Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront
data with them and analyze or visualize the results. The package supports
rules that are per-field, in-record, cross-record or cross-dataset. Rules
can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut],
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.1.4 dated 2016-04-15 and 0.1.5 dated 2016-06-24
DESCRIPTION | 8 +-- MD5 | 34 +++++++-------- NEWS | 5 ++ R/compare.R | 20 +++++---- R/confrontation.R | 25 ++++++----- R/functions.R | 8 +++ R/retailers.R | 5 +- R/yaml.R | 2 inst/doc/intro.html | 71 +++++++++++++++++--------------- inst/doc/rule-files.Rmd | 27 +++++++++++- inst/doc/rule-files.html | 81 ++++++++++++++++++++++--------------- man/compare.Rd | 4 - man/confront.Rd | 4 + man/retailers.Rd | 5 +- tests/testthat/testConfrontation.R | 4 + tests/testthat/testParse.R | 2 tests/testthat/testUtils.R | 4 - vignettes/rule-files.Rmd | 27 +++++++++++- 18 files changed, 222 insertions(+), 114 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix
design, along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.2.1 dated 2016-06-01 and 1.2.2 dated 2016-06-24
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS | 6 ++++++ R/MainBar.R | 12 ++++++++---- R/SizeBar.R | 33 ++++++++++++++++++++++++++++++--- R/upset.R | 12 ++++++++---- man/upset.Rd | 7 ++++++- 8 files changed, 71 insertions(+), 23 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 1.8-11.1 dated 2016-01-29 and 1.8-12 dated 2016-06-24
DESCRIPTION | 10 ++-- MD5 | 82 ++++++++++++++++++++++++++--------- NEWS | 27 +++++++++++ R/BIOSPELL_to_STS.R | 54 ++++++++++++----------- R/dissmfac.R | 3 - R/plot.stslist.R | 5 +- R/seqST.R | 30 ++++++++++-- R/seqdef.R | 52 +++++++++++----------- R/seqtab.R | 36 ++++++++------- build/vignette.rds |binary data/bfspell.RData |only data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/CITATION | 9 ++- inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 man/bfspell.Rd |only man/biofam.Rd | 9 +++ man/seqST.Rd | 18 +++++-- man/seqdiff.Rd | 4 - man/seqformat.Rd | 23 +++++++-- src/src |only vignettes/Graphiques |only 24 files changed, 246 insertions(+), 118 deletions(-)
Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal
image video files, plotting and converting binary raw data into estimates of
temperature. First published 2015-03-26. Written primarily for research purposes in
biological applications of thermal images. v1 included the base calculations for
converting thermal image binary values to temperatures. v2 included additional equations
for providing heat transfer calculations.
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>
Diff between Thermimage versions 2.1 dated 2016-05-18 and 2.1.1 dated 2016-06-24
DESCRIPTION | 12 +++++++----- MD5 | 28 +++++++++++++++++----------- R/Prandtl.R | 16 ++++++++++++++-- R/Te.R | 4 ++-- R/Teq.R |only R/airdensity.R |only R/airspecificheat.R |only man/Ld.Rd | 2 +- man/Te.Rd | 4 ++-- man/Teq.Rd |only man/airdensity.Rd |only man/airspecificheat.Rd |only man/palette.choose.Rd | 5 +---- man/qcond.Rd | 4 ---- man/raw2temp.Rd | 6 +----- man/slopeEveryN.Rd | 4 ---- man/slopebypoint.Rd | 5 ----- man/temp2raw.Rd | 4 ---- 18 files changed, 45 insertions(+), 49 deletions(-)
Title: Sparse and Regularized Discriminant Analysis
Description: A collection of sparse and regularized discriminant analysis
methods intended for small-sample, high-dimensional data sets. The package
features the High-Dimensional Regularized Discriminant Analysis classifier.
Author: John A. Ramey <johnramey@gmail.com>
Maintainer: John A. Ramey <johnramey@gmail.com>
Diff between sparsediscrim versions 0.2 dated 2014-03-31 and 0.2.3 dated 2016-06-24
sparsediscrim-0.2.3/sparsediscrim/DESCRIPTION | 13 sparsediscrim-0.2.3/sparsediscrim/LICENSE | 2 sparsediscrim-0.2.3/sparsediscrim/MD5 | 172 +++---- sparsediscrim-0.2.3/sparsediscrim/NAMESPACE | 26 + sparsediscrim-0.2.3/sparsediscrim/NEWS | 60 ++ sparsediscrim-0.2.3/sparsediscrim/R/data-block-autocorrelation.r | 44 + sparsediscrim-0.2.3/sparsediscrim/R/dlda.r | 68 +- sparsediscrim-0.2.3/sparsediscrim/R/dqda.r | 68 +- sparsediscrim-0.2.3/sparsediscrim/R/estimates.r | 26 - sparsediscrim-0.2.3/sparsediscrim/R/hdrda.r | 242 ++++++---- sparsediscrim-0.2.3/sparsediscrim/R/helper-cov.r | 4 sparsediscrim-0.2.3/sparsediscrim/R/helper-intercept.r | 1 sparsediscrim-0.2.3/sparsediscrim/R/helper.r | 64 ++ sparsediscrim-0.2.3/sparsediscrim/R/lda-pseudo.r | 75 +-- sparsediscrim-0.2.3/sparsediscrim/R/lda-schafer.r | 79 +-- sparsediscrim-0.2.3/sparsediscrim/R/lda-thomaz.r | 74 +-- sparsediscrim-0.2.3/sparsediscrim/R/mdeb.r | 71 +- sparsediscrim-0.2.3/sparsediscrim/R/mdmeb.r | 74 +-- sparsediscrim-0.2.3/sparsediscrim/R/mdmp.r | 74 +-- sparsediscrim-0.2.3/sparsediscrim/R/sdlda.r | 79 +-- sparsediscrim-0.2.3/sparsediscrim/R/sdqda.r | 81 +-- sparsediscrim-0.2.3/sparsediscrim/R/smdlda.r | 68 +- sparsediscrim-0.2.3/sparsediscrim/R/smdqda.r | 64 +- sparsediscrim-0.2.3/sparsediscrim/R/stein-shrinkage.r | 90 +-- sparsediscrim-0.2.3/sparsediscrim/R/tong-shrinkage.r | 1 sparsediscrim-0.2.3/sparsediscrim/README.md | 54 +- sparsediscrim-0.2.3/sparsediscrim/man/center_data.Rd | 17 sparsediscrim-0.2.3/sparsediscrim/man/cov_autocorrelation.Rd | 27 - sparsediscrim-0.2.3/sparsediscrim/man/cov_block_autocorrelation.Rd | 40 - sparsediscrim-0.2.3/sparsediscrim/man/cov_eigen.Rd | 40 - sparsediscrim-0.2.3/sparsediscrim/man/cov_intraclass.Rd | 32 - sparsediscrim-0.2.3/sparsediscrim/man/cov_list.Rd | 17 sparsediscrim-0.2.3/sparsediscrim/man/cov_mle.Rd | 28 - sparsediscrim-0.2.3/sparsediscrim/man/cov_pool.Rd | 15 sparsediscrim-0.2.3/sparsediscrim/man/cov_shrink_diag.Rd | 42 - sparsediscrim-0.2.3/sparsediscrim/man/cv_partition.Rd | 43 - sparsediscrim-0.2.3/sparsediscrim/man/diag_estimates.Rd | 96 +-- sparsediscrim-0.2.3/sparsediscrim/man/dlda.Rd | 142 ++--- sparsediscrim-0.2.3/sparsediscrim/man/dmvnorm_diag.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/dqda.Rd | 144 ++--- sparsediscrim-0.2.3/sparsediscrim/man/generate_blockdiag.Rd | 100 ++-- sparsediscrim-0.2.3/sparsediscrim/man/generate_intraclass.Rd | 85 +-- sparsediscrim-0.2.3/sparsediscrim/man/h.Rd | 23 sparsediscrim-0.2.3/sparsediscrim/man/hdrda.Rd | 171 ++----- sparsediscrim-0.2.3/sparsediscrim/man/hdrda_cv.Rd | 49 -- sparsediscrim-0.2.3/sparsediscrim/man/lda_pseudo.Rd | 131 ++--- sparsediscrim-0.2.3/sparsediscrim/man/lda_schafer.Rd | 139 ++--- sparsediscrim-0.2.3/sparsediscrim/man/lda_thomaz.Rd | 138 ++--- sparsediscrim-0.2.3/sparsediscrim/man/log_determinant.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/mdeb.Rd | 130 ++--- sparsediscrim-0.2.3/sparsediscrim/man/mdmeb.Rd | 134 ++--- sparsediscrim-0.2.3/sparsediscrim/man/mdmp.Rd | 129 ++--- sparsediscrim-0.2.3/sparsediscrim/man/no_intercept.Rd | 18 sparsediscrim-0.2.3/sparsediscrim/man/plot.hdrda_cv.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/posterior_probs.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.dlda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.dqda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.hdrda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.lda_pseudo.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.lda_schafer.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.lda_thomaz.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.mdeb.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.mdmeb.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.mdmp.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.sdlda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.sdqda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.smdlda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/print.smdqda.Rd |only sparsediscrim-0.2.3/sparsediscrim/man/quadform.Rd | 20 sparsediscrim-0.2.3/sparsediscrim/man/quadform_inv.Rd | 20 sparsediscrim-0.2.3/sparsediscrim/man/rda_cov.Rd | 24 sparsediscrim-0.2.3/sparsediscrim/man/rda_weights.Rd | 23 sparsediscrim-0.2.3/sparsediscrim/man/regdiscrim_estimates.Rd | 84 +-- sparsediscrim-0.2.3/sparsediscrim/man/risk_stein.Rd | 45 - sparsediscrim-0.2.3/sparsediscrim/man/sdlda.Rd | 174 +++---- sparsediscrim-0.2.3/sparsediscrim/man/sdqda.Rd | 173 +++---- sparsediscrim-0.2.3/sparsediscrim/man/smdlda.Rd | 156 ++---- sparsediscrim-0.2.3/sparsediscrim/man/smdqda.Rd | 147 ++---- sparsediscrim-0.2.3/sparsediscrim/man/solve_chol.Rd | 8 sparsediscrim-0.2.3/sparsediscrim/man/tong_mean_shrinkage.Rd | 24 sparsediscrim-0.2.3/sparsediscrim/man/update_hdrda.Rd | 24 sparsediscrim-0.2.3/sparsediscrim/man/var_shrinkage.Rd | 31 - sparsediscrim-0.2.3/sparsediscrim/tests |only sparsediscrim-0.2/sparsediscrim/inst |only 84 files changed, 2230 insertions(+), 2327 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Easily implement a variety of simulation models, with a focus on
spatially explicit agent based models. These include raster-based,
event-based, and agent-based models. The core simulation components are
built upon a discrete event simulation framework that facilitates
modularity, and easily enables the user to include additional functionality
