Title: Data Management for Hydrology and Beyond Using the Observations
Data Model
Description: Data management in hydrology and other fields is facilitated with functions to enter and modify data in a database according to the Observations Data Model (ODM) standard by CUASHI (Consortium of Universities for the Advancement of Hydrologic Science). While this data model has been developed in hydrology, it is also useful for other fields. RObsDat helps in the setup of the database within one of the free database systems MariaDB, PostgreSQL or SQLite. It imports the controlled water vocabulary from the CUASHI web service and provides a smart interface between the analyst and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designs to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. When querying data from the database, it is stored in a spacetime objects within R for subsequent processing.
Author: Dominik Reusser
Maintainer: Dominik Reusser <reusser@pik-potsdam.de>
Diff between RObsDat versions 15.08 dated 2015-08-03 and 16.03 dated 2016-03-31
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/RObsDat_Einstiegstutorial.pdf |binary inst/setting_up_test_environment.sh | 2 +- man/RObsDat-package.Rd | 2 +- vignettes/RObsDat.bib | 24 ++++++++++++------------ 7 files changed, 25 insertions(+), 25 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with
bibliographic references. It greatly enhances the 'bibentry' class by
providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references,
supports 'UTF-8' encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files
can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez',
'CrossRef', and 'Zotero' are provided for importing references and
references can be created from locally stored 'PDF' files using 'Poppler'. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.10.6 dated 2016-02-15 and 0.10.12 dated 2016-03-31
DESCRIPTION | 12 +- MD5 | 39 ++++----- NAMESPACE | 2 R/04InternalFunctions.R | 6 - R/06BibEntry.R | 8 + R/07makeBibLatexAuthoryear.R | 16 ++- R/ReadCrossRef.R | 13 +-- R/ReadGS.R | 5 - R/ReadPubMed.R | 6 - R/asdataframe.R | 7 + README.md | 177 ----------------------------------------- inst/NEWS | 16 +++ inst/doc/TestAlphabetic.html | 4 inst/doc/TestRmd.html | 4 inst/doc/manual.pdf |binary man/BibEntry.Rd | 5 - tests/test-all.R | 2 tests/testthat/test-BibEntry.R |only tests/testthat/test-as.R | 11 ++ tests/testthat/test-authors.R | 4 tests/testthat/test-crossref.R | 17 +++ 21 files changed, 116 insertions(+), 238 deletions(-)
More information about processcontrol at CRAN
Permanent link
Title: Fast Hierarchical Clustering Routines for R and Python
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: linkage() in the SciPy package
'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
'flashClust' package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner <daniel@danifold.net>
Diff between fastcluster versions 1.1.16 dated 2015-02-17 and 1.1.20 dated 2016-03-31
DESCRIPTION | 16 ++--- INSTALL | 39 +++++++++----- MD5 | 31 +++++------ NEWS | 16 +++++ build/vignette.rds |binary inst/doc/fastcluster.Rtex | 4 - inst/doc/fastcluster.pdf |binary man/hclust.vector.Rd | 2 src/fastcluster.cpp | 27 +++++++++ src/fastcluster_python.cpp | 2 src/python/fastcluster.py | 2 src/python/setup.py | 76 ++++++++++++++++----------- src/python/test/__init__.py |only src/python/test/nantest.py | 115 +++++++++++++++++++++++++----------------- src/python/test/test.py | 66 +++++++++++++----------- src/python/test/vectortest.py | 56 ++++++++++++-------- vignettes/fastcluster.Rtex | 4 - 17 files changed, 284 insertions(+), 172 deletions(-)
Title: Efficient Effect Size Computation
Description: A collection of functions to compute the standardized
effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A).
The computation algorithms have been optimized to allow efficient computation even
with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano <marco.torchiano@polito.it>
Diff between effsize versions 0.6.1 dated 2016-02-26 and 0.6.2 dated 2016-03-31
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/CohenD.R | 14 ++++++++++++-- man/cohen.d.Rd | 3 ++- man/effsize-package.Rd | 1 + tests/testCohenD.R | 9 +++++++++ tests/testCohenD.Rout.save | 10 ++++++++++ 7 files changed, 44 insertions(+), 13 deletions(-)
Title: Fast Text Mining Framework for Vectorization and Word Embeddings
Description: Very fast and memory-friendly tools for text vectorization and
state-of-the-art word embeddings (GloVe). This package provides a
source-agnostic streaming API, which allows researchers to perform analysis
of collections of documents which are much larger than available RAM. All
core functions are parallelized to benefit from multicore machines.
Author: Dmitriy Selivanov [aut, cre],
Lincoln Mullen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between text2vec versions 0.2.0 dated 2016-01-10 and 0.3.0 dated 2016-03-31
text2vec-0.2.0/text2vec/R/analogues.R |only text2vec-0.2.0/text2vec/R/corpus.R |only text2vec-0.2.0/text2vec/R/feature_hasher.R |only text2vec-0.2.0/text2vec/man/check_analogue_accuracy.Rd |only text2vec-0.2.0/text2vec/man/create_vocab_corpus.Rd |only text2vec-0.2.0/text2vec/man/dtm_get_idf.Rd |only text2vec-0.2.0/text2vec/man/dtm_get_tf.Rd |only text2vec-0.2.0/text2vec/man/feature_hasher.Rd |only text2vec-0.2.0/text2vec/man/filter_commons_transformer.Rd |only text2vec-0.2.0/text2vec/man/prepare_analogue_questions.Rd |only text2vec-0.2.0/text2vec/man/split_vector.Rd |only text2vec-0.2.0/text2vec/man/tf_transformer.Rd |only text2vec-0.2.0/text2vec/man/to_lda_c.Rd |only text2vec-0.2.0/text2vec/man/vocabulary.Rd |only text2vec-0.3.0/text2vec/DESCRIPTION | 33 - text2vec-0.3.0/text2vec/LICENSE | 2 text2vec-0.3.0/text2vec/MD5 | 127 ++-- text2vec-0.3.0/text2vec/NAMESPACE | 44 - text2vec-0.3.0/text2vec/R/analogies.R |only text2vec-0.3.0/text2vec/R/data.R | 24 text2vec-0.3.0/text2vec/R/dtm.R |only text2vec-0.3.0/text2vec/R/glove.R | 96 +-- text2vec-0.3.0/text2vec/R/iterators.R | 266 +++++---- text2vec-0.3.0/text2vec/R/matrix.R | 131 ---- text2vec-0.3.0/text2vec/R/tcm.R |only text2vec-0.3.0/text2vec/R/text2vec.R | 15 text2vec-0.3.0/text2vec/R/transformers.R | 117 ++-- text2vec-0.3.0/text2vec/R/utils.R | 129 +++- text2vec-0.3.0/text2vec/R/vectorizers.R |only text2vec-0.3.0/text2vec/R/vocabulary.R | 246 +++++--- text2vec-0.3.0/text2vec/R/zzz.R | 2 text2vec-0.3.0/text2vec/README.md | 52 - text2vec-0.3.0/text2vec/build/vignette.rds |binary text2vec-0.3.0/text2vec/inst/doc/advanced.R |only text2vec-0.3.0/text2vec/inst/doc/advanced.Rmd |only text2vec-0.3.0/text2vec/inst/doc/advanced.html |only text2vec-0.3.0/text2vec/inst/doc/glove.R | 60 -- text2vec-0.3.0/text2vec/inst/doc/glove.Rmd | 123 ++-- text2vec-0.3.0/text2vec/inst/doc/glove.html | 102 +-- text2vec-0.3.0/text2vec/inst/doc/text-vectorization.R | 167 ++--- text2vec-0.3.0/text2vec/inst/doc/text-vectorization.Rmd | 243 +++----- text2vec-0.3.0/text2vec/inst/doc/text-vectorization.html | 288 ++++------ text2vec-0.3.0/text2vec/man/check_analogy_accuracy.Rd |only text2vec-0.3.0/text2vec/man/create_corpus.Rd |only text2vec-0.3.0/text2vec/man/create_dtm.Rd |only text2vec-0.3.0/text2vec/man/create_tcm.Rd |only text2vec-0.3.0/text2vec/man/create_vocabulary.Rd |only text2vec-0.3.0/text2vec/man/get_dtm.Rd | 47 - text2vec-0.3.0/text2vec/man/get_idf.Rd |only text2vec-0.3.0/text2vec/man/get_tcm.Rd | 22 text2vec-0.3.0/text2vec/man/get_tf.Rd |only text2vec-0.3.0/text2vec/man/glove.Rd | 102 +-- text2vec-0.3.0/text2vec/man/ifiles.Rd | 21 text2vec-0.3.0/text2vec/man/ilines.Rd | 15 text2vec-0.3.0/text2vec/man/itoken.Rd | 88 ++- text2vec-0.3.0/text2vec/man/movie_review.Rd | 24 text2vec-0.3.0/text2vec/man/prepare_analogy_questions.Rd |only text2vec-0.3.0/text2vec/man/prune_vocabulary.Rd | 18 text2vec-0.3.0/text2vec/man/split_into.Rd |only text2vec-0.3.0/text2vec/man/text2vec.Rd | 6 text2vec-0.3.0/text2vec/man/transform_filter_commons.Rd |only text2vec-0.3.0/text2vec/man/transform_tf.Rd |only text2vec-0.3.0/text2vec/man/vectorizers.Rd |only text2vec-0.3.0/text2vec/src/Corpus.h | 9 text2vec-0.3.0/text2vec/src/GloveFit.h | 2 text2vec-0.3.0/text2vec/src/HashCorpus.h | 31 - text2vec-0.3.0/text2vec/src/SparseTripletMatrix.h | 10 text2vec-0.3.0/text2vec/src/VocabCorpus.cpp | 2 text2vec-0.3.0/text2vec/src/VocabCorpus.h | 44 - text2vec-0.3.0/text2vec/src/Vocabulary.cpp | 5 text2vec-0.3.0/text2vec/src/Vocabulary.h | 121 +--- text2vec-0.3.0/text2vec/src/text2vec.h | 13 text2vec-0.3.0/text2vec/src/utils.cpp | 145 +++-- text2vec-0.3.0/text2vec/tests/testthat/not-test-glove.R | 14 text2vec-0.3.0/text2vec/tests/testthat/not-test-perf.R |only text2vec-0.3.0/text2vec/tests/testthat/test-hash-corpus.R | 12 text2vec-0.3.0/text2vec/tests/testthat/test-iterators.R | 16 text2vec-0.3.0/text2vec/tests/testthat/test-tcm.R |only text2vec-0.3.0/text2vec/tests/testthat/test-vocab-corpus.R | 91 ++- text2vec-0.3.0/text2vec/tests/testthat/test-vocab-high-level.R |only text2vec-0.3.0/text2vec/vignettes/advanced.Rmd |only text2vec-0.3.0/text2vec/vignettes/glove.Rmd | 123 ++-- text2vec-0.3.0/text2vec/vignettes/text-vectorization.Rmd | 243 +++----- 83 files changed, 1800 insertions(+), 1691 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-29 0.5
Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between poweRlaw versions 0.50.0 dated 2015-08-11 and 0.60.0 dated 2016-03-31
DESCRIPTION | 19 - MD5 | 159 ++++++---- NAMESPACE | 34 +- NEWS | 13 R/AllGenerics.R | 1 R/aaa_all_classes.R | 20 - R/bootstrap.R | 63 ++- R/bootstrap_p.R | 49 ++- R/compare_distributions.R | 1 R/def_conexp.R | 2 R/def_conlorm.R | 1 R/def_conweibull.R |only R/def_dislnorm.R | 1 R/def_displ.R | 6 R/def_dispois.R | 1 R/estimate_xmin.R | 107 ++++-- R/lines_methods.R | 2 R/plcon.R | 2 R/plot_methods.R | 6 R/show_methods.R | 1 R/timer.R |only build/vignette.rds |binary data/bootstrap_moby.RData |binary data/bootstrap_p_moby.RData |binary inst/doc/a_introduction.R | 8 inst/doc/a_introduction.Rnw | 27 + inst/doc/a_introduction.pdf |binary inst/doc/b_powerlaw_examples.R | 10 inst/doc/b_powerlaw_examples.Rnw | 8 inst/doc/b_powerlaw_examples.pdf |binary inst/doc/c_comparing_distributions.R | 11 inst/doc/c_comparing_distributions.Rnw | 25 + inst/doc/c_comparing_distributions.pdf |binary inst/doc/d_jss_paper.pdf |binary man/bootstrap_moby.Rd | 15 man/compare_distributions.Rd | 46 +- man/displ.Rd | 22 - man/dist_cdf-methods.Rd | 28 + man/dist_data_cdf-methods.Rd | 4 man/dist_ll-methods.Rd | 11 man/dist_pdf-methods.Rd | 15 man/dist_rand-methods.Rd | 13 man/dplcon.Rd | 19 - man/dpldis.Rd | 32 +- man/estimate_pars.Rd | 8 man/estimate_xmin.Rd | 72 ++-- man/get_KS_statistic-deprecated.Rd |only man/get_n.Rd | 4 man/get_ntail.Rd | 6 man/moby.Rd | 6 man/native_american.Rd | 6 man/plot-distribution-ANY-method.Rd | 14 man/plot.bs_xmin.Rd | 4 man/population.Rd | 4 man/poweRlaw-package.Rd | 10 man/show-distribution-method.Rd | 6 man/swiss_prot.Rd | 16 - tests |only vignettes/a_introduction-concordance.tex |only vignettes/a_introduction.Rnw | 27 + vignettes/b_powerlaw_examples-concordance.tex |only vignettes/b_powerlaw_examples.Rnw | 8 vignettes/c_comparing_distributions.Rnw | 25 + vignettes/figure1.ps |only vignettes/figure2.ps |only vignettes/figure3.ps |only vignettes/figure4.ps |only vignettes/figure5.ps |only vignettes/jsslogo.ps |only vignettes/knitr_cache_poweRlaw |only vignettes/knitr_figure_compare |only vignettes/knitr_figure_examples |only vignettes/knitr_figure_poweRlaw/graphics-do_we_have_a_power-1.pdf |binary vignettes/knitr_figure_poweRlaw/graphics-unnamed-chunk-15-1.pdf |binary vignettes/knitr_figure_poweRlaw/graphics-unnamed-chunk-25-1.pdf |binary vignettes/knitr_figure_poweRlaw/graphics-unnamed-chunk-34-1.pdf |binary 76 files changed, 617 insertions(+), 381 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of various epidemiological statistics where the use of population data such as population counts and hazards is required.
Relatively high computation speed achieved by using data.table.
Author: Joonas Miettinen [aut, cre],
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.2.1 dated 2015-09-29 and 0.3.0 dated 2016-03-31
popEpi-0.2.1/popEpi/R/survival.R |only popEpi-0.2.1/popEpi/inst/doc/sir.Rmd |only popEpi-0.2.1/popEpi/inst/doc/survtab_examples.Rmd |only popEpi-0.2.1/popEpi/man/as.pe.Lexis.Rd |only popEpi-0.2.1/popEpi/man/as.pe.data.table.Rd |only popEpi-0.2.1/popEpi/man/as.pe.list.Rd |only popEpi-0.2.1/popEpi/man/expr.by.cj.Rd |only popEpi-0.2.1/popEpi/man/plot.pe.Rd |only popEpi-0.2.1/popEpi/man/survtab.Rd |only popEpi-0.2.1/popEpi/vignettes |only popEpi-0.3.0/popEpi/DESCRIPTION | 26 popEpi-0.3.0/popEpi/MD5 | 205 popEpi-0.3.0/popEpi/NAMESPACE | 120 popEpi-0.3.0/popEpi/NEWS | 209 popEpi-0.3.0/popEpi/NEWS.md |only popEpi-0.3.0/popEpi/R/S3_definitions.R | 1847 ++++--- popEpi-0.3.0/popEpi/R/aggregating.R |only popEpi-0.3.0/popEpi/R/data_document.R | 235 popEpi-0.3.0/popEpi/R/direct_adjusting.R |only popEpi-0.3.0/popEpi/R/flexyargs.R |only popEpi-0.3.0/popEpi/R/incidence_rates.R |only popEpi-0.3.0/popEpi/R/lexpand.R | 1937 +++---- popEpi-0.3.0/popEpi/R/lifetime_function.R |only popEpi-0.3.0/popEpi/R/ltable.R | 476 - popEpi-0.3.0/popEpi/R/mean_survival.R | 1011 ++- popEpi-0.3.0/popEpi/R/popEpi_package.r | 64 popEpi-0.3.0/popEpi/R/pophaz.R |only popEpi-0.3.0/popEpi/R/relative_poisson.R | 652 +- popEpi-0.3.0/popEpi/R/relative_poisson_net_survival.R | 333 - popEpi-0.3.0/popEpi/R/sir_devaus.R | 2302 ++++---- popEpi-0.3.0/popEpi/R/splitLexisDT.R | 384 - popEpi-0.3.0/popEpi/R/splitMulti.R | 452 - popEpi-0.3.0/popEpi/R/splitting_utility_functions.R | 1574 ++++-- popEpi-0.3.0/popEpi/R/startup_message.R | 30 popEpi-0.3.0/popEpi/R/survival_aggregated.R |only popEpi-0.3.0/popEpi/R/survival_lexis.R |only popEpi-0.3.0/popEpi/R/survival_utility_functions.R | 795 ++- popEpi-0.3.0/popEpi/R/utility_functions.R | 2571 ++++++---- popEpi-0.3.0/popEpi/R/weighted_table.R |only popEpi-0.3.0/popEpi/README.md | 372 - popEpi-0.3.0/popEpi/build/vignette.rds |binary popEpi-0.3.0/popEpi/data/ICSS.rdata |binary popEpi-0.3.0/popEpi/data/popmort.rdata |binary popEpi-0.3.0/popEpi/data/sibr.rdata |binary popEpi-0.3.0/popEpi/data/sire.rdata |binary popEpi-0.3.0/popEpi/data/stdpop101.rdata |only popEpi-0.3.0/popEpi/data/stdpop18.rdata |only popEpi-0.3.0/popEpi/inst/doc/sir.R | 128 popEpi-0.3.0/popEpi/inst/doc/sir.html | 646 -- popEpi-0.3.0/popEpi/inst/doc/survtab_examples.R | 258 - popEpi-0.3.0/popEpi/inst/doc/survtab_examples.html | 862 +-- popEpi-0.3.0/popEpi/man/ICSS.Rd | 51 popEpi-0.3.0/popEpi/man/RPL.Rd | 36 popEpi-0.3.0/popEpi/man/adjust.Rd |only popEpi-0.3.0/popEpi/man/aggre.Rd |only popEpi-0.3.0/popEpi/man/all_names_present.Rd | 58 popEpi-0.3.0/popEpi/man/as.Date.yrs.Rd |only popEpi-0.3.0/popEpi/man/as.aggre.Rd |only popEpi-0.3.0/popEpi/man/as.data.frame.ratetable.Rd | 66 popEpi-0.3.0/popEpi/man/as.data.table.ratetable.Rd | 66 popEpi-0.3.0/popEpi/man/cast_simple.Rd | 101 popEpi-0.3.0/popEpi/man/cut_bound.Rd | 58 popEpi-0.3.0/popEpi/man/direct_standardization.Rd |only popEpi-0.3.0/popEpi/man/fac2num.Rd | 74 popEpi-0.3.0/popEpi/man/flexible_argument.Rd |only popEpi-0.3.0/popEpi/man/get.yrs.Rd | 128 popEpi-0.3.0/popEpi/man/is.Date.Rd | 78 popEpi-0.3.0/popEpi/man/is_leap_year.Rd | 57 popEpi-0.3.0/popEpi/man/lexpand.Rd | 669 +- popEpi-0.3.0/popEpi/man/lines.sirspline.Rd |only popEpi-0.3.0/popEpi/man/lines.survmean.Rd |only popEpi-0.3.0/popEpi/man/lines.survtab.Rd | 90 popEpi-0.3.0/popEpi/man/longDF2ratetable.Rd | 59 popEpi-0.3.0/popEpi/man/lower_bound.Rd | 38 popEpi-0.3.0/popEpi/man/ltable.Rd | 240 popEpi-0.3.0/popEpi/man/makeWeightsDT.Rd |only popEpi-0.3.0/popEpi/man/na2zero.Rd | 53 popEpi-0.3.0/popEpi/man/plot.sir.Rd | 157 popEpi-0.3.0/popEpi/man/plot.sirspline.Rd | 81 popEpi-0.3.0/popEpi/man/plot.survmean.Rd |only popEpi-0.3.0/popEpi/man/plot.survtab.Rd | 104 popEpi-0.3.0/popEpi/man/poisson.ci.Rd | 52 popEpi-0.3.0/popEpi/man/popEpi.Rd | 76 popEpi-0.3.0/popEpi/man/pophaz.Rd |only popEpi-0.3.0/popEpi/man/popmort.Rd | 42 popEpi-0.3.0/popEpi/man/prepExpo.Rd |only popEpi-0.3.0/popEpi/man/print.aggre.Rd |only popEpi-0.3.0/popEpi/man/print.sir.Rd | 40 popEpi-0.3.0/popEpi/man/print.sirspline.Rd | 40 popEpi-0.3.0/popEpi/man/print.survtab.Rd |only popEpi-0.3.0/popEpi/man/rate.Rd |only popEpi-0.3.0/popEpi/man/relpois.Rd | 212 popEpi-0.3.0/popEpi/man/relpois_ag.Rd |only popEpi-0.3.0/popEpi/man/robust_values.Rd | 91 popEpi-0.3.0/popEpi/man/rpcurve.Rd | 126 popEpi-0.3.0/popEpi/man/setaggre.Rd |only popEpi-0.3.0/popEpi/man/setclass.Rd | 56 popEpi-0.3.0/popEpi/man/setcolsnull.Rd | 64 popEpi-0.3.0/popEpi/man/shift.var.Rd | 67 popEpi-0.3.0/popEpi/man/sibr.Rd | 62 popEpi-0.3.0/popEpi/man/sir.Rd | 367 - popEpi-0.3.0/popEpi/man/sire.Rd | 60 popEpi-0.3.0/popEpi/man/sirspline.Rd | 266 - popEpi-0.3.0/popEpi/man/splitLexisDT.Rd | 144 popEpi-0.3.0/popEpi/man/splitMulti.Rd | 242 popEpi-0.3.0/popEpi/man/stdpop101.Rd |only popEpi-0.3.0/popEpi/man/stdpop18.Rd |only popEpi-0.3.0/popEpi/man/summary.aggre.Rd |only popEpi-0.3.0/popEpi/man/summary.survtab.Rd |only popEpi-0.3.0/popEpi/man/survmean.Rd | 386 + popEpi-0.3.0/popEpi/man/survtab_ag.Rd |only popEpi-0.3.0/popEpi/man/try2int.Rd | 49 popEpi-0.3.0/popEpi/tests/testthat.R | 21 popEpi-0.3.0/popEpi/tests/testthat/test_aggre.R |only popEpi-0.3.0/popEpi/tests/testthat/test_expo.R |only popEpi-0.3.0/popEpi/tests/testthat/test_lexpand.R | 517 +- popEpi-0.3.0/popEpi/tests/testthat/test_mean_survival.R | 368 + popEpi-0.3.0/popEpi/tests/testthat/test_rate.R |only popEpi-0.3.0/popEpi/tests/testthat/test_relpois_mean_curve.R | 119 popEpi-0.3.0/popEpi/tests/testthat/test_sir.R | 345 - popEpi-0.3.0/popEpi/tests/testthat/test_splitLexisDT.R | 247 popEpi-0.3.0/popEpi/tests/testthat/test_splitMulti.R | 198 popEpi-0.3.0/popEpi/tests/testthat/test_survtab_bad_surv_ints.R | 173 popEpi-0.3.0/popEpi/tests/testthat/test_survtab_observed.R | 182 popEpi-0.3.0/popEpi/tests/testthat/test_survtab_relative.R | 295 - popEpi-0.3.0/popEpi/tests/testthat/test_survtab_usage.R |only popEpi-0.3.0/popEpi/tests/testthat/test_utils.R |only popEpi-0.3.0/popEpi/tests/testthat/test_weighter.R |only 128 files changed, 14352 insertions(+), 10308 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.3.3 dated 2016-03-23 and 0.4.0 dated 2016-03-31
DESCRIPTION | 8 MD5 | 10 - R/mdmr.R | 356 ++++++++++++++++++++++++++++++++------------ inst/doc/mdmr-vignette.html | 52 +++--- man/delta.Rd | 8 man/mdmr.Rd | 9 - 6 files changed, 310 insertions(+), 133 deletions(-)
Title: Bi-Level Optimization of Metabolic Network Models
Description: Initial metabolic networks often inaccurately predict in-silico growth or non-growth if compared to in-vivo data. This package refines metabolic network models by making networks changes (i.e., removing, adding, changing reversibility of reactions; adding and removing biomass metabolites) and simultaneously matching sets of experimental growth and non-growth data (e.g., KO-mutants, mutants grown under different media conditions,...)
Author: Daniel Hartleb
Maintainer: Daniel Hartleb <daniel.hartleb@hhu.de>
Diff between GlobalFit versions 1.0 dated 2015-04-29 and 1.1 dated 2016-03-31
GlobalFit-1.0/GlobalFit/data/additional_biomass_mets.rda |only GlobalFit-1.0/GlobalFit/data/additional_reactions_list.rda |only GlobalFit-1.0/GlobalFit/data/influxes.rda |only GlobalFit-1.0/GlobalFit/data/not_delete_back.rda |only GlobalFit-1.0/GlobalFit/data/not_delete_for.rda |only GlobalFit-1.0/GlobalFit/data/off.rda |only GlobalFit-1.0/GlobalFit/data/on.rda |only GlobalFit-1.0/GlobalFit/data/opt_net.rda |only GlobalFit-1.0/GlobalFit/data/p_list.rda |only GlobalFit-1.0/GlobalFit/data/remove_biomass_mets.rda |only GlobalFit-1.0/GlobalFit/data/reverse_reaction_list.rda |only GlobalFit-1.0/GlobalFit/data/test.rda |only GlobalFit-1.0/GlobalFit/man/additional_biomass_mets.Rd |only GlobalFit-1.0/GlobalFit/man/additional_reactions_list.Rd |only GlobalFit-1.0/GlobalFit/man/influxes.Rd |only GlobalFit-1.0/GlobalFit/man/initialize-methods.Rd |only GlobalFit-1.0/GlobalFit/man/not_delete_back.Rd |only GlobalFit-1.0/GlobalFit/man/not_delete_for.Rd |only GlobalFit-1.0/GlobalFit/man/off.Rd |only GlobalFit-1.0/GlobalFit/man/on.Rd |only GlobalFit-1.0/GlobalFit/man/opt_net.Rd |only GlobalFit-1.0/GlobalFit/man/p_list.Rd |only GlobalFit-1.0/GlobalFit/man/remove_biomass_mets.Rd |only GlobalFit-1.0/GlobalFit/man/reverse_reaction_list.Rd |only GlobalFit-1.0/GlobalFit/man/test.Rd |only GlobalFit-1.1/GlobalFit/DESCRIPTION | 8 GlobalFit-1.1/GlobalFit/MD5 | 48 GlobalFit-1.1/GlobalFit/NAMESPACE | 1 GlobalFit-1.1/GlobalFit/R/FastGlobalFit.R |only GlobalFit-1.1/GlobalFit/R/GlobalFit.R | 522 +++++--- GlobalFit-1.1/GlobalFit/R/GlobalFit_methods.R | 613 ++++++++-- GlobalFit-1.1/GlobalFit/build |only GlobalFit-1.1/GlobalFit/data/example_net1.rda |only GlobalFit-1.1/GlobalFit/data/example_net2.rda |only GlobalFit-1.1/GlobalFit/data/example_net3.rda |only GlobalFit-1.1/GlobalFit/man/GlobalFit-package.Rd | 243 ++- GlobalFit-1.1/GlobalFit/man/bilevel_optimize.Rd | 345 +++-- GlobalFit-1.1/GlobalFit/man/example_net1.Rd |only GlobalFit-1.1/GlobalFit/man/example_net2.Rd |only GlobalFit-1.1/GlobalFit/man/example_net3.Rd |only GlobalFit-1.1/GlobalFit/man/sysBiolAlg_FastGlobalFit-class.Rd |only GlobalFit-1.1/GlobalFit/man/sysBiolAlg_GlobalFit-class.Rd | 15 42 files changed, 1267 insertions(+), 528 deletions(-)
Title: Calculations for All Common Subsequences
Description: Implements several string comparison algorithms, including calACS (count all common subsequences), lenACS (calculate the lengths of all common subsequences), and lenLCS (calculate the length of the longest common subsequence). Some algorithms differentiate between the more strict definition of subsequence, where a common subsequence cannot be separated by any other items, from its looser counterpart, where a common subsequence can be interrupted by other items. This difference is shown in the suffix of the algorithm (-Strict vs -Loose). For example, q-w is a common subsequence of q-w-e-r and q-e-w-r on the looser definition, but not on the more strict definition. calACSLoose Algorithm from Wang, H. All common subsequences (2007) IJCAI International Joint Conference on Artificial Intelligence, pp. 635-640.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between calACS versions 2.2.1 dated 2016-01-31 and 2.2.2 dated 2016-03-31
calACS-2.2.1/calACS/man/GeneratePossibleSubsequences.Rd |only calACS-2.2.1/calACS/man/calACSstrLoose.Rd |only calACS-2.2.1/calACS/man/calACSstrStrict.Rd |only calACS-2.2.1/calACS/man/is.subvector.Rd |only calACS-2.2.1/calACS/man/lenACSstrStrict.Rd |only calACS-2.2.1/calACS/man/lenLCSstrStrict.Rd |only calACS-2.2.2/calACS/DESCRIPTION | 20 +++----------- calACS-2.2.2/calACS/MD5 | 20 +++++--------- calACS-2.2.2/calACS/R/GeneratePossibleSubsequences.r | 12 ++++---- calACS-2.2.2/calACS/R/calACSstrLoose.r | 18 ++++++------- calACS-2.2.2/calACS/R/calACSstrStrict.R | 22 ++++++++-------- calACS-2.2.2/calACS/R/is.subvector.r | 10 +++---- calACS-2.2.2/calACS/R/lenACSstrStrict.r | 16 +++++------ calACS-2.2.2/calACS/R/lenLCSstrStrict.r | 14 +++++----- 14 files changed, 58 insertions(+), 74 deletions(-)
Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.1.5 dated 2016-03-06 and 1.2.0 dated 2016-03-31
DESCRIPTION | 18 - MD5 | 135 ++++++------ NAMESPACE | 6 NEWS | 26 ++ R/build_run_modify.r | 321 ++++++++++++---------------- R/fit_and_reporting.r | 382 +++++++++++++++++++--------------- R/hermine_original_twinHetMulAceCon.R | 40 +-- R/misc_and_utility.r | 177 +++++++++++---- R/model_builders.r | 109 +++++++-- R/xmu.r | 365 ++++++++++++++++---------------- man/RMSEA.MxModel.Rd | 2 man/RMSEA.Rd | 2 man/RMSEA.summary.mxmodel.Rd | 2 man/confint.MxModel.Rd | 2 man/extractAIC.MxModel.Rd | 2 man/figures/ACEcov.png |only man/figures/Duncan.pdf |only man/figures/Duncan.png |only man/figures/set_default_app.png |only man/figures/umxEFA.png |only man/figures/umx_help_figures.graffle |binary man/loadings.MxModel.Rd |only man/loadings.Rd |only man/logLik.Rd | 2 man/plot.MxModel.Rd | 34 +-- man/residuals.MxModel.Rd | 2 man/summaryAPA.Rd | 8 man/umx.Rd | 51 +--- man/umxACE.Rd | 33 +- man/umxACESexLim.Rd | 4 man/umxACEcov.Rd | 42 --- man/umxCI.Rd | 2 man/umxCI_boot.Rd | 2 man/umxCP.Rd | 8 man/umxCompare.Rd | 2 man/umxEFA.Rd | 53 +++- man/umxExpCov.Rd | 2 man/umxExpMeans.Rd | 4 man/umxFitIndices.Rd | 2 man/umxIP.Rd | 8 man/umxPath.Rd | 6 man/umxPlotACE.Rd | 8 man/umxPlotACEcov.Rd | 10 man/umxPlotCP.Rd | 9 man/umxPlotIP.Rd | 8 man/umxRAM.Rd | 2 man/umxSetParameters.Rd | 2 man/umxSummary.MxModel.Rd | 13 - man/umxSummaryACE.Rd | 10 man/umxSummaryACEcov.Rd | 14 - man/umxSummaryCP.Rd | 12 - man/umxSummaryGxE.Rd | 4 man/umxSummaryIP.Rd | 8 man/umx_APA_pval.Rd | 8 man/umx_aggregate.Rd | 17 - man/umx_drop_ok.Rd | 2 man/umx_get_checkpoint.Rd | 4 man/umx_get_cores.Rd | 4 man/umx_get_optimizer.Rd | 4 man/umx_has_means.Rd | 2 man/umx_print.Rd | 10 man/umx_set_auto_plot.Rd | 6 man/umx_set_auto_run.Rd | 4 man/umx_set_checkpoint.Rd | 4 man/umx_set_cores.Rd | 4 man/umx_set_optimizer.Rd | 4 man/umx_set_plot_format.Rd |only man/umx_set_table_format.Rd |only man/umx_show.Rd | 14 - man/umx_standardize_RAM.Rd | 2 man/umx_time.Rd | 8 man/xmu_dot_make_paths.Rd | 10 man/xmu_dot_make_residuals.Rd | 4 73 files changed, 1130 insertions(+), 935 deletions(-)
Title: 'dplyr' Functionality for Matched Tree and Data Objects
Description: Matches phylogenetic trees and trait data, and
allows simultaneous manipulation of the tree and data using 'dplyr'.
Author: Josef Uyeda
Maintainer: Josef Uyeda <josef.uyeda@gmail.com>
Diff between treeplyr versions 0.1 dated 2016-03-03 and 0.1.1 dated 2016-03-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/treeplyr_functions.R | 10 +++++----- man/group_by_.treedata.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: A Tool for Downloading Functional Traits Data for Plant Species
Description: Plant ecologists often need to collect "traits" data
about plant species which are often scattered among various
databases: TR8 contains a set of tools which take care of
automatically retrieving some of those functional traits data
for plant species from publicly available databases (Biolflor,
The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg
values for Italian Flora, Mycorrhizal intensity databases, Catminat, BROT,
PLANTS, Jepson Flora Project).
The TR8 name, inspired by "car plates" jokes, was chosen since
it both reminds of the main object of the package and is
extremely short to type.
Author: Gionata Bocci <boccigionata@gmail.com>
Maintainer: Gionata Bocci <boccigionata@gmail.com>
Diff between TR8 versions 0.9.13 dated 2015-03-22 and 0.9.14 dated 2016-03-31
TR8-0.9.13/TR8/data/ECOFLORA_df.rda |only TR8-0.9.13/TR8/vignettes/_region_.tex |only TR8-0.9.14/TR8/DESCRIPTION | 15 TR8-0.9.14/TR8/MD5 | 101 ++-- TR8-0.9.14/TR8/NAMESPACE | 8 TR8-0.9.14/TR8/NEWS |only TR8-0.9.14/TR8/R/LEDA.R | 2 TR8-0.9.14/TR8/R/PLANTS.R |only TR8-0.9.14/TR8/R/PLANTS_download.R |only TR8-0.9.14/TR8/R/TR8-package.R | 16 TR8-0.9.14/TR8/R/biolflor.R | 50 +- TR8-0.9.14/TR8/R/brot_data.R |only TR8-0.9.14/TR8/R/catminat_download.R | 255 ++++++----- TR8-0.9.14/TR8/R/create_brico_ref.R |only TR8-0.9.14/TR8/R/ecoflora.R | 26 - TR8-0.9.14/TR8/R/ecoflora_download_url.R |only TR8-0.9.14/TR8/R/eflora.R |only TR8-0.9.14/TR8/R/flowering_italy.R | 97 ++-- TR8-0.9.14/TR8/R/leda_download.R | 2 TR8-0.9.14/TR8/R/leda_general.R | 4 TR8-0.9.14/TR8/R/local_storage.R | 12 TR8-0.9.14/TR8/R/myco.R | 2 TR8-0.9.14/TR8/R/tr8.R | 394 ++++++++++------- TR8-0.9.14/TR8/R/tr8_gui.R | 32 + TR8-0.9.14/TR8/build/vignette.rds |binary TR8-0.9.14/TR8/data/available_tr8.rda |binary TR8-0.9.14/TR8/data/biolflor_lookup.rda |binary TR8-0.9.14/TR8/data/column_list.rda |binary TR8-0.9.14/TR8/data/leda_lookup.rda |binary TR8-0.9.14/TR8/data/pignatti.rda |binary TR8-0.9.14/TR8/data/ref_PLANTS.rda |only TR8-0.9.14/TR8/data/traits_Biolflor.rda |binary TR8-0.9.14/TR8/data/traits_eco.rda |binary TR8-0.9.14/TR8/inst/doc/Expanding_TR8.pdf |binary TR8-0.9.14/TR8/inst/doc/TR8.R | 10 TR8-0.9.14/TR8/inst/doc/TR8.Rnw | 70 ++- TR8-0.9.14/TR8/inst/doc/TR8.pdf |binary TR8-0.9.14/TR8/inst/doc/TR8_workflow.R | 29 - TR8-0.9.14/TR8/inst/doc/TR8_workflow.Rnw | 41 + TR8-0.9.14/TR8/inst/doc/TR8_workflow.pdf |binary TR8-0.9.14/TR8/man/ECOFLORA_df.Rd | 5 TR8-0.9.14/TR8/man/TR8-package.Rd | 50 +- TR8-0.9.14/TR8/man/Tr8-class.Rd | 3 TR8-0.9.14/TR8/man/available_tr8.Rd | 2 TR8-0.9.14/TR8/man/available_traits.Rd | 3 TR8-0.9.14/TR8/man/biolflor_lookup.Rd | 2 TR8-0.9.14/TR8/man/column_list.Rd | 20 TR8-0.9.14/TR8/man/leda_download_to_local_directory.Rd | 2 TR8-0.9.14/TR8/man/leda_lookup.Rd | 2 TR8-0.9.14/TR8/man/ref_PLANTS.Rd |only TR8-0.9.14/TR8/man/tr8.Rd | 49 +- TR8-0.9.14/TR8/man/traits_eco.Rd | 4 TR8-0.9.14/TR8/man/traits_pollen_Biolflor.Rd |only TR8-0.9.14/TR8/man/traits_special_Biolflor.Rd |only TR8-0.9.14/TR8/vignettes/TR8.Rnw | 70 ++- TR8-0.9.14/TR8/vignettes/TR8_workflow.Rnw | 41 + TR8-0.9.14/TR8/vignettes/temp.ps | 2 TR8-0.9.14/TR8/vignettes/tr8.bib | 39 + 58 files changed, 963 insertions(+), 497 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 1.6.0 dated 2016-03-06 and 1.7.0 dated 2016-03-31
textmineR-1.6.0/textmineR/data/acq2.rda |only textmineR-1.6.0/textmineR/man/acq2.Rd |only textmineR-1.7.0/textmineR/DESCRIPTION | 16 - textmineR-1.7.0/textmineR/MD5 | 68 +++--- textmineR-1.7.0/textmineR/R/CalcLikelihood.R | 7 textmineR-1.7.0/textmineR/R/CalcProbCoherence.R |only textmineR-1.7.0/textmineR/R/CalcTopicModelR2.R | 11 - textmineR-1.7.0/textmineR/R/Cluster2TopicModel.R |only textmineR-1.7.0/textmineR/R/Dtm2Docs.R | 7 textmineR-1.7.0/textmineR/R/FitLdaModel.R | 133 +++++++++--- textmineR-1.7.0/textmineR/R/FitLsaModel.R |only textmineR-1.7.0/textmineR/R/FormatRawLdaOutput.R | 13 - textmineR-1.7.0/textmineR/R/GetPhiPrime.R | 5 textmineR-1.7.0/textmineR/R/GetProbableTerms.R | 11 - textmineR-1.7.0/textmineR/R/GetTopTerms.R | 5 textmineR-1.7.0/textmineR/R/LabelTopics.R | 9 textmineR-1.7.0/textmineR/R/MakeSparseDTM.R | 2 textmineR-1.7.0/textmineR/R/ProbCoherence.R | 12 - textmineR-1.7.0/textmineR/R/TermDocFreq.R | 5 textmineR-1.7.0/textmineR/R/Vec2Dtm.R | 146 +++++++------- textmineR-1.7.0/textmineR/README.md | 16 - textmineR-1.7.0/textmineR/data/nih_sample.rda |only textmineR-1.7.0/textmineR/data/nih_sample_dtm.rda |only textmineR-1.7.0/textmineR/data/nih_sample_topic_model.rda |only textmineR-1.7.0/textmineR/man/CalcLikelihood.Rd | 7 textmineR-1.7.0/textmineR/man/CalcProbCoherence.Rd |only textmineR-1.7.0/textmineR/man/CalcTopicModelR2.Rd | 8 textmineR-1.7.0/textmineR/man/Cluster2TopicModel.Rd |only textmineR-1.7.0/textmineR/man/Dtm2Docs.Rd | 7 textmineR-1.7.0/textmineR/man/FitLdaModel.Rd | 43 +++- textmineR-1.7.0/textmineR/man/FitLsaModel.Rd |only textmineR-1.7.0/textmineR/man/FormatRawLdaOutput.Rd | 11 - textmineR-1.7.0/textmineR/man/GetPhiPrime.Rd | 5 textmineR-1.7.0/textmineR/man/GetProbableTerms.Rd | 9 textmineR-1.7.0/textmineR/man/GetTopTerms.Rd | 5 textmineR-1.7.0/textmineR/man/LabelTopics.Rd | 8 textmineR-1.7.0/textmineR/man/MakeSparseDTM.Rd | 2 textmineR-1.7.0/textmineR/man/ProbCoherence.Rd | 5 textmineR-1.7.0/textmineR/man/TermDocFreq.Rd | 5 textmineR-1.7.0/textmineR/man/Vec2Dtm.Rd | 26 +- textmineR-1.7.0/textmineR/man/nih.Rd |only 41 files changed, 375 insertions(+), 232 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph] (Copyright holder of the code in
/src/distributions/jags, src/distributions/DPar1.*, configure.ac,
and original copyright holder of some modified code where
indicated)
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.0.2-8 dated 2015-09-14 and 2.0.3-2 dated 2016-03-31
runjags-2.0.2-8/runjags/inst/doc/UserGuide.Rtex |only runjags-2.0.2-8/runjags/inst/doc/UserGuide.pdf |only runjags-2.0.2-8/runjags/vignettes/UserGuide.Rtex |only runjags-2.0.3-2/runjags/CHANGELOG | 44 +++ runjags-2.0.3-2/runjags/DESCRIPTION | 8 runjags-2.0.3-2/runjags/MD5 | 121 ++++----- runjags-2.0.3-2/runjags/NAMESPACE | 3 runjags-2.0.3-2/runjags/R/autoextend.jags.R | 29 +- runjags-2.0.3-2/runjags/R/combine.mcmc.R | 2 runjags-2.0.3-2/runjags/R/dump.list.format.R | 8 runjags-2.0.3-2/runjags/R/extend.jags.R | 12 runjags-2.0.3-2/runjags/R/extract.runjags.R | 10 runjags-2.0.3-2/runjags/R/load.module.runjags.R | 16 - runjags-2.0.3-2/runjags/R/results.jags.R | 19 + runjags-2.0.3-2/runjags/R/run.jags.study.R | 10 runjags-2.0.3-2/runjags/R/runjags.readin.R | 6 runjags-2.0.3-2/runjags/R/runjags.start.R | 35 +- runjags-2.0.3-2/runjags/R/runjags.summaries.R | 40 +-- runjags-2.0.3-2/runjags/R/runjagsclass.R | 26 +- runjags-2.0.3-2/runjags/R/setup.jags.jagsfile.R | 62 ++-- runjags-2.0.3-2/runjags/R/summary.R | 28 +- runjags-2.0.3-2/runjags/R/template.jags.R | 8 runjags-2.0.3-2/runjags/R/utilities.R | 40 ++- runjags-2.0.3-2/runjags/R/utilities.invisible.R | 73 ++++- runjags-2.0.3-2/runjags/R/xgrid.run.R | 4 runjags-2.0.3-2/runjags/R/xgrid.utilities.R | 2 runjags-2.0.3-2/runjags/README | 74 ++++- runjags-2.0.3-2/runjags/build/vignette.rds |binary runjags-2.0.3-2/runjags/inst/doc/quickjags.R | 4 runjags-2.0.3-2/runjags/inst/doc/quickjags.Rmd | 4 runjags-2.0.3-2/runjags/inst/doc/quickjags.html | 126 +++++----- runjags-2.0.3-2/runjags/inst/doc/userguide.Rtex |only runjags-2.0.3-2/runjags/inst/doc/userguide.pdf |only runjags-2.0.3-2/runjags/man/add.summary.Rd | 4 runjags-2.0.3-2/runjags/man/autorun.jags.Rd | 2 runjags-2.0.3-2/runjags/man/run.jags.Rd | 2 runjags-2.0.3-2/runjags/man/runjags-class.Rd | 14 + runjags-2.0.3-2/runjags/man/runjags.options.Rd | 15 - runjags-2.0.3-2/runjags/src/Makevars.in | 63 +---- runjags-2.0.3-2/runjags/src/Makevars.win | 61 +++- runjags-2.0.3-2/runjags/src/distributions/DGenPar.h | 3 runjags-2.0.3-2/runjags/src/distributions/DHalfCauchy.h | 3 runjags-2.0.3-2/runjags/src/distributions/DLomax.h | 3 runjags-2.0.3-2/runjags/src/distributions/DMouchel.h | 3 runjags-2.0.3-2/runjags/src/distributions/DPar1.h | 3 runjags-2.0.3-2/runjags/src/distributions/DPar2.h | 3 runjags-2.0.3-2/runjags/src/distributions/DPar3.h | 3 runjags-2.0.3-2/runjags/src/distributions/DPar4.h | 3 runjags-2.0.3-2/runjags/src/distributions/jags/DFunction.cc | 5 runjags-2.0.3-2/runjags/src/distributions/jags/DFunction.h | 4 runjags-2.0.3-2/runjags/src/distributions/jags/DPQFunction.cc | 5 runjags-2.0.3-2/runjags/src/distributions/jags/DPQFunction.h | 4 runjags-2.0.3-2/runjags/src/distributions/jags/PFunction.cc | 5 runjags-2.0.3-2/runjags/src/distributions/jags/PFunction.h | 5 runjags-2.0.3-2/runjags/src/distributions/jags/QFunction.cc | 5 runjags-2.0.3-2/runjags/src/distributions/jags/QFunction.h | 5 runjags-2.0.3-2/runjags/src/distributions/jags/RScalarDist.cc | 3 runjags-2.0.3-2/runjags/src/distributions/jags/RScalarDist.h | 3 runjags-2.0.3-2/runjags/src/jagsversions.h |only runjags-2.0.3-2/runjags/src/runjags.cc | 4 runjags-2.0.3-2/runjags/src/testrunjags.cc | 22 + runjags-2.0.3-2/runjags/tests/checkmethods.R | 2 runjags-2.0.3-2/runjags/tests/checkmodule.R | 19 + runjags-2.0.3-2/runjags/vignettes/quickjags.Rmd | 4 runjags-2.0.3-2/runjags/vignettes/userguide.Rtex |only 65 files changed, 675 insertions(+), 419 deletions(-)
Title: Phylogenetic ANalyses of DiversificAtion
Description: Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, and Drury et al. (2016) <DOI:10.1093/sysbio/syw020>.
Author: Hélène Morlon [aut, cre, cph]
Maintainer: Hélène Morlon <morlon@biologie.ens.fr>
Diff between RPANDA versions 1.1 dated 2015-09-14 and 1.2 dated 2016-03-31
DESCRIPTION | 13 +++++++------ MD5 | 32 +++++++++++++++++++++++++++----- NAMESPACE | 6 +++++- R/CreateGeoObject.R |only R/DDexp.rescale.R |only R/DDexp.rescale.geog.R |only R/DDlin.rescale.R |only R/DDlin.rescale.geog.R |only R/JSDtree_cluster.R | 11 +++++++++-- R/MC.rescale.R |only R/MC.rescale_geog.R |only R/fit_t_comp.R |only R/likelihood_t_DD.R |only R/likelihood_t_DD_geog.R |only R/likelihood_t_MC.R |only R/likelihood_t_MC_geog.R |only R/sim_t_comp.R |only README.md | 6 +++--- data/Anolis.data.rda |only man/Anolis.data.Rd |only man/CreateGeoObject.Rd |only man/JSDtree_cluster.Rd | 9 ++++++--- man/fit_t_comp.Rd |only man/likelihood_t_DD.Rd |only man/likelihood_t_DD_geog.Rd |only man/likelihood_t_MC.Rd |only man/likelihood_t_MC_geog.Rd |only man/sim_t_comp.Rd |only 28 files changed, 57 insertions(+), 20 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: http://sdmx.org .
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.5 dated 2015-11-26 and 1.6 dated 2016-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/java/SDMX.jar |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, unit conversions.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 1.0-2 dated 2016-03-18 and 1.0-3 dated 2016-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/fitBB.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
Author: Yi Wang, Ulrike Naumann, Stephen Wright, Dirk Eddelbuettel and David Warton
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 3.11.5 dated 2015-11-24 and 3.11.7 dated 2016-03-31
mvabund-3.11.5/mvabund/cleanup |only mvabund-3.11.7/mvabund/DESCRIPTION | 8 +++--- mvabund-3.11.7/mvabund/MD5 | 29 +++++++++++------------- mvabund-3.11.7/mvabund/R/anova.manyglm.R | 11 ++++----- mvabund-3.11.7/mvabund/R/default.plot.manyglm.R | 14 ++++++----- mvabund-3.11.7/mvabund/R/manyany.R | 2 - mvabund-3.11.7/mvabund/R/manyglm.R | 15 ++++++------ mvabund-3.11.7/mvabund/R/predict.traitglm.R | 22 ++++++++++++++---- mvabund-3.11.7/mvabund/R/summary.manyglm.R | 15 ++++++++---- mvabund-3.11.7/mvabund/README.md | 2 - mvabund-3.11.7/mvabund/man/anova.manyglm.Rd | 3 -- mvabund-3.11.7/mvabund/man/manyglm.Rd | 17 +++++++------- mvabund-3.11.7/mvabund/man/summary.manyglm.Rd | 7 ++--- mvabund-3.11.7/mvabund/src/Rinterface.cpp | 2 + mvabund-3.11.7/mvabund/src/glm.cpp | 1 mvabund-3.11.7/mvabund/src/resampTest.h | 1 16 files changed, 87 insertions(+), 62 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between mclust versions 5.1 dated 2015-10-27 and 5.2 dated 2016-03-31
DESCRIPTION | 14 MD5 | 84 +-- NAMESPACE | 8 R/bootstrap.R | 328 +++++++++++-- R/densityMclust.R | 52 -- R/icl.R | 88 +-- R/init.R | 12 R/mclust.R | 760 ++++++++++++++------------------ R/mclustda.R | 8 R/mclustdr.R | 57 +- R/util.R | 206 +++++++- build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/NEWS | 18 inst/doc/mclust.R | 23 inst/doc/mclust.Rmd | 25 - inst/doc/mclust.html | 176 +++---- man/Mclust.Rd | 17 man/MclustBootstrap.Rd | 27 - man/coordProj.Rd | 21 man/defaultPrior.Rd | 14 man/dens.Rd | 14 man/densityMclust.Rd | 44 - man/mclust-internal.Rd | 5 man/mclust1Dplot.Rd | 4 man/mclust2Dplot.Rd | 16 man/mclustBootstrapLRT.Rd | 2 man/mclustICL.Rd | 14 man/plot.Mclust.Rd | 5 man/plot.densityMclust.Rd | 36 - man/priorControl.Rd | 11 man/surfacePlot.Rd | 13 man/uncerPlot.Rd | 3 src/mclust.f | 4 src/mclustaddson.f | 38 - vignettes/mclust.Rmd | 25 - 43 files changed, 1267 insertions(+), 905 deletions(-)
Title: Selecting the Best Set of Relevant Environmental Variables along
with the Optimal Regularization Multiplier for Maxent Niche
Modeling
Description: Complex niche models show low performance in identifying
the most important range-limiting environmental variables and in
transferring habitat suitability to novel environmental conditions
(Warren and Seifert, 2011; Warren et al., 2014). This package helps to
identify the most important set of uncorrelated variables and to
fine-tune Maxent's regularization multiplier. In combination, this
allows to constrain complexity and increase performance of Maxent niche
models (assessed by information criteria, such as AICc (Akaike, 1974) ,
and by the area under the receiver operating characteristic (AUC)
(Fielding and Bell, 1997). Users of this package should be familiar with
Maxent niche modelling.
Author: Alexander Jueterbock
Maintainer: "Alexander Jueterbock" <Alexander-Jueterbock@web.de>
Diff between MaxentVariableSelection versions 1.0-0 dated 2015-09-22 and 1.0-1 dated 2016-03-31
DESCRIPTION | 11 ++-- MD5 | 14 +++-- NEWS.md |only README.md |only build/vignette.rds |binary inst/CITATION |only man/MaxentVariableSelection-package.Rd | 16 ++---- vignettes/MaxentVariableSelection.Rmd | 14 +++-- vignettes/MaxentVariableSelection.html | 85 +++++++++++++++++++++++++-------- vignettes/auto |only 10 files changed, 96 insertions(+), 44 deletions(-)
More information about MaxentVariableSelection at CRAN
Permanent link
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions.
Author: Edzer Pebesma [aut, cre],
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 1.1-2 dated 2016-02-23 and 1.1-3 dated 2016-03-31
DESCRIPTION | 6 MD5 | 76 - NAMESPACE | 2 R/krige0.R | 216 ++- build/vignette.rds |binary data/DE_RB_2005.rda |only data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary demo/00Index | 4 demo/stkrige-crossvalidation.R |only demo/stkrige-prediction.R |only demo/stkrige.R | 434 +++--- inst/NEWS.Rd | 18 inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.Rnw | 413 +++--- inst/doc/spatio-temporal-kriging.bib | 1732 +------------------------- inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/DE_RB_2005.Rd |only man/krigeST.Rd | 11 vignettes/figures/allVgmsDiffWireframe.png |only vignettes/figures/allVgmsWireframe.png |binary vignettes/figures/daily_means_PM10.png |binary vignettes/figures/diffs_daily_means_PM10.png |only vignettes/figures/pred_daily_means_PM10.png |binary vignettes/figures/singleStationTimeSeries.png |binary vignettes/figures/vgmVsMetricDist.png |binary vignettes/spatio-temporal-kriging.Rnw | 413 +++--- vignettes/spatio-temporal-kriging.bib | 1732 +------------------------- 42 files changed, 1202 insertions(+), 3855 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.1.0 dated 2016-03-18 and 2.1.1 dated 2016-03-31
DESCRIPTION | 11 +++-- MD5 | 79 ++++++++++++++++++++++-------------------- NAMESPACE | 8 ++++ NEWS | 7 +++ R/annotation-raster-tern.R |only R/coord-tern.R | 23 ++++++------ R/doc-data.R | 37 +++++++++++++++---- R/geom-confidence-tern.R | 9 ++-- R/geom-crosshair-tern.R | 8 ++-- R/geom-density-tern.R | 4 +- R/geom-errorbarX.R | 8 ++-- R/geom-interpolate-tern.R | 4 +- R/geom-mask.R | 9 ++-- R/geom-point-swap.R |only R/geom-smooth-tern.R | 8 ++-- R/legend-draw-tern.R | 14 +++++++ R/plot-build.R | 11 +++-- R/stat-confidence-tern.R | 8 ++-- R/stat-density-tern.R | 9 ++-- R/stat-interpolate-tern.R | 7 ++- R/stat-smooth-tern.R | 11 +++-- R/strip-unapproved.R | 2 + R/theme-bordersontop.R |only R/theme-defaults.R | 3 + R/theme-elements.R | 7 ++- R/theme-gridsontop.R | 9 ++++ R/utilities.R | 18 +++++++-- build/partial.rdb |binary data/FeldsparRaster.RData |only man/annotation-raster-tern.Rd |only man/data_sets_Feldspar.Rd | 31 +++++++++++++--- man/draw_key_tern.Rd | 3 + man/geom_confidence_tern.Rd | 19 ++++------ man/geom_crosshair_tern.Rd | 14 +++---- man/geom_density_tern.Rd | 15 +++---- man/geom_errorbarX.Rd | 14 +++---- man/geom_interpolate_tern.Rd | 18 ++++----- man/geom_point_swap.Rd |only man/geom_smooth_tern.Rd | 26 ++++++------- man/stat_density_tern.Rd | 14 +++---- man/theme_bordersontop.Rd |only man/theme_elements.Rd | 3 + man/theme_gridsontop.Rd | 6 ++- man/undocumented.Rd | 11 +++++ 44 files changed, 305 insertions(+), 183 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: Provides the next iteration of the EMU Speech
Database Management System (EMU_SDMS) with database management, data
extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between emuR versions 0.1.6 dated 2016-03-24 and 0.1.7 dated 2016-03-31
DESCRIPTION | 8 MD5 | 27 NEWS.md | 7 R/emuR-convert_TextGridCollection.R | 5 R/emuR-create_DBconfigFromTextGrid.R | 5 R/emuR-create_filePairList.R | 4 R/emuR-database.files.R | 2 README.md | 5 build/vignette.rds |binary inst/doc/EQL.R |only inst/doc/EQL.Rmd | 968 +++++++++++++++++++++++------------ inst/doc/EQL.html | 927 +++++++++++++++++++++++++-------- inst/doc/emuDB.html | 10 inst/doc/emuR_intro.html | 6 tests/testthat/test_emuR-database.R | 6 15 files changed, 1404 insertions(+), 576 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: The facilities can roughly be grouped as:
1) Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Sren Hjsgaard <sorenh@math.aau.dk> and Ulrich Halekoh <uhalekoh@health.sdu.dk>
Maintainer: Sren Hjsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.5-14 dated 2015-12-29 and 4.5-15 dated 2016-03-31
doBy-4.5-14/doBy/R/LSmeans.R |only doBy-4.5-14/doBy/R/linestMatrix.R |only doBy-4.5-15/doBy/ChangeLog | 8 doBy-4.5-15/doBy/DESCRIPTION | 11 doBy-4.5-15/doBy/MD5 | 24 - doBy-4.5-15/doBy/NAMESPACE | 32 +- doBy-4.5-15/doBy/R/linest.R | 53 +-- doBy-4.5-15/doBy/R/linestGet.R | 462 ++++++++++++++-------------------- doBy-4.5-15/doBy/R/linestLSmatrix.R |only doBy-4.5-15/doBy/R/linestUtilities.R |only doBy-4.5-15/doBy/inst/doc/LSmeans.pdf |binary doBy-4.5-15/doBy/inst/doc/doBy.pdf |binary doBy-4.5-15/doBy/man/doBy-internal.Rd | 67 +++- doBy-4.5-15/doBy/man/esticon.Rd | 3 doBy-4.5-15/doBy/man/is_estimable.Rd |only doBy-4.5-15/doBy/man/null_basis.Rd |only 16 files changed, 321 insertions(+), 339 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse
the tree in various orders. Aggregate, cumulate, print, plot, convert to and from
data.frame and more. Useful for decision trees, machine learning,
finance, conversion from and to JSON, and many other applications.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.3.0 dated 2016-02-12 and 0.3.5 dated 2016-03-31
DESCRIPTION | 8 MD5 | 57 ++--- NAMESPACE | 1 NEWS | 26 ++ R/node.R | 8 R/node_conversion_dataframe.R | 4 R/node_conversion_list.R | 76 +++++-- R/node_methods.R | 41 ++++ README.md | 2 build/vignette.rds |binary data/acme.rda |binary data/mushroom.rda |binary inst/doc/applications.R | 49 ++-- inst/doc/applications.Rmd | 65 ++++-- inst/doc/applications.html | 346 ++++++++++++++++++++--------------- inst/doc/data.tree.R | 12 - inst/doc/data.tree.Rmd | 14 - inst/doc/data.tree.html | 229 ++++++++++++++--------- man/Climb.Rd | 2 man/FindNode.Rd |only man/NODE_RESERVED_NAMES_CONST.Rd | 2 man/Node.Rd | 1 man/as.Node.data.frame.Rd | 2 man/as.Node.list.Rd | 16 + man/as.data.frame.Node.Rd | 2 man/as.list.Node.Rd | 2 tests/testthat/test-treeConversion.R | 94 +++++++++ tests/testthat/test-treeMethods.R | 36 +++ vignettes/applications.Rmd | 65 ++++-- vignettes/data.tree.Rmd | 14 - 30 files changed, 785 insertions(+), 389 deletions(-)
Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Diff between cancerTiming versions 3.1.5 dated 2016-02-09 and 3.1.6 dated 2016-03-31
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 + R/labelSeg.R | 14 +++++++------- R/mut2seg.R | 12 ++++++------ 5 files changed, 23 insertions(+), 22 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from
Liang et al (2008)
<http://dx.doi.org/10.1198/016214507000001337>
for linear models or mixtures of
g-priors in GLMs of Li and Clyde (2015)
<http://arxiv.org/abs/1503.06913 >. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models and for large p truncated priors on the model
space. The user may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.9 dated 2016-02-03 and 1.1.0 dated 2016-03-31
BAS-1.0.9/BAS/inst/doc |only BAS-1.1.0/BAS/CHANGELOG | 8 +++++++ BAS-1.1.0/BAS/DESCRIPTION | 22 ++++++++++++------- BAS-1.1.0/BAS/MD5 | 31 ++++++++++++++------------- BAS-1.1.0/BAS/NAMESPACE | 4 +-- BAS-1.1.0/BAS/R/bas.R | 9 +++++-- BAS-1.1.0/BAS/R/image.bma.R | 2 - BAS-1.1.0/BAS/R/modelpriors.R | 13 +++++++++++ BAS-1.1.0/BAS/R/plot.bma.R | 10 ++++---- BAS-1.1.0/BAS/R/predict.bma.R | 22 +++++++++---------- BAS-1.1.0/BAS/man/bas.Rd | 18 +++++++-------- BAS-1.1.0/BAS/man/image.bma.Rd | 8 +++---- BAS-1.1.0/BAS/man/plot.bma.Rd | 17 +++++++-------- BAS-1.1.0/BAS/man/trunc.beta.binomial.Rd |only BAS-1.1.0/BAS/man/trunc.poisson.Rd |only BAS-1.1.0/BAS/src/mcmc_new.c | 8 +++++-- BAS-1.1.0/BAS/src/probabilities.c | 35 ++++++++++++++++++++++++++++++- BAS-1.1.0/BAS/src/sampling.h | 2 + 18 files changed, 139 insertions(+), 70 deletions(-)
Title: Phylogenetic Methods for Multiple Gene Data
Description: Toolkit for the analysis of multiple gene data. Apex implements
the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle
aligned DNA sequences from multiple genes.
Author: Thibaut Jombart [aut, cre],
Zhian Namir Kamvar [aut],
Klaus Schliep [aut],
Eric Archer [aut],
Rebecca Harris [aut]
Maintainer: Thibaut Jombart <t.jombart@imperial.ac.uk>
Diff between apex versions 1.0.1 dated 2015-09-07 and 1.0.2 dated 2016-03-31
DESCRIPTION | 17 MD5 | 83 +- NAMESPACE | 12 R/accessors.R | 189 ++++- R/internal.R | 16 R/readfiles.R | 12 R/show.R | 2 R/subset.R | 4 README.md | 405 ++++++++---- inst/doc/apex.R | 96 +- inst/doc/apex.Rmd | 190 +++-- inst/doc/apex.html | 1146 ++++++++++++++--------------------- man/accessors.Rd | 79 +- man/add.gaps.Rd | 2 man/apex.Rd | 2 man/concatenate.Rd | 3 man/dist.multidna.Rd | 4 man/getTree.Rd | 4 man/initialize-multidna-method.Rd | 4 man/initialize-multiphyDat-method.Rd | 3 man/multidna.Rd | 4 man/multidna2alignment.Rd | 2 man/multidna2genind.Rd | 4 man/multidna2multiphyDat.Rd | 4 man/multiphyDat.Rd | 3 man/plot-multidna-ANY-method.Rd | 3 man/readfiles.Rd | 7 man/rm.gaps.Rd | 2 man/show-multidna-method.Rd | 2 man/show-multiphyDat-method.Rd | 2 man/subset.multidna.Rd | 6 vignettes/apex.Rmd | 122 ++- vignettes/apex.md |only vignettes/figs/class-1.png |binary vignettes/figs/class-2.png |binary vignettes/figs/concat-1.png |binary vignettes/figs/concat-2.png |binary vignettes/figs/handling-1.png |binary vignettes/figs/handling-2.png |binary vignettes/figs/multidnaclass-1.png |only vignettes/figs/multidnaclass-2.png |only vignettes/figs/plotMultiPhylo-1.png |binary vignettes/figs/plotPhyloSingle-1.png |binary vignettes/figs/readfiles-1.png |binary 44 files changed, 1378 insertions(+), 1056 deletions(-)
Title: Adverse Outcome Pathway Analysis
Description: Provides tools for analyzing adverse outcome pathways
(AOPs) for pharmacological and toxicological research. Functionality
includes the ability to perform causal network analysis of networks
developed in and exported from Cytoscape or existing as R graph objects, and
identifying the point of departure/screening/risk value from concentration-
response data.
Author: Lyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
Maintainer: Lyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
Diff between aop versions 0.99.5 dated 2015-06-16 and 1.0.0 dated 2016-03-31
DESCRIPTION | 27 - MD5 | 45 +- NAMESPACE | 49 +- R/aop_graph_analysis.R | 418 ++++++++++++------------- R/bmr_Class.R |only R/pod_analysis.R |only README.md |only build/vignette.rds |binary data |only inst/doc/aop.R | 51 +-- inst/doc/aop.Rmd | 148 ++++---- inst/doc/aop.html | 224 ++++++------- inst/doc/concentration-response_analysis.R |only inst/doc/concentration-response_analysis.Rmd |only inst/doc/concentration-response_analysis.html |only man/aop_backdoor.Rd | 100 ++--- man/aop_cytoscape-class.Rd | 50 +- man/aop_cytoscape-methods.Rd | 62 +-- man/bmr-class.Rd |only man/bootstrap_metaregression.Rd |only man/calculate_confidence_and_median.Rd |only man/convert_aop_to_graph.Rd | 62 +-- man/convert_cytoscape_to_aop.Rd | 58 +-- man/internal_model_fits.Rd |only man/oxybenzone.Rd |only man/plot_metaregression_confidence_envelope.Rd |only man/plot_metaregression_spaghetti_plot.Rd |only man/plot_slope_analysis.Rd |only man/pod_envelope_analysis.Rd |only man/pod_slope_analysis.Rd |only man/slope_pod_analysis.Rd |only vignettes/aop.Rmd | 2 vignettes/concentration-response_analysis.Rmd |only 33 files changed, 663 insertions(+), 633 deletions(-)
Title: Tools for Collecting Social Media Data and Generating Networks
for Analysis
Description: A suite of tools for collecting and constructing networks from
social media data. Provides easy-to-use functions for collecting data across
popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating
different types of networks for analysis.
Author: Timothy Graham & Robert Ackland with contribution from Chung-hong Chan
Maintainer: Timothy Graham <timothy.graham3@uq.net.au>
Diff between SocialMediaLab versions 0.19.0 dated 2015-11-26 and 0.20.0 dated 2016-03-30
DESCRIPTION | 15 - MD5 | 92 +++++---- NAMESPACE | 97 ++++++--- R/Authenticate.R |only R/AuthenticateWithFacebookAPI.R | 56 +++++ R/AuthenticateWithInstagramAPI.R | 48 ++++ R/AuthenticateWithTwitterAPI.R | 40 +++ R/AuthenticateWithYoutubeAPI.R | 29 ++ R/Collect.R |only R/CollectDataFacebook.R | 105 +++++++++- R/CollectDataInstagram.R | 113 ++++++++++- R/CollectDataTwitter.R | 85 ++++++++ R/CollectDataYoutube.R | 362 +++++++++++++++++++++++++++++++++++- R/CollectEgoInstagram.R |only R/Create.R |only R/CreateActorNetwork.R | 80 +++++++ R/CreateActorNetwork.list.R | 1 R/CreateActorNetwork.twitter.R | 1 R/CreateActorNetwork.youtube.R | 1 R/CreateBimodalNetwork.R | 84 ++++++++ R/CreateBimodalNetwork.facebook.R | 1 R/CreateBimodalNetwork.instagram.R | 1 R/CreateBimodalNetwork.list.R | 1 R/CreateBimodalNetwork.twitter.R | 1 R/CreateDynamicNetwork.R | 86 ++++++++ R/CreateEgoNetwork.R | 73 +++++++ R/CreateEgoNetworkFromData.R |only R/CreateSemanticNetwork.R | 99 +++++++++ R/CreateSemanticNetwork.list.R | 1 R/CreateSemanticNetwork.twitter.R | 1 R/GetYoutubeVideoIDs.R | 48 ++++ R/SocialMediaLab-package.R |only man/Authenticate.Rd |only man/AuthenticateWithFacebookAPI.Rd | 90 +++++--- man/AuthenticateWithInstagramAPI.Rd | 75 ++++--- man/AuthenticateWithTwitterAPI.Rd | 76 +++---- man/AuthenticateWithYoutubeAPI.Rd | 53 ++--- man/Collect.Rd |only man/CollectDataFacebook.Rd | 131 ++++++++----- man/CollectDataInstagram.Rd | 148 ++++++++------ man/CollectDataTwitter.Rd | 126 +++++++----- man/CollectDataYoutube.Rd | 115 +++++++---- man/CollectEgoInstagram.Rd |only man/Create.Rd |only man/CreateActorNetwork.Rd | 96 ++++++--- man/CreateBimodalNetwork.Rd | 108 ++++++---- man/CreateDynamicNetwork.Rd | 108 ++++++---- man/CreateEgoNetwork.Rd | 122 +++++++----- man/CreateEgoNetworkFromData.Rd |only man/CreateSemanticNetwork.Rd | 136 ++++++++----- man/GetYoutubeVideoIDs.Rd | 56 +++-- man/SaveCredential.Rd |only man/SocialMediaLab-package.Rd | 37 ++- 53 files changed, 2345 insertions(+), 653 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Relative Contribution of Effects in a Regression Model
Description: Functions to facilitate inference on the relative importance of predictors in a linear or generalized linear model, and a couple of useful Tcl/Tk widgets.
Author: David Firth with contributions from Heather Turner and John Fox
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between relimp versions 1.0-4 dated 2015-02-03 and 1.0-5 dated 2016-03-30
DESCRIPTION | 13 - MD5 | 8 NAMESPACE | 9 R/showData.R | 598 +++++++++++++++++++++++++------------------------------- man/showData.Rd | 4 5 files changed, 290 insertions(+), 342 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Description: Functions to compute quasi variances and associated measures of approximation error.
Author: David Firth
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between qvcalc versions 0.8-9 dated 2015-02-03 and 0.9-0 dated 2016-03-30
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 4 ++++ 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Package Management Tool
Description: Tools to more conveniently perform tasks associated with
add-on packages. pacman conveniently wraps library and package
related functions and names them in an intuitive and consistent
fashion. It seeks to combine functionality from lower level
functions which can speed up workflow.
Author: Tyler Rinker [aut, cre, ctb], Dason Kurkiewicz [aut, ctb],
Keith Hughitt [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between pacman versions 0.3.0 dated 2015-02-20 and 0.4.1 dated 2016-03-30
DESCRIPTION | 37 +++-- MD5 | 163 +++++++++++++------------ NAMESPACE | 11 + NEWS | 33 ++++- R/p_author.R | 6 R/p_boot.R |only R/p_citation.R | 6 R/p_cran.R | 4 R/p_data.R | 6 R/p_delete_single.R | 2 R/p_depends.R | 4 R/p_exists.R | 2 R/p_functions.R | 4 R/p_help.R | 8 - R/p_information.R | 2 R/p_install.R | 26 +++- R/p_install_gh.R | 2 R/p_install_version_gh.R |only R/p_install_version_single.R | 2 R/p_install_version_single_gh.R |only R/p_interactive.R | 12 - R/p_load_current_gh.R |only R/p_load_current_single_gh.R |only R/p_loaded.R | 2 R/p_news.R | 2 R/p_old.R |only R/p_path.R | 18 ++ R/p_search_library.R | 2 R/p_unload.R | 4 R/p_update.R | 4 R/p_version.R | 120 ++++++++++++++++++ R/p_vignette.R | 6 R/p_zip.R | 8 - R/utils.R | 12 - README.md | 10 + build/vignette.rds |binary inst/CITATION | 10 - inst/doc/Introduction_to_pacman.R | 54 ++++---- inst/doc/Introduction_to_pacman.Rmd | 4 inst/doc/Introduction_to_pacman.html | 177 +++++++++++++++------------- inst/doc/pacman_functions_quick_reference.R | 14 +- man/p_author.Rd | 2 man/p_base.Rd | 10 - man/p_boot.Rd |only man/p_citation.Rd | 8 - man/p_cran.Rd | 4 man/p_data.Rd | 6 man/p_delete.Rd | 14 +- man/p_depends.Rd | 20 +-- man/p_detectOS.Rd | 2 man/p_exists.Rd | 6 man/p_extract.Rd | 8 - man/p_functions.Rd | 6 man/p_help.Rd | 10 - man/p_information.Rd | 12 - man/p_install.Rd | 8 - man/p_install_gh.Rd | 6 man/p_install_version.Rd | 8 - man/p_install_version_gh.Rd |only man/p_interactive.Rd | 4 man/p_isinstalled.Rd | 2 man/p_library.Rd | 8 - man/p_load.Rd | 22 +-- man/p_load_current_gh.Rd |only man/p_load_gh.Rd | 20 +-- man/p_loaded.Rd | 14 +- man/p_news.Rd | 4 man/p_old.Rd |only man/p_opendir.Rd | 2 man/p_path.Rd | 9 + man/p_search_any.Rd | 12 - man/p_search_library.Rd | 12 - man/p_set_cranrepo.Rd | 2 man/p_temp.Rd | 2 man/p_unload.Rd | 14 +- man/p_unlock.Rd | 14 +- man/p_update.Rd | 10 - man/p_version.Rd | 31 ++++ man/p_vignette.Rd | 16 +- man/print.p_version_diff.Rd |only man/print.search_any.Rd | 2 man/print.wide_table.Rd | 2 tests/testthat/test-p_author.R | 8 - tests/testthat/test-p_install.R | 8 - tests/testthat/test-p_install_gh.R | 2 tests/testthat/test-p_install_version.R | 16 +- tests/testthat/test-p_version.R | 2 vignettes/Introduction_to_pacman.Rmd | 4 88 files changed, 708 insertions(+), 441 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut]
Maintainer: Jared E. Knowles <jknowles@gmail.com>
Diff between merTools versions 0.2.0 dated 2016-02-19 and 0.2.1 dated 2016-03-30
DESCRIPTION | 12 +++---- MD5 | 10 +++--- NEWS.md | 4 ++ README.md | 60 ++++++++++++++++++------------------ inst/doc/Using_predictInterval.html | 43 ++++++++++++------------- inst/doc/merToolsIntro.html | 21 ++++++------ 6 files changed, 76 insertions(+), 74 deletions(-)
Title: Test of Stationarity and Localized Autocovariance
Description: Provides test of second-order stationarity for time
series (for dyadic and arbitrary-n length data). Provides
localized autocovariance, with confidence intervals,
for locally stationary (nonstationary) time series.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <g.p.nason@bristol.ac.uk>
Diff between locits versions 1.4 dated 2013-10-18 and 1.7.1 dated 2016-03-30
locits-1.4/locits/R/locits-internal.R |only locits-1.7.1/locits/DESCRIPTION | 17 +++-- locits-1.7.1/locits/MD5 | 45 ++++++++++----- locits-1.7.1/locits/NAMESPACE | 44 ++++++++++++++ locits-1.7.1/locits/R/AutoBestBW.R | 2 locits-1.7.1/locits/R/EstBetaCov.R |only locits-1.7.1/locits/R/StoreStatistics.R | 2 locits-1.7.1/locits/R/hwt.R |only locits-1.7.1/locits/R/hwtos.R |only locits-1.7.1/locits/R/hwtos2.R | 8 ++ locits-1.7.1/locits/R/plot.hwtANYN.R |only locits-1.7.1/locits/R/plot.tosANYN.R |only locits-1.7.1/locits/R/print.hwtANYN.R |only locits-1.7.1/locits/R/print.tosANYN.R |only locits-1.7.1/locits/R/summary.hwtANYN.R |only locits-1.7.1/locits/R/summary.tosANYN.R |only locits-1.7.1/locits/R/zeropad.R |only locits-1.7.1/locits/inst/CHANGES | 40 +++++++++++++ locits-1.7.1/locits/man/AutoBestBW.Rd | 2 locits-1.7.1/locits/man/EstBetaCov.Rd |only locits-1.7.1/locits/man/hwt.Rd |only locits-1.7.1/locits/man/hwtos.Rd |only locits-1.7.1/locits/man/hwtos2.Rd | 5 + locits-1.7.1/locits/man/locits-package.Rd | 9 ++- locits-1.7.1/locits/man/plot.hwtANYN.Rd |only locits-1.7.1/locits/man/plot.tos.Rd | 15 ++--- locits-1.7.1/locits/man/plot.tosANYN.Rd |only locits-1.7.1/locits/man/print.hwtANYN.Rd |only locits-1.7.1/locits/man/print.tosANYN.Rd |only locits-1.7.1/locits/man/summary.hwtANYN.Rd |only locits-1.7.1/locits/man/summary.tos.Rd | 3 - locits-1.7.1/locits/man/summary.tosANYN.Rd |only locits-1.7.1/locits/man/zeropad.Rd |only locits-1.7.1/locits/src/CPkPlj.c | 86 ++++++++++++++++++++++++----- 34 files changed, 228 insertions(+), 50 deletions(-)
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to 'stats::lowess' function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting "Venn" diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gplots versions 3.0.0 dated 2016-03-28 and 3.0.1 dated 2016-03-30
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 13 +++++++++++++ R/plot.lowess.R | 7 ++++--- inst/ChangeLog | 25 +++++++++++++++++++++++++ inst/NEWS | 13 +++++++++++++ inst/doc/venn.pdf |binary man/heatmap.2.Rd | 2 +- man/lowess.Rd | 24 +++++++++++++++++++++++- 10 files changed, 117 insertions(+), 18 deletions(-)
Title: Visualization of Functional Analysis Data
Description: Implementation of multilayered visualizations for enhanced
graphical representation of functional analysis data. It combines and integrates
omics data derived from expression and functional annotation enrichment
analyses. Its plotting functions have been developed with an hierarchical
structure in mind: starting from a general overview to identify the most
enriched categories (modified bar plot, bubble plot) to a more detailed one
displaying different types of relevant information for the molecules in a given
set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).
Author: Wencke Walter [aut, cre],
Fatima Sanchez-Cabo [aut]
Maintainer: Wencke Walter <wencke.walter@arcor.de>
Diff between GOplot versions 1.0.1 dated 2015-07-16 and 1.0.2 dated 2016-03-30
GOplot-1.0.1/GOplot/man/bezier.Rd |only GOplot-1.0.1/GOplot/man/circleFun.Rd |only GOplot-1.0.1/GOplot/man/draw_table.Rd |only GOplot-1.0.1/GOplot/man/get_overlap.Rd |only GOplot-1.0.1/GOplot/man/get_overlap2.Rd |only GOplot-1.0.1/GOplot/man/theme_blank.Rd |only GOplot-1.0.2/GOplot/DESCRIPTION | 40 +-- GOplot-1.0.2/GOplot/MD5 | 63 ++--- GOplot-1.0.2/GOplot/NAMESPACE | 4 GOplot-1.0.2/GOplot/NEWS.md |only GOplot-1.0.2/GOplot/R/GOCluster.R | 69 +++-- GOplot-1.0.2/GOplot/R/GOCore.R | 276 ++++++++++------------ GOplot-1.0.2/GOplot/R/GOHeat.R |only GOplot-1.0.2/GOplot/R/GOVenn.R | 183 -------------- GOplot-1.0.2/GOplot/R/Helper.R |only GOplot-1.0.2/GOplot/README.md | 4 GOplot-1.0.2/GOplot/build/vignette.rds |binary GOplot-1.0.2/GOplot/inst/CITATION |only GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.R | 30 ++ GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.Rmd | 78 ++++-- GOplot-1.0.2/GOplot/inst/doc/GOplot_vignette.html | 71 +++-- GOplot-1.0.2/GOplot/man/EC.Rd | 2 GOplot-1.0.2/GOplot/man/GOBar.Rd | 22 - GOplot-1.0.2/GOplot/man/GOBubble.Rd | 43 +-- GOplot-1.0.2/GOplot/man/GOChord.Rd | 64 +++-- GOplot-1.0.2/GOplot/man/GOCircle.Rd | 53 ++-- GOplot-1.0.2/GOplot/man/GOCluster.Rd | 28 +- GOplot-1.0.2/GOplot/man/GOHeat.Rd |only GOplot-1.0.2/GOplot/man/GOVenn.Rd | 32 +- GOplot-1.0.2/GOplot/man/chord_dat.Rd | 41 --- GOplot-1.0.2/GOplot/man/circle_dat.Rd | 28 +- GOplot-1.0.2/GOplot/man/reduce_overlap.Rd |only GOplot-1.0.2/GOplot/vignettes/GOBar.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble1.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble2.png |binary GOplot-1.0.2/GOplot/vignettes/GOBubble3.png |only GOplot-1.0.2/GOplot/vignettes/GOBubble4.png |only GOplot-1.0.2/GOplot/vignettes/GOHeat_lfc.png |only GOplot-1.0.2/GOplot/vignettes/GOHeat_nolfc.png |only GOplot-1.0.2/GOplot/vignettes/GOplot_vignette.Rmd | 76 ++++-- GOplot-1.0.2/GOplot/vignettes/Titel.png |only 41 files changed, 576 insertions(+), 631 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalization trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.4 dated 2016-02-10 and 1.4.5 dated 2016-03-30
gaston-1.4.5/gaston/DESCRIPTION | 8 - gaston-1.4.5/gaston/MD5 | 47 ++++++----- gaston-1.4.5/gaston/NAMESPACE | 8 + gaston-1.4.5/gaston/NEWS | 6 + gaston-1.4.5/gaston/R/bm.r | 4 gaston-1.4.5/gaston/R/bm_genomic_sex.r |only gaston-1.4.5/gaston/R/bm_stats.r | 34 +++----- gaston-1.4.5/gaston/inst/doc/gaston.R | 110 ++++++++++++++------------- gaston-1.4.5/gaston/inst/doc/gaston.Rnw | 37 +++++++-- gaston-1.4.5/gaston/inst/doc/gaston.pdf |binary gaston-1.4.5/gaston/man/set.genomic.sex.Rd |only gaston-1.4.5/gaston/man/set.hwe.Rd | 4 gaston-1.4.5/gaston/man/set.stats.Rd | 2 gaston-1.4.5/gaston/src/ai-reml-1k-covar.h | 66 +++++++++++++--- gaston-1.4.5/gaston/src/ai-reml-1k.h | 67 +++++++++++++--- gaston-1.4.5/gaston/src/ai-reml-nk-covar.h | 70 +++++++++++++---- gaston-1.4.5/gaston/src/ai-reml-nk.h | 78 ++++++++++++++----- gaston-1.4.5/gaston/src/any.h |only gaston-1.4.5/gaston/src/export-aireml-nk.cpp | 1 gaston-1.4.5/gaston/src/m4_kinship.cpp | 65 +++++++++------ gaston-1.4.5/gaston/src/m4_kinship_p.cpp | 77 ++++++++++-------- gaston-1.4.5/gaston/vignettes/gaston-028.pdf |only gaston-1.4.5/gaston/vignettes/gaston-032.pdf |only gaston-1.4.5/gaston/vignettes/gaston-039.pdf |only gaston-1.4.5/gaston/vignettes/gaston-041.pdf |only gaston-1.4.5/gaston/vignettes/gaston-043.pdf |only gaston-1.4.5/gaston/vignettes/gaston-047.pdf |only gaston-1.4.5/gaston/vignettes/gaston-053.pdf |only gaston-1.4.5/gaston/vignettes/gaston.Rnw | 37 +++++++-- gaston-1.4/gaston/vignettes/lapin |only 30 files changed, 486 insertions(+), 235 deletions(-)
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 1.2-3 dated 2016-02-04 and 2.0 dated 2016-03-30
DESCRIPTION | 10 MD5 | 27 - NAMESPACE | 3 R/functions.r | 838 ++++++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/NEWS | 10 inst/doc/equateIRT.pdf |binary man/bisectorec.Rd | 26 - man/convert.Rd | 2 man/eqc.Rd | 8 man/equateIRT-internal.Rd | 9 man/equateIRT-package.Rd | 18 man/itm.Rd | 27 + man/score.Rd |only man/summary.meqc.Rd | 2 15 files changed, 794 insertions(+), 186 deletions(-)
Title: Network Reconstruction and Changepoint Detection
Description: Package EDISON (Estimation of Directed Interactions from
Sequences Of Non-homogeneous gene expression) runs an MCMC
simulation to reconstruct networks from time series data, using
a non-homogeneous, time-varying dynamic Bayesian network.
Networks segments and changepoints are inferred concurrently,
and information sharing priors provide a reduction of the
inference uncertainty.
Author: Frank Dondelinger, Sophie Lebre
Maintainer: Frank Dondelinger <fdondelinger.work@gmail.com>
Diff between EDISON versions 1.1 dated 2014-09-14 and 1.1.1 dated 2016-03-30
DESCRIPTION | 9 + MD5 | 127 ++++++++++++++-------------- NAMESPACE | 3 NEWS |only R/EDISON-package.R | 2 R/dinvgamma.R | 6 - man/AcceptableMove.Rd | 5 - man/BinoHyperMove.Rd | 3 man/BinoHyperRatio.Rd | 3 man/CalculateChanges.Rd | 3 man/CalculateLikelihoodRatio.Rd | 3 man/CalculatePriorRatio.Rd | 3 man/CollectNetworkInfo.Rd | 3 man/EDISON-package.Rd | 8 + man/EDISON.run.Rd | 15 +-- man/ExpHyperMove.Rd | 3 man/ExpHyperRatioTarget.Rd | 3 man/HyperParms.Rd | 3 man/HyperparameterMove.Rd | 3 man/NetworkProbBino.Rd | 3 man/NetworkProbExp.Rd | 3 man/NetworkRatioBino.Rd | 3 man/NetworkRatioExp.Rd | 3 man/PriorRatioPoisson.Rd | 3 man/ProposeDiscrete.Rd | 5 - man/addProposalNetworkInfo.Rd | 9 + man/bp.computeAlpha.Rd | 3 man/buildXY.Rd | 3 man/calculateCPPGlobal.Rd | 3 man/calculateCPProbabilities.Rd | 5 - man/calculateEdgeProbabilities.Rd | 7 + man/calculateEdgeProbabilitiesSegs.Rd | 3 man/calculateEdgeProbabilitiesTimePoints.Rd | 3 man/computePx.Rd | 3 man/computeRho4.Rd | 3 man/convert_nets.Rd | 3 man/cp.birth.Rd | 3 man/cp.death.Rd | 3 man/cp.shift.Rd | 3 man/defaultOptions.Rd | 7 + man/dinvgamma.Rd | 7 + man/fix_eigenvalues.Rd | 3 man/generateNetwork.Rd | 7 + man/init.Rd | 3 man/main.Rd | 3 man/make_structure_move.Rd | 7 - man/output.Rd | 3 man/phase.update.Rd | 3 man/proposalTuning.Rd | 3 man/proposeContinuous.Rd | 5 - man/psrf.Rd | 8 + man/psrf_check.Rd | 3 man/psrf_check_hyper.Rd | 3 man/readDataTS.Rd | 3 man/rinvgamma.Rd | 7 + man/runDBN.Rd | 7 - man/sampleBinit.Rd | 3 man/sampleBxy.Rd | 3 man/sampleDelta2.Rd | 3 man/sampleK.Rd | 3 man/sampleParms.Rd | 3 man/sampleSig2.Rd | 3 man/simulateNetwork.Rd | 13 +- man/updateSigMulti.Rd | 3 man/updateSigSolo.Rd | 3 65 files changed, 243 insertions(+), 155 deletions(-)
Title: Reading EDF(+) and BDF(+) Files
Description: Reads European Data Format files EDF and EDF+, see http://www.edfplus.info,
BioSemi Data Format files BDF, see http://www.biosemi.com/faq/file_format.htm,
and BDF+ files, see http://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html.
The files are read in two steps: first the header is read
and then the signals (using the header object as a parameter).
Author: Jan Vis [aut, cre]
Maintainer: Jan Vis <jan@visconsultancy.eu>
Diff between edfReader versions 1.0.0 dated 2016-02-07 and 1.1.0 dated 2016-03-30
edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD.bdf |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_annotations.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_data.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_header.txt |only edfReader-1.0.0/edfReader/inst/extdata/bdfPlusD_signals.txt |only edfReader-1.0.0/edfReader/tests/testthat/testSampleFiles.R |only edfReader-1.1.0/edfReader/DESCRIPTION | 9 edfReader-1.1.0/edfReader/MD5 | 49 edfReader-1.1.0/edfReader/NAMESPACE | 1 edfReader-1.1.0/edfReader/NEWS.md |only edfReader-1.1.0/edfReader/R/edfReader.R | 9 edfReader-1.1.0/edfReader/R/readHeaderFunctions.R | 61 edfReader-1.1.0/edfReader/R/readSignalFunctions.R | 492 ++++-- edfReader-1.1.0/edfReader/R/s3functions.R | 418 +++-- edfReader-1.1.0/edfReader/build/vignette.rds |binary edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.R | 57 edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.Rmd | 275 ++- edfReader-1.1.0/edfReader/inst/doc/edfReaderVignette.html | 720 +++++----- edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC.bdf |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_annotations.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_data.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_header.txt |only edfReader-1.1.0/edfReader/inst/extdata/bdfPlusC_signals.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC.edf |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_annotations.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_header.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfAnnonC_signals.txt |only edfReader-1.1.0/edfReader/inst/extdata/edfPlusD.edf |only edfReader-1.1.0/edfReader/man/edfReader.Rd | 6 edfReader-1.1.0/edfReader/man/readEdfSignals.Rd | 14 edfReader-1.1.0/edfReader/tests/testthat/testCSampleFiles.R |only edfReader-1.1.0/edfReader/tests/testthat/testDSampleFiles.R |only edfReader-1.1.0/edfReader/tests/testthat/testFromTill.R | 302 ++-- edfReader-1.1.0/edfReader/tests/testthat/testReadEdfSignalsParams.R | 132 + edfReader-1.1.0/edfReader/vignettes/edfReaderVignette.Rmd | 275 ++- 35 files changed, 1722 insertions(+), 1098 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.5.1 dated 2016-03-25 and 3.5.2 dated 2016-03-30
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS | 5 +++++ R/startup_messages.R | 2 +- inst/doc/a-introduction.html | 16 +++++++++++++++- inst/doc/h-creating-your-own-maps.html | 2 +- 6 files changed, 33 insertions(+), 14 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.1-2 dated 2016-01-27 and 0.1-3 dated 2016-03-30
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS | 9 ++++ R/blav_object_methods.R | 2 + R/blav_utils.R | 34 +++++++++++++++++ R/blavaan.R | 68 ++++++++++++++++++++++++---------- R/lav_export_jags.R | 95 ++++++++++++++++++++++++++++++++++-------------- R/set_priors.R | 2 + 8 files changed, 174 insertions(+), 58 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as
defined by Kalbfleisch and Prentice. The underlying survival functions of the
event of interest in each group can be estimated using either the (weighted)
Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition
probabilities in Markov multi-state models. Right-censored and left-truncated
data is supported. Moreover, the difference in restricted mean survival can be
estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.3 dated 2015-10-30 and 1.4 dated 2016-03-30
AHR-1.3/AHR/inst |only AHR-1.4/AHR/DESCRIPTION | 17 ++++++-- AHR-1.4/AHR/MD5 | 53 ++++++++++++++------------- AHR-1.4/AHR/NAMESPACE | 2 - AHR-1.4/AHR/NEWS.md |only AHR-1.4/AHR/R/ahr.R | 56 +++++++++++++++------------- AHR-1.4/AHR/R/quantiles.R | 40 ++++++++++++-------- AHR-1.4/AHR/R/rmean.R | 34 ++++++++++------- AHR-1.4/AHR/R/wkm.R | 64 ++++++++++++++++++++------------- AHR-1.4/AHR/README.md |only AHR-1.4/AHR/man/AHR.Rd | 5 +- AHR-1.4/AHR/man/ahrAJ.Rd | 2 - AHR-1.4/AHR/man/ahrKM.Rd | 2 - AHR-1.4/AHR/man/ahrWKM.Rd | 11 +++-- AHR-1.4/AHR/man/aj.Rd | 4 +- AHR-1.4/AHR/man/avgHR.Rd | 2 - AHR-1.4/AHR/man/fastkm.Rd | 2 - AHR-1.4/AHR/man/print.ahr.Rd | 2 - AHR-1.4/AHR/man/print.rmd.Rd | 2 - AHR-1.4/AHR/man/print.survQuantile.Rd | 2 - AHR-1.4/AHR/man/rmeanDiff.Rd | 6 ++- AHR-1.4/AHR/man/rmeanDiff.ahr.Rd | 2 - AHR-1.4/AHR/man/wkm.Rd | 17 ++++---- AHR-1.4/AHR/man/wkmCompareQuantiles.Rd | 2 - AHR-1.4/AHR/man/wkmQuantile.Rd | 6 +-- AHR-1.4/AHR/tests |only 26 files changed, 191 insertions(+), 142 deletions(-)
Title: Improved False Positive Control of Gene-Permuting GSEA with
Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Diff between AbsFilterGSEA versions 1.0 dated 2016-03-16 and 1.2 dated 2016-03-30
DESCRIPTION | 10 ++--- MD5 | 18 +++++----- NAMESPACE | 18 ++++++---- R/GenePermGSEA.R | 85 ++++++++++++++++++++++++++++++++++++++++---------- R/RcppExports.R | 22 ++++++------ data/example.rda |binary man/GenePermGSEA.Rd | 31 ++++++++++-------- man/example.Rd | 10 +---- src/AbsFilterGSEA.cpp | 7 ++++ vignettes |only 10 files changed, 133 insertions(+), 68 deletions(-)
Title: A Boosted Tweedie Compound Poisson Model
Description: A boosted Tweedie compound Poisson model using the gradient boosting. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing interactions among predictors.
Author: Yi Yang <yi.yang6@mcgill.ca>, Wei Qian <wxqsma@rit.edu>, Hui Zou <hzou@stat.umn.edu>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Diff between TDboost versions 1.1 dated 2015-03-15 and 1.2 dated 2016-03-30
ChangeLog | 12 ++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 10 ++++++++++ R/TDboost.R | 5 +++-- man/TDboost.Rd | 6 ++---- man/TDboost.object.Rd | 2 +- man/TDboost.perf.Rd | 9 ++------- man/plot.TDboost.Rd | 4 +--- man/predict.TDboost.Rd | 9 +++++++-- man/relative.influence.Rd | 4 ++-- man/summary.TDboost.Rd | 3 +-- 12 files changed, 58 insertions(+), 40 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: James P. Howard, II [aut, cre]
Maintainer: "James P. Howard, II" <jh@jameshoward.us>
Diff between phonics versions 0.6.3 dated 2016-02-15 and 0.7.3 dated 2016-03-30
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++++----------- NAMESPACE | 1 + R/cologne.R |only README.md | 3 ++- man/caverphone.Rd | 8 ++++---- man/cologne.Rd |only man/lein.Rd | 7 ++++--- man/metaphone.Rd | 7 ++++--- man/mra.Rd | 7 ++++--- man/nysiis.Rd | 7 ++++--- man/rogerroot.Rd | 7 ++++--- man/soundex.Rd | 7 ++++--- man/statcan.Rd | 7 ++++--- tests/testthat/cologne.csv |only tests/testthat/test-cologne.R |only 16 files changed, 57 insertions(+), 43 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.5 dated 2016-03-19 and 1.6 dated 2016-03-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/hisse.R | 9 +++++++++ R/marginRecon.R | 9 +++++++++ man/hisse.Rd | 4 +++- man/hisseNull4.Rd | 5 ++++- man/marginRecon.Rd | 7 ++++++- man/supportRegion.Rd | 2 +- 8 files changed, 43 insertions(+), 15 deletions(-)
Title: Forecastable Component Analysis
Description: Implementation of Forecastable Component Analysis ('ForeCA'),
including main algorithms and auxiliary function (summary, plotting, etc.) to
apply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel dimension
reduction (DR) technique for temporally dependent signals. Contrary to other
popular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time dependency
explicitly into account and searches for the most ''forecastable'' signal.
The measure of forecastability is based on the Shannon entropy of the spectral
density of the transformed signal.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between ForeCA versions 0.2.2 dated 2015-04-29 and 0.2.4 dated 2016-03-30
DESCRIPTION | 27 +++---- MD5 | 76 ++++++++++----------- NAMESPACE | 7 + NEWS | 12 +++ R/ForeCA-package.R | 1 R/Omega.R | 11 +-- R/complete_controls.R | 2 R/foreca-utils.R | 2 R/foreca.R | 62 ++++++++--------- R/initialize_weightvector.R | 2 R/mvspectrum.R | 4 - R/quadratic_form.R | 8 -- R/spectral_entropy.R | 13 +-- R/whiten.R | 117 +++++++++++++++++++++----------- man/ForeCA-package.Rd | 17 ++-- man/Omega.Rd | 32 ++++---- man/common-arguments.Rd | 26 +++---- man/complete-controls.Rd | 32 ++++---- man/continuous_entropy.Rd | 11 +-- man/discrete_entropy.Rd | 30 ++++---- man/foreca-utils.Rd | 13 +-- man/foreca.EM-aux.Rd | 59 ++++++++-------- man/foreca.EM.one_weightvector.Rd | 27 +++---- man/foreca.Rd | 121 ++++++++++++++++------------------ man/foreca.one_weightvector-utils.Rd | 21 +++-- man/initialize_weightvector.Rd | 26 +++---- man/mvspectrum-utils.Rd | 10 +- man/mvspectrum.Rd | 82 ++++++++++++----------- man/mvspectrum2wcov.Rd | 24 +++--- man/quadratic_form.Rd | 18 +++-- man/sfa.Rd | 25 +++---- man/spectral_entropy.Rd | 36 +++++----- man/whiten.Rd | 57 +++++++++------- tests/testthat/test_foreca.EM-aux.R | 39 +++++----- tests/testthat/test_foreca.R | 34 +++++---- tests/testthat/test_mvspectrum2wcov.R | 5 - tests/testthat/test_quadratic_form.R | 23 +++++- tests/testthat/test_sfa.R | 6 + tests/testthat/test_whiten.R | 18 +++-- 39 files changed, 620 insertions(+), 516 deletions(-)
Title: Bindings to the CommonMark Reference Implementation
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the libcmark reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.7 dated 2016-01-20 and 0.8 dated 2016-03-30
DESCRIPTION | 8 MD5 | 36 NEWS | 3 src/cmark/blocks.c | 664 +++--- src/cmark/buffer.c | 5 src/cmark/chunk.h | 8 src/cmark/cmark.h | 6 src/cmark/cmark_version.h | 4 src/cmark/commonmark.c | 35 src/cmark/html.c | 16 src/cmark/inlines.c | 22 src/cmark/latex.c | 8 src/cmark/main.c | 2 src/cmark/man.c | 5 src/cmark/node.c | 4 src/cmark/parser.h | 2 src/cmark/render.c | 26 src/cmark/scanners.c | 5051 ++++++++++++++++++++++------------------------ src/cmark/xml.c | 20 19 files changed, 2958 insertions(+), 2967 deletions(-)
Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa, and betta_random() permits random effects modelling.
Author: Amy Willis and John Bunge
Maintainer: Amy Willis <adw96@cornell.edu>
Diff between breakaway versions 2.0 dated 2015-10-01 and 3.0 dated 2016-03-30
DESCRIPTION | 11 +-- MD5 | 29 +++++++-- NAMESPACE | 8 ++ R/betta.R | 87 ++++++++++++++--------------- R/betta_pic.R |only R/betta_random.R |only R/breakaway.R | 105 +++++++++++++++++------------------ R/breakaway_nof1.R | 136 +++++++++++++++++++++++----------------------- R/chao1.R |only R/chao1_bc.R |only R/chao_bunge.R |only R/wlrm_transformed.R |only R/wlrm_untransformed.R |only man/betta.Rd | 25 +++++--- man/betta_pic.Rd | 22 +++---- man/betta_random.Rd |only man/breakaway-package.Rd | 17 +++-- man/chao1.Rd |only man/chao1_bc.Rd |only man/chao_bunge.Rd |only man/wlrm_transformed.Rd |only man/wlrm_untransformed.Rd |only 22 files changed, 231 insertions(+), 209 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R
without printing the content of graphics windows to an embosser of some kind. This
is not as immediate as is required for efficient access to statistical output.
The functions here are created so that blind people can make even better use
of R. This includes the text descriptions of graphs, convenience functions
to replace the functionality offered in many GUI front ends, and experimental
functionality for optimising graphical content to prepare it for embossing as
tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Duncan Murdoch [ctb], Greg Snow
[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie
[ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.24.1 dated 2016-03-19 and 0.24.2 dated 2016-03-29
DESCRIPTION | 10 ++-- MD5 | 10 ++-- inst/NEWS | 3 + inst/doc/BrailleRHistory.html | 36 ++++++++--------- inst/doc/Ex1histograms.html | 87 +++++++++++++++++++++--------------------- man/BrailleR-package.Rd | 4 - 6 files changed, 77 insertions(+), 73 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, plots, and static web content.
Author: JJ Allaire
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rsconnect versions 0.4.2 dated 2016-03-20 and 0.4.2.1 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/proxies.Rd | 8 +------- 3 files changed, 7 insertions(+), 13 deletions(-)
Title: An Individual-Based Population Genetic Simulation Environment
Description: An interface between R and the metasim simulation engine.
The simulation environment is documented in: "A
Strand. Metasim 1.0: an individual-based environment for
simulating population genetics of complex population
dynamics. Mol. Ecol. Notes, 2:373-376, 2002".
The current version has eliminated the backend encoded output routines.
These routines were accessed using "landscape.write.foreign". Now only
output to GenePop files remains.
R based routines for population genetic data analysis have improved dramatically
and many can use the 'genind' format defined by the adegenet package.
There is now a new function called "landscape.make.genind" which converts
a landscape to a genind object. Please contact the maintainer if other
output formats are needed.
Author: Allan Strand <stranda@cofc.edu>,
James Niehaus
Maintainer: Allan Strand <stranda@cofc.edu>
Diff between rmetasim versions 2.0.4.1 dated 2016-02-26 and 3.0.2 dated 2016-03-29
rmetasim-2.0.4.1/rmetasim/R/ape_interface.R |only rmetasim-2.0.4.1/rmetasim/R/output_formats.R |only rmetasim-2.0.4.1/rmetasim/R/simcoal.R |only rmetasim-3.0.2/rmetasim/CHANGELOG | 24 rmetasim-3.0.2/rmetasim/DESCRIPTION | 37 rmetasim-3.0.2/rmetasim/MD5 | 135 +- rmetasim-3.0.2/rmetasim/NAMESPACE | 39 rmetasim-3.0.2/rmetasim/R/amova.R | 14 rmetasim-3.0.2/rmetasim/R/assign.R | 4 rmetasim-3.0.2/rmetasim/R/create_landscape.R | 113 - rmetasim-3.0.2/rmetasim/R/diversity.R | 10 rmetasim-3.0.2/rmetasim/R/dnadiversity.R | 63 - rmetasim-3.0.2/rmetasim/R/landscape.allelefreq.R | 2 rmetasim-3.0.2/rmetasim/R/landscape.coalinput.R |only rmetasim-3.0.2/rmetasim/R/landscape.freq.locnames.R |only rmetasim-3.0.2/rmetasim/R/landscape.ind.freq.R |only rmetasim-3.0.2/rmetasim/R/landscape.make.genind.R |only rmetasim-3.0.2/rmetasim/R/landscape.make.genpop.R |only rmetasim-3.0.2/rmetasim/R/landscape.mig.matrix.R | 3 rmetasim-3.0.2/rmetasim/R/landscape.sample.R | 148 +- rmetasim-3.0.2/rmetasim/R/landscape.write.foreign.R |only rmetasim-3.0.2/rmetasim/R/landscape.write.genepop.R |only rmetasim-3.0.2/rmetasim/R/landscapeIO.R | 19 rmetasim-3.0.2/rmetasim/R/loci.R | 25 rmetasim-3.0.2/rmetasim/R/pegas_interface.R |only rmetasim-3.0.2/rmetasim/README.md |only rmetasim-3.0.2/rmetasim/inst/doc/CreatingLandscapes.R |only rmetasim-3.0.2/rmetasim/inst/doc/Simulating.R |only rmetasim-3.0.2/rmetasim/man/SimulationComponents.Rd | 12 rmetasim-3.0.2/rmetasim/man/landscape.Fst.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.allelecount.Rd | 16 rmetasim-3.0.2/rmetasim/man/landscape.allelefreq.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.amova.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.amova.locus.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.clean.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.coalinput.Rd | 8 rmetasim-3.0.2/rmetasim/man/landscape.compress.Rd | 7 rmetasim-3.0.2/rmetasim/man/landscape.demography.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.exp.het.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.freq.locnames.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.ind.freq.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.locus.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.locus.states.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.make.genind.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.make.genpop.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.mismatchdist.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.modify.epoch.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.empty.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.epoch.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.example.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.floatparam.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.new.individuals.Rd | 10 rmetasim-3.0.2/rmetasim/man/landscape.new.intparam.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.new.local.demo.Rd | 5 rmetasim-3.0.2/rmetasim/man/landscape.new.locus.Rd | 16 rmetasim-3.0.2/rmetasim/man/landscape.new.switchparam.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.sample.Rd | 19 rmetasim-3.0.2/rmetasim/man/landscape.simulate.Rd | 2 rmetasim-3.0.2/rmetasim/man/landscape.states.Rd | 4 rmetasim-3.0.2/rmetasim/man/landscape.theta.h.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.theta.k.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.theta.s.Rd |only rmetasim-3.0.2/rmetasim/man/landscape.write.foreign.Rd | 32 rmetasim-3.0.2/rmetasim/src/AlleleObj.cc | 21 rmetasim-3.0.2/rmetasim/src/AlleleTbl.cc | 4 rmetasim-3.0.2/rmetasim/src/Democlass.cc | 5 rmetasim-3.0.2/rmetasim/src/Eigen.h | 5 rmetasim-3.0.2/rmetasim/src/FastAllele.cc | 21 rmetasim-3.0.2/rmetasim/src/FastSeqAllele.cc | 10 rmetasim-3.0.2/rmetasim/src/Landscape.cc | 852 --------------- rmetasim-3.0.2/rmetasim/src/Landscape.h | 56 rmetasim-3.0.2/rmetasim/src/Makevars | 6 rmetasim-3.0.2/rmetasim/src/PackedIndividual.h | 8 rmetasim-3.0.2/rmetasim/src/RandLib.h | 8 rmetasim-3.0.2/rmetasim/src/TransMat.cc | 12 rmetasim-3.0.2/rmetasim/src/metasim.h | 4 rmetasim-3.0.2/rmetasim/src/rmetasim.cc | 211 --- rmetasim-3.0.2/rmetasim/src/rmetasim.h | 13 rmetasim-3.0.2/rmetasim/vignettes |only 79 files changed, 493 insertions(+), 1556 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a
Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <mdramins@ipipan.waw.pl>
Diff between rmcfs versions 1.1.0 dated 2016-03-28 and 1.1.1 dated 2016-03-29
rmcfs-1.1.0/rmcfs/man/info.Rd |only rmcfs-1.1.1/rmcfs/DESCRIPTION | 14 - rmcfs-1.1.1/rmcfs/MD5 | 44 ++-- rmcfs-1.1.1/rmcfs/NAMESPACE | 10 - rmcfs-1.1.1/rmcfs/R/onLoad.R | 16 - rmcfs-1.1.1/rmcfs/R/rmcfs.R | 38 +++- rmcfs-1.1.1/rmcfs/R/rmcfs.plot.R | 10 - rmcfs-1.1.1/rmcfs/R/utils.R | 16 - rmcfs-1.1.1/rmcfs/inst/java/dmLab.jar |binary rmcfs-1.1.1/rmcfs/java/src/dmLab/DMLabInfo.java | 4 rmcfs-1.1.1/rmcfs/java/src/dmLab/array/loader/fileLoader/FileLoader.java | 14 - rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/MCFSParams.java | 93 +++++----- rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/mcfsEngine/MCFSExperiment.java | 21 +- rmcfs-1.1.1/rmcfs/java/src/dmLab/mcfs/mcfsEngine/framework/MCFSFramework.java | 7 rmcfs-1.1.1/rmcfs/man/artificial.data.Rd | 2 rmcfs-1.1.1/rmcfs/man/build.idgraph.Rd | 6 rmcfs-1.1.1/rmcfs/man/export.result.Rd | 6 rmcfs-1.1.1/rmcfs/man/filter.data.Rd | 8 rmcfs-1.1.1/rmcfs/man/import.result.Rd | 6 rmcfs-1.1.1/rmcfs/man/mcfs.Rd | 37 ++- rmcfs-1.1.1/rmcfs/man/plot.idgraph.Rd | 6 rmcfs-1.1.1/rmcfs/man/plot.mcfs.Rd | 8 rmcfs-1.1.1/rmcfs/man/print.mcfs.Rd | 6 rmcfs-1.1.1/rmcfs/man/showme.Rd |only 24 files changed, 209 insertions(+), 163 deletions(-)
Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture
Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>
Diff between GMCM versions 1.2.2 dated 2015-08-05 and 1.2.3 dated 2016-03-29
GMCM-1.2.2/GMCM/inst/tests |only GMCM-1.2.3/GMCM/DESCRIPTION | 8 - GMCM-1.2.3/GMCM/MD5 | 140 +++++++++++++-------------- GMCM-1.2.3/GMCM/R/EMAlgortihm.R | 2 GMCM-1.2.3/GMCM/R/EStep.R | 2 GMCM-1.2.3/GMCM/R/GMCM-package.R | 12 +- GMCM-1.2.3/GMCM/R/PseudoEMAlgorithm.R | 2 GMCM-1.2.3/GMCM/R/SimulateGMCMData.R | 30 ++++- GMCM-1.2.3/GMCM/R/Uhat.R | 2 GMCM-1.2.3/GMCM/R/choose.theta.R | 2 GMCM-1.2.3/GMCM/R/colSds.R | 2 GMCM-1.2.3/GMCM/R/cummean.R | 2 GMCM-1.2.3/GMCM/R/dgmcm.loglik.R | 2 GMCM-1.2.3/GMCM/R/fit.full.GMCM.R | 2 GMCM-1.2.3/GMCM/R/fit.meta.GMCM.R | 2 GMCM-1.2.3/GMCM/R/full2meta.R | 2 GMCM-1.2.3/GMCM/R/get.IDR2.R | 2 GMCM-1.2.3/GMCM/R/is.theta.R | 2 GMCM-1.2.3/GMCM/R/logit.R | 2 GMCM-1.2.3/GMCM/R/rho.transform.R | 2 GMCM-1.2.3/GMCM/R/rtheta.R | 2 GMCM-1.2.3/GMCM/R/tt.R | 4 GMCM-1.2.3/GMCM/README.md | 14 +- GMCM-1.2.3/GMCM/build/vignette.rds |binary GMCM-1.2.3/GMCM/inst/CITATION | 63 +++++++----- GMCM-1.2.3/GMCM/inst/NEWS.Rd | 15 ++ GMCM-1.2.3/GMCM/inst/doc/GMCM-JStatSoft.Rnw | 13 +- GMCM-1.2.3/GMCM/inst/doc/GMCM-JStatSoft.pdf |binary GMCM-1.2.3/GMCM/man/EMAlgorithm.Rd | 2 GMCM-1.2.3/GMCM/man/EStep.Rd | 2 GMCM-1.2.3/GMCM/man/GMCM-package.Rd | 10 + GMCM-1.2.3/GMCM/man/PseudoEMAlgorithm.Rd | 2 GMCM-1.2.3/GMCM/man/SimulateGMCMData.Rd | 30 ++++- GMCM-1.2.3/GMCM/man/Uhat.Rd | 2 GMCM-1.2.3/GMCM/man/choose.theta.Rd | 2 GMCM-1.2.3/GMCM/man/colSds.Rd | 2 GMCM-1.2.3/GMCM/man/cummean.Rd | 2 GMCM-1.2.3/GMCM/man/dgmcm.loglik.Rd | 2 GMCM-1.2.3/GMCM/man/fit.full.GMCM.Rd | 2 GMCM-1.2.3/GMCM/man/fit.meta.GMCM.Rd | 2 GMCM-1.2.3/GMCM/man/freshVsFrozen.Rd | 2 GMCM-1.2.3/GMCM/man/full2meta.Rd | 2 GMCM-1.2.3/GMCM/man/get.IDR.Rd | 2 GMCM-1.2.3/GMCM/man/is.theta.Rd | 2 GMCM-1.2.3/GMCM/man/logit.Rd | 2 GMCM-1.2.3/GMCM/man/rho.transform.Rd | 2 GMCM-1.2.3/GMCM/man/rtheta.Rd | 2 GMCM-1.2.3/GMCM/man/tt.Rd | 4 GMCM-1.2.3/GMCM/man/u133VsExon.Rd | 2 GMCM-1.2.3/GMCM/tests/test-all.R | 8 - GMCM-1.2.3/GMCM/tests/testthat |only GMCM-1.2.3/GMCM/vignettes/GMCM-JStatSoft.Rnw | 13 +- 52 files changed, 250 insertions(+), 182 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Routines for dealing with markers on the X-chromosome are included.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.5.5 dated 2015-02-26 and 1.5.6 dated 2016-03-29
DESCRIPTION | 11 +- MD5 | 118 +++++++++++++++++------------ NAMESPACE | 4 - R/AFtest.R |only R/Chisquare.R | 5 - R/Chisquare.x.R |only R/Chisquarex.R |only R/CombineExact.R | 2 R/HW.chi.mat.R |only R/HWAlltests.R | 52 +++++++------ R/HWChisq.R | 119 +++++++++++++++++++++--------- R/HWChisqStats.R |only R/HWClo.R |only R/HWData.R | 156 ++++++++++++++++++++++++++------------- R/HWExact.R | 170 ++++++++++++++++++++++++++++++------------- R/HWExactPrevious.R |only R/HWExactStats.R |only R/HWGenotypePlot.R | 4 - R/HWLratio.R | 92 ++++++++++++++++++----- R/HWPerm.R | 62 ++++++++++++++- R/HWTernaryPlot.R | 35 +++----- R/MakeCounts.R | 9 +- R/UniqueGenotypeCounts.R | 9 +- R/agcounts.R |only R/auxiliartable.R |only R/generate.outcomes.R |only R/mac.R | 3 R/make.outcomes.R |only R/n.outcomes.R |only R/recode.R | 90 +++++++++++++++++----- R/sample.prob.R |only R/sample.prob.last.R |only R/subsamples.prob.R |only R/vaf.R | 22 +---- build/vignette.rds |binary inst/CITATION | 2 inst/doc/HardyWeinberg.R | 105 ++++++++++++++++++++------ inst/doc/HardyWeinberg.Rnw | 122 ++++++++++++++++++++++++++---- inst/doc/HardyWeinberg.pdf |binary man/AFtest.Rd |only man/HWAlltests.Rd | 8 +- man/HWAlr.Rd | 2 man/HWAlrPlot.Rd | 2 man/HWChisq.Rd | 49 ++++++++++-- man/HWChisqMat.Rd | 2 man/HWChisqStats.Rd |only man/HWClo.Rd |only man/HWClr.Rd | 2 man/HWClrPlot.Rd | 2 man/HWData.Rd | 43 ++++++++-- man/HWExact.Rd | 19 +++- man/HWExactMat.Rd | 2 man/HWExactPrevious.Rd |only man/HWExactStats.Rd |only man/HWGenotypePlot.Rd | 3 man/HWIlr.Rd | 2 man/HWIlrPlot.Rd | 2 man/HWLratio.Rd | 16 +++- man/HWMissing.Rd | 4 - man/HWPerm.Rd | 16 +++- man/HWPower.Rd | 2 man/HWTernaryPlot.Rd | 8 -- man/HardyWeinberg-package.Rd | 13 +-- man/MakeCounts.Rd | 9 +- man/Markers.Rd | 2 man/UniqueGenotypeCounts.Rd | 5 - man/agcounts.Rd |only man/recode.Rd | 20 +++-- man/vaf.Rd | 11 +- vignettes/HardyWeinberg.Rnw | 122 ++++++++++++++++++++++++++---- vignettes/HardyWeinberg.bib | 18 ++++ 71 files changed, 1137 insertions(+), 439 deletions(-)
Title: Aligned Rank Transform
Description: The Aligned Rank Transform for nonparametric
factorial ANOVAs as described by J. O. Wobbrock,
L. Findlater, D. Gergle, & J. J. Higgins, "The Aligned
Rank Transform for nonparametric factorial analyses
using only ANOVA procedures", CHI 2011 <DOI:10.1145/1978942.1978963>.
Author: Matthew Kay [aut, cre],
Jacob O. Wobbrock [aut]
Maintainer: Matthew Kay <mjskay@uw.edu>
Diff between ARTool versions 0.10.0 dated 2016-01-11 and 0.10.2 dated 2016-03-29
DESCRIPTION | 15 - MD5 | 19 - NEWS | 69 ++-- R/release.questions.R |only build/vignette.rds |binary inst/doc/art-contrasts.R | 27 - inst/doc/art-contrasts.Rmd | 580 ++++++++++++++++++++---------------------- inst/doc/art-contrasts.html | 99 +++---- inst/doc/art-effect-size.R |only inst/doc/art-effect-size.Rmd |only inst/doc/art-effect-size.html |only vignettes/art-contrasts.Rmd | 580 ++++++++++++++++++++---------------------- vignettes/art-effect-size.Rmd |only 13 files changed, 696 insertions(+), 693 deletions(-)
Title: Time to Target Plot
Description: Implementation of Time to Target plot based on the work
of Ribeiro and Rosseti (2015) <DOI:10.1007/s11590-014-0760-8>,
that describe a numerical method that gives the probability of
an algorithm A finds a solution at least as good as a given
target value in smaller computation time than algorithm B.
Author: Carlos A. Martinez [aut, cre] based on the work of Ribeiro and Rosseti (2015).
Maintainer: Carlos A. Martinez <amartin@unal.edu.co>
Diff between tttplot versions 1.0 dated 2016-03-20 and 1.1.1 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/RCode.R | 42 ++++++++++++++++-------------------------- man/tttPlot.Rd | 10 +++++----- man/tttPlotCompare.Rd | 21 ++++++++++++--------- 6 files changed, 43 insertions(+), 50 deletions(-)
Title: Partition-Assisted Clustering
Description: Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering.
The package also provides functions for effectively visualizing the clustering results.
It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.
Author: Dangna Li, Henry Li
Maintainer: Dangna Li <ldangna@gmail.com>
Diff between PAC versions 1.0.2 dated 2016-03-29 and 1.0.3 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + R/PAC.R | 1 + src/bsp.cc | 4 ++-- 5 files changed, 11 insertions(+), 9 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.1.1 dated 2016-03-27 and 1.1.2 dated 2016-03-29
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/diag.r | 68 +++++++++++++++++++++++++++++++++---------------------- man/csmf.diag.Rd | 29 ++++++----------------- 4 files changed, 56 insertions(+), 55 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets,
also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.3 dated 2016-03-11 and 0.3.1 dated 2016-03-29
DESCRIPTION | 17 +++++++++-------- MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS.md |only R/dynamize.R | 2 ++ README.md | 4 ++++ tests/testthat/test_dynamise.R | 6 ++++++ tests/testthat/test_edges.R | 12 ++++++++++++ tests/testthat/test_nodes.R | 4 ++++ 9 files changed, 46 insertions(+), 16 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.2.3 dated 2016-01-21 and 2.3 dated 2016-03-29
DESCRIPTION | 8 +- MD5 | 8 +- R/evenn.R | 169 ++++++++++++++++++++++++++++----------------------- man/eVenn-package.Rd | 4 - man/evenn.Rd | 12 ++- 5 files changed, 110 insertions(+), 91 deletions(-)
Title: Combined Analysis of Pleiotropy and Epistasis
Description: Combines complementary information across multiple related
phenotypes to infer directed epistatic interactions between genetic markers.
This analysis can be applied to a variety of engineered and natural populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Greg W.
Carter
Maintainer: Anna L. Tyler <Anna.Tyler@jax.org>
Diff between cape versions 1.3 dated 2014-09-26 and 2.0 dated 2016-03-29
cape-1.3/cape/R/create.covar.R |only cape-1.3/cape/R/linkage.blocks.stepwise.R |only cape-1.3/cape/R/one.pairscan.R |only cape-1.3/cape/R/remove.ind.with.missing.pheno.R |only cape-1.3/cape/R/set.covar.R |only cape-1.3/cape/R/set.pairscan.thresh.R |only cape-1.3/cape/man/create.covar.Rd |only cape-1.3/cape/man/linkage.blocks.stepwise.Rd |only cape-1.3/cape/man/one.pairscan.Rd |only cape-1.3/cape/man/remove.ind.with.missing.pheno.Rd |only cape-1.3/cape/man/set.covar.Rd |only cape-1.3/cape/man/set.pairscan.thresh.Rd |only cape-1.3/cape/vignettes/Network_Collapsed.pdf |only cape-1.3/cape/vignettes/Network_Full.pdf |only cape-1.3/cape/vignettes/pair_regression.pdf |only cape-1.3/cape/vignettes/svd.pdf |only cape-1.3/cape/vignettes/variant_influences.pdf |only cape-2.0/cape/DESCRIPTION | 23 cape-2.0/cape/MD5 | 209 +++-- cape-2.0/cape/NAMESPACE | 9 cape-2.0/cape/R/bin.vector.R |only cape-2.0/cape/R/calc.p.R | 45 - cape-2.0/cape/R/direct.influence.R | 79 -- cape-2.0/cape/R/error.prop.R | 74 +- cape-2.0/cape/R/filter.hwe.R |only cape-2.0/cape/R/filter.maf.R |only cape-2.0/cape/R/genome.wide.threshold.1D.R | 35 cape-2.0/cape/R/genome.wide.threshold.1D.parallel.R |only cape-2.0/cape/R/get.chr.markers.R |only cape-2.0/cape/R/get.col.R |only cape-2.0/cape/R/get.covar.R | 88 +- cape-2.0/cape/R/get.eigentraits.R | 31 cape-2.0/cape/R/get.geno.R |only cape-2.0/cape/R/get.geno.with.covar.R |only cape-2.0/cape/R/get.linearly.independent.R | 40 - cape-2.0/cape/R/get.marker.chr.R |only cape-2.0/cape/R/get.marker.idx.R |only cape-2.0/cape/R/get.marker.location.R |only cape-2.0/cape/R/get.marker.name.R |only cape-2.0/cape/R/get.marker.num.R |only cape-2.0/cape/R/get.marker.val.R |only cape-2.0/cape/R/get.network.R | 50 + cape-2.0/cape/R/get.pairs.for.pairscan.R | 19 cape-2.0/cape/R/get.pheno.R |only cape-2.0/cape/R/histPheno.R |only cape-2.0/cape/R/impute.missing.geno.R |only cape-2.0/cape/R/kinship.R |only cape-2.0/cape/R/kinship.on.the.fly.R |only cape-2.0/cape/R/linkage.blocks.network.R |only cape-2.0/cape/R/make.data.obj.R |only cape-2.0/cape/R/marker2covar.R |only cape-2.0/cape/R/myImagePlot.R | 89 -- cape-2.0/cape/R/one.pairscan.parallel.R |only cape-2.0/cape/R/one.singlescan.R | 14 cape-2.0/cape/R/pairscan.R | 128 +-- cape-2.0/cape/R/pairscan.kin.R |only cape-2.0/cape/R/pairscan.noKin.R |only cape-2.0/cape/R/pairscan.null.R | 154 ++-- cape-2.0/cape/R/pheno2covar.R |only cape-2.0/cape/R/plotCollapsedVarInf.R | 2 cape-2.0/cape/R/plotNetwork.R | 125 ++- cape-2.0/cape/R/plotPairscan.R | 52 - cape-2.0/cape/R/plotPheno.R |only cape-2.0/cape/R/plotPhenoCor.R |only cape-2.0/cape/R/plotSVD.R | 29 cape-2.0/cape/R/plotSinglescan.R | 323 ++++++--- cape-2.0/cape/R/plotSinglescan.heat.R | 10 cape-2.0/cape/R/plotVariantInfluences.R | 133 +-- cape-2.0/cape/R/qqPheno.R |only cape-2.0/cape/R/read.geno.R |only cape-2.0/cape/R/read.pheno.R |only cape-2.0/cape/R/read.population.R | 424 ++++++----- cape-2.0/cape/R/remove.ind.R |only cape-2.0/cape/R/remove.markers.R |only cape-2.0/cape/R/select.by.chr.R | 6 cape-2.0/cape/R/select.markers.for.pairscan.R | 162 +--- cape-2.0/cape/R/singlescan.R | 392 ++++++---- cape-2.0/cape/R/sortByThenBy.R |only cape-2.0/cape/R/sortCross.R |only cape-2.0/cape/R/writeVariantInfluences.R | 29 cape-2.0/cape/build/vignette.rds |binary cape-2.0/cape/data/obesity.cross.rda |binary cape-2.0/cape/inst/doc/cape.R | 194 +++-- cape-2.0/cape/inst/doc/cape.Rnw | 607 +++++++---------- cape-2.0/cape/inst/doc/cape.pdf |binary cape-2.0/cape/man/bin.vector.Rd |only cape-2.0/cape/man/calc.p.Rd | 9 cape-2.0/cape/man/direct.influence.Rd | 5 cape-2.0/cape/man/error.prop.Rd | 8 cape-2.0/cape/man/filter.hwe.Rd |only cape-2.0/cape/man/filter.maf.Rd |only cape-2.0/cape/man/genome.wide.threshold.1D.Rd | 10 cape-2.0/cape/man/genome.wide.threshold.1D.parallel.Rd |only cape-2.0/cape/man/get.chr.markers.Rd |only cape-2.0/cape/man/get.col.Rd |only cape-2.0/cape/man/get.col.num.Rd | 3 cape-2.0/cape/man/get.covar.Rd | 24 cape-2.0/cape/man/get.geno.Rd |only cape-2.0/cape/man/get.geno.with.covar.Rd |only cape-2.0/cape/man/get.linearly.independent.Rd | 6 cape-2.0/cape/man/get.marker.chr.Rd |only cape-2.0/cape/man/get.marker.idx.Rd |only cape-2.0/cape/man/get.marker.location.Rd |only cape-2.0/cape/man/get.marker.name.Rd |only cape-2.0/cape/man/get.marker.num.Rd |only cape-2.0/cape/man/get.marker.val.Rd |only cape-2.0/cape/man/get.network.Rd | 21 cape-2.0/cape/man/get.pairs.for.pairscan.Rd | 19 cape-2.0/cape/man/get.pheno.Rd |only cape-2.0/cape/man/histPheno.Rd |only cape-2.0/cape/man/impute.missing.geno.Rd |only cape-2.0/cape/man/kinship.Rd |only cape-2.0/cape/man/kinship.on.the.fly.Rd |only cape-2.0/cape/man/linkage.blocks.network.Rd |only cape-2.0/cape/man/make.data.obj.Rd |only cape-2.0/cape/man/marker2covar.Rd |only cape-2.0/cape/man/norm.pheno.Rd | 11 cape-2.0/cape/man/one.pairscan.parallel.Rd |only cape-2.0/cape/man/one.singlescan.Rd | 5 cape-2.0/cape/man/pairscan.Rd | 63 + cape-2.0/cape/man/pairscan.kin.Rd |only cape-2.0/cape/man/pairscan.noKin.Rd |only cape-2.0/cape/man/pairscan.null.Rd | 22 cape-2.0/cape/man/pheno2covar.Rd |only cape-2.0/cape/man/plotCollapsedVarInf.Rd | 2 cape-2.0/cape/man/plotNetwork.Rd | 15 cape-2.0/cape/man/plotPairscan.Rd | 18 cape-2.0/cape/man/plotPheno.Rd |only cape-2.0/cape/man/plotPhenoCor.Rd |only cape-2.0/cape/man/plotSVD.Rd | 14 cape-2.0/cape/man/plotSinglescan.Rd | 58 + cape-2.0/cape/man/plotSinglescan.heat.Rd | 15 cape-2.0/cape/man/plotVariantInfluences.Rd | 26 cape-2.0/cape/man/qqPheno.Rd |only cape-2.0/cape/man/read.geno.Rd |only cape-2.0/cape/man/read.pheno.Rd |only cape-2.0/cape/man/read.population.Rd | 8 cape-2.0/cape/man/remove.ind.Rd |only cape-2.0/cape/man/remove.markers.Rd |only cape-2.0/cape/man/select.by.chr.Rd | 16 cape-2.0/cape/man/select.markers.for.pairscan.Rd | 37 - cape-2.0/cape/man/singlescan.Rd | 55 + cape-2.0/cape/man/sortByThenBy.Rd |only cape-2.0/cape/man/sortCross.Rd |only cape-2.0/cape/vignettes/cape-017.pdf |only cape-2.0/cape/vignettes/cape-019.pdf |only cape-2.0/cape/vignettes/cape.Rnw | 607 +++++++---------- cape-2.0/cape/vignettes/cape.bib | 47 + cape-2.0/cape/vignettes/interaction_fig.pdf |binary cape-2.0/cape/vignettes/reparam.pdf |binary 150 files changed, 2583 insertions(+), 2116 deletions(-)
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
Diff between binaryLogic versions 0.3.2 dated 2016-01-19 and 0.3.4 dated 2016-03-29
DESCRIPTION | 6 +- LICENSE | 2 MD5 | 20 ++++---- NAMESPACE | 2 R/BinaryS3.R | 27 ++++++++--- R/binHelper.R | 51 ++++++++++++++++++++ README.md | 42 +++++++++++++++-- man/as.binary.Rd | 6 ++ man/bin2gray.Rd |only man/gray2bin.Rd |only tests/testthat/test-BinaryS3.R | 28 +++++++++++ tests/testthat/test-binHelper.R | 98 ++++++++++++++++++++++++++++++++++++++++ 12 files changed, 259 insertions(+), 23 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility
'API'
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF').
'GBIF' is a database of species occurrence records from sources all
over the globe. 'rgbif' includes functions for searching for
taxonomic names, retrieving information on data providers,
getting species occurrence records, and getting counts of
occurrence records.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 0.9.2 dated 2016-02-02 and 0.9.3 dated 2016-03-29
DESCRIPTION | 11 MD5 | 66 +-- NAMESPACE | 3 R/check_wkt.r | 19 - R/gbifmap.r | 8 R/geometry_utils.R |only R/name_usage.r | 12 R/occ_data.R | 22 - R/occ_download.R | 10 R/occ_search.r | 48 +- R/rgbif-package.r | 1 R/wkt_parse.R |only R/zzz.r | 8 README.md | 119 +++--- build/vignette.rds |binary inst/assets/img/unnamed-chunk-8-1.png |binary inst/doc/issues_vignette.Rmd | 206 +++++----- inst/doc/issues_vignette.html | 206 +++++----- inst/doc/rgbif_vignette.html | 641 +++++++++++++++++----------------- inst/vign/figure/gbifmap1-1.png |binary inst/vign/issues_vignette.md | 206 +++++----- inst/vign/rgbif_vignette.md | 641 +++++++++++++++++----------------- man/check_wkt.Rd | 3 man/occ_data.Rd | 128 ++++++ man/occ_search.Rd | 124 ++++++ man/wkt_parse.Rd |only tests/testthat/test-count_facet.r | 11 tests/testthat/test-elevation.R | 5 tests/testthat/test-name_suggest.r | 1 tests/testthat/test-nodes.r | 10 tests/testthat/test-occ_data.R | 80 ++++ tests/testthat/test-occ_issues.R | 2 tests/testthat/test-occ_search.r | 81 ++++ tests/testthat/test-wkt_large.R |only vignettes/issues_vignette.Rmd | 206 +++++----- vignettes/rgbif_vignette.Rmd | 641 +++++++++++++++++----------------- 36 files changed, 2012 insertions(+), 1507 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.7.13).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre],
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-25 dated 2016-03-15 and 0.4-26 dated 2016-03-29
CHANGELOG | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/attributes.R | 3 ++- R/classifiers.R | 6 ++++-- R/filters.R | 3 ++- build/vignette.rds |binary inst/doc/RWeka.pdf |binary 8 files changed, 22 insertions(+), 14 deletions(-)
Title: Build Regression Models Quickly and Display the Results Using
'ggplot2'
Description: A set of functions to extract results from regression models and
plot the effect size using 'ggplot2' seamlessly. While 'broom' is useful to
convert statistical analysis objects into tidy data frames, 'coefplot' is adept at showing
multivariate regression results. With specific outcome, this package could build regression models
automatically, extract results into a data frame and provide a quicker way to summarize
models' statistical findings using 'ggplot2'.
Author: Xikun Han [aut, cre]
Maintainer: Xikun Han <hanxikun2014@163.com>
Diff between quickReg versions 0.0.1 dated 2016-03-03 and 0.0.2 dated 2016-03-29
DESCRIPTION | 12 ++-- MD5 | 45 ++++++++--------- NAMESPACE | 1 NEWS |only R/data.R | 2 R/dataframe.R | 2 R/dataframe.reg.R | 12 +++- R/detail.R | 2 R/detail.reg.R | 2 R/display.data.frame.R | 50 +++++++++++-------- R/display.reg.R | 66 +++++++++++++------------ R/plot.reg.R | 108 +++++++++++++++++++++-------------------- R/reg.R | 56 +++++++++++++-------- build/vignette.rds |binary inst/doc/quickReg.R | 28 ++++++++-- inst/doc/quickReg.Rmd | 26 ++++++++-- inst/doc/quickReg.html | 119 +++++++++++++++++++--------------------------- man/dataframe.reg.Rd | 4 + man/diabetes.Rd | 2 man/display.data.frame.Rd | 14 +++-- man/display.reg.Rd | 3 - man/plot.reg.Rd | 9 +-- man/reg.Rd | 2 vignettes/quickReg.Rmd | 26 ++++++++-- 24 files changed, 336 insertions(+), 255 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexis@ci.tuwien.ac.at>
Diff between kernlab versions 0.9-23 dated 2016-01-26 and 0.9-24 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 42 +++++++++++++++++++++--------------------- R/gausspr.R | 2 +- R/kfa.R | 2 +- R/kha.R | 2 +- R/kkmeans.R | 2 +- R/kpca.R | 2 +- R/kqr.R | 2 +- R/ksvm.R | 2 +- R/lssvm.R | 2 +- R/rvm.R | 2 +- R/sigest.R | 2 +- R/specc.R | 2 +- build/vignette.rds |binary data/income.rda |binary data/musk.rda |binary data/promotergene.rda |binary data/reuters.rda |binary data/spam.rda |binary data/spirals.rda |binary data/ticdata.rda |binary inst/CITATION | 8 ++++---- 22 files changed, 39 insertions(+), 39 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.count versions 3.2.0 dated 2015-06-19 and 3.2.2 dated 2016-03-29
DESCRIPTION | 8 ++-- LICENSE | 2 - MD5 | 38 +++++++++++------------ R/InitReference.R | 9 +++++ R/InitWtErgmTerm.R | 9 +++++ R/InitWtMHP.R | 9 +++++ R/zzz.R | 13 +++++++ inst/CITATION | 11 ++++-- inst/NEWS.Rd | 75 +++++++++++++++++++++++++++++++--------------- man/ergm-references.Rd | 9 +++++ man/ergm-terms.Rd | 9 +++++ man/ergm.count-package.Rd | 11 ++++++ man/zach.Rd | 9 +++++ src/include_stubs.c | 18 +++++++++++ src/wtMHproposals.c | 18 +++++++++++ src/wtMHproposals.h | 18 +++++++++++ src/wtchangestats.c | 18 +++++++++++ src/wtchangestats.h | 18 +++++++++++ tests/valued_fit.R | 11 ++++++ tests/valued_sim.R | 9 +++++ 20 files changed, 267 insertions(+), 55 deletions(-)
More information about CrossClustering at CRAN
Permanent link
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of predicates (is_* functions) to check the state of your
variables, and assertions (assert_* functions) to throw errors if they
aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.3-2 dated 2016-03-08 and 0.3-3 dated 2016-03-29
DESCRIPTION | 10 MD5 | 10 NAMESPACE | 2 NEWS | 1 R/exports-reflection.R | 508 ++++++++++++++++++++++++------------------------- man/is_r.Rd | 2 6 files changed, 271 insertions(+), 262 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.9.3 dated 2016-03-24 and 1.9.4 dated 2016-03-29
DESCRIPTION | 12 MD5 | 20 NEWS | 9 NEWS.md | 19 R/sjPlotFrequencies.R | 1568 ++++++------- R/sjPlotGLME.R | 5116 ++++++++++++++++++++++----------------------- R/sjPlotStackFrequencies.R | 908 +++---- build/partial.rdb |binary man/sjPlot-package.Rd | 4 man/sjp.frq.Rd | 602 ++--- man/sjp.stackfrq.Rd | 2 11 files changed, 4146 insertions(+), 4114 deletions(-)
Title: An Imgur.com API Client Package
Description: A complete API client for the image hosting service Imgur.com, including the an imgur graphics device, enabling the easy upload and sharing of plots.
Author: Thomas J. Leeper [aut, cre],
Aaron Statham [ctb],
Yihui Xie [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between imguR versions 1.0.1 dated 2016-02-19 and 1.0.3 dated 2016-03-29
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 65 +++++++++++++++++++++++++++++++++++++++++++++ NEWS | 4 ++ R/http.r | 85 ++++++++++++++++++++++++++++++++++-------------------------- README.md | 2 - 6 files changed, 128 insertions(+), 48 deletions(-)
Title: Simple Metrics to Summarize Growth Curves
Description: This is a simple package that fits the logistic equation to
microbial growth curve data (e.g., repeated absorbance measurements
taken from a plate reader over time). From this fit, a variety of
metrics are provided, including the maximum growth rate,
the doubling time, the carrying capacity, the area under the logistic
curve, and the time to the inflection point.
Author: Kathleen sprouffske [aut, cre]
Maintainer: Kathleen sprouffske <sprouffske@gmail.com>
Diff between growthcurver versions 0.2.0 dated 2016-03-09 and 0.2.1 dated 2016-03-29
DESCRIPTION | 8 - MD5 | 30 +++--- R/fit-logistic.R | 33 ++++--- R/helpers.R | 26 +++-- R/summarize-growth-by-plate.R | 27 +++-- R/summarize-growth.R | 84 ++++++++++++------ R/utils.R | 2 build/vignette.rds |binary inst/doc/Growthcurver-vignette.R | 12 ++ inst/doc/Growthcurver-vignette.Rmd | 85 ++++++++++++------ inst/doc/Growthcurver-vignette.html | 155 ++++++++++++++++++++++------------ man/SummarizeGrowth.Rd | 12 +- man/SummarizeGrowthByPlate.Rd | 21 ++-- man/gcvals.Rd | 5 - tests/testthat/test_SummarizeGrowth.R | 12 ++ vignettes/Growthcurver-vignette.Rmd | 85 ++++++++++++------ 16 files changed, 404 insertions(+), 193 deletions(-)
Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data,
tweening is necessary. This package provides a range of functions for
creating tweened data that plugs right into functions such as gg_animate()
from the 'gganimate' package. Furthermore it adds a number of vectorized
interpolaters for common R data types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tweenr versions 0.1.2 dated 2016-02-11 and 0.1.3 dated 2016-03-29
DESCRIPTION | 9 ++-- MD5 | 4 - README.md | 125 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++--- 3 files changed, 127 insertions(+), 11 deletions(-)
Title: Linear/Nonlinear SVM Classification Solver Based on ADMM and
IADMM Algorithms
Description:
Solve large-scale regularised linear/kernel classification by using ADMM and IADMM algorithms. This package provides linear L2-regularised primal classification (both ADMM and IADMM are available), kernel L2-regularised dual classification (IADMM) as well as L1-regularised primal classification (both ADMM and IADMM are available).
Author: Ben DAI <bendai2-c@my.cityu.edu.hk>; Junhui Wang <j.h.wang@cityu.edu.hk>
Maintainer: Ben DAI <bendai2-c@my.cityu.edu.hk>
Diff between svmadmm versions 0.2 dated 2016-03-17 and 0.3 dated 2016-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/kerneliadmm.c | 3 +-- src/linear_math.c | 44 ++++++++++++++++++++++---------------------- src/linearadmm.c | 5 ++--- 5 files changed, 32 insertions(+), 34 deletions(-)
Title: Tools for Analyzing Content Homogeneity and News Diffusion using
Computational Text Analysis
Description: A collection of tools for measuring the similarity of news content and tracing the flow of (news) messages over
time and across media.
Author: Kasper Welbers & Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between RNewsflow versions 1.0 dated 2016-02-21 and 1.0.1 dated 2016-03-29
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Generate Random Strings
Description: Generate random strings of a dictated size of symbol set and
distribution of the lengths of strings.
Author: Alan Gu
Maintainer: Alan Gu <alan.on.ca@gmail.com>
Diff between randstr versions 0.1.1 dated 2016-03-28 and 0.2.0 dated 2016-03-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/generatelens.r | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Partition-Assisted Clustering
Description: Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering.
The package also provides functions for effectively visualizing the clustering results.
It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.
Author: Dangna Li, Henry Li
Maintainer: Dangna Li <ldangna@gmail.com>
Diff between PAC versions 1.0.1 dated 2016-03-27 and 1.0.2 dated 2016-03-29
PAC-1.0.1/PAC/configure.ac |only PAC-1.0.2/PAC/DESCRIPTION | 6 +++--- PAC-1.0.2/PAC/MD5 | 8 ++++---- PAC-1.0.2/PAC/R/PAC.R | 1 - PAC-1.0.2/PAC/cleanup.win |only PAC-1.0.2/PAC/src/Makevars | 4 +++- 6 files changed, 10 insertions(+), 9 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. Probably the most important function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.2 dated 2016-02-05 and 0.6.4 dated 2016-03-29
DESCRIPTION | 12 +- MD5 | 38 ++++----- NEWS | 8 + R/RcppExports.R | 2 R/dU.R | 4 R/pU.R | 4 R/qU.R | 8 + man/estimate-moments.Rd | 2 src/skewness.cpp | 3 tests/testthat/test_H_gamma.R | 3 tests/testthat/test_IGMM.R | 34 ++++---- tests/testthat/test_LambertW_fit_methods.R | 7 - tests/testthat/test_MLE_LambertW.R | 20 ++-- tests/testthat/test_W.R | 17 ---- tests/testthat/test_W_gamma.R | 13 +-- tests/testthat/test_dpqr_LambertW.R | 12 +- tests/testthat/test_dpqr_U.R | 122 +++++++++++++++++++++++++++++ tests/testthat/test_get_support.R | 8 + tests/testthat/test_lp_norm.R | 8 - tests/testthat/test_theta_tau.R | 11 ++ 20 files changed, 239 insertions(+), 97 deletions(-)
Title: Group Sequential Bayes Design
Description: Group Sequential Operating Characteristics for Clinical,
Bayesian two-arm Trials with known Sigma and Normal Endpoints.
Author: Florian Gerber, Thomas Gsponer
Maintainer: Florian Gerber <florian.gerber@math.uzh.ch>
Diff between gsbDesign versions 0.96-3 dated 2015-07-08 and 1.00 dated 2016-03-29
ChangeLog | 6 +++++ DESCRIPTION | 10 ++++---- MD5 | 29 ++++++++++++++++--------- R/package.r | 21 ++++++++++++++++-- build |only demo |only inst/CITATION | 55 +++++++++++++++++++++++++++++-------------------- inst/doc |only man/gsb-package.Rd | 28 +++++++++++------------- man/gsb.Rd | 23 ++++++++------------ man/gsbBayesUpdate.Rd | 2 - man/gsbCriteria.Rd | 2 - man/plot.gsbMainOut.Rd | 2 - man/tab.Rd | 2 - vignettes |only 15 files changed, 108 insertions(+), 72 deletions(-)
Title: Identify Favorable Subsets of Germplasm Collections
Description: Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.
Author: Ryan C. Graebner and Alfonso Cuesta-Marcos
Maintainer: Ryan C. Graebner <ryan.graebner@gmail.com>
Diff between GeneticSubsetter versions 0.6 dated 2015-10-14 and 0.7 dated 2016-03-29
GeneticSubsetter-0.6/GeneticSubsetter/man/PIC.Rd |only GeneticSubsetter-0.7/GeneticSubsetter/DESCRIPTION | 6 ++-- GeneticSubsetter-0.7/GeneticSubsetter/MD5 | 14 +++++----- GeneticSubsetter-0.7/GeneticSubsetter/R/CoreSetOptimizer.R | 1 GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetOptimizer.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetter.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/CoreSetterCombined.Rd | 2 - GeneticSubsetter-0.7/GeneticSubsetter/man/GeneticSubsetter.Rd | 4 +- GeneticSubsetter-0.7/GeneticSubsetter/man/HET.Rd |only 9 files changed, 15 insertions(+), 16 deletions(-)
More information about GeneticSubsetter at CRAN
Permanent link
Title: Visualizes Random Forests with Feature Contributions
Description: Form visualizations of high dimensional mapping structures of random forests and feature contributions.
Author: Soeren Havelund Welling
Maintainer: Soeren Havelund Welling <SOWE@DTU.DK>
Diff between forestFloor versions 1.9.1 dated 2016-01-03 and 1.9.3 dated 2016-03-29
DESCRIPTION | 10 +-- MD5 | 50 ++++++++-------- NAMESPACE | 7 +- NEWS | 14 ++++ R/RcppExports.R | 8 +- R/Xtestmerger.R |only R/checkPlotTest.R |only R/fcol.R | 29 +++++++++ R/forestFloor_randomForest_multiClass.R | 97 ++++++++++++++++++++++++++++---- R/forestFloor_randomForest_regression.R | 63 +++++++++++++++++--- R/forestFloor_source.R | 35 +++++++---- R/plot.forestFloor_multiClass.R | 21 +++++- R/plot.forestFloor_regression.R | 16 ++++- R/show3d.R | 39 ++++++++++++ man/Xtestmerger.Rd |only man/fcol.Rd | 6 + man/forestFloor.Rd | 23 +++++-- man/plot.forestFloor.Rd | 7 ++ man/plot_simplex3.Rd | 2 man/recTree.Rd | 20 +++++- man/show3d.Rd | 11 +++ src/RcppExports.cpp | 14 ++-- src/testcpp_rec6.cpp | 51 ++++++++++++++-- tests/allExamples.R | 70 +++++++++++------------ tests/stdUsage.R | 68 ++++++++++++++++------ tests/testBinaryClass.R | 17 ++++- tests/testMultiClass.cpp.R | 59 ++++++++++++++----- tests/test_Xtestmerger.R |only 28 files changed, 564 insertions(+), 173 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.1-0 dated 2016-03-25 and 3.1-1 dated 2016-03-29
DESCRIPTION | 14 ++-- MD5 | 6 +- NEWS | 4 + man/effects-package.Rd | 143 ++++++++++++++++++++++++------------------------- 4 files changed, 86 insertions(+), 81 deletions(-)
Title: Interface to Bold Systems 'API'
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic 'barcode' data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.3.4 dated 2016-03-23 and 0.3.5 dated 2016-03-29
DESCRIPTION | 10 +++++----- MD5 | 35 +++++++++++++++++++---------------- NEWS.md | 15 +++++++++++++-- R/bold_identify.R | 7 ++++--- R/bold_tax_id.R | 5 ++--- R/bold_tax_name.R | 4 ++-- R/zzz.R | 2 +- README.md | 20 ++++++++++---------- inst/doc/bold_vignette.Rmd | 2 +- inst/doc/bold_vignette.html | 2 +- man/bold_identify.Rd | 5 +++-- man/bold_tax_id.Rd | 5 ++--- man/bold_tax_name.Rd | 4 ++-- tests/testthat/test-bold_identify.R |only tests/testthat/test-bold_seq.R | 16 +++++++++------- tests/testthat/test-bold_seqspec.R | 18 ++++++++++-------- tests/testthat/test-bold_specimens.R | 18 +++++++++++------- tests/testthat/test-bold_tax_id.R |only tests/testthat/test-bold_tax_name.R |only vignettes/bold_vignette.Rmd | 2 +- 20 files changed, 96 insertions(+), 74 deletions(-)
Title: Assertions for Checking the State of R
Description: A set of predicates and assertions for checking the state and
capabilities of R, the operating system it is running on, and the IDE
being used. This is mainly for use by other package developers who
want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.reflection versions 0.0-2 dated 2016-03-06 and 0.0-3 dated 2016-03-29
DESCRIPTION | 10 MD5 | 36 - NAMESPACE | 2 NEWS | 2 R/assert-is-r-version.R | 7 R/assert-r-has-capability.R | 308 +++++++------- R/is-current.R | 26 + R/is-ide.R | 352 ++++++++-------- R/is-r-mode.R | 8 R/is-r-version.R | 12 R/r-has-capability.R | 710 ++++++++++++++++----------------- man/is_package_current.Rd | 2 man/is_r.Rd | 14 man/r_can_find_tools.Rd | 146 +++--- tests/testthat.R | 12 tests/testthat/test-is-32-64-bit.R | 34 - tests/testthat/test-is-decimal-point.R | 176 ++++---- tests/testthat/test-is-ide.R | 244 +++++------ tests/testthat/test-is-r-mode.R | 82 +-- 19 files changed, 1118 insertions(+), 1065 deletions(-)
More information about assertive.reflection at CRAN
Permanent link
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between textreuse versions 0.1.2 dated 2015-11-06 and 0.1.3 dated 2016-03-28
textreuse-0.1.2/textreuse/NEWS |only textreuse-0.1.3/textreuse/DESCRIPTION | 10 +-- textreuse-0.1.3/textreuse/MD5 | 32 +++++----- textreuse-0.1.3/textreuse/NEWS.md |only textreuse-0.1.3/textreuse/R/conversion-functions.R | 6 - textreuse-0.1.3/textreuse/R/lsh_candidates.R | 9 +- textreuse-0.1.3/textreuse/R/lsh_compare.R | 4 - textreuse-0.1.3/textreuse/R/lsh_query.R | 2 textreuse-0.1.3/textreuse/R/similarity.R | 2 textreuse-0.1.3/textreuse/README.md | 6 - textreuse-0.1.3/textreuse/build/vignette.rds |binary textreuse-0.1.3/textreuse/inst/doc/textreuse-alignment.html | 17 ++--- textreuse-0.1.3/textreuse/inst/doc/textreuse-introduction.html | 17 ++--- textreuse-0.1.3/textreuse/inst/doc/textreuse-minhash.html | 31 ++++----- textreuse-0.1.3/textreuse/inst/doc/textreuse-pairwise.html | 19 ++--- textreuse-0.1.3/textreuse/man/similarity-functions.Rd | 2 textreuse-0.1.3/textreuse/tests/testthat/test-TextReuseCorpus.R | 4 - textreuse-0.1.3/textreuse/tests/testthat/test-lsh.R | 3 18 files changed, 80 insertions(+), 84 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library (http://sourceforge.net/projects/libxls/) and '.xlsx' via
the embedded 'RapidXML' C++ library (http://rapidxml.sourceforge.net). Works on
Windows, Mac and Linux without external dependencies.
Author: Hadley Wickham [aut, cre],
RStudio [cph] (Copyright holder of all R code and all C/C++ code
without explicit copyright attribution),
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Komarov Valery [ctb, cph] (Author of included libxls code),
Christophe Leitienne [ctb, cph] (Author of included libxls code),
Bob Colbert [ctb, cph] (Author of included libxls code),
David Hoerl [ctb, cph] (Author of included libxls code)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between readxl versions 0.1.0 dated 2015-04-14 and 0.1.1 dated 2016-03-28
DESCRIPTION | 17 +++++++------ MD5 | 27 ++++++++++++---------- NAMESPACE | 2 - NEWS.md |only R/xlsx.R | 2 - README.md | 10 +++++++- man/excel_sheets.Rd | 2 - man/read_excel.Rd | 2 - src/Makevars | 2 - src/XlsWorkSheet.h | 2 - src/XlsxCell.h | 44 ------------------------------------ src/XlsxString.h |only src/XlsxWorkBook.h | 2 - tests/testthat/new_line_errors.xlsx |only tests/testthat/test-dates.R | 4 +-- tests/testthat/test-richtext.R | 7 +++++ 16 files changed, 50 insertions(+), 73 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.7 dated 2016-03-17 and 0.4.7-1 dated 2016-03-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/resources/init-rprofile.R | 2 +- inst/resources/init.R | 2 +- tests/test-cranlike-repositories.R | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES).
Author: Christopher Endres
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 0.6.3 dated 2016-02-25 and 0.6.3.1 dated 2016-03-28
DESCRIPTION | 8 +-- MD5 | 22 ++++---- R/nhanes.R | 99 ++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/Introducing_nhanesA.R | 18 ++++-- inst/doc/Introducing_nhanesA.Rmd | 30 ++++++----- inst/doc/Introducing_nhanesA.html | 41 ++++++++------- man/browseNHANES.Rd | 4 - man/nhanesSearch.Rd | 16 ++++-- man/nhanesTableVars.Rd | 4 - man/nhanesTables.Rd | 4 - vignettes/Introducing_nhanesA.Rmd | 30 ++++++----- 12 files changed, 168 insertions(+), 108 deletions(-)
Title: Query Cache for HTTP Clients
Description: In order to improve performance for HTTP API clients, 'httpcache'
provides simple tools for caching and invalidating cache. It includes the
HTTP verb functions GET, PUT, PATCH, POST, and DELETE, which are drop-in
replacements for those in the 'httr' package. These functions are cache-aware
and provide default settings for cache invalidation suitable for RESTful
APIs; the package also enables custom cache-management strategies.
Finally, 'httpcache' includes a basic logging framework to facilitate the
measurement of HTTP request time and cache performance.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httpcache versions 0.1.2 dated 2016-02-23 and 0.1.4 dated 2016-03-28
httpcache-0.1.2/httpcache/tests/testthat/mocks.R |only httpcache-0.1.4/httpcache/DESCRIPTION | 9 ++-- httpcache-0.1.4/httpcache/MD5 | 25 ++++++------- httpcache-0.1.4/httpcache/R/cache.R | 23 +++++++---- httpcache-0.1.4/httpcache/R/http-verbs.R | 21 +++++----- httpcache-0.1.4/httpcache/R/log.R | 2 - httpcache-0.1.4/httpcache/man/startLog.Rd | 2 - httpcache-0.1.4/httpcache/man/uncached.Rd | 6 +-- httpcache-0.1.4/httpcache/tests/testthat/helper-mocks.R |only httpcache-0.1.4/httpcache/tests/testthat/helper.R | 6 --- httpcache-0.1.4/httpcache/tests/testthat/test-cache.R | 22 +++++++++-- httpcache-0.1.4/httpcache/tests/testthat/test-drop-cache.R | 19 +++++++++ httpcache-0.1.4/httpcache/tests/testthat/test-logging.R | 5 +- httpcache-0.1.4/httpcache/tests/testthat/test-zzz-helper.R | 8 +++- httpcache-0.1.4/httpcache/vignettes |only 15 files changed, 94 insertions(+), 54 deletions(-)
Title: Estimation of Extreme Value Dependence for Time Series Data
Description: Estimation of the sample univariate, cross and return time extremograms. The package can also add empirical confidence bands to each of the extremogram plots via a permutation procedure under the assumption that the data are independent. Finally, the stationary bootstrap allows us to construct credible confidence bands for the extremograms.
Author: Nadezda Frolova, Ivor Cribben
Maintainer: Nadezda Frolova <nfrolova@ualberta.ca>
Diff between extremogram versions 1.0.0 dated 2015-09-29 and 1.0.1 dated 2016-03-28
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/bootconf1.R | 19 ++++++++++++------- R/bootconf2.R | 13 ++++++------- R/bootconfr.R | 11 ++++------- R/extremogram1.R | 18 +++++++++++++----- R/extremogram2.R | 8 +++----- R/extremogramr.R | 24 +++++++++++++++++------- man/bootconf1.Rd | 4 +++- man/bootconf2.Rd | 4 +++- man/bootconfr.Rd | 4 +++- man/extremogram1.Rd | 5 ++++- man/extremogram2.Rd | 4 +++- man/extremogramr.Rd | 4 +++- 14 files changed, 91 insertions(+), 61 deletions(-)
Title: Average and Conditional Effects
Description: Use structural equation modeling to estimate average and
conditional effects of a treatment variable on an outcome variable, taking into
account multiple continuous and categorical covariates.
Author: Axel Mayer [aut, cre],
Lisa Dietzfelbinger [ctb]
Maintainer: Axel Mayer <amayer2010@gmail.com>
Diff between EffectLiteR versions 0.4-1 dated 2015-10-18 and 0.4-2 dated 2016-03-28
DESCRIPTION | 18 MD5 | 46 - NAMESPACE | 4 R/00class.R |only R/00documentation.R |only R/00methods.R |only R/effectliter.R | 1653 ------------------------------------- R/elr_compute_propensity_score.R |only R/elr_compute_results.R |only R/elr_create_input.R |only R/elr_create_parnames.R |only R/elr_create_syntax.R |only R/elr_generate_measurement_model.R |only R/elr_plot_condeffects.R |only R/elr_predict.R |only R/elr_read_data.R |only R/elr_shiny.R |only data/example_multilevel.RData |binary inst/elrshiny/server.R | 146 ++- inst/elrshiny/ui.R | 407 +++++---- man/EffectLiteR.Rd | 4 man/conditionalEffectsPlot.Rd | 9 man/effectLite.Rd | 31 man/effectLiteGUI.Rd | 4 man/elrPredict.Rd |only man/elrReadData.Rd | 10 man/example01.Rd | 4 man/example02lv.Rd | 4 man/example_multilevel.Rd | 7 man/generateMeasurementModel.Rd | 27 man/nonortho.Rd | 4 31 files changed, 500 insertions(+), 1878 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut],
Jordan Read [ctb],
Lindsay Carr [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.5.2 dated 2016-03-04 and 2.5.3 dated 2016-03-28
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/importWaterML1.r | 3 ++- R/readNWISdata.r | 11 +++++++---- R/whatNWISsites.R | 4 +--- R/zeroPad.r | 6 +++++- README.md | 2 +- build/vignette.rds |binary man/readNWISdata.Rd | 7 ++++++- 9 files changed, 35 insertions(+), 24 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.3.4 dated 2015-12-22 and 0.3.5 dated 2016-03-28
DESCRIPTION | 10 +- MD5 | 63 ++++++++-------- NAMESPACE | 1 NEWS | 10 ++ R/chordDiagram.R | 79 +++++++++++++++++++-- R/genomic.R | 23 ++---- R/global.R | 3 R/link.R | 2 R/plot.R | 71 +++++++++++++++++- build/vignette.rds |binary inst/doc/circlize.R | 9 +- inst/doc/circlize.Rnw | 12 ++- inst/doc/circlize.pdf |binary inst/doc/circular_phylogenetic_tree.pdf |binary inst/doc/circular_visualization_of_matrix.pdf |binary inst/doc/genomic_plot.R | 4 - inst/doc/genomic_plot.Rnw | 2 inst/doc/genomic_plot.pdf |binary inst/doc/interesting_graphics.pdf |binary inst/doc/visualize_relations_by_chord_diagram.R | 2 inst/doc/visualize_relations_by_chord_diagram.Rnw | 4 - inst/doc/visualize_relations_by_chord_diagram.pdf |binary man/chordDiagram.rd | 46 +++++++++++- man/circos.genomicLink.rd | 2 man/circos.link.rd | 2 man/circos.par.rd | 3 man/circos.text.rd | 4 - man/degree.rd |only man/smartAlign.rd | 1 vignettes/circlize.Rnw | 12 ++- vignettes/genomic_plot.Rnw | 2 vignettes/src/intro-11-axis.R | 2 vignettes/visualize_relations_by_chord_diagram.Rnw | 4 - 33 files changed, 286 insertions(+), 87 deletions(-)
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System. These tools address common challenges
associated with continuous time series data for environmental decision
making.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between SWMPr versions 2.1.4 dated 2015-10-07 and 2.1.5 dated 2016-03-28
SWMPr-2.1.4/SWMPr/man/import_remote.Rd |only SWMPr-2.1.5/SWMPr/DESCRIPTION | 14 ++- SWMPr-2.1.5/SWMPr/MD5 | 88 +++++++++++----------- SWMPr-2.1.5/SWMPr/NAMESPACE | 4 - SWMPr-2.1.5/SWMPr/R/globalVariables.R |only SWMPr-2.1.5/SWMPr/R/swmpr_analyze.R | 119 +++++++++++++++++++++++++----- SWMPr-2.1.5/SWMPr/R/swmpr_misc.R | 10 +- SWMPr-2.1.5/SWMPr/R/swmpr_organize.R | 44 +++++++++-- SWMPr-2.1.5/SWMPr/R/swmpr_retrieval.R | 64 +++------------- SWMPr-2.1.5/SWMPr/man/aggremetab.Rd | 2 SWMPr-2.1.5/SWMPr/man/aggreswmp.Rd | 20 ++++- SWMPr-2.1.5/SWMPr/man/all_params.Rd | 3 SWMPr-2.1.5/SWMPr/man/all_params_dtrng.Rd | 5 - SWMPr-2.1.5/SWMPr/man/apacpnut.Rd | 2 SWMPr-2.1.5/SWMPr/man/apacpwq.Rd | 2 SWMPr-2.1.5/SWMPr/man/apadbwq.Rd | 2 SWMPr-2.1.5/SWMPr/man/apaebmet.Rd | 2 SWMPr-2.1.5/SWMPr/man/calckl.Rd | 2 SWMPr-2.1.5/SWMPr/man/comb.Rd | 10 +- SWMPr-2.1.5/SWMPr/man/decomp.Rd | 7 + SWMPr-2.1.5/SWMPr/man/decomp_cj.Rd | 8 +- SWMPr-2.1.5/SWMPr/man/ecometab.Rd | 4 - SWMPr-2.1.5/SWMPr/man/gradcols.Rd | 2 SWMPr-2.1.5/SWMPr/man/hist.swmpr.Rd | 2 SWMPr-2.1.5/SWMPr/man/import_local.Rd | 11 +- SWMPr-2.1.5/SWMPr/man/map_reserve.Rd | 7 + SWMPr-2.1.5/SWMPr/man/metab_day.Rd | 2 SWMPr-2.1.5/SWMPr/man/na.approx.swmpr.Rd | 4 - SWMPr-2.1.5/SWMPr/man/overplot.Rd | 4 - SWMPr-2.1.5/SWMPr/man/param_names.Rd | 2 SWMPr-2.1.5/SWMPr/man/parser.Rd | 2 SWMPr-2.1.5/SWMPr/man/plot.swmpr.Rd | 4 - SWMPr-2.1.5/SWMPr/man/plot_metab.Rd | 2 SWMPr-2.1.5/SWMPr/man/plot_summary.Rd | 26 +++++- SWMPr-2.1.5/SWMPr/man/qaqc.Rd | 2 SWMPr-2.1.5/SWMPr/man/qaqcchk.Rd | 3 SWMPr-2.1.5/SWMPr/man/rem_reps.Rd | 2 SWMPr-2.1.5/SWMPr/man/setstep.Rd | 2 SWMPr-2.1.5/SWMPr/man/single_param.Rd | 3 SWMPr-2.1.5/SWMPr/man/site_codes.Rd | 2 SWMPr-2.1.5/SWMPr/man/site_codes_ind.Rd | 2 SWMPr-2.1.5/SWMPr/man/smoother.Rd | 2 SWMPr-2.1.5/SWMPr/man/stat_locs.Rd | 2 SWMPr-2.1.5/SWMPr/man/subset.swmpr.Rd | 4 - SWMPr-2.1.5/SWMPr/man/swmpr.Rd | 2 SWMPr-2.1.5/SWMPr/man/time_vec.Rd | 2 46 files changed, 318 insertions(+), 190 deletions(-)
Title: Diverse Basic Statistical and Graphical Functions
Description: Contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Herv
Maintainer: Maxime Herv <mx.herve@gmail.com>
Diff between RVAideMemoire versions 0.9-53 dated 2016-02-28 and 0.9-54 dated 2016-03-28
RVAideMemoire-0.9-53/RVAideMemoire/R/summary.least.rect.R |only RVAideMemoire-0.9-54/RVAideMemoire/DESCRIPTION | 8 RVAideMemoire-0.9-54/RVAideMemoire/MD5 | 23 +- RVAideMemoire-0.9-54/RVAideMemoire/NAMESPACE | 4 RVAideMemoire-0.9-54/RVAideMemoire/NEWS | 85 +++++----- RVAideMemoire-0.9-54/RVAideMemoire/R/MVA.scoreplot.R | 10 + RVAideMemoire-0.9-54/RVAideMemoire/R/dummy.R |only RVAideMemoire-0.9-54/RVAideMemoire/R/least.rect.R | 70 +++++++- RVAideMemoire-0.9-54/RVAideMemoire/R/prop.multinom.R | 2 RVAideMemoire-0.9-54/RVAideMemoire/R/spearman.cor.multcomp.R |only RVAideMemoire-0.9-54/RVAideMemoire/R/zzz.R | 2 RVAideMemoire-0.9-54/RVAideMemoire/man/RVAideMemoire-package.Rd | 4 RVAideMemoire-0.9-54/RVAideMemoire/man/dummy.Rd |only RVAideMemoire-0.9-54/RVAideMemoire/man/least.rect.Rd | 6 RVAideMemoire-0.9-54/RVAideMemoire/man/spearman.cor.multcomp.Rd |only 15 files changed, 145 insertions(+), 69 deletions(-)
Title: Application Directories: Determine Where to Save Data, Caches,
and Logs
Description: An easy way to determine which directories on the users computer
you should use to save data, caches and logs. A port of Python's 'Appdirs'
(\url{https://github.com/ActiveState/appdirs}) to R.
Author: Hadley Wickham [trl, cre, cph],
RStudio [cph],
Sridhar Ratnakumar [aut],
Trent Mick [aut],
ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated
from appdirs),
Eddy Petrisor [ctb],
Trevor Davis [trl, aut],
Gabor Csardi [ctb],
Gregory Jefferis [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rappdirs versions 0.3 dated 2014-09-02 and 0.3.1 dated 2016-03-28
rappdirs-0.3.1/rappdirs/DESCRIPTION | 19 ++++---- rappdirs-0.3.1/rappdirs/LICENSE | 2 rappdirs-0.3.1/rappdirs/MD5 | 22 ++++----- rappdirs-0.3.1/rappdirs/NAMESPACE | 2 rappdirs-0.3.1/rappdirs/NEWS.md |only rappdirs-0.3.1/rappdirs/man/app_dir.Rd | 5 +- rappdirs-0.3.1/rappdirs/man/rappdirs-package.Rd | 46 ++++++++++---------- rappdirs-0.3.1/rappdirs/man/site_data_dir.Rd | 19 ++++---- rappdirs-0.3.1/rappdirs/man/user_cache_dir.Rd | 15 +++--- rappdirs-0.3.1/rappdirs/man/user_data_dir.Rd | 21 ++++----- rappdirs-0.3.1/rappdirs/man/user_log_dir.Rd | 17 +++---- rappdirs-0.3.1/rappdirs/tests/testthat/test-utils.r | 1 rappdirs-0.3/rappdirs/NEWS |only 13 files changed, 88 insertions(+), 81 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.3.1 dated 2015-10-25 and 3.4.0 dated 2016-03-28
tergm-3.3.1/tergm/tests/examples.R |only tergm-3.4.0/tergm/DESCRIPTION | 12 +-- tergm-3.4.0/tergm/LICENSE | 2 tergm-3.4.0/tergm/MD5 | 24 +++--- tergm-3.4.0/tergm/NAMESPACE | 15 ++- tergm-3.4.0/tergm/R/stergm.CMLE.R | 8 +- tergm-3.4.0/tergm/R/stergm.EGMME.GD.R | 2 tergm-3.4.0/tergm/R/stergm.EGMME.SA.R | 10 +- tergm-3.4.0/tergm/R/zzz.R | 4 - tergm-3.4.0/tergm/inst/NEWS.Rd | 50 ++++++++---- tergm-3.4.0/tergm/inst/doc/STERGM.pdf |binary tergm-3.4.0/tergm/man/stergm.Rd | 4 - tergm-3.4.0/tergm/tests/requireNamespaceTest.R |only tergm-3.4.0/tergm/tests/tergm_offset_tests.R | 100 ++++++++++++------------- 14 files changed, 128 insertions(+), 103 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 0.13.1 dated 2016-02-17 and 0.13.2 dated 2016-03-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ inst/doc/events.html | 15 +++++++-------- inst/www/shared/shiny.min.js | 2 +- man/htmlTemplate.Rd | 8 ++++++-- 6 files changed, 28 insertions(+), 20 deletions(-)
Title: Data.frame-Like Operations on Sparse and Dense Matrix Objects
Description: Implements data manipulation methods such as cast, aggregate, and merge/join for Matrix and matrix-like objects.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between Matrix.utils versions 0.5 dated 2015-12-15 and 0.9.0 dated 2016-03-28
DESCRIPTION | 14 +- MD5 | 15 +-- NAMESPACE | 3 R/Matrix.utils.R | 235 ++++++++++++++++++++++++++++++++++++++---------- man/Matrix.utils.Rd | 6 - man/aggregate.Matrix.Rd | 2 man/dMcast.Rd | 5 - man/merge.Matrix.Rd | 104 ++++++++++++++------- man/rBind.fill.Rd |only 9 files changed, 287 insertions(+), 97 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.2.0 dated 2016-03-23 and 1.2.2 dated 2016-03-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/GDM_Table_Funcs.R | 28 +++++++++++++++++----------- inst/doc/gdmVignette.pdf |binary src/Gdmlib.cpp | 2 +- 5 files changed, 26 insertions(+), 20 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson
<jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles
Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.5.18 dated 2016-03-08 and 4.5.19 dated 2016-03-28
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/vignette.rds |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Finding Files in Project Subdirectories
Description: Robust, reliable and flexible paths to files below a
project root. The 'root' of a project is defined as a directory
that matches a certain criterion, e.g., it contains a certain
regular file.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between rprojroot versions 1.0-1 dated 2016-03-27 and 1.0-2 dated 2016-03-28
rprojroot-1.0-1/rprojroot/R/zzz-autoroxy.R |only rprojroot-1.0-2/rprojroot/DESCRIPTION | 8 ++++---- rprojroot-1.0-2/rprojroot/MD5 | 7 +++---- rprojroot-1.0-2/rprojroot/NEWS.md | 10 ++++++++++ rprojroot-1.0-2/rprojroot/tests/testthat/test-make.R | 3 ++- 5 files changed, 19 insertions(+), 9 deletions(-)
Title: Nonparametric Combination of Hypothesis Tests
Description: An implementation of nonparametric combination of hypothesis tests.
