Title: An R Package for Stepwise Cluster Analysis
Description: A statistical tool for multivariate modeling and clustering using stepwise cluster analysis. The modeling output of rSCA is constructed as a cluster tree to represent the complicated relationships between multiple dependent and independent variables. A free tool (named rSCA Tree Generator) for visualizing the cluster tree from rSCA is also released and it can be downloaded at <rscatree.weebly.com>.
Author: Xiuquan Wang [aut] ,
Xiuquan Wang [cre]
Maintainer: Xiuquan (Xander) Wang <xiuquan.wang@gmail.com>
Diff between rSCA versions 3.1 dated 2020-03-10 and 3.2 dated 2026-07-26
DESCRIPTION | 24 +++++++++++++++++------- MD5 | 4 ++-- man/rSCA.modeling.Rd | 2 +- 3 files changed, 20 insertions(+), 10 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] ,
Google Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between cld3 versions 1.6.1 dated 2024-10-04 and 1.6.2 dated 2026-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 39 ++++++++++++++++++++++++++++----------- 4 files changed, 38 insertions(+), 18 deletions(-)
Title: Binary Image Thinning Algorithms
Description: Thinning (skeletonization) algorithms for binary raster
images. Provides seven algorithms behind a single dispatching
function: Zhang-Suen (Zhang and Suen 1984)
<doi:10.1145/357994.358023>, Guo-Hall (Guo and Hall 1989)
<doi:10.1145/62065.62074>, a 2-D adaptation of Lee
(Lee, Kashyap, and Chu 1994) <doi:10.1006/cgip.1994.1042>, K3M
(Saeed, Tabedzki, Rybnik, and Adamski 2010)
<doi:10.2478/v10006-010-0024-4>, the parallel form commonly
attributed to Hilditch (1969, in 'Machine Intelligence 4'),
OPTA / SPTA (Naccache and Shinghal 1984), and Holt and colleagues
(1987) <doi:10.1145/12527.12531>. Also provides the medial axis
transform (Blum 1967) and a distance transform implementation
following Felzenszwalb and Huttenlocher (2012)
<doi:10.4086/toc.2012.v008a019>. The thin() API selects the
algorithm by name, defaulting to Zhang-Suen. Complements the
morphology in the 'EBImage' package, which does not provide a
thinning operator.
Author: Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between thinr versions 0.2.0 dated 2026-05-27 and 0.3.0 dated 2026-07-26
thinr-0.2.0/thinr/R/thin_image.R |only thinr-0.2.0/thinr/man/thinImage.Rd |only thinr-0.3.0/thinr/DESCRIPTION | 14 thinr-0.3.0/thinr/MD5 | 59 - thinr-0.3.0/thinr/NAMESPACE | 1 thinr-0.3.0/thinr/NEWS.md | 56 + thinr-0.3.0/thinr/R/distance_transform.R | 10 thinr-0.3.0/thinr/R/medial_axis.R | 2 thinr-0.3.0/thinr/R/thin.R | 77 +- thinr-0.3.0/thinr/R/thinr-package.R | 13 thinr-0.3.0/thinr/README.md | 11 thinr-0.3.0/thinr/build/partial.rdb |binary thinr-0.3.0/thinr/build/vignette.rds |binary thinr-0.3.0/thinr/inst/WORDLIST | 16 thinr-0.3.0/thinr/inst/doc/choosing-a-method.R | 6 thinr-0.3.0/thinr/inst/doc/choosing-a-method.Rmd | 28 thinr-0.3.0/thinr/inst/doc/choosing-a-method.html | 186 ++--- thinr-0.3.0/thinr/inst/doc/correctness-properties.R |only thinr-0.3.0/thinr/inst/doc/correctness-properties.Rmd |only thinr-0.3.0/thinr/inst/doc/correctness-properties.html |only thinr-0.3.0/thinr/man/distance_transform.Rd | 10 thinr-0.3.0/thinr/man/medial_axis.Rd | 2 thinr-0.3.0/thinr/man/thin.Rd | 39 - thinr-0.3.0/thinr/man/thinr-package.Rd | 13 thinr-0.3.0/thinr/src/distance_transform.cpp | 17 thinr-0.3.0/thinr/src/hilditch.cpp | 42 - thinr-0.3.0/thinr/src/lee.cpp | 7 thinr-0.3.0/thinr/src/opta.cpp | 103 +- thinr-0.3.0/thinr/tests/testthat/test-coercion-helpers.R |only thinr-0.3.0/thinr/tests/testthat/test-distance-transform.R | 40 + thinr-0.3.0/thinr/tests/testthat/test-medial-axis.R | 25 thinr-0.3.0/thinr/tests/testthat/test-thin.R | 468 ++++++++++++- thinr-0.3.0/thinr/vignettes/choosing-a-method.Rmd | 28 thinr-0.3.0/thinr/vignettes/correctness-properties.Rmd |only 34 files changed, 1017 insertions(+), 256 deletions(-)
Title: Generates Multivariate Nonnormal Data and Determines How Many
Factors to Retain
Description: The GenDataSample() and GenDataPopulation() functions create,
respectively, a sample or population of multivariate nonnormal data
using methods described in Ruscio and Kaczetow (2008). Both of these
functions call a FactorAnalysis() function to reproduce a correlation
matrix. The EFACompData() function allows users to determine how many
factors to retain in an exploratory factor analysis of an empirical data
set using a method described in Ruscio and Roche (2012). The latter
function uses populations of comparison data created by calling the
GenDataPopulation() function.
<DOI: 10.1080/00273170802285693>.
<DOI: 10.1037/a0025697>.
Author: John Ruscio [aut, cre]
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RGenData versions 1.0 dated 2018-11-14 and 1.0.1 dated 2026-07-26
DESCRIPTION | 15 +++++++++------ MD5 | 6 +++--- man/GenDataPopulation.Rd | 4 ++-- man/GenDataSample.Rd | 2 +- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Polyspherical Kernel Density Estimation
Description: Kernel density estimation on the polysphere, (hyper)sphere, and
circle. Includes functions for density estimation, regression estimation,
ridge estimation, bandwidth selection, kernels, samplers, and homogeneity
tests. Companion package to García-Portugués and Meilán-Vila (2025)
<doi:10.1080/01621459.2025.2521898> and García-Portugués and Meilán-Vila
(2023) <doi:10.1007/978-3-031-32729-2_4>.
Author: Eduardo Garcia-Portugues [aut, cre] ,
Andrea Meilan-Vila [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between polykde versions 1.2.0 dated 2026-07-25 and 1.2.1 dated 2026-07-26
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 +++++- tests/testthat/Rplots.pdf |binary tests/testthat/tests_bwd.R | 1 + tests/testthat/tests_distr.R | 7 +++++-- tests/testthat/tests_grad_hess.R | 1 + tests/testthat/tests_kde.R | 3 ++- tests/testthat/tests_kre.R | 8 -------- tests/testthat/tests_samplers.R | 10 ++++++++++ tests/testthat/tests_tests.R | 5 ++++- 11 files changed, 42 insertions(+), 27 deletions(-)
Title: Just Analysis Methods Base
Description: Just analysis methods ('jam') base functions
focused on bioinformatics.
Version- and gene-centric alphanumeric sort,
unique name and version assignment, colorized console and 'HTML' output,
color ramp and palette manipulation,
'Rmarkdown' cache import, styled 'Excel' worksheet import and export,
interpolated raster output from smooth scatter and image plots,
list to delimited vector, efficient list tools.
