Title: Program for Inferring Immunoglobulin Allele Similarity Clusters
and Genotypes
Description: Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires.
The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes.
The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.
Author: Ayelet Peres [aut, cre],
William Lees [aut],
Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <ayelet.peres@yale.edu>
This is a re-admission after prior archival of version 1.0.7 dated 2025-04-09
Diff between piglet versions 1.0.7 dated 2025-04-09 and 1.2.0 dated 2026-02-17
piglet-1.0.7/piglet/man/GermlineCluster-class.Rd |only piglet-1.2.0/piglet/DESCRIPTION | 58 piglet-1.2.0/piglet/MD5 | 66 piglet-1.2.0/piglet/NAMESPACE | 60 piglet-1.2.0/piglet/NEWS.md | 58 piglet-1.2.0/piglet/R/GermlineCluster-class.R |only piglet-1.2.0/piglet/R/allele_cluster.R | 944 ++++++---- piglet-1.2.0/piglet/R/allele_genotype.R | 62 piglet-1.2.0/piglet/R/community_detection.R |only piglet-1.2.0/piglet/R/piglet.R | 16 piglet-1.2.0/piglet/R/visualization.R |only piglet-1.2.0/piglet/build/partial.rdb |binary piglet-1.2.0/piglet/build/vignette.rds |binary piglet-1.2.0/piglet/inst/doc/PIgLET-vignette.R | 211 -- piglet-1.2.0/piglet/inst/doc/PIgLET-vignette.Rmd | 189 -- piglet-1.2.0/piglet/inst/doc/PIgLET-vignette.html | 41 piglet-1.2.0/piglet/inst/doc/PIgLET_biomed_asc.R |only piglet-1.2.0/piglet/inst/doc/PIgLET_biomed_asc.Rmd |only piglet-1.2.0/piglet/inst/doc/PIgLET_biomed_asc.html |only piglet-1.2.0/piglet/man/GermlineCluster.Rd |only piglet-1.2.0/piglet/man/assignAlleleClusters.Rd | 12 piglet-1.2.0/piglet/man/compute_distance.Rd |only piglet-1.2.0/piglet/man/detect_communities_leiden.Rd |only piglet-1.2.0/piglet/man/distance_to_graph.Rd |only piglet-1.2.0/piglet/man/dot-create_iuis_labels_with_markers.Rd |only piglet-1.2.0/piglet/man/dot-getNClusters.Rd |only piglet-1.2.0/piglet/man/igClust.Rd |only piglet-1.2.0/piglet/man/igDistance.Rd |only piglet-1.2.0/piglet/man/ighvClust.Rd | 19 piglet-1.2.0/piglet/man/ighvDistance.Rd | 16 piglet-1.2.0/piglet/man/inferAlleleClusters.Rd | 105 - piglet-1.2.0/piglet/man/new_germline_cluster.Rd |only piglet-1.2.0/piglet/man/optimize_resolution.Rd |only piglet-1.2.0/piglet/man/piglet-package.Rd | 4 piglet-1.2.0/piglet/man/plot.GermlineCluster.Rd |only piglet-1.2.0/piglet/man/plotClusterComparison.Rd |only piglet-1.2.0/piglet/man/plotCommunityNetwork.Rd |only piglet-1.2.0/piglet/man/plotSilhouetteOptimization.Rd |only piglet-1.2.0/piglet/man/plotTruncatedTree.Rd |only piglet-1.2.0/piglet/man/print.GermlineCluster.Rd |only piglet-1.2.0/piglet/man/summary.GermlineCluster.Rd |only piglet-1.2.0/piglet/tests |only piglet-1.2.0/piglet/vignettes/PIgLET-vignette.Rmd | 189 -- piglet-1.2.0/piglet/vignettes/PIgLET_biomed_asc.Rmd |only 44 files changed, 1124 insertions(+), 926 deletions(-)
Title: Visualizing Topological Loops and Voids
Description: Visualizations to explain the results of a topological
data analysis. The goal of topological data analysis is to identify
persistent topological structures, such as loops (topological circles)
and voids (topological spheres), in data sets. The output of an
analysis using the 'TDA' package is a Rips diagram (named after the
mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in
these holes in the data by providing tools to visualize the features
that help explain the structures found in the Rips diagram. See McGee
and colleagues (2024) <doi:10.1101/2024.05.16.593927>.
Author: Kevin R. Coombes [aut, cre],
Jake Reed [aut],
RB McGee [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RPointCloud versions 0.8.0 dated 2024-08-19 and 0.9.1 dated 2026-02-17
DESCRIPTION | 8 - MD5 | 38 ++++---- R/01-disentangle.R | 20 ++-- build/vignette.rds |binary data/CLL.rda |binary data/cytof.rda |binary data/treg.rda |binary inst/doc/clinical.R | 57 ++++++------- inst/doc/clinical.Rmd | 9 +- inst/doc/clinical.html | 113 ++++++++++++++++--------- inst/doc/cytof.R | 27 +++--- inst/doc/cytof.Rmd | 9 +- inst/doc/cytof.html | 60 +++++-------- inst/doc/treg.R | 29 +++--- inst/doc/treg.Rmd | 9 +- inst/doc/treg.html | 214 +++++++++++++++++++++++-------------------------- man/m03-disentangle.Rd | 3 vignettes/clinical.Rmd | 9 +- vignettes/cytof.Rmd | 9 +- vignettes/treg.Rmd | 9 +- 20 files changed, 331 insertions(+), 292 deletions(-)
Title: Pharmacokinetic Bioanalysis Experiments Design and Exploration
Description: Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations.
The package impose regulatory constrains and sanity checking for common bioanalytical procedures.
Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.
Author: Omar Elashkar [aut, cre]
Maintainer: Omar Elashkar <omar.i.elashkar@gmail.com>
Diff between PKbioanalysis versions 0.4.0 dated 2026-01-14 and 0.5.0 dated 2026-02-17
PKbioanalysis-0.4.0/PKbioanalysis/man/has_default_RT.Rd |only PKbioanalysis-0.4.0/PKbioanalysis/tests/exp/test-chrom_parsers.R |only PKbioanalysis-0.4.0/PKbioanalysis/tests/exp/test-filter_chrom.R |only PKbioanalysis-0.4.0/PKbioanalysis/tests/exp/test-peak_integerate.R |only PKbioanalysis-0.4.0/PKbioanalysis/tests/exp/test-process_chroms.R |only PKbioanalysis-0.4.0/PKbioanalysis/tests/exp/test-smoothing.R |only PKbioanalysis-0.5.0/PKbioanalysis/DESCRIPTION | 24 PKbioanalysis-0.5.0/PKbioanalysis/MD5 | 87 - PKbioanalysis-0.5.0/PKbioanalysis/NAMESPACE | 8 PKbioanalysis-0.5.0/PKbioanalysis/NEWS.md | 3 PKbioanalysis-0.5.0/PKbioanalysis/R/PKbioanalysis-package.R | 5 PKbioanalysis-0.5.0/PKbioanalysis/R/chrom_anomaly_plots.R | 14 PKbioanalysis-0.5.0/PKbioanalysis/R/chrom_app.R | 470 ++++-- PKbioanalysis-0.5.0/PKbioanalysis/R/chrom_parsers.R | 16 PKbioanalysis-0.5.0/PKbioanalysis/R/chrom_utils.R | 2 PKbioanalysis-0.5.0/PKbioanalysis/R/chromatogram.R | 4 PKbioanalysis-0.5.0/PKbioanalysis/R/class.R | 3 PKbioanalysis-0.5.0/PKbioanalysis/R/config.R | 7 PKbioanalysis-0.5.0/PKbioanalysis/R/genAI.R | 7 PKbioanalysis-0.5.0/PKbioanalysis/R/gen_studydesign.R | 34 PKbioanalysis-0.5.0/PKbioanalysis/R/generate_test_set.R | 86 + PKbioanalysis-0.5.0/PKbioanalysis/R/injec_list.R | 3 PKbioanalysis-0.5.0/PKbioanalysis/R/linearitycheck.R | 166 +- PKbioanalysis-0.5.0/PKbioanalysis/R/peak_integerate.R | 696 +++++----- PKbioanalysis-0.5.0/PKbioanalysis/R/quant_app.R | 347 ++++ PKbioanalysis-0.5.0/PKbioanalysis/R/quant_object.R | 70 - PKbioanalysis-0.5.0/PKbioanalysis/R/quant_parsers.R | 15 PKbioanalysis-0.5.0/PKbioanalysis/R/samples_profiles.R | 315 +++- PKbioanalysis-0.5.0/PKbioanalysis/R/utils.R | 33 PKbioanalysis-0.5.0/PKbioanalysis/R/zzz.R | 18 PKbioanalysis-0.5.0/PKbioanalysis/README.md | 234 ++- PKbioanalysis-0.5.0/PKbioanalysis/inst/dist/install_PKbioanalysis.bat | 2 PKbioanalysis-0.5.0/PKbioanalysis/inst/dist/install_PKbioanalysis.zip |binary PKbioanalysis-0.5.0/PKbioanalysis/inst/extdata/08122019_MTG_injeclist_parsed.csv |only PKbioanalysis-0.5.0/PKbioanalysis/inst/extdata/parse_mtg.py |only PKbioanalysis-0.5.0/PKbioanalysis/inst/extdata/parse_mtg_to_csv.py |only PKbioanalysis-0.5.0/PKbioanalysis/inst/pysrc/src/__pycache__/masslynx_parser.cpython-313.pyc |only PKbioanalysis-0.5.0/PKbioanalysis/man/export_pk_profiles.Rd |only PKbioanalysis-0.5.0/PKbioanalysis/man/extract_peak_bounds.Rd | 8 PKbioanalysis-0.5.0/PKbioanalysis/man/has_default_bounds.Rd |only PKbioanalysis-0.5.0/PKbioanalysis/man/nca_table.Rd |only PKbioanalysis-0.5.0/PKbioanalysis/man/pkmerge.Rd |only PKbioanalysis-0.5.0/PKbioanalysis/man/read_experiment_results.Rd | 9 PKbioanalysis-0.5.0/PKbioanalysis/man/update_RT.Rd | 32 PKbioanalysis-0.5.0/PKbioanalysis/tests/exp/test-chrom_res.R | 31 PKbioanalysis-0.5.0/PKbioanalysis/tests/exp/test-update_RT.R | 36 PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/helper-global.R | 6 PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-chrom_parsers.R |only PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-filter_chrom.R |only PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-genai.R | 177 ++ PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-peak_integerate.R |only PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-pkmerge.R |only PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test-smoothing.R |only PKbioanalysis-0.5.0/PKbioanalysis/tests/testthat/test_quant_object.R | 2 54 files changed, 2145 insertions(+), 825 deletions(-)
Title: Running Local LLMs with 'llama.cpp' Backend
Description: Provides R bindings to the 'llama.cpp' library for running large language models.
The package uses a lightweight architecture where the C++ backend library is downloaded
at runtime rather than bundled with the package.
Package features include text generation, reproducible generation, and parallel inference.