This package performs nonparametric combination (Pesarin and Salmaso 2010),
a permutation-based procedure for jointly testing multiple hypotheses. The
tests are conducted under the global "sharp" null hypothesis of no effects,
and the component tests are combined on the metric of their p-values. A
key feature of nonparametric combination is that it accounts for the
dependence among tests under the null hypothesis. In addition to the
"NPC" function, which performs nonparametric combination itself, the
package also contains a number of helper functions, many of which calculate
a test statistic given an input of data.
Author: Devin Caughey [aut, cre]
Maintainer: Devin Caughey <devin.caughey@gmail.com>
Diff between NPC versions 1.0.2 dated 2015-10-21 and 1.1.0 dated 2016-03-28
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NAMESPACE | 5 ++++- NEWS.md | 2 +- R/FWE.R | 1 + R/NPC.R | 10 ++++++---- man/NPC.Rd | 21 ++++++++------------- 7 files changed, 31 insertions(+), 29 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of R markdown instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.4.4 dated 2016-03-01 and 3.4.6 dated 2016-03-28
lessR-3.4.4/lessR/man/set.Rd |only lessR-3.4.6/lessR/DESCRIPTION | 10 lessR-3.4.6/lessR/MD5 | 93 +++--- lessR-3.4.6/lessR/NAMESPACE | 1 lessR-3.4.6/lessR/NEWS | 72 +++++ lessR-3.4.6/lessR/R/ANOVAz1.R | 8 lessR-3.4.6/lessR/R/BarChart.R | 42 ++- lessR-3.4.6/lessR/R/BoxPlot.R | 7 lessR-3.4.6/lessR/R/Correlation.R | 4 lessR-3.4.6/lessR/R/Density.R | 5 lessR-3.4.6/lessR/R/Help.R | 20 - lessR-3.4.6/lessR/R/Histogram.R | 10 lessR-3.4.6/lessR/R/LineChart.R | 5 lessR-3.4.6/lessR/R/Read.R | 22 + lessR-3.4.6/lessR/R/ScatterPlot.R | 214 +++++++++++---- lessR-3.4.6/lessR/R/SummaryStats.R | 4 lessR-3.4.6/lessR/R/bc.data.frame.R | 8 lessR-3.4.6/lessR/R/bc.zmain.R | 118 ++++---- lessR-3.4.6/lessR/R/bx.zmain.R | 6 lessR-3.4.6/lessR/R/corEFA.R | 1 lessR-3.4.6/lessR/R/cr.data.frame.R | 28 +- lessR-3.4.6/lessR/R/details.R | 8 lessR-3.4.6/lessR/R/dn.zmain.R | 2 lessR-3.4.6/lessR/R/dp.zmain.R | 19 - lessR-3.4.6/lessR/R/dpmat.zmain.R | 15 - lessR-3.4.6/lessR/R/hst.zmain.R | 5 lessR-3.4.6/lessR/R/lc.zmain.R | 2 lessR-3.4.6/lessR/R/logit.z4Pred.R | 47 +-- lessR-3.4.6/lessR/R/pc.zmain.R | 2 lessR-3.4.6/lessR/R/plt.zlegend.R | 9 lessR-3.4.6/lessR/R/plt.zmain.R | 398 ++++++++++++++++++----------- lessR-3.4.6/lessR/R/reg.z3resfitResidual.R | 38 +- lessR-3.4.6/lessR/R/reg.z5Plot.R | 10 lessR-3.4.6/lessR/R/set.R | 270 ------------------- lessR-3.4.6/lessR/R/ss.zdata.frame.R | 3 lessR-3.4.6/lessR/R/ss.zfactor.R | 56 ++-- lessR-3.4.6/lessR/R/theme.R |only lessR-3.4.6/lessR/R/ttest.R | 7 lessR-3.4.6/lessR/R/ttp2zgraph.R | 52 +-- lessR-3.4.6/lessR/R/zzz.R | 135 +++++---- lessR-3.4.6/lessR/man/ANOVA.Rd | 8 lessR-3.4.6/lessR/man/BarChart.Rd | 49 +-- lessR-3.4.6/lessR/man/Correlation.Rd | 3 lessR-3.4.6/lessR/man/Histogram.Rd | 3 lessR-3.4.6/lessR/man/LineChart.Rd | 4 lessR-3.4.6/lessR/man/Regression.Rd | 32 +- lessR-3.4.6/lessR/man/ScatterPlot.Rd | 145 ++++++---- lessR-3.4.6/lessR/man/corCFA.Rd | 2 lessR-3.4.6/lessR/man/theme.Rd |only 49 files changed, 1084 insertions(+), 918 deletions(-)
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to 'stats::lowess' function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting "Venn" diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gplots versions 2.17.0 dated 2015-05-02 and 3.0.0 dated 2016-03-28
ChangeLog | 1612 +++++++++++++++++++------------------------ DESCRIPTION | 16 MD5 | 45 - NAMESPACE | 27 NEWS | 58 + R/angleAxis.R |only R/boxplot2.R | 4 R/heatmap.2.R | 71 + R/layout_set.R |only R/lmplot2.R | 308 ++++---- R/lowess.R | 90 +- R/plot.lowess.R |only R/plot.venn.R | 81 +- R/smartlegend.R | 52 - R/venn.R | 256 +++--- R/vennMembers.R |only inst/ChangeLog | 1612 +++++++++++++++++++------------------------ inst/NEWS | 58 + inst/doc/venn.pdf |binary man/angleAxis.Rd |only man/gplots-defunct.Rd | 36 man/gplots-deprecated.Rd | 17 man/heatmap.2.Rd | 4 man/lowess.Rd | 90 +- man/venn.Rd | 62 - tests/heatmap2Test.Rout.save | 38 - 26 files changed, 2247 insertions(+), 2290 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time. Especially important for small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.3.1 dated 2016-01-20 and 1.3.2 dated 2016-03-28
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS | 4 ++++ R/kmciFunctions.R | 18 +++++++++++++----- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/discreteBPCP.Rnw | 2 +- inst/doc/discreteBPCP.pdf |binary man/bpcp-package.Rd | 8 ++++---- man/kmciALL.Rd | 4 ++-- tests/FirstObsCensored.R |only vignettes/discreteBPCP.Rnw | 2 +- 12 files changed, 42 insertions(+), 29 deletions(-)
Title: Tools for Accessing Various Datasets Developed by the Foundation
SmarterPoland.pl
Description: Tools for accessing and processing datasets prepared by the Foundation SmarterPoland.pl. Among all: access to API of Google Maps, Central Statistical Office of Poland, MojePanstwo, Eurostat, WHO and other sources.
Author: Przemyslaw Biecek (Foundation SmarterPoland.pl)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between SmarterPoland versions 1.5 dated 2015-01-30 and 1.7 dated 2016-03-28
DESCRIPTION | 13 +- MD5 | 25 ++-- NAMESPACE | 6 - R/BankDanychLokalnych.R | 217 +++++++++++++++++++++++++------------------ R/getGoogleMapsAddress.R | 8 - R/getMillwardBrown.R | 72 ++++++++++---- R/getWeatherForecast.R | 2 data/BDLtree.rda |binary data/cities_lon_lat.rda |binary data/countries.rda |only data/datalist |only data/maturaExam.rda |only man/BankDanychLokalnych.Rd | 34 ++++-- man/SmarterPoland-package.Rd | 19 +-- man/countries.Rd |only man/maturaExam.Rd |only 16 files changed, 243 insertions(+), 153 deletions(-)
Title: Polygon Clipping
Description: R port of Angus Johnson's open source library Clipper. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines. Computes Minkowski Sum of general polygons. There is a function for removing self-intersections from polygon data.
Author: Angus Johnson [aut] (C++ original,
http://www.angusj.com/delphi/clipper.php),
Adrian Baddeley [aut, trl, cre],
Brian D. Ripley [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between polyclip versions 1.4-1 dated 2016-02-14 and 1.5-1 dated 2016-03-28
DESCRIPTION | 29 MD5 | 23 NAMESPACE | 5 R/First.R | 7 R/clipper.R | 40 + man/polyclip.Rd | 3 man/polylineoffset.Rd | 6 man/polyminkowski.Rd |only man/polyoffset.Rd | 6 man/polysimplify.Rd | 3 src/clipper.cpp | 1739 ++++++++++++++++++++++++-------------------------- src/clipper.h | 182 ++--- src/interface.cpp | 93 ++ 13 files changed, 1144 insertions(+), 992 deletions(-)
Title: Geometric Median, k-Median Clustering and Robust Median PCA
Description: Fast algorithms based on averaged stochastic gradient for robust estimation with large samples. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.
Author: Herve Cardot
Maintainer: Herve Cardot <herve.cardot@u-bourgogne.fr>
Diff between Gmedian versions 1.0 dated 2016-03-27 and 1.1 dated 2016-03-28
DESCRIPTION | 12 ++++++------ MD5 | 17 +++++++++-------- NAMESPACE | 4 ++-- NEWS |only build/partial.rdb |binary man/Gmedian-package.Rd | 2 +- man/Gmedian.Rd | 14 +++++++------- man/GmedianCov.Rd | 12 ++++++------ man/kGmedian.Rd | 2 +- src/Gmedian.cpp | 19 +++++++------------ 10 files changed, 39 insertions(+), 43 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.3.1.1 dated 2016-02-29 and 1.4.1.1 dated 2016-03-28
pomp-1.3.1.1/pomp/R/abc-methods.R |only pomp-1.3.1.1/pomp/R/basic-probes.R |only pomp-1.3.1.1/pomp/R/dmeasure-pomp.R |only pomp-1.3.1.1/pomp/R/dprior-pomp.R |only pomp-1.3.1.1/pomp/R/dprocess-pomp.R |only pomp-1.3.1.1/pomp/R/init-state-pomp.R |only pomp-1.3.1.1/pomp/R/mif-methods.R |only pomp-1.3.1.1/pomp/R/mif2-methods.R |only pomp-1.3.1.1/pomp/R/nlf-funcs.R |only pomp-1.3.1.1/pomp/R/nlf-guts.R |only pomp-1.3.1.1/pomp/R/nlf-objfun.R |only pomp-1.3.1.1/pomp/R/pfilter-methods.R |only pomp-1.3.1.1/pomp/R/plot-pomp.R |only pomp-1.3.1.1/pomp/R/pmcmc-methods.R |only pomp-1.3.1.1/pomp/R/pomp-class.R |only pomp-1.3.1.1/pomp/R/pomp-fun.R |only pomp-1.3.1.1/pomp/R/pomp-methods.R |only pomp-1.3.1.1/pomp/R/probe-match.R |only pomp-1.3.1.1/pomp/R/profile-design.R |only pomp-1.3.1.1/pomp/R/rmeasure-pomp.R |only pomp-1.3.1.1/pomp/R/rprior-pomp.R |only pomp-1.3.1.1/pomp/R/rprocess-pomp.R |only pomp-1.3.1.1/pomp/R/simulate-pomp.R |only pomp-1.3.1.1/pomp/R/skeleton-pomp.R |only pomp-1.3.1.1/pomp/R/slice-design.R |only pomp-1.3.1.1/pomp/R/spect-match.R |only pomp-1.3.1.1/pomp/R/traj-match.R |only pomp-1.3.1.1/pomp/R/trajectory-pomp.R |only pomp-1.3.1.1/pomp/man/builder.Rd |only pomp-1.4.1.1/pomp/DESCRIPTION | 30 - pomp-1.4.1.1/pomp/MD5 | 89 ++-- pomp-1.4.1.1/pomp/R/abc_methods.R |only pomp-1.4.1.1/pomp/R/basic_probes.R |only pomp-1.4.1.1/pomp/R/builder.R | 621 ++++++++++++++------------------- pomp-1.4.1.1/pomp/R/dmeasure_pomp.R |only pomp-1.4.1.1/pomp/R/dprior_pomp.R |only pomp-1.4.1.1/pomp/R/dprocess_pomp.R |only pomp-1.4.1.1/pomp/R/initstate_pomp.R |only pomp-1.4.1.1/pomp/R/mif2.R | 5 pomp-1.4.1.1/pomp/R/mif2_methods.R |only pomp-1.4.1.1/pomp/R/mif_methods.R |only pomp-1.4.1.1/pomp/R/nlf_funcs.R |only pomp-1.4.1.1/pomp/R/nlf_guts.R |only pomp-1.4.1.1/pomp/R/nlf_objfun.R |only pomp-1.4.1.1/pomp/R/pfilter_methods.R |only pomp-1.4.1.1/pomp/R/plot_pomp.R |only pomp-1.4.1.1/pomp/R/pmcmc_methods.R |only pomp-1.4.1.1/pomp/R/pomp.R | 67 ++- pomp-1.4.1.1/pomp/R/pomp_class.R |only pomp-1.4.1.1/pomp/R/pomp_fun.R |only pomp-1.4.1.1/pomp/R/pomp_methods.R |only pomp-1.4.1.1/pomp/R/probe_match.R |only pomp-1.4.1.1/pomp/R/profile_design.R |only pomp-1.4.1.1/pomp/R/rmeasure_pomp.R |only pomp-1.4.1.1/pomp/R/rprior_pomp.R |only pomp-1.4.1.1/pomp/R/rprocess_pomp.R |only pomp-1.4.1.1/pomp/R/simulate_pomp.R |only pomp-1.4.1.1/pomp/R/skeleton_pomp.R |only pomp-1.4.1.1/pomp/R/slice_design.R |only pomp-1.4.1.1/pomp/R/spect_match.R |only pomp-1.4.1.1/pomp/R/traj_match.R |only pomp-1.4.1.1/pomp/R/trajectory_pomp.R |only pomp-1.4.1.1/pomp/build/partial.rdb |binary pomp-1.4.1.1/pomp/data/LondonYorke.rda |binary pomp-1.4.1.1/pomp/data/ewcitmeas.rda |binary pomp-1.4.1.1/pomp/data/ewmeas.rda |binary pomp-1.4.1.1/pomp/inst/CITATION | 106 ++--- pomp-1.4.1.1/pomp/inst/NEWS | 21 + pomp-1.4.1.1/pomp/inst/NEWS.Rd | 19 - pomp-1.4.1.1/pomp/inst/doc/index.html | 3 pomp-1.4.1.1/pomp/man/package.Rd | 2 pomp-1.4.1.1/pomp/man/pmcmc.Rd | 6 pomp-1.4.1.1/pomp/man/pomp.Rd | 17 pomp-1.4.1.1/pomp/src/simulate.c | 2 74 files changed, 487 insertions(+), 501 deletions(-)
Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between openVA versions 1.0 dated 2016-03-12 and 1.0.1 dated 2016-03-28
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 6 +++++- R/CSMF.r | 50 +++++++++++++++++++++++++++++++++++++++++++++++++- R/VAmain.r | 32 +++++++++++++++++--------------- man/codeVA.Rd | 4 ++-- man/getIndivProb.Rd |only 7 files changed, 84 insertions(+), 29 deletions(-)
Title: Attaches and Installs Packages
Description: A simple function for easier package loading and auto-installation.
Author: Josh Katz [aut, cre]
Maintainer: Josh Katz <josh.katz@nytimes.com>
Diff between needs versions 0.0.2 dated 2015-12-18 and 0.0.3 dated 2016-03-28
DESCRIPTION | 8 +-- LICENSE | 2 MD5 | 16 +++--- NAMESPACE | 1 R/needs-package.R | 8 ++- R/needs.R | 132 ++++++++++++++++++++++++++++++++------------------- R/prioritize.R |only man/needs-package.Rd | 7 ++ man/needs.Rd | 28 +++++++--- man/prioritize.Rd |only 10 files changed, 131 insertions(+), 71 deletions(-)
Title: A Wrapper for the 'Highcharts' Library
Description: A wrapper for the 'Highcharts' library including
shortcut functions to plot R objects. 'Highcharts'
<http://www.highcharts.com/> is a charting library offering
numerous chart types with a simple configuration syntax.
Author: Joshua Kunst <jbkunst@gmail.com>
Maintainer: Joshua Kunst <jbkunst@gmail.com>
Diff between highcharter versions 0.2.0 dated 2016-02-25 and 0.3.0 dated 2016-03-28
DESCRIPTION | 13 - MD5 | 103 +++++--- NAMESPACE | 29 ++ NEWS.md | 24 ++ R/api-hc-extras.R | 17 + R/api-hc.R | 29 ++ R/export-hc.R |only R/hchart.R | 127 +++++++++++ R/helpers.R | 112 +++++++++ R/highcharter-package.R | 5 R/shortcuts-ts-xts.R | 7 R/shortcuts.R | 57 +--- R/theme-538.R | 22 + R/theme-chalk.R | 11 R/theme-darkunica.R | 11 R/theme-db.R | 10 R/theme-economist.R | 18 + R/theme-flat.R |only R/theme-ft.R |only R/theme-google.R | 11 R/theme-gridlight.R | 11 R/theme-handdrawn.R | 11 R/theme-null.R | 11 R/theme-sandsignika.R | 11 R/theme-smpl.R |only R/theme.R | 4 README.md | 17 + build/vignette.rds |binary inst/doc/replicating-highcharts-demos.Rmd | 2 inst/doc/replicating-highcharts-demos.html | 21 - inst/htmlwidgets/highchart.js | 10 inst/htmlwidgets/highchart.yaml | 8 inst/htmlwidgets/lib/highcharts-4.2.3/modules/funnel.js |only inst/htmlwidgets/lib/highcharts-4.2.3/modules/solid-gauge.js |only man/colorize_vector.Rd |only man/export_hc.Rd |only man/hc_add_series_flags.Rd | 4 man/hc_add_series_scatter.Rd | 34 -- man/hc_add_series_xts.Rd | 3 man/hc_colors.Rd |only man/hc_pane.Rd |only man/hc_theme.Rd | 2 man/hc_theme_538.Rd | 13 + man/hc_theme_chalk.Rd | 5 man/hc_theme_darkunica.Rd | 5 man/hc_theme_db.Rd | 5 man/hc_theme_economist.Rd | 9 man/hc_theme_flat.Rd |only man/hc_theme_ft.Rd |only man/hc_theme_google.Rd | 5 man/hc_theme_gridlight.Rd | 5 man/hc_theme_handdrawn.Rd | 5 man/hc_theme_merge.Rd | 2 man/hc_theme_null.Rd | 5 man/hc_theme_sandsignika.Rd | 5 man/hc_theme_smpl.Rd |only man/hex_to_rgba.Rd |only man/highcarter-exports.Rd | 1 man/tooltip_table.Rd |only vignettes/replicating-highcharts-demos.Rmd | 2 60 files changed, 648 insertions(+), 174 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.3.4 dated 2016-01-06 and 0.4.0 dated 2016-03-28
DESCRIPTION | 13 ++++++------ MD5 | 28 +++++++++++++++---------- NAMESPACE | 3 ++ NEWS.md | 6 +++++ R/ggMarginal.R | 8 +++++-- R/ggMarginalGadget.R |only README.md | 22 +++++++++++++------- build/vignette.rds |binary inst/doc/overview.R | 2 - inst/doc/overview.Rmd | 16 ++++++++------ inst/doc/overview.html | 41 ++++++++++++++++++++------------------ inst/examples/ggMarginal/server.R | 2 - inst/gadgets |only inst/img |only inst/rstudio |only man/ggMarginalGadget.Rd |only vignettes/overview.Rmd | 16 ++++++++------ 17 files changed, 96 insertions(+), 61 deletions(-)
Title: Modular Differential Evolution for Experimenting with Operators
Description: Modular implementation of the Differential Evolution algorithm for
experimenting with different types of operators.
Author: Felipe Campelo [aut, cre],
Moises Botelho [aut]
Maintainer: Felipe Campelo <fcampelo@ufmg.br>
Diff between ExpDE versions 0.1.1 dated 2016-03-26 and 0.1.2 dated 2016-03-28
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- README.md | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 65 insertions(+), 6 deletions(-)
Title: Process activPAL Events Files
Description: Performs estimation of physical activity and sedentary behavior variables from activPAL (PAL Technologies, Glasgow, Scotland) events files. See <http://paltechnologies.com> for more information on the activPAL.
Author: Kate Lyden
Maintainer: Kate Lyden <activpalProcessing@gmail.com>
Diff between activpalProcessing versions 1.0 dated 2016-01-25 and 1.0.1 dated 2016-03-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/process.AP.R | 5 ++++- man/process.AP.Rd | 8 ++++---- 4 files changed, 15 insertions(+), 12 deletions(-)
More information about activpalProcessing at CRAN
Permanent link
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files, sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.5.0 dated 2016-03-06 and 3.5.1 dated 2016-03-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 5 +++++ R/Matlab.R | 6 ------ man/Matlab.Rd | 6 ------ 5 files changed, 13 insertions(+), 20 deletions(-)
Title: Quantile-Based Spectral Analysis of Time Series
Description: Methods to determine, smooth and plot quantile periodograms for
univariate and multivariate time series.
Author: Tobias Kley [aut, cre],
Stefan Birr [ctb] (Contributions to lag window estimation)
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between quantspec versions 1.2-0 dated 2015-10-20 and 1.2-1 dated 2016-03-27
DESCRIPTION | 11 MD5 | 262 +++++------ NAMESPACE | 2 NEWS | 8 R/Class-ClippedFT.R | 6 R/Class-QuantilePG.R | 6 R/Class-QuantileSD.R | 4 R/Class-SmoothedPG.R | 9 R/RcppExports.R | 4 R/models.R | 2 R/quantspec-package.R | 18 build/vignette.rds |binary inst/CITATION | 34 - inst/doc/quantspec.R | 48 -- inst/doc/quantspec.Rnw | 799 ++++++++++++++++++++-------------- inst/doc/quantspec.pdf |binary inst/examples/QuantilePG.R | 2 man/BootPos-class.Rd | 2 man/ClippedCov-class.Rd | 16 man/ClippedCov-constructor.Rd | 8 man/ClippedFT-class.Rd | 8 man/ClippedFT-constructor.Rd | 8 man/FreqRep-class.Rd | 2 man/IntegrQuantileSD-class.Rd | 2 man/IntegrQuantileSD-constructor.Rd | 4 man/KernelWeight-class.Rd | 16 man/KernelWeight-constructor.Rd | 2 man/LagEstimator-class.Rd | 6 man/LagEstimator-constructor.Rd | 8 man/LagKernelWeight-class.Rd | 12 man/LagKernelWeight-constructor.Rd | 2 man/LagOperator-class.Rd | 4 man/MovingBlocks-class.Rd | 2 man/MovingBlocks-constructor.Rd | 2 man/QRegEstimator-class.Rd | 4 man/QRegEstimator-constructor.Rd | 2 man/QSpecQuantity-class.Rd | 2 man/QuantilePG-class.Rd | 10 man/QuantilePG-constructor.Rd | 4 man/QuantileSD-class.Rd | 8 man/QuantileSD-constructor.Rd | 4 man/SmoothedPG-class.Rd | 4 man/SmoothedPG-constructor.Rd | 2 man/SpecDistrWeight-class.Rd | 2 man/SpecDistrWeight-constructor.Rd | 2 man/Weight-class.Rd | 2 man/closest.pos.Rd | 2 man/data-sp500.Rd | 2 man/data-wheatprices.Rd | 2 man/frequenciesValidator.Rd | 4 man/generics-accessors.Rd | 4 man/generics-associations.Rd | 4 man/generics-functions.Rd | 4 man/getB-FreqRep.Rd | 2 man/getB-LagOperator.Rd | 2 man/getBootPos-FreqRep.Rd | 2 man/getBootPos-LagOperator.Rd | 2 man/getBw-KernelWeight.Rd | 2 man/getBw-LagKernelWeight.Rd | 2 man/getCoherency-QuantileSD.Rd | 2 man/getCoherency-SmoothedPG.Rd | 2 man/getCoherencySdNaive-SmoothedPG.Rd | 7 man/getDescr-Weight.Rd | 2 man/getFreqRep-QuantilePG.Rd | 2 man/getFrequencies-FreqRep.Rd | 4 man/getFrequencies-QSpecQuantity.Rd | 2 man/getIsRankBased-FreqRep.Rd | 2 man/getIsRankBased-LagOperator.Rd | 2 man/getLagOperator-LagEstimator.Rd | 2 man/getLevels-FreqRep.Rd | 4 man/getLevels-LagOperator.Rd | 2 man/getLevels-QSpecQuantity.Rd | 2 man/getMaxLag-LagOperator.Rd | 2 man/getMeanPG-QuantileSD.Rd | 2 man/getN-QuantileSD.Rd | 2 man/getParallel-QRegEstimator.Rd | 2 man/getPointwiseCIs-LagEstimator.Rd | 4 man/getPointwiseCIs-SmoothedPG.Rd | 6 man/getPositions-MovingBlocks.Rd | 2 man/getQuantilePG-QuantileSD.Rd | 4 man/getQuantilePG-SmoothedPG.Rd | 2 man/getQuantileSD-IntegrQuantileSD.Rd | 2 man/getR-QuantileSD.Rd | 2 man/getSdBoot-LagEstimator.Rd | 2 man/getSdBoot-SmoothedPG.Rd | 2 man/getSdNaive-LagEstimator.Rd | 8 man/getSdNaive-SmoothedPG.Rd | 2 man/getStdError-QuantileSD.Rd | 2 man/getTs-QuantileSD.Rd | 2 man/getType-QuantileSD.Rd | 2 man/getValues-FreqRep.Rd | 4 man/getValues-IntegrQuantileSD.Rd | 2 man/getValues-KernelWeight.Rd | 2 man/getValues-LagEstimator.Rd | 2 man/getValues-LagKernelWeight.Rd | 2 man/getValues-LagOperator.Rd | 2 man/getValues-QuantilePG.Rd | 2 man/getValues-QuantileSD.Rd | 2 man/getValues-SmoothedPG.Rd | 2 man/getValues-SpecDistrWeight.Rd | 6 man/getW-KernelWeight.Rd | 2 man/getW-LagKernelWeight.Rd | 2 man/getWeight-LagEstimator.Rd | 2 man/getWeight-SmoothedPG.Rd | 2 man/getWnj-KernelWeight.Rd | 4 man/getY-FreqRep.Rd | 4 man/increasePrecision-QuantileSD.Rd | 4 man/is.wholenumber.Rd | 4 man/kernels.Rd | 2 man/lenTS.Rd | 4 man/plot-FreqRep.Rd | 4 man/plot-IntegrQuantileSD.Rd | 2 man/plot-KernelWeight.Rd | 2 man/plot-LagEstimator.Rd | 8 man/plot-LagKernelWeight.Rd | 4 man/plot-LagOperator.Rd | 2 man/plot-QuantilePG.Rd | 2 man/plot-QuantileSD.Rd | 2 man/plot-SmoothedPG.Rd | 2 man/plot-SpecDistrWeight.Rd | 2 man/quantspec-defunct.Rd | 2 man/quantspec-package.Rd | 22 man/timeSeriesValidator.Rd | 2 man/ts-models-AR1.Rd | 6 man/ts-models-AR2.Rd | 2 man/ts-models-ARCH1.Rd | 3 man/ts-models-QAR1.Rd | 2 man/ts-models.Rd | 6 src/computeCoherency.cpp | 2 src/computeSdNaive.cpp | 2 vignettes/quantspec-refs.bib | 56 +- vignettes/quantspec.Rnw | 799 ++++++++++++++++++++-------------- 132 files changed, 1421 insertions(+), 1053 deletions(-)
Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including new heterogeneity tests and measures that are robust to outliers, and measures of publication bias.
Author: Lifeng Lin and Haitao Chu
Maintainer: Lifeng Lin <linl@umn.edu>
Diff between altmeta versions 1.0 dated 2016-02-29 and 2.0 dated 2016-03-27
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++++-- NAMESPACE | 4 ++-- R/metapb.R |only data/ha.rda |only data/lcj.rda |only data/slf.rda |only man/ha.Rd |only man/lcj.Rd |only man/metapb.Rd |only man/slf.Rd |only 11 files changed, 17 insertions(+), 9 deletions(-)
Title: Finding Files in Project Subdirectories
Description: Robust, reliable and flexible paths to files below a
project root. The 'root' of a project is defined as a directory
that matches a certain criterion, e.g., it contains a certain
regular file.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between rprojroot versions 1.0 dated 2016-03-26 and 1.0-1 dated 2016-03-27
rprojroot-1.0-1/rprojroot/DESCRIPTION | 6 +++--- rprojroot-1.0-1/rprojroot/MD5 | 20 ++------------------ rprojroot-1.0-1/rprojroot/NEWS.md | 2 +- rprojroot-1.0/rprojroot/inst/NEWS.Rd |only rprojroot-1.0/rprojroot/inst/staticdocs |only rprojroot-1.0/rprojroot/inst/web |only 6 files changed, 6 insertions(+), 22 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.1 dated 2016-03-10 and 1.1.1 dated 2016-03-27
DESCRIPTION | 10 +++---- MD5 | 25 +++++++++--------- NAMESPACE | 1 R/get_indiv.r | 65 +++++++++++++++++++++++++++++++++++++++++------- R/insilico_core.r | 2 - R/insilico_standard.r | 4 +- R/insilico_train.r | 2 - R/report.r | 15 +++++++++-- man/get.indiv.Rd | 19 +++++++------- man/insilico.Rd | 4 +- man/insilico.fit.Rd | 2 - man/insilico.train.Rd | 4 +- man/summary.insilico.Rd | 3 ++ man/updateIndiv.Rd |only 14 files changed, 110 insertions(+), 46 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.7 include: (1) Higher subpopulation detection specificity, in particular for small subpopulations. (2) Higher accuracy for mutation assignment to subpopulations. (3) Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations. (4) Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation. (5) New subpopulation plotting options (function plotSPs). (6) New phylogeny plotting option: user can choose between consensus and germline population to be included as control. (7) 50 simulated samples of various genetic complexities and measurement precision included for user testing. Special thanks to Dr. Ryan Morin for his contributions that have led to higher accuracy measures during simulations for mutation assignment to subpopulations, as well as advanced visualization features of assigned mutations. Further documentation and FAQ available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.7 dated 2016-03-26 and 1.7.1 dated 2016-03-27
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/runExPANdS.R | 1 + inst/doc/expands.pdf |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Constructs nested and crossed block designs
for unstructured treatment sets with arbitrary replication not necessarily all equal.
Blocks can be nested to any required depth of nesting and blocks are optimized
hierarchically from the top down with successive nested blocks strata optimized within
the levels of all preceding blocks strata. Block sizes are all equal in any one stratum if the number
of blocks in that stratum exactly divides the number of plots, otherwise they differ by at most one plot.
The design output is a data table showing a randomised allocation of treatments to blocks together with
plans showing the allocation of treatments to blocks for each block in the bottom stratum of the design.
D and A-efficiency factors are shown for each stratum together with A-efficiency upper bounds,
where available.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 2.0 dated 2016-02-07 and 2.1 dated 2016-03-27
DESCRIPTION | 8 MD5 | 6 R/blocks.r | 602 ++++++++++++++++++++++++++++++---------------------------- man/blocks.Rd | 54 ++--- 4 files changed, 349 insertions(+), 321 deletions(-)
Title: Replicate Tariff Method for Verbal Autopsy
Description: Implement the Tariff algorithm for coding cause-of-death from verbal autopsies. The Tariff method was originally proposed in James et al (2011) <DOI:10.1186/1478-7954-9-31> and later refined as Tariff 2.0 in Serina, et al. (2015) <DOI:10.1186/s12916-015-0527-9>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist between the this implementation and the implementation available from IHME.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between Tariff versions 1.0.1 dated 2016-03-08 and 1.0.2 dated 2016-03-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/Tariff.r | 18 +++++++++++------- R/zzz.R | 7 ++++++- data/RandomVA3.rda |binary man/tariff.Rd | 7 ++++--- 6 files changed, 31 insertions(+), 21 deletions(-)
Title: Tools for Simulating and Plotting Quantities of Interest
Estimated from Cox Proportional Hazards Models
Description: Simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between simPH versions 1.3.5 dated 2015-12-15 and 1.3.7 dated 2016-03-27
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 ++ NEWS | 16 ++++++++++++++-- R/IntervalConstrict.R | 4 ++-- R/MinMaxLines.R | 36 ++++++++++++++++++------------------ R/coxsimInteract.R | 16 ++++++++-------- R/coxsimLinear.R | 22 ++++++++++++---------- R/coxsimPoly.R | 14 +++++++++----- R/coxsimSpline.R | 10 +++++----- R/coxsimtvc.R | 14 ++++++++------ R/simGG.siminteract.R | 12 ++++++------ R/simGG.simlinear.R | 12 ++++++------ R/simGG.simpoly.R | 12 ++++++------ R/simGG.simtvc.R | 12 ++++++------ README.md | 10 +++++----- build/vignette.rds |binary man/coxsimPoly.Rd | 2 +- 18 files changed, 130 insertions(+), 108 deletions(-)
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' also includes
a colour picker widget, a colour picker RStudio addin, and can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.5.0 dated 2016-03-19 and 0.5.2 dated 2016-03-27
shinyjs-0.5.0/shinyjs/inst/gadgets/colourpicker/helpers.R |only shinyjs-0.5.0/shinyjs/inst/gadgets/colourpicker/server.R |only shinyjs-0.5.0/shinyjs/inst/gadgets/colourpicker/ui.R |only shinyjs-0.5.0/shinyjs/inst/gadgets/colourpicker/www |only shinyjs-0.5.2/shinyjs/DESCRIPTION | 6 shinyjs-0.5.2/shinyjs/MD5 | 51 - shinyjs-0.5.2/shinyjs/NAMESPACE | 2 shinyjs-0.5.2/shinyjs/NEWS.md | 12 shinyjs-0.5.2/shinyjs/R/colourInput.R | 35 - shinyjs-0.5.2/shinyjs/R/colourPickerGadget.R | 271 +++++++++- shinyjs-0.5.2/shinyjs/R/colourPickerGadgetUtils.R |only shinyjs-0.5.2/shinyjs/README.md | 89 +-- shinyjs-0.5.2/shinyjs/inst/doc/overview.Rmd | 50 + shinyjs-0.5.2/shinyjs/inst/doc/overview.html | 48 - shinyjs-0.5.2/shinyjs/inst/examples/colourInput/app.R | 27 shinyjs-0.5.2/shinyjs/inst/examples/colourInput/www/app.css | 1 shinyjs-0.5.2/shinyjs/inst/gadgets/colourpicker/css |only shinyjs-0.5.2/shinyjs/inst/gadgets/colourpicker/img |only shinyjs-0.5.2/shinyjs/inst/gadgets/colourpicker/js |only shinyjs-0.5.2/shinyjs/inst/img/colourpickerscrnshot.png |only shinyjs-0.5.2/shinyjs/inst/rstudio/addins.dcf | 2 shinyjs-0.5.2/shinyjs/inst/srcjs/input_binding_colour.js | 6 shinyjs-0.5.2/shinyjs/inst/srcjs/shinyjs-default-funcs.js | 2 shinyjs-0.5.2/shinyjs/inst/www/shared/colourpicker/css/colourpicker.css | 7 shinyjs-0.5.2/shinyjs/inst/www/shared/colourpicker/css/colourpicker.min.css | 2 shinyjs-0.5.2/shinyjs/inst/www/shared/colourpicker/js/colourpicker.js | 37 + shinyjs-0.5.2/shinyjs/inst/www/shared/colourpicker/js/colourpicker.min.js | 2 shinyjs-0.5.2/shinyjs/man/colourInput.Rd | 18 shinyjs-0.5.2/shinyjs/man/colourPicker.Rd | 8 shinyjs-0.5.2/shinyjs/man/updateColourInput.Rd | 9 shinyjs-0.5.2/shinyjs/vignettes/overview.Rmd | 50 + 31 files changed, 549 insertions(+), 186 deletions(-)
Title: Robust Periodogram and Periodicity Detection Methods
Description: Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer() calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit(). Artificial light curves can be generated using the function tsgen(). For more details see the corresponding article: Thieler, Fried and Rathjens (2016), Journal of Statistical Software 69(9), 1-36, <doi:10.18637/jss.v069.i09>.
Author: Anita M. Thieler [aut],
Jonathan Rathjens [aut, cre],
Roland Fried [aut],
Brenton R. Clarke [ctb] (function betaCvMfit()),
Uwe Ligges [ctb] (function TK95()),
Matias Salibian-Barrera [ctb] (functions FastS() and FastTau()),
Gert Willems [ctb] (function FastTau()),
Victor Yohai [ctb] (function FastS())
Maintainer: Jonathan Rathjens <jonathan.rathjens@tu-dortmund.de>
Diff between RobPer versions 1.2.1 dated 2015-03-02 and 1.2.2 dated 2016-03-27
RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.R |only RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.Rnw |only RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.pdf |only RobPer-1.2.1/RobPer/vignettes/RobPer_Art.bib |only RobPer-1.2.1/RobPer/vignettes/RobPer_Vignette.Rnw |only RobPer-1.2.1/RobPer/vignettes/diagbox.sty |only RobPer-1.2.1/RobPer/vignettes/subfigure.sty |only RobPer-1.2.2/RobPer/DESCRIPTION | 24 ++- RobPer-1.2.2/RobPer/MD5 | 49 +++---- RobPer-1.2.2/RobPer/NAMESPACE | 7 - RobPer-1.2.2/RobPer/build/vignette.rds |binary RobPer-1.2.2/RobPer/inst/CITATION |only RobPer-1.2.2/RobPer/inst/doc/RobPer_vignette.R |only RobPer-1.2.2/RobPer/inst/doc/RobPer_vignette.Rnw |only RobPer-1.2.2/RobPer/inst/doc/RobPer_vignette.pdf |only RobPer-1.2.2/RobPer/man/FastS.Rd | 144 +++++++++++----------- RobPer-1.2.2/RobPer/man/FastTau.Rd | 8 - RobPer-1.2.2/RobPer/man/Mrk421.Rd | 144 +++++++++++----------- RobPer-1.2.2/RobPer/man/Mrk501.Rd | 144 +++++++++++----------- RobPer-1.2.2/RobPer/man/RobPer-package.rd | 44 +++--- RobPer-1.2.2/RobPer/man/RobPer.Rd | 56 ++++---- RobPer-1.2.2/RobPer/man/TK95.Rd | 10 - RobPer-1.2.2/RobPer/man/TK95_uneq.Rd | 10 - RobPer-1.2.2/RobPer/man/Xgen.Rd | 4 RobPer-1.2.2/RobPer/man/betaCvMfit.Rd | 18 +- RobPer-1.2.2/RobPer/man/disturber.Rd | 4 RobPer-1.2.2/RobPer/man/lc_noise.Rd | 4 RobPer-1.2.2/RobPer/man/sampler.Rd | 4 RobPer-1.2.2/RobPer/man/signalgen.Rd | 4 RobPer-1.2.2/RobPer/man/tsgen.Rd | 4 RobPer-1.2.2/RobPer/vignettes/RobPer_vignette.Rnw |only RobPer-1.2.2/RobPer/vignettes/v69i09.bib |only 32 files changed, 344 insertions(+), 338 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.1-3 dated 2015-12-21 and 1.1-7 dated 2016-03-27
ChangeLog | 59 ++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 +++--- MD5 | 44 ++++++++++++++--------------- NAMESPACE | 2 - R/ogr.R | 17 ++--------- R/ogr_sp.R | 46 +++++++++++++++++-------------- R/ogr_write.R | 10 ++++++ build/vignette.rds |binary configure | 18 ++++++------ inst/ChangeLog | 59 ++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 - inst/doc/OGR_shape_encoding.pdf |binary inst/pictures/Rlogo.jpg |binary inst/pictures/logo.jpg |binary man/readOGR.Rd | 16 ++++++---- man/showWKT.Rd | 5 +++ man/writeOGR.Rd | 7 ++++ src/Makevars.in | 1 src/Makevars.win | 2 - src/init.c | 1 src/ogr_proj.cpp | 27 ++++++++++++++++++ src/ogrsource.cpp | 13 +++++--- src/rgdal.h | 1 23 files changed, 253 insertions(+), 87 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.8.0 dated 2016-03-25 and 2.8.1 dated 2016-03-27
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/AllClasses.R | 3 ++- R/RCLRMIX.R | 2 +- R/RCLSMIX.R | 2 +- R/REBMIX.R | 2 +- R/RNGMIX.R | 2 +- inst/NEWS.Rd | 6 ++++++ inst/doc/rebmix.R | 8 ++++---- inst/doc/rebmix.Rnw | 10 +++++----- inst/doc/rebmix.pdf |binary src/base.cpp | 2 +- src/rebmixf.cpp | 2 +- src/rebmvnormf.cpp | 6 +++--- src/rngmixf.cpp | 2 +- vignettes/rebmix.Rnw | 10 +++++----- vignettes/rebmix.bib | 4 ++-- 17 files changed, 53 insertions(+), 46 deletions(-)
Title: Partition-Assisted Clustering
Description: Implements Partition-Assisted Clustering, which utilizes a collection of partition based nonparametric density estimation techniques to improve the robustness and accuracy of downstream clustering.
The package also provides functions for effectively visualizing the clustering results.
It is particularly useful for finding and visualizing subpopulations in single-cell data analysis.
Author: Dangna Li, Henry Li
Maintainer: Dangna Li <ldangna@gmail.com>
Diff between PAC versions 1.0.0 dated 2016-03-25 and 1.0.1 dated 2016-03-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/PAC.R | 1 + configure.ac | 17 +++++++++++++++++ 4 files changed, 24 insertions(+), 6 deletions(-)
Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series
and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis [aut, cre],
Christophe Sax [ctb]
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>
Diff between ggseas versions 0.3.0 dated 2016-03-14 and 0.4.0 dated 2016-03-27
DESCRIPTION | 14 ++++++++---- MD5 | 21 ++++++++++-------- R/decompose-seasonal.R | 25 +++++++++++++++++---- R/ggsdc.R | 56 +++++++++++++++++++++++++++++++++---------------- R/stl-seasonal.R | 24 ++++++++++++++++----- R/x13-seasonal.R | 53 +++++++++++++++++++++++++++++++++++++--------- man/ggsdc.Rd | 17 +++++++------- man/stat_decomp.Rd | 14 ++++++------ man/stat_seas.Rd | 29 ++++++++++++++++--------- man/stat_stl.Rd | 12 +++++----- tests |only 11 files changed, 182 insertions(+), 83 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between DataCombine versions 0.2.19 dated 2016-03-07 and 0.2.20 dated 2016-03-27
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS | 9 +++++++++ R/DropNA.R | 10 +++++++++- R/slide.R | 7 +++---- R/utils.R | 15 ++++++++++----- man/DropNA.Rd | 6 +++++- man/dMerge.Rd | 7 ++++--- 9 files changed, 54 insertions(+), 27 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-08 1.0.10-2
2014-12-21 1.0.10
2014-08-20 1.0.9-3
2014-08-11 1.0.9
Title: Tools Developed for Structured Sufficient Dimension Reduction
(sSDR)
Description: Performs structured OLS (sOLS) and structured SIR (sSIR).
Author: Yang Liu <zjubioly@gmail.com>, Francesca Chiaromonte, Bing Li
Maintainer: Yang Liu <zjubioly@gmail.com>
Diff between sSDR versions 1.1.0 dated 2016-01-14 and 1.2.0 dated 2016-03-26
DESCRIPTION | 8 - MD5 | 14 +- R/sSDR.R | 341 +++++++++++++++-------------------------------------- man/gOLS.Rd | 21 --- man/gOLS.comp.d.Rd | 7 - man/gSIR.Rd | 21 --- man/gSIR.comp.d.Rd | 7 - man/sOLS.comp.d.Rd | 8 - 8 files changed, 124 insertions(+), 303 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.7-5 dated 2016-02-23 and 0.7-6 dated 2016-03-26
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/LRT.trend.R | 58 ++++++++++++++---------------------------------- R/rds.estimates.local.R | 5 ++-- 4 files changed, 28 insertions(+), 49 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,
Qiang Kou, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.3 dated 2016-01-10 and 0.12.4 dated 2016-03-26
ChangeLog | 219 +++++++ DESCRIPTION | 8 MD5 | 264 ++++---- R/Attributes.R | 7 README.md | 2 build/Rcpp.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 38 + inst/doc/Rcpp-FAQ.R | 34 - inst/doc/Rcpp-FAQ.Rnw | 225 ++++++- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.R | 2 inst/doc/Rcpp-sugar.Rnw | 10 inst/doc/Rcpp-sugar.pdf |binary inst/doc/Rcpp-unitTests.pdf |binary inst/doc/Rcpp.bib | 2 inst/examples/ConvolveBenchmarks/exampleRCode.r | 2 inst/examples/ConvolveBenchmarks/overhead.r | 16 inst/examples/FastLM/benchmark.r | 5 inst/examples/FastLM/benchmarkLongley.r | 2 inst/examples/FastLM/fastLMviaArmadillo.r | 2 inst/examples/FastLM/fastLMviaGSL.r | 2 inst/examples/FastLM/lmArmadillo.R | 10 inst/examples/FastLM/lmGSL.R | 10 inst/examples/Misc/fibonacci.r | 4 inst/examples/Misc/ifelseLooped.r | 2 inst/examples/Misc/newFib.r | 2 inst/examples/Misc/piBySimulation.r | 2 inst/examples/OpenMP/OpenMPandInline.r | 2 inst/examples/RcppInline/RObject.r | 2 inst/examples/RcppInline/RcppInlineExample.r | 2 inst/examples/RcppInline/RcppInlineWithLibsExamples.r | 70 +- inst/examples/RcppInline/RcppSimpleExample.r | 2 inst/examples/RcppInline/UncaughtExceptions.r | 2 inst/examples/RcppInline/external_pointer.r | 2 inst/examples/SugarPerformance/sugarBenchmarks.R | 2 inst/examples/functionCallback/newApiExample.r | 7 inst/include/Rcpp/Fast.h | 18 inst/include/Rcpp/Nullable.h | 21 inst/include/Rcpp/config.h | 6 inst/include/Rcpp/stats/beta.h | 4 inst/include/Rcpp/stats/binom.h | 4 inst/include/Rcpp/stats/cauchy.h | 30 inst/include/Rcpp/stats/chisq.h | 4 inst/include/Rcpp/stats/dpq/dpq.h | 527 ++++++++--------- inst/include/Rcpp/stats/exp.h | 73 +- inst/include/Rcpp/stats/f.h | 4 inst/include/Rcpp/stats/gamma.h | 25 inst/include/Rcpp/stats/geom.h | 4 inst/include/Rcpp/stats/hyper.h | 4 inst/include/Rcpp/stats/lnorm.h | 47 - inst/include/Rcpp/stats/logis.h | 73 +- inst/include/Rcpp/stats/nbeta.h | 4 inst/include/Rcpp/stats/nbinom.h | 4 inst/include/Rcpp/stats/nbinom_mu.h | 4 inst/include/Rcpp/stats/nchisq.h | 4 inst/include/Rcpp/stats/nf.h | 4 inst/include/Rcpp/stats/norm.h | 73 +- inst/include/Rcpp/stats/nt.h | 4 inst/include/Rcpp/stats/pois.h | 4 inst/include/Rcpp/stats/random/random.h | 558 +++++++++--------- inst/include/Rcpp/stats/random/rbeta.h | 25 inst/include/Rcpp/stats/random/rbinom.h | 23 inst/include/Rcpp/stats/random/rcauchy.h | 43 - inst/include/Rcpp/stats/random/rchisq.h | 27 inst/include/Rcpp/stats/random/rexp.h | 39 - inst/include/Rcpp/stats/random/rf.h | 76 +- inst/include/Rcpp/stats/random/rgamma.h | 25 inst/include/Rcpp/stats/random/rgeom.h | 27 inst/include/Rcpp/stats/random/rhyper.h | 24 inst/include/Rcpp/stats/random/rlnorm.h | 66 +- inst/include/Rcpp/stats/random/rlogis.h | 72 +- inst/include/Rcpp/stats/random/rnbinom.h | 32 - inst/include/Rcpp/stats/random/rnbinom_mu.h | 31 - inst/include/Rcpp/stats/random/rnchisq.h | 49 - inst/include/Rcpp/stats/random/rnorm.h | 89 +- inst/include/Rcpp/stats/random/rpois.h | 23 inst/include/Rcpp/stats/random/rsignrank.h | 22 inst/include/Rcpp/stats/random/rt.h | 39 - inst/include/Rcpp/stats/random/runif.h | 62 -- inst/include/Rcpp/stats/random/rweibull.h | 50 - inst/include/Rcpp/stats/random/rwilcox.h | 22 inst/include/Rcpp/stats/stats.h | 10 inst/include/Rcpp/stats/t.h | 4 inst/include/Rcpp/stats/unif.h | 40 - inst/include/Rcpp/stats/weibull.h | 41 - inst/include/Rcpp/sugar/functions/cbind.h |only inst/include/Rcpp/sugar/functions/functions.h | 4 inst/include/Rcpp/sugar/functions/median.h |only inst/include/Rcpp/vector/Subsetter.h | 18 inst/unitTests/cpp/Vector.cpp | 5 inst/unitTests/cpp/misc.cpp | 26 inst/unitTests/cpp/sugar.cpp | 309 +++++++++ inst/unitTests/runit.DataFrame.R | 2 inst/unitTests/runit.Date.R | 2 inst/unitTests/runit.Function.R | 2 inst/unitTests/runit.InternalFunction.R | 2 inst/unitTests/runit.InternalFunctionCPP11.R | 2 inst/unitTests/runit.Language.R | 2 inst/unitTests/runit.Matrix.R | 2 inst/unitTests/runit.Module.R | 2 inst/unitTests/runit.Module.client.package.R | 2 inst/unitTests/runit.RObject.R | 2 inst/unitTests/runit.Reference.R | 2 inst/unitTests/runit.S4.R | 2 inst/unitTests/runit.String.R | 2 inst/unitTests/runit.Vector.R | 11 inst/unitTests/runit.XPTr.R | 2 inst/unitTests/runit.as.R | 2 inst/unitTests/runit.attributes.R | 2 inst/unitTests/runit.binary.package.R | 2 inst/unitTests/runit.client.package.R | 2 inst/unitTests/runit.environments.R | 2 inst/unitTests/runit.misc.R | 21 inst/unitTests/runit.modref.R | 2 inst/unitTests/runit.na.R | 2 inst/unitTests/runit.rmath.R | 2 inst/unitTests/runit.stats.R | 2 inst/unitTests/runit.subset.R | 2 inst/unitTests/runit.sugar.R | 339 ++++++++++ inst/unitTests/runit.sugar.var.R | 2 inst/unitTests/runit.support.R | 2 inst/unitTests/runit.table.R | 2 inst/unitTests/runit.wrap.R | 2 inst/unitTests/runit.wstring.R | 2 vignettes/Rcpp-FAQ.Rnw | 225 ++++++- vignettes/Rcpp-sugar.Rnw | 10 vignettes/Rcpp.bib | 2 134 files changed, 2852 insertions(+), 1601 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate an play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.2.3 dated 2015-11-07 and 0.3.3 dated 2016-03-26
DESCRIPTION | 11 MD5 | 146 +++++----- NAMESPACE | 7 NEWS | 50 +++ R/02PTCell.r | 9 R/03PTTrack.r | 2 R/09playing_routines.r | 631 ++++++++++++++++++++++++++++++++++------------ R/10ModArchiveHelpers.r |only R/ProTrackR.r | 113 ++++---- man/PTBlock.Rd | 5 man/PTCell-class.Rd | 36 -- man/PTCell-method.Rd | 18 - man/PTModule-class.Rd | 43 --- man/PTPattern-class.Rd | 27 - man/PTPattern-method.Rd | 23 - man/PTSample-class.Rd | 51 --- man/PTSample-method.Rd | 48 --- man/PTTrack-class.Rd | 4 man/PTTrack-method.Rd | 8 man/ProTrackR.Rd | 113 ++++---- man/appendPattern.Rd | 67 ---- man/as.character.Rd | 27 - man/as.raw.Rd | 17 - man/clearSamples.Rd | 44 --- man/clearSong.Rd | 44 --- man/deletePattern.Rd | 68 ---- man/effect.Rd | 23 - man/fineTune.Rd | 49 --- man/funk_table.Rd | 2 man/loopLength.Rd | 59 ---- man/loopSample.Rd | 63 ---- man/loopStart.Rd | 59 ---- man/loopState.Rd | 60 ---- man/mod.intro.Rd | 2 man/modArchive.Rd |only man/modToWave.Rd | 44 --- man/moduleSize.Rd | 45 --- man/name.Rd | 61 ---- man/note.Rd | 69 ----- man/noteManipulation.Rd | 28 +- man/noteToPeriod.Rd | 50 --- man/nybble.Rd | 38 +- man/nybbleToSignedInt.Rd | 40 +- man/octave.Rd | 43 --- man/pasteBlock.Rd | 27 - man/patternLength.Rd | 66 ---- man/patternOrder.Rd | 67 +--- man/patternOrderLength.Rd | 69 +---- man/paula_clock.Rd | 2 man/periodToChar.Rd | 63 ---- man/period_table.Rd | 18 - man/playMod.Rd | 48 --- man/playSample.Rd | 63 ---- man/playWave.Rd | 9 man/playingtable.Rd | 43 --- man/plot.Rd | 2 man/print.Rd | 2 man/proTrackerVibrato.Rd | 2 man/rawToCharNull.Rd | 35 -- man/rawToSignedInt.Rd | 36 -- man/rawToUnsignedInt.Rd | 36 -- man/read.module.Rd | 51 --- man/read.sample.Rd | 61 ---- man/resample.Rd | 2 man/sampleLength.Rd | 51 --- man/sampleNumber.Rd | 22 - man/sampleRate.Rd | 62 +--- man/signedIntToNybble.Rd | 42 +-- man/signedIntToRaw.Rd | 36 -- man/trackerFlag.Rd | 42 --- man/unsignedIntToRaw.Rd | 36 -- man/volume.Rd | 49 --- man/waveform.Rd | 61 +--- man/write.module.Rd | 51 --- man/write.sample.Rd | 61 ---- 75 files changed, 1269 insertions(+), 2293 deletions(-)
Title: Weighted k-Nearest Neighbors
Description: Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
Author: Klaus Schliep [aut, cre],
Klaus Hechenbichler [aut],
Antoine Lizee [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between kknn versions 1.3.0 dated 2015-07-09 and 1.3.1 dated 2016-03-26
DESCRIPTION | 20 ++++++++----- MD5 | 14 ++++----- NAMESPACE | 2 - NEWS | 14 ++++++++- R/kknn.R | 81 +++++++++++++++++++++++++++++++++++++++--------------- R/specClust.R | 4 +- README.md | 1 man/train.kknn.Rd | 5 ++- 8 files changed, 99 insertions(+), 42 deletions(-)
Title: Graphical Analysis of Structural Causal Models
Description: A port of the web-based software 'DAGitty', available at
<http://dagitty.net>, for analyzing structural causal models
(also known as directed acyclic graphs or DAGs).
This package computes covariate adjustment sets for estimating causal
effects, enumerates instrumental variables, derives testable
implications (d-separation and vanishing tetrads), generates equivalent
models, and includes a simple facility for data simulation.
Author: Johannes Textor, Benito van der Zander
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between dagitty versions 0.1-9 dated 2016-03-22 and 0.1-10 dated 2016-03-26
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- R/dagitty.r | 8 ++++---- inst/doc/dagitty4semusers.html | 6 +++--- man/dagitty.Rd | 2 +- man/names.dagitty.Rd | 6 +++--- 6 files changed, 24 insertions(+), 23 deletions(-)
Title: Beta-Diversity of Species Interactions
Description: Measures of beta-diversity in networks, and easy visualization of why two networks are different.
Author: Timothee Poisot <tim@poisotlab.io>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between betalink versions 2.2.0 dated 2015-12-22 and 2.2.1 dated 2016-03-26
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 5 +++++ R/betalink.r | 8 ++++---- R/metaweb.r | 6 ++++++ 5 files changed, 24 insertions(+), 13 deletions(-)
Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences.
Provides interfaces to the C++ implementation of cSPADE by
Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from
Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>
Diff between arulesSequences versions 0.2-13 dated 2016-01-26 and 0.2-14 dated 2016-03-26
CHANGELOG | 6 DESCRIPTION | 8 - MD5 | 44 +++---- NAMESPACE | 6 R/02sequences.R | 9 + R/03rules.R | 2 R/05read_write.R | 12 - R/10timed.R | 21 +-- R/20support.R | 11 - R/30similarity.R | 93 ++++++++++---- data/zaki.rda |binary man/cspade.Rd | 2 man/match-methods.Rd | 1 man/read_baskets.Rd | 2 man/timedsequences-class.Rd | 5 src/ptree.c | 274 ++++++++++++++++++++++++++++++++++++++++++-- tests/arules.Rout.save | 2 tests/idlists.Rout.save | 2 tests/makebin.Rout.save | 2 tests/native.Rout.save | 2 tests/ptree.Rout.save | 2 tests/similarity.Rout.save | 2 tests/zaki.Rout.save | 2 23 files changed, 413 insertions(+), 97 deletions(-)
More information about arulesSequences at CRAN
Permanent link
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.4 dated 2015-10-14 and 2.4-1 dated 2016-03-26
treemap-2.4-1/treemap/DESCRIPTION | 10 ++-- treemap-2.4-1/treemap/MD5 | 38 +++++++++--------- treemap-2.4-1/treemap/NAMESPACE | 12 ++++- treemap-2.4-1/treemap/NEWS | 4 + treemap-2.4-1/treemap/R/datasets.R | 15 ++++--- treemap-2.4-1/treemap/R/pkg.R | 9 ---- treemap-2.4-1/treemap/R/treecolors.R | 2 treemap-2.4-1/treemap/R/treemap.R | 23 +++++----- treemap-2.4-1/treemap/build/vignette.rds |binary treemap-2.4-1/treemap/data/GNI2014.rda |only treemap-2.4-1/treemap/man/GNI2014.Rd |only treemap-2.4-1/treemap/man/business.Rd | 4 - treemap-2.4-1/treemap/man/itreemap.Rd | 2 treemap-2.4-1/treemap/man/random.hierarchical.data.Rd | 2 treemap-2.4-1/treemap/man/tmPlot.Rd | 2 treemap-2.4-1/treemap/man/treecolors.Rd | 2 treemap-2.4-1/treemap/man/treegraph.Rd | 8 +-- treemap-2.4-1/treemap/man/treemap-package.Rd | 13 ------ treemap-2.4-1/treemap/man/treemap.Rd | 18 ++++---- treemap-2.4-1/treemap/man/treepalette.Rd | 4 - treemap-2.4/treemap/data/GNI2010.rda |only treemap-2.4/treemap/man/GNI2010.Rd |only 22 files changed, 83 insertions(+), 85 deletions(-)
More information about TotalCopheneticIndex at CRAN
Permanent link
Title: Collect Data Programmatically by POST Methods to Google Forms
Description: GET and POST data to Google Forms; more secure than having to
expose Google Sheets in order to POST data.
Author: Steve Simpson [aut, cre]
Maintainer: Steve Simpson <steven.troy.simpson@gmail.com>
Diff between googleformr versions 0.0.1 dated 2016-01-06 and 0.0.2 dated 2016-03-26
googleformr-0.0.1/googleformr/R/why_R_u_thankful.R |only googleformr-0.0.1/googleformr/man/why_R_u_thankful.Rd |only googleformr-0.0.2/googleformr/DESCRIPTION | 6 ++-- googleformr-0.0.2/googleformr/MD5 | 14 +++++----- googleformr-0.0.2/googleformr/NAMESPACE | 2 - googleformr-0.0.2/googleformr/R/gformr.R | 4 +- googleformr-0.0.2/googleformr/R/why_R_u_opensource.R |only googleformr-0.0.2/googleformr/README.md | 22 ++++++++-------- googleformr-0.0.2/googleformr/man/gformr.Rd | 2 - googleformr-0.0.2/googleformr/man/why_R_u_opensource.Rd |only 10 files changed, 25 insertions(+), 25 deletions(-)
Title: Tableplot, a Visualization of Large Datasets
Description: A tableplot is a visualisation of a (large)
dataset with a dozen of variables, both numeric and
categorical. Each column represents a variable and each
row bin is an aggregate of a certain number of records.
Numeric variables are visualized as bar charts, and
categorical variables as stacked bar charts. Missing
values are taken into account. Also supports large ffdf
datasets from the ff package.
Author: Martijn Tennekes and Edwin de Jonge
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tabplot versions 1.1 dated 2014-02-24 and 1.3 dated 2016-03-26
tabplot-1.1/tabplot/vignettes/figure |only tabplot-1.3/tabplot/DESCRIPTION | 13 - tabplot-1.3/tabplot/MD5 | 114 ++++------ tabplot-1.3/tabplot/NAMESPACE | 29 ++ tabplot-1.3/tabplot/NEWS | 12 + tabplot-1.3/tabplot/R/bin_data.R | 11 tabplot-1.3/tabplot/R/columnTable.R | 11 tabplot-1.3/tabplot/R/coorNumCol.R | 52 +++- tabplot-1.3/tabplot/R/itableplot.R | 2 tabplot-1.3/tabplot/R/num2fac.R | 37 +-- tabplot-1.3/tabplot/R/pkg.R | 16 - tabplot-1.3/tabplot/R/plotCatCol.R | 11 tabplot-1.3/tabplot/R/plotNumCol.R | 148 +++++++++---- tabplot-1.3/tabplot/R/plot_tabplot.r | 61 +++-- tabplot-1.3/tabplot/R/save_loadPrepare.R |only tabplot-1.3/tabplot/R/scaleNumCol.R | 9 tabplot-1.3/tabplot/R/sysdata.rda |binary tabplot-1.3/tabplot/R/tablePalettes.R | 6 tabplot-1.3/tabplot/R/tablePrepare.R | 16 - tabplot-1.3/tabplot/R/tableSave.R | 113 +++++----- tabplot-1.3/tabplot/R/tableplot.R | 98 ++++++-- tabplot-1.3/tabplot/R/tableplot_checkCols.R | 10 tabplot-1.3/tabplot/R/tableplot_checkNumPals.R | 9 tabplot-1.3/tabplot/R/tableplot_checkPals.R | 2 tabplot-1.3/tabplot/R/tableplot_checkRevLeg.R |only tabplot-1.3/tabplot/R/tableplot_processCols.R |only tabplot-1.3/tabplot/R/tableplots_diff.R | 29 +- tabplot-1.3/tabplot/R/tabplot_object.R | 2 tabplot-1.3/tabplot/build/vignette.rds |binary tabplot-1.3/tabplot/inst/doc/tabplot-timings.R | 9 tabplot-1.3/tabplot/inst/doc/tabplot-timings.html | 139 ++++++------ tabplot-1.3/tabplot/inst/doc/tabplot-vignette.R | 20 - tabplot-1.3/tabplot/inst/doc/tabplot-vignette.Rmd | 10 tabplot-1.3/tabplot/inst/doc/tabplot-vignette.html | 198 +++++++++-------- tabplot-1.3/tabplot/inst/shinyapp/ui.R | 2 tabplot-1.3/tabplot/man/bin_data.Rd | 21 - tabplot-1.3/tabplot/man/bin_hcc_data.Rd | 9 tabplot-1.3/tabplot/man/datetime2fac.Rd | 19 - tabplot-1.3/tabplot/man/itableplot.Rd | 14 - tabplot-1.3/tabplot/man/loadPrepare.Rd |only tabplot-1.3/tabplot/man/num2fac.Rd | 42 +-- tabplot-1.3/tabplot/man/plot.tabplot.Rd | 58 ++--- tabplot-1.3/tabplot/man/print.tabplot.Rd | 6 tabplot-1.3/tabplot/man/savePrepare.Rd |only tabplot-1.3/tabplot/man/summary.tabplot.Rd | 9 tabplot-1.3/tabplot/man/tableChange.Rd | 44 +-- tabplot-1.3/tabplot/man/tablePalettes.Rd | 59 +---- tabplot-1.3/tabplot/man/tablePrepare.Rd | 38 +-- tabplot-1.3/tabplot/man/tableSave.Rd | 46 +--- tabplot-1.3/tabplot/man/tableplot.Rd | 237 ++++++--------------- tabplot-1.3/tabplot/man/tableplot_comparison.Rd | 17 - tabplot-1.3/tabplot/man/tabplot-object.Rd | 15 - tabplot-1.3/tabplot/man/tabplot-package.Rd | 44 +-- tabplot-1.3/tabplot/man/tabplot_compare-object.Rd | 8 tabplot-1.3/tabplot/vignettes/tabplot-vignette.Rmd | 10 55 files changed, 982 insertions(+), 903 deletions(-)
Title: Determine Optimal Clustering Algorithm and Number of Clusters
Description: Cluster analysis using statistical and biological
validation measures for both continuous and count data.
Author: Michael Sekula <michael.sekula@louisville.edu>,
Somnath Datta <somnath.datta@louisville.edu>,
and Susmita Datta <susmita.datta@louisville.edu>
Maintainer: Michael Sekula <michael.sekula@louisville.edu>
Diff between optCluster versions 1.0.1 dated 2015-10-19 and 1.1.0 dated 2016-03-26
DESCRIPTION | 8 +- MD5 | 12 +-- R/optCluster-Functions.R | 23 +++++-- man/arabid.Rd | 38 ++++++------ man/optCluster.Rd | 147 ++++++++++++++++++++++++++++++----------------- man/optHeatmap.Rd | 8 +- man/repRankAggreg.Rd | 39 +++++++++++- 7 files changed, 178 insertions(+), 97 deletions(-)
Title: Network Assisted Algorithm for Epigenetic Studies Using Mean and
Variance Combined Signals
Description: Package for a Network assisted algorithm for Epigenetic studies using mean and variance Combined signals: NEpiC. NEpiC combines both signals in mean and variance differences in methylation level between case and control groups searching for differentially methylated sub-networks (modules) using the protein-protein interaction network.
Author: Peifeng Ruan
Maintainer: Peifeng Ruan <pruan12@fudan.edu.cn>
Diff between NEpiC versions 1.0 dated 2015-11-26 and 1.0.1 dated 2016-03-26
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 5 +++-- R/permutation.r |only man/permutation.Rd |only 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Data Exploration with Information Theory (Weight-of-Evidence and
Information Value)
Description: Performs exploratory data analysis and variable screening for
binary classification models using weight-of-evidence (WOE) and information
value (IV). In order to make the package as efficient as possible, aggregations
are done in data.table and creation of WOE vectors can be distributed across
multiple cores. The package also supports exploration for uplift models (NWOE
and NIV).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between Information versions 0.0.7 dated 2015-11-19 and 0.0.8 dated 2016-03-26
DESCRIPTION | 16 ++- MD5 | 45 ++++----- NAMESPACE | 2 NEWS.md |only R/Aggregate.R | 10 +- R/NWOE.R | 2 R/Penalty.R | 6 - R/WOE.R | 2 R/create_infotables.R | 4 build/vignette.rds |binary inst/doc/Information-vignette.html | 182 ++++++++++++++++++++----------------- man/Aggregate.Rd | 2 man/CheckInputs.Rd | 4 man/Information.Rd | 14 +- man/MultiPlot.Rd | 2 man/NWOE.Rd | 2 man/SinglePlot.Rd | 2 man/WOE.Rd | 2 man/create_infotables.Rd | 3 man/is.binary.Rd | 2 man/penalty.Rd | 2 man/plot_infotables.Rd | 5 - man/train.Rd | 2 man/valid.Rd | 2 24 files changed, 175 insertions(+), 138 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre],
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between HiveR versions 0.2.46 dated 2016-01-25 and 0.2.55 dated 2016-03-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/plotHive.R | 12 ++++++------ build/vignette.rds |binary inst/doc/HiveR.pdf |binary 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models.
HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses
(in two dimensions) and ellipsoids (in three dimensions). The related "candisc" package provides visualizations
in a reduced-rank canonical discriminant space when there are more than a few response variables.
Author: John Fox [aut], Michael Friendly [aut, cre], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.0-16 dated 2015-07-12 and 1.1-0 dated 2016-03-26
DESCRIPTION | 18 MD5 | 156 ++- NAMESPACE | 56 - NEWS | 15 R/boxM.R |only R/colDevs.R |only R/covEllipses.R |only R/logdetCI.R |only R/pairs.mlm.R | 57 - R/plot.boxM.R |only build/vignette.rds |binary data/AddHealth.RData |only data/Adopted.RData |binary data/Bees.rda |binary data/FootHead.rda |binary data/Headache.RData |binary data/Hernior.RData |binary data/MockJury.RData |binary data/NLSY.RData |binary data/Oslo.RData |binary data/Plastic.rda |binary data/Pottery2.RData |binary data/Probe1.RData |binary data/Probe2.RData |binary data/RatWeight.RData |binary data/ReactTime.RData |binary data/Rohwer.rda |binary data/RootStock.rda |binary data/Sake.RData |binary data/Skulls.RData |binary data/SocGrades.RData |binary data/VocabGrowth.rda |binary data/WeightLoss.RData |binary data/schooldata.RData |binary inst/doc/HE-examples.R | 1096 +++++++++++++-------------- inst/doc/repeated.R | 1266 ++++++++++++++++---------------- man/AddHealth.Rd |only man/boxM.Rd |only man/colDevs.Rd |only man/covEllipses.Rd |only man/heplot-package.Rd | 9 man/logdetCI.Rd |only man/pairs.mlm.Rd | 6 man/plot.boxM.Rd |only vignettes/fig/plot-Ortho-fm1.pdf |binary vignettes/fig/plot-Ortho-fm3.pdf |binary vignettes/fig/plot-grades-can-class.pdf |binary vignettes/fig/plot-grades-can-gpa.pdf |binary vignettes/fig/plot-grades-can-sex.pdf |binary vignettes/fig/plot-grades-pairs.pdf |binary vignettes/fig/plot-hern-can-age.pdf |binary vignettes/fig/plot-hern-can-build.pdf |binary vignettes/fig/plot-hern-can-cardiac.pdf |binary vignettes/fig/plot-hern-can-pstat.pdf |binary vignettes/fig/plot-hern-pairs.pdf |binary vignettes/fig/plot-jury-can1.pdf |binary vignettes/fig/plot-jury-mod1-HE.pdf |binary vignettes/fig/plot-jury-mod1-pairs.pdf |binary vignettes/fig/plot-jury-mod2-HE.pdf |binary vignettes/fig/plot-jury-mod3-eff.pdf |binary vignettes/fig/plot-obk-HE1.pdf |binary vignettes/fig/plot-obk-HE2.pdf |binary vignettes/fig/plot-obk-HE3.pdf |binary vignettes/fig/plot-obk2-HE1.pdf |binary vignettes/fig/plot-obk2-HE2.pdf |binary vignettes/fig/plot-ortho-HE.pdf |binary vignettes/fig/plot-ortho-nonlin-HE.pdf |binary vignettes/fig/plot-ortho-xyplot1.pdf |binary vignettes/fig/plot-ortho-xyplot2.pdf |binary vignettes/fig/plot-plastic2.pdf |binary vignettes/fig/plot-rohwer-HE1.pdf |binary vignettes/fig/plot-rohwer-HE2.pdf |binary vignettes/fig/plot-rohwer-HE3.pdf |binary vignettes/fig/plot-rohwer-HE4.pdf |binary vignettes/fig/plot-skulls-HE-pairs.pdf |binary vignettes/fig/plot-skulls-bwplot.pdf |binary vignettes/fig/plot-skulls-can2.pdf |binary vignettes/fig/plot-skulls4.pdf |binary vignettes/fig/plot-voc1.pdf |binary vignettes/fig/plot-voc4.pdf |binary vignettes/fig/plot-voc8.pdf |binary vignettes/fig/plot-wl-HE1.pdf |binary vignettes/fig/plot-wl-HE2.pdf |binary vignettes/fig/plot-wl-HE3.pdf |binary vignettes/fig/plot-wl-means.pdf |binary 85 files changed, 1370 insertions(+), 1309 deletions(-)
Title: Expanding Ploidy and Allele-Frequency on Nested Subpopulations
Description: Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (http://www.ncbi.nlm.nih.gov/pubmed/24177718). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 1.7 include: (1) Higher subpopulation detection specificity, in particular for small subpopulations. (2) Higher accuracy for mutation assignment to subpopulations. (3) Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations. (4) Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation. (5) New subpopulation plotting options (function plotSPs). (6) New phylogeny plotting option: user can choose between consensus and germline population to be included as control. (7) 50 simulated samples of various genetic complexities and noise levels included for user testing. Special thanks to Dr. Ryan Morin for his contributions that have led to higher accuracy measures during simulations for mutation assignment to subpopulations, as well as advanced visualization features of assigned mutations. Further documentation and FAQ available at http://dna-discovery.stanford.edu/software/expands.
Author: Noemi Andor
Maintainer: Noemi Andor <expands.r@gmail.com>
Diff between expands versions 1.6.1 dated 2015-12-03 and 1.7 dated 2016-03-26
expands-1.6.1/expands/java/expands.jar |only expands-1.7/expands/DESCRIPTION | 14 - expands-1.7/expands/MD5 | 47 +-- expands-1.7/expands/NAMESPACE | 2 expands-1.7/expands/R/addColumn.R | 20 - expands-1.7/expands/R/assignMutations.R | 186 +++++++++++--- expands-1.7/expands/R/assignQuantityToMutation.R | 166 ++++++------ expands-1.7/expands/R/buildPhylo.R | 121 ++++++--- expands-1.7/expands/R/cellfrequency_pdf.R | 164 ++++++------ expands-1.7/expands/R/clusterCellFrequencies.R | 53 +-- expands-1.7/expands/R/computeCellFrequencyDistributions.R | 1 expands-1.7/expands/R/plotSPs.R | 85 +++++- expands-1.7/expands/R/runExPANdS.R | 93 +++++-- expands-1.7/expands/data/simulation.rda |only expands-1.7/expands/inst/doc/expands.Rnw | 8 expands-1.7/expands/inst/doc/expands.pdf |binary expands-1.7/expands/inst/java/expands.jar |binary expands-1.7/expands/java/Common.java |only expands-1.7/expands/java/ExPANdS.java |only expands-1.7/expands/man/assignMutations.Rd | 17 - expands-1.7/expands/man/assignQuantityToSP.Rd | 2 expands-1.7/expands/man/buildMultiSamplePhylo.Rd | 2 expands-1.7/expands/man/buildPhylo.Rd | 7 expands-1.7/expands/man/plotSPs.Rd | 23 + expands-1.7/expands/man/runExPANdS.Rd | 8 expands-1.7/expands/man/simulation.Rd |only expands-1.7/expands/vignettes/expands.Rnw | 8 27 files changed, 681 insertions(+), 346 deletions(-)
Title: Calculation of Thermal Comfort Indices
Description: Functions to calculate various common and less common thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>
Diff between comf versions 0.1.1 dated 2016-03-06 and 0.1.2 dated 2016-03-26
comf-0.1.1/comf/man/calcMeanBias.Rd |only comf-0.1.2/comf/DESCRIPTION | 9 ++++---- comf-0.1.2/comf/MD5 | 36 +++++++++++++++++--------------- comf-0.1.2/comf/NAMESPACE | 2 - comf-0.1.2/comf/NEWS |only comf-0.1.2/comf/R/ComfortIndices.r | 6 ++--- comf-0.1.2/comf/R/dfField.R |only comf-0.1.2/comf/R/fct2Node.r | 19 ++++++++-------- comf-0.1.2/comf/R/fctHBxStSt.r | 2 - comf-0.1.2/comf/R/fctHelp.r | 11 ++++++--- comf-0.1.2/comf/R/fctOther.r | 4 +++ comf-0.1.2/comf/data |only comf-0.1.2/comf/man/calc2Node.Rd | 8 ++++--- comf-0.1.2/comf/man/calcBias.Rd |only comf-0.1.2/comf/man/calcComfInd.Rd | 2 - comf-0.1.2/comf/man/calcHbExSteady.Rd | 10 ++++---- comf-0.1.2/comf/man/calcHbExUnsteady.Rd | 2 - comf-0.1.2/comf/man/calcPMVPPD.Rd | 2 + comf-0.1.2/comf/man/calcTAdapt.Rd | 6 ++++- comf-0.1.2/comf/man/calcdTNZ.Rd | 2 - comf-0.1.2/comf/man/comf-package.Rd | 12 +++++----- comf-0.1.2/comf/man/dfField.Rd |only 22 files changed, 76 insertions(+), 57 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.7.2 dated 2015-08-13 and 2.8.0 dated 2016-03-25
rebmix-2.7.2/rebmix/R/extractTheta.R |only rebmix-2.7.2/rebmix/R/print.REBMIX.R |only rebmix-2.7.2/rebmix/R/print.RNGMIX.R |only rebmix-2.7.2/rebmix/R/print.boot.REBMIX.R |only rebmix-2.7.2/rebmix/R/summary.REBMIX.R |only rebmix-2.7.2/rebmix/R/summary.boot.REBMIX.R |only rebmix-2.7.2/rebmix/man/print.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/print.RNGMIX.Rd |only rebmix-2.7.2/rebmix/man/print.boot.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/summary.REBMIX.Rd |only rebmix-2.7.2/rebmix/man/summary.boot.REBMIX.Rd |only rebmix-2.7.2/rebmix/src/Makevars |only rebmix-2.8.0/rebmix/DESCRIPTION | 13 rebmix-2.8.0/rebmix/MD5 | 164 rebmix-2.8.0/rebmix/NAMESPACE | 79 rebmix-2.8.0/rebmix/R/AllClasses.R |only rebmix-2.8.0/rebmix/R/AllGenerics.R |only rebmix-2.8.0/rebmix/R/IC.R | 238 - rebmix-2.8.0/rebmix/R/RCLRMIX.R |only rebmix-2.8.0/rebmix/R/RCLSMIX.R | 267 - rebmix-2.8.0/rebmix/R/REBMIX.R | 740 +-- rebmix-2.8.0/rebmix/R/RNGMIX.R | 277 - rebmix-2.8.0/rebmix/R/boot.REBMIX.R | 389 + rebmix-2.8.0/rebmix/R/coef.REBMIX.R | 97 rebmix-2.8.0/rebmix/R/demix.R | 34 rebmix-2.8.0/rebmix/R/dfmix.R | 87 rebmix-2.8.0/rebmix/R/dfmvnorm.x.R |only rebmix-2.8.0/rebmix/R/dfmvnorm.xy.R |only rebmix-2.8.0/rebmix/R/extractThetaA.R |only rebmix-2.8.0/rebmix/R/extractThetaB.R |only rebmix-2.8.0/rebmix/R/is.error.R |only rebmix-2.8.0/rebmix/R/is.number.R |only rebmix-2.8.0/rebmix/R/pemix.R | 6 rebmix-2.8.0/rebmix/R/pfmix.R | 87 rebmix-2.8.0/rebmix/R/pfmvnorm.x.R |only rebmix-2.8.0/rebmix/R/pfmvnorm.xy.R |only rebmix-2.8.0/rebmix/R/plot.RCLRMIX.R |only rebmix-2.8.0/rebmix/R/plot.RCLSMIX.R |only rebmix-2.8.0/rebmix/R/plot.REBMIX.R | 1233 +++++ rebmix-2.8.0/rebmix/R/summary.R |only rebmix-2.8.0/rebmix/data/iris.rda |only rebmix-2.8.0/rebmix/demo/rebmix.galaxy.R | 7 rebmix-2.8.0/rebmix/demo/rebmix.mixed.continuous.discrete.R | 39 rebmix-2.8.0/rebmix/demo/rebmix.multivariate.normal.R | 37 rebmix-2.8.0/rebmix/demo/rebmix.truck.R | 38 rebmix-2.8.0/rebmix/demo/rebmix.univariate.normal.R | 56 rebmix-2.8.0/rebmix/demo/rebmix.weibullnormal.R | 38 rebmix-2.8.0/rebmix/inst/NEWS.Rd | 16 rebmix-2.8.0/rebmix/inst/doc/rebmix.R | 406 + rebmix-2.8.0/rebmix/inst/doc/rebmix.Rnw | 423 +- rebmix-2.8.0/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.8.0/rebmix/man/AIC.Rd | 46 rebmix-2.8.0/rebmix/man/AWE.Rd | 20 rebmix-2.8.0/rebmix/man/BIC.Rd | 19 rebmix-2.8.0/rebmix/man/CLC.Rd | 19 rebmix-2.8.0/rebmix/man/HQC.Rd | 19 rebmix-2.8.0/rebmix/man/ICL.Rd | 19 rebmix-2.8.0/rebmix/man/ICLBIC.Rd | 19 rebmix-2.8.0/rebmix/man/MDL.Rd | 24 rebmix-2.8.0/rebmix/man/PC.Rd | 19 rebmix-2.8.0/rebmix/man/PRD.Rd | 23 rebmix-2.8.0/rebmix/man/RCLRMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RCLRMIX.Rd |only rebmix-2.8.0/rebmix/man/RCLSMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RCLSMIX.Rd | 188 rebmix-2.8.0/rebmix/man/REBMIX-class.Rd |only rebmix-2.8.0/rebmix/man/REBMIX.Rd | 161 rebmix-2.8.0/rebmix/man/REBMIX.boot-class.Rd |only rebmix-2.8.0/rebmix/man/RNGMIX-class.Rd |only rebmix-2.8.0/rebmix/man/RNGMIX.Rd | 164 rebmix-2.8.0/rebmix/man/SSE.Rd | 19 rebmix-2.8.0/rebmix/man/adult.Rd | 50 rebmix-2.8.0/rebmix/man/boot.REBMIX.Rd | 106 rebmix-2.8.0/rebmix/man/coef.REBMIX.Rd | 47 rebmix-2.8.0/rebmix/man/demix.Rd | 29 rebmix-2.8.0/rebmix/man/dfmix.Rd | 79 rebmix-2.8.0/rebmix/man/galaxy.Rd | 6 rebmix-2.8.0/rebmix/man/iris.Rd |only rebmix-2.8.0/rebmix/man/kseq.Rd | 9 rebmix-2.8.0/rebmix/man/logL.Rd | 18 rebmix-2.8.0/rebmix/man/pemix.Rd | 22 rebmix-2.8.0/rebmix/man/pfmix.Rd | 77 rebmix-2.8.0/rebmix/man/plot.REBMIX.Rd | 72 rebmix-2.8.0/rebmix/man/rebmix-internal.Rd |only rebmix-2.8.0/rebmix/man/truck.Rd | 3 rebmix-2.8.0/rebmix/man/weibull.Rd | 2 rebmix-2.8.0/rebmix/man/weibullnormal.Rd | 3 rebmix-2.8.0/rebmix/man/wine.Rd | 98 rebmix-2.8.0/rebmix/src/Rrebmix.cpp | 1338 +++--- rebmix-2.8.0/rebmix/src/Rrebmvnorm.cpp |only rebmix-2.8.0/rebmix/src/base.cpp | 281 + rebmix-2.8.0/rebmix/src/base.h | 36 rebmix-2.8.0/rebmix/src/rebmix.cpp | 14 rebmix-2.8.0/rebmix/src/rebmixf.cpp | 2528 +++++------- rebmix-2.8.0/rebmix/src/rebmixf.h | 58 rebmix-2.8.0/rebmix/src/rebmvnormf.cpp |only rebmix-2.8.0/rebmix/src/rebmvnormf.h |only rebmix-2.8.0/rebmix/src/rngmixf.cpp | 376 - rebmix-2.8.0/rebmix/src/rngmixf.h | 30 rebmix-2.8.0/rebmix/src/rngmvnormf.cpp |only rebmix-2.8.0/rebmix/src/rngmvnormf.h |only rebmix-2.8.0/rebmix/vignettes/rebmix.Rnw | 423 +- rebmix-2.8.0/rebmix/vignettes/rebmix.bib | 46 103 files changed, 6806 insertions(+), 4475 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA.
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between missMDA versions 1.9 dated 2015-12-15 and 1.10 dated 2016-03-25
DESCRIPTION | 13 +++++++------ MD5 | 27 ++++++++++++++------------- R/estim_ncpFAMD.R | 3 ++- inst |only man/gene.Rd | 2 ++ man/geno.Rd | 3 ++- man/imputeFAMD.Rd | 2 ++ man/imputeMCA.Rd | 2 ++ man/imputeMFA.Rd | 3 ++- man/imputePCA.Rd | 2 ++ man/missMDA-package.Rd | 2 ++ man/orange.Rd | 3 ++- man/ozone.Rd | 3 +++ man/snorena.Rd | 3 +++ man/vnf.Rd | 3 +++ 15 files changed, 48 insertions(+), 23 deletions(-)
Title: Monte Carlo Standard Errors for MCMC
Description: Provides tools for computing Monte Carlo standard
errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. MCSE
computation for expectation and quantile estimators is
supported as well as multivariate estimations. The package also provides
functions for computing effective sample size and for plotting
Monte Carlo estimates versus sample size.
Author: James M. Flegal <jflegal@ucr.edu>, John Hughes
<hughesj@umn.edu> and Dootika Vats <vatsx007@umn.edu>
Maintainer: James M. Flegal <jflegal@ucr.edu>
Diff between mcmcse versions 1.1-2 dated 2015-08-24 and 1.2-1 dated 2016-03-25
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++------------- NAMESPACE | 1 + R/mcse_multi.R | 11 +++++++---- R/minESS.R |only build/vignette.rds |binary inst/doc/mcmcse_vignette.R | 12 ++++++++++++ inst/doc/mcmcse_vignette.Rnw | 35 +++++++++++++++++++++++++++++++++-- inst/doc/mcmcse_vignette.pdf |binary man/ess.Rd | 5 +++++ man/mcmcse-package.Rd | 4 ++++ man/mcse.Rd | 4 ++++ man/minESS.Rd |only man/multiESS.Rd | 9 +++++++-- vignettes/mcmcse_vignette.Rnw | 35 +++++++++++++++++++++++++++++++++-- vignettes/mcse.bib | 12 +++++++++--- 16 files changed, 135 insertions(+), 31 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 0.1.1 dated 2015-12-04 and 0.1.2 dated 2016-03-25
GetoptLong-0.1.1/GetoptLong/man/source.rd |only GetoptLong-0.1.2/GetoptLong/DESCRIPTION | 10 GetoptLong-0.1.2/GetoptLong/MD5 | 47 ++-- GetoptLong-0.1.2/GetoptLong/NAMESPACE | 1 GetoptLong-0.1.2/GetoptLong/NEWS | 6 GetoptLong-0.1.2/GetoptLong/R/0_global.R | 39 ++- GetoptLong-0.1.2/GetoptLong/R/GetoptLong.R | 106 ++++++---- GetoptLong-0.1.2/GetoptLong/R/qq.R | 43 +++- GetoptLong-0.1.2/GetoptLong/build/vignette.rds |binary GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.R | 26 -- GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.Rnw | 78 +++---- GetoptLong-0.1.2/GetoptLong/inst/doc/GetoptLong.pdf |binary GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.R | 14 + GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.Rnw | 57 ++++- GetoptLong-0.1.2/GetoptLong/inst/doc/variable_interpolation.pdf |binary GetoptLong-0.1.2/GetoptLong/inst/tests/test_GetoptLong.R | 4 GetoptLong-0.1.2/GetoptLong/man/GetOptions.rd | 10 GetoptLong-0.1.2/GetoptLong/man/GetoptLong.options.rd | 19 + GetoptLong-0.1.2/GetoptLong/man/GetoptLong.rd | 20 + GetoptLong-0.1.2/GetoptLong/man/get_scriptname.rd | 16 + GetoptLong-0.1.2/GetoptLong/man/qq.options.rd | 20 + GetoptLong-0.1.2/GetoptLong/man/qq.rd | 23 +- GetoptLong-0.1.2/GetoptLong/man/qqcat.rd | 25 +- GetoptLong-0.1.2/GetoptLong/vignettes/GetoptLong.Rnw | 78 +++---- GetoptLong-0.1.2/GetoptLong/vignettes/variable_interpolation.Rnw | 57 ++++- 25 files changed, 448 insertions(+), 251 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 3.0.0 dated 2016-01-21 and 3.0.1 dated 2016-03-25
geomorph-3.0.0/geomorph/R/geomorph.utils.R |only geomorph-3.0.0/geomorph/R/gridPar.R |only geomorph-3.0.0/geomorph/R/integration.test.R |only geomorph-3.0.0/geomorph/R/modularity.test.R |only geomorph-3.0.0/geomorph/R/nested.update.R |only geomorph-3.0.0/geomorph/R/phylo.integration.R |only geomorph-3.0.0/geomorph/R/phylo.modularity.R |only geomorph-3.0.0/geomorph/R/procD.allometry.R |only geomorph-3.0.0/geomorph/R/trajectory.analysis.R |only geomorph-3.0.1/geomorph/DESCRIPTION | 11 geomorph-3.0.1/geomorph/MD5 | 146 ++-- geomorph-3.0.1/geomorph/NAMESPACE | 1 geomorph-3.0.1/geomorph/NEWS | 52 - geomorph-3.0.1/geomorph/R/advanced.procD.lm.r | 16 geomorph-3.0.1/geomorph/R/digitize2d.r | 29 geomorph-3.0.1/geomorph/R/digitsurface.r | 2 geomorph-3.0.1/geomorph/R/geomorph.support.code.r | 473 +++++++------ geomorph-3.0.1/geomorph/R/geomorph.utils.r |only geomorph-3.0.1/geomorph/R/gpagen.r | 8 geomorph-3.0.1/geomorph/R/gridPar.r |only geomorph-3.0.1/geomorph/R/integration.test.r |only geomorph-3.0.1/geomorph/R/modularity.test.r |only geomorph-3.0.1/geomorph/R/morphol.disparity.r | 4 geomorph-3.0.1/geomorph/R/nested.update.r |only geomorph-3.0.1/geomorph/R/phylo.integration.r |only geomorph-3.0.1/geomorph/R/phylo.modularity.r |only geomorph-3.0.1/geomorph/R/plotGMPhyloMorphoSpace.r | 34 geomorph-3.0.1/geomorph/R/plotOutliers.r | 4 geomorph-3.0.1/geomorph/R/procD.allometry.r |only geomorph-3.0.1/geomorph/R/procD.lm.r | 2 geomorph-3.0.1/geomorph/R/procD.pgls.r | 13 geomorph-3.0.1/geomorph/R/trajectory.analysis.r |only geomorph-3.0.1/geomorph/README.md | 17 geomorph-3.0.1/geomorph/man/digitsurface.Rd | 2 geomorph-3.0.1/geomorph/man/gpagen.Rd | 3 geomorph-3.0.1/geomorph/man/gridPar.Rd | 2 geomorph-3.0.1/geomorph/man/integration.test.Rd | 2 geomorph-3.0.1/geomorph/man/modularity.test.Rd | 2 geomorph-3.0.1/geomorph/man/morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/nested.update.Rd | 35 geomorph-3.0.1/geomorph/man/phylo.integration.Rd | 12 geomorph-3.0.1/geomorph/man/phylo.modularity.Rd | 2 geomorph-3.0.1/geomorph/man/plot.CR.Rd | 2 geomorph-3.0.1/geomorph/man/plot.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/plot.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/plot.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/plot.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/plot.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/plot.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/plot.pls.Rd | 2 geomorph-3.0.1/geomorph/man/plot.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/plot.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/plot.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/plotGMPhyloMorphoSpace.Rd | 2 geomorph-3.0.1/geomorph/man/print.CR.Rd | 2 geomorph-3.0.1/geomorph/man/print.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/print.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/print.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/print.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/print.evolrate1.Rd | 2 geomorph-3.0.1/geomorph/man/print.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/print.morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/print.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/print.pls.Rd | 2 geomorph-3.0.1/geomorph/man/print.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/print.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/print.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/procD.allometry.Rd | 11 geomorph-3.0.1/geomorph/man/procD.pgls.Rd | 2 geomorph-3.0.1/geomorph/man/summary.CR.Rd | 2 geomorph-3.0.1/geomorph/man/summary.CR.phylo.Rd | 2 geomorph-3.0.1/geomorph/man/summary.advanced.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/summary.bilat.symmetry.Rd | 2 geomorph-3.0.1/geomorph/man/summary.evolrate.Rd | 2 geomorph-3.0.1/geomorph/man/summary.evolrate1.Rd | 2 geomorph-3.0.1/geomorph/man/summary.gpagen.Rd | 2 geomorph-3.0.1/geomorph/man/summary.morphol.disparity.Rd | 2 geomorph-3.0.1/geomorph/man/summary.physignal.Rd | 2 geomorph-3.0.1/geomorph/man/summary.pls.Rd | 2 geomorph-3.0.1/geomorph/man/summary.procD.allometry.Rd | 2 geomorph-3.0.1/geomorph/man/summary.procD.lm.Rd | 2 geomorph-3.0.1/geomorph/man/summary.trajectory.analysis.Rd | 2 geomorph-3.0.1/geomorph/man/trajectory.analysis.Rd | 2 83 files changed, 540 insertions(+), 425 deletions(-)
Title: Coarse Approximation Linear Function
Description: Contains a greedy algorithm for coarse approximation linear function.
Author: Stephanie Lane [aut, cre], Clark Jeffries [aut], Diana Perkins [aut]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between CALF versions 0.1.1 dated 2016-01-04 and 0.1.2 dated 2016-03-25
CALF-0.1.1/CALF/R/CALF.R |only CALF-0.1.2/CALF/DESCRIPTION | 9 +++++---- CALF-0.1.2/CALF/MD5 | 18 +++++++++++------- CALF-0.1.2/CALF/NAMESPACE | 8 +++++++- CALF-0.1.2/CALF/R/CALF-package.R | 11 ++++++----- CALF-0.1.2/CALF/R/calf_internal.R |only CALF-0.1.2/CALF/R/calf_wrappers.R |only CALF-0.1.2/CALF/R/print.calf.R |only CALF-0.1.2/CALF/man/CALF-package.Rd | 12 ++++++------ CALF-0.1.2/CALF/man/CaseControl.Rd | 2 +- CALF-0.1.2/CALF/man/calf.Rd | 8 ++++++-- CALF-0.1.2/CALF/man/calf_randomize.Rd |only CALF-0.1.2/CALF/man/calf_subset.Rd |only 13 files changed, 42 insertions(+), 26 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.6-1 dated 2016-01-24 and 2.7-0 dated 2016-03-25
DESCRIPTION | 8 MD5 | 36 NAMESPACE | 2 R/ensemble.analogue.R | 1 R/ensemble.batch.R | 39 - R/ensemble.mean.R | 14 R/ensemble.novel.R | 1 R/ensemble.plot.R |only R/ensemble.raster.R | 3 R/ensemble.test.R | 9 R/ensemble.zones.R | 1 R/evaluation.strip.data.R | 19 R/evaluation.strip.plot.R | 31 inst/ChangeLog | 24 inst/doc |only inst/etc/BiodiversityGUI.R | 1488 ++++++++++++++++++++++++++++++++++++++- inst/etc/BiodiversityR-menus.txt | 37 inst/etc/Rcmdr-menus.txt | 40 - man/ensemble.batch.Rd | 41 - man/evaluation.strip.Rd | 14 20 files changed, 1746 insertions(+), 62 deletions(-)
Title: Tools for Archiving, Managing and Sharing R Objects via GitHub
Description: The extension of the 'archivist' package integrating the archivist with GitHub via GitHub API, 'git2r' packages and 'httr' package.
Author: Marcin Kosinski [aut, cre],
Przemyslaw Biecek [aut]
Maintainer: Marcin Kosinski <m.p.kosinski@gmail.com>
Diff between archivist.github versions 0.1 dated 2016-02-17 and 0.1.1 dated 2016-03-25
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/archive.R | 4 ++-- README.md | 9 ++++++--- man/archive.Rd | 2 +- 6 files changed, 26 insertions(+), 19 deletions(-)
More information about archivist.github at CRAN
Permanent link
Title: Template Model Builder: A General Random Effect Tool Inspired by
ADMB
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
CppAD (C++ automatic differentiation), Eigen (templated matrix-vector
library) and CHOLMOD (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through BLAS and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.6.6 dated 2016-01-30 and 1.7.0 dated 2016-03-25
TMB-1.6.6/TMB/man/mcmc.Rd |only TMB-1.6.6/TMB/man/mcmc.hmc.Rd |only TMB-1.6.6/TMB/man/mcmc.nuts.Rd |only TMB-1.6.6/TMB/man/mcmc.rwm.Rd |only TMB-1.7.0/TMB/DESCRIPTION | 27 +++++----- TMB-1.7.0/TMB/MD5 | 69 +++++++++++++------------- TMB-1.7.0/TMB/NAMESPACE | 3 - TMB-1.7.0/TMB/NEWS | 13 ++++ TMB-1.7.0/TMB/R/examples.R | 6 +- TMB-1.7.0/TMB/R/mcmc.R | 23 ++++---- TMB-1.7.0/TMB/R/sdreport.R | 74 +++++++++++++++++++++++++++- TMB-1.7.0/TMB/inst/CITATION | 39 +++++++++----- TMB-1.7.0/TMB/inst/examples/mcmc_examples.R | 6 +- TMB-1.7.0/TMB/inst/include/tmb_core.hpp | 63 ++++++++++++++++------- TMB-1.7.0/TMB/man/MakeADFun.Rd | 2 TMB-1.7.0/TMB/man/Rinterface.Rd | 2 TMB-1.7.0/TMB/man/as.list.sdreport.Rd |only TMB-1.7.0/TMB/man/benchmark.Rd | 2 TMB-1.7.0/TMB/man/compile.Rd | 2 TMB-1.7.0/TMB/man/config.Rd | 2 TMB-1.7.0/TMB/man/confint.tmbprofile.Rd | 2 TMB-1.7.0/TMB/man/dynlib.Rd | 2 TMB-1.7.0/TMB/man/gdbsource.Rd | 2 TMB-1.7.0/TMB/man/newton.Rd | 2 TMB-1.7.0/TMB/man/newtonOption.Rd | 2 TMB-1.7.0/TMB/man/oneStepPredict.Rd | 2 TMB-1.7.0/TMB/man/openmp.Rd | 2 TMB-1.7.0/TMB/man/plot.tmbprofile.Rd | 2 TMB-1.7.0/TMB/man/precompile.Rd | 2 TMB-1.7.0/TMB/man/print.sdreport.Rd | 2 TMB-1.7.0/TMB/man/runExample.Rd | 6 +- TMB-1.7.0/TMB/man/runSymbolicAnalysis.Rd | 2 TMB-1.7.0/TMB/man/run_mcmc.Rd |only TMB-1.7.0/TMB/man/run_mcmc.hmc.Rd |only TMB-1.7.0/TMB/man/run_mcmc.nuts.Rd |only TMB-1.7.0/TMB/man/run_mcmc.rwm.Rd |only TMB-1.7.0/TMB/man/sdreport.Rd | 6 +- TMB-1.7.0/TMB/man/summary.sdreport.Rd | 2 TMB-1.7.0/TMB/man/template.Rd | 2 TMB-1.7.0/TMB/man/tmbprofile.Rd | 2 40 files changed, 249 insertions(+), 124 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.7-8 dated 2015-11-09 and 0.7-9 dated 2016-03-25
DESCRIPTION | 8 ++--- MD5 | 31 +++++++++++----------- R/aucJM.JMbayes.R | 43 +++++++++++++++++++++++-------- R/check_td.R | 3 -- R/dns.R | 3 -- R/dwish.R | 3 -- R/fastSumID.R | 3 -- R/fastSumID2.R | 3 -- R/find_positions.R | 3 -- R/makepredictcall.dns.R | 3 -- R/prederrJM.JMbayes.R | 66 +++++++++++++++++++++++++++++++++++++----------- R/rocJM.JMbayes.R | 42 +++++++++++++++++++++++------- R/survfitJM.JMbayes.R | 2 - README.md |only inst/NEWS | 6 ++++ man/JMbayes.Rd | 4 +- man/pbc.Rd | 4 -- 17 files changed, 152 insertions(+), 75 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JM versions 1.4-2 dated 2015-11-09 and 1.4-4 dated 2016-03-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/cumHaz.R | 7 ++++++- R/log.posterior.b2.R | 4 ++-- R/phGH.fit.R | 2 +- inst/NEWS | 16 ++++++++++++++-- man/JM.Rd | 4 ++-- man/pbc.Rd | 4 ---- 8 files changed, 36 insertions(+), 23 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description:
Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 3.0-7 dated 2016-02-20 and 3.1-0 dated 2016-03-25
DESCRIPTION | 12 MD5 | 33 - NEWS | 4 R/Effect.R | 783 +++++++++++++--------------- R/plot-methods.R | 1300 +++++++++++++++++++++++------------------------ R/utilities.R | 874 +++++++++++++------------------ data/Arrests.rda |binary data/BEPS.rda |binary data/Cowles.rda |binary data/Hartnagel.rda |binary data/Prestige.rda |binary data/TitanicSurvival.rda |binary data/WVS.rda |binary data/Wells.rda |binary man/effect.Rd | 1204 +++++++++++++++++++++---------------------- man/effects-package.Rd | 4 man/summary.effect.Rd | 29 - tests/effect-tests-2.R |only 18 files changed, 2052 insertions(+), 2191 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.5.0 dated 2016-02-28 and 3.5.1 dated 2016-03-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/choropleth.R | 14 ++++++++++++-- R/startup_messages.R | 9 ++++----- build/vignette.rds |binary inst/doc/h-creating-your-own-maps.html | 2 +- 7 files changed, 32 insertions(+), 17 deletions(-)
Title: Estimate Parameter of Bivariate Copula
Description: Implement an interval censor method
to break ties when using data with ties to fitting a
bivariate copula.
Author: Yan Li, Yang Li, Yichen Qin, and Jun yan
Maintainer: Yan Li <YanLi_stats@hotmail.com>
Diff between censorcopula versions 1.0 dated 2016-03-13 and 2.0 dated 2016-03-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary man/censorcopula-package.Rd | 4 ++-- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Companion to Applied Regression
Description:
Functions and Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 2.1-1 dated 2015-12-14 and 2.1-2 dated 2016-03-25
DESCRIPTION | 12 - MD5 | 114 ++++++------ NEWS | 454 ++++++++++++++++++++++++------------------------ R/scatter3d.R | 3 build/vignette.rds |binary data/AMSsurvey.rda |binary data/Adler.rda |binary data/Angell.rda |binary data/Anscombe.rda |binary data/Baumann.rda |binary data/Bfox.rda |binary data/Blackmore.rda |binary data/Burt.rda |binary data/CanPop.rda |binary data/Chile.rda |binary data/Chirot.rda |binary data/Cowles.rda |binary data/Davis.rda |binary data/DavisThin.rda |binary data/Depredations.rda |binary data/Duncan.rda |binary data/Ericksen.rda |binary data/Florida.rda |binary data/Freedman.rda |binary data/Friendly.rda |binary data/Ginzberg.rda |binary data/Greene.rda |binary data/Guyer.rda |binary data/Hartnagel.rda |binary data/Highway1.rda |binary data/KosteckiDillon.rda |binary data/Leinhardt.rda |binary data/LoBD.rda |binary data/Mandel.rda |binary data/Migration.rda |binary data/Moore.rda |binary data/Mroz.rda |binary data/OBrienKaiser.rda |binary data/Ornstein.rda |binary data/Pottery.rda |binary data/Prestige.rda |binary data/Quartet.rda |binary data/Robey.rda |binary data/SLID.rda |binary data/Sahlins.rda |binary data/Salaries.rda |binary data/Soils.rda |binary data/States.rda |binary data/Transact.rda |binary data/UN.rda |binary data/USPop.rda |binary data/Vocab.rda |binary data/WeightLoss.rda |binary data/Womenlf.rda |binary data/Wong.rda |binary data/Wool.rda |binary inst/doc/embedding.pdf |binary man/car-package.Rd | 72 +++---- 58 files changed, 328 insertions(+), 327 deletions(-)
Title: Tools for Temporal Social Network Analysis
Description: Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.
Author: Skye Bender-deMoll [aut, cre],
Martina Morris [aut],
James Moody [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between tsna versions 0.1.3 dated 2015-10-01 and 0.2.0 dated 2016-03-25
ChangeLog |only DESCRIPTION | 13 +- MD5 | 24 ++-- NAMESPACE | 14 ++ R/durations.R | 7 - R/randomwalk.R |only R/summaryStats.R | 27 ++++- build/vignette.rds |binary inst/doc/tsna_vignette.Rmd | 7 - inst/doc/tsna_vignette.html | 231 ++++++++++++++++++++++---------------------- man/tErgmStats.Rd | 10 + man/tSnaStats.Rd | 8 + tests/statsWrapper_tests.R | 14 ++ vignettes/tsna_vignette.Rmd | 7 - 14 files changed, 216 insertions(+), 146 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.5.1 dated 2015-10-24 and 3.6.0 dated 2016-03-25
ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.R |only ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.Rmd |only ergm-3.5.1/ergm/inst/doc/ergm-term-crossRef.html |only ergm-3.5.1/ergm/man/robust.inverse.Rd |only ergm-3.5.1/ergm/tests/off |only ergm-3.6.0/ergm/BUGS | 5 ergm-3.6.0/ergm/DESCRIPTION | 15 - ergm-3.6.0/ergm/LICENSE | 2 ergm-3.6.0/ergm/MD5 | 109 +++++----- ergm-3.6.0/ergm/NAMESPACE | 33 +-- ergm-3.6.0/ergm/R/InitErgmTerm.R | 66 ++++-- ergm-3.6.0/ergm/R/InitErgmTerm.dgw_sp.R |only ergm-3.6.0/ergm/R/InitWtErgmTerm.R | 179 +++++++++++++++- ergm-3.6.0/ergm/R/MHproposal.R | 28 +- ergm-3.6.0/ergm/R/approx.hotelling.diff.test.R | 13 - ergm-3.6.0/ergm/R/build_term_index.R | 4 ergm-3.6.0/ergm/R/coef.ergm.R | 5 ergm-3.6.0/ergm/R/control.ergm.R | 6 ergm-3.6.0/ergm/R/ergm.CD.fixed.R | 22 +- ergm-3.6.0/ergm/R/ergm.MCMLE.R | 14 - ergm-3.6.0/ergm/R/ergm.R | 3 ergm-3.6.0/ergm/R/ergm.bridge.R | 4 ergm-3.6.0/ergm/R/ergm.estimate.R | 6 ergm-3.6.0/ergm/R/ergm.getCDsample.R | 2 ergm-3.6.0/ergm/R/ergm.getMCMCsample.R | 4 ergm-3.6.0/ergm/R/ergm.getmodel.R | 100 +++------ ergm-3.6.0/ergm/R/ergm.logitreg.R | 5 ergm-3.6.0/ergm/R/ergm.pen.glm.R | 8 ergm-3.6.0/ergm/R/ergm.robmon.R | 2 ergm-3.6.0/ergm/R/ergm.stepping.R | 97 ++++++--- ergm-3.6.0/ergm/R/ergm.stocapprox.R | 2 ergm-3.6.0/ergm/R/ergm.utility.R | 23 ++ ergm-3.6.0/ergm/R/gof.ergm.R | 28 +- ergm-3.6.0/ergm/R/is.inCH.R | 68 +++--- ergm-3.6.0/ergm/R/mcmc.diagnostics.ergm.R | 10 ergm-3.6.0/ergm/R/parallel.utils.R | 5 ergm-3.6.0/ergm/R/robust.inverse.R | 1 ergm-3.6.0/ergm/R/simulate.ergm.R | 28 ++ ergm-3.6.0/ergm/R/summary.ergm.R | 6 ergm-3.6.0/ergm/R/zzz.R | 5 ergm-3.6.0/ergm/build/vignette.rds |binary ergm-3.6.0/ergm/inst/NEWS.Rd | 115 ++++++++-- ergm-3.6.0/ergm/inst/doc/ergm.pdf |binary ergm-3.6.0/ergm/man/control.ergm.Rd | 24 +- ergm-3.6.0/ergm/man/ergm-terms.Rd | 234 ++++++++-------------- ergm-3.6.0/ergm/man/ergm_deprecated.Rd | 2 ergm-3.6.0/ergm/man/gof.ergm.Rd | 5 ergm-3.6.0/ergm/man/is.inCH.Rd | 12 - ergm-3.6.0/ergm/man/samplk.Rd | 27 +- ergm-3.6.0/ergm/man/sampson.Rd | 6 ergm-3.6.0/ergm/man/summary.ergm.Rd | 4 ergm-3.6.0/ergm/src/changestats.c | 22 ++ ergm-3.6.0/ergm/src/changestats.dgw_sp.c |only ergm-3.6.0/ergm/src/changestats.dgw_sp.h |only ergm-3.6.0/ergm/src/wtchangestats.c | 78 +++++++ ergm-3.6.0/ergm/tests/Rplots.pdf |only ergm-3.6.0/ergm/tests/gw_sp_tests.R |only ergm-3.6.0/ergm/tests/requireNamespaceTest.R |only ergm-3.6.0/ergm/tests/termTests.bipartite.R | 27 ++ ergm-3.6.0/ergm/tests/termTests.valued.R |only ergm-3.6.0/ergm/vignettes/ergm-term-crossRef.html |only 61 files changed, 965 insertions(+), 499 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral sciences and related fields. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial(Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of means, which are easily interpretable for behavioral researchers. BANOVA uses JAGS as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 0.2 dated 2014-06-29 and 0.4 dated 2016-03-25
DESCRIPTION | 15 +- MD5 | 122 +++++++++---------- NAMESPACE | 67 +++++----- R/BANOVA.Bern.R | 4 R/BANOVA.BernNormal.R | 123 ++++++++++--------- R/BANOVA.Bin.R | 4 R/BANOVA.BinNormal.R | 133 +++++++++++---------- R/BANOVA.MultiNormal.R | 157 +++++++++++++----------- R/BANOVA.Multinomial.R | 4 R/BANOVA.Normal.R | 4 R/BANOVA.NormalNormal.R | 114 +++++++++--------- R/BANOVA.PNormal.R | 123 ++++++++++--------- R/BANOVA.Poisson.R | 4 R/BANOVA.T.R | 4 R/BANOVA.TNormal.R | 114 +++++++++--------- R/BANOVA.ordMultiNormal.R | 153 +++++++++++++----------- R/BANOVA.ordMultinomial.R | 4 R/JAGSgen.PNormal.R | 175 ++++++++++++++++----------- R/JAGSgen.TNormal.R | 173 ++++++++++++++++----------- R/JAGSgen.bernNormal.R | 164 +++++++++++++++---------- R/JAGSgen.binNormal.R | 165 +++++++++++++++----------- R/JAGSgen.multiNormal.R | 171 ++++++++++++++++----------- R/JAGSgen.normalNormal.R | 169 +++++++++++++++----------- R/JAGSgen.ordmultiNormal.R | 202 ++++++++++++++++++-------------- R/conv.geweke.heidel.R | 55 ++++---- R/print.conv.diag.R | 23 ++- R/print.summary.BANOVA.Bern.R | 33 ++--- R/print.summary.BANOVA.Bin.R | 33 ++--- R/print.summary.BANOVA.Multinomial.R | 33 ++--- R/print.summary.BANOVA.Normal.R | 33 ++--- R/print.summary.BANOVA.Poisson.R | 33 ++--- R/print.summary.BANOVA.T.R | 33 ++--- R/print.summary.BANOVA.ordMultinomial.R | 33 ++--- R/ssquares.R | 68 +++++----- R/summary.BANOVA.Bern.R | 16 +- R/summary.BANOVA.Bin.R | 16 +- R/summary.BANOVA.Multinomial.R | 16 +- R/summary.BANOVA.Normal.R | 16 +- R/summary.BANOVA.Poisson.R | 16 +- R/summary.BANOVA.T.R | 16 +- R/summary.BANOVA.ordMultinomial.R | 16 +- R/table.ANCOVA.R | 66 +++++----- man/BANOVA-package.Rd | 12 + man/BANOVA.Bern.Rd | 164 +++++++++++++------------ man/BANOVA.Bin.Rd | 175 ++++++++++++++------------- man/BANOVA.Multinomial.Rd | 194 +++++++++++++++--------------- man/BANOVA.Normal.Rd | 169 ++++++++++++++------------ man/BANOVA.Poisson.Rd | 174 ++++++++++++++------------- man/BANOVA.T.Rd | 157 +++++++++++++----------- man/BANOVA.ordMultinomial.Rd | 176 ++++++++++++++------------- man/BAnova.Rd | 96 +++++++-------- man/bernlogtime.Rd | 86 ++++++------- man/bpndata.Rd | 104 ++++++++-------- man/choicedata.Rd | 2 man/colorad.Rd | 84 ++++++------- man/colorad2.Rd | 90 +++++++------- man/conv.diag.Rd | 108 ++++++++--------- man/goalstudy.Rd | 102 ++++++++-------- man/ipadstudy.Rd | 98 +++++++-------- man/table.means.Rd | 48 +++---- man/table.pvalues.Rd | 86 ++++++------- man/trace.plot.Rd | 50 +++---- 62 files changed, 2746 insertions(+), 2352 deletions(-)
Title: Social Relation Model (SRM) Analyses for Single or Multiple
Groups
Description: Social Relation Model (SRM) analyses for single or multiple
round-robin groups are performed. These analyses are either based on one
manifest variable, one latent construct measured by two manifest variables,
two manifest variables and their bivariate relations, or two latent
constructs each measured by two manifest variables. Within-group t-tests
for variance components and covariances are provided for single groups.
For multiple groups two types of significance tests are provided:
between-groups t-tests (as in SOREMO) and enhanced standard errors based on
Lashley and Bond (1997). Handling for missing values is provided.
Author: F. D. Schönbrodt, M. D. Back, S. C. Schmukle
Maintainer: Felix Schönbrodt <felix.schoenbrodt@psy.lmu.de>
Diff between TripleR versions 1.4.1 dated 2015-04-30 and 1.5.0 dated 2016-03-24
DESCRIPTION | 16 MD5 | 25 - NAMESPACE | 17 NEWS | 12 R/00-Skinning.R |only R/LashleyBond.R |only R/RR.r | 834 +++++++++++++------------------------------------ R/helpers.R |only R/imports.R |only R/impute.R |only R/plots.R | 3 R/print.RR.R |only R/weighted.t.test.R |only inst/CITATION | 6 inst/doc/TripleR.pdf |binary man/RR.Rd | 14 man/TripleR-package.Rd | 5 17 files changed, 305 insertions(+), 627 deletions(-)
Title: Learn R, in R
Description: Use the R console as an interactive learning
environment. Users receive immediate feedback as they are guided through
self-paced lessons in data science and R programming.
Author: Sean Kross [aut, cre],
Nick Carchedi [aut],
Bill Bauer [aut],
Gina Grdina [aut],
Filip Schouwenaars [ctb],
Wush Wu [ctb]
Maintainer: Sean Kross <sean@seankross.com>
Diff between swirl versions 2.2.21 dated 2015-01-04 and 2.4.0 dated 2016-03-24
DESCRIPTION | 36 +++-- LICENSE |only MD5 | 118 ++++++++++-------- NAMESPACE | 11 + NEWS.md |only R/actions.R |only R/answerTests2.R | 8 - R/args_specification.R |only R/courseraCheck.R | 66 +++++----- R/install_course.R | 224 ++++++++++++++++++++++++++---------- R/instructionSet.R | 47 ++++--- R/languages.R |only R/log.R |only R/menu.R | 131 ++++++++++++++------- R/options.R |only R/parse_content.R | 16 ++ R/phrases.R | 74 +++++------ R/post.R |only R/progress.R | 12 + R/rmatch_calls.R | 18 +- R/swirl.R | 161 +++++++++---------------- R/sysdata.rda |only R/utilities.R | 18 +- R/zzz.R | 14 +- README.md | 3 inst/Courses/suggested_courses.yaml | 13 +- inst/test |only man/AnswerTests.Rd | 56 ++++----- man/InstallCourses.Rd | 29 ++-- man/any_of_exprs.Rd | 18 +- man/bye.Rd | 2 man/delete_progress.Rd | 6 man/email_admin.Rd | 2 man/expr_creates_var.Rd | 16 +- man/expr_identical_to.Rd | 16 +- man/expr_is_a.Rd | 18 +- man/expr_uses_func.Rd | 16 +- man/func_of_newvar_equals.Rd | 16 +- man/info.Rd | 24 --- man/install_course.Rd |only man/install_course_directory.Rd | 21 +-- man/install_course_dropbox.Rd | 21 +-- man/install_course_github.Rd | 21 +-- man/install_course_google_drive.Rd | 21 +-- man/install_course_url.Rd | 21 +-- man/install_course_zip.Rd | 21 +-- man/install_from_swirl.Rd | 27 ++-- man/is_robust_match.Rd | 4 man/main.Rd | 2 man/nxt.Rd | 2 man/omnitest.Rd | 30 ++-- man/play.Rd | 2 man/reset.Rd | 2 man/restart.Rd |only man/rmatch_calls.Rd | 32 ++--- man/select_language.Rd |only man/skip.Rd | 2 man/submit.Rd | 2 man/swirl.Rd | 10 - man/swirl_options.Rd |only man/uninstall_all_courses.Rd | 28 ++-- man/uninstall_course.Rd | 21 +-- man/val_has_length.Rd | 18 +- man/val_matches.Rd | 18 +- man/var_is_a.Rd | 16 +- man/zip_course.Rd | 23 +-- tests/testthat/test-encoding.R |only tests/testthat/test-uses_func.R |only 68 files changed, 864 insertions(+), 690 deletions(-)
Title: Stubbing Framework for R
Description: Create stubs of functions for use while testing.
Author: Sainath Adapa [aut, cre],
Nitin Madasu [aut]
Maintainer: Sainath Adapa <adapasainath@gmail.com>
Diff between stubthat versions 0.1.0 dated 2015-12-13 and 1.0.0 dated 2016-03-24
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Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures or other covariance structures in R.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.3 dated 2016-03-09 and 1.4 dated 2016-03-24
CHANGELOG | 12 + DESCRIPTION | 14 - MD5 | 52 +++-- NAMESPACE | 11 - R/AI.R | 441 ++++++++++++++++++++++++++++-------------------- R/AI2.R | 2 R/AI3.R | 2 R/EM.R | 270 ++++++++++++++++++----------- R/EM2.R |only R/atcg1234.R | 40 ++++ R/bag.R | 2 R/big.peaks.col.R |only R/brewer.pal.R |only R/map.plot2.R | 61 ++++++ R/mmer.R | 84 ++++++++- R/mmer2.R | 8 data/Technow_data.RData |only data/datalist | 1 inst/CITATION | 4 man/AI.Rd | 4 man/CPdata.Rd | 2 man/EM.Rd | 3 man/EM2.Rd |only man/PolyData.Rd | 4 man/Technow_data.Rd |only man/atcg1234.Rd | 3 man/big.peaks.col.Rd |only man/brewer.pal.Rd |only man/mmer.Rd | 79 ++++++-- man/mmer2.Rd | 85 +++++++-- man/sommer-package.Rd | 62 ++++-- 31 files changed, 851 insertions(+), 395 deletions(-)
Title: Six Sigma Tools for Quality Control and Improvement
Description: Functions and utilities to perform
Statistical Analyses in the Six Sigma way.
Through the DMAIC cycle (Define, Measure, Analyze, Improve, Control),
you can manage several Quality Management studies:
Gage R&R, Capability Analysis, Control Charts, Loss Function Analysis,
etc. Data frames used in the books "Six Sigma with R" (Springer, 2012)
and "Quality Control with R" (Springer, 2015)
are also included in the package.
Author: Emilio L. Cano, Javier M. Moguerza, Mariano Prieto and Andrés Redchuk
Maintainer: Emilio L. Cano <emilio.lopez@urjc.es>
Diff between SixSigma versions 0.9-2 dated 2016-02-05 and 0.9-3 dated 2016-03-24
DESCRIPTION | 8 MD5 | 20 - NEWS | 9 R/SixSigma-package.R | 2 R/ss.ci.R | 305 ++++++++++--------- R/ss.rr.R | 550 ++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/HelicopterInstructions.pdf |binary inst/doc/ShewhartConstants.pdf |binary man/SixSigma.Rd | 2 man/ss.rr.Rd | 47 ++- 11 files changed, 560 insertions(+), 383 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.2.0 dated 2015-08-20 and 0.2.2 dated 2016-03-24
DESCRIPTION | 10 +- MD5 | 20 ++-- NAMESPACE | 20 ++-- NEWS | 14 +++ R/SeqFeatR_GUI.R | 174 +++++++++++++++++++++++++++++------------ R/assocpoint.R | 75 +++++------------ R/smallmanhattan.R |only build/vignette.rds |binary inst/doc/SeqFeatR_tutorial.pdf |binary inst/extdata/config.cfg | 3 man/assocpoint.Rd | 15 --- man/smallmanhattan.Rd |only 12 files changed, 199 insertions(+), 132 deletions(-)
Title: JavaScript Charts API Tool
Description: API for using 'AmCharts' Library. Based on the 'htmlwidgets'
package, it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced
but can easily be added in the constructors. Complex properties (e.g.
'JavaScript' object) can be passed as named list. See examples at <http://
datastorm-open.github.io/introduction_ramcharts/>. and <http://www.amcharts.com/> for
more information about the library. The package includes the free version of
'AmCharts' Library. Its only limitation is that a small link to the web site
will be displayed in your charts. If you enjoy this library, do not hesitate
to refer to this page <http://www.amcharts.com/online-store/> to purchase a
licence, and thus support its creators and get a period of Priority Support.
See also <http://www.amcharts.com/about/> for more information about
'AmCharts' company.
Author: Jeffery Petit [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Benoit Thieurmel [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Jeffery Petit <jeffery.petit@datastorm.fr>
Diff between rAmCharts versions 1.1.2 dated 2015-10-19 and 2.0.0 dated 2016-03-24
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rAmCharts-2.0.0/rAmCharts/man/AmGraph-class.Rd | 15 rAmCharts-2.0.0/rAmCharts/man/AmGraph.Rd |only rAmCharts-2.0.0/rAmCharts/man/AmLegend-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/AmObject-class.Rd | 12 rAmCharts-2.0.0/rAmCharts/man/AmStockChart-class.Rd | 22 rAmCharts-2.0.0/rAmCharts/man/AmStockChart.Rd |only rAmCharts-2.0.0/rAmCharts/man/AxisBase-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/CategoryAxis-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/ChartCursor-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/ChartScrollbar-class.Rd | 15 rAmCharts-2.0.0/rAmCharts/man/DataSet-class.Rd | 25 rAmCharts-2.0.0/rAmCharts/man/DataSet.Rd |only rAmCharts-2.0.0/rAmCharts/man/DataSetSelector-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/DataSetSelector.Rd |only rAmCharts-2.0.0/rAmCharts/man/GaugeArrow-class.Rd | 16 rAmCharts-2.0.0/rAmCharts/man/GaugeArrow.Rd |only rAmCharts-2.0.0/rAmCharts/man/GaugeAxis-class.Rd | 14 rAmCharts-2.0.0/rAmCharts/man/GaugeAxis.Rd |only rAmCharts-2.0.0/rAmCharts/man/GaugeBand-class.Rd | 14 rAmCharts-2.0.0/rAmCharts/man/GaugeBand.Rd |only rAmCharts-2.0.0/rAmCharts/man/Guide-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/Label-class.Rd | 13 rAmCharts-2.0.0/rAmCharts/man/Label.Rd |only rAmCharts-2.0.0/rAmCharts/man/PeriodSelector-class.Rd | 18 rAmCharts-2.0.0/rAmCharts/man/StockEvent-class.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/StockPanel-class.Rd | 56 rAmCharts-2.0.0/rAmCharts/man/Title-class.Rd | 18 rAmCharts-2.0.0/rAmCharts/man/Title.Rd |only rAmCharts-2.0.0/rAmCharts/man/TrendLine-class.Rd | 8 rAmCharts-2.0.0/rAmCharts/man/TrendLine.Rd |only rAmCharts-2.0.0/rAmCharts/man/ValueAxis-class.Rd | 12 rAmCharts-2.0.0/rAmCharts/man/amAngularGauge.Rd |only rAmCharts-2.0.0/rAmCharts/man/amBarplot.Rd |only rAmCharts-2.0.0/rAmCharts/man/amBoxplot.Rd | 117 + rAmCharts-2.0.0/rAmCharts/man/amBullet.Rd |only rAmCharts-2.0.0/rAmCharts/man/amCandlestick.Rd |only rAmCharts-2.0.0/rAmCharts/man/amChartsOutput.Rd | 20 rAmCharts-2.0.0/rAmCharts/man/amFloatingBar.Rd |only rAmCharts-2.0.0/rAmCharts/man/amFunnel.Rd |only rAmCharts-2.0.0/rAmCharts/man/amHist.Rd | 90 - rAmCharts-2.0.0/rAmCharts/man/amLines.Rd |only rAmCharts-2.0.0/rAmCharts/man/amMekko.Rd |only rAmCharts-2.0.0/rAmCharts/man/amOHLC.Rd |only rAmCharts-2.0.0/rAmCharts/man/amOptions.Rd |only rAmCharts-2.0.0/rAmCharts/man/amPie.Rd |only rAmCharts-2.0.0/rAmCharts/man/amPlot.Rd |only rAmCharts-2.0.0/rAmCharts/man/amRadar.Rd |only rAmCharts-2.0.0/rAmCharts/man/amSolidGauge.Rd |only rAmCharts-2.0.0/rAmCharts/man/amWaterfall.Rd |only rAmCharts-2.0.0/rAmCharts/man/amWind.Rd |only rAmCharts-2.0.0/rAmCharts/man/api.Rd | 2 rAmCharts-2.0.0/rAmCharts/man/controlShinyPlot.Rd | 12 rAmCharts-2.0.0/rAmCharts/man/data_AirPassengers.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_bar.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_candleStick1.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_candleStick2.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_fbar.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_funnel.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_gbar.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_gdp.Rd | 6 rAmCharts-2.0.0/rAmCharts/man/data_mekko.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_pie.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_radar.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_stock1.Rd | 6 rAmCharts-2.0.0/rAmCharts/man/data_waterfall.Rd |only rAmCharts-2.0.0/rAmCharts/man/data_wind.Rd |only rAmCharts-2.0.0/rAmCharts/man/initialize-AmChart.Rd | 370 ++--- rAmCharts-2.0.0/rAmCharts/man/initialize-AmLegend.Rd | 24 rAmCharts-2.0.0/rAmCharts/man/initialize-AxisBase.Rd | 11 rAmCharts-2.0.0/rAmCharts/man/initialize-CategoryAxis.Rd | 27 rAmCharts-2.0.0/rAmCharts/man/initialize-ChartCursor.Rd | 26 rAmCharts-2.0.0/rAmCharts/man/initialize-ChartScrollbar.Rd | 30 rAmCharts-2.0.0/rAmCharts/man/initialize-Guide.Rd | 27 rAmCharts-2.0.0/rAmCharts/man/initialize-PeriodSelector.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/initialize-StockEvent.Rd | 13 rAmCharts-2.0.0/rAmCharts/man/initialize-StockPanel.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/initialize-ValueAxis.Rd | 24 rAmCharts-2.0.0/rAmCharts/man/listProperties-AmObject.Rd | 115 - rAmCharts-2.0.0/rAmCharts/man/methods-AmObject.Rd | 48 rAmCharts-2.0.0/rAmCharts/man/plot.AmChart.Rd | 8 rAmCharts-2.0.0/rAmCharts/man/print-AmObject-method.Rd | 17 rAmCharts-2.0.0/rAmCharts/man/renderAmCharts.Rd | 14 rAmCharts-2.0.0/rAmCharts/man/runExamples.Rd |only rAmCharts-2.0.0/rAmCharts/man/shared-generics.Rd | 41 rAmCharts-2.0.0/rAmCharts/man/show-AmChart-method.Rd | 24 rAmCharts-2.0.0/rAmCharts/man/show-AmObject-method.Rd | 13 rAmCharts-2.0.0/rAmCharts/man/stockGraph.Rd | 10 rAmCharts-2.0.0/rAmCharts/man/stockLegend.Rd | 14 rAmCharts-2.0.0/rAmCharts/tests/testthat.R | 3 rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amBarplot.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amBoxplot.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amBullet.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amCandlestick.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amFloatingBar.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amFunnel.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amHist.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amMekko.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amOHLC.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amOptions.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amPie.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amPlot.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amRadar.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amSolidGauge.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amTests.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amWaterfall.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amWind.R |only rAmCharts-2.0.0/rAmCharts/tests/testthat/test_amchart_setters.R |only 312 files changed, 3169 insertions(+), 2165 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.5.0 dated 2016-02-28 and 0.5.1 dated 2016-03-24
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NEWS | 8 ++++ R/tcc.R | 97 ++++++++++++++++++++++++++++++++++++----------------- build/vignette.rds |binary man/tcc.Rd | 14 ++++--- 6 files changed, 93 insertions(+), 44 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-41 dated 2015-11-09 and 0.9.42 dated 2016-03-24
mkin-0.9-41/mkin/vignettes/FOCUS_D_cache |only mkin-0.9-41/mkin/vignettes/FOCUS_D_files |only mkin-0.9-41/mkin/vignettes/FOCUS_L_cache |only mkin-0.9-41/mkin/vignettes/FOCUS_L_files |only mkin-0.9.42/mkin/DESCRIPTION | 10 - mkin-0.9.42/mkin/MD5 | 121 ++-------------- mkin-0.9.42/mkin/NEWS.md | 16 ++ mkin-0.9.42/mkin/R/mkinfit.R | 15 +- mkin-0.9.42/mkin/R/mkinmod.R | 6 mkin-0.9.42/mkin/README.md | 31 ---- mkin-0.9.42/mkin/build/vignette.rds |binary mkin-0.9.42/mkin/inst/doc/FOCUS_D.R | 20 ++ mkin-0.9.42/mkin/inst/doc/FOCUS_D.html | 42 +++-- mkin-0.9.42/mkin/inst/doc/FOCUS_L.R | 95 +++++++++++++ mkin-0.9.42/mkin/inst/doc/FOCUS_L.html | 180 ++++++++++++------------- mkin-0.9.42/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9.42/mkin/inst/doc/compiled_models.R | 37 +++-- mkin-0.9.42/mkin/inst/doc/compiled_models.Rmd | 41 +++-- mkin-0.9.42/mkin/inst/doc/compiled_models.html | 120 +++++++++------- mkin-0.9.42/mkin/inst/doc/mkin.pdf |binary mkin-0.9.42/mkin/man/mkinfit.Rd | 8 + mkin-0.9.42/mkin/vignettes/compiled_models.Rmd | 41 +++-- 22 files changed, 433 insertions(+), 350 deletions(-)
Title: Multivariate Random Forest for Linearly Related Output Features
Description: In Random Forest, prediction has been done for single
output feature, while linear relation between the
output features has not been considered in other
packages. In this package, using linear relation of
the output features, a multivariate random forest
prediction has been done, which can predict all the
output features with one Random forest. If there is
high correlation among the features, this MRF
prediction gives better result than the individual
RFs.
Author: Raziur Rahman <razeeebuet@gmail.com>
Maintainer: Raziur Rahman <razeeebuet@gmail.com>
Diff between MultivariateRandomForest versions 1.0 dated 2016-03-13 and 1.1 dated 2016-03-24
DESCRIPTION | 17 +++++++++--- MD5 | 38 ++++++++++++++-------------- R/CrossValidation.R | 6 ++-- R/Imputation.R | 11 ++++---- R/Multi_D_mod.R | 25 ++++++++++++++---- R/MultivariateRandomForest.R | 53 +++++++++++++++++++++++++++++++--------- R/build_single_tree.R | 17 +++++++----- R/predicting.R | 18 +++++++++---- R/single_tree_prediction.R | 17 ++++++------ R/split_node.R | 29 ++++++++++++++------- R/spliting.R | 35 +++++++++++++++++++------- man/CrossValidation.Rd | 6 ++-- man/Imputation.Rd | 8 +++--- man/Multi_D_mod.Rd | 28 ++++++++++++++++----- man/MultivariateRandomForest.Rd | 49 +++++++++++++++++++++++++++--------- man/build_single_tree.Rd | 18 ++++++++----- man/predicting.Rd | 19 +++++++++----- man/single_tree_prediction.Rd | 16 ++++++------ man/split_node.Rd | 28 ++++++++++++++------- man/spliting.Rd | 35 +++++++++++++++++++------- 20 files changed, 320 insertions(+), 153 deletions(-)
More information about MultivariateRandomForest at CRAN
Permanent link
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for
reproducible model validation, calibration, and comparison.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 3.0 dated 2016-01-04 and 3.6 dated 2016-03-24
DESCRIPTION | 10 +- MD5 | 52 +++++++------ NAMESPACE | 1 NEWS.md | 15 +++ R/10.hdnom.compare.calibrate.R | 75 +++++++++++-------- R/11.hdnom.color.palette.R |only R/3.hdnom.validate.R | 74 +++++++++++-------- R/4.hdnom.calibrate.R | 43 ++++++----- R/5.hdnom.external.validate.R | 16 +++- R/6.hdnom.external.calibrate.R | 43 ++++++----- R/7.hdnom.kmplot.R | 49 +++++++++--- R/9.hdnom.compare.validate.R | 136 +++++++++++++++++++---------------- README.md | 4 - build/vignette.rds |binary inst/doc/hdnom.Rmd | 33 +++++++- inst/doc/hdnom.html | 130 +++++++++++++++++++++------------ man/hdnom.kmplot.Rd | 7 + man/kmplot.Rd | 5 + man/palette.aaas.Rd |only man/palette.jco.Rd |only man/palette.lancet.Rd |only man/palette.npg.Rd |only man/plot.hdnom.calibrate.Rd | 7 + man/plot.hdnom.compare.calibrate.Rd | 6 + man/plot.hdnom.compare.validate.Rd | 7 + man/plot.hdnom.external.calibrate.Rd | 6 + man/plot.hdnom.external.validate.Rd | 7 + man/plot.hdnom.validate.Rd | 7 + vignettes/hdnom.Rmd | 33 +++++++- vignettes/hdnom.css |only 30 files changed, 500 insertions(+), 266 deletions(-)
More information about futureheatwaves at CRAN
Permanent link
Title: Functions for Simple Fisheries Stock Assessment Methods
Description: Functions to perform a variety of simple fish stock assessment
methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.5 dated 2016-02-14 and 0.8.6 dated 2016-03-24
DESCRIPTION | 8 +-- MD5 | 51 ++++++++++---------- NEWS.md |only R/FSA-internals.R | 51 ++++++++++++++------ R/alkPlot.R | 40 +++++++++++++--- R/alkSummaries.R | 3 - R/hist.formula.R | 86 +++++++++++++++++++++++------------ R/knitUtil.R | 18 ++++++- R/lencat.R | 28 ++++++----- R/psdAdd.R | 18 ++++--- R/psdPlot.R | 28 ++++++----- R/psdVal.R | 16 +++--- R/vbStarts.R | 3 - man/FSA-internals.Rd | 1 man/hist.formula.Rd | 20 ++++++-- man/knitUtil.Rd | 6 +- man/lencat.Rd | 22 ++++---- man/psdAdd.Rd | 14 +++-- man/psdPlot.Rd | 17 +++--- man/psdVal.Rd | 8 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test_AgeComparisons.R | 12 ++-- tests/testthat/test_AgeLengthKey.R | 29 ++++++----- tests/testthat/test_Internals.R | 32 +++++++++++++ tests/testthat/test_PSD.R | 61 +++++++++++++----------- tests/testthat/test_WSWR.R | 21 ++++---- tests/testthat/test_histFormula.R | 37 +++++++++++++-- 27 files changed, 405 insertions(+), 225 deletions(-)
Title: Ecological Inference
Description: Software accompanying Gary King's book: A Solution to the Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-0691012407.
Author: Gary King <king@harvard.edu>, Molly Roberts <molly.e.roberts@gmail.com>
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between ei versions 1.3 dated 2016-01-20 and 1.3-2 dated 2016-03-24
DESCRIPTION | 11 ++++++----- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 - R/tomogRxc3d.R | 35 ++++++++++++++++++++--------------- inst/doc/ei.pdf |binary man/bounds1.Rd | 8 ++++---- man/census1910.Rd | 6 +++--- man/ei.Rd | 2 +- man/ei.sim.Rd | 2 +- man/eiread.Rd | 2 +- man/plot.ei.Rd | 2 +- man/summary.ei.Rd | 2 +- man/tomogRxC.Rd | 2 +- man/tomogRxC3d.Rd | 2 +- 14 files changed, 53 insertions(+), 48 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.6 dated 2016-01-07 and 0.7 dated 2016-03-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/dynRB-internal.R | 11 +++++++++++ R/dynRB_Pn.R | 6 ++++++ R/dynRB_VPa.R | 15 ++++++++++++++- R/dynRB_Vn.R | 8 +++++++- man/dynRB-package.Rd | 4 ++-- man/dynRB_VPa.Rd | 9 ++++++++- 9 files changed, 60 insertions(+), 16 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich (R package)
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.2.1 dated 2016-02-27 and 1.2.2 dated 2016-03-24
bartMachine-1.2.1/bartMachine/man/predict.Rd |only bartMachine-1.2.1/bartMachine/vignettes/bart_package_paper.bib |only bartMachine-1.2.1/bartMachine/vignettes/images |only bartMachine-1.2.1/bartMachine/vignettes/jss_style |only bartMachine-1.2.2/bartMachine/CHANGELOG | 8 bartMachine-1.2.2/bartMachine/DESCRIPTION | 8 bartMachine-1.2.2/bartMachine/MD5 | 110 bartMachine-1.2.2/bartMachine/NAMESPACE | 4 bartMachine-1.2.2/bartMachine/R/bart_arrays.R |only bartMachine-1.2.2/bartMachine/R/bart_package_builders.R | 2 bartMachine-1.2.2/bartMachine/R/bart_package_f_tests.R | 9 bartMachine-1.2.2/bartMachine/R/bart_package_inits.R | 2 bartMachine-1.2.2/bartMachine/R/bart_package_predicts.R | 2 bartMachine-1.2.2/bartMachine/R/zzz.R | 8 bartMachine-1.2.2/bartMachine/build/vignette.rds |binary bartMachine-1.2.2/bartMachine/data/benchmark_datasets.RData |only bartMachine-1.2.2/bartMachine/inst/CITATION | 29 bartMachine-1.2.2/bartMachine/inst/COPYRIGHTS | 2 bartMachine-1.2.2/bartMachine/inst/doc/bartMachine.Rnw | 1934 +++++++--- bartMachine-1.2.2/bartMachine/inst/doc/bartMachine.pdf |binary bartMachine-1.2.2/bartMachine/man/bartMachine.Rd | 8 bartMachine-1.2.2/bartMachine/man/bartMachineArr.Rd |only bartMachine-1.2.2/bartMachine/man/bartMachineCV.Rd | 5 bartMachine-1.2.2/bartMachine/man/benchmark_datasets.Rd |only bartMachine-1.2.2/bartMachine/man/calc_prediction_intervals.Rd | 4 bartMachine-1.2.2/bartMachine/man/cov_importance_test.Rd | 4 bartMachine-1.2.2/bartMachine/man/interaction_investigator.Rd | 4 bartMachine-1.2.2/bartMachine/man/investigate_var_importance.Rd | 4 bartMachine-1.2.2/bartMachine/man/linearity_test.Rd |only bartMachine-1.2.2/bartMachine/man/pd_plot.Rd | 4 bartMachine-1.2.2/bartMachine/man/predict.bartMachine.Rd |only bartMachine-1.2.2/bartMachine/man/predict_bartMachineArr.Rd |only bartMachine-1.2.2/bartMachine/man/var_selection_by_permute.Rd | 4 bartMachine-1.2.2/bartMachine/man/var_selection_by_permute_cv.Rd | 4 bartMachine-1.2.2/bartMachine/vignettes/bartMachine.Rnw | 1934 +++++++--- bartMachine-1.2.2/bartMachine/vignettes/bart_normality_heteroskedasticity_2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/convergence_diagnostics4.pdf |only bartMachine-1.2.2/bartMachine/vignettes/cov_test_body_style2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/cov_test_omnibus2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/cov_test_top_10_2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/cov_test_width2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/covariate_test_age3.pdf |only bartMachine-1.2.2/bartMachine/vignettes/friedman_function_interactions2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/glucose_partial_dependence2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/pdp_horsepower2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/pdp_stroke2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/plot_y_vs_y_hat_cred_ints2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/plot_y_vs_y_hat_pred_ints2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/rmse_num_trees_3.pdf |only bartMachine-1.2.2/bartMachine/vignettes/speed_full4.pdf |only bartMachine-1.2.2/bartMachine/vignettes/speed_zoomed4.pdf |only bartMachine-1.2.2/bartMachine/vignettes/v70i04.bib |only bartMachine-1.2.2/bartMachine/vignettes/var_imp_automobile_cc2.pdf |only bartMachine-1.2.2/bartMachine/vignettes/var_selection_plot2.pdf |only 54 files changed, 2878 insertions(+), 1215 deletions(-)
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (including memory profiling) in a visually appealing way.
It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.3.1 dated 2015-10-09 and 0.3.2 dated 2016-03-24
DESCRIPTION | 9 +++--- MD5 | 22 ++++++++-------- NAMESPACE | 2 - R/aprof.R | 64 ++++++++++++++++++------------------------------- man/aprof.Rd | 12 ++++----- man/is.aprof.Rd | 2 - man/plot.Rd | 7 ++--- man/print.Rd | 2 - man/profileplot.Rd | 2 - man/readLineDensity.Rd | 2 - man/summary.Rd | 2 - man/targetedSummary.Rd | 10 +------ 12 files changed, 57 insertions(+), 79 deletions(-)
Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and
exploration of data from environmental monitoring programs.
The package name stands for "water quality" and reflects the
original focus on time series data for physical and chemical
properties of water, as well as the biota. Intended for
programs that sample approximately monthly, quarterly or
annually at discrete stations, a feature of many legacy data
sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject
matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>
Diff between wq versions 0.4.6 dated 2016-03-20 and 0.4.7 dated 2016-03-24
wq-0.4.6/wq/R/ruleN.R |only wq-0.4.7/wq/DESCRIPTION | 13 ++++--- wq-0.4.7/wq/MD5 | 35 +++++++++++---------- wq-0.4.7/wq/NAMESPACE | 1 wq-0.4.7/wq/NEWS | 21 ++++++++---- wq-0.4.7/wq/R/eof.R | 57 ++++++++++++++++++++--------------- wq-0.4.7/wq/R/eofNum.R | 50 +++++++++++------------------- wq-0.4.7/wq/R/eofPlot.R | 23 ++++++-------- wq-0.4.7/wq/R/plotSeason.R | 27 +++++++--------- wq-0.4.7/wq/R/plotTsAnom.R | 20 ++++++------ wq-0.4.7/wq/R/plotTsTile.R | 4 +- wq-0.4.7/wq/build/partial.rdb |binary wq-0.4.7/wq/build/vignette.rds |only wq-0.4.7/wq/inst/doc |only wq-0.4.7/wq/man/eof.Rd | 29 +++++++++++------ wq-0.4.7/wq/man/eofNum.Rd | 45 +++++++++++---------------- wq-0.4.7/wq/man/eofPlot.Rd | 28 ++++++----------- wq-0.4.7/wq/man/plotTsTile.Rd | 14 ++++---- wq-0.4.7/wq/vignettes/wq-package.Rmd | 10 +++--- 19 files changed, 188 insertions(+), 189 deletions(-)
Title: Convert Between Spatial Objects and Well-Known Binary Geometry
Description: Utility functions to convert between the 'Spatial' classes
specified by the package 'sp', and the well-known binary '(WKB)'
representation for geometry specified by the Open Geospatial Consortium.
Supports 'Spatial' objects of class 'SpatialPoints',
'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame',
'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry
types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and
'MultiPolygon'. Includes extensions to enable creation of maps with
'TIBCO Spotfire'.
Author: TIBCO Software Inc.
Maintainer: Ian Cook <ianmcook@gmail.com>
Diff between wkb versions 0.2-0 dated 2015-09-28 and 0.3-0 dated 2016-03-24
DESCRIPTION | 27 ++++++++++++++------------- LICENSE | 2 +- MD5 | 17 ++++++++++------- R/XYListToWKBLineString.R |only R/contourLinesToWKB.R |only R/coordPairsStringToWKBPolygon.R |only R/hex2raw.R | 3 ++- R/writeWKB.R | 23 ++++++++++++----------- tests/testthat/testmultipoint.R | 4 ++-- tests/testthat/testmultipolygon.R | 4 ++-- tests/testthat/testpolygon.R | 4 ++-- 11 files changed, 45 insertions(+), 39 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.3 dated 2015-11-19 and 1.7.4 dated 2016-03-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/TimeInstantDataFrame.R | 31 +++++++++++++++++++++---------- R/TimeIntervalDataFrame.R | 4 +++- R/split.R | 1 + README | 10 ++++++++++ man/timetools-package.Rd | 4 ++-- 7 files changed, 47 insertions(+), 23 deletions(-)
Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Timo Aspelmeier [cre, aut],
Thomas Hotz [aut],
Hannes Sieling [aut],
Pein Florian [ctb]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between stepR versions 1.0-3 dated 2015-06-18 and 1.0-4 dated 2016-03-24
ChangeLog | 6 ++++++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 ++- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.9.2 dated 2016-03-02 and 1.9.3 dated 2016-03-24
DESCRIPTION | 12 MD5 | 137 - NAMESPACE | 3 NEWS | 21 NEWS.md | 32 R/helpfunctions.R | 52 R/sjPlotAncovaLSMeans.R | 1248 ++++++++-------- R/sjPlotAnova.R | 650 ++++---- R/sjPlotClusterAnalysis.R | 1792 +++++++++++------------ R/sjPlotCorr.R | 712 ++++----- R/sjPlotFrequencies.R | 1568 ++++++++++---------- R/sjPlotGLME.R | 182 +- R/sjPlotGroupFrequencies.R | 11 R/sjPlotGroupPropTable.R | 525 +++--- R/sjPlotInteractions.R | 162 +- R/sjPlotLikert.R | 1322 ++++++++--------- R/sjPlotLinreg.R | 3080 ++++++++++++++++++++-------------------- R/sjPlotLinregMultiple.R | 927 +++++------- R/sjPlotOdds.R | 2073 +++++++++++++------------- R/sjPlotOddsMultiple.R | 43 R/sjPlotPCA.R | 940 ++++++------ R/sjPlotPearsonsChi2Test.R | 290 +-- R/sjPlotPolynomials.R | 580 +++---- R/sjPlotPropTable.R | 1042 ++++++------- R/sjPlotScatter.R | 754 ++++----- R/sjPlotSetTheme.R | 1 R/sjPlotStackFrequencies.R | 30 R/sjTabCorr.R | 1020 ++++++------- R/sjTabDataFrame.R | 6 R/sjTabFrequencies.R | 11 R/sjTabGrpmean.R | 432 ++--- R/sjTabItemAnalysis.R | 808 +++++----- R/sjTabLinReg.R | 192 ++ R/sjTabMannWhitney.R | 172 +- R/sjTabOdds.R | 216 ++ R/sjTabPCA.R | 1188 +++++++-------- R/sjTabPropTable.R | 1162 +++++++-------- R/sjTabSPSS.R | 828 +++++----- R/sjTabStackFrq.R | 1032 ++++++------- R/zzz.R | 12 README.md | 84 - build |only man/sjPlot-package.Rd | 4 man/sjp.glm.Rd | 11 man/sjp.glmer.Rd | 46 man/sjp.glmm.Rd | 21 man/sjp.grpfrq.Rd | 2 man/sjp.int.Rd | 25 man/sjp.likert.Rd | 4 man/sjp.lm.Rd | 3 man/sjp.lmer.Rd | 19 man/sjp.lmm.Rd | 29 man/sjp.xtab.Rd | 2 man/sjt.df.Rd | 4 man/sjt.frq.Rd | 7 man/sjt.glm.Rd | 18 man/sjt.glmer.Rd | 28 man/sjt.itemanalysis.Rd | 4 man/sjt.lm.Rd | 15 man/sjt.lmer.Rd | 30 man/sjt.stackfrq.Rd | 4 man/sjt.xtab.Rd | 4 tests/testthat.R | 12 tests/testthat/test_sjpfrq.R | 290 +-- tests/testthat/test_sjpgrpfrq.R | 50 tests/testthat/test_sjpint.R | 8 tests/testthat/test_sjplikert.R | 148 - tests/testthat/test_sjtglm.R | 358 ++-- tests/testthat/test_sjtlm.R | 466 +++--- tests/testthat/test_sjtxtab.R | 198 +- 70 files changed, 13800 insertions(+), 13362 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/),
Speros Kokenes [aut, cph] (d3-lasso-plugin library,
https://github.com/skokenes/D3-Lasso-Plugin)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.6.1 dated 2016-02-29 and 0.6.2 dated 2016-03-24
DESCRIPTION | 8 +-- MD5 | 14 ++--- NEWS | 9 +++ R/scatterD3.R | 6 ++ build/vignette.rds |binary inst/doc/introduction.html | 62 ++++++++++++------------- inst/htmlwidgets/lib/d3-lasso-plugin/lasso.css | 4 - inst/htmlwidgets/scatterD3.js | 4 + 8 files changed, 61 insertions(+), 46 deletions(-)
Title: Moving-Window Add-on for 'plyr'
Description: Apply a function in a moving window, then
combine the results in a data frame.
Author: "Alexandre Genin <alex@lecairn.org> [aut, cre]"
Maintainer: Alexandre Genin <alex@lecairn.org>
Diff between rollply versions 0.4.2 dated 2015-09-21 and 0.5.0 dated 2016-03-24
rollply-0.4.2/rollply/vignettes/rollply_intro.html |only rollply-0.5.0/rollply/DESCRIPTION | 20 +- rollply-0.5.0/rollply/MD5 | 40 ++-- rollply-0.5.0/rollply/NAMESPACE | 2 rollply-0.5.0/rollply/NEWS |only rollply-0.5.0/rollply/R/RcppExports.R | 4 rollply-0.5.0/rollply/R/build_grid_ahull_crop.R | 38 ++-- rollply-0.5.0/rollply/R/build_grid_ahull_fill.R | 132 +++++++++------ rollply-0.5.0/rollply/R/meadow.R |only rollply-0.5.0/rollply/R/rollply.R | 173 ++++++++++++-------- rollply-0.5.0/rollply/README.md |only rollply-0.5.0/rollply/build |only rollply-0.5.0/rollply/data/meadow.rda |binary rollply-0.5.0/rollply/inst |only rollply-0.5.0/rollply/man/build_grid_ahull_crop.Rd | 32 ++- rollply-0.5.0/rollply/man/build_grid_ahull_fill.Rd | 56 ++++-- rollply-0.5.0/rollply/man/build_grid_identical.Rd | 14 - rollply-0.5.0/rollply/man/build_grid_squaretile.Rd | 12 - rollply-0.5.0/rollply/man/meadow.Rd |only rollply-0.5.0/rollply/man/rollply.Rd | 132 ++++++++++----- rollply-0.5.0/rollply/src/RcppExports.cpp | 13 + rollply-0.5.0/rollply/src/inahull_cpp.cpp |only rollply-0.5.0/rollply/tests/testthat/test_grids.R | 4 rollply-0.5.0/rollply/tests/testthat/test_inahull.R |only rollply-0.5.0/rollply/vignettes/rollply.Rmd |only 25 files changed, 437 insertions(+), 235 deletions(-)
Title: Access and Plot CanVec and CanVec+ Data for Rapid Basemap
Creation in Canada
Description: Provides an interface to the National Topographic System (NTS),
which is the way in which a number of freely available Canadian datasets are
organized. CanVec and CanVec+ datasets, which include all data used to create
Canadian topographic maps, are two such datasets that are useful in creating
vector-based maps for locations across Canada. This packages searches CanVec
data by location, plots it using pretty defaults, and exports it to human-
readable shapefiles for use in another GIS.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rcanvec versions 0.1.4 dated 2016-01-13 and 0.1.6 dated 2016-03-24
DESCRIPTION | 23 ++++++++++--------- MD5 | 50 +++++++++++++++++++++---------------------- NAMESPACE | 4 --- R/canvec.R | 12 +++++----- README.md | 12 ++++++---- man/canvec.cachedir.Rd | 2 - man/canvec.cleanup.Rd | 2 - man/canvec.defaultoptions.Rd | 2 - man/canvec.download.Rd | 3 +- man/canvec.export.Rd | 15 +++++++----- man/canvec.findlayer.Rd | 6 ++--- man/canvec.load.Rd | 3 +- man/canvec.loadfromdir.Rd | 2 - man/canvec.plot.Rd | 2 - man/canvec.qplot.Rd | 17 +++++++------- man/canvec.url.Rd | 2 - man/canvec_layers.Rd | 2 - man/nts.Rd | 3 +- man/nts.SCALE250K.Rd | 9 ++++--- man/nts.SCALE50K.Rd | 9 ++++--- man/nts.SCALESERIES.Rd | 5 +--- man/nts.bbox.Rd | 3 +- man/nts.bybbox.Rd | 2 - man/nts.idat.Rd | 4 +-- man/ntsstring.Rd | 5 ++-- man/rcanvec-package.Rd | 2 - 26 files changed, 107 insertions(+), 94 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.7-3 dated 2016-03-01 and 1.8-0 dated 2016-03-24
DESCRIPTION | 8 - MD5 | 42 ++--- R/GoogleMapsPlot.R | 2 R/TaylorDiagram.R | 3 R/calendarPlot.R | 254 +++++++++++++++++--------------- R/checkPrep.R | 17 +- R/cutData.R | 412 ++++++++++++++++++++++++++-------------------------- R/polarPlot.R | 162 +++++++++++++++++--- R/quickText.R | 4 R/scatterPlot.R | 44 ++++- R/smoothTrend.R | 2 R/timeProp.R | 13 - R/trajCluster.R | 4 R/utilities.R | 18 ++ R/windRose.R | 6 README.md | 3 data/mydata.rda |binary man/calendarPlot.Rd | 226 +++++++++++++++------------- man/cutData.Rd | 68 +++----- man/polarPlot.Rd | 51 +++--- man/timeProp.Rd | 7 man/trajCluster.Rd | 4 22 files changed, 766 insertions(+), 584 deletions(-)
Title: Wald Test of Nonlinear Restrictions and Nonlinear CI
Description: Wald Test for nonlinear restrictions on model parameters and confidence
intervals for nonlinear functions of parameters using delta-method. Applicable
after ANY model, provided parameters estimates and their covariance matrix are
available.
Author: Oleh Komashko
Maintainer: Oleh Komashko <oleg_komashko@ukr.net>
Diff between nlWaldTest versions 1.0.1 dated 2014-09-18 and 1.1.3 dated 2016-03-24
nlWaldTest-1.0.1/nlWaldTest/R/nlWald25.R |only nlWaldTest-1.1.3/nlWaldTest/DESCRIPTION | 25 ++- nlWaldTest-1.1.3/nlWaldTest/MD5 | 14 +- nlWaldTest-1.1.3/nlWaldTest/NAMESPACE | 4 nlWaldTest-1.1.3/nlWaldTest/NEWS |only nlWaldTest-1.1.3/nlWaldTest/R/nlConfint.R |only nlWaldTest-1.1.3/nlWaldTest/R/nlWaldTest-internal.R |only nlWaldTest-1.1.3/nlWaldTest/R/nlWaldtest.R |only nlWaldTest-1.1.3/nlWaldTest/man/CESdata.Rd | 2 nlWaldTest-1.1.3/nlWaldTest/man/nlConfint.Rd |only nlWaldTest-1.1.3/nlWaldTest/man/nlWaldtest.Rd | 127 ++++++++++---------- 11 files changed, 92 insertions(+), 80 deletions(-)
Title: Computes Pdf, Cdf, Quantile and Random Numbers, Measures of
Inference for 19 General Families of Distributions
Description: Computes the probability density function, cumulative distribution function, quantile function, random numbers and measures of inference for the following general families of distributions (each family defined in terms of an arbitrary cdf G): Marshall Olkin G distributions, exponentiated G distributions, beta G distributions, gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions, beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions, exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions, and exponentiated exponential Poisson G distributions.
Author: Saralees Nadarajah, Ricardo Rocha
Maintainer: Saralees Nadarajah <Saralees.Nadarajah@manchester.ac.uk>
Diff between Newdistns versions 2.0 dated 2015-03-04 and 2.1 dated 2016-03-24
DESCRIPTION | 8 ++++---- MD5 | 45 +++++++++++++++++++++++---------------------- NAMESPACE | 6 +++++- inst |only man/Newdistns-package.Rd | 6 +++--- man/beg.Rd | 2 +- man/betaexpg.Rd | 2 +- man/betag.Rd | 2 +- man/eepg.Rd | 2 +- man/eg.Rd | 2 +- man/expg.Rd | 2 +- man/expkumg.Rd | 2 +- man/gammag.Rd | 2 +- man/gammag1.Rd | 2 +- man/gammag2.Rd | 2 +- man/gbg.Rd | 2 +- man/gepg.Rd | 2 +- man/kumg.Rd | 2 +- man/loggammag1.Rd | 2 +- man/loggammag2.Rd | 2 +- man/mbetag.Rd | 2 +- man/mog.Rd | 2 +- man/tessg.Rd | 2 +- man/weibullg.Rd | 2 +- 24 files changed, 54 insertions(+), 49 deletions(-)
Title: Machine Coded Genetic Algorithms for Real-Valued Optimization
Problems
Description: Machine coded genetic algorithm (MCGA) is a fast tool for
real-valued optimization problems. It uses the byte
representation of variables rather than real-values. It
performs the classical crossover operations (uniform) on these
byte representations. Mutation operator is also similar to
classical mutation operator, which is to say, it changes a
randomly selected byte value of a chromosome by +1 or -1 with
probability 1/2. In MCGAs there is no need for
encoding-decoding process and the classical operators are
directly applicable on real-values. It is fast and can handle a
wide range of a search space with high precision. Using a
256-unary alphabet is the main disadvantage of this algorithm
but a moderate size population is convenient for many problems.
Package also includes multi_mcga function for multi objective
optimization problems. This function sorts the chromosomes
using their ranks calculated from the non-dominated sorting
algorithm.
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between mcga versions 2.0.9 dated 2014-03-25 and 3.0 dated 2016-03-24
DESCRIPTION | 52 +++++++++++++++------------- MD5 | 49 +++++++++++++++++++++++--- NAMESPACE | 13 ++++--- R/RcppExports.R |only R/oplibrary.R |only R/zzz.r | 9 ++++ inst |only man/ByteCodeMutation.Rd |only man/ByteCodeMutationUsingDoubles.Rd |only man/ByteCodeMutationUsingDoublesRandom.Rd |only man/ByteVectorToDoubles.Rd |only man/BytesToDouble.Rd |only man/DoubleToBytes.Rd |only man/DoubleVectorToBytes.Rd |only man/EnsureBounds.Rd |only man/MaxDouble.Rd |only man/OnePointCrossOver.Rd |only man/OnePointCrossOverOnDoublesUsingBytes.Rd |only man/SizeOfDouble.Rd |only man/SizeOfInt.Rd |only man/SizeOfLong.Rd |only man/TwoPointCrossOver.Rd |only man/TwoPointCrossOverOnDoublesUsingBytes.Rd |only man/UniformCrossOver.Rd |only man/UniformCrossOverOnDoublesUsingBytes.Rd |only man/arithmetic_crossover.Rd |only man/blx_crossover.Rd |only man/byte_crossover.Rd |only man/byte_crossover_1p.Rd |only man/byte_crossover_2p.Rd |only man/byte_mutation.Rd |only man/byte_mutation_dynamic.Rd |only man/byte_mutation_random.Rd |only man/byte_mutation_random_dynamic.Rd |only man/flat_crossover.Rd |only man/linear_crossover.Rd |only man/mcga.Rd | 2 - man/mcga2.Rd |only man/sbx_crossover.Rd |only man/unfair_average_crossover.Rd |only src/RcppExports.cpp |only src/mcga.c | 35 ++++++++++++------ src/multi_mcga.c | 35 ++++++++++++------ src/typeconversations.cpp |only 44 files changed, 135 insertions(+), 60 deletions(-)
Title: Kolmogorov-Zurbenko Adaptive Filters
Description: Time Series Analysis including break detection, spectral analysis, KZ Fourier Transforms.
Author: Brian Close <brian.close@gmail.com> and Igor Zurbenko <IZurbenko@albany.edu>
Maintainer: Brian Close <brian.close@gmail.com>
Diff between kza versions 3.2.0 dated 2016-01-29 and 4.0.0 dated 2016-03-24
kza-3.2.0/kza/cleanup |only kza-3.2.0/kza/configure |only kza-3.2.0/kza/configure.ac |only kza-3.2.0/kza/data |only kza-3.2.0/kza/man/fars.Rd |only kza-3.2.0/kza/src/Makevars.in |only kza-3.2.0/kza/src/Makevars.win |only kza-3.2.0/kza/src/build |only kza-3.2.0/kza/src/ckzft.c |only kza-3.2.0/kza/src/config.h |only kza-3.2.0/kza/src/fftw3.h |only kza-3.2.0/kza/src/kzft.c |only kza-3.2.0/kza/src/kzft.h |only kza-3.2.0/kza/src/kzp.c |only kza-3.2.0/kza/src/kztp.c |only kza-4.0.0/kza/DESCRIPTION | 8 - kza-4.0.0/kza/MD5 | 33 +--- kza-4.0.0/kza/R/kza.R | 2 kza-4.0.0/kza/R/kzft.R | 303 ++++++++++------------------------------- kza-4.0.0/kza/README | 2 kza-4.0.0/kza/man/kza.Rd | 3 kza-4.0.0/kza/man/kzft.Rd | 28 --- kza-4.0.0/kza/man/kzp.Rd | 13 - kza-4.0.0/kza/src/Rkza.c | 11 - 24 files changed, 102 insertions(+), 301 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of
variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.2.0 dated 2016-03-17 and 0.1.2.1 dated 2016-03-24
DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS.md | 6 ++- inst/doc/interplot-vignette.R | 21 ++++++++++- inst/doc/interplot-vignette.Rmd | 49 ++++++++++++++++++++++++-- inst/doc/interplot-vignette.html | 72 +++++++++++++++++++++++++++++---------- vignettes/interplot-vignette.Rmd | 5 -- 7 files changed, 134 insertions(+), 37 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 0.7 dated 2015-11-13 and 0.7.1 dated 2016-03-24
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- R/flexsurvreg.R | 70 ++++++++++++++++++++++++++--------------- R/spline.R | 8 +++- build/vignette.rds |binary inst/NEWS | 9 +++++ inst/doc/flexsurv-examples.pdf |binary inst/doc/flexsurv.pdf |binary man/flexsurvreg.Rd | 2 - tests/testthat/test_deriv.R | 53 ++++++++++++++----------------- 10 files changed, 99 insertions(+), 69 deletions(-)
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between explor versions 0.2 dated 2016-03-03 and 0.2.1 dated 2016-03-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 8 ++++++++ R/explor_PCA.R | 2 +- R/prepare_results_MCA.R | 6 ++++-- build/vignette.rds |binary inst/doc/introduction_en.html | 4 ++-- inst/doc/introduction_fr.html | 4 ++-- tests/testthat/test_prepare_results_MCA.R | 2 +- 9 files changed, 30 insertions(+), 20 deletions(-)
Title: Analysis of Discretely Observed Linear
Birth-and-Death(-and-Immigration) Markov Chains
Description: Provides Frequentist (EM) and Bayesian (MCMC) Methods for Inference of Birth-Death-Immigration Markov Chains.
Author: Charles Doss, Vladimir Minin, Marc Suchard
Maintainer: Charles Doss <cdoss@umn.edu>
Diff between DOBAD versions 1.0.4 dated 2014-12-01 and 1.0.5 dated 2016-03-24
DOBAD-1.0.4/DOBAD/README |only DOBAD-1.0.4/DOBAD/vignettes/Makefile |only DOBAD-1.0.5/DOBAD/DESCRIPTION | 16 ++++++------ DOBAD-1.0.5/DOBAD/MD5 | 20 +++++++++------ DOBAD-1.0.5/DOBAD/NAMESPACE | 4 +++ DOBAD-1.0.5/DOBAD/build |only DOBAD-1.0.5/DOBAD/inst/doc/BD_EM.Rnw |only DOBAD-1.0.5/DOBAD/inst/doc/BD_EM.pdf |binary DOBAD-1.0.5/DOBAD/inst/doc/BD_EM_wImmig.R |only DOBAD-1.0.5/DOBAD/inst/doc/BD_EM_wImmig.Rnw |only DOBAD-1.0.5/DOBAD/inst/doc/BD_MCMC.R |only DOBAD-1.0.5/DOBAD/inst/doc/BD_MCMC.Rnw |only DOBAD-1.0.5/DOBAD/inst/doc/BD_MCMC.pdf |binary DOBAD-1.0.5/DOBAD/inst/doc/sim_condBD.R |only DOBAD-1.0.5/DOBAD/inst/doc/sim_condBD.Rnw |only DOBAD-1.0.5/DOBAD/vignettes/BD_EM.Rnw | 37 ++++++++++++++-------------- 16 files changed, 44 insertions(+), 33 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include combinatorial search (all possible subset regression), productivity evaluation using distance measures: DDF (directional distance function), DEA (data envelopment analysis), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.0 dated 2016-02-06 and 2.1 dated 2016-03-24
DESCRIPTION | 6 - MD5 | 60 +++++----- NEWS | 13 ++ R/DJL-internal.R | 251 ++++++++++++++++++++++------------------------ R/dm.ddf.R | 3 R/dm.dea.R | 4 R/dm.sbm.R | 1 R/dm.sf.R | 3 R/map.soa.ddf.R | 1 R/map.soa.dea.R | 1 R/map.soa.sbm.R | 1 R/map.soa.sf.R | 1 R/roc.dea.R | 7 - R/roc.sf.R | 3 R/target.arrival.dea.R | 1 R/target.arrival.sf.R | 3 R/target.spec.dea.R | 25 +++- man/dm.ddf.Rd | 10 - man/dm.dea.Rd | 10 - man/dm.sbm.Rd | 8 - man/dm.sf.Rd | 12 +- man/ma.aps.reg.Rd | 10 - man/map.soa.ddf.Rd | 16 +- man/map.soa.dea.Rd | 16 +- man/map.soa.sbm.Rd | 12 +- man/map.soa.sf.Rd | 18 +-- man/roc.dea.Rd | 30 ++--- man/roc.sf.Rd | 18 +-- man/target.arrival.dea.Rd | 14 +- man/target.arrival.sf.Rd | 18 +-- man/target.spec.dea.Rd | 28 ++--- 31 files changed, 323 insertions(+), 281 deletions(-)
Title: Exploratory Chemometrics for Spectroscopy
Description: A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.
Author: Bryan A. Hanson DePauw University, Greencastle Indiana USA
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec versions 4.2.8 dated 2016-01-26 and 4.3.17 dated 2016-03-24
DESCRIPTION | 10 ++++----- MD5 | 38 ++++++++++++++++++++---------------- NAMESPACE | 6 ++--- NEWS | 13 ++++++++++++ R/baselineSpectra.R | 47 ++++++++++++++++++++++++++++++++++++++++----- R/check4Gaps.R | 2 - R/files2SpectraObject.R | 10 ++++----- R/normSpectra.R | 11 ++++++++++ R/plotScores.R | 2 - R/plotSpectraDist.R |only R/sgfSpectra.R |only R/sumSpectra.R | 23 +++++++++++++--------- R/surveySpectra.R | 26 +++++++++++++++++------- build/vignette.rds |binary inst/doc/ChemoSpec.Rnw | 13 ++++++------ inst/doc/ChemoSpec.pdf |binary man/baselineSpectra.Rd | 9 +++++--- man/normSpectra.Rd | 4 +-- man/plotSpectraDist.Rd |only man/sgfSpectra.Rd |only vignettes/ChemoSpec.Rnw | 13 ++++++------ vignettes/chemometrics.bib | 2 - 22 files changed, 157 insertions(+), 72 deletions(-)
Title: Calculate and Analyze Blau Status for Measuring Social Distance
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to organizations. Relational (network) data may be incorporated for additional analyses.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <cwang3@nd.edu>
Diff between Blaunet versions 2.0.1 dated 2015-12-27 and 2.0.2 dated 2016-03-24
Blaunet-2.0.1/Blaunet/inst/scripts/diagnostic.R |only Blaunet-2.0.2/Blaunet/DESCRIPTION | 6 +- Blaunet-2.0.2/Blaunet/MD5 | 18 +++--- Blaunet-2.0.2/Blaunet/data/BSANet.rda |binary Blaunet-2.0.2/Blaunet/inst/scripts/blaububbles.R | 69 +++++++++++++++++------ Blaunet-2.0.2/Blaunet/inst/scripts/blaunetgui.R | 10 +-- Blaunet-2.0.2/Blaunet/inst/scripts/command.pdf |binary Blaunet-2.0.2/Blaunet/inst/scripts/dynamics.R | 28 ++++----- Blaunet-2.0.2/Blaunet/inst/scripts/graphic.pdf |binary Blaunet-2.0.2/Blaunet/inst/scripts/nicheplot.R |only Blaunet-2.0.2/Blaunet/man/blaunet-package.Rd | 4 - 11 files changed, 84 insertions(+), 51 deletions(-)
Title: IRT Item-Person Map with 'ConQuest' Integration
Description: A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The 'WrightMap' package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. 'TAM', 'mirt', 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.), 'WrightMap' features special integration with 'ConQuest' to facilitate reading and plotting its output directly.The 'wrightMap' function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The 'CQmodel' function reads output files created using 'ConQuest' software and creates a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The 'wrightMap' function can take a 'CQmodel' object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Author: David Torres Irribarra & Rebecca Freund
Maintainer: David Torres Irribarra <dti@berkeley.edu>
Diff between WrightMap versions 1.2 dated 2016-03-18 and 1.2.1 dated 2016-03-23
DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NEWS | 2 ++ R/CQmodel.R | 46 +++++++++++++++------------------------------- R/itemClassic.R | 13 ++++++++----- R/itemHist.R | 12 ++++++------ R/itemModern.R | 9 +++++---- R/personDens.R | 13 +++++++------ R/personHist.R | 33 +++++++++++++-------------------- R/plotCI.R | 2 +- R/wrightMap.R | 32 ++++++++++++++++++++------------ README.md | 6 ++---- inst/extdata/ex7a.eap |only inst/extdata/ex7a.shw |only man/WrightMap-package.Rd | 3 +++ man/plotCI.Rd | 2 +- man/wrightMap.Rd | 1 + 17 files changed, 105 insertions(+), 109 deletions(-)
Title: Variance Component Analysis
Description: ANOVA-type estimation (prediction) of random effects in linear mixed models is implemented, following
Searle et al. (1991, ANOVA for unbalanced data). For better performance the SWEEP-Operator is implemented
for generating the ANOVA Type-1 error sum of squares. Restricted Maximum Likelihood (REML) estimation is
also available making use of the 'lme4' package.
The primary objective of this package is to perform Variance Component Analyses (VCA).
This is a special type of analysis frequently used in verifying the precision performance of diagnostics.
The Satterthwaite approximation of the total degrees of freedom and for individual variance components is
implemented for models fitted by ANOVA as well as for models fitted by REML. These are used in the Chi-Squared
tests against a claimed value, and in the respective confidence intervals.