by running user-built simulation modules. Included are numerous tools to
visualize raster and other maps. The suggested package `fastshp` can be
installed with `install.packages("fastshp", repos="http://rforge.net",
type="source")`.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES versions 1.1.4 dated 2016-04-20 and 1.2.0 dated 2016-06-24
DESCRIPTION | 24 MD5 | 468 NAMESPACE | 989 - NEWS | 483 R/SELES.R | 555 R/agent.R | 176 R/check.R | 546 R/checkpoint.R | 676 - R/copy.R | 78 R/environment.R | 408 R/experiment.R | 1321 +- R/helpers.R | 259 R/initialize.R | 719 - R/load.R | 610 - R/mapReduce.R | 164 R/mergeRaster.R |only R/misc-methods.R | 1452 +- R/module-dependencies-class.R | 450 R/module-dependencies-methods.R | 536 R/module-repository.R | 899 - R/module-template.R | 1564 +- R/moduleCoverage.R | 300 R/moduleMetadata.R | 152 R/movement.R | 252 R/neighbourhood.R | 1547 +- R/numerical-comparisons.R | 72 R/plotting-classes.R | 580 - R/plotting-colours.R | 1144 + R/plotting-diagrams.R | 612 - R/plotting-helpers.R | 1516 +- R/plotting-other.R | 768 - R/plotting.R | 3980 +++--- R/priority.R | 86 R/probability.R | 94 R/progress.R | 234 R/save.R | 296 R/shine.R | 694 - R/simList-accessors.R | 5777 +++++----- R/simList-class.R | 512 R/simulation.R | 2000 +-- R/spades-classes.R | 72 R/spades-package.R | 843 - R/splitRaster.R | 281 R/spread-process.R | 2021 ++- R/times.R | 907 - R/zzz.R | 30 README.md | 149 build/vignette.rds |binary demo/00Index | 4 demo/spades-simulation.R | 102 inst/doc/i-introduction.R | 78 inst/doc/i-introduction.Rmd | 660 - inst/doc/i-introduction.html | 740 - inst/doc/ii-modules.R | 705 - inst/doc/ii-modules.Rmd | 1617 +- inst/doc/ii-modules.html | 2081 +-- inst/doc/iii-plotting.R | 306 inst/doc/iii-plotting.Rmd | 824 - inst/doc/iii-plotting.html | 771 - inst/examples |only inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R | 44 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd | 88 inst/sampleModules/caribouMovement/caribouMovement.R | 308 inst/sampleModules/fireSpread/fireSpread.R | 368 inst/sampleModules/randomLandscapes/randomLandscapes.R | 232 man/Plot.Rd | 621 - man/SELESagentLocation.Rd | 58 man/SELESnumAgents.Rd | 60 man/SELESprobInit.Rd | 86 man/SELEStransitions.Rd | 62 man/SpaDES-package.Rd | 802 - man/addDepends.Rd | 58 man/adj.Rd | 198 man/append_attr.Rd | 78 man/arrangeViewports.Rd | 48 man/arrangement-class.Rd | 144 man/assignSpaDES.Rd | 66 man/cache.Rd | 103 man/changeObjEnv.Rd | 124 man/checkModule.Rd | 58 man/checkObject.Rd | 112 man/checkParams.Rd | 72 man/checkPath.Rd | 76 man/checkpoint.Rd | 102 man/checksums.Rd | 92 man/cir.Rd | 248 man/classFilter.Rd | 202 man/clearPlot.Rd | 80 man/clearStubArtifacts.Rd | 58 man/copy.Rd | 58 man/crw.Rd | 154 man/defineModule.Rd | 114 man/defineParameter.Rd | 108 man/depsEdgeList.Rd | 72 man/depsGraph.Rd | 68 man/depsLoadOrder.Rd | 68 man/depsPruneEdges.Rd | 54 man/dev.Rd | 63 man/digest.Rd | 54 man/directions.Rd |only man/distances.Rd |only man/divergentColors.Rd | 98 man/doEvent.Rd | 86 man/downloadData.Rd | 70 man/downloadModule.Rd | 128 man/dwrpnorm2.Rd | 88 man/emptyEventList.Rd | 120 man/emptyMetadata.Rd | 48 man/equalExtent.Rd | 44 man/eventDiagram.Rd | 110 man/existsSpaDES.Rd | 52 man/experiment.Rd | 821 - man/fileExt.Rd | 42 man/fileName.Rd | 42 man/fileTable.Rd | 74 man/fillInputRows.Rd | 34 man/fillOutputRows.Rd | 34 man/findFactors.Rd | 38 man/findObjects.Rd |only man/ganttStatus.Rd | 58 man/gaussmap.Rd | 98 man/getColors.Rd | 68 man/getFileName.Rd | 54 man/getModuleVersion.Rd | 58 man/getSpaDES.Rd | 48 man/grid-functions.Rd | 46 man/heading.Rd | 128 man/identifyGrobToPlot.Rd | 78 man/inRange.Rd | 60 man/initialize-method.Rd | 34 man/initiateAgents.Rd | 161 man/inputObjects.Rd | 62 man/layerNames.Rd | 90 man/loadFiles.Rd | 176 man/loadPackages.Rd | 102 man/ls-method.Rd | 58 man/ls_str-method.Rd | 58 man/makeColorMatrix.Rd | 110 man/makeDigestible.Rd | 88 man/makeLayout.Rd | 66 man/makeLines.Rd | 115 man/makeList.Rd | 54 man/makeSpadesPlot.Rd | 88 man/makeViewports.Rd | 56 man/maxTimeunit.Rd | 52 man/mergeRaster.Rd |only man/minTimeunit.Rd | 54 man/moduleCoverage.Rd | 128 man/moduleDeps-class.Rd | 146 man/moduleDiagram.Rd | 80 man/moduleMetadata.Rd | 82 man/newModule.Rd | 232 man/newPlot.Rd | 58 man/newProgressBar.Rd | 50 man/nlayers.Rd | 77 man/normPath.Rd | 68 man/objectDiagram.Rd | 68 man/objectNames.Rd | 64 man/openModules.Rd | 106 man/packages.Rd | 50 man/paddedFloatToChar.Rd | 72 man/parseArgs.Rd | 58 man/parseModule.Rd | 54 man/patchSize.Rd | 30 man/plotGrob.Rd | 215 man/prepareRaster.Rd | 66 man/priority.Rd | 64 man/randomPolygons.Rd | 109 man/rasterToMemory.Rd | 62 man/rasterizeReduce.Rd | 120 man/rings.Rd |only man/rndstr.Rd | 130 man/saveFiles.Rd | 138 man/scheduleEvent.Rd | 132 man/setColors.Rd | 194 man/shine.Rd | 136 man/show-method.Rd | 32 man/sim2gantt.Rd | 72 man/simDeps-class.Rd | 44 man/simInit.Rd | 390 man/simList-accessors-envir.Rd | 96 man/simList-accessors-events.Rd | 194 man/simList-accessors-inout.Rd | 610 - man/simList-accessors-modules.Rd | 174 man/simList-accessors-objects.Rd | 158 man/simList-accessors-params.Rd | 300 man/simList-accessors-paths.Rd | 210 man/simList-accessors-times.Rd | 343 man/simList-class.Rd | 222 man/simList_-class.Rd | 46 man/sortDotsFirst.Rd | 48 man/spades-classes.Rd | 90 man/spades.Rd | 214 man/spadesEnv.Rd | 30 man/spadesGrob-class.Rd | 102 man/spadesMaps.Rd | 50 man/spadesMouseClicks.Rd | 136 man/spadesPlot-class.Rd | 96 man/spadesPlotObjects-class.Rd | 44 man/spadesPlottables-class.Rd | 46 man/spadesTime.Rd | 160 man/spatialObjects-class.Rd | 46 man/specnumperpatch-probs.Rd | 82 man/splitRaster.Rd | 203 man/spread.Rd | 699 - man/timeConversion.Rd | 186 man/unittrim.Rd | 44 man/unparsed.Rd | 50 man/updateList.Rd | 104 man/updateSpadesPlot.Rd | 62 man/versionWarning.Rd | 74 man/wrap.Rd | 172 man/zipModule.Rd | 80 tests/test-all.R | 4 tests/testthat/test-Plot.R | 1240 +- tests/testthat/test-adj.R | 635 - tests/testthat/test-checkPath.R | 144 tests/testthat/test-checkpoint.R | 76 tests/testthat/test-downloadModule.R | 193 tests/testthat/test-environment.R | 22 tests/testthat/test-examples.R | 6 tests/testthat/test-experiment.R | 406 tests/testthat/test-inRange.R | 38 tests/testthat/test-load.R | 571 tests/testthat/test-mapReduce.R | 206 tests/testthat/test-module-deps-methods.R | 302 tests/testthat/test-module-template.R | 94 tests/testthat/test-paths.R | 112 tests/testthat/test-save.R | 195 tests/testthat/test-simList.R | 441 tests/testthat/test-simulation.R | 220 tests/testthat/test-splitRaster.R |only tests/testthat/test-spread.R | 1175 +- tests/testthat/test-timeunits.R | 214 tests/testthat/test-updateList.R | 32 vignettes/bibliography.bib | 270 vignettes/i-introduction.Rmd | 660 - vignettes/ii-modules.Rmd | 1617 +- vignettes/iii-plotting.Rmd | 824 - 239 files changed, 38253 insertions(+), 34636 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a
probabilistic programming language that implements full Bayesian statistical
inference via Markov Chain Monte Carlo, rough Bayesian inference via variational
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need
to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cph] (R/cxxfunplus.R),
The R Core Team [cph] (R/pairs.R),
Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R),
Hadley Wickham [cph] (R/rtools.R),
Joel de Guzman [cph] (Boost),
John Fletcher [cph] (Boost),
Thomas Heller [cph] (Boost),
Eric Niebler [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.9.0-3 dated 2016-02-11 and 2.10.1 dated 2016-06-24
rstan-2.10.1/rstan/DESCRIPTION | 57 rstan-2.10.1/rstan/MD5 | 189 - rstan-2.10.1/rstan/NAMESPACE | 1 rstan-2.10.1/rstan/R/AllClass.R | 2 rstan-2.10.1/rstan/R/Rcpp_module_def.R | 2 rstan-2.10.1/rstan/R/chains.R | 2 rstan-2.10.1/rstan/R/cxxdso-class.R | 8 rstan-2.10.1/rstan/R/cxxfunplus.R | 6 rstan-2.10.1/rstan/R/expose_stan_functions.R | 23 rstan-2.10.1/rstan/R/git_rstan_head.R | 3 rstan-2.10.1/rstan/R/lookup.R | 6 rstan-2.10.1/rstan/R/makefile_op.R | 2 rstan-2.10.1/rstan/R/misc.R | 12 rstan-2.10.1/rstan/R/monitor.R | 2 rstan-2.10.1/rstan/R/options.R | 2 rstan-2.10.1/rstan/R/pairs.R | 16 rstan-2.10.1/rstan/R/plugin.R | 34 rstan-2.10.1/rstan/R/rstan.R | 2 rstan-2.10.1/rstan/R/rstan_package_skeleton.R | 22 rstan-2.10.1/rstan/R/rtools.R | 2 rstan-2.10.1/rstan/R/stan_csv.R | 4 rstan-2.10.1/rstan/R/stan_demo.R | 11 rstan-2.10.1/rstan/R/stan_plot.R | 42 rstan-2.10.1/rstan/R/stan_plot_helpers.R | 42 rstan-2.10.1/rstan/R/stanc.R | 8 rstan-2.10.1/rstan/R/stanfit-class.R | 24 rstan-2.10.1/rstan/R/stanmodel-class.R | 32 rstan-2.10.1/rstan/R/sysdata.rda |binary rstan-2.10.1/rstan/R/zzz.R | 2 rstan-2.10.1/rstan/build/vignette.rds |binary rstan-2.10.1/rstan/inst/CITATION | 10 rstan-2.10.1/rstan/inst/NEWS | 10 rstan-2.10.1/rstan/inst/doc/rstan.R |only rstan-2.10.1/rstan/inst/doc/rstan.Rmd |only rstan-2.10.1/rstan/inst/doc/rstan.html |only rstan-2.10.1/rstan/inst/doc/stanfit-objects.R |only rstan-2.10.1/rstan/inst/doc/stanfit-objects.Rmd |only rstan-2.10.1/rstan/inst/doc/stanfit-objects.html |only