Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <https://curl.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between RCurl versions 1.98-1.7 dated 2022-06-09 and 1.98-1.8 dated 2022-07-30
DESCRIPTION | 6 +++--- MD5 | 38 +++++++++++++++++++------------------- data/mimeTypeExtensions.rda |binary inst/doc/philosophy.html | 36 ++++++++++++++++++------------------ inst/doc/withCookies.html | 22 +++++++++++----------- man/MultiCURLHandle-class.Rd | 2 +- man/basicHeaderGatherer.Rd | 4 ++-- man/basicTextGatherer.Rd | 20 ++++++++++---------- man/binaryBuffer.Rd | 4 ++-- man/chunkToLineReader.Rd | 8 +++++--- man/curlPerform.Rd | 8 ++++---- man/curlSetOpt.Rd | 4 ++-- man/dynCurlReader.Rd | 8 ++++---- man/getBinaryURL.Rd | 2 +- man/getCurlHandle.Rd | 6 +++--- man/getCurlInfo.Rd | 4 ++-- man/getFormParams.Rd | 4 ++-- man/getURIAsynchronous.Rd | 6 +++--- man/getURL.Rd | 38 +++++++++++++++++++------------------- man/url.exists.Rd | 4 ++-- 20 files changed, 113 insertions(+), 111 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] ,
Albrecht Gebhardt [trl] ,
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-58 dated 2022-07-14 and 7.3-58.1 dated 2022-07-27
MASS-7.3-58.1/MASS/ChangeLog | 7 ++++++- MASS-7.3-58.1/MASS/DESCRIPTION | 12 +++++------- MASS-7.3-58.1/MASS/tests/glmmPQL.R | 6 +++++- MASS-7.3-58.1/MASS/tests/polr.R | 2 ++ MASS-7.3-58.1/MASS/tests/solr.rda |only MASS-7.3-58/MASS/MD5 |only 6 files changed, 18 insertions(+), 9 deletions(-)
Title: Statistical Inference in High Dimensional Regression
Description: Inference procedures in the high-dimensional setting for
(1) linear functionals in generalized linear regression ('Cai et al.' (2019) <arXiv:1904.12891>, 'Guo et al.' (2020) <arXiv:2012.07133>, 'Cai et al.' (2021)),
(2) individual treatment effects in generalized linear regression,
(3) quadratic functionals in linear regression ('Guo et al.' (2019) <arXiv:1909.01503>).
Author: Prabrisha Rakshit, Zhenyu Wang, Tony Cai, Zijian Guo
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between SIHR versions 0.2.0 dated 2021-10-07 and 1.0.0 dated 2022-07-25
SIHR-0.2.0/SIHR/R/GLM_binary.R |only SIHR-0.2.0/SIHR/R/LF_linear.R |only SIHR-0.2.0/SIHR/R/LF_logistic.R |only SIHR-0.2.0/SIHR/R/Source_GLM.R |only SIHR-0.2.0/SIHR/R/Source_Linear.R |only SIHR-0.2.0/SIHR/build |only SIHR-0.2.0/SIHR/inst/REFERENCES.bib |only SIHR-0.2.0/SIHR/inst/doc |only SIHR-0.2.0/SIHR/man/Direction_fixedtuning.Rd |only SIHR-0.2.0/SIHR/man/Direction_searchtuning.Rd |only SIHR-0.2.0/SIHR/man/GLM_binary.Rd |only SIHR-0.2.0/SIHR/man/ITE_Logistic.Rd |only SIHR-0.2.0/SIHR/man/LF_logistic.Rd |only SIHR-0.2.0/SIHR/vignettes |only SIHR-1.0.0/SIHR/DESCRIPTION | 26 SIHR-1.0.0/SIHR/MD5 | 50 - SIHR-1.0.0/SIHR/NAMESPACE | 46 - SIHR-1.0.0/SIHR/R/ITE.R |only SIHR-1.0.0/SIHR/R/LF.R |only SIHR-1.0.0/SIHR/R/Methods.R |only SIHR-1.0.0/SIHR/R/Projection_Directions.R | 178 ++--- SIHR-1.0.0/SIHR/R/QF.R | 377 +++++------ SIHR-1.0.0/SIHR/R/check.R |only SIHR-1.0.0/SIHR/R/helpers.R |only SIHR-1.0.0/SIHR/README.md | 858 +++++++++++--------------- SIHR-1.0.0/SIHR/inst/references.bib |only SIHR-1.0.0/SIHR/man/ITE.Rd | 146 ++-- SIHR-1.0.0/SIHR/man/LF.Rd | 114 +-- SIHR-1.0.0/SIHR/man/QF.Rd | 108 +-- SIHR-1.0.0/SIHR/man/ci.ITE.Rd |only SIHR-1.0.0/SIHR/man/ci.LF.Rd |only SIHR-1.0.0/SIHR/man/ci.QF.Rd |only SIHR-1.0.0/SIHR/man/ci.Rd |only SIHR-1.0.0/SIHR/man/print.summary.ITE.Rd |only SIHR-1.0.0/SIHR/man/print.summary.LF.Rd |only SIHR-1.0.0/SIHR/man/print.summary.QF.Rd |only SIHR-1.0.0/SIHR/man/summary.ITE.Rd |only SIHR-1.0.0/SIHR/man/summary.LF.Rd |only SIHR-1.0.0/SIHR/man/summary.QF.Rd |only 39 files changed, 885 insertions(+), 1018 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' can do more, is easier to use, and it is faster.
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Karl Forner [ctb],
Jeroen Ooms [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.5-34 dated 2022-06-09 and 1.6-3 dated 2022-07-25
terra-1.5-34/terra/R/gridDistance.R |only terra-1.5-34/terra/man/subset-vector.Rd |only terra-1.6-3/terra/DESCRIPTION | 11 terra-1.6-3/terra/MD5 | 417 ++++++++-------- terra-1.6-3/terra/NAMESPACE | 3 terra-1.6-3/terra/NEWS.md | 47 + terra-1.6-3/terra/R/Agenerics.R | 25 terra-1.6-3/terra/R/Arith_generics.R | 91 +-- terra-1.6-3/terra/R/RGB.R | 16 terra-1.6-3/terra/R/SpatRasterDataset.R | 20 terra-1.6-3/terra/R/SpatVectorCollection.R | 8 terra-1.6-3/terra/R/Zdeprecated.R | 17 terra-1.6-3/terra/R/aggregate.R | 74 +- terra-1.6-3/terra/R/animate.R | 2 terra-1.6-3/terra/R/app.R | 36 - terra-1.6-3/terra/R/approximate.R | 6 terra-1.6-3/terra/R/arith.R | 4 terra-1.6-3/terra/R/autocor.R | 22 terra-1.6-3/terra/R/cells.R | 24 terra-1.6-3/terra/R/clean.R | 2 terra-1.6-3/terra/R/click.R | 26 terra-1.6-3/terra/R/coerce.R | 242 +++++---- terra-1.6-3/terra/R/colors.R | 48 + terra-1.6-3/terra/R/crosstab.R | 10 terra-1.6-3/terra/R/crs.R | 47 - terra-1.6-3/terra/R/deprecated.R |only terra-1.6-3/terra/R/dimensions.R | 52 - terra-1.6-3/terra/R/distance.R | 28 - terra-1.6-3/terra/R/draw.R | 16 terra-1.6-3/terra/R/expand.R | 4 terra-1.6-3/terra/R/extent.R | 140 ++--- terra-1.6-3/terra/R/extract.R | 79 +-- terra-1.6-3/terra/R/focal.R | 12 terra-1.6-3/terra/R/gcp.R | 6 terra-1.6-3/terra/R/gdal.R | 8 terra-1.6-3/terra/R/generics.R | 421 +++++++++------- terra-1.6-3/terra/R/geom.R | 237 +++++++-- terra-1.6-3/terra/R/hist.R | 18 terra-1.6-3/terra/R/ifelse.R | 8 terra-1.6-3/terra/R/image.R | 4 terra-1.6-3/terra/R/init.R | 4 terra-1.6-3/terra/R/inset.R | 10 terra-1.6-3/terra/R/interpolate.R | 6 terra-1.6-3/terra/R/lapp.R | 38 + terra-1.6-3/terra/R/layerCor.R | 2 terra-1.6-3/terra/R/levels.R | 207 +++---- terra-1.6-3/terra/R/lines.R | 6 terra-1.6-3/terra/R/makeVRT.R | 40 - terra-1.6-3/terra/R/match.R | 5 terra-1.6-3/terra/R/math.R | 14 terra-1.6-3/terra/R/merge.R | 23 terra-1.6-3/terra/R/mergeTime.R | 26 terra-1.6-3/terra/R/messages.R | 10 terra-1.6-3/terra/R/names.R | 73 +- terra-1.6-3/terra/R/ncdf.R | 70 +- terra-1.6-3/terra/R/options.R | 24 terra-1.6-3/terra/R/pack.R | 62 +- terra-1.6-3/terra/R/plot.R | 44 - terra-1.6-3/terra/R/plot2rasters.R | 8 terra-1.6-3/terra/R/plotExtent.R | 8 terra-1.6-3/terra/R/plotRGB.R | 10 terra-1.6-3/terra/R/plot_cartogram.R | 2 terra-1.6-3/terra/R/plot_legend.R | 18 terra-1.6-3/terra/R/plot_let.R |only terra-1.6-3/terra/R/plot_raster.R | 172 ++++-- terra-1.6-3/terra/R/plot_scale.R | 30 - terra-1.6-3/terra/R/plot_vector.R | 131 +++-- terra-1.6-3/terra/R/predict.R | 16 terra-1.6-3/terra/R/rapp.R | 8 terra-1.6-3/terra/R/rast.R | 109 ++-- terra-1.6-3/terra/R/rasterize.R | 39 - terra-1.6-3/terra/R/read.R | 10 terra-1.6-3/terra/R/readsvg.R | 2 terra-1.6-3/terra/R/relate.R | 34 - terra-1.6-3/terra/R/replace.R | 103 ++- terra-1.6-3/terra/R/sample.R | 89 +-- terra-1.6-3/terra/R/select.R | 6 terra-1.6-3/terra/R/selectHigh.R | 2 terra-1.6-3/terra/R/show.R | 116 ++-- terra-1.6-3/terra/R/spatDF.R | 80 ++- terra-1.6-3/terra/R/spatvec.R | 60 +- terra-1.6-3/terra/R/subset.R | 152 ++++- terra-1.6-3/terra/R/tapp.R | 41 + terra-1.6-3/terra/R/tempfiles.R | 6 terra-1.6-3/terra/R/tiles.R | 4 terra-1.6-3/terra/R/time.R | 133 ++++- terra-1.6-3/terra/R/values.R | 97 +-- terra-1.6-3/terra/R/vect.R | 120 ++-- terra-1.6-3/terra/R/window.R | 4 terra-1.6-3/terra/R/write.R | 20 terra-1.6-3/terra/R/zonal.R | 96 +++ terra-1.6-3/terra/R/zoom.R | 18 terra-1.6-3/terra/R/zzz.R | 2 terra-1.6-3/terra/inst/tinytest/test_cats.R | 22 terra-1.6-3/terra/inst/tinytest/test_extract.R | 102 +++ terra-1.6-3/terra/man/RGB.Rd | 6 terra-1.6-3/terra/man/aggregate.Rd | 3 terra-1.6-3/terra/man/as.list.Rd | 11 terra-1.6-3/terra/man/as.spatvector.Rd | 10 terra-1.6-3/terra/man/catalyze.Rd | 2 terra-1.6-3/terra/man/cellSize.Rd | 3 terra-1.6-3/terra/man/centroids.Rd | 2 terra-1.6-3/terra/man/coerce.Rd | 5 terra-1.6-3/terra/man/colors.Rd | 10 terra-1.6-3/terra/man/combineGeoms.Rd |only terra-1.6-3/terra/man/concats.Rd |only terra-1.6-3/terra/man/cover.Rd | 4 terra-1.6-3/terra/man/crop.Rd | 9 terra-1.6-3/terra/man/crs.Rd | 3 terra-1.6-3/terra/man/deprecated.Rd | 9 terra-1.6-3/terra/man/distance.Rd | 3 terra-1.6-3/terra/man/erase.Rd | 16 terra-1.6-3/terra/man/ext.Rd | 2 terra-1.6-3/terra/man/extract.Rd | 11 terra-1.6-3/terra/man/factors.Rd | 49 - terra-1.6-3/terra/man/focalCpp.Rd | 4 terra-1.6-3/terra/man/freq.Rd | 3 terra-1.6-3/terra/man/geometry.Rd | 11 terra-1.6-3/terra/man/global.Rd | 2 terra-1.6-3/terra/man/gridDistance.Rd | 7 terra-1.6-3/terra/man/image.Rd | 2 terra-1.6-3/terra/man/inplace.Rd | 3 terra-1.6-3/terra/man/lapp.Rd | 17 terra-1.6-3/terra/man/mask.Rd | 4 terra-1.6-3/terra/man/merge.Rd | 1 terra-1.6-3/terra/man/names.Rd | 2 terra-1.6-3/terra/man/plet.Rd |only terra-1.6-3/terra/man/plot.Rd | 42 - terra-1.6-3/terra/man/project.Rd | 6 terra-1.6-3/terra/man/rast.Rd | 8 terra-1.6-3/terra/man/rasterize.Rd | 1 terra-1.6-3/terra/man/rectify.Rd | 2 terra-1.6-3/terra/man/resample.Rd | 6 terra-1.6-3/terra/man/sapp.Rd | 14 terra-1.6-3/terra/man/segregate.Rd | 6 terra-1.6-3/terra/man/selectHigh.Rd | 2 terra-1.6-3/terra/man/shade.Rd | 4 terra-1.6-3/terra/man/sharedPaths.Rd | 8 terra-1.6-3/terra/man/simplify.Rd | 11 terra-1.6-3/terra/man/sort.Rd |only terra-1.6-3/terra/man/subset.Rd | 56 +- terra-1.6-3/terra/man/subst.Rd | 10 terra-1.6-3/terra/man/tapp.Rd | 8 terra-1.6-3/terra/man/terra-package.Rd | 133 ++--- terra-1.6-3/terra/man/terraOptions.Rd | 2 terra-1.6-3/terra/man/terrain.Rd | 4 terra-1.6-3/terra/man/time.Rd | 31 - terra-1.6-3/terra/man/union.Rd | 6 terra-1.6-3/terra/man/unique.Rd | 8 terra-1.6-3/terra/man/vect.Rd | 2 terra-1.6-3/terra/man/voronoi.Rd | 3 terra-1.6-3/terra/man/vrt.Rd | 2 terra-1.6-3/terra/man/writeRaster.Rd | 6 terra-1.6-3/terra/man/zonal.Rd | 34 + terra-1.6-3/terra/src/NA.h | 2 terra-1.6-3/terra/src/RcppFunctions.cpp | 52 - terra-1.6-3/terra/src/RcppModule.cpp | 190 +++++-- terra-1.6-3/terra/src/arith.cpp | 62 +- terra-1.6-3/terra/src/crs.cpp | 12 terra-1.6-3/terra/src/crs.h | 17 terra-1.6-3/terra/src/date.h | 2 terra-1.6-3/terra/src/distRaster.cpp | 441 ++++++++-------- terra-1.6-3/terra/src/distance.cpp | 10 terra-1.6-3/terra/src/distance.h | 2 terra-1.6-3/terra/src/extract.cpp | 198 +++++-- terra-1.6-3/terra/src/file_utils.cpp | 25 terra-1.6-3/terra/src/file_utils.h | 17 terra-1.6-3/terra/src/focal.cpp | 68 +- terra-1.6-3/terra/src/gcp.cpp | 4 terra-1.6-3/terra/src/gdal_algs.cpp | 166 +++--- terra-1.6-3/terra/src/gdal_multidimensional.cpp | 138 +++-- terra-1.6-3/terra/src/gdalio.cpp | 83 +-- terra-1.6-3/terra/src/gdalio.h | 19 terra-1.6-3/terra/src/geos_methods.cpp | 360 +++++++++---- terra-1.6-3/terra/src/geos_spat.h | 17 terra-1.6-3/terra/src/geosphere.cpp | 82 +-- terra-1.6-3/terra/src/graticule.cpp | 2 terra-1.6-3/terra/src/math_utils.cpp | 4 terra-1.6-3/terra/src/math_utils.h | 2 terra-1.6-3/terra/src/mediancut.cpp | 17 terra-1.6-3/terra/src/memory.cpp | 14 terra-1.6-3/terra/src/ncdf.cpp | 2 terra-1.6-3/terra/src/ram.cpp | 17 terra-1.6-3/terra/src/ram.h | 17 terra-1.6-3/terra/src/raster_methods.cpp | 625 +++++++++++++++++------- terra-1.6-3/terra/src/raster_stats.cpp | 277 +++++++--- terra-1.6-3/terra/src/rasterize.cpp | 98 +-- terra-1.6-3/terra/src/read.cpp | 12 terra-1.6-3/terra/src/read_gdal.cpp | 184 +++---- terra-1.6-3/terra/src/read_ogr.cpp | 94 ++- terra-1.6-3/terra/src/recycle.h | 2 terra-1.6-3/terra/src/sample.cpp | 56 +- terra-1.6-3/terra/src/spatBase.cpp | 123 +++- terra-1.6-3/terra/src/spatBase.h | 2 terra-1.6-3/terra/src/spatDataframe.cpp | 457 +++++++++++++---- terra-1.6-3/terra/src/spatDataframe.h | 30 - terra-1.6-3/terra/src/spatFactor.cpp |only terra-1.6-3/terra/src/spatFactor.h | 166 +----- terra-1.6-3/terra/src/spatRaster.cpp | 152 +++-- terra-1.6-3/terra/src/spatRaster.h | 34 - terra-1.6-3/terra/src/spatRasterMultiple.h | 2 terra-1.6-3/terra/src/spatSources.cpp | 53 +- terra-1.6-3/terra/src/spatTime.cpp | 24 terra-1.6-3/terra/src/spatTime.h | 31 + terra-1.6-3/terra/src/spatVector.cpp | 83 ++- terra-1.6-3/terra/src/spatVector.h | 45 + terra-1.6-3/terra/src/string_utils.cpp | 10 terra-1.6-3/terra/src/string_utils.h | 16 terra-1.6-3/terra/src/vecmath.cpp | 2 terra-1.6-3/terra/src/vecmath.h | 3 terra-1.6-3/terra/src/vector_methods.cpp | 168 +++++- terra-1.6-3/terra/src/write.cpp | 22 terra-1.6-3/terra/src/write_gdal.cpp | 107 ++-- terra-1.6-3/terra/src/write_ogr.cpp | 92 ++- 214 files changed, 6538 insertions(+), 3868 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] ,
George Athanasopoulos [aut] ,
Christoph Bergmeir [aut] ,
Gabriel Caceres [aut] ,
Leanne Chhay [aut],
Kirill Kuroptev [aut],
Mitchell O'Hara-Wild [aut] ,
Fotios Petropoulos [aut] ,
Slava Razbash [aut],
Earo Wang [aut] ,
F [...truncated...]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.16 dated 2022-01-09 and 8.17.0 dated 2022-07-25
forecast-8.16/forecast/man/accuracy.Rd |only forecast-8.16/forecast/man/forecast.Rd |only forecast-8.16/forecast/tests/testthat/Rplots.pdf |only forecast-8.17.0/forecast/DESCRIPTION | 40 +++-- forecast-8.17.0/forecast/MD5 | 87 ++++++------ forecast-8.17.0/forecast/NAMESPACE | 3 forecast-8.17.0/forecast/NEWS.md | 6 forecast-8.17.0/forecast/R/DM2.R | 58 +++++--- forecast-8.17.0/forecast/R/HoltWintersNew.R | 5 forecast-8.17.0/forecast/R/arfima.R | 2 forecast-8.17.0/forecast/R/arima.R | 6 forecast-8.17.0/forecast/R/attach.R | 20 +- forecast-8.17.0/forecast/R/bats.R | 6 forecast-8.17.0/forecast/R/calendar.R | 4 forecast-8.17.0/forecast/R/checkresiduals.R | 10 - forecast-8.17.0/forecast/R/clean.R | 6 forecast-8.17.0/forecast/R/dshw.r | 17 +- forecast-8.17.0/forecast/R/errors.R | 10 - forecast-8.17.0/forecast/R/ets.R | 19 +- forecast-8.17.0/forecast/R/etsforecast.R | 4 forecast-8.17.0/forecast/R/findfrequency.R |only forecast-8.17.0/forecast/R/forecast-package.R | 11 + forecast-8.17.0/forecast/R/forecast.R | 101 --------------- forecast-8.17.0/forecast/R/forecast2.R | 6 forecast-8.17.0/forecast/R/lm.R | 4 forecast-8.17.0/forecast/R/mforecast.R | 4 forecast-8.17.0/forecast/R/modelAR.R | 4 forecast-8.17.0/forecast/R/mstl.R | 4 forecast-8.17.0/forecast/R/naive.R | 2 forecast-8.17.0/forecast/R/newarima2.R | 8 - forecast-8.17.0/forecast/R/nnetar.R | 4 forecast-8.17.0/forecast/R/simulate.R | 2 forecast-8.17.0/forecast/R/simulate_tbats.R |only forecast-8.17.0/forecast/R/spline.R | 2 forecast-8.17.0/forecast/R/tbats.R | 6 forecast-8.17.0/forecast/build/vignette.rds |binary forecast-8.17.0/forecast/inst/doc/JSS2008.pdf |binary forecast-8.17.0/forecast/man/accuracy.default.Rd |only forecast-8.17.0/forecast/man/bizdays.Rd | 2 forecast-8.17.0/forecast/man/dm.test.Rd | 32 ++-- forecast-8.17.0/forecast/man/ets.Rd | 4 forecast-8.17.0/forecast/man/findfrequency.Rd | 2 forecast-8.17.0/forecast/man/forecast-package.Rd | 53 ++++++- forecast-8.17.0/forecast/man/forecast.ts.Rd |only forecast-8.17.0/forecast/man/reexports.Rd | 4 forecast-8.17.0/forecast/man/simulate.ets.Rd | 13 + forecast-8.17.0/forecast/tests/testthat/test-calendar.R | 6 forecast-8.17.0/forecast/tests/testthat/test-newarima2.R | 4 48 files changed, 297 insertions(+), 284 deletions(-)
Title: Raster-Based Spatial Stratification Algorithms
Description: Algorithms for the spatial stratification of landscapes, sampling and modeling of
spatially-varying phenomena. These algorithms offer a simple framework for the stratification
of geographic space based on raster layers representing landscape factors and/or factor scales.
The stratification process follows a hierarchical approach, which is based on first level units
(i.e., classification units) and second-level units (i.e., stratification units). Nonparametric
techniques allow to measure the correspondence between the geographic space and the landscape
configuration represented by the units. These correspondence metrics are useful to define
sampling schemes and to model the spatial variability of environmental phenomena. The
theoretical background of the algorithms and code examples are presented in Fuentes, Dorantes,
and Tipton (2021). <doi:10.31223/X50S57>.
Author: Bryan A. Fuentes [aut, cre] ,
Minerva J. Dorantes [aut] ,
John R. Tipton [aut] ,
Robert J. Hijmans [ctb] ,
Andrew G. Brown [ctb]
Maintainer: Bryan A. Fuentes <bryandrep@gmail.com>
Diff between rassta versions 1.0.3 dated 2022-02-25 and 1.0.4 dated 2022-07-25
DESCRIPTION | 24 +- MD5 | 58 +++--- NEWS.md | 55 ++++-- R/dummies.r | 71 +++++--- R/locations.r | 331 ++++++++++++++++++++------------------ R/observation.r | 134 +++++++-------- R/predict_functions.r | 407 +++++++++++++++++++++++++++++++---------------- R/select_functions.r | 2 R/signature.r | 36 +--- R/similarity.r | 64 +++---- R/som_pam.r | 65 ++++--- R/strata.r | 33 +-- README.md | 9 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/classunits.html | 278 ++++++++++++++++++++++++++++++-- inst/doc/modeling.Rmd | 6 inst/doc/modeling.html | 256 +++++++++++++++++++++++++++-- inst/doc/sampling.html | 286 ++++++++++++++++++++++++++++++--- inst/doc/signature.html | 297 +++++++++++++++++++++++++++++++--- inst/doc/similarity.html | 231 +++++++++++++++++++++++++- inst/doc/stratunits.html | 255 ++++++++++++++++++++++++++++- man/dummies.Rd | 2 man/locations.Rd | 13 - man/observation.Rd | 8 man/predict_functions.Rd | 97 ++++++++--- man/select_functions.Rd | 2 man/som_pam.Rd | 31 ++- man/strata.Rd | 12 - vignettes/modeling.Rmd | 6 30 files changed, 2377 insertions(+), 692 deletions(-)
Title: Parametric Time-to-Event Analysis with Variable Incubation
Phases
Description: Fit parametric models for time-to-event data that show an initial
'incubation period', i.e., a variable delay phase where the hazard is zero. The
delayed Weibull distribution serves as the foundational data model. The
specific method of 'MPSE' (maximum product of spacings estimation) is used for parameter
estimation. Bootstrap confidence intervals for parameters and significance
tests in a two group setting are provided.
Author: Matthias Kuhn [aut, cre]
Maintainer: Matthias Kuhn <matthias.kuhn@tu-dresden.de>
Diff between incubate versions 1.1.8 dated 2022-05-04 and 1.2.0 dated 2022-07-25
incubate-1.1.8/incubate/man/geomSpaceFactory.Rd |only incubate-1.1.8/incubate/man/near.Rd |only incubate-1.2.0/incubate/DESCRIPTION | 22 incubate-1.2.0/incubate/MD5 | 61 incubate-1.2.0/incubate/NAMESPACE | 3 incubate-1.2.0/incubate/NEWS.md | 20 incubate-1.2.0/incubate/R/data.R | 2 incubate-1.2.0/incubate/R/delay.R | 12 incubate-1.2.0/incubate/R/delay_estimation.R | 631 ++++++---- incubate-1.2.0/incubate/R/delay_test.R | 144 +- incubate-1.2.0/incubate/R/incubate-package.R | 4 incubate-1.2.0/incubate/R/utils.R | 21 incubate-1.2.0/incubate/README.md | 49 incubate-1.2.0/incubate/data/stankovic.rda |binary incubate-1.2.0/incubate/inst |only incubate-1.2.0/incubate/man/DelayedExponential.Rd | 4 incubate-1.2.0/incubate/man/DelayedWeibull.Rd | 6 incubate-1.2.0/incubate/man/as_percent.Rd |only incubate-1.2.0/incubate/man/bsDataStep.Rd | 8 incubate-1.2.0/incubate/man/confint.incubate_fit.Rd | 14 incubate-1.2.0/incubate/man/delay_fit.Rd | 5 incubate-1.2.0/incubate/man/delay_model.Rd | 10 incubate-1.2.0/incubate/man/figures/README-example_fit-1.png |binary incubate-1.2.0/incubate/man/figures/README-example_inf-1.png |binary incubate-1.2.0/incubate/man/getPars.Rd | 13 incubate-1.2.0/incubate/man/objFunFactory.Rd |only incubate-1.2.0/incubate/man/power_diff.Rd | 2 incubate-1.2.0/incubate/man/stankovic.Rd | 2 incubate-1.2.0/incubate/man/test_GOF.Rd | 5 incubate-1.2.0/incubate/man/test_diff.Rd | 6 incubate-1.2.0/incubate/man/transform.incubate_fit.Rd |only incubate-1.2.0/incubate/tests/testthat/test-delay_estimation.R | 64 - incubate-1.2.0/incubate/tests/testthat/test-delay_test.R | 13 33 files changed, 658 insertions(+), 463 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-02 0.2.32
2022-03-21 0.2.28
2021-08-13 0.2.17
2021-06-04 0.2.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-01 0.2.15
2022-06-22 0.2.6
2022-06-18 0.2.5
2022-04-26 0.2.3
2021-08-22 0.1.38
2021-08-14 0.1.37
2021-03-29 0.1.29
2021-03-17 0.1.28
2021-03-09 0.1.19
2021-03-05 0.1.10
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the
'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged: it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.4.2 dated 2021-04-18 and 1.4.3 dated 2022-07-24
DESCRIPTION | 19 - MD5 | 22 - NEWS.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 39 --- inst/doc/alphordering-numbers.html | 114 +++++--- inst/doc/argument-matching.html | 196 ++++++++------- inst/doc/before-and-after.html | 135 ++++++---- inst/doc/important-miscellany.html | 240 ++++++++++-------- inst/doc/numbers-in-strings.html | 478 +++++++++++++++++++------------------ man/str_nth_number_before_mth.Rd | 7 12 files changed, 692 insertions(+), 564 deletions(-)
Title: Random Walk Clustering on Weighted Graphs
Description: Implements the random walk clustering algorithm for weighted graphs as found in Harel and Koren (2001) <https://link.springer.com/chapter/10.1007/3-540-45294-X_3>.
Author: Carson Sprock [aut, cre]
Maintainer: Carson Sprock <csprock@gmail.com>
Diff between Rwclust versions 0.0.1 dated 2022-05-17 and 0.1.0 dated 2022-07-24
Rwclust-0.0.1/Rwclust/man/rwclust_.Rd |only Rwclust-0.1.0/Rwclust/DESCRIPTION | 8 +- Rwclust-0.1.0/Rwclust/MD5 | 34 +++++--- Rwclust-0.1.0/Rwclust/NAMESPACE | 13 +++ Rwclust-0.1.0/Rwclust/NEWS.md | 7 + Rwclust-0.1.0/Rwclust/R/matrix_functions.R | 4 - Rwclust-0.1.0/Rwclust/R/metrics.R | 6 + Rwclust-0.1.0/Rwclust/R/rwclust.R | 76 ++++++++------------ Rwclust-0.1.0/Rwclust/R/user_input.R | 1 Rwclust-0.1.0/Rwclust/R/utils.R |only Rwclust-0.1.0/Rwclust/README.md | 13 +++ Rwclust-0.1.0/Rwclust/inst/doc/basic_usage.R | 12 +-- Rwclust-0.1.0/Rwclust/inst/doc/basic_usage.Rmd | 12 +-- Rwclust-0.1.0/Rwclust/inst/doc/basic_usage.html | 19 ++--- Rwclust-0.1.0/Rwclust/man/adjacency.Rd |only Rwclust-0.1.0/Rwclust/man/new_rwclust.Rd |only Rwclust-0.1.0/Rwclust/man/plot.rwclust.Rd |only Rwclust-0.1.0/Rwclust/man/rwclust.Rd | 14 ++- Rwclust-0.1.0/Rwclust/tests/testthat/test-rwclust.R | 3 Rwclust-0.1.0/Rwclust/tests/testthat/test-utils.R |only Rwclust-0.1.0/Rwclust/vignettes/basic_usage.Rmd | 12 +-- 21 files changed, 125 insertions(+), 109 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
three public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>) and
the 'ISRCTN' (<http://www.isrctn.com/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite' or 'MongoDB'; via package 'nodbi').
Functions are included to identify de-duplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries.
The package can be used for meta-analysis and trend-analysis of
the design and conduct as well as for results of clinical trials.
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.10.0 dated 2022-07-06 and 1.10.1 dated 2022-07-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/ctrdata-registers.R | 4 ++-- README.md | 13 ++++++------- build/vignette.rds |binary inst/tinytest/ctrdata_euctr.R | 2 +- inst/tinytest/test_ctrdata_other_functions.R | 2 +- man/ctrdata-registers.Rd | 4 ++-- 9 files changed, 29 insertions(+), 25 deletions(-)
Title: Artificial Intelligence Systems and Observer Performance
Description: Analyzing the performance of artificial intelligence
(AI) systems/algorithms characterized by a 'search-and-report'
strategy. Historically observer performance has dealt with
measuring radiologists' performances in search tasks, e.g., searching
for lesions in medical images and reporting them, but the implicit
location information has been ignored. The implemented methods apply
to analyzing the absolute and relative performances of AI systems,
comparing AI performance to a group of human readers or optimizing the
reporting threshold of an AI system. In addition to performing historical
receiver operating receiver operating characteristic (ROC) analysis
(localization information ignored), the software also performs
free-response receiver operating characteristic (FROC)
analysis, where lesion localization information is used. A book
using the software has been published: Chakraborty DP: Observer
Performance Methods for Diagnostic Imaging - Foundations, Modeling,
and Applications with R-Based Examples, Taylor-Francis LLC; 2017.
Online updates to this book, which use the software, are at
<https://dpc10ster.github.io/RJafrocQuickStart/>,
<https://dpc10ster.github.io/RJafrocRocBook/> and at
<https://dpc10ster.github.io/RJafrocFrocBook/>. Supported data
collection paradigms are the ROC, FROC and the location ROC (LROC).
ROC data consists of single ratings per images, where a rating is
the perceived confidence level that the image is that of a diseased
patient. An ROC curve is a plot of true positive fraction vs. false
positive fraction. FROC data consists of a variable number (zero or
more) of mark-rating pairs per image, where a mark is the location
of a reported suspicious region and the rating is the confidence
level that it is a real lesion. LROC data consists of a rating and a
location of the most suspicious region, for every image. Four models
of observer performance, and curve-fitting software, are implemented:
the binormal model (BM), the contaminated binormal model (CBM), the
correlated contaminated binormal model (CORCBM), and the radiological
search model (RSM). Unlike the binormal model, CBM, CORCBM and RSM
predict 'proper' ROC curves that do not inappropriately cross the
chance diagonal. Additionally, RSM parameters are related to search
performance (not measured in conventional ROC analysis) and
classification performance. Search performance refers to finding
lesions, i.e., true positives, while simultaneously not finding false
positive locations. Classification performance measures the ability to
distinguish between true and false positive locations. Knowing these
separate performances allows principled optimization of reader or AI
system performance. This package supersedes Windows JAFROC (jackknife
alternative FROC) software V4.2.1,
<https://github.com/dpc10ster/WindowsJafroc>. Package functions are
organized as follows. Data file related function names are preceded
by 'Df', curve fitting functions by 'Fit', included data sets by 'dataset',
plotting functions by 'Plot', significance testing functions by 'St',
sample size related functions by 'Ss', data simulation functions by
'Simulate' and utility functions by 'Util'. Implemented are figures of
merit (FOMs) for quantifying performance and functions for visualizing
empirical or fitted operating characteristics: e.g., ROC, FROC, alternative
FROC (AFROC) and weighted AFROC (wAFROC) curves. For fully crossed study
designs significance testing of reader-averaged FOM differences between
modalities is implemented via either Dorfman-Berbaum-Metz or the
Obuchowski-Rockette methods. Also implemented is single treatment analysis,
which allows comparison of performance of a group of radiologists to a
specified value, or comparison of AI to a group of radiologists interpreting
the same cases. Crossed-modality analysis is implemented wherein there are
two crossed treatment factors and the aim is to determined performance in
each treatment factor averaged over all levels of the second factor. Sample
size estimation tools are provided for ROC and FROC studies; these use
estimates of the relevant variances from a pilot study to predict required
numbers of readers and cases in a pivotal study to achieve the desired power.
Utility and data file manipulation functions allow data to be read in any of
the currently used input formats, including Excel, and the results of the
analysis can be viewed in text or Excel output files. The methods are
illustrated with several included datasets from the author's collaborations.
This update includes improvements to the code, some as a result of
user-reported bugs and new feature requests, and others discovered during
ongoing testing and code simplification.
Author: Dev Chakraborty [cre, aut, cph],
Peter Phillips [ctb],
Xuetong Zhai [aut]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>
Diff between RJafroc versions 2.0.1 dated 2020-12-15 and 2.1.0 dated 2022-07-24
RJafroc-2.0.1/RJafroc/R/Compare3ProperRocFits.R |only RJafroc-2.0.1/RJafroc/R/MyFom_ij.R |only RJafroc-2.0.1/RJafroc/R/UtilLesionDistr.R |only RJafroc-2.0.1/RJafroc/R/UtilLesionWeightsDistr.R |only RJafroc-2.0.1/RJafroc/inst/ANALYZED |only RJafroc-2.0.1/RJafroc/inst/MRMCRuns |only RJafroc-2.0.1/RJafroc/man/Compare3ProperRocFits.Rd |only RJafroc-2.0.1/RJafroc/man/UtilLesionDistr.Rd |only RJafroc-2.0.1/RJafroc/man/UtilLesionWeightsDistr.Rd |only RJafroc-2.1.0/RJafroc/DESCRIPTION | 128 +- RJafroc-2.1.0/RJafroc/MD5 | 555 ++++++++-- RJafroc-2.1.0/RJafroc/NAMESPACE | 18 RJafroc-2.1.0/RJafroc/NEWS.md | 150 ++ RJafroc-2.1.0/RJafroc/R/ChisqrGoodnessOfFit.R | 17 RJafroc-2.1.0/RJafroc/R/DfBinDataset.R | 1 RJafroc-2.1.0/RJafroc/R/DfExtractDataset.R | 19 RJafroc-2.1.0/RJafroc/R/DfReadCrossedModalities.R | 13 RJafroc-2.1.0/RJafroc/R/DfReadDataFile.R | 69 - RJafroc-2.1.0/RJafroc/R/DfReadIowaFormats.R | 13 RJafroc-2.1.0/RJafroc/R/DfReadLrocDataFile.R |only RJafroc-2.1.0/RJafroc/R/DfSaveDataFile.R | 202 +-- RJafroc-2.1.0/RJafroc/R/DfWriteExcelDataFile.R |only RJafroc-2.1.0/RJafroc/R/FitRsmRoc.R | 32 RJafroc-2.1.0/RJafroc/R/PlotRsmOperatingCharacteristics.R | 75 - RJafroc-2.1.0/RJafroc/R/ReadJAFROCNewFormat.R | 39 RJafroc-2.1.0/RJafroc/R/ReadJAFROCOldFormat.R | 4 RJafroc-2.1.0/RJafroc/R/SimulateFrocDataset.R | 1 RJafroc-2.1.0/RJafroc/R/SimulateFrocFromLrocDataset.R | 1 RJafroc-2.1.0/RJafroc/R/SimulateLrocDataset.R | 1 RJafroc-2.1.0/RJafroc/R/SimulateRocDataset.R | 1 RJafroc-2.1.0/RJafroc/R/SsFrocNhRsmModel.R | 123 +- RJafroc-2.1.0/RJafroc/R/StSignificanceTesting.R | 7 RJafroc-2.1.0/RJafroc/R/StSignificanceTestingCadVsRad.R | 28 RJafroc-2.1.0/RJafroc/R/StSignificanceTestingCrossedModalities.R | 7 RJafroc-2.1.0/RJafroc/R/UtilAnalyticalAucsRSM.R | 65 - RJafroc-2.1.0/RJafroc/R/UtilFigureOfMerit.R | 1 RJafroc-2.1.0/RJafroc/R/UtilFigureOfMerit_ij.R |only RJafroc-2.1.0/RJafroc/R/UtilIntrinsic2PhysicalRSM.R | 1 RJafroc-2.1.0/RJafroc/R/UtilLesionDistrVector.R |only RJafroc-2.1.0/RJafroc/R/UtilLesionWeightsMatrix.R |only RJafroc-2.1.0/RJafroc/R/UtilOutputReport.R | 22 RJafroc-2.1.0/RJafroc/R/UtilPhysical2IntrinsicRSM.R | 1 RJafroc-2.1.0/RJafroc/R/datasets.R | 11 RJafroc-2.1.0/RJafroc/R/rsmFormulae.R | 321 +++++ RJafroc-2.1.0/RJafroc/R/test2Functions.R |only RJafroc-2.1.0/RJafroc/inst/cranSubmission/cranSubmission.R | 86 + RJafroc-2.1.0/RJafroc/inst/extdata/CadFrocData.xlsx |only RJafroc-2.1.0/RJafroc/inst/extdata/CrossedModalities.xlsx |only RJafroc-2.1.0/RJafroc/inst/extdata/JT.xlsx |only RJafroc-2.1.0/RJafroc/inst/extdata/JT2Rdrs.xlsx |only RJafroc-2.1.0/RJafroc/inst/extdata/NicoRadRoc.xlsx |only RJafroc-2.1.0/RJafroc/inst/extdata/findings.txt |only RJafroc-2.1.0/RJafroc/inst/extdata/toyFiles |only RJafroc-2.1.0/RJafroc/inst/temp |only RJafroc-2.1.0/RJafroc/man/ChisqrGoodnessOfFit.Rd | 18 RJafroc-2.1.0/RJafroc/man/DfBinDataset.Rd | 3 RJafroc-2.1.0/RJafroc/man/DfReadCrossedModalities.Rd | 17 RJafroc-2.1.0/RJafroc/man/DfReadDataFile.Rd | 44 RJafroc-2.1.0/RJafroc/man/DfReadLrocDataFile.Rd |only RJafroc-2.1.0/RJafroc/man/DfSaveDataFile.Rd | 17 RJafroc-2.1.0/RJafroc/man/DfWriteExcelDataFile.Rd |only RJafroc-2.1.0/RJafroc/man/FitRsmRoc.Rd | 29 RJafroc-2.1.0/RJafroc/man/PlotRsmOperatingCharacteristics.Rd | 22 RJafroc-2.1.0/RJafroc/man/RJafroc-package.Rd | 88 - RJafroc-2.1.0/RJafroc/man/RSM_erf.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_pdfD.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_pdfN.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_xFROC.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_xROC.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_yFROC.Rd |only RJafroc-2.1.0/RJafroc/man/RSM_yROC.Rd |only RJafroc-2.1.0/RJafroc/man/SimulateFrocDataset.Rd | 3 RJafroc-2.1.0/RJafroc/man/SimulateFrocFromLrocDataset.Rd | 1 RJafroc-2.1.0/RJafroc/man/SimulateLrocDataset.Rd | 3 RJafroc-2.1.0/RJafroc/man/SimulateRocDataset.Rd | 3 RJafroc-2.1.0/RJafroc/man/SsFrocNhRsmModel.Rd | 48 RJafroc-2.1.0/RJafroc/man/StSignificanceTesting.Rd | 7 RJafroc-2.1.0/RJafroc/man/StSignificanceTestingCadVsRad.Rd | 24 RJafroc-2.1.0/RJafroc/man/StSignificanceTestingCrossedModalities.Rd | 7 RJafroc-2.1.0/RJafroc/man/UtilAnalyticalAucsRSM.Rd | 23 RJafroc-2.1.0/RJafroc/man/UtilFigureOfMerit.Rd | 1 RJafroc-2.1.0/RJafroc/man/UtilIntrinsic2PhysicalRSM.Rd | 3 RJafroc-2.1.0/RJafroc/man/UtilLesionDistrVector.Rd |only RJafroc-2.1.0/RJafroc/man/UtilLesionWeightsMatrix.Rd |only RJafroc-2.1.0/RJafroc/man/UtilOutputReport.Rd | 21 RJafroc-2.1.0/RJafroc/man/UtilPhysical2IntrinsicRSM.Rd | 3 RJafroc-2.1.0/RJafroc/man/dataset05.Rd | 6 RJafroc-2.1.0/RJafroc/man/dataset10.Rd | 2 RJafroc-2.1.0/RJafroc/man/datasetCrossedModality.Rd | 2 RJafroc-2.1.0/RJafroc/man/funs.Rd |only RJafroc-2.1.0/RJafroc/src/CommonFuncs.h | 11 RJafroc-2.1.0/RJafroc/src/RcppExports.cpp | 25 RJafroc-2.1.0/RJafroc/src/RsmFuncs.cpp | 141 -- RJafroc-2.1.0/RJafroc/tests |only 94 files changed, 1824 insertions(+), 760 deletions(-)
Title: Credit Risk Scorecard
Description: The `scorecard` package makes the development of credit risk scorecard
easier and efficient by providing functions for some common tasks,
such as data partition, variable selection, woe binning, scorecard scaling,
performance evaluation and report generation. These functions can also used
in the development of machine learning models.
The references including:
1. Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard:
Development and Implementation Using SAS.
2. Siddiqi, N. (2006, ISBN: 9780471754510). Credit risk scorecards.
Developing and Implementing Intelligent Credit Scoring.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between scorecard versions 0.3.8 dated 2022-07-09 and 0.3.9 dated 2022-07-24
DESCRIPTION | 6 +-- MD5 | 15 ++++--- NEWS.md | 5 ++ R/condition_fun.R | 10 ++++- R/report.R | 11 ++++- R/var_filter.R | 102 ++++++++++++++++++++++++++++++++++++---------------- R/woebin.R | 24 ++++++------ inst/extdata/demo.R |only man/var_filter.Rd | 10 +++-- 9 files changed, 124 insertions(+), 59 deletions(-)
Title: Prediction Performance Metrics
Description: A compilation of more than 80 functions designed to quantitatively and visually evaluate prediction performance of regression (continuous variables) and classification (categorical variables) of point-forecast models (e.g. APSIM, DSSAT, DNDC, supervised Machine Learning). For regression, it includes functions to generate plots (scatter, tiles, density, & Bland-Altman plot), and to estimate error metrics (e.g. MBE, MAE, RMSE), error decomposition (e.g. lack of accuracy-precision), model efficiency (e.g. NSE, E1, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), adjusted correlation coefficients (e.g. CCC, dcorr), symmetric regression coefficients (intercept, slope), and mean absolute scaled error (MASE) for time series predictions. For classification (binomial and multinomial), it offers functions to generate and plot confusion matrices, and to estimate performance metrics such as accuracy, precision, recall, specificity, F-score, Cohen's Kappa, G-mean, and many more. For more details visit the vignettes <https://adriancorrendo.github.io/metrica/>.
Author: Adrian A. Correndo [cre, cph] ,
Adrian A. Correndo [aut] ,
Luiz H. Moro Rosso [aut] ,
Rai Schwalbert [aut] ,
Carlos Hernandez [aut] ,
Leonardo M. Bastos [aut] ,
Luciana Nieto [aut] ,
Dean Holzworth [aut],
Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <correndo@ksu.edu>
Diff between metrica versions 2.0.0 dated 2022-07-05 and 2.0.1 dated 2022-07-24
DESCRIPTION | 16 ++-- MD5 | 42 +++++----- NEWS.md | 30 +++++-- R/class_confusion_matrix.R | 52 +++++++------ R/plot_density.R | 4 - R/plot_scatter.R | 4 - R/plot_tiles.R | 4 - R/reg_d1r.R | 3 README.md | 53 ++++++++++--- inst/doc/apsim_open.Rmd | 2 inst/doc/apsim_open.html | 8 +- inst/doc/available_metrics_classification.html | 4 - inst/doc/available_metrics_regression.html | 4 - inst/doc/classification_case.Rmd | 2 inst/doc/classification_case.html | 8 +- inst/doc/regression_case.html | 100 ++++++++++++------------- man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/metrica-package.Rd | 4 - vignettes/apsim_open.Rmd | 2 vignettes/classification_case.Rmd | 2 22 files changed, 197 insertions(+), 147 deletions(-)
Title: Ordered Random Forests
Description: An implementation of the Ordered Forest estimator as developed
in Lechner & Okasa (2019) <arXiv:1907.02436>. The Ordered Forest flexibly
estimates the conditional probabilities of models with ordered categorical
outcomes (so-called ordered choice models). Additionally to common machine
learning algorithms the 'orf' package provides functions for estimating
marginal effects as well as statistical inference thereof and thus provides
similar output as in standard econometric models for ordered choice. The
core forest algorithm relies on the fast C++ forest implementation from
the 'ranger' package (Wright & Ziegler, 2017) <arXiv:1508.04409>.
Author: Gabriel Okasa [aut, cre], Michael Lechner [ctb]
Maintainer: Gabriel Okasa <okasa.gabriel@gmail.com>
Diff between orf versions 0.1.3 dated 2020-01-31 and 0.1.4 dated 2022-07-23
DESCRIPTION | 12 MD5 | 31 +- NEWS.md | 6 R/orf_package.R | 4 R/orf_user.R | 6 README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/doc/orf_vignette.Rmd | 7 inst/doc/orf_vignette.html | 643 +++++++++++++++++---------------------------- man/odata.Rd | 4 man/orf-package.Rd | 4 man/orf.Rd | 4 src/RcppExports.cpp | 5 vignettes/library.bib | 14 vignettes/orf_vignette.Rmd | 7 17 files changed, 318 insertions(+), 439 deletions(-)
Title: Make Requests from the Bureau of Labor Statistics API
Description: Implements v2 of the B.L.S. API for requests of survey information
and time series data through 3-tiered API that allows users to interact with
the raw API directly, create queries through a functional interface, and
re-shape the data structures returned to fit common uses. The API definition
is located at: <https://www.bls.gov/developers/api_signature_v2.htm>.
