Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre] ,
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-7 dated 2025-05-19 and 1.0-8 dated 2026-07-02
GET-1.0-7/GET/R/appl_hotspots.r |only GET-1.0-7/GET/R/roadcrash.r |only GET-1.0-7/GET/data/roadcrash.RData |only GET-1.0-7/GET/inst/doc/HotSpots.pdf |only GET-1.0-7/GET/inst/doc/HotSpots.tex.rsp |only GET-1.0-7/GET/man/MatClust.lppm.Rd |only GET-1.0-7/GET/man/hotspots.MatClustlpp.Rd |only GET-1.0-7/GET/man/hotspots.poislpp.Rd |only GET-1.0-7/GET/man/pois.lppm.Rd |only GET-1.0-7/GET/man/rMatClustlpp.Rd |only GET-1.0-7/GET/man/roadcrash.Rd |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param_obs.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param_sim.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_sim.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_covariates.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_covariates_subwin.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_crashes.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_crashes_thin.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_density.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_poisson_EIP.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_poisson_K.pdf |only GET-1.0-7/GET/vignettes/HotSpots-fdrenvelope.pdf |only GET-1.0-7/GET/vignettes/HotSpots-fdrenvelope_cset.pdf |only GET-1.0-7/GET/vignettes/HotSpots.Rnw.orig |only GET-1.0-7/GET/vignettes/HotSpots.tex.rsp |only GET-1.0-8/GET/DESCRIPTION | 20 +- GET-1.0-8/GET/MD5 | 108 ++++------- GET-1.0-8/GET/NAMESPACE | 13 - GET-1.0-8/GET/NEWS | 6 GET-1.0-8/GET/R/appl_variogram.r | 8 GET-1.0-8/GET/R/curve-set.r | 6 GET-1.0-8/GET/R/fclustering.r | 10 - GET-1.0-8/GET/R/fdr.r | 12 + GET-1.0-8/GET/R/glm.R | 73 ++++--- GET-1.0-8/GET/R/plot_envelope_helper.R | 35 +-- GET-1.0-8/GET/build/vignette.rds |binary GET-1.0-8/GET/data/GDP.RData |binary GET-1.0-8/GET/data/GDPtax.RData |binary GET-1.0-8/GET/data/abide_9002_23.RData |binary GET-1.0-8/GET/data/adult_trees.RData |binary GET-1.0-8/GET/data/cgec.RData |binary GET-1.0-8/GET/data/datalist | 1 GET-1.0-8/GET/data/fallen_trees.RData |binary GET-1.0-8/GET/data/imageset3.RData |binary GET-1.0-8/GET/data/naturalness.RData |binary GET-1.0-8/GET/data/popgrowthmillion.RData |binary GET-1.0-8/GET/data/rimov.RData |binary GET-1.0-8/GET/data/saplings.RData |binary GET-1.0-8/GET/inst/doc/FDRenvelopes.pdf |binary GET-1.0-8/GET/inst/doc/FDRenvelopes.tex.rsp | 2 GET-1.0-8/GET/inst/doc/GET.pdf |binary GET-1.0-8/GET/inst/doc/GET.tex.rsp | 6 GET-1.0-8/GET/inst/doc/QuantileRegression.pdf |binary GET-1.0-8/GET/inst/doc/QuantileRegression.tex.rsp | 4 GET-1.0-8/GET/inst/doc/pointpatterns.pdf |binary GET-1.0-8/GET/inst/doc/pointpatterns.tex.rsp | 2 GET-1.0-8/GET/man/GET.variogram.Rd | 4 GET-1.0-8/GET/man/geom_central_region.Rd | 8 GET-1.0-8/GET/man/graph.flm.Rd | 3 GET-1.0-8/GET/vignettes/FDRenvelopes.Rnw.orig | 6 GET-1.0-8/GET/vignettes/FDRenvelopes.tex.rsp | 2 GET-1.0-8/GET/vignettes/GET.Rnw.orig | 4 GET-1.0-8/GET/vignettes/GET.tex.rsp | 6 GET-1.0-8/GET/vignettes/QuantileRegression.Rnw.orig | 4 GET-1.0-8/GET/vignettes/QuantileRegression.tex.rsp | 4 GET-1.0-8/GET/vignettes/pointpatterns.Rnw.orig | 2 GET-1.0-8/GET/vignettes/pointpatterns.tex.rsp | 2 68 files changed, 179 insertions(+), 172 deletions(-)
Title: Simulation of Discrete Random Variables with Marginal
Distributions and Correlation Matrix and via a Gaussian or
Student's t Copula
Description: A Gaussian or Student's t copula-based procedure for generating samples from discrete random variables with prescribed correlation matrix and marginal distributions.
Author: Alessandro Barbiero [aut, cre],
Pier Alda Ferrari [aut]
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between GenOrd versions 2.0.0 dated 2025-09-22 and 2.1.0 dated 2026-07-02
DESCRIPTION | 12 ++-- MD5 | 39 ++++++++------- NAMESPACE | 49 ++++++++++-------- R/contord.R | 129 +++++++++++++++++++++++++++++--------------------- R/estcontord.R | 31 ++++++------ R/logL.R | 14 ----- R/logLfull.R | 52 +++++++++++--------- R/logLfullz.R |only R/p_rect_t.R |only R/pmvt.alt.R | 14 ++--- README.md |only man/GenOrd-package.Rd | 14 +++-- man/contord.Rd | 44 +++++++++++++---- man/corrcheck.Rd | 6 +- man/estcontord.Rd | 52 ++++++++++++++------ man/logL.Rd | 16 +++--- man/logL_mle2.Rd | 11 ++-- man/logLfull.Rd | 17 +++--- man/logLfullz.Rd |only man/ordcont.Rd | 38 ++++++++++++-- man/ordsample.Rd | 26 +++++----- man/p_rect_t.Rd |only man/pmvt.alt.Rd | 29 ++++++----- 23 files changed, 362 insertions(+), 231 deletions(-)
Title: Parse Front Matter from Documents
Description: Extracts and parses structured metadata ('YAML' or 'TOML')
from the beginning of text documents. Front matter is a common pattern
in 'Quarto' documents, 'R Markdown' documents, static site generators,
documentation systems, content management tools and even 'Python' and
'R' scripts where metadata is placed at the top of a document,
separated from the main content by delimiter fences.
Author: Garrick Aden-Buie [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between frontmatter versions 0.2.0 dated 2026-02-09 and 0.3.0 dated 2026-07-02
DESCRIPTION | 8 MD5 | 25 +- NEWS.md | 23 ++ R/frontmatter-package.R | 1 R/parse_front_matter.R | 4 R/write_front_matter.R | 145 +++++++++++-- README.md | 61 +++++ man/format_front_matter.Rd | 66 ++++-- man/frontmatter-package.Rd | 6 man/parse_front_matter.Rd | 6 src/extract_front_matter.cpp | 338 ++++++++++++++++++++++++++----- tests/testthat/_snaps/sql-formats.md |only tests/testthat/test-shebang.R |only tests/testthat/test-sql-formats.R |only tests/testthat/test-write_front_matter.R | 109 +++++++++ 15 files changed, 685 insertions(+), 107 deletions(-)
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.2.3 dated 2026-02-26 and 1.3.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 36 - NAMESPACE | 1 NEWS.md | 7 R/estimate_griddap_size.R |only R/grid.R | 144 ++++ R/zzz.r | 31 build/vignette.rds |binary inst/doc/Using_rerddap.R | 43 + inst/doc/Using_rerddap.Rmd | 235 ++++--- inst/doc/Using_rerddap.html | 1366 ++++++++++++++++++++++--------------------- man/cache_delete.Rd | 8 man/cache_details.Rd | 8 man/cache_list.Rd | 8 man/cache_setup.Rd | 8 man/disk.Rd | 4 man/estimate_griddap_size.Rd |only man/eurl.Rd | 4 man/griddap.Rd | 12 vignettes/Using_rerddap.Rmd | 235 ++++--- 20 files changed, 1285 insertions(+), 875 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc_node_en.html> for more information).
Choose observational time series from meteorological stations with 'selectDWD()'.
Find raster data from radar and interpolation according to <https://brry.github.io/rdwd/raster-data.html>.
Download (multiple) data sets with progress bars and no re-downloads through 'dataDWD()'.
Read both tabular observational data and binary gridded datasets with 'readDWD()'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.9.8 dated 2025-12-21 and 1.9.17 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 72 +++++----- NEWS.md | 13 + R/checkUpdates.R | 4 R/dataDWD.R | 43 +++++ R/indexFTP.R | 1 R/locdir.R | 2 R/plotRadar.R | 6 R/readDWD.R | 34 ++-- R/runLocalTests.R | 4 R/updateIndexes.R | 11 + README.md | 11 - build/vignette.rds |binary data/fileIndex.rda |binary data/formatIndex.rda |binary data/geoIndex.rda |binary data/gridIndex.rda |binary data/metaIndex.rda |binary inst/shinyapps/compare_years/app.R | 6 inst/shinyapps/compare_years/rsconnect/shinyapps.io/brry/wetter.dcf | 2 man/checkUpdates.Rd | 4 man/dataDWD.Rd | 17 ++ man/dwdbase.Rd | 5 man/dwdparams.Rd | 4 man/locdir.Rd | 4 man/plotDWD.Rd | 4 man/plotRadar.Rd | 2 man/projectRasterDWD.Rd | 10 - man/readDWD.Rd | 4 man/readDWD.deriv.Rd | 2 man/readDWD.grib2.Rd | 2 man/readDWD.hyras.Rd | 7 man/readDWD.nc.Rd | 9 - man/readDWD.radar.Rd | 10 - man/readDWD.raster.Rd | 2 man/updateIndexes.Rd | 6 man/validFileTypes.Rd | 5 37 files changed, 203 insertions(+), 113 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package 'randomForest', written by Andy Liaw.
Author: Nicolai Meinshausen [aut, cre],
Loris Michel [aut]
Maintainer: Nicolai Meinshausen <meinshausen@gmail.com>
Diff between quantregForest versions 1.3-7.1 dated 2024-10-07 and 1.4-0 dated 2026-07-02
quantregForest-1.3-7.1/quantregForest/R/MDSplot.R |only quantregForest-1.3-7.1/quantregForest/R/classCenter.R |only quantregForest-1.3-7.1/quantregForest/R/combine.R |only quantregForest-1.3-7.1/quantregForest/R/convert.R |only quantregForest-1.3-7.1/quantregForest/R/getTree.R |only quantregForest-1.3-7.1/quantregForest/R/grow.R |only quantregForest-1.3-7.1/quantregForest/R/importance.R |only quantregForest-1.3-7.1/quantregForest/R/margin.R |only quantregForest-1.3-7.1/quantregForest/R/na.roughfix.R |only quantregForest-1.3-7.1/quantregForest/R/outlier.R |only quantregForest-1.3-7.1/quantregForest/R/partialPlot.R |only quantregForest-1.3-7.1/quantregForest/R/rfImpute.R |only quantregForest-1.3-7.1/quantregForest/R/rfcv.R |only quantregForest-1.3-7.1/quantregForest/R/treesize.R |only quantregForest-1.3-7.1/quantregForest/R/tuneRF.R |only quantregForest-1.3-7.1/quantregForest/R/varImpPlot.R |only quantregForest-1.3-7.1/quantregForest/R/varUsed.R |only quantregForest-1.3-7.1/quantregForest/R/zzz.R |only quantregForest-1.3-7.1/quantregForest/src |only quantregForest-1.4-0/quantregForest/DESCRIPTION | 25 quantregForest-1.4-0/quantregForest/MD5 | 37 quantregForest-1.4-0/quantregForest/NAMESPACE | 10 quantregForest-1.4-0/quantregForest/NEWS |only quantregForest-1.4-0/quantregForest/R/parallelRandomForest.R | 514 ---------- quantregForest-1.4-0/quantregForest/R/predict.quantregForest.R | 103 +- quantregForest-1.4-0/quantregForest/R/quantregForest.R | 59 - 26 files changed, 133 insertions(+), 615 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://developers.openalex.org/>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 3.0.1 dated 2026-01-14 and 3.1.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 82 +++---- NAMESPACE | 1 NEWS.md | 17 + R/data.R | 8 R/oa2bibliometrix.R | 2 R/oa2df.R | 426 ++++++++++++++------------------------- R/oa_fetch.R | 130 +++++++---- R/oa_ngrams.R | 6 R/oa_options.R |only R/oa_snowball.R | 4 R/simplify.R | 4 R/utils.R | 2 README.md | 145 +++++++++---- data/oa2df_coverage.rda |binary man/authors2df.Rd | 4 man/concepts2df.Rd | 4 man/countrycode.Rd | 4 man/funders2df.Rd | 4 man/institutions2df.Rd | 4 man/keywords2df.Rd | 2 man/oa2bibliometrix.Rd | 2 man/oa2df.Rd | 32 -- man/oa2df_coverage.Rd | 4 man/oa_fetch.Rd | 62 ++--- man/oa_ngrams.Rd | 6 man/oa_options.Rd |only man/oa_query.Rd | 36 +-- man/oa_request.Rd | 6 man/oa_snowball.Rd | 4 man/openalexR-package.Rd | 3 man/process_paper_authors.Rd | 2 man/publishers2df.Rd | 4 man/show_authors.Rd | 2 man/show_works.Rd | 2 man/sources2df.Rd | 4 man/topics2df.Rd | 4 man/works2df.Rd | 4 tests/testthat/fixtures |only tests/testthat/test-coverage.R | 2 tests/testthat/test-oa2df.R | 56 +++++ tests/testthat/test-oa_fetch.R | 178 +++++++++++++++- tests/testthat/test-oa_options.R |only tests/testthat/test-oa_query.R | 15 + 44 files changed, 730 insertions(+), 557 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.20 dated 2026-06-01 and 1.0.21 dated 2026-07-02
DESCRIPTION | 15 +- MD5 | 66 +++++----- R/check_model_da.R | 2 R/construct_matrices_da.R | 7 - R/equations_lms.R | 45 +++++-- R/equations_qml.R | 4 R/generics_modsem_da.R | 8 - R/lav_syntax_functions.R | 18 ++ R/lexer.R | 6 R/mod_msg.R | 15 ++ R/model_da.R | 1 R/modsem_da.R | 32 +++-- R/modsem_data_da.R | 30 +++- R/modsem_mplus.R | 82 +++++++++++- R/ordered_mc_correction.R | 192 ++++++++++++++++++++++++++---- R/parser.R | 69 +++++++--- R/print_partable.R | 12 - R/simple_slopes.R | 44 ++---- R/summarize_partable.R | 8 - R/tokenizer.R | 39 ++++-- R/utils.R | 13 +- R/utils_da.R | 12 + R/zzz.R | 65 ++++++++++ README.md | 4 inst/doc/customize_plot_interactions.html | 2 inst/doc/observed_lms_qml.html | 6 inst/doc/plot_interactions.html | 8 - man/modsem-package.Rd | 5 man/modsem_da.Rd | 31 +++- man/modsem_mplus.Rd | 5 src/equations_lms.cpp | 86 ++----------- tests/testthat/test_composites_da.R | 3 tests/testthat/test_intchecks.R | 20 +++ tests/testthat/test_missing.R | 36 +++++ 34 files changed, 690 insertions(+), 301 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.9.0 dated 2026-02-15 and 3.10.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 677 NAMESPACE | 358 NEWS.md | 1065 - R/as_gt.R | 164 R/as_rtf.R | 504 R/as_table.R | 120 R/binomialExactPValues.R |only R/binomialPowerTable.R | 316 R/globals.R | 20 R/gsBinomial.R | 910 - R/gsBinomialExact.R | 921 - R/gsCP.R | 1061 - R/gsDesign-package.R | 8 R/gsDesign.R | 3498 ++-- R/gsMethods.R | 2147 +- R/gsNormalGrid.R | 260 R/gsSimulate.R | 242 R/gsSpending.R | 3672 ++-- R/gsSurv-eEvents.R | 668 R/gsSurv-interim.R | 90 R/gsSurv-method.R | 1098 - R/gsSurv-nSurv.R | 1378 - R/gsSurv-utils.R | 95 R/gsSurv-xtable.R | 162 R/gsSurv.R | 714 R/gsSurvCalendar.R | 436 R/gsSurvPower.R |only R/gsSurvival.R | 620 R/gsUtilities.R | 654 R/gsWTPT.R | 234 R/gsqplot.R | 2382 +- R/nBinomial1Sample.R | 82 R/nEvents.R | 118 R/nNormal.R | 284 R/sequentialPValue.R | 225 R/sfXG.R | 406 R/simBinomialSeasonalExact.R |only R/ssrCP.R | 1352 - R/toBinomialExact.R | 498 R/toInteger.R | 523 R/varBinomial.R | 640 R/xtable.R | 254 README.md | 87 build/vignette.rds |binary inst/doc/ConditionalErrorSpending.R | 420 inst/doc/ConditionalErrorSpending.Rmd | 790 inst/doc/ConditionalErrorSpending.html | 4770 ++--- inst/doc/ConditionalPowerPlot.R | 188 inst/doc/ConditionalPowerPlot.Rmd | 364 inst/doc/ConditionalPowerPlot.html | 1186 - inst/doc/GentleIntroductionToGSD.R | 206 inst/doc/GentleIntroductionToGSD.Rmd | 560 inst/doc/GentleIntroductionToGSD.html | 1416 - inst/doc/GraphicalMultiplicity.Rmd | 22 inst/doc/GraphicalMultiplicity.html | 524 inst/doc/HarmBound.R |only inst/doc/HarmBound.Rmd |only inst/doc/HarmBound.html |only inst/doc/MultiSeasonRareEvents.R |only inst/doc/MultiSeasonRareEvents.Rmd |only inst/doc/MultiSeasonRareEvents.html |only inst/doc/PoissonMixtureModel.R | 438 inst/doc/PoissonMixtureModel.Rmd | 708 inst/doc/PoissonMixtureModel.html | 2374 +- inst/doc/SelectiveBoundTesting.R |only inst/doc/SelectiveBoundTesting.Rmd |only inst/doc/SelectiveBoundTesting.html |only inst/doc/SeqDesignSurvival.R |only inst/doc/SeqDesignSurvival.Rmd |only inst/doc/SeqDesignSurvival.html |only inst/doc/SpendingFunctionOverview.R | 22 inst/doc/SpendingFunctionOverview.Rmd | 112 inst/doc/SpendingFunctionOverview.html | 646 inst/doc/SurvivalOverview.R | 388 inst/doc/SurvivalOverview.Rmd | 864 - inst/doc/SurvivalOverview.html | 2141 +- inst/doc/VaccineEfficacy.R | 562 inst/doc/VaccineEfficacy.Rmd | 929 - inst/doc/VaccineEfficacy.html | 5306 +++--- inst/doc/binomialSPRTExample.R | 122 inst/doc/binomialSPRTExample.Rmd | 312 inst/doc/binomialSPRTExample.html | 2912 +-- inst/doc/binomialTwoSample.R | 454 inst/doc/binomialTwoSample.Rmd | 782 inst/doc/binomialTwoSample.html | 8480 +++++----- inst/doc/gsDesignPackageOverview.R | 38 inst/doc/gsDesignPackageOverview.Rmd | 142 inst/doc/gsDesignPackageOverview.html | 910 - inst/doc/gsSurvBasicExamples.R | 508 inst/doc/gsSurvBasicExamples.Rmd | 848 - inst/doc/gsSurvBasicExamples.html | 4491 ++--- inst/doc/gsSurvPower.R |only inst/doc/gsSurvPower.Rmd |only inst/doc/gsSurvPower.html |only inst/doc/hGraph.Rmd | 22 inst/doc/hGraph.html | 522 inst/doc/nNormal.R | 162 inst/doc/nNormal.Rmd | 420 inst/doc/nNormal.html | 1428 - inst/doc/toInteger.R | 296 inst/doc/toInteger.Rmd | 523 inst/doc/toInteger.html | 1306 - inst/slides |only man/as_gt.Rd | 156 man/as_rtf.Rd | 292 man/as_table.Rd | 84 man/binomialPowerTable.Rd | 198 man/checkScalar.Rd | 270 man/eEvents.Rd | 270 man/gsBinomialExact.Rd | 612 man/gsBound.Rd | 284 man/gsBoundCP.Rd | 150 man/gsBoundSummary.Rd | 704 man/gsCP.Rd | 528 man/gsDensity.Rd | 242 man/gsDesign-package.Rd | 65 man/gsDesign.Rd | 828 man/gsProbability.Rd | 276 man/gsSurvCalendar.Rd | 455 man/gsSurvPower.Rd |only man/nNormal.Rd | 238 man/nSurv.Rd | 1364 - man/nSurvival.Rd | 570 man/normalGrid.Rd | 230 man/plot.gsDesign.Rd | 336 man/repeatedPValueBinomialExact.Rd |only man/sequentiaPValue.Rd | 170 man/sequentialPValueBinomialExact.Rd |only man/sfDistribution.Rd | 340 man/sfExponential.Rd | 222 man/sfHSD.Rd | 180 man/sfLDOF.Rd | 250 man/sfLinear.Rd | 298 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tests/testthat/test-outputs.R | 326 tests/testthat/test-plot_inputs.R | 30 tests/testthat/test-selective-bounds.R |only tests/testthat/test-sequentialPValue.R | 64 tests/testthat/test-sequentialPValueInputs.R | 40 tests/testthat/test-sf_inputs.R | 150 vignettes/ConditionalErrorSpending.Rmd | 790 vignettes/ConditionalPowerPlot.Rmd | 364 vignettes/GentleIntroductionToGSD.Rmd | 560 vignettes/GraphicalMultiplicity.Rmd | 22 vignettes/HarmBound.Rmd |only vignettes/MultiSeasonRareEvents.Rmd |only vignettes/PoissonMixtureModel.Rmd | 708 vignettes/SelectiveBoundTesting.Rmd |only vignettes/SeqDesignSurvival.Rmd |only vignettes/SpendingFunctionOverview.Rmd | 112 vignettes/SurvivalOverview.Rmd | 864 - vignettes/VaccineEfficacy.Rmd | 929 - vignettes/binomialSPRTExample.Rmd | 312 vignettes/binomialTwoSample.Rmd | 782 vignettes/gsDesign.bib | 714 vignettes/gsDesignPackageOverview.Rmd | 142 vignettes/gsDesignVsProcSeqdesign.html |only vignettes/gsSurvBasicExamples.Rmd | 848 - vignettes/gsSurvPower.Rmd 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Title: Plotting Tool for Brain Atlases
Description: Provides a 'ggplot2' geom and position for visualizing brain
region data on cortical, subcortical, and white matter tract atlases.
Brain atlas geometries are stored as polygon data, enabling
seamless integration with the 'ggplot2' ecosystem including faceting,
custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Ramiro Magno [ctb] ,
Center for Lifespan Changes in Brain and Cognition, University of Oslo,
Norway [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 2.2.0 dated 2026-06-22 and 2.2.1 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ inst/doc/external-data.html | 2 +- inst/doc/ggseg.html | 12 ++++++------ inst/doc/positioning-views.html | 4 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/helpers.R | 14 ++++++++++++++ tests/testthat/test-coords.R | 7 ++++--- tests/testthat/test-geom-brain-polygon.R | 5 +---- tests/testthat/test-geom-brain.R | 3 +-- 11 files changed, 48 insertions(+), 31 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.2.0 dated 2026-06-18 and 1.2.1 dated 2026-07-02
DESCRIPTION | 6 MD5 | 20 NEWS.md | 6 R/erafyCohort.R | 30 R/plots.R | 18 R/summariseDiscontinuationAsSurvival.R | 8 R/summariseDrugUtilisation.R | 3 R/tables.R | 2 inst/doc/create_cohorts.html | 220 inst/doc/drug_utilisation.html | 4296 ++++++++--------- tests/testthat/test-generateDrugUtilisationCohortSet.R | 5 11 files changed, 2317 insertions(+), 2297 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
three different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; and 'Nager.Date' for public holidays.
