Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock [aut, cre],
Theo Michelot [aut]
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.5.5 dated 2022-10-18 and 1.5.6 dated 2025-07-21
DESCRIPTION | 22 +++++++++++----- MD5 | 43 +++++++++++++++++---------------- NEWS | 7 +++++ R/AIC_momentuHMM.R | 2 - R/AICweights.R | 2 - R/MIfitHMM.R | 14 ++++++++-- R/MIpool.R | 12 +++++++-- R/crawlWrap.R | 18 +++++++++++-- R/plotSat.R | 2 - R/pseudoRes.R | 6 +++- R/randomEffects.R | 6 +++- R/simData.R | 6 +++- R/simHierData.R | 6 +++- R/timeInStates.R | 6 +++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 ++++-- man/AIC.momentuHMM.Rd | 2 - man/AICweights.Rd | 2 - man/MIfitHMM.Rd | 2 - man/plotSat.Rd | 2 - vignettes/plot_buffaloExampleCT011.pdf |only vignettes/plot_buffaloResultsCT.pdf |only vignettes/plot_buffaloStatesCT.pdf |only 24 files changed, 119 insertions(+), 50 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 25.1.0 dated 2025-07-03 and 25.1.1 dated 2025-07-21
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/msigdbr-collections.R | 7 +++++-- R/msigdbr-species.R | 3 +++ R/msigdbr.R | 17 +++++++++++++++-- man/msigdbr.Rd | 19 +++++++++++++++++-- man/msigdbr_collections.Rd | 9 +++++++-- man/msigdbr_species.Rd | 3 +++ tests/testthat/test-msigdbr-collections.R | 3 +++ tests/testthat/test-msigdbr.R | 3 +++ 11 files changed, 73 insertions(+), 21 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Richard Li [aut, cre],
Tyler McCormick [aut],
Sam Clark [aut]
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.4.0 dated 2022-09-29 and 1.4.2 dated 2025-07-21
DESCRIPTION | 26 +++++++++++++----- MD5 | 24 ++++++++-------- NEWS.md | 6 +++- R/diag.r | 6 ++-- R/insilico_core.r | 34 ++++++++++++++++-------- R/insilico_standard.r | 8 +++-- R/insilico_train.r | 6 ++-- inst/java/Insilico.jar |binary java/Insilico/src/sampler/InsilicoSampler2.java | 11 +++++++ man/csmf.diag.Rd | 6 ++-- man/insilico.Rd | 5 ++- man/insilico.fit.Rd | 3 ++ man/insilico.train.Rd | 3 ++ 13 files changed, 94 insertions(+), 44 deletions(-)
Title: Microbiome Analysis Tools
Description: We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faith’s PD for a set of communities, and calculating the core UniFrac distance between two sets of communities. All functions rely on construction of a core community phylogeny, which is a phylogeny where branches are defined based on their presence in multiple samples from a single type of habitat. Our package provides two options for constructing the core community phylogeny, a tip-based approach, where the core community phylogeny is identified based on incidence of leaf nodes and a branch-based approach, where the core community phylogeny is identified based on incidence of individual branches. We suggest use of the microViz package.
Author: Sharon Bewick [aut, cre],
Benjamin Camper [aut],
National Science Foundation Division of Integrative Organismal Systems
[fnd]
Maintainer: Sharon Bewick <sbewick@clemson.edu>
Diff between holobiont versions 0.1.2 dated 2024-10-16 and 0.1.3 dated 2025-07-21
DESCRIPTION | 13 +-- MD5 | 48 +++++++---- NAMESPACE | 19 ++++ R/basic_branch.R |only R/basic_np.R |only R/basic_tip.R |only R/coreEdges.R |only R/coreFaithsPD.R | 145 ++++++++++++++------------------- R/coreJaccard.R | 44 ++++++++-- R/corePhyloVenn.R | 158 +++++++++++++++++++++++++----------- R/coreRichness.R |only R/coreTaxa.R |only R/coreTree.R | 121 ++++++++++++---------------- R/coreUniFrac.R | 220 +++++++++++++++++++-------------------------------- R/coreVenn.R |only R/coreVennTree.R | 148 ++++++++++++++++------------------ R/shade_branch.R |only R/shade_np.R |only R/shade_tip.R |only man/basic_branch.Rd |only man/basic_np.Rd |only man/basic_tip.Rd |only man/coreEdges.Rd |only man/coreFaithsPD.Rd | 41 ++++++--- man/coreJaccard.Rd | 30 ++++++ man/corePhyloVenn.Rd | 42 ++++++++- man/coreRichness.Rd |only man/coreTaxa.Rd |only man/coreTree.Rd | 43 +++++++-- man/coreUniFrac.Rd | 34 ++++++- man/coreVenn.Rd |only man/coreVennTree.Rd | 40 ++++++++- man/shade_branch.Rd |only man/shade_np.Rd |only man/shade_tip.Rd |only 35 files changed, 674 insertions(+), 472 deletions(-)
Title: Analysis of Niche Evolution using Niche and Distribution Models
Description: Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Author: Dan Warren [aut, cre] ,
Russell Dinnage [aut]
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between ENMTools versions 1.1.4 dated 2025-07-13 and 1.1.5 dated 2025-07-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/testthat/test_ENMTools.R | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Datasets and Functions to Accompany Analisis De Datos Con R
Description: Datasets and functions to accompany the book 'Analisis de datos con el programa
estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109).
The package helps carry out data management, exploratory analyses, and model fitting.
Author: Christian Salas-Eljatib [aut, cre] ,
Campos Nicolas [ctb] ,
Pino Nicolas [ctb] ,
Riquelme Joaquin [ctb]
Maintainer: Christian Salas-Eljatib <cseljatib@gmail.com>
Diff between datana versions 1.1.0 dated 2025-06-12 and 1.1.1 dated 2025-07-21
datana-1.1.0/datana/R/skew.r |only datana-1.1.0/datana/man/skew.Rd |only datana-1.1.1/datana/DESCRIPTION | 11 datana-1.1.1/datana/MD5 | 203 +++++++++------- datana-1.1.1/datana/NAMESPACE | 10 datana-1.1.1/datana/R/data-beetles.r | 6 datana-1.1.1/datana/R/data-beetles2.r | 10 datana-1.1.1/datana/R/data-endfid2.r |only datana-1.1.1/datana/R/data-imacec2.r |only datana-1.1.1/datana/R/data-rendesc2.r |only datana-1.1.1/datana/R/data-simce2.r |only datana-1.1.1/datana/R/datana-package.R | 2 datana-1.1.1/datana/R/descstat.r | 8 datana-1.1.1/datana/R/histbxp.r |only datana-1.1.1/datana/R/skewn.r |only datana-1.1.1/datana/R/tabtexanova.r |only datana-1.1.1/datana/R/tabtexregre.r |only datana-1.1.1/datana/R/upperleft.r |only datana-1.1.1/datana/R/xyboxplot.r | 327 +++++++++++++++++++++++---- datana-1.1.1/datana/build/partial.rdb |binary datana-1.1.1/datana/data/aboutrsq.rda |binary datana-1.1.1/datana/data/aboutrsq2.rda |binary datana-1.1.1/datana/data/airnyc.rda |binary datana-1.1.1/datana/data/airnyc2.rda |binary datana-1.1.1/datana/data/annualppCities.rda |binary datana-1.1.1/datana/data/annualppCities2.rda |binary datana-1.1.1/datana/data/bears.rda |binary datana-1.1.1/datana/data/bears2.rda |binary datana-1.1.1/datana/data/bearsdepu.rda |binary datana-1.1.1/datana/data/bearsdepu2.rda |binary datana-1.1.1/datana/data/beetles.rda |binary datana-1.1.1/datana/data/beetles2.rda |binary datana-1.1.1/datana/data/cameratrap.rda |binary datana-1.1.1/datana/data/cameratrap2.rda |binary datana-1.1.1/datana/data/carAccidents.rda |binary datana-1.1.1/datana/data/caribou.rda |binary datana-1.1.1/datana/data/caribou2.rda |binary datana-1.1.1/datana/data/casen.rda |binary datana-1.1.1/datana/data/chicksw.rda |binary datana-1.1.1/datana/data/chicksw2.rda |binary datana-1.1.1/datana/data/co2temp.rda |binary datana-1.1.1/datana/data/corkoak.rda |binary datana-1.1.1/datana/data/corkoak2.rda |binary datana-1.1.1/datana/data/election.rda |binary datana-1.1.1/datana/data/election2.rda |binary datana-1.1.1/datana/data/endfid2.rda |only datana-1.1.1/datana/data/eucaleaf.rda |binary datana-1.1.1/datana/data/eucaleaf2.rda |binary datana-1.1.1/datana/data/eucaleafAll.rda |binary datana-1.1.1/datana/data/eucaleafAll2.rda |binary datana-1.1.1/datana/data/fdamage.rda |binary datana-1.1.1/datana/data/fdamage2.rda |binary datana-1.1.1/datana/data/fertiliza.rda |binary datana-1.1.1/datana/data/fertiliza2.rda |binary datana-1.1.1/datana/data/ficdiamgr.rda |binary datana-1.1.1/datana/data/ficdiamgr2.rda |binary datana-1.1.1/datana/data/fishgrowth.rda |binary datana-1.1.1/datana/data/fishgrowth2.rda |binary datana-1.1.1/datana/data/forestfire.rda |binary datana-1.1.1/datana/data/forestfire2.rda |binary datana-1.1.1/datana/data/gasoline.rda |binary datana-1.1.1/datana/data/gasoline2.rda |binary datana-1.1.1/datana/data/gdpcap.rda |binary datana-1.1.1/datana/data/hgrdfir.rda |binary datana-1.1.1/datana/data/hgrdfir2.rda |binary datana-1.1.1/datana/data/idahohd.rda |binary datana-1.1.1/datana/data/idahohd2.rda |binary datana-1.1.1/datana/data/imacec2.rda |only datana-1.1.1/datana/data/landcover.rda |binary datana-1.1.1/datana/data/landcover2.rda |binary datana-1.1.1/datana/data/largetrees.rda |binary datana-1.1.1/datana/data/largetrees2.rda |binary datana-1.1.1/datana/data/lifexpect.rda |binary datana-1.1.1/datana/data/llancahue.rda |binary datana-1.1.1/datana/data/llancahue2.rda |binary datana-1.1.1/datana/data/papersdocstu.rda |binary datana-1.1.1/datana/data/pesohojas.rda |binary datana-1.1.1/datana/data/presenceIce.rda |binary datana-1.1.1/datana/data/president.rda |binary datana-1.1.1/datana/data/primarias.rda |binary datana-1.1.1/datana/data/pspLlancahue.rda |binary datana-1.1.1/datana/data/pspruca.rda |binary datana-1.1.1/datana/data/pspruca2.rda |binary datana-1.1.1/datana/data/ptaeda.rda |binary datana-1.1.1/datana/data/ptaeda2.rda |binary datana-1.1.1/datana/data/rainfallCA.rda |binary datana-1.1.1/datana/data/raulihg.rda |binary datana-1.1.1/datana/data/raulihg2.rda |binary datana-1.1.1/datana/data/rendesc2.rda |only datana-1.1.1/datana/data/simce2.rda |only datana-1.1.1/datana/data/sludge.rda |binary datana-1.1.1/datana/data/sludge2.rda |binary datana-1.1.1/datana/data/snaspe.rda |binary datana-1.1.1/datana/data/snaspe2.rda |binary datana-1.1.1/datana/data/soiltreat.rda |binary datana-1.1.1/datana/data/soiltreat2.rda |binary datana-1.1.1/datana/data/spataustria.rda |binary datana-1.1.1/datana/data/treevol.rda |binary datana-1.1.1/datana/data/treevol2.rda |binary datana-1.1.1/datana/data/treevolroble.rda |binary datana-1.1.1/datana/data/treevolroble2.rda |binary datana-1.1.1/datana/inst/CITATION | 4 datana-1.1.1/datana/man/beetles.Rd | 6 datana-1.1.1/datana/man/beetles2.Rd | 10 datana-1.1.1/datana/man/endfid2.Rd |only datana-1.1.1/datana/man/histbxp.Rd |only datana-1.1.1/datana/man/imacec2.Rd |only datana-1.1.1/datana/man/rendesc2.Rd |only datana-1.1.1/datana/man/simce2.Rd |only datana-1.1.1/datana/man/skewn.Rd |only datana-1.1.1/datana/man/tabtexregre.Rd |only datana-1.1.1/datana/man/upperleft.Rd |only datana-1.1.1/datana/man/xyboxplot.Rd | 147 ++++++++++-- datana-1.1.1/datana/tests |only 114 files changed, 566 insertions(+), 178 deletions(-)
Title: High Performance Tables Using 'Cheetah Grid'
Description: An R interface to 'Cheetah Grid', a high-performance JavaScript table widget.