Author: Guillermo Roditi Dominguez [aut, cre]
Maintainer: Guillermo Roditi Dominguez <guillermo@newriverinvestments.com>
Diff between blsR versions 0.3.0 dated 2022-04-11 and 0.3.1 dated 2022-07-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ R/merge_tables.R | 18 +++++++++++++++++- man/merge_tables.Rd | 3 ++- tests/testthat/test-merge.R | 17 +++++++++++++++++ 6 files changed, 54 insertions(+), 10 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 1.1.3 dated 2022-06-29 and 1.2.0 dated 2022-07-23
DESCRIPTION | 8 MD5 | 28 - NAMESPACE | 1 R/BranchGLM.R | 209 +++++++---- R/VariableSelection.R | 29 + inst/doc/BranchGLM-Vignette.R | 5 inst/doc/BranchGLM-Vignette.Rmd | 24 - inst/doc/BranchGLM-Vignette.html | 687 +++++++++++++++++++-------------------- man/BranchGLM.Rd | 57 ++- man/VariableSelection.Rd | 14 src/BranchGLMHelpers.cpp | 76 ++-- src/ParBranchGLMHelpers.cpp | 45 +- src/ParVariableSelection.cpp | 85 +++- tests/testthat/test-BranchGLM.R | 28 + vignettes/BranchGLM-Vignette.Rmd | 24 - 15 files changed, 779 insertions(+), 541 deletions(-)
Title: Template Engine Inspired by 'Jinja'
Description: Template engine powered by the 'inja' C++ library. Users
write a template document, using syntax inspired by the 'Jinja' Python
package, and then render the final document by passing data from R.
The template syntax supports features such as variables, loops,
conditions and inheritance.
Author: David Hall [aut, cre, cph] ,
Lars Berscheid [cph] ,
Niels Lohmann [cph]
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between jinjar versions 0.2.0 dated 2022-06-24 and 0.3.0 dated 2022-07-23
DESCRIPTION | 10 ++-- MD5 | 44 ++++++++++-------- NAMESPACE | 2 NEWS.md | 13 +++++ R/check.R | 21 +++++++- R/condition.R |only R/config.R | 28 ++++++----- R/knit.R | 2 R/loader.R | 35 ++++++++++++-- R/parse.R | 25 +++++----- R/print.R |only R/render.R | 10 ++-- README.md | 16 +++--- man/parse.Rd | 4 + man/print.Rd |only man/render.Rd | 2 src/condition.cpp |only src/condition.h |only src/template.cpp | 27 +++++++---- tests/testthat/_snaps/config.md | 76 +++++++++++++++++++++++++++++++- tests/testthat/_snaps/loader.md |only tests/testthat/_snaps/parse.md |only tests/testthat/_snaps/render.md | 95 +++++++++++++++++++++++++++++++++++++--- tests/testthat/test-config.R | 15 ++++-- tests/testthat/test-loader.R | 35 ++++++++++---- tests/testthat/test-parse.R |only tests/testthat/test-render.R | 21 +++++--- 27 files changed, 367 insertions(+), 114 deletions(-)
Title: Multivariate Menu for Radiant: Business Analytics using R and
Shiny
Description: The Radiant Multivariate menu includes interfaces for perceptual
mapping, factor analysis, cluster analysis, and conjoint analysis. The
application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.multivariate versions 1.4.1 dated 2021-11-22 and 1.4.4 dated 2022-07-23
DESCRIPTION | 12 +- MD5 | 22 ++-- NEWS.md | 4 README.md | 10 - inst/app/init.R | 3 inst/app/tools/analysis/conjoint_ui.R | 158 +++++++++++++++++++++---------- inst/app/tools/analysis/full_factor_ui.R | 122 +++++++++++++++-------- inst/app/tools/analysis/hclus_ui.R | 96 ++++++++++++------ inst/app/tools/analysis/kclus_ui.R | 74 ++++++++++---- inst/app/tools/analysis/mds_ui.R | 59 ++++++++--- inst/app/tools/analysis/pre_factor_ui.R | 49 +++++++-- inst/app/tools/analysis/prmap_ui.R | 97 +++++++++++++------ 12 files changed, 491 insertions(+), 215 deletions(-)
More information about radiant.multivariate at CRAN
Permanent link
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.4.4 dated 2022-05-25 and 1.4.6 dated 2022-07-23
DESCRIPTION | 10 - MD5 | 50 ++--- NEWS.md | 5 R/dtree.R | 129 +++++++++----- R/logistic.R | 3 R/nn.R | 249 +++++++++++++++++++++++++++ R/regress.R | 209 ++++++++++++++--------- README.md | 2 inst/app/tools/analysis/crs_ui.R | 59 ++++-- inst/app/tools/analysis/crtree_ui.R | 109 ++++++++---- inst/app/tools/analysis/dtree_ui.R | 289 +++++++++++++++++++------------- inst/app/tools/analysis/evalbin_ui.R | 95 +++++++--- inst/app/tools/analysis/evalreg_ui.R | 47 +++-- inst/app/tools/analysis/gbt_ui.R | 155 +++++++++++------ inst/app/tools/analysis/logistic_ui.R | 137 ++++++++++----- inst/app/tools/analysis/mnl_ui.R | 129 +++++++++----- inst/app/tools/analysis/naivebayes_ui.R | 120 +++++++++---- inst/app/tools/analysis/nn_ui.R | 146 +++++++++++----- inst/app/tools/analysis/regress_ui.R | 137 ++++++++++----- inst/app/tools/analysis/rforest_ui.R | 149 +++++++++++----- inst/app/tools/analysis/simulater_ui.R | 176 ++++++++++++------- inst/app/tools/help/dtree.Rmd | 4 inst/app/tools/help/dtree.md | 4 inst/app/www/js/store.js | 24 ++ man/summary.regress.Rd | 4 man/var_check.Rd | 2 26 files changed, 1746 insertions(+), 697 deletions(-)
Title: Design Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Design menu includes interfaces for design of
experiments, sampling, and sample size calculation. The application extends
the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.design versions 1.4.1 dated 2021-11-18 and 1.4.4 dated 2022-07-23
DESCRIPTION | 12 ++-- MD5 | 16 ++--- NEWS.md | 4 + README.md | 10 +-- inst/app/tools/analysis/doe_ui.R | 19 +++++- inst/app/tools/analysis/randomizer_ui.R | 35 ++++++++--- inst/app/tools/analysis/sample_size_comp_ui.R | 50 ++++++++++++---- inst/app/tools/analysis/sample_size_ui.R | 78 ++++++++++++++++++-------- inst/app/tools/analysis/sampling_ui.R | 42 ++++++++++---- 9 files changed, 189 insertions(+), 77 deletions(-)
More information about radiant.design at CRAN
Permanent link
Title: Basics Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Basics menu includes interfaces for probability
calculation, central limit theorem simulation, comparing means and proportions,
goodness-of-fit testing, cross-tabs, and correlation. The application extends
the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.basics versions 1.4.1 dated 2021-11-18 and 1.4.4 dated 2022-07-23
DESCRIPTION | 10 +-- MD5 | 24 +++---- NEWS.md | 4 + README.md | 10 +-- inst/app/tools/analysis/clt_ui.R | 47 ++++++++++----- inst/app/tools/analysis/compare_means_ui.R | 67 ++++++++++++++++----- inst/app/tools/analysis/compare_props_ui.R | 64 ++++++++++++++++---- inst/app/tools/analysis/correlation_ui.R | 89 ++++++++++++++++++++--------- inst/app/tools/analysis/cross_tabs_ui.R | 19 +++++- inst/app/tools/analysis/goodness_ui.R | 56 ++++++++++++++---- inst/app/tools/analysis/prob_calc_ui.R | 19 +++++- inst/app/tools/analysis/single_mean_ui.R | 19 +++++- inst/app/tools/analysis/single_prop_ui.R | 19 +++++- 13 files changed, 335 insertions(+), 112 deletions(-)
More information about radiant.basics at CRAN
Permanent link
Title: A Tool for Sensitivity Analysis in Structural Equation Modeling
Description: Perform sensitivity analysis in structural equation modeling using
meta-heuristic optimization methods (e.g., ant colony optimization and others).
The references for the proposed methods are:
(1) Leite, W., & Shen, Z., Marcoulides, K., Fish, C., & Harring, J. (2022).
<doi:10.1080/10705511.2021.1881786>
(2) Harring, J. R., McNeish, D. M., & Hancock, G. R. (2017)
<doi:10.1080/10705511.2018.1506925>;
(3) Fisk, C., Harring, J., Shen, Z., Leite, W., Suen, K., & Marcoulides, K.
(2022). <doi:10.1177/00131644211073121>;
(4) Socha, K., & Dorigo, M. (2008) <doi:10.1016/j.ejor.2006.06.046>.
We also thank Dr. Krzysztof Socha for sharing his research on ant colony optimization
algorithm with continuous domains and associated R code,
which provided the base for the development of this package.
Author: Walter Leite [aut, cre],
Zuchao Shen [aut],
Charles Fisk [aut],
Gail Fish [ctb],
YongSeok Lee [ctb],
Sanaz Nazari [ctb],
Jia Quan [ctb],
Eric Wright [ctb],
Huibin Zhang [ctb]
Maintainer: Walter Leite <walter.leite@coe.ufl.edu>
Diff between SEMsens versions 1.0.5 dated 2022-06-22 and 1.2.5 dated 2022-07-22
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 +++- R/sa.aco.R | 2 +- R/sa.sa.R |only build/vignette.rds |binary inst/doc/Hom-vignette.html | 4 ++-- inst/doc/SEMsens.html | 4 ++-- inst/doc/Smith12vignette.html | 4 ++-- inst/doc/Smith19_6phantom3.html | 4 ++-- man/sa.aco.Rd | 2 +- man/sa.sa.Rd |only 13 files changed, 29 insertions(+), 24 deletions(-)
Title: Kaya Identity Data for Nations and Regions
Description: Provides data for Kaya identity variables (population, gross
domestic product, primary energy consumption, and energy-related
CO2 emissions) for the world and for individual nations, and
utility functions for looking up data, plotting trends of
Kaya variables, and plotting the fuel mix for a given country
or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori,
"Environment, Energy, and Economy: Strategies for Sustainability"
(United Nations University Press, 1998) and
<https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's
or region's greenhouse gas emissions in terms of its population,
per-capita Gross Domestic Product, the energy intensity of its
economy, and the carbon-intensity of its energy supply.
Author: Jonathan Gilligan [cre, aut]
Maintainer: Jonathan Gilligan <jonathan.gilligan@vanderbilt.edu>
Diff between kayadata versions 1.1.0 dated 2022-04-14 and 1.2.0 dated 2022-07-22
DESCRIPTION | 10 LICENSE | 2 MD5 | 52 +-- NEWS.md | 6 R/data.R | 12 R/kaya.R | 14 - build/partial.rdb |binary build/vignette.rds |binary data/fuel_mix.rda |binary data/kaya_data.rda |binary data/td_trends.rda |binary data/td_values.rda |binary inst/doc/kayadata.html | 40 +- inst/doc/policy_analysis.html | 70 ++--- man/figures/README-plot-fuel-mix-1.png |binary man/figures/README-plot-kaya-1.png |binary man/figures/README-plot-kaya-world-1.png |binary man/get_kaya_data.Rd | 10 man/get_top_down_values.Rd | 4 man/kaya_data.Rd | 8 man/project_top_down.Rd | 4 man/td_values.Rd | 4 tests/testthat/_snaps/plot_kaya/fuel-mix-collapsed.svg | 20 - tests/testthat/_snaps/plot_kaya/fuel-mix-colors.svg | 24 - tests/testthat/_snaps/plot_kaya/fuel-mix-full.svg | 24 - tests/testthat/_snaps/plot_kaya/kaya-plot-with-colors.svg | 173 ++++++------ tests/testthat/_snaps/plot_kaya/kaya-plot.svg | 189 +++++++------- 27 files changed, 339 insertions(+), 327 deletions(-)
Title: Transport Accessibility Measures
Description: A set of fast and convenient functions to calculate multiple
transport accessibility measures. Given a pre-computed travel cost
matrix and a land use dataset (containing the location of jobs,
healthcare and population, for example), the package allows one to
calculate active and passive accessibility levels using multiple
accessibility measures, such as: cumulative opportunities (using
either travel cost cutoffs or intervals), minimum travel cost to
closest N number of activities, gravity-based (with different decay
functions) and different floating catchment area methods.
Author: Rafael H. M. Pereira [aut] ,
Daniel Herszenhut [aut, cre] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between accessibility versions 0.1.0 dated 2022-06-30 and 1.0.0 dated 2022-07-22
accessibility-0.1.0/accessibility/R/fca_2sfca.R |only accessibility-0.1.0/accessibility/R/fca_bfca.R |only accessibility-0.1.0/accessibility/R/gravity_model.R |only accessibility-0.1.0/accessibility/R/time_to_closest.R |only accessibility-0.1.0/accessibility/inst/doc/intro_accessibility.R |only accessibility-0.1.0/accessibility/inst/doc/intro_accessibility.Rmd |only accessibility-0.1.0/accessibility/inst/doc/intro_accessibility.html |only accessibility-0.1.0/accessibility/inst/extdata/ttm_bho.rds |only accessibility-0.1.0/accessibility/man/cumulative_time_cutoff.Rd |only accessibility-0.1.0/accessibility/man/cumulative_time_interval.Rd |only accessibility-0.1.0/accessibility/man/fca_2sfca.Rd |only accessibility-0.1.0/accessibility/man/fca_bfca.Rd |only accessibility-0.1.0/accessibility/man/gravity_access.Rd |only accessibility-0.1.0/accessibility/man/roxygen/templates/by_col.R |only accessibility-0.1.0/accessibility/man/roxygen/templates/opportunity_col.R |only accessibility-0.1.0/accessibility/man/roxygen/templates/travel_cost_col.R |only accessibility-0.1.0/accessibility/man/time_to_closest.Rd |only accessibility-0.1.0/accessibility/tests/testthat/test-gravity_access.R |only accessibility-0.1.0/accessibility/tests/testthat/test-time_to_closest.R |only accessibility-0.1.0/accessibility/vignettes/intro_accessibility.Rmd |only accessibility-0.1.0/accessibility/vignettes/references.bib |only accessibility-1.0.0/accessibility/DESCRIPTION | 58 accessibility-1.0.0/accessibility/LICENSE | 4 accessibility-1.0.0/accessibility/MD5 | 135 - accessibility-1.0.0/accessibility/NAMESPACE | 10 accessibility-1.0.0/accessibility/NEWS.md |only accessibility-1.0.0/accessibility/R/accessibility.R | 98 accessibility-1.0.0/accessibility/R/assert_and_assign.R |only accessibility-1.0.0/accessibility/R/cost_to_closest.R |only accessibility-1.0.0/accessibility/R/cumulative_cutoff.R | 174 + accessibility-1.0.0/accessibility/R/cumulative_interval.R | 289 +- accessibility-1.0.0/accessibility/R/decay_binary.R | 69 accessibility-1.0.0/accessibility/R/decay_exponential.R | 69 accessibility-1.0.0/accessibility/R/decay_linear.R | 71 accessibility-1.0.0/accessibility/R/decay_power.R | 69 accessibility-1.0.0/accessibility/R/decay_stepped.R |only accessibility-1.0.0/accessibility/R/do_fill_missing_ids.R |only accessibility-1.0.0/accessibility/R/floating_catchment_area.R | 388 ++- accessibility-1.0.0/accessibility/R/gravity.R |only accessibility-1.0.0/accessibility/R/merge_by_reference.R |only accessibility-1.0.0/accessibility/R/warn_extra_cols.R |only accessibility-1.0.0/accessibility/README.md | 222 +- accessibility-1.0.0/accessibility/build/partial.rdb |binary accessibility-1.0.0/accessibility/build/vignette.rds |binary accessibility-1.0.0/accessibility/inst/REFERENCES.bib |only accessibility-1.0.0/accessibility/inst/doc/accessibility.R |only accessibility-1.0.0/accessibility/inst/doc/accessibility.Rmd |only accessibility-1.0.0/accessibility/inst/doc/accessibility.html |only accessibility-1.0.0/accessibility/inst/doc/decay_functions.R | 153 - accessibility-1.0.0/accessibility/inst/doc/decay_functions.Rmd | 412 ++- accessibility-1.0.0/accessibility/inst/doc/decay_functions.html | 1070 ++++------ accessibility-1.0.0/accessibility/inst/extdata/land_use_data.rds |only accessibility-1.0.0/accessibility/inst/extdata/travel_matrix.rds |only accessibility-1.0.0/accessibility/man/accessibility.Rd | 20 accessibility-1.0.0/accessibility/man/cost_to_closest.Rd |only accessibility-1.0.0/accessibility/man/cumulative_cutoff.Rd |only accessibility-1.0.0/accessibility/man/cumulative_interval.Rd |only accessibility-1.0.0/accessibility/man/decay_binary.Rd | 30 accessibility-1.0.0/accessibility/man/decay_exponential.Rd | 30 accessibility-1.0.0/accessibility/man/decay_linear.Rd | 31 accessibility-1.0.0/accessibility/man/decay_power.Rd | 29 accessibility-1.0.0/accessibility/man/decay_stepped.Rd |only accessibility-1.0.0/accessibility/man/floating_catchment_area.Rd | 192 - accessibility-1.0.0/accessibility/man/gravity.Rd |only accessibility-1.0.0/accessibility/man/roxygen/templates/active.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/arguments_fca.R | 8 accessibility-1.0.0/accessibility/man/roxygen/templates/decay_function.R | 14 accessibility-1.0.0/accessibility/man/roxygen/templates/description_generic_cost.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/fill_missing_ids_combinations.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/group_by.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/input_data.R | 10 accessibility-1.0.0/accessibility/man/roxygen/templates/land_use_data.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/opportunity.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/return_accessibility.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/return_decay_function.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/travel_cost.R |only accessibility-1.0.0/accessibility/man/roxygen/templates/travel_matrix.R |only accessibility-1.0.0/accessibility/tests/test_rafa/decay_functions_ggplot.R | 66 accessibility-1.0.0/accessibility/tests/test_rafa/generate_inst_data.R | 216 +- accessibility-1.0.0/accessibility/tests/test_rafa/reprex_logo.R | 228 +- accessibility-1.0.0/accessibility/tests/test_rafa/test_rafa.R | 400 +-- accessibility-1.0.0/accessibility/tests/testthat.R | 8 accessibility-1.0.0/accessibility/tests/testthat/setup.R | 14 accessibility-1.0.0/accessibility/tests/testthat/test-cost_to_closest.R |only accessibility-1.0.0/accessibility/tests/testthat/test-cumulative_cutoff.R | 311 ++ accessibility-1.0.0/accessibility/tests/testthat/test-cumulative_interval.R | 383 ++- accessibility-1.0.0/accessibility/tests/testthat/test-decay_binary.R | 66 accessibility-1.0.0/accessibility/tests/testthat/test-decay_exponential.R | 80 accessibility-1.0.0/accessibility/tests/testthat/test-decay_linear.R | 81 accessibility-1.0.0/accessibility/tests/testthat/test-decay_power.R | 81 accessibility-1.0.0/accessibility/tests/testthat/test-decay_stepped.R |only accessibility-1.0.0/accessibility/tests/testthat/test-do_fill_missing_ids.R |only accessibility-1.0.0/accessibility/tests/testthat/test-floating_catchment_area.R | 378 ++- accessibility-1.0.0/accessibility/tests/testthat/test-gravity.R |only accessibility-1.0.0/accessibility/vignettes/accessibility.Rmd |only accessibility-1.0.0/accessibility/vignettes/decay_functions.Rmd | 412 ++- 96 files changed, 3722 insertions(+), 2657 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.2.0 dated 2022-05-24 and 0.3.0 dated 2022-07-22
audubon-0.2.0/audubon/R/strj-tinyseg.R |only audubon-0.3.0/audubon/DESCRIPTION | 10 audubon-0.3.0/audubon/MD5 | 56 +- audubon-0.3.0/audubon/NAMESPACE | 2 audubon-0.3.0/audubon/NEWS.md | 7 audubon-0.3.0/audubon/R/pack.R | 2 audubon-0.3.0/audubon/R/prettify.R |only audubon-0.3.0/audubon/R/strj-fill.R | 14 audubon-0.3.0/audubon/R/strj-japanese.R | 14 audubon-0.3.0/audubon/R/strj-normalize.R | 4 audubon-0.3.0/audubon/R/strj-rewrite.R | 4 audubon-0.3.0/audubon/R/strj-segment.R | 59 +- audubon-0.3.0/audubon/R/strj-tokenize.R | 169 +++++- audubon-0.3.0/audubon/README.md | 272 +++++----- audubon-0.3.0/audubon/inst/WORDLIST | 15 audubon-0.3.0/audubon/man/get_dict_features.Rd |only audubon-0.3.0/audubon/man/pack.Rd | 2 audubon-0.3.0/audubon/man/prettify.Rd |only audubon-0.3.0/audubon/man/read_rewrite_def.Rd | 2 audubon-0.3.0/audubon/man/strj_fill_iter_mark.Rd | 4 audubon-0.3.0/audubon/man/strj_hiraganize.Rd | 4 audubon-0.3.0/audubon/man/strj_katakanize.Rd | 4 audubon-0.3.0/audubon/man/strj_normalize.Rd | 4 audubon-0.3.0/audubon/man/strj_rewrite_as_def.Rd | 2 audubon-0.3.0/audubon/man/strj_romanize.Rd | 2 audubon-0.3.0/audubon/man/strj_segment.Rd | 15 audubon-0.3.0/audubon/man/strj_tinyseg.Rd | 9 audubon-0.3.0/audubon/man/strj_tokenize.Rd | 26 audubon-0.3.0/audubon/man/strj_transcribe_num.Rd | 4 audubon-0.3.0/audubon/tests/testthat/test_strj-fill.R | 2 audubon-0.3.0/audubon/tests/testthat/test_strj-tokenize-and-segment.R | 41 + 31 files changed, 496 insertions(+), 253 deletions(-)
Title: Creating Demographic Table
Description: Functions for creating demographic table with simple summary
statistics, with optional comparison(s) over one or more groups.
Numeric variables are summarized in means, standard deviations,
medians, inter-quartile-ranges (IQR), skewness, Shapiro-Wilk
normality test and ranges, and compared using two-sample t-test,
Wilcoxon test, ANOVA and/or Kruskal-Wallis test. Logical and
factor variables are summarized in counts and percentages and
compared using chi-squared test and/or Fisher's exact test.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.1.5 dated 2022-06-24 and 0.1.6 dated 2022-07-22
DESCRIPTION | 31 +++++++++++++++---------------- MD5 | 6 +++--- NEWS.md | 2 ++ R/DemographicTable.R | 7 ++++++- 4 files changed, 26 insertions(+), 20 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Bayesian Probit Choice Modeling
Description: Bayes estimation of probit choice models, both in the cross-sectional and
panel setting. The package can analyze binary, multivariate, ordered, and
ranked choices, and places a special focus on modeling heterogeneity of
choice behavior among deciders. The main functionality includes model
fitting via Markov chain Monte Carlo methods, tools for convergence
diagnostic, choice data simulation, in-sample and out-of-sample choice
prediction, and model selection using information criteria and Bayes
factors. The latent class model extension facilitates preference-based
decider classification, where the number of latent classes can be inferred
via the Dirichlet process or a weight-based updating scheme. This allows for
flexible modeling of choice behavior without the need to impose structural
constraints. For a reference on the method see Oelschlaeger and Bauer (2021)
<https://trid.trb.org/view/1759753>.
Author: Lennart Oelschlaeger [aut, cre]
,
Dietmar Bauer [aut] ,
Sebastian Buescher [ctb],
Manuel Batram [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.0.0 dated 2021-11-12 and 1.1.0 dated 2022-07-22
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Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.26.1 dated 2022-05-27 and 1.27.0 dated 2022-07-22
future-1.26.1/future/R/rng.R |only future-1.26.1/future/man/as_lecyer_cmrg_seed.Rd |only future-1.26.1/future/man/make_rng_seeds.Rd |only future-1.27.0/future/DESCRIPTION | 10 - future-1.27.0/future/MD5 | 54 +++--- future-1.27.0/future/NAMESPACE | 1 future-1.27.0/future/NEWS.md | 16 + future-1.27.0/future/R/Future-class.R | 7 future-1.27.0/future/R/FutureResult-class.R | 3 future-1.27.0/future/R/UniprocessFuture-class.R | 2 future-1.27.0/future/R/multicore.R | 12 - future-1.27.0/future/R/multisession.R | 8 future-1.27.0/future/R/rng_utils.R |only future-1.27.0/future/R/utils,conditions.R |only future-1.27.0/future/R/utils.R | 12 - future-1.27.0/future/build/vignette.rds |binary future-1.27.0/future/inst/WORDLIST | 1 future-1.27.0/future/inst/doc/future-4-non-exportable-objects.html | 77 ++++++++- future-1.27.0/future/inst/doc/future-4-non-exportable-objects.md.rsp | 81 +++++++++- future-1.27.0/future/inst/doc/future-7-for-package-developers.html | 2 future-1.27.0/future/inst/doc/future-7-for-package-developers.md.rsp | 2 future-1.27.0/future/inst/doc/future-8-how-future-is-validated.html | 5 future-1.27.0/future/inst/doc/future-8-how-future-is-validated.md.rsp | 7 future-1.27.0/future/man/multicore.Rd | 7 future-1.27.0/future/man/multisession.Rd | 4 future-1.27.0/future/tests/cluster.R | 22 +- future-1.27.0/future/tests/incl/start,load-only.R | 6 future-1.27.0/future/tests/rng_utils.R |only future-1.27.0/future/vignettes/future-4-non-exportable-objects.md.rsp | 81 +++++++++- future-1.27.0/future/vignettes/future-7-for-package-developers.md.rsp | 2 future-1.27.0/future/vignettes/future-8-how-future-is-validated.md.rsp | 7 31 files changed, 318 insertions(+), 111 deletions(-)
Title: Correction Factors for Tree Plot Areas Intersected by Stand
Boundaries
Description: The German national forest inventory uses angle count sampling,
a sampling method first published as `Bitterlich, W.: Die Winkelzählmessung.
Allgemeine Forst- und Holzwirtschaftliche Zeitung, 58. Jahrg., Folge 11/12
vom Juni 1947` and extended by Grosenbaugh
(<https://academic.oup.com/jof/article-abstract/50/1/32/4684174>)
as probability proportional to size sampling.
When plots are located near stand boundaries, their sizes and hence
their probabilities need to be corrected.
Author: Andreas Dominik Cullmann [aut, cre],
Bernhard Boesch [ctb],
Christoph Fischer [ctb],
Gerald Kaendler [ctb]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between treePlotArea versions 1.0.0 dated 2022-07-14 and 1.1.0 dated 2022-07-22
treePlotArea-1.0.0/treePlotArea/R/plot.R |only treePlotArea-1.1.0/treePlotArea/DESCRIPTION | 12 treePlotArea-1.1.0/treePlotArea/MD5 | 61 ++-- treePlotArea-1.1.0/treePlotArea/NAMESPACE | 3 treePlotArea-1.1.0/treePlotArea/NEWS.md | 22 + treePlotArea-1.1.0/treePlotArea/R/add_boundaries_to_plot.R |only treePlotArea-1.1.0/treePlotArea/R/bw2bwi2022de.R | 3 treePlotArea-1.1.0/treePlotArea/R/check_boundaries.R |only treePlotArea-1.1.0/treePlotArea/R/delete_extraneous_boundaries.R | 6 treePlotArea-1.1.0/treePlotArea/R/get_boundary_polygons.R | 25 + treePlotArea-1.1.0/treePlotArea/R/get_correction_factors.R | 148 +++++++--- treePlotArea-1.1.0/treePlotArea/R/get_intersection.R |only treePlotArea-1.1.0/treePlotArea/R/plot_tree_plot_area.R |only treePlotArea-1.1.0/treePlotArea/R/points2equation.R | 1 treePlotArea-1.1.0/treePlotArea/R/secant_intersections.R | 7 treePlotArea-1.1.0/treePlotArea/R/tree_and_boundary.R |only treePlotArea-1.1.0/treePlotArea/R/validate_data.R |only treePlotArea-1.1.0/treePlotArea/R/vector_length.R | 21 + treePlotArea-1.1.0/treePlotArea/README.md | 2 treePlotArea-1.1.0/treePlotArea/inst/NEWS.rd | 24 + treePlotArea-1.1.0/treePlotArea/inst/doc/An_Introduction_to_treePlotArea.R | 52 ++- treePlotArea-1.1.0/treePlotArea/inst/doc/An_Introduction_to_treePlotArea.Rnw | 41 ++ treePlotArea-1.1.0/treePlotArea/inst/doc/An_Introduction_to_treePlotArea.pdf |binary treePlotArea-1.1.0/treePlotArea/inst/runit_tests/runit-get_boundary_polygons.R |only treePlotArea-1.1.0/treePlotArea/inst/runit_tests/runit-get_correction_factors.R | 37 +- treePlotArea-1.1.0/treePlotArea/inst/tinytest/test_plot.R | 2 treePlotArea-1.1.0/treePlotArea/inst/vignettes_code/An_Introduction_to_treePlotArea.R | 52 ++- treePlotArea-1.1.0/treePlotArea/man/get_boundary_polygons.Rd | 23 + treePlotArea-1.1.0/treePlotArea/man/get_correction_factors.Rd | 46 ++- treePlotArea-1.1.0/treePlotArea/man/get_intersection.Rd |only treePlotArea-1.1.0/treePlotArea/man/plot_tree_plot_area.Rd | 14 treePlotArea-1.1.0/treePlotArea/man/points2equation.Rd | 6 treePlotArea-1.1.0/treePlotArea/man/secant_intersections.Rd | 6 treePlotArea-1.1.0/treePlotArea/man/select_valid_angle_count_trees.Rd | 3 treePlotArea-1.1.0/treePlotArea/man/validate_data.Rd |only treePlotArea-1.1.0/treePlotArea/man/vector_length.Rd |only treePlotArea-1.1.0/treePlotArea/vignettes/An_Introduction_to_treePlotArea.Rnw | 41 ++ 37 files changed, 520 insertions(+), 138 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional
data frame.
Author: Kirill Mueller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
Jennifer Bryan [ctb],
RStudio [cph, fnd]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>
Diff between tibble versions 3.1.7 dated 2022-05-03 and 3.1.8 dated 2022-07-22
tibble-3.1.7/tibble/tests/testthat/zzz-output |only tibble-3.1.8/tibble/DESCRIPTION | 14 - tibble-3.1.8/tibble/MD5 | 95 ++------- tibble-3.1.8/tibble/NAMESPACE | 1 tibble-3.1.8/tibble/NEWS.md | 9 tibble-3.1.8/tibble/R/as_tibble.R | 3 tibble-3.1.8/tibble/R/pillar.R | 4 tibble-3.1.8/tibble/R/subsetting.R | 13 + tibble-3.1.8/tibble/R/tbl_df.R | 1 tibble-3.1.8/tibble/R/tibble-package.R | 1 tibble-3.1.8/tibble/inst/doc/invariants.html | 59 +++--- tibble-3.1.8/tibble/inst/doc/numbers.R | 4 tibble-3.1.8/tibble/inst/doc/numbers.Rmd | 7 tibble-3.1.8/tibble/inst/doc/numbers.html | 96 +++++----- tibble-3.1.8/tibble/inst/doc/tibble.html | 29 +-- tibble-3.1.8/tibble/inst/doc/types.html | 51 ++--- tibble-3.1.8/tibble/man/name-repair-superseded.Rd | 6 tibble-3.1.8/tibble/man/tibble-package.Rd | 2 tibble-3.1.8/tibble/tests/testthat/_snaps/print.md | 15 + tibble-3.1.8/tibble/tests/testthat/_snaps/subsetting.md | 48 ++--- tibble-3.1.8/tibble/tests/testthat/_snaps/vignette-invariants/invariants.md | 12 + tibble-3.1.8/tibble/tests/testthat/_snaps/vignette-numbers/numbers.md | 14 + tibble-3.1.8/tibble/tests/testthat/_snaps/vignette-tibble/tibble.md | 18 + tibble-3.1.8/tibble/tests/testthat/_snaps/zzz-trunc-mat.md |only tibble-3.1.8/tibble/tests/testthat/helper-zzz.R | 5 tibble-3.1.8/tibble/tests/testthat/test-tribble.R | 1 tibble-3.1.8/tibble/tests/testthat/test-zzz-tribble.R | 1 tibble-3.1.8/tibble/vignettes/numbers.Rmd | 7 28 files changed, 280 insertions(+), 236 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests.
Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony',
'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.3.3 dated 2022-05-16 and 1.3.4 dated 2022-07-22
TestDesign-1.3.3/TestDesign/R/item_functions.R |only TestDesign-1.3.3/TestDesign/R/test_operators.R |only TestDesign-1.3.3/TestDesign/src/item_functions.cpp |only TestDesign-1.3.3/TestDesign/src/item_functions.h |only TestDesign-1.3.4/TestDesign/DESCRIPTION | 32 TestDesign-1.3.4/TestDesign/MD5 | 125 - TestDesign-1.3.4/TestDesign/NAMESPACE | 40 TestDesign-1.3.4/TestDesign/NEWS.md | 17 TestDesign-1.3.4/TestDesign/R/RcppExports.R | 288 ++ TestDesign-1.3.4/TestDesign/R/bayes_functions.R | 164 - TestDesign-1.3.4/TestDesign/R/calc_escore_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_fisher_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_hessian_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_jacobian_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_location_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_loglikelihood_functions.r |only TestDesign-1.3.4/TestDesign/R/calc_prob_functions.r |only TestDesign-1.3.4/TestDesign/R/cpp_documents.R | 152 + TestDesign-1.3.4/TestDesign/R/eligibility_functions.R | 25 TestDesign-1.3.4/TestDesign/R/exposure_control_functions.R | 2 TestDesign-1.3.4/TestDesign/R/import.R | 3 TestDesign-1.3.4/TestDesign/R/item_pool_operators.R | 8 TestDesign-1.3.4/TestDesign/R/loading_functions.R | 288 +- TestDesign-1.3.4/TestDesign/R/other_functions.R | 124 - TestDesign-1.3.4/TestDesign/R/plot_functions.R | 1121 ++++------ TestDesign-1.3.4/TestDesign/R/shadow_class.R | 106 TestDesign-1.3.4/TestDesign/R/shadow_functions.R | 224 - TestDesign-1.3.4/TestDesign/R/sim_resp_functions.r |only TestDesign-1.3.4/TestDesign/R/simulation_data_cache_class.r |only TestDesign-1.3.4/TestDesign/R/simulation_data_cache_operators.r |only TestDesign-1.3.4/TestDesign/R/static_functions.R | 10 TestDesign-1.3.4/TestDesign/R/summary_class.R | 10 TestDesign-1.3.4/TestDesign/R/theta_functions.R | 206 + TestDesign-1.3.4/TestDesign/build/vignette.rds |binary TestDesign-1.3.4/TestDesign/inst/doc/constraints.html | 525 ++++ TestDesign-1.3.4/TestDesign/inst/doc/rsymphony.html | 294 ++ TestDesign-1.3.4/TestDesign/inst/doc/split.html | 224 + TestDesign-1.3.4/TestDesign/man/Shadow-methods.Rd | 10 TestDesign-1.3.4/TestDesign/man/calcEscore-methods.Rd | 4 TestDesign-1.3.4/TestDesign/man/calcFisher-methods.Rd | 2 TestDesign-1.3.4/TestDesign/man/calcHessian-methods.Rd | 26 TestDesign-1.3.4/TestDesign/man/calcJacobian-methods.Rd | 30 TestDesign-1.3.4/TestDesign/man/calcLocation-methods.Rd | 2 TestDesign-1.3.4/TestDesign/man/calcLogLikelihood-methods.Rd | 2 TestDesign-1.3.4/TestDesign/man/calcProb-methods.Rd | 2 TestDesign-1.3.4/TestDesign/man/createShadowTestConfig.Rd | 1 TestDesign-1.3.4/TestDesign/man/e_item.Rd |only TestDesign-1.3.4/TestDesign/man/eap-methods.Rd | 2 TestDesign-1.3.4/TestDesign/man/h_item.Rd |only TestDesign-1.3.4/TestDesign/man/j_item.Rd |only TestDesign-1.3.4/TestDesign/man/makeSimulationDataCache-methods.Rd |only TestDesign-1.3.4/TestDesign/man/makeTest-methods.Rd | 8 TestDesign-1.3.4/TestDesign/man/makeTestCluster-methods.Rd | 14 TestDesign-1.3.4/TestDesign/man/simResp-methods.Rd | 25 TestDesign-1.3.4/TestDesign/man/simulation_data_cache-class.Rd |only TestDesign-1.3.4/TestDesign/man/test-class.Rd | 9 TestDesign-1.3.4/TestDesign/man/test_cluster-class.Rd | 8 TestDesign-1.3.4/TestDesign/man/test_operators.Rd | 2 TestDesign-1.3.4/TestDesign/src/Makevars.win |only TestDesign-1.3.4/TestDesign/src/RcppExports.cpp | 642 +++++ TestDesign-1.3.4/TestDesign/src/expected_score.cpp |only TestDesign-1.3.4/TestDesign/src/expected_score.h |only TestDesign-1.3.4/TestDesign/src/hessian.cpp |only TestDesign-1.3.4/TestDesign/src/hessian.h |only TestDesign-1.3.4/TestDesign/src/info_array_functions.cpp | 3 TestDesign-1.3.4/TestDesign/src/item_information.cpp |only TestDesign-1.3.4/TestDesign/src/item_information.h |only TestDesign-1.3.4/TestDesign/src/item_probability.cpp |only TestDesign-1.3.4/TestDesign/src/item_probability.h |only TestDesign-1.3.4/TestDesign/src/jacobian.cpp |only TestDesign-1.3.4/TestDesign/src/jacobian.h |only TestDesign-1.3.4/TestDesign/src/other_functions.cpp | 1 TestDesign-1.3.4/TestDesign/src/posterior_functions.cpp | 2 TestDesign-1.3.4/TestDesign/src/posterior_functions.h | 8 TestDesign-1.3.4/TestDesign/src/theta_functions.cpp | 1 TestDesign-1.3.4/TestDesign/tests/testthat/test-gfi.R | 2 TestDesign-1.3.4/TestDesign/tests/testthat/test-refresh-methods.R | 4 TestDesign-1.3.4/TestDesign/tests/testthat/test-theta-methods.R | 2 TestDesign-1.3.4/TestDesign/tests/testthat/test_unidimensional.r |only 79 files changed, 3397 insertions(+), 1403 deletions(-)
Title: Location Identify Tool
Description: Determine the sea area where the fishing boat operates.
The latitude and longitude of geographic coordinates are used to match oceanic areas and economic sea areas.
You can plot the distribution map with dotplot() function.
Please refer to Flanders Marine Institute (2020) <doi:10.14284/403>.
