Title: The Symmetric Group: Permutations of a Finite Set
Description: Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between permutations versions 1.0-2 dated 2017-01-25 and 1.0-4 dated 2019-04-11
DESCRIPTION | 12 +++++----- MD5 | 48 ++++++++++++++++++++++++------------------ R/perm_ops.R | 6 ++--- R/permfuns.R | 50 ++++++++++++++++++++++++++++++++++++++++---- R/validity_funs.R | 19 ++++++++++------ build/partial.rdb |only build/vignette.rds |binary data/megaminx.rda |binary inst/code.R |only inst/code2.R |only inst/data.txt |only inst/doc/permutations.R | 14 ++++++------ inst/doc/permutations.Rnw | 5 +--- inst/doc/permutations.pdf |binary inst/read.me |only inst/representation.Rmd |only man/Ops.permutation.Rd | 1 man/allperms.Rd | 6 ----- man/cayley.Rd |only man/conjugate.Rd | 1 man/cyclist.Rd | 2 - man/derangement.Rd | 4 --- man/permutation.Rd | 11 +++++---- man/permutations-package.Rd |only man/print.Rd | 28 ++++++++++++++++++++++-- man/shape.Rd | 4 +-- man/valid.Rd | 30 ++++++++++++-------------- tests/tests.R | 10 ++++++++ vignettes/permutations.Rnw | 5 +--- 29 files changed, 168 insertions(+), 88 deletions(-)
Title: Sitree Extensions
Description: Provides extensions for package 'sitree' for allometric variables, growth, mortality, recruitment, management, tree removal and external modifiers functions.
Author: Clara Anton Fernandez [aut, cre]
Maintainer: Clara Anton Fernandez <caf@nibio.no>
Diff between sitreeE versions 0.0-2 dated 2018-06-01 and 0.0-3 dated 2019-04-11
DESCRIPTION | 10 MD5 | 18 - NAMESPACE | 2 R/AM2016ClimateSensitiveSI.R | 2 R/Biomass_Norway.R | 523 +++++++++++++++++++++---------------------- R/PlotDataToLong.R |only README.md | 3 man/PBAL.Rd | 5 man/PlotDataToLong.Rd |only man/biomass.birch.S2014.Rd | 5 man/top.height.Rd | 5 11 files changed, 286 insertions(+), 287 deletions(-)
Title: Single Tree Simulator
Description: Forecasts plots at tree level.
Author: Clara Anton Fernandez [aut, cre],
Nikolas von Lupke [ctb]
Maintainer: Clara Anton Fernandez <caf@nibio.no>
Diff between sitree versions 0.1-4 dated 2018-10-25 and 0.1-6 dated 2019-04-11
DESCRIPTION | 11 ++++++----- MD5 | 14 ++++++++------ R/sitree.R | 4 ++-- R/sitree2dataframe.R |only build/vignette.rds |binary inst/doc/TestEquations.html | 32 ++++++++++++-------------------- man/dbhi.BN2009.Rd | 5 +---- man/sitree2dataframe.Rd |only man/tree.age.Rd | 5 +---- 9 files changed, 30 insertions(+), 41 deletions(-)
Title: Clustering High Dimensional Data with Hidden Markov Model on
Variable Blocks
Description: Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <http://jmlr.org/papers/v18/16-342.html>.
Author: Yevhen Tupikov [aut],
Lin Lin [aut],
Lixiang Zhang [aut],
Jia Li [aut, cre]
Maintainer: Jia Li <jiali@psu.edu>
Diff between HDclust versions 1.0 dated 2018-07-29 and 1.0.3 dated 2019-04-11
HDclust-1.0.3/HDclust/DESCRIPTION | 28 +- HDclust-1.0.3/HDclust/MD5 | 67 ++--- HDclust-1.0.3/HDclust/NAMESPACE | 8 HDclust-1.0.3/HDclust/R/AllClass.R | 12 HDclust-1.0.3/HDclust/R/AllGeneric.R | 16 - HDclust-1.0.3/HDclust/R/AllMethod.R | 79 ++++-- HDclust-1.0.3/HDclust/R/RcppExports.R | 8 HDclust-1.0.3/HDclust/R/clustControl.R | 9 HDclust-1.0.3/HDclust/R/clustModes.R |only HDclust-1.0.3/HDclust/R/hmmvbBIC.R | 25 +- HDclust-1.0.3/HDclust/R/hmmvbClust.R | 1 HDclust-1.0.3/HDclust/R/hmmvbFindModes.R |only HDclust-1.0.3/HDclust/R/package-HDclust.R | 8 HDclust-1.0.3/HDclust/build/vignette.rds |binary HDclust-1.0.3/HDclust/configure | 2 HDclust-1.0.3/HDclust/data/sim2.RData |binary HDclust-1.0.3/HDclust/inst/doc/HDclust.R | 42 +++ HDclust-1.0.3/HDclust/inst/doc/HDclust.Rmd | 73 +++++ HDclust-1.0.3/HDclust/inst/doc/HDclust.html | 114 +++++++-- HDclust-1.0.3/HDclust/man/HDclust-package.Rd | 2 HDclust-1.0.3/HDclust/man/HMMVB-class.Rd | 2 HDclust-1.0.3/HDclust/man/HMMVBBIC-class.Rd | 13 - HDclust-1.0.3/HDclust/man/HMMVBclust-class.Rd | 7 HDclust-1.0.3/HDclust/man/clustControl.Rd | 6 HDclust-1.0.3/HDclust/man/clustModes.Rd |only HDclust-1.0.3/HDclust/man/getLoglikehd.Rd |only HDclust-1.0.3/HDclust/man/getNumst.Rd | 11 HDclust-1.0.3/HDclust/man/hmmvbClust.Rd | 4 HDclust-1.0.3/HDclust/man/hmmvbFindModes.Rd |only HDclust-1.0.3/HDclust/man/mkhmmvb.Rd | 4 HDclust-1.0.3/HDclust/src/RcppExports.cpp | 23 + HDclust-1.0.3/HDclust/src/hmm.h | 3 HDclust-1.0.3/HDclust/src/rcpp_findModes.cpp |only HDclust-1.0.3/HDclust/src/rcpp_testsync.cpp | 309 +++++++++++++------------ HDclust-1.0.3/HDclust/src/rcpp_trainmaster.cpp | 30 +- HDclust-1.0.3/HDclust/src/utils_rcpp.cpp |only HDclust-1.0.3/HDclust/src/utils_rcpp.h |only HDclust-1.0.3/HDclust/vignettes/HDclust.Rmd | 73 +++++ HDclust-1.0/HDclust/man/getConfigList.Rd |only 39 files changed, 660 insertions(+), 319 deletions(-)
Title: Retrieve and Analyze Information on Clinical Trials from Public
Registers
Description: Provides functions for querying, retrieving and analysing protocol- and results-related information on clinical trials from two public registers, the European Union Clinical Trials Register (EUCTR, <https://www.clinicaltrialsregister.eu/>) and ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The information is transformed and then stored in a database (mongo). Functions are provided for accessing and analysing the locally stored information on the clinical trials, as well as for identifying duplicate records. The package is motivated by the need for aggregating and trend-analysing the design, conduct and outcomes across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 0.17.0 dated 2019-03-27 and 0.18 dated 2019-04-11
DESCRIPTION | 6 MD5 | 40 - NEWS.md | 7 R/main.R | 2 R/onload.R | 7 R/utils.R | 74 + README.md | 97 +- build/vignette.rds |binary inst/doc/ctrdata_get_started.R | 99 -- inst/doc/ctrdata_get_started.Rmd | 136 +-- inst/doc/ctrdata_get_started.html | 170 +--- inst/doc/ctrdata_usage_examples.R | 454 +++++------ inst/doc/ctrdata_usage_examples.Rmd | 477 +++++------ inst/doc/ctrdata_usage_examples.html | 1399 +++++++++++++++++------------------ man/dbCTRLoadJSONFiles.Rd | 2 tests/testthat/testfunctions.R | 109 ++ vignettes/ctrdata_get_started.Rmd | 136 +-- vignettes/ctrdata_usage_examples.Rmd | 477 +++++------ vignettes/ctrdatapvaluesphase23.png |binary vignettes/ph1paedoncopen.png |binary vignettes/phase1_paed_oncol.png |binary 21 files changed, 1877 insertions(+), 1815 deletions(-)
Title: Cognitive Mapping Tools Based on Coding of Textual Sources
Description: Functions for building cognitive maps based on qualitative data. Inputs are textual sources (articles, transcription of qualitative interviews of agents,...). These sources have been coded using relations and are linked to (i) a table describing the variables (or concepts) used for the coding and (ii) a table describing the sources (typology of agents, ...). Main outputs are Individual Cognitive Maps (ICM), Social Cognitive Maps (all sources or group of sources) and a list of quotes linked to relations. This package is linked to the work done during the PhD of Frederic M. Vanwindekens (CRA-W / UCL) hold the 13 of May 2014 at University of Louvain in collaboration with the Walloon Agricultural Research Centre (project MIMOSA, MOERMAN fund).