rstan-2.10.1/rstan/inst/include/rstan/rstan_writer.hpp | 138 - rstan-2.10.1/rstan/inst/include/rstan/stan_args.hpp | 4 rstan-2.10.1/rstan/inst/include/rstan/stan_fit.hpp | 157 - rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_1.csv | 2 rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_2.csv | 2 rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_3.csv | 2 rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_4.csv | 2 rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_incomplete_1.csv | 2 rstan-2.10.1/rstan/inst/misc/rstan_doc_ex_incomplete_2.csv | 2 rstan-2.10.1/rstan/man/As.mcmc.list.Rd |only rstan-2.10.1/rstan/man/expose_stan_functions.Rd | 62 rstan-2.10.1/rstan/man/extract_sparse_parts.Rd | 23 rstan-2.10.1/rstan/man/lookup.Rd | 12 rstan-2.10.1/rstan/man/monitor.Rd | 61 rstan-2.10.1/rstan/man/plotting-functions.Rd | 4 rstan-2.10.1/rstan/man/print.stanfit.Rd | 44 rstan-2.10.1/rstan/man/rstan-internal.Rd | 4 rstan-2.10.1/rstan/man/rstan.Rd | 52 rstan-2.10.1/rstan/man/stan.Rd | 214 - rstan-2.10.1/rstan/man/stan_model.Rd | 93 rstan-2.10.1/rstan/man/stan_plot.Rd | 91 rstan-2.10.1/rstan/man/stan_plot_diagnostics.Rd | 8 rstan-2.10.1/rstan/man/stan_plot_options.Rd | 2 rstan-2.10.1/rstan/man/stanc.Rd | 33 rstan-2.10.1/rstan/man/stanfit-class.Rd | 295 +- rstan-2.10.1/rstan/man/stanfit-method-extract.Rd | 59 rstan-2.10.1/rstan/man/stanfit-method-logprob.Rd | 30 rstan-2.10.1/rstan/man/stanfit-method-pairs.Rd | 9 rstan-2.10.1/rstan/man/stanfit-method-plot.Rd | 42 rstan-2.10.1/rstan/man/stanfit-method-summary.Rd |only rstan-2.10.1/rstan/man/stanfit-method-traceplot.Rd | 20 rstan-2.10.1/rstan/man/stanfit2array-method.Rd | 28 rstan-2.10.1/rstan/man/stanmodel-class.Rd | 6 rstan-2.10.1/rstan/man/stanmodel-method-optimizing.Rd | 128 - rstan-2.10.1/rstan/man/stanmodel-method-sampling.Rd | 121 rstan-2.10.1/rstan/man/stanmodel-method-vb.Rd | 113 rstan-2.10.1/rstan/src/Makevars | 5 rstan-2.10.1/rstan/src/Makevars.win | 3 rstan-2.10.1/rstan/src/chains.cpp | 2 rstan-2.10.1/rstan/src/init.cpp | 2 rstan-2.10.1/rstan/src/lang__ast_def.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__bare_type_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__expression07_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__expression_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__functions_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__indexes_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__program_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__semantic_actions.cpp |only rstan-2.10.1/rstan/src/lang__grammars__statement_2_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__statement_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__term_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__var_deccls_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/lang__grammars__whitespace_grammar_inst.cpp | 2 rstan-2.10.1/rstan/src/misc.cpp | 2 rstan-2.10.1/rstan/src/stanc.cpp | 2 rstan-2.10.1/rstan/tools/stan-functions.R | 315 +- rstan-2.10.1/rstan/tools/stan-functions.txt | 1246 +++++----- rstan-2.10.1/rstan/vignettes/rstan.Rmd |only rstan-2.10.1/rstan/vignettes/rstan.bib | 4 rstan-2.10.1/rstan/vignettes/schools.stan | 12 rstan-2.10.1/rstan/vignettes/stanfit-objects.Rmd |only rstan-2.9.0-3/rstan/inst/doc/rstan_vignette.R |only rstan-2.9.0-3/rstan/inst/doc/rstan_vignette.Rnw |only rstan-2.9.0-3/rstan/inst/doc/rstan_vignette.pdf |only rstan-2.9.0-3/rstan/vignettes/rstan_vignette.Rnw |only 103 files changed, 2168 insertions(+), 1892 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0.4 dated 2016-04-25 and 1.0.5 dated 2016-06-24
DESCRIPTION | 10 MD5 | 26 - NAMESPACE | 4 R/find.ladder.R | 1107 +++++++++++++++++++++++++++------------------- R/ladder.info.attach.R | 10 R/overview.R | 9 R/overview2.R | 101 ++-- R/score.easy.R | 3 R/storing.inds.R | 99 ++-- man/Fragman-package.Rd | 44 + man/find.ladder.Rd | 4 man/ladder.info.attach.Rd | 14 man/overview2.Rd | 6 man/score.easy.Rd | 100 +++- 14 files changed, 983 insertions(+), 554 deletions(-)
Title: Chunkwise Text-File Processing for 'dplyr'
Description: Text data can be processed chunkwise using 'dplyr' commands. These
are recorded and executed per data chunk, so large files can be processed with
limited memory using the 'LaF' package.
Author: Edwin de Jonge
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between chunked versions 0.2.1 dated 2016-04-07 and 0.3 dated 2016-06-24
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/write.R | 21 +++++++++++++-------- tests/testthat/test-print.R | 7 ++----- 4 files changed, 24 insertions(+), 22 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three
S3 generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance, which
provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between broom versions 0.4.0 dated 2015-11-30 and 0.4.1 dated 2016-06-24
DESCRIPTION | 34 +++-- MD5 | 255 +++++++++++++++++++++------------------- NAMESPACE | 27 ++++ R/anova_tidiers.R | 7 - R/extras.R | 21 ++- R/gam_tidiers.R | 44 ++++++ R/glmnet_tidiers.R | 2 R/globals.R | 4 R/gmm_tidiers.R |only R/htest_tidiers.R | 8 + R/kde_tidiers.R |only R/list_tidiers.R | 10 + R/lm_tidiers.R | 40 ++++-- R/lme4_tidiers.R | 2 R/lmodel2_tidiers.R |only R/mclust_tidiers.R |only R/mcmc_tidiers.R | 22 ++- R/orcutt_tidiers.R |only R/plm_tidiers.R | 3 R/polca_tidiers.R |only R/prcomp_tidiers.R |only R/ridgelm_tidiers.R | 4 R/rstanarm_tidiers.R |only R/sparse_tidiers.R |only R/stats_tidiers.R | 150 ++++++++++++++++++++++- R/summary_tidiers.R | 2 R/survival_tidiers.R | 15 ++ R/svd_tidiers.R | 13 -- R/utilities.R | 28 +++- R/vector_tidiers.R |only R/zoo_tidiers.R | 2 README.md | 52 ++++++-- build/vignette.rds |binary inst/doc/bootstrapping.R | 16 -- inst/doc/bootstrapping.Rmd | 21 --- inst/doc/bootstrapping.html | 34 +---- inst/doc/broom.html | 20 +-- inst/doc/broom_and_dplyr.html | 9 - inst/doc/kmeans.html | 8 - man/Arima_tidiers.Rd | 4 man/aareg_tidiers.Rd | 4 man/acf_tidiers.Rd |only man/anova_tidiers.Rd | 4 man/auc_tidiers.Rd | 14 +- man/augment.Rd | 2 man/augment_columns.Rd | 2 man/biglm_tidiers.Rd | 10 - man/binDesign_tidiers.Rd | 5 man/binWidth_tidiers.Rd | 8 - man/boot_tidiers.Rd | 5 man/bootstrap.Rd | 9 + man/broom.Rd | 2 man/btergm_tidiers.Rd | 9 - man/cch_tidiers.Rd | 16 +- man/compact.Rd | 2 man/confint.geeglm.Rd | 2 man/confint_tidy.Rd | 2 man/coxph_tidiers.Rd | 7 - man/cv.glmnet_tidiers.Rd | 22 +-- man/data.frame_tidiers.Rd | 4 man/ergm_tidiers.Rd | 11 - man/felm_tidiers.Rd | 15 +- man/finish_glance.Rd | 4 man/fitdistr_tidiers.Rd | 3 man/fix_data_frame.Rd | 2 man/gam_tidiers.Rd | 6 man/gamlss_tidiers.Rd | 4 man/geeglm_tidiers.Rd | 4 man/glance.Rd | 2 man/glm_tidiers.Rd | 4 man/glmnet_tidiers.Rd | 16 +- man/gmm_tidiers.Rd |only man/htest_tidiers.Rd | 8 - man/inflate.Rd | 2 man/insert_NAs.Rd | 2 man/kappa_tidiers.Rd | 4 man/kde_tidiers.Rd |only man/kmeans_tidiers.Rd | 4 man/list_tidiers.Rd | 8 - man/lm_tidiers.Rd | 17 ++ man/lme4_tidiers.Rd | 9 - man/lmodel2_tidiers.Rd |only man/loess_tidiers.Rd | 8 - man/matrix_tidiers.Rd | 4 man/mclust_tidiers.Rd |only man/mcmc_tidiers.Rd | 29 ++-- man/mle2_tidiers.Rd | 8 - man/multcomp_tidiers.Rd | 3 man/multinom_tidiers.Rd | 14 +- man/nlme_tidiers.Rd | 10 - man/nls_tidiers.Rd | 4 man/optim_tidiers.Rd | 4 man/orcutt_tidiers.Rd |only man/plm_tidiers.Rd | 12 + man/poLCA_tidiers.Rd |only man/prcomp_tidiers.Rd |only man/process_ergm.Rd | 2 man/process_geeglm.Rd | 2 man/process_lm.Rd | 2 man/process_rq.Rd | 2 man/pyears_tidiers.Rd | 8 - man/rcorr_tidiers.Rd | 12 + man/ridgelm_tidiers.Rd | 7 - man/rlm_tidiers.Rd | 4 man/rowwise_df_tidiers.Rd | 6 man/rq_tidiers.Rd | 10 - man/rstanarm_tidiers.Rd |only man/sexpfit_tidiers.Rd | 4 man/smooth.spline_tidiers.Rd | 4 man/sp_tidiers.Rd | 3 man/sparse_tidiers.Rd |only man/summary_tidiers.Rd | 4 man/survfit_tidiers.Rd | 29 ++-- man/survreg_tidiers.Rd | 4 man/svd_tidiers.Rd | 3 man/tidy.NULL.Rd | 2 man/tidy.Rd | 2 man/tidy.TukeyHSD.Rd | 18 ++ man/tidy.coeftest.Rd | 6 man/tidy.default.Rd | 4 man/tidy.density.Rd | 2 man/tidy.dist.Rd |only man/tidy.ftable.Rd | 4 man/tidy.manova.Rd | 17 ++ man/tidy.map.Rd | 3 man/tidy.pairwise.htest.Rd | 6 man/tidy.power.htest.Rd | 4 man/tidy.spec.Rd | 4 man/tidy.table.Rd | 4 man/tidy.ts.Rd | 2 man/unrowname.Rd | 2 man/vector_tidiers.Rd |only man/xyz_tidiers.Rd | 4 man/zoo_tidiers.Rd | 8 - tests/testthat/test-bootstrap.R |only tests/testthat/test-dplyr.R | 8 - tests/testthat/test-gam.R |only tests/testthat/test-rowwise.R | 4 tests/testthat/test-rstanarm.R |only tests/testthat/test-tidy.R | 2 vignettes/bootstrapping.Rmd | 21 --- 141 files changed, 943 insertions(+), 497 deletions(-)
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal
shaped particles based on the same measured quantities of corresponding planar
section profiles. A single trivariate discretized version of the (stereological)
integral equation in the case of prolate and oblate spheroids is solved
numerically by the EM algorithm. The estimation of diameter distribution of
spheres from planar sections (Wicksell's corpuscle problem) is also implemented.