Satterthwaite's approximation of denominator degrees of freedom in t-/F-tests of fixed effects are also
available. For models fitted by (REML) the variance-covariance matrix of the variance components is approximated
by the method pointed out in Giesbrecht & Burns (1985), which is required for applying the Satterthwaite approximation
of the degrees of freedom. For models fitted by ANOVA the method pointed out in Searle et al. (1991) employing quadratic
forms generating ANOVA sum of squares is also available.
There are several functions for extracting, random effects, fixed effects, variance-covariance
matrices of random and fixed effects. Residuals (marginal, conditional) can be extracted as raw, standardized
and studentized residuals.
Additionally, plotting methods for residuals and random effects and a variability chart are available. The latter
is useful for visualizing the variability in sub-classes emerging from the experimental design.
Author: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.2.1 dated 2015-11-24 and 1.3 dated 2016-03-23
DESCRIPTION | 27 MD5 | 66 NAMESPACE | 6 R/plot.R | 990 +++++----- R/vca.R | 3346 +++++++++++++++++++++++++----------- data/ReproData1.RData |only inst/ChangeLog.txt | 23 inst/UnitTests/runit.VCAinference.R | 204 +- inst/UnitTests/runit.anovaMM.R | 2 inst/UnitTests/runit.anovaVCA.R | 360 +-- inst/UnitTests/runit.misc.R | 315 +++ inst/UnitTests/runit.remlMM.R |only inst/UnitTests/runit.remlVCA.R |only man/ReproData1.Rd |only man/Solve.Rd | 4 man/Trace.Rd | 4 man/VCA-Package.Rd | 54 man/VCAinference.Rd | 15 man/anovaDF.Rd | 24 man/anovaMM.Rd | 10 man/anovaVCA.Rd | 16 man/check4MKL.Rd |only man/coef.VCA.Rd | 4 man/getGB.Rd |only man/getV.Rd | 4 man/lmerG.Rd |only man/lmerMatrices.Rd |only man/lmerSummary.Rd |only man/load_if_installed.Rd |only man/lsmMat.Rd | 6 man/ranef.VCA.Rd | 4 man/remlMM.Rd |only man/remlVCA.Rd |only man/residuals.VCA.Rd | 4 man/test.fixef.Rd | 40 man/test.lsmeans.Rd | 37 man/varPlot.Rd | 3 man/vcov.VCA.Rd | 4 man/vcovFixed.Rd | 8 man/vcovVC.Rd | 12 40 files changed, 3779 insertions(+), 1813 deletions(-)
Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of SQL and
SQL/MR functions running in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre],
Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.4.2 dated 2016-01-22 and 0.5.1 dated 2016-03-23
DESCRIPTION | 17 - MD5 | 47 ++-- NAMESPACE | 11 + NEWS | 32 +++ R/computeGraph.R |only R/computeTfIdf.R | 11 - R/maps.R | 2 R/misc.R | 58 +++++ R/showData.R | 2 R/showGraph.R |only R/toaster.R | 3 R/utils.R | 295 +++++++++++++++++++--------- man/computeEgoGraph.Rd |only man/computeGraph.Rd |only man/computeGraphHistogram.Rd |only man/computeGraphMetric.Rd |only man/createMap.Rd | 3 man/getNullCounts.Rd | 16 + man/getTableSummary.Rd | 3 man/getWindowFunction.Rd |only man/isTable.Rd | 23 +- man/makeFromClause.Rd |only man/showData.Rd | 2 man/showGraph.Rd |only man/toaGraph.Rd |only tests/testthat/test-computeEgoGraph.R |only tests/testthat/test-computeGraph.R |only tests/testthat/test-computeGraphHistogram.R |only tests/testthat/test-computeGraphMetric.R |only tests/testthat/test-computeHistogram.R | 3 tests/testthat/test-showGraph.R |only tests/testthat/test-utils.R | 39 +++ 32 files changed, 430 insertions(+), 137 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions
for searching for bird observations by geographic location (latitude,
longitude), eBird hotspots, location identifiers, by notable sightings, by
region, and by taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut],
Andy Teucher [aut],
Sebastian Pardo [aut, cre]
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 0.2 dated 2015-07-09 and 0.3.0 dated 2016-03-23
DESCRIPTION | 25 +++---- LICENSE | 2 MD5 | 43 ++++++------- NAMESPACE | 2 NEWS.md |only R/ebirdregioncheck.R | 7 -- R/getlatlng.R | 4 - R/nearestobs.R | 4 - R/zzz.R | 18 ++--- README.md | 125 ++++++++++++++++++++------------------- build/vignette.rds |binary man/ebirdfreq.Rd | 33 ++++------ man/ebirdgeo.Rd | 4 - man/ebirdhotspot.Rd | 2 man/ebirdloc.Rd | 22 +++--- man/ebirdnotable.Rd | 2 man/ebirdregion.Rd | 2 man/ebirdregioncheck.Rd | 2 man/ebirdtaxonomy.Rd | 16 ++-- man/getlatlng.Rd | 2 man/nearestobs.Rd | 6 - man/rebird-package.Rd | 8 +- tests/testthat/test-nearestobs.R | 4 - 23 files changed, 169 insertions(+), 164 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.3.0 dated 2016-02-03 and 0.3.3 dated 2016-03-23
DESCRIPTION | 8 MD5 | 10 - R/mdmr.R | 388 +++++++++++++++++++++++++------------------- inst/doc/mdmr-vignette.html | 231 ++++++++++++++------------ man/delta.Rd | 31 ++- man/summary.mdmr.Rd | 2 6 files changed, 391 insertions(+), 279 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors and for
the comparison of predictive errors between models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.5 dated 2016-02-12 and 0.1.6 dated 2016-03-23
DESCRIPTION | 16 ++++++++-------- MD5 | 34 +++++++++++++++++----------------- R/compare.R | 11 +++++------ R/extract_log_lik.R | 5 +++-- R/helpers.R | 31 +++++++++++++++++++++---------- R/loo.R | 6 ++++-- R/print.R | 15 +++++++++------ R/psislw.R | 9 ++++++--- R/waic.R | 6 ++++-- R/zzz.R | 8 ++++---- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/Example.R | 5 +++-- inst/doc/Example.Rmd | 5 +++-- inst/doc/Example.html | 18 ++++++++++-------- man/compare.Rd | 4 ++-- tests/testthat/test_compare.R | 15 ++++++--------- vignettes/Example.Rmd | 5 +++-- 18 files changed, 110 insertions(+), 87 deletions(-)
Title: Functions for Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models.
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@al.umces.edu>
Diff between gdm versions 1.1.7 dated 2016-01-09 and 1.2.0 dated 2016-03-23
gdm-1.1.7/gdm/vignettes/gdmVignette.Rmd |only gdm-1.1.7/gdm/vignettes/gdmVignette.bib |only gdm-1.2.0/gdm/DESCRIPTION | 12 gdm-1.2.0/gdm/MD5 | 25 gdm-1.2.0/gdm/NAMESPACE | 12 gdm-1.2.0/gdm/R/GDM_Table_Funcs.R | 942 +++++++++++++++++++++++---- gdm-1.2.0/gdm/build/vignette.rds |binary gdm-1.2.0/gdm/data/gdm.RData |binary gdm-1.2.0/gdm/inst/doc/gdmVignette.pdf |binary gdm-1.2.0/gdm/man/formatsitepair.Rd | 37 - gdm-1.2.0/gdm/man/gd.varImp.Rd |only gdm-1.2.0/gdm/man/permutateSitePair.Rd |only gdm-1.2.0/gdm/man/permutateVarSitePair.Rd |only gdm-1.2.0/gdm/man/plot.gdm.Rd | 130 +-- gdm-1.2.0/gdm/man/plotUncertainty.Rd |only gdm-1.2.0/gdm/man/removeSitesFromSitePair.Rd |only gdm-1.2.0/gdm/src/Gdmlib.cpp | 44 - 17 files changed, 954 insertions(+), 248 deletions(-)
Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to identify
combinatorial effects of multiple treatments and/or perturbations on pathways
and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics
data.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between directPA versions 1.2 dated 2015-06-18 and 1.3 dated 2016-03-23
directPA-1.2/directPA/R/directEnrichPlot2d.R |only directPA-1.2/directPA/man/directEnrichPlot2d.Rd |only directPA-1.3/directPA/DESCRIPTION | 14 ++- directPA-1.3/directPA/MD5 | 27 +++--- directPA-1.3/directPA/NAMESPACE | 8 +- directPA-1.3/directPA/R/directPA.R | 95 ++++++++++-------------- directPA-1.3/directPA/R/geneStats.R | 2 directPA-1.3/directPA/R/kinasePA.R |only directPA-1.3/directPA/R/perturbPlot2d.R |only directPA-1.3/directPA/README.md |only directPA-1.3/directPA/man/directExplorer2d.Rd | 15 ++- directPA-1.3/directPA/man/directPA.Rd | 82 +++++++------------- directPA-1.3/directPA/man/geneStats.Rd | 11 +- directPA-1.3/directPA/man/kinasePA.Rd |only directPA-1.3/directPA/man/pathwayStats.Rd | 13 +-- directPA-1.3/directPA/man/perturbPlot2d.Rd |only directPA-1.3/directPA/man/rotate2d.Rd | 3 directPA-1.3/directPA/man/rotate3d.Rd | 3 18 files changed, 128 insertions(+), 145 deletions(-)
Title: Three-Way Data Analysis Through Densities
Description: The three-way data consists of a set of variables measured on several groups of individuals. To each group is associated an estimated probability density function. The package provides functional methods (principal component analysis, multidimensional scaling, discriminant analysis...) for such probability densities.
Author: Rachid Boumaza, Pierre Santagostini, Smail Yousfi, Sabine Demotes-Mainard
Maintainer: Rachid Boumaza <rachid.boumaza@agrocampus-ouest.fr>
Diff between dad versions 1.0.2 dated 2015-11-05 and 1.1.0 dated 2016-03-23
DESCRIPTION | 10 +- MD5 | 34 ++++--- R/append.df2fh.R |only R/fdiscd.misclass.R | 7 - R/fdiscd.predict.R | 7 - R/folderh.R | 204 +++++++++++++++++++++++++++++++---------------- R/folderh2df.R | 2 R/folderh2folder.R | 4 R/plot.fmdsd.R | 2 R/plot.fpcad.R | 4 data/roseflowers.rda |binary data/roseleaves.rda |only man/append.df2folderh.Rd |only man/folderh.Rd | 78 ++++++++--------- man/folderh2df.Rd | 8 - man/folderh2folder.Rd | 8 - man/plot.fmdsd.Rd | 5 - man/plot.fpcad.Rd | 5 - man/roseflowers.Rd | 2 man/roseleaves.Rd |only 20 files changed, 229 insertions(+), 151 deletions(-)
Title: Interface to Bold Systems 'API'
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic 'barcode' data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.3.0 dated 2015-09-16 and 0.3.4 dated 2016-03-23
bold-0.3.0/bold/NEWS |only bold-0.3.4/bold/DESCRIPTION | 17 +++---- bold-0.3.4/bold/LICENSE | 2 bold-0.3.4/bold/MD5 | 54 +++++++++++------------ bold-0.3.4/bold/NAMESPACE | 15 +++--- bold-0.3.4/bold/NEWS.md |only bold-0.3.4/bold/R/bold-package.R | 2 bold-0.3.4/bold/R/bold_identify.R | 33 +++++++------- bold-0.3.4/bold/R/bold_seq.R | 6 +- bold-0.3.4/bold/R/bold_seqspec.R | 50 +++++++++++++++------ bold-0.3.4/bold/R/bold_specimens.R | 12 +++-- bold-0.3.4/bold/R/bold_tax_id.R | 19 +++++--- bold-0.3.4/bold/R/bold_tax_name.R | 10 ++-- bold-0.3.4/bold/R/bold_trace.R | 24 +++++++--- bold-0.3.4/bold/R/zzz.R | 47 +++++++++++--------- bold-0.3.4/bold/README.md | 64 +++++++++++++++------------- bold-0.3.4/bold/build/vignette.rds |binary bold-0.3.4/bold/inst/doc/bold_vignette.Rmd | 2 bold-0.3.4/bold/inst/doc/bold_vignette.html | 2 bold-0.3.4/bold/man/bold-package.Rd | 12 ++--- bold-0.3.4/bold/man/bold_identify.Rd | 2 bold-0.3.4/bold/man/bold_seq.Rd | 14 +++--- bold-0.3.4/bold/man/bold_seqspec.Rd | 25 +++++++--- bold-0.3.4/bold/man/bold_specimens.Rd | 16 +++---- bold-0.3.4/bold/man/bold_tax_id.Rd | 2 bold-0.3.4/bold/man/bold_tax_name.Rd | 2 bold-0.3.4/bold/man/bold_trace.Rd | 32 +++++++------- bold-0.3.4/bold/man/sequences.Rd | 6 +- bold-0.3.4/bold/vignettes/bold_vignette.Rmd | 2 29 files changed, 272 insertions(+), 200 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-10 dated 2016-03-14 and 5.0-11 dated 2016-03-22
DESCRIPTION | 8 +++--- MD5 | 8 +++--- R/create-json.R | 11 +++++++- R/model-zelig.R | 7 +++-- inst/JSON/zelig5models.json | 56 ++++++++++++++++++++++++++++++++------------ 5 files changed, 63 insertions(+), 27 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.0.3 dated 2015-07-27 and 1.0.4 dated 2016-03-22
sitar-1.0.3/sitar/R/lms2z.R |only sitar-1.0.3/sitar/man/lms2z.Rd |only sitar-1.0.4/sitar/DESCRIPTION | 8 - sitar-1.0.4/sitar/MD5 | 34 ++++---- sitar-1.0.4/sitar/NEWS | 19 ++++ sitar-1.0.4/sitar/R/LMS2z.R |only sitar-1.0.4/sitar/R/ifun.R | 20 ++-- sitar-1.0.4/sitar/R/plot.sitar.R | 7 + sitar-1.0.4/sitar/R/predict.sitar.R | 7 + sitar-1.0.4/sitar/R/sitar.R | 28 +++--- sitar-1.0.4/sitar/R/update.sitar.R | 148 +++++++++++++++--------------------- sitar-1.0.4/sitar/man/LMS2z.Rd |only sitar-1.0.4/sitar/man/LMSfit.Rd | 6 - sitar-1.0.4/sitar/man/bupdate.Rd | 4 sitar-1.0.4/sitar/man/cLMS.Rd | 18 ++-- sitar-1.0.4/sitar/man/ifun.Rd | 27 +++--- sitar-1.0.4/sitar/man/sitar.Rd | 4 sitar-1.0.4/sitar/man/uk90.Rd | 5 - sitar-1.0.4/sitar/man/ukwhopt.Rd | 3 sitar-1.0.4/sitar/man/who06.Rd | 2 20 files changed, 179 insertions(+), 161 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.7 dated 2016-02-21 and 0.8 dated 2016-03-22
SimDesign-0.7/SimDesign/R/SimDesign_functions.R |only SimDesign-0.7/SimDesign/man/SimDesign_functions.Rd |only SimDesign-0.7/SimDesign/man/analyse.Rd |only SimDesign-0.7/SimDesign/man/generate.Rd |only SimDesign-0.7/SimDesign/man/summarise.Rd |only SimDesign-0.8/SimDesign/DESCRIPTION | 8 SimDesign-0.8/SimDesign/MD5 | 40 ++- SimDesign-0.8/SimDesign/NAMESPACE | 6 SimDesign-0.8/SimDesign/R/SimAnova.R |only SimDesign-0.8/SimDesign/R/SimClean.R |only SimDesign-0.8/SimDesign/R/SimDesign.R | 56 ++++ SimDesign-0.8/SimDesign/R/SimFunctions.R |only SimDesign-0.8/SimDesign/R/analysis.R | 16 - SimDesign-0.8/SimDesign/R/functions.R | 79 ++++-- SimDesign-0.8/SimDesign/R/runSimulation.R | 225 ++++++++++++------- SimDesign-0.8/SimDesign/R/summary_functions.R | 14 + SimDesign-0.8/SimDesign/build/vignette.rds |binary SimDesign-0.8/SimDesign/data |only SimDesign-0.8/SimDesign/man/Analyse.Rd |only SimDesign-0.8/SimDesign/man/BF_sim.Rd |only SimDesign-0.8/SimDesign/man/BF_sim_alternative.Rd |only SimDesign-0.8/SimDesign/man/ECR.Rd | 9 SimDesign-0.8/SimDesign/man/Generate.Rd |only SimDesign-0.8/SimDesign/man/SimAnova.Rd |only SimDesign-0.8/SimDesign/man/SimClean.Rd |only SimDesign-0.8/SimDesign/man/SimFunctions.Rd |only SimDesign-0.8/SimDesign/man/Summarise.Rd |only SimDesign-0.8/SimDesign/man/runSimulation.Rd | 202 ++++++++++------- SimDesign-0.8/SimDesign/tests/tests/test-SimDesign.R | 23 + 29 files changed, 467 insertions(+), 211 deletions(-)
Title: R Interface to Experigen
Description: Provides convenience functions to communicate with
an Experigen server. It is especially helpful with registered experiments, as
authentication with the server has to happen.
Author: Daniel Szeredi [aut, cre]
Maintainer: Daniel Szeredi <daniel@szeredi.hu>
Diff between Rexperigen versions 0.1.0 dated 2016-02-27 and 0.2.0 dated 2016-03-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/download.R | 33 ++++++++++++++++++++++++--------- tests/testthat/test-download.R | 28 ++++++++++++++++++++++------ 5 files changed, 59 insertions(+), 22 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package randomForests, written by Andy Liaw.
Author: Nicolai Meinshausen, Lukas Schiesser
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between quantregForest versions 1.1 dated 2015-09-09 and 1.2 dated 2016-03-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/predict.all.R | 4 +--- R/predict.quantregForest.R | 6 +++--- build/vignette.rds |binary man/predict.quantregForest.Rd | 5 ++++- 6 files changed, 17 insertions(+), 16 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Description: Screens and sorts phylogenetic trees in both traditional and
extended Newick format. Allows for the fast and flexible screening (within
a tree) of Exclusive clades that comprise only the target taxa and/or Non-
Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Debashish Bhattacharya [aut],
Mark Ragan [aut],
Cheong Xin Chan [aut, cph] (Original Perl implementation)
Maintainer: Timothy Stephens <timothy.stephens1@uqconnect.edu.au>
Diff between PhySortR versions 1.0.5 dated 2016-01-11 and 1.0.6 dated 2016-03-22
DESCRIPTION | 8 - MD5 | 12 +- NAMESPACE | 12 +- R/sortTrees.R | 210 +++++++++++++++++++++------------------------ man/PhySortR.Rd | 68 +++++++------- man/convert.eNewick.Rd | 52 +++++------ man/sortTrees.Rd | 228 ++++++++++++++++++++++++------------------------- 7 files changed, 290 insertions(+), 300 deletions(-)
Title: A Permutation Based Test for Biomarker Discovery in Microbiome
Data
Description: All the functions compiled in this package were created to perform permutation-based non-parametric analysis on microbiome data for biomarker discovery aims. This test executes thousands of comparisons in pairwise manner, after random shuffling of data into the different groups of study.
Author: Alfonso Benitez-Paez
Maintainer: Alfonso Benitez-Paez <abenitez@iata.csic.es>
Diff between permubiome versions 1.0 dated 2016-02-08 and 1.1 dated 2016-03-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get.data.R | 20 ++++++++++++++++++++ R/plots.R | 2 +- build/partial.rdb |binary man/get.data.Rd | 39 +++++++++++++++++++++++++++++++++++++-- man/permubiome.Rd | 2 +- man/plots.Rd | 2 +- 8 files changed, 71 insertions(+), 16 deletions(-)
Title: Customisable Images of OpenStreetMap Data
Description: Produces customisable images of OpenStreetMap (OSM) data and enables data visualisation using OSM objects.
Author: Mark Padgham [aut, cre]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmplotr versions 0.1-2 dated 2016-03-03 and 0.1-3 dated 2016-03-22
osmplotr-0.1-2/osmplotr/R/get-xylims.R |only osmplotr-0.1-2/osmplotr/R/group-osm-objects.R |only osmplotr-0.1-2/osmplotr/data/datalist |only osmplotr-0.1-2/osmplotr/man/get_xylims.Rd |only osmplotr-0.1-2/osmplotr/man/group_osm_objects.Rd |only osmplotr-0.1-3/osmplotr/DESCRIPTION | 13 - osmplotr-0.1-3/osmplotr/MD5 | 84 +++--- osmplotr-0.1-3/osmplotr/NAMESPACE | 13 - osmplotr-0.1-3/osmplotr/NEWS |only osmplotr-0.1-3/osmplotr/R/add-axes.R |only osmplotr-0.1-3/osmplotr/R/add-colourbar.R |only osmplotr-0.1-3/osmplotr/R/add-osm-groups.R |only osmplotr-0.1-3/osmplotr/R/add-osm-objects.R | 20 + osmplotr-0.1-3/osmplotr/R/add-osm-surface.R |only osmplotr-0.1-3/osmplotr/R/adjust_colours.R |only osmplotr-0.1-3/osmplotr/R/click-map.R | 4 osmplotr-0.1-3/osmplotr/R/extract-highway.R | 33 +- osmplotr-0.1-3/osmplotr/R/extract-highways.R | 15 - osmplotr-0.1-3/osmplotr/R/extract-osm-objects.R | 57 ++-- osmplotr-0.1-3/osmplotr/R/get-bbox.R |only osmplotr-0.1-3/osmplotr/R/highways2polygon.R | 4 osmplotr-0.1-3/osmplotr/R/make-osm-map.R | 32 +- osmplotr-0.1-3/osmplotr/R/osm-structures.R | 7 osmplotr-0.1-3/osmplotr/R/osmplotr.R | 68 ++++- osmplotr-0.1-3/osmplotr/R/plot-osm-basemap.R | 19 - osmplotr-0.1-3/osmplotr/build/vignette.rds |binary osmplotr-0.1-3/osmplotr/data/london.rda |binary osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.R | 23 + osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.Rmd | 23 + osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.html | 19 - osmplotr-0.1-3/osmplotr/inst/doc/making-maps.R | 148 ++++++----- osmplotr-0.1-3/osmplotr/inst/doc/making-maps.Rmd | 186 +++++++------- osmplotr-0.1-3/osmplotr/inst/doc/making-maps.html | 218 ++++++++--------- osmplotr-0.1-3/osmplotr/man/add_axes.Rd |only osmplotr-0.1-3/osmplotr/man/add_colourbar.Rd |only osmplotr-0.1-3/osmplotr/man/add_osm_groups.Rd |only osmplotr-0.1-3/osmplotr/man/add_osm_objects.Rd | 4 osmplotr-0.1-3/osmplotr/man/add_osm_surface.Rd |only osmplotr-0.1-3/osmplotr/man/adjust_colours.Rd |only osmplotr-0.1-3/osmplotr/man/click_map.Rd | 2 osmplotr-0.1-3/osmplotr/man/extract_highway.Rd | 4 osmplotr-0.1-3/osmplotr/man/extract_highways.Rd | 10 osmplotr-0.1-3/osmplotr/man/extract_osm_objects.Rd | 19 + osmplotr-0.1-3/osmplotr/man/get_bbox.Rd |only osmplotr-0.1-3/osmplotr/man/highways2polygon.Rd | 4 osmplotr-0.1-3/osmplotr/man/make_osm_map.Rd | 6 osmplotr-0.1-3/osmplotr/man/osm_structures.Rd | 7 osmplotr-0.1-3/osmplotr/man/osmplotr.Rd | 77 +++++- osmplotr-0.1-3/osmplotr/man/plot_osm_basemap.Rd | 11 osmplotr-0.1-3/osmplotr/vignettes/downloading-data.Rmd | 23 + osmplotr-0.1-3/osmplotr/vignettes/downloading-data.md |only osmplotr-0.1-3/osmplotr/vignettes/making-maps.Rmd | 186 +++++++------- osmplotr-0.1-3/osmplotr/vignettes/making-maps.md |only 53 files changed, 810 insertions(+), 529 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets.
The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 0.7 dated 2016-03-04 and 0.8 dated 2016-03-22
MXM-0.7/MXM/R/censIndLR.R |only MXM-0.7/MXM/man/censIndLR.Rd |only MXM-0.7/MXM/man/testIndMVReg.Rd |only MXM-0.7/MXM/man/testIndNB.Rd |only MXM-0.7/MXM/man/testIndRQ.Rd |only MXM-0.7/MXM/man/testIndSpearman.Rd |only MXM-0.7/MXM/man/testIndZIP.Rd |only MXM-0.8/MXM/DESCRIPTION | 10 - MXM-0.8/MXM/MD5 | 84 ++++++++-------- MXM-0.8/MXM/NAMESPACE | 14 +- MXM-0.8/MXM/R/MMPC.R | 194 ++++++++++--------------------------- MXM-0.8/MXM/R/SES.R | 100 +++++++++++++------ MXM-0.8/MXM/R/cat.ci.R | 5 MXM-0.8/MXM/R/censIndCR.R |only MXM-0.8/MXM/R/censIndWR.R |only MXM-0.8/MXM/R/cv.ses.R | 21 ++-- MXM-0.8/MXM/R/gSquare.R | 4 MXM-0.8/MXM/R/mmhc.skel.R | 6 - MXM-0.8/MXM/R/model.R | 135 ++++++++++++++----------- MXM-0.8/MXM/R/pc.con.R | 65 +++++++----- MXM-0.8/MXM/R/pc.skel.R | 52 ++++----- MXM-0.8/MXM/R/testIndBeta.R | 20 +-- MXM-0.8/MXM/R/testIndClogit.R |only MXM-0.8/MXM/R/testIndFisher.R | 22 ++-- MXM-0.8/MXM/R/testIndGLMM.R | 20 +-- MXM-0.8/MXM/R/testIndLogistic.R | 34 +++--- MXM-0.8/MXM/R/testIndMVreg.R | 22 ++-- MXM-0.8/MXM/R/testIndNB.R | 22 ++-- MXM-0.8/MXM/R/testIndPois.R | 22 ++-- MXM-0.8/MXM/R/testIndRQ.R | 24 ++-- MXM-0.8/MXM/R/testIndReg.R | 23 ++-- MXM-0.8/MXM/R/testIndSpearman.R | 24 ++-- MXM-0.8/MXM/R/testIndSpeedglm.R |only MXM-0.8/MXM/R/testIndZIP.R | 57 +++++----- MXM-0.8/MXM/man/MXM-package.Rd | 13 +- MXM-0.8/MXM/man/MXMCondIndTests.Rd | 22 ++-- MXM-0.8/MXM/man/SES.Rd | 23 ++-- MXM-0.8/MXM/man/censIndCR.Rd |only MXM-0.8/MXM/man/cv.ses.Rd | 2 MXM-0.8/MXM/man/gSquare.Rd | 12 +- MXM-0.8/MXM/man/mmhc.skel.Rd | 3 MXM-0.8/MXM/man/pc.skel.Rd | 5 MXM-0.8/MXM/man/testIndBeta.Rd | 4 MXM-0.8/MXM/man/testIndClogit.Rd |only MXM-0.8/MXM/man/testIndFisher.Rd | 30 +++-- MXM-0.8/MXM/man/testIndGLMM.Rd | 2 MXM-0.8/MXM/man/testIndLogistic.Rd | 15 +- MXM-0.8/MXM/man/testIndPois.Rd | 36 +++++- MXM-0.8/MXM/man/testIndReg.Rd | 47 ++++++-- MXM-0.8/MXM/man/testIndSpeedglm.Rd |only 50 files changed, 638 insertions(+), 556 deletions(-)
Title: L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
Description: Extensive functions for the theory of L-moments (LMs) in addition to probability-weighted moments (PWMs), and parameter (p) estimation for numerous familiar and not-so-familiar distributions. Estimation of LMs for the same distributions is provided as are L-moment ratio diagrams. Estimation of LMs for right-tail and left-tail censoring by known or unknown threshold and also by indicator variable is available. Asymmetric trimmed LMs (TL-moments, TLMs) are supported as are numerical integrations to dynamically compute trajectories of select TLM ratios for TL-moment ratio diagram construction. LMs of residual (resid.) and reversed (rev.) resid. life are implemented along with 13 operators on quantile functions that are useful in reliability, lifetime, and survival analysis. Exact analytical bootstrap estimates of order statistics, LMs, and variances-covariances of LMs are provided. The Harri-Coble Tau34-squared Test for Normality is available. Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail censoring (RC) encompasses: Asymmetric (Asy.) Exponential (Exp.) Power [L], Asy. Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen.) Exp. Poisson [L], Gen. Extreme Value [L], Gen. Lambda [L,TL], Gen. Logistic [L), Gen. Normal [L], Gen. Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev. Gumbel [L+RC], Rice/Rician (L), Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L]. LMs have multivariate analogs; the sample L-comoments (LCMs) are implemented and might have considerable application with copulas because LCMs measure asymmetric association and higher comoments or comovements of variables.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between lmomco versions 2.1.4 dated 2015-04-21 and 2.2.2 dated 2016-03-22
lmomco-2.1.4/lmomco/R/genci.R |only lmomco-2.1.4/lmomco/R/qua2ci.R |only lmomco-2.1.4/lmomco/man/genci.Rd |only lmomco-2.1.4/lmomco/man/qua2ci.Rd |only lmomco-2.2.2/lmomco/DESCRIPTION | 13 lmomco-2.2.2/lmomco/MD5 | 340 +++++++------- lmomco-2.2.2/lmomco/NAMESPACE | 20 lmomco-2.2.2/lmomco/NEWS | 116 ++++ lmomco-2.2.2/lmomco/R/BEhypergeo.R | 2 lmomco-2.2.2/lmomco/R/TLmom.R | 7 lmomco-2.2.2/lmomco/R/TLmoms.R | 15 lmomco-2.2.2/lmomco/R/add.lmomco.axis.R | 28 - lmomco-2.2.2/lmomco/R/add.log.axis.R |only lmomco-2.2.2/lmomco/R/are.par.valid.R | 3 lmomco-2.2.2/lmomco/R/cdf2lmom.R | 42 - lmomco-2.2.2/lmomco/R/cdf2lmoms.R | 3 lmomco-2.2.2/lmomco/R/cdfaep4.R | 40 - lmomco-2.2.2/lmomco/R/cdfcau.R | 12 lmomco-2.2.2/lmomco/R/cdfemu.R | 42 - lmomco-2.2.2/lmomco/R/cdfexp.R | 10 lmomco-2.2.2/lmomco/R/cdfgam.R | 15 lmomco-2.2.2/lmomco/R/cdfgep.R | 6 lmomco-2.2.2/lmomco/R/cdfgev.R | 37 - lmomco-2.2.2/lmomco/R/cdfgld.R | 62 +- lmomco-2.2.2/lmomco/R/cdfglo.R | 37 - lmomco-2.2.2/lmomco/R/cdfgno.R | 35 - lmomco-2.2.2/lmomco/R/cdfgov.R | 34 - lmomco-2.2.2/lmomco/R/cdfgpa.R | 38 - lmomco-2.2.2/lmomco/R/cdfgum.R | 8 lmomco-2.2.2/lmomco/R/cdfkap.R | 53 -- lmomco-2.2.2/lmomco/R/cdfkmu.R | 79 ++- lmomco-2.2.2/lmomco/R/cdfkur.R | 13 lmomco-2.2.2/lmomco/R/cdflap.R | 14 lmomco-2.2.2/lmomco/R/cdflmrq.R | 34 - lmomco-2.2.2/lmomco/R/cdfln3.R | 16 lmomco-2.2.2/lmomco/R/cdfnor.R | 7 lmomco-2.2.2/lmomco/R/cdfpe3.R | 39 - lmomco-2.2.2/lmomco/R/cdfray.R | 15 lmomco-2.2.2/lmomco/R/cdfrevgum.R | 15 lmomco-2.2.2/lmomco/R/cdfrice.R | 32 - lmomco-2.2.2/lmomco/R/cdfsla.R | 26 - lmomco-2.2.2/lmomco/R/cdfst3.R | 13 lmomco-2.2.2/lmomco/R/cdftexp.R | 31 - lmomco-2.2.2/lmomco/R/cdftri.R | 20 lmomco-2.2.2/lmomco/R/cdfwak.R | 79 +-- lmomco-2.2.2/lmomco/R/check.pdf.R | 49 +- lmomco-2.2.2/lmomco/R/disfitqua.R |only lmomco-2.2.2/lmomco/R/dlmomco.R | 3 lmomco-2.2.2/lmomco/R/genci.simple.R |only lmomco-2.2.2/lmomco/R/gini.mean.diff.R | 6 lmomco-2.2.2/lmomco/R/hlmomco.R | 1 lmomco-2.2.2/lmomco/R/lmomemu.R | 3 lmomco-2.2.2/lmomco/R/lmomkmu.R | 57 -- lmomco-2.2.2/lmomco/R/lmomrice.R | 3 lmomco-2.2.2/lmomco/R/lmoms.cov.R |only lmomco-2.2.2/lmomco/R/lmomtri.R | 58 +- lmomco-2.2.2/lmomco/R/lmrdia.R | 15 lmomco-2.2.2/lmomco/R/nonexceeds.R | 23 lmomco-2.2.2/lmomco/R/partri.R | 55 +- lmomco-2.2.2/lmomco/R/pdfaep4.R | 12 lmomco-2.2.2/lmomco/R/pdfcau.R | 12 lmomco-2.2.2/lmomco/R/pdfemu.R | 51 +- lmomco-2.2.2/lmomco/R/pdfexp.R | 16 lmomco-2.2.2/lmomco/R/pdfgam.R | 16 lmomco-2.2.2/lmomco/R/pdfgep.R | 17 lmomco-2.2.2/lmomco/R/pdfgev.R | 40 - lmomco-2.2.2/lmomco/R/pdfgld.R | 34 - lmomco-2.2.2/lmomco/R/pdfglo.R | 34 - lmomco-2.2.2/lmomco/R/pdfgno.R | 36 - lmomco-2.2.2/lmomco/R/pdfgov.R | 24 lmomco-2.2.2/lmomco/R/pdfgpa.R | 31 - lmomco-2.2.2/lmomco/R/pdfgum.R | 17 lmomco-2.2.2/lmomco/R/pdfkap.R | 57 -- lmomco-2.2.2/lmomco/R/pdfkmu.R | 103 ++-- lmomco-2.2.2/lmomco/R/pdfkur.R | 17 lmomco-2.2.2/lmomco/R/pdflap.R | 12 lmomco-2.2.2/lmomco/R/pdflmrq.R | 17 lmomco-2.2.2/lmomco/R/pdfln3.R | 8 lmomco-2.2.2/lmomco/R/pdfnor.R | 7 lmomco-2.2.2/lmomco/R/pdfpe3.R | 57 -- lmomco-2.2.2/lmomco/R/pdfray.R | 20 lmomco-2.2.2/lmomco/R/pdfrevgum.R | 12 lmomco-2.2.2/lmomco/R/pdfrice.R | 27 - lmomco-2.2.2/lmomco/R/pdfsla.R | 28 - lmomco-2.2.2/lmomco/R/pdfst3.R | 10 lmomco-2.2.2/lmomco/R/pdftexp.R | 31 - lmomco-2.2.2/lmomco/R/pdftri.R | 42 - lmomco-2.2.2/lmomco/R/pdfwak.R | 29 - lmomco-2.2.2/lmomco/R/pfactor.bernstein.R | 2 lmomco-2.2.2/lmomco/R/prettydist.R | 2 lmomco-2.2.2/lmomco/R/qua2ci.cov.R |only lmomco-2.2.2/lmomco/R/qua2ci.simple.R |only lmomco-2.2.2/lmomco/R/quaaep4.R | 36 - lmomco-2.2.2/lmomco/R/quaaep4kapmix.R | 3 lmomco-2.2.2/lmomco/R/quacau.R | 12 lmomco-2.2.2/lmomco/R/quaemu.R | 17 lmomco-2.2.2/lmomco/R/quaexp.R | 7 lmomco-2.2.2/lmomco/R/quagam.R | 14 lmomco-2.2.2/lmomco/R/quagep.R | 12 lmomco-2.2.2/lmomco/R/quagev.R | 27 - lmomco-2.2.2/lmomco/R/quagld.R | 20 lmomco-2.2.2/lmomco/R/quaglo.R | 28 - lmomco-2.2.2/lmomco/R/quagno.R | 21 lmomco-2.2.2/lmomco/R/quagov.R | 17 lmomco-2.2.2/lmomco/R/quagpa.R | 25 - lmomco-2.2.2/lmomco/R/quagum.R | 13 lmomco-2.2.2/lmomco/R/quakap.R | 49 -- lmomco-2.2.2/lmomco/R/quakmu.R | 106 ++-- lmomco-2.2.2/lmomco/R/quakur.R | 13 lmomco-2.2.2/lmomco/R/qualap.R | 11 lmomco-2.2.2/lmomco/R/qualmrq.R | 1 lmomco-2.2.2/lmomco/R/qualn3.R | 6 lmomco-2.2.2/lmomco/R/quanor.R | 7 lmomco-2.2.2/lmomco/R/quape3.R | 45 - lmomco-2.2.2/lmomco/R/quaray.R | 13 lmomco-2.2.2/lmomco/R/quarevgum.R | 15 lmomco-2.2.2/lmomco/R/quarice.R | 33 - lmomco-2.2.2/lmomco/R/quasla.R | 26 - lmomco-2.2.2/lmomco/R/quatexp.R | 29 - lmomco-2.2.2/lmomco/R/quatri.R | 14 lmomco-2.2.2/lmomco/R/quawak.R | 50 -- lmomco-2.2.2/lmomco/R/rmlmomco.R | 17 lmomco-2.2.2/lmomco/R/rmvarlmomco.R | 14 lmomco-2.2.2/lmomco/R/rrmlmomco.R | 16 lmomco-2.2.2/lmomco/R/rrmvarlmomco.R | 14 lmomco-2.2.2/lmomco/R/supdist.R | 41 + lmomco-2.2.2/lmomco/R/tau34sq.normtest.R | 28 - lmomco-2.2.2/lmomco/R/theoTLmoms.R | 20 lmomco-2.2.2/lmomco/R/vec2par.R | 4 lmomco-2.2.2/lmomco/R/x2xlo.R | 10 lmomco-2.2.2/lmomco/R/z.par2cdf.R | 35 - lmomco-2.2.2/lmomco/R/z.par2qua.R | 42 + lmomco-2.2.2/lmomco/inst/ACKNOWLEDGEMENTS | 2 lmomco-2.2.2/lmomco/inst/CITATION | 18 lmomco-2.2.2/lmomco/inst/ERRATA_FOR_ISBN9781463508418.txt | 10 lmomco-2.2.2/lmomco/man/TLmoms.Rd | 6 lmomco-2.2.2/lmomco/man/add.lmomco.axis.Rd | 11 lmomco-2.2.2/lmomco/man/add.log.axis.Rd |only lmomco-2.2.2/lmomco/man/are.par.valid.Rd | 3 lmomco-2.2.2/lmomco/man/cdf2lmoms.Rd | 2 lmomco-2.2.2/lmomco/man/cdfgld.Rd | 7 lmomco-2.2.2/lmomco/man/cdfkmu.Rd | 51 +- lmomco-2.2.2/lmomco/man/cdfwak.Rd | 4 lmomco-2.2.2/lmomco/man/check.pdf.Rd | 17 lmomco-2.2.2/lmomco/man/disfitqua.Rd |only lmomco-2.2.2/lmomco/man/dist.list.Rd | 19 lmomco-2.2.2/lmomco/man/gen.freq.curves.Rd | 6 lmomco-2.2.2/lmomco/man/genci.simple.Rd |only lmomco-2.2.2/lmomco/man/lmomco-package.Rd | 6 lmomco-2.2.2/lmomco/man/lmomgov.Rd | 2 lmomco-2.2.2/lmomco/man/lmomkmu.Rd | 2 lmomco-2.2.2/lmomco/man/lmoms.bootbarvar.Rd | 2 lmomco-2.2.2/lmomco/man/lmoms.cov.Rd |only lmomco-2.2.2/lmomco/man/lmomsRCmark.Rd | 15 lmomco-2.2.2/lmomco/man/lmomtri.Rd | 56 +- lmomco-2.2.2/lmomco/man/lmrdia.Rd | 3 lmomco-2.2.2/lmomco/man/nonexceeds.Rd | 5 lmomco-2.2.2/lmomco/man/parglo.Rd | 12 lmomco-2.2.2/lmomco/man/parkmu.Rd | 3 lmomco-2.2.2/lmomco/man/pdfemu.Rd | 6 lmomco-2.2.2/lmomco/man/pdfgld.Rd | 6 lmomco-2.2.2/lmomco/man/pdfkmu.Rd | 6 lmomco-2.2.2/lmomco/man/pdfrice.Rd | 36 - lmomco-2.2.2/lmomco/man/pdfwei.Rd | 6 lmomco-2.2.2/lmomco/man/pmoms.Rd | 2 lmomco-2.2.2/lmomco/man/prettydist.Rd | 3 lmomco-2.2.2/lmomco/man/qua2ci.cov.Rd |only lmomco-2.2.2/lmomco/man/qua2ci.simple.Rd |only lmomco-2.2.2/lmomco/man/quagep.Rd | 2 lmomco-2.2.2/lmomco/man/quagld.Rd | 4 lmomco-2.2.2/lmomco/man/quagpa.Rd | 12 lmomco-2.2.2/lmomco/man/quakmu.Rd | 11 lmomco-2.2.2/lmomco/man/quarice.Rd | 7 lmomco-2.2.2/lmomco/man/quatexp.Rd | 5 lmomco-2.2.2/lmomco/man/rmvarlmomco.Rd | 9 lmomco-2.2.2/lmomco/man/supdist.Rd | 12 lmomco-2.2.2/lmomco/man/theoTLmoms.Rd | 71 ++ lmomco-2.2.2/lmomco/man/z.par2cdf.Rd | 45 + lmomco-2.2.2/lmomco/man/z.par2qua.Rd | 31 - 179 files changed, 2040 insertions(+), 1952 deletions(-)
Title: Basic Statistical Functions for Package 'ff'
Description: Extends the out of memory vectors of 'ff' with
statistical functions and other utilities to ease their usage.
Author: Edwin de Jonge, Jan Wijffels, Jan van der Laan
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between ffbase versions 0.12.1 dated 2015-06-05 and 0.12.3 dated 2016-03-22
ffbase-0.12.1/ffbase/tests/testthat/tmp.fwf |only ffbase-0.12.3/ffbase/DESCRIPTION | 13 ffbase-0.12.3/ffbase/MD5 | 322 ++++----- ffbase-0.12.3/ffbase/NAMESPACE | 448 ++++++------ ffbase-0.12.3/ffbase/NEWS | 259 +++---- ffbase-0.12.3/ffbase/R/Summary_ff.R | 236 +++--- ffbase-0.12.3/ffbase/R/as.R | 204 ++--- ffbase-0.12.3/ffbase/R/auxilary.R | 318 ++++---- ffbase-0.12.3/ffbase/R/bigglm.R | 134 +-- ffbase-0.12.3/ffbase/R/binned_sum.R | 162 ++-- ffbase-0.12.3/ffbase/R/binned_sumsq.R | 156 ++-- ffbase-0.12.3/ffbase/R/binned_tabulate.R | 190 ++--- ffbase-0.12.3/ffbase/R/byMean.R | 160 ++-- ffbase-0.12.3/ffbase/R/bySum.R | 140 +-- ffbase-0.12.3/ffbase/R/chunkify.R | 118 +-- ffbase-0.12.3/ffbase/R/compact.R | 112 +-- ffbase-0.12.3/ffbase/R/cumsum.R | 142 +-- ffbase-0.12.3/ffbase/R/cut_ff.R | 106 +- ffbase-0.12.3/ffbase/R/date_formatting.R | 56 - ffbase-0.12.3/ffbase/R/diff_ff.R | 66 - ffbase-0.12.3/ffbase/R/droplevels.R | 108 +-- ffbase-0.12.3/ffbase/R/duplicated.R | 158 ++-- ffbase-0.12.3/ffbase/R/expand_ffgrid.R | 140 +-- ffbase-0.12.3/ffbase/R/extract.R | 189 +++-- ffbase-0.12.3/ffbase/R/ffappend.R | 268 +++---- ffbase-0.12.3/ffbase/R/ffdfdply.R | 226 +++--- ffbase-0.12.3/ffbase/R/ffdfsave.R | 64 - ffbase-0.12.3/ffbase/R/ffdfwith.R | 144 ++-- ffbase-0.12.3/ffbase/R/ffifelse.R | 68 - ffbase-0.12.3/ffbase/R/ffmatch.R | 226 +++--- ffbase-0.12.3/ffbase/R/ffordered.R | 106 +- ffbase-0.12.3/ffbase/R/ffrandom.R | 74 +- ffbase-0.12.3/ffbase/R/ffrep.R | 116 +-- ffbase-0.12.3/ffbase/R/ffseq.R | 298 ++++---- ffbase-0.12.3/ffbase/R/ffwhich.R | 166 ++-- ffbase-0.12.3/ffbase/R/hist2d.R | 86 +- ffbase-0.12.3/ffbase/R/hist_ff.R | 106 +- ffbase-0.12.3/ffbase/R/ikey.R | 44 - ffbase-0.12.3/ffbase/R/isNA.R | 80 +- ffbase-0.12.3/ffbase/R/laf_to_ffdf.R | 118 +-- ffbase-0.12.3/ffbase/R/logging.R | 66 - ffbase-0.12.3/ffbase/R/mean.R | 70 - ffbase-0.12.3/ffbase/R/merge.R | 232 +++--- ffbase-0.12.3/ffbase/R/pkg.R | 153 ++-- ffbase-0.12.3/ffbase/R/quantile_ff.R | 70 - ffbase-0.12.3/ffbase/R/rbind_ffdf.R | 96 +- ffbase-0.12.3/ffbase/R/rev_ff.R | 26 ffbase-0.12.3/ffbase/R/rle_ff.R | 94 +- ffbase-0.12.3/ffbase/R/save_ffdf.R | 436 ++++++------ ffbase-0.12.3/ffbase/R/subset.R | 100 +- ffbase-0.12.3/ffbase/R/table_ff.R | 230 +++--- ffbase-0.12.3/ffbase/R/tabulate_ff.R | 128 +-- ffbase-0.12.3/ffbase/R/transform.R | 78 +- ffbase-0.12.3/ffbase/R/tsum.R | 164 ++-- ffbase-0.12.3/ffbase/R/unique.R | 192 ++--- ffbase-0.12.3/ffbase/R/with.R | 284 +++---- ffbase-0.12.3/ffbase/R/zzz.R | 6 ffbase-0.12.3/ffbase/man/all.ff.Rd | 48 - ffbase-0.12.3/ffbase/man/any.ff.Rd | 48 - ffbase-0.12.3/ffbase/man/as.Date.ff_vector.Rd | 44 - ffbase-0.12.3/ffbase/man/as.character.ff.Rd | 64 - ffbase-0.12.3/ffbase/man/as.ffdf.ffdf.Rd | 34 ffbase-0.12.3/ffbase/man/as.ram.ffdf.Rd | 40 - ffbase-0.12.3/ffbase/man/bigglm.ffdf.Rd | 92 +- ffbase-0.12.3/ffbase/man/binned_sum.Rd | 60 - ffbase-0.12.3/ffbase/man/binned_sumsq.Rd | 84 +- ffbase-0.12.3/ffbase/man/binned_tabulate.Rd | 76 +- ffbase-0.12.3/ffbase/man/byMean.Rd | 52 - ffbase-0.12.3/ffbase/man/bySum.Rd | 60 - ffbase-0.12.3/ffbase/man/c.ff.Rd | 42 - ffbase-0.12.3/ffbase/man/chunkexpr.Rd | 48 - ffbase-0.12.3/ffbase/man/chunkify.Rd | 40 - ffbase-0.12.3/ffbase/man/compact.Rd | 48 - ffbase-0.12.3/ffbase/man/condMean.Rd | 48 - ffbase-0.12.3/ffbase/man/condSum.Rd | 48 - ffbase-0.12.3/ffbase/man/cumsum.ff.Rd | 110 +-- ffbase-0.12.3/ffbase/man/cut.ff.Rd | 56 - ffbase-0.12.3/ffbase/man/diff.ff.Rd | 42 - ffbase-0.12.3/ffbase/man/droplevels.ff.Rd | 56 - ffbase-0.12.3/ffbase/man/droplevels.ffdf.Rd | 60 - ffbase-0.12.3/ffbase/man/duplicated.ff.Rd | 136 +-- ffbase-0.12.3/ffbase/man/expand.ffgrid.Rd | 84 +- ffbase-0.12.3/ffbase/man/ff_arithmetic.Rd | 90 +- ffbase-0.12.3/ffbase/man/ff_math.Rd | 236 +++--- ffbase-0.12.3/ffbase/man/ff_ops.Rd | 104 +- ffbase-0.12.3/ffbase/man/ffappend.Rd | 56 - ffbase-0.12.3/ffbase/man/ffbase-package.Rd | 186 ++--- ffbase-0.12.3/ffbase/man/ffdfappend.Rd | 60 - ffbase-0.12.3/ffbase/man/ffdfdply.Rd | 144 ++-- ffbase-0.12.3/ffbase/man/ffdfrbind.fill.Rd | 68 - ffbase-0.12.3/ffbase/man/ffdfwith.Rd | 80 +- ffbase-0.12.3/ffbase/man/ffextract.Rd | 130 +-- ffbase-0.12.3/ffbase/man/ffextractffdf.Rd |only ffbase-0.12.3/ffbase/man/ffifelse.Rd | 72 +- ffbase-0.12.3/ffbase/man/ffmatch.Rd | 140 +-- ffbase-0.12.3/ffbase/man/ffordered.Rd | 86 +- ffbase-0.12.3/ffbase/man/ffrandom.Rd | 94 +- ffbase-0.12.3/ffbase/man/ffrep.int.Rd | 84 +- ffbase-0.12.3/ffbase/man/ffseq.Rd | 102 +- ffbase-0.12.3/ffbase/man/ffseq_len.Rd | 78 +- ffbase-0.12.3/ffbase/man/ffwhich.Rd | 78 +- ffbase-0.12.3/ffbase/man/format.ff_vector.Rd | 44 - ffbase-0.12.3/ffbase/man/grouprunningcumsum.Rd | 46 - ffbase-0.12.3/ffbase/man/hist.ff.Rd | 48 - ffbase-0.12.3/ffbase/man/hist2d.ff.Rd | 26 ffbase-0.12.3/ffbase/man/ikey.Rd | 62 - ffbase-0.12.3/ffbase/man/is.na.ff.Rd | 91 +- ffbase-0.12.3/ffbase/man/laf_to_ffdf.Rd | 48 - ffbase-0.12.3/ffbase/man/load.ffdf.Rd | 96 +- ffbase-0.12.3/ffbase/man/mean.ff.Rd | 60 - ffbase-0.12.3/ffbase/man/merge.ffdf.Rd | 226 +++--- ffbase-0.12.3/ffbase/man/min.ff.Rd | 86 +- ffbase-0.12.3/ffbase/man/move.ffdf.Rd | 106 +- ffbase-0.12.3/ffbase/man/pack.ffdf.Rd | 96 +- ffbase-0.12.3/ffbase/man/pkg-deprecated.Rd | 42 - ffbase-0.12.3/ffbase/man/quantile.ff.Rd | 54 - ffbase-0.12.3/ffbase/man/rle_ff.Rd | 64 - ffbase-0.12.3/ffbase/man/save.ffdf.Rd | 144 ++-- ffbase-0.12.3/ffbase/man/set_ffbase_logging.Rd | 34 ffbase-0.12.3/ffbase/man/subset.ff.Rd | 46 - ffbase-0.12.3/ffbase/man/sum.ff.Rd | 48 - ffbase-0.12.3/ffbase/man/table.Rd | 84 +- ffbase-0.12.3/ffbase/man/tabulate.ff.Rd | 70 - ffbase-0.12.3/ffbase/man/transform.ffdf.Rd | 54 - ffbase-0.12.3/ffbase/man/unique.ff.Rd | 130 +-- ffbase-0.12.3/ffbase/man/unpack.ffdf.Rd | 100 +- ffbase-0.12.3/ffbase/man/with.ffdf.Rd | 82 +- ffbase-0.12.3/ffbase/man/within.ffdf.Rd | 60 - ffbase-0.12.3/ffbase/src/binned_sumsq.c | 2 ffbase-0.12.3/ffbase/tests/testthat.R | 6 ffbase-0.12.3/ffbase/tests/testthat/testSummary.R | 146 ++-- ffbase-0.12.3/ffbase/tests/testthat/testchunkify.R | 44 - ffbase-0.12.3/ffbase/tests/testthat/testcumsum.R | 90 +- ffbase-0.12.3/ffbase/tests/testthat/testcut_ff.R | 24 ffbase-0.12.3/ffbase/tests/testthat/testdroplevels.R | 58 - ffbase-0.12.3/ffbase/tests/testthat/testduplicated.R | 44 - ffbase-0.12.3/ffbase/tests/testthat/testextract.R | 22 ffbase-0.12.3/ffbase/tests/testthat/testffappend.R | 196 ++--- ffbase-0.12.3/ffbase/tests/testthat/testffdfplyr.R | 56 - ffbase-0.12.3/ffbase/tests/testthat/testffifelse.R | 72 +- ffbase-0.12.3/ffbase/tests/testthat/testffmatch.R | 102 +- ffbase-0.12.3/ffbase/tests/testthat/testffranfrom.R | 26 ffbase-0.12.3/ffbase/tests/testthat/testffwhich.R | 74 +- ffbase-0.12.3/ffbase/tests/testthat/testikey.R | 44 - ffbase-0.12.3/ffbase/tests/testthat/testisna.R | 64 - ffbase-0.12.3/ffbase/tests/testthat/testlaf.R | 110 +-- ffbase-0.12.3/ffbase/tests/testthat/testmean.ff.R | 16 ffbase-0.12.3/ffbase/tests/testthat/testmerge.R | 180 ++--- ffbase-0.12.3/ffbase/tests/testthat/testmin.ff.R | 78 +- ffbase-0.12.3/ffbase/tests/testthat/testrange_ff.R | 28 ffbase-0.12.3/ffbase/tests/testthat/testrisplit.R | 58 - ffbase-0.12.3/ffbase/tests/testthat/testrle_ff.R | 46 - ffbase-0.12.3/ffbase/tests/testthat/testsave_ffdf.R | 20 ffbase-0.12.3/ffbase/tests/testthat/testseq.R | 108 +-- ffbase-0.12.3/ffbase/tests/testthat/testsops.R | 640 +++++++++--------- ffbase-0.12.3/ffbase/tests/testthat/testsubset.R | 102 +- ffbase-0.12.3/ffbase/tests/testthat/testsum_ff.R | 30 ffbase-0.12.3/ffbase/tests/testthat/testtable_ff.R | 106 +- ffbase-0.12.3/ffbase/tests/testthat/testtabulate_ff.R | 26 ffbase-0.12.3/ffbase/tests/testthat/testtransform.R | 30 ffbase-0.12.3/ffbase/tests/testthat/testunique.R | 48 - ffbase-0.12.3/ffbase/tests/testthat/testwith.R | 102 +- ffbase-0.12.3/ffbase/tests/testthat/testwithin.R | 30 163 files changed, 8468 insertions(+), 8367 deletions(-)
Title: Chunkwise Text-File Processing for 'dplyr'
Description: Text data can be processed chunkwise using 'dplyr' commands. These
are recorded and executed per data chunk, so large files can be processed with
limited memory using the 'LaF' package.
Author: Edwin de Jonge
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between chunked versions 0.1.1 dated 2015-10-12 and 0.2.0 dated 2016-03-22
DESCRIPTION | 14 +- MD5 | 56 ++++---- NAMESPACE | 77 +++++------ NEWS.md |only R/chunkwise.R | 266 +++++++++++++++++++------------------- R/head.R | 24 +-- R/insert_chunk_into.R | 104 +++++++------- R/pkg.R | 96 ++++++------- R/print.R | 28 ++-- R/read.R | 154 +++++++++++----------- R/unsupported.R | 62 ++++---- R/verbs.R | 225 +++++++++++++++++--------------- R/write.R | 262 ++++++++++++++++++------------------- README.md | 264 +++++++++++++++++++------------------ man/chunked-package.Rd | 110 +++++++-------- man/insert_chunkwise_into.Rd | 56 ++++---- man/read_chunks.Rd | 150 +++++++++++---------- man/read_chunkwise.Rd | 62 ++++---- man/write_chunkwise.Rd | 62 ++++---- man/write_csv.Rd | 136 ++++++++++--------- tests/testthat.R | 8 - tests/testthat/test-head.R | 21 +-- tests/testthat/test-insert-into.R | 46 +++--- tests/testthat/test-print.R |only tests/testthat/test-read.R | 72 +++++----- tests/testthat/test-tbl-chunk.R | 34 ++-- tests/testthat/test-unsupported.R | 60 ++++---- tests/testthat/test-verbs.R | 204 ++++++++++++++++------------- tests/testthat/test-write.R | 64 ++++----- tests/testthat/util.R | 44 +++--- 30 files changed, 1423 insertions(+), 1338 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen, Kathleen Gates, and Mikko Rönkkö.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.6 dated 2016-03-06 and 0.4.7 dated 2016-03-22
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- R/miive.R | 7 ++++--- R/miivs.R | 20 ++++++++++++++++++-- 4 files changed, 29 insertions(+), 11 deletions(-)
Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory
(IRT) models. The current implementation includes IRT models for binary and ordinal
responses, along with dynamic and hierarchical IRT models with binary responses. The
latter two models are derived and implemented using variational EM. Subsequent edits
also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <jameslo@princeton.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <jameslo@princeton.edu>
Diff between emIRT versions 0.0.5 dated 2015-03-01 and 0.0.6 dated 2016-03-22
ChangeLog |only DESCRIPTION | 13 +-- MD5 | 67 +++++++++++++++--- NAMESPACE | 7 + R/binIRT.R | 120 +++++++++++++++++++++++++++++++-- R/bootstrap.R |only R/getStarts.R | 100 +++++++++++++++++++++++++++ R/makePriors.R | 29 +++++++ R/networkIRT.R |only R/poisIRT.R |only data/datalist | 2 data/manifesto.rda |only data/ustweet.rda |only man/binIRT.Rd | 74 +++++++++++++++++--- man/boot_emIRT.Rd |only man/manifesto.Rd |only man/networkIRT.Rd |only man/ordIRT.Rd | 2 man/poisIRT.Rd |only man/ustweet.Rd |only src/checkConv.cpp | 58 +++++++++++++++ src/checkConv.h | 15 ++++ src/checkConv_poisIRT.cpp |only src/checkConv_poisIRT.h |only src/endorseIRT_estimate.cpp |only src/estimate_endorseIRT.cpp |only src/estimate_endorseIRT.h |only src/estimate_poisIRT.cpp |only src/estimate_poisIRT.h |only src/getEalpha_endorseIRT.cpp |only src/getEalpha_endorseIRT.h |only src/getEalpha_poisIRT.cpp |only src/getEalpha_poisIRT.h |only src/getEbeta_endorseIRT.cpp |only src/getEbeta_endorseIRT.h |only src/getEbeta_poisIRT.cpp |only src/getEbeta_poisIRT.h |only src/getEgamma_endorseIRT.cpp |only src/getEgamma_endorseIRT.h |only src/getEpsi_poisIRT.cpp |only src/getEpsi_poisIRT.h |only src/getEtheta_endorseIRT.cpp |only src/getEtheta_endorseIRT.h |only src/getEw_endorseIRT.cpp |only src/getEw_endorseIRT.h |only src/getEx_poisIRT.cpp |only src/getEx_poisIRT.h |only src/getExi_poisIRT.cpp |only src/getExi_poisIRT.h |only src/getEystar_endorseIRT.cpp |only src/getEystar_endorseIRT.h |only src/getVbeta_poisIRT.cpp |only src/getVbeta_poisIRT.h |only src/getVx_poisIRT.cpp |only src/getVx_poisIRT.h |only src/poisIRT_estimate.cpp |only src/updateHigherMoments_endorseIRT.cpp |only src/updateHigherMoments_endorseIRT.h |only 58 files changed, 453 insertions(+), 34 deletions(-)
Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to
Bayesian Statistics, Bolstad, W.M. (2007), John Wiley & Sons ISBN 0-471-27020-2.
Author: James Curran <j.curran@auckland.ac.nz>
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Bolstad versions 0.2-30 dated 2016-03-17 and 0.2-32 dated 2016-03-22
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 49 --- R/as.data.frame.Bolstad.R | 2 R/bayes.lin.reg.r | 743 +++++++++++++++++++++++----------------------- R/nvaricp.r | 440 +++++++++++++-------------- R/quantile.Bolstad.R | 1 R/sd.R | 5 R/var.R | 1 man/nvaricp.Rd | 41 -- 10 files changed, 617 insertions(+), 691 deletions(-)
Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma et al (2013) <DOI:10.1080/15533174.2012.707849>).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.3 dated 2016-03-09 and 1.1.4 dated 2016-03-22
clere-1.1.3/clere/man/is.clere.Rd |only clere-1.1.4/clere/DESCRIPTION | 8 clere-1.1.4/clere/MD5 | 27 +-- clere-1.1.4/clere/NAMESPACE | 3 clere-1.1.4/clere/R/Clere.R | 17 -- clere-1.1.4/clere/R/fitClere.R | 226 ++++++++++++++-------------- clere-1.1.4/clere/build/vignette.rds |binary clere-1.1.4/clere/data/algoComp.RData |binary clere-1.1.4/clere/data/numExpRealData.RData |binary clere-1.1.4/clere/data/numExpSimData.RData |binary clere-1.1.4/clere/inst/doc/clere.Rnw | 24 +- clere-1.1.4/clere/inst/doc/clere.pdf |binary clere-1.1.4/clere/man/clere-package.Rd | 4 clere-1.1.4/clere/src/Model.cpp | 6 clere-1.1.4/clere/vignettes/clere.Rnw | 24 +- 15 files changed, 164 insertions(+), 175 deletions(-)
Title: SQL Server R Database Interface (DBI) and dplyr SQL Backend
Description: Utilises The jTDS Project's JDBC 3.0 SQL Server
driver to extend the RJDBC classes and DBI methods. It defines a
SQLServerDriver, SQLServerConnection & SQLServerRsult S4 classes as
extensions of the RJDBC equivalent classes with most DBI
methods being thin extensions of the methods defined by RJDBC classes.
However, the dbConnect interface is more convenient, and the data reading
and writing capabilities found in RJDBC's fetch and dbWriteTable methods
have been refined. The package also implements a SQL backend to the dplyr
package.
Author: Imanuel Costigan [aut, cre],
The jTDS Project (for MSSQL Server driver) [aut],
Simon Urbanek [ctb],
Hadley Wickham [ctb],
Romain Francois [ctb],
RStudio [cph],
The Legion Of The Bouncy Castle [cph, ctb]
Maintainer: Imanuel Costigan <i.costigan@me.com>
Diff between RSQLServer versions 0.1.1 dated 2014-10-10 and 0.2.0 dated 2016-03-22
RSQLServer-0.1.1/RSQLServer/NEWS |only RSQLServer-0.1.1/RSQLServer/R/DBConnection.R |only RSQLServer-0.1.1/RSQLServer/R/DBDriver.R |only RSQLServer-0.1.1/RSQLServer/R/DBResult.R |only RSQLServer-0.1.1/RSQLServer/inst/java/jtds-1.3.1.jar |only RSQLServer-0.1.1/RSQLServer/java/jTDS1.3.1 |only RSQLServer-0.1.1/RSQLServer/man/dbConnect-SQLServerDriver-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbGetInfo-SQLServerConnection-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbGetInfo-SQLServerDriver-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbIsValid-SQLServerConnection-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbIsValid-SQLServerResult-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbListConnections-SQLServerDriver-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbSendQuery-SQLServerConnection-character-method.Rd |only RSQLServer-0.1.1/RSQLServer/man/dbUnloadDriver-SQLServerDriver-method.Rd |only RSQLServer-0.2.0/RSQLServer/DESCRIPTION | 65 ++- RSQLServer-0.2.0/RSQLServer/MD5 | 203 +++++----- RSQLServer-0.2.0/RSQLServer/NAMESPACE | 91 ++++ RSQLServer-0.2.0/RSQLServer/NEWS.md |only RSQLServer-0.2.0/RSQLServer/R/RSQLServer.R | 19 RSQLServer-0.2.0/RSQLServer/R/Utils.R | 143 +++++-- RSQLServer-0.2.0/RSQLServer/R/dbi-classes.R |only RSQLServer-0.2.0/RSQLServer/R/dbi-methods.R |only RSQLServer-0.2.0/RSQLServer/R/dbi-shims.R |only RSQLServer-0.2.0/RSQLServer/R/dplyr-imports.R |only RSQLServer-0.2.0/RSQLServer/R/dplyr.R |only RSQLServer-0.2.0/RSQLServer/R/jdbc-methods.R |only RSQLServer-0.2.0/RSQLServer/R/onLoad.R | 6 RSQLServer-0.2.0/RSQLServer/R/sql-backends.R |only RSQLServer-0.2.0/RSQLServer/R/sql-methods.R |only RSQLServer-0.2.0/RSQLServer/README.md | 97 ++++ RSQLServer-0.2.0/RSQLServer/inst/extdata |only RSQLServer-0.2.0/RSQLServer/inst/java/jtds-1.2.8.jar |only RSQLServer-0.2.0/RSQLServer/java/jTDS1.2.8 |only RSQLServer-0.2.0/RSQLServer/man/RSQLServer.Rd | 19 RSQLServer-0.2.0/RSQLServer/man/SQLServer.Rd |only RSQLServer-0.2.0/RSQLServer/man/SQLServerConnection-class.Rd | 49 +- RSQLServer-0.2.0/RSQLServer/man/SQLServerDriver-class.Rd | 45 -- RSQLServer-0.2.0/RSQLServer/man/SQLServerResult-class.Rd | 35 + RSQLServer-0.2.0/RSQLServer/man/get_server_details.Rd |only RSQLServer-0.2.0/RSQLServer/man/have_test_server.Rd |only RSQLServer-0.2.0/RSQLServer/man/setops.Rd |only RSQLServer-0.2.0/RSQLServer/man/src_sqlserver.Rd |only RSQLServer-0.2.0/RSQLServer/tests |only 43 files changed, 530 insertions(+), 242 deletions(-)
Title: Analyse Text Documents Using Ecological Tools
Description: A set of functions and a graphical user interface
to analyse and compare texts, using classical text mining
functions, as well as those from theoretical ecology.
Author: Rebaudo Francois (IRD, UMR EGCE, Univ.ParisSud-CNRS-IRD-
Univ.ParisSaclay)
Maintainer: Rebaudo Francois <francois.rebaudo@ird.fr>
Diff between inpdfr versions 0.1.1 dated 2016-02-24 and 0.1.2 dated 2016-03-22
DESCRIPTION | 10 MD5 | 84 ++-- NEWS.md | 10 R/inpdfr_ALL_quickFunctions.R | 109 ++++- R/inpdfr_ANA_ECO_entropart.R | 126 ++++-- R/inpdfr_ANA_ECO_metacom.R | 67 ++- R/inpdfr_ANA_barplot.R | 102 +++-- R/inpdfr_ANA_cluster.R | 116 ++++-- R/inpdfr_ANA_correspAnalysis.R | 57 ++- R/inpdfr_ANA_freqWordCor.R | 219 +++++++---- R/inpdfr_ANA_hist.R | 42 +- R/inpdfr_ANA_occur.R | 39 +- R/inpdfr_ANA_wordcloud.R | 55 +- R/inpdfr_PRO_extractTxt.R | 68 ++- R/inpdfr_PRO_manageFiles.R | 22 - R/inpdfr_PRO_processDF.R | 62 ++- R/inpdfr_PRO_processTxt.R | 50 +- R/inpdfr_PRO_stopwords.R | 46 +- R/inpdfr_RGtk2_GUI.R | 771 +++++++++++++++++++++-------------------- inst/doc/inpdfr-vignette.html | 4 man/doCA.Rd | 24 + man/doCluster.Rd | 23 + man/doKmeansClust.Rd | 23 + man/doMetacomEntropart.Rd | 25 + man/doMetacomMetacom.Rd | 24 + man/excludeStopWords.Rd | 2 man/getAllAnalysis.Rd | 35 + man/getListFiles.Rd | 2 man/getMostFreqWord.Rd | 24 + man/getMostFreqWordCor.Rd | 24 + man/getPDF.Rd | 2 man/getSummaryStatsBARPLOT.Rd | 26 + man/getSummaryStatsHISTO.Rd | 25 + man/getSummaryStatsOCCUR.Rd | 7 man/getTXT.Rd | 19 - man/getXFreqWord.Rd | 20 - man/getwordOccuDF.Rd | 23 + man/makeWordcloud.Rd | 9 man/mergeWordFreq.Rd | 20 - man/postProcTxt.Rd | 15 man/preProcTxt.Rd | 13 man/quitSpaceFromChars.Rd | 2 man/truncNumWords.Rd | 2 43 files changed, 1559 insertions(+), 889 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Provides new statistics to locate and tag peaks and valleys in 2D
plots, a statistics to add a label with the equation of a polynomial fitted
with lm(), or R^2 or adjusted R^2 or information criteria for any model
fitted with function lm(). Provides a function for flexibly converting time
series to data frames suitable for plotting with ggplot(). In addition
provides two statistics and two geometry useful for diagnosing what data are
passed to compute_group() and compute_panel() functions and to geometries.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.2.6 dated 2016-02-25 and 0.2.7 dated 2016-03-22
DESCRIPTION | 22 +- MD5 | 39 ++-- NAMESPACE | 4 NEWS | 16 + R/geom-debug.R |only R/ggpmisc.R | 21 ++ R/stat-debug-group.R | 51 +++-- R/stat-debug-panel.R | 23 +- R/stat-poly-eq.R | 41 ++++ README.md | 14 + build/vignette.rds |binary inst/doc/examples.R | 146 ++++++++++++++++- inst/doc/examples.Rmd | 216 +++++++++++++++++++++++-- inst/doc/examples.html | 411 ++++++++++++++++++++++++++++++++++++++++++++---- man/geom_debug.Rd |only man/geom_null.Rd |only man/ggpmisc-ggproto.Rd | 6 man/ggpmisc-package.Rd | 35 ++-- man/stat_debug_group.Rd | 25 +- man/stat_debug_panel.Rd | 8 man/stat_poly_eq.Rd | 11 - vignettes/examples.Rmd | 216 +++++++++++++++++++++++-- 22 files changed, 1144 insertions(+), 161 deletions(-)
Title: An Interface to the NOAA Operational Model Archive and
Distribution System
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>
Diff between rNOMADS versions 2.1.7 dated 2016-01-14 and 2.2.0 dated 2016-03-21
rNOMADS-2.1.7/rNOMADS/man/RTModelProfile.Rd |only rNOMADS-2.2.0/rNOMADS/DESCRIPTION | 12 - rNOMADS-2.2.0/rNOMADS/MD5 | 29 +-- rNOMADS-2.2.0/rNOMADS/NEWS | 9 + rNOMADS-2.2.0/rNOMADS/R/GetDODS.R | 7 rNOMADS-2.2.0/rNOMADS/R/RNomadsTools.R | 179 ++++++++--------------- rNOMADS-2.2.0/rNOMADS/man/ArchiveGribGrab.Rd | 7 rNOMADS-2.2.0/rNOMADS/man/BuildProfile.Rd | 30 ++- rNOMADS-2.2.0/rNOMADS/man/CheckNOMADSArchive.Rd | 6 rNOMADS-2.2.0/rNOMADS/man/DODSGrab.Rd | 2 rNOMADS-2.2.0/rNOMADS/man/GetClosestForecasts.Rd | 45 +++-- rNOMADS-2.2.0/rNOMADS/man/GetDODSModelRunInfo.Rd | 3 rNOMADS-2.2.0/rNOMADS/man/LinkExtractor.Rd | 6 rNOMADS-2.2.0/rNOMADS/man/ModelGrid.Rd | 17 -- rNOMADS-2.2.0/rNOMADS/man/PlotWindProfile.Rd | 51 ++---- rNOMADS-2.2.0/rNOMADS/man/rNOMADS-package.Rd | 19 +- 16 files changed, 199 insertions(+), 223 deletions(-)
Title: Expectation-Maximization Binary Clustering
Description: Unsupervised, multivariate, clustering algorithm for meaningful binary clustering and taking into account the uncertainty in the data. A specific constructor for trajectory movement analysis yields behavioural annotation of the tracks based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator.
Author: Joan Garriga, John R.B. Palmer, Aitana Oltra, Frederic Bartumeus
Maintainer: Joan Garriga <jgarriga@ceab.csic.es>
Diff between EMbC versions 1.9.3 dated 2015-07-28 and 1.9.4 dated 2016-03-21
DESCRIPTION | 10 - MD5 | 18 +- NEWS.md |only R/classes.R | 31 +-- R/functions.R | 38 ++-- R/methods.R | 404 +++++++++++++++++++++++----------------------- R/mvbc.R | 60 +++--- build/vignette.rds |binary man/sctr.Rd | 4 man/view.Rd | 8 vignettes/imgs/pkml01.png |only 11 files changed, 298 insertions(+), 275 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.40 dated 2016-02-18 and 1.41 dated 2016-03-21
DESCRIPTION | 8 +- MD5 | 20 +++--- NAMESPACE | 2 R/MTaSPUs.R | 94 +++++----------------------- R/estcov.R | 4 - R/minP.R | 4 - R/util.R | 175 +++++++++++++++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary man/MTaSPUs.Rd | 12 +-- man/estcov.Rd | 4 - man/minP.Rd | 4 - 11 files changed, 222 insertions(+), 105 deletions(-)
Title: Conditional Logistic Regression: A Two-Step Estimation Method
Description: Conditional logistic regression with longitudinal follow up and
individual-level random coefficients: A stable and efficient
two-step estimation method.
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie Baillargeon
Maintainer: Thierry Duchesne <thierry.duchesne@mat.ulaval.ca>
Diff between TwoStepCLogit versions 1.2.4 dated 2015-12-07 and 1.2.5 dated 2016-03-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Ts.estim.R | 16 +++++++++++++--- R/TwoStepCLogit.R | 4 ++-- inst/NEWS.Rd | 6 ++++++ man/TwoStepCLogit-package.Rd | 4 ++-- 6 files changed, 32 insertions(+), 16 deletions(-)
Title: Fast and Simple MongoDB Client for R
Description: High-level, high-performance MongoDB client based on libmongoc and
jsonlite. Includes support for aggregation, indexing, map-reduce, streaming,
SSL encryption and SASL authentication. The vignette gives a brief overview
of the available methods in the package.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.8 dated 2016-01-23 and 0.8.1 dated 2016-03-21
DESCRIPTION | 6 +-- MD5 | 36 +++++++++--------- NEWS | 3 + build/vignette.rds |binary configure | 2 - inst/doc/intro.html | 70 ++++++++++++++++++++++++++++++------ src/Makevars.win | 8 ++-- src/bson/bson-stdint.h | 2 - src/bson/bson-version.h | 6 +-- src/mongoc/mongoc-client.c | 16 ++++++-- src/mongoc/mongoc-cluster-private.h | 2 + src/mongoc/mongoc-cluster.c | 64 ++++++++++++++++++++++++++------ src/mongoc/mongoc-collection.c | 2 + src/mongoc/mongoc-cursor-private.h | 4 +- src/mongoc/mongoc-cursor.c | 13 +++++- src/mongoc/mongoc-database.c | 5 +- src/mongoc/mongoc-stream-tls.c | 6 +++ src/mongoc/mongoc-version.h | 6 +-- src/mongoc/mongoc-write-command.c | 28 +++++++++----- 19 files changed, 203 insertions(+), 76 deletions(-)
Title: Connect MonetDB to R
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Thomas Lumley [ctb]
Maintainer: Hannes Muehleisen <hannes@cwi.nl>
Diff between MonetDB.R versions 1.0.0 dated 2015-11-25 and 1.0.1 dated 2016-03-21
DESCRIPTION | 17 +++----- MD5 | 23 +++++------ NAMESPACE | 22 ++-------- NEWS | 7 ++- R/control.R | 86 ++++++++++++++++-------------------------- R/dbi.R | 98 ++++++++++++++++++++++++++++++++++-------------- R/dplyr.R | 42 +++++++++++++++----- man/MonetDB.R.Rd | 9 +--- man/MonetDBLite.Rd | 6 +- man/control.Rd | 9 +++- man/monetdb.read.csv.Rd | 38 +++++++++--------- man/sqlitecompat.Rd |only man/src_monetdb.Rd | 3 - 13 files changed, 203 insertions(+), 157 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from the Manifesto
Corpus and to the Manifesto Project's Main Dataset and routines to analyse this
data. The Manifesto Project (https://manifesto-project.wzb.eu) collects and
analyses election programmes across time and space to measure the political
preferences of parties. The Manifesto Corpus contains the collected and
annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut, cre],
Nicolas Merz [aut],
Sven Regel [ctb],
Pola Lehmann [ctb]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between manifestoR versions 1.1-1 dated 2015-11-12 and 1.2 dated 2016-03-21
ChangeLog | 21 ++++ DESCRIPTION | 32 +++--- MD5 | 135 +++++++++++++++------------- NAMESPACE | 13 ++ R/cache.R | 2 R/clarity.R |only R/codes.R | 63 ++++++++++--- R/corpus.R | 2 R/dataset.R | 10 ++ R/db_api.R | 18 ++- R/issue_attention.R | 2 R/manifesto.R | 179 ++++++++++++++++++++++++++------------ R/manifestoR-package.r | 9 + R/nicheness.R | 2 R/pipe_helpers.R | 11 ++ R/scaling_functions.R | 182 ++++++++++++++++++++++++++++++++++++++- R/scaling_general.R | 2 R/scaling_rile.R | 9 + inst/doc/manifestoRworkflow.pdf |binary inst/extdata |only man/ManifestoAvailability.Rd | 16 ++- man/ManifestoCorpus.Rd | 3 man/ManifestoDocument.Rd | 6 - man/ManifestoDocumentMeta.Rd | 2 man/ManifestoSource.Rd | 2 man/aggregate_pers.Rd | 8 + man/attach_year.Rd |only man/categories.Rd | 2 man/clarity_dimensions.Rd |only man/cmp_codes.Rd | 4 man/codes.Rd | 2 man/corpusupdate.Rd | 5 - man/count_codes.Rd | 2 man/formatids.Rd | 2 man/formatmpds.Rd | 2 man/franzmann_kaiser.Rd |only man/get_mpdb.Rd | 12 +- man/get_viacache.Rd | 2 man/iff.Rd | 2 man/issue_attention_diversity.Rd | 4 man/manifestoR.Rd | 2 man/median_voter.Rd | 6 - man/mp_availability.Rd | 6 - man/mp_bootstrap.Rd | 2 man/mp_cite.Rd | 2 man/mp_clarity.Rd |only man/mp_coreversions.Rd | 4 man/mp_corpus.Rd | 4 man/mp_corpusversions.Rd | 2 man/mp_emptycache.Rd | 2 man/mp_interpolate.Rd | 2 man/mp_load_cache.Rd | 2 man/mp_maindataset.Rd | 27 +++++ man/mp_metadata.Rd | 4 man/mp_nicheness.Rd | 8 - man/mp_rmps.Rd |only man/mp_save_cache.Rd | 2 man/mp_scale.Rd | 4 man/mp_setapikey.Rd | 4 man/mp_use_corpus_version.Rd | 2 man/mp_view_originals.Rd | 2 man/mpdb_api_request.Rd | 2 man/na_action.Rd |only man/null_to_na.Rd | 2 man/prefix.Rd | 2 man/readManifesto.Rd | 2 man/rep.data.frame.Rd | 2 man/rescale.Rd | 2 man/rile.Rd | 2 man/scale.Rd | 3 man/split_belgium.Rd |only man/vanilla.Rd | 8 - vignettes/manifestoRworkflow.Rmd | 25 ++++- 73 files changed, 651 insertions(+), 254 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters
heaped data, i.e. data which are rounded (to a possibly different degree
of coarseness). While this is mostly a minor problem in parametric density
estimation the bias can be very large for non-parametric methods such as kernel
density estimation. This package implements a partly Bayesian algorithm treating
the true unknown values as additional parameters and estimates the rounding
parameters to give a corrected kernel density estimate. It supports various
standard bandwidth selection methods. Varying rounding probabilities (depending
on the true value) and asymmetric rounding is estimable as well. Additionally,
bivariate non-parametric density estimation for rounded data is supported.
Author: Marcus Gross
Maintainer: Marcus Gross <marcus.gross@fu-berlin.de>
Diff between Kernelheaping versions 1.2 dated 2015-12-07 and 1.5 dated 2016-03-21
DESCRIPTION | 11 +-- MD5 | 10 +-- NAMESPACE | 5 - R/functions.R | 174 +++++++++++++++++++++++++++++++++++++++++++++++++++++- data/students.rda |binary man/dclass.Rd |only man/dshapebivr.Rd |only 7 files changed, 187 insertions(+), 13 deletions(-)
Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness
correlations (HFCs) based on microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre],
Mareike Esser [aut],
Joseph Hoffman [aut],
Marty Kardos [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>
Diff between inbreedR versions 0.3.0 dated 2015-11-30 and 0.3.1 dated 2016-03-21
DESCRIPTION | 23 +- MD5 | 40 ++-- NAMESPACE | 2 R/convert_raw.R | 2 R/g2_microsats.R | 27 +-- R/g2_snps.R | 310 ++++++++++++++++++------------------ R/inbreedR.R | 3 R/plot.inbreed.R | 38 ---- R/print.inbreed.R | 6 R/r2_Wf.R | 9 - R/r2_hf.R | 107 ------------ README.md | 2 build/vignette.rds |binary man/convert_raw.Rd | 2 man/g2_microsats.Rd | 4 man/g2_snps.Rd | 4 man/inbreedR.Rd | 3 man/r2_Wf.Rd | 5 man/r2_hf.Rd | 13 - tests/testthat/test-r2_hf.R | 8 vignettes/inbreedR_step_by_step.Rmd | 61 ++++--- 21 files changed, 281 insertions(+), 388 deletions(-)
Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Testing. It is recommended for research purposes only.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>
Diff between IMak versions 1.1.0 dated 2016-03-03 and 1.1.1 dated 2016-03-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/buildfa.R | 46 +++++++++++++++++++++++----------------------- R/plotfa.R | 20 ++++++++++---------- man/IMak.Rd | 4 ++-- man/build_fa.Rd | 14 +++++++------- man/plot_fa.Rd | 10 +++++----- 7 files changed, 56 insertions(+), 56 deletions(-)
Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: RStudio, Inc.
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between htmltools versions 0.3 dated 2015-12-29 and 0.3.5 dated 2016-03-21
htmltools-0.3.5/htmltools/DESCRIPTION | 13 +- htmltools-0.3.5/htmltools/MD5 | 37 +++--- htmltools-0.3.5/htmltools/NAMESPACE | 4 htmltools-0.3.5/htmltools/NEWS | 29 +++++ htmltools-0.3.5/htmltools/R/RcppExports.R |only htmltools-0.3.5/htmltools/R/html_dependency.R | 108 ++++++++++++++----- htmltools-0.3.5/htmltools/R/html_escape.R | 4 htmltools-0.3.5/htmltools/R/tags.R | 47 +++++--- htmltools-0.3.5/htmltools/R/template.R | 66 ++++++----- htmltools-0.3.5/htmltools/man/builder.Rd | 6 - htmltools-0.3.5/htmltools/man/copyDependencyToDir.Rd | 7 - htmltools-0.3.5/htmltools/man/htmlDependencies.Rd | 24 ++++ htmltools-0.3.5/htmltools/man/htmlDependency.Rd | 7 + htmltools-0.3.5/htmltools/man/htmlTemplate.Rd | 8 + htmltools-0.3.5/htmltools/src |only htmltools-0.3.5/htmltools/tests/test-all.R | 2 htmltools-0.3.5/htmltools/tests/testthat |only htmltools-0.3/htmltools/inst |only 18 files changed, 259 insertions(+), 103 deletions(-)
Title: Robust Estimation Using Heavy-Tailed Distributions
Description: Functions to perform robust estimation considering heavy-tailed distributions.
Currently, the package includes linear regression, linear mixed-effect models, multivariate
location and scatter estimation, multivariate regression, penalized splines and random
variate generation.
Author: Felipe Osorio
Maintainer: Felipe Osorio <felipe.osorio@ucv.cl>
Diff between heavy versions 0.2-35 dated 2014-09-01 and 0.3 dated 2016-03-21
DESCRIPTION | 24 +-- MD5 | 63 ++++---- NAMESPACE | 35 +++- R/control.R | 13 - R/heavyFit.R | 2 R/lm.R | 308 +++++++++++++++++++++++++++------------ R/lme.R | 20 -- R/ps.R | 394 +++++++++++++++++++++++++-------------------------- data/dialyzer.rda |only inst/CITATION | 12 - man/dialyzer.Rd |only man/heavy.control.Rd | 8 - man/heavyFit.Rd | 2 man/heavyLm.Rd | 28 ++- man/heavyPS.Rd | 17 +- src/Makevars | 1 src/base.h | 10 - src/family.c | 74 +++++++++ src/family.h | 1 src/init.c | 2 src/lm_fit.c | 13 + src/lm_fit.h | 3 src/lme_fit.c | 11 + src/lme_fit.h | 1 src/matrix.c | 26 +-- src/matrix.h | 2 src/mlm_fit.c |only src/mv_fit.c | 15 + src/optim.c | 216 +++++++++------------------ src/ps_fit.c | 102 ++++++------- src/ps_fit.h | 6 src/random.c | 167 +++++++++++++++------ src/random.h | 5 src/specfun.c | 107 ++++++------- 34 files changed, 966 insertions(+), 722 deletions(-)
Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between hdi versions 0.1-5 dated 2016-03-11 and 0.1-6 dated 2016-03-21
DESCRIPTION | 8 ++--- MD5 | 27 ++++++++++--------- R/multi-split.R | 5 ++- build/partial.rdb |binary inst/NEWS.Rd | 19 ++++++++++++- man/clusterGroupBound.rd | 40 ++++++++++++++-------------- man/groupBound.rd | 26 ++++++++++-------- man/hdi.Rd | 2 - man/lasso.proj.Rd | 24 ++++++++++------- man/plotClusterGroupBound.rd | 32 ++++++++++------------- tests/ex-clusterGroupBound.R |only tests/ex-lasso.proj.R |only tests/ex-plotClusterGroupBound.R |only tests/groupTsts.R | 51 ++++++++++++++++++------------------ tests/test-lasso.R | 54 +++++++++++++++++++++++---------------- tests/test-stability.R | 4 ++ 16 files changed, 165 insertions(+), 127 deletions(-)
Title: Simulation of Dynamic Microbial Inactivation
Description: Prediction and adjustment to experimental data of microbial
inactivation. Several models available in the literature are implemented.
Author: Alberto Garre [aut, cre],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioinactivation versions 1.1.1 dated 2016-02-04 and 1.1.2 dated 2016-03-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/geeraerd_model.R | 2 +- R/make_predictions.R | 1 - inst/doc/inactivation.html | 25 ++++++++++++------------- 5 files changed, 20 insertions(+), 22 deletions(-)
More information about bioinactivation at CRAN
Permanent link
Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen <bent.nielsen@nuffield.ox.ac.uk>
Diff between apc versions 1.1 dated 2015-04-13 and 1.2 dated 2016-03-21
apc-1.1/apc/CHANGES |only apc-1.1/apc/build |only apc-1.1/apc/inst/CHANGES |only apc-1.1/apc/inst/doc |only apc-1.1/apc/man/apc_1.1-package.Rd |only apc-1.1/apc/vignettes |only apc-1.2/apc/DESCRIPTION | 9 apc-1.2/apc/MD5 | 79 +-- apc-1.2/apc/NAMESPACE | 4 apc-1.2/apc/NEWS | 49 +- apc-1.2/apc/R/apc_data.R | 532 ++++++++++++++++--------- apc-1.2/apc/R/apc_fit.R | 14 apc-1.2/apc/R/apc_forecast.R |only apc-1.2/apc/R/apc_get_index.R | 156 +++---- apc-1.2/apc/R/apc_identify.R | 27 - apc-1.2/apc/R/apc_plot_data.R | 477 +++++++++++++++------- apc-1.2/apc/R/apc_plot_fit.R | 51 ++ apc-1.2/apc/R/internal.R |only apc-1.2/apc/inst/CITATION | 1 apc-1.2/apc/man/apc.data.list.Rd | 43 +- apc-1.2/apc/man/apc.data.list.subset.Rd | 24 + apc-1.2/apc/man/apc.data.sums.Rd | 14 apc-1.2/apc/man/apc.fit.model.Rd | 3 apc-1.2/apc/man/apc.forecast.Rd |only apc-1.2/apc/man/apc.forecast.ac.Rd |only apc-1.2/apc/man/apc.forecast.ap.Rd |only apc-1.2/apc/man/apc.get.design.Rd | 2 apc-1.2/apc/man/apc.identify.Rd | 4 apc-1.2/apc/man/apc.plot.data.all.Rd | 6 apc-1.2/apc/man/apc.plot.data.level.Rd |only apc-1.2/apc/man/apc.plot.data.sparsity.Rd | 8 apc-1.2/apc/man/apc.plot.data.within.Rd | 36 + apc-1.2/apc/man/apc.plot.fit.Rd | 2 apc-1.2/apc/man/apc.plot.fit.all.Rd |only apc-1.2/apc/man/apc.plot.fit.residuals.Rd |only apc-1.2/apc/man/apc.polygon.Rd |only apc-1.2/apc/man/apc_1.2-package.Rd |only apc-1.2/apc/man/data.Belgian.lung.cancer.Rd | 5 apc-1.2/apc/man/data.Italian.bladder.cancer.Rd | 5 apc-1.2/apc/man/data.Japanese.breast.cancer.Rd | 5 apc-1.2/apc/man/data.US.prostate.cancer.Rd |only apc-1.2/apc/man/data.aids.Rd |only apc-1.2/apc/man/data.asbestos.Rd | 3 apc-1.2/apc/man/data.loss.BZ.Rd | 3 apc-1.2/apc/man/data.loss.TA.Rd | 3 apc-1.2/apc/man/data.loss.VNJ.Rd | 13 apc-1.2/apc/man/internal.Rd |only 47 files changed, 1052 insertions(+), 526 deletions(-)
Title: Experience Life Tables
Description: Build experience life tables.
Author: Julien Tomas, Frederic Planchet, Wassim Youssef
Maintainer: Wassim Youssef <Wassim.G.Youssef@gmail.com>
Diff between ELT versions 1.4 dated 2015-09-03 and 1.5 dated 2016-03-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/S01.R | 2 +- man/ELT-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.6 dated 2016-01-08 and 1.1.7 dated 2016-03-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/Clickstream.r | 4 ++-- R/clickstream-package.R | 2 +- man/clickstream-package.Rd | 2 +- 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Exploring Water Quality Monitoring Data
Description: Functions to assist in the processing and
exploration of data from environmental monitoring programs.
The package name stands for "water quality" and reflects the
original focus on time series data for physical and chemical
properties of water, as well as the biota. Intended for
programs that sample approximately monthly, quarterly or
annually at discrete stations, a feature of many legacy data
sets. Most of the functions should be useful for analysis of
similar-frequency time series regardless of the subject
matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby <wq@fastmail.net>
Diff between wq versions 0.4.5 dated 2015-12-21 and 0.4.6 dated 2016-03-20
wq-0.4.5/wq/build/vignette.rds |only wq-0.4.5/wq/inst/doc |only wq-0.4.5/wq/vignettes/limnology_and_oceanography.bst |only wq-0.4.5/wq/vignettes/wq-package.Rnw |only wq-0.4.5/wq/vignettes/wqFlow.pdf |only wq-0.4.6/wq/DESCRIPTION | 29 +- wq-0.4.6/wq/MD5 | 107 ++++----- wq-0.4.6/wq/NAMESPACE | 2 wq-0.4.6/wq/NEWS | 18 + wq-0.4.6/wq/R/R2pss.R | 7 wq-0.4.6/wq/R/WqData-class.R | 23 +- wq-0.4.6/wq/R/date2decyear.R | 3 wq-0.4.6/wq/R/decompTs.R | 116 ++++------ wq-0.4.6/wq/R/decyear2date.R | 3 wq-0.4.6/wq/R/ec2pss.R | 60 ++--- wq-0.4.6/wq/R/eof.R | 31 -- wq-0.4.6/wq/R/eofNum.R | 45 +--- wq-0.4.6/wq/R/eofPlot.R | 73 ++---- wq-0.4.6/wq/R/interpTs.R | 47 +--- wq-0.4.6/wq/R/layerMean.R | 13 - wq-0.4.6/wq/R/leapYear.R | 7 wq-0.4.6/wq/R/mannKen.R | 207 +++++++++---------- wq-0.4.6/wq/R/meanSub.R | 5 wq-0.4.6/wq/R/monthCor.R | 13 - wq-0.4.6/wq/R/monthNum.R | 6 wq-0.4.6/wq/R/mts2ts.R | 19 - wq-0.4.6/wq/R/oxySol.R | 28 -- wq-0.4.6/wq/R/pett.R |only wq-0.4.6/wq/R/phenoAmp.R | 26 -- wq-0.4.6/wq/R/phenoPhase.R | 27 -- wq-0.4.6/wq/R/plotSeason.R | 22 -- wq-0.4.6/wq/R/plotTs.R | 58 ++--- wq-0.4.6/wq/R/plotTsAnom.R | 62 +++-- wq-0.4.6/wq/R/plotTsTile.R | 173 +++++++-------- wq-0.4.6/wq/R/ruleN.R | 17 - wq-0.4.6/wq/R/seaKen.R | 113 +++++----- wq-0.4.6/wq/R/seaRoll.R | 104 ++++----- wq-0.4.6/wq/R/seasonTrend.R | 142 ++++--------- wq-0.4.6/wq/R/trendHomog.R | 40 ++- wq-0.4.6/wq/R/ts2df.R | 24 -- wq-0.4.6/wq/R/tsMake.R | 10 wq-0.4.6/wq/R/tsSub.R | 30 +- wq-0.4.6/wq/R/wqData.R | 22 +- wq-0.4.6/wq/R/years.R | 2 wq-0.4.6/wq/README | 42 +-- wq-0.4.6/wq/build/partial.rdb |only wq-0.4.6/wq/man/decompTs.Rd | 39 +-- wq-0.4.6/wq/man/mannKen.Rd | 54 +++- wq-0.4.6/wq/man/pett.Rd |only wq-0.4.6/wq/man/plotSeason.Rd | 2 wq-0.4.6/wq/man/plotTs.Rd | 26 +- wq-0.4.6/wq/man/plotTsAnom.Rd | 16 - wq-0.4.6/wq/man/seaKen.Rd | 77 +++---- wq-0.4.6/wq/man/seaRoll.Rd |only wq-0.4.6/wq/man/seasonTrend.Rd | 68 ++---- wq-0.4.6/wq/man/wq-package.Rd | 106 +++------ wq-0.4.6/wq/vignettes/wq-package.Rmd |only wq-0.4.6/wq/vignettes/wq.bib | 15 + wq-0.4.6/wq/vignettes/wqflow.png |only 59 files changed, 989 insertions(+), 1190 deletions(-)
Title: A Social Media Search and Analytic Tool
Description: Social media search and analytic tool that takes one or multiple URL(s) and returns the information about the popularity and reach of the URL(s) on social media. The function get_socialmedia() retrieves the number of shares, likes, pins, and hits on Facebook (www.facebook.com), Pinterest (www.pinterest.com), StumbleUpon (www.stumbleupon.com), LinkedIn (www.linkedin.com), and Reddit (www.reddit.com). The package also includes dedicated functions for each social network platform and a function to resolve shortened URLs.
Author: Marco T. Bastos
Maintainer: Marco T. Bastos <marco@toledobastos.com>
Diff between SocialMediaMineR versions 0.2 dated 2016-01-15 and 0.3 dated 2016-03-20
SocialMediaMineR-0.2/SocialMediaMineR/R/SocialMediaMineR-internal.R |only SocialMediaMineR-0.3/SocialMediaMineR/ChangeLog | 2 SocialMediaMineR-0.3/SocialMediaMineR/DESCRIPTION | 12 +-- SocialMediaMineR-0.3/SocialMediaMineR/MD5 | 33 ++++------ SocialMediaMineR-0.3/SocialMediaMineR/R/get_facebook.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/R/get_linkedin.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/R/get_pinterest.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/R/get_reddit.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/R/get_socialmedia.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/R/get_stumbleupon.R | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/SocialMediaMineR-package.Rd | 8 +- SocialMediaMineR-0.3/SocialMediaMineR/man/get_facebook.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_linkedin.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_pinterest.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_reddit.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_socialmedia.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_stumbleupon.Rd | 2 SocialMediaMineR-0.3/SocialMediaMineR/man/get_url.Rd | 2 18 files changed, 41 insertions(+), 40 deletions(-)
More information about SocialMediaMineR at CRAN
Permanent link
Title: LInear Regression in Astronomy
Description: Performs Bayesian linear regression in astronomy. The method accounts for heteroscedastic errors in both the independent and the dependent variables, intrinsic scatters (in both variables), time evolution of slopes, normalization and scatters, Malmquist and Eddington bias, and break of linearity. The posterior distribution of the regression parameters is sampled with a Gibbs method exploiting the JAGS library.
Author: Mauro Sereno
Maintainer: Mauro Sereno <mauro.sereno@unibo.it>
Diff between lira versions 1.0 dated 2015-09-17 and 1.2.0 dated 2016-03-20
DESCRIPTION | 10 - MD5 | 6 - R/lira.R | 302 +++++++++++++++++++++++++++++++++++++++++++++++------------- man/lira.Rd | 67 ++++++++++--- 4 files changed, 297 insertions(+), 88 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.17.4 dated 2016-03-19 and 0.17.5 dated 2016-03-20
ChangeLog | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 14 +++++------ NEWS | 10 +++++++ R/install.R | 12 ++++++--- R/updateR.R | 16 ++++++------ man/install.R.Rd | 2 - man/install.URL.Rd | 6 +++- 8 files changed, 110 insertions(+), 25 deletions(-)
Title: Get Meteorological Data for Hydrologic Models
Description: Hydrologic models often require users to collect and format input meteorological data. This package contains functions for sourcing, formatting, and
editing meteorological data for hydrologic models.
Author: Andrew Sommerlot [aut, cre],
Daniel Fuka [aut],
Zachary Easton [aut]
Maintainer: Andrew Sommerlot <andrewrs@vt.edu>
Diff between getMet versions 0.2.1 dated 2015-11-13 and 0.3.2 dated 2016-03-20
DESCRIPTION | 12 +- MD5 | 20 ++-- NAMESPACE | 4 R/SWATsubGage.R |only R/genSWATdates.R | 83 ++++++++---------- R/getMet.R | 46 +++++----- R/getSWATcfsr.R | 191 ++++++++++++++++++++----------------------- R/getSWATdates.R | 88 +++++++++---------- R/getSWATwunderForecast.R |only man/SWATsubGage.Rd |only man/getMet.Rd | 6 - man/getSWATcfsr.Rd | 4 man/getSWATwunderForecast.Rd |only 13 files changed, 221 insertions(+), 233 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of k-Shape, TADPole and fuzzy clustering are available.
The functionality can be easily extended with custom distance measures
and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 2.1.0 dated 2016-02-21 and 2.1.1 dated 2016-03-20
dtwclust-2.1.0/dtwclust/tests/testthat/fc.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/hc_all.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/hc_lbi.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/i386 |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_colMeans.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_dba.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_dtw.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_dtw2.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_dtw_lb.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_l2.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_lbi.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_lbk.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_list.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_matrix.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_mean.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_median.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_ndtw.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_ndtw2.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_pam.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_sbd.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_shape.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pc_tadp.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pdist_dtw_lb.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pdist_lbi.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pdist_lbk.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/pdist_sbd.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/rep_median.rds |only dtwclust-2.1.0/dtwclust/tests/testthat/rep_pampre.rds |only dtwclust-2.1.1/dtwclust/DESCRIPTION | 18 dtwclust-2.1.1/dtwclust/MD5 | 86 dtwclust-2.1.1/dtwclust/R/all_cent.R | 393 +-- dtwclust-2.1.1/dtwclust/R/dtwclust-methods.R | 1055 +++++----- dtwclust-2.1.1/dtwclust/R/dtwclust.R | 1636 ++++++++-------- dtwclust-2.1.1/dtwclust/R/kcca-list.R | 241 +- dtwclust-2.1.1/dtwclust/R/pkg.R | 352 +-- dtwclust-2.1.1/dtwclust/R/shape-extraction.R | 229 +- dtwclust-2.1.1/dtwclust/R/utils.R | 464 ++-- dtwclust-2.1.1/dtwclust/README.md | 39 dtwclust-2.1.1/dtwclust/inst/NEWS.Rd | 12 dtwclust-2.1.1/dtwclust/inst/dtwclust-examples.R | 320 +-- dtwclust-2.1.1/dtwclust/man/DBA.Rd | 194 - dtwclust-2.1.1/dtwclust/man/NCCc.Rd | 54 dtwclust-2.1.1/dtwclust/man/SBD.Rd | 124 - dtwclust-2.1.1/dtwclust/man/TADPole.Rd | 198 - dtwclust-2.1.1/dtwclust/man/dtw_lb.Rd | 240 +- dtwclust-2.1.1/dtwclust/man/dtwclust-class.Rd | 122 - dtwclust-2.1.1/dtwclust/man/dtwclust-methods.Rd | 180 - dtwclust-2.1.1/dtwclust/man/dtwclust-package.Rd | 198 - dtwclust-2.1.1/dtwclust/man/dtwclust.Rd | 1024 +++++----- dtwclust-2.1.1/dtwclust/man/dtwclustControl-class.Rd | 172 - dtwclust-2.1.1/dtwclust/man/dtwclustFamily-class.Rd | 62 dtwclust-2.1.1/dtwclust/man/lb_improved.Rd | 164 - dtwclust-2.1.1/dtwclust/man/lb_keogh.Rd | 168 - dtwclust-2.1.1/dtwclust/man/reinterpolate.Rd | 42 dtwclust-2.1.1/dtwclust/man/shape_extraction.Rd | 120 - dtwclust-2.1.1/dtwclust/man/zscore.Rd | 48 dtwclust-2.1.1/dtwclust/tests/testthat/helper_all.R | 66 57 files changed, 4008 insertions(+), 4013 deletions(-)
Title: Technical Trading Rules
Description: Functions and data to construct technical trading rules with R.
Author: Joshua Ulrich
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.23-0 dated 2015-07-10 and 0.23-1 dated 2016-03-20
TTR-0.23-0/TTR/tests/unitTests |only TTR-0.23-1/TTR/DESCRIPTION | 8 +++---- TTR-0.23-1/TTR/MD5 | 43 ++++++++++++++++++-------------------- TTR-0.23-1/TTR/R/GMMA.R | 3 +- TTR-0.23-1/TTR/R/MovingAverages.R | 17 +++++++++++++++ TTR-0.23-1/TTR/R/runFun.R | 29 +++++++++++++++++++++++++ TTR-0.23-1/TTR/inst |only TTR-0.23-1/TTR/tests/doRUnit.R | 29 ++++++++++++++----------- 8 files changed, 89 insertions(+), 40 deletions(-)
Title: Public Subject Attention via Wikipedia Page View Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied. For the omnipresent Wikipedia those access statistics
are made available via 'http://stats.grok.se' a server
providing the information as file dumps as well as as web API.
This package provides an easy to use, consistent and traffic
minimizing approach to make those data accessible within R.
Author: Peter Meissner [aut, cre], R Core Team [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 1.1.7 dated 2015-09-23 and 1.1.10 dated 2016-03-20
wikipediatrend-1.1.10/wikipediatrend/DESCRIPTION | 34 wikipediatrend-1.1.10/wikipediatrend/MD5 | 128 wikipediatrend-1.1.10/wikipediatrend/NAMESPACE | 5 wikipediatrend-1.1.10/wikipediatrend/NEWS | 31 wikipediatrend-1.1.10/wikipediatrend/R/html.R | 4 wikipediatrend-1.1.10/wikipediatrend/R/wp_cache.R | 262 wikipediatrend-1.1.10/wikipediatrend/R/wp_check_date_inputs.R | 75 wikipediatrend-1.1.10/wikipediatrend/R/wp_date_functions.r | 6 wikipediatrend-1.1.10/wikipediatrend/R/wp_df.R | 129 wikipediatrend-1.1.10/wikipediatrend/R/wp_download_data.R | 1 wikipediatrend-1.1.10/wikipediatrend/R/wp_expand_ts.R | 26 wikipediatrend-1.1.10/wikipediatrend/R/wp_get_data.R | 3 wikipediatrend-1.1.10/wikipediatrend/R/wp_http_header.R | 2 wikipediatrend-1.1.10/wikipediatrend/R/wp_jsons_to_df.R | 117 wikipediatrend-1.1.10/wikipediatrend/R/wp_linked_pages.R | 5 wikipediatrend-1.1.10/wikipediatrend/R/wp_load_and_save.r | 244 wikipediatrend-1.1.10/wikipediatrend/R/wp_prepare_urls.R | 1 wikipediatrend-1.1.10/wikipediatrend/R/wp_trend.R | 264 wikipediatrend-1.1.10/wikipediatrend/README.md |only wikipediatrend-1.1.10/wikipediatrend/build/vignette.rds |binary wikipediatrend-1.1.10/wikipediatrend/inst/doc/using-wikipediatrend.R | 532 wikipediatrend-1.1.10/wikipediatrend/inst/doc/using-wikipediatrend.Rmd | 1051 wikipediatrend-1.1.10/wikipediatrend/inst/doc/using-wikipediatrend.html | 1056 wikipediatrend-1.1.10/wikipediatrend/inst/extdata/json |only wikipediatrend-1.1.10/wikipediatrend/inst/extdata/wikipediatrend_cache.csv |14228 +++++----- wikipediatrend-1.1.10/wikipediatrend/man/html.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/html2.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/prev_month_end.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/prev_month_start.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/print.wp_df.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/read_utf8_csv.Rd | 6 wikipediatrend-1.1.10/wikipediatrend/man/toUTF8.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_add_to_cache.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_cache.Rd | 5 wikipediatrend-1.1.10/wikipediatrend/man/wp_cache_default.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_cache_file.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_cache_load.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_cache_reset.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_check_date_inputs.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_date.Rd | 14 wikipediatrend-1.1.10/wikipediatrend/man/wp_day.Rd | 6 wikipediatrend-1.1.10/wikipediatrend/man/wp_download_data.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_expand_ts.Rd | 8 wikipediatrend-1.1.10/wikipediatrend/man/wp_get_cache.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_get_data.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_http_header.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_jsons_to_df.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_linked_pages.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_load.Rd | 4 wikipediatrend-1.1.10/wikipediatrend/man/wp_month.Rd | 8 wikipediatrend-1.1.10/wikipediatrend/man/wp_prepare_urls.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_save.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_save_cache.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_set_cache_file.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_set_print_options.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/man/wp_trend.Rd | 78 wikipediatrend-1.1.10/wikipediatrend/man/wp_wday.Rd | 16 wikipediatrend-1.1.10/wikipediatrend/man/wp_year.Rd | 6 wikipediatrend-1.1.10/wikipediatrend/man/wp_yearmonth.Rd | 6 wikipediatrend-1.1.10/wikipediatrend/man/write_utf8_csv.Rd | 2 wikipediatrend-1.1.10/wikipediatrend/tests/testthat/extdata/wikipediatrend_cache.csv |12278 ++++---- wikipediatrend-1.1.10/wikipediatrend/tests/testthat/test.csv | 62 wikipediatrend-1.1.10/wikipediatrend/tests/testthat/test_caching_gathering.R | 222 wikipediatrend-1.1.10/wikipediatrend/tests/testthat/test_date_functions.R | 16 wikipediatrend-1.1.10/wikipediatrend/vignettes/using-wikipediatrend.Rmd | 81 wikipediatrend-1.1.7/wikipediatrend/R/aa_pversion_inc.r |only wikipediatrend-1.1.7/wikipediatrend/man/pversion_inc.Rd |only 67 files changed, 16534 insertions(+), 14534 deletions(-)
More information about wikipediatrend at CRAN
Permanent link
Title: Change-Point Estimation using Shape-Restricted Splines
Description: In a scatterplot where the response variable is Gaussian, Poisson or binomial, we consider the case in which the mean function is smooth with a change-point, which is a mode, an inflection point or a jump point. The main routine estimates the mean curve and the change-point as well using shape-restricted B-splines. An optional subroutine delivering a bootstrap confidence interval for the change-point is incorporated in the main routine.
Author: Xiyue Liao and Mary C Meyer
Maintainer: Xiyue Liao <xiyue@rams.colostate.edu>
Diff between ShapeChange versions 1.2 dated 2016-01-14 and 1.3 dated 2016-03-20
DESCRIPTION | 8 - MD5 | 8 - R/ShapeChange.R | 315 ++++++++++++++++++++++++++++++++++++--------- man/ShapeChange-package.Rd | 4 man/changept.Rd | 5 5 files changed, 268 insertions(+), 72 deletions(-)
Title: Automatic Marking of R Assignments
Description: Automatic marking of R assignments for students and teachers based
on 'testthat' test suites.
Author: Mans Magnusson, Oscar Pettersson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between markmyassignment versions 0.4.0 dated 2016-01-18 and 0.5.0 dated 2016-03-20
markmyassignment-0.4.0/markmyassignment/README.md |only markmyassignment-0.5.0/markmyassignment/DESCRIPTION | 11 +++-- markmyassignment-0.5.0/markmyassignment/MD5 | 13 +++--- markmyassignment-0.5.0/markmyassignment/R/set_assignment.R | 2 - markmyassignment-0.5.0/markmyassignment/inst/doc/markmyassignment.html | 8 ++-- markmyassignment-0.5.0/markmyassignment/tests/testthat/test-mark_my_assignment.R | 20 +++------- markmyassignment-0.5.0/markmyassignment/tests/testthat/test-mark_my_file.R | 20 +++++----- markmyassignment-0.5.0/markmyassignment/tests/testthat/test-set_assignment.R | 16 ++++---- 8 files changed, 43 insertions(+), 47 deletions(-)
More information about markmyassignment at CRAN
Permanent link
Title: Interpreting Time Series and Autocorrelated Data Using GAMMs
Description: GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999)
as implemented in the R package mgcv (Wood, S.N., 2006; 2011) is a nonlinear
regression analysis which is particularly useful for time course data such as
EEG, pupil dilation, gaze data (eye tracking), and articulography recordings,
but also for behavioral data such as reaction times and response data. As time
course measures are sensitive to autocorrelation problems, GAMMs implements
methods to reduce the autocorrelation problems. This package includes functions
for the evaluation of GAMM models (e.g., model comparisons, determining regions
of significance, inspection of autocorrelational structure in residuals)
and interpreting of GAMMs (e.g., visualization of complex interactions, and
contrasts).
Author: Jacolien van Rij [aut, cre],
Martijn Wieling [aut],
R. Harald Baayen [aut],
Hedderik van Rijn [ctb]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Diff between itsadug versions 1.0.1 dated 2015-07-02 and 2.0 dated 2016-03-20
itsadug-1.0.1/itsadug/R/acf.n.plots.R |only itsadug-1.0.1/itsadug/R/acf.plot.R |only itsadug-1.0.1/itsadug/R/acf_resid.R |only itsadug-1.0.1/itsadug/R/basic_plots.R |only itsadug-1.0.1/itsadug/R/compareML.R |only itsadug-1.0.1/itsadug/R/data_utility_functions.R |only itsadug-1.0.1/itsadug/R/find_difference.R |only itsadug-1.0.1/itsadug/R/fvisgam.R |only itsadug-1.0.1/itsadug/R/helpers.R |only itsadug-1.0.1/itsadug/R/inspect_random.R |only itsadug-1.0.1/itsadug/R/inspect_residuals.R |only itsadug-1.0.1/itsadug/R/model_utility_functions.R |only itsadug-1.0.1/itsadug/R/plotSurface.R |only itsadug-1.0.1/itsadug/R/plot_diff.R |only itsadug-1.0.1/itsadug/R/plot_parametric.R |only itsadug-1.0.1/itsadug/R/plot_smooth.R |only itsadug-1.0.1/itsadug/R/plot_topo.R |only itsadug-1.0.1/itsadug/R/plot_utility_functions.R |only itsadug-1.0.1/itsadug/R/predictions.R |only itsadug-1.0.1/itsadug/R/pvisgam.R |only itsadug-1.0.1/itsadug/R/resid_gam.R |only itsadug-1.0.1/itsadug/R/start_event.R |only itsadug-1.0.1/itsadug/R/version.R |only itsadug-1.0.1/itsadug/inst/doc/overview.R |only itsadug-1.0.1/itsadug/inst/doc/overview.Rmd |only itsadug-1.0.1/itsadug/inst/doc/overview.html |only itsadug-1.0.1/itsadug/man/countValues.Rd |only itsadug-1.0.1/itsadug/man/getCountData.Rd |only itsadug-1.0.1/itsadug/man/horiz_error.Rd |only itsadug-1.0.1/itsadug/vignettes/overview.Rmd |only itsadug-2.0/itsadug/DESCRIPTION | 41 - itsadug-2.0/itsadug/MD5 | 191 ++--- itsadug-2.0/itsadug/NAMESPACE | 24 itsadug-2.0/itsadug/R/acf.R |only itsadug-2.0/itsadug/R/data.R | 5 itsadug-2.0/itsadug/R/eval.R |only itsadug-2.0/itsadug/R/inspect.R |only itsadug-2.0/itsadug/R/itsadug.R | 177 +++- itsadug-2.0/itsadug/R/pca.R |only itsadug-2.0/itsadug/R/plot.R |only itsadug-2.0/itsadug/R/predict.R |only itsadug-2.0/itsadug/R/test.R |only itsadug-2.0/itsadug/R/util.R |only itsadug-2.0/itsadug/build/vignette.rds |binary itsadug-2.0/itsadug/inst/NEWS | 144 +-- itsadug-2.0/itsadug/inst/doc/acf.R | 244 +++--- itsadug-2.0/itsadug/inst/doc/acf.Rmd | 339 ++++----- itsadug-2.0/itsadug/inst/doc/acf.html | 806 ++++++---------------- itsadug-2.0/itsadug/inst/doc/inspect.R |only itsadug-2.0/itsadug/inst/doc/inspect.Rmd |only itsadug-2.0/itsadug/inst/doc/inspect.html |only itsadug-2.0/itsadug/inst/doc/test.R |only itsadug-2.0/itsadug/inst/doc/test.Rmd |only itsadug-2.0/itsadug/inst/doc/test.html |only itsadug-2.0/itsadug/man/acf_n_plots.Rd | 59 - itsadug-2.0/itsadug/man/acf_plot.Rd | 34 itsadug-2.0/itsadug/man/acf_resid.Rd | 49 - itsadug-2.0/itsadug/man/addInterval.Rd | 36 itsadug-2.0/itsadug/man/add_bars.Rd |only itsadug-2.0/itsadug/man/alpha.Rd | 32 itsadug-2.0/itsadug/man/alphaPalette.Rd | 41 - itsadug-2.0/itsadug/man/check_normaldist.Rd | 26 itsadug-2.0/itsadug/man/check_resid.Rd | 72 + itsadug-2.0/itsadug/man/color_contour.Rd | 44 - itsadug-2.0/itsadug/man/compareML.Rd | 69 + itsadug-2.0/itsadug/man/convertNonAlphanumeric.Rd | 25 itsadug-2.0/itsadug/man/derive_timeseries.Rd |only itsadug-2.0/itsadug/man/diagnostics.Rd |only itsadug-2.0/itsadug/man/diff_terms.Rd | 19 itsadug-2.0/itsadug/man/dotplot_error.Rd | 53 - itsadug-2.0/itsadug/man/drawArrows.Rd |only itsadug-2.0/itsadug/man/eeg.Rd | 6 itsadug-2.0/itsadug/man/emptyPlot.Rd | 60 - itsadug-2.0/itsadug/man/errorBars.Rd | 72 + itsadug-2.0/itsadug/man/fadeRug.Rd | 45 - itsadug-2.0/itsadug/man/fill_area.Rd | 42 - itsadug-2.0/itsadug/man/findAbsMin.Rd | 22 itsadug-2.0/itsadug/man/find_difference.Rd | 38 - itsadug-2.0/itsadug/man/find_n_neighbors.Rd | 20 itsadug-2.0/itsadug/man/fvisgam.Rd | 109 +- itsadug-2.0/itsadug/man/gamtabs.Rd | 38 - itsadug-2.0/itsadug/man/getCoords.Rd | 67 + itsadug-2.0/itsadug/man/getDec.Rd |only itsadug-2.0/itsadug/man/getFigCoords.Rd | 38 - itsadug-2.0/itsadug/man/getProps.Rd |only itsadug-2.0/itsadug/man/getRange.Rd |only itsadug-2.0/itsadug/man/get_coefs.Rd | 24 itsadug-2.0/itsadug/man/get_difference.Rd | 45 - itsadug-2.0/itsadug/man/get_fitted.Rd |only itsadug-2.0/itsadug/man/get_modelterm.Rd | 56 - itsadug-2.0/itsadug/man/get_pca_predictions.Rd |only itsadug-2.0/itsadug/man/get_predictions.Rd | 46 - itsadug-2.0/itsadug/man/get_random.Rd | 28 itsadug-2.0/itsadug/man/gradientLegend.Rd | 79 +- itsadug-2.0/itsadug/man/group_sort.Rd | 24 itsadug-2.0/itsadug/man/info.Rd | 8 itsadug-2.0/itsadug/man/infoMessages.Rd | 9 itsadug-2.0/itsadug/man/inspect_random.Rd | 53 - itsadug-2.0/itsadug/man/itsadug.Rd | 130 +-- itsadug-2.0/itsadug/man/list2str.Rd |only itsadug-2.0/itsadug/man/marginDensityPlot.Rd |only itsadug-2.0/itsadug/man/missing_est.Rd | 19 itsadug-2.0/itsadug/man/move_n_point.Rd | 25 itsadug-2.0/itsadug/man/plot_data.Rd |only itsadug-2.0/itsadug/man/plot_diff.Rd | 70 + itsadug-2.0/itsadug/man/plot_diff2.Rd | 49 - itsadug-2.0/itsadug/man/plot_error.Rd | 70 + itsadug-2.0/itsadug/man/plot_image.Rd |only itsadug-2.0/itsadug/man/plot_modelfit.Rd |only itsadug-2.0/itsadug/man/plot_parametric.Rd | 60 - itsadug-2.0/itsadug/man/plot_pca_surface.Rd |only itsadug-2.0/itsadug/man/plot_smooth.Rd | 116 +-- itsadug-2.0/itsadug/man/plot_topo.Rd | 71 - itsadug-2.0/itsadug/man/plotsurface.Rd | 64 + itsadug-2.0/itsadug/man/print_summary.Rd | 20 itsadug-2.0/itsadug/man/pvisgam.Rd | 103 +- itsadug-2.0/itsadug/man/report_stats.Rd |only itsadug-2.0/itsadug/man/resid_gam.Rd | 66 + itsadug-2.0/itsadug/man/rug_model.Rd |only itsadug-2.0/itsadug/man/se.Rd | 15 itsadug-2.0/itsadug/man/simdat.Rd | 6 itsadug-2.0/itsadug/man/start_event.Rd | 24 itsadug-2.0/itsadug/man/start_value_rho.Rd |only itsadug-2.0/itsadug/man/summary_data.Rd | 20 itsadug-2.0/itsadug/man/timeBins.Rd | 28 itsadug-2.0/itsadug/man/wald_gam.Rd |only itsadug-2.0/itsadug/vignettes/acf.Rmd | 339 ++++----- itsadug-2.0/itsadug/vignettes/inspect.Rmd |only itsadug-2.0/itsadug/vignettes/test.Rmd |only 129 files changed, 2499 insertions(+), 2255 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling.
Markov models (homogeneous and non-homogeneous)
for health economic evaluation. Model comparison,
sensitivity and probabilistic analysis.
Author: Kevin Zarca [aut], Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.2.0 dated 2016-02-08 and 0.3.0 dated 2016-03-20
COPYING | 2 DESCRIPTION | 10 - MD5 | 111 ++++++------- NAMESPACE | 17 +- R/errors.R |only R/gho_mortality.R |only R/imports.R | 14 + R/matrix.R | 35 +++- R/model.R | 79 ++++----- R/parameters.R | 13 + R/resamp.R | 12 + R/run_model.R | 81 ++++++--- R/sensitivity.R | 44 +++-- R/states.R | 10 + R/utils.R | 8 README.md | 14 + build/vignette.rds |binary inst/doc/homogeneous.R | 29 ++- inst/doc/homogeneous.Rmd | 37 ++-- inst/doc/homogeneous.html | 184 +++++++++++++--------- inst/doc/introduction.R | 14 + inst/doc/introduction.Rmd | 25 ++- inst/doc/introduction.html | 138 ++++++++++------ inst/doc/non-homogeneous.R | 39 ---- inst/doc/non-homogeneous.Rmd | 74 +++----- inst/doc/non-homogeneous.html | 249 +++++++++++++++--------------- inst/doc/probabilistic.R | 12 + inst/doc/probabilistic.Rmd | 21 ++ inst/doc/probabilistic.html | 122 +++++++++----- inst/doc/sensitivity.R | 2 inst/doc/sensitivity.Rmd | 3 inst/doc/sensitivity.html | 79 +++++---- inst/examples/example_define_model.R | 10 - inst/examples/example_run_models.R | 4 inst/examples/example_run_newdata.R | 2 inst/examples/example_run_probabilistic.R | 2 inst/examples/example_run_sensitivity.R | 2 man/define_matrix.Rd | 16 + man/define_model.Rd | 20 -- man/define_parameters.Rd | 9 - man/define_state.Rd | 5 man/define_state_list.Rd | 6 man/discount.Rd | 2 man/get_who_mr_.Rd |only man/normalize_ce.Rd | 4 man/run_models.Rd | 20 +- man/run_newdata.Rd | 2 man/run_probabilistic.Rd | 4 man/run_sensitivity.Rd | 2 tests/testthat/test_model.R | 112 ++++++++----- tests/testthat/test_newdata.R | 8 tests/testthat/test_run_model.R | 28 +-- tests/testthat/test_states.R | 2 vignettes/homogeneous.Rmd | 37 ++-- vignettes/introduction.Rmd | 25 ++- vignettes/non-homogeneous.Rmd | 74 +++----- vignettes/probabilistic.Rmd | 21 ++ vignettes/sensitivity.Rmd | 3 58 files changed, 1102 insertions(+), 796 deletions(-)
Title: Highest (Posterior) Density Intervals
Description: A generic function and a set of methods to calculate highest density intervals for a variety of classes of objects which can specify a probability density distribution, including MCMC output, fitted density objects, and functions.
Author: Mike Meredith and John Kruschke
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between HDInterval versions 0.1.1 dated 2016-02-17 and 0.1.2 dated 2016-03-20
DESCRIPTION | 10 +++---- MD5 | 15 ++++++----- NEWS | 12 +++++++++ R/checkCredMass.R | 2 - R/hdi.R | 28 +++++++-------------- R/hdiVector.R |only inst/tests/testthat/test-hdi.R | 43 +++++++++++++++++++++------------ inst/tests/testthat/test-hdi_density.R | 6 ++-- man/hdi.Rd | 4 ++- 9 files changed, 70 insertions(+), 50 deletions(-)
Title: Graphical User Interface for bayesTFR, bayesLife and bayesPop
Description: Provides graphical user interface for the packages 'bayesTFR', 'bayesLife' and 'bayesPop'.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesDem versions 2.4-1 dated 2014-04-29 and 2.5-0 dated 2016-03-20
ChangeLog | 8 ++ DESCRIPTION | 18 ++--- MD5 | 16 ++-- NAMESPACE | 4 - R/bayesDem_ini.R | 2 R/handlers_and_fncs.R | 4 - R/pop-predict.R | 8 +- R/pop-results.R | 160 ++++++++++++++++++++++++++++++++++++++++++++++++ man/bayesDem-package.Rd | 4 - 9 files changed, 199 insertions(+), 25 deletions(-)
Title: Binary Classifier and Regression Model Interpretation Functions
Description: Compute permutation- based performance measures and create partial
dependence plots for (cross-validated) 'randomForest' and 'ada' models.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@GMail.com>
Diff between interpretR versions 0.2.3 dated 2015-06-23 and 0.2.4 dated 2016-03-19
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 7 ++++++- R/parDepPlot.R | 27 +++++++++++++++++++-------- inst/NEWS | 4 ++++ man/parDepPlot.Rd | 4 +++- 6 files changed, 42 insertions(+), 20 deletions(-)
Title: An API Client for the Internet Archive
Description: Search the Internet Archive, retrieve metadata, and download
files.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between internetarchive versions 0.1.4 dated 2015-09-28 and 0.1.5 dated 2016-03-19
internetarchive-0.1.4/internetarchive/NEWS |only internetarchive-0.1.5/internetarchive/DESCRIPTION | 11 - internetarchive-0.1.5/internetarchive/MD5 | 48 ++-- internetarchive-0.1.5/internetarchive/NAMESPACE | 3 internetarchive-0.1.5/internetarchive/NEWS.md |only internetarchive-0.1.5/internetarchive/R/ia_download.R | 6 internetarchive-0.1.5/internetarchive/R/ia_get_item.R | 5 internetarchive-0.1.5/internetarchive/R/ia_keyword_search.R | 4 internetarchive-0.1.5/internetarchive/R/ia_search.R | 4 internetarchive-0.1.5/internetarchive/R/internetarchive-package.R | 3 internetarchive-0.1.5/internetarchive/build/vignette.rds |binary internetarchive-0.1.5/internetarchive/inst/doc/internet-archive.R | 20 - internetarchive-0.1.5/internetarchive/inst/doc/internet-archive.Rmd | 17 - internetarchive-0.1.5/internetarchive/inst/doc/internet-archive.html | 103 +++++----- internetarchive-0.1.5/internetarchive/man/ia_browse.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_download.Rd | 6 internetarchive-0.1.5/internetarchive/man/ia_files.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_get_items.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_item_id.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_keyword_search.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_list_fields.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_metadata.Rd | 2 internetarchive-0.1.5/internetarchive/man/ia_search.Rd | 2 internetarchive-0.1.5/internetarchive/man/internetarchive.Rd | 2 internetarchive-0.1.5/internetarchive/tests/testthat/hecker_meta.rds |binary internetarchive-0.1.5/internetarchive/vignettes/internet-archive.Rmd | 15 - 26 files changed, 121 insertions(+), 142 deletions(-)
More information about internetarchive at CRAN
Permanent link
Title: Morphological Analysis and Spell Checker for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex or manual document.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between hunspell versions 1.1 dated 2016-03-12 and 1.2 dated 2016-03-19
hunspell-1.1/hunspell/inst/dict/en_US |only hunspell-1.2/hunspell/DESCRIPTION | 9 - hunspell-1.2/hunspell/MD5 | 35 +++-- hunspell-1.2/hunspell/NAMESPACE | 5 hunspell-1.2/hunspell/NEWS | 6 hunspell-1.2/hunspell/R/RcppExports.R | 16 +- hunspell-1.2/hunspell/R/hunspell.R | 190 +++++++++++++++++++++-------- hunspell-1.2/hunspell/inst/dict/README.txt |only hunspell-1.2/hunspell/inst/dict/en_US.aff |only hunspell-1.2/hunspell/inst/dict/en_US.dic |only hunspell-1.2/hunspell/man/hunspell.Rd | 115 ++++++++++++----- hunspell-1.2/hunspell/src/Makevars.in | 4 hunspell-1.2/hunspell/src/Makevars.win | 4 hunspell-1.2/hunspell/src/RcppExports.cpp | 67 +++++++--- hunspell-1.2/hunspell/src/check.cpp | 100 ++++----------- hunspell-1.2/hunspell/src/find.cpp | 140 ++++++++++++++------- hunspell-1.2/hunspell/src/utils.h |only hunspell-1.2/hunspell/tests |only 18 files changed, 450 insertions(+), 241 deletions(-)
Title: Generate Functions to Get or Set Global Options
Description: It provides more controls on the option values such as validation
and filtering on the values, making options invisible or private.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GlobalOptions versions 0.0.8 dated 2015-08-18 and 0.0.9 dated 2016-03-19
GlobalOptions-0.0.8/GlobalOptions/inst/doc/GlobalOptions.Rnw |only GlobalOptions-0.0.8/GlobalOptions/inst/doc/GlobalOptions.pdf |only GlobalOptions-0.0.8/GlobalOptions/vignettes/GlobalOptions.Rnw |only GlobalOptions-0.0.9/GlobalOptions/DESCRIPTION | 10 GlobalOptions-0.0.9/GlobalOptions/MD5 | 27 - GlobalOptions-0.0.9/GlobalOptions/NEWS | 5 GlobalOptions-0.0.9/GlobalOptions/R/class.R | 46 +- GlobalOptions-0.0.9/GlobalOptions/R/setGlobalOptions.R | 129 +++++- GlobalOptions-0.0.9/GlobalOptions/build/vignette.rds |binary GlobalOptions-0.0.9/GlobalOptions/inst/doc/GlobalOptions.R | 211 +++++++--- GlobalOptions-0.0.9/GlobalOptions/inst/doc/GlobalOptions.Rmd |only GlobalOptions-0.0.9/GlobalOptions/inst/doc/GlobalOptions.html |only GlobalOptions-0.0.9/GlobalOptions/inst/tests/test.R | 94 ++++ GlobalOptions-0.0.9/GlobalOptions/man/Assign.GlobalOptionsFun.rd | 13 GlobalOptions-0.0.9/GlobalOptions/man/Subset.GlobalOptionsFun.rd | 11 GlobalOptions-0.0.9/GlobalOptions/man/setGlobalOptions.rd | 17 GlobalOptions-0.0.9/GlobalOptions/vignettes/GlobalOptions.Rmd |only GlobalOptions-0.0.9/GlobalOptions/vignettes/custom.css |only 18 files changed, 461 insertions(+), 102 deletions(-)
Title: End-Member Modelling of Grain-Size Data
Description: End-member modelling analysis of grain-size data.
Author: Michael Dietze, Elisabeth Dietze
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>
Diff between EMMAgeo versions 0.9.1 dated 2013-10-14 and 0.9.4 dated 2016-03-19
EMMAgeo-0.9.1/EMMAgeo/R/test.L.R |only EMMAgeo-0.9.1/EMMAgeo/R/test.lw.R |only EMMAgeo-0.9.1/EMMAgeo/data/X.artificial.rda |only EMMAgeo-0.9.1/EMMAgeo/man/X.artificial.Rd |only EMMAgeo-0.9.1/EMMAgeo/man/test.L.Rd |only EMMAgeo-0.9.1/EMMAgeo/man/test.lw.Rd |only EMMAgeo-0.9.4/EMMAgeo/DESCRIPTION | 24 - EMMAgeo-0.9.4/EMMAgeo/MD5 | 91 ++-- EMMAgeo-0.9.4/EMMAgeo/NAMESPACE | 62 ++ EMMAgeo-0.9.4/EMMAgeo/NEWS | 32 + EMMAgeo-0.9.4/EMMAgeo/R/EMMA.R | 512 ++++++++++++++--------- EMMAgeo-0.9.4/EMMAgeo/R/EMMAgeo-internal.R | 250 +++++------ EMMAgeo-0.9.4/EMMAgeo/R/EMMAgeo-package.R |only EMMAgeo-0.9.4/EMMAgeo/R/GUI.R |only EMMAgeo-0.9.4/EMMAgeo/R/Mqs.uncertainty.R | 292 ++++++------- EMMAgeo-0.9.4/EMMAgeo/R/check.data.R | 136 +++--- EMMAgeo-0.9.4/EMMAgeo/R/convert.units.R | 67 +-- EMMAgeo-0.9.4/EMMAgeo/R/create.EM.R | 107 ++-- EMMAgeo-0.9.4/EMMAgeo/R/define.limits.R | 73 +-- EMMAgeo-0.9.4/EMMAgeo/R/get.l.R |only EMMAgeo-0.9.4/EMMAgeo/R/get.l.opt.R |only EMMAgeo-0.9.4/EMMAgeo/R/get.limits.R |only EMMAgeo-0.9.4/EMMAgeo/R/get.q.R |only EMMAgeo-0.9.4/EMMAgeo/R/interpolate.classes.R | 147 +++--- EMMAgeo-0.9.4/EMMAgeo/R/mix.EM.R | 104 ++-- EMMAgeo-0.9.4/EMMAgeo/R/model.em.R |only EMMAgeo-0.9.4/EMMAgeo/R/residual.EM.R | 95 +--- EMMAgeo-0.9.4/EMMAgeo/R/robust.EM.R | 308 ++++++++----- EMMAgeo-0.9.4/EMMAgeo/R/test.factors.R |only EMMAgeo-0.9.4/EMMAgeo/R/test.l.R |only EMMAgeo-0.9.4/EMMAgeo/R/test.l.max.R |only EMMAgeo-0.9.4/EMMAgeo/R/test.parameters.R | 501 +++++++++++++--------- EMMAgeo-0.9.4/EMMAgeo/R/test.robustness.R | 317 +++++++------- EMMAgeo-0.9.4/EMMAgeo/data/TR.rda |only EMMAgeo-0.9.4/EMMAgeo/data/X.rda |only EMMAgeo-0.9.4/EMMAgeo/data/rEM.rda |only EMMAgeo-0.9.4/EMMAgeo/inst |only EMMAgeo-0.9.4/EMMAgeo/man/EMMA.Rd | 205 ++++----- EMMAgeo-0.9.4/EMMAgeo/man/EMMAgeo-package.Rd | 43 - EMMAgeo-0.9.4/EMMAgeo/man/GUI.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/Mqs.uncertainty.Rd | 249 ++++++----- EMMAgeo-0.9.4/EMMAgeo/man/TR.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/X.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/check.data.Rd | 100 ++-- EMMAgeo-0.9.4/EMMAgeo/man/convert.units.Rd | 72 +-- EMMAgeo-0.9.4/EMMAgeo/man/create.EM.Rd | 117 ++--- EMMAgeo-0.9.4/EMMAgeo/man/define.limits.Rd | 87 ++- EMMAgeo-0.9.4/EMMAgeo/man/get.l.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/get.l.opt.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/get.limits.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/get.q.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/interpolate.classes.Rd | 77 ++- EMMAgeo-0.9.4/EMMAgeo/man/mix.EM.Rd | 115 ++--- EMMAgeo-0.9.4/EMMAgeo/man/model.em.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/rEM.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/residual.EM.Rd | 108 ++-- EMMAgeo-0.9.4/EMMAgeo/man/robust.EM.Rd | 192 ++++---- EMMAgeo-0.9.4/EMMAgeo/man/test.factors.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/test.l.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/test.l.max.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/test.parameters.Rd | 194 +++++--- EMMAgeo-0.9.4/EMMAgeo/man/test.robustness.Rd | 258 ++++++----- 62 files changed, 2781 insertions(+), 2154 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-10 0.2.1
2014-08-04 0.2.0
2014-05-07 0.1.6
2014-01-23 0.1.5
2014-01-07 0.1.4
2013-11-18 0.1.3
2013-10-01 0.1.2
2013-06-26 0.1.1
2013-06-24 0.1.0
Title: Perform Common JavaScript Operations in Shiny Apps using Plain R
Code
Description: Perform common JavaScript operations in Shiny applications without
having to know any JavaScript. Examples include: hiding an element, disabling
an input, resetting an input back to its original value, delaying code execution
by a few seconds, and many more useful functions. 'shinyjs' also includes
a colour picker widget, a colour picker RStudio addin, and can also be used to
easily run your own custom JavaScript functions from R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyjs versions 0.4.0 dated 2016-01-21 and 0.5.0 dated 2016-03-19
DESCRIPTION | 16 +++++----- MD5 | 55 ++++++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 12 +++++++ R/colourInput.R | 1 R/colourPickerGadget.R |only R/extendShinyjs.R | 8 ----- R/ignoreme.R |only R/jsFunc-classFuncs.R | 2 - R/jsFunc-stateFuncs.R | 2 - R/jsFunc-visibilityFuncs.R | 2 - R/shinyjs.R | 5 +-- README.md | 24 +++++++++++---- build/vignette.rds |binary inst/doc/overview.Rmd | 16 +++++++--- inst/doc/overview.html | 18 +++++++---- inst/examples/colourInput/app.R | 8 +++-- inst/examples/demo/ui.R | 13 ++++---- inst/examples/sandbox/ui.R | 16 +++++----- inst/gadgets |only inst/img/colourPickerGadget.gif |only inst/rstudio |only inst/srcjs/shinyjs-default-funcs.js | 14 +++++++-- man/classFuncs.Rd | 2 - man/colourInput.Rd | 1 man/colourPicker.Rd |only man/shinyjs.Rd | 5 +-- man/stateFuncs.Rd | 2 - man/visibilityFuncs.Rd | 2 - vignettes/overview.Rmd | 16 +++++++--- 30 files changed, 156 insertions(+), 85 deletions(-)
Title: Using R to Install Stuff (Such As: R, Rtools, RStudio, Git, and
More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.17.0 dated 2015-09-14 and 0.17.4 dated 2016-03-19
ChangeLog | 158 +++++++++++++++++++++ DESCRIPTION | 10 - MD5 | 196 +++++++++++++-------------- NAMESPACE | 2 NEWS | 37 +++++ R/RStudio_CRAN_data.R | 14 - R/geo_functions.R | 4 R/install.R | 38 +++-- R/startup.R | 6 R/updateR.R | 41 +++-- R/xlsx2csv.R | 2 README.md | 7 TODO | 5 man/R_version_in_a_folder.Rd | 4 man/add.installr.GUI.Rd | 6 man/add_load_installr_on_startup_menu.Rd | 2 man/add_remove_installr_from_startup_menu.Rd | 2 man/add_to_.First_in_Rprofile.site.Rd | 2 man/ask.user.for.a.row.Rd | 6 man/ask.user.yn.question.Rd | 14 - man/barplot_package_users_per_day.Rd | 8 - man/browse.latest.R.NEWS.Rd | 8 - man/check.for.updates.R.Rd | 12 - man/check.integer.Rd | 2 man/checkMD5sums2.Rd | 2 man/copy.packages.between.libraries.Rd | 12 - man/cranometer.Rd | 16 +- man/create.global.library.Rd | 2 man/download_RStudio_CRAN_data.Rd | 10 - man/fetch_tag_from_Rd.Rd | 6 man/file.name.from.url.Rd | 2 man/format_RStudio_CRAN_data.Rd | 10 - man/freegeoip.Rd | 4 man/get.installed.R.folders.Rd | 12 - man/get_Rscript_PID.Rd | 10 - man/get_pid.Rd | 4 man/get_tasklist.Rd | 8 - man/install.7zip.Rd | 2 man/install.CMake.Rd | 11 - man/install.Cygwin.Rd | 2 man/install.FFmpeg.Rd | 4 man/install.GitHub.Rd | 2 man/install.GraphicsMagick.Rd | 2 man/install.ImageMagick.Rd | 2 man/install.LaTeX2RTF.Rd | 2 man/install.LyX.Rd | 4 man/install.MikTeX.Rd | 2 man/install.R.Rd | 10 - man/install.RStudio.Rd | 2 man/install.Rdevel.Rd | 12 - man/install.Rtools.Rd | 8 - man/install.SWFTools.Rd | 4 man/install.Texmaker.Rd | 2 man/install.URL.Rd | 2 man/install.git.Rd | 8 - man/install.notepadpp.Rd | 2 man/install.npptor.Rd | 2 man/install.packages.zip.Rd | 2 man/install.pandoc.Rd | 10 - man/installr-package.Rd | 2 man/installr.Rd | 6 man/is.RStudio.Rd | 4 man/is.Rgui.Rd | 4 man/is.empty.Rd | 12 - man/is.exe.installed.Rd | 4 man/is.windows.Rd | 2 man/is_in_.First_in_Rprofile.site.Rd | 2 man/kill_all_Rscript_s.Rd | 10 - man/kill_pid.Rd | 8 - man/kill_process.Rd | 8 - man/lineplot_package_downloads.Rd | 10 - man/load_installr_on_startup.Rd | 4 man/most_downloaded_packages.Rd | 8 - man/myip.Rd | 6 man/os.hibernate.Rd | 8 - man/os.lock.Rd | 6 man/os.manage.Rd | 14 - man/os.restart.Rd | 4 man/os.shutdown.Rd | 6 man/os.sleep.Rd | 4 man/package_authors.Rd | 10 - man/pkgDNLs_worldmapcolor.Rd | 8 - man/read_RStudio_CRAN_data.Rd | 8 - man/remove.installr.GUI.Rd | 2 man/remove_from_.First_in_Rprofile.site.Rd | 2 man/rename_r_to_R.Rd | 10 - man/require2.Rd | 2 man/restart_RGui.Rd | 2 man/rm_installr_from_startup.Rd | 4 man/source.https.Rd | 6 man/system.PATH.Rd | 6 man/turn.number.version.Rd | 4 man/turn.version.to.number.Rd | 2 man/turn.version.to.number1.Rd | 2 man/uninstall.R.Rd | 6 man/uninstall.packages.Rd | 6 man/up_folder.Rd | 2 man/updateR.Rd | 12 - man/xlsx2csv.Rd | 4 99 files changed, 622 insertions(+), 389 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.4 dated 2016-01-07 and 1.5 dated 2016-03-19
DESCRIPTION | 8 - MD5 | 12 +- R/supportRegion.R | 14 +-- README.md | 2 inst/doc/hisse-vignette.Rmd | 19 ++-- inst/doc/hisse-vignette.html | 192 +++++++++++++++++++++++-------------------- vignettes/hisse-vignette.Rmd | 19 ++-- 7 files changed, 143 insertions(+), 123 deletions(-)
Title: Fuzzy Measure Tools for R
Description: Various tools for handling fuzzy measures, calculating Shapley value and Interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using 'lpsolve' package, whose source in C adapted to the R environment
is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package.
Author: Gleb Beliakov [aut, cre],
Quan Vu [ctb],
Andrei Kelarev [ctb],
Michel Berkelaar [ctb],
Kjell Eikland [ctb],
Samuel E. Buttrey and others [ctb]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>
Diff between Rfmtool versions 1.1 dated 2016-03-17 and 1.2 dated 2016-03-19
DESCRIPTION | 4 ++-- MD5 | 8 ++++---- inst/doc/Rfmtool_manual.pdf |binary src/fuzzymeasurefit.cpp | 8 ++++++++ src/wrapper.cpp | 2 +- 5 files changed, 15 insertions(+), 7 deletions(-)
Title: Circle Plot with Bundled Edges
Description: Generates interactive circle plots with the nodes around the
circumference and linkages between the connected nodes using hierarchical
edge bundling via the D3 JavaScript library. See <http://d3js.org/> for more
information on D3.
Author: Mike Bostock [aut, cph] (d3.js library and much of edgebundle code in
htmlwidgets/lib, http://d3js.org),
Ellis Patrick [aut],
Kent Russell [ctb],
Garth Tarr [aut, cre]
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between edgebundleR versions 0.1.2 dated 2015-11-16 and 0.1.4 dated 2016-03-19
DESCRIPTION | 21 ++++++++++++++------- MD5 | 9 ++++++--- README.md | 12 ++++++++++-- inst/htmlwidgets/edgebundleR.yaml | 5 ++++- inst/htmlwidgets/lib/d3 |only 5 files changed, 34 insertions(+), 13 deletions(-)
Title: Print Nicely Formatted Comments for Use in Script Files
Description: Functions to
produce nicely formatted comments to use in R-scripts (or
Latex/HTML/markdown etc). A comment with formatting is printed to the
console and can then be copied to a script.
Author: Erik Bulow
Maintainer: Erik Bulow <erik.bulow@rccvast.se>
Diff between commentr versions 1.0.1 dated 2015-08-19 and 1.0.4 dated 2016-03-19
DESCRIPTION | 12 +++++----- MD5 | 23 ++++++++++--------- NAMESPACE | 2 - NEWS.md |only README.md | 16 +++++-------- man/comment.Rd | 42 +++++++++++++++++------------------ man/comment_end.Rd | 2 - man/comment_start.Rd | 2 - man/comment_width.Rd | 3 +- man/empty_line.Rd | 2 - man/full_line.Rd | 2 - man/out.Rd | 4 +-- tests/testthat/test-help_functions.R | 21 ++++++++--------- 13 files changed, 66 insertions(+), 65 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R
without printing the content of graphics windows to an embosser of some kind. This
is not as immediate as is required for efficient access to statistical output.
The functions here are created so that blind people can make even better use
of R. This includes the text descriptions of graphs, convenience functions
to replace the functionality offered in many GUI front ends, and experimental
functionality for optimising graphical content to prepare it for embossing as
tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Duncan Murdoch [ctb], Greg Snow
[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie
[ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.24.0 dated 2016-03-17 and 0.24.1 dated 2016-03-19
DESCRIPTION | 8 +-- MD5 | 28 ++++++------- R/Options.R | 27 +++++++------ R/SetupBrailleR.R | 36 ++++++++++------- R/zzz.R | 9 ++-- inst/NEWS | 6 ++ inst/doc/BrailleRHistory.html | 33 ++++++++-------- inst/doc/Ex1histograms.html | 85 ++++++++++++++++++++---------------------- inst/doc/GettingStarted.R | 8 +-- inst/doc/GettingStarted.Rmd | 4 - inst/doc/GettingStarted.html | 3 - man/BrailleR-package.Rd | 4 - man/SetOptions.Rd | 26 +++++------- man/SetupBrailleR.Rd | 6 +- vignettes/GettingStarted.Rmd | 4 - 15 files changed, 150 insertions(+), 137 deletions(-)
Title: Fitting Routines for the Vitality Family of Mortality Models
Description: Provides fitting routines for four versions of the
Vitality family of mortality models.
Author: Gregor Passolt, James J. Anderson, Ting Li, David H. Salinger, David J. Sharrow
Maintainer: David J. Sharrow <dsharrow@uw.edu>
Diff between vitality versions 1.1 dated 2014-12-10 and 1.2 dated 2016-03-19
DESCRIPTION | 9 +-- MD5 | 54 ++++++++++-------- NAMESPACE | 21 ++++++- R/mortality_rate.R | 28 +++++++++ R/vitality.4p.R | 107 ++++++++++++++++++++++++++++++------ R/vitality.6p.R | 151 ++++++++++++++++++++++++++++------------------------ data/daphnia.rda |only man/SurvFn.4p.Rd | 6 +- man/SurvFn.6p.Rd | 6 +- man/SurvFn.ex.4p.Rd |only man/SurvFn.ex.6p.Rd |only man/SurvFn.in.4p.Rd |only man/SurvFn.in.6p.Rd |only man/daphnia.Rd |only man/dataPrep.Rd | 2 man/ft.6p.Rd | 2 man/indexFinder.Rd | 4 - man/mu.vd1.6p.Rd | 2 man/mu.vd2.6p.Rd | 4 - man/mu.vd3.6p.Rd |only man/mu.vd4.6p.Rd |only man/plotting.4p.Rd | 4 - man/plotting.6p.Rd | 8 +- man/plotting.k.Rd | 4 - man/plotting.ku.Rd | 2 man/vft.4p.Rd | 2 man/vft.6p.Rd | 2 man/vitality.4p.Rd | 50 +++++++++++++---- man/vitality.6p.Rd | 48 ++++++++++++---- man/vitality.Rd | 47 ++++++++-------- man/vitality.k.Rd | 39 ++++++++++--- man/vitality.ku.Rd | 41 ++++++++++---- 32 files changed, 438 insertions(+), 205 deletions(-)
Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between NAM versions 1.4.3 dated 2016-01-28 and 1.4.4 dated 2016-03-19
DESCRIPTION | 10 - MD5 | 24 +- R/gibbs.R | 319 +++++++++++++++++++++++++++++++++++++- R/gwas3c.R | 4 R/wrapGE.R | 203 ++++++++++++++++++------ inst/doc/Bioinformatics_2015.pdf |only inst/doc/gwa_GxE_Interactions.pdf |only inst/doc/vignette2.Rmd | 68 +------- inst/doc/vignette2.html | 64 ------- man/Internals.Rd | 1 man/NAM-package.Rd | 4 man/gibbs.Rd | 9 - man/gwas.Rd | 10 - vignettes/vignette2.Rmd | 68 +------- 14 files changed, 536 insertions(+), 248 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data. Includes fast algorithm for computing non-parametric maximum likelihood estimator.
Author: Clifford Anderson-Bergman; uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.3.3 dated 2016-01-07 and 1.3.4 dated 2016-03-19
icenReg-1.3.3/icenReg/src/Eigen_local |only icenReg-1.3.4/icenReg/DESCRIPTION | 13 icenReg-1.3.4/icenReg/MD5 | 306 -------- icenReg-1.3.4/icenReg/NAMESPACE | 5 icenReg-1.3.4/icenReg/NEWS | 8 icenReg-1.3.4/icenReg/R/Utilities.R | 59 + icenReg-1.3.4/icenReg/R/referenceClasses.R | 75 +- icenReg-1.3.4/icenReg/R/user_functions.R | 361 ++++++++-- icenReg-1.3.4/icenReg/data/IR_diabetes.RData |binary icenReg-1.3.4/icenReg/man/ic_np.Rd |only icenReg-1.3.4/icenReg/man/ic_par.Rd | 2 icenReg-1.3.4/icenReg/man/ic_sp.Rd | 11 icenReg-1.3.4/icenReg/man/imputeCens.Rd | 3 icenReg-1.3.4/icenReg/src/icenReg.cpp | 7 icenReg-1.3.4/icenReg/src/icenReg_files/EMICM.cpp |only icenReg-1.3.4/icenReg/src/icenReg_files/EMICM.h |only icenReg-1.3.4/icenReg/src/icenReg_files/basicUtilities.cpp | 82 ++ icenReg-1.3.4/icenReg/src/icenReg_files/experimentalCode.cpp | 4 icenReg-1.3.4/icenReg/src/icenReg_files/ic_sp_ch.cpp | 188 +---- icenReg-1.3.4/icenReg/src/icenReg_files/ic_sp_ch.h | 13 icenReg-1.3.4/icenReg/src/icenReg_files/ic_sp_gradDescent.cpp | 157 ++-- icenReg-1.3.4/icenReg/src/icenReg_files/regressionTransforms.cpp | 4 icenReg-1.3.4/icenReg/src/icenReg_files/regressionTransforms.h | 3 23 files changed, 713 insertions(+), 588 deletions(-)
Title: Graph-Based Change-Point Detection (g-Segmentation)
Description: Using an approach based on similarity graph to estimate change-point(s) and the corresponding p-values. Can be applied to any type of data (high-dimensional, non-Euclidean, etc.) as long as a reasonable similarity measure is available.
Author: Hao Chen and Nancy R. Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gSeg versions 0.2 dated 2015-11-08 and 0.3 dated 2016-03-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/gSeg.r | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.3-1 dated 2015-12-14 and 1.4-0 dated 2016-03-19
DESCRIPTION | 8 - MD5 | 108 +++++++------- NAMESPACE | 18 +- R/AAADefs.R | 22 +-- R/AllClasses.R | 28 --- R/AllGenerics.R | 18 ++ R/abbreviate.R | 81 +++++------ R/associations.R | 20 ++ R/eclat.R | 5 R/interestMeasures.R | 47 ++---- R/is.redundant.R | 27 --- R/is.superset.R | 4 R/itemMatrix.R | 7 R/random.transactions.R | 6 R/read_write.R | 2 R/tidLists.R | 13 + R/transactions.R | 31 ++-- README.md | 7 build/vignette.rds |binary data/Adult.rda |binary data/AdultUCI.rda |binary data/Epub.rda |binary data/Groceries.rda |binary data/Income.rda |binary data/IncomeESL.rda |binary data/Mushroom.rda |binary data/SunBai.rda |binary inst/NEWS | 16 ++ inst/doc/arules.R | 4 inst/doc/arules.Rnw | 6 inst/doc/arules.pdf |binary man/SunBai.Rd | 2 man/abbreviate.Rd | 27 +-- man/aggregate.Rd | 4 man/associations-class.Rd | 2 man/interestMeasure.Rd | 7 man/is.redundant.Rd | 22 ++- man/is.superset.Rd | 4 man/itemCoding.Rd | 2 man/itemMatrix-class.Rd | 10 + man/match.Rd | 2 man/pmml.Rd | 28 +-- man/ruleInduction.Rd | 3 man/rules-class.Rd | 9 - man/sort.Rd | 29 +++ man/tidLists-class.Rd | 1 man/transactions-class.Rd | 23 ++- src/ptree.c | 148 ++++++++++++++++++-- src/similarity.c | 26 +++ tests/testthat/test-associations.R | 271 +++++++++++++++++++------------------ tests/testthat/test-itemMatrix.R | 34 ++++ tests/testthat/test-measures.R | 1 tests/testthat/test-tidLists.R | 6 tests/testthat/test-warm.R | 17 -- vignettes/arules.Rnw | 6 55 files changed, 710 insertions(+), 452 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.2 dated 2015-12-11 and 1.4 dated 2016-03-18
tmap-1.2/tmap/R/itmap.R |only tmap-1.2/tmap/R/leaflet_functions.R |only tmap-1.2/tmap/R/tm_misc.R |only tmap-1.2/tmap/man/itmap.Rd |only tmap-1.4/tmap/DESCRIPTION | 20 tmap-1.4/tmap/MD5 | 201 +++--- tmap-1.4/tmap/NAMESPACE | 41 - tmap-1.4/tmap/NEWS | 19 tmap-1.4/tmap/R/animation_tmap.R | 5 tmap-1.4/tmap/R/append_data.R | 14 tmap-1.4/tmap/R/bb.R | 39 - tmap-1.4/tmap/R/cat2pal.R | 43 - tmap-1.4/tmap/R/col2hex.R |only tmap-1.4/tmap/R/geocode_OSM.R |only tmap-1.4/tmap/R/get_asp_ratio.R | 24 tmap-1.4/tmap/R/get_proj4_code.R | 9 tmap-1.4/tmap/R/get_raster_data.R | 52 + tmap-1.4/tmap/R/get_sp_coordinates.R |only tmap-1.4/tmap/R/gridplot.R | 130 +++- tmap-1.4/tmap/R/kde2D.R | 2 tmap-1.4/tmap/R/line_functions.R |only tmap-1.4/tmap/R/map2scale.R | 6 tmap-1.4/tmap/R/map_coloring.R | 22 tmap-1.4/tmap/R/meta_plot.R | 171 +++-- tmap-1.4/tmap/R/num2pal.R | 77 +- tmap-1.4/tmap/R/onLoad.R | 2 tmap-1.4/tmap/R/pkg.R | 23 tmap-1.4/tmap/R/plot_all.R | 180 ++--- tmap-1.4/tmap/R/plot_map.R | 62 - tmap-1.4/tmap/R/plot_misc_functions.R | 162 +++- tmap-1.4/tmap/R/preprocess_gt.R |only tmap-1.4/tmap/R/preprocess_shapes.R |only tmap-1.4/tmap/R/print_tmap.R | 447 ++++++++----- tmap-1.4/tmap/R/process_bubbles.R | 36 - tmap-1.4/tmap/R/process_col_vector.R | 17 tmap-1.4/tmap/R/process_color.R | 72 ++ tmap-1.4/tmap/R/process_data.R | 14 tmap-1.4/tmap/R/process_facet_layout.R |only tmap-1.4/tmap/R/process_fill.R | 19 tmap-1.4/tmap/R/process_layers.R | 83 +- tmap-1.4/tmap/R/process_lines.R | 93 +- tmap-1.4/tmap/R/process_meta.R | 92 ++ tmap-1.4/tmap/R/process_raster.R | 86 -- tmap-1.4/tmap/R/process_shapes.R | 132 +--- tmap-1.4/tmap/R/process_text.R | 45 + tmap-1.4/tmap/R/process_tm.R | 166 ++--- tmap-1.4/tmap/R/qtm.R | 75 +- tmap-1.4/tmap/R/read_GPX.R | 4 tmap-1.4/tmap/R/read_osm.R | 19 tmap-1.4/tmap/R/read_shape.R | 10 tmap-1.4/tmap/R/sample_dots.R | 70 +- tmap-1.4/tmap/R/save_tmap.R | 180 ++++- tmap-1.4/tmap/R/set_projection.R | 92 ++ tmap-1.4/tmap/R/smooth_map.R | 5 tmap-1.4/tmap/R/split_shps.R | 11 tmap-1.4/tmap/R/split_tm.R | 2 tmap-1.4/tmap/R/tm_layers.R | 79 +- tmap-1.4/tmap/R/tm_layout.R | 64 + tmap-1.4/tmap/R/tm_misc_elements.R | 39 - tmap-1.4/tmap/R/tm_shape.R | 8 tmap-1.4/tmap/R/tm_view.R |only tmap-1.4/tmap/R/tmap_mode.R |only tmap-1.4/tmap/R/to_raster.R | 23 tmap-1.4/tmap/R/view_tmap.R |only tmap-1.4/tmap/build/vignette.rds |binary tmap-1.4/tmap/data/Europe.rda |binary tmap-1.4/tmap/data/NLD_muni.rda |binary tmap-1.4/tmap/data/NLD_prov.rda |binary tmap-1.4/tmap/data/World.rda |binary tmap-1.4/tmap/inst/doc/tmap-modes.R |only tmap-1.4/tmap/inst/doc/tmap-modes.Rmd |only tmap-1.4/tmap/inst/doc/tmap-modes.html |only tmap-1.4/tmap/inst/doc/tmap-nutshell.R | 142 ++-- tmap-1.4/tmap/inst/doc/tmap-nutshell.Rmd | 336 +++++++--- tmap-1.4/tmap/inst/doc/tmap-nutshell.html | 974 ++++++++++++++---------------- tmap-1.4/tmap/man/animation_tmap.Rd | 30 tmap-1.4/tmap/man/bb.Rd | 30 tmap-1.4/tmap/man/calc_densities.Rd | 10 tmap-1.4/tmap/man/double_line.Rd |only tmap-1.4/tmap/man/geocode_OSM.Rd |only tmap-1.4/tmap/man/get_asp_ratio.Rd | 13 tmap-1.4/tmap/man/get_proj4.Rd | 5 tmap-1.4/tmap/man/land.Rd | 2 tmap-1.4/tmap/man/map_coloring.Rd | 10 tmap-1.4/tmap/man/poly_to_raster.Rd | 8 tmap-1.4/tmap/man/polygons.Rd | 26 tmap-1.4/tmap/man/print.tmap.Rd | 21 tmap-1.4/tmap/man/qtm.Rd | 31 tmap-1.4/tmap/man/read_GPX.Rd | 51 - tmap-1.4/tmap/man/read_osm.Rd | 75 +- tmap-1.4/tmap/man/sample_dots.Rd | 128 ++- tmap-1.4/tmap/man/save_tmap.Rd | 56 + tmap-1.4/tmap/man/set_projection.Rd | 5 tmap-1.4/tmap/man/smooth_map.Rd | 99 +++ tmap-1.4/tmap/man/tm_bubbles.Rd | 32 tmap-1.4/tmap/man/tm_compass.Rd | 12 tmap-1.4/tmap/man/tm_credits.Rd | 7 tmap-1.4/tmap/man/tm_facets.Rd | 85 ++ tmap-1.4/tmap/man/tm_grid.Rd | 8 tmap-1.4/tmap/man/tm_layout.Rd | 114 ++- tmap-1.4/tmap/man/tm_lines.Rd | 57 + tmap-1.4/tmap/man/tm_raster.Rd | 48 - tmap-1.4/tmap/man/tm_scale_bar.Rd | 9 tmap-1.4/tmap/man/tm_shape.Rd | 17 tmap-1.4/tmap/man/tm_text.Rd | 28 tmap-1.4/tmap/man/tm_view.Rd |only tmap-1.4/tmap/man/tmap-element.Rd | 2 tmap-1.4/tmap/man/tmap-package.Rd | 21 tmap-1.4/tmap/man/tmap_leaflet.Rd |only tmap-1.4/tmap/man/tmap_mode.Rd |only tmap-1.4/tmap/man/tmap_style.Rd |only tmap-1.4/tmap/vignettes/images |only tmap-1.4/tmap/vignettes/tmap-modes.Rmd |only tmap-1.4/tmap/vignettes/tmap-nutshell.Rmd | 159 +++- 114 files changed, 3626 insertions(+), 2312 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-68 dated 2016-02-21 and 0.1-69 dated 2016-03-18
DESCRIPTION | 8 MD5 | 6 NEWS | 2 R/ICA.BinBin.Grid.Sample.R | 2992 ++++++++++++++++++++++----------------------- 4 files changed, 1499 insertions(+), 1509 deletions(-)
Title: Spatial Position Models
Description: Computes spatial position models: Stewart potentials, Reilly
catchment areas, Huff catchment areas.
Author: Timothée Giraud [cre, aut],
Hadrien Commenges [aut],
Joël Boulier [ctb]
Maintainer: Timothée Giraud <timothee.giraud@ums-riate.fr>
Diff between SpatialPosition versions 1.0 dated 2015-12-04 and 1.1 dated 2016-03-18
DESCRIPTION | 12 ++-- MD5 | 48 +++++++++------- NAMESPACE | 2 NEWS | 14 ++++ R/contourStewart.R | 120 ++++++------------------------------------ R/gridandmat.R | 10 ++- R/package.R | 11 ++- R/quickStewart.R |only R/rasterToContourPoly.R |only R/stewart.R | 7 +- README.md | 5 + build/vignette.rds |binary inst/doc/SpatialPosition.R | 2 inst/doc/SpatialPosition.Rmd | 2 inst/doc/SpatialPosition.html | 27 ++++----- inst/doc/StewartExample.R | 15 ++--- inst/doc/StewartExample.Rmd | 15 ++--- inst/doc/StewartExample.html | 42 +++++++------- man/SpatialPosition.Rd | 11 ++- man/contourStewart.Rd | 21 +++++-- man/plotStewart.Rd | 2 man/quickStewart.Rd |only man/rasterStewart.Rd | 2 man/rasterToContourPoly.Rd |only man/stewart.Rd | 3 - vignettes/SpatialPosition.Rmd | 2 vignettes/StewartExample.Rmd | 15 ++--- 27 files changed, 173 insertions(+), 215 deletions(-)
More information about SpatialPosition at CRAN
Permanent link
Title: Morphometrics using R
Description: A complete toolkit for morphometrics, from data extraction to multivariate analyses.
Most common 2D morphometrics approaches are included:
outlines, open outlines, configurations of landmarks, traditional morphometrics,
and facilities for data preparation, manipulation and visualization
with a consistent grammar throughout.
Momocs allows reproducible, complex morphometric analyses,
paves the way for a pure open-source workflow in R,
and other morphometrics approaches should be easy to plug in,
or develop from, on top of this canvas.
Author: Vincent Bonhomme [aut, cre],
Julien Claude [aut]
Maintainer: Vincent Bonhomme <bonhomme.vincent@gmail.com>
Diff between Momocs versions 0.2-6 dated 2014-03-07 and 1.0.0 dated 2016-03-18
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Momocs-1.0.0/Momocs/man/import_jpg.Rd |only Momocs-1.0.0/Momocs/man/import_jpg1.Rd |only Momocs-1.0.0/Momocs/man/import_tps.Rd |only Momocs-1.0.0/Momocs/man/import_txt.Rd |only Momocs-1.0.0/Momocs/man/is.Rd |only Momocs-1.0.0/Momocs/man/is_closed.Rd |only Momocs-1.0.0/Momocs/man/l2a.Rd | 75 - Momocs-1.0.0/Momocs/man/l2m.Rd | 67 - Momocs-1.0.0/Momocs/man/ldk_check.Rd |only Momocs-1.0.0/Momocs/man/ldk_chull.Rd |only Momocs-1.0.0/Momocs/man/ldk_confell.Rd |only Momocs-1.0.0/Momocs/man/ldk_contour.Rd |only Momocs-1.0.0/Momocs/man/ldk_labels.Rd |only Momocs-1.0.0/Momocs/man/ldk_links.Rd |only Momocs-1.0.0/Momocs/man/lf_structure.Rd |only Momocs-1.0.0/Momocs/man/links_all.Rd |only Momocs-1.0.0/Momocs/man/links_delaunay.Rd |only Momocs-1.0.0/Momocs/man/m2a.Rd |only Momocs-1.0.0/Momocs/man/m2d.Rd |only Momocs-1.0.0/Momocs/man/m2l.Rd | 64 - Momocs-1.0.0/Momocs/man/m2ll.Rd |only Momocs-1.0.0/Momocs/man/measure.Rd |only Momocs-1.0.0/Momocs/man/mshapes.Rd |only Momocs-1.0.0/Momocs/man/mutate.Rd |only Momocs-1.0.0/Momocs/man/nef2Coe.Rd | 93 -- Momocs-1.0.0/Momocs/man/npoly.Rd |only Momocs-1.0.0/Momocs/man/ntsrow2Coo.Rd |only Momocs-1.0.0/Momocs/man/opoly.Rd |only Momocs-1.0.0/Momocs/man/pProcrustes.Rd |only Momocs-1.0.0/Momocs/man/panel.Coo.Rd |only Momocs-1.0.0/Momocs/man/panel2.Rd |only Momocs-1.0.0/Momocs/man/perm.Rd |only Momocs-1.0.0/Momocs/man/pix2chc.Rd | 91 -- Momocs-1.0.0/Momocs/man/plot.Coo.Rd |only Momocs-1.0.0/Momocs/man/plot.LDA.Rd |only Momocs-1.0.0/Momocs/man/plot.PCA.Rd |only Momocs-1.0.0/Momocs/man/plot2.PCA.Rd |only Momocs-1.0.0/Momocs/man/plot3.PCA.Rd |only Momocs-1.0.0/Momocs/man/plot_CV.Rd |only Momocs-1.0.0/Momocs/man/plot_CV2.Rd |only Momocs-1.0.0/Momocs/man/plot_devsegments.Rd |only Momocs-1.0.0/Momocs/man/poly_i.Rd |only Momocs-1.0.0/Momocs/man/pos.shapes.Rd |only Momocs-1.0.0/Momocs/man/reLDA.Rd |only Momocs-1.0.0/Momocs/man/rePCA.Rd |only Momocs-1.0.0/Momocs/man/reexports.Rd |only Momocs-1.0.0/Momocs/man/rename.Rd |only Momocs-1.0.0/Momocs/man/rescale.Rd |only Momocs-1.0.0/Momocs/man/rfourier.Rd | 140 +-- Momocs-1.0.0/Momocs/man/rfourier_i.Rd |only Momocs-1.0.0/Momocs/man/rfourier_shape.Rd |only Momocs-1.0.0/Momocs/man/rm_asym.Rd |only Momocs-1.0.0/Momocs/man/rm_harm.Rd |only Momocs-1.0.0/Momocs/man/rm_uncomplete.Rd |only Momocs-1.0.0/Momocs/man/rw_rule.Rd |only Momocs-1.0.0/Momocs/man/sample_frac.Rd |only Momocs-1.0.0/Momocs/man/sample_n.Rd |only Momocs-1.0.0/Momocs/man/scree.Rd |only Momocs-1.0.0/Momocs/man/select.Rd |only Momocs-1.0.0/Momocs/man/slice.Rd |only Momocs-1.0.0/Momocs/man/slidings_scheme.Rd |only Momocs-1.0.0/Momocs/man/stack.Coo.Rd |only Momocs-1.0.0/Momocs/man/stack2.Rd |only Momocs-1.0.0/Momocs/man/subset.Rd |only Momocs-1.0.0/Momocs/man/symmetry.Rd |only Momocs-1.0.0/Momocs/man/table.Rd |only Momocs-1.0.0/Momocs/man/tfourier.Rd | 156 +-- Momocs-1.0.0/Momocs/man/tfourier_i.Rd |only Momocs-1.0.0/Momocs/man/tfourier_shape.Rd |only Momocs-1.0.0/Momocs/man/tie_jpg_txt.Rd |only Momocs-1.0.0/Momocs/man/tps2coo.Rd |only Momocs-1.0.0/Momocs/man/tps2d.Rd | 66 - Momocs-1.0.0/Momocs/man/tps_arr.Rd |only Momocs-1.0.0/Momocs/man/tps_grid.Rd |only Momocs-1.0.0/Momocs/man/tps_iso.Rd |only Momocs-1.0.0/Momocs/man/tps_raw.Rd |only Momocs-1.0.0/Momocs/man/transmute.Rd |only Momocs-1.0.0/Momocs/man/truss.Rd |only Momocs-1.0.0/Momocs/man/validate.Rd |only Momocs-1.0.0/Momocs/man/vecs_param.Rd |only Momocs-1.0.0/Momocs/man/which_out.Rd |only Momocs-1.0.0/Momocs/tests |only Momocs-1.0.0/Momocs/vignettes |only 397 files changed, 1701 insertions(+), 943 deletions(-)
Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including
sequence data from 'NCBI', plant trait data from 'BETYdb', invasive species
data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
Author: Scott Chamberlain [aut, cre],
Zachary Foster [aut],
Ignasi Bartomeus [aut],
David LeBauer [aut],
David Harris [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between traits versions 0.1.2 dated 2015-09-12 and 0.2.0 dated 2016-03-18
DESCRIPTION | 14 +++-- LICENSE | 2 MD5 | 74 +++++++++++++++--------------- NAMESPACE | 19 ++++--- R/betydb.R | 31 +++++------- R/birdlife.R | 22 +++++--- R/coral.R | 8 +-- R/deprecated.R |only R/eol_invasive.R | 7 +- R/fe_native.R | 92 +++++++++++++++++++------------------ R/g_invasive.R | 20 ++++---- R/is_native.R | 59 ++++++++++++----------- R/leda.R | 105 ++++++++++++++++++++++++++---------------- R/ncbi_byid.R | 106 ++++++++++++++++++++++++++++++------------- R/ncbi_byname.R | 61 ++++++++++++------------ R/ncbi_searcher.R | 34 ++++++------- R/taxa_search.R |only R/traitbank.R | 2 R/traits-package.r | 6 ++ R/zzz.R | 15 ++++++ README.md | 56 +++++++++++----------- build/vignette.rds |binary man/betydb.Rd | 6 +- man/birdlife_habitat.Rd | 2 man/birdlife_threats.Rd | 2 man/coral.Rd | 2 man/eol_invasive_.Rd | 2 man/fe_native.Rd | 3 - man/g_invasive.Rd | 3 - man/is_native.Rd | 20 ++++---- man/leda.Rd | 36 ++++++++++++-- man/ncbi_byid.Rd | 28 ++++++----- man/ncbi_byname.Rd | 6 +- man/ncbi_searcher.Rd | 6 +- man/plantatt.Rd | 2 man/taxa_search.Rd |only man/traitbank.Rd | 2 man/traits-deprecated.Rd |only man/traits-package.Rd | 3 - tests/testthat/test-betydb.R | 8 +-- 40 files changed, 505 insertions(+), 359 deletions(-)
Title: Provides R-Language Code to Examine Quantitative Risk Management
Concepts
Description: Accompanying package to the book
Quantitative Risk Management: Concepts, Techniques and Tools by
Alexander J. McNeil, Rüdiger Frey, and Paul Embrechts.