'cheetahR' allows users to render millions of rows in just a few milliseconds,
making it an excellent alternative to other R table widgets. The package wraps
the 'Cheetah Grid' JavaScript functions and makes them readily available for R users.
The underlying grid implementation is based on 'Cheetah Grid'
<https://github.com/future-architect/cheetah-grid>.
Author: Olajoke Oladipo [aut, cre],
David Granjon [aut],
cynkra GmbH [fnd]
Maintainer: Olajoke Oladipo <olajoke@cynkra.com>
Diff between cheetahR versions 0.2.0 dated 2025-05-12 and 0.3.0 dated 2025-07-21
DESCRIPTION | 6 MD5 | 31 NAMESPACE | 5 NEWS.md | 9 R/cheetah.R | 122 R/cheetah_proxy.R |only R/cheetah_utils.R | 251 R/utils.R | 75 inst/doc/cheetahR.R | 220 inst/doc/cheetahR.html |32777 -------------------------------------------- inst/doc/cheetahR.qmd | 264 inst/htmlwidgets/cheetah.js |32193 ------------------------------------------- man/add_row.Rd |only man/cheetah.Rd | 103 man/cheetah_proxy.Rd |only man/delete_row.Rd |only man/number_format.Rd |only tests/testthat/test-utils.R | 46 vignettes/cheetahR.qmd | 264 19 files changed, 1801 insertions(+), 64565 deletions(-)
Title: Parametric Linkage and Other Pedigree Analysis in R
Description: NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PEDSUITE'
PACKAGES (<https://magnusdv.github.io/pedsuite/>). 'PARAMLINK' IS
MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW
PROJECTS. A suite of tools for analysing pedigrees with marker data,
including parametric linkage analysis, forensic computations,
relatedness analysis and marker simulations. The core of the package
is an implementation of the Elston-Stewart algorithm for pedigree
likelihoods, extended to allow mutations as well as complex
inbreeding. Features for linkage analysis include singlepoint LOD
scores, power analysis, and multipoint analysis (the latter through a
wrapper to the 'MERLIN' software). Forensic applications include
exclusion probabilities, genotype distributions and conditional
simulations. Data from the 'Familias' software can be imported and
analysed in 'paramlink'. Finally, 'paramlink' offers many utility
functions for creating, manipulating and plotting pedigrees with or
without marker [...truncated...]
Author: Magnus Dehli Vigeland [aut, cre],
Thore Egeland [ctb],
Guro Doerum [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between paramlink versions 1.1-5 dated 2022-04-15 and 1.1-6 dated 2025-07-21
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 - NEWS | 8 ++++---- R/linkage.power.R | 3 +-- R/plot.linkdat.R | 4 ++-- R/zzz.R | 2 +- README.md | 24 ++++++++++++------------ man/linkage.power.Rd | 3 +-- man/paramlink-package.Rd | 2 +- man/plot.linkdat.Rd | 4 ++-- 11 files changed, 39 insertions(+), 42 deletions(-)
Title: R Client for the Microsoft Cognitive Services 'Text-to-Speech'
REST API
Description: R Client for the Microsoft Cognitive Services
'Text-to-Speech' REST API, including voice synthesis. A valid account
must be registered at the Microsoft Cognitive Services website
<https://azure.microsoft.com/en-us/products/ai-services/> in order to
obtain a (free) API key. Without an API key, this package will not
work properly.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mscstts versions 0.6.3 dated 2022-06-10 and 0.6.4 dated 2025-07-21
DESCRIPTION | 17 +++++++++-------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ R/create_ssml.R | 2 +- R/ms_list_voices.R | 4 ++-- R/ms_locale_names.R | 4 ++-- R/ms_synthesize.R | 6 +++--- R/ms_tts_auth.R | 4 ++-- README.md | 9 +++++---- man/ms_create_ssml.Rd | 2 +- man/ms_get_tts_key.Rd | 2 +- man/ms_get_tts_token.Rd | 2 +- man/ms_list_voices.Rd | 4 ++-- man/ms_locale_names.Rd | 2 +- man/ms_locales_df.Rd | 2 +- man/ms_synthesize.Rd | 6 +++--- tests/testthat/test-locales.R | 12 ++++++++---- 17 files changed, 62 insertions(+), 52 deletions(-)
Title: Iterative Hard Thresholding Extensions to Cyclops
Description: Fits large-scale regression models with a penalty that
restricts the maximum number of non-zero regression coefficients
to a prespecified value. While Chu et al (2020) <doi:10.1093/gigascience/giaa044>
describe the basic algorithm, this package uses Cyclops for an efficient implementation.
Author: Marc A. Suchard [aut, cre],
Patrick Ryan [aut],
Observational Health Data Sciences and Informatics [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between IterativeHardThresholding versions 1.0.2 dated 2022-09-08 and 1.0.3 dated 2025-07-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/FastIhtPrior.R | 2 +- R/Prior.R | 2 +- README.md | 20 ++++++-------------- man/createFastIhtPrior.Rd | 2 +- man/createIhtPrior.Rd | 2 +- 7 files changed, 21 insertions(+), 29 deletions(-)
More information about IterativeHardThresholding at CRAN
Permanent link
Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including
likelihood ratios for relationship testing, general relatedness
inference, marker simulation, and power analysis. 'forrel' is part of
the 'pedsuite', a collection of packages for pedigree analysis,
further described in the book 'Pedigree Analysis in R' (Vigeland,
2021, ISBN:9780128244302). Several functions deal specifically with
power analysis in missing person cases, implementing methods described
in Vigeland et al. (2020) <doi:10.1016/j.fsigen.2020.102376>. Data
import from the 'Familias' software (Egeland et al. (2000)
<doi:10.1016/S0379-0738(00)00147-X>) is supported through the
'pedFamilias' package.
Author: Magnus Dehli Vigeland [aut, cre] ,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between forrel versions 1.8.0 dated 2025-05-07 and 1.8.1 dated 2025-07-21
DESCRIPTION | 6 +- MD5 | 20 +++++---- NEWS.md | 10 ++++ R/checkPairwise.R | 77 +++++++++++++++++++---------------- R/data.R | 96 +++++++++++++++++--------------------------- build/partial.rdb |binary data/FORCE.rda |binary data/XFORCE.rda |only inst |only man/FORCE.Rd | 45 ++++++++++++++------ man/NorwegianFrequencies.Rd | 5 +- man/checkPairwise.Rd | 4 + 12 files changed, 144 insertions(+), 119 deletions(-)
Title: Estimating Environmental Suitability for Plants
Description: The ecocrop model estimates environmental suitability for plants using a limiting factor approach for plant growth following Hackett (1991) <doi:10.1007/BF00045728>. The implementation in this package is fast and flexible: it allows for the use of any (environmental) predictor variable. Predictors can be either static (for example, soil pH) or dynamic (for example, monthly precipitation).
Author: Robert J. Hijmans [cre, aut],
Rhys Manners [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between Recocrop versions 0.4-1 dated 2022-10-24 and 0.4-2 dated 2025-07-21
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- build/partial.rdb |binary man/parameters.Rd | 2 +- man/spatial.Rd | 2 +- 5 files changed, 11 insertions(+), 12 deletions(-)
Title: Prediction and Interpretation in Decision Trees for
Classification and Regression
Description: Optimization of conditional inference trees from the package 'party'
for classification and regression.
For optimization, the model space is searched for the best tree on the full sample by
means of repeated subsampling. Restrictions are allowed so that only trees are accepted
which do not include pre-specified uninterpretable split results (cf. Weihs & Buschfeld, 2021a).