The package enables users to explore various aspects of Colombia such as
geographic locations, cultural attractions, economic indicators, demographic
data, and public holidays. Additionally, 'ColombiAPI' includes curated
datasets covering Bogota air stations, business and holiday dates, public
schools, Colombian coffee exports, cannabis licenses, Medellin rainfall,
malls in Bogota, as well as datasets on indigenous languages, student
admissions and school statistics, forest liana mortality, municipal and
regional data, connectivity and digital infrastructure, program graduates,
vehicle counts, international visitors, [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.3.2 dated 2026-05-06 and 0.4.0 dated 2026-07-02
ColombiAPI-0.3.2/ColombiAPI/R/get_country_info_co.R |only ColombiAPI-0.3.2/ColombiAPI/man/get_country_info_co.Rd |only ColombiAPI-0.3.2/ColombiAPI/tests/testthat/test-get_country_info_co.R |only ColombiAPI-0.4.0/ColombiAPI/DESCRIPTION | 40 +- ColombiAPI-0.4.0/ColombiAPI/MD5 | 163 ++++------ ColombiAPI-0.4.0/ColombiAPI/NAMESPACE | 1 ColombiAPI-0.4.0/ColombiAPI/NEWS.md | 21 + ColombiAPI-0.4.0/ColombiAPI/R/colombiapi-package.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/data-documentation.R | 5 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_airports.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_attractions.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_child_mortality.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_cities.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_cpi.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_departments.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_energy_use.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_gdp.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_holidays.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_hospital_beds.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_invasive_species.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_life_expectancy.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_literacy_rate.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_native_communities.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_natural_areas.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_population.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_presidents.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_radios.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_regions.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_typical_dishes.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_unemployment.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/utils.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/view_datasets_ColombiAPI.R | 2 ColombiAPI-0.4.0/ColombiAPI/README.md | 12 ColombiAPI-0.4.0/ColombiAPI/build/vignette.rds |binary ColombiAPI-0.4.0/ColombiAPI/inst/CITATION | 2 ColombiAPI-0.4.0/ColombiAPI/inst/doc/colombiAPI_vignette.Rmd | 11 ColombiAPI-0.4.0/ColombiAPI/inst/doc/colombiAPI_vignette.html | 25 - ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSE | 4 ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSE.md | 51 +-- ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSES_DETAILS.md | 3 ColombiAPI-0.4.0/ColombiAPI/man/Cartagena_wifi_tbl_df.Rd | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_airstations_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_business_Date.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_holidays_Date.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_malls_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bucaramanga_wifi_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Cartagena_wifi_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Colombia_coffee_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Medellin_rain_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-admitted_students_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-dead_lianas_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-digital_centers_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-digital_graduates_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-foreign_visitors_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-gdp_departments_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_airports.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_attractions.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_child_mortality.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_cities.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_cpi.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_departments.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_energy_use.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_gdp.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_holidays.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_hospital_beds.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_invasive_species.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_life_expectancy.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_literacy_rate.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_native_communities.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_natural_areas.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_population.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_presidents.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_radios.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_regions.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_typical_dishes.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_unemployment.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-indigenous_vocabulary_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-municipalities_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-school_levels_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-vehicle_count_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-view_datasets_ColombiAPI.R | 2 ColombiAPI-0.4.0/ColombiAPI/vignettes/colombiAPI_vignette.Rmd | 11 84 files changed, 240 insertions(+), 243 deletions(-)
Title: Access Chilean Data via APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'FINDIC API', 'World Bank API', and 'Nager.Date',
retrieving real-time or historical data related to Chile such as financial indicators,
holidays, and more.
Additionally, the package includes curated datasets related to Chile, covering topics
such as human rights violations during the Pinochet regime, electoral data, census samples,
health surveys, seismic events, territorial codes, and environmental measurements.
The package supports research and analysis focused on Chile by integrating open APIs with
high-quality datasets from multiple domains. For more information on the APIs, see:
'FINDIC' <https://findic.cl/>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
and 'Nager.Date' <https://date.nager.at/Api>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ChileDataAPI versions 0.2.0 dated 2025-09-11 and 0.3.0 dated 2026-07-02
ChileDataAPI-0.2.0/ChileDataAPI/R/get_country_info_cl.R |only ChileDataAPI-0.2.0/ChileDataAPI/man/get_country_info_cl.Rd |only ChileDataAPI-0.2.0/ChileDataAPI/tests/testthat/test-get_country_info_cl.R |only ChileDataAPI-0.3.0/ChileDataAPI/DESCRIPTION | 13 ChileDataAPI-0.3.0/ChileDataAPI/MD5 | 125 ++++----- ChileDataAPI-0.3.0/ChileDataAPI/NAMESPACE | 2 ChileDataAPI-0.3.0/ChileDataAPI/NEWS.md | 22 + ChileDataAPI-0.3.0/ChileDataAPI/R/chiledataapi-package.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/data-documentation.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_bitcoin.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_child_mortality.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_copper_pound.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_cpi.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_dollar.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_energy_use.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_euro.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_gdp.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_holidays.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_hospital_beds.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_ipsa.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_life_expectancy.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_literacy_rate.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_population.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_uf.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_unemployment.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_utm.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_yen.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/utils.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/view_datasets_ChileDataAPI.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/README.md | 10 ChileDataAPI-0.3.0/ChileDataAPI/build/vignette.rds |binary ChileDataAPI-0.3.0/ChileDataAPI/inst/CITATION | 4 ChileDataAPI-0.3.0/ChileDataAPI/inst/doc/ChileDataAPI_vignette.Rmd | 30 -- ChileDataAPI-0.3.0/ChileDataAPI/inst/doc/ChileDataAPI_vignette.html | 132 ++++------ ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSE | 4 ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSE.md | 34 -- ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSES_DETAILS.md | 5 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-census_chile_2017_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_earthquakes_tbl_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_election_2021_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_health_survey_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_plebiscite_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_bitcoin.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_child_mortality.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_copper_pound.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_cpi.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_dollar.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_energy_use.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_euro.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_gdp.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_holidays.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_hospital_beds.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_ipsa.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_life_expectancy.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_literacy_rate.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_population.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_uf.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_unemployment.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_utm.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_yen.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-malleco_tree_rings_ts.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-pinochet_regime_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-territorial_codes_tbl_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-view_datasets_ChileDataAPI.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/vignettes/ChileDataAPI_vignette.Rmd | 30 -- 65 files changed, 297 insertions(+), 310 deletions(-)
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Dony Unardi [aut, cre],
Joe Zhu [aut] ,
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkof [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.clinical versions 0.12.0 dated 2025-12-03 and 0.13.0 dated 2026-07-02
teal.modules.clinical-0.12.0/teal.modules.clinical/man/select_decorators.Rd |only teal.modules.clinical-0.12.0/teal.modules.clinical/man/srv_decorate_teal_data.Rd |only teal.modules.clinical-0.13.0/teal.modules.clinical/DESCRIPTION | 24 - teal.modules.clinical-0.13.0/teal.modules.clinical/MD5 | 218 ++++------ teal.modules.clinical-0.13.0/teal.modules.clinical/NEWS.md | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/argument_convention.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/R/arm_ref_comp.R | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_a_gee.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_a_mmrm.R | 30 - teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_barchart_simple.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_ci.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_forest_rsp.R | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_forest_tte.R | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_ipp.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_km.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_lineplot.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_adverse_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_patient_timeline.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_therapy.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_vitals.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_abnormality.R | 64 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_abnormality_by_worst_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_ancova.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_binary_outcome.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_coxreg.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_by_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_patyear.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_summary.R | 14 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_exposure.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_glm_counts.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_logistic.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_mult_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_pp_medical_history.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_arm.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_arm_by_worst.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_smq.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_summary.R | 45 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_summary_by.R | 47 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_tte.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/utils.R | 132 ------ teal.modules.clinical-0.13.0/teal.modules.clinical/README.md | 14 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/WORDLIST | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/decorate-module-output.html | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.R | 8 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.Rmd | 8 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.html | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/quickstart_substitute.html | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/teal-modules-clinical.html | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/module_arguments.Rd | 5 teal.modules.clinical-0.13.0/teal.modules.clinical/man/split_choices.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/man/teal.modules.clinical-package.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_abnormality.Rd | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_arguments.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_g_km.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_summary.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_tte.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_binary_outcome.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_summary.Rd | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_summary_by.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_tte.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_g_ipp.md | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_t_abnormality.md | 51 ++ teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_t_summary.md | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/helper-TealAppDriver.R | 19 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/helper-testing-depth.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/setup-options.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-examples.R | 29 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_a_gee.R | 62 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_a_mmrm.R | 61 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_barchart_simple.R | 69 +-- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_ci.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_forest_rsp.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_forest_tte.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_ipp.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_km.R | 78 +-- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_lineplot.R | 63 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R | 38 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R | 111 +---- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_therapy.R | 27 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_vitals.R | 29 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_abnormality.R | 23 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_ancova.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_binary_outcome.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_coxreg.R | 24 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events.R | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_by_grade.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_patyear.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_summary.R | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_exposure.R | 28 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_logistic.R | 26 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_mult_events.R | 21 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_basic_info.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_laboratory.R | 143 +++--- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_medical_history.R | 30 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_prior_medication.R | 36 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm.R | 25 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm_by_worst.R | 36 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_grade.R | 26 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_smq.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_summary.R | 19 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_summary_by.R | 27 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_tte.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_abnormality.R | 20 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_glm_counts.R | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_summary.R | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_summary_by.R | 75 +++ teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-utils.R | 152 ++++++ teal.modules.clinical-0.13.0/teal.modules.clinical/vignettes/generate_tmc_test_data.Rmd | 8 111 files changed, 1403 insertions(+), 1391 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.27 dated 2026-05-25 and 1.28 dated 2026-07-02
DESCRIPTION | 8 MD5 | 90 ++--- NEWS.md | 31 + R/class-color.R | 10 R/class-workbook-utils.R | 60 +++ R/class-workbook-wrappers.R | 3 R/class-workbook.R | 55 ++- R/get-named-regions.R | 19 - R/helper-functions.R | 3 R/openxlsx2-package.R | 14 R/standardize.R | 2 R/utils.R | 2 R/wb_load.R | 43 ++ README.md | 20 - build/vignette.rds |binary inst/AUTHORS | 1 inst/WORDLIST | 3 inst/doc/openxlsx2.R | 4 inst/doc/openxlsx2.Rmd | 5 inst/doc/openxlsx2_charts_manual.R | 2 inst/doc/openxlsx2_charts_manual.Rmd | 2 inst/doc/openxlsx2_charts_manual.html | 10 inst/include/pugixml/pugiconfig.hpp | 15 inst/include/pugixml/pugixml.cpp | 459 ++++++++++++++++++++------- inst/include/pugixml/pugixml.hpp | 107 +++--- man/named_region-wb.Rd | 5 man/openxlsx2-package.Rd | 8 man/wbWorkbook.Rd | 6 man/wb_add_data_table.Rd | 3 man/wb_dims.Rd | 2 src/helper_functions.cpp | 53 ++- src/openxlsx2.h | 5 src/write_file.cpp | 12 tests/testthat/test-class-workbook.R | 65 +++ tests/testthat/test-conditional_formatting.R | 2 tests/testthat/test-helper-functions.R | 35 ++ tests/testthat/test-loading_workbook.R | 62 +++ tests/testthat/test-named_regions.R | 2 tests/testthat/test-read_sources.R | 19 + tests/testthat/test-standardize.R | 28 + tests/testthat/test-tables.R | 26 + tests/testthat/test-utils.R | 5 tests/testthat/test-wb_styles.R | 24 + tests/testthat/test-write.R | 7 vignettes/openxlsx2.Rmd | 5 vignettes/openxlsx2_charts_manual.Rmd | 2 46 files changed, 1031 insertions(+), 313 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 4.0.0 dated 2026-06-19 and 4.0.1 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/byTileAOP.R | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Providing Fast and Flexible Functions for Distance Correlation
Analysis
Description: Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <doi:10.48550/arXiv.1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Author: Dominic Edelmann [aut, cre],
Jochen Fiedler [aut]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Diff between dcortools versions 0.1.7 dated 2025-12-09 and 0.2.0 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 16 +- NEWS.md | 10 + R/auxiliary_functions.R | 2 R/distcov_test2.R | 360 ++++++++++++++++++++++++++++++++++++++---------- R/methods_test.R | 14 + R/perm_algorithms2.R | 279 ++++++++++++++++++------------------- build/partial.rdb |binary man/distcov.test.Rd | 16 +- 9 files changed, 475 insertions(+), 233 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic trees contain components such as nodes, edges,
branches, and associated data. As the core data manipulation tool in the
'ggtree' ecosystem, 'tidytree' provides tools for converting tree objects
to tidy data frames and tidy interfaces for manipulating, analyzing, and
visualizing tree data.
Author: Guangchuang Yu [aut, cre, cph] ,
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.4.7 dated 2026-01-08 and 0.4.8 dated 2026-07-02
DESCRIPTION | 14 +++-- MD5 | 25 +++++----- NEWS.md | 13 +++++ R/AllClasses.R | 3 - R/as-tibble.R | 14 +++-- R/full-join.R | 2 R/left-join.R | 16 ++++++ R/method-as-ultrametric.R | 51 ++++++++++++--------- R/offspring.R | 91 ++++++++++++++++++++++++++++++-------- R/tree-subset.R | 53 +++++++++++----------- man/reexports.Rd | 12 ++--- man/tidytree-package.Rd | 63 ++++++++++++++------------ tests/testthat/test-innerjoin.R | 2 tests/testthat/test-tree-subset.R |only 14 files changed, 233 insertions(+), 126 deletions(-)
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Lluis Revilla Sancho [aut] ,
Dony Unardi [rev, cre],
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [aut],
Andrew Bates [aut],
Mahmoud Halla [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.slice versions 0.8.0 dated 2026-06-04 and 0.8.1 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/teal_slice.R | 4 ++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 0.2.1 dated 2026-03-17 and 1.0.0 dated 2026-07-02
DESCRIPTION | 12 MD5 | 57 + NEWS.md | 68 ++ R/aaa.R | 3 R/client-auth.R |only R/client-http.R |only R/client.R | 1019 +++++++++++++++++++++++++++++---- R/connect.R |only R/protocol-version.R | 6 R/server.R | 376 ++++++++++-- R/session.R | 202 ++++++ R/tools.R | 18 R/utils.R | 68 ++ README.md | 29 build/vignette.rds |binary inst/doc/server.Rmd | 37 + inst/doc/server.html | 33 + inst/example-config-remote.json | 7 man/client.Rd | 71 +- man/mcptools-package.Rd | 1 man/server.Rd | 27 tests/testthat/fixtures |only tests/testthat/helper.R | 122 +++ tests/testthat/test-client-auth.R |only tests/testthat/test-client-http.R |only tests/testthat/test-client.R | 237 +++++++ tests/testthat/test-connect.R |only tests/testthat/test-protocol-version.R | 31 + tests/testthat/test-server.R | 420 +++++++++++++ tests/testthat/test-session.R | 182 +++++ tests/testthat/test-tools.R | 139 ++++ tests/testthat/test-utils.R | 33 + vignettes/server.Rmd | 37 + 33 files changed, 2987 insertions(+), 248 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb] ,
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.6.0 dated 2026-01-18 and 0.6.1 dated 2026-07-02
DESCRIPTION | 16 MD5 | 86 +-- NEWS.md | 5 R/geom-label-pairwise.r | 236 ++++++---- R/geom-text-pairwise.R | 187 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/grammar-extensions.Rmd | 2 inst/doc/grammar-extensions.html | 6 man/birch.df.Rd | 2 man/geom_plot.Rd | 4 man/geom_quadrant_lines.Rd | 6 man/geom_table.Rd | 4 man/geom_text_pairwise.Rd | 25 + man/geom_x_margin_arrow.Rd | 6 man/geom_x_margin_grob.Rd | 6 man/geom_x_margin_point.Rd | 6 man/ggpp-ggproto.Rd | 2 man/ggpp-package.Rd | 5 man/ivy.df.Rd | 72 +-- man/position_dodgenudge.Rd | 18 man/position_dodgenudge_to.Rd | 18 man/position_jitternudge.Rd | 18 man/position_nudge_center.Rd | 18 man/position_nudge_keep.Rd | 18 man/position_nudge_line.Rd | 18 man/position_nudge_to.Rd | 18 man/position_stacknudge.Rd | 18 man/position_stacknudge_to.Rd | 18 man/quadrant_example.df.Rd | 2 man/stat_dens1d_filter.Rd | 8 man/stat_dens1d_labels.Rd | 8 man/stat_dens2d_filter.Rd | 8 man/stat_dens2d_labels.Rd | 8 man/stat_panel_counts.Rd | 6 man/stat_quadrant_counts.Rd | 6 man/volcano_example.df.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/geom-label/geom-label-npc4.svg | 2 tests/testthat/_snaps/geom-table/geom-table-parsed-all.svg | 104 ++-- tests/testthat/_snaps/geom-table/geom-table-parsed-partial-dark.svg | 102 ++-- tests/testthat/_snaps/geom-table/geom-table-parsed-partial.svg | 102 ++-- tests/testthat/_snaps/geom-text/geom-text-npc4.svg | 2 vignettes/grammar-extensions.Rmd | 2 44 files changed, 705 insertions(+), 495 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Provides a collection of 'ggplot2' extensions and utilities
for creating geometric layers, applying themes, working with legends,
and modifying plot objects.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.2.0 dated 2025-07-15 and 0.2.1 dated 2026-07-02
ggfun-0.2.0/ggfun/inst/doc/ggfun.Rmd |only ggfun-0.2.0/ggfun/vignettes/ggfun.Rmd |only ggfun-0.2.1/ggfun/DESCRIPTION | 29 - ggfun-0.2.1/ggfun/MD5 | 44 + ggfun-0.2.1/ggfun/NAMESPACE | 4 ggfun-0.2.1/ggfun/NEWS.md | 9 ggfun-0.2.1/ggfun/R/geom-hist.r |only ggfun-0.2.1/ggfun/R/geom_segment_c.R | 176 +++---- ggfun-0.2.1/ggfun/R/ggelement.R | 35 - ggfun-0.2.1/ggfun/R/operator.R | 24 - ggfun-0.2.1/ggfun/R/set_font.R | 19 ggfun-0.2.1/ggfun/R/utilities.R | 4 ggfun-0.2.1/ggfun/README.md |only ggfun-0.2.1/ggfun/build/vignette.rds |binary ggfun-0.2.1/ggfun/inst/doc/ggfun.R | 248 ++++++++-- ggfun-0.2.1/ggfun/inst/doc/ggfun.html | 694 ++++++++++++++++++++--------- ggfun-0.2.1/ggfun/inst/doc/ggfun.qmd |only ggfun-0.2.1/ggfun/man/element_roundrect.Rd | 6 ggfun-0.2.1/ggfun/man/geom_hist.Rd |only ggfun-0.2.1/ggfun/man/geom_segment_c.Rd | 3 ggfun-0.2.1/ggfun/man/geom_xspline.Rd | 308 ++++++------ ggfun-0.2.1/ggfun/man/ggfun-package.Rd | 57 +- ggfun-0.2.1/ggfun/man/reexports.Rd | 4 ggfun-0.2.1/ggfun/tests |only ggfun-0.2.1/ggfun/vignettes/ggfun.qmd |only 25 files changed, 1075 insertions(+), 589 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson [aut, cre] ,
Julie Josse [aut],
Sebastien Le [aut],
Jeremy Mazet [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.15 dated 2026-06-11 and 2.16 dated 2026-07-02
FactoMineR-2.15/FactoMineR/NEWS |only FactoMineR-2.15/FactoMineR/README |only FactoMineR-2.16/FactoMineR/DESCRIPTION | 8 - FactoMineR-2.16/FactoMineR/MD5 | 71 ++++----- FactoMineR-2.16/FactoMineR/NAMESPACE | 29 ++- FactoMineR-2.16/FactoMineR/NEWS.md |only FactoMineR-2.16/FactoMineR/R/CA.R | 7 FactoMineR-2.16/FactoMineR/R/FAMD.R | 12 - FactoMineR-2.16/FactoMineR/R/HCPC.R | 10 - FactoMineR-2.16/FactoMineR/R/MCA.R | 10 - FactoMineR-2.16/FactoMineR/R/MFA.R | 17 +- FactoMineR-2.16/FactoMineR/R/PCA.R | 6 FactoMineR-2.16/FactoMineR/R/catdes.r | 12 + FactoMineR-2.16/FactoMineR/R/ellipseCA.R | 21 ++ FactoMineR-2.16/FactoMineR/R/meansComp.R | 2 FactoMineR-2.16/FactoMineR/R/plot.CA.R | 29 ++- FactoMineR-2.16/FactoMineR/R/plot.FAMD.R | 15 +- FactoMineR-2.16/FactoMineR/R/plot.MCA.R | 29 ++- FactoMineR-2.16/FactoMineR/R/plot.MFA.R | 40 +++-- FactoMineR-2.16/FactoMineR/R/plot.PCA.R | 41 +++-- FactoMineR-2.16/FactoMineR/R/plot.catdes.R | 154 +++++++++++---------- FactoMineR-2.16/FactoMineR/R/plot.meansComp.R | 26 ++- FactoMineR-2.16/FactoMineR/R/svd.triplet.R | 2 FactoMineR-2.16/FactoMineR/R/theme_factominer.R |only FactoMineR-2.16/FactoMineR/man/CA.Rd | 5 FactoMineR-2.16/FactoMineR/man/FAMD.Rd | 3 FactoMineR-2.16/FactoMineR/man/MCA.Rd | 3 FactoMineR-2.16/FactoMineR/man/MFA.Rd | 3 FactoMineR-2.16/FactoMineR/man/PCA.Rd | 3 FactoMineR-2.16/FactoMineR/man/catdes.Rd | 5 FactoMineR-2.16/FactoMineR/man/ellipseCA.Rd | 2 FactoMineR-2.16/FactoMineR/man/plot.CA.Rd | 12 - FactoMineR-2.16/FactoMineR/man/plot.FAMD.Rd | 4 FactoMineR-2.16/FactoMineR/man/plot.MCA.Rd | 12 - FactoMineR-2.16/FactoMineR/man/plot.MFA.Rd | 4 FactoMineR-2.16/FactoMineR/man/plot.PCA.Rd | 13 - FactoMineR-2.16/FactoMineR/man/plot.catdes.Rd | 7 FactoMineR-2.16/FactoMineR/man/plot.meansComp.Rd | 3 FactoMineR-2.16/FactoMineR/man/theme_factominer.Rd |only 39 files changed, 364 insertions(+), 256 deletions(-)
Title: Structural Data for Norway
Description: Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.
