Title: Analysing Prognostic Studies
Description: Functions that help with analysis of prognostic study data. This allows users with little experience of developing models to develop models and assess the performance of the prognostic models. This also summarises the information, so the performance of multiple models can be displayed simultaneously. This minor update fixes issues related to memory requirements with large number of simulations and deals with situations when there is overfitting of data. Gurusamy, K (2026)<https://github.com/kurinchi2k/EQUALPrognosis>.
Author: Kurinchi Gurusamy [aut, cre]
Maintainer: Kurinchi Gurusamy <k.gurusamy@ucl.ac.uk>
Diff between EQUALPrognosis versions 0.1.2 dated 2026-02-04 and 0.1.3 dated 2026-03-20
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/calculate_actual_predicted.R | 2 +- R/compile_results.R | 26 +++++++++++++------------- 4 files changed, 22 insertions(+), 22 deletions(-)
More information about EQUALPrognosis at CRAN
Permanent link
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Benoît Depaire [cre],
Gert Janssenswillen [aut],
Gerard van Hulzen [ctb],
Marijke Swennen [ctb],
Ivan Esin [ctb],
Felix Mannhardt [ctb],
Hasselt University [cph]
Maintainer: Benoît Depaire <benoit.depaire@uhasselt.be>
Diff between edeaR versions 1.0.0 dated 2025-11-29 and 1.0.1 dated 2026-03-20
edeaR-1.0.0/edeaR/R/ifilter.R |only edeaR-1.0.0/edeaR/man/ifilter.Rd |only edeaR-1.0.1/edeaR/DESCRIPTION | 6 edeaR-1.0.1/edeaR/MD5 | 144 ++--- edeaR-1.0.1/edeaR/R/activity_frequency.R | 222 ++++---- edeaR-1.0.1/edeaR/R/activity_presence.R | 198 +++---- edeaR-1.0.1/edeaR/R/calculate_queuing_times.R | 114 ++-- edeaR-1.0.1/edeaR/R/edeaR.R | 70 +- edeaR-1.0.1/edeaR/R/end_activities.R | 228 ++++---- edeaR-1.0.1/edeaR/R/filter_activity.R | 146 ++--- edeaR-1.0.1/edeaR/R/filter_activity_frequency.R | 318 ++++++------ edeaR-1.0.1/edeaR/R/filter_activity_instance.R | 150 ++--- edeaR-1.0.1/edeaR/R/filter_activity_presence.R | 320 ++++++------ edeaR-1.0.1/edeaR/R/filter_case.R | 148 ++--- edeaR-1.0.1/edeaR/R/filter_case_condition.R | 76 +- edeaR-1.0.1/edeaR/R/filter_endpoints.R | 234 ++++----- edeaR-1.0.1/edeaR/R/filter_endpoints_condition.R | 270 +++++----- edeaR-1.0.1/edeaR/R/filter_lifecycle.R | 146 ++--- edeaR-1.0.1/edeaR/R/filter_lifecycle_presence.R | 268 +++++----- edeaR-1.0.1/edeaR/R/filter_precedence.R | 390 +++++++-------- edeaR-1.0.1/edeaR/R/filter_precedence_condition.R | 268 +++++----- edeaR-1.0.1/edeaR/R/filter_precedence_resource.R | 434 ++++++++--------- edeaR-1.0.1/edeaR/R/filter_processing_time.R | 294 +++++------ edeaR-1.0.1/edeaR/R/filter_resource.R | 140 ++--- edeaR-1.0.1/edeaR/R/filter_resource_frequency.R | 320 ++++++------ edeaR-1.0.1/edeaR/R/filter_throughput_time.R | 242 ++++----- edeaR-1.0.1/edeaR/R/filter_time_period.R | 404 +++++++-------- edeaR-1.0.1/edeaR/R/filter_trace_frequency.R | 238 ++++----- edeaR-1.0.1/edeaR/R/filter_trace_length.R | 252 ++++----- edeaR-1.0.1/edeaR/R/filter_trim.R | 316 ++++++------ edeaR-1.0.1/edeaR/R/filter_trim_lifecycle.R | 258 +++++----- edeaR-1.0.1/edeaR/R/groupby_helpers.R | 158 +++--- edeaR-1.0.1/edeaR/R/idle_time.R | 270 +++++----- edeaR-1.0.1/edeaR/R/idle_time_case.R | 114 ++-- edeaR-1.0.1/edeaR/R/idle_time_resource.R | 112 ++-- edeaR-1.0.1/edeaR/R/idle_time_trace.R | 42 - edeaR-1.0.1/edeaR/R/number_of_repetitions.R | 414 ++++++++-------- edeaR-1.0.1/edeaR/R/number_of_selfloops.R | 416 ++++++++-------- edeaR-1.0.1/edeaR/R/number_of_traces.R | 106 ++-- edeaR-1.0.1/edeaR/R/plot.activity_frequency.R | 102 +-- edeaR-1.0.1/edeaR/R/plot.activity_presence.R | 40 - edeaR-1.0.1/edeaR/R/plot.end_activity.R | 138 ++--- edeaR-1.0.1/edeaR/R/plot.idle_time.R | 90 +-- edeaR-1.0.1/edeaR/R/plot.number_of_repetitions.R | 188 +++---- edeaR-1.0.1/edeaR/R/plot.number_of_selfloops.R | 188 +++---- edeaR-1.0.1/edeaR/R/plot.processing_time.R | 130 ++--- edeaR-1.0.1/edeaR/R/plot.referral_matrix.R | 38 - edeaR-1.0.1/edeaR/R/plot.resource_frequency.R | 130 ++--- edeaR-1.0.1/edeaR/R/plot.resource_involvement.R | 94 +-- edeaR-1.0.1/edeaR/R/plot.resource_specialisation.R | 96 +-- edeaR-1.0.1/edeaR/R/plot.start_activities.R | 136 ++--- edeaR-1.0.1/edeaR/R/plot.throughput_time.R | 106 ++-- edeaR-1.0.1/edeaR/R/plot.trace_coverage.R | 114 ++-- edeaR-1.0.1/edeaR/R/plot.trace_length.R | 94 +-- edeaR-1.0.1/edeaR/R/processing_time.R | 354 ++++++------- edeaR-1.0.1/edeaR/R/processing_time_case.R | 56 +- edeaR-1.0.1/edeaR/R/processing_time_trace.R | 54 +- edeaR-1.0.1/edeaR/R/redo_repetitions_referral_matrix.R | 98 +-- edeaR-1.0.1/edeaR/R/redo_selfloops_referral_matrix.R | 92 +-- edeaR-1.0.1/edeaR/R/resource_frequency.R | 250 ++++----- edeaR-1.0.1/edeaR/R/resource_involvement.R | 178 +++--- edeaR-1.0.1/edeaR/R/resource_specialisation.R | 200 +++---- edeaR-1.0.1/edeaR/R/size_of_repetitions.R | 268 +++++----- edeaR-1.0.1/edeaR/R/size_of_selfloops.R | 278 +++++----- edeaR-1.0.1/edeaR/R/start_activities.R | 228 ++++---- edeaR-1.0.1/edeaR/R/throughput_time.R | 312 ++++++------ edeaR-1.0.1/edeaR/R/throughput_time_activity.R | 50 - edeaR-1.0.1/edeaR/R/throughput_time_trace.R | 48 - edeaR-1.0.1/edeaR/R/trace_coverage.R | 150 ++--- edeaR-1.0.1/edeaR/R/trace_length.R | 224 ++++---- edeaR-1.0.1/edeaR/inst/doc/filters.html | 4 edeaR-1.0.1/edeaR/inst/doc/metrics.html | 66 +- edeaR-1.0.1/edeaR/inst/doc/queue.html | 19 edeaR-1.0.1/edeaR/inst/doc/work_schedules.html | 4 74 files changed, 6435 insertions(+), 6428 deletions(-)
Title: Analysing SNP Data to Identify Sex-Linked Markers
Description: Identifies, filters and exports sex linked markers using 'SNP'
(single nucleotide polymorphism) data. To install the other packages, we
recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'.