The function PrInDT() represents the basic resampling loop for 2-class classification (cf. Weihs
& Buschfeld, 2021a). The function RePrInDT() (repeated PrInDT()) allows for repeated
applications of PrInDT() for different percentages of the observations of the large and the
small classes (cf. Weihs & Buschfeld, 2021c). The function NesPrInDT() (nested PrInDT())
allows for an extra layer of subsampling for a specific factor variable (cf. Weihs & Buschfeld,
2021b). The functions PrInDTMulev() and PrInDTMulab() deal with multilevel and multilabel
classification. In addition to these PrInDT() variants for c [...truncated...]
Author: Claus Weihs [aut, cre],
Sarah Buschfeld [aut],
Niklas Nitsch [ctb]
Maintainer: Claus Weihs <claus.weihs@tu-dortmund.de>
Diff between PrInDT versions 1.0.1 dated 2023-05-09 and 2.0.0 dated 2025-07-21
PrInDT-1.0.1/PrInDT/man/FindSubstr.Rd |only PrInDT-2.0.0/PrInDT/DESCRIPTION | 29 + PrInDT-2.0.0/PrInDT/MD5 | 87 +++-- PrInDT-2.0.0/PrInDT/NAMESPACE | 37 ++ PrInDT-2.0.0/PrInDT/R/C2SPrInDT.R |only PrInDT-2.0.0/PrInDT/R/FindSubstr.R | 2 PrInDT-2.0.0/PrInDT/R/Mix2SPrInDT.R |only PrInDT-2.0.0/PrInDT/R/NesPrInDT.R | 49 ++- PrInDT-2.0.0/PrInDT/R/OptPrInDT.R |only PrInDT-2.0.0/PrInDT/R/PrInDT.R | 383 ++++++++++++++++++++------ PrInDT-2.0.0/PrInDT/R/PrInDTAll.R | 107 ++++++- PrInDT-2.0.0/PrInDT/R/PrInDTAllparts.R | 41 ++ PrInDT-2.0.0/PrInDT/R/PrInDTCstruc.R |only PrInDT-2.0.0/PrInDT/R/PrInDTMulab.R | 97 ++++-- PrInDT-2.0.0/PrInDT/R/PrInDTMulabAll.R | 98 +++++- PrInDT-2.0.0/PrInDT/R/PrInDTMulev.R | 80 ++++- PrInDT-2.0.0/PrInDT/R/PrInDTMulevALL.R | 45 +-- PrInDT-2.0.0/PrInDT/R/PrInDTRstruc.R |only PrInDT-2.0.0/PrInDT/R/PrInDTreg.R | 141 ++++++--- PrInDT-2.0.0/PrInDT/R/PrInDTregAll.R | 46 ++- PrInDT-2.0.0/PrInDT/R/PrInDTstruc1.R |only PrInDT-2.0.0/PrInDT/R/PrInDTstruc2.R |only PrInDT-2.0.0/PrInDT/R/R2SPrInDT.R |only PrInDT-2.0.0/PrInDT/R/RePrInDT.R | 87 +++-- PrInDT-2.0.0/PrInDT/R/SimCPrInDT.R |only PrInDT-2.0.0/PrInDT/R/SimMixPrInDT.R |only PrInDT-2.0.0/PrInDT/R/SimRPrInDT.R |only PrInDT-2.0.0/PrInDT/R/data.R | 16 + PrInDT-2.0.0/PrInDT/R/sysdata.rda |binary PrInDT-2.0.0/PrInDT/data/data_land.rda |binary PrInDT-2.0.0/PrInDT/data/data_speaker.rda |binary PrInDT-2.0.0/PrInDT/data/data_vowel.rda |binary PrInDT-2.0.0/PrInDT/data/data_zero.rda |binary PrInDT-2.0.0/PrInDT/data/participant_zero.rda |only PrInDT-2.0.0/PrInDT/man/C2SPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/Mix2SPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/NesPrInDT.Rd | 14 PrInDT-2.0.0/PrInDT/man/OptPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/PrInDT.Rd | 61 +++- PrInDT-2.0.0/PrInDT/man/PrInDTAll.Rd | 35 ++ PrInDT-2.0.0/PrInDT/man/PrInDTAllparts.Rd | 13 PrInDT-2.0.0/PrInDT/man/PrInDTCstruc.Rd |only PrInDT-2.0.0/PrInDT/man/PrInDTMulab.Rd | 25 + PrInDT-2.0.0/PrInDT/man/PrInDTMulabAll.Rd | 14 PrInDT-2.0.0/PrInDT/man/PrInDTMulev.Rd | 16 - PrInDT-2.0.0/PrInDT/man/PrInDTMulevAll.Rd | 11 PrInDT-2.0.0/PrInDT/man/PrInDTRstruc.Rd |only PrInDT-2.0.0/PrInDT/man/PrInDTreg.Rd | 43 +- PrInDT-2.0.0/PrInDT/man/PrInDTregAll.Rd | 14 PrInDT-2.0.0/PrInDT/man/R2SPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/RePrInDT.Rd | 21 + PrInDT-2.0.0/PrInDT/man/SimCPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/SimMixPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/SimRPrInDT.Rd |only PrInDT-2.0.0/PrInDT/man/data_land.Rd | 3 PrInDT-2.0.0/PrInDT/man/participant_zero.Rd |only 56 files changed, 1227 insertions(+), 388 deletions(-)
Title: Analyze the Structure of Musical Scales
Description: Analysis of musical scales (& modes, grooves, etc.) in the vein of
Sherrill 2025 <doi:10.1215/00222909-11595194>.
The initials MCT in the package title refer to the article's title: "Modal
Color Theory." Offers support for conventional musical pitch class set
theory as developed by Forte (1973, ISBN: 9780300016109) and David Lewin
(1987, ISBN: 9780300034936), as well as for the continuous geometries of
Callender, Quinn, & Tymoczko (2008) <doi:10.1126/science.1153021>.
Identifies structural properties of scales and calculates derived values
(sign vector, color number, brightness ratio, etc.). Creates plots such as
"brightness graphs" which visualize these properties.
Author: Paul Sherrill [aut, cre, cph]
Maintainer: Paul Sherrill <paul.sherrill@utah.edu>
Diff between musicMCT versions 0.1.2 dated 2025-06-05 and 0.2.0 dated 2025-07-21
DESCRIPTION | 11 +- MD5 | 118 +++++++++++++++------------- NAMESPACE | 11 ++ NEWS.md | 53 ++++++++++++ R/OPTC_test.R | 2 R/asword.R | 2 R/brightness_comparisons.R | 6 - R/brightnessgraph.R | 14 +-- R/colornum.R | 6 - R/data.R | 25 +++++ R/dft.R |only R/make_offset_ineqmat.R |only R/make_white_ineqmat.R | 76 +++++++++++++++++- R/makeineqmat.R | 8 + R/propriety.R | 36 ++++++-- R/quantize_color.R | 75 ++++++++++++++--- R/set_from_signvector.R | 27 ++++-- R/set_theory.R | 81 ++++++++++++++++++- R/signvector.R | 2 R/sim.R | 43 +++++++++- R/subsets.R | 2 R/utils.R | 54 +++++++++++- R/vlsig.R | 7 - README.md | 18 +++- data/roth_ineqmats.rda |only inst/CITATION | 3 inst/doc/visualizing_higher_dimensions.html | 12 +- man/brightnessgraph.Rd | 2 man/clockface.Rd |only man/colornum.Rd | 6 - man/dft.Rd |only man/figures/logo.png |only man/howfree.Rd | 6 - man/ianring.Rd |only man/make_black_ineqmat.Rd |only man/make_offset_ineqmat.Rd |only man/make_roth_ineqmat.Rd | 10 +- man/make_white_ineqmat.Rd | 22 +++-- man/musicMCT-package.Rd | 5 - man/populate_flat.Rd | 6 - man/primary_hue.Rd | 8 - man/project_onto.Rd | 6 - man/quantize_color.Rd | 21 +++- man/quantize_hue.Rd | 22 ++++- man/roth_ineqmats.Rd |only man/set_from_signvector.Rd | 19 ++-- man/set_to_distribution.Rd |only man/signvector.Rd | 6 - man/sim.Rd | 30 ++++++- man/simplify_scale.Rd | 6 - man/step_signvector.Rd | 6 - man/svzero_fingerprint.Rd | 6 - man/whichsvzeroes.Rd | 8 - man/writeSCL.Rd | 6 - tests/testthat/_snaps/make_white_ineqmat.md | 14 +++ tests/testthat/_snaps/set_theory |only tests/testthat/test-dft.R |only tests/testthat/test-make_offset_ineqmat.R |only tests/testthat/test-make_white_ineqmat.R | 13 ++- tests/testthat/test-makeineqmat.R | 5 + tests/testthat/test-propriety.R | 5 + tests/testthat/test-quantize_color.R | 15 +++ tests/testthat/test-set_from_signvector.R | 8 + tests/testthat/test-set_theory.R | 10 ++ tests/testthat/test-sim.R | 24 +++++ tests/testthat/test-utils.R |only tests/testthat/test-vlsig.R | 3 67 files changed, 782 insertions(+), 208 deletions(-)
Title: Inference of Species Associations from Co-Occurrence Data
Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.
Author: Benjamin Blonder [aut, cre],
Naia Morueta-Holme [aut]
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between netassoc versions 0.7.0 dated 2022-07-20 and 0.7.1 dated 2025-07-21
DESCRIPTION | 18 +++++++++++++----- MD5 | 8 ++++---- man/make_netassoc_network.Rd | 2 +- man/partial_correlation.Rd | 13 +++++-------- man/plot_netassoc_network.Rd | 2 +- 5 files changed, 24 insertions(+), 19 deletions(-)
Title: Introduction to Sports Analytics using R (ISAR) Data
Description: We provide data sets used in the textbook "Introduction to Sports Analytics using R" by Elmore and Urbaczweski (2025).
