Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.9.8.7 dated 2026-04-25 and 1.9.9.1 dated 2026-09-10
DESCRIPTION | 10 ++-- MD5 | 16 ++++--- inst/NEWS.Rd | 6 ++ inst/doc/haplostats.R | 14 +++--- inst/doc/haplostats.Rmd | 53 +++++++++++++----------- inst/doc/haplostats.html | 88 ++++++++++++++++++++--------------------- tests/testthat/cchladf.rds |only tests/testthat/cctestdf.rds |only tests/testthat/test.haplo.cc.R | 37 ++++++++++------- vignettes/haplostats.Rmd | 53 +++++++++++++----------- 10 files changed, 150 insertions(+), 127 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgleish [aut, cre] ,
Yonghong Wang [aut],
Jack Zhu [aut],
Paul Meltzer [aut, sad]
Maintainer: James Dalgleish <jamesdalg@gmail.com>
Diff between CNVScope versions 3.7.6 dated 2026-07-04 and 3.7.7 dated 2026-09-10
DESCRIPTION | 8 +++--- MD5 | 36 ++++++++++++++-------------- NEWS.md | 16 ++++++++++++ R/CNVScopeserver.R | 2 - R/calcCNVKernelProbDist.R | 2 - R/downsample_genomic_matrix.R | 11 +++----- R/formSampleMatrixFromRawGDCData.R | 5 +++ R/getBlockAverageMatrixFromBreakpoints.R | 2 - R/getInterchromosomalInteractivePlot.R | 2 - R/importBreakpointBed.R | 2 - R/rebinGenomicInteractions.R | 2 - man/CNVScopeserver.Rd | 3 ++ man/calcCNVKernelProbDist.Rd | 9 +++++++ man/downsample_genomic_matrix.Rd | 3 ++ man/formSampleMatrixFromRawGDCData.Rd | 22 +++++++++++++++++ man/getBlockAverageMatrixFromBreakpoints.Rd | 10 +++++++ man/getInterchromosomalInteractivePlot.Rd | 3 ++ man/importBreakpointBed.Rd | 3 ++ man/rebinGenomicInteractions.Rd | 11 ++++++++ 19 files changed, 116 insertions(+), 36 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matthew Heaton [ctb] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.13.0 dated 2026-06-10 and 0.14.0 dated 2026-09-10
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spmodel-0.14.0/spmodel/inst/doc/introduction.html | 189 spmodel-0.14.0/spmodel/inst/references.bib | 529 - spmodel-0.14.0/spmodel/man/anova.spmodel.Rd | 25 spmodel-0.14.0/spmodel/man/augment.spmodel.Rd | 24 spmodel-0.14.0/spmodel/man/conditional.Rd |only spmodel-0.14.0/spmodel/man/confint.spmodel.Rd | 6 spmodel-0.14.0/spmodel/man/decorrelate.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_data.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_grid.Rd |only spmodel-0.14.0/spmodel/man/decorrelate_newdata.Rd |only spmodel-0.14.0/spmodel/man/eacf.Rd | 6 spmodel-0.14.0/spmodel/man/esv.Rd | 6 spmodel-0.14.0/spmodel/man/kcv.Rd |only spmodel-0.14.0/spmodel/man/lake.Rd | 3 spmodel-0.14.0/spmodel/man/loocv.Rd | 51 spmodel-0.14.0/spmodel/man/moss.Rd | 4 spmodel-0.14.0/spmodel/man/plot.spmodel.Rd | 2 spmodel-0.14.0/spmodel/man/predict.spmodel.Rd | 103 spmodel-0.14.0/spmodel/man/print.spmodel.Rd | 40 spmodel-0.14.0/spmodel/man/recorrelate_newdata.Rd |only spmodel-0.14.0/spmodel/man/satterthwaite.Rd |only spmodel-0.14.0/spmodel/man/seal.Rd | 3 spmodel-0.14.0/spmodel/man/spautor.Rd | 12 spmodel-0.14.0/spmodel/man/spautorRF.Rd | 3 spmodel-0.14.0/spmodel/man/spcov_initial.Rd | 2 spmodel-0.14.0/spmodel/man/spglm.Rd | 2 spmodel-0.14.0/spmodel/man/splm.Rd | 14 spmodel-0.14.0/spmodel/man/splmRF.Rd | 6 spmodel-0.14.0/spmodel/man/spmodel-package.Rd | 7 spmodel-0.14.0/spmodel/man/sprnorm.Rd | 8 spmodel-0.14.0/spmodel/man/summary.spmodel.Rd | 18 spmodel-0.14.0/spmodel/man/texas.Rd | 3 spmodel-0.14.0/spmodel/man/varcomp.Rd | 30 spmodel-0.14.0/spmodel/man/vcov.spmodel.Rd | 16 spmodel-0.14.0/spmodel/tests/testthat/_snaps |only spmodel-0.14.0/spmodel/tests/testthat/setup.R |only spmodel-0.14.0/spmodel/tests/testthat/test-conditional.R |only spmodel-0.14.0/spmodel/tests/testthat/test-cov-initial-search.R |only spmodel-0.14.0/spmodel/tests/testthat/test-decorrelate.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-block-predict.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-conditional.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-decorrelate.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-exact.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-kcv.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-offset.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-satterthwaite.R |only spmodel-0.14.0/spmodel/tests/testthat/test-extras-spautor.R | 1485 ++- spmodel-0.14.0/spmodel/tests/testthat/test-extras-spautorRF.R | 95 spmodel-0.14.0/spmodel/tests/testthat/test-extras-spgautor.R | 431 - spmodel-0.14.0/spmodel/tests/testthat/test-extras-spglm.R | 568 + spmodel-0.14.0/spmodel/tests/testthat/test-extras-splm.R | 2566 +++--- spmodel-0.14.0/spmodel/tests/testthat/test-extras-splmRF.R | 98 spmodel-0.14.0/spmodel/tests/testthat/test-extras.R | 3814 +++++----- spmodel-0.14.0/spmodel/tests/testthat/test-print.R |only spmodel-0.14.0/spmodel/tests/testthat/test-spautor.R | 64 spmodel-0.14.0/spmodel/tests/testthat/test-spgautor.R | 23 spmodel-0.14.0/spmodel/tests/testthat/test-spglm.R | 34 spmodel-0.14.0/spmodel/tests/testthat/test-splm.R | 78 spmodel-0.14.0/spmodel/tests/testthat/test-utils.R | 22 spmodel-0.14.0/spmodel/vignettes/introduction.Rmd | 29 314 files changed, 14783 insertions(+), 12274 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows
Description: Provides tools for implementing Retrieval-Augmented
Generation (RAG) workflows with Large Language Models (LLM). Includes
functions for document processing, text chunking, embedding
generation, storage management, and content retrieval. Supports
various document types and embedding providers ('Ollama', 'OpenAI'),
with 'DuckDB' as the default storage backend. Integrates with the
'ellmer' package to equip chat objects with retrieval capabilities.
Designed to offer both sensible defaults and customization options
with transparent access to intermediate outputs. For a review of
retrieval-augmented generation methods, see Gao et al. (2023)
"Retrieval-Augmented Generation for Large Language Models: A Survey"
<doi:10.48550/arXiv.2312.10997>.
