Title: Graph-Based Two-Sample Tests
Description: Four graph-based tests are provided for testing whether two samples are from the same distribution. It works for both continuous data and discrete data.
Author: Hao Chen and Jingru Zhang
Maintainer: Hao Chen <hxchen@ucdavis.edu>
Diff between gTests versions 0.1 dated 2016-09-30 and 0.2 dated 2017-12-06
DESCRIPTION | 13 ++++++----- MD5 | 32 ++++++++++++++++++++++----- NAMESPACE | 8 ++++-- R/gTests.r | 37 ++++++++++++++++++++++++-------- R/gTests_discrete.r |only R/graphConstruct.r |only data/datalist |only data/example.rda |binary data/example_discrete.rda |only man/counts1.Rd |only man/counts2.Rd |only man/counts3.Rd |only man/dfs.Rd |only man/ds1.Rd |only man/ds2.Rd |only man/ds3.Rd |only man/g.tests.Rd | 17 ++++++++------ man/g.tests_discrete.Rd |only man/gTests-package.Rd | 53 +++++++++++++++++++++++++--------------------- man/getComdist.Rd |only man/getGraph.Rd |only man/getMV_discrete.Rd |only man/getR1R2_discrete.Rd |only man/nnlink.Rd |only man/nnlink_Com.Rd |only man/nnlink_K.Rd |only man/permute_discrete.Rd |only 27 files changed, 105 insertions(+), 55 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC) at <www.cbioportal.org>.
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.2.6 dated 2017-04-11 and 1.2.8 dated 2017-12-06
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/cgdsr.R | 20 ++++++++++---------- inst/doc/cgdsr.Rnw | 5 +++-- inst/doc/cgdsr.pdf |binary man/cgdsr-getMutationData.Rd | 5 +++-- vignettes/cgdsr.Rnw | 5 +++-- 8 files changed, 32 insertions(+), 28 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <http://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [cph],
Jana Straková [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.2 dated 2017-11-13 and 0.2.1 dated 2017-12-06
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 9 +++++++++ R/RcppExports.R | 4 ++++ R/nlp_phrase_sequences.R |only R/udpipe_train.R | 1 + R/utils.R | 4 ++-- build/vignette.rds |binary inst/doc/udpipe-annotation.html | 6 +++--- inst/doc/udpipe-train.html | 6 +++--- man/as_phrasemachine.Rd |only man/phrases.Rd |only src/RcppExports.cpp | 14 ++++++++++++++ src/rcpp_phrases.cpp |only src/udpipe.cpp | 14 ++++++++++---- 16 files changed, 66 insertions(+), 26 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre],
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL
Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-2 dated 2017-11-18 and 0.7-3 dated 2017-12-06
DESCRIPTION | 8 +-- MD5 | 28 ++++++----- R/matrix.R | 3 + R/tokenizer.R | 25 +++++++--- R/utils.R | 1 inst/NEWS.Rd | 10 ++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/PlainTextDocument.Rd | 14 ++--- man/readPDF.Rd | 11 +++- man/termFreq.Rd | 4 - src/remove.c | 15 +++++- src/scan.c | 73 +++++++++++++++++++++---------- tests/testthat/test-TermDocumentMatrix.R | 24 ++++++++++ tests/testthat/test-Tokenizer.R |only tests/testthat/test-Transformation.R |only 16 files changed, 155 insertions(+), 61 deletions(-)
Title: Utility Functions for Building Web Databrowsers
Description: A suite of utility functions providing standardized functionality
often needed in web services including: logging, cache management
and parsing of http request headers.
Author: Jonathan Callahan [aut, cre]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaWebUtils versions 0.1.4 dated 2017-11-02 and 0.1.5 dated 2017-12-06
DESCRIPTION | 6 +- MD5 | 11 ++--- NAMESPACE | 1 R/httpResponse.R | 81 +++++++++++++++++++++++++--------------- man/httpResponse.contentType.Rd | 2 man/httpResponse.header.Rd | 6 +- man/mimeType.Rd |only 7 files changed, 65 insertions(+), 42 deletions(-)
More information about MazamaWebUtils at CRAN
Permanent link
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.1.6 dated 2017-12-05 and 1.1.7 dated 2017-12-06
DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/network_permutation.R | 5 +++ R/network_swap.R | 62 +++++++++++++++++++++++++++++++++++++++++++----- man/asnipe-package.Rd | 4 +-- man/network_swap.Rd | 24 +++++++++++++++++- 6 files changed, 93 insertions(+), 20 deletions(-)
Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with
package 'leaflet'. These charts can be used to represent at same time multiple
variables on a single map.