Author: James M. Ward [aut, cre, cph]
Maintainer: James M. Ward <jmw86069@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2025-03-23
Diff between jamba versions 1.0.4 dated 2025-03-23 and 1.0.5 dated 2026-07-26
jamba-1.0.4/jamba/man/figures/writeopenxlsx.png |only jamba-1.0.5/jamba/DESCRIPTION | 14 jamba-1.0.5/jamba/LICENSE | 4 jamba-1.0.5/jamba/MD5 | 364 jamba-1.0.5/jamba/NAMESPACE | 299 jamba-1.0.5/jamba/NEWS.md | 5508 +++++++-------- jamba-1.0.5/jamba/R/jam-calc-density.R | 2 jamba-1.0.5/jamba/R/jam-call-fn-ellipsis.R | 111 jamba-1.0.5/jamba/R/jamba-axis.R | 52 jamba-1.0.5/jamba/R/jamba-clrange.R | 273 jamba-1.0.5/jamba/R/jamba-colors-hsl.R | 4 jamba-1.0.5/jamba/R/jamba-colors.r | 34 jamba-1.0.5/jamba/R/jamba-export.r | 231 jamba-1.0.5/jamba/R/jamba-heatmap-order.R | 2 jamba-1.0.5/jamba/R/jamba-hmcellfunlabel.R | 2 jamba-1.0.5/jamba/R/jamba-imagebycolors.R | 14 jamba-1.0.5/jamba/R/jamba-kable-coloring.R | 8 jamba-1.0.5/jamba/R/jamba-lldf.R | 21 jamba-1.0.5/jamba/R/jamba-load-qmd-cache.R |only jamba-1.0.5/jamba/R/jamba-mixedSort.R | 4 jamba-1.0.5/jamba/R/jamba-package.R | 83 jamba-1.0.5/jamba/R/jamba-plots.r | 58 jamba-1.0.5/jamba/R/jamba-printdebug.R | 195 jamba-1.0.5/jamba/R/jamba-rainbow2.R | 2 jamba-1.0.5/jamba/R/jamba-showcolors.R | 202 jamba-1.0.5/jamba/R/jamba-string.r | 49 jamba-1.0.5/jamba/R/jamba-utils.R | 2 jamba-1.0.5/jamba/R/jamba.r | 55 jamba-1.0.5/jamba/README.md | 896 +- jamba-1.0.5/jamba/build/vignette.rds |binary jamba-1.0.5/jamba/inst/CITATION | 22 jamba-1.0.5/jamba/inst/doc/jamba-vignette.R | 434 - jamba-1.0.5/jamba/inst/doc/jamba-vignette.Rmd | 1142 +-- jamba-1.0.5/jamba/inst/doc/jamba-vignette.html | 2349 +++--- jamba-1.0.5/jamba/man/adjustAxisLabelMargins.Rd | 210 jamba-1.0.5/jamba/man/alpha2col.Rd | 126 jamba-1.0.5/jamba/man/applyCLrange.Rd | 316 jamba-1.0.5/jamba/man/applyXlsxCategoricalFormat.Rd | 230 jamba-1.0.5/jamba/man/applyXlsxConditionalFormat.Rd | 374 - jamba-1.0.5/jamba/man/asDate.Rd | 72 jamba-1.0.5/jamba/man/asSize.Rd | 186 jamba-1.0.5/jamba/man/breakDensity.Rd | 249 jamba-1.0.5/jamba/man/breaksByVector.Rd | 240 jamba-1.0.5/jamba/man/cPaste.Rd | 456 - jamba-1.0.5/jamba/man/call_fn_ellipsis.Rd | 227 jamba-1.0.5/jamba/man/cell_fun_label.Rd | 266 jamba-1.0.5/jamba/man/checkLightMode.Rd | 169 jamba-1.0.5/jamba/man/check_pkg_installed.Rd | 227 jamba-1.0.5/jamba/man/col2alpha.Rd | 106 jamba-1.0.5/jamba/man/col2hcl.Rd | 160 jamba-1.0.5/jamba/man/col2hsl.Rd | 196 jamba-1.0.5/jamba/man/col2hsv.Rd | 126 jamba-1.0.5/jamba/man/colNum2excelName.Rd | 147 jamba-1.0.5/jamba/man/color2gradient.Rd | 300 jamba-1.0.5/jamba/man/color_dither.Rd | 229 jamba-1.0.5/jamba/man/coordPresets.Rd | 402 - jamba-1.0.5/jamba/man/dateToDaysOld.Rd | 74 jamba-1.0.5/jamba/man/decideMfrow.Rd | 220 jamba-1.0.5/jamba/man/deg2rad.Rd | 76 jamba-1.0.5/jamba/man/drawLabels.Rd | 494 - jamba-1.0.5/jamba/man/exp2signed.Rd | 149 jamba-1.0.5/jamba/man/fillBlanks.Rd | 126 jamba-1.0.5/jamba/man/fixYellow.Rd | 154 jamba-1.0.5/jamba/man/fixYellowHue.Rd | 154 jamba-1.0.5/jamba/man/formatInt.Rd | 142 jamba-1.0.5/jamba/man/getAxisLabel.Rd | 221 jamba-1.0.5/jamba/man/getColorRamp.Rd | 464 - jamba-1.0.5/jamba/man/getDate.Rd | 80 jamba-1.0.5/jamba/man/getPlotAspect.Rd | 166 jamba-1.0.5/jamba/man/grepls.Rd | 162 jamba-1.0.5/jamba/man/groupedAxis.Rd | 232 jamba-1.0.5/jamba/man/gsubOrdered.Rd | 196 jamba-1.0.5/jamba/man/gsubs.Rd | 188 jamba-1.0.5/jamba/man/handleArgsText.Rd | 204 jamba-1.0.5/jamba/man/hcl2col.Rd | 240 jamba-1.0.5/jamba/man/heads.Rd | 118 jamba-1.0.5/jamba/man/heatmap_column_order.Rd | 268 jamba-1.0.5/jamba/man/heatmap_row_order.Rd | 130 jamba-1.0.5/jamba/man/hsl2col.Rd | 186 jamba-1.0.5/jamba/man/hsv2col.Rd | 130 jamba-1.0.5/jamba/man/igrep.Rd | 84 jamba-1.0.5/jamba/man/igrepHas.Rd | 132 jamba-1.0.5/jamba/man/igrepl.Rd | 94 jamba-1.0.5/jamba/man/imageByColors.Rd | 458 - jamba-1.0.5/jamba/man/imageDefault.Rd | 342 jamba-1.0.5/jamba/man/isColor.Rd | 112 jamba-1.0.5/jamba/man/isFALSEV.Rd | 121 jamba-1.0.5/jamba/man/isTRUEV.Rd | 121 jamba-1.0.5/jamba/man/jamCalcDensity.Rd | 92 jamba-1.0.5/jamba/man/jam_rapply.Rd | 118 jamba-1.0.5/jamba/man/jamba-package.Rd | 260 jamba-1.0.5/jamba/man/jargs.Rd | 317 jamba-1.0.5/jamba/man/kable_coloring.Rd | 453 - jamba-1.0.5/jamba/man/list2df.Rd | 118 jamba-1.0.5/jamba/man/lldf.Rd | 194 jamba-1.0.5/jamba/man/log2signed.Rd | 165 jamba-1.0.5/jamba/man/makeColorDarker.Rd | 220 jamba-1.0.5/jamba/man/makeNames.Rd | 270 jamba-1.0.5/jamba/man/make_html_styles.Rd | 234 jamba-1.0.5/jamba/man/make_styles.Rd | 258 jamba-1.0.5/jamba/man/mergeAllXY.Rd | 222 jamba-1.0.5/jamba/man/middle.Rd | 137 jamba-1.0.5/jamba/man/minorLogTicks.Rd | 419 - jamba-1.0.5/jamba/man/minorLogTicksAxis.Rd | 564 - jamba-1.0.5/jamba/man/mixedOrder.Rd | 378 - jamba-1.0.5/jamba/man/mixedSort.Rd | 298 jamba-1.0.5/jamba/man/mixedSortDF.Rd | 362 jamba-1.0.5/jamba/man/mixedSorts.Rd | 420 - jamba-1.0.5/jamba/man/mmixedOrder.Rd | 194 jamba-1.0.5/jamba/man/nameVector.Rd | 176 jamba-1.0.5/jamba/man/nameVectorN.Rd | 198 jamba-1.0.5/jamba/man/newestFile.Rd | 133 jamba-1.0.5/jamba/man/noiseFloor.Rd | 190 jamba-1.0.5/jamba/man/normScale.Rd | 198 jamba-1.0.5/jamba/man/nullPlot.Rd | 266 jamba-1.0.5/jamba/man/padInteger.Rd | 112 jamba-1.0.5/jamba/man/padString.Rd | 118 jamba-1.0.5/jamba/man/pasteByRow.Rd | 224 jamba-1.0.5/jamba/man/pasteByRowOrdered.Rd | 248 jamba-1.0.5/jamba/man/plotPolygonDensity.Rd | 612 - jamba-1.0.5/jamba/man/plotRidges.Rd | 252 jamba-1.0.5/jamba/man/plotSmoothScatter.Rd | 540 - jamba-1.0.5/jamba/man/printDebug.Rd | 793 +- jamba-1.0.5/jamba/man/provigrep.Rd | 280 jamba-1.0.5/jamba/man/rad2deg.Rd | 76 jamba-1.0.5/jamba/man/rainbow2.Rd | 130 jamba-1.0.5/jamba/man/rbindList.Rd | 206 jamba-1.0.5/jamba/man/readOpenxlsx.Rd | 332 jamba-1.0.5/jamba/man/relist_named.Rd | 208 jamba-1.0.5/jamba/man/reload_qmd_cache.Rd |only jamba-1.0.5/jamba/man/reload_rmarkdown_cache.Rd | 249 jamba-1.0.5/jamba/man/renameColumn.Rd | 181 jamba-1.0.5/jamba/man/rgb2col.Rd | 266 jamba-1.0.5/jamba/man/rlengths.Rd | 148 jamba-1.0.5/jamba/man/rmInfinite.Rd | 121 jamba-1.0.5/jamba/man/rmNA.Rd | 199 jamba-1.0.5/jamba/man/rmNAs.Rd | 209 jamba-1.0.5/jamba/man/rmNULL.Rd | 129 jamba-1.0.5/jamba/man/rowGroupMeans.Rd | 368 - jamba-1.0.5/jamba/man/rowRmMadOutliers.Rd | 374 - jamba-1.0.5/jamba/man/sclass.Rd | 124 jamba-1.0.5/jamba/man/sdim.Rd | 342 jamba-1.0.5/jamba/man/setCLranges.Rd | 251 