Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dawid Kaledkowski [aut, cre],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.modules.general versions 0.5.0 dated 2025-08-20 and 0.5.1 dated 2025-10-22
DESCRIPTION | 12 MD5 | 188 - NAMESPACE | 67 NEWS.md | 720 ++-- R/teal.modules.general.R | 43 R/tm_a_pca.R | 2324 ++++++------- R/tm_a_regression.R | 2110 +++++------ R/tm_data_table.R | 698 +-- R/tm_file_viewer.R | 510 +- R/tm_front_page.R | 528 +- R/tm_g_association.R | 1160 +++--- R/tm_g_bivariate.R | 2240 ++++++------ R/tm_g_distribution.R | 2840 ++++++++-------- R/tm_g_response.R | 1254 +++---- R/tm_g_scatterplot.R | 2200 ++++++------ R/tm_g_scatterplotmatrix.R | 1220 +++--- R/tm_missing_data.R | 2836 +++++++-------- R/tm_outliers.R | 2746 +++++++-------- R/tm_t_crosstable.R | 1040 ++--- R/tm_variable_browser.R | 2536 +++++++------- R/utils.R | 752 ++-- build/vignette.rds |binary inst/WORDLIST | 31 inst/doc/decorate-module-output.R | 840 ++-- inst/doc/decorate-module-output.html | 1750 ++++----- inst/doc/teal-modules-general.R | 154 inst/doc/teal-modules-general.html | 998 ++--- inst/doc/using-association-plot.R | 544 +-- inst/doc/using-association-plot.html | 1320 +++---- inst/doc/using-bivariate-plot.R | 1182 +++--- inst/doc/using-bivariate-plot.html | 1958 +++++------ inst/doc/using-cross-table.R | 224 - inst/doc/using-cross-table.html | 992 ++--- inst/doc/using-data-table.R | 162 inst/doc/using-data-table.html | 934 ++--- inst/doc/using-outliers-module.R | 326 - inst/doc/using-outliers-module.html | 1100 +++--- inst/doc/using-regression-plots.R | 478 +- inst/doc/using-regression-plots.html | 1254 +++---- inst/doc/using-response-plot.R | 698 +-- inst/doc/using-response-plot.html | 1474 ++++---- inst/doc/using-scatterplot-matrix.R | 254 - inst/doc/using-scatterplot-matrix.html | 1032 ++--- inst/doc/using-scatterplot.R | 686 +-- inst/doc/using-scatterplot.html | 1462 ++++---- man/srv_decorate_teal_data.Rd | 72 man/tm_a_pca.Rd | 414 +- man/tm_a_regression.Rd | 492 +- man/tm_g_association.Rd | 418 +- man/tm_g_bivariate.Rd | 560 +-- man/tm_g_distribution.Rd | 396 +- man/tm_g_response.Rd | 472 +- man/tm_g_scatterplot.Rd | 660 +-- man/tm_g_scatterplotmatrix.Rd | 476 +- man/tm_missing_data.Rd | 350 - man/tm_outliers.Rd | 418 +- man/tm_t_crosstable.Rd | 448 +- tests/testthat/helper-TealAppDriver.R | 96 tests/testthat/test-examples.R | 360 +- tests/testthat/test-shinytest2-tm_a_pca.R | 526 +- tests/testthat/test-shinytest2-tm_a_regression.R | 368 +- tests/testthat/test-shinytest2-tm_data_table.R | 210 - tests/testthat/test-shinytest2-tm_file_viewer.R | 198 - tests/testthat/test-shinytest2-tm_front_page.R | 144 tests/testthat/test-shinytest2-tm_g_association.R | 228 - tests/testthat/test-shinytest2-tm_g_bivariate.R | 488 +- tests/testthat/test-shinytest2-tm_g_distribution.R | 254 - tests/testthat/test-shinytest2-tm_g_response.R | 228 - tests/testthat/test-shinytest2-tm_g_scatterplot.R | 414 +- tests/testthat/test-shinytest2-tm_g_scatterplotmatrix.R | 238 - tests/testthat/test-shinytest2-tm_misssing_data.R | 358 +- tests/testthat/test-shinytest2-tm_outliers.R | 642 +-- tests/testthat/test-shinytest2-tm_t_crosstable.R | 222 - tests/testthat/test-shinytest2-tm_variable_browser.R | 462 +- tests/testthat/test_bivariate_ggplot_call.R | 195 - 75 files changed, 29319 insertions(+), 29365 deletions(-)
More information about teal.modules.general at CRAN
Permanent link
Title: Modelling of Extreme Values
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes (Dombry, Engelke and Oesting, 2016, <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] ,
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut] ,
Raphael Huser [aut] ,
Scott D. Grimshaw [aut] ,
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 1.17 dated 2024-07-09 and 2.0 dated 2025-10-22
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Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
Diff between biodosetools versions 3.7 dated 2025-10-14 and 3.7.1 dated 2025-10-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/utils-md.R | 45 ++++++++++++++++++++++++--------------------- inst/doc/interlab.html | 12 ++++++------ 4 files changed, 36 insertions(+), 33 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for exploring and quantifying acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals (Araya-Salas et al 2016 <doi:10.1111/2041-210X.12624>).
Author: Marcelo Araya-Salas [aut, cre] ,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
This is a re-admission after prior archival of version 1.1.36 dated 2025-07-28
Diff between warbleR versions 1.1.36 dated 2025-07-28 and 1.1.37 dated 2025-10-22
DESCRIPTION | 6 MD5 | 60 +++--- NEWS.md | 8 R/acoustic_activity.R | 27 +- R/consolidate.R | 2 R/cross_correlation.R | 2 R/fix_wavs.R | 2 R/freq_ts.R | 4 R/query_xc.R | 313 --------------------------------- R/selection_table.R | 4 R/simulate_songs.R | 2 R/spectro_analysis.R | 2 R/warbleR-package.R | 2 R/xc_maps.R | 311 -------------------------------- README.md | 11 - build/vignette.rds |binary data/comp_matrix.rda |binary data/lbh_selec_table.rda |binary data/sim_coor_sing.rda |binary data/sth_annotations.rda |binary inst/doc/a_warbleR.html | 48 ++--- inst/doc/b_annotation_data_format.html | 92 ++++----- inst/doc/c_warbleR_workflow_02.html | 12 - man/acoustic_activity.Rd | 23 +- man/consolidate.Rd | 2 man/fix_wavs.Rd | 2 man/freq_ts.Rd | 4 man/map_xc.Rd | 17 - man/query_xc.Rd | 46 ---- man/simulate_songs.Rd | 2 man/warbleR.Rd | 2 31 files changed, 180 insertions(+), 826 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre],
Michael https://github.com/MichaelChirico [ctb],
R Core Team [cph]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.22 dated 2025-03-18 and 1.4.23 dated 2025-10-22
unitizer-1.4.22/unitizer/tests/not-cran.R |only unitizer-1.4.23/unitizer/DESCRIPTION | 8 ++++---- unitizer-1.4.23/unitizer/MD5 | 13 ++++++------- unitizer-1.4.23/unitizer/NEWS.md | 7 +++++++ unitizer-1.4.23/unitizer/R/demo.R | 1 + unitizer-1.4.23/unitizer/R/load.R | 6 ++++++ unitizer-1.4.23/unitizer/build/vignette.rds |binary unitizer-1.4.23/unitizer/tests/_helper/init.R | 3 +++ 8 files changed, 27 insertions(+), 11 deletions(-)
Title: Download and Analyze Crash Data
Description: Easily Download Analysis-Ready Crash Data from the U.S. National Highway Traffic Safety Administration.
Author: Steve Jackson [aut, cre]
Maintainer: Steve Jackson <steve.jackson@toxcel.com>
This is a re-admission after prior archival of version 2.0.1 dated 2025-10-02
Diff between rfars versions 2.0.1 dated 2025-10-02 and 2.0.2 dated 2025-10-22
DESCRIPTION | 12 MD5 | 62 R/counts.R | 11 R/get_fars.R | 17 R/get_gescrss.R | 17 R/sysdata.rda |only README.md | 5633 ++++++++++++++-- data/fars_codebook.rda |binary data/geo_relations.rda |binary data/gescrss_codebook.rda |binary inst/doc/Alcohol_Counts.R | 230 inst/doc/Alcohol_Counts.Rmd | 74 inst/doc/Alcohol_Counts.html | 41 inst/doc/Counts.R | 196 inst/doc/Counts.Rmd | 105 inst/doc/Counts.html |11483 ++++++++++++++++++++++++++++++++- inst/doc/Crash_sequence_of_events.R | 162 inst/doc/Crash_sequence_of_events.Rmd | 197 inst/doc/Crash_sequence_of_events.html | 358 - inst/doc/Searchable_Codebooks.R | 28 inst/doc/Searchable_Codebooks.Rmd | 49 inst/doc/Searchable_Codebooks.html | 5861 +++++++++------- man/get_fars.Rd | 9 man/get_gescrss.Rd | 9 tests |only vignettes/Alcohol_Counts.Rmd | 74 vignettes/Counts.Rmd | 105 vignettes/Crash_sequence_of_events.Rmd | 197 vignettes/Searchable_Codebooks.Rmd | 49 29 files changed, 21131 insertions(+), 3848 deletions(-)
Title: Abstractions for Promise-Based Asynchronous Programming
Description: Provides fundamental abstractions for doing asynchronous
programming in R using promises. Asynchronous programming is useful
for allowing a single R process to orchestrate multiple tasks in the
background while also attending to something else. Semantics are
similar to 'JavaScript' promises, but with a syntax that is idiomatic
R.
Author: Joe Cheng [aut],
Barret Schloerke [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between promises versions 1.3.3 dated 2025-05-29 and 1.4.0 dated 2025-10-22
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Title: Power Analysis for Differential Expression Studies
Description: Provides a convenient framework to simulate, test, power, and visualize
data for differential expression studies with lognormal or negative binomial
outcomes. Supported designs are two-sample comparisons of independent or
dependent outcomes. Power may be summarized in the context of controlling the
per-family error rate or family-wise error rate. Negative binomial methods are
described in Yu, Fernandez, and Brock (2017) <doi:10.1186/s12859-017-1648-2>
and Yu, Fernandez, and Brock (2020) <doi:10.1186/s12859-020-3541-7>.
Author: Brett Klamer [aut, cre] ,
Lianbo Yu [aut]
Maintainer: Brett Klamer <code@brettklamer.com>
Diff between depower versions 2025.1.20 dated 2025-01-23 and 2025.10.21 dated 2025-10-22
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Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox& [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.4.1 dated 2025-04-08 and 1.4.2 dated 2025-10-22
DESCRIPTION | 8 MD5 | 1011 +++++----- NAMESPACE | 336 +-- NEWS.md | 730 +++---- R/acsaf_box_mergetime.R | 856 ++++---- R/add_grid_info.R | 210 +- R/arith_wrapper.R | 446 ++-- R/arithc_wrapper.R | 248 +- R/box_mergetime.R | 796 ++++---- R/calc_allDatesNc.R | 76 R/calc_field.R | 74 R/calc_overlapping_time.R | 328 +-- R/calc_regres_coef_a.R | 30 R/calc_regres_coef_b.R | 30 R/calc_timestepNc.R | 250 +- R/calc_timx_result.R | 122 - R/calc_trend.R | 136 - R/calc_trend_advanced.R | 254 +- R/change_att.R | 226 +- R/check.coordinate.system.R | 80 R/check_constant.R | 10 R/check_dims.R | 58 R/check_format.R | 20 R/check_infile.R | 18 R/check_infiles.R | 24 R/check_nc_version.R | 26 R/check_outfile.R | 18 R/check_overwrite.R | 14 R/check_variable.R | 10 R/cmsaf.abs.R | 302 +-- R/cmsaf.add.R | 168 - R/cmsaf.addc.R | 134 - R/cmsaf.adjust.two.files.R | 514 ++--- R/cmsaf.cat.R | 482 ++--- R/cmsaf.detrend.R | 378 +-- R/cmsaf.div.R | 168 - R/cmsaf.divc.R | 134 - R/cmsaf.mk.test.R | 406 ++-- R/cmsaf.mul.R | 168 - R/cmsaf.mulc.R | 136 - R/cmsaf.regres.R | 352 +-- R/cmsaf.stats.R | 244 +- R/cmsaf.stats.station.data.R | 428 ++-- R/cmsaf.sub.R | 166 - R/cmsaf.sub.rel.R | 294 +-- R/cmsaf.subc.R | 136 - R/cmsaf.transform.coordinate.system.R | 220 +- R/cmsafops.R | 198 +- R/constants.R | 280 +- R/correct_filename.R | 20 R/dayavg.R | 132 - R/daymax.R | 124 - R/daymean.R | 132 - R/daymin.R | 124 - R/daypctl.R | 130 - R/dayrange.R | 364 +-- R/daysd.R | 124 - R/daysum.R | 122 - R/dayvar.R | 124 - R/dayx_wrapper.R | 302 +-- R/define_dims.R | 86 R/define_vars.R | 46 R/define_vars_mk.test.R | 62 R/define_vars_trend.R | 84 R/define_vars_trend_advanced.R | 102 - R/divdpm.R | 132 - R/extract.level.R | 402 ++-- R/extract.period.R | 526 ++--- R/fld_cor_covar_wrapper.R | 286 +- R/fldcor.R | 152 - R/fldcovar.R | 152 - R/fldmax.R | 126 - R/fldmean.R | 126 - R/fldmin.R | 126 - R/fldrange.R | 128 - R/fldsd.R | 126 - R/fldsum.R | 126 - R/fldx_wrapper.R | 210 +- R/getDateID.R | 28 R/getTimeRange.R | 78 R/get_basename.R | 68 R/get_climatology.R | 58 R/get_cor_data.R | 62 R/get_cor_data_fld.R | 32 R/get_date_time.R | 68 R/get_dimensions.R | 110 - R/get_nc_version.R | 34 R/get_processing_time_string.R | 40 R/get_time.R | 198 +- R/get_time_bnds_1.R | 14 R/get_time_bnds_from_file.R | 16 R/get_time_bnds_mul.R | 28 R/get_time_bounds.R | 26 R/get_time_bounds_doy.R | 26 R/get_time_bounds_hour.R | 26 R/get_time_bounds_month.R | 26 R/get_time_bounds_run.R | 18 R/get_time_bounds_timrange.R | 54 R/get_time_bounds_year.R | 26 R/get_time_info.R | 42 R/get_var_atts.R | 36 R/get_var_from_vars.R | 26 R/get_var_from_vars_all.R | 26 R/get_var_prec.R | 16 R/gridboxmax.R | 130 - R/gridboxmean.R | 130 - R/gridboxmin.R | 130 - R/gridboxrange.R | 130 - R/gridboxsd.R | 130 - R/gridboxsum.R | 130 - R/gridboxvar.R | 130 - R/gridboxx_wrapper.R | 558 ++--- R/hourmean.R | 128 - R/hoursum.R | 128 - R/hourx_wrapper.R | 236 +- R/is_leap_year.R | 6 R/is_url.R | 4 R/keep_sig_alongside.R |only R/levbox_mergetime.R | 186 - R/map_regular.R | 598 +++--- R/mermean.R | 126 - R/merx_wrapper.R | 218 +- R/mon.anomaly.R | 420 ++-- R/mon.anomaly.climatology.R | 357 +-- R/mon_num_above.R | 130 - R/mon_num_below.R | 130 - R/mon_num_equal.R | 130 - R/mon_num_wrapper.R | 276 +- R/monavg.R | 136 - R/mondaymean.R | 400 ++-- R/monmax.R | 124 - R/monmean.R | 136 - R/monmin.R | 124 - R/monpctl.R | 134 - R/monsd.R | 126 - R/monsum.R | 124 - R/monvar.R | 126 - R/monx_wrapper.R | 342 +-- R/muldpm.R | 130 - R/multimonmean.R | 342 +-- R/multimonsum.R | 364 +-- R/multiplelm.R | 34 R/ncinfo.R | 242 +- R/num_above.R | 134 - R/num_below.R | 134 - R/num_equal.R | 134 - R/num_wrapper.R | 182 - R/read_file.R | 163 - R/read_file_all.R | 144 - R/read_gridfile.R | 54 R/read_ncvar.R | 174 - R/redefine_grid_vars.R | 72 R/release_questions.R | 36 R/remap.R | 660 +++--- R/runmax.R | 132 - R/runmean.R | 126 - R/runmin.R | 130 - R/runrange.R | 126 - R/runsd.R | 132 - R/runsum.R | 132 - R/runx_wrapper.R | 310 +-- R/seas.anomaly.R | 464 ++-- R/seasmean.R | 128 - R/seassd.R | 128 - R/seassum.R | 128 - R/seasvar.R | 130 - R/seasx_wrapper.R | 322 +-- R/sellonlatbox.R | 446 ++-- R/selmon.R | 310 +-- R/selperiod.R | 356 +-- R/selpoint.R | 506 ++--- R/selpoint.multi.R | 800 ++++---- R/seltime.R | 310 +-- R/selyear.R | 314 +-- R/set_seasons.R | 54 R/simplelm.R | 46 R/simplelm2.R | 50 R/tim_cor_covar_wrapper.R | 356 +-- R/timavg.R | 138 - R/timcor.R | 152 - R/timcovar.R | 152 - R/timcumsum.R | 598 +++--- R/timmax.R | 124 - R/timmean.R | 126 - R/timmin.R | 124 - R/timpctl.R | 134 - R/timsd.R | 126 - R/timselmean.R | 124 - R/timselsum.R | 130 - R/timselx_wrapper.R | 238 +- R/timsum.R | 126 - R/timx_wrapper.R | 164 - R/trend.R | 296 +-- R/trend_advanced.R | 332 +-- R/wfldmean.R | 130 - R/write_output_file.R | 222 +- R/write_output_file_mk.test.R | 228 +- R/write_output_file_trend.R | 264 +- R/write_output_file_trend_advanced.R | 284 +- R/xdpm_wrapper.R | 244 +- R/ydaymax.R | 124 - R/ydaymean.R | 322 +-- R/ydaymin.R | 124 - R/ydayrange.R | 124 - R/ydaysd.R | 126 - R/ydaysum.R | 122 - R/ydayx_wrapper.R | 270 +- R/ydrunmean.R | 132 - R/ydrunsd.R | 132 - R/ydrunsum.R | 132 - R/ydrunx_wrapper.R | 98 - R/year.anomaly.R | 318 +-- R/yearmax.R | 126 - R/yearmean.R | 308 +-- R/yearmin.R | 124 - R/yearrange.R | 126 - R/yearsd.R | 126 - R/yearsum.R | 308 +-- R/yearvar.R | 124 - R/yearx_wrapper.R | 258 +- R/ymonmax.R | 126 - R/ymonmean.R | 126 - R/ymonmedian.R | 126 - R/ymonmin.R | 126 - R/ymonsd.R | 126 - R/ymonsum.R | 126 - R/ymonx_wrapper.R | 270 +- R/yseasmax.R | 126 - R/yseasmean.R | 132 - R/yseasmin.R | 126 - R/yseassd.R | 126 - R/yseasx_wrapper.R | 256 +- R/zonmean.R | 126 - R/zonsum.R | 126 - R/zonx_wrapper.R | 230 +- inst/WORDLIST | 363 +-- man/acsaf_box_mergetime.Rd | 118 - man/add_grid_info.Rd | 76 man/box_mergetime.Rd | 244 +- man/calc_allDatesNc.Rd | 32 man/calc_overlapping_time.Rd | 76 man/calc_timestepNc.Rd | 32 man/change_att.Rd | 178 - man/check.coordinate.system.Rd | 40 man/cmsaf.abs.Rd | 188 - man/cmsaf.add.Rd | 240 +- man/cmsaf.addc.Rd | 198 +- man/cmsaf.adjust.two.files.Rd | 112 - man/cmsaf.cat.Rd | 168 - man/cmsaf.detrend.Rd | 198 +- man/cmsaf.div.Rd | 240 +- man/cmsaf.divc.Rd | 198 +- man/cmsaf.mk.test.Rd | 208 +- man/cmsaf.mul.Rd | 240 +- man/cmsaf.mulc.Rd | 200 +- man/cmsaf.regres.Rd | 196 +- man/cmsaf.stats.Rd | 118 - man/cmsaf.stats.station.data.Rd | 96 - man/cmsaf.sub.Rd | 238 +- man/cmsaf.sub.rel.Rd | 110 - man/cmsaf.subc.Rd | 200 +- man/cmsaf.transform.coordinate.system.Rd | 74 man/dayavg.Rd | 206 +- man/daymax.Rd | 196 +- man/daymean.Rd | 206 +- man/daymin.Rd | 196 +- man/daypctl.Rd | 204 +- man/dayrange.Rd | 198 +- man/daysd.Rd | 196 +- man/daysum.Rd | 196 +- man/dayvar.Rd | 196 +- man/divdpm.Rd | 194 +- man/extract.level.Rd | 222 +- man/extract.period.Rd | 200 +- man/fldcor.Rd | 214 +- man/fldcovar.Rd | 214 +- man/fldmax.Rd | 180 - man/fldmean.Rd | 180 - man/fldmin.Rd | 180 - man/fldrange.Rd | 182 - man/fldsd.Rd | 180 - man/fldsum.Rd | 180 - man/get_basename.Rd | 66 man/get_date_time.Rd | 54 man/get_dimensions.Rd | 32 man/get_nc_version.Rd | 28 man/get_processing_time_string.Rd | 42 man/get_time.Rd | 52 man/get_time_info.Rd | 36 man/gridboxmax.Rd | 194 +- man/gridboxmean.Rd | 194 +- man/gridboxmin.Rd | 194 +- man/gridboxrange.Rd | 194 +- man/gridboxsd.Rd | 194 +- man/gridboxsum.Rd | 194 +- man/gridboxvar.Rd | 194 +- man/hourmean.Rd | 174 - man/hoursum.Rd | 174 - man/levbox_mergetime.Rd | 256 +- man/map_regular.Rd | 166 - man/mermean.Rd | 162 - man/mon.anomaly.Rd | 210 +- man/mon.anomaly.climatology.Rd | 81 man/mon_num_above.Rd | 216 +- man/mon_num_below.Rd | 216 +- man/mon_num_equal.Rd | 216 +- man/monavg.Rd | 220 +- man/mondaymean.Rd | 208 +- man/monmax.Rd | 208 +- man/monmean.Rd | 220 +- man/monmin.Rd | 208 +- man/monpctl.Rd | 220 +- man/monsd.Rd | 210 +- man/monsum.Rd | 208 +- man/monvar.Rd | 210 +- man/muldpm.Rd | 194 +- man/multimonmean.Rd | 222 +- man/multimonsum.Rd | 220 +- man/ncinfo.Rd | 126 - man/num_above.Rd | 206 +- man/num_below.Rd | 206 +- man/num_equal.Rd | 206 +- man/read_file.Rd | 39 man/read_ncvar.Rd | 128 - man/remap.Rd | 264 +- man/runmax.Rd | 194 +- man/runmean.Rd | 190 - man/runmin.Rd | 192 +- man/runrange.Rd | 190 - man/runsd.Rd | 194 +- man/runsum.Rd | 194 +- man/seas.anomaly.Rd | 184 - man/seasmean.Rd | 188 - man/seassd.Rd | 188 - man/seassum.Rd | 188 - man/seasvar.Rd | 188 - man/sellonlatbox.Rd | 212 +- man/selmon.Rd | 192 +- man/selperiod.Rd | 198 +- man/selpoint.Rd | 216 +- man/selpoint.multi.Rd | 254 +- man/seltime.Rd | 192 +- man/selyear.Rd | 194 +- man/timavg.Rd | 210 +- man/timcor.Rd | 214 +- man/timcovar.Rd | 214 +- man/timcumsum.Rd | 86 man/timmax.Rd | 196 +- man/timmean.Rd | 198 +- man/timmin.Rd | 196 +- man/timpctl.Rd | 208 +- man/timsd.Rd | 198 +- man/timselmean.Rd | 174 - man/timselsum.Rd | 178 - man/timsum.Rd | 198 +- man/trend.Rd | 238 +- man/trend_advanced.Rd | 258 +- man/wfldmean.Rd | 184 - man/ydaymax.Rd | 196 +- man/ydaymean.Rd | 198 +- man/ydaymin.Rd | 196 +- man/ydayrange.Rd | 196 +- man/ydaysd.Rd | 198 +- man/ydaysum.Rd | 196 +- man/ydrunmean.Rd | 194 +- man/ydrunsd.Rd | 194 +- man/ydrunsum.Rd | 194 +- man/year.anomaly.Rd | 182 - man/yearmax.Rd | 182 - man/yearmean.Rd | 182 - man/yearmin.Rd | 182 - man/yearrange.Rd | 182 - man/yearsd.Rd | 182 - man/yearsum.Rd | 182 - man/yearvar.Rd | 182 - man/ymonmax.Rd | 210 +- man/ymonmean.Rd | 210 +- man/ymonmedian.Rd | 210 +- man/ymonmin.Rd | 210 +- man/ymonsd.Rd | 210 +- man/ymonsum.Rd | 210 +- man/yseasmax.Rd | 186 - man/yseasmean.Rd | 192 +- man/yseasmin.Rd | 186 - man/yseassd.Rd | 186 - man/zonmean.Rd | 170 - man/zonsum.Rd | 170 - tests/spelling.R | 6 tests/testdata/SelpointRef_A.csv | 74 tests/testdata/SelpointRef_B.csv | 74 tests/testthat.R | 8 tests/testthat/create_testdata.R | 2964 +++++++++++++++---------------- tests/testthat/helper.R | 16 tests/testthat/test_add_grid_info.R | 1252 ++++++------- tests/testthat/test_box_mergetime.R | 2314 ++++++++++++------------ tests/testthat/test_change_att.R | 1384 +++++++------- tests/testthat/test_cmsaf.abs.R | 406 ++-- tests/testthat/test_cmsaf.add.R | 1934 ++++++++++---------- tests/testthat/test_cmsaf.addc.R | 1954 ++++++++++---------- tests/testthat/test_cmsaf.cat.R | 1562 ++++++++-------- tests/testthat/test_cmsaf.detrend.R | 394 ++-- tests/testthat/test_cmsaf.div.R | 1978 ++++++++++---------- tests/testthat/test_cmsaf.divc.R | 1808 +++++++++--------- tests/testthat/test_cmsaf.mul.R | 1944 ++++++++++---------- tests/testthat/test_cmsaf.mulc.R | 1946 ++++++++++---------- tests/testthat/test_cmsaf.regres.R | 378 +-- tests/testthat/test_cmsaf.sub.R | 1890 +++++++++---------- tests/testthat/test_cmsaf.subc.R | 1934 ++++++++++---------- tests/testthat/test_dayavg.R | 1376 +++++++------- tests/testthat/test_daymax.R | 1376 +++++++------- tests/testthat/test_daymean.R | 1376 +++++++------- tests/testthat/test_daymin.R | 1376 +++++++------- tests/testthat/test_daypctl.R | 1376 +++++++------- tests/testthat/test_dayrange.R | 1256 ++++++------- tests/testthat/test_daysd.R | 1376 +++++++------- tests/testthat/test_daysum.R | 1376 +++++++------- tests/testthat/test_dayvar.R | 1376 +++++++------- tests/testthat/test_divdpm.R | 1180 ++++++------ tests/testthat/test_extract.level.R | 1546 +++------------- tests/testthat/test_extract.period.R | 744 +++---- tests/testthat/test_fldcor.R | 168 - tests/testthat/test_fldcovar.R | 168 - tests/testthat/test_fldmax.R | 392 ++-- tests/testthat/test_fldmean.R | 390 ++-- tests/testthat/test_fldmin.R | 390 ++-- tests/testthat/test_fldrange.R | 392 ++-- tests/testthat/test_fldsd.R | 392 ++-- tests/testthat/test_fldsum.R | 392 ++-- tests/testthat/test_gridboxmax.R | 244 +- tests/testthat/test_gridboxmean.R | 244 +- tests/testthat/test_gridboxmin.R | 244 +- tests/testthat/test_gridboxrange.R | 244 +- tests/testthat/test_gridboxsd.R | 244 +- tests/testthat/test_gridboxsum.R | 244 +- tests/testthat/test_gridboxvar.R | 244 +- tests/testthat/test_levbox_mergetime.R | 192 +- tests/testthat/test_mermean.R | 184 - tests/testthat/test_mon.anomaly.R | 226 +- tests/testthat/test_monavg.R | 422 ++-- tests/testthat/test_monmax.R | 412 ++-- tests/testthat/test_monmean.R | 410 ++-- tests/testthat/test_monmin.R | 410 ++-- tests/testthat/test_monpctl.R | 428 ++-- tests/testthat/test_monsd.R | 416 ++-- tests/testthat/test_monsum.R | 414 ++-- tests/testthat/test_monvar.R | 428 ++-- tests/testthat/test_muldpm.R | 178 - tests/testthat/test_multimonmean.R | 178 - tests/testthat/test_multimonsum.R | 180 - tests/testthat/test_runmax.R | 188 - tests/testthat/test_runmean.R | 192 +- tests/testthat/test_runmin.R | 190 - tests/testthat/test_runrange.R | 172 - tests/testthat/test_runsd.R | 188 - tests/testthat/test_runsum.R | 190 - tests/testthat/test_seasmean.R | 178 - tests/testthat/test_seassd.R | 260 +- tests/testthat/test_seassum.R | 178 - tests/testthat/test_seasvar.R | 260 +- tests/testthat/test_sellonlatbox.R | 2264 +++++++++++------------ tests/testthat/test_selmon.R | 1834 +++++++++---------- tests/testthat/test_selperiod.R | 1832 +++++++++---------- tests/testthat/test_selpoint.R | 1728 +++++++++--------- tests/testthat/test_selpoint.multi.R | 144 - tests/testthat/test_seltime.R | 1518 +++++++-------- tests/testthat/test_selyear.R | 1832 +++++++++---------- tests/testthat/test_timavg.R | 1462 +++++++-------- tests/testthat/test_timcor.R | 234 +- tests/testthat/test_timcovar.R | 232 +- tests/testthat/test_timcumsum.R | 762 +++---- tests/testthat/test_timmax.R | 1612 ++++++++-------- tests/testthat/test_timmean.R | 1462 +++++++-------- tests/testthat/test_timmin.R | 1612 ++++++++-------- tests/testthat/test_timpctl.R | 1922 ++++++++++---------- tests/testthat/test_timsd.R | 1608 ++++++++-------- tests/testthat/test_timselmean.R | 192 +- tests/testthat/test_timselsum.R | 192 +- tests/testthat/test_timsum.R | 1460 +++++++-------- tests/testthat/test_wfldmean.R | 382 +-- tests/testthat/test_ydaymax.R | 534 ++--- tests/testthat/test_ydaymean.R | 508 ++--- tests/testthat/test_ydaymin.R | 534 ++--- tests/testthat/test_ydayrange.R | 466 ++-- tests/testthat/test_ydaysd.R | 466 ++-- tests/testthat/test_ydaysum.R | 534 ++--- tests/testthat/test_ydrunmean.R | 242 +- tests/testthat/test_ydrunsd.R | 246 +- tests/testthat/test_ydrunsum.R | 238 +- tests/testthat/test_year.anomaly.R | 386 ++-- tests/testthat/test_yearmax.R | 406 ++-- tests/testthat/test_yearmean.R | 388 ++-- tests/testthat/test_yearmin.R | 406 ++-- tests/testthat/test_yearrange.R | 406 ++-- tests/testthat/test_yearsd.R | 406 ++-- tests/testthat/test_yearsum.R | 396 ++-- tests/testthat/test_yearvar.R | 406 ++-- tests/testthat/test_ymonmax.R | 886 ++++----- tests/testthat/test_ymonmean.R | 408 ++-- tests/testthat/test_ymonmin.R | 408 ++-- tests/testthat/test_ymonsd.R | 414 ++-- tests/testthat/test_ymonsum.R | 408 ++-- tests/testthat/test_yseasmax.R | 404 ++-- tests/testthat/test_yseasmean.R | 404 ++-- tests/testthat/test_yseasmin.R | 404 ++-- tests/testthat/test_yseassd.R | 408 ++-- tests/testthat/test_zonmean.R | 176 - tests/testthat/test_zonsum.R | 176 - 507 files changed, 79228 insertions(+), 80102 deletions(-)
Title: Sparse Gaussian Graphical Modeling with Variable Clustering
Description: Perform sparse estimation of a Gaussian graphical model (GGM) with node aggregation through variable clustering. Currently, the package implements the clusterpath estimator of the Gaussian graphical model (CGGM) (Touw, Alfons, Groenen & Wilms, 2025; <doi:10.48550/arXiv.2407.00644>).