Author: shiao chih hao [aut, cre, ctb],
chang shu ting [aut, ctb]
Maintainer: shiao chih hao <chihhao@ofdc.org.tw>
Diff between oceanic versions 0.1.3 dated 2022-03-22 and 0.1.4 dated 2022-07-22
DESCRIPTION | 14 +++++++------- MD5 | 16 +++++++++++----- NAMESPACE | 32 +++++++++++++++++--------------- R/data.R | 9 ++++++++- R/idfocean.R | 1 + R/idfport.R |only R/sixtytoten.R |only data/port.rda |only man/eez_rg.Rd | 2 +- man/idfport.Rd |only man/port.Rd |only man/sixtytoten.Rd |only 12 files changed, 45 insertions(+), 29 deletions(-)
Title: Functions for 'Ecdat'
Description: Functions and vignettes to update
data sets in 'Ecdat' and to create, manipulate,
plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.2-6 dated 2022-06-15 and 0.3-0 dated 2022-07-21
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 27 +++++--- build/vignette.rds |binary inst/WORDLIST | 16 ++++ inst/doc/UpdatingUSGDPpresidents.Rmd | 2 inst/doc/UpdatingUSGDPpresidents.html | 4 - inst/doc/nuclearArmageddon.html | 104 +++++++++++++++---------------- inst/doc/update_nuclearWeaponStates.html | 4 - man/read.transpose.Rd | 40 ++++++----- man/subNonStandardCharacters.Rd | 4 - vignettes/UpdatingUSGDPpresidents.Rmd | 2 12 files changed, 130 insertions(+), 103 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 1.3.4 dated 2022-03-25 and 1.3.5 dated 2022-07-21
DESCRIPTION | 8 ++-- MD5 | 12 +++--- R/visvow.R | 64 ++++++++++++++++++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/visvow.pdf |binary tests/testthat/data/Nearey_IIF.csv | 52 +++++++++++++++--------------- 7 files changed, 85 insertions(+), 51 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Mueller [aut, cre] ,
Antoine Fabri [ctb],
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
Indrajeet Patil [ctb] ,
Maelle Salmon [ctb] ,
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>
Diff between dm versions 0.3.0 dated 2022-07-06 and 1.0.0 dated 2022-07-21
dm-0.3.0/dm/R/rows-truncate.R |only dm-0.3.0/dm/man/dm_add_tbl.Rd |only dm-0.3.0/dm/man/dm_bind.Rd |only dm-0.3.0/dm/man/dm_get_filters.Rd |only dm-0.3.0/dm/man/dm_rm_tbl.Rd |only dm-0.3.0/dm/man/enum_pk_candidates.Rd |only dm-0.3.0/dm/man/rows_truncate.Rd |only dm-1.0.0/dm/DESCRIPTION | 29 dm-1.0.0/dm/MD5 | 604 +++--- dm-1.0.0/dm/NAMESPACE | 116 - dm-1.0.0/dm/NEWS.md | 93 dm-1.0.0/dm/R/aaa-dbplyr.R | 2 dm-1.0.0/dm/R/aaa-dplyr.R | 2 dm-1.0.0/dm/R/add-tbl.R | 68 dm-1.0.0/dm/R/bind.R | 65 dm-1.0.0/dm/R/check-cardinalities.R | 323 ++- dm-1.0.0/dm/R/code-generation.R | 34 dm-1.0.0/dm/R/datamodelr-code.R | 21 dm-1.0.0/dm/R/db-interface.R | 2 dm-1.0.0/dm/R/deconstruct.R |only dm-1.0.0/dm/R/disambiguate.R | 34 dm-1.0.0/dm/R/dm.R | 340 ++- dm-1.0.0/dm/R/dm_from_con.R | 5 dm-1.0.0/dm/R/dm_get_con.R | 2 dm-1.0.0/dm/R/dm_get_tables.R |only dm-1.0.0/dm/R/dm_gui.R |only dm-1.0.0/dm/R/dm_unnest_tbl.R | 4 dm-1.0.0/dm/R/dplyr-src.R | 8 dm-1.0.0/dm/R/dplyr.R | 254 ++ dm-1.0.0/dm/R/draw-dm.R | 12 dm-1.0.0/dm/R/error-helpers.R | 18 dm-1.0.0/dm/R/examine-cardinalities.R | 59 dm-1.0.0/dm/R/examine-constraints.R | 53 dm-1.0.0/dm/R/filter-dm.R | 231 +- dm-1.0.0/dm/R/filter-helpers.R | 5 dm-1.0.0/dm/R/financial.R | 2 dm-1.0.0/dm/R/flatten.R | 96 dm-1.0.0/dm/R/foreign-keys.R | 40 dm-1.0.0/dm/R/global.R | 13 dm-1.0.0/dm/R/gui-check.R |only dm-1.0.0/dm/R/gui-dm.R |only dm-1.0.0/dm/R/gui-dmSVG.R |only dm-1.0.0/dm/R/gui-dm_to_svg.R |only dm-1.0.0/dm/R/gui-expect_mw_cg_snapshot.R |only dm-1.0.0/dm/R/gui-gui_global.R |only dm-1.0.0/dm/R/gui-gui_run.R |only dm-1.0.0/dm/R/gui-gui_server.R |only dm-1.0.0/dm/R/gui-gui_ui.R |only dm-1.0.0/dm/R/gui-mw_cg.R |only dm-1.0.0/dm/R/gui-mw_cg_enum_dm_add_fk.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_add_fk.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_add_pk.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_disentangle.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_rename.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_rm_fk.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_select.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_select_tbl.R |only dm-1.0.0/dm/R/gui-mw_cg_make_dm_set_colors.R |only dm-1.0.0/dm/R/gui-ops_stack.R |only dm-1.0.0/dm/R/gui-shiny_input.R |only dm-1.0.0/dm/R/gui-zzz.R |only dm-1.0.0/dm/R/key-helpers.R | 260 +- dm-1.0.0/dm/R/learn.R | 5 dm-1.0.0/dm/R/nest.R | 28 dm-1.0.0/dm/R/nycflights13.R | 2 dm-1.0.0/dm/R/pack_join.R | 2 dm-1.0.0/dm/R/paste.R | 2 dm-1.0.0/dm/R/pixarfilms.R | 2 dm-1.0.0/dm/R/primary-keys.R | 17 dm-1.0.0/dm/R/ptype.R | 2 dm-1.0.0/dm/R/reexport.R | 3 dm-1.0.0/dm/R/rows-dm.R | 14 dm-1.0.0/dm/R/schema.R | 2 dm-1.0.0/dm/R/select-tbl.R | 10 dm-1.0.0/dm/R/select.R | 6 dm-1.0.0/dm/R/table-surgery.R | 12 dm-1.0.0/dm/R/tidyr.R | 50 dm-1.0.0/dm/R/upgrade.R | 11 dm-1.0.0/dm/R/utils.R | 14 dm-1.0.0/dm/R/validate.R | 12 dm-1.0.0/dm/R/zoom.R | 27 dm-1.0.0/dm/R/zzx-deprecated.R | 203 ++ dm-1.0.0/dm/R/zzz.R | 2 dm-1.0.0/dm/README.md | 40 dm-1.0.0/dm/build/vignette.rds |binary dm-1.0.0/dm/demo/basel.R | 4 dm-1.0.0/dm/demo/hamburg.R | 4 dm-1.0.0/dm/demo/nyc.R | 4 dm-1.0.0/dm/demo/seattle.R | 4 dm-1.0.0/dm/demo/zurich2.R | 2 dm-1.0.0/dm/inst/doc/dm.R | 108 - dm-1.0.0/dm/inst/doc/dm.Rmd | 10 dm-1.0.0/dm/inst/doc/dm.html | 267 -- dm-1.0.0/dm/inst/doc/howto-dm-copy.R | 196 +- dm-1.0.0/dm/inst/doc/howto-dm-copy.Rmd | 6 dm-1.0.0/dm/inst/doc/howto-dm-copy.html | 359 --- dm-1.0.0/dm/inst/doc/howto-dm-db.R | 148 - dm-1.0.0/dm/inst/doc/howto-dm-db.Rmd | 6 dm-1.0.0/dm/inst/doc/howto-dm-db.html | 354 --- dm-1.0.0/dm/inst/doc/howto-dm-df.R | 116 - dm-1.0.0/dm/inst/doc/howto-dm-df.html | 592 ------ dm-1.0.0/dm/inst/doc/howto-dm-rows.R | 188 - dm-1.0.0/dm/inst/doc/howto-dm-rows.Rmd | 6 dm-1.0.0/dm/inst/doc/howto-dm-rows.html | 351 --- dm-1.0.0/dm/inst/doc/howto-dm-theory.R | 98 - dm-1.0.0/dm/inst/doc/howto-dm-theory.html | 291 --- dm-1.0.0/dm/inst/doc/tech-dm-cdm.R | 12 dm-1.0.0/dm/inst/doc/tech-dm-cdm.html | 77 dm-1.0.0/dm/inst/doc/tech-dm-class.R | 124 - dm-1.0.0/dm/inst/doc/tech-dm-class.Rmd | 24 dm-1.0.0/dm/inst/doc/tech-dm-class.html | 184 - dm-1.0.0/dm/inst/doc/tech-dm-draw.R | 52 dm-1.0.0/dm/inst/doc/tech-dm-draw.Rmd | 2 dm-1.0.0/dm/inst/doc/tech-dm-draw.html | 576 ----- dm-1.0.0/dm/inst/doc/tech-dm-filter.R | 104 - dm-1.0.0/dm/inst/doc/tech-dm-filter.Rmd | 58 dm-1.0.0/dm/inst/doc/tech-dm-filter.html | 373 --- dm-1.0.0/dm/inst/doc/tech-dm-join.R | 71 dm-1.0.0/dm/inst/doc/tech-dm-join.Rmd | 23 dm-1.0.0/dm/inst/doc/tech-dm-join.html | 243 -- dm-1.0.0/dm/inst/doc/tech-dm-keyed.R |only dm-1.0.0/dm/inst/doc/tech-dm-keyed.Rmd |only dm-1.0.0/dm/inst/doc/tech-dm-keyed.html |only dm-1.0.0/dm/inst/doc/tech-dm-low-level.R | 78 dm-1.0.0/dm/inst/doc/tech-dm-low-level.html | 165 - dm-1.0.0/dm/inst/doc/tech-dm-naming.Rmd | 6 dm-1.0.0/dm/inst/doc/tech-dm-naming.html | 6 dm-1.0.0/dm/inst/doc/tech-dm-zoom.R | 218 +- dm-1.0.0/dm/inst/doc/tech-dm-zoom.Rmd | 21 dm-1.0.0/dm/inst/doc/tech-dm-zoom.html | 970 +--------- dm-1.0.0/dm/inst/htmlwidgets |only dm-1.0.0/dm/man/check_key.Rd | 22 dm-1.0.0/dm/man/check_set_equality.Rd | 34 dm-1.0.0/dm/man/check_subset.Rd | 25 dm-1.0.0/dm/man/copy_dm_to.Rd | 2 dm-1.0.0/dm/man/decompose_table.Rd | 6 dm-1.0.0/dm/man/deprecated.Rd | 50 dm-1.0.0/dm/man/dm.Rd | 50 dm-1.0.0/dm/man/dm_add_fk.Rd | 2 dm-1.0.0/dm/man/dm_add_pk.Rd | 2 dm-1.0.0/dm/man/dm_disambiguate_cols.Rd | 19 dm-1.0.0/dm/man/dm_draw.Rd | 2 dm-1.0.0/dm/man/dm_enum_fk_candidates.Rd | 8 dm-1.0.0/dm/man/dm_enum_pk_candidates.Rd |only dm-1.0.0/dm/man/dm_examine_cardinalities.Rd | 16 dm-1.0.0/dm/man/dm_examine_constraints.Rd | 14 dm-1.0.0/dm/man/dm_filter.Rd | 93 dm-1.0.0/dm/man/dm_financial.Rd | 2 dm-1.0.0/dm/man/dm_flatten_to_tbl.Rd | 60 dm-1.0.0/dm/man/dm_from_con.Rd | 2 dm-1.0.0/dm/man/dm_get_all_fks.Rd | 2 dm-1.0.0/dm/man/dm_get_all_pks.Rd | 4 dm-1.0.0/dm/man/dm_get_con.Rd | 2 dm-1.0.0/dm/man/dm_get_tables.Rd |only dm-1.0.0/dm/man/dm_gui.Rd |only dm-1.0.0/dm/man/dm_has_pk.Rd | 2 dm-1.0.0/dm/man/dm_mutate_tbl.Rd | 2 dm-1.0.0/dm/man/dm_nrow.Rd | 5 dm-1.0.0/dm/man/dm_nycflights13.Rd | 2 dm-1.0.0/dm/man/dm_paste.Rd | 2 dm-1.0.0/dm/man/dm_pixarfilms.Rd | 2 dm-1.0.0/dm/man/dm_ptype.Rd | 2 dm-1.0.0/dm/man/dm_rename.Rd | 2 dm-1.0.0/dm/man/dm_rm_fk.Rd | 2 dm-1.0.0/dm/man/dm_rm_pk.Rd | 2 dm-1.0.0/dm/man/dm_select.Rd | 2 dm-1.0.0/dm/man/dm_select_tbl.Rd | 5 dm-1.0.0/dm/man/dm_set_colors.Rd | 2 dm-1.0.0/dm/man/dm_zoom_to.Rd | 11 dm-1.0.0/dm/man/dplyr_join.Rd | 52 dm-1.0.0/dm/man/dplyr_src.Rd | 6 dm-1.0.0/dm/man/dplyr_table_manipulation.Rd | 84 dm-1.0.0/dm/man/examine_cardinality.Rd | 167 + dm-1.0.0/dm/man/figures/README-draw.svg | 18 dm-1.0.0/dm/man/glimpse.dm.Rd | 6 dm-1.0.0/dm/man/materialize.Rd | 4 dm-1.0.0/dm/man/pack_join.Rd | 4 dm-1.0.0/dm/man/pull_tbl.Rd | 18 dm-1.0.0/dm/man/reexports.Rd | 3 dm-1.0.0/dm/man/reunite_parent_child.Rd | 6 dm-1.0.0/dm/man/rows-dm.Rd | 7 dm-1.0.0/dm/man/tidyr_table_manipulation.Rd | 40 dm-1.0.0/dm/man/utils_table_manipulation.Rd | 20 dm-1.0.0/dm/tests/testthat/_snaps/add-tbl.md | 30 dm-1.0.0/dm/tests/testthat/_snaps/bind.md | 73 dm-1.0.0/dm/tests/testthat/_snaps/check-cardinalities.md | 117 - dm-1.0.0/dm/tests/testthat/_snaps/code-generation.md | 33 dm-1.0.0/dm/tests/testthat/_snaps/datamodelr-code |only dm-1.0.0/dm/tests/testthat/_snaps/datamodelr-code.md |only dm-1.0.0/dm/tests/testthat/_snaps/deconstruct.md |only dm-1.0.0/dm/tests/testthat/_snaps/disambiguate.md | 20 dm-1.0.0/dm/tests/testthat/_snaps/disentangle.md | 4 dm-1.0.0/dm/tests/testthat/_snaps/dm.md | 466 ++++ dm-1.0.0/dm/tests/testthat/_snaps/dplyr.md | 77 dm-1.0.0/dm/tests/testthat/_snaps/draw-dm.md | 53 dm-1.0.0/dm/tests/testthat/_snaps/draw-dm/empty-table-in-dm.svg | 6 dm-1.0.0/dm/tests/testthat/_snaps/draw-dm/nycflight-dm-types.svg | 18 dm-1.0.0/dm/tests/testthat/_snaps/draw-dm/nycflight-dm.svg | 30 dm-1.0.0/dm/tests/testthat/_snaps/draw-dm/single-empty-table-dm.svg | 2 dm-1.0.0/dm/tests/testthat/_snaps/enumerate_all_paths.md | 4 dm-1.0.0/dm/tests/testthat/_snaps/error-helpers.md | 16 dm-1.0.0/dm/tests/testthat/_snaps/examine-cardinalities.md | 29 dm-1.0.0/dm/tests/testthat/_snaps/examine-constraints.md | 40 dm-1.0.0/dm/tests/testthat/_snaps/filter-dm.md | 122 + dm-1.0.0/dm/tests/testthat/_snaps/foreign-keys.md | 1 dm-1.0.0/dm/tests/testthat/_snaps/key-helpers.md | 81 dm-1.0.0/dm/tests/testthat/_snaps/pack_join.md | 2 dm-1.0.0/dm/tests/testthat/_snaps/paste.md | 4 dm-1.0.0/dm/tests/testthat/_snaps/primary-keys.md | 1 dm-1.0.0/dm/tests/testthat/_snaps/rows-dm.md | 18 dm-1.0.0/dm/tests/testthat/_snaps/tidyr.md | 8 dm-1.0.0/dm/tests/testthat/_snaps/upgrade.md | 32 dm-1.0.0/dm/tests/testthat/_snaps/waldo.md | 20 dm-1.0.0/dm/tests/testthat/_snaps/zoom.md | 35 dm-1.0.0/dm/tests/testthat/dm/v3.rds |only dm-1.0.0/dm/tests/testthat/dm/v3_zoomed.rds |only dm-1.0.0/dm/tests/testthat/helper-expectations.R | 5 dm-1.0.0/dm/tests/testthat/helper-src.R | 35 dm-1.0.0/dm/tests/testthat/test-add-tbl.R | 31 dm-1.0.0/dm/tests/testthat/test-bind.R | 32 dm-1.0.0/dm/tests/testthat/test-check-cardinalities.R | 368 +++ dm-1.0.0/dm/tests/testthat/test-code-generation.R | 10 dm-1.0.0/dm/tests/testthat/test-datamodelr-code.R |only dm-1.0.0/dm/tests/testthat/test-db-interface.R | 3 dm-1.0.0/dm/tests/testthat/test-deconstruct.R |only dm-1.0.0/dm/tests/testthat/test-dm.R | 289 ++ dm-1.0.0/dm/tests/testthat/test-dm_wrap.R | 20 dm-1.0.0/dm/tests/testthat/test-dplyr-src.R | 8 dm-1.0.0/dm/tests/testthat/test-dplyr.R | 105 - dm-1.0.0/dm/tests/testthat/test-draw-dm.R | 12 dm-1.0.0/dm/tests/testthat/test-examine-cardinalities.R | 13 dm-1.0.0/dm/tests/testthat/test-examine-constraints.R | 23 dm-1.0.0/dm/tests/testthat/test-filter-dm.R | 115 - dm-1.0.0/dm/tests/testthat/test-flatten.R | 149 - dm-1.0.0/dm/tests/testthat/test-foreign-keys.R | 2 dm-1.0.0/dm/tests/testthat/test-key-helpers.R | 304 +++ dm-1.0.0/dm/tests/testthat/test-nest.R | 22 dm-1.0.0/dm/tests/testthat/test-pack_join.R | 2 dm-1.0.0/dm/tests/testthat/test-paste.R | 2 dm-1.0.0/dm/tests/testthat/test-primary-keys.R | 2 dm-1.0.0/dm/tests/testthat/test-rows-dm.R | 3 dm-1.0.0/dm/tests/testthat/test-tidyr.R | 32 dm-1.0.0/dm/tests/testthat/test-upgrade.R | 30 dm-1.0.0/dm/tests/testthat/test-utils.R | 4 dm-1.0.0/dm/tests/testthat/test-validate.R | 2 dm-1.0.0/dm/tests/testthat/test-waldo.R | 33 dm-1.0.0/dm/tests/testthat/test-zoom.R | 16 dm-1.0.0/dm/tests/testthat/test-zzx-deprecated.R | 2 dm-1.0.0/dm/vignettes/dm.Rmd | 10 dm-1.0.0/dm/vignettes/flights_dm_w_many_keys_and_color.svg |only dm-1.0.0/dm/vignettes/howto-dm-copy.Rmd | 6 dm-1.0.0/dm/vignettes/howto-dm-db.Rmd | 6 dm-1.0.0/dm/vignettes/howto-dm-rows.Rmd | 6 dm-1.0.0/dm/vignettes/setup/setup.R | 9 dm-1.0.0/dm/vignettes/tech-dm-class.Rmd | 24 dm-1.0.0/dm/vignettes/tech-dm-draw.Rmd | 2 dm-1.0.0/dm/vignettes/tech-dm-filter.Rmd | 58 dm-1.0.0/dm/vignettes/tech-dm-join.Rmd | 23 dm-1.0.0/dm/vignettes/tech-dm-keyed.Rmd |only dm-1.0.0/dm/vignettes/tech-dm-naming.Rmd | 6 dm-1.0.0/dm/vignettes/tech-dm-zoom.Rmd | 21 261 files changed, 6500 insertions(+), 7344 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.14.0 dated 2022-02-02 and 2.14.1 dated 2022-07-21
rebmix-2.14.0/rebmix/R/dist.xy.R |only rebmix-2.14.1/rebmix/DESCRIPTION | 8 rebmix-2.14.1/rebmix/MD5 | 179 - rebmix-2.14.1/rebmix/NAMESPACE | 11 rebmix-2.14.1/rebmix/R/AllClasses.R | 280 ++ rebmix-2.14.1/rebmix/R/AllGenerics.R | 33 rebmix-2.14.1/rebmix/R/EMMIX.R | 54 rebmix-2.14.1/rebmix/R/IC.R | 415 ++-- rebmix-2.14.1/rebmix/R/RCLRMIX.R | 252 +- rebmix-2.14.1/rebmix/R/RCLSMIX.R | 10 rebmix-2.14.1/rebmix/R/REBMIX.R | 392 ++- rebmix-2.14.1/rebmix/R/RNGMIX.R | 4 rebmix-2.14.1/rebmix/R/bins.R | 21 rebmix-2.14.1/rebmix/R/boot.REBMIX.R | 4 rebmix-2.14.1/rebmix/R/demix.R | 353 ++- rebmix-2.14.1/rebmix/R/densHistogram.x.R | 2 rebmix-2.14.1/rebmix/R/densHistogram.xy.R | 2 rebmix-2.14.1/rebmix/R/densK.x.R |only rebmix-2.14.1/rebmix/R/densK.xy.R |only rebmix-2.14.1/rebmix/R/densKDE.x.R | 2 rebmix-2.14.1/rebmix/R/densKDE.xy.R | 2 rebmix-2.14.1/rebmix/R/densKNearestNeighbour.x.R | 2 rebmix-2.14.1/rebmix/R/densKNearestNeighbour.xy.R | 2 rebmix-2.14.1/rebmix/R/dfmix.R | 22 rebmix-2.14.1/rebmix/R/dist.x.R | 35 rebmix-2.14.1/rebmix/R/histogram.R |only rebmix-2.14.1/rebmix/R/legendA.R | 2 rebmix-2.14.1/rebmix/R/mapclusters.R |only rebmix-2.14.1/rebmix/R/optbins.R | 21 rebmix-2.14.1/rebmix/R/pemix.R | 140 + rebmix-2.14.1/rebmix/R/pfmix.R | 12 rebmix-2.14.1/rebmix/R/plot.RCLRMIX.R | 74 rebmix-2.14.1/rebmix/R/plot.REBMIX.R | 608 +++-- rebmix-2.14.1/rebmix/R/summary.R | 4 rebmix-2.14.1/rebmix/R/zaccessors.R | 71 rebmix-2.14.1/rebmix/build/partial.rdb |binary rebmix-2.14.1/rebmix/build/vignette.rds |binary rebmix-2.14.1/rebmix/data/adult.rda |binary rebmix-2.14.1/rebmix/data/bearings.rda |binary rebmix-2.14.1/rebmix/data/galaxy.rda |binary rebmix-2.14.1/rebmix/data/iris.rda |binary rebmix-2.14.1/rebmix/data/sensorlessdrive.rda |binary rebmix-2.14.1/rebmix/data/steelplates.rda |binary rebmix-2.14.1/rebmix/data/truck.rda |binary rebmix-2.14.1/rebmix/data/weibull.rda |binary rebmix-2.14.1/rebmix/data/weibullnormal.rda |binary rebmix-2.14.1/rebmix/data/wine.rda |binary rebmix-2.14.1/rebmix/demo/rebmix.truck.R | 4 rebmix-2.14.1/rebmix/demo/rebmix.weibullnormal.R | 4 rebmix-2.14.1/rebmix/inst/CITATION | 6 rebmix-2.14.1/rebmix/inst/NEWS.Rd | 10 rebmix-2.14.1/rebmix/inst/doc/rebmix.Rnw | 1619 +++++++-------- rebmix-2.14.1/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.14.1/rebmix/man/AIC.Rd | 4 rebmix-2.14.1/rebmix/man/EM.Control-class.Rd | 8 rebmix-2.14.1/rebmix/man/EMMIX.Rd | 2 rebmix-2.14.1/rebmix/man/HQC.Rd | 2 rebmix-2.14.1/rebmix/man/Histogram-class.Rd |only rebmix-2.14.1/rebmix/man/MDL.Rd | 2 rebmix-2.14.1/rebmix/man/PRD.Rd | 2 rebmix-2.14.1/rebmix/man/RCLRMIX-class.Rd | 2 rebmix-2.14.1/rebmix/man/RCLRMIX.Rd | 4 rebmix-2.14.1/rebmix/man/REBMIX-class.Rd | 10 rebmix-2.14.1/rebmix/man/REBMIX.Rd | 14 rebmix-2.14.1/rebmix/man/REBMIX.plot.Rd | 2 rebmix-2.14.1/rebmix/man/bearings.Rd | 2 rebmix-2.14.1/rebmix/man/bins.Rd | 7 rebmix-2.14.1/rebmix/man/chistogram.Rd |only rebmix-2.14.1/rebmix/man/demix.Rd | 2 rebmix-2.14.1/rebmix/man/dfmix.Rd | 2 rebmix-2.14.1/rebmix/man/fhistogram.Rd |only rebmix-2.14.1/rebmix/man/galaxy.Rd | 8 rebmix-2.14.1/rebmix/man/mapclusters.Rd |only rebmix-2.14.1/rebmix/man/optbins.Rd | 5 rebmix-2.14.1/rebmix/man/pemix.Rd | 2 rebmix-2.14.1/rebmix/man/pfmix.Rd | 2 rebmix-2.14.1/rebmix/man/rebmix-internal.Rd | 19 rebmix-2.14.1/rebmix/src/Rrebmix.cpp | 1311 +++++++++--- rebmix-2.14.1/rebmix/src/Rrebmvnorm.cpp | 748 +++++-- rebmix-2.14.1/rebmix/src/base.cpp | 88 rebmix-2.14.1/rebmix/src/base.h | 64 rebmix-2.14.1/rebmix/src/emf.cpp | 233 +- rebmix-2.14.1/rebmix/src/emf.h | 49 rebmix-2.14.1/rebmix/src/init.c | 63 rebmix-2.14.1/rebmix/src/rebmix.cpp | 2 rebmix-2.14.1/rebmix/src/rebmixf.cpp | 2253 ++++++++++++++++------ rebmix-2.14.1/rebmix/src/rebmixf.h | 168 - rebmix-2.14.1/rebmix/src/rebmvnormf.cpp | 164 - rebmix-2.14.1/rebmix/src/rebmvnormf.h | 32 rebmix-2.14.1/rebmix/src/rngmixf.cpp | 64 rebmix-2.14.1/rebmix/src/rngmixf.h | 22 rebmix-2.14.1/rebmix/src/rngmvnormf.cpp | 8 rebmix-2.14.1/rebmix/src/rngmvnormf.h | 2 rebmix-2.14.1/rebmix/vignettes/rebmix.Rnw | 1619 +++++++-------- rebmix-2.14.1/rebmix/vignettes/rebmix.bib | 2 95 files changed, 7251 insertions(+), 4402 deletions(-)
Title: Fast and Light-Weight Caching (Memoization) of Objects and
Results to Speed Up Computations
Description: Memoization can be used to speed up repetitive and computational expensive function calls. The first time a function that implements memoization is called the results are stored in a cache memory. The next time the function is called with the same set of parameters, the results are momentarily retrieved from the cache avoiding repeating the calculations. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.cache versions 0.15.0 dated 2021-04-30 and 0.16.0 dated 2022-07-21
R.cache-0.15.0/R.cache/NEWS |only R.cache-0.16.0/R.cache/DESCRIPTION | 7 ++++--- R.cache-0.16.0/R.cache/MD5 | 12 ++++++------ R.cache-0.16.0/R.cache/NEWS.md |only R.cache-0.16.0/R.cache/R/getCachePath.R | 15 +++++++++++++-- R.cache-0.16.0/R.cache/R/memoizedCall.R | 12 +++++++++++- R.cache-0.16.0/R.cache/man/R.cache-package.Rd | 1 - R.cache-0.16.0/R.cache/man/getCachePath.Rd | 2 ++ 8 files changed, 36 insertions(+), 13 deletions(-)
Title: General-Purpose Phase-Type Functions
Description: General implementation of core function from phase-type
theory. 'PhaseTypeR' can be used to model continuous and discrete
phase-type distributions, both univariate and multivariate. The
package includes functions for outputting the mean and (co)variance of
phase-type distributions; their density, probability and quantile
functions; functions for random draws; functions for
reward-transformation; and functions for plotting the distributions as
networks. For more information on these functions please refer to
Bladt and Nielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro
(2019)
<https://orbit.dtu.dk/en/publications/order-statistics-and-multivariate-discrete-phase-type-distributio>.
Author: Iker Rivas-Gonzalez [aut, cre]
,
Asger Hobolth [aut],
Lars Noervang Andersen [aut],
Colin Guetemme [aut]
Maintainer: Iker Rivas-Gonzalez <ikerrivas96@gmail.com>
Diff between PhaseTypeR versions 1.0.3 dated 2022-07-14 and 1.0.4 dated 2022-07-21
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/phase_type_to_network.R | 5 +++-- inst/doc/PhaseTypeR.R | 9 ++++++--- inst/doc/PhaseTypeR.Rmd | 9 ++++++--- inst/doc/PhaseTypeR.html | 17 ++++++++++------- man/phase_type_to_network.Rd | 5 +++-- vignettes/PhaseTypeR.Rmd | 9 ++++++--- 9 files changed, 50 insertions(+), 31 deletions(-)
Title: Random Forests, Linear Trees, and Gradient Boosting for
Inference and Interpretability
Description: Provides fast implementations of Honest Random Forests,
Gradient Boosting, and Linear Random Forests, with an emphasis on inference
and interpretability. Additionally contains methods for variable
importance, out-of-bag prediction, regression monotonicity, and
several methods for missing data imputation. Soren R. Kunzel,
Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon (2019) <arXiv:1906.06463>.
Author: Soeren Kuenzel [aut],
Theo Saarinen [aut, cre],
Simon Walter [aut],
Edward Liu [aut],
Allen Tang [aut],
Jasjeet Sekhon [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
Diff between Rforestry versions 0.9.0.95 dated 2022-03-09 and 0.9.0.116 dated 2022-07-21
DESCRIPTION | 6 MD5 | 32 ++-- R/RcppExports.R | 8 - R/compute_rf_lp.R | 2 R/forestry.R | 250 ++++++++++++++++++++++++------------ R/plottree.R | 16 -- man/plot-forestry.Rd | 16 -- man/predict-forestry.Rd | 31 ++++ src/RcppExports.cpp | 21 +-- src/forestry.cpp | 103 ++++++++++---- src/forestry.h | 3 src/forestryTree.cpp | 195 +++++++++++++++++----------- src/forestryTree.h | 11 - src/rcpp_cppBuildInterface.cpp | 113 +++++++++++----- src/utils.cpp | 14 ++ tests/testthat/test-groupSampling.R | 34 ++++ tests/testthat/test-hold_out_idx.R |only tests/testthat/test-trainingIdx.R |only 18 files changed, 566 insertions(+), 289 deletions(-)
Title: Discovery of Process Models with the Heuristics Miner
Description: Provides the heuristics miner algorithm for process discovery
as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The
algorithm builds a causal net from an event log created with the 'bupaR'
package. Event logs are a set of ordered sequences of events for which
'bupaR' provides the S3 class eventlog(). The discovered causal nets
can be visualised as 'htmlwidgets' and it is possible to annotate them with
the occurrence frequency or processing and waiting time of process
activities.
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>
Diff between heuristicsmineR versions 0.2.6 dated 2022-07-14 and 0.2.7 dated 2022-07-21
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/utils.R | 7 +++++-- README.md | 2 +- build/partial.rdb |binary man/causal_performance.Rd | 4 ++-- 7 files changed, 23 insertions(+), 16 deletions(-)
More information about heuristicsmineR at CRAN
Permanent link
Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre]
,
Nussaïbah Raja-Schoob [aut, ctb],
Ádam Kocsis [aut, ctb],
Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>
Diff between fossilbrush versions 1.0.2 dated 2022-05-23 and 1.0.3 dated 2022-07-21
DESCRIPTION | 10 MD5 | 27 - R/GTS2020_changelog.R |only R/add_itp.R | 136 ++--- R/check_taxonomy.R | 986 ++++++++++++++++++------------------- R/plot_dprofile.R | 147 ++--- R/revise_ranges.R | 721 +++++++++++++-------------- data/GTS2020.rda |binary data/GTS2020_changelog.rda |only inst/doc/fossilbrush_vignette.R | 8 inst/doc/fossilbrush_vignette.Rmd | 12 inst/doc/fossilbrush_vignette.pdf |binary man/GTS2020_changelog.Rd |only man/add_itp.Rd | 8 man/plot_dprofile.Rd | 6 vignettes/fossilbrush_vignette.Rmd | 12 16 files changed, 1058 insertions(+), 1015 deletions(-)
Title: Tools for Poisson Data
Description: Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.
Author: Andrew Wheeler [aut, cre]
Maintainer: Andrew Wheeler <apwheele@gmail.com>
Diff between ptools versions 1.0.0 dated 2022-07-16 and 1.0.1 dated 2022-07-21
ptools-1.0.0/ptools/tests/testthat/test-spf.R |only ptools-1.0.1/ptools/DESCRIPTION | 12 +-- ptools-1.0.1/ptools/MD5 | 17 ++-- ptools-1.0.1/ptools/R/check_pois.R | 2 ptools-1.0.1/ptools/R/sp_features.R | 94 +++++++++++++++++++++--- ptools-1.0.1/ptools/README.md | 16 ++-- ptools-1.0.1/ptools/inst/doc/spat-feateng.html | 37 ++++----- ptools-1.0.1/ptools/man/check_pois.Rd | 2 ptools-1.0.1/ptools/man/vor_sp.Rd | 5 - ptools-1.0.1/ptools/tests/testthat/test-exact.R | 16 ++-- 10 files changed, 143 insertions(+), 58 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates to be annotated
to express unspecified date components,
approximate or uncertain date components,
date ranges, and sets of dates.
This is useful for describing and analysing temporal information,
whether historical or recent, where date precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 0.3.0 dated 2022-06-02 and 0.3.1 dated 2022-07-21
messydates-0.3.0/messydates/R/stats.R |only messydates-0.3.0/messydates/man/stats.Rd |only messydates-0.3.0/messydates/tests/testthat/test-skimr.R |only messydates-0.3.1/messydates/DESCRIPTION | 12 - messydates-0.3.1/messydates/MD5 | 42 +++--- messydates-0.3.1/messydates/NAMESPACE | 11 + messydates-0.3.1/messydates/NEWS.md | 14 ++ messydates-0.3.1/messydates/R/battles.R | 5 messydates-0.3.1/messydates/R/contract.R | 7 - messydates-0.3.1/messydates/R/expand.R | 28 ++-- messydates-0.3.1/messydates/R/logical.R | 21 ++- messydates-0.3.1/messydates/R/report.R |only messydates-0.3.1/messydates/README.md | 80 +---------- messydates-0.3.1/messydates/build/vignette.rds |binary messydates-0.3.1/messydates/data/battles.rda |binary messydates-0.3.1/messydates/inst/doc/messydates.Rmd | 24 ++- messydates-0.3.1/messydates/inst/doc/messydates.html | 89 +++++-------- messydates-0.3.1/messydates/man/battles.Rd | 11 + messydates-0.3.1/messydates/man/expand.Rd | 3 messydates-0.3.1/messydates/man/logical-class.Rd | 15 ++ messydates-0.3.1/messydates/man/mreport.Rd |only messydates-0.3.1/messydates/tests/testthat/test-contract.R | 6 messydates-0.3.1/messydates/tests/testthat/test-logical.R | 10 + messydates-0.3.1/messydates/tests/testthat/test-report.R |only messydates-0.3.1/messydates/vignettes/messydates.Rmd | 24 ++- 25 files changed, 212 insertions(+), 190 deletions(-)
Title: Data from the Doctor Who Series
Description: Explore data related to the Doctor Who TV series.
Author: Jonathan Kitt [aut, cre]
Maintainer: Jonathan Kitt <jonathan.kitt@protonmail.com>
Diff between datardis versions 0.0.2 dated 2021-11-15 and 0.0.3 dated 2022-07-21
datardis-0.0.2/datardis/data/directors.rda |only datardis-0.0.2/datardis/data/episodes.rda |only datardis-0.0.2/datardis/data/writers.rda |only datardis-0.0.2/datardis/man/directors.Rd |only datardis-0.0.2/datardis/man/episodes.Rd |only datardis-0.0.2/datardis/man/writers.Rd |only datardis-0.0.3/datardis/DESCRIPTION | 8 - datardis-0.0.3/datardis/LICENSE | 4 datardis-0.0.3/datardis/MD5 | 34 +++--- datardis-0.0.3/datardis/NAMESPACE | 7 - datardis-0.0.3/datardis/NEWS.md | 6 + datardis-0.0.3/datardis/R/datasets.R | 91 +++++++++++++++-- datardis-0.0.3/datardis/README.md | 41 ++++--- datardis-0.0.3/datardis/data/drwho_directors.rda |only datardis-0.0.3/datardis/data/drwho_episodes.rda |only datardis-0.0.3/datardis/data/drwho_writers.rda |only datardis-0.0.3/datardis/data/torchwood_directors.rda |only datardis-0.0.3/datardis/data/torchwood_episodes.rda |only datardis-0.0.3/datardis/data/torchwood_writers.rda |only datardis-0.0.3/datardis/man/drwho_directors.Rd |only datardis-0.0.3/datardis/man/drwho_episodes.Rd |only datardis-0.0.3/datardis/man/drwho_writers.Rd |only datardis-0.0.3/datardis/man/torchwood_directors.Rd |only datardis-0.0.3/datardis/man/torchwood_episodes.Rd |only datardis-0.0.3/datardis/man/torchwood_writers.Rd |only datardis-0.0.3/datardis/tests/testthat.R | 8 - datardis-0.0.3/datardis/tests/testthat/test-episodes.R | 2 27 files changed, 146 insertions(+), 55 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.0.0 dated 2022-06-22 and 2.1.0 dated 2022-07-21
DESCRIPTION | 8 MD5 | 143 ++++++------ NAMESPACE | 1 NEWS.md | 9 R/image_reg.R | 18 + R/mrs_data_display.R | 25 +- R/mrs_data_proc.R | 50 ++++ build/vignette.rds |binary inst/doc/abfit-baseline-opts.html | 260 ++++++++++++++++++++++- inst/doc/spant-basis-simulation.html | 226 +++++++++++++++++++- inst/doc/spant-intro.html | 333 +++++++++++++++++++++++------- inst/doc/spant-metabolite-simulation.html | 236 ++++++++++++++++++++- inst/doc/spant-preprocessing.html | 209 ++++++++++++++++++ man/acquire.Rd | 46 ++-- man/append_coils.Rd | 38 +-- man/append_dyns.Rd | 38 +-- man/apply_axes.Rd | 60 ++--- man/apply_mrs.Rd | 44 +-- man/auto_phase.Rd | 50 ++-- man/bbase.Rd | 46 ++-- man/calc_ed_from_lambda.Rd | 42 +-- man/calc_peak_info_vec.Rd | 40 +-- man/calc_spec_diff.Rd | 42 +-- man/calc_spec_snr.Rd | 88 +++---- man/crop_td_pts.Rd | 42 +-- man/ecc.Rd | 52 ++-- man/fit_amps.Rd | 58 ++--- man/fp_phase_correct.Rd | 44 +-- man/get_1h_brain_basis_paras.Rd | 48 ++-- man/get_1h_brain_basis_paras_v1.Rd | 48 ++-- man/get_1h_brain_basis_paras_v2.Rd | 48 ++-- man/get_mrsi_voxel.Rd | 50 ++-- man/get_mrsi_voxel_xy_psf.Rd | 50 ++-- man/get_seg_ind.Rd | 42 +-- man/get_voi_seg.Rd | 38 +-- man/get_voi_seg_psf.Rd | 38 +-- man/get_voxel.Rd | 54 ++-- man/grid_shift_xy.Rd | 42 +-- man/mean.list.Rd |only man/mrs_data2basis.Rd | 42 +-- man/mrs_data2vec.Rd | 54 ++-- man/nifti_flip_lr.Rd | 42 +-- man/peak_info.Rd | 72 +++--- man/plot.mrs_data.Rd | 3 man/plot_bc.Rd | 36 +-- man/plot_slice_map.Rd | 94 ++++---- man/read_lcm_coord.Rd | 36 +-- man/read_mrs_tqn.Rd | 64 ++--- man/read_tqn_result.Rd | 48 ++-- man/resample_img.Rd | 42 +-- man/reslice_to_mrs.Rd | 4 man/seq_cpmg_ideal.Rd | 50 ++-- man/seq_mega_press_ideal.Rd | 84 +++---- man/seq_press_ideal.Rd | 50 ++-- man/seq_pulse_acquire.Rd | 42 +-- man/seq_pulse_acquire_31p.Rd | 42 +-- man/seq_slaser_ideal.Rd | 54 ++-- man/seq_spin_echo_ideal.Rd | 46 ++-- man/seq_spin_echo_ideal_31p.Rd | 46 ++-- man/seq_steam_ideal.Rd | 50 ++-- man/set_lw.Rd | 42 +-- man/sim_basis.Rd | 64 ++--- man/sim_basis_1h_brain.Rd | 70 +++--- man/sim_basis_1h_brain_press.Rd | 70 +++--- man/sim_basis_tqn.Rd | 66 ++--- man/sim_brain_1h.Rd | 82 +++---- man/sim_mol.Rd | 80 +++---- man/spin_sys.Rd | 42 +-- man/spm_pve2categorical.Rd | 38 +-- man/td_conv_filt.Rd | 42 +-- man/varpro_3_para_opts.Rd | 100 ++++----- man/varpro_opts.Rd | 96 ++++---- man/write_basis_tqn.Rd | 46 ++-- 73 files changed, 2839 insertions(+), 1706 deletions(-)
Title: R Utilities for GFF Files
Description: R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.
Author: Juan Antonio Garcia-Martin [cre, aut]
,
Juan Carlos Oliveros [aut, ctb]
,
Rafael Torres-Perez [aut, ctb]
Maintainer: Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>
Diff between Rgff versions 0.1.2 dated 2022-06-27 and 0.1.3 dated 2022-07-21
DESCRIPTION | 6 MD5 | 18 NEWS.md | 10 R/Rgff.R | 597 +++++++++++++++---------- inst/doc/Using_Rgff.html | 24 - inst/extdata/AthSmall.gff3.gene.ncRNA_gene.saf | 12 inst/extdata/AthSmall.gff3.gene.saf | 4 inst/extdata/AthSmall.gff3.paths | 60 +- inst/extdata/AthSmall.gtf.gff3 | 2 man/check_gff.Rd | 2 10 files changed, 451 insertions(+), 284 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Marc Becker [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.13.3 dated 2022-03-01 and 0.13.4 dated 2022-07-21
DESCRIPTION | 8 MD5 | 378 +++++++++++------------ NAMESPACE | 13 NEWS.md | 10 R/BenchmarkResult.R | 10 R/DataBackendMatrix.R | 2 R/Learner.R | 33 +- R/LearnerClassifDebug.R | 2 R/LearnerClassifFeatureless.R | 2 R/LearnerClassifRpart.R | 2 R/LearnerRegrDebug.R | 2 R/LearnerRegrFeatureless.R | 2 R/LearnerRegrRpart.R | 2 R/Measure.R | 14 R/MeasureAIC.R | 2 R/MeasureBIC.R | 2 R/MeasureClassifCosts.R | 2 R/MeasureDebug.R | 2 R/MeasureElapsedTime.R | 8 R/MeasureOOBError.R | 2 R/MeasureSelectedFeatures.R | 2 R/MeasureSimple.R | 101 +++--- R/Prediction.R | 9 R/ResampleResult.R | 18 - R/Resampling.R | 10 R/ResamplingBootstrap.R | 2 R/ResamplingCV.R | 2 R/ResamplingCustom.R | 2 R/ResamplingCustomCV.R | 2 R/ResamplingHoldout.R | 2 R/ResamplingInsample.R | 2 R/ResamplingLOO.R | 2 R/ResamplingRepeatedCV.R | 2 R/ResamplingSubsampling.R | 2 R/Task.R | 75 +++- R/TaskClassif.R | 34 +- R/TaskGenerator.R | 10 R/TaskGenerator2DNormals.R | 2 R/TaskGeneratorCassini.R | 2 R/TaskGeneratorCircle.R | 2 R/TaskGeneratorFriedman1.R | 2 R/TaskGeneratorMoons.R | 2 R/TaskGeneratorSimplex.R | 2 R/TaskGeneratorSmiley.R | 2 R/TaskGeneratorSpirals.R | 2 R/TaskGeneratorXor.R | 2 R/as_task_classif.R | 51 ++- R/as_task_regr.R | 30 + R/benchmark.R | 25 - R/bibentries.R | 2 R/helper.R | 5 R/helper_exec.R | 18 - R/helper_print.R | 6 R/mlr_reflections.R | 10 R/resample.R | 21 - R/worker.R | 8 R/zzz.R | 9 README.md | 67 +--- build/partial.rdb |binary inst/testthat/helper_autotest.R | 112 ++++-- inst/testthat/helper_expectations.R | 31 - man/BenchmarkResult.Rd | 73 ++-- man/DataBackend.Rd | 20 - man/DataBackendDataTable.Rd | 48 +- man/DataBackendMatrix.Rd | 50 +-- man/HotstartStack.Rd | 36 +- man/Learner.Rd | 87 ++--- man/LearnerClassif.Rd | 42 +- man/LearnerRegr.Rd | 42 +- man/Measure.Rd | 38 +- man/MeasureClassif.Rd | 30 - man/MeasureRegr.Rd | 30 - man/MeasureSimilarity.Rd | 30 - man/Prediction.Rd | 38 +- man/PredictionClassif.Rd | 36 +- man/PredictionRegr.Rd | 30 - man/ResampleResult.Rd | 73 ++-- man/Resampling.Rd | 50 +-- man/ResultData.Rd | 90 ++--- man/Task.Rd | 145 ++++---- man/TaskClassif.Rd | 82 ++-- man/TaskGenerator.Rd | 30 - man/TaskRegr.Rd | 78 ++-- man/TaskSupervised.Rd | 78 ++-- man/TaskUnsupervised.Rd | 64 +-- man/as_data_backend.Rd | 2 man/as_task_classif.Rd | 36 +- man/as_task_regr.Rd | 40 ++ man/benchmark.Rd | 20 - man/benchmark_grid.Rd | 2 man/mlr3-package.Rd | 11 man/mlr_learners_classif.debug.Rd | 69 +--- man/mlr_learners_classif.featureless.Rd | 70 ++-- man/mlr_learners_classif.rpart.Rd | 79 ++-- man/mlr_learners_regr.debug.Rd | 58 +-- man/mlr_learners_regr.featureless.Rd | 70 ++-- man/mlr_learners_regr.rpart.Rd | 79 ++-- man/mlr_measures_aic.Rd | 48 +- man/mlr_measures_bic.Rd | 42 +- man/mlr_measures_classif.acc.Rd | 6 man/mlr_measures_classif.auc.Rd | 6 man/mlr_measures_classif.bacc.Rd | 6 man/mlr_measures_classif.bbrier.Rd | 6 man/mlr_measures_classif.ce.Rd | 6 man/mlr_measures_classif.costs.Rd | 48 +- man/mlr_measures_classif.dor.Rd | 6 man/mlr_measures_classif.fbeta.Rd | 14 man/mlr_measures_classif.fdr.Rd | 6 man/mlr_measures_classif.fn.Rd | 6 man/mlr_measures_classif.fnr.Rd | 6 man/mlr_measures_classif.fomr.Rd | 6 man/mlr_measures_classif.fp.Rd | 6 man/mlr_measures_classif.fpr.Rd | 6 man/mlr_measures_classif.logloss.Rd | 6 man/mlr_measures_classif.mbrier.Rd | 6 man/mlr_measures_classif.mcc.Rd | 6 man/mlr_measures_classif.npv.Rd | 6 man/mlr_measures_classif.ppv.Rd | 6 man/mlr_measures_classif.prauc.Rd | 6 man/mlr_measures_classif.precision.Rd | 6 man/mlr_measures_classif.recall.Rd | 6 man/mlr_measures_classif.sensitivity.Rd | 6 man/mlr_measures_classif.specificity.Rd | 6 man/mlr_measures_classif.tn.Rd | 6 man/mlr_measures_classif.tnr.Rd | 6 man/mlr_measures_classif.tp.Rd | 6 man/mlr_measures_classif.tpr.Rd | 6 man/mlr_measures_debug.Rd | 48 +- man/mlr_measures_elapsed_time.Rd | 44 +- man/mlr_measures_oob_error.Rd | 42 +- man/mlr_measures_regr.bias.Rd | 6 man/mlr_measures_regr.ktau.Rd | 6 man/mlr_measures_regr.mae.Rd | 6 man/mlr_measures_regr.mape.Rd | 6 man/mlr_measures_regr.maxae.Rd | 6 man/mlr_measures_regr.medae.Rd | 6 man/mlr_measures_regr.medse.Rd | 6 man/mlr_measures_regr.mse.Rd | 6 man/mlr_measures_regr.msle.Rd | 6 man/mlr_measures_regr.pbias.Rd | 6 man/mlr_measures_regr.rae.Rd | 6 man/mlr_measures_regr.rmse.Rd | 6 man/mlr_measures_regr.rmsle.Rd | 6 man/mlr_measures_regr.rrse.Rd | 6 man/mlr_measures_regr.rse.Rd | 6 man/mlr_measures_regr.rsq.Rd | 6 man/mlr_measures_regr.sae.Rd | 6 man/mlr_measures_regr.smape.Rd | 6 man/mlr_measures_regr.srho.Rd | 6 man/mlr_measures_regr.sse.Rd | 6 man/mlr_measures_selected_features.Rd | 48 +- man/mlr_measures_sim.jaccard.Rd | 6 man/mlr_measures_sim.phi.Rd | 6 man/mlr_reflections.Rd | 4 man/mlr_resamplings_bootstrap.Rd | 44 +- man/mlr_resamplings_custom.Rd | 52 +-- man/mlr_resamplings_custom_cv.Rd | 52 +-- man/mlr_resamplings_cv.Rd | 44 +- man/mlr_resamplings_holdout.Rd | 44 +- man/mlr_resamplings_insample.Rd | 44 +- man/mlr_resamplings_loo.Rd | 44 +- man/mlr_resamplings_repeated_cv.Rd | 60 +-- man/mlr_resamplings_subsampling.Rd | 44 +- man/mlr_task_generators_2dnormals.Rd | 50 +-- man/mlr_task_generators_cassini.Rd | 50 +-- man/mlr_task_generators_circle.Rd | 48 +- man/mlr_task_generators_friedman1.Rd | 42 +- man/mlr_task_generators_moons.Rd | 48 +- man/mlr_task_generators_simplex.Rd | 51 +-- man/mlr_task_generators_smiley.Rd | 49 +- man/mlr_task_generators_spirals.Rd | 49 +- man/mlr_task_generators_xor.Rd | 48 +- man/mlr_tasks_boston_housing.Rd | 14 man/mlr_tasks_breast_cancer.Rd | 14 man/mlr_tasks_german_credit.Rd | 14 man/mlr_tasks_iris.Rd | 16 man/mlr_tasks_mtcars.Rd | 14 man/mlr_tasks_penguins.Rd | 14 man/mlr_tasks_pima.Rd | 14 man/mlr_tasks_sonar.Rd | 14 man/mlr_tasks_spam.Rd | 14 man/mlr_tasks_wine.Rd | 14 man/mlr_tasks_zoo.Rd | 14 man/resample.Rd | 20 - tests/testthat/test_Learner.R | 9 tests/testthat/test_Measure.R | 6 tests/testthat/test_Task.R | 27 + tests/testthat/test_convert_task.R | 35 +- tests/testthat/test_mlr_learners_classif_debug.R | 17 + tests/testthat/test_mlr_measures.R | 2 190 files changed, 2572 insertions(+), 2233 deletions(-)
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] ,
Michael Sumner [ctb] ,
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.5-5 dated 2021-12-18 and 0.5-6 dated 2022-07-21
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Title: Adaptive Semiparametric Additive Regression with Simultaneous
Confidence Bands and Specification Tests
Description: Fits semiparametric additive regression models with spatially adaptive penalized splines and computes simultaneous confidence bands and associated specification (lack-of-fit) tests. Simultaneous confidence bands cover the entire curve with a prescribed level of confidence and allow us to assess the estimation uncertainty for the whole curve. In contrast to pointwise confidence bands, they permit statements about the statistical significance of certain features (e.g. bumps) in the underlying curve.The method allows for handling of spatially heterogeneous functions and their derivatives as well as heteroscedasticity in the data. See Wiesenfarth et al. (2012) <doi:10.1080/01621459.2012.682809>.
Author: Manuel Wiesenfarth [aut, cre],
Tatyana Krivobokova [aut],
Matt Wand [ctb] ,
Catherine Loader [cph, ctb] ,
Jiayang Sun [cph, ctb] ,
Lucent Technologies [cph]
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>
Diff between AdaptFitOS versions 0.68 dated 2022-02-25 and 0.69 dated 2022-07-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary src/local.h | 2 +- src/smisc.c | 6 +++--- 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.32.0 dated 2022-06-07 and 1.32.1 dated 2022-07-21
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ R/makeClusterPSOCK.R | 1 + R/options.R | 20 ++++++++++---------- man/availableCores.Rd | 6 +++--- man/parallelly.options.Rd | 20 ++++++++++---------- tests/makeClusterPSOCK.R | 3 +++ 8 files changed, 48 insertions(+), 34 deletions(-)
More information about nextGenShinyApps at CRAN
Permanent link
Title: Minimalist Async Evaluation Framework for R
Description: Extremely simple and lightweight method for concurrent /
parallel code execution, built on 'nanonext' and 'NNG' (Nanomsg Next Gen)
technology.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.5.0 dated 2022-06-21 and 0.5.2 dated 2022-07-21
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 3 ++- NEWS.md | 4 ++++ R/mirai-package.R | 5 ++--- R/mirai.R | 10 +++++----- 6 files changed, 23 insertions(+), 19 deletions(-)
Title: Model-Based Clustering for Functional Data with Covariates
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Author: Natalya Pya Arnqvist[aut, cre],
Per Arnqvist [aut, cre],
Sara Sjoestedt de Luna [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Diff between fdaMocca versions 0.1-0 dated 2021-10-21 and 0.1-1 dated 2022-07-21
ChangeLog |only DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/fitmocca.r | 10 +++++----- man/mocca.Rd | 2 +- man/summary.mocca.Rd | 2 +- 6 files changed, 16 insertions(+), 15 deletions(-)
More information about EnrichIntersect at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-04 0.91.3
2020-01-09 0.91.2
2019-12-12 0.91.1
2019-11-06 0.91
Title: Revisiting Base Rapply
Description: The minimal 'rrapply'-package contains a single function rrapply(), providing an extended implementation of 'R'-base rapply() by allowing to recursively apply a function to elements of a nested list based on a general condition function and including the possibility to prune or aggregate nested list elements from the result. In addition, special arguments can be supplied to access the name, location, parents and siblings in the nested list of the element under evaluation. The rrapply() function builds upon rapply()'s native 'C' implementation and requires no other package dependencies.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between rrapply versions 1.2.4 dated 2022-03-07 and 1.2.5 dated 2022-07-21
rrapply-1.2.4/rrapply/README.md |only rrapply-1.2.4/rrapply/inst/doc/rrapply.R |only rrapply-1.2.4/rrapply/inst/doc/rrapply.Rnw |only rrapply-1.2.4/rrapply/inst/doc/rrapply.pdf |only rrapply-1.2.4/rrapply/vignettes/rrapply.Rnw |only rrapply-1.2.5/rrapply/DESCRIPTION | 10 rrapply-1.2.5/rrapply/MD5 | 33 - rrapply-1.2.5/rrapply/NEWS.md | 39 +- rrapply-1.2.5/rrapply/R/rrapply.R | 252 +++++++++----- rrapply-1.2.5/rrapply/build/vignette.rds |binary rrapply-1.2.5/rrapply/inst/doc/rrapply_cheatsheet.Rnw |only rrapply-1.2.5/rrapply/inst/doc/rrapply_cheatsheet.pdf |only rrapply-1.2.5/rrapply/inst/unit_tests/unit_test_rrapply.R | 172 ++++++++- rrapply-1.2.5/rrapply/man/rrapply.Rd | 192 ++++++---- rrapply-1.2.5/rrapply/src/flatten.c | 64 ++- rrapply-1.2.5/rrapply/src/init.c | 4 rrapply-1.2.5/rrapply/src/list.c | 64 ++- rrapply-1.2.5/rrapply/src/rrapply.c | 235 +++++++++---- rrapply-1.2.5/rrapply/src/rrapply.h | 36 +- rrapply-1.2.5/rrapply/src/utils.c | 100 ++++- rrapply-1.2.5/rrapply/vignettes/cheatsheet.pdf |only rrapply-1.2.5/rrapply/vignettes/rrapply_cheatsheet.Rnw |only 22 files changed, 844 insertions(+), 357 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.7 dated 2021-12-06 and 1.8 dated 2022-07-21
overlapping-1.7/overlapping/NEWS |only overlapping-1.8/overlapping/DESCRIPTION | 8 ++++---- overlapping-1.8/overlapping/MD5 | 8 ++++---- overlapping-1.8/overlapping/NEWS.md |only overlapping-1.8/overlapping/R/overlap.R | 24 ++++++++++++++---------- overlapping-1.8/overlapping/build/partial.rdb |binary 6 files changed, 22 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-21 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-02 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-24 0.1.2
2016-08-16 0.1.1
2016-06-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-03 1.8.18
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-17 2.1
2019-03-21 2.0
2017-03-26 1.3
2016-09-30 1.2
2016-03-09 1.1
2016-02-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-28 1.0.4
2016-07-25 1.0.3
2016-05-04 1.0.2
2016-03-04 1.0.1
2016-03-02 1.0
Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize
Twitter data via Twitter's REST and stream Application Program
Interfaces (API), which can be found at the following URL:
<https://developer.twitter.com/en/docs>.