jamba-1.0.5/jamba/man/setPrompt.Rd | 399 - jamba-1.0.5/jamba/man/setTextContrastColor.Rd | 318 jamba-1.0.5/jamba/man/set_xlsx_colwidths.Rd | 148 jamba-1.0.5/jamba/man/set_xlsx_rowheights.Rd | 170 jamba-1.0.5/jamba/man/shadowText.Rd | 296 jamba-1.0.5/jamba/man/shadowText_options.Rd | 334 jamba-1.0.5/jamba/man/showColors.Rd | 414 - jamba-1.0.5/jamba/man/sizeAsNum.Rd | 172 jamba-1.0.5/jamba/man/smoothScatterJam.Rd | 306 jamba-1.0.5/jamba/man/sqrtAxis.Rd | 206 jamba-1.0.5/jamba/man/tcount.Rd | 154 jamba-1.0.5/jamba/man/ucfirst.Rd | 124 jamba-1.0.5/jamba/man/unalpha.Rd | 128 jamba-1.0.5/jamba/man/unigrep.Rd | 84 jamba-1.0.5/jamba/man/uniques.Rd | 164 jamba-1.0.5/jamba/man/unnestList.Rd | 224 jamba-1.0.5/jamba/man/unvigrep.Rd | 90 jamba-1.0.5/jamba/man/usrBox.Rd | 146 jamba-1.0.5/jamba/man/vgrep.Rd | 84 jamba-1.0.5/jamba/man/vigrep.Rd | 78 jamba-1.0.5/jamba/man/warpAroundZero.Rd | 188 jamba-1.0.5/jamba/man/warpRamp.Rd | 192 jamba-1.0.5/jamba/man/writeOpenxlsx.Rd | 737 +- jamba-1.0.5/jamba/tests/testthat.R | 8 jamba-1.0.5/jamba/tests/testthat/test-asSize.R | 62 jamba-1.0.5/jamba/tests/testthat/test-cPaste.R | 262 jamba-1.0.5/jamba/tests/testthat/test-call-fn-ellipsis.R |only jamba-1.0.5/jamba/tests/testthat/test-color2gradient.R | 72 jamba-1.0.5/jamba/tests/testthat/test-getColorRamp.R | 280 jamba-1.0.5/jamba/tests/testthat/test-grep.R | 150 jamba-1.0.5/jamba/tests/testthat/test-groupedAxis.R | 104 jamba-1.0.5/jamba/tests/testthat/test-gsubs.R | 58 jamba-1.0.5/jamba/tests/testthat/test-kable-coloring.R | 88 jamba-1.0.5/jamba/tests/testthat/test-makeNames.R | 154 jamba-1.0.5/jamba/tests/testthat/test-mixedSort.R | 314 jamba-1.0.5/jamba/tests/testthat/test-mixedSortDF.R | 332 jamba-1.0.5/jamba/tests/testthat/test-rbindList.R | 140 jamba-1.0.5/jamba/tests/testthat/test-rmNULL-rmNA.R | 104 jamba-1.0.5/jamba/tests/testthat/test-rmRowMadOutliers.R | 124 jamba-1.0.5/jamba/tests/testthat/test-rowGroupMeans.R | 314 jamba-1.0.5/jamba/tests/testthat/test-writeOpenxlsx.R | 199 jamba-1.0.5/jamba/vignettes/jamba-vignette.Rmd | 1142 +-- 185 files changed, 23614 insertions(+), 22883 deletions(-)
Title: 'DataSHIELD' RO-Crate Governance Functions
Description: Tools for wrapping 'DataSHIELD' analyses into RO-Crate
(Research Object Crate) objects. Provides functions to create structured
metadata for federated data analysis projects, enabling governance
tracking of data access, project membership, analysis execution and
output validation across distributed data sources.
Author: Roberto Villegas-Diaz [aut, cre] ,
Becca Wilson [aut] ,
Olly Butters [aut] ,
Stuart Wheater [aut] ,
University of Liverpool [cph]
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@outlook.com>
Diff between dsROCrate versions 0.1.0 dated 2026-06-01 and 0.2.0 dated 2026-07-26
DESCRIPTION | 10 MD5 | 94 +- NAMESPACE | 34 NEWS.md | 32 R/audit.R | 37 R/audit_engine.R | 68 - R/backend-generic.R |only R/backend-opal.R |only R/check_permissions.R | 25 R/dsROCrate.R | 15 R/print.R | 53 + R/report.R | 23 R/safe-call-utils.R |only R/safe-call.R |only R/safe-reference.R |only R/safe-symbol-utils.R |only R/safe-symbol.R |only R/safe_data.R | 12 R/safe_output.R | 245 ++++- R/safe_people.R | 10 R/safe_project.R | 77 - R/safe_setting.R | 16 R/symbol-registry.R |only R/utils-armadillo.R | 5 R/utils-audit.R | 39 R/utils-connection.R | 118 -- R/utils-cr8tor.R | 74 + R/utils-opal.R | 98 -- R/utils-safe_data.R | 2 R/utils-safe_people.R | 71 + R/utils-safe_project.R | 2 inst/WORDLIST | 23 inst/doc/audit-permissions.R | 4 inst/doc/audit-permissions.Rmd | 7 inst/doc/audit-permissions.html | 5 inst/doc/getting-started.html | 1378 +++++--------------------------- man/armadillo_login.Rd | 5 man/check_permissions.Rd | 9 man/init.Rd | 5 man/report.Rd | 6 man/safe_data.Rd | 5 man/safe_output.Rd | 5 man/safe_people.Rd | 5 man/safe_project.Rd | 37 man/safe_setting.Rd | 5 tests/testthat/helper-mock-opal.R |only tests/testthat/test-audit.R |only tests/testthat/test-audit_engine.R |only tests/testthat/test-check_permissions.R |only tests/testthat/test-dsROCrate-package.R | 4 tests/testthat/test-report.R | 8 tests/testthat/test-utils-opal.R | 4 tests/testthat/test-utils-safe_people.R | 68 + vignettes/audit-permissions.Rmd | 7 54 files changed, 1093 insertions(+), 1657 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <https://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] ,
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-49 dated 2026-07-13 and 0.4-50 dated 2026-07-26
RWeka-0.4-49/RWeka/inst/arff/diabetes.arff |only RWeka-0.4-50/RWeka/CHANGELOG | 12 ++++++++++++ RWeka-0.4-50/RWeka/DESCRIPTION | 6 +++--- RWeka-0.4-50/RWeka/MD5 | 11 +++++------ RWeka-0.4-50/RWeka/build/partial.rdb |binary RWeka-0.4-50/RWeka/inst/doc/RWeka.pdf |binary RWeka-0.4-50/RWeka/man/Weka_classifier_trees.Rd | 12 ------------ 7 files changed, 20 insertions(+), 21 deletions(-)
Title: Visualizations of Paired Comparisons
Description: Convert a logical vector or a vector of p-values or a correlation,
difference, or distance matrix into a display identifying the pairs for
which the differences were not significantly different. Designed for use
in conjunction with the output of functions like TukeyHSD, dist (stats),
simint, simtest, csimint, csimtest (multcomp), friedmanmc, kruskalmc (pgirmess).
Author: Spencer Graves [aut],
Hans-Peter Piepho [aut],
Luciano Selzer [aut, cre],
Sundar Dorai-Raj [ctb]
Maintainer: Luciano Selzer <luciano.selzer@gmail.com>
Diff between multcompView versions 0.1-11 dated 2026-02-16 and 0.1-12 dated 2026-07-26
DESCRIPTION | 11 +++++++---- MD5 | 21 ++++++++++++++------- NEWS.md |only R/multcompLetters.R | 16 ++++++++-------- R/multcompTs.R | 6 +----- R/vec2mat.R | 26 -------------------------- man/multcompLetters.Rd | 9 +++------ man/multcompTs.Rd | 6 +----- man/vec2mat.Rd | 26 -------------------------- tests |only 10 files changed, 34 insertions(+), 87 deletions(-)
Title: Extra Functionality for the 'xpose' Package
Description: Adding some at-present missing functionality, or functions
unlikely to be added to the base 'xpose' package. This includes some
diagnostic plots that have been missing in translation from 'xpose4',
but also some useful features that truly extend the capabilities of what
can be done with 'xpose'. These extensions include the concept of a set of
'xpose' objects, and diagnostics for likelihood-based models.