Author: Ryan Elmore [cre, aut]
Maintainer: Ryan Elmore <Ryan.Elmore@du.edu>
Diff between ISAR versions 0.1.12 dated 2023-07-08 and 1.0.0 dated 2025-07-21
DESCRIPTION | 12 +++--- MD5 | 68 +++++++++++++++++++++++++++++++++---- NEWS.md | 5 ++ R/avs_roster_2022.R |only R/avs_stats_2022.R |only R/draftkings-edm-col.R |only R/draftkings-nyr-car.R |only R/epl_gk_stats_2023.R |only R/epl_gk_stats_2024.R |only R/epl_player_stats_2022.R | 2 - R/epl_player_stats_2023.R |only R/epl_player_stats_2024.R |only R/epl_team_stats_2023.R |only R/epl_team_stats_2024.R |only R/nba_advanced_team_2024.R |only R/nba_advanced_team_2025.R |only R/nba_four_factors_team_2023.R | 2 - R/nba_four_factors_team_2024.R |only R/nba_four_factors_team_2025.R |only R/nba_games_2024.R |only R/nba_games_2025.R |only R/nhl_data_hockey_reference.R |only R/nhl_team_stats_2022.R |only README.md | 4 +- data/avs_roster_2022.rda |only data/avs_stats_2022.rda |only data/dk_edm_col.rda |only data/dk_nyr_car.rda |only data/epl_gk_stats_2023.rda |only data/epl_gk_stats_2024.rda |only data/epl_player_stats_2023.rda |only data/epl_player_stats_2024.rda |only data/epl_team_stats_2023.rda |only data/epl_team_stats_2024.rda |only data/nba_adv_team_2024.rda |only data/nba_adv_team_2025.rda |only data/nba_ff_team_2024.rda |only data/nba_ff_team_2025.rda |only data/nba_games_2024.rda |only data/nba_games_2025.rda |only data/nhl_data_hockey_reference.rda |only data/nhl_team_stats_2022.rda |only man/avs_roster_2022.Rd |only man/avs_stats_2022.Rd |only man/dk_edm_col.Rd |only man/dk_nyr_car.Rd |only man/epl_gk_stats_2023.Rd |only man/epl_gk_stats_2024.Rd |only man/epl_player_stats_2022.Rd | 2 - man/epl_player_stats_2023.Rd |only man/epl_player_stats_2024.Rd |only man/epl_team_stats_2023.Rd |only man/epl_team_stats_2024.Rd |only man/nba_adv_team_2024.Rd |only man/nba_adv_team_2025.Rd |only man/nba_ff_team_2023.Rd | 2 - man/nba_ff_team_2024.Rd |only man/nba_ff_team_2025.Rd |only man/nba_games_2024.Rd |only man/nba_games_2025.Rd |only man/nhl_data_hockey_reference.Rd |only man/nhl_team_stats_2022.Rd |only 62 files changed, 79 insertions(+), 18 deletions(-)
Title: Eigenvectors from Eigenvalues Sparse Principal Component
Analysis (EESPCA)
Description: Contains logic for computing sparse principal components via the EESPCA method,
which is based on an approximation of the eigenvector/eigenvalue identity.
Includes logic to support execution of the TPower and rifle sparse PCA methods,
as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle
via cross-validation to minimize the out-of-sample reconstruction error.
H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.
Author: H. Robert Frost [aut, cre]
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between EESPCA versions 0.7.0 dated 2022-06-15 and 0.8.0 dated 2025-07-21
DESCRIPTION | 12 ++++++++---- MD5 | 21 +++++++++++---------- NEWS |only build/vignette.rds |binary inst/doc/EESPCA_Example.R | 24 ++++++++++++------------ inst/doc/EESPCA_Example.Rnw | 26 +++++++++++++------------- inst/doc/EESPCA_Example.pdf |binary man/EESPCACV.Rd | 2 +- man/RifleInit.Rd | 2 +- man/RiflePCACV.Rd | 2 +- man/TpowerPCACV.Rd | 2 +- vignettes/EESPCA_Example.Rnw | 26 +++++++++++++------------- 12 files changed, 61 insertions(+), 56 deletions(-)
Title: A Clustering Method for Time-Series Whole-Brain Activity Data of
'C. elegans'
Description: A toolkit to detect clusters from distance matrices.
The distance matrices are assumed to be calculated between the cells of
multiple animals ('Caenorhabditis elegans') from input time-series matrices.
Some functions for generating distance matrices, performing clustering,
evaluating the clustering, and visualizing the results of clustering and
evaluation are available. We're also providing the download function to
retrieve the calculated distance matrices from
'figshare' <https://figshare.com>.
Author: Kentaro Yamamoto [aut, cre],
Koki Tsuyuzaki [aut],
Itoshi Nikaido [aut]
Maintainer: Kentaro Yamamoto <yamaken37.the.answer@gmail.com>
Diff between WormTensor versions 0.1.1 dated 2024-07-23 and 0.1.2 dated 2025-07-21
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 4 ++ R/worm_download.R | 12 ++++---- inst/doc/WormTensor.R | 2 - inst/doc/WormTensor.html | 64 +++++++++++++++++++++-------------------------- 6 files changed, 48 insertions(+), 50 deletions(-)
Title: Plotting Methods for 'simmer'
Description: A set of plotting methods for 'simmer' trajectories and simulations.
Author: Inaki Ucar [aut, cph, cre] ,
Bart Smeets [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between simmer.plot versions 0.1.18 dated 2023-07-17 and 0.1.19 dated 2025-07-21
DESCRIPTION | 11 +++-- MD5 | 22 +++++------ NEWS.md | 4 ++ R/plot.trajectory.R | 4 +- R/simmer.plot.R | 3 - build/vignette.rds |binary inst/doc/plot.simmer.R | 12 +++--- inst/doc/plot.simmer.html | 81 +++++++++++++++++++++--------------------- inst/doc/plot.trajectory.R | 14 +++---- inst/doc/plot.trajectory.html | 67 +++++++++++++++++----------------- man/plot.trajectory.Rd | 4 +- man/simmer.plot-package.Rd | 1 12 files changed, 115 insertions(+), 108 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.42.0 dated 2025-03-25 and 1.43.0 dated 2025-07-21
reticulate-1.42.0/reticulate/tests/testthat/resources/figure |only reticulate-1.42.0/reticulate/tests/testthat/resources/test-custom-root-dir.md |only reticulate-1.43.0/reticulate/DESCRIPTION | 8 - reticulate-1.43.0/reticulate/MD5 | 51 +++--- reticulate-1.43.0/reticulate/NAMESPACE | 3 reticulate-1.43.0/reticulate/NEWS.md | 34 +++- reticulate-1.43.0/reticulate/R/array.R | 25 +++ reticulate-1.43.0/reticulate/R/conda.R | 23 ++- reticulate-1.43.0/reticulate/R/conversion.R | 17 +- reticulate-1.43.0/reticulate/R/install-python.R | 59 ++++--- reticulate-1.43.0/reticulate/R/miniconda.R | 9 + reticulate-1.43.0/reticulate/R/package.R | 7 reticulate-1.43.0/reticulate/R/py_require.R | 76 ++++++++-- reticulate-1.43.0/reticulate/R/pyenv.R | 6 reticulate-1.43.0/reticulate/R/utils.R | 2 reticulate-1.43.0/reticulate/R/zzz.R | 1 reticulate-1.43.0/reticulate/build/vignette.rds |binary reticulate-1.43.0/reticulate/inst/doc/arrays.html | 5 reticulate-1.43.0/reticulate/inst/doc/calling_python.html | 5 reticulate-1.43.0/reticulate/inst/doc/package.html | 5 reticulate-1.43.0/reticulate/inst/doc/python_dependencies.html | 5 reticulate-1.43.0/reticulate/inst/doc/python_packages.html | 5 reticulate-1.43.0/reticulate/inst/doc/python_primer.html | 5 reticulate-1.43.0/reticulate/inst/doc/versions.html | 5 reticulate-1.43.0/reticulate/man/install_python.Rd | 33 ++-- reticulate-1.43.0/reticulate/tests/testthat/_snaps/py_require.md | 18 +- reticulate-1.43.0/reticulate/tests/testthat/test-py_require.R | 26 ++- 27 files changed, 306 insertions(+), 127 deletions(-)
Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with
'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between RcppXPtrUtils versions 0.1.2 dated 2022-05-24 and 0.1.3 dated 2025-07-21
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/cppXPtr.R | 4 ++-- man/cppXPtr.Rd | 4 ++-- 5 files changed, 18 insertions(+), 13 deletions(-)
Title: National Emergency Medical Service Quality Alliance Measure
Calculations
Description: Designed to automate the calculation of Emergency Medical
Service (EMS) quality metrics, 'nemsqar' implements measures defined
by the National EMS Quality Alliance (NEMSQA). By providing reliable,
evidence-based quality assessments, the package supports EMS agencies,
healthcare providers, and researchers in evaluating and improving
patient outcomes. Users can find details on all approved NEMSQA
measures at <https://www.nemsqa.org/measures>. Full technical
specifications, including documentation and pseudocode used to develop
'nemsqar', are available on the NEMSQA website after creating a user
profile at <https://www.nemsqa.org>.
Author: Nicolas Foss [aut, cre],
Samuel Kordik [aut] ,
Alyssa Green [ctb],
Iowa Department of Health and Human Services [cph]
Maintainer: Nicolas Foss <nicolas.foss@hhs.iowa.gov>
Diff between nemsqar versions 1.1.1 dated 2025-07-16 and 1.1.2 dated 2025-07-21
DESCRIPTION | 6 - MD5 | 9 +- NEWS.md | 4 + R/nemsqa_binomial_confint.R | 125 +++++++++++++++++++++-------------------- build |only man/nemsqa_binomial_confint.Rd | 4 - 6 files changed, 81 insertions(+), 67 deletions(-)
Title: Read Spectrometric Data and Metadata
Description: Parse various reflectance/transmittance/absorbance spectra file
formats to extract spectral data and metadata, as described in Gruson, White
& Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import
files from 'Avantes' <https://www.avantes.com/>, 'CRAIC'
<https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight'
<https://www.oceanoptics.com/> brands.