Author: Jalal-Edine ZAWAM [aut, cre],
Francois Guillem [aut],
RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>
Diff between leaflet.minicharts versions 0.5.1 dated 2017-08-17 and 0.5.2 dated 2017-12-06
DESCRIPTION | 16 MD5 | 46 +- NEWS | 116 ++--- R/add_flows.R | 222 ++++----- R/add_minicharts.R | 528 +++++++++++------------ R/data-doc.R | 70 +-- R/minicharts_deps.R | 36 - R/popup_args.R | 58 +- R/prepare_js_args.R | 346 +++++++-------- R/preprocess_args.R | 72 +-- R/sync_with.R | 86 +-- R/zzz.R | 18 README.md | 98 ++-- build/vignette.rds |binary inst/doc/introduction.Rmd | 368 ++++++++-------- inst/doc/introduction.html | 88 +-- inst/font-awesome-4.7.0/css/font-awesome.min.css | 8 inst/minicharts.css | 304 ++++++------- tests/testthat.R | 8 tests/testthat/test-flows.R | 64 +- tests/testthat/test-minicharts.R | 264 +++++------ tests/testthat/test-prepare_js_args.R | 406 ++++++++--------- tests/testthat/test-preprocess_args.R | 80 +-- vignettes/introduction.Rmd | 368 ++++++++-------- 24 files changed, 1849 insertions(+), 1821 deletions(-)
More information about leaflet.minicharts at CRAN
Permanent link
Title: Sparsed Sliced Inverse Regression via Lasso
Description: Estimate the sufficient dimension reduction space using sparsed sliced inverse regression via Lasso (Lasso-SIR) introduced in Lin, Zhao, and Liu (2017) <arxiv:1611.06655>. The Lasso-SIR is consistent and achieve the optimal convergence rate under certain sparsity conditions for the multiple index models.
Author: Zhigen Zhao, Qian Lin, Jun Liu
Maintainer: Zhigen Zhao <zhigen.zhao@gmail.com>
Diff between LassoSIR versions 0.1 dated 2017-10-27 and 0.1.1 dated 2017-12-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/LassoSIR.R | 31 +++++++------------------------ build/partial.rdb |binary 4 files changed, 14 insertions(+), 31 deletions(-)
Title: Read/Write Files in Key-Value-Hierarchy Format
Description: The format KVH is a lightweight format that can be read/written both by humans and machines.
It can be useful in situations where XML or alike formats seem to be an overkill.
We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between kvh versions 1.0.1 dated 2017-10-09 and 1.1 dated 2017-12-06
DESCRIPTION | 9 ++-- MD5 | 19 ++++++--- NAMESPACE | 2 NEWS |only R/kvh.R | 96 ++++++++++++++++++++++++++++++---------------- README.md |only cleanup |only man/esc_kvh_k.Rd |only man/esc_kvh_v.Rd |only man/obj2kvh.Rd | 6 +- man/obj_by_keys.Rd |only src/rcpp_kvh.cpp | 31 +++++++------- tests/testthat/res.RData |only tests/testthat/test_kvh.R | 4 + 14 files changed, 106 insertions(+), 61 deletions(-)
Title: Inventory Models
Description: Determination of the optimal policy in inventory problems from a game-theoretic perspective.
Author: Alejandro Saavedra Nieves
Maintainer: Alejandro Saavedra Nieves <alejandro.saavedra.nieves@gmail.com>
Diff between Inventorymodel versions 1.0.6 dated 2017-12-02 and 1.1.0 dated 2017-12-06
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/EOQcoo.R | 12 ++++++++++-- R/EPQcoo.R | 23 ++++++++++++++++------- R/STIcoo.R | 29 ++++++++++++++++++++--------- R/mct.R | 10 ++++++++-- R/mfoc.R | 14 +++++++++++--- R/mwhc.R | 51 +++++++++++++++++++++++++++++++-------------------- R/mwhc2c.R | 23 ++++++++++++++++------- R/mwhcct.R | 14 ++++++++++++-- man/EOQcoo.Rd | 2 +- man/EPQcoo.Rd | 2 +- man/STIcoo.Rd | 2 +- man/mct.Rd | 2 +- man/mfoc.Rd | 2 +- man/mwhc.Rd | 2 +- man/mwhc2c.Rd | 2 +- man/mwhcct.Rd | 3 +-- 18 files changed, 153 insertions(+), 82 deletions(-)
More information about Inventorymodel at CRAN
Permanent link
Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre],
Ben Armstrong [aut],
Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.3.2 dated 2017-01-16 and 2.3.4 dated 2017-12-06