Author: John Prybylski [aut, cre, cph]
Maintainer: John Prybylski <jprybylski@gmail.com>
Diff between xpose.xtras versions 0.1.4 dated 2026-04-21 and 0.2.0 dated 2026-07-26
DESCRIPTION | 22 MD5 | 231 ++++--- NAMESPACE | 40 + NEWS.md | 49 + R/bbr.R |only R/categorical.R | 333 ++++++++++- R/colinearity.R | 244 ++++++++ R/confusion.R | 6 R/covariates.R | 159 +++++ R/fit_stats.R |only R/fixes.R | 206 ++++++ R/modavg_xpdb.R | 18 R/nlmixr_examples.R | 55 + R/process_preset.R |only R/utils.R | 12 R/xp_xtras.R | 90 ++ R/xplot_binned.R |only R/xplot_forest.R |only R/xplot_heatmap.R |only R/xplot_pairs.R | 8 R/xpose.xtras-package.R | 2 R/xpose_set.R | 65 +- R/xset_features.R | 2 R/xset_plots.R | 30 R/xtra_labs.R |only R/xtra_pars.R | 905 +++++++++++++++++++++++++++++- R/xtra_plot_all.R |only R/xtra_plots.R | 186 ++++++ R/xtra_watermark.R |only R/xtras_options.R |only R/zzz.R | 21 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary data/pheno_base.rda |binary data/pheno_final.rda |binary data/pheno_saem.rda |binary data/pheno_set.rda |binary data/pkpd_m3.rda |binary data/pkpd_m3_df.rda |binary data/vismo_dtmm.rda |binary data/vismo_pomod.rda |binary data/vismodegib.rda |binary data/xpdb_set.rda |binary data/xpdb_x.rda |binary inst/WORDLIST | 45 + inst/doc/a01-the-xp_xtra-object.R | 30 inst/doc/a01-the-xp_xtra-object.Rmd | 43 + inst/doc/a01-the-xp_xtra-object.html | 136 +++- inst/doc/a02-xpose-sets.R | 4 inst/doc/a02-xpose-sets.Rmd | 7 inst/doc/a02-xpose-sets.html | 131 ++-- inst/doc/a03-useful_plots.R | 16 inst/doc/a03-useful_plots.Rmd | 29 inst/doc/a03-useful_plots.html | 63 +- inst/doc/a04-plot-output-and-options.R |only inst/doc/a04-plot-output-and-options.Rmd |only inst/doc/a04-plot-output-and-options.html |only man/add_cov_association.Rd |only man/add_process_preset.Rd |only man/add_watermark.Rd |only man/apply_default_labs.Rd |only man/catdv_vs_ipred.Rd |only man/catdv_vs_occ.Rd |only man/check_levels.Rd | 5 man/cormat.Rd |only man/cov_forest.Rd |only man/diagnose_constants.Rd | 2 man/figures/README-cormat-1.png |only man/figures/README-m3-1.png |binary man/figures/README-m3_roc-1.png |binary man/focus_xpdb.Rd | 28 man/get_cov_matrix.Rd |only man/get_xtras_option.Rd |only man/ggsave_xp.Rd |only man/grapes-p-grapes.Rd | 4 man/ind_plots_sample.Rd |only man/is_franken_xpdb.Rd |only man/join_backfill.Rd |only man/left_join_x.Rd |only man/levelers.Rd | 8 man/list_dv_probs.Rd | 4 man/logLik.xpose_data.Rd |only man/modify_xpdb.Rd | 2 man/nlmixr_example.Rd | 7 man/patch_condn.Rd |only man/persist_process_presets.Rd |only man/plot.xpose_data.Rd |only man/prm_cov.Rd |only man/reexports.Rd | 2 man/set_default_labs.Rd |only man/set_default_plots.Rd |only man/set_default_watermark.Rd |only man/set_dv_probs.Rd | 10 man/set_option.Rd | 9 man/set_var_levels.Rd | 9 man/set_var_types.Rd | 6 man/set_var_types.default.Rd | 6 man/set_var_types.xp_xtra.Rd | 6 man/set_var_types_x.Rd | 6 man/set_xtras_options.Rd |only man/summarise_xpdb.Rd | 2 man/val2lvl.Rd | 5 man/xp_from_bbr.Rd |only man/xplot_binned.Rd |only man/xplot_forest.Rd |only man/xplot_heatmap.Rd |only man/xpose.xtras-package.Rd | 5 man/xset_fitstats.Rd |only tests/testthat/helper-bbr.R |only tests/testthat/test-bbr.R |only tests/testthat/test-categorical.R | 309 ++++++++++ tests/testthat/test-colinearity.R |only tests/testthat/test-confusion.R | 77 ++ tests/testthat/test-covariates.R | 204 ++++++ tests/testthat/test-diag_constants.R | 75 ++ tests/testthat/test-fit_stats.R |only tests/testthat/test-fixes.R | 498 ++++++++++++++++ tests/testthat/test-modavg_xpdb.R | 30 tests/testthat/test-nlmixr2.R | 305 +++++++++- tests/testthat/test-process_preset.R |only tests/testthat/test-utils.R | 22 tests/testthat/test-xp_xtras.R | 120 +++ tests/testthat/test-xplot_binned.R |only tests/testthat/test-xplot_boxplot.R | 24 tests/testthat/test-xplot_forest.R |only tests/testthat/test-xplot_heatmap.R |only tests/testthat/test-xplot_pairs.R | 243 ++++++++ tests/testthat/test-xplot_rocplot.R | 83 ++ tests/testthat/test-xpose_set.R | 120 +++ tests/testthat/test-xset_features.R | 22 tests/testthat/test-xset_plots.R | 94 +++ tests/testthat/test-xset_shark.R | 21 tests/testthat/test-xset_waterfall.R | 16 tests/testthat/test-xtra_labs.R |only tests/testthat/test-xtra_pars.R | 559 ++++++++++++++++++ tests/testthat/test-xtra_plot_all.R |only tests/testthat/test-xtra_plots.R | 148 ++++ tests/testthat/test-xtra_watermark.R |only tests/testthat/test-xtras_options.R |only tests/testthat/test-zzz.R |only vignettes/a01-the-xp_xtra-object.Rmd | 43 + vignettes/a02-xpose-sets.Rmd | 7 vignettes/a03-useful_plots.Rmd | 29 vignettes/a04-plot-output-and-options.Rmd |only 145 files changed, 6061 insertions(+), 310 deletions(-)
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH)
Data
Description: A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.