Author: Eddie Yang [aut] ,
Yaosheng Xu [aut, cre]
Maintainer: Yaosheng Xu <xu2009@purdue.edu>
Diff between localLLM versions 1.1.0 dated 2025-12-17 and 1.2.0 dated 2026-02-17
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md |only R/annotations.R | 25 +++++++++++++++++++++++++ R/install.R | 4 ++-- inst/doc/tutorial-model-comparison.R | 2 +- inst/doc/tutorial-model-comparison.Rmd | 2 +- inst/doc/tutorial-model-comparison.html | 2 +- vignettes/tutorial-model-comparison.Rmd | 2 +- 9 files changed, 43 insertions(+), 17 deletions(-)
More information about LifeTableFertility at CRAN
Permanent link
Title: Delayed Read for 'GDAL' Vector Data Sources
Description: Lazy read for drawings. A 'dplyr' back end for data sources supported by
'GDAL' vector drivers, that allows working with local or remote sources as if they
are in-memory data frames. Basic features works with any drawing format ('GDAL vector
data source') supported by the 'sf' package.
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between lazysf versions 0.2.0 dated 2025-04-03 and 0.3.0 dated 2026-02-17
DESCRIPTION | 18 ++++++++++-------- MD5 | 9 +++++---- NAMESPACE | 4 ++++ NEWS.md | 4 ++++ R/dbplyr.R |only build/vignette.rds |binary 6 files changed, 23 insertions(+), 12 deletions(-)
Title: Tidyverse-Compatible Bootstrapping
Description: Compute arbitrary non-parametric bootstrap statistics on data in
tidy data frames.
Author: Mika Braginsky [aut, cre],
Daniel Yurovsky [aut]
Maintainer: Mika Braginsky <mika.br@gmail.com>
Diff between tidyboot versions 0.1.1 dated 2018-03-14 and 0.1.3 dated 2026-02-17
DESCRIPTION | 11 +++---- MD5 | 18 ++++++------- NEWS.md | 6 +++- R/tidyboot.R | 40 +++++++++++++++++------------ R/util.R | 4 +- README.md | 62 +++++++++++++++++++++++++-------------------- man/tidyboot.data.frame.Rd | 23 ++++++++++++---- man/tidyboot.logical.Rd | 11 ++++++- man/tidyboot.numeric.Rd | 11 ++++++- man/tidyboot_mean.Rd | 5 ++- 10 files changed, 118 insertions(+), 73 deletions(-)
Title: Spatial Logistic Gaussian Process for Field Density Estimation
Description: Provides tools for conditional and spatially dependent
density estimation using Spatial Logistic Gaussian Processes (SLGPs).
The approach represents probability densities through finite-rank
Gaussian process priors transformed via a spatial logistic density
transformation, enabling flexible non-parametric modeling of
heterogeneous data. Functionality includes density prediction,
quantile and moment estimation, sampling methods, and preprocessing
routines for basis functions. Applications arise in spatial statistics,
machine learning, and uncertainty quantification.
The methodology builds on the framework of Leonard (1978)
<doi:10.1111/j.2517-6161.1978.tb01655.x>, Lenk (1988) <doi:10.1080/01621459.1988.10478625>,
Tokdar (2007) <doi:10.1198/106186007X210206>, Tokdar (2010) <doi:10.1214/10-BA605>,
and is further aligned with recent developments
in Bayesian non-parametric modelling: see Gautier (2023) <https://boristheses.unibe.ch/4377/>,
and Gautier (2025) &l [...truncated...]
Author: Athenais Gautier [aut, cre]
Maintainer: Athenais Gautier <athenais.gautier@onera.fr>
Diff between SLGP versions 1.0.1 dated 2026-01-20 and 1.0.2 dated 2026-02-17
DESCRIPTION | 6 +-- MD5 | 24 ++++++------- R/PredictAndSimulate.R | 69 ++++++++++++++++++++++++++++------------ R/slgp.R | 5 +- inst/doc/IntroductionSLGP.html | 4 +- inst/doc/SLGPdiscrete.html | 2 - inst/extdata/composed_model.rds |binary inst/extdata/simple_model.rds |binary man/predictSLGP_cdf.Rd | 5 ++ man/predictSLGP_moments.Rd | 5 ++ man/predictSLGP_newNode.Rd | 5 ++ man/predictSLGP_quantiles.Rd | 5 ++ man/sampleSLGP.Rd | 5 ++ 13 files changed, 89 insertions(+), 46 deletions(-)
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<https://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre] ,
Manuel Leiva [aut] ,
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 1.0.4 dated 2025-01-26 and 1.2.0 dated 2026-02-17
DESCRIPTION | 12 - MD5 | 8 R/ChileAirQuality.R | 33 +-- R/ChileClimateData.R | 311 +++++++++++----------------- README.md | 553 +++++++++++++++------------------------------------ 5 files changed, 314 insertions(+), 603 deletions(-)
Title: Generation of Artificial Binary Data
Description: Generation of correlated artificial binary data.
Author: Friedrich Leisch [aut] ,
Andreas Weingessel [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between bindata versions 0.9-23 dated 2026-01-11 and 0.9-24 dated 2026-02-17
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- R/sysdata.rda |binary build/partial.rdb |binary inst/REFERENCES.R |only man/SimulVals.Rd | 7 ++----- man/bincorr2commonprob.Rd | 7 ++----- man/check.commonprob.Rd | 7 ++----- man/commonprob2sigma.Rd | 7 ++----- man/rmvbin.Rd | 7 +------ man/simul.commonprob.Rd | 7 ++----- 11 files changed, 24 insertions(+), 43 deletions(-)
Title: Credential Chain for Seamless 'OAuth 2.0' Authentication to
'Azure Services'
Description: Implements a credential chain for 'Azure OAuth 2.0' authentication
based on the package 'httr2''s 'OAuth' framework. Sequentially attempts authentication
methods until one succeeds. During development allows interactive
browser-based flows ('Device Code' and 'Auth Code' flows) and non-interactive
flow ('Client Secret') in batch mode.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between azr versions 0.2.1 dated 2026-01-07 and 0.3.0 dated 2026-02-17
azr-0.2.1/azr/R/azure-clients.R |only azr-0.3.0/azr/DESCRIPTION | 8 azr-0.3.0/azr/MD5 | 56 +++-- azr-0.3.0/azr/NAMESPACE | 7 azr-0.3.0/azr/NEWS.md | 8 azr-0.3.0/azr/R/api-client.R | 119 ++++++++---- azr-0.3.0/azr/R/api-resource.R | 2 azr-0.3.0/azr/R/api-services.R | 10 - azr-0.3.0/azr/R/azure-graph-client.R |only azr-0.3.0/azr/R/azure-storage-client.R |only azr-0.3.0/azr/R/constants.R | 1 azr-0.3.0/azr/R/credential-azure-cli.R | 203 +++++++++++++++++++-- azr-0.3.0/azr/R/credential-cached-token.R |only azr-0.3.0/azr/R/credential-interactive.R | 70 +++++-- azr-0.3.0/azr/R/credential-refresh-token.R |only azr-0.3.0/azr/R/default-credential.R | 62 ++++++ azr-0.3.0/azr/R/defaults.R | 25 ++ azr-0.3.0/azr/R/zzz.R | 4 azr-0.3.0/azr/man/AuthCodeCredential.Rd | 6 azr-0.3.0/azr/man/AzureCLICredential.Rd | 12 - azr-0.3.0/azr/man/CachedTokenCredential.Rd |only azr-0.3.0/azr/man/DeviceCodeCredential.Rd | 6 azr-0.3.0/azr/man/InteractiveCredential.Rd | 12 + azr-0.3.0/azr/man/RefreshTokenCredential.Rd |only azr-0.3.0/azr/man/api_client.Rd | 109 ++++++++--- azr-0.3.0/azr/man/api_graph_resource.Rd | 2 azr-0.3.0/azr/man/api_resource.Rd | 2 azr-0.3.0/azr/man/api_storage_client.Rd |only azr-0.3.0/azr/man/az_cli_get_cached_token.Rd |only azr-0.3.0/azr/man/azr_graph_client.Rd | 2 azr-0.3.0/azr/man/azr_storage_client.Rd |only azr-0.3.0/azr/man/cached_token_credential_chain.Rd |only azr-0.3.0/azr/man/default_refresh_token.Rd |only azr-0.3.0/azr/man/environment_variables.Rd | 2 azr-0.3.0/azr/man/get_credential_provider.Rd | 10 - 35 files changed, 588 insertions(+), 150 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.7.0 dated 2025-10-30 and 0.7.1 dated 2026-02-17
DESCRIPTION | 6 +-- MD5 | 30 +++++++-------- NEWS.md | 14 +++++++ R/freeze.R | 2 - R/import_man.R | 7 ++- R/import_misc.R | 7 ++- R/import_readme.R | 4 +- R/import_vignettes.R | 2 - R/rd2qmd.R | 24 ++++++------ R/render_docs.R | 6 +-- R/settings_docute.R | 4 +- R/settings_mkdocs.R | 2 - R/utils.R | 11 ++++- tests/testthat/_snaps/docsify/render_docs/index.html | 2 - tests/testthat/test-import_man.R | 5 ++ tests/testthat/test-render_docs.R | 38 +++++++++++++++++-- 16 files changed, 114 insertions(+), 50 deletions(-)
Title: Diagnostics for Lists of Codes Based on Measurements
Description: Diagnostics of list of codes based on concepts from the domains measurement and observation. This package works for data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Marta Alcalde-Herraiz [aut]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between MeasurementDiagnostics versions 0.2.0 dated 2025-12-17 and 0.3.0 dated 2026-02-17
MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.R |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.Rmd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/inst/doc/summariseMeasurementUse.html |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/man/timeScaleDoc.Rd |only MeasurementDiagnostics-0.2.0/MeasurementDiagnostics/vignettes/summariseMeasurementUse.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/DESCRIPTION | 17 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/MD5 | 65 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/documentationHelpers.R | 15 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/mockMeasurementDiagnostics.R | 4 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/plotMeasurementSummary.R | 35 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/plotMeasurementValueAsNumeric.R | 1 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/summariseCohortMeasurementUse.R | 14 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/summariseMeasurementUse.R | 382 ++- MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/tableMeasurementSummary.R | 29 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/tableMeasurementValueAsConcept.R | 8 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/tableMeasurementValueAsNumeric.R | 17 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/R/utilities.R |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/README.md | 1090 +++++++++- MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/build/vignette.rds |binary MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a01_summariseMeasurementUse.R |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a01_summariseMeasurementUse.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a01_summariseMeasurementUse.html |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a02_summariseCohortMeasurementUse.R |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a02_summariseCohortMeasurementUse.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a02_summariseCohortMeasurementUse.html |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a03_resultsVisualisation.R |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a03_resultsVisualisation.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/inst/doc/a03_resultsVisualisation.html |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/figures/README-unnamed-chunk-10-1.png |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/plotMeasurementSummary.Rd | 14 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/plotMeasurementValueAsNumber.Rd | 3 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/summariseCohortMeasurementUse.Rd | 18 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/summariseMeasurementDoc.Rd | 8 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/summariseMeasurementUse.Rd | 16 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/tableMeasurementSummary.Rd | 2 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/man/tableMeasurementValueAsNumber.Rd | 2 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementSummary.R | 15 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/tests/testthat/test-plotMeasurementValueAsNumeric.R | 2 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/tests/testthat/test-summariseCohortMeasurementUse.R | 51 MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/tests/testthat/test-summariseMeasurementUse.R | 165 + MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/vignettes/a01_summariseMeasurementUse.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/vignettes/a02_summariseCohortMeasurementUse.Rmd |only MeasurementDiagnostics-0.3.0/MeasurementDiagnostics/vignettes/a03_resultsVisualisation.Rmd |only 43 files changed, 1677 insertions(+), 296 deletions(-)
More information about MeasurementDiagnostics at CRAN
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More information about VariableSelection at CRAN
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Title: Complete Environment for Bayesian Inference
Description: Provides a complete environment for Bayesian inference using a variety of different samplers (see ?LaplacesDemon for an overview).