Author: Bernhard Pfaff [aut, cre],
Marius Hofert [ctb],
Alexander McNeil [aut] (S-Plus original (QRMlib)),
Scott Ulmann [trl] (First R port as package QRMlib)
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between QRM versions 0.4-10 dated 2014-05-16 and 0.4-13 dated 2016-03-18
DESCRIPTION | 20 +++--- MD5 | 74 +++++++++++------------ NAMESPACE | 13 +++- R/GIG.R | 25 +++---- R/Student.R | 4 - R/game.R | 101 +++++++++++++++++++++----------- data/DJ.RData |binary data/DJ.df.RData |binary data/FXGBP.RData |binary data/FXGBP.df.RData |binary data/cac40.RData |binary data/cac40.df.RData |binary data/danish.RData |binary data/danish.df.RData |binary data/dji.RData |binary data/dji.df.RData |binary data/ftse100.RData |binary data/ftse100.df.RData |binary data/hsi.RData |binary data/hsi.df.RData |binary data/nasdaq.RData |binary data/nasdaq.df.RData |binary data/nikkei.RData |binary data/nikkei.df.RData |binary data/smi.RData |binary data/smi.df.RData |binary data/sp500.RData |binary data/sp500.df.RData |binary data/spdata.RData |binary data/spdata.df.RData |binary data/spdata.raw.RData |binary data/spdata.raw.df.RData |binary data/xdax.RData |binary data/xdax.df.RData |binary demo/game.R | 148 ++++++++++++++++++++++++++++++----------------- man/CopulaStudent.Rd | 2 man/game-aux.Rd | 41 ++++++------- man/game.Rd | 7 +- 38 files changed, 262 insertions(+), 173 deletions(-)
Title: Preprocessing of Aligned Sequences from HTS Analyses
Description: Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charl<c3><a8>ne Innocenti, Pierre Ferrier, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil@mssm.edu>
Diff between Pasha versions 0.99.18 dated 2015-10-16 and 0.99.21 dated 2016-03-18
DESCRIPTION | 13 - MD5 | 22 +- NAMESPACE | 3 NEWS | 2 R/pipelineChipSeq.R | 222 ++++++++++++++++++---- R/test_functional.R | 9 inst/doc/Pasha.Rnw | 180 ++++++++++------- inst/doc/Pasha.pdf |binary inst/extdata/resultsFromFunctionalTestsWIG.tar.gz |binary man/processPipeline.Rd | 48 +++- tests/test_Pasha.Rout.save | 27 +- vignettes/Pasha.Rnw | 180 ++++++++++------- 12 files changed, 471 insertions(+), 235 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.0.1 dated 2016-01-16 and 2.1.0 dated 2016-03-18
ggtern-2.0.1/ggtern/R/scales-.R |only ggtern-2.1.0/ggtern/DESCRIPTION | 32 ++++---- ggtern-2.1.0/ggtern/MD5 | 80 +++++++++++----------- ggtern-2.1.0/ggtern/NAMESPACE | 30 ++++++-- ggtern-2.1.0/ggtern/NEWS | 23 ++++++ ggtern-2.1.0/ggtern/R/aes.R | 12 ++- ggtern-2.1.0/ggtern/R/coord-tern.R | 23 ++++-- ggtern-2.1.0/ggtern/R/doc-theme-convenience.R | 23 +++--- ggtern-2.1.0/ggtern/R/geom-Xisoprop.R | 6 - ggtern-2.1.0/ggtern/R/geom-Xline.R | 60 ++++++++-------- ggtern-2.1.0/ggtern/R/geom-crosshair-tern.R |only ggtern-2.1.0/ggtern/R/geom-errorbarX.R | 6 + ggtern-2.1.0/ggtern/R/geom-interpolate-tern.R | 18 ++--- ggtern-2.1.0/ggtern/R/gg-internal.R | 2 ggtern-2.1.0/ggtern/R/ggtern-constructor.R | 4 - ggtern-2.1.0/ggtern/R/legend-draw-tern.R |only ggtern-2.1.0/ggtern/R/onLoad.R | 4 - ggtern-2.1.0/ggtern/R/plot-build.R | 54 +++++---------- ggtern-2.1.0/ggtern/R/plot-construction.R | 1 ggtern-2.1.0/ggtern/R/plot.R | 2 ggtern-2.1.0/ggtern/R/stat-confidence-tern.R | 6 + ggtern-2.1.0/ggtern/R/stat-density-tern.R | 3 ggtern-2.1.0/ggtern/R/stat-interpolate-methods.R |only ggtern-2.1.0/ggtern/R/stat-interpolate-tern.R | 82 +++++++++++++++-------- ggtern-2.1.0/ggtern/R/strip-unapproved.R | 16 +++- ggtern-2.1.0/ggtern/R/theme-defaults.R | 8 +- ggtern-2.1.0/ggtern/R/theme-elements.R | 4 - ggtern-2.1.0/ggtern/R/utilities.R | 7 + ggtern-2.1.0/ggtern/README.md | 8 +- ggtern-2.1.0/ggtern/TODO | 6 - ggtern-2.1.0/ggtern/build/partial.rdb |binary ggtern-2.1.0/ggtern/man/convenience_functions.Rd | 23 +++--- ggtern-2.1.0/ggtern/man/draw_key_tern.Rd |only ggtern-2.1.0/ggtern/man/geom_Xisoprop.Rd | 38 +++++----- ggtern-2.1.0/ggtern/man/geom_Xline.Rd | 38 +++++----- ggtern-2.1.0/ggtern/man/geom_confidence_tern.Rd | 34 +++++---- ggtern-2.1.0/ggtern/man/geom_crosshair_tern.Rd |only ggtern-2.1.0/ggtern/man/geom_density_tern.Rd | 34 +++++---- ggtern-2.1.0/ggtern/man/geom_errorbarX.Rd | 41 +++++------ ggtern-2.1.0/ggtern/man/geom_interpolate_tern.Rd | 54 ++++++++------- ggtern-2.1.0/ggtern/man/geom_smooth_tern.Rd | 34 +++++---- ggtern-2.1.0/ggtern/man/ggtern_themes.Rd | 7 + ggtern-2.1.0/ggtern/man/stat_density_tern.Rd | 34 +++++---- ggtern-2.1.0/ggtern/man/undocumented.Rd | 13 --- 44 files changed, 496 insertions(+), 374 deletions(-)
Title: Programmatic Access to the European Central Bank's Statistical
Data Warehouse (SDW)
Description: Provides an interface to the European Central Bank's Statistical
Data Warehouse API, allowing for programmatic retrieval of a vast quantity
of statistical data.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>
Diff between ecb versions 0.1 dated 2015-12-11 and 0.2 dated 2016-03-18
ecb-0.1/ecb/README.md |only ecb-0.2/ecb/DESCRIPTION | 11 ++- ecb-0.2/ecb/MD5 | 30 +++++----- ecb-0.2/ecb/NAMESPACE | 2 ecb-0.2/ecb/R/main.R | 7 +- ecb-0.2/ecb/build/vignette.rds |binary ecb-0.2/ecb/inst/doc/ecb_sdw.R | 33 +++++------ ecb-0.2/ecb/inst/doc/ecb_sdw.Rmd | 10 ++- ecb-0.2/ecb/inst/doc/ecb_sdw.html | 99 ++++++++++++++++++---------------- ecb-0.2/ecb/man/convert_dates.Rd | 2 ecb-0.2/ecb/man/get_data.Rd | 4 - ecb-0.2/ecb/man/get_dataflows.Rd | 2 ecb-0.2/ecb/man/get_description.Rd | 2 ecb-0.2/ecb/man/get_dimensions.Rd | 2 ecb-0.2/ecb/tests |only ecb-0.2/ecb/vignettes/ecb_sdw.Rmd | 10 ++- ecb-0.2/ecb/vignettes/hicp_plot-1.png |only 17 files changed, 115 insertions(+), 99 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Provides implementations of functions which have been introduced in
R since version 3.0.0. The backports are conditionally exported which
results in R resolving the function names to the version shipped with R (if
available) and uses the implemented backports as fallback. This way package
developers can make use of the new functions without worrying about the
minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.0.1 dated 2016-03-10 and 1.0.2 dated 2016-03-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/file.x.r | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: IRT Item-Person Map with 'ConQuest' Integration
Description: A powerful yet simple graphical tool available in the field of psychometrics is the Wright Map (also known as item maps or item-person maps), which presents the location of both respondents and items on the same scale. Wright Maps are commonly used to present the results of dichotomous or polytomous item response models. The 'WrightMap' package provides functions to create these plots from item parameters and person estimates stored as R objects. Although the package can be used in conjunction with any software used to estimate the IRT model (e.g. 'eRm' or 'IRToys' in 'R', or 'Stata', 'Mplus', etc.), 'WrightMap' features special integration with 'ConQuest' to facilitate reading and plotting its output directly.The 'wrightMap' function creates Wright Maps based on person estimates and item parameters produced by an item response analysis. The 'CQmodel' function reads output files created using 'ConQuest' software and creates a set of data frames for easy data manipulation, bundled in a 'CQmodel' object. The 'wrightMap' function can take a 'CQmodel' object as input or it can be used to create Wright Maps directly from data frames of person and item parameters.
Author: David Torres Irribarra & Rebecca Freund
Maintainer: David Torres Irribarra <dti@berkeley.edu>
Diff between WrightMap versions 1.1 dated 2014-03-31 and 1.2 dated 2016-03-18
WrightMap-1.1/WrightMap/R/FitPlot.R |only WrightMap-1.1/WrightMap/R/wrightMap.CQmodel.R |only WrightMap-1.1/WrightMap/R/wrightMap.character.R |only WrightMap-1.1/WrightMap/R/wrightMap.default.R |only WrightMap-1.2/WrightMap/DESCRIPTION | 12 - WrightMap-1.2/WrightMap/MD5 | 63 ++++-- WrightMap-1.2/WrightMap/NAMESPACE | 34 +++ WrightMap-1.2/WrightMap/NEWS |only WrightMap-1.2/WrightMap/R/CQmodel.R | 152 ++++++++++---- WrightMap-1.2/WrightMap/R/cutLines.R |only WrightMap-1.2/WrightMap/R/difplot.CQmodel.R |only WrightMap-1.2/WrightMap/R/difplot.R |only WrightMap-1.2/WrightMap/R/difplot.character.R |only WrightMap-1.2/WrightMap/R/difplot.default.R |only WrightMap-1.2/WrightMap/R/fitgraph.CQmodel.R | 29 +- WrightMap-1.2/WrightMap/R/fitgraph.default.R | 6 WrightMap-1.2/WrightMap/R/fitgraph.numeric.R |only WrightMap-1.2/WrightMap/R/itemClassic.R |only WrightMap-1.2/WrightMap/R/itemData.CQmodel.R |only WrightMap-1.2/WrightMap/R/itemData.R |only WrightMap-1.2/WrightMap/R/itemData.character.R |only WrightMap-1.2/WrightMap/R/itemData.default.R |only WrightMap-1.2/WrightMap/R/itemHist.R |only WrightMap-1.2/WrightMap/R/itemModern.R |only WrightMap-1.2/WrightMap/R/make.deltas.CQmodel.R | 84 ++++---- WrightMap-1.2/WrightMap/R/make.thresholds.CQmodel.R | 6 WrightMap-1.2/WrightMap/R/make.thresholds.default.R | 189 ++++++++++-------- WrightMap-1.2/WrightMap/R/make.thresholds.matrix.R |only WrightMap-1.2/WrightMap/R/personData.CQmodel.R |only WrightMap-1.2/WrightMap/R/personData.R |only WrightMap-1.2/WrightMap/R/personData.character.R |only WrightMap-1.2/WrightMap/R/personData.default.R |only WrightMap-1.2/WrightMap/R/personDens.R |only WrightMap-1.2/WrightMap/R/personHist.R |only WrightMap-1.2/WrightMap/R/plotCI.R |only WrightMap-1.2/WrightMap/R/ppPlot.R |only WrightMap-1.2/WrightMap/R/wrightMap.R | 73 ++++++ WrightMap-1.2/WrightMap/README.md | 6 WrightMap-1.2/WrightMap/inst/extdata/ex6a.shw |only WrightMap-1.2/WrightMap/man/CQmodel.Rd | 7 WrightMap-1.2/WrightMap/man/WrightMap-package.Rd | 85 +++----- WrightMap-1.2/WrightMap/man/fitgraph.Rd | 25 +- WrightMap-1.2/WrightMap/man/item.person.data.Rd |only WrightMap-1.2/WrightMap/man/item.side.Rd |only WrightMap-1.2/WrightMap/man/make.thresholds.Rd | 22 +- WrightMap-1.2/WrightMap/man/person.side.Rd |only WrightMap-1.2/WrightMap/man/plotCI.Rd |only WrightMap-1.2/WrightMap/man/ppPlot.Rd |only WrightMap-1.2/WrightMap/man/wrightMap.Rd | 209 +++----------------- 49 files changed, 563 insertions(+), 439 deletions(-)
Title: A 'Whoapi' API Client
Description: Retrieve data from the 'Whoapi' (https://whoapi.com) store of
domain information, including a domain's geographic location, registration
status and search prominence.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between whoapi versions 0.1.0 dated 2015-06-25 and 0.1.1 dated 2016-03-18
DESCRIPTION | 14 ++++++++------ MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 2 +- R/domain_info.R | 8 ++++++-- R/domain_metadata.R | 12 ++++++++---- build/vignette.rds |binary inst/doc/Whoapi.html | 13 +++++++++---- man/certificate_info.Rd | 4 +++- man/domain_location.Rd | 4 +++- man/domain_metadata.Rd | 4 +++- man/domain_rank.Rd | 4 +++- man/domain_search.Rd | 4 +++- man/is_blacklisted.Rd | 2 +- man/is_taken.Rd | 5 ++++- man/whoapi.Rd | 2 +- man/whoapi_token.Rd | 2 +- man/whois_info.Rd | 4 +++- tests/testthat/test_info.R | 32 ++++++++++++++++++++------------ tests/testthat/test_metadata.R | 33 ++++++++++++++++++++------------- 19 files changed, 115 insertions(+), 70 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, unit conversions.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 1.0 dated 2015-11-19 and 1.0-2 dated 2016-03-18
plantecophys-1.0-2/plantecophys/DESCRIPTION | 7 +- plantecophys-1.0-2/plantecophys/MD5 | 52 ++++-------------- plantecophys-1.0-2/plantecophys/NAMESPACE | 2 plantecophys-1.0-2/plantecophys/R/LeafEnergyBalance.R | 2 plantecophys-1.0-2/plantecophys/R/fitBB.R | 4 - plantecophys-1.0-2/plantecophys/R/fitaci.R | 1 plantecophys-1.0-2/plantecophys/R/fitacis.R | 22 +++++-- plantecophys-1.0-2/plantecophys/man/AciC4.Rd | 4 - plantecophys-1.0-2/plantecophys/man/Conversions.Rd | 10 +-- plantecophys-1.0-2/plantecophys/man/FARAO.Rd | 2 plantecophys-1.0-2/plantecophys/man/Photosyn.Rd | 48 ++++++++-------- plantecophys-1.0-2/plantecophys/man/PhotosynEB.Rd | 4 - plantecophys-1.0-2/plantecophys/man/acidata1.Rd | 2 plantecophys-1.0-2/plantecophys/man/fitBB.Rd | 11 ++- plantecophys-1.0-2/plantecophys/man/fitaci.Rd | 23 ++++--- plantecophys-1.0/plantecophys/inst/web |only 16 files changed, 91 insertions(+), 103 deletions(-)
Title: Manage Google Spreadsheets from R
Description: Interact with Google Sheets from R.
Author: Jennifer Bryan [aut, cre],
Joanna Zhao [aut]
Maintainer: Jennifer Bryan <jenny@stat.ubc.ca>
Diff between googlesheets versions 0.1.0 dated 2015-07-05 and 0.2.0 dated 2016-03-18
googlesheets-0.1.0/googlesheets/R/http_requests.R |only googlesheets-0.1.0/googlesheets/R/permissions.R |only googlesheets-0.1.0/googlesheets/inst/mini-gap.csv |only googlesheets-0.1.0/googlesheets/inst/mini-gap.ods |only googlesheets-0.1.0/googlesheets/inst/mini-gap.tsv |only googlesheets-0.1.0/googlesheets/inst/mini-gap.txt |only googlesheets-0.1.0/googlesheets/inst/mini-gap.xlsx |only googlesheets-0.1.0/googlesheets/man/gdrive_GET.Rd |only googlesheets-0.1.0/googlesheets/man/gdrive_POST.Rd |only googlesheets-0.1.0/googlesheets/man/gdrive_PUT.Rd |only googlesheets-0.1.0/googlesheets/man/get_google_token.Rd |only googlesheets-0.1.0/googlesheets/man/gs_auth_suspend.Rd |only googlesheets-0.1.0/googlesheets/man/gs_user.Rd |only googlesheets-0.1.0/googlesheets/man/gsheets_DELETE.Rd |only googlesheets-0.1.0/googlesheets/man/gsheets_GET.Rd |only googlesheets-0.1.0/googlesheets/man/gsheets_POST.Rd |only googlesheets-0.1.0/googlesheets/man/gsheets_PUT.Rd |only googlesheets-0.1.0/googlesheets/man/token_exists.Rd |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/gap_sheet5_get_via_cf.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/gap_sheet5_get_via_lf.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/gap_sheet5_gs_read_cellfeed.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/gap_sheet5_gs_read_listfeed.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/iris_pvt_get_via_lf.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/iris_pvt_gs_read_cellfeed.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/for_reference/iris_pvt_gs_read_listfeed.rds |only googlesheets-0.1.0/googlesheets/tests/testthat/test-gs-create-delete-copy.R |only googlesheets-0.1.0/googlesheets/tests/testthat/test-gs-download.R |only googlesheets-0.2.0/googlesheets/DESCRIPTION | 16 googlesheets-0.2.0/googlesheets/LICENSE | 2 googlesheets-0.2.0/googlesheets/MD5 | 259 - googlesheets-0.2.0/googlesheets/NAMESPACE | 14 googlesheets-0.2.0/googlesheets/NEWS.md |only googlesheets-0.2.0/googlesheets/R/gd_metadata.R |only googlesheets-0.2.0/googlesheets/R/gd_permissions.R |only googlesheets-0.2.0/googlesheets/R/gd_user.R |only googlesheets-0.2.0/googlesheets/R/googlesheet.R | 38 googlesheets-0.2.0/googlesheets/R/googlesheets.R | 1 googlesheets-0.2.0/googlesheets/R/gs_add_row.R | 51 googlesheets-0.2.0/googlesheets/R/gs_auth.R | 310 - googlesheets-0.2.0/googlesheets/R/gs_browse.R |only googlesheets-0.2.0/googlesheets/R/gs_copy.R | 50 googlesheets-0.2.0/googlesheets/R/gs_delete.R | 35 googlesheets-0.2.0/googlesheets/R/gs_download.R | 68 googlesheets-0.2.0/googlesheets/R/gs_edit_cells.R | 73 googlesheets-0.2.0/googlesheets/R/gs_example-sheet-setup.R | 123 googlesheets-0.2.0/googlesheets/R/gs_inspect.R | 11 googlesheets-0.2.0/googlesheets/R/gs_ls.R | 10 googlesheets-0.2.0/googlesheets/R/gs_new.R | 39 googlesheets-0.2.0/googlesheets/R/gs_old-sheets.R | 2 googlesheets-0.2.0/googlesheets/R/gs_read.R | 54 googlesheets-0.2.0/googlesheets/R/gs_read_cellfeed.R | 97 googlesheets-0.2.0/googlesheets/R/gs_read_csv.R | 109 googlesheets-0.2.0/googlesheets/R/gs_read_listfeed.R | 206 - googlesheets-0.2.0/googlesheets/R/gs_register.R | 42 googlesheets-0.2.0/googlesheets/R/gs_rename.R |only googlesheets-0.2.0/googlesheets/R/gs_reshape_cellfeed.R | 138 googlesheets-0.2.0/googlesheets/R/gs_simplify_cellfeed.R | 100 googlesheets-0.2.0/googlesheets/R/gs_upload.R | 68 googlesheets-0.2.0/googlesheets/R/gs_webapp.R | 3 googlesheets-0.2.0/googlesheets/R/gs_ws.R | 111 googlesheets-0.2.0/googlesheets/R/httr-helpers.R |only googlesheets-0.2.0/googlesheets/R/utils.R | 109 googlesheets-0.2.0/googlesheets/R/zzz.R | 11 googlesheets-0.2.0/googlesheets/README.md | 113 googlesheets-0.2.0/googlesheets/build/vignette.rds |binary googlesheets-0.2.0/googlesheets/inst/doc/basic-usage.R | 284 + googlesheets-0.2.0/googlesheets/inst/doc/basic-usage.Rmd | 309 + googlesheets-0.2.0/googlesheets/inst/doc/basic-usage.html | 1679 +++++----- googlesheets-0.2.0/googlesheets/inst/doc/formulas-and-formatted-numbers.R |only googlesheets-0.2.0/googlesheets/inst/doc/formulas-and-formatted-numbers.Rmd |only googlesheets-0.2.0/googlesheets/inst/doc/formulas-and-formatted-numbers.html |only googlesheets-0.2.0/googlesheets/inst/doc/managing-auth-tokens.R |only googlesheets-0.2.0/googlesheets/inst/doc/managing-auth-tokens.Rmd |only googlesheets-0.2.0/googlesheets/inst/doc/managing-auth-tokens.html |only googlesheets-0.2.0/googlesheets/inst/mini-gap |only googlesheets-0.2.0/googlesheets/man/cell-specification.Rd | 3 googlesheets-0.2.0/googlesheets/man/construct_url_from_key.Rd | 2 googlesheets-0.2.0/googlesheets/man/construct_ws_feed_from_key.Rd | 6 googlesheets-0.2.0/googlesheets/man/example-sheets.Rd | 83 googlesheets-0.2.0/googlesheets/man/extract_key_from_url.Rd | 3 googlesheets-0.2.0/googlesheets/man/gd_user.Rd |only googlesheets-0.2.0/googlesheets/man/google_token.Rd |only googlesheets-0.2.0/googlesheets/man/google_user.Rd | 4 googlesheets-0.2.0/googlesheets/man/googlesheet.Rd | 10 googlesheets-0.2.0/googlesheets/man/googlesheets.Rd | 2 googlesheets-0.2.0/googlesheets/man/gs_add_row.Rd | 10 googlesheets-0.2.0/googlesheets/man/gs_auth.Rd | 70 googlesheets-0.2.0/googlesheets/man/gs_browse.Rd |only googlesheets-0.2.0/googlesheets/man/gs_copy.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_deauth.Rd |only googlesheets-0.2.0/googlesheets/man/gs_delete.Rd | 6 googlesheets-0.2.0/googlesheets/man/gs_download.Rd | 13 googlesheets-0.2.0/googlesheets/man/gs_edit_cells.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_grepdel.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_inspect.Rd | 4 googlesheets-0.2.0/googlesheets/man/gs_ls.Rd | 5 googlesheets-0.2.0/googlesheets/man/gs_new.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_perm_add.Rd | 5 googlesheets-0.2.0/googlesheets/man/gs_perm_delete.Rd | 5 googlesheets-0.2.0/googlesheets/man/gs_perm_edit.Rd | 5 googlesheets-0.2.0/googlesheets/man/gs_perm_ls.Rd | 7 googlesheets-0.2.0/googlesheets/man/gs_read.Rd | 91 googlesheets-0.2.0/googlesheets/man/gs_read_cellfeed.Rd | 70 googlesheets-0.2.0/googlesheets/man/gs_read_csv.Rd | 68 googlesheets-0.2.0/googlesheets/man/gs_read_listfeed.Rd | 136 googlesheets-0.2.0/googlesheets/man/gs_rename.Rd |only googlesheets-0.2.0/googlesheets/man/gs_reshape_cellfeed.Rd | 70 googlesheets-0.2.0/googlesheets/man/gs_simplify_cellfeed.Rd | 70 googlesheets-0.2.0/googlesheets/man/gs_upload.Rd | 5 googlesheets-0.2.0/googlesheets/man/gs_webapp_auth_url.Rd | 10 googlesheets-0.2.0/googlesheets/man/gs_webapp_get_token.Rd | 2 googlesheets-0.2.0/googlesheets/man/gs_ws.Rd | 2 googlesheets-0.2.0/googlesheets/man/gs_ws_delete.Rd | 6 googlesheets-0.2.0/googlesheets/man/gs_ws_ls.Rd | 2 googlesheets-0.2.0/googlesheets/man/gs_ws_modify.Rd | 2 googlesheets-0.2.0/googlesheets/man/gs_ws_new.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_ws_rename.Rd | 3 googlesheets-0.2.0/googlesheets/man/gs_ws_resize.Rd | 5 googlesheets-0.2.0/googlesheets/man/is_legit_token.Rd | 6 googlesheets-0.2.0/googlesheets/man/print.googlesheet.Rd | 3 googlesheets-0.2.0/googlesheets/man/token_available.Rd |only googlesheets-0.2.0/googlesheets/tests/testthat/for_reference/ff.rds |only googlesheets-0.2.0/googlesheets/tests/testthat/for_reference/ff_cellfeed.rds |only googlesheets-0.2.0/googlesheets/tests/testthat/for_reference/gap_oceania_listfeed_query.rds |only googlesheets-0.2.0/googlesheets/tests/testthat/for_reference/iris_pvt.rds |only googlesheets-0.2.0/googlesheets/tests/testthat/for_reference/pts_special_chars.rds |binary googlesheets-0.2.0/googlesheets/tests/testthat/helper01_setup-sheets.R | 24 googlesheets-0.2.0/googlesheets/tests/testthat/helper02_unique-slug.R | 2 googlesheets-0.2.0/googlesheets/tests/testthat/helper04_activate-test-token.R |only googlesheets-0.2.0/googlesheets/tests/testthat/test-auth.R | 57 googlesheets-0.2.0/googlesheets/tests/testthat/test-cell-edit.R | 54 googlesheets-0.2.0/googlesheets/tests/testthat/test-consume-data-private.R | 34 googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-create-delete-copy-rename.R |only googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-ls.R | 4 googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-permissions.R | 4 googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-register.R | 48 googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-upload.R | 7 googlesheets-0.2.0/googlesheets/tests/testthat/test-gs-yy-download.R |only googlesheets-0.2.0/googlesheets/tests/testthat/test-inspect.R | 7 googlesheets-0.2.0/googlesheets/tests/testthat/test-interactive.R |only googlesheets-0.2.0/googlesheets/tests/testthat/test-utils.R | 29 googlesheets-0.2.0/googlesheets/tests/testthat/test-ws-edits.R | 10 googlesheets-0.2.0/googlesheets/tests/testthat/test-yy-axe-oauth-token.R | 8 googlesheets-0.2.0/googlesheets/tests/testthat/test-yy-consume-data-public-selective.R | 100 googlesheets-0.2.0/googlesheets/tests/testthat/test-yy-consume-data-public-tricky.R | 123 googlesheets-0.2.0/googlesheets/tests/testthat/test-yy-consume-data-public-whole-sheets.R | 73 googlesheets-0.2.0/googlesheets/tests/testthat/test-zz-clean-up.R | 10 googlesheets-0.2.0/googlesheets/vignettes/basic-usage.Rmd | 309 + googlesheets-0.2.0/googlesheets/vignettes/formulas-and-formatted-numbers.Rmd |only googlesheets-0.2.0/googlesheets/vignettes/img |only googlesheets-0.2.0/googlesheets/vignettes/managing-auth-tokens.Rmd |only 151 files changed, 3943 insertions(+), 2304 deletions(-)
Title: Comparison of Alternative Multiple Sequence Alignments
Description: Methods for comparing two alternative multiple
sequence alignments (MSAs) to determine whether they align homologous residues in
the same columns as one another. It then classifies similarities and differences
into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative
to the other. Summarising these categories for each MSA column yields information
on which sequence regions are agreed upon my both MSAs, and which differ. Several
plotting functions enable easily visualisation of the comparison data for analysis.
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>
Diff between AlignStat versions 1.1.1 dated 2016-03-16 and 1.1.3 dated 2016-03-18
DESCRIPTION | 6 ++-- MD5 | 14 +++++------ R/Plots.R | 52 ++++++++++++++++++++---------------------- R/compare_alignments.R | 14 ++++++++--- README.md | 27 +++++++++++++-------- data/comparison_alignment.rda |binary data/reference_alignment.rda |binary tests/testthat/test-align.R | 48 +++++++++++++++++++------------------- 8 files changed, 86 insertions(+), 75 deletions(-)
Title: Download, Manipulate, and Present American Community Survey and
Decennial Data from the US Census
Description: Provides a general toolkit for downloading, managing,
analyzing, and presenting data from the U.S. Census, including SF1
(Decennial short-form), SF3 (Decennial long-form), and the American
Community Survey (ACS). Confidence intervals provided with ACS data
are converted to standard errors to be bundled with estimates in
complex acs objects. Package provides new methods to conduct
standard operations on acs objects and present/plot data in
statistically appropriate ways. Current version is 2.0 +/- .033.
Author: Ezra Haber Glenn [aut, cre]
Maintainer: Ezra Haber Glenn <eglenn@mit.edu>
Diff between acs versions 1.2 dated 2014-01-22 and 2.0 dated 2016-03-17
acs-1.2/acs/inst |only acs-2.0/acs/DESCRIPTION | 32 acs-2.0/acs/MD5 | 67 acs-2.0/acs/NAMESPACE | 9 acs-2.0/acs/R/acs.R | 2470 ++++++++++++------------- acs-2.0/acs/README.md |only acs-2.0/acs/cleanup |only acs-2.0/acs/configure |only acs-2.0/acs/data/cpi.rda |binary acs-2.0/acs/data/fips.american.indian.area.rda |binary acs-2.0/acs/data/fips.county.rda |binary acs-2.0/acs/data/fips.county.subdivision.rda |binary acs-2.0/acs/data/fips.place.rda |binary acs-2.0/acs/data/fips.school.rda |binary acs-2.0/acs/data/fips.state.rda |binary acs-2.0/acs/data/kansas07.rda |binary acs-2.0/acs/data/kansas09.rda |binary acs-2.0/acs/data/lawrence10.rda |binary acs-2.0/acs/man/acs-class.Rd | 23 acs-2.0/acs/man/acs-package.Rd | 46 acs-2.0/acs/man/acs.fetch.Rd | 94 acs-2.0/acs/man/acs.lookup-class.Rd | 3 acs-2.0/acs/man/acs.lookup.Rd | 73 acs-2.0/acs/man/acs.tables.install.Rd |only acs-2.0/acs/man/api.key.install.Rd | 13 acs-2.0/acs/man/api.key.migrate.Rd |only acs-2.0/acs/man/cpi.Rd | 10 acs-2.0/acs/man/currency.convert.Rd | 12 acs-2.0/acs/man/currency.year.Rd | 6 acs-2.0/acs/man/divide.acs.Rd | 47 acs-2.0/acs/man/geo.lookup.Rd | 2 acs-2.0/acs/man/geo.make.Rd | 67 acs-2.0/acs/man/geography.Rd | 6 acs-2.0/acs/man/rbind.acs.Rd | 6 acs-2.0/acs/man/read.acs.Rd | 8 acs-2.0/acs/man/sum-methods.Rd | 2 36 files changed, 1567 insertions(+), 1429 deletions(-)
Title: Fetch and Analyze Data from 'WaterML' and 'WaterOneFlow' Web
Services
Description: Lets you connect to any of the Consortium of Universities for the Advancement
of Hydrologic Sciences, Inc. ('CUAHSI') Water Data Center 'WaterOneFlow' web services
and read any 'WaterML' hydrological time series data file. To see list of available
web services, see <http://hiscentral.cuahsi.org>. All versions of 'WaterML'
(1.0, 1.1 and 2.0) and both types of the web service protocol ('SOAP' and 'REST') are supported.
The package has six data download functions: GetServices(): show all public web
services from the HIS Central Catalog. HISCentral_GetSites() and HISCentral_GetSeriesCatalog():
search for sites or time series from the HIS Central catalog based on geographic bounding box,
server, or keyword. GetVariables(): Show a data.frame with all variables on the server.
GetSites(): Show a data.frame with all sites on the server. GetSiteInfo(): Show what variables,
methods and quality control levels are available at the specific site. GetValues(): Given a site
code, variable code, start time and end time, fetch a data.frame of all the observation time
series data values. The GetValues() function can also parse 'WaterML' data from a custom URL or
from a local file. The package also has five data upload functions:
AddSites(), AddVariables(), AddMethods(), AddSources(), and AddValues().
These functions can be used for uploading data to a 'HydroServer Lite' Observations
Data Model ('ODM') database via the 'JSON' data upload web service interface.
Author: Jiri Kadlec [aut, cre]
Maintainer: Jiri Kadlec <jirikadlec2@gmail.com>
Diff between WaterML versions 1.7.0 dated 2016-02-17 and 1.7.1 dated 2016-03-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/GetValues.R | 9 +++++++-- build/vignette.rds |binary inst/doc/WaterML-Tutorial.html | 15 +++------------ 5 files changed, 17 insertions(+), 21 deletions(-)
Title: Estimate Gene-Treatment Interaction Exploiting Randomization
Description: Estimation of gene-treatment interactions in randomized clinical trials exploiting gene-treatment independence.
Author: James Dai [aut, cre],
Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Diff between TwoPhaseInd versions 1.1.0 dated 2016-01-29 and 1.1.1 dated 2016-03-17
DESCRIPTION | 8 MD5 | 23 +- inst/doc/TwoPhaseInd.R | 238 ++++++++++++-------------- inst/doc/TwoPhaseInd.Rnw | 421 ++++++++++++++++++++-------------------------- inst/doc/TwoPhaseInd.pdf |binary man/aco1arm.Rd | 2 man/aco2arm.Rd | 2 man/acoarm.Rd | 2 man/acodata.Rd | 16 - man/caseonly.Rd | 4 vignettes/TwoPhaseInd.Rnw | 421 ++++++++++++++++++++-------------------------- vignettes/TwoPhaseInd.bib | 70 +++++++ vignettes/figure1new.png |only 13 files changed, 591 insertions(+), 616 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.6-1 dated 2015-11-05 and 0.4.7 dated 2016-03-17
packrat-0.4.6-1/packrat/R/install_github.R |only packrat-0.4.6-1/packrat/man/install_github.Rd |only packrat-0.4.6-1/packrat/tests/testthat/test-cranlike-repositories.R |only packrat-0.4.7/packrat/DESCRIPTION | 8 packrat-0.4.7/packrat/MD5 | 88 ++-- packrat-0.4.7/packrat/NAMESPACE | 1 packrat-0.4.7/packrat/R/aaa-globals.R | 2 packrat-0.4.7/packrat/R/bundle.R | 180 ---------- packrat-0.4.7/packrat/R/cache.R | 2 packrat-0.4.7/packrat/R/clean-search-path.R | 2 packrat-0.4.7/packrat/R/cranlike-repositories.R | 39 +- packrat-0.4.7/packrat/R/dependencies.R | 46 +- packrat-0.4.7/packrat/R/descfile.R | 2 packrat-0.4.7/packrat/R/disable.R | 3 packrat-0.4.7/packrat/R/downloader.R | 22 + packrat-0.4.7/packrat/R/env.R |only packrat-0.4.7/packrat/R/external.R | 4 packrat-0.4.7/packrat/R/github.R |only packrat-0.4.7/packrat/R/hide-site-libraries.R | 6 packrat-0.4.7/packrat/R/hooks.R | 2 packrat-0.4.7/packrat/R/install-local.R | 4 packrat-0.4.7/packrat/R/install.R | 2 packrat-0.4.7/packrat/R/library-support.R | 174 ++++----- packrat-0.4.7/packrat/R/lockfile.R | 35 + packrat-0.4.7/packrat/R/migrate-packrat.R | 8 packrat-0.4.7/packrat/R/options.R | 39 +- packrat-0.4.7/packrat/R/packrat-mode.R | 27 + packrat-0.4.7/packrat/R/packrat.R | 6 packrat-0.4.7/packrat/R/paths.R | 96 +---- packrat-0.4.7/packrat/R/pkg.R | 20 - packrat-0.4.7/packrat/R/pretty-print.R | 14 packrat-0.4.7/packrat/R/restore.R | 63 ++- packrat-0.4.7/packrat/R/snapshot.R | 15 packrat-0.4.7/packrat/R/status.R | 2 packrat-0.4.7/packrat/R/utils.R | 53 +- packrat-0.4.7/packrat/R/zzz.R |only packrat-0.4.7/packrat/README.md | 4 packrat-0.4.7/packrat/inst/resources/init-rprofile.R | 2 packrat-0.4.7/packrat/inst/resources/init.R | 2 packrat-0.4.7/packrat/man/bundle.Rd | 5 packrat-0.4.7/packrat/man/packrat-options.Rd | 22 - packrat-0.4.7/packrat/tests/test-cranlike-repositories.R |only packrat-0.4.7/packrat/tests/testthat/helper-bundle.R | 2 packrat-0.4.7/packrat/tests/testthat/helper-packrat.R | 31 + packrat-0.4.7/packrat/tests/testthat/projects/emptydesc |only packrat-0.4.7/packrat/tests/testthat/test-bundle.R | 73 +--- packrat-0.4.7/packrat/tests/testthat/test-github.R |only packrat-0.4.7/packrat/tests/testthat/test-packrat.R | 15 packrat-0.4.7/packrat/tests/testthat/test-rmarkdown.R | 5 49 files changed, 520 insertions(+), 606 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 2.0-3 dated 2016-02-24 and 2.0-4 dated 2016-03-17
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- R/mma.r | 59 ++++++++++++++++++++++++++++++++++-------------- man/boot.med.binx.Rd | 2 - man/boot.med.contx.Rd | 2 - man/data.org.Rd | 2 - man/med.binx.Rd | 6 ++-- man/med.contx.Rd | 6 ++-- man/mma-package.Rd | 8 +++--- man/mma.Rd | 8 +++--- man/plot.mma.Rd | 2 - man/print.mma.Rd | 2 - man/summary.med_iden.Rd | 15 +++++------- man/summary.mma.Rd | 2 - 14 files changed, 87 insertions(+), 61 deletions(-)
Title: Plot the Effects of Variables in Interaction Terms
Description: Plots the conditional coefficients ("marginal effects") of
variables included in multiplicative interaction terms.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between interplot versions 0.1.1.1 dated 2016-02-15 and 0.1.2.0 dated 2016-03-17
DESCRIPTION | 6 - MD5 | 39 +++--- NAMESPACE | 1 NEWS.md | 6 + R/Interplot.R | 11 + R/Interplot_default.R | 118 +++++++++++--------- R/Interplot_mi.R | 224 +++++++++++++++++++++------------------ R/Interplot_mlm.R | 198 ++++++++++++++++++---------------- R/Interplot_mlmmi.R | 201 ++++++++++++++++++---------------- R/Interplot_plot.R | 102 +++++++++++++++-- README.md | 2 inst/doc/interplot-vignette.Rmd | 2 inst/doc/interplot-vignette.html | 19 --- man/interplot.Rd | 19 ++- man/interplot.default.Rd | 19 ++- man/interplot.lmerMod.Rd | 19 ++- man/interplot.lmmi.Rd | 19 ++- man/interplot.mlmmi.Rd | 19 ++- man/interplot.plot.Rd | 19 ++- vignettes/interplot-vignette.Rmd | 50 ++++++++ vignettes/vignette.bib |only 21 files changed, 693 insertions(+), 400 deletions(-)
Title: Birnbaum-Saunders Model Based on Skew-Normal Distribution
Description: It provides the density, distribution function, quantile function, random number generator, reliability function, failure rate, likelihood function,
moments and EM algorithm for Maximum Likelihood estimators, also empirical quantile and generated envelope for a given sample, all this for the three parameter
Birnbaum-Saunders model based on Skew-Normal Distribution.
Additionally, it provides the random number generator for the mixture of Birnbaum-Saunders model based on Skew-Normal distribution.
Author: Rocio Paola Maehara <rmaeharaa@gmail.com> and Luis Benites Sanchez <lbenitesanchez@gmail.com>
Maintainer: Rocio Paola Maehara <rmaeharaa@gmail.com>
Diff between bssn versions 0.6 dated 2015-09-08 and 0.7 dated 2016-03-17
DESCRIPTION | 8 MD5 | 22 - NAMESPACE | 37 +-- R/EMbssn.R | 86 +++---- R/algEMbssn.R | 242 ++++++++++---------- R/functions.R | 572 ++++++++++++++++++++++++++----------------------- data/ozone.txt.gz |binary man/EMbssn.Rd | 249 ++++++++++----------- man/bssn.Rd | 336 ++++++++++++++-------------- man/momentsbssn.Rd | 128 +++++----- man/ozone.Rd | 60 ++--- man/reliabilitybssn.Rd | 180 +++++++-------- 12 files changed, 987 insertions(+), 933 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes. Now extended to include multivariate and unsupervised forests.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.0.7 dated 2016-01-15 and 2.1.0 dated 2016-03-17
DESCRIPTION | 11 MD5 | 70 +-- R/data.utilities.R | 16 R/factor.utilities.R | 8 R/find.interaction.R | 12 R/generic.impute.rfsrc.R | 8 R/generic.predict.rfsrc.R | 78 ++- R/impute.rfsrc.R | 8 R/max.subtree.R | 8 R/plot.competing.risk.R | 8 R/plot.rfsrc.R | 8 R/plot.survival.R | 8 R/plot.variable.R | 15 R/predict.rfsrc.R | 10 R/print.rfsrc.R | 8 R/rf2rfz.R | 8 R/rfsrc.R | 37 - R/rfsrc.news.R | 8 R/rfsrcSyn.R | 8 R/stat.split.R | 8 R/utilities.R | 119 +++-- R/var.select.R | 25 - R/vimp.R | 21 R/zzz.R | 8 configure.ac | 2 inst/CITATION | 4 inst/NEWS | 16 inst/doc/rsf-Rnews.pdf |binary man/find.interaction.Rd | 17 man/nutrigenomic.Rd | 3 man/predict.rfsrc.Rd | 4 man/rfsrc.Rd | 31 - man/var.select.Rd | 23 - man/vimp.Rd | 2 src/randomForestSRC.c | 1003 ++++++++++++++++++++-------------------------- src/randomForestSRC.h | 27 - 36 files changed, 836 insertions(+), 814 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.5 dated 2016-03-06 and 0.1.6 dated 2016-03-17
DESCRIPTION | 8 ++-- MD5 | 28 ++++++++-------- NEWS.md | 3 + R/helpers.R | 23 ------------- R/time_cluster_data.R | 40 +++++++++++++++-------- R/time_sequence_data.R | 35 +++++++++++++++++--- build/vignette.rds |binary inst/doc/divergence_vignette.html | 9 ++--- inst/doc/growth_curve_analysis_vignette.html | 4 +- inst/doc/onset_contingent_analysis_vignette.html | 4 +- inst/doc/preparing_your_data_vignette.html | 4 +- inst/doc/window_analysis_vignette.html | 4 +- man/analyze_time_bins.Rd | 10 +++++ man/make_time_cluster_data.Rd | 13 ++++++- tests/testthat/test_cluster_analysis.R | 22 ++++++++++++ 15 files changed, 132 insertions(+), 75 deletions(-)
Title: Canadian Forest Fire Danger Rating System
Description: This project provides a group of new functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS) at various time scales: the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System. Some functions have two versions, table and raster based.
Author: Xianli Wang, Alan Cantin, Marc-Andre Parisien, Mike Wotton, Kerry Anderson, Brett Moore, and Mike Flannigan
Maintainer: Alan Cantin <Alan.Cantin@Canada.ca>
Diff between cffdrs versions 1.7.1 dated 2016-02-22 and 1.7.3 dated 2016-03-17
DESCRIPTION | 12 - MD5 | 69 ++++--- R/BEcalc.r | 43 +++- R/BROScalc.r | 51 ++++- R/C6calc.r | 78 ++++++-- R/CFBcalc.r | 51 ++++- R/DISTtcalc.r | 37 +++- R/FBPcalc.r | 415 ++++++++++++++++++++++++++++----------------- R/FIcalc.r | 25 ++ R/FMCcalc.r | 62 +++++- R/FROScalc.r | 27 ++ R/ISIcalc.r | 46 ++++- R/LBcalc.r | 38 +++- R/LBtcalc.r | 41 +++- R/ROScalc.r | 138 +++++++++++---- R/ROStcalc.r | 35 +++ R/ROSthetacalc.r | 43 +++- R/SFCcalc.r | 92 ++++++++-- R/Slopecalc.r | 361 ++++++++++++++++++++++++++------------- R/TFCcalc.r | 50 ++++- R/buiCalc.R |only R/dcCalc.R |only R/dmcCalc.R |only R/fbp.r | 79 ++++++-- R/fbpRaster.r | 213 ++++++++++++++--------- R/ffmcCalc.R |only R/fireSeason.r | 82 +++++++-- R/fwi.r | 248 +++++++++++++++------------ R/fwiCalc.R |only R/fwiRaster.r | 454 ++++++++++++++++++++++++++++++++------------------ R/gfmc.r | 162 ++++++++++++----- R/hffmc.r | 168 ++++++++++++------ R/hffmcRaster.r | 194 +++++++++++++-------- R/sdmc.r | 121 +++++++++---- R/winter_DC.r | 41 +++- man/cffdrs-package.Rd | 4 man/fbp.Rd | 2 man/fbpRaster.Rd | 2 38 files changed, 2430 insertions(+), 1054 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via Gibbs sampling with optional resampling techniques and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <xaviera@purdue.edu>
Diff between bWGR versions 1.3 dated 2015-11-19 and 1.3.1 dated 2016-03-17
DESCRIPTION | 8 ++--- MD5 | 20 ++++++++----- R/RcppExports.R | 4 ++ R/bmen.R |only R/mkr.R | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++- R/wGELA.R |only inst/CITATION | 6 +-- inst/doc |only man/bWGR.Rd | 4 +- man/bmen.Rd |only man/mkr.Rd | 1 src/GSEN.cpp |only src/RcppExports.cpp | 18 +++++++++++ 13 files changed, 124 insertions(+), 17 deletions(-)
Title: Smoothing Splines for Large Samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Six marginal spline types are supported: cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between bigsplines versions 1.0-7 dated 2015-08-09 and 1.0-8 dated 2016-03-17
ChangeLog | 27 ++++++++++++++++ DESCRIPTION | 10 +++--- MD5 | 70 ++++++++++++++++++++++-------------------- R/bigspline.R | 13 ++++++- R/bigssa.R | 6 +-- R/bigssp.R | 4 +- R/imagebar.R | 11 +++--- R/makerkm.R | 15 ++++++--- R/makessa.R | 21 +++++++++--- R/makessg.R | 9 +++++ R/makessp.R | 15 +++++++-- R/predict.bigspline.R | 17 +++++++++- R/predict.bigssa.R | 4 +- R/predict.bigssg.R | 4 +- R/predict.bigssp.R | 4 +- R/remlri.R | 48 +++++++++++++++++++++++++++-- R/remlvc.R | 75 +++++++++++++++++++++++++++++++++++++++++++--- R/ssawork.R | 5 ++- R/ssgwork.R | 5 ++- R/sspwork.R | 5 ++- man/bigspline.Rd | 19 ++++++----- man/bigsplines-package.Rd | 8 +++- man/bigssa.Rd | 26 +++++++-------- man/bigssg.Rd | 18 +++-------- man/bigssp.Rd | 20 ++++++------ man/bigtps.Rd | 6 +-- man/makessa.Rd | 13 +++---- man/makessg.Rd | 13 +------ man/makessp.Rd | 13 +++---- man/predict.bigspline.Rd | 6 +-- man/predict.bigssa.Rd | 10 +++--- man/predict.bigssg.Rd | 12 ++----- man/predict.bigssp.Rd | 12 ++++--- man/predict.bigtps.Rd | 4 +- src/linker.f |only src/linkersym.f |only src/ordker.f |only src/ordkersym.f |only 38 files changed, 369 insertions(+), 179 deletions(-)
Title: Quantitative Analysis Made Accessible
Description: Contains a number of functions that serve
two goals: first, make R more accessible to people migrating from
SPSS by adding a number of functions that behave roughly like their
SPSS equivalents; and second, make a number of slightly more
advanced functions more user friendly to relatively novice users.
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between userfriendlyscience versions 0.4-0 dated 2016-01-21 and 0.4-1 dated 2016-03-17
userfriendlyscience-0.4-0/userfriendlyscience/man/userfriendlyscience-associationMatrix.Rd |only userfriendlyscience-0.4-0/userfriendlyscience/man/userfriendlyscience-convert.Rd |only userfriendlyscience-0.4-0/userfriendlyscience/man/userfriendlyscience-printMethods.Rd |only userfriendlyscience-0.4-0/userfriendlyscience/man/userfriendlyscience-regr.Rd |only userfriendlyscience-0.4-0/userfriendlyscience/man/userfriendlyscience-userfriendlyscienceBasics.Rd |only userfriendlyscience-0.4-0/userfriendlyscience/tests/sysRevExampleTemplate.r |only userfriendlyscience-0.4-1/userfriendlyscience/DESCRIPTION | 8 +- userfriendlyscience-0.4-1/userfriendlyscience/MD5 | 35 +++++----- userfriendlyscience-0.4-1/userfriendlyscience/NAMESPACE | 4 - userfriendlyscience-0.4-1/userfriendlyscience/R/associationMatrix.R | 17 ++++ userfriendlyscience-0.4-1/userfriendlyscience/R/asymmetricalScatterMatrix.R | 21 ++++-- userfriendlyscience-0.4-1/userfriendlyscience/R/convert.R | 8 ++ userfriendlyscience-0.4-1/userfriendlyscience/R/descr.R | 2 userfriendlyscience-0.4-1/userfriendlyscience/R/fullFact.R |only userfriendlyscience-0.4-1/userfriendlyscience/R/powerHist.R | 9 +- userfriendlyscience-0.4-1/userfriendlyscience/R/regr.R | 17 ++++ userfriendlyscience-0.4-1/userfriendlyscience/R/sort.associationMatrix.R | 18 ++++- userfriendlyscience-0.4-1/userfriendlyscience/man/associationMatrix.Rd |only userfriendlyscience-0.4-1/userfriendlyscience/man/asymmetricalScatterMatrix.Rd | 7 ++ userfriendlyscience-0.4-1/userfriendlyscience/man/convert.Rd |only userfriendlyscience-0.4-1/userfriendlyscience/man/fullFact.Rd |only userfriendlyscience-0.4-1/userfriendlyscience/man/printMethods.Rd |only userfriendlyscience-0.4-1/userfriendlyscience/man/regr.Rd |only userfriendlyscience-0.4-1/userfriendlyscience/man/userfriendlyscience-powerHist.Rd | 7 +- userfriendlyscience-0.4-1/userfriendlyscience/man/userfriendlyscienceBasics.Rd |only 25 files changed, 115 insertions(+), 38 deletions(-)
More information about userfriendlyscience at CRAN
Permanent link
Title: Improved Prediction Intervals for ARIMA Processes and Structural
Time Series
Description: Prediction intervals for ARIMA and structural time series
models using importance sampling approach with uninformative priors for model
parameters, leading to more accurate coverage probabilities in frequentist
sense. Instead of sampling the future observations and hidden states of the
state space representation of the model, only model parameters are sampled,
and the method is based solving the equations corresponding to the conditional
coverage probability of the prediction intervals. This makes method relatively
fast compared to for example MCMC methods, and standard errors of prediction
limits can also be computed straightforwardly.
Author: Jouni Helske
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between tsPI versions 1.0.0 dated 2015-11-09 and 1.0.1 dated 2016-03-17
ChangeLog |only DESCRIPTION | 19 + MD5 | 35 +-- NAMESPACE | 76 +++---- R/arima_pi.R | 390 ++++++++++++++++++++-------------------- R/struct_pi.R | 328 ++++++++++++++++----------------- R/tsPI-package.R | 66 +++--- inst/CITATION | 17 + man/acv_arma.Rd | 68 +++--- man/arima_pi.Rd | 181 +++++++++--------- man/avg_coverage_arima.Rd | 110 +++++------ man/avg_coverage_struct.Rd | 122 ++++++------ man/dacv_arma.Rd | 52 ++--- man/information_arma.Rd | 62 +++--- man/priors.Rd | 74 +++---- man/struct_pi.Rd | 154 +++++++-------- man/tsPI.Rd | 68 +++--- tests/testthat/test-arima_pi.R | 124 ++++++------ tests/testthat/test-struct_pi.R | 100 +++++----- 19 files changed, 1037 insertions(+), 1009 deletions(-)
Title: Linear/Nonlinear SVM Classification Solver Based on ADMM and
IADMM Algorithms
Description:
Solve large-scale regularised linear/kernel classification by using ADMM and IADMM algorithms. This package provides linear L2-regularised primal classification (both ADMM and IADMM are available), kernel L2-regularised dual classification (IADMM) as well as L1-regularised primal classification (both ADMM and IADMM are available).
Author: Ben DAI <bendai2-c@my.cityu.edu.hk>; Junhui Wang <j.h.wang@cityu.edu.hk>
Maintainer: Ben DAI <bendai2-c@my.cityu.edu.hk>
Diff between svmadmm versions 0.1 dated 2016-03-07 and 0.2 dated 2016-03-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/linear_math.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Spatial Modeling on Stream Networks
Description: Geostatistical modeling for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including covariates, can be fit with ML or REML. Mapping and other graphical functions are included.
Author: Jay Ver Hoef and Erin Peterson
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.6 dated 2015-08-23 and 1.1.7 dated 2016-03-17
SSN-1.1.6/SSN/R/additive.function.jay.R |only SSN-1.1.6/SSN/R/glmssn2.R |only SSN-1.1.6/SSN/inst/vignRnw |only SSN-1.1.7/SSN/DESCRIPTION | 8 SSN-1.1.7/SSN/MD5 | 34 +- SSN-1.1.7/SSN/R/CrossValidationSSN.r | 12 SSN-1.1.7/SSN/R/CrossValidationStatsSSN.r | 17 - SSN-1.1.7/SSN/R/SSN-methods.R | 7 SSN-1.1.7/SSN/R/additive.function.R | 138 +++++++-- SSN-1.1.7/SSN/R/createDistMat.R | 28 - SSN-1.1.7/SSN/data/mf04.rda |binary SSN-1.1.7/SSN/data/mf04p.rda |binary SSN-1.1.7/SSN/data/modelFits.rda |binary SSN-1.1.7/SSN/inst/doc/SSN.R | 423 ++++++++++++------------------ SSN-1.1.7/SSN/inst/doc/SSN.pdf |binary SSN-1.1.7/SSN/inst/doc/STARS.pdf |binary SSN-1.1.7/SSN/man/CrossValidationSSN.Rd | 15 - SSN-1.1.7/SSN/man/SimulateOnSSN.Rd | 6 SSN-1.1.7/SSN/man/createSSN.Rd | 2 19 files changed, 335 insertions(+), 355 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.6 dated 2015-11-10 and 1.3.7 dated 2016-03-17
ChangeLog |only DESCRIPTION | 9 +-- MD5 | 27 ++++----- NAMESPACE | 24 ++++---- R/RcppExports.R | 46 +++++++-------- R/ecg.R | 32 +++++------ configure.ac | 54 +++++++++--------- man/ECG.Rd | 45 ++++++++------- man/Rlibeemd.Rd | 60 ++++++++++---------- man/ceemdan.Rd | 162 ++++++++++++++++++++++++++++---------------------------- man/eemd.Rd | 154 ++++++++++++++++++++++++++--------------------------- man/emd.Rd | 93 +++++++++++++++----------------- man/extrema.Rd | 99 +++++++++++++++++----------------- man/nIMFs.Rd | 42 +++++++------- src/Makevars.in | 2 15 files changed, 427 insertions(+), 422 deletions(-)
Title: Importance Measure and Selection for Groups of Variables with
Random Forests
Description: Variable selection tools for groups of variables and functional data based on a new grouped variable importance with random forests.
Author: Baptiste Gregorutti
Maintainer: Baptiste Gregorutti <baptiste.gregorutti@safety-line.fr>
Diff between RFgroove versions 1.0 dated 2015-05-18 and 1.1 dated 2016-03-17
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 4 ++++ R/plot.importance.R |only R/selectLevel.R | 9 ++++++--- R/varImpGroup.R | 3 ++- man/RFgroove-package.Rd | 4 ++-- man/plot.importance.Rd |only man/selectFunctional.Rd | 4 ++-- man/varImpGroup.Rd | 8 ++++---- src/RFGroupImp.c | 45 --------------------------------------------- 11 files changed, 34 insertions(+), 69 deletions(-)
Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits (morphometric, function-valued, etc.) including ancestral state reconstruction, estimating phylogenetic signal, and assessing correlated trait evolution. Visit http://www.phylocurve.org for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 1.3.0 dated 2015-06-17 and 2.0.2 dated 2016-03-17
phylocurve-1.3.0/phylocurve/man/compare.multivar.rate.mult.Rd |only phylocurve-1.3.0/phylocurve/man/compare.rate.mult.Rd |only phylocurve-1.3.0/phylocurve/man/get_aligned_function_data.Rd |only phylocurve-1.3.0/phylocurve/man/get_tip_coefficients.Rd |only phylocurve-1.3.0/phylocurve/man/pgls.mult.Rd |only phylocurve-1.3.0/phylocurve/man/print.lr.test.Rd |only phylocurve-1.3.0/phylocurve/man/print.rate.mult.Rd |only phylocurve-1.3.0/phylocurve/man/rate.mult.Rd |only phylocurve-1.3.0/phylocurve/man/sim.mult.Rd |only phylocurve-2.0.2/phylocurve/DESCRIPTION | 21 phylocurve-2.0.2/phylocurve/MD5 | 54 phylocurve-2.0.2/phylocurve/NAMESPACE | 76 phylocurve-2.0.2/phylocurve/R/RcppExports.R |only phylocurve-2.0.2/phylocurve/R/fast_geomorph_functions.R |only phylocurve-2.0.2/phylocurve/R/phylocurve.R | 3559 ++++++---- phylocurve-2.0.2/phylocurve/man/GP.fit.Rd | 4 phylocurve-2.0.2/phylocurve/man/K.mult.Rd | 40 phylocurve-2.0.2/phylocurve/man/compare.models.Rd |only phylocurve-2.0.2/phylocurve/man/evo.model.Rd |only phylocurve-2.0.2/phylocurve/man/fast.geomorph.compare.evol.rates.Rd |only phylocurve-2.0.2/phylocurve/man/fast.geomorph.compare.multi.evol.rates.Rd |only phylocurve-2.0.2/phylocurve/man/fast.geomorph.phylo.integration.Rd |only phylocurve-2.0.2/phylocurve/man/fast.geomorph.physignal.Rd |only phylocurve-2.0.2/phylocurve/man/fast.geomorph.procD.pgls.Rd |only phylocurve-2.0.2/phylocurve/man/get.aligned.function.data.Rd |only phylocurve-2.0.2/phylocurve/man/get.tip.coefficients.Rd |only phylocurve-2.0.2/phylocurve/man/multipic.Rd |only phylocurve-2.0.2/phylocurve/man/nonlinear.fit.Rd | 4 phylocurve-2.0.2/phylocurve/man/paint.edges.Rd |only phylocurve-2.0.2/phylocurve/man/phylocurve-package.Rd | 12 phylocurve-2.0.2/phylocurve/man/phylocurve.Rd | 12 phylocurve-2.0.2/phylocurve/man/phylocurve.generalized.Rd | 4 phylocurve-2.0.2/phylocurve/man/phylocurve.trim.Rd | 4 phylocurve-2.0.2/phylocurve/man/polynomial.fit.Rd | 4 phylocurve-2.0.2/phylocurve/man/prep_multipic.Rd |only phylocurve-2.0.2/phylocurve/man/print.evo.model.Rd |only phylocurve-2.0.2/phylocurve/man/sim.curves.Rd | 6 phylocurve-2.0.2/phylocurve/man/sim.traits.Rd |only phylocurve-2.0.2/phylocurve/man/ultraFastAnc.Rd |only phylocurve-2.0.2/phylocurve/src |only 40 files changed, 2342 insertions(+), 1458 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between KFAS versions 1.2.1 dated 2016-02-05 and 1.2.2 dated 2016-03-17
ChangeLog | 30 - DESCRIPTION | 8 MD5 | 66 +- R/SSMcustom.R | 2 R/fitSSM.R | 11 R/importanceSSM.R | 4 R/interval.R | 14 R/logLik.SSModel.R | 10 R/predict.SSModel.R | 5 R/simulateSSM.R | 24 build/vignette.rds |binary data/GlobalTemp.rda |binary data/alcohol.rda |binary data/boat.rda |binary data/sexratio.rda |binary inst/doc/KFAS.R | 110 +-- inst/doc/KFAS.Rnw | 1018 +++++++++++++++++----------------- inst/doc/KFAS.pdf |binary man/KFAS.Rd | 1078 ++++++++++++++++++------------------- man/KFS.Rd | 442 +++++++-------- man/fitSSM.Rd | 4 man/ldl.Rd | 64 +- man/logLik.SSModel.Rd | 10 man/predict.SSModel.Rd | 5 man/simulateSSM.Rd | 190 +++--- src/declarations.h | 2 src/init.c | 2 src/simgaussianuncond.f95 | 13 tests/testthat/testBasics.R | 11 tests/testthat/testImportanceSSM.R | 14 tests/testthat/testNumerical.R | 7 tests/testthat/testPredict.R | 67 +- tests/testthat/testSimulateSSM.R | 12 vignettes/KFAS.Rnw | 1018 +++++++++++++++++----------------- 34 files changed, 2136 insertions(+), 2105 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 2.0-4 dated 2016-03-13 and 2.0-5 dated 2016-03-17
DESCRIPTION | 8 +-- MD5 | 10 +-- R/predict.glmnet.R | 2 R/predict.multnet.R | 4 - inst/doc/Coxnet.pdf |binary inst/doc/glmnet_beta.html | 116 +++++++++++++++++++++++----------------------- 6 files changed, 70 insertions(+), 70 deletions(-)
Title: Abbreviating Items Measures using Genetic Algorithms
Description: The GAabbreviate package uses Genetic Algorithms as an optimization tool for scale abbreviation or subset selection that maximally captures the variance in the original data.
Author: Luca Scrucca [aut],
Baljinder K. Sahdra [aut, cre]
Maintainer: Baljinder K. Sahdra <baljinder.sahdra@acu.edu.au>
Diff between GAabbreviate versions 1.1 dated 2016-02-26 and 1.2 dated 2016-03-17
GAabbreviate-1.1/GAabbreviate/R/zzz.R |only GAabbreviate-1.2/GAabbreviate/DESCRIPTION | 8 GAabbreviate-1.2/GAabbreviate/MD5 | 11 GAabbreviate-1.2/GAabbreviate/R/GAabbreviate.R | 335 ++++++------- GAabbreviate-1.2/GAabbreviate/inst/NEWS | 6 GAabbreviate-1.2/GAabbreviate/man/GAabbreviate-internal.Rd | 1 GAabbreviate-1.2/GAabbreviate/man/GAabbreviate.Rd | 16 7 files changed, 202 insertions(+), 175 deletions(-)
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ddpcr versions 1.0.1 dated 2016-02-19 and 1.1.2 dated 2016-03-17
ddpcr-1.0.1/ddpcr/inst/sample_data/small/B06_filled.csv |only ddpcr-1.0.1/ddpcr/inst/sample_data/small/small_B01_Amplitude.csv |only ddpcr-1.0.1/ddpcr/inst/sample_data/small/small_B06_Amplitude.csv |only ddpcr-1.0.1/ddpcr/inst/sample_data/small/small_C06_Amplitude.csv |only ddpcr-1.0.1/ddpcr/inst/sample_data/small/small_C08_Amplitude.csv |only ddpcr-1.1.2/ddpcr/DESCRIPTION | 10 ddpcr-1.1.2/ddpcr/MD5 | 114 ddpcr-1.1.2/ddpcr/R/plate.R | 4 ddpcr-1.1.2/ddpcr/R/plot.R | 2 ddpcr-1.1.2/ddpcr/R/pnpp_experiment-calculate_neg_freq.R | 2 ddpcr-1.1.2/ddpcr/R/pnpp_experiment-filled.R | 8 ddpcr-1.1.2/ddpcr/R/pnpp_experiment-plot.R | 2 ddpcr-1.1.2/ddpcr/R/sample_data.R |only ddpcr-1.1.2/ddpcr/R/subset.R | 28 ddpcr-1.1.2/ddpcr/R/type-wildtype_mutant_pnpp.R | 2 ddpcr-1.1.2/ddpcr/R/utils.R | 60 ddpcr-1.1.2/ddpcr/README.md | 205 ddpcr-1.1.2/ddpcr/build/vignette.rds |binary ddpcr-1.1.2/ddpcr/inst/doc/algorithm.Rmd | 8 ddpcr-1.1.2/ddpcr/inst/doc/algorithm.html | 21 ddpcr-1.1.2/ddpcr/inst/doc/extend.html | 41 ddpcr-1.1.2/ddpcr/inst/doc/overview.R | 16 ddpcr-1.1.2/ddpcr/inst/doc/overview.Rmd | 32 ddpcr-1.1.2/ddpcr/inst/doc/overview.html | 199 ddpcr-1.1.2/ddpcr/inst/sample_data/empty_plate.rds |binary ddpcr-1.1.2/ddpcr/inst/sample_data/large/large.rds |binary ddpcr-1.1.2/ddpcr/inst/sample_data/small/A05_filled.csv |only ddpcr-1.1.2/ddpcr/inst/sample_data/small/analyzed.rds |binary ddpcr-1.1.2/ddpcr/inst/sample_data/small/analyzed_pnpp.rds |binary ddpcr-1.1.2/ddpcr/inst/sample_data/small/small.csv | 15 ddpcr-1.1.2/ddpcr/inst/sample_data/small/small.rds |binary ddpcr-1.1.2/ddpcr/inst/sample_data/small/small_A01_Amplitude.csv |only ddpcr-1.1.2/ddpcr/inst/sample_data/small/small_A05_Amplitude.csv |only ddpcr-1.1.2/ddpcr/inst/sample_data/small/small_C01_Amplitude.csv |29535 ++++------ ddpcr-1.1.2/ddpcr/inst/sample_data/small/small_C05_Amplitude.csv |only ddpcr-1.1.2/ddpcr/inst/sample_data/small/small_F05_Amplitude.csv |only ddpcr-1.1.2/ddpcr/inst/shiny/data |only ddpcr-1.1.2/ddpcr/inst/shiny/server/tab-dataset.R | 2 ddpcr-1.1.2/ddpcr/inst/shiny/server/tab-results.R | 3 ddpcr-1.1.2/ddpcr/inst/shiny/server/tab-settings.R | 4 ddpcr-1.1.2/ddpcr/inst/shiny/ui/tab-settings.R | 9 ddpcr-1.1.2/ddpcr/man/calculate_neg_freq_single.Rd | 2 ddpcr-1.1.2/ddpcr/man/get_filled_border.Rd | 4 ddpcr-1.1.2/ddpcr/man/get_filled_drops.Rd | 4 ddpcr-1.1.2/ddpcr/man/is_range.Rd | 8 ddpcr-1.1.2/ddpcr/man/plot.ddpcr_plate.Rd | 2 ddpcr-1.1.2/ddpcr/man/plot.pnpp_experiment.Rd | 2 ddpcr-1.1.2/ddpcr/man/plot.wildtype_mutant_pnpp.Rd | 2 ddpcr-1.1.2/ddpcr/man/sample_data.Rd | 5 ddpcr-1.1.2/ddpcr/man/subset.ddpcr_plate.Rd | 20 ddpcr-1.1.2/ddpcr/man/well_info.Rd | 2 ddpcr-1.1.2/ddpcr/man/wells_used.Rd | 2 ddpcr-1.1.2/ddpcr/tests/testthat/test-custom_thresholds.R | 10 ddpcr-1.1.2/ddpcr/tests/testthat/test-empty.R | 16 ddpcr-1.1.2/ddpcr/tests/testthat/test-failures.R | 8 ddpcr-1.1.2/ddpcr/tests/testthat/test-outliers.R | 6 ddpcr-1.1.2/ddpcr/tests/testthat/test-plate.R | 10 ddpcr-1.1.2/ddpcr/tests/testthat/test-pnpp_experiment-calculate_neg_freq.R | 10 ddpcr-1.1.2/ddpcr/tests/testthat/test-pnpp_experiment-filled.R | 18 ddpcr-1.1.2/ddpcr/tests/testthat/test-pnpp_experiment.R | 4 ddpcr-1.1.2/ddpcr/tests/testthat/test-subset.R | 56 ddpcr-1.1.2/ddpcr/tests/testthat/test-utils.R | 20 ddpcr-1.1.2/ddpcr/vignettes/algorithm.Rmd | 8 ddpcr-1.1.2/ddpcr/vignettes/overview.Rmd | 32 64 files changed, 14751 insertions(+), 15822 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R
without printing the content of graphics windows to an embosser of some kind. This
is not as immediate as is required for efficient access to statistical output.
The functions here are created so that blind people can make even better use
of R. This includes the text descriptions of graphs, convenience functions
to replace the functionality offered in many GUI front ends, and experimental
functionality for optimising graphical content to prepare it for embossing as
tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Duncan Murdoch [ctb], Greg Snow
[ctb], Henrik Bengtsson [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie
[ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.22.0 dated 2015-06-26 and 0.24.0 dated 2016-03-17
BrailleR-0.22.0/BrailleR/R/Premiere100.R |only BrailleR-0.22.0/BrailleR/inst/DEFAULTS |only BrailleR-0.24.0/BrailleR/DESCRIPTION | 31 + BrailleR-0.24.0/BrailleR/MD5 | 116 +++-- BrailleR-0.24.0/BrailleR/NAMESPACE | 15 BrailleR-0.24.0/BrailleR/R/BRLThis.R | 26 - BrailleR-0.24.0/BrailleR/R/BrailleRHome.R |only BrailleR-0.24.0/BrailleR/R/GettingStarted.R | 18 BrailleR-0.24.0/BrailleR/R/Internal.R | 18 BrailleR-0.24.0/BrailleR/R/JoinBlindRUG.R |only BrailleR-0.24.0/BrailleR/R/MakeAllFormats.R |only BrailleR-0.24.0/BrailleR/R/MakeBatch.R | 26 - BrailleR-0.24.0/BrailleR/R/MakeReadable.R |only BrailleR-0.24.0/BrailleR/R/MakeRmdFiles.R | 14 BrailleR-0.24.0/BrailleR/R/MakeRprofile.R | 5 BrailleR-0.24.0/BrailleR/R/MakeSlideShow.R |only BrailleR-0.24.0/BrailleR/R/NewFunction.R |only BrailleR-0.24.0/BrailleR/R/OneFactor.R | 49 +- BrailleR-0.24.0/BrailleR/R/OnePredictor.R | 43 +- BrailleR-0.24.0/BrailleR/R/Options.R | 214 +++++++--- BrailleR-0.24.0/BrailleR/R/Premier100.R |only BrailleR-0.24.0/BrailleR/R/PrepareWriteR.R | 8 BrailleR-0.24.0/BrailleR/R/R2txtJG.R | 2 BrailleR-0.24.0/BrailleR/R/SVGThis.R | 4 BrailleR-0.24.0/BrailleR/R/SetupBrailleR.R |only BrailleR-0.24.0/BrailleR/R/TwoFactors.R | 67 +-- BrailleR-0.24.0/BrailleR/R/UniDesc.R | 69 +-- BrailleR-0.24.0/BrailleR/R/VIMethod1_JG.R | 4 BrailleR-0.24.0/BrailleR/R/VIMethod2_TB.R | 4 BrailleR-0.24.0/BrailleR/R/WTF.R |only BrailleR-0.24.0/BrailleR/R/WhereXY.R | 7 BrailleR-0.24.0/BrailleR/R/WriteR.R |only BrailleR-0.24.0/BrailleR/R/history.R |only BrailleR-0.24.0/BrailleR/R/zzz.R | 29 + BrailleR-0.24.0/BrailleR/inst/BrailleROptions |only BrailleR-0.24.0/BrailleR/inst/NEWS | 111 ++++- BrailleR-0.24.0/BrailleR/inst/Python/FixLineBreaks.py |only BrailleR-0.24.0/BrailleR/inst/Python/RemoveTabs.py |only BrailleR-0.24.0/BrailleR/inst/Python/WriteR/HelpPage.Rmd | 51 +- BrailleR-0.24.0/BrailleR/inst/Python/WriteR/HelpPage.html | 59 +- BrailleR-0.24.0/BrailleR/inst/Python/WriteR/WriteR.pyw | 172 +++++--- BrailleR-0.24.0/BrailleR/inst/WriteROptions |only BrailleR-0.24.0/BrailleR/inst/css/JGSlides.css |only BrailleR-0.24.0/BrailleR/inst/doc/BrailleRHistory.html | 166 +++++-- BrailleR-0.24.0/BrailleR/inst/doc/BrailleRHistory.rmd | 11 BrailleR-0.24.0/BrailleR/inst/doc/Ex1histograms.html | 150 +++---- BrailleR-0.24.0/BrailleR/inst/doc/Ex2BasicNumerical.html | 48 +- BrailleR-0.24.0/BrailleR/inst/doc/Ex3UnivariateDescription.html | 46 +- BrailleR-0.24.0/BrailleR/inst/doc/Ex4SingleResponseOneGroupingFactor.html | 46 +- BrailleR-0.24.0/BrailleR/inst/doc/GettingStarted.R | 3 BrailleR-0.24.0/BrailleR/inst/doc/GettingStarted.Rmd | 13 BrailleR-0.24.0/BrailleR/inst/doc/GettingStarted.html | 66 ++- BrailleR-0.24.0/BrailleR/inst/foo.pandoc |only BrailleR-0.24.0/BrailleR/man/BrailleR-package.Rd | 6 BrailleR-0.24.0/BrailleR/man/BrailleRHome.Rd |only BrailleR-0.24.0/BrailleR/man/Embossers.Rd | 15 BrailleR-0.24.0/BrailleR/man/Internal.Rd | 8 BrailleR-0.24.0/BrailleR/man/JoinBlindRUG.Rd |only BrailleR-0.24.0/BrailleR/man/MakeAllFormats.Rd |only BrailleR-0.24.0/BrailleR/man/MakeReadable.Rd |only BrailleR-0.24.0/BrailleR/man/MakeSlideShow.Rd |only BrailleR-0.24.0/BrailleR/man/NewFunction.Rd |only BrailleR-0.24.0/BrailleR/man/PrepareWriteR.Rd | 14 BrailleR-0.24.0/BrailleR/man/SVGThis.Rd | 11 BrailleR-0.24.0/BrailleR/man/SetOptions.Rd | 44 +- BrailleR-0.24.0/BrailleR/man/SetupBrailleR.Rd |only BrailleR-0.24.0/BrailleR/man/TwoFactors.Rd | 8 BrailleR-0.24.0/BrailleR/man/VI.Rd | 5 BrailleR-0.24.0/BrailleR/man/WTF.Rd |only BrailleR-0.24.0/BrailleR/man/history.Rd |only BrailleR-0.24.0/BrailleR/vignettes/BrailleRHistory.rmd | 11 BrailleR-0.24.0/BrailleR/vignettes/BrailleRPublications.bib | 2 BrailleR-0.24.0/BrailleR/vignettes/GettingStarted.Rmd | 13 73 files changed, 1207 insertions(+), 641 deletions(-)
Title: Functions for Elementary Bayesian Inference
Description: A set of R functions and data sets for the book Introduction to
Bayesian Statistics, Bolstad, W.M. (2007), John Wiley & Sons ISBN 0-471-27020-2.
Author: James Curran <j.curran@auckland.ac.nz>
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Bolstad versions 0.2-25 dated 2013-06-17 and 0.2-30 dated 2016-03-17
Bolstad-0.2-25/Bolstad/INDEX |only Bolstad-0.2-30/Bolstad/DESCRIPTION | 20 Bolstad-0.2-30/Bolstad/MD5 | 125 ++- Bolstad-0.2-30/Bolstad/NAMESPACE | 111 ++- Bolstad-0.2-30/Bolstad/R/Bolstad-package.R |only Bolstad-0.2-30/Bolstad/R/IQR.R |only Bolstad-0.2-30/Bolstad/R/as.data.frame.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/bayes.lin.reg.r | 631 +++++++++++--------- Bolstad-0.2-30/Bolstad/R/bayes.lm.R |only Bolstad-0.2-30/Bolstad/R/bayes.t.test.R |only Bolstad-0.2-30/Bolstad/R/binobp.r | 93 ++ Bolstad-0.2-30/Bolstad/R/binodp.r | 93 ++ Bolstad-0.2-30/Bolstad/R/binogcp.r | 149 +++- Bolstad-0.2-30/Bolstad/R/binomixp.r | 314 ++++++--- Bolstad-0.2-30/Bolstad/R/cdf.R |only Bolstad-0.2-30/Bolstad/R/createPrior.R |only Bolstad-0.2-30/Bolstad/R/createPrior.default.R |only Bolstad-0.2-30/Bolstad/R/cumDistFun.R |only Bolstad-0.2-30/Bolstad/R/decomp.R |only Bolstad-0.2-30/Bolstad/R/lines.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/mean.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/median.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/mvnmvnp.R |only Bolstad-0.2-30/Bolstad/R/normdp.r | 64 +- Bolstad-0.2-30/Bolstad/R/normgcp.r | 123 +++ Bolstad-0.2-30/Bolstad/R/normmixp.r | 390 +++++++----- Bolstad-0.2-30/Bolstad/R/normnp.r | 212 ++++-- Bolstad-0.2-30/Bolstad/R/nvaricp.r | 67 ++ Bolstad-0.2-30/Bolstad/R/plot.Bolstad.r | 83 ++ Bolstad-0.2-30/Bolstad/R/poisdp.r | 72 ++ Bolstad-0.2-30/Bolstad/R/poisgamp.r | 107 ++- Bolstad-0.2-30/Bolstad/R/poisgcp.r | 88 ++ Bolstad-0.2-30/Bolstad/R/print.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/print.sintegral.R |only Bolstad-0.2-30/Bolstad/R/print.sscamp.R |only Bolstad-0.2-30/Bolstad/R/print.summary.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/qFun.R |only Bolstad-0.2-30/Bolstad/R/quantile.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/sd.R |only Bolstad-0.2-30/Bolstad/R/sintegral.r | 119 ++- Bolstad-0.2-30/Bolstad/R/sscsample.r | 339 +++++----- Bolstad-0.2-30/Bolstad/R/summary.Bolstad.R |only Bolstad-0.2-30/Bolstad/R/sysdata.rda |binary Bolstad-0.2-30/Bolstad/R/var.R |only Bolstad-0.2-30/Bolstad/R/xdesign.r | 58 + Bolstad-0.2-30/Bolstad/README.md |only Bolstad-0.2-30/Bolstad/data |only Bolstad-0.2-30/Bolstad/man/Bolstad-package.Rd |only Bolstad-0.2-30/Bolstad/man/IQR.Rd |only Bolstad-0.2-30/Bolstad/man/as.data.frame.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/bayes.lin.reg.Rd | 196 +++--- Bolstad-0.2-30/Bolstad/man/bayes.lm.Rd |only Bolstad-0.2-30/Bolstad/man/bayes.t.test.Rd |only Bolstad-0.2-30/Bolstad/man/bears.Rd |only Bolstad-0.2-30/Bolstad/man/binobp.Rd | 130 +--- Bolstad-0.2-30/Bolstad/man/binodp.Rd | 145 ++-- Bolstad-0.2-30/Bolstad/man/binogcp.Rd | 184 +++-- Bolstad-0.2-30/Bolstad/man/binomixp.Rd | 157 ++-- Bolstad-0.2-30/Bolstad/man/cdf.Rd |only Bolstad-0.2-30/Bolstad/man/createPrior.Rd |only Bolstad-0.2-30/Bolstad/man/createPrior.default.Rd |only Bolstad-0.2-30/Bolstad/man/decomp.Rd |only Bolstad-0.2-30/Bolstad/man/lines.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/mean.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/median.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/mvnmvnp.Rd |only Bolstad-0.2-30/Bolstad/man/normdp.Rd | 123 ++- Bolstad-0.2-30/Bolstad/man/normgcp.Rd | 209 +++--- Bolstad-0.2-30/Bolstad/man/normmixp.Rd | 123 ++- Bolstad-0.2-30/Bolstad/man/normnp.Rd | 120 ++- Bolstad-0.2-30/Bolstad/man/nvaricp.Rd | 146 ++-- Bolstad-0.2-30/Bolstad/man/plot.Bolstad.Rd | 98 ++- Bolstad-0.2-30/Bolstad/man/poisdp.Rd | 135 ++-- Bolstad-0.2-30/Bolstad/man/poisgamp.Rd | 141 ++-- Bolstad-0.2-30/Bolstad/man/poisgcp.Rd | 206 +++--- Bolstad-0.2-30/Bolstad/man/print.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/print.sscsamp.Rd |only Bolstad-0.2-30/Bolstad/man/quantile.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/sd.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/sd.Rd |only Bolstad-0.2-30/Bolstad/man/sintegral.Rd | 127 ++-- Bolstad-0.2-30/Bolstad/man/slug.Rd |only Bolstad-0.2-30/Bolstad/man/sscsample.Rd | 100 +-- Bolstad-0.2-30/Bolstad/man/sscsample.data.Rd |only Bolstad-0.2-30/Bolstad/man/summary.Bolstad.Rd |only Bolstad-0.2-30/Bolstad/man/var.Rd |only Bolstad-0.2-30/Bolstad/man/xdesign.Rd | 92 +- 87 files changed, 3613 insertions(+), 2077 deletions(-)
Title: Remove Weekends and Holidays from ggplot2 Axes
Description: Provides a continuous date scale, omitting weekends and holidays.
Author: Dave Mills [aut, cre]
Maintainer: Dave Mills <dave.a.mills@gmail.com>
Diff between bdscale versions 1.2 dated 2014-11-12 and 2.0.0 dated 2016-03-17
DESCRIPTION | 25 +++++---- MD5 | 34 +++++++------ NAMESPACE | 10 ++- R/data.R |only R/scale_bd.R | 43 +++++++++-------- R/yahoo_dates.R | 3 - README.md | 31 ++++++------ build/vignette.rds |binary data |only inst/doc/bdscale.R | 14 ++--- inst/doc/bdscale.Rmd | 4 - inst/doc/bdscale.html | 126 +++++++++++++++++++++++++++++--------------------- man/bd2t.Rd | 6 +- man/bd_breaks.Rd | 5 + man/nyse.Rd |only man/scale_x_bd.Rd | 11 ++-- man/yahoo.Rd | 3 - tests |only vignettes/bdscale.Rmd | 4 - 19 files changed, 183 insertions(+), 136 deletions(-)
Title: Advanced Analysis of B Cell Receptor Repertoire Data
Description: Methods for advanced analysis of B cell receptor repertoire
data, like gene usage, mutations, clones, diversity, distance measures and
multidimensional scaling and their visualisation.
Author: Julia Bischof
Maintainer: Julia Bischof <Julia.Bischof@uksh.de>
Diff between bcRep versions 1.3.1 dated 2016-02-25 and 1.3.2 dated 2016-03-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/compare.geneUsage.R | 4 ++-- R/sequences.geneComb.R | 12 ++++++------ inst/NEWS.Rmd | 8 ++++++++ inst/doc/NEWS.pdf |binary 6 files changed, 25 insertions(+), 17 deletions(-)
Title: Supervised Component Generalized Linear Regression
Description: The Fisher Scoring Algorithm is extended so as to combine Partial
Least Squares regression with Generalized Linear Model estimation in the
multivariate context.
Author: Guillaume Cornu [cre, aut],
Frederic Mortier [aut],
Catherine Trottier [aut],
Xavier Bry [aut]
Maintainer: Guillaume Cornu <gcornu@cirad.fr>
Diff between SCGLR versions 2.0.2 dated 2015-02-16 and 2.0.3 dated 2016-03-16
DESCRIPTION | 19 ++++++---- MD5 | 64 ++++++++++++++++++------------------ NAMESPACE | 21 ++++++++++- NEWS | 5 ++ R/infoCriterion.r | 2 + R/metric.r | 1 R/multivariateGlm.fit.r | 1 R/multivariateGlm.r | 3 + R/multivariatePredictGlm.r | 2 + R/package.r | 2 - R/plot.r | 74 ++++++++++++++++++++++++++++++++++-------- R/scglr.r | 5 ++ R/scglrCrossVal.r | 5 ++ R/summary.r | 2 + build/vignette.rds |binary inst/doc/scglrVignettes.R | 11 ------ inst/doc/scglrVignettes.pdf |binary man/barplot.SCGLR.Rd | 8 ++-- man/critConvergence.Rd | 4 +- man/customize.Rd | 2 - man/genus.Rd | 12 +++--- man/infoCriterion.Rd | 8 ++-- man/method.Rd | 2 - man/multivariateFormula.Rd | 2 - man/multivariateGlm.Rd | 16 ++++----- man/multivariatePredictGlm.Rd | 12 +++--- man/pairs.SCGLR.Rd | 2 - man/plot.SCGLR.Rd | 4 +- man/print.SCGLR.Rd | 2 - man/scglr-package.Rd | 11 ++---- man/scglr.Rd | 16 ++++----- man/scglrCrossVal.Rd | 16 ++++----- man/summary.SCGLR.Rd | 2 - 33 files changed, 209 insertions(+), 127 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.5-2 dated 2016-03-15 and 0.5-3 dated 2016-03-16
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/SDMXGenericData-methods.R | 9 +++++---- R/rsdmx.R | 4 ++-- README.md | 2 +- inst/doc/quickstart.Rmd | 2 +- inst/doc/quickstart.html | 2 +- man/rsdmx.Rd | 4 ++-- vignettes/quickstart.Rmd | 2 +- 9 files changed, 25 insertions(+), 24 deletions(-)
Title: Joint Estimation in Linear Quantile Regression
Description: Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
Author: Surya Tokdar <tokdar@stat.duke.edu>
Maintainer: Surya Tokdar <tokdar@stat.duke.edu>
Diff between qrjoint versions 0.1-1 dated 2015-07-14 and 1.0-0 dated 2016-03-16
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/qrjoint.R | 80 ++++++++++++++++++++++++++++++--------------------------- man/qrjoint.Rd | 2 - src/qrjoint.c | 8 +++-- 5 files changed, 57 insertions(+), 49 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.4 dated 2015-12-26 and 1.7.5 dated 2016-03-16
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 11 +++++++++-- R/Contlcmm.R | 6 +++--- R/Jointlcmm.R | 6 +++--- R/Ordlcmm.R | 6 +++--- R/hlme.R | 8 ++++---- R/lcmm.R | 10 +++++----- R/multlcmm.R | 15 ++++++++++++--- R/plotfit.R | 2 +- R/predictL.multlcmm.R | 23 ++++++++++++++++++++++- R/predictY.multlcmm.R | 17 +++++++++++++++++ R/summary.Jointlcmm.R | 4 ++-- R/summary.hlme.R | 6 +++--- R/summary.lcmm.R | 4 ++-- R/summary.multlcmm.R | 16 +++++++++++++--- man/Jointlcmm.Rd | 10 ++++++++-- man/hlme.Rd | 14 ++++++++++---- man/lcmm-package.Rd | 6 +++--- man/lcmm.Rd | 19 +++++++++++++------ man/multlcmm.Rd | 10 +++++++--- src/hetmixCont.f90 | 4 +++- 22 files changed, 168 insertions(+), 79 deletions(-)
Title: Scalable Rejection Sampling for Bayesian Hierarchical Models
Description: Functions for implementing the Braun and Damien (2015) rejection
sampling algorithm for Bayesian hierarchical models. The algorithm generates
posterior samples in parallel, and is scalable when the individual units are
conditionally independent.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>
Diff between bayesGDS versions 0.6.1 dated 2015-03-31 and 0.6.2 dated 2016-03-16
DESCRIPTION | 20 ++- MD5 | 31 +++--- NAMESPACE | 3 NEWS | 13 +- NEWS.md |only R/bayesGDS-package.R | 3 build/vignette.rds |binary inst/vignette_sources/binary/binary.Rnw | 15 +- inst/vignette_sources/binary/binary_chunks.R | 2 man/Deprecated.Rd | 29 +---- man/bayesGDS-package.Rd | 14 -- man/binary-data.Rd | 10 - man/binary.Rd | 12 -- man/get.LML.Rd | 52 ++++------ man/get.cutoffs.Rd | 22 ++-- man/sample.GDS.Rd | 139 +++++++++++++-------------- tests/testthat/test_binary.R | 9 - 17 files changed, 178 insertions(+), 196 deletions(-)
More information about MatrixCorrelation at CRAN
Permanent link
Title: GPU Functions for R Objects
Description: Provides GPU enabled functions for R objects in a simple and
approachable manner. New 'gpu*' and 'vcl*' classes have been provided to
wrap typical R objects (e.g. vector, matrix), in both host and device
spaces, to mirror typical R syntax without the need to know OpenCL.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr. <cdetermanjr@gmail.com>
Diff between gpuR versions 1.0.1 dated 2015-11-21 and 1.1.0 dated 2016-03-16
gpuR-1.0.1/gpuR/configure.ac |only gpuR-1.0.1/gpuR/inst/include/gpuR/dynEigen.hpp |only gpuR-1.0.1/gpuR/inst/include/gpuR/vcl_helpers.hpp |only gpuR-1.0.1/gpuR/man/Arith-gpuMatrix-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/Arith-gpuVector-gpuVector-method.Rd |only gpuR-1.0.1/gpuR/man/Arith-vclMatrix-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/Arith-vclVector-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/Compare-gpuVector-vector-method.Rd |only gpuR-1.0.1/gpuR/man/Compare-vector-gpuVector-method.Rd |only gpuR-1.0.1/gpuR/man/Math-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/Math-gpuVector-method.Rd |only gpuR-1.0.1/gpuR/man/Math-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/Math-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/dim-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/dim-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/extract-gpuMatrix.Rd |only gpuR-1.0.1/gpuR/man/extract-gpuVector.Rd |only gpuR-1.0.1/gpuR/man/extract-vclMatrix.Rd |only gpuR-1.0.1/gpuR/man/extract-vclVector.Rd |only gpuR-1.0.1/gpuR/man/gpuInfo.Rd |only gpuR-1.0.1/gpuR/man/gpuMatrix.cov.Rd |only gpuR-1.0.1/gpuR/man/gpuVector-prods.Rd |only gpuR-1.0.1/gpuR/man/grapes-o-grapes-gpuVector-gpuVector-method.Rd |only gpuR-1.0.1/gpuR/man/grapes-o-grapes-vclVector-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/grapes-times-grapes-gpuMatrix-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/grapes-times-grapes-vclMatrix-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/grapes-times-grapes-vclVector-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/log-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/log-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/log-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/nrow.gpuMatrix.Rd |only gpuR-1.0.1/gpuR/man/nrow.vclMatrix.Rd |only gpuR-1.0.1/gpuR/man/typeof-gpuMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/typeof-gpuVector-method.Rd |only gpuR-1.0.1/gpuR/man/typeof-vclMatrix-method.Rd |only gpuR-1.0.1/gpuR/man/typeof-vclVector-method.Rd |only gpuR-1.0.1/gpuR/man/vclMatrix.cov.Rd |only gpuR-1.0.1/gpuR/src/Makevars.in |only gpuR-1.0.1/gpuR/src/detectCPUs.cpp |only gpuR-1.0.1/gpuR/src/detectGPUs.cpp |only gpuR-1.0.1/gpuR/src/detectPlatforms.cpp |only gpuR-1.0.1/gpuR/src/device_has_double.cpp |only gpuR-1.0.1/gpuR/src/dynEigen.cpp |only gpuR-1.0.1/gpuR/src/gpuInfo.cpp |only gpuR-1.0.1/gpuR/src/platformInfo.cpp |only gpuR-1.0.1/gpuR/tools |only gpuR-1.1.0/gpuR/DESCRIPTION | 17 gpuR-1.1.0/gpuR/MD5 | 409 gpuR-1.1.0/gpuR/NAMESPACE | 13 gpuR-1.1.0/gpuR/R/RcppExports.R | 373 gpuR-1.1.0/gpuR/R/class-gpuMatrix.R | 25 gpuR-1.1.0/gpuR/R/class-gpuVector.R | 34 gpuR-1.1.0/gpuR/R/class-vclMatrix.R | 26 gpuR-1.1.0/gpuR/R/class-vclVector.R | 30 gpuR-1.1.0/gpuR/R/eigen.R | 8 gpuR-1.1.0/gpuR/R/generics.R | 73 gpuR-1.1.0/gpuR/R/gpuMatrix.R | 277 gpuR-1.1.0/gpuR/R/gpuVector.R | 90 gpuR-1.1.0/gpuR/R/methods-gpuMatrix.R | 506 + gpuR-1.1.0/gpuR/R/methods-gpuVector.R | 235 gpuR-1.1.0/gpuR/R/methods-vclMatrix.R | 512 + gpuR-1.1.0/gpuR/R/methods-vclVector.R | 187 gpuR-1.1.0/gpuR/R/print.R | 1 gpuR-1.1.0/gpuR/R/typeof.R | 56 gpuR-1.1.0/gpuR/R/utils.R | 2 gpuR-1.1.0/gpuR/R/vclMatrix.R | 146 gpuR-1.1.0/gpuR/R/vclVector.R | 82 gpuR-1.1.0/gpuR/R/wrappers-gpuVector.R | 497 + gpuR-1.1.0/gpuR/R/wrappers-utils.R | 57 gpuR-1.1.0/gpuR/R/wrappers-vclMatrix.R | 767 + gpuR-1.1.0/gpuR/R/wrappers-vclVector.R | 346 gpuR-1.1.0/gpuR/R/wrappers.R | 528 + gpuR-1.1.0/gpuR/R/zzz.R | 11 gpuR-1.1.0/gpuR/README.md | 20 gpuR-1.1.0/gpuR/build/vignette.rds |binary gpuR-1.1.0/gpuR/configure | 4304 ---------- gpuR-1.1.0/gpuR/inst/NEWS.Rd | 26 gpuR-1.1.0/gpuR/inst/doc/gpuR.R | 20 gpuR-1.1.0/gpuR/inst/doc/gpuR.Rnw | 120 gpuR-1.1.0/gpuR/inst/doc/gpuR.pdf |binary gpuR-1.1.0/gpuR/inst/include/gpuR/dynEigenMat.hpp |only gpuR-1.1.0/gpuR/inst/include/gpuR/dynEigenVec.hpp | 41 gpuR-1.1.0/gpuR/inst/include/gpuR/dynVCLMat.hpp |only gpuR-1.1.0/gpuR/inst/include/gpuR/dynVCLVec.hpp |only gpuR-1.1.0/gpuR/inst/include/gpuR/eigen_helpers.hpp | 107 gpuR-1.1.0/gpuR/inst/testWithGPU |only gpuR-1.1.0/gpuR/man/Arith-methods.Rd |only gpuR-1.1.0/gpuR/man/Compare-methods.Rd |only gpuR-1.1.0/gpuR/man/Math-methods.Rd |only gpuR-1.1.0/gpuR/man/Summary-methods.Rd |only gpuR-1.1.0/gpuR/man/as.gpuMatrix-methods.Rd | 4 gpuR-1.1.0/gpuR/man/as.gpuVector-methods.Rd | 4 gpuR-1.1.0/gpuR/man/cov-methods.Rd |only gpuR-1.1.0/gpuR/man/currentContext.Rd |only gpuR-1.1.0/gpuR/man/currentDevice.Rd |only gpuR-1.1.0/gpuR/man/currentPlatform.Rd |only gpuR-1.1.0/gpuR/man/detectCPUs.Rd | 2 gpuR-1.1.0/gpuR/man/detectGPUs.Rd | 2 gpuR-1.1.0/gpuR/man/detectPlatforms.Rd | 2 gpuR-1.1.0/gpuR/man/deviceHasDouble.Rd | 2 gpuR-1.1.0/gpuR/man/deviceInfo.Rd |only gpuR-1.1.0/gpuR/man/dgpuMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/dgpuVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/dim-methods.Rd |only gpuR-1.1.0/gpuR/man/dist-vclMatrix.Rd | 33 gpuR-1.1.0/gpuR/man/dvclMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/dvclVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/eigen-gpuMatrix.Rd | 8 gpuR-1.1.0/gpuR/man/extract-methods.Rd |only gpuR-1.1.0/gpuR/man/fgpuMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/fgpuVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/fvclMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/fvclVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/gpuMatrix-class.Rd | 21 gpuR-1.1.0/gpuR/man/gpuMatrix-crossprod.Rd | 2 gpuR-1.1.0/gpuR/man/gpuMatrix-methods.Rd | 15 gpuR-1.1.0/gpuR/man/gpuMatrix.colSums.Rd | 2 gpuR-1.1.0/gpuR/man/gpuR-block.Rd |only gpuR-1.1.0/gpuR/man/gpuR-deepcopy.Rd |only gpuR-1.1.0/gpuR/man/gpuR-package.Rd | 24 gpuR-1.1.0/gpuR/man/gpuR-slice.Rd |only gpuR-1.1.0/gpuR/man/gpuVector-class.Rd | 14 gpuR-1.1.0/gpuR/man/gpuVector-methods.Rd | 6 gpuR-1.1.0/gpuR/man/grapes-o-grapes-methods.Rd |only gpuR-1.1.0/gpuR/man/grapes-times-grapes-methods.Rd |only gpuR-1.1.0/gpuR/man/has_cpu_skip.Rd | 2 gpuR-1.1.0/gpuR/man/has_double_skip.Rd | 2 gpuR-1.1.0/gpuR/man/has_gpu_skip.Rd | 2 gpuR-1.1.0/gpuR/man/igpuMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/igpuVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/ivclMatrix-class.Rd | 4 gpuR-1.1.0/gpuR/man/ivclVector-class.Rd | 2 gpuR-1.1.0/gpuR/man/length-methods.Rd | 8 gpuR-1.1.0/gpuR/man/listContexts.Rd |only gpuR-1.1.0/gpuR/man/log-methods.Rd |only gpuR-1.1.0/gpuR/man/nrow-gpuR.Rd |only gpuR-1.1.0/gpuR/man/platformInfo.Rd | 2 gpuR-1.1.0/gpuR/man/print.gpuMatrix.Rd | 4 gpuR-1.1.0/gpuR/man/setContext.Rd |only gpuR-1.1.0/gpuR/man/typeof-gpuR-methods.Rd |only gpuR-1.1.0/gpuR/man/vclMatrix-class.Rd | 19 gpuR-1.1.0/gpuR/man/vclMatrix-crossprod.Rd | 2 gpuR-1.1.0/gpuR/man/vclMatrix-methods.Rd | 12 gpuR-1.1.0/gpuR/man/vclMatrix.colSums.Rd | 2 gpuR-1.1.0/gpuR/man/vclVector-class.Rd | 14 gpuR-1.1.0/gpuR/man/vclVector-methods.Rd | 4 gpuR-1.1.0/gpuR/src/Makevars.win | 5 gpuR-1.1.0/gpuR/src/RcppExports.cpp | 1360 ++- gpuR-1.1.0/gpuR/src/context.cpp |only gpuR-1.1.0/gpuR/src/device.cpp |only gpuR-1.1.0/gpuR/src/dynEigenMat.cpp |only gpuR-1.1.0/gpuR/src/dynEigenVec.cpp | 42 gpuR-1.1.0/gpuR/src/dynVCLMat.cpp |only gpuR-1.1.0/gpuR/src/dynVCLVec.cpp |only gpuR-1.1.0/gpuR/src/gpuEigenPtr.cpp | 415 gpuR-1.1.0/gpuR/src/gpuMatrix_iaxpy.cpp | 40 gpuR-1.1.0/gpuR/src/gpuMatrix_igemm.cpp | 51 gpuR-1.1.0/gpuR/src/gpuVector_iaxpy.cpp | 24 gpuR-1.1.0/gpuR/src/gpu_vector_algebra.cpp | 17 gpuR-1.1.0/gpuR/src/platform.cpp |only gpuR-1.1.0/gpuR/src/trunc_gpuMat.cpp | 31 gpuR-1.1.0/gpuR/src/utils-vcl.cpp | 28 gpuR-1.1.0/gpuR/src/utils.cpp | 147 gpuR-1.1.0/gpuR/src/vclPtr.cpp | 507 - gpuR-1.1.0/gpuR/src/vienna_blas1.cpp | 4206 +++++++-- gpuR-1.1.0/gpuR/src/vienna_blas3.cpp | 354 gpuR-1.1.0/gpuR/src/vienna_eigen.cpp | 94 gpuR-1.1.0/gpuR/src/vienna_stats.cpp | 635 + gpuR-1.1.0/gpuR/tests/testthat/test_cpu_deepcopy.R |only gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrixBlock_algebra.R |only gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_algebra.R | 446 - gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_classes.R | 133 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_cov.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_dist.R | 172 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_eigen.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_math.R | 80 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_row_col.R | 255 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuMatrix_utils.R | 13 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuVector_algebra.R | 499 - gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuVector_classes.R | 58 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuVector_math.R | 204 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_gpuVector_utils.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrixBlock_algebra.R |only gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_algebra.R | 72 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_classes.R | 95 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_cov.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_dist.R | 173 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_eigen.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrix_row_col.R | 236 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrtix_math.R | 86 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclMatrtix_utils.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclVector_algebra.R | 404 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclVector_classes.R | 68 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclVector_math.R | 111 gpuR-1.1.0/gpuR/tests/testthat/test_cpu_vclVector_utils.R | 4 gpuR-1.1.0/gpuR/tests/testthat/test_deepcopy.R |only gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrixBlock_algebra.R |only gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_algebra.R | 392 gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_classes.R | 182 gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_dist.R | 169 gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_math.R | 73 gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_row_col.R | 251 gpuR-1.1.0/gpuR/tests/testthat/test_gpuMatrix_utils.R | 9 gpuR-1.1.0/gpuR/tests/testthat/test_gpuVector_algebra.R | 382 gpuR-1.1.0/gpuR/tests/testthat/test_gpuVector_classes.R | 63 gpuR-1.1.0/gpuR/tests/testthat/test_gpuVector_math.R | 205 gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrixBlock_algebra.R |only gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_algebra.R | 487 - gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_classes.R | 88 gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_dist.R | 172 gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_eigen.R | 8 gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_math.R | 70 gpuR-1.1.0/gpuR/tests/testthat/test_vclMatrix_row_col.R | 239 gpuR-1.1.0/gpuR/tests/testthat/test_vclVector_algebra.R | 395 gpuR-1.1.0/gpuR/tests/testthat/test_vclVector_classes.R | 67 gpuR-1.1.0/gpuR/tests/testthat/test_vclVector_math.R | 103 gpuR-1.1.0/gpuR/vignettes/gpuR-concordance.tex | 2 gpuR-1.1.0/gpuR/vignettes/gpuR.Rnw | 120 218 files changed, 17223 insertions(+), 7539 deletions(-)
Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre],
Dylan Kesler [aut],
Elisabeth Webb [aut],
Nicole Michel [ctb]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>
Diff between DiversityOccupancy versions 1.0.1 dated 2016-03-11 and 1.0.2 dated 2016-03-16
DESCRIPTION | 14 +++--- MD5 | 13 +++--- NAMESPACE | 2 R/DiversityOccu.R | 94 ++++++++++++++++++++++++++++++++++++++++------ inst/doc/my-vignette.html | 4 - man/batchoccu.Rd | 11 ++++- man/diversityoccu.Rd | 6 ++ man/occupancy.predict.Rd |only 8 files changed, 115 insertions(+), 29 deletions(-)
More information about DiversityOccupancy at CRAN
Permanent link
Title: Directional Statistics
Description: A collection of R functions for directional data analysis.
Author: Michail Tsagris, Giorgos Athineou
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 1.7.5 dated 2016-02-12 and 1.8 dated 2016-03-16
Directional-1.7.5/Directional/R/vmfkde.tune_2.R |only Directional-1.7.5/Directional/R/vmkde.tune_2.R |only Directional-1.7.5/Directional/man/circ.cor2.Rd |only Directional-1.7.5/Directional/man/embed.aov.Rd |only Directional-1.7.5/Directional/man/embed.circaov.Rd |only Directional-1.7.5/Directional/man/het.aov.Rd |only Directional-1.7.5/Directional/man/het.circaov.Rd |only Directional-1.7.5/Directional/man/lr.aov.Rd |only Directional-1.7.5/Directional/man/lr.circaov.Rd |only Directional-1.7.5/Directional/man/vmfkde.tune_2.Rd |only Directional-1.7.5/Directional/man/vmkde.tune_2.Rd |only Directional-1.8/Directional/DESCRIPTION | 10 - Directional-1.8/Directional/MD5 | 138 ++++++++--------- Directional-1.8/Directional/NAMESPACE | 1 Directional-1.8/Directional/R/bic.mixvmf.R | 30 ++- Directional-1.8/Directional/R/circ.cor1.R | 12 - Directional-1.8/Directional/R/circ.cor2.R | 24 +- Directional-1.8/Directional/R/circ.summary.R | 30 +-- Directional-1.8/Directional/R/circlin.cor.R | 14 - Directional-1.8/Directional/R/conc.test.R | 6 Directional-1.8/Directional/R/dirknn.R | 45 ++--- Directional-1.8/Directional/R/dirknn.tune.R | 94 ++++++----- Directional-1.8/Directional/R/embed.aov.R | 12 - Directional-1.8/Directional/R/embed.circaov.R | 10 - Directional-1.8/Directional/R/f.rbing.R | 32 ++- Directional-1.8/Directional/R/fb.saddle.R | 21 +- Directional-1.8/Directional/R/fishkent.R | 14 - Directional-1.8/Directional/R/hcf.aov.R | 16 - Directional-1.8/Directional/R/hcf.circaov.R | 20 +- Directional-1.8/Directional/R/het.aov.R | 10 - Directional-1.8/Directional/R/het.circaov.R | 14 - Directional-1.8/Directional/R/knn.reg.R |only Directional-1.8/Directional/R/knnreg.tune.R |only Directional-1.8/Directional/R/kuiper.R |only Directional-1.8/Directional/R/lambert.R | 8 Directional-1.8/Directional/R/lambert.inv.R | 10 - Directional-1.8/Directional/R/lr.aov.R | 24 +- Directional-1.8/Directional/R/lr.circaov.R | 10 - Directional-1.8/Directional/R/meandir.test.R | 24 +- Directional-1.8/Directional/R/mix.vmf.R | 33 ++-- Directional-1.8/Directional/R/rbingham.R | 4 Directional-1.8/Directional/R/rfb.R | 21 +- Directional-1.8/Directional/R/rot.matrix.R | 2 Directional-1.8/Directional/R/rotation.R | 14 - Directional-1.8/Directional/R/rvmf.R | 51 +++--- Directional-1.8/Directional/R/rvnomises.R | 12 - Directional-1.8/Directional/R/spher.cor.R | 12 - Directional-1.8/Directional/R/spher.reg.R | 14 - Directional-1.8/Directional/R/spml.reg.R | 55 +++--- Directional-1.8/Directional/R/vm.kde.R | 46 +++-- Directional-1.8/Directional/R/vmf.da.R | 20 +- Directional-1.8/Directional/R/vmf.kde.R | 44 +++-- Directional-1.8/Directional/R/vmf.kerncontour.R | 23 +- Directional-1.8/Directional/R/vmfda.pred.R | 10 - Directional-1.8/Directional/R/vmfkde.tune.R | 25 +-- Directional-1.8/Directional/R/vmkde.tune.R | 45 +---- Directional-1.8/Directional/R/watson.R |only Directional-1.8/Directional/man/Directional-package.Rd | 4 Directional-1.8/Directional/man/bic.mixvmf.Rd | 14 + Directional-1.8/Directional/man/circ.cor1.Rd | 33 +++- Directional-1.8/Directional/man/circ.summary.Rd | 2 Directional-1.8/Directional/man/circlin.cor.Rd | 4 Directional-1.8/Directional/man/conc.test.Rd | 4 Directional-1.8/Directional/man/dirknn.tune.Rd | 54 ++++-- Directional-1.8/Directional/man/hcf.aov.Rd | 40 +++- Directional-1.8/Directional/man/hcf.circaov.Rd | 38 +++- Directional-1.8/Directional/man/knn.reg.Rd |only Directional-1.8/Directional/man/knnreg.tune.Rd |only Directional-1.8/Directional/man/kuiper.Rd |only Directional-1.8/Directional/man/mix.vmf.Rd | 12 + Directional-1.8/Directional/man/rvmf.Rd | 2 Directional-1.8/Directional/man/rvonmises.Rd | 2 Directional-1.8/Directional/man/spher.reg.Rd | 2 Directional-1.8/Directional/man/spml.reg.Rd | 24 -- Directional-1.8/Directional/man/tang.conc.Rd | 2 Directional-1.8/Directional/man/vm.kde.Rd | 7 Directional-1.8/Directional/man/vmf.kde.Rd | 2 Directional-1.8/Directional/man/vmfkde.tune.Rd | 31 +-- Directional-1.8/Directional/man/vmkde.tune.Rd | 32 +-- 79 files changed, 741 insertions(+), 628 deletions(-)
Title: Request Data from the U.S. Bureau of Labor Statistics API
Description: Allows users to request data for one or multiple series through the
U.S. Bureau of Labor Statistics API. Users provide parameters as specified in
http://www.bls.gov/developers/api_signature.htm and the function returns a JSON
string.
Author: Michael Silva <mike.a.silva@gmail.com>
Maintainer: Michael Silva <mike.a.silva@gmail.com>
Diff between blsAPI versions 0.1.2 dated 2015-09-10 and 0.1.3 dated 2016-03-16
DESCRIPTION | 11 ++++++++--- MD5 | 10 ++++++---- NAMESPACE | 4 +++- R/blsAPI.R | 43 ++++++++++++++++++++++++++----------------- R/blsQCEW.R |only man/blsAPI.Rd | 15 ++++++++++----- man/blsQCEW.Rd |only 7 files changed, 53 insertions(+), 30 deletions(-)
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test.
Author: Michael Thrun, Onno Hansen-Goos, Rabea Griese, Catharina Lippmann, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between AdaptGauss versions 1.1.0 dated 2015-10-14 and 1.2.0 dated 2016-03-16
AdaptGauss-1.1.0/AdaptGauss/R/BayesForMixes.R |only AdaptGauss-1.1.0/AdaptGauss/R/Intersect2Mixes.R |only AdaptGauss-1.1.0/AdaptGauss/R/PlotGaussMixesAndBoundaries.R |only AdaptGauss-1.1.0/AdaptGauss/R/PlotGaussianMixtures.R |only AdaptGauss-1.1.0/AdaptGauss/R/paretoDensityEstimationForGMM.R |only AdaptGauss-1.1.0/AdaptGauss/R/paretoRadiusForGMM.R |only AdaptGauss-1.1.0/AdaptGauss/R/qqplotGMM.R |only AdaptGauss-1.1.0/AdaptGauss/R/randomLogGMM.R |only AdaptGauss-1.1.0/AdaptGauss/man/BayesForMixes.Rd |only AdaptGauss-1.1.0/AdaptGauss/man/Intersect2Mixes.Rd |only AdaptGauss-1.1.0/AdaptGauss/man/PlotGaussMixesAndBoundaries.Rd |only AdaptGauss-1.1.0/AdaptGauss/man/PlotGaussianMixtures.Rd |only AdaptGauss-1.1.0/AdaptGauss/man/paretoDensityEstimationForGMM.Rd |only AdaptGauss-1.1.0/AdaptGauss/man/paretoRadiusForGMM.Rd |only AdaptGauss-1.2.0/AdaptGauss/DESCRIPTION | 10 AdaptGauss-1.2.0/AdaptGauss/MD5 | 60 +-- AdaptGauss-1.2.0/AdaptGauss/NAMESPACE | 4 AdaptGauss-1.2.0/AdaptGauss/R/AdaptGauss.R | 197 +++++----- AdaptGauss-1.2.0/AdaptGauss/R/Bayes4Mixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/BayesDecisionBoundaries.R | 2 AdaptGauss-1.2.0/AdaptGauss/R/Chi2testMixtures.R | 8 AdaptGauss-1.2.0/AdaptGauss/R/InformationCriteria4GMM.R |only AdaptGauss-1.2.0/AdaptGauss/R/Intersect2Mixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/KStestMixtures.R | 8 AdaptGauss-1.2.0/AdaptGauss/R/LikelihoodRatio4Mixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/LogLikelihood4Mixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/ParetoDensityEstimation.R |only AdaptGauss-1.2.0/AdaptGauss/R/ParetoRadius.R |only AdaptGauss-1.2.0/AdaptGauss/R/Pdf4Mixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/PlotMixtures.R |only AdaptGauss-1.2.0/AdaptGauss/R/PlotMixturesAndBoundaries.R |only AdaptGauss-1.2.0/AdaptGauss/R/QQplotGMM.R |only AdaptGauss-1.2.0/AdaptGauss/R/RandomLogGMM.R |only AdaptGauss-1.2.0/AdaptGauss/man/AdaptGauss-package.Rd | 2 AdaptGauss-1.2.0/AdaptGauss/man/Bayes4Mixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/BayesDecisionBoundaries.Rd | 2 AdaptGauss-1.2.0/AdaptGauss/man/ClassifyByDecisionBoundaries.Rd | 2 AdaptGauss-1.2.0/AdaptGauss/man/InformationCriteria4GMM.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/Intersect2Mixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/LikelihoodRatio4Mixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/LogLikelihood4Mixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/OptimalNoBins.Rd | 2 AdaptGauss-1.2.0/AdaptGauss/man/ParetoDensityEstimation.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/ParetoRadius.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/Pdf4Mixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/PlotMixtures.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/PlotMixturesAndBoundaries.Rd |only AdaptGauss-1.2.0/AdaptGauss/man/qqplotGMM.Rd | 11 AdaptGauss-1.2.0/AdaptGauss/man/randomLogGMM.Rd | 8 49 files changed, 166 insertions(+), 150 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.6.500.4.0 dated 2016-01-27 and 0.6.600.4.0 dated 2016-03-16
RcppArmadillo-0.6.500.4.0/RcppArmadillo/inst/include/armadillo_bits/constants_compat.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/ChangeLog | 26 + RcppArmadillo-0.6.600.4.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.6.600.4.0/RcppArmadillo/MD5 | 108 ++--- RcppArmadillo-0.6.600.4.0/RcppArmadillo/README.md | 2 RcppArmadillo-0.6.600.4.0/RcppArmadillo/build/vignette.rds |binary RcppArmadillo-0.6.600.4.0/RcppArmadillo/configure | 12 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/NEWS.Rd | 15 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo | 8 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 6 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 127 +++--- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 6 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 26 - RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/Op_bones.hpp | 4 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/SizeCube_meat.hpp | 14 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 6 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 64 +-- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 4 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_bones.hpp | 4 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 36 - RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 3 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 9 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp.cmake | 9 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/constants.hpp | 2 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/constants_old.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 22 - RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 49 +- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_inv.hpp | 6 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_max.hpp | 34 + RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_mean.hpp | 18 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_min.hpp | 34 + RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_misc.hpp | 2 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_shift.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_spsolve.hpp | 6 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_sqrtmat.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/fn_sum.hpp | 19 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_bones.hpp | 15 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_max_meat.hpp | 132 ++++++ RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_bones.hpp | 15 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_min_meat.hpp | 134 ++++++ RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 8 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/gmm_diag_meat.hpp | 8 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_inv_meat.hpp | 12 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_max_bones.hpp | 18 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_max_meat.hpp | 204 +++++++++- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_bones.hpp | 20 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_mean_meat.hpp | 182 ++++++++ RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_min_bones.hpp | 18 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_min_meat.hpp | 204 +++++++++- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_shift_bones.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_shift_meat.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sqrtmat_bones.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sqrtmat_meat.hpp |only RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_bones.hpp | 19 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/op_sum_meat.hpp | 204 +++++++++- RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_bones.hpp | 4 RcppArmadillo-0.6.600.4.0/RcppArmadillo/inst/include/armadillo_bits/subview_field_meat.hpp | 32 + 59 files changed, 1621 insertions(+), 297 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.3 dated 2015-05-30 and 1.6.4 dated 2016-03-16
ChangeLog | 88 +++++++++++++++- DESCRIPTION | 15 +- MD5 | 99 ++++++++++-------- NAMESPACE | 4 R/common.interval.R | 4 R/detrend.R | 35 +++--- R/detrend.series.R | 64 ++++++++++-- R/helpers.R | 6 - R/rasterPlot.R | 206 +++++++++++++++++++++++++++++---------- R/read.crn.R | 6 - R/read.tridas.R | 57 ++++++---- R/read.tucson.R | 6 - R/redfit.R | 12 +- R/rwi.stats.running.R | 4 R/sea.R | 16 ++- R/skel.plot.R | 12 +- R/treeMean.R |only R/wavelet.plot.R | 32 +++++- R/write.compact.R | 9 - R/write.tucson.R | 29 +++-- TODO | 28 +++-- build/vignette.rds |binary data/anos1.rda |binary data/wa082.rda |only inst/doc/chron-dplR.R |only inst/doc/chron-dplR.pdf |only inst/doc/intro-dplR.pdf |binary inst/doc/timeseries-dplR.pdf |binary inst/doc/xdate-dplR.pdf |binary inst/po/fi/LC_MESSAGES/R-dplR.mo |binary man/combine.rwl.Rd | 2 man/detrend.Rd | 16 ++- man/detrend.series.Rd | 37 +++++-- man/rasterPlot.Rd | 147 +++++++++++++++++++++++---- man/read.compact.Rd | 6 - man/read.fh.Rd | 9 - man/read.rwl.Rd | 9 - man/read.tucson.Rd | 6 - man/redfit.Rd | 4 man/sea.Rd | 12 +- man/skel.plot.Rd | 5 man/treeMean.Rd |only man/wa082.Rd |only man/wavelet.plot.Rd | 6 - man/xskel.ccf.plot.Rd | 2 man/xskel.plot.Rd | 2 po/R-dplR.pot | 43 ++++++-- po/R-fi.po | 49 ++++++--- vignettes/chron-dplR.Rnw |only vignettes/dplR.bib | 16 +++ vignettes/dplR.sty | 11 +- vignettes/intro-dplR.Rnw | 8 - vignettes/timeseries-dplR.Rnw | 14 +- vignettes/xdate-dplR.Rnw | 12 +- 54 files changed, 835 insertions(+), 313 deletions(-)
Title: Comparison of Alternative Multiple Sequence Alignments
Description: Methods for comparing two alternative multiple
sequence alignments (MSAs) to determine whether they align homologous residues in
the same columns as one another. It then classifies similarities and differences
into conserved gaps, conserved sequence, merges, splits or shifts of one MSA relative
to the other. Summarising these categories for each MSA column yields information
on which sequence regions are agreed upon my both MSAs, and which differ. Several
plotting functions enable easily visualisation of the comparison data for analysis.
Author: Thomas Shafee, Ira Cooke
Maintainer: Thomas Shafee <thomas.shafee@gmail.com>
Diff between AlignStat versions 1.1 dated 2016-03-14 and 1.1.1 dated 2016-03-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-align.R | 10 ---------- 3 files changed, 6 insertions(+), 16 deletions(-)
Title: Improved False Positive Control of Gene-Permuting GSEA with
Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Diff between AbsFilterGSEA versions 0.1 dated 2016-01-04 and 1.0 dated 2016-03-16
AbsFilterGSEA-0.1/AbsFilterGSEA/data/datalist |only AbsFilterGSEA-1.0/AbsFilterGSEA/DESCRIPTION | 11 +-- AbsFilterGSEA-1.0/AbsFilterGSEA/MD5 | 11 +-- AbsFilterGSEA-1.0/AbsFilterGSEA/NAMESPACE | 1 AbsFilterGSEA-1.0/AbsFilterGSEA/R/GenePermGSEA.R | 61 ++++++++++++------ AbsFilterGSEA-1.0/AbsFilterGSEA/man/GenePermGSEA.Rd | 16 ++-- AbsFilterGSEA-1.0/AbsFilterGSEA/src/AbsFilterGSEA.cpp | 57 ++++++++++++---- 7 files changed, 104 insertions(+), 53 deletions(-)
Title: Spatial Individual-Plant Modelling
Description: A platform for experimenting with spatially explicit individual-based vegetation models.
Author: Oscar Garcia
Maintainer: Oscar Garcia <garcia@dasometrics.net>
Diff between siplab versions 1.1 dated 2014-05-11 and 1.2 dated 2016-03-16
DESCRIPTION | 12 ++++++------ MD5 | 25 +++++++++++++------------ R/pairwise.R | 2 +- R/spurr.ker.R | 2 +- inst |only man/assimilation.Rd | 26 ++++++++++++++------------ man/boreas.Rd | 4 ++-- man/edges.Rd | 4 ++-- man/efficiency.Rd | 3 ++- man/influence.Rd | 3 ++- man/kernel.Rd | 13 +++++++++---- man/pairwise.Rd | 18 ++++++++++-------- man/select.Rd | 12 +++++++----- man/siplab-package.Rd | 36 ++++++++++++++++++++++++++---------- 14 files changed, 95 insertions(+), 65 deletions(-)
More information about ROpenWeatherMap at CRAN
Permanent link
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 1.0.0 dated 2015-12-28 and 1.1.0 dated 2016-03-16
DESCRIPTION | 8 +-- MD5 | 14 ++--- build/partial.rdb |binary inst/News.Rd | 18 ++++++- man/lamW-package.Rd | 4 - man/lamW.Rd | 2 src/lambertW.cpp | 109 ++++++++++++++++++++++++++++++--------------- tests/testthat/test-lamW.R | 4 - 8 files changed, 105 insertions(+), 54 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0.2 dated 2015-11-12 and 1.0.3 dated 2016-03-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/find.ladder.R | 22 +++++++++++----------- R/ladder.info.attach.R | 10 +++++++--- man/Fragman-package.Rd | 47 +++++++++++++++++++++++++++++++++++------------ man/find.ladder.Rd | 6 +++++- man/jm.conv.Rd | 2 +- man/score.easy.Rd | 10 +++++----- 8 files changed, 75 insertions(+), 44 deletions(-)
Title: Divide and Recombine for Large, Complex Data
Description: Methods for dividing data into subsets, applying analytical
methods to the subsets, and recombining the results. Comes with a generic
MapReduce interface as well. Works with key-value pairs stored in memory,
on local disk, or on HDFS, in the latter case using the R and Hadoop
Integrated Programming Environment (RHIPE).
Author: Ryan Hafen [aut, cre],
Landon Sego [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between datadr versions 0.8.4 dated 2016-03-14 and 0.8.5 dated 2016-03-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 1 + tests/testthat/test-quantile.R | 22 +++++++++++----------- 4 files changed, 19 insertions(+), 18 deletions(-)
Title: Unicode Data and Utilities
Description: Data from Unicode 8.0.0 and related utilities.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between Unicode versions 0.1-5 dated 2014-11-28 and 8.0.0-1 dated 2016-03-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/sysdata.rda |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: R/Weka Interface Jars
Description: External jars required for package 'RWeka'.
Author: Kurt Hornik [aut, cre],
University of Waikato [ctb, cph] (Weka Java library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWekajars versions 3.7.12-1 dated 2015-01-25 and 3.7.13-1 dated 2016-03-15
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- inst/java/weka.jar |binary 3 files changed, 8 insertions(+), 8 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.7.13).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre],
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-24 dated 2015-01-25 and 0.4-25 dated 2016-03-15
CHANGELOG | 4 +++ DESCRIPTION | 20 ++++++++-------- MD5 | 24 ++++++++++---------- build/vignette.rds |binary inst/CITATION | 54 ++++++++++++++++++--------------------------- inst/doc/RWeka.pdf |binary inst/java/RWeka.jar |binary java/RWekaInterfaces.class |binary java/RWekaInterfaces.java | 4 +-- man/WOW.Rd | 2 - man/Weka_interfaces.Rd | 2 - man/read.arff.Rd | 2 - man/write.arff.Rd | 2 - 13 files changed, 54 insertions(+), 60 deletions(-)
Title: ViennaCL C++ Header Files
Description: ViennaCL is a free open-source linear algebra library
for computations on many-core architectures (GPUs, MIC) and
multi-core CPUs. The library is written in C++ and supports CUDA,
OpenCL, and OpenMP (including switches at runtime).
I have placed these libraries in this package as a more efficient
distribution system for CRAN. The idea is that you can write a package
that depends on the ViennaCL library and yet you do not need to
distribute a copy of this code with your package.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr <cdetermanjr@gmail.com>
Diff between RViennaCL versions 1.7.1-0 dated 2016-01-22 and 1.7.1-1 dated 2016-03-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 5 +++-- inst/include/viennacl/ocl/backend.hpp | 6 ++++++ inst/include/viennacl/ocl/context.hpp | 6 ++++++ 7 files changed, 26 insertions(+), 13 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <kamvarz@science.oregonstate.edu>
Diff between poppr versions 2.1.0 dated 2015-12-01 and 2.1.1 dated 2016-03-15
poppr-2.1.0/poppr/inst/msn_explorer |only poppr-2.1.1/poppr/DESCRIPTION | 8 poppr-2.1.1/poppr/MD5 | 156 ++++---- poppr-2.1.1/poppr/NEWS | 36 + poppr-2.1.1/poppr/R/Index_calculations.r | 177 ++++++--- poppr-2.1.1/poppr/R/aaaMLGclass.R | 2 poppr-2.1.1/poppr/R/bitwise.r | 165 +++++---- poppr-2.1.1/poppr/R/bruvo.r | 10 poppr-2.1.1/poppr/R/classes.r | 22 + poppr-2.1.1/poppr/R/data_subset.r | 363 ++++---------------- poppr-2.1.1/poppr/R/distances.r | 22 - poppr-2.1.1/poppr/R/file_handling.r | 14 poppr-2.1.1/poppr/R/filter_stats.R | 74 ++-- poppr-2.1.1/poppr/R/imsn.R | 4 poppr-2.1.1/poppr/R/internal.r | 100 ++++- poppr-2.1.1/poppr/R/internal_methods.R | 317 +++++++++++------ poppr-2.1.1/poppr/R/messages.r | 58 ++- poppr-2.1.1/poppr/R/methods.r | 193 +++++----- poppr-2.1.1/poppr/R/mlg.r | 181 --------- poppr-2.1.1/poppr/R/poppr.R | 140 ++++--- poppr-2.1.1/poppr/R/round_robin.R | 329 +++++++++++++----- poppr-2.1.1/poppr/README.md | 57 +-- poppr-2.1.1/poppr/build/vignette.rds |binary poppr-2.1.1/poppr/inst/doc/algo.pdf |binary poppr-2.1.1/poppr/inst/doc/how_to_migrate.pdf |binary poppr-2.1.1/poppr/inst/doc/mlg.R | 135 +++---- poppr-2.1.1/poppr/inst/doc/mlg.Rmd | 135 +++---- poppr-2.1.1/poppr/inst/doc/mlg.html | 293 ++++++++-------- poppr-2.1.1/poppr/inst/doc/poppr_manual.pdf |binary poppr-2.1.1/poppr/inst/shiny |only poppr-2.1.1/poppr/man/MLG-class.Rd | 2 poppr-2.1.1/poppr/man/bitwise.dist.Rd | 61 ++- poppr-2.1.1/poppr/man/bitwise.ia.Rd | 47 +- poppr-2.1.1/poppr/man/bruvo.boot.Rd | 2 poppr-2.1.1/poppr/man/bruvo.dist.Rd | 2 poppr-2.1.1/poppr/man/bruvo.msn.Rd | 2 poppr-2.1.1/poppr/man/clonecorrect.Rd | 17 poppr-2.1.1/poppr/man/cutoff_predictor.Rd | 18 poppr-2.1.1/poppr/man/diss.dist.Rd | 11 poppr-2.1.1/poppr/man/filter_stats.Rd | 43 +- poppr-2.1.1/poppr/man/fix_replen.Rd | 2 poppr-2.1.1/poppr/man/genclone-class.Rd | 23 + poppr-2.1.1/poppr/man/genetic_distance.Rd | 12 poppr-2.1.1/poppr/man/ia.Rd | 3 poppr-2.1.1/poppr/man/imsn.Rd | 2 poppr-2.1.1/poppr/man/missingno.Rd | 25 - poppr-2.1.1/poppr/man/mlg.Rd | 12 poppr-2.1.1/poppr/man/mlg.filter.Rd | 21 - poppr-2.1.1/poppr/man/mll-method.Rd | 3 poppr-2.1.1/poppr/man/pgen.Rd | 62 +-- poppr-2.1.1/poppr/man/plot_filter_stats.Rd | 3 poppr-2.1.1/poppr/man/poppr-package.Rd | 143 ++++--- poppr-2.1.1/poppr/man/poppr.Rd | 97 +++-- poppr-2.1.1/poppr/man/popsub.Rd | 9 poppr-2.1.1/poppr/man/psex.Rd | 25 - poppr-2.1.1/poppr/man/rare_allele_correction.Rd |only poppr-2.1.1/poppr/man/recode_polyploids.Rd | 27 - poppr-2.1.1/poppr/man/rraf.Rd | 75 ++-- poppr-2.1.1/poppr/man/samp.ia.Rd | 19 - poppr-2.1.1/poppr/man/test_replen.Rd | 2 poppr-2.1.1/poppr/man/win.ia.Rd | 9 poppr-2.1.1/poppr/src/mlg_clustering.c | 11 poppr-2.1.1/poppr/tests/testthat/test-MLG-class.R | 4 poppr-2.1.1/poppr/tests/testthat/test-amova.R | 6 poppr-2.1.1/poppr/tests/testthat/test-errors.R | 9 poppr-2.1.1/poppr/tests/testthat/test-filter.R | 39 +- poppr-2.1.1/poppr/tests/testthat/test-genclone.R | 8 poppr-2.1.1/poppr/tests/testthat/test-import.R | 35 + poppr-2.1.1/poppr/tests/testthat/test-locustable.R | 2 poppr-2.1.1/poppr/tests/testthat/test-missing.R | 21 - poppr-2.1.1/poppr/tests/testthat/test-mlg.R | 58 ++- poppr-2.1.1/poppr/tests/testthat/test-msn.R | 6 poppr-2.1.1/poppr/tests/testthat/test-plots.R | 89 ++-- poppr-2.1.1/poppr/tests/testthat/test-polyploids.R | 2 poppr-2.1.1/poppr/tests/testthat/test-poppr.R | 16 poppr-2.1.1/poppr/tests/testthat/test-round-robin.R | 67 +++ poppr-2.1.1/poppr/tests/testthat/test-sampling.R | 20 - poppr-2.1.1/poppr/tests/testthat/test-values.R | 5 poppr-2.1.1/poppr/vignettes/mlg.Rmd | 135 +++---- 79 files changed, 2415 insertions(+), 1888 deletions(-)
Title: Solve Nonlinear Optimization with Nonlinear Constraints
Description: Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
Author: Xianyan Chen <xychen@uga.edu>, Xiangrong Yin <yinxiangrong@uky.edu>
Maintainer: Xianyan Chen <xychen@uga.edu>
Diff between NlcOptim versions 0.3 dated 2015-12-21 and 0.4 dated 2016-03-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/NlcOptim.R | 26 +++++++++++++++----------- R/solqp.R | 19 ++++++++++--------- 4 files changed, 31 insertions(+), 26 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models. Threshold selection methods.
Author: Leo Belzile [aut, cre],
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut],
Claire L. Coleman [aut],
Jin. Zhang [ctb],
Michael A. Newton [ctb],
Art Owen [ctb]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>
Diff between mev versions 1.6 dated 2016-03-08 and 1.6.1 dated 2016-03-15
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++--------- NEWS | 7 ++++- R/Northrop_Coleman_Extremes_2014.R | 46 ++++++++++++++++++++----------------- R/Wadsworth_Technometrics_2016.R | 1 R/bivpot_methods.R | 2 - R/rmev_wrapper.R | 28 +++++++++++++++++++++- man/NC.diag.Rd | 3 +- man/gp.fit.Rd | 2 - man/ibvpot.Rd | 2 - man/rmev.Rd | 7 ++++- src/ev_sampling.cpp | 4 +-- 12 files changed, 87 insertions(+), 45 deletions(-)
Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes.
Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
currency codes, ISO 15924 script codes, and the ISO 8859 character codes
as well as the UN M.49 area codes.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between ISOcodes versions 2015.04.04 dated 2015-04-04 and 2016.03.15 dated 2016-03-15
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- data/ISO_15924.rda |binary data/ISO_3166_1.rda |binary data/ISO_3166_2.rda |binary data/ISO_3166_3.rda |binary data/ISO_4217.rda |binary data/ISO_4217_Historic.rda |binary data/ISO_639_2.rda |binary data/ISO_639_3.rda |binary data/ISO_639_3_Retirements.rda |binary data/ISO_639_5.rda |binary data/ISO_8859.rda |binary data/UN_M.49_Countries.rda |binary data/UN_M.49_Regions.rda |binary 15 files changed, 18 insertions(+), 18 deletions(-)
Title: Tools for Multiple Imputation in Multilevel Modeling
Description: Provides tools for multiple imputation of missing data in multilevel
modeling. Includes a user-friendly interface to the packages 'pan' and 'jomo',
and several functions for visualization, data management and the analysis
of multiply imputed data sets.
Author: Simon Grund [aut,cre], Alexander Robitzsch [aut], Oliver Luedtke [aut]
Maintainer: Simon Grund <grund@ipn.uni-kiel.de>
Diff between mitml versions 0.2-4 dated 2015-10-19 and 0.3-0 dated 2016-03-15
DESCRIPTION | 14 ++--- MD5 | 43 +++++++++-------- NAMESPACE | 2 NEWS | 18 +++++++ R/as.mitml.list.R | 2 R/internal-convergence.R |only R/internal-model.R |only R/internal-zzz.R |only R/jomoImpute.R |only R/mitmlComplete.R | 61 ++++++++++++++++++++---- R/panImpute.R | 116 ++++++++++------------------------------------- R/plot.mitml.R | 70 +++++++++++++++++++++++----- R/summary.mitml.R | 7 ++ R/zzz.R | 72 ----------------------------- man/jomoImpute.Rd |only man/mitml-package.Rd | 3 - man/mitmlComplete.Rd | 8 +-- man/panImpute.Rd | 11 +++- man/plot.mitml.Rd | 8 +-- man/read.mitml.Rd | 2 man/summary.mitml.Rd | 4 - man/write.mitml.Rd | 4 - man/write.mitmlMplus.Rd | 4 - man/write.mitmlSAV.Rd | 4 - man/write.mitmlSPSS.Rd | 4 - 25 files changed, 222 insertions(+), 235 deletions(-)
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 1.0 dated 2016-02-25 and 1.1 dated 2016-03-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/partial.rdb |binary man/jmuOutlier-package.Rd | 4 ++-- man/rmd.test.Rd | 6 +++--- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.1.3 dated 2014-08-05 and 2.2.3 dated 2016-03-15
dlnm-2.1.3/dlnm/R/Lag2.R |only dlnm-2.1.3/dlnm/R/check.R |only dlnm-2.1.3/dlnm/R/get.R |only dlnm-2.1.3/dlnm/inst/doc/biblioVignette.bib |only dlnm-2.2.3/dlnm/DESCRIPTION | 19 - dlnm-2.2.3/dlnm/MD5 | 136 ++++----- dlnm-2.2.3/dlnm/NAMESPACE | 17 - dlnm-2.2.3/dlnm/R/checkcrossbasis.R |only dlnm-2.2.3/dlnm/R/checkgroup.R |only dlnm-2.2.3/dlnm/R/checkonebasis.R |only dlnm-2.2.3/dlnm/R/coef.crosspred.R | 10 dlnm-2.2.3/dlnm/R/coef.crossreduce.R | 10 dlnm-2.2.3/dlnm/R/crossbasis.R | 193 ++++++------ dlnm-2.2.3/dlnm/R/crosspred.R | 207 ++++++------- dlnm-2.2.3/dlnm/R/crossreduce.R | 97 +++--- dlnm-2.2.3/dlnm/R/equalknots.R | 49 +-- dlnm-2.2.3/dlnm/R/exphist.R | 84 ++--- dlnm-2.2.3/dlnm/R/fci.R | 68 ++-- dlnm-2.2.3/dlnm/R/getcoef.R |only dlnm-2.2.3/dlnm/R/getlink.R |only dlnm-2.2.3/dlnm/R/getvcov.R |only dlnm-2.2.3/dlnm/R/integer.R | 11 dlnm-2.2.3/dlnm/R/lin.R | 46 +-- dlnm-2.2.3/dlnm/R/lines.crosspred.R | 262 ++++++++--------- dlnm-2.2.3/dlnm/R/lines.crossreduce.R | 105 +++---- dlnm-2.2.3/dlnm/R/logknots.R | 53 +-- dlnm-2.2.3/dlnm/R/mkXpred.R |only dlnm-2.2.3/dlnm/R/mkat.R |only dlnm-2.2.3/dlnm/R/mkcen.R |only dlnm-2.2.3/dlnm/R/mklag.R | 2 dlnm-2.2.3/dlnm/R/onAttach.R | 9 dlnm-2.2.3/dlnm/R/onebasis.R | 88 ++--- dlnm-2.2.3/dlnm/R/plot.crosspred.R | 418 +++++++++++++--------------- dlnm-2.2.3/dlnm/R/plot.crossreduce.R | 117 +++---- dlnm-2.2.3/dlnm/R/points.crosspred.R | 258 ++++++++--------- dlnm-2.2.3/dlnm/R/points.crossreduce.R | 101 +++--- dlnm-2.2.3/dlnm/R/poly.R | 48 +-- dlnm-2.2.3/dlnm/R/seqlag.R | 12 dlnm-2.2.3/dlnm/R/strata.R | 80 ++--- dlnm-2.2.3/dlnm/R/summary.crossbasis.R | 17 - dlnm-2.2.3/dlnm/R/summary.crosspred.R | 45 +-- dlnm-2.2.3/dlnm/R/summary.crossreduce.R | 69 ++-- dlnm-2.2.3/dlnm/R/summary.onebasis.R | 5 dlnm-2.2.3/dlnm/R/thr.R | 68 ++-- dlnm-2.2.3/dlnm/R/vcov.crosspred.R | 10 dlnm-2.2.3/dlnm/R/vcov.crossreduce.R | 10 dlnm-2.2.3/dlnm/build/vignette.rds |binary dlnm-2.2.3/dlnm/inst/ChangeLog | 65 ++++ dlnm-2.2.3/dlnm/inst/Changesince200 | 4 dlnm-2.2.3/dlnm/inst/Changesince220 |only dlnm-2.2.3/dlnm/inst/doc/dlnmExtended.R | 68 ++-- dlnm-2.2.3/dlnm/inst/doc/dlnmExtended.Rnw | 36 +- dlnm-2.2.3/dlnm/inst/doc/dlnmExtended.pdf |binary dlnm-2.2.3/dlnm/inst/doc/dlnmOverview.R | 9 dlnm-2.2.3/dlnm/inst/doc/dlnmOverview.Rnw | 55 ++- dlnm-2.2.3/dlnm/inst/doc/dlnmOverview.pdf |binary dlnm-2.2.3/dlnm/inst/doc/dlnmTS.R | 47 +-- dlnm-2.2.3/dlnm/inst/doc/dlnmTS.Rnw | 111 +++---- dlnm-2.2.3/dlnm/inst/doc/dlnmTS.pdf |binary dlnm-2.2.3/dlnm/man/crossbasis.Rd | 242 ++++++++-------- dlnm-2.2.3/dlnm/man/crosspred.Rd | 41 +- dlnm-2.2.3/dlnm/man/crossreduce.Rd | 24 + dlnm-2.2.3/dlnm/man/dlnm-internal.Rd | 54 ++- dlnm-2.2.3/dlnm/man/equalknots.Rd | 8 dlnm-2.2.3/dlnm/man/integer.Rd | 11 dlnm-2.2.3/dlnm/man/lin.Rd | 10 dlnm-2.2.3/dlnm/man/logknots.Rd | 16 - dlnm-2.2.3/dlnm/man/onebasis.Rd | 47 +-- dlnm-2.2.3/dlnm/man/plot.crosspred.Rd | 296 +++++++++---------- dlnm-2.2.3/dlnm/man/plot.crossreduce.Rd | 12 dlnm-2.2.3/dlnm/man/poly.Rd | 10 dlnm-2.2.3/dlnm/man/strata.Rd | 18 - dlnm-2.2.3/dlnm/man/thr.Rd | 10 dlnm-2.2.3/dlnm/vignettes/dlnmExtended.Rnw | 36 +- dlnm-2.2.3/dlnm/vignettes/dlnmOverview.Rnw | 55 ++- dlnm-2.2.3/dlnm/vignettes/dlnmTS.Rnw | 111 +++---- 76 files changed, 2100 insertions(+), 2020 deletions(-)
Title: R Interface to Bloomberg
Description: An R Interface to Bloomberg is provided via the Blp API.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.2 dated 2015-12-07 and 0.3.3 dated 2016-03-15
ChangeLog | 103 ++++++++++ DESCRIPTION | 11 - LICENSE | 13 - MD5 | 58 +++-- NAMESPACE | 2 R/RcppExports.R | 16 + R/bdh.R | 19 + R/bds.R | 15 + R/bsrch.R |only R/fieldInfo.R |only R/subscribe.R | 4 README.md | 2 build/vignette.rds |binary configure | 2 inst/NEWS.Rd | 22 ++ inst/doc/rblpapi-intro.html | 13 - inst/unitTests |only man/bdh.Rd | 13 - man/bds.Rd | 12 - man/bsrch.Rd |only man/fieldInfo.Rd |only man/subscribe.Rd | 4 src/RcppExports.cpp | 42 +++- src/bdh.cpp | 50 +++-- src/bdp.cpp | 47 ++-- src/bds.cpp | 196 +++++++++++++++++-- src/blpapi_utils.cpp | 433 +++++++++++++++++++++++--------------------- src/blpapi_utils.h | 31 +-- src/bsrch.cpp |only src/getFieldInfo.cpp |only src/rblpapi_types.h |only src/subscribe.cpp | 2 tests |only 33 files changed, 756 insertions(+), 354 deletions(-)
Title: Tools for Thermoluminescences Dating
Description: A series of function to make thermoluminescence dating using the MAAD or the SAR protocol.
This package completes the R package "Luminescence."
Author: David Strebler [aut, cre],
Dominik Brill [ths],
Helmut Brückner [ths]
Maintainer: David Strebler <david.strebler@uni-koeln.de>
Diff between TLdating versions 0.1.0 dated 2016-03-08 and 0.1.1 dated 2016-03-15
DESCRIPTION | 8 +- MD5 | 42 +++++------ NAMESPACE | 8 ++ R/TLdating-package.R | 10 +- R/TLum-class.R | 7 - R/TLum.Analysis-class.R | 163 ++++++++++++++----------------------------- R/TLum.BIN.File-class.R | 65 +++++++++++++---- R/TLum.Data-class.R | 11 +- R/TLum.Data.Curve-class.R | 95 +++++++++++++++++++------ R/TLum.Results-class.R | 58 ++++++++++----- R/script_TL.MAAD.R | 2 R/script_TL.SAR.R | 4 - R/script_TL.plateau.R | 4 - man/TLdating-package.Rd | 10 +- man/TLum.Analysis-class.Rd | 48 +++++++++++- man/TLum.BIN.File-class.Rd | 46 ++++++++++-- man/TLum.Data-class.Rd | 3 man/TLum.Data.Curve-class.Rd | 60 +++++++++++++++ man/TLum.Results-class.Rd | 30 +++++++ man/script_TL.MAAD.Rd | 2 man/script_TL.SAR.Rd | 4 - man/script_TL.plateau.Rd | 4 - 22 files changed, 455 insertions(+), 229 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data.
Author: Beata Nowok, Gillian M Raab, Joshua Snoke and Chris Dibben
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.2-0 dated 2016-02-03 and 1.2-1 dated 2016-03-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 9 +++++++++ R/sampler.syn.r | 2 ++ R/syn.r | 32 ++++++++++++++++++-------------- inst/doc/synthpop.pdf |binary man/synthpop-package.Rd | 4 ++-- 7 files changed, 41 insertions(+), 26 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between questionr versions 0.4.3 dated 2015-03-31 and 0.5 dated 2016-03-15
questionr-0.4.3/questionr/R/addNAstr.r |only questionr-0.4.3/questionr/R/datasets.r |only questionr-0.4.3/questionr/R/describe.r |only questionr-0.4.3/questionr/R/icut.r |only questionr-0.4.3/questionr/R/irec.r |only questionr-0.4.3/questionr/R/lookfor.r |only questionr-0.4.3/questionr/R/odds.ratio.r |only questionr-0.4.3/questionr/R/questionr-package.r |only questionr-0.4.3/questionr/R/recode.r |only questionr-0.4.3/questionr/R/stats.r |only questionr-0.4.3/questionr/R/table.multi.r |only questionr-0.4.3/questionr/R/tables.r |only questionr-0.4.3/questionr/R/tools.r |only questionr-0.4.3/questionr/R/utils.r |only questionr-0.4.3/questionr/R/weighting.r |only questionr-0.4.3/questionr/data/happy.rda |only questionr-0.4.3/questionr/data/hdv2003.rda |only questionr-0.4.3/questionr/data/rp99.rda |only questionr-0.4.3/questionr/po/R-en.po |only questionr-0.5/questionr/DESCRIPTION | 23 questionr-0.5/questionr/MD5 | 143 questionr-0.5/questionr/NAMESPACE | 8 questionr-0.5/questionr/NEWS | 16 questionr-0.5/questionr/R/addNAstr.R |only questionr-0.5/questionr/R/datasets.R |only questionr-0.5/questionr/R/describe.R |only questionr-0.5/questionr/R/icut.R |only questionr-0.5/questionr/R/iorder.R | 482 questionr-0.5/questionr/R/irec.R |only questionr-0.5/questionr/R/lookfor.R |only questionr-0.5/questionr/R/odds.ratio.R |only questionr-0.5/questionr/R/questionr-package.R |only questionr-0.5/questionr/R/recode.R |only questionr-0.5/questionr/R/shiny-utils.R |only questionr-0.5/questionr/R/stats.R |only questionr-0.5/questionr/R/table.multi.R |only questionr-0.5/questionr/R/tables.R |only questionr-0.5/questionr/R/tools.R |only questionr-0.5/questionr/R/utils.R |only questionr-0.5/questionr/R/weighting.R |only questionr-0.5/questionr/data/fecondite.RData |only questionr-0.5/questionr/data/happy.RData |only questionr-0.5/questionr/data/hdv2003.RData |only questionr-0.5/questionr/data/rp99.RData |only questionr-0.5/questionr/inst/po/en/LC_MESSAGES/R-questionr.mo |binary questionr-0.5/questionr/inst/po/en@quot/LC_MESSAGES/R-questionr.mo |binary questionr-0.5/questionr/inst/po/fr/LC_MESSAGES/R-questionr.mo |binary questionr-0.5/questionr/inst/rstudio |only questionr-0.5/questionr/inst/shiny/css/ifuncs.css | 2 questionr-0.5/questionr/inst/shiny/js/iorder.js | 27 questionr-0.5/questionr/inst/shiny/js/jquery-ui.js |17410 ++-------- questionr-0.5/questionr/man/addNAstr.Rd | 10 questionr-0.5/questionr/man/chisq.residuals.Rd | 4 questionr-0.5/questionr/man/clipcopy.Rd | 4 questionr-0.5/questionr/man/cprop.Rd | 4 questionr-0.5/questionr/man/cramer.v.Rd | 4 questionr-0.5/questionr/man/cross.multi.table.Rd | 12 questionr-0.5/questionr/man/describe.Rd | 6 questionr-0.5/questionr/man/duplicated2.Rd | 8 questionr-0.5/questionr/man/enfants.Rd |only questionr-0.5/questionr/man/escape_regex.Rd |only questionr-0.5/questionr/man/fecondite.Rd |only questionr-0.5/questionr/man/femmes.Rd |only questionr-0.5/questionr/man/first_non_null.Rd |only questionr-0.5/questionr/man/format.proptab.Rd | 4 questionr-0.5/questionr/man/freq.Rd | 4 questionr-0.5/questionr/man/freq.na.Rd | 4 questionr-0.5/questionr/man/hdv2003.Rd | 4 questionr-0.5/questionr/man/icut.Rd | 11 questionr-0.5/questionr/man/ifunc_get_css.Rd |only questionr-0.5/questionr/man/ifunc_run_as_addin.Rd |only questionr-0.5/questionr/man/ifunc_show_alert.Rd |only questionr-0.5/questionr/man/iorder.Rd | 8 questionr-0.5/questionr/man/irec.Rd | 13 questionr-0.5/questionr/man/lookfor.Rd | 4 questionr-0.5/questionr/man/menages.Rd |only questionr-0.5/questionr/man/multi.split.Rd | 5 questionr-0.5/questionr/man/multi.table.Rd | 4 questionr-0.5/questionr/man/na.rm.Rd | 8 questionr-0.5/questionr/man/odds.ratio.Rd | 36 questionr-0.5/questionr/man/print.proptab.Rd | 4 questionr-0.5/questionr/man/prop.Rd | 4 questionr-0.5/questionr/man/qload.Rd | 10 questionr-0.5/questionr/man/qscan.Rd | 12 questionr-0.5/questionr/man/quant.cut.Rd | 4 questionr-0.5/questionr/man/questionr.Rd | 4 questionr-0.5/questionr/man/recode.na.Rd | 6 questionr-0.5/questionr/man/rename.variable.Rd | 4 questionr-0.5/questionr/man/rm.unused.levels.Rd | 4 questionr-0.5/questionr/man/rp99.Rd | 4 questionr-0.5/questionr/man/rprop.Rd | 4 questionr-0.5/questionr/man/wtd.mean.Rd | 4 questionr-0.5/questionr/man/wtd.table.Rd | 4 questionr-0.5/questionr/po/R-fr.mo |binary questionr-0.5/questionr/po/R-fr.po | 174 questionr-0.5/questionr/po/R-questionr.pot | 100 questionr-0.5/questionr/tests |only 97 files changed, 5055 insertions(+), 13555 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models.
Author: Adrien Taudiere, Cyrille Violle with contribution by Francois Munoz
Maintainer: Adrien Taudiere <adrien.taudiere@cefe.cnrs.fr>
Diff between cati versions 0.99 dated 2015-05-29 and 0.99.1 dated 2016-03-15
cati-0.99.1/cati/DESCRIPTION | 6 +++--- cati-0.99.1/cati/MD5 | 20 ++++++++++---------- cati-0.99.1/cati/NAMESPACE | 3 +++ cati-0.99.1/cati/R/allfunctions_cati.R |only cati-0.99.1/cati/inst/CITATION | 2 +- cati-0.99.1/cati/man/ComIndex.Rd | 11 +++++++++-- cati-0.99.1/cati/man/ComIndexMulti.Rd | 9 ++++++++- cati-0.99.1/cati/man/Fred.Rd | 19 ++++++++++++++----- cati-0.99.1/cati/man/RaoRel.Rd | 4 ++-- cati-0.99.1/cati/man/Tstats.Rd | 1 + cati-0.99.1/cati/man/cati-package.Rd | 2 +- cati-0.99/cati/R/allfunctions_cati.r |only 12 files changed, 52 insertions(+), 25 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using MCMC.
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.6.2 dated 2015-07-20 and 0.6.3 dated 2016-03-15
bsts-0.6.2/bsts/R/plot.dynamic.distribution.R |only bsts-0.6.2/bsts/man/plot.dynamic.distribution.Rd |only bsts-0.6.2/bsts/src/btlm.cc |only bsts-0.6.2/bsts/src/state_space.cc |only bsts-0.6.3/bsts/DESCRIPTION | 10 bsts-0.6.3/bsts/MD5 | 49 bsts-0.6.3/bsts/NAMESPACE | 9 bsts-0.6.3/bsts/R/add.dynamic.regression.R | 91 bsts-0.6.3/bsts/R/add.trig.R |only bsts-0.6.3/bsts/R/bsts.R | 1517 ++---------- bsts-0.6.3/bsts/R/diagnostics.R |only bsts-0.6.3/bsts/R/format.learning.data.R |only bsts-0.6.3/bsts/R/format.prediction.data.R |only bsts-0.6.3/bsts/R/mixed.frequency.R | 13 bsts-0.6.3/bsts/R/plots.R |only bsts-0.6.3/bsts/R/predict.bsts.R |only bsts-0.6.3/bsts/R/summary.bsts.R |only bsts-0.6.3/bsts/R/utils.R |only bsts-0.6.3/bsts/man/add.dynamic.regression.Rd | 9 bsts-0.6.3/bsts/man/add.trig.Rd |only bsts-0.6.3/bsts/man/bsts.Rd | 44 bsts-0.6.3/bsts/man/plot.bsts.prediction.Rd | 10 bsts-0.6.3/bsts/man/predict.bsts.Rd | 13 bsts-0.6.3/bsts/src/bsts.cc |only bsts-0.6.3/bsts/src/mixed_frequency.cc | 25 bsts-0.6.3/bsts/src/model_manager.cc |only bsts-0.6.3/bsts/src/model_manager.h |only bsts-0.6.3/bsts/src/state_space_gaussian_model_manager.cc |only bsts-0.6.3/bsts/src/state_space_gaussian_model_manager.h |only bsts-0.6.3/bsts/src/state_space_logit_model_manager.cc |only bsts-0.6.3/bsts/src/state_space_logit_model_manager.h |only bsts-0.6.3/bsts/src/state_space_poisson_model_manager.cc |only bsts-0.6.3/bsts/src/state_space_poisson_model_manager.h |only bsts-0.6.3/bsts/src/state_space_regression_model_manager.cc |only bsts-0.6.3/bsts/src/state_space_regression_model_manager.h |only bsts-0.6.3/bsts/src/state_space_student_model_manager.cc |only bsts-0.6.3/bsts/src/state_space_student_model_manager.h |only bsts-0.6.3/bsts/src/utils.cc |only bsts-0.6.3/bsts/src/utils.h | 95 39 files changed, 604 insertions(+), 1281 deletions(-)
Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression a la McCulloch and George (1997).
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between BoomSpikeSlab versions 0.5.2 dated 2014-12-04 and 0.5.3 dated 2016-03-15
DESCRIPTION | 12 MD5 | 39 +- NAMESPACE | 27 + R/lm.spike.R | 121 +++----- R/logit.spike.R | 128 ++------- R/model.matrix.R |only R/poisson.spike.R | 69 +--- R/spike.slab.prior.R | 393 +++++++++++++++++++++++++++- man/independent.spike.slab.prior.Rd | 5 man/independent.student.spike.slab.prior.Rd |only man/logit.spike.Rd | 30 +- man/logit.zellner.prior.Rd |only man/make.spike.slab.prior.Rd | 6 man/model.matrix.Rd |only man/plot.lm.spike.Rd | 7 man/plot.logit.spike.Rd | 28 + man/plot.poisson.spike.Rd |only man/poisson.zellner.prior.Rd |only man/spike.slab.glm.prior.Rd |only man/student.spike.slab.prior.Rd |only man/summary.logit.spike.Rd | 5 src/logit_spike_slab_wrapper.cc | 47 --- src/poisson_spike_slab_wrapper.cc | 14 src/spike_slab_wrapper.cc | 27 + src/utils.h |only 25 files changed, 657 insertions(+), 301 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on
Markov chain Monte Carlo. Although boom contains a few R utilities
(mainly plotting functions), its primary purpose is to install the
BOOM C++ library on your system so that other packages can link
against it.
Author: Steven L. Scott is the sole author and creator of the BOOM
project. Some code in the BOOM libraries has been modified from
other open source projects. These include Cephes (obtained from
Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell,
obtained from Powell's web site), and a modified version of the R
math libraries (R core development team). Original copyright
notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications
made to the original code.