If you want understand the applied rational to identify sexlinked markers
and/or want to cite 'dartR.sexlinked', you find the information by typing
citation('dartR.sexlinked') in the console.
Author: Diana Robledo-Ruiz [aut, cre],
Floriaan Devloo-Delva [aut],
Bernd Gruber [aut],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb]
Maintainer: Diana Robledo-Ruiz <diana.robledoruiz1@monash.edu>
Diff between dartR.sexlinked versions 1.0.5 dated 2024-06-24 and 1.2.2 dated 2026-03-20
DESCRIPTION | 17 - MD5 | 24 - NAMESPACE | 3 R/gl.drop.sexlinked.r | 660 ------------------------------------------- R/gl.filter.sexlinked.r |only R/gl.infer.sex.r | 288 +++++++++++-------- R/gl.keep.sexlinked.r | 678 +++++++++++++++++++++++++-------------------- R/gl.report.sexlinked.r | 565 +++++++++++++++++++++---------------- R/zzz.r | 2 man/gl.drop.sexlinked.Rd | 80 ----- man/gl.filter.sexlinked.Rd |only man/gl.infer.sex.Rd | 69 ++-- man/gl.keep.sexlinked.Rd | 55 +-- man/gl.report.sexlinked.Rd | 71 ++-- 14 files changed, 1033 insertions(+), 1479 deletions(-)
More information about dartR.sexlinked at CRAN
Permanent link
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.1.0 dated 2026-03-03 and 1.2.0 dated 2026-03-20
DESCRIPTION | 9 MD5 | 139 ++++-- NAMESPACE | 26 + NEWS.md | 126 +++++ R/RcppExports.R | 4 R/matching_cem.R |only R/matching_core.R | 60 +- R/matching_diagnostics.R | 210 +++++++++ R/matching_distance.R | 52 +- R/matching_full.R |only R/matching_interop.R |only R/matching_join.R | 57 ++ R/matching_output.R |only R/matching_parallel.R | 6 R/matching_plots.R | 10 R/matching_subclass.R |only R/utils.R | 3 R/zzz.R | 19 README.md | 64 ++ inst/WORDLIST | 2 inst/doc/algorithms.html | 4 inst/doc/comparison.R | 139 +++--- inst/doc/comparison.Rmd | 52 +- inst/doc/comparison.html | 134 ++++-- inst/doc/getting-started.R | 12 inst/doc/getting-started.Rmd | 44 +- inst/doc/getting-started.html | 393 ++++++++++-------- inst/doc/matching-workflows.R | 205 +++++++++ inst/doc/matching-workflows.Rmd | 312 ++++++++++++++ inst/doc/matching-workflows.html | 495 ++++++++++++++++++++++- inst/doc/pixel-morphing.html | 4 inst/doc/troubleshooting.html | 6 inst/extdata/icons/circleA_40.png |only inst/extdata/icons/circleA_80.png |only inst/extdata/icons/circleB_40.png |only inst/extdata/icons/circleB_80.png |only inst/extdata/icons/circle_color_walk.png |only inst/extdata/icons/circle_exact.png |only inst/extdata/icons/circle_recursive.png |only inst/extdata/morphs/image_color_walk.png |only inst/extdata/morphs/image_exact.png |only inst/extdata/morphs/image_recursive.png |only inst/extdata/work |only man/as_matchit.Rd |only man/bal.tab.matching_result.Rd |only man/balance_diagnostics.Rd | 43 + man/build_cost_matrix.Rd | 3 man/cem_match.Rd |only man/compute_distance_matrix.Rd | 17 man/dot-auto_breaks.Rd |only man/dot-blocks_parallel.Rd | 3 man/dot-couples_blocked.Rd | 3 man/dot-couples_single.Rd | 3 man/full_match.Rd |only man/greedy_couples.Rd | 7 man/greedy_couples_blocked.Rd | 3 man/greedy_couples_single.Rd | 3 man/join_matched.Rd | 25 - man/match_couples.Rd | 7 man/match_couples_blocked.Rd | 3 man/match_couples_single.Rd | 3 man/match_data.Rd |only man/print.cem_result.Rd |only man/print.full_matching_result.Rd |only man/print.subclass_result.Rd |only man/subclass_match.Rd |only src/Makevars | 4 src/Makevars.win | 4 src/RcppExports.cpp | 14 src/rcpp_interface.cpp | 6 src/solvers/solve_full_matching.cpp |only src/solvers/solve_full_matching.h |only src/solvers/solve_full_matching_rcpp.cpp |only tests/testthat/test-lap-solve-batch-coverage-3.R | 6 tests/testthat/test-lap-solve-batch-coverage.R | 17 tests/testthat/test-matching-cem.R |only tests/testthat/test-matching-full-optimal.R |only tests/testthat/test-matching-full.R |only tests/testthat/test-matching-interop.R |only tests/testthat/test-matching-mahalanobis.R |only tests/testthat/test-matching-output.R |only tests/testthat/test-matching-subclass.R |only vignettes/comparison.Rmd | 52 +- vignettes/getting-started.Rmd | 44 +- vignettes/images/ImageA_80.png |only vignettes/images/ImageB_80.png |only vignettes/images/circleA_80.png |only vignettes/images/circleB_80.png |only vignettes/matching-workflows.Rmd | 312 ++++++++++++++ 89 files changed, 2698 insertions(+), 471 deletions(-)
Title: Create Publication-Ready Regression Tables with Panels
Description: Create an automated regression table that is well-suited for models that are estimated with multiple dependent variables. 'panelsummary' extends 'modelsummary' (Arel-Bundock, V. (2022) <doi:10.18637/jss.v103.i01>) by allowing regression tables to be split into multiple sections with a simple function call. Utilize familiar arguments such as fmt, estimate, statistic, vcov, conf_level, stars, coef_map, coef_omit, coef_rename, gof_map, and gof_omit from 'modelsummary' to clean the table, and additionally, add a row for the mean of the dependent variable without external manipulation.