Author: Michael W. Kearney [aut] ,
Lluis Revilla Sancho [aut, cre]
,
Hadley Wickham [aut] ,
Andrew Heiss [rev] ,
Francois Briatte [rev],
Jonathan Sidi [ctb]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between rtweet versions 0.7.0 dated 2020-01-08 and 1.0.2 dated 2022-07-21
rtweet-0.7.0/rtweet/R/access_level.R |only rtweet-0.7.0/rtweet/R/as_screenname.R |only rtweet-0.7.0/rtweet/R/get-my-timeline.R |only rtweet-0.7.0/rtweet/R/imports.R |only rtweet-0.7.0/rtweet/R/join_rtweet.R |only rtweet-0.7.0/rtweet/R/parse_twitter.R |only rtweet-0.7.0/rtweet/R/post.R |only rtweet-0.7.0/rtweet/R/renv.R |only rtweet-0.7.0/rtweet/R/suggested.R |only rtweet-0.7.0/rtweet/R/varnames.R |only rtweet-0.7.0/rtweet/data |only rtweet-0.7.0/rtweet/inst/assets |only rtweet-0.7.0/rtweet/inst/doc/FAQ.R |only rtweet-0.7.0/rtweet/inst/doc/FAQ.Rmd |only rtweet-0.7.0/rtweet/inst/doc/FAQ.html |only rtweet-0.7.0/rtweet/inst/doc/intro.R |only rtweet-0.7.0/rtweet/inst/doc/intro.Rmd |only rtweet-0.7.0/rtweet/inst/doc/intro.html |only rtweet-0.7.0/rtweet/inst/doc/stream.R |only rtweet-0.7.0/rtweet/man/get_collections.Rd |only rtweet-0.7.0/rtweet/man/get_my_timeline.Rd |only rtweet-0.7.0/rtweet/man/get_retweeters.Rd |only rtweet-0.7.0/rtweet/man/get_tokens.Rd |only rtweet-0.7.0/rtweet/man/lookup_statuses.Rd |only rtweet-0.7.0/rtweet/man/network_graph.Rd |only rtweet-0.7.0/rtweet/man/reexports.Rd |only rtweet-0.7.0/rtweet/man/search_30day.Rd |only rtweet-0.7.0/rtweet/man/suggested_users.Rd |only rtweet-0.7.0/rtweet/man/tweets_data.Rd |only rtweet-0.7.0/rtweet/tests/testthat/test_aaa.R |only rtweet-0.7.0/rtweet/tests/testthat/test_access_level.R |only rtweet-0.7.0/rtweet/tests/testthat/test_bearer.R |only rtweet-0.7.0/rtweet/tests/testthat/test_collections.R |only rtweet-0.7.0/rtweet/tests/testthat/test_direct_messages.R |only rtweet-0.7.0/rtweet/tests/testthat/test_friendships.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_favorites.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_followers.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_friends.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_my_timeline.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_timelines.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_trends.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_trends_closest.R |only rtweet-0.7.0/rtweet/tests/testthat/test_graph.R |only rtweet-0.7.0/rtweet/tests/testthat/test_lists_funs.R |only rtweet-0.7.0/rtweet/tests/testthat/test_lookup_coords.R |only rtweet-0.7.0/rtweet/tests/testthat/test_lookup_statuses.R |only rtweet-0.7.0/rtweet/tests/testthat/test_lookup_users.R |only rtweet-0.7.0/rtweet/tests/testthat/test_mentions.R |only rtweet-0.7.0/rtweet/tests/testthat/test_plain_tweets.R |only rtweet-0.7.0/rtweet/tests/testthat/test_rate_limit.R |only rtweet-0.7.0/rtweet/tests/testthat/test_retweets.R |only rtweet-0.7.0/rtweet/tests/testthat/test_save_as_csv.R |only rtweet-0.7.0/rtweet/tests/testthat/test_scroller.R |only rtweet-0.7.0/rtweet/tests/testthat/test_search_tweets.R |only rtweet-0.7.0/rtweet/tests/testthat/test_search_users.R |only rtweet-0.7.0/rtweet/tests/testthat/test_set_renv.R |only rtweet-0.7.0/rtweet/tests/testthat/test_stream_tweets.R |only rtweet-0.7.0/rtweet/tests/testthat/test_tokens.R |only rtweet-0.7.0/rtweet/tests/testthat/test_trends_available.R |only rtweet-0.7.0/rtweet/tests/testthat/test_tweet_shot.R |only rtweet-0.7.0/rtweet/tests/testthat/test_username.R |only rtweet-0.7.0/rtweet/tests/testthat/test_zzz.R |only rtweet-0.7.0/rtweet/tools |only rtweet-0.7.0/rtweet/vignettes/FAQ.Rmd |only rtweet-0.7.0/rtweet/vignettes/files/accesskeys.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-1.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-2.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-3.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-4.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-5.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-6.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-7.png |only rtweet-0.7.0/rtweet/vignettes/files/created.png |only rtweet-0.7.0/rtweet/vignettes/files/creating.png |only rtweet-0.7.0/rtweet/vignettes/files/gen_token.png |only rtweet-0.7.0/rtweet/vignettes/files/keys.png |only rtweet-0.7.0/rtweet/vignettes/intro.Rmd |only rtweet-1.0.2/rtweet/DESCRIPTION | 72 rtweet-1.0.2/rtweet/MD5 | 503 ++++-- rtweet-1.0.2/rtweet/NAMESPACE | 82 - 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rtweet-1.0.2/rtweet/R/lists_subscriptions.R | 136 - rtweet-1.0.2/rtweet/R/lists_users.R | 31 rtweet-1.0.2/rtweet/R/mentions.R | 113 - rtweet-1.0.2/rtweet/R/next_cursor.R | 499 ------ rtweet-1.0.2/rtweet/R/plain_tweets.R | 5 rtweet-1.0.2/rtweet/R/post-block.R |only rtweet-1.0.2/rtweet/R/post-favorite.R |only rtweet-1.0.2/rtweet/R/post-list.R |only rtweet-1.0.2/rtweet/R/post-message.R |only rtweet-1.0.2/rtweet/R/post-tweet.R |only rtweet-1.0.2/rtweet/R/post-user.R |only rtweet-1.0.2/rtweet/R/post_destroy.R |only rtweet-1.0.2/rtweet/R/premium.R | 336 +--- rtweet-1.0.2/rtweet/R/rate_limit.R | 426 +---- rtweet-1.0.2/rtweet/R/retweets.R | 148 - rtweet-1.0.2/rtweet/R/rtweet-package.R | 31 rtweet-1.0.2/rtweet/R/save_as_csv.R | 12 rtweet-1.0.2/rtweet/R/search_tweets.R | 478 +----- rtweet-1.0.2/rtweet/R/search_users.R | 159 -- rtweet-1.0.2/rtweet/R/statuses.R | 111 - rtweet-1.0.2/rtweet/R/stream.R | 715 ++------- rtweet-1.0.2/rtweet/R/timeline.R | 264 +-- rtweet-1.0.2/rtweet/R/tokens.R | 617 -------- rtweet-1.0.2/rtweet/R/trends.R | 96 - rtweet-1.0.2/rtweet/R/ts_plot.R | 67 rtweet-1.0.2/rtweet/R/tweet_embed.R |only rtweet-1.0.2/rtweet/R/tweet_object.R |only rtweet-1.0.2/rtweet/R/tweet_shot.R | 24 rtweet-1.0.2/rtweet/R/tweet_threading.R |only rtweet-1.0.2/rtweet/R/tweets_and_users.R | 757 ---------- rtweet-1.0.2/rtweet/R/user_id.R |only rtweet-1.0.2/rtweet/R/user_object.R |only rtweet-1.0.2/rtweet/R/users.R | 165 -- rtweet-1.0.2/rtweet/R/utils.R | 495 ------ rtweet-1.0.2/rtweet/README.md | 377 ---- rtweet-1.0.2/rtweet/build/vignette.rds |binary rtweet-1.0.2/rtweet/inst/doc/auth.R | 74 rtweet-1.0.2/rtweet/inst/doc/auth.Rmd | 232 +-- rtweet-1.0.2/rtweet/inst/doc/auth.html | 353 ++-- rtweet-1.0.2/rtweet/inst/doc/rtweet.Rmd |only rtweet-1.0.2/rtweet/inst/doc/rtweet.html |only rtweet-1.0.2/rtweet/inst/doc/stream.Rmd | 232 +-- rtweet-1.0.2/rtweet/inst/doc/stream.html | 262 ++- rtweet-1.0.2/rtweet/man/TWIT_paginate_max_id.Rd |only rtweet-1.0.2/rtweet/man/as_screenname.Rd | 69 rtweet-1.0.2/rtweet/man/auth_as.Rd |only rtweet-1.0.2/rtweet/man/auth_get.Rd |only rtweet-1.0.2/rtweet/man/auth_save.Rd |only rtweet-1.0.2/rtweet/man/auth_setup_default.Rd |only rtweet-1.0.2/rtweet/man/auth_sitrep.Rd |only rtweet-1.0.2/rtweet/man/bearer_token.Rd | 56 rtweet-1.0.2/rtweet/man/create_token.Rd | 48 rtweet-1.0.2/rtweet/man/direct_messages.Rd | 103 - rtweet-1.0.2/rtweet/man/direct_messages_received.Rd | 53 rtweet-1.0.2/rtweet/man/do_call_rbind.Rd | 16 rtweet-1.0.2/rtweet/man/emojis.Rd | 11 rtweet-1.0.2/rtweet/man/figures/lifecycle-archived.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-defunct.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-deprecated.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-experimental.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-maturing.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-questioning.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-stable.svg |only rtweet-1.0.2/rtweet/man/figures/lifecycle-superseded.svg |only rtweet-1.0.2/rtweet/man/flatten.Rd | 30 rtweet-1.0.2/rtweet/man/get_favorites.Rd | 106 - rtweet-1.0.2/rtweet/man/get_followers.Rd | 153 -- rtweet-1.0.2/rtweet/man/get_friends.Rd | 142 - rtweet-1.0.2/rtweet/man/get_mentions.Rd | 103 - rtweet-1.0.2/rtweet/man/get_retweets.Rd | 43 rtweet-1.0.2/rtweet/man/get_timeline.Rd | 144 + rtweet-1.0.2/rtweet/man/get_token.Rd |only rtweet-1.0.2/rtweet/man/get_trends.Rd | 25 rtweet-1.0.2/rtweet/man/invalidate_bearer.Rd | 7 rtweet-1.0.2/rtweet/man/langs.Rd | 11 rtweet-1.0.2/rtweet/man/lat_lng.Rd | 31 rtweet-1.0.2/rtweet/man/lists_members.Rd | 120 - rtweet-1.0.2/rtweet/man/lists_memberships.Rd |only rtweet-1.0.2/rtweet/man/lists_statuses.Rd | 71 rtweet-1.0.2/rtweet/man/lists_subscribers.Rd | 95 - rtweet-1.0.2/rtweet/man/lists_subscriptions.Rd | 95 - rtweet-1.0.2/rtweet/man/lists_users.Rd | 27 rtweet-1.0.2/rtweet/man/lookup_collections.Rd | 53 rtweet-1.0.2/rtweet/man/lookup_coords.Rd | 28 rtweet-1.0.2/rtweet/man/lookup_friendships.Rd | 21 rtweet-1.0.2/rtweet/man/lookup_tweets.Rd |only rtweet-1.0.2/rtweet/man/lookup_users.Rd | 74 rtweet-1.0.2/rtweet/man/max_id.Rd |only rtweet-1.0.2/rtweet/man/my_friendships.Rd | 24 rtweet-1.0.2/rtweet/man/network_data.Rd |only rtweet-1.0.2/rtweet/man/next_cursor.Rd | 77 - rtweet-1.0.2/rtweet/man/parse_stream.Rd | 25 rtweet-1.0.2/rtweet/man/plain_tweets.Rd | 5 rtweet-1.0.2/rtweet/man/post_destroy.Rd |only rtweet-1.0.2/rtweet/man/post_favorite.Rd | 18 rtweet-1.0.2/rtweet/man/post_follow.Rd | 26 rtweet-1.0.2/rtweet/man/post_friendship.Rd | 14 rtweet-1.0.2/rtweet/man/post_list.Rd | 68 rtweet-1.0.2/rtweet/man/post_message.Rd | 14 rtweet-1.0.2/rtweet/man/post_tweet.Rd | 57 rtweet-1.0.2/rtweet/man/previous_cursor.Rd |only rtweet-1.0.2/rtweet/man/rate_limit.Rd | 79 - rtweet-1.0.2/rtweet/man/rtweet-package.Rd | 30 rtweet-1.0.2/rtweet/man/rtweet_user.Rd |only rtweet-1.0.2/rtweet/man/search_fullarchive.Rd | 128 + rtweet-1.0.2/rtweet/man/search_tweets.Rd | 267 +-- rtweet-1.0.2/rtweet/man/search_users.Rd | 92 - rtweet-1.0.2/rtweet/man/stopwordslangs.Rd | 14 rtweet-1.0.2/rtweet/man/stream_tweets.Rd | 211 -- rtweet-1.0.2/rtweet/man/stream_tweets2.Rd |only rtweet-1.0.2/rtweet/man/trends_available.Rd | 22 rtweet-1.0.2/rtweet/man/ts_data.Rd | 17 rtweet-1.0.2/rtweet/man/ts_plot.Rd | 35 rtweet-1.0.2/rtweet/man/tweet_embed.Rd |only rtweet-1.0.2/rtweet/man/tweet_shot.Rd | 8 rtweet-1.0.2/rtweet/man/tweet_threading.Rd |only rtweet-1.0.2/rtweet/man/tweets_with_users.Rd | 49 rtweet-1.0.2/rtweet/man/user_block.Rd |only rtweet-1.0.2/rtweet/man/users_data.Rd | 56 rtweet-1.0.2/rtweet/man/write_as_csv.Rd | 2 rtweet-1.0.2/rtweet/tests/fixtures |only rtweet-1.0.2/rtweet/tests/testthat.R | 15 rtweet-1.0.2/rtweet/tests/testthat/_snaps |only rtweet-1.0.2/rtweet/tests/testthat/setup-rtweet.R |only rtweet-1.0.2/rtweet/tests/testthat/test-auth.R |only rtweet-1.0.2/rtweet/tests/testthat/test-block.R |only rtweet-1.0.2/rtweet/tests/testthat/test-collections.R |only rtweet-1.0.2/rtweet/tests/testthat/test-coords.R |only rtweet-1.0.2/rtweet/tests/testthat/test-direct_messages.R |only rtweet-1.0.2/rtweet/tests/testthat/test-entities_objects.R |only rtweet-1.0.2/rtweet/tests/testthat/test-extractors.R |only rtweet-1.0.2/rtweet/tests/testthat/test-favorites.R |only rtweet-1.0.2/rtweet/tests/testthat/test-followers.R |only rtweet-1.0.2/rtweet/tests/testthat/test-friends.R |only rtweet-1.0.2/rtweet/tests/testthat/test-geo_objects.R |only rtweet-1.0.2/rtweet/tests/testthat/test-graph-network.R |only rtweet-1.0.2/rtweet/tests/testthat/test-http.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lat_lng.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_members.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_memberships.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_statuses.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_subscribers.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_subscriptions.R |only rtweet-1.0.2/rtweet/tests/testthat/test-lists_users.R |only rtweet-1.0.2/rtweet/tests/testthat/test-mentions.R |only rtweet-1.0.2/rtweet/tests/testthat/test-next_cursor.R |only rtweet-1.0.2/rtweet/tests/testthat/test-post-block.R |only rtweet-1.0.2/rtweet/tests/testthat/test-post-favorite.R |only rtweet-1.0.2/rtweet/tests/testthat/test-post-message.R |only rtweet-1.0.2/rtweet/tests/testthat/test-post-tweet.R |only rtweet-1.0.2/rtweet/tests/testthat/test-post-user.R |only rtweet-1.0.2/rtweet/tests/testthat/test-premium.R |only rtweet-1.0.2/rtweet/tests/testthat/test-rate_limit.R |only rtweet-1.0.2/rtweet/tests/testthat/test-retweets.R |only rtweet-1.0.2/rtweet/tests/testthat/test-save_as_csv.R |only rtweet-1.0.2/rtweet/tests/testthat/test-search_tweets.R |only rtweet-1.0.2/rtweet/tests/testthat/test-search_users.R |only rtweet-1.0.2/rtweet/tests/testthat/test-statuses.R |only rtweet-1.0.2/rtweet/tests/testthat/test-stream.R |only rtweet-1.0.2/rtweet/tests/testthat/test-timeline.R |only rtweet-1.0.2/rtweet/tests/testthat/test-tokens.R |only rtweet-1.0.2/rtweet/tests/testthat/test-trends.R |only rtweet-1.0.2/rtweet/tests/testthat/test-ts_plot.R |only rtweet-1.0.2/rtweet/tests/testthat/test-tweet_embed.R |only rtweet-1.0.2/rtweet/tests/testthat/test-tweet_object.R |only rtweet-1.0.2/rtweet/tests/testthat/test-tweet_shot.R |only rtweet-1.0.2/rtweet/tests/testthat/test-tweet_threading.R |only rtweet-1.0.2/rtweet/tests/testthat/test-user_id.R |only rtweet-1.0.2/rtweet/tests/testthat/test-users.R |only rtweet-1.0.2/rtweet/tests/testthat/tweet.gif |only rtweet-1.0.2/rtweet/tests/testthat/tweet.mp4 |only rtweet-1.0.2/rtweet/vignettes/app-info.png |only rtweet-1.0.2/rtweet/vignettes/auth.Rmd | 232 +-- rtweet-1.0.2/rtweet/vignettes/files/plot1-1.png |only rtweet-1.0.2/rtweet/vignettes/files/ts_plot-1.png |only rtweet-1.0.2/rtweet/vignettes/keys-tokens.png |only rtweet-1.0.2/rtweet/vignettes/rtweet.Rmd |only rtweet-1.0.2/rtweet/vignettes/rtweet.Rmd.orig |only rtweet-1.0.2/rtweet/vignettes/stream.Rmd | 232 +-- rtweet-1.0.2/rtweet/vignettes/stream.Rmd.orig |only 284 files changed, 4641 insertions(+), 9429 deletions(-)
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.filesets versions 2.14.0 dated 2020-12-08 and 2.15.0 dated 2022-07-21
R.filesets-2.14.0/R.filesets/NEWS |only R.filesets-2.15.0/R.filesets/DESCRIPTION | 6 +- R.filesets-2.15.0/R.filesets/MD5 | 14 ++--- R.filesets-2.15.0/R.filesets/NEWS.md |only R.filesets-2.15.0/R.filesets/R/GenericDataFileSet.PARALLEL.R | 25 +--------- R.filesets-2.15.0/R.filesets/R/TabularTextFile.R | 5 +- R.filesets-2.15.0/R.filesets/man/R.filesets-package.Rd | 2 R.filesets-2.15.0/R.filesets/man/dsApplyInPairs.GenericDataFileSet.Rd | 4 - R.filesets-2.15.0/R.filesets/tests/VectorAndListAPI.R | 2 9 files changed, 20 insertions(+), 38 deletions(-)
Title: Monotonic Binning for Credit Rating Models
Description: Performs monotonic binning of numeric risk factor in credit rating models (PD, LGD, EAD)
development. All functions handle both binary and continuous target variable.
Functions that use isotonic regression in the first stage of binning process have an additional
feature for correction of minimum percentage of observations and minimum target rate per bin.
Additionally, monotonic trend can be identified based on raw data or, if known in advance,
forced by functions' argument. Missing values and other possible special values are treated
separately from so-called complete cases.
Author: Andrija Djurovic [aut, cre]
Maintainer: Andrija Djurovic <djandrija@gmail.com>
Diff between monobin versions 0.2.3 dated 2022-04-18 and 0.2.4 dated 2022-07-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/07_MDT_BINNING.R | 4 ++-- README.md | 2 +- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Fiber Length Determination
Description: Routines for estimating tree fiber (tracheid) length distributions in the standing tree
based on increment core samples. Two types of data can be used with the package, increment
core data measured by means of an optical fiber analyzer (OFA), e.g. such as the Kajaani
Fiber Lab, or measured by microscopy. Increment core data analyzed by OFAs consist of the cell
lengths of both cut and uncut fibres (tracheids) and fines (such as ray parenchyma cells)
without being able to identify which cells are cut or if they are fines or fibres. The
microscopy measured data consist of the observed lengths of the uncut fibres in the increment
core. A censored version of a mixture of the fine and fiber length distributions is proposed to
fit the OFA data, under distributional assumptions (Svensson et al., 2006) <doi:10.1111/j.1467-9469.2006.00501.x>. The package offers two choices for the
assumptions of the underlying density functions of the true fiber (fine) lenghts of those fibers
(fines) that at least partially appear in the increment core, being the generalized gamma and
the log normal densities.
Author: Natalya Pya Arnqvist[aut, cre],
Sara Sjoestedt de Luna [aut],
Konrad Abramowicz [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Diff between fiberLD versions 0.1-6 dated 2019-02-18 and 0.1-7 dated 2022-07-21
ChangeLog |only DESCRIPTION | 16 ++- MD5 | 20 +++- NAMESPACE | 3 R/fiber.r | 225 +++++++++++++++++++++++++++++-------------------------- R/plot.fled.r | 8 + R/summary.fled.r | 2 man/fled.Rd | 15 ++- src |only 9 files changed, 163 insertions(+), 126 deletions(-)
Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut] ,
Enrico Crema [aut, cre] ,
R. Kyle Bocinsky [ctb],
Martin Hinz [ctb],
Philip Riris [ctb],
Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>
Diff between rcarbon versions 1.4.3 dated 2022-02-17 and 1.4.4 dated 2022-07-21
DESCRIPTION | 8 MD5 | 20 R/aggregation.R | 25 R/calibration.R | 4 R/plots.R | 18 build/vignette.rds |binary inst/doc/rcarbon.Rmd | 17 inst/doc/rcarbon.html | 1481 +++++++++++++++++++++++++++++++++++++++++------- man/plot.stackCalSPD.Rd | 11 man/stackspd.Rd | 2 vignettes/rcarbon.Rmd | 17 11 files changed, 1336 insertions(+), 267 deletions(-)
Title: Collinearity Detection in a Multiple Linear Regression Model
Description: The detection of worrying approximate collinearity in a multiple linear regression model is a problem addressed in all existing statistical packages. However, we have detected deficits regarding to the incorrect treatment of qualitative independent variables and the role of the intercept of the model. The objective of this package is to correct these deficits. In this package will be available detection and treatment techniques traditionally used as the recently developed.
Author: R. Salmeron, C. Garcia and J. Garcia
Maintainer: R. Salmeron <romansg@ugr.es>
Diff between multiColl versions 1.0 dated 2019-07-18 and 2.0 dated 2022-07-21
DESCRIPTION | 21 +++++++-------------- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/PROPs.R | 2 +- R/VIF.R | 12 +++--------- R/ki.R | 21 +++++++++------------ R/multiCol.R | 14 +++++++++++++- R/multiColLM.R | 4 ++-- data/KG.rda |binary data/theil.rda |binary man/multiCol.Rd | 3 ++- man/multiColLM.Rd | 3 ++- man/multiColl-package.Rd | 4 +++- 13 files changed, 55 insertions(+), 54 deletions(-)
Title: Rmetrics - Importing Economic and Financial Data
Description: Provides a collection of utility functions
to download and manage data sets from the Internet or from other
sources.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fImport versions 3042.85 dated 2017-11-20 and 4021.86 dated 2022-07-21
fImport-3042.85/fImport/NEWS |only fImport-4021.86/fImport/DESCRIPTION | 27 ++++++++---- fImport-4021.86/fImport/MD5 | 19 ++++----- fImport-4021.86/fImport/NAMESPACE | 23 +++++++++-- fImport-4021.86/fImport/NEWS.md |only fImport-4021.86/fImport/inst/_pkgdown.yml |only fImport-4021.86/fImport/man/00fImport-package.Rd | 38 +++++++++--------- fImport-4021.86/fImport/man/class-fWEBDATA.Rd | 2 fImport-4021.86/fImport/man/import-fred.Rd | 10 +++- fImport-4021.86/fImport/man/provider-listings.Rd | 8 +++ fImport-4021.86/fImport/man/utils-download.Rd | 48 +++++++++-------------- fImport-4021.86/fImport/man/utils-split.Rd | 12 +---- 12 files changed, 105 insertions(+), 82 deletions(-)
Title: Package for Brik, Fabrik and Fdebrik Algorithms to Initialise
Kmeans
Description: Implementation of the BRIk, FABRIk and FDEBRIk algorithms
to initialise k-means. These methods are intended for the
clustering of multivariate and functional data, respectively.
They make use of the Modified Band Depth and bootstrap to
identify appropriate initial seeds for k-means, which are
proven to be better options than many techniques in the
literature. Torrente and Romo (2021) <doi:10.1007/s00357-020-09372-3>
It makes use of the functions kma and kma.similarity, from the
archived package fdakma, by Alice Parodi et al.
Author: Javier Albert Smet <javas@kth.se> and
Aurora Torrente <etorrent@est-econ.uc3m.es>.
Alice Parodi, Mirco Patriarca, Laura Sangalli, Piercesare Secchi,
Simone Vantini and Valeria Vitelli, as contributors.
Maintainer: Aurora Torrente <etorrent@est-econ.uc3m.es>
Diff between briKmeans versions 0.1 dated 2021-02-15 and 1.0 dated 2022-07-21
DESCRIPTION | 28 +++++++++++++++++----------- MD5 | 14 ++++++++++---- NAMESPACE | 11 +++++++++-- R/fdebrik.R |only R/kma.R |only R/kma.similarity.R |only R/plotKmeansClustering.R | 2 +- man/elbowRule.Rd | 16 ++++++++-------- man/fdebrik.Rd |only man/kma.Rd |only man/kma.similarity.Rd |only 11 files changed, 45 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-18 0.13.2
2021-03-05 0.13.0
2021-01-15 0.12.3
2021-01-05 0.12.2
2020-12-11 0.12.1
2020-03-16 0.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-13 1.0
2014-08-16 0.9.1
2013-06-19 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-07 1.0.2
Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also given.
Set partitions and now compositions and riffle shuffles are
included.
Author: Robin K. S. Hankin [aut, cre] ,
Paul Egeler [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.10-4 dated 2021-10-23 and 1.10-7 dated 2022-07-20
DESCRIPTION | 15 ++--- MD5 | 51 ++++++++--------- NAMESPACE | 3 + R/partitions.R | 21 ++++++- README.md | 87 ++++++++++++++++++++++++----- build/partial.rdb |binary build/partitions.pdf |binary build/vignette.rds |binary inst/doc/partitionspaper.R | 10 +-- inst/doc/partitionspaper.Rnw | 9 +-- inst/doc/partitionspaper.pdf |binary inst/doc/scrabble.R | 4 - inst/doc/scrabble.Rnw | 5 + inst/doc/scrabble.pdf |binary inst/doc/setpartitions.R | 14 ++-- inst/doc/setpartitions.Rnw | 6 +- inst/doc/setpartitions.pdf |binary man/conjugate.Rd | 12 ++-- man/partitions.package.Rd | 2 man/parts.Rd | 125 +++++++++--------------------------------- man/perms.Rd | 7 -- man/riffle.Rd |only man/setparts.Rd | 24 ++++++-- man/summary.partition.Rd | 2 vignettes/partitionspaper.Rnw | 9 +-- vignettes/scrabble.Rnw | 5 + vignettes/setpartitions.Rnw | 6 +- 27 files changed, 227 insertions(+), 190 deletions(-)
Title: Facilitates 'PhenoCam' Data Access and Time Series
Post-Processing
Description: Programmatic interface to the 'PhenoCam' web services (<https://phenocam.nau.edu/webcam>).
Allows for easy downloading of 'PhenoCam' data directly to your R workspace
or your computer and provides post-processing routines for consistent and easy
timeseries outlier detection, smoothing and estimation of phenological transition dates.
Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between phenocamr versions 1.1.4 dated 2020-03-22 and 1.1.5 dated 2022-07-20
DESCRIPTION | 32 - MD5 | 52 +- NAMESPACE | 2 R/contract_phenocam.r | 2 R/detect_outliers.r | 2 R/expand_phenocam.r | 2 R/grvi.r | 2 R/list_rois.r | 2 R/list_sites.r | 4 R/merge_daymet.r | 2 R/merge_modis.R | 2 R/phenophases.r | 2 R/smooth_ts.r | 2 R/transition_dates.r | 2 R/truncate_phenocam.r | 2 R/write_phenocam.r | 2 R/zzz.R | 10 build/vignette.rds |binary inst/CITATION | 2 inst/doc/phenocamr-vignette.R | 2 inst/doc/phenocamr-vignette.Rmd | 12 inst/doc/phenocamr-vignette.html | 614 +++++++++++++++++------------- inst/shiny/phenocam_explorer/server.R | 12 inst/shiny/phenocam_explorer/ui.R | 38 + tests/testthat/test_ancillary_functions.r | 17 tests/testthat/test_download_function.r | 231 ++++++----- vignettes/phenocamr-vignette.Rmd | 12 27 files changed, 616 insertions(+), 448 deletions(-)
Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, eight different methods for smoothing parameter selection, and flexible tools for prediction and inference.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between npreg versions 1.0-8 dated 2022-03-31 and 1.0-9 dated 2022-07-20
npreg-1.0-8/npreg/R/resid.R |only npreg-1.0-8/npreg/man/resid.Rd |only npreg-1.0-9/npreg/ChangeLog | 52 ++++++++++++++ npreg-1.0-9/npreg/DESCRIPTION | 8 +- npreg-1.0-9/npreg/MD5 | 74 +++++++++++++-------- npreg-1.0-9/npreg/NAMESPACE | 57 +++++++++++----- npreg-1.0-9/npreg/R/boot.gsm.R | 11 +-- npreg-1.0-9/npreg/R/boot.sm.R | 12 +-- npreg-1.0-9/npreg/R/boot.ss.R | 50 ++++++++++---- npreg-1.0-9/npreg/R/coef.R |only npreg-1.0-9/npreg/R/cooks.distance.R |only npreg-1.0-9/npreg/R/cov.ratio.R |only npreg-1.0-9/npreg/R/deviance.R |only npreg-1.0-9/npreg/R/dfbeta.R |only npreg-1.0-9/npreg/R/dfbetas.R |only npreg-1.0-9/npreg/R/diagnostic.plots.R |only npreg-1.0-9/npreg/R/fit_gsm.R | 7 + npreg-1.0-9/npreg/R/fit_sm.R | 4 - npreg-1.0-9/npreg/R/fit_ssi.R |only npreg-1.0-9/npreg/R/fitted.R | 18 ----- npreg-1.0-9/npreg/R/gsm.R | 5 + npreg-1.0-9/npreg/R/hatvalues.R |only npreg-1.0-9/npreg/R/model.matrix.R | 9 +- npreg-1.0-9/npreg/R/residuals.R |only npreg-1.0-9/npreg/R/rstandard.R |only npreg-1.0-9/npreg/R/rstudent.R |only npreg-1.0-9/npreg/R/smooth.influence.R |only npreg-1.0-9/npreg/R/smooth.influence.measures.R |only npreg-1.0-9/npreg/R/ss.R | 31 +++++++- npreg-1.0-9/npreg/R/summary.gsm.R | 9 -- npreg-1.0-9/npreg/R/summary.sm.R | 15 +--- npreg-1.0-9/npreg/R/varimp.R | 8 +- npreg-1.0-9/npreg/R/varinf.R |only npreg-1.0-9/npreg/R/vcov.R |only npreg-1.0-9/npreg/R/weights.R |only npreg-1.0-9/npreg/build/partial.rdb |binary npreg-1.0-9/npreg/man/coef.Rd |only npreg-1.0-9/npreg/man/deviance.Rd |only npreg-1.0-9/npreg/man/diagnostic.plots.Rd |only npreg-1.0-9/npreg/man/fitted.Rd | 12 --- npreg-1.0-9/npreg/man/gsm.Rd | 65 +++++++++++++++--- npreg-1.0-9/npreg/man/npreg-internals.Rd | 5 - npreg-1.0-9/npreg/man/residuals.Rd |only npreg-1.0-9/npreg/man/sm.Rd | 61 +++++++++++++---- npreg-1.0-9/npreg/man/smooth.influence.Rd |only npreg-1.0-9/npreg/man/smooth.influence.measures.Rd |only npreg-1.0-9/npreg/man/ss.Rd | 74 ++++++++++++++++----- npreg-1.0-9/npreg/man/summary.Rd | 2 npreg-1.0-9/npreg/man/varimp.Rd | 7 + npreg-1.0-9/npreg/man/varinf.Rd |only npreg-1.0-9/npreg/man/vcov.Rd |only npreg-1.0-9/npreg/man/weights.Rd |only 52 files changed, 422 insertions(+), 174 deletions(-)
Title: Create ToxPi Prioritization Models
Description: Enables users to build 'ToxPi' prioritization models and provides
functionality within the grid framework for plotting ToxPi graphs.
'toxpiR' allows for more customization than the 'ToxPi GUI'
(<https://toxpi.org>) and integration into existing workflows for greater
ease-of-use, reproducibility, and transparency.
toxpiR package behaves nearly identically to the GUI; the package
documentation includes notes about all differences.
The vignettes download example files from
<https://github.com/ToxPi/ToxPi-example-files>.
Author: Dayne L Filer [aut, cre, fnd] ,
Dillon T Lloyd [aut],
Preethi Thunga [aut] ,
Skylar W Marvel [aut],
Alison A Motsinger-Reif [fnd] ,
David M Reif [aut, fnd]
Maintainer: Dayne L Filer <dayne.filer@gmail.com>
Diff between toxpiR versions 1.0.3 dated 2022-02-18 and 1.2.1 dated 2022-07-20
DESCRIPTION | 8 MD5 | 64 ++-- NAMESPACE | 6 NEWS.md |only R/allClasses.R | 13 R/allGenerics.R | 5 R/methods-TxpModel.R | 18 + R/methods-TxpModelList.R | 6 R/methods-TxpResult.R | 17 - R/methods-TxpResultParam.R |only R/methods-TxpTransFuncList.R | 2 R/txpCalculateScores.R | 84 ++---- R/txpExportGui.R |only R/txpImportGui.R | 15 - R/utils.R | 41 ++ build/vignette.rds |binary inst/doc/exportToGui.R |only inst/doc/exportToGui.html |only inst/doc/exportToGui.rmd |only inst/doc/importFromGui.R | 2 inst/doc/importFromGui.Rmd | 4 inst/doc/importFromGui.html | 229 +++++++++++++++- inst/doc/introduction.Rmd | 46 +-- inst/doc/introduction.html | 371 ++++++++++++++++++++++++--- man/TxpModel-class.Rd | 8 man/TxpResult-class.Rd | 7 man/TxpResultParam-class.Rd |only man/txpCalculateScores.Rd | 15 - man/txpExportGui.Rd |only man/txpGenerics.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/guiFiles/gui_test_data.csv |only tests/testthat/guiFiles/gui_test_results.csv |only tests/testthat/test-TxpModel.R | 3 tests/testthat/test-txpExportGui.R |only tests/testthat/test-vsGuiResults.R |only vignettes/embeddedFigures/txp_explain.png |only vignettes/exportToGui.rmd |only vignettes/importFromGui.Rmd | 4 vignettes/introduction.Rmd | 46 +-- 40 files changed, 823 insertions(+), 194 deletions(-)
Title: Post-Process 'ggplot2' Plots with 'TikZ' Code Using Plot
Coordinates
Description: Annotation of 'ggplot2' plots with arbitrary 'TikZ' code, using absolute data or relative plot coordinates.
Author: Oliver Thomas [aut, cre]
Maintainer: Oliver Thomas <oliver.thomas@sgbm.uni-freiburg.de>
Diff between ggtikz versions 0.1.0 dated 2021-11-04 and 0.1.1 dated 2022-07-20
ggtikz-0.1.0/ggtikz/tests/visualtests |only ggtikz-0.1.1/ggtikz/DESCRIPTION | 12 ++--- ggtikz-0.1.1/ggtikz/MD5 | 28 ++++++------- ggtikz-0.1.1/ggtikz/NEWS.md | 5 ++ ggtikz-0.1.1/ggtikz/R/ggtikzTransform.R | 13 ------ ggtikz-0.1.1/ggtikz/R/ggtikzUninfinite.R | 3 - ggtikz-0.1.1/ggtikz/R/padding.R | 4 + ggtikz-0.1.1/ggtikz/R/unclip.R | 22 +++++++++- ggtikz-0.1.1/ggtikz/build/vignette.rds |binary ggtikz-0.1.1/ggtikz/inst/doc/examples.pdf |binary ggtikz-0.1.1/ggtikz/inst/testdata |only ggtikz-0.1.1/ggtikz/man/tikz_exts_pattern.Rd |only ggtikz-0.1.1/ggtikz/tests/testthat/helpers.R | 14 +++--- ggtikz-0.1.1/ggtikz/tests/testthat/test-ggtikzTransform.R | 27 ------------ ggtikz-0.1.1/ggtikz/tests/testthat/test-ggtikzUninfinite.R | 20 --------- ggtikz-0.1.1/ggtikz/tests/testthat/test-unclip.R | 21 +++++++++ 16 files changed, 78 insertions(+), 91 deletions(-)
Title: Efficient Implementation of Binary Segmentation
Description: Standard template library
containers are used to implement an efficient binary segmentation
algorithm, which is log-linear on average and quadratic in the
worst case.
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between binsegRcpp versions 2022.1.24 dated 2022-01-26 and 2022.7.19 dated 2022-07-20
binsegRcpp-2022.1.24/binsegRcpp/man/binsegRcpp-package.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/coef.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/plot.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/man/print.binseg_normal.Rd |only binsegRcpp-2022.1.24/binsegRcpp/src/binseg_normal.cpp |only binsegRcpp-2022.1.24/binsegRcpp/src/binseg_normal.h |only binsegRcpp-2022.1.24/binsegRcpp/tests/testthat/test-CRAN-binseg.R |only binsegRcpp-2022.7.19/binsegRcpp/DESCRIPTION | 11 binsegRcpp-2022.7.19/binsegRcpp/MD5 | 78 + binsegRcpp-2022.7.19/binsegRcpp/NAMESPACE | 18 binsegRcpp-2022.7.19/binsegRcpp/NEWS | 117 +- binsegRcpp-2022.7.19/binsegRcpp/R/RcppExports.R | 36 binsegRcpp-2022.7.19/binsegRcpp/R/binseg.R |only binsegRcpp-2022.7.19/binsegRcpp/R/binseg_normal.R | 96 -- binsegRcpp-2022.7.19/binsegRcpp/R/binseg_normal_cv.R | 2 binsegRcpp-2022.7.19/binsegRcpp/R/complexity.R | 475 ++++++++-- binsegRcpp-2022.7.19/binsegRcpp/R/cum_median.R |only binsegRcpp-2022.7.19/binsegRcpp/build/vignette.rds |binary binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.R |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.Rmd |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/comparisons.html |only binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.R | 214 ++-- binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.Rmd | 214 ++-- binsegRcpp-2022.7.19/binsegRcpp/inst/doc/cross-validation.html | 240 ++--- binsegRcpp-2022.7.19/binsegRcpp/man/binseg.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/binseg_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/binseg_normal.Rd | 20 binsegRcpp-2022.7.19/binsegRcpp/man/check_sizes.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/coef.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/cum_median.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/cum_median_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/depth_first_interface.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity.Rd | 130 ++ binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_heuristic_equal_breadth_full.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_heuristic_equal_depth_full.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_cost.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_splits.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_best_optimal_tree.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_empirical.Rd | 9 binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_extreme.Rd | 8 binsegRcpp-2022.7.19/binsegRcpp/man/get_complexity_worst.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_distribution_info.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/get_tree_empirical.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/plot.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/print.binsegRcpp.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/qp.x.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/size_to_splits.Rd |only binsegRcpp-2022.7.19/binsegRcpp/man/tree_layout.Rd |only binsegRcpp-2022.7.19/binsegRcpp/src/PiecewiseFunction.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/PiecewiseFunction.h |only binsegRcpp-2022.7.19/binsegRcpp/src/RcppExports.cpp | 53 - binsegRcpp-2022.7.19/binsegRcpp/src/binseg.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/binseg.h |only binsegRcpp-2022.7.19/binsegRcpp/src/cum_median.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/cum_median.h |only binsegRcpp-2022.7.19/binsegRcpp/src/depth_first.cpp |only binsegRcpp-2022.7.19/binsegRcpp/src/depth_first.h |only binsegRcpp-2022.7.19/binsegRcpp/src/interface.cpp | 179 +++ binsegRcpp-2022.7.19/binsegRcpp/tests/testthat/test-CRAN.R |only binsegRcpp-2022.7.19/binsegRcpp/vignettes/comparisons.Rmd |only binsegRcpp-2022.7.19/binsegRcpp/vignettes/cross-validation.Rmd | 214 ++-- 61 files changed, 1384 insertions(+), 730 deletions(-)
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
cache management and date-time parsing. Functions for date-time parsing and
formatting require that time zones be specified explicitly, avoiding a common
source of error when working with environmental time series.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Spencer Pease [ctb],
Thomas Bergamaschi [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.4.10 dated 2021-11-11 and 0.4.12 dated 2022-07-20
DESCRIPTION | 6 - MD5 | 32 +++++----- NEWS.md | 11 +++ R/errorHandling.R | 124 ++++++++++++++++++++++++++++------------- R/html_getLinks.R | 8 +- R/html_getTables.R | 14 ++-- R/initializeLogging.R | 12 +-- R/loadDataFile.R | 13 ---- R/timeStamp.R | 8 -- inst/doc/cache-management.html | 1 inst/doc/date-parsing.html | 1 inst/doc/error-handling.html | 56 +++++++++--------- inst/doc/logging.html | 58 +++++++++---------- man/html_getLinks.Rd | 2 man/html_getTables.Rd | 2 man/stopOnError.Rd | 99 ++++++++++++++++++++++++-------- man/timeStamp.Rd | 8 -- 17 files changed, 281 insertions(+), 174 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.6.1 dated 2015-10-27 and 1.7.0 dated 2022-07-20
aroma.cn-1.6.1/aroma.cn/NEWS |only aroma.cn-1.7.0/aroma.cn/DESCRIPTION | 17 aroma.cn-1.7.0/aroma.cn/MD5 | 195 aroma.cn-1.7.0/aroma.cn/NAMESPACE | 12 aroma.cn-1.7.0/aroma.cn/NEWS.md |only aroma.cn-1.7.0/aroma.cn/R/000.R | 10 aroma.cn-1.7.0/aroma.cn/R/006.fixVarArgs.R | 8 aroma.cn-1.7.0/aroma.cn/R/009.setup.R | 13 aroma.cn-1.7.0/aroma.cn/R/021.dynamic_imports.R | 2 aroma.cn-1.7.0/aroma.cn/R/999.DEPRECATED.R | 44 aroma.cn-1.7.0/aroma.cn/R/999.NonDocumentedObjects.R | 6 aroma.cn-1.7.0/aroma.cn/R/AbstractCurveNormalization.R | 1243 ++-- aroma.cn-1.7.0/aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R | 585 - aroma.cn-1.7.0/aroma.cn/R/C1C2.R | 46 aroma.cn-1.7.0/aroma.cn/R/CBS.findAtomicAberrations.R | 174 aroma.cn-1.7.0/aroma.cn/R/CartesianSnpData.R | 205 aroma.cn-1.7.0/aroma.cn/R/CopyNumberRegions.findAtomicAberrations.R | 115 aroma.cn-1.7.0/aroma.cn/R/MultiSourceCopyNumberNormalization.R | 2962 ++++------ aroma.cn-1.7.0/aroma.cn/R/MultiSourceCopyNumberNormalization.XTRAS.R | 273 aroma.cn-1.7.0/aroma.cn/R/NaiveFracBGenotyping.R | 539 - 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aroma.cn-1.7.0/aroma.cn/R/segmentByPruneCBS.R | 799 +- aroma.cn-1.7.0/aroma.cn/R/testAllelicBalanceByBAFs.R | 376 - aroma.cn-1.7.0/aroma.cn/R/testEquality.R | 359 - aroma.cn-1.7.0/aroma.cn/R/utils.R |only aroma.cn-1.7.0/aroma.cn/R/zzz.R | 22 aroma.cn-1.7.0/aroma.cn/inst/CITATION | 208 aroma.cn-1.7.0/aroma.cn/inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R | 350 - aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01a.downloadAllAnnotationData.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01b.downloadAllRawDataSet.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/01c.installAllPackages.R | 54 aroma.cn-1.7.0/aroma.cn/inst/testScripts/setup/99a.cleanupRootDirectories.R | 100 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex | 22 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex | 6 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex | 6 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp | 4 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/segmentation/20091110,CBS.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/tracks/20091010,TCGA,plot.Rex | 2 aroma.cn-1.7.0/aroma.cn/inst/testScripts/system/tracks/utils.R | 2 aroma.cn-1.7.0/aroma.cn/man/AbstractCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 10 aroma.cn-1.7.0/aroma.cn/man/PairedPscbsModel.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/PrincipalCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnBinnedSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnKernelSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TotalCnSmoothing.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/TumorBoostNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/XYCurveNormalization.Rd | 2 aroma.cn-1.7.0/aroma.cn/man/aroma.cn-package.Rd | 4 aroma.cn-1.7.0/aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd | 6 100 files changed, 8957 insertions(+), 9533 deletions(-)
Title: Command Line Option Parser
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Steve Lianoglou [ctb],
Jim Nikelski [ctb],
Kirill Mueller [ctb],
Peter Humburg [ctb],
Rich FitzJohn [ctb],
Gyu Jin Choi [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between optparse versions 1.7.1 dated 2021-10-08 and 1.7.3 dated 2022-07-20
DESCRIPTION | 16 ++-- MD5 | 20 +++--- NEWS.md | 11 +++ R/optparse.R | 132 +++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/COPYRIGHTS | 6 - inst/doc/optparse.R | 23 +++---- inst/doc/optparse.Rrst | 23 +++---- inst/doc/optparse.html | 51 +++++++-------- tests/testthat/test-optparse.R | 2 vignettes/optparse.Rrst | 23 +++---- 11 files changed, 180 insertions(+), 127 deletions(-)
Title: Flexible Segment Geoms with Arrows for 'ggplot2'
Description: Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.