Author: Byron Hall [aut],
Martina Hall [aut],
Statisticat, LLC [aut, cph],
Charles J. Geyer [ctb, cph] ,
Eric Brown [ctb],
Richard Hermanson [ctb],
Emmanuel Charpentier [ctb],
Daniel Heck [ctb],
Stephane Laurent [ctb],
Quentin F. Gronau [ctb],
Henrik Singman [...truncated...]
Maintainer: Henrik Singmann <singmann+LaplacesDemon@gmail.com>
Diff between LaplacesDemon versions 16.1.6 dated 2021-07-09 and 16.1.8 dated 2026-02-17
CHANGELOG | 6 + DESCRIPTION | 14 ++-- MD5 | 86 ++++++++++++------------ R/LaplaceApproximation.R | 6 - R/Validate.R | 2 R/distributions.R | 7 -- R/is.proper.R | 6 - R/plot.demonoid.hpc.R | 2 R/plot.demonoid.ppc.R | 2 R/plot.iterquad.R | 2 R/plot.iterquad.ppc.R | 2 R/plot.laplace.R | 2 R/plot.laplace.ppc.R | 2 R/plot.pmc.R | 2 R/plot.pmc.ppc.R | 2 R/plot.vb.R | 2 R/plot.vb.ppc.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 104 ++++++++++++++--------------- inst/doc/BayesianInference.pdf |binary inst/doc/Examples.pdf |binary inst/doc/LaplacesDemonTutorial.pdf |binary man/LML.Rd | 2 man/LaplaceApproximation.Rd | 2 man/LaplacesDemon.Rd | 2 man/LossMatrix.Rd | 4 - man/MISS.Rd | 2 man/Matrices.Rd | 2 man/PMC.Rd | 2 man/caterpillar.plot.Rd | 2 man/data.demonfx.Rd | 2 man/data.demontexas.Rd | 122 +++++++++++++++++------------------ man/dist.Inverse.Wishart.Cholesky.Rd | 8 +- man/dist.Inverse.Wishart.Rd | 8 +- man/print.demonoid.Rd | 2 man/print.heidelberger.Rd | 2 man/print.iterquad.Rd | 2 man/print.laplace.Rd | 2 man/print.miss.Rd | 2 man/print.pmc.Rd | 2 man/print.raftery.Rd | 2 man/print.vb.Rd | 2 vignettes/References.bib | 8 +- 44 files changed, 221 insertions(+), 212 deletions(-)
Title: Estimators DID with Multiple Groups and Periods
Description: Estimators of Difference-in-Differences based on de Chaisemartin and D'Haultfoeuille.
Author: Anzony Quispe [aut, cre],
Diego Ciccia [aut],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Shuo Zhang [aut],
Clement de Chaisemartin [aut]
Maintainer: Anzony Quispe <anzony.quispe@gmail.com>
Diff between DIDmultiplegt versions 2.0.0 dated 2024-07-16 and 2.1.0 dated 2026-02-17
DESCRIPTION | 22 MD5 | 14 NAMESPACE | 23 R/data.R | 28 R/did_multiplegt.R | 111 +-- R/did_multiplegt_old.R | 1566 +++++++++++++++++++++++----------------------- man/did_multiplegt.Rd | 4 man/did_multiplegt_old.Rd | 65 - 8 files changed, 915 insertions(+), 918 deletions(-)
Title: Comparative Shortest Path Forest Stand Segmentation from LiDAR
Data
Description: Functionality for segmenting individual trees from a forest stand scanned with a close-range (e.g., terrestrial or mobile) laser scanner. The complete workflow from a raw point cloud to a complete tabular forest inventory is provided. The package contains several algorithms for detecting tree bases and a graph-based algorithm to attach all remaining points to these tree bases. It builds heavily on the 'lidR' package. A description of the segmentation algorithm can be found in Larysch et al. (2025) <doi:10.1007/s10342-025-01796-z>.
Author: Julian Frey [aut, cre] ,
Zoe Schindler [ctb] ,
Katja Kroener [ctb]
Maintainer: Julian Frey <julian.frey@wwd.uni-freiburg.de>
Diff between CspStandSegmentation versions 0.1.2 dated 2025-10-28 and 0.2.0 dated 2026-02-17
DESCRIPTION | 12 MD5 | 24 - NEWS.md |only R/csp_cost_functions.R | 59 +++ R/forest_inventory.R | 597 +++++++++++++++++++++------------------ R/merge_las_objects.R | 41 ++ R/zzz.R | 3 README.md | 5 man/comparative_shortest_path.Rd | 6 man/csp_cost_segmentation.Rd | 5 man/forest_inventory.Rd | 125 ++++---- man/las_merge.Rd | 17 - man/ransac_circle_fit.Rd | 4 tests/testthat/test-merge_las.R |only 14 files changed, 534 insertions(+), 364 deletions(-)
More information about CspStandSegmentation at CRAN
Permanent link
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.13.1 dated 2025-12-08 and 0.14.0 dated 2026-02-17
DESCRIPTION | 8 MD5 | 63 NAMESPACE | 1 NEWS.md | 22 R/collapse_by_group.R |only R/estimate_contrast_methods.R | 282 ++- R/estimate_means.R | 14 R/estimate_slopes.R | 80 - R/get_emmeans.R | 46 R/get_marginalcontrasts.R | 82 - R/p_adjust.R | 129 + R/pool.R | 45 R/standardize_methods.R | 44 R/summary.R | 56 R/tinyplot.R | 9 R/utils.R | 63 R/visualisation_recipe.R | 98 - R/visualisation_recipe_internal.R | 211 +- README.md | 18 inst/WORDLIST | 3 man/collapse_by_group.Rd |only man/estimate_contrasts.Rd | 7 man/estimate_means.Rd | 7 man/estimate_slopes.Rd | 41 man/get_emmeans.Rd | 10 man/visualisation_recipe.estimate_predicted.Rd | 41 tests/testthat/test-estimate_contrasts.R | 1161 +++++++++++++--- tests/testthat/test-estimate_contrasts_counterfactual.R | 27 tests/testthat/test-estimate_contrasts_inequality.R | 146 +- tests/testthat/test-estimate_slopes.R | 209 ++ tests/testthat/test-ordinal.R | 7 tests/testthat/test-plot-show_data.R |only tests/testthat/test-plot.R | 238 +-- tests/testthat/test-vcov.R | 22 34 files changed, 2276 insertions(+), 914 deletions(-)
Title: 'Galaxy' API Implementation
Description: On 'Galaxy' platforms like 'Galaxy Europe' <https://usegalaxy.eu>, many tools and workflows can run directly on a high-performance computer. 'GalaxyR' connects R with 'Galaxy' platforms API <https://usegalaxy.eu/api/docs> and allows credential management, uploading data, invoking workflows or tools, checking their status, and downloading results.
Author: Julian Frey [aut, cre] ,
Zoe Schindler [ctb]
Maintainer: Julian Frey <julian.frey@wwd.uni-freiburg.de>
Diff between GalaxyR versions 0.1.0 dated 2026-02-04 and 0.1.1 dated 2026-02-17
DESCRIPTION | 6 MD5 | 41 NAMESPACE | 2 NEWS.md | 20 R/2025-10-27_JF_R_Galaxy_functions.R | 2034 +++++++++++++++---------------- R/2026-01-21_s4_class_methods.R | 2296 ++++++++++++++++++----------------- README.md | 7 inst/CITATION | 24 man/dot-resolve_galaxy_url.Rd | 42 man/dot-rtrim.Rd | 42 man/galaxy_delete_dataset.Rd | 124 - man/galaxy_delete_datasets.Rd | 94 - man/galaxy_download_rocrate.Rd |only man/galaxy_get_file_info.Rd | 82 - man/galaxy_get_tool.Rd | 76 - man/galaxy_get_tool_id.Rd | 110 - man/galaxy_has_key.Rd | 38 man/galaxy_history_size.Rd | 86 - man/galaxy_list_histories.Rd | 48 man/galaxy_list_invocations.Rd | 42 man/galaxy_list_tools.Rd | 102 - man/galaxy_list_workflows.Rd | 80 - 22 files changed, 2766 insertions(+), 2630 deletions(-)
Title: Test Theory Analysis and Biclustering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.8.0 dated 2025-12-10 and 1.8.1 dated 2026-02-17
DESCRIPTION | 6 +-- MD5 | 12 +++---- NEWS.md | 28 +++++++++++++++++ R/00_GridSearch.R | 10 ++++-- R/01_dataFormat.R | 72 ++++++++++++-------------------------------- R/13_LRA_rated.R | 2 - R/16_Biclustering_ordinal.R | 9 ++++- 7 files changed, 74 insertions(+), 65 deletions(-)
Title: Tutorials for Learning 'Positron' and for Using AI
Description: Collection of tutorials for working with 'Positron'
and for learning how to apply generative AI when coding with R.
Covers scripts, 'Quarto' documents, 'Git', 'GitHub', and
'Quarto' websites. Makes extensive use of the tools in the
'tutorial.helpers' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between positron.tutorials versions 0.2.0 dated 2025-06-08 and 0.2.1 dated 2026-02-17
positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/01-code/images/start-up-2.png |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/02-quarto/images/example-chunk.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/02-quarto/images/example-quarto.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/03-terminal/images/download.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/03-terminal/tutorial.html |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/04-github-1/tutorial_files |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/05-github-2/images/quarto-1-1.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/05-github-2/images/quarto-1-2.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/05-github-2/images/quarto-2-1.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/05-github-2/images/quarto-2-2.txt |only positron.tutorials-0.2.0/positron.tutorials/inst/tutorials/07-websites-2/tutorial.html |only positron.tutorials-0.2.0/positron.tutorials/tests/testthat/test-render.R |only positron.tutorials-0.2.1/positron.tutorials/DESCRIPTION | 22 positron.tutorials-0.2.1/positron.tutorials/MD5 | 46 positron.tutorials-0.2.1/positron.tutorials/NAMESPACE | 3 positron.tutorials-0.2.1/positron.tutorials/NEWS.md | 8 positron.tutorials-0.2.1/positron.tutorials/R |only positron.tutorials-0.2.1/positron.tutorials/README.md | 75 + positron.tutorials-0.2.1/positron.tutorials/inst/extdata |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/01-code/images/positron-interface.jpeg |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/01-code/tutorial.Rmd | 500 +--------- positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/02-quarto/tutorial.Rmd | 71 - positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/03-terminal/tutorial.Rmd | 40 positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/04-github-1/tutorial.Rmd | 7 positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/05-github-2/tutorial.Rmd | 96 + positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/06-websites-1/tutorial.Rmd | 5 positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/07-websites-2/tutorial.Rmd | 32 positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/r4ds-1 |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/r4ds-2 |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/r4ds-3 |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/r4ds-4 |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/r4ds-5 |only positron.tutorials-0.2.1/positron.tutorials/inst/tutorials/tidycensus-1 |only positron.tutorials-0.2.1/positron.tutorials/man |only positron.tutorials-0.2.1/positron.tutorials/tests/testthat/test-tutorials.R |only 35 files changed, 363 insertions(+), 542 deletions(-)
More information about positron.tutorials at CRAN
Permanent link
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>),
and grammatical differential evolution (O'Neill, M. and Brabazon, A. (2006) in
Arabinia, H. (2006, ISBN:978-193-241596-3).