Further, the package provides routines for the simulation of a Poisson germ-
grain process with either spheroids, spherocylinders or spheres as grains together
with functions for planar sections. For the purpose of exact simulation a bivariate size-shape
distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.5.7 dated 2016-06-24 and 0.5.8 dated 2016-06-24
DESCRIPTION | 6 - MD5 | 20 +++--- src/GeometricPrimitives.cpp | 17 ++--- src/GeometricPrimitives.h | 23 +++---- src/Intersector.cpp | 27 -------- src/Intersector.h | 135 ++++++++++++++++++++------------------------ src/SimCylinder.cpp | 2 src/SimEllipsoid.cpp | 2 src/directions.h | 9 ++ src/ellipt.cpp | 134 +++++++++++++++++++++++-------------------- src/unfold.cpp | 73 ++++++++++++----------- 11 files changed, 218 insertions(+), 230 deletions(-)
Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of
JSON like document that support JavaScript typed data (https://github.com/tercen/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>
Diff between rtson versions 1.1 dated 2015-12-02 and 1.2 dated 2016-06-24
DESCRIPTION | 12 ++-- MD5 | 18 +++--- NAMESPACE | 2 R/deserializer.R | 64 ++++++++++------------- R/rtson.R | 122 +++++++++++++++++++++++++++++++++----------- R/serializer.R | 47 +++++++--------- README.md | 10 +++ man/fromTSON.Rd | 4 - man/readTSON.Rd |only man/writeTSON.Rd |only tests/testthat/test_rtson.R | 2 11 files changed, 171 insertions(+), 110 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.4.3 dated 2015-09-01 and 0.5.0 dated 2016-06-24
dplyr-0.4.3/dplyr/R/chain.r |only dplyr-0.4.3/dplyr/R/cluster.R |only dplyr-0.4.3/dplyr/R/frame-data.R |only dplyr-0.4.3/dplyr/R/glimpse.R |only dplyr-0.4.3/dplyr/R/grouped-dt.r |only dplyr-0.4.3/dplyr/R/rbind.r |only dplyr-0.4.3/dplyr/R/tbl-dt.r |only dplyr-0.4.3/dplyr/R/type-sum.r |only dplyr-0.4.3/dplyr/R/utils-dt.R |only dplyr-0.4.3/dplyr/demo |only dplyr-0.4.3/dplyr/inst/include/dplyr/JoinFactorFactorVisitor_SameLevels.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/Result/First.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Last.h |only dplyr-0.4.3/dplyr/inst/include/dplyr/Result/Nth.h |only dplyr-0.4.3/dplyr/man/all.equal.tbl_df.Rd |only dplyr-0.4.3/dplyr/man/as_data_frame.Rd |only dplyr-0.4.3/dplyr/man/chain.Rd |only dplyr-0.4.3/dplyr/man/data_frame.Rd |only dplyr-0.4.3/dplyr/man/dplyr-cluster.Rd |only dplyr-0.4.3/dplyr/man/dplyr-formatting.Rd |only dplyr-0.4.3/dplyr/man/frame_data.Rd |only dplyr-0.4.3/dplyr/man/glimpse.Rd |only dplyr-0.4.3/dplyr/man/grouped_dt.Rd |only 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dplyr-0.5.0/dplyr/man/summarise.Rd | 15 dplyr-0.5.0/dplyr/man/summarise_all.Rd |only dplyr-0.5.0/dplyr/man/summarise_each.Rd | 37 dplyr-0.5.0/dplyr/man/tally.Rd | 10 dplyr-0.5.0/dplyr/man/tbl.Rd | 2 dplyr-0.5.0/dplyr/man/tbl_cube.Rd | 6 dplyr-0.5.0/dplyr/man/tbl_df.Rd | 19 dplyr-0.5.0/dplyr/man/tbl_sql.Rd | 2 dplyr-0.5.0/dplyr/man/tbl_vars.Rd | 2 dplyr-0.5.0/dplyr/man/testing.Rd |only dplyr-0.5.0/dplyr/man/top_n.Rd | 31 dplyr-0.5.0/dplyr/man/translate_sql.Rd | 115 dplyr-0.5.0/dplyr/man/vars.Rd |only dplyr-0.5.0/dplyr/man/with_order.Rd | 4 dplyr-0.5.0/dplyr/src/Makevars | 3 dplyr-0.5.0/dplyr/src/RcppExports.cpp | 100 dplyr-0.5.0/dplyr/src/address.cpp | 8 dplyr-0.5.0/dplyr/src/api.cpp | 150 + dplyr-0.5.0/dplyr/src/arrange.cpp | 65 dplyr-0.5.0/dplyr/src/bind.cpp | 124 - dplyr-0.5.0/dplyr/src/combine_variables.cpp | 4 dplyr-0.5.0/dplyr/src/distinct.cpp | 12 dplyr-0.5.0/dplyr/src/dplyr.cpp | 733 ++---- dplyr-0.5.0/dplyr/src/filter.cpp | 12 dplyr-0.5.0/dplyr/src/init.cpp | 4 dplyr-0.5.0/dplyr/src/join.cpp | 118 dplyr-0.5.0/dplyr/src/nth.cpp |only dplyr-0.5.0/dplyr/src/strings_addresses.cpp | 4 dplyr-0.5.0/dplyr/src/summarise.cpp | 2 dplyr-0.5.0/dplyr/src/test.cpp | 8 dplyr-0.5.0/dplyr/src/window.cpp | 19 dplyr-0.5.0/dplyr/tests/testthat.R | 11 dplyr-0.5.0/dplyr/tests/testthat/helper-output.R |only dplyr-0.5.0/dplyr/tests/testthat/helper-src.R |only dplyr-0.5.0/dplyr/tests/testthat/output |only dplyr-0.5.0/dplyr/tests/testthat/test-arrange.r | 85 dplyr-0.5.0/dplyr/tests/testthat/test-as-data-frame.R |only dplyr-0.5.0/dplyr/tests/testthat/test-binds.R |only dplyr-0.5.0/dplyr/tests/testthat/test-case-when.R |only dplyr-0.5.0/dplyr/tests/testthat/test-coalesce.R |only dplyr-0.5.0/dplyr/tests/testthat/test-colwise.R | 78 dplyr-0.5.0/dplyr/tests/testthat/test-combine.R |only dplyr-0.5.0/dplyr/tests/testthat/test-compute.R |only dplyr-0.5.0/dplyr/tests/testthat/test-count.r | 33 dplyr-0.5.0/dplyr/tests/testthat/test-data_frame.R | 60 dplyr-0.5.0/dplyr/tests/testthat/test-distinct.R | 43 dplyr-0.5.0/dplyr/tests/testthat/test-do.R | 84 dplyr-0.5.0/dplyr/tests/testthat/test-equality.r | 48 dplyr-0.5.0/dplyr/tests/testthat/test-equiv-manip.r | 27 dplyr-0.5.0/dplyr/tests/testthat/test-filter-windowed.R | 50 dplyr-0.5.0/dplyr/tests/testthat/test-filter.r | 143 - dplyr-0.5.0/dplyr/tests/testthat/test-group-by.r | 104 dplyr-0.5.0/dplyr/tests/testthat/test-group-size.R | 2 dplyr-0.5.0/dplyr/tests/testthat/test-if-else.R |only dplyr-0.5.0/dplyr/tests/testthat/test-joins.r | 238 + dplyr-0.5.0/dplyr/tests/testthat/test-lazy-ops.R |only dplyr-0.5.0/dplyr/tests/testthat/test-mutate-windowed.R | 51 dplyr-0.5.0/dplyr/tests/testthat/test-mutate.r | 178 + dplyr-0.5.0/dplyr/tests/testthat/test-na-if.R |only dplyr-0.5.0/dplyr/tests/testthat/test-near.R |only dplyr-0.5.0/dplyr/tests/testthat/test-nth-value.R | 21 dplyr-0.5.0/dplyr/tests/testthat/test-output.R |only dplyr-0.5.0/dplyr/tests/testthat/test-recode.R |only dplyr-0.5.0/dplyr/tests/testthat/test-sample.R | 4 dplyr-0.5.0/dplyr/tests/testthat/test-select-helpers.R |only dplyr-0.5.0/dplyr/tests/testthat/test-select.r | 94 dplyr-0.5.0/dplyr/tests/testthat/test-sets.R | 48 dplyr-0.5.0/dplyr/tests/testthat/test-slice.r | 25 dplyr-0.5.0/dplyr/tests/testthat/test-sql-build.R |only dplyr-0.5.0/dplyr/tests/testthat/test-sql-escape.r | 11 dplyr-0.5.0/dplyr/tests/testthat/test-sql-joins.R | 30 dplyr-0.5.0/dplyr/tests/testthat/test-sql-render.R |only dplyr-0.5.0/dplyr/tests/testthat/test-sql-translation.r | 106 dplyr-0.5.0/dplyr/tests/testthat/test-summarise.r | 172 + dplyr-0.5.0/dplyr/tests/testthat/test-tally.R |only dplyr-0.5.0/dplyr/tests/testthat/test-tbl-cube.R | 52 dplyr-0.5.0/dplyr/tests/testthat/test-tbl-sql.r | 18 dplyr-0.5.0/dplyr/tests/testthat/test-union-all.R |only dplyr-0.5.0/dplyr/tests/testthat/test-window.R | 52 dplyr-0.5.0/dplyr/vignettes/data_frames.Rmd | 97 dplyr-0.5.0/dplyr/vignettes/databases.Rmd | 119 dplyr-0.5.0/dplyr/vignettes/hybrid-evaluation.Rmd | 4 dplyr-0.5.0/dplyr/vignettes/introduction.Rmd | 16 dplyr-0.5.0/dplyr/vignettes/new-sql-backend.Rmd | 40 dplyr-0.5.0/dplyr/vignettes/notes/postgres-setup.Rmd | 20 dplyr-0.5.0/dplyr/vignettes/nse.Rmd | 12 dplyr-0.5.0/dplyr/vignettes/two-table.Rmd | 2 dplyr-0.5.0/dplyr/vignettes/window-functions.Rmd | 4 400 files changed, 8236 insertions(+), 7772 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between devtools versions 1.11.1 dated 2016-04-21 and 1.12.0 dated 2016-06-24
DESCRIPTION | 6 MD5 | 145 ++++++++-------- NAMESPACE | 27 +++ NEWS.md | 65 +++++++ R/aaa.r |only R/check-cran.r | 2 R/check-doc.r | 37 ++-- R/compile-dll.r | 5 R/deps.R | 205 ++++++++++++++--------- R/doctor.R | 2 R/download-method.R |only R/git.R | 33 +++ R/github.R | 38 +++- R/imports-env.r | 59 +++--- R/infrastructure-git.R | 39 +++- R/infrastructure.R | 52 +++++ R/install-bioc.r |only R/install-bitbucket.r | 24 +- R/install-cran.r |only R/install-git.r | 26 +- R/install-github.r | 42 ++-- R/install-local.r | 31 +++ R/install-remote.R | 121 ++++++++++++- R/install-svn.r | 86 +++++++-- R/install-url.r | 15 + R/install.r | 57 +++++- R/load-dll.r | 157 +++++------------ R/load.r | 21 +- R/namespace-env.r | 221 +++---------------------- R/release.r | 10 - R/revdep.R | 14 + R/rtools.r | 9 + R/run-source.r | 40 +++- R/unload.r | 16 + R/utils.r | 80 ++++++++- R/vignettes.r | 2 R/zzz.r | 8 README.md | 24 +- build/vignette.rds |binary inst/doc/dependencies.html | 4 inst/templates/codecov.yml |only inst/templates/revdep.R | 3 man/check_man.Rd | 1 man/dr_devtools.Rd | 2 man/infrastructure.Rd | 9 + man/install.Rd | 10 - man/install_bioc.Rd |only man/install_bitbucket.Rd | 10 - man/install_cran.Rd |only man/install_deps.Rd | 9 - man/install_git.Rd | 17 - man/install_github.Rd | 15 - man/install_svn.Rd | 10 - man/install_url.Rd | 10 - man/install_version.Rd | 10 - man/load_all.Rd | 5 man/package_deps.Rd | 9 - man/revdep_check.Rd | 8 man/source_gist.Rd | 13 + man/uninstall.Rd | 10 - man/update_packages.Rd | 7 man/use_github.Rd | 7 man/use_github_links.Rd | 11 + tests/testthat/infrastructure/DESCRIPTION | 3 tests/testthat/infrastructure/README.md | 9 - tests/testthat/infrastructure/Rbuildignore | 11 - tests/testthat/infrastructure/codecov.yml |only tests/testthat/infrastructure/cran-comments.md | 4 tests/testthat/infrastructure/data/x.rda |binary tests/testthat/infrastructure/revdep/check.R | 2 tests/testthat/infrastructure/travis.yml | 3 tests/testthat/test-bioconductor.r |only tests/testthat/test-extraction.R |only tests/testthat/test-git.R |only tests/testthat/test-github-connections.R | 17 + tests/testthat/test-remotes.r | 100 ++++++----- tests/testthat/test-update.R | 29 +-- tests/testthat/test-vignettes.r | 2 vignettes/dependencies.Rmd | 3 79 files changed, 1288 insertions(+), 794 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-08 1.0.1
2014-05-11 1.0.0
Title: Parse XML
Description: Work with XML files using a simple, consistent interface. Built on
top of the 'libxml2' C library.