Author: Tomasz Kalinowski [aut, cre],
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between ragnar versions 0.3.0 dated 2026-01-23 and 0.3.1 dated 2026-09-10
ragnar-0.3.0/ragnar/inst/python/_ragnartools/__pycache__ |only ragnar-0.3.1/ragnar/DESCRIPTION | 21 - ragnar-0.3.1/ragnar/MD5 | 75 ++-- ragnar-0.3.1/ragnar/NAMESPACE | 250 ++++++++------- ragnar-0.3.1/ragnar/NEWS.md | 23 + ragnar-0.3.1/ragnar/R/aaa-utils.R | 7 ragnar-0.3.1/ragnar/R/embed-vertex.R | 2 ragnar-0.3.1/ragnar/R/embed.R | 4 ragnar-0.3.1/ragnar/R/ingest.R | 7 ragnar-0.3.1/ragnar/R/legacy.R | 2 ragnar-0.3.1/ragnar/R/markdown-chunk.R | 2 ragnar-0.3.1/ragnar/R/markdown-document.R | 2 ragnar-0.3.1/ragnar/R/markdown-segment.R | 2 ragnar-0.3.1/ragnar/R/ragnar-package.R | 20 - ragnar-0.3.1/ragnar/R/retrieve.R | 10 ragnar-0.3.1/ragnar/R/store.R | 35 +- ragnar-0.3.1/ragnar/build/partial.rdb |binary ragnar-0.3.1/ragnar/build/vignette.rds |binary ragnar-0.3.1/ragnar/inst/python/_ragnartools/atlas.py | 29 - ragnar-0.3.1/ragnar/man/MarkdownDocument.Rd | 3 ragnar-0.3.1/ragnar/man/MarkdownDocumentChunks.Rd | 3 ragnar-0.3.1/ragnar/man/embed_ollama.Rd | 2 ragnar-0.3.1/ragnar/man/mcp_serve_store.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar-package.Rd | 1 ragnar-0.3.1/ragnar/man/ragnar_chunk.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar_find_links.Rd | 2 ragnar-0.3.1/ragnar/man/ragnar_retrieve.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_bm25.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_vss.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_retrieve_vss_and_bm25.Rd | 8 ragnar-0.3.1/ragnar/man/ragnar_store_atlas.Rd | 23 + ragnar-0.3.1/ragnar/tests/testthat/test-embed-gemini.R | 27 - ragnar-0.3.1/ragnar/tests/testthat/test-frame.R | 2 ragnar-0.3.1/ragnar/tests/testthat/test-ragnar-package.R |only ragnar-0.3.1/ragnar/tests/testthat/test-retrieve.R | 27 + ragnar-0.3.1/ragnar/tests/testthat/test-store-atlas.R |only ragnar-0.3.1/ragnar/tools/configure_deps.R | 16 37 files changed, 362 insertions(+), 271 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut] ,
Rafael H. M. Pereira [aut, cre] ,
Gabriel Garcia de Almeida [aut] ,
Lucas Mation [aut]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between enderecobr versions 0.5.0 dated 2026-01-10 and 0.6.0 dated 2026-09-10
DESCRIPTION | 38 LICENSE | 4 MD5 | 170 - NAMESPACE | 40 NEWS.md | 231 +- R/codigos.R | 78 R/correspondencia_campos.R | 168 - R/correspondencia_logradouro.R | 118 - R/enderecobr.R | 56 R/erro.R | 32 R/extendr-wrappers.R | 118 - R/mensagem.R | 16 R/padronizar_bairros.R | 66 R/padronizar_ceps.R | 284 +- R/padronizar_complementos.R | 65 R/padronizar_enderecos.R | 540 ++-- R/padronizar_estados.R | 100 R/padronizar_logradouros.R | 68 R/padronizar_logradouros_completos.R | 602 ++--- R/padronizar_municipios.R | 96 R/padronizar_numeros.R | 218 - R/padronizar_tipos_de_logradouro.R | 66 R/warning.R | 22 README.md | 324 +- build/vignette.rds |binary cleanup |only cleanup.win |only configure | 4 configure.win | 4 inst/doc/enderecobr.R | 388 +-- inst/doc/enderecobr.Rmd | 842 +++---- inst/doc/enderecobr.html | 1614 +++++++------- man/codigos_estados.Rd | 58 man/codigos_municipios.Rd | 58 man/correspondencia_campos.Rd | 114 man/correspondencia_logradouro.Rd | 86 man/enderecobr.Rd | 67 man/figures/logo.svg | 304 +- man/padronizar_bairros.Rd | 78 man/padronizar_ceps.Rd | 76 man/padronizar_complementos.Rd | 78 man/padronizar_enderecos.Rd | 210 - man/padronizar_estados.Rd | 98 man/padronizar_logradouros.Rd | 80 man/padronizar_logradouros_completos.Rd | 162 - man/padronizar_municipios.Rd | 102 man/padronizar_numeros.Rd | 90 man/padronizar_tipos_de_logradouro.Rd | 78 src/Makevars.in | 14 src/Makevars.win.in | 93 src/enderecobr-win.def | 4 src/entrypoint.c | 2 src/rust/Cargo.lock | 74 src/rust/Cargo.toml | 41 src/rust/README.md |only src/rust/document.c |only src/rust/document.rs |only src/rust/src/lib.rs | 589 ++--- src/rust/vendor.tar.xz |binary tests/testes_nao_automaticos/rust-bench.R | 130 - tests/testes_nao_automaticos/test-grandes_bases.R | 112 tests/testthat.R | 24 tests/testthat/_snaps/correspondencia_campos.md | 16 tests/testthat/_snaps/correspondencia_logradouro.md | 16 tests/testthat/_snaps/erro.md | 18 tests/testthat/_snaps/padronizar_ceps.md | 126 - tests/testthat/_snaps/padronizar_enderecos.md | 404 +-- tests/testthat/_snaps/padronizar_logradouros_completos.md | 166 - tests/testthat/_snaps/padronizar_numeros.md | 16 tests/testthat/_snaps/warning.md | 18 tests/testthat/helper-mensagens.R |only tests/testthat/test-correspondencia_campos.R | 104 tests/testthat/test-correspondencia_logradouro.R | 86 tests/testthat/test-erro.R | 24 tests/testthat/test-mensagem.R | 36 tests/testthat/test-padronizar_bairros.R | 38 tests/testthat/test-padronizar_ceps.R | 128 - tests/testthat/test-padronizar_complementos.R | 34 tests/testthat/test-padronizar_enderecos.R | 842 +++---- tests/testthat/test-padronizar_estados.R | 126 - tests/testthat/test-padronizar_logradouros.R | 34 tests/testthat/test-padronizar_logradouros_completos.R | 420 +-- tests/testthat/test-padronizar_municipios.R | 58 tests/testthat/test-padronizar_numeros.R | 280 +- tests/testthat/test-padronizar_tipos_de_logradouro.R | 610 ++--- tests/testthat/test-warning.R | 24 tools/config.R | 244 +- tools/msrv.R | 232 +- vignettes/enderecobr.Rmd | 842 +++---- 89 files changed, 7168 insertions(+), 6968 deletions(-)
Title: Assessment of Cluster Stability by Randomized Maps
Description: The reliability of clusters is estimated using random projections.
A set of stability measures is provided to assess the reliability of the clusters
discovered by a generic clustering algorithm.
The stability measures are taylored to high dimensional data (e.g. DNA microarray data)
(Valentini, G (2005), <doi:10.1093/bioinformatics/bti817>.
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between clusterv versions 1.1.1 dated 2025-05-14 and 1.1.2 dated 2026-09-10
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- build/vignette.rds |binary 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Surface Fire Spread Model
Description: Implements the surface fire spread model of Rothermel (1972)
<doi:10.2737/INT-RP-115> in R. Additional utilities support uncertainty
propagation, selection among standard fuel models, optimization of fuel
model parameters by genetic algorithms, and example datasets.
Author: Giorgio Vacchiano [aut, cre] ,
Davide Ascoli [ctb]
Maintainer: Giorgio Vacchiano <gvacchiano@gmail.com>
This is a re-admission after prior archival of version 1.2 dated 2014-11-10
Diff between Rothermel versions 1.2 dated 2014-11-10 and 1.4.1 dated 2026-09-10
DESCRIPTION | 35 +++++++++++++++++++++++++---------- MD5 | 26 ++++++++++++++------------ NAMESPACE | 7 ++++--- R/bestFM.R | 6 ++++-- R/gaRoth.R | 13 ++++++++----- R/ros.R | 5 +++-- R/rosunc.R | 28 +++++++++++++++------------- build |only inst/CITATION | 29 +++++++++++++++-------------- man/Rothermel-package.Rd | 17 +++++++---------- man/firexp.Rd | 4 ++-- man/gaRoth.Rd | 12 ++++++------ man/ros.Rd | 8 ++++++-- man/scenarios.Rd | 2 +- tests |only 15 files changed, 110 insertions(+), 82 deletions(-)
Title: Robust Marginal Bayesian Variable Selection for Gene-Environment
Interactions
Description: Recently, multiple marginal variable selection methods have been developed and shown to be effective in Gene-Environment interactions studies. We propose a novel marginal Bayesian variable selection method for Gene-Environment interactions studies. In particular, our marginal Bayesian method is robust to data contamination and outliers in the outcome variables. With the incorporation of spike-and-slab priors, we have implemented the Gibbs sampler based on Markov Chain Monte Carlo. The core algorithms of the package have been developed in 'C++'.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu0521@gmail.com>
Diff between marble versions 0.0.3 dated 2024-04-04 and 0.0.4 dated 2026-09-10
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector'
objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://web.archive.org/web/20250719184025/https://www.wim.uni-mannheim.de/schlather/publications/software> and <https://github.com/cran/RandomFields>.
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 2.0.10 dated 2026-02-26 and 2.2.0 dated 2026-09-10
geostatsp-2.0.10/geostatsp/R/grfConditional.R |only geostatsp-2.2.0/geostatsp/DESCRIPTION | 20 geostatsp-2.2.0/geostatsp/MD5 | 97 + geostatsp-2.2.0/geostatsp/NAMESPACE | 7 geostatsp-2.2.0/geostatsp/NEWS |only geostatsp-2.2.0/geostatsp/R/0gm.R | 51 - geostatsp-2.2.0/geostatsp/R/RFsimulate.R | 2 geostatsp-2.2.0/geostatsp/R/forInla.R | 20 geostatsp-2.2.0/geostatsp/R/glgm.R | 22 geostatsp-2.2.0/geostatsp/R/krige.R | 10 geostatsp-2.2.0/geostatsp/R/lgm.R | 5 geostatsp-2.2.0/geostatsp/R/lgm.Raster.R | 2 geostatsp-2.2.0/geostatsp/R/maternGmrfPrec.R | 1119 +++++++++++------------ geostatsp-2.2.0/geostatsp/R/onload.R | 1 geostatsp-2.2.0/geostatsp/R/profLlgm.R | 316 +++--- geostatsp-2.2.0/geostatsp/build/stage23.rdb |binary geostatsp-2.2.0/geostatsp/build/vignette.rds |binary geostatsp-2.2.0/geostatsp/inst/doc/glgm.R | 8 geostatsp-2.2.0/geostatsp/inst/doc/glgm.Rnw | 8 geostatsp-2.2.0/geostatsp/inst/doc/glgm.pdf |binary geostatsp-2.2.0/geostatsp/inst/doc/lgcp.R | 6 geostatsp-2.2.0/geostatsp/inst/doc/lgcp.Rnw | 6 geostatsp-2.2.0/geostatsp/inst/doc/lgcp.pdf |binary geostatsp-2.2.0/geostatsp/inst/extR/loaloaData.R | 4 geostatsp-2.2.0/geostatsp/man/RFsimulate.Rd | 14 geostatsp-2.2.0/geostatsp/man/excProb.Rd | 6 geostatsp-2.2.0/geostatsp/man/geostatData.Rd |only geostatsp-2.2.0/geostatsp/man/glgm.Rd | 16 geostatsp-2.2.0/geostatsp/man/inlaAvailable.Rd |only geostatsp-2.2.0/geostatsp/man/krige.Rd | 7 geostatsp-2.2.0/geostatsp/man/murder.Rd | 2 geostatsp-2.2.0/geostatsp/man/postExp.Rd | 6 geostatsp-2.2.0/geostatsp/man/simLgcp.Rd | 4 geostatsp-2.2.0/geostatsp/man/stackRasterList.Rd | 4 geostatsp-2.2.0/geostatsp/man/swissRainR.Rd | 2 geostatsp-2.2.0/geostatsp/src/geostatsp.h | 24 geostatsp-2.2.0/geostatsp/src/matern.c | 236 ---- geostatsp-2.2.0/geostatsp/src/maternPoint.c |only geostatsp-2.2.0/geostatsp/tests/RFsimulate.R | 14 geostatsp-2.2.0/geostatsp/tests/geostatData.R |only geostatsp-2.2.0/geostatsp/tests/krige.R | 4 geostatsp-2.2.0/geostatsp/tests/lgcp.R | 12 geostatsp-2.2.0/geostatsp/tests/lgm.R | 2 geostatsp-2.2.0/geostatsp/tests/lgmRaster.R | 2 geostatsp-2.2.0/geostatsp/tests/likfitLgm.R | 2 geostatsp-2.2.0/geostatsp/tests/matern.R | 2 geostatsp-2.2.0/geostatsp/tests/maternGmrfPrec.R | 10 geostatsp-2.2.0/geostatsp/tests/maternPoint.R |only geostatsp-2.2.0/geostatsp/tests/profLlgm.R | 14 geostatsp-2.2.0/geostatsp/tests/simLgcp.R | 18 geostatsp-2.2.0/geostatsp/vignettes/Makefile | 4 geostatsp-2.2.0/geostatsp/vignettes/glgm.Rnw | 8 geostatsp-2.2.0/geostatsp/vignettes/lgcp.Rnw | 6 53 files changed, 1036 insertions(+), 1087 deletions(-)
Title: Robust Bayesian Elastic Net
Description: As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in 'C++' and R.