DESCRIPTION | 8 MD5 | 168 ++-- NAMESPACE | 148 +-- NEWS.md | 14 R/Predict.matrix.cb.smooth.R | 58 - R/cbPen.R | 108 +- R/checkcrossbasis.R | 80 +- R/checkgroup.R | 26 R/checkonebasis.R | 90 +- R/coef.crosspred.R | 8 R/coef.crossreduce.R | 8 R/cr.R | 112 +-- R/crossbasis.R | 206 ++--- R/crosspred.R | 378 +++++----- R/crossreduce.R | 329 ++++---- R/equalknots.R | 50 - R/exphist.R | 70 - R/fci.R | 70 - R/findrank.R | 24 R/getcoef.R | 40 - R/getlink.R | 38 - R/getvcov.R | 44 - R/integer.R | 64 - R/lin.R | 46 - R/lines.crosspred.R | 260 +++--- R/lines.crossreduce.R | 104 +- R/logknots.R | 54 - R/mkXpred.R | 100 +- R/mkaddSlag.R | 52 - R/mkat.R | 58 - R/mkcen.R | 96 +- R/mklag.R | 32 R/onAttach.R | 34 R/onebasis.R | 74 - R/plot.crosspred.R | 416 +++++------ R/plot.crossreduce.R | 116 +-- R/points.crosspred.R | 256 +++--- R/points.crossreduce.R | 100 +- R/poly.R | 48 - R/ps.R | 122 +-- R/seqlag.R | 12 R/smooth.construct.cb.smooth.spec.R | 282 +++---- R/strata.R | 82 +- R/summary.crossbasis.R | 70 - R/summary.crosspred.R | 46 - R/summary.crossreduce.R | 68 - R/summary.onebasis.R | 42 - R/thr.R | 68 - R/vcov.crosspred.R | 10 R/vcov.crossreduce.R | 10 README.md | 120 +-- build/vignette.rds |binary inst/NEWS | 1226 ++++++++++++++++----------------- inst/doc/dlnmExtended.Rnw | 1202 ++++++++++++++++---------------- inst/doc/dlnmExtended.pdf |binary inst/doc/dlnmOverview.Rnw | 658 ++++++++--------- inst/doc/dlnmOverview.pdf |binary inst/doc/dlnmPenalized.Rnw | 200 ++--- inst/doc/dlnmPenalized.pdf |binary inst/doc/dlnmTS.Rnw | 912 ++++++++++++------------ inst/doc/dlnmTS.pdf |binary man/cbPen.Rd | 3 man/cr.Rd | 2 man/crossbasis.Rd | 8 man/crosspred.Rd | 476 ++++++------ man/crossreduce.Rd | 272 +++---- man/dlnm-internal.Rd | 216 ++--- man/dlnm-package.Rd | 14 man/equalknots.Rd | 106 +- man/exphist.Rd | 132 +-- man/integer.Rd | 96 +- man/lin.Rd | 106 +- man/logknots.Rd | 146 +-- man/onebasis.Rd | 250 +++--- man/plot.crosspred.Rd | 8 man/plot.crossreduce.Rd | 208 ++--- man/poly.Rd | 118 +-- man/ps.Rd | 6 man/smooth.construct.cb.smooth.spec.Rd | 2 man/strata.Rd | 124 +-- man/thr.Rd | 120 +-- vignettes/dlnmExtended.Rnw | 1202 ++++++++++++++++---------------- vignettes/dlnmOverview.Rnw | 658 ++++++++--------- vignettes/dlnmPenalized.Rnw | 200 ++--- vignettes/dlnmTS.Rnw | 912 ++++++++++++------------ 85 files changed, 7265 insertions(+), 7237 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'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.8.100.1.0 dated 2017-10-11 and 0.8.300.1.0 dated 2017-12-06
ChangeLog | 72 + DESCRIPTION | 8 MD5 | 129 +-- R/RcppArmadillo.package.skeleton.R | 38 build/vignette.rds |binary configure | 97 +- configure.ac | 66 - inst/NEWS.Rd | 21 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloAs.h | 14 inst/include/RcppArmadilloConfig.h | 10 inst/include/RcppArmadilloConfigGenerated.h.in | 6 inst/include/armadillo | 7 inst/include/armadillo_bits/Cube_meat.hpp | 136 +-- inst/include/armadillo_bits/Glue_bones.hpp | 11 inst/include/armadillo_bits/MapMat_bones.hpp | 29 inst/include/armadillo_bits/MapMat_meat.hpp | 206 ----- inst/include/armadillo_bits/Mat_meat.hpp | 148 +-- inst/include/armadillo_bits/SpMat_bones.hpp | 21 inst/include/armadillo_bits/SpMat_meat.hpp | 126 ++- inst/include/armadillo_bits/SpSubview_bones.hpp | 17 inst/include/armadillo_bits/SpSubview_meat.hpp | 19 inst/include/armadillo_bits/SpValProxy_bones.hpp | 12 inst/include/armadillo_bits/SpValProxy_meat.hpp | 34 inst/include/armadillo_bits/arma_forward.hpp | 108 ++ inst/include/armadillo_bits/arma_rng_cxx11.hpp | 63 + inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/auxlib_bones.hpp | 35 inst/include/armadillo_bits/auxlib_meat.hpp | 452 ++++++++++- inst/include/armadillo_bits/band_helper.hpp |only inst/include/armadillo_bits/compiler_extra.