Author: Michael Topper [aut, cre],
Vincent Arel-Bundock [cph]
Maintainer: Michael Topper <miketopper123@gmail.com>
Diff between panelsummary versions 0.1.2.1 dated 2023-08-16 and 0.1.3 dated 2026-03-20
DESCRIPTION | 9 - MD5 | 46 +++---- NEWS.md | 5 R/clean_raw.R | 9 + R/helper_functions.R | 2 R/panelsummary_raw.R | 34 +++++ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/adding_rows.R | 2 inst/doc/adding_rows.html | 4 inst/doc/panelsummary.R | 2 inst/doc/panelsummary.Rmd | 4 inst/doc/panelsummary.html | 237 +++++++++++++++++++++++++++++++++---- inst/doc/with_fixest.R | 2 inst/doc/with_fixest.Rmd | 2 inst/doc/with_fixest.html | 151 ++++++++++++----------- man/clean_raw.Rd | 8 + man/panelsummary-package.Rd | 1 man/panelsummary.Rd | 41 +++--- man/panelsummary_raw.Rd | 45 ++++--- tests/testthat/test-create_means.R | 26 ++-- vignettes/panelsummary.Rmd | 4 vignettes/with_fixest.Rmd | 2 24 files changed, 454 insertions(+), 184 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 1.0.1 dated 2026-01-08 and 1.0.2 dated 2026-03-20
BayesSIM-1.0.1/BayesSIM/man/predict.bsim.Rd |only BayesSIM-1.0.2/BayesSIM/DESCRIPTION | 6 BayesSIM-1.0.2/BayesSIM/MD5 | 90 ++--- BayesSIM-1.0.2/BayesSIM/NAMESPACE | 8 BayesSIM-1.0.2/BayesSIM/R/bayesSIM.R | 2 BayesSIM-1.0.2/BayesSIM/R/bsFisher-sampler.R | 33 ++ BayesSIM-1.0.2/BayesSIM/R/bsFisher.R | 58 ++- BayesSIM-1.0.2/BayesSIM/R/bsPolar.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/bsSphere-functions.R | 14 BayesSIM-1.0.2/BayesSIM/R/bsSphere-sampler.R | 17 - BayesSIM-1.0.2/BayesSIM/R/bsSphere.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/bsSpike.R | 48 ++- BayesSIM-1.0.2/BayesSIM/R/generics.R | 262 +++++++++++++---- BayesSIM-1.0.2/BayesSIM/R/gpFisher.R | 49 ++- BayesSIM-1.0.2/BayesSIM/R/gpPolar-functions.R | 160 ++++++---- BayesSIM-1.0.2/BayesSIM/R/gpPolar-sampler.R | 158 +++++++--- BayesSIM-1.0.2/BayesSIM/R/gpPolar.R | 80 +++-- BayesSIM-1.0.2/BayesSIM/R/gpPolarTemp.R | 45 ++ BayesSIM-1.0.2/BayesSIM/R/gpSphere-united.R | 46 ++ BayesSIM-1.0.2/BayesSIM/R/gpspike-functions.R | 1 BayesSIM-1.0.2/BayesSIM/R/gpspike-sampler.R | 8 BayesSIM-1.0.2/BayesSIM/R/gpspike.R | 88 ++++- BayesSIM-1.0.2/BayesSIM/R/initial-params.R | 6 BayesSIM-1.0.2/BayesSIM/man/BayesSIM.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/as.data.frame.bsimPred.Rd |only BayesSIM-1.0.2/BayesSIM/man/as_bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsFisher.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsPolar.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsSphere.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/bsSpike.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/coef.bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/compileModelAndMCMC.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/fitted.bsim.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/genBasic.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/getFunction.Rd | 14 BayesSIM-1.0.2/BayesSIM/man/getInit.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gof.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpFisher.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpPolar.Rd | 22 - BayesSIM-1.0.2/BayesSIM/man/gpSphere.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/gpSpike.Rd | 4 BayesSIM-1.0.2/BayesSIM/man/nimTraceplot.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/plot.Rd | 2 BayesSIM-1.0.2/BayesSIM/man/predict.Rd |only BayesSIM-1.0.2/BayesSIM/man/summary.bsim.Rd | 4 BayesSIM-1.0.2/BayesSIM/man/summary.bsimPred.Rd |only BayesSIM-1.0.2/BayesSIM/tests/testthat/test-BayesSIM.R | 2 BayesSIM-1.0.2/BayesSIM/tests/testthat/test-generic.R | 14 48 files changed, 951 insertions(+), 416 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-24 0.0.2
2019-08-27 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-05 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-29 0.1.3
2025-11-25 0.1.2
2025-11-19 0.1.1
2025-11-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-04 0.8-3
2015-07-05 0.7-6
2015-05-25 0.6-16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-22 2.1.2
2018-10-02 2.1.1
2018-07-05 2.1.0
2017-08-30 2.0.3
2017-04-13 2.0.1
2017-01-10 2.0.0
2016-08-29 1.1.0
2016-08-13 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-05 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-10 1.3.4.1
2022-11-10 1.3.4
2021-10-28 1.3.3
2020-02-13 1.3.2
2018-09-14 1.3.1
2015-01-06 1.3.0
2014-11-16 1.2.11
2014-01-08 1.2.10
2013-07-27 1.2.9
2013-07-16 1.2.8
2013-05-23 1.2.7
2013-02-12 1.2.6
2012-11-15 1.2.5
2012-07-06 1.2.4
2012-04-20 1.2.3
2012-03-15 1.2.1
2012-02-15 1.2.0
2012-02-13 1.1.9
2012-02-08 1.1.8
2012-01-10 1.1.7
2011-07-28 1.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-12 0.0.3
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb],
Ivan Krylov [cre]
Maintainer: Ivan Krylov <ikrylov@disroot.org>
Diff between XML versions 3.99-0.22 dated 2026-02-10 and 3.99-0.23 dated 2026-03-20
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/Utils.c | 2 +- src/XMLEventParse.c | 5 +++-- src/schema.c | 8 +++++--- 6 files changed, 21 insertions(+), 14 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.1.0 dated 2026-02-11 and 2.2.0 dated 2026-03-20