Author: Richard Aubrey White [aut, cre] ,
Chi Zhang [aut]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdata versions 2026.3.30 dated 2026-03-31 and 2026.7.2 dated 2026-07-02
DESCRIPTION | 9 LICENSE | 2 MD5 | 70 NAMESPACE | 1 NEWS.md | 8 R/add_variable_to_data_set.R | 33 R/config_aa_environments.r | 43 R/location_code_to.R | 45 R/nor_locations_hierarchy.R | 308 ++- R/nor_locations_names.R | 57 R/nor_locations_redistricting.R | 53 R/nor_population_by_age_cats.R | 140 + R/nor_population_by_sex_age_cats.R |only R/sysdata.rda |binary build/vignette.rds |binary inst/doc/csdata.Rmd | 18 inst/doc/csdata.html | 2574 ++++++++++++++++-------------- inst/doc/locations_norway.Rmd | 4 inst/doc/locations_norway.html | 877 +++++----- inst/doc/population_norway.Rmd | 8 inst/doc/population_norway.html | 2680 +++++++++++++++++--------------- man/add_granularity_geo_to_data_set.Rd | 20 man/add_iso3_to_data_set.Rd | 13 man/config.Rd | 16 man/location_code_to_granularity_geo.Rd | 25 man/location_code_to_iso3.Rd | 18 man/nb.Rd | 10 man/nor_locations_hierarchy_from_to.Rd | 42 man/nor_locations_names.Rd | 39 man/nor_locations_redistricting.Rd | 36 man/nor_population_by_age_cats.Rd | 57 man/nor_population_by_sex_age_cats.Rd |only man/se.Rd | 10 man/set_config.Rd | 17 vignettes/csdata.Rmd | 18 vignettes/locations_norway.Rmd | 4 vignettes/population_norway.Rmd | 8 37 files changed, 3985 insertions(+), 3278 deletions(-)
Title: Composite Indicators Functions
Description: A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.
Author: Francesco Vidoli [aut, cre],
Elisa Fusco [aut]
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 3.4 dated 2025-05-16 and 3.5 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++++------ NAMESPACE | 1 + NEWS | 35 +++++++++++++---------------------- R/ci_bod_time_decomp.R |only data/desktop.ini |only desktop.ini |only inst/desktop.ini |only inst/doc/Compind_vignette.pdf |binary man/ci_bod_constr_bad.Rd | 20 ++++++++++---------- man/ci_bod_time_decomp.Rd |only man/ci_rbod_constr_bad_Q.Rd | 30 +++++++++++++++--------------- vignettes/desktop.ini |only 13 files changed, 55 insertions(+), 57 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Circumplex models, which organize constructs in a circle around two
underlying dimensions, are popular for studying interpersonal functioning,
mood/affect, and vocational preferences/environments. This package provides
tools for analyzing and visualizing circular data, including scoring
functions for relevant instruments and a generalization of the bootstrapped
structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results.
Author: Jeffrey Girard [aut, cre] ,
Johannes Zimmermann [aut] ,
Aidan Wright [aut]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 1.1.0 dated 2026-05-24 and 1.2.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 86 NEWS.md | 57 R/instrument_oop.R | 4 R/ssm_analysis.R | 88 R/ssm_bootstrap.R | 40 R/ssm_oop.R | 20 R/ssm_plot.R | 1064 +++++----- R/ssm_table.R | 2 R/tidying_functions.R | 49 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/intermediate-ssm-analysis.Rmd | 2 inst/doc/intermediate-ssm-analysis.html | 67 inst/doc/introduction-to-ssm-analysis.Rmd | 6 inst/doc/introduction-to-ssm-analysis.html | 19 inst/doc/using-instruments.html | 2 man/norm_standardize.Rd | 5 man/score.Rd | 3 man/ssm_analyze.Rd | 34 man/ssm_parameters.Rd | 8 man/ssm_plot_circle.Rd | 2 man/ssm_plot_contrast.Rd | 2 man/ssm_plot_curve.Rd | 4 man/ssm_score.Rd | 3 src/parameters.cpp | 30 tests/testthat/_snaps/instrument_oop.md | 2 tests/testthat/_snaps/ssm_plot/group-constrast-correlation-ssm.svg | 165 - tests/testthat/_snaps/ssm_plot/many-circle-plots.svg | 8 tests/testthat/_snaps/ssm_plot/many-circle-repel.svg | 14 tests/testthat/_snaps/ssm_plot/measure-contrast-circle-ssm.svg | 4 tests/testthat/_snaps/ssm_plot/measure-contrast-ssm.svg | 294 +- tests/testthat/_snaps/ssm_plot/single-group-correlation-ssm.svg | 2 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm-no-palette.svg | 2 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm.svg | 2 tests/testthat/test-ssm_analysis.R | 209 + tests/testthat/test-ssm_bootstrap.R | 60 tests/testthat/test-ssm_oop.R | 50 tests/testthat/test-ssm_plot.R | 28 tests/testthat/test-tidying_functions.R | 58 tests/testthat/test-utils.R | 14 vignettes/intermediate-ssm-analysis.Rmd | 2 vignettes/introduction-to-ssm-analysis.Rmd | 6 44 files changed, 1607 insertions(+), 918 deletions(-)
Title: Bayesian Synthetic Likelihood
Description: Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>)
is an alternative to standard, non-parametric approximate Bayesian
computation (ABC). BSL assumes a multivariate normal distribution
for the summary statistic likelihood and it is suitable when the
distribution of the model summary statistics is sufficiently regular.
This package provides a Metropolis Hastings Markov chain Monte Carlo
implementation of four methods (BSL, uBSL, semiBSL and BSLmisspec) and two
shrinkage estimators (graphical lasso and Warton's estimator).
uBSL (Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) uses
an unbiased estimator to the normal density. A semi-parametric version
of BSL (semiBSL, An et al. (2020) <doi:10.1007/s11222-019-09904-x>) is more robust
to non-normal summary statistics. BSLmisspec (Frazier et al. 2021
<doi:10.1080/10618600.2021.1875839>) estimates the Gaussian synthetic likelihood whilst
acknowledging that there may be [...truncated...]
Author: Ziwen An [aut] ,
Leah F. South [aut, cre] ,
Christopher C. Drovandi [aut]
Maintainer: Leah F. South <l1.south@qut.edu.au>
This is a re-admission after prior archival of version 3.2.5 dated 2022-11-03
Diff between BSL versions 3.2.5 dated 2022-11-03 and 3.2.6 dated 2026-07-02
DESCRIPTION | 24 +++++++++++++----------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/s4-MODEL.R | 19 ++++++++++++------- build/partial.rdb |binary inst/REFERENCES.bib | 39 ++++++++++++++++++++++++--------------- man/MODEL-class.Rd | 19 ++++++++++++------- man/cell.Rd | 8 ++++---- man/ma2.Rd | 10 +++++----- man/toad.Rd | 8 ++++---- src/Makevars.win | 5 +---- 12 files changed, 99 insertions(+), 68 deletions(-)
Title: Access Brazilian Data via APIs and Curated Datasets
Description: Provides functions to access data from the 'BrasilAPI', 'Nager.Date API',
and 'World Bank API', related to Brazil's postal codes, banks, holidays,
company registrations, and economic development data. Additionally, the package includes
curated datasets related to Brazil, covering topics such as demographic data (males and
females by state and year), river levels, environmental emission factors, film festivals,
and yellow fever outbreak records. The package supports research and analysis focused on
Brazil by integrating open APIs with high-quality datasets from multiple domains. For more
information on the APIs, see:
'BrasilAPI' <https://brasilapi.com.br/>,
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between BrazilDataAPI versions 0.2.0 dated 2025-09-15 and 0.3.0 dated 2026-07-02
BrazilDataAPI-0.2.0/BrazilDataAPI/R/get_brazil_vehicle_brands.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/R/get_country_info_br.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/man/get_brazil_vehicle_brands.Rd |only BrazilDataAPI-0.2.0/BrazilDataAPI/man/get_country_info_br.Rd |only BrazilDataAPI-0.2.0/BrazilDataAPI/tests/testthat/test-get_brazil_vehicle_brands.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/tests/testthat/test-get_country_info_br.R |only BrazilDataAPI-0.3.0/BrazilDataAPI/DESCRIPTION | 27 - BrazilDataAPI-0.3.0/BrazilDataAPI/MD5 | 118 ++---- BrazilDataAPI-0.3.0/BrazilDataAPI/NAMESPACE | 3 BrazilDataAPI-0.3.0/BrazilDataAPI/NEWS.md | 18 BrazilDataAPI-0.3.0/BrazilDataAPI/R/brazildataapi-package.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/data-documentation.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_banks.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cep.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_child_mortality.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cnpj.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cpi.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_energy_use.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_gdp.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_holidays.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_hospital_beds.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_life_expectancy.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_literacy_rate.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_municipalities.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_population.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_rate_name.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_rates.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_unemployment.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/utils.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/view_datasets_BrazilDataAPI.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/README.md | 10 BrazilDataAPI-0.3.0/BrazilDataAPI/build/vignette.rds |binary BrazilDataAPI-0.3.0/BrazilDataAPI/inst/CITATION | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.R | 9 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.Rmd | 24 - BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.html | 190 ++++------ BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSE | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSE.md | 37 - BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSES_DETAILS.md | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brasil_females_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brasil_males_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brazil_films_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Yellow_Fever_list.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_banks.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cep.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_child_mortality.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cnpj.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cpi.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_energy_use.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_gdp.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_holidays.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_hospital_beds.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_life_expectancy.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_literacy_rate.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_municipalities.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_population.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_rate_name.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_rates.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_unemployment.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-manaus_ts.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-sp_emission_factors_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-view_datasets_BrazilDataAPI.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/vignettes/BrazilDataAPI_vignette.Rmd | 24 - 63 files changed, 285 insertions(+), 359 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
[...truncated...]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 3.6.3 dated 2021-06-04 and 3.7.1 dated 2026-07-02
arsenal-3.6.3/arsenal/man/arsenal.Rd |only arsenal-3.7.1/arsenal/DESCRIPTION | 14 arsenal-3.7.1/arsenal/MD5 | 114 arsenal-3.7.1/arsenal/NAMESPACE | 14 arsenal-3.7.1/arsenal/NEWS.md | 60 arsenal-3.7.1/arsenal/R/arsenal.R | 4 arsenal-3.7.1/arsenal/R/arsenal_table.R | 46 arsenal-3.7.1/arsenal/R/formulize.R | 11 arsenal-3.7.1/arsenal/R/modelsum.R | 2 arsenal-3.7.1/arsenal/R/paired.R | 20 arsenal-3.7.1/arsenal/R/paired.control.R | 6 arsenal-3.7.1/arsenal/R/paired.stat.tests.R | 2 arsenal-3.7.1/arsenal/R/summary.tableby.R | 25 arsenal-3.7.1/arsenal/R/tableby.R | 19 arsenal-3.7.1/arsenal/R/tableby.control.R | 11 arsenal-3.7.1/arsenal/R/tableby.internal.R | 85 arsenal-3.7.1/arsenal/R/tableby.stat.tests.R | 28 arsenal-3.7.1/arsenal/R/tableby.stats.R | 291 + arsenal-3.7.1/arsenal/README.md | 1 arsenal-3.7.1/arsenal/build/vignette.rds |binary arsenal-3.7.1/arsenal/inst/doc/comparedf.R | 12 arsenal-3.7.1/arsenal/inst/doc/comparedf.html | 844 +++- arsenal-3.7.1/arsenal/inst/doc/freqlist.R | 8 arsenal-3.7.1/arsenal/inst/doc/freqlist.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/freqlist.html | 784 +++- arsenal-3.7.1/arsenal/inst/doc/labels.html | 517 ++ arsenal-3.7.1/arsenal/inst/doc/modelsum.R | 84 arsenal-3.7.1/arsenal/inst/doc/modelsum.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/modelsum.html | 2777 +++++++++------ arsenal-3.7.1/arsenal/inst/doc/paired.R | 2 arsenal-3.7.1/arsenal/inst/doc/paired.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/paired.html | 436 +- arsenal-3.7.1/arsenal/inst/doc/tableby.R | 191 - arsenal-3.7.1/arsenal/inst/doc/tableby.Rmd | 91 arsenal-3.7.1/arsenal/inst/doc/tableby.html | 2269 +++++++++--- arsenal-3.7.1/arsenal/inst/doc/write2.R | 290 - arsenal-3.7.1/arsenal/inst/doc/write2.html | 842 +++- arsenal-3.7.1/arsenal/man/arsenal-package.Rd |only arsenal-3.7.1/arsenal/man/arsenal_table.Rd | 3 arsenal-3.7.1/arsenal/man/formulize.Rd | 2 arsenal-3.7.1/arsenal/man/internal.functions.Rd | 6 arsenal-3.7.1/arsenal/man/padjust.Rd | 3 arsenal-3.7.1/arsenal/man/paired.Rd | 2 arsenal-3.7.1/arsenal/man/paired.control.Rd | 6 arsenal-3.7.1/arsenal/man/summary.modelsum.Rd | 4 arsenal-3.7.1/arsenal/man/summary.tableby.Rd | 4 arsenal-3.7.1/arsenal/man/tableby.control.Rd | 5 arsenal-3.7.1/arsenal/man/tableby.stats.Rd | 50 arsenal-3.7.1/arsenal/man/tableby.stats.internal.Rd | 40 arsenal-3.7.1/arsenal/tests/testthat/test_formulize.R | 10 arsenal-3.7.1/arsenal/tests/testthat/test_paired.R | 28 arsenal-3.7.1/arsenal/tests/testthat/test_tableby.R | 195 + arsenal-3.7.1/arsenal/tests/testthat/test_write2.R | 3 arsenal-3.7.1/arsenal/tests/testthat/write2.lm.pdf.Rmd | 8 arsenal-3.7.1/arsenal/tests/testthat/write2.yaml.pdf.Rmd | 8 arsenal-3.7.1/arsenal/vignettes/freqlist.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/modelsum.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/paired.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/tableby.Rmd | 91 59 files changed, 7219 insertions(+), 3161 deletions(-)
Title: Sequential Change Point Detection for High-Dimensional VAR
Models
Description: Implements the algorithm introduced in Tian, Y., and Safikhani, A. (2024)
<doi:10.5705/ss.202024.0182>, "Sequential Change Point Detection in High-dimensional
Vector Auto-regressive Models". This package provides tools for detecting change points
in the transition matrices of VAR models, effectively identifying shifts in temporal
and cross-correlations within high-dimensional time series data.
Author: Yuhan Tian [aut, cre],
Abolfazl Safikhani [aut]
Maintainer: Yuhan Tian <tyh9293@gmail.com>
Diff between VARcpDetectOnline versions 0.2.0 dated 2025-02-13 and 0.2.1 dated 2026-07-02
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 12 insertions(+), 8 deletions(-)
More information about VARcpDetectOnline at CRAN
Permanent link
Title: Parse 'User-Agent' Strings
Description: Parses HTTP user agent strings and returns user agent, device and OS information. This is a 'V8'-backed package
based on the 'ua-parser' project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb],
Jim Vine [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.3.8 dated 2026-05-09 and 0.4.0 dated 2026-07-02
uaparserjs-0.3.8/uaparserjs/R/uaparserjs-package.R |only uaparserjs-0.3.8/uaparserjs/R/utils-mappers.R |only uaparserjs-0.4.0/uaparserjs/DESCRIPTION | 24 - uaparserjs-0.4.0/uaparserjs/MD5 | 28 - uaparserjs-0.4.0/uaparserjs/NAMESPACE | 4 uaparserjs-0.4.0/uaparserjs/NEWS.md | 6 uaparserjs-0.4.0/uaparserjs/R/uaparser.R | 144 +++++--- uaparserjs-0.4.0/uaparserjs/R/utils.R |only uaparserjs-0.4.0/uaparserjs/R/zzz.r | 4 uaparserjs-0.4.0/uaparserjs/README.md | 14 uaparserjs-0.4.0/uaparserjs/inst/js/bundle.js | 2 uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_exhaustive.R | 178 +++++++++-- uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_multirow.R |only uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_uaparserjs.R | 119 +++++++ uaparserjs-0.4.0/uaparserjs/inst/tinytest/tests/test_ua.yaml | 6 uaparserjs-0.4.0/uaparserjs/man/ua_parse.Rd | 33 +- uaparserjs-0.4.0/uaparserjs/man/uaparserjs.Rd | 12 17 files changed, 441 insertions(+), 133 deletions(-)
Title: Simple Colour Manipulation
Description: Functions for easily manipulating colours, creating colour scales and calculating colour distances.
Author: Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between shades versions 1.4.0 dated 2019-08-02 and 1.5.0 dated 2026-07-02
shades-1.4.0/shades/tests/testthat |only shades-1.4.0/shades/tests/testthat.R |only shades-1.5.0/shades/DESCRIPTION | 21 - shades-1.5.0/shades/MD5 | 90 ++--- shades-1.5.0/shades/NAMESPACE | 5 shades-1.5.0/shades/NEWS | 27 + shades-1.5.0/shades/R/adaptation.R | 2 shades-1.5.0/shades/R/distance.R | 34 +- shades-1.5.0/shades/R/properties.R | 67 ++- shades-1.5.0/shades/R/scales.R | 14 shades-1.5.0/shades/R/shade.R | 161 +++++++-- shades-1.5.0/shades/R/swatch.R | 57 ++- shades-1.5.0/shades/R/tinytest.R |only shades-1.5.0/shades/R/zzz.R | 6 shades-1.5.0/shades/README.md | 86 +++-- shades-1.5.0/shades/inst |only shades-1.5.0/shades/man/coords.Rd | 4 shades-1.5.0/shades/man/dichromat.Rd | 11 shades-1.5.0/shades/man/distance.Rd | 30 + shades-1.5.0/shades/man/gradient.Rd | 8 shades-1.5.0/shades/man/mixtures.Rd | 2 shades-1.5.0/shades/man/properties.Rd | 24 - shades-1.5.0/shades/man/shade.Rd | 43 +- shades-1.5.0/shades/man/space.Rd | 2 shades-1.5.0/shades/man/swatch.Rd | 17 - shades-1.5.0/shades/man/tinytest.Rd |only shades-1.5.0/shades/man/warp.Rd | 22 - shades-1.5.0/shades/tests/tinytest.R |only shades-1.5.0/shades/tools/figures/addmix-1.svg | 46 ++ shades-1.5.0/shades/tools/figures/dichromat-1.svg | 51 ++- shades-1.5.0/shades/tools/figures/dichromat-2.svg | 51 ++- shades-1.5.0/shades/tools/figures/ggplot-1.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/gradients-1.svg | 45 ++ shades-1.5.0/shades/tools/figures/gradients-2.svg | 45 ++ shades-1.5.0/shades/tools/figures/missing-1.svg | 45 ++ shades-1.5.0/shades/tools/figures/saturation-1.svg | 59 ++- shades-1.5.0/shades/tools/figures/scales-1.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/scales-2.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/submix-1.svg | 46 ++ shades-1.5.0/shades/tools/figures/tinyplot-1.svg |only shades-1.5.0/shades/tools/figures/tinyplot-2.svg |only 41 files changed, 1139 insertions(+), 1047 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] ,
Susie Lu [aut, cph] ,
Speros Kokenes [aut, cph] ,
Evan Wang [aut, cph]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between scatterD3 versions 1.0.1 dated 2021-10-06 and 1.0.2 dated 2026-07-02
DESCRIPTION | 10 MD5 | 22 NEWS.md | 201 +++---- R/scatterD3.R | 9 README.md | 17 build/vignette.rds |binary inst/doc/introduction.R | 44 - inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 1181 ++++++++++++++++++++++++------------------ inst/htmlwidgets/scatterD3.js | 2 man/scatterD3.Rd | 6 vignettes/introduction.Rmd | 8 12 files changed, 858 insertions(+), 650 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.9-0 dated 2026-03-13 and 1.10-0 dated 2026-07-02
RBesT-1.10-0/RBesT/DESCRIPTION | 16 RBesT-1.10-0/RBesT/MD5 | 229 +++- RBesT-1.10-0/RBesT/NAMESPACE | 11 RBesT-1.10-0/RBesT/NEWS.md | 43 RBesT-1.10-0/RBesT/R/RBesT-package.R | 13 RBesT-1.10-0/RBesT/R/asthma.R |only RBesT-1.10-0/RBesT/R/decision1S_boundary.R | 90 + RBesT-1.10-0/RBesT/R/decision2S_boundary.R | 154 ++- RBesT-1.10-0/RBesT/R/forest_plot.R | 19 RBesT-1.10-0/RBesT/R/gMAP.R | 352 +++++-- RBesT-1.10-0/RBesT/R/gMAP_draws.R |only RBesT-1.10-0/RBesT/R/integrate_gauss_quadrature.R |only RBesT-1.10-0/RBesT/R/integrate_logit_log.R | 85 + RBesT-1.10-0/RBesT/R/mixdiff.R | 18 RBesT-1.10-0/RBesT/R/mixess.R | 22 RBesT-1.10-0/RBesT/R/mixfit.R | 18 RBesT-1.10-0/RBesT/R/mixstanvar.R | 5 RBesT-1.10-0/RBesT/R/nsamples.R | 5 RBesT-1.10-0/RBesT/R/oc1S.R | 89 + RBesT-1.10-0/RBesT/R/oc2S.R | 93 + RBesT-1.10-0/RBesT/R/plot_gMAP.R | 18 RBesT-1.10-0/RBesT/R/pos1S.R | 113 +- RBesT-1.10-0/RBesT/R/pos2S.R | 90 + RBesT-1.10-0/RBesT/R/posterior.R | 114 +- RBesT-1.10-0/RBesT/R/postmix.R | 7 RBesT-1.10-0/RBesT/R/predict_gMAP.R | 72 - RBesT-1.10-0/RBesT/R/sigma_from_family.R |only RBesT-1.10-0/RBesT/R/sysdata.rda |binary RBesT-1.10-0/RBesT/build/vignette.rds |binary RBesT-1.10-0/RBesT/data/AS.rda |binary RBesT-1.10-0/RBesT/data/asthma.rda |only RBesT-1.10-0/RBesT/data/colitis.rda |binary RBesT-1.10-0/RBesT/data/crohn.rda |binary RBesT-1.10-0/RBesT/data/transplant.rda |binary RBesT-1.10-0/RBesT/demo/00Index | 1 RBesT-1.10-0/RBesT/demo/oc2S_interim.R |only RBesT-1.10-0/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.10-0/RBesT/inst/doc/introduction.html | 81 - RBesT-1.10-0/RBesT/inst/extra/oc2S_interim.R |only RBesT-1.10-0/RBesT/inst/sbc/sbc_report.html | 36 RBesT-1.10-0/RBesT/man/RBesT-package.Rd | 18 RBesT-1.10-0/RBesT/man/asthma.Rd |only RBesT-1.10-0/RBesT/man/decision1S.Rd | 8 RBesT-1.10-0/RBesT/man/decision1S_boundary.Rd | 47 RBesT-1.10-0/RBesT/man/decision2S.Rd | 8 RBesT-1.10-0/RBesT/man/decision2S_boundary.Rd | 30 RBesT-1.10-0/RBesT/man/dot-gmap_all_diag_df.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_all_draws.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_diag_df.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_divergence_count.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_diag_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_draws_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_extract_diag_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_extract_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_mcmc_metadata.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_sampler_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_thin_draws.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_warn_no_samples.Rd |only RBesT-1.10-0/RBesT/man/draws-RBesT.Rd | 5 RBesT-1.10-0/RBesT/man/ess.Rd | 4 RBesT-1.10-0/RBesT/man/gMAP.Rd | 13 RBesT-1.10-0/RBesT/man/integrate_density.Rd |only RBesT-1.10-0/RBesT/man/integrate_density_log.Rd | 57 - RBesT-1.10-0/RBesT/man/integrate_gauss_quadrature.Rd |only RBesT-1.10-0/RBesT/man/mix.Rd | 12 RBesT-1.10-0/RBesT/man/mixbeta.Rd | 10 RBesT-1.10-0/RBesT/man/mixcombine.Rd | 10 RBesT-1.10-0/RBesT/man/mixfit.Rd | 4 RBesT-1.10-0/RBesT/man/mixgamma.Rd | 10 RBesT-1.10-0/RBesT/man/mixjson.Rd | 16 RBesT-1.10-0/RBesT/man/mixmvnorm.Rd | 10 RBesT-1.10-0/RBesT/man/mixnorm.Rd | 10 RBesT-1.10-0/RBesT/man/mixplot.Rd | 12 RBesT-1.10-0/RBesT/man/mixstanvar.Rd | 2 RBesT-1.10-0/RBesT/man/oc1S.Rd | 38 RBesT-1.10-0/RBesT/man/oc2S.Rd | 30 RBesT-1.10-0/RBesT/man/plot.EM.Rd | 4 RBesT-1.10-0/RBesT/man/pos1S.Rd | 38 RBesT-1.10-0/RBesT/man/pos2S.Rd | 30 RBesT-1.10-0/RBesT/man/resolve_sigma_family.Rd |only RBesT-1.10-0/RBesT/man/sigma_from_family.Rd |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-compact |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-compact-src |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-mcmc-src |only RBesT-1.10-0/RBesT/tests/testthat/helper-compressed-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-mixstanvar.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-utils.R | 14 RBesT-1.10-0/RBesT/tests/testthat/test-EM.R | 290 +++--- RBesT-1.10-0/RBesT/tests/testthat/test-design1S-family.R |only RBesT-1.10-0/RBesT/tests/testthat/test-design2S-family.R |only RBesT-1.10-0/RBesT/tests/testthat/test-gMAP-compact-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/test-gMAP.R | 314 ------ RBesT-1.10-0/RBesT/tests/testthat/test-integrate-GQ.R |only RBesT-1.10-0/RBesT/tests/testthat/test-mixdiff.R | 143 +-- RBesT-1.10-0/RBesT/tests/testthat/test-mixdist.R | 146 +-- RBesT-1.10-0/RBesT/tests/testthat/test-mixstanvar-sampling.R |only RBesT-1.10-0/RBesT/tests/testthat/test-mixstanvar.R | 473 ---------- RBesT-1.10-0/RBesT/tests/testthat/test-oc1S.R | 191 ++-- RBesT-1.10-0/RBesT/tests/testthat/test-oc2S.R | 359 +++---- RBesT-1.10-0/RBesT/tests/testthat/test-pos1S.R | 100 +- RBesT-1.10-0/RBesT/tests/testthat/test-pos2S.R | 226 +++- RBesT-1.10-0/RBesT/tests/testthat/test-posterior.R | 117 +- RBesT-1.10-0/RBesT/tests/testthat/test-postmix.R | 7 RBesT-1.10-0/RBesT/tests/testthat/test-preddist.R | 69 - RBesT-1.10-0/RBesT/tests/testthat/test-utils.R | 251 ++--- RBesT-1.9-0/RBesT/R/SimSum.R |only RBesT-1.9-0/RBesT/man/SimSum.Rd |only 111 files changed, 2621 insertions(+), 2299 deletions(-)
Title: Confidence Intervals and Tests for Comparisons of Binomial
Proportions or Poisson Rates
Description: Computes confidence intervals for binomial or Poisson rates
and their differences or ratios. Including the rate (or risk)
difference ('RD') or rate ratio (or relative risk, 'RR') for binomial
proportions or Poisson rates, and odds ratio ('OR', binomial only).