Author: Mian Zhong [aut] ,
Margaux Goetschmann [aut] ,
Colin Walder [aut] ,
Lars Schoebitz [aut, cre] ,
Global Health Engineering, ETH Zurich [cph]
Maintainer: Lars Schoebitz <lschoebitz@ethz.ch>
Diff between washr versions 1.0.1 dated 2024-11-07 and 1.0.2 dated 2026-07-26
DESCRIPTION | 26 +++++----- MD5 | 47 ++++++++++--------- NEWS.md | 23 +++++++++ R/setup_dictionary.R | 16 ------ R/setup_readme.R | 13 ++++- R/setup_roxygen.R | 8 --- R/setup_website.R | 6 -- R/update_citation.R | 59 +++++++++++++++--------- R/update_description.R | 26 ++++++++-- build/vignette.rds |binary inst/doc/washr.R | 6 +- inst/doc/washr.html | 5 +- man/fill_dictionary.Rd | 8 --- man/setup_dictionary.Rd | 8 --- man/setup_readme.Rd | 6 ++ man/setup_roxygen.Rd | 8 --- man/setup_website.Rd | 6 -- man/update_citation.Rd | 20 +++----- man/update_description.Rd | 3 + tests/testthat/_snaps |only tests/testthat/helper.R | 23 ++------- tests/testthat/test_setup_rawdata.R | 1 tests/testthat/test_setup_readme.R | 21 ++++++++ tests/testthat/test_update_citation.R |only tests/testthat/test_update_description.R | 76 +++++++++++++++++++++++++++++-- 25 files changed, 257 insertions(+), 158 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 1.6 dated 2026-04-13 and 2.0.0 dated 2026-07-26
huge-1.6/huge/inst/doc/huge-content.pdf |only huge-2.0.0/huge/DESCRIPTION | 15 huge-2.0.0/huge/MD5 | 103 - huge-2.0.0/huge/NAMESPACE | 1 huge-2.0.0/huge/NEWS.md | 272 +++ huge-2.0.0/huge/R/RcppExports.R | 12 huge-2.0.0/huge/R/huge-internal.R | 332 ++++ huge-2.0.0/huge/R/huge-package.R | 1 huge-2.0.0/huge/R/huge.R | 96 - huge-2.0.0/huge/R/huge.ct.R | 98 - huge-2.0.0/huge/R/huge.generator.R | 163 +- huge-2.0.0/huge/R/huge.glasso.R | 46 huge-2.0.0/huge/R/huge.inference.R | 113 + huge-2.0.0/huge/R/huge.mb.R | 97 - huge-2.0.0/huge/R/huge.npn.R | 56 huge-2.0.0/huge/R/huge.plot.R | 21 huge-2.0.0/huge/R/huge.roc.R | 36 huge-2.0.0/huge/R/huge.select.R | 319 +++- huge-2.0.0/huge/R/huge.tiger.R | 113 + huge-2.0.0/huge/build |only huge-2.0.0/huge/configure | 95 + huge-2.0.0/huge/configure.ac | 22 huge-2.0.0/huge/inst/doc/huge.pdf |binary huge-2.0.0/huge/man/huge.Rd | 52 huge-2.0.0/huge/man/huge.ct.Rd | 26 huge-2.0.0/huge/man/huge.generator.Rd | 33 huge-2.0.0/huge/man/huge.glasso.Rd | 21 huge-2.0.0/huge/man/huge.inference.Rd | 12 huge-2.0.0/huge/man/huge.mb.Rd | 19 huge-2.0.0/huge/man/huge.npn.Rd | 6 huge-2.0.0/huge/man/huge.roc.Rd | 4 huge-2.0.0/huge/man/huge.select.Rd | 11 huge-2.0.0/huge/man/huge.tiger.Rd | 26 huge-2.0.0/huge/man/plot.sim.Rd | 2 huge-2.0.0/huge/src/Makevars.in | 1 huge-2.0.0/huge/src/Makevars.win | 1 huge-2.0.0/huge/src/RIC.cpp | 43 huge-2.0.0/huge/src/RcppExports.cpp | 35 huge-2.0.0/huge/src/SPMBgraph.cpp | 56 huge-2.0.0/huge/src/SPMBgraphsqrt.cpp | 83 - huge-2.0.0/huge/src/huge/blas_config.h | 8 huge-2.0.0/huge/src/huge/huge_core.h | 27 huge-2.0.0/huge/src/huge_core.cpp | 1328 ++++++++++++++++--- huge-2.0.0/huge/src/huge_r_threads.h |only huge-2.0.0/huge/src/hugeglasso.cpp | 30 huge-2.0.0/huge/tests/testthat/test-ct.R | 158 ++ huge-2.0.0/huge/tests/testthat/test-generator.R | 277 +++ huge-2.0.0/huge/tests/testthat/test-glasso.R | 236 +++ huge-2.0.0/huge/tests/testthat/test-graphics-state.R |only huge-2.0.0/huge/tests/testthat/test-inference.R | 156 ++ huge-2.0.0/huge/tests/testthat/test-invariants.R |only huge-2.0.0/huge/tests/testthat/test-mb.R | 123 + huge-2.0.0/huge/tests/testthat/test-regressions.R |only huge-2.0.0/huge/tests/testthat/test-select.R | 358 +++++ huge-2.0.0/huge/tests/testthat/test-tiger.R | 546 +++++++ huge-2.0.0/huge/tests/testthat/test-validation.R |only 56 files changed, 4918 insertions(+), 771 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.9 dated 2026-06-30 and 1.1.10 dated 2026-07-26
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NEWS.md | 3 +++ R/checkTimeBetween.R | 14 ++++++++++++-- inst/doc/IntroductionToDrugExposureDiagnostics.html | 6 +++--- inst/shiny/ResultsExplorer/dataTest |only inst/testCases |only tests/testthat/test-SyntheaSqlServer.R | 12 ++++++++---- 8 files changed, 36 insertions(+), 17 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Optimal, Fast, and Reproducible Univariate Clustering
Description: Fast, optimal, and reproducible univariate
clustering by dynamic programming. Four problems are solved, including
univariate k-means (Wang & Song 2011) <doi:10.32614/RJ-2011-015>
(Song & Zhong 2020) <doi:10.1093/bioinformatics/btaa613>, k-median,
k-segments, and multi-channel weighted k-means. Dynamic programming
is used to minimize the sum of (weighted) within-cluster distances
using respective metrics. It substantially outperforms heuristic
clustering in both efficiency and accuracy as the number of clusters
increases. Multi-channel weighted k-means groups multiple univariate
signals into k clusters. An auxiliary function generates histograms
adaptive to patterns in data. This package provides a powerful set
of tools for univariate data analysis with guaranteed optimality,
efficiency, and reproducibility, useful for peak calling on temporal,
spatial, and spectral data in addition to univariate clustering.
Author: Joe Song [aut, cre] ,
Hua Zhong [aut] ,
Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@nmsu.edu>
Diff between Ckmeans.1d.dp versions 4.3.5 dated 2023-08-19 and 4.3.6 dated 2026-07-26
DESCRIPTION | 26 ++++++------ MD5 | 26 ++++++------ NEWS.md | 17 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Ckmeans.1d.dp.R | 10 ++-- inst/doc/Ckmeans.1d.dp.html | 92 +++++++++++++++++++++---------------------- inst/doc/Weights.html | 4 - inst/doc/ahist.R | 14 +++--- inst/doc/ahist.html | 15 +++---- man/Ckmeans.1d.dp.Rd | 18 +++++++- man/plot.Cksegs.1d.dp.Rd | 4 - tests/testthat/Rplots.pdf |binary tests/testthat/test_MC_WUC.R | 9 ++++ 14 files changed, 137 insertions(+), 98 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 1.2.0 dated 2026-07-21 and 1.2.1 dated 2026-07-26
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ README.md | 20 ++++++++++---------- inst/CITATION | 6 +++--- tests/testthat/test_ResultAssignerArchive.R | 2 +- tests/testthat/test_ResultAssignerSurrogate.R | 2 +- tests/testthat/test_TunerADBO.R | 2 +- tests/testthat/test_TunerAsyncMbo.R | 2 +- 9 files changed, 32 insertions(+), 28 deletions(-)
Title: Gaussian Model Invariant by Permutation Symmetry
Description: Find the permutation symmetry group such that the covariance
matrix of the given data is approximately invariant under it.
Discovering such a permutation decreases the number of observations
needed to fit a Gaussian model, which is of great use when it is
smaller than the number of variables. Even if that is not the case,
the covariance matrix found with 'gips' approximates the actual
covariance with less statistical error. The methods implemented in
this package are described in Graczyk et al. (2022)
<doi:10.1214/22-AOS2174>. Documentation about 'gips' is
provided via its website at <https://przechoj.github.io/gips/> and
the paper by Chojecki, Morgen, Kołodziejek
(2025, <doi:10.18637/jss.v112.i07>).