Author: Frédéric M. Vanwindekens [aut, cre]
(<https://orcid.org/0000-0002-9117-7543>),
Didier Stilmant [aut, ths],
Philippe V. Baret [aut, ths]
Maintainer: Frédéric M. Vanwindekens <f.vanwindekens@cra.wallonie.be>
Diff between cogmapr versions 0.9 dated 2019-04-09 and 0.9.1 dated 2019-04-11
cogmapr-0.9.1/cogmapr/DESCRIPTION | 16 ++++++++------- cogmapr-0.9.1/cogmapr/MD5 | 21 ++++++-------------- cogmapr-0.9.1/cogmapr/NAMESPACE | 3 -- cogmapr-0.9.1/cogmapr/R/cogmapr-comp.R | 2 - cogmapr-0.9.1/cogmapr/R/cogmapr.R | 14 +------------ cogmapr-0.9.1/cogmapr/inst/THANKS | 2 - cogmapr-0.9.1/cogmapr/man/EdgCMap.Rd | 2 - cogmapr-0.9.1/cogmapr/tests/testthat/test-cogmapr.R | 10 +-------- cogmapr-0.9/cogmapr/R/cogmapr-report.R |only cogmapr-0.9/cogmapr/inst/rmarkdown |only cogmapr-0.9/cogmapr/man/ReportICM.Rd |only cogmapr-0.9/cogmapr/man/ReportSCM.Rd |only cogmapr-0.9/cogmapr/man/SheetCoding.Rd |only 13 files changed, 23 insertions(+), 47 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.11 dated 2019-03-12 and 0.12 dated 2019-04-11
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/install.R | 34 ++++++++++++++++++++-------------- R/latex.R | 14 +++++++++++++- inst |only 5 files changed, 40 insertions(+), 21 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Estimation-bias corrections are available.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>),
Bruno Herault [aut] (<https://orcid.org/0000-0002-6950-7286>)
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between entropart versions 1.5-3 dated 2018-02-05 and 1.6-1 dated 2019-04-11
entropart-1.5-3/entropart/NEWS |only entropart-1.5-3/entropart/inst/doc/docs.Rmd |only entropart-1.5-3/entropart/inst/doc/docs.html |only entropart-1.5-3/entropart/inst/doc/rd.Rmd |only entropart-1.5-3/entropart/inst/doc/rd.html |only entropart-1.5-3/entropart/vignettes/Tree.png |only entropart-1.5-3/entropart/vignettes/docs.Rmd |only entropart-1.5-3/entropart/vignettes/rd.Rmd |only entropart-1.5-3/entropart/vignettes/rd_index.yaml |only entropart-1.6-1/entropart/DESCRIPTION | 31 entropart-1.6-1/entropart/MD5 | 136 ++- entropart-1.6-1/entropart/NAMESPACE | 428 ++++++------ entropart-1.6-1/entropart/NEWS.md |only entropart-1.6-1/entropart/R/AbdFreqCount.R | 51 + entropart-1.6-1/entropart/R/Accumulation.R |only entropart-1.6-1/entropart/R/ArgumentOriginalName.R | 2 entropart-1.6-1/entropart/R/CEnvelope.R | 4 entropart-1.6-1/entropart/R/CheckentropartArguments.R | 48 + entropart-1.6-1/entropart/R/CommunityProfile.R | 29 entropart-1.6-1/entropart/R/Coverage.R | 185 +++-- entropart-1.6-1/entropart/R/DivEst.R | 69 + entropart-1.6-1/entropart/R/DivPart.R | 19 entropart-1.6-1/entropart/R/DivProfile.R | 108 ++- entropart-1.6-1/entropart/R/Diversity.R | 33 entropart-1.6-1/entropart/R/EntropyCI.R | 8 entropart-1.6-1/entropart/R/GenSimpson.R | 62 - entropart-1.6-1/entropart/R/HurlbertD.R | 2 entropart-1.6-1/entropart/R/MCdiversity.R | 17 entropart-1.6-1/entropart/R/MCentropy.R | 16 entropart-1.6-1/entropart/R/PhyloValue.R | 34 entropart-1.6-1/entropart/R/Richness.R | 189 +++-- entropart-1.6-1/entropart/R/Shannon.R | 68 + entropart-1.6-1/entropart/R/SimTest.R | 23 entropart-1.6-1/entropart/R/Simpson.R | 55 + entropart-1.6-1/entropart/R/SpeciesDistribution.R | 344 +++++++-- entropart-1.6-1/entropart/R/Tsallis.R | 80 +- entropart-1.6-1/entropart/README.md | 10 entropart-1.6-1/entropart/build/vignette.rds |binary entropart-1.6-1/entropart/inst/doc/entropart.R |only entropart-1.6-1/entropart/inst/doc/entropart.Rmd |only entropart-1.6-1/entropart/inst/doc/entropart.html |only entropart-1.6-1/entropart/man/AbdFreqCount.Rd | 20 entropart-1.6-1/entropart/man/Accumulation.Rd |only entropart-1.6-1/entropart/man/CommunityProfile.Rd | 15 entropart-1.6-1/entropart/man/Coverage.Rd | 22 entropart-1.6-1/entropart/man/DivEst.Rd | 17 entropart-1.6-1/entropart/man/DivPart.Rd | 4 entropart-1.6-1/entropart/man/DivProfile.Rd | 22 entropart-1.6-1/entropart/man/Diversity.Rd | 47 + entropart-1.6-1/entropart/man/EightSpTree.Rd | 6 entropart-1.6-1/entropart/man/EntropyCI.Rd | 5 entropart-1.6-1/entropart/man/MCdiversity.Rd | 4 entropart-1.6-1/entropart/man/MCentropy.Rd | 4 entropart-1.6-1/entropart/man/PhyloApply.Rd | 2 entropart-1.6-1/entropart/man/PhyloEntropy.Rd | 2 entropart-1.6-1/entropart/man/PhyloValue.Rd | 14 entropart-1.6-1/entropart/man/Preprocess.Tree.Rd | 4 entropart-1.6-1/entropart/man/RAC.Rd |only entropart-1.6-1/entropart/man/Richness.Rd | 35 entropart-1.6-1/entropart/man/Shannon.Rd | 36 - entropart-1.6-1/entropart/man/SimTest.Rd | 36 - entropart-1.6-1/entropart/man/Simpson.Rd | 21 entropart-1.6-1/entropart/man/SpeciesDistribution.Rd | 28 entropart-1.6-1/entropart/man/Tsallis.Rd | 51 + entropart-1.6-1/entropart/man/figures |only entropart-1.6-1/entropart/man/mergeandlabel.Rd | 2 entropart-1.6-1/entropart/man/rCommunity.Rd | 2 entropart-1.6-1/entropart/tests/testthat.R | 2 entropart-1.6-1/entropart/tests/testthat/testCProfile.R |only entropart-1.6-1/entropart/tests/testthat/testCoverage.R |only entropart-1.6-1/entropart/tests/testthat/testDivProfile.R |only entropart-1.6-1/entropart/tests/testthat/testDqZ.R |only entropart-1.6-1/entropart/tests/testthat/testHurlbert.R |only entropart-1.6-1/entropart/tests/testthat/testLevel.R |only entropart-1.6-1/entropart/tests/testthat/testMissingNorP.R |only entropart-1.6-1/entropart/tests/testthat/testNoSp.R |only entropart-1.6-1/entropart/tests/testthat/testOrder2.R | 20 entropart-1.6-1/entropart/tests/testthat/testPhyloEntropy.R | 37 - entropart-1.6-1/entropart/tests/testthat/testTsallis.R | 62 + entropart-1.6-1/entropart/tests/testthat/testlnqexpq.R | 10 entropart-1.6-1/entropart/vignettes/entropart.Rmd |only entropart-1.6-1/entropart/vignettes/entropart.bib | 27 82 files changed, 1889 insertions(+), 719 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common univariate
statistics in concise tables available in a variety of
formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.9.2 dated 2019-02-22 and 0.9.3 dated 2019-04-11
summarytools-0.9.2/summarytools/R/useTranslations.R |only summarytools-0.9.2/summarytools/man/useTranslations.Rd |only summarytools-0.9.3/summarytools/DESCRIPTION | 10 summarytools-0.9.3/summarytools/MD5 | 61 - summarytools-0.9.3/summarytools/NAMESPACE | 14 summarytools-0.9.3/summarytools/NEWS.md | 41 summarytools-0.9.3/summarytools/R/args_validation.R |only summarytools-0.9.3/summarytools/R/ctable.R | 92 +- summarytools-0.9.3/summarytools/R/define_keywords.R |only summarytools-0.9.3/summarytools/R/descr.R | 2 summarytools-0.9.3/summarytools/R/dfSummary.R | 253 ++++-- summarytools-0.9.3/summarytools/R/freq.R | 212 ++--- summarytools-0.9.3/summarytools/R/helpers.R | 421 ---------- summarytools-0.9.3/summarytools/R/parse_args.R | 54 + summarytools-0.9.3/summarytools/R/print.summarytools.R | 207 +++- summarytools-0.9.3/summarytools/R/st_options.R | 49 - summarytools-0.9.3/summarytools/R/stby.R | 10 summarytools-0.9.3/summarytools/R/sysdata.rda |binary summarytools-0.9.3/summarytools/R/tb.R |only summarytools-0.9.3/summarytools/R/use_custom_lang.R |only summarytools-0.9.3/summarytools/R/zzz.R | 15 summarytools-0.9.3/summarytools/README | 2 summarytools-0.9.3/summarytools/build/vignette.rds |binary summarytools-0.9.3/summarytools/inst/doc/Introduction.R | 21 summarytools-0.9.3/summarytools/inst/doc/Introduction.Rmd | 154 ++- summarytools-0.9.3/summarytools/inst/doc/Introduction.html | 359 ++++++-- summarytools-0.9.3/summarytools/inst/doc/Recommendations-rmarkdown.html | 37 summarytools-0.9.3/summarytools/inst/includes/language_template.csv |only summarytools-0.9.3/summarytools/man/ctable.Rd | 10 summarytools-0.9.3/summarytools/man/define_keywords.Rd |only summarytools-0.9.3/summarytools/man/freq.Rd | 35 summarytools-0.9.3/summarytools/man/st_options.Rd | 21 summarytools-0.9.3/summarytools/man/stby.Rd | 4 summarytools-0.9.3/summarytools/man/tb.Rd |only summarytools-0.9.3/summarytools/man/use_custom_lang.Rd |only summarytools-0.9.3/summarytools/vignettes/Introduction.Rmd | 154 ++- summarytools-0.9.3/summarytools/vignettes/define_keywords.png |only 37 files changed, 1323 insertions(+), 915 deletions(-)
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.66 dated 2018-10-24 and 1.67 dated 2019-04-11
Changelog | 59 ++++++++++ DESCRIPTION | 8 - MD5 | 53 +++++---- R/Functions.R | 135 +++++++++++++++---------- R/blockwiseData.R | 5 R/blockwiseModulesC.R | 205 ++++++++++++++++++++++++-------------- R/consensusCalculations.R | 24 ++-- R/consensusTOM.R | 14 ++ R/exportFunctions.R | 5 R/hierarchicalConsensusModules.R | 5 R/internalConstants.R | 2 R/modulePreservation.R | 12 +- R/zzz.R | 58 +++++----- man/TOMsimilarity.Rd | 33 ++++-- man/TOMsimilarityFromExpr.Rd | 13 ++ man/blockwiseConsensusModules.Rd | 5 man/blockwiseIndividualTOMs.Rd | 19 ++- man/blockwiseModules.Rd | 10 + man/consensusCalculation.Rd | 3 man/consensusTOM.Rd | 5 man/formatLabels.Rd | 3 man/hierarchicalConsensusKME.Rd | 5 man/multiGSub.Rd | 9 + man/newConsensusOptions.Rd | 6 - man/newNetworkOptions.Rd | 9 + man/projectiveKMeans.Rd | 5 man/sizeRestrictedClusterMerge.Rd |only src/networkFunctions.c | 67 ++++++++++-- 28 files changed, 542 insertions(+), 235 deletions(-)
Title: Tools to Retrieve Economic Policy Institute Data Library
Extracts
Description: The Economic Policy Institute (<http://www.epi.org/>) provides
researchers, media, and the public with easily accessible, up-to-date, and
comprehensive historical data on the American labor force. It is compiled
from Economic Policy Institute analysis of government data sources. Use
it to research wages, inequality, and other economic indicators over time
and among demographic groups. Data is usually updated monthly.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rud.is>
Diff between epidata versions 0.2.0 dated 2018-04-03 and 0.3.0 dated 2019-04-11
DESCRIPTION | 14 +-- MD5 | 88 +++++++++++++----------- NAMESPACE | 4 + NEWS.md | 17 ++-- R/aaa.r | 9 ++ R/annual-wages-by-wage-group.R |only R/compensation-wages-benefits.R |only R/employment.r | 18 +++- R/epi_query.r | 11 ++- R/epidata-package.R | 1 R/gaps.r | 23 +++--- R/health.r | 3 R/minimum-wage.R |only R/pension.r | 3 R/poverty.R |only R/productivity.r | 3 R/union.r | 4 - R/utils.r | 8 +- R/wage_decomposition.r | 3 R/wages.r | 7 + R/wages_and_hours.r | 4 - README.md |only man/epidata.Rd | 1 man/figures |only man/get_annual_wages_and_work_hours.Rd | 2 man/get_annual_wages_by_wage_group.Rd |only man/get_black_white_wage_gap.Rd | 2 man/get_college_wage_premium.Rd | 2 man/get_compensation_wages_and_benefits.Rd |only man/get_employment_to_population_ratio.Rd | 2 man/get_gender_wage_gap.Rd | 2 man/get_health_insurance_coverage.Rd | 2 man/get_hispanic_white_wage_gap.Rd | 2 man/get_labor_force_participation_rate.Rd | 2 man/get_long_term_unemployment.Rd | 2 man/get_median_and_mean_wages.Rd | 2 man/get_minimum_wage.Rd |only man/get_non_high_school_wage_penalty.Rd | 2 man/get_pension_coverage.Rd | 2 man/get_poverty_level_wages.Rd |only man/get_productivity_and_hourly_compensation.Rd | 2 man/get_underemployment.Rd | 2 man/get_unemployment.Rd | 2 man/get_unemployment_by_state.Rd | 2 man/get_union_coverage.Rd | 2 man/get_wage_decomposition.Rd | 2 man/get_wage_ratios.Rd | 2 man/get_wages_by_education.Rd | 2 man/get_wages_by_percentile.Rd | 2 tests/testthat/test-epidata.R | 8 +- 50 files changed, 161 insertions(+), 110 deletions(-)
Title: Import XY-Data into R
Description: Provides access to the 'xylib' C library for to import xy
data from powder diffraction, spectroscopy and other experimental methods.