Also confidence intervals for RD, RR or OR for paired binomial data,
and estimation of a proportion from clustered binomial data. Includes
skewness-corrected asymptotic score ('SCAS') methods, which have been
developed in Laud (2017) <doi:10.1002/pst.1813> from Miettinen and
Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart and Nam (1988)
<doi:10.2307/2531848>, and in Laud (2026, under review) for paired
proportions. In each case, the same score produces hypothesis tests that are
improved versions of the non-inferiority test for binomial RD and RR
by Farrington and Manning (1990) <doi:10.1002/sim.4780091208>, or a
generalisation of the McNemar test for paired data. The package also
includes MOVER metho [...truncated...]
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <pete@sheffstat.co.uk>
Diff between ratesci versions 1.0.0 dated 2025-06-20 and 1.1.0 dated 2026-07-02
ratesci-1.0.0/ratesci/vignettes/bmj.csl |only ratesci-1.1.0/ratesci/DESCRIPTION | 62 ratesci-1.1.0/ratesci/MD5 | 127 ratesci-1.1.0/ratesci/NAMESPACE | 69 ratesci-1.1.0/ratesci/NEWS.md | 414 +- ratesci-1.1.0/ratesci/R/clusterpci.R | 198 - ratesci-1.1.0/ratesci/R/data.R | 100 ratesci-1.1.0/ratesci/R/moverci.R | 902 ++-- ratesci-1.1.0/ratesci/R/moverpairci.R |only ratesci-1.1.0/ratesci/R/orci.R |only ratesci-1.1.0/ratesci/R/orpairci.R |only ratesci-1.1.0/ratesci/R/pairbinci.R | 2353 ++++++----- ratesci-1.1.0/ratesci/R/rateci.R | 819 ++-- ratesci-1.1.0/ratesci/R/ratesci-package.R | 182 ratesci-1.1.0/ratesci/R/rdci.R |only ratesci-1.1.0/ratesci/R/rdpairci.R |only ratesci-1.1.0/ratesci/R/rrci.R |only ratesci-1.1.0/ratesci/R/rrpairci.R |only ratesci-1.1.0/ratesci/R/scoreci.R | 3728 +++++++++---------- ratesci-1.1.0/ratesci/R/scorepairci.R |only ratesci-1.1.0/ratesci/R/utils.R | 566 +- ratesci-1.1.0/ratesci/build/partial.rdb |binary ratesci-1.1.0/ratesci/build/vignette.rds |binary ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.R | 170 ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.Rmd | 393 +- ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.html | 1485 ++++--- ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.R | 94 ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.Rmd | 233 - ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.html | 1210 +++--- ratesci-1.1.0/ratesci/inst/doc/single_rate.R | 183 ratesci-1.1.0/ratesci/inst/doc/single_rate.Rmd | 365 - ratesci-1.1.0/ratesci/inst/doc/single_rate.html | 1401 +++---- ratesci-1.1.0/ratesci/inst/doc/stratified.R | 106 ratesci-1.1.0/ratesci/inst/doc/stratified.Rmd | 188 ratesci-1.1.0/ratesci/inst/doc/stratified.html | 1055 ++--- ratesci-1.1.0/ratesci/inst/doc/tests.R | 178 ratesci-1.1.0/ratesci/inst/doc/tests.Rmd | 356 + ratesci-1.1.0/ratesci/inst/doc/tests.html | 1403 +++---- ratesci-1.1.0/ratesci/man/cisapride.Rd | 54 ratesci-1.1.0/ratesci/man/clusterpci.Rd | 150 ratesci-1.1.0/ratesci/man/compress.Rd | 56 ratesci-1.1.0/ratesci/man/crash.Rd | 58 ratesci-1.1.0/ratesci/man/jeffreysci.Rd | 150 ratesci-1.1.0/ratesci/man/moverbci.Rd | 146 ratesci-1.1.0/ratesci/man/moverci.Rd | 244 - ratesci-1.1.0/ratesci/man/moverpairci.Rd |only ratesci-1.1.0/ratesci/man/orci.Rd |only ratesci-1.1.0/ratesci/man/orpairci.Rd |only ratesci-1.1.0/ratesci/man/pairbinci.Rd | 454 +- ratesci-1.1.0/ratesci/man/rateci.Rd | 179 ratesci-1.1.0/ratesci/man/ratesci-package.Rd | 229 - ratesci-1.1.0/ratesci/man/rdci.Rd |only ratesci-1.1.0/ratesci/man/rdpairci.Rd |only ratesci-1.1.0/ratesci/man/rrci.Rd |only ratesci-1.1.0/ratesci/man/rrpairci.Rd |only ratesci-1.1.0/ratesci/man/scasci.Rd | 336 - ratesci-1.1.0/ratesci/man/scaspci.Rd | 138 ratesci-1.1.0/ratesci/man/scoreci.Rd | 718 +-- ratesci-1.1.0/ratesci/man/scorepairci.Rd |only ratesci-1.1.0/ratesci/man/tdasci.Rd | 342 - ratesci-1.1.0/ratesci/tests/testthat.R | 24 ratesci-1.1.0/ratesci/tests/testthat/Table2x.Rdata |only ratesci-1.1.0/ratesci/tests/testthat/Table3x.Rdata |only ratesci-1.1.0/ratesci/tests/testthat/test1.R | 759 +-- ratesci-1.1.0/ratesci/tests/testthat/test2.R | 400 +- ratesci-1.1.0/ratesci/tests/testthat/test3.R | 1398 +++---- ratesci-1.1.0/ratesci/tests/testthat/test4.R | 866 ++-- ratesci-1.1.0/ratesci/tests/testthat/test5.R | 72 ratesci-1.1.0/ratesci/vignettes/REFERENCES.bib | 808 ++-- ratesci-1.1.0/ratesci/vignettes/basic_contrasts.Rmd | 393 +- ratesci-1.1.0/ratesci/vignettes/paired_contrasts.Rmd | 233 - ratesci-1.1.0/ratesci/vignettes/single_rate.Rmd | 365 - ratesci-1.1.0/ratesci/vignettes/stratified.Rmd | 188 ratesci-1.1.0/ratesci/vignettes/tests.Rmd | 356 + 74 files changed, 14583 insertions(+), 12873 deletions(-)
Title: Open Knowledge Format (OKF) Ingestion
Description: Read, validate, and load Open Knowledge Format (OKF) bundles (a
directory of markdown files with YAML frontmatter) into a portable DuckDB
catalog, build the concept graph, render to HTML, and optionally embed
concept bodies for semantic search. Deterministic and agent-free: the same
bundle always yields the same catalog, graph, and render, with no LLM calls
in the core. Conformant and permissive per the OKF v0.1 specification.
Author: Travis Jakel [aut, cre]
Maintainer: Travis Jakel <travis.s.jakel@gmail.com>
Diff between okf versions 0.5.2 dated 2026-06-30 and 0.7.0 dated 2026-07-02
DESCRIPTION | 6 +-- MD5 | 14 +++++--- NAMESPACE | 2 + NEWS.md |only R/okf.R | 74 ++++++++++++++++++++++++++++++++++++++++--- R/okf_diff.R |only man/okf_diff.Rd |only man/okf_extract_wikilinks.Rd |only man/okf_links.Rd | 3 + tests/testthat/test-core.R | 49 ++++++++++++++++++++++++++++ 10 files changed, 134 insertions(+), 14 deletions(-)
Title: Aggregate Data Modelling
Description: Fit pharmacokinetic/pharmacodynamic (PK/PD) models to aggregate-level data (mean vector
and covariance matrix per study) rather than individual-level data. Integrates
with the 'nlmixr2'/'rxode2' ecosystem via four estimation methods: a First-Order ('FO')
analytical estimator, a Monte Carlo (MC) estimator, a Gauss-Hermite quadrature ('GH')
estimator, and an Iterative Reweighting Monte Carlo ('IRMC') estimator. Methods are
based on Välitalo (2021) <doi:10.1007/s10928-021-09760-1>; software described in
van de Beek et al. (2025) <doi:10.1007/s10928-025-10011-w>.
Author: H. van de Beek [aut, cre],
P.A.J. Vaelitalo [aut],
L.B. Zwep [aut],
J.G.C. van Hasselt [aut]
Maintainer: H. van de Beek <h.van.de.beek@lacdr.leidenuniv.nl>
Diff between admixr2 versions 0.1.0 dated 2026-06-02 and 0.2.0 dated 2026-07-02
DESCRIPTION | 20 MD5 | 93 - NAMESPACE | 3 NEWS.md | 66 R/adfo.R | 1902 ++++++++++++------------- R/adgh.R |only R/adirmc.R | 173 +- R/admc.R | 428 +++-- R/datagen.R | 559 ++++--- R/model.R | 277 ++- R/parse.R | 49 R/plot.R | 203 ++ R/simulate.R | 148 - R/utils.R | 94 + R/zzz.R | 32 README.md | 321 ++-- inst/doc/admixr2.Rmd | 390 ++--- inst/doc/admixr2.html | 65 man/adfoControl.Rd | 321 ++-- man/adghControl.Rd |only man/adirmcControl.Rd | 458 +++--- man/admClearCache.Rd |only man/admControl.Rd | 416 ++--- man/admData.Rd | 40 man/datagen.Rd | 229 +-- man/datagenControl.Rd | 111 - man/nlmixr2Est.adgh.Rd |only man/plot.admFit.Rd | 194 +- src/nll.cpp | 27 tests/manual |only tests/testthat/helper-integration.R | 1253 +++++++++++----- tests/testthat/setup.R |only tests/testthat/test-adgh-nodes.R |only tests/testthat/test-control-adfo.R | 346 ++-- tests/testthat/test-control-objects.R | 364 ++++ tests/testthat/test-datagen.R |only tests/testthat/test-fo-nll.R | 952 ++++++------ tests/testthat/test-grad-analytic.R | 386 ++--- tests/testthat/test-grad-kernels.R | 6 tests/testthat/test-integration-adfo.R | 243 +-- tests/testthat/test-integration-adgh.R |only tests/testthat/test-integration-cold-session.R |only tests/testthat/test-integration-cov.R | 283 ++- tests/testthat/test-integration-grad.R | 403 ++--- tests/testthat/test-integration-irmc.R | 150 + tests/testthat/test-integration-parallel.R |only tests/testthat/test-integration-pipeline.R |only tests/testthat/test-model.R |only tests/testthat/test-nll-kernels.R | 16 tests/testthat/test-parse.R | 117 + tests/testthat/test-progress-formatting.R | 54 tests/testthat/test-restart-output-var.R |only tests/testthat/test-traceplot.R |only tests/testthat/test-utils.R | 161 ++ vignettes/admixr2.Rmd | 390 ++--- 55 files changed, 6936 insertions(+), 4807 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.2.1 dated 2026-03-23 and 1.3.0 dated 2026-07-02
btw-1.2.1/btw/tests/testthat/_snaps/cli.md |only btw-1.3.0/btw/DESCRIPTION | 24 btw-1.3.0/btw/MD5 | 161 +- btw-1.3.0/btw/NAMESPACE | 4 btw-1.3.0/btw/NEWS.md | 28 btw-1.3.0/btw/R/btw_client_app.R | 360 ++++- btw-1.3.0/btw/R/btw_this.R | 8 btw-1.3.0/btw/R/mcp.R | 32 btw-1.3.0/btw/R/task_create_readme.R | 4 btw-1.3.0/btw/R/tool-agent-subagent.R | 19 btw-1.3.0/btw/R/tool-docs.R | 4 btw-1.3.0/btw/R/tool-env-df.R | 4 btw-1.3.0/btw/R/tool-env.R | 2 btw-1.3.0/btw/R/tool-files-patch.R |only btw-1.3.0/btw/R/tool-sessioninfo.R | 2 btw-1.3.0/btw/R/tool-skills.R | 301 +++- btw-1.3.0/btw/R/tools.R | 9 btw-1.3.0/btw/R/utils-ellmer.R | 220 +++ btw-1.3.0/btw/R/utils-r.R | 5 btw-1.3.0/btw/R/zzz.R | 12 btw-1.3.0/btw/exec/btw.R | 643 +++++++++- btw-1.3.0/btw/inst/cli-skill/r-btw-cli/SKILL.md | 60 btw-1.3.0/btw/inst/icons/ink-eraser.svg |only btw-1.3.0/btw/inst/js/app/btw_app.css | 55 btw-1.3.0/btw/inst/js/app/btw_app.js | 84 + btw-1.3.0/btw/inst/js/run-r/btw-run-r.css | 53 btw-1.3.0/btw/inst/js/run-r/btw-run-r.js | 58 btw-1.3.0/btw/man/btw-package.Rd | 1 btw-1.3.0/btw/man/btw.Rd | 2 btw-1.3.0/btw/man/btw_agent_tool.Rd | 2 btw-1.3.0/btw/man/btw_client.Rd | 20 btw-1.3.0/btw/man/btw_skill_install_github.Rd | 7 btw-1.3.0/btw/man/btw_skill_install_package.Rd | 7 btw-1.3.0/btw/man/btw_skill_install_project.Rd |only btw-1.3.0/btw/man/btw_task.Rd | 8 btw-1.3.0/btw/man/btw_task_create_btw_md.Rd | 10 btw-1.3.0/btw/man/btw_task_create_readme.Rd | 10 btw-1.3.0/btw/man/btw_task_create_skill.Rd | 10 btw-1.3.0/btw/man/btw_this.Rd | 8 btw-1.3.0/btw/man/btw_this.character.Rd | 10 btw-1.3.0/btw/man/btw_this.data.frame.Rd | 13 btw-1.3.0/btw/man/btw_this.environment.Rd | 8 btw-1.3.0/btw/man/btw_tool_cran_package.Rd | 4 btw-1.3.0/btw/man/btw_tool_cran_search.Rd | 4 btw-1.3.0/btw/man/btw_tool_docs_package_news.Rd | 2 btw-1.3.0/btw/man/btw_tool_env_describe_data_frame.Rd | 4 btw-1.3.0/btw/man/btw_tool_env_describe_environment.Rd | 4 btw-1.3.0/btw/man/btw_tool_files_edit.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_list.Rd | 15 btw-1.3.0/btw/man/btw_tool_files_patch.Rd |only btw-1.3.0/btw/man/btw_tool_files_read.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_replace.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_search.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_write.Rd | 13 btw-1.3.0/btw/man/btw_tool_git_branch_checkout.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_branch_create.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_branch_list.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_commit.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_diff.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_log.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_status.Rd | 16 btw-1.3.0/btw/man/btw_tool_package_docs.Rd | 4 btw-1.3.0/btw/man/btw_tool_pkg_check.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_coverage.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_document.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_load_all.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_test.Rd | 10 btw-1.3.0/btw/man/btw_tool_sessioninfo_is_package_installed.Rd | 6 btw-1.3.0/btw/man/btw_tool_sessioninfo_package.Rd | 6 btw-1.3.0/btw/man/btw_tool_sessioninfo_platform.Rd | 6 btw-1.3.0/btw/man/btw_tool_skill.Rd | 26 btw-1.3.0/btw/man/btw_tool_web_read_url.Rd | 2 btw-1.3.0/btw/man/btw_tools.Rd | 10 btw-1.3.0/btw/man/mcp.Rd | 38 btw-1.3.0/btw/man/use_btw_md.Rd | 2 btw-1.3.0/btw/tests/testthat/_snaps/tool-docs.md | 68 - btw-1.3.0/btw/tests/testthat/_snaps/tool-files-patch.md |only btw-1.3.0/btw/tests/testthat/helpers.R | 19 btw-1.3.0/btw/tests/testthat/test-btw_client.R | 217 +++ btw-1.3.0/btw/tests/testthat/test-btw_task.R | 1 btw-1.3.0/btw/tests/testthat/test-cli.R | 207 +-- btw-1.3.0/btw/tests/testthat/test-tool-agent-subagent.R | 41 btw-1.3.0/btw/tests/testthat/test-tool-files-patch.R |only btw-1.3.0/btw/tests/testthat/test-tool-session-package-installed.R | 3 btw-1.3.0/btw/tests/testthat/test-tool_skills.R | 220 +++ 85 files changed, 2692 insertions(+), 712 deletions(-)
Title: Interactive 3D Brain Atlas Visualization
Description: Plot brain atlases as interactive 3D meshes using 'Three.js'
via 'htmlwidgets', or render publication-quality static images through
'rgl' and 'rayshader'. A pipe-friendly API lets you map data onto
brain regions, control camera angles, toggle region edges, overlay
glass brains, and snapshot or ray-trace the result. Additional
atlases are available through the 'ggsegverse' r-universe. Mowinckel
& Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Center for Lifespan Changes in Brain and Cognition , University
of Oslo [cph],
three.js authors [ctb, cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg3d versions 2.1.1 dated 2026-04-22 and 2.1.2 dated 2026-07-02
ggseg3d-2.1.1/ggseg3d/tests/testthat/test-data_merge.R |only ggseg3d-2.1.2/ggseg3d/DESCRIPTION | 6 ggseg3d-2.1.2/ggseg3d/MD5 | 12 ggseg3d-2.1.2/ggseg3d/NEWS.md | 5 ggseg3d-2.1.2/ggseg3d/tests/testthat/helper-atlas-fixtures.R |only ggseg3d-2.1.2/ggseg3d/tests/testthat/helper-visual.R | 43 -- ggseg3d-2.1.2/ggseg3d/tests/testthat/test-brain-mesh.R | 37 - ggseg3d-2.1.2/ggseg3d/tests/testthat/test-ggseg3d.R | 227 ++++------- 8 files changed, 123 insertions(+), 207 deletions(-)
Title: Splitting-Coalescence-Estimation Method
Description: We introduce improved methods for statistically assessing birth seasonality and intra-annual variation. The first method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. One can use the function SCEM() to implement this method. The second method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits_OLS(), while makeFits_initial() is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach. One can use the function makeFits() to generate parametric birth seasonality estimates using either initialization. Detailed description can be found here: Chazin Hannah, Soudeep Deb, Joshua Falk, and Arun Srinivasan (2019) <doi:10.1111/arcm.12432> "New Statistica [...truncated...]
Author: Hannah Chazin [aut, cre],
Soudeep Deb [aut],
Joshua Falk [aut],
Arun Srinivasan [aut],
Kyung Serk Cho [aut]
Maintainer: Hannah Chazin <h.chazin@columbia.edu>
This is a re-admission after prior archival of version 1.1.0 dated 2021-09-02
Diff between SCEM versions 1.1.0 dated 2021-09-02 and 1.2.0 dated 2026-07-02
SCEM-1.1.0/SCEM/README.md |only SCEM-1.1.0/SCEM/build/SCEM.pdf |only SCEM-1.2.0/SCEM/DESCRIPTION | 30 - SCEM-1.2.0/SCEM/MD5 | 81 +- SCEM-1.2.0/SCEM/NAMESPACE | 35 - SCEM-1.2.0/SCEM/R/EBIC.R | 124 ++-- SCEM-1.2.0/SCEM/R/EstTrend.R | 100 +-- SCEM-1.2.0/SCEM/R/SCEM.R | 196 +++--- SCEM-1.2.0/SCEM/R/SCalgo.R | 92 +-- SCEM-1.2.0/SCEM/R/calculateRSS.R | 134 ++-- SCEM-1.2.0/SCEM/R/convertParameters.R | 110 +-- SCEM-1.2.0/SCEM/R/iteration.R | 142 ++-- SCEM-1.2.0/SCEM/R/kernel.R | 46 - SCEM-1.2.0/SCEM/R/makeFits.R | 90 +-- SCEM-1.2.0/SCEM/R/makeFits_OLS.R | 124 ++-- SCEM-1.2.0/SCEM/R/makeFits_initial.R | 136 ++-- SCEM-1.2.0/SCEM/R/sineFit.R | 92 +-- SCEM-1.2.0/SCEM/R/sine_OLS.R | 102 +-- SCEM-1.2.0/SCEM/R/sine_initial.R | 122 ++-- SCEM-1.2.0/SCEM/build/stage23.rdb |only SCEM-1.2.0/SCEM/build/vignette.rds |binary SCEM-1.2.0/SCEM/inst/CITATION | 32 - SCEM-1.2.0/SCEM/inst/doc/SCEM_example.R | 186 +++--- SCEM-1.2.0/SCEM/inst/doc/SCEM_example.Rmd | 240 ++++---- SCEM-1.2.0/SCEM/inst/doc/SCEM_example.html | 723 +++++++++++++++---------- SCEM-1.2.0/SCEM/man/EBIC.Rd | 88 +-- SCEM-1.2.0/SCEM/man/EstTrend.Rd | 64 +- SCEM-1.2.0/SCEM/man/SCEM.Rd | 102 +-- SCEM-1.2.0/SCEM/man/SCalgo.Rd | 58 +- SCEM-1.2.0/SCEM/man/calculateRSS.Rd | 82 +- SCEM-1.2.0/SCEM/man/convertParameters.Rd | 58 +- SCEM-1.2.0/SCEM/man/data-armenia.Rd | 60 +- SCEM-1.2.0/SCEM/man/iteration.Rd | 70 +- SCEM-1.2.0/SCEM/man/kernel.Rd | 50 - SCEM-1.2.0/SCEM/man/makeFits.Rd | 96 +-- SCEM-1.2.0/SCEM/man/makeFits_OLS.Rd | 74 +- SCEM-1.2.0/SCEM/man/makeFits_initial.Rd | 86 +- SCEM-1.2.0/SCEM/man/sineFit.Rd | 82 +- SCEM-1.2.0/SCEM/man/sine_OLS.Rd | 66 +- SCEM-1.2.0/SCEM/man/sine_initial.Rd | 80 +- SCEM-1.2.0/SCEM/tests/testthat.R | 8 SCEM-1.2.0/SCEM/tests/testthat/test-makeFits.R | 6 SCEM-1.2.0/SCEM/vignettes/SCEM_example.Rmd | 240 ++++---- 43 files changed, 2255 insertions(+), 2052 deletions(-)
Title: Example Metabolomics Data Sets
Description: Data sets from a variety of biological sample matrices,
analysed using a number of mass spectrometry based metabolomic analytical techniques.