All algorithms reuse basic adaptive mechanisms for performance optimization.
For 'xega''s architecture, see Gey [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.18 dated 2025-11-28 and 0.9.0.23 dated 2026-02-17
DESCRIPTION | 10 +- MD5 | 18 ++- NAMESPACE | 3 NEWS | 27 +++++ R/xegaDebug.R |only R/xegaRerun.R | 62 ++++++++++++- R/xegaRun.R | 251 ++++++++++++++++++++++++++++++++++++++++--------------- R/xegaVersion.R | 6 - man/xegaDebug.Rd |only man/xegaReRun.Rd | 7 + man/xegaRun.Rd | 211 +++++++++++++++++++++++++++++++++------------- 11 files changed, 444 insertions(+), 151 deletions(-)
Title: Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Author: Mohammad Ferdosi [aut, cre],
Cedric Gondro [aut]
Maintainer: Mohammad Ferdosi <mhferdosi@yahoo.com>
Diff between hsphase versions 2.0.4 dated 2025-04-05 and 3.0.0 dated 2026-02-17
DESCRIPTION | 14 +-- MD5 | 159 +++++++++++++++++++++++-------------- NAMESPACE | 5 - R/aio.R | 4 R/bmh.R | 17 +++ R/cs.R | 4 R/fastDist.R | 12 +- R/fixBothStrandSireOrigin.R |only R/fixRotation.R |only R/fixSwitches.R |only R/groupMatSingle.R |only R/hsphase.R | 92 +++++++++++++++++++++ R/hss.R | 18 +++- R/ibdCluster.R |only R/imageplot.R | 61 +++++++------- R/maf.R | 22 +---- R/ohg.R | 7 - R/oneRowhaplotpe2twoRowhaplotype.R |only R/para.R | 15 +-- R/prCalus.R | 57 +++++++++++-- R/prManual.R | 56 +++++++++++-- R/prSimple.R | 63 ++++++++++++-- R/rpoh.R | 8 - R/rpohhsphase.R | 75 ++++++++++++++++- R/simulateHalfsib.R | 2 R/switch.R |only R/switchDetector.R |only R/two2oneRow.R |only build/vignette.rds |binary data/genotypes.rda |binary data/map.txt.gz |binary data/pedigree.txt.gz |binary demo/hsphase.R | 65 +++++++++++++-- inst/CITATION | 145 +++++++++++++++++++++------------ inst/doc/hsphase.Rnw | 6 - inst/doc/hsphase.pdf |binary man/addSwitch.Rd |only man/aio.Rd | 72 ++++++++-------- man/bmh.Rd | 68 +++++++++------ man/co.Rd | 41 +++------ man/cs.Rd | 27 ++---- man/dot-fastdist.Rd | 12 +- man/dot-fillGap.Rd |only man/dot-fixBothStrand.Rd |only man/dot-fixRotation.Rd |only man/dot-hblock.Rd |only man/dot-ibdCluster.Rd |only man/dot-maf.Rd | 17 +-- man/dot-o2tH.Rd |only man/dot-phfnoGenotype.Rd |only man/dot-prCalus.Rd |only man/dot-prManual.Rd |only man/dot-prSimple.Rd |only man/dot-ptr2por.Rd |only man/dot-rpohhsphase.Rd |only man/fixSW.Rd |only man/genotypes.Rd | 18 ++-- man/groupMatSingle.Rd |only man/hbp.Rd | 37 ++++---- man/hh.Rd | 50 +++++------ man/hsphase-package.Rd | 59 +++++++------ man/hss.Rd | 6 - man/imageplot.Rd | 55 ++++++------ man/map.Rd | 18 ++-- man/ohd.Rd | 55 ++++-------- man/ohg.Rd | 39 +++------ man/para.Rd | 6 + man/pedigree.Rd | 16 +-- man/pedigreeNaming.Rd | 34 ++----- man/phf.Rd | 38 ++++---- man/pm.Rd | 48 ++++++----- man/pogc.Rd | 47 +++++----- man/readGenotype.Rd | 45 +++------- man/recombinations.Rd | 38 +++----- man/rplot.Rd | 67 +++++++-------- man/ssp.Rd | 40 ++++----- man/switchDetector.Rd |only src/FastDist.cpp | 2 src/FillGap.cpp |only src/FillGap.h |only src/FixBothStrand.cpp |only src/FixBothStrand.h |only src/Makevars | 6 - src/Makevars.win | 3 src/SwitchAdd.cpp |only src/SwitchAdd.h |only src/SwitchDetector.cpp |only src/SwitchDetector.h |only src/fixRotation.cpp |only src/fixRotation.h |only src/hsp.cpp | 56 +++---------- src/ibdcluster.cpp |only src/ibdcluster.h |only src/main.cpp | 12 ++ src/memory.cpp | 8 - src/mhMat.cpp |only src/mhMat.h |only src/ohg.cpp |only src/ohg.h |only src/ohp.cpp |only src/ohp.h |only vignettes/hsphase.Rnw | 6 - 102 files changed, 1156 insertions(+), 797 deletions(-)
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and group-specific factors using a flexible multi-level factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) obtain estimates of the parameters of the factor-augmented quantile regressions together with their standard deviations; (iv) recover full predictive conditional densities from estimated quantiles; (v) obtain risk measures based on extreme quantiles of the conditional densities; (vi) estimate the conditional density and the corresponding extreme quantiles when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.7.1 dated 2025-11-05 and 0.8.0 dated 2026-02-17
FARS-0.7.1/FARS/R/orthogonalize_factors.R |only FARS-0.7.1/FARS/man/orthogonalize_factors.Rd |only FARS-0.8.0/FARS/DESCRIPTION | 8 FARS-0.8.0/FARS/MD5 | 30 - FARS-0.8.0/FARS/NAMESPACE | 4 FARS-0.8.0/FARS/R/apply_identifications.R | 155 +++------- FARS-0.8.0/FARS/R/fars_methods.R | 114 ++++++- FARS-0.8.0/FARS/R/mldfm.R | 18 + FARS-0.8.0/FARS/R/mldfm_subsampling.R | 25 + FARS-0.8.0/FARS/R/multiple_blocks.R | 18 - FARS-0.8.0/FARS/R/single_block.R | 23 - FARS-0.8.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf |binary FARS-0.8.0/FARS/man/AIC.fars.Rd |only FARS-0.8.0/FARS/man/BIC.fars.Rd |only FARS-0.8.0/FARS/man/apply_identifications.Rd | 27 - FARS-0.8.0/FARS/man/logLik.fars.Rd | 13 FARS-0.8.0/FARS/man/mldfm.Rd | 6 FARS-0.8.0/FARS/man/mldfm_subsampling.Rd | 6 18 files changed, 256 insertions(+), 191 deletions(-)
Title: Genetic Population Level Functions
Description: This collection of gene representation-independent functions
implements the population layer of extended evolutionary and genetic
algorithms and its support
for the R-package 'xega' <https://CRAN.R-project.org/package=xega>.
The population layer consists of functions
for initializing, logging, observing, evaluating a population of genes,
as well as of computing the next population. For parallel evaluation of a
population of genes 4 execution models - named Sequential, MultiCore,
FutureApply, and Cluster - are provided. They are implemented by
configuring the lapply() function. The execution model FutureApply can be
externally configured as recommended by Bengtsson (2021)
<doi:10.32614/RJ-2021-048>. Configurable acceptance rules and cooling
schedules (see Kirkpatrick, S., Gelatt, C. D. J, and Vecchi, M. P. (1983)
<doi:10.1126/science.220.4598.671>, and Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7) offer simulated annealing or greedy randomized
approximate search [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPopulation versions 1.0.0.11 dated 2025-11-26 and 1.0.0.12 dated 2026-02-17
DESCRIPTION | 12 +++++----- MD5 | 46 +++++++++++++++++++++------------------ NAMESPACE | 4 +++ NEWS | 8 ++++++ R/asPipeline.R |only R/xegaEvalPopulation.R | 38 +++++++++++++------------------- R/xegaNextPopulation.R | 5 ++-- man/AcceptFactory.Rd | 1 man/ApplyFactory.Rd | 1 man/CoolingFactory.Rd | 1 man/CrossRateFactory.Rd | 1 man/MutationRateFactory.Rd | 1 man/TerminationFactory.Rd | 1 man/asPipeline.Rd | 7 +++-- man/asPipelineG.Rd |only man/asPipelineID.Rd |only man/checkTerminationFactory.Rd | 1 man/xegaAsPipelineFactory.Rd |only man/xegaConfiguration.Rd | 1 man/xegaEvalPopulation.Rd | 7 +++++ man/xegaEvalPopulationFactory.Rd | 1 man/xegaNextPopulation.Rd | 1 man/xegaRepEvalPopulation.Rd | 3 +- man/xegaRepairPop.Rd | 4 ++- tests/testthat/test-replicate.R | 3 ++ tests/testthat/test-replicate2.R | 4 +++ 26 files changed, 95 insertions(+), 56 deletions(-)
More information about xegaPopulation at CRAN
Permanent link
Title: Curve Registration for Exponential Family Functional Data
Description: A method for performing joint registration and functional principal
component analysis for curves (functional data) that are generated from exponential family distributions. This
mainly implements the algorithms described in 'Wrobel et al. (2019)' <doi:10.1111/biom.12963> and further adapts them to potentially
incomplete curves where (some) curves are not observed from the beginning and/or until the end of the common domain. Curve registration
can be used to better understand patterns in functional data by separating curves into phase and amplitude variability.
This software handles both binary and continuous functional data, and is
especially applicable in accelerometry and wearable technology.