Author: Xi Lu [aut, cre],
Cen Wu [aut]
Maintainer: Xi Lu <xilu0521@gmail.com>
Diff between Bayenet versions 0.3 dated 2025-03-19 and 0.4 dated 2026-09-10
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Latent Dirichlet Allocation Using 'tidyverse' Conventions
Description: Implements an algorithm for Latent Dirichlet
Allocation (LDA), Blei et al. (2003) <https://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf>,
using style conventions from the 'tidyverse',
Wickham et al. (2019)<doi:10.21105/joss.01686>,
and 'tidymodels', Kuhn et al.<https://tidymodels.github.io/model-implementation-principles/>.
Fitting is done via 'warpLDA', a Metropolis-Hastings sampler,
Chen et al. (2016) <doi:10.48550/arXiv.1510.08628>.
Also implements several novel features for LDA such as guided models and
transfer learning.
Author: Tommy Jones [aut, cre] ,
Brendan Knapp [ctb] ,
Barum Park [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between tidylda versions 0.1.0 dated 2026-08-28 and 0.1.1 dated 2026-09-10
tidylda-0.1.0/tidylda/src/Makevars |only tidylda-0.1.1/tidylda/DESCRIPTION | 6 ++-- tidylda-0.1.1/tidylda/MD5 | 16 ++++++------ tidylda-0.1.1/tidylda/NEWS.md | 11 ++++++++ tidylda-0.1.1/tidylda/cleanup |only tidylda-0.1.1/tidylda/configure |only tidylda-0.1.1/tidylda/inst/WORDLIST | 7 +++++ tidylda-0.1.1/tidylda/inst/doc/probabilistic-coherence.html | 4 +-- tidylda-0.1.1/tidylda/inst/doc/tLDA.html | 4 +-- tidylda-0.1.1/tidylda/inst/doc/tidylda-intro.html | 4 +-- tidylda-0.1.1/tidylda/src/Makevars.in |only 11 files changed, 36 insertions(+), 16 deletions(-)
Title: Prepare 'WEXTOR' Data
Description: Facilitate data preparation for data collected on 'WEXTOR' <https://wextor.eu>, created by Reips and Neuhaus (2002) <doi:10.3758/bf03195449>. Perform plausibility and other checks and make use of cool color palettes and themes for data visualization.
Author: Annika Tave Overlander [aut, cre] ,
Ulf-Dietrich Reips [ths, cph]
Maintainer: Annika Tave Overlander <annika-tave.overlander@uni.kn>
Diff between rextor versions 1.1.0 dated 2026-05-21 and 1.2.0 dated 2026-09-10
DESCRIPTION | 15 +++++++++------ MD5 | 25 ++++++++++++++++--------- NAMESPACE | 2 ++ NEWS.md | 13 ++++++++++++- R/BiFiX_data_raw.R | 2 +- R/fake_wextor_log.R |only R/read_WEXTOR.R | 18 ++++++++++++++++++ R/read_WEXTOR_log.R |only R/scale_rextor.R | 24 ++++++++++++++---------- R/tidy_WEXTOR_log.R |only README.md | 2 +- inst/extdata/fake_wextor_log.txt |only man/BiFiX_data_raw.Rd | 2 +- man/fake_wextor_log.Rd |only man/read_WEXTOR_log.Rd |only man/scale_rextor.Rd | 6 +++++- man/tidy_WEXTOR_log.Rd |only 17 files changed, 79 insertions(+), 30 deletions(-)
Title: Alocă Pe Ore Lecțiile Zilei
Description: Lecțiile prof/cls trebuie completate cu un câmp "ora", astfel ca
oricare două lecții prof/cls/ora să nu se suprapună într-o aceeași oră.
The prof/cls lessons must be completed with a "hour" field ('ora), so that
any two prof/cls/ora lessons do not overlap in the same hour.
<https://vlad.bazon.net/>.
Author: Vlad Bazon [aut, cre]
Maintainer: Vlad Bazon <vlad.bazon@gmail.com>
Diff between hours2lessons versions 0.1.5 dated 2026-09-05 and 1.0.0 dated 2026-09-10
hours2lessons-0.1.5/hours2lessons/R/on_tuples.R |only hours2lessons-0.1.5/hours2lessons/data/LSS.rda |only hours2lessons-0.1.5/hours2lessons/data/Tuplaje.rda |only hours2lessons-0.1.5/hours2lessons/man/LSS.Rd |only hours2lessons-0.1.5/hours2lessons/man/Tuplaje.Rd |only hours2lessons-0.1.5/hours2lessons/man/on_tuples.Rd |only hours2lessons-1.0.0/hours2lessons/DESCRIPTION | 8 hours2lessons-1.0.0/hours2lessons/MD5 | 41 +- hours2lessons-1.0.0/hours2lessons/NAMESPACE | 30 +- hours2lessons-1.0.0/hours2lessons/NEWS.md | 9 hours2lessons-1.0.0/hours2lessons/R/data.R | 28 + hours2lessons-1.0.0/hours2lessons/R/globals.R |only hours2lessons-1.0.0/hours2lessons/R/hlp.R | 4 hours2lessons-1.0.0/hours2lessons/R/long2matrix.R | 4 hours2lessons-1.0.0/hours2lessons/R/mount_hours.R | 82 ++--- hours2lessons-1.0.0/hours2lessons/build/vignette.rds |binary hours2lessons-1.0.0/hours2lessons/data/dayLessons.rda |only hours2lessons-1.0.0/hours2lessons/data/dayTuples.rda |only hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.R | 8 hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.Rmd | 36 +- hours2lessons-1.0.0/hours2lessons/inst/doc/orarul-zilei.html | 141 +++++----- hours2lessons-1.0.0/hours2lessons/man/dayLessons.Rd |only hours2lessons-1.0.0/hours2lessons/man/dayTuples.Rd |only hours2lessons-1.0.0/hours2lessons/man/hours2lessons-package.Rd | 5 hours2lessons-1.0.0/hours2lessons/man/long2matrix.Rd | 2 hours2lessons-1.0.0/hours2lessons/man/mount_hours.Rd | 19 - hours2lessons-1.0.0/hours2lessons/vignettes/orarul-zilei.Rmd | 36 +- 27 files changed, 242 insertions(+), 211 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.7.0 dated 2026-08-29 and 1.7.1 dated 2026-09-10
DESCRIPTION | 8 ++-- MD5 | 35 +++++++++++++------ NAMESPACE | 2 + NEWS.md | 6 +++ R/gtdd_get_yield_curve.R | 38 ++++++++++++++++++--- R/td_get.R | 17 +++++++++ R/td_get2.R |only R/td_get_current.R | 6 +-- README.md | 54 ++++++++++++++---------------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-retired.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/td_get.Rd | 7 +++ man/td_get2.Rd |only man/td_get_current.Rd | 2 - tests/testthat/test-importing-data.R | 27 +++++++++++++-- tests/testthat/test-td-get2.R |only 25 files changed, 149 insertions(+), 53 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546>, Doc2vec (Le & Mikolov, 2014) <doi:10.48550/arXiv.1405.4053> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.6.3 dated 2026-07-28 and 0.6.4 dated 2026-09-10
DESCRIPTION | 6 ++-- MD5 | 35 +++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 7 ++++ R/as.doc2vec.R | 10 +++--- R/as.word2vec.R |only R/utils.R | 40 +++++++++++++++++++++----- R/word2vec.R | 2 - man/as.textmodel_doc2vec.Rd | 6 ++-- man/as.textmodel_word2vec.Rd |only man/perplexity.Rd | 4 -- man/probability.Rd | 31 +++----------------- man/probability.textmodel_wordvector.Rd |only man/similarity.Rd | 29 +++---------------- man/similarity.textmodel_wordvector.Rd |only man/textmodel_word2vec.Rd | 2 - tests/testthat/test-as.doc2vec.R | 24 ++++++++++++++-- tests/testthat/test-as.word2vec.R |only tests/testthat/test-doc2vec.R | 2 - tests/testthat/test-utils.R | 48 ++++++++++++++++++++++++++------ tests/testthat/test-word2vec.R | 2 - 21 files changed, 149 insertions(+), 103 deletions(-)
Title: Optimal Stratification of Univariate Populations
Description: Determines Optimum Strata Boundaries (OSB) and Optimum Sample
Sizes (OSS) for univariate stratified sampling designs under Neyman
allocation. The stratification variable is described by a best-fitting
parametric distribution, selected automatically by AIC from a set of
continuous families (normal, log-normal, gamma, Weibull, exponential,
Cauchy, uniform, Pareto, triangular and right-triangular), and the
optimum boundaries are obtained by minimising the Neyman objective.
Version 2.0 keeps the original globally optimal Dynamic Programming (DP)
solver of Reddy and Khan (2020) as the default and adds two faster
derivative-free alternatives for interactive and large-scale use: a
multi-start 'COBYLA' solver and a two-phase 'global' solver that couples
'DIRECT-L' with 'COBYLA' refinement. It also provides cost-constrained
allocation with unequal per-stratum costs, a design-efficiency comparison
(compare_designs), two- and three-dimensional and interactive
visualisations, solution-quality di [...truncated...]