Author: Hugo Gruson [cre, aut, cph] ,
Rafael Maia [aut, cph] ,
Thomas White [aut, cph] ,
Kotya Karapetyan [ctb, cph] )
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between lightr versions 1.8.0 dated 2024-12-01 and 1.9.0 dated 2025-07-21
DESCRIPTION | 17 MD5 | 112 NAMESPACE | 2 NEWS.md | 55 R/compute_processed.R | 2 R/convert_tocsv.R | 58 R/dispatch_parser.R | 34 R/get_metadata.R | 52 R/get_spec.R | 71 R/parse_avantes_binary.R | 260 R/parse_avantes_converted.R | 35 R/parse_csv.R |only R/parse_generic.R | 30 R/parse_jdx.R | 64 R/parse_oceanoptics_converted.R | 94 R/parse_procspec.R | 74 R/parse_spc.R | 87 R/utils.R | 31 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/batch_import.R | 2 inst/doc/batch_import.Rmd | 3 inst/doc/batch_import.html | 6 inst/doc/design-principles.R |only inst/doc/design-principles.Rmd |only inst/doc/design-principles.html |only inst/doc/renormalise.html | 9 inst/doc/true_example.R | 10 inst/doc/true_example.Rmd | 37 inst/doc/true_example.html | 15 inst/testdata/compare/Avantes/1904090M1_0007.Raw8 |only inst/testdata/compare/Avantes/1904090M1_0007_1904090M1.TXT |only inst/testdata/tampered_procspec.zip |only man/dispatch_parser.Rd | 6 man/lr_convert_tocsv.Rd | 13 man/lr_get_metadata.Rd | 9 man/lr_get_spec.Rd | 13 man/lr_parse_csv.Rd |only man/lr_parse_generic.Rd | 4 man/lr_parse_jaz.Rd | 6 man/lr_parse_jdx.Rd | 4 man/lr_parse_procspec.Rd | 11 man/lr_parse_spc.Rd | 4 man/lr_parse_trm.Rd | 14 man/lr_parse_ttt.Rd | 6 tests/spelling.R | 8 tests/testthat.R | 2 tests/testthat/_snaps/getspec.md | 7752 ++++++++++--- tests/testthat/_snaps/metadata.md | 292 tests/testthat/_snaps/parsers.md |only tests/testthat/setup.R | 22 tests/testthat/setup_options.R |only tests/testthat/test_compare_official.R | 80 tests/testthat/test_convert.R | 55 tests/testthat/test_dispatch.R | 32 tests/testthat/test_getspec.R | 89 tests/testthat/test_metadata.R | 38 tests/testthat/test_parsers.R | 240 vignettes/architecture.svg |only vignettes/batch_import.Rmd | 3 vignettes/design-principles.Rmd |only vignettes/true_example.Rmd | 37 63 files changed, 7701 insertions(+), 2200 deletions(-)
Title: An Interactive and Feature-Rich Data Viewer
Description: Provides an interactive viewer for 'data.frame' and 'tibble' objects using 'shiny' <https://shiny.posit.co/> and 'DT' <https://rstudio.github.io/DT/>. It supports complex filtering, column selection, and automatic generation of reproducible 'dplyr' <https://dplyr.tidyverse.org/> code for data manipulation. The package is designed for ease of use in data exploration and reporting workflows.
Author: Madhan Kumar N [aut, cre]
Maintainer: Madhan Kumar N <madhanmanoj1999@gmail.com>
Diff between dataviewR versions 0.1.0 dated 2025-06-14 and 0.1.1 dated 2025-07-21
DESCRIPTION | 11 + MD5 | 9 - NEWS.md |only R/dataviewer.R | 17 +- README.md | 268 ++++++++++++++++++++++++++++++++++----- tests/testthat/test-dataviewer.R | 2 6 files changed, 261 insertions(+), 46 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 1.14.0 dated 2025-05-13 and 1.15.0 dated 2025-07-21
TreeTools-1.14.0/TreeTools/tests/testthat/_snaps/helper_functions |only TreeTools-1.15.0/TreeTools/DESCRIPTION | 11 TreeTools-1.15.0/TreeTools/MD5 | 81 +++--- TreeTools-1.15.0/TreeTools/NAMESPACE | 5 TreeTools-1.15.0/TreeTools/NEWS.md | 13 TreeTools-1.15.0/TreeTools/R/MatchStrings.R |only TreeTools-1.15.0/TreeTools/R/PhyToString.R |only TreeTools-1.15.0/TreeTools/R/Reweight.R |only TreeTools-1.15.0/TreeTools/R/Splits.R | 2 TreeTools-1.15.0/TreeTools/R/helper_functions.R | 3 TreeTools-1.15.0/TreeTools/R/parse_files.R | 134 ---------- TreeTools-1.15.0/TreeTools/R/tree_rearrangement.R | 70 +++-- TreeTools-1.15.0/TreeTools/build/partial.rdb |binary TreeTools-1.15.0/TreeTools/inst/REFERENCES.bib | 22 + TreeTools-1.15.0/TreeTools/inst/WORDLIST | 4 TreeTools-1.15.0/TreeTools/inst/doc/filesystem-navigation.html | 4 TreeTools-1.15.0/TreeTools/inst/doc/load-data.html | 4 TreeTools-1.15.0/TreeTools/inst/doc/load-trees.html | 4 TreeTools-1.15.0/TreeTools/inst/include/TreeTools/ClusterTable.h | 13 TreeTools-1.15.0/TreeTools/inst/include/TreeTools/SplitList.h | 16 - TreeTools-1.15.0/TreeTools/inst/include/TreeTools/keep_tip.h | 4 TreeTools-1.15.0/TreeTools/inst/include/TreeTools/types.h | 12 TreeTools-1.15.0/TreeTools/man/Decompose.Rd | 1 TreeTools-1.15.0/TreeTools/man/EndSentence.Rd | 1 TreeTools-1.15.0/TreeTools/man/MatchStrings.Rd |only TreeTools-1.15.0/TreeTools/man/MatrixToPhyDat.Rd | 1 TreeTools-1.15.0/TreeTools/man/MorphoBankDecode.Rd | 1 TreeTools-1.15.0/TreeTools/man/PhyToString.Rd | 5 TreeTools-1.15.0/TreeTools/man/Reweight.Rd |only TreeTools-1.15.0/TreeTools/man/RightmostCharacter.Rd | 1 TreeTools-1.15.0/TreeTools/man/RootTree.Rd | 16 - TreeTools-1.15.0/TreeTools/man/Unquote.Rd | 1 TreeTools-1.15.0/TreeTools/src/as_newick.cpp | 2 TreeTools-1.15.0/TreeTools/src/descendant_edges.cpp | 2 TreeTools-1.15.0/TreeTools/src/int_to_tree.cpp | 4 TreeTools-1.15.0/TreeTools/src/splits.cpp | 8 TreeTools-1.15.0/TreeTools/src/tips_in_splits.cpp | 2 TreeTools-1.15.0/TreeTools/src/tree_shape.cpp | 4 TreeTools-1.15.0/TreeTools/tests/testthat/test-MatchStrings.R |only TreeTools-1.15.0/TreeTools/tests/testthat/test-PhyToString.R |only TreeTools-1.15.0/TreeTools/tests/testthat/test-ReadTntTree.R | 25 + TreeTools-1.15.0/TreeTools/tests/testthat/test-Reweight.R |only TreeTools-1.15.0/TreeTools/tests/testthat/test-Splits.R | 7 TreeTools-1.15.0/TreeTools/tests/testthat/test-helper_functions.R | 26 - TreeTools-1.15.0/TreeTools/tests/testthat/test-parsers.R | 44 --- TreeTools-1.15.0/TreeTools/tests/testthat/test-tree_rearrange.R | 24 + 46 files changed, 256 insertions(+), 321 deletions(-)
Title: 'OpenID Connect' Discovery and Authentication
Description: Discover 'OpenID Connect' endpoints and authenticate
using device flow. Used by 'MOLGENIS' packages.
Author: Fleur Kelpin [aut] ,
Tommy de Boer [aut] ,
Sido Haakma [aut] ,
Mariska Slofstra [aut, cre] ,
Tim Cadman [aut] ,
MOLGENIS org [cph, fnd]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between MolgenisAuth versions 0.0.25 dated 2023-02-20 and 1.0.0 dated 2025-07-21
DESCRIPTION | 30 ++- MD5 | 16 - NAMESPACE | 14 - NEWS.md | 5 R/auth.R | 254 +++++++++++++++++++++------- man/MolgenisAuth-package.Rd | 1 man/device_flow_auth.Rd | 3 man/discover.Rd | 2 tests/testthat/test-auth.R | 393 +++++++++++++++++++++++++++++++++++--------- 9 files changed, 553 insertions(+), 165 deletions(-)
Title: Keyword Assisted Topic Models
Description: Fits keyword assisted topic models (keyATM) using collapsed Gibbs samplers. The keyATM combines the latent dirichlet allocation (LDA) models with a small number of keywords selected by researchers in order to improve the interpretability and topic classification of the LDA. The keyATM can also incorporate covariates and directly model time trends. The keyATM is proposed in Eshima, Imai, and Sasaki (2024) <doi:10.1111/ajps.12779>.