Maintainer: Steve Scott <stevescott@google.com>
Diff between Boom versions 0.2 dated 2014-12-03 and 0.3 dated 2016-03-15
Boom-0.2/Boom/inst/include/Models/CompositeEmMixtureComponent.hpp |only Boom-0.2/Boom/inst/include/Models/Policies/ConjugatePriorPolicy.hpp |only Boom-0.2/Boom/inst/include/Models/StateSpace/Filters/ScalarHomogeneousKalmanFilter.hpp |only Boom-0.2/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanFilter.hpp |only Boom-0.2/Boom/inst/include/TargetFun/FpTargetFun.hpp |only Boom-0.2/Boom/src/Models/CompositeEmMixtureComponent.cpp |only Boom-0.2/Boom/src/Models/EmMixtureComponent.cpp |only Boom-0.2/Boom/src/Models/StateSpace/Filters/ScalarHomogeneousKalmanFilter.cpp |only Boom-0.3/Boom/DESCRIPTION | 9 Boom-0.3/Boom/MD5 | 1273 +++++----- Boom-0.3/Boom/NAMESPACE | 7 Boom-0.3/Boom/R/check.data.R | 7 Boom-0.3/Boom/R/compare.many.densities.R | 14 Boom-0.3/Boom/R/histabunch.R |only Boom-0.3/Boom/R/plot.dynamic.distribution.R | 98 Boom-0.3/Boom/R/prior_specification.R | 54 Boom-0.3/Boom/R/suggest_burn_log_likelihood.R |only Boom-0.3/Boom/inst/include/LinAlg/Array.hpp | 51 Boom-0.3/Boom/inst/include/LinAlg/CorrelationMatrix.hpp | 6 Boom-0.3/Boom/inst/include/LinAlg/DiagonalMatrix.hpp | 253 + Boom-0.3/Boom/inst/include/LinAlg/LinAlgExceptions.hpp | 8 Boom-0.3/Boom/inst/include/LinAlg/Matrix.hpp | 541 ++-- Boom-0.3/Boom/inst/include/LinAlg/Selector.hpp | 210 + Boom-0.3/Boom/inst/include/LinAlg/SpdMatrix.hpp | 55 Boom-0.3/Boom/inst/include/LinAlg/Types.hpp | 3 Boom-0.3/Boom/inst/include/LinAlg/Vector.hpp | 50 Boom-0.3/Boom/inst/include/LinAlg/VectorView.hpp | 23 Boom-0.3/Boom/inst/include/LinAlg/blas.hpp | 5 Boom-0.3/Boom/inst/include/Models/Bart/Bart.hpp | 22 Boom-0.3/Boom/inst/include/Models/Bart/GaussianBartModel.hpp | 8 Boom-0.3/Boom/inst/include/Models/Bart/GaussianLinearBartModel.hpp | 6 Boom-0.3/Boom/inst/include/Models/Bart/LogitBartModel.hpp | 8 Boom-0.3/Boom/inst/include/Models/Bart/PoissonBartModel.hpp | 8 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/BartPosteriorSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.hpp | 39 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.hpp | 39 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.hpp | 35 Boom-0.3/Boom/inst/include/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.hpp | 39 Boom-0.3/Boom/inst/include/Models/Bart/ProbitBartModel.hpp | 8 Boom-0.3/Boom/inst/include/Models/BetaBinomialModel.hpp | 54 Boom-0.3/Boom/inst/include/Models/BetaModel.hpp | 28 Boom-0.3/Boom/inst/include/Models/BinomialModel.hpp | 45 Boom-0.3/Boom/inst/include/Models/CategoricalData.hpp | 66 Boom-0.3/Boom/inst/include/Models/ChisqModel.hpp | 18 Boom-0.3/Boom/inst/include/Models/CompositeData.hpp | 4 Boom-0.3/Boom/inst/include/Models/CompositeModel.hpp | 10 Boom-0.3/Boom/inst/include/Models/ConstrainedVectorParams.hpp | 48 Boom-0.3/Boom/inst/include/Models/DataPair.hpp | 4 Boom-0.3/Boom/inst/include/Models/DataTypes.hpp | 81 Boom-0.3/Boom/inst/include/Models/DirichletModel.hpp | 69 Boom-0.3/Boom/inst/include/Models/DiscreteUniformModel.hpp |only Boom-0.3/Boom/inst/include/Models/DoubleModel.hpp | 16 Boom-0.3/Boom/inst/include/Models/EmMixtureComponent.hpp | 12 Boom-0.3/Boom/inst/include/Models/ExponentialModel.hpp | 40 Boom-0.3/Boom/inst/include/Models/FiniteMixtureModel.hpp | 28 Boom-0.3/Boom/inst/include/Models/GammaModel.hpp | 44 Boom-0.3/Boom/inst/include/Models/GaussianModel.hpp | 34 Boom-0.3/Boom/inst/include/Models/GaussianModelBase.hpp | 51 Boom-0.3/Boom/inst/include/Models/GaussianModelGivenSigma.hpp | 12 Boom-0.3/Boom/inst/include/Models/Glm/AggregatedRegressionModel.hpp | 48 Boom-0.3/Boom/inst/include/Models/Glm/BinomialLogitModel.hpp | 54 Boom-0.3/Boom/inst/include/Models/Glm/BinomialRegressionData.hpp | 38 Boom-0.3/Boom/inst/include/Models/Glm/ChoiceData.hpp | 20 Boom-0.3/Boom/inst/include/Models/Glm/CumulativeLogitModel.hpp | 12 Boom-0.3/Boom/inst/include/Models/Glm/CumulativeProbitModel.hpp | 12 Boom-0.3/Boom/inst/include/Models/Glm/Glm.hpp | 224 - Boom-0.3/Boom/inst/include/Models/Glm/GlmCoefs.hpp | 12 Boom-0.3/Boom/inst/include/Models/Glm/GlmMvnPriorBase.hpp | 28 Boom-0.3/Boom/inst/include/Models/Glm/HierarchicalPoissonRegression.hpp | 8 Boom-0.3/Boom/inst/include/Models/Glm/LogisticRegressionModel.hpp | 69 Boom-0.3/Boom/inst/include/Models/Glm/ModelSelectionConcepts.hpp | 32 Boom-0.3/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp | 82 Boom-0.3/Boom/inst/include/Models/Glm/MultinomialProbitModel.hpp | 72 Boom-0.3/Boom/inst/include/Models/Glm/MvReg2.hpp | 154 - Boom-0.3/Boom/inst/include/Models/Glm/MvnGivenX.hpp | 48 Boom-0.3/Boom/inst/include/Models/Glm/MvnGivenXandSigma.hpp | 16 Boom-0.3/Boom/inst/include/Models/Glm/MvtRegModel.hpp | 32 Boom-0.3/Boom/inst/include/Models/Glm/OrdinalCutpointModel.hpp | 48 Boom-0.3/Boom/inst/include/Models/Glm/PoissonRegressionData.hpp | 31 Boom-0.3/Boom/inst/include/Models/Glm/PoissonRegressionModel.hpp | 26 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.hpp | 43 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.hpp | 38 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.hpp | 32 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.hpp | 38 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.hpp | 30 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp | 62 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.hpp | 15 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.hpp | 15 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/DAFE_MLM.hpp | 45 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.hpp | 21 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/LogitSampler.hpp | 22 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/LogitSamplerBma.hpp | 11 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MLAuxMixSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MLVS.hpp | 17 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MLVS_data_imputer.hpp | 18 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MlogitRwm.hpp | 16 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.hpp | 14 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MnpBetaSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.hpp | 4 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.hpp | 5 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MvRegSampler.hpp | 13 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/MvtRegSampler.hpp | 12 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.hpp | 4 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/PartRegSampler.hpp | 40 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.hpp | 34 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.hpp | 20 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/ProbitRegressionSampler.hpp | 17 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.hpp | 17 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionConjSampler.hpp | 20 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/SpikeSlabSampler.hpp | 48 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/TDataImputer.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/TRegressionSampler.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/VsPriorSampler.hpp | 15 Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/ProbitRegression.hpp | 28 Boom-0.3/Boom/inst/include/Models/Glm/RegressionModel.hpp | 258 +- Boom-0.3/Boom/inst/include/Models/Glm/TRegression.hpp | 82 Boom-0.3/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp | 38 Boom-0.3/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 68 Boom-0.3/Boom/inst/include/Models/Glm/ZeroInflatedLognormalRegression.hpp |only Boom-0.3/Boom/inst/include/Models/Glm/ZeroInflatedPoissonRegression.hpp |only Boom-0.3/Boom/inst/include/Models/HMM/Clickstream/NestedHmm.hpp | 38 Boom-0.3/Boom/inst/include/Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/HMM/Clickstream/Session.hpp | 2 Boom-0.3/Boom/inst/include/Models/HMM/Clickstream/Stream.hpp | 4 Boom-0.3/Boom/inst/include/Models/HMM/HMM2.hpp | 20 Boom-0.3/Boom/inst/include/Models/HMM/HealthStateModel.hpp | 20 Boom-0.3/Boom/inst/include/Models/HMM/HmmFilter.hpp | 16 Boom-0.3/Boom/inst/include/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/HMM/hmm_tools.hpp | 6 Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalDirichletModel.hpp |only Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalGammaModel.hpp | 14 Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalModel.hpp |only Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalPoissonModel.hpp | 50 Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.hpp | 25 Boom-0.3/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp | 20 Boom-0.3/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.hpp |only Boom-0.3/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.hpp | 27 Boom-0.3/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/IRT/DafePcr.hpp | 42 Boom-0.3/Boom/inst/include/Models/IRT/DafePcrRwm.hpp | 26 Boom-0.3/Boom/inst/include/Models/IRT/IrtModel.hpp | 14 Boom-0.3/Boom/inst/include/Models/IRT/Item.hpp | 84 Boom-0.3/Boom/inst/include/Models/IRT/ItemDataPolicy.hpp | 2 Boom-0.3/Boom/inst/include/Models/IRT/ItemSliceSampler.hpp | 6 Boom-0.3/Boom/inst/include/Models/IRT/PartialCreditModel.hpp | 56 Boom-0.3/Boom/inst/include/Models/IRT/PcrNid.hpp | 12 Boom-0.3/Boom/inst/include/Models/IRT/Subject.hpp | 16 Boom-0.3/Boom/inst/include/Models/IRT/SubjectPrior.hpp | 38 Boom-0.3/Boom/inst/include/Models/IRT/SubjectSliceSampler.hpp | 13 Boom-0.3/Boom/inst/include/Models/IRT/Subject_prior.hpp | 12 Boom-0.3/Boom/inst/include/Models/IRT/multisubscale_logit_cutpoint_model.hpp | 8 Boom-0.3/Boom/inst/include/Models/IndependentMvnModel.hpp | 88 Boom-0.3/Boom/inst/include/Models/IndependentMvnModelGivenScalarSigma.hpp | 16 Boom-0.3/Boom/inst/include/Models/LognormalModel.hpp |only Boom-0.3/Boom/inst/include/Models/MarginallyUniformCorrelationModel.hpp | 6 Boom-0.3/Boom/inst/include/Models/MarkovModel.hpp | 94 Boom-0.3/Boom/inst/include/Models/Mixtures/ConditionalFiniteMixtureModel.hpp | 16 Boom-0.3/Boom/inst/include/Models/Mixtures/DirichletProcessMvnModel.hpp |only Boom-0.3/Boom/inst/include/Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.hpp |only Boom-0.3/Boom/inst/include/Models/ModelTypes.hpp | 150 - Boom-0.3/Boom/inst/include/Models/MultinomialModel.hpp | 66 Boom-0.3/Boom/inst/include/Models/MvnBase.hpp | 95 Boom-0.3/Boom/inst/include/Models/MvnGivenScalarSigma.hpp | 35 Boom-0.3/Boom/inst/include/Models/MvnGivenSigma.hpp | 36 Boom-0.3/Boom/inst/include/Models/MvnModel.hpp | 47 Boom-0.3/Boom/inst/include/Models/MvtModel.hpp | 43 Boom-0.3/Boom/inst/include/Models/Nonparametric |only Boom-0.3/Boom/inst/include/Models/ParamTypes.hpp | 80 Boom-0.3/Boom/inst/include/Models/PointProcess/CosinePoissonProcess.hpp | 16 Boom-0.3/Boom/inst/include/Models/PointProcess/HomogeneousPoissonProcess.hpp | 44 Boom-0.3/Boom/inst/include/Models/PointProcess/MarkovModulatedPoissonProcess.hpp | 16 Boom-0.3/Boom/inst/include/Models/PointProcess/PointProcess.hpp | 8 Boom-0.3/Boom/inst/include/Models/PointProcess/PoissonClusterProcess.hpp | 26 Boom-0.3/Boom/inst/include/Models/PointProcess/PoissonProcess.hpp | 2 Boom-0.3/Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PointProcess/PosteriorSamplers/PoissonClusterPosteriorSampler.hpp | 6 Boom-0.3/Boom/inst/include/Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PointProcess/WeeklyCyclePoissonProcess.hpp | 74 Boom-0.3/Boom/inst/include/Models/PoissonGammaModel.hpp | 10 Boom-0.3/Boom/inst/include/Models/PoissonModel.hpp | 54 Boom-0.3/Boom/inst/include/Models/Policies/CompositeParamPolicy.hpp | 10 Boom-0.3/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp | 15 Boom-0.3/Boom/inst/include/Models/Policies/ManyParamPolicy.hpp | 7 Boom-0.3/Boom/inst/include/Models/Policies/MixtureDataPolicy.hpp | 12 Boom-0.3/Boom/inst/include/Models/Policies/NonparametricParamPolicy.hpp | 4 Boom-0.3/Boom/inst/include/Models/Policies/NullDataPolicy.hpp | 6 Boom-0.3/Boom/inst/include/Models/Policies/NullParamPolicy.hpp | 6 Boom-0.3/Boom/inst/include/Models/Policies/ParamPolicy_1.hpp | 17 Boom-0.3/Boom/inst/include/Models/Policies/ParamPolicy_2.hpp | 13 Boom-0.3/Boom/inst/include/Models/Policies/ParamPolicy_3.hpp | 13 Boom-0.3/Boom/inst/include/Models/Policies/ParamPolicy_4.hpp | 13 Boom-0.3/Boom/inst/include/Models/Policies/PriorPolicy.hpp | 30 Boom-0.3/Boom/inst/include/Models/Policies/SufstatDataPolicy.hpp | 5 Boom-0.3/Boom/inst/include/Models/Policies/SufstatOnlyDataPolicy.hpp | 2 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.hpp | 34 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.hpp | 210 + Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/BetaBinomialSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/BetaPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/CompositeModelSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/CompositeSampler.hpp | 21 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/CorrelationSampler.hpp | 29 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/DirichletPosteriorSampler.hpp | 398 ++- Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ExchangeableDirichletSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ExponentialGammaSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/FiniteMixturePosteriorSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/FixedProbBinomialSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/FixedSpdSampler.hpp | 18 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/FixedUnivariateSampler.hpp | 10 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/GammaPosteriorSampler.hpp | 14 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/GaussianConjSampler.hpp | 16 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/GaussianMeanSampler.hpp | 10 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/GaussianVarSampler.hpp | 26 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/GenericGaussianVarianceSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/Imputer.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/IndependentMvnConjSampler.hpp | 28 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/IndependentMvnVarSampler.hpp |only Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MarkovConjSampler.hpp | 40 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MarkovConjShrinkageSampler.hpp | 18 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MultinomialDirichletSampler.hpp | 17 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MvnConjSampler.hpp | 27 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MvnIndependentVarianceSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MvnMeanSampler.hpp | 32 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/MvnVarSampler.hpp | 22 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/PoissonGammaSampler.hpp | 14 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp | 41 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.hpp | 10 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/SepStratSampler.hpp | 32 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/SharedSigsqSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedLognormalPosteriorSampler.hpp | 9 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp | 14 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.hpp | 12 Boom-0.3/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.hpp | 17 Boom-0.3/Boom/inst/include/Models/ProductDirichletModel.hpp | 44 Boom-0.3/Boom/inst/include/Models/ProductModel.hpp | 4 Boom-0.3/Boom/inst/include/Models/ScaledChisqModel.hpp | 11 Boom-0.3/Boom/inst/include/Models/SpdData.hpp | 54 Boom-0.3/Boom/inst/include/Models/SpdModel.hpp | 6 Boom-0.3/Boom/inst/include/Models/SpdParams.hpp | 16 Boom-0.3/Boom/inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp | 114 Boom-0.3/Boom/inst/include/Models/StateSpace/Filters/KalmanTools.hpp | 62 Boom-0.3/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanStorage.hpp | 21 Boom-0.3/Boom/inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp | 128 - Boom-0.3/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp | 449 ++- Boom-0.3/Boom/inst/include/Models/StateSpace/Filters/SparseVector.hpp | 31 Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.hpp | 15 Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/StateSpace/PosteriorSamplers/SufstatManager.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 28 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp | 32 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/Holiday.hpp | 24 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp | 32 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 30 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.hpp | 44 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp | 30 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/RegressionStateModel.hpp | 24 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp | 32 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 9 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp | 38 Boom-0.3/Boom/inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceLogitModel.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp | 32 Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 171 - Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceNormalMixture.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpacePoissonModel.hpp |only Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp | 50 Boom-0.3/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp |only Boom-0.3/Boom/inst/include/Models/Sufstat.hpp | 12 Boom-0.3/Boom/inst/include/Models/TimeSeries/ArModel.hpp | 42 Boom-0.3/Boom/inst/include/Models/TimeSeries/NonzeroMeanAr1Model.hpp | 26 Boom-0.3/Boom/inst/include/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.hpp | 7 Boom-0.3/Boom/inst/include/Models/TimeSeries/TimeSeries.hpp | 6 Boom-0.3/Boom/inst/include/Models/TimeSeries/TimeSeriesDataPolicy.hpp | 2 Boom-0.3/Boom/inst/include/Models/TimeSeries/TimeSeriesSufstatDataPolicy.hpp | 6 Boom-0.3/Boom/inst/include/Models/TruncatedGammaModel.hpp | 2 Boom-0.3/Boom/inst/include/Models/UniformCorrelationModel.hpp | 6 Boom-0.3/Boom/inst/include/Models/UniformModel.hpp | 30 Boom-0.3/Boom/inst/include/Models/VectorModel.hpp | 40 Boom-0.3/Boom/inst/include/Models/WeightedData.hpp | 4 Boom-0.3/Boom/inst/include/Models/WeightedGaussianSuf.hpp | 20 Boom-0.3/Boom/inst/include/Models/WeightedMvnModel.hpp | 56 Boom-0.3/Boom/inst/include/Models/WishartModel.hpp | 100 Boom-0.3/Boom/inst/include/Models/ZeroInflatedGammaModel.hpp | 18 Boom-0.3/Boom/inst/include/Models/ZeroInflatedLognormalModel.hpp | 29 Boom-0.3/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 24 Boom-0.3/Boom/inst/include/Models/ZeroMeanGaussianModel.hpp | 29 Boom-0.3/Boom/inst/include/Models/ZeroMeanMvnModel.hpp | 27 Boom-0.3/Boom/inst/include/Samplers/ARMS.hpp | 18 Boom-0.3/Boom/inst/include/Samplers/DirectProposal.hpp |only Boom-0.3/Boom/inst/include/Samplers/ImportanceResampler.hpp |only Boom-0.3/Boom/inst/include/Samplers/MH_Proposals.hpp | 89 Boom-0.3/Boom/inst/include/Samplers/MetropolisHastings.hpp | 16 Boom-0.3/Boom/inst/include/Samplers/RejectionSampler.hpp |only Boom-0.3/Boom/inst/include/Samplers/Sampler.hpp | 13 Boom-0.3/Boom/inst/include/Samplers/ScalarAdaptiveRejectionSampler.hpp |only Boom-0.3/Boom/inst/include/Samplers/ScalarLangevinSampler.hpp |only Boom-0.3/Boom/inst/include/Samplers/ScalarSliceSampler.hpp | 13 Boom-0.3/Boom/inst/include/Samplers/SliceSampler.hpp | 10 Boom-0.3/Boom/inst/include/Samplers/TIM.hpp | 7 Boom-0.3/Boom/inst/include/Samplers/UnivariateLangevinSampler.hpp |only Boom-0.3/Boom/inst/include/Samplers/UnivariateSliceSampler.hpp | 58 Boom-0.3/Boom/inst/include/TargetFun/JacobianChecker.hpp |only Boom-0.3/Boom/inst/include/TargetFun/LogPost.hpp | 14 Boom-0.3/Boom/inst/include/TargetFun/Loglike.hpp | 14 Boom-0.3/Boom/inst/include/TargetFun/ScalarLogpostTF.hpp | 2 Boom-0.3/Boom/inst/include/TargetFun/TargetFun.hpp | 119 Boom-0.3/Boom/inst/include/TargetFun/Transformation.hpp |only Boom-0.3/Boom/inst/include/cpputil/Date.hpp | 61 Boom-0.3/Boom/inst/include/cpputil/ParamHolder.hpp | 20 Boom-0.3/Boom/inst/include/cpputil/ProgressTracker.hpp | 2 Boom-0.3/Boom/inst/include/cpputil/file_utils.hpp | 3 Boom-0.3/Boom/inst/include/cpputil/lse.hpp | 16 Boom-0.3/Boom/inst/include/cpputil/permute.hpp | 2 Boom-0.3/Boom/inst/include/cpputil/rep.hpp | 4 Boom-0.3/Boom/inst/include/cpputil/stream.hpp |only Boom-0.3/Boom/inst/include/cpputil/string_utils.hpp | 31 Boom-0.3/Boom/inst/include/distributions.hpp | 274 +- Boom-0.3/Boom/inst/include/distributions/Markov.hpp | 8 Boom-0.3/Boom/inst/include/numopt/NumericalDerivatives.hpp |only Boom-0.3/Boom/inst/include/r_interface/boom_r_tools.hpp | 12 Boom-0.3/Boom/inst/include/r_interface/create_state_model.hpp | 3 Boom-0.3/Boom/inst/include/r_interface/list_io.hpp | 116 Boom-0.3/Boom/inst/include/r_interface/prior_specification.hpp | 134 - Boom-0.3/Boom/inst/include/stats/Bspline.hpp |only Boom-0.3/Boom/inst/include/stats/ChiSquareTest.hpp | 8 Boom-0.3/Boom/inst/include/stats/DataTable.hpp | 157 - Boom-0.3/Boom/inst/include/stats/Design.hpp | 87 Boom-0.3/Boom/inst/include/stats/FreqDist.hpp | 70 Boom-0.3/Boom/inst/include/stats/NaturalSpline.hpp | 44 Boom-0.3/Boom/inst/include/stats/Resampler.hpp | 98 Boom-0.3/Boom/inst/include/stats/Spline.hpp | 18 Boom-0.3/Boom/inst/include/stats/diff.hpp | 6 Boom-0.3/Boom/inst/include/stats/moments.hpp | 12 Boom-0.3/Boom/inst/include/stats/ols.hpp | 2 Boom-0.3/Boom/inst/include/stats/regression.hpp | 2 Boom-0.3/Boom/inst/include/uint.hpp | 4 Boom-0.3/Boom/man/check.data.Rd | 2 Boom-0.3/Boom/man/compare.many.densities.Rd | 4 Boom-0.3/Boom/man/histabunch.Rd |only Boom-0.3/Boom/man/normal.prior.Rd | 6 Boom-0.3/Boom/man/plot.dynamic.distribution.Rd | 18 Boom-0.3/Boom/man/suggest.burn.log.likelihood.Rd |only Boom-0.3/Boom/src/Bmath/Bmath.hpp | 26 Boom-0.3/Boom/src/LinAlg/Array.cpp | 1165 ++++----- Boom-0.3/Boom/src/LinAlg/CorrelationMatrix.cpp | 51 Boom-0.3/Boom/src/LinAlg/DiagonalMatrix.cpp | 529 ++-- Boom-0.3/Boom/src/LinAlg/LU.cpp | 23 Boom-0.3/Boom/src/LinAlg/LinAlgExceptions.cpp | 4 Boom-0.3/Boom/src/LinAlg/Matrix.cpp | 608 ++-- Boom-0.3/Boom/src/LinAlg/SVD.cpp | 4 Boom-0.3/Boom/src/LinAlg/SWEEP.cpp | 16 Boom-0.3/Boom/src/LinAlg/Selector.cpp | 589 ++-- Boom-0.3/Boom/src/LinAlg/SpdMatrix.cpp | 34 Boom-0.3/Boom/src/LinAlg/SubMatrix.cpp | 3 Boom-0.3/Boom/src/LinAlg/Vector.cpp | 95 Boom-0.3/Boom/src/LinAlg/VectorView.cpp | 8 Boom-0.3/Boom/src/LinAlg/blas.cpp | 80 Boom-0.3/Boom/src/Makevars | 13 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/BartPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/GaussianLinearBartPosteriorSampler.cpp | 9 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/BetaBinomialModel.cpp | 90 Boom-0.3/Boom/src/Models/BetaModel.cpp | 12 Boom-0.3/Boom/src/Models/BinomialModel.cpp | 26 Boom-0.3/Boom/src/Models/CategoricalData.cpp | 292 +- Boom-0.3/Boom/src/Models/ChisqModel.cpp | 11 Boom-0.3/Boom/src/Models/ConstrainedVectorParams.cpp | 46 Boom-0.3/Boom/src/Models/DataTypes.cpp | 119 Boom-0.3/Boom/src/Models/DirichletModel.cpp | 122 Boom-0.3/Boom/src/Models/DiscreteUniformModel.cpp |only Boom-0.3/Boom/src/Models/ExponentialModel.cpp | 21 Boom-0.3/Boom/src/Models/FiniteMixtureModel.cpp | 28 Boom-0.3/Boom/src/Models/GammaModel.cpp | 18 Boom-0.3/Boom/src/Models/GaussianModel.cpp | 86 Boom-0.3/Boom/src/Models/GaussianModelBase.cpp | 28 Boom-0.3/Boom/src/Models/GaussianModelGivenSigma.cpp | 4 Boom-0.3/Boom/src/Models/Glm/AggregatedRegressionModel.cpp | 16 Boom-0.3/Boom/src/Models/Glm/BinomialLogitModel.cpp | 68 Boom-0.3/Boom/src/Models/Glm/BinomialRegressionData.cpp | 31 Boom-0.3/Boom/src/Models/Glm/ChoiceData.cpp | 16 Boom-0.3/Boom/src/Models/Glm/CumulativeLogitModel.cpp | 4 Boom-0.3/Boom/src/Models/Glm/CumulativeProbitModel.cpp | 4 Boom-0.3/Boom/src/Models/Glm/Glm.cpp | 44 Boom-0.3/Boom/src/Models/Glm/GlmCoefs.cpp | 27 Boom-0.3/Boom/src/Models/Glm/LogisticRegressionModel.cpp | 109 Boom-0.3/Boom/src/Models/Glm/MultinomialLogitModel.cpp | 302 -- Boom-0.3/Boom/src/Models/Glm/MultinomialProbitModel.cpp | 58 Boom-0.3/Boom/src/Models/Glm/MvReg2.cpp | 136 - Boom-0.3/Boom/src/Models/Glm/MvnGivenX.cpp | 28 Boom-0.3/Boom/src/Models/Glm/MvnGivenXandSigma.cpp | 16 Boom-0.3/Boom/src/Models/Glm/MvtRegModel.cpp | 44 Boom-0.3/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 313 +- Boom-0.3/Boom/src/Models/Glm/PoissonRegressionData.cpp | 41 Boom-0.3/Boom/src/Models/Glm/PoissonRegressionModel.cpp | 14 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/AggregatedRegressionSampler.cpp | 6 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.cpp | 33 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.cpp | 187 - Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.cpp | 22 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.cpp | 14 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.cpp | 26 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.cpp | 111 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 75 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.cpp | 13 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.cpp | 14 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/DAFE_MLM.cpp | 134 - Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.cpp | 12 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/LogitSampler.cpp | 22 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/LogitSamplerBma.cpp | 33 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MLAuxMixSampler.cpp | 8 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MLVS.cpp | 28 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MLVS_data_imputer.cpp | 6 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MlogitRwm.cpp | 15 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MnpBetaGivenSigmaSampler.cpp | 32 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MnpBetaSampler.cpp | 15 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.cpp | 8 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.cpp | 6 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MvRegSampler.cpp | 21 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/MvtRegSampler.cpp | 17 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/PartRegSampler.cpp | 50 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.cpp | 61 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionRwmSampler.cpp | 11 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.cpp | 24 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/ProbitRegressionSampler.cpp | 18 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.cpp | 33 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/RegressionConjSampler.cpp | 16 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.cpp | 10 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/SpikeSlabSampler.cpp | 32 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/TDataImputer.cpp |only Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/TRegressionSampler.cpp |only Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/TRegressionSpikeSlabSampler.cpp |only Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/VsPriorSampler.cpp | 46 Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/ZeroInflatedLognormalRegressionPosteriorSampler.cpp |only Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.cpp |only Boom-0.3/Boom/src/Models/Glm/PosteriorSamplers/draw_logit_lambda.cpp | 5 Boom-0.3/Boom/src/Models/Glm/ProbitRegression.cpp | 38 Boom-0.3/Boom/src/Models/Glm/RegressionModel.cpp | 72 Boom-0.3/Boom/src/Models/Glm/TRegression.cpp | 284 -- Boom-0.3/Boom/src/Models/Glm/VariableSelectionPrior.cpp | 50 Boom-0.3/Boom/src/Models/Glm/WeightedRegressionModel.cpp | 247 - Boom-0.3/Boom/src/Models/Glm/ZeroInflatedLognormalRegression.cpp |only Boom-0.3/Boom/src/Models/Glm/ZeroInflatedPoissonRegression.cpp |only Boom-0.3/Boom/src/Models/HMM/Clickstream/NestedHmm.cpp | 58 Boom-0.3/Boom/src/Models/HMM/Clickstream/PosteriorSamplers/NestedHmmPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/HMM/HMM2.cpp | 22 Boom-0.3/Boom/src/Models/HMM/HealthStateModel.cpp | 6 Boom-0.3/Boom/src/Models/HMM/HmmDataImputer.cpp | 2 Boom-0.3/Boom/src/Models/HMM/HmmFilter.cpp | 27 Boom-0.3/Boom/src/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.cpp | 9 Boom-0.3/Boom/src/Models/HMM/hmm_tools.cpp | 6 Boom-0.3/Boom/src/Models/Hierarchical/HierarchicalDirichletModel.cpp |only Boom-0.3/Boom/src/Models/Hierarchical/HierarchicalPoissonModel.cpp | 93 Boom-0.3/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.cpp | 12 Boom-0.3/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.cpp | 6 Boom-0.3/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalDirichletPosteriorSampler.cpp |only Boom-0.3/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalGammaSampler.cpp | 6 Boom-0.3/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.cpp | 10 Boom-0.3/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedGammaSampler.cpp | 18 Boom-0.3/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalZeroInflatedPoissonSampler.cpp | 28 Boom-0.3/Boom/src/Models/IRT/DafePcrDataImputer.cpp | 52 Boom-0.3/Boom/src/Models/IRT/DafePcrItemSampler.cpp | 53 Boom-0.3/Boom/src/Models/IRT/DafePcrRwmItemSampler.cpp | 32 Boom-0.3/Boom/src/Models/IRT/DafePcrRwmSubject.cpp | 36 Boom-0.3/Boom/src/Models/IRT/DafePcrSubject.cpp | 69 Boom-0.3/Boom/src/Models/IRT/IrtModel.cpp | 36 Boom-0.3/Boom/src/Models/IRT/Item.cpp | 20 Boom-0.3/Boom/src/Models/IRT/PartialCreditModel.cpp | 155 - Boom-0.3/Boom/src/Models/IRT/Subject.cpp | 17 Boom-0.3/Boom/src/Models/IRT/SubjectPrior.cpp | 4 Boom-0.3/Boom/src/Models/IRT/SubjectSliceSampler.cpp | 20 Boom-0.3/Boom/src/Models/IndependentMvnModel.cpp | 56 Boom-0.3/Boom/src/Models/LognormalModel.cpp |only Boom-0.3/Boom/src/Models/MarginallyUniformCorrelationModel.cpp | 6 Boom-0.3/Boom/src/Models/MarkovModel.cpp | 97 Boom-0.3/Boom/src/Models/Mixtures/DirichletProcessMvnModel.cpp |only Boom-0.3/Boom/src/Models/Mixtures/PosteriorSamplers/ConditionalFiniteMixtureSampler.cpp | 5 Boom-0.3/Boom/src/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.cpp |only Boom-0.3/Boom/src/Models/ModelTypes.cpp | 58 Boom-0.3/Boom/src/Models/MultinomialModel.cpp | 126 Boom-0.3/Boom/src/Models/MvnBase.cpp | 144 - Boom-0.3/Boom/src/Models/MvnGivenScalarSigma.cpp | 24 Boom-0.3/Boom/src/Models/MvnGivenSigma.cpp | 26 Boom-0.3/Boom/src/Models/MvnModel.cpp | 26 Boom-0.3/Boom/src/Models/MvtModel.cpp | 53 Boom-0.3/Boom/src/Models/ParamTypes.cpp | 109 Boom-0.3/Boom/src/Models/PointProcess/BoundedPoissonProcessSimulator.cpp | 2 Boom-0.3/Boom/src/Models/PointProcess/HomogeneousPoissonProcess.cpp | 14 Boom-0.3/Boom/src/Models/PointProcess/PoissonClusterProcess.cpp | 22 Boom-0.3/Boom/src/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.cpp | 9 Boom-0.3/Boom/src/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/PointProcess/PosteriorSamplers/WeeklyCyclePoissonProcessSampler.cpp | 34 Boom-0.3/Boom/src/Models/PointProcess/WeeklyCyclePoissonProcess.cpp | 76 Boom-0.3/Boom/src/Models/PoissonGammaModel.cpp | 4 Boom-0.3/Boom/src/Models/PoissonModel.cpp | 40 Boom-0.3/Boom/src/Models/Policies/CompositeParamPolicy.cpp | 13 Boom-0.3/Boom/src/Models/Policies/ManyParamPolicy.cpp | 4 Boom-0.3/Boom/src/Models/Policies/NullParamPolicy.cpp | 4 Boom-0.3/Boom/src/Models/PosteriorSamplers/AbsorbingMarkovConjSampler.cpp | 199 - Boom-0.3/Boom/src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp | 325 ++ Boom-0.3/Boom/src/Models/PosteriorSamplers/BetaBinomialSampler.cpp | 7 Boom-0.3/Boom/src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp | 11 Boom-0.3/Boom/src/Models/PosteriorSamplers/CompositeModelSampler.cpp | 5 Boom-0.3/Boom/src/Models/PosteriorSamplers/CompositeSampler.cpp | 18 Boom-0.3/Boom/src/Models/PosteriorSamplers/CorrelationSampler.cpp | 14 Boom-0.3/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 669 ++++- Boom-0.3/Boom/src/Models/PosteriorSamplers/ExchangeableDirichletSampler.cpp | 20 Boom-0.3/Boom/src/Models/PosteriorSamplers/ExponentialGammaSampler.cpp | 9 Boom-0.3/Boom/src/Models/PosteriorSamplers/FixedProbBinomialSampler.cpp | 6 Boom-0.3/Boom/src/Models/PosteriorSamplers/GammaPosteriorSampler.cpp | 20 Boom-0.3/Boom/src/Models/PosteriorSamplers/GaussianConjSampler.cpp | 10 Boom-0.3/Boom/src/Models/PosteriorSamplers/GaussianMeanSampler.cpp | 12 Boom-0.3/Boom/src/Models/PosteriorSamplers/GaussianVarSampler.cpp | 45 Boom-0.3/Boom/src/Models/PosteriorSamplers/GenericGaussianVarianceSampler.cpp | 11 Boom-0.3/Boom/src/Models/PosteriorSamplers/IndependentMvnConjSampler.cpp | 32 Boom-0.3/Boom/src/Models/PosteriorSamplers/IndependentMvnVarSampler.cpp |only Boom-0.3/Boom/src/Models/PosteriorSamplers/MarkovConjSampler.cpp | 71 Boom-0.3/Boom/src/Models/PosteriorSamplers/MarkovConjShrinkageSampler.cpp | 42 Boom-0.3/Boom/src/Models/PosteriorSamplers/MultinomialDirichletSampler.cpp | 23 Boom-0.3/Boom/src/Models/PosteriorSamplers/MvnConjSampler.cpp | 31 Boom-0.3/Boom/src/Models/PosteriorSamplers/MvnIndependentVarianceSampler.cpp | 10 Boom-0.3/Boom/src/Models/PosteriorSamplers/MvnMeanSampler.cpp | 52 Boom-0.3/Boom/src/Models/PosteriorSamplers/MvnVarSampler.cpp | 38 Boom-0.3/Boom/src/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/PosteriorSamplers/PoissonGammaSampler.cpp | 12 Boom-0.3/Boom/src/Models/PosteriorSamplers/PosteriorSampler.cpp | 24 Boom-0.3/Boom/src/Models/PosteriorSamplers/ProductDirichletPosteriorSampler.cpp | 23 Boom-0.3/Boom/src/Models/PosteriorSamplers/SepStratSampler.cpp | 30 Boom-0.3/Boom/src/Models/PosteriorSamplers/SharedSigsqSampler.cpp | 6 Boom-0.3/Boom/src/Models/PosteriorSamplers/ZeroInflatedGammaPosteriorSampler.cpp | 12 Boom-0.3/Boom/src/Models/PosteriorSamplers/ZeroInflatedPoissonSampler.cpp | 30 Boom-0.3/Boom/src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp | 17 Boom-0.3/Boom/src/Models/PosteriorSamplers/ZeroMeanMvnConjSampler.cpp | 18 Boom-0.3/Boom/src/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.cpp | 28 Boom-0.3/Boom/src/Models/ProductDirichletModel.cpp | 40 Boom-0.3/Boom/src/Models/ScaledChisqModel.cpp | 22 Boom-0.3/Boom/src/Models/SpdData.cpp | 48 Boom-0.3/Boom/src/Models/SpdParams.cpp | 16 Boom-0.3/Boom/src/Models/StateSpace/AggregatedStateSpaceRegression.cpp | 71 Boom-0.3/Boom/src/Models/StateSpace/Filters/KalmanTools.cpp | 40 Boom-0.3/Boom/src/Models/StateSpace/Filters/SparseKalmanTools.cpp | 65 Boom-0.3/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp | 284 +- Boom-0.3/Boom/src/Models/StateSpace/Filters/SparseVector.cpp | 86 Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.cpp |only Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp |only Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp | 9 Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.cpp |only Boom-0.3/Boom/src/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.cpp | 6 Boom-0.3/Boom/src/Models/StateSpace/StateModels/ArStateModel.cpp | 12 Boom-0.3/Boom/src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp | 18 Boom-0.3/Boom/src/Models/StateSpace/StateModels/Holiday.cpp | 6 Boom-0.3/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp | 8 Boom-0.3/Boom/src/Models/StateSpace/StateModels/LocalLinearTrend.cpp | 14 Boom-0.3/Boom/src/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.cpp | 10 Boom-0.3/Boom/src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp | 8 Boom-0.3/Boom/src/Models/StateSpace/StateModels/RegressionStateModel.cpp | 8 Boom-0.3/Boom/src/Models/StateSpace/StateModels/SeasonalStateModel.cpp | 24 Boom-0.3/Boom/src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp | 12 Boom-0.3/Boom/src/Models/StateSpace/StateModels/TrigStateModel.cpp |only Boom-0.3/Boom/src/Models/StateSpace/StateSpaceLogitModel.cpp |only Boom-0.3/Boom/src/Models/StateSpace/StateSpaceModel.cpp | 30 Boom-0.3/Boom/src/Models/StateSpace/StateSpaceModelBase.cpp | 390 +-- Boom-0.3/Boom/src/Models/StateSpace/StateSpaceNormalMixture.cpp |only Boom-0.3/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp |only Boom-0.3/Boom/src/Models/StateSpace/StateSpaceRegressionModel.cpp | 129 - Boom-0.3/Boom/src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp |only Boom-0.3/Boom/src/Models/Sufstat.cpp | 10 Boom-0.3/Boom/src/Models/TimeSeries/ArModel.cpp | 34 Boom-0.3/Boom/src/Models/TimeSeries/NonzeroMeanAr1Model.cpp | 18 Boom-0.3/Boom/src/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.cpp | 25 Boom-0.3/Boom/src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp | 6 Boom-0.3/Boom/src/Models/UniformCorrelationModel.cpp | 6 Boom-0.3/Boom/src/Models/UniformModel.cpp | 10 Boom-0.3/Boom/src/Models/WeightedGaussianSuf.cpp | 14 Boom-0.3/Boom/src/Models/WeightedMvnModel.cpp | 46 Boom-0.3/Boom/src/Models/WishartModel.cpp | 64 Boom-0.3/Boom/src/Models/ZeroInflatedLognormalModel.cpp | 23 Boom-0.3/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 12 Boom-0.3/Boom/src/Models/ZeroMeanGaussianModel.cpp | 18 Boom-0.3/Boom/src/Models/ZeroMeanMvnModel.cpp | 16 Boom-0.3/Boom/src/Samplers/ARMS.cpp | 15 Boom-0.3/Boom/src/Samplers/DirectProposal.cpp |only Boom-0.3/Boom/src/Samplers/ImportanceResampler.cpp |only Boom-0.3/Boom/src/Samplers/MH_Proposals.cpp | 38 Boom-0.3/Boom/src/Samplers/MetropolisHastings.cpp | 83 Boom-0.3/Boom/src/Samplers/RejectionSampler.cpp |only Boom-0.3/Boom/src/Samplers/Sampler.cpp | 10 Boom-0.3/Boom/src/Samplers/ScalarAdaptiveRejectionSampler.cpp |only Boom-0.3/Boom/src/Samplers/ScalarLangevinSampler.cpp |only Boom-0.3/Boom/src/Samplers/ScalarSliceSampler.cpp | 125 Boom-0.3/Boom/src/Samplers/SliceSampler.cpp | 9 Boom-0.3/Boom/src/Samplers/TIM.cpp | 26 Boom-0.3/Boom/src/Samplers/UnivariateLangevinSampler.cpp |only Boom-0.3/Boom/src/Samplers/UnivariateSliceSampler.cpp | 115 Boom-0.3/Boom/src/TargetFun/JacobianChecker.cpp |only Boom-0.3/Boom/src/TargetFun/LogPost.cpp | 12 Boom-0.3/Boom/src/TargetFun/ScalarLogpostTF.cpp | 4 Boom-0.3/Boom/src/TargetFun/TargetFun.cpp | 83 Boom-0.3/Boom/src/TargetFun/Transformation.cpp |only Boom-0.3/Boom/src/boom_r_tools.cpp | 43 Boom-0.3/Boom/src/cpputil/Date.cpp | 39 Boom-0.3/Boom/src/cpputil/ParamHolder.cpp | 12 Boom-0.3/Boom/src/cpputil/lse.cpp | 17 Boom-0.3/Boom/src/cpputil/parse_range.cpp | 4 Boom-0.3/Boom/src/cpputil/print_columns.cpp | 68 Boom-0.3/Boom/src/cpputil/rep.cpp | 10 Boom-0.3/Boom/src/cpputil/split.cpp | 5 Boom-0.3/Boom/src/create_mixture_component.cpp | 88 Boom-0.3/Boom/src/create_state_model.cpp | 70 Boom-0.3/Boom/src/distributions/BoundedAdaptiveRejectionSampler.cpp | 3 Boom-0.3/Boom/src/distributions/DoublyBoundedAdaptiveRejectionSampler.cpp | 5 Boom-0.3/Boom/src/distributions/Markov.cpp | 34 Boom-0.3/Boom/src/distributions/Rmath_dist.cpp | 47 Boom-0.3/Boom/src/distributions/Wishart.cpp | 39 Boom-0.3/Boom/src/distributions/dirichlet.cpp | 36 Boom-0.3/Boom/src/distributions/inverse_gaussian.cpp | 23 Boom-0.3/Boom/src/distributions/matrix_normal.cpp | 32 Boom-0.3/Boom/src/distributions/mvn.cpp | 52 Boom-0.3/Boom/src/distributions/mvt.cpp | 14 Boom-0.3/Boom/src/distributions/random_cor.cpp | 2 Boom-0.3/Boom/src/distributions/rmulti.cpp | 4 Boom-0.3/Boom/src/distributions/rtriangle.cpp | 15 Boom-0.3/Boom/src/distributions/trun_exp.cpp | 55 Boom-0.3/Boom/src/distributions/usp.cpp | 49 Boom-0.3/Boom/src/error.cpp | 2 Boom-0.3/Boom/src/extract_mixture_data.cpp | 18 Boom-0.3/Boom/src/list_io.cpp | 22 Boom-0.3/Boom/src/numopt/Negate.cpp | 6 Boom-0.3/Boom/src/numopt/NumericalDerivatives.cpp |only Boom-0.3/Boom/src/numopt/ScalarLaplaceApproximation.cpp | 26 Boom-0.3/Boom/src/numopt/ScalarNewtonMax.cpp | 9 Boom-0.3/Boom/src/numopt/bfgs.cpp | 23 Boom-0.3/Boom/src/numopt/conj_grad.cpp | 15 Boom-0.3/Boom/src/numopt/max_nd.cpp | 78 Boom-0.3/Boom/src/numopt/nelder_mead.cpp | 18 Boom-0.3/Boom/src/numopt/newton.cpp | 188 - Boom-0.3/Boom/src/numopt/simulated_annealing.cpp | 8 Boom-0.3/Boom/src/prior_specification.cpp | 116 Boom-0.3/Boom/src/spike_slab_prior.cpp | 34 Boom-0.3/Boom/src/stats/Bspline.cpp |only Boom-0.3/Boom/src/stats/ChiSquareTest.cpp | 10 Boom-0.3/Boom/src/stats/DataTable.cpp | 479 ++- Boom-0.3/Boom/src/stats/Design.cpp | 498 +++ Boom-0.3/Boom/src/stats/FreqDist.cpp | 129 - Boom-0.3/Boom/src/stats/IQagent.cpp | 4 Boom-0.3/Boom/src/stats/NaturalSpline.cpp | 53 Boom-0.3/Boom/src/stats/Resampler.cpp | 46 Boom-0.3/Boom/src/stats/Spline.cpp | 12 Boom-0.3/Boom/src/stats/diff.cpp | 10 Boom-0.3/Boom/src/stats/moments.cpp | 30 Boom-0.3/Boom/src/stats/regression.cpp | 7 674 files changed, 16222 insertions(+), 12051 deletions(-)
Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.5-1 dated 2016-02-02 and 0.5-2 dated 2016-03-15
rsdmx-0.5-1/rsdmx/R/Class-SDMXRESTRequestBuilder.R |only rsdmx-0.5-1/rsdmx/R/SDMXRESTRequestBuilder-methods.R |only rsdmx-0.5-1/rsdmx/man/SDMXRESTRequestBuilder.Rd |only rsdmx-0.5-2/rsdmx/DESCRIPTION | 58 + rsdmx-0.5-2/rsdmx/MD5 | 256 ++++---- rsdmx-0.5-2/rsdmx/NAMESPACE | 43 - rsdmx-0.5-2/rsdmx/R/Class-SDMX.R | 3 rsdmx-0.5-2/rsdmx/R/Class-SDMXAttribute.R | 10 rsdmx-0.5-2/rsdmx/R/Class-SDMXCode.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXCodelist.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXCompactData.R | 2 rsdmx-0.5-2/rsdmx/R/Class-SDMXConcept.R | 12 rsdmx-0.5-2/rsdmx/R/Class-SDMXConceptScheme.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXCrossSectionalData.R | 2 rsdmx-0.5-2/rsdmx/R/Class-SDMXData.R |only rsdmx-0.5-2/rsdmx/R/Class-SDMXDataFlow.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXDataStructure.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXDataStructureDefinition.R | 5 rsdmx-0.5-2/rsdmx/R/Class-SDMXDimension.R | 6 rsdmx-0.5-2/rsdmx/R/Class-SDMXDotStatRequestBuilder.R |only rsdmx-0.5-2/rsdmx/R/Class-SDMXFooterMessage.R | 18 rsdmx-0.5-2/rsdmx/R/Class-SDMXGenericData.R | 2 rsdmx-0.5-2/rsdmx/R/Class-SDMXHeader.R | 73 +- rsdmx-0.5-2/rsdmx/R/Class-SDMXMessageGroup.R | 2 rsdmx-0.5-2/rsdmx/R/Class-SDMXPrimaryMeasure.R | 5 rsdmx-0.5-2/rsdmx/R/Class-SDMXREST20RequestBuilder.R |only rsdmx-0.5-2/rsdmx/R/Class-SDMXREST21RequestBuilder.R |only rsdmx-0.5-2/rsdmx/R/Class-SDMXRequestBuilder.R | 35 - rsdmx-0.5-2/rsdmx/R/Class-SDMXRequestParams.R |only rsdmx-0.5-2/rsdmx/R/Class-SDMXSchema.R | 28 rsdmx-0.5-2/rsdmx/R/Class-SDMXStructureSpecificData.R | 2 rsdmx-0.5-2/rsdmx/R/Class-SDMXStructureType.R | 30 rsdmx-0.5-2/rsdmx/R/Class-SDMXTimeDimension.R | 8 rsdmx-0.5-2/rsdmx/R/Class-SDMXType.R | 36 - rsdmx-0.5-2/rsdmx/R/Class-SDMXUtilityData.R | 2 rsdmx-0.5-2/rsdmx/R/SDMX-methods.R | 110 ++- rsdmx-0.5-2/rsdmx/R/SDMXAttribute-methods.R | 13 rsdmx-0.5-2/rsdmx/R/SDMXCode-methods.R | 13 rsdmx-0.5-2/rsdmx/R/SDMXCodelist-methods.R | 14 rsdmx-0.5-2/rsdmx/R/SDMXCodelists-methods.R | 28 rsdmx-0.5-2/rsdmx/R/SDMXCompactData-methods.R | 37 - rsdmx-0.5-2/rsdmx/R/SDMXComponents-methods.R | 111 ++- rsdmx-0.5-2/rsdmx/R/SDMXConcept-methods.R | 13 rsdmx-0.5-2/rsdmx/R/SDMXConceptScheme-methods.R | 16 rsdmx-0.5-2/rsdmx/R/SDMXConcepts-methods.R | 33 - rsdmx-0.5-2/rsdmx/R/SDMXCrossSectionalData-methods.R | 32 - rsdmx-0.5-2/rsdmx/R/SDMXData-methods.R |only rsdmx-0.5-2/rsdmx/R/SDMXDataFlow-methods.R | 41 + rsdmx-0.5-2/rsdmx/R/SDMXDataFlows-methods.R | 33 - rsdmx-0.5-2/rsdmx/R/SDMXDataStructure-methods.R | 10 rsdmx-0.5-2/rsdmx/R/SDMXDataStructureDefinition-methods.R | 13 rsdmx-0.5-2/rsdmx/R/SDMXDataStructures-methods.R | 22 rsdmx-0.5-2/rsdmx/R/SDMXDimension-methods.R | 8 rsdmx-0.5-2/rsdmx/R/SDMXDotStatRequestBuilder-methods.R |only rsdmx-0.5-2/rsdmx/R/SDMXFooter-methods.R | 8 rsdmx-0.5-2/rsdmx/R/SDMXGenericData-methods.R | 42 - rsdmx-0.5-2/rsdmx/R/SDMXHeader-methods.R | 7 rsdmx-0.5-2/rsdmx/R/SDMXMessageGroup-methods.R | 27 rsdmx-0.5-2/rsdmx/R/SDMXPrimaryMeasure-methods.R | 8 rsdmx-0.5-2/rsdmx/R/SDMXREST20RequestBuilder-methods.R |only rsdmx-0.5-2/rsdmx/R/SDMXREST21RequestBuilder-methods.R |only rsdmx-0.5-2/rsdmx/R/SDMXRequestBuilder-methods.R | 55 + rsdmx-0.5-2/rsdmx/R/SDMXRequestParams-methods.R |only rsdmx-0.5-2/rsdmx/R/SDMXSchema-methods.R | 25 rsdmx-0.5-2/rsdmx/R/SDMXServiceProvider-methods.R | 316 +++++++--- rsdmx-0.5-2/rsdmx/R/SDMXServiceProviders-methods.R | 11 rsdmx-0.5-2/rsdmx/R/SDMXStructureSpecificData-methods.R | 15 rsdmx-0.5-2/rsdmx/R/SDMXStructureType-methods.R | 30 rsdmx-0.5-2/rsdmx/R/SDMXTimeDimension-methods.R | 8 rsdmx-0.5-2/rsdmx/R/SDMXType-methods.R | 7 rsdmx-0.5-2/rsdmx/R/SDMXUtilityData-methods.R | 15 rsdmx-0.5-2/rsdmx/R/profile.R | 6 rsdmx-0.5-2/rsdmx/R/readSDMX.R | 171 ++++- rsdmx-0.5-2/rsdmx/R/rsdmx.R | 4 rsdmx-0.5-2/rsdmx/README.md | 150 +++- rsdmx-0.5-2/rsdmx/inst/doc/quickstart.R | 20 rsdmx-0.5-2/rsdmx/inst/doc/quickstart.Rmd | 35 + rsdmx-0.5-2/rsdmx/inst/doc/quickstart.html | 141 +++- rsdmx-0.5-2/rsdmx/man/SDMX.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXAttribute.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXCode.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXCodelist.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXCodelists.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXCompactData.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXComponents.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXConcept.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXConceptScheme.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXConcepts.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXCrossSectionalData.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXData.Rd |only rsdmx-0.5-2/rsdmx/man/SDMXDataFlow.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDataFlows.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDataStructure.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDataStructureDefinition.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDataStructures.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDimension.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXDotStatRequestBuilder.Rd |only rsdmx-0.5-2/rsdmx/man/SDMXFooter.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXGenericData.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXHeader.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXMessageGroup.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXPrimaryMeasure.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXREST20RequestBuilder.Rd |only rsdmx-0.5-2/rsdmx/man/SDMXREST21RequestBuilder.Rd |only rsdmx-0.5-2/rsdmx/man/SDMXRequestBuilder.Rd | 61 + rsdmx-0.5-2/rsdmx/man/SDMXRequestParams.Rd |only rsdmx-0.5-2/rsdmx/man/SDMXSchema.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXServiceProvider.Rd | 2 rsdmx-0.5-2/rsdmx/man/SDMXStructureSpecificData.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXStructureType.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXTimeDimension.Rd | 4 rsdmx-0.5-2/rsdmx/man/SDMXUtilityData.Rd | 4 rsdmx-0.5-2/rsdmx/man/addSDMXServiceProvider.Rd | 2 rsdmx-0.5-2/rsdmx/man/findNamespace.Rd | 5 rsdmx-0.5-2/rsdmx/man/getRegistryInterfaceResult.Rd |only rsdmx-0.5-2/rsdmx/man/isRegistryInterfaceEnvelope.Rd |only rsdmx-0.5-2/rsdmx/man/isSoapRequestEnvelope.Rd | 4 rsdmx-0.5-2/rsdmx/man/readSDMX.Rd | 26 rsdmx-0.5-2/rsdmx/man/rsdmx.Rd | 4 rsdmx-0.5-2/rsdmx/man/setDSD.Rd |only rsdmx-0.5-2/rsdmx/tests/testthat/test_Codelists.R | 10 rsdmx-0.5-2/rsdmx/tests/testthat/test_CompactData.R | 4 rsdmx-0.5-2/rsdmx/tests/testthat/test_Concepts.R | 11 rsdmx-0.5-2/rsdmx/tests/testthat/test_CrossSectionalData.R | 4 rsdmx-0.5-2/rsdmx/tests/testthat/test_Data.R |only rsdmx-0.5-2/rsdmx/tests/testthat/test_DataFlows.R | 5 rsdmx-0.5-2/rsdmx/tests/testthat/test_DataStructureDefinition.R | 8 rsdmx-0.5-2/rsdmx/tests/testthat/test_DataStructures.R | 10 rsdmx-0.5-2/rsdmx/tests/testthat/test_Footer.R | 10 rsdmx-0.5-2/rsdmx/tests/testthat/test_GenericData.R | 12 rsdmx-0.5-2/rsdmx/tests/testthat/test_Header.R | 8 rsdmx-0.5-2/rsdmx/tests/testthat/test_Main_Helpers.R | 230 ++++++- rsdmx-0.5-2/rsdmx/tests/testthat/test_MessageGroup.R | 8 rsdmx-0.5-2/rsdmx/tests/testthat/test_Namespaces.R | 4 rsdmx-0.5-2/rsdmx/tests/testthat/test_RequestBuilder.R | 114 +++ rsdmx-0.5-2/rsdmx/tests/testthat/test_Schema.R | 17 rsdmx-0.5-2/rsdmx/tests/testthat/test_ServiceProvider.R | 39 - rsdmx-0.5-2/rsdmx/tests/testthat/test_Soap.R | 8 rsdmx-0.5-2/rsdmx/tests/testthat/test_StructureSpecificData.R | 4 rsdmx-0.5-2/rsdmx/vignettes/quickstart.Rmd | 35 + 140 files changed, 2154 insertions(+), 925 deletions(-)
Title: Lightweight GitHub Package Installer
Description: A lightweight, vectorized drop-in replacement for 'devtools::install_github()' that uses native git and R methods to clone and install a package from GitHub.
Author: Thomas J. Leeper [aut, cre]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between ghit versions 0.2.0 dated 2016-02-15 and 0.2.5 dated 2016-03-15
DESCRIPTION | 10 ++++--- MD5 | 20 +++++++------- NEWS | 13 +++++++++ R/build_and_insert.R | 2 - R/checkout_pkg.R | 32 ++++++++++++++--------- R/install.R | 56 +++++++++++++++++++++++++++-------------- README.md | 3 ++ man/ghit.Rd | 2 - man/install.Rd | 4 +- tests/testthat/test_install.R | 34 +++++++++++++----------- tests/testthat/test_internal.R | 3 -- 11 files changed, 113 insertions(+), 66 deletions(-)
Title: Digital PCR Analysis
Description: Analysis, visualisation and simulation of digital polymerase chain
reaction (dPCR).
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut],
Bart Jacobs [aut],
Piotr Sobczyk [ctb]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between dpcR versions 0.2 dated 2015-12-11 and 0.3 dated 2016-03-15
CHANGELOG | 111 DESCRIPTION | 42 MD5 | 335 NAMESPACE | 207 R/AUCtest.R | 136 R/BioradCNV.R |only R/White.R | 170 R/adpcr2panel.R | 160 R/adpcr2ppp.R | 136 R/analyze_pooled.R |only R/binarize.R | 92 R/bind_dpcr.R | 400 R/bioamp.R | 152 R/calc_breaks.R | 24 R/calc_coordinates.R | 90 R/calc_lambda.R | 40 R/classes.R | 546 R/compare_dens.R | 118 R/count_test-class.R | 292 R/create_dpcr.R | 146 R/dPCRmethyl.R | 32 R/dpcR-package.R | 140 R/dpcReport_gui.R | 22 R/dpcr_calculator.R | 32 R/dpcr_density.R | 200 R/dpcr_density_gui.R | 24 R/dpcr_density_table.R | 86 R/extract_dpcr.R | 150 R/fit_adpcr.R | 62 R/fl.R | 2 R/get_k_n.R | 24 R/limit_cq.R | 344 R/many_peaks.R | 38 R/moments.R | 194 R/num2int.R | 40 R/pds.R | 162 R/pds_raw.R | 250 R/plot_distr.R | 92 R/plot_panel.R | 290 R/plot_vf_circ.R | 6 R/plot_vic_fam.R | 260 R/print_summary.R | 66 R/qdpcr.R | 190 R/qpcr2pp.R | 238 R/qpcr_analyser.R | 320 R/read_dpcr.R | 426 R/rename_dpcr.R | 54 R/rtadpcr.R | 62 R/safe_efficiency.R | 20 R/show_dpcr.R | 84 R/sim_adpcr.R | 200 R/sim_ddpcr.R | 182 R/sim_ddpcr_bkm.R | 596 - R/simulations.R | 130 R/six_panels.R | 38 R/summary_dpcr.R | 212 R/test_counts.R | 467 R/test_counts_gui.R | 22 R/test_panel.R | 114 R/test_peaks.R | 210 R/test_ratio.R | 306 R/valid_amp.R | 10 R/y_val_conf.R | 26 README.md | 60 build/vignette.rds |binary data/BioradCNV.rda |only data/White.rda |binary data/dPCRmethyl.rda |binary data/datalist | 13 data/many_peaks.rda |binary data/pds.rda |binary data/pds_raw.rda |binary data/six_panels.rda |binary inst/CITATION | 28 inst/doc/overview.R | 496 inst/doc/overview.Rmd | 898 - inst/doc/overview.html | 2032 +-- inst/dpcReport/about.Rmd | 106 inst/dpcReport/about.md | 128 inst/dpcReport/data_summary/data_summary_table1.md | 28 inst/dpcReport/data_summary/summary_input.R | 10 inst/dpcReport/download_report1.md | 22 inst/dpcReport/dpcr.bib | 118 inst/dpcReport/input_file1.md | 36 inst/dpcReport/input_file2.md | 6 inst/dpcReport/plot_panel/plot_panel.R | 24 inst/dpcReport/plot_panel/plot_panel0.md | 4 inst/dpcReport/plot_panel/plot_panel1.md | 10 inst/dpcReport/plot_panel/plot_panel2.md | 2 inst/dpcReport/plot_panel/subpanel_summary.R | 34 inst/dpcReport/plot_panel/test_panel.R | 14 inst/dpcReport/prob_distr/get_kn.R | 20 inst/dpcReport/prob_distr/plot_density.R | 28 inst/dpcReport/prob_distr/prob_distr1.md | 6 inst/dpcReport/prob_distr/prob_distr2.md | 16 inst/dpcReport/prob_distr/prob_distr3.md | 10 inst/dpcReport/prob_distr/prob_distr4.md | 24 inst/dpcReport/prob_distr/single_run_moments.R | 6 inst/dpcReport/r_code_gen.R | 244 inst/dpcReport/report.css | 214 inst/dpcReport/report_template.Rmd | 334 inst/dpcReport/server.R | 1138 +- inst/dpcReport/server_data.R | 216 inst/dpcReport/summary_plots/data_summary_scatterchart1.md | 10 inst/dpcReport/summary_plots/data_summary_scatterchart2.md | 6 inst/dpcReport/summary_plots/summary_exprep_plot.R | 28 inst/dpcReport/summary_plots/summary_plot.R | 22 inst/dpcReport/test_counts/test_counts1.md | 10 inst/dpcReport/test_counts/test_counts2.md | 10 inst/dpcReport/test_counts/test_counts3.md | 2 inst/dpcReport/test_counts/test_counts_group.R | 8 inst/dpcReport/test_counts/test_counts_plot.R | 48 inst/dpcReport/test_counts/test_counts_res.R | 16 inst/dpcReport/ui.R | 264 inst/dpcr_density_gui/server.R | 146 inst/dpcr_density_gui/ui.R | 48 inst/test_counts_gui/readme.md | 20 inst/test_counts_gui/server.R | 92 inst/test_counts_gui/ui.R | 54 man/BioradCNV.Rd |only man/White.Rd | 186 man/adpcr-class.Rd | 114 man/adpcr2panel.Rd | 98 man/adpcr2ppp.Rd | 124 man/analyze_pooled.Rd |only man/binarize.Rd | 72 man/bind_dpcr-methods.Rd | 132 man/bioamp.Rd | 106 man/calc_coordinates.Rd | 64 man/compare_dens.Rd | 74 man/count_test-class.Rd | 134 man/create_dpcr.Rd | 178 man/dPCRmethyl.Rd | 50 man/ddpcr-class.Rd | 86 man/dpcR-package.Rd | 122 man/dpcReport.Rd | 40 man/dpcr-class.Rd | 116 man/dpcr_density.Rd | 152 man/dpcr_density_gui.Rd | 46 man/dpcr_density_table.Rd | 110 man/extract_dpcr.Rd | 120 man/limit_cq.Rd | 198 man/many_peaks.Rd | 46 man/moments-methods.Rd | 116 man/num2int.Rd | 44 man/pds.Rd | 184 man/pds_raw.Rd | 274 man/plot.qdpcr.Rd | 88 man/plot_panel.Rd | 238 man/plot_vic_fam.Rd | 148 man/qdpcr-class.Rd | 66 man/qpcr2pp.Rd | 222 man/qpcr_analyser.Rd | 228 man/read_BioMark.Rd | 60 man/read_QX100.Rd | 56 man/read_dpcr.Rd | 80 man/read_raw.Rd | 64 man/rename_dpcr.Rd | 44 man/rtadpcr-class.Rd | 76 man/show-methods.Rd | 80 man/sim_adpcr.Rd | 234 man/sim_ddpcr.Rd | 176 man/six_panels.Rd | 48 man/summary-methods.Rd | 188 man/test_counts.Rd | 175 man/test_counts_gui.Rd | 46 man/test_panel.Rd | 164 man/test_peaks.Rd | 180 man/test_ratio.Rd | 204 vignettes/dpcr.bib | 7114 ++++++------- vignettes/overview.Rmd | 898 - 171 files changed, 15341 insertions(+), 15251 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.0-0 dated 2015-10-29 and 1.0-1 dated 2016-03-15
VGAM-1.0-0/VGAM/man/expint.Rd |only VGAM-1.0-0/VGAM/man/log1pexp.Rd |only VGAM-1.0-1/VGAM/DESCRIPTION | 8 VGAM-1.0-1/VGAM/MD5 | 414 ++-- VGAM-1.0-1/VGAM/NAMESPACE | 33 VGAM-1.0-1/VGAM/NEWS | 103 + VGAM-1.0-1/VGAM/R/aamethods.q | 66 VGAM-1.0-1/VGAM/R/calibrate.q | 4 VGAM-1.0-1/VGAM/R/cao.R | 2 VGAM-1.0-1/VGAM/R/cao.fit.q | 10 VGAM-1.0-1/VGAM/R/coef.vlm.q | 31 VGAM-1.0-1/VGAM/R/cqo.R | 2 VGAM-1.0-1/VGAM/R/family.actuary.R | 412 ++-- VGAM-1.0-1/VGAM/R/family.aunivariate.R | 164 + VGAM-1.0-1/VGAM/R/family.basics.R | 126 + VGAM-1.0-1/VGAM/R/family.binomial.R | 242 ++ VGAM-1.0-1/VGAM/R/family.bivariate.R | 301 +-- VGAM-1.0-1/VGAM/R/family.categorical.R | 1105 ++++++++++- VGAM-1.0-1/VGAM/R/family.censored.R | 163 - VGAM-1.0-1/VGAM/R/family.circular.R | 153 - VGAM-1.0-1/VGAM/R/family.exp.R | 20 VGAM-1.0-1/VGAM/R/family.extremes.R | 283 ++ VGAM-1.0-1/VGAM/R/family.genetic.R | 29 VGAM-1.0-1/VGAM/R/family.glmgam.R | 131 - VGAM-1.0-1/VGAM/R/family.loglin.R | 49 VGAM-1.0-1/VGAM/R/family.math.R | 96 VGAM-1.0-1/VGAM/R/family.mixture.R | 265 +- VGAM-1.0-1/VGAM/R/family.nonlinear.R | 38 VGAM-1.0-1/VGAM/R/family.normal.R | 204 +- VGAM-1.0-1/VGAM/R/family.others.R | 525 ++++- VGAM-1.0-1/VGAM/R/family.positive.R | 763 +++++-- VGAM-1.0-1/VGAM/R/family.qreg.R | 307 ++- VGAM-1.0-1/VGAM/R/family.rcim.R | 3 VGAM-1.0-1/VGAM/R/family.rcqo.R | 2 VGAM-1.0-1/VGAM/R/family.robust.R | 30 VGAM-1.0-1/VGAM/R/family.rrr.R | 14 VGAM-1.0-1/VGAM/R/family.sur.R | 5 VGAM-1.0-1/VGAM/R/family.survival.R | 60 VGAM-1.0-1/VGAM/R/family.ts.R | 95 VGAM-1.0-1/VGAM/R/family.univariate.R | 1935 +++++++++++-------- VGAM-1.0-1/VGAM/R/family.zeroinf.R | 2636 ++++++++++++++++----------- VGAM-1.0-1/VGAM/R/links.q | 79 VGAM-1.0-1/VGAM/R/lrwaldtest.R | 6 VGAM-1.0-1/VGAM/R/mux.q | 8 VGAM-1.0-1/VGAM/R/plot.vglm.q | 2 VGAM-1.0-1/VGAM/R/predict.vglm.q | 98 - VGAM-1.0-1/VGAM/R/predict.vlm.q | 14 VGAM-1.0-1/VGAM/R/print.vglm.q | 27 VGAM-1.0-1/VGAM/R/qtplot.q | 8 VGAM-1.0-1/VGAM/R/residuals.vlm.q | 4 VGAM-1.0-1/VGAM/R/rrvglm.fit.q | 2 VGAM-1.0-1/VGAM/R/summary.vglm.q | 166 + VGAM-1.0-1/VGAM/R/summary.vlm.q | 5 VGAM-1.0-1/VGAM/R/vgam.control.q | 2 VGAM-1.0-1/VGAM/R/vglm.R | 1 VGAM-1.0-1/VGAM/R/vglm.control.q | 9 VGAM-1.0-1/VGAM/R/vglm.fit.q | 75 VGAM-1.0-1/VGAM/R/vlm.wfit.q | 2 VGAM-1.0-1/VGAM/R/vsmooth.spline.q | 6 VGAM-1.0-1/VGAM/build/vignette.rds |binary VGAM-1.0-1/VGAM/data/Huggins89.t1.rda |binary VGAM-1.0-1/VGAM/data/Huggins89table1.rda |binary VGAM-1.0-1/VGAM/data/alclevels.rda |binary VGAM-1.0-1/VGAM/data/alcoff.rda |binary VGAM-1.0-1/VGAM/data/auuc.rda |binary VGAM-1.0-1/VGAM/data/backPain.rda |binary VGAM-1.0-1/VGAM/data/beggs.rda |binary VGAM-1.0-1/VGAM/data/car.all.rda |binary VGAM-1.0-1/VGAM/data/cfibrosis.rda |binary VGAM-1.0-1/VGAM/data/corbet.rda |binary VGAM-1.0-1/VGAM/data/crashbc.rda |binary VGAM-1.0-1/VGAM/data/crashf.rda |binary VGAM-1.0-1/VGAM/data/crashi.rda |binary VGAM-1.0-1/VGAM/data/crashmc.rda |binary VGAM-1.0-1/VGAM/data/crashp.rda |binary VGAM-1.0-1/VGAM/data/crashtr.rda |binary VGAM-1.0-1/VGAM/data/deermice.rda |binary VGAM-1.0-1/VGAM/data/ducklings.rda |binary VGAM-1.0-1/VGAM/data/finney44.rda |binary VGAM-1.0-1/VGAM/data/flourbeetle.rda |binary VGAM-1.0-1/VGAM/data/hspider.rda |binary VGAM-1.0-1/VGAM/data/lakeO.rda |binary VGAM-1.0-1/VGAM/data/leukemia.rda |binary VGAM-1.0-1/VGAM/data/marital.nz.rda |binary VGAM-1.0-1/VGAM/data/melbmaxtemp.rda |binary VGAM-1.0-1/VGAM/data/pneumo.rda |binary VGAM-1.0-1/VGAM/data/prinia.rda |binary VGAM-1.0-1/VGAM/data/ruge.rda |binary VGAM-1.0-1/VGAM/data/toxop.rda |binary VGAM-1.0-1/VGAM/data/venice.rda |binary VGAM-1.0-1/VGAM/data/venice90.rda |binary VGAM-1.0-1/VGAM/data/wine.rda |binary VGAM-1.0-1/VGAM/inst/doc/categoricalVGAM.pdf |binary VGAM-1.0-1/VGAM/inst/doc/crVGAM.pdf |binary VGAM-1.0-1/VGAM/man/AR1.Rd | 52 VGAM-1.0-1/VGAM/man/CommonVGAMffArguments.Rd | 78 VGAM-1.0-1/VGAM/man/UtilitiesVGAM.Rd |only VGAM-1.0-1/VGAM/man/acat.Rd | 3 VGAM-1.0-1/VGAM/man/alaplace3.Rd | 4 VGAM-1.0-1/VGAM/man/betaII.Rd | 3 VGAM-1.0-1/VGAM/man/betaR.Rd | 4 VGAM-1.0-1/VGAM/man/betabinomUC.Rd | 81 VGAM-1.0-1/VGAM/man/betabinomial.Rd | 10 VGAM-1.0-1/VGAM/man/betabinomialff.Rd | 4 VGAM-1.0-1/VGAM/man/betaff.Rd | 1 VGAM-1.0-1/VGAM/man/bigamma.mckay.Rd | 2 VGAM-1.0-1/VGAM/man/bilogistic.Rd | 3 VGAM-1.0-1/VGAM/man/binom2.or.Rd | 7 VGAM-1.0-1/VGAM/man/binom2.rho.Rd | 37 VGAM-1.0-1/VGAM/man/binormal.Rd | 2 VGAM-1.0-1/VGAM/man/bisa.Rd | 17 VGAM-1.0-1/VGAM/man/bistudentt.Rd | 2 VGAM-1.0-1/VGAM/man/cauchy.Rd | 4 VGAM-1.0-1/VGAM/man/cens.gumbel.Rd | 4 VGAM-1.0-1/VGAM/man/cens.normal.Rd | 14 VGAM-1.0-1/VGAM/man/cloglog.Rd | 1 VGAM-1.0-1/VGAM/man/coefvgam.Rd |only VGAM-1.0-1/VGAM/man/coefvlm.Rd | 3 VGAM-1.0-1/VGAM/man/cratio.Rd | 12 VGAM-1.0-1/VGAM/man/dagum.Rd | 3 VGAM-1.0-1/VGAM/man/double.cens.normal.Rd | 8 VGAM-1.0-1/VGAM/man/double.expbinomial.Rd | 10 VGAM-1.0-1/VGAM/man/expint3.Rd |only VGAM-1.0-1/VGAM/man/fisk.Rd | 3 VGAM-1.0-1/VGAM/man/fittedvlm.Rd | 2 VGAM-1.0-1/VGAM/man/freund61.Rd | 5 VGAM-1.0-1/VGAM/man/gamma2.Rd | 23 VGAM-1.0-1/VGAM/man/gammaR.Rd | 3 VGAM-1.0-1/VGAM/man/genbetaII.Rd | 11 VGAM-1.0-1/VGAM/man/gengamma.Rd | 12 VGAM-1.0-1/VGAM/man/genpoisson.Rd | 3 VGAM-1.0-1/VGAM/man/geometric.Rd | 2 VGAM-1.0-1/VGAM/man/gev.Rd | 13 VGAM-1.0-1/VGAM/man/gpd.Rd | 4 VGAM-1.0-1/VGAM/man/gumbel.Rd | 4 VGAM-1.0-1/VGAM/man/gumbelII.Rd | 3 VGAM-1.0-1/VGAM/man/huber.Rd | 4 VGAM-1.0-1/VGAM/man/inv.gaussianff.Rd | 2 VGAM-1.0-1/VGAM/man/inv.lomax.Rd | 6 VGAM-1.0-1/VGAM/man/inv.paralogistic.Rd | 2 VGAM-1.0-1/VGAM/man/laplace.Rd | 4 VGAM-1.0-1/VGAM/man/lerch.Rd | 3 VGAM-1.0-1/VGAM/man/levy.Rd | 5 VGAM-1.0-1/VGAM/man/lgammaff.Rd | 3 VGAM-1.0-1/VGAM/man/lino.Rd | 4 VGAM-1.0-1/VGAM/man/lms.bcg.Rd | 2 VGAM-1.0-1/VGAM/man/lms.bcn.Rd | 9 VGAM-1.0-1/VGAM/man/lms.yjn.Rd | 4 VGAM-1.0-1/VGAM/man/log1mexp.Rd |only VGAM-1.0-1/VGAM/man/logistic.Rd | 7 VGAM-1.0-1/VGAM/man/logit.Rd | 2 VGAM-1.0-1/VGAM/man/logitoffsetlink.Rd |only VGAM-1.0-1/VGAM/man/loglinb2.Rd | 11 VGAM-1.0-1/VGAM/man/loglinb3.Rd | 8 VGAM-1.0-1/VGAM/man/lognormal.Rd | 8 VGAM-1.0-1/VGAM/man/lomax.Rd | 2 VGAM-1.0-1/VGAM/man/makeham.Rd | 1 VGAM-1.0-1/VGAM/man/margeff.Rd | 94 VGAM-1.0-1/VGAM/man/mccullagh89.Rd | 6 VGAM-1.0-1/VGAM/man/micmen.Rd | 16 VGAM-1.0-1/VGAM/man/mix2exp.Rd | 2 VGAM-1.0-1/VGAM/man/mix2normal.Rd | 7 VGAM-1.0-1/VGAM/man/mix2poisson.Rd | 2 VGAM-1.0-1/VGAM/man/multinomial.Rd | 3 VGAM-1.0-1/VGAM/man/nbcanlink.Rd | 10 VGAM-1.0-1/VGAM/man/negbinomial.Rd | 198 +- VGAM-1.0-1/VGAM/man/negbinomial.size.Rd | 2 VGAM-1.0-1/VGAM/man/normal.vcm.Rd | 5 VGAM-1.0-1/VGAM/man/notdocumentedyet.Rd | 31 VGAM-1.0-1/VGAM/man/ozibetaUC.Rd |only VGAM-1.0-1/VGAM/man/paralogistic.Rd | 4 VGAM-1.0-1/VGAM/man/pgamma.deriv.Rd | 3 VGAM-1.0-1/VGAM/man/poissonff.Rd | 2 VGAM-1.0-1/VGAM/man/posnegbinomial.Rd | 95 VGAM-1.0-1/VGAM/man/posnormal.Rd | 4 VGAM-1.0-1/VGAM/man/pospoisson.Rd | 11 VGAM-1.0-1/VGAM/man/prentice74.Rd | 7 VGAM-1.0-1/VGAM/man/quasibinomialff.Rd | 3 VGAM-1.0-1/VGAM/man/quasipoissonff.Rd | 5 VGAM-1.0-1/VGAM/man/rec.normal.Rd | 3 VGAM-1.0-1/VGAM/man/riceff.Rd | 4 VGAM-1.0-1/VGAM/man/sc.studentt2.Rd | 2 VGAM-1.0-1/VGAM/man/simplex.Rd | 7 VGAM-1.0-1/VGAM/man/sinmad.Rd | 3 VGAM-1.0-1/VGAM/man/skellam.Rd | 2 VGAM-1.0-1/VGAM/man/slash.Rd | 3 VGAM-1.0-1/VGAM/man/sratio.Rd | 4 VGAM-1.0-1/VGAM/man/studentt.Rd | 4 VGAM-1.0-1/VGAM/man/summaryvglm.Rd | 20 VGAM-1.0-1/VGAM/man/tikuv.Rd | 10 VGAM-1.0-1/VGAM/man/tobit.Rd | 6 VGAM-1.0-1/VGAM/man/truncweibull.Rd | 6 VGAM-1.0-1/VGAM/man/undocumented-methods.Rd | 44 VGAM-1.0-1/VGAM/man/uninormal.Rd | 2 VGAM-1.0-1/VGAM/man/vglmff-class.Rd | 10 VGAM-1.0-1/VGAM/man/vonmises.Rd | 5 VGAM-1.0-1/VGAM/man/weibull.mean.Rd | 2 VGAM-1.0-1/VGAM/man/weibullR.Rd | 3 VGAM-1.0-1/VGAM/man/yip88.Rd | 10 VGAM-1.0-1/VGAM/man/zabinomial.Rd | 17 VGAM-1.0-1/VGAM/man/zageometric.Rd | 6 VGAM-1.0-1/VGAM/man/zanegbinomial.Rd | 74 VGAM-1.0-1/VGAM/man/zapoisson.Rd | 31 VGAM-1.0-1/VGAM/man/zero.Rd | 13 VGAM-1.0-1/VGAM/man/zeta.Rd | 11 VGAM-1.0-1/VGAM/man/zetaff.Rd | 2 VGAM-1.0-1/VGAM/man/zibinomial.Rd | 16 VGAM-1.0-1/VGAM/man/zigeometric.Rd | 6 VGAM-1.0-1/VGAM/man/zinegbinomial.Rd | 137 + VGAM-1.0-1/VGAM/man/zipebcom.Rd | 2 VGAM-1.0-1/VGAM/man/zipoisson.Rd | 43 VGAM-1.0-1/VGAM/src/tyeepolygamma3.c | 52 212 files changed, 9011 insertions(+), 3946 deletions(-)
Title: Convert R Markdown Files to DataCamp Light HTML Files
Description: DataCamp Light (<https://github.com/datacamp/datacamp-light>) is a light-weight implementation of the DataCamp UI,
that allows you to embed interactive exercises inside HTML documents. The 'tutorial' package makes it easy to create these
HTML files from R Markdown files. A wrapper around the 'rmarkdown' package, 'tutorial' pre-detects code chunks with the 'ex' and 'type'
properties, and replaces the chunks with DataCamp Light readable chunks in the resulting HTML file.
Author: Filip Schouwenaars
Maintainer: Filip Schouwenaars <filip@datacamp.com>
Diff between tutorial versions 0.2.1 dated 2016-03-14 and 0.2.2 dated 2016-03-15
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- README.md | 1 + 3 files changed, 8 insertions(+), 5 deletions(-)
Title: Calculate Agreement or Consensus in Ordered Rating Scales
Description: Calculate agreement or consensus in ordered rating scales. The package implements van der Eijk's (2001) measure of agreement A, which can be used to describe agreement, consensus, or polarization among respondents. It also implements measures of consensus (dispersion) by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, and Garcia-Montalvo and Reynal-Querol. Furthermore, an implementation of Galtungs AJUS-system is provided to classify distributions, as well as a function to identify the position of multiple modes.
Author: Didier Ruedin
Maintainer: Didier Ruedin <didier.ruedin@wolfson.oxon.org>
Diff between agrmt versions 1.39.3 dated 2015-12-07 and 1.40.1 dated 2016-03-15
DESCRIPTION | 14 - MD5 | 21 - NEWS |only R/MRQ.R | 2 build/vignette.rds |binary inst/doc/agrmt.R | 38 +-- inst/doc/agrmt.Rnw | 580 ++++++++++++++++++++++++++++------------------------ inst/doc/agrmt.pdf |binary man/MRQ.Rd | 17 + man/consensus.Rd | 2 vignettes/agrmt.Rnw | 580 ++++++++++++++++++++++++++++------------------------ vignettes/agrmt.bib | 96 ++++++-- 12 files changed, 755 insertions(+), 595 deletions(-)
Title: Optimization of Sample Configurations using Spatial Simulated
Annealing
Description: Methods to optimize spatial sample configurations using spatial simulated annealing. Multiple
objective functions are implemented for various purposes, such as variogram estimation, spatial trend
estimation, and spatial interpolation. A general purpose spatial simulated annealing function enables the
user to define his/her own objective function.
Author: Alessandro Samuel-Rosa [aut, cre],
Lucia Helena Cunha dos Anjos [ths],
Gustavo de Mattos Vasques [ths],
Gerard B M Heuvelink [ths],
Edzer Pebesma [ctb],
Jon Skoien [ctb],
Joshua French [ctb],
Pierre Roudier [ctb],
Dick Brus [ctb],
Murray Lark [ctb]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between spsann versions 1.0-2 dated 2015-10-25 and 2.0-0 dated 2016-03-15
spsann-1.0-2/spsann/man/spJitterFinite.Rd |only spsann-2.0-0/spsann/DESCRIPTION | 53 -- spsann-2.0-0/spsann/MD5 | 90 ++-- spsann-2.0-0/spsann/NAMESPACE | 8 spsann-2.0-0/spsann/NEWS.md |only spsann-2.0-0/spsann/R/AAA.R | 11 spsann-2.0-0/spsann/R/SPSANNtools.R | 111 ++--- spsann-2.0-0/spsann/R/ZZZ.R |only spsann-2.0-0/spsann/R/check-first-chain.R |only spsann-2.0-0/spsann/R/check-spsann-arguments.R | 46 -- spsann-2.0-0/spsann/R/check-suggests.R | 3 spsann-2.0-0/spsann/R/minmaxPareto.R |only spsann-2.0-0/spsann/R/optimACDC.R | 408 ++++++++---------- spsann-2.0-0/spsann/R/optimCLHS.R | 394 ++++++++--------- spsann-2.0-0/spsann/R/optimCORR.R | 315 +++++++------- spsann-2.0-0/spsann/R/optimDIST.R | 273 +++++++----- spsann-2.0-0/spsann/R/optimMKV.R | 316 +++++++------- spsann-2.0-0/spsann/R/optimMSSD.R | 268 ++++++------ spsann-2.0-0/spsann/R/optimPPL.R | 389 ++++++++++------- spsann-2.0-0/spsann/R/optimSPAN.R | 448 ++++++++++---------- spsann-2.0-0/spsann/R/optimUSER.R | 214 ++++----- spsann-2.0-0/spsann/R/plot-and-jitter.R | 24 - spsann-2.0-0/spsann/R/plot-method.R |only spsann-2.0-0/spsann/R/plotting-options.R | 6 spsann-2.0-0/spsann/R/prepare-acdc-covars.R | 7 spsann-2.0-0/spsann/R/prepare-jittering.R | 34 - spsann-2.0-0/spsann/R/prepare-output.R | 66 ++ spsann-2.0-0/spsann/R/prepare-points.R | 27 - spsann-2.0-0/spsann/R/scheduleSPSANN.R |only spsann-2.0-0/spsann/R/set-progress.R |only spsann-2.0-0/spsann/R/spJitter.R | 195 ++++++-- spsann-2.0-0/spsann/R/spsann.R | 166 ++++--- spsann-2.0-0/spsann/R/update-progress.R |only spsann-2.0-0/spsann/README.md | 2 spsann-2.0-0/spsann/build |only spsann-2.0-0/spsann/inst |only spsann-2.0-0/spsann/man/SPSANNtools.Rd | 18 spsann-2.0-0/spsann/man/minmaxPareto.Rd |only spsann-2.0-0/spsann/man/optimACDC.Rd | 479 +++++---------------- spsann-2.0-0/spsann/man/optimCLHS.Rd | 382 +++++------------ spsann-2.0-0/spsann/man/optimCORR.Rd | 400 ++++-------------- spsann-2.0-0/spsann/man/optimDIST.Rd | 427 ++++--------------- spsann-2.0-0/spsann/man/optimMKV.Rd | 352 +++------------ spsann-2.0-0/spsann/man/optimMSSD.Rd | 331 +++----------- spsann-2.0-0/spsann/man/optimPPL.Rd | 455 ++++++-------------- spsann-2.0-0/spsann/man/optimSPAN.Rd | 553 +++++-------------------- spsann-2.0-0/spsann/man/optimUSER.Rd | 304 ++----------- spsann-2.0-0/spsann/man/plot-method.Rd |only spsann-2.0-0/spsann/man/scheduleSPSANN.Rd |only spsann-2.0-0/spsann/man/spJitter.Rd |only spsann-2.0-0/spsann/man/spsann-package.Rd | 163 ++++--- spsann-2.0-0/spsann/src/spJitterCpp.cpp | 2 spsann-2.0-0/spsann/vignettes |only 53 files changed, 3146 insertions(+), 4594 deletions(-)
Title: Numerical Estimation of Sparse Hessians
Description: Estimates Hessian of a scalar-valued function, and returns it
in a sparse Matrix format. The sparsity pattern must be known in advance. The
algorithm is especially efficient for hierarchical models with a large number of
heterogeneous units.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>
Diff between sparseHessianFD versions 0.2.0 dated 2015-02-04 and 0.3.0 dated 2016-03-15
sparseHessianFD-0.2.0/sparseHessianFD/LICENSE |only sparseHessianFD-0.2.0/sparseHessianFD/R/sparseHessianFD-new.R |only sparseHessianFD-0.2.0/sparseHessianFD/inst/Rfunc_old.cpp |only sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.Rmd |only sparseHessianFD-0.2.0/sparseHessianFD/inst/doc/sparseHessianFD.html |only sparseHessianFD-0.2.0/sparseHessianFD/inst/examples |only sparseHessianFD-0.2.0/sparseHessianFD/inst/include |only sparseHessianFD-0.2.0/sparseHessianFD/inst/misc |only sparseHessianFD-0.2.0/sparseHessianFD/man/Coord.to.Pattern.Matrix.Rd |only sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD-deprecated.Rd |only sparseHessianFD-0.2.0/sparseHessianFD/man/sparseHessianFD.new.Rd |only sparseHessianFD-0.2.0/sparseHessianFD/src/FDHS-DSSM.c |only sparseHessianFD-0.2.0/sparseHessianFD/src/rcpp_module.cpp |only sparseHessianFD-0.2.0/sparseHessianFD/vignettes/sparseHessianFD.Rmd |only sparseHessianFD-0.3.0/sparseHessianFD/DESCRIPTION | 40 - sparseHessianFD-0.3.0/sparseHessianFD/MD5 | 81 +-- sparseHessianFD-0.3.0/sparseHessianFD/NAMESPACE | 4 sparseHessianFD-0.3.0/sparseHessianFD/NEWS | 30 + sparseHessianFD-0.3.0/sparseHessianFD/NEWS.md |only sparseHessianFD-0.3.0/sparseHessianFD/R/RcppExports.R |only sparseHessianFD-0.3.0/sparseHessianFD/R/binary-data.R | 32 + sparseHessianFD-0.3.0/sparseHessianFD/R/binary.R | 83 +-- sparseHessianFD-0.3.0/sparseHessianFD/R/coloring.R |only sparseHessianFD-0.3.0/sparseHessianFD/R/deprecated.R | 87 ++- sparseHessianFD-0.3.0/sparseHessianFD/R/matrices.R | 249 +++++++-- sparseHessianFD-0.3.0/sparseHessianFD/R/sparseHessianFD-class.R | 267 ++++++++-- sparseHessianFD-0.3.0/sparseHessianFD/R/sparseHessianFD.R | 37 - sparseHessianFD-0.3.0/sparseHessianFD/build/vignette.rds |binary sparseHessianFD-0.3.0/sparseHessianFD/data/binary.rda |binary sparseHessianFD-0.3.0/sparseHessianFD/data/binary_large.rda |only sparseHessianFD-0.3.0/sparseHessianFD/data/binary_small.rda |only sparseHessianFD-0.3.0/sparseHessianFD/data/binary_super.rda |only sparseHessianFD-0.3.0/sparseHessianFD/inst/CITATION | 3 sparseHessianFD-0.3.0/sparseHessianFD/inst/doc/sparseHessianFD.R | 116 ++-- sparseHessianFD-0.3.0/sparseHessianFD/inst/doc/sparseHessianFD.Rnw |only sparseHessianFD-0.3.0/sparseHessianFD/inst/doc/sparseHessianFD.pdf |only sparseHessianFD-0.3.0/sparseHessianFD/man/Coord.to.Pointers.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/man/Matrix.to.Coord.Rd | 34 - sparseHessianFD-0.3.0/sparseHessianFD/man/Matrix.to.Pointers.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/man/binary-data.Rd | 26 sparseHessianFD-0.3.0/sparseHessianFD/man/binary.Rd | 30 - sparseHessianFD-0.3.0/sparseHessianFD/man/coloring.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/man/deprecated.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/man/get_colors.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/man/sparseHessianFD-class.Rd | 111 +++- sparseHessianFD-0.3.0/sparseHessianFD/man/sparseHessianFD-package.Rd | 47 - sparseHessianFD-0.3.0/sparseHessianFD/man/subst.Rd |only sparseHessianFD-0.3.0/sparseHessianFD/src/Makevars | 4 sparseHessianFD-0.3.0/sparseHessianFD/src/Makevars.win | 8 sparseHessianFD-0.3.0/sparseHessianFD/src/RcppExports.cpp |only sparseHessianFD-0.3.0/sparseHessianFD/src/color.cpp |only sparseHessianFD-0.3.0/sparseHessianFD/src/subst.cpp |only sparseHessianFD-0.3.0/sparseHessianFD/tests/testthat/test_binary.R | 101 +-- sparseHessianFD-0.3.0/sparseHessianFD/tests/testthat/test_mat2.R |only sparseHessianFD-0.3.0/sparseHessianFD/tests/testthat/test_matrices.R | 127 +++- sparseHessianFD-0.3.0/sparseHessianFD/vignettes/fig_timings.pdf |only sparseHessianFD-0.3.0/sparseHessianFD/vignettes/sparseHessianFD.Rnw |only sparseHessianFD-0.3.0/sparseHessianFD/vignettes/sparseHessianFD.bib |only sparseHessianFD-0.3.0/sparseHessianFD/vignettes/timings.pdf |only 59 files changed, 1092 insertions(+), 425 deletions(-)
More information about sparseHessianFD at CRAN
Permanent link
Title: Multichannel Wavelet Deconvolution with Additive Long Memory
Noise
Description: Computes the Wavelet deconvolution estimate of a common signal
present in multiple channels that have possible different levels of blur
and long memory additive error.
Author: Justin Rory Wishart
Maintainer: Justin Rory Wishart <justin.wishart@mq.edu.au>
Diff between mwaved versions 1.1.1 dated 2015-01-07 and 1.1.2 dated 2016-03-15
DESCRIPTION | 11 MD5 | 68 +- NAMESPACE | 19 R/RcppExports.R |only R/functions.R | 1210 +++++++++++++++++++++++----------------------- R/makeFunctions.R | 1 build/vignette.rds |binary cleanup | 2 inst/doc/mWaveD.R | 578 ++++++++++----------- inst/doc/mWaveD.html | 1182 +++++++++++++++++++++++--------------------- inst/mWaveDDemo/rsconnect |only inst/mWaveDDemo/ui.R | 160 +++--- man/blurSignal.Rd | 3 man/boxcarBlur.Rd | 2 man/detectBlur.Rd | 2 man/directBlur.Rd | 2 man/gammaBlur.Rd | 2 man/mWaveDDemo.Rd | 2 man/makeSignals.Rd | 2 man/multiCoef.Rd | 2 man/multiEstimate.Rd | 5 man/multiNoise.Rd | 2 man/multiProj.Rd | 6 man/multiSigma.Rd | 3 man/multiThresh.Rd | 3 man/multiWaveD.Rd | 5 man/mwaved.Rd | 2 man/plot.mWaveD.Rd | 2 man/plot.waveletCoef.Rd | 2 man/resolutionMethod.Rd | 2 man/sigmaSNR.Rd | 4 man/summary.mWaveD.Rd | 4 man/theoreticalEta.Rd | 2 man/waveletThresh.Rd | 14 src/Makevars.win | 2 src/RcppExports.cpp | 258 ++++----- 36 files changed, 1801 insertions(+), 1763 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: Spencer Aiello, Tom Kraljevic and Petr Maj, with contributions from the
H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.6.0.8 dated 2015-11-24 and 3.8.1.3 dated 2016-03-15
h2o-3.6.0.8/h2o/man/Frame-Extract.Rd |only h2o-3.6.0.8/h2o/man/Frame.Rd |only h2o-3.6.0.8/h2o/man/as.character.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.data.frame.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.matrix.Frame.Rd |only h2o-3.6.0.8/h2o/man/as.vector.Rd |only h2o-3.6.0.8/h2o/man/dim.Frame.Rd |only h2o-3.6.0.8/h2o/man/dimnames.Frame.Rd |only h2o-3.6.0.8/h2o/man/h2o.startGLMJob.Rd |only h2o-3.6.0.8/h2o/man/names.Frame.Rd |only h2o-3.6.0.8/h2o/man/print.Frame.Rd |only h2o-3.6.0.8/h2o/man/range.Frame.Rd |only h2o-3.6.0.8/h2o/man/str.Frame.Rd |only h2o-3.8.1.3/h2o/DESCRIPTION | 8 h2o-3.8.1.3/h2o/MD5 | 303 +- h2o-3.8.1.3/h2o/NAMESPACE | 121 - h2o-3.8.1.3/h2o/NEWS |only h2o-3.8.1.3/h2o/R/astfun.R | 6 h2o-3.8.1.3/h2o/R/classes.R | 46 h2o-3.8.1.3/h2o/R/communication.R | 64 h2o-3.8.1.3/h2o/R/connection.R | 142 - h2o-3.8.1.3/h2o/R/constants.R | 19 h2o-3.8.1.3/h2o/R/deeplearning.R | 156 - h2o-3.8.1.3/h2o/R/export.R | 19 h2o-3.8.1.3/h2o/R/frame.R | 1144 ++++++----- h2o-3.8.1.3/h2o/R/gbm.R | 39 h2o-3.8.1.3/h2o/R/glm.R | 230 +- h2o-3.8.1.3/h2o/R/glrm.R | 108 - h2o-3.8.1.3/h2o/R/grid.R | 46 h2o-3.8.1.3/h2o/R/import.R | 11 h2o-3.8.1.3/h2o/R/kmeans.R | 23 h2o-3.8.1.3/h2o/R/kvstore.R | 42 h2o-3.8.1.3/h2o/R/models.R | 613 +++-- h2o-3.8.1.3/h2o/R/naivebayes.R | 16 h2o-3.8.1.3/h2o/R/parse.R | 14 h2o-3.8.1.3/h2o/R/pca.R | 35 h2o-3.8.1.3/h2o/R/randomforest.R | 35 h2o-3.8.1.3/h2o/R/svd.R | 15 h2o-3.8.1.3/h2o/R/word2vec.R | 12 h2o-3.8.1.3/h2o/inst/branch.txt | 2 h2o-3.8.1.3/h2o/inst/buildnum.txt | 2 h2o-3.8.1.3/h2o/man/H2OClusteringModel-class.Rd | 2 h2o-3.8.1.3/h2o/man/H2OConnection-class.Rd | 2 h2o-3.8.1.3/h2o/man/H2OFrame-Extract.Rd |only h2o-3.8.1.3/h2o/man/H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/H2OGrid-class.Rd | 2 h2o-3.8.1.3/h2o/man/H2OModel-class.Rd | 2 h2o-3.8.1.3/h2o/man/Logical-or.Rd |only h2o-3.8.1.3/h2o/man/and-and.Rd |only h2o-3.8.1.3/h2o/man/apply.Rd | 6 h2o-3.8.1.3/h2o/man/as.character.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/as.data.frame.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/as.factor.Rd | 2 h2o-3.8.1.3/h2o/man/as.h2o.Rd | 4 h2o-3.8.1.3/h2o/man/as.matrix.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/as.numeric.Rd | 2 h2o-3.8.1.3/h2o/man/as.vector.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/colnames.Rd | 6 h2o-3.8.1.3/h2o/man/dim.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/dimnames.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/h2o-package.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.aic.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.anomaly.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.anyFactor.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.assign.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.auc.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.betweenss.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.biases.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.cbind.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.centers.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.centersSTD.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.centroid_stats.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.cluster_sizes.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.confusionMatrix.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.createFrame.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.cut.Rd | 8 h2o-3.8.1.3/h2o/man/h2o.day.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.dayOfWeek.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.dct.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.ddply.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.deepfeatures.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.deeplearning.Rd | 146 - h2o-3.8.1.3/h2o/man/h2o.describe.Rd |only h2o-3.8.1.3/h2o/man/h2o.downloadCSV.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.download_pojo.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.entropy.Rd |only h2o-3.8.1.3/h2o/man/h2o.exportFile.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.gainsLift.Rd |only h2o-3.8.1.3/h2o/man/h2o.gbm.Rd | 36 h2o-3.8.1.3/h2o/man/h2o.getGrid.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.getId.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.getTypes.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.giniCoef.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.glm.Rd | 52 h2o-3.8.1.3/h2o/man/h2o.glrm.Rd | 29 h2o-3.8.1.3/h2o/man/h2o.grid.Rd | 27 h2o-3.8.1.3/h2o/man/h2o.group_by.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.head.Rd | 14 h2o-3.8.1.3/h2o/man/h2o.hist.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.hit_ratio_table.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.hour.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.importFile.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.impute.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.init.Rd | 26 h2o-3.8.1.3/h2o/man/h2o.insertMissingValues.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.interaction.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.kmeans.Rd | 17 h2o-3.8.1.3/h2o/man/h2o.levels.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.logloss.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.lstrip.Rd |only h2o-3.8.1.3/h2o/man/h2o.match.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.mean.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.mean_residual_deviance.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.median.Rd | 8 h2o-3.8.1.3/h2o/man/h2o.merge.Rd | 20 h2o-3.8.1.3/h2o/man/h2o.metric.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.month.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.mse.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.nacnt.Rd |only h2o-3.8.1.3/h2o/man/h2o.naiveBayes.Rd | 11 h2o-3.8.1.3/h2o/man/h2o.nlevels.Rd |only h2o-3.8.1.3/h2o/man/h2o.no_progress.Rd |only h2o-3.8.1.3/h2o/man/h2o.null_deviance.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.null_dof.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.parseRaw.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.parseSetup.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.performance.Rd | 15 h2o-3.8.1.3/h2o/man/h2o.prcomp.Rd | 32 h2o-3.8.1.3/h2o/man/h2o.pro_substrings_words.Rd |only h2o-3.8.1.3/h2o/man/h2o.proj_archetypes.Rd |only h2o-3.8.1.3/h2o/man/h2o.quantile.Rd | 18 h2o-3.8.1.3/h2o/man/h2o.r2.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.randomForest.Rd | 33 h2o-3.8.1.3/h2o/man/h2o.rbind.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.reconstruct.Rd |only h2o-3.8.1.3/h2o/man/h2o.removeVecs.Rd | 6 h2o-3.8.1.3/h2o/man/h2o.rep_len.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.residual_deviance.Rd | 5 h2o-3.8.1.3/h2o/man/h2o.residual_dof.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.rm.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.round.Rd |only h2o-3.8.1.3/h2o/man/h2o.rstrip.Rd |only h2o-3.8.1.3/h2o/man/h2o.runif.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.scale.Rd | 8 h2o-3.8.1.3/h2o/man/h2o.scoreHistory.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.sd.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.show_progress.Rd |only h2o-3.8.1.3/h2o/man/h2o.signif.Rd |only h2o-3.8.1.3/h2o/man/h2o.splitFrame.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.substring.Rd |only h2o-3.8.1.3/h2o/man/h2o.summary.Rd | 19 h2o-3.8.1.3/h2o/man/h2o.svd.Rd | 8 h2o-3.8.1.3/h2o/man/h2o.table.Rd | 15 h2o-3.8.1.3/h2o/man/h2o.tabulate.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.tolower.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.tot_withinss.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.totss.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.toupper.Rd | 2 h2o-3.8.1.3/h2o/man/h2o.unique.Rd |only h2o-3.8.1.3/h2o/man/h2o.var.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.varimp.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.week.Rd | 10 h2o-3.8.1.3/h2o/man/h2o.weights.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.which.Rd |only h2o-3.8.1.3/h2o/man/h2o.withinss.Rd | 4 h2o-3.8.1.3/h2o/man/h2o.year.Rd | 10 h2o-3.8.1.3/h2o/man/is.character.Rd |only h2o-3.8.1.3/h2o/man/is.factor.Rd | 2 h2o-3.8.1.3/h2o/man/is.numeric.Rd | 2 h2o-3.8.1.3/h2o/man/na.omit.Rd | 8 h2o-3.8.1.3/h2o/man/names.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/predict.H2OModel.Rd | 8 h2o-3.8.1.3/h2o/man/predict_leaf_node_assignment.H2OModel.Rd |only h2o-3.8.1.3/h2o/man/print.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/range.H2OFrame.Rd |only h2o-3.8.1.3/h2o/man/str.H2OFrame.Rd |only 176 files changed, 2540 insertions(+), 1652 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.6 dated 2015-12-23 and 4.7 dated 2016-03-15
ftsa-4.6/ftsa/R/DataPostProc.R |only ftsa-4.6/ftsa/R/L1median2.R |only ftsa-4.6/ftsa/R/MISE.R |only ftsa-4.6/ftsa/R/ParseControlStructure.R |only ftsa-4.6/ftsa/R/ParseDevString.R |only ftsa-4.6/ftsa/R/Qn.R |only ftsa-4.6/ftsa/R/ScaleAdv.R |only ftsa-4.6/ftsa/R/aveISFE.R |only ftsa-4.6/ftsa/R/colQn.R |only ftsa-4.6/ftsa/R/hossjercroux.R |only ftsa-4.6/ftsa/R/hyman.filter.R |only ftsa-4.6/ftsa/R/isfe.fts.R |only ftsa-4.6/ftsa/R/loadSgnU.R |only ftsa-4.6/ftsa/R/matrix.rank.R |only ftsa-4.6/ftsa/R/metri.p.R |only ftsa-4.6/ftsa/R/mrobj.R |only ftsa-4.6/ftsa/R/nicerange.R |only ftsa-4.6/ftsa/R/norm.R |only ftsa-4.6/ftsa/R/norme.R |only ftsa-4.6/ftsa/R/pegelsna.R |only ftsa-4.6/ftsa/R/rapca.R |only ftsa-4.6/ftsa/R/repmat.R |only ftsa-4.6/ftsa/R/rstep.R |only ftsa-4.6/ftsa/R/rw.drift.R |only ftsa-4.6/ftsa/R/spl.coef.conv.R |only ftsa-4.6/ftsa/R/struct.forecast.R |only ftsa-4.7/ftsa/ChangeLog | 4 ftsa-4.7/ftsa/DESCRIPTION | 10 - ftsa-4.7/ftsa/MD5 | 85 +++++---- ftsa-4.7/ftsa/R/DataPostProc.r |only ftsa-4.7/ftsa/R/L1median2.r |only ftsa-4.7/ftsa/R/MISE.r |only ftsa-4.7/ftsa/R/ParseControlStructure.r |only ftsa-4.7/ftsa/R/ParseDevString.r |only ftsa-4.7/ftsa/R/Qn.r |only ftsa-4.7/ftsa/R/ScaleAdv.r |only ftsa-4.7/ftsa/R/aveISFE.r |only ftsa-4.7/ftsa/R/colQn.r |only ftsa-4.7/ftsa/R/farforecast.R | 6 ftsa-4.7/ftsa/R/hossjercroux.r |only ftsa-4.7/ftsa/R/hyman.filter.r |only ftsa-4.7/ftsa/R/isfe.fts.r |only ftsa-4.7/ftsa/R/loadSgnU.r |only ftsa-4.7/ftsa/R/matrix.rank.r |only ftsa-4.7/ftsa/R/metri.p.r |only ftsa-4.7/ftsa/R/mrobj.r |only ftsa-4.7/ftsa/R/nicerange.r |only ftsa-4.7/ftsa/R/norm.r |only ftsa-4.7/ftsa/R/norme.r |only ftsa-4.7/ftsa/R/pegelsna.r |only ftsa-4.7/ftsa/R/rapca.r |only ftsa-4.7/ftsa/R/repmat.r |only ftsa-4.7/ftsa/R/rstep.r |only ftsa-4.7/ftsa/R/rw.drift.r |only ftsa-4.7/ftsa/R/spl.coef.conv.r |only ftsa-4.7/ftsa/R/struct.forecast.r |only ftsa-4.7/ftsa/build/vignette.rds |binary ftsa-4.7/ftsa/inst/doc/ftsa.Rnw | 4 ftsa-4.7/ftsa/inst/doc/ftsa.pdf |binary ftsa-4.7/ftsa/inst/doc/ftsa_test.Rnw |only ftsa-4.7/ftsa/inst/doc/ftsa_test.pdf |only ftsa-4.7/ftsa/man/MFDM.Rd | 6 ftsa-4.7/ftsa/man/dynamic_FLR.Rd | 2 ftsa-4.7/ftsa/man/farforecast.Rd | 2 ftsa-4.7/ftsa/man/forecast.ftsm.Rd | 2 ftsa-4.7/ftsa/man/fplsr.Rd | 266 +++++++++++++++--------------- ftsa-4.7/ftsa/man/ftsa-package.Rd | 4 ftsa-4.7/ftsa/vignettes/KokoszkaShang.bib |only ftsa-4.7/ftsa/vignettes/ftsa.Rnw | 4 ftsa-4.7/ftsa/vignettes/ftsa_test.Rnw |only ftsa-4.7/ftsa/vignettes/ibm.pdf |only ftsa-4.7/ftsa/vignettes/pm10.pdf |only ftsa-4.7/ftsa/vignettes/pm10_ftsm.pdf |only 73 files changed, 204 insertions(+), 191 deletions(-)
Title: Analyzing Dichotomous Choice Contingent Valuation Data
Description: Functions for analyzing dichotomous choice contingent valuation (CV) data. It provides
functions for estimating parametric and nonparametric models for single- and double-bounded
CV data.
Author: Tomoaki Nakatani [aut, cph] (original developer),
Hideo Aizaki [aut, cre] (code patches),
Kazuo Sato [ctb] (theoretical part of the manual)
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between DCchoice versions 0.0.13-3 dated 2015-09-15 and 0.0.14 dated 2016-03-15
DESCRIPTION | 11 - MD5 | 55 +++-- NAMESPACE | 16 + R/bootCI.R | 31 ++ R/dbchoice.R | 116 ++++------ R/krCI.R | 19 + R/kristrom.R | 11 - R/logLik.dbchoice.R |only R/logLik.sbchoice.R |only R/plot.dbchoice.R |only R/plot.sbchoice.R |only R/predict.dbchoice.R |only R/predict.sbchoice.R |only R/sbchoice.R | 131 +++++------- R/turnbull_db.R | 14 + R/turnbull_sb.R | 11 - R/update.dbchoice.R |only R/update.sbchoice.R |only R/vcov.dbchoice.R |only R/vcov.sbchoice.R |only R/wtp.R |only inst/CITATION | 38 +-- man/bootCI.Rd | 6 man/dbchoice.Rd | 522 ++++++++++++++++++++++++++---------------------- man/krCI.Rd | 6 man/kristrom.Rd | 245 +++++++++++----------- man/plot.dbchoice.Rd |only man/plot.kristrom.Rd | 76 +++--- man/plot.sbchoice.Rd |only man/predict.dbchoice.Rd |only man/predict.sbchoice.Rd |only man/sbchoice.Rd | 389 +++++++++++++++++++---------------- man/summary.kristrom.Rd | 70 +++--- man/summary.sbchoice.Rd | 154 +++++++------- man/turnbull.Rd | 5 man/update.dbchoice.Rd |only man/update.sbchoice.Rd |only 37 files changed, 1040 insertions(+), 886 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.49 dated 2015-12-29 and 1.51 dated 2016-03-14
Changelog | 34 ++++++++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- R/Functions.R | 48 +++++++++++++++++------------ R/blockwiseModulesC.R | 21 ++++++++++-- R/branchSplit.R | 4 +- R/consensusRepresentatives.R |only R/consensusTOM.R | 6 +++ R/corFunctions.R | 2 - R/heatmapWithLegend.R | 59 +++++++++++++++++++++--------------- R/matchLabels.R | 3 + man/TOMsimilarityFromExpr.Rd | 5 +++ man/WGCNA-package.Rd | 4 +- man/blockwiseConsensusModules.Rd | 9 +++++ man/blockwiseIndividualTOMs.Rd | 7 ++++ man/blockwiseModules.Rd | 9 +++++ man/consensusProjectiveKMeans.Rd | 2 - man/consensusRepresentatives.Rd |only man/consensusTOM.Rd | 14 ++++++++ man/selectFewestConsensusMissing.Rd |only src/corFunctions-unified.c | 30 ++++++++++++++---- src/networkFunctions.c | 33 ++++++++++++++------ 22 files changed, 248 insertions(+), 89 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from Turboveg (<http://www.synbiosys.alterra.nl/turboveg/>) and other sources (<http://www.vegetweb.de>). Taxonomic harmonization given appropriate taxonomic lists (e.g. the German taxonomical standard list "GermanSL", <http://www.botanik.uni-greifswald.de/GermanSL.html>).
Author: Florian Jansen <jansen@uni-greifswald.de>
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between vegdata versions 0.8.7 dated 2016-02-23 and 0.8.9 dated 2016-03-14
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 +- R/internal.r | 2 +- R/monotypic.r | 7 +++++-- R/taxval.r | 15 +++++++++------ R/tv.coverperc.r | 2 +- R/tv.obs.r | 5 ++++- R/tv.site.r | 41 ++++++++++++++++++++++++----------------- R/vegetweb.r | 35 ++++++++--------------------------- inst/doc/vegdata.R | 2 +- inst/doc/vegdata.Rnw | 4 ++-- man/tv.site.Rd | 5 +++-- vignettes/vegdata.Rnw | 4 ++-- 14 files changed, 78 insertions(+), 80 deletions(-)
Title: Parameter Space Exploration with Latin Hypercubes
Description: Functions for creating Latin Hypercubes with
prescribed correlations and performing parameter space exploration.
Also implements the PLUE method.
Based on the package sensitivity, by Gilles Pujol,
Bertrand Iooss & Alexandre Janon.
Author: Andre Chalom, Paulo Inacio Knegt Lopez de Prado
Maintainer: Andre Chalom <andrechalom@gmail.com>
Diff between pse versions 0.4.3 dated 2015-09-24 and 0.4.5 dated 2016-03-14
pse-0.4.3/pse/man/decoupling.Rd |only pse-0.4.3/pse/man/plotcv.Rd |only pse-0.4.3/pse/man/plotecdf.Rd |only pse-0.4.3/pse/man/plotscatter.Rd |only pse-0.4.3/pse/src/Makevars |only pse-0.4.5/pse/DESCRIPTION | 17 +- pse-0.4.5/pse/MD5 | 69 +++++----- pse-0.4.5/pse/NAMESPACE | 53 +++++--- pse-0.4.5/pse/NEWS | 6 pse-0.4.5/pse/R/LHS.R | 105 +++++++++++++++ pse-0.4.5/pse/R/LHScorcorr.R | 115 ++++++++++++----- pse-0.4.5/pse/R/PLUE.R | 102 +++++++++------ pse-0.4.5/pse/R/accessors.R | 43 ++++++ pse-0.4.5/pse/R/cluster.R | 22 +++ pse-0.4.5/pse/R/external.R | 7 + pse-0.4.5/pse/R/pic.R | 62 ++++++--- pse-0.4.5/pse/R/plotcv.R | 29 ++-- pse-0.4.5/pse/R/plotecdf.R | 45 ++++++ pse-0.4.5/pse/R/plotprcc.R | 2 pse-0.4.5/pse/R/plotscatter.R | 22 +-- pse-0.4.5/pse/R/sbma.R | 39 +++++ pse-0.4.5/pse/R/target.sbma.R | 15 ++ pse-0.4.5/pse/build/vignette.rds |binary pse-0.4.5/pse/inst/doc/multiple.R | 3 pse-0.4.5/pse/inst/doc/multiple.Rnw | 3 pse-0.4.5/pse/inst/doc/multiple.pdf |binary pse-0.4.5/pse/inst/doc/pse_tutorial.pdf |binary pse-0.4.5/pse/man/LHS.Rd | 211 ++++++++++++++++---------------- pse-0.4.5/pse/man/LHScorcorr.Rd | 84 ++++++------ pse-0.4.5/pse/man/PLUE.Rd | 119 ++++++++---------- pse-0.4.5/pse/man/accessors.Rd | 72 +++++----- pse-0.4.5/pse/man/cv.Rd | 20 +-- pse-0.4.5/pse/man/external.Rd |only pse-0.4.5/pse/man/machinefile.Rd | 46 ++---- pse-0.4.5/pse/man/pic.Rd | 60 +++++---- pse-0.4.5/pse/man/plots.Rd |only pse-0.4.5/pse/man/sbma.Rd | 60 ++++++--- pse-0.4.5/pse/man/target.sbma.Rd | 97 +++++++------- pse-0.4.5/pse/vignettes/multiple.Rnw | 3 39 files changed, 981 insertions(+), 550 deletions(-)
Title: NBD-Dirichlet Model of Consumer Buying Behavior for Marketing
Research
Description: The Dirichlet (aka NBD-Dirichlet) model describes the
purchase incidence and brand choice of consumer products. We
estimate the model and summarize various theoretical quantities
of interest to marketing researchers. Also provides functions
for making tables that compare observed and theoretical
statistics.
Author: Feiming Chen
Maintainer: Feiming Chen <feimingchen@yahoo.com>
Diff between NBDdirichlet versions 1.01 dated 2011-09-10 and 1.3 dated 2016-03-14
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- NAMESPACE | 3 +++ man/plot.dirichlet.Rd | 2 +- man/print.dirichlet.Rd | 5 +++-- man/summary.dirichlet.Rd | 2 +- 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman eta l. 1993 JVS) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between eHOF versions 1.6 dated 2015-11-06 and 1.7 dated 2016-03-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Para.deriv.r | 6 +++--- R/Para.opt.r | 2 +- R/print.HOF.r | 2 +- man/HOF.Rd | 2 +- man/plot.HOF.Rd | 23 ++++++++--------------- 7 files changed, 24 insertions(+), 31 deletions(-)
Title: Ace Editor Bindings for Shiny
Description: Ace editor bindings to enable a rich text editing environment
within Shiny.
Author: Trestle Technology, LLC [aut],
Jeff Allen [cre],
Institut de Radioprotection et de Surete Nucleaire [cph],
Ajax.org B.V. [ctb, cph] (Ace)
Maintainer: Jeff Allen <cran@trestletechnology.net>
Diff between shinyAce versions 0.1.0 dated 2013-11-05 and 0.2.1 dated 2016-03-14
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Title: Steady and Unsteady Open-Channel Flow Computation
Description: A tool for undergraduate and graduate courses in open-channel
hydraulics. Provides functions for computing normal and critical depths,
steady-state water surface profiles (e.g. backwater curves) and unsteady flow
computations (e.g. flood wave routing).
Author: Michael C Koohafkan [aut, cre]
Maintainer: Michael C Koohafkan <michael.koohafkan@gmail.com>
Diff between rivr versions 1.1 dated 2015-10-16 and 1.2 dated 2016-03-14
DESCRIPTION | 17 ++++---- MD5 | 38 ++++++++++++------- NAMESPACE | 3 + NEWS |only R/graduallyvariedflow_v2.r | 11 +++-- R/shinydemos.r |only build/vignette.rds |binary inst/CITATION |only inst/doc/publication-reproduction.R |only inst/doc/publication-reproduction.Rmd |only inst/doc/publication-reproduction.html |only inst/doc/quickstart.html | 4 +- inst/shiny-examples |only man/channel_geom.Rd | 6 +-- man/compute_profile.Rd | 30 +++++++-------- man/conveyance.Rd | 6 +-- man/critical_depth.Rd | 10 ++--- man/demo_shiny.Rd |only man/froude.Rd | 12 +++--- man/normal_depth.Rd | 10 ++--- man/rivr-package.Rd | 13 +++--- man/route_wave.Rd | 64 ++++++++++++++++----------------- man/waterolympics.Rd | 14 +++---- vignettes/publication-reproduction.Rmd |only 24 files changed, 126 insertions(+), 112 deletions(-)
Title: Regression Discontinuity Estimation
Description: Provides the tools to undertake estimation in
Regression Discontinuity Designs. Both sharp and fuzzy designs are
supported. Estimation is accomplished using local linear regression.
A provided function will utilize Imbens-Kalyanaraman optimal
bandwidth calculation. A function is also included to test the
assumption of no-sorting effects.
Author: Drew Dimmery
Maintainer: Drew Dimmery <drewd@nyu.edu>
Diff between rdd versions 0.56 dated 2013-10-11 and 0.57 dated 2016-03-14
DESCRIPTION | 13 - MD5 | 38 +-- NAMESPACE | 19 + NEWS | 3 R/DCdensity.R | 473 +++++++++++++++++++++++---------------------- R/IKbandwidth.R | 205 +++++++++---------- R/RDestimate.R | 547 ++++++++++++++++++++++++++--------------------------- R/kernelwts.R | 100 ++++----- R/plot.RD.R | 5 R/print.RD.R | 40 +-- R/rdd-package.R | 30 +- R/summary.RD.R | 191 +++++++++--------- man/DCdensity.Rd | 133 +++++------- man/IKbandwidth.Rd | 80 +++---- man/RDestimate.Rd | 259 +++++++++++-------------- man/kernelwts.Rd | 85 +++----- man/plot.RD.Rd | 60 ++--- man/print.RD.Rd | 45 ++-- man/rdd-package.Rd | 50 ++-- man/summary.RD.Rd | 58 ++--- 20 files changed, 1206 insertions(+), 1228 deletions(-)
Title: Maximal Information-Based Nonparametric Exploration R Package
for Variable Analysis
Description: R wrapper for 'cmine' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation 'cmine'
can be found at 'http://mpba.fbk.eu/cmine'.
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide
Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman
[ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi <filosi@fbk.eu>
Diff between minerva versions 1.4.1 dated 2014-08-26 and 1.4.5 dated 2016-03-14
DESCRIPTION | 21 +++--- MD5 | 22 +++--- NAMESPACE | 3 NEWS | 7 ++ R/mine.R | 136 ++++++++++++++++++++++++++++++------------ inst |only man/mine.Rd | 7 +- man/minerva-package.Rd | 4 - src/mine.c | 155 ++++++++++++++++++++++++++++++++++++++++++------- src/mine.h | 16 ++++- src/mine_interface.c | 35 ++++++++--- tests/test_minepy.R |only tests/testspellman0.R | 2 13 files changed, 315 insertions(+), 93 deletions(-)
Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>
Diff between ggmcmc versions 0.7.3 dated 2016-01-04 and 0.8 dated 2016-03-14
DESCRIPTION | 9 +++-- MD5 | 67 +++++++++++++++++++++++++------------------- NEWS | 35 ++++++++++++++++++++++ R/functions.R | 2 - R/ggs.R | 35 ++++++++++++++++++---- R/ggs_Rhat.R | 9 +++-- R/ggs_autocorrelation.R | 19 +++++++++--- R/ggs_caterpillar.R | 12 +++++-- R/ggs_compare_partial.R | 11 +++++-- R/ggs_crosscorrelation.R | 7 +++- R/ggs_density.R | 9 ++++- R/ggs_geweke.R | 6 +++ R/ggs_histogram.R | 13 ++++++-- R/ggs_pairs.R | 15 +++++++-- R/ggs_running.R | 11 +++++-- R/ggs_separation.R | 55 +++++++++++++++++++----------------- R/ggs_traceplot.R | 9 ++++- build |only inst/doc |only man/custom.sort.Rd |only man/ggs_Rhat.Rd | 4 +- man/ggs_autocorrelation.Rd | 4 +- man/ggs_caterpillar.Rd | 4 +- man/ggs_compare_partial.Rd | 5 ++- man/ggs_crosscorrelation.Rd | 4 +- man/ggs_density.Rd | 4 +- man/ggs_geweke.Rd | 4 +- man/ggs_histogram.Rd | 4 +- man/ggs_pairs.Rd | 4 +- man/ggs_running.Rd | 5 ++- man/ggs_separation.Rd | 9 +++-- man/ggs_traceplot.Rd | 4 +- vignettes |only 33 files changed, 269 insertions(+), 110 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: Provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm or numerical integration. PACE is useful for the analysis of data that have been generated by a sample of underlying (but usually not fully observed) random trajectories. It does not rely on pre-smoothing of trajectories, which is problematic if functional data are sparsely sampled. PACE provides options for functional regression and correlation, for Longitudinal Data Analysis, the analysis of stochastic processes from samples of realized trajectories, and for the analysis of underlying dynamics. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Xiongtao Dai,
Pantelis Z. Hadjipantelis,
Hao Ji,
Hans-Georg Mueller,
Jane-Ling Wang
Maintainer: Pantelis Z. Hadjipantelis <pantelis@ucdavis.edu>
Diff between fdapace versions 0.1.0 dated 2016-03-13 and 0.1.1 dated 2016-03-14
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/GetCrCovYX.R | 2 +- inst/doc/fdapaceVignette.pdf |binary man/GetCrCovYX.Rd | 2 +- src/CPPlwls1d.cpp | 2 +- src/Rmullwlsk.cpp | 5 +++-- src/RmullwlskCC.cpp | 3 ++- 8 files changed, 20 insertions(+), 18 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 5.0-9 dated 2015-12-01 and 5.0-10 dated 2016-03-14
DESCRIPTION | 20 +- MD5 | 200 +++++++++++++---------- NAMESPACE | 12 - R/create-json.R | 29 +++ R/model-ar.R |only R/model-arima.R |only R/model-bayes.R | 8 R/model-binchoice-gee.R | 5 R/model-binchoice-survey.R |only R/model-exp.R | 10 - R/model-factor-bayes.R | 8 R/model-gamma-survey.R |only R/model-gamma.R | 16 + R/model-gee.R | 20 +- R/model-glm.R | 11 - R/model-logit-bayes.R | 1 R/model-logit-survey.R |only R/model-lognorm.R | 26 +-- R/model-ls.R | 12 + R/model-ma.R |only R/model-negbinom.R | 16 + R/model-normal-survey.R |only R/model-normal.R | 18 +- R/model-poisson-gee.R | 4 R/model-poisson-survey.R |only R/model-probit-gee.R | 1 R/model-probit-survey.R |only R/model-quantile.R | 14 + R/model-relogit.R | 10 - R/model-survey.R |only R/model-timeseries.R |only R/model-tobit.R | 23 +- R/model-weibull.R | 26 +-- R/model-zelig.R | 205 ++++++++++++++++++++++- R/plots.R | 308 ++++++++++++++++++++++++++---------- R/utils.R | 3 R/wrappers.R | 8 data/friendship.RData |binary data/sna.ex.RData |binary inst/JSON/zelig5models.json | 78 +++++++++ man/Median.Rd | 2 man/Mode.Rd | 2 man/Zelig-ar-class.Rd |only man/Zelig-arima-class.Rd |only man/Zelig-bayes-class.Rd | 5 man/Zelig-binchoice-class.Rd | 2 man/Zelig-binchoice-gee-class.Rd | 6 man/Zelig-binchoice-survey-class.Rd |only man/Zelig-class.Rd | 9 - man/Zelig-exp-class.Rd | 5 man/Zelig-factor-bayes-class.Rd | 5 man/Zelig-gamma-class.Rd | 2 man/Zelig-gamma-gee-class.Rd | 2 man/Zelig-gamma-survey-class.Rd |only man/Zelig-gee-class.Rd | 5 man/Zelig-glm-class.Rd | 5 man/Zelig-logit-bayes-class.Rd | 2 man/Zelig-logit-class.Rd | 2 man/Zelig-logit-gee-class.Rd | 2 man/Zelig-logit-survey-class.Rd |only man/Zelig-lognorm-class.Rd | 5 man/Zelig-ls-class.Rd | 5 man/Zelig-ma-class.Rd |only man/Zelig-mlogit-bayes-class.Rd | 2 man/Zelig-negbin-class.Rd | 5 man/Zelig-normal-bayes-class.Rd | 2 man/Zelig-normal-class.Rd | 2 man/Zelig-normal-gee-class.Rd | 2 man/Zelig-normal-survey-class.Rd |only man/Zelig-oprobit-bayes-class.Rd | 2 man/Zelig-poisson-bayes-class.Rd | 2 man/Zelig-poisson-class.Rd | 2 man/Zelig-poisson-gee-class.Rd | 2 man/Zelig-poisson-survey-class.Rd |only man/Zelig-probit-bayes-class.Rd | 2 man/Zelig-probit-class.Rd | 2 man/Zelig-probit-gee-class.Rd | 2 man/Zelig-probit-survey-class.Rd |only man/Zelig-quantile-class.Rd | 5 man/Zelig-relogit-class.Rd | 5 man/Zelig-survey-class.Rd |only man/Zelig-timeseries-class.Rd |only man/Zelig-tobit-bayes-class.Rd | 2 man/Zelig-tobit-class.Rd | 5 man/Zelig-weibull-class.Rd | 5 man/avg.Rd | 2 man/ci.plot.Rd | 11 - man/cluster.formula.Rd | 2 man/coef-Zelig-method.Rd | 2 man/fitted-Zelig-method.Rd | 2 man/plot-Zelig-ANY-method.Rd | 2 man/predict-Zelig-method.Rd | 2 man/qi.plot.Rd | 4 man/reduce.Rd | 2 man/relogit.Rd | 2 man/rocplot.Rd | 4 man/setfactor.Rd | 2 man/setval.Rd | 2 man/setx.Rd | 8 man/sim.Rd | 10 - man/simacf.Rd |only man/simulations.plot.Rd | 2 man/stat.Rd | 2 man/statlevel.Rd | 6 man/statmat.Rd | 6 man/summary-Zelig-method.Rd | 2 man/table.levels.Rd | 2 man/vcov-Zelig-method.Rd | 2 man/zelig.Rd | 4 man/zeligACFplot.Rd |only man/zeligARMAbreakforecaster.Rd |only man/zeligARMAlongrun.Rd |only man/zeligARMAnextstep.Rd |only man/zeligArimaWrapper.Rd |only man/zeligPlyrMutate.Rd | 2 115 files changed, 900 insertions(+), 392 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 1.0.15 dated 2016-03-11 and 1.0.16 dated 2016-03-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/gershunov.R | 3 +++ inst/Changelog | 4 ++++ 4 files changed, 13 insertions(+), 6 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.5 dated 2016-02-11 and 1.6 dated 2016-03-14
DESCRIPTION | 10 MD5 | 106 +++++----- NAMESPACE | 20 + NEWS | 23 ++ NEWS.md | 22 +- R/S3-methods.R | 96 +++++++-- R/as_labelled.R | 46 ++++ R/cronb.R | 14 - R/cv.R | 27 ++ R/drop_labels.R |only R/fill_labels.R | 2 R/frq.R | 65 +++++- R/get_label.R | 9 R/get_labels.R | 502 ++++++++++++++++++++++++-------------------------- R/group_var.R | 434 +++++++++++++++++++++---------------------- R/icc.R | 107 +++++++--- R/mean_n.R | 164 ++++++++-------- R/mic.R | 6 R/overdisp.R | 163 ++++++++++------ R/pseudo_r2.R | 117 +++++++++++ R/rec.R | 12 + R/rec_pattern.R |only R/ref_lvl.R | 7 R/set_label.R | 353 +++++++++++++++++------------------ R/set_labels.R | 12 - R/str_contains.R |only R/to_factor.R | 9 R/to_long.R | 260 +++++++++++++------------ R/unlabel.R | 17 - R/weight.R | 193 ++++++++++--------- R/zap_labels.R | 6 README.md | 85 ++++---- build |only man/cronb.Rd | 6 man/cv.Rd | 5 man/drop_labels.Rd |only man/fill_labels.Rd | 3 man/frq.Rd | 5 man/get_frq.Rd |only man/get_label.Rd | 3 man/get_labels.Rd | 4 man/group_var.Rd | 14 - man/icc.Rd | 116 ++++++----- man/lbl_df.Rd |only man/mic.Rd | 6 man/overdisp.Rd | 51 ++++- man/r2.Rd |only man/rec_pattern.Rd |only man/set_label.Rd | 3 man/set_labels.Rd | 3 man/sjmisc-package.Rd | 4 man/str_contains.Rd |only man/to_factor.Rd | 3 man/to_long.Rd | 10 man/unlabel.Rd | 15 - man/weight.Rd | 7 man/weight2.Rd | 1 man/zap_labels.Rd | 3 man/zap_unlabelled.Rd | 3 59 files changed, 1803 insertions(+), 1349 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>
Diff between piecewiseSEM versions 1.0.3 dated 2016-02-01 and 1.1 dated 2016-03-14
DESCRIPTION | 10 +-- MD5 | 78 +++++++++++++------------ NAMESPACE | 8 +- NEWS.md | 19 ++++++ R/filter.exogenous.R | 50 ++++++---------- R/get.basis.set.R | 13 +--- R/get.dag.R | 62 +++++++++++++++----- R/get.model.control.R | 4 - R/get.random.formula.R | 14 ++-- R/get.scaled.data.R | 55 ++++++++++++------ R/get.scaled.model.R |only R/get.sort.dag.R |only R/partial.resid.R | 112 ++++++++++++++++++++++-------------- R/sem.aic.R | 12 +-- R/sem.basis.set.R | 117 ++++++++++++++++++++++++++++++-------- R/sem.coefs.R | 60 ++++++++++++++----- R/sem.fisher.c.R | 10 +-- R/sem.fit.R | 22 ++----- R/sem.lavaan.R | 6 + R/sem.missing.paths.R | 134 +++++++++++++++++++++++++++++++------------- R/sem.model.fits.R | 55 ++++++++++++------ R/sem.plot.R |only R/sem.predict.R | 13 ++-- README.md | 63 ++++++++++---------- build/vignette.rds |binary inst/doc/piecewiseSEM.R | 7 +- inst/doc/piecewiseSEM.Rmd | 12 ++- inst/doc/piecewiseSEM.html | 129 +++++++++++++++++++++++++----------------- man/filter.exogenous.Rd | 2 man/get.scaled.model.Rd |only man/get.sort.dag.Rd |only man/piecewiseSEM-package.Rd | 10 +-- man/sem.aic.Rd | 8 -- man/sem.basis.set.Rd | 2 man/sem.coefs.Rd | 4 - man/sem.fisher.c.Rd | 8 -- man/sem.fit.Rd | 79 +++++++++++++------------ man/sem.lavaan.Rd | 42 ++++++------- man/sem.missing.paths.Rd | 22 ++++--- man/sem.model.fits.Rd | 2 man/sem.plot.Rd |only man/sem.predict.Rd | 2 vignettes/piecewiseSEM.Rmd | 12 ++- 43 files changed, 778 insertions(+), 480 deletions(-)
Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph
proposed by Rosenbaum is useful
for checking some properties of various
sorts of latent scale, this program generates commands
to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between latdiag versions 0.2-1 dated 2015-01-16 and 0.2-2 dated 2016-03-14
latdiag-0.2-1/latdiag/inst/doc |only latdiag-0.2-2/latdiag/DESCRIPTION | 20 +++++++++++--------- latdiag-0.2-2/latdiag/MD5 | 7 +++---- latdiag-0.2-2/latdiag/NEWS | 6 +++++- latdiag-0.2-2/latdiag/man/latdiag-package.Rd | 2 +- 5 files changed, 20 insertions(+), 15 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Author: Martin Loos, Christian Gerber
Maintainer: Martin Loos <martin.loos@alumni.ethz.ch>
Diff between enviPat versions 2.0 dated 2015-06-05 and 2.1 dated 2016-03-14
DESCRIPTION | 8 MD5 | 24 NAMESPACE | 3 NEWS | 6 R/check_chemform.R | 9 R/enviPat.R | 2 R/getR.R | 12 data/isotopes.rda |binary man/check_chemform.Rd | 3 man/check_ded.Rd | 2 man/isowrap.Rd | 1 src/data.h | 2728 -------------------------------------------------- src/main.c | 2 13 files changed, 46 insertions(+), 2754 deletions(-)
Title: R Interface for PreSens Fiber Optic Data
Description: Makes output files from select PreSens Fiber Optic Oxygen
Transmitters easier to work with in R. See http://www.presens.de for more
information about PreSens (Precision Sensing GmbH).
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between presens versions 1.0.0 dated 2015-02-10 and 2.0.0 dated 2016-03-14
DESCRIPTION | 15 ++++--- MD5 | 16 +++---- NAMESPACE | 3 - NEWS | 6 ++ R/import_o2.R | 106 ++++++++++++++++++++++++++++------------------------ R/o2_unit_conv.R | 77 ++++++++++++++++++++++++++----------- man/import_o2.Rd | 33 +++++++++------- man/o2_unit_conv.Rd | 36 +++++++++++++---- man/presens.Rd | 2 9 files changed, 185 insertions(+), 109 deletions(-)
Title: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos <Martin.Loos@eawag.ch>
Diff between nontarget versions 1.7 dated 2015-01-17 and 1.8 dated 2016-03-14
DESCRIPTION | 14 MD5 | 54 +- NAMESPACE | 8 NEWS | 9 R/adduct.search.R | 14 R/combine.R | 8 R/homol.search.R | 972 +++++++++++++++++++++++++++++++++++++---------- R/make.isos.R | 6 R/nontarget.R | 2 R/pattern.search.R | 572 ++++++++++++++------------- R/pattern.search2.R | 137 +++--- R/plotcomp.R | 6 R/plothomol.R | 37 + R/rm.sat.R | 8 man/adduct.search.Rd | 4 man/combine.Rd | 32 - man/homol.search.Rd | 125 +++--- man/make.isos.Rd | 2 man/nontarget-package.Rd | 38 - man/pattern.search.Rd | 6 man/pattern.search2.Rd | 16 man/plotcomp.Rd | 4 man/plothomol.Rd | 40 + man/rm.sat.Rd | 7 src/homologues.cpp | 511 +++++++++++------------- src/massCpp.cpp | 18 src/quantization.cpp | 20 src/searchTree.cpp | 778 +++++++++++++++++++++++++++++++++++-- 28 files changed, 2409 insertions(+), 1039 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-125 dated 2016-02-27 and 3.1-126 dated 2016-03-14
ChangeLog | 6 ++++ DESCRIPTION | 8 ++--- MD5 | 14 +++++----- R/lmList.R | 27 ++++++++------------ R/nlme.R | 40 ++++++++++++----------------- R/nlsList.R | 47 +++++++++++++++------------------- tests/augPred_lab.R | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++++ tests/nlme2.R | 37 +++++++++++++++++++++++++++ 8 files changed, 173 insertions(+), 76 deletions(-)
Title: Peak Picking for High Resolution Mass Spectrometry Data
Description: Sequential partitioning, clustering and peak detection of
centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw
data plot.
Author: Martin Loos
Maintainer: Martin Loos <Martin.Loos@eawag.ch>
Diff between enviPick versions 1.3 dated 2014-11-29 and 1.4 dated 2016-03-14
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 4 ++++ NEWS | 4 ++++ R/enviPick.R | 2 +- R/mzagglom.r | 2 +- R/mzclust.R | 34 +++++++++++++++++----------------- R/mzpick.R | 3 ++- R/readMSdata.R | 6 +++++- 9 files changed, 47 insertions(+), 34 deletions(-)
Title: A Tool for Calculation and Optimization of the Expected Gain
from Multi-Stage Selection
Description: Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.
Author: Xuefei Mi, Jose Marulanda, H. Friedrich Utz, Albrecht E. Melchinger (Project contact person: Melchinger@uni-hohenheim.de )
Maintainer: Xuefei Mi <mi_xue_fei@hotmail.com>
Diff between selectiongain versions 2.0.40 dated 2014-12-29 and 2.0.50.1 dated 2016-03-14
DESCRIPTION | 16 +-- MD5 | 18 +-- NAMESPACE | 5 - R/multistagecor.R | 161 ++++++++++++++++++++++++++++++-- R/multistagegain.R | 73 ++++++++++++-- R/multistageoptimum.grid.R | 196 ++++++++++++++++++++++++++++++---------- R/multistageoptimum.search.R | 192 +++++++++++++++++++++++++++++++++------ man/multistagegain.Rd | 4 man/multistageoptimum.grid.Rd | 20 +++- man/multistageoptimum.search.Rd | 23 +++- 10 files changed, 579 insertions(+), 129 deletions(-)
Title: Boosting Functional Regression Models
Description: Regression models for functional data, i.e., scalar-on-function,
function-on-scalar and function-on-function regression models, are fitted
by a component-wise gradient boosting algorithm.
Author: Sarah Brockhaus [aut, cre],
David Ruegamer [ctb],
Torsten Hothorn [ctb],
with contributions by many others (see inst/CONTRIBUTIONS) [ctb]
Maintainer: Sarah Brockhaus <Sarah.Brockhaus@stat.uni-muenchen.de>
Diff between FDboost versions 0.0-8 dated 2015-02-16 and 0.1-0 dated 2016-03-14
FDboost-0.0-8/FDboost/R/internalsMboost.R |only FDboost-0.1-0/FDboost/DESCRIPTION | 36 FDboost-0.1-0/FDboost/MD5 | 117 + FDboost-0.1-0/FDboost/NAMESPACE | 65 + FDboost-0.1-0/FDboost/R/FDboost.R | 923 ++++++++++---- FDboost-0.1-0/FDboost/R/FDboostLSS.R |only FDboost-0.1-0/FDboost/R/baselearners.R | 944 ++++++++++---- FDboost-0.1-0/FDboost/R/baselearnersX.R |only FDboost-0.1-0/FDboost/R/constrainedX.R |only FDboost-0.1-0/FDboost/R/crossvalidation.R | 612 +++++---- FDboost-0.1-0/FDboost/R/hmatrix.R |only FDboost-0.1-0/FDboost/R/methods.R | 1338 +++++++++++++-------- FDboost-0.1-0/FDboost/R/utilityFunctions.R | 232 +++ FDboost-0.1-0/FDboost/build/vignette.rds |binary FDboost-0.1-0/FDboost/inst/CITATION | 16 FDboost-0.1-0/FDboost/inst/CONTRIBUTIONS |only FDboost-0.1-0/FDboost/inst/NEWS.Rd |only FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.R | 4 FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.Rnw | 11 FDboost-0.1-0/FDboost/inst/doc/FLAM_canada.pdf |binary FDboost-0.1-0/FDboost/inst/doc/FLAM_fuel.Rnw | 10 FDboost-0.1-0/FDboost/inst/doc/FLAM_fuel.pdf |binary FDboost-0.1-0/FDboost/inst/doc/FLAM_viscosity.Rnw | 9 FDboost-0.1-0/FDboost/inst/doc/FLAM_viscosity.pdf |binary FDboost-0.1-0/FDboost/inst/sim/readme.txt |only FDboost-0.1-0/FDboost/inst/sim/run_FDboost.R | 1 FDboost-0.1-0/FDboost/inst/sim/run_pffr.R | 1 FDboost-0.1-0/FDboost/inst/sim/simfuns.R | 4 FDboost-0.1-0/FDboost/inst/simHist |only FDboost-0.1-0/FDboost/man/FDboost.Rd | 391 ++++-- FDboost-0.1-0/FDboost/man/FDboostLSS.Rd |only FDboost-0.1-0/FDboost/man/anisotropic_Kronecker.Rd |only FDboost-0.1-0/FDboost/man/bbsc.Rd | 27 FDboost-0.1-0/FDboost/man/bhistx.Rd |only FDboost-0.1-0/FDboost/man/bsignal.Rd | 162 +- FDboost-0.1-0/FDboost/man/coef.FDboost.Rd | 28 FDboost-0.1-0/FDboost/man/cvrisk.FDboostLSS.Rd |only FDboost-0.1-0/FDboost/man/extract.blg.Rd | 16 FDboost-0.1-0/FDboost/man/fitted.FDboost.Rd | 8 FDboost-0.1-0/FDboost/man/fuelSubset.Rd | 120 + FDboost-0.1-0/FDboost/man/funMRD.Rd | 2 FDboost-0.1-0/FDboost/man/funMSE.Rd | 2 FDboost-0.1-0/FDboost/man/funRsquared.Rd | 2 FDboost-0.1-0/FDboost/man/funplot.Rd | 5 FDboost-0.1-0/FDboost/man/getTime.Rd |only FDboost-0.1-0/FDboost/man/getTime.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/grapes-Xc-grapes.Rd |only FDboost-0.1-0/FDboost/man/hmatrix.Rd |only FDboost-0.1-0/FDboost/man/integrationWeights.Rd | 16 FDboost-0.1-0/FDboost/man/is.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/o_control.Rd | 2 FDboost-0.1-0/FDboost/man/plot.FDboost.Rd | 33 FDboost-0.1-0/FDboost/man/plot.validateFDboost.Rd | 36 FDboost-0.1-0/FDboost/man/predict.FDboost.Rd | 11 FDboost-0.1-0/FDboost/man/print.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/residuals.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/sub-.hmatrix.Rd |only FDboost-0.1-0/FDboost/man/summary.FDboost.Rd | 2 FDboost-0.1-0/FDboost/man/truncateTime.Rd | 2 FDboost-0.1-0/FDboost/man/validateFDboost.Rd | 201 ++- FDboost-0.1-0/FDboost/man/viscosity.Rd | 124 - FDboost-0.1-0/FDboost/man/wide2long.Rd |only FDboost-0.1-0/FDboost/vignettes/FLAM_canada.Rnw | 11 FDboost-0.1-0/FDboost/vignettes/FLAM_fuel.Rnw | 10 FDboost-0.1-0/FDboost/vignettes/FLAM_viscosity.Rnw | 9 65 files changed, 3766 insertions(+), 1781 deletions(-)
Title: Dandelion Plot for R-Mode Exploratory Factor Analysis
Description: Contains the function used to create the Dandelion Plot. Dandelion Plot is a visualization method for R-mode Exploratory Factor Analysis.
Author: Artur Manukyan, Ahmet Sedef, Erhan Cene, Ibrahim Demir
Maintainer: Artur Manukyan <artur-man@hotmail.com>
Diff between DandEFA versions 1.5 dated 2014-04-25 and 1.6 dated 2016-03-14
DESCRIPTION | 16 +- MD5 | 12 - NAMESPACE | 4 R/dandelion.R | 370 +++++++++++++++++++++++++++---------------------------- man/dandelion.Rd | 18 +- man/factload.Rd | 5 man/timss2011.Rd | 4 7 files changed, 218 insertions(+), 211 deletions(-)
Title: 'stats' for Seasonal Adjustment on the Fly with 'ggplot2'
Description: Provides 'ggplot2' 'stats' that estimate seasonally adjusted series
and rolling summaries such as rolling average on the fly for time series.
Author: Peter Ellis <peter.ellis2013nz@gmail.com>
Maintainer: Peter Ellis <peter.ellis2013nz@gmail.com>
Diff between ggseas versions 0.2.1 dated 2016-02-29 and 0.3.0 dated 2016-03-14
DESCRIPTION | 10 ++++----- MD5 | 25 ++++++++++++++--------- NAMESPACE | 3 ++ R/decompose-seasonal.R | 32 ++++++++++++++++++++++++------ R/ggsdc.R | 48 ++++++++++++++++++++++++++++++++------------- R/helper_funcs.R |only R/stat_index.R |only R/stat_rollapplyr.R |only R/stl-seasonal.R | 34 ++++++++++++++++++++++++-------- R/x13-seasonal.R | 32 ++++++++++++++++++++++++------ man/ggsdc.Rd | 15 +++++++++++++- man/stat_decomp.Rd | 52 +++++++++++++++++++++++++++++++++++++------------ man/stat_index.Rd |only man/stat_rollapplyr.Rd |only man/stat_seas.Rd | 51 ++++++++++++++++++++++++++++++++++++------------ man/stat_stl.Rd | 48 +++++++++++++++++++++++++++++++++------------ 16 files changed, 264 insertions(+), 86 deletions(-)
Title: Provide the 'x13ashtml' Seasonal Adjustment Binary
Description: The US Census provides a seasonal adjustment program now
called 'X-13ARIMA-SEATS' building on both earlier Census programs called
X-11 and X-12 as well as the SEATS program by the Bank of Spain. Census
offers both source and binary versions -- which this package integrates
for use by other R packages.
Author: Dirk Eddelbuettel and Christoph Sax
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between x13binary versions 0.1.1 dated 2016-02-10 and 0.1.2 dated 2016-03-14
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 2 +- configure | 4 ++-- configure.win | 28 ++++++++++++++-------------- 6 files changed, 40 insertions(+), 26 deletions(-)
Title: Statistical Significance of the Sharpe Ratio
Description: A collection of tools for analyzing significance of trading
strategies, based on the Sharpe ratio and overfit of the same.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between SharpeR versions 1.0.0 dated 2015-06-18 and 1.1.0 dated 2016-03-14
SharpeR-1.0.0/SharpeR/inst/tests |only SharpeR-1.0.0/SharpeR/tests/run-all.R |only SharpeR-1.1.0/SharpeR/.Rinstignore | 1 SharpeR-1.1.0/SharpeR/DESCRIPTION | 15 - SharpeR-1.1.0/SharpeR/MD5 | 107 ++++----- SharpeR-1.1.0/SharpeR/NAMESPACE | 32 ++ SharpeR-1.1.0/SharpeR/R/SharpeR.r | 16 + SharpeR-1.1.0/SharpeR/R/distributions.r | 19 - SharpeR-1.1.0/SharpeR/R/estimation.r | 108 ++++++--- SharpeR-1.1.0/SharpeR/R/sr.r | 139 +++++++++--- SharpeR-1.1.0/SharpeR/R/tests.r | 15 - SharpeR-1.1.0/SharpeR/R/utils.r | 12 - SharpeR-1.1.0/SharpeR/README.md | 42 +++ SharpeR-1.1.0/SharpeR/build/vignette.rds |binary SharpeR-1.1.0/SharpeR/inst/doc/SharpeR.pdf |binary SharpeR-1.1.0/SharpeR/inst/doc/SharpeRatio.pdf |binary SharpeR-1.1.0/SharpeR/inst/extdata/autocorr_study.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/haircut_study.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/hotelling_power_rule.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/ret_data.rda |binary SharpeR-1.1.0/SharpeR/inst/extdata/skew_study.rda |binary SharpeR-1.1.0/SharpeR/man/NEWS.Rd | 19 + SharpeR-1.1.0/SharpeR/man/SharpeR.Rd | 47 +--- SharpeR-1.1.0/SharpeR/man/as.del_sropt.Rd | 24 +- SharpeR-1.1.0/SharpeR/man/as.sr.Rd | 40 +-- SharpeR-1.1.0/SharpeR/man/as.sropt.Rd | 36 +-- SharpeR-1.1.0/SharpeR/man/confint.Rd | 53 +--- SharpeR-1.1.0/SharpeR/man/del_sropt.Rd | 43 +-- SharpeR-1.1.0/SharpeR/man/dsr.Rd | 50 +--- SharpeR-1.1.0/SharpeR/man/dsropt.Rd | 48 +--- SharpeR-1.1.0/SharpeR/man/inference.Rd | 35 +-- SharpeR-1.1.0/SharpeR/man/is.del_sropt.Rd | 5 SharpeR-1.1.0/SharpeR/man/is.sr.Rd | 28 -- SharpeR-1.1.0/SharpeR/man/is.sropt.Rd | 17 - SharpeR-1.1.0/SharpeR/man/ism_vcov.Rd | 21 - SharpeR-1.1.0/SharpeR/man/pco_sropt.Rd | 36 +-- SharpeR-1.1.0/SharpeR/man/plambdap.Rd | 30 -- SharpeR-1.1.0/SharpeR/man/power.sr_test.Rd | 63 ++--- SharpeR-1.1.0/SharpeR/man/power.sropt_test.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/predint.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/print.Rd | 29 -- SharpeR-1.1.0/SharpeR/man/reannualize.Rd | 44 +-- SharpeR-1.1.0/SharpeR/man/se.Rd | 31 -- SharpeR-1.1.0/SharpeR/man/sm_vcov.Rd | 15 - SharpeR-1.1.0/SharpeR/man/sr.Rd | 51 +--- SharpeR-1.1.0/SharpeR/man/sr_equality_test.Rd | 55 +--- SharpeR-1.1.0/SharpeR/man/sr_test.Rd | 41 +-- SharpeR-1.1.0/SharpeR/man/sr_unpaired_test.Rd | 42 +-- SharpeR-1.1.0/SharpeR/man/sr_vcov.Rd | 52 ++-- SharpeR-1.1.0/SharpeR/man/sric.Rd |only SharpeR-1.1.0/SharpeR/man/sropt.Rd | 40 +-- SharpeR-1.1.0/SharpeR/man/sropt_test.Rd | 30 +- SharpeR-1.1.0/SharpeR/man/summary.Rd |only SharpeR-1.1.0/SharpeR/tests/testthat |only SharpeR-1.1.0/SharpeR/tests/testthat.R |only 55 files changed, 835 insertions(+), 780 deletions(-)
Title: Provides Access to Databases Through the ODBC Interface
Description: An implementation of R's DBI interface using ODBC package as a
back-end. This allows R to connect to any DBMS that has a ODBC driver.
Author: Nagi Teramo [aut, cre],
Shinichi Takayanagi [aut]
Maintainer: Nagi Teramo <teramonagi@gmail.com>
Diff between RODBCDBI versions 0.1 dated 2015-12-02 and 0.1.1 dated 2016-03-14
DESCRIPTION | 15 +++- LICENSE | 2 MD5 | 50 ++++++++------- NAMESPACE | 4 - R/ODBCConnection.R | 27 +++++++- R/ODBCDriver.R | 60 ++++++++++++++----- R/ODBCResult.R | 38 +++++++----- R/RODBCDBI.R | 16 ++--- README.md | 38 ++++++++++-- man/ODBC.Rd | 15 +++- man/ODBCConnection-class.Rd | 11 --- man/ODBCDriver-class.Rd | 11 ++- man/ODBCResult-class.Rd | 6 - man/RODBCDBI.Rd | 4 - man/dbConnect-ODBCDriver-method.Rd |only man/dbDisconnect.Rd | 2 man/dbExistsTable-ODBCConnection-character-method.Rd | 5 + man/dbGetInfo-ODBCConnection-method.Rd |only man/dbListFields-ODBCConnection-character-method.Rd | 2 man/dbListTables-ODBCConnection-method.Rd | 2 man/dbReadTable-ODBCConnection-character-method.Rd | 6 - man/dbRemoveTable-ODBCConnection-character-method.Rd | 2 man/dbWriteTable.Rd | 10 +-- man/odbc-meta.Rd | 5 + man/odbc-query.Rd | 8 -- tests/testthat/test-ODBCConnection.R | 16 +++-- tests/testthat/test-ODBCDriver.R |only tests/testthat/test-ODBCResult.R |only 28 files changed, 237 insertions(+), 118 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut, cph],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 2.0.16 dated 2015-12-20 and 3.4.1 dated 2016-03-14
plotly-2.0.16/plotly/R/build_function.R |only plotly-2.0.16/plotly/R/colour_conversion.R |only plotly-2.0.16/plotly/R/corresp_one_one.R |only plotly-2.0.16/plotly/R/marker_conversion.R |only plotly-2.0.16/plotly/R/trace_generation.R |only plotly-2.0.16/plotly/man/ggplot_build2.Rd |only plotly-2.0.16/plotly/man/group2NA.Rd |only plotly-2.0.16/plotly/man/layer2traces.Rd |only plotly-2.0.16/plotly/man/paramORdefault.Rd |only plotly-2.0.16/plotly/man/toFill.Rd |only plotly-2.0.16/plotly/man/toWidget.Rd |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-build2.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-categorical.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-environment.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-legend-name.R |only plotly-2.0.16/plotly/tests/testthat/test-ggplot-stack.R |only plotly-2.0.16/plotly/tests/testthat/test-unimplemented.R |only plotly-3.4.1/plotly/DESCRIPTION | 20 plotly-3.4.1/plotly/MD5 | 181 - plotly-3.4.1/plotly/NAMESPACE | 57 plotly-3.4.1/plotly/NEWS | 175 + plotly-3.4.1/plotly/R/figure.R | 2 plotly-3.4.1/plotly/R/ggplotly.R | 1729 ++++------ plotly-3.4.1/plotly/R/imports.R |only plotly-3.4.1/plotly/R/layers2traces.R |only plotly-3.4.1/plotly/R/plotly.R | 157 plotly-3.4.1/plotly/R/plotly_IMAGE.R | 8 plotly-3.4.1/plotly/R/plotly_POST.R | 69 plotly-3.4.1/plotly/R/print.R | 74 plotly-3.4.1/plotly/R/process.R | 5 plotly-3.4.1/plotly/R/shiny.R | 28 plotly-3.4.1/plotly/R/signup.R | 2 plotly-3.4.1/plotly/R/subplots.R | 10 plotly-3.4.1/plotly/R/toRGB.R |only plotly-3.4.1/plotly/R/utils.R | 110 plotly-3.4.1/plotly/README.md | 48 plotly-3.4.1/plotly/build/vignette.rds |binary plotly-3.4.1/plotly/inst/doc/intro.R | 3 plotly-3.4.1/plotly/inst/doc/intro.Rmd | 6 plotly-3.4.1/plotly/inst/doc/intro.html | 98 plotly-3.4.1/plotly/inst/examples/Movies/server.R | 2 plotly-3.4.1/plotly/inst/examples/lmGadget |only plotly-3.4.1/plotly/inst/examples/map_click |only plotly-3.4.1/plotly/inst/examples/onRenderHover |only plotly-3.4.1/plotly/inst/examples/plotly3DEvents |only plotly-3.4.1/plotly/inst/examples/plotlyEvents |only plotly-3.4.1/plotly/inst/examples/plotlyLinkedBrush |only plotly-3.4.1/plotly/inst/examples/plotlyLinkedClick |only plotly-3.4.1/plotly/inst/htmlwidgets/lib/plotlyjs/LICENSE | 2 plotly-3.4.1/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 75 plotly-3.4.1/plotly/inst/htmlwidgets/plotly.js | 76 plotly-3.4.1/plotly/inst/htmlwidgets/plotly.yaml | 2 plotly-3.4.1/plotly/inst/plotlyjs.R | 22 plotly-3.4.1/plotly/man/as.widget.Rd |only plotly-3.4.1/plotly/man/bbox.Rd |only plotly-3.4.1/plotly/man/config.Rd | 40 plotly-3.4.1/plotly/man/embed_notebook.Rd | 12 plotly-3.4.1/plotly/man/event_data.Rd |only plotly-3.4.1/plotly/man/geom2trace.Rd |only plotly-3.4.1/plotly/man/gg2list.Rd | 14 plotly-3.4.1/plotly/man/ggplotly.Rd | 35 plotly-3.4.1/plotly/man/knit_print.plotly.Rd | 2 plotly-3.4.1/plotly/man/plot_ly.Rd | 6 plotly-3.4.1/plotly/man/plotly_IMAGE.Rd | 2 plotly-3.4.1/plotly/man/plotly_POST.Rd | 32 plotly-3.4.1/plotly/man/print.plotly.Rd | 2 plotly-3.4.1/plotly/man/toRGB.Rd | 6 plotly-3.4.1/plotly/man/to_basic.Rd |only plotly-3.4.1/plotly/tests/testthat.R | 2 plotly-3.4.1/plotly/tests/testthat/test-cookbook-axes.R | 165 plotly-3.4.1/plotly/tests/testthat/test-cookbook-lines.R | 107 plotly-3.4.1/plotly/tests/testthat/test-cookbook-scatterplots.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-abline.R | 5 plotly-3.4.1/plotly/tests/testthat/test-ggplot-area.R | 59 plotly-3.4.1/plotly/tests/testthat/test-ggplot-bar.R | 79 plotly-3.4.1/plotly/tests/testthat/test-ggplot-boxplot.R | 23 plotly-3.4.1/plotly/tests/testthat/test-ggplot-contour.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-date.R | 40 plotly-3.4.1/plotly/tests/testthat/test-ggplot-density.R | 30 plotly-3.4.1/plotly/tests/testthat/test-ggplot-density2d.R | 64 plotly-3.4.1/plotly/tests/testthat/test-ggplot-errorbar-horizontal.R | 10 plotly-3.4.1/plotly/tests/testthat/test-ggplot-errorbar.R | 36 plotly-3.4.1/plotly/tests/testthat/test-ggplot-facets.R | 95 plotly-3.4.1/plotly/tests/testthat/test-ggplot-heatmap.R | 43 plotly-3.4.1/plotly/tests/testthat/test-ggplot-hex.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-histogram.R | 77 plotly-3.4.1/plotly/tests/testthat/test-ggplot-hline.R | 5 plotly-3.4.1/plotly/tests/testthat/test-ggplot-labels.R | 25 plotly-3.4.1/plotly/tests/testthat/test-ggplot-legend.R | 132 plotly-3.4.1/plotly/tests/testthat/test-ggplot-map.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-path.R | 66 plotly-3.4.1/plotly/tests/testthat/test-ggplot-point.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-polygons.R | 132 plotly-3.4.1/plotly/tests/testthat/test-ggplot-rect.R | 47 plotly-3.4.1/plotly/tests/testthat/test-ggplot-segment.R | 61 plotly-3.4.1/plotly/tests/testthat/test-ggplot-smooth.R | 25 plotly-3.4.1/plotly/tests/testthat/test-ggplot-step.R | 2 plotly-3.4.1/plotly/tests/testthat/test-ggplot-text.R | 37 plotly-3.4.1/plotly/tests/testthat/test-ggplot-theme.R | 53 plotly-3.4.1/plotly/tests/testthat/test-ggplot-ticks.R | 298 - plotly-3.4.1/plotly/tests/testthat/test-ggplot-tooltip.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-violin.R |only plotly-3.4.1/plotly/tests/testthat/test-ggplot-vline.R | 9 plotly-3.4.1/plotly/tests/testthat/test-ggplot-ylim.R | 17 plotly-3.4.1/plotly/tests/testthat/test-mean-error-bars.R | 192 - plotly-3.4.1/plotly/tests/testthat/test-plotly-getfigure.R | 16 plotly-3.4.1/plotly/tests/testthat/test-plotly-subplot.R | 3 plotly-3.4.1/plotly/tests/testthat/test-plotly.R | 32 plotly-3.4.1/plotly/vignettes/intro.Rmd | 6 109 files changed, 2521 insertions(+), 2602 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package evaluates the mass balance and extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to check the compound names associated to Chemical Entities of Biological Interest (ChEBI) database <https://www.ebi.ac.uk/chebi>.
Author: Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco
[aut]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.1 dated 2016-02-16 and 0.2 dated 2016-03-14
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++--------------------- NEWS | 4 +++ R/chebi.formula.R | 2 - R/chebi.id.R | 4 +-- R/compartments.R | 10 +++---- R/is.chebi.R | 10 ++----- R/is.validsyntax.R | 4 +-- R/metabolites.R | 30 +++++++++++----------- R/minval-internal.R | 21 +++++++++++----- R/orphan.products.R | 13 +++++---- R/orphan.reactants.R | 10 +++---- R/products.R | 21 +++++++++------- R/reactants.R | 21 +++++++++------- R/toChEBI.R | 34 +++++++++++++------------ R/unbalanced.R | 63 ++++++++++++++++-------------------------------- data/chebi.RData |binary man/chebi.candidates.Rd | 18 ------------- man/chebi.formula.Rd | 6 ---- man/compartments.Rd | 2 + man/glugln.Rd | 2 - man/metabolites.Rd | 24 +++++++++--------- man/minval-package.Rd | 4 +-- man/orphan.products.Rd | 2 - man/orphan.reactants.Rd | 14 +++++----- man/products.Rd | 4 +-- man/reactants.Rd | 4 +-- man/unbalanced.Rd | 6 ++-- 28 files changed, 186 insertions(+), 209 deletions(-)
Title: Binary Dimensionality Reduction
Description: Dimensionality reduction techniques for binary data including
logistic PCA.
Author: Andrew J. Landgraf
Maintainer: Andrew J. Landgraf <andland@gmail.com>
Diff between logisticPCA versions 0.1 dated 2015-10-05 and 0.2 dated 2016-03-14
DESCRIPTION | 15 LICENSE | 4 MD5 | 75 +- NAMESPACE | 58 - NEWS.md |only R/convexLogisticPCA.R | 917 +++++++++++++------------- R/data.R | 58 - R/logisticPCA-package.R | 24 R/logisticPCA.R | 1068 ++++++++++++++++--------------- R/logisticSVD.R | 970 ++++++++++++++-------------- README.md | 97 +- build/vignette.rds |binary inst/CITATION | 36 - inst/doc/logisticPCA.R | 115 +-- inst/doc/logisticPCA.Rmd | 343 +++++---- inst/doc/logisticPCA.html | 475 ++++++------- man/convexLogisticPCA.Rd | 160 ++-- man/cv.clpca.Rd | 92 +- man/cv.lpca.Rd | 92 +- man/cv.lsvd.Rd | 84 +- man/fitted.lpca.Rd | 72 +- man/fitted.lsvd.Rd | 72 +- man/house_votes84.Rd | 76 +- man/inv.logit.mat.Rd | 50 - man/log_like_Bernoulli.Rd | 42 - man/logisticPCA-package.Rd | 28 man/logisticPCA.Rd | 161 ++-- man/logisticSVD.Rd | 164 ++-- man/plot.clpca.Rd | 76 +- man/plot.cv.lpca.Rd | 64 - man/plot.lpca.Rd | 76 +- man/plot.lsvd.Rd | 76 +- man/predict.clpca.Rd | 86 +- man/predict.lpca.Rd | 86 +- man/predict.lsvd.Rd | 122 +-- man/project.Fantope.Rd | 42 - tests/testthat/test-dimensions.R | 375 +++++----- tests/testthat/test-dimensions_missing.R | 365 ++++------ vignettes/logisticPCA.Rmd | 343 +++++---- 39 files changed, 3575 insertions(+), 3484 deletions(-)
Title: Learning Data Cleaning, Visual Analysis and Model Performance
Description: Learn data cleaning, visual data analysis and model performance assessment (KS, AUC and ROC), package core is in the vignette documentation explaining last topics as a tutorial.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>
Diff between funModeling versions 1.0 dated 2016-02-07 and 1.1 dated 2016-03-14
funModeling-1.0/funModeling/man/cross_iterator.Rd |only funModeling-1.1/funModeling/DESCRIPTION | 8 funModeling-1.1/funModeling/MD5 | 18 - funModeling-1.1/funModeling/NEWS |only funModeling-1.1/funModeling/R/cross_plot.R | 267 ++++++++---------- funModeling-1.1/funModeling/inst/doc/funModeling.R | 11 funModeling-1.1/funModeling/inst/doc/funModeling.Rmd | 25 - funModeling-1.1/funModeling/inst/doc/funModeling.html | 18 - funModeling-1.1/funModeling/man/cross_plot.Rd | 13 funModeling-1.1/funModeling/man/massive_cross_plot.Rd | 11 funModeling-1.1/funModeling/vignettes/funModeling.Rmd | 25 - 11 files changed, 180 insertions(+), 216 deletions(-)
Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of
flow cytometry samples using the curvHDR method.
Author: Matt Wand [aut, cre],
George Luta [aut],
Ulrike Naumann [aut],
Mathew W. McLean [ctb],
Dai Feng [ctb],
Luke Tierney [ctb],
Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>
Diff between curvHDR versions 1.0-3 dated 2011-12-23 and 1.1-0 dated 2016-03-14
curvHDR-1.0-3/curvHDR/doc |only curvHDR-1.1-0/curvHDR/DESCRIPTION | 30 +++++++++++---- curvHDR-1.1-0/curvHDR/MD5 | 20 ++++++---- curvHDR-1.1-0/curvHDR/NAMESPACE | 34 +++++++++++++++++- curvHDR-1.1-0/curvHDR/R/curvHDRfilter.r | 49 ++++++++++++++------------ curvHDR-1.1-0/curvHDR/R/inpolygon.r |only curvHDR-1.1-0/curvHDR/R/plot.curvHDRfilter.r | 2 - curvHDR-1.1-0/curvHDR/R/plot3D.r | 4 +- curvHDR-1.1-0/curvHDR/R/separateTriPolyh.r | 8 +--- curvHDR-1.1-0/curvHDR/R/t2ve.r |only curvHDR-1.1-0/curvHDR/R/vertexTriangles.r |only curvHDR-1.1-0/curvHDR/man/curvHDR-internal.Rd | 2 - curvHDR-1.1-0/curvHDR/src |only curvHDR-1.1-0/curvHDR/vignettes |only 14 files changed, 101 insertions(+), 48 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.13.1 dated 2015-12-10 and 0.14.0 dated 2016-03-13
git2r-0.13.1/git2r/configure.win |only git2r-0.13.1/git2r/src/http-parser |only git2r-0.13.1/git2r/src/libgit2/annotated_commit.c |only git2r-0.13.1/git2r/src/libgit2/annotated_commit.h |only git2r-0.13.1/git2r/src/libgit2/array.h |only git2r-0.13.1/git2r/src/libgit2/attr.c |only git2r-0.13.1/git2r/src/libgit2/attr.h |only git2r-0.13.1/git2r/src/libgit2/attr_file.c |only git2r-0.13.1/git2r/src/libgit2/attr_file.h |only git2r-0.13.1/git2r/src/libgit2/attrcache.c |only git2r-0.13.1/git2r/src/libgit2/attrcache.h |only git2r-0.13.1/git2r/src/libgit2/bitvec.h |only git2r-0.13.1/git2r/src/libgit2/blame.c |only git2r-0.13.1/git2r/src/libgit2/blame.h |only git2r-0.13.1/git2r/src/libgit2/blame_git.c |only git2r-0.13.1/git2r/src/libgit2/blame_git.h |only git2r-0.13.1/git2r/src/libgit2/blob.c |only git2r-0.13.1/git2r/src/libgit2/blob.h |only git2r-0.13.1/git2r/src/libgit2/branch.c |only git2r-0.13.1/git2r/src/libgit2/branch.h |only git2r-0.13.1/git2r/src/libgit2/buf_text.c |only 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git2r-0.13.1/git2r/src/libgit2/refs.h |only git2r-0.13.1/git2r/src/libgit2/refspec.c |only git2r-0.13.1/git2r/src/libgit2/refspec.h |only git2r-0.13.1/git2r/src/libgit2/remote.c |only git2r-0.13.1/git2r/src/libgit2/remote.h |only git2r-0.13.1/git2r/src/libgit2/repo_template.h |only git2r-0.13.1/git2r/src/libgit2/repository.c |only git2r-0.13.1/git2r/src/libgit2/repository.h |only git2r-0.13.1/git2r/src/libgit2/reset.c |only git2r-0.13.1/git2r/src/libgit2/revert.c |only git2r-0.13.1/git2r/src/libgit2/revparse.c |only git2r-0.13.1/git2r/src/libgit2/revwalk.c |only git2r-0.13.1/git2r/src/libgit2/revwalk.h |only git2r-0.13.1/git2r/src/libgit2/settings.c |only git2r-0.13.1/git2r/src/libgit2/sha1_lookup.c |only git2r-0.13.1/git2r/src/libgit2/sha1_lookup.h |only git2r-0.13.1/git2r/src/libgit2/signature.c |only git2r-0.13.1/git2r/src/libgit2/signature.h |only git2r-0.13.1/git2r/src/libgit2/socket_stream.c |only git2r-0.13.1/git2r/src/libgit2/socket_stream.h |only git2r-0.13.1/git2r/src/libgit2/sortedcache.c |only git2r-0.13.1/git2r/src/libgit2/sortedcache.h |only git2r-0.13.1/git2r/src/libgit2/stash.c |only git2r-0.13.1/git2r/src/libgit2/status.c |only git2r-0.13.1/git2r/src/libgit2/status.h |only git2r-0.13.1/git2r/src/libgit2/stransport_stream.h |only git2r-0.13.1/git2r/src/libgit2/stream.h |only git2r-0.13.1/git2r/src/libgit2/strmap.c |only git2r-0.13.1/git2r/src/libgit2/strmap.h |only git2r-0.13.1/git2r/src/libgit2/strnlen.h |only git2r-0.13.1/git2r/src/libgit2/submodule.c |only git2r-0.13.1/git2r/src/libgit2/submodule.h |only git2r-0.13.1/git2r/src/libgit2/sysdir.c |only git2r-0.13.1/git2r/src/libgit2/sysdir.h |only git2r-0.13.1/git2r/src/libgit2/tag.c |only git2r-0.13.1/git2r/src/libgit2/tag.h |only git2r-0.13.1/git2r/src/libgit2/thread-utils.c |only git2r-0.13.1/git2r/src/libgit2/thread-utils.h |only git2r-0.13.1/git2r/src/libgit2/tls_stream.c |only git2r-0.13.1/git2r/src/libgit2/tls_stream.h |only git2r-0.13.1/git2r/src/libgit2/trace.c |only git2r-0.13.1/git2r/src/libgit2/trace.h |only git2r-0.13.1/git2r/src/libgit2/transaction.c |only git2r-0.13.1/git2r/src/libgit2/transport.c |only git2r-0.13.1/git2r/src/libgit2/transports |only git2r-0.13.1/git2r/src/libgit2/tree-cache.c |only git2r-0.13.1/git2r/src/libgit2/tree-cache.h |only git2r-0.13.1/git2r/src/libgit2/tree.c |only git2r-0.13.1/git2r/src/libgit2/tree.h |only git2r-0.13.1/git2r/src/libgit2/tsort.c |only git2r-0.13.1/git2r/src/libgit2/unix |only git2r-0.13.1/git2r/src/libgit2/userdiff.h |only git2r-0.13.1/git2r/src/libgit2/util.c |only git2r-0.13.1/git2r/src/libgit2/util.h |only git2r-0.13.1/git2r/src/libgit2/vector.c |only git2r-0.13.1/git2r/src/libgit2/vector.h |only git2r-0.13.1/git2r/src/libgit2/win32 |only git2r-0.13.1/git2r/src/libgit2/xdiff |only git2r-0.13.1/git2r/src/libgit2/zstream.c |only git2r-0.13.1/git2r/src/libgit2/zstream.h |only git2r-0.13.1/git2r/src/regex |only git2r-0.13.1/git2r/src/winhttp |only git2r-0.14.0/git2r/DESCRIPTION | 10 git2r-0.14.0/git2r/MD5 | 740 +- git2r-0.14.0/git2r/NEWS | 22 git2r-0.14.0/git2r/R/checkout.r | 49 git2r-0.14.0/git2r/R/commit.r | 31 git2r-0.14.0/git2r/R/fetch.r | 34 git2r-0.14.0/git2r/R/libgit2.r | 2 git2r-0.14.0/git2r/R/status.r | 3 git2r-0.14.0/git2r/cleanup | 11 git2r-0.14.0/git2r/configure | 3661 +++++----- git2r-0.14.0/git2r/configure.ac | 379 - git2r-0.14.0/git2r/inst/AUTHORS | 5 git2r-0.14.0/git2r/man/fetch-methods.Rd | 27 git2r-0.14.0/git2r/src/Makevars.in | 129 git2r-0.14.0/git2r/src/Makevars.win | 131 git2r-0.14.0/git2r/src/git2r.c | 4 git2r-0.14.0/git2r/src/git2r_config.c | 143 git2r-0.14.0/git2r/src/git2r_remote.c | 82 git2r-0.14.0/git2r/src/git2r_remote.h | 4 git2r-0.14.0/git2r/src/git2r_transfer.h | 3 git2r-0.14.0/git2r/src/libgit2/deps |only git2r-0.14.0/git2r/src/libgit2/include/git2/blame.h | 12 git2r-0.14.0/git2r/src/libgit2/include/git2/blob.h | 4 git2r-0.14.0/git2r/src/libgit2/include/git2/commit.h | 31 git2r-0.14.0/git2r/src/libgit2/include/git2/common.h | 48 git2r-0.14.0/git2r/src/libgit2/include/git2/config.h | 48 git2r-0.14.0/git2r/src/libgit2/include/git2/cred_helpers.h | 2 git2r-0.14.0/git2r/src/libgit2/include/git2/diff.h | 44 git2r-0.14.0/git2r/src/libgit2/include/git2/errors.h | 6 git2r-0.14.0/git2r/src/libgit2/include/git2/index.h | 39 git2r-0.14.0/git2r/src/libgit2/include/git2/merge.h | 60 git2r-0.14.0/git2r/src/libgit2/include/git2/rebase.h | 36 git2r-0.14.0/git2r/src/libgit2/include/git2/remote.h | 13 git2r-0.14.0/git2r/src/libgit2/include/git2/repository.h | 2 git2r-0.14.0/git2r/src/libgit2/include/git2/stash.h | 4 git2r-0.14.0/git2r/src/libgit2/include/git2/submodule.h | 13 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/config.h | 14 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/filter.h | 59 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/index.h | 2 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/odb_backend.h | 4 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/refdb_backend.h | 4 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/stream.h | 13 git2r-0.14.0/git2r/src/libgit2/include/git2/sys/transport.h | 28 git2r-0.14.0/git2r/src/libgit2/include/git2/transport.h | 11 git2r-0.14.0/git2r/src/libgit2/include/git2/version.h | 6 git2r-0.14.0/git2r/src/libgit2/src |only git2r-0.14.0/git2r/tests/add-force.R | 3 git2r-0.14.0/git2r/tests/bare_repository.R | 3 git2r-0.14.0/git2r/tests/blame.R | 3 git2r-0.14.0/git2r/tests/blob.R | 3 git2r-0.14.0/git2r/tests/branch.R | 3 git2r-0.14.0/git2r/tests/checkout-named-branch.R | 3 git2r-0.14.0/git2r/tests/checkout.R | 3 git2r-0.14.0/git2r/tests/checkout_branch.R | 3 git2r-0.14.0/git2r/tests/checkout_commit.R | 3 git2r-0.14.0/git2r/tests/checkout_tag.R | 3 git2r-0.14.0/git2r/tests/clone_bare.R | 3 git2r-0.14.0/git2r/tests/clone_branch.R | 3 git2r-0.14.0/git2r/tests/commit.R | 3 git2r-0.14.0/git2r/tests/config.R | 3 git2r-0.14.0/git2r/tests/diff.R | 3 git2r-0.14.0/git2r/tests/fast_forward_merge.R | 3 git2r-0.14.0/git2r/tests/fetch.R | 3 git2r-0.14.0/git2r/tests/graph.R | 3 git2r-0.14.0/git2r/tests/index.R | 3 git2r-0.14.0/git2r/tests/invalid-conf-var.R |only git2r-0.14.0/git2r/tests/libgit2.R | 3 git2r-0.14.0/git2r/tests/merge.R | 3 git2r-0.14.0/git2r/tests/merge_named_branch.R | 3 git2r-0.14.0/git2r/tests/normal_merge.R | 3 git2r-0.14.0/git2r/tests/note.R | 3 git2r-0.14.0/git2r/tests/odb_blobs.R | 3 git2r-0.14.0/git2r/tests/pre-process-path.R | 3 git2r-0.14.0/git2r/tests/pull.R | 3 git2r-0.14.0/git2r/tests/push-force.R | 3 git2r-0.14.0/git2r/tests/push.R | 3 git2r-0.14.0/git2r/tests/reference.R | 3 git2r-0.14.0/git2r/tests/reflog.R | 3 git2r-0.14.0/git2r/tests/refspec.R | 3 git2r-0.14.0/git2r/tests/remotes.R | 3 git2r-0.14.0/git2r/tests/remove.R | 3 git2r-0.14.0/git2r/tests/repository.R | 3 git2r-0.14.0/git2r/tests/reset.R | 3 git2r-0.14.0/git2r/tests/revparse.R | 3 git2r-0.14.0/git2r/tests/signature.R | 3 git2r-0.14.0/git2r/tests/stash.R | 3 git2r-0.14.0/git2r/tests/status.R | 9 git2r-0.14.0/git2r/tests/tag.R | 3 git2r-0.14.0/git2r/tests/time.R | 3 git2r-0.14.0/git2r/tests/tree.R | 3 git2r-0.14.0/git2r/tests/when.R | 3 git2r-0.14.0/git2r/tools/config.guess | 334 git2r-0.14.0/git2r/tools/config.sub | 106 git2r-0.14.0/git2r/tools/install-sh | 364 git2r-0.14.0/git2r/tools/libcurl.m4 |only git2r-0.14.0/git2r/tools/missing | 4 git2r-0.14.0/git2r/tools/winlibs.R |only 306 files changed, 3715 insertions(+), 3204 deletions(-)
Title: Density Estimation with a Penalized Mixture Approach
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Diff between pendensity versions 0.2.9 dated 2016-03-01 and 0.2.10 dated 2016-03-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plot.pendensity.R | 35 ++++++++++++++++++----------------- man/pendensity-package.Rd | 4 ++-- 4 files changed, 27 insertions(+), 26 deletions(-)
More information about MultivariateRandomForest at CRAN
Permanent link
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 2.0-3 dated 2016-02-23 and 2.0-4 dated 2016-03-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/predict.glmnet.R | 2 +- R/predict.multnet.R | 4 ++-- inst/doc/Coxnet.pdf |binary inst/doc/glmnet_beta.html | 28 ++++++++++++++-------------- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: Fit a Generalized Linear Mixed Model
Description: Conduct inference about generalized linear mixed models, with a
choice about which method to use to approximate the likelihood. In addition
to the Laplace and adaptive Gaussian quadrature approximations, which are
borrowed from 'lme4', the likelihood may be approximated by the sequential
reduction approximation, or an importance sampling approximation. These
methods provide an accurate approximation to the likelihood in some
situations where it is not possible to use adaptive Gaussian quadrature.
Author: Helen Ogden [aut, cre]
Maintainer: Helen Ogden <heogden12@gmail.com>
Diff between glmmsr versions 0.1.0 dated 2016-03-09 and 0.1.1 dated 2016-03-13
DESCRIPTION | 6 +- MD5 | 18 +++---- README.md | 10 +++- build/vignette.rds |binary inst/doc/glmmsr-vignette.pdf |binary inst/include/Graph.h | 37 +++++++++++---- src/BasisLevel.cpp | 8 +-- src/Graph.cpp | 105 +++++++++++++++++++++++++++++-------------- src/LogitLink.cpp | 4 - src/QuadratureRule.cpp | 9 ++- 10 files changed, 130 insertions(+), 67 deletions(-)
Title: Spell Checker and Text Parser for R
Description: A spell checker and morphological analyzer library designed for
languages with rich morphology and complex word compounding or character
encoding. The package can check and analyze individual words as well as
search for incorrect words within a text, latex or manual document.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between hunspell versions 1.0 dated 2016-03-10 and 1.1 dated 2016-03-12
hunspell-1.0/hunspell/src/bindings.cpp |only hunspell-1.1/hunspell/DESCRIPTION | 19 ++++++++------- hunspell-1.1/hunspell/MD5 | 25 ++++++++++++++------ hunspell-1.1/hunspell/NEWS |only hunspell-1.1/hunspell/R/RcppExports.R | 8 +++--- hunspell-1.1/hunspell/R/hunspell.R | 36 +++++++++++++++++++----------- hunspell-1.1/hunspell/man/hunspell.Rd | 35 ++++++++++++++++++----------- hunspell-1.1/hunspell/src/Makevars.in | 17 ++++++++++++-- hunspell-1.1/hunspell/src/Makevars.win | 16 +++++++++---- hunspell-1.1/hunspell/src/RcppExports.cpp | 30 ++++++++++++------------- hunspell-1.1/hunspell/src/check.cpp |only hunspell-1.1/hunspell/src/find.cpp |only hunspell-1.1/hunspell/src/parsers |only 13 files changed, 117 insertions(+), 69 deletions(-)
Title: Functions for Analysis of Data with General Recognition Theory
Description: Tools associated with General
Recognition Theory (Townsend & Ashby, 1986), including Gaussian model fitting of 2x2 and more
general designs, associated plotting and model comparison tools,
and tests of marginal response invariance and report independence.