Author: Hadley Wickham [aut, cre],
James Hester [aut],
Jeroen Ooms [ctb],
RStudio [cph],
R Foundation [ctb] (Copy of R-project homepage cached as example)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between xml2 versions 0.1.2 dated 2015-09-01 and 1.0.0 dated 2016-06-24
DESCRIPTION | 17 - MD5 | 121 +++++---- NAMESPACE | 78 ++++++ NEWS.md |only R/RcppExports.R | 100 +++++++- R/as_list.R | 5 R/classes.R | 56 ++++ R/utils.R | 31 ++ R/xml_attr.R | 97 +++++++ R/xml_children.R | 54 ++++ R/xml_find.R | 171 +++++++++++-- R/xml_modify.R |only R/xml_name.R | 30 ++ R/xml_namespaces.R | 21 + R/xml_parse.R | 122 +++++++++ R/xml_path.R | 4 R/xml_structure.R | 7 R/xml_text.R | 95 +++++++ R/xml_type.R | 5 R/xml_url.R | 5 R/xml_write.R | 18 - README.md | 13 - build |only inst/doc |only man/as_list.Rd | 2 man/read_xml.Rd | 43 +++ man/url_absolute.Rd | 2 man/url_escape.Rd | 2 man/url_parse.Rd | 2 man/write_xml.Rd | 6 man/xml_attr.Rd | 18 + man/xml_children.Rd | 27 ++ man/xml_find_all.Rd | 47 ++- man/xml_name-set.Rd |only man/xml_name.Rd | 2 man/xml_new_document.Rd |only man/xml_ns.Rd | 4 man/xml_ns_strip.Rd |only man/xml_path.Rd | 2 man/xml_replace.Rd |only man/xml_set_namespace.Rd |only man/xml_structure.Rd | 2 man/xml_text.Rd | 23 + man/xml_type.Rd | 2 man/xml_url.Rd | 2 src/Makevars.win | 15 - src/RcppExports.cpp | 290 ++++++++++++++++++++--- src/xml2_doc.cpp | 39 ++- src/xml2_namespace.cpp | 23 + src/xml2_node.cpp | 404 ++++++++++++++++++++++++++++++--- src/xml2_types.h | 8 src/xml2_url.cpp | 3 src/xml2_utils.h | 62 ++--- src/xml2_xpath.cpp | 93 +++---- tests/testthat/cd_catalog.xml.bz2 |only tests/testthat/ns-multiple-aliases.xml |only tests/testthat/test-format.R |only tests/testthat/test-modify-xml.R |only tests/testthat/test-namespaces.R | 22 + tests/testthat/test-read-xml.R | 40 +++ tests/testthat/test-url.R |only tests/testthat/test-xml_attrs.R | 113 +++++++++ tests/testthat/test-xml_children.R |only tests/testthat/test-xml_find.R | 91 +++++++ tests/testthat/test-xml_missing.R |only tests/testthat/test-xml_name.R | 20 + tests/testthat/test-xml_structure.R |only tests/testthat/test-xml_text.R |only tools/winlibs.R | 4 vignettes |only 70 files changed, 2106 insertions(+), 357 deletions(-)
Title: Google Search Console R Client
Description: Provides an interface with the Google Search Console,
formally called Google Webmaster Tools.
Author: Mark Edmondson [aut, cre],
Jennifer Bryan [ctb]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between searchConsoleR versions 0.2.0 dated 2016-04-03 and 0.2.1 dated 2016-06-24
DESCRIPTION | 8 +- MD5 | 16 ++-- R/getData.R | 80 ++++++++++++++++++++---- README.md | 119 +++++++++++++++---------------------- build/vignette.rds |binary inst/doc/searchConsoleR-intro.Rmd | 2 inst/doc/searchConsoleR-intro.html | 11 +-- man/search_analytics.Rd | 42 +++++++++++-- vignettes/searchConsoleR-intro.Rmd | 2 9 files changed, 172 insertions(+), 108 deletions(-)
More information about searchConsoleR at CRAN
Permanent link
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+extraDistr@gmail.com>
Diff between extraDistr versions 1.7.1 dated 2016-06-18 and 1.7.2 dated 2016-06-24
extraDistr-1.7.1/extraDistr/src/half-distributions.cpp |only extraDistr-1.7.2/extraDistr/DESCRIPTION | 8 extraDistr-1.7.2/extraDistr/MD5 | 148 +++++----- extraDistr-1.7.2/extraDistr/NEWS.md | 7 extraDistr-1.7.2/extraDistr/R/RcppExports.R | 48 ++- extraDistr-1.7.2/extraDistr/R/beta-binomial-distribution.R | 12 extraDistr-1.7.2/extraDistr/R/beta-negative-binomial-distribution.R | 16 - extraDistr-1.7.2/extraDistr/R/beta-prime-distribution.R | 10 extraDistr-1.7.2/extraDistr/R/bivariate-poisson-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/dirichlet-distribution.R | 3 extraDistr-1.7.2/extraDistr/R/dirichlet-multinomial-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/discrete-normal-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/discrete-uniform-distribution.R | 10 extraDistr-1.7.2/extraDistr/R/discrete-weibull-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/frechet-distribution.R | 10 extraDistr-1.7.2/extraDistr/R/gamma-poisson-distribution.R | 12 extraDistr-1.7.2/extraDistr/R/gev-distribution.R | 20 - extraDistr-1.7.2/extraDistr/R/gpd-distribution.R | 18 - extraDistr-1.7.2/extraDistr/R/gumbel-distribution.R | 10 extraDistr-1.7.2/extraDistr/R/half-cauchy-distribution.R | 8 extraDistr-1.7.2/extraDistr/R/half-normal-distribution.R | 8 extraDistr-1.7.2/extraDistr/R/half-t-distribution.R | 8 extraDistr-1.7.2/extraDistr/R/inverse-gamma-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/kumaraswamy-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/laplace-distribution.R | 14 extraDistr-1.7.2/extraDistr/R/mixture-of-normal-distributions.R | 2 extraDistr-1.7.2/extraDistr/R/mixture-of-poisson-distributions.R | 2 extraDistr-1.7.2/extraDistr/R/pareto-distribution.R | 4 extraDistr-1.7.2/extraDistr/R/proportion-distribution.R | 8 extraDistr-1.7.2/extraDistr/R/skellam-distribution.R | 2 extraDistr-1.7.2/extraDistr/R/truncated-normal-distribution.R | 10 extraDistr-1.7.2/extraDistr/man/BetaBinom.Rd | 10 extraDistr-1.7.2/extraDistr/man/BetaNegBinom.Rd | 16 - extraDistr-1.7.2/extraDistr/man/BetaPrime.Rd | 10 extraDistr-1.7.2/extraDistr/man/BivPoiss.Rd | 4 extraDistr-1.7.2/extraDistr/man/DirMnom.Rd | 4 extraDistr-1.7.2/extraDistr/man/Dirichlet.Rd | 2 extraDistr-1.7.2/extraDistr/man/DiscrWeibull.Rd | 4 extraDistr-1.7.2/extraDistr/man/DiscreteNormal.Rd | 4 extraDistr-1.7.2/extraDistr/man/DiscreteUniform.Rd | 7 extraDistr-1.7.2/extraDistr/man/Frechet.Rd | 10 extraDistr-1.7.2/extraDistr/man/GEV.Rd | 20 - extraDistr-1.7.2/extraDistr/man/GPD.Rd | 18 - extraDistr-1.7.2/extraDistr/man/GammaPoiss.Rd | 12 extraDistr-1.7.2/extraDistr/man/Gumbel.Rd | 10 extraDistr-1.7.2/extraDistr/man/InvGamma.Rd | 4 extraDistr-1.7.2/extraDistr/man/Kumaraswamy.Rd | 4 extraDistr-1.7.2/extraDistr/man/Laplace.Rd | 14 extraDistr-1.7.2/extraDistr/man/NormalMix.Rd | 2 extraDistr-1.7.2/extraDistr/man/Pareto.Rd | 4 extraDistr-1.7.2/extraDistr/man/PoissonMix.Rd | 2 extraDistr-1.7.2/extraDistr/man/PropBeta.Rd | 8 extraDistr-1.7.2/extraDistr/man/Skellam.Rd | 2 extraDistr-1.7.2/extraDistr/man/TruncNormal.Rd | 10 extraDistr-1.7.2/extraDistr/src/RcppExports.cpp | 138 ++++++++- extraDistr-1.7.2/extraDistr/src/beta-binomial-distribution.cpp | 10 extraDistr-1.7.2/extraDistr/src/beta-negative-binomial-distribution.cpp | 10 extraDistr-1.7.2/extraDistr/src/birnbaum-saunders-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/categorical-distribution.cpp | 72 ++-- extraDistr-1.7.2/extraDistr/src/const.h | 7 extraDistr-1.7.2/extraDistr/src/dirichlet-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/discrete-uniform-distribution.cpp | 15 - extraDistr-1.7.2/extraDistr/src/gamma-poisson-distribution.cpp | 10 extraDistr-1.7.2/extraDistr/src/half-cauchy-distribution.cpp |only extraDistr-1.7.2/extraDistr/src/half-normal-distribution.cpp |only extraDistr-1.7.2/extraDistr/src/half-t-distribution.cpp |only extraDistr-1.7.2/extraDistr/src/huber-distribution.cpp | 15 - extraDistr-1.7.2/extraDistr/src/logarithmic-series-distribution.cpp | 5 extraDistr-1.7.2/extraDistr/src/mixture-of-normal-distributions.cpp | 18 - extraDistr-1.7.2/extraDistr/src/mixture-of-poisson-distributions.cpp | 18 - extraDistr-1.7.2/extraDistr/src/multinomial-distribution.cpp | 14 extraDistr-1.7.2/extraDistr/src/non-standard-t-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/non-standart-beta-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/pareto-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/proportion-distribution.cpp | 2 extraDistr-1.7.2/extraDistr/src/shared.cpp | 2 extraDistr-1.7.2/extraDistr/src/slash-distribution.cpp | 5 77 files changed, 554 insertions(+), 400 deletions(-)
Title: JAR Dependencies for the XLConnect Package
Description: Provides external JAR dependencies for the XLConnect package.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] (Apache POI, Apache XMLBeans)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnectJars versions 0.2-9 dated 2014-08-14 and 0.2-12 dated 2016-06-24
XLConnectJars-0.2-12/XLConnectJars/DESCRIPTION | 14 +++++----- XLConnectJars-0.2-12/XLConnectJars/MD5 | 12 ++++---- XLConnectJars-0.2-12/XLConnectJars/NEWS | 3 ++ XLConnectJars-0.2-12/XLConnectJars/R/onLoad.R | 2 - XLConnectJars-0.2-12/XLConnectJars/inst/java/ooxml-schemas-1.3.jar |only XLConnectJars-0.2-12/XLConnectJars/java/README | 2 - XLConnectJars-0.2-12/XLConnectJars/man/XLConnectJars-package.Rd | 5 +-- XLConnectJars-0.2-9/XLConnectJars/inst/java/ooxml-schemas-1.1.jar |only 8 files changed, 20 insertions(+), 18 deletions(-)
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons
Codec),
Stephen Colebourne [ctb, cph] (Joda-Time Java library),
Graph Builder [ctb, cph] (Curvesapi Java library)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 0.2-11 dated 2015-03-01 and 0.2-12 dated 2016-06-24
XLConnect-0.2-11/XLConnect/inst/java/XLConnect-0.2-11.jar |only XLConnect-0.2-11/XLConnect/inst/java/commons-codec-1.9.jar |only XLConnect-0.2-11/XLConnect/inst/java/poi-3.12-beta1.jar |only XLConnect-0.2-11/XLConnect/inst/java/poi-ooxml-3.12-beta1.jar |only XLConnect-0.2-12/XLConnect/DESCRIPTION | 19 XLConnect-0.2-12/XLConnect/MD5 | 276 +++++---- XLConnect-0.2-12/XLConnect/NAMESPACE | 1 XLConnect-0.2-12/XLConnect/NEWS | 17 XLConnect-0.2-12/XLConnect/R/XLConnectSettings.R | 6 XLConnect-0.2-12/XLConnect/R/aref.R | 2 XLConnect-0.2-12/XLConnect/R/aref2idx.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.operators.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.setBorder.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.setDataFormat.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.setFillBackgroundColor.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.setFillForegroundColor.R | 2 XLConnect-0.2-12/XLConnect/R/cellstyle.setFillPattern.R | 2 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More information about VetResearchLMM at CRAN