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 23 inst/include/armadillo_bits/config.hpp | 2 inst/include/armadillo_bits/config.hpp.cmake | 2 inst/include/armadillo_bits/constants.hpp | 2 inst/include/armadillo_bits/def_hdf5.hpp | 12 inst/include/armadillo_bits/def_lapack.hpp | 50 + inst/include/armadillo_bits/diskio_bones.hpp | 4 inst/include/armadillo_bits/diskio_meat.hpp | 212 ++--- inst/include/armadillo_bits/fn_chol.hpp | 2 inst/include/armadillo_bits/fn_intersect.hpp |only inst/include/armadillo_bits/fn_normpdf.hpp |only inst/include/armadillo_bits/fn_spsolve.hpp | 27 inst/include/armadillo_bits/glue_affmul_bones.hpp | 9 inst/include/armadillo_bits/glue_affmul_meat.hpp | 260 ++++++ inst/include/armadillo_bits/glue_intersect_bones.hpp |only inst/include/armadillo_bits/glue_intersect_meat.hpp |only inst/include/armadillo_bits/glue_max_meat.hpp | 4 inst/include/armadillo_bits/glue_min_meat.hpp | 4 inst/include/armadillo_bits/glue_solve_bones.hpp | 3 inst/include/armadillo_bits/glue_solve_meat.hpp | 38 inst/include/armadillo_bits/gmm_diag_meat.hpp | 4 inst/include/armadillo_bits/gmm_full_meat.hpp | 6 inst/include/armadillo_bits/hdf5_misc.hpp | 33 inst/include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp | 5 inst/include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp | 5 inst/include/armadillo_bits/op_chol_bones.hpp | 4 inst/include/armadillo_bits/op_chol_meat.hpp | 26 inst/include/armadillo_bits/operator_times.hpp | 28 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 20 inst/include/armadillo_bits/subview_field_meat.hpp | 80 - inst/include/armadillo_bits/wrapper_lapack.hpp | 115 ++ inst/skeleton/Makevars | 12 inst/skeleton/Makevars.win | 12 inst/unitTests/runit.sparseConversion.R | 8 man/RcppArmadillo-package.Rd | 9 68 files changed, 2061 insertions(+), 851 deletions(-)
Title: Pakistan Social and Living Standards Measurement Survey 2014-15
Description: Data and statistics of Pakistan Social and Living Standards Measurement (PSLM) survey 2014-15 from Pakistan Bureau of Statistics (<http://www.pbs.gov.pk/>).
Author: Muhammad Yaseen [aut, cre],
Muhammad Arfan Dilber [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PSLM2015 versions 0.1.0 dated 2017-11-22 and 0.2.0 dated 2017-12-06
PSLM2015-0.1.0/PSLM2015/R/AssetLiability.R |only PSLM2015-0.1.0/PSLM2015/R/Income.R |only PSLM2015-0.1.0/PSLM2015/R/Land.R |only PSLM2015-0.1.0/PSLM2015/R/NonAgriculture.R |only PSLM2015-0.1.0/PSLM2015/R/OtherIncome.R |only PSLM2015-0.1.0/PSLM2015/R/PaidReceived.R |only PSLM2015-0.1.0/PSLM2015/R/SurveyInfo.R |only PSLM2015-0.1.0/PSLM2015/data/AssetLiability.RData |only PSLM2015-0.1.0/PSLM2015/data/Income.RData |only PSLM2015-0.1.0/PSLM2015/data/Land.RData |only PSLM2015-0.1.0/PSLM2015/data/NonAgriculture.RData |only PSLM2015-0.1.0/PSLM2015/data/OtherIncome.RData |only PSLM2015-0.1.0/PSLM2015/data/PaidReceived.RData |only PSLM2015-0.1.0/PSLM2015/data/SurveyInfo.RData |only PSLM2015-0.1.0/PSLM2015/man/AssetLiability.Rd |only PSLM2015-0.1.0/PSLM2015/man/Income.Rd |only PSLM2015-0.1.0/PSLM2015/man/Land.Rd |only PSLM2015-0.1.0/PSLM2015/man/NonAgriculture.Rd |only PSLM2015-0.1.0/PSLM2015/man/OtherIncome.Rd |only PSLM2015-0.1.0/PSLM2015/man/PaidReceived.Rd |only PSLM2015-0.1.0/PSLM2015/man/SurveyInfo.Rd |only PSLM2015-0.2.0/PSLM2015/DESCRIPTION | 8 PSLM2015-0.2.0/PSLM2015/MD5 | 69 +++----- PSLM2015-0.2.0/PSLM2015/NAMESPACE | 4 PSLM2015-0.2.0/PSLM2015/NEWS.md | 5 PSLM2015-0.2.0/PSLM2015/R/Agriculture.R | 168 +++++++++++++++++--- PSLM2015-0.2.0/PSLM2015/R/Education.R | 108 ++++++++----- PSLM2015-0.2.0/PSLM2015/R/Employment.R | 123 +++++++++------ PSLM2015-0.2.0/PSLM2015/R/Expenditure.R | 80 +++++---- PSLM2015-0.2.0/PSLM2015/R/HHRoster.R |only PSLM2015-0.2.0/PSLM2015/R/Housing.R |only PSLM2015-0.2.0/PSLM2015/R/ICT.R | 107 +++++++------ PSLM2015-0.2.0/PSLM2015/R/LiveStock.R | 177 ++++++++++++++++++---- PSLM2015-0.2.0/PSLM2015/data/Agriculture.RData |binary PSLM2015-0.2.0/PSLM2015/data/Education.RData |binary PSLM2015-0.2.0/PSLM2015/data/Employment.RData |binary PSLM2015-0.2.0/PSLM2015/data/Expenditure.RData |binary PSLM2015-0.2.0/PSLM2015/data/HHRoster.RData |only PSLM2015-0.2.0/PSLM2015/data/Housing.RData |only PSLM2015-0.2.0/PSLM2015/data/LiveStock.RData |binary PSLM2015-0.2.0/PSLM2015/data/datalist | 9 - PSLM2015-0.2.0/PSLM2015/man/Agriculture.Rd | 157 ++++++++++++++++--- PSLM2015-0.2.0/PSLM2015/man/Education.Rd | 97 +++++++----- PSLM2015-0.2.0/PSLM2015/man/Employment.Rd | 110 ++++++++----- PSLM2015-0.2.0/PSLM2015/man/Expenditure.Rd | 70 ++++---- PSLM2015-0.2.0/PSLM2015/man/HHRoster.Rd |only PSLM2015-0.2.0/PSLM2015/man/Housing.Rd |only PSLM2015-0.2.0/PSLM2015/man/ICT.Rd | 96 ++++++----- PSLM2015-0.2.0/PSLM2015/man/LiveStock.Rd | 168 +++++++++++++++++--- 49 files changed, 1076 insertions(+), 480 deletions(-)
Title: Joint Models for Longitudinal Measurements and Competing Risks
Failure Time Data
Description: Fit joint models of continuous or ordinal longitudinal data and time-to-event data with competing risks. For a detailed information, see Robert Elashoff, Gang li and Ning Li (2016, ISBN:9781439807828) ; Robert M. Elashoff,Gang Li and Ning Li (2008) <doi:10.1111/j.1541-0420.2007.00952.x> ; Ning Li, Robert Elashoff, Gang Li and Jeffrey Saver (2010) <doi:10.1002/sim.3798> .
Author: Hong Wang<wh@csu.edu.cn>, Ning Li<nli@biomath.ucla.edu> and Gang Li<vli@ucla.edu>
Maintainer: Hong Wang <wh@csu.edu.cn>
Diff between JMcmprsk versions 0.9.1 dated 2017-12-04 and 0.9.2 dated 2017-12-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/JMcmprsk.html | 4 ++-- src/jmc.cpp | 10 +++++----- src/jmo.cpp | 10 +++++----- 5 files changed, 20 insertions(+), 20 deletions(-)
Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for glm(), glm.nb(), polr() and multinom().
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 2.5-1 dated 2017-05-23 and 3.0-0 dated 2017-12-06
DESCRIPTION | 10 - MD5 | 58 ++++-- NAMESPACE | 10 - R/basepredict.R |only R/basepredict.glm.R |only R/basepredict.multinom.R |only R/basepredict.polr.R |only R/dc.R |only R/dc.glm.R |only R/dc.multinom.R |only R/dc.polr.R |only R/discrete.change.R | 83 -------- R/discrete.changes.R | 399 ------------------------------------------- R/getBaseCombinations.R |only R/getCombinations.R |only R/getDummies.R | 9 R/getFactorCombinations.R |only R/getLabel.R |only R/getNames.R |only R/getProducts.R |only R/getResultMatrix.R |only R/getValues.R |only R/inizialize_data.frame.R |only R/mode.R |only R/nominal_discrete.change.R | 66 ------- R/nominal_discrete.changes.R | 367 --------------------------------------- R/ordinal_discrete.changes.R | 376 ---------------------------------------- R/ordinal_discrete_change.R | 75 -------- R/predict_glm.R | 64 ------ R/predict_multinom.R | 57 ------ R/predict_polr.R | 67 ------- R/predicts.R |only R/predicts_glm.R | 353 -------------------------------------- R/predicts_multinom.R | 319 ---------------------------------- R/predicts_polr.R | 328 ----------------------------------- man/basepredict.Rd |only man/basepredict.glm.Rd |only man/basepredict.multinom.Rd |only man/basepredict.polr.Rd |only man/dc.Rd |only man/dc.glm.Rd |only man/dc.multinom.Rd |only man/dc.polr.Rd |only man/predicts.Rd |only 44 files changed, 89 insertions(+), 2552 deletions(-)
Title: Create Meme
Description: The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976).