Author: Sebastian Kreutzer [aut, trl, cre]
(<https://orcid.org/0000-0002-0734-2199>),
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
RLum Team [ctb],
Marcin Wojdyr [cph] (C++ library 'xylib'),
Peng Zhang [cph] (C++ library 'xylib')
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between rxylib versions 0.2.1 dated 2017-12-20 and 0.2.3 dated 2019-04-11
DESCRIPTION | 21 +++++---- MD5 | 26 ++++++----- NEWS | 6 ++ NEWS.md |only R/convert_xy2TKA.R | 10 +++- R/rxylib.R | 4 - README.md |only inst/include/xylib/spectra.h | 83 ++++++++++++++++++-------------------- inst/include/xylib/util.h | 1 man/convert_xy2TKA.Rd | 10 +++- man/rxylib-package.Rd | 4 - src/Makevars | 19 ++++++-- src/xylib/winspec_spe.cpp | 2 src/xylib/xsyg.cpp | 2 tests/testthat/test_read_xyData.R | 4 - 15 files changed, 111 insertions(+), 81 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.9-4 dated 2019-01-03 and 4.9-5 dated 2019-04-11
meta-4.9-4/meta/R/baujat.meta.R |only meta-4.9-4/meta/R/bubble.metareg.R |only meta-4.9-4/meta/R/chkmetafor.R |only meta-4.9-4/meta/R/cilayout.R |only meta-4.9-4/meta/R/forest.meta.R |only meta-4.9-4/meta/R/forest.metabind.R |only meta-4.9-4/meta/R/funnel.default.R |only meta-4.9-4/meta/R/funnel.meta.R |only meta-4.9-4/meta/R/labbe.default.R |only meta-4.9-4/meta/R/labbe.metabin.R |only meta-4.9-4/meta/R/metabias.default.R |only meta-4.9-4/meta/R/metabias.meta.R |only meta-4.9-4/meta/R/print.metabias.R |only meta-4.9-4/meta/R/print.rm5.R |only meta-4.9-4/meta/R/print.summary.meta.R |only meta-4.9-4/meta/R/print.summary.rm5.R |only meta-4.9-4/meta/R/radial.default.R |only meta-4.9-4/meta/R/radial.meta.R |only meta-4.9-4/meta/R/trimfill.default.R |only meta-4.9-4/meta/R/trimfill.meta.R |only meta-4.9-4/meta/data/Fleiss93.txt.gz |only meta-4.9-4/meta/data/Fleiss93_CR.csv.gz |only meta-4.9-4/meta/data/Fleiss93cont.txt.gz |only meta-4.9-4/meta/data/Olkin95.txt.gz |only meta-4.9-4/meta/data/amlodipine.txt.gz |only meta-4.9-4/meta/data/cisapride.txt.gz |only meta-4.9-4/meta/data/lungcancer.txt.gz |only meta-4.9-4/meta/data/smoking.txt.gz |only meta-4.9-4/meta/data/woodyplants.txt.gz |only meta-4.9-4/meta/man/print.rm5.Rd |only meta-4.9-5/meta/DESCRIPTION | 24 meta-4.9-5/meta/MD5 | 220 meta-4.9-5/meta/NAMESPACE | 203 meta-4.9-5/meta/NEWS | 80 meta-4.9-5/meta/R/Fleiss93.R |only meta-4.9-5/meta/R/Fleiss93cont.R |only meta-4.9-5/meta/R/Olkin95.R |only meta-4.9-5/meta/R/TE.seTE.ci.R |only meta-4.9-5/meta/R/TE.seTE.iqr.R |only meta-4.9-5/meta/R/TE.seTE.iqr.range.R |only meta-4.9-5/meta/R/TE.seTE.range.R |only meta-4.9-5/meta/R/amlodipine.R |only meta-4.9-5/meta/R/as.data.frame.meta.R | 58 meta-4.9-5/meta/R/baujat.R | 212 meta-4.9-5/meta/R/bubble.R | 346 + meta-4.9-5/meta/R/chklength.R | 11 meta-4.9-5/meta/R/ci.R | 41 meta-4.9-5/meta/R/cisapride.R |only meta-4.9-5/meta/R/estimate.missing.R | 4 meta-4.9-5/meta/R/forest-internal.R | 2 meta-4.9-5/meta/R/forest.R | 6917 ++++++++++++++++++++++++++- meta-4.9-5/meta/R/funnel.R | 701 ++ meta-4.9-5/meta/R/gs.R | 46 meta-4.9-5/meta/R/hetcalc.R | 10 meta-4.9-5/meta/R/labbe.R | 776 +++ meta-4.9-5/meta/R/meta-internal.R | 27 meta-4.9-5/meta/R/meta-package.R |only meta-4.9-5/meta/R/metabias.R | 689 ++ meta-4.9-5/meta/R/metabias.rm5.R | 73 meta-4.9-5/meta/R/metabin.R | 750 ++ meta-4.9-5/meta/R/metabind.R | 59 meta-4.9-5/meta/R/metacont.R | 478 + meta-4.9-5/meta/R/metacor.R | 341 + meta-4.9-5/meta/R/metacr.R | 128 meta-4.9-5/meta/R/metacum.R | 104 meta-4.9-5/meta/R/metagen.R | 1081 ++++ meta-4.9-5/meta/R/metainc.R | 555 ++ meta-4.9-5/meta/R/metainf.R | 108 meta-4.9-5/meta/R/metamean.R | 344 + meta-4.9-5/meta/R/metaprop.R | 728 ++ meta-4.9-5/meta/R/metarate.R | 463 + meta-4.9-5/meta/R/metareg.R | 278 - meta-4.9-5/meta/R/or2smd.R |only meta-4.9-5/meta/R/print.meta.R | 143 meta-4.9-5/meta/R/radial.R | 223 meta-4.9-5/meta/R/read.mtv.R | 75 meta-4.9-5/meta/R/read.rm5.R | 208 meta-4.9-5/meta/R/seTE.pval.R |only meta-4.9-5/meta/R/setchar.R | 54 meta-4.9-5/meta/R/settings.meta.R | 198 meta-4.9-5/meta/R/smd2or.R |only meta-4.9-5/meta/R/smoking.R |only meta-4.9-5/meta/R/subgroup.R | 57 meta-4.9-5/meta/R/summary.meta.R | 1067 ++++ meta-4.9-5/meta/R/summary.rm5.R | 88 meta-4.9-5/meta/R/trimfill.R | 814 +++ meta-4.9-5/meta/R/update.meta.R | 213 meta-4.9-5/meta/R/weights.meta.R | 62 meta-4.9-5/meta/R/woodyplants.R |only meta-4.9-5/meta/data/Fleiss93.rda |only meta-4.9-5/meta/data/Fleiss93cont.rda |only meta-4.9-5/meta/data/Olkin95.rda |only meta-4.9-5/meta/data/amlodipine.rda |only meta-4.9-5/meta/data/cisapride.rda |only meta-4.9-5/meta/data/lungcancer.rda |only meta-4.9-5/meta/data/smoking.rda |only meta-4.9-5/meta/data/woodyplants.rda |only meta-4.9-5/meta/inst/extdata/Fleiss93_CR.csv |only meta-4.9-5/meta/man/Fleiss93.Rd | 53 meta-4.9-5/meta/man/Fleiss93cont.Rd | 66 meta-4.9-5/meta/man/Olkin95.Rd | 46 meta-4.9-5/meta/man/amlodipine.Rd | 79 meta-4.9-5/meta/man/as.data.frame.meta.Rd | 65 meta-4.9-5/meta/man/baujat.Rd | 179 meta-4.9-5/meta/man/bubble.Rd | 202 meta-4.9-5/meta/man/ci.Rd | 67 meta-4.9-5/meta/man/cisapride.Rd | 90 meta-4.9-5/meta/man/forest.Rd | 1966 ++++--- meta-4.9-5/meta/man/funnel.Rd | 425 - meta-4.9-5/meta/man/gs.Rd | 37 meta-4.9-5/meta/man/labbe.Rd | 333 - meta-4.9-5/meta/man/meta-package.Rd | 227 meta-4.9-5/meta/man/metabias.Rd | 414 - meta-4.9-5/meta/man/metabias.rm5.Rd |only meta-4.9-5/meta/man/metabin.Rd | 1265 ++-- meta-4.9-5/meta/man/metabind.Rd | 88 meta-4.9-5/meta/man/metacont.Rd | 959 +-- meta-4.9-5/meta/man/metacor.Rd | 674 +- meta-4.9-5/meta/man/metacr.Rd | 231 meta-4.9-5/meta/man/metacum.Rd | 181 meta-4.9-5/meta/man/metagen.Rd | 989 ++- meta-4.9-5/meta/man/metainc.Rd | 1003 ++- meta-4.9-5/meta/man/metainf.Rd | 187 meta-4.9-5/meta/man/metamean.Rd | 704 +- meta-4.9-5/meta/man/metaprop.Rd | 1184 ++-- meta-4.9-5/meta/man/metarate.Rd | 855 +-- meta-4.9-5/meta/man/metareg.Rd | 177 meta-4.9-5/meta/man/or2smd.Rd |only meta-4.9-5/meta/man/print.meta.Rd | 426 - meta-4.9-5/meta/man/radial.Rd |only meta-4.9-5/meta/man/read.mtv.Rd | 104 meta-4.9-5/meta/man/read.rm5.Rd | 324 - meta-4.9-5/meta/man/settings.meta.Rd | 220 meta-4.9-5/meta/man/smd2or.Rd |only meta-4.9-5/meta/man/smoking.Rd | 90 meta-4.9-5/meta/man/summary.meta.Rd |only meta-4.9-5/meta/man/summary.rm5.Rd |only meta-4.9-5/meta/man/trimfill.Rd | 451 - meta-4.9-5/meta/man/update.meta.Rd | 498 + meta-4.9-5/meta/man/weights.meta.Rd | 82 meta-4.9-5/meta/man/woodyplants.Rd | 93 141 files changed, 26492 insertions(+), 7601 deletions(-)
Title: Finding Feedback Effects in SEM and Testing for Their
Significance
Description: Provides two main functionalities.