Permanent link
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.7.4 dated 2016-03-24 and 1.8.0 dated 2016-06-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/TimeInstantDataFrame.R | 42 +++++++++++++++++++++++++++++++++++++++--- R/TimeIntervalDataFrame.R | 42 +++++++++++++++++++++++++++++++++++++++--- R/split.R | 4 ++-- README | 10 ++++++++++ man/timetools-package.Rd | 4 ++-- 7 files changed, 102 insertions(+), 20 deletions(-)
Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code, vignettes, or function documentation. There is a shared object containing part of the CVODES library, but it is not accessible from R. StanHeaders is only useful for developers who want to utilize the LinkingTo directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or variational methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, templated statistical and linear algebra functions that can handle the automatically differentiable scalar types (and doubles, ints, etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut],
Joshua Pritikin [ctb],
Andrew Gelman [aut],
Bob Carpenter [aut],
Matt Hoffman [aut],
Daniel Lee [aut],
Michael Betancourt [aut],
Marcus Brubaker [aut],
Jiqiang Guo [aut],
Peter Li [aut],
Allen Riddell [aut],
Marco Inacio [aut],
Mitzi Morris [aut],
Jeffrey Arnold [aut],
Rob Goedman [aut],
Brian Lau [aut],
Rob Trangucci [aut],
Jonah Gabry [aut],
Alp Kucukelbir [aut],
Robert Grant [aut],
Dustin Tran [aut],
Michael Malecki [aut],
Yuanjun Gao [aut],
Trustees of Columbia University [cph],
Lawrence Livermore National Security [cph] (CVODES),
The Regents of the University of California [cph] (CVODES),
Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between StanHeaders versions 2.10.0 dated 2016-06-22 and 2.10.0-2 dated 2016-06-24
StanHeaders-2.10.0-2/StanHeaders/DESCRIPTION | 8 StanHeaders-2.10.0-2/StanHeaders/MD5 | 82 +++++----- StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_band.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_bandpre.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_bbdpre.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_dense.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_diag.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_direct.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_klu.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_lapack.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_sparse.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_spbcgs.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_spgmr.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_spils.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_sptfqmr.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/cvodes/cvodes_superlumt.h |only StanHeaders-2.10.0-2/StanHeaders/inst/include/nvector |only StanHeaders-2.10.0-2/StanHeaders/inst/include/sundials |only StanHeaders-2.10.0-2/StanHeaders/src/Makevars | 6 StanHeaders-2.10.0-2/StanHeaders/src/Makevars.win | 6 StanHeaders-2.10.0/StanHeaders/inst/include/cvodes/cvodes |only StanHeaders-2.10.0/StanHeaders/inst/include/cvodes/nvector |only StanHeaders-2.10.0/StanHeaders/inst/include/cvodes/sundials |only 24 files changed, 51 insertions(+), 51 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of
classification, regression, survival and probability prediction trees are supported. Data from
genome-wide association studies can be analyzed efficiently. In addition to data frames, datasets of
class 'gwaa.data' (R package 'GenABEL') can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.4.0 dated 2016-04-07 and 0.5.0 dated 2016-06-24
DESCRIPTION | 20 - MD5 | 83 ++-- NAMESPACE | 2 NEWS | 8 R/RcppExports.R | 4 R/getTerminalNodeIDs.R | 2 R/holdoutRF.R |only R/importance.R | 89 ++++ R/predict.R | 78 ++-- R/print.R | 1 R/ranger.R | 228 +++++++++-- man/getTerminalNodeIDs.Rd | 2 man/holdoutRF.Rd |only man/importance.ranger.Rd | 6 man/importance_pvalues.Rd |only man/ranger.Rd | 58 ++ src/AAA_check_cpp11.cpp | 3 src/Forest.cpp | 102 +++-- src/Forest.h | 18 src/ForestProbability.cpp | 11 src/RcppExports.cpp | 9 src/Tree.cpp | 115 +++-- src/Tree.h | 8 src/TreeClassification.cpp | 4 src/TreeProbability.cpp | 142 ++++--- src/TreeProbability.h | 12 src/TreeRegression.cpp | 121 ++++++ src/TreeRegression.h | 9 src/TreeSurvival.cpp | 142 ++++++- src/TreeSurvival.h | 2 src/globals.h | 25 + src/rangerCpp.cpp | 4 src/utility.cpp | 302 +++++++++++++++ src/utility.h | 171 ++++++++ src/version.h | 2 tests/testthat/test_char.R |only tests/testthat/test_classification.R |only tests/testthat/test_csrf.R | 10 tests/testthat/test_importance.R |only tests/testthat/test_importance_pvalues.R |only tests/testthat/test_inbag.R |only tests/testthat/test_maxstat.R |only tests/testthat/test_predict.R |only tests/testthat/test_print.R |only tests/testthat/test_probability.R |only tests/testthat/test_ranger.R | 601 ++----------------------------- tests/testthat/test_regression.R |only tests/testthat/test_seed.R |only tests/testthat/test_splitweights.R |only tests/testthat/test_survival.R |only tests/testthat/test_unordered.R |only 51 files changed, 1496 insertions(+), 898 deletions(-)
Title: Random Effects Latent Class Analysis
Description: Fits standard and random effects latent class models. The single level random effects model is described in Qu et al <doi:10.2307/2533043> and the two level random effects model in Beath and Heller <doi:10.1177/1471082X0800900302>. Examples are given for their use in diagnostic testing.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between randomLCA versions 1.0-8 dated 2016-05-20 and 1.0-9 dated 2016-06-24
DESCRIPTION | 12 - MD5 | 28 +-- NAMESPACE | 1 R/fitAdaptRandom.R | 57 ++++--- R/fitAdaptRandom2.R | 79 ++++++---- R/fitFixed.R | 345 ++++++++++++++++++++++----------------------- R/outcomeProbs.R | 12 - R/randomLCA.R | 9 - build/vignette.rds |binary inst/NEWS | 12 + man/randomLCA.Rd | 2 src/bernoulliprob.c | 11 - src/bernoulliprobrandom.c | 18 +- src/bernoulliprobrandom2.c | 18 +- src/lcemalgorith.c | 21 +- 15 files changed, 340 insertions(+), 285 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more empirical distributions.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.2 dated 2016-02-08 and 1.3 dated 2016-06-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/final.plot.R | 10 ++++++---- R/overlap.R | 7 ++++--- man/cutnumeric.Rd | 2 +- man/overlap.Rd | 1 + 7 files changed, 28 insertions(+), 18 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Package also contains tools useful for performing Monte Carlo simulations
for studying the behaviour of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 0.8 dated 2016-02-24 and 0.9 dated 2016-06-24
DESCRIPTION | 12 ++--- MD5 | 36 ++++++++-------- NEWS.md | 6 ++ R/ShinyGUIClass.R | 10 ++++ R/findNextCATItem.R | 29 ++++++++----- R/generate.mirt_object.R | 2 R/generate_pattern.R | 4 - R/mirtCAT.R | 5 ++ R/selection_criteria.R | 74 +++++++++------------------------- R/server.R | 9 +--- R/util.R | 10 ++++ build/vignette.rds |binary man/findNextItem.Rd | 12 ++++- man/mirtCAT.Rd | 5 ++ tests/GUI-tests/GUI-tests.R | 5 ++ tests/tests/test-mirtCAT_classify.R | 10 ++-- tests/tests/test-mirtCAT_multi.R | 11 +---- tests/tests/test-mirtCAT_ordered.R | 20 ++++----- tests/tests/test-mirtCAT_uni.R | 78 ++++++++++++++++++------------------ 19 files changed, 178 insertions(+), 160 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.17.1 dated 2016-04-27 and 1.18 dated 2016-06-24
DESCRIPTION | 8 - MD5 | 96 +++++++++--------- NAMESPACE | 2 NEWS.md | 26 +++++ R/02-item_methods.R | 187 +++++++++++++++++++++--------------- R/03-estimation.R | 124 +++++++++++++++-------- R/DTF.R | 4 R/Discrete-methods.R | 6 - R/EMstep.group.R | 32 +++--- R/EMstep.utils.R | 45 ++++++-- R/LoadPars.R | 118 ++++++++++++---------- R/MHRM.group.R | 29 +++++ R/MultipleGroup-methods.R | 1 R/PLCI.mirt.R | 139 +++++++++++++++++++++----- R/PrepData.R | 46 ++++---- R/SE.methods.R | 21 ++-- R/SingleGroup-methods.R | 4 R/boot.LR.R |only R/createGroup.R |only R/createItem.R | 2 R/itemfit.R | 2 R/lagrange.R | 81 +++++++-------- R/mdirt.R | 29 ++--- R/mirt.R | 25 ++-- R/model.elements.R | 9 - R/simdata.R | 15 +- R/utils.R | 65 ++++++++++-- build/vignette.rds |binary man/DTF.Rd | 4 man/PLCI.mirt.Rd | 18 +++ man/boot.LR.Rd |only man/createGroup.Rd |only man/createItem.Rd | 2 man/lagrange.Rd | 44 +++----- man/mdirt.Rd | 22 +--- man/mirt.Rd | 23 +++- man/simdata.Rd | 2 src/Misc.cpp | 25 ++++ src/dpars.cpp | 80 +++++++++++++-- src/traceLinePts.cpp | 16 +-- src/traceLinePts.h | 2 tests/extratests/test-02-wideData.R | 6 - tests/tests/test-01-mirtOne.R | 2 tests/tests/test-02-mirtTwo.R | 8 - tests/tests/test-03-bfactor.R | 10 - tests/tests/test-04-multipleGroup.R | 40 +++---- tests/tests/test-06-confmirtTwo.R | 14 +- tests/tests/test-07-mixedmirt.R | 34 +++--- tests/tests/test-09-mirt.model.R | 5 tests/tests/test-10-extras.R | 31 ++--- tests/tests/test-11-discrete.R | 17 +-- 51 files changed, 964 insertions(+), 557 deletions(-)
Title: A Future API for R
Description: A Future API for R is provided. In programming, a future is an
abstraction for a value that may be available at some point in the future.