Author: Julia Wrobel [aut, cre] ,
Alexander Bauer [aut],
Erin McDonnell [aut],
Fabian Scheipl [ctb],
Jeff Goldsmith [aut]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
This is a re-admission after prior archival of version 2.1.0 dated 2022-10-02
Diff between registr versions 2.1.0 dated 2022-10-02 and 2.2.1 dated 2026-02-17
registr-2.1.0/registr/cleanup |only registr-2.2.1/registr/DESCRIPTION | 19 registr-2.2.1/registr/MD5 | 42 - registr-2.2.1/registr/NEWS.md | 13 registr-2.2.1/registr/R/gfpca_twoStep.R | 4 registr-2.2.1/registr/R/help.R | 4 registr-2.2.1/registr/R/registr-package.R |only registr-2.2.1/registr/README.md | 55 +- registr-2.2.1/registr/build/partial.rdb |only registr-2.2.1/registr/build/vignette.rds |binary registr-2.2.1/registr/inst/doc/incomplete_curves.html | 421 +++++++++--------- registr-2.2.1/registr/inst/doc/registr.R | 2 registr-2.2.1/registr/inst/doc/registr.Rmd | 2 registr-2.2.1/registr/inst/doc/registr.html | 382 ++++++++-------- registr-2.2.1/registr/man/bfpca.Rd | 7 registr-2.2.1/registr/man/bfpca_optimization.Rd | 7 registr-2.2.1/registr/man/fpca_gauss_optimization.Rd | 7 registr-2.2.1/registr/man/gfpca_twoStep.Rd | 4 registr-2.2.1/registr/man/loss_h_gradient.Rd | 9 registr-2.2.1/registr/man/registr-package.Rd |only registr-2.2.1/registr/man/registr.Rd | 9 registr-2.2.1/registr/src/Makevars | 8 registr-2.2.1/registr/src/Makevars.ucrt |only registr-2.2.1/registr/src/Makevars.win |only registr-2.2.1/registr/vignettes/registr.Rmd | 2 25 files changed, 494 insertions(+), 503 deletions(-)
Title: Construct Parsers for Structured Text Files
Description: Construct parser combinator functions, higher order functions that
parse input. Construction of such parsers is transparent and easy. Their main
application is the parsing of structured text files like those generated by
laboratory instruments. Based on a paper by Hutton (1992)
<doi:10.1017/S0956796800000411>.
Author: Douwe Molenaar [aut, cre, cph]
Maintainer: Douwe Molenaar <d.molenaar@vu.nl>
Diff between parcr versions 0.6.0 dated 2026-02-15 and 0.6.1 dated 2026-02-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ R/parsers_error.R | 3 ++- R/stringparser_constructor.R | 13 ++++++------- man/stringparser.Rd | 7 +++---- tests/testthat/test-parsers_error.R | 6 +++++- tests/testthat/test-stringparser_constructor.R | 5 +++++ 8 files changed, 41 insertions(+), 23 deletions(-)
Title: Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling
Framework
Description: Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.
Author: Marc Scherstjanoi [aut, cre],
Rene Dechow [aut]
Maintainer: Marc Scherstjanoi <marc.scherstjanoi@thuenen.de>
Diff between sorcering versions 1.2.1 dated 2025-10-13 and 1.2.2 dated 2026-02-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/partial.rdb |binary build/sorcering.pdf |binary build/stage23.rdb |binary inst/doc/sorcering.pdf |binary man/sorcering.Rd | 2 +- 8 files changed, 17 insertions(+), 12 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 8.0 dated 2025-12-04 and 8.1 dated 2026-02-17
DESCRIPTION | 20 +++--- MD5 | 68 ++++++++++----------- NAMESPACE | 5 - R/ait.knn.R | 6 - R/alfa.pcr.R | 10 ++- R/alfa.tune.R | 43 +++++++------ R/alfareg.tune.R | 48 +++++++-------- R/el.test2.R | 60 +++++++++---------- R/glmpcr.tune.R | 36 ++++++----- R/hellinger.compreg.R | 75 +++++++++++------------- R/js.compreg.R | 42 ++++++------- R/kernreg.tune.R | 56 ++++++++--------- R/kl.compreg.R | 34 ++++++---- R/multinompcr.tune.R | 37 ++++++----- R/ols.compreg.R | 44 ++++++++------ R/pcr.tune.R | 38 +++++------- R/rda.tune.R | 46 +++++++++----- R/ridge.tune.R | 36 +++++------ R/scls.R | 134 ++++++++++++++++++++++++++++++++----------- R/scls.betest.R | 2 R/symkl.compreg.R | 34 +++++----- R/tflr.betest.R | 30 +++++---- R/tflr.indeptest.R | 104 ++++++--------------------------- R/tflr.irls.R | 32 ++++++++-- R/tv.compreg.R | 35 +++++------ R/zadr.R | 69 ++-------------------- R/zadr2.R | 75 ++---------------------- man/Compositional-package.Rd | 4 - man/aeqdist.etest.Rd | 2 man/alfareg.tune.Rd | 4 - man/scls.Rd | 8 +- man/tflr.Rd | 2 man/tflr.betest.Rd | 7 +- man/tflr.indeptest.Rd | 5 + man/zadr.Rd | 20 +----- 35 files changed, 603 insertions(+), 668 deletions(-)
Title: Create Visual Predictive Checks
Description: Visual predictive checks are a commonly used diagnostic plot in pharmacometrics, showing how certain statistics (percentiles) for observed data compare to those same statistics for data simulated from a model. The package can generate VPCs for continuous, categorical, censored, and (repeated) time-to-event data.
Author: Ron Keizer [aut, cre],
Bill Denney [aut]
Maintainer: Ron Keizer <ron@insight-rx.com>
Diff between vpc versions 1.2.2 dated 2021-01-11 and 1.2.4 dated 2026-02-17
vpc-1.2.2/vpc/R/sim_data.R |only vpc-1.2.2/vpc/man/loq_perc.Rd |only vpc-1.2.2/vpc/man/show_default_tte.Rd |only vpc-1.2.2/vpc/man/sim_data.Rd |only vpc-1.2.2/vpc/tests/test-add_sim_index_number.R |only vpc-1.2.2/vpc/tests/test-filter_dv.R |only vpc-1.2.2/vpc/tests/test-labeller.R |only vpc-1.2.2/vpc/tests/test-scales.R |only vpc-1.2.2/vpc/tests/test-softwaretype.R |only vpc-1.2.2/vpc/tests/test-strat-col-detection.R |only vpc-1.2.2/vpc/tests/test-vpc.R |only vpc-1.2.2/vpc/tests/test-vpc_cat.R |only vpc-1.2.2/vpc/tests/test-vpc_cens.R |only vpc-1.2.2/vpc/tests/test-vpc_tte.R |only vpc-1.2.4/vpc/DESCRIPTION | 28 vpc-1.2.4/vpc/MD5 | 152 + vpc-1.2.4/vpc/NAMESPACE | 15 vpc-1.2.4/vpc/NEWS.md | 12 vpc-1.2.4/vpc/R/add_noise.R | 2 vpc-1.2.4/vpc/R/add_sim_index_number.R | 6 vpc-1.2.4/vpc/R/add_stratification.R | 30 vpc-1.2.4/vpc/R/as_vpcdb.R |only vpc-1.2.4/vpc/R/binning.R | 8 vpc-1.2.4/vpc/R/calc_pred_corr_continuous.R |only vpc-1.2.4/vpc/R/calc_vpc_continuous.R |only vpc-1.2.4/vpc/R/check_stratification_columns_available.R | 19 vpc-1.2.4/vpc/R/compute_kaplan.R | 110 - vpc-1.2.4/vpc/R/compute_kmmc.R | 6 vpc-1.2.4/vpc/R/create_vpc_theme.R | 7 vpc-1.2.4/vpc/R/datasets.R | 2 vpc-1.2.4/vpc/R/define_bins.R |only vpc-1.2.4/vpc/R/define_data_columns.R | 4 vpc-1.2.4/vpc/R/define_loq.R |only vpc-1.2.4/vpc/R/draw_params_mvr.R | 2 vpc-1.2.4/vpc/R/filter_dv.R | 38 vpc-1.2.4/vpc/R/format_vpc_input_data.R | 199 ++ vpc-1.2.4/vpc/R/functions.R | 28 vpc-1.2.4/vpc/R/label_vpc_tte.R |only vpc-1.2.4/vpc/R/new_vpc_theme.R | 99 - vpc-1.2.4/vpc/R/pk_functions.R | 22 vpc-1.2.4/vpc/R/plot_vpc.R | 983 ++++++++---- vpc-1.2.4/vpc/R/quantile_cens.R | 67 vpc-1.2.4/vpc/R/read_table_nm.R | 3 vpc-1.2.4/vpc/R/read_vpc.R |only vpc-1.2.4/vpc/R/replace_list_elements.R | 10 vpc-1.2.4/vpc/R/show_default.R | 93 - vpc-1.2.4/vpc/R/themes.R | 16 vpc-1.2.4/vpc/R/triangle_to_full.R | 5 vpc-1.2.4/vpc/R/vpc-package.R | 11 vpc-1.2.4/vpc/R/vpc.R | 406 +--- vpc-1.2.4/vpc/R/vpc_cat.R | 183 -- vpc-1.2.4/vpc/R/vpc_cens.R | 237 +- vpc-1.2.4/vpc/R/vpc_tte.R | 388 +--- vpc-1.2.4/vpc/R/zzz.R | 10 vpc-1.2.4/vpc/man/add_stratification.Rd | 6 vpc-1.2.4/vpc/man/as_vpcdb.Rd |only vpc-1.2.4/vpc/man/auto_bin.Rd | 2 vpc-1.2.4/vpc/man/calc_pred_corr_continuous.Rd |only vpc-1.2.4/vpc/man/calc_vpc_continuous.Rd |only vpc-1.2.4/vpc/man/check_stratification_columns_available.Rd | 9 vpc-1.2.4/vpc/man/create_vpc_theme.Rd | 3 vpc-1.2.4/vpc/man/define_bins.Rd |only vpc-1.2.4/vpc/man/define_loq.Rd |only vpc-1.2.4/vpc/man/filter_dv.Rd |only vpc-1.2.4/vpc/man/format_vpc_input_data.Rd |only vpc-1.2.4/vpc/man/ggplot.vpcdb_continuous.Rd |only vpc-1.2.4/vpc/man/ggplot2_label_variable.Rd |only vpc-1.2.4/vpc/man/label_vpc_tte.Rd |only vpc-1.2.4/vpc/man/loq_frac.Rd |only vpc-1.2.4/vpc/man/new_vpc_theme.Rd | 50 vpc-1.2.4/vpc/man/pk_iv_1cmt.Rd | 6 vpc-1.2.4/vpc/man/pk_oral_1cmt.Rd | 6 vpc-1.2.4/vpc/man/plot_vpc.Rd | 6 vpc-1.2.4/vpc/man/plot_vpc_helper.Rd |only vpc-1.2.4/vpc/man/pred_correction_core.Rd |only vpc-1.2.4/vpc/man/quantile_cens.Rd | 23 vpc-1.2.4/vpc/man/read_vpc.Rd |only vpc-1.2.4/vpc/man/replace_list_elements.Rd | 2 vpc-1.2.4/vpc/man/show_default.Rd | 6 vpc-1.2.4/vpc/man/simple_data.Rd | 2 vpc-1.2.4/vpc/man/standardize_column.Rd |only vpc-1.2.4/vpc/man/vpc-package.Rd | 20 vpc-1.2.4/vpc/man/vpc.Rd | 17 vpc-1.2.4/vpc/man/vpc_cat.Rd | 24 vpc-1.2.4/vpc/man/vpc_cens.Rd | 26 vpc-1.2.4/vpc/man/vpc_ggplot.Rd |only vpc-1.2.4/vpc/man/vpc_tte.Rd | 36 vpc-1.2.4/vpc/tests/testthat |only vpc-1.2.4/vpc/tests/testthat.R |only 89 files changed, 1888 insertions(+), 1557 deletions(-)
Title: Multi-Category Classification Accuracy
Description: It contains six common multi-category classification accuracy evaluation measures.