1 - Given a system of simultaneous equation,
it decomposes the matrix of coefficients weighting the endogenous variables
into three submatrices: one includes the subset of coefficients that have a causal nature
in the model, two include the subset of coefficients that have a interdependent nature
in the model, either at systematic level or induced by the correlation between error terms.
2 - Given a decomposed model,
it tests for the significance of the interdependent relationships acting in the system,
via Maximum likelihood and Wald test, which can be built starting from the function output.
For theoretical reference see Faliva (1992) <doi:10.1007/BF02589085> and
Faliva and Zoia (1994) <doi:10.1007/BF02589041>.
Author: Gianmarco Vacca [aut, cre]
Maintainer: Gianmarco Vacca <gianmarco.vacca@unicatt.it>
Diff between SIRE versions 1.0.2 dated 2018-07-30 and 1.1.0 dated 2019-04-11
SIRE-1.0.2/SIRE/R/causal_decompose_sim.R |only SIRE-1.0.2/SIRE/man/causal.decompose.Rd |only SIRE-1.0.2/SIRE/man/causal.decompose.sim.Rd |only SIRE-1.0.2/SIRE/man/dec.calc.Rd |only SIRE-1.0.2/SIRE/man/feedback.ml.Rd |only SIRE-1.0.2/SIRE/man/rho.calc.Rd |only SIRE-1.1.0/SIRE/DESCRIPTION | 8 SIRE-1.1.0/SIRE/MD5 | 24 SIRE-1.1.0/SIRE/NAMESPACE | 13 SIRE-1.1.0/SIRE/R/causal_decompose.R | 733 +++++++++++----------------- SIRE-1.1.0/SIRE/R/dec_calc.R | 6 SIRE-1.1.0/SIRE/R/feedback_ml.R | 244 +++------ SIRE-1.1.0/SIRE/R/rho_calc.R | 186 +++---- SIRE-1.1.0/SIRE/man/causal_decompose.Rd |only SIRE-1.1.0/SIRE/man/dec_calc.Rd |only SIRE-1.1.0/SIRE/man/feedback_ml.Rd |only SIRE-1.1.0/SIRE/man/macroIT.Rd | 68 +- SIRE-1.1.0/SIRE/man/rho_calc.Rd |only 18 files changed, 530 insertions(+), 752 deletions(-)
Title: Statistical Trending for Medical Devices Surveillance
Description: A collection of common statistical algorithms used in active
surveillance of medical device events. Context includes post-market
surveillance, pharmacovigilance, signal detection and trending, and
regulatory reporting. Primary inputs are device-event time series. Outputs
include trending results with the ability to run multiple algorithms at
once. This package works well with the 'mds' package, but does not require
it.
Author: Gary Chung [aut, cre],
Zhiheng Xu [ctb] (derived code for `cp_mean()`),
Stephane Bottine [ctb] (derived code from 'SPRT' package),
Ismaïl Ahmed [ctb] (derived code from 'PhViD' package),
John Ihrie [ctb] (derived code from 'openEBGM' package)
Maintainer: Gary Chung <gchung05@gmail.com>
Diff between mdsstat versions 0.2.2 dated 2019-01-24 and 0.3.0 dated 2019-04-11
mdsstat-0.2.2/mdsstat/tests/testthat/test_shewhart.R |only mdsstat-0.3.0/mdsstat/DESCRIPTION | 20 mdsstat-0.3.0/mdsstat/MD5 | 112 +- mdsstat-0.3.0/mdsstat/NAMESPACE | 71 - mdsstat-0.3.0/mdsstat/NEWS.md | 117 +- mdsstat-0.3.0/mdsstat/R/additional.R | 432 ++++----- mdsstat-0.3.0/mdsstat/R/bcpnn.R | 620 ++++++------- mdsstat-0.3.0/mdsstat/R/cp_mean.R |only mdsstat-0.3.0/mdsstat/R/cusum.R | 460 +++++----- mdsstat-0.3.0/mdsstat/R/data.R | 138 +-- mdsstat-0.3.0/mdsstat/R/ewma.R |only mdsstat-0.3.0/mdsstat/R/gps.R | 796 ++++++++--------- mdsstat-0.3.0/mdsstat/R/prr.R | 470 +++++----- mdsstat-0.3.0/mdsstat/R/ror.R | 470 +++++----- mdsstat-0.3.0/mdsstat/R/shewhart.R | 504 +++++------ mdsstat-0.3.0/mdsstat/R/sprt.R | 672 +++++++------- mdsstat-0.3.0/mdsstat/R/stats.R | 523 +++++------ mdsstat-0.3.0/mdsstat/R/utils.R | 318 +++---- mdsstat-0.3.0/mdsstat/R/xbar.R |only mdsstat-0.3.0/mdsstat/README.md | 78 + mdsstat-0.3.0/mdsstat/build/vignette.rds |binary mdsstat-0.3.0/mdsstat/data/mds_ts.rda |binary mdsstat-0.3.0/mdsstat/inst/doc/mdsstat_intro.R | 24 mdsstat-0.3.0/mdsstat/inst/doc/mdsstat_intro.Rmd | 421 ++++----- mdsstat-0.3.0/mdsstat/inst/doc/mdsstat_intro.html | 855 +++++++++++-------- mdsstat-0.3.0/mdsstat/man/E2x2.Rd | 42 mdsstat-0.3.0/mdsstat/man/bcpnn.Rd | 342 +++---- mdsstat-0.3.0/mdsstat/man/char_to_df.Rd | 48 - mdsstat-0.3.0/mdsstat/man/convert_date.Rd | 60 - mdsstat-0.3.0/mdsstat/man/cp_mean.Rd |only mdsstat-0.3.0/mdsstat/man/cusum.Rd | 246 ++--- mdsstat-0.3.0/mdsstat/man/define_algos.Rd | 72 - mdsstat-0.3.0/mdsstat/man/ewma.Rd |only mdsstat-0.3.0/mdsstat/man/fNA.Rd | 48 - mdsstat-0.3.0/mdsstat/man/gps.Rd | 394 ++++---- mdsstat-0.3.0/mdsstat/man/input_param_checker.Rd | 66 - mdsstat-0.3.0/mdsstat/man/maude.Rd | 98 +- mdsstat-0.3.0/mdsstat/man/mds_ts.Rd | 42 mdsstat-0.3.0/mdsstat/man/next_dev.Rd | 42 mdsstat-0.3.0/mdsstat/man/next_ev.Rd | 42 mdsstat-0.3.0/mdsstat/man/poisson_rare.Rd | 222 ++-- mdsstat-0.3.0/mdsstat/man/prr.Rd | 266 ++--- mdsstat-0.3.0/mdsstat/man/ror.Rd | 268 ++--- mdsstat-0.3.0/mdsstat/man/run_algos.Rd | 130 +- mdsstat-0.3.0/mdsstat/man/sales.Rd | 54 - mdsstat-0.3.0/mdsstat/man/shewhart.Rd | 251 ++--- mdsstat-0.3.0/mdsstat/man/sprt.Rd | 344 +++---- mdsstat-0.3.0/mdsstat/man/test_as_row.Rd | 40 mdsstat-0.3.0/mdsstat/man/xbar.Rd |only mdsstat-0.3.0/mdsstat/tests/testthat.R | 8 mdsstat-0.3.0/mdsstat/tests/testthat/test_addtl.R | 298 +++--- mdsstat-0.3.0/mdsstat/tests/testthat/test_bcpnn.R | 474 +++++----- mdsstat-0.3.0/mdsstat/tests/testthat/test_cp_mean.R |only mdsstat-0.3.0/mdsstat/tests/testthat/test_cusum.R | 348 +++---- mdsstat-0.3.0/mdsstat/tests/testthat/test_ewma.R |only mdsstat-0.3.0/mdsstat/tests/testthat/test_gps.R | 602 ++++++------- mdsstat-0.3.0/mdsstat/tests/testthat/test_prr.R | 430 ++++----- mdsstat-0.3.0/mdsstat/tests/testthat/test_ror.R | 428 ++++----- mdsstat-0.3.0/mdsstat/tests/testthat/test_sprt.R | 440 ++++----- mdsstat-0.3.0/mdsstat/tests/testthat/test_stats.R | 290 +++--- mdsstat-0.3.0/mdsstat/tests/testthat/test_xbar.R |only mdsstat-0.3.0/mdsstat/vignettes/mdsstat_intro.Rmd | 421 ++++----- 62 files changed, 7153 insertions(+), 6804 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman <broman@wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.68-2 dated 2018-07-25 and 0.69-5 dated 2019-04-11