DESCRIPTION | 12 MD5 | 574 +- NAMESPACE | 1026 +-- NEWS.md | 1244 ++-- R/AddTip.R | 550 +- R/ArtificialExtinction.R | 242 R/Cherries.R | 5 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/Consensus.R | 300 - R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/DropTip.R | 12 R/EdgeRatio.R |only R/ImposeConstraint.R | 278 - R/Information.R | 502 - R/KeptPaths.R | 94 R/KeptVerts.R | 126 R/LongBranchScore.R | 150 R/MatchNodes.R | 216 R/MatchStrings.R | 66 R/PathLengths.R | 96 R/PhyToString.R | 286 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 64 R/RcppExports.R | 16 R/ReadMrBayes.R | 180 R/ReadTntTree.R | 580 +- R/Reweight.R | 220 R/RoguePlot.R | 618 +- R/SplitFunctions.R | 912 +-- R/Splits.R | 1294 ++-- R/Stemwardness.R | 218 R/Support.R | 348 - R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TotalCopheneticIndex.R | 316 - R/TreeNumber.R | 1042 ++- R/TreeTools-package.R | 50 R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/parse_files.R | 1830 +++--- R/phylo.R | 644 +- R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_descendants.R | 274 - R/tree_display.R | 292 - R/tree_generation.R | 998 +-- R/tree_information.R | 206 R/tree_numbering.R | 56 R/tree_properties.R | 1096 +--- R/tree_rearrangement.R | 1294 ++-- R/tree_shape.R | 572 +- R/tree_write.R | 262 R/zzz.R | 68 build/partial.rdb |binary build/vignette.rds |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 34 inst/REFERENCES.bib | 745 +- inst/WORDLIST | 251 inst/apa-old-doi-prefix.csl | 4541 ++++++++--------- inst/doc/filesystem-navigation.Rmd | 104 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 - inst/doc/load-data.html | 4 inst/doc/load-trees.Rmd | 250 inst/doc/load-trees.html | 4 inst/extdata/input/dataset.nex | 44 inst/extdata/input/notes.nex | 54 inst/extdata/output/named.tre | 6 inst/extdata/output/numbered.tre | 8 inst/extdata/tests/ape-tree.nex | 10 inst/extdata/tests/continuous.nex | 44 inst/extdata/tests/encoding.nex | 48 inst/extdata/tests/parse-nexus.nexus | 510 - inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/include/TreeTools/SplitList.h | 29 inst/include/TreeTools/tree_number.h |only man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 106 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 101 man/CladeSizes.Rd | 96 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 104 man/ConsensusWithout.Rd | 211 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 166 man/DescendantEdges.Rd | 162 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 124 man/EdgeDistances.Rd | 104 man/EdgeRatio.Rd |only man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 188 man/Hamming.Rd | 156 man/ImposeConstraint.Rd | 148 man/J1Index.Rd | 190 man/KeptPaths.Rd | 132 man/KeptVerts.Rd | 138 man/LabelSplits.Rd | 172 man/LeafLabelInterchange.Rd | 118 man/ListAncestors.Rd | 218 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 129 man/MRCA.Rd | 134 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 137 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 156 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 92 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 171 man/NTip.Rd | 139 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NodeDepth.Rd | 126 man/NodeNumbers.Rd | 113 man/NodeOrder.Rd | 108 man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 117 man/PhyToString.Rd | 212 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 288 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 556 +- man/Reweight.Rd | 156 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 104 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 161 man/SplitInformation.Rd | 247 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 161 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 251 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 85 man/TreeNumber.Rd | 421 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 80 man/Treeness.Rd | 113 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 124 man/Unquote.Rd | 64 man/UnrootedTreesMatchingSplit.Rd | 96 man/UnshiftTree.Rd | 116 man/WriteTntCharacters.Rd | 140 man/as.Newick.Rd | 96 man/as.multiPhylo.Rd | 106 man/brewer.Rd | 66 man/dot-RandomParent.Rd | 54 man/doubleFactorials.Rd | 52 man/edge_to_splits.Rd | 98 man/is.TreeNumber.Rd | 64 man/logDoubleFactorials.Rd | 46 man/match.Splits.Rd | 136 man/match.multiPhylo.Rd | 144 man/nRootedShapes.Rd | 56 man/print.TreeNumber.Rd | 44 man/root_on_node.Rd | 58 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports-manual.cpp | 6 src/RcppExports.cpp | 55 src/consensus.cpp | 169 src/int_to_tree.cpp | 168 src/node_depth.cpp |only src/renumber_tips.cpp |only src/splits.cpp | 97 src/tips_in_splits.cpp | 4 tests/figs/rogueplot.svg | 68 tests/spelling.R | 8 tests/testthat.R | 8 tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg | 82 tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg | 94 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/_snaps/Support/labelsplits.svg | 148 tests/testthat/_snaps/mst/mst-plotting.svg | 142 tests/testthat/_snaps/tree_display/sorted-tree.svg | 270 - tests/testthat/test-AddTip.R | 356 - tests/testthat/test-ArtificialExtinction.R | 94 tests/testthat/test-Cherries.R | 24 