Author: Adam Przemyslaw Chojecki [aut, cre] ,
Pawel Morgen [aut],
Bartosz Kolodziejek [aut]
Maintainer: Adam Przemyslaw Chojecki <adam.prze.choj@gmail.com>
Diff between gips versions 1.2.3 dated 2025-03-18 and 1.3.0 dated 2026-07-26
gips-1.2.3/gips/R/gips_class.R |only gips-1.2.3/gips/man/figures/README-example_mean_known4-1.png |only gips-1.2.3/gips/tests/testthat/Rplots.pdf |only gips-1.3.0/gips/DESCRIPTION | 28 gips-1.3.0/gips/MD5 | 127 + gips-1.3.0/gips/NAMESPACE | 2 gips-1.3.0/gips/NEWS.md | 78 + gips-1.3.0/gips/R/RcppExports.R |only gips-1.3.0/gips/R/calculate_gamma_function.R | 83 - gips-1.3.0/gips/R/find_MAP.R | 365 +++-- gips-1.3.0/gips/R/get_structure_constants.R | 2 gips-1.3.0/gips/R/gips_constructors.R |only gips-1.3.0/gips/R/gips_methods.R |only gips-1.3.0/gips/R/gips_perm_class.R | 36 gips-1.3.0/gips/R/gips_plot.R |only gips-1.3.0/gips/R/log_posteriori_of_gips.R | 253 +++ gips-1.3.0/gips/R/prepare_orthogonal_matrix.R | 65 - gips-1.3.0/gips/R/project_matrix.R | 192 -- gips-1.3.0/gips/R/rcpp.R |only gips-1.3.0/gips/R/sysdata.rda |binary gips-1.3.0/gips/R/utils.R | 29 gips-1.3.0/gips/README.md | 24 gips-1.3.0/gips/inst/WORDLIST | 18 gips-1.3.0/gips/inst/doc/Optimizers.R | 122 + gips-1.3.0/gips/inst/doc/Optimizers.Rmd | 164 ++ gips-1.3.0/gips/inst/doc/Optimizers.html | 524 +++++--- gips-1.3.0/gips/inst/doc/Theory.Rmd | 26 gips-1.3.0/gips/inst/doc/Theory.html | 84 - gips-1.3.0/gips/inst/doc/gips.R | 88 + gips-1.3.0/gips/inst/doc/gips.Rmd | 157 ++ gips-1.3.0/gips/inst/doc/gips.html | 244 ++- gips-1.3.0/gips/man/AIC.gips.Rd | 10 gips-1.3.0/gips/man/as.character.gips.Rd | 4 gips-1.3.0/gips/man/as.character.gips_perm.Rd | 2 gips-1.3.0/gips/man/calculate_gamma_function.Rd | 12 gips-1.3.0/gips/man/compare_posteriories_of_perms.Rd | 11 gips-1.3.0/gips/man/figures/README-example_mean_known1_1-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_known3_1-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_known6-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_unknown2-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_unknown4-1.png |binary gips-1.3.0/gips/man/find_MAP.Rd | 32 gips-1.3.0/gips/man/forget_perms.Rd | 4 gips-1.3.0/gips/man/get_probabilities_from_gips.Rd | 13 gips-1.3.0/gips/man/get_structure_constants.Rd | 2 gips-1.3.0/gips/man/gips.Rd | 70 - gips-1.3.0/gips/man/gips_perm.Rd | 4 gips-1.3.0/gips/man/logLik.gips.Rd | 13 gips-1.3.0/gips/man/log_posteriori_of_gips.Rd | 19 gips-1.3.0/gips/man/plot.gips.Rd | 75 - gips-1.3.0/gips/man/prepare_orthogonal_matrix.Rd | 9 gips-1.3.0/gips/man/print.gips.Rd | 17 gips-1.3.0/gips/man/print.gips_perm.Rd | 2 gips-1.3.0/gips/man/project_matrix.Rd | 22 gips-1.3.0/gips/man/summary.gips.Rd | 25 gips-1.3.0/gips/src |only gips-1.3.0/gips/tests/testthat/test-calculate_gamma_function.R | 104 + gips-1.3.0/gips/tests/testthat/test-find_MAP.R | 39 gips-1.3.0/gips/tests/testthat/test-gips_class.R | 641 ++-------- gips-1.3.0/gips/tests/testthat/test-gips_mult.R |only gips-1.3.0/gips/tests/testthat/test-gips_perm_class.R | 21 gips-1.3.0/gips/tests/testthat/test-gips_plot.R |only gips-1.3.0/gips/tests/testthat/test-log_posteriori_of_gips.R | 57 gips-1.3.0/gips/tests/testthat/test-plot_multi.R |only gips-1.3.0/gips/tests/testthat/test-prepare_orthogonal_matrix.R | 18 gips-1.3.0/gips/tests/testthat/test-project_matrix.R | 121 - gips-1.3.0/gips/tests/testthat/test-utils.R | 28 gips-1.3.0/gips/vignettes/Optimizers.Rmd | 164 ++ gips-1.3.0/gips/vignettes/Theory.Rmd | 26 gips-1.3.0/gips/vignettes/gips.Rmd | 157 ++ 70 files changed, 2891 insertions(+), 1542 deletions(-)
Title: Diagnostic Test Accuracy Meta-Analysis using Template Model
Builder
Description: Fits the hierarchical summary receiver operating characteristic (HSROC) model of
Rutter and Gatsonis (2001) <doi:10.1002/sim.942>, the bivariate binomial-normal model of
Reitsma et al. (2005) <doi:10.1016/j.jclinepi.2005.02.022>, the threshold-based bivariate
time-to-event model of Hoyer et al. (2018) <doi:10.1002/jrsm.1273>, and the latent class
extensions of Liu et al. (2015) <doi:10.1111/biom.12264> for diagnostic studies without
a perfect reference standard. Provides subgroup analyses, HSROC meta-regression,
likelihood-ratio tests, summary ROC plots, and coupled forest plots.
Author: Claus Nowak [aut, cre]
Maintainer: Claus Nowak <claus.nowak@donau-uni.ac.at>
Diff between dtametaTMB versions 0.1.0 dated 2026-07-16 and 0.1.1 dated 2026-07-26
dtametaTMB-0.1.0/dtametaTMB/R/TMB.R |only dtametaTMB-0.1.0/dtametaTMB/R/getesti_V_g.R |only dtametaTMB-0.1.1/dtametaTMB/DESCRIPTION | 17 dtametaTMB-0.1.1/dtametaTMB/MD5 | 154 +- dtametaTMB-0.1.1/dtametaTMB/NAMESPACE | 33 dtametaTMB-0.1.1/dtametaTMB/R/LogLik.R | 72 dtametaTMB-0.1.1/dtametaTMB/R/as_revman.R | 265 +++ dtametaTMB-0.1.1/dtametaTMB/R/check2_data.R |only dtametaTMB-0.1.1/dtametaTMB/R/dtametaTMB.R | 7 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsma.R | 34 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaSubgroup.R | 52 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonis.R | 14 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisReg.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisSubgroup.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/forestCochrane.R | 13 dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneSubgroup.R | 46 dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/getWEIGHTSLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/pap.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotHoyerAFT.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsma.R | 22 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaSubgroup.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonis.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisSubgroup.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plot_SESPGRID.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/printHoyerAFT.R | 11 dtametaTMB-0.1.1/dtametaTMB/R/printReitsma.R | 20 dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaSubgroup.R | 18 dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonis.R | 14 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisReg.R | 9 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisSubgroup.R | 10 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/rename_hsrocsubLCA_rows.R |only dtametaTMB-0.1.1/dtametaTMB/R/rename_reitsubLCA_rows.R |only dtametaTMB-0.1.1/dtametaTMB/R/schuetz.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/summaryReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonis.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/tub.R |only dtametaTMB-0.1.1/dtametaTMB/README.md | 37 dtametaTMB-0.1.1/dtametaTMB/build/vignette.rds |binary dtametaTMB-0.1.1/dtametaTMB/data/pap.rda |only dtametaTMB-0.1.1/dtametaTMB/data/tub.rda |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.R |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.pdf |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.qmd |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.R | 38 dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.pdf |binary dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.qmd | 49 dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.R | 4 dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.pdf |binary dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.qmd | 121 - dtametaTMB-0.1.1/dtametaTMB/man/anova.dtametaTMB.Rd | 12 dtametaTMB-0.1.1/dtametaTMB/man/as_revman.dtametaTMB.Rd | 19 dtametaTMB-0.1.1/dtametaTMB/man/dtametaTMB.Rd | 15 dtametaTMB-0.1.1/dtametaTMB/man/fitReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisSubgroup.Rd | 2 dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/forest.CochraneLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/forest.CochraneSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/logLik.dtametaTMB.Rd | 12 dtametaTMB-0.1.1/dtametaTMB/man/pap.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/schuetz.Rd | 4 dtametaTMB-0.1.1/dtametaTMB/man/summary.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonis.Rd | 2 dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/tub.Rd |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/ReitsmaLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/ReitsmaSubgroupLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/RutterGatsonisLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/RutterGatsonisSubgroupLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/dtametaTMB_TMBExports.cpp | 12 dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-fitLCA.R |only dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-fitReitsmaSubgroup.R | 2 dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-plotLCA.R |only dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-plotReitsmaSubgroup.R |only dtametaTMB-0.1.1/dtametaTMB/vignettes/LCA.html |only dtametaTMB-0.1.1/dtametaTMB/vignettes/LCA.qmd |only dtametaTMB-0.1.1/dtametaTMB/vignettes/Meta-Regression.html | 767 ++++++---- dtametaTMB-0.1.1/dtametaTMB/vignettes/Meta-Regression.qmd | 49 dtametaTMB-0.1.1/dtametaTMB/vignettes/dtametaTMB.html | 439 ++--- dtametaTMB-0.1.1/dtametaTMB/vignettes/dtametaTMB.qmd | 121 - 108 files changed, 1653 insertions(+), 891 deletions(-)
Title: Demographic Analysis
Description: Tool for demographic modeling and analysis, combining stochastic
simulation-based projections with classic demographic methods. Provides
utilities for disaggregating population data using Karup-King interpolation,
fitting Brass relational logit models, calculating fertility and mortality
metrics, building complete and abridged life tables with model-based
separation factors, estimating child mortality indirectly from children
ever born and surviving (Brass-Trussell method), decomposing and
standardizing rates, and performing hierarchical subnational population
projections. Relational life table estimation and interpolation
methods are described in Brass (1975) "Methods for Estimating Fertility and
Mortality from Limited and Defective Data", Preston et al. (2001,
ISBN:978-0631226161) "Demography: Measuring and Modeling Population
Processes", Siegel and Swanson (2004, ISBN:978-0126419559) "The Methods and
Materials of Demography", and Raftery et al. (2012) "Bayesian probabilistic
populat [...truncated...]