Author: Matthew Hall [aut, cre]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Diff between ggarchery versions 0.2.0 dated 2022-02-25 and 0.3.0 dated 2022-07-20
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 8 ++++++-- R/geom-arrowsegment.R | 8 ++++++-- R/position-attractsegment.R | 11 ++++++++--- README.md | 19 +++++++++++++------ man/geom_arrowsegment.Rd | 5 ++++- man/position_attractsegment.Rd | 5 ++++- 8 files changed, 53 insertions(+), 27 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Winston Chang [aut],
Jennifer Bryan [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between devtools versions 2.4.3 dated 2021-11-30 and 2.4.4 dated 2022-07-20
devtools-2.4.3/devtools/man/devtools.Rd |only devtools-2.4.4/devtools/DESCRIPTION | 62 +- devtools-2.4.4/devtools/MD5 | 133 +++-- devtools-2.4.4/devtools/NAMESPACE | 4 devtools-2.4.4/devtools/NEWS.md | 20 devtools-2.4.4/devtools/R/active.R | 19 devtools-2.4.4/devtools/R/build-manual.R | 2 devtools-2.4.4/devtools/R/build-readme.R | 11 devtools-2.4.4/devtools/R/check-devtools.R | 4 devtools-2.4.4/devtools/R/check-doc.R | 6 devtools-2.4.4/devtools/R/check-mac.R | 19 devtools-2.4.4/devtools/R/check-win.R | 45 + devtools-2.4.4/devtools/R/check.R | 47 - devtools-2.4.4/devtools/R/dev-mode.R | 14 devtools-2.4.4/devtools/R/devtools-package.R |only devtools-2.4.4/devtools/R/document.R | 2 devtools-2.4.4/devtools/R/install.R | 10 devtools-2.4.4/devtools/R/lint.R | 20 devtools-2.4.4/devtools/R/package.R | 49 - devtools-2.4.4/devtools/R/pkgbuild.R | 2 devtools-2.4.4/devtools/R/r-hub.R | 2 devtools-2.4.4/devtools/R/release.R | 115 +--- devtools-2.4.4/devtools/R/reload.R | 4 devtools-2.4.4/devtools/R/run-examples.R | 16 devtools-2.4.4/devtools/R/run-source.R | 44 + devtools-2.4.4/devtools/R/show-news.R | 2 devtools-2.4.4/devtools/R/sitrep.R | 32 + devtools-2.4.4/devtools/R/test.R | 24 devtools-2.4.4/devtools/R/uninstall.R | 16 devtools-2.4.4/devtools/R/usethis.R | 2 devtools-2.4.4/devtools/R/utils.R | 8 devtools-2.4.4/devtools/R/vignette-r.R | 6 devtools-2.4.4/devtools/R/vignettes.R | 47 - devtools-2.4.4/devtools/R/wd.R | 4 devtools-2.4.4/devtools/R/zzz.R | 35 - devtools-2.4.4/devtools/README.md | 5 devtools-2.4.4/devtools/inst/WORDLIST | 32 - devtools-2.4.4/devtools/inst/doc/dependencies.html | 247 +++++++++- devtools-2.4.4/devtools/man/as.package.Rd | 6 devtools-2.4.4/devtools/man/build.Rd | 5 devtools-2.4.4/devtools/man/build_vignettes.Rd | 2 devtools-2.4.4/devtools/man/check.Rd | 4 devtools-2.4.4/devtools/man/check_mac_release.Rd | 5 devtools-2.4.4/devtools/man/check_man.Rd | 1 devtools-2.4.4/devtools/man/check_win.Rd | 11 devtools-2.4.4/devtools/man/devtools-package.Rd |only devtools-2.4.4/devtools/man/figures/lifecycle-archived.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-defunct.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-deprecated.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-experimental.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-maturing.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-questioning.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-stable.svg |only devtools-2.4.4/devtools/man/figures/lifecycle-superseded.svg |only devtools-2.4.4/devtools/man/lint.Rd | 20 devtools-2.4.4/devtools/man/load_all.Rd | 48 + devtools-2.4.4/devtools/man/run_examples.Rd | 13 devtools-2.4.4/devtools/man/uninstall.Rd | 14 devtools-2.4.4/devtools/tests/testthat/_snaps |only devtools-2.4.4/devtools/tests/testthat/helper.R | 26 - devtools-2.4.4/devtools/tests/testthat/test-active.R | 10 devtools-2.4.4/devtools/tests/testthat/test-build-readme.R | 61 +- devtools-2.4.4/devtools/tests/testthat/test-check-doc.R | 4 devtools-2.4.4/devtools/tests/testthat/test-check-win.R |only devtools-2.4.4/devtools/tests/testthat/test-install.R | 21 devtools-2.4.4/devtools/tests/testthat/test-package.R |only devtools-2.4.4/devtools/tests/testthat/test-reload.R | 5 devtools-2.4.4/devtools/tests/testthat/test-run-source.R | 41 - devtools-2.4.4/devtools/tests/testthat/test-sitrep.R | 52 +- devtools-2.4.4/devtools/tests/testthat/test-vignettes.R | 85 --- devtools-2.4.4/devtools/tests/testthat/testError/R/error.R | 2 devtools-2.4.4/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-warn.R | 2 72 files changed, 885 insertions(+), 663 deletions(-)
Title: Interpretable Bivariate Density Visualization with 'ggplot2'
Description: The 'ggplot2' package provides simple functions for visualizing contours
of 2-d kernel density estimates. 'ggdensity' implements several additional density estimators
as well as more interpretable visualizations based on highest density regions instead of
the traditional height of the estimated density surface.
Author: James Otto [aut, cre] ,
David Kahle [aut]
Maintainer: James Otto <jamesotto852@gmail.com>
Diff between ggdensity versions 0.0.1 dated 2022-02-15 and 0.1.0 dated 2022-07-20
ggdensity-0.0.1/ggdensity/man/figures |only ggdensity-0.1.0/ggdensity/DESCRIPTION | 14 +- ggdensity-0.1.0/ggdensity/MD5 | 48 +++------ ggdensity-0.1.0/ggdensity/NAMESPACE | 10 + ggdensity-0.1.0/ggdensity/NEWS.md |only ggdensity-0.1.0/ggdensity/R/hdr.R | 12 +- ggdensity-0.1.0/ggdensity/R/hdr_fun.R | 12 +- ggdensity-0.1.0/ggdensity/R/hdr_lines.R | 1 ggdensity-0.1.0/ggdensity/R/hdr_lines_fun.R | 1 ggdensity-0.1.0/ggdensity/R/hdr_points.R |only ggdensity-0.1.0/ggdensity/R/hdr_points_fun.R |only ggdensity-0.1.0/ggdensity/R/hdr_rug.R |only ggdensity-0.1.0/ggdensity/R/iso.R | 100 +++++++++++++++++-- ggdensity-0.1.0/ggdensity/R/marginals.R |only ggdensity-0.1.0/ggdensity/man/geom_hdr.Rd | 9 - ggdensity-0.1.0/ggdensity/man/geom_hdr_fun.Rd | 13 +- ggdensity-0.1.0/ggdensity/man/geom_hdr_points.Rd |only ggdensity-0.1.0/ggdensity/man/geom_hdr_points_fun.Rd |only ggdensity-0.1.0/ggdensity/man/geom_hdr_rug.Rd |only 19 files changed, 157 insertions(+), 63 deletions(-)
Title: Fast Simulation of Simple Temporal Exponential Random Graph
Models
Description: Provides functions for the computationally efficient simulation of
dynamic networks estimated with the statistical framework of temporal
exponential random graph models, implemented in the 'tergm' package.
Author: Samuel M. Jenness [aut, cre],
Chad Klumb [aut]
Maintainer: Samuel M. Jenness <samuel.m.jenness@emory.edu>
Diff between tergmLite versions 2.5.5 dated 2021-11-11 and 2.6.1 dated 2022-07-20
DESCRIPTION | 10 MD5 | 18 - NEWS.md | 2 R/network.R | 6 R/tergmLite-package.r | 4 man/get_vertex_attribute.Rd | 2 man/network_initialize.Rd | 2 man/set_vertex_attribute.Rd | 2 man/tergmLite-package.Rd | 4 tests/testthat/test-networkLite.R | 404 +++++++++++++++++++------------------- 10 files changed, 239 insertions(+), 215 deletions(-)
Title: Super Imposition by Translation and Rotation Growth Curve
Analysis
Description: Functions for fitting and plotting SITAR (Super
Imposition by Translation And Rotation) growth curve models. SITAR is
a shape-invariant model with a regression B-spline mean curve and
subject-specific random effects on both the measurement and age
scales. The model was first described by Lindstrom (1995)
<doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole
et al (2010) <doi:10.1093/ije/dyq115>.
Author: Tim Cole [aut, cre]
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>
Diff between sitar versions 1.2.0 dated 2021-04-22 and 1.3.0 dated 2022-07-20
DESCRIPTION | 8 MD5 | 77 +- NAMESPACE | 16 NEWS | 12 R/BICadj.R | 2 R/LMS2z.R | 7 R/LMSfit.R | 4 R/berkeley.R | 1 R/deren.R | 13 R/dfpower.R | 2 R/dfset.R | 2 R/functions.R |only R/getData.sitar.R | 2 R/getPeakTrough.R | 2 R/ifun.R | 2 R/mplot.R | 2 R/ob_convertr.R | 671 +++++++++++++++-------- R/optimal_design.R | 2 R/pdLMS.R | 2 R/plot.sitar.R | 36 - R/plotclean.R | 16 R/predict.sitar.R | 110 +-- R/sitar.R | 41 - R/sitarlib.R | 16 R/timegap.R | 2 R/who0607.R | 2 R/xyadj.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/berkeley.rda |binary data/deren.rda |binary inst/doc/Fitting_models_with_SITAR.html | 316 +++++++++- inst/doc/Optimal_design_for_centile_studies.html | 360 ++++++++++-- man/berkeley.Rd | 1 man/deren.Rd | 13 man/ob_convertr.Rd | 209 +++++-- man/plot.sitar.Rd | 29 man/predict.sitar.Rd | 4 man/sitar.Rd | 12 man/who0607.Rd | 2 40 files changed, 1484 insertions(+), 514 deletions(-)
Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) <doi:10.1214/08-STS254> . This test is useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers [aut, cre],
Mark Fredrickson [aut],
Ben Hansen [aut],
Josh Errickson [ctb]
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.1-18 dated 2022-02-28 and 0.3-0 dated 2022-07-20
RItools-0.1-18/RItools/R/data.R |only RItools-0.1-18/RItools/R/xBalance.make.stratwts.R |only RItools-0.1-18/RItools/man/xBalance.make.stratwts.Rd |only RItools-0.1-18/RItools/man/xBalance.makeMM.Rd |only RItools-0.1-18/RItools/man/xBalanceEngine.Rd |only RItools-0.3-0/RItools/DESCRIPTION | 14 RItools-0.3-0/RItools/MD5 | 112 ++-- RItools-0.3-0/RItools/NAMESPACE | 15 RItools-0.3-0/RItools/NEWS.md | 91 ++- RItools-0.3-0/RItools/R/Design.R |only RItools-0.3-0/RItools/R/balanceTest.R |only RItools-0.3-0/RItools/R/balanceTest.make.stratwts.R |only RItools-0.3-0/RItools/R/balanceTestEngine.R |only RItools-0.3-0/RItools/R/harmonic.R | 49 + RItools-0.3-0/RItools/R/naImpute.R | 33 - RItools-0.3-0/RItools/R/nuclearplants.R |only RItools-0.3-0/RItools/R/plot.balancetest.R |only RItools-0.3-0/RItools/R/plot.xbal.R | 44 + RItools-0.3-0/RItools/R/print.xbal.R | 256 +++++++--- RItools-0.3-0/RItools/R/utils.R | 172 ++++++ RItools-0.3-0/RItools/R/xBalance.R | 59 -- RItools-0.3-0/RItools/R/xBalance.find.goodstrats.R | 1 RItools-0.3-0/RItools/R/xBalance.make.stratwts.old.R |only RItools-0.3-0/RItools/R/xBalance.makeMM.R | 6 RItools-0.3-0/RItools/R/xBalance.makepooledsd.R | 19 RItools-0.3-0/RItools/R/xBalanceEngine.R | 52 -- RItools-0.3-0/RItools/R/xbal_tidiers.R |only RItools-0.3-0/RItools/R/xtable.xbal.R | 21 RItools-0.3-0/RItools/R/ym_long.R |only RItools-0.3-0/RItools/R/ym_short.R |only RItools-0.3-0/RItools/README.md | 72 +- RItools-0.3-0/RItools/data/ym_long.rda |only RItools-0.3-0/RItools/data/ym_short.rda |only RItools-0.3-0/RItools/inst/CITATION | 6 RItools-0.3-0/RItools/inst/examples/plot.xbal.R | 9 RItools-0.3-0/RItools/inst/extdata |only RItools-0.3-0/RItools/man/CovsAlignedToADesign-class.Rd |only RItools-0.3-0/RItools/man/DesignOptions-class.Rd |only RItools-0.3-0/RItools/man/DesignWeights.Rd |only RItools-0.3-0/RItools/man/HB08.Rd |only RItools-0.3-0/RItools/man/HB08_2016.Rd |only RItools-0.3-0/RItools/man/ModelMatrixPlus-class.Rd |only RItools-0.3-0/RItools/man/StratumWeightedDesignOptions-class.Rd |only RItools-0.3-0/RItools/man/aggregateDesigns.Rd |only RItools-0.3-0/RItools/man/alignDesignsByStrata.Rd |only RItools-0.3-0/RItools/man/balanceTest.Rd |only RItools-0.3-0/RItools/man/balanceTest.make.stratwts.Rd |only RItools-0.3-0/RItools/man/balanceTestEngine.Rd |only RItools-0.3-0/RItools/man/balanceplot.Rd | 17 RItools-0.3-0/RItools/man/designToDescriptives.Rd |only RItools-0.3-0/RItools/man/effectOfTreatmentOnTreated.Rd |only RItools-0.3-0/RItools/man/formula.xbal.Rd | 1 RItools-0.3-0/RItools/man/harmonic.Rd | 3 RItools-0.3-0/RItools/man/harmonic_times_mean_weight.Rd |only RItools-0.3-0/RItools/man/identify_NM_vars.Rd |only RItools-0.3-0/RItools/man/makeDesigns.Rd |only RItools-0.3-0/RItools/man/model_matrix.Rd |only RItools-0.3-0/RItools/man/naImpute.Rd | 6 RItools-0.3-0/RItools/man/nuclearplants.Rd | 2 RItools-0.3-0/RItools/man/original_units_var_formatter.Rd |only RItools-0.3-0/RItools/man/plot.balancetest.Rd |only RItools-0.3-0/RItools/man/plot.xbal.Rd | 12 RItools-0.3-0/RItools/man/print.xbal.Rd | 39 - RItools-0.3-0/RItools/man/sparseToVec.Rd |only RItools-0.3-0/RItools/man/subset.xbal.Rd | 5 RItools-0.3-0/RItools/man/tidy.xbal.Rd |only RItools-0.3-0/RItools/man/xBalance.Rd | 15 RItools-0.3-0/RItools/man/xBalance.find.goodstrats.Rd | 1 RItools-0.3-0/RItools/man/xBalance.makepooledsd.Rd | 1 RItools-0.3-0/RItools/man/xtable.xbal.Rd | 18 RItools-0.3-0/RItools/man/ym_long.Rd |only RItools-0.3-0/RItools/man/ym_short.Rd |only RItools-0.3-0/RItools/tests/testthat/test.Design.R |only RItools-0.3-0/RItools/tests/testthat/test.balanceTest.R |only RItools-0.3-0/RItools/tests/testthat/test.clusters.R |only RItools-0.3-0/RItools/tests/testthat/test.plot.balancetest.R |only RItools-0.3-0/RItools/tests/testthat/test.plot.xbal.R | 9 RItools-0.3-0/RItools/tests/testthat/test.utils.R | 192 ++++++- RItools-0.3-0/RItools/tests/testthat/test.xBalance.R | 93 +-- RItools-0.3-0/RItools/tests/xBalanceTests2.Rout.save | 10 80 files changed, 996 insertions(+), 459 deletions(-)
Title: R Client for the Daisi Microservice Platform
Description: Connect, execute, and parse results from the Daisi Microservice Platform <https://www.daisi.io/>. The rdaisi client
includes a set of functionality that allows remote execution of microservices directly from R.
Daisis allow R users to access a wide variety of Python functionality and interact with them natively.
Author: Daisi Technology, Inc. [aut],
Jean-Marie Laigle [aut],
Eric Hare [aut, cre]
Maintainer: Eric Hare <eric.hare@daisi.io>
Diff between rdaisi versions 0.1.2 dated 2022-07-05 and 0.1.3 dated 2022-07-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/rdaisi.R | 2 +- README.md | 5 ++--- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Retrieve Records from the Urban Institute's Education Data
Portal API
Description: Allows R users to retrieve and parse data from the Urban
Institute's Education Data API <https://educationdata.urban.org/> into a
'data.frame' for analysis.
Author: Erika Tyagi [cre],
Kyle Ueyama [aut],
The Urban Institute [cph]
Maintainer: Erika Tyagi <etyagi@urban.org>
Diff between educationdata versions 0.1.1 dated 2021-05-31 and 0.1.2 dated 2022-07-20
DESCRIPTION | 18 - MD5 | 20 - NEWS.md | 8 R/construct-url.R | 8 R/validate-args.R | 9 README.md | 330 +++++++++++++------------- build/vignette.rds |binary inst/doc/introducing-educationdata.Rmd | 4 inst/doc/introducing-educationdata.html | 397 ++++++++++++++++++++++++++------ tests/testthat/test-validation.R | 4 vignettes/introducing-educationdata.Rmd | 4 11 files changed, 535 insertions(+), 267 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre]
,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.9 dated 2022-07-16 and 0.1.10 dated 2022-07-20
DESCRIPTION | 8 MD5 | 85 - R/check_installation.R | 98 + R/github.R | 15 R/worcs_checklist.R | 1 R/worcs_project.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/setup-docker.html | 13 inst/doc/setup.Rmd | 21 inst/doc/setup.html | 31 inst/doc/workflow.Rmd | 4 inst/doc/workflow.html | 7 inst/rstudio/addins.dcf | 6 inst/rstudio/templates/project/licenses/cc_by-nc-nd_4.0.txt | 806 +++++------ inst/rstudio/templates/project/licenses/cc_by-nc-sa_4.0.txt | 876 ++++++------ inst/rstudio/templates/project/licenses/cc_by-nc_4.0.txt | 816 +++++------ inst/rstudio/templates/project/licenses/cc_by-nd_4.0.txt | 782 +++++----- inst/rstudio/templates/project/licenses/cc_by-sa_4.0.txt | 856 +++++------ inst/rstudio/templates/project/licenses/cc_by_4.0.txt | 792 +++++----- man/add_manuscript.Rd | 196 +- man/add_preregistration.Rd | 124 - man/check_worcs.Rd | 60 man/check_worcs_installation.Rd | 102 - man/cite_all.Rd | 78 - man/cite_essential.Rd | 78 - man/codebook.Rd | 140 - man/data_label.Rd | 76 - man/data_unlabel.Rd | 54 man/descriptives.Rd | 44 man/export_project.Rd | 70 man/git_user.Rd | 72 man/has_git_user.Rd | 42 man/load_data.Rd | 144 - man/load_entrypoint.Rd | 84 - man/open_data.Rd | 156 +- man/skew_kurtosis.Rd | 60 man/worcs_badge.Rd | 82 - man/worcs_checklist.Rd | 72 man/worcs_project.Rd | 154 +- tests/testthat/test-check_worcs_installation.R |only tests/testthat/test-worcsfile.R | 78 - vignettes/setup.Rmd | 21 vignettes/workflow.Rmd | 4 44 files changed, 3656 insertions(+), 3564 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
,
Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.7.2 dated 2022-05-24 and 1.7.3 dated 2022-07-20
DESCRIPTION | 12 MD5 | 65 ++--- NEWS.md | 9 R/Splits.R | 9 R/Support.R | 1 R/TreeNumber.R | 66 ++--- R/parse_files.R | 346 ++++++++++++++-------------- R/zzz.R | 3 build/partial.rdb |binary inst/REFERENCES.bib | 5 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.html | 4 inst/doc/load-trees.html | 4 inst/extdata/tests/tnt-bare-tree.tnt |only inst/extdata/tests/tnt-tree.tre | 2 inst/extdata/tests/tnt-trees-and-matrix.tnt | 5 man/ApeTime.Rd | 6 man/DoubleFactorial.Rd | 10 man/DropTip.Rd | 8 man/ExtractTaxa.Rd | 18 - man/ImposeConstraint.Rd | 4 man/ListAncestors.Rd | 4 man/MatrixToPhyDat.Rd | 12 man/NRooted.Rd | 20 - man/PhyToString.Rd | 6 man/ReadCharacters.Rd | 29 -- man/ReadTntTree.Rd | 22 - man/Reorder.Rd | 10 man/SplitFrequency.Rd | 8 man/match.Splits.Rd | 2 src/int_to_tree.cpp | 23 + tests/testthat/test-SplitFunctions.R | 24 - tests/testthat/test-TreeNumber.R | 9 tests/testthat/test-parsers.R | 229 ++++++++++-------- 34 files changed, 519 insertions(+), 460 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.4.0 dated 2022-03-23 and 2.4.1 dated 2022-07-20
TreeDist-2.4.0/TreeDist/R/ClusterTable.R |only TreeDist-2.4.0/TreeDist/build/TreeDist.pdf |only TreeDist-2.4.0/TreeDist/man/ClusterTable-methods.Rd |only TreeDist-2.4.0/TreeDist/man/ClusterTable.Rd |only TreeDist-2.4.0/TreeDist/tests/testthat/test-ClusterTable.R |only TreeDist-2.4.1/TreeDist/DESCRIPTION | 15 TreeDist-2.4.1/TreeDist/MD5 | 134 +- TreeDist-2.4.1/TreeDist/NAMESPACE | 8 TreeDist-2.4.1/TreeDist/NEWS.md | 16 TreeDist-2.4.1/TreeDist/R/Information.R | 38 TreeDist-2.4.1/TreeDist/R/RcppExports.R | 12 TreeDist-2.4.1/TreeDist/R/lap.R | 14 TreeDist-2.4.1/TreeDist/R/plot.R | 1 TreeDist-2.4.1/TreeDist/R/tree_distance.R | 18 TreeDist-2.4.1/TreeDist/R/tree_distance_info.R | 35 TreeDist-2.4.1/TreeDist/R/tree_distance_kendall-colijn.R | 82 - TreeDist-2.4.1/TreeDist/R/tree_distance_mast.R | 12 TreeDist-2.4.1/TreeDist/R/tree_distance_msd.R | 11 TreeDist-2.4.1/TreeDist/R/tree_distance_nni.R | 16 TreeDist-2.4.1/TreeDist/R/tree_distance_nye.R | 17 TreeDist-2.4.1/TreeDist/R/tree_distance_path.R | 37 TreeDist-2.4.1/TreeDist/R/tree_distance_rf.R | 21 TreeDist-2.4.1/TreeDist/build/partial.rdb |only TreeDist-2.4.1/TreeDist/build/vignette.rds |binary TreeDist-2.4.1/TreeDist/inst/CITATION | 10 TreeDist-2.4.1/TreeDist/inst/REFERENCES.bib | 9 TreeDist-2.4.1/TreeDist/inst/WORDLIST | 1 TreeDist-2.4.1/TreeDist/inst/doc/Generalized-RF.html | 375 ++++++- TreeDist-2.4.1/TreeDist/inst/doc/Robinson-Foulds.html | 370 ++++++- TreeDist-2.4.1/TreeDist/inst/doc/Using-TreeDist.html | 276 ++++- TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.R |only TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.Rmd |only TreeDist-2.4.1/TreeDist/inst/doc/compare-treesets.html |only TreeDist-2.4.1/TreeDist/inst/doc/information.html | 459 +++++++- TreeDist-2.4.1/TreeDist/inst/doc/treespace.R | 64 - TreeDist-2.4.1/TreeDist/inst/doc/treespace.Rmd | 85 - TreeDist-2.4.1/TreeDist/inst/doc/treespace.html | 495 +++++++-- TreeDist-2.4.1/TreeDist/inst/doc/using-distances.html | 469 +++++++-- TreeDist-2.4.1/TreeDist/inst/treespace/app.R | 516 +++++----- TreeDist-2.4.1/TreeDist/man/AllSplitPairings.Rd | 10 TreeDist-2.4.1/TreeDist/man/CalculateTreeDistance.Rd | 7 TreeDist-2.4.1/TreeDist/man/GeneralizedRF.Rd | 16 TreeDist-2.4.1/TreeDist/man/JaccardRobinsonFoulds.Rd | 27 TreeDist-2.4.1/TreeDist/man/KendallColijn.Rd | 64 - TreeDist-2.4.1/TreeDist/man/LAPJV.Rd | 9 TreeDist-2.4.1/TreeDist/man/MASTSize.Rd | 11 TreeDist-2.4.1/TreeDist/man/MSTSegments.Rd | 8 TreeDist-2.4.1/TreeDist/man/MapTrees.Rd | 1 TreeDist-2.4.1/TreeDist/man/MappingQuality.Rd | 1 TreeDist-2.4.1/TreeDist/man/MatchingSplitDistance.Rd | 21 TreeDist-2.4.1/TreeDist/man/MeilaVariationOfInformation.Rd | 9 TreeDist-2.4.1/TreeDist/man/NNIDist.Rd | 16 TreeDist-2.4.1/TreeDist/man/NyeSimilarity.Rd | 19 TreeDist-2.4.1/TreeDist/man/PathDist.Rd | 36 TreeDist-2.4.1/TreeDist/man/Robinson-Foulds.Rd | 36 TreeDist-2.4.1/TreeDist/man/SpectralEigens.Rd | 1 TreeDist-2.4.1/TreeDist/man/SplitEntropy.Rd | 7 TreeDist-2.4.1/TreeDist/man/SplitSharedInformation.Rd | 19 TreeDist-2.4.1/TreeDist/man/TreeDist-package.Rd | 4 TreeDist-2.4.1/TreeDist/man/TreeDistance.Rd | 35 TreeDist-2.4.1/TreeDist/man/median.multiPhylo.Rd | 1 TreeDist-2.4.1/TreeDist/src/RcppExports.cpp | 36 TreeDist-2.4.1/TreeDist/src/day_1985.cpp | 26 TreeDist-2.4.1/TreeDist/src/mast.cpp | 4 TreeDist-2.4.1/TreeDist/src/nni_distance.cpp | 4 TreeDist-2.4.1/TreeDist/src/tree_distances.cpp | 14 TreeDist-2.4.1/TreeDist/tests/testthat/_snaps/plot/mst-example-plot.svg | 8 TreeDist-2.4.1/TreeDist/tests/testthat/test-day_1985.cpp.r | 8 TreeDist-2.4.1/TreeDist/tests/testthat/test-plot.R | 3 TreeDist-2.4.1/TreeDist/tests/testthat/test-tree_distance_kc.R | 18 TreeDist-2.4.1/TreeDist/vignettes/Batch1.svg |only TreeDist-2.4.1/TreeDist/vignettes/Batch2.svg |only TreeDist-2.4.1/TreeDist/vignettes/compare-treesets.Rmd |only TreeDist-2.4.1/TreeDist/vignettes/treespace.Rmd | 85 - 74 files changed, 2923 insertions(+), 1257 deletions(-)
Title: Solve for Leaf Temperature Using Energy Balance
Description: Implements models of leaf temperature using energy balance. It uses units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately as in Foster and Smith (1986) <doi:10.1111/j.1365-3040.1986.tb02108.x>. It's straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind. It can also model leaf temperature over trait gradients such as leaf size or stomatal conductance. Other references are Monteith and Unsworth (2013, ISBN:9780123869104), Nobel (2009, ISBN:9780123741431), and Okajima et al. (2012) <doi:10.1007/s11284-011-0905-5>.
Author: Chris Muir [aut, cre]
Maintainer: Chris Muir <cdmuir@hawaii.edu>
Diff between tealeaves versions 1.0.5 dated 2020-06-18 and 1.0.6 dated 2022-07-20
DESCRIPTION | 12 - MD5 | 26 +- NEWS.md | 8 R/tleaves.R | 2 README.md | 50 ++--- build/vignette.rds |binary inst/CITATION | 4 inst/doc/parameter-functions.html | 142 ++++++++++----- inst/doc/tealeaves-intermediate.html | 142 ++++++++++----- inst/doc/tealeaves-introduction.R | 67 +++---- inst/doc/tealeaves-introduction.Rmd | 3 inst/doc/tealeaves-introduction.html | 325 ++++++++++++++++++++++------------- man/dot-get_Sr.Rd | 2 vignettes/tealeaves-introduction.Rmd | 3 14 files changed, 490 insertions(+), 296 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.3.1 dated 2022-06-07 and 2.4 dated 2022-07-20
DESCRIPTION | 6 - MD5 | 26 +++-- NEWS.md | 19 ++++ R/bib.R | 24 ++++- README.md | 81 +++++++++--------- build/partial.rdb |binary inst/REFERENCES.bib | 6 - inst/doc/Inserting_bibtex_references.pdf |binary inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary man/insert_all_ref.Rd | 5 - man/macros/refmacros.Rd | 2 tests/testthat/dummyArticle.rds |only tests/testthat/test-bib.R | 39 ++++++++ vignettes/Inserting_bibtex_references.md |only vignettes/Inserting_bibtex_references.org | 11 ++ 15 files changed, 157 insertions(+), 62 deletions(-)
Title: A 'pkgdown' Template
Description: This is an accessible template for 'pkgdown'. It uses two
bootstrap themes, Flatly and Darkly and utilizes the
'prefers-color-scheme' CSS variable to automatically serve either of
the two based on user’s operating system setting, or allowing them to
manually toggle between them.
Author: Amir Masoud Abdol [aut, cre]
Maintainer: Amir Masoud Abdol <i@amirmasoudabdol.name>
Diff between preferably versions 0.4 dated 2021-12-02 and 0.4.1 dated 2022-07-20
DESCRIPTION | 11 - MD5 | 22 +- NAMESPACE | 2 NEWS.md | 8 + R/preferably-package.R | 3 README.md | 8 - build/vignette.rds |binary inst/doc/in-the-wild.Rmd | 3 inst/doc/in-the-wild.html | 264 ++++++++++++++++++++++++++++++--- inst/pkgdown/BS5/assets/preferably.css | 28 +++ inst/pkgdown/BS5/templates/navbar.html | 2 vignettes/in-the-wild.Rmd | 3 12 files changed, 311 insertions(+), 43 deletions(-)
Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a
statistical method that allows to predict survival from
high-dimensional longitudinal predictors. PRC is described in
Signorelli et al. (2021, <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 1.2.1 dated 2022-06-22 and 1.2.2 dated 2022-07-20
DESCRIPTION | 6 MD5 | 24 - R/fit_lmms.R | 8 R/fit_mlpmms.R | 6 R/fit_prclmm.R | 6 R/summarize_lmms.R | 45 ++ inst/NEWS.md | 10 inst/doc/pencal-vignette.R | 12 inst/doc/pencal-vignette.Rmd | 644 ++++++++++++++++++++---------------------- inst/doc/pencal-vignette.html | 83 ++--- man/fit_lmms.Rd | 6 man/fit_mlpmms.Rd | 6 vignettes/pencal-vignette.Rmd | 644 ++++++++++++++++++++---------------------- 13 files changed, 769 insertions(+), 731 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.4 dated 2022-07-19 and 0.5.5 dated 2022-07-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS.md | 5 +++++ R/boundary_datasets.R | 17 +++++++++++++++++ inst/doc/advanced_network.html | 2 +- man/get_boundaries.Rd |only 7 files changed, 33 insertions(+), 9 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder, Naia Morueta-Holme
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between netassoc versions 0.6.3 dated 2017-06-05 and 0.7.0 dated 2022-07-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/plot.R | 2 +- man/plot_netassoc_network.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Estimation and Plotting of IDF Curves
Description: Intensity-duration-frequency (IDF) curves are a widely used analysis-tool
in hydrology to assess extreme values of precipitation
[e.g. Mailhot et al., 2007, <doi:10.1016/j.jhydrol.2007.09.019>].
The package 'IDF' provides functions to estimate IDF parameters for given
precipitation time series on the basis of a duration-dependent
generalized extreme value distribution
[Koutsoyiannis et al., 1998, <doi:10.1016/S0022-1694(98)00097-3>].
Author: Felix S. Fauer [aut, cre],
Jana Ulrich [aut],
Laura Mack [ctb],
Oscar E. Jurado [ctb],
Christoph Ritschel [aut],
Carola Detring [ctb],
Sarah Joedicke [ctb]
Maintainer: Felix S. Fauer <felix.fauer@met.fu-berlin.de>
Diff between IDF versions 2.1.1 dated 2022-03-03 and 2.1.2 dated 2022-07-20
DESCRIPTION | 24 ++++++++++++------------ MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 19 insertions(+), 14 deletions(-)
Title: Side Grammar Graphics
Description: The grammar of graphics as shown in 'ggplot2' has provided
an expressive API for users to build plots. 'ggside' extends 'ggplot2'
by allowing users to add graphical information about one of the main panel's
axis using a familiar 'ggplot2' style API with tidy data. This package is
particularly useful for visualizing metadata on a discrete axis, or summary
graphics on a continuous axis such as a boxplot or a density distribution.
Author: Justin Landis [aut, cre]
Maintainer: Justin Landis <jtlandis314@gmail.com>
Diff between ggside versions 0.2.0 dated 2021-12-11 and 0.2.1 dated 2022-07-20
DESCRIPTION | 19 MD5 | 95 +- NAMESPACE | 12 NEWS.md | 24 R/Layer.r | 426 ---------- R/aab-other_utils.r | 4 R/geom-sidebar.r | 1 R/geom-sideboxplot.r | 1 R/geom-sidefreqpoly.r | 1 R/geom-sidefunction.r |only R/geom-sidehistogram.r | 1 R/geom-sidelabel.r |only R/geom-sidepath.r | 2 R/ggside.R | 9 R/plot-construction.R | 52 - R/scales-sides-.R | 7 R/sideCoord--utils.R | 3 R/sideFacet--utils.R | 95 +- R/sideFacet-Grid.R | 54 + R/sideFacet-Null.R | 17 R/sideFacet-Wrap.R | 34 R/sideLayer.R | 13 README.md | 15 build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/ggside_aes_mapping.html | 268 +++++- inst/doc/ggside_basic_usage.R | 2 inst/doc/ggside_basic_usage.Rmd | 2 inst/doc/ggside_basic_usage.html | 388 ++++++++- man/figures/README-example-1.png |binary man/figures/README-example-mix-scales-1.png |binary man/figures/README-example-side-themes-1.png |binary man/geom_xsidebar.Rd | 4 man/geom_xsideboxplot.Rd | 78 - man/geom_xsidefreqpoly.Rd | 4 man/geom_xsidefunction.Rd |only man/geom_xsidehistogram.Rd | 4 man/geom_xsidelabel.Rd |only man/geom_xsidetext.Rd | 6 man/ggside-ggproto-facets.Rd | 13 man/ggside-ggproto-geoms.Rd | 11 man/ggside.Rd | 6 tests/testthat/_snaps/ggside_axis_polts/xyside-strip-main.svg |only tests/testthat/_snaps/vdiff_irisScatter/collapsed-histo.svg | 174 ---- tests/testthat/_snaps/vdiff_irisScatter/facetgrid-collapsed-density.svg | 30 tests/testthat/_snaps/vdiff_irisScatter/stacked-side-density.svg | 32 tests/testthat/_snaps/vdiff_irisScatter/yside-histo.svg | 177 ---- tests/testthat/test_FacetGrid_ggside_themes.R | 1 tests/testthat/test_ggside_axis_polts.R | 6 tests/testthat/test_ggside_scales.R | 27 vignettes/ggside_basic_usage.Rmd | 2 51 files changed, 1093 insertions(+), 1029 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers (Read et al. (2015) <doi:10.1111/ecog.01880>).
Author: Jordan Read [aut],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut, cre],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between geoknife versions 1.6.6 dated 2021-12-10 and 1.6.7 dated 2022-07-20
geoknife-1.6.6/geoknife/R/algorithmVersion-webprocess.R |only geoknife-1.6.6/geoknife/R/bufferPoint.R |only geoknife-1.6.6/geoknife/R/check.R |only geoknife-1.6.6/geoknife/R/dodsReplace.R |only geoknife-1.6.6/geoknife/R/geoknife-generic.R |only geoknife-1.6.6/geoknife/R/geoknifeUtils.R |only geoknife-1.6.6/geoknife/R/initializeProcessInputs.R |only geoknife-1.6.6/geoknife/R/parseCategorical.R |only geoknife-1.6.6/geoknife/R/parseTimeseries.R |only geoknife-1.6.6/geoknife/R/query-webdata.R |only geoknife-1.6.6/geoknife/R/query-webgeom.R |only geoknife-1.6.6/geoknife/R/query-webprocess.R |only geoknife-1.6.6/geoknife/R/setJobState.R |only geoknife-1.6.6/geoknife/R/setProcessInputs.R |only geoknife-1.6.6/geoknife/R/show-datagroup.R |only geoknife-1.6.6/geoknife/R/show-geojob.R |only geoknife-1.6.6/geoknife/R/show-simplegeom.R |only geoknife-1.6.6/geoknife/R/show-webdata.R |only geoknife-1.6.6/geoknife/R/show-webgeom.R |only geoknife-1.6.6/geoknife/R/show-webprocess.R |only geoknife-1.6.6/geoknife/R/successful.R |only geoknife-1.6.6/geoknife/R/waitUntilFinished.R |only geoknife-1.6.6/geoknife/inst/extdata/nasa_data.zip |only geoknife-1.6.7/geoknife/DESCRIPTION | 16 geoknife-1.6.7/geoknife/MD5 | 130 - geoknife-1.6.7/geoknife/NAMESPACE | 14 geoknife-1.6.7/geoknife/NEWS.md | 11 geoknife-1.6.7/geoknife/R/00-gconfig.R | 50 geoknife-1.6.7/geoknife/R/02-webgeom-obj.R | 3 geoknife-1.6.7/geoknife/R/03-webdata-obj.R | 38 geoknife-1.6.7/geoknife/R/04-webprocess-obj.R | 10 geoknife-1.6.7/geoknife/R/06-simplegeom-obj.R | 119 + geoknife-1.6.7/geoknife/R/08-geoknife-function.R |only geoknife-1.6.7/geoknife/R/cancel-geojob.R | 2 geoknife-1.6.7/geoknife/R/check-geojob.R |only geoknife-1.6.7/geoknife/R/processInputsToXML.R | 8 geoknife-1.6.7/geoknife/R/query.R |only geoknife-1.6.7/geoknife/R/show.R |only geoknife-1.6.7/geoknife/R/util-bufferPoint.R |only geoknife-1.6.7/geoknife/R/util-geoknife.R |only geoknife-1.6.7/geoknife/R/util-initializeProcessInputs.R |only geoknife-1.6.7/geoknife/R/util-parseCategorical.R |only geoknife-1.6.7/geoknife/R/util-parseTimeseries.R |only geoknife-1.6.7/geoknife/R/util-setJobState.R |only geoknife-1.6.7/geoknife/R/util-setProcessInputs.R |only geoknife-1.6.7/geoknife/R/wait-geojob.R |only geoknife-1.6.7/geoknife/build/vignette.rds |binary geoknife-1.6.7/geoknife/inst/doc/custom_data_sources.R | 66 geoknife-1.6.7/geoknife/inst/doc/custom_data_sources.html | 292 +++ geoknife-1.6.7/geoknife/inst/doc/geoknife.Rmd | 14 geoknife-1.6.7/geoknife/inst/doc/geoknife.html | 769 +++++++--- geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.R | 74 geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.Rmd | 52 geoknife-1.6.7/geoknife/inst/doc/plot_geotiff.html | 296 +++ geoknife-1.6.7/geoknife/inst/unnamed-chunk-6-1.png |only geoknife-1.6.7/geoknife/man/bufferPoint.Rd | 2 geoknife-1.6.7/geoknife/man/canStart.Rd | 2 geoknife-1.6.7/geoknife/man/cancel-methods.Rd | 2 geoknife-1.6.7/geoknife/man/check-geojob.Rd | 2 geoknife-1.6.7/geoknife/man/datagroup-methods.Rd | 4 geoknife-1.6.7/geoknife/man/defaultProcessInputs.Rd | 2 geoknife-1.6.7/geoknife/man/gconfig.Rd | 1 geoknife-1.6.7/geoknife/man/gcontent.Rd | 2 geoknife-1.6.7/geoknife/man/geoknife-methods.Rd | 6 geoknife-1.6.7/geoknife/man/getJobState.Rd | 2 geoknife-1.6.7/geoknife/man/parseCategorical.Rd | 2 geoknife-1.6.7/geoknife/man/parseTimeseries.Rd | 2 geoknife-1.6.7/geoknife/man/query.Rd | 11 geoknife-1.6.7/geoknife/man/retryVERB.Rd | 2 geoknife-1.6.7/geoknife/man/setJobState.Rd | 2 geoknife-1.6.7/geoknife/man/simplegeom-class.Rd | 65 geoknife-1.6.7/geoknife/man/simplegeom-methods.Rd | 24 geoknife-1.6.7/geoknife/man/successful-methods.Rd | 2 geoknife-1.6.7/geoknife/man/wait.Rd | 35 geoknife-1.6.7/geoknife/man/webdata-class.Rd | 2 geoknife-1.6.7/geoknife/man/webgeom-methods.Rd | 3 geoknife-1.6.7/geoknife/man/webprocess-class.Rd | 4 geoknife-1.6.7/geoknife/tests/testthat/data/test_simplegeom_two_points.rds |binary geoknife-1.6.7/geoknife/tests/testthat/test-geoknife_setters.R | 17 geoknife-1.6.7/geoknife/tests/testthat/test-parseCategorical.R | 3 geoknife-1.6.7/geoknife/tests/testthat/test-waitUntilFinished.R | 7 geoknife-1.6.7/geoknife/tests/testthat/test-webprocess_input.R | 2 geoknife-1.6.7/geoknife/vignettes/geoknife.Rmd | 14 geoknife-1.6.7/geoknife/vignettes/plot_geotiff.Rmd | 52 84 files changed, 1584 insertions(+), 654 deletions(-)
Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown'
documents and 'Shiny' apps. These icons can be inserted into HTML content
through inline 'SVG' tags or 'i' tags. There is also a utility function for
exporting 'Font Awesome' icons as 'PNG' images for those situations where
raster graphics are needed.
Author: Richard Iannone [aut, cre] ,
Christophe Dervieux [ctb] ,
Winston Chang [ctb],
Dave Gandy [ctb, cph] ,
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between fontawesome versions 0.2.2 dated 2021-07-02 and 0.3.0 dated 2022-07-20
fontawesome-0.2.2/fontawesome/R/fa_tbl.R |only fontawesome-0.2.2/fontawesome/R/fa_v4_v5.R |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-brands-400.woff |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-regular-400.woff |only fontawesome-0.2.2/fontawesome/inst/fontawesome/webfonts/fa-solid-900.woff |only fontawesome-0.3.0/fontawesome/DESCRIPTION | 15 fontawesome-0.3.0/fontawesome/MD5 | 56 fontawesome-0.3.0/fontawesome/NEWS.md | 8 fontawesome-0.3.0/fontawesome/R/fa.R | 247 fontawesome-0.3.0/fontawesome/R/fa_brands.R | 461 fontawesome-0.3.0/fontawesome/R/fa_i.R | 73 fontawesome-0.3.0/fontawesome/R/fa_metadata.R | 9 fontawesome-0.3.0/fontawesome/R/fa_version.R | 2 fontawesome-0.3.0/fontawesome/R/knit_print.R | 10 fontawesome-0.3.0/fontawesome/R/staticimports.R |only fontawesome-0.3.0/fontawesome/R/sysdata.rda |only fontawesome-0.3.0/fontawesome/R/utils.R | 7 fontawesome-0.3.0/fontawesome/R/zzz.R | 26 fontawesome-0.3.0/fontawesome/README.md | 2 fontawesome-0.3.0/fontawesome/inst/apps/138-icon-fontawesome/app.R | 18 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/all.css | 8411 ++++++---- fontawesome-0.3.0/fontawesome/inst/fontawesome/css/all.min.css | 5 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/v4-shims.css | 808 fontawesome-0.3.0/fontawesome/inst/fontawesome/css/v4-shims.min.css | 5 fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-brands-400.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-brands-400.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-regular-400.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-regular-400.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-solid-900.ttf |binary fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-solid-900.woff2 |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-v4compatibility.ttf |only fontawesome-0.3.0/fontawesome/inst/fontawesome/webfonts/fa-v4compatibility.woff2 |only fontawesome-0.3.0/fontawesome/man/fa_html_dependency.Rd | 6 fontawesome-0.3.0/fontawesome/man/fa_i.Rd | 10 fontawesome-0.3.0/fontawesome/tests/testthat/test-fa_icon.R | 133 35 files changed, 6549 insertions(+), 3763 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.0 dated 2022-01-13 and 2.1.1 dated 2022-07-20
DESCRIPTION | 10 - MD5 | 44 ++-- NEWS.md | 5 R/Rogue-package.R | 8 R/RogueTaxa.R | 4 R/SPIC.R | 10 - R/stability.R | 44 ++-- R/utilities.R | 2 R/zz_RogueNaRok.R | 6 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Bayesian.R | 36 +-- inst/doc/Bayesian.Rmd | 41 +--- inst/doc/Bayesian.html | 383 +++++++++++++++++++++++++++++++-------- man/Rogue-package.Rd | 8 man/RogueTaxa.Rd | 8 man/TipInstability.Rd | 4 tests/testthat/test-RogueNaRok.R | 2 tests/testthat/test-spic.R | 3 tests/testthat/test-stability.R | 10 - tests/testthat/test-utilities.R | 4 vignettes/Bayesian.Rmd | 41 +--- 23 files changed, 440 insertions(+), 235 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.7-3 dated 2021-11-10 and 0.3.7-4 dated 2022-07-20
DESCRIPTION | 12 MD5 | 36 NEWS | 2 R/inverter.R | 2 build/vignette.rds |binary inst/doc/a_1_getting_started.html | 1306 +++++++++++--------------- inst/doc/a_2_mlrCPO_core.R | 8 inst/doc/a_2_mlrCPO_core.Rmd | 8 inst/doc/a_2_mlrCPO_core.html | 1476 ++++++++++++----------------- inst/doc/a_3_all_CPOs.html | 1290 ++++++++++--------------- inst/doc/a_4_custom_CPOs.html | 1594 +++++++++++++------------------- inst/doc/z_1_getting_started_terse.html | 488 ++------- inst/doc/z_2_mlrCPO_core_terse.R | 8 inst/doc/z_2_mlrCPO_core_terse.html | 568 +++-------- inst/doc/z_3_all_CPOs_terse.html | 434 ++------ inst/doc/z_4_custom_CPOs_terse.html | 898 ++++++------------ man/cpoFilterPermutationImportance.Rd | 4 tests/testthat/test_core_targetop.R | 4 vignettes/a_2_mlrCPO_core.Rmd | 8 19 files changed, 3251 insertions(+), 4895 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen [aut, cre]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.4.0 dated 2022-07-03 and 0.5.0 dated 2022-07-20
DESCRIPTION | 6 ++-- MD5 | 22 +++++++-------- NEWS.md | 6 ++++ R/corrected_lasso.R | 4 +- R/corrected_lasso_glm.R | 6 ++-- R/project_gradient.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/hdme.html | 44 +++++++++++++++---------------- man/corrected_lasso.Rd | 4 +- tests/testthat/test_corrected_lasso.R | 18 +++++++++++- tests/testthat/test_cv_corrected_lasso.R | 8 ++--- 12 files changed, 71 insertions(+), 49 deletions(-)
Title: Process Map Token Replay Animation
Description: Provides animated process maps based on the 'procesmapR' package.
Cases stored in event logs created with with 'bupaR' S3 class eventlog() are
rendered as tokens (SVG shapes) and animated according to their occurrence
times on top of the process map. For rendering SVG animations ('SMIL') and the
'htmlwidget' package are used.