tests/testthat/test-ClusterTable.R | 284 - tests/testthat/test-Decompose.R | 152 tests/testthat/test-DropTip.R | 6 tests/testthat/test-EdgeRatio.R |only tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-ImposeConstraint.R | 275 - tests/testthat/test-KeptPaths.R | 40 tests/testthat/test-KeptVerts.R | 172 tests/testthat/test-LongBranchScore.R | 36 tests/testthat/test-MatchNodes.R | 148 tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PathLengths.R | 70 tests/testthat/test-PhyToString.R | 150 tests/testthat/test-RUtreebalance.R | 128 tests/testthat/test-ReadMrBayes.R | 8 tests/testthat/test-ReadTntTree.R | 290 - tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 362 - tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Splits.R | 1154 ++-- tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-Support.R | 162 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TotalCopheneticIndex.R | 152 tests/testthat/test-TreeNumber.R | 293 - tests/testthat/test-Treeness.R | 38 tests/testthat/test-as.matrix.R | 14 tests/testthat/test-as.multiPhylo.R | 70 tests/testthat/test-combinatorics.R | 178 tests/testthat/test-consensus.R | 236 tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 76 tests/testthat/test-int_to_tree.cpp.R | 129 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-parsers.R | 442 - tests/testthat/test-phylo.R | 112 tests/testthat/test-root_tree.h.R | 226 tests/testthat/test-sort.R | 44 tests/testthat/test-split_analysis.R | 22 tests/testthat/test-splits.cpp.R | 74 tests/testthat/test-tree_ancestors.R | 40 tests/testthat/test-tree_comparison.R | 48 tests/testthat/test-tree_descendants.R | 168 tests/testthat/test-tree_display.R | 128 tests/testthat/test-tree_generation-random.R | 90 tests/testthat/test-tree_generation.R | 438 - tests/testthat/test-tree_information.R | 38 tests/testthat/test-tree_numbering.R | 102 tests/testthat/test-tree_properties.R | 364 - tests/testthat/test-tree_rearrange.R | 830 +-- tests/testthat/test-tree_shape.R | 318 - tests/testthat/test-tree_write.R | 98 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 291 files changed, 30003 insertions(+), 29147 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute
distance, correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis
of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad
Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman [aut],
Aviezer Lifshitz [aut, cre]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between tgstat versions 2.3.29 dated 2025-11-12 and 2.3.32 dated 2026-03-20
DESCRIPTION | 8 ++-- MD5 | 14 ++++---- NEWS.md | 11 ++++++ R/knn.R | 3 - R/zzz.R | 3 - src/tgstat.cpp | 69 +++++++++++++++++++++++++++++++++++++++--- src/tgstat.h | 1 tests/testthat/test-cor-knn.R |only tests/testthat/test-tmpdir.R |only 9 files changed, 90 insertions(+), 19 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.0.1 dated 2025-12-09 and 5.0.2 dated 2026-03-20
DESCRIPTION | 15 MD5 | 338 +++++----- NAMESPACE | 7 NEWS.md | 29 R/CTS.R | 2 R/RcppExports.R | 38 - R/dsl.R | 12 R/err.R | 8 R/et.R | 49 + R/geom-amt.R | 7 R/mix.R | 4 R/mu.R | 2 R/piping-model.R | 6 R/piping.R | 37 + R/print.R | 2 R/reexport.R | 5 R/rudf.R | 14 R/rxParams.R | 6 R/rxRaw.R | 62 + R/rxShiny.R | 4 R/rxUiGet.R | 5 R/rxode-options.R | 71 -- R/rxode2.R | 47 + R/rxode2_md5.R | 2 R/rxrandom.R | 66 +- R/rxsolve.R | 4 R/summary.R | 4 R/symengine.R | 2 R/ui-assign-parts.R | 10 R/ui-bind.R | 3 R/ui-rename.R | 7 R/ui.R | 17 R/utils.R | 13 R/version.R | 7 README.md | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rxode2-syntax.html | 717 +++++++++++++--------- inst/include/rxode2.h | 2 inst/include/rxode2_model_shared.c | 2 inst/include/rxode2parseGetTime.h | 58 + inst/include/rxode2parseHandleEvid.h | 22 inst/include/rxode2parseStruct.h | 10 inst/include/rxode2parseVer.h | 4 inst/tools/workaround.R | 3 inst/tutorials/rxode2-00-syntax/RxODE00syntax.Rmd | 110 +-- inst/tutorials/rxode2-01-events/rxode01events.Rmd | 380 +++++------ man/dot-rxGetSeed.Rd |only man/dot-rxSetSeed.Rd |only man/eventTable.Rd | 10 man/ini.Rd | 14 man/mix.Rd | 4 man/reexports.Rd | 3 man/rmdhunks/rxode2-intro-chunk.Rmd | 24 man/rxAppendModel.Rd | 3 man/rxDemoteAddErr.Rd | 6 man/rxErrTypeCombine.Rd | 2 man/rxFun.Rd | 2 man/rxGetDefaultSerialize.Rd |only man/rxGetSeed.Rd | 2 man/rxGetSerialType_.Rd | 2 man/rxOldQsDes.Rd |only man/rxRawToC.Rd | 6 man/rxRename.Rd | 6 man/rxSetCovariateNamesForPiping.Rd | 4 man/rxSyncOptions.Rd | 3 man/rxVersion.Rd | 8 man/rxode2.Rd | 81 +- man/stat_amt.Rd | 7 src/RcppExports.cpp | 118 +-- src/approx.cpp | 2 src/codegen.c | 47 - src/codegen2.h | 2 src/forder.cpp | 8 src/handle_evid.cpp | 9 src/init.c | 5 src/linCmt.cpp | 2 src/macros2micros.h | 1 src/par_solve.cpp | 340 +++++++++- src/par_solve.h | 55 + src/qs.cpp | 14 src/rxDerived.cpp | 12 src/rxode2_df.cpp | 18 src/seed.cpp | 62 - src/utilc.cpp | 78 +- tests/testthat.R | 4 tests/testthat/_problems |only tests/testthat/test-001-sum.R | 2 tests/testthat/test-100-cmt.R | 6 tests/testthat/test-alag.R | 30 tests/testthat/test-as-ini.R | 18 tests/testthat/test-backward.R | 10 tests/testthat/test-bad-dose.R | 8 tests/testthat/test-cmt-order.R | 10 tests/testthat/test-cov.R | 18 tests/testthat/test-data-table.R | 6 tests/testthat/test-deSolve-events.R | 4 tests/testthat/test-dollar-names.R | 6 tests/testthat/test-dplyr.R | 24 tests/testthat/test-et.R | 137 ++-- tests/testthat/test-etTrans.R | 28 tests/testthat/test-evid2.R | 10 tests/testthat/test-evid3.R | 24 tests/testthat/test-expand-grid.R | 12 tests/testthat/test-focei-variances.R | 126 +-- tests/testthat/test-iCov.R | 12 tests/testthat/test-ind-lin.R | 18 tests/testthat/test-ini.R | 8 tests/testthat/test-interp.R | 4 tests/testthat/test-keep.R | 43 - tests/testthat/test-lag.R | 58 - tests/testthat/test-lhs-ifelse.R | 8 tests/testthat/test-lincmt-solve.R | 434 ++++++------- tests/testthat/test-llik.R | 104 +-- tests/testthat/test-load.R | 1 tests/testthat/test-logit.R | 6 tests/testthat/test-missing-evid.R | 16 tests/testthat/test-mix.R | 36 - tests/testthat/test-model-rate.R | 86 +- tests/testthat/test-mtime.R | 134 ++++ tests/testthat/test-mu2.R | 4 tests/testthat/test-nearpd.R | 6 tests/testthat/test-nesting.R | 10 tests/testthat/test-newind.R | 8 tests/testthat/test-nmtest.R | 4 tests/testthat/test-nopred-ui.R | 2 tests/testthat/test-occ.R | 30 tests/testthat/test-off.R | 16 tests/testthat/test-par-solve.R | 6 tests/testthat/test-parsing.R | 10 tests/testthat/test-pipeline.R | 52 - tests/testthat/test-piping-ini.R | 50 - tests/testthat/test-print.R | 26 tests/testthat/test-rbind.R | 12 tests/testthat/test-resample.R | 28 tests/testthat/test-reset.R | 28 tests/testthat/test-rxIs.R | 24 tests/testthat/test-rxode-issue-005.R | 6 tests/testthat/test-rxode-issue-067.R | 3 tests/testthat/test-rxode-issue-163.R | 8 tests/testthat/test-rxode-issue-272.R | 10 tests/testthat/test-rxode-issue-349.R | 4 tests/testthat/test-rxode-issue-352.R | 12 tests/testthat/test-rxode-issue-375.R | 28 tests/testthat/test-rxode-issue-435.R | 16 tests/testthat/test-rxode-issue-445.R | 32 tests/testthat/test-rxode-issue-450.R | 8 tests/testthat/test-rxui-ctl.R | 8 tests/testthat/test-seq.R | 36 - tests/testthat/test-sim-zeros.R | 20 tests/testthat/test-solComp.R | 34 - tests/testthat/test-state-dep-dur.R |only tests/testthat/test-state-dep-f.R |only tests/testthat/test-state-dep-lag.R |only tests/testthat/test-state-dep-rate.R |only tests/testthat/test-state-dep-sort.R |only tests/testthat/test-steady-state.R | 118 +-- tests/testthat/test-symmetric.R | 2 tests/testthat/test-tad.R | 60 - tests/testthat/test-transit.R | 4 tests/testthat/test-ui-assign-model-parts.R | 10 tests/testthat/test-ui-drop-lines.R | 14 tests/testthat/test-ui-dv.R | 6 tests/testthat/test-ui-fix-unfix.R | 16 tests/testthat/test-ui-ini-lotri.R | 4 tests/testthat/test-ui-ini-str.R | 4 tests/testthat/test-ui-mod-functions.R | 36 - tests/testthat/test-ui-piping-single-endpoint.R | 12 tests/testthat/test-ui-piping.R | 264 ++++---- tests/testthat/test-ui-promote.R | 10 tests/testthat/test-ui-rename.R | 118 +++ tests/testthat/test-ui-simulation.R | 116 +-- tests/testthat/test-utils.R | 4 tests/testthat/test-zzzz-plot.R | 466 +++++++------- tests/testthat/testthat-problems.rds |only 175 files changed, 3706 insertions(+), 2747 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] ,
Gabi Melman [aut] ,
Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.27 dated 2026-02-12 and 0.0.28 dated 2026-03-20
ChangeLog | 13 +++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ src/RcppExports.cpp | 32 ++++++++++++++++---------------- 7 files changed, 46 insertions(+), 26 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.1 dated 2026-03-01 and 0.3.2 dated 2026-03-20
quickSentiment-0.3.1/quickSentiment/R/evaluation.R |only quickSentiment-0.3.1/quickSentiment/man/evaluate_metrics.Rd |only quickSentiment-0.3.2/quickSentiment/DESCRIPTION | 12 - quickSentiment-0.3.2/quickSentiment/LICENSE | 4 quickSentiment-0.3.2/quickSentiment/MD5 | 29 +-- quickSentiment-0.3.2/quickSentiment/NAMESPACE | 11 - quickSentiment-0.3.2/quickSentiment/NEWS.md | 19 -- quickSentiment-0.3.2/quickSentiment/R/evaluate_performance.R |only quickSentiment-0.3.2/quickSentiment/R/pipeline.R | 59 +------ quickSentiment-0.3.2/quickSentiment/R/prediction.R | 22 +- quickSentiment-0.3.2/quickSentiment/R/print.quickSentiment_eval.R |only quickSentiment-0.3.2/quickSentiment/R/route_prediction.R | 8 quickSentiment-0.3.2/quickSentiment/README.md | 30 +-- quickSentiment-0.3.2/quickSentiment/build/vignette.rds |binary quickSentiment-0.3.2/quickSentiment/inst/doc/introduction-to-quickSentiment.html | 82 +++++----- quickSentiment-0.3.2/quickSentiment/man/evaluate_performance.Rd |only quickSentiment-0.3.2/quickSentiment/man/plot.quickSentiment_prc.Rd |only quickSentiment-0.3.2/quickSentiment/man/plot.quickSentiment_roc.Rd |only quickSentiment-0.3.2/quickSentiment/man/predict_sentiment.Rd | 2 19 files changed, 122 insertions(+), 156 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Recreates Some 'SAS®' Procedures in 'R'
Description: Contains functions to simulate the most commonly used
'SAS®' procedures. Specifically, the package aims to
simulate the functionality of 'proc freq', 'proc means', 'proc ttest',
'proc reg', 'proc transpose', 'proc sort', and 'proc print'.
The simulation will include recreating
all statistics with the highest fidelity possible.