Author: Karuna G. Reddy [aut, cre],
M. G. M. Khan [aut]
Maintainer: Karuna G. Reddy <karuna.reddy@auckland.ac.nz>
Diff between stratifyR versions 1.0-5 dated 2026-06-23 and 2.0-1 dated 2026-09-10
stratifyR-1.0-5/stratifyR/R/mode.val.r |only stratifyR-1.0-5/stratifyR/README.md |only stratifyR-2.0-1/stratifyR/DESCRIPTION | 61 stratifyR-2.0-1/stratifyR/MD5 | 60 stratifyR-2.0-1/stratifyR/NAMESPACE | 53 stratifyR-2.0-1/stratifyR/NEWS.md | 71 stratifyR-2.0-1/stratifyR/R/app.R |only stratifyR-2.0-1/stratifyR/R/cobyla.optim.R |only stratifyR-2.0-1/stratifyR/R/compare_designs.R |only stratifyR-2.0-1/stratifyR/R/create.mat.R | 2 stratifyR-2.0-1/stratifyR/R/data.alloc.R | 25 stratifyR-2.0-1/stratifyR/R/data.optim.R | 23 stratifyR-2.0-1/stratifyR/R/data.root.R | 45 stratifyR-2.0-1/stratifyR/R/distr.alloc.R | 37 stratifyR-2.0-1/stratifyR/R/distr.optim.R | 23 stratifyR-2.0-1/stratifyR/R/distr.root.R | 28 stratifyR-2.0-1/stratifyR/R/fit_distribution.R |only stratifyR-2.0-1/stratifyR/R/mode.val.R |only stratifyR-2.0-1/stratifyR/R/plot.strata.R |only stratifyR-2.0-1/stratifyR/R/print.strata.R |only stratifyR-2.0-1/stratifyR/R/realloc.R | 10 stratifyR-2.0-1/stratifyR/R/strata.data.R | 699 +++- stratifyR-2.0-1/stratifyR/R/strata.distr.R | 519 ++- stratifyR-2.0-1/stratifyR/R/summary.strata.R | 14 stratifyR-2.0-1/stratifyR/build/vignette.rds |binary stratifyR-2.0-1/stratifyR/inst/app |only stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.R | 129 stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.Rmd | 325 ++ stratifyR-2.0-1/stratifyR/inst/doc/stratifyR-vignette.html | 1857 +++++++++++-- stratifyR-2.0-1/stratifyR/man/compare_designs.Rd |only stratifyR-2.0-1/stratifyR/man/plot.strata.Rd |only stratifyR-2.0-1/stratifyR/man/print.strata.Rd |only stratifyR-2.0-1/stratifyR/man/strata.data.Rd | 29 stratifyR-2.0-1/stratifyR/man/strata.distr.Rd | 31 stratifyR-2.0-1/stratifyR/man/stratifyRApp.Rd |only stratifyR-2.0-1/stratifyR/man/summary.strata.Rd | 11 stratifyR-2.0-1/stratifyR/vignettes/library.bib | 19 stratifyR-2.0-1/stratifyR/vignettes/stratifyR-vignette.Rmd | 325 ++ 38 files changed, 3422 insertions(+), 974 deletions(-)
Title: Covariate Selection Based on VIMP Permutation-Like Testing
Description: A statistical method for reducing the number of covariates in
an analysis by evaluating Variable Importance Measures (VIMPs) derived
from the Random Forest algorithm. It performs statistical tests on the
VIMPs and outputs whether the covariate is significant along with the
p-values.
Author: Tim Mueller [aut, cre],
Oktawia Miluch [aut],
Staburo GmbH [cph, fnd]
Maintainer: Tim Mueller <mueller@staburo.de>
Diff between shadowVIMP versions 1.0.2 dated 2025-06-19 and 1.0.3 dated 2026-09-10
shadowVIMP-1.0.2/shadowVIMP/vignettes/figure-html |only shadowVIMP-1.0.3/shadowVIMP/DESCRIPTION | 22 shadowVIMP-1.0.3/shadowVIMP/MD5 | 52 shadowVIMP-1.0.3/shadowVIMP/NEWS.md | 22 shadowVIMP-1.0.3/shadowVIMP/R/plot_vimps.R | 894 +++++----- shadowVIMP-1.0.3/shadowVIMP/R/print.shadow_vimp.R | 220 +- shadowVIMP-1.0.3/shadowVIMP/R/shadow_vimp.R | 776 ++++---- shadowVIMP-1.0.3/shadowVIMP/R/vim_perm_sim.R | 340 +-- shadowVIMP-1.0.3/shadowVIMP/README.md | 24 shadowVIMP-1.0.3/shadowVIMP/build/vignette.rds |binary shadowVIMP-1.0.3/shadowVIMP/inst/doc/shadowVIMP-vignette.Rmd | 754 ++++---- shadowVIMP-1.0.3/shadowVIMP/inst/doc/shadowVIMP-vignette.html | 85 shadowVIMP-1.0.3/shadowVIMP/man/figures/README-example_cont-1.png |binary shadowVIMP-1.0.3/shadowVIMP/man/print.shadow_vimp.Rd | 46 shadowVIMP-1.0.3/shadowVIMP/man/shadowVIMP-package.Rd | 66 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/helper.R | 74 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-add_test_results.R | 74 shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-plot_vimps.R | 298 +-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-print.shadow_vimp.R | 340 +-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-shadow_vimp.R | 390 ++-- shadowVIMP-1.0.3/shadowVIMP/tests/testthat/test-vim_perm_sim.R | 80 shadowVIMP-1.0.3/shadowVIMP/vignettes/shadowVIMP-vignette.Rmd | 754 ++++---- 22 files changed, 2643 insertions(+), 2668 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chenghua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 1.0.0 dated 2026-08-21 and 1.0.1 dated 2026-09-10
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/timeSeries.R | 11 ++++++----- man/sentopics_sentiment.Rd | 8 ++++---- tests/testthat/test-rJST-sentiment.R |only 6 files changed, 23 insertions(+), 16 deletions(-)
Title: Model Order Selection for Clustering
Description: Stability based methods for model order selection in clustering problems
(Valentini, G (2007), <doi:10.1093/bioinformatics/btl600>).
Using multiple perturbations of the data the stability of clustering solutions is assessed. Different
perturbations may be used: resampling techniques, random projections and noise injection. Stability measures
for the estimate of clustering solutions and statistical tests to assess their significance are provided.
Author: Giorgio Valentini [aut],
Jessica Gliozzo [cre]
Maintainer: Jessica Gliozzo <jessica.gliozzo@gmail.com>
Diff between mosclust versions 1.0.2 dated 2025-05-27 and 1.0.3 dated 2026-09-10
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Calculation of Comorbidity and Frailty Scores
Description: Computes comorbidity indices and combined frailty scores for multiple ICD coding systems, including ICD-10-CA, ICD-10-CM, and ICD-11. The package provides tools to preprocess episode data, map diagnosis codes to chronic categories, propagate conditions across episodes, and generate comorbidity and frailty measures. The methods implemented are original to this package and were developed by the authors for research applications; a manuscript describing the methodology is currently in preparation.
Author: Azadeh Bayani [aut, cre] ,
Jean Noel Nikiema [ctb],
Michele Bally [ctb]
Maintainer: Azadeh Bayani <azadeh.bayani@umontreal.ca>
Diff between LABTNSCPSS versions 1.0.3 dated 2026-09-05 and 1.0.4 dated 2026-09-10
DESCRIPTION | 9 +++++---- MD5 | 11 +++++++---- R/setup_package.R |only README.md | 43 +++++++++++++++++++++++++++++++------------ build |only inst/CITATION |only man/LABTNSCPSS-package.Rd | 1 + man/LABTNSCPSS.Rd | 2 ++ 8 files changed, 46 insertions(+), 20 deletions(-)
Title: Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov
Models
Description: Inference, goodness-of-fit tests, and predictions for continuous and discrete univariate Hidden Markov Models (HMM), including zero-inflated distributions. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Nasri et al (2020) <doi:10.1029/2019WR025122>.
Author: Bouchra R. Nasri [aut, cre, cph],
Mamadou Yamar Thioub [aut, cph],
Bruno N. Remillard [aut, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GenHMM1d versions 0.2.6 dated 2025-09-07 and 0.2.8 dated 2026-09-10
DESCRIPTION | 10 +-- MD5 | 26 ++++---- R/CDF.R | 39 ++++++------- R/CDF_est.R | 31 ++++++---- R/EstHMMGen.R | 161 +++++++++++++++++++++++++++++++------------------------ R/GofHMMGen.R | 4 + R/PDF.R | 29 ++++++--- R/PDF_unc.R | 43 +++++++++----- R/QUANTILE.R | 22 +++---- R/SimHMMGen.R | 37 +++++++----- R/alpha2theta.R | 46 +++++++++------ R/theta2alpha.R | 49 ++++++++++------ man/GofHMMGen.Rd | 4 + man/SimHMMGen.Rd | 5 - 14 files changed, 291 insertions(+), 215 deletions(-)
Title: A Genetic Algorithm for Learning Directed Acyclic Graphs
Description: Learns sparse large Directed Acyclic Graphs with a combination of a convex program and a tailored genetic algorithm.