Author: Felix Mannhardt [aut, cre],
Gert Janssenswillen [ctb]
Maintainer: Felix Mannhardt <f.mannhardt@tue.nl>
Diff between processanimateR versions 1.0.4 dated 2021-10-11 and 1.0.5 dated 2022-07-20
DESCRIPTION | 9 MD5 | 28 NEWS.md | 4 R/processanimateR.R | 7 R/renderer.R | 2 README.md | 2 build/vignette.rds |binary data/example_log.rda |binary inst/doc/use-external-data-to-change-tokens.html | 4517 ++++++++++++++++++ inst/doc/use-shiny-selections.html | 209 inst/doc/use-timestamp-change-token-aes.html | 4543 ++++++++++++++++++- inst/doc/use-token_scales.html | 4517 ++++++++++++++++++ inst/doc/use-with-shiny.html | 208 man/renderer_graphviz.Rd | 6 vignettes/use-external-data-to-change-activites.R |only vignettes/use-external-data-to-change-activites.html |only 16 files changed, 13932 insertions(+), 120 deletions(-)
More information about processanimateR at CRAN
Permanent link
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://serpstat.com/api/>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.1.0 dated 2021-01-10 and 0.2.0 dated 2022-07-20
DESCRIPTION | 9 +- MD5 | 41 +++++------ NAMESPACE | 2 NEWS.md | 9 ++ R/backlinks.R |only R/rank_tracker.R | 133 +++++++++++++++++++++--------------- R/search_analytics.R | 147 +++++++++++++++++++++------------------- R/utility_functions.R | 2 README.md | 18 ++++ man/sst_bl_domain_summary.Rd |only man/sst_bl_referring_domains.Rd |only man/sst_call_api_method.Rd | 2 man/sst_rt_competitors.Rd | 24 ++++-- man/sst_rt_positions_history.Rd | 29 ++++--- man/sst_rt_project_regions.Rd | 5 + man/sst_rt_serp_history.Rd | 27 ++++--- man/sst_sa_database_info.Rd | 7 + man/sst_sa_domain_keywords.Rd | 26 +++---- man/sst_sa_domains_info.Rd | 11 +- man/sst_sa_keyword_top.Rd | 11 +- man/sst_sa_keywords.Rd | 26 +++---- man/sst_sa_keywords_info.Rd | 11 +- man/sst_sa_stats.Rd | 2 23 files changed, 320 insertions(+), 222 deletions(-)
Title: Extending Base R List
Description: Extends the functionality of base R list and
provides specialized data structures deque,
set, dict, and 'dict.table', the latter to extend the 'data.table'
package.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between container versions 1.0.1 dated 2022-02-19 and 1.0.2 dated 2022-07-20
container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark1_6ac35304b28e6737d8dd724111c5601e.rdx |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark2_3d1d0bb6beeea34d8d3970f97c4d64d0.rdx |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.RData |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.rdb |only container-1.0.1/container/vignettes/manage-data-columns_cache/html/benchmark3_8438e5c0342d468e3740c0deb509a403.rdx |only container-1.0.2/container/DESCRIPTION | 10 +- container-1.0.2/container/MD5 | 40 +++++----- container-1.0.2/container/NEWS.md | 17 ++-- container-1.0.2/container/build/vignette.rds |binary container-1.0.2/container/inst/doc/code-development.html | 1 container-1.0.2/container/inst/doc/container.html | 1 container-1.0.2/container/inst/doc/deque-set-dict.html | 1 container-1.0.2/container/inst/doc/manage-data-columns.html | 12 +-- container-1.0.2/container/inst/doc/parameter-list.html | 1 container-1.0.2/container/inst/doc/reference-semantics.html | 1 container-1.0.2/container/inst/tinytest/test_Ops-extract.R | 1 container-1.0.2/container/vignettes/manage-data-columns_cache/html/__packages | 1 container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark1_a03288235c212473fcd09376fad1de40.rdx |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark2_20930831ad0f4db7cc46c8caa705c962.rdx |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.RData |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.rdb |only container-1.0.2/container/vignettes/manage-data-columns_cache/html/benchmark3_4fefa0c6a9310ad08e13ee597b4687e6.rdx |only 30 files changed, 49 insertions(+), 37 deletions(-)
Title: Hyperbolic Geometry
Description: Hyperbolic geometry in the Minkowski model and the Poincaré
model. The methods are based on the gyrovector space theory developed
by A. A. Ungar that can be found in the book 'Analytic Hyperbolic
Geometry: Mathematical Foundations And Applications'
<doi:10.1142/5914>. The package provides functions to plot
three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings
of the Poincaré disk.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between gyro versions 1.0.1 dated 2022-06-13 and 1.1.0 dated 2022-07-20
DESCRIPTION | 30 +- MD5 | 45 ++-- NAMESPACE | 85 ++++---- NEWS.md | 7 R/RcppExports.R | 8 R/aaa.R | 2 R/examples.R |only R/gyro.R | 516 ++++---------------------------------------------- R/gyro_operations.R |only R/gyrocentroid.R |only R/gyromidpoint.R |only R/gyrosegment.R |only R/gyrosubdiv.R |only R/hdelaunay.R |only R/internal.R | 3 R/isomorphisms.R |only R/misc.R |only R/plot.R |only README.md | 2 build/vignette.rds |binary man/changesOfSign.Rd | 2 man/gyroABt.Rd | 60 ++--- man/gyrocentroid.Rd |only man/gyrodemos.Rd | 2 man/gyrosegment.Rd | 160 +++++++-------- man/gyrotriangle.Rd | 190 +++++++++--------- man/gyrotube.Rd | 108 +++++----- man/hdelaunay.Rd |only man/plotGyrohull3d.Rd | 360 +++++++++++++++++----------------- man/plotHdelaunay.Rd |only 30 files changed, 601 insertions(+), 979 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models for conditional quantile functions:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press,
<doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression,
CRC Press, <doi:10.1201/9781315120256>.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] ,
Pin Tian Ng [ctb] ,
Blaise Melly [ctb] ,
Achim Zeileis [ctb] ,
Philip Grosjean [ctb] ,
Cleve Moler [ctb] ,
Yousef Saad [ctb] ,
Victor Chernozhukov [ctb] ,
Ivan Fernandez-Val [ctb] ,
Brian D Ripley [tr [...truncated...]
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.93 dated 2022-05-02 and 5.94 dated 2022-07-20
DESCRIPTION | 17 ++- MD5 | 28 +++--- R/crq.R | 1 R/dynrq.R | 68 +++++++-------- R/quantreg.R | 89 ++++++++++--------- R/rqss.R | 232 ++++++++++++++++++++++++++-------------------------- demo/cobar.R | 2 demo/hinged.R | 4 inst/ChangeLog | 28 ++++++ man/plot.rqss.Rd | 5 - man/predict.rqss.Rd | 4 man/qss.Rd | 2 man/rqss.Rd | 2 man/rqss.object.Rd | 2 man/summary.crq.Rd | 4 15 files changed, 260 insertions(+), 228 deletions(-)
Title: Rmetrics - Nonlinear and Chaotic Time Series Modelling
Description: Provides a collection of functions for testing various aspects of
univariate time series including independence and neglected
nonlinearities. Further provides functions to investigate the chaotic
behavior of time series processes and to simulate different types of chaotic
time series maps.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [aut],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fNonlinear versions 3042.79 dated 2017-11-16 and 4021.80 dated 2022-07-20
ChangeLog | 6 +++ DESCRIPTION | 23 +++++++------ MD5 | 11 +++--- R/NonLinStatistics.R | 20 ++++++------ R/NonLinTests.R | 10 +++--- src/Tisean.c | 84 +++++++++++++++++++++++++-------------------------- src/init.c |only 7 files changed, 83 insertions(+), 71 deletions(-)
Title: Rmetrics - Bivariate Dependence Structures with Copulae
Description: Provides a collection of functions to
manage, to investigate and to analyze bivariate financial returns by
Copulae. Included are the families of Archemedean, Elliptical,
Extreme Value, and Empirical Copulae.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [ctb],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fCopulae versions 3042.82.1 dated 2020-03-07 and 4021.84 dated 2022-07-20
fCopulae-3042.82.1/fCopulae/inst/obsolete |only fCopulae-4021.84/fCopulae/ChangeLog | 9 +++++++++ fCopulae-4021.84/fCopulae/DESCRIPTION | 21 ++++++++++++--------- fCopulae-4021.84/fCopulae/MD5 | 19 +++---------------- fCopulae-4021.84/fCopulae/R/EllipticalCopulae.R | 8 +++++--- 5 files changed, 29 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-27 1.1.0
2020-06-29 1.0.4
2020-04-21 1.0.3
Title: Managing Larger Data on a GitHub Repository
Description: Because larger (> 50 MB) data files cannot easily be committed to git,
a different approach is required to manage data associated with an analysis in a
GitHub repository. This package provides a simple work-around by allowing larger
(up to 2 GB) data files to piggyback on a repository as assets attached to individual
GitHub releases. These files are not handled by git in any way, but instead are
uploaded, downloaded, or edited directly by calls through the GitHub API. These
data files can be versioned manually by creating different releases. This approach
works equally well with public or private repositories. Data can be uploaded
and downloaded programmatically from scripts. No authentication is required to
download data from public repositories.
Author: Carl Boettiger [aut, cre, cph]
,
Tan Ho [aut] ,
Mark Padgham [ctb] ,
Jeffrey O Hanson [ctb] ,
Kevin Kuo [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between piggyback versions 0.1.3 dated 2022-05-19 and 0.1.4 dated 2022-07-19
piggyback-0.1.3/piggyback/R/pb_new_release.R |only piggyback-0.1.3/piggyback/man/pb_new_release.Rd |only piggyback-0.1.3/piggyback/tests/testthat/test-errors.R |only piggyback-0.1.3/piggyback/tests/testthat/test-gh.R |only piggyback-0.1.3/piggyback/tests/testthat/test-on-cran.R |only piggyback-0.1.3/piggyback/tests/testthat/test-timestamps.R |only piggyback-0.1.3/piggyback/tests/testthat/test-with-auth.R |only piggyback-0.1.3/piggyback/tests/testthat/test-without-auth.R |only piggyback-0.1.3/piggyback/tests/testthat/test-zzz-teardown.R |only piggyback-0.1.4/piggyback/DESCRIPTION | 23 ++-- piggyback-0.1.4/piggyback/MD5 | 59 +++++------ piggyback-0.1.4/piggyback/NAMESPACE | 2 piggyback-0.1.4/piggyback/NEWS.md | 13 ++ piggyback-0.1.4/piggyback/R/pb_delete.R | 2 piggyback-0.1.4/piggyback/R/pb_download.R | 21 ++- piggyback-0.1.4/piggyback/R/pb_info.R | 27 ++--- piggyback-0.1.4/piggyback/R/pb_release_create.R |only piggyback-0.1.4/piggyback/R/pb_release_delete.R |only piggyback-0.1.4/piggyback/R/pb_upload.R | 41 ++++--- piggyback-0.1.4/piggyback/R/utils.R | 48 -------- piggyback-0.1.4/piggyback/build/vignette.rds |binary piggyback-0.1.4/piggyback/inst/doc/alternatives.html | 4 piggyback-0.1.4/piggyback/inst/doc/intro.Rmd | 2 piggyback-0.1.4/piggyback/inst/doc/intro.html | 8 - piggyback-0.1.4/piggyback/inst/iris_upload.tsv.gz |only piggyback-0.1.4/piggyback/inst/mtcars_upload.tsv.gz |only piggyback-0.1.4/piggyback/man/pb_delete.Rd | 3 piggyback-0.1.4/piggyback/man/pb_download.Rd | 7 - piggyback-0.1.4/piggyback/man/pb_download_url.Rd | 3 piggyback-0.1.4/piggyback/man/pb_list.Rd | 3 piggyback-0.1.4/piggyback/man/pb_release_create.Rd |only piggyback-0.1.4/piggyback/man/pb_release_delete.Rd |only piggyback-0.1.4/piggyback/man/pb_upload.Rd | 7 - piggyback-0.1.4/piggyback/man/piggyback-package.Rd | 6 - piggyback-0.1.4/piggyback/tests/testthat.R | 1 piggyback-0.1.4/piggyback/tests/testthat/test-pb_download.R |only piggyback-0.1.4/piggyback/tests/testthat/test-pb_info.R |only piggyback-0.1.4/piggyback/tests/testthat/test-utils.R |only piggyback-0.1.4/piggyback/tests/testthat/test-with_auth.R |only piggyback-0.1.4/piggyback/vignettes/intro.Rmd | 2 40 files changed, 134 insertions(+), 148 deletions(-)
Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser.
Enables embedding a JB2 genome browser in a Shiny app or R Markdown
document. The browser can also be launched from an interactive R console.
The browser can be loaded with a variety of common genomics data types,
and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] ,
the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>
Diff between JBrowseR versions 0.9.0 dated 2021-10-17 and 0.9.1 dated 2022-07-19
DESCRIPTION | 6 MD5 | 19 +- NAMESPACE | 1 NEWS.md | 5 R/text-index.R |only inst/doc/JBrowseR.html | 267 +++++++++++++++++++++++++++++-- inst/doc/creating-urls.html | 240 +++++++++++++++++++++++++++- inst/doc/custom-browser-tutorial.html | 287 +++++++++++++++++++++++++++++++--- inst/doc/json-tutorial.html | 244 +++++++++++++++++++++++++++- inst/htmlwidgets/JBrowseR.js | 187 ++++++++++++---------- man/text_index.Rd |only tests/testthat/test-text-index.R |only 12 files changed, 1093 insertions(+), 163 deletions(-)
Title: Semi-Parametric Dimension Reduction Models Using Orthogonality
Constrained Optimization
Description: Utilize an orthogonality constrained optimization algorithm of
Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of
dimension reduction problems in the semiparametric framework, such as
Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013)
<DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2019) <arXiv:1704.05046>
and Zhou, Zhu & Zeng (2021) <arXiv:1802.06156>. It also serves as a general
purpose optimization solver for problems with orthogonality constraints.
Parallel computing for approximating the gradient is enabled
through 'OpenMP'.
Author: Ruilin Zhao [aut, cph],
Ruoqing Zhu [aut, cre, cph] ,
Jiyang Zhang [aut, cph],
Wenzhuo Zhou [aut, cph],
Peng Xu [aut, cph],
James Joseph Balamuta [ctb]
Maintainer: Ruoqing Zhu <teazrq@gmail.com>
Diff between orthoDr versions 0.6.4 dated 2019-09-05 and 0.6.5 dated 2022-07-19
orthoDr-0.6.4/orthoDr/man/param_check.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_pdose.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_reg.Rd |only orthoDr-0.6.4/orthoDr/man/predict_orthoDr_surv.Rd |only orthoDr-0.6.4/orthoDr/man/print.Rd |only orthoDr-0.6.5/orthoDr/DESCRIPTION | 51 ++- orthoDr-0.6.5/orthoDr/MD5 | 126 ++++----- orthoDr-0.6.5/orthoDr/NAMESPACE | 54 ++- orthoDr-0.6.5/orthoDr/R/CP_SIR.r | 121 +++++--- orthoDr-0.6.5/orthoDr/R/RcppExports.R | 93 ++++-- orthoDr-0.6.5/orthoDr/R/dist_cross.r | 31 +- orthoDr-0.6.5/orthoDr/R/distance.r | 112 ++++---- orthoDr-0.6.5/orthoDr/R/hMave.r | 270 ++++++++++--------- orthoDr-0.6.5/orthoDr/R/kernel_weight.r | 35 +- orthoDr-0.6.5/orthoDr/R/orthoDr-package.R |only orthoDr-0.6.5/orthoDr/R/orthoDr_pdose.r | 211 ++++++++------- orthoDr-0.6.5/orthoDr/R/orthoDr_reg.r | 239 +++++++++-------- orthoDr-0.6.5/orthoDr/R/orthoDr_surv.r | 214 ++++++++------- orthoDr-0.6.5/orthoDr/R/ortho_optim.r | 271 ++++++++++--------- orthoDr-0.6.5/orthoDr/R/pSAVE.r | 97 +++---- orthoDr-0.6.5/orthoDr/R/param_check.r | 91 +++--- orthoDr-0.6.5/orthoDr/R/predict.r | 289 +++++++++++---------- orthoDr-0.6.5/orthoDr/R/print.r | 59 ++-- orthoDr-0.6.5/orthoDr/R/silverman.r | 20 - orthoDr-0.6.5/orthoDr/R/skcm.r | 52 ++- orthoDr-0.6.5/orthoDr/R/view_dr_surv.r | 143 +++++----- orthoDr-0.6.5/orthoDr/README.md |only orthoDr-0.6.5/orthoDr/build |only orthoDr-0.6.5/orthoDr/inst/CITATION | 78 ++++- orthoDr-0.6.5/orthoDr/man/CP_SIR.Rd | 38 +- orthoDr-0.6.5/orthoDr/man/dist_cross.Rd | 16 - orthoDr-0.6.5/orthoDr/man/distance.Rd | 31 +- orthoDr-0.6.5/orthoDr/man/gen_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/hMave.Rd | 31 +- orthoDr-0.6.5/orthoDr/man/kernel_weight.Rd | 20 - orthoDr-0.6.5/orthoDr/man/local_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/orthoDr-package.Rd |only orthoDr-0.6.5/orthoDr/man/orthoDr_pdose.Rd | 105 ++++--- orthoDr-0.6.5/orthoDr/man/orthoDr_reg.Rd | 78 +++-- orthoDr-0.6.5/orthoDr/man/orthoDr_surv.Rd | 96 ++++-- orthoDr-0.6.5/orthoDr/man/ortho_optim.Rd | 62 +++- orthoDr-0.6.5/orthoDr/man/pSAVE.Rd | 18 - orthoDr-0.6.5/orthoDr/man/pdose_direct_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/pdose_semi_solver.Rd | 29 +- orthoDr-0.6.5/orthoDr/man/phd_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/predict.orthoDr.Rd | 77 +++-- orthoDr-0.6.5/orthoDr/man/print.orthoDr.Rd |only orthoDr-0.6.5/orthoDr/man/save_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/seff_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/silverman.Rd | 4 orthoDr-0.6.5/orthoDr/man/sir_solver.Rd | 27 + orthoDr-0.6.5/orthoDr/man/skcm.clinical.Rd | 22 + orthoDr-0.6.5/orthoDr/man/skcm.melgene.Rd | 16 - orthoDr-0.6.5/orthoDr/man/surv_dm_solver.Rd | 28 +- orthoDr-0.6.5/orthoDr/man/surv_dn_solver.Rd | 28 +- orthoDr-0.6.5/orthoDr/man/surv_forward_solver.Rd | 25 + orthoDr-0.6.5/orthoDr/man/view_dr_surv.Rd | 51 ++- orthoDr-0.6.5/orthoDr/src/RcppExports.cpp | 5 orthoDr-0.6.5/orthoDr/src/gen_solver.cpp | 12 orthoDr-0.6.5/orthoDr/src/pdose_direct_solver.cpp | 7 orthoDr-0.6.5/orthoDr/src/pdose_semi_solver.cpp | 7 orthoDr-0.6.5/orthoDr/src/reg_local_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_phd_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_save_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_seff_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/reg_sir_solver.cpp | 8 orthoDr-0.6.5/orthoDr/src/surv_dm_solver.cpp | 11 orthoDr-0.6.5/orthoDr/src/surv_dn_solver.cpp | 9 orthoDr-0.6.5/orthoDr/src/surv_forward_solver.cpp | 8 69 files changed, 2204 insertions(+), 1520 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamas Nepusz <ntamas@gmail.com>
Diff between igraph versions 1.3.3 dated 2022-07-14 and 1.3.4 dated 2022-07-19
DESCRIPTION | 6 - MD5 | 27 ++--- NEWS.md | 22 ++++ R/games.R | 43 ++++---- R/layout.R | 60 +++++++++--- inst/NEWS.md | 22 ++++ man/layout_nicely.Rd | 14 ++ man/layout_with_fr.Rd | 2 man/layout_with_kk.Rd | 5 - man/sample_bipartite.Rd | 20 ++-- man/sample_pref.Rd | 4 src/core/connectivity/components.c | 6 + src/core/games/preference.c | 58 ++++++----- src/rinterface.c | 178 +++++++++++++++++++++++------------- tests/testthat/test_layout_nicely.R |only 15 files changed, 317 insertions(+), 150 deletions(-)
Title: Delete or Merge Regressors Algorithms for Linear and Logistic
Model Selection and High-Dimensional Data
Description: Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <https://projecteuclid.org/euclid.ejs/1440507392>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka Sołtys, Michał Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831–863. <doi:10.1111/sjos.12546>.
Author: Agnieszka Prochenka-Soltys [aut] ,
Piotr Pokarowski [aut],
Szymon Nowakowski [aut, cre]
Maintainer: Szymon Nowakowski <s.nowakowski@mimuw.edu.pl>
Diff between DMRnet versions 0.2.0 dated 2018-03-24 and 0.3.1 dated 2022-07-19
DMRnet-0.2.0/DMRnet/R/DMRnet-package.r |only DMRnet-0.2.0/DMRnet/R/cvfolds.R |only DMRnet-0.3.1/DMRnet/DESCRIPTION | 26 ++- DMRnet-0.3.1/DMRnet/MD5 | 128 ++++++++++------- DMRnet-0.3.1/DMRnet/NEWS.md |only DMRnet-0.3.1/DMRnet/R/DMR.R | 34 ++-- DMRnet-0.3.1/DMRnet/R/DMR4glm.R | 67 ++++++--- DMRnet-0.3.1/DMRnet/R/DMR4glm_help.R | 15 +- DMRnet-0.3.1/DMRnet/R/DMR4lm.R | 125 ++++++++++------- DMRnet-0.3.1/DMRnet/R/DMR4lm_help.R | 12 + DMRnet-0.3.1/DMRnet/R/DMRnet-package.R |only DMRnet-0.3.1/DMRnet/R/DMRnet.R | 99 +++++++++---- DMRnet-0.3.1/DMRnet/R/DMRnet4glm.R | 53 +++++-- DMRnet-0.3.1/DMRnet/R/DMRnet4glm_help.R | 4 DMRnet-0.3.1/DMRnet/R/DMRnet4lm.R | 93 ++++++++---- DMRnet-0.3.1/DMRnet/R/DMRnet4lm_help.R | 5 DMRnet-0.3.1/DMRnet/R/SOSnet4glm.R | 16 +- DMRnet-0.3.1/DMRnet/R/SOSnet4glm_help.R | 4 DMRnet-0.3.1/DMRnet/R/SOSnet4lm.R | 64 +++++--- DMRnet-0.3.1/DMRnet/R/SOSnet4lm_help.R | 55 +++++-- DMRnet-0.3.1/DMRnet/R/clusters_4glm_help.R |only DMRnet-0.3.1/DMRnet/R/clusters_4lm_help.R |only DMRnet-0.3.1/DMRnet/R/coef.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/coef.cv.DMR.R | 24 ++- DMRnet-0.3.1/DMRnet/R/coef.gic.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/cv.DMR.R | 85 ++--------- DMRnet-0.3.1/DMRnet/R/cv.DMRnet.R | 131 ++++++++---------- DMRnet-0.3.1/DMRnet/R/cv_GIC_indexed.R |only DMRnet-0.3.1/DMRnet/R/cv_MD_indexed.R |only DMRnet-0.3.1/DMRnet/R/cv_compute_model.R |only DMRnet-0.3.1/DMRnet/R/cv_indexation.mode_distribute.R |only DMRnet-0.3.1/DMRnet/R/gic.DMR.R | 14 - DMRnet-0.3.1/DMRnet/R/glamer_4glm.R |only DMRnet-0.3.1/DMRnet/R/glamer_4glm_help.R |only DMRnet-0.3.1/DMRnet/R/glamer_4lm.R |only DMRnet-0.3.1/DMRnet/R/glamer_4lm_help.R |only DMRnet-0.3.1/DMRnet/R/glamer_stats.R |only DMRnet-0.3.1/DMRnet/R/miete.R | 4 DMRnet-0.3.1/DMRnet/R/part2beta_glm_help.R | 35 ++-- DMRnet-0.3.1/DMRnet/R/part2beta_help.R | 91 +++++++----- DMRnet-0.3.1/DMRnet/R/plot.DMR.R | 10 - DMRnet-0.3.1/DMRnet/R/plot.cv.DMR.R | 9 - DMRnet-0.3.1/DMRnet/R/plot.gic.DMR.R | 8 - DMRnet-0.3.1/DMRnet/R/predict.DMR.R | 67 +++++++-- DMRnet-0.3.1/DMRnet/R/predict.cv.DMR.R | 29 ++- DMRnet-0.3.1/DMRnet/R/predict.gic.DMR.R | 16 +- DMRnet-0.3.1/DMRnet/R/print.DMR.R | 6 DMRnet-0.3.1/DMRnet/R/promoter.R | 2 DMRnet-0.3.1/DMRnet/R/release_questions.R |only DMRnet-0.3.1/DMRnet/R/t_stats.R | 2 DMRnet-0.3.1/DMRnet/R/w_stats.R | 5 DMRnet-0.3.1/DMRnet/README.md |only DMRnet-0.3.1/DMRnet/build |only DMRnet-0.3.1/DMRnet/inst |only DMRnet-0.3.1/DMRnet/man/DMR.Rd | 38 +++-- DMRnet-0.3.1/DMRnet/man/DMRnet-package.Rd | 40 +++-- DMRnet-0.3.1/DMRnet/man/DMRnet.Rd | 95 +++++++++---- DMRnet-0.3.1/DMRnet/man/coef.DMR.Rd | 5 DMRnet-0.3.1/DMRnet/man/coef.cv.DMR.Rd | 11 - DMRnet-0.3.1/DMRnet/man/coef.gic.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/cv.DMR.Rd | 37 +++-- DMRnet-0.3.1/DMRnet/man/cv.DMRnet.Rd | 44 +++--- DMRnet-0.3.1/DMRnet/man/gic.DMR.Rd | 15 -- DMRnet-0.3.1/DMRnet/man/miete.Rd | 11 - DMRnet-0.3.1/DMRnet/man/plot.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/plot.cv.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/plot.gic.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/predict.DMR.Rd | 22 ++- DMRnet-0.3.1/DMRnet/man/predict.cv.DMR.Rd | 22 ++- DMRnet-0.3.1/DMRnet/man/predict.gic.DMR.Rd | 15 +- DMRnet-0.3.1/DMRnet/man/print.DMR.Rd | 7 DMRnet-0.3.1/DMRnet/man/promoter.Rd | 9 - DMRnet-0.3.1/DMRnet/vignettes |only 73 files changed, 1065 insertions(+), 688 deletions(-)
Title: SPAtial Resolution-SEnsitive Models of Outbreak Dynamics
Description: Implementation of spatially-explicit, stochastic disease models with customizable time windows that describe how parameter values fluctuate during outbreaks (e.g., in response to public health or conservation interventions).
Author: Joseph Mihaljevic [aut, cre] ,
Toby Hocking [ctb] ,
Seth Borkovec [ctb] ,
Saikanth Ratnavale [ctb]
Maintainer: Joseph Mihaljevic <Joseph.Mihaljevic@nau.edu>
Diff between SPARSEMODr versions 1.1.0 dated 2021-07-01 and 1.2.0 dated 2022-07-19
SPARSEMODr-1.1.0/SPARSEMODr/man/Time-varying-R0.Rd |only SPARSEMODr-1.1.0/SPARSEMODr/man/figures |only SPARSEMODr-1.2.0/SPARSEMODr/DESCRIPTION | 7 SPARSEMODr-1.2.0/SPARSEMODr/MD5 | 78 SPARSEMODr-1.2.0/SPARSEMODr/NEWS | 12 SPARSEMODr-1.2.0/SPARSEMODr/R/model_interface.R | 8 SPARSEMODr-1.2.0/SPARSEMODr/R/time_windows.R | 74 SPARSEMODr-1.2.0/SPARSEMODr/README.md | 171 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.R | 130 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.Rmd | 134 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model-vary-hosp.html | 937 +++++----- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.R | 109 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.Rmd | 127 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/covid-19-model.html | 801 ++++---- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.R | 59 SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.Rmd | 87 SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/key-features.html | 201 +- SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.R | 107 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.Rmd | 125 - SPARSEMODr-1.2.0/SPARSEMODr/inst/doc/seir-model.html | 625 +++--- SPARSEMODr-1.2.0/SPARSEMODr/man/Movement.Rd | 4 SPARSEMODr-1.2.0/SPARSEMODr/man/SPARSEMOD-package.Rd | 2 SPARSEMODr-1.2.0/SPARSEMODr/man/model_interface.Rd | 47 SPARSEMODr-1.2.0/SPARSEMODr/man/model_parallel.Rd | 47 SPARSEMODr-1.2.0/SPARSEMODr/man/seir_control.Rd | 3 SPARSEMODr-1.2.0/SPARSEMODr/man/time_windows.Rd | 59 SPARSEMODr-1.2.0/SPARSEMODr/src/RcppExports.cpp | 5 SPARSEMODr-1.2.0/SPARSEMODr/src/covid19_model.cpp | 251 +- SPARSEMODr-1.2.0/SPARSEMODr/src/covid19_model.h | 14 SPARSEMODr-1.2.0/SPARSEMODr/src/general_model.h | 4 SPARSEMODr-1.2.0/SPARSEMODr/src/interface.cpp | 30 SPARSEMODr-1.2.0/SPARSEMODr/src/seir_model.cpp | 230 +- SPARSEMODr-1.2.0/SPARSEMODr/src/seir_model.h | 14 SPARSEMODr-1.2.0/SPARSEMODr/src/time_window_utils.cpp | 22 SPARSEMODr-1.2.0/SPARSEMODr/src/time_window_utils.h | 52 SPARSEMODr-1.2.0/SPARSEMODr/tests/testthat/test-model.R | 14 SPARSEMODr-1.2.0/SPARSEMODr/vignettes/covid-19-model-vary-hosp.Rmd | 134 - SPARSEMODr-1.2.0/SPARSEMODr/vignettes/covid-19-model.Rmd | 127 - SPARSEMODr-1.2.0/SPARSEMODr/vignettes/key-features.Rmd | 87 SPARSEMODr-1.2.0/SPARSEMODr/vignettes/seir-model.Rmd | 125 - 40 files changed, 2556 insertions(+), 2507 deletions(-)
Title: Functions for Web Development
Description: Organizational framework for web development in R including functions to
serve static and dynamic content via HTTP methods, includes the html5 package to
create HTML pages, and offers other utility functions for common tasks related
to web development.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between webdeveloper versions 1.0.1 dated 2022-07-06 and 1.0.2 dated 2022-07-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/webdeveloper.R | 23 +++++++++++------------ 3 files changed, 16 insertions(+), 17 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Gruen <dominic.gruen@gmail.com>
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.2.3 dated 2021-04-08 and 0.2.4 dated 2022-07-19
DESCRIPTION | 10 +- MD5 | 16 +-- R/VarID_functions.R | 2 build/vignette.rds |binary data/cc_genes.RData |binary data/intestinalData.RData |binary data/intestinalDataSmall.RData |binary inst/doc/RaceID.html | 194 +++++++++++++++++++---------------------- src/RcppExports.cpp | 5 + 9 files changed, 111 insertions(+), 116 deletions(-)
Title: Create HTML Content with Bootstrap 5 Classes and Layouts
Description: Functions are pre-configured to utilize Bootstrap 5 classes and
HTML structures to create Bootstrap-styled HTML quickly and easily. Includes
functions for creating common Bootstrap elements such as containers, rows, cols,
navbars, etc. Intended to be used with the html5 package. Learn more at
<https://getbootstrap.com/>.
Author: Timothy Conwell
Maintainer: Timothy Conwell <timconwell@gmail.com>
Diff between bsTools versions 1.0.0 dated 2022-06-22 and 1.0.2 dated 2022-07-19
DESCRIPTION | 6 ++-- MD5 | 8 +++--- R/bsTools2.R | 68 +++++++++++++++++++++++++++++++++++-------------------- man/bs_card.Rd | 17 ++++++++++++- man/bs_navbar.Rd | 3 ++ 5 files changed, 70 insertions(+), 32 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.2.0 dated 2022-06-08 and 1.2.1 dated 2022-07-19
DESCRIPTION | 8 LICENSE | 4 MD5 | 296 ++++---- NEWS.md | 19 R/00_global_variables.R | 18 R/autoplot-combined-dist.R | 558 +++++++-------- R/autoplot-four-graphs.R | 176 ++-- R/autoplot-multi-dist.R | 724 ++++++++++---------- R/autoplot-randomwalk.R | 374 +++++----- R/combine-multi-single-dist-tbl.R | 239 +++--- R/combine-tidy-distributions-tbl.R | 2 R/empirical-tidy-bootstrap.R | 190 ++--- R/empirical-tidy.R | 278 +++---- R/est-param-beta.R | 318 ++++---- R/est-param-binomial.R | 336 ++++----- R/est-param-cauchy.R | 194 ++--- R/est-param-exponential.R | 208 ++--- R/est-param-gamma.R | 250 +++--- R/est-param-geometric.R | 238 +++--- R/est-param-hypergeometric.R | 436 ++++++------ R/est-param-logistic.R | 272 +++---- R/est-param-lognormal.R | 228 +++--- R/est-param-negative-binomial.R | 296 ++++---- R/est-param-normal.R | 228 +++--- R/est-param-pareto.R | 240 +++--- R/est-param-poisson.R | 214 ++--- R/est-param-uniform.R | 218 +++--- R/est-param-weibull.R | 202 ++--- R/palette-color-blind.R | 80 +- R/random-tidy-beta.R | 252 +++--- R/random-tidy-binomial.R | 256 +++---- R/random-tidy-burr-inverse.R | 2 R/random-tidy-burr.R | 2 R/random-tidy-cauchy.R | 248 +++--- R/random-tidy-chisquare.R | 248 +++--- R/random-tidy-exponential-inverse.R | 2 R/random-tidy-exponential.R | 234 +++--- R/random-tidy-f.R | 252 +++--- R/random-tidy-gamma-inverse.R | 2 R/random-tidy-gamma.R | 258 +++---- R/random-tidy-general-beta.R | 2 R/random-tidy-general-pareto.R | 2 R/random-tidy-geom.R | 236 +++--- R/random-tidy-hypergeometric.R | 254 +++---- R/random-tidy-logistic.R | 240 +++--- R/random-tidy-lognormal.R | 248 +++--- R/random-tidy-mixture.R | 298 ++++---- R/random-tidy-negative-binomial.R | 2 R/random-tidy-normal-inverse.R | 266 +++---- R/random-tidy-normal.R | 254 +++---- R/random-tidy-paralogistic.R | 268 +++---- R/random-tidy-pareto-inverse.R | 2 R/random-tidy-pareto-single-param.R | 2 R/random-tidy-pareto.R | 2 R/random-tidy-poisson.R | 240 +++--- R/random-tidy-t.R | 250 +++--- R/random-tidy-uniform.R | 242 +++--- R/random-tidy-weibull-inverse.R | 2 R/random-tidy-weibull.R | 248 +++--- R/random-tidy-zero-truc-poisson.R | 2 R/random-tidy-zero-trunc-geometric.R | 2 R/random-tidy-zero-truncated-binomial.R | 2 R/random-zero-trunc-negative-binomial.R | 2 R/stats-beta-tbl.R | 170 ++-- R/stats-binomial-tbl.R | 174 ++-- R/stats-cauchy-tbl.R | 170 ++-- R/stats-chisquare-tbl.R | 180 ++-- R/stats-confidence-intervals.R | 130 +-- R/stats-exponential-tbl.R | 172 ++-- R/stats-f-tbl.R | 208 ++--- R/stats-gamma-tbl.R | 168 ++-- R/stats-geometric-tbl.R | 176 ++-- R/stats-hypergeometric-tbl.R | 196 ++--- R/stats-logistic-tbl.R | 172 ++-- R/stats-lognormal-tbl.R | 174 ++-- R/stats-negative-binomial-tbl.R | 174 ++-- R/stats-normal-tbl.R | 170 ++-- R/stats-pareto-tbl.R | 172 ++-- R/stats-poisson-tbl.R | 170 ++-- R/stats-t-tbl.R | 170 ++-- R/stats-uniform-tbl.R | 176 ++-- R/stats-weibull-tbl.R | 194 ++--- R/tidy-random-walk.R | 19 R/tidy_distribution_summary_tbl.R | 164 ++-- R/util-distribution-comparison.R | 500 +++++++------ R/utils-pipe.R | 28 R/utils-tidy-eval.R | 214 ++--- README.md | 25 build/vignette.rds |binary inst/doc/getting-started.Rmd | 122 +-- inst/doc/getting-started.html | 43 - man/bootstrap_unnest_tbl.Rd | 80 +- man/ci_hi.Rd | 76 +- man/ci_lo.Rd | 76 +- man/color_blind.Rd | 22 man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/pipe.Rd | 40 - man/td_scale_color_colorblind.Rd | 32 man/td_scale_fill_colorblind.Rd | 32 man/tidy_bootstrap.Rd | 108 +- man/tidy_burr.Rd | 2 man/tidy_distribution_comparison.Rd | 124 +-- man/tidy_four_autoplot.Rd | 168 ++-- man/tidy_generalized_beta.Rd | 2 man/tidy_generalized_pareto.Rd | 2 man/tidy_inverse_burr.Rd | 2 man/tidy_inverse_exponential.Rd | 2 man/tidy_inverse_gamma.Rd | 2 man/tidy_inverse_pareto.Rd | 2 man/tidy_inverse_weibull.Rd | 2 man/tidy_mixture_density.Rd | 128 +-- man/tidy_negative_binomial.Rd | 2 man/tidy_pareto.Rd | 2 man/tidy_pareto1.Rd | 2 man/tidy_t.Rd | 170 ++-- man/tidy_zero_truncated_binomial.Rd | 2 man/tidy_zero_truncated_geometric.Rd | 2 man/tidy_zero_truncated_negative_binomial.Rd | 2 man/tidy_zero_truncated_poisson.Rd | 2 man/tidyeval.Rd | 196 ++--- man/util_beta_stats_tbl.Rd | 120 +-- man/util_binomial_stats_tbl.Rd | 126 +-- man/util_cauchy_param_estimate.Rd | 136 +-- man/util_cauchy_stats_tbl.Rd | 118 +-- man/util_chisquare_stats_tbl.Rd | 116 +-- man/util_exponential_stats_tbl.Rd | 120 +-- man/util_f_stats_tbl.Rd | 116 +-- man/util_gamma_stats_tbl.Rd | 120 +-- man/util_geometric_stats_tbl.Rd | 120 +-- man/util_hypergeometric_stats_tbl.Rd | 118 +-- man/util_logistic_stats_tbl.Rd | 120 +-- man/util_lognormal_stats_tbl.Rd | 118 +-- man/util_negative_binomial_stats_tbl.Rd | 112 +-- man/util_normal_stats_tbl.Rd | 120 +-- man/util_pareto_stats_tbl.Rd | 124 +-- man/util_poisson_stats_tbl.Rd | 120 +-- man/util_t_stats_tbl.Rd | 116 +-- man/util_uniform_param_estimate.Rd | 136 +-- man/util_uniform_stats_tbl.Rd | 118 +-- man/util_weibull_param_estimate.Rd | 138 +-- man/util_weibull_stats_tbl.Rd | 120 +-- vignettes/getting-started.Rmd | 122 +-- 149 files changed, 10083 insertions(+), 9970 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1> and for a tutorial on some of the main functions available here, see Gilleland (2022) <doi: 10.5065/4px3-5a05>.
Author: Eric Gilleland [aut, cre],
Kim Elmore [ctb],
Caren Marzban [ctb],
Matt Pocernich [ctb],
Gregor Skok [ctb]
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.9 dated 2022-01-27 and 1.0 dated 2022-07-19
DESCRIPTION | 12 ++++++------ MD5 | 43 ++++++++++++++++++++++--------------------- NAMESPACE | 1 + R/FeatureTable.R | 2 +- R/Features.R | 10 +++++----- R/G2IL.R | 2 ++ R/Gbeta.R | 2 ++ R/GbetaIL.R | 2 ++ R/Hoods2d.R | 6 +++--- R/LocMeasures.R | 2 +- R/MergeForce.R | 2 +- R/Vgrams.R | 6 +++--- R/binarizer.R | 22 +++++++++++----------- R/compositer.R | 2 +- R/deltamm.R | 8 ++++---- R/functionals.R | 2 +- R/gmm.R | 2 +- R/interester.R | 2 +- R/minboundmatch.R | 2 +- R/spct.R | 4 ++-- R/warper.R | 2 +- inst |only man/hoods2d.Rd | 2 +- 23 files changed, 73 insertions(+), 65 deletions(-)
Title: Extract Muscle Synergies from Electromyography
Description: Provides a framework to factorise electromyography (EMG) data.
Tools are provided for raw data pre-processing, non negative matrix factorisation,
classification of factorised data and plotting of obtained outcomes.
In particular, reading from ASCII files is supported, along with wide-used
filtering approaches to process EMG data. All steps include one or more sensible
defaults that aim at simplifying the workflow. Yet, all functions are largely
tunable at need. Example data sets are included.
Author: Alessandro Santuz [aut, cre]
Maintainer: Alessandro Santuz <alessandro.santuz@gmail.com>
Diff between musclesyneRgies versions 1.1.3 dated 2022-02-10 and 1.2.5 dated 2022-07-19
DESCRIPTION | 12 - MD5 | 77 +++++---- NEWS.md | 171 +++++++++++++++++++++ R/HFD.R | 18 ++ R/Hurst.R | 28 +++ R/classify_kmeans.R | 57 +++---- R/filtEMG.R | 10 - R/normEMG.R | 14 - R/plot_classified_syns.R | 6 R/plot_rawEMG.R | 4 R/rawdata.R | 63 +++++-- R/sMLE.R | 6 R/subsetEMG.R | 28 ++- R/synsNMF.R | 48 ++++-- README.md | 76 ++++++--- build/partial.rdb |binary build/vignette.rds |binary data/RAW_DATA.RData |binary inst/CITATION |only inst/doc/analysis.R | 2 inst/doc/analysis.Rmd | 2 inst/doc/analysis.html | 209 +++++++++++++++++++++++++- inst/doc/plots.html | 223 +++++++++++++++++++++++++++- inst/doc/pro_tips.html | 214 ++++++++++++++++++++++++++- inst/doc/workflow.html | 268 ++++++++++++++++++++++++++++++---- man/HFD.Rd | 14 + man/Hurst.Rd | 26 +++ man/classify_kmeans.Rd | 11 + man/filtEMG.Rd | 2 man/normEMG.Rd | 2 man/rawdata.Rd | 15 + tests/testthat/test-EMG.R | 15 + tests/testthat/test-HFD.R | 5 tests/testthat/test-Hurst.R | 5 tests/testthat/test-classify_kmeans.R |only tests/testthat/test-filtEMG.R |only tests/testthat/test-normEMG.R |only tests/testthat/test-plots.R | 17 +- tests/testthat/test-sMLE.R | 4 tests/testthat/test-subsetEMG.R |only tests/testthat/test-synsNMF.R | 7 vignettes/analysis.Rmd | 2 42 files changed, 1428 insertions(+), 233 deletions(-)
More information about musclesyneRgies at CRAN
Permanent link
Title: Create R Markdown from Lists
Description: Programmatically create R Markdown documents from lists.