All of these measures could be found in Li and Ming (2019) <doi:10.1002/sim.8103>. Specifically,
Hypervolume Under Manifold (HUM), described in
Li and Fine (2008) <doi:10.1093/biostatistics/kxm050>.
Correct Classification Percentage (CCP), Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), R-Squared Value (RSQ), described in
Li, Jiang and Fine (2013) <doi:10.1093/biostatistics/kxs047>.
Polytomous Discrimination Index (PDI), described in
Van Calster et al. (2012) <doi:10.1007/s10654-012-9733-3>.
Li et al. (2018) <doi:10.1177/0962280217692830>.
PDI with variance estimation using Dover et al. (2021) <doi:10.1002/sim.9187>.
We described all these above measures and our mcca package in
Li, Gao and D'Agostino (2019) <doi:10.1002/sim.8103>.
Author: Ming Gao [aut],
Jialiang Li [aut, cre],
Pan Liu [aut],
Ben Van Calster [aut]
Maintainer: Jialiang Li <stalj@nus.edu.sg>
Diff between mcca versions 0.7.0 dated 2019-12-20 and 0.8.1 dated 2026-02-17
DESCRIPTION | 26 +++++-- MD5 | 12 +-- NAMESPACE | 31 ++++---- R/pdi.R | 164 ++++++++++++++++++++++++++++++++++++++++++++++ R/utils.R | 164 ++++++++++++++++++++++++++-------------------- man/mcca-package.Rd | 8 +- man/pdi_var.Rd |only man/print.mcca.pdi.var.Rd |only 8 files changed, 305 insertions(+), 100 deletions(-)
Title: A Versatile Visualization Suite
Description: A visualization suite primarily designed for single-cell
RNA-sequencing data analysis applications but well-suited for
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, alluvial and volcano plots)
for ease of usage and flexibility.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between henna versions 0.3.4 dated 2025-10-19 and 0.7.5 dated 2026-02-17
henna-0.3.4/henna/man/figures |only henna-0.7.5/henna/DESCRIPTION | 20 ++- henna-0.7.5/henna/MD5 | 96 +++++++++++------- henna-0.7.5/henna/NAMESPACE | 9 + henna-0.7.5/henna/NEWS | 9 + henna-0.7.5/henna/R/class_plot.R | 36 +++--- henna-0.7.5/henna/R/density_plot.R | 107 ++++++++++---------- henna-0.7.5/henna/R/documentation.R |only henna-0.7.5/henna/R/geometry.R | 5 henna-0.7.5/henna/R/hull_plot.R | 44 +++++--- henna-0.7.5/henna/R/label_points.R |only henna-0.7.5/henna/R/network_plot.R | 72 +++++++++---- henna-0.7.5/henna/R/palettes.R | 71 ++++++++++--- henna-0.7.5/henna/R/radial_plot.R | 21 +--- henna-0.7.5/henna/R/rank_plot.R | 31 +++--- henna-0.7.5/henna/R/river_plot.R | 15 -- henna-0.7.5/henna/R/tile_plot.R | 65 ++++++++---- henna-0.7.5/henna/R/utils.R | 38 ------- henna-0.7.5/henna/R/volcano_plot.R |only henna-0.7.5/henna/README.md | 129 ++++++++++++++----------- henna-0.7.5/henna/inst |only henna-0.7.5/henna/man/classPlot.Rd | 41 +++++-- henna-0.7.5/henna/man/connectedComponents.Rd | 5 henna-0.7.5/henna/man/correlationPlot.Rd | 9 - henna-0.7.5/henna/man/createLabelDFTemplate.Rd |only henna-0.7.5/henna/man/densityPlot.Rd | 71 ++++++++++--- henna-0.7.5/henna/man/documentFun.Rd |only henna-0.7.5/henna/man/dpColors.Rd | 10 + henna-0.7.5/henna/man/hullPlot.Rd | 49 +++++++-- henna-0.7.5/henna/man/labelPoints.Rd | 48 ++++++++- henna-0.7.5/henna/man/networkPlot.Rd | 30 +++-- henna-0.7.5/henna/man/networkPlotDF.Rd | 5 henna-0.7.5/henna/man/radialPlot.Rd | 11 -- henna-0.7.5/henna/man/rankPlot.Rd | 22 +++- henna-0.7.5/henna/man/reorderDF.Rd |only henna-0.7.5/henna/man/riverPlot.Rd | 13 +- henna-0.7.5/henna/man/tilePlot.Rd | 43 +++++--- henna-0.7.5/henna/man/volcanoPlot.Rd |only henna-0.7.5/henna/tests/testthat/test-henna.R | 38 ++++++- 39 files changed, 732 insertions(+), 431 deletions(-)
Title: Plot Columns of Two Matrices Against Each Other Using 'ggplot2'
Description: A quick and easy way of plotting the columns of two matrices or
data frames against each other using 'ggplot2'. Although 'ggmatplot' doesn't
provide the same flexibility as 'ggplot2', it can be used as a workaround for
having to wrangle wide format data into long format for plotting with
'ggplot2'.
Author: Xuan Liang [aut, cre] ,
Francis K. C. Hui [aut] ,
Emi Tanaka [aut] ,
Dilinie Seimon [aut]
Maintainer: Xuan Liang <xuan.liang@anu.edu.au>
Diff between ggmatplot versions 0.1.2 dated 2022-05-16 and 0.1.2.1 dated 2026-02-17
DESCRIPTION | 15 - MD5 | 12 build/vignette.rds |binary inst/doc/ggmatplot.R | 2 inst/doc/ggmatplot.Rmd | 2 inst/doc/ggmatplot.html | 628 +++++++++++++++++++++++++++++++++--------------- vignettes/ggmatplot.Rmd | 2 7 files changed, 459 insertions(+), 202 deletions(-)
Title: The R Package Ada for Stochastic Boosting
Description: Performs discrete, real, and gentle boost under both exponential and
logistic loss on a given data set. The package ada provides a straightforward,
well-documented, and broad boosting routine for classification, ideally suited
for small to moderate-sized data sets.
Author: Mark Culp [aut, cre],
Kjell Johnson [aut],
George Michailidis [aut]
Maintainer: Mark Culp <mvculp@mail.wvu.edu>
Diff between ada versions 2.0-5 dated 2016-05-13 and 2.0-5.1 dated 2026-02-17
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 6 +++--- data/soldat.rda |binary man/ada.Rd | 2 +- 4 files changed, 21 insertions(+), 9 deletions(-)
Title: Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Description: Write 'YAML' front matter for R Markdown and related
documents. Work with 'YAML' objects more naturally and write the
resulting 'YAML' to your clipboard or to 'YAML' files related to your
project.
Author: Malcolm Barrett [aut, cre] ,
Richard Iannone [aut] ,
RStudio [cph, fnd]
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>
Diff between ymlthis versions 0.1.7 dated 2022-08-05 and 1.0.0 dated 2026-02-17
DESCRIPTION | 13 MD5 | 102 ++-- NEWS.md | 19 R/markdownr.R | 6 R/use_yml.R | 4 R/yml.R | 2 R/yml_blogdown.R | 12 R/yml_bookdown.R | 4 R/yml_params.R | 4 R/yml_rmarkdown.R | 4 R/yml_rsconnect.R | 4 README.md | 13 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/introduction-to-ymlthis.R | 4 inst/doc/introduction-to-ymlthis.Rmd | 6 inst/doc/introduction-to-ymlthis.html | 709 ++++++++++++++++------------------ inst/doc/yaml-fieldguide.R | 4 inst/doc/yaml-fieldguide.html | 10 inst/doc/yaml-overview.R | 10 inst/doc/yaml-overview.html | 191 ++++----- man/asis_yaml_output.Rd | 2 man/bib2yml.Rd | 2 man/draw_yml_tree.Rd | 2 man/gitbook_config.Rd | 2 man/has_field.Rd | 2 man/read_json.Rd | 2 man/use_file_yml.Rd | 6 man/use_yml_defaults.Rd | 2 man/yml_author.Rd | 2 man/yml_blogdown_opts.Rd | 12 man/yml_bookdown_opts.Rd | 4 man/yml_citations.Rd | 2 man/yml_clean.Rd | 2 man/yml_distill_opts.Rd | 2 man/yml_latex_opts.Rd | 2 man/yml_output.Rd | 2 man/yml_pagedown_opts.Rd | 2 man/yml_params.Rd | 12 man/yml_pkgdown.Rd | 2 man/yml_reference.Rd | 2 man/yml_replace.Rd | 4 man/yml_resource_files.Rd | 2 man/yml_rsconnect_email.Rd | 4 man/yml_rticles_opts.Rd | 2 man/yml_runtime.Rd | 4 man/yml_site_opts.Rd | 4 man/yml_toc.Rd | 2 man/yml_vignette.Rd | 2 tests/testthat/_snaps/markdownr.md | 28 + tests/testthat/test-markdownr.R | 14 vignettes/introduction-to-ymlthis.Rmd | 6 52 files changed, 663 insertions(+), 597 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 1.7.2 dated 2025-11-24 and 1.7.3 dated 2026-02-17
DESCRIPTION | 8 LICENSE | 4 MD5 | 148 NAMESPACE | 60 NEWS.md | 386 R/artifact_registry.R | 898 R/cache.R | 244 R/download.R | 102 R/file_utilities.R | 760 R/model_deps.R | 190 R/predict_values.R | 650 R/seed_example_helpers.R | 96 R/writeAlizer.R | 102 README.md | 383 build/vignette.rds |binary inst/CITATION | 26 inst/WORDLIST | 114 inst/doc/scoring-model-development.Rmd | 8402 +- inst/doc/scoring-model-development.html |69730 +++++++++++----------- inst/doc/writealizer-getting-started.R | 16 inst/doc/writealizer-getting-started.Rmd | 762 inst/doc/writealizer-getting-started.html | 2082 inst/extdata/sample_coh.csv | 8 inst/extdata/sample_gamet.csv | 8 inst/extdata/sample_rb.csv | 8 inst/metadata/artifacts.csv | 102 man/import_coh.Rd | 66 man/import_gamet.Rd | 66 man/import_merge_gamet_rb.Rd | 82 man/import_rb.Rd | 74 man/model_deps.Rd | 92 man/predict_quality.Rd | 172 man/preprocess.Rd | 86 man/wa_cache_clear.Rd | 72 man/wa_cache_dir.Rd | 68 man/wa_download.Rd | 112 man/wa_seed_example_models.Rd | 82 man/writeAlizer-package.Rd | 144 tests/testthat.R | 24 tests/testthat/helper-network.R | 136 tests/testthat/helper-quiet.R | 16 tests/testthat/helper-sample-paths.R | 72 tests/testthat/helper-urls.R | 20 tests/testthat/setup-cache.R | 10 tests/testthat/setup-reset-options.R | 6 tests/testthat/test-artifact-registry-downloads.R | 192 tests/testthat/test-artifact-registry-paths.R | 56 tests/testthat/test-artifact-registry-registry.R | 278 tests/testthat/test-artifact-registry.R | 540 tests/testthat/test-cache-api-more.R | 168 tests/testthat/test-cache-api-preview.R | 152 tests/testthat/test-cache-api.R | 196 tests/testthat/test-cache-checksum.R | 30 tests/testthat/test-cache-minor.R | 12 tests/testthat/test-download-snapshots.R | 20 tests/testthat/test-download.R | 212 tests/testthat/test-file-utilities-branches.R | 218 tests/testthat/test-file-utilities-files.R | 202 tests/testthat/test-file-utilities-more.R | 202 tests/testthat/test-file-utilities.R | 88 tests/testthat/test-helper-urls.R | 22 tests/testthat/test-import-rb-namebased.R | 64 tests/testthat/test-import-validation.R | 96 tests/testthat/test-integration-predict_quality.R | 496 tests/testthat/test-keep_stem_before_txt.R | 66 tests/testthat/test-model-deps.R | 244 tests/testthat/test-predict-values-input.R | 64 tests/testthat/test-predict-values-negative.R | 176 tests/testthat/test-preprocess-and-download.R | 326 tests/testthat/test-smoke-basic.R | 42 tests/testthat/test-smoke-rb_mod3all-mocked.R | 92 vignettes/apa.csl | 4266 - vignettes/references.bib | 150 vignettes/scoring-model-development.Rmd | 8402 +- vignettes/writealizer-getting-started.Rmd | 762 75 files changed, 52265 insertions(+), 52258 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.8 dated 2026-01-13 and 0.8.9 dated 2026-02-17
DESCRIPTION | 6 ++--- MD5 | 8 +++---- NEWS.md | 3 ++ src/populate.cpp | 34 ++++++++++++++++++++++++++++++++- tests/testthat/test_populate.R | 42 +++++++++++++++++++++++++++++++++++++++++ 5 files changed, 85 insertions(+), 8 deletions(-)
Title: Functions to Calculate Optimal Fourth Down Decisions in the
National Football League
Description: A set of functions to estimate outcomes of fourth down plays
in the National Football League and obtain fourth down plays from
<https://www.nfl.com/> and <https://www.espn.com/>.