The state of a future can either be unresolved or resolved. As soon as it is
resolved, the value is available. Futures are useful constructs in for instance
concurrent evaluation, e.g. parallel processing and distributed processing on
compute clusters. The purpose of this package is to provide a lightweight
interface for using futures in R. Functions 'future()' and 'value()' exist for
creating futures and requesting their values, e.g.
'f <- future({ mandelbrot(-0.75, 0, side=3) })' and 'v <- value(f)'.
The 'resolved()' function can be used to check if a future is resolved or not.
An infix assignment operator '%<-%' exists for creating futures whose values
are accessible by the assigned variables (as promises), e.g.
'v %<-% { mandelbrot(-0.75, 0, side=3) }'.
This package implements synchronous "lazy" and "eager" futures, and asynchronous
"multicore", "multisession" and ad hoc "cluster" futures.
Globals variables and functions are automatically identified and exported.
Required packages are attached in external R sessions whenever needed.
All types of futures are designed to behave the same such that the exact
same code work regardless of futures used or number of cores, background
sessions or cluster nodes available.
Additional types of futures are provided by other packages enhancing
this package.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 0.15.0 dated 2016-06-14 and 1.0.0 dated 2016-06-24
future-0.15.0/future/tests/parseCmdArgs.R |only future-1.0.0/future/DESCRIPTION | 10 future-1.0.0/future/MD5 | 150 +++---- future-1.0.0/future/NAMESPACE | 10 future-1.0.0/future/NEWS | 35 + future-1.0.0/future/R/ClusterFuture-class.R | 12 future-1.0.0/future/R/ClusterRegistry.R | 2 future-1.0.0/future/R/Future-class.R | 40 + future-1.0.0/future/R/availableCores.R | 4 future-1.0.0/future/R/globals.R | 36 + future-1.0.0/future/R/mandelbrot.R |only future-1.0.0/future/R/multicore.R | 14 future-1.0.0/future/R/options.R |only future-1.0.0/future/R/plan.R | 66 ++- future-1.0.0/future/R/remote.R | 23 - future-1.0.0/future/R/resolve.R | 46 -- future-1.0.0/future/R/tweak.R | 6 future-1.0.0/future/R/utils.R | 159 +++++++ future-1.0.0/future/R/zzz.R | 81 +++ future-1.0.0/future/build/vignette.rds |binary future-1.0.0/future/demo/mandelbrot.R | 222 +++------- future-1.0.0/future/inst/doc/future-1-overview.html | 131 ++---- future-1.0.0/future/inst/doc/future-2-issues.html | 169 +++----- future-1.0.0/future/inst/doc/future-2-issues.md.rsp | 232 +++++++---- future-1.0.0/future/man/availableCores.Rd | 2 future-1.0.0/future/man/future.options.Rd |only future-1.0.0/future/man/mandelbrot.Rd |only future-1.0.0/future/man/plan.Rd | 63 ++ future-1.0.0/future/man/requestCore.Rd | 8 future-1.0.0/future/man/resolve.Rd | 2 future-1.0.0/future/tests/ClusterRegistry.R | 22 - future-1.0.0/future/tests/Future-class.R | 30 - future-1.0.0/future/tests/FutureError.R | 11 future-1.0.0/future/tests/FutureRegistry.R | 13 future-1.0.0/future/tests/availableCores.R | 44 +- future-1.0.0/future/tests/backtrace.R | 11 future-1.0.0/future/tests/cluster.R | 16 future-1.0.0/future/tests/constant.R | 13 future-1.0.0/future/tests/demo.R | 11 future-1.0.0/future/tests/deprecated.R |only future-1.0.0/future/tests/dotdotdot.R | 11 future-1.0.0/future/tests/eager.R | 11 future-1.0.0/future/tests/early-signaling.R | 11 future-1.0.0/future/tests/flapply.R | 20 future-1.0.0/future/tests/future.R | 53 ++ future-1.0.0/future/tests/futureAssign.R | 12 future-1.0.0/future/tests/futureAssign_OP.R | 13 future-1.0.0/future/tests/futureAssign_OP_with_environment.R | 10 future-1.0.0/future/tests/futureAssign_OP_with_listenv.R | 12 future-1.0.0/future/tests/futureCall.R | 12 future-1.0.0/future/tests/futureOf.R | 12 future-1.0.0/future/tests/futureOf_with_environment.R | 14 future-1.0.0/future/tests/futureOf_with_listenv.R | 10 future-1.0.0/future/tests/futures.R | 12 future-1.0.0/future/tests/globals,NSE.R |only future-1.0.0/future/tests/globals,resolve.R | 10 future-1.0.0/future/tests/globals,toolarge.R |only future-1.0.0/future/tests/globals,tricky.R | 21 future-1.0.0/future/tests/globalsOf,tweaks.R | 12 future-1.0.0/future/tests/incl |only future-1.0.0/future/tests/invalid-owner.R | 10 future-1.0.0/future/tests/lazy.R | 24 - future-1.0.0/future/tests/mandelbrot.R |only future-1.0.0/future/tests/multicore.R | 10 future-1.0.0/future/tests/multiprocess.R | 15 future-1.0.0/future/tests/multisession.R | 15 future-1.0.0/future/tests/nbrOfWorkers.R | 13 future-1.0.0/future/tests/nested_futures,mc.cores.R | 10 future-1.0.0/future/tests/plan.R | 13 future-1.0.0/future/tests/remote.R | 21 future-1.0.0/future/tests/requestCore.R | 27 - future-1.0.0/future/tests/requestNode.R |only future-1.0.0/future/tests/resolve.R | 62 ++ future-1.0.0/future/tests/rng.R | 12 future-1.0.0/future/tests/startup.R |only future-1.0.0/future/tests/transparent.R | 11 future-1.0.0/future/tests/tweak.R | 7 future-1.0.0/future/tests/utils.R | 66 ++- future-1.0.0/future/tests/uuid.R | 14 future-1.0.0/future/tests/whichIndex.R | 5 future-1.0.0/future/vignettes/future-2-issues.md.rsp | 232 +++++++---- 81 files changed, 1454 insertions(+), 1063 deletions(-)
Title: Data Representation: Bayesian Approach That's Sparse
Description: Feed longitudinal data into a Bayesian Latent Factor Model to obtain a low-rank representation. Parameters are estimated using a Hamiltonian Monte Carlo algorithm with STAN. See G. Weinrott, B. Fontez, N. Hilgert and S. Holmes, "Bayesian Latent Factor Model for Functional Data Analysis", Actes des JdS 2016.
Author: Gabrielle Weinrott [aut, cre],
Brigitte Charnomordic [aut],
Benedicte Fontez [aut],
Nadine Hilgert [aut],
Susan Holmes [aut]
Maintainer: Gabrielle Weinrott <gabrielle.weinrott@supagro.inra.fr>
Diff between DrBats versions 0.1.3 dated 2016-05-18 and 0.1.4 dated 2016-06-24
DrBats-0.1.3/DrBats/R/visualize.R |only DrBats-0.1.3/DrBats/man/clean.mcmc.Rd |only DrBats-0.1.3/DrBats/man/interval.pca.Deville.Rd |only DrBats-0.1.3/DrBats/man/main.modelFit.Rd |only DrBats-0.1.4/DrBats/DESCRIPTION | 8 DrBats-0.1.4/DrBats/MD5 | 36 - DrBats-0.1.4/DrBats/NAMESPACE | 2 DrBats-0.1.4/DrBats/R/dimRed.R | 69 --- DrBats-0.1.4/DrBats/R/modelEval.R | 400 +++++++++++++++------- DrBats-0.1.4/DrBats/R/modelFit.R | 369 +++++++++----------- DrBats-0.1.4/DrBats/R/simul.R | 39 ++ DrBats-0.1.4/DrBats/data/stanfit.rda |binary DrBats-0.1.4/DrBats/data/toydata.rda |binary DrBats-0.1.4/DrBats/man/calc.loglik.Rd | 2 DrBats-0.1.4/DrBats/man/modelFit.Rd | 11 DrBats-0.1.4/DrBats/man/postdens.Rd | 23 - DrBats-0.1.4/DrBats/man/visW.Rd | 31 - DrBats-0.1.4/DrBats/man/visbeta.Rd | 25 - DrBats-0.1.4/DrBats/vignettes/DrBats.Rmd | 41 -- DrBats-0.1.4/DrBats/vignettes/ModelEvaluation.Rmd | 28 - DrBats-0.1.4/DrBats/vignettes/ModelFit.Rmd | 41 -- 21 files changed, 571 insertions(+), 554 deletions(-)
Title: Detecting Breakpoints and Estimating Segments in Trend
Description: A program for analyzing vegetation time series, with two algorithms: 1) change detection algorithm that detects trend changes, determines their type (abrupt or non-abrupt), and estimates their timing, magnitude, number, and direction; 2) generalization algorithm that simplifies the temporal trend into main features. The user can set the number of major breakpoints or magnitude of greatest changes of interest for detection, and can control the generalization process by setting an additional parameter of generalization-percentage.