Author: Daniel J.W. Touw [aut] ,
Andreas Alfons [aut, cre] ,
Ines Wilms [aut] ,
Patrick J.F. Groenen [ths]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between clusterGGM versions 0.1.0 dated 2025-10-17 and 0.1.1 dated 2025-10-22
clusterGGM-0.1.0/clusterGGM/src/clock.h |only clusterGGM-0.1.1/clusterGGM/DESCRIPTION | 8 +- clusterGGM-0.1.1/clusterGGM/MD5 | 16 ++--- clusterGGM-0.1.1/clusterGGM/NEWS |only clusterGGM-0.1.1/clusterGGM/R/cggm.R | 3 - clusterGGM-0.1.1/clusterGGM/R/cggm_wrapper.R | 2 clusterGGM-0.1.1/clusterGGM/build/partial.rdb |binary clusterGGM-0.1.1/clusterGGM/man/cggm.Rd | 3 - clusterGGM-0.1.1/clusterGGM/src/cggm_export.cpp | 66 ------------------------ clusterGGM-0.1.1/clusterGGM/src/utils.cpp | 14 +++++ 10 files changed, 26 insertions(+), 86 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous and continuous response data using latent factor by both 1PL LSIRM and 2PL LSIRM as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>. It includes original 1PL LSIRM and 2PL LSIRM provided for binary response data and its extension for continuous response data. Bayesian model selection with spike-and-slab prior and method for dealing data with missing value under missing at random, missing completely at random are also supported. Various diagnostic plots are available to inspect the latent space and summary of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 1.3.8 dated 2025-10-14 and 1.3.9 dated 2025-10-22
DESCRIPTION | 8 MD5 | 162 ++++++------- R/RcppExports.R | 144 ++++++------ R/lsirm.R | 243 ++++++++++---------- R/lsirm1pl_fixed_gamma.R | 11 R/lsirm1pl_fixed_gamma_mar.R | 10 R/lsirm1pl_fixed_gamma_mcar.R | 11 R/lsirm1pl_mar.R | 9 R/lsirm1pl_mar_ss.R | 14 - R/lsirm1pl_mcar.R | 9 R/lsirm1pl_mcar_ss.R | 8 R/lsirm1pl_normal_fixed_gamma.R | 12 - R/lsirm1pl_normal_fixed_gamma_mar.R | 14 - R/lsirm1pl_normal_fixed_gamma_mcar.R | 14 - R/lsirm1pl_normal_mar.R | 16 - R/lsirm1pl_normal_mar_ss.R | 18 - R/lsirm1pl_normal_mcar.R | 17 - R/lsirm1pl_normal_mcar_ss.R | 18 - R/lsirm1pl_normal_o.R | 12 - R/lsirm1pl_normal_ss.R | 18 - R/lsirm1pl_o.R | 8 R/lsirm1pl_ss.R | 8 R/lsirm2pl_fixed_gamma.R | 12 - R/lsirm2pl_fixed_gamma_mar.R | 14 - R/lsirm2pl_fixed_gamma_mcar.R | 14 - R/lsirm2pl_mar.R | 14 - R/lsirm2pl_mar_ss.R | 18 - R/lsirm2pl_mcar.R | 14 - R/lsirm2pl_mcar_ss.R | 18 - R/lsirm2pl_normal_fixed_gamma.R | 14 - R/lsirm2pl_normal_fixed_gamma_mar.R | 16 - R/lsirm2pl_normal_fixed_gamma_mcar.R | 16 - R/lsirm2pl_normal_mar.R | 18 - R/lsirm2pl_normal_mar_ss.R | 18 - R/lsirm2pl_normal_mcar.R | 18 - R/lsirm2pl_normal_mcar_ss.R | 18 - R/lsirm2pl_normal_o.R | 12 - R/lsirm2pl_normal_ss.R | 14 - R/lsirm2pl_o.R | 313 +++++++++++++------------- R/lsirm2pl_ss.R | 16 - man/lsirm1pl.Rd | 6 man/lsirm1pl_fixed_gamma.Rd | 8 man/lsirm1pl_fixed_gamma_mar.Rd | 8 man/lsirm1pl_fixed_gamma_mcar.Rd | 8 man/lsirm1pl_mar.Rd | 8 man/lsirm1pl_mar_ss.Rd | 8 man/lsirm1pl_mcar.Rd | 8 man/lsirm1pl_mcar_ss.Rd | 8 man/lsirm1pl_normal_fixed_gamma.Rd | 8 man/lsirm1pl_normal_fixed_gamma_mar.Rd | 8 man/lsirm1pl_normal_fixed_gamma_mcar.Rd | 8 man/lsirm1pl_normal_mar.Rd | 8 man/lsirm1pl_normal_mar_ss.Rd | 8 man/lsirm1pl_normal_mcar.Rd | 8 man/lsirm1pl_normal_mcar_ss.Rd | 8 man/lsirm1pl_normal_o.Rd | 8 man/lsirm1pl_normal_ss.Rd | 8 man/lsirm1pl_o.Rd | 8 man/lsirm1pl_ss.Rd | 8 man/lsirm2pl.Rd | 9 man/lsirm2pl_fixed_gamma.Rd | 11 man/lsirm2pl_fixed_gamma_mar.Rd | 11 man/lsirm2pl_fixed_gamma_mcar.Rd | 11 man/lsirm2pl_mar.Rd | 11 man/lsirm2pl_mar_ss.Rd | 11 man/lsirm2pl_mcar.Rd | 11 man/lsirm2pl_mcar_ss.Rd | 11 man/lsirm2pl_normal_fixed_gamma.Rd | 11 man/lsirm2pl_normal_fixed_gamma_mar.Rd | 11 man/lsirm2pl_normal_fixed_gamma_mcar.Rd | 11 man/lsirm2pl_normal_mar.Rd | 11 man/lsirm2pl_normal_mar_ss.Rd | 11 man/lsirm2pl_normal_mcar.Rd | 11 man/lsirm2pl_normal_mcar_ss.Rd | 11 man/lsirm2pl_normal_o.Rd | 11 man/lsirm2pl_normal_ss.Rd | 11 man/lsirm2pl_o.Rd | 11 man/lsirm2pl_ss.Rd | 11 src/RcppExports.cpp | 378 +++++++++++++++++++------------- src/lsirm1pl.cpp | 256 ++++++++++++--------- src/lsirm2pl.cpp | 334 +++++++++++++++------------- src/utility_cpp.cpp | 93 ++++--- 82 files changed, 1623 insertions(+), 1156 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp [aut, cre]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.13.1 dated 2025-06-02 and 0.13.2 dated 2025-10-22
DESCRIPTION | 7 MD5 | 512 ++-- NAMESPACE | 400 +-- NEWS | 382 +-- R/00_codeOrganization.R | 44 R/00_steps_to_implement_distribution.R | 20 R/00_steps_to_implement_estimator.R | 18 R/00_steps_to_implement_model.R | 30 R/01_classes.R | 444 ++-- R/02_algebrahelpers_Solve.R | 122 - R/02_algebrahelpers_blockToeplitz.R | 40 R/02_algebrahelpers_checkJacobian.R | 250 +- R/02_algebrahelpers_expected_latent_residual_covs.R | 124 - R/02_algebrahelpers_expectedmodel.R | 48 R/02_algebrahelpers_kronecker.R | 2 R/02_algebrahelpers_lavUtils.R | 48 R/02_algebrahelpers_matrixexponent.R | 20 R/02_algebrahelpers_maxcor.R | 22 R/02_algebrahelpers_modelMatrix.R | 26 R/02_algebrahelpers_quantiletransform.R | 20 R/02_algebrahelpers_spectralshift.R | 50 R/02_algebrahelpers_trysolve.R | 52 R/02_algebrahelpers_vectorize.R | 56 R/02_algebrahelpers_vectorizeMatrices.R | 116 - R/02_algebrahelpers_weighted_geomean.R | 2 R/02_modelformation_PCCPDC.R | 32 R/03_modelformation_adjust_p_values.R | 116 - R/03_modelformation_defaultoptimizer.R | 6 R/03_modelformation_factorstart.R | 40 R/03_modelformation_fixAdj.R | 162 - R/03_modelformation_fixMatrix.R | 160 - R/03_modelformation_fixMu.R | 82 R/03_modelformation_fixTau.R | 170 - R/03_modelformation_formModelMatrices.R | 152 - R/03_modelformation_generateParameterTable.R | 540 ++-- R/03_modelformation_impliedcovstructures.R | 272 +- R/03_modelformation_labtoind.R | 56 R/03_modelformation_matrixSetup_Isingbeta.R | 65 R/03_modelformation_matrixSetup_Isingtau.R | 54 R/03_modelformation_matrixSetup_SD.R | 102 R/03_modelformation_matrixSetup_beta.R | 76 R/03_modelformation_matrixSetup_cholesky.R | 126 - R/03_modelformation_matrixSetup_delta.R | 124 - R/03_modelformation_matrixSetup_isingomega.R | 64 R/03_modelformation_matrixSetup_kappa.R | 134 - R/03_modelformation_matrixSetup_lambda.R | 452 ++-- R/03_modelformation_matrixSetup_mu.R | 68 R/03_modelformation_matrixSetup_omega.R | 200 - R/03_modelformation_matrixSetup_rho.R | 104 R/03_modelformation_matrixSetup_sigma.R | 130 - R/03_modelformation_matrixSetup_tau.R | 74 R/03_modelformation_missingpatterns.R | 314 +- R/03_modelformation_missingpatterns_covs.R | 174 - R/03_modelformation_samplestats.R | 16 R/03_modelformation_samplestats_norawts.R | 1304 ++++++------ R/03_modelformation_samplestats_rawts.R | 192 - R/03_modelformation_sparseordense.R | 90 R/03_modelformation_startvaluesandbounds.R | 104 R/03_modelformation_tsData.R | 344 +-- R/04_generalFit_fitfunction.R | 88 R/04_generalFit_gradient.R | 258 +- R/04_generalFit_logLikelihood.R | 36 R/04_generalfit_FisherInformation.R | 468 ++-- R/04_generalfit_VCOV.R | 28 R/04_generalfit_impliedModel.R | 80 R/04_generalfit_loglikelihood_Ising.R | 176 - R/04_generalfit_loglikelihood_gauss.R | 232 +- R/04_generalfit_prepareModel.R | 154 - R/04_modelformation_matrixSetup_flexcov.R | 138 - R/05_MLestimator_expected_hessian_Gauss.R | 126 - R/05_MLestimator_expected_hessian_Ising.R | 178 - R/05_MLestimator_fit_Gauss.R | 36 R/05_MLestimator_fit_Ising.R | 76 R/05_MLestimator_fitfunction.R | 22 R/05_MLestimator_gradient_Gauss.R | 146 - R/05_MLestimator_gradient_Ising.R | 164 - R/06_ULS_expectedHessian.R | 64 R/06_ULS_fitfunction.R | 154 - R/06_ULS_gradient.R | 124 - R/06_weightsMatrix.R | 76 R/07_FIMLestimator_expected_hessian_Gauss.R | 302 +- R/07_FIMLestimator_fit_Gauss.R | 194 - R/07_FIMLestimator_fitfunction.R | 20 R/07_FIMLestimator_gradient_Gauss.R | 302 +- R/08_outputHelpers_NAtoFALSE.R | 4 R/08_outputHelpers_NAtoTRUE.R | 4 R/08_outputHelpers_goodNum.R | 92 R/08_outputHelpers_logo.R | 72 R/09_modelmodification_clearpars.R | 40 R/09_modelmodifivation_emergencystart.R | 166 - R/14_varcov_derivatives.R | 434 ++-- R/14_varcov_implied.R | 92 R/14_varcov_prepare.R | 136 - R/15_lvm_derivatives.R | 428 +-- R/15_lvm_identify.R | 436 ++-- R/15_lvm_implied.R | 122 - R/15_lvm_prepare.R | 122 - R/16_var1_derivatives.R | 362 +-- R/16_var1_implied.R | 150 - R/16_var1_prepare.R | 188 - R/18_dlvm1_derivatives.R | 814 +++---- R/18_dlvm1_identify.R | 518 ++-- R/18_dlvm1_implied.R | 258 +- R/18_dlvm1_prepare.R | 116 - R/19_tsdlvm1_derivatives.R | 424 +-- R/19_tsdlvm1_identify.R | 396 +-- R/19_tsdlvm1_implied.R | 218 +- R/19_tsdlvm1_prepare.R | 116 - R/20_meta_varcov_derivatives.R | 584 ++--- R/20_meta_varcov_implied.R | 148 - R/20_meta_varcov_prepare.R | 98 R/21_Ising_derivatives.R | 57 R/21_Ising_helperfunctions.R | 32 R/21_Ising_identify.R | 146 - R/21_Ising_implied.R | 33 R/21_Ising_prepare.R | 128 - R/22_ml_lvm_derivatives.R | 424 +-- R/22_ml_lvm_identify.R | 576 ++--- R/22_ml_lvm_implied.R | 258 +- R/22_ml_lvm_prepare.R | 116 - R/RcppExports.R | 1342 ++++++------ R/a_models_Ising.R | 478 ++-- R/a_models_bifactor.R | 90 R/a_models_cholesky.R | 18 R/a_models_corr.R | 18 R/a_models_dlvm1.R | 2166 ++++++++++---------- R/a_models_frombootnet.R | 78 R/a_models_ggm.R | 18 R/a_models_gvar.R | 8 R/a_models_joingroups.R | 244 +- R/a_models_latentgrowth.R | 198 - R/a_models_lnm.R | 6 R/a_models_lrnm.R | 6 R/a_models_lvm.R | 858 +++---- R/a_models_meta_ggm.R | 4 R/a_models_meta_varcov.R | 1310 ++++++------ R/a_models_ml_lnm.R | 4 R/a_models_ml_lrnm.R | 4 R/a_models_ml_lvm.R | 1196 +++++------ R/a_models_ml_rnm.R | 4 R/a_models_ml_tsdlvm1.R | 356 +-- R/a_models_ml_tslvgvar.R | 44 R/a_models_panelgvar.R | 154 - R/a_models_precision.R | 18 R/a_models_ri_clpm.R | 450 ++-- R/a_models_rnm.R | 6 R/a_models_sem.R | 6 R/a_models_tsdlvm1.R | 826 +++---- R/a_models_tslvgvar.R | 6 R/a_models_var1.R | 642 ++--- R/a_models_varcov.R | 812 +++---- R/b_modelexpansions_addMIs.R | 450 ++-- R/b_modelexpansions_addSEs.R | 206 - R/b_modelexpansions_addfit.R | 560 ++--- R/b_modelexpansions_identify.R | 70 R/b_modelexpansions_updateModel.R | 32 R/c_runmodel.R | 1732 +++++++-------- R/d_stepup.R | 890 ++++---- R/e_modelmodifications_fixpar.R | 218 +- R/e_modelmodifications_fixstart.R | 72 R/e_modelmodifications_freepar.R | 264 +- R/e_modelmodifications_groupequal.R | 266 +- R/e_modelmodifications_groupfree.R | 252 +- R/e_modelmodifications_intersectionmodel.R | 414 +-- R/e_modelmodifications_partialprune.R | 708 +++--- R/e_modelmodifications_prune.R | 634 ++--- R/e_modelmodifications_ri_clpm_stationarity.R | 214 - R/e_modelmodifications_setequal.R | 110 - R/e_modelmodifications_transmod.R | 574 ++--- R/e_modelmodifications_unionmodel.R | 404 +-- R/f_conveneince_changedata.R | 168 - R/f_conveneince_fake_optimr.R | 60 R/f_conveneince_generate.R | 66 R/f_conveneince_setEstimator.R | 6 R/f_conveneince_setoptimizer.R | 56 R/f_conveneince_setverbose.R | 8 R/f_conveneince_usecpp.R | 22 R/f_convenience_CIplot.R | 878 ++++---- R/f_convenience_MIs.R | 268 +- R/f_convenience_aggregate_bootstraps.R | 414 +-- R/f_convenience_bootstrap.R | 174 - R/f_convenience_bootstrap_SEs.R | 12 R/f_convenience_bootstrap_warning.R | 4 R/f_convenience_covML.R | 24 R/f_convenience_ergodicity.R | 450 ++-- R/f_convenience_factorscores.R | 164 - R/f_convenience_fit.R | 98 R/f_convenience_getmatrix.R | 298 +- R/f_convenience_logbook.R | 84 R/f_convenience_parameters.R | 346 +-- R/f_convenience_printMethod.R | 236 +- R/f_convenience_printMethod_bootstrap.R | 180 - R/f_convenience_residuals.R | 64 R/f_convenience_simplestructure.R | 22 R/g_simulations_replicator.R | 154 - R/h_modelsearch.R | 878 ++++---- build/partial.rdb |binary man/CIplot.Rd | 232 +- man/Ising.Rd | 366 +-- man/Jonas.Rd | 64 man/MIs.Rd | 134 - man/StarWars.Rd | 76 man/aggregate_bootstraps.Rd | 64 man/algebraMatrices.Rd | 86 man/bifactor.Rd | 72 man/bootstrap.Rd | 78 man/changedata.Rd | 82 man/convenience.Rd | 116 - man/covML.Rd | 94 man/diagnostics.Rd | 106 man/dlvm1_family.Rd | 482 ++-- man/emergencystart.Rd | 54 man/esa.Rd | 140 - man/factorscores.Rd | 56 man/fit.Rd | 96 man/fixpar_freepar.Rd | 126 - man/fixstart.Rd | 68 man/generate.Rd | 54 man/getVCOV.Rd | 56 man/getmatrix.Rd | 134 - man/groupequal_groupfree.Rd | 108 man/latentgrowth.Rd | 146 - man/logbook.Rd | 52 man/lvm_family.Rd | 1102 +++++----- man/meta_varcov.Rd | 268 +- man/ml_lvm.Rd | 396 +-- man/ml_tsdlvm1.Rd | 124 - man/modelsearch.Rd | 182 - man/modelupdate.Rd | 102 man/parameters.Rd | 96 man/parequal.Rd | 80 man/partialprune.Rd | 190 - man/prune.Rd | 182 - man/psychonetrics-class.Rd | 128 - man/psychonetrics-package.Rd | 50 man/psychonetrics_bootstrap-class.Rd | 88 man/psychonetrics_log-class.Rd | 68 man/ri_clpm.Rd | 128 - man/runmodel.Rd | 186 - man/setverbose.Rd | 52 man/simplestructure.Rd | 44 man/stepup.Rd | 204 - man/transmod.Rd | 158 - man/tsdlvm1_family.Rd | 426 +-- man/unionmodel_intersectionmodel.Rd | 94 man/var1_family.Rd | 478 ++-- man/varcov_family.Rd | 478 ++-- src/02_algebrahelpers_RcppHelpers.cpp | 4 src/05_MLestimator_gradient_Ising_cpp.cpp | 2 src/06_ULS_fitfunction_cpp.cpp | 2 src/06_ULS_gradient_cpp.cpp | 2 src/06_WLS_Wmat.cpp | 6 src/14_varcov_derivatives_cpp.cpp | 6 src/21_Ising_derivatives.cpp | 13 src/21_Ising_expectedHessian.cpp | 2 src/21_Ising_implied_cpp.cpp | 43 src/21_Ising_prepare_cpp.cpp | 5 257 files changed, 27068 insertions(+), 26941 deletions(-)
Title: Describe, Package, and Share Biodiversity Data
Description: The Darwin Core data standard is widely used to share
biodiversity information, most notably by the Global Biodiversity Information
Facility and its partner nodes; but converting data to this standard can be
tricky. 'galaxias' is functionally similar to 'devtools', but with a focus on
building Darwin Core Archives rather than R packages, enabling data to be
shared and re-used with relative ease. For details see
Wieczorek and colleagues (2012) <doi:10.1371/journal.pone.0029715>.
Author: Martin Westgate [aut, cre],
Shandiya Balasubramaniam [aut],
Dax Kellie [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galaxias versions 0.1.0 dated 2025-07-07 and 0.1.1 dated 2025-10-22
DESCRIPTION | 6 MD5 | 24 +-- NEWS.md | 7 R/build_archive.R | 3 R/use_data.R | 6 build/vignette.rds |binary inst/doc/events-example.R | 4 inst/doc/events-example.html | 8 - inst/doc/occurrences-example.R | 4 inst/doc/occurrences-example.html | 255 +++++++++++++++++------------------- inst/doc/quick_start_guide.R | 82 +++++------ tests/testthat/test-build_archive.R | 6 tests/testthat/test-use_data.R | 20 ++ 13 files changed, 229 insertions(+), 196 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.2 dated 2025-07-02 and 7.3 dated 2025-10-22
DESCRIPTION | 12 +++++----- MD5 | 54 ++++++++++++++++++++++----------------------- R/cardio.mle.R | 23 ++++++++++++------- R/group.gof.R | 1 R/kuiper.R | 1 R/tang.conc.R | 1 R/watson.R | 1 man/Directional-package.Rd | 8 +++++- man/bic.mixvmf.Rd | 3 +- man/dirda.Rd | 3 +- man/dirda.cv.Rd | 4 +-- man/dmixvmf.Rd | 3 +- man/dsespc.Rd | 2 - man/dvm.Rd | 6 ++--- man/iag.reg.Rd | 7 ++--- man/mixvmf.mle.Rd | 3 +- man/pc.test.Rd | 6 ++--- man/rmixvmf.Rd | 3 +- man/rsespc.Rd | 6 +++-- man/score.cipc.Rd | 4 ++- man/sespc.mle.Rd | 4 ++- man/sespc.reg.Rd | 6 +++-- man/spcauchy2test.Rd | 3 +- man/spher.sespc.contour.Rd | 4 ++- man/spml.mle.Rd | 7 +++-- man/vmf.contour.Rd | 3 +- man/vmf.mle.Rd | 9 ++++--- man/vmfreg.Rd | 3 +- 28 files changed, 112 insertions(+), 78 deletions(-)
Title: Harness ArcGIS Data Services
Description: Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or
'ArcGIS Platform' to read, write, publish, or manage vector and raster
data via ArcGIS location services REST API endpoints
<https://developers.arcgis.com/rest/>.
Author: Josiah Parry [aut, cre] ,
Eli Pousson [ctb] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Antony Barja [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgislayers versions 0.5.0 dated 2025-09-19 and 0.5.1 dated 2025-10-22
arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-16-1.png |only arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-4-1.png |only arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-7-1.png |only arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-8-1.png |only arcgislayers-0.5.1/arcgislayers/DESCRIPTION | 6 arcgislayers-0.5.1/arcgislayers/MD5 | 52 - arcgislayers-0.5.1/arcgislayers/NEWS.md | 8 arcgislayers-0.5.1/arcgislayers/R/arc-add-delete.R | 2 arcgislayers-0.5.1/arcgislayers/R/arc-read.R | 72 + arcgislayers-0.5.1/arcgislayers/R/import-standalone-obj-type.R | 46 - arcgislayers-0.5.1/arcgislayers/R/import-standalone-types-check.R | 281 +++--- arcgislayers-0.5.1/arcgislayers/man/encode_field_values.Rd | 7 arcgislayers-0.5.1/arcgislayers/man/modify.Rd | 2 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-arc-select-respect-crs.R | 1 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-arc_raster.R | 1 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-arc_select.R | 9 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-attachments.R | 23 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-date-parsing.R | 1 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-encode-field-values.R | 445 ---------- arcgislayers-0.5.1/arcgislayers/tests/testthat/test-get-layer.R | 61 + arcgislayers-0.5.1/arcgislayers/tests/testthat/test-get-layers.R | 60 + arcgislayers-0.5.1/arcgislayers/tests/testthat/test-map-services.R | 5 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-page-size.R | 2 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-pbf.R | 6 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-raster-fns.R | 4 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-return-geometry.R | 4 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-returned-fields.R | 27 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-unset-token.R | 1 arcgislayers-0.5.1/arcgislayers/tests/testthat/test-update-fields.R | 8 29 files changed, 462 insertions(+), 672 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.2.5 dated 2025-09-05 and 0.2.6 dated 2025-10-22
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + R/scidca.coxph.R | 1 + R/scidca.scisvycoxph.R |only man/scidca.scisvycoxph.Rd |only 6 files changed, 10 insertions(+), 6 deletions(-)
Title: Generate Predicted Writing Quality Scores
Description: Imports variables from 'ReaderBench' (Dascalu et al.,
2018)<doi:10.1007/978-3-319-66610-5_48>, 'Coh-Metrix' (McNamara et
al., 2014)<doi:10.1017/CBO9780511894664>, and/or 'GAMET' (Crossley et
al., 2019) <doi:10.17239/jowr-2019.11.02.01> output files; downloads
predictive scoring models described in Mercer & Cannon
(2022)<doi:10.31244/jero.2022.01.03> and Mercer et
al.(2021)<doi:10.1177/0829573520987753>; and generates predicted
writing quality and curriculum-based measurement (McMaster & Espin,
2007)<doi:10.1177/00224669070410020301> scores.
Author: Sterett H. Mercer [aut, cre]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Diff between writeAlizer versions 1.6.4 dated 2025-09-30 and 1.7.0 dated 2025-10-21
writeAlizer-1.6.4/writeAlizer/R/internal_example_helpers.R |only writeAlizer-1.6.4/writeAlizer/R/writeAlizer-package.R |only writeAlizer-1.6.4/writeAlizer/build/partial.rdb |only writeAlizer-1.6.4/writeAlizer/man/dot-wa_rb_keep_exclude_from_sample.Rd |only writeAlizer-1.6.4/writeAlizer/man/writeAlizer.Rd |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-ensure-file.R |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-loaders.R |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-more.R |only writeAlizer-1.7.0/writeAlizer/DESCRIPTION | 18 writeAlizer-1.7.0/writeAlizer/LICENSE |only writeAlizer-1.7.0/writeAlizer/MD5 | 88 +- writeAlizer-1.7.0/writeAlizer/NAMESPACE | 5 writeAlizer-1.7.0/writeAlizer/NEWS.md | 72 + writeAlizer-1.7.0/writeAlizer/R/artifact_registry.R | 388 ++++++---- writeAlizer-1.7.0/writeAlizer/R/cache.R | 2 writeAlizer-1.7.0/writeAlizer/R/download.R | 40 - writeAlizer-1.7.0/writeAlizer/R/file_utilities.R | 137 ++- writeAlizer-1.7.0/writeAlizer/R/model_deps.R | 23 writeAlizer-1.7.0/writeAlizer/R/predict_values.R | 118 ++- writeAlizer-1.7.0/writeAlizer/R/seed_example_helpers.R |only writeAlizer-1.7.0/writeAlizer/R/writeAlizer.R | 73 - writeAlizer-1.7.0/writeAlizer/README.md | 49 - writeAlizer-1.7.0/writeAlizer/build/vignette.rds |only writeAlizer-1.7.0/writeAlizer/inst/CITATION | 45 - writeAlizer-1.7.0/writeAlizer/inst/doc |only writeAlizer-1.7.0/writeAlizer/man/wa_cache_dir.Rd | 2 writeAlizer-1.7.0/writeAlizer/man/wa_download.Rd | 26 writeAlizer-1.7.0/writeAlizer/man/wa_seed_example_models.Rd | 83 +- writeAlizer-1.7.0/writeAlizer/man/writeAlizer-package.Rd | 57 + writeAlizer-1.7.0/writeAlizer/tests/testthat/_snaps |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-network.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-quiet.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-sample-paths.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-urls.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/setup-cache.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/setup-reset-options.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-downloads.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-paths.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-registry.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry.R | 286 ++++++- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-cache-checksum.R | 55 - writeAlizer-1.7.0/writeAlizer/tests/testthat/test-download-snapshots.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-download.R | 73 + writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities-branches.R | 82 +- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities-files.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities.R | 50 - writeAlizer-1.7.0/writeAlizer/tests/testthat/test-helper-urls.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-import-rb-namebased.R | 25 writeAlizer-1.7.0/writeAlizer/tests/testthat/test-import-validation.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-integration-predict_quality.R | 197 +++-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-model-deps.R | 125 +-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-predict-values-input.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-predict-values-negative.R | 71 + writeAlizer-1.7.0/writeAlizer/tests/testthat/test-preprocess-and-download.R | 123 +-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-smoke-basic.R | 4 writeAlizer-1.7.0/writeAlizer/tests/testthat/test-smoke-rb_mod3all-mocked.R | 58 - writeAlizer-1.7.0/writeAlizer/vignettes |only 57 files changed, 1665 insertions(+), 710 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.1.2 dated 2025-10-21 and 5.1.3 dated 2025-10-21
ChangeLog | 2 +- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/ARIMAmodel.h | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph] ,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Arsene Druel [aut] ,
Julien Ruffault [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Francois Pimont [ctb] ,
Herve Cochar [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.8.3 dated 2025-08-27 and 4.8.4 dated 2025-10-21
DESCRIPTION | 10 +- MD5 | 68 ++++++++-------- NAMESPACE | 3 R/RcppExports.R | 4 R/defaultControl.R | 9 -- R/extract.R | 33 +++++--- R/plot.spwb.R | 24 +++++ R/plot_internals.R | 83 ++++++++++++++------ R/shinyplot.R | 66 ++++++++++------ R/summary.spwb.R | 9 +- data/SpParamsDefinition.rda |binary man/defaultControl.Rd | 6 - man/extract.Rd | 2 man/plot.spwb.Rd | 13 +++ man/shinyplot.Rd | 3 man/summary.spwb.Rd | 13 ++- src/RcppExports.cpp | 9 +- src/communication_structures.cpp | 31 ++++++- src/communication_structures.h | 2 src/growth.cpp | 13 +-- src/inner_sureau.cpp | 138 +++++++++++++++++++++++++++------- src/inner_sureau.h | 2 src/modelInput.cpp | 16 ++- src/phenology.cpp | 13 ++- src/spwb.cpp | 15 ++- src/spwb_day.cpp | 94 +++++++++++------------ src/spwb_day.h | 2 src/struct_sureau.h | 1 src/transpiration_advanced.cpp | 37 +++++---- src/transpiration_basic.cpp | 8 + tests/testthat/Rplots.pdf |binary tests/testthat/test_fordyn.R | 11 ++ tests/testthat/test_growth.R | 8 + tests/testthat/test_post_processing.R | 21 +++++ tests/testthat/test_spwb.R | 45 +++++++++++ 35 files changed, 579 insertions(+), 233 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.9.7 dated 2023-12-07 and 0.9.8 dated 2025-10-21
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/svmd.R | 1 + man/RSSL-package.Rd | 2 +- src/utils.cpp | 3 +-- 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Robust Functional Linear Regression
Description: Functions for implementing robust methods for functional linear regression. In the functional linear regression, we consider scalar-on-function linear regression and function-on-function linear regression.
Author: Ufuk Beyaztas [aut, cre, cph] ,
Han Lin Shang [aut]
Maintainer: Ufuk Beyaztas <ufukbeyaztas@gmail.com>
Diff between robflreg versions 1.2 dated 2024-01-23 and 1.3 dated 2025-10-21
ChangeLog | 5 +++++ DESCRIPTION | 18 ++++++++++-------- MD5 | 35 ++++++++++++++++++++++++++++++----- NAMESPACE | 13 ++++++++++++- R/BIC_fun.R |only R/BIC_fun_JAS.R |only R/calculate_percentile.R |only R/check_loss.R |only R/fpqr.R |only R/fpqr_dgp.R |only R/getAmat.R |only R/par_opt.R |only R/paramCV.R |only R/pen2SLS_est.R |only R/pqr.R |only R/predict_fpqr.R |only R/predict_sffr2SLS.R |only R/qcov.R |only R/sff_dgp.R |only R/sffr_pen2SLS.R |only R/smooth_fun.R |only R/svd_flip.R |only R/utils.R |only R/var.sel.R | 42 +++++++++++++++++++++--------------------- man/fpqr.Rd |only man/fpqr_dgp.Rd |only man/predict_fpqr.Rd |only man/predict_sffr2SLS.Rd |only man/robflreg-package.Rd | 40 +++++++++++++++++++++++++++++----------- man/sff_dgp.Rd |only man/sffr_pen2SLS.Rd |only 31 files changed, 107 insertions(+), 46 deletions(-)
Title: Loglikelihood Adjustment for Extreme Value Models
Description: Performs adjusted inferences based on model objects fitted, using
maximum likelihood estimation, by the extreme value analysis packages
'eva' <https://cran.r-project.org/package=eva>,
'evd' <https://cran.r-project.org/package=evd>,
'evir' <https://cran.r-project.org/package=evir>,
'extRemes' <https://cran.r-project.org/package=extRemes>,
'fExtremes' <https://cran.r-project.org/package=fExtremes>,
'ismev' <https://cran.r-project.org/package=ismev>,
'mev' <https://cran.r-project.org/package=mev>,
'POT' <https://cran.r-project.org/package=POT> and
'texmex' <https://cran.r-project.org/package=texmex>.
Adjusted standard errors and an adjusted loglikelihood are provided, using
the 'chandwich' package <https://cran.r-project.org/package=chandwich>
and the object-oriented features of the 'sandwich' package
<https://cran.r-project.org/package=sandwich>. The adjustment is based on a
robust sandwich estimator of the parameter covar [...truncated...]
Author: Paul J. Northrop [aut, cre, cph],
Camellia Yin [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between lax versions 1.2.3 dated 2024-02-25 and 1.2.4 dated 2025-10-21
DESCRIPTION | 10 ++++---- MD5 | 44 +++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 7 +++++ R/alogLik_methods.R | 16 +++++++++++-- R/bernoulli.R | 4 +-- R/lax-internal.R | 4 +-- R/mev.R | 32 +++++++++++++++++--------- R/mev_egp.R | 13 ++++++++-- R/return_level.R | 4 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lax-vignette.R | 16 ++++++------- inst/doc/lax-vignette.Rmd | 2 - inst/doc/lax-vignette.html | 10 ++++---- man/alogLik.Rd | 2 - man/bernoulli.Rd | 4 +-- man/lax-internal.Rd | 2 - man/logLik.logLikVec.Rd | 16 ++++++++++++- man/logLikVec.Rd | 12 +++++++++ man/return_level.Rd | 2 - tests/testthat/test-logLik-mev.R | 48 ++++++++++++++++++++++++++------------- vignettes/lax-vignette.Rmd | 2 - 23 files changed, 168 insertions(+), 83 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.2.0 dated 2025-07-16 and 1.3.0 dated 2025-10-21
IssueTrackeR-1.2.0/IssueTrackeR/inst/data_issues/list_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/DESCRIPTION | 8 IssueTrackeR-1.3.0/IssueTrackeR/LICENSE | 4 IssueTrackeR-1.3.0/IssueTrackeR/MD5 | 76 IssueTrackeR-1.3.0/IssueTrackeR/NAMESPACE | 13 IssueTrackeR-1.3.0/IssueTrackeR/NEWS.md | 29 IssueTrackeR-1.3.0/IssueTrackeR/R/IssueTrackeR-package.R | 38 IssueTrackeR-1.3.0/IssueTrackeR/R/check.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/comments.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/finding-objects.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/format.R | 66 IssueTrackeR-1.3.0/IssueTrackeR/R/print.R | 518 +++-- IssueTrackeR-1.3.0/IssueTrackeR/R/summary.R | 92 IssueTrackeR-1.3.0/IssueTrackeR/R/update_database.R | 178 - IssueTrackeR-1.3.0/IssueTrackeR/R/utils.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_issues.R | 958 +++++----- IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_labels.R | 90 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_milestones.R | 76 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_issues.R | 74 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_repo.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/zzz.R | 22 IssueTrackeR-1.3.0/IssueTrackeR/README.md | 58 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/closed_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/generate-files.R |only IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/list_labels.yaml | 25 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/list_milestones.yaml | 3 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/open_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/man/IssueTrackeR-package.Rd | 48 IssueTrackeR-1.3.0/IssueTrackeR/man/figures/logo.svg |only IssueTrackeR-1.3.0/IssueTrackeR/man/format_labels.Rd | 74 IssueTrackeR-1.3.0/IssueTrackeR/man/format_milestones.Rd | 76 IssueTrackeR-1.3.0/IssueTrackeR/man/get.Rd | 3 IssueTrackeR-1.3.0/IssueTrackeR/man/get_all_repos.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/new_issue.Rd | 15 IssueTrackeR-1.3.0/IssueTrackeR/man/new_issues.Rd | 8 IssueTrackeR-1.3.0/IssueTrackeR/man/print.Rd | 8 IssueTrackeR-1.3.0/IssueTrackeR/man/summary.Rd | 5 IssueTrackeR-1.3.0/IssueTrackeR/man/update_database.Rd | 114 - IssueTrackeR-1.3.0/IssueTrackeR/man/with_labels.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/with_text.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/write.Rd | 2 IssueTrackeR-1.3.0/IssueTrackeR/tests/spelling.R | 14 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat.R | 24 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/helper.R | 64 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/test-check.R |only IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/test-get_issues.R | 114 - 46 files changed, 1589 insertions(+), 1308 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock [aut, cre],
Theo Michelot [aut]
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.5.6 dated 2025-07-21 and 1.5.7 dated 2025-10-21
momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloExampleCT011.pdf |only momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloResultsCT.pdf |only momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloStatesCT.pdf |only momentuHMM-1.5.7/momentuHMM/DESCRIPTION | 10 +-- momentuHMM-1.5.7/momentuHMM/MD5 | 31 ++++------ momentuHMM-1.5.7/momentuHMM/NEWS | 7 ++ momentuHMM-1.5.7/momentuHMM/R/fitHMM.R | 12 --- momentuHMM-1.5.7/momentuHMM/R/momentuHMM_utils.R | 7 ++ momentuHMM-1.5.7/momentuHMM/R/simData.R | 4 - momentuHMM-1.5.7/momentuHMM/README.md | 2 momentuHMM-1.5.7/momentuHMM/build/partial.rdb |binary momentuHMM-1.5.7/momentuHMM/build/vignette.rds |binary momentuHMM-1.5.7/momentuHMM/inst/doc/momentuHMM.pdf |binary momentuHMM-1.5.7/momentuHMM/man/simData.Rd | 2 momentuHMM-1.5.7/momentuHMM/src/densities.h | 26 ++++---- momentuHMM-1.5.7/momentuHMM/src/nLogLike.cpp | 2 momentuHMM-1.5.7/momentuHMM/vignettes/examples/buffaloExample.R | 14 ++++ momentuHMM-1.5.7/momentuHMM/vignettes/examples/elephantExample.R | 8 -- 18 files changed, 71 insertions(+), 54 deletions(-)
More information about AgeTopicModels at CRAN
Permanent link
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015)
<https://journal.r-project.org/articles/RJ-2015-018/>.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@u-bordeaux.fr>
Diff between VSURF versions 1.2.0 dated 2022-12-15 and 1.2.1 dated 2025-10-21
VSURF-1.2.0/VSURF/tests/testthat/case_win32_test_iris.R |only VSURF-1.2.0/VSURF/tests/testthat/case_win32b_test_orange.R |only VSURF-1.2.0/VSURF/tests/testthat/testthat-problems.rds |only VSURF-1.2.1/VSURF/DESCRIPTION | 13 +- VSURF-1.2.1/VSURF/MD5 | 36 ++--- VSURF-1.2.1/VSURF/NEWS | 4 VSURF-1.2.1/VSURF/R/VSURF.R | 4 VSURF-1.2.1/VSURF/R/VSURF_interp.R | 52 ++++---- VSURF-1.2.1/VSURF/R/VSURF_pred.R | 60 ++++----- VSURF-1.2.1/VSURF/R/VSURF_thres.R | 2 VSURF-1.2.1/VSURF/R/plot.VSURF.R | 2 VSURF-1.2.1/VSURF/R/predict.VSURF.R | 8 - VSURF-1.2.1/VSURF/man/VSURF.Rd | 4 VSURF-1.2.1/VSURF/man/VSURF_interp.Rd | 2 VSURF-1.2.1/VSURF/man/VSURF_pred.Rd | 2 VSURF-1.2.1/VSURF/man/VSURF_thres.Rd | 2 VSURF-1.2.1/VSURF/man/plot.VSURF.Rd | 2 VSURF-1.2.1/VSURF/man/predict.VSURF.Rd | 8 - VSURF-1.2.1/VSURF/tests/testthat/test_iris.R | 30 +--- VSURF-1.2.1/VSURF/tests/testthat/test_irisParallel.R |only VSURF-1.2.1/VSURF/tests/testthat/test_orange.R | 83 +++++++------ 21 files changed, 161 insertions(+), 153 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector
Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Thomas Lin Pedersen [cre, aut] ,
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] ,
David Gohel [ctb] ,
Yixuan Qiu [ctb] ,
Hakon Malmedal [ctb] ,
Posit Software, PBC [cph, fnd [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between svglite versions 2.2.1 dated 2025-05-12 and 2.2.2 dated 2025-10-21
svglite-2.2.1/svglite/inst/doc/fonts.R |only svglite-2.2.1/svglite/inst/doc/fonts.Rmd |only svglite-2.2.1/svglite/inst/doc/fonts.html |only svglite-2.2.1/svglite/vignettes/fonts.Rmd |only svglite-2.2.2/svglite/DESCRIPTION | 8 +- svglite-2.2.2/svglite/MD5 | 42 ++++++--------- svglite-2.2.2/svglite/NEWS.md | 5 + svglite-2.2.2/svglite/R/SVG.R | 2 svglite-2.2.2/svglite/R/fonts.R | 2 svglite-2.2.2/svglite/R/inlineSVG.R | 2 svglite-2.2.2/svglite/README.md | 4 - svglite-2.2.2/svglite/build/vignette.rds |binary svglite-2.2.2/svglite/inst/doc/scaling.html | 9 +-- svglite-2.2.2/svglite/man/editSVG.Rd | 2 svglite-2.2.2/svglite/man/htmlSVG.Rd | 2 svglite-2.2.2/svglite/man/stringSVG.Rd | 2 svglite-2.2.2/svglite/man/svglite.Rd | 2 svglite-2.2.2/svglite/man/xmlSVG.Rd | 2 svglite-2.2.2/svglite/src/SvgStream.h | 3 - svglite-2.2.2/svglite/tests/testthat/test-clip.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-no-clip.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-scale-text.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-text.R | 12 ---- svglite-2.2.2/svglite/tests/testthat/test-text.svg | 4 + 24 files changed, 63 insertions(+), 52 deletions(-)
Title: Haplotype-Aware CNV Analysis from scRNA-Seq
Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Author: Teng Gao [cre, aut],
Ruslan Soldatov [aut],
Hirak Sarkar [aut],
Evan Biederstedt [aut],
Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Diff between numbat versions 1.4.2 dated 2024-09-20 and 1.5.1 dated 2025-10-21
DESCRIPTION | 8 +- MD5 | 28 ++++++--- NEWS.md | 8 ++ R/diagnostics.R | 90 ++++++++++++++++++++++++++++--- R/main.R | 37 +++++++----- R/vis.R | 12 ++-- README.md | 6 ++ inst/bin/get_binned_atac.R |only inst/bin/get_binned_rna.R |only inst/bin/get_gene_binned_intersections.R |only inst/bin/input_prep.R |only inst/bin/pileup_and_phase.R | 25 +++++++- inst/bin/run_numbat_multiome.R |only inst/extdata |only man/annot_consensus.Rd | 4 - man/check_gtf_input.Rd |only man/plot_phylo_heatmap.Rd | 3 + man/run_numbat.Rd | 6 ++ 18 files changed, 183 insertions(+), 44 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.7 dated 2025-08-30 and 1.3.8 dated 2025-10-21
DESCRIPTION | 10 MD5 | 97 NAMESPACE | 2 NEWS.md | 4 R/WA-estimands.R | 2 R/binomial.regression.R | 868 ++++++ R/cifreg.R | 4 R/phreg.R | 18 R/phreg_rct.R | 7 R/ratio.regression.R | 19 R/recreg.R | 3074 ++++++++++++------------ R/recurrent.marginal.R | 16 R/restricted.mean.R | 7 R/sim-pc-hazard.R | 100 build/vignette.rds |binary inst/doc/basic-dutils.html | 12 inst/doc/binomial-family.html | 12 inst/doc/binomial-twin.html | 12 inst/doc/binreg-TRS.html | 12 inst/doc/binreg-ate.R | 38 inst/doc/binreg-ate.Rmd | 45 inst/doc/binreg-ate.html | 527 ++-- inst/doc/binreg.html | 12 inst/doc/cifreg.html | 12 inst/doc/cooking-survival-data.R | 210 - inst/doc/cooking-survival-data.Rmd | 329 +- inst/doc/cooking-survival-data.html | 937 +++---- inst/doc/glm-utility.html | 12 inst/doc/haplo-discrete-ttp.html | 12 inst/doc/interval-discrete-survival.html | 12 inst/doc/marginal-cox.html | 12 inst/doc/mediation-survival.html | 12 inst/doc/phreg_rct.Rmd | 4 inst/doc/phreg_rct.html | 17 inst/doc/recurrent-events.html | 14 inst/doc/rmst-ate.html | 32 inst/doc/survival-ate.html | 172 - inst/doc/time-to-event-family-studies-arev.html | 16 inst/doc/twostage-survival.html | 12 inst/doc/while-alive.html | 12 inst/tinytest/test_cluster.R |only man/binregATE.Rd | 13 man/binregG.Rd | 3 man/binregRatio.Rd | 17 man/phreg_rct.Rd | 5 man/sim.cif.Rd | 9 man/sim.recurrent.Rd | 4 vignettes/binreg-ate.Rmd | 45 vignettes/cooking-survival-data.Rmd | 329 +- vignettes/phreg_rct.Rmd | 4 50 files changed, 3991 insertions(+), 3163 deletions(-)
Title: Tools for Nonparametric Martingale Posterior Sampling
Description: Performs Bayesian nonparametric density estimation using Martingale
posterior distributions including the Copula Resampling (CopRe) algorithm.
Also included are a Gibbs sampler for the marginal Gibbs-type mixture model and
an extension to include full uncertainty quantification via a predictive
sequence resampling (SeqRe) algorithm. The CopRe and SeqRe samplers generate
random nonparametric distributions as output, leading to complete nonparametric
inference on posterior summaries. Routines for calculating arbitrary
functionals from the sampled distributions are included as well as an important
algorithm for finding the number and location of modes, which can then be used
to estimate the clusters in the data using, for example, k-means.
Implements work developed in Moya B., Walker S. G. (2022).
<doi:10.48550/arxiv.2206.08418>, Fong, E., Holmes, C., Walker, S. G. (2021)
<doi:10.48550/arxiv.2103.15671>, and Escobar M. D., West, M. (1995)
<doi:10.1080/01621459.1995.10476550 [...truncated...]
Author: Blake Moya [cre, aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Blake Moya <blakemoya@utexas.edu>
Diff between copre versions 0.2.1 dated 2024-05-21 and 0.2.2 dated 2025-10-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 14 +++++++++----- build/partial.rdb |binary src/seq_measures.cpp | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.2.9 dated 2024-09-30 and 1.3.0 dated 2025-10-21
DESCRIPTION | 12 MD5 | 62 +-- NAMESPACE | 17 NEWS.md | 8 R/fieldmean_and_anomaly_map.R | 13 R/getColors.R | 631 +++++++++++++++++++++++++++++++++ R/helper_time_series_compare.R | 4 R/plot_abs_map.R | 43 +- R/plot_fieldmean.R | 108 ++++- R/plot_fieldmean_and_map.R | 138 ++++--- R/plot_warming_stripes.R | 491 ++++++++++++------------- R/ranking.R | 44 +- R/recalculateImageDimensions.R | 10 R/render_plot.R | 262 +++++++++++-- R/render_plot_1d.R | 11 R/render_plot_1d_advanced.R | 12 R/render_plot_hist_compare.R | 1 R/render_plot_hovmoller.R | 18 R/render_plot_side_by_side.R | 1 R/render_plot_time_series_compare.R | 12 R/render_region_plot.R | 515 +++++++++++++++----------- R/trend_plot.R | 4 inst/WORDLIST | 5 inst/extdata/quicklook_config.yml | 20 + man/render_plot.Rd | 8 man/render_plot_1d.Rd | 12 man/render_plot_1d_advanced.Rd | 12 man/render_plot_hist_compare.Rd | 3 man/render_plot_hovmoller.Rd | 6 man/render_plot_side_by_side.Rd | 3 man/render_plot_time_series_compare.Rd | 12 man/render_region_plot.Rd | 86 +--- 32 files changed, 1843 insertions(+), 741 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of
Machine Learning (ML) techniques as easy and accessible as possible,
particularly within the framework of the Knowledge Discovery in
Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive
or classification modeling workflow, aligning closely with the
fundamental steps of the KDD methodology, from data selection and
preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis.
The 'MLwrap' workflow is organized into four core steps;
preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to
data preparation and transformation, model construction,
hyperparameter optimization, and sensitivity analysis. The user can
access comprehensive model evaluation results including fit
assessment metrics, plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.2.0 dated 2025-10-11 and 0.2.1 dated 2025-10-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/create_xgboost.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: High-Dimensional Model Selection
Description: Model selection and averaging for regression, generalized linear models, generalized additive models, graphical models and mixtures, focusing on Bayesian model selection and information criteria (Bayesian information criterion etc.). See Rossell (2025) <doi:10.5281/zenodo.17119597> (see the URL field below for its URL) for a hands-on book describing the methods, examples and suggested citations if you use the package.