Author: Ben Baldwin [aut, cre, cph],
Sebastian Carl [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>
Diff between nfl4th versions 1.0.5 dated 2026-02-10 and 1.0.6 dated 2026-02-17
DESCRIPTION | 6 ++--- MD5 | 6 ++--- NEWS.md | 6 +++++ R/cache.R | 69 ++++++++++++++++++++++++++++++++++++++++++++++-------------- 4 files changed, 66 insertions(+), 21 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.9.4 dated 2026-02-04 and 0.9.5 dated 2026-02-17
DESCRIPTION | 10 +-- MD5 | 46 ++++++++++------- NAMESPACE | 4 + NEWS.md | 27 ++++++++++ R/default.R | 2 R/dsvg.R | 21 +------- R/element_interactive.R | 5 + R/fonts.R | 64 ++++++------------------ R/girafe.R | 25 +++++++++ R/girafe_class.R |only R/girafe_options.R | 20 ++++++- R/guide_interactive.R | 3 + inst/examples/shiny/css_class |only inst/examples/shiny/linked_scale |only inst/htmlwidgets/girafe.js | 2 inst/tinytest/test-dsvg_text.R | 2 man/dsvg.Rd | 21 +------- man/girafe.Rd | 24 ++++++--- man/girafe_class.Rd |only man/guide_bins_interactive.Rd | 102 ++++++++++++++++++--------------------- man/opts_hover.Rd | 10 +++ man/opts_selection.Rd | 6 +- man/validated_fonts.Rd | 21 +++----- 23 files changed, 229 insertions(+), 186 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.46 dated 2026-01-08 and 4.48 dated 2026-02-17
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 27 ++++++++++++++++++++++++++- R/cleanCoords.R | 6 +++--- R/getRegion.R | 5 ++--- inst/CITATION | 39 ++++++++++++++++++++++++++++----------- man/cleanCoords.Rd | 2 +- man/fuzzySim-package.Rd | 4 ++-- man/getRegion.Rd | 2 +- man/timer.Rd | 4 ++-- 10 files changed, 78 insertions(+), 37 deletions(-)
Title: Extract-Transform-Load Framework for Medium Data
Description: A predictable and pipeable framework for performing ETL
(extract-transform-load) operations on publicly-accessible medium-sized data
set. This package sets up the method structure and implements generic
functions. Packages that depend on this package download specific data sets
from the Internet, clean them up, and import them into a local or remote
relational database management system.
Author: Benjamin S. Baumer [aut, cre] ,
Carson Sievert [ctb],
Natalia Iannucci [ctb]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between etl versions 0.4.2 dated 2025-07-24 and 0.4.3 dated 2026-02-17
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- NEWS.md | 4 +++ R/etl.R | 8 +++--- R/etl_transform.R | 2 + R/utils.R | 2 - README.md | 8 +++--- build/vignette.rds |binary inst/doc/extending_etl.html | 53 ++++++++++++++++++++++++-------------------- inst/doc/using_etl.Rmd | 2 - inst/doc/using_etl.html | 21 +++++++++-------- man/etl.Rd | 8 +++--- man/src_mysql_cnf.Rd | 4 +-- vignettes/using_etl.Rmd | 2 - 14 files changed, 80 insertions(+), 68 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut],
Sanford Weisberg [aut],
Brad Price [aut, cre],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb],
R Core Team [ctb]
Maintainer: Brad Price <brad.price@mail.wvu.edu>
Diff between effects versions 4.2-4 dated 2025-07-29 and 4.2-5 dated 2026-02-17
effects-4.2-4/effects/inst/doc/effects-hex.pdf |only effects-4.2-5/effects/DESCRIPTION | 24 +++++----- effects-4.2-5/effects/MD5 | 23 ++++----- effects-4.2-5/effects/NEWS | 6 ++ effects-4.2-5/effects/inst/doc/functions-supported-by-effects.pdf |binary effects-4.2-5/effects/inst/doc/partial-residuals.pdf |binary effects-4.2-5/effects/inst/doc/predictor-effects-gallery.Rnw | 2 effects-4.2-5/effects/inst/doc/predictor-effects-gallery.pdf |binary effects-4.2-5/effects/man/effCoef.Rd | 2 effects-4.2-5/effects/man/effSources.Rd | 4 - effects-4.2-5/effects/man/effect.Rd | 6 +- effects-4.2-5/effects/man/predictorEffects.Rd | 6 +- effects-4.2-5/effects/vignettes/predictor-effects-gallery.Rnw | 2 13 files changed, 39 insertions(+), 36 deletions(-)
Title: Tidying Methods for Mixed Models
Description: Convert fitted objects from various R mixed-model packages
into tidy data frames along the lines of the 'broom' package.
The package provides three
S3 generics for each model: tidy(), which summarizes a model's statistical findings such as
coefficients of a regression; augment(), which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance(), which
provides a one-row summary of model-level statistics.
Author: Ben Bolker [aut, cre] ,
David Robinson [aut],
Dieter Menne [ctb],
Jonah Gabry [ctb],
Paul Buerkner [ctb],
Christopher Hua [ctb],
William Petry [ctb] ,
Joshua Wiley [ctb] ,
Patrick Kennedy [ctb],
Eduard Szoecs [ctb] ,
Indrajeet Patil [ctb],
Vincent Are [...truncated...]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between broom.mixed versions 0.2.9.6 dated 2024-10-15 and 0.2.9.7 dated 2026-02-17
DESCRIPTION | 31 +++--- MD5 | 37 ++++---- NAMESPACE | 3 NEWS.md | 13 ++ R/TMB_tidiers.R | 14 +++ R/VarCorr_tidiers.R |only R/brms_tidiers.R | 6 - R/glmmTMB_tidiers.R | 16 +-- R/glmm_tidiers.R | 4 R/lme4_tidiers.R | 11 +- R/nlme_tidiers.R | 184 ++++++++++++++++++++-------------------- R/ordinal_tidiers.R | 2 R/rstanarm_tidiers.R | 9 + build/vignette.rds |binary inst/doc/broom_mixed_intro.html | 33 +++---- man/rstanarm_tidiers.Rd | 6 - man/tidy.VarCorr.lme.Rd |only tests/testthat/test-VarCorr.R |only tests/testthat/test-glmmTMB.R | 7 + tests/testthat/test-lme4.R | 46 +++++++--- tests/testthat/test-rstanarm.R | 16 +++ 21 files changed, 261 insertions(+), 177 deletions(-)
Title: Species Distribution Models as a Function of Biotic, Abiotic and
Movement Factors (BAM)
Description: Species Distribution Modeling (SDM) is a practical
methodology that aims to estimate the area of distribution of a
species. However, most of the work has focused on estimating static
expressions of the correlation between environmental variables. The
outputs of correlative species distribution models can be interpreted
as maps of the suitable environment for a species but not generally as
maps of its actual distribution. Soberón and Peterson (2005)
<doi:10.17161/bi.v2i0.4> presented the BAM scheme, a heuristic
framework that states that the occupied area of a species occurs on
sites that have been accessible through dispersal (M) and have both
favorable biotic (B) and abiotic conditions (A). The 'bamm' package
implements classes and functions to operate on each element of the BAM
and by using a cellular automata model where the occupied area of a
species at time t is estimated by the multiplication of three binary
matrices: one matrix represents movements (M), another abiotic - [...truncated...]