It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity.
The internet memes are captioned photos that are intended to be funny, ridiculous.
Memes behave like infectious viruses and travel from person to person quickly through social media.
The 'meme' package allows users to make custom memes.
Author: Guangchuang Yu [aut, cre] (0000-0002-6485-8781)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between meme versions 0.0.7 dated 2017-11-02 and 0.1.1 dated 2017-12-06
DESCRIPTION | 11 ++++++----- MD5 | 23 ++++++++++++++--------- NAMESPACE | 5 ++++- NEWS | 5 +++++ R/font_import.R |only R/utilities.R | 12 +++++++----- inst/doc/meme.R | 29 +++++++++++++++++++++++++---- inst/doc/meme.Rmd | 49 +++++++++++++++++++++++++++++++++++++++++++++---- inst/doc/meme.html | 38 ++++++++++++++++++++++++++++++++------ inst/fonts |only man/asp.Rd | 2 ++ man/font-import.Rd |only vignettes/meme.Rmd | 49 +++++++++++++++++++++++++++++++++++++++++++++---- 13 files changed, 185 insertions(+), 38 deletions(-)
Title: Correction of the P-Value after Multiple Coding in Generalized
Linear Models
Description: We propose to determine the correction of the significance level after multiple coding of an explanatory variable in Generalized Linear Model. The different methods of correction of the p-value are the Single step Bonferroni procedure, and resampling based methods developed by P.H.Westfall in 1993. Resampling methods are based on the permutation and the parametric bootstrap procedure. If some continuous, and dichotomous transformations are performed this package offers an exact correction of the p-value developed by B.Liquet & D.Commenges in 2005. The naive method with no correction is also available.
Author: Jeremie Riou, and Benoit Liquet
Maintainer: Jeremie Riou <jeremie.riou@univ-angers.fr>
Diff between CPMCGLM versions 1.1 dated 2013-11-06 and 1.2 dated 2017-12-06
DESCRIPTION | 21 - MD5 | 27 - NAMESPACE | 6 R/CPMCGLM.R | 895 +++++++++++++++++++++++++------------------------- R/Codage.R | 41 +- R/FP.R |only R/bestcod.R | 315 +++++++++-------- R/codcut.R | 4 R/print.CPMCGLM.R | 140 ++++--- R/test.liquet.R | 147 ++++---- R/test.score.R | 82 ++-- R/tmultboot.R | 105 +++-- R/transf.R | 328 ++++++++++++------ man/CPMCGLM.Rd | 420 ++++++++++++----------- man/ForInternalUse.Rd | 25 - 15 files changed, 1411 insertions(+), 1145 deletions(-)
Title: Clustering with Overlaps
Description: Provide functions for overlaps clustering, fuzzy clustering and interval-valued data manipulation. The package implement the following algorithms:
OKM (Overlapping Kmeans) from Cleuziou, G. (2007) <doi:10.1109/icpr.2008.4761079> ;
NEOKM (Non-exhaustive overlapping Kmeans) from Whang, J. J., Dhillon, I. S., and Gleich, D. F. (2015) <doi:10.1137/1.9781611974010.105> ;
Fuzzy Cmeans from Bezdek, J. C. (1981) <doi:10.1007/978-1-4757-0450-1> ;
Fuzzy I-Cmeans from de A.T. De Carvalho, F. (2005) <doi:10.1016/j.patrec.2006.08.014>.
Author: Guillaume Cleuziou [cre],
Nicolas Hiot [aut]
Maintainer: Guillaume Cleuziou <guillaume.cleuziou@univ-orleans.fr>
Diff between COveR versions 1.0.1 dated 2017-11-27 and 1.0.3 dated 2017-12-06
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/r1okm.R | 1 - R/r2okm.R | 1 - src/icmeans/icmeans.h | 4 +++- src/ikmeans/ikmeans.h | 4 +++- src/ineokm/ineokm.h | 4 +++- src/neokm/neokm.h | 4 +++- src/r1okm/r1okm.h | 4 +++- src/r2okm/r2okm.h | 4 +++- 10 files changed, 30 insertions(+), 20 deletions(-)
Title: Rubik's Cube Solving
Description: Functions for visualizing, animating, solving and
analyzing the Rubik's cube. Includes data structures for
solvable and unsolvable cubes, random moves and random
state scrambles and cubes, 3D displays and animations
using 'OpenGL', patterned cube generation, and lightweight
solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the
Kociemba solver.