Author: David Bosak [aut, cre],
Diyu Yang [aut],
Athenkosi Nkonyeni [aut],
Kevin Kramer [ctb],
Brian Varney [ctb],
Duong Tran [ctb],
Yifei Chen [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between procs versions 1.0.7 dated 2025-07-27 and 1.0.8 dated 2026-03-20
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procs-1.0.8/procs/vignettes/procs-ttest.Rmd | 51 + procs-1.0.8/procs/vignettes/procs.Rmd | 28 124 files changed, 8397 insertions(+), 2655 deletions(-)
Title: Gaussian and Student-t Copula Models for Count Time Series
Description: Provides likelihood-based inference for Gaussian and Student-t
copula models for univariate count time series. Supports Poisson,
negative binomial, binomial, beta-binomial, and zero-inflated
marginals with ARMA dependence structures. Includes simulation,
maximum-likelihood estimation, residual diagnostics, and predictive
inference. Implements Time Series Minimax Exponential Tilting (TMET)
<doi:10.1016/j.csda.2026.108344>, an adaptation of minimax exponential
tilting of Botev (2017) <doi:10.1111/rssb.12162>. Also provides a
linear-cost implementation of the Geweke–Hajivassiliou–Keane (GHK)
simulator following Masarotto and Varin (2012) <doi:10.1214/12-EJS721>,
and the Continuous Extension (CE) approximation of Nguyen and
De Oliveira (2025) <doi:10.1080/02664763.2025.2498502>. The package
follows the S3 design philosophy of 'gcmr' but is developed independently.
Author: Quynh Nguyen [aut, cre],
Victor De Oliveira [aut]
Maintainer: Quynh Nguyen <nqnhu2209@gmail.com>
Diff between gctsc versions 0.2.0 dated 2026-03-13 and 0.2.3 dated 2026-03-20
gctsc-0.2.0/gctsc/data/KCWC.csv |only gctsc-0.2.0/gctsc/data/datalist |only gctsc-0.2.0/gctsc/data/rota.csv |only gctsc-0.2.0/gctsc/src/mvphi.f |only gctsc-0.2.3/gctsc/DESCRIPTION | 8 +-- gctsc-0.2.3/gctsc/MD5 | 22 ++++------ gctsc-0.2.3/gctsc/R/residuals.R | 2 gctsc-0.2.3/gctsc/inst/doc/gctsc_vignette.html | 44 ++++++++++----------- gctsc-0.2.3/gctsc/inst/t_copula_examples/Poisson.R | 2 gctsc-0.2.3/gctsc/man/plot.gctsc.Rd | 2 gctsc-0.2.3/gctsc/src/gauss_utils.cpp | 27 ++++++------ gctsc-0.2.3/gctsc/src/gauss_utils.h | 9 ++-- gctsc-0.2.3/gctsc/src/pred_mvn.cpp | 9 +++- gctsc-0.2.3/gctsc/src/pred_mvt.cpp | 5 +- 14 files changed, 68 insertions(+), 62 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
('ODE', 'DAE', 'DDE')
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations ('ODE'), of
partial differential equations ('PDE'), of differential
algebraic equations ('DAE'), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK'
collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk'
and a C-implementation of solvers of the 'Runge-Kutta' family with
fixed or variable time steps. The package contains routines
designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D
partial differential equations ('PDE') that have been converted
to 'ODEs' by numerical differencing.
Author: Karline Soetaert [aut] ,
Thomas Petzoldt [aut, cre] ,
R. Woodrow Setzer [aut] ,
Peter N. Brown [ctb] ,
George D. Byrne [ctb] ,
Ernst Hairer [ctb] ,
Alan C. Hindmarsh [ctb] ,
Cleve Moler [ctb] ,
Linda R. Petzold [ctb] ,
Youcef Saad [ctb] ,
Clement W. [...truncated...]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.41 dated 2026-02-06 and 1.42 dated 2026-03-20
DESCRIPTION | 6 MD5 | 46 +-- NEWS.md | 581 +++++++++++++++++++++++----------------------- build/partial.rdb |binary build/vignette.rds |binary data/ccl4data.rda |binary inst/doc/compiledCode.pdf |binary inst/doc/deSolve.pdf |binary src/call_daspk.c | 26 +- src/call_lsoda.c | 14 - src/call_radau.c | 8 src/call_zvode.c | 14 - src/deSolve_utils.c | 45 +-- src/ex_Aquaphy.c | 4 src/ex_CCL4model.c | 2 src/ex_ChemicalDAE.c | 2 src/ex_SCOC.c | 2 src/forcings.c | 4 src/lags.c | 30 +- src/rk_auto.c | 6 src/rk_fixed.c | 4 src/rk_implicit.c | 8 src/rk_util.c | 21 + src/twoDmap.c | 6 24 files changed, 418 insertions(+), 411 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-32 dated 2025-04-02 and 0.9-33 dated 2026-03-20
DESCRIPTION | 15 +++++----- MD5 | 24 ++++++++-------- R/dbarts.R | 14 +++++++++ build/vignette.rds |binary inst/doc/gibbs_sampler_mixture_model.pdf |binary inst/doc/working_with_saved_trees.pdf |binary src/R_interface.cpp | 2 + src/R_interface_crossvalidate.cpp | 2 - src/R_interface_sampler.cpp | 45 +++++++++++++++++++++++++++++++ src/R_interface_sampler.hpp | 3 ++ src/external/randomBase.c | 14 ++++----- src/include/rc/util.h | 6 ++++ src/rc/util.c | 2 - 13 files changed, 99 insertions(+), 28 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Emily Stringer [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [c [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 1.2.2 dated 2026-03-12 and 1.2.3 dated 2026-03-20
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Title: PolyaGamma Sampling
Description: Tools for sampling from the PolyaGamma distribution based on Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Useful for logistic regression.