The example data sets are stored remotely using GitHub releases
<https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package.
The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://github.com/aberHRML/FIEmspro> <doi:10.1038/nprot.2007.511>.
Author: Jasen Finch [aut, cre] ,
Manfred Beckmann [ctb],
David Enot [ctb],
Wanchang Lin [ctb]
Maintainer: Jasen Finch <jsnfnch4@gmail.com>
Diff between metaboData versions 0.6.3 dated 2022-02-15 and 0.6.4 dated 2026-07-02
DESCRIPTION | 16 ++-- MD5 | 17 ++-- NEWS.md | 8 ++ R/reexports.R | 7 + build/vignette.rds |binary inst/doc/metaboData.R | 34 ++++---- inst/doc/metaboData.html | 174 ++++++++++++++++++++++++++------------------- man/reexports.Rd | 17 +--- vignettes/metaboData_files |only 9 files changed, 157 insertions(+), 116 deletions(-)
Title: Computing Key Indicators of the Spatial Distribution of Economic
Activities
Description: Computes a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. Most of the functions use matrix calculus and are based on bipartite (incidence) matrices consisting of region - industry pairs. These are described in Balland (2017) <http://econ.geo.uu.nl/peeg/peeg1709.pdf>.
Author: Pierre-Alexandre Balland [aut, cre, cph]
Maintainer: Pierre-Alexandre Balland <pierre.alex.balland@gmail.com>
Diff between EconGeo versions 2.0 dated 2023-06-26 and 2.1 dated 2026-07-02
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/index.html>.
Author: Christoph Scheuch [aut, cre, cph] ,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.7.0 dated 2026-06-25 and 0.8.0 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 101 ++++++----- NAMESPACE | 6 NEWS.md | 55 ++++++ R/download_data.R | 42 ++++ R/download_data_huggingface.R | 18 +- R/download_data_jkp.R |only R/download_data_osap.R | 25 ++ R/download_data_pastor_stambaugh.R |only R/download_data_stambaugh_yuan.R |only R/list_supported_datasets.R | 9 + R/tidyfinance-package.R | 2 R/validate.R | 1 README.md | 161 ++++++++++++++++--- build/vignette.rds |only inst/CITATION | 2 inst/doc |only man/create_summary_statistics.Rd | 1 man/download_data.Rd | 14 + man/download_data_constituents.Rd | 3 man/download_data_factors_ff.Rd | 3 man/download_data_factors_q.Rd | 3 man/download_data_fred.Rd | 3 man/download_data_huggingface.Rd | 3 man/download_data_jkp.Rd |only man/download_data_macro_predictors.Rd | 3 man/download_data_osap.Rd | 22 ++ man/download_data_pastor_stambaugh.Rd |only man/download_data_risk_free.Rd | 3 man/download_data_stambaugh_yuan.Rd |only man/download_data_stock_prices.Rd | 3 man/download_factor_library_grid.Rd | 3 man/download_factor_library_ids.Rd | 3 man/get_available_huggingface_files.Rd | 1 man/list_supported_datasets.Rd | 1 man/list_supported_datasets_ff.Rd | 1 man/list_supported_datasets_ff_legacy.Rd | 1 man/list_supported_datasets_macro_predictors.Rd | 1 man/list_supported_datasets_other.Rd | 1 man/list_supported_datasets_pseudo.Rd | 1 man/list_supported_datasets_wrds.Rd | 1 man/list_supported_indexes.Rd | 1 man/list_supported_jkp_factors.Rd |only man/list_tidy_finance_chapters.Rd | 1 man/open_tidy_finance_website.Rd | 1 man/tidyfinance-package.Rd | 2 man/trim.Rd | 1 man/validate_dates.Rd | 1 man/winsorize.Rd | 1 tests/testthat/_snaps/list_supported_datasets.md | 25 +- tests/testthat/test-download_data.R | 46 +++++ tests/testthat/test-download_data_huggingface.R | 42 ++++ tests/testthat/test-download_data_jkp.R |only tests/testthat/test-download_data_osap.R | 9 - tests/testthat/test-download_data_pastor_stambaugh.R |only tests/testthat/test-download_data_stambaugh_yuan.R |only vignettes |only 57 files changed, 521 insertions(+), 117 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.2.0 dated 2026-06-23 and 3.4.0 dated 2026-07-02
ggRandomForests-3.2.0/ggRandomForests/tests/testthat/Rplots.pdf |only ggRandomForests-3.4.0/ggRandomForests/DESCRIPTION | 8 ggRandomForests-3.4.0/ggRandomForests/MD5 | 88 +- ggRandomForests-3.4.0/ggRandomForests/NAMESPACE | 18 ggRandomForests-3.4.0/ggRandomForests/NEWS.md | 72 + ggRandomForests-3.4.0/ggRandomForests/R/gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/R/gg_beta_varpro.R | 12 ggRandomForests-3.4.0/ggRandomForests/R/gg_isopro.R | 12 ggRandomForests-3.4.0/ggRandomForests/R/gg_ivarpro.R | 13 ggRandomForests-3.4.0/ggRandomForests/R/gg_partial_rfsrc.R | 36 ggRandomForests-3.4.0/ggRandomForests/R/gg_partial_varpro.R | 247 +++++- ggRandomForests-3.4.0/ggRandomForests/R/gg_partialpro.R | 4 ggRandomForests-3.4.0/ggRandomForests/R/gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_partial_varpro.R | 106 ++ ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/README.md | 22 ggRandomForests-3.4.0/ggRandomForests/build/vignette.rds |binary ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-regression.html | 36 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-regression.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-survival.html | 44 - ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-survival.qmd | 11 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests.html | 4 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.html |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.qmd |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.R | 13 ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.html | 386 ++++++---- ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.qmd | 150 +-- ggRandomForests-3.4.0/ggRandomForests/man/gg_beta_uvarpro.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/gg_partial_rfsrc.Rd | 3 ggRandomForests-3.4.0/ggRandomForests/man/gg_partial_varpro.Rd | 40 - ggRandomForests-3.4.0/ggRandomForests/man/gg_sdependent.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_beta_uvarpro.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_partial_varpro.Rd | 64 + ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_sdependent.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/print.gg.Rd | 11 ggRandomForests-3.4.0/ggRandomForests/man/summary.gg.Rd | 15 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_beta_varpro.R | 7 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_isopro.R | 9 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_ivarpro.R | 9 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_partial_rfsrc.R |only ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_partial_varpro.R | 180 ++++ ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests-regression.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests-survival.qmd | 11 ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/vignettes/precompute_varpro.R | 9 ggRandomForests-3.4.0/ggRandomForests/vignettes/uvarpro.qmd |only ggRandomForests-3.4.0/ggRandomForests/vignettes/varpro.qmd | 150 +-- ggRandomForests-3.4.0/ggRandomForests/vignettes/varpro_precomputed.rds |binary 53 files changed, 1274 insertions(+), 524 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: R Library for 'Harmony'
Description: 'Harmony' is a tool using AI which allows you to compare items from questionnaires and identify similar content. You can try 'Harmony' at <https://harmonydata.ac.uk/app/> and you can read our blog at <https://harmonydata.ac.uk/blog/> or at <https://fastdatascience.com/how-does-harmony-work/>. Documentation at <https://harmonydata.ac.uk/harmony-r-released/>.
Author: Omar Hassoun [aut, cre],
Thomas Wood [ctb],
Alex, Nikic [ctb],
Ulster University [cph]
Maintainer: Omar Hassoun <omtarful@gmail.com>
Diff between harmonydata versions 0.3.1 dated 2025-04-20 and 0.3.2 dated 2026-07-02
DESCRIPTION | 8 +++--- MD5 | 11 +++++--- NEWS.md | 29 ++++++++++++++++------- R/match_instruments.R | 58 ++++++++++++++++++++++++++++++++++++++++++++++- man/match_instruments.Rd | 24 ++++++++++++++++++- tests |only 6 files changed, 111 insertions(+), 19 deletions(-)
Title: Coverage Correlation Coefficient and Testing for Independence
Description: Computes the coverage correlation coefficient introduced in <doi:10.48550/arXiv.2508.06402> , a statistical measure that quantifies dependence between two random vectors by computing the union volume of data-centered hypercubes in a uniform space.
Author: Tengyao Wang [aut, cre],
Mona Azadkia [aut, ctb],
Xuzhi Yang [aut, ctb]
Maintainer: Tengyao Wang <t.wang59@lse.ac.uk>
Diff between covercorr versions 1.0.0 dated 2025-08-25 and 1.1.0 dated 2026-07-02
DESCRIPTION | 13 MD5 | 28 + NAMESPACE | 10 NEWS.md |only R/Visualise_density.R |only R/covercorr-methods.R |only R/covercorr.R | 765 ++++++++++++++++++++++++++++++++++++- inst/doc/coverage_correlation.R | 95 ++++ inst/doc/coverage_correlation.Rmd | 273 +++++++++++-- inst/doc/coverage_correlation.html | 352 +++++++++++++---- man/coverage_correlation_K.Rd |only man/coverage_correlation_K_grid.Rd |only man/coverage_correlation_grid.Rd |only man/covercorr.Rd |only man/visualise_density.Rd |only tests |only vignettes/coverage_correlation.Rmd | 273 +++++++++++-- 17 files changed, 1628 insertions(+), 181 deletions(-)
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Maximilian Muecke [aut, cre] ,
Sebastian Fischer [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3fda versions 0.6.0 dated 2026-06-01 and 0.7.0 dated 2026-07-02
DESCRIPTION | 17 ++++---- MD5 | 59 +++++++++++++++++-------------- NAMESPACE | 2 + NEWS.md | 8 ++++ R/PipeOpFDABsignal.R | 4 +- R/PipeOpFDACatch22.R |only R/PipeOpFDAFlatten.R | 6 --- R/PipeOpFDAIntegrate.R |only R/PipeOpFDARandomEffect.R | 2 - R/PipeOpFDAScaleRange.R | 12 ++---- R/PipeOpFDATsfeatures.R | 2 - R/PipeOpFDAWavelets.R | 5 +- R/PipeOpFDAZoom.R | 6 +-- R/PipeOpFPCA.R | 4 -- R/bibentries.R | 8 ++-- R/hash_input.R | 6 --- R/zzz.R | 10 +---- README.md | 2 + build/partial.rdb |binary man/mlr_pipeops_fda.bsignal.Rd | 2 + man/mlr_pipeops_fda.catch22.Rd |only man/mlr_pipeops_fda.fourier.Rd | 2 - man/mlr_pipeops_fda.integrate.Rd |only man/mlr_pipeops_fda.random_effect.Rd | 2 + man/mlr_pipeops_fda.tsfeats.Rd | 2 + man/mlr_pipeops_fda.wavelets.Rd | 2 + man/mlr_tasks_dti.Rd | 2 - man/mlr_tasks_fuel.Rd | 2 - man/mlr_tasks_phoneme.Rd | 2 - tests/testthat/helper.R | 2 - tests/testthat/test_PipeOpFDACatch22.R |only tests/testthat/test_PipeOpFDAIntegrate.R |only tests/testthat/test_PipeOpFDAWavelets.R | 6 +-- tests/testthat/test_zzz.R |only 34 files changed, 93 insertions(+), 84 deletions(-)
Title: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data
Downloading and Importing
Description: Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
Author: John Elizarraras [aut, ctb],
Zhiao Shi [cre]
Maintainer: Zhiao Shi <zhiao.shi@gmail.com>
Diff between clinicalomicsdbR versions 1.0.5 dated 2024-06-26 and 1.0.6 dated 2026-07-02
DESCRIPTION | 16 +++++++++------- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 15 insertions(+), 9 deletions(-)
More information about clinicalomicsdbR at CRAN
Permanent link
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of
covariate-dependent binomial probabilities, and the Dirichlet Kernel Process (DKP) for
categorical or multinomial response data. Scalable global-local approximations
are provided through TwinBKP and TwinDKP, using twinning-selected global subsets
and local nearest-neighbour updates.
Functions are included for model fitting, predictive inference with
uncertainty quantification, posterior simulation,
and visualization in one- and two-dimensional input spaces.
Gaussian, Matern 5/2, Matern 3/2, and Wendland kernels are supported,
with hyperparameters selected by multi-start derivative-free optimization.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.3 dated 2025-09-22 and 0.3.0 dated 2026-07-02
BKP-0.2.3/BKP/tests/testthat/Rplots.pdf |only BKP-0.2.3/BKP/tests/testthat/test-simualte_DKP.R |only BKP-0.3.0/BKP/DESCRIPTION | 27 BKP-0.3.0/BKP/MD5 | 201 ++-- BKP-0.3.0/BKP/NAMESPACE | 57 + BKP-0.3.0/BKP/NEWS.md | 32 BKP-0.3.0/BKP/R/BKP-package.R | 111 +- BKP-0.3.0/BKP/R/RcppExports.R |only BKP-0.3.0/BKP/R/fit_BKP.R | 686 +++++++++----- BKP-0.3.0/BKP/R/fit_DKP.R | 684 +++++++++----- BKP-0.3.0/BKP/R/fit_TwinBKP.R |only BKP-0.3.0/BKP/R/fit_TwinDKP.R |only BKP-0.3.0/BKP/R/fitted_BKP.R | 159 ++- BKP-0.3.0/BKP/R/fitted_DKP.R | 106 +- BKP-0.3.0/BKP/R/fitted_TwinBKP.R |only BKP-0.3.0/BKP/R/fitted_TwinDKP.R |only BKP-0.3.0/BKP/R/get_prior.R | 302 ++++-- BKP-0.3.0/BKP/R/kernel_matrix.R | 209 ++-- BKP-0.3.0/BKP/R/loss_fun.R | 362 ++++--- BKP-0.3.0/BKP/R/parameter_BKP.R | 164 ++- BKP-0.3.0/BKP/R/parameter_DKP.R | 98 +- BKP-0.3.0/BKP/R/parameter_TwinBKP.R |only BKP-0.3.0/BKP/R/parameter_TwinDKP.R |only BKP-0.3.0/BKP/R/plot_BKP.R | 709 +++++++++------ BKP-0.3.0/BKP/R/plot_DKP.R | 660 ++++++++------ BKP-0.3.0/BKP/R/plot_TwinBKP.R |only BKP-0.3.0/BKP/R/plot_TwinDKP.R |only BKP-0.3.0/BKP/R/predict_BKP.R | 613 ++++++++----- BKP-0.3.0/BKP/R/predict_DKP.R | 448 ++++++--- BKP-0.3.0/BKP/R/predict_TwinBKP.R |only BKP-0.3.0/BKP/R/predict_TwinDKP.R |only BKP-0.3.0/BKP/R/print_BKP.R | 671 +++++++------- BKP-0.3.0/BKP/R/print_DKP.R | 665 +++++++------- BKP-0.3.0/BKP/R/print_TwinBKP.R |only BKP-0.3.0/BKP/R/print_TwinDKP.R |only BKP-0.3.0/BKP/R/quantile_BKP.R | 207 ++-- BKP-0.3.0/BKP/R/quantile_DKP.R | 166 ++- BKP-0.3.0/BKP/R/quantile_TwinBKP.R |only BKP-0.3.0/BKP/R/quantile_TwinDKP.R |only BKP-0.3.0/BKP/R/simulate_BKP.R | 434 +++++---- BKP-0.3.0/BKP/R/simulate_DKP.R | 289 +++--- BKP-0.3.0/BKP/R/simulate_TwinBKP.R |only BKP-0.3.0/BKP/R/simulate_TwinDKP.R |only BKP-0.3.0/BKP/R/summary_BKP.R | 240 ++--- BKP-0.3.0/BKP/R/summary_DKP.R | 184 +--- BKP-0.3.0/BKP/R/summary_TwinBKP.R |only BKP-0.3.0/BKP/R/summary_TwinDKP.R |only BKP-0.3.0/BKP/R/utils.R | 827 ++++++++++++++++-- BKP-0.3.0/BKP/README.md | 103 +- BKP-0.3.0/BKP/inst/CITATION | 23 BKP-0.3.0/BKP/inst/COPYRIGHTS |only BKP-0.3.0/BKP/inst/WORDLIST |only BKP-0.3.0/BKP/inst/include |only BKP-0.3.0/BKP/man/BKP-package.Rd | 102 +- BKP-0.3.0/BKP/man/bkp_check_unique_locations.Rd |only BKP-0.3.0/BKP/man/bkp_compute_posterior.Rd |only BKP-0.3.0/BKP/man/bkp_ess_calibration.Rd |only BKP-0.3.0/BKP/man/bkp_ess_none_info.Rd |only BKP-0.3.0/BKP/man/bkp_shepard_m.Rd |only BKP-0.3.0/BKP/man/bkp_shepard_m_loo.Rd |only BKP-0.3.0/BKP/man/dkp_compute_posterior.Rd |only BKP-0.3.0/BKP/man/fit_BKP.Rd | 376 ++++---- BKP-0.3.0/BKP/man/fit_DKP.Rd | 385 +++++--- BKP-0.3.0/BKP/man/fit_TwinBKP.Rd |only BKP-0.3.0/BKP/man/fit_TwinDKP.Rd |only BKP-0.3.0/BKP/man/fitted.Rd | 241 +++-- BKP-0.3.0/BKP/man/get_prior.Rd | 125 +- BKP-0.3.0/BKP/man/kernel_matrix.Rd | 105 +- BKP-0.3.0/BKP/man/loss_fun.Rd | 87 + BKP-0.3.0/BKP/man/make_plot_grid.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_class.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_class_ggplot.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_ggplot.Rd |only BKP-0.3.0/BKP/man/parameter.Rd | 247 +++-- BKP-0.3.0/BKP/man/plot.Rd | 200 +++- BKP-0.3.0/BKP/man/posterior_summary.Rd |only BKP-0.3.0/BKP/man/predict.Rd | 321 ++++-- BKP-0.3.0/BKP/man/print.Rd | 203 ++-- BKP-0.3.0/BKP/man/quantile.Rd | 257 +++-- BKP-0.3.0/BKP/man/simulate.Rd | 183 ++- BKP-0.3.0/BKP/man/summary.Rd | 177 +-- BKP-0.3.0/BKP/src |only BKP-0.3.0/BKP/tests/testthat.R | 4 BKP-0.3.0/BKP/tests/testthat/helper-BKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-DKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fit_BKP.R | 371 +++++--- BKP-0.3.0/BKP/tests/testthat/test-fit_DKP.R | 451 ++++++--- BKP-0.3.0/BKP/tests/testthat/test-fit_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fit_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fitted_BKP.R | 323 ++++--- BKP-0.3.0/BKP/tests/testthat/test-fitted_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fitted_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-get_prior.R | 130 ++ BKP-0.3.0/BKP/tests/testthat/test-kernel_matrix.R | 288 ++++++ BKP-0.3.0/BKP/tests/testthat/test-loss_fun.R | 130 ++ BKP-0.3.0/BKP/tests/testthat/test-parameter_BKP.R | 128 +- BKP-0.3.0/BKP/tests/testthat/test-parameter_DKP.R | 132 +- BKP-0.3.0/BKP/tests/testthat/test-parameter_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-parameter_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-plot_BKP.R | 195 ++-- BKP-0.3.0/BKP/tests/testthat/test-plot_DKP.R | 238 +++-- BKP-0.3.0/BKP/tests/testthat/test-plot_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-plot_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-predict_BKP.R | 192 ++-- BKP-0.3.0/BKP/tests/testthat/test-predict_DKP.R | 220 ++-- BKP-0.3.0/BKP/tests/testthat/test-predict_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-predict_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-print_BKP.R | 103 +- BKP-0.3.0/BKP/tests/testthat/test-print_DKP.R | 105 +- BKP-0.3.0/BKP/tests/testthat/test-print_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-print_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-quantile_BKP.R | 158 +-- BKP-0.3.0/BKP/tests/testthat/test-quantile_DKP.R | 232 ++--- BKP-0.3.0/BKP/tests/testthat/test-quantile_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-quantile_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-simulate_BKP.R | 232 ++--- BKP-0.3.0/BKP/tests/testthat/test-simulate_DKP.R | 201 +++- BKP-0.3.0/BKP/tests/testthat/test-simulate_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-simulate_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-summary_BKP.R | 169 +-- BKP-0.3.0/BKP/tests/testthat/test-summary_DKP.R | 187 ++-- BKP-0.3.0/BKP/tests/testthat/test-summary_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-summary_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-utils.R | 214 ++-- 127 files changed, 10501 insertions(+), 6348 deletions(-)
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://api-docs.serpstat.com/docs/serpstat-public-api/jenasqbwtxdlr-introduction-to-serpstat-api>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.4.2 dated 2026-06-09 and 0.4.3 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/serp_crawling.R |only R/utility_functions.R | 13 +++++++++++-- README.md | 14 ++++++++++++++ man/sst_sc_add_task.Rd |only man/sst_sc_get_task_result.Rd |only tests/testthat/test_serp_crawling.R |only 10 files changed, 45 insertions(+), 10 deletions(-)
Title: Phenotypic Index Measures for Oak Decline Severity
Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2021) <doi:10.1016/j.foreco.2021.118948>.
Author: Jasen Finch [aut, cre]
Maintainer: Jasen Finch <jsnfnch4@gmail.com>
Diff between pdi versions 0.4.2 dated 2021-02-09 and 0.4.3 dated 2026-07-02
DESCRIPTION | 19 - MD5 | 26 - NAMESPACE | 1 NEWS.md | 12 R/reexports.R | 9 R/siteAdjustment.R | 62 ++- R/siteAdjustmentFactors.R | 46 +- README.md | 6 build/vignette.rds |binary inst/doc/pdi-example.R | 4 inst/doc/pdi-example.html | 695 ++++++++++++++++++++++++++++++------------- man/reexports.Rd | 21 - man/siteAdjustment.Rd | 9 man/siteAdjustmentFactors.Rd | 7 14 files changed, 617 insertions(+), 300 deletions(-)
Title: A Set of Color Palettes Inspired by OK Go Music Videos for
'ggplot2' in R
Description: A collection of aesthetically appealing color palettes for effective data visualization with 'ggplot2'. Palettes support both discrete and continuous data.