Author: David Rossell [aut, cre],
John D. Cook [ctb],
Donatello Telesca [aut],
P. Roebuck [ctb],
Oriol Abril [aut],
Miquel Torrens [aut],
Peter Mueller [ctb],
William Hallahan [ctb]
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between modelSelection versions 1.0.3 dated 2025-09-21 and 1.0.4 dated 2025-10-21
modelSelection-1.0.3/modelSelection/tests/testthat/testthat-problems.rds |only modelSelection-1.0.4/modelSelection/ChangeLog |only modelSelection-1.0.4/modelSelection/DESCRIPTION | 14 - modelSelection-1.0.4/modelSelection/MD5 | 44 ++--- modelSelection-1.0.4/modelSelection/NAMESPACE | 3 modelSelection-1.0.4/modelSelection/R/RcppExports.R | 12 - modelSelection-1.0.4/modelSelection/R/bms_ortho.R | 34 ++-- modelSelection-1.0.4/modelSelection/R/cil.R | 16 - modelSelection-1.0.4/modelSelection/R/eBayes.R | 14 - modelSelection-1.0.4/modelSelection/R/greedyGLM.R | 14 - modelSelection-1.0.4/modelSelection/R/infocriteria.R | 85 +++++++--- modelSelection-1.0.4/modelSelection/R/localnulltest.R | 26 +-- modelSelection-1.0.4/modelSelection/R/modelSelection.R | 52 +++--- modelSelection-1.0.4/modelSelection/R/modelSelectionGLM.R | 18 +- modelSelection-1.0.4/modelSelection/R/modelsearch.R | 14 - modelSelection-1.0.4/modelSelection/README.md | 4 modelSelection-1.0.4/modelSelection/man/bestBIC.Rd | 30 +++ modelSelection-1.0.4/modelSelection/man/localnulltest.Rd | 10 - modelSelection-1.0.4/modelSelection/man/modelSelection.Rd | 43 ++--- modelSelection-1.0.4/modelSelection/src/RcppExports.cpp | 24 +- modelSelection-1.0.4/modelSelection/src/modelSel_regression.cpp | 30 +-- modelSelection-1.0.4/modelSelection/src/modelSel_regression.h | 6 modelSelection-1.0.4/modelSelection/tests/testthat/test-modelSelection-enum.R | 16 - modelSelection-1.0.4/modelSelection/tests/testthat/test-modelSelection-gibbs.R | 12 - 24 files changed, 301 insertions(+), 220 deletions(-)
More information about modelSelection at CRAN
Permanent link
Title: 'Domino Data R SDK'
Description: A wrapper on top of the 'Domino Data Python SDK' library. It lets
you query and access 'Domino Data Sources' directly from your R environment.
Under the hood, 'Domino Data R SDK' leverages the API provided by the
'Domino Data Python SDK', which must be installed as a prerequisite.
'Domino' is a platform that makes it easy to run your code on scalable
hardware, with integrated version control and collaboration features
designed for analytical workflows. See
<https://docs.dominodatalab.com/en/latest/api_guide/140b48/domino-data-api>
for more information.
Author: Gabriel Haim [aut, cre]
Maintainer: Gabriel Haim <gabriel.haim@dominodatalab.com>
Diff between DominoDataR versions 0.2.3 dated 2023-08-17 and 0.3.0 dated 2025-10-21
DESCRIPTION | 10 ++-- MD5 | 39 ++++++++++++------ NAMESPACE | 9 ++++ R/client.R | 44 ++++++++++++++++++-- R/config.R | 26 +++++++++--- R/http.R | 91 ++++++++++++++++++++++++++++++++++++++++-- R/netapp_volumes.R |only R/python.R | 2 R/zzz.R | 6 ++ README.md | 17 ++++++- man/datasource_client.Rd | 11 ++++- man/encode_url_path.Rd |only man/get_file_url.Rd |only man/get_netapp_token.Rd |only man/get_volume.Rd |only man/list_files.Rd |only man/list_snapshots.Rd |only man/list_volumes.Rd |only man/load_oauth_credentials.Rd | 6 +- man/make_request.Rd |only man/netapp_volume_client.Rd |only man/put_volume_object.Rd |only man/py_select_interpreter.Rd | 2 man/query.Rd | 2 man/save_volume_object.Rd |only man/upload_volume_object.Rd |only tests/testthat/test-client.R | 14 ++++++ 27 files changed, 237 insertions(+), 42 deletions(-)
Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>
Diff between R2MLwiN versions 0.8-9 dated 2024-01-29 and 0.8-10 dated 2025-10-21
DESCRIPTION | 24 ++-- MD5 | 38 +++--- NAMESPACE | 291 ++++++++++++++++++++++++------------------------- NEWS | 15 ++ R/Formula.translate.R | 54 +++++++++ R/R2MLwiN-package.R | 3 R/data-tutorial.R | 2 R/init.R | 4 R/mlwin2bugs.R | 97 ++++------------ R/runMLwiN.R | 197 +++++++++++++++++++++++++++++++-- R/sixway.R | 2 build/partial.rdb |binary demo/MCMCGuide07.R | 14 +- demo/MCMCGuide08.R | 7 + demo/MCMCGuide17.R | 5 man/R2MLwiN-package.Rd | 6 - man/mlwin2bugs.Rd | 52 +------- man/runMLwiN.Rd | 4 man/sixway.Rd | 2 man/tutorial.Rd | 2 20 files changed, 495 insertions(+), 324 deletions(-)
Title: A GUI for Dual and Bulk RNA-Sequencing Analysis
Description: A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.
Author: Carmine Fruggiero [aut, cre],
Gaetano Aufiero [aut]
Maintainer: Carmine Fruggiero <fruggierocarmine3@gmail.com>
Diff between inDAGO versions 1.0.2 dated 2025-09-19 and 1.0.3 dated 2025-10-21
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 4 R/BulkAlignment.R | 62 + R/CombinedAlignment.R | 41 - R/SequentialAlignment.R | 1178 ++++++++++++++++++------------------- R/app.R | 7 R/mappingBulkServerLogic.R | 505 +++++++-------- R/mappingBulkUserInterface.R | 681 ++++++++++----------- R/mappingSequentialServerLogic.R | 639 ++++++++++---------- R/mappingSequentialUserInterface.R | 742 +++++++++++------------ R/zzz.R | 8 man/BulkAlignment.Rd | 3 tests/testthat.R | 24 tests/testthat/test-inDAGO_shiny.R | 22 15 files changed, 1978 insertions(+), 1980 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2025.5.24 dated 2025-05-27 and 2025.9.30 dated 2025-10-21
DESCRIPTION | 17 MD5 | 100 +-- NAMESPACE | 44 - NEWS | 462 +++++++------- R/atime.R | 503 ++++++---------- R/atime_grid.R |only R/predict.R | 246 +++---- R/references.R | 370 +++++------ R/test.R | 771 ++++++++++++------------ R/versions.R | 396 ++++++------ build/vignette.rds |binary inst/doc/Custom_Plots.R | 135 ++-- inst/doc/Custom_Plots.Rmd | 195 +++--- inst/doc/Custom_Plots.html | 445 +++++++------- inst/doc/Custom_References.R | 122 +-- inst/doc/Custom_References.Rmd | 279 ++++---- inst/doc/Custom_References.html | 633 ++++++++++---------- inst/doc/Custom_Units.R | 124 +-- inst/doc/Custom_Units.Rmd | 315 ++++------ inst/doc/Custom_Units.html | 609 ++++++++++--------- inst/doc/cum_median.R | 56 - inst/doc/cum_median.Rmd | 101 +-- inst/doc/cum_median.html | 344 +++++------ inst/doc/regex.R | 120 +-- inst/doc/regex.Rmd | 215 +++--- inst/doc/regex.html | 520 +++++++++------- inst/doc/sparse.R | 378 +++++------- inst/doc/sparse.Rmd | 698 +++++++++++----------- inst/doc/sparse.html | 1248 ++++++++++++++++++++++------------------ inst/example_tests.R | 82 +- inst/global_edit.R | 82 +- man/atime.Rd | 130 ++-- man/atime_grid.Rd | 200 +++--- man/atime_pkg.Rd | 238 +++---- man/atime_test.Rd | 128 ++-- man/atime_test_list.Rd | 164 ++--- man/atime_versions.Rd | 202 +++--- man/atime_versions_exprs.Rd | 180 ++--- man/atime_versions_remove.Rd | 32 - man/glob_find_replace.Rd | 38 - man/references_best.Rd | 104 +-- tests/testthat.R | 4 tests/testthat/test-CRAN.R | 1077 +++++++++++++++++----------------- vignettes/Custom_Plots.Rmd | 195 +++--- vignettes/Custom_References.Rmd | 279 ++++---- vignettes/Custom_Units.Rmd | 315 ++++------ vignettes/cum_median.Rmd | 101 +-- vignettes/data.table__files |only vignettes/git__files |only vignettes/images |only vignettes/regex.Rmd | 215 +++--- vignettes/sparse.Rmd | 698 +++++++++++----------- 52 files changed, 7046 insertions(+), 6864 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability
of linear structural equation models as described in Drton, Foygel, and
Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012)
<doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical
representation of structural equation models.
Author: Rina Foygel Barber [aut],
Mathias Drton [aut],
Luca Weihs [aut],
Nils Sturma [cre, aut]
Maintainer: Nils Sturma <nils.sturma@epfl.ch>
Diff between SEMID versions 0.4.1 dated 2023-07-19 and 0.4.2 dated 2025-10-21
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 3 +++ R/FlowGraph.R | 14 ++++++-------- man/updateEdgeCapacities.Rd | 2 +- 5 files changed, 21 insertions(+), 20 deletions(-)
Title: An R Package for the Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frederic Santos [aut, cre]
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 4.0.3 dated 2023-11-29 and 4.1.0 dated 2025-10-21
DESCRIPTION | 9 ++--- MD5 | 24 ++++++------- NEWS.md | 9 +++++ R/mmd.R | 15 +++----- R/small_utils.R | 1 build/vignette.rds |binary inst/doc/intro_AnthropMMD.R | 6 +-- inst/doc/intro_AnthropMMD.Rmd | 30 ++++++++++------- inst/doc/intro_AnthropMMD.html | 71 ++++++++++++++++++++++++----------------- man/mmd.Rd | 4 +- tests/testthat/test-mmd.R | 68 +++++++++++++++++++++++++-------------- vignettes/biblio.bib | 9 +++++ vignettes/intro_AnthropMMD.Rmd | 30 ++++++++++------- 13 files changed, 171 insertions(+), 105 deletions(-)
Title: Mapping Cortical Folding Patterns
Description: Visualizes sulcal morphometry data derived from 'BrainVisa' <https://brainvisa.info/> including width, depth, surface area, and length. The package enables mapping of statistical group results or subject-level values onto cortical surface maps, with options to focus on all sulci or only selected regions of interest. Users can display all four measures simultaneously or restrict plots to chosen measures, creating composite, publication-quality brain visualizations in R to support the analysis and interpretation of sulcal morphology.
Author: Mahan Shafie [aut, cre],
Fabrizio Pizzagalli [aut]
Maintainer: Mahan Shafie <mahan.shafie@unito.it>
Diff between sulcimap versions 1.0.5 dated 2025-10-14 and 1.0.6 dated 2025-10-21
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 7 ++++--- NEWS.md | 4 ++++ inst/CITATION |only man/sulcimap-package.Rd | 7 ++++++- 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Jakub Grzywaczewski [aut, cre],
Tymoteusz Kwiecinski [aut] ,
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Jakub Grzywaczewski <jakubzgrzywaczewski@gmail.com>
Diff between SerolyzeR versions 1.3.0 dated 2025-07-18 and 1.3.1 dated 2025-10-21
SerolyzeR-1.3.0/SerolyzeR/tests/testthat/Rplots.pdf |only SerolyzeR-1.3.0/SerolyzeR/tests/testthat/normalised_data |only SerolyzeR-1.3.1/SerolyzeR/DESCRIPTION | 18 SerolyzeR-1.3.1/SerolyzeR/MD5 | 48 SerolyzeR-1.3.1/SerolyzeR/R/classes-plate.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/classes-plate_builder.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/get-nmfi.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/helpers.R | 31 SerolyzeR-1.3.1/SerolyzeR/R/merge-plate-outputs.R | 175 - SerolyzeR-1.3.1/SerolyzeR/R/parser-xponent.R | 6 SerolyzeR-1.3.1/SerolyzeR/R/plots-standard_curve.R | 1 SerolyzeR-1.3.1/SerolyzeR/R/process-dir.R | 40 SerolyzeR-1.3.1/SerolyzeR/R/process-file.R | 19 SerolyzeR-1.3.1/SerolyzeR/build/partial.rdb |binary SerolyzeR-1.3.1/SerolyzeR/build/vignette.rds |binary SerolyzeR-1.3.1/SerolyzeR/inst/doc/example_script.R | 204 - SerolyzeR-1.3.1/SerolyzeR/inst/doc/example_script.html | 1598 +++++----- SerolyzeR-1.3.1/SerolyzeR/inst/extdata/random_blanks.csv |only SerolyzeR-1.3.1/SerolyzeR/inst/img/EU.jpg |binary SerolyzeR-1.3.1/SerolyzeR/inst/img/overview.png |binary SerolyzeR-1.3.1/SerolyzeR/man/merge_plate_outputs.Rd | 102 SerolyzeR-1.3.1/SerolyzeR/man/try_cast_as_numeric.Rd |only SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-helpers.R | 17 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-model.R | 1 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-parser-xponent.R | 5 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-parser.R | 1 26 files changed, 1158 insertions(+), 1114 deletions(-)
Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more
accessible to students and professionals from Epidemiology and
Public Health related disciplines. Includes a function to report
coefficients and confidence intervals from models using robust
standard errors (when available), functions that expand 'ggplot2'
plots and functions relevant for introductory papers in Epidemiology
or Public Health. Please note that use of the
provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre],
Frank Harell [ctb],
John Fox [ctb],
R-Core [ctb]
Maintainer: Josie Athens <josie.athens@gmail.com>
Diff between pubh versions 2.0.0 dated 2024-10-08 and 3.0.0 dated 2025-10-21
pubh-2.0.0/pubh/man/axis_labs.Rd |only pubh-2.0.0/pubh/man/box_plot.Rd |only pubh-2.0.0/pubh/man/gf_star.Rd |only pubh-2.0.0/pubh/man/hist_norm.Rd |only pubh-3.0.0/pubh/DESCRIPTION | 19 pubh-3.0.0/pubh/MD5 | 61 +- pubh-3.0.0/pubh/NAMESPACE | 25 - pubh-3.0.0/pubh/R/data.R | 23 - pubh-3.0.0/pubh/R/descriptive_functions.R | 102 ++++ pubh-3.0.0/pubh/R/epi_functions.R | 45 -- pubh-3.0.0/pubh/R/misc_functions.R | 147 ++++++- pubh-3.0.0/pubh/R/plot_functions.R | 604 ++++++++--------------------- pubh-3.0.0/pubh/build/vignette.rds |binary pubh-3.0.0/pubh/inst/doc/introduction.R | 88 +--- pubh-3.0.0/pubh/inst/doc/introduction.Rmd | 90 +--- pubh-3.0.0/pubh/inst/doc/introduction.html | 504 +++++++++++++----------- pubh-3.0.0/pubh/man/Fentress.Rd | 2 pubh-3.0.0/pubh/man/Hodgkin.Rd | 8 pubh-3.0.0/pubh/man/Kirkwood.Rd | 4 pubh-3.0.0/pubh/man/Sharples.Rd | 6 pubh-3.0.0/pubh/man/Tuzson.Rd | 3 pubh-3.0.0/pubh/man/bar_error.Rd | 34 - pubh-3.0.0/pubh/man/bland_altman.Rd | 46 -- pubh-3.0.0/pubh/man/bmj.Rd |only pubh-3.0.0/pubh/man/cosm_reg.Rd |only pubh-3.0.0/pubh/man/cosm_sum.Rd |only pubh-3.0.0/pubh/man/cross_tbl.Rd |only pubh-3.0.0/pubh/man/effect_plot.Rd |only pubh-3.0.0/pubh/man/gen_bst_df.Rd | 15 pubh-3.0.0/pubh/man/gg_star.Rd |only pubh-3.0.0/pubh/man/multiple.Rd | 13 pubh-3.0.0/pubh/man/odds_trend.Rd | 25 - pubh-3.0.0/pubh/man/predict_inv.Rd | 5 pubh-3.0.0/pubh/man/qq_plot.Rd | 28 - pubh-3.0.0/pubh/man/strip_error.Rd | 61 -- pubh-3.0.0/pubh/man/theme_pubh.Rd |only pubh-3.0.0/pubh/vignettes/introduction.Rmd | 90 +--- 37 files changed, 949 insertions(+), 1099 deletions(-)
Title: Initialization of Numerical Optimization
Description: Analysis of the initialization for numerical optimization of
real-valued functions, particularly likelihood functions of statistical
models. See <https://loelschlaeger.de/ino/> for more details.
Author: Lennart Oelschlaeger [aut, cre] ,
Marius Oetting [aut] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ino versions 1.1.0 dated 2025-07-05 and 1.1.1 dated 2025-10-21
DESCRIPTION | 8 MD5 | 56 NAMESPACE | 158 - NEWS.md | 4 R/autoplot.R | 672 ++--- R/ino-package.R | 232 - R/nop.R | 3140 ++++++++++++------------- README.md | 278 +- build/vignette.rds |binary inst/doc/example_hmm.R | 245 - inst/doc/example_hmm.Rmd | 82 inst/doc/example_hmm.html | 1491 +++++------ inst/doc/ino.R | 310 +- inst/doc/ino.Rmd | 922 +++---- inst/doc/ino.html | 2118 ++++++++-------- man/Nop.Rd | 1510 ++++++------ man/Nop_hmm.Rd | 40 man/autoplot.Nop.Rd | 132 - man/ino-package.Rd | 72 tests/testthat.R | 8 tests/testthat/test-nop.R | 490 +-- vignettes/example_hmm.Rmd | 82 vignettes/figures/hmm-optimization-time-1.png |binary vignettes/figures/hmm-plot-dax-data-1.png |binary vignettes/figures/ino-estimated-mixtures-1.png |binary vignettes/figures/ino-faithful-plot-1.png |binary vignettes/figures/ino-plot-seconds-1.png |binary vignettes/ino.Rmd | 922 +++---- vignettes/ref.bib | 302 +- 29 files changed, 6689 insertions(+), 6585 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths] ,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.5 dated 2025-03-05 and 2.1.6 dated 2025-10-21
DESCRIPTION | 28 - MD5 | 80 +-- NEWS.md | 15 R/fplot.R | 59 ++ R/ger_summary.R | 96 +++- R/webTable.R | 11 build/vignette.rds |binary inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 4 inst/GerminaQuant/server.R | 117 +++-- inst/GerminaQuant/ui.R | 11 inst/doc/GerminaR.R | 11 inst/doc/GerminaR.Rmd | 11 inst/doc/GerminaR.html | 119 ++--- inst/doc/introduction.Rmd | 19 inst/doc/introduction.html | 139 +----- man/GerminaQuant.Rd | 50 +- man/fplot.Rd | 216 +++++----- man/ger_ASG.Rd | 54 +- man/ger_CVG.Rd | 50 +- man/ger_GRP.Rd | 72 +-- man/ger_GRS.Rd | 52 +- man/ger_GSP.Rd | 50 +- man/ger_MGR.Rd | 64 +- man/ger_MGT.Rd | 70 +-- man/ger_SDG.Rd | 50 +- man/ger_SYN.Rd | 72 +-- man/ger_UNC.Rd | 70 +-- man/ger_VGT.Rd | 50 +- man/ger_boxp.Rd | 146 +++--- man/ger_intime.Rd | 104 ++-- man/ger_summary.Rd | 65 +-- man/ger_testcomp.Rd | 86 +-- man/gquant_analysis.Rd | 122 ++--- man/osmp.Rd | 54 +- man/prosopis.Rd | 56 +- man/reexports.Rd | 32 - man/rep_row.Rd | 38 - man/textcolor.Rd | 68 +-- man/webTable.Rd | 68 +-- vignettes/GerminaR.Rmd | 11 vignettes/introduction.Rmd | 19 41 files changed, 1307 insertions(+), 1202 deletions(-)
Title: Ecological Inference in 2x2 Tables
Description: Implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008 <doi:10.1093/pan/mpm017>) and (2011 <doi:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
Author: Kosuke Imai [aut, cre],
Ying Lu [aut],
Aaron Strauss [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@Harvard.Edu>
This is a re-admission after prior archival of version 4.0-3 dated 2022-11-03
Diff between eco versions 4.0-3 dated 2022-11-03 and 4.0-4 dated 2025-10-21
ChangeLog | 1 DESCRIPTION | 34 +++++++++-------------------- MD5 | 62 +++++++++++++++++++++++++++--------------------------- R/Qfun.R | 1 R/eco.R | 2 - R/ecoNP.R | 7 +++--- R/emeco.R | 8 +++--- R/predict.eco.R | 2 - R/varcov.R | 1 inst/CITATION | 6 +---- man/Qfun.Rd | 3 ++ man/eco.Rd | 2 - man/ecoML.Rd | 8 +++--- man/ecoNP.Rd | 7 +++--- man/varcov.Rd | 3 ++ src/bayes.c | 4 +-- src/fintegrate.c | 30 +++++++++++++------------- src/gibbsBase.c | 2 - src/gibbsBase2C.c | 4 +-- src/gibbsBaseRC.c | 4 +-- src/gibbsDP.c | 8 +++--- src/gibbsEM.c | 25 +++++++++++++-------- src/gibbsXBase.c | 4 +-- src/gibbsXDP.c | 10 ++++---- src/gibbsZBase.c | 16 ++++++------- src/preBaseX.c | 4 +-- src/preDP.c | 4 +-- src/preDPX.c | 4 +-- src/rand.c | 6 ++--- src/sample.c | 22 +++++++++---------- src/subroutines.c | 22 +++++++++---------- src/vector.c | 15 ++++++------- 32 files changed, 168 insertions(+), 163 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre],
Antonio Canale [ctb],
Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 1.0.2 dated 2022-07-15 and 1.1.0 dated 2025-10-21
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 19 ++++++++++--------- build/partial.rdb |only build/vignette.rds |binary data/CPP.RData |binary inst/doc/BNPmix.pdf |binary man/BNPmix-package.Rd | 12 +++++++++++- src/DdpFunctions.cpp | 17 ++++++++++++----- src/Distributions.cpp | 37 +++++++++++++++++++++++++++---------- src/Makevars | 2 +- src/Makevars.win | 2 +- 11 files changed, 81 insertions(+), 34 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.2 dated 2025-10-01 and 1.4.3 dated 2025-10-21
DESCRIPTION | 10 +- MD5 | 10 +- NEWS.md | 7 + R/VWRfirstrun.R | 133 +++++++++++++++------------ inst/doc/VertexWiseR_surface_extraction.html | 51 +++++----- vignettes/VertexWiseR_surface_extraction.Rmd | 14 +- 6 files changed, 130 insertions(+), 95 deletions(-)
Title: Stochastic Gradient Descent for Scalable Estimation
Description: A fast and flexible set of tools for large scale estimation. It
features many stochastic gradient methods, built-in models, visualization
tools, automated hyperparameter tuning, model checking, interval estimation,
and convergence diagnostics.
Author: Junhyung Lyle Kim [cre, aut],
Dustin Tran [aut],
Panos Toulis [aut],
Tian Lian [ctb],
Ye Kuang [ctb],
Edoardo Airoldi [ctb]
Maintainer: Junhyung Lyle Kim <jlylekim@gmail.com>
Diff between sgd versions 1.1.2 dated 2024-01-31 and 1.1.3 dated 2025-10-21
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NEWS.md |only R/print.sgd.R | 2 +- README.md | 5 ++--- build/vignette.rds |binary man/print.sgd.Rd | 2 +- src/sgd/explicit_sgd.h | 2 +- src/sgd/implicit_sgd.h | 2 +- src/sgd/momentum_sgd.h | 2 +- src/sgd/nesterov_sgd.h | 2 +- src/validity-check/validity_check.h | 2 +- 12 files changed, 25 insertions(+), 25 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] ,
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Luis De Araujo [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
This is a re-admission after prior archival of version 4.21.0 dated 2024-11-14
Diff between umx versions 4.21.0 dated 2024-11-14 and 4.59.0 dated 2025-10-21
umx-4.21.0/umx/man/umx_set_plot_use_hrbrthemes.Rd |only umx-4.21.0/umx/man/xmu_scale_wide_data.Rd |only umx-4.59.0/umx/DESCRIPTION | 22 umx-4.59.0/umx/MD5 | 360 +- umx-4.59.0/umx/NAMESPACE | 13 umx-4.59.0/umx/NEWS.md | 40 umx-4.59.0/umx/R/build_run_modify.R | 34 umx-4.59.0/umx/R/financial_functions.R |only umx-4.59.0/umx/R/fit_and_reporting.R | 179 - umx-4.59.0/umx/R/misc_and_utility.R | 1737 +++---------- umx-4.59.0/umx/R/tmx.R | 47 umx-4.59.0/umx/R/umxCLPM.R | 86 umx-4.59.0/umx/R/umxDoC.R | 56 umx-4.59.0/umx/R/umxDoC2.R |only umx-4.59.0/umx/R/umxMRDoC.R | 1049 ++++++- umx-4.59.0/umx/R/umxMatrixFree.R | 2 umx-4.59.0/umx/R/umxPower.R | 2 umx-4.59.0/umx/R/umx_build_umxGxEbiv.R | 5 umx-4.59.0/umx/R/umx_build_umxSexLim.R | 9 umx-4.59.0/umx/R/umx_build_umxSimplex.R | 10 umx-4.59.0/umx/R/xmu.R | 393 ++ umx-4.59.0/umx/R/xmu_update_covar.R |only umx-4.59.0/umx/build/partial.rdb |binary umx-4.59.0/umx/inst/WORDLIST | 17 umx-4.59.0/umx/man/bucks.Rd | 4 umx-4.59.0/umx/man/deg2rad.Rd | 2 umx-4.59.0/umx/man/figures/umx_help_figures.graffle |binary umx-4.59.0/umx/man/fin_JustifiedPE.Rd | 4 umx-4.59.0/umx/man/fin_NI.Rd | 4 umx-4.59.0/umx/man/fin_expected.Rd |only umx-4.59.0/umx/man/fin_interest.Rd | 8 umx-4.59.0/umx/man/fin_net_present_value.Rd |only umx-4.59.0/umx/man/fin_percent.Rd | 4 umx-4.59.0/umx/man/fin_ticker.Rd | 4 umx-4.59.0/umx/man/fin_valuation.Rd | 4 umx-4.59.0/umx/man/ggAddR.Rd | 1 umx-4.59.0/umx/man/install.OpenMx.Rd | 4 umx-4.59.0/umx/man/libs.Rd | 9 umx-4.59.0/umx/man/plot.MxLISRELModel.Rd | 1 umx-4.59.0/umx/man/plot.MxModel.Rd | 1 umx-4.59.0/umx/man/plot.MxModelTwinMaker.Rd | 1 umx-4.59.0/umx/man/plot.percent.Rd | 2 umx-4.59.0/umx/man/print.percent.Rd | 2 umx-4.59.0/umx/man/prolific_anonymize.Rd | 9 umx-4.59.0/umx/man/qm.Rd | 4 umx-4.59.0/umx/man/rad2deg.Rd | 2 umx-4.59.0/umx/man/tmx_show.MxMatrix.Rd | 29 umx-4.59.0/umx/man/tmx_show.MxModel.Rd | 5 umx-4.59.0/umx/man/tmx_show.Rd | 5 umx-4.59.0/umx/man/umx.Rd | 9 umx-4.59.0/umx/man/umxBrownie.Rd | 2 umx-4.59.0/umx/man/umxCLPM.Rd | 6 umx-4.59.0/umx/man/umxDoC.Rd | 4 umx-4.59.0/umx/man/umxLav2RAM.Rd | 4 umx-4.59.0/umx/man/umxMRDoC.Rd | 39 umx-4.59.0/umx/man/umxMatrixFree.Rd | 2 umx-4.59.0/umx/man/umxModel.Rd | 3 umx-4.59.0/umx/man/umxModelNames.Rd | 4 umx-4.59.0/umx/man/umxPlot.Rd | 13 umx-4.59.0/umx/man/umxPlotACE.Rd | 1 umx-4.59.0/umx/man/umxPlotACEcov.Rd | 1 umx-4.59.0/umx/man/umxPlotACEv.Rd | 1 umx-4.59.0/umx/man/umxPlotCP.Rd | 1 umx-4.59.0/umx/man/umxPlotDoC.Rd | 3 umx-4.59.0/umx/man/umxPlotFun.Rd | 4 umx-4.59.0/umx/man/umxPlotGxE.Rd | 1 umx-4.59.0/umx/man/umxPlotGxEbiv.Rd | 1 umx-4.59.0/umx/man/umxPlotIP.Rd | 1 umx-4.59.0/umx/man/umxPlotPredict.Rd |only umx-4.59.0/umx/man/umxPlotSexLim.Rd | 1 umx-4.59.0/umx/man/umxPlotSimplex.Rd | 1 umx-4.59.0/umx/man/umxPower.Rd | 2 umx-4.59.0/umx/man/umxRAM2Lav.Rd | 4 umx-4.59.0/umx/man/umxRenameMatrix.Rd | 3 umx-4.59.0/umx/man/umxSummaryDoC.Rd | 2 umx-4.59.0/umx/man/umxVersion.Rd | 4 umx-4.59.0/umx/man/umx_APA_pval.Rd | 3 umx-4.59.0/umx/man/umx_array_shift.Rd | 4 umx-4.59.0/umx/man/umx_as_numeric.Rd | 2 umx-4.59.0/umx/man/umx_find_object.Rd | 4 umx-4.59.0/umx/man/umx_fun_mean_sd.Rd | 3 umx-4.59.0/umx/man/umx_get_alphas.Rd |only umx-4.59.0/umx/man/umx_get_bracket_addresses.Rd | 3 umx-4.59.0/umx/man/umx_get_checkpoint.Rd | 2 umx-4.59.0/umx/man/umx_get_options.Rd | 2 umx-4.59.0/umx/man/umx_long2wide.Rd | 4 umx-4.59.0/umx/man/umx_lower.tri.Rd | 4 umx-4.59.0/umx/man/umx_make.Rd | 7 umx-4.59.0/umx/man/umx_make_TwinData.Rd | 2 umx-4.59.0/umx/man/umx_make_twin_data_nice.Rd | 2 umx-4.59.0/umx/man/umx_msg.Rd | 4 umx-4.59.0/umx/man/umx_open_CRAN_page.Rd | 4 umx-4.59.0/umx/man/umx_pad.Rd | 4 umx-4.59.0/umx/man/umx_print.Rd | 4 umx-4.59.0/umx/man/umx_residualize.Rd | 2 umx-4.59.0/umx/man/umx_scale_wide_twin_data.Rd | 2 umx-4.59.0/umx/man/umx_set_auto_plot.Rd | 2 umx-4.59.0/umx/man/umx_set_auto_run.Rd | 2 umx-4.59.0/umx/man/umx_set_checkpoint.Rd | 2 umx-4.59.0/umx/man/umx_set_condensed_slots.Rd | 2 umx-4.59.0/umx/man/umx_set_cores.Rd | 2 umx-4.59.0/umx/man/umx_set_data_variance_check.Rd | 2 umx-4.59.0/umx/man/umx_set_dollar_symbol.Rd | 2 umx-4.59.0/umx/man/umx_set_optimization_options.Rd | 2 umx-4.59.0/umx/man/umx_set_optimizer.Rd | 2 umx-4.59.0/umx/man/umx_set_plot_file_suffix.Rd | 2 umx-4.59.0/umx/man/umx_set_plot_format.Rd | 2 umx-4.59.0/umx/man/umx_set_separator.Rd | 2 umx-4.59.0/umx/man/umx_set_silent.Rd | 2 umx-4.59.0/umx/man/umx_set_table_format.Rd | 2 umx-4.59.0/umx/man/umx_standardize.Rd | 3 umx-4.59.0/umx/man/umx_string_to_algebra.Rd | 3 umx-4.59.0/umx/man/umx_strings2numeric.Rd | 4 umx-4.59.0/umx/man/umx_wide2long.Rd | 96 umx-4.59.0/umx/man/umx_wide2longTwinData.Rd |only umx-4.59.0/umx/man/umx_wide4lmer.Rd |only umx-4.59.0/umx/man/xmuHasSquareBrackets.Rd | 3 umx-4.59.0/umx/man/xmuLabel_MATRIX_Model.Rd | 3 umx-4.59.0/umx/man/xmuLabel_Matrix.Rd | 3 umx-4.59.0/umx/man/xmuLabel_RAM_Model.Rd | 3 umx-4.59.0/umx/man/xmuMI.Rd | 3 umx-4.59.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 3 umx-4.59.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 3 umx-4.59.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 3 umx-4.59.0/umx/man/xmuMaxLevels.Rd | 3 umx-4.59.0/umx/man/xmuMinLevels.Rd | 3 umx-4.59.0/umx/man/xmuPropagateLabels.Rd | 3 umx-4.59.0/umx/man/xmuRAM2Ordinal.Rd | 3 umx-4.59.0/umx/man/xmuTwinSuper_Continuous.Rd | 3 umx-4.59.0/umx/man/xmuTwinSuper_NoBinary.Rd | 3 umx-4.59.0/umx/man/xmuTwinUpgradeMeansToCovariateModel.Rd | 3 umx-4.59.0/umx/man/xmu_CI_merge.Rd | 3 umx-4.59.0/umx/man/xmu_CI_stash.Rd | 3 umx-4.59.0/umx/man/xmu_DF_to_mxData_TypeCov.Rd | 3 umx-4.59.0/umx/man/xmu_PadAndPruneForDefVars.Rd | 3 umx-4.59.0/umx/man/xmu_bracket_address2rclabel.Rd | 3 umx-4.59.0/umx/man/xmu_cell_is_on.Rd | 3 umx-4.59.0/umx/man/xmu_check_levels_identical.Rd | 3 umx-4.59.0/umx/man/xmu_check_needs_means.Rd | 3 umx-4.59.0/umx/man/xmu_check_variance.Rd | 7 umx-4.59.0/umx/man/xmu_clean_label.Rd | 3 umx-4.59.0/umx/man/xmu_data_missing.Rd | 3 umx-4.59.0/umx/man/xmu_data_swap_a_block.Rd | 5 umx-4.59.0/umx/man/xmu_describe_data_WLS.Rd | 3 umx-4.59.0/umx/man/xmu_dot_define_shapes.Rd | 2 umx-4.59.0/umx/man/xmu_dot_make_paths.Rd | 3 umx-4.59.0/umx/man/xmu_dot_make_residuals.Rd | 3 umx-4.59.0/umx/man/xmu_dot_maker.Rd | 3 umx-4.59.0/umx/man/xmu_dot_mat2dot.Rd | 2 umx-4.59.0/umx/man/xmu_dot_move_ranks.Rd | 3 umx-4.59.0/umx/man/xmu_dot_rank.Rd | 2 umx-4.59.0/umx/man/xmu_dot_rank_str.Rd | 3 umx-4.59.0/umx/man/xmu_extract_column.Rd | 3 umx-4.59.0/umx/man/xmu_get_CI.Rd | 5 umx-4.59.0/umx/man/xmu_lavaan_process_group.Rd | 3 umx-4.59.0/umx/man/xmu_make_TwinSuperModel.Rd | 3 umx-4.59.0/umx/man/xmu_make_bin_cont_pair_data.Rd | 26 umx-4.59.0/umx/man/xmu_make_mxData.Rd | 3 umx-4.59.0/umx/man/xmu_match.arg.Rd | 3 umx-4.59.0/umx/man/xmu_name_from_lavaan_str.Rd | 3 umx-4.59.0/umx/man/xmu_path2twin.Rd | 3 umx-4.59.0/umx/man/xmu_path_regex.Rd | 3 umx-4.59.0/umx/man/xmu_print_algebras.Rd | 3 umx-4.59.0/umx/man/xmu_rclabel_2_bracket_address.Rd | 3 umx-4.59.0/umx/man/xmu_relevel_factors.Rd | 3 umx-4.59.0/umx/man/xmu_safe_run_summary.Rd | 3 umx-4.59.0/umx/man/xmu_set_sep_from_suffix.Rd | 3 umx-4.59.0/umx/man/xmu_show_fit_or_comparison.Rd | 3 umx-4.59.0/umx/man/xmu_simplex_corner.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACE.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACEcov.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACEv.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_CP.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_IP.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_RAM.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_SexLim.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_Simplex.Rd | 3 umx-4.59.0/umx/man/xmu_start_value_list.Rd | 3 umx-4.59.0/umx/man/xmu_starts.Rd | 3 umx-4.59.0/umx/man/xmu_summary_RAM_group_parameters.Rd | 3 umx-4.59.0/umx/man/xmu_twin_add_WeightMatrices.Rd | 3 umx-4.59.0/umx/man/xmu_twin_check.Rd | 3 umx-4.59.0/umx/man/xmu_twin_get_var_names.Rd | 3 umx-4.59.0/umx/man/xmu_twin_make_def_means_mats_and_alg.Rd | 3 umx-4.59.0/umx/man/xmu_twin_upgrade_selDvs2SelVars.Rd | 3 umx-4.59.0/umx/man/xmu_update_covar.Rd |only umx-4.59.0/umx/tests/testthat.R | 13 187 files changed, 2698 insertions(+), 2033 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 2.0.1 dated 2025-05-04 and 2.0.2 dated 2025-10-21
DESCRIPTION | 8 MD5 | 44 ++-- NEWS.md | 3 R/coro.R | 24 +- R/oa2bibliometrix.R | 46 +++- R/oa2df.R | 350 ++++++++++++++++++++++++++++---------- R/oa_fetch.R | 223 +++++++++++++++--------- R/oa_ngrams.R | 58 ++++-- R/oa_snowball.R | 35 ++- R/openalexR-internal.R | 2 R/simplify.R | 42 +++- R/utils.R | 60 ++++-- README.md | 46 +++- data/concept_abbrev.rda |binary data/oa2df_coverage.rda |binary man/oa_fetch.Rd | 7 man/show_authors.Rd | 4 man/show_works.Rd | 4 tests/testthat/test-coverage.R | 5 tests/testthat/test-group_by.R | 5 tests/testthat/test-oa_fetch.R | 20 ++ tests/testthat/test-oa_snowball.R | 16 + tests/testthat/test-utils.R | 10 - 23 files changed, 701 insertions(+), 311 deletions(-)
Title: An Interface to the Reptile Database
Description: Provides tools to retrieve and summarize taxonomic information and synonymy data for reptile species using data scraped from The Reptile Database website (<https://reptile-database.reptarium.cz/>). Outputs include clean and structured data frames useful for ecological, evolutionary, and conservation research.