Author: Nicholas G. Polson [aut, cph],
James G. Scott [aut, cph],
Jesse Windle [aut, cre, cph],
Jari Oksanen [ctb],
James Balamuta [ctb]
Maintainer: Jesse Windle <jesse.windle@gmail.com>
Diff between BayesLogit versions 2.1 dated 2019-09-26 and 2.3 dated 2026-03-20
BayesLogit-2.1/BayesLogit/inst/dev/data |only BayesLogit-2.3/BayesLogit/DESCRIPTION | 8 ++-- BayesLogit-2.3/BayesLogit/MD5 | 15 +++---- BayesLogit-2.3/BayesLogit/NEWS.md | 31 +++++++++++----- BayesLogit-2.3/BayesLogit/R/PolyaGammaApproxAlt.R | 4 +- BayesLogit-2.3/BayesLogit/R/SaddlePointApprox.R | 30 +++++++-------- BayesLogit-2.3/BayesLogit/README.md | 4 -- BayesLogit-2.3/BayesLogit/inst/CITATION | 42 +++++++++++++++------- BayesLogit-2.3/BayesLogit/man/rpg.Rd | 2 - 9 files changed, 81 insertions(+), 55 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre] ,
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb],
Stephen Roecker [aut, ctb],
David Rossiter [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.3 dated 2026-01-17 and 2.3.1 dated 2026-03-20
aqp-2.3.1/aqp/DESCRIPTION | 6 aqp-2.3.1/aqp/MD5 | 138 ++-- aqp-2.3.1/aqp/NAMESPACE | 6 aqp-2.3.1/aqp/NEWS.md | 34 + aqp-2.3.1/aqp/R/Class-SoilProfileCollection.R | 19 aqp-2.3.1/aqp/R/SoilProfileCollection-methods.R | 157 ++++- aqp-2.3.1/aqp/R/SoilProfileCollection-operators.R | 11 aqp-2.3.1/aqp/R/SoilProfileCollection-setters.R | 32 - aqp-2.3.1/aqp/R/SoilProfileCollection-spatial.R | 3 aqp-2.3.1/aqp/R/addBracket.R | 303 ++++++---- aqp-2.3.1/aqp/R/aggregateColor.R | 2 aqp-2.3.1/aqp/R/col2Munsell.R | 4 aqp-2.3.1/aqp/R/colorChart.R | 105 ++- aqp-2.3.1/aqp/R/colorQuantiles.R | 11 aqp-2.3.1/aqp/R/colorVariation.R | 183 ++++-- aqp-2.3.1/aqp/R/data-documentation.R | 16 aqp-2.3.1/aqp/R/estimateSoilColor.R | 218 +++++-- aqp-2.3.1/aqp/R/fillHzGaps.R | 36 - aqp-2.3.1/aqp/R/hzOffset.R | 260 +++++++- aqp-2.3.1/aqp/R/launderMunsell.R |only aqp-2.3.1/aqp/R/mixMunsell.R | 32 - aqp-2.3.1/aqp/R/mutate_profile.R | 9 aqp-2.3.1/aqp/R/parseMunsell.R | 2 aqp-2.3.1/aqp/R/plotSPC.R | 10 aqp-2.3.1/aqp/R/reduceSPC.R |only aqp-2.3.1/aqp/R/repairMissingHzDepths.R | 2 aqp-2.3.1/aqp/R/simulateColor.R | 6 aqp-2.3.1/aqp/R/soilColorSignature.R | 59 + aqp-2.3.1/aqp/R/spc2mpspline.R | 17 aqp-2.3.1/aqp/R/spec2Munsell.R | 2 aqp-2.3.1/aqp/R/validateMunsell.R |only aqp-2.3.1/aqp/R/warpHorizons.R | 4 aqp-2.3.1/aqp/data/Ohz.colors.rda |only aqp-2.3.1/aqp/data/datalist | 1 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 6 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 8 aqp-2.3.1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 112 +-- aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.R | 53 + aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.Rmd | 88 ++ aqp-2.3.1/aqp/inst/doc/Munsell-color-conversion.html | 110 +++ aqp-2.3.1/aqp/inst/doc/aqp-overview.Rmd | 4 aqp-2.3.1/aqp/inst/doc/aqp-overview.html | 8 aqp-2.3.1/aqp/man/Ohz.colors.Rd |only aqp-2.3.1/aqp/man/SoilProfileCollection-plotting-methods.Rd | 3 aqp-2.3.1/aqp/man/addBracket.Rd | 148 ++-- aqp-2.3.1/aqp/man/addDiagnosticBracket.Rd | 43 + aqp-2.3.1/aqp/man/colorChart.Rd | 18 aqp-2.3.1/aqp/man/colorVariation.Rd | 68 ++ aqp-2.3.1/aqp/man/dollarsign.Rd | 8 aqp-2.3.1/aqp/man/estimateSoilColor.Rd | 59 + aqp-2.3.1/aqp/man/grepSPC.Rd | 2 aqp-2.3.1/aqp/man/hzOffset.Rd | 180 +++++ aqp-2.3.1/aqp/man/initSpatial.Rd | 4 aqp-2.3.1/aqp/man/launderMunsell.Rd |only aqp-2.3.1/aqp/man/mixMunsell.Rd | 4 aqp-2.3.1/aqp/man/mutate_profile.Rd | 2 aqp-2.3.1/aqp/man/names.Rd | 12 aqp-2.3.1/aqp/man/parseMunsell.Rd | 3 aqp-2.3.1/aqp/man/reduceSPC.Rd | 2 aqp-2.3.1/aqp/man/simulateColor.Rd | 2 aqp-2.3.1/aqp/man/site.Rd | 4 aqp-2.3.1/aqp/man/soilColorSignature.Rd | 2 aqp-2.3.1/aqp/man/subApply.Rd | 2 aqp-2.3.1/aqp/man/validateMunsell.Rd |only aqp-2.3.1/aqp/tests/testthat/Rplots.pdf |binary aqp-2.3.1/aqp/tests/testthat/test-colorVariation.R |only aqp-2.3.1/aqp/tests/testthat/test-estimateSoilColor.R | 96 +++ aqp-2.3.1/aqp/tests/testthat/test-hzOffset.R | 44 + aqp-2.3.1/aqp/tests/testthat/test-plotSPC.R | 5 aqp-2.3.1/aqp/tests/testthat/test-reduceSPC.R | 9 aqp-2.3.1/aqp/tests/testthat/test-validateMunsell.R |only aqp-2.3.1/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 8 aqp-2.3.1/aqp/vignettes/Munsell-color-conversion.Rmd | 88 ++ aqp-2.3.1/aqp/vignettes/aqp-overview.Rmd | 4 aqp-2.3/aqp/R/reduce.R |only 75 files changed, 2223 insertions(+), 674 deletions(-)
Title: Versatile R Server
Description: Rserve is a versatile, scalable server enabling the
efficient use of R from other applications through
variety of protocols including QAP, WebSockets, HTTP
and HTTPS. It acts as a server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for many popular languages allowing applications
to use facilities of R without the need of linking to
the R binary. Rserve supports remote connections,
user authentication and file transfer. A simple R client
is included in this package as well. It also supports
OCAP mode for secure remote procedure calls,
including support for full event loop, asynchronous
results/graphics and console I/O.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-17 dated 2026-02-02 and 1.8-18 dated 2026-03-20
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS | 4 ++++ inst/java/REngine.jar |binary inst/java/Rserve.jar |binary src/Rsrv.h | 4 ++-- src/client/cxx/Rsrv.h | 4 ++-- src/client/java/Rserve/Rserve.jar |binary src/oc.h | 1 + src/rcompat.h | 17 +++++++++++++++++ 10 files changed, 38 insertions(+), 16 deletions(-)