Author: Nelson de O. Quesado Filho [aut, cre],
Ana Flavia Teles Silveira [aut]
Maintainer: Nelson de O. Quesado Filho <nquesado@gmail.com>
Diff between okcolors versions 0.1.0 dated 2025-05-14 and 0.1.2 dated 2026-07-02
DESCRIPTION | 9 ++--- MD5 | 26 +++++++------- NAMESPACE | 1 NEWS.md | 11 ++++++ R/palettes.R | 46 ++++++++----------------- R/scales.R | 73 +++++++++++++++++++++-------------------- R/utils.R | 64 +++++++++++++++++++++++++++++++++++ README.md |only man/okcolors.Rd | 28 ++++++--------- man/scale_color_okcolors.Rd | 35 +++++++++---------- man/scale_fill_okcolors.Rd | 34 +++++++++---------- man/valid_palettes.Rd |only tests/testthat/test-okcolors.R | 35 ++++++++----------- tests/testthat/test-palettes.R | 12 +++++- tests/testthat/test-scales.R | 14 ++++++- 15 files changed, 231 insertions(+), 157 deletions(-)
Title: Interface to 'NetMHCIIpan'
Description: The field of immunology benefits from software that can
predict which peptide sequences trigger an immune response.
'NetMHCIIpan' is a such a tool: it predicts the
binding strength of a short peptide to a Major Histocompatibility
Complex class II (MHC-II) molecule.
'NetMHCIIpan' can be used from a web server at
<https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/>
or from the command-line, using a local installation. This package
allows to call 'NetMHCIIpan' from R.
Author: Richel J.C. Bilderbeek [aut, cre] ,
Lue Ping Zhao [ctb],
Byungkuk Min [ctb]
Maintainer: Richel J.C. Bilderbeek <rjcbilderbeek@gmail.com>
Diff between netmhc2pan versions 1.3.2 dated 2023-11-08 and 1.3.3 dated 2026-07-02
netmhc2pan-1.3.2/netmhc2pan/R/netmhc2pan.R |only netmhc2pan-1.3.2/netmhc2pan/man/figures/TravisCI.png |only netmhc2pan-1.3.3/netmhc2pan/DESCRIPTION | 16 ++++++++-------- netmhc2pan-1.3.3/netmhc2pan/MD5 | 11 +++++------ netmhc2pan-1.3.3/netmhc2pan/R/netmhc2pan-package.R |only netmhc2pan-1.3.3/netmhc2pan/R/netmhc2pan_report.R | 2 +- netmhc2pan-1.3.3/netmhc2pan/build/vignette.rds |binary netmhc2pan-1.3.3/netmhc2pan/inst/doc/demo.html | 6 +++--- 8 files changed, 17 insertions(+), 18 deletions(-)
Title: Create Data with Identical Statistics
Description: Creates data with identical statistics (metamers) using an iterative
algorithm proposed by Matejka & Fitzmaurice (2017) <DOI:10.1145/3025453.3025912>.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metamer versions 0.3.0 dated 2022-06-23 and 0.3.1 dated 2026-07-02
DESCRIPTION | 18 ++++++++++-------- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ README.md | 18 +++++++----------- build/partial.rdb |binary man/delayed_with.Rd | 16 ++++++++-------- man/densify.Rd | 16 ++++++++-------- man/draw_data.Rd | 16 ++++++++-------- man/figures/README-unnamed-chunk-6-1.gif |binary man/figures/README-unnamed-chunk-8-1.gif |binary man/mean_dist_to.Rd | 16 ++++++++-------- man/mean_dist_to_sf.Rd | 16 ++++++++-------- man/mean_self_proximity.Rd | 16 ++++++++-------- man/metamer-package.Rd | 8 +++++++- man/moments_n.Rd | 16 ++++++++-------- man/rounding.Rd | 25 ++++++++----------------- 16 files changed, 107 insertions(+), 108 deletions(-)
Title: Brain Atlas Data Structures for the 'ggsegverse' Ecosystem
Description: Provides the 'ggseg_atlas' S3 class used across the 'ggsegverse'
ecosystem for 2D and 3D brain visualisation. Ships four bundled atlases
('Desikan-Killiany', 'FreeSurfer' 'aseg', 'TRACULA', 'SUIT') and functions
for querying, subsetting, renaming, and enriching atlas objects. Also
includes readers for 'FreeSurfer' statistics files.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Center for Lifespan Changes in Brain and Cognition , University
of Oslo [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg.formats versions 0.0.3 dated 2026-06-18 and 0.0.4 dated 2026-07-02
DESCRIPTION | 6 MD5 | 57 ++-- NEWS.md | 225 ++++++++-------- R/atlas_accessors.R | 13 R/atlas_convert.R | 4 R/atlas_polygons.R | 4 R/compat_dataframe.R | 52 +++ R/ggseg_atlas.R | 29 +- R/ggseg_atlas_data.R | 20 - R/read_freesurfer.R | 2 R/sysdata.rda |binary inst/WORDLIST | 6 inst/doc/atlas-manipulation.html | 6 inst/doc/ggseg.formats.html | 344 ++++--------------------- tests/testthat/_snaps |only tests/testthat/helper-polygons.R | 7 tests/testthat/test-atlas_accessors.R | 19 + tests/testthat/test-atlas_convert.R | 17 - tests/testthat/test-atlas_polygon_converters.R | 3 tests/testthat/test-atlas_polygon_ops.R | 5 tests/testthat/test-atlas_polygons.R | 39 +- tests/testthat/test-atlas_utils.R | 16 - tests/testthat/test-atlases.R | 12 tests/testthat/test-compat_dataframe.R | 39 ++ tests/testthat/test-ggseg-atlas-plots.R | 30 ++ tests/testthat/test-ggseg_atlas.R | 22 - tests/testthat/test-ggseg_atlas_data.R | 18 - tests/testthat/test-migrate_atlas_files.R | 15 - 28 files changed, 483 insertions(+), 527 deletions(-)
Title: Easy Plotting of Periodic Data with 'ggplot2'
Description: Implements methods to plot periodic data in any arbitrary range on the fly.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between ggperiodic versions 1.0.3 dated 2023-03-22 and 1.0.4 dated 2026-07-02
DESCRIPTION | 15 ++-- MD5 | 24 +++---- NEWS.md | 4 + R/fortify.R | 35 ----------- R/periodic.R | 1 R/unperiodic.R | 12 +-- README.md | 13 ---- build/vignette.rds |binary inst/doc/wraping-around-ggplot2.html | 95 +++++++++++++++---------------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/ggperiodic.Rd | 9 ++ man/reexports.Rd | 2 13 files changed, 89 insertions(+), 121 deletions(-)
Title: Open-Access Computational Biology Datasets
Description: Efficiently access the 'Bedrock Bio' library of open-access
computational biology datasets. Lazily query datasets backed by 'DuckDB'
and 'Apache Iceberg', with support for predicate pushdown and column
projection to the cloud storage backend. This enables quick, iterative
access to otherwise massive, unwieldy datasets without downloading them
in full. See <https://bedrock.bio> for available datasets and
documentation.
Author: Liam Abbott [aut, cre, cph]
Maintainer: Liam Abbott <liam@bedrock.bio>
Diff between bedrockbio versions 1.4.0 dated 2026-05-28 and 2.0.0 dated 2026-07-02
DESCRIPTION | 15 +- MD5 | 46 +++--- NEWS.md | 23 +++ R/describe_namespace.R | 15 -- R/describe_table.R | 32 +--- R/list_namespaces.R | 7 R/list_tables.R | 25 ++- R/load_table.R | 19 +- R/utils.R | 105 ++++---------- R/zzz.R | 12 + README.md | 22 +-- man/bedrockbio-package.Rd | 4 man/describe_namespace.Rd | 15 -- man/describe_table.Rd | 15 +- man/list_namespaces.Rd | 6 man/list_tables.Rd | 14 + man/load_table.Rd | 9 - tests/testthat/helper-v2.R |only tests/testthat/test-describe_namespace.R | 37 ++--- tests/testthat/test-describe_table.R | 62 ++++---- tests/testthat/test-env.R |only tests/testthat/test-list_namespaces.R | 2 tests/testthat/test-list_tables.R | 35 ++++ tests/testthat/test-load_table.R | 39 ++++- tests/testthat/test-utils.R | 225 +++++++++---------------------- 25 files changed, 387 insertions(+), 397 deletions(-)
Title: 'Material UI' for 'shiny' Apps and 'Quarto'
Description: Wraps the 'Material UI' React components <https://mui.com/> for use in R, 'shiny'
applications and 'quarto' documents, including inputs, layouts, navigation, and
surfaces. All inputs come with R usage examples.
Author: Felix Luginbuhl [aut, cre, cph] ,
MUI [cph] ,
Emotion team [cph] ,
Meta Platforms, Inc. and affiliates [cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between muiMaterial versions 0.2.1 dated 2026-06-28 and 0.2.2 dated 2026-07-02
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 10 ++ README.md | 4 inst/www/muiMaterial/mui-material.js | 113 +++++++++++++---------- inst/www/muiMaterial/mui-material.js.LICENSE.txt | 12 +- 6 files changed, 94 insertions(+), 61 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 1.1.1 dated 2026-05-20 and 1.2.0 dated 2026-07-02
maestro-1.1.1/maestro/R/show_network.R |only maestro-1.1.1/maestro/man/show_network.Rd |only maestro-1.1.1/maestro/tests/testthat/test-show_network.R |only maestro-1.2.0/maestro/DESCRIPTION | 10 maestro-1.2.0/maestro/MD5 | 85 +- maestro-1.2.0/maestro/NAMESPACE | 4 maestro-1.2.0/maestro/NEWS.md | 23 maestro-1.2.0/maestro/R/MaestroPipeline.R | 155 ++++ maestro-1.2.0/maestro/R/MaestroPipelineList.R | 340 +++++++++- maestro-1.2.0/maestro/R/MaestroSchedule.R | 45 - maestro-1.2.0/maestro/R/build_schedule.R | 39 - maestro-1.2.0/maestro/R/build_schedule_entry.R | 84 +- maestro-1.2.0/maestro/R/get_labels.R |only maestro-1.2.0/maestro/R/get_network.R | 1 maestro-1.2.0/maestro/R/maestro_tags.R | 66 + maestro-1.2.0/maestro/R/roxy_maestro.R | 41 + maestro-1.2.0/maestro/build/vignette.rds |binary maestro-1.2.0/maestro/inst/doc/maestro-1-quick-start.html | 2 maestro-1.2.0/maestro/inst/doc/maestro-3-advanced-scheduling.html | 6 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.R | 3 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.Rmd | 5 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.html | 84 +- maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.R |only maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.Rmd |only maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.html |only maestro-1.2.0/maestro/inst/doc/maestro-5-logging.html | 56 - maestro-1.2.0/maestro/inst/doc/maestro-7-tag-reference.html | 30 maestro-1.2.0/maestro/inst/doc/maestro-7-tag-reference.qmd | 42 + maestro-1.2.0/maestro/inst/doc/maestro-8-conditionals.html | 34 - maestro-1.2.0/maestro/man/MaestroPipeline.Rd | 169 ++++ maestro-1.2.0/maestro/man/MaestroPipelineList.Rd | 42 + maestro-1.2.0/maestro/man/MaestroSchedule.Rd | 14 maestro-1.2.0/maestro/man/build_schedule.Rd | 6 maestro-1.2.0/maestro/man/get_labels.Rd |only maestro-1.2.0/maestro/man/get_network.Rd | 3 maestro-1.2.0/maestro/man/maestro_tags.Rd | 70 ++ maestro-1.2.0/maestro/tests/testthat/_snaps/fan-in-collect.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/fanout.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/labels.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/multicore.md | 42 + maestro-1.2.0/maestro/tests/testthat/test-build_schedule_entry.R | 52 + maestro-1.2.0/maestro/tests/testthat/test-fan-in-collect.R |only maestro-1.2.0/maestro/tests/testthat/test-fanout.R |only maestro-1.2.0/maestro/tests/testthat/test-labels.R |only maestro-1.2.0/maestro/tests/testthat/test-multicore.R | 87 ++ maestro-1.2.0/maestro/tests/testthat/test-roclets.R | 4 maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_in |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_in_chained |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_out |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_out_collect |only maestro-1.2.0/maestro/vignettes/maestro-4-directed-acyclic-graphs.Rmd | 5 maestro-1.2.0/maestro/vignettes/maestro-4b-directed-acyclic-graphs.Rmd |only maestro-1.2.0/maestro/vignettes/maestro-7-tag-reference.qmd | 42 + 53 files changed, 1434 insertions(+), 257 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph] ,
Finnish Biodiversity Information Facility [cph] ,
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.14 dated 2026-04-17 and 0.10.0 dated 2026-07-02
finbif-0.10.0/finbif/DESCRIPTION | 11 finbif-0.10.0/finbif/MD5 | 159 finbif-0.10.0/finbif/NAMESPACE | 12 finbif-0.10.0/finbif/NEWS.md | 598 - finbif-0.10.0/finbif/R/api_get.R | 40 finbif-0.10.0/finbif/R/dates.R | 2 finbif-0.10.0/finbif/R/finbif_check_taxa.R | 8 finbif-0.10.0/finbif/R/finbif_clear_cache.R | 4 finbif-0.10.0/finbif/R/finbif_collections.R | 103 finbif-0.10.0/finbif/R/finbif_informal_groups.R | 15 finbif-0.10.0/finbif/R/finbif_metadata.R | 15 finbif-0.10.0/finbif/R/finbif_occurrence.R | 98 finbif-0.10.0/finbif/R/finbif_occurrence_load.R | 99 finbif-0.10.0/finbif/R/finbif_records.R | 31 finbif-0.10.0/finbif/R/finbif_request_token.R | 4 finbif-0.10.0/finbif/R/finbif_taxa.R | 3 finbif-0.10.0/finbif/R/finbif_update_cache.R | 4 finbif-0.10.0/finbif/R/methods.R | 4 finbif-0.10.0/finbif/R/sysdata.R | 60 finbif-0.10.0/finbif/R/sysdata.rda |binary finbif-0.10.0/finbif/R/utils.R | 43 finbif-0.10.0/finbif/R/variables.R | 217 finbif-0.10.0/finbif/R/zzz.R | 30 finbif-0.10.0/finbif/README.md | 2 finbif-0.10.0/finbif/build/vignette.rds |binary finbif-0.10.0/finbif/inst/doc/finbif.Rmd | 209 finbif-0.10.0/finbif/inst/doc/finbif.html | 271 finbif-0.10.0/finbif/inst/doc/v02_occurrence_data.Rmd | 352 finbif-0.10.0/finbif/inst/doc/v02_occurrence_data.html | 336 finbif-0.10.0/finbif/inst/doc/v03_selecting_variables.Rmd | 210 finbif-0.10.0/finbif/inst/doc/v03_selecting_variables.html | 202 finbif-0.10.0/finbif/inst/doc/v04_metadata.Rmd | 253 finbif-0.10.0/finbif/inst/doc/v04_metadata.html | 255 finbif-0.10.0/finbif/inst/doc/v05_filtering.Rmd | 449 - finbif-0.10.0/finbif/inst/doc/v05_filtering.html | 413 finbif-0.10.0/finbif/man/finbif-package.Rd | 5 finbif-0.10.0/finbif/man/finbif_clear_cache.Rd | 3 finbif-0.10.0/finbif/man/finbif_update_cache.Rd | 3 finbif-0.10.0/finbif/man/variables.Rd | 217 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_db_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_file_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_check_taxa.yml | 8 finbif-0.10.0/finbif/tests/fixtures/finbif_collections.yml | 3238 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_informal_groups.yml | 4 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod1.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod2.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod3.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_metadata.yml | 840 +- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence.yml | 4183 ++++++---- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_aggregate.yml | 3321 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_api_error.yml | 4 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_compute_var_from_id_zero_rows.yml | 3264 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_dates.yml | 3298 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_load.yml | 370 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_print.yml | 18 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_select_local_area.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_taxa.yml | 8 finbif-0.10.0/finbif/tests/testthat/_snaps/caching.md | 93 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_collections.md | 98 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_metadata.md | 29 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_occurrence.md | 160 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_occurrence_load.md | 500 - finbif-0.10.0/finbif/tests/testthat/laji-data-new-col.tsv | 2 finbif-0.10.0/finbif/tests/testthat/laji-data-pap.tsv | 2 finbif-0.10.0/finbif/tests/testthat/laji-data.tsv | 2 finbif-0.10.0/finbif/tests/testthat/test-finbif_check_taxa.R | 17 finbif-0.10.0/finbif/tests/testthat/test-finbif_collections.R | 2 finbif-0.10.0/finbif/tests/testthat/test-finbif_informal_groups.R | 4 finbif-0.10.0/finbif/tests/testthat/test-finbif_metadata.R | 4 finbif-0.10.0/finbif/tests/testthat/test-finbif_occurrence.R | 63 finbif-0.10.0/finbif/tests/testthat/test-finbif_occurrence_load.R | 13 finbif-0.10.0/finbif/tests/testthat/test-finbif_request_token.R | 11 finbif-0.10.0/finbif/tests/testthat/test-finbif_taxa.R | 13 finbif-0.10.0/finbif/tests/testthat/test-to_dwc.R | 6 finbif-0.10.0/finbif/vignettes/finbif.Rmd | 209 finbif-0.10.0/finbif/vignettes/v02_occurrence_data.Rmd | 352 finbif-0.10.0/finbif/vignettes/v03_selecting_variables.Rmd | 210 finbif-0.10.0/finbif/vignettes/v04_metadata.Rmd | 253 finbif-0.10.0/finbif/vignettes/v05_filtering.Rmd | 449 - finbif-0.9.14/finbif/tests/testthat/test-zzz.R |only 81 files changed, 16168 insertions(+), 9728 deletions(-)
Title: Explore Catálogo Taxônomico da Fauna do Brasil Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Catálogo Taxônomico da Fauna do Brasil. For more information about the dataset, please visit <https://fauna.jbrj.gov.br/fauna/listaBrasil/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Diff between faunabr versions 1.0.1 dated 2026-04-19 and 1.1.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 25 - NAMESPACE | 7 NEWS.md | 6 R/data.R | 2 R/fauna_discrepancies.R | 87 +++- R/get_faunabr.R | 2 R/globals.R |only R/helpers.R | 786 +++++++++++++++++++++++++++------------------ R/load_faunabr.R | 8 R/merge_data.R |only man/fauna_discrepancies.Rd | 1 man/load_faunabr.Rd | 6 man/merge_data.Rd |only man/occurrences.Rd | 2 15 files changed, 570 insertions(+), 368 deletions(-)
Title: R Interface to 'DuckDB' Database with Spatial Extension
Description: Fast and memory-efficient functions to analyze and manipulate large
spatial datasets. It leverages the fast analytical
capabilities of ‘DuckDB’ and its spatial extension (see
<https://duckdb.org/docs/stable/core_extensions/spatial/overview>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckspatial versions 1.1.2 dated 2026-06-22 and 1.2.0 dated 2026-07-02
DESCRIPTION | 21 - MD5 | 82 ++++--- NAMESPACE | 14 + NEWS.md | 40 +++ R/db_extension.R | 184 +++++++++++----- R/ddbs_geom_conversion.R | 314 +++++++++++++++++++++++++++- R/ddbs_mvt.R |only R/ddbs_ops_unary.R | 176 +++++++++++++++ R/ddbs_ops_unary_line.R | 55 ++++ R/ddbs_queries.R | 36 +++ R/ddbs_templates.R | 150 +++++++++++++ R/ddbs_union.R | 152 +++++++++++++ R/utils_not_exported.R | 75 ++++++ R/zzz.R | 2 inst/doc/aw_interpolation.R | 10 inst/doc/aw_interpolation.html | 4 inst/doc/aw_interpolation.qmd | 10 inst/doc/benchmark.html | 4 inst/doc/duckspatial.R | 10 inst/doc/duckspatial.html | 12 - inst/doc/duckspatial.qmd | 10 inst/doc/spatial_joins.R | 10 inst/doc/spatial_joins.html | 4 inst/doc/spatial_joins.qmd | 10 man/ddbs_as_format.Rd | 26 ++ man/ddbs_as_mvt_geom.Rd |only man/ddbs_extension_info.Rd |only man/ddbs_geom_from.Rd |only man/ddbs_get_npoints.Rd | 20 + man/ddbs_install.Rd | 20 + man/ddbs_intersection_agg.Rd |only man/ddbs_line_node.Rd |only man/ddbs_normalize.Rd |only man/ddbs_reduce_precision.Rd |only man/ddbs_reverse.Rd |only man/ddbs_write_mbtiles.Rd |only man/duckspatial-package.Rd | 2 tests/testthat/test-db_extension.R | 66 +++++ tests/testthat/test-ddbs_geom_conversion.R | 245 +++++++++++++++++++++ tests/testthat/test-ddbs_intersection_agg.R |only tests/testthat/test-ddbs_macros.R | 70 ++++-- tests/testthat/test-ddbs_mvt.R |only tests/testthat/test-ddbs_ops_unary.R | 226 ++++++++++++++++++++ tests/testthat/test-ddbs_ops_unary_line.R | 81 +++++++ tests/testthat/test-ddbs_queries.R | 238 +++++++++++++++++++++ vignettes/aw_interpolation.qmd | 10 vignettes/duckspatial.qmd | 10 vignettes/spatial_joins.qmd | 10 48 files changed, 2258 insertions(+), 151 deletions(-)
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 1.0.0 dated 2026-06-17 and 1.1.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 228 +++++++++----- NAMESPACE | 11 NEWS.md | 19 + R/0_utils.R | 6 R/aaa.R | 46 ++ R/autoint-fit.R | 190 +++++++++--- R/autoint-predict.R | 4 R/autoplot.R | 4 R/brulee-package.R | 1 R/checks.R | 18 - R/chronos2-fit.R | 34 +- R/chronos2-misc.R | 4 R/chronos2-predict.R | 257 ++++++---------- R/coef.R | 11 R/linear_reg-fit.R | 40 +- R/linear_reg-predict.R | 8 R/logistic_reg-fit.R | 46 +- R/logistic_reg-predict.R | 8 R/mlp-fit.R | 58 +-- R/mlp-predict.R | 15 R/multinomial_reg-fit.R | 44 +- R/multinomial_reg-predict.R | 8 R/outcome_processing.R | 6 R/resnet-fit.R | 27 + R/resnet-predict.R | 6 R/rln-fit.R | 29 + R/rln-predict.R | 6 R/saint-fit.R | 233 ++++++++++---- R/saint-predict.R | 4 R/summary.R | 28 + R/tabicl-attention.R |only R/tabicl-download.R |only R/tabicl-embedding.R |only R/tabicl-ensemble.R |only R/tabicl-fit.R |only R/tabicl-interaction.R |only R/tabicl-layers.R |only R/tabicl-learning.R |only R/tabicl-load.R |only R/tabicl-model.R |only R/tabicl-predict.R |only R/tabicl-preprocess.R |only R/tabicl-quantile.R |only R/tabicl-rope.R |only R/training_loop.R | 164 +++++++--- R/validation.R | 22 - README.md | 89 ++--- inst/WORDLIST | 14 inst/check_stages.R |only man/brulee-autoplot.Rd | 4 man/brulee-coefs.Rd | 4 man/brulee_auto_int.Rd | 26 + man/brulee_chronos.Rd | 20 - man/brulee_linear_reg.Rd | 17 - man/brulee_logistic_reg.Rd | 17 - man/brulee_mlp.Rd | 19 - man/brulee_multinomial_reg.Rd | 15 man/brulee_resnet.Rd | 17 - man/brulee_rln.Rd | 15 man/brulee_saint.Rd | 40 +- man/brulee_tab_icl.Rd |only man/predict.brulee_auto_int.Rd | 2 man/predict.brulee_chronos.Rd | 54 +-- man/predict.brulee_linear_reg.Rd | 4 man/predict.brulee_logistic_reg.Rd | 4 man/predict.brulee_mlp.Rd | 4 man/predict.brulee_multinomial_reg.Rd | 4 man/predict.brulee_resnet.Rd | 4 man/predict.brulee_rln.Rd | 4 man/predict.brulee_saint.Rd | 2 man/predict.brulee_tab_icl.Rd |only man/summary.brulee.Rd | 2 man/tab_icl_download_weights.Rd |only tests/testthat/_snaps/autoint.md | 16 + tests/testthat/_snaps/chronos2-predict.md | 64 ---- tests/testthat/_snaps/mlp-binary.md |only tests/testthat/_snaps/saint.md | 26 + tests/testthat/_snaps/tabicl-download.md |only tests/testthat/_snaps/tabicl-fit.md |only tests/testthat/_snaps/tabicl-load.md |only tests/testthat/_snaps/tabicl-preprocess.md |only tests/testthat/fixtures |only tests/testthat/helper-chronos2.R | 6 tests/testthat/helper-tabicl.R |only tests/testthat/setup.R |only tests/testthat/test-autoint.R | 75 ++++ tests/testthat/test-chronos2-fit.R | 5 tests/testthat/test-chronos2-predict.R | 456 +++++++++-------------------- tests/testthat/test-device-support.R | 2 tests/testthat/test-linear_reg-fit.R | 87 +++++ tests/testthat/test-logistic_reg-fit.R | 32 -- tests/testthat/test-mlp-binary.R | 72 +++- tests/testthat/test-mlp-multinomial.R | 28 - tests/testthat/test-mlp-regression.R | 54 ++- tests/testthat/test-multinomial_reg-fit.R | 40 +- tests/testthat/test-penalty-integration.R | 16 - tests/testthat/test-penalty.R | 10 tests/testthat/test-saint.R | 75 ++++ tests/testthat/test-schedulers.R | 2 tests/testthat/test-tabicl-attention.R |only tests/testthat/test-tabicl-download.R |only tests/testthat/test-tabicl-embedding.R |only tests/testthat/test-tabicl-ensemble.R |only tests/testthat/test-tabicl-fit.R |only tests/testthat/test-tabicl-interaction.R |only tests/testthat/test-tabicl-learning.R |only tests/testthat/test-tabicl-load.R |only tests/testthat/test-tabicl-preprocess.R |only tests/testthat/test-tabicl-quantile.R |only tests/testthat/test-tabicl-rope.R |only 111 files changed, 1840 insertions(+), 1202 deletions(-)
Title: A 'C++20' API for R
Description: A header-only 'C++20' API for manipulating R data structures
from 'C++'. Provides 'C++20' concepts specific to R, custom scalar and
vector classes with built-in NA handling, automatic object protection,
'SIMD' (single-instruction-multiple-data), parallelisation, and a
streamlined system for registering 'C++' functions, including
templates, to R. Full API reference and documentation are available at
<https://nicchr.github.io/cppally/>.