Author: Joao Paulo dos Santos Vieira-Alencar [aut, cre] ,
Christoph Liedtke [aut]
Maintainer: Joao Paulo dos Santos Vieira-Alencar <joaopaulo.valencar@gmail.com>
Diff between letsRept versions 1.0.1 dated 2025-08-23 and 1.1.0 dated 2025-10-21
letsRept-1.0.1/letsRept/build/partial.rdb |only letsRept-1.1.0/letsRept/DESCRIPTION | 8 letsRept-1.1.0/letsRept/MD5 | 70 - letsRept-1.1.0/letsRept/NEWS.md | 37 letsRept-1.1.0/letsRept/R/data_allReptiles.R | 2 letsRept-1.1.0/letsRept/R/data_br_snakes_atlas.r |only letsRept-1.1.0/letsRept/R/data_synonymsRef.R | 6 letsRept-1.1.0/letsRept/R/internal_functions.R | 537 +++----- letsRept-1.1.0/letsRept/R/reptAdvancedSearch.R | 5 letsRept-1.1.0/letsRept/R/reptCompare.R | 155 +- letsRept-1.1.0/letsRept/R/reptSearch.R | 12 letsRept-1.1.0/letsRept/R/reptSpecies.R | 67 - letsRept-1.1.0/letsRept/R/reptSplitCheck.R | 17 letsRept-1.1.0/letsRept/R/reptStats.R | 7 letsRept-1.1.0/letsRept/R/reptSync.R | 24 letsRept-1.1.0/letsRept/R/reptSynonyms.R | 135 -- letsRept-1.1.0/letsRept/R/reptTidySyn.R | 2 letsRept-1.1.0/letsRept/README.md | 37 letsRept-1.1.0/letsRept/build/vignette.rds |binary letsRept-1.1.0/letsRept/data/allReptiles.rda |binary letsRept-1.1.0/letsRept/data/allSynonymsRef.rda |binary letsRept-1.1.0/letsRept/data/br_snakes_atlas.rda |only letsRept-1.1.0/letsRept/inst/CITATION | 26 letsRept-1.1.0/letsRept/inst/doc/case-study.R |only letsRept-1.1.0/letsRept/inst/doc/case-study.Rmd |only letsRept-1.1.0/letsRept/inst/doc/case-study.html |only letsRept-1.1.0/letsRept/inst/doc/letsRept.R | 23 letsRept-1.1.0/letsRept/inst/doc/letsRept.Rmd | 74 - letsRept-1.1.0/letsRept/inst/doc/letsRept.html | 910 ++++++-------- letsRept-1.1.0/letsRept/man/allReptiles.Rd | 2 letsRept-1.1.0/letsRept/man/allSynonymsRef.Rd | 6 letsRept-1.1.0/letsRept/man/br_snakes_atlas.Rd |only letsRept-1.1.0/letsRept/man/reptCompare.Rd | 28 letsRept-1.1.0/letsRept/man/reptSpecies.Rd | 13 letsRept-1.1.0/letsRept/man/reptSplitCheck.Rd | 11 letsRept-1.1.0/letsRept/man/reptSync.Rd | 6 letsRept-1.1.0/letsRept/man/reptSynonyms.Rd | 24 letsRept-1.1.0/letsRept/tests/testthat/test-reptCompare.R | 4 letsRept-1.1.0/letsRept/vignettes/case-study.Rmd |only letsRept-1.1.0/letsRept/vignettes/letsRept.Rmd | 74 - 40 files changed, 1200 insertions(+), 1122 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.5.0 dated 2025-10-19 and 0.5.1 dated 2025-10-21
DESCRIPTION | 12 - MD5 | 12 - NAMESPACE | 1 NEWS.md | 10 + R/plot_multiple_answers.R | 185 ++++++++++++++++++++++++++-- man/plot_multiple_answers.Rd | 42 +++++- tests/testthat/test-plot_multiple_answers.R | 32 ++++ 7 files changed, 272 insertions(+), 22 deletions(-)
Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching.
The contents include themes for plots, functions for simulating
quantities of interest from regression models, functions for simulating various
forms of fake data for instructional/research purposes, and many more. All told, the functions
provided here are broadly useful for data organization, data presentation, data recoding,
and data simulation.
Author: Steve Miller [aut, cre],
Ben Bolker [ctb],
Dave Armstrong [ctb],
John Fox [ctb],
Winston Chang [ctb],
Brian Ripley [ctb],
Bill Venables [ctb],
Pascal van Kooten [ctb],
Gerko Vink [ctb],
Paul Williamson [ctb],
Andreas Beger [ctb] ,
Vincent Arel-Bundoc [...truncated...]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevemisc versions 1.8.0 dated 2024-08-23 and 1.9.0 dated 2025-10-21
DESCRIPTION | 17 +++++----- MD5 | 35 +++++++++++----------- NAMESPACE | 3 + NEWS.md | 6 +++ R/at.R | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++ R/db_lselect.R | 4 +- R/linloess_plot.R | 74 ++++++++++++++++++++++++++++++++++++----------- R/print_refs.R | 51 ++++++++++++++++++++++++-------- R/ps_btscs.R | 2 - R/rd_plot.R | 11 ++++--- R/sbtscs.R | 2 - inst |only man/at.Rd | 18 +++++++++++ man/db_lselect.Rd | 4 +- man/linloess_plot.Rd | 41 ++++++++++++++++++-------- man/print_refs.Rd | 43 +++++++++++++++++++-------- man/ps_btscs.Rd | 2 - man/rd_plot.Rd | 7 +++- man/sbtscs.Rd | 2 - 19 files changed, 309 insertions(+), 93 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <hanchenphd@gmail.com>
Diff between MAGEE versions 1.4.3 dated 2025-07-12 and 1.4.4 dated 2025-10-21
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- build/vignette.rds |binary data/example.rda |binary inst/doc/MAGEE.R | 9 ++++++--- inst/doc/MAGEE.Rnw | 23 ++++++++++++++++------- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- src/fitglmm.cpp | 4 ++-- src/fitmagee.cpp | 2 +- vignettes/MAGEE.Rnw | 23 ++++++++++++++++------- 11 files changed, 59 insertions(+), 38 deletions(-)
Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant [aut, cre] ,
David Ginsbourger [aut] ,
Yves Deville [aut] ,
Clement Chevalier [ctb],
Yann Richet [ctb]
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>
Diff between DiceKriging versions 1.6.0 dated 2021-02-23 and 1.6.1 dated 2025-10-21
DiceKriging-1.6.0/DiceKriging/README.md |only DiceKriging-1.6.1/DiceKriging/CHANGELOG | 14 +++- DiceKriging-1.6.1/DiceKriging/DESCRIPTION | 39 +++++++++-- DiceKriging-1.6.1/DiceKriging/MD5 | 40 ++++++------ DiceKriging-1.6.1/DiceKriging/R/kmEstimate.R | 6 + DiceKriging-1.6.1/DiceKriging/R/kmStruct.R | 2 DiceKriging-1.6.1/DiceKriging/R/logLikFun.R | 4 - DiceKriging-1.6.1/DiceKriging/build |only DiceKriging-1.6.1/DiceKriging/inst/CITATION | 28 +++----- DiceKriging-1.6.1/DiceKriging/man/DiceKriging-package.Rd | 16 +--- DiceKriging-1.6.1/DiceKriging/man/covIso-class.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/covTensorProduct-class.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/covVector.dx.Rd | 4 - DiceKriging-1.6.1/DiceKriging/man/km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOut.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOutFun.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOutGrad.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/logLik.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/nuggetvalue.Rd | 10 +-- DiceKriging-1.6.1/DiceKriging/man/predict.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/update.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/tests/testthat/test-km.R | 13 ++- 22 files changed, 113 insertions(+), 81 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.1.1 dated 2025-07-21 and 5.1.2 dated 2025-10-21
UComp-5.1.1/UComp/src/oldBSMmodel.h |only UComp-5.1.2/UComp/ChangeLog | 3 UComp-5.1.2/UComp/DESCRIPTION | 8 UComp-5.1.2/UComp/MD5 | 41 UComp-5.1.2/UComp/R/ARIMAS3functions.R | 5 UComp-5.1.2/UComp/R/ARIMAmodel.R | 11 UComp-5.1.2/UComp/R/ETSS3functions.R | 5 UComp-5.1.2/UComp/R/ETSmodel.R | 4 UComp-5.1.2/UComp/R/ETSvalidate.R | 4 UComp-5.1.2/UComp/R/TETSS3functions.R | 5 UComp-5.1.2/UComp/R/TETSmodel.R | 4 UComp-5.1.2/UComp/R/TETSvalidate.R | 4 UComp-5.1.2/UComp/R/UCestim.R | 35 UComp-5.1.2/UComp/R/UCmodel.R | 4 UComp-5.1.2/UComp/R/tools.R | 249 - UComp-5.1.2/UComp/man/plotSlide.Rd | 84 UComp-5.1.2/UComp/man/slide.Rd | 130 UComp-5.1.2/UComp/src/ARIMAmodel.h | 34 UComp-5.1.2/UComp/src/BSMmodel.h | 6379 ++++++++++++++++----------------- UComp-5.1.2/UComp/src/ETSmodel.h | 52 UComp-5.1.2/UComp/src/SSpace.h | 14 UComp-5.1.2/UComp/src/UCompC.cpp | 33 22 files changed, 3621 insertions(+), 3487 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-20 4.1.0
2025-05-28 4.0.4
2024-11-25 4.0.3
2024-08-16 4.0.2
2024-07-10 4.0.1
2023-12-13 3.0.2
2023-05-15 3.0.1
2023-02-09 2.3.0
2022-09-02 2.2.0
2022-06-15 2.1.1
2022-04-02 2.1.0
2022-02-22 2.0.2
2022-01-06 2.0.1
2021-02-04 1.5.3
2021-01-05 1.5.2
2020-06-01 1.5.1
2020-05-29 1.5.0
2020-03-17 1.4.3
2019-10-19 1.4.2
2019-09-03 1.4.1
2019-06-06 1.4.0
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb],
Ryan A. Hill [ctb],
Marc Weber [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.3.1 dated 2025-09-30 and 0.4.0 dated 2025-10-21
DESCRIPTION | 16 MD5 | 104 +-- NEWS.md | 17 R/AIC_deprecated.R | 266 ++++----- R/AICc.R | 140 ++--- R/AUROC.R | 42 - R/SSN2.R | 62 +- R/Torgegram.R | 616 +++++++++++------------ R/anova.R | 518 +++++++++---------- R/augment.R | 566 ++++++++++----------- R/checks.R | 366 ++++++------- R/cov_matrix.R | 718 +++++++++++++------------- R/cov_vector.R | 588 ++++++++++----------- R/data.R | 254 ++++----- R/emmeans.R | 108 ++-- R/get_cov_vector.R | 132 ++-- R/get_data_object_bigdata.R | 517 ++++++++++--------- R/get_data_object_bigdata_glm.R | 39 - R/get_dist_object_bigdata.R | 584 ++++++++++----------- R/get_model_stats_bigdata_glm.R | 440 ++++++++-------- R/glance.R | 126 ++-- R/glances.R | 302 +++++------ R/initial.R | 636 +++++++++++------------ R/local.R | 8 R/logLik.R | 104 +-- R/loocv_glm.R | 476 ++++++++--------- R/plot.R | 576 ++++++++++----------- R/predict.R | 4 R/predict_glm.R | 1044 +++++++++++++++++++-------------------- R/predict_terms.R | 226 ++++---- R/ssn_glm.R | 3 R/ssn_import.R | 586 ++++++++++----------- R/ssn_lm.R | 5 R/ssn_simulate.R | 234 ++++---- R/utils.R | 170 +++--- R/zzz.R | 30 - README.md | 518 +++++++++---------- inst/doc/introduction.R | 368 ++++++------- inst/doc/introduction.Rmd | 2 inst/doc/introduction.pdf |binary inst/references.bib | 1044 ++++++++++++++++++++------------------- man/SSN2-package.Rd | 2 man/predict.SSN2.Rd | 4 man/ssn_glm.Rd | 6 man/ssn_lm.Rd | 4 tests/testthat/helper-data.R | 34 - tests/testthat/test-Torgegram.R | 156 ++--- tests/testthat/test-extras.R | 608 +++++++++++----------- tests/testthat/test-local.R | 194 +++---- tests/testthat/test-ssn-object.R | 228 ++++---- tests/testthat/test-ssn_glm.R | 618 +++++++++++------------ tests/testthat/test-ssn_lm.R | 602 +++++++++++----------- vignettes/introduction.Rmd | 2 53 files changed, 7553 insertions(+), 7460 deletions(-)
Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features
(i.e. lines and polygons) to make them more aesthetically pleasing.
Smooth curves, fill holes, and remove small fragments from lines and
polygons.
Author: Matthew Strimas-Mackey [aut, cre]
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>
Diff between smoothr versions 1.1.0 dated 2025-06-25 and 1.2.1 dated 2025-10-21
smoothr-1.1.0/smoothr/data/jagged_raster.rda |only smoothr-1.1.0/smoothr/man/jagged_raster.Rd |only smoothr-1.2.1/smoothr/DESCRIPTION | 10 +++--- smoothr-1.2.1/smoothr/MD5 | 19 +++++------- smoothr-1.2.1/smoothr/NEWS.md | 5 +++ smoothr-1.2.1/smoothr/R/data.r | 12 ------- smoothr-1.2.1/smoothr/build/vignette.rds |binary smoothr-1.2.1/smoothr/inst/doc/smoothr.R | 9 +++-- smoothr-1.2.1/smoothr/inst/doc/smoothr.Rmd | 11 +++---- smoothr-1.2.1/smoothr/inst/doc/smoothr.html | 41 ++++++++++++++------------- smoothr-1.2.1/smoothr/inst/extdata |only smoothr-1.2.1/smoothr/vignettes/smoothr.Rmd | 11 +++---- 12 files changed, 58 insertions(+), 60 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.8.2 dated 2025-09-05 and 1.9.0 dated 2025-10-21
DESCRIPTION | 10 MD5 | 16 NEWS.md | 3 R/RCM_assess.R | 757 ++++++++++++++++++++++----------------------- R/define_S4_generic_RCM.R | 4 inst/include/RCM.hpp | 35 +- inst/include/ns/ns_RCM.hpp | 38 +- man/RCM.Rd | 4 man/RCM_assess.Rd | 11 9 files changed, 459 insertions(+), 419 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.7-4 dated 2024-05-11 and 0.7-5 dated 2025-10-21
DESCRIPTION | 21 MD5 | 24 NEWS.md | 9 R/nplmodel.R | 6 build/partial.rdb |binary build/vignette.rds |binary demo/MathExam14W.R | 10 demo/VerbalAggression.R | 12 demo/toolbox1.R | 2 demo/toolbox2.R | 2 inst/doc/toolbox-simulation.pdf |binary man/itemresp.Rd | 2 tests/Examples/psychotools-Ex.Rout.save | 6883 ++++++++++++++++---------------- 13 files changed, 3502 insertions(+), 3469 deletions(-)
Title: Maps of Peru
Description: Information of the centroids and geographical limits of the regions, departments, provinces and districts of Peru.
Author: Jorge L. C. Musaja [aut, cre]
Maintainer: Jorge L. C. Musaja <musajajorge@gmail.com>
Diff between mapsPERU versions 2.0.0 dated 2023-08-14 and 2.0.1 dated 2025-10-21
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/map_DEP.R | 1 + R/map_DIST.R | 36 ++++++++++++++++++------------------ R/map_PROV.R | 1 + R/map_REG.R | 1 + data/map_DEP.rda |binary data/map_DIST.rda |binary data/map_PROV.rda |binary data/map_REG.rda |binary man/map_DEP.Rd | 1 + man/map_DIST.Rd | 2 +- man/map_PROV.Rd | 1 + man/map_REG.Rd | 1 + 14 files changed, 42 insertions(+), 36 deletions(-)
Title: Create 'Makefiles' Using R
Description: A user-friendly interface for the construction of
'Makefiles'.
Author: Andreas Dominik Cullmann [aut, cre],
Kirill Mueller [aut]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between MakefileR versions 1.0 dated 2016-01-08 and 1.1.0 dated 2025-10-21
MakefileR-1.0/MakefileR/inst/doc/demo.R |only MakefileR-1.0/MakefileR/inst/doc/demo.Rmd |only MakefileR-1.0/MakefileR/inst/doc/demo.html |only MakefileR-1.0/MakefileR/inst/web |only MakefileR-1.0/MakefileR/vignettes/demo.Rmd |only MakefileR-1.1.0/MakefileR/.Rinstignore |only MakefileR-1.1.0/MakefileR/DESCRIPTION | 34 ++-- MakefileR-1.1.0/MakefileR/MD5 | 81 ++++------ MakefileR-1.1.0/MakefileR/NEWS.md | 19 ++ MakefileR-1.1.0/MakefileR/R/MakefileR-package.R |only MakefileR-1.1.0/MakefileR/R/comment.R | 2 MakefileR-1.1.0/MakefileR/R/def.R | 14 + MakefileR-1.1.0/MakefileR/R/file.R | 2 MakefileR-1.1.0/MakefileR/R/group.R | 6 MakefileR-1.1.0/MakefileR/R/rule.R | 2 MakefileR-1.1.0/MakefileR/R/text.R | 2 MakefileR-1.1.0/MakefileR/R/throw.R |only MakefileR-1.1.0/MakefileR/R/zzz-autoroxy.R |only MakefileR-1.1.0/MakefileR/README.md | 64 +++++++ MakefileR-1.1.0/MakefileR/build/vignette.rds |binary MakefileR-1.1.0/MakefileR/inst/NEWS.rd |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.R |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.Rmd |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.html |only MakefileR-1.1.0/MakefileR/inst/runit_tests |only MakefileR-1.1.0/MakefileR/inst/tinytest |only MakefileR-1.1.0/MakefileR/inst/vignettes_code |only MakefileR-1.1.0/MakefileR/man/Concatenation.Rd | 3 MakefileR-1.1.0/MakefileR/man/MakefileR-package.Rd |only MakefileR-1.1.0/MakefileR/man/make_comment.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_def.Rd | 17 +- MakefileR-1.1.0/MakefileR/man/make_group.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_rule.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_text.Rd | 12 - MakefileR-1.1.0/MakefileR/man/makefile.Rd | 3 MakefileR-1.1.0/MakefileR/man/throw.Rd |only MakefileR-1.1.0/MakefileR/man/write_makefile.Rd | 1 MakefileR-1.1.0/MakefileR/tests/runit.R |only MakefileR-1.1.0/MakefileR/tests/testthat.R | 2 MakefileR-1.1.0/MakefileR/tests/testthat/test-def.R | 2 MakefileR-1.1.0/MakefileR/tests/testthat/test-file.R | 6 MakefileR-1.1.0/MakefileR/tests/testthat/test-rule.R | 6 MakefileR-1.1.0/MakefileR/tests/testthat/test-throw.R |only MakefileR-1.1.0/MakefileR/tests/testthat/test-write.R |only MakefileR-1.1.0/MakefileR/tests/tinytest.R |only MakefileR-1.1.0/MakefileR/vignettes/An_Introduction_to_MakefileR.Rmd |only 46 files changed, 200 insertions(+), 114 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.87 dated 2025-09-29 and 2.0.88 dated 2025-10-21
DESCRIPTION | 8 MD5 | 68 +- NEWS | 12 R/epi.nomogram.R | 68 +- R/epi.ssdxsesp.R | 50 + R/rsu.dxtest.R | 805 +++++++++++++++++++++++++---- inst/doc/epiR_descriptive.R | 60 +- inst/doc/epiR_descriptive.Rmd | 176 ++++-- inst/doc/epiR_descriptive.html | 225 +++----- inst/doc/epiR_measures_of_association.R | 78 +- inst/doc/epiR_measures_of_association.Rmd | 137 ++-- inst/doc/epiR_measures_of_association.html | 163 ++--- inst/doc/epiR_sample_size.Rmd | 14 inst/doc/epiR_sample_size.html | 22 inst/doc/epiR_surveillance.R | 52 + inst/doc/epiR_surveillance.Rmd | 68 +- inst/doc/epiR_surveillance.html | 35 - man/epi.bohning.Rd | 2 man/epi.nomogram.Rd | 14 man/epi.ssdxsesp.Rd | 37 + man/rsu.dxtest.Rd | 104 ++- man/rsu.sssep.rs.Rd | 22 vignettes/epiR_descriptive.Rmd | 176 ++++-- vignettes/epiR_measures_of_association.Rmd | 137 ++-- vignettes/epiR_sample_size.Rmd | 14 vignettes/epiR_surveillance.Rmd | 68 +- vignettes/epidemic_curve-01.png |only vignettes/epidemic_curve-02.png |only vignettes/epidemic_curve-03.png |only vignettes/epidemic_curve-04.png |only vignettes/epidemic_curve-05.png |only vignettes/epidemic_curve-06.png |only vignettes/epidemic_curve-07.png |only vignettes/epidemic_curve-08.png |only vignettes/epidemic_curve-09.png |only vignettes/low_bw_adjusted_or.png |only vignettes/low_bw_unadjusted_or.png |only vignettes/map-01.png |only vignettes/map-02.png |only vignettes/prob_dis_freedom.png |only vignettes/ranked_error_bar-01.png |only vignettes/ranked_error_bar-02.png |only vignettes/styles.css | 15 43 files changed, 1761 insertions(+), 869 deletions(-)
Title: Zero-Variance Control Variates
Description: Stein control variates can be used to improve Monte Carlo estimates of expectations when the derivatives of the log target are available. This package implements a variety of such methods, including zero-variance control variates (ZV-CV, Mira et al. (2013) <doi:10.1007/s11222-012-9344-6>), regularised ZV-CV (South et al., 2023 <doi:10.1214/22-BA1328>), control functionals (CF, Oates et al. (2017) <doi:10.1111/rssb.12185>) and semi-exact control functionals (SECF, South et al., 2022 <doi:10.1093/biomet/asab036>). ZV-CV is a parametric approach that is exact for (low order) polynomial integrands with Gaussian targets. CF is a non-parametric alternative that offers better than the standard Monte Carlo convergence rates. SECF has both a parametric and a non-parametric component and it offers the advantages of both for an additional computational cost. Functions for applying ZV-CV and CF to two estimators for the normalising constant of the posterior distribution in [...truncated...]
Author: Leah F. South [aut, cre]
Maintainer: Leah F. South <leah.south@hdr.qut.edu.au>
Diff between ZVCV versions 2.1.2 dated 2022-11-02 and 2.1.3 dated 2025-10-20
DESCRIPTION | 15 +++++----- MD5 | 44 +++++++++++++++---------------- NEWS.md | 10 ++++++- R/Expand_Temperatures.R | 2 - R/RcppExports.R | 10 +++---- R/ZVCV_package.R | 14 +++++----- R/evidence_CTI.R | 2 - R/kernel_methods.R | 62 ++++++++++++++++++++++----------------------- R/zvcv.R | 4 +- man/CF.Rd | 16 +++++------ man/CF_crossval.Rd | 16 +++++------ man/Expand_Temperatures.Rd | 2 - man/K0_fn.Rd | 10 +++---- man/Phi_fn.Rd | 4 +- man/SECF.Rd | 20 +++++++------- man/SECF_crossval.Rd | 20 +++++++------- man/ZVCV_package.Rd | 15 +++++----- man/aSECF.Rd | 16 +++++------ man/aSECF_crossval.Rd | 16 +++++------ man/evidence.Rd | 10 +++---- man/zvcv.Rd | 8 ++--- src/fnToExport.cpp | 10 +++---- src/getPoly.cpp | 7 +++-- 23 files changed, 173 insertions(+), 160 deletions(-)
Title: Test Investment Strategies with English-Like Code
Description: Design, backtest, and analyze portfolio strategies using simple,
English-like function chains. Includes technical indicators, flexible stock
selection, portfolio construction methods (equal weighting, signal weighting,
inverse volatility, hierarchical risk parity), and a compact backtesting
engine for portfolio returns, drawdowns, and summary metrics.
Author: Alberto Pallotta [aut, cre]
Maintainer: Alberto Pallotta <pallottaalberto@gmail.com>
Diff between PortfolioTesteR versions 0.1.2 dated 2025-09-29 and 0.1.3 dated 2025-10-20
PortfolioTesteR-0.1.2/PortfolioTesteR/man/figures |only PortfolioTesteR-0.1.3/PortfolioTesteR/DESCRIPTION | 14 PortfolioTesteR-0.1.3/PortfolioTesteR/MD5 | 114 +- PortfolioTesteR-0.1.3/PortfolioTesteR/NAMESPACE | 17 PortfolioTesteR-0.1.3/PortfolioTesteR/NEWS.md | 102 +- PortfolioTesteR-0.1.3/PortfolioTesteR/R/filters.R | 111 -- PortfolioTesteR-0.1.3/PortfolioTesteR/R/globals.R | 4 PortfolioTesteR-0.1.3/PortfolioTesteR/R/ml.R | 433 ++++++---- PortfolioTesteR-0.1.3/PortfolioTesteR/R/ml_helper.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/R/performance_analytics.R | 429 ++++++--- PortfolioTesteR-0.1.3/PortfolioTesteR/R/utils.R | 406 +++++++++ PortfolioTesteR-0.1.3/PortfolioTesteR/R/weighting.R | 48 - PortfolioTesteR-0.1.3/PortfolioTesteR/README.md | 4 PortfolioTesteR-0.1.3/PortfolioTesteR/build/vignette.rds |binary PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.Rmd |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/Getting_Started_Advanced.html |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.Rmd | 11 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/getting-started.html | 13 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/optimization-walkforward.Rmd | 3 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/doc/optimization-walkforward.html | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/cap_exposure_caps.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_quality_momentum_inverse_vol.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_regime_hrp_momentum.R | 1 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/demo_wf_full_diagnostics.R | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/limit_positions_selection_basic.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_sequence_gru_pooled.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_tabular_ensemble.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/ml_tabular_xgb_sector_neutral.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/inst/examples/vol_target_momentum_top10_eq.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/PortfolioTesteR-package.Rd | 6 PortfolioTesteR-0.1.3/PortfolioTesteR/man/analyze_by_period.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/analyze_vs_benchmark.Rd | 42 PortfolioTesteR-0.1.3/PortfolioTesteR/man/calculate_daily_values.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/cap_exposure.Rd | 74 + PortfolioTesteR-0.1.3/PortfolioTesteR/man/combine_scores.Rd | 24 PortfolioTesteR-0.1.3/PortfolioTesteR/man/demo_sector_map.Rd | 35 PortfolioTesteR-0.1.3/PortfolioTesteR/man/download_sp500_sectors.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/join_panels.Rd | 13 PortfolioTesteR-0.1.3/PortfolioTesteR/man/limit_positions.Rd | 52 - PortfolioTesteR-0.1.3/PortfolioTesteR/man/load_mixed_symbols.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/make_labels.Rd | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_add_interactions.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_ic_series_on_scores.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_ensemble.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_model.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_make_seq_model.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_panel_op.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_panel_reduce.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_plot_ic_roll.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/ml_prepare_features.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/panel_lag.Rd | 17 PortfolioTesteR-0.1.3/PortfolioTesteR/man/panel_returns_simple.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/perf_metrics.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/portfolio_returns.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/roll_ic_stats.Rd | 16 PortfolioTesteR-0.1.3/PortfolioTesteR/man/run_example.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/select_top_k_scores_by_group.Rd | 38 PortfolioTesteR-0.1.3/PortfolioTesteR/man/sql_adapter.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/sql_adapter_adjusted.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/man/tune_ml_backtest.Rd | 114 +- PortfolioTesteR-0.1.3/PortfolioTesteR/man/validate_group_map.Rd | 22 PortfolioTesteR-0.1.3/PortfolioTesteR/man/vol_target.Rd |only PortfolioTesteR-0.1.3/PortfolioTesteR/man/weight_by_risk_parity.Rd | 46 - PortfolioTesteR-0.1.3/PortfolioTesteR/man/wf_sweep_tabular.Rd | 108 +- PortfolioTesteR-0.1.3/PortfolioTesteR/man/yahoo_adapter.Rd | 2 PortfolioTesteR-0.1.3/PortfolioTesteR/tests/testthat/test-ml-helpers.R |only PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/Getting_Started_Advanced.Rmd |only PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/getting-started.Rmd | 11 PortfolioTesteR-0.1.3/PortfolioTesteR/vignettes/optimization-walkforward.Rmd | 3 71 files changed, 1610 insertions(+), 783 deletions(-)
More information about PortfolioTesteR at CRAN
Permanent link
Title: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix
Factorizations to Count Data
Description: Implements fast, scalable optimization algorithms for
fitting topic models ("grade of membership" models) and
non-negative matrix factorizations to count data. The methods
exploit the special relationship between the multinomial topic
model (also, "probabilistic latent semantic indexing") and Poisson
non-negative matrix factorization. The package provides tools to
compare, annotate and visualize model fits, including functions to
efficiently create "structure plots" and identify key features in
topics. The 'fastTopics' package is a successor to the
'CountClust' package. For more information, see
<doi:10.48550/arXiv.2105.13440> and
<doi:10.1186/s13059-023-03067-9>. Please also see the GitHub
repository for additional vignettes not included in the package on
CRAN.
Author: Peter Carbonetto [aut, cre],
Kevin Luo [aut],
Kushal Dey [aut],
Joyce Hsiao [ctb],
Abhishek Sarkar [ctb],
Anthony Hung [ctb],
Xihui Lin [ctb],
Paul C. Boutros [ctb],
Minzhe Wang [ctb],
Tracy Ke [ctb],
Eric Weine [ctb],
Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between fastTopics versions 0.6-192 dated 2024-07-09 and 0.7-30 dated 2025-10-20
DESCRIPTION | 11 +++++----- LICENSE | 2 - MD5 | 35 ++++++++++++++++++++------------- NAMESPACE | 6 +++++ R/annotation_heatmap.R |only R/fit_poisson_nmf.R | 16 ++++++++++----- R/newsgroups.R |only R/structure_plot.R | 28 ++++++++++++++++---------- README.md | 2 - build/vignette.rds |binary data/newsgroups.RData |only inst/doc/relationship.html | 11 +++++----- inst/doc/single_cell_rnaseq_basic.R |only inst/doc/single_cell_rnaseq_basic.Rmd |only inst/doc/single_cell_rnaseq_basic.html |only inst/doc/topics_vs_clusters.html | 6 ++--- man/annotation_heatmap.Rd |only man/fit_poisson_nmf.Rd | 14 +++++++++---- man/newsgroups.Rd |only man/structure_plot.Rd | 19 ++++++++++++++++- src/Makevars | 2 - src/Makevars.win | 2 - vignettes/single_cell_rnaseq_basic.Rmd |only 23 files changed, 103 insertions(+), 51 deletions(-)
Title: Group Sequential Design for Historical Control Trial with
Survival Outcome
Description: It provides functions to design historical controlled trials with survival outcome by group sequential method. The options for interim look boundaries are efficacy only, efficacy & futility or futility only. It also provides the function to monitor the trial for any unplanned look. The package is based on Jianrong Wu, Xiaoping Xiong (2016) <doi:10.1002/pst.1756> and Jianrong Wu, Yimei Li (2020) <doi:10.1080/10543406.2019.1684305>.
Author: Tushar Patni [aut, cre],
Yimei Li [aut],
Jianrong Wu [aut]
Maintainer: Tushar Patni <tushar.patni006@gmail.com>
Diff between HCTDesign versions 0.7.3 dated 2025-08-29 and 0.7.4 dated 2025-10-20
DESCRIPTION | 8 +- MD5 | 40 ++++++------ NAMESPACE | 2 R/EffIM.R | 2 R/FuttIM.R | 2 R/HCT.R | 12 ++- R/IM.R | 2 R/SM.R | 163 ++++++++++++++++++++++++++++----------------------- R/alpha.R | 11 ++- R/beta.R | 11 ++- R/calendar_time.R |only R/sf.R | 2 build/partial.rdb |binary man/EffDesign.Rd | 2 man/EffIM.Rd | 2 man/FutDesign.Rd | 2 man/FutIM.Rd | 2 man/HCTSurvDesign.Rd | 2 man/IM.Rd | 2 man/SM.Rd | 6 - man/calendar_time.Rd |only man/sf.Rd | 2 22 files changed, 156 insertions(+), 119 deletions(-)
More information about SimplicialComplex at CRAN
Permanent link
Title: Extract Data from Professional Volleyball Leagues in North
America
Description: Gather boxscore, play-by-play, and auxiliary data from Major League Volleyball (MLV) <https://provolleyball.com>, League One Volleyball Pro (LOVB Pro) <https://www.lovb.com/pro-league>, and Athletes Unlimited Pro Volleyball <https://auprosports.com/volleyball/> to create a repository of basic and advanced statistics for teams and players.
Author: David Awosoga [aut, cre, cph] ,
Matthew Chow [aut] ,
Ryan Du [aut]
Maintainer: David Awosoga <odo.awosoga@gmail.com>
Diff between rvolleydata versions 1.0.0 dated 2025-09-02 and 1.1.0 dated 2025-10-20
DESCRIPTION | 6 - MD5 | 31 +++++--- NAMESPACE | 4 + NEWS.md | 11 ++- R/lovb.R | 119 +++++++++++++++++++++++++++++++++ R/mlv.R | 123 ++++++++++++++++++++++++++++++++++- README.md | 10 ++ inst/doc/rvolleydata-how-to-use.R | 12 ++- inst/doc/rvolleydata-how-to-use.Rmd | 32 +++++++-- inst/doc/rvolleydata-how-to-use.html | 98 ++++++++++++++++++++++++--- man/figures/logo.svg |only man/load_lovb_player_boxscore.Rd | 58 +++++++++------- man/load_lovb_player_info.Rd |only man/load_lovb_team_boxscore.Rd |only man/load_mlv_player_boxscore.Rd | 59 +++++++++------- man/load_mlv_player_info.Rd |only man/load_mlv_team_boxscore.Rd |only tests/testthat/test_get_data.R | 16 ++-- vignettes/rvolleydata-how-to-use.Rmd | 32 +++++++-- 19 files changed, 501 insertions(+), 110 deletions(-)
Title: Feature Selection
Description: Feature subset selection algorithms modularized in search algorithms and measure utilities.
Author: Alfonso Jimenez-Vilchez [aut, cre],
Francisco Aragon-Royon [aut],
Adan M. Rodriguez [aut],
Antonio Arauzo-Azofra [aut],
Jose Manuel Benitez [aut]
Maintainer: Alfonso Jimenez-Vilchez <i52jivia@uco.es>
This is a re-admission after prior archival of version 2.0.5 dated 2020-11-23
Diff between FSinR versions 2.0.5 dated 2020-11-23 and 2.0.8 dated 2025-10-20
DESCRIPTION | 20 MD5 | 167 ++- NAMESPACE | 1 NEWS |only NEWS.md |only R/Jd.R | 50 - R/LCC.R | 2 R/RFSM.R | 4 R/chi2.R | 4 R/consistency.R | 40 R/determinationCoefficient.R | 2 R/directFeatureSelection.R | 2 R/directSearchGenerator.R | 4 R/discrete.R | 11 R/entropy.R | 28 R/exhaustiveSearch.R | 8 R/fScore.R | 6 R/featureSelection.R | 2 R/filterGenerator.R | 5 R/gini.R | 11 R/hybridFeatureSelection.R | 2 R/hybridSearchGenerator.R | 2 R/localSearch.R | 8 R/mdlc.R | 9 R/metaheuristic.R | 16 R/probabilistic.R | 11 R/relief.R | 389 +++------ R/searchGenerator.R | 4 R/selectIndividualFeatures.R | 24 R/sequentialSelection.R | 33 R/wrapperGenerator.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FSinR.R | 34 inst/doc/FSinR.html | 601 ++++++++------ inst/doc/methods.R | 12 inst/doc/methods.Rmd | 2 inst/doc/methods.html | 1219 ++++++++++++----------------- man/IEConsistency.Rd | 11 man/IEPConsistency.Rd | 11 man/Jd.Rd | 4 man/LCC.Rd | 2 man/LasVegas.Rd | 9 man/MDLC.Rd | 9 man/ReliefFeatureSetMeasure.Rd | 2 man/antColony.Rd | 4 man/binaryConsistency.Rd | 9 man/breadthFirst.Rd | 4 man/chiSquared.Rd | 2 man/cramer.Rd | 2 man/deepFirst.Rd | 4 man/determinationCoefficient.Rd | 2 man/directFeatureSelection.Rd | 2 man/directSearchAlgorithm.Rd | 4 man/featureSelection.Rd | 2 man/filterEvaluator.Rd | 2 man/fscore.Rd | 2 man/gainRatio.Rd | 10 man/geneticAlgorithm.Rd | 4 man/giniIndex.Rd | 11 man/hillClimbing.Rd | 4 man/hybridFeatureSelection.Rd | 2 man/hybridSearchAlgorithm.Rd | 2 man/is.discrete.Rd |only man/mutualInformation.Rd | 10 man/normalizedRelief.Rd | 2 man/normalizedReliefFeatureSetMeasure.Rd | 2 man/relief.Rd | 2 man/roughsetConsistency.Rd | 9 man/searchAlgorithm.Rd | 4 man/selectDifference.Rd | 4 man/selectKBest.Rd | 4 man/selectPercentile.Rd | 4 man/selectSlope.Rd | 4 man/selectThreshold.Rd | 4 man/selectThresholdRange.Rd | 4 man/sequentialBackwardSelection.Rd | 4 man/sequentialFloatingBackwardSelection.Rd | 4 man/sequentialFloatingForwardSelection.Rd | 6 man/sequentialForwardSelection.Rd | 4 man/simulatedAnnealing.Rd | 4 man/symmetricalUncertain.Rd | 8 man/tabu.Rd | 4 man/whaleOptimization.Rd | 4 man/wrapperEvaluator.Rd | 2 vignettes/methods.Rmd | 2 86 files changed, 1445 insertions(+), 1505 deletions(-)
More information about compIndexBuilder at CRAN
Permanent link
Title: Design and Analyze Choice-Based Conjoint Experiments
Description: Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, frequency-based designs, and D-optimal designs, as well as "labeled" designs (also known as "alternative-specific designs"), designs with "no choice" options, and designs with dominant alternatives removed. Conveniently inspect and compare designs using a variety of metrics, including design balance, overlap, and D-error, and simulate choice data for a survey design either randomly or according to a utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Bayesian D-efficient designs using the 'cea' and 'modfed' methods are obtained using the 'idefix' package by Traets et al (2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package by He [...truncated...]
Author: John Helveston [cre, aut, cph]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between cbcTools versions 0.6.4 dated 2025-09-23 and 0.7.1 dated 2025-10-20
cbcTools-0.6.4/cbcTools/R/decode.R |only cbcTools-0.6.4/cbcTools/tests/testthat/test_decode.R |only cbcTools-0.7.1/cbcTools/DESCRIPTION | 6 cbcTools-0.7.1/cbcTools/MD5 | 89 - cbcTools-0.7.1/cbcTools/NAMESPACE | 10 cbcTools-0.7.1/cbcTools/NEWS.md | 11 cbcTools-0.7.1/cbcTools/R/choices.R | 69 - cbcTools-0.7.1/cbcTools/R/compare.R | 17 cbcTools-0.7.1/cbcTools/R/depreciated.R |only cbcTools-0.7.1/cbcTools/R/design.R | 165 +- cbcTools-0.7.1/cbcTools/R/design_optim.R | 6 cbcTools-0.7.1/cbcTools/R/encode.R |only cbcTools-0.7.1/cbcTools/R/input_checks.R | 41 cbcTools-0.7.1/cbcTools/R/inspect.R | 288 +++- cbcTools-0.7.1/cbcTools/R/methods.R | 447 +++++- cbcTools-0.7.1/cbcTools/R/power.R | 3 cbcTools-0.7.1/cbcTools/R/util.R | 1 cbcTools-0.7.1/cbcTools/R/validate_design.R |only cbcTools-0.7.1/cbcTools/README.md | 18 cbcTools-0.7.1/cbcTools/build/vignette.rds |binary cbcTools-0.7.1/cbcTools/inst/doc/choices.R | 10 cbcTools-0.7.1/cbcTools/inst/doc/choices.Rmd | 10 cbcTools-0.7.1/cbcTools/inst/doc/choices.html | 264 +-- cbcTools-0.7.1/cbcTools/inst/doc/design.R | 20 cbcTools-0.7.1/cbcTools/inst/doc/design.Rmd | 51 cbcTools-0.7.1/cbcTools/inst/doc/design.html | 727 +++++------ cbcTools-0.7.1/cbcTools/inst/doc/encoding.R |only cbcTools-0.7.1/cbcTools/inst/doc/encoding.Rmd |only cbcTools-0.7.1/cbcTools/inst/doc/encoding.html |only cbcTools-0.7.1/cbcTools/inst/doc/getting-started.R | 2 cbcTools-0.7.1/cbcTools/inst/doc/getting-started.Rmd | 6 cbcTools-0.7.1/cbcTools/inst/doc/getting-started.html | 293 +--- cbcTools-0.7.1/cbcTools/inst/doc/power.R | 26 cbcTools-0.7.1/cbcTools/inst/doc/power.Rmd | 32 cbcTools-0.7.1/cbcTools/inst/doc/power.html | 666 +++++----- cbcTools-0.7.1/cbcTools/man/cbc_decode.Rd | 34 cbcTools-0.7.1/cbcTools/man/cbc_encode.Rd |only cbcTools-0.7.1/cbcTools/man/cbc_inspect.Rd | 2 cbcTools-0.7.1/cbcTools/man/infer_categorical_structure.Rd |only cbcTools-0.7.1/cbcTools/man/infer_encoding.Rd |only cbcTools-0.7.1/cbcTools/man/infer_from_coded_columns.Rd |only cbcTools-0.7.1/cbcTools/man/reconstruct_design_attributes.Rd |only cbcTools-0.7.1/cbcTools/man/validate_design_object.Rd |only cbcTools-0.7.1/cbcTools/man/validate_or_reconstruct.Rd |only cbcTools-0.7.1/cbcTools/tests/testthat/test_choices.R | 31 cbcTools-0.7.1/cbcTools/tests/testthat/test_design.R | 12 cbcTools-0.7.1/cbcTools/tests/testthat/test_encode.R |only cbcTools-0.7.1/cbcTools/tests/testthat/test_inspection.R | 153 -- cbcTools-0.7.1/cbcTools/tests/testthat/test_power.R | 187 -- cbcTools-0.7.1/cbcTools/vignettes/choices.Rmd | 10 cbcTools-0.7.1/cbcTools/vignettes/design.Rmd | 51 cbcTools-0.7.1/cbcTools/vignettes/encoding.Rmd |only cbcTools-0.7.1/cbcTools/vignettes/getting-started.Rmd | 6 cbcTools-0.7.1/cbcTools/vignettes/power.Rmd | 32 54 files changed, 2042 insertions(+), 1754 deletions(-)
Title: Calculation of the Water Deficit Index (WDI) and the Evaporative
Fraction (EF) on Rasters
Description: Provides functions to calculate the Water Deficit Index (WDI) and
the Evaporative Fraction (EF) using geospatial raster data such as fractional
vegetation cover (FVC) and surface-air temperature difference (TS-TA).