Author: Shusei Eshima [aut, cre] ,
Tomoya Sasaki [aut],
Kosuke Imai [aut],
Chung-hong Chan [ctb] ,
Romain Francois [ctb] ,
Martin Feldkircher [ctb] ,
William Lowe [ctb],
Seo-young Silvia Kim [ctb]
Maintainer: Shusei Eshima <shuseieshima@gmail.com>
Diff between keyATM versions 0.5.3 dated 2025-03-30 and 0.5.4 dated 2025-07-21
DESCRIPTION | 21 MD5 | 122 ++--- NAMESPACE | 1 NEWS.md | 5 R/analysis_covariates.R | 162 ++++--- R/keyATM-package.R | 1 R/keyATM.R | 99 +++- R/keyATMvb.R | 158 ++++--- R/model.R | 659 ++++++++++++++++++++---------- R/multiPGreg.R | 114 ++--- R/plots.R | 425 +++++++++++++------ R/posterior.R | 475 +++++++++++++-------- R/predict.R | 219 +++++---- R/utils.R | 215 ++++++--- R/zzz.R | 14 data/keyATM_data_bills.rda |binary man/refine_keywords.Rd |only src/LDA_base.cpp | 43 - src/LDA_base.h | 41 - src/LDA_weight.cpp | 23 - src/LDA_weight.h | 67 +-- src/LDA_weightCov.cpp | 27 - src/LDA_weightCov.h | 28 - src/LDA_weightHMM.cpp | 34 - src/LDA_weightHMM.h | 25 - src/count.cpp | 3 src/helper.cpp | 8 src/initialize.cpp | 48 -- src/initialize.h | 125 ++--- src/keyATM_HMM.cpp | 218 ++++----- src/keyATM_HMM.h | 163 +++---- src/keyATM_base.cpp | 76 +-- src/keyATM_base.h | 77 +-- src/keyATM_cov.cpp | 118 ++--- src/keyATM_cov.h | 103 ++-- src/keyATM_covPG.cpp | 85 +-- src/keyATM_covPG.h | 65 +- src/keyATM_meta.cpp | 182 +++----- src/keyATM_meta.h | 479 ++++++++++----------- src/keyATMvb_call.cpp | 10 src/keyATMvb_main.cpp | 325 +++++--------- src/keyATMvb_main.h | 226 +++++----- src/read.cpp | 10 src/sampler.cpp | 144 +++--- src/sampler.h | 21 src/train.cpp | 36 - src/utils.cpp | 40 - src/utils.h | 21 tests/testthat/test-Initialization.R | 183 +++++--- tests/testthat/test-checks.R | 40 + tests/testthat/test-diagnosis.R | 24 - tests/testthat/test-keyATMBase.R | 126 +++-- tests/testthat/test-keyATMCovDirMulti.R | 332 +++++++++++---- tests/testthat/test-keyATMCovPG.R | 353 +++++++++++----- tests/testthat/test-keyATMDynamic.R | 20 tests/testthat/test-keyATMHeterogeneity.R | 134 ++++-- tests/testthat/test-keyATMvb.R | 46 +- tests/testthat/test-plot.R | 197 ++++++-- tests/testthat/test-read_keywords.R | 145 ++++-- tests/testthat/test-read_texts.R | 16 tests/testthat/test-refine_keywords.R |only tests/testthat/test-resume.R | 324 ++++++++++---- tests/testthat/test-weightedLDA.R | 52 +- 63 files changed, 4423 insertions(+), 3130 deletions(-)
Title: Efficient and Accessible Discrete Choice Experiments
Description: Design, conduct and analyze 'DCEs' from a virtual interface in shiny. Reference: Perez-Troncoso, D. (2022) <https://github.com/danielpereztr/DCEtool>.
Author: Daniel Perez Troncoso [aut, cre]
Maintainer: Daniel Perez Troncoso <dpereztr@gmail.com>
Diff between DCEtool versions 1.1.1 dated 2025-05-18 and 1.2.0 dated 2025-07-21
DESCRIPTION | 12 MD5 | 9 NAMESPACE | 24 + R/app.R | 741 ++++++++++++++++++++++++++++++++++++++++---------- inst/doc/DCEtool.html | 2 inst/www |only 6 files changed, 633 insertions(+), 155 deletions(-)
Title: Repel Visually Similar Colors for Colorblind Users in Various
Plots
Description: Iterate and repel visually similar colors away in various 'ggplot2' plots. When many groups are plotted at the same time on multiple axes, for instance stacked bars or scatter plots, effectively ordering colors becomes difficult. This tool iterates through color combinations to find the best solution to maximize visual distinctness of nearby groups, so plots are more friendly toward colorblind users. This is achieved by two distance measurements, distance between groups within the plot, and CIELAB color space distances between colors as described in Carter et al., (2018) <doi:10.25039/TR.015.2018>.
Author: Rui Fu [cre, aut, cph]
Maintainer: Rui Fu <raysinensis@gmail.com>
Diff between colorrepel versions 0.4.1 dated 2025-01-18 and 0.4.3 dated 2025-07-21
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/color_repel.R | 8 ++++---- R/interactive.R | 16 +++++++++++----- R/wrappers.R | 19 +------------------ README.md | 10 +++++----- inst/stackbar_example.png |binary man/ggplotly_background.Rd | 4 +++- 9 files changed, 46 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-22 1.2.10
2023-02-17 1.2.9
2022-12-18 1.2.8
2022-01-03 1.2.5
2021-04-20 1.2.4
2020-06-18 1.2.3
2020-02-15 1.2.2
2020-01-26 1.2.1
2019-11-10 1.2.0
Title: A Centralized Metadata Object Focus on Clinical Trial Data
Programming Workflows
Description: Create an immutable container holding metadata for the
purpose of better enabling programming activities and functionality of
other packages within the clinical programming workflow.
Author: Liam Hobby [aut, cre],
Christina Fillmore [aut] ,
Bill Denney [aut],
Maya Gans [aut] ,
Ashley Tarasiewicz [aut],
Mike Stackhouse [aut] ,
Tamara Senior [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Liam Hobby <liam.f.hobby@gsk.com>
Diff between metacore versions 0.2.0 dated 2025-07-14 and 0.2.1 dated 2025-07-21
DESCRIPTION | 6 +-- MD5 | 8 ++-- NAMESPACE | 1 NEWS.md | 115 ++++++++++++++++++++++++++++++------------------------------ R/zzz.R | 2 - 5 files changed, 68 insertions(+), 64 deletions(-)
Title: Curved Text in 'ggplot2'
Description: A 'ggplot2' extension that allows text to follow curved paths.
Curved text makes it easier to directly label paths or neatly annotate in
polar co-ordinates.
Author: Allan Cameron [aut, cre],
Teun van den Brand [aut]
Maintainer: Allan Cameron <Allan.Cameron@nhs.scot>
Diff between geomtextpath versions 0.1.5 dated 2025-01-14 and 0.2.0 dated 2025-07-21
DESCRIPTION | 14 ++++++++------ MD5 | 23 ++++++++++++----------- NEWS.md | 2 ++ R/geom_textsf.R | 14 +++++--------- R/onload.R | 3 +++ R/sf_helpers.R | 6 +++--- R/text_placement.R | 2 +- R/utils.R | 13 +++++++++++++ README.md | 2 +- inst/doc/aesthetics.html | 8 +++----- inst/doc/curved_polar.html | 16 ++++++++++------ tests/testthat/_snaps/coord_curvedpolar.md |only tests/testthat/test-coord_curvedpolar.R | 9 ++++++--- 13 files changed, 67 insertions(+), 45 deletions(-)
Title: Cronbach's Alpha
Description: Cronbach's alpha and various formulas for confidence intervals. The relevant paper is Tsagris M., Frangos C.C. and Frangos C.C. (2013). "Confidence intervals for Cronbach's reliability coefficient". Recent Techniques in Educational Science, 14-16 May, Athens, Greece.
Author: Michail Tsagris [aut, cre],
Constantinos Frangos [aut],
Christos Frangos [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Cronbach versions 0.2 dated 2024-12-17 and 0.3 dated 2025-07-21
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NAMESPACE | 6 +++--- R/cron.ci.R | 28 +++++++++++++++++++++++++++- R/cronbach.R | 12 +++++++----- man/Cronbach-package.Rd | 4 ++-- man/cron.ci.Rd | 6 ++++-- man/cronfree.ci.Rd | 6 +++--- 8 files changed, 61 insertions(+), 31 deletions(-)
Title: Access INKAR Database
Description: Retrieve and import data from the INKAR database (Indikatoren und Karten zur Raum- und Stadtentwicklung Datenbank, <https://www.inkar.de>) of the Federal Office for Building and Regional Planning (BBSR) in Bonn using their JSON API.
Author: Moritz Marbach [aut, cre]
Maintainer: Moritz Marbach <m.marbach@ucl.ac.uk>
Diff between bonn versions 1.0.2 dated 2023-03-20 and 1.0.3 dated 2025-07-21
DESCRIPTION | 11 ++++++----- MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 +++++ R/bonn-package.R | 20 ++++++-------------- R/get_data.R | 12 ++++++++++-- R/get_geographies.R | 15 +++++++++++---- R/get_metadata.R | 11 +++++++++-- R/get_themes.R | 11 +++++++++-- R/get_variables.R | 15 +++++++++++---- man/bonn-package.Rd | 14 ++++++++++++-- man/get_data.Rd | 12 ++++++++++-- man/get_geographies.Rd | 15 +++++++++++---- man/get_metadata.Rd | 11 +++++++++-- man/get_themes.Rd | 11 +++++++++-- man/get_variables.Rd | 15 +++++++++++---- 15 files changed, 143 insertions(+), 63 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.1 dated 2025-04-02 and 5.1.1 dated 2025-07-21
UComp-5.1.1/UComp/ChangeLog | 3 UComp-5.1.1/UComp/DESCRIPTION | 11 UComp-5.1.1/UComp/MD5 | 42 - UComp-5.1.1/UComp/R/RcppExports.R | 4 UComp-5.1.1/UComp/R/UCS3functions.R | 69 ++ UComp-5.1.1/UComp/R/UCestim.R | 506 +++++++++++++++++---- UComp-5.1.1/UComp/R/UCmodel.R | 77 +-- UComp-5.1.1/UComp/man/UC.Rd | 4 UComp-5.1.1/UComp/man/UCcomponents.Rd | 2 UComp-5.1.1/UComp/man/UCdisturb.Rd | 2 UComp-5.1.1/UComp/man/UCfilter.Rd | 2 UComp-5.1.1/UComp/man/UCforecast.Rd | 4 UComp-5.1.1/UComp/man/UChp.Rd | 2 UComp-5.1.1/UComp/man/UCsetup.Rd | 2 UComp-5.1.1/UComp/man/UCsmooth.Rd | 2 UComp-5.1.1/UComp/man/UCvalidate.Rd | 2 UComp-5.1.1/UComp/src/BSMmodel.h | 99 ++-- UComp-5.1.1/UComp/src/RcppExports.cpp | 29 - UComp-5.1.1/UComp/src/SSpace.h | 3 UComp-5.1.1/UComp/src/UCompC.cpp | 788 +++++++++++++++++++++------------- UComp-5.1.1/UComp/src/oldBSMmodel.h |only UComp-5.1/UComp/R/UCcomponents.R |only UComp-5.1/UComp/R/UCfilter.R |only UComp-5.1/UComp/R/UCvalidate.R |only 24 files changed, 1122 insertions(+), 531 deletions(-)
Title: Causal Inference with Continuous (Multiple Time Point)
Interventions
Description: Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.