broman-0.68-2/broman/R/zzz.R |only broman-0.68-2/broman/inst |only broman-0.69-5/broman/DESCRIPTION | 14 - broman-0.69-5/broman/MD5 | 219 +++++++++---------- broman-0.69-5/broman/NAMESPACE | 7 broman-0.69-5/broman/NEWS | 22 + broman-0.69-5/broman/R/add_commas.R | 2 broman-0.69-5/broman/R/align_stuff.R | 2 broman-0.69-5/broman/R/arrowlocator.R | 7 broman-0.69-5/broman/R/attrnames.R | 2 broman-0.69-5/broman/R/brocolors.R | 16 - broman-0.69-5/broman/R/cf.R | 6 broman-0.69-5/broman/R/ciplot.R |only broman-0.69-5/broman/R/compare_rows.R | 7 broman-0.69-5/broman/R/convert2hex.R | 8 broman-0.69-5/broman/R/dotplot.R | 18 - broman-0.69-5/broman/R/excel_fig.R | 14 - broman-0.69-5/broman/R/fisher.R | 12 - broman-0.69-5/broman/R/get_precision.R | 2 broman-0.69-5/broman/R/grayplot.R | 2 broman-0.69-5/broman/R/grayplot_na.R | 2 broman-0.69-5/broman/R/help.R | 7 broman-0.69-5/broman/R/histlines.R | 26 +- broman-0.69-5/broman/R/holmans_triangle.R | 10 broman-0.69-5/broman/R/jiggle.R | 12 - broman-0.69-5/broman/R/kbdate.R | 2 broman-0.69-5/broman/R/lenuniq.R | 8 broman-0.69-5/broman/R/make.R | 6 broman-0.69-5/broman/R/manyboxplot.R | 9 broman-0.69-5/broman/R/mypairs.R | 9 broman-0.69-5/broman/R/myround.R | 5 broman-0.69-5/broman/R/normalize.R | 7 broman-0.69-5/broman/R/not_in.R |only broman-0.69-5/broman/R/numbers.R | 6 broman-0.69-5/broman/R/objectsizes.R | 6 broman-0.69-5/broman/R/openfile.R | 16 - broman-0.69-5/broman/R/pastedot.R | 34 +- broman-0.69-5/broman/R/permtest.R | 32 +- broman-0.69-5/broman/R/pick_more_precise.R | 2 broman-0.69-5/broman/R/pushbullet.R | 29 +- broman-0.69-5/broman/R/qqline2.R | 10 broman-0.69-5/broman/R/qr.R | 7 broman-0.69-5/broman/R/quantileSE.R | 16 - broman-0.69-5/broman/R/revgray.R |only broman-0.69-5/broman/R/revrainbow.R | 10 broman-0.69-5/broman/R/rmvn.R | 8 broman-0.69-5/broman/R/runningmean.R | 24 +- broman-0.69-5/broman/R/setRNGparallel.R | 4 broman-0.69-5/broman/R/simp.R | 8 broman-0.69-5/broman/R/spell_out.R |only broman-0.69-5/broman/R/strwidth2lines.R | 6 broman-0.69-5/broman/R/strwidth2xlim.R | 11 broman-0.69-5/broman/R/switchv.R | 4 broman-0.69-5/broman/R/theme_karl.R | 6 broman-0.69-5/broman/R/venn_diagram.R | 2 broman-0.69-5/broman/R/winsorize.R | 4 broman-0.69-5/broman/R/xlimlabel.R | 9 broman-0.69-5/broman/data/numbers-cap.RData |binary broman-0.69-5/broman/data/numbers.RData |binary broman-0.69-5/broman/man/arrowlocator.Rd | 17 - broman-0.69-5/broman/man/brocolors.Rd | 6 broman-0.69-5/broman/man/bromanversion.Rd | 2 broman-0.69-5/broman/man/chisq.Rd | 11 broman-0.69-5/broman/man/ciplot.Rd |only broman-0.69-5/broman/man/convert2hex.Rd | 2 broman-0.69-5/broman/man/crayons.Rd | 4 broman-0.69-5/broman/man/done.Rd | 9 broman-0.69-5/broman/man/dotplot.Rd | 13 - broman-0.69-5/broman/man/errors2pushbullet.Rd | 5 broman-0.69-5/broman/man/excel_fig.Rd | 8 broman-0.69-5/broman/man/fisher.Rd | 13 - broman-0.69-5/broman/man/grayplot.Rd | 8 broman-0.69-5/broman/man/h.Rd | 6 broman-0.69-5/broman/man/hex2dec.Rd | 4 broman-0.69-5/broman/man/histlines.Rd | 17 - broman-0.69-5/broman/man/jiggle.Rd | 7 broman-0.69-5/broman/man/kbdate.Rd | 2 broman-0.69-5/broman/man/make.Rd | 6 broman-0.69-5/broman/man/manyboxplot.Rd | 8 broman-0.69-5/broman/man/mypairs.Rd | 12 - broman-0.69-5/broman/man/myround.Rd | 4 broman-0.69-5/broman/man/normalize.Rd | 18 - broman-0.69-5/broman/man/note.Rd | 8 broman-0.69-5/broman/man/notin.Rd |only broman-0.69-5/broman/man/numbers.Rd | 1 broman-0.69-5/broman/man/objectsizes.Rd | 9 broman-0.69-5/broman/man/openfile.Rd | 12 - broman-0.69-5/broman/man/paired.perm.test.Rd | 18 - broman-0.69-5/broman/man/paste..Rd | 16 - broman-0.69-5/broman/man/paste00.Rd | 18 - broman-0.69-5/broman/man/perm.test.Rd | 18 - broman-0.69-5/broman/man/plot_crayons.Rd | 12 - broman-0.69-5/broman/man/pushbullet_devices.Rd | 3 broman-0.69-5/broman/man/qqline2.Rd | 10 broman-0.69-5/broman/man/qr2.Rd | 6 broman-0.69-5/broman/man/quantileSE.Rd | 16 - broman-0.69-5/broman/man/revgray.Rd |only broman-0.69-5/broman/man/revrainbow.Rd | 8 broman-0.69-5/broman/man/rmvn.Rd | 6 broman-0.69-5/broman/man/runningmean.Rd | 12 - broman-0.69-5/broman/man/runningratio.Rd | 6 broman-0.69-5/broman/man/simp.Rd | 8 broman-0.69-5/broman/man/spell_out.Rd |only broman-0.69-5/broman/man/stop_sending_errors.Rd | 3 broman-0.69-5/broman/man/strwidth2xlim.Rd | 2 broman-0.69-5/broman/man/switchv.Rd | 4 broman-0.69-5/broman/man/theme_karl.Rd | 6 broman-0.69-5/broman/man/venn.Rd | 8 broman-0.69-5/broman/man/winsorize.Rd | 4 broman-0.69-5/broman/man/xlimlabel.Rd | 4 broman-0.69-5/broman/src/normalize.c | 2 broman-0.69-5/broman/src/normalize.h | 2 broman-0.69-5/broman/src/runningmean.c | 2 broman-0.69-5/broman/src/runningmean.h | 2 broman-0.69-5/broman/tests/testthat/test-notin.R |only broman-0.69-5/broman/tests/testthat/test-spell_out.R |only 116 files changed, 572 insertions(+), 553 deletions(-)
Title: Infinitesimally Robust Estimators for Preprocessing -Omics Data
Description: Functions for the determination of optimally robust influence curves and
estimators for preprocessing omics data, in particular gene expression data.
Author: Matthias Kohl [aut, cre, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobLoxBioC versions 1.1.0 dated 2018-08-03 and 1.2.0 dated 2019-04-11
DESCRIPTION | 24 ++++++++++++------------ MD5 | 4 ++-- man/0RobLoxBioC-package.Rd | 16 +++++++--------- 3 files changed, 21 insertions(+), 23 deletions(-)
Title: Divisia Monetary Aggregates Index
Description: Functions to calculate Divisia monetary aggregates index as given in Barnett, W. A. (1980) (<DOI:10.1016/0304-4076(80)90070-6>).
Author: Muhammad Yaseen [aut, cre],
Ahmad Nadeem [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between dmai versions 0.1.0 dated 2018-11-02 and 0.3.0 dated 2019-04-11
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 5 ++ R/dmai.R | 121 +++++++++++++++++++++++++++++++++++++++--------------------- man/dmai.Rd | 31 ++++++++++++--- 5 files changed, 119 insertions(+), 54 deletions(-)
Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstIO' package
provides basic functionalities to read and write KST data from/to
files to be used together with the 'kst', 'kstMatrix', 'pks' or
'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstIO versions 0.2-0 dated 2018-09-11 and 0.3-0 dated 2019-04-11
Changelog | 15 + DESCRIPTION | 13 - MD5 | 50 ++-- NAMESPACE | 7 R/read_kbase.R | 25 +- R/read_kdata.R | 22 +- R/read_kfamset.R |only R/read_kspace.R | 30 ++ R/read_kstructure.R | 25 ++ R/read_surmiserelation.R |only R/write_surmiserelation.R |only build/vignette.rds |binary inst/doc/kstIO.R | 14 - inst/doc/kstIO.Rnw | 60 ++++- inst/doc/kstIO.pdf |binary man/kstIO-package.Rd | 26 ++ man/read_kbase.Rd | 12 - man/read_kdata.Rd | 13 - man/read_kfamset.Rd |only man/read_kspace.Rd | 22 +- man/read_kstructure.Rd | 12 - man/read_surmiserelation.Rd |only man/write_kbase.Rd | 2 man/write_kdata.Rd | 2 man/write_kspace.Rd | 4 man/write_kstructure.Rd | 2 man/write_surmiserelation.Rd |only vignettes/kst.bib | 446 ++++++++++++++++++++++++++++++++++--------- vignettes/kstIO.Rnw | 60 ++++- 29 files changed, 659 insertions(+), 203 deletions(-)
Title: Weighted Dependence Measures
Description: Provides efficient implementations of weighted dependence measures
and related asymptotic tests for independence. Implemented measures are
the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta, and
Hoeffding's D; see, e.g., Nelsen (2006) <doi:10.1007/0-387-28678-0> and
Hollander et al. (2015, ISBN:9780470387375).