The package automates regression-based edge fitting and produces continuous
spatial maps of surface moisture and evaporative dynamics.
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>
Diff between wdiEF versions 1.0.3 dated 2025-02-19 and 1.0.4 dated 2025-10-20
DESCRIPTION | 29 +++++++++---- MD5 | 10 ++-- NAMESPACE | 1 NEWS.md | 5 -- R/calculate_EF.R | 115 +++++++++++++++++++++--------------------------------- R/calculate_WDI.R | 101 ++++++++++++++++++++--------------------------- 6 files changed, 117 insertions(+), 144 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut, cre],
Julian Zhou [aut],
Nima Nouri [aut],
Noah Yann Lee [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between shazam versions 1.2.0 dated 2023-10-02 and 1.3.0 dated 2025-10-20
shazam-1.2.0/shazam/vignettes/Baseline-Vignette.md |only shazam-1.3.0/shazam/DESCRIPTION | 16 - shazam-1.3.0/shazam/MD5 | 111 ++++----- shazam-1.3.0/shazam/NAMESPACE | 1 shazam-1.3.0/shazam/NEWS.md | 56 ++++- shazam-1.3.0/shazam/R/Baseline.R | 56 ++--- shazam-1.3.0/shazam/R/Core.R | 10 shazam-1.3.0/shazam/R/Deprecated.R | 2 shazam-1.3.0/shazam/R/DistToNearest.R | 167 ++++++++++----- shazam-1.3.0/shazam/R/MutationProfiling.R | 83 +++---- shazam-1.3.0/shazam/R/RegionDefinitions.R | 6 shazam-1.3.0/shazam/R/RegionsExtend.R | 12 - shazam-1.3.0/shazam/R/Shazam.R | 9 shazam-1.3.0/shazam/R/Shmulate.R | 12 - shazam-1.3.0/shazam/R/TargetingModels.R | 44 +-- shazam-1.3.0/shazam/README.md | 10 shazam-1.3.0/shazam/build/partial.rdb |binary shazam-1.3.0/shazam/build/vignette.rds |binary shazam-1.3.0/shazam/inst/CITATION | 11 shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.R | 100 ++++---- shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.Rmd | 4 shazam-1.3.0/shazam/inst/doc/Baseline-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.R | 14 - shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/DistToNearest-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.R | 38 +-- shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.Rmd | 42 +-- shazam-1.3.0/shazam/inst/doc/Mutation-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Shmulate-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/Shmulate-Vignette.pdf |binary shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.R | 42 +-- shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.Rmd | 2 shazam-1.3.0/shazam/inst/doc/Targeting-Vignette.pdf |binary shazam-1.3.0/shazam/man/Baseline-class.Rd | 2 shazam-1.3.0/shazam/man/IMGT_SCHEMES.Rd | 6 shazam-1.3.0/shazam/man/TargetingModel-class.Rd | 2 shazam-1.3.0/shazam/man/calcObservedMutations.Rd | 4 shazam-1.3.0/shazam/man/collapseClones.Rd | 8 shazam-1.3.0/shazam/man/createBaseline.Rd | 2 shazam-1.3.0/shazam/man/createMutabilityMatrix.Rd | 6 shazam-1.3.0/shazam/man/createSubstitutionMatrix.Rd | 6 shazam-1.3.0/shazam/man/createTargetingModel.Rd | 6 shazam-1.3.0/shazam/man/distToNearest.Rd | 17 - shazam-1.3.0/shazam/man/expectedMutations.Rd | 2 shazam-1.3.0/shazam/man/observedMutations.Rd | 4 shazam-1.3.0/shazam/man/plotBaselineDensity.Rd | 2 shazam-1.3.0/shazam/man/plotBaselineSummary.Rd | 2 shazam-1.3.0/shazam/man/shazam-package.Rd | 3 shazam-1.3.0/shazam/man/shazam.Rd | 3 shazam-1.3.0/shazam/man/shmulateSeq.Rd | 9 shazam-1.3.0/shazam/man/slideWindowTunePlot.Rd | 2 shazam-1.3.0/shazam/man/testBaseline.Rd | 6 shazam-1.3.0/shazam/vignettes/Baseline-Vignette.Rmd | 4 shazam-1.3.0/shazam/vignettes/DistToNearest-Vignette.Rmd | 2 shazam-1.3.0/shazam/vignettes/Mutation-Vignette.Rmd | 42 +-- shazam-1.3.0/shazam/vignettes/Shmulate-Vignette.Rmd | 2 shazam-1.3.0/shazam/vignettes/Targeting-Vignette.Rmd | 2 57 files changed, 558 insertions(+), 438 deletions(-)
Title: Viral Quasispecies Comparison from Long-Read Sequencing Data
Description: Performs variety of viral quasispecies diversity analyses [see Pamornchainavakul et al. (2024) <doi:10.21203/rs.3.rs-4637890/v1>] based on long-read sequence alignment. Main functions include 1) sequencing error and other noise minimization and read sampling, 2) Single nucleotide variant (SNV) profiles comparison, and 3) viral quasispecies profiles comparison and visualization.
Author: Nakarin Pamornchainavakul [aut, cre]
Maintainer: Nakarin Pamornchainavakul <pamornakarin@gmail.com>
Diff between longreadvqs versions 0.1.3 dated 2024-08-26 and 0.1.4 dated 2025-10-20
DESCRIPTION | 20 ++++++++++---------- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- NEWS.md | 7 +++++++ R/AAcompare.R | 9 +++++++-- R/otucompare.R | 7 ++++++- R/pctopt.R | 1 - R/vqsassess.R | 6 +++--- R/vqscompare.R | 11 ++++++++--- R/vqscustompct.R | 6 +++--- R/vqsresub.R | 4 ++-- R/vqssub.R | 6 +++--- README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/longreadvqs-vignette.html | 22 +++++++++++----------- 16 files changed, 77 insertions(+), 56 deletions(-)
Title: Fast Data Summary Reports
Description: Generates an RMarkdown data report with two components:
a summary of an input dataset and a diff of the dataset relative to an old version.
Author: Bryant Cong [aut, cre]
Maintainer: Bryant Cong <bryant.bcp@gmail.com>
Diff between datareportR versions 0.1 dated 2025-10-16 and 0.1.1 dated 2025-10-20
datareportR-0.1.1/datareportR/DESCRIPTION | 6 +++--- datareportR-0.1.1/datareportR/MD5 | 10 +++------- datareportR-0.1.1/datareportR/R/render_data_report.R | 2 +- datareportR-0.1.1/datareportR/README.md | 8 +++++++- datareportR-0.1/datareportR/inst |only datareportR-0.1/datareportR/tests |only 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Hierarchical Heatmaps
Description: Allows users to create high-quality heatmaps from labelled, hierarchical data. Specifically, for data with a two-level hierarchical structure, it will produce a heatmap where each row and column represents a category at the lower level. These rows and columns are then grouped by the higher-level group each category belongs to, with the names for each category and groups shown in the margins. While other packages (e.g. 'dendextend') allow heatmap rows and columns to be arranged by groups only, 'hhmR' also allows the labelling of the data at both the category and group level.
Author: Michael Mahony [cre, aut, cph] ,
Francisco Rowe [aut] ,
Carmen Cabrera-Arnau [aut]
Maintainer: Michael Mahony <michael.mahony@cantab.net>
Diff between hhmR versions 0.0.1 dated 2025-01-14 and 0.0.1.1 dated 2025-10-20
DESCRIPTION | 17 MD5 | 12 build/vignette.rds |binary data/example_migration.RData |binary data/example_time_series.RData |binary inst/doc/hhmR_overview.R | 2136 ++++++++++++++++++++--------------------- inst/doc/hhmR_overview.html | 1743 ++++++++++++++++----------------- 7 files changed, 1955 insertions(+), 1953 deletions(-)
Title: Scale Invariant Probabilistic Neural Networks
Description: Scale invariant version of the original PNN proposed by Specht (1990) <doi:10.1016/0893-6080(90)90049-q> with the added functionality of allowing for smoothing along multiple dimensions while accounting for covariances within the data set. It is written in the R statistical programming language. Given a data set with categorical variables, we use this algorithm to estimate the probabilities of a new observation vector belonging to a specific category. This type of neural network provides the benefits of fast training time relative to backpropagation and statistical generalization with only a small set of known observations.
Author: Romin Ebrahimi [aut, cre]
Maintainer: Romin Ebrahimi <romin.ebrahimi@utexas.edu>
Diff between spnn versions 1.2.1 dated 2020-01-08 and 1.3.0 dated 2025-10-20
DESCRIPTION | 14 +++++++++----- MD5 | 15 ++++++++------- NEWS | 9 ++++++++- README.md |only build/partial.rdb |binary man/spnn-package.Rd | 8 ++++---- src/Makevars | 13 +++---------- src/Makevars.win | 13 +++---------- src/cpp-internal.cpp | 2 +- 9 files changed, 36 insertions(+), 38 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 4.0.4 dated 2025-05-28 and 4.1.0 dated 2025-10-20
DESCRIPTION | 8 MD5 | 42 +-- NEWS.md | 8 R/bimets_ts_functions.R | 581 +++++++++++++++++++++++++++++++++++++++++- R/sysdata.rda |binary README.md | 15 + build/vignette.rds |binary data/FRB__MCAP__WP__MODEL.rda |binary data/FRB__MODEL.rda |binary data/LONGBASE.rda |binary inst/doc/bimets.R | 164 ++++++----- inst/doc/bimets.Rnw | 32 ++ inst/doc/bimets.pdf |binary inst/doc/frb2bimets.pdf |binary man/BIMETS2CSV.Rd |only man/CSV2BIMETS.Rd |only man/as.bimets.Rd | 2 man/bimets-package.Rd | 34 ++ man/bimetsConf.Rd | 2 man/fromBIMETStoTS.Rd | 2 man/fromBIMETStoXTS.Rd | 2 man/idxOver.Rd | 2 vignettes/bimets.Rnw | 32 ++ 23 files changed, 824 insertions(+), 102 deletions(-)
Title: Numerical Methods and Optimization in Finance
Description: Functions, examples and data from the first and
the second edition of "Numerical Methods and Optimization in
Finance" by M. Gilli, D. Maringer and E. Schumann (2019,
ISBN:978-0128150658). The package provides implementations
of optimisation heuristics (Differential Evolution, Genetic
Algorithms, Particle Swarm Optimisation, Simulated Annealing
and Threshold Accepting), and other optimisation tools, such
as grid search and greedy search. There are also functions
for the valuation of financial instruments such as bonds and
options, for portfolio selection and functions that help
with stochastic simulations.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between NMOF versions 2.10-1 dated 2024-11-03 and 2.11-0 dated 2025-10-20
DESCRIPTION | 11 +++++----- MD5 | 44 ++++++++++++++++++++-------------------- NAMESPACE | 14 ++++++++++-- NEWS | 43 +++++++++++++++++++++++++++------------ R/market_data.R | 37 ++++++++++++++++++++++++++------- R/portfolio.R | 2 + R/probBO.R |only README.md | 3 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview.pdf |binary inst/doc/DEnss.pdf |binary inst/doc/LSqueens.pdf |binary inst/doc/LSselect.pdf |binary inst/doc/PSlms.pdf |binary inst/doc/TAportfolio.pdf |binary inst/doc/portfolio.pdf |binary inst/doc/qTableEx.pdf |binary inst/doc/repair.pdf |binary inst/doc/vectorise.pdf |binary inst/unitTests/test_results.txt | 30 +++++++++++++-------------- man/French.Rd | 5 ++++ man/PBO.Rd |only man/Ritter.Rd | 22 +++++++------------- 24 files changed, 132 insertions(+), 79 deletions(-)
Title: Many Data on State and State-Like Actors in the International
System
Description: Comprehensively identifying states and state-like actors is difficult.
This package provides data on states and state-like entities in the international system across time.
The package combines and cross-references several existing datasets consistent with the aims and functions of the manydata package.
It also includes functions for identifying state references in text, and for generating fictional state names.
Author: James Hollway [cre, aut, ctb] ,
Bernhard Bieri [ctb] ,
Mylan Evrard [ctb] ,
Esther Peev [ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manystates versions 1.0.2 dated 2025-10-14 and 1.0.3 dated 2025-10-20
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 13 ++ R/generate_states.R | 162 ++++++++++++---------------------- README.md | 20 +++- man/generate_states.Rd | 25 +---- tests/testthat/test-generate_states.R | 2 7 files changed, 106 insertions(+), 136 deletions(-)
Title: Enhanced R Package for 'GEMPACK' .har and .sl4 Files
Description: Provides tools for processing and analyzing .har and .sl4 files, making it easier
for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets.
It simplifies the management of multiple experiment results, enabling faster
and more efficient comparisons without complexity. Users can extract, restructure,
and merge data seamlessly, ensuring compatibility across different tools.
The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or
any software that supports Text, CSV, or 'Excel' formats.
Author: Pattawee Puangchit [aut, cre]
Maintainer: Pattawee Puangchit <ppuangch@purdue.edu>
Diff between HARplus versions 1.1.0 dated 2025-10-19 and 1.1.2 dated 2025-10-20
HARplus-1.1.0/HARplus/inst/docs/HARplus_1.1.0.pdf |only HARplus-1.1.2/HARplus/DESCRIPTION | 6 - HARplus-1.1.2/HARplus/MD5 | 27 ++++-- HARplus-1.1.2/HARplus/NAMESPACE | 5 + HARplus-1.1.2/HARplus/R/save_har.R | 79 +++++++++++++++++-- HARplus-1.1.2/HARplus/R/shock_cal.R |only HARplus-1.1.2/HARplus/README.md | 50 +++++++++++- HARplus-1.1.2/HARplus/inst/doc/introduction.R | 6 - HARplus-1.1.2/HARplus/inst/doc/introduction.Rmd | 13 +-- HARplus-1.1.2/HARplus/inst/doc/introduction.html | 25 ++---- HARplus-1.1.2/HARplus/inst/docs/HARplus_1.1.2.pdf |only HARplus-1.1.2/HARplus/inst/extdata/baserate.har |only HARplus-1.1.2/HARplus/man/create_calc_config.Rd |only HARplus-1.1.2/HARplus/man/create_initial_config.Rd |only HARplus-1.1.2/HARplus/man/create_target_config.Rd |only HARplus-1.1.2/HARplus/man/save_har.Rd | 37 ++++++++ HARplus-1.1.2/HARplus/man/shock_calculate.Rd |only HARplus-1.1.2/HARplus/man/shock_calculate_uniform.Rd |only HARplus-1.1.2/HARplus/vignettes/introduction.Rmd | 13 +-- 19 files changed, 208 insertions(+), 53 deletions(-)
Title: A Combined Interaction Test for Unreplicated Two-Way Tables
Description: There are several non-functional-form-based interaction tests for testing interaction in unreplicated two-way layouts. However, no single test can detect all patterns of possible interaction and the tests are sensitive to a particular pattern of interaction. This package combines six non-functional-form-based interaction tests for testing additivity. These six tests were proposed by Boik (1993) <doi:10.1080/02664769300000004>, Piepho (1994), Kharrati-Kopaei and Sadooghi-Alvandi (2007) <doi:10.1080/03610920701386851>, Franck et al. (2013) <doi:10.1016/j.csda.2013.05.002>, Malik et al. (2016) <doi:10.1080/03610918.2013.870196> and Kharrati-Kopaei and Miller (2016) <doi:10.1080/00949655.2015.1057821>. The p-values of these six tests are combined by Bonferroni, Sidak, Jacobi polynomial expansion, and the Gaussian copula methods to provide researchers with a testing approach which leverages many existing methods to detect disparate forms of non-additivity. This [...truncated...]
Author: Zahra Shenavari [aut],
Hossein Haghbin [aut, cre] ,
Mahmood Kharrati-Kopaei [aut] ,
Seyed Morteza Najibi [aut]
Maintainer: Hossein Haghbin <haghbin@pgu.ac.ir>
Diff between combinIT versions 2.0.0 dated 2022-10-21 and 2.0.1 dated 2025-10-20
DESCRIPTION | 14 ++++++++------ MD5 | 9 +++++---- NEWS.md | 34 ++++++++++++++++++++++++++++++++++ README.md |only src/Makevars | 15 +++------------ src/Makevars.win | 6 +++++- 6 files changed, 55 insertions(+), 23 deletions(-)
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.1-1 dated 2025-05-07 and 1.1-2 dated 2025-10-20
DESCRIPTION | 6 - MD5 | 112 ++++++++++++------- NEWS.md | 13 ++ R/clifford.R | 177 +++++++++++++++---------------- R/print.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/dot.rda |binary inst/CITATION | 11 - inst/doc/clifford.R | 14 +- inst/doc/clifford.Rnw | 6 - inst/doc/clifford.pdf |binary inst/doc/complex_clifford.R |only inst/doc/complex_clifford.Rmd |only inst/doc/complex_clifford.html |only inst/doc/conformal_algebra_clifford.R |only inst/doc/conformal_algebra_clifford.Rmd |only inst/doc/conformal_algebra_clifford.html |only inst/doc/cramer_clifford.R |only inst/doc/cramer_clifford.Rmd |only inst/doc/cramer_clifford.html |only inst/doc/determinants_clifford.R |only inst/doc/determinants_clifford.Rmd |only inst/doc/determinants_clifford.html |only inst/doc/getcoeffs.R |only inst/doc/getcoeffs.Rmd |only inst/doc/getcoeffs.html |only inst/doc/lorentz_clifford.Rmd | 4 inst/doc/lorentz_clifford.html | 26 ++-- inst/doc/pauli_clifford.R |only inst/doc/pauli_clifford.Rmd |only inst/doc/pauli_clifford.html |only inst/doc/pseudoscalar.R |only inst/doc/pseudoscalar.Rmd |only inst/doc/pseudoscalar.html |only inst/doc/quaternion_clifford.R |only inst/doc/quaternion_clifford.Rmd |only inst/doc/quaternion_clifford.html |only inst/doc/signature.Rmd | 8 - inst/doc/signature.html | 24 ++-- inst/dot.Rmd | 2 inst/hankin_aaca_revision3.tex |only inst/nectarines.Rmd | 2 man/Ops.clifford.Rd | 32 ++--- man/cartan.Rd | 4 man/clifford-package.Rd | 10 + man/const.Rd | 14 +- man/dot.Rd | 2 man/grade.Rd | 4 man/horner.Rd | 4 man/lowlevel.Rd | 4 man/magnitude.Rd | 3 man/numeric_to_clifford.Rd | 4 man/print.Rd | 7 - man/rcliff.Rd | 10 - man/signature.Rd | 14 +- man/term.Rd | 1 man/vector.Rd | 4 man/zap.Rd | 4 src/clifford.cpp | 64 ++++++++--- src/clifford.h | 48 ++++---- tests/testthat/test_aak.R |only vignettes/clifford.Rnw | 6 - vignettes/clifford.bib | 48 ++++++++ vignettes/complex_clifford.Rmd |only vignettes/conformal_algebra_clifford.Rmd |only vignettes/cramer_clifford.Rmd |only vignettes/determinants_clifford.Rmd |only vignettes/getcoeffs.Rmd |only vignettes/lorentz_clifford.Rmd | 4 vignettes/pauli_clifford.Rmd |only vignettes/pseudoscalar.Rmd |only vignettes/quaternion_clifford.Rmd |only vignettes/signature.Rmd | 8 - 74 files changed, 420 insertions(+), 286 deletions(-)
Title: Maximum Likelihood Estimation of Various Univariate and
Multivariate Distributions
Description: Several functions for maximum likelihood estimation of various univariate and multivariate distributions. The list includes more than 100 functions for univariate continuous and discrete distributions, distributions that lie on the real line, the positive line, interval restricted, circular distributions. Further, multivariate continuous and discrete distributions, distributions for compositional and directional data, etc. Some references include Johnson N. L., Kotz S. and Balakrishnan N. (1994). "Continuous Univariate Distributions, Volume 1" <ISBN:978-0-471-58495-7>, Johnson, Norman L. Kemp, Adrianne W. Kotz, Samuel (2005). "Univariate Discrete Distributions". <ISBN:978-0-471-71580-1> and Mardia, K. V. and Jupp, P. E. (2000). "Directional Statistics". <ISBN:978-0-471-95333-3>.
Author: Michail Tsagris [aut, cre],
Sofia Piperaki [aut],
Muhammad Imran [ctb],
Rafail Vargiakakis [aut],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MLE versions 1.5 dated 2025-04-03 and 1.6 dated 2025-10-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/colprop.mle.R | 10 ++++++---- R/colreal.mle.R | 14 +++++++++++++- R/prop.mle.R | 3 +++ R/real.mle.R | 14 ++++++++++++-- man/MLE-package.Rd | 4 ++-- man/colprop.mle.Rd | 2 +- man/prop.mle.Rd | 3 ++- 9 files changed, 51 insertions(+), 23 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cm [...truncated...]
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.5.2 dated 2024-09-27 and 3.6.0 dated 2025-10-20
DESCRIPTION | 16 +- MD5 | 10 - NEWS.md | 4 inst/toolbox/global.R | 31 ++++ inst/toolbox/server.R | 337 ++++++++++++++++++++++++++++++++++++-------------- inst/toolbox/ui.R | 56 +++++++- 6 files changed, 339 insertions(+), 115 deletions(-)
Title: Strategy Estimation
Description: Variants of strategy estimation (Dal Bo & Frechette, 2011, <doi:10.1257/aer.101.1.411>), including the model with parameters for the choice probabilities of the strategies (Breitmoser, 2015, <doi:10.1257/aer.20130675>), and the model with individual level covariates for the selection of strategies by individuals (Dvorak & Fehrler, 2018, <doi:10.2139/ssrn.2986445>).
Author: Fabian Dvorak [aut, cre]
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>
Diff between stratEst versions 1.1.7 dated 2025-04-01 and 1.1.8 dated 2025-10-20
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- src/stratEst.cpp | 24 ++++++++++++------------ 3 files changed, 20 insertions(+), 19 deletions(-)
Title: Ready-to-Use Omics Formatting, Analysis, and Visualization
Pipeline
Description: Provides a flexible and streamlined pipeline for formatting, analyzing, and
visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics,
metabolomics). The package includes tools for shaping input data into analysis-ready
structures, fitting linear or mixed-effect models, extracting key contrasts, and
generating a rich variety of ready-to-use publication-quality plots.
Designed for transparency and reproducibility across a wide range of study designs,
with customizable components for statistical modeling.
Author: Laura Martinez-Gili [cre, aut, cph]
Maintainer: Laura Martinez-Gili <martinez.gili.laura@gmail.com>
Diff between readyomics versions 0.1.2 dated 2025-09-18 and 0.2.0 dated 2025-10-20
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 6 +- R/utils_analysis.R | 106 ++++++++++++++++++++++++++++---------- man/adjust_pval.Rd | 31 +++++++---- tests/testthat/test-adjust_pval.R | 58 ++++++++++++++++++++ 6 files changed, 168 insertions(+), 49 deletions(-)
Title: Approximate Algorithm for Horseshoe Prior
Description: Provides exact and approximate algorithms for the horseshoe prior
in linear regression models, which were proposed by Johndrow et al. (2020)
<https://www.jmlr.org/papers/v21/19-536.html>.
Author: Kang Mingi [aut, cre],
Lee Kyoungjae [aut]
Maintainer: Kang Mingi <leehuimin115@g.skku.edu>
Diff between Mhorseshoe versions 0.1.4 dated 2025-03-16 and 0.1.5 dated 2025-10-20
DESCRIPTION | 10 MD5 | 18 - NEWS.md | 56 ++-- R/approximate_algorithm.R | 506 ++++++++++++++++++++++----------------------- R/exact_algorithm.R | 388 +++++++++++++++++----------------- build/vignette.rds |binary inst/doc/Mhorseshoe.R | 21 - inst/doc/Mhorseshoe.Rmd | 517 ++++++++++++++++++++++------------------------ inst/doc/Mhorseshoe.html | 188 +++++++--------- vignettes/Mhorseshoe.Rmd | 517 ++++++++++++++++++++++------------------------ 10 files changed, 1071 insertions(+), 1150 deletions(-)
Title: Storing, Manipulating and Analysis Spectroscopy and Associated
Data
Description: Stores and eases the manipulation of spectra and associated data,
with dedicated classes for spatial and soil-related data.
Author: Pierre Roudier [aut, cre],
Max Kuhn [ctb],
Kristian Hovde Liland [ctb],
Bjorn-Helge Mevik [ctb],
Hadley Wickham [ctb],
Raphael Viscarra Rossel [dtc]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
This is a re-admission after prior archival of version 0.5-4 dated 2023-07-07
Diff between spectacles versions 0.5-4 dated 2023-07-07 and 0.5-5 dated 2025-10-20
DESCRIPTION | 10 MD5 | 30 R/Spectra-methods.R | 2530 +++++++++++++++++------------------ R/SpectraDataFrame-methods.R | 1032 +++++++------- R/australia.R | 10 R/preprocessing.R | 560 +++---- R/spectacles-package.R | 3 build/vignette.rds |binary inst/doc/interfacing-with-caret.R | 220 +-- inst/doc/interfacing-with-caret.html | 1269 ++++++++--------- inst/doc/quickstart.R | 130 - inst/doc/quickstart.html | 1003 ++++++------- man/australia.Rd | 10 man/base_line.Rd | 2 man/continuum_removal.Rd | 2 man/spectacles-package.Rd | 1 16 files changed, 3411 insertions(+), 3401 deletions(-)
Title: Radix Tree and Trie-Based String Distances
Description: A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>.
Author: Travers Ching [aut, cre, cph],
Martin Moene [ctb, cph] ,
Steve Hanov [ctb] ,
Martin Leitner-Ankerl [ctb]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between seqtrie versions 0.2.9 dated 2025-03-02 and 0.3.5 dated 2025-10-20
seqtrie-0.2.9/seqtrie/R/covid_cdr3.r |only seqtrie-0.3.5/seqtrie/ChangeLog | 14 seqtrie-0.3.5/seqtrie/DESCRIPTION | 11 seqtrie-0.3.5/seqtrie/MD5 | 68 seqtrie-0.3.5/seqtrie/R/RadixForest.R | 4 seqtrie-0.3.5/seqtrie/R/RadixTree.R | 38 seqtrie-0.3.5/seqtrie/R/RadixTree_search_helpers.R | 8 seqtrie-0.3.5/seqtrie/R/RcppExports.R | 16 seqtrie-0.3.5/seqtrie/R/covid_cdr3.R |only seqtrie-0.3.5/seqtrie/R/pairwise.R | 19 seqtrie-0.3.5/seqtrie/R/utils.R | 210 - seqtrie-0.3.5/seqtrie/README.md | 159 - seqtrie-0.3.5/seqtrie/build/vignette.rds |binary seqtrie-0.3.5/seqtrie/inst/doc/vignette.R | 56 seqtrie-0.3.5/seqtrie/inst/doc/vignette.html | 481 ++-- seqtrie-0.3.5/seqtrie/inst/doc/vignette.rmd | 47 seqtrie-0.3.5/seqtrie/inst/fix_rd_subsections.R |only seqtrie-0.3.5/seqtrie/inst/include/seqtrie/pairwise.h | 73 seqtrie-0.3.5/seqtrie/inst/include/seqtrie/radixmap.h | 1139 +++++++--- seqtrie-0.3.5/seqtrie/inst/include/seqtrie/utility.h | 15 seqtrie-0.3.5/seqtrie/inst/include/simple_progress/simple_progress.h | 1 seqtrie-0.3.5/seqtrie/man/RadixForest.Rd | 56 seqtrie-0.3.5/seqtrie/man/RadixTree.Rd | 106 seqtrie-0.3.5/seqtrie/man/covid_cdr3.Rd | 2 seqtrie-0.3.5/seqtrie/man/dist_matrix.Rd | 13 seqtrie-0.3.5/seqtrie/man/dist_pairwise.Rd | 13 seqtrie-0.3.5/seqtrie/man/dist_search.Rd | 13 seqtrie-0.3.5/seqtrie/man/generate_cost_matrix.Rd | 23 seqtrie-0.3.5/seqtrie/src/RadixForest.cpp | 13 seqtrie-0.3.5/seqtrie/src/RadixTree.cpp | 82 seqtrie-0.3.5/seqtrie/src/RcppExports.cpp | 49 seqtrie-0.3.5/seqtrie/src/pairwise.cpp | 86 seqtrie-0.3.5/seqtrie/src/seqtrie_types.h | 278 +- seqtrie-0.3.5/seqtrie/tests/test_RadixTree.R | 2 seqtrie-0.3.5/seqtrie/tests/test_pairwise.R | 36 seqtrie-0.3.5/seqtrie/tests/test_single_gap_search.R |only seqtrie-0.3.5/seqtrie/vignettes/vignette.rmd | 47 37 files changed, 1970 insertions(+), 1208 deletions(-)
Title: Joint Inference for Competing Risks Data Using Multiple
Endpoints
Description: Tools for competing risks trials that allow simultaneous inference on
recovery and mortality endpoints. Provides data preparation helpers, standard
cumulative incidence estimators (restricted mean time gained/lost), and severity
weighted extensions that integrate longitudinal ordinal outcomes to summarise
treatment benefit. Methods follow Wen, Hu, and Wang (2023) Biometrics 79(3):1635-1645
<doi:10.1111/biom.13752>.
Author: Wenqing Zhang [aut, cre],
Jiyang Wen [aut],
Chen Hu [aut],
Meicheng Wang [aut]
Maintainer: Wenqing Zhang <wzhan115@jhu.edu>
Diff between jointCompRisk versions 0.1.0 dated 2025-10-14 and 0.1.1 dated 2025-10-20
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NEWS.md |only R/cif_inference.R | 2 +- R/weighted_cif.R | 2 +- inst/doc/Example_analysis.html | 12 ++++++------ inst/doc/Vignette.Rmd | 6 +++++- inst/doc/Vignette.html | 40 ++++++++++++++++++++++------------------ vignettes/Vignette.Rmd | 6 +++++- 9 files changed, 53 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-22 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-20 0.3.0
2020-10-29 0.2.0
2020-09-18 0.1.0
Title: 'WhiteboxTools' R Frontend
Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. [...truncated...]
Author: Qiusheng Wu [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between whitebox versions 2.4.2 dated 2025-10-14 and 2.4.3 dated 2025-10-20
DESCRIPTION | 6 +-- MD5 | 25 ++++++------ NEWS.md | 16 ++++++++ R/wbt.R | 1 R/whitebox-package.R | 55 ++++++++++++++++----------- README.md | 26 ++++++------- inst/CITATION | 4 +- inst/doc/datasets.html | 3 - inst/doc/demo.html | 33 ++++++++-------- inst/doc/wbt-method.html | 59 ++++++++++++++---------------- inst/extdata/DEM.tif |only man/extdata-gis.Rd | 9 +--- man/figures/README-terra-plot-facc-1.jpeg |binary tests/testthat/test-wbt_source.R | 6 +++ 14 files changed, 135 insertions(+), 108 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] ,
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between multcomp versions 1.4-28 dated 2025-01-29 and 1.4-29 dated 2025-10-20
multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.R |only multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.Rnw |only multcomp-1.4-28/multcomp/inst/doc/multcomp-examples.pdf |only multcomp-1.4-28/multcomp/tests/Examples |only multcomp-1.4-28/multcomp/vignettes/multcomp-examples.Rnw |only multcomp-1.4-29/multcomp/DESCRIPTION | 11 ++--- multcomp-1.4-29/multcomp/MD5 | 32 +++++++-------- multcomp-1.4-29/multcomp/R/print.R | 6 +- multcomp-1.4-29/multcomp/build/vignette.rds |binary multcomp-1.4-29/multcomp/data/cholesterol.rda |binary multcomp-1.4-29/multcomp/data/litter.rda |binary multcomp-1.4-29/multcomp/demo/Ch_Appl.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_GLM.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Intro.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Misc.Rout.save |only multcomp-1.4-29/multcomp/demo/Ch_Theory.Rout.save |only multcomp-1.4-29/multcomp/inst/NEWS | 4 + multcomp-1.4-29/multcomp/inst/doc/chfls1.pdf |binary multcomp-1.4-29/multcomp/inst/doc/generalsiminf.pdf |binary multcomp-1.4-29/multcomp/man/fattyacid.Rd | 2 multcomp-1.4-29/multcomp/man/methods.Rd | 2 multcomp-1.4-29/multcomp/man/mmm.Rd | 4 - 22 files changed, 33 insertions(+), 28 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728>).
Author: Pierre Roudier [aut, cre],
Colby Brugnard [ctb],
Dylan Beaudette [ctb],
Benjamin Louis [ctb],
Kiri Daust [ctb],
David Clifford [ctb],
Andrew Brown [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.9.0 dated 2021-10-14 and 0.9.2 dated 2025-10-20
DESCRIPTION | 22 + MD5 | 34 +- NAMESPACE | 2 NEWS.md | 40 +-- R/clhs-data.frame.R | 61 +++-- R/clhs-package.R | 2 R/clhs-sf.R | 2 R/clhs-terra.R |only R/similarity.R | 6 README.md | 2 build/vignette.rds |binary inst/CITATION | 20 - inst/doc/intro-clhs.html | 443 +++++++++++++++++++++++++++++---------- man/similarity_buffer.Rd | 5 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test-clhs-gower.R | 4 tests/testthat/test-spdf.R | 4 tests/testthat/test-terra.R |only 19 files changed, 453 insertions(+), 198 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between av versions 0.9.5 dated 2025-08-25 and 0.9.6 dated 2025-10-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/fft.R | 4 +++- src/fft.c | 23 ++++++++++++++--------- 5 files changed, 27 insertions(+), 17 deletions(-)
Title: Aster Models
Description: Aster models (Geyer, Wagenius, and Shaw, 2007,
<doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and
Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson,
and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family
regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, life table analysis,
zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the ex [...truncated...]
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between aster versions 1.3-5 dated 2025-06-03 and 1.3-6 dated 2025-10-20
CHANGES | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 29 ++++++++++++++++++----------- R/reaster.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary data/grey_cloud_2015.rda |only inst/doc/delta.R |only inst/doc/delta.Rnw |only inst/doc/delta.pdf |only inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary man/aster.Rd | 2 ++ man/grey_cloud_2015.Rd |only man/vcov.Rd | 46 ++++++++++++++++++++++++++++++++++++++++++++++ vignettes/delta.Rnw |only vignettes/rout.rda |only 19 files changed, 75 insertions(+), 18 deletions(-)
Title: Assessment of Diagnostic and Prognostic Markers
Description: Provides estimations of the Receiver Operating Characteristic (ROC) curve and the Area Under the Curve (AUC) based on the two-stages mixed-subjects ROC curve estimator (Diaz-Coto et al. (2020) <doi:10.1515/ijb-2019-0097> and Diaz-Coto et al. (2020) <doi:10.1080/00949655.2020.1736071>).
Author: Susana Diaz-Coto [aut],
Susana Diaz-Coto [cre]
Maintainer: Susana Diaz-Coto <susanacoto@gmail.com>
Diff between sMSROC versions 0.1.2 dated 2023-12-07 and 0.1.3 dated 2025-10-19
DESCRIPTION | 7 +++---- MD5 | 16 ++++++++-------- R/ComputeROC.R | 26 ++++++++++++++------------ R/Summary.R | 10 ++++++---- build/partial.rdb |binary man/evol_auc.Rd | 4 ++-- man/explore_table.Rd | 2 +- man/probs_pred.Rd | 4 ++-- man/sMSROC_plot.Rd | 6 +++--- 9 files changed, 39 insertions(+), 36 deletions(-)
Title: Refined Modified Stahel-Donoho Estimators for Outlier Detection
Description: A function for multivariate outlier detection named Modified Stahel-Donoho (MSD) estimators is contained. The function is for elliptically distributed datasets and recognizes outliers based on Mahalanobis distance.
The function is called the single core version in Wada & Tsubaki (2013) <doi:10.1109/CLOUDCOM-ASIA.2013.86> and evaluated with other methods in Wada, Kawano & Tsubaki (2020) <doi:10.17713/ajs.v49i2.872>.
Author: Kazumi Wada [aut, cre]
Maintainer: Kazumi Wada <kazwd2008@gmail.com>
Diff between RMSD versions 0.1.0 dated 2023-11-06 and 0.1.1 dated 2025-10-19
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- man/RMSD.Rd | 2 +- tests/testthat/test01.r | 12 +++++++++++- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Monte Carlo Confidence Intervals in Structural Equation Modeling
Description: Monte Carlo confidence intervals for free and defined parameters
in models fitted in the structural equation modeling package 'lavaan'
can be generated using the 'semmcci' package.
'semmcci' has three main functions, namely, MC(), MCMI(), and MCStd().
The output of 'lavaan' is passed as the first argument
to the MC() function or the MCMI() function to generate Monte Carlo confidence intervals.
Monte Carlo confidence intervals for the standardized estimates
can also be generated by passing the output of the MC() function or the MCMI() function
to the MCStd() function.
A description of the package and code examples
are presented in Pesigan and Cheung (2024) <doi:10.3758/s13428-023-02114-4>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Shu Fai Cheung [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between semmcci versions 1.1.4 dated 2024-03-17 and 1.1.5 dated 2025-10-19
DESCRIPTION | 20 LICENSE | 2 MD5 | 129 +- NAMESPACE | 1 NEWS.md | 8 R/lavHelper-lav-2-ram-dot.R | 12 R/lavHelper-ram-2-lav-dot.R | 2 R/lavHelper-std-lav-dot.R | 10 R/lavHelper-std-ram-dot.R | 12 R/lavHelper-theta-hat-dot.R | 46 - R/linearAlgebra-positive-definite-test-dot.R | 8 R/miHelper-ariv-dot.R | 27 R/miHelper-mi-combine-dot.R | 21 R/miHelper-total-adj-dot.R | 15 R/nBootstrap-ci-format-dot.R | 2 R/nBootstrap-pc-ci-dot.R | 12 R/nBootstrap-pc-probs-dot.R | 8 R/randomGaussian-location-dot.R | 12 R/randomGaussian-random-gaussian-chol-dot.R | 4 R/randomGaussian-random-gaussian-eigen-dot.R | 12 R/randomGaussian-random-gaussian-svd-dot.R | 12 R/randomGaussian-random-gaussian-z-dot.R | 14 R/semmcci-func.R | 6 R/semmcci-mc-ci-dot.R | 8 R/semmcci-mc-def-dot.R | 31 R/semmcci-mc-func.R | 51 - R/semmcci-mc-generic.R | 18 R/semmcci-mc-mi.R | 28 R/semmcci-mc-std.R | 41 R/semmcci-mc.R | 8 R/semmcci-methods.R | 79 + R/semmcci-theta-hat-star-dot.R | 8 build/partial.rdb |binary inst/CITATION | 3 man/Func.Rd | 4 man/MC.Rd | 2 man/MCFunc.Rd | 4 man/MCGeneric.Rd | 2 man/MCMI.Rd | 2 man/MCStd.Rd | 2 man/print.semmcci.Rd | 2 man/semmcci-package.Rd | 2 tests/testthat/test-semmcci-mc-func-simple-med.R | 439 +++++++--- tests/testthat/test-semmcci-mc-generic-simple-med-defined.R | 341 +++++-- tests/testthat/test-semmcci-mc-latent-med-defined-none.R | 191 ++-- tests/testthat/test-semmcci-mc-latent-med-defined.R | 181 +++- tests/testthat/test-semmcci-mc-latent-med-std-defined-none.R | 216 +++- tests/testthat/test-semmcci-mc-latent-med-std-defined.R | 208 +++- tests/testthat/test-semmcci-mc-moment.R | 77 - tests/testthat/test-semmcci-mc-simple-med-defined-equality.R | 251 ++++- tests/testthat/test-semmcci-mc-simple-med-defined-inequality.R | 251 ++++- tests/testthat/test-semmcci-mc-simple-med-defined-meanstructure.R | 275 ++++-- tests/testthat/test-semmcci-mc-simple-med-defined-mi-amelia.R | 97 +- tests/testthat/test-semmcci-mc-simple-med-defined-mi-list.R | 97 +- tests/testthat/test-semmcci-mc-simple-med-defined-mi-mice.R | 99 +- tests/testthat/test-semmcci-mc-simple-med-defined-none.R | 239 +++-- tests/testthat/test-semmcci-mc-simple-med-defined.R | 271 ++++-- tests/testthat/test-semmcci-mc-simple-med-std-defined-meanstructure.R | 258 ++++- tests/testthat/test-semmcci-mc-simple-med-std-defined-none-random-x.R | 260 ++++- tests/testthat/test-semmcci-mc-simple-med-std-defined-none.R | 10 tests/testthat/test-semmcci-mc-simple-med-std-defined.R | 264 ++++-- tests/testthat/test-semmcci-methods.R | 105 +- tests/testthat/test-semmcci-npd.R | 80 + tests/testthat/test-semmcci-zzz-coverage.R | 21 tests/testthat/test-semmcci-zzz-heywood.R | 69 - tests/testthat/test-semmcci.R |only 66 files changed, 3326 insertions(+), 1664 deletions(-)
Title: Classify RGB Images into Forest or Non-Forest
Description: Implements two out-of box classifiers presented in <doi:10.1002/env.2848> for
distinguishing forest and non-forest terrain images. Under these algorithms, there are
frequentist approaches: one parametric, using stable distributions, and another one-
non-parametric, using the squared Mahalanobis distance. The package also contains functions for
data handling and building of new classifiers as well as some test data set.