Author: Michael Schomaker [aut, cre],
Leo Fuhrhop [ctb]
Maintainer: Michael Schomaker <michael.schomaker@stat.uni-muenchen.de>
Diff between CICI versions 0.9.5 dated 2025-05-20 and 0.9.6 dated 2025-07-21
DESCRIPTION | 13 +++++++------ MD5 | 18 +++++++++++------- NAMESPACE | 5 +++-- R/contrast.R |only R/gformula.r | 9 ++++----- R/helper.r | 20 ++++++++++---------- R/mi.boot.r | 2 +- R/print.contrastResult.R |only man/CICI-package.Rd | 4 ++-- man/contrast.Rd |only man/gformula.Rd | 2 +- man/print.contrastResult.Rd |only 12 files changed, 39 insertions(+), 34 deletions(-)
More information about ShrinkageTrees at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-12 0.0.5
2025-07-06 0.0.4
Title: Probabilistic Reconciliation via Conditioning
Description: Provides methods for probabilistic reconciliation of hierarchical forecasts of time series.
The available methods include analytical Gaussian reconciliation (Corani et al., 2021)
<doi:10.1007/978-3-030-67664-3_13>,
MCMC reconciliation of count time series (Corani et al., 2024)
<doi:10.1016/j.ijforecast.2023.04.003>,
Bottom-Up Importance Sampling (Zambon et al., 2024)
<doi:10.1007/s11222-023-10343-y>,
methods for the reconciliation of mixed hierarchies (Mix-Cond and TD-cond)
(Zambon et al., 2024) <https://proceedings.mlr.press/v244/zambon24a.html>.
Author: Dario Azzimonti [aut, cre] ,
Nicolo Rubattu [aut] ,
Lorenzo Zambon [aut] ,
Giorgio Corani [aut]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between bayesRecon versions 0.3.2 dated 2024-11-04 and 0.3.3 dated 2025-07-21
bayesRecon-0.3.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_b5653210a4dc5c04299b83d18464324f.RData |only bayesRecon-0.3.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_b5653210a4dc5c04299b83d18464324f.rdb |only bayesRecon-0.3.2/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_b5653210a4dc5c04299b83d18464324f.rdx |only bayesRecon-0.3.3/bayesRecon/DESCRIPTION | 22 +- bayesRecon-0.3.3/bayesRecon/MD5 | 64 ++--- bayesRecon-0.3.3/bayesRecon/NEWS.md | 4 bayesRecon-0.3.3/bayesRecon/R/PMF.R | 109 ++++++++-- bayesRecon-0.3.3/bayesRecon/R/bayesRecon-package.R | 3 bayesRecon-0.3.3/bayesRecon/R/hierarchy.R | 11 - bayesRecon-0.3.3/bayesRecon/R/reconc_MixCond.R | 3 bayesRecon-0.3.3/bayesRecon/R/reconc_TDcond.R | 6 bayesRecon-0.3.3/bayesRecon/R/shrink_cov.R | 5 bayesRecon-0.3.3/bayesRecon/R/utils.R | 2 bayesRecon-0.3.3/bayesRecon/README.md | 6 bayesRecon-0.3.3/bayesRecon/build/partial.rdb |binary bayesRecon-0.3.3/bayesRecon/build/vignette.rds |binary bayesRecon-0.3.3/bayesRecon/inst/doc/bayesRecon.R | 8 bayesRecon-0.3.3/bayesRecon/inst/doc/bayesRecon.Rmd | 8 bayesRecon-0.3.3/bayesRecon/inst/doc/bayesRecon.html | 34 +-- bayesRecon-0.3.3/bayesRecon/inst/doc/mixed_reconciliation.R | 40 +-- bayesRecon-0.3.3/bayesRecon/inst/doc/mixed_reconciliation.Rmd | 40 +-- bayesRecon-0.3.3/bayesRecon/inst/doc/mixed_reconciliation.html | 45 ++-- bayesRecon-0.3.3/bayesRecon/inst/doc/reconciliation_properties.R | 2 bayesRecon-0.3.3/bayesRecon/inst/doc/reconciliation_properties.Rmd | 2 bayesRecon-0.3.3/bayesRecon/inst/doc/reconciliation_properties.html | 14 - bayesRecon-0.3.3/bayesRecon/man/bayesRecon-package.Rd | 6 bayesRecon-0.3.3/bayesRecon/man/reconc_MixCond.Rd | 3 bayesRecon-0.3.3/bayesRecon/man/reconc_TDcond.Rd | 3 bayesRecon-0.3.3/bayesRecon/tests/testthat/test-schaferStrimmer.R | 13 + bayesRecon-0.3.3/bayesRecon/vignettes/bayesRecon.Rmd | 8 bayesRecon-0.3.3/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_a1e8d8fd15099b693549111bf0ad7931.RData |only bayesRecon-0.3.3/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_a1e8d8fd15099b693549111bf0ad7931.rdb |only bayesRecon-0.3.3/bayesRecon/vignettes/bayesRecon_cache/html/hier-fore_a1e8d8fd15099b693549111bf0ad7931.rdx |only bayesRecon-0.3.3/bayesRecon/vignettes/mixed_reconciliation.Rmd | 40 +-- bayesRecon-0.3.3/bayesRecon/vignettes/reconciliation_properties.Rmd | 2 bayesRecon-0.3.3/bayesRecon/vignettes/references.bib | 32 ++ 36 files changed, 345 insertions(+), 190 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 2.1.0 dated 2025-05-20 and 2.1.1 dated 2025-07-21
DESCRIPTION | 10 +++---- MD5 | 22 +++++++-------- NEWS.md | 6 +++- R/normalize_feature.R | 18 ++++++------ inst/doc/bdd.html | 45 +++++--------------------------- inst/doc/bdd.qmd | 2 - inst/doc/how-it-works.html | 39 +++------------------------ inst/doc/migration-to-2-0-0.html | 2 - inst/doc/reference-gherkin.html | 2 - tests/testthat/_snaps/local/examples.md | 4 +- tests/testthat/test-normalize_feature.R | 28 +++++++++++++++++++ vignettes/bdd.qmd | 2 - 12 files changed, 77 insertions(+), 103 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
re [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.23.0 dated 2025-07-02 and 1.24.0 dated 2025-07-21
DESCRIPTION | 8 MD5 | 136 +-- NAMESPACE | 3 NEWS.md | 11 R/ctrFindActiveSubstanceSynonyms.R | 2 R/ctrGenerateQueries.R | 110 +- R/ctrGetQueryUrl.R | 2 R/ctrLoadQueryIntoDb.R | 46 - R/ctrLoadQueryIntoDbCtgov2.R | 7 R/ctrLoadQueryIntoDbCtis.R | 3 R/ctrLoadQueryIntoDbEuctr.R | 18 R/ctrLoadQueryIntoDbIsrctn.R | 1 R/ctrOpenSearchPagesInBrowser.R | 27 R/ctrShowOneTrial.R | 2 R/ctrdata-trial-concepts.R | 21 R/dbFindFields.R | 2 R/dbFindIdsUniqueTrials.R | 11 R/dbGetFieldsIntoDf.R | 47 - R/dbQueryHistory.R | 2 R/dfMergeVariablesRelevel.R | 2 R/dfName2Value.R | 2 R/dfTrials2Long.R | 2 R/f_assignmentType.R |only R/f_controlType.R | 52 - R/f_externalLinks.R |only R/f_hasResults.R |only R/f_isMedIntervTrial.R | 24 R/f_isUniqueTrial.R | 4 R/f_likelyPlatformTrial.R | 4 R/f_numSites.R | 6 R/f_numTestArmsSubstances.R | 6 R/f_primaryEndpointDescription.R | 4 R/f_primaryEndpointResults.R | 4 R/f_resultsDate.R | 4 R/f_sampleSize.R | 4 R/f_sponsorType.R | 190 +++- R/f_startDate.R | 4 R/f_statusRecruitment.R | 6 R/f_trialObjectives.R | 4 R/f_trialPhase.R | 4 R/f_trialPopulation.R | 4 R/f_trialTitle.R | 4 R/util_fields.R | 2 R/util_functions.R | 45 README.md | 196 ++-- inst/WORDLIST | 4 inst/doc/ctrdata_install.Rmd | 2 inst/doc/ctrdata_install.html | 2 inst/doc/ctrdata_retrieve.R | 33 inst/doc/ctrdata_retrieve.Rmd | 46 - inst/doc/ctrdata_retrieve.html | 678 +++++++-------- inst/doc/ctrdata_summarise.R | 56 - inst/doc/ctrdata_summarise.Rmd | 62 - inst/doc/ctrdata_summarise.html | 100 -- inst/tinytest/ctrdata_euctr.R | 10 inst/tinytest/ctrdata_isrctn.R | 69 + inst/tinytest/test_ctrdata_function_ctrgeneratequeries.R | 70 + inst/tinytest/test_ctrdata_function_trial-concepts.R | 13 inst/tinytest/test_ctrdata_function_various.R | 42 man/ctrGenerateQueries.Rd | 15 man/ctrLoadQueryIntoDb.Rd | 24 man/ctrdata-trial-concepts.Rd | 18 man/dbGetFieldsIntoDf.Rd | 13 man/f.assignmentType.Rd |only man/f.externalLinks.Rd |only man/f.hasResults.Rd |only man/f.sponsorType.Rd | 7 man/figures/README-ctrdata_across_registers.png |binary man/figures/README-ctrdata_results_neuroblastoma.png |binary vignettes/ctrdata_install.Rmd | 2 vignettes/ctrdata_retrieve.Rmd | 46 - vignettes/ctrdata_summarise.Rmd | 62 - 72 files changed, 1367 insertions(+), 1043 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.0.1 dated 2025-07-17 and 4.0.2 dated 2025-07-21
DESCRIPTION | 6 ++-- MD5 | 20 ++++++------- NAMESPACE | 1 NEWS.md | 9 ++++++ R/rbind.R | 6 +++- R/rxode2_md5.R | 2 - inst/doc/rxode2-syntax.html | 27 ++++++++---------- inst/include/rxode2parseVer.h | 4 +- inst/tools/workaround.R | 3 +- src/codegen.c | 27 ++++++++++++++++-- src/codegen2.h | 61 +++++++++++++++++++++--------------------- 11 files changed, 101 insertions(+), 65 deletions(-)
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.6.2 dated 2025-05-01 and 1.6.3 dated 2025-07-21
HLAtools-1.6.2/HLAtools/R/buildGazeteer.R |only HLAtools-1.6.2/HLAtools/data/HLAgazeteer.rda |only HLAtools-1.6.2/HLAtools/man/HLAgazeteer.Rd |only HLAtools-1.6.2/HLAtools/man/buildGazeteer.Rd |only HLAtools-1.6.3/HLAtools/DESCRIPTION | 6 - HLAtools-1.6.3/HLAtools/MD5 | 56 +++++++++--------- HLAtools-1.6.3/HLAtools/NAMESPACE | 2 HLAtools-1.6.3/HLAtools/NEWS.md | 7 ++ HLAtools-1.6.3/HLAtools/R/UpdateAll.R | 26 ++++---- HLAtools-1.6.3/HLAtools/R/alignmentFull.R | 30 ++++----- HLAtools-1.6.3/HLAtools/R/atlasFull.R | 8 +- HLAtools-1.6.3/HLAtools/R/atlasMaker.R | 8 +- HLAtools-1.6.3/HLAtools/R/buildAlignments.R | 14 ++-- HLAtools-1.6.3/HLAtools/R/buildGazetteer.R |only HLAtools-1.6.3/HLAtools/R/data.R | 16 ++--- HLAtools-1.6.3/HLAtools/R/fragmentFeatureNames.R | 6 - HLAtools-1.6.3/HLAtools/R/globals.R | 2 HLAtools-1.6.3/HLAtools/R/locusValidator.R | 24 +++---- HLAtools-1.6.3/HLAtools/README.md | 18 ++--- HLAtools-1.6.3/HLAtools/data/HLAatlas.rda |binary HLAtools-1.6.3/HLAtools/data/HLAgazetteer.rda |only HLAtools-1.6.3/HLAtools/data/fragmentFeatureNames.rda |binary HLAtools-1.6.3/HLAtools/inst/doc/HLAtools.Rmd | 34 +++++----- HLAtools-1.6.3/HLAtools/inst/doc/HLAtools.html | 46 +++++++------- HLAtools-1.6.3/HLAtools/man/HLAgazetteer.Rd |only HLAtools-1.6.3/HLAtools/man/alignmentFull.Rd | 6 - HLAtools-1.6.3/HLAtools/man/alleleListHistory.Rd | 2 HLAtools-1.6.3/HLAtools/man/buildGazetteer.Rd |only HLAtools-1.6.3/HLAtools/man/getAlignmentNames.Rd | 2 HLAtools-1.6.3/HLAtools/man/multiLocusValidation.Rd | 8 +- HLAtools-1.6.3/HLAtools/man/updateAll.Rd | 2 HLAtools-1.6.3/HLAtools/man/validateLocus.Rd | 6 - HLAtools-1.6.3/HLAtools/vignettes/HLAtools.Rmd | 34 +++++----- 33 files changed, 185 insertions(+), 178 deletions(-)
Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests.