Author: Robert X.D. Hawkins <rxdh@stanford.edu>, Joe Houpt
<joseph.houpt@wright.edu>, Noah Silbert <noahpoah@gmail.com>, Leslie
Blaha <Leslie.Blaha@wpafb.af.mil>, Thomas D. Wickens
<twickens@socrates.berkeley.edu>
Maintainer: Robert X.D. Hawkins <rxdh@stanford.edu>
Diff between mdsdt versions 1.1 dated 2015-09-01 and 1.2 dated 2016-03-12
mdsdt-1.1/mdsdt/README.md |only mdsdt-1.1/mdsdt/data/thomasA.rda |only mdsdt-1.1/mdsdt/data/thomasB.rda |only mdsdt-1.1/mdsdt/man/thomasA.Rd |only mdsdt-1.1/mdsdt/man/thomasB.Rd |only mdsdt-1.2/mdsdt/DESCRIPTION | 12 +- mdsdt-1.2/mdsdt/MD5 | 39 +++--- mdsdt-1.2/mdsdt/R/grt-data.R | 40 +++++- mdsdt-1.2/mdsdt/R/grt_base.R | 211 ++++++++++++++++++++++-------------- mdsdt-1.2/mdsdt/data/silbert09a.rda |binary mdsdt-1.2/mdsdt/data/silbert09b.rda |binary mdsdt-1.2/mdsdt/data/thomas01a.rda |only mdsdt-1.2/mdsdt/data/thomas01b.rda |only mdsdt-1.2/mdsdt/data/thomas15a.rda |only mdsdt-1.2/mdsdt/data/thomas15b.rda |only mdsdt-1.2/mdsdt/man/GOF.Rd | 6 - mdsdt-1.2/mdsdt/man/fit.grt.Rd | 17 +- mdsdt-1.2/mdsdt/man/mriTest.Rd | 4 mdsdt-1.2/mdsdt/man/plot.grt.Rd | 9 + mdsdt-1.2/mdsdt/man/riTest.Rd | 4 mdsdt-1.2/mdsdt/man/silbert09a.Rd | 2 mdsdt-1.2/mdsdt/man/silbert09b.Rd | 2 mdsdt-1.2/mdsdt/man/silbert12.Rd | 2 mdsdt-1.2/mdsdt/man/thomas01a.Rd |only mdsdt-1.2/mdsdt/man/thomas01b.Rd |only mdsdt-1.2/mdsdt/man/thomas15a.Rd |only mdsdt-1.2/mdsdt/man/thomas15b.Rd |only 27 files changed, 217 insertions(+), 131 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat. 'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.60 dated 2016-03-08 and 0.62 dated 2016-03-12
DESCRIPTION | 23 MD5 | 159 ++--- NAMESPACE | 103 +++ R/PLS_chill_force.R | 501 +++++++++++++----- R/PLS_pheno.R | 412 ++++++++++---- R/VIP.R | 69 ++ R/YEARMODA2Date.R | 32 - R/bloom_prediction.R | 268 +++++++-- R/chile_agromet2chillR.R | 105 ++- R/chillR-package.R |only R/chillR.R | 2 R/chilling.R | 419 ++++++++++----- R/chilling_hourtable.R | 372 +++++++++---- R/color_bar_maker.R | 60 +- R/daily_chill.R | 210 ++++++- R/fix_weather.R | 186 ++++-- R/get_last_date.R | 47 + R/get_weather.R | 182 ++++-- R/handle_chile_agromet.R | 343 ++++++++---- R/handle_cimis.R | 554 ++++++++++++-------- R/handle_gsod.R | 434 ++++++++++----- R/handle_ucipm.R | 399 +++++++++----- R/handle_wunderground.R | 357 ++++++++---- R/interpolate_gaps.R | 121 ++-- R/leap_year.R | 26 R/make_all_day_table.R | 99 ++- R/make_california_UCIPM_station_list.R | 80 +- R/make_chill_plot.R | 219 ++++--- R/make_daily_chill_figures.R | 263 +++++++-- R/make_daily_chill_plot.R | 405 ++++++++------ R/make_hourly_temps.R | 194 ++++--- R/make_multi_pheno_trend_plot.R | 348 +++++++----- R/make_pheno_trend_plot.R | 360 ++++++++----- R/plot_pheno_results.R | 825 +++++++++++++++++------------- R/runn_mean.R | 51 + R/stack_hourly_temps.R | 101 ++- R/tempResponse.R | 192 ++++-- R/temp_models.R | 420 +++++++++++---- R/weather2chillR.R | 97 ++- man/Chilling_Hours.Rd | 104 ++- man/Dynamic_Model.Rd | 99 ++- man/GDH.Rd | 91 +-- man/KA_bloom.Rd | 62 +- man/KA_weather.Rd | 65 +- man/PLS_chill_force.Rd | 428 +++++++++------ man/PLS_pheno.Rd | 272 ++++++--- man/Utah_Model.Rd | 99 ++- man/VIP.Rd | 111 ++-- man/YEARMODA2Date.Rd | 63 +- man/bloom_prediction.Rd | 298 ++++++---- man/california_stations.Rd | 60 +- man/chile_agromet2chillR.Rd | 108 ++- man/chillR-package.Rd | 144 +++-- man/chilling.Rd | 305 ++++++----- man/chilling_hourtable.Rd | 281 ++++++---- man/color_bar_maker.Rd | 110 ++-- man/daily_chill.Rd | 287 ++++++---- man/fix_weather.Rd | 120 ++-- man/get_last_date.Rd | 70 +- man/get_weather.Rd | 197 ++++--- man/handle_chile_agromet.Rd | 187 ++++-- man/handle_cimis.Rd | 209 ++++--- man/handle_gsod.Rd | 210 ++++--- man/handle_ucipm.Rd | 196 ++++--- man/handle_wunderground.Rd | 204 ++++--- man/interpolate_gaps.Rd | 95 +-- man/leap_year.Rd | 69 +- man/make_all_day_table.Rd | 82 +- man/make_california_UCIPM_station_list.Rd | 66 +- man/make_chill_plot.Rd | 115 ++-- man/make_daily_chill_figures.Rd | 293 ++++++---- man/make_daily_chill_plot.Rd | 136 +++- man/make_hourly_temps.Rd | 120 ++-- man/make_multi_pheno_trend_plot.Rd | 138 +++-- man/make_pheno_trend_plot.Rd | 243 +++++--- man/plot_PLS.Rd | 216 +++++-- man/runn_mean.Rd | 59 +- man/stack_hourly_temps.Rd | 99 ++- man/step_model.Rd | 115 ++-- man/tempResponse.Rd | 158 +++-- man/weather2chillR.Rd | 139 ++--- 81 files changed, 10025 insertions(+), 5536 deletions(-)
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness. This is the 'lite' version of the more complete 'viridis' package
that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.1.2 dated 2016-03-04 and 0.1.3 dated 2016-03-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/viridis.R | 10 ++++++++-- README.md | 2 +- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3.3 dated 2016-03-04 and 0.3.4 dated 2016-03-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/viridis.R | 10 ++++++++-- README.md | 2 +- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Phylogenetic Comparative Tools for Missing Data and
Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between Rphylopars versions 0.1.1 dated 2015-06-02 and 0.2.1 dated 2016-03-12
Rphylopars-0.1.1/Rphylopars/man/phylopars.crossvalidate.Rd |only Rphylopars-0.1.1/Rphylopars/man/phylopars.pca.Rd |only Rphylopars-0.1.1/Rphylopars/man/phylopars.predict.Rd |only Rphylopars-0.1.1/Rphylopars/man/phylopars.rerun.Rd |only Rphylopars-0.1.1/Rphylopars/man/plot.crossvalidate.Rd |only Rphylopars-0.1.1/Rphylopars/man/print.crossvalidate.Rd |only Rphylopars-0.2.1/Rphylopars/DESCRIPTION | 13 Rphylopars-0.2.1/Rphylopars/MD5 | 28 Rphylopars-0.2.1/Rphylopars/NAMESPACE | 25 Rphylopars-0.2.1/Rphylopars/R/RcppExports.R | 60 Rphylopars-0.2.1/Rphylopars/R/phylopars_main.R | 1796 -------- Rphylopars-0.2.1/Rphylopars/R/phylopars_update.R |only Rphylopars-0.2.1/Rphylopars/README.md |only Rphylopars-0.2.1/Rphylopars/man/Rphylopars-package.Rd | 27 Rphylopars-0.2.1/Rphylopars/man/phylopars.Rd | 126 Rphylopars-0.2.1/Rphylopars/man/phylopars.lm.Rd | 123 Rphylopars-0.2.1/Rphylopars/man/simtraits.Rd | 19 Rphylopars-0.2.1/Rphylopars/src/RcppExports.cpp | 429 -- Rphylopars-0.2.1/Rphylopars/src/phylopars_rcpp.cpp | 2687 ++----------- 19 files changed, 936 insertions(+), 4397 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Jeroen Ooms [aut],
Carl Boettiger [aut],
Scott Chamberlain [aut],
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-6 dated 2016-02-18 and 1.0.17-7 dated 2016-03-12
redland-1.0.17-6/redland/inst/Makefile |only redland-1.0.17-6/redland/inst/config.log |only redland-1.0.17-6/redland/inst/config.status |only redland-1.0.17-6/redland/tools/Makefile |only redland-1.0.17-6/redland/tools/NEWS |only redland-1.0.17-6/redland/tools/README |only redland-1.0.17-6/redland/tools/aclocal.m4 |only redland-1.0.17-6/redland/tools/config.log |only redland-1.0.17-6/redland/tools/config.status |only redland-1.0.17-7/redland/DESCRIPTION | 8 +- redland-1.0.17-7/redland/MD5 | 35 ++++-------- redland-1.0.17-7/redland/NEWS | 9 +++ redland-1.0.17-7/redland/R/redland.R | 4 - redland-1.0.17-7/redland/README.md | 19 +++++- redland-1.0.17-7/redland/tests/testthat/test.Model.R | 16 ++--- redland-1.0.17-7/redland/tests/testthat/test.Node.R | 8 -- redland-1.0.17-7/redland/tests/testthat/test.Parser.R | 22 +++---- redland-1.0.17-7/redland/tests/testthat/test.Query.R | 8 +- redland-1.0.17-7/redland/tests/testthat/test.Serializer.R | 22 +++---- redland-1.0.17-7/redland/tests/testthat/test.Statement.R | 12 ++-- redland-1.0.17-7/redland/tests/testthat/test.Storage.R | 4 - redland-1.0.17-7/redland/tests/testthat/test.World.R | 2 redland-1.0.17-7/redland/tests/testthat/test.redland_base.R | 12 ++-- 23 files changed, 96 insertions(+), 85 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between PVAClone versions 0.1-5 dated 2016-02-05 and 0.1-6 dated 2016-03-12
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 4 ++-- R/pva-methods.R | 19 +++++++++++++------ inst/ChangeLog | 8 ++++++++ 5 files changed, 34 insertions(+), 19 deletions(-)
Title: The Guardian API Wrapper
Description: Provides an interface to the Open Platform's Content API of the Guardian Media Group. It retrieves content from news outlets The Observer, The Guardian, and guardian.co.uk from 1999 to current day.
Author: Marco T. Bastos & Cornelius Puschmann
Maintainer: Marco T. Bastos <marco@toledobastos.com>
Diff between GuardianR versions 0.5 dated 2014-09-16 and 0.6 dated 2016-03-12
ChangeLog | 8 +++++++- DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/guardianr.R | 12 ++++++++---- man/GuardianR-package.Rd | 8 ++++---- man/get_guardian.Rd | 8 ++++---- man/get_json.Rd | 2 +- man/parse_json_to_df.Rd | 2 +- 9 files changed, 41 insertions(+), 30 deletions(-)
Title: Fermi Large Area Telescope Catalogs
Description: Data from various catalogs of astrophysical gamma-ray sources
detected by NASA's Large Area Telescope (The Astrophysical Journal, 697, 1071,
2009 June 1), on board the Fermi gamma-ray satellite. More information on
Fermi and its data products is available from the Fermi Science Support Center
(http://fermi.gsfc.nasa.gov/ssc/).
Author: Pablo Saz Parkinson [aut, cre]
Maintainer: Pablo Saz Parkinson <sazpark2@gmail.com>
Diff between fermicatsR versions 1.3 dated 2015-05-28 and 1.4 dated 2016-03-12
DESCRIPTION | 17 +-- MD5 | 40 ++++--- R/fermicatsR.R | 285 ++++++++++++++++++++++++++++++++++++++++++++++++++--- data/DF1.rdata |only data/FGL0.rdata |binary data/FGL1.rdata |binary data/FGL2.rdata |binary data/FGL3.rdata |binary data/FHL2.rdata |only data/FIG1.rdata |only data/LAC3_HI.rdata |only data/LAC3_LO.rdata |only data/datalist | 5 data/pulsars.rdata |binary man/DF1.Rd |only man/FGL0.Rd | 12 +- man/FGL1.Rd | 22 ++-- man/FGL2.Rd | 26 ++-- man/FGL3.Rd | 36 +++--- man/FHL1.Rd | 82 +++++++-------- man/FHL2.Rd |only man/FIG1.Rd |only man/LAC3_HI.Rd |only man/LAC3_LO.Rd |only man/fermicatsR.Rd | 32 +++-- man/pulsars.Rd | 15 +- 26 files changed, 425 insertions(+), 147 deletions(-)
Title: Hierarchical Models Made Easy with Data Cloning
Description: S4 classes around infrastructure provided by the
'coda' and 'dclone' packages to make package development easy as a breeze
with data cloning for hierarchical models.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dcmle versions 0.3-0 dated 2016-01-14 and 0.3-1 dated 2016-03-12
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 ++-- R/dcmle-methods.R | 4 +++- inst/ChangeLog | 7 +++++++ tests/dcmle_tests.R | 8 ++++---- 6 files changed, 26 insertions(+), 17 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing
maximum likelihood estimating procedures for
complex models using data cloning and Bayesian
Markov chain Monte Carlo methods.
Sequential and parallel MCMC support
for JAGS, WinBUGS and OpenBUGS.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dclone versions 2.1-1 dated 2016-01-12 and 2.1-2 dated 2016-03-12
dclone-2.1-1/dclone/R/snowWrapper.R |only dclone-2.1-1/dclone/man/snowWrapper.Rd |only dclone-2.1-2/dclone/DESCRIPTION | 12 dclone-2.1-2/dclone/MD5 | 86 +- dclone-2.1-2/dclone/NAMESPACE | 1 dclone-2.1-2/dclone/R/bugs.parfit.R | 2 dclone-2.1-2/dclone/R/codaSamples.R | 31 dclone-2.1-2/dclone/R/dc.parfit.R | 4 dclone-2.1-2/dclone/R/jags.parfit.R | 2 dclone-2.1-2/dclone/R/parCodaSamples.R | 99 +- dclone-2.1-2/dclone/inst/CITATION | 36 - dclone-2.1-2/dclone/inst/ChangeLog | 845 ++++++++++++------------ dclone-2.1-2/dclone/man/DcloneEnv.Rd | 206 ++--- dclone-2.1-2/dclone/man/bugs.fit.Rd | 318 ++++----- dclone-2.1-2/dclone/man/bugs.parfit.Rd | 292 ++++---- dclone-2.1-2/dclone/man/clusterSize.Rd | 170 ++-- dclone-2.1-2/dclone/man/clusterSplitSB.Rd | 186 ++--- dclone-2.1-2/dclone/man/codaSamples.Rd | 17 dclone-2.1-2/dclone/man/coef.mcmc.list.Rd | 230 +++--- dclone-2.1-2/dclone/man/dc.fit.Rd | 530 +++++++-------- dclone-2.1-2/dclone/man/dc.parfit.Rd | 632 ++++++++--------- dclone-2.1-2/dclone/man/dcFit.Rd | 212 +++--- dclone-2.1-2/dclone/man/dclone-package.Rd | 189 ++--- dclone-2.1-2/dclone/man/dclone.Rd | 364 +++++----- dclone-2.1-2/dclone/man/dcoptions.Rd | 122 +-- dclone-2.1-2/dclone/man/dctable.Rd | 430 ++++++------ dclone-2.1-2/dclone/man/errlines.Rd | 188 ++--- dclone-2.1-2/dclone/man/evalParallelArgument.Rd | 86 +- dclone-2.1-2/dclone/man/jags.fit.Rd | 256 +++---- dclone-2.1-2/dclone/man/jags.parfit.Rd | 294 ++++---- dclone-2.1-2/dclone/man/lambdamax.diag.Rd | 164 ++-- dclone-2.1-2/dclone/man/make.symmetric.Rd | 90 +- dclone-2.1-2/dclone/man/mclapplySB.Rd | 4 dclone-2.1-2/dclone/man/mcmcapply.Rd | 120 +-- dclone-2.1-2/dclone/man/nclones.Rd | 80 +- dclone-2.1-2/dclone/man/ovenbird.Rd | 82 +- dclone-2.1-2/dclone/man/pairs.mcmc.list.Rd | 152 ++-- dclone-2.1-2/dclone/man/parCodaSamples.Rd | 17 dclone-2.1-2/dclone/man/parDosa.Rd | 291 ++++---- dclone-2.1-2/dclone/man/parJagsModel.Rd | 2 dclone-2.1-2/dclone/man/parUpdate.Rd | 2 dclone-2.1-2/dclone/man/parallel.inits.Rd | 136 +-- dclone-2.1-2/dclone/man/regmod.Rd | 104 +- dclone-2.1-2/dclone/man/update.mcmc.list.Rd | 254 +++---- dclone-2.1-2/dclone/man/write.jags.model.Rd | 286 ++++---- 45 files changed, 3820 insertions(+), 3804 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.8 dated 2015-12-10 and 1.0.9 dated 2016-03-12
rscala-1.0.8/rscala/inst/doc/readme.html |only rscala-1.0.8/rscala/inst/java/rscala_2.10-1.0.8.jar |only rscala-1.0.8/rscala/inst/java/rscala_2.11-1.0.8.jar |only rscala-1.0.8/rscala/java/rscala_2.10-1.0.8-sources.jar |only rscala-1.0.8/rscala/java/rscala_2.11-1.0.8-sources.jar |only rscala-1.0.9/rscala/DESCRIPTION | 8 +++---- rscala-1.0.9/rscala/MD5 | 19 ++++++++--------- rscala-1.0.9/rscala/NEWS | 4 +++ rscala-1.0.9/rscala/R/protocol.R | 2 - rscala-1.0.9/rscala/R/scalaInterpreter.R | 12 +++++----- rscala-1.0.9/rscala/inst/README |only rscala-1.0.9/rscala/inst/doc/index.html |only rscala-1.0.9/rscala/inst/java/rscala_2.10-1.0.9.jar |only rscala-1.0.9/rscala/inst/java/rscala_2.11-1.0.9.jar |only rscala-1.0.9/rscala/java/rscala_2.10-1.0.9-sources.jar |only rscala-1.0.9/rscala/java/rscala_2.11-1.0.9-sources.jar |only 16 files changed, 25 insertions(+), 20 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between mboost versions 2.5-0 dated 2015-08-14 and 2.6-0 dated 2016-03-12
mboost-2.5-0/mboost/man/helper.Rd |only mboost-2.6-0/mboost/DESCRIPTION | 32 ++--- mboost-2.6-0/mboost/MD5 | 47 ++++---- mboost-2.6-0/mboost/NAMESPACE | 7 - mboost-2.6-0/mboost/R/bkronecker.R | 15 +- mboost-2.6-0/mboost/R/bl.R | 15 +- mboost-2.6-0/mboost/R/btree.R | 23 ++-- mboost-2.6-0/mboost/R/crossvalidation.R | 8 - mboost-2.6-0/mboost/R/helpers.R | 20 ++- mboost-2.6-0/mboost/R/mboost.R | 94 +++++++++++++---- mboost-2.6-0/mboost/R/mboost_intern.R |only mboost-2.6-0/mboost/R/methods.R | 1 mboost-2.6-0/mboost/build/vignette.rds |binary mboost-2.6-0/mboost/inst/NEWS.Rd | 68 ++++++++++-- mboost-2.6-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary mboost-2.6-0/mboost/inst/doc/mboost.pdf |binary mboost-2.6-0/mboost/inst/doc/mboost_illustrations.Rnw | 2 mboost-2.6-0/mboost/inst/doc/mboost_illustrations.pdf |binary mboost-2.6-0/mboost/inst/doc/mboost_tutorial.pdf |binary mboost-2.6-0/mboost/man/blackboost.Rd | 5 mboost-2.6-0/mboost/man/glmboost.Rd | 17 +-- mboost-2.6-0/mboost/man/mboost.Rd | 4 mboost-2.6-0/mboost/man/mboost_intern.Rd |only mboost-2.6-0/mboost/man/mboost_package.Rd | 28 ++++- mboost-2.6-0/mboost/man/methods.Rd | 5 mboost-2.6-0/mboost/vignettes/mboost_illustrations.Rnw | 2 26 files changed, 274 insertions(+), 119 deletions(-)
Title: Test Analysis Modules
Description:
Includes marginal maximum likelihood estimation of uni- and
multidimensional item response models (Rasch, 2PL, 3PL,
Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models)
and joint maximum likelihood estimation for models
from the Rasch family.
Latent regression models and plausible value imputation are
also supported.
Author:
Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 1.16-0 dated 2016-02-01 and 1.17-0 dated 2016-03-11
DESCRIPTION | 20 +-- MD5 | 130 +++++++++++-------- NAMESPACE | 250 ++++++++++++++++++++------------------ R/DescribeBy.R |only R/IRTLikelihood.cfa.R | 2 R/IRTLikelihood.ctt.R |only R/Scale.R |only R/TAM-internal_helper.R | 4 R/WLErel.R |only R/plot.tam.R | 4 R/print.tam.R |only R/print.tam.wle.R |only R/summary.tam.R | 12 - R/summary.tam.modelfit.R | 6 R/tam.jml2.R | 11 - R/tam.mml.2pl.R | 11 - R/tam.mml.3pl.R | 11 - R/tam.mml.3pl.est.guessing.R | 8 - R/tam.mml.R | 3 R/tam.mml.mfr.R | 4 R/tam.modelfit.R | 6 R/tam.pv.R | 10 - R/tam.wle.R | 68 +++++++--- R/tamaan.R | 2 R/tampv2datalist.R | 2 R/weighted_mean.R |only R/weighted_quantile.R |only R/weighted_skewness.R |only R/weighted_table.R |only R/weighted_var.R |only R/zzz.R | 11 - data/data.cqc01.rda |binary data/data.cqc02.rda |binary data/data.cqc03.rda |binary data/data.cqc04.rda |binary data/data.cqc05.rda |binary data/data.ctest1.rda |binary data/data.ctest2.rda |binary data/data.ex08.rda |binary data/data.ex10.rda |binary data/data.ex11.rda |binary data/data.ex12.rda |binary data/data.ex14.rda |binary data/data.ex15.rda |binary data/data.exJ03.rda |binary data/data.fims.Aus.Jpn.raw.rda |binary data/data.fims.Aus.Jpn.scored.rda |binary data/data.geiser.rda |binary data/data.gpcm.rda |binary data/data.janssen.rda |binary data/data.janssen2.rda |binary data/data.mc.rda |binary data/data.numeracy.rda |binary data/data.sim.facets.rda |binary data/data.sim.mfr.rda |binary data/data.sim.rasch.missing.rda |binary data/data.sim.rasch.pweights.rda |binary data/data.sim.rasch.rda |binary data/data.timssAusTwn.rda |binary data/data.timssAusTwn.scored.rda |binary inst/NEWS | 45 ++++++ man/DescribeBy.Rd |only man/IRTLikelihood.ctt.Rd |only man/Scale.Rd |only man/TAM-package.Rd | 18 +- man/WLErel.Rd |only man/tam.latreg.Rd | 6 man/tam.mml.3pl.Rd | 63 +++++++++ man/tam.mml.Rd | 47 ++++++- man/tam.pv.Rd | 17 +- man/tam.wle.Rd | 8 + man/tamaan.Rd | 14 ++ man/tampv2datalist.Rd | 4 man/weighted_Stats.Rd |only 74 files changed, 527 insertions(+), 270 deletions(-)
Title: Interface to the 'Handsontable.js' Library
Description: An R interface to the 'Handsontable' JavaScript library, which is a
minimalist Excel-like data grid editor.
Author: Jonathan Owen [aut, cre, cph],
Jeff Allen [ctb],
Yihui Xie [ctb],
Enzo Martoglio [ctb],
Warpechowski Marcin [ctb, cph] (Handsontable.js library),
Handsoncode sp. z o.o. [ctb, cph] (Handsontable.js library),
Aisch Gregor [ctb, cph] (Chroma.js library),
Wood Tim [ctb, cph] (Moment.js library),
Chernev Iskren [ctb, cph] (Moment.js library),
Moment.js contributors [ctb, cph] (Moment.js library),
Bushell David [ctb, cph] (Pikaday.js library),
jQuery Foundation [ctb, cph] (jQuery.js library),
Splunk Inc [ctb, cph] (Sparkline.js library),
Rohan Jon [ctb, cph] (ZeroClipboard library),
Greene James [ctb, cph] (ZeroClipboard library)
Maintainer: Jonathan Owen <jonathanro@gmail.com>
Diff between rhandsontable versions 0.3 dated 2016-02-01 and 0.3.1 dated 2016-03-11
rhandsontable-0.3.1/rhandsontable/DESCRIPTION | 8 rhandsontable-0.3.1/rhandsontable/MD5 | 30 - rhandsontable-0.3.1/rhandsontable/NEWS | 13 rhandsontable-0.3.1/rhandsontable/R/rhandsontable.R | 73 ++-- rhandsontable-0.3.1/rhandsontable/inst/doc/intro_rhandsontable.R | 103 ++--- rhandsontable-0.3.1/rhandsontable/inst/doc/intro_rhandsontable.Rmd | 112 +++--- rhandsontable-0.3.1/rhandsontable/inst/doc/intro_rhandsontable.html | 178 +++++----- rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/lib/chroma/chroma.min.js |only rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.css | 4 rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/lib/handsontable/handsontable.full.min.js | 39 -- rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/lib/jquery/jquery.min.js |only rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/lib/sparkline/jquery.sparkline.min.js |only rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/rhandsontable.js | 12 rhandsontable-0.3.1/rhandsontable/inst/htmlwidgets/rhandsontable.yaml | 14 rhandsontable-0.3.1/rhandsontable/man/hot_table.Rd | 5 rhandsontable-0.3.1/rhandsontable/vignettes/intro_rhandsontable.Rmd | 112 +++--- rhandsontable-0.3/rhandsontable/inst/htmlwidgets/lib/chroma/chroma.js |only rhandsontable-0.3/rhandsontable/inst/htmlwidgets/lib/jquery/jquery.js |only rhandsontable-0.3/rhandsontable/inst/htmlwidgets/lib/sparkline/jquery.sparkline.js |only 19 files changed, 369 insertions(+), 334 deletions(-)
Title: Randomization for Clinical Trials
Description: This tool enables the user to choose a randomization procedure
based on sound scientific criteria. It comprises the generation of
randomization sequences as well the assessment of randomization procedures
based on carefully selected criteria. Furthermore, randomizeR provides a
function for the comparison of randomization procedures.
Author: David Schindler [aut],
Diane Uschner [aut, cre],
Martin Manolov [ctb],
Thi Mui Pham [ctb],
Ralf-Dieter Hilgers [aut, ths],
Nicole Heussen [aut, ths]
Maintainer: Diane Uschner <duschner@ukaachen.de>
Diff between randomizeR versions 1.1.0 dated 2016-01-19 and 1.2.0 dated 2016-03-11
DESCRIPTION | 26 ++++++++------ MD5 | 30 ++++++++-------- NAMESPACE | 1 NEWS.md |only R/assess.R | 51 ++++++++++++++-------------- R/ebcPar.R | 6 --- R/randSeq.R | 40 ++++++++++----------- R/randomizeRPackage.R | 3 + build/vignette.rds |binary inst/doc/comparison-example.Rnw | 2 - inst/doc/comparison-example.pdf |binary inst/doc/randomizeR-refCard.pdf |binary man/plotSeq.Rd | 2 - man/randomizeR-package.Rd | 2 - tests/testthat/test_sequenceProbability.R | 2 - vignettes/comparison-example.Rnw | 2 - vignettes/randomizeRQuickReferenceGuide.pdf |only 17 files changed, 86 insertions(+), 81 deletions(-)
Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
Diff between FRESA.CAD versions 2.1.3 dated 2015-09-04 and 2.2.0 dated 2016-03-11
DESCRIPTION | 10 MD5 | 80 +++--- NAMESPACE | 2 NEWS | 21 + R/FRESA.Model.R | 32 +- R/ForwardSelection.Model.Bin.R | 24 +- R/ForwardSelection.Model.Res.R | 17 + R/backVarElimination.Bin.R | 32 +- R/backVarElimination.Res.R | 31 +- R/baggedModel.R |only R/bootstrapValidation.Bin.R | 37 --- R/bootstrapValidation.Res.R | 50 ++-- R/bootstrapVarElimination.Bin.R | 93 ++++--- R/bootstrapVarElimination.Res.R | 188 ++++++++------- R/crossValidationFeatureSelection.Bin.R | 176 ++++++++------ R/crossValidationFeatureSelection.Res.R | 321 +++++++++++++++------------ R/getKNNpredictionFromFormula.R | 32 ++ R/heatMaps.R | 341 ++++++++++++++++++----------- R/listTopCorrelatedVariables.R | 21 + R/medianPredict.R | 83 +++++-- R/plot.bootstrapValidation.Bin.R | 2 R/plot.bootstrapValidation.Res.R | 2 R/plotModels.ROC.R | 90 +++++-- R/residualtForFRESA.R | 20 - R/uniRankVar.R | 76 +++++- R/updateModel.Bin.R | 61 +---- R/updateModel.Res.R | 50 ---- man/FRESA.CAD-package.Rd | 4 man/FRESA.Model.Rd | 12 - man/ForwardModel.Bin.Rd | 5 man/ForwardModel.Res.Rd | 3 man/baggedModel.Rd |only man/bootstrapValidation.Bin.Rd | 3 man/crossValidationFeatureSelection.Bin.Rd | 14 + man/crossValidationFeatureSelection.Res.Rd | 20 + man/heatMaps.Rd | 18 - man/medianPredict.Rd | 4 man/plotModels.ROC.Rd | 20 + src/FRESAcommons.cpp | 93 +++++-- src/FRESAcommons.h | 3 src/binaryFeatureSelectionCpp.cpp | 140 +++++++---- src/regresionFeatureSelectionCpp.cpp | 155 ++++++------- 42 files changed, 1418 insertions(+), 968 deletions(-)
Title: Statistical Comparisons of Two or more Alpha Coefficients
Description: Statistical tests for the comparison between two or more alpha
coefficients based on either dependent or independent groups of individuals.
A web interface is available at http://comparingcronbachalphas.org. A plugin
for the R GUI and IDE RKWard is included. Please install RKWard from https://
rkward.kde.org to use this feature. The respective R package 'rkward' cannot be
installed directly from a repository, as it is a part of RKWard.
Author: Birk Diedenhofen [aut, cre]
Maintainer: Birk Diedenhofen <mail@birkdiedenhofen.de>
Diff between cocron versions 1.0-0 dated 2013-09-21 and 1.0-1 dated 2016-03-11
cocron-1.0-0/cocron/R/helper.r |only cocron-1.0-1/cocron/ChangeLog | 4 cocron-1.0-1/cocron/DESCRIPTION | 32 +-- cocron-1.0-1/cocron/MD5 | 36 +-- cocron-1.0-1/cocron/NAMESPACE | 4 cocron-1.0-1/cocron/R/0helper.r |only cocron-1.0-1/cocron/R/cocron-package.R | 13 - cocron-1.0-1/cocron/inst/CITATION | 22 +- cocron-1.0-1/cocron/inst/rkward/cocron.pluginmap | 23 +- cocron-1.0-1/cocron/inst/rkward/plugins/ComparingCronbachalphas.js | 32 +-- cocron-1.0-1/cocron/inst/rkward/plugins/ComparingCronbachalphas.rkh | 50 ++++ cocron-1.0-1/cocron/inst/rkward/plugins/ComparingCronbachalphas.xml | 46 ++-- cocron-1.0-1/cocron/inst/rkward/rkwarddev.cocron.plugin.script.R | 41 ++- cocron-1.0-1/cocron/man/cocron-package.Rd | 30 +- cocron-1.0-1/cocron/man/cocron.Rd | 74 ++----- cocron-1.0-1/cocron/man/cocron.n.coefficients.Rd | 99 ++++----- cocron-1.0-1/cocron/man/cocron.two.coefficients.Rd | 105 ++++------ cocron-1.0-1/cocron/man/cronbach.alpha.CI.Rd | 63 ++---- cocron-1.0-1/cocron/man/cronbach.alpha.Rd | 61 ++--- cocron-1.0-1/cocron/man/knowledge.Rd | 3 20 files changed, 376 insertions(+), 362 deletions(-)
Title: A Collection of Functions to Help with Analysis of Coarsely
Observed Data
Description: Functions to analyze coarse data.
Specifically, it contains functions to (1) fit parametric accelerated
failure time models to interval-censored survival time data, and (2)
estimate the case-fatality ratio in scenarios with under-reporting.
This package's development was motivated by applications to infectious
disease: in particular, problems with estimating the incubation period and
the case fatality ratio of a given disease. Sample data files are included
in the package.
Author: Nicholas G. Reich <nick@schoolph.umass.edu>, Justin Lessler
<jlessler@jhsph.edu>, Andrew Azman <andrewazman@gmail.com>
Maintainer: Nicholas G. Reich <nick@schoolph.umass.edu>
Diff between coarseDataTools versions 0.6-2 dated 2013-08-05 and 0.6-3 dated 2016-03-11
ChangeLog | 4 +++- DESCRIPTION | 14 +++++++------- MD5 | 11 ++++++----- NAMESPACE | 12 ++++++++++-- README.md | 9 +++++++++ build |only inst/doc/CFR_vignette.pdf |binary 7 files changed, 35 insertions(+), 15 deletions(-)
More information about coarseDataTools at CRAN
Permanent link
Title: Chaos Game
Description: The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities (IFSP) is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between ChaosGame versions 0.1 dated 2016-02-23 and 0.2 dated 2016-03-11
ChaosGame-0.1/ChaosGame/R/plot_hist3D.R |only ChaosGame-0.1/ChaosGame/man/plot_hist3D.Rd |only ChaosGame-0.2/ChaosGame/DESCRIPTION | 8 +++---- ChaosGame-0.2/ChaosGame/MD5 | 10 ++++---- ChaosGame-0.2/ChaosGame/R/ChaosGame-internal.R | 11 +++++++-- ChaosGame-0.2/ChaosGame/R/plot_word3D.R |only ChaosGame-0.2/ChaosGame/man/ChaosGame-package.Rd | 26 +++++++++++------------ ChaosGame-0.2/ChaosGame/man/plot_word3D.Rd |only 8 files changed, 30 insertions(+), 25 deletions(-)
Title: Reproducible, Accessible & Shareable Species Distribution
Modelling
Description: Reproducible and remixable species distribution modelling. The
package reads user submitted modules from an online repository, runs full
SDM workflows and returns output that is fully reproducible.
Author: Tim Lucas, Nick Golding, Tom August, Greg McInerny, Emiel van Loon
Maintainer: Tom August <tomaug@ceh.ac.uk>
Diff between zoon versions 0.4.21 dated 2015-12-10 and 0.4.23 dated 2016-03-11
zoon-0.4.21/zoon/vignettes/Building_a_module.md |only zoon-0.4.21/zoon/vignettes/basic-zoon-usage.md |only zoon-0.4.21/zoon/vignettes/interactive_zoon_usage.md |only zoon-0.4.23/zoon/DESCRIPTION | 8 zoon-0.4.23/zoon/MD5 | 64 - zoon-0.4.23/zoon/NAMESPACE | 2 zoon-0.4.23/zoon/R/BuildModule.R | 8 zoon-0.4.23/zoon/R/ChangeWorkflow.R | 2 zoon-0.4.23/zoon/R/HelpFunctions.R | 3 zoon-0.4.23/zoon/R/RerunWorkflow.R | 2 zoon-0.4.23/zoon/R/zoon.R | 2 zoon-0.4.23/zoon/R/zoonHelpers.R | 25 zoon-0.4.23/zoon/README.md | 34 zoon-0.4.23/zoon/build/vignette.rds |binary zoon-0.4.23/zoon/inst/doc/Building_a_module.R | 39 zoon-0.4.23/zoon/inst/doc/Building_a_module.Rmd | 54 - zoon-0.4.23/zoon/inst/doc/Building_a_module.html | 888 ++++++++---------- zoon-0.4.23/zoon/inst/doc/basic-zoon-usage.R | 31 zoon-0.4.23/zoon/inst/doc/basic-zoon-usage.Rmd | 83 - zoon-0.4.23/zoon/inst/doc/basic-zoon-usage.html | 266 ++--- zoon-0.4.23/zoon/inst/doc/interactive_zoon_usage.R | 6 zoon-0.4.23/zoon/inst/doc/interactive_zoon_usage.Rmd | 20 zoon-0.4.23/zoon/inst/doc/interactive_zoon_usage.html | 116 -- zoon-0.4.23/zoon/man/BuildModule.Rd | 4 zoon-0.4.23/zoon/man/ChangeWorkflow.Rd | 2 zoon-0.4.23/zoon/man/ExtractAndCombData.Rd |only zoon-0.4.23/zoon/man/RerunWorkflow.Rd | 2 zoon-0.4.23/zoon/man/RunModels.Rd | 2 zoon-0.4.23/zoon/man/workflow.Rd | 2 zoon-0.4.23/zoon/tests/testthat/Rplots.pdf |binary zoon-0.4.23/zoon/tests/testthat/testSortArgs.R | 6 zoon-0.4.23/zoon/tests/testthat/testSplitCall.R | 6 zoon-0.4.23/zoon/vignettes/Building_a_module.Rmd | 54 - zoon-0.4.23/zoon/vignettes/basic-zoon-usage.Rmd | 83 - zoon-0.4.23/zoon/vignettes/interactive_zoon_usage.Rmd | 20 35 files changed, 880 insertions(+), 954 deletions(-)
More information about polychaosbasics at CRAN
Permanent link
Title: High-Dimensional Inference
Description: Implementation of multiple approaches to perform inference in high-dimensional models.
Author: Lukas Meier [aut, cre], Ruben Dezeure [aut], Nicolai Meinshausen [aut], Martin Maechler [aut], Peter Buehlmann [aut]
Maintainer: Lukas Meier <meier@stat.math.ethz.ch>
Diff between hdi versions 0.1-2 dated 2014-08-11 and 0.1-5 dated 2016-03-11
DESCRIPTION | 26 - MD5 | 66 ++- NAMESPACE | 44 +- R/hdi.R | 11 R/helpers.R | 446 +++++++++++++++++------- R/helpers.nodewise.R | 127 +++---- R/lasso-proj.R | 138 ++++--- R/lower-bound.R | 485 +++++++++++++-------------- R/methods.R | 166 ++++----- R/multi-split.R | 770 ++++++++++++++++++++++--------------------- R/multi-split.hierarchical.R |only R/reference.datasets.R |only R/ridge-proj.R | 49 +- R/stability.R | 7 build |only data/riboflavin.RData |binary inst |only man/clusterGroupBound.rd | 145 +++----- man/fdr.adjust.Rd | 2 man/glm.pval.Rd | 4 man/groupBound.rd | 141 ++++--- man/hdi-package.Rd | 49 +- man/hdi.Rd | 28 - man/lasso.cv.Rd | 45 +- man/lasso.firstq.Rd | 35 + man/lasso.proj.Rd | 96 ++++- man/multi.split.Rd | 178 ++++++--- man/plotClusterGroupBound.rd | 63 +-- man/rXb.rd |only man/riboflavin.Rd | 12 man/ridge.proj.Rd | 74 ++-- man/stability.Rd | 25 - tests/groupTsts.R |only tests/test-lasso.R | 63 ++- tests/test-multisplit.R |only tests/test-ridge.R | 7 tests/test-stability.R | 53 -- 37 files changed, 1865 insertions(+), 1490 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between gamboostLSS versions 1.2-0 dated 2015-08-19 and 1.2-1 dated 2016-03-11
DESCRIPTION | 12 ++++++------ MD5 | 26 ++++++++++++++------------ NAMESPACE | 3 +-- R/gamboostLSS_intern.R |only R/mboostLSS.R | 15 +++++++++++++-- R/methods.R | 17 ++++++++++++----- build/vignette.rds |binary data/india.RData |binary data/india.bnd.RData |binary inst/CITATION | 3 ++- inst/NEWS.Rd | 36 +++++++++++++++++++++++++++++++++--- inst/doc/gamboostLSS_Tutorial.pdf |binary man/gamboostLSS_intern.Rd |only tests/bugfixes.R | 20 ++++++++++++++++++++ tests/regtest-stabilization.R | 15 +++++++++++---- 15 files changed, 112 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-15 0.1.6
2014-12-10 0.1.5
2014-10-05 0.1.4
2014-07-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-20 1.3
2015-06-15 1.1
2015-06-01 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-18 2.0.5
2015-06-30 2.0.3
Title: Presmoothed Estimation in Survival Analysis
Description: Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data.
Author: Ignacio Lopez de Ullibarri and Maria Amalia Jacome
Maintainer: Ignacio Lopez de Ullibarri <ilu@udc.es>
Diff between survPresmooth versions 1.1-8 dated 2013-09-05 and 1.1-9 dated 2016-03-11
ChangeLog | 14 ++++++++++ DESCRIPTION | 10 +++---- MD5 | 14 +++++----- NAMESPACE | 4 ++ R/presmooth.R | 64 +++++++++++++++++++---------------------------- man/control.presmooth.Rd | 12 +++++--- man/presmooth.Rd | 8 ++--- man/pscheck.Rd | 2 - 8 files changed, 68 insertions(+), 60 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.3-4 dated 2016-02-11 and 1.3-5 dated 2016-03-11
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- README | 20 ++++++++------------ src/Makevars.win |only 4 files changed, 15 insertions(+), 18 deletions(-)
Title: Determining and Evaluating High-Risk Zones
Description: Functions for determining and evaluating high-risk zones and
simulating and thinning point process data, as described in 'Determining
high risk zones using point process methodology - Realization by building
an R package' (Seibold, 2012) and 'Determining high-risk zones for
unexploded World War II bombs by using point process methodology' (Mahling
et al., 2013).
Author: Heidi Seibold <Heidi.Seibold@uzh.ch>, Monia Mahling
<monia.mahling@stat.uni-muenchen.de>, Sebastian Linne
<Sebastian.Linne@campus.lmu.de>
Maintainer: Heidi Seibold <Heidi.Seibold@uzh.ch>
Diff between highriskzone versions 1.3 dated 2015-11-16 and 1.3-1 dated 2016-03-11
DESCRIPTION | 15 ++++--- MD5 | 82 +++++++++++++++++++++---------------------- NAMESPACE | 2 - R/est_intens_spde.R | 4 +- data/craterA.RData |binary data/craterB.RData |binary man/bootcor.Rd | 4 +- man/bootcor_restr.Rd | 6 +-- man/bootcorr.Rd | 4 +- man/check_det_hrz_input.Rd | 18 ++++----- man/craterA.Rd | 2 - man/craterB.Rd | 2 - man/det_alpha.Rd | 6 +-- man/det_area.Rd | 6 +-- man/det_hrz.Rd | 42 +++++++++++----------- man/det_hrz_restr.Rd | 2 - man/det_nnarea.Rd | 4 +- man/det_nsintens.Rd | 4 +- man/det_nsintens_restr.Rd | 2 - man/det_radius.Rd | 6 +-- man/det_threshold.Rd | 4 +- man/det_thresholdfromarea.Rd | 4 +- man/est_intens.Rd | 2 - man/est_intens_spde.Rd | 6 +-- man/est_intens_weight.Rd | 6 +-- man/eval_hrz.Rd | 16 ++++---- man/eval_method.Rd | 49 +++++++++++++------------ man/highriskzone-package.Rd | 4 +- man/plot.bootcorr.Rd | 2 - man/plot.highriskzone.Rd | 4 +- man/plot.hrzeval.Rd | 8 ++-- man/print.bootcorr.Rd | 2 - man/print.highriskzone.Rd | 2 - man/print.hrzeval.Rd | 2 - man/read_pppdata.Rd | 6 +-- man/sim_intens.Rd | 2 - man/sim_nsppp.Rd | 9 ++-- man/sim_nsprocess.Rd | 4 +- man/summary.bootcorr.Rd | 2 - man/summary.highriskzone.Rd | 2 - man/summary.hrzeval.Rd | 2 - man/thin.Rd | 4 +- 42 files changed, 178 insertions(+), 175 deletions(-)
Title: Who Are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: This open-source software package enables researchers to predict
individual ethnicity using his/her surname, geolocation, and other attributes
such as gender and age. The method utilizes the Bayes' rule to compute the
posterior probability of each racial category for any given individual voter.
The package implements methods described in Imai and Khanna (2016) <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre], Kosuke Imai [aut, cre]
Maintainer: Kabir Khanna <kkhanna@princeton.edu>
Diff between wru versions 0.0-1 dated 2015-12-09 and 0.0-2 dated 2016-03-11
ChangeLog |only DESCRIPTION | 20 ++++++++++++-------- MD5 | 15 ++++++++------- NAMESPACE | 1 + R/name.clean.R | 26 ++++++++++++++++++-------- data/State.FIPS.RData |binary data/names.all.RData |binary data/pid.RData |binary data/voters.RData |binary 9 files changed, 39 insertions(+), 23 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 1.0.13 dated 2015-11-26 and 1.0.15 dated 2016-03-11
treeclim-1.0.13/treeclim/tests/testthat/test_moving_windows.R |only treeclim-1.0.15/treeclim/DESCRIPTION | 8 treeclim-1.0.15/treeclim/MD5 | 39 +--- treeclim-1.0.15/treeclim/NAMESPACE | 2 treeclim-1.0.15/treeclim/R/dcc.R | 2 treeclim-1.0.15/treeclim/R/generics.R | 26 +- treeclim-1.0.15/treeclim/R/gershunov.R | 90 ++++----- treeclim-1.0.15/treeclim/R/make_pmat.R | 35 ++- treeclim-1.0.15/treeclim/R/seascorr.R | 15 + treeclim-1.0.15/treeclim/R/skills.R | 96 +++++----- treeclim-1.0.15/treeclim/R/tc_design.R | 10 - treeclim-1.0.15/treeclim/R/tc_mfunc.R | 16 - treeclim-1.0.15/treeclim/R/truncate_input.R | 48 ++--- treeclim-1.0.15/treeclim/README.md | 4 treeclim-1.0.15/treeclim/inst/Changelog | 10 + treeclim-1.0.15/treeclim/man/g_test.Rd | 20 -- treeclim-1.0.15/treeclim/man/make_pmat.Rd | 14 - treeclim-1.0.15/treeclim/man/skills.Rd | 24 +- treeclim-1.0.15/treeclim/man/tc_design.Rd | 5 treeclim-1.0.15/treeclim/man/truncate_input.Rd | 3 treeclim-1.0.15/treeclim/tests/testthat/test_truncation.R | 10 - 21 files changed, 260 insertions(+), 217 deletions(-)
Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to various methods in the kernel for enforcing security
restrictions. AppArmor can apply mandatory access control (MAC) policies on
a given task (process) via security profiles with detailed ACL definitions.
In addition the package has kernel bindings for setting the process hardware
resource limits (rlimit), uid, gid, affinity and priority. The high level R
function 'eval.secure' builds on these methods to do dynamic sandboxing:
it evaluates a single R expression within a temporary fork which acts as a
sandbox by enforcing fine grained restrictions without affecting the main R
process.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RAppArmor versions 2.0 dated 2016-03-09 and 2.0.1 dated 2016-03-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ configure | 9 +++++++-- tests/run-all.R | 6 +++--- 5 files changed, 21 insertions(+), 12 deletions(-)
Title: Allows to Explore Monophyly (or Lack of it) of Taxonomic Groups
in a Phylogeny
Description: Requires rooted resolved phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways.
Author: Orlando Schwery
Maintainer: Orlando Schwery <oschwery@vols.utk.edu>
Diff between MonoPhy versions 1.0 dated 2015-10-19 and 1.1 dated 2016-03-11
DESCRIPTION | 10 MD5 | 47 +-- R/AssessMonophyly.R | 63 ++-- R/GetAncNodes.R | 33 +- R/GetIntruderTaxa.R | 40 +- R/GetIntruderTips.R | 28 + R/GetOutlierTaxa.R | 18 - R/GetOutlierTips.R | 36 +- R/GetResultMonophyly.R | 18 - R/GetSummaryMonophyly.R | 18 - R/PlotMonophyly.R | 22 - README.md |only build/vignette.rds |binary inst/doc/MonoPhyVignette.R | 2 inst/doc/MonoPhyVignette.Rmd | 20 - inst/doc/MonoPhyVignette.html | 630 +++++++++++++----------------------------- man/AssessMonophyly.Rd | 6 man/GetAncNodes.Rd | 4 man/GetIntruderTaxa.Rd | 6 man/GetResultMonophyly.Rd | 4 man/MonoPhy-package.Rd | 6 man/MonophylyData.Rd | 2 man/PlotMonophyly.Rd | 8 tests |only vignettes/MonoPhyVignette.Rmd | 20 - 25 files changed, 455 insertions(+), 586 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets, also provides function to build vertices (meta-data) and create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.2 dated 2016-02-26 and 0.3 dated 2016-03-11
graphTweets-0.2/graphTweets/tests/testthat/test_dat.RData |only graphTweets-0.3/graphTweets/DESCRIPTION | 10 +- graphTweets-0.3/graphTweets/MD5 | 29 ++++---- graphTweets-0.3/graphTweets/NAMESPACE | 2 graphTweets-0.3/graphTweets/R/dynamize.R |only graphTweets-0.3/graphTweets/R/getEdges.R | 45 +++++++----- graphTweets-0.3/graphTweets/R/getNodes.R | 47 ++++++------- graphTweets-0.3/graphTweets/R/graphTweets.R | 18 ++++ graphTweets-0.3/graphTweets/R/utils.R | 38 ++++++++++ graphTweets-0.3/graphTweets/README.md | 16 +++- graphTweets-0.3/graphTweets/man/dynamise.Rd |only graphTweets-0.3/graphTweets/man/getEdges.Rd | 32 ++++---- graphTweets-0.3/graphTweets/man/getNodes.Rd | 27 +++---- graphTweets-0.3/graphTweets/man/graphTweets.Rd | 18 ++++ graphTweets-0.3/graphTweets/tests/testthat/test_dynamise.R |only graphTweets-0.3/graphTweets/tests/testthat/test_edges.R | 14 ++- graphTweets-0.3/graphTweets/tests/testthat/test_nodes.R | 23 ++---- graphTweets-0.3/graphTweets/tests/testthat/tweets.RData |only 18 files changed, 204 insertions(+), 115 deletions(-)
Title: Building Diversity Models from Multiple Species Occupancy Models
Description: Predictions of alpha diversity are fitted from presence data, first abundance is modeled from occupancy models and then, several diversity indices are calculated and finally GLM models are used to predict diversity in different environments and select priority areas.
Author: Derek Corcoran [aut, cre],
Dylan Kesler [aut],
Elisabeth Webb [aut],
Nicole Michel [aut]
Maintainer: Derek Corcoran <derek.corcoran.barrios@gmail.com>
Diff between DiversityOccupancy versions 1.0.0 dated 2016-03-09 and 1.0.1 dated 2016-03-11
DESCRIPTION | 17 ++++++++++------- MD5 | 6 +++--- R/DiversityOccu.R | 6 ++---- inst/doc/my-vignette.html | 4 ++-- 4 files changed, 17 insertions(+), 16 deletions(-)
More information about DiversityOccupancy at CRAN
Permanent link
Title: Intermittent Time Series Forecasting
Description: Functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>
Diff between tsintermittent versions 1.8 dated 2015-09-24 and 1.9 dated 2016-03-10
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/crost.R | 25 ++++++++++++++++++++----- R/crost.ma.R | 30 +++++++++++++++++++++++------- man/crost.Rd | 1 + man/crost.ma.Rd | 1 + 7 files changed, 59 insertions(+), 22 deletions(-)
More information about tsintermittent at CRAN
Permanent link
Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>
Diff between tablaxlsx versions 1.0.6 dated 2016-02-23 and 1.0.8 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/escribirTabla.R | 17 ++++++++++++++--- data/estilosDGE.rda |binary inst/img/logoJMR.png |binary 5 files changed, 22 insertions(+), 11 deletions(-)
Title: Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Description: Sparse modeling provides a mean selecting a small number of non-zero effects from a large possible number of candidate effects. This package includes a suite of methods for sparse modeling: estimation via EM or MCMC, approximate confidence intervals with nominal coverage, and diagnostic and summary plots. The method can implement sparse linear regression and sparse probit regression. Beyond regression analyses, applications include subgroup analysis, particularly for conjoint experiments, and panel data. Future versions will include extensions to models with truncated outcomes, propensity score, and instrumental variable analysis.
Author: Marc Ratkovic and Dustin Tingley
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Diff between sparsereg versions 1.1 dated 2015-10-01 and 1.2 dated 2016-03-10
ChangeLog | 3 DESCRIPTION | 10 +- MD5 | 16 ++-- NAMESPACE | 3 R/cleandata.R | 35 ++++++++++ R/subgroup.R | 158 ++++++++++++++++++++++++++++++++++------------ R/utility.R | 6 + man/sparsereg-internal.Rd | 1 man/sparsereg.Rd | 32 +++++---- 9 files changed, 193 insertions(+), 71 deletions(-)
Title: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>
Diff between sparr versions 0.3-7 dated 2015-09-17 and 0.3-8 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/tolerance.R | 2 ++ R/zzz.R | 2 +- man/sparr-package.Rd | 4 ++-- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Read and Write 'SAS' 'XPORT' Files
Description: Functions for reading, listing
the contents of, and writing 'SAS' 'xport' format files.
The functions support reading and writing of either
individual data frames or sets of data frames. Further,
a mechanism has been provided for customizing how
variables of different data types are stored.
Author: Unless otherwise noted, the contents of this package were written by
Gregory R. Warnes <greg@warnes.net> and are provided under the
terms of the GNU General Public License, version 2.0 or later.
--
The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from
BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John
Muuss, Copyright (c) 2004-2007 United States Government as
represented by the U.S. Army Research Laboratory, and is utilized
and redistributed under the terms of the GNU Lesser General Public
License, version 2.1.
--
The files 'R/AFirst.lib.s', 'R/all.is.numeric.R',
'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R',
'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the
'Hmisc' package created by Frank E. Harrell, Jr.
<f.harrell@vanderbilt.edu>, and are utilized and redistributed under
the terms of the GNU General Public License, version 2.0 or later.
--
The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and
'src/foreign.h' are copied or adapted from the 'R' 'foreign' package
created by Douglas M. Bates <bates@stat.wisc.edu> and Saikat DebRoy
<saikat@stat.wisc.edu>, and are utilized and redistributed under the
terms of the GNU General Public License, version 2.0 or later.
--
The creation of this package was partially funded by Metrum Institute
<http://metruminstitute.org>.
Maintainer: Gabor Csardi <gcsardi@mango-solutions.com>
Diff between SASxport versions 1.5.2 dated 2016-02-15 and 1.5.3 dated 2016-03-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/read.xport.R | 2 +- man/read.xport.Rd | 6 ++++++ 5 files changed, 16 insertions(+), 8 deletions(-)
Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between RVsharing versions 1.3.4 dated 2015-05-11 and 1.4.0 dated 2016-03-10
DESCRIPTION | 11 ++++---- MD5 | 68 +++++++++++++++++++++++++++++++++++++++++++++----- NAMESPACE | 3 +- R/RVgene.R |only R/extract_carriers.R |only R/ped2trio.R | 32 ++++++++++++++--------- R/pvalue_functions.R |only data/ex.ped.mat.RData |only inst |only man/GeneDropSim.fn.Rd | 6 ++-- man/RVgene.Rd |only man/RVsharing.Rd | 2 - man/ex.ped.mat.Rd |only man/get.psubset.Rd |only man/ped.list.Rd | 2 - 15 files changed, 95 insertions(+), 29 deletions(-)
Title: Friendly Regular Expressions
Description: A friendly interface for the construction of regular expressions.
Author: Kevin Ushey [aut],
Jim Hester [aut, cre],
Robert Krzyzanowski [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between rex versions 1.0.1 dated 2015-04-27 and 1.1.1 dated 2016-03-10
rex-1.0.1/rex/inst/doc/stackoverflow.R |only rex-1.0.1/rex/inst/doc/stackoverflow.Rmd |only rex-1.0.1/rex/inst/doc/stackoverflow.html |only rex-1.0.1/rex/tests/testthat/test-zzz.R |only rex-1.0.1/rex/vignettes/stackoverflow.Rmd |only rex-1.1.1/rex/DESCRIPTION | 10 - rex-1.1.1/rex/LICENSE | 2 rex-1.1.1/rex/MD5 | 65 +++---- rex-1.1.1/rex/NAMESPACE | 2 rex-1.1.1/rex/NEWS.md |only rex-1.1.1/rex/R/match.R | 4 rex-1.1.1/rex/R/shortcuts.R | 23 ++ rex-1.1.1/rex/R/utils.R | 2 rex-1.1.1/rex/R/zzz.R | 6 rex-1.1.1/rex/build/vignette.rds |binary rex-1.1.1/rex/man/as.regex.Rd | 2 rex-1.1.1/rex/man/capture.Rd | 28 --- rex-1.1.1/rex/man/character_class.Rd | 23 -- rex-1.1.1/rex/man/character_class_escape.Rd | 2 rex-1.1.1/rex/man/counts.Rd | 25 -- rex-1.1.1/rex/man/escape.Rd | 2 rex-1.1.1/rex/man/group.Rd | 27 --- rex-1.1.1/rex/man/lookarounds.Rd | 24 -- rex-1.1.1/rex/man/not.Rd | 27 --- rex-1.1.1/rex/man/or.Rd | 27 --- rex-1.1.1/rex/man/pipe.Rd | 2 rex-1.1.1/rex/man/re_matches.Rd | 2 rex-1.1.1/rex/man/re_substitutes.Rd | 2 rex-1.1.1/rex/man/regex.Rd | 2 rex-1.1.1/rex/man/register_shortcuts.Rd | 2 rex-1.1.1/rex/man/rex.Rd | 27 --- rex-1.1.1/rex/man/rex_mode.Rd | 2 rex-1.1.1/rex/man/shortcuts.Rd | 245 +++++++++++++--------------- rex-1.1.1/rex/man/single_shortcuts.Rd | 40 ++-- rex-1.1.1/rex/man/wildcards.Rd | 23 -- rex-1.1.1/rex/vignettes/log_parsing.Rmd | 2 rex-1.1.1/rex/vignettes/stackoverflow.R |only 37 files changed, 270 insertions(+), 380 deletions(-)
Title: A Simple General Purpose N-Gram Tokenizer
Description: A simple n-gram (contiguous sequences of n items from a
given sequence of text) tokenizer to be used with the 'tm' package with no
'rJava'/'RWeka' dependency.
Author: Chung-hong Chan <chainsawtiney@gmail.com>
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between ngramrr versions 0.1.1 dated 2015-04-06 and 0.2.0 dated 2016-03-10
DESCRIPTION | 17 ++++++++++------- MD5 | 12 ++++++++---- NAMESPACE | 5 ++++- R/dtm2.R |only R/ngramrr.R | 12 ++++++++---- README.md |only man/dtmwrappers.Rd |only man/ngramrr.Rd | 4 ++-- tests/testthat/test_charngram.R |only 9 files changed, 32 insertions(+), 18 deletions(-)
Title: Replicate and Analyse InterVA4
Description: Provides an R version of the InterVA4 software for
coding cause of death from verbal autopsies. It also provides simple
graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InterVA4 versions 1.7 dated 2016-03-03 and 1.7.1 dated 2016-03-10
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/InterVA.plot.R | 105 ++++++++++++++++++++++++++++++++-------------- R/InterVA.summary.r | 12 +++-- man/CSMF.Rd | 8 +-- man/Population.summary.Rd | 6 +- man/summary.interVA.Rd | 5 +- 7 files changed, 104 insertions(+), 52 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with InSilicoVA
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.0 dated 2015-12-04 and 1.1 dated 2016-03-10
InSilicoVA-1.0/InSilicoVA/R/insilico_java.r |only InSilicoVA-1.0/InSilicoVA/R/insilico_java2.r |only InSilicoVA-1.0/InSilicoVA/R/insilico_java3.r |only InSilicoVA-1.0/InSilicoVA/man/insilico.dev.Rd |only InSilicoVA-1.1/InSilicoVA/DESCRIPTION | 10 InSilicoVA-1.1/InSilicoVA/MD5 | 61 ++-- InSilicoVA-1.1/InSilicoVA/NAMESPACE | 10 InSilicoVA-1.1/InSilicoVA/R/diag.r | 12 InSilicoVA-1.1/InSilicoVA/R/extct_prob.r |only InSilicoVA-1.1/InSilicoVA/R/get_indiv.r |only InSilicoVA-1.1/InSilicoVA/R/groupplot.r |only InSilicoVA-1.1/InSilicoVA/R/indivplot.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_core.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_standard.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_train.r |only InSilicoVA-1.1/InSilicoVA/R/phy_debias.r | 14 - InSilicoVA-1.1/InSilicoVA/R/plot.r | 73 ++--- InSilicoVA-1.1/InSilicoVA/R/print_insilico.r | 4 InSilicoVA-1.1/InSilicoVA/R/print_insilico_summary.r | 86 +++--- InSilicoVA-1.1/InSilicoVA/R/report.r | 41 ++- InSilicoVA-1.1/InSilicoVA/R/zzz.R | 2 InSilicoVA-1.1/InSilicoVA/data/RandomPhysician.rda |binary InSilicoVA-1.1/InSilicoVA/data/RandomVA1.rda |binary InSilicoVA-1.1/InSilicoVA/data/RandomVA2.rda |binary InSilicoVA-1.1/InSilicoVA/data/SampleCategory.rda |binary InSilicoVA-1.1/InSilicoVA/data/condprobnum.rda |only InSilicoVA-1.1/InSilicoVA/inst/java/Insilico.jar |binary InSilicoVA-1.1/InSilicoVA/man/RandomVA1.Rd | 11 InSilicoVA-1.1/InSilicoVA/man/RandomVA2.rd | 7 InSilicoVA-1.1/InSilicoVA/man/condprobnum.Rd |only InSilicoVA-1.1/InSilicoVA/man/csmf.diag.Rd | 14 - InSilicoVA-1.1/InSilicoVA/man/extract.prob.Rd |only InSilicoVA-1.1/InSilicoVA/man/get.indiv.Rd |only InSilicoVA-1.1/InSilicoVA/man/indivplot.Rd |only InSilicoVA-1.1/InSilicoVA/man/insilico.Rd | 241 ++++++++++++------- InSilicoVA-1.1/InSilicoVA/man/insilico.fit.Rd |only InSilicoVA-1.1/InSilicoVA/man/insilico.train.Rd |only InSilicoVA-1.1/InSilicoVA/man/physician_debias.Rd | 4 InSilicoVA-1.1/InSilicoVA/man/plot.insilico.Rd | 71 ++--- InSilicoVA-1.1/InSilicoVA/man/stackplot.Rd |only InSilicoVA-1.1/InSilicoVA/man/summary.insilico.Rd | 14 - 41 files changed, 397 insertions(+), 278 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.7 dated 2016-03-02 and 2.0.8 dated 2016-03-10
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/FedDataTester.R | 3 ++- man/FedData-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 12 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin <davidbolin@gmail.com> and Finn Lindgren <finn.lindgren@gmail.com>
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.0.16 dated 2015-02-09 and 2.1.1 dated 2016-03-10
excursions-2.0.16/excursions/README.md |only excursions-2.1.1/excursions/DESCRIPTION | 13 excursions-2.1.1/excursions/MD5 | 53 - excursions-2.1.1/excursions/NAMESPACE | 32 excursions-2.1.1/excursions/R/contourmap.R | 37 - excursions-2.1.1/excursions/R/contourmap.inla.R | 2 excursions-2.1.1/excursions/R/contourutil.R | 210 +++++ excursions-2.1.1/excursions/R/excursions.R | 24 excursions-2.1.1/excursions/R/excursions.inla.R | 4 excursions-2.1.1/excursions/R/gaussint.R | 22 excursions-2.1.1/excursions/R/geometry.R | 357 ++++++---- excursions-2.1.1/excursions/R/inlautils.R | 15 excursions-2.1.1/excursions/R/interface.mc.R |only excursions-2.1.1/excursions/R/simconf.R | 43 - excursions-2.1.1/excursions/R/simconf.inla.R | 41 - excursions-2.1.1/excursions/R/simconf.mixture.R | 76 +- excursions-2.1.1/excursions/R/utils.R | 216 +++++- excursions-2.1.1/excursions/man/continuous.Rd | 12 excursions-2.1.1/excursions/man/contourmap.Rd | 3 excursions-2.1.1/excursions/man/contourmap.inla.Rd | 2 excursions-2.1.1/excursions/man/contourmap.mc.Rd |only excursions-2.1.1/excursions/man/excursions.mc.Rd |only excursions-2.1.1/excursions/man/simconf.inla.Rd | 2 excursions-2.1.1/excursions/man/simconf.mc.Rd |only excursions-2.1.1/excursions/man/simconf.mixture.Rd | 2 excursions-2.1.1/excursions/man/submesh.grid.Rd |only excursions-2.1.1/excursions/man/submesh.mesh.Rd |only excursions-2.1.1/excursions/src/CAMD/Source/Makefile | 2 excursions-2.1.1/excursions/src/SuiteSparse_config/Makefile | 2 excursions-2.1.1/excursions/tests/testthat/helper-data.R | 2 excursions-2.1.1/excursions/tests/testthat/test.integration.R | 18 31 files changed, 922 insertions(+), 268 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and manipulation
utilities.
Author: Lahti Leo [aut, cre],
Biecek Przemyslaw [aut],
Kainu Markus [aut],
Huovari Janne [aut]
Maintainer: Lahti Leo <louhos@googlegroups.com>
Diff between eurostat versions 1.2.13 dated 2016-01-19 and 1.2.21 dated 2016-03-10
DESCRIPTION | 12 MD5 | 43 +- NAMESPACE | 1 R/get_eurostat.R | 117 ++++-- R/get_eurostat_json.R |only R/get_eurostat_raw.R | 4 R/label_eurostat.R | 5 R/tidy_eurostat.R | 44 +- README.md | 12 inst/doc/eurostat_tutorial.R | 28 + inst/doc/eurostat_tutorial.Rmd | 71 ++- inst/doc/eurostat_tutorial.pdf |binary man/convert_time_col.Rd |only man/get_eurostat.Rd | 65 ++- man/get_eurostat_json.Rd |only man/get_eurostat_raw.Rd | 4 man/label_eurostat.Rd | 4 tests/testthat/test-all.R | 14 vignettes/2015-RJournal/lahti-huovari-kainu-biecek.tex | 8 vignettes/eurostat_tutorial.Rmd | 71 ++- vignettes/eurostat_tutorial.html | 326 ++++++++++++----- vignettes/fig/plotGallery-1.pdf |binary vignettes/fig/trains_plot-1.pdf |binary vignettes/fig/trains_plot-1.png |binary 24 files changed, 616 insertions(+), 213 deletions(-)
Title: Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms
Description: Contains methods for detection of clusters in hierarchical clustering dendrograms.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Bin Zhang <binzhang.ucla@gmail.com>,
with contributions from Steve Horvath <SHorvath@mednet.ucla.edu>
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between dynamicTreeCut versions 1.62 dated 2014-04-22 and 1.63-1 dated 2016-03-10
Changelog | 14 ++++++++++ DESCRIPTION | 12 ++++---- MD5 | 22 +++++++-------- NAMESPACE | 4 ++ R/treeCut.R | 58 ++++++++++++++++++++++++++++++++++-------- man/cutreeDynamic.Rd | 2 - man/cutreeDynamicTree.Rd | 2 - man/cutreeHybrid.Rd | 2 - man/dynamicTreeCut-package.Rd | 7 ++--- man/indentSpaces.Rd | 2 - man/merge2Clusters.Rd | 2 - man/printFlush.Rd | 2 - 12 files changed, 92 insertions(+), 37 deletions(-)
More information about dynamicTreeCut at CRAN
Permanent link
Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at
coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 0.1-0 dated 2015-10-14 and 1.2-1 dated 2016-03-10
downscale-0.1-0/downscale/R/ExtendRaster.R |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale30.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale32.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale33.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale34.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale35.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale36.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale38.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale40.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale41.pdf |only downscale-1.2-1/downscale/DESCRIPTION | 18 - downscale-1.2-1/downscale/MD5 | 50 +- downscale-1.2-1/downscale/NEWS | 17 downscale-1.2-1/downscale/R/upgrain.R | 105 +++--- downscale-1.2-1/downscale/build/vignette.rds |binary downscale-1.2-1/downscale/inst/doc/Downscaling.Rnw | 173 +++++----- downscale-1.2-1/downscale/inst/doc/Downscaling.pdf |binary downscale-1.2-1/downscale/inst/doc/Upgraining.Rnw | 18 - downscale-1.2-1/downscale/inst/doc/Upgraining.pdf |binary downscale-1.2-1/downscale/man/upgrain.Rd | 5 downscale-1.2-1/downscale/vignettes/Downscaling-downscale30.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale32.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale33.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale34.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale36.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale38.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale40.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale41.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale42.png |binary downscale-1.2-1/downscale/vignettes/Downscaling.Rnw | 173 +++++----- downscale-1.2-1/downscale/vignettes/Upgraining.Rnw | 18 - 31 files changed, 319 insertions(+), 258 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.7.2 dated 2016-02-25 and 1.7.3 dated 2016-03-10
DESCRIPTION | 18 ++-- MD5 | 141 +++++++++++++++++----------------- NAMESPACE | 7 + R/asInteger.r | 10 -- R/assert.r | 16 +-- R/checkAtomic.r | 2 R/checkCharacter.r | 4 R/checkDataFrame.r | 2 R/checkDataTable.r | 2 R/checkDate.r |only R/checkDirectory.r | 13 +-- R/checkFactor.r | 5 - R/checkFile.r | 29 +++++- R/checkFunction.r | 2 R/checkList.r | 4 R/checkOS.r | 12 +- R/checkPathForOutput.r | 15 +-- R/checkString.r | 2 R/coalesce.r | 2 R/helper.r | 6 - R/makeAssertion.r | 11 +- R/makeExpectation.r | 2 R/makeTest.r | 5 - R/qassert.r | 8 - R/qassertr.r | 8 - R/zzz.r | 1 inst/NEWS.md | 8 + inst/doc/checkmate.html | 76 +++++++++--------- man/asInteger.Rd | 13 +-- man/assert.Rd | 10 +- man/checkAccess.Rd | 10 +- man/checkArray.Rd | 10 +- man/checkAtomic.Rd | 22 +---- man/checkAtomicVector.Rd | 10 +- man/checkCharacter.Rd | 10 +- man/checkChoice.Rd | 10 +- man/checkClass.Rd | 10 +- man/checkComplex.Rd | 10 +- man/checkCount.Rd | 10 +- man/checkDataFrame.Rd | 10 +- man/checkDataTable.Rd | 10 +- man/checkDate.Rd |only man/checkDirectory.Rd | 10 +- man/checkEnvironment.Rd | 12 +- man/checkFactor.Rd | 10 +- man/checkFile.Rd | 23 +++-- man/checkFlag.Rd | 10 +- man/checkFunction.Rd | 10 +- man/checkInt.Rd | 10 +- man/checkInteger.Rd | 10 +- man/checkIntegerish.Rd | 10 +- man/checkList.Rd | 10 +- man/checkLogical.Rd | 10 +- man/checkMatrix.Rd | 10 +- man/checkNamed.Rd | 10 +- man/checkNames.Rd | 10 +- man/checkNull.Rd | 10 +- man/checkNumber.Rd | 10 +- man/checkNumeric.Rd | 12 +- man/checkOS.Rd | 6 - man/checkPathForOutput.Rd | 10 +- man/checkScalar.Rd | 10 +- man/checkScalarNA.Rd | 10 +- man/checkSetEqual.Rd | 10 +- man/checkString.Rd | 10 +- man/checkSubset.Rd | 10 +- man/checkVector.Rd | 10 +- man/makeAssertion.Rd | 9 +- man/qassert.Rd | 8 - man/qassertr.Rd | 8 - tests/testthat/test_checkDate.r |only tests/testthat/test_checkFilesystem.r | 6 + tests/testthat/test_checkOS.r | 20 ++++ 73 files changed, 462 insertions(+), 408 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.7-0 dated 2016-01-30 and 4.8-0 dated 2016-03-10
DESCRIPTION | 8 +- MD5 | 96 +++++++++++++++++----------------- NAMESPACE | 3 + R/itemfit.sx2.R | 6 ++ R/numerical_Hessian.R |only R/osink.R |only R/print.din.R | 10 ++- R/print.gdina.R | 10 ++- R/print.gdm.R | 12 ++-- R/print.mcdina.R | 10 ++- R/print.slca.R | 10 ++- R/print.summary.din.R | 4 + R/summary.din.R | 8 +- R/summary.gdina.R | 13 +++- R/summary.gdm.R | 9 ++- R/summary.mcdina.R | 8 ++ R/summary.slca.R | 10 ++- data/data.Students.rda |binary data/data.cdm01.rda |binary data/data.cdm02.rda |binary data/data.dcm.rda |binary data/data.dtmr.rda |binary data/data.ecpe.rda |binary data/data.fraction1.rda |binary data/data.fraction2.rda |binary data/data.hr.rda |binary data/data.jang.rda |binary data/data.melab.rda |binary data/data.mg.rda |binary data/data.pgdina.rda |binary data/data.sda6.rda |binary data/data.timss03.G8.su.rda |binary data/data.timss07.G4.lee.rda |binary data/data.timss11.G4.AUT.part.rda |binary data/data.timss11.G4.AUT.rda |binary data/fraction.subtraction.data.rda |binary data/fraction.subtraction.qmatrix.rda |binary data/sim.dina.rda |binary data/sim.dino.rda |binary data/sim.qmatrix.rda |binary inst/NEWS | 23 +++++++- man/CDM-package.Rd | 84 +++++++++++++++-------------- man/din.Rd | 3 + man/din.deterministic.Rd | 2 man/gdina.Rd | 6 +- man/gdm.Rd | 4 + man/mcdina.Rd | 6 +- man/numerical_Hessian.Rd |only man/osink.Rd |only man/slca.Rd | 4 + man/summary.din.Rd | 5 + 51 files changed, 225 insertions(+), 129 deletions(-)
Title: Stochastic Model for Analysis of Longitudinal Data
Description: Utilities to estimate parameters of stochastic process and modeling survival trajectories
and time-to-event outcomes observed from longitudinal studies.
Miscellaneous function for data preparation is also provided.
For more information, see: "Stochastic model for analysis of longitudinal data on aging
and mortality" by Yashin A. et al, 2007, Mathematical Biosciences, 208(2), 538-551
<DOI:10.1016/j.mbs.2006.11.006>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.0 dated 2016-02-08 and 1.1.2 dated 2016-03-10
DESCRIPTION | 10 +- MD5 | 45 ++++----- NAMESPACE | 3 R/prepare_data.R | 3 R/simdata_cont.R | 109 ++++++++++++++++++++-- R/simdata_discr.R | 38 ++++--- R/spm.R | 109 +++++++++++++--------- R/spm_continuous.R | 192 ++++++++++++++++++++++++-------------- R/spm_discrete.R | 30 +++--- R/spm_projection.R |only R/spm_time-dependent.R | 20 ++-- README.md | 21 ++-- man/optimize.Rd | 6 - man/simdata_cont.Rd | 8 - man/simdata_cont2.Rd |only man/simdata_discr.Rd | 6 - man/spm.Rd | 27 ++++- man/spm_continuous.Rd | 22 ++-- man/spm_discrete.Rd | 8 - man/spm_projection.Rd |only man/spm_time_dep.Rd | 10 +- src/simdataND.cpp | 1 src/spm_integral_MD.cpp | 201 +++++++++++++++++++++++++++++++++++++++- vignettes/stpm-vignette.Rmd | 30 ++---- vignettes/stpm-vignette.html | 212 ++++++++++++++++++++++--------------------- 25 files changed, 757 insertions(+), 354 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by M. Adepeju;
Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.44-1 dated 2015-12-29 and 1.45-0 dated 2016-03-10
DESCRIPTION | 16 MD5 | 757 ++++++++++++++++++++++--------------------- NAMESPACE | 106 +++++- NEWS | 337 +++++++++++++++++++ R/Fest.R | 16 R/Hest.R | 5 R/Iest.R | 2 R/Jinhom.R | 4 R/Kest.R | 57 +-- R/Tstat.R | 4 R/addvar.R | 4 R/allstats.R | 6 R/alltypes.R | 6 R/anova.mppm.R | 28 + R/anova.ppm.R | 6 R/areainter.R | 16 R/as.im.R | 5 R/badgey.R | 6 R/bermantest.R | 14 R/blur.R | 4 R/boundingbox.R | 8 R/breakpts.R | 29 + R/bw.optim.R | 10 R/cdftest.R | 16 R/clickppp.R | 21 - R/close3Dpairs.R | 74 +++- R/closepairs.R | 197 +++++++++-- R/clusterset.R | 6 R/colourtables.R | 14 R/compileK.R | 4 R/concom.R | 6 R/density.lpp.R | 16 R/density.ppp.R | 6 R/detpointprocfamilyfun.R | 1 R/diagnoseppm.R | 26 + R/dist2dpath.R | 19 - R/distcdf.R | 4 R/distfunlpp.R | 2 R/dppm.R | 37 +- R/dppmclass.R | 2 R/dummify.R | 4 R/edgeRipley.R | 2 R/edgeTrans.R | 40 +- R/effectfun.R | 6 R/envelope.R | 31 + R/envelope3.R | 9 R/envelopelpp.R | 14 R/eval.fasp.R | 4 R/eval.fv.R | 12 R/eval.im.R | 12 R/evalcovar.R | 4 R/ewcdf.R | 4 R/factors.R | 2 R/fasp.R | 6 R/fii.R | 4 R/fiksel.R | 4 R/fitted.ppm.R | 51 ++ R/fryplot.R | 4 R/funxy.R | 46 ++ R/fv.R | 26 + R/geyer.R | 66 ++- R/hackglmm.R | 6 R/hexagons.R | 6 R/hierhard.R | 4 R/hierpair.family.R | 4 R/hierstrauss.R | 4 R/hierstrhard.R | 4 R/hybrid.R | 6 R/hybrid.family.R | 6 R/hyperframe.R | 18 - R/hypersub.R | 8 R/idw.R | 3 R/images.R | 21 - R/indices.R |only R/infline.R | 4 R/interactions.R | 42 +- R/ippm.R | 6 R/kppm.R | 40 +- R/laslett.R |only R/layered.R | 10 R/lennard.R | 4 R/leverage.R | 211 ++++++++---- R/linalg.R | 28 + R/linfun.R | 31 + R/linim.R | 21 - R/linnet.R | 111 +++++- R/linnetsurgery.R |only R/lintess.R |only R/localpcf.R | 4 R/logistic.R | 2 R/lpp.R | 129 ++++--- R/lppm.R | 46 +- R/lurking.R | 11 R/markcorr.R | 10 R/marks.R | 23 - R/measures.R | 16 R/mincontrast.R | 12 R/morisita.R | 4 R/mpl.R | 184 ++++++---- R/mppm.R | 51 ++ R/multihard.R | 4 R/multistrauss.R | 2 R/multistrhard.R | 4 R/nnclean.R | 8 R/nndist.R | 6 R/nndistlpp.R | 20 - R/nnmap.R | 4 R/objsurf.R | 10 R/options.R | 5 R/pairs.im.R | 14 R/pairsat.family.R | 17 R/pairwise.family.R | 6 R/parres.R | 4 R/pcf.R | 80 +++- R/pcfinhom.R | 35 + R/penttinen.R | 4 R/persp.im.R | 4 R/pixellate.R | 6 R/plot.anylist.R | 10 R/plot.fasp.R | 4 R/plot.fv.R | 16 R/plot.im.R | 10 R/plot.mppm.R | 8 R/plot.owin.R | 24 - R/plot.plotppm.R | 8 R/plot.ppp.R | 28 - R/pool.R | 5 R/pp3.R | 4 R/ppm.R | 17 R/ppmclass.R | 19 - R/ppp.R | 4 R/ppx.R | 20 - R/predict.ppm.R | 57 ++- R/profilepl.R | 42 +- R/progress.R | 4 R/psp.R | 12 R/psp2pix.R | 4 R/pspcross.R | 24 + R/qqplotppm.R | 419 ++++++++++++----------- R/quadclass.R | 18 - R/quadratcount.R | 8 R/quadrattest.R | 16 R/quadscheme.R | 6 R/quantess.R | 4 R/random.R | 8 R/reduceformula.R | 3 R/replace.ppp.R | 2 R/resid4plot.R | 10 R/residppm.R | 29 - R/rho2hat.R | 13 R/rhohat.R | 6 R/rmh.default.R | 6 R/rmh.ppm.R | 6 R/rmhcontrol.R | 8 R/rmhexpand.R | 4 R/rmhmodel.R | 6 R/rmhmodel.ppm.R | 15 R/rmhstart.R | 6 R/rshift.R | 6 R/satpiece.R | 4 R/scanstat.R | 7 R/sigtrace.R | 2 R/slrm.R | 24 - R/smooth.ppp.R | 20 - R/smoothfun.R | 4 R/softcore.R | 4 R/sparse3Darray.R |only R/sparsecommon.R |only R/sparselinalg.R |only R/split.ppx.R | 4 R/strauss.R | 13 R/strausshard.R | 4 R/subfits.R | 791 ++++++++++++++++++++++++--------------------- R/subset.R | 18 - R/summary.mppm.R | 4 R/summary.ppm.R | 8 R/superimpose.R | 46 +- R/symbolmap.R | 60 ++- R/tess.R | 14 R/texture.R | 27 - R/triplets.R | 4 R/unique.ppp.R | 2 R/unnormdensity.R | 16 R/update.ppm.R | 11 R/util.R | 89 ++--- R/varblock.R | 26 - R/vcov.mppm.R | 49 ++ R/vcov.ppm.R | 100 +++-- R/versions.R | 7 R/window.R | 11 R/wingeom.R | 42 +- R/xypolygon.R | 4 R/zclustermodel.R | 2 demo/spatstat.R | 3 inst/CITATION | 40 +- inst/doc/datasets.R | 129 +++---- inst/doc/datasets.Rnw | 1 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.R | 142 ++++---- inst/doc/replicated.Rnw | 18 - inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 8 inst/doc/updates.Rnw | 293 +++++++++++++++- inst/doc/updates.pdf |binary man/Emark.Rd | 2 man/Extract.fasp.Rd | 10 man/Extract.layered.Rd | 5 man/Extract.linnet.Rd | 35 + man/Extract.lpp.Rd | 30 + man/Extract.msr.Rd | 6 man/Extract.ppp.Rd | 41 +- man/Extract.splitppp.Rd | 2 man/Fest.Rd | 2 man/Gcross.Rd | 4 man/Gdot.Rd | 2 man/Gest.Rd | 2 man/Geyer.Rd | 20 - man/Gmulti.Rd | 17 man/Jcross.Rd | 18 - man/Jdot.Rd | 10 man/Jest.Rd | 2 man/Jmulti.Rd | 17 man/Kcross.Rd | 2 man/Kcross.inhom.Rd | 29 - man/Kdot.Rd | 14 man/Kdot.inhom.Rd | 21 - man/Kest.fft.Rd | 3 man/Kinhom.Rd | 7 man/Kmark.Rd | 2 man/Kmulti.Rd | 21 - man/Kmulti.inhom.Rd | 6 man/Lcross.inhom.Rd | 18 - man/Ldot.inhom.Rd | 21 - man/Poisson.Rd | 31 - man/Smooth.msr.Rd | 6 man/anova.lppm.Rd | 6 man/ants.Rd | 2 man/applynbd.Rd | 39 +- man/as.im.Rd | 2 man/as.linfun.Rd |only man/as.lpp.Rd | 5 man/bdist.points.Rd | 2 man/clarkevans.Rd | 2 man/closepairs.Rd | 28 + man/closepairs.pp3.Rd | 21 - man/coef.mppm.Rd | 36 +- man/complement.owin.Rd | 4 man/connected.linnet.Rd |only man/connected.ppp.Rd | 2 man/convexhull.Rd | 2 man/crossing.psp.Rd | 22 + man/cut.ppp.Rd | 23 - man/deletebranch.Rd | 24 - man/density.lpp.Rd | 9 man/diagnose.ppm.Rd | 12 man/dirichletWeights.Rd | 2 man/discretise.Rd | 8 man/distfun.Rd | 24 - man/distfun.lpp.Rd | 21 - man/divide.linnet.Rd |only man/dppm.Rd | 15 man/dummy.ppm.Rd | 2 man/edge.Ripley.Rd | 2 man/edge.Trans.Rd | 14 man/eem.Rd | 2 man/envelope.Rd | 24 + man/envelope.lpp.Rd | 8 man/envelope.pp3.Rd | 6 man/eval.linim.Rd | 14 man/fitted.ppm.Rd | 6 man/fixef.mppm.Rd | 16 man/funxy.Rd | 21 - man/harmonic.Rd | 27 - man/harmonise.fv.Rd | 2 man/humberside.Rd | 2 man/idw.Rd | 9 man/im.Rd | 23 + man/influence.ppm.Rd | 4 man/insertVertices.Rd |only man/laslett.Rd |only man/leverage.ppm.Rd | 4 man/lineardisc.Rd | 12 man/linim.Rd | 5 man/linnet.Rd | 17 man/lintess.Rd |only man/lpp.Rd | 18 - man/lppm.Rd | 5 man/markconnect.Rd | 2 man/markcorr.Rd | 4 man/marks.Rd | 15 man/marks.psp.Rd | 13 man/markstat.Rd | 21 - man/methods.linfun.Rd | 9 man/methods.linim.Rd | 16 man/methods.linnet.Rd | 44 +- man/methods.lpp.Rd | 2 man/methods.lppm.Rd | 2 man/methods.objsurf.Rd | 3 man/mppm.Rd | 52 ++ man/nbfires.Rd | 444 ++++++++++++------------- man/nncorr.Rd | 2 man/nndist.lpp.Rd | 2 man/nnwhich.lpp.Rd | 2 man/nvertices.Rd |only man/osteo.Rd | 2 man/overlap.owin.Rd | 2 man/owin.Rd | 8 man/owin.object.Rd | 24 - man/pairdist.lpp.Rd | 2 man/pcf.Rd | 17 man/pcf.fv.Rd | 15 man/pcf.ppp.Rd | 34 + man/pcfinhom.Rd | 27 + man/periodify.Rd | 2 man/plot.laslett.Rd |only man/plot.linim.Rd | 10 man/plot.linnet.Rd | 3 man/plot.lpp.Rd | 8 man/plot.lppm.Rd | 6 man/plot.msr.Rd | 6 man/plot.ppp.Rd | 31 + man/plot.psp.Rd | 4 man/ppp.Rd | 2 man/ppp.object.Rd | 2 man/pppdist.Rd | 444 ++++++++++++------------- man/pppmatching.Rd | 2 man/predict.lppm.Rd | 4 man/predict.mppm.Rd | 2 man/print.owin.Rd | 2 man/psp.Rd | 5 man/quad.object.Rd | 4 man/quad.ppm.Rd | 7 man/quadrat.test.Rd | 2 man/quadratcount.Rd | 2 man/quadrats.Rd | 2 man/quadscheme.Rd | 8 man/quadscheme.logi.Rd | 5 man/ranef.mppm.Rd | 17 man/reload.or.compute.Rd | 2 man/requireversion.Rd |only man/rescale.owin.Rd | 2 man/residuals.ppm.Rd | 11 man/rmh.default.Rd | 8 man/rmhcontrol.Rd | 2 man/rthin.Rd | 2 man/run.simplepanel.Rd | 57 +++ man/scan.test.Rd | 6 man/selfcut.psp.Rd | 10 man/simplepanel.Rd | 9 man/simplify.owin.Rd | 13 man/spatstat-internal.Rd | 150 +++++++- man/spatstat-package.Rd | 93 +++-- man/split.ppp.Rd | 26 - man/subfits.Rd | 24 - man/subset.ppp.Rd | 29 + man/summary.owin.Rd | 2 man/summary.ppm.Rd | 13 man/summary.ppp.Rd | 19 - man/superimpose.Rd | 4 man/symbolmap.Rd | 21 - man/texturemap.Rd | 18 - man/textureplot.Rd | 16 man/thinNetwork.Rd |only man/transect.im.Rd | 2 man/treebranchlabels.Rd | 16 man/treeprune.Rd | 32 + man/unmark.Rd | 6 man/vcov.ppm.Rd | 9 src/PerfectPenttinen.h | 4 src/bdrymask.c | 4 src/close3pair.c | 3 src/closefuns.h | 373 ++++++++++++++++++++- src/closepair.c | 1 src/knngrid.h | 4 src/linSnncross.h | 9 src/linequad.c | 24 - src/linknnd.c | 11 src/linvknndist.c | 12 src/methas.c | 2 src/sparselinalg.c |only src/spasumsymout.h |only src/whist.c | 4 tests/alltests.R | 390 ++++++++++++++++++---- vignettes/datasets.Rnw | 1 vignettes/packagesizes.txt | 1 vignettes/replicated.Rnw | 18 - vignettes/updates.Rnw | 293 +++++++++++++++- 389 files changed, 6955 insertions(+), 3646 deletions(-)
Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal
Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide
Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.3 dated 2016-02-18 and 1.3.1 dated 2016-03-10
idm-1.3.1/idm/DESCRIPTION | 8 idm-1.3.1/idm/MD5 | 17 - idm-1.3.1/idm/NAMESPACE | 2 idm-1.3.1/idm/R/i_pca.r | 466 ++++++++++++++++++++-------------------- idm-1.3.1/idm/R/update.i_pca.R | 3 idm-1.3.1/idm/man/i_pca.Rd | 2 idm-1.3.1/idm/man/idm.Rd | 62 ++--- idm-1.3.1/idm/man/plot.i_pca.Rd | 3 idm-1.3.1/idm/man/tweet.Rd | 58 ++-- idm-1.3/idm/man/transform_z.Rd |only 10 files changed, 311 insertions(+), 310 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Provides implementations of functions which have been introduced in
R since version 3.0.0. The backports are conditionally exported which
results in R resolving the function names to the version shipped with R (if
available) and uses the implemented backports as fallback. This way package
developers can make use of the new functions without worrying about the
minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.0.0 dated 2016-02-19 and 1.0.1 dated 2016-03-10
DESCRIPTION | 10 +++++----- MD5 | 9 ++++++--- NAMESPACE | 3 +++ NEWS.md | 8 ++++++-- R/file.x.r |only man/file.size.Rd |only tests/testthat/test_file.x.r |only 7 files changed, 20 insertions(+), 10 deletions(-)
Title: Applications of Empirical Dynamic Modeling from Time Series
Description: Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described by Sugihara et al. (2012) <DOI:10.1126/science.1227079>.
Author: Hao Ye, Adam Clark, Ethan Deyle
Maintainer: Hao Ye <hye@ucsd.edu>
Diff between rEDM versions 0.4.5 dated 2016-03-07 and 0.4.7 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- inst/doc/rEDM_tutorial.html | 14 +++++++------- inst/tests/Rplots.pdf |only inst/tests/test_lnlp.R | 2 ++ src/block_lnlp.cpp | 7 +++++-- src/block_lnlp.h | 2 +- src/lnlp.cpp | 4 +++- src/lnlp.h | 2 +- src/xmap.cpp | 5 ++++- src/xmap.h | 2 +- 11 files changed, 38 insertions(+), 27 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-3 dated 2015-10-29 and 0.1-4 dated 2016-03-10
DESCRIPTION | 10 +-- MD5 | 141 +++++++++++++++++++++++++-------------------- NAMESPACE | 12 +++ R/DAYMET_tiles-data.R |only R/breeding.density.R | 3 R/daymet.point.R |only R/daymet.tiles.R |only R/download.hansen.R | 2 R/download.prism.R | 5 - R/effect.size.R |only R/logistic.regression.R | 31 ++++++--- R/plot.effect.size.R |only R/plot.loess.boot.R | 2 R/print.effect.size.R |only R/pseudo.absence.R | 29 ++++----- R/sample.annulus.R |only R/sample.line.R | 4 - R/se.news.R |only R/sp.na.omit.R | 66 +++++++++++---------- R/spatialEcoNews.R |only R/summary.effect.size.R |only R/tri.R | 2 R/zzz.R |only data/DAYMET_tiles.rda |only inst/CITATION | 4 - inst/NEWS | 15 +++- man/DAYMET_tiles.Rd |only man/ants.Rd | 2 man/bearing.distance.Rd | 7 -- man/breeding.density.Rd | 21 +----- man/concordance.Rd | 21 +----- man/conf.interval.Rd | 5 - man/correlogram.Rd | 20 ++---- man/csi.Rd | 14 +--- man/daymet.point.Rd |only man/daymet.tiles.Rd |only man/dispersion.Rd | 12 --- man/download.daymet.Rd | 32 +++------- man/download.hansen.Rd | 15 +--- man/download.prism.Rd | 24 ++----- man/effect.size.Rd |only man/gaussian.kernel.Rd | 3 man/group.pdf.Rd | 8 -- man/hexagons.Rd | 5 - man/idw.smoothing.Rd | 11 --- man/insert.values.Rd | 6 - man/kl.divergence.Rd | 8 -- man/land.metrics.Rd | 18 +---- man/local.min.max.Rd | 12 +-- man/loess.boot.Rd | 32 +++------- man/loess.ci.Rd | 15 +--- man/logistic.regression.Rd | 48 +++++++-------- man/moments.Rd | 35 +++++------ man/nni.Rd | 9 -- man/o.ring.Rd | 12 --- man/optimal.k.Rd | 7 -- man/outliers.Rd | 7 -- man/parea.sample.Rd | 8 -- man/plot.effect.size.Rd |only man/plot.loess.boot.Rd | 9 -- man/point.in.poly.Rd | 4 - man/pp.subsample.Rd | 24 +------ man/print.effect.size.Rd |only man/pseudo.absence.Rd | 55 ++++++----------- man/pu.Rd | 5 - man/raster.entropy.Rd | 11 --- man/raster.vol.Rd | 6 - man/sample.annulus.Rd |only man/sample.line.Rd | 10 --- man/sample.poly.Rd | 6 - man/se.news.Rd |only man/separability.Rd | 36 +++-------- man/shannons.Rd | 10 --- man/similarity.Rd | 12 --- man/sp.na.omit.Rd | 43 ++++++------- man/stratified.random.Rd | 8 -- man/summary.effect.size.Rd |only man/tpi.Rd | 7 -- man/trend.line.Rd | 3 man/tri.Rd | 9 -- man/wt.centroid.Rd | 11 --- man/zonal.stats.Rd | 11 --- 82 files changed, 408 insertions(+), 615 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively
adjust alpha in order to maintain the consumer risk in ABEL studies
and adapt the sample size for the loss in power.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-3 dated 2016-01-15 and 1.3-4 dated 2016-03-10
PowerTOST-1.3-3/PowerTOST/R/power_scABEL2.R |only PowerTOST-1.3-4/PowerTOST/DESCRIPTION | 8 +-- PowerTOST-1.3-4/PowerTOST/MD5 | 50 ++++++++++---------- PowerTOST-1.3-4/PowerTOST/NEWS | 7 ++ PowerTOST-1.3-4/PowerTOST/R/SampleSize_HVNTID.R | 10 ++-- PowerTOST-1.3-4/PowerTOST/R/exppower.R | 3 - PowerTOST-1.3-4/PowerTOST/R/power2.R |only PowerTOST-1.3-4/PowerTOST/R/power_RSABE.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_RSABE_NTID.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_RSABE_pure.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_TOST_sim.R | 5 +- PowerTOST-1.3-4/PowerTOST/R/power_scABEL.R | 29 ++++++----- PowerTOST-1.3-4/PowerTOST/R/power_scABEL_2.R |only PowerTOST-1.3-4/PowerTOST/R/power_scABEL_lo.R |only PowerTOST-1.3-4/PowerTOST/R/power_scABEL_pure.R | 6 ++ PowerTOST-1.3-4/PowerTOST/R/sampleN.scABEL.ad.R | 25 +++++----- PowerTOST-1.3-4/PowerTOST/R/samplesize_RSABE.R | 10 ++-- PowerTOST-1.3-4/PowerTOST/R/samplesize_RSABE_NTID.R | 11 ++-- PowerTOST-1.3-4/PowerTOST/R/samplesize_scABEL.R | 14 ++--- PowerTOST-1.3-4/PowerTOST/R/scABEL.ad.R | 5 +- PowerTOST-1.3-4/PowerTOST/man/power.HVNTID.Rd | 2 PowerTOST-1.3-4/PowerTOST/man/power.NTIDFDA.Rd | 4 + PowerTOST-1.3-4/PowerTOST/man/sampleN.HVNTID.Rd | 17 ++++-- PowerTOST-1.3-4/PowerTOST/man/sampleN.NTIDFDA.Rd | 13 ++++- PowerTOST-1.3-4/PowerTOST/man/sampleN.RSABE.Rd | 10 +++- PowerTOST-1.3-4/PowerTOST/man/sampleN.scABEL.Rd | 13 +++-- PowerTOST-1.3-4/PowerTOST/man/sampleN.scABEL.ad.Rd | 5 +- PowerTOST-1.3-4/PowerTOST/man/scABEL.ad.Rd | 9 ++- 28 files changed, 162 insertions(+), 97 deletions(-)
Title: Non-Negative Lasso and Elastic Net Penalized Generalized Linear
Models
Description: Estimates of coefficients of lasso penalized linear regression and generalized linear models subject to non-negativity constraints on the parameters using multiplicative iterative algorithm. Entire regularization path for a sequence of lambda values can be obtained. Functions are available for creating plots of regularization path, cross validation and estimating coefficients at a given lambda value. There is also provision for obtaining standard error of coefficient estimates.
Author: Baidya Nath Mandal <mandal.stat@gmail.com> and Jun Ma <jun.ma@mq.edu.au>
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Diff between nnlasso versions 0.2 dated 2015-04-10 and 0.3 dated 2016-03-10
DESCRIPTION | 14 +++++------ MD5 | 46 ++++++++++++++++++------------------- NAMESPACE | 2 + R/nnlasso.r | 50 ++++++++++++++++++++--------------------- man/bars.Rd | 2 - man/coef.nnlasso.Rd | 3 +- man/cv.nnlasso.Rd | 12 ++++----- man/cv.nnlasso.binomial.Rd | 5 ++-- man/cv.nnlasso.normal.Rd | 5 ++-- man/cv.nnlasso.poisson.Rd | 5 ++-- man/fold.Rd | 2 - man/kfold.Rd | 2 - man/msefun.binomial.Rd | 2 - man/msefun.normal.Rd | 2 - man/msefun.poisson.Rd | 2 - man/nnlasso.Rd | 16 ++++++++++++- man/nnlasso.binomial.Rd | 4 ++- man/nnlasso.binomial.lambda.Rd | 4 +-- man/nnlasso.normal.Rd | 3 +- man/nnlasso.normal.lambda.Rd | 2 - man/nnlasso.poisson.Rd | 4 ++- man/nnlasso.poisson.lambda.Rd | 2 - man/plot.nnlasso.Rd | 5 +++- man/predict.nnlasso.Rd | 5 +++- 24 files changed, 115 insertions(+), 84 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.22-1 dated 2016-02-07 and 2.23 dated 2016-03-10
DESCRIPTION | 16 - MD5 | 49 +++-- NAMESPACE | 28 ++- R/glht-support.R | 26 ++- R/helpers.R | 8 R/lsmeans.R | 16 + R/rbind.R | 11 - R/ref.grid.R | 98 ++++++++--- R/summary.R | 123 +++++++++----- R/transformations.R |only R/xtable-method.R |only inst/NEWS | 24 ++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 228 +++++++++++++++++---------- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 361 ++++++++++++++++++++++++++++++-------------- man/contrast.Rd | 10 - man/glht.Rd | 14 + man/lsmeans.Rd | 14 - man/make.tran.Rd |only man/models.Rd | 2 man/ref.grid.Rd | 7 man/summary.Rd | 41 +++- man/update.Rd | 22 +- tests/tests1.Rout.save | 26 ++- vignettes/lsmeans.bib | 40 +++- vignettes/using-lsmeans.rnw | 361 ++++++++++++++++++++++++++++++-------------- 27 files changed, 1024 insertions(+), 501 deletions(-)
Title: Epistasis Test in Meta-Analysis
Description: Traditional meta-regression based method has been developed for using meta-analysis data, but it faced the challenge of inconsistent estimates. This package purpose a new statistical method to detect epistasis using incomplete information summary, and have proven it not only successfully let consistency of evidence, but also increase the power compared with traditional method (Detailed tutorial is shown in website <http://rpubs.com/chinlin/ETMA>).
Author: Chin Lin
Maintainer: Chin Lin <xup6fup@gmail.com>
Diff between etma versions 1.0-6 dated 2015-10-01 and 1.0-8 dated 2016-03-10
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 +++++++++---- build/partial.rdb |binary build/vignette.rds |only inst |only man/ETMA.Rd | 5 +++-- man/etma-package.Rd | 1 + vignettes |only 8 files changed, 23 insertions(+), 14 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Package DoE.base creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 0.27-1 dated 2015-08-21 and 0.28 dated 2016-03-10
DESCRIPTION | 8 - MD5 | 26 +++-- NAMESPACE | 11 +- R/SCFTs.R | 45 ++++++++-- R/cross.design.R | 4 R/expansive.replace.R |only R/paramtowide.R | 2 R/show.oas.R | 6 + R/sysdata.rda |binary inst/NEWS | 21 ++++ man/GRind.Rd | 16 ++- man/arrays.Rd | 209 +++++++++++++++++++++++++++++++++-------------- man/expansive.replace.Rd |only man/oacat.Rd | 75 +++++++++++++--- man/show.oas.Rd | 10 +- 15 files changed, 324 insertions(+), 109 deletions(-)
Title: R 'Htmlwidget' to Add Pan and Zoom to Almost any R Graphic
Description: This 'htmlwidget' provides pan and zoom interactivity to R
graphics, including 'base', 'lattice', and 'ggplot2'. The interactivity is
provided through the 'svg-pan-zoom.js' library. Various options to the widget
can tailor the pan and zoom experience to nearly any user desire.
Author: Anders Riutta et. al. [aut, cph] (svg-pan-zoom.js BSD-licensed library
in htmlwidgets/lib, https://github.com/ariutta/svg-pan-zoom),
Jorik Tangelder [aut, cph] (hammer.js MIT-licensed touch library in
htmlwidgets/lib, https://github.com/hammerjs/hammer),
Kent Russell [aut, cre] (R interface to svg-pan-zoom.js)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between svgPanZoom versions 0.3.0 dated 2015-09-11 and 0.3.2 dated 2016-03-09
DESCRIPTION | 19 ++--- LICENSE | 2 MD5 | 19 ++--- NAMESPACE | 2 NEWS.md | 11 +++ R/svgPanZoom.R | 29 +++++--- inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.js |only inst/htmlwidgets/lib/svg-pan-zoom/dist/svg-pan-zoom.min.js | 6 - inst/htmlwidgets/svgPanZoom.js | 45 +++++++------ man/svgPanZoom-shiny.Rd | 6 - man/svgPanZoom.Rd | 29 +++++--- 11 files changed, 100 insertions(+), 68 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.2 dated 2016-02-07 and 1.3 dated 2016-03-09
CHANGELOG | 32 +++ DESCRIPTION | 10 - MD5 | 71 +++---- NAMESPACE | 7 R/AI.R | 62 +++++- R/AI2.R | 397 +++++++++++++++++++++------------------ R/AI3.R | 394 +++++++++++++++++++++------------------ R/D.mat.R | 60 ++---- R/EM.R | 500 ++++++++++++++++++++++++-------------------------- R/EMMA.R | 234 +++++++++++++---------- R/atcg1234.R | 108 ++++++---- R/bag.R |only R/fdr.R | 15 - R/hdm.R | 41 ++-- R/jet.colors.R |only R/mmer.R | 116 +++++++++-- R/mmer2.R | 113 +++++------ R/score.calc.R | 1 man/A.mat.Rd | 4 man/AI.Rd | 46 +++- man/CPdata.Rd | 41 ++-- man/D.mat.Rd | 48 +++- man/E.mat.Rd | 4 man/EM.Rd | 16 + man/EMMA.Rd | 19 + man/HDdata.Rd | 28 ++ man/PolyData.Rd | 45 +++- man/atcg1234.Rd | 8 man/bag.Rd |only man/bathy.colors.Rd |only man/cornHybrid.Rd | 62 +++--- man/fdr.Rd | 11 + man/hdm.Rd | 28 ++ man/jet.colors.Rd |only man/map.plot2.Rd | 9 man/mmer.Rd | 273 +++++++++++++++++++-------- man/mmer2.Rd | 94 ++++++--- man/sommer-package.Rd | 173 +++++++++++------ man/wheatLines.Rd | 57 ++++- 39 files changed, 1895 insertions(+), 1232 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow
Archive. The package contains R wrappers to the UK NRFA data temporary-API.
There are functions to retrieve stations falling in a bounding box,
to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre], Matthew Fry [ctb]
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 0.4.3 dated 2016-02-25 and 0.5.1 dated 2016-03-09
rnrfa-0.4.3/rnrfa/R/CMRmeta.R |only rnrfa-0.4.3/rnrfa/R/CMRmulti.R |only rnrfa-0.4.3/rnrfa/R/GDFmeta.R |only rnrfa-0.4.3/rnrfa/R/GDFmulti.R |only rnrfa-0.4.3/rnrfa/man/CMRmeta.Rd |only rnrfa-0.4.3/rnrfa/man/CMRmulti.Rd |only rnrfa-0.4.3/rnrfa/man/GDFmeta.Rd |only rnrfa-0.4.3/rnrfa/man/GDFmulti.Rd |only rnrfa-0.5.1/rnrfa/DESCRIPTION | 6 +- rnrfa-0.5.1/rnrfa/MD5 | 34 ++++++-------- rnrfa-0.5.1/rnrfa/NAMESPACE | 10 ++-- rnrfa-0.5.1/rnrfa/R/CMR.R | 36 ++++----------- rnrfa-0.5.1/rnrfa/R/FindInfo.R | 41 ++++++++++------- rnrfa-0.5.1/rnrfa/R/GDF.R | 37 ++++----------- rnrfa-0.5.1/rnrfa/R/OSGparse.R | 13 ++--- rnrfa-0.5.1/rnrfa/R/catalogue.R | 81 ++++++++++++++++++++-------------- rnrfa-0.5.1/rnrfa/R/getTS.R |only rnrfa-0.5.1/rnrfa/R/plotRainFlow.R |only rnrfa-0.5.1/rnrfa/man/CMR.Rd | 13 +++-- rnrfa-0.5.1/rnrfa/man/GDF.Rd | 14 +++-- rnrfa-0.5.1/rnrfa/man/OSGparse.Rd | 10 ++-- rnrfa-0.5.1/rnrfa/man/catalogue.Rd | 10 ++-- rnrfa-0.5.1/rnrfa/man/getTS.Rd |only rnrfa-0.5.1/rnrfa/man/plotRainFlow.Rd |only 24 files changed, 153 insertions(+), 152 deletions(-)
Title: Solvers for Large Scale Eigenvalue and SVD Problems
Description: Previously an R wrapper of the 'ARPACK' library
<http://www.caam.rice.edu/software/ARPACK/>, and now a shell of the
R package 'RSpectra', an R interface to the 'Spectra' library
<http://yixuan.cos.name/spectra/> for solving large scale
eigenvalue/vector problems. The current version of 'rARPACK'
simply imports and exports the functions provided by 'RSpectra'.
New users of 'rARPACK' are advised to switch to the 'RSpectra' package.
Author: Yixuan Qiu, Jiali Mei and authors of the ARPACK library. See file
AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between rARPACK versions 0.10-0 dated 2016-01-18 and 0.11-0 dated 2016-03-09
rARPACK-0.10-0/rARPACK/R/10_eigs_real_gen.R |only rARPACK-0.10-0/rARPACK/R/20_eigs_real_sym.R |only rARPACK-0.10-0/rARPACK/R/40_svds_real_gen.R |only rARPACK-0.10-0/rARPACK/R/50_svds_real_sym.R |only rARPACK-0.10-0/rARPACK/R/zzz.R |only rARPACK-0.10-0/rARPACK/inst/include |only rARPACK-0.10-0/rARPACK/src |only rARPACK-0.11-0/rARPACK/DESCRIPTION | 32 ++--- rARPACK-0.11-0/rARPACK/MD5 | 70 +----------- rARPACK-0.11-0/rARPACK/NAMESPACE | 23 ---- rARPACK-0.11-0/rARPACK/R/00_eigs.R | 152 +--------------------------- rARPACK-0.11-0/rARPACK/R/30_svds.R | 40 ------- rARPACK-0.11-0/rARPACK/README.md | 27 +++- rARPACK-0.11-0/rARPACK/inst/NEWS.Rd | 9 + rARPACK-0.11-0/rARPACK/man/eigs.Rd | 44 +------- rARPACK-0.11-0/rARPACK/man/svds.Rd | 18 --- 16 files changed, 72 insertions(+), 343 deletions(-)
Title: Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Description: Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data.
Includes Cauchit, Log-Log, Logistic, and Probit link functions for Bernoulli distributed RR data.
Author: Jean-Paul Fox [aut], Konrad Klotzke [aut], Duco Veen [aut]
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>
Diff between GLMMRR versions 0.1.1 dated 2016-03-09 and 0.1.2 dated 2016-03-09
GLMMRR-0.1.1/GLMMRR/R/PlagiarismRR.R |only GLMMRR-0.1.1/GLMMRR/data/PlagiarismRR.rda |only GLMMRR-0.1.1/GLMMRR/man/PlagiarismRR.Rd |only GLMMRR-0.1.2/GLMMRR/DESCRIPTION | 15 GLMMRR-0.1.2/GLMMRR/MD5 | 56 +-- GLMMRR-0.1.2/GLMMRR/NAMESPACE | 48 +- GLMMRR-0.1.2/GLMMRR/R/Plagiarism.R |only GLMMRR-0.1.2/GLMMRR/R/RRglm.R | 218 ++++++------- GLMMRR-0.1.2/GLMMRR/R/RRglmGOF.R | 416 ++++++++++++------------- GLMMRR-0.1.2/GLMMRR/R/RRglmer.R | 268 ++++++++-------- GLMMRR-0.1.2/GLMMRR/R/RRlink_cauchit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_cloglog.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_logit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/RRlink_probit.R | 56 +-- GLMMRR-0.1.2/GLMMRR/R/getRRparameters.R | 270 ++++++++-------- GLMMRR-0.1.2/GLMMRR/R/hello.R | 8 GLMMRR-0.1.2/GLMMRR/R/print.R | 124 +++---- GLMMRR-0.1.2/GLMMRR/R/summary.R | 422 +++++++++++++------------- GLMMRR-0.1.2/GLMMRR/data/Plagiarism.rda |only GLMMRR-0.1.2/GLMMRR/man/Plagiarism.Rd |only GLMMRR-0.1.2/GLMMRR/man/RRglm.Rd | 104 +++--- GLMMRR-0.1.2/GLMMRR/man/RRglmGOF.Rd | 88 ++--- GLMMRR-0.1.2/GLMMRR/man/RRglmer.Rd | 128 +++---- GLMMRR-0.1.2/GLMMRR/man/RRlink.cauchit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.cloglog.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.logit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/RRlink.probit.Rd | 42 +- GLMMRR-0.1.2/GLMMRR/man/getRRparameters.Rd | 48 +- GLMMRR-0.1.2/GLMMRR/man/hello.Rd | 24 - GLMMRR-0.1.2/GLMMRR/man/print.RRglmGOF.Rd | 38 +- GLMMRR-0.1.2/GLMMRR/man/summary.RRglm.Rd | 48 +- GLMMRR-0.1.2/GLMMRR/man/summary.RRglmerMod.Rd | 48 +- 32 files changed, 1385 insertions(+), 1378 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.5 dated 2016-02-28 and 0.6 dated 2016-03-09
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NEWS | 18 +++++++++++++++--- R/isat.R | 4 +++- man/coef.arx.Rd | 2 +- man/coef.gets.Rd | 24 +++++------------------- man/gets-package.Rd | 4 ++-- man/paths.Rd |only 8 files changed, 38 insertions(+), 37 deletions(-)
Title: Fuzzy Forests
Description: Fuzzy forests, a new algorithm based on random forests,
is designed to reduce the bias seen in random forest feature selection
caused by the presence of correlated features. Fuzzy forests uses
recursive feature elimination random forests to select
features from separate blocks of correlated features where the
correlation within each block of features is high
and the correlation between blocks of features is low.
One final random forest is fit using the surviving features.
This package fits random forests using the 'randomForest' package and
allows for easy use of 'WGCNA' to split features into distinct blocks.
Author: Daniel Conn [aut, cre],
Tuck Ngun [aut],
Christina M. Ramirez [aut]
Maintainer: Daniel Conn <djconn17@gmail.com>
Diff between fuzzyforest versions 1.0.0 dated 2016-02-18 and 1.0.1 dated 2016-03-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/select_RF.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Time-Dependent ROC Curve Estimators and Expected Utility
Functions
Description: Contains functions in order to estimate diagnostic and prognostic capacities of continuous markers. More precisely, one function concerns the estimation of time-dependent ROC (ROCt) curve, as proposed by Heagerty et al. (2000) <DOI: 10.1111/j.0006-341X.2000.00337.x>. One function concerns the adaptation of the ROCt theory for studying the capacity of a marker to predict the excess of mortality of a specific population compared to the general population. This last part is based on additive relative survival models and the work of Pohar-Perme et al. (2012) <DOI: 10.1111/j.1541-0420.2011.01640.x>. We also propose two functions for cut-off estimation in medical decision making by maximizing time-dependent expected utility function. Finally, we propose confounder-adjusted estimators of ROC and ROCt curves by using the Inverse Probability Weighting (IPW) approach. For the confounder-adjusted ROC curve (without censoring), we also proposed the implementation of the estimator based on placement values proposed by Pepe and Cai (2004) <DOI: 10.1111/j.0006-341X.2004.00200.x>.
Author: Y. Foucher, E. Dantan, P. Tessier, F. Le Borgne, and M. Lorent
Maintainer: Y. Foucher <Yohann.Foucher@univ-nantes.fr>
Diff between ROCt versions 0.8 dated 2013-12-20 and 0.9.4 dated 2016-03-09
ROCt-0.8/ROCt/man/allcause.ROCt.Rd |only ROCt-0.9.4/ROCt/DESCRIPTION | 18 ROCt-0.9.4/ROCt/MD5 | 33 - ROCt-0.9.4/ROCt/NAMESPACE | 7 ROCt-0.9.4/ROCt/R/prog.R | 666 +++++++++++++++++++++++++++++++- ROCt-0.9.4/ROCt/data/dataDIVAT.rda |binary ROCt-0.9.4/ROCt/data/dataKTFS.rda |only ROCt-0.9.4/ROCt/data/datalist | 1 ROCt-0.9.4/ROCt/data/fr.ratetable.rda |binary ROCt-0.9.4/ROCt/data/rein.ratetable.rda |binary ROCt-0.9.4/ROCt/man/AUC.Rd |only ROCt-0.9.4/ROCt/man/EUt1.Rd |only ROCt-0.9.4/ROCt/man/EUt2.Rd |only ROCt-0.9.4/ROCt/man/ROCt-package.Rd | 37 + ROCt-0.9.4/ROCt/man/adjusted.ROC.Rd |only ROCt-0.9.4/ROCt/man/adjusted.ROCt.Rd |only ROCt-0.9.4/ROCt/man/crude.ROCt.Rd |only ROCt-0.9.4/ROCt/man/dataDIVAT.Rd | 4 ROCt-0.9.4/ROCt/man/dataKTFS.Rd |only ROCt-0.9.4/ROCt/man/fr.ratetable.Rd | 8 ROCt-0.9.4/ROCt/man/net.ROCt.Rd | 57 +- ROCt-0.9.4/ROCt/man/rein.ratetable.Rd | 6 22 files changed, 738 insertions(+), 99 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic agent-based, and stochastic network models. Network models use
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features
an easy API for extending these templates to address novel scientific research
aims.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 1.2.4 dated 2016-02-01 and 1.2.5 dated 2016-03-09
DESCRIPTION | 8 - MD5 | 59 +++++----- NEWS | 15 ++ R/EpiModel-package.r | 4 R/control.R | 5 R/dendo.R | 195 ++++++++++++++++++++++------------ R/netdx.R | 3 R/netest.R | 22 --- R/netsim.R | 141 ++++++++++++++++-------- R/param.R | 3 R/test.R | 140 ++++++------------------ inst/doc/Intro.Rmd | 2 inst/doc/Intro.html | 21 +-- man/EpiModel-package.Rd | 4 man/as.network.transmat.Rd | 2 man/as.phylo.transmat.Rd | 32 +++-- man/control.net.Rd | 25 ++-- man/netest.Rd | 7 - man/netsim.Rd | 9 - man/param.net.Rd | 3 man/plot.transmat.Rd | 2 tests/testthat/test-dcm.R | 11 + tests/testthat/test-icm-long.R | 5 tests/testthat/test-icm.R | 23 ++++ tests/testthat/test-netdx.R | 46 +++++++- tests/testthat/test-netest.R | 55 +++++++++ tests/testthat/test-netsim-parallel.R |only tests/testthat/test-netsim.R | 51 ++++++++ tests/testthat/test-print.R | 30 ++--- tests/testthat/test-transmat-dendo.R | 26 ++++ vignettes/Intro.Rmd | 2 31 files changed, 598 insertions(+), 353 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.2 dated 2016-03-05 and 0.2.2.1 dated 2016-03-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/fdouble_metaphone.c | 14 +++++--------- 3 files changed, 10 insertions(+), 14 deletions(-)
Title: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing
Description: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing.
Author: Dirk de Weerd, Lennart Johansson
Maintainer: Lennart Johansson <l.johansson@umcg.nl>
Diff between NIPTeR versions 1.0.1 dated 2016-01-02 and 1.0.2 dated 2016-03-09
DESCRIPTION | 14 +++---- MD5 | 22 +++++------ NAMESPACE | 1 R/bin_sample.R | 1 R/diagnose_control_group.R | 2 - R/prepare_ncv_template.R | 14 +++---- R/regression.R | 4 +- R/z_score.R | 2 - build/vignette.rds |binary inst/doc/NIPTeR.Rmd | 2 - inst/doc/NIPTeR.html | 84 +++++++++++++++++++++++++++++++++++---------- vignettes/NIPTeR.Rmd | 2 - 12 files changed, 98 insertions(+), 50 deletions(-)
Title: Simple Metrics to Summarize Growth Curves
Description: This is a simple package that fits the logistic equation to
microbial growth curve data (e.g., repeated absorbance measurements
taken from a plate reader over time). From this fit, a variety of
metrics are provided, including the maximum growth rate,
the doubling time, the carrying capacity, the area under the logistic
curve, and the time to the inflection point.
Author: Kathleen sprouffske [aut, cre]
Maintainer: Kathleen sprouffske <sprouffske@gmail.com>
Diff between growthcurver versions 0.1.0 dated 2015-11-03 and 0.2.0 dated 2016-03-09
DESCRIPTION | 12 - MD5 | 26 +-- NAMESPACE | 1 R/fit-logistic.R | 4 R/helpers.R | 42 +++++ R/summarize-growth-by-plate.R |only R/summarize-growth.R | 82 +++++++++-- README.md | 6 inst/doc/Growthcurver-vignette.R | 136 ++++++++++++------ inst/doc/Growthcurver-vignette.Rmd | 190 +++++++++++++++++--------- inst/doc/Growthcurver-vignette.html | 247 +++++++++++++++++++++++++--------- man/SummarizeGrowth.Rd | 18 ++ man/SummarizeGrowthByPlate.Rd |only tests/testthat/test_SummarizeGrowth.R | 2 vignettes/Growthcurver-vignette.Rmd | 190 +++++++++++++++++--------- 15 files changed, 686 insertions(+), 270 deletions(-)
Title: Emoji Fonts for using in R
Description: An implementation of using emoji font in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between emojifont versions 0.3.1 dated 2016-02-26 and 0.3.2 dated 2016-03-09
DESCRIPTION | 6 - MD5 | 14 ++- README.md | 130 +++++-------------------------------- build/vignette.rds |binary inst/doc/emojifont.Rmd | 40 ++++++++++- inst/doc/emojifont.html | 72 +++++++++++++++----- vignettes/emojifont.Rmd | 40 ++++++++++- vignettes/figures/apple_emoji2.png |only vignettes/figures/fontawesome.png |only 9 files changed, 159 insertions(+), 143 deletions(-)
Title: Bayesian Estimation of Incoherent Neutron Scattering Backgrounds
Description: We implemented a Bayesian-statistics approach for
subtraction of incoherent scattering from neutron total-scattering data.
In this approach, the estimated background signal associated with
incoherent scattering maximizes the posterior probability, which combines
the likelihood of this signal in reciprocal and real spaces with the prior
that favors smooth lines.
Author: Anton Gagin and Igor Levin with contributions from Charles R. Hogg III
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between BBEST versions 0.1-5 dated 2015-09-15 and 0.1-6 dated 2016-03-09
ChangeLog | 9 DESCRIPTION | 8 MD5 | 16 - README.md | 6 inst/gui/help/help.html | 540 ++++++++++++++++++++++++------------------------ inst/gui/server.R | 31 ++ inst/gui/ui.R | 3 man/do.fit.Rd | 2 man/set.control.Rd | 2 9 files changed, 326 insertions(+), 291 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.5.4 dated 2016-01-16 and 0.5.6 dated 2016-03-09
DESCRIPTION | 8 +- MD5 | 56 ++++++++--------- R/linarpr.R | 8 -- R/linarpt.R | 5 - R/linarr.R | 31 ++++----- R/lingini.R | 18 ++--- R/lingini2.R | 18 ++--- R/lingpg.R | 55 ++++++++-------- R/linpoormed.R | 9 +- R/linqsr.R | 132 ++++++++++++++++++++-------------------- R/linrmir.R | 8 -- R/linrmpg.R | 5 - R/vardchangannual.R | 16 ++-- R/vardchanges.R | 157 ++++++++++++++++++++++++++---------------------- R/vardchangespoor.R | 102 +++++++++++++++++-------------- R/vardcros.R | 49 ++++++-------- R/vardcrospoor.R | 19 +---- R/vardomh.R | 7 +- R/variance_est.R | 26 +++---- R/variance_othstr.R | 86 ++++++++++---------------- R/varpoord.R | 8 +- inst/CITATION | 4 - inst/NEWS | 9 ++ man/vardchangannual.Rd | 5 - man/vardchanges.Rd | 8 -- man/vardchangespoor.Rd | 6 - man/vardcros.Rd | 9 -- man/vardcrospoor.Rd | 5 - man/vardpoor-package.Rd | 4 - 29 files changed, 420 insertions(+), 453 deletions(-)
Title: Global, Parameterwise and Joint Shrinkage Factor Estimation
Description: The predictive value of a statistical model can often be improved
by applying shrinkage methods. This can be achieved, e.g., by regularized
regression or empirical Bayes approaches. Various types of shrinkage factors can
also be estimated after a maximum likelihood. While global shrinkage modifies
all regression coefficients by the same factor, parameterwise shrinkage factors
differ between regression coefficients. With variables which are either highly
correlated or associated with regard to contents, such as several columns of a
design matrix describing a nonlinear effect, parameterwise shrinkage factors are
not interpretable and a compromise between global and parameterwise shrinkage,
termed 'joint shrinkage', is a useful extension. A computational shortcut to
resampling-based shrinkage factor estimation based on DFBETA residuals can be
applied. Global, parameterwise and joint shrinkage for models fitted by lm(),
glm(), coxph(), or mfp() is available.
Author: Daniela Dunkler [aut, cre],
Georg Heinze [aut]
Maintainer: Daniela Dunkler <daniela.dunkler@meduniwien.ac.at>
Diff between shrink versions 1.2.0 dated 2014-10-02 and 1.2.1 dated 2016-03-09
shrink-1.2.0/shrink/Changelog |only shrink-1.2.0/shrink/R/additionalfunctions.r |only shrink-1.2.0/shrink/R/coef.shrink.r |only shrink-1.2.0/shrink/R/predict.shrink.r |only shrink-1.2.0/shrink/R/print.shrink.r |only shrink-1.2.0/shrink/R/shrink.coxph.r |only shrink-1.2.0/shrink/R/shrink.glm.r |only shrink-1.2.0/shrink/R/shrink.lm.r |only shrink-1.2.0/shrink/R/shrink.r |only shrink-1.2.0/shrink/R/summary.shrink.r |only shrink-1.2.0/shrink/R/vcov.shrink.r |only shrink-1.2.0/shrink/data/GBSG.txt.gz |only shrink-1.2.0/shrink/data/deepvein.txt.gz |only shrink-1.2.1/shrink/DESCRIPTION | 49 ++- shrink-1.2.1/shrink/MD5 | 62 ++-- shrink-1.2.1/shrink/NAMESPACE | 41 ++- shrink-1.2.1/shrink/R/GBSG.R |only shrink-1.2.1/shrink/R/coef.shrink.R |only shrink-1.2.1/shrink/R/deepvein.R |only shrink-1.2.1/shrink/R/predict.shrink.R |only shrink-1.2.1/shrink/R/print.shrink.R |only shrink-1.2.1/shrink/R/shrink.R |only shrink-1.2.1/shrink/R/shrink.coxph.R |only shrink-1.2.1/shrink/R/shrink.glm.R |only shrink-1.2.1/shrink/R/shrink.lm.R |only shrink-1.2.1/shrink/R/summary.shrink.R |only shrink-1.2.1/shrink/R/utility.R |only shrink-1.2.1/shrink/R/vcov.shrink.R |only shrink-1.2.1/shrink/R/zzz.R |only shrink-1.2.1/shrink/build |only shrink-1.2.1/shrink/data/GBSG.rda |only shrink-1.2.1/shrink/data/deepvein.rda |only shrink-1.2.1/shrink/inst/CITATION | 40 +-- shrink-1.2.1/shrink/inst/NEWS.Rd |only shrink-1.2.1/shrink/inst/doc |only shrink-1.2.1/shrink/man/GBSG.Rd | 62 ++-- shrink-1.2.1/shrink/man/coef.shrink.Rd | 49 +-- shrink-1.2.1/shrink/man/deepvein.Rd | 120 +++------ shrink-1.2.1/shrink/man/isrcs.Rd |only shrink-1.2.1/shrink/man/predict.shrink.Rd | 124 ++++++--- shrink-1.2.1/shrink/man/print.shrink.Rd | 46 +-- shrink-1.2.1/shrink/man/shrink-package.Rd | 116 ++++---- shrink-1.2.1/shrink/man/shrink.Rd | 361 ++++++++++++++-------------- shrink-1.2.1/shrink/man/shrink.coxph.Rd |only shrink-1.2.1/shrink/man/shrink.glm.Rd |only shrink-1.2.1/shrink/man/shrink.lm.Rd |only shrink-1.2.1/shrink/man/summary.shrink.Rd | 52 +--- shrink-1.2.1/shrink/man/vcov.shrink.Rd | 50 +-- shrink-1.2.1/shrink/vignettes |only 49 files changed, 595 insertions(+), 577 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.6 dated 2015-11-18 and 1.6.1 dated 2016-03-09
ChangeLog | 21 ++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 36 ++++++++++++------------ R/draic.R | 9 ++++-- R/hmm.R | 5 ++- R/msm.R | 50 ++++++++++++++++++++++++++------- build/vignette.rds |binary inst/NEWS | 15 ++++++++++ inst/doc/msm-manual.pdf |binary man/draic.msm.Rd | 8 ++++- man/msm.Rd | 30 ++++++++++---------- src/lik.c | 7 ++-- src/msm.h | 1 tests/testthat/helper.r | 9 +----- tests/testthat/test_datasumm.r | 2 - tests/testthat/test_deriv.r | 51 +++++++++++++++++----------------- tests/testthat/test_models.r | 7 +++- tests/testthat/test_models_hmmmulti.r | 11 ++++--- tests/testthat/test_models_misc.r | 5 +++ 19 files changed, 179 insertions(+), 96 deletions(-)
Title: Functional Data Analysis and Partial Differential Equations;
Statistical Analysis of Functional and Spatial Data, Based on
Regression with Partial Differential Regularizations
Description: An implementation of regression models with partial differential regularizations, making use of the Finite Element Method. The models efficiently handle data distributed over irregularly shaped domains and can comply with various conditions at the boundaries of the domain. A priori information about the spatial structure of the phenomenon under study can be incorporated in the model via the differential regularization.
Author: Eardi Lila [aut, cre],
Laura M. Sangalli [aut],
Jim Ramsay [aut],
Luca Formaggia [aut]
Maintainer: Eardi Lila <el425@cam.ac.uk>
Diff between fdaPDE versions 0.1-1 dated 2016-01-15 and 0.1-2 dated 2016-03-09
DESCRIPTION | 18 ++--- MD5 | 88 +++++++++++++------------ R/fdaPDE.checkParameters.R |only R/fdaPDE.locator.R | 23 ++++-- R/fdaPDE.objects.R | 41 ++++++------ R/fdaPDE.smoothing.R | 133 ++++++++++++++++++++++++++++++--------- R/fdaPDE.smoothing_CPP.R | 6 - R/fdaPDE.smoothing_R.R | 14 +++- R/mesh.2D.R | 29 +++----- README.md |only man/FEM.Rd | 8 +- man/MeuseBorder.Rd | 2 man/MeuseData.Rd | 8 +- man/R_elementProperties.Rd | 8 +- man/R_eval.FEM.Rd | 4 - man/R_eval.FEM.basis.Rd | 6 - man/R_mass.Rd | 4 - man/R_smooth.FEM.basis.Rd | 4 - man/R_stiff.Rd | 4 - man/create.FEM.basis.Rd | 28 +++----- man/create.MESH.2D.Rd | 32 ++++----- man/eval.FEM.Rd | 4 - man/image.FEM.Rd | 4 - man/mesh.2D.rectangular.Rd | 2 man/mesh.2D.simple.Rd | 2 man/plot.FEM.Rd | 4 - man/plot.MESH2D.Rd | 2 man/refine.MESH.2D.Rd | 18 ++--- man/smooth.FEM.PDE.basis.Rd | 29 ++++---- man/smooth.FEM.PDE.sv.basis.Rd | 51 +++++++++----- man/smooth.FEM.basis.Rd | 27 ++++--- src/FEMeval.cpp | 3 src/evaluator.h | 2 src/evaluator_imp.h | 30 +++++--- src/fdaPDE.cpp | 50 +++++++------- src/finite_element_imp.h | 7 +- src/mesh.h | 2 src/mesh_imp.h | 41 ++++++------ src/mesh_objects.h | 1 src/mesh_objects_imp.h | 10 +- src/mixedFERegression_imp.h | 31 +++++---- src/triangle.c | 1 tests/testsmoothingPDE.R | 2 tests/testsmoothingPDESV.R | 14 ++-- tests/testsmoothingbaseCPPcode.R | 2 tests/testsmoothingbaseRcode.R | 2 46 files changed, 470 insertions(+), 331 deletions(-)
Title: Simulation of Time-to-Event Family Data and Penetrance
Estimation
Description: Generates time-to-event family data associated with mutated genes arising from various family study designs such as population-based, clinic- based, or multi-stage designs and provides functions to fit family data accounting for the study design and estimate age-dependent penetrance functions. It also provides carrier probabilities for those with missing genotypes and penetrance estimations are based on an Expectation-Maximization algorithm when genotypes are missing.
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
Diff between FamEvent versions 1.0 dated 2016-02-09 and 1.1 dated 2016-03-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/inv.surv.R | 2 +- R/penmodelEM.R | 15 ++++++++++----- R/plot.simfam.R | 14 ++++++++------ man/plot.simfam.Rd | 19 +++++++++---------- man/simfam.Rd | 2 +- 7 files changed, 39 insertions(+), 33 deletions(-)
Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.4 dated 2015-11-27 and 0.3.5 dated 2016-03-09
DVHmetrics-0.3.4/DVHmetrics/R/loessSelSpan.R |only DVHmetrics-0.3.5/DVHmetrics/DESCRIPTION | 10 - DVHmetrics-0.3.5/DVHmetrics/MD5 | 68 +++--- DVHmetrics-0.3.5/DVHmetrics/NAMESPACE | 95 +++++---- DVHmetrics-0.3.5/DVHmetrics/R/convertDVH.R | 178 ++++++------------ DVHmetrics-0.3.5/DVHmetrics/R/convertDVHsmooth.R |only DVHmetrics-0.3.5/DVHmetrics/R/getDMEAN.R | 51 +++-- DVHmetrics-0.3.5/DVHmetrics/R/getHI.R |only DVHmetrics-0.3.5/DVHmetrics/R/getMeanDVH.R | 20 -- DVHmetrics-0.3.5/DVHmetrics/R/getMetric.R | 36 ++- DVHmetrics-0.3.5/DVHmetrics/R/getNTCP.R | 5 DVHmetrics-0.3.5/DVHmetrics/R/parseCadplan.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseConstraint.R | 7 DVHmetrics-0.3.5/DVHmetrics/R/parseEclipse.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseHiArt.R | 15 - DVHmetrics-0.3.5/DVHmetrics/R/parseMasterplan.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/parseMetric.R | 21 +- DVHmetrics-0.3.5/DVHmetrics/R/parseMonaco.R | 31 ++- DVHmetrics-0.3.5/DVHmetrics/R/parsePinnacleDVH.R | 33 +-- DVHmetrics-0.3.5/DVHmetrics/R/parseRayStation.R | 4 DVHmetrics-0.3.5/DVHmetrics/R/showDVH.R | 2 DVHmetrics-0.3.5/DVHmetrics/R/smoothDVH.R | 2 DVHmetrics-0.3.5/DVHmetrics/inst/ChangeLog | 27 ++ DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/helper.R | 5 DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/server.R | 12 - DVHmetrics-0.3.5/DVHmetrics/inst/DVHshiny/ui.R | 25 +- DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHmetrics.Rnw | 3 DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHmetrics.pdf |binary DVHmetrics-0.3.5/DVHmetrics/inst/doc/DVHshiny.pdf |binary DVHmetrics-0.3.5/DVHmetrics/man/DVHmetrics-package.Rd | 4 DVHmetrics-0.3.5/DVHmetrics/man/convertDVH.Rd | 17 - DVHmetrics-0.3.5/DVHmetrics/man/convertDVHsmooth.Rd |only DVHmetrics-0.3.5/DVHmetrics/man/getDMEAN.Rd | 3 DVHmetrics-0.3.5/DVHmetrics/man/getMeanDVH.Rd | 13 - DVHmetrics-0.3.5/DVHmetrics/man/getMetric.Rd | 1 DVHmetrics-0.3.5/DVHmetrics/man/readDVH.Rd | 2 DVHmetrics-0.3.5/DVHmetrics/vignettes/DVHmetrics.Rnw | 3 37 files changed, 374 insertions(+), 331 deletions(-)
Title: Automated C Code Generation for Use with the 'deSolve' and
'bvpSolve' Packages
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
Diff between cOde versions 0.2 dated 2015-06-10 and 0.2.1 dated 2016-03-09
cOde-0.2.1/cOde/DESCRIPTION | 8 ++++---- cOde-0.2.1/cOde/MD5 | 14 ++++++-------- cOde-0.2.1/cOde/NAMESPACE | 3 +++ cOde-0.2.1/cOde/R/cOde.R | 22 +++++++++++++++------- cOde-0.2.1/cOde/R/derivedEquations.R | 2 +- cOde-0.2.1/cOde/R/symbolics.R | 7 ++++--- cOde-0.2.1/cOde/man/funC.Rd | 5 ++++- cOde-0.2/cOde/data |only 8 files changed, 37 insertions(+), 24 deletions(-)
Title: Recovering a Basic Space from Issue Scales
Description: Conducts Aldrich-McKelvey and Blackbox Scaling to Recover
Latent Dimensions of Judgment.
Author: Keith Poole <ktpoole@uga.edu>, Howard Rosenthal
<hr31@nyu.edu>, Jeffrey Lewis <jblewis@ucla.edu>,
James Lo <jameslo@princeton.edu> and Royce Carroll
<rcarroll@rice.edu>
Maintainer: James Lo <jameslo@princeton.edu>
Diff between basicspace versions 0.15 dated 2014-11-19 and 0.17 dated 2016-03-09
ChangeLog | 17 +++++------------ DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- NAMESPACE | 11 +++++++++++ build |only inst/CITATION |only man/Issues1980.Rd | 2 +- man/LC1980.Rd | 2 +- man/aldmck.Rd | 6 +++++- man/blackbox.Rd | 4 ++++ man/blackbox_transpose.Rd | 4 ++++ man/boot_aldmck.Rd | 6 +++++- 12 files changed, 52 insertions(+), 30 deletions(-)
Title: Hierarchical Models for Parametric and Semi-Parametric Analyses
of Semi-Competing Risks Data
Description: Parametric and semi-parametric analyses of semi-competing risks/univariate survival data.
Author: Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between SemiCompRisks versions 2.3 dated 2015-12-04 and 2.4 dated 2016-03-09
DESCRIPTION | 10 MD5 | 18 - R/BayesID.R | 80 +++---- R/BayesSurv.R | 28 +- R/initiate.startValues.R | 442 +++++++++++++++++++++++++++++++++++-------- R/methods.R | 169 ++++++++++++---- man/BayesID.Rd | 10 man/BayesSurv.Rd | 10 man/SemiCompRisks-package.Rd | 8 man/initiate.startValues.Rd | 39 +++ 10 files changed, 614 insertions(+), 200 deletions(-)
Title: Read ODS Files
Description: Read ODS (OpenDocument Spreadsheet) and puts them into data frames.
Author: Gerrit-Jan Schutten, Chung-hong Chan
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 1.4 dated 2014-07-07 and 1.6.2 dated 2016-03-09
readODS-1.4/readODS/man/getNrOfSheetsInODS.Rd |only readODS-1.4/readODS/man/getODSRoot.Rd |only readODS-1.4/readODS/man/lettersToNumber.Rd |only readODS-1.4/readODS/man/numberToLetters.Rd |only readODS-1.4/readODS/man/odsPreParser.Rd |only readODS-1.4/readODS/tests/runAllTests.R |only readODS-1.4/readODS/tests/testdata/content_googledocs.xml |only readODS-1.4/readODS/tests/testdata/content_layout_test.xml |only readODS-1.4/readODS/tests/testdata/content_lotsofnothing_test.xml |only readODS-1.4/readODS/tests/testdata/content_mergerandgreaterthanlibreoffice.xml |only readODS-1.4/readODS/tests/testdata/content_multisheet.xml |only readODS-1.4/readODS/tests/testdata/content_sum.xml |only readODS-1.4/readODS/tests/testdata/content_table.xml |only readODS-1.4/readODS/tests/testdata/content_test.xml |only readODS-1.4/readODS/tests/testthat/test_readODS.R |only readODS-1.6.2/readODS/DESCRIPTION | 24 readODS-1.6.2/readODS/MD5 | 35 readODS-1.6.2/readODS/NAMESPACE | 9 readODS-1.6.2/readODS/R/readODS.R | 679 +++------- readODS-1.6.2/readODS/README.md | 91 - readODS-1.6.2/readODS/man/get_num_sheet_in_ods.Rd |only readODS-1.6.2/readODS/man/ods_sheets.Rd |only readODS-1.6.2/readODS/man/read.ods.Rd | 18 readODS-1.6.2/readODS/man/read_ods.Rd |only readODS-1.6.2/readODS/tests/testdata/1996-2000.ods |only readODS-1.6.2/readODS/tests/testdata/datasets.ods |only readODS-1.6.2/readODS/tests/testdata/merged.ods |only readODS-1.6.2/readODS/tests/testdata/smartSheetTest.ods |only readODS-1.6.2/readODS/tests/testthat.R |only readODS-1.6.2/readODS/tests/testthat/test_legacy.R |only readODS-1.6.2/readODS/tests/testthat/test_read_ods.R |only 31 files changed, 345 insertions(+), 511 deletions(-)
Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.devices versions 2.13.2 dated 2015-12-16 and 2.14.0 dated 2016-03-09
DESCRIPTION | 8 - MD5 | 30 ++-- NAMESPACE | 1 NEWS | 10 + R/capturePlot.R |only R/devOptions.R | 6 R/deviceUtils.R | 24 +++ R/utils.R |only build/vignette.rds |binary inst/doc/R.devices-overview.pdf |binary man/R.devices-package.Rd | 4 man/capturePlot.Rd |only tests/capabilitiesX11.R | 2 tests/capturePlot.R |only tests/devEqualTypes.R | 82 ++++++------- tests/devEval.R | 4 tests/devNew.R | 242 ++++++++++++++++++++-------------------- tests/toNNN.R | 57 ++++----- 18 files changed, 250 insertions(+), 220 deletions(-)
Title: Bindings to AppArmor and Security Related Linux Tools
Description: Bindings to various methods in the kernel for enforcing security
restrictions. AppArmor can apply mandatory access control (MAC) policies on
a given task (process) via security profiles with detailed ACL definitions.
In addition the package has kernel bindings for setting the process hardware
resource limits (rlimit), uid, gid, affinity and priority. The high level R
function 'eval.secure' builds on these methods to do dynamic sandboxing:
it evaluates a single R expression within a temporary fork which acts as a
sandbox by enforcing fine grained restrictions without affecting the main R
process.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RAppArmor versions 1.0.1 dated 2013-12-18 and 2.0 dated 2016-03-09
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More information about DiversityOccupancy at CRAN
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Title: Simultaneous Variables Clustering and Regression
Description: Implements an empirical Bayes approach for simultaneous variable clustering and regression. This version also (re)implements in C++ an R script proposed by Howard Bondell that fits the Pairwise Absolute Clustering and Sparsity (PACS) methodology (see Sharma et al (2013) <DOI:10.1080/15533174.2012.707849>).
Author: Loic Yengo, Mickael Canouil
Maintainer: Loic Yengo <loic.yengo@gmail.com>
Diff between clere versions 1.1.2 dated 2015-10-08 and 1.1.3 dated 2016-03-09
clere-1.1.2/clere/inst/doc/RJpaper-vignette.ltx |only clere-1.1.2/clere/inst/doc/RJpaper-vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf |only clere-1.1.2/clere/inst/doc/Vignette.pdf.asis |only clere-1.1.2/clere/vignettes/Vignette.pdf.asis |only clere-1.1.3/clere/DESCRIPTION | 14 ++---- clere-1.1.3/clere/MD5 | 42 +++++++++++-------- clere-1.1.3/clere/NAMESPACE | 22 +++++++++ clere-1.1.3/clere/R/Clere.R | 13 +++++ clere-1.1.3/clere/build/vignette.rds |binary clere-1.1.3/clere/data/algoComp.RData |binary clere-1.1.3/clere/data/numExpRealData.RData |binary clere-1.1.3/clere/data/numExpSimData.RData |binary clere-1.1.3/clere/inst/doc/ExampleProstate.R |only clere-1.1.3/clere/inst/doc/Methods.R |only clere-1.1.3/clere/inst/doc/RealDataExample.R |only clere-1.1.3/clere/inst/doc/SEM_vs_MCEM_simulations.R |only clere-1.1.3/clere/inst/doc/SimulatedDataExample.R |only clere-1.1.3/clere/inst/doc/clere.R |only clere-1.1.3/clere/inst/doc/clere.Rnw |only clere-1.1.3/clere/inst/doc/clere.pdf |only clere-1.1.3/clere/man/algoComp.Rd | 3 - clere-1.1.3/clere/man/clere-package.Rd | 4 - clere-1.1.3/clere/man/numExpRealData.Rd | 1 clere-1.1.3/clere/man/numExpSimData.Rd | 3 - clere-1.1.3/clere/vignettes/RJournal.sty |only clere-1.1.3/clere/vignettes/biblio.bib |only clere-1.1.3/clere/vignettes/clere.Rnw |only clere-1.1.3/clere/vignettes/environ.sty |only clere-1.1.3/clere/vignettes/inconsolata.sty |only clere-1.1.3/clere/vignettes/trimspaces.sty |only clere-1.1.3/clere/vignettes/upquote.sty |only 32 files changed, 72 insertions(+), 30 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms.
Author: Daniel Sabanes Bove <sabanesd@roche.com>
Maintainer: Daniel Sabanes Bove <sabanesd@roche.com>
Diff between bfp versions 0.0-27 dated 2013-12-10 and 0.0-30 dated 2016-03-09
ChangeLog | 312 +++++++++++++++++++++++++------------------------- DESCRIPTION | 23 ++- MD5 | 20 +-- NAMESPACE | 132 +++++++++++---------- R/plotCurveEstimate.R | 38 +++--- data/ozone.RData |binary src/dataStructure.cpp | 1 src/hyp2f1.c | 6 src/hyperg.cpp | 2 src/hyperg.h | 12 + src/mconf.h | 6 11 files changed, 285 insertions(+), 267 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as verifying species names, and getting taxonomic 'hierarchies'.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut],
James O'Donnell [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.7.0 dated 2015-11-30 and 0.7.4 dated 2016-03-08
taxize-0.7.0/taxize/man/get_genes-deprecated.Rd |only taxize-0.7.0/taxize/man/get_genes_avail-deprecated.Rd |only taxize-0.7.0/taxize/man/get_seqs-deprecated.Rd |only taxize-0.7.4/taxize/DESCRIPTION | 20 taxize-0.7.4/taxize/LICENSE | 2 taxize-0.7.4/taxize/MD5 | 339 +++--- taxize-0.7.4/taxize/NAMESPACE | 26 taxize-0.7.4/taxize/NEWS.md |only taxize-0.7.4/taxize/R/apg.R | 4 taxize-0.7.4/taxize/R/children.R | 4 taxize-0.7.4/taxize/R/classification.R | 86 - taxize-0.7.4/taxize/R/col_children.R | 57 - taxize-0.7.4/taxize/R/col_classification.R | 59 - taxize-0.7.4/taxize/R/col_downstream.R | 97 - taxize-0.7.4/taxize/R/col_search.R | 23 taxize-0.7.4/taxize/R/comm2sci.R | 8 taxize-0.7.4/taxize/R/downstream.R | 80 - taxize-0.7.4/taxize/R/eol_dataobjects.R | 21 taxize-0.7.4/taxize/R/eol_hierarchy.R | 34 taxize-0.7.4/taxize/R/eol_invasive.R | 128 -- taxize-0.7.4/taxize/R/eol_pages.R | 42 taxize-0.7.4/taxize/R/eol_search.R | 3 taxize-0.7.4/taxize/R/eubon.R | 6 taxize-0.7.4/taxize/R/fungorum.R | 50 - taxize-0.7.4/taxize/R/gbif_downstream.R | 33 taxize-0.7.4/taxize/R/gbif_name_usage.R |only taxize-0.7.4/taxize/R/gbif_parse.R | 2 taxize-0.7.4/taxize/R/genbank2uid.R | 11 taxize-0.7.4/taxize/R/get_boldid.R | 4 taxize-0.7.4/taxize/R/get_colid.R | 6 taxize-0.7.4/taxize/R/get_eolid.R | 51 - taxize-0.7.4/taxize/R/get_gbifid.R | 16 taxize-0.7.4/taxize/R/get_tsn.R | 13 taxize-0.7.4/taxize/R/get_ubioid.R | 2 taxize-0.7.4/taxize/R/get_uid.R | 40 taxize-0.7.4/taxize/R/getkey.R |only taxize-0.7.4/taxize/R/gisd_isinvasive.R | 64 - taxize-0.7.4/taxize/R/gni_details.R | 3 taxize-0.7.4/taxize/R/gni_parse.R | 2 taxize-0.7.4/taxize/R/gni_search.R | 3 taxize-0.7.4/taxize/R/gnr_resolve.R | 21 taxize-0.7.4/taxize/R/ion.R | 21 taxize-0.7.4/taxize/R/iplant_resolve.R | 2 taxize-0.7.4/taxize/R/ipni_search.R | 2 taxize-0.7.4/taxize/R/itis.R | 382 +++---- taxize-0.7.4/taxize/R/itis_downstream.R | 38 taxize-0.7.4/taxize/R/itis_hierarchy.R | 2 taxize-0.7.4/taxize/R/iucn_id.R | 48 taxize-0.7.4/taxize/R/iucn_summary.R | 143 ++ taxize-0.7.4/taxize/R/lowest_common.R |only taxize-0.7.4/taxize/R/nbn_classification.R | 2 taxize-0.7.4/taxize/R/nbn_search.R | 7 taxize-0.7.4/taxize/R/nbn_synonyms.R | 4 taxize-0.7.4/taxize/R/ncbi_children.R | 6 taxize-0.7.4/taxize/R/ncbi_get_taxon_summary.R | 11 taxize-0.7.4/taxize/R/ncbi_getbyid.R | 50 - taxize-0.7.4/taxize/R/ncbi_getbyname.R | 138 -- taxize-0.7.4/taxize/R/ncbi_search.R | 178 --- taxize-0.7.4/taxize/R/ping.R | 31 taxize-0.7.4/taxize/R/plantminer.R | 2 taxize-0.7.4/taxize/R/sci2comm.R | 8 taxize-0.7.4/taxize/R/scrapenames.r | 4 taxize-0.7.4/taxize/R/synonyms.R | 18 taxize-0.7.4/taxize/R/taxize-package.R | 32 taxize-0.7.4/taxize/R/taxize_ldfast.R |only taxize-0.7.4/taxize/R/tnrs.R | 8 taxize-0.7.4/taxize/R/tnrs_sources.r | 4 taxize-0.7.4/taxize/R/tp_accnames.R | 14 taxize-0.7.4/taxize/R/tp_classification.R | 25 taxize-0.7.4/taxize/R/tp_dist.R | 2 taxize-0.7.4/taxize/R/tp_refs.R | 2 taxize-0.7.4/taxize/R/tp_search.R | 28 taxize-0.7.4/taxize/R/tp_summary.R | 2 taxize-0.7.4/taxize/R/tp_synonyms.R | 2 taxize-0.7.4/taxize/R/tpl_families.r | 16 taxize-0.7.4/taxize/R/tpl_get.r | 11 taxize-0.7.4/taxize/R/upstream.R | 40 taxize-0.7.4/taxize/R/vascan_search.r | 10 taxize-0.7.4/taxize/R/zzz.R | 189 --- taxize-0.7.4/taxize/README.md | 72 - taxize-0.7.4/taxize/data/rank_ref.RData |binary taxize-0.7.4/taxize/inst/CITATION | 8 taxize-0.7.4/taxize/inst/doc/taxize_vignette.Rmd | 491 +++++----- taxize-0.7.4/taxize/inst/doc/taxize_vignette.html | 491 +++++----- taxize-0.7.4/taxize/inst/ignore/nature_serve.R |only taxize-0.7.4/taxize/inst/ignore/taxonid.R |only taxize-0.7.4/taxize/inst/vign/taxize_vignette.md | 491 +++++----- taxize-0.7.4/taxize/man/children.Rd | 4 taxize-0.7.4/taxize/man/col_children.Rd | 13 taxize-0.7.4/taxize/man/col_classification-defunct.Rd | 35 taxize-0.7.4/taxize/man/col_downstream.Rd | 14 taxize-0.7.4/taxize/man/downstream.Rd | 74 - taxize-0.7.4/taxize/man/eol_dataobjects.Rd | 10 taxize-0.7.4/taxize/man/eol_hierarchy-defunct.Rd | 23 taxize-0.7.4/taxize/man/eol_invasive-defunct.Rd | 73 - taxize-0.7.4/taxize/man/eol_pages.Rd | 23 taxize-0.7.4/taxize/man/eubon.Rd | 3 taxize-0.7.4/taxize/man/fungorum.Rd | 4 taxize-0.7.4/taxize/man/gbif_downstream.Rd | 14 taxize-0.7.4/taxize/man/gbif_name_usage.Rd | 2 taxize-0.7.4/taxize/man/get_boldid.Rd | 2 taxize-0.7.4/taxize/man/get_eolid.Rd | 11 taxize-0.7.4/taxize/man/get_genes-defunct.Rd |only taxize-0.7.4/taxize/man/get_genes_avail-defunct.Rd |only taxize-0.7.4/taxize/man/get_seqs-defunct.Rd |only taxize-0.7.4/taxize/man/get_tsn.Rd | 2 taxize-0.7.4/taxize/man/get_ubioid-defunct.Rd | 2 taxize-0.7.4/taxize/man/get_uid.Rd | 6 taxize-0.7.4/taxize/man/getacceptednamesfromtsn.Rd | 7 taxize-0.7.4/taxize/man/getcommentdetailfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getcommonnamesfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getcoremetadatafromtsn.Rd | 4 taxize-0.7.4/taxize/man/getcoveragefromtsn.Rd | 4 taxize-0.7.4/taxize/man/getcredibilityratingfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getcredibilityratings.Rd | 2 taxize-0.7.4/taxize/man/getcurrencyfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getexpertsfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getfullhierarchyfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getfullrecordfromlsid.Rd | 2 taxize-0.7.4/taxize/man/getfullrecordfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getgeographicdivisionsfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getgeographicvalues.Rd | 2 taxize-0.7.4/taxize/man/getglobalspeciescompletenessfromtsn.Rd | 2 taxize-0.7.4/taxize/man/gethierarchydownfromtsn.Rd | 2 taxize-0.7.4/taxize/man/gethierarchyupfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getitisterms.Rd | 2 taxize-0.7.4/taxize/man/getitistermsfromcommonname.Rd | 4 taxize-0.7.4/taxize/man/getitistermsfromscientificname.Rd | 2 taxize-0.7.4/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getkey.Rd | 2 taxize-0.7.4/taxize/man/getlsidfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getothersourcesfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getpublicationsfromtsn.Rd | 2 taxize-0.7.4/taxize/man/getsynonymnamesfromtsn.Rd | 4 taxize-0.7.4/taxize/man/getvernacularlanguages.Rd | 2 taxize-0.7.4/taxize/man/gisd_invasive-defunct.Rd | 43 taxize-0.7.4/taxize/man/itis_downstream.Rd | 18 taxize-0.7.4/taxize/man/itis_searchcommon.Rd | 2 taxize-0.7.4/taxize/man/iucn_id.Rd | 15 taxize-0.7.4/taxize/man/iucn_summary.Rd | 22 taxize-0.7.4/taxize/man/lowest_common.Rd |only taxize-0.7.4/taxize/man/ncbi_getbyid-defunct.Rd | 21 taxize-0.7.4/taxize/man/ncbi_getbyname-defunct.Rd | 30 taxize-0.7.4/taxize/man/ncbi_search-defunct.Rd | 44 taxize-0.7.4/taxize/man/searchbycommonname.Rd | 2 taxize-0.7.4/taxize/man/searchbycommonnamebeginswith.Rd | 2 taxize-0.7.4/taxize/man/searchbycommonnameendswith.Rd | 2 taxize-0.7.4/taxize/man/searchforanymatch.Rd | 4 taxize-0.7.4/taxize/man/searchforanymatchpaged.Rd | 4 taxize-0.7.4/taxize/man/taxize-defunct.Rd | 23 taxize-0.7.4/taxize/man/taxize_ldfast.Rd | 2 taxize-0.7.4/taxize/man/tp_classification-defunct.Rd | 15 taxize-0.7.4/taxize/man/tp_search.Rd | 13 taxize-0.7.4/taxize/man/tpl_families.Rd | 5 taxize-0.7.4/taxize/man/tpl_get.Rd | 4 taxize-0.7.4/taxize/man/upstream.Rd | 32 taxize-0.7.4/taxize/man/vascan_search.Rd | 6 taxize-0.7.4/taxize/tests/testthat/Rplots.pdf |binary taxize-0.7.4/taxize/tests/testthat/test-apgscraping.R | 32 taxize-0.7.4/taxize/tests/testthat/test-classification.R | 28 taxize-0.7.4/taxize/tests/testthat/test-col_downstream.R | 2 taxize-0.7.4/taxize/tests/testthat/test-eol_dataobjects.R | 21 taxize-0.7.4/taxize/tests/testthat/test-eol_pages.R | 15 taxize-0.7.4/taxize/tests/testthat/test-fungorum.R | 16 taxize-0.7.4/taxize/tests/testthat/test-gbif_downstream.R | 8 taxize-0.7.4/taxize/tests/testthat/test-get_ids.R | 2 taxize-0.7.4/taxize/tests/testthat/test-get_tpsid.R | 21 taxize-0.7.4/taxize/tests/testthat/test-get_tsn.R | 4 taxize-0.7.4/taxize/tests/testthat/test-get_uid.R | 2 taxize-0.7.4/taxize/tests/testthat/test-gni_search.R | 6 taxize-0.7.4/taxize/tests/testthat/test-gnr_resolve.R | 6 taxize-0.7.4/taxize/tests/testthat/test-ipni_search.R | 10 taxize-0.7.4/taxize/tests/testthat/test-itis_downstream.R | 2 taxize-0.7.4/taxize/tests/testthat/test-iucn_id.R | 8 taxize-0.7.4/taxize/tests/testthat/test-iucn_summary.R | 50 - taxize-0.7.4/taxize/tests/testthat/test-lowest_common.R |only taxize-0.7.4/taxize/tests/testthat/test-tp_search.R | 22 taxize-0.7.4/taxize/vignettes/taxize_vignette.Rmd | 491 +++++----- 178 files changed, 2613 insertions(+), 3219 deletions(-)
Title: R Markdown Format for 'reveal.js' Presentations
Description: R Markdown format for 'reveal.js' presentations, a framework
for easily creating beautiful presentations using HTML.
Author: Hakim El Hattab [aut, cph] (reveal.js-3.2.0,
https://github.com/hakimel/reveal.js),
JJ Allaire [aut, cre],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between revealjs versions 0.5.0 dated 2016-01-31 and 0.6 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ inst/NEWS |only inst/reveal.js-3.2.0/css/theme/beige.css | 4 ++-- inst/reveal.js-3.2.0/css/theme/league.css | 7 ++++--- inst/reveal.js-3.2.0/css/theme/solarized.css | 5 ++--- man/revealjs_presentation.Rd | 12 ++++++------ tests/testthat/test_themes.R | 4 +++- 8 files changed, 28 insertions(+), 25 deletions(-)
Title: Penalized Parametric and Semiparametric Bayesian Survival Models
with Shrinkage and Grouping Priors
Description: Algorithms for fitting penalized parametric and semiparametric Bayesian survival models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee <klee@hsph.harvard.edu>
Diff between psbcGroup versions 1.2 dated 2015-09-17 and 1.3 dated 2016-03-08
DESCRIPTION | 18 +++++++++--------- MD5 | 12 +++++++++--- NAMESPACE | 3 +++ R/aftGL.R |only man/aftGL.Rd |only man/psbcGroup.Rd | 14 +++++++++----- src |only 7 files changed, 30 insertions(+), 17 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color
from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-4 dated 2016-01-27 and 0.5-5 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 5 +++++ R/summary.rspec.R | 18 ++++++++++++------ 4 files changed, 24 insertions(+), 13 deletions(-)
Title: A System for Embedded Scientific Computing and Reproducible
Research with R
Description: The OpenCPU system exposes an HTTP API for embedded scientific
computing with R. This provides scalable foundations for integrating R
based analysis and visualization modules into pipelines, web applications
or big data infrastructures. The OpenCPU server can run either as a
single-user development server within the interactive R session, or as a
high performance multi-user cloud server that builds on Linux, Nginx and
rApache. The current R package forms the core of the system. When loaded
in R, it automatically initiates the single-user server and displays the
web address in the console. Visit the OpenCPU website for detailed
information and documentation on the API.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between opencpu versions 1.5.1 dated 2015-09-25 and 1.5.4 dated 2016-03-08
opencpu-1.5.1/opencpu/inst/doc/opencpu-paper.Rnw |only opencpu-1.5.1/opencpu/vignettes/opencpu-paper.Rnw |only opencpu-1.5.1/opencpu/vignettes/references.bib |only opencpu-1.5.4/opencpu/DESCRIPTION | 10 +++++----- opencpu-1.5.4/opencpu/MD5 | 17 ++++++++--------- opencpu-1.5.4/opencpu/NEWS | 4 ++++ opencpu-1.5.4/opencpu/R/eval_fork.R | 15 ++++++++++++++- opencpu-1.5.4/opencpu/build/vignette.rds |binary opencpu-1.5.4/opencpu/inst/doc/opencpu-paper.pdf |binary opencpu-1.5.4/opencpu/inst/doc/opencpu-paper.pdf.asis |only opencpu-1.5.4/opencpu/inst/doc/opencpu-server.pdf |binary opencpu-1.5.4/opencpu/vignettes/opencpu-paper.pdf.asis |only 12 files changed, 31 insertions(+), 15 deletions(-)
Title: Estimate Copy Number for Digital PCR
Description: The assay sensitivity is the minimum number of copies that the digital PCR assay can detect. Users provide serial dilution results in the format of counts of positive and total reaction wells. The output is the estimated assay sensitivity and the copy number per well in the initial dilute.
Author: Xutao Deng
Maintainer: Xutao Deng <xutaodeng@gmail.com>
Diff between digitalPCR versions 1.0 dated 2014-12-31 and 1.1.0 dated 2016-03-08
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NAMESPACE | 3 ++- R/digitalPCR.R | 10 ++++++---- R/likelihood.R | 4 +++- R/poisson.param.R | 4 ++-- man/digitalPCR.Rd | 17 ++++++++++------- 7 files changed, 35 insertions(+), 26 deletions(-)
Title: Data Checking
Description: Checks column names,
column classes, values, keys, joins, vectors and scalars.
If the user-defined conditions are met the function
returns an invisible copy of the data frame, vector or scalar.
Otherwise the function throws an informative error.
Author: Joe Thorley [aut, cre]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between datacheckr versions 0.1.0 dated 2016-01-26 and 0.1.1 dated 2016-03-08
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- NEWS.md | 12 +++++++++--- inst/doc/datacheckr.html | 17 ++++++++--------- inst/doc/nycflights13.html | 17 ++++++++--------- tests/testthat/test-check-values.R | 2 +- 6 files changed, 35 insertions(+), 30 deletions(-)
Title: Censored Autoregressive Model with Exogenous Covariates
Description: A censored time series class is designed. An estimation procedure
is implemented to estimate the Censored AutoRegressive time series with
eXogenous covariates (CARX), assuming normality of the innovations. Some other
functions that might be useful are also included.
Author: Chao Wang [aut, cre],
Kung-Sik Chan [aut]
Maintainer: Chao Wang <chao-wang@uiowa.edu>
Diff between carx versions 0.6.1 dated 2016-01-19 and 0.6.2 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/carx_default.R | 14 +++++++------- 3 files changed, 13 insertions(+), 13 deletions(-)
Title: Estimation of the Number of Fatalities from Carcass Searches
Description: The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.
Author: Fraenzi Korner-Nievergelt, Ivo Niermann, Oliver Behr, Matthew A. Etterson, Robert Brinkmann, Pius Korner, Barbara Hellriegel, Tobias Roth, Manuela M. P. Huso, Dan Dalthorp
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@oikostat.ch>
Diff between carcass versions 1.5 dated 2015-11-29 and 1.6 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/estimateN.r | 5 ++++- 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Various actuarial science functionalities, mostly in the
fields of loss distributions, risk theory (including ruin theory),
simulation of compound hierarchical models and credibility theory.
The package also features 17 probability laws commonly used in
insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 1.1-10 dated 2015-07-22 and 1.2-0 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/CTE.R | 16 +++++----------- R/quantile.aggregateDist.R | 12 ++++++------ build/vignette.rds |binary inst/NEWS.Rd | 13 +++++++++++++ inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.pdf |binary inst/doc/lossdist.Rnw | 2 +- inst/doc/lossdist.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary man/CTE.Rd | 29 +++++++++++++++++++++++------ vignettes/lossdist.Rnw | 2 +- 15 files changed, 67 insertions(+), 43 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.8 dated 2015-05-13 and 0.2.9 dated 2016-03-08
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 13 +++++++------ NEWS |only R/rglobi.R | 13 ++++++------- README.md | 7 ++++--- build/vignette.rds |binary man/get_interaction_matrix.Rd | 4 ++-- 8 files changed, 25 insertions(+), 24 deletions(-)
Title: The Multivariate Normal and t Distributions
Description: Functions are provided for computing the density and the
distribution function of multivariate normal and "t" random variables,
and for generating random vectors sampled from these distributions.
Probabilities are computed via non-Monte Carlo methods; different routines
are used in the case d=1, d=2, d>2, if d denotes the number of dimensions.
Author: Fortran code by Alan Genz, R code by Adelchi Azzalini
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between mnormt versions 1.5-3 dated 2015-05-25 and 1.5-4 dated 2016-03-08
ChangeLog |only DESCRIPTION | 12 ++++++------ INDEX |only MD5 | 16 +++++++++------- NAMESPACE | 5 +++-- NEWS | 42 +++++++++++++++++++++++------------------- R/mnormt.R | 32 +++++++++++++++----------------- man/dmnorm.Rd | 38 ++++++++++++++++++++++++-------------- man/dmt.Rd | 39 ++++++++++++++++----------------------- man/pd.solve.Rd | 4 ++-- 10 files changed, 98 insertions(+), 90 deletions(-)
Title: Calculate Textures from Grey-Level Co-Occurrence Matrices
(GLCMs)
Description: Enables calculation of image textures derived from grey-level
co-occurrence matrices (GLCMs). Supports processing images that cannot
fit in memory.
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff <azvoleff@conservation.org>
Diff between glcm versions 1.4 dated 2015-11-21 and 1.6.1 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS | 15 +++++++++++---- R/glcm.R | 5 +++-- README.md | 7 +++---- man/glcm.Rd | 2 +- src/Makevars |only 7 files changed, 28 insertions(+), 20 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network representation that
offers unmatched efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop, simulated annealing, stochastic
gradient) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon),
but it is first and foremost an efficient computational engine. Users can
easily implement their algorithms by taking advantage of fast gradient computing
routines, as well as network reconstruction functionality (removing weights
and redundant neurons, reordering inputs, merging networks). Networks can be
exported to C functions in order to integrate them into virtually any software
solution.
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.6.1 dated 2016-03-07 and 0.6.2 dated 2016-03-08
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- src/fcnn/fcnncfg.R.h | 11 +++++------ 3 files changed, 11 insertions(+), 13 deletions(-)
Title: Interface to 'Dygraphs' Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
JJ Allaire [aut, cre] (R interface),
RStudio [cph],
Jonathan Owen [aut, cph],
Daniel Gromer [aut, cph],
Petr Shevtsov [aut, cph],
Benoit Thieurmel [aut, cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between dygraphs versions 0.7 dated 2016-02-02 and 0.8 dated 2016-03-08
DESCRIPTION | 8 - MD5 | 8 - inst/NEWS | 8 + inst/examples/examples.html | 237 +++++++++++++++++++++++++------------------ inst/htmlwidgets/dygraphs.js | 29 +++++ 5 files changed, 184 insertions(+), 106 deletions(-)
Title: Statistical Comparisons with Distance-Function Based Permutation
Tests
Description: Provides tools for making statistical comparisons with distance-function based permutation tests developed by P. W. Mielke, Jr. and colleagues at Colorado State University (Mielke, P. W. & Berry, K. J. Permutation Methods: A Distance Function Approach (Springer, New York, 2001)) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U. S. Geological Survey.
Author: Marian Talbert, Jon Richards, Paul Mielke, and Brian Cade
Maintainer: Marian Talbert <mtalbert@usgs.gov>
Diff between Blossom versions 1.3 dated 2015-10-14 and 1.4 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 3 ++- inst |only 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it is possible to create and manipulate multivariate network
data with different formats, and there are effective ways available to treat multiple networks
with routines that combine algebraic systems like the partially ordered semigroup or the
semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. As well an algebraic approach for two-mode networks is made
through Galois derivations between families of the pair of subsets.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.8.1 dated 2016-03-04 and 1.8.2 dated 2016-03-08
DESCRIPTION | 7 MD5 | 11 - R/bundles.R | 391 +++++++++++++++++++++---------------------- build |only inst/CHANGELOG | 6 inst/doc/TwoModeNetworks.R |only inst/doc/TwoModeNetworks.Rnw |only man/multiplex-package.Rd | 4 8 files changed, 212 insertions(+), 207 deletions(-)
Title: Half-Normal Plots with Simulation Envelopes
Description: Generates (half-)normal plots with simulation envelopes using different diagnostics from a range of different fitted models. A few example datasets are included.
Author: Rafael de Andrade Moral [aut, cre], John Hinde [aut], Clarice Garcia Borges Demetrio [aut]
Maintainer: Rafael de Andrade Moral <rafael_moral@yahoo.com.br>
Diff between hnp versions 1.1 dated 2015-09-12 and 1.2 dated 2016-03-08
DESCRIPTION | 12 MD5 | 34 NAMESPACE | 50 - R/hnp-internal.R |only R/hnp.R | 2232 +++++++++++++++++++++++++++------------------------- R/newhnp.R |only R/plot.hnp.R | 58 - data/cbb.rda |binary data/chryso.rda |binary data/corn.rda |binary data/fungi.rda |binary data/oil.rda |binary data/orange.rda |only data/progeny.rda |binary data/wolbachia.rda |binary man/hnp-internal.Rd |only man/hnp.Rd | 536 ++++++------ man/newhnp.Rd |only man/oil.Rd | 162 +-- man/orange.Rd |only man/plot.hnp.Rd | 120 +- 21 files changed, 1691 insertions(+), 1513 deletions(-)
Title: Microsoft Word, Microsoft PowerPoint and HTML Documents
Generation
Description: Create 'Microsoft Word' document (>=2007),
'Microsoft PowerPoint' document (>=2007) and 'HTML' documents from R. There are
several features to let you format and present R outputs ; e.g. Editable
Vector Graphics, functions for complex tables reporting, reuse of corporate
template document. You can use the package as a tool for fast reporting
and as a tool for reporting automation. The package does not require
any installation of Microsoft product to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Bootstrap [ctb, cph] (Bootstrap development team),
jQuery [ctb, cph] (The jQuery Foundation)
Maintainer: David Gohel <david.gohel@lysis-consultants.fr>
Diff between ReporteRs versions 0.8.5 dated 2016-02-26 and 0.8.6 dated 2016-03-08
ReporteRs-0.8.5/ReporteRs/man/borderDashed.Rd |only ReporteRs-0.8.5/ReporteRs/man/borderDotted.Rd |only ReporteRs-0.8.5/ReporteRs/man/borderNone.Rd |only ReporteRs-0.8.5/ReporteRs/man/borderSolid.Rd |only ReporteRs-0.8.5/ReporteRs/man/parCenter.Rd |only ReporteRs-0.8.5/ReporteRs/man/parJustify.Rd |only ReporteRs-0.8.5/ReporteRs/man/parLeft.Rd |only ReporteRs-0.8.5/ReporteRs/man/parRight.Rd |only ReporteRs-0.8.5/ReporteRs/man/textBold.Rd |only ReporteRs-0.8.5/ReporteRs/man/textBoldItalic.Rd |only ReporteRs-0.8.5/ReporteRs/man/textItalic.Rd |only ReporteRs-0.8.5/ReporteRs/man/textNormal.Rd |only ReporteRs-0.8.6/ReporteRs/DESCRIPTION | 23 ReporteRs-0.8.6/ReporteRs/MD5 | 99 -- ReporteRs-0.8.6/ReporteRs/NAMESPACE | 8 ReporteRs-0.8.6/ReporteRs/NEWS | 18 ReporteRs-0.8.6/ReporteRs/R/01_tools.R | 5 ReporteRs-0.8.6/ReporteRs/R/FlexTableFormatTools.R | 110 +- ReporteRs-0.8.6/ReporteRs/R/FlexTablePublicAPI.R | 489 ++++------ ReporteRs-0.8.6/ReporteRs/R/ReporteRs.R | 2 ReporteRs-0.8.6/ReporteRs/R/addCodeBlock.R | 39 ReporteRs-0.8.6/ReporteRs/R/addFlexTable.R | 65 - ReporteRs-0.8.6/ReporteRs/R/addFooter.pptx.R | 8 ReporteRs-0.8.6/ReporteRs/R/addImage.R | 82 + ReporteRs-0.8.6/ReporteRs/R/addPlot.R | 99 +- ReporteRs-0.8.6/ReporteRs/R/addSlide.R | 4 ReporteRs-0.8.6/ReporteRs/R/borderProperties.R | 17 ReporteRs-0.8.6/ReporteRs/R/cellProperties.R | 23 ReporteRs-0.8.6/ReporteRs/R/chprop.FlexTable.R |only ReporteRs-0.8.6/ReporteRs/R/colorProperties.R |only ReporteRs-0.8.6/ReporteRs/R/format.properties.R | 282 +---- ReporteRs-0.8.6/ReporteRs/R/java_description.R | 1 ReporteRs-0.8.6/ReporteRs/R/parProperties.R | 11 ReporteRs-0.8.6/ReporteRs/R/textProperties.R | 34 ReporteRs-0.8.6/ReporteRs/inst/java/ReporteRs-0.8.jar |binary ReporteRs-0.8.6/ReporteRs/java/ReporteRs-0.8-src.jar |binary ReporteRs-0.8.6/ReporteRs/man/FlexTable-alter.Rd | 37 ReporteRs-0.8.6/ReporteRs/man/ReporteRs-package.Rd | 2 ReporteRs-0.8.6/ReporteRs/man/addCodeBlock.Rd | 34 ReporteRs-0.8.6/ReporteRs/man/addFlexTable.Rd | 473 --------- ReporteRs-0.8.6/ReporteRs/man/addFooter.pptx.Rd | 17 ReporteRs-0.8.6/ReporteRs/man/addFooterRow.Rd | 6 ReporteRs-0.8.6/ReporteRs/man/addHeaderRow.Rd | 24 ReporteRs-0.8.6/ReporteRs/man/addImage.Rd | 83 - ReporteRs-0.8.6/ReporteRs/man/addPlot.Rd | 84 + ReporteRs-0.8.6/ReporteRs/man/addSlide.Rd | 4 ReporteRs-0.8.6/ReporteRs/man/borderProperties.Rd | 3 ReporteRs-0.8.6/ReporteRs/man/cellProperties.Rd | 5 ReporteRs-0.8.6/ReporteRs/man/chprop.FlexTable.Rd |only ReporteRs-0.8.6/ReporteRs/man/colorProperties.Rd |only ReporteRs-0.8.6/ReporteRs/man/parProperties.Rd | 3 ReporteRs-0.8.6/ReporteRs/man/setFlexTableBackgroundColors.Rd | 6 ReporteRs-0.8.6/ReporteRs/man/setFlexTableBorders.Rd | 8 ReporteRs-0.8.6/ReporteRs/man/shortcut_properties.Rd |only ReporteRs-0.8.6/ReporteRs/man/spanFlexTableColumns.Rd | 2 ReporteRs-0.8.6/ReporteRs/man/spanFlexTableRows.Rd | 2 ReporteRs-0.8.6/ReporteRs/man/textProperties.Rd | 3 ReporteRs-0.8.6/ReporteRs/tests/testthat/test-pptx-img.R | 4 ReporteRs-0.8.6/ReporteRs/tests/testthat/test-pptx-plot.R | 4 59 files changed, 895 insertions(+), 1328 deletions(-)
Title: Multivariate Extreme Value Distributions
Description: Exact simulation from max-stable processes and multivariate extreme value distributions for various parametric models. Threshold selection methods.