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between wdm versions 0.2.0 dated 2019-02-07 and 0.2.1 dated 2019-04-11
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/indep_test.R | 2 +- R/wdm.R | 2 +- build/partial.rdb |binary man/indep_test.Rd | 2 +- man/wdm.Rd | 2 +- src/Makevars | 5 ----- 9 files changed, 21 insertions(+), 21 deletions(-)
Title: Univariate Kernel Density Estimation
Description: Provides an efficient implementation of univariate local polynomial
kernel density estimators that can handle bounded and discrete data. See
Geenens (2014) <arXiv:1303.4121>,
Geenens and Wang (2018) <arXiv:1602.04862>,
Nagler (2018a) <arXiv:1704.07457>,
Nagler (2018b) <arXiv:1705.05431>.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kde1d versions 0.2.1 dated 2018-05-28 and 0.4.0 dated 2019-04-11
kde1d-0.2.1/kde1d/tests/testthat/Rplots.pdf |only kde1d-0.4.0/kde1d/DESCRIPTION | 8 +-- kde1d-0.4.0/kde1d/MD5 | 35 +++++++------- kde1d-0.4.0/kde1d/NEWS.md | 12 +++-- kde1d-0.4.0/kde1d/R/RcppExports.R | 13 +++-- kde1d-0.4.0/kde1d/R/kde1d.R | 23 +++++++-- kde1d-0.4.0/kde1d/R/kde1d_methods.R | 4 + kde1d-0.4.0/kde1d/R/tools.R | 18 +++++++ kde1d-0.4.0/kde1d/README.md | 13 ++++- kde1d-0.4.0/kde1d/inst/include/dpik.hpp | 47 +++++++++++++------ kde1d-0.4.0/kde1d/inst/include/lpdens.hpp | 35 ++++++++++---- kde1d-0.4.0/kde1d/inst/include/stats.hpp | 46 ++++++++++++++++++- kde1d-0.4.0/kde1d/man/dkde1d.Rd | 1 kde1d-0.4.0/kde1d/man/kde1d.Rd | 12 ++++- kde1d-0.4.0/kde1d/man/plot.kde1d.Rd | 1 kde1d-0.4.0/kde1d/src/Makevars | 5 -- kde1d-0.4.0/kde1d/src/RcppExports.cpp | 32 ++++++++++--- kde1d-0.4.0/kde1d/src/wrappers.cpp | 19 +++++-- kde1d-0.4.0/kde1d/tests/testthat/test_kde1d.R | 62 ++++++++++++++++---------- 19 files changed, 281 insertions(+), 105 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Øyvind Langsrud [aut, cre],
Jan Bruusgaard [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 0.2.0 dated 2018-10-12 and 0.3.0 dated 2019-04-11
PxWebApiData-0.2.0/PxWebApiData/README.md |only PxWebApiData-0.3.0/PxWebApiData/DESCRIPTION | 19 ++- PxWebApiData-0.3.0/PxWebApiData/MD5 | 16 ++- PxWebApiData-0.3.0/PxWebApiData/NAMESPACE | 3 PxWebApiData-0.3.0/PxWebApiData/R/ApiData.R | 131 ++++++++++++++++++++----- PxWebApiData-0.3.0/PxWebApiData/build |only PxWebApiData-0.3.0/PxWebApiData/inst |only PxWebApiData-0.3.0/PxWebApiData/man/ApiData.Rd | 47 +++++++- PxWebApiData-0.3.0/PxWebApiData/tests |only PxWebApiData-0.3.0/PxWebApiData/vignettes |only 10 files changed, 176 insertions(+), 40 deletions(-)
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and plot linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
Author: Philipp Adämmer [aut, cre] (<https://orcid.org/0000-0003-3770-0097>),
James P. LeSage [ctb],
Mehmet Balcilar [ctb]
Maintainer: Philipp Adämmer <adaemmer@hsu-hh.de>
Diff between lpirfs versions 0.1.4 dated 2018-12-11 and 0.1.5 dated 2019-04-11
DESCRIPTION | 6 MD5 | 40 ++-- NAMESPACE | 2 NEWS.md | 20 ++ R/create_nl_data.R | 2 R/create_panel_data.R | 32 ++- R/data-documentation.R | 2 R/get_vals_switching.R | 53 ++++- R/lp_lin_iv.R | 10 - R/lp_lin_panel.R | 53 ++++- R/lp_nl.R | 17 + R/lp_nl_panel.R | 74 +++++-- R/plot_lin.R | 4 README.md | 28 +- man/get_vals_switching.Rd | 4 man/lp_lin_iv.Rd | 2 man/lp_lin_panel.Rd | 6 man/lp_nl_panel.Rd | 6 tests/testthat/test-lp_lin_panel.R | 230 ++++++++++++++++------- tests/testthat/test-lp_nl.R | 5 tests/testthat/test-lp_nl_panel.R | 357 ++++++++++++++++++++++++++++++++++++- 21 files changed, 769 insertions(+), 184 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre] (<https://orcid.org/0000-0001-5537-637X>),
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.3.4 dated 2019-04-07 and 3.3.5 dated 2019-04-11
DESCRIPTION | 8 MD5 | 32 README.md | 2 inst/doc/blogposts.html | 4 inst/doc/cheatsheet.html | 4 inst/doc/eurostat_tutorial.R | 110 +- inst/doc/eurostat_tutorial.Rmd | 56 - inst/doc/eurostat_tutorial.pdf | 1526 +++++++++++++++++++-------------------- inst/doc/publications.html | 4 vignettes/eurostat_tutorial.Rmd | 56 - vignettes/eurostat_tutorial.html | 160 ---- vignettes/eurostat_tutorial.md | 176 ---- vignettes/fig/map1ex-1.pdf |binary vignettes/fig/maps2-1.pdf |binary vignettes/fig/plotGallery-1.pdf |binary vignettes/fig/plotGallery-1.png |binary vignettes/fig/trains_plot-1.pdf |binary 17 files changed, 917 insertions(+), 1221 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Satu Helske [aut] (<https://orcid.org/0000-0003-0532-0153>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.0.11 dated 2019-04-09 and 1.0.12 dated 2019-04-11
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 8 ++++++-- inst/doc/seqHMM.pdf | 38 +++++++++++++++++++------------------- inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf |binary src/log_objective.cpp | 4 +--- src/log_objectivex.cpp | 5 +---- src/objectivex.cpp | 4 +--- 10 files changed, 41 insertions(+), 44 deletions(-)
Title: Ensemble Penalized Cox Regression for Survival Prediction
Description: The top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge <https://www.synapse.org/ProstateCancerChallenge> presented in Guinney J, Wang T, Laajala TD, et al. (2017) <doi:10.1016/S1470-2045(16)30560-5> is provided here-in, together with the corresponding follow-up work. While initially aimed at modeling the most advanced stage of prostate cancer, metastatic Castration-Resistant Prostate Cancer (mCRPC), the modeling framework has subsequently been extended to cover also the non-metastatic form of advanced prostate cancer (CRPC). Readily fitted ensemble-based model S4-objects are provided, and a simulated example dataset based on a real-life cohort is provided from the Turku University Hospital, to illustrate the use of the package. Functionality of the ePCR methodology relies on constructing ensembles of strata in patient cohorts and averaging over them, with each ensemble member consisting of a highly optimized penalized/regularized Cox regression model. Various cross-validation and other modeling schema are provided for constructing novel model objects.
Author: Teemu Daniel Laajala <teelaa@utu.fi> [aut, cre], Mika Murtoj<e4>rvi <mianmu2@hotmail.com> [ctb]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between ePCR versions 0.9.9-6 dated 2018-05-29 and 0.9.9-9 dated 2019-04-11
DESCRIPTION | 17 ++++++------- MD5 | 36 +++++++++++++-------------- NAMESPACE | 2 - NEWS | 25 +++++++++++++++++++ R/int.R | 8 +++--- R/psp.R | 62 +++++++++++++++++++++++++++++++++++++----------- R/roxygen.R | 8 +++--- build/vignette.rds |binary inst/doc/ePCR_guide.pdf |binary man/NelsonAalen.Rd | 4 +-- man/PSP-methods.Rd | 4 +-- man/TYKS.Rd | 2 - man/TYKSSIMU.Rd | 2 - man/TYKS_reduced.Rd | 2 - man/TimeSurvProb.Rd | 4 +-- man/cv.grid.Rd | 4 +-- man/ePCR.Rd | 4 +-- man/heatcv.Rd | 7 +++-- man/score.iAUC.Rd | 4 ++- 19 files changed, 129 insertions(+), 66 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy Studies with Several
Cutpoints
Description: Provides methods by Steinhauser et al. (2016) <DOI:10.1186/s12874-016-0196-1> for meta-analysis of diagnostic accuracy studies with several cutpoints.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Susanne Steinhauser [aut],
Srinath Kolampally [aut],
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between diagmeta versions 0.3-0 dated 2018-12-11 and 0.3-1 dated 2019-04-11
DESCRIPTION | 33 +++--- MD5 | 50 ++++----- NAMESPACE | 7 + NEWS | 22 +++- R/Schneider2017.R | 53 +++++----- R/as.data.frame.diagmeta.R | 8 - R/diagmeta-package.R | 24 ++-- R/diagmeta.R | 94 ++++++++++-------- R/diagstats.R | 14 +- R/ipd2diag.R | 16 +-- R/plot.diagmeta.R | 214 ++++++++++++++++++++++-------------------- R/print.diagmeta.R | 14 +- R/print.diagstats.R | 8 - R/print.summary.diagmeta.R | 17 ++- R/summary.diagmeta.R | 20 ++- man/Schneider2017.Rd | 47 ++++----- man/as.data.frame.diagmeta.Rd | 4 man/diagmeta-package.Rd | 17 +-- man/diagmeta.Rd | 24 ++-- man/diagstats.Rd | 11 -- man/ipd2diag.Rd | 7 - man/plot.diagmeta.Rd | 50 +++++---- man/print.diagmeta.Rd | 8 - man/print.diagstats.Rd | 4 man/print.summary.diagmeta.Rd | 10 - man/summary.diagmeta.Rd | 7 - 26 files changed, 434 insertions(+), 349 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all
previous 'R' versions and their release dates.
Author: Gábor Csárdi [aut, cre],
Jeroen Ooms [ctb],
R Consortium [fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rversions versions 1.0.3 dated 2016-08-02 and 1.1.0 dated 2019-04-11
DESCRIPTION | 20 ++- MD5 | 29 +++-- NAMESPACE | 4 R/keep-head.R |only R/macos.R |only R/nicks.R |only R/rversions-package.R |only R/rversions.R | 89 +++++++++------ R/tarball.R |only R/urls.R |only R/win.R |only inst/NEWS.md | 13 +- inst/README.md | 262 ++++++++++++++++++++++++----------------------- man/r_oldrel.Rd | 5 man/r_release.Rd | 5 man/r_release_macos.Rd |only man/r_release_tarball.Rd |only man/r_release_win.Rd |only man/r_versions.Rd | 5 man/rversions-package.Rd |only tests |only 21 files changed, 239 insertions(+), 193 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.0.3 dated 2019-03-18 and 2.0.4 dated 2019-04-11
DESCRIPTION | 8 - MD5 | 6 - R/phylgls.R | 222 ++++++++++++++++++++++++++++++++++++++++++----- man/mvSLOUCH-internal.Rd | 1 4 files changed, 208 insertions(+), 29 deletions(-)
Title: Movement Data Visualization
Description: Tools to visualize movement data (e.g. from GPS tracking) and temporal changes of environmental data (e.g. from remote sensing) by creating video animations.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Diff between moveVis versions 0.10.0 dated 2019-03-20 and 0.10.1 dated 2019-04-11
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS.md | 59 +++++++++++++++++++++++++++++++++++++++++---------- R/moveVis-internal.R | 59 +++++++++++++++++++++++++++------------------------ README.md | 45 ++++++++++++++++++++++++++++++++------ 5 files changed, 126 insertions(+), 53 deletions(-)
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.3 dated 2018-11-26 and 0.1.4 dated 2019-04-11
raptr-0.1.3/raptr/src/Makevars |only raptr-0.1.4/raptr/DESCRIPTION | 8 - raptr-0.1.4/raptr/MD5 | 11 - raptr-0.1.4/raptr/NEWS.md | 6 - raptr-0.1.4/raptr/README.md | 2 raptr-0.1.4/raptr/build/vignette.rds |binary raptr-0.1.4/raptr/inst/doc/raptr.html | 197 +++++++++++++++++----------------- 7 files changed, 116 insertions(+), 108 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.0.0.7 dated 2018-09-19 and 1.0.1.2 dated 2019-04-11
DESCRIPTION | 12 +- MD5 | 75 ++++++++--------- NAMESPACE | 2 R/CreateDataCV.R | 61 ++++++++----- R/OnlyA_CV.R | 7 + R/OnlyF_CV.R | 7 + R/PAFit.R | 179 ++++++++++++++++++++++++----------------- R/generate_net.R | 25 ++++- R/get_statistics.R | 39 +++++++- R/joint_estimate.R | 2 R/one_cycle.R | 173 ++++++++++++++++++++++++++------------- R/only_A_estimate.R | 17 ++- R/performCV_core_new_new.R | 146 +++++++++++---------------------- R/performCV_old_new.R | 17 ++- R/plot.Full_PAFit_result.R | 25 +++++ R/plot.pa_result.R | 3 R/plot.pafit_result.r | 3 build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 18 +++- inst/doc/Tutorial.pdf |binary man/Newman.rd | 9 +- man/PAFit-package.Rd | 18 ++-- man/as.PAFit_net.rd | 3 man/generate_BB.rd | 2 man/generate_fit_only.rd | 2 man/generate_net.Rd | 4 man/get_statistics.Rd | 4 man/joint_estimate.rd | 59 ++++++++++++- man/only_A_estimate.rd | 39 ++++++++ man/test_linear_PA.rd | 4 src/Cpp_code.cpp | 17 ++- tests/fit_node_no_new_edge.R |only tests/test_cv_data.R |only tests/test_isolated_node.R | 74 +++++++++------- tests/test_isolated_node_2.R | 40 +++++---- tests/test_joint_estimate.R | 37 +++++--- tests/test_non_log_linear_PA.R |only tests/test_only_A.R | 33 +++---- tests/test_test_linear_PA.R | 4 40 files changed, 721 insertions(+), 443 deletions(-)
Title: Variable Table
Description: Automatically generates HTML variable documentation including variable names, labels, classes, value labels (if applicable), value ranges, and summary statistics. See the vignette "vtable" for a package overview.