Includes tools for stubbing 'HTTP' requests, including expected
request conditions and response conditions. Match on
'HTTP' method, query parameters, request body, headers and
more. Can be used for unit tests or outside of a testing
context.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [ctb] ,
rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between webmockr versions 2.1.0 dated 2025-06-29 and 2.2.0 dated 2025-07-21
webmockr-2.1.0/webmockr/R/globals.R |only webmockr-2.1.0/webmockr/tests/testthat/test-b-no-cassette-in-use.R |only webmockr-2.1.0/webmockr/tests/testthat/test-writing-to-disk-write_disk_path.R |only webmockr-2.2.0/webmockr/DESCRIPTION | 9 webmockr-2.2.0/webmockr/MD5 | 94 +++--- webmockr-2.2.0/webmockr/NAMESPACE | 2 webmockr-2.2.0/webmockr/NEWS.md | 10 webmockr-2.2.0/webmockr/R/adapter-crul.R | 32 -- webmockr-2.2.0/webmockr/R/adapter-httr.R | 1 webmockr-2.2.0/webmockr/R/adapter-httr2.R | 1 webmockr-2.2.0/webmockr/R/adapter.R | 83 ----- webmockr-2.2.0/webmockr/R/flipswitch.R | 24 + webmockr-2.2.0/webmockr/R/mocking-disk-writing.R | 2 webmockr-2.2.0/webmockr/R/pluck_body.R | 8 webmockr-2.2.0/webmockr/R/stub_request.R | 143 ---------- webmockr-2.2.0/webmockr/R/webmockr-package.R | 3 webmockr-2.2.0/webmockr/R/zzz.R | 13 webmockr-2.2.0/webmockr/man/mocking-disk-writing.Rd | 2 webmockr-2.2.0/webmockr/man/stub_request.Rd | 143 ---------- webmockr-2.2.0/webmockr/man/webmockr-package.Rd | 1 webmockr-2.2.0/webmockr/tests/testthat/_snaps/Adapter.md | 20 - webmockr-2.2.0/webmockr/tests/testthat/_snaps/flipswitch.md |only webmockr-2.2.0/webmockr/tests/testthat/helper-webmockr.R | 2 webmockr-2.2.0/webmockr/tests/testthat/httr2_obj.rda |binary webmockr-2.2.0/webmockr/tests/testthat/httr2_obj_auth.rda |binary webmockr-2.2.0/webmockr/tests/testthat/httr_obj.rda |binary webmockr-2.2.0/webmockr/tests/testthat/httr_obj_auth.rda |binary webmockr-2.2.0/webmockr/tests/testthat/test-Adapter.R | 10 webmockr-2.2.0/webmockr/tests/testthat/test-CrulAdapter.R | 42 -- webmockr-2.2.0/webmockr/tests/testthat/test-Httr2Adapter.R | 64 ---- webmockr-2.2.0/webmockr/tests/testthat/test-HttrAdapter.R | 93 ------ webmockr-2.2.0/webmockr/tests/testthat/test-RequestPattern.R | 4 webmockr-2.2.0/webmockr/tests/testthat/test-Response.R | 4 webmockr-2.2.0/webmockr/tests/testthat/test-StubbedRequest.R | 32 +- webmockr-2.2.0/webmockr/tests/testthat/test-auth_handling.R | 4 webmockr-2.2.0/webmockr/tests/testthat/test-flipswitch.R | 13 webmockr-2.2.0/webmockr/tests/testthat/test-last_request.R | 1 webmockr-2.2.0/webmockr/tests/testthat/test-partial_matching.R | 42 +- webmockr-2.2.0/webmockr/tests/testthat/test-request_registry.R | 1 webmockr-2.2.0/webmockr/tests/testthat/test-stub_body_diff.R | 9 webmockr-2.2.0/webmockr/tests/testthat/test-stub_requests_crul.R | 18 - webmockr-2.2.0/webmockr/tests/testthat/test-to_return.R | 4 webmockr-2.2.0/webmockr/tests/testthat/test-to_return_body.R | 2 webmockr-2.2.0/webmockr/tests/testthat/test-to_return_then.R | 4 webmockr-2.2.0/webmockr/tests/testthat/test-uri_regex.R | 7 webmockr-2.2.0/webmockr/tests/testthat/test-webmockr_reset.R | 2 webmockr-2.2.0/webmockr/tests/testthat/test-wi_th.R | 3 webmockr-2.2.0/webmockr/tests/testthat/test-within_test_that_blocks.R | 2 webmockr-2.2.0/webmockr/tests/testthat/test-writing-to-disk.R | 2 webmockr-2.2.0/webmockr/tests/testthat/test-zutils.R | 3 50 files changed, 232 insertions(+), 727 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Roger Bivand [ctb] ,
Andrew Brown [ctb] ,
Michael Chirico [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-54 dated 2025-06-01 and 1.8-60 dated 2025-07-21
DESCRIPTION | 29 +++++------ MD5 | 80 +++++++++++++++--------------- NEWS.md | 52 ++++++++++++++----- R/extract.R | 9 +++ R/gdal.R | 1 R/layerCor.R | 4 - R/plot_legend_continuous.R | 4 + R/tapp.R | 14 ++++- R/tiles.R | 20 ++++--- R/vect.R | 2 R/zonal.R | 20 ++++--- build/partial.rdb |binary inst/tinytest/test_extract.R | 78 +++++++++++++++++++++++++++++ man/freq.Rd | 4 + man/layerCor.Rd | 17 ++---- man/plot.Rd | 1 man/vrt.Rd | 12 ++-- src/RcppModule.cpp | 14 ++--- src/arith.cpp | 12 +++- src/distRaster.cpp | 4 - src/distValueRaster.cpp | 2 src/distance.cpp | 4 - src/extract.cpp | 40 +++++++-------- src/focal.cpp | 34 ++++++------ src/gcp.cpp | 2 src/gdal_algs.cpp | 8 +-- src/gdal_multidimensional.cpp | 34 ++++++++---- src/gdalio.cpp | 13 +++- src/geos_methods.cpp | 23 +++++++- src/movingWindow.cpp | 4 - src/nearest.cpp | 2 src/raster_methods.cpp | 24 +++++---- src/read_gdal.cpp | 50 +++++++++++-------- src/sample.cpp | 2 src/spatRaster.cpp | 110 +++++++++++++++++++++--------------------- src/spatRaster.h | 57 ++++++++++----------- src/spatSources.cpp | 6 +- src/spatVector.cpp | 16 +++--- src/surfArea.cpp | 2 src/vector_methods.cpp | 11 +++- src/write.cpp | 8 +-- 41 files changed, 510 insertions(+), 319 deletions(-)
Title: Loop Functions for Extreme Value Distributions
Description: Performs extreme value analysis at multiple locations using functions from the 'evd' package. Supports both point-based and gridded input data using the 'terra' package, enabling flexible looping across spatial datasets for batch processing of generalised extreme value, Gumbel fits.
Author: Julian O'Grady [aut, cre]
Maintainer: Julian O'Grady <julian.ogrady@csiro.au>
Diff between loopevd versions 1.0.1 dated 2025-06-23 and 1.0.2 dated 2025-07-21
DESCRIPTION | 6 +-- MD5 | 11 +++-- NAMESPACE | 1 R/loopFuns.R | 82 +++++++++++++++++++++++++++++++++++++++++- inst/doc/Into_to_loopevd.html | 8 ++-- man/df_fevd.Rd |only man/raster_fevd.Rd | 2 - 7 files changed, 96 insertions(+), 14 deletions(-)