Author: Jesper Muren [aut] ,
Dmitry Otryakhin [aut, cre]
Maintainer: Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>
Diff between deforestable versions 3.1.1 dated 2022-10-15 and 3.1.2 dated 2025-10-19
DESCRIPTION | 19 ++++++++++--------- MD5 | 7 ++++--- inst/CITATION |only src/Makevars | 13 +------------ src/Makevars.win | 13 +------------ 5 files changed, 16 insertions(+), 36 deletions(-)
Title: Robust Confidence Intervals for Standardized Regression
Coefficients
Description: Generates robust confidence intervals for standardized regression coefficients
using heteroskedasticity-consistent standard errors for models fitted by lm()
as described in Dudgeon (2017) <doi:10.1007/s11336-017-9563-z>.
The package can also be used to generate confidence intervals for R-squared,
adjusted R-squared, and differences of standardized regression coefficients.
A description of the package and code examples
are presented in Pesigan, Sun, and Cheung (2023) <doi:10.1080/00273171.2023.2201277>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaSandwich versions 1.0.7 dated 2024-04-14 and 1.0.8 dated 2025-10-19
DESCRIPTION | 12 LICENSE | 2 MD5 | 123 ++-- NAMESPACE | 3 NEWS.md | 6 R/betaSandwich-acov-hc-dot.R | 4 R/betaSandwich-acov-sem-inverse-dot.R | 8 R/betaSandwich-beta-adf.R | 10 R/betaSandwich-beta-ci-dot.R | 22 R/betaSandwich-beta-hc.R | 10 R/betaSandwich-beta-mvn.R | 10 R/betaSandwich-cov-hc-dot.R | 4 R/betaSandwich-diff-beta-ci-dot.R | 20 R/betaSandwich-diff-beta-sandwich.R | 8 R/betaSandwich-gamma-hc-dot.R | 30 - R/betaSandwich-jacobian-diff-beta-star-wrt-beta-star-dot.R | 2 R/betaSandwich-methods-beta-sandwich.R | 91 ++- R/betaSandwich-methods-diff-beta-sandwich.R | 83 ++- R/betaSandwich-methods-r-sq-beta-sandwich.R | 87 ++- R/betaSandwich-q-mat-dot.R | 73 +- R/betaSandwich-r-sq-beta-sandwich.R | 24 R/betaSandwich-r-sq-ci-dot.R | 22 R/betaSandwich-r-sq-vcov-dot.R | 8 R/gammaADF-gamma-adf-consistent-dot.R | 34 - R/gammaADF-gamma-adf-unbiased-dot.R | 34 - R/gammaN-gamma-mvn-dot.R | 16 R/linearAlgebra-d-mat-dot.R | 22 R/linearAlgebra-d-of-mat-dot.R | 12 R/linearAlgebra-pinv-of-d-mat-dot.R | 16 R/linearAlgebra-vec-dot.R | 2 R/linearAlgebra-vech-dot.R | 14 R/linearAlgebra-vech-names-dot.R | 4 R/processLM-dif-dot.R | 10 R/processLM-process-lm-dot.R | 100 +--- R/rhoMatrix-rho-of-sigma-dot.R | 8 R/strRegression-beta-star-of-rho-dot.R | 26 - R/strRegression-jacobian-vech-sigma-wrt-theta-dot.R | 4 R/strRegression-jacobian-vech-sigma-wrt-theta-std-dot.R | 4 R/strRegression-moments-index-dot.R | 34 - R/strRegression-p-cor-sq-dot.R | 8 R/strRegression-r-sq-bar-dot.R | 6 R/strRegression-r-sq-of-sigma-dot.R | 20 R/strRegression-s-p-cor-dot.R | 16 R/strRegression-theta-index-dot.R | 34 - R/strRegression-theta-star-index-dot.R | 77 +-- R/wald-ci-wald-dot.R | 6 R/wald-probs-of-alpha-dot.R | 21 build/partial.rdb |binary data/nas1982.rda |binary inst/CITATION | 1 man/print.betasandwich.Rd | 2 man/print.diffbetasandwich.Rd | 2 man/print.rsqbetasandwich.Rd | 2 tests/testthat/test-betaSandwich-beta-sandwich-adf.R | 38 + tests/testthat/test-betaSandwich-beta-sandwich-hc.R | 130 ++++- tests/testthat/test-betaSandwich-beta-sandwich-methods.R | 111 ++-- tests/testthat/test-betaSandwich-beta-sandwich-mvn.R | 38 + tests/testthat/test-betaSandwich-diff-beta-sandwich-methods.R | 148 +++-- tests/testthat/test-betaSandwich-diff-beta-sandwich.R | 248 +++++++++- tests/testthat/test-betaSandwich-r-sq-beta-sandwich-methods.R | 111 ++-- tests/testthat/test-betaSandwich-r-sq-beta-sandwich.R | 144 ++++- tests/testthat/test-betaSandwich.R |only tests/testthat/test-zzz-coverage.R | 111 ++-- 63 files changed, 1350 insertions(+), 926 deletions(-)
Title: Bootstrap for Regression Effect Sizes
Description: Generates nonparametric bootstrap confidence intervals
(Efron and Tibshirani, 1993: <doi:10.1201/9780429246593>)
for standardized regression coefficients (beta) and other effect sizes,
including multiple correlation, semipartial correlations,
improvement in R-squared, squared partial correlations,
and differences in standardized regression coefficients,
for models fitted by lm().
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaNB versions 1.0.5 dated 2025-01-09 and 1.0.6 dated 2025-10-19
DESCRIPTION | 12 +- LICENSE | 2 MD5 | 93 ++++++++--------- NAMESPACE | 1 NEWS.md | 6 + R/betaNB-beta-nb.R | 14 -- R/betaNB-ci.R | 4 R/betaNB-delta-r-sq-nb.R | 30 ++--- R/betaNB-diff-beta-nb.R | 6 - R/betaNB-methods-beta-nb.R | 118 +++++++++++---------- R/betaNB-nb.R | 40 +++---- R/betaNB-p-cor-nb.R | 12 -- R/betaNB-r-sq-nb.R | 12 -- R/betaNB-s-cor-nb.R | 28 ++--- R/linearAlgebra-d-mat-dot.R | 22 +--- R/linearAlgebra-pinv-of-d-mat-dot.R | 16 +- R/linearAlgebra-vec-dot.R | 2 R/linearAlgebra-vech-dot.R | 14 +- R/nBootstrap-acceleration-dot.R | 8 - R/nBootstrap-bc-ci-dot.R | 12 -- R/nBootstrap-bc-probs-dot.R | 6 - R/nBootstrap-bca-ci-dot.R | 12 -- R/nBootstrap-bca-probs-dot.R | 12 -- R/nBootstrap-ci-format-dot.R | 2 R/nBootstrap-pc-ci-dot.R | 12 -- R/nBootstrap-pc-probs-dot.R | 8 - R/nBootstrap-z0-dot.R | 10 - R/nBootstrap-z1-dot.R | 4 R/processLM-dif-dot.R | 10 - R/processLM-process-lm-dot.R | 94 ++++++++--------- R/rhoMatrix-rho-of-sigma-dot.R | 8 - R/strRegression-beta-star-of-rho-dot.R | 26 ++-- R/strRegression-beta-star-of-sigma-dot.R | 14 +- R/strRegression-p-cor-sq-dot.R | 8 - R/strRegression-r-sq-bar-dot.R | 6 - R/strRegression-r-sq-of-sigma-dot.R | 20 +-- R/strRegression-s-p-cor-dot.R | 16 +- build/partial.rdb |binary data/nas1982.rda |binary inst/CITATION | 2 tests/testthat/test-betaNB-beta-nb-est.R | 101 +++++++++++------- tests/testthat/test-betaNB-delta-r-sq-nb-est.R | 50 +++++---- tests/testthat/test-betaNB-diff-beta-nb-est.R | 50 +++++---- tests/testthat/test-betaNB-nb.R | 136 ++++++++++++------------- tests/testthat/test-betaNB-p-cor-nb-est.R | 50 +++++---- tests/testthat/test-betaNB-r-sq-nb-est.R | 74 +++++++------ tests/testthat/test-betaNB-s-cor-nb-est.R | 50 +++++---- tests/testthat/test-betaNB.R |only 48 files changed, 623 insertions(+), 610 deletions(-)
Title: Monte Carlo for Regression Effect Sizes
Description: Generates Monte Carlo confidence intervals
for standardized regression coefficients (beta) and other effect sizes,
including multiple correlation, semipartial correlations,
improvement in R-squared, squared partial correlations,
and differences in standardized regression coefficients,
for models fitted by lm().
'betaMC' combines ideas from Monte Carlo confidence intervals for the indirect effect
(Pesigan and Cheung, 2024 <doi:10.3758/s13428-023-02114-4>)
and the sampling covariance matrix of regression coefficients
(Dudgeon, 2017 <doi:10.1007/s11336-017-9563-z>)
to generate confidence intervals effect sizes in regression.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaMC versions 1.3.2 dated 2024-04-14 and 1.3.3 dated 2025-10-19
DESCRIPTION | 14 LICENSE | 2 MD5 | 175 ++--- NAMESPACE | 2 NEWS.md | 6 R/betaMC-beta-mc.R | 28 R/betaMC-ci-dot.R | 10 R/betaMC-cov-dot.R | 2 R/betaMC-delta-r-sq-mc.R | 4 R/betaMC-diff-beta-mc.R | 12 R/betaMC-j.R | 24 R/betaMC-mc-bias.R | 36 - R/betaMC-mc-dot.R | 6 R/betaMC-mc-mi.R | 28 R/betaMC-mc-rmse.R | 46 - R/betaMC-mc-theta-hat-dot.R | 20 R/betaMC-mc-var.R | 56 - R/betaMC-mc.R | 12 R/betaMC-methods-beta-mc.R | 107 +-- R/betaMC-methods-mc.R | 57 + R/betaMC-p-cor-mc.R | 20 R/betaMC-r-sq-mc.R | 14 R/betaMC-s-cor-mc.R | 20 R/betaSandwich-acov-hc-dot.R | 4 R/betaSandwich-acov-sem-inverse-dot.R | 8 R/betaSandwich-cov-hc-dot.R | 4 R/betaSandwich-gamma-hc-dot.R | 30 R/betaSandwich-q-mat-dot.R | 73 -- R/gammaADF-gamma-adf-consistent-dot.R | 34 - R/gammaADF-gamma-adf-unbiased-dot.R | 34 - R/gammaN-gamma-mvn-dot.R | 16 R/linearAlgebra-d-mat-dot.R | 22 R/linearAlgebra-d-of-mat-dot.R | 12 R/linearAlgebra-pinv-of-d-mat-dot.R | 16 R/linearAlgebra-positive-definite-2-test-dot.R | 35 - R/linearAlgebra-positive-definite-test-dot.R | 8 R/linearAlgebra-vec-dot.R | 2 R/linearAlgebra-vech-dot.R | 14 R/linearAlgebra-vech-names-dot.R | 4 R/miHelper-ariv-dot.R | 27 R/miHelper-mi-combine-dot.R | 21 R/miHelper-total-adj-dot.R | 15 R/nBootstrap-ci-format-dot.R | 2 R/nBootstrap-pc-ci-dot.R | 12 R/nBootstrap-pc-probs-dot.R | 8 R/processLM-dif-dot.R | 10 R/processLM-process-lm-dot.R | 100 +-- R/randomGaussian-location-dot.R | 12 R/randomGaussian-random-gaussian-chol-dot.R | 4 R/randomGaussian-random-gaussian-eigen-dot.R | 12 R/randomGaussian-random-gaussian-svd-dot.R | 12 R/randomGaussian-random-gaussian-z-dot.R | 14 R/rhoMatrix-rho-of-sigma-dot.R | 8 R/semmcci-theta-hat-star-dot.R | 8 R/strRegression-beta-star-dot.R | 10 R/strRegression-beta-star-of-rho-dot.R | 26 R/strRegression-jacobian-vech-sigma-wrt-theta-dot.R | 4 R/strRegression-moments-index-dot.R | 34 - R/strRegression-p-cor-sq-dot.R | 8 R/strRegression-r-sq-bar-dot.R | 6 R/strRegression-r-sq-of-sigma-dot.R | 20 R/strRegression-s-p-cor-dot.R | 16 R/strRegression-sigma-y-sq-dot.R | 12 R/strRegression-sigma-yx-dot.R | 10 R/strRegression-theta-index-dot.R | 34 - build/partial.rdb |binary data/nas1982.rda |binary inst/CITATION | 5 man/MC.Rd | 2 man/MCMI.Rd | 2 man/betaMC-package.Rd | 2 tests/testthat/test-betaMC-beta-mc-est-mi.R | 95 ++- tests/testthat/test-betaMC-beta-mc-est.R | 77 +- tests/testthat/test-betaMC-delta-r-sq-mc-est-mi.R | 74 +- tests/testthat/test-betaMC-delta-r-sq-mc-est.R | 56 + tests/testthat/test-betaMC-diff-beta-mc-est-mi.R | 74 +- tests/testthat/test-betaMC-diff-beta-mc-est.R | 56 + tests/testthat/test-betaMC-mc-fixed-x-mi.R | 605 +++++++++++++++++--- tests/testthat/test-betaMC-mc-fixed-x.R | 499 ++++++++++++++-- tests/testthat/test-betaMC-mc-mi.R | 495 ++++++++++++++-- tests/testthat/test-betaMC-mc.R | 522 ++++++++++++++--- tests/testthat/test-betaMC-p-cor-mc-est-mi.R | 74 +- tests/testthat/test-betaMC-p-cor-mc-est.R | 56 + tests/testthat/test-betaMC-r-sq-mc-est-mi.R | 93 +-- tests/testthat/test-betaMC-r-sq-mc-est.R | 75 +- tests/testthat/test-betaMC-s-cor-mc-est-mi.R | 74 +- tests/testthat/test-betaMC-s-cor-mc-est.R | 56 + tests/testthat/test-betaMC.R |only tests/testthat/test-zzz-coverage.R | 133 ++-- 89 files changed, 3144 insertions(+), 1443 deletions(-)
Title: Confidence Intervals for Standardized Regression Coefficients
Description: Generates confidence intervals for standardized regression coefficients
using delta method standard errors for models fitted by lm()
as described in Yuan and Chan (2011) <doi:10.1007/s11336-011-9224-6>
and Jones and Waller (2015) <doi:10.1007/s11336-013-9380-y>.
The package can also be used to generate confidence intervals for
differences of standardized regression coefficients
and as a general approach to performing the delta method.
A description of the package and code examples
are presented in Pesigan, Sun, and Cheung (2023) <doi:10.1080/00273171.2023.2201277>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaDelta versions 1.0.5 dated 2024-04-14 and 1.0.6 dated 2025-10-19
DESCRIPTION | 12 LICENSE | 2 MD5 | 109 ++++---- NAMESPACE | 2 NEWS.md | 6 R/betaDelta-beta-ci-dot.R | 22 - R/betaDelta-beta-delta-dot.R | 12 R/betaDelta-beta-delta.R | 10 R/betaDelta-diff-beta-ci-dot.R | 20 - R/betaDelta-diff-beta-delta.R | 8 R/betaDelta-gamma-dot.R | 2 R/betaDelta-methods-beta-delta.R | 83 +++--- R/betaDelta-methods-diff-beta-delta.R | 83 +++--- R/betaSandwich-jacobian-diff-beta-star-wrt-beta-star-dot.R | 2 R/deltaMethod-acov-delta.R | 8 R/deltaMethod-delta-ci-dot.R | 22 - R/deltaMethod-delta-generic.R | 12 R/deltaMethod-delta.R | 8 R/deltaMethod-methods.R | 36 +- R/gammaADF-gamma-adf-consistent-dot.R | 34 +- R/gammaADF-gamma-adf-unbiased-dot.R | 34 +- R/gammaN-gamma-mvn-dot.R | 16 - R/linearAlgebra-d-mat-dot.R | 22 - R/linearAlgebra-d-of-mat-dot.R | 12 R/linearAlgebra-diag-of-vech-dot.R | 20 - R/linearAlgebra-pinv-of-d-mat-dot.R | 16 - R/linearAlgebra-vec-dot.R | 2 R/linearAlgebra-vech-dot.R | 14 - R/linearAlgebra-vech-names-dot.R | 4 R/processLM-dif-dot.R | 10 R/processLM-process-lm-dot.R | 100 +++---- R/rhoMatrix-rho-of-sigma-dot.R | 8 R/strRegression-beta-star-of-rho-dot.R | 26 - R/strRegression-jacobian-beta-star-wrt-vech-sigma-dot.R | 4 R/strRegression-moments-index-dot.R | 34 +- R/strRegression-p-cor-sq-dot.R | 8 R/strRegression-r-sq-bar-dot.R | 6 R/strRegression-r-sq-of-sigma-dot.R | 20 - R/strRegression-s-p-cor-dot.R | 16 - R/wald-ci-wald-dot.R | 6 R/wald-probs-of-alpha-dot.R | 21 - build/partial.rdb |binary data/nas1982.rda |binary inst/CITATION | 1 man/Delta.Rd | 4 man/print.betadelta.Rd | 2 man/print.diffbetadelta.Rd | 2 tests/testthat/test-betaDelta-beta-delta-adf.R | 38 +- tests/testthat/test-betaDelta-beta-delta-methods.R | 85 +++--- tests/testthat/test-betaDelta-beta-delta-mvn.R | 38 +- tests/testthat/test-betaDelta-diff-beta-delta-methods.R | 57 ++-- tests/testthat/test-betaDelta-diff-beta-delta.R | 64 +++- tests/testthat/test-betaDelta.R |only tests/testthat/test-deltaMethod-delta-generic.R | 155 ++++++++--- tests/testthat/test-deltaMethod-delta.R | 177 +++++++++---- tests/testthat/test-zzz-coverage.R | 75 +++-- 56 files changed, 910 insertions(+), 680 deletions(-)
Title: High-Dimensional Shrinkage Optimal Portfolios
Description: Constructs shrinkage estimators of high-dimensional mean-variance portfolios and performs
high-dimensional tests on optimality of a given portfolio. The techniques developed in
Bodnar et al. (2018 <doi:10.1016/j.ejor.2017.09.028>, 2019 <doi:10.1109/TSP.2019.2929964>,
2020 <doi:10.1109/TSP.2020.3037369>, 2021 <doi:10.1080/07350015.2021.2004897>)
are central to the package. They provide simple and feasible estimators and tests for optimal
portfolio weights, which are applicable for 'large p and large n' situations where p is the
portfolio dimension (number of stocks) and n is the sample size. The package also includes tools
for constructing portfolios based on shrinkage estimators of the mean vector and covariance matrix
as well as a new Bayesian estimator for the Markowitz efficient frontier recently developed by
Bauder et al. (2021) <doi:10.1080/14697688.2020.1748214>.
Author: Taras Bodnar [aut] ,
Solomiia Dmytriv [aut] ,
Yarema Okhrin [aut] ,
Dmitry Otryakhin [aut, cre] ,
Nestor Parolya [aut]
Maintainer: Dmitry Otryakhin <d.otryakhin.acad@protonmail.ch>
Diff between HDShOP versions 0.1.5 dated 2024-03-25 and 0.1.6 dated 2025-10-19
DESCRIPTION | 23 +++++++----- MD5 | 33 +++++++++--------- NEWS.md | 4 ++ R/Plot_frontier.R | 2 - build/partial.rdb |binary inst/CITATION |only tests/testthat.R | 9 ++++ tests/testthat/test_CovarEstim.R | 21 ++++------- tests/testthat/test_EU_vs_GMV.R | 10 ++--- tests/testthat/test_MVShrinkportfolio.R | 26 +++++++------- tests/testthat/test_T_stat.R | 2 - tests/testthat/test_alphas.R | 14 +++---- tests/testthat/test_custom_portfolio.R | 14 +++---- tests/testthat/test_misc_expressions.R | 2 - tests/testthat/test_naive_covar_estims.R | 2 - tests/testthat/test_portf_prototypes_on_data_frames.R | 2 - tests/testthat/test_portf_prototypes_on_matrices.R | 2 - tests/testthat/test_shrink_covar_methods.R | 10 ++--- 18 files changed, 94 insertions(+), 82 deletions(-)
Title: A Versatile Visualization Suite
Description: A visualization suite primarily designed for single-cell
RNA-sequencing data analysis applications, but adaptable to
other purposes as well. It introduces novel plots to represent two-variable
and frequency data and optimizes some commonly used plotting options
(e.g., correlation, network, density and alluvial plots) for ease of usage
and flexibility.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between henna versions 0.2.5 dated 2025-09-18 and 0.3.4 dated 2025-10-19
DESCRIPTION | 10 +-- MD5 | 49 ++++++++-------- NAMESPACE | 1 R/density_plot.R | 13 +++- R/hull_plot.R | 57 +++++++++++++------ R/network_plot.R | 35 ++++++++--- R/palettes.R | 8 ++ R/radial_plot.R | 126 +++++++++++++++++++++++-------------------- R/rank_plot.R | 23 +++++-- README.md | 30 ++++++---- man/circleCoords.Rd | 14 ++-- man/classPlot.Rd | 3 - man/densityPlot.Rd | 2 man/distFreq.Rd | 16 +++-- man/dpColors.Rd | 2 man/figures/network_plot.png |binary man/figures/radial_plot.png |binary man/hullPlot.Rd | 22 +++++-- man/networkPlot.Rd | 24 +++++--- man/pointsOnCircle.Rd |only man/radialPlot.Rd | 40 +++++++++---- man/rankPlot.Rd | 20 ++++-- man/rankSummary.Rd | 2 man/splitHull.Rd | 19 ++++-- man/tilePlot.Rd | 3 - tests/testthat/test-henna.R | 33 +++++++---- 26 files changed, 348 insertions(+), 204 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.3.3 dated 2025-10-11 and 1.3.4 dated 2025-10-19
DESCRIPTION | 6 MD5 | 24 +-- NAMESPACE | 1 NEWS.md | 12 + R/from.R | 29 ++-- R/what.R |only build/build_and_release_process.R | 2 inst/doc/import.R | 15 +- inst/doc/import.Rmd | 267 +++++++++++++++++++++++-------------- inst/doc/import.html | 269 ++++++++++++++++++++++---------------- man/importfunctions.Rd | 40 ++++- tests/test_import/test_from.R | 11 + tests/test_import/test_what.R |only vignettes/import.Rmd | 267 +++++++++++++++++++++++-------------- 14 files changed, 590 insertions(+), 353 deletions(-)
Title: Visualization 2D of Binary Classification Models
Description: Visual contour and 2D point and contour plots for binary classification modeling under algorithms such as 'glm', 'rf', 'gbm', 'nnet' and 'svm', presented over two dimensions generated by 'famd' and 'mca' methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses under the 'XAI' paradigm.
Author: Javier Portela [aut, cre]
Maintainer: Javier Portela <javipgm@gmail.com>
Diff between visualpred versions 0.1.1 dated 2024-11-07 and 0.1.2 dated 2025-10-19
DESCRIPTION | 11 +- MD5 | 54 +++++----- NAMESPACE | 4 NEWS.md | 6 + R/famdcontour.R | 215 ++++++++++++++++++++++++------------------- R/famdcontourlabel.R | 49 ++++++--- R/mcacontour.R | 106 ++++++++++++--------- R/mcacontourjitter.R | 2 R/mcamodelo.R | 32 ++---- build/vignette.rds |binary inst/doc/Advanced.Rmd | 4 inst/doc/Advanced.html | 209 ++++++++++++++++++------------------------ inst/doc/Basic_example.R | 6 - inst/doc/Basic_example.Rmd | 19 ++- inst/doc/Basic_example.html | 217 +++++++++++++++++++------------------------- inst/doc/Comparing.R | 2 inst/doc/Comparing.Rmd | 6 - inst/doc/Comparing.html | 205 +++++++++++++++++------------------------ inst/doc/Outliers.Rmd | 4 inst/doc/Outliers.html | 205 +++++++++++++++++------------------------ man/famdcontour.Rd | 32 ++++-- man/famdcontourlabel.Rd | 17 +++ man/mcacontour.Rd | 15 ++- man/mcamodelobis.Rd | 2 vignettes/Advanced.Rmd | 4 vignettes/Basic_example.Rmd | 19 ++- vignettes/Comparing.Rmd | 6 - vignettes/Outliers.Rmd | 4 28 files changed, 717 insertions(+), 738 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.6-6 dated 2025-06-17 and 1.7-0 dated 2025-10-19
DESCRIPTION | 10 - MD5 | 68 +++++------ NAMESPACE | 22 +++ R/R.R | 278 ++++++++++++++++++++++++++++++++++++++++++++- R/ctm.R | 1 R/distr.R | 88 +++++++++----- R/loglik.R | 16 ++ R/methods.R | 6 R/mlt.R | 96 +++++++++++---- R/mltoptim.R | 168 ++++++++++++++++++++++----- R/mmlt.R | 32 ++--- R/sample.R | 5 R/utils.R | 5 inst/NEWS.Rd | 33 +++++ man/ctm.Rd | 6 man/mlt.Rd | 14 +- man/mltoptim.Rd | 83 +++++++++++-- man/mmlt.Rd | 12 + tests/2sample.R | 1 tests/2sample.Rout.save | 61 +++++---- tests/Cox-Ex.R | 15 -- tests/Cox-Ex.Rout.save | 64 ++++------ tests/bugfixes.Rout.save | 8 - tests/distr-Ex.R | 71 +++++++++++ tests/dpq-Ex.Rout.save | 40 +++--- tests/glm-Ex.Rout.save | 8 - tests/lm-Ex.R | 5 tests/lm-Ex.Rout.save | 25 +--- tests/missing-responses.R | 2 tests/polr-Ex.R | 1 tests/polr-Ex.Rout.save | 65 +++++----- tests/predict-Ex.Rout.save | 8 - tests/subset.Rout.save | 8 - tests/surv-Ex.R | 1 tests/surv-Ex.Rout.save | 230 +++++++++++++++++-------------------- 35 files changed, 1101 insertions(+), 455 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.4.1 dated 2025-09-16 and 0.5.0 dated 2025-10-19
DESCRIPTION | 11 ++++++----- MD5 | 15 ++++++++++----- NAMESPACE | 2 ++ NEWS.md | 10 +++++++++- R/combine_answers.R |only R/plot_multiple_answers.R |only R/plot_proportions.R | 2 +- man/combine_answers.Rd |only man/plot_multiple_answers.Rd |only man/plot_proportions.Rd | 2 +- tests/testthat/test-plot_multiple_answers.R |only 11 files changed, 29 insertions(+), 13 deletions(-)
Title: 'shiny' Application for Statistical Test Assumption Checking and
Guidance
Description: A 'shiny' application to assess statistical assumptions and guide users toward appropriate tests. The app is designed for researchers with minimal statistical training and provides diagnostics, plots, and test recommendations for a wide range of analyses. Many statistical assumptions are implemented using the package 'rstatix' (Kassambara, 2019) <doi:10.32614/CRAN.package.rstatix> and 'performance' (Lüdecke et al., 2021) <doi:10.21105/joss.03139>.
Author: Ahmed Bargheet [aut, cre]
Maintainer: Ahmed Bargheet <ahmed.bargheet@yahoo.com>
Diff between AssumpSure versions 1.1.1 dated 2025-09-18 and 1.1.2 dated 2025-10-19
DESCRIPTION | 8 MD5 | 10 NEWS.md | 13 + R/launch_app.R | 6 R/zzz.R | 6 inst/app/app.R | 593 ++++++++++++++++++++++++++++++++++++++++++++++++++------- 6 files changed, 554 insertions(+), 82 deletions(-)
Title: Access and Analyze eBird Status and Trends Data Products
Description: Tools for accessing and analyzing eBird Status and
Trends Data Products
(<https://science.ebird.org/en/status-and-trends>). eBird
(<https://ebird.org/home>) is a global database of bird observations
collected by member of the public. eBird Status and Trends uses these
data to model global bird distributions, abundances, and population trends
at a high spatial and temporal resolution.
Author: Matthew Strimas-Mackey [aut, cre] ,
Shawn Ligocki [aut],
Tom Auer [aut] ,
Daniel Fink [aut] ,
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between ebirdst versions 3.2023.0 dated 2025-05-07 and 3.2023.1 dated 2025-10-19
DESCRIPTION | 12 - MD5 | 50 +++---- NAMESPACE | 2 NEWS.md | 7 R/sample.R | 21 +- R/trends.R | 118 ++++++++++++++++ R/utils.R | 6 build/vignette.rds |binary inst/doc/applications.R | 3 inst/doc/applications.Rmd | 3 inst/doc/applications.html | 5 inst/doc/product-changelog.Rmd | 6 inst/doc/product-changelog.html | 26 +-- inst/doc/status.R | 3 inst/doc/status.Rmd | 3 inst/doc/status.html | 5 inst/doc/trends.R | 58 ++++++++ inst/doc/trends.Rmd | 69 +++++++++ inst/doc/trends.html | 276 ++++++++++++++++++++++++--------------- man/convert_ppy_to_cumulative.Rd |only man/grid_sample.Rd | 12 - man/vectorize_trends.Rd |only tests/testthat/test_utils.R | 2 vignettes/applications.Rmd | 3 vignettes/product-changelog.Rmd | 6 vignettes/status.Rmd | 3 vignettes/trends.Rmd | 69 +++++++++ 27 files changed, 583 insertions(+), 185 deletions(-)
Title: Simplified Access to Brazilian Financial and Macroeconomic Data
Description: It offers simplified access to Brazilian macroeconomic and financial indicators selected from official sources, such as the 'IBGE' (Brazilian Institute of Geography and Statistics) via the 'SIDRA' API and the 'Central Bank of Brazil' via the 'SGS' API. It allows users to quickly retrieve and visualize data series such as the unemployment rate and the Selic interest rate. This package was developed for data access and visualization purposes, without generating forecasts or statistical results. For more information, see the official APIs: <https://sidra.ibge.gov.br/> and <https://dadosabertos.bcb.gov.br/dataset/>.
Author: Joao Paulo dos Santos Pereira Barbosa [aut, cre]
Maintainer: Joao Paulo dos Santos Pereira Barbosa <joao.31582129@gmail.com>
Diff between brfinance versions 0.2.1 dated 2025-10-17 and 0.2.2 dated 2025-10-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/plot_unemployment.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Portfolio Management with R
Description: Tools for the practical management of financial
portfolios: backtesting investment and trading strategies,
computing profit/loss and returns, analysing trades,
handling lists of transactions, reporting, and more. The
package provides a small set of reliable, efficient and
convenient tools for processing and analysing
trade/portfolio data. The manual provides all the details;
it is available from
<https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>.
Examples and descriptions of new features are provided at
<https://enricoschumann.net/notes/PMwR/>.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between PMwR versions 1.0-1 dated 2024-10-19 and 1.1-0 dated 2025-10-19
DESCRIPTION | 11 - MD5 | 99 ++++++------ NAMESPACE | 2 NEWS | 30 +++ R/NAVseries.R | 69 +++----- R/btest.R | 12 - R/instrument.R |only R/internal.R | 4 R/journal.R | 73 ++------- R/pl.R | 4 R/position.R | 216 ++++++++++++++++++++++++---- R/rc.R | 123 +++++---------- R/rebalance.R | 4 R/unit_prices.R | 2 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/An_overview_of_PMwR.pdf |binary inst/doc/Computing_returns.R | 2 inst/doc/Computing_returns.Rnw | 4 inst/doc/Computing_returns.pdf |binary inst/doc/Drawdowns_streaks.pdf |binary inst/doc/FinTeX.pdf |binary inst/doc/pl_open_positions.pdf |binary inst/doc/q32.pdf |binary inst/tinytest/test_btest_initial.position.R | 45 +++++ inst/tinytest/test_internal.R | 38 ++++ inst/tinytest/test_pl.R | 61 +++++++ inst/tinytest/test_position.R | 53 ++++++ inst/tinytest/test_position_00.R | 11 + inst/tinytest/test_position_ops.R | 109 +++++++++++++- inst/tinytest/test_rc.R | 129 ++++++++++++++++ man/NAVseries.Rd | 138 +++++++++-------- man/PMwR-internal.Rd | 3 man/PMwR-package.Rd | 4 man/adjust-series.Rd | 6 man/btest.Rd | 2 man/drawdowns.Rd | 2 man/instrument.Rd | 2 man/journal.Rd | 17 +- man/pl.Rd | 4 man/plot_trading_hours.Rd | 2 man/position.Rd | 57 +++++-- man/pricetable.Rd | 2 man/rc.Rd | 22 ++ man/rebalance.Rd | 6 man/returns.Rd | 2 man/scale1.Rd | 2 man/streaks.Rd | 2 man/unit_prices.Rd | 2 vignettes/Computing_returns.Rnw | 4 51 files changed, 993 insertions(+), 393 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-30 1.0.3
2023-12-21 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-22 0.5.1
2025-08-26 0.3.1
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.14.0 dated 2025-09-29 and 0.15.0 dated 2025-10-19
DESCRIPTION | 6 MD5 | 220 ++-- NEWS.md | 26 R/aaa_class.R | 8 R/build_tt.R | 59 - R/expand_style.R | 242 +--- R/grid_colspan.R | 9 R/grid_style.R | 54 R/group_tt_j.R | 16 R/html_finalize.R | 18 R/html_style.R | 403 ++++--- R/json.R | 23 R/plot_tt.R | 281 ++++- R/sanity.R | 2 R/style_tt.R | 126 +- R/tabularray_style.R | 308 +++-- R/tabulator_build.R | 15 R/tabulator_columns.R | 547 ++-------- R/tabulator_css.R | 1 R/tabulator_data.R | 34 R/tabulator_finalize.R | 152 ++ R/tabulator_plot.R |only R/tabulator_search.R | 151 +- R/tabulator_style.R | 348 ++++-- R/tabulator_stylesheet.R | 49 R/theme_html.R | 29 R/theme_html_tabulator.R | 11 R/theme_striped.R | 8 R/typst_style.R | 185 ++- R/typst_tt.R | 6 README.md | 2 build/partial.rdb |binary inst/tabulator.scss |only inst/tabulator_tinytable.css |only inst/tabulator_tinytable.css.map |only inst/tabulator_tinytable.min.css |only inst/tabulator_tinytable.min.css.map |only inst/tabulator_tinytable.scss |only inst/templates/html.html | 1 inst/templates/tabulator.html | 18 inst/tinytable.js | 174 +++ inst/tinytest/_tinysnapshot/ansi-style_groupj_01.md | 2 inst/tinytest/_tinysnapshot/ansi-styles_01.md | 2 inst/tinytest/_tinysnapshot/docx-issue98_01.txt | 2 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.html | 16 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.typ | 4 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.html | 16 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.typ | 4 inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 8 inst/tinytest/_tinysnapshot/group-3level.md | 4 inst/tinytest/_tinysnapshot/group-3level.typ | 25 inst/tinytest/_tinysnapshot/group-delim-all-delim.md | 2 inst/tinytest/_tinysnapshot/group-delim-some-delim.md | 2 inst/tinytest/_tinysnapshot/group-delim-x-delim.md | 2 inst/tinytest/_tinysnapshot/group-html_tutorial_01.html | 20 inst/tinytest/_tinysnapshot/group-issue165_extra_row.html | 32 inst/tinytest/_tinysnapshot/group-issue165_extra_row.md | 2 inst/tinytest/_tinysnapshot/group-issue165_extra_row.typ | 4 inst/tinytest/_tinysnapshot/group-issue165_html_centering_style.html | 40 inst/tinytest/_tinysnapshot/group-multilevel-basic.html | 20 inst/tinytest/_tinysnapshot/group-multilevel-basic.md | 2 inst/tinytest/_tinysnapshot/group-multilevel-basic.typ | 6 inst/tinytest/_tinysnapshot/group-multilevel-complex.html | 32 inst/tinytest/_tinysnapshot/group-multilevel-complex.md | 4 inst/tinytest/_tinysnapshot/group-multilevel-complex.typ | 14 inst/tinytest/_tinysnapshot/group-multilevel-empty.html | 42 inst/tinytest/_tinysnapshot/group-multilevel-empty.md | 4 inst/tinytest/_tinysnapshot/group-multilevel-empty.tex | 2 inst/tinytest/_tinysnapshot/group-multilevel-empty.typ | 13 inst/tinytest/_tinysnapshot/group-nse.html | 4 inst/tinytest/_tinysnapshot/group-shared-level-spanning.md | 2 inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.html | 8 inst/tinytest/_tinysnapshot/html-alignment.html | 32 inst/tinytest/_tinysnapshot/html-borders.html | 2 inst/tinytest/_tinysnapshot/html-conditional_styling.html | 8 inst/tinytest/_tinysnapshot/html-font_size.html | 12 inst/tinytest/_tinysnapshot/html-individual_cells.html | 8 inst/tinytest/_tinysnapshot/html-issue355a.html | 52 inst/tinytest/_tinysnapshot/html-issue355b.html | 20 inst/tinytest/_tinysnapshot/html-issue575.html | 40 inst/tinytest/_tinysnapshot/html-issue58.html | 24 inst/tinytest/_tinysnapshot/html-issue88.html | 8 inst/tinytest/_tinysnapshot/html-issue92.html | 16 inst/tinytest/_tinysnapshot/html-spanning_cells.html | 8 inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 24 inst/tinytest/_tinysnapshot/latex-background_na_values.tex |only inst/tinytest/_tinysnapshot/markdown-group_j_wider_1.txt | 2 inst/tinytest/_tinysnapshot/markdown-group_j_wider_2.txt | 2 inst/tinytest/_tinysnapshot/markdown-group_tt.txt | 2 inst/tinytest/_tinysnapshot/markdown-issue605.txt |only inst/tinytest/_tinysnapshot/markdown-long_column_group.txt | 2 inst/tinytest/_tinysnapshot/markdown-long_mixed_groups.txt | 2 inst/tinytest/_tinysnapshot/style-align_partial.html | 40 inst/tinytest/_tinysnapshot/style-groupj_colnames.md | 2 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.html | 44 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.md | 2 inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.typ | 4 inst/tinytest/_tinysnapshot/style-issue514_white_blue.html | 12 inst/tinytest/_tinysnapshot/style-issue514_white_blue.typ | 20 inst/tinytest/_tinysnapshot/style-smallcap.html | 20 inst/tinytest/_tinysnapshot/theme-issue531_style_colors_override_stripes.html | 24 inst/tinytest/_tinysnapshot/typst-complicated.typ | 4 inst/tinytest/_tinysnapshot/typst-group_columns.typ | 5 inst/tinytest/_tinysnapshot/typst-issue-139_misaligned_rule_with_group_tt.typ | 4 inst/tinytest/_tinysnapshot/typst-issue323_group_tt_style_tt.typ | 5 inst/tinytest/_tinysnapshot/typst-issue592.typ |only inst/tinytest/_tinysnapshot/typst-no_headers.typ | 7 inst/tinytest/test-group.R | 23 inst/tinytest/test-latex.R | 11 inst/tinytest/test-markdown.R | 33 inst/tinytest/test-typst.R | 71 + man/plot_tt.Rd | 30 man/plot_vector.Rd | 7 man/style_tt.Rd | 24 man/theme_html.Rd | 17 man/tt.Rd | 2 116 files changed, 2753 insertions(+), 1794 deletions(-)
Title: Synthetic Control Group Method for Comparative Case Studies
Description: Implements the synthetic control group method for comparative case studies
as described in Abadie and Gardeazabal (2003) and Abadie, Diamond, and Hainmueller
(2010, 2011, 2014). The synthetic control method allows for effect estimation in
settings where a single unit (a state, country, firm, etc.) is exposed to an event
or intervention. It provides a data-driven procedure to construct synthetic control
units based on a weighted combination of comparison units that approximates the
characteristics of the unit that is exposed to the intervention. A combination of
comparison units often provides a better comparison for the unit exposed to the
intervention than any comparison unit alone.