Author: Edward Owusu Manu [aut, cre]
Maintainer: Edward Owusu Manu <edward.manu@statsghana.gov.gh>
Diff between DemogAnr versions 0.1.0 dated 2026-07-23 and 0.2.0 dated 2026-07-26
DESCRIPTION | 15 +- MD5 | 55 +++++++--- NAMESPACE | 46 ++++++++ NEWS.md | 78 +++++++++++---- R/CDR_ASDR.R | 16 ++- R/Dem-package.R | 5 R/Fertility.R | 17 +++ R/age_quality.R |only R/child_mortality_indirect.R |only R/data.R | 40 +++++++ R/globals.R | 8 + R/lifetables.R | 176 +++++++++++++++++++++++++--------- R/newPPP.R | 27 +++++ R/plots.R |only R/standardization.R |only data/ghmort2021.rda |only data/ghpop2021.rda |only man/DemogAnr-package.Rd | 2 man/age_ratio.Rd |only man/chm_brass.Rd |only man/decompose_LE.Rd |only man/decompose_rates.Rd |only man/dem.cdr.Rd | 5 man/dem.fert.Rd | 5 man/ghmort2021.Rd |only man/ghpop2021.Rd |only man/lifetable.Rd | 60 +++++++++-- man/myers.Rd |only man/project_population.Rd | 5 man/pyramid.Rd |only man/sex_ratio.Rd |only man/standardize.Rd |only man/un_age_sex_accuracy.Rd |only man/whipple.Rd |only tests/testthat/test-age-quality.R |only tests/testthat/test-chm-brass.R |only tests/testthat/test-lifetable-nax.R |only tests/testthat/test-plots.R |only tests/testthat/test-projections.R | 4 tests/testthat/test-standardization.R |only 40 files changed, 463 insertions(+), 101 deletions(-)
Title: Bayesian Generalized Linear Models (IID Samples)
Description: Provides Bayesian linear and generalized linear model fitting
with independent and identically distributed (iid) posterior samples. The
main functions mirror R's lm() and glm() interfaces while adding prior
family specifications for Gaussian, Poisson, binomial, and Gamma models
with log-concave likelihoods. Sampling for supported non-conjugate models
uses accept-reject methods based on likelihood subgradients as in Nygren
and Nygren (2006) <doi:10.1198/016214506000000357>. The package also
includes tools for prior setup, posterior summaries, prediction,
diagnostics, simulation, vignettes, and optional 'OpenCL' acceleration for
larger models.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between glmbayes versions 0.9.7 dated 2026-07-19 and 0.9.72 dated 2026-07-26
DESCRIPTION | 8 - MD5 | 90 ++++++++-------- NEWS.md | 15 ++ build/partial.rdb |binary configure.win | 9 - inst/doc/Chapter-01.html | 12 +- inst/doc/Chapter-02-S01.html | 4 inst/doc/Chapter-02-S02.html | 4 inst/doc/Chapter-02-S03.html | 4 inst/doc/Chapter-02-S04.html | 4 inst/doc/Chapter-02-S05.html | 4 inst/doc/Chapter-03.html | 4 inst/doc/Chapter-04.html | 4 inst/doc/Chapter-05.html | 164 +++++++++++++++--------------- inst/doc/Chapter-06.html | 168 +++++++++++++++---------------- inst/doc/Chapter-07.html | 4 inst/doc/Chapter-08.html | 50 ++++----- inst/doc/Chapter-09.html | 82 +++++++-------- inst/doc/Chapter-10.html | 82 +++++++-------- inst/doc/Chapter-11.html | 50 ++++----- inst/doc/Chapter-13.html | 12 +- inst/doc/Chapter-14.html | 34 +++--- inst/doc/Chapter-17.html | 18 +-- inst/doc/Chapter-18.html | 4 inst/doc/Chapter-A01.html | 22 ++-- inst/doc/Chapter-A02.html | 4 inst/doc/Chapter-A03.html | 120 +++++++++++----------- inst/doc/Chapter-A04.html | 4 inst/doc/Chapter-A05.html | 4 inst/doc/Chapter-A06.html | 4 inst/doc/Chapter-A07.html | 4 inst/doc/Chapter-A08.html | 4 inst/doc/Chapter-A09.html | 4 inst/doc/Chapter-A10.html | 4 inst/doc/Chapter-A11.html | 4 inst/doc/Chapter-A12.html | 4 inst/examples/Ex_Prior_Setup.R | 27 +++- inst/examples/Ex_pfamily.R | 15 ++ inst/examples/Ex_rGamma_reg.R | 6 - inst/examples/Ex_rNormalGamma_reg.R | 5 inst/examples/Ex_rNormal_reg.R | 18 ++- inst/examples/Ex_rindepNormalGamma_reg.R | 6 - man/Prior_Setup.Rd | 27 +++- man/pfamily.Rd | 15 ++ man/simfuncs.Rd | 35 ++++-- src/Makevars.win | 4 46 files changed, 633 insertions(+), 537 deletions(-)
Title: Genetic Tools for Colony Management
Description: Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical
Approach for Designing Breeding Groups to Maximize Genetic Diversity in a
Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatta')".
It provides a 'Shiny' application with an exposed API.
The application supports five groups of functions:
(1) Quality control of studbooks contained in text files or 'Excel'
workbooks and of pedigrees within 'LabKey' Electronic Health Records
(EHR);
(2) Creation of pedigrees from a list of animals using the 'LabKey' EHR
integration;
(3) Creation and display of an age by sex pyramid plot of the living
animals within the designated pedigree;
(4) Generation of genetic value analysis reports; and
(5) Creation of potential breeding groups with and without proscribed sex
ratios and defined maximum kinships.
Author: Michael Raboin [aut],
Terry Therneau [aut],
Amanda Vinson [aut, dtc],
R. Mark Sharp [aut, cre, cph, dtc] ,
Matthew Schultz [aut] ,
Southwest National Primate Research Center NIH grant P51 RR13986 [fnd],
Oregon National Primate Research Center grant P [...truncated...]
Maintainer: R. Mark Sharp <rmsharp@me.com>
This is a re-admission after prior archival of version 1.0.8 dated 2025-07-25
Diff between nprcgenekeepr versions 1.0.8 dated 2025-07-25 and 2.0.0 dated 2026-07-26
nprcgenekeepr-1.0.8/nprcgenekeepr/R/agePyramidPlot.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/fixGenotypeCols.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getLogo.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getMinParentAge.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getSimSires.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/makeGrpNum.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/nprcgenekeeper.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/_pkgdown.yml |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/application |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/software_design_doc.qmd |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/submission.txt |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/trulyUnknownParents.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/man/getLogo.Rd |only nprcgenekeepr-1.0.8/nprcgenekeepr/man/nprcgenekeepr.Rd |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_fixGenotypeCols.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_getLogo.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_getMinParentAge.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_makeGeneticDiversityDashboard.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/vignettes/manual_components/_bg_algorithm.Rmd |only nprcgenekeepr-1.0.8/nprcgenekeepr/vignettes/manual_components/_bg_formation.Rmd |only nprcgenekeepr-2.0.0/nprcgenekeepr/DESCRIPTION | 31 nprcgenekeepr-2.0.0/nprcgenekeepr/LICENSE | 2 nprcgenekeepr-2.0.0/nprcgenekeepr/MD5 | 1266 + nprcgenekeepr-2.0.0/nprcgenekeepr/NAMESPACE | 170 nprcgenekeepr-2.0.0/nprcgenekeepr/NEWS.md | 269 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addAnimalsWithNoRelative.R | 21 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addBackSecondParents.R | 11 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addErrTxt.R | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addGenotype.R | 27 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addGroupOfUnusedAnimals.R | 14 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addIdRecords.R | 20 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addKinshipValueCount.R | 15 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addParents.R | 10 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addSexAndAgeToGroup.R | 20 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addUIds.R | 23 nprcgenekeepr-2.0.0/nprcgenekeepr/R/allTrueNoNA.R | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/R/alleleFreq.R | 15 nprcgenekeepr-2.0.0/nprcgenekeepr/R/appServer.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/appUI.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/applyKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/applyKinshipOverridesToMatrix.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/assertRequiredColsPresent.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/assignAlleles.R | 13 nprcgenekeepr-2.0.0/nprcgenekeepr/R/autoIdFormat.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcA.R | 32 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcAge.R | 13 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcFE.R | 61 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcFEFG.R | 90 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nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSiteConfig.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_coverage.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_ggplots.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_kinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_parity.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_popovers.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_relationships.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_moduleContract.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_monolith_removed.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_muffleIncompleteFinalLine.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_normalizeGvReport.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscateDate.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscateId.R | 19 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscatePed.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_orderReport.R | 110 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_pkgdown_reference_config.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_prepareKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_print.summary.nprcgenekeeprErr.R | 5 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_print.summary.nprcgenekeeprGV.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_qcStudbook.R | 113 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rankSubjects.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_readKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeAutoGenIds.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeDuplicates.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeEarlyDates.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeUninformativeFounders.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeUnknownAnimals.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_reportGV.R | 712 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resetGroup.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resetPopulation.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resolveBreedingAge.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rhesusGenotypes.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rhesusPedigree.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_runModularApp_alias.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_runQcStudbook.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_saveDataframesAsFiles.R | 23 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_setExit.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_setLabKeyDefaults.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_sexCodes.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shinytest2_workflow_coverage.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shouldShowChangedColsTab.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shouldShowOripTab.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_species_first_class.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summarizeKinshipValues.R | 54 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summary.nprcgenekeeprErr.R | 11 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summary.nprcgenekeeprGV.R | 47 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_trimPedigree.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_vignettes_no_deprecated_minParentAge.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_withinIntegerRange.R | 5 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/a2interactive.Rmd | 34 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/gvaConvergence.Rmd |only nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_breeding_group_algorithm.Rmd | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_breeding_group_formation.Rmd | 98 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_genetic_value_analysis.Rmd | 105 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_genome_uniqueness_algorithm.Rmd | 7 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_gv_and_bg_desc.Rmd | 49 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_input.Rmd | 84 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_introduction.Rmd | 2 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_pedigree_browser.Rmd | 78 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_running_shiny_application.Rmd | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_summary_statistics.Rmd | 99 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/simulatedKValues.Rmd | 83 775 files changed, 15263 insertions(+), 10318 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.8.5 dated 2026-03-07 and 0.8.6 dated 2026-07-26
DESCRIPTION | 10 +++-- MD5 | 30 ++++++++-------- R/ExpandDH.R | 16 +++++--- R/Objs.R | 6 +++ R/SolComp3.R | 20 +++++++---- R/cmpChi.R | 14 ++++--- R/hSkew.R | 16 ++++---- R/nComp.R | 7 ++- R/nlr.R | 32 ++++++++++------- R/pComp.R | 15 ++++---- R/pProf.R | 2 - R/wnl5.R | 6 --- inst/NEWS.Rd | 101 +++++++++++++++++++++++++++++++------------------------- man/SolComp3.Rd | 2 - man/nlr.Rd | 4 +- man/wnl5.Rd | 4 +- 16 files changed, 163 insertions(+), 122 deletions(-)
Title: Power Analysis of Flexible ANOVA Designs and Related Tests
Description: Provides functions for conducting power analysis in ANOVA designs, including between-, within-, and mixed-factor designs, with full support for both main effects and interactions. The package allows calculation of statistical power, required total sample size, significance level, and minimal detectable effect sizes expressed as partial eta squared or Cohen's f for ANOVA terms and planned contrasts. In addition, complementary functions are included for common related tests such as t-tests and correlation tests, making the package a convenient toolkit for power analysis in experimental psychology and related fields.