Author: Nick Christofides [aut, cre, cph] ,
Martin Leitner-Ankerl [cph] ,
Malte Skarupke [cph] ,
Posit Software, PBC [cph]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppally versions 0.1.0 dated 2026-04-28 and 1.0.0 dated 2026-07-02
cppally-0.1.0/cppally/inst/include/cppally/r_coerce_impl.h |only cppally-0.1.0/cppally/inst/include/cppally/r_scalar_methods.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_copy.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_identical.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_vec_methods.h |only cppally-1.0.0/cppally/DESCRIPTION | 8 cppally-1.0.0/cppally/MD5 | 159 - cppally-1.0.0/cppally/NAMESPACE | 3 cppally-1.0.0/cppally/NEWS.md | 126 - cppally-1.0.0/cppally/R/cpp_source.R | 763 +++--- cppally-1.0.0/cppally/R/register.R | 81 cppally-1.0.0/cppally/R/use_check_data_frames.R |only cppally-1.0.0/cppally/R/use_check_factors.R |only cppally-1.0.0/cppally/R/use_copy_on_modify.R |only cppally-1.0.0/cppally/R/use_cppally.R | 221 - cppally-1.0.0/cppally/README.md | 221 + cppally-1.0.0/cppally/build/vignette.rds |binary cppally-1.0.0/cppally/inst/COPYRIGHTS | 32 cppally-1.0.0/cppally/inst/doc/cppally.R | 480 +++ cppally-1.0.0/cppally/inst/doc/cppally.Rmd | 918 +++++-- cppally-1.0.0/cppally/inst/doc/cppally.html | 1252 ++++++---- cppally-1.0.0/cppally/inst/doc/functionals.R |only cppally-1.0.0/cppally/inst/doc/functionals.Rmd |only cppally-1.0.0/cppally/inst/doc/functionals.html |only cppally-1.0.0/cppally/inst/doc/protection.R | 8 cppally-1.0.0/cppally/inst/doc/protection.Rmd | 793 +++--- cppally-1.0.0/cppally/inst/doc/protection.html | 64 cppally-1.0.0/cppally/inst/doc/vector_name_hashing.R |only cppally-1.0.0/cppally/inst/doc/vector_name_hashing.Rmd |only cppally-1.0.0/cppally/inst/doc/vector_name_hashing.html |only cppally-1.0.0/cppally/inst/include/cppally.hpp | 22 cppally-1.0.0/cppally/inst/include/cppally/r_attrs.h | 99 cppally-1.0.0/cppally/inst/include/cppally/r_coerce.h | 416 +-- cppally-1.0.0/cppally/inst/include/cppally/r_coerce_scalars.h |only cppally-1.0.0/cppally/inst/include/cppally/r_concepts.h | 239 + cppally-1.0.0/cppally/inst/include/cppally/r_copy.h |only cppally-1.0.0/cppally/inst/include/cppally/r_cplx.h | 12 cppally-1.0.0/cppally/inst/include/cppally/r_date.h | 4 cppally-1.0.0/cppally/inst/include/cppally/r_dbl.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_df.h | 288 +- cppally-1.0.0/cppally/inst/include/cppally/r_df_methods.h |only cppally-1.0.0/cppally/inst/include/cppally/r_dispatch.h | 28 cppally-1.0.0/cppally/inst/include/cppally/r_factor.h | 434 ++- cppally-1.0.0/cppally/inst/include/cppally/r_hash_names.h |only cppally-1.0.0/cppally/inst/include/cppally/r_identical.h |only cppally-1.0.0/cppally/inst/include/cppally/r_int.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_int64.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_length.h |only cppally-1.0.0/cppally/inst/include/cppally/r_lgl.h | 17 cppally-1.0.0/cppally/inst/include/cppally/r_list_helpers.h | 50 cppally-1.0.0/cppally/inst/include/cppally/r_nas.h | 101 cppally-1.0.0/cppally/inst/include/cppally/r_pmap.h |only cppally-1.0.0/cppally/inst/include/cppally/r_protect.h | 13 cppally-1.0.0/cppally/inst/include/cppally/r_psxct.h | 8 cppally-1.0.0/cppally/inst/include/cppally/r_raw.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_scalar_ops.h |only cppally-1.0.0/cppally/inst/include/cppally/r_setup.h | 9 cppally-1.0.0/cppally/inst/include/cppally/r_sexp.h | 60 cppally-1.0.0/cppally/inst/include/cppally/r_sexp_types.h | 9 cppally-1.0.0/cppally/inst/include/cppally/r_str.h | 30 cppally-1.0.0/cppally/inst/include/cppally/r_sym.h | 12 cppally-1.0.0/cppally/inst/include/cppally/r_types.h | 50 cppally-1.0.0/cppally/inst/include/cppally/r_utils.h | 18 cppally-1.0.0/cppally/inst/include/cppally/r_vec.h | 760 ++++-- cppally-1.0.0/cppally/inst/include/cppally/r_vec_ops.h |only cppally-1.0.0/cppally/inst/include/cppally/r_vec_utils.h | 70 cppally-1.0.0/cppally/inst/include/cppally/r_visit.h | 369 ++ cppally-1.0.0/cppally/inst/include/cppally/sugar/r_combine.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_equal.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_groups.h | 221 + cppally-1.0.0/cppally/inst/include/cppally/sugar/r_hash.h | 53 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_list_pmap.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_make_vec.h | 15 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_match.h | 144 + cppally-1.0.0/cppally/inst/include/cppally/sugar/r_math.h | 310 +- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_n_unique.h | 55 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_paste.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_recycle.h | 3 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_rep.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_replace_at.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_seq.h | 133 - cppally-1.0.0/cppally/inst/include/cppally/sugar/r_sexp_methods.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_sort.h | 350 +- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_stats.h | 302 -- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_subset.h | 257 -- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_unique.h | 50 cppally-1.0.0/cppally/inst/include/cppally_light.hpp | 5 cppally-1.0.0/cppally/inst/include/ska_sort/ska_sort.hpp | 123 cppally-1.0.0/cppally/man/cpp_register.Rd | 3 cppally-1.0.0/cppally/man/cpp_source.Rd | 70 cppally-1.0.0/cppally/man/cppally-package.Rd | 5 cppally-1.0.0/cppally/man/use_check_data_frames.Rd |only cppally-1.0.0/cppally/man/use_check_factors.Rd |only cppally-1.0.0/cppally/man/use_copy_on_modify.Rd |only cppally-1.0.0/cppally/vignettes/cppally.Rmd | 918 +++++-- cppally-1.0.0/cppally/vignettes/functionals.Rmd |only cppally-1.0.0/cppally/vignettes/protection.Rmd | 793 +++--- cppally-1.0.0/cppally/vignettes/vector_name_hashing.Rmd |only 98 files changed, 7644 insertions(+), 4437 deletions(-)
Title: High-Dimensional Methods via Generalised Singular Decomposition
Description: Construct a Canonical Variate Analysis Biplot via the Generalised Singular Value Decomposition, for cases when the number of samples is less than the number of variables. For more information on these biplots, see Ganey, R., & Gardner-Lubbe, S. (2026) <doi:10.1007/s10260-025-00831-y>.
Author: Raeesa Ganey [aut, cre]
Maintainer: Raeesa Ganey <Raeesa.ganey@wits.ac.za>
Diff between wideRhino versions 1.0.2 dated 2025-06-11 and 1.2.0 dated 2026-07-02
wideRhino-1.0.2/wideRhino/R/CVAbiplot.R |only wideRhino-1.2.0/wideRhino/DESCRIPTION | 11 wideRhino-1.2.0/wideRhino/MD5 | 24 - wideRhino-1.2.0/wideRhino/NEWS.md | 5 wideRhino-1.2.0/wideRhino/R/CVAgsvd.R |only wideRhino-1.2.0/wideRhino/R/axes_coordinates.R | 9 wideRhino-1.2.0/wideRhino/R/globals.R | 3 wideRhino-1.2.0/wideRhino/R/gsvd.R | 196 +++++++++++- wideRhino-1.2.0/wideRhino/R/plot.R | 96 ++--- wideRhino-1.2.0/wideRhino/README.md | 12 wideRhino-1.2.0/wideRhino/man/CVAbiplot.Rd | 14 wideRhino-1.2.0/wideRhino/man/CVAgsvd.Rd | 8 wideRhino-1.2.0/wideRhino/man/figures/README-example1-1.png |binary wideRhino-1.2.0/wideRhino/man/figures/README-example2-1.png |binary 14 files changed, 278 insertions(+), 100 deletions(-)
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between robmixglm versions 1.2-5 dated 2025-10-31 and 1.2-8 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 32 +-- NAMESPACE | 10 - R/RcppExports.R | 38 ++-- R/binomial.fit.robmixglm.R | 372 ++++++++++++++++++++--------------------- R/gamma.fit.robmixglm.R | 166 +++++++++--------- R/gaussian.fit.robmixglm.R | 188 ++++++++++---------- R/nbinom.fit.robmixglm.R | 324 +++++++++++++++++------------------ R/outlierTest.robmixglm.R | 10 - R/poisson.fit.robmixglm.R | 244 +++++++++++++++----------- R/robmixglm.R | 12 - R/truncpoisson.fit.robmixglm.R | 255 ++++++++++++++-------------- build/vignette.rds |binary inst/NEWS | 14 + inst/doc/robmixglm-package.pdf |binary man/outlierTest.robmixglm.Rd | 6 man/robmixglm.Rd | 6 17 files changed, 888 insertions(+), 800 deletions(-)
Title: Bayesian Power Analysis Using 'brms' and 'INLA'
Description: Provides tools for Bayesian power analysis and assurance calculations using the statistical frameworks of 'brms' and 'INLA'. Includes simulation-based approaches, support for multiple decision rules (direction, threshold, ROPE), sequential designs, and visualisation helpers. Methods are based on Kruschke (2014, ISBN:9780124058880) "Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan", O'Hagan & Stevens (2001) <doi:10.1177/0272989X0102100307> "Bayesian Assessment of Sample Size for Clinical Trials of Cost-Effectiveness", Kruschke (2018) <doi:10.1177/2515245918771304> "Rejecting or Accepting Parameter Values in Bayesian Estimation", Rue et al. (2009) <doi:10.1111/j.1467-9868.2008.00700.x> "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations", and Bürkner (2017) <doi:10.18637/jss.v080.i01> "brms: An R Package for Bayesian Multilevel Models using Stan".
Author: Tony Myers [aut, cre]
Maintainer: Tony Myers <admyers@aol.com>
Diff between powerbrmsINLA versions 1.2.0 dated 2026-06-02 and 1.3.0 dated 2026-07-02
powerbrmsINLA-1.2.0/powerbrmsINLA/R/plotting-helpers.R |only powerbrmsINLA-1.2.0/powerbrmsINLA/tests/testthat/sequencial-test.R |only powerbrmsINLA-1.2.0/powerbrmsINLA/tests/testthat/set-up.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/DESCRIPTION | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/MD5 | 67 ++-- powerbrmsINLA-1.3.0/powerbrmsINLA/NAMESPACE | 8 powerbrmsINLA-1.3.0/powerbrmsINLA/NEWS.md | 86 +++++ powerbrmsINLA-1.3.0/powerbrmsINLA/R/compute-assurance.R | 2 powerbrmsINLA-1.3.0/powerbrmsINLA/R/decision-helpers.R | 23 + powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-main.R | 50 ++- powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-sequential-trial.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-sequential.R | 37 +- powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-two-stage.R | 9 powerbrmsINLA-1.3.0/powerbrmsINLA/R/globals.R | 2 powerbrmsINLA-1.3.0/powerbrmsINLA/R/plotting-power.R | 6 powerbrmsINLA-1.3.0/powerbrmsINLA/R/sequential-analysis.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/R/utils-helpers.R | 6 powerbrmsINLA-1.3.0/powerbrmsINLA/README.md | 154 +++++++-- powerbrmsINLA-1.3.0/powerbrmsINLA/build/partial.rdb |binary powerbrmsINLA-1.3.0/powerbrmsINLA/build/vignette.rds |binary powerbrmsINLA-1.3.0/powerbrmsINLA/inst/doc/validation.R | 164 +++++----- powerbrmsINLA-1.3.0/powerbrmsINLA/inst/doc/validation.html | 3 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_power_sequential.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_power_two_stage.Rd | 4 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_sequential_trial.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-add_contour_lines.Rd | 21 - powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-geom_line_lw.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-geom_point_lw.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-gg_line_arg.Rd | 14 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-plot_decision_assurance_curve_from_summary.Rd | 5 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-sample_design_prior.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-seq_design_fingerprint.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/plot_sequential_monitor.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_design.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_monitor.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_trial.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/sequential_analysis.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/sequential_design.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/setup.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-regression-effectname-decide.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-analysis.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-stopping.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-trial.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-validation-bayesassurance.R | 104 ------ 44 files changed, 479 insertions(+), 326 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut] ,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 4.2.3 dated 2026-02-11 and 4.3.0 dated 2026-07-02
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 15 ++++ R/nretention.r | 2 build/vignette.rds |binary data/crops.obic.rda |binary inst/doc/description-of-the-columns.html | 4 - inst/doc/obic_introduction.html | 100 +++++++++++++------------------ inst/doc/obic_score_aggregation.html | 24 +++---- inst/doc/obic_water_functions.html | 35 +++++----- inst/doc/obic_workability.html | 11 +-- man/crops.obic.Rd | 2 12 files changed, 111 insertions(+), 112 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-05 1.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-20 1.1.0
2024-02-14 1.0.0
Title: Designing Stated Preference Experiments
Description: Contemporary software commonly used to design stated preference experiments are expensive and the code is closed source. This is a free software package with an easy to use interface to make flexible stated preference experimental designs using state-of-the-art methods. For an overview of stated choice experimental design theory, see e.g., Rose, J. M. & Bliemer, M. C. J. (2014) in Hess S. & Daly. A. <doi:10.4337/9781781003152>. The package website can be accessed at <https://spdesign.edsandorf.me>. We acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant INSPiRE (Grant agreement ID: 793163). The package features in Mariel et al. (2025) Environmental Valuation with Discrete Choice Experiments in R. (<doi:10.1007/978-3-031-89338-4>).
Author: Erlend Dancke Sandorf [aut, cre],
Danny Campbell [aut]
Maintainer: Erlend Dancke Sandorf <erlend.dancke.sandorf@nmbu.no>
Diff between spdesign versions 0.0.5 dated 2024-10-18 and 0.0.6 dated 2026-07-02
DESCRIPTION | 12 MD5 | 99 - NEWS.md | 10 R/DEPRECATED-set-defaults.R | 2 R/assertions.R | 39 R/block.R | 26 R/derive.R | 26 R/design.R | 194 ++- R/draws.R | 20 R/efficiency-criteria.R | 41 R/evaluate.R | 57 R/exclusions-and-conditions.R | 2 R/extract.R | 7 R/federov.R | 173 +- R/level-balance.R | 8 R/methods.R | 16 R/parsing.R | 96 + R/print.R | 7 R/priors.R | 27 R/probabilities.R | 4 R/random.R | 93 + R/remove.R | 2 R/rsc.R | 110 + R/xj.R | 23 R/zzz.R | 33 build/partial.rdb |binary build/vignette.rds |binary inst/doc/examples.R | 604 +++++----- inst/doc/examples.html | 243 ++-- inst/doc/syntax.Rmd | 8 inst/doc/syntax.html | 30 man/federov.Rd | 3 man/generate_design.Rd | 5 man/level_occurrences_specified.Rd |only man/random.Rd | 3 man/reexports.Rd | 2 man/rsc.Rd | 3 man/spdesign-package.Rd | 5 tests/testthat/test-assertions.R | 30 vignettes/examples/mnl-c-efficiency.R | 23 vignettes/examples/mnl-design-advanced.R | 17 vignettes/examples/mnl-design-bayesian-priors.R | 17 vignettes/examples/mnl-design-dummy-coding.R | 11 vignettes/examples/mnl-design-random-with-specified-level-occurrence.R | 11 vignettes/examples/mnl-design-with-alternative-specific-attributres.R | 23 vignettes/examples/mnl-design-with-exclusions.R | 19 vignettes/examples/mnl-design-with-interactions.R | 13 vignettes/examples/mnl-design-with-multiway-interactions.R | 13 vignettes/examples/mnl-design-with-sq-and-names.R | 21 vignettes/examples/mnl-design-with-supplied-candidate-set.R | 25 vignettes/syntax.Rmd | 8 51 files changed, 1402 insertions(+), 862 deletions(-)
Title: Statistical Pattern Recognition and daTing using Archaeological
Artefacts assemblageS
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages.
Package of statistical tools for archaeology.
hclustcompro()/perioclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021, ISBN:978-3-030-60103-4).
mapclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>.
seriograph(): Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>.
cerardat(): Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Author: Arthur Coulon [aut, cre],
Lise Bellanger [aut],
Philippe Husi [aut],
Bruno Desachy [ctb],
Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>
Diff between SPARTAAS versions 1.2.5 dated 2026-03-26 and 1.2.6 dated 2026-07-02
DESCRIPTION | 19 MD5 | 33 - NAMESPACE | 4 R/cerardat.R | 402 ++++++++++--- R/mapclust.R | 4 R/perioclust.R | 6 R/util.R | 13 R/zzz.R | 2 build/partial.rdb |binary inst/shiny-examples/hclustcompro.app/server.R | 216 ++++--- inst/shiny-examples/hclustcompro.app/ui.R | 777 +++++++++++++------------- inst/shiny-examples/map.app/server.R | 38 - man/arrangePlot.Rd |only man/cerardat.Rd | 92 +-- man/cerardat_estim_nf.Rd | 44 + man/extract_results.Rd | 15 man/plot.cerardat_obj.Rd | 81 +- man/seriograph.Rd | 45 + 18 files changed, 1062 insertions(+), 729 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Optimize and compress local and online image files with the
'reSmush.it' 'API' <https://resmush.it/api/>. Process individual files
or entire directories. The 'API' is free for personal use, accepts
files smaller than 5 'MB' and supports 'PNG', 'JPEG', 'GIF', 'BMP' and
'TIFF' files.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 1.0.1 dated 2026-05-29 and 1.0.2 dated 2026-07-02
DESCRIPTION | 16 ++- MD5 | 70 +++++++-------- NAMESPACE | 16 +-- NEWS.md | 28 +++--- R/resmush-package.R | 12 ++ R/resmush_clean_dir.R | 40 ++++---- R/resmush_dir.R | 50 ++++++----- R/resmush_file.R | 71 +++++++-------- R/resmush_url.R | 70 +++++++-------- R/show_report.R | 18 ++-- R/sysdata.rda |binary R/utils.R | 87 ++++++++++++++----- README.md | 143 +++++++++++++++++--------------- build/vignette.rds |binary inst/REFERENCES.bib | 30 +++--- inst/WORDLIST | 55 ++++++------ inst/doc/resmush.html | 96 ++++++++++----------- inst/doc/resmush.qmd | 128 +++++++++++++++------------- inst/schemaorg.json | 6 - man/resmush-package.Rd | 17 ++- man/resmush_clean_dir.Rd | 27 ++---- man/resmush_dir.Rd | 59 +++++++------ man/resmush_file.Rd | 54 ++++++------ man/resmush_url.Rd | 61 +++++++------ man/roxygen/meta.R | 4 tests/testthat/_snaps/formats.md | 4 tests/testthat/_snaps/remush_url.md | 26 +++-- tests/testthat/_snaps/resmuh_dir.md | 2 tests/testthat/_snaps/resmush_file.md | 11 ++ tests/testthat/_snaps/show_report.md | 32 +++---- tests/testthat/test-formats.R | 2 tests/testthat/test-remush_url.R | 84 ++++++++++++------ tests/testthat/test-resmush_clean_dir.R | 2 tests/testthat/test-resmush_file.R | 84 +++++++++++------- vignettes/REFERENCES.bib | 30 +++--- vignettes/resmush.qmd | 128 +++++++++++++++------------- 36 files changed, 880 insertions(+), 683 deletions(-)
Title: Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy
Description: Tools for Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy (MAIHDA) for intersectional inequality research.
Methods are described in Merlo (2018) <doi:10.1016/j.socscimed.2017.12.026>
and Evans et al. (2018) <doi:10.1016/j.socscimed.2017.11.011>. The package
creates intersectional strata, fits multilevel MAIHDA models, estimates
variance partition coefficients, proportional change in variance, stratum
effects, and discriminatory-accuracy summaries, and provides diagnostic and
presentation plots.