Author: Sadegh Jamali, Hristo Tomov
Maintainer: Hristo Tomov <tomov.hristo@gmail.com>
Diff between DBEST versions 1.2 dated 2016-06-15 and 1.3 dated 2016-06-24
DESCRIPTION | 8 +-- MD5 | 8 ++- data/TREND.Site1.rda |only data/TREND.Site2.rda |only man/DBEST.Rd | 127 +++++++++++++++++++++++++++++---------------------- man/TREND.Site1.Rd |only man/TREND.Site2.Rd |only 7 files changed, 83 insertions(+), 60 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 0.4-5 dated 2015-08-17 and 0.4-7 dated 2016-06-24
ASMap-0.4-5/ASMap/R/mstmap10.R |only ASMap-0.4-7/ASMap/DESCRIPTION | 8 +++---- ASMap-0.4-7/ASMap/MD5 | 27 +++++++++++++------------- ASMap-0.4-7/ASMap/NAMESPACE | 4 ++- ASMap-0.4-7/ASMap/R/mstmap11.R |only ASMap-0.4-7/ASMap/build/vignette.rds |binary ASMap-0.4-7/ASMap/inst/NEWS.Rd | 4 +++ ASMap-0.4-7/ASMap/inst/doc/asmapvignette.Rnw | 4 +-- ASMap-0.4-7/ASMap/man/alignCross.Rd |only ASMap-0.4-7/ASMap/man/profileGen.Rd | 3 +- ASMap-0.4-7/ASMap/man/profileMark.Rd | 3 +- ASMap-0.4-7/ASMap/man/statGen.Rd | 2 - ASMap-0.4-7/ASMap/man/statMark.Rd | 2 - ASMap-0.4-7/ASMap/src/MSTOpt.cpp | 26 +++++++++++++------------ ASMap-0.4-7/ASMap/src/linkage_group_DH.cpp | 4 +-- ASMap-0.4-7/ASMap/vignettes/asmapvignette.Rnw | 4 +-- 16 files changed, 51 insertions(+), 40 deletions(-)
Title: Stereological Unfolding for Spheroidal Particles
Description: Stereological unfolding as implemented in this package consists in
the estimation of the joint size-shape-orientation distribution of spheroidal
shaped particles based on the same measured quantities of corresponding planar
section profiles. A single trivariate discretized version of the (stereological)
integral equation in the case of prolate and oblate spheroids is solved
numerically by the EM algorithm. The estimation of diameter distribution of
spheres from planar sections (Wicksell's corpuscle problem) is also implemented.
Further, the package provides routines for the simulation of a Poisson germ-
grain process with either spheroids, spherocylinders or spheres as grains together
with functions for planar sections. For the purpose of exact simulation a bivariate size-shape
distribution is implemented.
Author: Markus Baaske [aut, cre], Felix Ballani [ctb]
Maintainer: Markus Baaske <markus.baaske@math.tu-freiberg.de>
Diff between unfoldr versions 0.5.6 dated 2016-06-22 and 0.5.7 dated 2016-06-24
DESCRIPTION | 6 ++-- MD5 | 18 +++++++------- src/Intersector.cpp | 57 +++++++++++++++++++++++---------------------- src/Intersector.h | 64 +++++++++++++++++++++++++++------------------------ src/SimCylinder.cpp | 20 +++++++-------- src/SimCylinder.h | 2 - src/SimEllipsoid.cpp | 39 +++++++++++++++---------------- src/SimEllipsoid.h | 2 - src/SimSphere.cpp | 14 +++++------ src/SimSphere.h | 2 - 10 files changed, 115 insertions(+), 109 deletions(-)
Title: 'dplyr' Functionality for Matched Tree and Data Objects
Description: Matches phylogenetic trees and trait data, and
allows simultaneous manipulation of the tree and data using 'dplyr'.
Author: Josef Uyeda
Maintainer: Josef Uyeda <josef.uyeda@gmail.com>
Diff between treeplyr versions 0.1.1 dated 2016-03-31 and 0.1.2 dated 2016-06-24
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NAMESPACE | 2 R/treeplyr_functions.R | 113 +++++++++++++++++++++++++++++++++++++++-------- man/getVector.Rd | 4 - man/treedply.treedata.Rd | 6 +- 6 files changed, 114 insertions(+), 31 deletions(-)
Title: Calculate Accurate Precision-Recall and Receiver Operator
Characteristics Curves
Description: Accurate calculations and visualization of Precision-Recall and Receiver Operator Characteristics
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.3.2 dated 2016-04-13 and 0.4.0 dated 2016-06-24
DESCRIPTION | 10 MD5 | 81 ++-- NAMESPACE | 8 R/RcppExports.R | 4 R/etc_utils_autoplot.R | 79 +++- R/etc_utils_dataframe.R |only R/etc_utils_fortify.R | 127 ------- R/etc_utils_plot.R | 127 ++++++- R/etc_utils_validate_args.R | 6 R/g_autoplot.R | 40 +- R/g_dataframe.R |only R/g_fortify.R | 43 +- R/g_plot.R | 12 R/g_print.R | 19 - R/main_evalmod.R | 5 R/mm3_reformat_data.R | 3 R/pl2_pipeline_main_basic.R | 35 +- R/pl3_create_confmats.R | 4 R/pl4_calc_measures.R | 40 ++ R/pl6_calc_average.R | 10 README.md | 29 - build/vignette.rds |binary inst/doc/introduction.R | 54 ++- inst/doc/introduction.Rmd | 102 +++++- inst/doc/introduction.html | 416 +++++++++++++++++++++++-- man/as.data.frame.Rd |only man/autoplot.Rd | 38 +- man/evalmod.Rd | 5 man/fortify.Rd | 16 man/plot.Rd | 22 - src/RcppExports.cpp | 8 src/calc_avg_point.cpp | 10 src/calc_basic_measures.cpp | 29 + src/create_confusion_matrices.cpp | 6 src/create_prc_curve.cpp | 2 src/create_roc_curve.cpp | 2 tests/testthat/test_g_autoplot3_points.R | 16 tests/testthat/test_g_datamatrix1_curves.R |only tests/testthat/test_g_datamatrix2_points.R |only tests/testthat/test_mm3_3_reformat_data_main.R | 6 tests/testthat/test_pl2_1_pl_main_basic.R | 67 ++++ tests/testthat/test_pl4_1_calc_measures.R | 45 ++ tests/testthat/test_pl6_1_calc_avg_points.R | 90 +++++ vignettes/introduction.Rmd | 102 +++++- 44 files changed, 1293 insertions(+), 425 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.5-20 dated 2016-03-06 and 0.5-38 dated 2016-06-24
DESCRIPTION | 12 +- MD5 | 71 ++++++++------- NAMESPACE | 28 +++--- R/backbonePhylo.R | 198 ++++++++++++++++++++++++++++++++++++-------- R/collapseTree.R | 3 R/consensus.edges.R |only R/contMap.R | 3 R/cophylo.R | 39 ++++++-- R/densityMap.R | 9 +- R/densityTree.R | 12 +- R/dotTree.R | 100 ++++++++++++++-------- R/evol.vcv.R | 183 +++++++++++++++++++++++----------------- R/fitMk.R | 88 +++++++++++++++++++ R/fitPagel.R | 216 ++++++++++++++++++++++++++++++++++++++++++++---- R/ls.consensus.R |only R/map.overlap.R | 70 +++++++++++++-- R/phylo.to.map.R | 120 +++++++++++++++++--------- R/plotSimmap.R | 33 ++++--- R/roundPhylogram.R | 17 ++- R/sim.history.R | 72 ++++++++++------ R/utilities.R | 126 ++++++++++++++++++++++++---- man/as.multiPhylo.Rd |only man/averageTree.Rd |only man/bind.tree.simmap.Rd |only man/consensus.edges.Rd |only man/cophylo.Rd | 2 man/densityTree.Rd | 7 + man/describe.simmap.Rd | 18 ++-- man/dotTree.Rd | 2 man/fitMk.Rd | 12 ++ man/fitPagel.Rd | 17 ++- man/map.overlap.Rd | 14 ++- man/mapped.states.Rd |only man/matchNodes.Rd | 4 man/multiC.Rd | 3 man/phenogram.Rd | 2 man/phylo.to.map.Rd | 6 - man/plotSimmap.Rd | 8 + man/roundPhylogram.Rd | 3 man/sim.history.Rd | 2 40 files changed, 1144 insertions(+), 356 deletions(-)
Title: Latent Variable Analysis with Shiny
Description: Interactive shiny application for working with different kinds of
latent variable analysis, with the 'lavaan' package. Graphical output for models
are provided and different estimators are supported.
Author: W. Kyle Hamilton <kyle.hamilton@gmail.com>
Maintainer: W. Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between lavaan.shiny versions 1.0 dated 2016-03-04 and 1.1 dated 2016-06-24
DESCRIPTION | 12 +-- MD5 | 8 +- NEWS |only README.md |only inst/shiny/server.R | 151 +++++++++++++++++++-------------------- inst/shiny/ui.R | 201 +++++++++++++++++++++++++++++++++------------------- 6 files changed, 215 insertions(+), 157 deletions(-)
Title: Download and Process Public Domain Works from Project Gutenberg
Description: Download and process public domain works in the Project
Gutenberg collection. Includes metadata for all Project Gutenberg works,
so that they can be searched and retrieved.
Author: David Robinson [aut, cre]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between gutenbergr versions 0.1.1 dated 2016-05-16 and 0.1.2 dated 2016-06-24
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/gutenberg_download.R | 6 +++--- R/gutenberg_works.R | 6 +++++- inst/doc/intro.html | 4 ++-- tests/testthat/test-download.R | 2 +- 7 files changed, 27 insertions(+), 18 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <niedballa@izw-berlin.de>
Diff between camtrapR versions 0.99.1 dated 2016-05-18 and 0.99.2 dated 2016-06-24
DESCRIPTION | 8 - MD5 | 42 +++--- NEWS | 13 ++ R/cameraOperation.R | 74 +++++++----- R/detectionHistory.R | 2 R/recordTable.R | 6 build/vignette.rds |binary inst/doc/DataExploration.R | 40 ++++++ inst/doc/DataExploration.Rmd | 50 +++++++- inst/doc/DataExploration.html | 73 +++++++++++- inst/doc/DataExtraction.R | 7 + inst/doc/DataExtraction.Rmd | 14 ++ inst/doc/DataExtraction.html | 157 ++++++++++++++------------ inst/doc/ImageOrganisation.Rmd | 26 +++- inst/doc/ImageOrganisation.html | 105 +++++++++++++---- inst/doc/SpeciesIndividualIdentification.html | 88 +++++++------- man/cameraOperation.Rd | 4 man/detectionHistory.Rd | 4 man/spatialDetectionHistory.Rd | 2 vignettes/DataExploration.Rmd | 50 +++++++- vignettes/DataExtraction.Rmd | 14 ++ vignettes/ImageOrganisation.Rmd | 26 +++- 22 files changed, 585 insertions(+), 220 deletions(-)
Title: Binary Logic
Description: Convert to binary numbers (Base2). Shift, rotate, summary. Based on logical vector.
Author: Daniel Dörrhöfer <ddo@openmailbox.org>
Maintainer: Daniel Dörrhöfer <ddo@openmailbox.org>
Diff between binaryLogic versions 0.3.4 dated 2016-03-29 and 0.3.5 dated 2016-06-24
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/BinaryS3.R | 26 ++++++++++++++++-- README.md | 52 +++++++++++++++++++------------------ tests/testthat/test-binOperators.R | 19 +++++++++++++ 5 files changed, 77 insertions(+), 34 deletions(-)