Author: Hiroyuki Muto [aut, cre]
Maintainer: Hiroyuki Muto <mutopsy@omu.ac.jp>
Diff between pwranova versions 1.0.3 dated 2026-01-19 and 1.1.5 dated 2026-07-26
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 29 R/cohensf_to_peta2.r | 84 +- R/peta2_to_cohensf.r | 84 +- R/pwranova.r | 737 +++++++++++----------- R/pwrcontrast.r | 33 - R/pwrcortest.r | 70 +- R/pwrttest.r | 58 + README.md | 373 +++++++---- inst/CITATION | 27 man/pwranova.Rd | 12 man/pwrcontrast.Rd | 2 man/pwrcortest.Rd | 29 man/pwrttest.Rd | 31 tests/testthat/expected/expected_pwranova.csv | 53 + tests/testthat/expected/expected_pwrcortest.csv | 26 tests/testthat/expected/expected_pwrttest.csv | 24 tests/testthat/test-cohensf_to_peta2.r | 62 + tests/testthat/test-peta2_to_cohensf.r | 72 +- tests/testthat/test-pwranova.r | 511 +++++++-------- tests/testthat/test-pwrcortest.r | 107 +++ tests/testthat/test-pwrttest.r | 777 ++++++++++++------------ 23 files changed, 1863 insertions(+), 1388 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.25 dated 2026-03-02 and 1.1.26 dated 2026-07-26
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++------------- NEWS | 7 ++ R/autotyp.feature.R | 14 ++++- R/grambank.feature.R | 23 +++++---- R/uralex.feature.R | 13 ++++- R/wals.feature.R | 4 + inst/doc/lingtypology_creating_maps.html | 4 - inst/doc/lingtypology_db_API.html | 4 - inst/doc/lingtypology_dplyr.html | 4 - inst/doc/lingtypology_glottolog_functions.html | 4 - inst/doc/lingtypology_intro.html | 4 - man/abvd.Rd | 2 man/autotyp.Rd | 2 man/autotyp.feature.Rd | 4 + man/bantu.Rd | 2 man/circassian.Rd | 2 man/countries.Rd | 2 man/eurasianphonology.Rd | 2 man/glottolog.Rd | 2 man/grambank.feature.Rd | 6 +- man/iso_639.Rd | 2 man/oto_mangueanIC.Rd | 2 man/phoible.Rd | 2 man/phonological_profiles.Rd | 2 man/providers.Rd | 2 man/soundcomparisons.Rd | 2 man/uralex.Rd | 2 man/uralex.feature.Rd | 4 + man/wals.Rd | 2 man/wals.feature.Rd | 2 31 files changed, 113 insertions(+), 82 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Description: Computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used. This package also includes a graphical tool which outputs path diagrams, heatmaps, goodness-of-fit indices and model selection criteria for each regularization parameter (Yamamoto, M., Hirose, K. and Nagata, H., 2017 <doi:10.1007/s41237-016-0007-3>). The user can change the regularization parameter interactively with a built-in self-contained HTML viewer (no additional packages required), which is helpful to find a suitable value of regularization parameter. As a penalty, we can choose either the minimax concave penalty (Hirose, K. and Yamamoto, M., 2015 <doi:10.1007/s11222-014-9458-0>; Hirose, K. and Yamamoto, M., 2014 <doi:10.1016/j.csda.2014.05.011>) or the product-based elastic net penalty (Hirose, K. and Terada, Y., 2023 <doi:10.1007/s11336-022-09868-4>).
Author: Kei Hirose [aut, cre] ,
Michio Yamamoto [aut],
Haruhisa Nagata [aut]
Maintainer: Kei Hirose <mail@keihirose.com>
Diff between fanc versions 2.3.13 dated 2026-06-04 and 2.4.0 dated 2026-07-26
DESCRIPTION | 15 MD5 | 23 NAMESPACE | 36 - R/fanc.R | 32 R/out.fanc.R | 7 R/plot.fanc.R | 1818 ++++++++++++++++++++--------------------------------- R/select.fanc.R | 7 man/fanc.Rd | 346 ++++------ man/out.fanc.Rd | 31 man/plot.fanc.Rd | 73 +- man/select.fanc.Rd | 32 src/fanc.c | 6 tests |only 13 files changed, 1041 insertions(+), 1385 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-23 1.0.4
2025-03-10 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-10 1.3.2
2014-08-21 1.3.1
2014-01-15 1.3.0
2013-10-30 1.2.1
2013-10-14 1.2
2013-09-26 1.1
Title: Extrema-Weighted Feature Extraction
Description: Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in van den Boom et al. (2018) <doi:10.1093/bioinformatics/bty120>.
Author: Willem van den Boom [aut, cre]
Maintainer: Willem van den Boom <willem@wvdboom.nl>
Diff between xwf versions 0.2-3 dated 2020-02-20 and 0.2-4 dated 2026-07-26
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 12 ++++++------ R/xwfGridsearch.R | 2 +- man/XWFpValues.Rd | 16 +++++++++++++--- man/xwf.Rd | 19 +++++++++++++++---- man/xwfGridsearch.Rd | 20 +++++++++++++++----- 7 files changed, 56 insertions(+), 25 deletions(-)
Title: Interface to the 'MinIO' Client
Description: An R interface to the 'MinIO' Client. The 'MinIO' Client ('mc')
provides a modern alternative to UNIX commands like 'ls', 'cat', 'cp',
'mirror', 'diff', 'find' etc. It supports 'filesystems' and Amazon "S3"
compatible cloud storage service ("AWS" Signature v2 and v4).
This package provides convenience functions for installing the 'MinIO'
client and running any operations, as described in the official
documentation, <https://docs.min.io/aistor/reference/cli/>.
This package provides a flexible and high-performance alternative to 'aws.s3'.
Author: Carl Boettiger [aut, cre] ,
Markus Skyttner [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between minioclient versions 0.0.6 dated 2023-11-07 and 0.0.7 dated 2026-07-26
DESCRIPTION | 11 ++++++----- MD5 | 26 ++++++++++++++------------ NEWS.md | 14 ++++++++++++++ R/install_mc.R | 15 +++++++++++---- R/mc.R | 2 +- R/mc_sql.R | 13 +++++++++++-- README.md | 8 ++++---- man/install_mc.Rd | 2 +- man/mc.Rd | 2 +- man/mc_alias_set.Rd | 2 +- man/mc_sql.Rd | 2 +- tests/testthat/helper-s3-select.R |only tests/testthat/test-mc.R | 5 ++++- tests/testthat/test-mc_bin.R |only tests/testthat/test-s3-select.R | 17 +++++++++++------ 15 files changed, 80 insertions(+), 39 deletions(-)