Author: Michael J. Kane [aut, cph, cre]
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Diff between listdown versions 0.4.1 dated 2020-12-07 and 0.5.2 dated 2022-07-19
listdown-0.4.1/listdown/tests/testthat.R |only listdown-0.4.1/listdown/tests/testthat/make-reference.r |only listdown-0.5.2/listdown/DESCRIPTION | 15 listdown-0.5.2/listdown/MD5 | 109 - listdown-0.5.2/listdown/NAMESPACE | 25 listdown-0.5.2/listdown/NEWS.md | 10 listdown-0.5.2/listdown/R/build-site.r |only listdown-0.5.2/listdown/R/cc-dendro.r | 9 listdown-0.5.2/listdown/R/chunk-options.r | 6 listdown-0.5.2/listdown/R/chunk-writer.r | 100 listdown-0.5.2/listdown/R/class-and-tag.r |only listdown-0.5.2/listdown/R/depth-first-pres-list-visitor.r | 1 listdown-0.5.2/listdown/R/headers.r | 2 listdown-0.5.2/listdown/R/ld-write-file.r | 54 listdown-0.5.2/listdown/build/vignette.rds |binary listdown-0.5.2/listdown/inst/CITATION |only listdown-0.5.2/listdown/inst/doc/listdown.html | 1029 ++++++---- listdown-0.5.2/listdown/inst/doc/listdown.rmd | 2 listdown-0.5.2/listdown/man/class_and_tag.Rd |only listdown-0.5.2/listdown/man/ld_build_html_site.Rd |only listdown-0.5.2/listdown/man/ld_bundle_doc.Rd |only listdown-0.5.2/listdown/man/ld_create_doc.Rd |only listdown-0.5.2/listdown/man/ld_make_chunks.Rd | 4 listdown-0.5.2/listdown/man/ld_site_yaml.Rd |only listdown-0.5.2/listdown/man/listdown.Rd | 22 listdown-0.5.2/listdown/tests/testthat.r |only listdown-0.5.2/listdown/tests/testthat/reference-data/as-yml.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/cc-dendro.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/cc-list.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-decorator-option-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-2.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-3.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/chunk-option-4.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/ld-cc-list-2-output.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/listdown-page-bundle-after-creation.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/listdown-page-bundle.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/option-check.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/option-chunk-check.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/site_yaml.rds |only listdown-0.5.2/listdown/tests/testthat/reference-data/test-make-chunks-1.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-make-chunks-2.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-no-package.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-print-ld.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-print-with-decorator.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-rmarkdown-header.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-setup-expr.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test-workflowr-header.rds |binary listdown-0.5.2/listdown/tests/testthat/reference-data/test_list.rds |binary listdown-0.5.2/listdown/tests/testthat/reference.r |only listdown-0.5.2/listdown/tests/testthat/test-add-chunk-elem-option.r | 67 listdown-0.5.2/listdown/tests/testthat/test-add-chunk-option.r | 40 listdown-0.5.2/listdown/tests/testthat/test-as-yml.r | 32 listdown-0.5.2/listdown/tests/testthat/test-cc-dendro.r | 42 listdown-0.5.2/listdown/tests/testthat/test-chunk-opts.r | 7 listdown-0.5.2/listdown/tests/testthat/test-create-doc.r |only listdown-0.5.2/listdown/tests/testthat/test-create-html-site.r |only listdown-0.5.2/listdown/tests/testthat/test-headers.r | 28 listdown-0.5.2/listdown/tests/testthat/test-list.r | 9 listdown-0.5.2/listdown/tests/testthat/test-make-chunks.r | 20 listdown-0.5.2/listdown/tests/testthat/test-no-package.r | 13 listdown-0.5.2/listdown/tests/testthat/test-setup-expr.r | 18 listdown-0.5.2/listdown/tests/testthat/test-site-yaml.r |only listdown-0.5.2/listdown/tests/testthat/test-write-file.r | 74 listdown-0.5.2/listdown/vignettes/listdown.rmd | 2 65 files changed, 1034 insertions(+), 706 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.0 dated 2022-05-31 and 1.0.0-2 dated 2022-07-19
DESCRIPTION | 6 +- MD5 | 26 +++++----- NEWS.md | 4 + R/CompareIsoGrowth_class.R | 5 - R/GlobalGrowthComparison_class.R | 5 - inst/doc/v02_growth_fitting.R | 5 + inst/doc/v02_growth_fitting.Rmd | 5 + inst/doc/v02_growth_fitting.html | 49 +++++++++---------- inst/doc/v03_growth_uncertainty.html | 12 ++-- inst/doc/v04_model_comparison.R | 10 ++- inst/doc/v04_model_comparison.Rmd | 10 ++- inst/doc/v04_model_comparison.html | 90 +++++++++++++++++------------------ vignettes/v02_growth_fitting.Rmd | 5 + vignettes/v04_model_comparison.Rmd | 10 ++- 14 files changed, 122 insertions(+), 120 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ts versions 0.2.0 dated 2022-06-09 and 0.2.1 dated 2022-07-19
DESCRIPTION | 8 MD5 | 280 ++++---- NAMESPACE | 10 NEWS.md | 18 R/00_global_variables.R | 6 R/arima-string.R | 120 +-- R/augment-ts-acceleration.R | 164 ++-- R/augment-ts-velocity.R | 158 ++-- R/boilerplate-autoarima-xgboost.R | 514 +++++++------- R/boilerplate-autoarima.R | 496 +++++++------- R/boilerplate-croston.R | 514 +++++++------- R/boilerplate-exp-smoothing.R | 522 +++++++-------- R/boilerplate-glmnet.R | 510 +++++++------- R/boilerplate-lm.R | 340 ++++----- R/boilerplate-mars.R | 502 +++++++------- R/boilerplate-misc-functions.R | 70 +- R/boilerplate-nnetar.R | 514 +++++++------- R/boilerplate-prophet-reg.R | 516 +++++++------- R/boilerplate-prophet-xgboost.R | 528 +++++++-------- R/boilerplate-smooth-es.R | 530 +++++++-------- R/boilerplate-svm-poly.R | 518 +++++++------- R/boilerplate-svm-rbf.R | 516 +++++++------- R/boilerplate-theta.R | 320 ++++----- R/boilerplate-xgboost.R | 504 +++++++------- R/calibrate-plot-list.R | 264 +++---- R/diagnostic_plots.R | 622 +++++++++--------- R/helper-model-extraction.R | 172 ++-- R/internal-event-backward.R |only R/internal-event-both.R |only R/internal-event-forward.R |only R/pallette-color-blind.R | 154 ++-- R/simulate-ts-arima.R | 416 ++++++------ R/stats-confidence-intervals.R |only R/step-ts-acceleration.R | 376 +++++----- R/step-ts-velocity.R | 376 +++++----- R/tidy-fft.R | 564 ++++++++-------- R/time-helpers.R |only R/ts-auto-recipe.R | 366 +++++----- R/ts-calendar-heatmap-plt.R | 248 +++---- R/ts-compare-data.R | 226 +++--- R/ts-event-analysis-plot.R |only R/ts-event-analysis-tbl.R |only R/ts-feature-cluster-plt.R | 350 +++++----- R/ts-feature-cluster-tbl.R | 382 +++++------ R/ts-info-tbl.R | 290 ++++---- R/ts-lag-correlation.R |only R/ts-ma-plt.R | 598 ++++++++--------- R/ts-model-compare.R | 496 +++++++------- R/ts-model-rank.R | 216 +++--- R/ts-model-tuner.R | 8 R/ts-qq-plot.R | 260 +++---- R/ts-skedactiy-plot.R | 262 +++---- R/ts-sma-plot.R | 270 +++---- R/ts-splits-plot.R | 142 ++-- R/ts-to-tbl.R | 122 +-- R/ts-tune-spec-template.R | 29 R/ts-vva-plot.R | 208 +++--- R/ts_fcst_sim.R | 548 +++++++-------- R/ts_random_walk.R | 162 ++-- R/vec-ts-acceleration.R | 114 +-- R/vec-ts-velocity.R | 114 +-- R/wfs-arima-boost.R | 362 +++++----- R/wfs-arima-reg.R | 214 +++--- R/wfs-ets-reg.R | 384 +++++------ R/wfs-linear-reg.R | 244 +++---- R/wfs-mars-reg.R | 268 +++---- R/wfs-nnetar-reg.R | 264 +++---- R/wfs-prophet-reg.R | 434 ++++++------ R/wfs-svm-poly-reg.R | 268 +++---- R/wfs-svm-rbf.R | 254 +++---- R/zzz.R | 258 +++---- README.md | 16 build/vignette.rds |binary inst/doc/getting-started.Rmd | 222 +++--- inst/doc/getting-started.html | 26 inst/doc/using-tidy-fft.Rmd | 574 ++++++++-------- inst/doc/using-tidy-fft.html | 16 man/arima_string.Rd | 36 - man/assign_value.Rd | 24 man/calibrate_and_plot.Rd | 206 +++-- man/chr_assign.Rd | 24 man/ci_hi.Rd |only man/ci_lo.Rd |only man/color_blind.Rd | 50 - man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/get_recipe_call.Rd | 24 man/internal_ts_backward_event_tbl.Rd |only man/internal_ts_both_event_tbl.Rd |only man/internal_ts_forward_event_tbl.Rd |only man/model_extraction_helper.Rd | 8 man/required_pkgs.healthyR.ts.Rd | 50 - man/step_ts_acceleration.Rd | 202 ++--- man/step_ts_velocity.Rd | 202 ++--- man/tidy_fft.Rd | 206 ++--- man/ts_acceleration_augment.Rd | 108 +-- man/ts_acceleration_vec.Rd | 106 +-- man/ts_arima_simulator.Rd | 176 ++--- man/ts_auto_arima.Rd | 248 +++---- man/ts_auto_arima_xgboost.Rd | 248 +++---- man/ts_auto_croston.Rd | 266 +++---- man/ts_auto_exp_smoothing.Rd | 264 +++---- man/ts_auto_glmnet.Rd | 246 +++---- man/ts_auto_lm.Rd | 220 +++--- man/ts_auto_mars.Rd | 246 +++---- man/ts_auto_nnetar.Rd | 246 +++---- man/ts_auto_prophet_boost.Rd | 254 +++---- man/ts_auto_prophet_reg.Rd | 252 +++---- man/ts_auto_recipe.Rd | 196 ++--- man/ts_auto_smooth_es.Rd | 264 +++---- man/ts_auto_svm_poly.Rd | 256 +++---- man/ts_auto_svm_rbf.Rd | 256 +++---- man/ts_auto_theta.Rd | 208 +++--- man/ts_auto_xgboost.Rd | 242 +++---- man/ts_compare_data.Rd | 5 man/ts_event_analysis_plot.Rd |only man/ts_feature_cluster.Rd | 224 +++--- man/ts_feature_cluster_plot.Rd | 208 +++--- man/ts_forecast_simulator.Rd | 176 ++--- man/ts_get_date_columns.Rd |only man/ts_info_tbl.Rd | 128 +-- man/ts_is_date_class.Rd |only man/ts_lag_correlation.Rd |only man/ts_ma_plot.Rd | 158 ++-- man/ts_model_auto_tune.Rd | 403 ++++++----- man/ts_model_compare.Rd | 260 +++---- man/ts_model_rank_tbl.Rd | 196 ++--- man/ts_model_spec_tune_template.Rd | 138 ++- man/ts_qq_plot.Rd | 205 +++-- man/ts_scale_color_colorblind.Rd | 52 - man/ts_scale_fill_colorblind.Rd | 52 - man/ts_scedacity_scatter_plot.Rd | 213 +++--- man/ts_sma_plot.Rd | 118 +-- man/ts_splits_plot.Rd | 118 +-- man/ts_time_event_analysis_tbl.Rd |only man/ts_to_tbl.Rd | 96 +- man/ts_velocity_augment.Rd | 108 +-- man/ts_velocity_vec.Rd | 106 +-- man/ts_vva_plot.Rd | 100 +- man/ts_wfs_arima_boost.Rd | 266 +++---- man/ts_wfs_auto_arima.Rd | 172 ++-- man/ts_wfs_ets_reg.Rd | 258 +++---- man/ts_wfs_lin_reg.Rd | 174 ++--- man/ts_wfs_mars.Rd | 208 +++--- man/ts_wfs_nnetar_reg.Rd | 220 +++--- man/ts_wfs_prophet_reg.Rd | 310 ++++---- man/ts_wfs_svm_poly.Rd | 214 +++--- man/ts_wfs_svm_rbf.Rd | 208 +++--- vignettes/getting-started.Rmd | 222 +++--- vignettes/using-tidy-fft.Rmd | 574 ++++++++-------- 150 files changed, 15878 insertions(+), 15683 deletions(-)
Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for
visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as
frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as
bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include
but are not limited to: points with multiple uncertainty intervals,
eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>,
density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>,
quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>,
complementary cumulative distribution function
barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>,
and fit curves with multiple uncertainty ribbons.
Author: Matthew Kay [aut, cre],
Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ggdist versions 3.1.1 dated 2022-02-27 and 3.2.0 dated 2022-07-19
DESCRIPTION | 21 MD5 | 173 - NAMESPACE | 34 NEWS.md | 63 R/abstract_stat_slabinterval.R | 231 + R/binning_methods.R | 4 R/cut_cdf_qi.R | 30 R/distributions.R | 90 R/geom_dotsinterval.R | 49 R/geom_slabinterval.R | 162 - R/guide_rampbar.R |only R/point_interval.R | 12 R/rd_slabinterval.R | 32 R/scale_.R | 10 R/scale_colour_ramp.R | 8 R/scale_thickness.R |only R/stat_dotsinterval.R | 45 R/stat_slabinterval.R | 284 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/dotsinterval.R | 20 inst/doc/dotsinterval.Rmd | 33 inst/doc/dotsinterval.html | 868 ++++- inst/doc/freq-uncertainty-vis.Rmd | 6 inst/doc/freq-uncertainty-vis.html | 356 ++ inst/doc/lineribbon.R | 30 inst/doc/lineribbon.Rmd | 85 inst/doc/lineribbon.html | 839 ++++- inst/doc/slabinterval.R | 99 inst/doc/slabinterval.Rmd | 167 - inst/doc/slabinterval.html | 1447 +++++++--- man/RankCorr.Rd | 6 man/cut_cdf_qi.Rd | 32 man/geom_dotsinterval.Rd | 20 man/geom_interval.Rd | 4 man/geom_pointinterval.Rd | 4 man/geom_slab.Rd | 4 man/guide_rampbar.Rd |only man/lkjcorr_marginal.Rd | 8 man/scale_colour_ramp.Rd | 9 man/scale_thickness.Rd |only man/scales.Rd | 23 man/stat_ccdfinterval.Rd | 21 man/stat_cdfinterval.Rd | 21 man/stat_eye.Rd | 19 man/stat_gradientinterval.Rd | 21 man/stat_halfeye.Rd | 15 man/stat_histinterval.Rd | 19 man/stat_interval.Rd | 14 man/stat_lineribbon.Rd | 14 man/stat_pointinterval.Rd | 14 man/stat_ribbon.Rd | 14 man/stat_slab.Rd | 19 man/stat_slabinterval.Rd | 15 man/student_t.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/test.geom_dotsinterval/bin-dot-order-kept.svg |only tests/testthat/_snaps/test.geom_dotsinterval/bin-dot-order.svg |only tests/testthat/_snaps/test.geom_dotsinterval/max-binwidth.svg | 74 tests/testthat/_snaps/test.geom_dotsinterval/min-binwidth.svg | 74 tests/testthat/_snaps/test.geom_dotsinterval/swarm-both.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/swarm-bottom.svg | 14 tests/testthat/_snaps/test.geom_dotsinterval/swarm-dot-order.svg | 124 tests/testthat/_snaps/test.geom_dotsinterval/varying-scale-side-just.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/varying-side-and-just.svg | 12 tests/testthat/_snaps/test.geom_dotsinterval/varying-side.svg | 18 tests/testthat/_snaps/test.geom_dotsinterval/weave-both.svg | 8 tests/testthat/_snaps/test.geom_dotsinterval/weave-bottom.svg | 10 tests/testthat/_snaps/test.geom_dotsinterval/weave-dot-order.svg | 124 tests/testthat/_snaps/test.geom_dotsinterval/weave-top.svg | 6 tests/testthat/_snaps/test.geom_slabinterval/slabinterval-with-nas-in-thickness.svg |only tests/testthat/_snaps/test.guide_rampbar |only tests/testthat/_snaps/test.scale_colour_ramp/fill-ramp-with-slab-and-nas.svg | 81 tests/testthat/_snaps/test.scale_thickness |only tests/testthat/_snaps/test.stat_dist_slabinterval/fill-type-gradient-with-two-groups-h.svg | 8 tests/testthat/_snaps/test.stat_dist_slabinterval/fill-type-gradient-with-two-groups.svg | 8 tests/testthat/_snaps/test.stat_dist_slabinterval/halfeye-multiple-dists-per-group.svg |only tests/testthat/_snaps/test.stat_sample_slabinterval/fill-type-gradient-with-two-groups-h.svg | 8 tests/testthat/_snaps/test.stat_sample_slabinterval/fill-type-gradient-with-two-groups.svg | 8 tests/testthat/test.distributions.R | 10 tests/testthat/test.geom_dotsinterval.R | 35 tests/testthat/test.geom_slabinterval.R | 20 tests/testthat/test.guide_rampbar.R |only tests/testthat/test.point_interval.R | 63 tests/testthat/test.scale_colour_ramp.R | 9 tests/testthat/test.scale_thickness.R |only tests/testthat/test.stat_dist_slabinterval.R | 100 tests/testthat/test.stat_sample_slabinterval.R | 28 vignettes/dotsinterval.Rmd | 33 vignettes/freq-uncertainty-vis.Rmd | 6 vignettes/lineribbon.Rmd | 85 vignettes/slabinterval.Rmd | 167 - 92 files changed, 4901 insertions(+), 1774 deletions(-)
Title: Reference Interval Estimation using Real-World Data
Description: Indirect method for the estimation of reference intervals using Real-World Data ('RWD'). It takes routine measurements
of diagnostic tests, containing pathological and non-pathological samples as input and uses sophisticated
statistical methods to derive a model describing the distribution of the non-pathological samples. This distribution can then be
used to derive reference intervals.
Furthermore, the package offers functions for printing and plotting the results of the algorithm. See ?refineR for a more comprehensive description of the features.
Version 1.0 of the algorithm is described in detail in Ammer T., Schuetzenmeister A., Prokosch H.-U., Rauh M., Rank C.M., Zierk J. "refineR: A Novel Algorithm for Reference Interval Estimation from Real-World Data". Scientific Reports (2021) <doi:10.1038/s41598-021-95301-2>.
Author: Tatjana Ammer [aut, cre],
Christopher M Rank [aut],
Andre Schuetzenmeister [aut]
Maintainer: Tatjana Ammer <tatjana.ammer@roche.com>
Diff between refineR versions 1.5.0 dated 2022-06-03 and 1.5.1 dated 2022-07-19
refineR-1.5.0/refineR/build/partial.rdb |only refineR-1.5.0/refineR/inst/ChangeLog.txt |only refineR-1.5.1/refineR/DESCRIPTION | 10 +++-- refineR-1.5.1/refineR/MD5 | 28 ++++++++------ refineR-1.5.1/refineR/NEWS.md | 14 +++++-- refineR-1.5.1/refineR/R/algoInvHist.R | 52 +++++++++++++-------------- refineR-1.5.1/refineR/R/plot.R | 6 +-- refineR-1.5.1/refineR/R/utils.R | 34 ++++++++++++++--- refineR-1.5.1/refineR/build/vignette.rds |only refineR-1.5.1/refineR/inst/doc |only refineR-1.5.1/refineR/man/getRI.Rd | 4 +- refineR-1.5.1/refineR/man/plot.RWDRI.Rd | 6 +-- refineR-1.5.1/refineR/man/print.RWDRI.Rd | 4 +- refineR-1.5.1/refineR/man/refineR-Package.Rd | 7 +-- refineR-1.5.1/refineR/vignettes |only 15 files changed, 100 insertions(+), 65 deletions(-)
Title: 'Coroutines' for R
Description: Provides 'coroutines' for R, a family of functions that can
be suspended and resumed later on. This includes 'async' functions
(which await) and generators (which yield). 'Async' functions are
based on the concurrency framework of the 'promises' package.
Generators are based on a dependency free iteration protocol defined
in 'coro' and are compatible with iterators from the 'reticulate'
package.
Author: Lionel Henry [aut, cre],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between coro versions 1.0.2 dated 2021-12-03 and 1.0.3 dated 2022-07-19
DESCRIPTION | 39 ++++++++++++++++++++------------------- MD5 | 19 ++++++++++--------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/aaa.R | 4 ---- R/coro-package.R |only R/iterator.R | 16 +++++++--------- inst/doc/generator.html | 5 +++-- man/coro-package.Rd | 4 ++-- man/iterator.Rd | 34 +++++++++++++++++++++++++--------- tests/testthat/test-iterator.R | 17 +++++++++++++++++ 11 files changed, 92 insertions(+), 54 deletions(-)
Title: Easy to Make (Lazy) Tables
Description: Constructs tables of counts and proportions out of data sets with possibility to insert tables to Excel, Word, HTML, and PDF documents. Transforms tables to data suitable for modelling. Features Gibbs sampling based log-linear (NB2) and power analyses (original by Oleksandr Ocheredko <doi:10.35566/isdsa2019c5>) for tabulated data.
Author: Ocheredko Oleksandr
Maintainer: Ocheredko Oleksandr <Ocheredko@yahoo.com>
Diff between ltable versions 2.0.1 dated 2021-11-22 and 2.0.2 dated 2022-07-19
ltable-2.0.1/ltable/R/PowerPoisson.R |only ltable-2.0.1/ltable/R/Print.R |only ltable-2.0.1/ltable/R/RcppExports.R |only ltable-2.0.1/ltable/cleanup |only ltable-2.0.1/ltable/configure |only ltable-2.0.1/ltable/configure.ac |only ltable-2.0.1/ltable/inst/INSTALL.Rd |only ltable-2.0.1/ltable/man/powerpoisson.Rd |only ltable-2.0.1/ltable/src |only ltable-2.0.2/ltable/DESCRIPTION | 21 ++++------- ltable-2.0.2/ltable/MD5 | 40 ++++++++------------- ltable-2.0.2/ltable/NAMESPACE | 10 ++--- ltable-2.0.2/ltable/R/MCLogLin.R |only ltable-2.0.2/ltable/R/MCPower.R |only ltable-2.0.2/ltable/R/PrintPower.R |only ltable-2.0.2/ltable/inst/Doc/ltable.pdf |binary ltable-2.0.2/ltable/inst/NEWS.Rd | 8 ++-- ltable-2.0.2/ltable/man/MCLogLin.Rd |only ltable-2.0.2/ltable/man/MCPower.Rd |only ltable-2.0.2/ltable/man/ltable-package.Rd | 10 +++-- ltable-2.0.2/ltable/man/plot,powerClass-method.Rd | 6 ++- ltable-2.0.2/ltable/man/powerClass-class.Rd | 8 ++-- ltable-2.0.2/ltable/man/print,powerClass-method.Rd | 11 +++-- ltable-2.0.2/ltable/man/tableToData.Rd | 15 ++++--- ltable-2.0.2/ltable/man/table_f.Rd | 2 - ltable-2.0.2/ltable/man/z[,powerClass-method.Rd | 28 +++++++------- ltable-2.0.2/ltable/man/z[_-,powerClass-method.Rd | 23 ------------ 27 files changed, 83 insertions(+), 99 deletions(-)
Title: 2d, 2.5d, and 3d Delaunay Tessellations
Description: Construction and visualization of 2d Delaunay triangulations,
possibly constrained, 2.5d (i.e. elevated) Delaunay triangulations,
and 3d Delaunay triangulations.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between delaunay versions 1.0.0 dated 2022-07-06 and 1.1.0 dated 2022-07-19
delaunay-1.0.0/delaunay/src/Makevars |only delaunay-1.1.0/delaunay/DESCRIPTION | 9 ++++----- delaunay-1.1.0/delaunay/MD5 | 10 ++++++---- delaunay-1.1.0/delaunay/NEWS.md | 5 +++++ delaunay-1.1.0/delaunay/README.md | 1 + delaunay-1.1.0/delaunay/cleanup |only delaunay-1.1.0/delaunay/configure |only delaunay-1.1.0/delaunay/src/Makevars.in |only 8 files changed, 16 insertions(+), 9 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 3043.102 dated 2018-02-21 and 4021.104 dated 2022-07-19
ChangeLog | 12 +++++++ DESCRIPTION | 37 +++++++++++++++-------- MD5 | 36 ++++++++++++---------- NAMESPACE | 5 +-- NEWS.md |only R/calendar-firstDay.R | 35 +++++++++++++--------- R/calendar-onOrAfter.R | 58 ++++++++++++++++++------------------- R/holiday-Dates.R | 13 ++++++++ R/holiday-NYSE.R | 2 + R/holiday-TSX.R | 1 inst/_pkgdown.yml |only man/calendar-Easter.Rd | 3 + man/calendar-dayOfWeek.Rd | 13 -------- man/calendar-dayOfYear.Rd | 14 -------- man/calendar-endpoints.Rd | 4 +- man/holiday-Dates.Rd | 2 + man/holiday-Listing.Rd | 2 - man/options-RmetricsOptions.Rd | 2 - man/timeDate-DaylightSavingTime.Rd | 4 +- man/timeDate-whichFormat.Rd | 2 - 20 files changed, 137 insertions(+), 108 deletions(-)
Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data.
The philosophy of the package is described in Guo G. (2020)
<doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] ,
Miao Yu [aut],
Haoyue Song [aut],
Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between ORKM versions 0.3.0.0 dated 2022-06-10 and 0.4.0.0 dated 2022-07-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ORKMeans.R | 3 +-- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Clean the R Console and Environment
Description: Small package to clean the R console and the R environment
with the call of just one function.
Author: Jonathan M. Mang [aut, cre] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between cleaR versions 0.0.3 dated 2022-06-27 and 0.0.4 dated 2022-07-19
DESCRIPTION | 9 ++++----- MD5 | 4 ++-- R/clear.R | 2 +- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut, cre] ,
Leonardo Ramirez-Lopez [aut, cre] ,
Guillaume Hans [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.4 dated 2022-04-03 and 0.2.5 dated 2022-07-19
prospectr-0.2.4/prospectr/NEWS |only prospectr-0.2.5/prospectr/DESCRIPTION | 10 +-- prospectr-0.2.5/prospectr/MD5 | 32 +++++----- prospectr-0.2.5/prospectr/NEWS.md |only prospectr-0.2.5/prospectr/R/AAA.R | 2 prospectr-0.2.5/prospectr/R/baseline.R | 20 +++--- prospectr-0.2.5/prospectr/R/cochranTest.R | 2 prospectr-0.2.5/prospectr/R/e2m.R | 18 +++--- prospectr-0.2.5/prospectr/R/kenstone.R | 4 - prospectr-0.2.5/prospectr/R/msc.R | 8 +- prospectr-0.2.5/prospectr/R/spliceCorrection.R | 7 ++ prospectr-0.2.5/prospectr/README.md | 7 +- prospectr-0.2.5/prospectr/build/prospectr.pdf |binary prospectr-0.2.5/prospectr/build/vignette.rds |binary prospectr-0.2.5/prospectr/inst/doc/prospectr.html | 28 ++------- prospectr-0.2.5/prospectr/man/spliceCorrection.Rd | 2 prospectr-0.2.5/prospectr/tests/testthat/test-kenStone.R | 45 ++++++++++++--- prospectr-0.2.5/prospectr/tests/testthat/test-msc.R | 2 18 files changed, 105 insertions(+), 82 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data:
tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation;
forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping:
co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>);
extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful
for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>);
model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre]
,
Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 4.0.2 dated 2022-07-18 and 4.0.3 dated 2022-07-19
DESCRIPTION | 10 ++--- MD5 | 8 ++-- R/aba.R | 6 ++- R/tree_detection.R | 91 ++++++++++++++++++++++++++----------------------- man/tree_extraction.Rd | 13 +++++-- 5 files changed, 74 insertions(+), 54 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-25 0.1.6
2021-11-30 0.1.5
2021-10-15 0.1.4
2021-06-24 0.1.3
2021-05-04 0.1.2
2021-04-22 0.1.1
2020-12-16 0.1.0
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.20.0 dated 2022-02-16 and 1.20.1 dated 2022-07-19
DESCRIPTION | 8 +- MD5 | 80 ++++++++++---------- NEWS.md | 12 +++ R/LRCUSUM.runlength.R | 5 - R/boda.R | 75 ++++++++----------- R/earsC.R | 4 - R/ks.plot.unif.R | 49 +++--------- R/nowcast.R | 9 +- R/twinstim_siaf.R | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.Rnw | 4 - inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.Rnw | 8 +- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.pdf |binary inst/doc/twinstim.pdf |binary man/LRCUSUM.runlength.Rd | 6 - man/boda.Rd | 12 +-- man/categoricalCUSUM.Rd | 2 man/checkResidualProcess.Rd | 2 man/ks.plot.unif.Rd | 13 +-- man/m1.Rd | 4 - man/measles.weser.Rd | 13 +-- man/nowcast.Rd | 2 man/pairedbinCUSUM.Rd | 2 man/permutationTest.Rd | 4 - man/stsBP-class.Rd | 6 - man/stsNC-class.Rd | 6 - man/stsplot_spacetime.Rd | 26 +++--- man/twinSIR.Rd | 6 - src/init.c | 8 +- src/ks.c | 81 ++++++++++++--------- tests/testthat/test-hhh4_NA.R | 4 + vignettes/hhh4_spacetime.Rnw | 4 - vignettes/monitoringCounts-cache/boda.RData |binary vignettes/monitoringCounts-cache/boda.covars.RData |binary vignettes/monitoringCounts.Rnw | 8 +- 41 files changed, 230 insertions(+), 239 deletions(-)
Title: Interface to the 'PredictIt' API
Description: Wrapper to retrieve market data, explore available markets, and plot historical price data from the 'PredictIt' public API (<https://www.predictit.org/api/marketdata/all/>).
The package comes with a demo 'shiny' application for illustrating example use cases.
License to use data made available via the API is for non-commercial use and 'PredictIt' is the sole source of such data.
Author: Daniel Kovtun [cre, aut]
Maintainer: Daniel Kovtun <quantumfusetrader@gmail.com>
Diff between rpredictit versions 0.0.2 dated 2020-03-18 and 0.1.0 dated 2022-07-19
DESCRIPTION | 13 MD5 | 22 NEWS.md | 5 R/market_data.R | 16 README.md | 9 build/vignette.rds |binary inst/doc/rpredictit-vignette.R | 4 inst/doc/rpredictit-vignette.Rmd | 9 inst/doc/rpredictit-vignette.html | 1981 ++++++++++++++++++++++++++++++++++++-- man/format_market_data.Rd | 2 man/markets_table.Rd | 2 vignettes/rpredictit-vignette.Rmd | 9 12 files changed, 1937 insertions(+), 135 deletions(-)
Title: 'RStudio' Addins to Prettify 'JavaScript', 'C++', 'Python', and
More
Description: Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS',
'JavaScript', 'JSX', 'Markdown', 'C(++)', 'LaTeX', 'Python', 'Julia',
'XML', 'Java', 'JSON', 'Ruby', and to reindent 'C(++)', 'Fortran',
'Java', 'Julia', 'Python', 'SAS', 'Scala', 'Shell', 'SQL' and
"TypeScript". Two kinds of addins are provided: 'Prettify' and
'Indent'. The 'Indent' addins only reindent the code, while the
'Prettify' addins also modify the code, e.g. trailing semi-colons are
added to 'JavaScript' code when they are missing.
Author: Stephane Laurent [aut, cre],
James Long and contributors [cph] ,
Zeb Zhao [cph] ,
Marijn Haverbeke [cph] ,
George Leslie-Waksman and other contributors [cph] ,
Austin Cheney [cph] ,
John Schlinkert [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between prettifyAddins versions 2.4.0 dated 2022-01-25 and 2.5.0 dated 2022-07-19
DESCRIPTION | 73 ++++++++++------------- LICENSE.note | 27 ++++++++ MD5 | 18 +++-- NAMESPACE | 1 NEWS.md | 7 ++ R/addins.R | 4 - R/prettifyJULIA.R | 151 ++++++++++++++++++++++++------------------------ R/prettify_V8.R | 75 +++++++++++++++++++++++ inst/libraries |only inst/rstudio/addins.dcf | 5 + man/wordWrap.Rd |only 11 files changed, 237 insertions(+), 124 deletions(-)
More information about prettifyAddins at CRAN
Permanent link
Title: Jacobi Theta Functions and Related Functions
Description: Evaluation of the Jacobi theta functions and related
functions: Weierstrass elliptic function, Weierstrass sigma function,
Weierstrass zeta function, Klein j-function, Dedekind eta function,
lambda modular function, Jacobi elliptic functions, Neville theta
functions, and Eisenstein series. Complex values of the variable are
supported.
Author: Stephane Laurent [aut, cre],
Mikael Fremling [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jacobi versions 1.0.0 dated 2022-06-22 and 2.0.0 dated 2022-07-19
jacobi-1.0.0/jacobi/R/jtheta1primeprimeprime0.R |only jacobi-1.0.0/jacobi/R/p-weierstrass.R |only jacobi-1.0.0/jacobi/R/sigmaw.R |only jacobi-1.0.0/jacobi/man/En.Rd |only jacobi-1.0.0/jacobi/man/sigmaw.Rd |only jacobi-1.0.0/jacobi/tests/testthat/test-pweierstrass.R |only jacobi-1.0.0/jacobi/tests/testthat/test-sigmaw.R |only jacobi-2.0.0/jacobi/DESCRIPTION | 17 jacobi-2.0.0/jacobi/MD5 | 81 - jacobi-2.0.0/jacobi/NAMESPACE | 13 jacobi-2.0.0/jacobi/NEWS.md | 13 jacobi-2.0.0/jacobi/R/CostaMesh.R |only jacobi-2.0.0/jacobi/R/RcppExports.R | 108 +- jacobi-2.0.0/jacobi/R/agm.R | 2 jacobi-2.0.0/jacobi/R/am.R |only jacobi-2.0.0/jacobi/R/eisenstein.R | 16 jacobi-2.0.0/jacobi/R/eta-dedekind.R | 2 jacobi-2.0.0/jacobi/R/internal.R | 40 jacobi-2.0.0/jacobi/R/jellip.R | 4 jacobi-2.0.0/jacobi/R/jtheta.R | 119 +- jacobi-2.0.0/jacobi/R/jtheta1derivatives.R |only jacobi-2.0.0/jacobi/R/klein-j.R | 67 - jacobi-2.0.0/jacobi/R/lambda.R | 44 jacobi-2.0.0/jacobi/R/theta-neville.R | 54 - jacobi-2.0.0/jacobi/R/weierstrassStuff.R |only jacobi-2.0.0/jacobi/R/wp.R |only jacobi-2.0.0/jacobi/R/wpinv.R |only jacobi-2.0.0/jacobi/R/wsigma.R |only jacobi-2.0.0/jacobi/R/wzeta.R |only jacobi-2.0.0/jacobi/README.md | 28 jacobi-2.0.0/jacobi/man/CostaMesh.Rd |only jacobi-2.0.0/jacobi/man/EisensteinE.Rd |only jacobi-2.0.0/jacobi/man/am.Rd |only jacobi-2.0.0/jacobi/man/jellip.Rd | 4 jacobi-2.0.0/jacobi/man/jtheta1.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta2.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta3.Rd | 6 jacobi-2.0.0/jacobi/man/jtheta4.Rd | 6 jacobi-2.0.0/jacobi/man/kleinj.Rd | 27 jacobi-2.0.0/jacobi/man/lambda.Rd | 16 jacobi-2.0.0/jacobi/man/neville.Rd | 4 jacobi-2.0.0/jacobi/man/wp.Rd | 21 jacobi-2.0.0/jacobi/man/wpinv.Rd |only jacobi-2.0.0/jacobi/man/wsigma.Rd |only jacobi-2.0.0/jacobi/man/wzeta.Rd |only jacobi-2.0.0/jacobi/src/RcppExports.cpp | 336 ++++++ jacobi-2.0.0/jacobi/src/altjtheta.cpp |only jacobi-2.0.0/jacobi/src/jacobi.cpp | 850 ++++++++++++++++- jacobi-2.0.0/jacobi/src/jacobi_types.h | 14 jacobi-2.0.0/jacobi/tests/testthat/test-am.R |only jacobi-2.0.0/jacobi/tests/testthat/test-kleinj.R | 31 jacobi-2.0.0/jacobi/tests/testthat/test-wp.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wpinv.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wsigma.R |only jacobi-2.0.0/jacobi/tests/testthat/test-wzeta.R |only 55 files changed, 1697 insertions(+), 238 deletions(-)
Title: Tools for Stable Isotope Geochemistry
Description: This toolbox makes working with oxygen,
carbon, and clumped isotope data reproducible and straightforward.
Use it to quickly calculate isotope fractionation factors,
and apply paleothermometry equations.
Author: David Bajnai [aut, cre] ,
Julian Toedter [ctb]
Maintainer: David Bajnai <david.bajnai@uni-goettingen.de>
Diff between isogeochem versions 1.0.9 dated 2021-11-07 and 1.1.0 dated 2022-07-19
isogeochem-1.0.9/isogeochem/tests/testthat/Rplots.pdf |only isogeochem-1.1.0/isogeochem/DESCRIPTION | 14 isogeochem-1.1.0/isogeochem/MD5 | 55 +-- isogeochem-1.1.0/isogeochem/NAMESPACE | 1 isogeochem-1.1.0/isogeochem/NEWS.md | 89 ++--- isogeochem-1.1.0/isogeochem/R/a18.R | 23 + isogeochem-1.1.0/isogeochem/R/a18_c_H2O.R | 46 +- isogeochem-1.1.0/isogeochem/R/clumped.R | 2 isogeochem-1.1.0/isogeochem/R/d17O.R | 86 +++- isogeochem-1.1.0/isogeochem/R/data.R | 32 + isogeochem-1.1.0/isogeochem/R/quartz.R |only isogeochem-1.1.0/isogeochem/R/utils.R | 4 isogeochem-1.1.0/isogeochem/README.md | 90 +++-- isogeochem-1.1.0/isogeochem/build/partial.rdb |binary isogeochem-1.1.0/isogeochem/build/vignette.rds |binary isogeochem-1.1.0/isogeochem/data/meteoric_water.rda |only isogeochem-1.1.0/isogeochem/inst/WORDLIST | 264 ++++++++------- isogeochem-1.1.0/isogeochem/inst/doc/devils_hole.html | 238 ++++++++++++- isogeochem-1.1.0/isogeochem/inst/doc/kim_oneil_1997.html | 224 ++++++++++++ isogeochem-1.1.0/isogeochem/man/D47.Rd | 2 isogeochem-1.1.0/isogeochem/man/GTS2020.Rd | 3 isogeochem-1.1.0/isogeochem/man/LR04.Rd | 3 isogeochem-1.1.0/isogeochem/man/a18_CO2acid_c.Rd | 16 isogeochem-1.1.0/isogeochem/man/a18_c_H2O.Rd | 21 - isogeochem-1.1.0/isogeochem/man/d17O_c.Rd | 31 + isogeochem-1.1.0/isogeochem/man/d17O_qz.Rd |only isogeochem-1.1.0/isogeochem/man/devilshole.Rd | 3 isogeochem-1.1.0/isogeochem/man/meteoric_water.Rd |only isogeochem-1.1.0/isogeochem/man/mix_d17O.Rd | 27 + isogeochem-1.1.0/isogeochem/tests/testthat/test_a18.R | 22 - isogeochem-1.1.0/isogeochem/tests/testthat/test_d17O.R | 25 + 31 files changed, 993 insertions(+), 328 deletions(-)
Title: Simulation of Fossil and Taxonomy Data
Description: Simulating taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.3.0 dated 2022-04-19 and 2.3.1 dated 2022-07-19
DESCRIPTION | 8 MD5 | 50 - NEWS.md | 89 +- R/plot.fossils.R | 2 R/plot.taxonomy.R | 2 R/sim.fbd.R | 382 ++++----- R/sim.fossils.R | 30 R/sim.taxonomy.R | 48 - build/vignette.rds |binary inst/doc/SAtree.R | 42 - inst/doc/SAtree.html | 754 ++++++++++++------- inst/doc/fossils.R | 582 +++++++------- inst/doc/fossils.html | 1609 +++++++++++++++++++++++++---------------- inst/doc/intro.R | 62 - inst/doc/intro.html | 726 ++++++++++++------ inst/doc/paleotree.R | 44 - inst/doc/paleotree.html | 869 +++++++++++----------- inst/doc/simfbd.R | 48 - inst/doc/simfbd.html | 735 ++++++++++++------ inst/doc/taxonomy.R | 112 +- inst/doc/taxonomy.html | 978 ++++++++++++++++-------- man/sim.fbd.age.Rd | 17 man/sim.fbd.rateshift.taxa.Rd | 4 man/sim.fbd.taxa.Rd | 10 man/sim.fossils.environment.Rd | 7 man/sim.trait.values.Rd | 4 26 files changed, 4275 insertions(+), 2939 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.4.3 dated 2022-07-18 and 1.4.4 dated 2022-07-19
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NAMESPACE | 6 ++++++ NEWS.md | 2 +- R/aaa.R | 11 +++++++++++ inst/app/radiant.R | 2 +- inst/app/tools/data/manage_ui.R | 2 +- man/reexports.Rd | 7 +++++++ 8 files changed, 41 insertions(+), 16 deletions(-)
Title: Ternary Plots for Trinomial Regression Models
Description: An implementation of the ternary plot for interpreting regression
coefficients of trinomial regression models, as proposed in Santi, Dickson
and Espa (2019) <doi:10.1080/00031305.2018.1442368>. Ternary plots can be
drawn using either 'ggtern' package (based on 'ggplot2') or 'Ternary'
package (based on standard graphics). The package and its features are
illustrated in Santi, Dickson, Espa and Giuliani (2022)
<doi:10.18637/jss.v103.c01>.
Author: Flavio Santi [cre, aut] ,
Maria Michela Dickson [aut] ,
Giuseppe Espa [aut] ,
Diego Giuliani [aut]
Maintainer: Flavio Santi <flavio.santi@univr.it>
Diff between plot3logit versions 3.1.2 dated 2022-04-15 and 3.1.3 dated 2022-07-19
DESCRIPTION | 12 MD5 | 42 +-- NEWS.md | 11 R/conf_region.R | 3 R/data.R | 9 R/field3logit.R | 5 R/ggtern.R | 3 R/plot3logit-package.R | 3 README.md | 46 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 +-- inst/REFERENCES.bib | 11 inst/doc/plot3logit-overview.Rmd | 2 inst/doc/plot3logit-overview.html | 474 ++++++++++++++++++++++++++++++++------ man/USvote2016.Rd | 8 man/add_confregions.Rd | 3 man/autoplot.Hfield3logit.Rd | 10 man/field3logit.Rd | 5 man/gg3logit.Rd | 3 man/plot3logit-package.Rd | 3 vignettes/plot3logit-overview.Rmd | 2 22 files changed, 547 insertions(+), 146 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.3 dated 2022-05-27 and 0.5.4 dated 2022-07-19
DESCRIPTION | 6 MD5 | 28 +- NEWS.md | 4 R/downloading_tools.R | 552 ++++++++++++++++++++--------------------- R/get_oaproc.R | 2 R/index_nhdplus.R | 43 ++- build/vignette.rds |binary inst/doc/US_data.html | 487 ++++++++++++++++++++++++++++-------- inst/doc/advanced_network.html | 447 +++++++++++++++++++++++++++++---- inst/doc/indexing.html | 364 ++++++++++++++++++++++++--- inst/doc/nhdplusTools.html | 239 ++++++++++++++++- inst/doc/nhdplushr.html | 325 +++++++++++++++++++++--- inst/doc/plot_nhdplus.html | 304 ++++++++++++++++++++-- man/get_elev_along_path.Rd | 2 tests/testthat/test_index.R | 12 15 files changed, 2255 insertions(+), 560 deletions(-)
Title: Fast Covariance Estimation for Multivariate Sparse Functional
Data
Description: Multivariate functional principal component analysis via fast covariance estimation for
multivariate sparse functional data or longitudinal data proposed by Li, Xiao, and Luo (2020) <doi: 10.1002/sta4.245>.
Author: Cai Li [aut,cre] and Luo Xiao [aut]
Maintainer: Cai Li <cai.li.stats@gmail.com>
Diff between mfaces versions 0.1-3 dated 2021-04-30 and 0.1-4 dated 2022-07-19
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/face.sparse.inner.R | 6 ++++-- R/mface.sparse.R | 20 ++++++++++++++++---- R/predict.face.sparse.inner.R | 4 ++-- R/predict.mface.sparse.R | 6 +++--- build/partial.rdb |binary man/mface.sparse.Rd | 11 ++++++++--- man/mfaces-package.Rd | 6 +++--- man/predict.mface.sparse.Rd | 2 +- 10 files changed, 52 insertions(+), 33 deletions(-)
Title: Differential Expression Enrichment Tool
Description: RNA sequencing (RNA-seq) followed by differential gene expression analyses is a fundamental approach for making biological discoveries. Ongoing large-scale efforts to systematically process and normalize publicly available gene expression data facilitate rapid reanalyses of specific studies and the development of new methods for querying it. While there are several powerful tools for querying systematically processed publicly available RNA-seq data at the individual sample level, there are fewer options for querying differentially expressed gene (DEG) lists generated from these experiments. Here, we present the Differential Expression Enrichment Tool (DEET), which allows users to interact with 3162 consistently processed DEG lists curated from 142 RNA-seq datasets obtained from recount2 database, which contains data from consortiums (GTex, TCGA) and individual labs (SRA). To establish DEET we integrated systematically processed human RNA-seq data from recount2 with reported and predicted metadata from multiple sources and developed a CRAN R package and Shiny App where users can compare their genes, p-values, and coefficients against the DEG lists within DEET. Here we present DEET and demonstrate how it can facilitate hypothesis generation and provide biological insight from user-defined differential gene expression results. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Ellis,K., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).
Author: Dustin Sokolowski [aut, cre],
Jedid Ahn [aut],
Lauren Erdman [aut],
Kai Ellis [aut],
Huayun Hou [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between DEET versions 1.0.2 dated 2022-06-27 and 1.0.5 dated 2022-07-19
DESCRIPTION | 13 +- MD5 | 34 ++--- NAMESPACE | 88 +++++++------- R/DEET_data_download.R | 6 R/DEET_enrich.R | 43 ++++++- data/DEET_example_data.rda |binary data/example_DEET_enrich_input.rda |binary inst/doc/DEET_vignette.html | 4 man/DEET_data_download.Rd | 142 +++++++++++------------ man/DEET_enrich.Rd | 120 +++++++++---------- man/DEET_enrichment_plot.Rd | 152 ++++++++++++------------- man/DEET_example_data.Rd | 66 +++++----- man/DEET_feature_extract.Rd | 108 ++++++++--------- man/DEET_feature_extract_example_matrix.Rd | 42 +++--- man/DEET_feature_extract_example_response.Rd | 42 +++--- man/DEET_plot_correlation.Rd | 72 +++++------ man/example_DEET_enrich_input.Rd | 44 +++---- man/proccess_and_plot_DEET_enrich.Rd | 164 +++++++++++++-------------- 18 files changed, 590 insertions(+), 550 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.9.12 dated 2022-03-07 and 0.10.0 dated 2022-07-19
DESCRIPTION | 10 - MD5 | 92 ++++----- NAMESPACE | 2 NEWS | 8 R/bootstrap.R | 66 ++---- R/cfd.R | 196 +++++++++---------- R/cfda-package.R | 33 ++- R/dataPlot.R | 43 ++-- R/datasets.R | 63 +++++- R/encoding.R | 27 +- R/estimation.R | 2 R/fmca.print.R | 11 - R/plotEncoding.R | 11 - R/predict.R | 3 R/pretreatment.R | 197 +++++++++++++++++-- R/stat.R | 21 +- build/vignette.rds |binary data/flours.rda |only inst/doc/cfda.html | 370 ++++++++++++++++++++++++++++++++----- man/biofam2.Rd | 22 +- man/boxplot.timeSpent.Rd | 16 + man/care.Rd | 6 man/cfda-package.Rd | 33 ++- man/compute_duration.Rd | 13 + man/compute_number_jumps.Rd | 13 + man/compute_optimal_encoding.Rd | 28 ++ man/compute_time_spent.Rd | 13 + man/convertToCfd.Rd |only man/cut_data.Rd | 30 ++- man/estimate_pt.Rd | 13 + man/flours.Rd |only man/get_encoding.Rd | 11 + man/get_state.Rd | 1 man/hist.duration.Rd | 16 + man/hist.njump.Rd | 16 + man/matrixToCfd.Rd |only man/plot.fmca.Rd | 10 - man/plot.pt.Rd | 16 + man/plotComponent.Rd | 11 + man/plotData.Rd | 20 +- man/plotEigenvalues.Rd | 11 + man/predict.fmca.Rd | 10 - man/print.fmca.Rd | 16 + man/remove_duplicated_states.Rd | 15 + man/statetable.Rd | 14 + man/summary.fmca.Rd | 16 + man/summary_cfd.Rd | 17 + tests/testthat/test.pretreatment.R | 250 +++++++++++++++++++++++-- tests/testthat/test.stat.R | 32 +++ 49 files changed, 1435 insertions(+), 389 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <brandonedwards3@cmail.carleton.ca>
Diff between bbsBayes versions 2.5.0 dated 2022-07-11 and 2.5.1 dated 2022-07-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fetch-bbs-data.R | 3 +-- README.md | 4 ++-- 4 files changed, 10 insertions(+), 11 deletions(-)
Title: TV Show Themes and Color Palettes for 'ggplot2' Graphics
Description: Contains various 'ggplot2' themes and color palettes based on TV shows
such as 'Game of Thrones', 'Brooklyn Nine-Nine', 'Avatar: The Last Airbender',
'Spongebob Squarepants', and more.
Author: Ryo Nakagawara [aut, cre]
Maintainer: Ryo Nakagawara <ryonakagawara@gmail.com>
Diff between tvthemes versions 1.3.0 dated 2022-03-16 and 1.3.1 dated 2022-07-19
tvthemes-1.3.0/tvthemes/inst/fonts/ChelseaMarket |only tvthemes-1.3.0/tvthemes/inst/fonts/Cinzel |only tvthemes-1.3.0/tvthemes/inst/fonts/GravitationFalls/readme.txt |only tvthemes-1.3.0/tvthemes/inst/fonts/Roboto-Condensed |only tvthemes-1.3.0/tvthemes/inst/fonts/Titillium-Web |only tvthemes-1.3.0/tvthemes/man/import_chelseaMarket.Rd |only tvthemes-1.3.0/tvthemes/man/import_cinzel.Rd |only tvthemes-1.3.0/tvthemes/man/import_robotoCondensed.Rd |only tvthemes-1.3.0/tvthemes/man/import_roboto_condensed.Rd |only tvthemes-1.3.0/tvthemes/man/import_titilliumWeb.Rd |only tvthemes-1.3.0/tvthemes/man/import_titillium_web.Rd |only tvthemes-1.3.0/tvthemes/tests/spelling.R |only tvthemes-1.3.1/tvthemes/DESCRIPTION | 13 tvthemes-1.3.1/tvthemes/MD5 | 166 - tvthemes-1.3.1/tvthemes/NAMESPACE | 6 tvthemes-1.3.1/tvthemes/NEWS.md | 7 tvthemes-1.3.1/tvthemes/R/import_fonts.r | 139 - tvthemes-1.3.1/tvthemes/R/palette_hilda.R | 2 tvthemes-1.3.1/tvthemes/README.md | 6 tvthemes-1.3.1/tvthemes/inst/doc/examples.html | 997 +++++----- tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.R | 4 tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.Rmd | 6 tvthemes-1.3.1/tvthemes/inst/doc/fonts-and-colors.html | 119 - tvthemes-1.3.1/tvthemes/inst/doc/tvthemes-1_0_0.html | 132 - tvthemes-1.3.1/tvthemes/man/attackOnTitan_pal.Rd | 220 +- tvthemes-1.3.1/tvthemes/man/avatarTLA_pal.Rd | 226 +- tvthemes-1.3.1/tvthemes/man/avatar_pal.Rd | 264 +- tvthemes-1.3.1/tvthemes/man/bigHero6_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/brooklyn99_pal.Rd | 280 +- tvthemes-1.3.1/tvthemes/man/figures/README-b99header-1.png |binary tvthemes-1.3.1/tvthemes/man/figures/airnomads_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/attackontitan.png |binary tvthemes-1.3.1/tvthemes/man/figures/b99regpal_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/bighero6.png |binary tvthemes-1.3.1/tvthemes/man/figures/bobspog.bg.png |binary tvthemes-1.3.1/tvthemes/man/figures/crystalgems.png |binary tvthemes-1.3.1/tvthemes/man/figures/earthkingdom_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/firenation_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/gravityfalls.png |binary tvthemes-1.3.1/tvthemes/man/figures/hilda.png |binary tvthemes-1.3.1/tvthemes/man/figures/kimpossible.png |binary tvthemes-1.3.1/tvthemes/man/figures/lastairbender.png |binary tvthemes-1.3.1/tvthemes/man/figures/parksandrec_both.png |binary tvthemes-1.3.1/tvthemes/man/figures/rickmorty_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/simpsons_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/sponge_plot.png |binary tvthemes-1.3.1/tvthemes/man/figures/stevenuniverse.png |binary tvthemes-1.3.1/tvthemes/man/figures/watertribe_plot.png |binary tvthemes-1.3.1/tvthemes/man/gravityFalls_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/hilda_pal.Rd | 237 +- tvthemes-1.3.1/tvthemes/man/import_avatar.Rd | 32 tvthemes-1.3.1/tvthemes/man/import_gravitationFalls.Rd | 38 tvthemes-1.3.1/tvthemes/man/import_rickAndMorty.Rd | 34 tvthemes-1.3.1/tvthemes/man/import_simpsons.Rd | 38 tvthemes-1.3.1/tvthemes/man/import_spongeBob.Rd | 30 tvthemes-1.3.1/tvthemes/man/import_theLastAirbender.Rd | 32 tvthemes-1.3.1/tvthemes/man/kimPossible_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/paintBikiniBottom.Rd | 74 tvthemes-1.3.1/tvthemes/man/parksAndRec_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/rickAndMorty_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/simpsons_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/spongeBob_pal.Rd | 218 +- tvthemes-1.3.1/tvthemes/man/sponge_images.Rd | 30 tvthemes-1.3.1/tvthemes/man/stevenUniverse_pal.Rd | 264 +- tvthemes-1.3.1/tvthemes/man/theme_avatar.Rd | 164 - tvthemes-1.3.1/tvthemes/man/theme_brooklyn99.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_hildaDay.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_hildaDusk.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_hildaNight.Rd | 160 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRec.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRecLight.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_parksAndRec_light.Rd | 156 - tvthemes-1.3.1/tvthemes/man/theme_rickAndMorty.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_simpsons.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_spongeBob.Rd | 170 - tvthemes-1.3.1/tvthemes/man/theme_theLastAirbender.Rd | 146 - tvthemes-1.3.1/tvthemes/man/tvthemes.Rd | 80 tvthemes-1.3.1/tvthemes/man/westeros_pal.Rd | 276 +- tvthemes-1.3.1/tvthemes/tests/testthat/test-fonts.R | 12 tvthemes-1.3.1/tvthemes/vignettes/fonts-and-colors.Rmd | 6 80 files changed, 3594 insertions(+), 3668 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-10 1.2.3
2021-12-10 1.2.2
2021-10-11 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-21 0.7
2021-05-18 0.6
2018-11-29 0.5.2
2018-04-16 0.5
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut] ,
Barret Schloerke [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
RStudio [cph],
jQuery Foundation [cph] [...truncated...]