Author: Magali Champion [aut, cre],
Victor Picheny [aut],
Matthieu Vignes [aut]
Maintainer: Magali Champion <magali.champion@u-paris.fr>
Diff between GADAG versions 0.99.0 dated 2017-04-11 and 0.99.1 dated 2026-09-10
GADAG-0.99.0/GADAG/src/registerDynamicSymbol.c |only GADAG-0.99.1/GADAG/DESCRIPTION | 27 GADAG-0.99.1/GADAG/MD5 | 48 - GADAG-0.99.1/GADAG/NAMESPACE | 42 - GADAG-0.99.1/GADAG/R/GADAG_Analyze.R | 609 +++++++++++----------- GADAG-0.99.1/GADAG/R/GADAG_CV.R |only GADAG-0.99.1/GADAG/R/GADAG_Run.R | 680 +++++++++++-------------- GADAG-0.99.1/GADAG/R/RcppExports.R | 14 GADAG-0.99.1/GADAG/R/chrom.R | 72 +- GADAG-0.99.1/GADAG/R/create.population.R | 70 +- GADAG-0.99.1/GADAG/R/crossover.R | 145 ++--- GADAG-0.99.1/GADAG/R/evaluation.R | 234 ++++---- GADAG-0.99.1/GADAG/R/fitness.R | 114 ++-- GADAG-0.99.1/GADAG/R/generateToyData.R | 256 ++++----- GADAG-0.99.1/GADAG/R/mutation.R | 115 ++-- GADAG-0.99.1/GADAG/R/selection.R | 111 ++-- GADAG-0.99.1/GADAG/R/toy_data.R |only GADAG-0.99.1/GADAG/build/partial.rdb |binary GADAG-0.99.1/GADAG/man/GADAG-package.Rd | 174 +++--- GADAG-0.99.1/GADAG/man/GADAG_Analyze.Rd | 203 +++---- GADAG-0.99.1/GADAG/man/GADAG_CV.Rd |only GADAG-0.99.1/GADAG/man/GADAG_Run.Rd | 265 +++++---- GADAG-0.99.1/GADAG/man/evaluation.Rd | 174 +++--- GADAG-0.99.1/GADAG/man/fitness.Rd | 120 ++-- GADAG-0.99.1/GADAG/man/generateToyData.Rd | 135 ++-- GADAG-0.99.1/GADAG/man/toy_data.Rd | 34 - GADAG-0.99.1/GADAG/src/RcppExports.cpp | 17 27 files changed, 1868 insertions(+), 1791 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'Typst', 'RTF',
'Microsoft Word', 'Microsoft PowerPoint', R 'Grid Graphics' and
'patchwork'. 'R Markdown', 'Quarto' and the package 'officer' can be
used to produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.10.0 dated 2026-07-07 and 0.10.1 dated 2026-09-10
DESCRIPTION | 8 MD5 | 31 +- NAMESPACE | 367 +++++++++++++++++--------------- NEWS.md | 23 ++ R/docx_str.R | 15 - R/html_str.R | 16 + R/pptx_str.R | 9 R/read_structure.R | 101 +++++++- R/rtf_str.R | 6 R/runs_as_functions.R | 15 - R/typst_str.R | 29 ++ R/xtable_to_flextable.R | 2 tests/testthat/test-cell_content.R | 6 tests/testthat/test-deterministic-css.R |only tests/testthat/test-footers.R | 2 tests/testthat/test-headers.R | 4 tests/testthat/test-typst.R | 43 +++ 17 files changed, 427 insertions(+), 250 deletions(-)
Title: Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver", symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Jeroen van Raak [aut] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.29 dated 2026-05-04 and 1.30 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 10 - NEWS.md | 4 R/partition.R | 259 ++++++++++++++++++++++++++++++++++++++------ inst/doc/liver-example.html | 14 +- man/partition.Rd | 31 +++-- 6 files changed, 268 insertions(+), 56 deletions(-)
Title: Machine Learning Immunogenicity and Vaccine Response Analysis
Description: Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Author: Ivan Tomic [aut, cre, cph] ,
Adriana Tomic [aut, ctb, cph, fnd] ,
Stephanie Hao [aut]
Maintainer: Ivan Tomic <info@ivantomic.com>
Diff between immunaut versions 1.0.2 dated 2025-04-09 and 1.0.3 dated 2026-09-10
DESCRIPTION | 24 +- MD5 | 27 +- NAMESPACE | 2 NEWS.md | 23 ++ R/functions.R | 465 ++++++++++++++++++++++++--------------------- R/immunaut.R | 119 +++++++---- R/utils.R | 308 +++++++++++++++++++---------- README.md | 416 ++++++++++++++++++++-------------------- man/auto_simon_ml.Rd | 98 ++++----- man/immunaut.Rd | 8 man/plot_clustered_tsne.Rd | 2 man/preProcessData.Rd | 34 ++- man/preProcessResample.Rd | 27 +- tests |only 14 files changed, 883 insertions(+), 670 deletions(-)
Title: Multivariate Random Forest with Compositional Responses
Description: Multivariate random forests with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, or the alpha-transformation of Tsagris, Preston and Wood (2011), <doi:10.48550/arXiv.1106.1451>, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalRF versions 1.6 dated 2026-02-28 and 1.7 dated 2026-09-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/alfa.comp.rf.R | 21 +++++++++++++++------ R/cv.alfacomprf.R | 6 +++--- man/CompositionalRF-package.Rd | 4 ++-- 5 files changed, 28 insertions(+), 19 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: R Interface to the 'DieHarder' RNG Test Suite
Description: The 'RDieHarder' package provides an R interface to
the 'DieHarder' suite of random number generators and tests that
was developed by Robert G. Brown and David Bauer, extending
earlier work by George Marsaglia and others. The 'DieHarder'
library code is included.
Author: Dirk Eddelbuettel [aut, cre] ,
Robert G Brown [aut],
David Bauer [aut],
DieHarder Contributors [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RDieHarder versions 0.2.7 dated 2025-03-26 and 0.2.8 dated 2026-09-10
ChangeLog | 32 ++++++++++++++++++++++++++++++++ DESCRIPTION | 11 ++++++----- MD5 | 22 +++++++++++----------- build/vignette.rds |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/RDieHarder.R | 3 +-- inst/doc/RDieHarder.Rnw | 18 +++++++++--------- inst/doc/RDieHarder.pdf |binary man/dieharder.Rd | 4 ++-- vignettes/RDieHarder.Rnw | 18 +++++++++--------- vignettes/RDieHarder.bib | 31 ++++++++++++++++++------------- 12 files changed, 98 insertions(+), 61 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Elin Waring [ctb],
Thomas J. Faulkenberry [rev],
Robert Garrett [rev [...truncated...]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 1.3.1 dated 2026-04-26 and 1.4.0 dated 2026-09-10
DESCRIPTION | 26 MD5 | 266 +-- NAMESPACE | 10 NEWS.md | 26 R/assign_labels.R | 362 ++-- R/center.R | 708 ++++---- R/contrs.R | 201 +- R/convert_na_to.R | 434 ++--- R/data.R | 42 R/data_addprefix.R | 148 - R/data_arrange.R | 308 +-- R/data_codebook.R | 1144 +++++++------- R/data_duplicated.R | 210 +- R/data_extract.R | 310 +-- R/data_group.R | 158 - R/data_partition.R | 326 ++-- R/data_peek.R | 304 +-- R/data_read.R | 10 R/data_relocate.R | 354 ++-- R/data_rescale.R | 718 ++++----- R/data_restoretype.R | 100 - R/data_reverse.R | 624 +++---- R/data_rotate.R | 206 +- R/data_seek.R | 380 ++-- R/data_select.R | 88 - R/data_separate.R | 876 +++++------ R/data_tabulate.R | 94 + R/data_to_long.R | 764 ++++----- R/data_to_wide.R | 946 +++++------ R/data_unique.R | 308 +-- R/data_unite.R | 238 +- R/data_xtabulate.R | 9 R/datawizard-package.R | 42 R/demean.R | 4 R/describe_distribution.R | 1640 ++++++++++---------- R/descriptives.R | 426 ++--- R/extract_column_names.R | 360 ++-- R/format.R | 214 +- R/labels_to_levels.R | 216 +- R/makepredictcall.R | 166 +- R/mean_sd.R | 192 +- R/means_by_group.R | 19 R/ranktransform.R | 404 ++--- R/remove_empty.R | 254 +-- R/replace_nan_inf.R | 126 - R/rescale_weights.R | 950 +++++------ R/row_count.R | 266 +-- R/row_means.R | 428 ++--- R/select_nse.R | 1516 +++++++++---------- R/slide.R | 210 +- R/smoothness.R | 270 +-- R/standardize.R | 874 +++++----- R/to_factor.R | 284 +-- R/to_numeric.R | 674 ++++---- R/unnormalize.R | 332 ++-- R/unstandardize.R | 686 ++++---- R/utils-cols.R | 188 +- R/utils_standardize_center.R | 1056 ++++++------- R/visualisation_recipe.R | 184 +- R/weighted_mean_median_sd_mad.R | 328 ++-- R/winsorize.R | 298 +-- build/partial.rdb |binary build/vignette.rds |binary man/assign_labels.Rd | 296 +-- man/categorize.Rd | 528 +++--- man/center.Rd | 400 ++--- man/coef_var.Rd | 186 +- man/coerce_to_numeric.Rd | 44 man/colnames.Rd | 100 - man/contr.deviation.Rd | 22 man/convert_na_to.Rd | 344 ++-- man/convert_to_na.Rd | 252 +-- man/data_arrange.Rd | 70 man/data_duplicated.Rd | 218 +- man/data_extract.Rd | 294 +-- man/data_merge.Rd | 412 ++--- man/data_partition.Rd | 168 +- man/data_peek.Rd | 210 +- man/data_prefix_suffix.Rd | 214 +- man/data_read.Rd | 6 man/data_relocate.Rd | 310 +-- man/data_replicate.Rd | 200 +- man/data_restoretype.Rd | 70 man/data_rotate.Rd | 136 - man/data_seek.Rd | 136 - man/data_separate.Rd | 454 ++--- man/data_tabulate.Rd | 10 man/data_unique.Rd | 214 +- man/data_unite.Rd | 232 +- man/datawizard-package.Rd | 103 - man/distribution_mode.Rd | 68 man/efc.Rd | 24 man/extract_column_names.Rd | 398 ++--- man/labels_to_levels.Rd | 240 +-- man/makepredictcall.dw_transformer.Rd | 106 - man/mean_sd.Rd | 98 - man/means_by_group.Rd | 4 man/nhanes_sample.Rd | 28 man/normalize.Rd | 10 man/ranktransform.Rd | 288 +-- man/recode_into.Rd | 252 +-- man/reexports.Rd | 2 man/replace_nan_inf.Rd | 64 man/rescale.Rd | 390 ++-- man/reverse.Rd | 300 +-- man/row_count.Rd | 274 +-- man/row_means.Rd | 336 ++-- man/rownames.Rd | 110 - man/skewness.Rd | 296 +-- man/slide.Rd | 288 +-- man/smoothness.Rd | 74 man/standardize.Rd | 584 +++---- man/standardize.default.Rd | 200 +- man/text_format.Rd | 162 +- man/to_factor.Rd | 268 +-- man/to_numeric.Rd | 290 +-- man/visualisation_recipe.Rd | 60 man/weighted_mean.Rd | 112 - man/winsorize.Rd | 196 +- tests/testthat/_snaps/data_read.md | 240 +-- tests/testthat/_snaps/data_summary.md | 134 - tests/testthat/_snaps/data_tabulate.md | 1990 ++++++++++++------------- tests/testthat/_snaps/data_to_factor.md | 168 +- tests/testthat/_snaps/describe_distribution.md | 276 +-- tests/testthat/_snaps/discovr.md |only tests/testthat/test-convert_to_na.R | 4 tests/testthat/test-data_match.R | 3 tests/testthat/test-data_modify.R | 4 tests/testthat/test-data_read.R | 8 tests/testthat/test-data_recode.R | 20 tests/testthat/test-data_tabulate.R | 208 ++ tests/testthat/test-data_to_factor.R | 2 tests/testthat/test-describe_distribution.R | 29 tests/testthat/test-discovr.R |only tests/testthat/test-standardize_models.R | 910 +++++------ 135 files changed, 19451 insertions(+), 19001 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 2.4.0 dated 2026-06-02 and 2.4.1 dated 2026-09-10