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between cubing versions 1.0-0 dated 2017-12-04 and 1.0-1 dated 2017-12-06
DESCRIPTION | 8 MD5 | 41 +-- NAMESPACE | 2 R/gmcubes.R | 624 +++++++++++++++++++++++----------------------- R/patterns.R | 402 ++++++++--------------------- R/solver.R | 26 - R/struct.R | 51 ++- inst/doc/cubingintro.R | 113 ++++---- inst/doc/cubingintro.Rnw | 86 +++--- inst/doc/cubingintro.pdf |binary man/composition.Rd | 4 man/cubieCube.Rd | 25 + man/cycle.Rd | 2 man/getMovesPattern.Rd |only man/invCube.Rd | 2 man/invMoves.Rd | 2 man/plot.cube.Rd | 2 man/plot3d.cube.Rd | 2 man/rotate.Rd | 2 man/solver.Rd | 2 man/stickerCube.Rd | 25 + vignettes/cubingintro.Rnw | 86 +++--- 22 files changed, 700 insertions(+), 807 deletions(-)
Title: Wavelet Methods for Time Series Analysis
Description: Software to book Wavelet Methods for Time Series Analysis,
Donald B. Percival and Andrew T. Walden, Cambridge University
Press, 2000.
Author: William Constantine [cre, aut],
Donald Percival [aut]
Maintainer: William Constantine <wlbconstan@gmail.com>
Diff between wmtsa versions 2.0-2 dated 2016-06-13 and 2.0-3 dated 2017-12-06
DESCRIPTION | 6 ++--- MD5 | 13 +++++++---- NAMESPACE | 3 ++ R/wav_filt.R | 36 +++++++++++++++++++++++++++++++ R/wav_plot.R | 13 +++++++++++ R/wav_xform.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++ man/wavDWTMatrix.Rd |only man/wavEquivFilter.Rd |only man/wavStemPlot.Rd |only 9 files changed, 120 insertions(+), 8 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Kurt Hornik [aut],
Florian Gerber [ctb],
Michael Friendly [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-3 dated 2016-09-17 and 1.4-4 dated 2017-12-06
DESCRIPTION | 16 ++++++---- MD5 | 60 ++++++++++++++++++++--------------------- NAMESPACE | 13 ++------ R/agreementplot.R | 2 - R/labeling.R | 13 +++++--- R/loddsratio.R | 14 +++++---- R/structable.R | 2 - R/ternaryplot.R | 20 +++++++------ build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/NEWS.Rd | 10 ++++++ inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.pdf |binary man/Bundestag2005.Rd | 2 - man/assoc.Rd | 2 - man/legends.Rd | 2 - man/ternaryplot.Rd | 10 +++++- 31 files changed, 93 insertions(+), 73 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They
can be either drawn with or without replacement, or with distinct/ non-distinct
items (multiset). The generated sequences are in lexicographical order
(dictionary order). The algorithms to generate permutations and combinations are
memory efficient. These iterative algorithms enable users to process all sequences
without putting all results in the memory at the same time.
The algorithms are written in C/C++ for faster performance.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.3.3 dated 2017-09-12 and 0.3.4 dated 2017-12-06
DESCRIPTION | 24 ++++++++++++------------ MD5 | 18 +++++++++--------- R/iterpc.R | 14 ++++++++------ README.md | 4 ++-- build/vignette.rds |binary inst/doc/combinations.html | 4 ++-- inst/doc/permutations.html | 4 ++-- man/iterpc.Rd | 2 +- tests/testthat/test-combination.R | 3 +++ tests/testthat/test-permutation.R | 3 +++ 10 files changed, 42 insertions(+), 34 deletions(-)
Title: Utility Functions for 'INLA'
Description: A number of utility functions for 'INLA' <http://www.r-inla.org>. Additional diagnostic plots
and support for 'ggplot2'. Step wise regression with 'INLA'. Species distribution models
and other helper functions.
Author: Tim CD Lucas [aut, cre] (0000-0003-4694-8107),
Dave Redding [aut] (0000-0001-8615-1798)
Maintainer: Tim CD Lucas <timcdlucas@gmail.com>
Diff between INLAutils versions 0.0.4 dated 2017-08-05 and 0.0.5 dated 2017-12-06
DESCRIPTION | 14 +++++++------- MD5 | 4 ++-- inst/CITATION | 6 +++--- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in
the Lexis diagram, bootstrapping. Parametric proportional
hazards fitting with left truncation and right censoring for
common families of distributions, piecewise constant hazards,
and discrete models. AFT regression for left truncated and
right censored data.
