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: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh <uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <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(-)