DESCRIPTION | 15 MD5 | 585 +- NAMESPACE | 1036 +-- NEWS.md | 24 R/AddTip.R | 550 +- R/ArtificialExtinction.R | 1 R/Cherries.R | 68 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/Consensus.R | 38 R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/DropTip.R | 4 R/EdgeRatio.R | 70 R/ImposeConstraint.R | 278 - R/Information.R | 1 R/KeptPaths.R | 94 R/KeptVerts.R | 2 R/LongBranchScore.R | 150 R/MatchNodes.R | 216 R/MatchStrings.R | 66 R/PathLengths.R | 96 R/PhyToString.R | 284 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 7 R/RcppExports.R | 4 R/ReadMrBayes.R | 190 R/ReadTntTree.R | 580 +- R/Reweight.R | 220 R/RoguePlot.R | 9 R/SplitFunctions.R | 912 +-- R/Splits.R | 1336 ++-- R/Stemwardness.R | 218 R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TotalCopheneticIndex.R | 1 R/TreeNumber.R | 1166 ++-- R/TreeTools-package.R | 3 R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/fastmatch.R |only R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/parse_files.R | 17 R/phylo.R | 3 R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_display.R | 292 - R/tree_generation.R | 1006 +-- R/tree_information.R | 206 R/tree_numbering.R | 62 R/tree_properties.R | 1 R/tree_rearrangement.R | 2 R/tree_shape.R | 572 +- R/tree_write.R | 262 R/zzz.R | 16 build/partial.rdb |binary build/vignette.rds |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 35 inst/REFERENCES.bib | 778 +- inst/WORDLIST | 204 inst/apa-old-doi-prefix.csl | 4546 ++++++++--------- 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/statelabels-semicolon.nex |only inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-amp-continuation.tnt | 20 inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-cp1252-taxa.tnt | 12 inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-midline-xread.tnt | 12 inst/extdata/tests/tnt-multiline-comment.tnt | 26 inst/extdata/tests/tnt-multiline-taxa.tnt | 26 inst/extdata/tests/tnt-multitaxon-line.tnt | 10 inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-smartquote-taxa.tnt | 24 inst/extdata/tests/tnt-taxon-taxonomy.tnt | 14 inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/extdata/tests/tnt-xgroup.tnt | 32 inst/include/TreeTools/root_tree.h | 24 man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 108 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 108 man/CladeSizes.Rd | 98 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 152 man/ConsensusWithout.Rd | 212 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 168 man/DescendantEdges.Rd | 164 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 126 man/EdgeDistances.Rd | 106 man/EdgeRatio.Rd | 92 man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 202 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 | 192 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 130 man/MRCA.Rd | 136 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 140 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 158 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 100 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 172 man/NTip.Rd | 140 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NexusTokensToInteger.Rd | 128 man/NodeDepth.Rd | 128 man/NodeNumbers.Rd | 116 man/NodeOrder.Rd | 110 man/PaintTree.Rd | 196 man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 118 man/PhyToString.Rd | 214 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 314 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 550 +- man/Reweight.Rd | 158 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 106 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 180 man/SplitInformation.Rd | 256 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 162 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 252 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 86 man/TreeNumber.Rd | 432 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 93 man/Treeness.Rd | 114 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 126 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 | 62 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports.cpp | 13 src/consensus.cpp | 123 src/renumber_tips.cpp | 98 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 | 2 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 | 18 tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-ImposeConstraint.R | 4 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 | 4 tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 15 tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Splits.R | 16 tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TotalCopheneticIndex.R | 2 tests/testthat/test-TreeNumber.R | 360 - 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 | 419 + tests/testthat/test-fastmatch.R |only tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 84 tests/testthat/test-int_to_tree.cpp.R | 130 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-parsers.R | 42 tests/testthat/test-phylo.R | 2 tests/testthat/test-root_tree.h.R | 34 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_information.R | 38 tests/testthat/test-tree_numbering.R | 40 tests/testthat/test-tree_properties.R | 2 tests/testthat/test-tree_rearrange.R | 22 tests/testthat/test-tree_shape.R | 2 tests/testthat/test-tree_write.R | 2 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 295 files changed, 23198 insertions(+), 22655 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Most synthesising methods available in the package synthesise from conditional distributions where variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Methods that are not sequential, but synthesise all variables at once, are 'sample', 'ipf', and 'catall'. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb],
Timon Huijser [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.9-2 dated 2025-07-12 and 1.9-3 dated 2026-09-10
synthpop-1.9-2/synthpop/man/syn.pmm.Rd |only synthpop-1.9-3/synthpop/DESCRIPTION | 20 synthpop-1.9-3/synthpop/MD5 | 83 - synthpop-1.9-3/synthpop/NAMESPACE | 1 synthpop-1.9-3/synthpop/NEWS | 1147 +++++++++++------------ synthpop-1.9-3/synthpop/R/IO.r | 4 synthpop-1.9-3/synthpop/R/disclosure.R | 959 +++++++++---------- synthpop-1.9-3/synthpop/R/functions.syn.r | 81 - synthpop-1.9-3/synthpop/R/methods.syn.r | 9 synthpop-1.9-3/synthpop/R/syn.r | 5 synthpop-1.9-3/synthpop/R/syn.strata.r | 43 synthpop-1.9-3/synthpop/R/zzz.r | 2 synthpop-1.9-3/synthpop/build/partial.rdb |binary synthpop-1.9-3/synthpop/build/vignette.rds |binary synthpop-1.9-3/synthpop/inst/doc/disclosure.R | 8 synthpop-1.9-3/synthpop/inst/doc/disclosure.Rnw | 990 ++++++++++--------- synthpop-1.9-3/synthpop/inst/doc/disclosure.pdf |binary synthpop-1.9-3/synthpop/inst/doc/inference.R | 2 synthpop-1.9-3/synthpop/inst/doc/inference.pdf |binary synthpop-1.9-3/synthpop/inst/doc/synthpop.R | 2 synthpop-1.9-3/synthpop/inst/doc/synthpop.Rnw | 6 synthpop-1.9-3/synthpop/inst/doc/synthpop.pdf |binary synthpop-1.9-3/synthpop/inst/doc/utility.R | 2 synthpop-1.9-3/synthpop/inst/doc/utility.Rnw | 4 synthpop-1.9-3/synthpop/inst/doc/utility.pdf |binary synthpop-1.9-3/synthpop/man/SD2011.Rd | 2 synthpop-1.9-3/synthpop/man/disclosure.Rd | 403 ++++---- synthpop-1.9-3/synthpop/man/multi.disclosure.Rd | 397 +++---- synthpop-1.9-3/synthpop/man/syn.Rd | 8 synthpop-1.9-3/synthpop/man/syn.smooth.Rd | 2 synthpop-1.9-3/synthpop/man/synthpop-package.Rd | 116 +- synthpop-1.9-3/synthpop/man/utility.gen.Rd | 500 +++++----- synthpop-1.9-3/synthpop/man/utility.tab.Rd | 444 ++++---- synthpop-1.9-3/synthpop/man/utility.tables.Rd | 448 ++++---- synthpop-1.9-3/synthpop/vignettes/disclosure.Rnw | 990 ++++++++++--------- synthpop-1.9-3/synthpop/vignettes/disclosure.bib | 727 +++++++------- synthpop-1.9-3/synthpop/vignettes/fig2dis.png |binary synthpop-1.9-3/synthpop/vignettes/fig3dis.png |binary synthpop-1.9-3/synthpop/vignettes/inference.bib | 2 synthpop-1.9-3/synthpop/vignettes/synthpop.Rnw | 6 synthpop-1.9-3/synthpop/vignettes/synthpop.bib | 729 +++++++------- synthpop-1.9-3/synthpop/vignettes/utility.Rnw | 4 synthpop-1.9-3/synthpop/vignettes/utility.bib | 240 ++-- 43 files changed, 4329 insertions(+), 4057 deletions(-)
Title: Univariate Kernel Density Estimation
Description: Provides an efficient implementation of univariate local polynomial
kernel density estimators that can handle bounded, discrete, and zero-inflated
data. See Geenens and Wang (2018) <doi:10.48550/arXiv.1602.04862>,
Geenens (2014) <doi:10.48550/arXiv.1303.4121>,
Nagler (2018a) <doi:10.48550/arXiv.1704.07457>,
Nagler (2018b) <doi:10.48550/arXiv.1705.05431>.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kde1d versions 1.1.1 dated 2025-06-12 and 1.2.0 dated 2026-09-10