Author: Nick Huntington-Klein [aut, cre]
Maintainer: Nick Huntington-Klein <nhuntington-klein@fullerton.edu>
Diff between vtable versions 0.3.0 dated 2019-03-22 and 0.4.0 dated 2019-04-11
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- R/vtable.R | 60 +++++++++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/vtable.R | 14 +++++++++++ inst/doc/vtable.Rmd | 19 ++++++++++++++++ inst/doc/vtable.html | 25 ++++++++++++++++++--- man/vtable.Rd | 10 +++++++- vignettes/vtable.Rmd | 19 ++++++++++++++++ 9 files changed, 142 insertions(+), 29 deletions(-)
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 0.3.2 dated 2016-06-17 and 0.3.3 dated 2019-04-11
DESCRIPTION | 39 ++-- MD5 | 75 ++++---- NEWS.md | 10 - R/deprecated.R | 2 R/encoding.R | 9 - R/form.R | 15 + R/html.R | 4 R/minimal-html.R | 2 R/parse.R | 12 - R/rvest-package.R |only R/selectors.R | 38 ++-- R/session.R | 10 - R/table.R | 56 ++++-- R/utils.R | 2 README.md | 101 +++++++----- build/vignette.rds |binary inst/WORDLIST |only inst/doc/selectorgadget.Rmd | 14 - inst/doc/selectorgadget.html | 360 ++++++++++++++++++++++++++++++++++--------- man/encoding.Rd | 5 man/figures |only man/google_form.Rd | 1 man/html.Rd | 7 man/html_form.Rd | 3 man/html_nodes.Rd | 20 +- man/html_session.Rd | 8 man/html_table.Rd | 44 +++-- man/html_tag.Rd | 1 man/html_text.Rd | 11 - man/jump_to.Rd | 11 - man/minimal_html.Rd | 1 man/pipe.Rd | 3 man/pluck.Rd | 1 man/rvest-package.Rd |only man/session_history.Rd | 3 man/set_values.Rd | 1 man/submit_form.Rd | 9 - man/xml.Rd | 13 - tests/spelling.R |only tests/testthat/test-forms.R | 21 ++ vignettes/selectorgadget.Rmd | 14 - 41 files changed, 623 insertions(+), 303 deletions(-)
Title: Optimally Robust Estimation - Old Version
Description: Optimally robust estimation using S4 classes and methods. Old version still
needed for current versions of ROptRegTS and RobRex.
Author: Matthias Kohl [aut, cre, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between ROptEstOld versions 1.1.0 dated 2018-08-03 and 1.2.0 dated 2019-04-11
DESCRIPTION | 26 +++++++++++++------------- MD5 | 20 ++++++++++---------- R/getInfRobIC_asCov.R | 6 +++--- R/getInfRobIC_asHampel.R | 2 +- R/getInfStand.R | 2 +- R/infoPlot.R | 2 +- R/leastFavorableRadius.R | 2 +- R/optIC.R | 4 ++-- R/optRisk.R | 2 +- R/radiusMinimaxIC.R | 2 +- inst/NEWS | 7 +++++++ 11 files changed, 41 insertions(+), 34 deletions(-)
Title: Optimally Robust Influence Curves and Estimators for Location
and Scale
Description: Functions for the determination of optimally robust influence curves and
estimators in case of normal location and/or scale.
Author: Matthias Kohl [cre, cph],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RobLox versions 1.1.0 dated 2018-08-03 and 1.2.0 dated 2019-04-11
DESCRIPTION | 28 ++++----- MD5 | 16 ++--- R/rlOptIC.R | 4 - R/rlsOptIC_AL.R | 10 ++- R/roblox.R | 139 +++++++++++++++++++++++++++++++++---------------- R/rsOptIC.R | 10 ++- R/sysdata.rda |binary inst/NEWS | 9 +++ man/0RobLox-package.Rd | 17 ++--- 9 files changed, 146 insertions(+), 87 deletions(-)
Title: Y&R Miscellaneous R Functions
Description: Miscellaneous functions for data analysis, portfolio management, graphics, data manipulation, statistical investigation, including descriptive statistics, creating leading and lagging variables, portfolio return analysis, time series difference and percentage change calculation, stacking data for higher efficient analysis.
Author: Manuel Russon <RUSSONM@stjohns.edu>, Xuanhua (Peter) Yin <peteryin.sju@hotmail.com>
Maintainer: Xuanhua (Peter) Yin <peteryin.sju@hotmail.com>
Diff between YRmisc versions 0.1.3 dated 2019-01-02 and 0.1.4 dated 2019-04-11
DESCRIPTION | 8 +- MD5 | 158 +++++++++++++++++++++++++++++------------------ NEWS | 30 ++++++++ R/pt.alpha.R |only R/pt.annexrtn.R |only R/pt.annrtn.R |only R/pt.annsd.R |only R/pt.beta.R |only R/pt.btavg.R |only R/pt.cmexrtn.R |only R/pt.cmrtn.R |only R/pt.exploss.R |only R/pt.info.R |only R/pt.jalpha.R |only R/pt.m2.R |only R/pt.probloss.R |only R/pt.sdexrtn.R |only R/pt.semivar.R |only R/pt.sharp.R |only R/pt.sortino.R |only R/pt.te.R |only R/pt.treynor.R |only R/pt.udrtn.R |only R/pt.updwcap.R |only man/cor.lag.Rd | 50 +++++++------- man/cor.spearman.Rd | 38 +++++------ man/cv.annu.fv.Rd | 46 ++++++------- man/cv.annu.pv.Rd | 46 ++++++------- man/cv.axp.Rd | 46 ++++++------- man/cv.bondprice.Rd | 50 +++++++------- man/cv.diff.Rd | 40 +++++------ man/cv.drawdown.Rd | 40 +++++------ man/cv.lag.Rd | 42 ++++++------ man/cv.lead.Rd | 42 ++++++------ man/cv.logs.Rd | 46 ++++++------- man/cv.pctcng.Rd | 38 +++++------ man/cv.powers.Rd | 46 ++++++------- man/df.sortcol.Rd | 42 ++++++------ man/df.stack.Rd | 52 +++++++-------- man/ds.corm.Rd | 38 +++++------ man/ds.kurt.Rd | 34 +++++----- man/ds.skew.Rd | 38 +++++------ man/ds.summ.Rd | 42 ++++++------ man/pkg.reinstall.Rd | 38 +++++------ man/pkg.save.Rd | 36 +++++----- man/pl.2ts.Rd | 46 ++++++------- man/pl.2tsgg.Rd | 54 ++++++++-------- man/pl.3smoothtxt.Rd | 46 ++++++------- man/pl.3smoothtxtgg.Rd | 58 ++++++++--------- man/pl.3txt.Rd | 48 +++++++------- man/pl.3txtgg.Rd | 60 ++++++++--------- man/pl.coplot.Rd | 46 ++++++------- man/pl.hist.Rd | 38 +++++------ man/pl.histgg.Rd | 42 ++++++------ man/pl.hs.Rd | 50 +++++++------- man/pl.hsd.Rd | 38 +++++------ man/pl.hsdgg.Rd | 42 ++++++------ man/pl.s.Rd | 42 ++++++------ man/pl.sgg.Rd | 42 ++++++------ man/pl.sm.Rd | 42 ++++++------ man/pl.smgg.Rd | 48 +++++++------- man/pl.ts.Rd | 38 +++++------ man/pl.tsgg.Rd | 38 +++++------ man/pl.tss.Rd | 42 ++++++------ man/pt.alpha.Rd |only man/pt.annexrtn.Rd |only man/pt.annrtn.Rd |only man/pt.annsd.Rd |only man/pt.beta.Rd |only man/pt.btavg.Rd |only man/pt.cmexrtn.Rd |only man/pt.cmrtn.Rd |only man/pt.exploss.Rd |only man/pt.info.Rd |only man/pt.jalpha.Rd |only man/pt.m2.Rd |only man/pt.probloss.Rd |only man/pt.sdexrtn.Rd |only man/pt.semivar.Rd |only man/pt.sharp.Rd |only man/pt.sortino.Rd |only man/pt.te.Rd |only man/pt.treynor.Rd |only man/pt.udrtn.Rd |only man/pt.updwcap.Rd |only man/reg.adj.r.squared.Rd | 58 ++++++++--------- man/reg.aic.Rd | 48 +++++++------- man/reg.bic.Rd | 48 +++++++------- man/reg.dof.Rd | 42 ++++++------ man/reg.dw.Rd | 36 +++++----- man/reg.linreg.Rd | 42 ++++++------ man/reg.model.Rd | 38 +++++------ man/reg.r.squared.Rd | 52 +++++++-------- man/reg.std.err.Rd | 50 +++++++------- man/tr.log.Rd | 50 +++++++------- man/tr.logtb.Rd | 50 +++++++------- man/tr.nd.Rd | 42 ++++++------ man/tr.unli.Rd | 42 ++++++------ man/xd.avt.Rd | 64 +++++++++---------- man/xd.fred.Rd | 64 +++++++++---------- man/xd.fred.tickers.Rd | 28 ++++---- 101 files changed, 1386 insertions(+), 1314 deletions(-)
Title: Interim Analysis of Operational Futility in Randomized Trials
with Time-to-Event Endpoints and Fixed Follow-Up
Description: Randomized clinical trials commonly follow participants for a time-to-event efficacy endpoint for a fixed period of time. Consequently, at the time when the last enrolled participant completes their follow-up, the number of observed endpoints is a random variable. Assuming data collected through an interim timepoint, simulation-based estimation and inferential procedures in the standard right-censored failure time analysis framework are conducted for the distribution of the number of endpoints--in total as well as by treatment arm--at the end of the follow-up period. The future (i.e., yet unobserved) enrollment, endpoint, and dropout times are generated according to mechanisms specified in the simTrial() function in the 'seqDesign' package. A Bayesian model for the endpoint rate, offering the option to specify a robust mixture prior distribution, is used for generating future data (see the vignette for details). Inference can be restricted to participants who received treatment according to the protocol and are observed to be at risk for the endpoint at a specified timepoint. Plotting functions are provided for graphical display of results.