Author: Leo Belzile [aut, cre],
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut],
Claire L. Coleman [aut],
Jin. Zhang [ctb],
Michael A. Newton [ctb],
Art Owen [ctb]
Maintainer: Leo Belzile <leo.belzile@epfl.ch>
Diff between mev versions 1.5 dated 2016-02-15 and 1.6 dated 2016-03-08
DESCRIPTION | 16 - MD5 | 29 +- NAMESPACE | 5 NEWS | 23 +- R/Northrop_Coleman_Extremes_2014.R | 363 +++++++++++++++++++++++++++---------- R/RcppExports.R | 12 + R/Wadsworth_Technometrics_2016.R | 49 ++-- R/rmev_wrapper.R | 2 R/specdens.R |only man/NC.diag.Rd | 9 man/W.diag.Rd | 51 ++--- man/angmeas.Rd |only man/emplik.Rd |only man/gp.fit.Rd | 83 ++++++-- man/rmev.Rd | 2 src/RcppExports.cpp | 47 ++++ src/emp_lik.cpp |only src/zhang_stephens.cpp |only 18 files changed, 500 insertions(+), 191 deletions(-)
Title: R Functions to Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned
online by Google Trends is provided. Trends (number of hits) over the time as
well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.3.2 dated 2016-02-18 and 1.3.3 dated 2016-03-08
DESCRIPTION | 9 +- MD5 | 18 ++--- NEWS.md | 14 +++- R/countries.R | 2 R/gtrends.R | 176 ++++++++++++++++++++++++++++++++------------------- README.md | 5 - data/countries.RData |binary man/countries.Rd | 2 man/gconnect.Rd | 2 man/gtrends.Rd | 54 +++++++++++++-- 10 files changed, 192 insertions(+), 90 deletions(-)
Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-4 dated 2016-03-06 and 0.0-5 dated 2016-03-08
DESCRIPTION | 8 MD5 | 68 +++--- NAMESPACE | 116 +++++----- NEWS | 2 R/are-identical.R | 160 +++++++------- R/assert-are-identical.R | 122 +++++----- R/assert-identical-to-true-false-na.R | 270 ++++++++++++------------ R/cause.R | 324 ++++++++++++++-------------- R/engine.R | 240 ++++++++++----------- R/utils.R | 27 +- R/zzz.R | 8 man/Truth.Rd | 380 +++++++++++++++++----------------- man/are_identical.Rd | 128 +++++------ man/assert_engine.Rd | 86 +++---- man/assertionError.Rd | 98 ++++---- man/bapply.Rd | 60 ++--- man/call_and_name.Rd | 70 +++--- man/cause.Rd | 72 +++--- man/coerce_to.Rd | 82 +++---- man/dont_stop.Rd | 74 +++--- man/false.Rd | 44 +-- man/get_name_in_parent.Rd | 16 + man/is2.Rd | 66 ++--- man/na.Rd | 44 +-- man/parenthesize.Rd | 102 ++++----- man/print.vector_with_cause.Rd | 60 ++--- man/set_cause.Rd | 66 ++--- man/strip_attributes.Rd | 48 ++-- man/type_description.Rd | 36 +-- po/R-assertive.base.pot | 190 ++++++++--------- po/R-kr.po | 190 ++++++++--------- po/R-ua.po | 194 ++++++++--------- tests/testthat.R | 8 tests/testthat/test-are-identical.R | 26 +- tests/testthat/test-utils.R | 103 +++++++++ 35 files changed, 1861 insertions(+), 1727 deletions(-)
More information about assertive.base at CRAN
Permanent link
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson
<jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles
Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.5.17 dated 2016-03-01 and 4.5.18 dated 2016-03-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/bigmemory.R | 16 ++++------------ R/hello-bigmemory.R | 4 ---- man/bigmemory-package.Rd | 4 ---- src/BigMatrix.cpp | 24 ++++++------------------ tests/testthat/test_matrix_manips.R | 12 ++++++++++++ tests/testthat/test_readonly.R | 6 +++++- 8 files changed, 38 insertions(+), 50 deletions(-)
Title: Readable Check Functions to Ensure Code Integrity
Description: Lots of predicates (is_* functions) to check the state of your
variables, and assertions (assert_* functions) to throw errors if they
aren't in the right form.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive versions 0.3-1 dated 2015-10-08 and 0.3-2 dated 2016-03-08
assertive-0.3-1/assertive/man/is_set_equal.Rd |only assertive-0.3-2/assertive/DESCRIPTION | 29 assertive-0.3-2/assertive/MD5 | 274 ++-- assertive-0.3-2/assertive/NAMESPACE | 28 assertive-0.3-2/assertive/NEWS | 2 assertive-0.3-2/assertive/R/exports-properties.R | 21 assertive-0.3-2/assertive/R/exports-reflection.R | 504 +++---- assertive-0.3-2/assertive/R/exports-sets.R | 31 assertive-0.3-2/assertive/R/exports-strings.R | 9 assertive-0.3-2/assertive/R/exports-types.R | 657 +++++----- assertive-0.3-2/assertive/README.md | 478 +++---- assertive-0.3-2/assertive/inst/doc/checklists.Rmd | 4 assertive-0.3-2/assertive/inst/doc/introduction.Rmd | 25 assertive-0.3-2/assertive/inst/doc/introduction.html | 35 assertive-0.3-2/assertive/man/DIM.Rd | 2 assertive-0.3-2/assertive/man/Truth.Rd | 2 assertive-0.3-2/assertive/man/are_identical.Rd | 2 assertive-0.3-2/assertive/man/are_same_length.Rd | 4 assertive-0.3-2/assertive/man/are_set_equal.Rd |only assertive-0.3-2/assertive/man/assert_engine.Rd | 2 assertive-0.3-2/assertive/man/assert_is_all_of.Rd | 2 assertive-0.3-2/assertive/man/assertionError.Rd | 2 assertive-0.3-2/assertive/man/assertive.Rd | 10 assertive-0.3-2/assertive/man/bapply.Rd | 2 assertive-0.3-2/assertive/man/call_and_name.Rd | 2 assertive-0.3-2/assertive/man/cause.Rd | 2 assertive-0.3-2/assertive/man/changes.Rd | 16 assertive-0.3-2/assertive/man/character_to_list_of_integer_vectors.Rd | 8 assertive-0.3-2/assertive/man/coerce_to.Rd | 2 assertive-0.3-2/assertive/man/dont_stop.Rd | 2 assertive-0.3-2/assertive/man/false.Rd | 2 assertive-0.3-2/assertive/man/get_name_in_parent.Rd | 2 assertive-0.3-2/assertive/man/has_any_attributes.Rd | 2 assertive-0.3-2/assertive/man/has_arg.Rd | 8 assertive-0.3-2/assertive/man/has_attributes.Rd | 2 assertive-0.3-2/assertive/man/has_cols.Rd | 2 assertive-0.3-2/assertive/man/has_dims.Rd | 2 assertive-0.3-2/assertive/man/has_duplicates.Rd | 2 assertive-0.3-2/assertive/man/has_names.Rd | 2 assertive-0.3-2/assertive/man/has_slot.Rd |only assertive-0.3-2/assertive/man/has_terms.Rd | 2 assertive-0.3-2/assertive/man/is2.Rd | 2 assertive-0.3-2/assertive/man/is_array.Rd | 2 assertive-0.3-2/assertive/man/is_atomic.Rd | 6 assertive-0.3-2/assertive/man/is_batch_mode.Rd | 2 assertive-0.3-2/assertive/man/is_binding_locked.Rd | 8 assertive-0.3-2/assertive/man/is_cas_number.Rd | 2 assertive-0.3-2/assertive/man/is_character.Rd | 2 assertive-0.3-2/assertive/man/is_class.Rd | 2 assertive-0.3-2/assertive/man/is_complex.Rd | 2 assertive-0.3-2/assertive/man/is_connection.Rd | 2 assertive-0.3-2/assertive/man/is_credit_card_number.Rd | 2 assertive-0.3-2/assertive/man/is_data.frame.Rd | 2 assertive-0.3-2/assertive/man/is_data.table.Rd | 2 assertive-0.3-2/assertive/man/is_date.Rd | 2 assertive-0.3-2/assertive/man/is_date_string.Rd | 2 assertive-0.3-2/assertive/man/is_debugged.Rd | 8 assertive-0.3-2/assertive/man/is_diagonal_matrix.Rd | 2 assertive-0.3-2/assertive/man/is_dir.Rd | 2 assertive-0.3-2/assertive/man/is_divisible_by.Rd | 2 assertive-0.3-2/assertive/man/is_email_address.Rd | 2 assertive-0.3-2/assertive/man/is_empty.Rd | 2 assertive-0.3-2/assertive/man/is_empty_character.Rd | 4 assertive-0.3-2/assertive/man/is_empty_file.Rd | 2 assertive-0.3-2/assertive/man/is_empty_model.Rd | 2 assertive-0.3-2/assertive/man/is_environment.Rd | 2 assertive-0.3-2/assertive/man/is_equal_to.Rd | 2 assertive-0.3-2/assertive/man/is_error_free.Rd | 8 assertive-0.3-2/assertive/man/is_executable_file.Rd | 2 assertive-0.3-2/assertive/man/is_existing.Rd | 8 assertive-0.3-2/assertive/man/is_existing_file.Rd | 2 assertive-0.3-2/assertive/man/is_factor.Rd | 2 assertive-0.3-2/assertive/man/is_finite.Rd | 2 assertive-0.3-2/assertive/man/is_formula.Rd |only assertive-0.3-2/assertive/man/is_function.Rd | 2 assertive-0.3-2/assertive/man/is_hex_color.Rd | 2 assertive-0.3-2/assertive/man/is_honorific.Rd | 2 assertive-0.3-2/assertive/man/is_identity_matrix.Rd | 2 assertive-0.3-2/assertive/man/is_if_condition.Rd | 8 assertive-0.3-2/assertive/man/is_in_past.Rd | 2 assertive-0.3-2/assertive/man/is_in_range.Rd | 2 assertive-0.3-2/assertive/man/is_inherited_from.Rd | 2 assertive-0.3-2/assertive/man/is_integer.Rd | 2 assertive-0.3-2/assertive/man/is_ip_address.Rd | 2 assertive-0.3-2/assertive/man/is_isbn_code.Rd | 2 assertive-0.3-2/assertive/man/is_language.Rd | 2 assertive-0.3-2/assertive/man/is_leaf.Rd | 2 assertive-0.3-2/assertive/man/is_library.Rd | 2 assertive-0.3-2/assertive/man/is_list.Rd | 2 assertive-0.3-2/assertive/man/is_loaded.Rd | 8 assertive-0.3-2/assertive/man/is_logical.Rd | 2 assertive-0.3-2/assertive/man/is_lower_triangular_matrix.Rd | 2 assertive-0.3-2/assertive/man/is_nan.Rd | 2 assertive-0.3-2/assertive/man/is_null.Rd | 2 assertive-0.3-2/assertive/man/is_numeric.Rd | 6 assertive-0.3-2/assertive/man/is_numeric_string.Rd | 11 assertive-0.3-2/assertive/man/is_on_os_path.Rd | 2 assertive-0.3-2/assertive/man/is_package_current.Rd | 2 assertive-0.3-2/assertive/man/is_qr.Rd | 2 assertive-0.3-2/assertive/man/is_r.Rd | 2 assertive-0.3-2/assertive/man/is_r_current.Rd | 2 assertive-0.3-2/assertive/man/is_raster.Rd | 2 assertive-0.3-2/assertive/man/is_raw.Rd | 2 assertive-0.3-2/assertive/man/is_real.Rd | 2 assertive-0.3-2/assertive/man/is_relistable.Rd | 2 assertive-0.3-2/assertive/man/is_rstudio_current.Rd | 2 assertive-0.3-2/assertive/man/is_rstudio_desktop.Rd | 2 assertive-0.3-2/assertive/man/is_s4.Rd | 2 assertive-0.3-2/assertive/man/is_single_character.Rd | 8 assertive-0.3-2/assertive/man/is_square_matrix.Rd | 2 assertive-0.3-2/assertive/man/is_symmetric_matrix.Rd | 2 assertive-0.3-2/assertive/man/is_table.Rd | 2 assertive-0.3-2/assertive/man/is_tbl.Rd | 2 assertive-0.3-2/assertive/man/is_try_error.Rd | 2 assertive-0.3-2/assertive/man/is_ts.Rd | 2 assertive-0.3-2/assertive/man/is_uk_car_licence.Rd | 2 assertive-0.3-2/assertive/man/is_uk_national_insurance_number.Rd | 2 assertive-0.3-2/assertive/man/is_uk_postcode.Rd | 2 assertive-0.3-2/assertive/man/is_uk_telephone_number.Rd | 2 assertive-0.3-2/assertive/man/is_unsorted.Rd | 2 assertive-0.3-2/assertive/man/is_us_social_security_number.Rd | 2 assertive-0.3-2/assertive/man/is_us_telephone_number.Rd | 2 assertive-0.3-2/assertive/man/is_us_zip_code.Rd | 2 assertive-0.3-2/assertive/man/is_valid_r_code.Rd | 8 assertive-0.3-2/assertive/man/is_valid_variable_name.Rd | 8 assertive-0.3-2/assertive/man/is_whole_number.Rd | 2 assertive-0.3-2/assertive/man/is_windows.Rd | 2 assertive-0.3-2/assertive/man/is_xxx_for_decimal_point.Rd | 2 assertive-0.3-2/assertive/man/is_zero_matrix.Rd | 2 assertive-0.3-2/assertive/man/merge_dots_with_list.Rd | 2 assertive-0.3-2/assertive/man/n_elements.Rd | 2 assertive-0.3-2/assertive/man/na.Rd | 2 assertive-0.3-2/assertive/man/parenthesize.Rd | 2 assertive-0.3-2/assertive/man/r_can_find_tools.Rd | 4 assertive-0.3-2/assertive/man/r_has_jpeg_capability.Rd | 2 assertive-0.3-2/assertive/man/set_cause.Rd | 2 assertive-0.3-2/assertive/man/strip_attributes.Rd | 2 assertive-0.3-2/assertive/man/sys_get_locale.Rd | 2 assertive-0.3-2/assertive/man/use_first.Rd | 2 assertive-0.3-2/assertive/tests/testthat.R | 12 140 files changed, 1315 insertions(+), 1149 deletions(-)
Title: R Wrapper for the 'Wufoo.com' - The Form Building Service
Description: Allows form managers to download entries from their respondents
using Wufoo JSON API. Additionally, the Wufoo reports - when public - can be
also acquired programmatically. Note that building new forms within this package
is not supported.
Author: John Malc [aut, cre] (@dmpe),
Maksim Pecherskiy [ctb] (@MrMaksimize)
Maintainer: John Malc <cincenko@outlook.com>
Diff between WufooR versions 0.5.9 dated 2016-02-15 and 0.6.1 dated 2016-03-08
DESCRIPTION | 22 - MD5 | 42 +-- NAMESPACE | 30 +- NEWS | 31 +- R/Fields.R | 142 +++++----- R/Form.R | 320 ++++++++++++------------ R/Reports.R | 94 +++---- R/Users.R | 60 ++-- README.md | 92 +++---- build/vignette.rds |binary inst/doc/Tutorial.R | 62 ++-- inst/doc/Tutorial.Rmd | 154 +++++------ inst/doc/Tutorial.html | 583 +++++++++++++++++++++++---------------------- man/auth_name.Rd | 68 ++--- man/fields_info.Rd | 114 ++++---- man/form_entries.Rd | 122 ++++----- man/form_entriesCount.Rd | 72 ++--- man/form_entriesFromCSV.Rd | 80 +++--- man/form_info.Rd | 74 ++--- man/reports_info.Rd | 98 +++---- man/user_info.Rd | 66 ++--- vignettes/Tutorial.Rmd | 154 +++++------ 22 files changed, 1257 insertions(+), 1223 deletions(-)
Title: Replicate Tariff Method for Verbal Autopsy
Description: Implement Tariff algorithm for coding cause of death from verbal autopsies developed by James et al (2011). It also provides simple graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between Tariff versions 1.0 dated 2016-03-03 and 1.0.1 dated 2016-03-08
DESCRIPTION | 10 +++++----- MD5 | 21 ++++++++++++--------- R/Tariff.plot.r | 4 ++-- R/Tariff.r | 6 +++--- R/Tariff_1.0-package.R | 15 +++++++++++++++ R/Tarrif.summary.r | 8 ++++---- R/zzz.R |only data/RandomVA3.rda |binary data/SampleCategory3.rda |only man/SampleCategory3.Rd |only man/plot.tariff.Rd | 4 ++-- man/summary.tariff.Rd | 6 +++--- man/tariff.Rd | 8 ++++---- 13 files changed, 50 insertions(+), 32 deletions(-)
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro
Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 0.4.1 dated 2015-10-01 and 0.4.2 dated 2016-03-08
DESCRIPTION | 15 - MD5 | 68 ++-- NAMESPACE | 11 R/MetaLandSim.GUI.R | 13 R/iterate.graph.R | 30 +- R/list.stats.R | 21 + R/manage_expansion_sim.R | 8 R/metrics.graph.R | 2 R/range_expansion.R | 14 - R/range_raster.R | 27 + R/simulate_graph.R | 24 - R/span.graph.R | 574 ++++++++++++++++++++++-------------------- R/spom.R | 15 + build/vignette.rds |binary data/cabrera.rda |binary data/landscape_change.rda |binary data/mc_df.rda |binary data/occ.landscape.rda |binary data/occ.landscape2.rda |binary data/param1.rda |binary data/rg_exp.rda |binary data/rland.rda |binary inst/CITATION | 8 inst/doc/MetaLandSim.pdf |binary inst/doc/parametrization.R | 190 ++++++------- inst/doc/parametrization.Rnw | 2 inst/doc/parametrization.pdf |binary inst/doc/range_expansion.R | 84 +++--- man/MetaLandSim-package.Rd | 6 man/iterate.graph.Rd | 11 man/list.stats.Rd | 6 man/manage_expansion_sim.Rd | 4 man/param1.Rd | 72 ++--- man/range_expansion.Rd | 7 vignettes/parametrization.Rnw | 2 35 files changed, 641 insertions(+), 573 deletions(-)
Title: Moment-Based Estimation for Hierarchical Models
Description: Implements methods from the paper
"Fast Moment-Based Estimation for Hierarchical Models," by Perry (2016).
Author: Patrick O. Perry [aut, cre],
Timothy Sweetser [ctb]
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between mbest versions 0.4 dated 2015-10-19 and 0.5 dated 2016-03-08
mbest-0.4/mbest/inst/tests |only mbest-0.5/mbest/DESCRIPTION | 26 ++- mbest-0.5/mbest/MD5 | 54 +++---- mbest-0.5/mbest/NAMESPACE | 62 ++++---- mbest-0.5/mbest/R/firthglm.fit.R | 1 mbest-0.5/mbest/R/mhglm.R | 44 +++--- mbest-0.5/mbest/R/mhglm.fit.R | 126 ++++++++++++----- mbest-0.5/mbest/R/moment.est.R | 255 +++++++++++++++++++++-------------- mbest-0.5/mbest/R/rdglm.fit.R | 2 mbest-0.5/mbest/R/rdglm.group.fit.R | 90 +++++++----- mbest-0.5/mbest/README.md |only mbest-0.5/mbest/inst/CITATION | 22 +-- mbest-0.5/mbest/man/effects.Rd | 11 - mbest-0.5/mbest/man/mhglm.control.Rd | 7 mbest-0.5/mbest/src |only mbest-0.5/mbest/tests/test-all.R | 2 mbest-0.5/mbest/tests/testthat |only 17 files changed, 432 insertions(+), 270 deletions(-)
Title: An R Package for Text Analysis
Description: A set of tools to analyze texts. Includes, amongst others,
functions for automatic language detection, hyphenation, several indices of
lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability
(e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language
corpora are also provided, to enable frequency analyses (supports Celex and
Leipzig Corpora Collection file formats) and measures like tf-idf. Support for
additional languages can be added on-the-fly or by plugin packages. Note: For
full functionality a local installation of TreeTagger is recommended. 'koRpus'
also includes a plugin for the R GUI and IDE RKWard, providing graphical dialogs
for its basic features. The respective R package 'rkward' cannot be installed
directly from a repository, as it is a part of RKWard. To make full use of this
feature, please install RKWard from https://rkward.kde.org (plugins are detected
automatically). Due to some restrictions on CRAN, the full package sources are
only available from the project homepage. To ask for help, report bugs, suggest
feature improvements, or discuss the global development of the package, please
subscribe to the koRpus-dev mailing list (https://ml06.ispgateway.de/mailman/
listinfo/korpus-dev_r.reaktanz.de).
Author: m.eik michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: m.eik michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.05-6 dated 2015-06-30 and 0.06-4 dated 2016-03-08
koRpus-0.05-6/koRpus/R/freq.analysis.R |only koRpus-0.05-6/koRpus/R/hyphen.R |only koRpus-0.05-6/koRpus/R/lex.div.R |only koRpus-0.05-6/koRpus/R/read.corp.custom.R |only koRpus-0.05-6/koRpus/R/readability.R |only koRpus-0.05-6/koRpus/man/freq.analysis.Rd |only koRpus-0.05-6/koRpus/man/hyphen.Rd |only koRpus-0.05-6/koRpus/man/lex.div.Rd |only koRpus-0.05-6/koRpus/man/read.corp.custom.Rd |only koRpus-0.05-6/koRpus/man/readability.Rd |only koRpus-0.06-4/koRpus/ChangeLog | 79 koRpus-0.06-4/koRpus/DESCRIPTION | 55 koRpus-0.06-4/koRpus/MD5 | 283 +- koRpus-0.06-4/koRpus/NAMESPACE | 10 koRpus-0.06-4/koRpus/R/00_class_09_kRp.lang.R | 2 koRpus-0.06-4/koRpus/R/01_method_correct.R | 13 koRpus-0.06-4/koRpus/R/01_method_freq.analysis.R |only koRpus-0.06-4/koRpus/R/01_method_hyphen.R |only koRpus-0.06-4/koRpus/R/01_method_lex.div.R |only koRpus-0.06-4/koRpus/R/01_method_plot.kRp.tagged.R | 1 koRpus-0.06-4/koRpus/R/01_method_query.R | 2 koRpus-0.06-4/koRpus/R/01_method_read.corp.custom.R |only koRpus-0.06-4/koRpus/R/01_method_readability.R |only koRpus-0.06-4/koRpus/R/01_method_summary.kRp.readability.R | 7 koRpus-0.06-4/koRpus/R/01_method_summary.kRp.tagged.R | 2 koRpus-0.06-4/koRpus/R/flesch.R | 6 koRpus-0.06-4/koRpus/R/guess.lang.R | 4 koRpus-0.06-4/koRpus/R/kRp.POS.tags.R | 4 koRpus-0.06-4/koRpus/R/koRpus-internal.R | 175 - koRpus-0.06-4/koRpus/R/koRpus-internal.freq.analysis.R |only koRpus-0.06-4/koRpus/R/koRpus-internal.hyphen.R |only koRpus-0.06-4/koRpus/R/koRpus-internal.lexdiv.formulae.R | 456 ++++ koRpus-0.06-4/koRpus/R/koRpus-internal.rdb.formulae.R | 2 koRpus-0.06-4/koRpus/R/koRpus-internal.read.corp.custom.R |only koRpus-0.06-4/koRpus/R/koRpus-package.R | 8 koRpus-0.06-4/koRpus/R/lang.support-de.R | 2 koRpus-0.06-4/koRpus/R/lang.support-en.R | 3 koRpus-0.06-4/koRpus/R/lang.support-es.R | 2 koRpus-0.06-4/koRpus/R/lang.support-fr.R | 2 koRpus-0.06-4/koRpus/R/lang.support-it.R | 38 koRpus-0.06-4/koRpus/R/lang.support-ru.R | 2 koRpus-0.06-4/koRpus/R/read.tagged.R | 88 koRpus-0.06-4/koRpus/R/set.kRp.env.R | 26 koRpus-0.06-4/koRpus/R/set.lang.support.R |only koRpus-0.06-4/koRpus/R/treetag.R | 37 koRpus-0.06-4/koRpus/README.md |only koRpus-0.06-4/koRpus/inst/CITATION | 8 koRpus-0.06-4/koRpus/inst/NEWS.Rd | 110 + koRpus-0.06-4/koRpus/inst/README.languages | 47 koRpus-0.06-4/koRpus/inst/doc/koRpus_vignette.pdf |binary koRpus-0.06-4/koRpus/inst/rkward/koRpus.pluginmap | 250 +- koRpus-0.06-4/koRpus/inst/rkward/plugins/FrequencyAnalysis.js | 114 - koRpus-0.06-4/koRpus/inst/rkward/plugins/FrequencyAnalysis.xml | 104 koRpus-0.06-4/koRpus/inst/rkward/plugins/Hyphenation.js | 49 koRpus-0.06-4/koRpus/inst/rkward/plugins/Hyphenation.xml | 48 koRpus-0.06-4/koRpus/inst/rkward/plugins/LexicalDiversity.js | 336 +-- koRpus-0.06-4/koRpus/inst/rkward/plugins/LexicalDiversity.xml | 266 +- koRpus-0.06-4/koRpus/inst/rkward/plugins/Readability.js | 323 +-- koRpus-0.06-4/koRpus/inst/rkward/plugins/Readability.xml | 246 +- koRpus-0.06-4/koRpus/inst/rkward/plugins/TokenizingPOStagging.js | 135 - koRpus-0.06-4/koRpus/inst/rkward/plugins/TokenizingPOStagging.xml | 102 koRpus-0.06-4/koRpus/inst/rkward/po |only koRpus-0.06-4/koRpus/inst/rkward/rkwarddev_koRpus_plugin_script.R | 1045 +++++----- koRpus-0.06-4/koRpus/inst/shiny/demo/ui.R | 11 koRpus-0.06-4/koRpus/inst/templates |only koRpus-0.06-4/koRpus/man/ARI.Rd | 2 koRpus-0.06-4/koRpus/man/C.ld.Rd | 2 koRpus-0.06-4/koRpus/man/CTTR.Rd | 2 koRpus-0.06-4/koRpus/man/DRP.Rd | 2 koRpus-0.06-4/koRpus/man/ELF.Rd | 2 koRpus-0.06-4/koRpus/man/FOG.Rd | 2 koRpus-0.06-4/koRpus/man/FORCAST.Rd | 2 koRpus-0.06-4/koRpus/man/HDD.Rd | 2 koRpus-0.06-4/koRpus/man/K.ld.Rd | 2 koRpus-0.06-4/koRpus/man/LIX.Rd | 2 koRpus-0.06-4/koRpus/man/MATTR.Rd | 2 koRpus-0.06-4/koRpus/man/MSTTR.Rd | 2 koRpus-0.06-4/koRpus/man/MTLD.Rd | 2 koRpus-0.06-4/koRpus/man/R.ld.Rd | 2 koRpus-0.06-4/koRpus/man/RIX.Rd | 2 koRpus-0.06-4/koRpus/man/S.ld.Rd | 2 koRpus-0.06-4/koRpus/man/SMOG.Rd | 2 koRpus-0.06-4/koRpus/man/TRI.Rd | 2 koRpus-0.06-4/koRpus/man/TTR.Rd | 2 koRpus-0.06-4/koRpus/man/U.ld.Rd | 2 koRpus-0.06-4/koRpus/man/bormuth.Rd | 2 koRpus-0.06-4/koRpus/man/cTest-methods.Rd | 2 koRpus-0.06-4/koRpus/man/clozeDelete-methods.Rd | 2 koRpus-0.06-4/koRpus/man/coleman.Rd | 2 koRpus-0.06-4/koRpus/man/coleman.liau.Rd | 2 koRpus-0.06-4/koRpus/man/correct-methods.Rd | 11 koRpus-0.06-4/koRpus/man/dale.chall.Rd | 2 koRpus-0.06-4/koRpus/man/danielson.bryan.Rd | 2 koRpus-0.06-4/koRpus/man/dickes.steiwer.Rd | 2 koRpus-0.06-4/koRpus/man/farr.jenkins.paterson.Rd | 2 koRpus-0.06-4/koRpus/man/flesch.Rd | 6 koRpus-0.06-4/koRpus/man/flesch.kincaid.Rd | 2 koRpus-0.06-4/koRpus/man/freq.analysis-methods.Rd |only koRpus-0.06-4/koRpus/man/fucks.Rd | 2 koRpus-0.06-4/koRpus/man/get.kRp.env.Rd | 2 koRpus-0.06-4/koRpus/man/guess.lang.Rd | 2 koRpus-0.06-4/koRpus/man/harris.jacobson.Rd | 2 koRpus-0.06-4/koRpus/man/hyph.XX.Rd | 2 koRpus-0.06-4/koRpus/man/hyphen-methods.Rd |only koRpus-0.06-4/koRpus/man/jumbleWords.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.POS.tags.Rd | 6 koRpus-0.06-4/koRpus/man/kRp.TTR-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.analysis-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.cluster.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.corp.freq-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.filter.wclass.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.hyph.pat-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.hyphen-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.lang-class.Rd | 4 koRpus-0.06-4/koRpus/man/kRp.readability-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.tagged-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.taggedText-methods.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.text.analysis.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.text.paste.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.text.transform.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.txt.freq-class.Rd | 2 koRpus-0.06-4/koRpus/man/kRp.txt.trans-class.Rd | 2 koRpus-0.06-4/koRpus/man/koRpus-package.Rd | 11 koRpus-0.06-4/koRpus/man/lex.div-methods.Rd |only koRpus-0.06-4/koRpus/man/lex.div.num.Rd | 2 koRpus-0.06-4/koRpus/man/linsear.write.Rd | 2 koRpus-0.06-4/koRpus/man/maas.Rd | 2 koRpus-0.06-4/koRpus/man/manage.hyph.pat.Rd | 2 koRpus-0.06-4/koRpus/man/nWS.Rd | 2 koRpus-0.06-4/koRpus/man/plot-methods.Rd | 2 koRpus-0.06-4/koRpus/man/query-methods.Rd | 6 koRpus-0.06-4/koRpus/man/read.BAWL.Rd | 2 koRpus-0.06-4/koRpus/man/read.corp.LCC.Rd | 2 koRpus-0.06-4/koRpus/man/read.corp.celex.Rd | 2 koRpus-0.06-4/koRpus/man/read.corp.custom-methods.Rd |only koRpus-0.06-4/koRpus/man/read.hyph.pat.Rd | 2 koRpus-0.06-4/koRpus/man/read.tagged.Rd | 46 koRpus-0.06-4/koRpus/man/readability-methods.Rd |only koRpus-0.06-4/koRpus/man/readability.num.Rd | 2 koRpus-0.06-4/koRpus/man/segment.optimizer.Rd | 2 koRpus-0.06-4/koRpus/man/set.kRp.env.Rd | 7 koRpus-0.06-4/koRpus/man/set.lang.support.Rd |only koRpus-0.06-4/koRpus/man/show-methods.Rd | 20 koRpus-0.06-4/koRpus/man/spache.Rd | 2 koRpus-0.06-4/koRpus/man/strain.Rd | 2 koRpus-0.06-4/koRpus/man/summary-methods.Rd | 18 koRpus-0.06-4/koRpus/man/textFeatures.Rd | 2 koRpus-0.06-4/koRpus/man/tokenize.Rd | 36 koRpus-0.06-4/koRpus/man/traenkle.bailer.Rd | 2 koRpus-0.06-4/koRpus/man/treetag.Rd | 12 koRpus-0.06-4/koRpus/man/tuldava.Rd | 2 koRpus-0.06-4/koRpus/man/wheeler.smith.Rd | 2 koRpus-0.06-4/koRpus/tests/testthat/sample_text_hyphen_dput.txt | 308 +- koRpus-0.06-4/koRpus/tests/testthat/sample_text_readability_dput.txt | 10 koRpus-0.06-4/koRpus/tests/testthat/test_tokenizing_POS_tagging.R | 3 155 files changed, 2934 insertions(+), 2211 deletions(-)
Title: AMCE Estimator for Conjoint Experiments
Description: An R implementation of the Average Marginal Component-specific Effects (AMCE) estimator presented in Hainmueller, J., Hopkins, D., and Yamamoto T. (2014) Causal Inference in Conjoint Analysis: Understanding Multi-Dimensional Choices via Stated Preference Experiments. Political Analysis 22(1):1-30.
Author: Anton Strezhnev, Elissa Berwick, Jens Hainmueller, Daniel Hopkins, Teppei Yamamoto
Maintainer: Anton Strezhnev <astrezhnev@fas.harvard.edu>
Diff between cjoint versions 2.0.3 dated 2016-01-12 and 2.0.4 dated 2016-03-08
DESCRIPTION | 8 MD5 | 8 R/cjoint.R | 2104 +++++++++++++++++++++++------------------------------- demo/cjointdemo.R | 20 man/plot.amce.Rd | 8 5 files changed, 946 insertions(+), 1202 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat. 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.55 dated 2015-04-15 and 0.60 dated 2016-03-08
DESCRIPTION | 11 MD5 | 115 ++++-- NAMESPACE | 16 R/PLS_chill_force.R | 234 +++++++------ R/PLS_pheno.R | 224 +++++++----- R/VIP.R | 24 - R/YEARMODA2Date.R |only R/bloom_prediction.R | 112 +++--- R/chile_agromet2chillR.R |only R/chillR.R |only R/chilling.R | 266 +++++++------- R/chilling_hourtable.R | 223 ++++++------ R/color_bar_maker.R | 16 R/daily_chill.R | 141 +------ R/fix_weather.R |only R/get_last_date.R |only R/get_weather.R |only R/handle_chile_agromet.R |only R/handle_cimis.R |only R/handle_gsod.R |only R/handle_ucipm.R |only R/handle_wunderground.R |only R/interpolate_gaps.R | 76 ++-- R/leap_year.R |only R/make_all_day_table.R | 70 +-- R/make_california_UCIPM_station_list.R |only R/make_chill_plot.R |only R/make_daily_chill_figures.R | 124 +++--- R/make_daily_chill_plot.R |only R/make_hourly_temps.R | 140 +++---- R/make_multi_pheno_trend_plot.R |only R/make_pheno_trend_plot.R | 248 ++++++------- R/plot_pheno_results.R | 539 +++++++++++++++++++----------- R/runn_mean.R |only R/stack_hourly_temps.R | 45 +- R/tempResponse.R |only R/temp_models.R |only R/weather2chillR.R |only data/california_stations.rda |only man/Chilling_Hours.Rd |only man/Dynamic_Model.Rd |only man/GDH.Rd |only man/KA_bloom.Rd | 62 +-- man/KA_weather.Rd | 66 +-- man/PLS_chill_force.Rd | 308 ++++++++--------- man/PLS_pheno.Rd | 192 +++++----- man/Utah_Model.Rd |only man/VIP.Rd | 99 ++--- man/YEARMODA2Date.Rd |only man/bloom_prediction.Rd | 235 ++++++------- man/california_stations.Rd |only man/chile_agromet2chillR.Rd |only man/chillR-package.Rd | 125 +++--- man/chilling.Rd | 236 ++++++------- man/chilling_hourtable.Rd | 233 ++++++------ man/color_bar_maker.Rd | 92 ++--- man/daily_chill.Rd | 232 ++++++------ man/fix_weather.Rd |only man/get_last_date.Rd |only man/get_weather.Rd |only man/handle_chile_agromet.Rd |only man/handle_cimis.Rd |only man/handle_gsod.Rd |only man/handle_ucipm.Rd |only man/handle_wunderground.Rd |only man/interpolate_gaps.Rd | 83 ++-- man/leap_year.Rd |only man/make_all_day_table.Rd | 76 ++-- man/make_california_UCIPM_station_list.Rd |only man/make_chill_plot.Rd |only man/make_daily_chill_figures.Rd | 231 ++++++------ man/make_daily_chill_plot.Rd |only man/make_hourly_temps.Rd | 101 ++--- man/make_multi_pheno_trend_plot.Rd |only man/make_pheno_trend_plot.Rd | 192 +++++----- man/plot_PLS.Rd | 142 ++++--- man/runn_mean.Rd |only man/stack_hourly_temps.Rd | 81 ++-- man/step_model.Rd |only man/tempResponse.Rd |only man/weather2chillR.Rd |only 81 files changed, 2827 insertions(+), 2583 deletions(-)
Title: Clean Biological Occurrence Records
Description: Clean biological occurrence records. Includes functionality
for cleaning based on various aspects of spatial coordinates,
unlikely values due to political 'centroids', coordinates based on
where collections of specimens are held, and more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between scrubr versions 0.1.0 dated 2016-03-04 and 0.1.1 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 42 ++++++++++++++++++++++++------------------ NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/coord-funs.R | 10 +++++++--- R/dedup.R | 2 +- R/scrubr-package.R | 15 +-------------- R/scrubr_datasets.R |only R/taxonomy-funs.R | 8 ++++++-- README.md | 21 +++++++++++---------- data/sampledata3.rda |only data/sampledata4.rda |only inst/doc/scrubr_vignette.Rmd | 8 ++++++-- inst/doc/scrubr_vignette.html | 8 ++++++-- inst/vign/scrubr_vignette.Rmd | 8 ++++++-- inst/vign/scrubr_vignette.md | 8 ++++++-- man/coords.Rd | 10 +++++++--- man/sample_data_1.Rd | 17 ++++++++++++++--- man/sample_data_2.Rd | 15 ++++++++++++++- man/sample_data_3.Rd |only man/sample_data_4.Rd |only man/scrubr_datasets.Rd |only man/taxonomy.Rd | 8 ++++++-- tests/testthat/test-dates.R | 2 +- vignettes/scrubr_vignette.Rmd | 8 ++++++-- 25 files changed, 135 insertions(+), 72 deletions(-)
Title: Poly-Omic Prediction of Complex TRaits
Description: It provides functions to generate a correlation matrix
from a genetic dataset and to use this matrix to predict the phenotype of an
individual by using the phenotypes of the remaining individuals through
kriging. Kriging is a geostatistical method for optimal prediction or best
unbiased linear prediction. It consists of predicting the value of a
variable at an unobserved location as a weighted sum of the variable at
observed locations. Intuitively, it works as a reverse linear regression:
instead of computing correlation (univariate regression coefficients are
simply scaled correlation) between a dependent variable Y and independent
variables X, it uses known correlation between X and Y to predict Y.
Author: Hae Kyung Im, Heather E. Wheeler, Keston Aquino Michaels, Vassily
Trubetskoy
Maintainer: Hae Kyung Im <haky@uchicago.edu>
Diff between OmicKriging versions 1.3 dated 2014-06-18 and 1.4.0 dated 2016-03-07
DESCRIPTION | 19 ++++++------- MD5 | 32 +++++++++++----------- NAMESPACE | 12 +++++++- R/correlation_matrices.R | 7 ++++ R/input_pheno_GT.R | 6 ---- R/omic_KRIGR.R | 60 ++++++------------------------------------ README.md | 8 +++-- build/vignette.rds |binary inst/doc/OmicKriging.pdf |binary man/krigr_cross_validation.Rd | 30 ++++----------------- man/load_sample_data.Rd | 9 +----- man/make_GXM.Rd | 5 ++- man/make_PCs_irlba.Rd | 7 ++-- man/make_PCs_svd.Rd | 7 ++-- man/okriging.Rd | 35 ++++-------------------- man/read_GRMBin.Rd | 7 ++-- man/write_GRMBin.Rd | 10 ++++--- 17 files changed, 92 insertions(+), 162 deletions(-)
Title: Column-Linked and Row-Linked Matrices
Description: Matrices implemented as collections of matrix-like nodes, linked by
columns or rows.
Author: Gustavo de los Campos [aut],
Alexander Grueneberg [aut, cre]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between LinkedMatrix versions 1.0.0 dated 2015-10-22 and 1.1.0 dated 2016-03-07
LinkedMatrix-1.0.0/LinkedMatrix/man/apply-LinkedMatrix-method.Rd |only LinkedMatrix-1.0.0/LinkedMatrix/man/colMeans-LinkedMatrix-method.Rd |only LinkedMatrix-1.0.0/LinkedMatrix/man/colSums-LinkedMatrix-method.Rd |only LinkedMatrix-1.0.0/LinkedMatrix/man/rowMeans-LinkedMatrix-method.Rd |only LinkedMatrix-1.0.0/LinkedMatrix/man/rowSums-LinkedMatrix-method.Rd |only LinkedMatrix-1.0.0/LinkedMatrix/man/summary-LinkedMatrix-method.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/DESCRIPTION | 11 LinkedMatrix-1.1.0/LinkedMatrix/MD5 | 58 + LinkedMatrix-1.1.0/LinkedMatrix/NAMESPACE | 18 LinkedMatrix-1.1.0/LinkedMatrix/NEWS.md |only LinkedMatrix-1.1.0/LinkedMatrix/R/ColumnLinkedMatrix.R | 148 +++- LinkedMatrix-1.1.0/LinkedMatrix/R/LinkedMatrix.R | 279 +++------ LinkedMatrix-1.1.0/LinkedMatrix/R/RowLinkedMatrix.R | 141 +++- LinkedMatrix-1.1.0/LinkedMatrix/R/package.R | 15 LinkedMatrix-1.1.0/LinkedMatrix/R/utils.R |only LinkedMatrix-1.1.0/LinkedMatrix/README.md | 76 -- LinkedMatrix-1.1.0/LinkedMatrix/inst |only LinkedMatrix-1.1.0/LinkedMatrix/man/ColumnLinkedMatrix-class.Rd | 24 LinkedMatrix-1.1.0/LinkedMatrix/man/LinkedMatrix-class.Rd | 21 LinkedMatrix-1.1.0/LinkedMatrix/man/LinkedMatrix-package.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/LinkedMatrix.Rd | 37 + LinkedMatrix-1.1.0/LinkedMatrix/man/RowLinkedMatrix-class.Rd | 23 LinkedMatrix-1.1.0/LinkedMatrix/man/as.matrix.LinkedMatrix.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/cbind.ColumnLinkedMatrix.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/cbind.RowLinkedMatrix.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/index.Rd | 6 LinkedMatrix-1.1.0/LinkedMatrix/man/initialize-ColumnLinkedMatrix-method.Rd | 25 LinkedMatrix-1.1.0/LinkedMatrix/man/initialize-RowLinkedMatrix-method.Rd | 21 LinkedMatrix-1.1.0/LinkedMatrix/man/nNodes.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/nodes.Rd | 6 LinkedMatrix-1.1.0/LinkedMatrix/man/rbind.ColumnLinkedMatrix.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/rbind.RowLinkedMatrix.Rd |only LinkedMatrix-1.1.0/LinkedMatrix/man/show-LinkedMatrix-method.Rd | 12 LinkedMatrix-1.1.0/LinkedMatrix/man/sub-ColumnLinkedMatrix-method.Rd | 12 LinkedMatrix-1.1.0/LinkedMatrix/man/sub-RowLinkedMatrix-method.Rd | 11 LinkedMatrix-1.1.0/LinkedMatrix/man/subset-ColumnLinkedMatrix-method.Rd | 10 LinkedMatrix-1.1.0/LinkedMatrix/man/subset-RowLinkedMatrix-method.Rd | 9 LinkedMatrix-1.1.0/LinkedMatrix/tests/testthat/test-LinkedMatrix.R | 301 +++++----- 38 files changed, 741 insertions(+), 523 deletions(-)
Title: Short Term Forecasting via GMDH-Type Neural Network Algorithms
Description: Group method of data handling (GMDH) - type neural network algorithm is the heuristic self-organization method for modelling the complex systems. In this package, GMDH-type neural network algorithms are applied to make short term forecasting for a univariate time series.
Author: Osman Dag, Ceylan Yozgatligil
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH versions 1.2 dated 2015-12-28 and 1.3 dated 2016-03-07
DESCRIPTION | 8 +- MD5 | 12 +-- NAMESPACE | 6 - R/fcast.R | 190 ++++++++++++++++++++++++++++++++++++++++++++++++++++++---- man/GMDH.Rd | 4 - man/cancer.Rd | 2 man/fcast.Rd | 23 ++++--- 7 files changed, 208 insertions(+), 37 deletions(-)
Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network representation that
offers unmatched efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop, simulated annealing, stochastic
gradient) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon),
but it is first and foremost an efficient computational engine. Users can
easily implement their algorithms by taking advantage of fast gradient computing
routines, as well as network reconstruction functionality (removing weights
and redundant neurons, reordering inputs, merging networks). Networks can be
exported to C functions in order to integrate them into virtually any software
solution.
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.6.0 dated 2015-12-31 and 0.6.1 dated 2016-03-07
FCNN4R-0.6.0/FCNN4R/src/fcnn/version.h |only FCNN4R-0.6.1/FCNN4R/DESCRIPTION | 9 +-- FCNN4R-0.6.1/FCNN4R/MD5 | 70 +++++++++++++------------ FCNN4R-0.6.1/FCNN4R/NAMESPACE | 1 FCNN4R-0.6.1/FCNN4R/R/dataset.R | 2 FCNN4R-0.6.1/FCNN4R/R/fcnn4r.R | 2 FCNN4R-0.6.1/FCNN4R/R/mlp_gteach.R | 14 ++--- FCNN4R-0.6.1/FCNN4R/R/mlp_net.R | 72 ++++++++++++++++---------- FCNN4R-0.6.1/FCNN4R/R/mlp_plot.R | 2 FCNN4R-0.6.1/FCNN4R/R/mlp_prune.R | 2 FCNN4R-0.6.1/FCNN4R/R/mlp_teach.R | 14 +---- FCNN4R-0.6.1/FCNN4R/man/mlp_net-class.Rd | 2 FCNN4R-0.6.1/FCNN4R/man/mlp_net-display.Rd |only FCNN4R-0.6.1/FCNN4R/man/mlp_set_activation.Rd | 2 FCNN4R-0.6.1/FCNN4R/man/mlp_teach_grprop.Rd | 5 + FCNN4R-0.6.1/FCNN4R/man/mlp_teach_sa.Rd | 7 +- FCNN4R-0.6.1/FCNN4R/src/Makevars | 2 FCNN4R-0.6.1/FCNN4R/src/Makevars.win | 2 FCNN4R-0.6.1/FCNN4R/src/dataset.cpp | 3 - FCNN4R-0.6.1/FCNN4R/src/fcnn/activation.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/error.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/export.cpp | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/export.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/fcnncfg.R.h |only FCNN4R-0.6.1/FCNN4R/src/fcnn/fcnncfg.h |only FCNN4R-0.6.1/FCNN4R/src/fcnn/level1.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/level1_impl.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/level2.cpp | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/level2.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/level3.cpp | 16 ----- FCNN4R-0.6.1/FCNN4R/src/fcnn/level3.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/report.cpp | 10 +-- FCNN4R-0.6.1/FCNN4R/src/fcnn/report.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/struct.cpp | 26 ++++++--- FCNN4R-0.6.1/FCNN4R/src/fcnn/struct.h | 2 FCNN4R-0.6.1/FCNN4R/src/fcnn/utils.cpp | 10 +-- FCNN4R-0.6.1/FCNN4R/src/fcnn/utils.h | 2 FCNN4R-0.6.1/FCNN4R/src/interface.cpp | 2 38 files changed, 156 insertions(+), 143 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between diseasemapping versions 1.2.7 dated 2015-11-09 and 1.4.0 dated 2016-03-07
DESCRIPTION | 17 ++- MD5 | 20 ++-- R/bym.R | 214 +++++++++++++++++++++++++++++++++++++++++++++--- R/cancer-rates.info.R |only build |only data/casedata.RData |binary data/kentucky.RData |binary data/popdata.RData |binary data/referencepop.RData |binary inst/doc |only tests/bym.R | 18 +--- vignettes |only 12 files changed, 233 insertions(+), 36 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut],
Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 2.0.2 dated 2016-03-04 and 2.0.3 dated 2016-03-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + R/archivist-package.R | 1 + R/restoreLibraries.R | 17 ++++++++++------- 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) "DART: a software to analyse root system architecture and development from captured images", Plant and Soil, <DOI:10.1007/s11104-009-0005-2>), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) "Root System Markup Language: toward a unified root architecture description language", Plant Physiology, <DOI:10.1104/pp.114.253625>). More information can be found in Delory et al (2016) "archiDART: an R package for the automated computation of plant root architectural traits", Plant and Soil, <DOI:10.1007/s11104-015-2673-4>.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 1.3 dated 2016-03-06 and 1.4 dated 2016-03-07
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Sparklines and Graphical Tables for TeX and HTML
Description: Create sparklines and graphical tables for documents and websites.
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between sparkTable versions 1.1.0 dated 2015-11-11 and 1.2.0 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/methods.r | 10 +++++----- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: Semantically Rich I/O for the 'NeXML' Format
Description: Provides access to phyloinformatic data in 'NeXML' format. The
package should add new functionality to R such as the possibility to
manipulate 'NeXML' objects in more various and refined way and compatibility
with 'ape' objects.
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between RNeXML versions 2.0.5 dated 2015-12-30 and 2.0.6 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/nexml_read.R | 2 ++ R/nexml_write.R | 2 +- man/nexml_read.Rd | 2 ++ man/nexml_write.Rd | 2 +- 7 files changed, 21 insertions(+), 12 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including fixed and mixed-effects Cormack-Jolly-Seber(CJS) for survival
estimation and POPAN structured Jolly-Seber models for abundance
estimation. Includes a CJS models that concurrently estimates and corrects
for tag loss. Hidden Markov model (HMM) implementations of CJS and
multistate models with and without state uncertainty.
Author: Jeff Laake <jeff.laake@noaa.gov>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>
Maintainer: Jeff Laake <Jeff.Laake@noaa.gov>
Diff between marked versions 1.1.10 dated 2015-08-20 and 1.1.11 dated 2016-03-07
DESCRIPTION | 14 ++- MD5 | 152 ++++++++++++++++++++--------------------- NAMESPACE | 3 NEWS | 32 ++++++++ R/cjs.R | 28 +++++-- R/create.dm.R | 3 R/crm.R | 8 +- R/crm.wrapper.R | 36 +++++++-- R/mixed.model.r | 18 ++-- R/proc.formula.r | 3 R/set.initial.r | 1 build/vignette.rds |binary inst/cjs.tpl | 6 + inst/doc/markedVignette.R | 28 +++---- inst/doc/markedVignette.Rnw | 2 inst/doc/markedVignette.pdf |binary man/HMMLikelihood.Rd | 5 - man/Phi.mean.Rd | 2 man/R_HMMLikelihood.Rd | 2 man/backward_prob.Rd | 2 man/cjs.Rd | 2 man/cjs.accumulate.Rd | 2 man/cjs.hessian.Rd | 2 man/cjs.initial.Rd | 2 man/cjs.lnl.Rd | 96 ++++++++++++------------- man/cjs_delta.Rd | 4 - man/cjs_gamma.Rd | 2 man/coef.crm.Rd | 2 man/compute.real.Rd | 8 +- man/compute_matrices.Rd | 2 man/convert.link.to.real.Rd | 2 man/create.dm.Rd | 6 - man/create.dmdf.Rd | 54 +++++++------- man/create.fixed.matrix.Rd | 2 man/create.links.Rd | 2 man/crm.Rd | 16 ++-- man/crm.wrapper.Rd | 10 +- man/deriv_inverse.link.Rd | 2 man/dipper.Rd | 2 man/fix.parameters.Rd | 2 man/function.wrapper.Rd | 4 - man/global_decode.Rd | 2 man/hmmDemo.Rd | 4 - man/inverse.link.Rd | 2 man/js.Rd | 2 man/js.accumulate.Rd | 2 man/js.hessian.Rd | 2 man/js.lnl.Rd | 4 - man/local_decode.Rd | 2 man/make.design.data.Rd | 6 - man/merge_design.covariates.Rd | 4 - man/mixed.model.admb.Rd | 8 +- man/mscjs.Rd | 2 man/mstrata.Rd | 4 - man/mvms_design_data.Rd | 3 man/mvms_dmat.Rd | 4 - man/omega.Rd | 2 man/predict.crm.Rd | 4 - man/print.crm.Rd | 2 man/print.crmlist.Rd | 2 man/probitCJS.Rd | 28 +++---- man/proc.form.Rd | 8 +- man/process.ch.Rd | 8 +- man/process.data.Rd | 19 ++--- man/resight.matrix.Rd | 6 - man/sealions.Rd | 6 - man/set.fixed.Rd | 4 - man/set.initial.Rd | 2 man/set.scale.Rd | 6 - man/set_mvms.Rd | 12 +-- man/setup.model.Rd | 2 man/setup.parameters.Rd | 2 man/simHMM.Rd | 10 +- man/splitCH.Rd | 8 +- man/tagloss.Rd | 34 ++++----- man/valid.parameters.Rd | 2 vignettes/markedVignette.Rnw | 2 77 files changed, 439 insertions(+), 350 deletions(-)
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author:
Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.3-0 dated 2016-01-22 and 0.4-0 dated 2016-03-07
DESCRIPTION | 8 +-- MD5 | 93 ++++++++++++++++++++++------------------ NAMESPACE | 66 +++++++++++++++------------- R/agree_aicken.R |only R/anova_immer.R | 5 +- R/immer_FACETS.R | 2 R/immer_HRM.R | 2 R/immer_agree2.R |only R/immer_cml.R | 2 R/immer_collect_traces.R | 10 ++-- R/immer_identifiers_relabel.R | 4 - R/immer_install.R | 2 R/immer_mcmc_draw_variance.R | 2 R/immer_reshape_wideformat.R | 5 +- R/immer_unique_patterns.R |only R/inits_theta_1dim.R | 4 - R/lc2_agreement.R |only R/logLik.lc2_agreement.R |only R/loglik_HRM.R | 2 R/lpcm_inits.R | 3 - R/plot.immer_HRM.R | 2 R/probs2logits.R |only R/rtrnorm.R | 8 +-- R/sampling_hrm_a.R | 12 +++-- R/sampling_hrm_b.R | 16 +++--- R/sampling_hrm_mu_theta_1dim.R | 4 - R/sampling_hrm_phi.R | 12 ++--- R/sampling_hrm_psi.R | 12 ++--- R/sampling_hrm_theta_1dim.R | 8 +-- R/sampling_hrm_xi.R | 2 R/summary.immer_HRM.R | 2 R/summary.immer_agree2.R |only R/summary.immer_cml.R | 2 R/summary.lc2_agreement.R |only R/zzz.R | 4 - data/data.immer01a.rda |binary data/data.immer01b.rda |binary data/data.immer02.rda |binary data/data.immer03.rda |binary data/data.immer04a.rda |binary data/data.immer04b.rda |binary data/data.immer05.rda |binary data/data.immer06.rda |binary data/data.immer07.rda |binary data/data.immer08.rda |only inst/NEWS | 20 ++++++++ man/data.immer.Rd | 13 +++++ man/immer-package.Rd | 2 man/immer_agree2.Rd |only man/immer_cml.Rd | 4 - man/immer_reshape_wideformat.Rd | 4 - man/immer_unique_patterns.Rd |only man/lc2_agreement.Rd |only man/probs2logits.Rd |only 54 files changed, 197 insertions(+), 140 deletions(-)
Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>
Diff between forecTheta versions 2.0 dated 2016-03-02 and 2.1 dated 2016-03-07
ChangeLog | 11 +++++++++-- DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/crossValidationFunctions.R | 2 +- R/forecastFunctions.R | 14 +++++++++----- man/crossValidationFunctions.Rd | 17 ++++++++--------- man/errorMetricFunctions.Rd | 12 ++++++------ man/expSmoot.Rd | 2 +- man/forecTheta-package.Rd | 12 ++++++------ man/otm.arXiv.Rd | 7 +++---- man/plot.thetaModel.Rd | 4 ++-- man/thetaModels.Rd | 19 +++++++++++-------- 12 files changed, 71 insertions(+), 59 deletions(-)
Title: Computational Methods for Immune Cell-Type Subsets
Description: Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
Author: Yael Steuerman [aut, cre],
Irit Gat-Viks [aut]
Maintainer: Yael Steuerman <yaelsteu@mail.tau.ac.il>
Diff between ComICS versions 1.0.2 dated 2016-01-28 and 1.0.3 dated 2016-03-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/IterativeFilteration.R | 4 ++-- data/vocalEx.RData |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 1.9 dated 2016-01-10 and 2.0 dated 2016-03-07
cit-1.9/cit/src/citconlog2_perm_v5.cpp |only cit-2.0/cit/DESCRIPTION | 8 ++--- cit-2.0/cit/MD5 | 19 ++++++------ cit-2.0/cit/R/C_CIT_V12.R | 49 ++++++++++++++++++--------------- cit-2.0/cit/man/cit-package.Rd | 5 ++- cit-2.0/cit/man/cit.bp.Rd | 1 cit-2.0/cit/man/cit.cp.Rd | 1 cit-2.0/cit/man/fdr.cit.Rd | 25 ++++++++++++---- cit-2.0/cit/man/fdr.od.Rd | 15 ++++++---- cit-2.0/cit/man/iuq.Rd | 2 - cit-2.0/cit/src/citconlog3_perm_v5.cpp | 8 +++-- 11 files changed, 80 insertions(+), 53 deletions(-)
Title: (Robust) Canonical Correlation Analysis via Projection Pursuit
Description: Canonical correlation analysis and maximum correlation via
projection pursuit, as well as fast implementations of correlation
estimators, with a focus on robust and non-parametric methods.
Author: Andreas Alfons [aut, cre],
David Simcha [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between ccaPP versions 0.3.1 dated 2015-11-11 and 0.3.2 dated 2016-03-07
DESCRIPTION | 13 +++++++------ MD5 | 23 +++++++++++++++-------- NEWS | 7 +++++++ R/maxCor.R | 9 +++++++++ R/permTest.R | 11 ++++++++--- build/partial.rdb |binary build/vignette.rds |only inst |only man/ccaPP-package.Rd | 9 +++++++++ man/maxCorGrid.Rd | 9 +++++++++ man/permTest.Rd | 11 ++++++++--- vignettes |only 12 files changed, 72 insertions(+), 20 deletions(-)
Title: Tools for Easily Combining and Cleaning Data Sets
Description: Tools for combining and cleaning data sets, particularly
with grouped and time series data.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between DataCombine versions 0.2.18 dated 2015-12-24 and 0.2.19 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 8 ++++++++ R/FillIn.R | 6 ++++++ R/utils.R | 2 +- README.md | 4 ++-- 6 files changed, 26 insertions(+), 12 deletions(-)
Title: A Visual Tool for Behaviour Analysis
Description: A graphical tool designed to visualize and to give an overview of behavioural observations realized on individuals or groups. ViSiElse allows visualization of raw data during experimental observations of the realization of a procedure. It graphically presents an overview of individuals and group actions usually acquired from timestamps during video recorded sessions. Options of the package allow adding graphical information as statistical indicators (mean, standard deviation, quantile or statistical test) but also for each action green or black zones providing visual information about the accuracy of the realized actions.
Author: Nastasia Fouret [aut, cre, cph],
Mederic Descoins [aut, cph],
CEPOI - EA 7388 [cph]
Maintainer: Nastasia Fouret <nastasia.fouret@chu-reunion.fr>
Diff between ViSiElse versions 1.0.0 dated 2016-01-12 and 1.0.1 dated 2016-03-07
DESCRIPTION | 8 +- MD5 | 54 ++++++++-------- NAMESPACE | 2 R/ViSibook.r | 5 - data/intubation.rda |binary inst/doc/example_intubation.R | 13 +--- inst/doc/example_intubation.Rmd | 13 +--- inst/doc/example_intubation.html | 39 +++++------- inst/doc/introduction_ViSiElse.html | 87 +++++++++++++-------------- man/ConvertFromViSibook-ViSibook-methods.Rd | 2 man/ConvertoViSibook.Rd | 4 - man/ViSiElse.Rd | 38 +++++------ man/ViSibook-class.Rd | 14 ++-- man/ViSigrid-class.Rd | 6 - man/buildViSiGrid.Rd | 90 ++++++++++++++-------------- man/changeShoworder-ViSibook-methods.Rd | 2 man/dim-ViSibook-methods.Rd | 4 - man/get-ViSibook-methods.Rd | 2 man/initialize-ViSibook-methods.Rd | 2 man/intubation.Rd | 8 +- man/plot-ViSibook-methods.Rd | 4 - man/plot-ViSigrid-methods.Rd | 4 - man/print-ViSibook-methods.Rd | 4 - man/set-ViSibook-methods.Rd | 2 man/show-ViSibook-methods.Rd | 2 man/show-ViSigrid-methods.Rd | 2 man/summary-ViSigrid-methods.Rd | 2 vignettes/example_intubation.Rmd | 13 +--- 28 files changed, 211 insertions(+), 215 deletions(-)
Title: Fitting Semi-Parametric log-Symmetric Regression Models
Description: Set of tools to fit a semi-parametric regression model suitable for analysis of data sets in which the response variable is continuous, strictly positive, asymmetric and possibly, censored. Under this setup, both the median and the skewness of the response variable distribution are explicitly modeled by using semi-parametric functions, whose non-parametric components may be approximated by natural cubic splines or P-splines. Supported distributions for the model error include log-normal, log-Student-t, log-power-exponential, log-hyperbolic, log-contaminated-normal, log-slash, Birnbaum-Saunders and Birnbaum-Saunders-t distributions.
Author: Luis Hernando Vanegas <hvanegasp@gmail.com> and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas <hvanegasp@gmail.com>
Diff between ssym versions 1.5.4 dated 2015-10-22 and 1.5.5 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 32 +++++++++++++++++--------------- R/envelope.R | 16 +++++++++------- R/extra.parameter.R | 27 --------------------------- data/Baboons.rda |binary data/Biaxial.rda |binary data/Claims.rda |binary data/Erabbits.rda |binary data/Ovocytes.rda |binary data/Snacks.rda |binary data/Steel.rda |binary data/gdp.rda |binary data/myeloma.rda |only man/myeloma.Rd |only man/ssym-package.Rd | 4 ++-- man/ssym.l.Rd | 27 ++++++++++++++++++++++++++- man/ssym.l2.Rd | 27 +++++++++++++++++++++------ man/ssym.nl.Rd | 17 +++++++++-------- 18 files changed, 88 insertions(+), 70 deletions(-)
Title: Applications of Empirical Dynamic Modeling from Time Series
Description: Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described by Sugihara et al. (2012) <DOI:10.1126/science.1227079>.
Author: Hao Ye, Adam Clark, Ethan Deyle
Maintainer: Hao Ye <hye@ucsd.edu>
Diff between rEDM versions 0.4.4 dated 2016-03-05 and 0.4.5 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/rEDM_tutorial.html | 14 +++++++------- src/forecast_machine.cpp | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Find the Modes and Assess the Modality of Complex and Mixture
Distributions, Especially with Big Datasets
Description: Designed with a dual purpose of
accurately estimating the mode (or modes) as well as characterizing
the modality of data. The specific application area includes complex
or mixture distributions particularly in a big data environment.
The heterogeneous nature of (big) data may require deep introspective
statistical and machine learning techniques, but these statistical tools
often fail when applied without first understanding the data. In small
datasets, this often isn't a big issue, but when dealing with large scale
data analysis or big data thoroughly inspecting each dimension
typically yields an O(n^n-1) problem. As such, dealing with big data
require an alternative toolkit. This package not only identifies the
mode or modes for various data types, it also provides a programmatic
way of understanding the modality (i.e. unimodal, bimodal, etc.) of
a dataset (whether it's big data or not). See
<http://www.sdeevi.com/modes_package> for examples and discussion.
Author: Sathish Deevi [aut, cre],
4D Strategies [aut,own]
Maintainer: Sathish Deevi <SathishCDeevi@gmail.com>
Diff between modes versions 0.6.1 dated 2016-02-06 and 0.7.0 dated 2016-03-07
modes-0.6.1/modes/man/mode.Rd |only modes-0.7.0/modes/DESCRIPTION | 9 +++--- modes-0.7.0/modes/MD5 | 28 +++++++++--------- modes-0.7.0/modes/NAMESPACE | 1 modes-0.7.0/modes/R/Nonparametric_functions.R | 4 +- modes-0.7.0/modes/man/Ashmans_D.Rd | 22 +++++++------- modes-0.7.0/modes/man/amps.Rd | 4 +- modes-0.7.0/modes/man/bimodality_amplitude.Rd | 26 ++++++++--------- modes-0.7.0/modes/man/bimodality_coefficient.Rd | 4 +- modes-0.7.0/modes/man/bimodality_ratio.Rd | 36 ++++++++++++------------ modes-0.7.0/modes/man/bimodality_separation.Rd | 20 ++++++------- modes-0.7.0/modes/man/kurtosis.Rd | 4 +- modes-0.7.0/modes/man/modes-package.Rd | 1 modes-0.7.0/modes/man/modes.Rd |only modes-0.7.0/modes/man/nth_highest.Rd | 4 +- modes-0.7.0/modes/man/skewness.Rd | 6 ++-- 16 files changed, 85 insertions(+), 84 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.15 dated 2016-01-21 and 1.16 dated 2016-03-07
mirt-1.15/mirt/NEWS |only mirt-1.16/mirt/DESCRIPTION | 10 mirt-1.16/mirt/MD5 | 149 +++++----- mirt-1.16/mirt/NAMESPACE | 5 mirt-1.16/mirt/NEWS.md |only mirt-1.16/mirt/R/01-itemclass.R | 4 mirt-1.16/mirt/R/02-item_methods.R | 66 ++-- mirt-1.16/mirt/R/03-estimation.R | 127 ++++---- mirt-1.16/mirt/R/DIF.R | 2 mirt-1.16/mirt/R/Discrete-methods.R | 19 + mirt-1.16/mirt/R/EMstep.group.R | 60 ++-- mirt-1.16/mirt/R/EMstep.utils.R | 155 ++-------- mirt-1.16/mirt/R/LoadPars.R | 17 - mirt-1.16/mirt/R/M2.R | 5 mirt-1.16/mirt/R/MHRM.group.R | 215 +++++++++++--- mirt-1.16/mirt/R/Mixed-methods.R | 80 +++++ mirt-1.16/mirt/R/MultipleGroup-methods.R | 19 + mirt-1.16/mirt/R/PLCI.mirt.R | 147 +-------- mirt-1.16/mirt/R/PrepData.R | 11 mirt-1.16/mirt/R/SE.methods.R | 48 +-- mirt-1.16/mirt/R/SingleGroup-methods.R | 88 +++++ mirt-1.16/mirt/R/areainfo.R |only mirt-1.16/mirt/R/boot.mirt.R | 2 mirt-1.16/mirt/R/calcLogLik.R | 22 + mirt-1.16/mirt/R/createItem.R | 41 ++ mirt-1.16/mirt/R/empirical_plot.R | 17 - mirt-1.16/mirt/R/expected.test.R | 41 ++ mirt-1.16/mirt/R/extract.mirt.R | 5 mirt-1.16/mirt/R/fscores.R | 2 mirt-1.16/mirt/R/fscores.internal.R | 3 mirt-1.16/mirt/R/itemfit.R | 7 mirt-1.16/mirt/R/itemplot.internal.R | 2 mirt-1.16/mirt/R/lagrange.R |only mirt-1.16/mirt/R/mirt-package.R | 8 mirt-1.16/mirt/R/mirt.R | 51 +-- mirt-1.16/mirt/R/mirtCluster.R | 31 -- mirt-1.16/mirt/R/mixedmirt.R | 41 ++ mirt-1.16/mirt/R/model.elements.R | 5 mirt-1.16/mirt/R/personfit.R | 4 mirt-1.16/mirt/R/randef.R | 41 ++ mirt-1.16/mirt/R/simdata.R | 26 + mirt-1.16/mirt/R/testinfo.R | 26 + mirt-1.16/mirt/R/utils.R | 310 ++++++++++++++++----- mirt-1.16/mirt/R/wald.R | 5 mirt-1.16/mirt/README.md | 9 mirt-1.16/mirt/build/vignette.rds |binary mirt-1.16/mirt/man/Bock1997.Rd | 4 mirt-1.16/mirt/man/M2.Rd | 5 mirt-1.16/mirt/man/PLCI.mirt.Rd | 10 mirt-1.16/mirt/man/areainfo.Rd |only mirt-1.16/mirt/man/boot.mirt.Rd | 3 mirt-1.16/mirt/man/coef-method.Rd | 4 mirt-1.16/mirt/man/createItem.Rd | 42 ++ mirt-1.16/mirt/man/empirical_plot.Rd | 9 mirt-1.16/mirt/man/expected.test.Rd | 12 mirt-1.16/mirt/man/extract.mirt.Rd | 1 mirt-1.16/mirt/man/fscores.Rd | 2 mirt-1.16/mirt/man/lagrange.Rd |only mirt-1.16/mirt/man/logLik-method.Rd |only mirt-1.16/mirt/man/mirt.Rd | 53 +-- mirt-1.16/mirt/man/mirtCluster.Rd | 12 mirt-1.16/mirt/man/mixedmirt.Rd | 26 + mirt-1.16/mirt/man/numerical_deriv.Rd |only mirt-1.16/mirt/man/personfit.Rd | 2 mirt-1.16/mirt/man/simdata.Rd | 26 + mirt-1.16/mirt/man/summary-method.Rd | 9 mirt-1.16/mirt/man/testinfo.Rd | 14 mirt-1.16/mirt/man/vcov-method.Rd |only mirt-1.16/mirt/src/Estep.cpp | 90 +++--- mirt-1.16/mirt/src/Estep.h | 9 mirt-1.16/mirt/src/dpars.cpp | 137 +++++++-- mirt-1.16/mirt/tests/tests/test-00-basics.R | 6 mirt-1.16/mirt/tests/tests/test-01-mirtOne.R | 10 mirt-1.16/mirt/tests/tests/test-03-bfactor.R | 2 mirt-1.16/mirt/tests/tests/test-04-multipleGroup.R | 6 mirt-1.16/mirt/tests/tests/test-05-confmirtOne.R | 4 mirt-1.16/mirt/tests/tests/test-07-mixedmirt.R | 6 mirt-1.16/mirt/tests/tests/test-08-createItem.R | 2 mirt-1.16/mirt/tests/tests/test-10-extras.R | 8 mirt-1.16/mirt/tests/tests/test-11-discrete.R | 2 80 files changed, 1543 insertions(+), 899 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Ken Aho, Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Clint Cummins, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Dirk Eddelbuettel, Jeff Enos, Claus Ekstrom, Martin Elff, Kamil Erguler, Richard W. Farebrother, John Fox, Michael Friendly, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Richard Heiberger, Michael Hoehle, Christian W. Hoffmann, Torsten Hothorn, Markus Huerzeler, Wallace W. Hui, Pete Hurd, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Max Kuhn, Detlew Labes, Friederich Leisch, Jim Lemon, Dong Li, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Giovanni Millo, Yongyi Min, David Mitchell, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Hong Ooi, Nick Parsons, Sandrine Pavoine, Tony Plate, Roland Rapold, William Revelle, Tyler Rinker, Brian D. Ripley, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Mark Stevenson, Terry Therneau, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Rand R. Wilcox, Peter Wolf, Daniel Wollschlaeger, Thomas Yee, Achim Zeileis
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.15 dated 2015-10-25 and 0.99.16 dated 2016-03-07
DescTools-0.99.15/DescTools/R/FastDesc.R |only DescTools-0.99.15/DescTools/man/Desc.Date.Rd |only DescTools-0.99.15/DescTools/man/Desc.data.frame.Rd |only DescTools-0.99.15/DescTools/man/Desc.factor.Rd |only DescTools-0.99.15/DescTools/man/Desc.flags.Rd |only DescTools-0.99.15/DescTools/man/Desc.formula.Rd |only DescTools-0.99.15/DescTools/man/Desc.integer.Rd |only DescTools-0.99.15/DescTools/man/Desc.logical.Rd |only DescTools-0.99.15/DescTools/man/Desc.numeric.Rd |only DescTools-0.99.15/DescTools/man/Desc.table.Rd |only DescTools-0.99.15/DescTools/man/DescWrd.Rd |only DescTools-0.99.15/DescTools/man/GoodmanKruskalTauA.Rd |only DescTools-0.99.15/DescTools/man/PlotDesc.Rd |only DescTools-0.99.15/DescTools/man/RoundM.Rd |only DescTools-0.99.15/DescTools/man/WrdInsTab.Rd |only DescTools-0.99.15/DescTools/man/WrdSetFont.Rd |only DescTools-0.99.16/DescTools/DESCRIPTION | 14 DescTools-0.99.16/DescTools/MD5 | 156 DescTools-0.99.16/DescTools/NAMESPACE | 138 DescTools-0.99.16/DescTools/NEWS | 88 DescTools-0.99.16/DescTools/R/Desc.R |only DescTools-0.99.16/DescTools/R/DescTools.r |13804 ++------------- DescTools-0.99.16/DescTools/R/StatsAndCIs.r |only DescTools-0.99.16/DescTools/R/Tables.r | 18 DescTools-0.99.16/DescTools/R/Tests.r |only DescTools-0.99.16/DescTools/data/cards.rda |only DescTools-0.99.16/DescTools/data/roulette.rda |only DescTools-0.99.16/DescTools/data/tarot.rda |only DescTools-0.99.16/DescTools/inst/doc/TablesInR.pdf |binary DescTools-0.99.16/DescTools/man/AddMonths.Rd | 42 DescTools-0.99.16/DescTools/man/AddMonthsYM.Rd |only DescTools-0.99.16/DescTools/man/AllDuplicated.Rd | 4 DescTools-0.99.16/DescTools/man/AscToChar.Rd | 15 DescTools-0.99.16/DescTools/man/BarnardTest.Rd | 14 DescTools-0.99.16/DescTools/man/BartelsRankTest.Rd | 37 DescTools-0.99.16/DescTools/man/BinTree.Rd | 42 DescTools-0.99.16/DescTools/man/BreuschGodfreyTest.Rd |only DescTools-0.99.16/DescTools/man/ChooseColorDlg.Rd | 2 DescTools-0.99.16/DescTools/man/ConDisPairs.Rd | 14 DescTools-0.99.16/DescTools/man/Conf.Rd | 73 DescTools-0.99.16/DescTools/man/DatasetsforSimulation.Rd |only DescTools-0.99.16/DescTools/man/DateFunctions.Rd | 6 DescTools-0.99.16/DescTools/man/Desc.Rd | 397 DescTools-0.99.16/DescTools/man/DescTools-package.Rd | 34 DescTools-0.99.16/DescTools/man/DoCall.Rd | 3 DescTools-0.99.16/DescTools/man/DunnTest.Rd | 16 DescTools-0.99.16/DescTools/man/DurbinWatsonTest.Rd | 11 DescTools-0.99.16/DescTools/man/FctArgs.Rd | 12 DescTools-0.99.16/DescTools/man/Format.Rd | 114 DescTools-0.99.16/DescTools/man/GCD.Rd | 4 DescTools-0.99.16/DescTools/man/GetNewWrd.Rd | 16 DescTools-0.99.16/DescTools/man/GoodmanKruskalGamma.Rd | 18 DescTools-0.99.16/DescTools/man/GoodmanKruskalTau.Rd |only DescTools-0.99.16/DescTools/man/ICC.Rd | 17 DescTools-0.99.16/DescTools/man/IsDichotomous.Rd | 4 DescTools-0.99.16/DescTools/man/KendallTauA.Rd |only DescTools-0.99.16/DescTools/man/KendallTauB.Rd | 19 DescTools-0.99.16/DescTools/man/KendallW.Rd | 12 DescTools-0.99.16/DescTools/man/Lambda.Rd | 17 DescTools-0.99.16/DescTools/man/Lc.Rd | 39 DescTools-0.99.16/DescTools/man/Lookup.Rd |only DescTools-0.99.16/DescTools/man/MeanCI.Rd | 32 DescTools-0.99.16/DescTools/man/MedianCI.Rd | 16 DescTools-0.99.16/DescTools/man/PalDescTools.Rd | 11 DescTools-0.99.16/DescTools/man/PlotCorr.Rd | 24 DescTools-0.99.16/DescTools/man/PlotDot.Rd | 30 DescTools-0.99.16/DescTools/man/PlotFaces.Rd | 13 DescTools-0.99.16/DescTools/man/PlotFdist.Rd | 60 DescTools-0.99.16/DescTools/man/PlotLinesA.Rd | 36 DescTools-0.99.16/DescTools/man/PlotMiss.Rd | 6 DescTools-0.99.16/DescTools/man/PlotRCol.Rd | 15 DescTools-0.99.16/DescTools/man/PlotWeb.Rd | 33 DescTools-0.99.16/DescTools/man/RoundTo.Rd |only DescTools-0.99.16/DescTools/man/RunsTest.Rd | 32 DescTools-0.99.16/DescTools/man/SomersDelta.Rd | 27 DescTools-0.99.16/DescTools/man/Stamp.Rd | 4 DescTools-0.99.16/DescTools/man/StrAlign.Rd | 29 DescTools-0.99.16/DescTools/man/StrRight.Rd | 15 DescTools-0.99.16/DescTools/man/StrTrim.Rd | 7 DescTools-0.99.16/DescTools/man/StrVal.Rd | 6 DescTools-0.99.16/DescTools/man/StuartTauC.Rd | 22 DescTools-0.99.16/DescTools/man/TOne.Rd | 38 DescTools-0.99.16/DescTools/man/ToWide.Rd | 23 DescTools-0.99.16/DescTools/man/ToWrd.Rd |only DescTools-0.99.16/DescTools/man/Trim.Rd | 14 DescTools-0.99.16/DescTools/man/VarCI.Rd | 5 DescTools-0.99.16/DescTools/man/VarTest.Rd |only DescTools-0.99.16/DescTools/man/WrdCaption.Rd | 15 DescTools-0.99.16/DescTools/man/WrdFont.Rd |only DescTools-0.99.16/DescTools/man/WrdInsertBookmark.Rd | 4 DescTools-0.99.16/DescTools/man/WrdParagraphFormat.Rd |only DescTools-0.99.16/DescTools/man/WrdStyle.Rd |only DescTools-0.99.16/DescTools/man/WrdTable.Rd | 67 DescTools-0.99.16/DescTools/man/WrdText.Rd | 26 DescTools-0.99.16/DescTools/man/ZTest.Rd | 33 DescTools-0.99.16/DescTools/man/ZeroIfNA.Rd | 2 96 files changed, 3550 insertions(+), 12295 deletions(-)
Title: Data Package Manager for R
Description: Create, install, and summarise data packages that follow
the Open Knowledge Foundation's Data Package Protocol.
Author: Christopher Gandrud [aut, cre],
Yann-Ael Le Borgne [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between dpmr versions 0.1.7-1 dated 2015-05-22 and 0.1.9 dated 2016-03-07
DESCRIPTION | 17 ++++++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 5 ++++- NEWS | 13 +++++++++++++ R/datapackage_init.R | 40 +++++++++++++++++++++++++++------------- R/datapackage_install.R | 1 + R/github-utils.R | 2 ++ R/utils.R | 16 ++++++++-------- README.md | 5 ++++- man/datapackage_info.Rd | 3 ++- man/datapackage_init.Rd | 16 ++++++++++------ man/datapackage_install.Rd | 2 +- man/meta_template.Rd | 2 +- 13 files changed, 95 insertions(+), 51 deletions(-)
Title: Conformal Prediction for Regression and Classification
Description: Implementation of conformal prediction using caret models for classification and regression.
Author: Isidro Cortes <isidrolauscher@gmail.com>
Maintainer: Isidro Cortes <isidrolauscher@gmail.com>
Diff between conformal versions 0.1 dated 2015-01-21 and 0.2 dated 2016-03-07
DESCRIPTION | 14 +++--- MD5 | 22 +++++---- NAMESPACE | 32 ++++++++++---- R/ConformalClassification.R | 4 - R/ConformalRegression.R | 4 - R/misc.R | 6 +- data/LogS.RData |binary man/ConformalRegression.Rd | 5 ++ man/conformal.Rd | 26 +++++++---- man/figures/classificationScheme.pdf |binary man/figures/classificationScheme.svg | 78 +++++++++++++++++++++-------------- man/figures/regressionScheme.pdf |only man/figures/regressionScheme.svg |only 13 files changed, 119 insertions(+), 72 deletions(-)
Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.0.2 dated 2016-02-06 and 1.0.3 dated 2016-03-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ R/cdfquantreg.R | 2 +- R/qrPlot.R | 11 +++++------ build/vignette.rds |binary 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Assertions to Check Types of Variables
Description: A set of predicates and assertions for checking the types of
variables. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.types versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2016-03-07
DESCRIPTION | 24 MD5 | 77 +-- NAMESPACE | 13 NEWS | 3 R/assert-is-a-type.R | 195 ++++--- R/assert-is-formula.R |only R/assert-is-type-base.R | 713 ++++++++++++++-------------- R/is-a-type.R | 196 ++++--- R/is-formula.R |only R/is-type-base.R | 997 ++++++++++++++++++++-------------------- README.md | 120 ++-- man/assert_is_all_of.Rd | 2 man/is_array.Rd | 4 man/is_character.Rd | 13 man/is_class.Rd | 6 man/is_complex.Rd | 6 man/is_data.frame.Rd | 8 man/is_data.table.Rd | 6 man/is_date.Rd | 6 man/is_environment.Rd | 4 man/is_factor.Rd | 4 man/is_formula.Rd |only man/is_function.Rd | 6 man/is_inherited_from.Rd | 5 man/is_integer.Rd | 8 man/is_language.Rd | 6 man/is_leaf.Rd | 4 man/is_list.Rd | 4 man/is_logical.Rd | 6 man/is_numeric.Rd | 36 + man/is_qr.Rd | 4 man/is_raster.Rd | 8 man/is_raw.Rd | 8 man/is_relistable.Rd | 6 man/is_s4.Rd | 4 man/is_table.Rd | 4 man/is_tbl.Rd | 6 man/is_try_error.Rd | 6 man/is_ts.Rd | 4 tests/testthat.R | 6 tests/testthat/test-is-a-type.R | 17 41 files changed, 1324 insertions(+), 1221 deletions(-)
More information about assertive.types at CRAN
Permanent link
Title: Structural Equation Modelling in R with OpenMx
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.1.1 dated 2016-02-07 and 1.1.5 dated 2016-03-06
umx-1.1.1/umx/man/umxReRun.Rd |only umx-1.1.1/umx/man/umxStandardizeModel.Rd |only umx-1.1.1/umx/man/umx_SQL_from_Excel.Rd |only umx-1.1.1/umx/tests |only umx-1.1.5/umx/DESCRIPTION | 14 +- umx-1.1.5/umx/MD5 | 159 +++++++++++------------- umx-1.1.5/umx/NAMESPACE | 7 - umx-1.1.5/umx/NEWS | 6 umx-1.1.5/umx/R/build_run_modify.r | 140 ++++++++++----------- umx-1.1.5/umx/R/datasets_openmx.R |only umx-1.1.5/umx/R/deprecated.r | 4 umx-1.1.5/umx/R/fit_and_reporting.r | 179 ++++++++-------------------- umx-1.1.5/umx/R/misc_and_utility.r | 169 ++++++++++++++++++-------- umx-1.1.5/umx/R/xmu.r | 22 +++ umx-1.1.5/umx/README.md | 1 umx-1.1.5/umx/data/ex9_6.rda |only umx-1.1.5/umx/inst/CITATION | 38 +++++ umx-1.1.5/umx/man/RMSEA.MxModel.Rd | 4 umx-1.1.5/umx/man/RMSEA.Rd | 4 umx-1.1.5/umx/man/RMSEA.summary.mxmodel.Rd | 4 umx-1.1.5/umx/man/confint.MxModel.Rd | 4 umx-1.1.5/umx/man/dl_from_dropbox.Rd | 6 umx-1.1.5/umx/man/ex9_6.Rd |only umx-1.1.5/umx/man/extractAIC.MxModel.Rd | 4 umx-1.1.5/umx/man/getOpenMx.Rd |only umx-1.1.5/umx/man/logLik.Rd | 4 umx-1.1.5/umx/man/plot.MxModel.Rd | 4 umx-1.1.5/umx/man/residuals.MxModel.Rd | 4 umx-1.1.5/umx/man/umx-deprecated.Rd | 4 umx-1.1.5/umx/man/umx.Rd | 12 - umx-1.1.5/umx/man/umxACE.Rd | 3 umx-1.1.5/umx/man/umxCI.Rd | 4 umx-1.1.5/umx/man/umxCI_boot.Rd | 4 umx-1.1.5/umx/man/umxCP.Rd | 3 umx-1.1.5/umx/man/umxCompare.Rd | 8 - umx-1.1.5/umx/man/umxDiagnose.Rd | 4 umx-1.1.5/umx/man/umxExpCov.Rd | 4 umx-1.1.5/umx/man/umxExpMeans.Rd | 4 umx-1.1.5/umx/man/umxFactor.Rd | 7 - umx-1.1.5/umx/man/umxFitIndices.Rd | 4 umx-1.1.5/umx/man/umxFixAll.Rd | 1 umx-1.1.5/umx/man/umxGxE.Rd | 3 umx-1.1.5/umx/man/umxIP.Rd | 1 umx-1.1.5/umx/man/umxLabel.Rd | 4 umx-1.1.5/umx/man/umxLatent.Rd | 4 umx-1.1.5/umx/man/umxModify.Rd |only umx-1.1.5/umx/man/umxPath.Rd | 26 ++-- umx-1.1.5/umx/man/umxPlotACE.Rd | 4 umx-1.1.5/umx/man/umxPlotACEcov.Rd | 4 umx-1.1.5/umx/man/umxRAM.Rd | 6 umx-1.1.5/umx/man/umxRun.Rd | 4 umx-1.1.5/umx/man/umxSetParameters.Rd | 4 umx-1.1.5/umx/man/umxSummary.MxModel.Rd | 9 + umx-1.1.5/umx/man/umxSummaryACE.Rd | 14 +- umx-1.1.5/umx/man/umxSummaryACEcov.Rd | 3 umx-1.1.5/umx/man/umxSummaryCP.Rd | 6 umx-1.1.5/umx/man/umxSummaryGxE.Rd | 6 umx-1.1.5/umx/man/umxSummaryIP.Rd | 6 umx-1.1.5/umx/man/umxThresholdMatrix.Rd | 4 umx-1.1.5/umx/man/umxValues.Rd | 6 umx-1.1.5/umx/man/umx_check_parallel.Rd | 2 umx-1.1.5/umx/man/umx_drop_ok.Rd | 4 umx-1.1.5/umx/man/umx_fix_first_loadings.Rd | 4 umx-1.1.5/umx/man/umx_fix_latents.Rd | 4 umx-1.1.5/umx/man/umx_get_checkpoint.Rd | 1 umx-1.1.5/umx/man/umx_get_cores.Rd | 1 umx-1.1.5/umx/man/umx_get_optimizer.Rd | 1 umx-1.1.5/umx/man/umx_move_file.Rd | 4 umx-1.1.5/umx/man/umx_open.Rd | 4 umx-1.1.5/umx/man/umx_rename_file.Rd | 3 umx-1.1.5/umx/man/umx_set_auto_plot.Rd |only umx-1.1.5/umx/man/umx_set_auto_run.Rd | 1 umx-1.1.5/umx/man/umx_set_checkpoint.Rd | 1 umx-1.1.5/umx/man/umx_set_cores.Rd | 1 umx-1.1.5/umx/man/umx_set_optimizer.Rd | 1 umx-1.1.5/umx/man/umx_sql_from_excel.Rd |only umx-1.1.5/umx/man/umx_standardize_RAM.Rd |only umx-1.1.5/umx/man/umx_time.Rd | 16 +- 78 files changed, 531 insertions(+), 470 deletions(-)
Title: Function for Converting Cardinal to Ordinal Numbers by Adding a
Language Specific Ordinal Indicator to the Number
Description: Function for converting cardinal to ordinal numbers by adding a language specific ordinal indicator (http://en.wikipedia.org/wiki/Ordinal_indicator) to the number.
Author: Damian W. Betebenner [aut, cre],
Andrew Martin [ctb],
Jeff Erickson [ctb]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between toOrdinal versions 0.0-4 dated 2015-07-24 and 0.0-6 dated 2016-03-06
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/toOrdinal.R | 16 ++++++++-------- inst/CITATION | 8 ++++---- inst/NEWS | 8 ++++++++ man/toOrdinal-package.Rd | 4 ++-- tests/testthat/test_toOrdinal_english.R | 17 ++++++++--------- tests/testthat/test_toOrdinal_swedish.R | 21 ++++++++++----------- 8 files changed, 51 insertions(+), 45 deletions(-)
Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression',
specialised for modelling the association between a HPO-encoded phenotype
and binary genotype. A `no association' model is compared with one in which
the log odds of having a rare genotype is linked to the semantic similarity
between patient phenotype and a latent characteristic phenotype. The method
estimates the probability of an association together with an HPO-coded phenotype
characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 1.3 dated 2016-01-13 and 1.4 dated 2016-03-06
SimReg-1.3/SimReg/inst/doc/SimReg-guide.R |only SimReg-1.3/SimReg/inst/doc/SimReg-guide.Rmd |only SimReg-1.3/SimReg/inst/doc/SimReg-guide.html |only SimReg-1.3/SimReg/inst/examples |only SimReg-1.3/SimReg/vignettes/SimReg-guide.Rmd |only SimReg-1.4/SimReg/DESCRIPTION | 8 SimReg-1.4/SimReg/MD5 | 71 - SimReg-1.4/SimReg/NAMESPACE | 20 SimReg-1.4/SimReg/R/functions.R | 192 ++- SimReg-1.4/SimReg/R/generics.R |only SimReg-1.4/SimReg/R/multiSimReg.R |only SimReg-1.4/SimReg/R/plots.R | 52 SimReg-1.4/SimReg/R/simReg.R | 631 ++++++++-- SimReg-1.4/SimReg/build/vignette.rds |binary SimReg-1.4/SimReg/inst/doc/SimReg-Indroduction.R |only SimReg-1.4/SimReg/inst/doc/SimReg-Indroduction.Rmd |only SimReg-1.4/SimReg/inst/doc/SimReg-Indroduction.html |only SimReg-1.4/SimReg/inst/doc/SimReg-Priors.R |only SimReg-1.4/SimReg/inst/doc/SimReg-Priors.Rmd |only SimReg-1.4/SimReg/inst/doc/SimReg-Priors.html |only SimReg-1.4/SimReg/man/P-open-paren-gamma-equals-1-close-paren.Rd |only SimReg-1.4/SimReg/man/P_y_given_x.Rd |only SimReg-1.4/SimReg/man/SimReg-package.Rd | 4 SimReg-1.4/SimReg/man/acceptance_traces.Rd |only SimReg-1.4/SimReg/man/as.data.frame.sim_reg_summary.Rd |only SimReg-1.4/SimReg/man/final_sample.Rd |only SimReg-1.4/SimReg/man/log_odds_trace.Rd | 10 SimReg-1.4/SimReg/man/multi_sim_reg.Rd |only SimReg-1.4/SimReg/man/plot.sim_reg_samples.Rd |only SimReg-1.4/SimReg/man/plot.sim_reg_summary.Rd |only SimReg-1.4/SimReg/man/print.sim_reg_samples.Rd |only SimReg-1.4/SimReg/man/print.sim_reg_summary.Rd |only SimReg-1.4/SimReg/man/s.Rd |only SimReg-1.4/SimReg/man/s_phi.Rd |only SimReg-1.4/SimReg/man/s_x.Rd |only SimReg-1.4/SimReg/man/sim_reg.Rd | 70 - SimReg-1.4/SimReg/man/sim_reg_mc.Rd |only SimReg-1.4/SimReg/man/subset_sim_reg_samples.Rd |only SimReg-1.4/SimReg/man/summary.sim_reg_samples.Rd |only SimReg-1.4/SimReg/src/Chain.cpp | 103 + SimReg-1.4/SimReg/src/Chain.h | 3 SimReg-1.4/SimReg/src/HPO.cpp | 29 SimReg-1.4/SimReg/src/RcppExports.cpp | 43 SimReg-1.4/SimReg/src/RcppExports.h | 8 SimReg-1.4/SimReg/src/Similarity.cpp | 43 SimReg-1.4/SimReg/src/Similarity.h | 6 SimReg-1.4/SimReg/src/State.cpp | 21 SimReg-1.4/SimReg/src/State.h | 8 SimReg-1.4/SimReg/src/Update.cpp | 101 - SimReg-1.4/SimReg/src/Update.h | 22 SimReg-1.4/SimReg/vignettes/SimReg-Indroduction.Rmd |only SimReg-1.4/SimReg/vignettes/SimReg-Priors.Rmd |only 52 files changed, 1051 insertions(+), 394 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.5-10 dated 2015-12-10 and 0.5-20 dated 2016-03-06
DESCRIPTION | 8 +++---- MD5 | 52 ++++++++++++++++++++++++++---------------------- NAMESPACE | 12 +++++------ R/contMap.R | 6 +++-- R/cophylo.R | 4 ++- R/densityMap.R | 14 +++++++----- R/densityTree.R |only R/dotTree.R |only R/fitPagel.R | 20 ++++++++---------- R/map.to.singleton.R | 12 ++++++++++- R/phenogram.R | 35 +++++++++++++++++++++++++------- R/phylo.heatmap.R |only R/plotBranchbyTrait.R | 8 ++++++- R/plotSimmap.R | 9 +++----- R/read.newick.R | 8 +++---- R/utilities.R | 27 ++++++++++++++++-------- man/add.color.bar.Rd | 2 - man/contMap.Rd | 2 - man/cophylo.Rd | 2 - man/densityMap.Rd | 2 - man/densityTree.Rd |only man/dotTree.Rd |only man/fitMk.Rd | 2 - man/fitPagel.Rd | 5 ++-- man/map.to.singleton.Rd | 4 ++- man/nodeHeights.Rd | 7 +++--- man/phenogram.Rd | 2 - man/phylo.heatmap.Rd |only man/read.newick.Rd | 3 +- man/reroot.Rd | 4 +-- 30 files changed, 155 insertions(+), 95 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between mvSLOUCH versions 1.2.2 dated 2016-02-02 and 1.3 dated 2016-03-06
DESCRIPTION | 6 +- MD5 | 13 ++--- R/simulVasicekprocphyl.R | 98 +++++++++++++++++++++++++++------------ R/wrappers.R | 31 +++++++++--- man/drawPhylProcess.Rd |only man/simulBMProcPhylTree.Rd | 40 ++++++++++++++- man/simulMVSLOUCHProcPhylTree.Rd | 42 ++++++++++++++-- man/simulOUCHProcPhylTree.Rd | 42 +++++++++++++++- 8 files changed, 214 insertions(+), 58 deletions(-)
Title: Multilocus Random Mixed Linear Model for Genome-Wide Association
Study
Description: Conduct multi-locus random-SNP-effect mixed linear model analysis for genome-wide association study. First, each marker is scanned using random-SNP-effect mixed linear model method. Then, all the markers selected from the first step are included in the multi-locus model and their effects are estimated by an EM empirical Bayes method. No multiple test correction is needed.
Author: Wenlong Ren,Shibo Wang and Yuanming Zhang
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM versions 1.0 dated 2016-02-26 and 1.1 dated 2016-03-06
DESCRIPTION | 8 MD5 | 8 R/mrMLM.R | 382 ++++++++++++++++++++++++++++++++++------------- inst/doc/Instruction.pdf |binary man/mrMLM-package.Rd | 4 5 files changed, 293 insertions(+), 109 deletions(-)
Title: Linear Mixed Effect Model Splines for Modelling and Analysis of
Time Course Data
Description: Linear Mixed effect Model Splines ('lmms') implements linear mixed
effect model splines for modelling and differential expression for highly
dimensional data sets: investNoise() for quality control and filterNoise() for
removing non-informative trajectories; lmmSpline() to model time course expression
profiles and lmmsDE() performs differential expression analysis to identify
differential expression between groups, time and/or group x time interaction.
Author: Jasmin Straube [aut, cre],
Kim-Anh Le Cao [aut],
Emma Huang [aut],
Dominique Gorse [ctb]
Maintainer: Jasmin Straube <j.straube@qfab.org>
Diff between lmms versions 1.3 dated 2015-07-17 and 1.3.3 dated 2016-03-06
DESCRIPTION | 30 +++++++------- MD5 | 60 ++++++++++++++-------------- NAMESPACE | 25 +++++++----- R/deriv.lmmspline-method.R | 24 ++--------- R/filterNoise-method.R | 2 R/investNoise-method.R | 37 +++++++++-------- R/lmmSpline-method.R | 81 ++++++++++++++++++++------------------- R/lmmsDE-method.R | 26 +++++------- R/plot.lmmsde-method.R | 87 ++++++++++++++++++++++++------------------ R/plot.lmmspline-method.R | 67 ++++++++++++++++++-------------- R/plot.noise-method.R | 6 +- R/predict.lmmspline-method.R | 5 -- R/summary.lmmsde-methods.R | 2 data/kidneySimTimeGroup.RData |binary man/deriv.lmmspline.Rd | 6 -- man/filterNoise-methods.Rd | 10 ++-- man/investNoise-methods.Rd | 12 +---- man/lmmSpline-methods.Rd | 41 ++++++++----------- man/lmms-class.Rd | 2 man/lmms-package.Rd | 6 +- man/lmmsDE-methods.Rd | 6 +- man/lmmsde-class.Rd | 2 man/lmmspline-class.Rd | 2 man/noise-class.Rd | 2 man/plot.lmmsde.Rd | 10 ++-- man/plot.lmmspline.Rd | 16 +++---- man/plot.noise.Rd | 2 man/predict.lmmspline.Rd | 2 man/summary.lmmsde.Rd | 4 - man/summary.lmmspline.Rd | 2 man/summary.noise.Rd | 2 31 files changed, 290 insertions(+), 289 deletions(-)
Title: Various R Functions from the Kostas Lab
Description: A collection of R functions of common use in
the Kostas Lab for microbial ecology.
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.0.0 dated 2016-01-12 and 1.0.1 dated 2016-03-06
DESCRIPTION | 4 +-- MD5 | 12 +++++----- R/recplot2.R | 46 +++++++++++++++++++++++++++++++----------- README.md | 39 +++++++++++++++++++++-------------- man/enve.recplot2.Rd | 4 ++- man/enve.recplot2.__counts.Rd | 2 - man/plot.enve.RecPlot2.Rd | 5 ++-- 7 files changed, 73 insertions(+), 39 deletions(-)
Title: Mean and Variance Modeling of Count Data
Description: Modeling under- and over-dispersed count data using extended Poisson process models (EPPM).
Author: David M Smith, Malcolm J Faddy
Maintainer: David M. Smith <david.m.smith@truvenhealth.com>
Diff between CountsEPPM versions 2.0 dated 2014-11-01 and 2.1 dated 2016-03-06
CountsEPPM-2.0/CountsEPPM/R/CountsEPPM.distribution.R |only CountsEPPM-2.0/CountsEPPM/R/CountsEPPM.summary.R |only CountsEPPM-2.0/CountsEPPM/man/CountsEPPM.distribution.Rd |only CountsEPPM-2.0/CountsEPPM/man/CountsEPPM.summary.Rd |only CountsEPPM-2.1/CountsEPPM/DESCRIPTION | 14 +-- CountsEPPM-2.1/CountsEPPM/MD5 | 59 +++++++------- CountsEPPM-2.1/CountsEPPM/NAMESPACE | 3 CountsEPPM-2.1/CountsEPPM/R/CountsEPPM.R | 1 CountsEPPM-2.1/CountsEPPM/R/distribution.CountsEPPM.R |only CountsEPPM-2.1/CountsEPPM/R/logLik.CountsEPPM.R |only CountsEPPM-2.1/CountsEPPM/R/summary.CountsEPPM.R |only CountsEPPM-2.1/CountsEPPM/build |only CountsEPPM-2.1/CountsEPPM/data/Luningetal.litters.rda |binary CountsEPPM-2.1/CountsEPPM/data/Titanic.survivors.case.rda |binary CountsEPPM-2.1/CountsEPPM/data/Williams.litters.rda |binary CountsEPPM-2.1/CountsEPPM/data/ceriodaphnia.group.rda |binary CountsEPPM-2.1/CountsEPPM/data/herons.group.rda |binary CountsEPPM-2.1/CountsEPPM/data/takeover.bids.case.rda |binary CountsEPPM-2.1/CountsEPPM/man/CountsEPPM-package.Rd | 19 ++-- CountsEPPM-2.1/CountsEPPM/man/CountsEPPM.Rd | 16 ++- CountsEPPM-2.1/CountsEPPM/man/EPPMprob.Rd | 4 CountsEPPM-2.1/CountsEPPM/man/F.Regression.Counts.Rd | 4 CountsEPPM-2.1/CountsEPPM/man/Faddyprob.general.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/Faddyprob.limiting.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/LL.Regression.Counts.Rd | 4 CountsEPPM-2.1/CountsEPPM/man/Luningetal.litters.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/Model.Counts.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/Model.Faddy.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/Model.FaddyJMV.general.Rd | 4 CountsEPPM-2.1/CountsEPPM/man/Model.FaddyJMV.limiting.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/ceriodaphnia.group.Rd | 6 - CountsEPPM-2.1/CountsEPPM/man/distribution.CountsEPPM.Rd |only CountsEPPM-2.1/CountsEPPM/man/herons.group.Rd | 3 CountsEPPM-2.1/CountsEPPM/man/logLik.CountsEPPM.Rd |only CountsEPPM-2.1/CountsEPPM/man/summary.CountsEPPM.Rd |only CountsEPPM-2.1/CountsEPPM/man/takeover.bids.case.Rd | 8 - 36 files changed, 94 insertions(+), 69 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <oswaldosant@gmail.com>
Diff between capm versions 0.9.0 dated 2015-12-06 and 0.9.1 dated 2016-03-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 5 +++-- NEWS | 8 ++++++++ R/capm-package.R | 8 +++++--- inst/CITATION | 2 +- man/capm-package.Rd | 4 ++-- 7 files changed, 29 insertions(+), 18 deletions(-)
Title: A Lightweight Core of the 'assertive' Package
Description: A minimal set of predicates and assertions used by the assertive
package. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre],
Sunkyu Choi [trl],
Ivanka Skakun [trl],
Gergely Dar<c3><b3>czi [trl],
Anton Antonov [trl],
Hisham Ben Hamidane [trl],
Anja Billing [trl],
Aditya Bhagwat [trl],
Rasmus B<c3><a5><c3><a5>th [trl],
Mine Cetinkaya-Rundel [trl],
Aspasia Chatziefthymiou [trl]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.base versions 0.0-3 dated 2015-10-08 and 0.0-4 dated 2016-03-06
assertive.base-0.0-3/assertive.base/man/print_and_capture.Rd |only assertive.base-0.0-3/assertive.base/man/truncate.Rd |only assertive.base-0.0-4/assertive.base/DESCRIPTION | 15 assertive.base-0.0-4/assertive.base/MD5 | 81 ++-- assertive.base-0.0-4/assertive.base/NAMESPACE | 116 ++--- assertive.base-0.0-4/assertive.base/NEWS | 3 assertive.base-0.0-4/assertive.base/R/are-identical.R | 160 ++++---- assertive.base-0.0-4/assertive.base/R/assert-are-identical.R | 122 +++--- assertive.base-0.0-4/assertive.base/R/assert-identical-to-true-false-na.R | 20 - assertive.base-0.0-4/assertive.base/R/cause.R | 24 - assertive.base-0.0-4/assertive.base/R/coercion.R | 2 assertive.base-0.0-4/assertive.base/R/engine.R | 17 assertive.base-0.0-4/assertive.base/R/internal.R | 24 + assertive.base-0.0-4/assertive.base/R/utils.R | 138 +++++-- assertive.base-0.0-4/assertive.base/R/zzz.R |only assertive.base-0.0-4/assertive.base/README.md | 194 +++++----- assertive.base-0.0-4/assertive.base/inst/po/kr |only assertive.base-0.0-4/assertive.base/inst/po/ua |only assertive.base-0.0-4/assertive.base/man/Truth.Rd | 58 +- assertive.base-0.0-4/assertive.base/man/are_identical.Rd | 128 +++--- assertive.base-0.0-4/assertive.base/man/assert_engine.Rd | 11 assertive.base-0.0-4/assertive.base/man/assertionError.Rd | 98 ++--- assertive.base-0.0-4/assertive.base/man/bapply.Rd | 4 assertive.base-0.0-4/assertive.base/man/call_and_name.Rd | 6 assertive.base-0.0-4/assertive.base/man/cause.Rd | 2 assertive.base-0.0-4/assertive.base/man/coerce_to.Rd | 14 assertive.base-0.0-4/assertive.base/man/dont_stop.Rd | 30 - assertive.base-0.0-4/assertive.base/man/false.Rd | 2 assertive.base-0.0-4/assertive.base/man/get_name_in_parent.Rd | 2 assertive.base-0.0-4/assertive.base/man/is2.Rd | 6 assertive.base-0.0-4/assertive.base/man/merge.list.Rd | 21 - assertive.base-0.0-4/assertive.base/man/merge_dots_with_list.Rd | 19 assertive.base-0.0-4/assertive.base/man/na.Rd | 2 assertive.base-0.0-4/assertive.base/man/parenthesize.Rd | 14 assertive.base-0.0-4/assertive.base/man/print.vector_with_cause.Rd | 6 assertive.base-0.0-4/assertive.base/man/set_cause.Rd | 18 assertive.base-0.0-4/assertive.base/man/strip_attributes.Rd | 2 assertive.base-0.0-4/assertive.base/man/type_description.Rd | 2 assertive.base-0.0-4/assertive.base/man/use_first.Rd | 11 assertive.base-0.0-4/assertive.base/po/R-assertive.base.pot | 190 ++++----- assertive.base-0.0-4/assertive.base/po/R-kr.po |only assertive.base-0.0-4/assertive.base/po/R-ua.po |only assertive.base-0.0-4/assertive.base/tests/testthat.R | 6 assertive.base-0.0-4/assertive.base/tests/testthat/test-are-identical.R | 26 - assertive.base-0.0-4/assertive.base/tests/testthat/test-utils.R | 36 + 45 files changed, 899 insertions(+), 731 deletions(-)
More information about assertive.base at CRAN
Permanent link
Title: Plant Root System Architecture Analysis Using DART and RSML
Files
Description: Analysis of complex plant root system architectures (RSA) using the output files created by Data Analysis of Root Tracings (DART), an open-access software dedicated to the study of plant root architecture and development across time series (Le Bot et al (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, DOI: 10.1007/s11104-009-0005-2), and RSA data encoded with the Root System Markup Language (RSML) (Lobet et al (2015) Root System Markup Language: toward a unified root architecture description language, Plant Physiology, DOI: 10.1104/pp.114.253625). More information can be found in Delory et al (2016) archiDART: an R package for the automated computation of plant root architectural traits, Plant and Soil, DOI: 10.1007/s11104-015-2673-4.
Author: Benjamin M Delory, Caroline Baudson, Yves Brostaux, Guillaume Lobet, Patrick du Jardin, Loic Pages, Pierre Delaplace
Maintainer: Benjamin M Delory <Benjamin.Delory@leuphana.de>
Diff between archiDART versions 1.2 dated 2015-12-22 and 1.3 dated 2016-03-06
DESCRIPTION | 10 - MD5 | 16 +- R/rsmlToDART.R | 391 +++++++++++++++++++----------------------------------- R/xnodes.R |only R/ynodes.R |only man/archidraw.Rd | 4 man/archigrow.Rd | 4 man/architect.Rd | 4 man/latdist.Rd | 4 man/trajectory.Rd | 4 10 files changed, 168 insertions(+), 269 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files, sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.4.0 dated 2016-02-03 and 3.5.0 dated 2016-03-06
R.matlab-3.4.0/R.matlab/tests/octave-bug42562-empty.mat |only R.matlab-3.4.0/R.matlab/tests/octave-bug42562-scalar.mat |only R.matlab-3.4.0/R.matlab/tests/octave-bug42562-vector.mat |only R.matlab-3.5.0/R.matlab/DESCRIPTION | 14 R.matlab-3.5.0/R.matlab/MD5 | 22 - R.matlab-3.5.0/R.matlab/NEWS | 12 R.matlab-3.5.0/R.matlab/R/999.package.R | 2 R.matlab-3.5.0/R.matlab/R/readMat.R | 208 ++-------- R.matlab-3.5.0/R.matlab/inst/externals/MatlabServer.m | 24 - R.matlab-3.5.0/R.matlab/inst/mat-files/datetime,arraytype=17-v5.mat |only R.matlab-3.5.0/R.matlab/man/1._The_MATLAB_server_running_in_MATLAB.Rd | 24 - R.matlab-3.5.0/R.matlab/man/Matlab.Rd | 2 R.matlab-3.5.0/R.matlab/man/R.matlab-package.Rd | 4 R.matlab-3.5.0/R.matlab/man/readMat.Rd | 18 14 files changed, 110 insertions(+), 220 deletions(-)
Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rlist versions 0.4.5.1 dated 2015-09-09 and 0.4.6 dated 2016-03-06
DESCRIPTION | 9 +- MD5 | 144 ++++++++++++++++++++++---------------------- NAMESPACE | 3 NEWS | 2 R/list.clean.R | 15 ++-- R/list.common.R | 19 ++++- R/list.expand.R |only R/list.table.R | 11 ++- README.md | 2 man/List.Rd | 2 man/list.all.Rd | 2 man/list.any.Rd | 2 man/list.append.Rd | 2 man/list.apply.Rd | 2 man/list.cases.Rd | 2 man/list.cbind.Rd | 2 man/list.class.Rd | 2 man/list.clean.Rd | 14 ++-- man/list.common.Rd | 6 - man/list.count.Rd | 2 man/list.do.Rd | 2 man/list.exclude.Rd | 2 man/list.expand.Rd |only man/list.extract.Rd | 2 man/list.filter.Rd | 2 man/list.find.Rd | 2 man/list.findi.Rd | 2 man/list.first.Rd | 2 man/list.flatten.Rd | 2 man/list.group.Rd | 2 man/list.insert.Rd | 2 man/list.is.Rd | 2 man/list.iter.Rd | 2 man/list.join.Rd | 2 man/list.last.Rd | 2 man/list.load.Rd | 2 man/list.map.Rd | 2 man/list.maps.Rd | 2 man/list.mapv.Rd | 2 man/list.match.Rd | 2 man/list.merge.Rd | 2 man/list.names.Rd | 2 man/list.order.Rd | 2 man/list.parse.Rd | 2 man/list.prepend.Rd | 2 man/list.rbind.Rd | 2 man/list.remove.Rd | 2 man/list.reverse.Rd | 2 man/list.sample.Rd | 2 man/list.save.Rd | 2 man/list.search.Rd | 2 man/list.select.Rd | 2 man/list.serialize.Rd | 2 man/list.skip.Rd | 2 man/list.skipWhile.Rd | 2 man/list.sort.Rd | 2 man/list.stack.Rd | 2 man/list.subset.Rd | 2 man/list.table.Rd | 6 + man/list.take.Rd | 2 man/list.takeWhile.Rd | 2 man/list.ungroup.Rd | 2 man/list.unserialize.Rd | 2 man/list.unzip.Rd | 2 man/list.update.Rd | 2 man/list.which.Rd | 2 man/list.zip.Rd | 2 man/nyweather.Rd | 2 man/rlist-package.Rd | 2 man/subset.list.Rd | 2 man/tryEval.Rd | 2 man/tryGet.Rd | 2 tests/testthat/test-List.R | 2 tests/testthat/test-basic.R | 9 ++ 74 files changed, 196 insertions(+), 164 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
is more familiar to experienced R users. Also, implements various functions
related to topic modeling. It works well with with the "lda" package by J.
Chang.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 1.5.1 dated 2015-12-31 and 1.6.0 dated 2016-03-06
DESCRIPTION | 11 +++- MD5 | 32 ++++++------- R/CalcLikelihood.R | 12 +++-- R/CalcTopicModelR2.R | 13 +++-- R/DepluralizeDtm.R | 14 ++++-- R/Dtm2Docs.R | 10 +++- R/Files2Vec.R | 11 +++- R/ProbCoherence.R | 3 - R/TmParallelApply.R | 110 +++++++++++++++++++++++++++--------------------- R/Vec2Dtm.R | 5 +- README.md | 62 ++++++++++++++++----------- man/CalcLikelihood.Rd | 10 +++- man/CalcTopicModelR2.Rd | 10 +++- man/DepluralizeDtm.Rd | 10 +++- man/Dtm2Docs.Rd | 10 +++- man/Files2Vec.Rd | 10 +++- man/TmParallelApply.Rd | 6 ++ 17 files changed, 220 insertions(+), 119 deletions(-)
Title: XML-RPC Interface to NEOS
Description: Within this package the XML-RPC API to NEOS is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between rneos versions 0.2-8 dated 2014-12-28 and 0.3-1 dated 2016-03-06
DESCRIPTION | 16 +-- MD5 | 52 +++++----- man/CreateNeosComm.Rd | 6 - man/CreateXmlString.Rd | 130 +++++++++++++-------------- man/NemailHelp.Rd | 94 +++++++++---------- man/NeosAns-class.Rd | 6 - man/NeosComm-class.Rd | 2 man/NeosJob-class.Rd | 6 - man/NeosOff-class.Rd | 6 - man/NeosXml-class.Rd | 6 - man/NgetFinalResults.Rd | 128 +++++++++++++------------- man/NgetFinalResultsNonBlocking.Rd | 130 +++++++++++++-------------- man/NgetIntermediateResults.Rd | 142 ++++++++++++++--------------- man/NgetIntermediateResultsNonBlocking.Rd | 144 +++++++++++++++--------------- man/NgetJobInfo.Rd | 128 +++++++++++++------------- man/NgetJobStatus.Rd | 128 +++++++++++++------------- man/NgetSolverTemplate.Rd | 102 ++++++++++----------- man/Nhelp.Rd | 98 ++++++++++---------- man/NkillJob.Rd | 90 +++++++++--------- man/NlistAllSolvers.Rd | 96 ++++++++++---------- man/NlistCategories.Rd | 96 ++++++++++---------- man/NlistServersInCategory.Rd | 106 +++++++++++----------- man/Nping.Rd | 100 ++++++++++---------- man/NprintQueue.Rd | 98 ++++++++++---------- man/NsubmitJob.Rd | 90 +++++++++--------- man/Nversion.Rd | 100 ++++++++++---------- man/Nwelcome.Rd | 98 ++++++++++---------- 27 files changed, 1099 insertions(+), 1099 deletions(-)
Title: Gene and Splice Site Annotation Using Annotation Data from
Ensembl and UCSC Genome Browsers
Description: Contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between refGenome versions 1.5.8 dated 2015-07-28 and 1.6.0 dated 2016-03-06
ChangeLog | 12 DESCRIPTION | 8 MD5 | 44 +- NAMESPACE | 1 NEWS | 24 + R/refGenome.r | 687 ++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/readGTF.pdf |binary inst/doc/refGenome.R | 35 + inst/doc/refGenome.Rnw | 10 inst/doc/refGenome.pdf |binary inst/extdata/hs.ensembl.62.small.RData |binary man/extractByGeneID.Rd |only man/extractByGeneName.Rd | 4 man/getGenePositions.Rd | 7 man/refGenome-class.Rd | 4 man/refJunctions-class.Rd | 4 man/unifyJuncs.Rd | 32 + src/refGenome.cpp | 364 +++++++++-------- src/refGenome.h | 4 tests/test-all.R | 2 tests/test_overlap_juncs.r | 18 tests/test_unify_juncs.r |only vignettes/refGenome.Rnw | 10 24 files changed, 771 insertions(+), 499 deletions(-)
Title: Robust Data Envelopment Analysis (DEA) for R
Description: Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Author: Jaak Simm [aut, cre],
Galina Besstremyannaya [aut]
Maintainer: Jaak Simm <jaak.simm@gmail.com>
Diff between rDEA versions 1.2-2 dated 2015-08-04 and 1.2-3 dated 2016-03-06
rDEA-1.2-2/rDEA/src/tags |only rDEA-1.2-3/rDEA/DESCRIPTION | 6 +++--- rDEA-1.2-3/rDEA/MD5 | 11 +++++------ rDEA-1.2-3/rDEA/R/dea.env.robust.R | 14 ++++++++------ rDEA-1.2-3/rDEA/inst/CHANGELOG | 4 ++++ rDEA-1.2-3/rDEA/inst/tests/testthat/test-bootstrap.r | 6 +++--- rDEA-1.2-3/rDEA/man/dea_env_robust.Rd | 4 ++-- 7 files changed, 25 insertions(+), 20 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen, Kathleen Gates, and Mikko Rönkkö.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.5 dated 2016-03-04 and 0.4.6 dated 2016-03-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/miive.R | 4 ++-- R/miivs.R | 48 ++++++++++++++++++++++++++++++++++++++---------- R/print.miive.R | 2 +- 5 files changed, 48 insertions(+), 20 deletions(-)
Title: Eye-Tracking Data Analysis
Description: A set of tools that address tasks along the pipeline from raw
data to analysis and visualization for eye-tracking data. Offers several
popular types of analyses, including linear and growth curve time analyses,
onset-contingent reaction time analyses, as well as several non-parametric
bootstrapping approaches.
Author: Jacob Dink [aut, cre],
Brock Ferguson [aut]
Maintainer: Jacob Dink <jacobwdink@gmail.com>
Diff between eyetrackingR versions 0.1.4 dated 2016-01-26 and 0.1.5 dated 2016-03-06
DESCRIPTION | 8 - MD5 | 16 +-- NEWS.md | 3 R/time_sequence_data.R | 94 +++++++++++++++-------- inst/doc/divergence_vignette.html | 26 +++--- inst/doc/growth_curve_analysis_vignette.html | 25 ++---- inst/doc/onset_contingent_analysis_vignette.html | 23 ++--- inst/doc/preparing_your_data_vignette.html | 17 +--- inst/doc/window_analysis_vignette.html | 21 ++--- 9 files changed, 134 insertions(+), 99 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 0.1-9 dated 2015-03-09 and 0.1-12 dated 2016-03-06
deldir-0.1-12/deldir/ChangeLog | 69 ++++++++ deldir-0.1-12/deldir/DESCRIPTION | 12 - deldir-0.1-12/deldir/MD5 | 72 +++++---- deldir-0.1-12/deldir/NAMESPACE | 7 deldir-0.1-12/deldir/R/binsrt.R |only deldir-0.1-12/deldir/R/deldir.R | 139 ++++++++++++++--- deldir-0.1-12/deldir/R/divchain.R |only deldir-0.1-12/deldir/R/divchain.default.R |only deldir-0.1-12/deldir/R/divchain.deldir.R |only deldir-0.1-12/deldir/R/plot.divchain.R |only deldir-0.1-12/deldir/R/tile.list.R | 9 - deldir-0.1-12/deldir/R/triang.list.R | 16 +- deldir-0.1-12/deldir/inst/ratfor/binsrt.r | 10 - deldir-0.1-12/deldir/inst/ratfor/delout.r | 18 +- deldir-0.1-12/deldir/inst/ratfor/delseg.r | 14 - deldir-0.1-12/deldir/inst/ratfor/dirout.r | 17 +- deldir-0.1-12/deldir/inst/ratfor/dirseg.r | 22 +- deldir-0.1-12/deldir/inst/ratfor/dldins.r | 9 + deldir-0.1-12/deldir/inst/ratfor/master.r | 27 +-- deldir-0.1-12/deldir/man/deldir-internal.Rd | 4 deldir-0.1-12/deldir/man/deldir.Rd | 212 +++++++++++++++++---------- deldir-0.1-12/deldir/man/divchain.Rd |only deldir-0.1-12/deldir/man/divchain.default.Rd |only deldir-0.1-12/deldir/man/divchain.deldir.Rd |only deldir-0.1-12/deldir/man/duplicatedxy.Rd | 20 +- deldir-0.1-12/deldir/man/plot.deldir.Rd | 2 deldir-0.1-12/deldir/man/plot.divchain.Rd |only deldir-0.1-12/deldir/man/plot.tile.list.Rd | 6 deldir-0.1-12/deldir/man/plot.triang.list.Rd | 6 deldir-0.1-12/deldir/man/tile.centroids.Rd | 2 deldir-0.1-12/deldir/man/tile.list.Rd | 10 + deldir-0.1-12/deldir/man/tilePerim.Rd | 2 deldir-0.1-12/deldir/man/triMat.Rd | 2 deldir-0.1-12/deldir/man/triang.list.Rd | 32 ++-- deldir-0.1-12/deldir/src/binsrt.f | 6 deldir-0.1-12/deldir/src/delout.f | 15 - deldir-0.1-12/deldir/src/delseg.f | 14 - deldir-0.1-12/deldir/src/dirout.f | 17 +- deldir-0.1-12/deldir/src/dirseg.f | 30 ++- deldir-0.1-12/deldir/src/dldins.f | 9 + deldir-0.1-12/deldir/src/master.f | 59 +++---- deldir-0.1-9/deldir/R/declareGlobals.R |only 42 files changed, 576 insertions(+), 313 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
library. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot library.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.6.0 dated 2015-12-19 and 0.6.1 dated 2016-03-06
DESCRIPTION | 6 +-- MD5 | 59 +++++++++++++++++----------------- NAMESPACE | 1 NEWS | 6 +++ R/draw.R | 70 ++++++++++++++++++++++++++++++++++++++--- R/plot_grid.R | 2 - R/save.R | 10 ++--- R/switch_axis.R | 2 + R/themes.R | 3 + TODO | 5 ++ build/vignette.rds |binary inst/doc/axis_position.R | 22 +++++++++--- inst/doc/axis_position.Rmd | 24 ++++++++++---- inst/doc/axis_position.html | 38 ++++++++++++++-------- inst/doc/introduction.html | 36 +++++++++++---------- inst/doc/plot_annotations.html | 20 +++++------ inst/doc/plot_grid.R | 15 -------- inst/doc/plot_grid.Rmd | 19 ----------- inst/doc/plot_grid.html | 42 +++++++----------------- inst/doc/shared_legends.R | 2 - inst/doc/shared_legends.Rmd | 2 - inst/doc/shared_legends.html | 14 ++++---- man/draw_figure_label.Rd |only man/draw_line.Rd | 2 - man/draw_plot_label.Rd | 8 ++-- man/ggsave.Rd | 2 - man/plot_grid.Rd | 2 - man/save_plot.Rd | 8 ++-- vignettes/axis_position.Rmd | 24 ++++++++++---- vignettes/plot_grid.Rmd | 19 ----------- vignettes/shared_legends.Rmd | 2 - 31 files changed, 259 insertions(+), 206 deletions(-)
Title: Calculation of Thermal Comfort Indices
Description: Functions to calculate various common and less common thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and michael Kleber [ctr] and Boris Kingma [ctr] and masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>
Diff between comf versions 0.1 dated 2016-03-04 and 0.1.1 dated 2016-03-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ComfortIndices.r | 16 ++++++++-------- 3 files changed, 13 insertions(+), 13 deletions(-)
Title: Assertions to Check Properties of Strings
Description: A set of predicates and assertions for checking the properties of
strings. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.strings versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2016-03-06
DESCRIPTION | 15 ++-- MD5 | 36 ++++----- NAMESPACE | 7 + NEWS | 3 R/assert-is-empty-character.R | 18 ++++ R/assert-is-special-string.R | 41 +++++++++++ R/is-special-string.R | 31 +++++++- README.md | 102 ++++++++++++++-------------- man/character_to_list_of_integer_vectors.Rd | 2 man/create_regex.Rd | 2 man/d.Rd | 4 - man/is_empty_character.Rd | 12 ++- man/is_numeric_string.Rd | 26 ++++++- man/is_single_character.Rd | 8 +- man/matches_regex.Rd | 6 - man/recycle.Rd | 2 man/strip_invalid_chars.Rd | 8 +- tests/testthat.R | 7 - tests/testthat/test-is-special-string.R | 21 +++++ 19 files changed, 246 insertions(+), 105 deletions(-)
More information about assertive.strings at CRAN
Permanent link
Title: Assertions for Checking the State of R
Description: A set of predicates and assertions for checking the state and
capabilities of R, the operating system it is running on, and the IDE
being used. This is mainly for use by other package developers who
want to include run-time testing features in their own packages.
End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.reflection versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2016-03-06
DESCRIPTION | 13 - MD5 | 56 ++--- NAMESPACE | 342 ++++++++++++++++----------------- NEWS | 5 R/assert-r-has-capability.R | 12 - R/imports.R | 2 R/is-ide.R | 25 +- R/locale.R | 6 R/r-has-capability.R | 55 +++++ README.md | 130 ++++++------ man/is_batch_mode.Rd | 4 man/is_on_os_path.Rd | 4 man/is_package_current.Rd | 4 man/is_r.Rd | 8 man/is_r_current.Rd | 4 man/is_rstudio_current.Rd | 6 man/is_rstudio_desktop.Rd | 4 man/is_windows.Rd | 28 +- man/is_xxx_for_decimal_point.Rd | 30 +- man/locale_categories.Rd | 2 man/r_can_find_tools.Rd | 31 ++ man/r_has_jpeg_capability.Rd | 8 man/rstudio_version_info.Rd | 2 man/sys_get_locale.Rd | 12 - tests/testthat.R | 14 - tests/testthat/test-is-32-64-bit.R | 34 +-- tests/testthat/test-is-decimal-point.R | 176 ++++++++-------- tests/testthat/test-is-ide.R | 26 +- tests/testthat/test-is-r-mode.R | 82 +++---- 29 files changed, 619 insertions(+), 506 deletions(-)
More information about assertive.reflection at CRAN
Permanent link
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 0.4.3 dated 2015-11-26 and 0.4.3.1 dated 2016-03-05
ChangeLog | 5 + DESCRIPTION | 11 +- MD5 | 50 +++++----- NAMESPACE | 3 NEWS | 7 - R/0_classesAndMethods.R | 3 R/1_functions4Fitting.R | 24 ++--- data/blanden.rda |binary data/craigsendi.rda |binary data/holson.rda |binary data/preproglucacon.rda |binary data/rain.rda |binary inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/markovchainCrashIntro.pdf |binary man/randomSampler.Rd | 5 - src/2_probabilistic.cpp | 96 ++++++++++++++++---- tests/testthat/testBasic1.R | 2 tests/testthat/testHigerOrder.R | 2 tests/testthat/testInference.R | 2 tests/testthat/testMultinomCI.R | 2 tests/testthat/testParallelBootstrap.R | 2 tests/testthat/testPeriod.R | 2 tests/testthat/testPlot.R | 2 tests/testthat/testRecurrentClasses.R | 56 +++++------ tests/testthat/testetm.R | 2 tests/testthat/testmsm.R | 2 26 files changed, 176 insertions(+), 102 deletions(-)
Title: Interface to the 'HDF5' Library
Description: S4 Interface to the 'HDF5' library supporting fast storage and
retrieval of R-objects like vectors, matrices and arrays to binary files in
a language independent format. The 'HDF5' format can therefore be used as
an alternative to R's save/load mechanism. Since h5 is able to access only
subsets of stored data it can also handle data sets which do not fit into
memory.
Author: Mario Annau [aut, cre]
Maintainer: Mario Annau <mario.annau@gmail.com>
Diff between h5 versions 0.9.4 dated 2015-10-12 and 0.9.5 dated 2016-03-05
DESCRIPTION | 10 +++++----- MD5 | 38 ++++++++++++++++++++++---------------- R/Attribute.R | 2 +- R/DataSet.R | 8 ++------ R/DataSpace.R | 1 - R/H5Group.R | 2 +- inst/NEWS.Rd | 10 ++++++++++ inst/test-ascii-length-bug.h5 |only inst/test-ascii-length-bug.py |only man/Attribute.Rd | 2 +- man/DataSet.Rd | 16 ++++------------ man/DataSpace.Rd | 3 --- man/H5Group.Rd | 2 +- src/Dataset.cpp | 3 +++ src/Helpers.cpp | 2 +- tests/testthat/test-DataSet-IO.R | 15 +++++++++++++++ tests/testthat/test-DataSet.R | 2 +- tests/testthat/test-H5File.R | 12 ++++++------ tests/testthat/test-H5Group.R | 2 +- vignettes |only 20 files changed, 74 insertions(+), 56 deletions(-)
Title: Discover Probable Duplicates in Plant Genetic Resources
Collections
Description: Provides functions to aid the identification of probable/possible
duplicates in Plant Genetic Resources (PGR) collections using
'passport databases' comprising of information records of each constituent
sample. These include methods for cleaning the data, creation of a
searchable Key Word in Context (KWIC) index of keywords associated with
sample records and the identification of nearly identical records with
similar information by fuzzy, phonetic and semantic matching of keywords.
Author: J. Aravind [aut, cre],
J. Radhamani [aut],
Kalyani Srinivasan [aut],
B. Ananda Subhash [aut],
R. K. Tyagi [aut]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Diff between PGRdup versions 0.2.1 dated 2015-07-23 and 0.2.2 dated 2016-03-05
DESCRIPTION | 23 +-- MD5 | 93 +++++++------ NAMESPACE | 33 ++++ NEWS |only R/AddProbDup.R | 45 +++--- R/DataClean.R | 16 +- R/DisProbDup.R | 43 +++--- R/DoubleMetaphone.R | 18 +- R/KWCounts.R | 24 +-- R/KWIC.R | 40 ++--- R/MergeKW.R | 53 ++++--- R/MergeProbDup.R | 13 - R/PGRdup-package.R | 1 R/ParseProbDup.R | 28 ++-- R/ProbDup.R | 309 +++++++++++++++++++++++---------------------- R/ReconstructProbDup.R | 94 ++++++------- R/ReviewProbDup.R | 114 +++++++++------- R/SplitProbDup.R | 81 ++++++----- R/ValidatePrimKey.R | 18 +- R/ViewProbDup.R |only R/globals.R | 23 ++- R/print.KWIC.R | 5 R/print.ProbDup.R | 10 - R/read.genesys.R |only README.md | 26 ++- build/vignette.rds |binary inst/CITATION | 2 inst/doc/Introduction.Rmd | 178 +++++++++++++++---------- inst/doc/Introduction.pdf |binary man/AddProbDup.Rd | 58 ++++---- man/DataClean.Rd | 72 +++++----- man/DisProbDup.Rd | 42 +++--- man/DoubleMetaphone.Rd | 14 +- man/GN1000.Rd | 14 +- man/KWCounts.Rd | 32 ++-- man/KWIC.Rd | 40 ++--- man/MergeKW.Rd | 38 ++--- man/MergeProbDup.Rd | 18 +- man/PGRdup-package.Rd | 10 - man/ParseProbDup.Rd | 40 ++--- man/ProbDup.Rd | 197 ++++++++++++++-------------- man/ReconstructProbDup.Rd | 38 ++--- man/ReviewProbDup.Rd | 100 +++++++------- man/SplitProbDup.Rd | 24 +-- man/ValidatePrimKey.Rd | 36 ++--- man/ViewProbDup.Rd |only man/print.KWIC.Rd | 4 man/print.ProbDup.Rd | 4 man/read.genesys.Rd |only vignettes/Introduction.Rmd | 178 +++++++++++++++---------- 50 files changed, 1216 insertions(+), 1033 deletions(-)
Title: Format R Code Automatically
Description: Provides a function tidy_source() to format R source code. Spaces
and indent will be added to the code automatically, and comments will be
preserved under certain conditions, so that R code will be more
human-readable and tidy. There is also a Shiny app as a user interface in
this package (see tidy_app()).
Author: Yihui Xie
Maintainer: Yihui Xie <xie@yihui.name>
Diff between formatR versions 1.2.1 dated 2015-09-18 and 1.3 dated 2016-03-05
DESCRIPTION | 9 +++--- MD5 | 20 +++++++-------- NEWS | 10 +++++++ R/usage.R | 13 ++++------ R/utils.R | 8 +++--- build/vignette.rds |binary inst/doc/formatR.R | 3 ++ inst/doc/formatR.Rmd | 45 ++++++++-------------------------- inst/doc/formatR.html | 65 +++++++++++++------------------------------------- man/usage.Rd | 2 - vignettes/formatR.Rmd | 45 ++++++++-------------------------- 11 files changed, 80 insertions(+), 140 deletions(-)
Title: MA Birk's Functions
Description: Collection of tools to make R more convenient. Includes tools to
convert between units and dimensions of measurement and to summarize data
using statistics not available with base R.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between birk versions 2.0.0 dated 2016-01-18 and 2.1.0 dated 2016-03-05
DESCRIPTION | 15 +++++++-------- MD5 | 12 ++++++------ NEWS | 15 ++++----------- R/birk.R | 2 +- R/conv_unit.R | 19 ++++++++++++++----- man/birk.Rd | 2 +- man/conv_unit.Rd | 7 ++++--- 7 files changed, 37 insertions(+), 35 deletions(-)
Title: Student Growth Percentiles & Percentile Growth Trajectories
Description: Functions to calculate student growth percentiles and percentile growth projections/trajectories for students using large scale,
longitudinal assessment data. Functions use quantile regression to estimate the conditional density associated
with each student's achievement history. Percentile growth projections/trajectories are calculated using the coefficient matrices derived from
the quantile regression analyses and specify what percentile growth is required for students to reach future achievement targets.
Author: Damian W. Betebenner [aut, cre],
Adam R. Van Iwaarden [aut],
Ben Domingue [aut],
Yi Shang [aut],
Jonathan Weeks [ctb],
John Stewart [ctb],
Jinnie Choi [ctb],
Xin Wei [ctb],
Hi Shin Shim [ctb],
Xiaoyuan Tan [ctb] (Arizona Department of Education),
Carrie Giovannini [ctb] (Arizona Department of Education),
Sarah Polasky [ctb] (Arizona State University),
Rebecca Gau [ctb] (Arizona Charter School Association),
Jeffrey Dean [ctb] (University of Arkansas),
William Bonk [ctb] (Colorado Department of Education),
Marie Huchton [ctb] (Colorado Department of Education),
Allison Timberlake [ctb] (Georgia Department of Education),
Qi Qin [ctb] (Georgia Department of Education),
Melissa Fincher [ctb] (Georgia Department of Education),
Kiran Athota [ctb] (Georgia Department of Education),
Travis Allen [ctb] (Georgia Department of Education),
Glenn Hirata [ctb] (Hawaii Department of Education),
Glenn Nochi [ctb] (Hawaii Department of Education),
Joshua Lee [ctb] (Hawaii Department of Education),
Ayaka Nukui [ctb] (Idaho Department of Education),
Carissa Miller [ctb] (Idaho Department of Education),
Matthew Raimondi [ctb] (Elgin Area School District U46 (Illinois)),
Wes Bruce [ctb] (Indiana Department of Education),
Robert Hochsegang [ctb] (Indiana Department of Education),
Tony Moss [ctb] (Kansas State Department of Education),
Xuewen Sheng [ctb] (Kansas State Department of Education),
Kathy Flanagan [ctb] (Massachusetts Department of Elementary and Secondary Education),
Robert Lee [ctb] (Massachusetts Department of Elementary and Secondary Education),
Ji Zeng [ctb] (Michigan Department of Education),
Steve Viger [ctb] (Michigan Department of Education),
Joe DeCastra [ctb] (Mississippi Department of Education),
Ken Thompson [ctb] (Mississippi Department of Education),
Soo Yeon Cho [ctb] (Missouri Department of Education),
Jeff Halsell [ctb] (Clark County School District, Nevada),
Selcuk Ozdemir [ctb] (Washoe County School District, Nevada),
Roger Silva [ctb] (Nevada Department of Education),
Deb Wiswell [ctb] (New Hampshire Department of Education),
Katya Levitan-Reiner [ctb] (New Haven Public Schools),
Catherine McCaslin [ctb] (New Haven Public Schools),
Joshua Marland [ctb] (New York Education Department),
W Joshua Rew [ctb] (Oregon Department of Education),
Jason Becker [ctb] (Rhode Island Department of Education),
Jessica Bailey [ctb] (Rhode Island Department of Education),
Ana Karantonis [ctb] (Rhode Island Department of Education),
Deborah Jonas [ctb] (Virginia Department of Education),
Juan D'Brot [ctb] (West Virginia Department of Education),
Nate Hixson [ctb] (West Virginia Department of Education),
Deb Came [ctb] (Washington Office of Superintendent of Public Instruction),
Ashley Colburn [ctb] (Washington Office of Superintendent of Public Instruction),
Nick Hassell [ctb] (Washington Office of Superintendent of Public Instruction),
Krissy Johnson [ctb] (Washington Office of Superintendent of Public Instruction),
Daniel Bush [ctb] (Wisconsin Department of Education),
Justin Meyer [ctb] (Wisconsin Department of Education),
Joseph Newton [ctb] (Wisconsin Department of Education),
Nick Stroud [ctb] (Wisconsin Department of Education),
John Paul [ctb] (Wyoming Department of Education),
Michael Flicek [ctb] (Michael Flicek Projects LLC working with Wyoming Department of Education),
Phyllis Clay [ctb] (Albuquerque Public Schools),
Peter Kinyua [ctb] (Albuquerque Public Schools),
Brendan Houng [ctb] (University of Melbourne, Australia, NAPLAN),
Leslie Rosale [ctb] (Ministry of Education, Guatemala),
Nathan Wall [ctb] (eMetric working with Nevada Department of Education and South Dakota Department of Education),
Narek Sahakyan [ctb] (World Class Instruction and Design (WIDA))
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGP versions 1.4-0.0 dated 2016-01-10 and 1.5-0.0 dated 2016-03-04
DESCRIPTION | 12 - MD5 | 72 ++++--- NAMESPACE | 3 R/abcSGP.R | 11 - R/analyzeSGP.R | 54 +++-- R/createLongCutscores.R | 26 +- R/getAchievementLevel.R | 2 R/getMaxOrderForProgression.R | 9 R/getSGPColor.R |only R/getSGPConfig.R | 6 R/getStateAbbreviation.R | 4 R/gofSGP.R | 14 - R/growthAchievementPlot.R | 140 ++++++++++----- R/messageSGP.R |only R/outputSGP.R | 20 +- R/piecewiseTransform.R | 7 R/prepareSGP.R | 3 R/rliSGP.R | 52 +++-- R/startParallel.R | 1 R/studentGrowthPercentiles.R | 194 +++++++++++---------- R/studentGrowthProjections.R | 6 R/summarizeSGP.R | 6 R/summarizeSGP_Utilities.R | 2 R/testSGP.R | 365 ++++++++++++++++++++-------------------- R/transformScaleScore.R | 8 R/updateSGP.R | 10 - R/visualizeSGP.R | 34 --- R/zzz.R | 2 data/SGPstateData.rda |binary inst/CITATION | 9 inst/NEWS | 8 man/SGP-package.Rd | 4 man/abcSGP.Rd | 5 man/analyzeSGP.Rd | 3 man/growthAchievementPlot.Rd | 2 man/rliSGP.Rd | 4 man/studentGrowthPercentiles.Rd | 5 man/updateSGP.Rd | 5 38 files changed, 610 insertions(+), 498 deletions(-)
Title: Insolation for Palaeoclimate Studies
Description: R package to compute Incoming Solar Radiation (insolation) for palaeoclimate studies. Features three solutions: Berger (1978), Berger and Loutre (1991) and Laskar et al. (2004). Computes daily-mean, season-averaged and annual means for all latitudes.
Author: Michel Crucifix
Maintainer: Michel Crucifix <michel.crucifix@uclouvain.be>
Diff between palinsol versions 0.92 dated 2014-04-04 and 0.93 dated 2016-03-04
palinsol-0.92/palinsol/inst/orig |only palinsol-0.93/palinsol/CHANGES | 3 + palinsol-0.93/palinsol/DESCRIPTION | 14 ++-- palinsol-0.93/palinsol/MD5 | 37 ++++++------ palinsol-0.93/palinsol/NAMESPACE | 4 + palinsol-0.93/palinsol/R/astro.R | 93 +++++++++++++++++-------------- palinsol-0.93/palinsol/data/BER78.rda |binary palinsol-0.93/palinsol/data/BER90.rda |binary palinsol-0.93/palinsol/data/LA04.rda |binary palinsol-0.93/palinsol/inst/extdata |only palinsol-0.93/palinsol/man/BER78.Rd | 33 +++++------ palinsol-0.93/palinsol/man/Insol.Rd | 10 +-- palinsol-0.93/palinsol/man/Insol_l1l2.Rd | 2 palinsol-0.93/palinsol/man/LA04.Rd | 13 +--- palinsol-0.93/palinsol/man/astro.Rd | 40 ++++++++----- palinsol-0.93/palinsol/man/day2l.Rd | 6 +- 16 files changed, 141 insertions(+), 114 deletions(-)
Title: Functions for Nonlinear Least Squares Solutions
Description: Replacement for nls() tools for working with nonlinear least squares problems.
The calling structure is similar to, but much simpler than, that of the nls()
function. Moreover, where nls() specifically does NOT deal with small or zero
residual problems, nlmrt is quite happy to solve them. It also attempts to be
more robust in finding solutions, thereby avoiding 'singular gradient' messages
that arise in the Gauss-Newton method within nls(). The Marquardt-Nash approach
in nlmrt generally works more reliably to get a solution, though this may be
one of a set of possibilities, and may also be statistically unsatisfactory.
Added print and summary as of August 28, 2012.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash <nashjc@uottawa.ca>
Diff between nlmrt versions 2013-9.25 dated 2014-12-05 and 2016.3.2 dated 2016-03-04
DESCRIPTION | 24 ++++------ MD5 | 28 +++++------ NAMESPACE | 13 +++-- NEWS | 26 ++++++++--- R/model2jacfun.R | 6 ++ R/nlmrt.R | 10 ++-- R/nlxb.R | 9 +++ build/vignette.rds |binary inst/doc/nlmrt-vignette.R | 1 inst/doc/nlmrt-vignette.Rnw | 3 + inst/examples/eshl.R | 2 man/nlmrt-package.Rd | 101 +++++++++++++++++++++++++------------------ man/nlxb.Rd | 6 -- man/wrapnls.Rd | 4 + vignettes/nlmrt-vignette.Rnw | 4 + 15 files changed, 144 insertions(+), 93 deletions(-)
Title: Multilevel Mediation Analysis
Description: Used for mediation analysis with generalized multilevel models.
Author: Qingzhao Yu, Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mlma versions 1.0-0 dated 2015-10-31 and 2.0-0 dated 2016-03-04
DESCRIPTION | 6 MD5 | 16 NAMESPACE | 1 R/mlma.r | 894 ++++++++++++++++++++++++++++++++++++++--------- man/boot.mlma.Rd | 36 + man/data.org.Rd | 33 - man/mlma.Rd | 34 + man/plot.mlma.boot.Rd | 9 man/summary.mlma.boot.Rd | 9 9 files changed, 822 insertions(+), 216 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen, Kathleen Gates, and Mikko Rönkkö.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.4 dated 2015-11-30 and 0.4.5 dated 2016-03-04
DESCRIPTION | 9 +- MD5 | 10 +- R/MIIVsem.R | 3 R/miive.R | 24 ++++-- R/miivs.R | 221 +++++++++++++++++++++++++++++++++++++++------------------ man/MIIVsem.Rd | 3 6 files changed, 185 insertions(+), 85 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints objects are provided. Non-Gaussian models are fit using INLA, and Gaussian geostatistical models use Maximum Likelihood Estimation.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.3.10 dated 2015-11-09 and 1.4.0 dated 2016-03-04
DESCRIPTION | 18 ++-- MD5 | 35 +++++--- R/0gm.R | 1 R/RFsimulate.R | 5 - R/glgm.R | 191 ++++++++++++++++++++++++++++++++++++++++++------- R/lgcp.R | 4 - build |only data/gambiaUTM.RData |binary data/loaloa.RData |binary data/murder.RData |binary data/nn32.RData |binary data/rongelapUTM.RData |binary data/swissRain.RData |binary data/swissRainR.RData |binary data/torontoPop.RData |binary data/wheat.RData |binary inst/doc |only tests/glgm.R | 4 - vignettes |only 19 files changed, 202 insertions(+), 56 deletions(-)
Title: Generalized Competing Event Model
Description: Generalized competing event model based on Cox PH model and Fine-Gray model.
This function is designed to develop optimized risk-stratification methods for competing
risks data, such as described in:
1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F,
and Mell LK.(2014) Validated competing event model for thestage I-II endometrial cancer
population. Int J Radiat Oncol Biol Phys.89:888-98. <DOI:10.1016/j.ijrobp.2014.03.047>.
2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose
BS, Shen H, Vaida F, Murphy JD, and Mell LK. (2016) Improved method to stratify elderly
cancer patients at risk for competing events. J Clin Oncol.in press. <DOI:10.1200/JCO.2015.65.0739>.
Author: Hanjie Shen <has072@ucsd.edu>, Ruben Carmona
<ruben.carmona13@gmail.com>, Loren Mell <lmell@ucsd.edu>
Maintainer: Hanjie Shen <shenhanjie0418@gmail.com>
Diff between gcerisk versions 16.1.1 dated 2016-02-04 and 16.1.2 dated 2016-03-04
DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/gcecox.R | 76 ++++++++++++++++++++++++++++++++++++---------------------- R/gcefg.R | 41 ++++++++++++++----------------- man/gcecox.Rd | 2 - man/gcefg.Rd | 2 - 6 files changed, 78 insertions(+), 61 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Barret Schloerke [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.8 dated 2015-09-18 and 0.8.3 dated 2016-03-04
DESCRIPTION | 21 +++++++++++------ LICENSE | 2 - MD5 | 16 ++++++------- NEWS | 6 ++++ R/eval.r | 42 +++++++++++++++++++--------------- R/parse.r | 52 ++++++++++++++++++++++++++++--------------- man/evaluate.Rd | 36 +++++++++++++++-------------- man/parse_all.Rd | 4 ++- tests/testthat/test-errors.r | 2 - 9 files changed, 109 insertions(+), 72 deletions(-)
Title: Exploration and Graphics for RivEr Trends (EGRET)
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 2.3.1 dated 2015-08-13 and 2.4.3 dated 2016-03-04
DESCRIPTION | 9 - MD5 | 249 ++++++++++++++++++++--------------------- NAMESPACE | 2 R/boxConcThree.R | 29 +++- R/boxResidMonth.R | 23 ++- R/censoredSegments.R | 8 - R/fluxBiasEight.R | 1 R/makeRandomResiduals.R |only R/multiPlotDataOverview.R | 5 R/plotConcHist.R | 6 R/plotConcPred.R | 21 +-- R/plotConcQ.R | 11 + R/plotConcTime.R | 8 - R/plotConcTimeDaily.R | 11 - R/plotContours.R | 43 ++++--- R/plotDiffContours.R | 59 +++++---- R/plotFluxHist.R | 4 R/plotFluxPred.R | 19 +-- R/plotResidPred.R | 64 ++++++++-- R/plotResidQ.R | 79 ++++++++----- R/plotResidTime.R | 70 ++++++++--- R/populateDateColumns.r | 5 R/printSeries.R | 2 R/processQWData.r | 2 R/readMetaData.r | 2 R/setupYears.R | 2 README.md | 2 build/vignette.rds |binary man/Choptank_eList.Rd | 2 man/Constants.Rd | 2 man/EGRET-package.Rd | 6 man/INFOdataframe.Rd | 6 man/as.egret.Rd | 2 man/blankTime.Rd | 6 man/boxConcMonth.Rd | 8 - man/boxConcThree.Rd | 6 man/boxQTwice.Rd | 8 - man/boxResidMonth.Rd | 18 +- man/calculateMonthlyResults.Rd | 4 man/censoredSegments.Rd | 12 - man/checkStartEndDate.Rd | 2 man/compressData.Rd | 6 man/dataOverview.Rd | 2 man/dateFormatCheck.Rd | 2 man/estCrossVal.Rd | 10 - man/estDailyFromSurfaces.Rd | 4 man/estSurfaces.Rd | 12 - man/fixSampleFrame.Rd | 4 man/flowDuration.Rd | 20 +-- man/fluxBiasMulti.Rd | 10 - man/fluxBiasStat.Rd | 12 - man/fluxUnit-class.Rd | 14 +- man/formatCheckDate.Rd | 2 man/formatCheckParameterCd.Rd | 2 man/generalAxis.Rd | 2 man/genericEGRETDotPlot.Rd | 4 man/getDaily.Rd | 2 man/getInfo.Rd | 2 man/getSample.Rd | 2 man/getSurfaces.Rd | 2 man/is.egret.Rd | 2 man/logPretty1.Rd | 4 man/logPretty3.Rd | 6 man/makeAnnualSeries.Rd | 26 ++-- man/mergeReport.Rd | 4 man/modelEstimation.Rd | 8 - man/monthLabel-class.Rd | 2 man/multiPlotDataOverview.Rd | 10 - man/plot15.Rd | 2 man/plot1of15.Rd | 2 man/plotConcHist.Rd | 12 - man/plotConcPred.Rd | 8 - man/plotConcQ.Rd | 10 - man/plotConcQSmooth.Rd | 16 +- man/plotConcTime.Rd | 16 +- man/plotConcTimeDaily.Rd | 12 - man/plotConcTimeSmooth.Rd | 6 man/plotContours.Rd | 46 +++---- man/plotDiffContours.Rd | 42 +++--- man/plotFlowSingle.Rd | 6 man/plotFluxHist.Rd | 10 - man/plotFluxPred.Rd | 8 - man/plotFluxQ.Rd | 4 man/plotFluxTimeDaily.Rd | 10 - man/plotFour.Rd | 8 - man/plotFourStats.Rd | 6 man/plotQTimeDaily.Rd | 6 man/plotResidPred.Rd | 12 - man/plotResidQ.Rd | 10 - man/plotResidTime.Rd | 10 - man/plotSDLogQ.Rd | 12 - man/populateConcentrations.Rd | 2 man/populateDaily.Rd | 6 man/populateDateColumns.Rd | 4 man/populateParameterINFO.Rd | 2 man/populateSampleColumns.Rd | 2 man/populateSiteINFO.Rd | 2 man/print.egret.Rd | 2 man/printFluxUnitCheatSheet.Rd | 2 man/printSeries.Rd | 6 man/printqUnitCheatSheet.Rd | 2 man/processQWData.Rd | 4 man/qUnit-class.Rd | 6 man/readDataFromFile.Rd | 4 man/readNWISDaily.Rd | 6 man/readNWISSample.Rd | 4 man/readUserDaily.Rd | 4 man/readUserSample.Rd | 10 - man/readWQPSample.Rd | 6 man/removeDuplicates.Rd | 4 man/runSurvReg.Rd | 10 - man/saveResults.Rd | 11 + man/selectDays.Rd | 16 +- man/setPA.Rd | 10 - man/setSeasonLabel.Rd | 16 +- man/setSeasonLabelByUser.Rd | 16 +- man/setUpEstimation.Rd | 3 man/setupYears.Rd | 10 - man/surfaceIndex.Rd | 2 man/tableChange.Rd | 6 man/tableChangeSingle.Rd | 6 man/tableFlowChange.Rd | 6 man/tableResults.Rd | 4 man/triCube.Rd | 4 man/yPretty.Rd | 2 tests/testthat/tests_imports.R | 6 126 files changed, 826 insertions(+), 648 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from the
National Water Information System (NWIS) tools. Both EPA and USGS water
quality data are obtained from the Water Quality Portal.
Author: Robert Hirsch [aut],
Laura DeCicco [aut, cre],
David Lorenz [aut],
Jordan Read [ctb],
Lindsay Carr [ctb]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.3.1 dated 2015-08-14 and 2.5.2 dated 2016-03-04
dataRetrieval-2.3.1/dataRetrieval/R/whatNWISdata.r |only dataRetrieval-2.5.2/dataRetrieval/DESCRIPTION | 24 dataRetrieval-2.5.2/dataRetrieval/MD5 | 120 +-- dataRetrieval-2.5.2/dataRetrieval/NAMESPACE | 42 + dataRetrieval-2.5.2/dataRetrieval/NEWS | 12 dataRetrieval-2.5.2/dataRetrieval/R/AAA.R |only dataRetrieval-2.5.2/dataRetrieval/R/constructNWISURL.r | 40 - dataRetrieval-2.5.2/dataRetrieval/R/getWebServiceData.R | 70 +- dataRetrieval-2.5.2/dataRetrieval/R/importRDB1.r | 324 +++++----- dataRetrieval-2.5.2/dataRetrieval/R/importWQP.R | 203 +++--- dataRetrieval-2.5.2/dataRetrieval/R/importWaterML1.r | 109 +-- dataRetrieval-2.5.2/dataRetrieval/R/importWaterML2.r | 44 - dataRetrieval-2.5.2/dataRetrieval/R/readNWISdata.r | 111 +-- dataRetrieval-2.5.2/dataRetrieval/R/readNWISpCode.r | 2 dataRetrieval-2.5.2/dataRetrieval/R/readNWISqw.r | 29 dataRetrieval-2.5.2/dataRetrieval/R/readNWISsite.r | 4 dataRetrieval-2.5.2/dataRetrieval/R/readNWISunit.r | 179 +++-- dataRetrieval-2.5.2/dataRetrieval/R/readWQPdata.R | 17 dataRetrieval-2.5.2/dataRetrieval/R/readWQPqw.r | 2 dataRetrieval-2.5.2/dataRetrieval/R/renameColumns.R | 6 dataRetrieval-2.5.2/dataRetrieval/R/setAccess.R |only dataRetrieval-2.5.2/dataRetrieval/R/tabbedDataRetrievals.R | 14 dataRetrieval-2.5.2/dataRetrieval/R/whatNWISData.r |only dataRetrieval-2.5.2/dataRetrieval/R/whatNWISsites.R | 14 dataRetrieval-2.5.2/dataRetrieval/R/whatWQPsites.R | 56 - dataRetrieval-2.5.2/dataRetrieval/README.md | 3 dataRetrieval-2.5.2/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.5.2/dataRetrieval/inst/doc/dataRetrieval.pdf |binary dataRetrieval-2.5.2/dataRetrieval/man/checkWQPdates.Rd | 6 dataRetrieval-2.5.2/dataRetrieval/man/constructNWISURL.Rd | 9 dataRetrieval-2.5.2/dataRetrieval/man/constructWQPURL.Rd | 6 dataRetrieval-2.5.2/dataRetrieval/man/countyCd.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/dataRetrieval-package.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/getWebServiceData.Rd | 6 dataRetrieval-2.5.2/dataRetrieval/man/importRDB1.Rd | 35 - dataRetrieval-2.5.2/dataRetrieval/man/importWQP.Rd | 20 dataRetrieval-2.5.2/dataRetrieval/man/importWaterML1.Rd | 19 dataRetrieval-2.5.2/dataRetrieval/man/importWaterML2.Rd | 7 dataRetrieval-2.5.2/dataRetrieval/man/pCodeToName.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/parameterCdFile.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/readNWISdata.Rd | 40 - dataRetrieval-2.5.2/dataRetrieval/man/readNWISdv.Rd | 12 dataRetrieval-2.5.2/dataRetrieval/man/readNWISgwl.Rd | 13 dataRetrieval-2.5.2/dataRetrieval/man/readNWISmeas.Rd | 26 dataRetrieval-2.5.2/dataRetrieval/man/readNWISpCode.Rd | 6 dataRetrieval-2.5.2/dataRetrieval/man/readNWISpeak.Rd | 17 dataRetrieval-2.5.2/dataRetrieval/man/readNWISqw.Rd | 18 dataRetrieval-2.5.2/dataRetrieval/man/readNWISrating.Rd | 9 dataRetrieval-2.5.2/dataRetrieval/man/readNWISsite.Rd | 80 +- dataRetrieval-2.5.2/dataRetrieval/man/readNWISuv.Rd | 17 dataRetrieval-2.5.2/dataRetrieval/man/readWQPdata.Rd | 12 dataRetrieval-2.5.2/dataRetrieval/man/readWQPqw.Rd | 14 dataRetrieval-2.5.2/dataRetrieval/man/renameNWISColumns.Rd | 8 dataRetrieval-2.5.2/dataRetrieval/man/setAccess.Rd |only dataRetrieval-2.5.2/dataRetrieval/man/stateCd.Rd | 10 dataRetrieval-2.5.2/dataRetrieval/man/stateCdLookup.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/whatNWISdata.Rd | 10 dataRetrieval-2.5.2/dataRetrieval/man/whatNWISsites.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/man/whatWQPsites.Rd | 9 dataRetrieval-2.5.2/dataRetrieval/man/xmlcontent.Rd |only dataRetrieval-2.5.2/dataRetrieval/man/zeroPad.Rd | 2 dataRetrieval-2.5.2/dataRetrieval/tests/testthat/tests_general.R | 8 dataRetrieval-2.5.2/dataRetrieval/tests/testthat/tests_imports.R | 10 dataRetrieval-2.5.2/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 13 64 files changed, 1061 insertions(+), 818 deletions(-)
Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.1.0 dated 2015-11-30 and 1.2.0 dated 2016-03-04
BEDMatrix-1.1.0/BEDMatrix/tests/testthat/test-bedmatrix.R |only BEDMatrix-1.2.0/BEDMatrix/DESCRIPTION | 8 - BEDMatrix-1.2.0/BEDMatrix/MD5 | 19 +-- BEDMatrix-1.2.0/BEDMatrix/NAMESPACE | 3 BEDMatrix-1.2.0/BEDMatrix/NEWS.md | 16 ++ BEDMatrix-1.2.0/BEDMatrix/R/BEDMatrix.R | 80 +++++++++++--- BEDMatrix-1.2.0/BEDMatrix/R/package.R | 31 +++-- BEDMatrix-1.2.0/BEDMatrix/README.md | 59 ++++------ BEDMatrix-1.2.0/BEDMatrix/man/BEDMatrix-package.Rd |only BEDMatrix-1.2.0/BEDMatrix/man/BEDMatrix.Rd | 59 +++++++--- BEDMatrix-1.2.0/BEDMatrix/src/BEDMatrix.cpp | 12 +- BEDMatrix-1.2.0/BEDMatrix/tests/testthat/test-BEDMatrix.R |only 12 files changed, 188 insertions(+), 99 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut],
Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 2.0.1 dated 2016-02-21 and 2.0.2 dated 2016-03-04
archivist-2.0.1/archivist/inst/graphGallery/gallery/600bda83cb840947976bd1ce3a11879d.png |only archivist-2.0.1/archivist/inst/graphGallery/gallery/600bda83cb840947976bd1ce3a11879d.rda |only archivist-2.0.1/archivist/inst/graphGallery/gallery/70f4f83dbfef2a8afb2f495208d0a60f.png |only archivist-2.0.1/archivist/inst/graphGallery/gallery/70f4f83dbfef2a8afb2f495208d0a60f.rda |only archivist-2.0.2/archivist/DESCRIPTION | 6 archivist-2.0.2/archivist/MD5 | 98 +++++----- archivist-2.0.2/archivist/NAMESPACE | 1 archivist-2.0.2/archivist/NEWS.md | 7 archivist-2.0.2/archivist/R/aread.R | 4 archivist-2.0.2/archivist/R/asession.R | 2 archivist-2.0.2/archivist/R/atags.R | 2 archivist-2.0.2/archivist/R/loadFromRepo.R | 2 archivist-2.0.2/archivist/R/restoreLibraries.R |only archivist-2.0.2/archivist/R/saveToRepo.R | 2 archivist-2.0.2/archivist/demo/archivist_jss.r | 20 +- archivist-2.0.2/archivist/inst/graphGallery/backpack.db |binary archivist-2.0.2/archivist/inst/graphGallery/gallery/13b2724139eb2c62578b4dab0d7b2cea.png |only archivist-2.0.2/archivist/inst/graphGallery/gallery/13b2724139eb2c62578b4dab0d7b2cea.rda |only archivist-2.0.2/archivist/inst/graphGallery/gallery/1862bb3adaf78b7b3b9a30b46526bf7e.rda |only archivist-2.0.2/archivist/inst/graphGallery/gallery/2362b67ee86693d7326c95d3526a5cd8.rda |only archivist-2.0.2/archivist/inst/graphGallery/gallery/f05f0ed0662fe01850ec1b928830ef32.png |only archivist-2.0.2/archivist/inst/graphGallery/gallery/f05f0ed0662fe01850ec1b928830ef32.rda |only archivist-2.0.2/archivist/man/Repository.Rd | 2 archivist-2.0.2/archivist/man/Tags.Rd | 2 archivist-2.0.2/archivist/man/addHooksToPrint.Rd | 2 archivist-2.0.2/archivist/man/addTagsRepo.Rd | 2 archivist-2.0.2/archivist/man/aformat.Rd | 4 archivist-2.0.2/archivist/man/ahistory.Rd | 2 archivist-2.0.2/archivist/man/alink.Rd | 2 archivist-2.0.2/archivist/man/archivist-package.Rd | 2 archivist-2.0.2/archivist/man/archivistOptions.Rd | 2 archivist-2.0.2/archivist/man/aread.Rd | 6 archivist-2.0.2/archivist/man/asearch.Rd | 2 archivist-2.0.2/archivist/man/asession.Rd | 4 archivist-2.0.2/archivist/man/cache.Rd | 2 archivist-2.0.2/archivist/man/copyToRepo.Rd | 2 archivist-2.0.2/archivist/man/createEmptyRepo.Rd | 4 archivist-2.0.2/archivist/man/createMDGallery.Rd | 2 archivist-2.0.2/archivist/man/deleteLocalRepo.Rd | 4 archivist-2.0.2/archivist/man/getRemoteHook.Rd | 2 archivist-2.0.2/archivist/man/getTags.Rd | 4 archivist-2.0.2/archivist/man/loadFromRepo.Rd | 5 archivist-2.0.2/archivist/man/magrittr.Rd | 2 archivist-2.0.2/archivist/man/md5hash.Rd | 2 archivist-2.0.2/archivist/man/restoreLibs.Rd |only archivist-2.0.2/archivist/man/rmFromLocalRepo.Rd | 4 archivist-2.0.2/archivist/man/saveToRepo.Rd | 4 archivist-2.0.2/archivist/man/searchInRepo.Rd | 6 archivist-2.0.2/archivist/man/setRepo.Rd | 4 archivist-2.0.2/archivist/man/shinySearchInRepo.Rd | 2 archivist-2.0.2/archivist/man/showRepo.Rd | 2 archivist-2.0.2/archivist/man/splitTags.Rd | 2 archivist-2.0.2/archivist/man/summaryRepo.Rd | 2 archivist-2.0.2/archivist/man/zipRepo.Rd | 4 archivist-2.0.2/archivist/tests/testthat/test_aoptions.R | 12 - archivist-2.0.2/archivist/tests/testthat/test_jss_artilce.R | 42 +--- 56 files changed, 140 insertions(+), 149 deletions(-)
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness. This is the 'lite' version of the more complete 'viridis' package
that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.1.1 dated 2015-12-31 and 0.1.2 dated 2016-03-04
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/viridis.R | 44 ++++++++++++++++++++++++++++---------------- README.md | 16 ++++++++++++---- man/figures |only man/viridis.Rd | 10 ++++++++++ 6 files changed, 59 insertions(+), 28 deletions(-)
Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3.2 dated 2015-12-31 and 0.3.3 dated 2016-03-04
DESCRIPTION | 8 +- MD5 | 23 ++++---- R/scales.R | 36 ++++++++++++- R/viridis.R | 48 ++++++++++------- README.md | 2 inst/doc/intro-to-viridis.Rmd | 8 +- inst/doc/intro-to-viridis.html | 110 +++++++++++++++++++++++------------------ man/figures |only man/scale_viridis.Rd | 7 +- man/viridis.Rd | 10 +++ man/viridis_pal.Rd | 10 +++ vignettes/intro-to-viridis.Rmd | 8 +- 12 files changed, 176 insertions(+), 94 deletions(-)
Title: Tools for the Reading and Tokenization of R Code
Description: Tools for the reading and tokenization of R code.
The 'sourcetools' package provides both an R and C++ interface
for the tokenization of R code, and helpers for interacting
with the tokenized representation of R code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>
Diff between sourcetools versions 0.1.1 dated 2016-03-04 and 0.1.2 dated 2016-03-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-tokenize.R | 5 ----- 3 files changed, 5 insertions(+), 10 deletions(-)
Title: Analysis of Subjective Perspectives Using Q Methodology
Description: Analysis of Q methodology, used to identify distinct perspectives existing within a group.
This methodology is used across social, health and environmental sciences to understand diversity of attitudes, discourses, or decision-making styles (for more information, see http://qmethod.org).
A single function runs the full analysis. Each step can be run separately using the corresponding functions: for automatic flagging of Q-sorts (manual flagging is optional), for statement scores, for distinguishing and consensus statements, and for general characteristics of the factors.
Additional functions are available to import and export data, to print and plot, to import raw data from individual *.CSV files, and to make printable cards.
The package also offers functions to print Q cards and to generate Q distributions for study administration.
The package uses principal components and it allows manual or automatic flagging, a number of mathematical methods for rotation, and a number of correlation coefficients for the initial correlation matrix.
See further details in the package documentation, and in the web pages below, which include a cookbook, guidelines for more advanced analysis (how to perform manual flagging or change the sign of factors), data management, and a beta graphical user interface for online and offline use.
Author: Aiora Zabala [aut, cre] (Main author),
Maximilian Held [aut] (Author of additional data management functions)
Maintainer: Aiora Zabala <aiora.zabala@gmail.com>
Diff between qmethod versions 1.4.0 dated 2016-01-15 and 1.4.1 dated 2016-03-04
DESCRIPTION | 8 ++--- MD5 | 28 +++++++++--------- R/plot.QmethodRes.R | 5 ++- R/qbstep.R | 39 ++++++++++++-------------- R/qmb.plot.R | 73 ++++++++++++++++++++++++++++++++++--------------- R/qmb.summary.R | 10 ++++-- R/qmboots.R | 70 +++++++++++++++++++++++++--------------------- man/plot.QmethodRes.Rd | 4 ++ man/qbstep.Rd | 2 - man/qindtest.Rd | 3 -- man/qmb.plot.Rd | 25 ++++++++++------ man/qmb.summary.Rd | 2 - man/qmboots.Rd | 15 +++++++++- man/qmethod-package.Rd | 13 +++++++- man/qpcrustes.Rd | 2 - 15 files changed, 183 insertions(+), 116 deletions(-)
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench for evaluating Precision-Recall curves under various conditions.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 0.2.0 dated 2016-01-11 and 0.3.1 dated 2016-03-04
DESCRIPTION | 10 +- MD5 | 30 +++--- NAMESPACE | 1 R/prcbench.R | 1 R/tool_java.R | 22 ++++ R/tool_zzz.R | 9 +- README.md | 69 ++++++++++----- inst/doc/introduction.Rmd | 8 - inst/doc/introduction.html | 157 +++++++++++++++++++--------------- inst/java/auc2.jar |binary java/README.md | 13 ++ java/auc2/bin/auc2/AUCWrapper.class |binary java/auc2/lib/auc.jar |binary java/auc2/src/auc2/AUCWrapper.java | 162 ++++++++++++++++++------------------ tests/testthat/test_plot_autoplot.R | 2 vignettes/introduction.Rmd | 8 - 16 files changed, 286 insertions(+), 206 deletions(-)
Title: Extract Text and Data from PDF Documents
Description: Utilities based on libpoppler for extracting text,
fonts, attachments and metadata from a pdf file. Also implements
rendering of PDF to bitmaps on supported platforms.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between pdftools versions 0.1 dated 2016-02-25 and 0.2 dated 2016-03-04
DESCRIPTION | 14 ++++++++------ MD5 | 17 +++++++++-------- NEWS |only R/render.R | 18 ++++++++++-------- R/tools.R | 19 ++++++++++++------- configure | 16 ++++++++-------- man/pdf_render_page.Rd | 14 ++++++++------ man/pdftools.Rd | 20 +++++++++++++------- src/bindings.cpp | 2 +- src/init.cpp | 2 +- 10 files changed, 70 insertions(+), 52 deletions(-)
Title: Manipulation of Linear Systems of (in)Equalities
Description: Variable elimination (Gaussian elimination, Fourier-Motzkin elimination),
Moore-Penrose pseudoinverse, reduction to reduced row echelon form, value substitution,
projecting a vector on the convex polytope described by a system of (in)equations,
simplify systems by removing spurious columns and rows and collapse implied equalities,
test if a matrix is totally unimodilar, compute variable ranges implied by linear
(in)equalities.
Author: Mark van der Loo [aut, cre],
Edwin de Jonge [aut]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between lintools versions 0.1.0 dated 2016-01-22 and 0.1.1.1 dated 2016-03-04
lintools-0.1.0/lintools/man/sparseConstraints.Rd |only lintools-0.1.1.1/lintools/DESCRIPTION | 19 ++--- lintools-0.1.1.1/lintools/MD5 | 48 +++++++------ lintools-0.1.1.1/lintools/NAMESPACE | 8 +- lintools-0.1.1.1/lintools/NEWS | 9 ++ lintools-0.1.1.1/lintools/R/eliminate.R | 15 ++-- lintools-0.1.1.1/lintools/R/lintools-pkg.R | 1 lintools-0.1.1.1/lintools/R/pinv.R | 2 lintools-0.1.1.1/lintools/R/ranges.R |only lintools-0.1.1.1/lintools/R/spa.R | 6 - lintools-0.1.1.1/lintools/R/sparseConstraints.R | 45 +++++++----- lintools-0.1.1.1/lintools/R/unimodularity.R |only lintools-0.1.1.1/lintools/build/vignette.rds |binary lintools-0.1.1.1/lintools/inst/doc/project.R | 2 lintools-0.1.1.1/lintools/inst/doc/project.Rmd | 8 +- lintools-0.1.1.1/lintools/inst/doc/project.html | 23 ++---- lintools-0.1.1.1/lintools/man/allTotallyUnimodular.Rd |only lintools-0.1.1.1/lintools/man/eliminate.Rd | 5 + lintools-0.1.1.1/lintools/man/hellerTompkins.Rd |only lintools-0.1.1.1/lintools/man/is_totally_unimodular.Rd |only lintools-0.1.1.1/lintools/man/raghavachari.Rd |only lintools-0.1.1.1/lintools/man/ranges.Rd |only lintools-0.1.1.1/lintools/man/reduceMatrix.Rd |only lintools-0.1.1.1/lintools/man/sparse_constraints.Rd |only lintools-0.1.1.1/lintools/man/sparse_project.Rd | 4 - lintools-0.1.1.1/lintools/tests/testthat/test_eliminate.R | 18 ++++ lintools-0.1.1.1/lintools/tests/testthat/test_pinv.R | 7 + lintools-0.1.1.1/lintools/tests/testthat/test_ranges.R |only lintools-0.1.1.1/lintools/tests/testthat/test_spa.R | 4 - lintools-0.1.1.1/lintools/tests/testthat/test_unimodular.R |only lintools-0.1.1.1/lintools/vignettes/project.Rmd | 8 +- 31 files changed, 146 insertions(+), 86 deletions(-)
Title: Hypothesis Testing and Power Calculations for Comparing
Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>
Diff between HMP versions 1.4.2 dated 2016-01-15 and 1.4.3 dated 2016-03-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/DM.MoM.R | 2 +- R/Xsc.onesample.R | 2 +- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Heteroscedastic Discriminant Analysis
Description: Functions to perform dimensionality reduction for classification if the covariance matrices of the classes are unequal.