.Rinstignore |only DESCRIPTION | 14 MD5 | 62 +- NEWS.md | 52 + R/RcppExports.R | 16 R/jitter.R | 2 R/kde1d-methods.R | 2 R/kde1d.R | 55 +- inst/include/kde1d-cpp |only inst/include/kde1d-wrappers.hpp | 53 - inst/include/kde1d.hpp | 2 inst/include/kde1d/dpik.hpp | 176 ------ inst/include/kde1d/interpolation.hpp | 279 ---------- inst/include/kde1d/kde1d.hpp | 928 ----------------------------------- inst/include/kde1d/kdefft.hpp | 98 --- inst/include/kde1d/stats.hpp | 229 -------- inst/include/kde1d/tools.hpp | 128 ---- inst/include/kde1d/version.hpp | 26 man/dkde1d.Rd | 4 man/equi_jitter.Rd | 2 man/kde1d-package.Rd | 1 man/kde1d.Rd | 55 +- src/Makevars | 2 src/Makevars.win | 3 src/RcppExports.cpp | 9 src/kde1d-interface.cpp | 19 tests/testthat/Rplots.pdf |binary tests/testthat/cpp |only tests/testthat/test_cpp_headers.R |only tests/testthat/test_kde1d.R | 100 +++ 30 files changed, 323 insertions(+), 1994 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports cross-sectional network models for ordinal, binary, continuous, and mixed data,
fitted using the packages 'bgms' (default), 'BDgraph', and 'BGGM',
as well as network comparison tests fitted using the packages 'bgms' and 'BGGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.4.0 dated 2026-04-02 and 0.5.0 dated 2026-09-10
DESCRIPTION | 26 - MD5 | 59 +- NEWS.md |only R/AuxiliaryFunctions.R | 506 +++++++++++++++++++--- R/bgm_plot_class.R | 48 +- R/easybgm.R | 597 +++++++++++++++++++------- R/easybgm_compare.R | 376 +++++++++++----- R/functions.bdgraph.R | 4 R/functions.bggm.R | 6 R/functions.bgms.R | 208 +++++++-- R/functions.bgmscompare.R | 415 ++++++------------ R/plottingfunctions.bgmCompare.R | 140 +----- R/plottingfunctions.bgms.R | 86 +-- R/plottingfunctions.easybgm.R | 59 +- R/summary.easybgm.R | 90 +++ R/summary.easybgm_compare.R | 9 README.md | 6 man/HDI.Rd | 4 man/centrality.Rd | 6 man/clusterBayesfactor.Rd | 46 +- man/complexity_probs.Rd | 6 man/easybgm.Rd | 396 ++++++++++++----- man/easybgm_compare.Rd | 213 ++++++--- man/edgeevidence.Rd | 6 man/network.Rd | 11 man/prior_sensitivity.Rd | 4 man/structure.Rd | 4 man/structure_probs.Rd | 6 tests/testthat.R | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-easybgm.R | 887 ++++++++++++++++++++++++++------------- 31 files changed, 2817 insertions(+), 1408 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.3.0 dated 2026-08-20 and 0.4.0 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 78 ++++++------- NEWS.md | 21 +++ R/MCMC_Fit.R | 51 ++++++++ R/NUTS.R | 54 ++++++++- R/RTMB_Model.R | 28 +++- R/RTMB_Model_impl_classic.R | 168 ++++++++++++++++++++++++++++- R/RTMB_Model_impl_optimize.R | 4 R/RTMB_Model_impl_sampling.R | 73 +++++++++++- R/mcmc_continue.R |only R/plot.R | 13 +- R/posterior_predict.R | 16 ++ R/upgrade_fit.R | 7 - R/wrapper_corr.R | 45 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/analysis_reference.html | 1 inst/doc/introduction.html | 1 inst/doc/ja-analysis_reference.html | 156 +++++++++++--------------- inst/doc/ja-introduction.html | 33 ++--- inst/doc/ja-quick_start.html | 45 +++---- inst/doc/ja-rtmb_glmer.html | 1 inst/doc/ja-rtmb_internals.html | 1 inst/doc/ja-wrapper_functions.R | 22 +-- inst/doc/ja-wrapper_functions.Rmd | 22 +-- inst/doc/ja-wrapper_functions.html | 45 +++---- inst/doc/ja-writing_models.html | 38 +++--- inst/doc/quick_start.html | 11 + inst/doc/rtmb_glmer.html | 1 inst/doc/rtmb_internals.html | 1 inst/doc/wrapper_functions.html | 3 inst/doc/writing_models.html | 1 man/MCMC_Fit.Rd | 66 +++++++++++ man/RTMB_Model-class.Rd | 6 - man/plot_mdu.Rd | 6 - tests/testthat/test-fixed-jacobian.R | 31 +++++ tests/testthat/test-mcmc-continuation.R |only tests/testthat/test-optimize-marginal-df.R | 70 ++++++++++++ tests/testthat/test-plot.R | 20 +++ tests/testthat/test-posterior-predict.R | 10 + vignettes/ja-wrapper_functions.Rmd | 22 +-- 41 files changed, 887 insertions(+), 290 deletions(-)
Title: Bayesian Prediction of Complex Computer Codes
Description: Performs Bayesian prediction of complex computer codes when fast approximations are available. It uses a hierarchical version of the Gaussian process, originally proposed by Kennedy and O'Hagan (2000), Biometrika 87(1):1.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between approximator versions 1.2-8 dated 2023-08-24 and 1.3-0 dated 2026-09-10
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 3 ++- R/approximator.R | 47 +++++++++++++++++++++-------------------------- build/vignette.rds |binary data/genie.rda |binary data/toyapps.rda |binary inst/apprex_1d.R | 4 ---- inst/doc/apprex.R | 2 -- inst/doc/apprex.pdf |binary inst/hpafun_1d.R | 1 - man/H.fun.Rd | 2 +- man/is.consistent.Rd | 2 +- man/mdash.fun.Rd | 6 +++--- man/tee.fun.Rd | 2 +- 15 files changed, 59 insertions(+), 61 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.18.1 dated 2026-09-01 and 0.18.2 dated 2026-09-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 12 ++++++++++++ R/check_heteroscedasticity.R | 2 +- R/check_singularity.R | 2 +- tests/testthat/test-check_heteroskedasticity.R | 21 +++++++++++++++++++++ tests/testthat/test-check_outliers.R | 3 ++- 7 files changed, 47 insertions(+), 13 deletions(-)
Title: Bayesian Analysis of Non-Stationary Gaussian Process Models
Description: Enables off-the-shelf functionality for fully Bayesian, nonstationary Gaussian process modeling. The approach to nonstationary modeling involves a closed-form, convolution-based covariance function with spatially-varying parameters; these parameter processes can be specified either deterministically (using covariates or basis functions) or stochastically (using approximate Gaussian processes). Stationary Gaussian processes are a special case of our methodology, and we furthermore implement approximate Gaussian process inference to account for very large spatial data sets (Finley, et al (2017) <doi:10.48550/arXiv.1702.00434>). Bayesian inference is carried out using Markov chain Monte Carlo methods via the "nimble" package, and posterior prediction for the Gaussian process at unobserved locations is provided as a post-processing step. Also provided are nearest-neighbor Gaussian process components for use directly in user-written model code, where the spatial process is retained as [...truncated...]
Author: Daniel Turek [aut, cre],
Mark Risser [aut],
Fabian Ketwaroo [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between BayesNSGP versions 0.3.0 dated 2026-08-19 and 0.3.1 dated 2026-09-10
DESCRIPTION | 13 ++++++++----- MD5 | 15 ++++++++++----- R/v03_NNGP_density.R | 13 ++++++++++--- R/v03_NNGP_neighbors.R | 14 ++++++++------ build/partial.rdb |binary man/NNGP.pred.Rd | 13 ++++++++++--- tests |only 7 files changed, 46 insertions(+), 22 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using Stan
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.2 dated 2026-08-31 and 1.0.3 dated 2026-09-10
DESCRIPTION | 6 - MD5 | 50 ++++---- NEWS.md | 7 + R/bayes_factor.R | 6 - R/extract_param.R | 26 ++-- R/helpers.R | 152 +++++++++++++++++++++++--- R/set_priors.R | 7 - R/sim_bvarnet.R | 14 +- R/to_stan_data.R | 2 inst/doc/MCMC-Diagnostics.Rmd | 2 inst/doc/MCMC-Diagnostics.html | 2 man/bvarnet-package.Rd | 2 man/extract_draws.Rd | 39 +++++- man/prior.Rd | 3 man/set_priors.Rd | 3 man/sim_var.Rd | 6 - src/stan/model_ordinal.stan | 7 - tests/testthat/helper-fixtures.R | 54 +++++++-- tests/testthat/helper-oracles.R |only tests/testthat/test-extract_param.R | 189 ++++++++++++++++++++++++++++++++- tests/testthat/test-helpers.R | 2 tests/testthat/test-input-validation.R | 11 + tests/testthat/test-prior-scaling.R | 2 tests/testthat/test-sim_bvarnet.R | 6 - tests/testthat/test-stan-likelihood.R |only vignettes/MCMC-Diagnostics.Rmd | 2 vignettes/MCMC-Diagnostics.Rmd.orig | 2 27 files changed, 491 insertions(+), 111 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a 'log' or a 'logit' transformation respectively.
Author: Mikis Stasinopoulos [aut, cre, cph] ,
Robert Rigby [aut] ,
Calliope Akantziliotou [ctb],
Vlasios Voudouris [ctb],
Gillian Heller [ctb] ,
Fernanda De Bastiani [ctb] ,
Raydonal Ospina [ctb] ,
Nicoletta Motpan [ctb],
Fiona McElduff [ctb],
Majid Djennad [...truncated...]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss.dist versions 6.1-1 dated 2023-08-23 and 6.1-11 dated 2026-09-10
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Title: Data Envelopment Analysis
Description: Nonparametric efficiency measurement by data envelopment analysis.
Provides radial (Charnes-Cooper-Rhodes and Banker-Charnes-Cooper) technical
efficiency under constant, variable, non-increasing and non-decreasing
returns to scale, the slacks-based measure of Tone (2001), the additive
model of Charnes and others (1985), and the directional distance function
of Chambers, Chung and Fare (1996), all through one interface and one
result object. Efficiency estimates are accompanied by peers, slacks,
returns-to-scale classification, scale efficiency and the optimal
multipliers, and by bias-corrected estimates and confidence intervals from
the smoothed homogeneous bootstrap of Simar and Wilson (1998). Where
prices are known, cost, revenue and Nerlovian profit efficiency separate
the technical component from the allocative one; where they are not,
cross-efficiency with the secondary goals of Doyle and Green (1994) ranks
units that a self-appraisal leaves tied. This package succeeds the
arch [...truncated...]