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.7.1 dated 2021-10-02 and 1.7.2 dated 2022-07-18
shiny-1.7.1/shiny/inst/app_template/tests/shinytest |only shiny-1.7.1/shiny/inst/app_template/tests/shinytest.R |only shiny-1.7.1/shiny/tests/testthat/_snaps/test.md |only shiny-1.7.1/shiny/tests/testthat/test-test.R |only shiny-1.7.2/shiny/DESCRIPTION | 18 shiny-1.7.2/shiny/MD5 | 183 - shiny-1.7.2/shiny/NEWS.md | 58 shiny-1.7.2/shiny/R/app_template.R | 70 shiny-1.7.2/shiny/R/bookmark-state.R | 24 shiny-1.7.2/shiny/R/bootstrap-deprecated.R | 2 shiny-1.7.2/shiny/R/bootstrap-layout.R | 6 shiny-1.7.2/shiny/R/bootstrap.R | 28 shiny-1.7.2/shiny/R/conditions.R | 17 shiny-1.7.2/shiny/R/globals.R | 55 shiny-1.7.2/shiny/R/graph.R | 36 shiny-1.7.2/shiny/R/imageutils.R | 53 shiny-1.7.2/shiny/R/input-date.R | 10 shiny-1.7.2/shiny/R/input-file.R | 19 shiny-1.7.2/shiny/R/input-select.R | 19 shiny-1.7.2/shiny/R/input-slider.R | 19 shiny-1.7.2/shiny/R/input-utils.R | 2 shiny-1.7.2/shiny/R/jqueryui.R | 13 shiny-1.7.2/shiny/R/knitr.R | 4 shiny-1.7.2/shiny/R/middleware.R | 2 shiny-1.7.2/shiny/R/mock-session.R | 2 shiny-1.7.2/shiny/R/reactives.R | 10 shiny-1.7.2/shiny/R/render-plot.R | 6 shiny-1.7.2/shiny/R/run-url.R | 9 shiny-1.7.2/shiny/R/runapp.R | 4 shiny-1.7.2/shiny/R/server-input-handlers.R | 2 shiny-1.7.2/shiny/R/server.R | 8 shiny-1.7.2/shiny/R/shiny-options.R | 14 shiny-1.7.2/shiny/R/shiny.R | 53 shiny-1.7.2/shiny/R/shinyapp.R | 8 shiny-1.7.2/shiny/R/shinyui.R | 52 shiny-1.7.2/shiny/R/shinywrappers.R | 10 shiny-1.7.2/shiny/R/showcase.R | 42 shiny-1.7.2/shiny/R/staticimports.R |only shiny-1.7.2/shiny/R/utils.R | 85 shiny-1.7.2/shiny/README.md | 10 shiny-1.7.2/shiny/build/shiny.pdf |binary shiny-1.7.2/shiny/inst/app_template/tests/testthat.R | 10 shiny-1.7.2/shiny/inst/app_template/tests/testthat/test-server.R | 3 shiny-1.7.2/shiny/inst/app_template/tests/testthat/test-shinytest2.R |only shiny-1.7.2/shiny/inst/www/shared/shiny-autoreload.js | 6 shiny-1.7.2/shiny/inst/www/shared/shiny-autoreload.js.map |only shiny-1.7.2/shiny/inst/www/shared/shiny-showcase.css | 2 shiny-1.7.2/shiny/inst/www/shared/shiny-showcase.js | 4 shiny-1.7.2/shiny/inst/www/shared/shiny-showcase.js.map |only shiny-1.7.2/shiny/inst/www/shared/shiny-testmode.js | 4 shiny-1.7.2/shiny/inst/www/shared/shiny-testmode.js.map |only shiny-1.7.2/shiny/inst/www/shared/shiny.js | 1647 ++++------ shiny-1.7.2/shiny/inst/www/shared/shiny.js.map | 6 shiny-1.7.2/shiny/inst/www/shared/shiny.min.css | 2 shiny-1.7.2/shiny/inst/www/shared/shiny.min.js | 4 shiny-1.7.2/shiny/inst/www/shared/shiny.min.js.map | 6 shiny-1.7.2/shiny/man/MockShinySession.Rd | 174 - shiny-1.7.2/shiny/man/Progress.Rd | 48 shiny-1.7.2/shiny/man/bindCache.Rd | 58 shiny-1.7.2/shiny/man/bindEvent.Rd | 4 shiny-1.7.2/shiny/man/bootstrapPage.Rd | 2 shiny-1.7.2/shiny/man/createRenderFunction.Rd | 6 shiny-1.7.2/shiny/man/devmode.Rd | 30 shiny-1.7.2/shiny/man/diskCache.Rd | 2 shiny-1.7.2/shiny/man/downloadHandler.Rd | 8 shiny-1.7.2/shiny/man/fileInput.Rd | 16 shiny-1.7.2/shiny/man/fixedPage.Rd | 2 shiny-1.7.2/shiny/man/fluidPage.Rd | 2 shiny-1.7.2/shiny/man/loadSupport.Rd | 2 shiny-1.7.2/shiny/man/memoryCache.Rd | 2 shiny-1.7.2/shiny/man/navbarPage.Rd | 2 shiny-1.7.2/shiny/man/pageWithSidebar.Rd | 2 shiny-1.7.2/shiny/man/plotPNG.Rd | 37 shiny-1.7.2/shiny/man/reactlog.Rd | 8 shiny-1.7.2/shiny/man/reexports.Rd | 2 shiny-1.7.2/shiny/man/renderCachedPlot.Rd | 2 shiny-1.7.2/shiny/man/renderPlot.Rd | 4 shiny-1.7.2/shiny/man/req.Rd | 12 shiny-1.7.2/shiny/man/runApp.Rd | 2 shiny-1.7.2/shiny/man/runUrl.Rd | 9 shiny-1.7.2/shiny/man/shinyAppTemplate.Rd | 33 shiny-1.7.2/shiny/man/shinyOptions.Rd | 14 shiny-1.7.2/shiny/man/shinyServer.Rd | 2 shiny-1.7.2/shiny/man/tabPanel.Rd | 6 shiny-1.7.2/shiny/man/updateCheckboxGroupInput.Rd | 12 shiny-1.7.2/shiny/man/updateRadioButtons.Rd | 11 shiny-1.7.2/shiny/man/updateSliderInput.Rd | 5 shiny-1.7.2/shiny/man/validate.Rd | 6 shiny-1.7.2/shiny/man/varSelectInput.Rd | 4 shiny-1.7.2/shiny/tests/testthat/_snaps/test-shinyAppTemplate.md |only shiny-1.7.2/shiny/tests/testthat/_snaps/test-shinyAppTemplate.new.md |only shiny-1.7.2/shiny/tests/testthat/test-bookmarking.R | 52 shiny-1.7.2/shiny/tests/testthat/test-reactives.R | 25 shiny-1.7.2/shiny/tests/testthat/test-stacks-pruning.R | 45 shiny-1.7.2/shiny/tests/testthat/test-stacks.R | 30 shiny-1.7.2/shiny/tests/testthat/test-tabPanel.R | 2 shiny-1.7.2/shiny/tests/testthat/test-test-runTests.R |only shiny-1.7.2/shiny/tests/testthat/test-test-shinyAppTemplate.R |only shiny-1.7.2/shiny/tests/testthat/test-utils.R | 36 99 files changed, 1646 insertions(+), 1720 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features an API for
extending these templates to address novel scientific research aims. Full
methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Adrien Le Guillou [aut],
Chad Klumb [aut],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 2.2.1 dated 2022-02-02 and 2.3.0 dated 2022-07-18
EpiModel-2.2.1/EpiModel/R/EpiModel-package.r |only EpiModel-2.2.1/EpiModel/R/print.r |only EpiModel-2.2.1/EpiModel/R/util.R |only EpiModel-2.2.1/EpiModel/inst/EpiModel2 |only EpiModel-2.2.1/EpiModel/inst/JSS |only EpiModel-2.2.1/EpiModel/inst/NMGDemo.R |only EpiModel-2.2.1/EpiModel/inst/shiny/epinet/rsconnect |only EpiModel-2.2.1/EpiModel/inst/tests |only EpiModel-2.2.1/EpiModel/man/edgelist_meanage.Rd |only EpiModel-2.2.1/EpiModel/man/netsim_loop.Rd |only EpiModel-2.2.1/EpiModel/man/updater.net.Rd |only EpiModel-2.2.1/EpiModel/src/registerDynamicSymbol.c |only EpiModel-2.3.0/EpiModel/DESCRIPTION | 32 EpiModel-2.3.0/EpiModel/MD5 | 458 +- EpiModel-2.3.0/EpiModel/NAMESPACE | 25 EpiModel-2.3.0/EpiModel/NEWS.md | 550 +- EpiModel-2.3.0/EpiModel/R/EpiModel-package.R |only EpiModel-2.3.0/EpiModel/R/ErgmTerms.R | 101 EpiModel-2.3.0/EpiModel/R/as.data.frame.R | 12 EpiModel-2.3.0/EpiModel/R/dcm.inputs.R | 110 EpiModel-2.3.0/EpiModel/R/dcm.mods.R | 3 EpiModel-2.3.0/EpiModel/R/dendo.R | 130 EpiModel-2.3.0/EpiModel/R/el_cuml.R | 76 EpiModel-2.3.0/EpiModel/R/get.R | 100 EpiModel-2.3.0/EpiModel/R/icm.inputs.R | 61 EpiModel-2.3.0/EpiModel/R/icm.mod.init.R | 12 EpiModel-2.3.0/EpiModel/R/icm.mod.status.R | 28 EpiModel-2.3.0/EpiModel/R/icm.mod.vital.R | 24 EpiModel-2.3.0/EpiModel/R/icm.utils.R | 9 EpiModel-2.3.0/EpiModel/R/initialize.R | 9 EpiModel-2.3.0/EpiModel/R/merge.R | 91 EpiModel-2.3.0/EpiModel/R/modules.net.R | 10 EpiModel-2.3.0/EpiModel/R/net.accessor.R | 142 EpiModel-2.3.0/EpiModel/R/net.helpers.R | 46 EpiModel-2.3.0/EpiModel/R/net.inputs.R | 425 +- EpiModel-2.3.0/EpiModel/R/net.mod.infection.R | 44 EpiModel-2.3.0/EpiModel/R/net.mod.init.R | 54 EpiModel-2.3.0/EpiModel/R/net.mod.nwupdate.R | 52 EpiModel-2.3.0/EpiModel/R/net.mod.prevalence.R | 6 EpiModel-2.3.0/EpiModel/R/net.mod.recovery.R | 14 EpiModel-2.3.0/EpiModel/R/net.mod.simnet.R | 210 EpiModel-2.3.0/EpiModel/R/net.mod.trackers.R | 14 EpiModel-2.3.0/EpiModel/R/net.mod.updater.R | 74 EpiModel-2.3.0/EpiModel/R/net.mod.vital.R | 24 EpiModel-2.3.0/EpiModel/R/net.record.R | 51 EpiModel-2.3.0/EpiModel/R/net.scenarios.R |only EpiModel-2.3.0/EpiModel/R/net.utils.R | 260 - EpiModel-2.3.0/EpiModel/R/netdx.R | 552 +- EpiModel-2.3.0/EpiModel/R/netest.R | 238 - EpiModel-2.3.0/EpiModel/R/netsim.R | 215 - EpiModel-2.3.0/EpiModel/R/netsim_checkpoint.R |only EpiModel-2.3.0/EpiModel/R/network.R | 37 EpiModel-2.3.0/EpiModel/R/networkLite.R |only EpiModel-2.3.0/EpiModel/R/plot.R | 2107 ++-------- EpiModel-2.3.0/EpiModel/R/print.R |only EpiModel-2.3.0/EpiModel/R/saveout.R | 145 EpiModel-2.3.0/EpiModel/R/summary.R | 56 EpiModel-2.3.0/EpiModel/R/test.R | 4 EpiModel-2.3.0/EpiModel/R/update.R | 14 EpiModel-2.3.0/EpiModel/R/utils.R | 157 EpiModel-2.3.0/EpiModel/R/verbose.R | 34 EpiModel-2.3.0/EpiModel/build/partial.rdb |binary EpiModel-2.3.0/EpiModel/build/vignette.rds |binary EpiModel-2.3.0/EpiModel/inst/doc/Intro.Rmd | 8 EpiModel-2.3.0/EpiModel/inst/doc/Intro.html | 288 + EpiModel-2.3.0/EpiModel/inst/doc/attributes-and-summary-statistics.Rmd | 13 EpiModel-2.3.0/EpiModel/inst/doc/attributes-and-summary-statistics.html | 1137 +++-- EpiModel-2.3.0/EpiModel/inst/doc/model-parameters.R | 193 EpiModel-2.3.0/EpiModel/inst/doc/model-parameters.Rmd | 373 + EpiModel-2.3.0/EpiModel/inst/doc/model-parameters.html | 1741 ++++++-- EpiModel-2.3.0/EpiModel/inst/doc/network-objects.Rmd | 11 EpiModel-2.3.0/EpiModel/inst/doc/network-objects.html | 596 ++ EpiModel-2.3.0/EpiModel/man/EpiModel-package.Rd | 9 EpiModel-2.3.0/EpiModel/man/InitErgmTerm.absdiffby.Rd | 18 EpiModel-2.3.0/EpiModel/man/InitErgmTerm.absdiffnodemix.Rd | 11 EpiModel-2.3.0/EpiModel/man/InitErgmTerm.fuzzynodematch.Rd |only EpiModel-2.3.0/EpiModel/man/add_vertices.Rd | 7 EpiModel-2.3.0/EpiModel/man/apportion_lr.Rd | 18 EpiModel-2.3.0/EpiModel/man/arrivals.2g.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/arrivals.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/arrivals.icm.bip.Rd | 7 EpiModel-2.3.0/EpiModel/man/arrivals.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/as.data.frame.dcm.Rd | 5 EpiModel-2.3.0/EpiModel/man/as.data.frame.icm.Rd | 3 EpiModel-2.3.0/EpiModel/man/as.data.frame.netdx.Rd | 5 EpiModel-2.3.0/EpiModel/man/as.network.transmat.Rd | 24 EpiModel-2.3.0/EpiModel/man/as.phylo.transmat.Rd | 58 EpiModel-2.3.0/EpiModel/man/auto_update_attr.Rd | 10 EpiModel-2.3.0/EpiModel/man/brewer_ramp.Rd | 10 EpiModel-2.3.0/EpiModel/man/check_attr_lengths.Rd | 13 EpiModel-2.3.0/EpiModel/man/color_tea.Rd | 9 EpiModel-2.3.0/EpiModel/man/common_updater.Rd | 10 EpiModel-2.3.0/EpiModel/man/comp_plot.Rd | 6 EpiModel-2.3.0/EpiModel/man/control.dcm.Rd | 8 EpiModel-2.3.0/EpiModel/man/control.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/control.net.Rd | 103 EpiModel-2.3.0/EpiModel/man/copy_datattr_to_nwattr.Rd | 12 EpiModel-2.3.0/EpiModel/man/copy_nwattr_to_datattr.Rd | 10 EpiModel-2.3.0/EpiModel/man/create_dat_object.Rd | 8 EpiModel-2.3.0/EpiModel/man/create_scenario_list.Rd |only EpiModel-2.3.0/EpiModel/man/crosscheck.dcm.Rd | 10 EpiModel-2.3.0/EpiModel/man/dcm.mods.Rd | 3 EpiModel-2.3.0/EpiModel/man/deleteAttr.Rd | 5 EpiModel-2.3.0/EpiModel/man/delete_attr.Rd | 8 EpiModel-2.3.0/EpiModel/man/delete_vertices.Rd | 7 EpiModel-2.3.0/EpiModel/man/departures.2g.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/departures.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/departures.icm.bip.Rd | 7 EpiModel-2.3.0/EpiModel/man/departures.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/discord_edgelist.Rd | 11 EpiModel-2.3.0/EpiModel/man/dissolution_coefs.Rd | 17 EpiModel-2.3.0/EpiModel/man/edgelist_censor.Rd | 6 EpiModel-2.3.0/EpiModel/man/edges_correct.Rd | 6 EpiModel-2.3.0/EpiModel/man/format_param.Rd | 12 EpiModel-2.3.0/EpiModel/man/generate_random_params.Rd | 34 EpiModel-2.3.0/EpiModel/man/geom_bands.Rd | 6 EpiModel-2.3.0/EpiModel/man/get_args.Rd | 4 EpiModel-2.3.0/EpiModel/man/get_attr_history.Rd | 2 EpiModel-2.3.0/EpiModel/man/get_attr_prop.Rd | 14 EpiModel-2.3.0/EpiModel/man/get_cumulative_edgelist.Rd | 10 EpiModel-2.3.0/EpiModel/man/get_cumulative_edgelists_df.Rd | 10 EpiModel-2.3.0/EpiModel/man/get_current_timestep.Rd | 9 EpiModel-2.3.0/EpiModel/man/get_degree.Rd | 19 EpiModel-2.3.0/EpiModel/man/get_edgelist.Rd | 10 EpiModel-2.3.0/EpiModel/man/get_formula_term_attr.Rd | 15 EpiModel-2.3.0/EpiModel/man/get_network.Rd | 16 EpiModel-2.3.0/EpiModel/man/get_network_term_attr.Rd | 12 EpiModel-2.3.0/EpiModel/man/get_nwparam.Rd | 2 EpiModel-2.3.0/EpiModel/man/get_nwstats.Rd | 5 EpiModel-2.3.0/EpiModel/man/get_param_set.Rd | 2 EpiModel-2.3.0/EpiModel/man/get_partners.Rd | 13 EpiModel-2.3.0/EpiModel/man/get_sims.Rd | 13 EpiModel-2.3.0/EpiModel/man/get_vertex_attribute.Rd | 10 EpiModel-2.3.0/EpiModel/man/idgroup.Rd | 7 EpiModel-2.3.0/EpiModel/man/increment_timestep.Rd | 13 EpiModel-2.3.0/EpiModel/man/infection.2g.net.Rd | 7 EpiModel-2.3.0/EpiModel/man/infection.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/infection.icm.bip.Rd | 5 EpiModel-2.3.0/EpiModel/man/infection.net.Rd | 9 EpiModel-2.3.0/EpiModel/man/init.dcm.Rd | 29 EpiModel-2.3.0/EpiModel/man/init.icm.Rd | 29 EpiModel-2.3.0/EpiModel/man/init.net.Rd | 21 EpiModel-2.3.0/EpiModel/man/init_status.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/init_status.net.Rd | 27 EpiModel-2.3.0/EpiModel/man/init_tergmLite.Rd | 12 EpiModel-2.3.0/EpiModel/man/initialize.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/initialize.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/is_active_posit_ids.Rd | 9 EpiModel-2.3.0/EpiModel/man/is_active_unique_ids.Rd | 9 EpiModel-2.3.0/EpiModel/man/make_dissolution_stats.Rd | 10 EpiModel-2.3.0/EpiModel/man/make_formation_table.Rd | 10 EpiModel-2.3.0/EpiModel/man/mcat.Rd | 4 EpiModel-2.3.0/EpiModel/man/merge.icm.Rd | 6 EpiModel-2.3.0/EpiModel/man/merge.netsim.Rd | 20 EpiModel-2.3.0/EpiModel/man/modules.net.Rd | 10 EpiModel-2.3.0/EpiModel/man/mutate_epi.Rd | 4 EpiModel-2.3.0/EpiModel/man/net-accessor.Rd | 60 EpiModel-2.3.0/EpiModel/man/netdx.Rd | 80 EpiModel-2.3.0/EpiModel/man/netest.Rd | 44 EpiModel-2.3.0/EpiModel/man/netsim.Rd | 10 EpiModel-2.3.0/EpiModel/man/netsim_cond_msg.Rd | 18 EpiModel-2.3.0/EpiModel/man/networkLite.Rd | 68 EpiModel-2.3.0/EpiModel/man/networkLitemethods.Rd | 148 EpiModel-2.3.0/EpiModel/man/network_initialize.Rd | 28 EpiModel-2.3.0/EpiModel/man/nwupdate.net.Rd | 10 EpiModel-2.3.0/EpiModel/man/param.dcm.Rd | 56 EpiModel-2.3.0/EpiModel/man/param.icm.Rd | 53 EpiModel-2.3.0/EpiModel/man/param.net.Rd | 85 EpiModel-2.3.0/EpiModel/man/param.net_from_table.Rd |only EpiModel-2.3.0/EpiModel/man/param_random.Rd | 11 EpiModel-2.3.0/EpiModel/man/plot.dcm.Rd | 9 EpiModel-2.3.0/EpiModel/man/plot.icm.Rd | 44 EpiModel-2.3.0/EpiModel/man/plot.netdx.Rd | 71 EpiModel-2.3.0/EpiModel/man/plot.netsim.Rd | 60 EpiModel-2.3.0/EpiModel/man/plot.transmat.Rd | 25 EpiModel-2.3.0/EpiModel/man/prevalence.icm.Rd | 5 EpiModel-2.3.0/EpiModel/man/prevalence.icm.bip.Rd | 5 EpiModel-2.3.0/EpiModel/man/prevalence.net.Rd | 5 EpiModel-2.3.0/EpiModel/man/print.netdx.Rd |only EpiModel-2.3.0/EpiModel/man/print_nwstats_table.Rd | 6 EpiModel-2.3.0/EpiModel/man/process_out.net.Rd | 10 EpiModel-2.3.0/EpiModel/man/record_attr_history.Rd | 36 EpiModel-2.3.0/EpiModel/man/record_raw_object.Rd | 16 EpiModel-2.3.0/EpiModel/man/recovery.2g.net.Rd | 7 EpiModel-2.3.0/EpiModel/man/recovery.icm.Rd | 7 EpiModel-2.3.0/EpiModel/man/recovery.icm.bip.Rd | 7 EpiModel-2.3.0/EpiModel/man/recovery.net.Rd | 7 EpiModel-2.3.0/EpiModel/man/resim_nets.Rd | 8 EpiModel-2.3.0/EpiModel/man/saveout.dcm.Rd | 21 EpiModel-2.3.0/EpiModel/man/saveout.icm.Rd | 21 EpiModel-2.3.0/EpiModel/man/saveout.net.Rd | 23 EpiModel-2.3.0/EpiModel/man/set_current_timestep.Rd | 21 EpiModel-2.3.0/EpiModel/man/set_transmat.Rd | 14 EpiModel-2.3.0/EpiModel/man/set_vertex_attribute.Rd | 5 EpiModel-2.3.0/EpiModel/man/sim_nets_t1.Rd | 6 EpiModel-2.3.0/EpiModel/man/ssample.Rd | 3 EpiModel-2.3.0/EpiModel/man/summary.dcm.Rd | 10 EpiModel-2.3.0/EpiModel/man/summary.icm.Rd | 8 EpiModel-2.3.0/EpiModel/man/summary.netest.Rd | 14 EpiModel-2.3.0/EpiModel/man/summary.netsim.Rd | 8 EpiModel-2.3.0/EpiModel/man/trackers.net.Rd | 12 EpiModel-2.3.0/EpiModel/man/trim_netest.Rd |only EpiModel-2.3.0/EpiModel/man/truncate_sim.Rd | 7 EpiModel-2.3.0/EpiModel/man/unique_id-tools.Rd | 22 EpiModel-2.3.0/EpiModel/man/update_cumulative_edgelist.Rd | 23 EpiModel-2.3.0/EpiModel/man/update_dissolution.Rd | 22 EpiModel-2.3.0/EpiModel/man/update_list.Rd | 10 EpiModel-2.3.0/EpiModel/man/update_params.Rd | 23 EpiModel-2.3.0/EpiModel/man/update_unique_ids.Rd | 16 EpiModel-2.3.0/EpiModel/man/use_scenario.Rd |only EpiModel-2.3.0/EpiModel/man/verbose.dcm.Rd | 10 EpiModel-2.3.0/EpiModel/man/verbose.icm.Rd | 6 EpiModel-2.3.0/EpiModel/man/verbose.net.Rd | 10 EpiModel-2.3.0/EpiModel/src/RcppExports.cpp | 2 EpiModel-2.3.0/EpiModel/src/changestats.users.c | 44 EpiModel-2.3.0/EpiModel/src/changestats.users.h | 3 EpiModel-2.3.0/EpiModel/src/registerDynamicSymbol.cpp |only EpiModel-2.3.0/EpiModel/tests/testthat/test-cumulative_edgelist.R | 11 EpiModel-2.3.0/EpiModel/tests/testthat/test-dissolution-diagnostics.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-get.R | 10 EpiModel-2.3.0/EpiModel/tests/testthat/test-merge.R | 56 EpiModel-2.3.0/EpiModel/tests/testthat/test-net-long.R | 2 EpiModel-2.3.0/EpiModel/tests/testthat/test-net-tergmLite.R | 36 EpiModel-2.3.0/EpiModel/tests/testthat/test-netdx.R | 611 +- EpiModel-2.3.0/EpiModel/tests/testthat/test-netest.R | 55 EpiModel-2.3.0/EpiModel/tests/testthat/test-netsim-checkpoint.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-netsim.R | 243 - EpiModel-2.3.0/EpiModel/tests/testthat/test-networkLite.R | 1133 ++++- EpiModel-2.3.0/EpiModel/tests/testthat/test-parameters_df.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-random-params.R | 10 EpiModel-2.3.0/EpiModel/tests/testthat/test-scenarios.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-stergm.R | 49 EpiModel-2.3.0/EpiModel/tests/testthat/test-term-fuzzynodematch.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-terms.R |only EpiModel-2.3.0/EpiModel/tests/testthat/test-updater.R | 17 EpiModel-2.3.0/EpiModel/tests/testthat/test-utils.R | 4 EpiModel-2.3.0/EpiModel/vignettes/Intro.Rmd | 8 EpiModel-2.3.0/EpiModel/vignettes/attributes-and-summary-statistics.Rmd | 13 EpiModel-2.3.0/EpiModel/vignettes/model-parameters.Rmd | 373 + EpiModel-2.3.0/EpiModel/vignettes/network-objects.Rmd | 11 240 files changed, 10080 insertions(+), 6059 deletions(-)
Title: Gene Analysis Toolkit in R
Description: An analysis toolkit focused on genes. It mainly includes five
features (search, convert, analysis, plot, and export).
The user just needs to input feature id ('entrez', 'symbol', 'ensembl' or
'uniprot') to retrieve feature information and PubMed records, to convert id
types, to easily do enrichment analysis and draw publication-level plots of GO,
KEGG and GSEA, to plot group interaction and export results as sheets in one excel
file to easily share and communicate with others.
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>
Diff between genekitr versions 0.8.5 dated 2022-05-27 and 1.0.3 dated 2022-07-18
genekitr-0.8.5/genekitr/R/genGO.R |only genekitr-0.8.5/genekitr/R/genKEGG.R |only genekitr-0.8.5/genekitr/man/genGO.Rd |only genekitr-0.8.5/genekitr/man/genKEGG.Rd |only genekitr-1.0.3/genekitr/DESCRIPTION | 25 genekitr-1.0.3/genekitr/MD5 | 79 - genekitr-1.0.3/genekitr/NAMESPACE | 32 genekitr-1.0.3/genekitr/R/asEnrichdat.R | 2 genekitr-1.0.3/genekitr/R/data.R | 10 genekitr-1.0.3/genekitr/R/expoSheet.R | 35 genekitr-1.0.3/genekitr/R/genGSEA.R | 276 ++- genekitr-1.0.3/genekitr/R/genInfo.R | 172 +- genekitr-1.0.3/genekitr/R/genORA.R |only genekitr-1.0.3/genekitr/R/getPubmed.R | 52 genekitr-1.0.3/genekitr/R/importCP.R |only genekitr-1.0.3/genekitr/R/importPanther.R | 53 genekitr-1.0.3/genekitr/R/ploTheme.R | 34 genekitr-1.0.3/genekitr/R/plotEnrich.R | 1038 +++++++++------ genekitr-1.0.3/genekitr/R/plotEnrichAdv.R |only genekitr-1.0.3/genekitr/R/plotGSEA.R | 534 ++++--- genekitr-1.0.3/genekitr/R/plotVenn.R | 214 ++- genekitr-1.0.3/genekitr/R/plotVolcano.R | 102 - genekitr-1.0.3/genekitr/R/simGO.R |only genekitr-1.0.3/genekitr/R/transID.R | 50 genekitr-1.0.3/genekitr/R/transProbe.R |only genekitr-1.0.3/genekitr/R/utilities.R | 510 ++++--- genekitr-1.0.3/genekitr/R/zzz.R | 19 genekitr-1.0.3/genekitr/README.md | 84 - genekitr-1.0.3/genekitr/data/biocOrg_name.rda |binary genekitr-1.0.3/genekitr/data/deg.rda |binary genekitr-1.0.3/genekitr/data/ensOrg_name.rda |binary genekitr-1.0.3/genekitr/data/hsapiens_probe_platform.rda |only genekitr-1.0.3/genekitr/man/Datasets.Rd | 4 genekitr-1.0.3/genekitr/man/expoSheet.Rd | 6 genekitr-1.0.3/genekitr/man/genGSEA.Rd | 55 genekitr-1.0.3/genekitr/man/genInfo.Rd | 15 genekitr-1.0.3/genekitr/man/genORA.Rd |only genekitr-1.0.3/genekitr/man/getPubmed.Rd | 16 genekitr-1.0.3/genekitr/man/importCP.Rd |only genekitr-1.0.3/genekitr/man/plotEnrich.Rd | 70 - genekitr-1.0.3/genekitr/man/plotEnrichAdv.Rd |only genekitr-1.0.3/genekitr/man/plotGSEA.Rd | 45 genekitr-1.0.3/genekitr/man/plotVenn.Rd | 42 genekitr-1.0.3/genekitr/man/plotVolcano.Rd | 8 genekitr-1.0.3/genekitr/man/plot_theme.Rd | 5 genekitr-1.0.3/genekitr/man/simGO.Rd |only genekitr-1.0.3/genekitr/man/transId.Rd | 6 genekitr-1.0.3/genekitr/man/transProbe.Rd |only 48 files changed, 2191 insertions(+), 1402 deletions(-)
Title: Tools Inspired by 'Stata' to Manipulate Tabular Data
Description: A set of tools inspired by 'Stata' to explore data.frames ('summarize',
'tabulate', 'xtile', 'pctile', 'binscatter', elapsed quarters/month, lead/lag).
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez <mg3901@columbia.edu>
Diff between statar versions 0.7.3 dated 2020-11-19 and 0.7.4 dated 2022-07-18
DESCRIPTION | 8 MD5 | 18 - R/elapsed_dates.R | 1 README.md | 2 build/vignette.rds |binary inst/doc/data-frames.html | 535 +++++++++++++++++++++++++++----------------- inst/doc/graph.html | 456 ++++++++++++++++++++++++++----------- inst/doc/panel-data.html | 557 ++++++++++++++++++++++++++++++---------------- inst/doc/vector.html | 490 +++++++++++++++++++++++++++------------- man/elapsed.Rd | 1 10 files changed, 1378 insertions(+), 690 deletions(-)
Title: Simplified Statistics for PA 606
Description: Simplifies functions assess normality for bivariate and multivariate statistical techniques. Includes functions designed to replicate plots and tables that would result from similar calls in 'SPSS', including hst(), box(), qq(), tab(), cormat(), and residplot(). Also includes simplified formulae, such as mode(), scatter(), p.corr(), ow.anova(), and rm.anova().
Author: Burrel Vann Jr [aut, cre]
Maintainer: Burrel Vann Jr <bvannjr@sdsu.edu>
Diff between vannstats versions 1.2.4.29 dated 2022-04-29 and 1.2.7.14 dated 2022-07-18
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 4 ++++ R/stata.plm.margins.R |only man/stata.plm.margins.Rd |only 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Hospital Data Analysis Workflow Tools
Description: Hospital data analysis workflow tools, modeling, and automations. This library
provides many useful tools to review common administrative hospital data. Some
of these include average length of stay, readmission rates, average net pay
amounts by service lines just to name a few. The aim is to provide a simple
and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR versions 0.1.9 dated 2022-04-25 and 0.2.0 dated 2022-07-18
DESCRIPTION | 8 MD5 | 80 +- NAMESPACE | 3 NEWS.md | 14 R/00_global_variables.R | 18 R/augment-service-line.R | 216 +++---- R/data_tbl_functions.R | 774 ++++++++++++------------- R/diverging-bar-plt.R | 260 ++++---- R/diverging-lollipop-plt.R | 218 +++---- R/gartner_magic_chart.R | 214 ++++--- R/kmeans-funcs.R | 996 ++++++++++++++++----------------- R/los_ra_index_plt.R | 318 +++++----- R/pallette-color-blind.R |only R/service-line-vec.R | 516 ++++++++--------- R/sql_string_split.R | 136 ++-- R/time_series_plots.R | 726 ++++++++++++------------ R/ts-census-los-tbl.R | 350 +++++------ R/ts_median_excess_plt.R | 268 ++++---- R/ts_signature_tbl.R | 148 ++-- R/umap_list.R | 406 ++++++------- R/zzz.R | 38 - README.md | 4 build/vignette.rds |binary inst/doc/getting-started.Rmd | 200 +++--- inst/doc/getting-started.html | 8 inst/doc/kmeans-umap.Rmd | 356 +++++------ inst/doc/kmeans-umap.html | 114 +-- man/color_blind.Rd |only man/diverging_bar_plt.Rd | 164 ++--- man/diverging_lollipop_plt.Rd | 126 ++-- man/figures/README-gartner_chart-1.png |binary man/gartner_magic_chart_plt.Rd | 47 + man/hr_scale_color_colorblind.Rd |only man/hr_scale_fill_colorblind.Rd |only man/kmeans_scree_data_tbl.Rd | 102 +-- man/kmeans_scree_plt.Rd | 100 +-- man/service_line_augment.Rd | 128 ++-- man/service_line_vec.Rd | 128 ++-- man/ts_signature_tbl.Rd | 96 +-- man/umap_list.Rd | 122 ++-- man/umap_plt.Rd | 130 ++-- vignettes/getting-started.Rmd | 200 +++--- vignettes/kmeans-umap.Rmd | 356 +++++------ 43 files changed, 4090 insertions(+), 3998 deletions(-)
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between clock versions 0.6.0 dated 2021-12-02 and 0.6.1 dated 2022-07-18
DESCRIPTION | 17 MD5 | 120 ++-- NAMESPACE | 1 NEWS.md | 29 R/arithmetic.R | 2 R/calendar.R | 4 R/clock-package.R | 1 R/date.R | 22 R/duration.R | 19 R/gregorian-year-day.R | 2 R/gregorian-year-month-day.R | 4 R/gregorian-year-month-weekday.R | 2 R/invalid.R | 2 R/iso-year-week-day.R | 4 R/naive-time.R | 5 R/posixt.R | 28 R/quarterly-year-quarter-day.R | 6 R/setters.R | 2 R/sys-time.R | 4 R/time-point.R | 6 R/weekday.R | 2 R/zoned-time.R | 4 build/vignette.rds |binary inst/doc/clock.html | 492 ++++++++++++++-- inst/doc/faq.html | 412 ++++++++++++-- inst/doc/recipes.html | 524 +++++++++++++++--- man/clock-arith.Rd | 5 man/clock-package.Rd | 2 man/date-sequence.Rd | 8 man/date-time-parse.Rd | 6 man/date_seq.Rd | 10 man/posixt-sequence.Rd | 8 man/seq.clock_duration.Rd | 14 man/seq.clock_iso_year_week_day.Rd | 4 man/seq.clock_time_point.Rd | 4 man/seq.clock_year_day.Rd | 4 man/seq.clock_year_month_day.Rd | 4 man/seq.clock_year_month_weekday.Rd | 4 man/seq.clock_year_quarter_day.Rd | 4 man/sys-parsing.Rd | 6 man/sys_time_info.Rd | 6 src/duration.cpp | 19 src/utils.h | 20 tests/testthat/_snaps/calendar.md | 21 tests/testthat/_snaps/date.md | 174 +++-- tests/testthat/_snaps/duration.md | 35 - tests/testthat/_snaps/gregorian-year-day.md | 3 tests/testthat/_snaps/gregorian-year-month-day.md | 6 tests/testthat/_snaps/gregorian-year-month-weekday.md | 3 tests/testthat/_snaps/iso-year-week-day.md | 3 tests/testthat/_snaps/naive-time.md | 29 tests/testthat/_snaps/posixt.md | 201 +++--- tests/testthat/_snaps/quarterly-year-quarter-day.md | 3 tests/testthat/_snaps/sys-time.md | 54 - tests/testthat/_snaps/time-point.md | 30 - tests/testthat/_snaps/utils.md | 3 tests/testthat/_snaps/zoned-time.md | 12 tests/testthat/helper-format.R | 10 tests/testthat/test-date.R | 32 - tests/testthat/test-duration.R | 18 tests/testthat/test-posixt.R | 50 + 61 files changed, 1821 insertions(+), 708 deletions(-)
Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 7.2.0 dated 2022-05-13 and 7.2.1 dated 2022-07-18
roxygen2-7.2.0/roxygen2/R/roxygen.R |only roxygen2-7.2.0/roxygen2/man/roxygen |only roxygen2-7.2.1/roxygen2/DESCRIPTION | 12 roxygen2-7.2.1/roxygen2/MD5 | 184 +- roxygen2-7.2.1/roxygen2/NAMESPACE | 11 roxygen2-7.2.1/roxygen2/NEWS.md | 76 roxygen2-7.2.1/roxygen2/R/markdown-escaping.R | 1 roxygen2-7.2.1/roxygen2/R/markdown-link.R | 8 roxygen2-7.2.1/roxygen2/R/markdown.R | 143 + roxygen2-7.2.1/roxygen2/R/namespace.R | 13 roxygen2-7.2.1/roxygen2/R/object-format.R | 1 roxygen2-7.2.1/roxygen2/R/object-s3.R | 1 roxygen2-7.2.1/roxygen2/R/options.R | 16 roxygen2-7.2.1/roxygen2/R/rd-describe-in.R | 217 ++ roxygen2-7.2.1/roxygen2/R/rd-eval.R |only roxygen2-7.2.1/roxygen2/R/rd-find-link-files.R | 2 roxygen2-7.2.1/roxygen2/R/rd-include-rmd.R | 33 roxygen2-7.2.1/roxygen2/R/rd-inherit.R | 6 roxygen2-7.2.1/roxygen2/R/rd-r6.R | 13 roxygen2-7.2.1/roxygen2/R/rd-raw.R | 2 roxygen2-7.2.1/roxygen2/R/rd-usage.R | 55 roxygen2-7.2.1/roxygen2/R/rd.R | 38 roxygen2-7.2.1/roxygen2/R/roclet.R | 1 roxygen2-7.2.1/roxygen2/R/roxygen2-package.R |only roxygen2-7.2.1/roxygen2/R/roxygenize.R | 3 roxygen2-7.2.1/roxygen2/R/tag-metadata.R |only roxygen2-7.2.1/roxygen2/R/tag-parser.R | 10 roxygen2-7.2.1/roxygen2/R/topic.R | 14 roxygen2-7.2.1/roxygen2/R/topics.R | 4 roxygen2-7.2.1/roxygen2/R/utils-rd.R | 8 roxygen2-7.2.1/roxygen2/R/utils.R | 18 roxygen2-7.2.1/roxygen2/R/vignette.R | 3 roxygen2-7.2.1/roxygen2/README.md | 14 roxygen2-7.2.1/roxygen2/build/vignette.rds |binary roxygen2-7.2.1/roxygen2/inst/doc/extending.Rmd | 72 roxygen2-7.2.1/roxygen2/inst/doc/index-crossref.R |only roxygen2-7.2.1/roxygen2/inst/doc/index-crossref.Rmd |only roxygen2-7.2.1/roxygen2/inst/doc/index-crossref.html |only roxygen2-7.2.1/roxygen2/inst/doc/namespace.R | 28 roxygen2-7.2.1/roxygen2/inst/doc/namespace.Rmd | 159 -- roxygen2-7.2.1/roxygen2/inst/doc/namespace.html | 198 +- roxygen2-7.2.1/roxygen2/inst/doc/rd-formatting.R | 126 - roxygen2-7.2.1/roxygen2/inst/doc/rd-formatting.Rmd | 535 ++---- roxygen2-7.2.1/roxygen2/inst/doc/rd-formatting.html | 636 ++------ roxygen2-7.2.1/roxygen2/inst/doc/rd-other.R |only roxygen2-7.2.1/roxygen2/inst/doc/rd-other.Rmd |only roxygen2-7.2.1/roxygen2/inst/doc/rd-other.html |only roxygen2-7.2.1/roxygen2/inst/doc/rd.R | 228 -- roxygen2-7.2.1/roxygen2/inst/doc/rd.Rmd | 688 -------- roxygen2-7.2.1/roxygen2/inst/doc/rd.html | 770 ---------- roxygen2-7.2.1/roxygen2/inst/doc/reuse.R |only roxygen2-7.2.1/roxygen2/inst/doc/reuse.Rmd |only roxygen2-7.2.1/roxygen2/inst/doc/reuse.html |only roxygen2-7.2.1/roxygen2/inst/doc/roxygen2.R | 34 roxygen2-7.2.1/roxygen2/inst/doc/roxygen2.Rmd | 135 - roxygen2-7.2.1/roxygen2/inst/doc/roxygen2.html | 71 roxygen2-7.2.1/roxygen2/inst/roxygen2-tags.yml |only roxygen2-7.2.1/roxygen2/man/RoxyTopic.Rd | 8 roxygen2-7.2.1/roxygen2/man/double_escape_md.Rd | 1 roxygen2-7.2.1/roxygen2/man/is_s3_generic.Rd | 1 roxygen2-7.2.1/roxygen2/man/load_options.Rd | 4 roxygen2-7.2.1/roxygen2/man/markdown-test.Rd | 6 roxygen2-7.2.1/roxygen2/man/markdown_pass1.Rd | 21 roxygen2-7.2.1/roxygen2/man/namespace_roclet.Rd | 5 roxygen2-7.2.1/roxygen2/man/object_format.Rd | 1 roxygen2-7.2.1/roxygen2/man/rd_roclet.Rd | 20 roxygen2-7.2.1/roxygen2/man/roclet_find.Rd | 1 roxygen2-7.2.1/roxygen2/man/roxygen2-package.Rd | 13 roxygen2-7.2.1/roxygen2/man/roxygenize.Rd | 2 roxygen2-7.2.1/roxygen2/man/tags-index-crossref.Rd |only roxygen2-7.2.1/roxygen2/man/tags-namespace.Rd |only roxygen2-7.2.1/roxygen2/man/tags-rd-formatting.Rd |only roxygen2-7.2.1/roxygen2/man/tags-rd-other.Rd |only roxygen2-7.2.1/roxygen2/man/tags-rd.Rd |only roxygen2-7.2.1/roxygen2/man/tags-reuse.Rd |only roxygen2-7.2.1/roxygen2/man/tags_list.Rd |only roxygen2-7.2.1/roxygen2/man/vignette_roclet.Rd | 8 roxygen2-7.2.1/roxygen2/src/parser2.cpp | 2 roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/markdown-code.md | 25 roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/markdown.md | 52 roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/rd-describe-in.md | 111 + roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/rd-include-rmd.md |only roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/rd-inherit.md | 8 roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/rd-r6.md | 26 roxygen2-7.2.1/roxygen2/tests/testthat/_snaps/rd-usage.md | 4 roxygen2-7.2.1/roxygen2/tests/testthat/example.Rmd |only roxygen2-7.2.1/roxygen2/tests/testthat/roxygen-block-3-B.Rd | 6 roxygen2-7.2.1/roxygen2/tests/testthat/roxygen-block-3-C.Rd | 8 roxygen2-7.2.1/roxygen2/tests/testthat/test-markdown-code.R | 64 roxygen2-7.2.1/roxygen2/tests/testthat/test-markdown-link.R | 20 roxygen2-7.2.1/roxygen2/tests/testthat/test-markdown.R | 51 roxygen2-7.2.1/roxygen2/tests/testthat/test-namespace.R | 5 roxygen2-7.2.1/roxygen2/tests/testthat/test-rd-describe-in.R | 191 +- roxygen2-7.2.1/roxygen2/tests/testthat/test-rd-include-rmd.R | 24 roxygen2-7.2.1/roxygen2/tests/testthat/test-rd-inherit.R | 1 roxygen2-7.2.1/roxygen2/tests/testthat/test-rd-r6.R | 27 roxygen2-7.2.1/roxygen2/tests/testthat/test-rd-usage.R | 22 roxygen2-7.2.1/roxygen2/tests/testthat/test-tag-metadata.R |only roxygen2-7.2.1/roxygen2/tests/testthat/test-utils.R | 6 roxygen2-7.2.1/roxygen2/vignettes/extending.Rmd | 72 roxygen2-7.2.1/roxygen2/vignettes/index-crossref.Rmd |only roxygen2-7.2.1/roxygen2/vignettes/namespace.Rmd | 159 -- roxygen2-7.2.1/roxygen2/vignettes/rd-formatting.Rmd | 535 ++---- roxygen2-7.2.1/roxygen2/vignettes/rd-other.Rmd |only roxygen2-7.2.1/roxygen2/vignettes/rd.Rmd | 688 -------- roxygen2-7.2.1/roxygen2/vignettes/reuse.Rmd |only roxygen2-7.2.1/roxygen2/vignettes/roxygen2.Rmd | 135 - 107 files changed, 2431 insertions(+), 4489 deletions(-)