Author: Gero Szepannek
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between hda versions 0.2-12 dated 2013-11-26 and 0.2-14 dated 2016-03-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 3 +++ man/hda.Rd | 2 +- man/showloadings.Rd | 2 +- 5 files changed, 13 insertions(+), 10 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.38-4 dated 2015-12-03 and 1.39-5 dated 2016-03-04
DESCRIPTION | 8 +++--- MD5 | 58 +++++++++++++++++++++++++------------------------- NAMESPACE | 1 R/est.rf.R | 21 ++++++++++++------ R/plot.scantwo.R | 10 +++++--- R/pull_stuff.R | 30 +++++++++++++++++++++++++ R/scantwo.R | 2 - R/viridis.R |only build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/INSTALL_ME.txt | 16 ++++++------- inst/STATUS.txt | 27 ++++++++++++++++++++++- inst/TODO.txt | 5 +++- inst/doc/rqtltour.pdf |binary man/map2table.Rd | 2 - man/plot.rf.Rd | 20 +++++++++++------ man/plot.scantwo.Rd | 31 +++++++++++++------------- man/readMWril.Rd | 17 +++++++++----- man/table2map.Rd |only src/forwsel.c | 4 +-- 31 files changed, 167 insertions(+), 85 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with
this package. Among other things, it is possible to create and manipulate multivariate network
data with different formats, and there are effective ways available to treat multiple networks
with routines that combine algebraic systems like the partially ordered semigroup or the
semiring structure together with the relational bundles occurring in different types of
multivariate network data sets. As well an algebraic approach for two-mode networks is made
through Galois derivations between families of the pair of subsets.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 1.7.1 dated 2015-09-03 and 1.8.1 dated 2016-03-04
multiplex-1.7.1/multiplex/build |only multiplex-1.7.1/multiplex/inst/doc/TwoModeNetworks.R |only multiplex-1.7.1/multiplex/inst/doc/TwoModeNetworks.Rnw |only multiplex-1.8.1/multiplex/DESCRIPTION | 35 +- multiplex-1.8.1/multiplex/MD5 | 49 +-- multiplex-1.8.1/multiplex/NAMESPACE | 1 multiplex-1.8.1/multiplex/R/as.signed.R | 24 + multiplex-1.8.1/multiplex/R/bundle.census.R | 2 multiplex-1.8.1/multiplex/R/bundles.R | 204 +++++++------ multiplex-1.8.1/multiplex/R/coor.R |only multiplex-1.8.1/multiplex/R/diagram.levels.R | 80 +++-- multiplex-1.8.1/multiplex/R/ngbs.R | 10 multiplex-1.8.1/multiplex/R/perm.R | 51 ++- multiplex-1.8.1/multiplex/R/print.gml.R |only multiplex-1.8.1/multiplex/R/read.gml.R | 188 ++++++++---- multiplex-1.8.1/multiplex/R/reduc.R | 43 ++ multiplex-1.8.1/multiplex/R/reducs.R | 4 multiplex-1.8.1/multiplex/R/rel.sys.R | 248 ++++++++++------- multiplex-1.8.1/multiplex/R/rm.isol.R | 1 multiplex-1.8.1/multiplex/R/signed.R | 122 ++------ multiplex-1.8.1/multiplex/inst/CHANGELOG | 30 +- multiplex-1.8.1/multiplex/man/as.signed.Rd | 5 multiplex-1.8.1/multiplex/man/bundles.Rd | 4 multiplex-1.8.1/multiplex/man/coor.Rd |only multiplex-1.8.1/multiplex/man/multiplex-package.Rd | 6 multiplex-1.8.1/multiplex/man/perm.Rd | 5 multiplex-1.8.1/multiplex/man/print.gml.Rd |only multiplex-1.8.1/multiplex/man/read.gml.Rd | 12 multiplex-1.8.1/multiplex/man/rel.sys.Rd | 11 29 files changed, 677 insertions(+), 458 deletions(-)
Title: Semiparametric Copula Bivariate Regression Models
Description: Routines for fitting copula bivariate models for binary and continuous responses with linear and nonlinear effects in the presence of associated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <r.radice@bbk.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between SemiParBIVProbit versions 3.6-1 dated 2015-12-07 and 3.7 dated 2016-03-04
ChangeLog | 5 DESCRIPTION | 12 MD5 | 161 +-- NAMESPACE | 19 R/AT.r | 260 ++--- R/AT2.r | 118 -- R/BCDF.r | 23 R/BiCDF.r | 14 R/LM.bpm.r | 8 R/OR.r | 198 +--- R/RR.r | 201 ++-- R/S.m.r | 36 R/SemiParBIVProbit.fit.R | 98 + R/SemiParBIVProbit.fit.post.r | 111 +- R/SemiParBIVProbit.r | 474 +++++---- R/adjCov.r | 114 ++ R/adjCovSD.r | 129 ++ R/bcont.R |only R/bcont23.R |only R/bcont3.R |only R/bcont32.R |only R/bprobgHs.r | 72 - R/bprobgHsCont.r | 78 - R/bprobgHsCont3.r | 91 - R/bprobgHsContUniv.r | 182 ++- R/bprobgHsContUniv3.r | 240 +++- R/bprobgHsPO.r | 49 R/bprobgHsPO0.r | 31 R/bprobgHsSS.r | 57 - R/conv.check.r | 4 R/copgHs.r | 609 ++++++------ R/copgHs2.r | 78 - R/copgHsAT.r | 187 +++ R/copgHsCont.r | 1640 +++++++++++++++++++++++++++++++-- R/copulaReg.fit.post.r |only R/copulaReg.r |only R/distrHs.r | 1816 ++++++++++++++++++++----------------- R/distrHsAT.r | 135 +- R/esp.tr.R |only R/eta.tr.R |only R/gt.bpm.R | 4 R/jc.probs.r |only R/logLik.SemiParBIVProbit.r | 2 R/numch.r |only R/numgh.r |only R/pen.r | 110 +- R/plot.SemiParBIVProbit.r | 24 R/polys.setup.r | 2 R/post.check.R | 57 - R/predict.SemiParBIVProbit.r | 8 R/prev.r | 46 R/print.AT.r | 27 R/print.OR.r | 22 R/print.RR.r | 19 R/print.SemiParBIVProbit.r | 155 +-- R/print.copulaReg.r |only R/print.summary.SemiParBIVProbit.r | 155 +-- R/print.summary.copulaReg.r |only R/probm.R |only R/regH.r | 19 R/resp.check.R | 126 +- R/summary.SemiParBIVProbit.r | 291 +---- R/summary.copulaReg.r |only R/teta.tr.R |only R/working.comp.r | 27 man/AT.Rd | 41 man/AT2.Rd | 8 man/LM.bpm.Rd | 6 man/OR.Rd | 30 man/RR.Rd | 30 man/SemiParBIVProbit-package.Rd | 16 man/SemiParBIVProbit.Rd | 168 ++- man/bcont.Rd |only man/bcont23.Rd |only man/bcont3.Rd |only man/bcont32.Rd |only man/bprobgHs.Rd | 2 man/bprobgHsCont.Rd | 2 man/bprobgHsCont3.Rd | 2 man/bprobgHsSS.Rd | 2 man/copulaReg.Rd |only man/copulaReg.fit.post.Rd |only man/copulaRegObject.Rd |only man/esp.tr.Rd |only man/eta.tr.Rd |only man/gt.bpm.Rd | 4 man/jc.probs.Rd |only man/logLik.SemiParBIVProbit.Rd | 4 man/numch.Rd |only man/numgh.Rd |only man/post.check.Rd | 12 man/print.copulaReg.Rd |only man/print.summary.copulaReg.Rd |only man/probm.Rd |only man/resp.check.Rd | 13 man/summary.SemiParBIVProbit.Rd | 3 man/summary.copulaReg.Rd |only man/teta.tr.Rd |only 98 files changed, 5567 insertions(+), 3120 deletions(-)
More information about SemiParBIVProbit at CRAN
Permanent link
Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for 'SVG', 'DrawingML' for
Microsoft Word and 'DrawingML' for Microsoft PowerPoint.
Author: David Gohel [aut, cre],
Bob Rudis [ctb] (the javascript code used by function set_attr),
Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.0.7 dated 2016-02-24 and 0.0.8 dated 2016-03-04
rvg-0.0.7/rvg/R/interactivePointsGrob.R |only rvg-0.0.7/rvg/R/interactivePolygonGrob.R |only rvg-0.0.7/rvg/R/interactivePolylineGrob.R |only rvg-0.0.7/rvg/R/interactiveRectGrob.R |only rvg-0.0.7/rvg/R/interactiveSegmentsGrob.R |only rvg-0.0.7/rvg/R/interactiveTextGrob.R |only rvg-0.0.7/rvg/man/drawDetails.interactivePointsGrob.Rd |only rvg-0.0.7/rvg/man/drawDetails.interactivePolygonGrob.Rd |only rvg-0.0.7/rvg/man/drawDetails.interactivePolylineGrob.Rd |only rvg-0.0.7/rvg/man/drawDetails.interactiveRectGrob.Rd |only rvg-0.0.7/rvg/man/drawDetails.interactiveSegmentsGrob.Rd |only rvg-0.0.7/rvg/man/drawDetails.interactiveTextGrob.Rd |only rvg-0.0.7/rvg/man/interactivePointsGrob.Rd |only rvg-0.0.7/rvg/man/interactivePolygonGrob.Rd |only rvg-0.0.7/rvg/man/interactivePolylineGrob.Rd |only rvg-0.0.7/rvg/man/interactiveRectGrob.Rd |only rvg-0.0.7/rvg/man/interactiveSegmentsGrob.Rd |only rvg-0.0.7/rvg/man/interactiveTextGrob.Rd |only rvg-0.0.7/rvg/man/send_click.Rd |only rvg-0.0.7/rvg/man/send_tooltip.Rd |only rvg-0.0.7/rvg/man/set_data_id.Rd |only rvg-0.0.8/rvg/DESCRIPTION | 14 - rvg-0.0.8/rvg/MD5 | 48 +--- rvg-0.0.8/rvg/NAMESPACE | 16 - rvg-0.0.8/rvg/NEWS | 7 rvg-0.0.8/rvg/R/RcppExports.R | 12 - rvg-0.0.8/rvg/R/utils.R | 71 ------ rvg-0.0.8/rvg/src/RcppExports.cpp | 39 --- rvg-0.0.8/rvg/src/body_pr.cpp | 9 rvg-0.0.8/rvg/src/clipper.cpp | 43 ---- rvg-0.0.8/rvg/src/clipper.h | 5 rvg-0.0.8/rvg/src/docx.cpp | 14 - rvg-0.0.8/rvg/src/dsvg.cpp | 71 ------ rvg-0.0.8/rvg/src/pptx.cpp | 31 +- rvg-0.0.8/rvg/tests/testthat/test-dml-editable.R |only rvg-0.0.8/rvg/tests/testthat/test-svg-interactive.R | 161 --------------- 36 files changed, 79 insertions(+), 462 deletions(-)
Title: Protracted Birth-Death Model of Diversification
Description: Conducts maximum likelihood analysis and simulation of the protracted speciation model.
Author: Rampal S. Etienne
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between PBD versions 1.1 dated 2015-09-29 and 1.2 dated 2016-03-04
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/pbd_ML.R | 10 +++++++--- R/pbd_loglik.R | 9 ++++++--- R/pbd_loglik_choosepar.R | 2 +- R/pbd_sim.R | 41 +++++++++++++++++++++++++++++++++-------- R/pbd_utils.R | 19 +++++++++++++++---- man/PBD-package.Rd | 6 ++++-- man/pbd_ML.Rd | 6 ++++-- man/pbd_sim.Rd | 10 +++++++--- 10 files changed, 90 insertions(+), 39 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets.
The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 0.5 dated 2015-09-29 and 0.7 dated 2016-03-04
DESCRIPTION | 21 +- MD5 | 97 ++++++++---- NAMESPACE | 71 ++++---- R/MMPC.R |only R/MMPC.temporal.R |only R/MMPC.temporal.output_script.R |only R/MMPCoutput_script.R |only R/SES.R | 304 ++++++++++++++++++++++++++++---------- R/SES.temporal.R |only R/SES.temporal.opoutput_script.R |only R/SESoutput_script.R | 12 + R/cat.ci.R |only R/censIndLR.R | 33 +--- R/condi.R |only R/cv.ses.R | 194 ++++++++++++++++++++++-- R/gSquare.R | 33 +--- R/mmhc.skel.R |only R/model.R |only R/nei.R |only R/pc.con.R |only R/pc.skel.R |only R/plota.R |only R/reg.fit.R |only R/ridge.plot.R |only R/ridge.reg.R |only R/ridgereg.cv.R |only R/testIndBeta.R | 39 ++-- R/testIndFisher.R | 20 +- R/testIndGLMM.R |only R/testIndLogistic.R | 62 +++---- R/testIndMVreg.R |only R/testIndNB.R | 18 -- R/testIndPois.R | 18 -- R/testIndRQ.R | 45 +++-- R/testIndReg.R | 72 +++++---- R/testIndSpearman.R |only R/testIndZIP.R |only man/MMPC.temporal.output-class.Rd |only man/MMPCoutput-class.Rd |only man/MXM-internal.Rd | 24 ++- man/MXM-package.Rd | 13 - man/MXMCondIndTests.Rd | 91 ++++++++--- man/SES.Rd | 144 +++++++++++------- man/SES.temporal.Rd |only man/SES.temporal.output-class.Rd |only man/SESoutput-class.Rd | 5 man/censIndLR.Rd | 45 +++-- man/cv.ses.Rd | 70 ++++++-- man/gSquare.Rd | 84 ++++++---- man/mmhc.skel.Rd |only man/model.Rd |only man/nei.Rd |only man/pc.skel.Rd |only man/plota.Rd |only man/reg.fit.Rd |only man/ridge.plot.Rd |only man/ridge.reg.Rd |only man/ridgereg.cv.Rd |only man/testIndBeta.Rd | 37 +++- man/testIndFisher.Rd | 50 +++--- man/testIndGLMM.Rd |only man/testIndLogistic.Rd | 72 +++++---- man/testIndMVReg.Rd |only man/testIndNB.Rd | 38 +++- man/testIndPois.Rd | 31 ++- man/testIndRQ.Rd | 40 +++-- man/testIndReg.Rd | 34 ++-- man/testIndSpearman.Rd |only man/testIndZIP.Rd |only 69 files changed, 1201 insertions(+), 616 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt <frederick-solt@uiowa.edu>, Yue Hu <yue-hu-1@uiowa.edu>
Maintainer: Yue Hu <yue-hu-1@uiowa.edu>
Diff between dotwhisker versions 0.2.0.4 dated 2016-02-15 and 0.2.0.5 dated 2016-03-04
DESCRIPTION | 12 ++++---- MD5 | 34 ++++++++++++------------ NAMESPACE | 2 - NEWS.md | 4 ++ R/add_brackets.R | 15 +++++----- R/dwplot.R | 2 - R/relabel_y_axis.R | 2 - README.md | 2 - inst/doc/dotwhisker-vignette.R | 9 +++--- inst/doc/dotwhisker-vignette.Rmd | 11 ++++---- inst/doc/dotwhisker-vignette.html | 52 +++++++++++++++++++------------------- inst/doc/dwplot-vignette.R | 8 ++--- inst/doc/kl2007_examples.R | 10 +++---- inst/doc/kl2007_examples.Rmd | 10 +++---- inst/doc/kl2007_examples.html | 31 ++++++++++------------ man/add_brackets.Rd | 11 +++----- vignettes/dotwhisker-vignette.Rmd | 11 ++++---- vignettes/kl2007_examples.Rmd | 10 +++---- 18 files changed, 119 insertions(+), 117 deletions(-)
Title: Tools for the Reading and Tokenization of R Code
Description: Tools for the reading and tokenization of R code.
The 'sourcetools' package provides both an R and C++ interface
for the tokenization of R code, and helpers for interacting
with the tokenized representation of R code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>
Diff between sourcetools versions 0.1.0 dated 2016-03-03 and 0.1.1 dated 2016-03-04
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/include/sourcetools/tokenization/Registration.h | 4 ++-- inst/include/sourcetools/tokenization/Token.h | 6 +++--- inst/include/sourcetools/tokenization/Tokenizer.h | 14 +++++++------- tests/testthat/test-tokenize.R | 6 +++--- 6 files changed, 23 insertions(+), 23 deletions(-)
Title: SA Counterparty Credit Risk under Basel III
Description: Computes the Exposure-At-Default based on standardized approach
of the Basel III Regulatory framework (SA-CCR). Currently, trade types of all
the five major asset classes have been created and, given the inheritance-
based structure of the application, the addition of further trade types is
straightforward. The application automatically separates the trades on the
corresponding hedging and netting sets including the basis and volatility
transactions. All the examples appearing on the regulatory paper (including the
margined and the un-margined workflow) have been implemented.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between SACCR versions 1.1 dated 2015-12-27 and 1.5 dated 2016-03-04
DESCRIPTION | 30 ++++++++++++++++++------------ MD5 | 42 +++++++++++++++++++++++++----------------- NAMESPACE | 6 +++++- R/CalcAddon.R | 16 ++++++++++------ R/Commodity.R | 23 +++++++++++++++++++---- R/ExampleBasisVol.R |only R/ExampleFX.R | 4 ++-- R/HandleBasisVol.R |only R/IRD.R | 42 ++++++++++++++++++++++++++++++------------ R/Swap.R |only R/Trade.R | 7 +++++-- R/Vol.R |only R/runExampleCalcs.R | 2 +- man/CSA-class.Rd | 1 - man/CalcAddon.Rd | 4 +++- man/CommSwap-class.Rd |only man/Commodity-class.Rd | 1 - man/CreditIndex-class.Rd | 1 - man/CreditSingle-class.Rd | 1 - man/ExampleBasisVol.Rd |only man/ExampleFX.Rd | 2 +- man/FXSwap-class.Rd | 1 - man/HandleBasisVol.Rd |only man/IRDSwap-class.Rd | 1 - man/IRDSwapVol-class.Rd |only man/IRDSwaption-class.Rd | 1 - 26 files changed, 119 insertions(+), 66 deletions(-)
Title: Client for the HuffPost Pollster API
Description: Client for the HuffPost Pollster API, which provides
access to U.S. opinion polls since 2004.
Author: Jeffrey B. Arnold [aut, cre],
Thomas J. Leeper [aut],
Drew Linzer [aut]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between pollstR versions 1.2.1 dated 2015-07-01 and 1.2.2 dated 2016-03-04
pollstR-1.2.1/pollstR/R/pollstR-package.R |only pollstR-1.2.2/pollstR/DESCRIPTION | 18 pollstR-1.2.2/pollstR/MD5 | 33 - pollstR-1.2.2/pollstR/NAMESPACE | 2 pollstR-1.2.2/pollstR/NEWS | 5 pollstR-1.2.2/pollstR/R/polls.R | 4 pollstR-1.2.2/pollstR/R/pollstr-package.R |only pollstR-1.2.2/pollstR/build/vignette.rds |binary pollstR-1.2.2/pollstR/inst/doc/introduction.Rmd | 166 +++--- pollstR-1.2.2/pollstR/inst/doc/introduction.html | 261 +++++----- pollstR-1.2.2/pollstR/inst/vign-src/figures |only pollstR-1.2.2/pollstR/inst/vign-src/introduction.md |only pollstR-1.2.2/pollstR/man/pollstR.Rd | 4 pollstR-1.2.2/pollstR/man/pollstr_chart.Rd | 2 pollstR-1.2.2/pollstR/man/pollstr_charts.Rd | 2 pollstR-1.2.2/pollstR/man/pollstr_polls.Rd | 2 pollstR-1.2.2/pollstR/vignettes/assets/obama-favorable-chart-1.png |binary pollstR-1.2.2/pollstR/vignettes/assets/obama-favorable-chart-2-1.png |binary pollstR-1.2.2/pollstR/vignettes/introduction.Rmd | 166 +++--- 19 files changed, 367 insertions(+), 298 deletions(-)
Title: Network Estimation for Time Series
Description: Sparse VAR estimation based on LASSO.
Author: Christian Brownlees
Maintainer: Christian Brownlees <christian.brownlees@upf.edu>
Diff between nets versions 0.1 dated 2013-03-04 and 0.8 dated 2016-03-04
nets-0.1/nets/demo/granger_network.R |only nets-0.1/nets/demo/lrparcor_network.R |only nets-0.1/nets/demo/parcor_network.R |only nets-0.8/nets/CHANGELOG | 12 nets-0.8/nets/DESCRIPTION | 17 nets-0.8/nets/MD5 | 23 nets-0.8/nets/NAMESPACE | 7 nets-0.8/nets/R/nets.R | 464 +++++++------- nets-0.8/nets/README |only nets-0.8/nets/demo/00Index | 6 nets-0.8/nets/demo/granger.R |only nets-0.8/nets/demo/nets.R |only nets-0.8/nets/demo/partial_correlation.R |only nets-0.8/nets/man/nets-package.Rd | 16 nets-0.8/nets/man/nets.Rd | 153 +++- nets-0.8/nets/src/nets.c | 989 ++++++++++++++++++++----------- 16 files changed, 1061 insertions(+), 626 deletions(-)
Title: Client for 'Turfjs' for 'Geospatial' Analysis
Description: Client for 'Turfjs' (http://turfjs.org/) for
'geospatial' analysis. The package revolves around using 'GeoJSON'
data. Functions are included for creating 'GeoJSON' data objects,
measuring aspects of 'GeoJSON', and combining, transforming,
and creating random 'GeoJSON' data objects.
Author: Scott Chamberlain [aut, cre],
Jeff Hollister [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between lawn versions 0.1.4 dated 2015-08-24 and 0.1.6 dated 2016-03-04
DESCRIPTION | 7 LICENSE | 2 MD5 | 165 +++---- NAMESPACE | 2 NEWS | 8 R/centroid.R | 2 R/zzz.R | 43 + build/vignette.rds |binary inst/doc/lawn_vignette.html | 10 inst/js/LICENSE-geojsonhint |only inst/js/geojsonhint.js | 905 ++++++++++++++++++++++-------------------- man/as.turf.Rd | 2 man/as_feature.Rd | 2 man/data-types.Rd | 2 man/georandom.Rd | 2 man/lawn-package.Rd | 2 man/lawn_aggregate.Rd | 11 man/lawn_along.Rd | 24 - man/lawn_area.Rd | 24 - man/lawn_average.Rd | 10 man/lawn_bbox_polygon.Rd | 22 - man/lawn_bearing.Rd | 22 - man/lawn_bezier.Rd | 10 man/lawn_buffer.Rd | 11 man/lawn_center.Rd | 22 - man/lawn_centroid.Rd | 24 - man/lawn_combine.Rd | 2 man/lawn_concave.Rd | 10 man/lawn_convex.Rd | 10 man/lawn_count.Rd | 10 man/lawn_data.Rd | 2 man/lawn_destination.Rd | 20 man/lawn_deviation.Rd | 10 man/lawn_distance.Rd | 22 - man/lawn_envelope.Rd | 22 - man/lawn_erase.Rd | 10 man/lawn_explode.Rd | 2 man/lawn_extent.Rd | 22 - man/lawn_featurecollection.Rd | 10 man/lawn_filter.Rd | 10 man/lawn_flip.Rd | 2 man/lawn_hex_grid.Rd | 10 man/lawn_inside.Rd | 4 man/lawn_intersect.Rd | 11 man/lawn_isolines.Rd | 11 man/lawn_jenks.Rd | 6 man/lawn_kinks.Rd | 2 man/lawn_line_distance.Rd | 20 man/lawn_line_slice.Rd | 2 man/lawn_linestring.Rd | 10 man/lawn_max.Rd | 10 man/lawn_median.Rd | 10 man/lawn_merge.Rd | 12 man/lawn_midpoint.Rd | 22 - man/lawn_min.Rd | 10 man/lawn_nearest.Rd | 7 man/lawn_planepoint.Rd | 10 man/lawn_point.Rd | 10 man/lawn_point_grid.Rd | 10 man/lawn_point_on_line.Rd | 2 man/lawn_point_on_surface.Rd | 20 man/lawn_polygon.Rd | 11 man/lawn_quantile.Rd | 6 man/lawn_random.Rd | 10 man/lawn_reclass.Rd | 6 man/lawn_remove.Rd | 10 man/lawn_sample.Rd | 10 man/lawn_simplify.Rd | 10 man/lawn_size.Rd | 22 - man/lawn_square.Rd | 22 - man/lawn_square_grid.Rd | 10 man/lawn_sum.Rd | 10 man/lawn_tag.Rd | 4 man/lawn_tin.Rd | 12 man/lawn_triangle_grid.Rd | 12 man/lawn_union.Rd | 11 man/lawn_variance.Rd | 10 man/lawn_within.Rd | 4 man/pipe.Rd | 2 man/print-methods.Rd | 2 man/type_sum.Rd | 2 man/view.Rd | 2 tests/testthat/test-count.R | 1 tests/testthat/test-sample.R | 2 84 files changed, 1012 insertions(+), 876 deletions(-)
Title: Statistical Analysis of Monthly Background Checks of Gun
Purchases
Description: Statistical analysis of monthly background checks of gun purchases for the New York Times
story "What Drives Gun Sales: Terrorism, Obama and Calls for Restrictions" at
<http://www.nytimes.com/interactive/2015/12/10/us/gun-sales-terrorism-obama-restrictions.html?> is provided.
Author: Gregor Aisch, Josh Keller and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between gunsales versions 0.1.0 dated 2016-02-28 and 0.1.1 dated 2016-03-04
DESCRIPTION | 11 ++++++----- MD5 | 29 +++++++++++++++-------------- NAMESPACE | 6 ++++-- R/analysis.R | 32 ++++++++++++++++++-------------- R/checkOS.R |only R/ggplot.R | 16 ++++++++-------- R/init.R | 4 ++++ R/plot.R | 12 ++++++------ README.md | 20 +++++++++++--------- inst/doc/gunsales.R | 21 +++++++++++++++------ inst/doc/gunsales.Rmd | 18 +++++++++++++++--- inst/doc/gunsales.html | 4 ++-- man/analysis.Rd | 14 +++++++++----- man/ggplot_gunsales.Rd | 6 +++--- man/plot_gunsales.Rd | 6 +++--- vignettes/gunsales.Rmd | 18 +++++++++++++++--- 16 files changed, 134 insertions(+), 83 deletions(-)
Title: Generalized Structured Component Analysis (GSCA)
Description: Fit a variety of component-based structural equation models.
Author: Heungsun Hwang, Sunmee Kim, Sungyoung Lee, Taesung Park
Maintainer: Sunmee Kim <sunmee.kim@mail.mcgill.ca>
Diff between gesca versions 1.0 dated 2016-03-02 and 1.0.1 dated 2016-03-04
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NAMESPACE | 4 +++- man/summary.gesca.Rd |only 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu) with code contribution from Bailey Fosdick (bfosdick@uw.edu) and Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 5.0-0 dated 2015-12-05 and 5.0-1 dated 2016-03-04
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/predict_tfr.R | 25 +++++++++++++++++++++---- man/bayesTFR-package.Rd | 4 ++-- 5 files changed, 37 insertions(+), 15 deletions(-)
Title: Miscellaneous Functions for Southwest Fisheries Science Center
Description: Collection of conversion, analytical, geodesic, mapping, and
plotting functions. Used to support packages and code written by
researchers at the Southwest Fisheries Science Center of the National
Oceanic and Atmospheric Administration.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between swfscMisc versions 1.0.9 dated 2016-02-08 and 1.1 dated 2016-03-03
DESCRIPTION | 10 +++++----- MD5 | 16 +++++++++------- NAMESPACE | 1 + NEWS.md | 38 +++++++++++++++----------------------- R/autoUnits.R |only R/destination.R | 2 +- R/sample.map.R | 9 ++++++--- man/autoUnits.Rd |only man/destination.Rd | 3 +-- man/sample.map.Rd | 7 ++++--- 10 files changed, 42 insertions(+), 44 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed.
Author: Eric Archer
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 1.9.3 dated 2016-02-08 and 2.0 dated 2016-03-03
rfPermute-1.9.3/rfPermute/R/calc.imp.pval.R |only rfPermute-1.9.3/rfPermute/inst |only rfPermute-1.9.3/rfPermute/man/calc.imp.pval.Rd |only rfPermute-2.0/rfPermute/DESCRIPTION | 13 ++-- rfPermute-2.0/rfPermute/MD5 | 48 ++++++++--------- rfPermute-2.0/rfPermute/NAMESPACE | 11 +++- rfPermute-2.0/rfPermute/NEWS.md | 31 +++++++---- rfPermute-2.0/rfPermute/R/clean.rf.data.R | 7 +- rfPermute-2.0/rfPermute/R/exptd.err.rate.R | 9 +-- rfPermute-2.0/rfPermute/R/internals.R |only rfPermute-2.0/rfPermute/R/plot.rfPermute.R | 32 ++++++----- rfPermute-2.0/rfPermute/R/plot.rp.importance.r | 18 +++--- rfPermute-2.0/rfPermute/R/proximity.plot.r | 59 ++++++++++++++-------- rfPermute-2.0/rfPermute/R/rfPermute.R | 59 ++++++++-------------- rfPermute-2.0/rfPermute/R/rfPermute.default.R | 45 ++++++++++------ rfPermute-2.0/rfPermute/R/rfPermute.formula.R | 15 ++++- rfPermute-2.0/rfPermute/R/rfpNews.R |only rfPermute-2.0/rfPermute/R/rp.combine.R | 26 +++++---- rfPermute-2.0/rfPermute/R/rp.importance.R | 41 +++++++++------ rfPermute-2.0/rfPermute/man/clean.rf.data.Rd | 7 +- rfPermute-2.0/rfPermute/man/exptd.err.rate.Rd | 8 +- rfPermute-2.0/rfPermute/man/plot.rfPermute.Rd | 4 + rfPermute-2.0/rfPermute/man/plot.rp.importance.Rd | 3 - rfPermute-2.0/rfPermute/man/proximity.plot.Rd | 20 ++++--- rfPermute-2.0/rfPermute/man/rfPermute.Rd | 48 ++++++++--------- rfPermute-2.0/rfPermute/man/rfpNews.Rd |only rfPermute-2.0/rfPermute/man/rp.combine.Rd | 14 ++--- rfPermute-2.0/rfPermute/man/rp.importance.Rd | 20 ++++--- 28 files changed, 310 insertions(+), 228 deletions(-)
Title: Regression and Similarity Evaluation for Memory-Based Learning
in Spectral Chemometrics
Description: Implementation of functions for spectral similarity/dissimilarity
analysis and memory-based learning (MBL) for non-linear modeling
in complex spectral datasets. In chemometrics MBL is also known as local modeling.
Author: Leonardo Ramirez-Lopez [aut, cre], Antoine Stevens [aut]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between resemble versions 1.2.1 dated 2016-02-02 and 1.2.2 dated 2016-03-03
DESCRIPTION | 11 ++-- MD5 | 22 ++++----- NEWS | 2 R/corDiss.R | 5 +- R/mbl.R | 109 +++++++++++++++++++++++++----------------------- R/mblControl.R | 1 R/resemble.R | 2 README.md | 43 +++--------------- man/corDiss.Rd | 2 man/locFitnpred.Rd | 6 +- man/mbl.Rd | 15 +++--- man/resemble-package.Rd | 2 12 files changed, 106 insertions(+), 114 deletions(-)
Title: Access to Facebook API via R
Description: Provides an interface to the Facebook API.
Author: Pablo Barbera <pablo.barbera@nyu.edu>, Michael Piccirilli
<mrp2181@columbia.edu>, Andrew Geisler
Maintainer: Pablo Barbera <pablo.barbera@nyu.edu>
Diff between Rfacebook versions 0.6 dated 2015-08-07 and 0.6.3 dated 2016-03-03
ChangeLog | 9 +++++ DESCRIPTION | 12 ++++--- MD5 | 21 +++++++------ NAMESPACE | 3 + R/fbOAuth.R | 35 +++++++++++++++++++--- R/getInsights.R | 82 +++++++++++++++++++++++++++++++++++++++++------------ R/getPage.R | 28 +++++++++++++----- R/utils.R | 18 +++++++++++ man/callAPI.Rd |only man/fbOAuth.Rd | 26 ++++++++++++++-- man/getInsights.Rd | 19 +++++++++--- man/getPage.Rd | 10 +++++- 12 files changed, 208 insertions(+), 55 deletions(-)
Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares <ajesusmp@cibio.up.pt>
Diff between PHENIX versions 1.2.1 dated 2016-01-28 and 1.2.2 dated 2016-03-03
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS | 4 ++-- inst |only 4 files changed, 9 insertions(+), 8 deletions(-)
More information about ProteinDescriptors at CRAN
Permanent link
Title: Customisable Images of OpenStreetMap Data
Description: Produces customisable images of OpenStreetMap data. Extracts OpenStreetMap data for specified key-value pairs (e.g. key="building") using the overpass API. Different OSM objects can be plotted in different colours using the function add_osm_objects(). The function group_osm_objects() enables customised highlighting of selected regions using different graphical schemes designed to contrast with surrounding backgrounds.
Author: Mark Padgham [aut, cre]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmplotr versions 0.1-1 dated 2016-03-02 and 0.1-2 dated 2016-03-03
DESCRIPTION | 8 +++---- MD5 | 44 ++++++++++++++++++++--------------------- NAMESPACE | 9 ++++++++ R/add-osm-objects.R | 1 R/click-map.R | 1 R/connect-highways.R | 1 R/extract-highway.R | 11 ++++------ R/extract-highways.R | 3 -- R/extract-osm-objects.R | 30 +++++++++++++++++---------- R/get-xylims.R | 1 R/group-osm-objects.R | 1 R/highways2polygon.R | 17 ++++++++------- R/make-osm-map.R | 1 R/plot-osm-basemap.R | 1 inst/doc/downloading-data.R | 9 +++----- inst/doc/downloading-data.Rmd | 16 ++++++++------ inst/doc/downloading-data.html | 11 ++++++---- inst/doc/making-maps.R | 17 +++++++-------- inst/doc/making-maps.Rmd | 23 +++++++++++---------- inst/doc/making-maps.html | 20 ++++++++++++------ man/extract_highway.Rd | 2 + vignettes/downloading-data.Rmd | 16 ++++++++------ vignettes/making-maps.Rmd | 23 +++++++++++---------- 23 files changed, 152 insertions(+), 114 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web APIs for chemical information.
Author: Eduard Szöcs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szöcs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.5.0 dated 2016-01-29 and 0.1.0.0 dated 2016-03-03
webchem-0.0.5.0/webchem/data/ppdb_idx.rda |only webchem-0.0.5.0/webchem/man/get_pcid.Rd |only webchem-0.0.5.0/webchem/man/pc_compinfo.Rd |only webchem-0.0.5.0/webchem/man/ppdb_buildidx.Rd |only webchem-0.0.5.0/webchem/man/ppdb_idx.Rd |only webchem-0.0.5.0/webchem/man/ppdb_query.Rd |only webchem-0.1.0.0/webchem/DESCRIPTION | 12 webchem-0.1.0.0/webchem/MD5 | 125 ++- webchem-0.1.0.0/webchem/NAMESPACE | 42 - webchem-0.1.0.0/webchem/NEWS | 36 + webchem-0.1.0.0/webchem/R/alanwood.R | 224 +++--- webchem-0.1.0.0/webchem/R/chemid.R | 245 +++---- webchem-0.1.0.0/webchem/R/chemspider.R | 493 +++++++-------- webchem-0.1.0.0/webchem/R/cir.R | 84 +- webchem-0.1.0.0/webchem/R/cts.R | 156 +++- webchem-0.1.0.0/webchem/R/etox.R | 460 +++++++------ webchem-0.1.0.0/webchem/R/extractors.R |only webchem-0.1.0.0/webchem/R/opsin.R |only webchem-0.1.0.0/webchem/R/pan.R | 168 ++--- webchem-0.1.0.0/webchem/R/physprop.R | 177 ++--- webchem-0.1.0.0/webchem/R/ppdb.R | 152 ---- webchem-0.1.0.0/webchem/R/pubchem.R | 286 +++++--- webchem-0.1.0.0/webchem/R/utils.R | 12 webchem-0.1.0.0/webchem/R/webchem-defunct.R | 27 webchem-0.1.0.0/webchem/R/webchem-deprecated.R | 64 - webchem-0.1.0.0/webchem/R/webchem.R | 26 webchem-0.1.0.0/webchem/R/wikidata.R | 224 ++++-- webchem-0.1.0.0/webchem/data/aw_idx.rda |only webchem-0.1.0.0/webchem/data/lc50.rda |binary webchem-0.1.0.0/webchem/man/aw_idx.Rd |only webchem-0.1.0.0/webchem/man/aw_query.Rd | 16 webchem-0.1.0.0/webchem/man/build_aw_idx.Rd |only webchem-0.1.0.0/webchem/man/ci_query.Rd | 33 - webchem-0.1.0.0/webchem/man/cir_query.Rd | 10 webchem-0.1.0.0/webchem/man/cs_compinfo.Rd | 16 webchem-0.1.0.0/webchem/man/cs_convert.Rd | 2 webchem-0.1.0.0/webchem/man/cs_extcompinfo.Rd | 19 webchem-0.1.0.0/webchem/man/cs_prop.Rd | 14 webchem-0.1.0.0/webchem/man/cts_compinfo.Rd | 16 webchem-0.1.0.0/webchem/man/cts_convert.Rd | 10 webchem-0.1.0.0/webchem/man/cts_from.Rd |only webchem-0.1.0.0/webchem/man/cts_to.Rd |only webchem-0.1.0.0/webchem/man/etox_basic.Rd | 12 webchem-0.1.0.0/webchem/man/etox_targets.Rd | 18 webchem-0.1.0.0/webchem/man/etox_tests.Rd | 5 webchem-0.1.0.0/webchem/man/extractors.Rd |only webchem-0.1.0.0/webchem/man/get_cid.Rd |only webchem-0.1.0.0/webchem/man/get_csid.Rd | 18 webchem-0.1.0.0/webchem/man/get_etoxid.Rd | 17 webchem-0.1.0.0/webchem/man/get_wdid.Rd | 17 webchem-0.1.0.0/webchem/man/lc50.Rd | 6 webchem-0.1.0.0/webchem/man/opsin_query.Rd |only webchem-0.1.0.0/webchem/man/pan_query.Rd | 21 webchem-0.1.0.0/webchem/man/pc_prop.Rd |only webchem-0.1.0.0/webchem/man/pc_synonyms.Rd |only webchem-0.1.0.0/webchem/man/pp_query.Rd | 12 webchem-0.1.0.0/webchem/man/ppdb_parse.Rd |only webchem-0.1.0.0/webchem/man/wd_ident.Rd | 4 webchem-0.1.0.0/webchem/man/webchem-defunct.Rd | 16 webchem-0.1.0.0/webchem/man/webchem-deprecated.Rd | 27 webchem-0.1.0.0/webchem/tests/testthat/test-alanwood.R | 64 - webchem-0.1.0.0/webchem/tests/testthat/test-chemid.R | 44 - webchem-0.1.0.0/webchem/tests/testthat/test-chemspider.R | 139 +--- webchem-0.1.0.0/webchem/tests/testthat/test-cir.R | 14 webchem-0.1.0.0/webchem/tests/testthat/test-cts.R | 34 - webchem-0.1.0.0/webchem/tests/testthat/test-etox.R | 176 ++--- webchem-0.1.0.0/webchem/tests/testthat/test-extractors.R |only webchem-0.1.0.0/webchem/tests/testthat/test-opsin.R |only webchem-0.1.0.0/webchem/tests/testthat/test-pan.R | 50 - webchem-0.1.0.0/webchem/tests/testthat/test-physprop.R | 30 webchem-0.1.0.0/webchem/tests/testthat/test-ppdb.R | 29 webchem-0.1.0.0/webchem/tests/testthat/test-pubchem.R | 55 - webchem-0.1.0.0/webchem/tests/testthat/test-utils.R | 5 webchem-0.1.0.0/webchem/tests/testthat/test-wikidata.R | 61 - 74 files changed, 2088 insertions(+), 1935 deletions(-)
Title: Make 'ggplot2' Graphics Interactive Using 'htmlwidgets'
Description: Create interactive 'ggplot2' graphics that are usable in the 'RStudio'
viewer pane, in 'R Markdown' documents and in 'Shiny' apps.
Author: David Gohel [aut, cre],
Mike Bostock [cph] (d3.js)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.1.0 dated 2016-01-28 and 0.2.0 dated 2016-03-03
ggiraph-0.1.0/ggiraph/inst/htmlwidgets/lib/bootstrap.min.css |only ggiraph-0.1.0/ggiraph/inst/htmlwidgets/lib/bootstrap.min.js |only ggiraph-0.1.0/ggiraph/inst/htmlwidgets/lib/jquery.min.js |only ggiraph-0.2.0/ggiraph/DESCRIPTION | 19 -- ggiraph-0.2.0/ggiraph/MD5 | 87 +++++---- ggiraph-0.2.0/ggiraph/NAMESPACE | 12 + ggiraph-0.2.0/ggiraph/NEWS |only ggiraph-0.2.0/ggiraph/R/geom_path_interactive.R | 4 ggiraph-0.2.0/ggiraph/R/geom_point_interactive.R | 30 +-- ggiraph-0.2.0/ggiraph/R/geom_polygon_interactive.R | 33 +-- ggiraph-0.2.0/ggiraph/R/geom_rect_interactive.R | 2 ggiraph-0.2.0/ggiraph/R/geom_segment_interactive.R | 2 ggiraph-0.2.0/ggiraph/R/geom_text_interactive.R | 2 ggiraph-0.2.0/ggiraph/R/ggiraph.R | 58 +++++- ggiraph-0.2.0/ggiraph/R/interactive_points_grob.R |only ggiraph-0.2.0/ggiraph/R/interactive_polygon_grob.R |only ggiraph-0.2.0/ggiraph/R/interactive_polyline_grob.R |only ggiraph-0.2.0/ggiraph/R/interactive_rect_grob.R |only ggiraph-0.2.0/ggiraph/R/interactive_segments_grob.R |only ggiraph-0.2.0/ggiraph/R/interactive_text_grob.R |only ggiraph-0.2.0/ggiraph/build/vignette.rds |binary ggiraph-0.2.0/ggiraph/inst/COPYRIGHTS | 77 ++------ ggiraph-0.2.0/ggiraph/inst/doc/custom_rendering.R |only ggiraph-0.2.0/ggiraph/inst/doc/custom_rendering.Rmd |only ggiraph-0.2.0/ggiraph/inst/doc/custom_rendering.html |only ggiraph-0.2.0/ggiraph/inst/doc/ggiraph.R | 25 -- ggiraph-0.2.0/ggiraph/inst/doc/ggiraph.Rmd | 32 +-- ggiraph-0.2.0/ggiraph/inst/doc/ggiraph.html | 64 ++---- ggiraph-0.2.0/ggiraph/inst/htmlwidgets/ggiraph.js | 95 +++++++--- ggiraph-0.2.0/ggiraph/inst/htmlwidgets/ggiraph.yaml | 11 - ggiraph-0.2.0/ggiraph/inst/htmlwidgets/lib/d3.min.js |only ggiraph-0.2.0/ggiraph/inst/shiny/ggplot.md | 8 ggiraph-0.2.0/ggiraph/inst/shiny/server.R | 8 ggiraph-0.2.0/ggiraph/inst/shiny/server.md | 2 ggiraph-0.2.0/ggiraph/inst/shiny/ui.R | 3 ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_points_grob.Rd |only ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_polygon_grob.Rd |only ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_polyline_grob.Rd |only ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_rect_grob.Rd |only ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_segments_grob.Rd |only ggiraph-0.2.0/ggiraph/man/drawDetails.interactive_text_grob.Rd |only ggiraph-0.2.0/ggiraph/man/geom_map_interactive.Rd | 5 ggiraph-0.2.0/ggiraph/man/geom_path_interactive.Rd | 12 - ggiraph-0.2.0/ggiraph/man/geom_point_interactive.Rd | 2 ggiraph-0.2.0/ggiraph/man/geom_polygon_interactive.Rd | 2 ggiraph-0.2.0/ggiraph/man/geom_rect_interactive.Rd | 2 ggiraph-0.2.0/ggiraph/man/geom_segment_interactive.Rd | 2 ggiraph-0.2.0/ggiraph/man/geom_text_interactive.Rd | 2 ggiraph-0.2.0/ggiraph/man/ggiraph.Rd | 22 +- ggiraph-0.2.0/ggiraph/man/ggiraphOutput.Rd | 6 ggiraph-0.2.0/ggiraph/man/interactive_points_grob.Rd |only ggiraph-0.2.0/ggiraph/man/interactive_polygon_grob.Rd |only ggiraph-0.2.0/ggiraph/man/interactive_polyline_grob.Rd |only ggiraph-0.2.0/ggiraph/man/interactive_rect_grob.Rd |only ggiraph-0.2.0/ggiraph/man/interactive_segments_grob.Rd |only ggiraph-0.2.0/ggiraph/man/interactive_text_grob.Rd |only ggiraph-0.2.0/ggiraph/vignettes/custom_rendering.Rmd |only ggiraph-0.2.0/ggiraph/vignettes/ggiraph.Rmd | 32 +-- 58 files changed, 367 insertions(+), 294 deletions(-)
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between explor versions 0.1 dated 2015-12-15 and 0.2 dated 2016-03-03
DESCRIPTION | 25 ++++--- MD5 | 43 +++++++----- NAMESPACE | 2 NEWS | 9 ++ R/explor.R | 25 ++++++- R/explor_CA.R | 84 ++++++++++++++++++------- R/explor_MCA.R | 81 ++++++++++++++++-------- R/explor_PCA.R | 56 +++++++++++----- R/prepare_results_MCA.R | 8 ++ R/prepare_results_dudi_mca.R | 22 ++++++ README.md | 19 ++++- build |only inst/doc |only inst/po/en@quot/LC_MESSAGES/R-explor.mo |binary inst/po/fr/LC_MESSAGES/R-explor.mo |binary po/R-explor.pot | 38 +++++++++-- po/R-fr.mo |binary po/R-fr.po | 40 +++++++++-- tests/testthat/test_prepare_results_MCA.R | 6 + tests/testthat/test_prepare_results_dudi.acm.R | 6 + vignettes/introduction_en.Rmd | 11 +-- vignettes/introduction_fr.Rmd | 11 +-- 22 files changed, 361 insertions(+), 125 deletions(-)
Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between bigrquery versions 0.1.0 dated 2015-01-13 and 0.2.0 dated 2016-03-03
bigrquery-0.1.0/bigrquery/tests/testthat/test-utils.r |only bigrquery-0.2.0/bigrquery/DESCRIPTION | 13 - bigrquery-0.2.0/bigrquery/MD5 | 76 +++++--- bigrquery-0.2.0/bigrquery/NAMESPACE | 16 + bigrquery-0.2.0/bigrquery/NEWS.md |only bigrquery-0.2.0/bigrquery/R/auth.r | 17 + bigrquery-0.2.0/bigrquery/R/bigrquery.r | 13 + bigrquery-0.2.0/bigrquery/R/datasets.r | 104 ++++++++++++ bigrquery-0.2.0/bigrquery/R/dplyr.r | 15 + bigrquery-0.2.0/bigrquery/R/id.R |only bigrquery-0.2.0/bigrquery/R/jobs.r | 2 bigrquery-0.2.0/bigrquery/R/query.r | 16 + bigrquery-0.2.0/bigrquery/R/request.r | 57 +++++- bigrquery-0.2.0/bigrquery/R/tabledata.r | 128 +++++++++++---- bigrquery-0.2.0/bigrquery/R/tables.r | 92 ++++++++++ bigrquery-0.2.0/bigrquery/R/upload.r | 40 +++- bigrquery-0.2.0/bigrquery/R/utils.r | 38 ---- bigrquery-0.2.0/bigrquery/R/zzz.r | 5 bigrquery-0.2.0/bigrquery/README.md | 20 +- bigrquery-0.2.0/bigrquery/man/bigrquery.Rd | 16 + bigrquery-0.2.0/bigrquery/man/copy_table.Rd |only bigrquery-0.2.0/bigrquery/man/delete_dataset.Rd |only bigrquery-0.2.0/bigrquery/man/delete_table.Rd | 4 bigrquery-0.2.0/bigrquery/man/format_dataset.Rd |only bigrquery-0.2.0/bigrquery/man/format_table.Rd |only bigrquery-0.2.0/bigrquery/man/get_access_cred.Rd | 4 bigrquery-0.2.0/bigrquery/man/get_dataset.Rd |only bigrquery-0.2.0/bigrquery/man/get_job.Rd | 6 bigrquery-0.2.0/bigrquery/man/get_table.Rd | 16 + bigrquery-0.2.0/bigrquery/man/insert_dataset.Rd |only bigrquery-0.2.0/bigrquery/man/insert_query_job.Rd | 6 bigrquery-0.2.0/bigrquery/man/insert_upload_job.Rd | 22 ++ bigrquery-0.2.0/bigrquery/man/list_datasets.Rd | 6 bigrquery-0.2.0/bigrquery/man/list_projects.Rd | 2 bigrquery-0.2.0/bigrquery/man/list_tabledata.Rd | 18 +- bigrquery-0.2.0/bigrquery/man/list_tables.Rd | 4 bigrquery-0.2.0/bigrquery/man/parse_dataset.Rd | 13 + bigrquery-0.2.0/bigrquery/man/parse_table.Rd | 13 + bigrquery-0.2.0/bigrquery/man/query_exec.Rd | 2 bigrquery-0.2.0/bigrquery/man/src_bigquery.Rd | 2 bigrquery-0.2.0/bigrquery/man/update_dataset.Rd |only bigrquery-0.2.0/bigrquery/man/wait_for.Rd | 8 bigrquery-0.2.0/bigrquery/tests/testthat/test-datasets.r |only bigrquery-0.2.0/bigrquery/tests/testthat/test-id.r |only bigrquery-0.2.0/bigrquery/tests/testthat/test-request.r |only bigrquery-0.2.0/bigrquery/tests/testthat/test-tables.r |only 46 files changed, 603 insertions(+), 191 deletions(-)
Title: Embedded JavaScript Engine
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 0.10 dated 2016-01-29 and 1.0.0 dated 2016-03-03
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 3 +++ R/RcppExports.R | 8 -------- R/V8.R | 6 +++--- inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.Rmd | 15 +++++++++++++++ inst/doc/v8_intro.html | 17 ++++++++++++++--- src/Makevars.in | 5 ----- src/Makevars.win | 4 +++- src/RcppExports.cpp | 32 ++++---------------------------- src/V8.cpp | 35 +++++++++++------------------------ vignettes/v8_intro.Rmd | 15 +++++++++++++++ 13 files changed, 86 insertions(+), 90 deletions(-)
Title: Predict Presence of Signal Peptides
Description: Predicts the presence of signal peptides in eukaryotic protein
using hidden semi-Markov models. The implemented algorithm can be accessed from
both the command line and GUI.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between signalHsmm versions 1.3 dated 2015-07-03 and 1.4 dated 2016-03-03
signalHsmm-1.3/signalHsmm/inst/logo.png |only signalHsmm-1.4/signalHsmm/CHANGELOG | 13 signalHsmm-1.4/signalHsmm/DESCRIPTION | 19 - signalHsmm-1.4/signalHsmm/MD5 | 80 ++-- signalHsmm-1.4/signalHsmm/NAMESPACE | 3 signalHsmm-1.4/signalHsmm/R/datasets.R | 4 signalHsmm-1.4/signalHsmm/R/find_nhc.R | 4 signalHsmm-1.4/signalHsmm/R/hsmm_pred.R | 81 ++-- signalHsmm-1.4/signalHsmm/R/hsmm_pred_list.R | 9 signalHsmm-1.4/signalHsmm/R/read_uniprot.R | 187 ++++------ signalHsmm-1.4/signalHsmm/R/run_signalHsmm.R | 140 ++----- signalHsmm-1.4/signalHsmm/R/signalHsmm.R | 4 signalHsmm-1.4/signalHsmm/R/train_hsmm.R | 94 ++--- signalHsmm-1.4/signalHsmm/R/utils.R | 29 + signalHsmm-1.4/signalHsmm/README.md | 6 signalHsmm-1.4/signalHsmm/data/aaaggregation.rda |binary signalHsmm-1.4/signalHsmm/inst/CITATION | 8 signalHsmm-1.4/signalHsmm/inst/signal_gui/logo.png |only signalHsmm-1.4/signalHsmm/inst/signal_gui/prots.txt | 8 signalHsmm-1.4/signalHsmm/inst/signal_gui/readme.md | 23 - signalHsmm-1.4/signalHsmm/inst/signal_gui/server.R | 38 +- signalHsmm-1.4/signalHsmm/inst/signal_gui/signalhsmm_report.Rmd | 24 + signalHsmm-1.4/signalHsmm/inst/signal_gui/ui.R | 4 signalHsmm-1.4/signalHsmm/man/aaaggregation.Rd | 8 signalHsmm-1.4/signalHsmm/man/add_k_mer_state.Rd | 4 signalHsmm-1.4/signalHsmm/man/benchmark_dat.Rd | 10 signalHsmm-1.4/signalHsmm/man/duration_viterbi.Rd | 2 signalHsmm-1.4/signalHsmm/man/find_nhc.Rd | 6 signalHsmm-1.4/signalHsmm/man/gui_signalHsmm.Rd | 2 signalHsmm-1.4/signalHsmm/man/hsmm_pred.Rd | 12 signalHsmm-1.4/signalHsmm/man/hsmm_pred_list.Rd | 2 signalHsmm-1.4/signalHsmm/man/is_protein.Rd | 2 signalHsmm-1.4/signalHsmm/man/plot.hsmm_pred.Rd | 9 signalHsmm-1.4/signalHsmm/man/pred2df.Rd | 2 signalHsmm-1.4/signalHsmm/man/predict.sighsmm_model.Rd | 2 signalHsmm-1.4/signalHsmm/man/read_txt.Rd | 4 signalHsmm-1.4/signalHsmm/man/read_uniprot.Rd | 19 - signalHsmm-1.4/signalHsmm/man/run_signalHsmm.Rd | 28 - signalHsmm-1.4/signalHsmm/man/signalHsmm.Rd | 25 - signalHsmm-1.4/signalHsmm/man/summary.hsmm_pred.Rd | 7 signalHsmm-1.4/signalHsmm/man/summary.hsmm_pred_list.Rd | 2 signalHsmm-1.4/signalHsmm/man/train_hsmm.Rd | 6 42 files changed, 501 insertions(+), 429 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools
<http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and
others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.1.0 dated 2015-10-16 and 2.2.0 dated 2016-03-03
DESCRIPTION | 18 ++- MD5 | 100 ++++++++++---------- NAMESPACE | 5 - NEWS | 21 ++++ R/affine.R | 124 +++++++++++++++---------- R/image.R | 17 +++ R/nifti.R | 22 +++- R/niftyreg.R | 72 +++++++------- R/transform.R | 11 +- man/affine.Rd | 27 +++-- man/applyTransform.Rd | 11 +- man/buildAffine.Rd | 2 man/composeTransforms.Rd | 4 man/decomposeAffine.Rd | 53 +++++----- man/deformationField.Rd | 2 man/dumpNifti.Rd | 13 ++ man/forward.Rd | 2 man/halfTransform.Rd | 2 man/internalImage.Rd | 2 man/invertAffine.Rd | 3 man/isImage.Rd | 4 man/jacobian.Rd | 2 man/ndim.Rd | 2 man/niftyreg.Rd | 53 +++++++--- man/niftyreg.linear.Rd | 11 +- man/niftyreg.nonlinear.Rd | 11 +- man/pixdim.Rd | 8 + man/readAffine.Rd | 3 man/readNifti.Rd | 4 man/updateNifti.Rd | 6 - man/voxelToWorld.Rd | 2 man/writeAffine.Rd | 11 +- man/writeNifti.Rd | 10 +- man/xform.Rd | 4 src/Makevars | 2 src/NiftiImage.cpp | 168 +++++++++++++++++++++++++++++++--- src/NiftiImage.h | 10 +- src/main.cpp | 33 +++--- src/reg-lib/_reg_f3d_sym.cpp | 2 src/reg-lib/cpu/_reg_KLdivergence.cpp | 4 src/reg-lib/cpu/_reg_dti.cpp | 4 src/reg-lib/cpu/_reg_femTrans.cpp | 2 src/reg-lib/cpu/_reg_lncc.cpp | 8 - src/reg-lib/cpu/_reg_localTrans.cpp | 24 ++-- src/reg-lib/cpu/_reg_maths.cpp | 2 src/reg-lib/cpu/_reg_resampling.cpp | 19 ++- src/reg-lib/cpu/_reg_ssd.cpp | 4 src/reg-lib/cpu/_reg_tools.cpp | 4 tests/testthat/test-05-nifti.R | 5 + tests/testthat/test-25-transform.R | 1 tests/testthat/test-30-multireg.R | 2 51 files changed, 629 insertions(+), 307 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.10.1 dated 2016-01-29 and 1.10.2 dated 2016-03-03
CHANGELOG | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/kda.R | 34 ++++++++++++++++++++-------------- R/kdde.R | 8 +++++--- R/kde.R | 11 ++++++----- build/vignette.rds |binary inst/doc/kde.pdf |binary man/kde.Rd | 5 +++-- 9 files changed, 51 insertions(+), 36 deletions(-)
Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Testing. It is recommended for research purposes only.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>
Diff between IMak versions 1.0.0 dated 2016-01-28 and 1.1.0 dated 2016-03-03
DESCRIPTION | 6 MD5 | 12 - R/buildfa.R | 359 ++++++++++++++++++++++++++++++-------------------------- R/plotfa.R | 160 ++++++++++++------------ man/IMak.Rd | 4 man/build_fa.Rd | 50 +++---- man/plot_fa.Rd | 70 +++++----- 7 files changed, 348 insertions(+), 313 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness
Estimation
Description: GAMs, GAMMs and other generalized ridge regression with
multiple smoothing parameter estimation by GCV, REML or UBRE/AIC.
Includes a gam() function, a wide variety of smoothers, JAGS
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-11 dated 2016-01-23 and 1.8-12 dated 2016-03-03
ChangeLog | 36 ++- DESCRIPTION | 6 MD5 | 55 ++-- NAMESPACE | 12 - R/bam.r | 16 - R/coxph.r | 22 - R/gam.fit3.r | 166 ++++++++++--- R/gam.fit4.r | 40 ++- R/gamm.r | 6 R/jagam.r | 2 R/mgcv.r | 164 +------------ R/misc.r | 76 ++++++ R/mvam.r | 8 R/plots.r | 8 R/smooth.r | 394 +++++++++++++++++++++++++-------- man/bam.Rd | 4 man/bandchol.Rd |only man/gam.Rd | 4 man/gamm.Rd | 4 man/missing.data.Rd |only man/negbin.Rd | 16 - man/random.effects.Rd | 6 man/sdiag.Rd |only man/smooth.construct.bs.smooth.spec.Rd |only man/smooth.construct.ps.smooth.spec.Rd | 55 ++++ man/smooth.construct.re.smooth.spec.Rd | 28 ++ man/trichol.Rd |only src/gdi.c | 66 ++++- src/init.c | 8 src/mat.c | 25 ++ src/mgcv.h | 8 31 files changed, 834 insertions(+), 401 deletions(-)
Title: Analyzing Wildlife Data with Detection Error
Description: Models for analyzing site occupancy and count data models
with detection error, including single-visit based models,
conditional distance sampling and time-removal models.
Package development was supported by the
Alberta Biodiversity Monitoring Institute (www.abmi.ca)
and the Boreal Avian Modelling Project (borealbirds.ca).
Author: Peter Solymos [cre, aut], Monica Moreno [aut], Subhash R. Lele [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between detect versions 0.3-2 dated 2014-05-16 and 0.4-0 dated 2016-03-03
DESCRIPTION | 28 +- MD5 | 163 ++++++------ NAMESPACE | 29 +- R/AUC.R | 6 R/AUC.svocc.R | 46 +-- R/bootstrap.R | 6 R/bootstrap.svisit.R | 126 ++++----- R/case.names.svisit.R | 12 R/cmulti.R | 8 R/coef.summary.svabu.R | 28 +- R/coef.summary.svocc.R | 26 - R/coef.svabu.R | 44 +-- R/coef.svocc.R | 28 +- R/confint.svabu.R | 118 ++++----- R/confint.svocc.R | 92 +++---- R/convertEDR.R | 34 +- R/drop.scope.svocc.R | 22 - R/drop1.svabu.R | 274 ++++++++++---------- R/drop1.svocc.R | 312 +++++++++++------------ R/extractAIC.svisit.R | 12 R/extractBOOT.R | 6 R/extractBOOT.svabu.R | 92 +++---- R/extractBOOT.svocc.R | 66 ++--- R/extractMLE.R | 6 R/extractMLE.svocc.R | 64 ++-- R/fitted.cmulti.R | 16 - R/fitted.svabu.R | 8 R/hbootindex.R | 71 ++--- R/is.present.R | 6 R/is.present.svisit.R | 43 +-- R/load_BAM_QPAD.R | 41 +-- R/logLik.cmulti.R | 12 R/logLik.svisit.R | 18 - R/model.frame.svisit.R | 12 R/model.matrix.svabu.R | 40 +-- R/model.matrix.svocc.R | 26 - R/plot.svabu.R | 162 ++++++------ R/predict.svabu.R | 132 +++++----- R/predict.svocc.R | 84 +++--- R/predictMCMC.R | 6 R/predictMCMC.svabu.R | 68 ++--- R/print.cmulti.R | 40 +-- R/print.summary.cmulti.R | 50 +-- R/print.summary.svabu.R | 106 ++++---- R/print.summary.svocc.R | 74 ++--- R/print.svabu.R | 66 ++--- R/print.svocc.R | 56 ++-- R/rocplot.R | 6 R/rocplot.svocc.R | 42 +-- R/simulate.svabu.R | 90 +++--- R/simulate.svocc.R | 48 +-- R/summary.cmulti.R | 42 +-- R/summary.svabu.R | 106 ++++---- R/summary.svocc.R | 102 +++---- R/svabu.R | 164 ++++++------ R/svabu.fit.R | 438 ++++++++++++++++----------------- R/svabu.step.R | 390 ++++++++++++++--------------- R/svabu_nb.fit.R |only R/svisitFormula.R | 144 +++++----- R/svocc.R | 112 ++++---- R/svocc.fit.R | 603 ++++++++++++++++++++++------------------------ R/svocc.step.R | 390 ++++++++++++++--------------- R/terms.svisit.R | 12 R/update.formula.svisit.R | 56 ++-- R/update.svisit.R | 102 +++---- R/variable.names.svisit.R | 12 R/vcov.cmulti.R | 16 - R/vcov.svabu.R | 102 +++---- R/vcov.svocc.R | 76 ++--- inst/ChangeLog | 117 +++++--- man/AUC.Rd | 62 ++-- man/bootstrap.Rd | 60 ++-- man/cmulti.Rd | 484 ++++++++++++++++++------------------ man/convertEDR.Rd | 114 ++++---- man/databu.Rd | 143 +++++----- man/datocc.Rd | 120 ++++----- man/detect-package.Rd | 128 ++++----- man/hbootindex.Rd | 102 +++---- man/internals.Rd | 90 +++--- man/load_BAM_QPAD.Rd | 79 ++---- man/oven.Rd | 74 ++--- man/svabu.Rd | 460 +++++++++++++++++------------------ man/svocc.Rd | 420 ++++++++++++++++---------------- 83 files changed, 4171 insertions(+), 4120 deletions(-)
Title: Reading ASD Binary Files in R
Description: A simple driver that reads binary data created by the ASD Inc.
portable spectrometer instruments, such as the FieldSpec (for more information,
see <http://www.asdi.com/products/fieldspec-spectroradiometers>). Spectral data
can be extracted from the ASD files as raw (DN), white reference, radiance, or
reflectance. Additionally, the metadata information contained in the ASD file
header can also be accessed.
Author: Pierre Roudier [aut, cre]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between asdreader versions 0.1-1 dated 2015-09-24 and 0.1-2 dated 2016-03-03
DESCRIPTION | 23 ++++++++++++----------- MD5 | 8 ++++---- R/asdreader.r | 24 +++++++++++++++++++++--- README.md | 3 ++- man/get_spectra.Rd | 18 ++++++++++++++++-- 5 files changed, 55 insertions(+), 21 deletions(-)
Title: Weighted Random Sampling without Replacement
Description: A collection of implementations of classical and novel
algorithms for weighted sampling without replacement.
Author: Kirill Müller [aut, cre]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between wrswoR versions 1.0 dated 2016-02-22 and 1.0-1 dated 2016-03-03
DESCRIPTION | 7 +- MD5 | 33 ++++++------- NEWS.md | 6 ++ R/sample_int_R.R | 7 ++ R/sample_int_ccrank.R | 8 ++- R/sample_int_crank.R | 8 ++- R/sample_int_expj.R | 10 ++-- R/sample_int_expjs.R | 10 ++-- R/sample_int_rank.R | 12 ++-- R/sample_int_rej.R | 8 ++- R/wrswoR-package.R | 2 inst/doc/wrswoR.R | 14 +++-- inst/doc/wrswoR.Rmd | 111 ++++++++++++++++++++++++++------------------- inst/doc/wrswoR.pdf |binary man/sample_int.Rd | 63 +++++++++++++++---------- man/wrswoR-package.Rd | 2 vignettes/pair_of_dice.pdf |only vignettes/wrswoR.Rmd | 111 ++++++++++++++++++++++++++------------------- 18 files changed, 241 insertions(+), 171 deletions(-)
Title: Some Additional Distributions
Description: Provides the density, distribution, quantile and generation
functions of some obscure probability distributions, including the doubly non-
central t, F, Beta, and Eta distributions; Lecoutre's lambda-prime and K-prime;
the upsilon distribution; the (weighted) sum of non-central chi-squares to a
power; the (weighted) sum of log non-central chi-squares; the product of non-
central chi-squares to powers; the product of doubly non-central F variates.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between sadists versions 0.2.1 dated 2015-06-11 and 0.2.2 dated 2016-03-03
DESCRIPTION | 21 +++++----- MD5 | 68 ++++++++++++++++---------------- NAMESPACE | 5 +- R/cumulants.r | 39 ------------------ R/dnbeta.r | 4 - R/dneta.r | 2 R/moments.r | 41 ------------------- R/prodchisqpow.r | 2 R/runExample.r | 4 - R/sadists.r | 8 +++ R/sumchisqpow.r | 5 +- R/sumlogchisq.r | 2 R/utils.r | 73 ++--------------------------------- README.md | 23 ++++++----- build/vignette.rds |binary inst/doc/sadists.R | 6 +- inst/doc/sadists.Rnw | 27 +++++++++++- inst/doc/sadists.pdf |binary inst/shiny-examples/sadists/server.R | 4 - man/NEWS.Rd | 9 +++- man/ddnbeta.Rd | 22 +++++----- man/ddneta.Rd | 22 +++++----- man/ddnf.Rd | 22 +++++----- man/ddnt.Rd | 20 ++++----- man/dkprime.Rd | 27 ++++++------ man/dlambdap.Rd | 25 ++++++----- man/dprodchisqpow.Rd | 28 ++++++------- man/dproddnf.Rd | 34 ++++++++-------- man/dsumchisqpow.Rd | 30 ++++++++------ man/dsumlogchisq.Rd | 22 +++++----- man/dupsilon.Rd | 32 +++++++-------- man/runExample.Rd | 12 ++--- man/sadists.Rd | 42 ++++++++++---------- tests |only vignettes/sadists.Rnw | 27 +++++++++++- 35 files changed, 322 insertions(+), 386 deletions(-)
Title: Data and Functions from the Book R Graphics, Second Edition
Description: Data and Functions from the book R Graphics, Second Edition. There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.
Author: Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between RGraphics versions 2.0-13 dated 2015-11-19 and 2.0-14 dated 2016-03-03
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Graphical Integrated Text Mining Solution
Description: An 'R Commander' plug-in providing an integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, vocabulary tables, terms
co-occurrences and documents similarity measures, time series analysis,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files, 'Twitter' queries,
as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between RcmdrPlugin.temis versions 0.7.4 dated 2015-08-19 and 0.7.5 dated 2016-03-03
DESCRIPTION | 16 ++++++++-------- MD5 | 10 ++++++---- NEWS | 3 +++ R/corpusCa.R | 2 +- R/corpusClustering.R | 2 +- inst/po/sl |only po/R-sl.po |only 7 files changed, 19 insertions(+), 14 deletions(-)
More information about RcmdrPlugin.temis at CRAN
Permanent link
Title: PDQ Functions via Gram Charlier, Edgeworth, and Cornish Fisher
Approximations
Description: A collection of tools for approximating the 'PDQ' functions (respectively, the
cumulative distribution, density, and quantile) of probability distributions via classical
expansions involving moments and cumulants.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between PDQutils versions 0.1.3 dated 2016-01-05 and 0.1.4 dated 2016-03-03
DESCRIPTION | 16 +++++++--------- MD5 | 10 +++++----- inst/doc/PDQutils.R | 6 +++--- inst/doc/PDQutils.Rnw | 6 +++--- inst/doc/PDQutils.pdf |binary vignettes/PDQutils.Rnw | 6 +++--- 6 files changed, 21 insertions(+), 23 deletions(-)
Title: Logistic Ordinal Regression Differential Item Functioning using
IRT
Description: Analysis of Differential Item Functioning (DIF) for
dichotomous and polytomous items using an iterative hybrid of
ordinal logistic regression and item response theory (IRT).
Author: Seung W. Choi, with contributions from Laura E. Gibbons and
Paul K. Crane
Maintainer: Seung W. Choi <choi.phd@gmail.com>
Diff between lordif versions 0.3-2 dated 2015-09-18 and 0.3-3 dated 2016-03-03
DESCRIPTION | 8 +-- MD5 | 67 ++++++++++++++++----------------- NAMESPACE | 2 R/DFIT.R | 4 - R/calcprob.R | 4 - R/calctheta.R | 2 R/extract.R | 6 +- R/getcutoff.R | 2 R/lordif-internal.R |only R/lordif.R | 101 +++++++++++++++++++++++++++++--------------------- R/montecarlo.R | 47 +++++++++++++---------- R/permute.R | 49 +++++++++++++----------- R/plot.lordif.MC.R | 14 +++--- R/plot.lordif.R | 10 +++- R/print.lordif.R | 3 - R/probgrm.R | 2 R/rundif.R | 6 +- R/runolr.R | 8 +-- R/separate.R | 2 data/Anxiety.rda |binary man/Anxiety.Rd | 3 - man/DFIT.Rd | 6 +- man/lordif-package.Rd | 42 ++++++++++++-------- man/lordif.Rd | 15 +++---- man/montecarlo.Rd | 22 +++++++--- man/permute.Rd | 22 ++++++---- man/plot.lordif.MC.Rd | 23 ++++++++--- man/plot.lordif.Rd | 27 +++++++++---- man/probgpcm.Rd | 27 ++++++++----- man/probgrm.Rd | 27 ++++++++----- man/recode.Rd | 15 +++++-- man/rundif.Rd | 26 ++++++++---- man/runolr.Rd | 29 ++++++++++---- man/separate.Rd | 16 +++++-- man/tcc.Rd | 20 ++++----- 35 files changed, 399 insertions(+), 258 deletions(-)
Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate georeferenced point data via
Inverse Path Distance Weighting. Useful for coastal marine applications where
barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek <jstachel@sfwmd.gov>
Maintainer: Joseph Stachelek <jstachel@sfwmd.gov>
Diff between ipdw versions 0.2-3 dated 2015-08-16 and 0.2-4 dated 2016-03-03
ipdw-0.2-3/ipdw/TODO |only ipdw-0.2-4/ipdw/DESCRIPTION | 13 +-- ipdw-0.2-4/ipdw/MD5 | 40 +++++---- ipdw-0.2-4/ipdw/NAMESPACE | 3 ipdw-0.2-4/ipdw/R/costrasterGen.R | 91 +++++++++++----------- ipdw-0.2-4/ipdw/R/errorGen.R | 54 ++++++------- ipdw-0.2-4/ipdw/R/ipdw.R | 13 +-- ipdw-0.2-4/ipdw/R/ipdwInterp.R | 123 +++++++++++++----------------- ipdw-0.2-4/ipdw/R/pathdistGen.R | 89 ++++++++++----------- ipdw-0.2-4/ipdw/build/vignette.rds |binary ipdw-0.2-4/ipdw/inst/doc/ipdw.R | 9 +- ipdw-0.2-4/ipdw/inst/doc/ipdw.Rnw | 11 +- ipdw-0.2-4/ipdw/inst/doc/ipdw.pdf |binary ipdw-0.2-4/ipdw/man/costrasterGen.Rd | 25 +++--- ipdw-0.2-4/ipdw/man/errorGen.Rd | 27 +++--- ipdw-0.2-4/ipdw/man/ipdw.Rd | 18 ++-- ipdw-0.2-4/ipdw/man/ipdwInterp.Rd | 24 ++--- ipdw-0.2-4/ipdw/man/pathdistGen.Rd | 28 +++--- ipdw-0.2-4/ipdw/man/rm_na_pointslayers.Rd |only ipdw-0.2-4/ipdw/tests |only ipdw-0.2-4/ipdw/vignettes/ipdw.Rnw | 11 +- 21 files changed, 295 insertions(+), 284 deletions(-)
Title: Replicate and Analyse InterVA4
Description: Provides an R version of the InterVA4 software for
coding cause of death from verbal autopsies. It also provides simple
graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InterVA4 versions 1.6 dated 2015-09-07 and 1.7 dated 2016-03-03
InterVA4-1.6/InterVA4/R/InterVA4_1.6-package.R |only InterVA4-1.7/InterVA4/DESCRIPTION | 8 +-- InterVA4-1.7/InterVA4/MD5 | 31 ++++++++------ InterVA4-1.7/InterVA4/NAMESPACE | 18 ++++++++ InterVA4-1.7/InterVA4/R/InterVA.R | 9 ++-- InterVA4-1.7/InterVA4/R/InterVA.plot.R | 44 ++++++++++++++------- InterVA4-1.7/InterVA4/R/InterVA.summary.r |only InterVA4-1.7/InterVA4/R/InterVA4_1.7-package.R |only InterVA4-1.7/InterVA4/man/CSMF.Rd | 21 ++++++---- InterVA4-1.7/InterVA4/man/CSMF.interVA4.Rd | 2 InterVA4-1.7/InterVA4/man/InterVA.Rd | 6 +- InterVA4-1.7/InterVA4/man/InterVA.plot.Rd | 2 InterVA4-1.7/InterVA4/man/InterVA4-package.Rd | 4 - InterVA4-1.7/InterVA4/man/Population.summary.Rd | 8 +-- InterVA4-1.7/InterVA4/man/SampleInput.Rd | 4 - InterVA4-1.7/InterVA4/man/causetext.Rd | 4 - InterVA4-1.7/InterVA4/man/print.interVA_summary.Rd |only InterVA4-1.7/InterVA4/man/probbase.Rd | 4 - InterVA4-1.7/InterVA4/man/summary.interVA.Rd |only 19 files changed, 107 insertions(+), 58 deletions(-)
Title: Quality Control for Graphics in R
Description: Functions to generate
graphics files, compare them with ``model'' files,
and report the results, including visual and textual
diffs of any differences.
Author: Stephen Gardiner and Paul Murrell
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between graphicsQC versions 1.0-6 dated 2014-12-21 and 1.0-7 dated 2016-03-03
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NAMESPACE | 2 ++ inst/doc/graphicsqc.pdf |binary 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.0 dated 2015-11-10 and 2.1.1 dated 2016-03-03
DESCRIPTION | 8 +-- MD5 | 22 ++++----- R/bammcolors.R | 14 +++++ R/getEventData.R | 2 R/setBAMMpriors.R | 30 ++++++++---- R/traitDependentBAMM.R | 109 +++++++++++----------------------------------- man/BAMMtools-internal.Rd | 44 ------------------ man/BAMMtools-package.Rd | 4 - man/addBAMMlegend.Rd | 2 man/plot.bammdata.Rd | 5 ++ man/setBAMMpriors.Rd | 2 man/traitDependentBAMM.Rd | 7 ++ 12 files changed, 92 insertions(+), 157 deletions(-)
Title: Fits Predator Preferences Model
Description: Fits and simulates data from our predator preferences model, <DOI:10.1007/s10651-016-0341-3>.
Author: Edward A. Roualdes [cre, aut],
Simon J. Bonner [aut]
Maintainer: Edward A. Roualdes <eroualdes@csuchico.edu>
Diff between spiders versions 1.0 dated 2014-12-10 and 1.2 dated 2016-03-02
spiders-1.0/spiders/man/getUnitCounts.Rd |only spiders-1.2/spiders/DESCRIPTION | 24 ++++-- spiders-1.2/spiders/MD5 | 73 +++++++++++---------- spiders-1.2/spiders/NAMESPACE | 5 - spiders-1.2/spiders/R/contrasts.R | 34 +++++---- spiders-1.2/spiders/R/estimate1.R | 16 ++-- spiders-1.2/spiders/R/estimateC.R | 21 +++--- spiders-1.2/spiders/R/estimateCs.R | 30 ++++++-- spiders-1.2/spiders/R/estimateCst.R | 39 ++++++++--- spiders-1.2/spiders/R/estimateCt.R | 38 ++++++++-- spiders-1.2/spiders/R/estimateGen.R | 10 +- spiders-1.2/spiders/R/hypotheses.R | 60 ++++++++--------- spiders-1.2/spiders/R/likelihood.R | 3 spiders-1.2/spiders/R/predPref.R | 29 ++++---- spiders-1.2/spiders/R/simPref.R | 14 ++-- spiders-1.2/spiders/R/summary.predPref.R | 57 ++++++++-------- spiders-1.2/spiders/R/util.R | 35 +++------- spiders-1.2/spiders/build |only spiders-1.2/spiders/inst |only spiders-1.2/spiders/man/calcHypotheses.Rd | 29 +++----- spiders-1.2/spiders/man/checkHypotheses.Rd | 5 - spiders-1.2/spiders/man/converged.Rd | 13 +-- spiders-1.2/spiders/man/est1.Rd | 23 ++---- spiders-1.2/spiders/man/estC.Rd | 23 ++---- spiders-1.2/spiders/man/estCs.Rd | 26 ++----- spiders-1.2/spiders/man/estCst.Rd | 23 ++---- spiders-1.2/spiders/man/estCt.Rd | 26 ++----- spiders-1.2/spiders/man/estGen.Rd | 27 +++---- spiders-1.2/spiders/man/getTimeCounts.Rd | 10 +- spiders-1.2/spiders/man/ll.Rd | 26 ++----- spiders-1.2/spiders/man/llEM.Rd | 21 ++---- spiders-1.2/spiders/man/predPref.Rd | 39 ++++------- spiders-1.2/spiders/man/print.summary.predPref.Rd |only spiders-1.2/spiders/man/simPref.Rd | 25 +++---- spiders-1.2/spiders/man/summary.predPref.Rd | 10 +- spiders-1.2/spiders/man/testC.Rd | 66 +++++++++--------- spiders-1.2/spiders/tests/testthat/test_predPref.R | 29 -------- spiders-1.2/spiders/vignettes |only 38 files changed, 451 insertions(+), 458 deletions(-)
Title: Assertions to Check Properties of Sets
Description: A set of predicates and assertions for checking the properties of
sets. This is mainly for use by other package developers who want to
include run-time testing features in their own packages. End-users will
usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.sets versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2016-03-02
assertive.sets-0.0-1/assertive.sets/man/is_set_equal.Rd |only assertive.sets-0.0-2/assertive.sets/DESCRIPTION | 15 - assertive.sets-0.0-2/assertive.sets/MD5 | 18 - assertive.sets-0.0-2/assertive.sets/NAMESPACE | 3 assertive.sets-0.0-2/assertive.sets/NEWS | 3 assertive.sets-0.0-2/assertive.sets/R/assert-is-set.R | 101 +++++----- assertive.sets-0.0-2/assertive.sets/R/is-set.R | 48 +++- assertive.sets-0.0-2/assertive.sets/README.md | 75 +++---- assertive.sets-0.0-2/assertive.sets/man/are_set_equal.Rd |only assertive.sets-0.0-2/assertive.sets/tests/testthat.R | 11 - assertive.sets-0.0-2/assertive.sets/tests/testthat/test-is-set.R | 28 ++ 11 files changed, 177 insertions(+), 125 deletions(-)
More information about assertive.sets at CRAN
Permanent link
Title: Assertions to Check Properties of Variables
Description: A set of predicates and assertions for checking the properties of
variables, such as length, names and attributes. This is mainly for use by
other package developers who want to include run-time testing features in
their own packages. End-users will usually want to use assertive directly.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between assertive.properties versions 0.0-1 dated 2015-10-06 and 0.0-2 dated 2016-03-02
assertive.properties-0.0-1/assertive.properties/inst |only assertive.properties-0.0-2/assertive.properties/DESCRIPTION | 20 - assertive.properties-0.0-2/assertive.properties/MD5 | 64 ++-- assertive.properties-0.0-2/assertive.properties/NAMESPACE | 146 +++++---- assertive.properties-0.0-2/assertive.properties/NEWS | 3 assertive.properties-0.0-2/assertive.properties/R/are-same-size.R | 2 assertive.properties-0.0-2/assertive.properties/R/assert-are-same-size.R | 8 assertive.properties-0.0-2/assertive.properties/R/assert-has-slot.R |only assertive.properties-0.0-2/assertive.properties/R/assert-is-atomic-recursive-vector.R | 26 + assertive.properties-0.0-2/assertive.properties/R/has-attributes.R | 151 +++++----- assertive.properties-0.0-2/assertive.properties/R/has-slot.R |only assertive.properties-0.0-2/assertive.properties/R/imports.R | 2 assertive.properties-0.0-2/assertive.properties/R/is-atomic-recursive-vector.R | 56 +++ assertive.properties-0.0-2/assertive.properties/R/is-empty-scalar.R | 2 assertive.properties-0.0-2/assertive.properties/R/is-unsorted.R | 6 assertive.properties-0.0-2/assertive.properties/README.md | 130 ++++---- assertive.properties-0.0-2/assertive.properties/man/DIM.Rd | 6 assertive.properties-0.0-2/assertive.properties/man/are_same_length.Rd | 20 - assertive.properties-0.0-2/assertive.properties/man/has_any_attributes.Rd | 64 ++-- assertive.properties-0.0-2/assertive.properties/man/has_attributes.Rd | 4 assertive.properties-0.0-2/assertive.properties/man/has_cols.Rd | 8 assertive.properties-0.0-2/assertive.properties/man/has_dims.Rd | 2 assertive.properties-0.0-2/assertive.properties/man/has_duplicates.Rd | 8 assertive.properties-0.0-2/assertive.properties/man/has_names.Rd | 12 assertive.properties-0.0-2/assertive.properties/man/has_slot.Rd |only assertive.properties-0.0-2/assertive.properties/man/is_atomic.Rd | 52 ++- assertive.properties-0.0-2/assertive.properties/man/is_empty.Rd | 10 assertive.properties-0.0-2/assertive.properties/man/is_null.Rd | 6 assertive.properties-0.0-2/assertive.properties/man/is_unsorted.Rd | 10 assertive.properties-0.0-2/assertive.properties/man/n_elements.Rd | 2 assertive.properties-0.0-2/assertive.properties/po/R-assertive.properties.pot | 134 ++++---- assertive.properties-0.0-2/assertive.properties/tests/testthat.R | 7 assertive.properties-0.0-2/assertive.properties/tests/testthat/test-has-attributes.R | 5 assertive.properties-0.0-2/assertive.properties/tests/testthat/test-is-atomic-recursive-vector.R | 27 + 34 files changed, 581 insertions(+), 412 deletions(-)
More information about assertive.properties at CRAN
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Title: A Multiple Comparison Perspective
Description: Accompanies "Designing experiments and analyzing data: A model comparison perspective"" (3rd ed.) Maxwell, Delaney, & Kelley (forthcoming). This package contains all of the data sets in the book. Information about the book is available here <http://www.DesigningExperiments.com>.
Author: Scott Maxwell [aut],
Harold Delaney [aut],
Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between AMCP versions 0.0.1 dated 2016-02-11 and 0.0.2 dated 2016-03-02
DESCRIPTION | 10 +-- MD5 | 104 ++++++++++++++++---------------- build/partial.rdb |binary data/chapter_4_table_1.rda |only man/chapter_10_table_5.Rd | 69 ++++++++++----------- man/chapter_10_table_9.Rd | 67 ++++++++++---------- man/chapter_11_table_1.Rd | 69 ++++++++++----------- man/chapter_11_table_19.Rd | 73 +++++++++++----------- man/chapter_11_table_20.Rd | 67 ++++++++++---------- man/chapter_11_table_4.Rd | 65 +++++++++----------- man/chapter_11_table_5.Rd | 69 ++++++++++----------- man/chapter_12_table_1.Rd | 73 +++++++++++----------- man/chapter_12_table_11.Rd | 63 +++++++++---------- man/chapter_12_table_15.Rd | 63 +++++++++---------- man/chapter_12_table_21.Rd | 75 +++++++++++------------ man/chapter_12_table_7.Rd | 63 +++++++++---------- man/chapter_12_table_9.Rd | 61 +++++++++--------- man/chapter_13_table_1.Rd | 69 ++++++++++----------- man/chapter_13_table_12.Rd | 65 +++++++++----------- man/chapter_13_table_14.Rd | 61 +++++++++--------- man/chapter_13_table_2.Rd | 63 +++++++++---------- man/chapter_13_table_5.Rd | 65 +++++++++----------- man/chapter_14_table_1.Rd | 65 +++++++++----------- man/chapter_14_table_10.Rd | 73 +++++++++++----------- man/chapter_14_table_3.Rd | 67 ++++++++++---------- man/chapter_14_table_4.Rd | 69 ++++++++++----------- man/chapter_14_table_5.Rd | 67 ++++++++++---------- man/chapter_14_table_8.Rd | 67 ++++++++++---------- man/chapter_15_table_1.Rd | 69 ++++++++++----------- man/chapter_16_table_1.Rd | 63 +++++++++---------- man/chapter_16_table_4.Rd | 73 +++++++++++----------- man/chapter_2_table_1.Rd | 87 +++++++++++++------------- man/chapter_3_table_1.Rd | 67 ++++++++++---------- man/chapter_3_table_3.Rd | 67 ++++++++++---------- man/chapter_3_table_7_and_9_raw_data.Rd | 74 +++++++++++----------- man/chapter_4_table_1.Rd |only man/chapter_4_table_7.Rd | 61 +++++++++--------- man/chapter_5_table_4.Rd | 65 +++++++++----------- man/chapter_6_table_1.Rd | 67 ++++++++++---------- man/chapter_7_table_1.Rd | 69 ++++++++++----------- man/chapter_7_table_11.Rd | 67 ++++++++++---------- man/chapter_7_table_15.Rd | 71 ++++++++++----------- man/chapter_7_table_23.Rd | 71 ++++++++++----------- man/chapter_7_table_5.Rd | 71 ++++++++++----------- man/chapter_7_table_9.Rd | 67 ++++++++++---------- man/chapter_8_table_12.Rd | 74 +++++++++++----------- man/chapter_9_extension_table_1.Rd | 63 +++++++++---------- man/chapter_9_table_1.Rd | 71 ++++++++++----------- man/chapter_9_table_11.Rd | 69 ++++++++++----------- man/chapter_9_table_7.Rd | 67 ++++++++++---------- man/tutorial_1_bdi.Rd | 1 man/tutorial_table_t1.Rd | 1 man/tutorial_table_t2.Rd | 63 +++++++++---------- man/tutorial_table_t3.Rd | 1 54 files changed, 1596 insertions(+), 1645 deletions(-)
More information about GoodmanKruskal at CRAN
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Title: Data Explorer
Description: Data exploration process for data analysis and model building, so
that users could focus on understanding data and extracting insights. The
package automatically scans through each variable and does data profiling.
Typical graphical techniques will be performed for both discrete and
continuous features.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>
Diff between DataExplorer versions 0.2.3 dated 2016-03-01 and 0.2.4 dated 2016-03-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 11 +++++++++++ R/GenerateReport.r | 7 +++++-- README.md | 4 +--- 5 files changed, 24 insertions(+), 12 deletions(-)
Title: Bayes Factors, Model Choice and Variable Selection in Linear
Models
Description: Conceived to calculate Bayes factors in linear models and then to provide a formal Bayesian answer to testing and variable selection problems. From a theoretical side, the emphasis in the package is placed on the prior distributions and BayesVarSel allows using a wide range of them: Jeffreys (1961); Zellner and Siow(1980)<DOI:10.1007/bf02888369>; Zellner and Siow(1984); Zellner (1986)<DOI:10.2307/2233941>; Fernandez et al. (2001)<DOI:10.1016/s0304-4076(00)00076-2>; Liang et al. (2008)<DOI:10.1198/016214507000001337> and Bayarri et al. (2012)<DOI:10.1214/12-aos1013>. The interaction with the package is through a friendly interface that syntactically mimics the well-known lm() command of R. The resulting objects can be easily explored providing the user very valuable information (like marginal, joint and conditional inclusion probabilities of potential variables; the highest posterior probability model, HPM; the median probability model, MPM) about the structure of the true -data generating- model. Additionally, "BayesVarSel" incorporates abilities to handle problems with a large number of potential explanatory variables through parallel and heuristic versions of the main commands, Garcia-Donato and Martinez-Beneito (2013)<DOI:10.1080/01621459.2012.742443>.
Author: Gonzalo Garcia-Donato and Anabel Forte
Maintainer: Anabel Forte <anabel.forte@uv.es>
Diff between BayesVarSel versions 1.6.1 dated 2015-01-26 and 1.6.2 dated 2016-03-02
DESCRIPTION | 12 +-- MD5 | 28 ++++---- NAMESPACE | 5 + R/Bvs.R | 66 +++++++++---------- R/GibbsBvs.R | 62 +++++++++--------- R/plotBvs.R | 13 +++ man/BayesFactor.Rd | 20 ++---- man/Bvs.Rd | 20 ++---- man/GibbsBvs.Rd | 11 +-- man/Hald.Rd | 2 man/Ozone35.Rd | 13 +-- man/PBvs.Rd | 14 +--- man/bayesvarsel-package.rd | 21 ++---- src/Gibbsauxiliaryfuncs.c | 55 +++++++++++----- src/mainGibbs.c | 150 +++++++++++++-------------------------------- 15 files changed, 226 insertions(+), 266 deletions(-)
Title: ABC-SMC Inference of STEPCAM
Description: STEPwise Community Assembly Model collection, applying ABC-SMC in order to infer different community assembly processes. Also includes several plotting functions in order to visualize found estimates.
Author: Thijs Janzen & Fons van der Plas
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between STEPCAM versions 1.1 dated 2015-08-07 and 1.1.1 dated 2016-03-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ABC_SMC.R | 6 +++--- man/STEPCAM-package.Rd | 21 ++++++++++----------- 4 files changed, 20 insertions(+), 21 deletions(-)
Title: Render SVG Images into PDF, PNG, PostScript, or Bitmap Arrays
Description: Renders vector-based 'svg' images into high-quality custom-size bitmap
arrays using 'librsvg'. The resulting bitmap can be written to e.g. 'png', 'jpeg'
or 'webp' format. In addition, the package can convert images directly to various
formats such as pdf or postscript.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between rsvg versions 0.4 dated 2016-01-28 and 0.5 dated 2016-03-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ configure | 18 ++++++++++-------- 4 files changed, 20 insertions(+), 14 deletions(-)
Title: Multiple-Output Directional Quantile Regression
Description: Contains basic tools for performing
multiple-output quantile regression and computing
regression quantile contours by means of directional
regression quantiles. In the location case, one can thus
obtain halfspace depth contours in two to six dimensions.
Author: Miroslav Šiman [aut], Pavel Boček [aut, cre]
Maintainer: Pavel Boček <bocek@utia.cas.cz>
Diff between modQR versions 0.1.0 dated 2015-06-18 and 0.1.1 dated 2016-03-02
ChangeLog | 4 ++++ DESCRIPTION | 15 +++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 5 ++++- R/addRow.R | 2 +- R/evalContour.R | 4 ++-- man/compContour.Rd | 2 +- man/evalContour.Rd | 2 +- man/getCTechST.Rd | 2 +- 9 files changed, 29 insertions(+), 23 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with
spatially correlated errors by robust and Gaussian (Restricted)
Maximum Likelihood and for computing robust and customary point
and block external-drift kriging predictions, along with utility
functions for variogram modelling in ad-hoc geostatistical analyses,
model building, model evaluation by cross-validation and for
unbiased back-transformation of kriging predictions of
log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.2-2 dated 2015-12-02 and 0.2-3 dated 2016-03-02
ChangeLog | 13 ++ DESCRIPTION | 26 ++--- MD5 | 32 +++--- NAMESPACE | 4 NEWS | 1 R/georob.S3methods.R | 2 R/georob.cv.R | 16 ++- R/georob.exported.functions.R | 2 R/georob.predict.R | 6 - R/georob.private.functions.R | 15 +-- R/variogram.R | 89 +++++++++++++++-- man/control.georob.Rd | 4 man/fit.variogram.model.Rd | 4 man/georob-package.Rd | 209 ++++++++++++++++++++++++++---------------- man/georob.Rd | 13 +- man/plot.georob.Rd | 45 +++++++-- man/predict.georob.Rd | 4 17 files changed, 329 insertions(+), 156 deletions(-)
Title: Forecasting Time Series by Theta Models
Description: Routines for forecasting univariate time series using Theta Models. Contains several cross-validation routines.
Author: Jose Augusto Fiorucci, Francisco Louzada and Bao Yiqi
Maintainer: Jose Augusto Fiorucci <jafiorucci@gmail.com>
Diff between forecTheta versions 1.1 dated 2015-08-02 and 2.0 dated 2016-03-02
forecTheta-1.1/forecTheta/man/forecastFunctions.Rd |only forecTheta-2.0/forecTheta/ChangeLog | 7 forecTheta-2.0/forecTheta/DESCRIPTION | 20 forecTheta-2.0/forecTheta/MD5 | 23 forecTheta-2.0/forecTheta/NAMESPACE | 17 forecTheta-2.0/forecTheta/R/crossValidationFunctions.R | 6 forecTheta-2.0/forecTheta/R/errorMetricFunctions.R | 4 forecTheta-2.0/forecTheta/R/forecastFunctions.R | 493 +++++++++++++- forecTheta-2.0/forecTheta/man/crossValidationFunctions.Rd | 38 - forecTheta-2.0/forecTheta/man/errorMetricFunctions.Rd | 4 forecTheta-2.0/forecTheta/man/expSmoot.Rd |only forecTheta-2.0/forecTheta/man/forecTheta-package.Rd | 57 - forecTheta-2.0/forecTheta/man/otm.arXiv.Rd |only forecTheta-2.0/forecTheta/man/plot.thetaModel.Rd |only forecTheta-2.0/forecTheta/man/thetaModels.Rd |only 15 files changed, 565 insertions(+), 104 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.6 dated 2016-02-21 and 2.0.7 dated 2016-03-02
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- man/FedData-package.Rd | 4 ++-- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Preparing Experimental Data for Statistical Analysis
Description: Prepares data for statistical analysis (e.g., analysis of variance
;ANOVA) by enabling the user to easily and quickly merge (using the
file_merge() function) raw data files into one merged table and then
aggregate the merged table (using the prep() function) into a finalized
table while keeping track and summarizing every step of the preparation.
The finalized table contain several possibilities for dependent measures of
the dependent variable. Most suitable when measuring variables in an
interval or ratio scale (e.g., reaction-times) and/or discrete values such
as accuracy. Main functions included are file_merge() and prep(). The
file_merge() function vertically merges individual data files (in a long
format) in which each line is a single observation to one single dataset.
The prep() function aggregates the single dataset according to any
combination of grouping variables (i.e., between-subjects and
within-subjects independent variables, respectively), and returns a data
frame with a number of dependent measures for further analysis for each cell
according to the combination of provided grouping variables. Dependent
measures for each cell include among others means before and after rejecting
all values according to a flexible standard deviation criteria, number of
rejected values according to the flexible standard deviation criteria,
proportions of rejected values according to the flexible standard deviation
criteria, number of values before rejection, means after rejecting values
according to procedures described in Van Selst & Jolicoeur (1994; suitable
when measuring reaction-times), standard deviations, medians, means according
to any percentile (e.g., 0.05, 0.25, 0.75, 0.95) and harmonic means. The data
frame prep() returns can also be exported as a txt file to be used for
statistical analysis in other statistical programs.
Author: Ayala S. Allon [aut, cre],
Roy Luria [aut],
James Grange [ctb],
Nachshon Meiran [ctb]
Maintainer: Ayala S. Allon <ayalaallon@gmail.com>
Diff between prepdat versions 1.0.6 dated 2016-02-28 and 1.0.7 dated 2016-03-02
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 7 + R/prep.R | 4 - README.md | 26 +++--- man/file_merge.Rd | 20 ++--- man/prep.Rd | 206 +++++++++++++++++++++++++++++++----------------------- 7 files changed, 161 insertions(+), 120 deletions(-)
Title: Deep Boosting Ensemble Modeling
Description: Provides deep boosting models training, evaluation, predicting and
hyper parameter optimising using grid search and cross validation.
Based on Google's Deep Boosting algorithm, and Google's C++ implementation.
Cortes, C., Mohri, M., & Syed, U. (2014) <URL:
http://machinelearning.wustl.edu/mlpapers/papers/icml2014c2_cortesb14>.
Author: Daniel Marcous [aut, cre], Yotam Sandbank [aut], Google Inc. [cph]
Maintainer: Daniel Marcous <dmarcous@gmail.com>
Diff between deepboost versions 0.1.3 dated 2016-03-01 and 0.1.4 dated 2016-03-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/deepboost-grid-search.R | 2 +- README.md | 4 ++-- src/boost.cc | 33 +++++++++++++++++---------------- src/deepboost_C.cc | 5 ----- src/deepboost_converters.cpp | 1 - src/tree.cc | 24 ++++++++++++------------ 8 files changed, 43 insertions(+), 48 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-4 dated 2015-11-10 and 1.0-5 dated 2016-03-02
adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.Rnw |only adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.pdf |only adegraphics-1.0-4/adegraphics/vignettes/adegraphics.Rnw |only adegraphics-1.0-5/adegraphics/DESCRIPTION | 16 adegraphics-1.0-5/adegraphics/MD5 | 38 - adegraphics-1.0-5/adegraphics/NAMESPACE | 23 adegraphics-1.0-5/adegraphics/R/ADEg.S2.R | 56 +- adegraphics-1.0-5/adegraphics/R/ADEgS.R | 2 adegraphics-1.0-5/adegraphics/R/S2.corcircle.R | 2 adegraphics-1.0-5/adegraphics/R/add.R |only adegraphics-1.0-5/adegraphics/R/ade4-kplot.R | 4 adegraphics-1.0-5/adegraphics/R/ade4-plot.R | 69 +- adegraphics-1.0-5/adegraphics/R/ade4-scatter.R | 8 adegraphics-1.0-5/adegraphics/R/genericMethod.R | 1 adegraphics-1.0-5/adegraphics/R/utils.R | 4 adegraphics-1.0-5/adegraphics/build/vignette.rds |binary adegraphics-1.0-5/adegraphics/inst/doc/adegraphics.R | 361 +++------------ adegraphics-1.0-5/adegraphics/inst/doc/adegraphics.Rmd |only adegraphics-1.0-5/adegraphics/inst/doc/adegraphics.html |only adegraphics-1.0-5/adegraphics/man/addtext.Rd |only adegraphics-1.0-5/adegraphics/man/adegraphics-package.Rd | 4 adegraphics-1.0-5/adegraphics/tests/add.R | 49 +- adegraphics-1.0-5/adegraphics/tests/adegraphics.R | 1 adegraphics-1.0-5/adegraphics/vignettes/adegraphics.Rmd |only 24 files changed, 267 insertions(+), 371 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 1.9.1 dated 2016-02-08 and 1.9.2 dated 2016-03-02
DESCRIPTION | 14 MD5 | 66 NAMESPACE | 2 NEWS | 25 NEWS.md | 43 R/helpfunctions.R | 21 R/sjPlotDist.R | 1044 +++++++------- R/sjPlotFrequencies.R | 2 R/sjPlotGLME.R | 121 + R/sjPlotGroupFrequencies.R | 1761 ++++++++++++------------ R/sjPlotGroupPropTable.R | 524 +++---- R/sjPlotInteractions.R | 69 R/sjPlotLikert.R | 17 R/sjPlotLinreg.R | 3005 ++++++++++++++++++++--------------------- R/sjPlotLinregMultiple.R | 25 R/sjPlotOdds.R | 1903 +++++++++++++------------ R/sjPlotOddsMultiple.R | 880 ++++++------ R/sjPlotPolynomials.R | 574 +++---- R/sjPlotPropTable.R | 1034 +++++++------- R/sjPlotScatter.R | 11 R/sjPlotStackFrequencies.R | 2 R/sjTabFrequencies.R | 1513 ++++++++++---------- README.md | 83 - man/sjPlot-package.Rd | 4 man/sjp.glm.Rd | 64 man/sjp.glmer.Rd | 6 man/sjp.glmm.Rd | 8 man/sjp.lmer.Rd | 5 man/sjp.lmm.Rd | 10 man/sjp.scatter.Rd | 4 man/sjp.xtab.Rd | 5 tests/testthat/test_sjpglmer.R | 328 ++-- tests/testthat/test_sjpint.R | 8 tests/testthat/test_sjplmer.R | 582 +++---- 34 files changed, 7062 insertions(+), 6701 deletions(-)
Title: Fast LXB File Reader
Description: Functions to quickly read LXB parameter data.
Author: Björn Winckler [aut, cre],
James K. Lawless [ctb, cph]
Maintainer: Björn Winckler <bjorn.winckler@gmail.com>
Diff between lxb versions 1.3 dated 2013-10-16 and 1.5 dated 2016-03-02
DESCRIPTION | 18 +++++++++++------- LICENSE | 4 ++-- MD5 | 6 +++--- src/lxb.c | 2 +- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Finding Unique or Duplicated Rows or Columns for Atomic Matrices
Description: An alternative implementation and extension (grpDuplicated) of base::duplicated.matrix, base:anyDuplicated.matrix and base::unique.matrix for matrices of atomic mode, avoiding the time consuming collapse of the matrix into a character vector.
Author: Long Qu [aut, cre]
Maintainer: Long Qu <long.qu@wright.edu>
Diff between uniqueAtomMat versions 0.1-1 dated 2016-02-29 and 0.1-2 dated 2016-03-01
DESCRIPTION | 8 MD5 | 28 +-- NAMESPACE | 32 +-- R/duplicated.matrix.R | 216 ++++++++++++------------ cleanup | 3 cleanup.win | 3 configure | 18 -- configure.win | 15 - man/grpDuplicated.Rd | 178 +++++++++---------- man/unique.Rd | 282 +++++++++++++++---------------- src/dupAtomMat.cpp | 4 src/dupAtomMatHash.cpp | 7 src/rcSetHash.h | 1 tests/testGrpDup.R | 440 ++++++++++++++++++++++++------------------------- tests/testUnique.R | 118 ++++++------- 15 files changed, 678 insertions(+), 675 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.2.2 dated 2016-01-27 and 1.3.0 dated 2016-03-01
DESCRIPTION | 10 +- MD5 | 77 ++++++++++++----- NAMESPACE | 3 NEWS | 15 +++ R/file.R |only R/match.R | 59 ++++++++++--- R/zzz.R | 8 + README.md | 39 ++++++++ man/matches.Rd | 13 ++ man/ore.file.Rd |only man/ore.ismatch.Rd | 7 + man/ore.search.Rd | 4 src/Makevars | 4 src/compile.c | 134 ++++++++++++++++++++++++------ src/compile.h | 8 + src/match.c | 179 +++++++++++++++++++++++++++++++++++------ src/match.h | 13 ++ src/onig/enc/big5.c |only src/onig/enc/cp1251.c |only src/onig/enc/cp932.c |only src/onig/enc/euc_jp.c |only src/onig/enc/euc_kr.c |only src/onig/enc/euc_tw.c |only src/onig/enc/gb18030.c |only src/onig/enc/iso8859_10.c |only src/onig/enc/iso8859_11.c |only src/onig/enc/iso8859_13.c |only src/onig/enc/iso8859_14.c |only src/onig/enc/iso8859_15.c |only src/onig/enc/iso8859_16.c |only src/onig/enc/iso8859_2.c |only src/onig/enc/iso8859_3.c |only src/onig/enc/iso8859_4.c |only src/onig/enc/iso8859_5.c |only src/onig/enc/iso8859_6.c |only src/onig/enc/iso8859_7.c |only src/onig/enc/iso8859_8.c |only src/onig/enc/iso8859_9.c |only src/onig/enc/jis |only src/onig/enc/koi8.c |only src/onig/enc/koi8_r.c |only src/onig/enc/sjis.c |only src/onig/enc/utf16_be.c |only src/onig/enc/utf16_le.c |only src/onig/enc/utf32_be.c |only src/onig/enc/utf32_le.c |only src/onig/oniguruma.h | 125 +++++++++++++--------------- src/print.c | 88 +++++++++++--------- src/print.h | 4 src/split.c | 4 src/subst.c | 16 +-- src/wcwidth.c |only src/wcwidth.h |only src/zzz.c | 4 tests/testthat/hello.bin |only tests/testthat/sjis.txt |only tests/testthat/test-10-match.R | 18 ++++ 57 files changed, 611 insertions(+), 221 deletions(-)
Title: Matrix Analysis and Normalization by Concordant Information
Enhancement
Description: High-dimensional data integration is a critical but difficult problem in genomics research because of potential biases from high-throughput experiments. We present MANCIE, a computational method for integrating two genomic data sets with homogenous dimensions from different sources based on a PCA procedure as an approximation to a Bayesian approach.
Author: Tao Wang, Chongzhi Zang
Maintainer: Tao Wang <tao.wang@utsouthwestern.edu>
Diff between MANCIE versions 1.2 dated 2015-09-25 and 1.4 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/summarize_mat.R | 13 ++++++++++--- man/summarize_mat.Rd | 7 +++++-- 5 files changed, 27 insertions(+), 13 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. kriging models, are
applied to global multiobjective optimization of black-box functions.
Multiobjective Expected Improvement and Step-wise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mickael.binois@mines-stetienne.fr>
Diff between GPareto versions 1.0.1 dated 2015-07-03 and 1.0.2 dated 2016-03-01
DESCRIPTION | 18 - MD5 | 89 ++++--- NAMESPACE | 132 +++++----- NEWS | 33 ++ R/CPF.R | 45 +-- R/EHI_2d.R | 12 R/GPareto-package.R | 153 +++++------- R/GParetoptim.R | 134 +++++++--- R/ParetoSetDensity.R |only R/SAA_MEI.R | 27 +- R/TestFunctions.R | 72 +++-- R/checkPredict.R | 30 +- R/crit_EHI.R | 9 R/crit_EMI.R | 6 R/crit_SMS.R | 103 ++++---- R/crit_SUR.R | 12 R/crit_optimizer.R | 71 ++++- R/easyGParetoptim.R |only R/fastfun.R | 56 +++- R/getDesign.R |only R/integration_design_optim.R | 2 R/plotGPareto.R |only R/plotParetoEmp.R | 6 R/plotParetoGrid.R | 17 - R/plotSymDevFun.R | 3 R/plot_uncertainty.R |only build |only inst |only man/CPF.Rd | 225 ++++++++--------- man/GPareto.Rd | 373 ++++++++++++++--------------- man/GParetoptim.Rd | 331 +++++++++++++------------- man/ParetoSetDensity.Rd |only man/TestFunctions.Rd | 205 ++++++++-------- man/checkPredict.Rd | 72 ++--- man/crit_EHI.Rd | 162 ++++++------ man/crit_EMI.Rd | 152 ++++++------ man/crit_SMS.Rd | 153 ++++++------ man/crit_SUR.Rd | 201 ++++++++------- man/crit_optimizer.Rd | 503 ++++++++++++++++++++-------------------- man/easyGParetoptim.Rd |only man/fastfun-class.Rd | 125 +++++---- man/fastfun.Rd | 176 ++++++------- man/getDesign.Rd |only man/integration_design_optim.Rd | 144 +++++------ man/plotGPareto.Rd |only man/plotParetoEmp.Rd | 78 +++--- man/plotParetoGrid.Rd | 62 ++-- man/plotSymDevFun.Rd | 129 +++++----- man/plotSymDifRNP.Rd | 76 +++--- man/plot_uncertainty.Rd |only vignettes |only 51 files changed, 2221 insertions(+), 1976 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.4.0 dated 2016-03-01 and 1.4.1 dated 2016-03-01
DESCRIPTION | 8 +-- MD5 | 20 +++---- R/glmmLasso_RE.R | 94 ++++++++++++++++++++++--------------- R/glmmLasso_noRE.R | 82 ++++++++++++++++++++------------ R/glmm_final.r | 2 R/glmm_final.smooth.r | 2 R/glmm_final.smooth_noRE.R | 2 R/glmm_final_multi_random.r | 2 R/glmm_final_multi_random_smooth.r | 2 R/glmm_final_noRE.R | 2 man/glmmLasso.rd | 4 - 11 files changed, 130 insertions(+), 90 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data
analysis by a unified model specification, along with some data manipulation
functions. This package covers fitting of variety models including Cox
regression models, linear regression models, Poisson regression models, logistic
models and others whose likelihood is expressed in negative binomial, gamma and
Weibull distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.5 dated 2016-02-01 and 0.0.6 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/calcAge.R | 30 +++++++++++++++++++++--------- R/modes.R | 2 +- R/pullOneValue.R | 17 +++++++++++++++-- man/calcAge.Rd | 2 +- man/modes.Rd | 2 +- man/pullOneValue.Rd | 5 ++++- 9 files changed, 61 insertions(+), 27 deletions(-)
Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>
Diff between caseMatch versions 1.0.5 dated 2016-02-02 and 1.0.6 dated 2016-03-01
DESCRIPTION | 8 MD5 | 4 R/case.match.R | 541 ++++++++++++++++++++++++--------------------------------- 3 files changed, 243 insertions(+), 310 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.0 dated 2015-09-04 and 2.1 dated 2016-03-01
BOIN-2.0/BOIN/R/conduct.comb.R |only BOIN-2.0/BOIN/man/BOIN-package.Rd |only BOIN-2.0/BOIN/man/conduct.comb.Rd |only BOIN-2.1/BOIN/DESCRIPTION | 35 - BOIN-2.1/BOIN/MD5 | 35 - BOIN-2.1/BOIN/NAMESPACE | 13 BOIN-2.1/BOIN/R/BOIN.R | 3 BOIN-2.1/BOIN/R/get.boundary.R | 299 +++++++++----- BOIN-2.1/BOIN/R/get.oc.R | 281 ++++++++----- BOIN-2.1/BOIN/R/get.oc.comb.R | 631 +++++++++++++++++++++++++++++-- BOIN-2.1/BOIN/R/get.oc.comb.phase12.R |only BOIN-2.1/BOIN/R/next.comb.R |only BOIN-2.1/BOIN/R/next.subtrial.R |only BOIN-2.1/BOIN/R/select.mtd.R | 235 +++++++---- BOIN-2.1/BOIN/R/select.mtd.comb.R | 196 +++++++-- BOIN-2.1/BOIN/man/get.boundary.Rd | 237 +++++------ BOIN-2.1/BOIN/man/get.oc.Rd | 216 ++++------ BOIN-2.1/BOIN/man/get.oc.comb.Rd | 246 ++++++------ BOIN-2.1/BOIN/man/get.oc.comb.phase12.Rd |only BOIN-2.1/BOIN/man/next.comb.Rd |only BOIN-2.1/BOIN/man/next.subtrial.Rd |only BOIN-2.1/BOIN/man/select.mtd.Rd | 153 +++---- BOIN-2.1/BOIN/man/select.mtd.comb.Rd | 186 ++++----- 23 files changed, 1820 insertions(+), 946 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-27 0.2.1
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre],
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.2 dated 2016-01-22 and 1.3 dated 2016-03-01
DESCRIPTION | 14 MD5 | 60 +- NAMESPACE | 11 NEWS | 13 R/getLocalOptimum.R |only R/getMeanFunction.R |only R/getRefPoint.R |only R/makeMultiObjectiveFunction.R | 16 R/makeObjectiveFunction.R | 23 R/makeSingleObjectiveFunction.R | 12 R/mof.dtlz1.R | 3 R/mof.dtlz2.R | 3 R/mof.dtlz3.R | 3 R/mof.dtlz4.R | 3 R/mof.dtlz5.R | 3 R/mof.dtlz6.R | 3 R/mof.zdt1.R | 5 R/mof.zdt2.R | 3 R/mof.zdt3.R | 3 R/mof.zdt4.R | 3 R/mof.zdt6.R | 3 R/sof.mpm2.R | 42 + inst/mpm2.py | 604 +++++++++++----------- man/getLocalOptimum.Rd |only man/getMeanFunction.Rd |only man/getRefPoint.Rd |only man/makeMPM2Function.Rd | 21 man/makeMultiObjectiveFunction.Rd | 13 man/makeSingleObjectiveFunction.Rd | 12 tests/testthat/Rplots.pdf |binary tests/testthat/test_helpers.R | 31 + tests/testthat/test_isMultiobjective.R | 6 tests/testthat/test_makeSingleObjectiveFunction.R | 18 tests/testthat/test_soofuns.R | 13 34 files changed, 568 insertions(+), 376 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.4 dated 2015-12-27 and 3.4.4 dated 2016-03-01
lessR-3.4.4/lessR/DESCRIPTION | 10 lessR-3.4.4/lessR/MD5 | 164 ++++---- lessR-3.4.4/lessR/NAMESPACE | 7 lessR-3.4.4/lessR/NEWS | 97 +++++ lessR-3.4.4/lessR/R/ANOVA.R | 28 + lessR-3.4.4/lessR/R/ANOVAz1.R | 12 lessR-3.4.4/lessR/R/BarChart.R | 50 +- lessR-3.4.4/lessR/R/BoxPlot.R | 41 +- lessR-3.4.4/lessR/R/Density.R | 40 +- lessR-3.4.4/lessR/R/Help.R | 202 +++++----- lessR-3.4.4/lessR/R/Histogram.R | 57 ++- lessR-3.4.4/lessR/R/LineChart.R | 21 - lessR-3.4.4/lessR/R/Merge.R | 2 lessR-3.4.4/lessR/R/PieChart.R | 4 lessR-3.4.4/lessR/R/Plot.R | 2 lessR-3.4.4/lessR/R/Read.R | 43 +- lessR-3.4.4/lessR/R/Regression.R | 48 +- lessR-3.4.4/lessR/R/ScatterPlot.R | 344 ++++++++++++------ lessR-3.4.4/lessR/R/SummaryStats.R | 21 - lessR-3.4.4/lessR/R/VariableLabels.R | 25 + lessR-3.4.4/lessR/R/anova.Rmd.R |only lessR-3.4.4/lessR/R/bc.data.frame.R | 10 lessR-3.4.4/lessR/R/bc.zmain.R | 225 +++++++---- lessR-3.4.4/lessR/R/bx.zmain.R | 39 +- lessR-3.4.4/lessR/R/corCFA.R | 29 - lessR-3.4.4/lessR/R/corEFA.R | 13 lessR-3.4.4/lessR/R/corFA.Rmd.R |only lessR-3.4.4/lessR/R/corScree.R | 8 lessR-3.4.4/lessR/R/cr.data.frame.R | 56 +- lessR-3.4.4/lessR/R/details.R | 7 lessR-3.4.4/lessR/R/dist.Rmd.R |only lessR-3.4.4/lessR/R/dn.zmain.R | 44 +- lessR-3.4.4/lessR/R/dp.zmain.R | 69 +++ lessR-3.4.4/lessR/R/dpmat.zmain.R |only lessR-3.4.4/lessR/R/hst.zmain.R | 37 + lessR-3.4.4/lessR/R/lc.zmain.R | 75 ++- lessR-3.4.4/lessR/R/logit.z4Pred.R | 20 - lessR-3.4.4/lessR/R/pc.zmain.R | 89 +--- lessR-3.4.4/lessR/R/plt.zmain.R | 546 +++++++++++++++++++---------- lessR-3.4.4/lessR/R/reg.z1bckBasic.R | 11 lessR-3.4.4/lessR/R/reg.z3dnResidual.R | 4 lessR-3.4.4/lessR/R/reg.z3resfitResidual.R | 14 lessR-3.4.4/lessR/R/reg.z5Plot.R | 55 +- lessR-3.4.4/lessR/R/reg.zRmd.R |only lessR-3.4.4/lessR/R/set.R | 2 lessR-3.4.4/lessR/R/simCImean.R | 3 lessR-3.4.4/lessR/R/simCLT.R | 10 lessR-3.4.4/lessR/R/simFlips.R | 8 lessR-3.4.4/lessR/R/simMeans.R | 15 lessR-3.4.4/lessR/R/ss.zdata.frame.R | 6 lessR-3.4.4/lessR/R/ss.zfactor.R | 19 - lessR-3.4.4/lessR/R/ss.znumeric.R | 17 lessR-3.4.4/lessR/R/tt.z1group.R | 5 lessR-3.4.4/lessR/R/tt.z2group.R | 14 lessR-3.4.4/lessR/R/tt.zformula.R | 39 +- lessR-3.4.4/lessR/R/ttest.R | 32 + lessR-3.4.4/lessR/R/ttp2zgraph.R | 43 +- lessR-3.4.4/lessR/R/zzz.R | 401 +++++++++++++++------ lessR-3.4.4/lessR/man/ANOVA.Rd | 15 lessR-3.4.4/lessR/man/BarChart.Rd | 57 ++- lessR-3.4.4/lessR/man/BoxPlot.Rd | 39 +- lessR-3.4.4/lessR/man/Correlation.Rd | 2 lessR-3.4.4/lessR/man/Density.Rd | 38 +- lessR-3.4.4/lessR/man/Help.Rd | 6 lessR-3.4.4/lessR/man/Histogram.Rd | 50 +- lessR-3.4.4/lessR/man/LineChart.Rd | 32 + lessR-3.4.4/lessR/man/Merge.Rd | 4 lessR-3.4.4/lessR/man/Nest.Rd | 2 lessR-3.4.4/lessR/man/PieChart.Rd | 5 lessR-3.4.4/lessR/man/Read.Rd | 10 lessR-3.4.4/lessR/man/Regression.Rd | 58 +-- lessR-3.4.4/lessR/man/ScatterPlot.Rd | 268 +++++++------- lessR-3.4.4/lessR/man/Subset.Rd | 17 lessR-3.4.4/lessR/man/SummaryStats.Rd | 2 lessR-3.4.4/lessR/man/Transform.Rd | 6 lessR-3.4.4/lessR/man/VariableLabels.Rd | 4 lessR-3.4.4/lessR/man/corCFA.Rd | 57 +-- lessR-3.4.4/lessR/man/corEFA.Rd | 13 lessR-3.4.4/lessR/man/dataMach4.Rd | 2 lessR-3.4.4/lessR/man/print_outpiece.Rd | 2 lessR-3.4.4/lessR/man/set.Rd | 2 lessR-3.4.4/lessR/man/to.Rd | 6 lessR-3.4/lessR/R/DotPlot.R |only lessR-3.4/lessR/R/anova.zknitr.R |only lessR-3.4/lessR/R/corFA.zknitr.R |only lessR-3.4/lessR/R/dist.zknitr.R |only lessR-3.4/lessR/R/dp.R |only lessR-3.4/lessR/R/hl.R |only lessR-3.4/lessR/R/reg.zknitr.R |only 89 files changed, 2477 insertions(+), 1403 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and
evaluation, ensemble of models.
Author: Wilfried Thuiller [aut, cre],
Damien Georges [aut, cre],
Robin Engler [aut],
Frank Breiner [aut]
Maintainer: Damien Georges <damien.georges2@gmail.com>
Diff between biomod2 versions 3.1-64 dated 2014-12-10 and 3.3-7 dated 2016-03-01
biomod2-3.1-64/biomod2/man/BinaryTransformation.Rd |only biomod2-3.3-7/biomod2/DESCRIPTION | 30 biomod2-3.3-7/biomod2/MD5 | 80 +- biomod2-3.3-7/biomod2/NAMESPACE | 32 biomod2-3.3-7/biomod2/NEWS | 31 biomod2-3.3-7/biomod2/R/BIOMOD_EnsembleForecasting.R | 36 biomod2-3.3-7/biomod2/R/BIOMOD_EnsembleModeling.R | 42 - biomod2-3.3-7/biomod2/R/BIOMOD_FormatingData.R | 4 biomod2-3.3-7/biomod2/R/BIOMOD_Modeling.R | 87 +- biomod2-3.3-7/biomod2/R/BIOMOD_ModelingOptions.R | 67 + biomod2-3.3-7/biomod2/R/BIOMOD_Projection.R | 13 biomod2-3.3-7/biomod2/R/BIOMOD_RangeSize.R | 25 biomod2-3.3-7/biomod2/R/BIOMOD_cv.R |only biomod2-3.3-7/biomod2/R/BIOMOD_presenceonly.R |only biomod2-3.3-7/biomod2/R/BIOMOD_tuning.R |only biomod2-3.3-7/biomod2/R/BinaryTransformation.R | 80 +- biomod2-3.3-7/biomod2/R/Biomod.Models_RE.R | 222 ++++- biomod2-3.3-7/biomod2/R/BiomodClass.R | 409 ++++------ biomod2-3.3-7/biomod2/R/CustomIndexMaker.R | 34 biomod2-3.3-7/biomod2/R/Evaluate.models.R | 126 ++- biomod2-3.3-7/biomod2/R/FilteringTransformation.R | 2 biomod2-3.3-7/biomod2/R/Prepare.Maxent.WorkDir.R | 113 ++ biomod2-3.3-7/biomod2/R/Projection.R | 36 biomod2-3.3-7/biomod2/R/Rescaler4.R | 1 biomod2-3.3-7/biomod2/R/biomod2_models-class.R | 534 ++++++++++---- biomod2-3.3-7/biomod2/R/deprecated_functions.R | 10 biomod2-3.3-7/biomod2/R/pseudo.abs.R | 248 ++++-- biomod2-3.3-7/biomod2/R/sample.factor.levels.R |only biomod2-3.3-7/biomod2/R/scope.R | 3 biomod2-3.3-7/biomod2/R/sre.R | 25 biomod2-3.3-7/biomod2/R/testnull.R | 1 biomod2-3.3-7/biomod2/R/transform.outputs.R | 4 biomod2-3.3-7/biomod2/R/variables_importance.R | 2 biomod2-3.3-7/biomod2/inst/doc/html/00Index.html | 15 biomod2-3.3-7/biomod2/man/BIOMOD.Model.Options-class.Rd | 3 biomod2-3.3-7/biomod2/man/BIOMOD.models.out-methods.Rd | 5 biomod2-3.3-7/biomod2/man/BIOMOD_FormatingData.Rd | 2 biomod2-3.3-7/biomod2/man/BIOMOD_Modeling.Rd | 23 biomod2-3.3-7/biomod2/man/BIOMOD_ModelingOptions.Rd | 45 - biomod2-3.3-7/biomod2/man/BIOMOD_cv.Rd |only biomod2-3.3-7/biomod2/man/BIOMOD_presenceonly.Rd |only biomod2-3.3-7/biomod2/man/BIOMOD_tuning.Rd |only biomod2-3.3-7/biomod2/man/BinaryTransformation-methods.Rd |only biomod2-3.3-7/biomod2/man/Find.Optim.Stat.Rd | 90 +- biomod2-3.3-7/biomod2/man/biomod2_model-class.Rd | 12 biomod2-3.3-7/biomod2/man/sample.factor.levels.Rd |only 46 files changed, 1620 insertions(+), 872 deletions(-)
Title: Calculate Accurate Precision-Recall and Receiver Operator
Characteristics Curves
Description: Accurate calculations and visualization of Precision-Recall and Receiver Operator Characteristics
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.2.0 dated 2015-12-21 and 0.3.1 dated 2016-03-01
DESCRIPTION | 15 +- MD5 | 15 +- NEWS.md |only README.md | 17 +-- inst/doc/introduction.Rmd | 7 + inst/doc/introduction.html | 165 +++++++++++++++++-------------- tests/testthat/test_g_autoplot2_curves.R | 8 - tests/testthat/test_g_autoplot3_points.R | 8 - vignettes/introduction.Rmd | 7 + 9 files changed, 139 insertions(+), 103 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 2.0 dated 2016-02-22 and 2.1 dated 2016-03-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/RFI.R | 10 ++++++++-- 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots (which include 'loaPlot', 'GoogleMap' and 'trianglePlot') use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>
Diff between loa versions 0.2.22 dated 2015-01-20 and 0.2.38 dated 2016-03-01
DESCRIPTION | 28 +-- MD5 | 48 +++-- NAMESPACE | 23 ++ NEWS | 73 ++++++++- R/formulaHandler.R | 147 +++++++++++++++++- R/key.handlers.R | 75 +++++++++ R/lims.and.scales.handlers.R | 70 +++++++- R/loaPlot.R | 21 ++ R/other.panel.functions.R | 8 R/panelPal.R | 76 ++++++++- R/plot.argument.handlers.R | 11 - R/specialist.panels.01.R | 292 +++++++++++++++++++++++++++++++++++- R/stackPlot.R |only R/trianglePlot.R | 11 + data/lat.lon.meuse.RData |binary data/roadmap.meuse.RData |binary inst/CITATION | 19 ++ man/1.1.loaPlot.Rd | 4 man/1.2.googleMap.Rd | 2 man/1.3.trianglePlot.Rd | 2 man/1.4.stackPlot.Rd |only man/2.1.specialist.panels.Rd | 224 ++++++++++++++++++--------- man/4.2.plot.structure.handlers.Rd | 33 +++- man/4.3.lims.and.scales.handlers.Rd | 20 +- man/4.6.key.handlers.Rd | 14 + man/loa-package.Rd | 6 26 files changed, 1047 insertions(+), 160 deletions(-)
Title: An Implementation of the Grammar of Graphics
Description: An implementation of the grammar of graphics in R. It combines the
advantages of both base and lattice graphics: conditioning and shared axes
are handled automatically, and you can still build up a plot step by step
from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map
data to aesthetic attributes. See http://ggplot2.org for more information,
documentation and examples.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ggplot2 versions 2.0.0 dated 2015-12-18 and 2.1.0 dated 2016-03-01
ggplot2-2.0.0/ggplot2/R/translate-qplot-base.r |only ggplot2-2.0.0/ggplot2/man/translate_qplot_base.Rd |only ggplot2-2.1.0/ggplot2/DESCRIPTION | 49 - ggplot2-2.1.0/ggplot2/MD5 | 344 ++++++------- ggplot2-2.1.0/ggplot2/NAMESPACE | 11 ggplot2-2.1.0/ggplot2/NEWS.md |only ggplot2-2.1.0/ggplot2/R/aes.r | 2 ggplot2-2.1.0/ggplot2/R/annotation-custom.r | 17 ggplot2-2.1.0/ggplot2/R/annotation.r | 3 ggplot2-2.1.0/ggplot2/R/bin.R |only ggplot2-2.1.0/ggplot2/R/data.R | 6 ggplot2-2.1.0/ggplot2/R/facet-grid-.r | 142 +---- ggplot2-2.1.0/ggplot2/R/facet-wrap.r | 29 - ggplot2-2.1.0/ggplot2/R/fortify.r | 9 ggplot2-2.1.0/ggplot2/R/geom-.r | 5 ggplot2-2.1.0/ggplot2/R/geom-abline.r | 9 ggplot2-2.1.0/ggplot2/R/geom-bar.r | 12 ggplot2-2.1.0/ggplot2/R/geom-bin2d.r | 10 ggplot2-2.1.0/ggplot2/R/geom-blank.r | 24 ggplot2-2.1.0/ggplot2/R/geom-boxplot.r | 32 - ggplot2-2.1.0/ggplot2/R/geom-contour.r | 15 ggplot2-2.1.0/ggplot2/R/geom-count.r | 10 ggplot2-2.1.0/ggplot2/R/geom-crossbar.r | 10 ggplot2-2.1.0/ggplot2/R/geom-curve.r | 15 ggplot2-2.1.0/ggplot2/R/geom-density.r | 10 ggplot2-2.1.0/ggplot2/R/geom-density2d.r | 15 ggplot2-2.1.0/ggplot2/R/geom-dotplot.r | 24 ggplot2-2.1.0/ggplot2/R/geom-errorbar.r | 9 ggplot2-2.1.0/ggplot2/R/geom-errorbarh.r | 10 ggplot2-2.1.0/ggplot2/R/geom-freqpoly.r | 20 ggplot2-2.1.0/ggplot2/R/geom-hex.r | 10 ggplot2-2.1.0/ggplot2/R/geom-histogram.r | 16 ggplot2-2.1.0/ggplot2/R/geom-hline.r | 3 ggplot2-2.1.0/ggplot2/R/geom-jitter.r | 11 ggplot2-2.1.0/ggplot2/R/geom-label.R | 16 ggplot2-2.1.0/ggplot2/R/geom-linerange.r | 10 ggplot2-2.1.0/ggplot2/R/geom-map.r | 10 ggplot2-2.1.0/ggplot2/R/geom-path.r | 18 ggplot2-2.1.0/ggplot2/R/geom-point.r | 42 - ggplot2-2.1.0/ggplot2/R/geom-pointrange.r | 10 ggplot2-2.1.0/ggplot2/R/geom-polygon.r | 12 ggplot2-2.1.0/ggplot2/R/geom-quantile.r | 14 ggplot2-2.1.0/ggplot2/R/geom-raster.r | 13 ggplot2-2.1.0/ggplot2/R/geom-rect.r | 11 ggplot2-2.1.0/ggplot2/R/geom-ribbon.r | 16 ggplot2-2.1.0/ggplot2/R/geom-rug.r | 11 ggplot2-2.1.0/ggplot2/R/geom-segment.r | 13 ggplot2-2.1.0/ggplot2/R/geom-smooth.r | 21 ggplot2-2.1.0/ggplot2/R/geom-spoke.r | 10 ggplot2-2.1.0/ggplot2/R/geom-text.r | 16 ggplot2-2.1.0/ggplot2/R/geom-tile.r | 14 ggplot2-2.1.0/ggplot2/R/geom-violin.r | 15 ggplot2-2.1.0/ggplot2/R/geom-vline.r | 3 ggplot2-2.1.0/ggplot2/R/ggproto.r | 7 ggplot2-2.1.0/ggplot2/R/guide-legend.r | 45 + ggplot2-2.1.0/ggplot2/R/hexbin.R |only ggplot2-2.1.0/ggplot2/R/labels.r | 10 ggplot2-2.1.0/ggplot2/R/layer.r | 70 ++ ggplot2-2.1.0/ggplot2/R/margins.R | 4 ggplot2-2.1.0/ggplot2/R/panel.r | 4 ggplot2-2.1.0/ggplot2/R/plot-build.r | 4 ggplot2-2.1.0/ggplot2/R/plot-construction.r | 2 ggplot2-2.1.0/ggplot2/R/plot.r | 2 ggplot2-2.1.0/ggplot2/R/position-jitterdodge.R | 15 ggplot2-2.1.0/ggplot2/R/position-nudge.R | 4 ggplot2-2.1.0/ggplot2/R/save.r | 2 ggplot2-2.1.0/ggplot2/R/scale-.r | 5 ggplot2-2.1.0/ggplot2/R/scale-discrete-.r | 34 - ggplot2-2.1.0/ggplot2/R/scale-shape.r | 2 ggplot2-2.1.0/ggplot2/R/scale-size.r | 16 ggplot2-2.1.0/ggplot2/R/scale-type.R |only ggplot2-2.1.0/ggplot2/R/scales-.r | 57 -- ggplot2-2.1.0/ggplot2/R/stat-bin.r | 171 +++--- ggplot2-2.1.0/ggplot2/R/stat-bin2d.r | 19 ggplot2-2.1.0/ggplot2/R/stat-bindot.r | 19 ggplot2-2.1.0/ggplot2/R/stat-binhex.r | 59 -- ggplot2-2.1.0/ggplot2/R/stat-boxplot.r | 10 ggplot2-2.1.0/ggplot2/R/stat-contour.r | 9 ggplot2-2.1.0/ggplot2/R/stat-count.r | 10 ggplot2-2.1.0/ggplot2/R/stat-density-2d.r | 19 ggplot2-2.1.0/ggplot2/R/stat-density.r | 24 ggplot2-2.1.0/ggplot2/R/stat-ecdf.r | 41 - ggplot2-2.1.0/ggplot2/R/stat-ellipse.R | 18 ggplot2-2.1.0/ggplot2/R/stat-function.r | 37 - ggplot2-2.1.0/ggplot2/R/stat-identity.r | 28 - ggplot2-2.1.0/ggplot2/R/stat-qq.r | 17 ggplot2-2.1.0/ggplot2/R/stat-quantile.r | 18 ggplot2-2.1.0/ggplot2/R/stat-smooth-methods.r | 6 ggplot2-2.1.0/ggplot2/R/stat-smooth.r | 19 ggplot2-2.1.0/ggplot2/R/stat-sum.r | 12 ggplot2-2.1.0/ggplot2/R/stat-summary-2d.r | 29 - ggplot2-2.1.0/ggplot2/R/stat-summary-bin.R | 18 ggplot2-2.1.0/ggplot2/R/stat-summary-hex.r | 55 -- ggplot2-2.1.0/ggplot2/R/stat-summary.r | 57 -- ggplot2-2.1.0/ggplot2/R/stat-unique.r | 14 ggplot2-2.1.0/ggplot2/R/stat-ydensity.r | 27 - ggplot2-2.1.0/ggplot2/R/theme-defaults.r | 35 + ggplot2-2.1.0/ggplot2/R/theme.r | 59 +- ggplot2-2.1.0/ggplot2/R/translate-qplot-lattice.r | 13 ggplot2-2.1.0/ggplot2/R/utilities-grid.r | 8 ggplot2-2.1.0/ggplot2/R/zxx.r | 29 + ggplot2-2.1.0/ggplot2/build/partial.rdb |binary ggplot2-2.1.0/ggplot2/build/vignette.rds |binary ggplot2-2.1.0/ggplot2/inst/CITATION | 4 ggplot2-2.1.0/ggplot2/inst/doc/extending-ggplot2.Rmd | 12 ggplot2-2.1.0/ggplot2/inst/doc/extending-ggplot2.html | 196 ++++--- ggplot2-2.1.0/ggplot2/inst/doc/ggplot2-specs.Rmd | 6 ggplot2-2.1.0/ggplot2/inst/doc/ggplot2-specs.html | 97 ++- ggplot2-2.1.0/ggplot2/inst/staticdocs/index.r | 3 ggplot2-2.1.0/ggplot2/man/aes_.Rd | 2 ggplot2-2.1.0/ggplot2/man/annotate.Rd | 6 ggplot2-2.1.0/ggplot2/man/annotation_custom.Rd | 17 ggplot2-2.1.0/ggplot2/man/discrete_scale.Rd | 5 ggplot2-2.1.0/ggplot2/man/facet_grid.Rd | 142 +---- ggplot2-2.1.0/ggplot2/man/geom_abline.Rd | 38 - ggplot2-2.1.0/ggplot2/man/geom_bar.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_bin2d.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_blank.Rd | 53 -- ggplot2-2.1.0/ggplot2/man/geom_boxplot.Rd | 56 +- ggplot2-2.1.0/ggplot2/man/geom_contour.Rd | 45 - ggplot2-2.1.0/ggplot2/man/geom_count.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_density.Rd | 50 + ggplot2-2.1.0/ggplot2/man/geom_density_2d.Rd | 45 - ggplot2-2.1.0/ggplot2/man/geom_dotplot.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_errorbarh.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_hex.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_histogram.Rd | 86 +-- ggplot2-2.1.0/ggplot2/man/geom_jitter.Rd | 54 +- ggplot2-2.1.0/ggplot2/man/geom_linerange.Rd | 48 - ggplot2-2.1.0/ggplot2/man/geom_map.Rd | 46 - ggplot2-2.1.0/ggplot2/man/geom_path.Rd | 46 - ggplot2-2.1.0/ggplot2/man/geom_point.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_polygon.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_quantile.Rd | 47 - ggplot2-2.1.0/ggplot2/man/geom_ribbon.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_rug.Rd | 40 - 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ggplot2-2.1.0/ggplot2/man/theme_update.Rd | 25 ggplot2-2.1.0/ggplot2/man/translate_qplot_lattice.Rd | 13 ggplot2-2.1.0/ggplot2/tests/testthat/Rplots.pdf |only ggplot2-2.1.0/ggplot2/tests/testthat/test-aes-setting.r | 19 ggplot2-2.1.0/ggplot2/tests/testthat/test-boxplot.r | 37 - ggplot2-2.1.0/ggplot2/tests/testthat/test-empty-data.r | 8 ggplot2-2.1.0/ggplot2/tests/testthat/test-facet-strips.r |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-boxplot.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-freqpoly.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-ribbon.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-tile.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-grid-utils.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-layer.r | 13 ggplot2-2.1.0/ggplot2/tests/testthat/test-scale-discrete.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-stat-bin.R | 84 +++ ggplot2-2.1.0/ggplot2/tests/testthat/test-stat-bin2d.R | 4 ggplot2-2.1.0/ggplot2/tests/testthat/test-stats-function.r | 11 ggplot2-2.1.0/ggplot2/vignettes/extending-ggplot2.Rmd | 12 ggplot2-2.1.0/ggplot2/vignettes/ggplot2-specs.Rmd | 6 180 files changed, 2732 insertions(+), 2154 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.7-1 dated 2015-10-12 and 0.8 dated 2016-03-01
gemtc-0.7-1/gemtc/inst/extdata/cipriani-efficacy.gemtc |only gemtc-0.7-1/gemtc/inst/extdata/luades-thrombolytic.gemtc |only gemtc-0.7-1/gemtc/inst/gemtc.study.baseline.priors.txt |only gemtc-0.7-1/gemtc/man/mtc.network.xml.Rd |only gemtc-0.7-1/gemtc/tests/data/fat-survival.data.txt |only gemtc-0.7-1/gemtc/tests/data/fat-survival.summaries.txt |only gemtc-0.7-1/gemtc/tests/data/luades-smoking.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-diff.data.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-shared.data-ab.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-shared.data-re.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson.txt |only gemtc-0.7-1/gemtc/tests/testthat/test-unit-mtc.model_data.re.R |only gemtc-0.7-1/gemtc/tests/testthat/test-unit-write.mtc.network.R |only gemtc-0.8/gemtc/DESCRIPTION | 33 gemtc-0.8/gemtc/MD5 | 152 ++- gemtc-0.8/gemtc/NAMESPACE | 5 gemtc-0.8/gemtc/NEWS | 27 gemtc-0.8/gemtc/R/anohe.R | 4 gemtc-0.8/gemtc/R/arrayize.R |only gemtc-0.8/gemtc/R/code.R | 35 gemtc-0.8/gemtc/R/data.R | 40 gemtc-0.8/gemtc/R/deviance.R | 42 - gemtc-0.8/gemtc/R/inits.R | 404 ++++++---- gemtc-0.8/gemtc/R/likelihoods.R | 31 gemtc-0.8/gemtc/R/ll.binom.cloglog.R | 7 gemtc-0.8/gemtc/R/ll.binom.log.R | 7 gemtc-0.8/gemtc/R/ll.binom.logit.R | 7 gemtc-0.8/gemtc/R/ll.normal.identity.R | 8 gemtc-0.8/gemtc/R/ll.poisson.log.R | 10 gemtc-0.8/gemtc/R/mtc.hy.prior.R |only gemtc-0.8/gemtc/R/mtc.model.R | 73 - gemtc-0.8/gemtc/R/mtc.model.regression.R |only gemtc-0.8/gemtc/R/mtc.network.R | 10 gemtc-0.8/gemtc/R/mtc.network.xml.R | 50 - gemtc-0.8/gemtc/R/mtc.result.R | 34 gemtc-0.8/gemtc/R/plotCovariateEffect.R |only gemtc-0.8/gemtc/R/rank.probability.R | 8 gemtc-0.8/gemtc/R/regression.R |only gemtc-0.8/gemtc/R/relative.effect.R | 46 - gemtc-0.8/gemtc/R/relative.effect.table.R | 5 gemtc-0.8/gemtc/R/solveLP.R |only gemtc-0.8/gemtc/R/stopIfNotConsistent.R |only gemtc-0.8/gemtc/R/template.R | 15 gemtc-0.8/gemtc/data/atrialFibrillation.rdata |only gemtc-0.8/gemtc/data/blocker.rdata |only gemtc-0.8/gemtc/data/certolizumab.rdata |only gemtc-0.8/gemtc/data/dietfat.rdata |only gemtc-0.8/gemtc/data/hfPrevention.rdata |only gemtc-0.8/gemtc/data/parkinson-diff.rdata |only gemtc-0.8/gemtc/data/parkinson-shared.rdata |only gemtc-0.8/gemtc/inst/gemtc.armeffect.likelihood.txt | 2 gemtc-0.8/gemtc/inst/gemtc.fixedeffect.txt | 2 gemtc-0.8/gemtc/inst/gemtc.likelihood.binom.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.binom.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.normal.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.normal.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.poisson.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.poisson.txt |only gemtc-0.8/gemtc/inst/gemtc.model.template.txt | 5 gemtc-0.8/gemtc/inst/gemtc.model.use.template.txt | 4 gemtc-0.8/gemtc/inst/gemtc.randomeffects.txt | 2 gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.power.r2.txt |only gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.power.rm.txt |only gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.r2.txt | 11 gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.rm.txt | 11 gemtc-0.8/gemtc/man/atrialFibrillation.Rd |only gemtc-0.8/gemtc/man/blocker.Rd |only gemtc-0.8/gemtc/man/certolizumab.Rd |only gemtc-0.8/gemtc/man/dietfat.Rd |only gemtc-0.8/gemtc/man/gemtc-package.Rd | 26 gemtc-0.8/gemtc/man/hfPrevention.Rd |only gemtc-0.8/gemtc/man/ll.call.Rd | 2 gemtc-0.8/gemtc/man/mtc.hy.prior.Rd | 4 gemtc-0.8/gemtc/man/mtc.model.Rd | 59 + gemtc-0.8/gemtc/man/mtc.network.Rd | 8 gemtc-0.8/gemtc/man/mtc.nodesplit.Rd | 2 gemtc-0.8/gemtc/man/mtc.run.Rd | 8 gemtc-0.8/gemtc/man/parkinson.Rd | 8 gemtc-0.8/gemtc/man/plotCovariateEffect.Rd |only gemtc-0.8/gemtc/man/rank.probability.Rd | 13 gemtc-0.8/gemtc/man/read.mtc.network.Rd |only gemtc-0.8/gemtc/man/relative.effect.Rd | 5 gemtc-0.8/gemtc/man/relative.effect.table.Rd | 3 gemtc-0.8/gemtc/tests/data/dietfat.fe.summaries.txt |only gemtc-0.8/gemtc/tests/data/dietfat.re.summaries.txt |only gemtc-0.8/gemtc/tests/data/parkinson-diff.summaries.txt | 75 - gemtc-0.8/gemtc/tests/data/parkinson-shared.summaries.txt | 76 - gemtc-0.8/gemtc/tests/data/parkinson.summaries.txt | 71 - gemtc-0.8/gemtc/tests/data/riskratio.summaries.txt | 2 gemtc-0.8/gemtc/tests/testthat/helper-regress.R | 17 gemtc-0.8/gemtc/tests/testthat/helper-validate.R | 42 - gemtc-0.8/gemtc/tests/testthat/test-regress-models.R | 129 ++- gemtc-0.8/gemtc/tests/testthat/test-unit-arrayize.R |only gemtc-0.8/gemtc/tests/testthat/test-unit-mtc.model_data.R | 107 +- gemtc-0.8/gemtc/tests/testthat/test-unit-mtc.model_inits.R | 292 +++++++ gemtc-0.8/gemtc/tests/testthat/test-unit-read.mtc.network.R | 6 gemtc-0.8/gemtc/tests/testthat/test-unit-regression.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-dietfat-fe.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-dietfat-re.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-parkinson-diff.R | 3 gemtc-0.8/gemtc/tests/testthat/test-validate-parkinson-shared.R | 4 101 files changed, 1374 insertions(+), 678 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE)
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations (ODE), of
partial differential equations (PDE), of differential
algebraic equations (DAE), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions lsoda, lsodar, lsode, lsodes of the ODEPACK
collection, to the FORTRAN functions dvode and daspk and a
C-implementation of solvers of the Runge-Kutta family with
fixed or variable time steps. The package contains routines
designed for solving ODEs resulting from 1-D, 2-D and 3-D
partial differential equations (PDE) that have been converted
to ODEs by numerical differencing.
Author: Karline Soetaert [aut],
Thomas Petzoldt [aut, cre],
R. Woodrow Setzer [aut],
odepack authors [cph]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.12 dated 2015-07-06 and 1.13 dated 2016-03-01
DESCRIPTION | 6 MD5 | 72 - NEWS | 14 R/Utilities.R | 16 R/checkevents.R | 4 R/daspk.R | 6 R/diagnostics.R | 360 ++++--- R/euler.R | 295 +++--- R/lsoda.R | 5 R/lsodar.R | 6 R/lsode.R | 6 R/matplot.R | 4 R/radau.R | 5 R/rk.R | 447 +++++---- R/rk4.R | 203 ++-- R/vode.R | 6 build/vignette.rds |binary data/ccl4data.rda |binary inst/CITATION | 48 - inst/doc/compiledCode.R | 708 +++++++-------- inst/doc/compiledCode.pdf |binary inst/doc/deSolve.R | 2074 +++++++++++++++++++++++----------------------- inst/doc/deSolve.pdf |binary man/deSolve.Rd | 14 man/events.Rd | 26 man/plot.deSolve.Rd | 2 man/rk.Rd | 4 man/rkMethod.Rd | 54 - src/call_daspk.c | 4 src/call_lsoda.c | 11 src/call_radau.c | 2 src/ex_SCOC.c | 8 src/forcings.c | 7 src/rk_auto.c | 24 src/rk_fixed.c | 21 src/rk_implicit.c | 81 - vignettes/.install_extras | 2 vignettes/integration.bib | 446 ++++----- 38 files changed, 2573 insertions(+), 2418 deletions(-)
Title: Query 'Team Cymru' 'IP' Address, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware'
Hash Data Services
Description: A toolkit for querying 'Team Cymru' <http://team-cymru.org> 'IP'
address, Autonomous System Number ('ASN'), Border Gateway Protocol ('BGP'), Bogon
and 'Malware' Hash Data Services.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between cymruservices versions 0.1.1 dated 2015-07-27 and 0.2.0 dated 2016-03-01
DESCRIPTION | 21 ++--- MD5 | 32 ++++---- NAMESPACE | 3 NEWS |only R/asn.R | 141 +++++++++++++++++++++++++++--------- R/bogons.R | 121 ++++++++++++++++++++++-------- R/cymruservices-package.r | 1 R/malwarehash.R | 37 ++++++--- R/utils.R | 2 README.md |only man/bulk_origin.Rd | 13 ++- man/bulk_origin_asn.Rd | 13 ++- man/bulk_peer.Rd | 13 ++- man/cymruservices.Rd | 2 man/ipv4_bogons.Rd | 6 + man/ipv6_bogons.Rd | 6 + man/malware_hash.Rd | 13 ++- tests/testthat/test-cymruservices.R | 31 +++++-- 18 files changed, 328 insertions(+), 127 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the
LZ77 algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip)
but offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.5 dated 2016-01-23 and 0.6 dated 2016-03-01
brotli-0.5/brotli/src/dec/streams.c |only brotli-0.5/brotli/src/dec/streams.h |only brotli-0.6/brotli/DESCRIPTION | 13 brotli-0.6/brotli/MD5 | 82 +- brotli-0.6/brotli/NAMESPACE | 2 brotli-0.6/brotli/NEWS | 4 brotli-0.6/brotli/inst/doc/benchmarks.html | 8 brotli-0.6/brotli/man/brotli.Rd | 2 brotli-0.6/brotli/src/Makevars | 14 brotli-0.6/brotli/src/dec/bit_reader.c | 6 brotli-0.6/brotli/src/dec/bit_reader.h | 46 - brotli-0.6/brotli/src/dec/context.h | 8 brotli-0.6/brotli/src/dec/decode.c | 473 ++++++---------- brotli-0.6/brotli/src/dec/decode.h | 136 +--- brotli-0.6/brotli/src/dec/dictionary.c | 2 brotli-0.6/brotli/src/dec/dictionary.h | 15 brotli-0.6/brotli/src/dec/huffman.c | 207 +++---- brotli-0.6/brotli/src/dec/huffman.h | 23 brotli-0.6/brotli/src/dec/port.h | 50 - brotli-0.6/brotli/src/dec/prefix.h | 2 brotli-0.6/brotli/src/dec/state.c | 26 brotli-0.6/brotli/src/dec/state.h | 23 brotli-0.6/brotli/src/dec/transform.h | 82 +- brotli-0.6/brotli/src/dec/types.h | 4 brotli-0.6/brotli/src/enc/backward_references.cc | 88 +- brotli-0.6/brotli/src/enc/backward_references.h | 2 brotli-0.6/brotli/src/enc/bit_cost.h | 2 brotli-0.6/brotli/src/enc/block_splitter.h | 2 brotli-0.6/brotli/src/enc/brotli_bit_stream.cc | 6 brotli-0.6/brotli/src/enc/brotli_bit_stream.h | 1 brotli-0.6/brotli/src/enc/command.h | 10 brotli-0.6/brotli/src/enc/compress_fragment.cc | 1 brotli-0.6/brotli/src/enc/compress_fragment_two_pass.cc | 1 brotli-0.6/brotli/src/enc/encode.cc | 17 brotli-0.6/brotli/src/enc/encode.h | 9 brotli-0.6/brotli/src/enc/encode_parallel.cc | 5 brotli-0.6/brotli/src/enc/hash.h | 312 +++++++++- brotli-0.6/brotli/src/enc/histogram.h | 4 brotli-0.6/brotli/src/enc/metablock.h | 2 brotli-0.6/brotli/src/enc/ringbuffer.h | 13 brotli-0.6/brotli/src/enc/streams.cc | 2 brotli-0.6/brotli/src/enc/streams.h | 10 brotli-0.6/brotli/src/wrapper.cc | 52 - 43 files changed, 907 insertions(+), 860 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-3 dated 2015-11-22 and 1.7-4 dated 2016-03-01
ChangeLog | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 18 +++++++------ NAMESPACE | 1 R/dpcoa.R | 6 ++-- R/mfa.R | 2 - R/plot.4thcorner.R | 6 ++-- R/randtest.dpcoa.R |only man/randtest.dpcoa.Rd |only man/testdim.Rd | 4 +- src/fourthcorner.c | 2 - 11 files changed, 94 insertions(+), 20 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson
<jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles
Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.5.11 dated 2016-02-22 and 4.5.17 dated 2016-03-01
DESCRIPTION | 8 +-- MD5 | 28 +++++----- NEWS | 2 R/bigmemory.R | 105 ++++++++++++++++++++++------------------- R/hello-bigmemory.R | 2 man/attach.big.matrix.Rd | 7 -- man/big.matrix.Rd | 22 -------- man/bigmemory-package.Rd | 2 man/flush-methods.Rd | 5 + man/sub.big.matrix.Rd | 4 - man/write.big.matrix.Rd | 21 +++++--- src/BigMatrix.cpp | 7 +- tests/testthat/test_create.R | 8 +-- tests/testthat/test_misc.R | 9 +-- tests/testthat/test_readonly.R | 54 ++++++++++----------- 15 files changed, 138 insertions(+), 146 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.8). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.8.0 dated 2016-02-23 and 0.3.2.8.1 dated 2016-03-01
ChangeLog | 15 DESCRIPTION | 8 MD5 | 18 inst/NEWS.Rd | 9 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/src/SparseCore/CompressedStorage.h | 5 inst/include/Eigen/src/SparseCore/SparseBlock.h | 1077 ++++++++---------- inst/include/Eigen/src/SparseCore/SparseMatrix.h | 12 inst/include/Eigen/src/SparseCore/SparseRedux.h | 4 inst/include/Eigen/src/SparseCore/SparseVector.h | 10 10 files changed, 592 insertions(+), 566 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.3.7 dated 2015-11-20 and 1.4.0 dated 2016-03-01
DESCRIPTION | 10 MD5 | 43 NAMESPACE | 19 R/family_acat.R |only R/family_cumulative.R |only R/glmmLasso.r | 107 - R/glmmLassoControl.r | 4 R/glmmLasso_RE.R | 2048 ++++++++++++++++++------------------- R/glmmLasso_noRE.R | 1858 ++++++++++++++------------------- R/glmm_final.r | 245 +--- R/glmm_final.smooth.r | 269 ++-- R/glmm_final.smooth_noRE.R | 196 +-- R/glmm_final_multi_random.r | 190 ++- R/glmm_final_multi_random_smooth.r | 206 ++- R/glmm_final_noRE.R | 185 +-- R/helpers.R |only R/likelihood.r | 33 R/logLik.glmmLasso.r | 67 - data/knee.RData |only demo/glmmLasso-soccer.r | 6 man/acat.Rd |only man/cumulative.Rd |only man/glmmLasso.rd | 45 man/glmmLassoControl.rd | 9 man/knee.Rd |only man/soccer.Rd | 6 26 files changed, 2617 insertions(+), 2929 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.3 dated 2015-06-30 and 3.98-1.4 dated 2016-03-01
DESCRIPTION | 8 - DESCRIPTION.in | 2 Docs/CreatingXML.xml | 2 Docs/MemoryManagement.html | 42 +++---- Docs/MemoryManagement.pdf |binary Docs/ModernDoc.Rdb | 4 Docs/ModernDoc.html | 16 +- Docs/ModernDoc.pdf |binary Docs/WritingXML.html | 2 Docs/description.nw | 2 Docs/description.xml | 4 Docs/htmlTable.xml | 2 Docs/shortIntro.xml | 6 - FAQ.html | 6 - GNUmakefile.admin | 2 MD5 | 182 +++++++++++++++++----------------- R/XMLClasses.R | 4 R/getRelativeURL.R | 20 +-- R/xmlInternalSource.R | 4 Rsamples/addChildren.R | 4 Rsamples/ns.R | 10 - Rsamples/tt.R | 2 Todo.xml | 6 - index.html | 14 +- index.html.in | 14 +- inst/exampleData/catalog.xml | 6 - inst/exampleData/cleanNamespace.xml | 4 inst/exampleData/longitudinalData.xml | 2 inst/exampleData/namespaces.xml | 4 inst/exampleData/namespaces2.xml | 4 inst/exampleData/redundantNS.xml | 4 inst/exampleData/tagnames.xml | 4 inst/exampleData/test.xml | 2 inst/exampleData/writeRS.xml | 2 inst/exampleData/xpathTest.xml | 4 inst/examples/GNUmakefile | 2 inst/examples/HTMLText.R | 2 inst/examples/RhelpInfo.xml | 2 inst/examples/catalog.R | 2 inst/examples/foo.html | 2 inst/examples/getElements.S | 4 inst/examples/gettingStarted.html | 38 +++---- inst/examples/newNodes.R | 2 inst/examples/prompt.xml | 2 inst/examples/xmlTags.xml | 4 man/AssignXMLNode.Rd | 2 man/addChildren.Rd | 4 man/append.XMLNode.Rd | 2 man/asXMLNode.Rd | 2 man/catalogResolve.Rd | 8 - man/catalogs.Rd | 4 man/dtdElement.Rd | 2 man/dtdElementValidEntry.Rd | 2 man/dtdIsAttribute.Rd | 2 man/dtdValidElement.Rd | 2 man/genericSAXHandlers.Rd | 2 man/getHTMLLinks.Rd | 6 - man/getNodeSet.Rd | 22 ++-- man/getRelativeURL.Rd | 2 man/getXMLErrors.Rd | 2 man/length.XMLNode.Rd | 2 man/libxmlVersion.Rd | 2 man/names.XMLNode.Rd | 2 man/newXMLDoc.Rd | 14 +- man/parseDTD.Rd | 2 man/parseURI.Rd | 14 +- man/parseXMLAndAdd.Rd | 4 man/print.Rd | 2 man/readHTMLList.Rd | 2 man/readHTMLTable.Rd | 2 man/saveXML.Rd | 2 man/supportsExpat.Rd | 2 man/xmlApply.Rd | 2 man/xmlAttributeType.Rd | 2 man/xmlContainsEntity.Rd | 2 man/xmlDOMApply.Rd | 2 man/xmlElementsByTagName.Rd | 4 man/xmlEventHandler.Rd | 2 man/xmlEventParse.Rd | 2 man/xmlGetAttr.Rd | 2 man/xmlHandler.Rd | 2 man/xmlName.Rd | 2 man/xmlNamespace.Rd | 4 man/xmlNode.Rd | 4 man/xmlOutput.Rd | 8 - man/xmlParseDoc.Rd | 4 man/xmlRoot.Rd | 2 man/xmlSize.Rd | 2 man/xmlSubset.Rd | 2 man/xmlTree.Rd | 12 +- man/xmlTreeParse.Rd | 2 man/xmlValue.Rd | 2 92 files changed, 316 insertions(+), 316 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: Functions for estimating split-duration regression models and
various associated generic function methods.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel Hill [aut],
Nils Metternich [aut],
Shahryar Minhas [aut],
Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.14.0 dated 2015-10-27 and 0.15.0 dated 2016-03-01
spduration-0.14.0/spduration/man/logLik.spdur.Rd |only spduration-0.14.0/spduration/man/nobs.spdur.Rd |only spduration-0.15.0/spduration/DESCRIPTION | 12 spduration-0.15.0/spduration/MD5 | 93 ++--- spduration-0.15.0/spduration/NAMESPACE | 11 spduration-0.15.0/spduration/NEWS |only spduration-0.15.0/spduration/NEWS.md |only spduration-0.15.0/spduration/R/accessors.spdur.R | 167 ++++++---- spduration-0.15.0/spduration/R/fit-stats.R |only spduration-0.15.0/spduration/R/plot.spdur.R | 80 ++-- spduration-0.15.0/spduration/R/predict.spdur.R | 58 ++- spduration-0.15.0/spduration/R/spdur.R | 57 ++- spduration-0.15.0/spduration/R/summary.spdur.R | 50 +- spduration-0.15.0/spduration/README.md | 5 spduration-0.15.0/spduration/data/model.coups.rda |binary spduration-0.15.0/spduration/man/AIC.spdur.Rd | 5 spduration-0.15.0/spduration/man/BIC.spdur.Rd | 5 spduration-0.15.0/spduration/man/accessors.Rd |only spduration-0.15.0/spduration/man/add_duration.Rd | 55 +-- spduration-0.15.0/spduration/man/as.data.frame.spdur.Rd | 11 spduration-0.15.0/spduration/man/attempt_date.Rd | 2 spduration-0.15.0/spduration/man/bscoup.Rd | 4 spduration-0.15.0/spduration/man/coups.Rd | 8 spduration-0.15.0/spduration/man/expand.call.Rd | 8 spduration-0.15.0/spduration/man/forecast.Rd | 2 spduration-0.15.0/spduration/man/forecast.default.Rd | 2 spduration-0.15.0/spduration/man/forecast.spdur.Rd | 9 spduration-0.15.0/spduration/man/hazard.Rd | 2 spduration-0.15.0/spduration/man/loglog.Rd | 2 spduration-0.15.0/spduration/man/loglog_lnl.Rd | 2 spduration-0.15.0/spduration/man/model.coups.Rd | 4 spduration-0.15.0/spduration/man/panel_lag.Rd | 13 spduration-0.15.0/spduration/man/plot.spdur.Rd | 7 spduration-0.15.0/spduration/man/plot_hazard.Rd | 30 + spduration-0.15.0/spduration/man/plot_hazard1.Rd | 2 spduration-0.15.0/spduration/man/plot_hazard2.Rd | 2 spduration-0.15.0/spduration/man/predict.spdur.Rd | 48 +- spduration-0.15.0/spduration/man/print.summary.spdur.Rd | 5 spduration-0.15.0/spduration/man/separationplot.spdur.Rd | 17 - spduration-0.15.0/spduration/man/spdur.Rd | 33 + spduration-0.15.0/spduration/man/spduration.Rd | 26 - spduration-0.15.0/spduration/man/sploglog.Rd | 2 spduration-0.15.0/spduration/man/sploglog_lnl.Rd | 2 spduration-0.15.0/spduration/man/spweib_lnl.Rd | 2 spduration-0.15.0/spduration/man/spweibull.Rd | 2 spduration-0.15.0/spduration/man/summary.spdur.Rd | 5 spduration-0.15.0/spduration/man/weib_lnl.Rd | 2 spduration-0.15.0/spduration/man/weibull.Rd | 2 spduration-0.15.0/spduration/man/xtable.spdur.Rd | 3 spduration-0.15.0/spduration/tests/testthat/Rplots.pdf |only spduration-0.15.0/spduration/tests/testthat/test_predict.spdur.R | 19 + 51 files changed, 524 insertions(+), 352 deletions(-)
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 12.0-0.0 dated 2015-12-04 and 13.0-0.0 dated 2016-03-01
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/zzz.R | 2 +- data/sgpData.rda |binary data/sgpData_INSTRUCTOR_NUMBER.rda |binary data/sgpData_LONG.rda |binary inst/CITATION | 8 ++++---- inst/NEWS | 6 ++++++ man/SGPdata-package.Rd | 4 ++-- man/sgpData.Rd | 20 ++++++++++---------- 10 files changed, 37 insertions(+), 31 deletions(-)
Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Sunthud Pornprasertmanit [aut, cre],
Patrick Miller [aut],
Alexander Schoemann [aut],
Yves Rosseel [aut],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb],
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher Preacher [ctb],
Donna Coffman [ctb],
Mijke Rhemtulla [ctb],
Alexander Robitzsch [ctb],
Craig Enders [ctb],
Ruber Arslan [ctb],
Bell Clinton [ctb],
Pavel Panko [ctb],
Edgar Merkle [ctb],
Terry Jorgensen [ctb],
Steven Chesnut [ctb],
Jarrett Byrnes [ctb],
Jason Rights [ctb]
Maintainer: Sunthud Pornprasertmanit <psunthud@gmail.com>
Diff between semTools versions 0.4-9 dated 2015-06-28 and 0.4-11 dated 2016-03-01
DESCRIPTION | 22 - MD5 | 144 ++++---- NAMESPACE | 13 R/NET.R | 8 R/PAVranking.R |only R/ci.reliability.R |only R/efa.R | 12 R/fitIndices.R | 2 R/imposeStart.R | 4 R/lavSpatialCorrect.R | 8 R/missingBootstrap.R | 276 ++++++++-------- R/monteCarloMed.R | 4 R/partialInvariance.R | 56 +-- R/partialInvarianceCat.R | 38 +- R/permuteMeasEq.R | 639 +++++++++++++++++++++++---------------- R/probeInteraction.R | 8 R/reliability.R | 10 R/runMI.R | 63 ++- R/wald.R | 6 build/vignette.rds |binary data/simParcel.rda |binary man/BootMiss-class.Rd | 10 man/EFA-class.Rd | 3 man/FitDiff-class.Rd | 2 man/PAVranking.Rd |only man/auxiliary.Rd | 4 man/bsBootMiss.Rd | 28 + man/ci.reliability.Rd |only man/clipboard.Rd | 2 man/combinequark.Rd | 2 man/compareFit.Rd | 2 man/efaUnrotate.Rd | 2 man/findRMSEApower.Rd | 2 man/findRMSEApowernested.Rd | 2 man/findRMSEAsamplesize.Rd | 2 man/findRMSEAsamplesizenested.Rd | 2 man/fitMeasuresMx.Rd | 2 man/impliedFactorStat.Rd | 2 man/imposeStart.Rd | 2 man/indProd.Rd | 2 man/kurtosis.Rd | 2 man/lavaanStar-class.Rd | 2 man/loadingFromAlpha.Rd | 2 man/longInvariance.Rd | 2 man/mardiaKurtosis.Rd | 2 man/mardiaSkew.Rd | 2 man/maximalRelia.Rd | 2 man/measurementInvariance.Rd | 2 man/measurementInvarianceCat.Rd | 4 man/miPowerFit.Rd | 2 man/moreFitIndices.Rd | 2 man/mvrnonnorm.Rd | 2 man/net.Rd | 3 man/nullMx.Rd | 2 man/partialInvariance.Rd | 2 man/permuteMeasEq-class.Rd | 18 - man/permuteMeasEq.Rd | 173 ++++------ man/plotProbe.Rd | 2 man/plotRMSEAdist.Rd | 2 man/plotRMSEApowernested.Rd | 2 man/probe2WayMC.Rd | 2 man/probe2WayRC.Rd | 2 man/probe3WayMC.Rd | 2 man/probe3WayRC.Rd | 2 man/quark.Rd | 2 man/reliability.Rd | 2 man/reliabilityL2.Rd | 2 man/residualCovariate.Rd | 2 man/rotate.Rd | 2 man/runMI.Rd | 15 man/saturateMx.Rd | 2 man/singleParamTest.Rd | 2 man/skew.Rd | 2 man/standardizeMx.Rd | 2 man/wald.Rd | 2 75 files changed, 912 insertions(+), 745 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between RCurl versions 1.95-4.7 dated 2015-06-30 and 1.95-4.8 dated 2016-03-01
Changes.html | 2 DESCRIPTION | 10 ++-- MD5 | 88 ++++++++++++++++++++--------------------- NAMESPACE | 1 R/getFormParams.R | 2 Todo.html | 2 getURL.html | 34 +++++++-------- inst/doc/FAQ.html | 6 +- inst/doc/RCurl.tex | 10 ++-- inst/doc/philosophy.html | 46 ++++++++++----------- inst/doc/philosophy.xml | 48 +++++++++++----------- inst/doc/withCookies.Rdb | 4 - inst/doc/withCookies.html | 22 +++++----- inst/examples/chunks.S | 2 inst/examples/concurrent.S | 2 inst/examples/concurrent.html | 14 +++--- inst/examples/concurrent.xml | 18 ++++---- inst/examples/curl.c | 2 inst/examples/encoding.R | 2 inst/examples/multi.S | 8 +-- inst/examples/nestedHTML.html | 6 +- inst/examples/nestedHTML.xml | 8 +-- inst/examples/omg.netrc | 2 inst/examples/postFormPasswd.R | 6 +- inst/examples/progress.S | 2 inst/examples/xmlParse.html | 4 - inst/examples/xmlParse.xml | 8 +-- man/MultiCURLHandle-class.Rd | 2 man/basicHeaderGatherer.Rd | 4 - man/basicTextGatherer.Rd | 20 ++++----- man/binaryBuffer.Rd | 4 - man/chunkToLineReader.Rd | 4 - man/curlPerform.Rd | 8 +-- man/curlSetOpt.Rd | 4 - man/dynCurlReader.Rd | 8 +-- man/getBinaryURL.Rd | 2 man/getCurlHandle.Rd | 6 +- man/getCurlInfo.Rd | 4 - man/getFormParams.Rd | 4 - man/getURIAsynchronous.Rd | 6 +- man/getURL.Rd | 36 ++++++++-------- man/url.exists.Rd | 4 - src/curl.c | 2 src/curl.c-expt | 2 tests/jpeg.R | 2 45 files changed, 241 insertions(+), 240 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.3 dated 2016-02-12 and 1.4 dated 2016-03-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gui.R | 22 +++++++++++----------- R/provenance.R | 7 ++++--- man/plot.ternary.Rd | 2 +- 5 files changed, 23 insertions(+), 22 deletions(-)
Title: Density Estimation with a Penalized Mixture Approach
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Diff between pendensity versions 0.2.8 dated 2015-04-08 and 0.2.9 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/plot.pendensity.R | 23 ++++++++++++----------- build/vignette.rds |binary man/pendensity-package.Rd | 4 ++-- man/plot.pendensity.Rd | 3 ++- 7 files changed, 28 insertions(+), 24 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.1-3 dated 2015-11-24 and 1.2-0 dated 2016-03-01
DESCRIPTION | 17 +- MD5 | 44 ++--- NAMESPACE | 16 + R/closepb.R | 13 - R/pbapply.R | 198 +++++++++++------------ R/pblapply.R | 38 ++-- R/pboptions.R | 32 +-- R/pbreplicate.R | 8 R/pbsapply.R | 22 +- R/timerProgressBar.R |only R/unix/dopb.R | 25 +- R/unix/getpb.R | 27 +-- R/unix/setpb.R | 27 +-- R/unix/startpb.R | 36 ++-- R/windows/dopb.R | 25 +- R/windows/getpb.R | 29 +-- R/windows/setpb.R | 29 +-- R/windows/startpb.R | 42 +++- R/zzz.R | 32 ++- inst/ChangeLog | 121 +++++++------- man/pbapply.Rd | 404 ++++++++++++++++++++++++------------------------ man/pboptions.Rd | 276 ++++++++++++++++---------------- man/timerProgressBar.Rd |only tests/tests.R | 82 ++++----- 24 files changed, 809 insertions(+), 734 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.7 dated 2016-02-22 and 1.7-3 dated 2016-03-01
DESCRIPTION | 8 MD5 | 38 - R/TaylorDiagram.R | 4 R/TheilSen.R | 1004 +++++++++++++++++++++++++++------------------------- R/checkPrep.R | 3 R/conditionalEval.R | 11 R/modStats.R | 20 - R/polarFreq.R | 2 R/scatterPlot.R | 9 R/smoothTrend.R | 846 +++++++++++++++++++++++-------------------- R/timeAverage.R | 30 + R/timePlot.R | 12 R/timeProp.R | 5 R/trajCluster.R | 34 + R/utilities.R | 191 ++++----- R/windRose.R | 2 man/TheilSen.Rd | 249 ++++++------ man/smoothTrend.Rd | 271 +++++++------- man/timeAverage.Rd | 22 - man/trajCluster.Rd | 12 20 files changed, 1460 insertions(+), 1313 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-2 dated 2015-11-22 and 0.3-3 dated 2016-03-01
mefa4-0.3-2/mefa4/R/mefa4extras.R |only mefa4-0.3-2/mefa4/inst/extras |only mefa4-0.3-3/mefa4/DESCRIPTION | 11 +++--- mefa4-0.3-3/mefa4/MD5 | 13 +++---- mefa4-0.3-3/mefa4/NAMESPACE | 3 + mefa4-0.3-3/mefa4/R/mefa4plus.R |only mefa4-0.3-3/mefa4/R/mefa4utilities.R | 47 ++++++++++++++++++++++++++ mefa4-0.3-3/mefa4/inst/ChangeLog | 61 ++++++++++++++++++++++++----------- mefa4-0.3-3/mefa4/man/nameAlnum.Rd | 26 +++++++++++++- 9 files changed, 128 insertions(+), 33 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-3 dated 2015-11-28 and 1.2-4 dated 2016-03-01
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++++---------------------- R/diagMatrix.R | 2 + R/sparseMatrix.R | 27 ++++++++++++++++------ TODO | 4 +++ build/vignette.rds |binary inst/NEWS.Rd | 21 +++++++++++++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/test-tools-Matrix.R | 3 -- man/Matrix-class.Rd | 7 ++++- man/bdiag.Rd | 11 +++++++++ man/spMatrix.Rd | 17 ++++++++----- man/sparseMatrix-class.Rd | 3 +- man/sparseMatrix.Rd | 17 ++++++++++++- src/CHOLMOD/Lib/Makefile | 5 ++++ src/Csparse.c | 6 ++++ src/Mutils.c | 9 ++++--- src/chm_common.c | 4 +-- src/dense.h | 2 - src/dgCMatrix.c | 2 - src/dgTMatrix.c | 55 ++++++++++++++++++++++++++++++++++++--------- src/factorizations.c | 21 +++++++++-------- src/init.c | 2 - tests/Simple.R | 28 +++++++++++++++++++++- 28 files changed, 227 insertions(+), 81 deletions(-)