Author: David Bernstein [aut, cre] ,
Zuleyka Diaz-Martinez [aut],
Jose Fernandez-Menendez [aut]
Maintainer: David Bernstein <davebernstein1@gmail.com>
This is a re-admission after prior archival of version 0.1-2 dated 2008-02-19
Diff between DEA versions 0.1-2 dated 2008-02-19 and 1.0.0 dated 2026-09-10
DEA-0.1-2/DEA/R/DEA-internal.R |only DEA-0.1-2/DEA/R/dea.add.env.R |only DEA-0.1-2/DEA/R/dea.add.mul.R |only DEA-0.1-2/DEA/R/dea.bcc.io.env.R |only DEA-0.1-2/DEA/R/dea.bcc.io.mul.R |only DEA-0.1-2/DEA/R/dea.bcc.oo.env.R |only DEA-0.1-2/DEA/R/dea.bcc.oo.mul.R |only DEA-0.1-2/DEA/R/dea.ccr.io.env.R |only DEA-0.1-2/DEA/R/dea.ccr.io.mul.R |only DEA-0.1-2/DEA/R/dea.ccr.oo.env.R |only DEA-0.1-2/DEA/R/dea.ccr.oo.mul.R |only DEA-0.1-2/DEA/R/dea.sbm.bcc.R |only DEA-0.1-2/DEA/R/dea.sbm.bcc.io.R |only DEA-0.1-2/DEA/R/dea.sbm.bcc.oo.R |only DEA-0.1-2/DEA/R/dea.sbm.ccr.R |only DEA-0.1-2/DEA/R/dea.sbm.ccr.io.R |only DEA-0.1-2/DEA/R/dea.sbm.ccr.oo.R |only DEA-0.1-2/DEA/R/zzz.R |only DEA-0.1-2/DEA/man/dea.add.env.Rd |only DEA-0.1-2/DEA/man/dea.add.mul.Rd |only DEA-0.1-2/DEA/man/dea.bcc.io.env.Rd |only DEA-0.1-2/DEA/man/dea.bcc.io.mul.Rd |only DEA-0.1-2/DEA/man/dea.bcc.oo.env.Rd |only DEA-0.1-2/DEA/man/dea.bcc.oo.mul.Rd |only DEA-0.1-2/DEA/man/dea.ccr.io.env.Rd |only DEA-0.1-2/DEA/man/dea.ccr.io.mul.Rd |only DEA-0.1-2/DEA/man/dea.ccr.oo.env.Rd |only DEA-0.1-2/DEA/man/dea.ccr.oo.mul.Rd |only DEA-0.1-2/DEA/man/dea.sbm.bcc.Rd |only DEA-0.1-2/DEA/man/dea.sbm.bcc.io.Rd |only DEA-0.1-2/DEA/man/dea.sbm.bcc.oo.Rd |only DEA-0.1-2/DEA/man/dea.sbm.ccr.Rd |only DEA-0.1-2/DEA/man/dea.sbm.ccr.io.Rd |only DEA-0.1-2/DEA/man/dea.sbm.ccr.oo.Rd |only DEA-0.1-2/DEA/src |only DEA-1.0.0/DEA/DESCRIPTION | 58 +++++++++++++++++++++++++++++------- DEA-1.0.0/DEA/MD5 |only DEA-1.0.0/DEA/NAMESPACE |only DEA-1.0.0/DEA/NEWS.md |only DEA-1.0.0/DEA/R/additive.R |only DEA-1.0.0/DEA/R/boot.R |only DEA-1.0.0/DEA/R/cross.R |only DEA-1.0.0/DEA/R/ddf.R |only DEA-1.0.0/DEA/R/dea.R |only DEA-1.0.0/DEA/R/lp.R |only DEA-1.0.0/DEA/R/methods.R |only DEA-1.0.0/DEA/R/price.R |only DEA-1.0.0/DEA/R/rts.R |only DEA-1.0.0/DEA/R/sbm.R |only DEA-1.0.0/DEA/R/sim.R |only DEA-1.0.0/DEA/R/utils.R |only DEA-1.0.0/DEA/README.md |only DEA-1.0.0/DEA/build |only DEA-1.0.0/DEA/data |only DEA-1.0.0/DEA/inst |only DEA-1.0.0/DEA/man/DEA-package.Rd |only DEA-1.0.0/DEA/man/charnes1981.Rd |only DEA-1.0.0/DEA/man/dea-methods.Rd |only DEA-1.0.0/DEA/man/dea.Rd |only DEA-1.0.0/DEA/man/dea_add.Rd |only DEA-1.0.0/DEA/man/dea_boot.Rd |only DEA-1.0.0/DEA/man/dea_cost.Rd |only DEA-1.0.0/DEA/man/dea_cross.Rd |only DEA-1.0.0/DEA/man/dea_ddf.Rd |only DEA-1.0.0/DEA/man/dea_rts.Rd |only DEA-1.0.0/DEA/man/dea_sbm.Rd |only DEA-1.0.0/DEA/man/dea_sim.Rd |only DEA-1.0.0/DEA/tests |only DEA-1.0.0/DEA/vignettes |only 69 files changed, 47 insertions(+), 11 deletions(-)
Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
Description: Many tools for making, manipulating, and modifying many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Tomas Diviak [ctb],
Henrique Sposito [ctb] ,
Christian Steglich [ctb],
Alvaro Uzaheta [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 2.3.1 dated 2026-08-28 and 2.3.4 dated 2026-09-10
DESCRIPTION | 6 MD5 | 123 +++++++++-------- NAMESPACE | 26 +++ NEWS.md | 126 ++++++++++++++++++ R/class_describe.R | 12 + R/class_interface.R | 99 ++++++++++---- R/class_marks.R | 17 +- R/class_measures.R | 27 --- R/class_members.R | 39 +++++ R/class_missing.R | 13 - R/class_validate.R | 15 +- R/coerce_graph.R | 63 +++++++-- R/data_ison.R | 9 + R/make_generate.R | 173 +++++++++++++++++++++++-- R/manip_changes.R | 21 ++- R/manip_globals.R | 117 ++++++++++++++++- R/manip_info.R | 52 +++++++ R/manip_nodes.R | 52 +++++++ R/mark_format.R | 42 ++++-- R/measure_properties.R | 98 +++++++++++++- R/modif_labels.R | 6 R/modif_motifs.R | 4 R/modif_project.R | 46 ++++++ R/modif_scope.R | 24 +++ R/modif_weight.R | 111 +++++++++++----- data/ison_southern_women.rda |binary inst/tutorials/manynet1/making.Rmd | 8 - inst/tutorials/manynet1/making.html | 100 +++++++------- inst/tutorials/manynet2/manipulating.html | 206 +++++++++++++++--------------- man/interface.Rd | 48 +++++- man/ison_southern_women.Rd | 55 ++++---- man/make_stochastic.Rd | 30 +++- man/manip_globals.Rd | 31 ++++ man/manip_nodes_num.Rd | 2 man/mark_format_tie.Rd | 23 ++- man/measure_dims.Rd | 4 man/member_names.Rd | 20 ++ man/modif_project.Rd | 4 man/modif_weight.Rd | 22 ++- man/progress.Rd | 5 tests/testthat/helper-functional.R | 12 + tests/testthat/helper-manynet.R | 8 + tests/testthat/test-class_interface.R |only tests/testthat/test-coercion.R | 59 ++++++++ tests/testthat/test-functional_from.R | 15 +- tests/testthat/test-functional_impute.R | 4 tests/testthat/test-functional_lists.R | 2 tests/testthat/test-functional_manips.R | 87 ++++++++++++ tests/testthat/test-functional_marks.R | 11 - tests/testthat/test-functional_prints.R | 67 ++++++++- tests/testthat/test-functional_to.R | 5 tests/testthat/test-make_collect.R | 4 tests/testthat/test-make_generate.R | 51 +++++++ tests/testthat/test-manip_add.R | 29 ++++ tests/testthat/test-manip_format.R | 97 +++++++++++++- tests/testthat/test-manip_layers.R | 26 +++ tests/testthat/test-manip_miss.R | 8 - tests/testthat/test-manip_nodes.R | 52 ++++++- tests/testthat/test-manip_transform.R | 73 ++++++---- tests/testthat/test-manynet-data.R | 16 +- tests/testthat/test-mark_is.R | 43 ++++++ tests/testthat/test-modif_proximity.R | 18 +- tests/testthat/test-to_motifs.R | 4 63 files changed, 2036 insertions(+), 534 deletions(-)
Title: Haplotype-Based Tracking of Admixed Population for Breed
Composition Estimation
Description: Simulate populations and track haplotypes over generations to evaluate population admixture. The 'HAPTRACE' supports customisable population parameters, including size, number of markers, mutation rates and recombination.
Author: Shweta Sahoo [aut, cre] ,
Sara de las Heras-Saldana [aut] ,
Julius H. J. van der Werf [aut] ,
Mohammad H. Ferdosi [aut]
Maintainer: Shweta Sahoo <queryhap01@gmail.com>
Diff between HAPTRACE versions 0.1.1 dated 2026-07-30 and 0.1.2 dated 2026-09-10
DESCRIPTION | 8 +-- MD5 | 19 ++++---- NAMESPACE | 54 +++++++++++++--------- R/Core_Simulation_function.R | 2 R/Extract_Phenotype.R | 2 R/Simulation_Data_function.R | 2 README.md |only inst/doc/Introduction_HAPTRACE.R | 9 ++- inst/doc/Introduction_HAPTRACE.Rmd | 9 ++- inst/doc/Introduction_HAPTRACE.html | 85 ++++++++++++++++++------------------ vignettes/Introduction_HAPTRACE.Rmd | 9 ++- 11 files changed, 106 insertions(+), 93 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths] ,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.6 dated 2025-10-21 and 2.1.7 dated 2026-09-10
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