Author: Jens Hainmueller [aut, cre],
Alexis Diamond [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between Synth versions 1.1-8 dated 2023-06-02 and 1.1-9 dated 2025-10-19
DESCRIPTION | 27 +++-- MD5 | 6 - man/fn.V.Rd | 12 +- man/synth.Rd | 310 +++++++++++------------------------------------------------ 4 files changed, 88 insertions(+), 267 deletions(-)
Title: Enhanced R Package for 'GEMPACK' .har and .sl4 Files
Description: Provides tools for processing and analyzing .har and .sl4 files, making it easier
for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets.
It simplifies the management of multiple experiment results, enabling faster
and more efficient comparisons without complexity. Users can extract, restructure,
and merge data seamlessly, ensuring compatibility across different tools.
The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or
any software that supports Text, CSV, or 'Excel' formats.
Author: Pattawee Puangchit [aut, cre]
Maintainer: Pattawee Puangchit <ppuangch@purdue.edu>
Diff between HARplus versions 1.0.1 dated 2025-03-13 and 1.1.0 dated 2025-10-19
HARplus-1.0.1/HARplus/vignettes/rsconnect |only HARplus-1.1.0/HARplus/DESCRIPTION | 8 HARplus-1.1.0/HARplus/MD5 | 28 HARplus-1.1.0/HARplus/NAMESPACE | 63 HARplus-1.1.0/HARplus/R/data_summary.R | 736 ++++----- HARplus-1.1.0/HARplus/R/get_data.R | 1638 +++++++++++----------- HARplus-1.1.0/HARplus/R/load_sl4x.R | 15 HARplus-1.1.0/HARplus/R/save_har.R |only HARplus-1.1.0/HARplus/README.md | 23 HARplus-1.1.0/HARplus/inst/doc/introduction.R | 20 HARplus-1.1.0/HARplus/inst/doc/introduction.Rmd | 44 HARplus-1.1.0/HARplus/inst/doc/introduction.html | 222 +- HARplus-1.1.0/HARplus/inst/docs |only HARplus-1.1.0/HARplus/man/export_data.Rd | 156 +- HARplus-1.1.0/HARplus/man/pivot_data_hierarchy.Rd | 152 +- HARplus-1.1.0/HARplus/man/save_har.Rd |only HARplus-1.1.0/HARplus/vignettes/introduction.Rmd | 44 17 files changed, 1669 insertions(+), 1480 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 3.1.13 dated 2025-07-22 and 3.1.18 dated 2025-10-19
DESCRIPTION | 8 MD5 | 49 ++-- NAMESPACE | 2 R/PVA.v3.r | 14 - R/byIndv4Times.r | 310 ++++++++++++++++++++++++++- R/calcs.r | 25 +- R/traitSmooth.r | 17 + build/partial.rdb |binary build/vignette.rds |binary inst/News.Rd | 26 ++ inst/doc/Rice.pdf |binary inst/doc/Tomato.pdf |binary inst/doc/growthPheno-manual.pdf |binary man/args4smoothing.Rd | 7 man/byIndv4Intvl_WaterUse.Rd | 2 man/byIndv4Times_GRsDiff.Rd | 6 man/byIndv4Times_SplinesGRs.Rd | 7 man/byIndv4Times_WaterUse.Rd |only man/byIndv4Times_periodicRates.Rd |only man/calcLagged.Rd | 3 man/growthPheno-pkg.Rd | 14 - man/plotCorrmatrix.Rd | 6 tests/testthat/data/water779DS.test.dat.rda |only tests/testthat/data/water797SH.check.dat.rda |only tests/testthat/data/water797SH.test.dat.rda |only tests/testthat/testTraitWrappers.r | 33 ++ tests/testthat/testbyIndv4Times.r | 105 +++++++++ tests/testthat/testexampleData.r | 2 28 files changed, 579 insertions(+), 57 deletions(-)
Title: Dataframe Difference Tool
Description: Functions for comparing two data.frames against
each other. The core functionality is to provide a detailed breakdown of any differences
between two data.frames as well as providing utility functions to help narrow down the
source of problems and differences.
Author: Craig Gower-Page [cre, aut],
Kieran Martin [aut]
Maintainer: Craig Gower-Page <craiggower@gmail.com>
Diff between diffdf versions 1.1.1 dated 2024-09-24 and 1.1.2 dated 2025-10-19
DESCRIPTION | 19 - LICENSE | 4 MD5 | 34 +- NEWS.md | 11 R/ascii_tables.R | 13 - R/diffdf.R | 32 -- R/identify.R | 2 R/print.R | 45 +++ build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/diffdf-basic.R | 6 inst/doc/diffdf-basic.html | 4 man/get_print_message.issue.Rd | 5 man/get_table.Rd | 3 man/print.diffdf.Rd | 21 + tests/testthat/_snaps/miscellaneous.md | 392 +++++++++++++++++++++++++++++++++ tests/testthat/test-miscellaneous.R | 154 ++++++++++++ tests/testthat/test-print_output.R | 40 +++ 18 files changed, 707 insertions(+), 79 deletions(-)
Title: Tidy Tools for Paleoenvironmental Archives
Description: Provides a set of functions with a common framework for age-depth model management,
stratigraphic visualization, and common statistical transformations. The focus of the
package is stratigraphic visualization, for which 'ggplot2' components are provided
to reproduce the scales, geometries, facets, and theme elements commonly used in
publication-quality stratigraphic diagrams. Helpers are also provided to reproduce
the exploratory statistical summaries that are frequently included on
stratigraphic diagrams. See Dunnington et al. (2021) <doi:10.18637/jss.v101.i07>.
Author: Dewey Dunnington [aut, cre, cph]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between tidypaleo versions 0.1.3 dated 2023-01-18 and 0.1.4 dated 2025-10-19
DESCRIPTION | 12 MD5 | 117 +++++- NEWS.md | 6 R/age_depth_model.R | 4 R/ggstrat-geoms.R | 12 R/ggstrat-plot_addons.R | 6 R/ggstrat-themes.R | 2 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/age_depth.R | 20 - inst/doc/age_depth.html | 89 ++-- inst/doc/nested_analysis.R | 6 inst/doc/nested_analysis.html | 424 +++++++++++------------ inst/doc/strat_diagrams.R | 68 +-- inst/doc/strat_diagrams.html | 620 +++++++++++++++++----------------- man/geom_point_exaggerate.Rd | 2 man/stat_nested_hclust.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps |only tests/testthat/test-age_depth_model.R | 4 tests/testthat/test-nested_chclust.R | 4 22 files changed, 741 insertions(+), 661 deletions(-)
Title: Cohort Data Analyses
Description: Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Diff between cohorttools versions 0.1.6 dated 2022-11-23 and 0.1.7 dated 2025-10-18
DESCRIPTION | 13 ++++++++----- MD5 | 12 ++++++------ NEWS.md | 2 +- R/cohorttools.R | 3 --- man/boxesLx.Rd | 3 --- man/mkratetable.Rd | 3 --- man/plotcuminc.Rd | 3 --- 7 files changed, 15 insertions(+), 24 deletions(-)
Title: Highlight Conserved Edits Across Versions of a Document
Description: Input multiple versions of a source document,
and receive HTML code for a highlighted version of the source document
indicating the frequency of occurrence of phrases in the different versions.
This method is described in Chapter 3 of
Rogers (2024) <https://digitalcommons.unl.edu/dissertations/AAI31240449/>.
Author: Center for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Rachel Rogers [aut, cre] ,
Susan VanderPlas [aut]
Maintainer: Rachel Rogers <rrogers.rpackages@gmail.com>
Diff between highlightr versions 1.1.2 dated 2025-06-26 and 1.2.0 dated 2025-10-18
DESCRIPTION | 8 MD5 | 56 +- NEWS.md | 14 R/collocate_comments.R | 163 +++--- R/collocate_comments_fuzzy.R | 28 - R/collocation_plot.R | 10 R/data.R | 88 +-- R/highlighted_text.R | 14 R/token_comments.R | 67 +- R/token_transcript.R | 67 +- R/transcript_frequency.R | 9 README.md | 31 + inst/doc/highlightr.R | 50 + inst/doc/highlightr.Rmd | 54 ++ inst/doc/highlightr.html | 291 ++++++---- inst/doc/wikipedia-highlighter.R | 69 +- inst/doc/wikipedia-highlighter.Rmd | 77 +- inst/doc/wikipedia-highlighter.html | 956 ++++++++++++++++++------------------ man/collocate_comments.Rd | 15 man/collocate_comments_fuzzy.Rd | 25 man/collocation_plot.Rd | 7 man/figures/highlight_example.PNG |binary man/highlighted_text.Rd | 11 man/token_comments.Rd | 2 man/token_transcript.Rd | 2 man/transcript_frequency.Rd | 6 man/wiki_pages.Rd | 2 vignettes/highlightr.Rmd | 54 ++ vignettes/wikipedia-highlighter.Rmd | 77 +- 29 files changed, 1362 insertions(+), 891 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-1 dated 2025-07-07 and 1.2-2 dated 2025-10-18
ChangeLog | 12 +++ DESCRIPTION | 8 +- MD5 | 14 +-- R/plotcpfa.R | 7 - inst/doc/cpfa.R | 83 ++++++++++++++++++++ inst/doc/cpfa.Rmd | 212 +++++++++++++++++++++++++++++++++++++++++++++++------ inst/doc/cpfa.pdf |binary vignettes/cpfa.Rmd | 212 +++++++++++++++++++++++++++++++++++++++++++++++------ 8 files changed, 488 insertions(+), 60 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre] ,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.14 dated 2025-07-11 and 1.2.15 dated 2025-10-18
DESCRIPTION | 10 ++-- MD5 | 42 +++++++++---------- NAMESPACE | 2 R/wiki_utils.R | 21 ++++++--- README.md | 4 - build/vignette.rds |binary inst/doc/wiki_utils.html | 39 +++++++++-------- man/filext.Rd | 58 +++++++++++++------------- man/getFiles.Rd | 102 +++++++++++++++++++++++------------------------ man/getWikiFiles.Rd | 88 ++++++++++++++++++++-------------------- man/httrGetJSON.Rd | 62 ++++++++++++++-------------- man/limitRequester.Rd | 3 - man/nametoWikiFrame.Rd | 74 +++++++++++++++++----------------- man/nametoWikiHtml.Rd | 70 ++++++++++++++++---------------- man/nametoWikiURL.Rd | 74 +++++++++++++++++----------------- man/preName.Rd | 60 +++++++++++++-------------- man/searchWiki.Rd | 96 ++++++++++++++++++++++---------------------- man/selectLang.Rd | 48 +++++++++++----------- man/urltoFrame.Rd | 70 ++++++++++++++++---------------- man/urltoHtml.Rd | 86 +++++++++++++++++++-------------------- man/validUrl.Rd | 56 ++++++++++++------------- man/w_query.Rd | 4 - 22 files changed, 537 insertions(+), 532 deletions(-)
Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting. The package is described in
Vollering et al. (2019; <doi:10.1002/ece3.5654>).
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph],
Michael Bedward [ctb]
Maintainer: Julien Vollering <julienvollering@gmail.com>
Diff between MIAmaxent versions 1.3.1 dated 2024-08-23 and 1.4.0 dated 2025-10-18
MIAmaxent-1.3.1/MIAmaxent/inst/doc/a-modeling-example.html.asis |only MIAmaxent-1.3.1/MIAmaxent/man/release_questions.Rd |only MIAmaxent-1.3.1/MIAmaxent/vignettes/a-modeling-example.html.asis |only MIAmaxent-1.4.0/MIAmaxent/DESCRIPTION | 12 MIAmaxent-1.4.0/MIAmaxent/MD5 | 32 MIAmaxent-1.4.0/MIAmaxent/NEWS.md | 158 ++-- MIAmaxent-1.4.0/MIAmaxent/R/deriveVars.R | 1 MIAmaxent-1.4.0/MIAmaxent/R/plotFOP.R | 2 MIAmaxent-1.4.0/MIAmaxent/R/testAUC.R | 9 MIAmaxent-1.4.0/MIAmaxent/R/utils.R | 30 MIAmaxent-1.4.0/MIAmaxent/README.md | 6 MIAmaxent-1.4.0/MIAmaxent/build/partial.rdb |binary MIAmaxent-1.4.0/MIAmaxent/build/vignette.rds |binary MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.R |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.Rmd |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/NCEAS.html |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.R |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.Rmd |only MIAmaxent-1.4.0/MIAmaxent/inst/doc/a-modeling-example.html | 323 +++++----- MIAmaxent-1.4.0/MIAmaxent/vignettes/NCEAS.Rmd |only MIAmaxent-1.4.0/MIAmaxent/vignettes/a-modeling-example.Rmd | 73 -- MIAmaxent-1.4.0/MIAmaxent/vignettes/references.bib |only 22 files changed, 330 insertions(+), 316 deletions(-)
Title: Marginal Modeling for Exposure Data with Values Below the LOD
Description: Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates. For more details see Chen IC, Bertke SJ, Curwin BD (2021) <doi:10.1038/s41370-021-00345-1>, Chen IC, Bertke SJ, Estill CF (2024) <doi:10.1038/s41370-024-00640-7>, Chen IC, Bertke SJ, Dahm MM (2024) <doi:10.1093/annweh/wxae068>, and Chen IC (2025) <doi:10.1038/s41370-025-00752-8>.
Author: I-Chen Chen [cre, aut] ,
Philip Westgate [ctb],
Liya Fu [ctb]
Maintainer: I-Chen Chen <flecsh@gmail.com>
Diff between marlod versions 0.2.1 dated 2025-05-27 and 0.2.2 dated 2025-10-18
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS.md | 62 +++++++++++++++-------------- R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/marlod.html | 106 +++++++++++++++++++++++++-------------------------- man/Fillin.Rd | 6 +- man/Modified.QIF.Rd | 12 ++--- 9 files changed, 109 insertions(+), 103 deletions(-)
Title: Interpretation of Heterogeneous Single-Cell Gene Expression Data
Description: We develop a novel matrix factorization tool named 'scINSIGHT' to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. Given multiple gene expression samples from different biological conditions, 'scINSIGHT' simultaneously identifies common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space. With the factorized results, the inferred expression levels and memberships of common gene modules can be used to cluster cells and detect cell identities, and the condition-specific gene modules can help compare functional differences in transcriptomes from distinct conditions. Please also see Qian K, Fu SW, Li HW, Li WV (2022) <doi:10.1186/s13059-022-02649-3>.
Author: Kun Qian [aut, ctb, cre] ,
Wei Vivian Li [aut, ctb]
Maintainer: Kun Qian <Kun_Qian@foxmail.com>
Diff between scINSIGHT versions 0.1.4 dated 2022-05-29 and 0.1.5 dated 2025-10-18
DESCRIPTION | 14 ++++++++------ MD5 | 9 +++++---- R/RcppExports.R | 30 +++++++++++++++--------------- README.md |only src/Makevars | 2 +- src/Makevars.win | 2 +- 6 files changed, 30 insertions(+), 27 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 2.1 dated 2025-06-17 and 2.2 dated 2025-10-18
DESCRIPTION | 8 +-- MD5 | 110 +++++++++++++++++++++++++++------------------------- R/ABWilcox.R | 2 R/ABbinomial.R | 9 ++-- R/ABdescrip.R | 3 - R/ABma.R | 16 ++++--- R/ABregres.R | 21 +++++++-- R/ABrf2.R | 3 - R/ABrobust.R | 7 +-- R/ABttest.R | 6 ++ R/Aregres.R | 17 +++++--- R/Arimadiff.R | 6 +- R/Arimama.R | 5 +- R/Arobust.R | 2 R/CDCabove.R | 9 ++-- R/CDCbelow.R | 9 ++-- R/Cchart.R | 14 +++--- R/GABrf2.R | 2 R/GABttest.R | 2 R/Gindex.R | 15 ++++--- R/IRDabove.R | 6 +- R/IRDbelow.R | 6 +- R/NAPabove.R | 6 +- R/NAPbelow.R | 6 +- R/PANDabove.R | 6 +- R/PANDbelow.R | 3 - R/PEMabove.R | 6 +- R/PEMbelow.R | 8 +-- R/PNDabove.R | 6 +- R/PNDbelow.R | 6 +- R/Pchart.R | 17 ++++---- R/RMEffectsize.R |only R/RMttest.R |only R/RSIQRline.R | 3 - R/RSPCline.R |only R/Rchart.R | 16 +------ R/Rchartsd.R | 6 +- R/RobustCDCabove.R | 11 ++--- R/RobustCDCbelow.R | 10 ++-- R/SPClegend.R | 8 ++- R/SPCline.R | 4 - R/XRchart.R | 11 ----- R/Xmrchart.R | 9 ---- R/diffchart.R | 12 +++-- R/meanabove.R | 7 ++- R/meanbelow.R | 11 +++-- R/medabove.R | 10 ++-- R/medbelow.R | 7 +-- R/metareg.R | 2 R/metaregi.R | 3 - R/regabove.R | 13 +++--- R/regbelow.R | 10 +++- R/robregabove.R | 12 ++--- R/robregbelow.R | 11 +++-- R/trimabove.R | 8 ++- R/trimbelow.R | 8 ++- man/RMEffectsize.Rd |only man/RMttest.Rd |only man/RSPCline.Rd |only 59 files changed, 292 insertions(+), 242 deletions(-)
Title: Flexible Client for the 'Financial Modeling Prep' API
Description: Provides a flexible interface to the 'Financial Modeling Prep' API
<https://site.financialmodelingprep.com/developer/docs>. The package
supports all available endpoints and parameters, enabling R users
to interact with a wide range of financial data.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between fmpapi versions 0.2.1 dated 2025-05-07 and 1.0.0 dated 2025-10-18
DESCRIPTION | 6 +- MD5 | 12 ++--- NEWS.md | 6 ++ R/fmp_get.R | 44 +++++++++++++++---- README.md | 8 --- man/fmp_get.Rd | 2 tests/testthat/test-fmp_get.R | 96 ++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 147 insertions(+), 27 deletions(-)
Title: Transition Network Analysis (TNA)
Description: Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)
<doi:10.1145/3706468.3706513> for more details on TNA.
Author: Mohammed Saqr [aut],
Santtu Tikka [aut],
Sonsoles Lopez-Pernas [aut, cre]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between tna versions 1.0.0 dated 2025-07-15 and 1.1.0 dated 2025-10-18
tna-1.0.0/tna/tests/testthat/test-tna.R |only tna-1.1.0/tna/DESCRIPTION | 16 tna-1.1.0/tna/MD5 | 152 +++-- tna-1.1.0/tna/NAMESPACE | 18 tna-1.1.0/tna/NEWS.md | 15 tna-1.1.0/tna/R/betweenness.R | 7 tna-1.1.0/tna/R/bootstrap.R | 143 ++++- tna-1.1.0/tna/R/build.R | 395 ++++++++++++-- tna-1.1.0/tna/R/centralities.R | 47 - tna-1.1.0/tna/R/check.R | 91 ++- tna-1.1.0/tna/R/cliques.R | 3 tna-1.1.0/tna/R/clusters.R | 549 ++++++-------------- tna-1.1.0/tna/R/coef.R |only tna-1.1.0/tna/R/colors.R | 8 tna-1.1.0/tna/R/communities.R | 17 tna-1.1.0/tna/R/compare.R | 192 ++++++ tna-1.1.0/tna/R/data.R | 257 ++++++--- tna-1.1.0/tna/R/groups.R |only tna-1.1.0/tna/R/indices.R |only tna-1.1.0/tna/R/mmm.R |only tna-1.1.0/tna/R/permutation.R | 59 +- tna-1.1.0/tna/R/plot.R | 393 +++++++++----- tna-1.1.0/tna/R/print.R | 222 +++++--- tna-1.1.0/tna/R/pruning.R | 6 tna-1.1.0/tna/R/summary.R | 41 + tna-1.1.0/tna/R/tna-package.R | 8 tna-1.1.0/tna/R/utilities.R | 74 ++ tna-1.1.0/tna/R/vcov.R |only tna-1.1.0/tna/R/zzz.R | 11 tna-1.1.0/tna/data/engagement.rda |binary tna-1.1.0/tna/data/engagement_mmm.rda |binary tna-1.1.0/tna/inst/doc/communities_and_cliques.html | 21 tna-1.1.0/tna/inst/doc/complete_tutorial.html | 8 tna-1.1.0/tna/inst/doc/grouped_sequences.html | 124 ++-- tna-1.1.0/tna/man/betweenness_network.Rd | 7 tna-1.1.0/tna/man/bootstrap.Rd | 10 tna-1.1.0/tna/man/bootstrap_cliques.Rd |only tna-1.1.0/tna/man/build_model.Rd | 125 +++- tna-1.1.0/tna/man/centralities.Rd | 10 tna-1.1.0/tna/man/cluster_sequences.Rd |only tna-1.1.0/tna/man/communities.Rd | 8 tna-1.1.0/tna/man/compare.Rd | 5 tna-1.1.0/tna/man/compare.group_tna.Rd | 9 tna-1.1.0/tna/man/compare_sequences.Rd |only tna-1.1.0/tna/man/estimate_centrality_stability.Rd | 40 + tna-1.1.0/tna/man/group_model.Rd | 53 + tna-1.1.0/tna/man/import_data.Rd | 5 tna-1.1.0/tna/man/import_onehot.Rd |only tna-1.1.0/tna/man/mmm_stats.Rd | 5 tna-1.1.0/tna/man/permutation_test.Rd | 3 tna-1.1.0/tna/man/permutation_test.group_tna.Rd | 9 tna-1.1.0/tna/man/plot.group_tna.Rd | 2 tna-1.1.0/tna/man/plot.group_tna_bootstrap.Rd | 4 tna-1.1.0/tna/man/plot.group_tna_communities.Rd | 2 tna-1.1.0/tna/man/plot.tna_comparison.Rd | 5 tna-1.1.0/tna/man/plot.tna_sequence_comparison.Rd |only tna-1.1.0/tna/man/plot_associations.Rd |only tna-1.1.0/tna/man/plot_compare.Rd | 5 tna-1.1.0/tna/man/plot_compare.group_tna.Rd | 5 tna-1.1.0/tna/man/plot_mosaic.group_tna.Rd | 2 tna-1.1.0/tna/man/plot_sequences.Rd | 11 tna-1.1.0/tna/man/prepare_data.Rd | 55 +- tna-1.1.0/tna/man/print.summary.group_tna.Rd | 2 tna-1.1.0/tna/man/print.tna.Rd | 7 tna-1.1.0/tna/man/print.tna_communities.Rd | 2 tna-1.1.0/tna/man/print.tna_comparison.Rd | 5 tna-1.1.0/tna/man/print.tna_data.Rd | 1 tna-1.1.0/tna/man/print.tna_sequence_comparison.Rd |only tna-1.1.0/tna/man/print.tna_stability.Rd | 2 tna-1.1.0/tna/man/rename_groups.Rd | 6 tna-1.1.0/tna/man/simulate.tna.Rd | 1 tna-1.1.0/tna/man/sna.Rd |only tna-1.1.0/tna/tests/testthat/helper-mock.R | 53 + tna-1.1.0/tna/tests/testthat/test-bootstrap.R | 8 tna-1.1.0/tna/tests/testthat/test-build.R |only tna-1.1.0/tna/tests/testthat/test-centralities.R | 4 tna-1.1.0/tna/tests/testthat/test-clusters.R | 123 ---- tna-1.1.0/tna/tests/testthat/test-compare.R | 17 tna-1.1.0/tna/tests/testthat/test-data.R | 76 ++ tna-1.1.0/tna/tests/testthat/test-groups.R |only tna-1.1.0/tna/tests/testthat/test-indices.R |only tna-1.1.0/tna/tests/testthat/test-mmm.R |only tna-1.1.0/tna/tests/testthat/test-permutation.R | 34 - tna-1.1.0/tna/tests/testthat/test-plot.R | 85 ++- tna-1.1.0/tna/tests/testthat/test-print.R | 31 + tna-1.1.0/tna/tests/testthat/test-pruning.R | 2 86 files changed, 2473 insertions(+), 1243 deletions(-)
Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between huito versions 0.2.5 dated 2024-09-05 and 0.2.6 dated 2025-10-18
huito-0.2.5/huito/inst/doc/labels.Rmd |only huito-0.2.5/huito/vignettes/labels.Rmd |only huito-0.2.6/huito/DESCRIPTION | 21 - huito-0.2.6/huito/MD5 | 50 +-- huito-0.2.6/huito/NEWS.md | 7 huito-0.2.6/huito/R/include_image.R | 3 huito-0.2.6/huito/R/include_text.R | 21 + huito-0.2.6/huito/R/label_layout.R | 7 huito-0.2.6/huito/R/label_print.R | 21 - huito-0.2.6/huito/build/vignette.rds |binary huito-0.2.6/huito/inst/doc/germinar.R | 7 huito-0.2.6/huito/inst/doc/germinar.Rmd | 9 huito-0.2.6/huito/inst/doc/germinar.html | 52 +-- huito-0.2.6/huito/inst/doc/huito.R | 6 huito-0.2.6/huito/inst/doc/huito.html | 4 huito-0.2.6/huito/inst/doc/labels.R | 37 +- huito-0.2.6/huito/inst/doc/labels.html | 465 +++++++++++-------------------- huito-0.2.6/huito/inst/doc/labels.qmd |only huito-0.2.6/huito/inst/doc/stickers.R | 32 +- huito-0.2.6/huito/inst/doc/stickers.Rmd | 32 +- huito-0.2.6/huito/inst/doc/stickers.html | 73 +++- huito-0.2.6/huito/man/fieldbook.Rd | 14 huito-0.2.6/huito/man/include_text.Rd | 8 huito-0.2.6/huito/man/label_layout.Rd | 7 huito-0.2.6/huito/man/label_print.Rd | 11 huito-0.2.6/huito/vignettes/germinar.Rmd | 9 huito-0.2.6/huito/vignettes/labels.qmd |only huito-0.2.6/huito/vignettes/stickers.Rmd | 32 +- 28 files changed, 479 insertions(+), 449 deletions(-)
Title: A 'ggplot2' Extension for Composable Visualization
Description: A 'ggplot2' extension providing an integrative framework for
composable visualization, enabling the creation of complex multi-plot
layouts such as insets, circular arrangements, and multi-panel compositions.
Built on the grammar of graphics, it offers tools to align, stack, and nest
plots, simplifying the construction of richly annotated figures for
high-dimensional data contexts—such as genomics, transcriptomics, and
microbiome studies—by making it easy to link related plots, overlay
clustering results, or highlight shared patterns.
Author: Yun Peng [aut, cre] ,
Shixiang Wang [aut] ,
Guangchuang Yu [ths]
Maintainer: Yun Peng <yunyunp96@163.com>
Diff between ggalign versions 1.1.0 dated 2025-09-11 and 1.2.0 dated 2025-10-18
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Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb] ,
Frederiek - Maarten Kerckhof [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.4 dated 2025-09-14 and 1.3.5 dated 2025-10-18
DESCRIPTION | 26 ++++-------- MD5 | 26 ++++++------ NEWS.md | 10 ++++ R/RcppExports.R | 4 + R/clustering_functions.R | 29 +++++++++++--- README.md | 20 ++------- build/vignette.rds |binary inst/doc/the_clusterR_package.html | 12 ++--- inst/include/ClusterRHeader.h | 76 ++++++++++++++++++++++++++++++++++++- man/predict_GMM.Rd | 3 - src/RcppExports.cpp | 15 +++++++ src/export_inst_folder_headers.cpp | 15 +++++++ src/init.c | 2 tests/testthat/test-gmm.R | 71 ++++++++++++++++++++++++++++++++++ 14 files changed, 251 insertions(+), 58 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.7.2 dated 2023-02-01 and 0.7.3 dated 2025-10-18
DESCRIPTION | 8 - MD5 | 44 ++++---- NEWS.md | 10 + R/box_m.R | 10 - R/sign_test.R | 2 R/wilcox_test.R | 2 README.md | 91 ++++++++---------- man/box_m.Rd | 10 - man/chisq_test.Rd | 2 man/cor_plot.Rd | 14 +- man/fisher_test.Rd | 8 - man/wilcox_test.Rd | 2 tests/testthat/test-remove_ns.R | 47 ++++++--- tests/testthat/test-wilcox_test.R | 32 +++++- tools/README-comaprison-against-reference-group-1.png |binary tools/README-comaprison-against-reference-group-2.png |binary tools/README-comparison-against-base-mean-1.png |binary tools/README-custoize-p-value-labels-1.png |binary tools/README-grouped-two-sample-t-test-1.png |binary tools/README-paired-t-test-1.png |binary tools/README-pairwise-comparisons-1.png |binary tools/README-unnamed-chunk-10-1.png |binary tools/README-unpaired-two-sample-t-test-1.png |binary 23 files changed, 161 insertions(+), 121 deletions(-)
Title: Non-Smooth Regularization for Structural Equation Models
Description: Provides regularized structural equation modeling
(regularized SEM) with non-smooth penalty functions (e.g., lasso) building
on 'lavaan'. The package is heavily inspired by the
['regsem'](<https://github.com/Rjacobucci/regsem>) and
['lslx'](<https://github.com/psyphh/lslx>) packages.
Author: Jannik H. Orzek [aut, cre, cph]
Maintainer: Jannik H. Orzek <jannik.orzek@mailbox.org>
Diff between lessSEM versions 1.5.6 dated 2025-08-25 and 1.5.7 dated 2025-10-18
DESCRIPTION | 6 +- MD5 | 30 +++++----- inst/doc/Definition-Variables-and-Multi-Group-SEM.html | 5 + inst/doc/Estimator-Settings.html | 5 + inst/doc/General-Purpose-Optimization.html | 5 + inst/doc/Mixed-Penalties.html | 5 + inst/doc/Parameter-transformations.html | 5 + inst/doc/The-Structural-Equation-Model.html | 5 + inst/doc/lessSEM.html | 5 + inst/include/lesstimate/include/lesstimate/bfgs.h | 2 inst/include/lesstimate/include/lesstimate/bfgsOptim.h | 4 - inst/include/lesstimate/include/lesstimate/glmnet_class.h | 4 - inst/include/lesstimate/include/lesstimate/glmnet_lsp.h | 2 inst/include/lesstimate/include/lesstimate/glmnet_mcp.h | 2 inst/include/lesstimate/include/lesstimate/ista_class.h | 6 +- inst/include/lesstimate/include/lesstimate/ista_mixedPenalty.h | 2 16 files changed, 51 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-11 0.3.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-06 2.1.16
2022-01-20 2.1.9
2021-12-02 2.1.7
2021-03-15 2.0.7
2020-12-16 2.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-06 0.6.3
2024-07-14 0.6.2
2024-04-09 0.6.1
2023-10-16 0.6.0
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani [aut, cre],
Maria Brigida Ferraro [aut],
Alessio Serafini [aut]
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 2.1.2 dated 2025-07-22 and 2.1.3 dated 2025-10-18
DESCRIPTION | 10 ++--- MD5 | 14 ++++---- NEWS.md | 4 ++ inst/CITATION | 2 - src/F.cpp | 4 +- src/FKM_rcpp.cpp | 92 +++++++++++++++++++++++++++---------------------------- src/func.cpp | 2 - src/memDeg.cpp | 2 - 8 files changed, 67 insertions(+), 63 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 3.1-8 dated 2025-08-18 and 3.1-9 dated 2025-10-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 16 ++++++++++++++++ data/austates.rda |binary data/shelling.rda |binary inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + 7 files changed, 28 insertions(+), 10 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Tommy Jones [aut, cre],
William Doane [ctb],
Mattias Attbom [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 3.0.5 dated 2021-06-28 and 3.0.6 dated 2025-10-18
DESCRIPTION | 11 MD5 | 68 - NEWS.md | 17 R/other_utilities.R | 5 R/textmineR.R | 3 R/topic_modeling_core.R | 22 README.md | 10 build/vignette.rds |binary inst/doc/a_start_here.R | 33 inst/doc/a_start_here.Rmd | 3 inst/doc/a_start_here.html | 604 ++++++++++------- inst/doc/b_document_clustering.R | 27 inst/doc/b_document_clustering.Rmd | 11 inst/doc/b_document_clustering.html | 353 +++++----- inst/doc/c_topic_modeling.R | 21 inst/doc/c_topic_modeling.Rmd | 11 inst/doc/c_topic_modeling.html | 1245 ++++++++++++++++++++---------------- inst/doc/d_text_embeddings.R | 14 inst/doc/d_text_embeddings.Rmd | 10 inst/doc/d_text_embeddings.html | 622 ++++++++++------- inst/doc/e_doc_summarization.R | 241 +++--- inst/doc/e_doc_summarization.Rmd | 27 inst/doc/e_doc_summarization.html | 536 ++++++++------- inst/doc/f_tidytext_example.R | 11 inst/doc/f_tidytext_example.Rmd | 11 inst/doc/f_tidytext_example.html | 317 +++++---- man/nih.Rd | 5 man/textmineR.Rd | 19 src/RcppExports.cpp | 5 vignettes/a_start_here.Rmd | 3 vignettes/b_document_clustering.Rmd | 11 vignettes/c_topic_modeling.Rmd | 11 vignettes/d_text_embeddings.Rmd | 10 vignettes/e_doc_summarization.Rmd | 27 vignettes/f_tidytext_example.Rmd | 11 35 files changed, 2485 insertions(+), 1850 deletions(-)
Title: Kalman Filter
Description: 'Rcpp' implementation of the multivariate Kalman filter for state space models that can handle missing values and exogenous data in the observation and state equations. There is also a function to handle time varying parameters.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kalmanfilter versions 2.1.1 dated 2024-03-07 and 2.2.0 dated 2025-10-18
kalmanfilter-2.1.1/kalmanfilter/man/Rginv.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/contains.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/gen_inv.Rd |only kalmanfilter-2.1.1/kalmanfilter/man/kalman_filter_cpp.Rd |only kalmanfilter-2.2.0/kalmanfilter/DESCRIPTION | 10 kalmanfilter-2.2.0/kalmanfilter/MD5 | 32 kalmanfilter-2.2.0/kalmanfilter/NEWS.md | 6 kalmanfilter-2.2.0/kalmanfilter/R/RcppExports.R | 61 kalmanfilter-2.2.0/kalmanfilter/build/partial.rdb |binary kalmanfilter-2.2.0/kalmanfilter/build/vignette.rds |binary kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.R | 729 +++++----- kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.Rmd | 3 kalmanfilter-2.2.0/kalmanfilter/inst/doc/kalmanfilter_vignette.html | 423 ++--- kalmanfilter-2.2.0/kalmanfilter/man/kalman_filter.Rd | 208 +- kalmanfilter-2.2.0/kalmanfilter/man/kalmanfilter-package.Rd | 30 kalmanfilter-2.2.0/kalmanfilter/man/sw_dcf.Rd | 48 kalmanfilter-2.2.0/kalmanfilter/man/treasuries.Rd | 42 kalmanfilter-2.2.0/kalmanfilter/src/kalmanfilter.cpp | 525 +++---- kalmanfilter-2.2.0/kalmanfilter/vignettes/kalmanfilter_vignette.Rmd | 3 19 files changed, 1033 insertions(+), 1087 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and (multivariate) longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>.
The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.5.1 dated 2025-07-23 and 1.5.2 dated 2025-10-18
DESCRIPTION | 11 MD5 | 45 - NAMESPACE | 4 NEWS.md | 4 R/CIF1mv.CR.R | 8 R/CIF2mv.CR.R | 8 R/FastJM.R | 2 R/Pkmv.us.R | 8 R/estepMV_worker.R |only R/estepMV_workerSF.R |only R/getbSig.R | 32 R/getbSig_grad.R | 13 R/getbSig_gradSF.R | 11 R/getbsigSF.R | 11 R/logLikCRmv.R |only R/mvdiff.R | 26 R/mvdiffSF.R | 20 R/mvjmcs.R | 585 +++++----------- R/survfitmvjmcs.R |only README.md | 631 +++++++++--------- man/mvjmcs.Rd | 9 man/survfitmvjmcs.Rd |only src/getmvCov.cpp | 16 src/getmvCovSF.cpp | 20 src/nonmix.cpp | 1691 +++++++++++++++++++++++++------------------------ src/normalApproxSF.cpp | 409 +++++------ 26 files changed, 1747 insertions(+), 1817 deletions(-)
Title: Probabilistic Regression Trees
Description: Implementation of Probabilistic Regression Trees (PRTree),
providing functions for model fitting and prediction, with specific adaptations
to handle missing values. The main computations are implemented in 'Fortran'
for high efficiency. The package is based on the PRTree methodology described in
Alkhoury et al. (2020), "Smooth and Consistent Probabilistic Regression Trees"
<https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Details on the treatment of missing data and implementation aspects are presented in
Prass, T.S.; Neimaier, A.S.; Pumi, G. (2025), "Handling Missing Data in Probabilistic Regression Trees:
Methods and Implementation in R" <doi:10.48550/arXiv.2510.03634>.
Author: Alisson Silva Neimaier [aut] ,
Taiane Schaedler Prass [aut, ths, cre]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between PRTree versions 1.0.0 dated 2025-10-09 and 1.0.1 dated 2025-10-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/prtree_main.R | 2 +- inst/news.md | 7 ++++++- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Breeding-Related Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.80 dated 2025-09-22 and 1.0.90 dated 2025-10-18
lme4breeding-1.0.80/lme4breeding/man/fillData.Rd |only lme4breeding-1.0.90/lme4breeding/ChangeLog | 15 lme4breeding-1.0.90/lme4breeding/DESCRIPTION | 8 lme4breeding-1.0.90/lme4breeding/MD5 | 82 lme4breeding-1.0.90/lme4breeding/NAMESPACE | 11 lme4breeding-1.0.90/lme4breeding/R/lmebreed.R | 420 +++- lme4breeding-1.0.90/lme4breeding/R/utils.R | 185 +- lme4breeding-1.0.90/lme4breeding/build/vignette.rds |binary lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.R | 178 +- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.Rmd | 215 +- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.gxe.html | 624 +++---- lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.R | 59 lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.Rmd | 79 lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.qg.html | 854 ++++------ lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.R |only lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.Rmd |only lme4breeding-1.0.90/lme4breeding/inst/doc/lmebreed.summaries.html |only lme4breeding-1.0.90/lme4breeding/man/DT_augment.Rd | 13 lme4breeding-1.0.90/lme4breeding/man/DT_big.Rd | 16 lme4breeding-1.0.90/lme4breeding/man/DT_btdata.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_cornhybrids.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_cpdata.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_example.Rd | 29 lme4breeding-1.0.90/lme4breeding/man/DT_expdesigns.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_fulldiallel.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_gryphon.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_h2.Rd | 21 lme4breeding-1.0.90/lme4breeding/man/DT_halfdiallel.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_ige.Rd | 5 lme4breeding-1.0.90/lme4breeding/man/DT_legendre.Rd | 17 lme4breeding-1.0.90/lme4breeding/man/DT_mohring.Rd | 3 lme4breeding-1.0.90/lme4breeding/man/DT_polyploid.Rd | 7 lme4breeding-1.0.90/lme4breeding/man/DT_rice.Rd | 11 lme4breeding-1.0.90/lme4breeding/man/DT_sleepstudy.Rd | 8 lme4breeding-1.0.90/lme4breeding/man/DT_technow.Rd | 6 lme4breeding-1.0.90/lme4breeding/man/DT_wheat.Rd | 24 lme4breeding-1.0.90/lme4breeding/man/DT_yatesoats.Rd | 14 lme4breeding-1.0.90/lme4breeding/man/Dtable.Rd |only lme4breeding-1.0.90/lme4breeding/man/getCi.Rd |only lme4breeding-1.0.90/lme4breeding/man/lme4breeding-package.Rd | 90 - lme4breeding-1.0.90/lme4breeding/man/lmebreed-class.Rd | 52 lme4breeding-1.0.90/lme4breeding/man/lmebreed.Rd | 104 - lme4breeding-1.0.90/lme4breeding/man/mkMmeIndex.Rd |only lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.gxe.Rmd | 215 +- lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.qg.Rmd | 79 lme4breeding-1.0.90/lme4breeding/vignettes/lmebreed.summaries.Rmd |only 46 files changed, 1923 insertions(+), 1567 deletions(-)
Title: Create Color-Coded Choropleth Maps in R
Description: Easily create color-coded (choropleth) maps in R. No knowledge of
cartography or shapefiles needed; go directly from your geographically
identified data to a highly customizable map with a single line of code!
Supported geographies: U.S. states, counties, census tracts, and zip codes,
world countries and sub-country regions (e.g., provinces, prefectures, etc.).