Author: Luis Osorio-Olvera [aut, cre] ,
Jorge Soberon [aut] ,
Rusby G. Contreras-Diaz [ctb]
Maintainer: Luis Osorio-Olvera <luismurao@gmail.com>
Diff between bamm versions 0.6.0 dated 2026-02-03 and 0.6.2 dated 2026-02-17
bamm-0.6.0/bamm/R/pol2pam.R |only bamm-0.6.0/bamm/inst/extdata/suam.rds |only bamm-0.6.0/bamm/inst/extdata/uicn.rds |only bamm-0.6.0/bamm/man/figures |only bamm-0.6.0/bamm/man/pol2pam.Rd |only bamm-0.6.0/bamm/src/sdm_sim.cpp |only bamm-0.6.2/bamm/DESCRIPTION | 24 bamm-0.6.2/bamm/MD5 | 86 bamm-0.6.2/bamm/NAMESPACE | 6 bamm-0.6.2/bamm/NEWS.md | 5 bamm-0.6.2/bamm/R/RcppExports.R | 4 bamm-0.6.2/bamm/R/adj_mat.R | 26 bamm-0.6.2/bamm/R/bam_classes.R | 64 bamm-0.6.2/bamm/R/bam_clusters.R | 21 bamm-0.6.2/bamm/R/bam_methods.R | 36 bamm-0.6.2/bamm/R/bam_sim.R | 5 bamm-0.6.2/bamm/R/community_sim.R | 8 bamm-0.6.2/bamm/R/csd_estimate.R | 12 bamm-0.6.2/bamm/R/csim2pam.R | 14 bamm-0.6.2/bamm/R/diversity_range_analysis.R | 15 bamm-0.6.2/bamm/R/model2sparse.R | 2 bamm-0.6.2/bamm/R/models2pam.R | 86 bamm-0.6.2/bamm/R/null_dispersion_field_distribution.R | 4 bamm-0.6.2/bamm/R/pam2richness.R | 2 bamm-0.6.2/bamm/R/sdm_sim.R | 211 bamm-0.6.2/bamm/R/sim2Animation.R | 207 bamm-0.6.2/bamm/R/sim2Raster.R | 17 bamm-0.6.2/bamm/build/partial.rdb |binary bamm-0.6.2/bamm/inst/WORDLIST | 12 bamm-0.6.2/bamm/inst/doc/bam.R | 5 bamm-0.6.2/bamm/inst/doc/bam.Rmd | 5 bamm-0.6.2/bamm/inst/doc/bam.html | 4076 ----------------- bamm-0.6.2/bamm/man/adj_mat.Rd | 27 bamm-0.6.2/bamm/man/bam_clusters.Rd | 5 bamm-0.6.2/bamm/man/community_sim.Rd | 9 bamm-0.6.2/bamm/man/csim2pam.Rd | 4 bamm-0.6.2/bamm/man/diversity_range_analysis.Rd | 4 bamm-0.6.2/bamm/man/g_area-class.Rd | 26 bamm-0.6.2/bamm/man/models2pam.Rd | 2 bamm-0.6.2/bamm/man/sdm_sim.Rd | 19 bamm-0.6.2/bamm/man/setA.Rd | 29 bamm-0.6.2/bamm/man/sim2Animation.Rd | 2 bamm-0.6.2/bamm/man/sim2Raster.Rd | 4 bamm-0.6.2/bamm/src/RcppExports.cpp | 21 bamm-0.6.2/bamm/tests/testthat/Rplots.pdf |binary bamm-0.6.2/bamm/tests/testthat/test-bam.R | 65 bamm-0.6.2/bamm/vignettes/bam.Rmd | 5 47 files changed, 450 insertions(+), 4725 deletions(-)
Title: R Bindings for 'Automerge' 'CRDT' Library
Description: Provides R bindings to the 'Automerge' Conflict-free
Replicated Data Type ('CRDT') library. 'Automerge' enables automatic
merging of concurrent changes without conflicts, making it ideal for
distributed systems, collaborative applications, and offline-first
architectures. The approach of local-first software was proposed in
Kleppmann, M., Wiggins, A., van Hardenberg, P., McGranaghan, M. (2019)
<doi:10.1145/3359591.3359737>. This package supports all 'Automerge'
data types (maps, lists, text, counters) and provides both low-level
and high-level synchronization protocols for seamless interoperability
with 'JavaScript' and other 'Automerge' implementations.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Authors of the dependency Rust crates [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between automerge versions 0.2.1 dated 2026-02-05 and 0.3.0 dated 2026-02-17
automerge-0.2.1/automerge/man/am_get_history.Rd |only automerge-0.2.1/automerge/man/am_sync_state_new.Rd |only automerge-0.2.1/automerge/tests/testthat/test-package.R |only automerge-0.3.0/automerge/DESCRIPTION | 8 automerge-0.3.0/automerge/MD5 | 214 +- automerge-0.3.0/automerge/NAMESPACE | 33 automerge-0.3.0/automerge/NEWS.md | 51 automerge-0.3.0/automerge/R/convenience.R | 1 automerge-0.3.0/automerge/R/cursors.R | 232 ++ automerge-0.3.0/automerge/R/document.R | 245 ++ automerge-0.3.0/automerge/R/methods.R | 3 automerge-0.3.0/automerge/R/objects.R | 169 + automerge-0.3.0/automerge/R/sync.R | 426 ++++ automerge-0.3.0/automerge/README.md | 2 automerge-0.3.0/automerge/configure | 2 automerge-0.3.0/automerge/configure.win | 2 automerge-0.3.0/automerge/inst/AUTHORS | 37 automerge-0.3.0/automerge/inst/doc/automerge.R | 163 + automerge-0.3.0/automerge/inst/doc/automerge.Rmd | 203 ++ automerge-0.3.0/automerge/inst/doc/automerge.html | 396 +++- automerge-0.3.0/automerge/inst/doc/crdt-concepts.R | 84 automerge-0.3.0/automerge/inst/doc/crdt-concepts.Rmd | 102 + automerge-0.3.0/automerge/inst/doc/crdt-concepts.html | 656 ++++--- automerge-0.3.0/automerge/inst/doc/cross-platform.R | 2 automerge-0.3.0/automerge/inst/doc/cross-platform.Rmd | 2 automerge-0.3.0/automerge/inst/doc/cross-platform.html | 2 automerge-0.3.0/automerge/inst/doc/quick-reference.R | 87 automerge-0.3.0/automerge/inst/doc/quick-reference.Rmd | 87 automerge-0.3.0/automerge/inst/doc/quick-reference.html | 149 + automerge-0.3.0/automerge/inst/doc/sync-protocol.R | 86 automerge-0.3.0/automerge/inst/doc/sync-protocol.Rmd | 102 - automerge-0.3.0/automerge/inst/doc/sync-protocol.html | 810 ++++---- automerge-0.3.0/automerge/man/am_apply_changes.Rd | 3 automerge-0.3.0/automerge/man/am_change_actor_id.Rd |only automerge-0.3.0/automerge/man/am_change_deps.Rd |only automerge-0.3.0/automerge/man/am_change_from_bytes.Rd |only automerge-0.3.0/automerge/man/am_change_hash.Rd |only automerge-0.3.0/automerge/man/am_change_message.Rd |only automerge-0.3.0/automerge/man/am_change_seq.Rd |only automerge-0.3.0/automerge/man/am_change_size.Rd |only automerge-0.3.0/automerge/man/am_change_time.Rd |only automerge-0.3.0/automerge/man/am_change_to_bytes.Rd |only automerge-0.3.0/automerge/man/am_clone.Rd |only automerge-0.3.0/automerge/man/am_commit_empty.Rd |only automerge-0.3.0/automerge/man/am_create.Rd | 1 automerge-0.3.0/automerge/man/am_cursor.Rd | 6 automerge-0.3.0/automerge/man/am_cursor_equal.Rd |only automerge-0.3.0/automerge/man/am_cursor_from_bytes.Rd |only automerge-0.3.0/automerge/man/am_cursor_from_string.Rd |only automerge-0.3.0/automerge/man/am_cursor_position.Rd | 6 automerge-0.3.0/automerge/man/am_cursor_to_bytes.Rd |only automerge-0.3.0/automerge/man/am_cursor_to_string.Rd |only automerge-0.3.0/automerge/man/am_equal.Rd |only automerge-0.3.0/automerge/man/am_fork.Rd | 15 automerge-0.3.0/automerge/man/am_get_actor.Rd | 1 automerge-0.3.0/automerge/man/am_get_actor_hex.Rd | 2 automerge-0.3.0/automerge/man/am_get_change_by_hash.Rd | 10 automerge-0.3.0/automerge/man/am_get_changes.Rd | 8 automerge-0.3.0/automerge/man/am_get_changes_added.Rd | 7 automerge-0.3.0/automerge/man/am_get_last_local_change.Rd | 6 automerge-0.3.0/automerge/man/am_get_missing_deps.Rd |only automerge-0.3.0/automerge/man/am_insert.Rd | 1 automerge-0.3.0/automerge/man/am_items.Rd |only automerge-0.3.0/automerge/man/am_list_get_all.Rd |only automerge-0.3.0/automerge/man/am_list_range.Rd |only automerge-0.3.0/automerge/man/am_load.Rd | 1 automerge-0.3.0/automerge/man/am_load_changes.Rd |only automerge-0.3.0/automerge/man/am_load_incremental.Rd |only automerge-0.3.0/automerge/man/am_map_get_all.Rd |only automerge-0.3.0/automerge/man/am_map_range.Rd |only automerge-0.3.0/automerge/man/am_mark_clear.Rd |only automerge-0.3.0/automerge/man/am_marks.Rd | 5 automerge-0.3.0/automerge/man/am_marks_at.Rd | 5 automerge-0.3.0/automerge/man/am_pending_ops.Rd |only automerge-0.3.0/automerge/man/am_put.Rd | 1 automerge-0.3.0/automerge/man/am_save.Rd | 1 automerge-0.3.0/automerge/man/am_save_incremental.Rd |only automerge-0.3.0/automerge/man/am_sync_decode.Rd | 4 automerge-0.3.0/automerge/man/am_sync_encode.Rd | 4 automerge-0.3.0/automerge/man/am_sync_state.Rd |only automerge-0.3.0/automerge/man/am_sync_state_decode.Rd |only automerge-0.3.0/automerge/man/am_sync_state_encode.Rd |only automerge-0.3.0/automerge/man/am_text_content.Rd | 1 automerge-0.3.0/automerge/man/am_text_splice.Rd | 1 automerge-0.3.0/automerge/man/am_text_update.Rd | 1 automerge-0.3.0/automerge/man/as.character.am_text.Rd | 1 automerge-0.3.0/automerge/man/as_automerge.Rd | 1 automerge-0.3.0/automerge/man/extract-am_object.Rd | 1 automerge-0.3.0/automerge/man/replace-am_object.Rd | 1 automerge-0.3.0/automerge/src/Makevars.in | 2 automerge-0.3.0/automerge/src/Makevars.win.in | 2 automerge-0.3.0/automerge/src/automerge.h | 67 automerge-0.3.0/automerge/src/automerge/rust/Cargo.lock | 155 - 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automerge-0.3.0/automerge/tests/testthat/test-errors.R | 11 automerge-0.3.0/automerge/tests/testthat/test-marks.R | 495 +++++ automerge-0.3.0/automerge/tests/testthat/test-methods.R | 2 automerge-0.3.0/automerge/tests/testthat/test-objects.R | 923 ++++++++++ automerge-0.3.0/automerge/tests/testthat/test-sync.R | 498 +++++ automerge-0.3.0/automerge/tools/patch-rust-msrv.sh | 54 automerge-0.3.0/automerge/tools/patch-sources.sh | 102 - automerge-0.3.0/automerge/tools/vendor-deps.sh | 21 automerge-0.3.0/automerge/vignettes/automerge.Rmd | 203 ++ automerge-0.3.0/automerge/vignettes/crdt-concepts.Rmd | 102 + automerge-0.3.0/automerge/vignettes/cross-platform.Rmd | 2 automerge-0.3.0/automerge/vignettes/quick-reference.Rmd | 87 automerge-0.3.0/automerge/vignettes/sync-protocol.Rmd | 102 - 126 files changed, 8061 insertions(+), 1512 deletions(-)