Author: Göran Broström [aut, cre]
Maintainer: Göran Broström <goran.brostrom@umu.se>
Diff between eha versions 2.5.0 dated 2017-10-11 and 2.5.1 dated 2017-12-06
ChangeLog | 16 ++ DESCRIPTION | 8 - MD5 | 20 +- NAMESPACE | 6 NEWS.md | 4 R/Pch.R | 54 +++++++ inst/doc/eha.html | 237 +++++++---------------------------- inst/doc/parametric.Rnw | 4 inst/doc/parametric.pdf |binary man/Pch.Rd |only vignettes/parametric-concordance.tex |only vignettes/parametric.Rnw | 4 12 files changed, 140 insertions(+), 213 deletions(-)
Title: Importing and Analysing Snp and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of
snp and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE. Other functions
are available for visualization after PCoA, or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip packages etc.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR versions 0.93 dated 2017-08-21 and 1.0 dated 2017-12-06
DESCRIPTION | 10 +++---- MD5 | 22 ++++++++++------- NAMESPACE | 9 ++++++ R/gl.report.maf.r |only R/gl2gi.r | 26 +++++++++++--------- R/gl2shp.R |only R/gl2structure.r |only inst/doc/IntroTutorial_dartR.R | 31 +++++++++++++++++++----- inst/doc/IntroTutorial_dartR.Rmd | 49 +++++++++++++++++++++++++++++++------- inst/doc/IntroTutorial_dartR.pdf |binary man/gl.report.maf.Rd |only man/gl2gi.Rd | 4 +-- man/gl2shp.Rd |only man/gl2structure.Rd |only vignettes/IntroTutorial_dartR.Rmd | 49 +++++++++++++++++++++++++++++++------- 15 files changed, 152 insertions(+), 48 deletions(-)
Title: A Bunch of Structure and Sequence Analysis
Description: Reads and plots phylogenetic placements obtained using the 'epa', 'pplacer' and 'guppy' softwares.
Author: Pierre Lefeuvre
Maintainer: Pierre Lefeuvre <pierre.lefeuvre@cirad.fr>
Diff between BoSSA versions 2.3 dated 2017-11-16 and 3.0 dated 2017-12-06
DESCRIPTION | 10 +- MD5 | 56 +++++++-------- NAMESPACE | 4 - R/plot.pplace.R | 48 ++++++++----- R/pplace_to_matrix.R | 63 +++++++++-------- R/pplace_to_table.R | 27 ++++--- R/pplace_to_taxonomy.R | 46 ++++++------ R/print.jplace.R | 4 - R/print.pplace.R | 7 + R/read_jplace.R | 45 ++++++++---- R/read_sqlite.R | 28 ++++--- R/refpkg.R | 3 R/sub_pplace.R | 35 +++++++-- R/write_jplace.R |only build/partial.rdb |binary data/pplace.rda |binary inst/doc/bossa-analysis.Rmd | 16 ++-- inst/doc/bossa-analysis.html | 158 +++++++++++++++++++++++++------------------ inst/doc/bossa-refpkg.Rmd | 2 inst/doc/bossa-refpkg.html | 10 +- inst/extdata/example.sqlite |binary man/plot.pplace.Rd | 11 ++ man/pplace_to_matrix.Rd | 13 ++- man/pplace_to_table.Rd | 5 + man/pplace_to_taxonomy.Rd | 5 + man/refpkg.Rd | 16 ++-- man/sub_pplace.Rd | 11 +- man/write_jplace.Rd |only vignettes/bossa-analysis.Rmd | 16 ++-- vignettes/bossa-refpkg.Rmd | 2 30 files changed, 387 insertions(+), 254 deletions(-)
Title: Generalized Linear Density Ratio Models
Description: Fits a generalized linear density ratio model (GLDRM).
A GLDRM is a semiparametric generalized linear model.
In contrast to a GLM, which assumes a particular exponential family distribution,
the GLDRM uses a semiparametric likelihood to estimate the reference distribution.
The reference distribution may be any discrete, continuous, or mixed exponential
family distribution. The model parameters, which include both the regression
coefficients and the cdf of the unspecified reference distribution, are estimated
by maximizing a semiparametric likelihood. Regression coefficients are estimated
with no loss of efficiency, i.e. the asymptotic variance is the same as if the
true exponential family distribution were known.
Author: Michael Wurm [aut, cre],
Paul Rathouz [aut]
Maintainer: Michael Wurm <wurm@uwalumni.com>
Diff between gldrm versions 1.1 dated 2017-06-28 and 1.4 dated 2017-12-06
DESCRIPTION | 12 +- MD5 | 14 +- R/getTheta.R | 4 R/gldrm.R | 2 R/gldrmCI.R | 324 +++++++++++++++++++++++++++++++++++++++++++-------------- R/gldrmFit.R | 2 man/gldrm.Rd | 2 man/gldrmCI.Rd | 15 +- 8 files changed, 274 insertions(+), 101 deletions(-)