Author: Ari Lamstein [aut],
Zhaochen He [ctb, cre],
Brian Johnson [ctb],
Trulia, Inc. [cph]
Maintainer: Zhaochen He <zhaochen.he@cnu.edu>
Diff between choroplethr versions 5.0.0 dated 2025-06-26 and 5.0.1 dated 2025-10-18
choroplethr-5.0.0/choroplethr/R/get_usa_demographics.R |only choroplethr-5.0.0/choroplethr/data/congress116.regions.rdata |only choroplethr-5.0.0/choroplethr/data/continental_us_states.rdata |only choroplethr-5.0.0/choroplethr/data/df_congress116_demographics.rdata |only choroplethr-5.0.0/choroplethr/data/df_congress116_party.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_country.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_county.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_ny_tract.rdata |only choroplethr-5.0.0/choroplethr/data/df_pop_state.rdata |only choroplethr-5.0.0/choroplethr/data/df_president_ts.rdata |only choroplethr-5.0.0/choroplethr/data/df_state_age_2010.rdata |only choroplethr-5.0.0/choroplethr/data/df_state_age_2015.rdata |only choroplethr-5.0.0/choroplethr/man/congress116.regions.Rd |only choroplethr-5.0.0/choroplethr/man/continental_us_states.Rd |only choroplethr-5.0.0/choroplethr/man/df_congress116_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/df_congress116_party.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_country.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_county.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_ny_tract.Rd |only choroplethr-5.0.0/choroplethr/man/df_pop_state.Rd |only choroplethr-5.0.0/choroplethr/man/df_president_ts.Rd |only choroplethr-5.0.0/choroplethr/man/df_state_age_2010.Rd |only choroplethr-5.0.0/choroplethr/man/df_state_age_2015.Rd |only choroplethr-5.0.0/choroplethr/man/get_admin1_map.Rd |only choroplethr-5.0.0/choroplethr/man/get_county_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/get_state_demographics.Rd |only choroplethr-5.0.0/choroplethr/man/get_tract_demographics.Rd |only choroplethr-5.0.1/choroplethr/DESCRIPTION | 28 choroplethr-5.0.1/choroplethr/LICENSE | 4 choroplethr-5.0.1/choroplethr/MD5 | 164 - choroplethr-5.0.1/choroplethr/NAMESPACE | 76 choroplethr-5.0.1/choroplethr/NEWS.md | 22 choroplethr-5.0.1/choroplethr/R/acs.R | 355 +-- choroplethr-5.0.1/choroplethr/R/admin1.R | 251 +- choroplethr-5.0.1/choroplethr/R/choropleth.R | 973 ++++------ choroplethr-5.0.1/choroplethr/R/country.R | 249 +- choroplethr-5.0.1/choroplethr/R/county.R | 237 +- choroplethr-5.0.1/choroplethr/R/data.R | 474 +--- choroplethr-5.0.1/choroplethr/R/init.R | 4 choroplethr-5.0.1/choroplethr/R/internal-docs.R | 133 - choroplethr-5.0.1/choroplethr/R/state.R | 221 +- choroplethr-5.0.1/choroplethr/R/tract.R | 212 +- choroplethr-5.0.1/choroplethr/R/zip.R |only choroplethr-5.0.1/choroplethr/README.md | 283 +- choroplethr-5.0.1/choroplethr/data/admin1.map.rda |only choroplethr-5.0.1/choroplethr/data/admin1.regions.rda |only choroplethr-5.0.1/choroplethr/data/country.map.rda |binary choroplethr-5.0.1/choroplethr/data/country.regions.rda |binary choroplethr-5.0.1/choroplethr/data/county.map.2015.rda |binary choroplethr-5.0.1/choroplethr/data/county.map.2024.rda |binary choroplethr-5.0.1/choroplethr/data/county.regions.2015.rda |binary choroplethr-5.0.1/choroplethr/data/county.regions.2024.rda |binary choroplethr-5.0.1/choroplethr/data/df_country_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_county_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_ny_tract_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/df_ri_zip_demographics.rda |only choroplethr-5.0.1/choroplethr/data/df_state_demographics.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.bigdc.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.hex.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.hires.rda |binary choroplethr-5.0.1/choroplethr/data/state.map.lores.rda |binary choroplethr-5.0.1/choroplethr/data/state.regions.rda |binary choroplethr-5.0.1/choroplethr/data/zip_lookup.rda |only choroplethr-5.0.1/choroplethr/man/Choropleth.Rd | 264 +- choroplethr-5.0.1/choroplethr/man/admin1.map.Rd |only choroplethr-5.0.1/choroplethr/man/admin1.regions.Rd |only choroplethr-5.0.1/choroplethr/man/admin1_choropleth.Rd | 358 +-- choroplethr-5.0.1/choroplethr/man/common_args.Rd | 251 +- choroplethr-5.0.1/choroplethr/man/country.map.Rd | 32 choroplethr-5.0.1/choroplethr/man/country.regions.Rd | 24 choroplethr-5.0.1/choroplethr/man/country_choropleth.Rd | 352 +-- choroplethr-5.0.1/choroplethr/man/county.map.2015.Rd | 30 choroplethr-5.0.1/choroplethr/man/county.map.2024.Rd | 30 choroplethr-5.0.1/choroplethr/man/county.regions.2015.Rd | 24 choroplethr-5.0.1/choroplethr/man/county.regions.2024.Rd | 24 choroplethr-5.0.1/choroplethr/man/county_choropleth.Rd | 310 +-- choroplethr-5.0.1/choroplethr/man/county_choropleth_acs.Rd | 105 - choroplethr-5.0.1/choroplethr/man/df_country_demographics.Rd | 34 choroplethr-5.0.1/choroplethr/man/df_county_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/df_japan_census.Rd | 35 choroplethr-5.0.1/choroplethr/man/df_ny_tract_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/df_president.Rd | 40 choroplethr-5.0.1/choroplethr/man/df_ri_zip_demographics.Rd |only choroplethr-5.0.1/choroplethr/man/df_state_demographics.Rd | 36 choroplethr-5.0.1/choroplethr/man/get_acs_data.Rd | 82 choroplethr-5.0.1/choroplethr/man/get_tract_map.Rd | 39 choroplethr-5.0.1/choroplethr/man/get_zip_map.Rd |only choroplethr-5.0.1/choroplethr/man/state.map.bigdc.Rd | 24 choroplethr-5.0.1/choroplethr/man/state.map.hex.Rd | 30 choroplethr-5.0.1/choroplethr/man/state.map.hires.Rd | 2 choroplethr-5.0.1/choroplethr/man/state.map.lores.Rd | 30 choroplethr-5.0.1/choroplethr/man/state.regions.Rd | 24 choroplethr-5.0.1/choroplethr/man/state_choropleth.Rd | 354 +-- choroplethr-5.0.1/choroplethr/man/state_choropleth_acs.Rd | 108 - choroplethr-5.0.1/choroplethr/man/tract_choropleth.Rd | 305 +-- choroplethr-5.0.1/choroplethr/man/zip_choropleth.Rd |only choroplethr-5.0.1/choroplethr/man/zip_lookup.Rd |only choroplethr-5.0.1/choroplethr/tests/testthat.R | 24 choroplethr-5.0.1/choroplethr/tests/testthat/superceeded/test_legacy.R | 492 ++--- choroplethr-5.0.1/choroplethr/tests/testthat/test-core.R | 98 - choroplethr-5.0.1/choroplethr/tests/testthat/test-country.R | 48 choroplethr-5.0.1/choroplethr/tests/testthat/test-county.R | 44 102 files changed, 3678 insertions(+), 3733 deletions(-)
Title: Robust Markov Chain Monte Carlo Methods
Description: Functions for simulating Markov chains using the Barker proposal
to compute Markov chain Monte Carlo (MCMC) estimates of expectations with
respect to a target distribution on a real-valued vector space. The Barker
proposal, described in Livingstone and Zanella (2022)
<doi:10.1111/rssb.12482>, is a gradient-based MCMC algorithm inspired by the
Barker accept-reject rule. It combines the robustness of simpler MCMC
schemes, such as random-walk Metropolis, with the efficiency of
gradient-based methods, such as the Metropolis adjusted Langevin algorithm.
The key function provided by the package is sample_chain(), which allows
sampling a Markov chain with a specified target distribution as its
stationary distribution. The chain is sampled by generating proposals and
accepting or rejecting them using a Metropolis-Hasting acceptance rule.
During an initial warm-up stage, the parameters of the proposal distribution
can be adapted, with adapters available to both: tune the scale of the
prop [...truncated...]
Author: Matthew M. Graham [aut, cre] ,
Samuel Livingstone [aut] ,
University College London [cph],
Engineering and Physical Sciences Research Council [fnd]
Maintainer: Matthew M. Graham <m.graham@ucl.ac.uk>
Diff between rmcmc versions 0.1.1 dated 2025-02-04 and 0.1.2 dated 2025-10-17
DESCRIPTION | 22 +++- MD5 | 38 ++++---- NEWS.md | 9 ++ R/adaptation.R | 4 R/barker.R | 2 R/bridges.R | 24 ++++- R/chains.R | 130 +++++++++++++++++------------ R/proposal.R | 6 - R/utils.R | 8 - README.md | 15 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/adjusting-noise-distribution.R | 2 inst/doc/adjusting-noise-distribution.Rmd | 2 inst/doc/adjusting-noise-distribution.html | 10 +- inst/doc/barker-proposal.html | 14 +-- man/target_distribution_from_stan_model.Rd | 6 + tests/testthat/test-adaptation.R | 8 + tests/testthat/test-bridges-stan.R | 100 +++++++++++++--------- vignettes/adjusting-noise-distribution.Rmd | 2 20 files changed, 251 insertions(+), 151 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
This is a re-admission after prior archival of version 0.9-2.2 dated 2025-08-27
Diff between rlibkriging versions 0.9-2.2 dated 2025-08-27 and 0.9-2.3 dated 2025-10-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/libK/cmake/update_version.sh | 2 +- src/libK/lbfgsb_cpp/include/lbfgsb_cpp/lbfgsb.hpp | 9 ++++++++- src/libK/travis-ci/common/before_script.sh | 2 +- src/libK/travis-ci/linux-macos/install.sh | 2 +- src/libK/travis-ci/linux-macos/loadenv.sh | 2 +- src/libK/travis-ci/linux-macos/test.sh | 2 +- 8 files changed, 24 insertions(+), 17 deletions(-)
Title: Kim Filter
Description: 'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference.
The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kimfilter versions 1.0.3 dated 2024-03-08 and 1.1.0 dated 2025-10-17
DESCRIPTION | 10 MD5 | 36 +- NEWS.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/kimfilter_vignette.R | 543 +++++++++++++++++++------------------- inst/doc/kimfilter_vignette.Rmd | 1 inst/doc/kimfilter_vignette.html | 549 +++++++++++++++++++-------------------- man/Rginv.Rd | 34 +- man/contains.Rd | 38 +- man/gen_inv.Rd | 34 +- man/kim_filter.Rd | 214 +++++++-------- man/kim_filter_cpp.Rd | 76 ++--- man/kimfilter-package.Rd | 30 +- man/self_rbind.Rd | 38 +- man/ss_prob.Rd | 62 ++-- man/sw_dcf.Rd | 48 +-- src/kimfilter.cpp | 2 vignettes/kimfilter_vignette.Rmd | 1 19 files changed, 867 insertions(+), 857 deletions(-)
Title: Access Data from the 'Impect' API
Description: Pull data from the 'Impect' Customer API <https://glossary.impect.com/api-design>. The package can retrieve data such as events or match sums.
Author: Impect GmbH [cph],
Florian Schmitt [aut, cre],
Thomas Walentin [ctb]
Maintainer: Florian Schmitt <florian.schmitt@impect.com>
Diff between impectR versions 2.5.1 dated 2025-10-15 and 2.5.2 dated 2025-10-17
DESCRIPTION | 6 +- MD5 | 18 ++++---- NEWS.md | 10 ++++ R/getEvents.R | 105 +++++++++++++++++++++++++++++------------------ R/getPlayerMatchScores.R | 92 +++++++++++++++++++++++------------------ R/getPlayerMatchsums.R | 75 ++++++++++++++++++++++----------- R/getSquadMatchScores.R | 75 ++++++++++++++++++++++----------- R/getSquadMatchsums.R | 75 ++++++++++++++++++++++----------- R/utils.R | 32 ++++++++++---- README.md | 6 +- 10 files changed, 318 insertions(+), 176 deletions(-)
Title: 'RSpace' API Wrapper
Description: Wrapper for the 'RSpace' Electronic Lab Notebook (<https://www.researchspace.com/>)
API. This packages provides convenience functions to browse, search, create,
and edit your 'RSpace' documents. In addition, it enables filling 'RSpace' templates
from R Markdown/Quarto templates or tabular data (e.g., 'Excel' files).
This R package is not developed or endorsed by 'Research Space'.
Author: Gerhard Burger [aut, cre] ,
Hanneke Leegwater [aut]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between rspacer versions 0.2.0 dated 2025-07-05 and 0.3.0 dated 2025-10-17
DESCRIPTION | 14 MD5 | 46 +- NAMESPACE | 3 NEWS.md | 13 R/documents.R | 75 ++-- R/fields.R | 55 ++- R/folders.R | 29 + R/mdtodoc.R | 104 ++++- R/utils.R | 77 ++++ README.md | 40 +- inst/CITATION |only inst/WORDLIST | 3 inst/doc/rspacer.Rmd | 653 +++++++++++++++++++++++++++++++++--- inst/doc/rspacer.html | 652 +++++++++++++++++++++++++++++++++-- man/document_create_from_tabular.Rd |only man/document_get_fields.Rd |only man/document_list_attachments.Rd | 16 man/document_search.Rd | 18 man/fields_to_data_frame.Rd |only man/folder_tree.Rd | 16 man/put_all_fields_in_one_field.Rd | 6 tests/testthat/test-documents.R | 24 - tests/testthat/test-fields.R | 18 tests/testthat/test-mdtodoc.R | 46 +- vignettes/rspacer.Rmd | 653 +++++++++++++++++++++++++++++++++--- vignettes/rspacer.Rmd.in | 18 26 files changed, 2239 insertions(+), 340 deletions(-)
More information about partialling.out at CRAN
Permanent link
Title: Parametric and Nonparametric Copula-Based Imputation Methods
Description: Copula-based imputation methods: parametric and nonparametric algorithms for missing multivariate data through conditional copulas.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Aurora Gatto [aut],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoImp versions 2.1.0 dated 2025-04-30 and 2.1.1 dated 2025-10-17
ChangeLog | 5 ++++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/InternalFunction.R | 6 +++--- R/NPCoImp.R | 12 ++++++------ inst/CITATION | 4 ++-- man/NPCoImp-class.Rd | 6 +++--- man/NPCoImp.Rd | 21 +++++++++++---------- 8 files changed, 40 insertions(+), 36 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.1.0 dated 2025-04-28 and 2.1.1 dated 2025-10-17
DESCRIPTION | 9 - MD5 | 52 ++--- NEWS.md | 2 R/ClustCpObj.R | 12 - R/DetectCpObj.R | 26 +- R/RcppExports.R | 42 ++-- R/clust_cp.R | 18 +- R/detect_cp.R | 61 +++--- README.md | 394 ++++++++++++++++++++++++--------------------- inst/doc/tutorial.R | 10 - inst/doc/tutorial.Rmd | 10 - inst/doc/tutorial.html | 228 ++++++++++++-------------- man/ClustCpObj.Rd | 4 man/DetectCpObj.Rd | 6 man/clust_cp.Rd | 16 - man/clust_cp_epi.Rd | 8 man/detect_cp.Rd | 37 +--- man/detect_cp_epi.Rd | 18 +- man/detect_cp_multi.Rd | 10 - man/detect_cp_uni.Rd | 8 man/plot.ClustCpObj.Rd | 4 man/plot.DetectCpObj.Rd | 2 man/print.DetectCpObj.Rd | 2 man/summary.DetectCpObj.Rd | 2 src/RcppExports.cpp | 20 +- src/code.cpp | 182 ++++++++++---------- vignettes/tutorial.Rmd | 10 - 27 files changed, 607 insertions(+), 586 deletions(-)
Title: Memory-Based Learning in Spectral Chemometrics
Description: Functions for dissimilarity analysis and memory-based learning
(MBL, a.k.a local modeling) in complex spectral data sets.
Most of these functions are based on the methods presented in
Ramirez-Lopez et al. (2013) <doi:10.1016/j.geoderma.2012.12.014>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Antoine Stevens [aut, ctb] ,
Claudio Orellano [ctb],
Raphael Viscarra Rossel [ctb] ,
Alex Wadoux [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between resemble versions 2.2.4 dated 2025-05-19 and 2.2.5 dated 2025-10-17
DESCRIPTION | 10 +- MD5 | 18 +-- NEWS.md | 8 + README.md | 216 ++++++++++++++++++++++++++++++++++++++++++++- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/resemble.html | 10 +- man/resemble-package.Rd | 2 src/diss_helpers.cpp | 8 - src/regression_methods.cpp | 5 - 10 files changed, 248 insertions(+), 29 deletions(-)
Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.
Author: Peter Bourke [aut, cre],
Geert van Geest [aut],
Roeland Voorrips [ctb],
Yanlin Liao [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>
Diff between polymapR versions 1.1.6 dated 2024-05-31 and 1.1.7 dated 2025-10-17
DESCRIPTION | 8 MD5 | 16 R/exported_functions.R | 71 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Vignette_genotype_probabilities.html | 72 +- inst/doc/Vignette_polymapR.Rmd | 2 inst/doc/Vignette_polymapR.html | 664 ++++++++++++-------------- vignettes/Vignette_polymapR.Rmd | 2 9 files changed, 409 insertions(+), 426 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.4 dated 2025-03-20 and 1.0.5 dated 2025-10-17
DESCRIPTION | 12 MD5 | 31 - NEWS.md | 5 R/clintrials_gov_convert.R | 2 R/eudract_convert.R | 2 R/relative_risk.R | 10 build/vignette.rds |binary inst/doc/eudract.html | 10 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/dotplot/dotplot-1group.svg | 94 ++-- tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 422 ++++++++++------------ tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 210 +++++----- tests/testthat/_snaps/dotplot/dotplot-ref.svg | 194 ++++------ tests/testthat/_snaps/dotplot/dotplot.svg | 194 ++++------ tests/testthat/data/four_groups |only tests/testthat/test_relative_risk.R | 8 16 files changed, 587 insertions(+), 607 deletions(-)
Title: Simplified Access to Brazilian Financial and Macroeconomic Data
Description: It offers simplified access to Brazilian macroeconomic and financial indicators selected from official sources, such as the 'IBGE' (Brazilian Institute of Geography and Statistics) via the 'SIDRA' API and the 'Central Bank of Brazil' via the 'SGS' API. It allows users to quickly retrieve and visualize data series such as the unemployment rate and the Selic interest rate. This package was developed for data access and visualization purposes, without generating forecasts or statistical results. For more information, see the official APIs: <https://sidra.ibge.gov.br/> and <https://dadosabertos.bcb.gov.br/dataset/>.
Author: Joao Paulo dos Santos Pereira Barbosa [aut, cre]
Maintainer: Joao Paulo dos Santos Pereira Barbosa <joao.31582129@gmail.com>
Diff between brfinance versions 0.2.0 dated 2025-10-16 and 0.2.1 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/globals.R | 6 +++++- R/plot_unemployment.R | 33 ++++++++++++++++++++++++--------- 4 files changed, 35 insertions(+), 16 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Goncalves Dosantos [aut, cre],
Ignacio Garcia Jurado [aut],
Julian Costa Bouzas [aut]
Maintainer: Juan Carlos Goncalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 2.0.2 dated 2024-10-24 and 2.1.4 dated 2025-10-17
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/ProjectManagement.R | 8 +------- R/function_pert_demora_unions.R | 12 ++++++++---- R/function_pert_estocastico_demora.R | 3 +++ R/function_pert_estocastico_demora_uniones.R | 24 ++++++++++++++++-------- man/ProjectManagement-package.Rd | 12 +++++++++++- 7 files changed, 51 insertions(+), 32 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains
functions and classes to be used in conjunction with other
'tidymodels' packages for finding reasonable values of
hyper-parameters in models, pre-processing methods, and
post-processing steps.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tune versions 2.0.0 dated 2025-09-01 and 2.0.1 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/parallel.R | 6 ++++-- tests/testthat/Rplots.pdf |binary 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of maximally distinct qualitative color palettes,
optionally tailored to color deficiency. A list of colors or a subspace
of a color space is used as input and then projected to the DIN99d color space,
where colors that are maximally distinct are chosen algorithmically.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <jolars@posteo.com>
Diff between qualpalr versions 1.0.0 dated 2025-08-18 and 1.0.1 dated 2025-10-17
DESCRIPTION | 6 - MD5 | 38 ++++++------ NEWS.md | 13 ++++ R/qualpal.R | 2 README.md | 5 + inst/CITATION | 58 +++++------------- inst/WORDLIST | 32 ++++++++-- inst/doc/comparisons.html | 46 +++++++------- inst/doc/introduction.html | 48 +++++++-------- inst/include/qualpal/analyze.h | 78 +++++++++++++++++------- inst/include/qualpal/color_difference.h | 59 +++++++++++++----- inst/include/qualpal/colors.h | 100 +++++++++++++++++++++++++------- inst/include/qualpal/matrix.h | 91 +++++++++++++++++++---------- inst/include/qualpal/metrics.h | 92 ++++++++++++++++++++--------- inst/include/qualpal/qualpal.h | 53 ++++++++++++---- inst/include/qualpal/threads.h | 36 +++++++---- man/analyze_palette.Rd | 2 man/qualpal.Rd | 2 man/qualpalr-package.Rd | 2 src/qualpal/colors.cpp | 6 - 20 files changed, 501 insertions(+), 268 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev] ,
Marcus Munch Gruenewald [rev] ,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.3.1 dated 2025-02-28 and 0.3.2 dated 2025-10-17
DESCRIPTION | 24 - MD5 | 48 +- NEWS.md | 347 ++++++++++---------- R/0_linters.R | 2 R/DiseasystoreBase.R | 2 R/test_diseasystore.R | 25 - README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/benchmarks.html | 2 inst/doc/diseasystore-ecdc-respiratory-viruses.html | 18 - inst/doc/diseasystore-google-covid-19.html | 14 inst/doc/diseasystore.html | 38 +- inst/doc/extending-diseasystore-example.html | 48 +- inst/extdata/benchmarks.rds |binary man/DiseasystoreBase.Rd | 2 man/DiseasystoreEcdcRespiratoryViruses.Rd | 2 man/DiseasystoreGoogleCovid19.Rd | 2 man/DiseasystoreSimulist.Rd | 2 man/FeatureHandler.Rd | 2 man/add_years.Rd | 2 man/age_on_date.Rd | 2 man/drop_diseasystore.Rd | 2 man/test_diseasystore.Rd | 25 - tests/testthat/test-age_helpers.R | 5 25 files changed, 312 insertions(+), 308 deletions(-)
Title: Statistical Tests for Covariance and Correlation Matrices and
their Structures
Description: A compilation of tests for hypotheses regarding covariance
and correlation matrices for one or more groups. The hypothesis can
be specified through a corresponding hypothesis matrix and a vector or
by choosing one of the basic hypotheses, while for the structure test,
only the latter works. Thereby Monte-Carlo and Bootstrap-techniques
are used, and the respective method must be chosen, and the functions
provide p-values and mostly also estimators of calculated covariance
matrices of test statistics. For more details on the methodology, see
Sattler et al. (2022) <doi:10.1016/j.jspi.2021.12.001>,
Sattler and Pauly (2024) <doi:10.1007/s11749-023-00906-6>, and
Sattler and Dobler (2025) <doi:10.48550/arXiv.2310.11799>.
Author: Paavo Sattler [aut] ,
Svenja Jedhoff [cre, aut] ,
Markus Pauly [ctb] ,
Arne C Bathke [ctb] ,
Dennis Dobler [ctb]
Maintainer: Svenja Jedhoff <jedhoff@statistik.tu-dortmund.de>
Diff between CovCorTest versions 1.0.0 dated 2025-06-06 and 1.1.0 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 11 ++++++++--- NAMESPACE | 1 + NEWS.md |only R/get_hypothesis.R |only README.md | 1 + man/get_extended_matrix.Rd |only man/get_hypothesis.Rd |only tests/testthat/test-gethypothesis.R |only 9 files changed, 13 insertions(+), 6 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, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 4041.110 dated 2024-09-22 and 4051.111 dated 2025-10-17
timeDate-4041.110/timeDate/R/options-currentYear.R |only timeDate-4041.110/timeDate/R/options-myFinCenter.R |only timeDate-4041.110/timeDate/R/options-myUnits.R |only timeDate-4051.111/timeDate/DESCRIPTION | 17 timeDate-4051.111/timeDate/MD5 | 106 ++-- timeDate-4051.111/timeDate/NAMESPACE | 30 - timeDate-4051.111/timeDate/NEWS.md | 78 ++- timeDate-4051.111/timeDate/R/AllClass.R | 75 ++ timeDate-4051.111/timeDate/R/base-format.R | 17 timeDate-4051.111/timeDate/R/base-round.R | 109 ++-- timeDate-4051.111/timeDate/R/calendar-align.R | 63 -- timeDate-4051.111/timeDate/R/calendar-firstDay.R | 98 ++- timeDate-4051.111/timeDate/R/calendar-nDay.R | 44 + timeDate-4051.111/timeDate/R/calendar-onOrAfter.R | 94 +-- timeDate-4051.111/timeDate/R/holiday-Dates.R | 16 timeDate-4051.111/timeDate/R/holiday-Listing.R | 259 +++++----- timeDate-4051.111/timeDate/R/methods-show.R | 46 + timeDate-4051.111/timeDate/R/options-RmetricsOptions.R | 34 - timeDate-4051.111/timeDate/R/pasteMat.R |only timeDate-4051.111/timeDate/R/stats-window.R | 11 timeDate-4051.111/timeDate/R/timeDate-listFinCenter.R | 8 timeDate-4051.111/timeDate/R/timeDate.R | 76 +- timeDate-4051.111/timeDate/R/timeInterval.R |only timeDate-4051.111/timeDate/README.md | 4 timeDate-4051.111/timeDate/inst/_pkgdown.yml | 34 - timeDate-4051.111/timeDate/inst/pkgdown.yml | 17 timeDate-4051.111/timeDate/inst/unitTests/runit.HolidayCalendars.R | 20 timeDate-4051.111/timeDate/man/00timeDate-package.Rd | 6 timeDate-4051.111/timeDate/man/base-diff.Rd | 28 - timeDate-4051.111/timeDate/man/base-difftimeDate.Rd | 32 - timeDate-4051.111/timeDate/man/base-round.Rd | 46 + timeDate-4051.111/timeDate/man/calendar-Easter.Rd | 19 timeDate-4051.111/timeDate/man/calendar-firstDay.Rd | 69 +- timeDate-4051.111/timeDate/man/calendar-isRegular.Rd | 9 timeDate-4051.111/timeDate/man/calendar-julian.Rd | 5 timeDate-4051.111/timeDate/man/calendar-nDay.Rd | 48 + timeDate-4051.111/timeDate/man/calendar-onOrAfter.Rd | 15 timeDate-4051.111/timeDate/man/class-timeDate.Rd | 64 +- timeDate-4051.111/timeDate/man/holiday-Dates.Rd | 61 +- timeDate-4051.111/timeDate/man/holiday-LONDON.Rd | 19 timeDate-4051.111/timeDate/man/holiday-Listing.Rd | 21 timeDate-4051.111/timeDate/man/holiday-NERC.Rd | 19 timeDate-4051.111/timeDate/man/holiday-NYSE.Rd | 22 timeDate-4051.111/timeDate/man/holiday-TSX.Rd | 19 timeDate-4051.111/timeDate/man/holiday-ZURICH.Rd | 20 timeDate-4051.111/timeDate/man/holiday.Rd | 22 timeDate-4051.111/timeDate/man/in_int.Rd |only timeDate-4051.111/timeDate/man/methods-mathOps.Rd | 20 timeDate-4051.111/timeDate/man/methods-show.Rd | 66 +- timeDate-4051.111/timeDate/man/options-RmetricsOptions.Rd | 4 timeDate-4051.111/timeDate/man/pasteMat.Rd |only timeDate-4051.111/timeDate/man/stats-kurtosis.Rd | 11 timeDate-4051.111/timeDate/man/stats-skewness.Rd | 6 timeDate-4051.111/timeDate/man/timeCeiling.Rd |only timeDate-4051.111/timeDate/man/timeDate-midnightStandard.Rd | 26 - timeDate-4051.111/timeDate/man/timeDate-whichFormat.Rd | 10 timeDate-4051.111/timeDate/man/timeDate.Rd | 71 ++ timeDate-4051.111/timeDate/man/timeInterval-class.Rd |only timeDate-4051.111/timeDate/man/timeInterval-methods.Rd |only 59 files changed, 1236 insertions(+), 778 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Author: Dayne L Filer [aut],
Jason Brown [ctb] ,
Madison Feshuk [cre] ,
Carter Thunes [ctb],
Sarah E Davidson-Fritz [ctb] ,
Kelly Carstens [ctb] ,
Elizabeth Gilson [ctb],
Lindsay Knupp [ctb],
Lori Kolaczkowski [ctb],
Ashley Ko [ctb],
Zhihui Zhao [ctb],
Kurt [...truncated...]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between tcpl versions 3.3.0 dated 2025-05-05 and 3.3.1 dated 2025-10-17
tcpl-3.3.0/tcpl/tests/testthat/ctx/api-ccte.epa.gov |only tcpl-3.3.0/tcpl/vignettes/api/0/api-ccte.epa.gov |only tcpl-3.3.1/tcpl/DESCRIPTION | 26 tcpl-3.3.1/tcpl/MD5 | 61 tcpl-3.3.1/tcpl/NAMESPACE | 2 tcpl-3.3.1/tcpl/NEWS.md | 6 tcpl-3.3.1/tcpl/R/tcplConf.R | 3 tcpl-3.3.1/tcpl/R/tcplLoadData.R | 4 tcpl-3.3.1/tcpl/R/tcplPlot.R | 4 tcpl-3.3.1/tcpl/R/tcplQueryAPI.R | 21 tcpl-3.3.1/tcpl/README.md | 2 tcpl-3.3.1/tcpl/data/test_api.rda |binary tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.R | 1433 +++++++++--------- tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.Rmd | 49 tcpl-3.3.1/tcpl/inst/doc/Introduction_Appendices.html | 301 +-- tcpl-3.3.1/tcpl/tests/testthat/ctx/comptox.epa.gov |only tcpl-3.3.1/tcpl/tests/testthat/test-tcplConf.R | 2 tcpl-3.3.1/tcpl/tests/testthat/test-tcplLoadAeid.R | 2 tcpl-3.3.1/tcpl/tests/testthat/test-tcplLoadData.R | 8 tcpl-3.3.1/tcpl/tests/testthat/test-tcplPlot.R | 8 tcpl-3.3.1/tcpl/tests/testthat/test-tcplggplot2.R | 76 tcpl-3.3.1/tcpl/vignettes/Introduction_Appendices.Rmd | 49 tcpl-3.3.1/tcpl/vignettes/api/0/comptox.epa.gov |only 23 files changed, 1032 insertions(+), 1025 deletions(-)
Title: Stable Balancing Weights for Causal Inference and Missing Data
Description: Implements the Stable Balancing Weights by Zubizarreta (2015) <DOI:10.1080/01621459.2015.1023805>. These are the weights of minimum variance that approximately balance the empirical distribution of the observed covariates. For an overview, see Chattopadhyay, Hase and Zubizarreta (2020) <DOI:10.1002/sim.8659>. To solve the optimization problem in 'sbw', the default solver is 'quadprog', which is readily available through CRAN. The solver 'osqp' is also posted on CRAN. To enhance the performance of 'sbw', users are encouraged to install other solvers such as 'gurobi' and 'Rmosek', which require special installation. For the installation of gurobi and pogs, please follow the instructions at <https://docs.gurobi.com/projects/optimizer/en/current/reference/r.html> and <http://foges.github.io/pogs/stp/r>.
Author: Jose R. Zubizarreta [aut, cre],
Yige Li [aut],
Kwangho Kim [aut],
Amine Allouah [ctb],
Noah Greifer [ctb]
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>
Diff between sbw versions 1.1.9 dated 2024-07-27 and 1.2 dated 2025-10-17
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/sbw.R | 2 +- R/summarize.R | 8 ++++---- man/sbw.Rd | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: 'shiny' App for TRAPD/ISPOR Survey Translation with LLMs
Description: A 'shiny' application to automate forward and back survey translation
with optional reconciliation using large language models (LLMs). Supports
OpenAI (GPT), Google Gemini, and Anthropic Claude models. It follows
the TRAPD (Translation, Review, Adjudication, Pretesting, Documentation)
framework and ISPOR (International Society for Pharmacoeconomics and
Outcomes Research) recommendations. See Harkness et al. (2010)
<doi:10.1002/9780470609927.ch7> and Wild et al. (2005)
<doi:10.1111/j.1524-4733.2005.04054.x>.
Author: Jonas R. Kunst [aut, cre]
Maintainer: Jonas R. Kunst <jonas.r.kunst@bi.no>
Diff between LLMTranslate versions 0.1.3 dated 2025-09-05 and 0.2.0 dated 2025-10-17
DESCRIPTION | 19 LICENSE | 4 MD5 | 29 NAMESPACE | 8 NEWS.md | 25 R/LLMTranslate-package.R | 112 +-- R/globals.R | 2 R/internal-helpers.R | 731 +++++++++++----------- R/run_app.R | 34 - README.md | 56 - inst/CITATION | 20 inst/WORDLIST |only inst/app/app.R | 1310 ++++++++++++++++++++++++---------------- man/LLMTranslate.Rd | 142 ++-- man/run_app.Rd | 44 - tests/testthat/test-internals.R | 164 ++--- 16 files changed, 1536 insertions(+), 1164 deletions(-)
Title: Utilities for Data Analysis in Agriculture
Description: Utilities designed to make the analysis of field trials easier and
more accessible for everyone working in plant breeding. It provides a simple
and intuitive interface for conducting single and multi-environmental trial
analysis, with minimal coding required. Whether you're a beginner or an
experienced user, 'agriutilities' will help you quickly and easily carry out
complex analyses with confidence. With built-in functions for fitting Linear
Mixed Models, 'agriutilities' is the ideal choice for anyone who wants to save
time and focus on interpreting their results.
Some of the functions require the R package 'asreml' for the 'ASReml' software,
this can be obtained upon purchase from 'VSN' international <https://vsni.co.uk/software/asreml-r/>.
Author: Johan Aparicio [aut, cre],
Alexia Bornhorst [aut],
The Alliance of Bioversity International and CIAT [cph]
Maintainer: Johan Aparicio <johanstevenapa@gmail.com>
This is a re-admission after prior archival of version 1.2.1 dated 2025-01-17
Diff between agriutilities versions 1.2.1 dated 2025-01-17 and 1.2.2 dated 2025-10-17
DESCRIPTION | 8 - MD5 | 24 ++--- R/utils_S3_methods.R | 4 README.md | 16 +-- build/vignette.rds |binary inst/doc/how-to-start.html | 27 +++--- inst/doc/repeated_measurements.html | 122 +++++++++++++++--------------- man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-11-2.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary 13 files changed, 100 insertions(+), 101 deletions(-)
Title: Linear Quantile Mixture Models
Description: Estimate linear quantile mixtures based on Time-Constant (TC) and/or Time-Varying (TV), discrete, random coefficients.
Author: Maria Francesca Marino [aut, cre],
Marco Alfo' [aut],
Nicola Salvati [aut],
Maria Giovanna Ranalli [aut]
Maintainer: Maria Francesca Marino <mariafrancesca.marino@unifi.it>
Diff between lqmix versions 1.1 dated 2025-03-21 and 1.2 dated 2025-10-17
DESCRIPTION | 14 - MD5 | 147 ++++++++------ NAMESPACE | 96 +++++---- NEWS | 8 R/cd4.R | 8 R/coef.lqmix.R | 12 - R/coef.lqr.R | 6 R/coef.seach_lqmix.R | 42 ++-- R/dal.R | 13 - R/logLik.lqmix.R | 8 R/logLik.lqr.R | 4 R/logLik.search_lqmix.R | 4 R/lqmix.R | 120 +++++------ R/lqmixTC.R | 177 ++++++----------- R/lqmixTCTV.fit_intermittent.R | 12 - R/lqmixTCTV_intermittent.R | 220 +++++++-------------- R/lqmixTV.fit_intermittent.R | 4 R/lqmixTV_intermittent.R | 196 ++++++------------- R/lqr.R | 104 +++++----- R/lqr.fit.R | 124 ++++++------ R/pain.R | 63 +++--- R/plot.lqmix.R | 133 ++++++------- R/plot.search_lqmix.R | 290 +++++++++++++++------------- R/postComputeTC.R | 18 - R/postComputeTV_intermittent.R | 6 R/predict.lqmix.R |only R/predict.lqr.R |only R/predict.search_lqmix.R |only R/print.lqmix.R | 4 R/print.lqr.R | 4 R/print.search_lqmix.R | 8 R/print.summary.lqmix.R | 4 R/print.summary.lqr.R | 56 ++--- R/print.summary.search_lqmix.R | 4 R/residuals.lqmix.R |only R/residuals.lqr.R |only R/residuals.search_lqmix.R |only R/search_lqmix.R | 171 +++++++--------- R/summary.lqmix.R | 388 +++++++++++++++++++------------------- R/summary.lqr.R | 4 R/summary.search_lqmix.R | 26 +- R/varAL.R | 14 + R/vcov.lqmix.R |only R/vcov.lqr.R |only R/vcov.search_lqmix.R |only R/xyBuildHOM.R |only R/xyBuildTC.R |only R/xyBuildTCTV.R |only R/xyBuildTV.R |only build/partial.rdb |binary inst/REFERENCES.bib | 51 +++- man/cd4.Rd | 7 man/coef.lqmix.Rd | 6 man/coef.lqr.Rd | 6 man/coef.search_lqmix.Rd | 6 man/dal.Rd | 12 - man/logLik.lqmix.Rd | 8 man/logLik.lqr.Rd | 4 man/logLik.search_lqmix.Rd | 4 man/lqmix-package.Rd | 6 man/lqmix.Rd | 68 +++--- man/lqr.Rd | 25 +- man/pain.Rd | 6 man/plot.lqmix.Rd | 6 man/plot.search_lqmix.Rd | 6 man/predict.lqmix.Rd |only man/predict.lqr.Rd |only man/predict.search_lqmix.Rd |only man/print.lqmix.Rd | 4 man/print.lqr.Rd | 4 man/print.search_lqmix.Rd | 4 man/print.summary.lqmix.Rd | 4 man/print.summary.lqr.Rd | 4 man/print.summary.search_lqmix.Rd | 4 man/residuals.lqmix.Rd |only man/residuals.lqr.Rd |only man/residuals.search_lqmix.Rd |only man/search_lqmix.Rd | 42 ++-- man/summary.lqmix.Rd | 10 man/summary.lqr.Rd | 4 man/summary.search_lqmix.Rd | 26 +- man/varAL.Rd | 17 + man/vcov.lqmix.Rd |only man/vcov.lqr.Rd |only man/vcov.search_lqmix.Rd |only tests |only 86 files changed, 1400 insertions(+), 1456 deletions(-)
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8.3 dated 2023-08-19 and 2.8.4 dated 2025-10-17
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/package.R | 3 +-- R/readMzXmlDir-functions.R | 2 -- R/readMzXmlFile-functions.R | 2 -- man/readMzXmlData-package.Rd | 1 + man/readMzXmlDir.Rd | 2 -- man/readMzXmlFile.Rd | 2 -- 9 files changed, 22 insertions(+), 25 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 1.0.4 dated 2025-09-17 and 1.0.5 dated 2025-10-17
DESCRIPTION | 7 ++- MD5 | 16 ++++---- NEWS.md | 5 ++ R/index_mean.R | 5 -- R/index_scale.R | 3 + R/sample_size_effect.R | 2 - inst/doc/more_descriptives.html | 39 ++------------------- inst/doc/ppi_diagnostics.html | 73 ++++++++++++---------------------------- inst/doc/spinebil.html | 41 +++------------------- 9 files changed, 54 insertions(+), 137 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.33.0 dated 2025-07-23 and 1.34.0 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/flip_img.R | 2 +- R/ortho2.R | 42 ++++++++++++++++++++++++++++++++++-------- R/overlay2.R | 12 ++++++++---- inst/doc/neurobase.html | 4 ++-- inst/doc/nifti_basics.html | 6 +++--- inst/doc/simple_io.html | 2 +- man/flip_img.Rd | 2 +- man/multi_overlay.Rd | 5 +++-- man/ortho2.Rd | 8 ++++++++ 12 files changed, 80 insertions(+), 36 deletions(-)