Author: Yingying Zhuang [aut],
Michal Juraska [aut, cre],
Doug Grove [ctb],
Peter Gilbert [ctb],
Alexander Luedtke [ctb],
Sanne Roels [ctb],
An Vandebosch [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between futility versions 0.3 dated 2019-02-06 and 0.4 dated 2019-04-11
DESCRIPTION | 8 MD5 | 8 R/futility.R | 484 ++++++++++++++++---------------- inst/doc/bayesianIncidenceRateModel.pdf |binary man/plotRCDF.byArm.Rd | 10 5 files changed, 261 insertions(+), 249 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with API's
for 'indices', documents, nodes, clusters, an interface to the cat API, and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.8.4 dated 2018-06-26 and 1.0.0 dated 2019-04-11
elastic-0.8.4/elastic/R/connect.R |only elastic-0.8.4/elastic/R/docs_bulk_plugins.R |only elastic-0.8.4/elastic/R/info.R |only elastic-0.8.4/elastic/inst/doc/elastic_intro.Rmd |only elastic-0.8.4/elastic/inst/doc/elastic_intro.html |only elastic-0.8.4/elastic/inst/vign/elastic_intro.Rmd |only elastic-0.8.4/elastic/inst/vign/elastic_intro.md |only elastic-0.8.4/elastic/man/es_auth.Rd |only elastic-0.8.4/elastic/man/index.Rd |only elastic-0.8.4/elastic/man/info.Rd |only elastic-0.8.4/elastic/tests/testthat/mtcars.json |only elastic-0.8.4/elastic/tests/testthat/mtcarslist.json |only elastic-0.8.4/elastic/vignettes/elastic_intro.Rmd |only elastic-1.0.0/elastic/DESCRIPTION | 15 elastic-1.0.0/elastic/LICENSE | 2 elastic-1.0.0/elastic/MD5 | 268 +++--- elastic-1.0.0/elastic/NAMESPACE | 36 elastic-1.0.0/elastic/NEWS.md | 42 elastic-1.0.0/elastic/R/Elasticsearch.R |only elastic-1.0.0/elastic/R/Search_uri.R | 26 elastic-1.0.0/elastic/R/alias.R | 165 ++- elastic-1.0.0/elastic/R/bulk_ci_generator.R |only elastic-1.0.0/elastic/R/bulk_df_fun_generator.R |only elastic-1.0.0/elastic/R/cat.r | 229 ++--- elastic-1.0.0/elastic/R/cluster.R | 95 +- elastic-1.0.0/elastic/R/count.r | 44 - elastic-1.0.0/elastic/R/defunct.R | 8 elastic-1.0.0/elastic/R/docs_bulk.r | 148 +-- elastic-1.0.0/elastic/R/docs_bulk_create.R |only elastic-1.0.0/elastic/R/docs_bulk_delete.R |only elastic-1.0.0/elastic/R/docs_bulk_index.R |only elastic-1.0.0/elastic/R/docs_bulk_prep.R | 28 elastic-1.0.0/elastic/R/docs_bulk_update.R | 81 - elastic-1.0.0/elastic/R/docs_bulk_utils.R | 43 elastic-1.0.0/elastic/R/docs_create.R | 44 - elastic-1.0.0/elastic/R/docs_delete.R | 33 elastic-1.0.0/elastic/R/docs_delete_by_query.R |only elastic-1.0.0/elastic/R/docs_get.r | 71 + elastic-1.0.0/elastic/R/docs_mget.r | 63 - elastic-1.0.0/elastic/R/docs_update.R | 42 elastic-1.0.0/elastic/R/docs_update_by_query.R |only elastic-1.0.0/elastic/R/elastic-package.r | 7 elastic-1.0.0/elastic/R/explain.R | 30 elastic-1.0.0/elastic/R/field_caps.R | 41 elastic-1.0.0/elastic/R/field_stats.R | 36 elastic-1.0.0/elastic/R/httr-verbs.R | 155 +-- elastic-1.0.0/elastic/R/index.R | 480 +++++------ elastic-1.0.0/elastic/R/index_templates.R | 86 + elastic-1.0.0/elastic/R/ingest.R |only elastic-1.0.0/elastic/R/mapping.R | 116 +- elastic-1.0.0/elastic/R/msearch.R | 29 elastic-1.0.0/elastic/R/mtermvectors.R | 27 elastic-1.0.0/elastic/R/nodes.R | 58 - elastic-1.0.0/elastic/R/percolater.R | 151 +-- elastic-1.0.0/elastic/R/ping.r | 22 elastic-1.0.0/elastic/R/reindex.R | 29 elastic-1.0.0/elastic/R/scroll-http.R |only elastic-1.0.0/elastic/R/scroll.R | 88 +- elastic-1.0.0/elastic/R/search.r | 30 elastic-1.0.0/elastic/R/search_body.R | 28 elastic-1.0.0/elastic/R/search_shards.R | 32 elastic-1.0.0/elastic/R/search_template.R | 120 +- elastic-1.0.0/elastic/R/searchapis.R | 2 elastic-1.0.0/elastic/R/tasks.R | 44 - elastic-1.0.0/elastic/R/termvectors.R | 41 elastic-1.0.0/elastic/R/tokenizer_set.R | 27 elastic-1.0.0/elastic/R/type_remover.R |only elastic-1.0.0/elastic/R/validate.R | 18 elastic-1.0.0/elastic/R/zzz.r | 122 +- elastic-1.0.0/elastic/README.md | 171 ++- elastic-1.0.0/elastic/build/vignette.rds |binary elastic-1.0.0/elastic/inst/doc/elastic.Rmd |only elastic-1.0.0/elastic/inst/doc/elastic.html |only elastic-1.0.0/elastic/inst/doc/search.Rmd | 117 +- elastic-1.0.0/elastic/inst/doc/search.html | 113 +- elastic-1.0.0/elastic/inst/examples/bar.json |only elastic-1.0.0/elastic/inst/examples/foo.json |only elastic-1.0.0/elastic/inst/examples/omdb.json | 222 ++--- elastic-1.0.0/elastic/inst/ignore/connect.R |only elastic-1.0.0/elastic/inst/ignore/docs_bulk_plugins.R |only elastic-1.0.0/elastic/inst/ignore/info.R |only elastic-1.0.0/elastic/inst/vign/elastic.Rmd |only elastic-1.0.0/elastic/inst/vign/elastic.md |only elastic-1.0.0/elastic/inst/vign/search.Rmd | 72 - elastic-1.0.0/elastic/inst/vign/search.md | 117 +- elastic-1.0.0/elastic/man/Search.Rd | 398 +++++---- elastic-1.0.0/elastic/man/Search_template.Rd | 68 + elastic-1.0.0/elastic/man/Search_uri.Rd | 188 ++-- elastic-1.0.0/elastic/man/alias.Rd | 97 +- elastic-1.0.0/elastic/man/cat.Rd | 144 +-- elastic-1.0.0/elastic/man/cluster.Rd | 66 - elastic-1.0.0/elastic/man/connect.Rd | 88 -- elastic-1.0.0/elastic/man/count.Rd | 40 elastic-1.0.0/elastic/man/docs_bulk.Rd | 114 +- elastic-1.0.0/elastic/man/docs_bulk_create.Rd |only elastic-1.0.0/elastic/man/docs_bulk_delete.Rd |only elastic-1.0.0/elastic/man/docs_bulk_index.Rd |only elastic-1.0.0/elastic/man/docs_bulk_prep.Rd | 32 elastic-1.0.0/elastic/man/docs_bulk_update.Rd | 35 elastic-1.0.0/elastic/man/docs_create.Rd | 31 elastic-1.0.0/elastic/man/docs_delete.Rd | 23 elastic-1.0.0/elastic/man/docs_delete_by_query.Rd |only elastic-1.0.0/elastic/man/docs_get.Rd | 49 - elastic-1.0.0/elastic/man/docs_mget.Rd | 42 elastic-1.0.0/elastic/man/docs_update.Rd | 37 elastic-1.0.0/elastic/man/docs_update_by_query.Rd |only elastic-1.0.0/elastic/man/elastic.Rd | 3 elastic-1.0.0/elastic/man/es_parse.Rd | 17 elastic-1.0.0/elastic/man/explain.Rd | 12 elastic-1.0.0/elastic/man/field_caps.Rd | 25 elastic-1.0.0/elastic/man/field_stats.Rd | 28 elastic-1.0.0/elastic/man/index_template.Rd | 35 elastic-1.0.0/elastic/man/indices.Rd |only elastic-1.0.0/elastic/man/info-defunct.Rd |only elastic-1.0.0/elastic/man/ingest.Rd |only elastic-1.0.0/elastic/man/mapping.Rd | 83 + elastic-1.0.0/elastic/man/msearch.Rd | 19 elastic-1.0.0/elastic/man/mtermvectors.Rd | 35 elastic-1.0.0/elastic/man/nodes.Rd | 39 elastic-1.0.0/elastic/man/percolate.Rd | 95 +- elastic-1.0.0/elastic/man/ping.Rd | 11 elastic-1.0.0/elastic/man/reindex.Rd | 16 elastic-1.0.0/elastic/man/scroll.Rd | 71 - elastic-1.0.0/elastic/man/search_body.Rd | 28 elastic-1.0.0/elastic/man/search_shards.Rd | 25 elastic-1.0.0/elastic/man/searchapis.Rd | 4 elastic-1.0.0/elastic/man/tasks.Rd | 18 elastic-1.0.0/elastic/man/termvectors.Rd | 32 elastic-1.0.0/elastic/man/tokenizer_set.Rd | 12 elastic-1.0.0/elastic/man/type_remover.Rd |only elastic-1.0.0/elastic/man/validate.Rd | 16 elastic-1.0.0/elastic/tests/testthat/helper-elastic.R | 29 elastic-1.0.0/elastic/tests/testthat/teardown.R |only elastic-1.0.0/elastic/tests/testthat/test-alias.R | 52 - elastic-1.0.0/elastic/tests/testthat/test-cat.R | 37 elastic-1.0.0/elastic/tests/testthat/test-cluster.R | 27 elastic-1.0.0/elastic/tests/testthat/test-connect.R | 21 elastic-1.0.0/elastic/tests/testthat/test-count.R | 29 elastic-1.0.0/elastic/tests/testthat/test-docs.R | 100 +- elastic-1.0.0/elastic/tests/testthat/test-docs_bulk.R | 82 - elastic-1.0.0/elastic/tests/testthat/test-docs_bulk_update.R | 223 +++-- elastic-1.0.0/elastic/tests/testthat/test-explain.R | 15 elastic-1.0.0/elastic/tests/testthat/test-indices.R | 96 +- elastic-1.0.0/elastic/tests/testthat/test-ingest.R |only elastic-1.0.0/elastic/tests/testthat/test-mappings.R | 71 - elastic-1.0.0/elastic/tests/testthat/test-msearch.R | 36 elastic-1.0.0/elastic/tests/testthat/test-mtermvectors.R | 21 elastic-1.0.0/elastic/tests/testthat/test-nodes.R | 29 elastic-1.0.0/elastic/tests/testthat/test-ping.R | 4 elastic-1.0.0/elastic/tests/testthat/test-scroll.R | 56 - elastic-1.0.0/elastic/tests/testthat/test-search.r | 119 +- elastic-1.0.0/elastic/tests/testthat/test-search_template.R | 83 + elastic-1.0.0/elastic/tests/testthat/test-search_uri.R | 23 elastic-1.0.0/elastic/tests/testthat/test-termvectors.R | 24 elastic-1.0.0/elastic/tests/testthat/test-type_remover.R |only elastic-1.0.0/elastic/tests/testthat/test-validate.R |only elastic-1.0.0/elastic/tools |only elastic-1.0.0/elastic/vignettes/elastic.Rmd |only elastic-1.0.0/elastic/vignettes/search.Rmd | 117 +- 159 files changed, 4255 insertions(+), 3229 deletions(-)