Author: Hamid Bulut [aut, cre]
Maintainer: Hamid Bulut <me@hamidbulut.com>
Diff between MAIHDA versions 0.1.11 dated 2026-06-18 and 0.2.0 dated 2026-07-02
MAIHDA-0.1.11/MAIHDA/R/maihda_ternary.R |only MAIHDA-0.1.11/MAIHDA/man/compute_maihda_ternary_data.Rd |only MAIHDA-0.1.11/MAIHDA/man/maihda_ternary_plot.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot.maihda_ternary.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot_maihda_ternary.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot_risk_vs_effect.Rd |only MAIHDA-0.1.11/MAIHDA/tests/testthat/test-maihda-ternary.R |only MAIHDA-0.2.0/MAIHDA/DESCRIPTION | 28 MAIHDA-0.2.0/MAIHDA/MD5 | 206 MAIHDA-0.2.0/MAIHDA/NAMESPACE | 15 MAIHDA-0.2.0/MAIHDA/NEWS.md | 46 MAIHDA-0.2.0/MAIHDA/R/app_modules.R | 24 MAIHDA-0.2.0/MAIHDA/R/calculate_pvc.R | 73 MAIHDA-0.2.0/MAIHDA/R/compare_maihda.R | 271 MAIHDA-0.2.0/MAIHDA/R/decompose_maihda.R | 40 MAIHDA-0.2.0/MAIHDA/R/design_weights.R | 75 MAIHDA-0.2.0/MAIHDA/R/discriminatory_accuracy.R | 164 MAIHDA-0.2.0/MAIHDA/R/fit_maihda.R | 106 MAIHDA-0.2.0/MAIHDA/R/information_criteria.R | 25 MAIHDA-0.2.0/MAIHDA/R/interactions.R | 342 - MAIHDA-0.2.0/MAIHDA/R/longitudinal.R | 22 MAIHDA-0.2.0/MAIHDA/R/maihda_table.R | 81 MAIHDA-0.2.0/MAIHDA/R/maihda_workflow.R | 364 - MAIHDA-0.2.0/MAIHDA/R/make_strata.R | 17 MAIHDA-0.2.0/MAIHDA/R/ordinal_engine.R | 96 MAIHDA-0.2.0/MAIHDA/R/plot_maihda.R | 3029 +++++----- MAIHDA-0.2.0/MAIHDA/R/plot_prediction_deviation_panels.R | 59 MAIHDA-0.2.0/MAIHDA/R/predict_maihda.R | 181 MAIHDA-0.2.0/MAIHDA/R/print_style.R |only MAIHDA-0.2.0/MAIHDA/R/run_app.R | 54 MAIHDA-0.2.0/MAIHDA/R/summary_maihda.R | 66 MAIHDA-0.2.0/MAIHDA/R/theme_maihda.R |only MAIHDA-0.2.0/MAIHDA/R/utils_maihda.R | 572 + MAIHDA-0.2.0/MAIHDA/R/vpc_response.R | 21 MAIHDA-0.2.0/MAIHDA/README.md | 60 MAIHDA-0.2.0/MAIHDA/build/vignette.rds |binary MAIHDA-0.2.0/MAIHDA/inst/doc/bayesian_sparse_maihda.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/binary_outcomes.html | 10 MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.R |only MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.Rmd |only MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.html |only MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.R | 3 MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.Rmd | 124 MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.html | 243 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.R | 7 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.Rmd | 31 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.html | 75 MAIHDA-0.2.0/MAIHDA/inst/doc/group_comparison.html | 63 MAIHDA-0.2.0/MAIHDA/inst/doc/interactive_app.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.R | 5 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.Rmd | 21 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.html | 58 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.R | 19 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.Rmd | 50 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.html | 268 MAIHDA-0.2.0/MAIHDA/inst/doc/longitudinal.html | 10 MAIHDA-0.2.0/MAIHDA/inst/doc/planning_a_study.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/reporting_results.html | 106 MAIHDA-0.2.0/MAIHDA/inst/shiny/app.R | 19 MAIHDA-0.2.0/MAIHDA/man/MAIHDA-package.Rd | 2 MAIHDA-0.2.0/MAIHDA/man/compare_maihda.Rd | 7 MAIHDA-0.2.0/MAIHDA/man/compare_maihda_groups.Rd | 22 MAIHDA-0.2.0/MAIHDA/man/fit_maihda.Rd | 29 MAIHDA-0.2.0/MAIHDA/man/maihda.Rd | 37 MAIHDA-0.2.0/MAIHDA/man/maihda_brms_ordinal_thresholds.Rd |only MAIHDA-0.2.0/MAIHDA/man/maihda_clmm_linpred.Rd | 12 MAIHDA-0.2.0/MAIHDA/man/maihda_discriminatory_accuracy.Rd | 17 MAIHDA-0.2.0/MAIHDA/man/maihda_interactions.Rd | 75 MAIHDA-0.2.0/MAIHDA/man/maihda_prepare_brms_sampling_weights.Rd | 6 MAIHDA-0.2.0/MAIHDA/man/maihda_table.Rd | 29 MAIHDA-0.2.0/MAIHDA/man/maihda_upset_size.Rd |only MAIHDA-0.2.0/MAIHDA/man/maihda_vpc_response.Rd | 2 MAIHDA-0.2.0/MAIHDA/man/maihda_wemix_linpred.Rd | 8 MAIHDA-0.2.0/MAIHDA/man/make_strata.Rd | 7 MAIHDA-0.2.0/MAIHDA/man/plot.maihda_analysis.Rd | 58 MAIHDA-0.2.0/MAIHDA/man/plot.maihda_model.Rd | 80 MAIHDA-0.2.0/MAIHDA/man/plot_group_comparison.Rd | 3 MAIHDA-0.2.0/MAIHDA/man/plot_obs_vs_shrunken.Rd | 16 MAIHDA-0.2.0/MAIHDA/man/plot_predicted_strata.Rd | 19 MAIHDA-0.2.0/MAIHDA/man/plot_stratum_trajectories.Rd | 16 MAIHDA-0.2.0/MAIHDA/man/plot_upset_strata.Rd |only MAIHDA-0.2.0/MAIHDA/man/predict_maihda.Rd | 27 MAIHDA-0.2.0/MAIHDA/man/stepwise_pcv.Rd | 5 MAIHDA-0.2.0/MAIHDA/man/sub-.maihda_group_comparison.Rd |only MAIHDA-0.2.0/MAIHDA/man/summary.maihda_model.Rd | 13 MAIHDA-0.2.0/MAIHDA/man/theme_maihda.Rd |only MAIHDA-0.2.0/MAIHDA/tests/testthat/test-auto_detect_family.R | 48 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-calculate_pvc.R | 9 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-compare_maihda_groups.R | 146 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-contextual.R | 30 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-correctness-regressions.R | 311 - MAIHDA-0.2.0/MAIHDA/tests/testthat/test-cross-classified.R | 32 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-design-weights.R | 281 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-discriminatory-accuracy.R | 165 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-information_criteria.R | 54 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-interactions.R | 519 + MAIHDA-0.2.0/MAIHDA/tests/testthat/test-longitudinal.R | 224 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-maihda-workflow.R | 117 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-maihda_table.R | 43 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-make_strata.R | 42 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-negbinomial.R | 1 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-ordinal-engine.R | 175 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-plot_predicted.R | 52 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-plot_upset.R |only MAIHDA-0.2.0/MAIHDA/tests/testthat/test-run_app.R | 22 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-vpc-response.R | 7 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-weighted-count-vpc.R |only MAIHDA-0.2.0/MAIHDA/vignettes/brfss_precomputed.rds |only MAIHDA-0.2.0/MAIHDA/vignettes/case_study_brfss.Rmd |only MAIHDA-0.2.0/MAIHDA/vignettes/cross_classified.Rmd | 124 MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_effect_decomp.png |only MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_upset.png |only MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_vpc.png |only MAIHDA-0.2.0/MAIHDA/vignettes/finding_interactions.Rmd | 31 MAIHDA-0.2.0/MAIHDA/vignettes/interpreting_plots.Rmd | 21 MAIHDA-0.2.0/MAIHDA/vignettes/introduction.Rmd | 50 116 files changed, 7111 insertions(+), 3044 deletions(-)
Title: Tree-Spatial Scan Statistic for Cluster Detection
Description: Implements the tree-spatial scan statistic for detecting clusters
that combine both spatial and hierarchical structures, as proposed by
Cancado et al. (2025) <doi:10.1007/s10651-025-00670-w>. The method extends
Kulldorff (1997) <doi:10.1080/03610929708831995> circular spatial scan
statistic and the tree-based scan statistic of Kulldorff et al. (2003)
<doi:10.1111/1541-0420.00039> by searching for anomalies in both
geographic regions and branches of hierarchical trees simultaneously. The
package also provides standalone implementations of Kulldorff's circular
spatial scan statistic and the tree-based scan statistic. Statistical
significance is assessed via Monte Carlo simulation under a Poisson or
binomial model, with optional 'OpenMP' parallelization.
Author: Allan Quadros [aut, cre] ,
Andre L. F. Cancado [aut] ,
Geiziane S. Oliveira [aut],
Luiz H. Duczmal [aut]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between treeSS versions 0.1.50 dated 2026-05-29 and 0.2.4 dated 2026-07-02
DESCRIPTION | 6 MD5 | 110 ++++++++-------- NEWS.md | 150 ++++++++++++++++++++++ R/aggregate_tree.R | 44 ++++-- R/circular_scan.R | 54 +++++--- R/data.R | 86 ++++++++++--- R/filter_clusters.R | 13 + R/generate_example_data.R | 17 +- R/get_cluster_regions.R | 13 + R/sequential_scan.R | 155 ++++++++++++++++------- R/tree_scan.R | 88 +++++++++---- R/treespatial_scan.R | 81 ++++++++---- R/vector_inputs.R | 43 ++++++ README.md | 38 +++-- data/rj_map.rda |only inst/doc/florida.R | 26 ++- inst/doc/florida.Rmd | 42 +++--- inst/doc/florida.html | 71 +++++----- inst/doc/introduction.R | 43 +++--- inst/doc/introduction.Rmd | 51 +++---- inst/doc/introduction.html | 116 ++++++++--------- inst/examples/example_brazil_rj.R | 40 +++--- inst/examples/example_chicago.R | 74 ++++++----- inst/examples/example_florida.R | 30 ++-- inst/examples/example_london.R | 26 ++- man/aggregate_tree.Rd | 31 ++-- man/chicago_map.Rd | 17 +- man/circular_scan.Rd | 39 +++-- man/filter_clusters.Rd | 76 ++++++----- man/fl_deaths.Rd | 46 +++++-- man/generate_example_data.Rd | 17 +- man/get_cluster_regions.Rd | 17 +- man/london_boroughs_map.Rd | 31 +++- man/print.circular_scan.Rd | 19 +- man/print.sequential_scan.Rd | 17 +- man/print.tree_scan.Rd | 19 +- man/print.treespatial_scan.Rd | 19 +- man/rj_map.Rd |only man/rj_mortality.Rd | 5 man/sequential_scan.Rd | 58 +++++--- man/summary.circular_scan.Rd | 15 +- man/summary.sequential_scan.Rd | 10 - man/summary.tree_scan.Rd | 15 +- man/summary.treespatial_scan.Rd | 17 +- man/treeSS-package.Rd | 2 man/tree_scan.Rd | 54 +++++--- man/treespatial_scan.Rd | 69 ++++++---- src/treescan_core.cpp | 197 ++++-------------------------- tests/testthat/test-binomial.R | 61 ++++----- tests/testthat/test-build-aggregate.R | 33 ++--- tests/testthat/test-circular-scan.R | 45 +++--- tests/testthat/test-get-cluster-regions.R | 30 +--- tests/testthat/test-sequential-scan.R | 102 ++++++--------- tests/testthat/test-tree-scan.R | 31 +++- tests/testthat/test-treespatial-scan.R | 78 +++++++---- vignettes/florida.Rmd | 42 +++--- vignettes/introduction.Rmd | 51 +++---- 57 files changed, 1554 insertions(+), 1126 deletions(-)
Title: Temporally Explicit Species Distribution Modelling
Description: Increases the ease of implementing a temporally-explicit modeling
methodology when building ecological niche and species distribution models.
Provides functions to assist with three major steps of temporally-explicit
models: (i) preprocessing species and environmental data and generating
suitable background or pseudoabsence data, (ii) building a niche model and
generating temporally-explicit predictions from that model, and (iii) model
postprocessing to explore spatiotemporal trends in model predictions.
Methodological and theoretical foundations are described in Ingenloff and
Peterson (2021) <doi:10.1111/2041-210X.13564>, Franklin (2010, ISBN:9780521700023),
Peterson et al. (2011, ISBN:9780691136882), Blonder (2018) <doi:10.1111/ecog.03187>,
Senay et al. (2013) <doi:10.1371/journal.pone.0071218>, and Li and Zhang (2024) <doi:10.48550/arXiv.2404.05933>.
Author: Connor Hughes [aut, cre] ,
Mariana Castaneda-Guzman [aut] ,
Luis E. Escobar [aut]
Maintainer: Connor Hughes <connorhughes926@gmail.com>
Diff between TemporalModelR versions 0.2.0 dated 2026-06-30 and 0.3.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 55 + NEWS.md | 14 R/analyze_temporal_patterns.R | 154 +++-- R/data_documentation.R | 24 R/generate_absences.R | 651 +++++++++++++++-------- R/helper_functions.R | 510 +++++++++--------- R/plot_model_assessment.R | 83 +- R/spatiotemporal_partition.R | 21 README.md | 13 data/tmr_absences.rda |binary data/tmr_absences_annual.rda |binary data/tmr_absences_user.rda |only data/tmr_partition.rda |binary data/tmr_partition_annual.rda |binary data/tmr_partition_small.rda |binary inst/doc/V2_Preprocessing.R | 57 +- inst/doc/V2_Preprocessing.Rmd | 77 ++ inst/doc/V2_Preprocessing.html | 207 +++++-- inst/doc/V3a_GLM.html | 6 inst/doc/V3b_GAM.html | 6 inst/doc/V3c_RF.html | 6 inst/doc/V3d_HV.html | 6 inst/doc/V4_Postprocessing.html | 26 inst/extdata/points/synthetic_user_presences.csv |only man/analyze_temporal_patterns.Rd | 80 +- man/extdata.Rd | 7 man/generate_absences.Rd | 53 + man/tmr_absences_user.Rd |only vignettes/V2_Preprocessing.Rmd | 77 ++ 30 files changed, 1404 insertions(+), 735 deletions(-)
More information about TemporalModelR at CRAN
Permanent link
Title: Simplified Statistical Analysis with Plain-English
Interpretation
Description: A toolkit for common statistical analyses including descriptive statistics, Student's t-tests (one-sample, independent, and paired), one-way and two-way Analysis of Variance (ANOVA), Multivariate Analysis of Variance (MANOVA), chi-square tests, Fisher's Exact Test, McNemar's Test, correlation analysis, simple and multiple linear regression, logistic regression, Friedman Test, and non-parametric tests (Mann-Whitney U, Wilcoxon Signed Rank, and Kruskal-Wallis). Additional tools include statistical power analysis and automated assumption checking. Each function automatically interprets results in plain English, reporting effect sizes, confidence intervals, and p-value interpretations. Post-hoc tests are automatically applied following significant results. A master function automatically detects the appropriate test based on the structure of the input data. Methods are based on Cohen, J. (1988) <doi:10.4324/9780203771587>, Tukey, J. W. (1949) <doi:10.2307/3001913>, and Shapiro [...truncated...]
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between statease versions 1.2.1 dated 2026-06-07 and 1.3.0 dated 2026-07-02
DESCRIPTION | 14 +- MD5 | 48 ++++++-- NAMESPACE | 17 +++ NEWS.md | 2 R/analyze.R | 177 +++++++++++++++++--------------- R/check_assumptions.R |only R/fisher_interpret.R |only R/friedman_interpret.R |only R/mcnemar_interpret.R |only R/nonparam_interpret.R | 10 + R/power_interpret.R |only R/run_app.R |only R/statease-package.R | 2 README.md | 55 +++++----- inst/doc/statease.R | 45 ++++++++ inst/doc/statease.Rmd | 87 ++++++++++++++++ inst/doc/statease.html | 249 ++++++++++++++++++++++++++++++++++++++++++++-- inst/shiny |only man/analyze.Rd | 76 +++++--------- man/check_assumptions.Rd |only man/fisher_interpret.Rd |only man/friedman_interpret.Rd |only man/mcnemar_interpret.Rd |only man/power_interpret.Rd |only man/run_app.Rd |only tests |only vignettes/statease.Rmd | 87 ++++++++++++++++ 27 files changed, 686 insertions(+), 183 deletions(-)
Title: Digitally Sign and Verify PDF Documents
Description: Digitally sign PDF documents with a 'PKCS#12' keystore and verify
their signatures. Signing produces a detached 'PKCS#7' / 'CMS' signature
('adbe.pkcs7.detached') over the document and is applied as an incremental
update, so existing signatures remain valid. The cryptography and PDF
manipulation are performed by a bundled, pure-'Rust' backend (the
'pdf_signer' crate); no Java runtime, 'OpenSSL', or external command-line
tools are required. Visible signature appearances with custom text are
supported.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Diogo Bezerra [aut],
Authors of the vendored Rust crates [ctb, cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pdfsigner versions 0.2.4 dated 2026-06-26 and 0.2.5 dated 2026-07-02
pdfsigner-0.2.4/pdfsigner/src/rust/pdf_signer |only pdfsigner-0.2.5/pdfsigner/DESCRIPTION | 6 +++--- pdfsigner-0.2.5/pdfsigner/MD5 | 22 ++++------------------ pdfsigner-0.2.5/pdfsigner/src/rust/Cargo.lock | 22 ++++++++++++++-------- pdfsigner-0.2.5/pdfsigner/src/rust/Cargo.toml | 2 +- pdfsigner-0.2.5/pdfsigner/src/rust/vendor.tar.xz |binary 6 files changed, 22 insertions(+), 30 deletions(-)
Title: Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'
Description: Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that
they can be rendered in R markdown documents and shiny apps.
Author: Matthias Gondan [aut, cre, cph] ,
Irene Alfarone [aut] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
This is a re-admission after prior archival of version 1.8 dated 2026-05-22
Diff between mathml versions 1.8 dated 2026-05-22 and 1.9 dated 2026-07-02
DESCRIPTION | 15 ++++++--------- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/mathml.html | 7 +++---- vignettes/bibliography.bibtex | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and
transparency in data processing. It provides functionality such as
automatic meta data creation and management, rudimentary quality
management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this
package to deliver everything what is needed to achieve full
reproducibility and transparency, but we believe that it supports
efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre] ,
Pascal Sauer [aut] ,
Lavinia Baumstark [aut] ,
Stephen Wirth [aut] ,
Anastasis Giannousakis [aut],
Renato Rodrigues [aut] ,
Benjamin Leon Bodirsky [aut] ,
Debbora Leip [aut] ,
Michael Crawford [aut] ,
Ulrich Kreidenw [...truncated...]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 3.15.6 dated 2024-12-19 and 3.37.1 dated 2026-07-02
madrat-3.15.6/madrat/R/madapply.R |only madrat-3.15.6/madrat/R/madlapply.R |only madrat-3.15.6/madrat/man/madapply.Rd |only madrat-3.15.6/madrat/man/madlapply.Rd |only madrat-3.37.1/madrat/DESCRIPTION | 68 - madrat-3.37.1/madrat/MD5 | 374 ++--- madrat-3.37.1/madrat/NAMESPACE | 21 madrat-3.37.1/madrat/R/addMapping.R | 61 madrat-3.37.1/madrat/R/cacheArgumentsHash.R | 32 madrat-3.37.1/madrat/R/cacheCleanup.R | 1 madrat-3.37.1/madrat/R/cacheCopy.R | 3 madrat-3.37.1/madrat/R/cacheGet.R | 45 madrat-3.37.1/madrat/R/cacheName.R | 115 - madrat-3.37.1/madrat/R/cachePut.R | 70 - madrat-3.37.1/madrat/R/calcOutput.R | 185 ++ madrat-3.37.1/madrat/R/checkBidirectional.R | 4 madrat-3.37.1/madrat/R/cleanComment.R | 1 madrat-3.37.1/madrat/R/compareData.R | 85 - madrat-3.37.1/madrat/R/compareMadratOutputs.R | 4 madrat-3.37.1/madrat/R/downloadSource.R | 13 madrat-3.37.1/madrat/R/findBottlenecks.R | 71 - madrat-3.37.1/madrat/R/fingerprint.R | 190 +- madrat-3.37.1/madrat/R/functionCallString.R | 3 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madrat-3.37.1/madrat/man/fingerprint.Rd | 18 madrat-3.37.1/madrat/man/functionCallString.Rd | 1 madrat-3.37.1/madrat/man/getCalculations.Rd | 6 madrat-3.37.1/madrat/man/getCode.Rd | 1 madrat-3.37.1/madrat/man/getConfig.Rd | 5 madrat-3.37.1/madrat/man/getDependencies.Rd | 6 madrat-3.37.1/madrat/man/getFlags.Rd | 1 madrat-3.37.1/madrat/man/getFromComment.Rd | 1 madrat-3.37.1/madrat/man/getISOlist.Rd | 7 madrat-3.37.1/madrat/man/getLinkFunction.Rd | 5 madrat-3.37.1/madrat/man/getLocation.Rd | 6 madrat-3.37.1/madrat/man/getMadratGraph.Rd | 6 madrat-3.37.1/madrat/man/getMadratInfo.Rd | 6 madrat-3.37.1/madrat/man/getMadratMessage.Rd | 6 madrat-3.37.1/madrat/man/getMainfolder.Rd | 1 madrat-3.37.1/madrat/man/getNonDefaultArguments.Rd | 14 madrat-3.37.1/madrat/man/getSourceFolder.Rd | 1 madrat-3.37.1/madrat/man/getSources.Rd | 6 madrat-3.37.1/madrat/man/initializeConfig.Rd | 1 madrat-3.37.1/madrat/man/installedMadratUniverse.Rd | 6 madrat-3.37.1/madrat/man/isWrapperActive.Rd | 1 madrat-3.37.1/madrat/man/madTempDir.Rd | 1 madrat-3.37.1/madrat/man/madrat-package.Rd | 23 madrat-3.37.1/madrat/man/madratAttach.Rd | 5 madrat-3.37.1/madrat/man/metadataGFZ.Rd | 4 madrat-3.37.1/madrat/man/prepComment.Rd | 1 madrat-3.37.1/madrat/man/prepExtendedComment.Rd | 1 madrat-3.37.1/madrat/man/prepFunctionName.Rd | 1 madrat-3.37.1/madrat/man/pucAggregate.Rd | 4 madrat-3.37.1/madrat/man/putMadratMessage.Rd | 6 madrat-3.37.1/madrat/man/readSource.Rd | 25 madrat-3.37.1/madrat/man/redirect.Rd | 16 madrat-3.37.1/madrat/man/redirectSource.Rd | 36 madrat-3.37.1/madrat/man/regionscode.Rd | 5 madrat-3.37.1/madrat/man/resetMadratMessages.Rd | 6 madrat-3.37.1/madrat/man/retrieveData.Rd | 7 madrat-3.37.1/madrat/man/returnCalcOutput.Rd |only madrat-3.37.1/madrat/man/robustOrder.Rd | 1 madrat-3.37.1/madrat/man/setConfig.Rd | 13 madrat-3.37.1/madrat/man/toolAggregate.Rd | 20 madrat-3.37.1/madrat/man/toolCodeLabels.Rd | 4 madrat-3.37.1/madrat/man/toolCompareStatusLogs.Rd |only 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Title: Interface for Large Language Models via 'llama.cpp'
Description: Provides R bindings to 'llama.cpp' for running large language
models locally, with optional GPU acceleration via 'ggmlR'. Supports text
generation, embeddings, chat-based workflows, tool calling, and multimodal
(vision) inference. Includes 'OpenAI'- and 'Anthropic'-compatible HTTP
servers for serving local models, along with device selection and
multi-GPU support.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between llamaR versions 0.2.4 dated 2026-05-27 and 0.2.5 dated 2026-07-02
llamaR-0.2.4/llamaR/src/Makevars.win |only llamaR-0.2.4/llamaR/src/models/cohere2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/gemma2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/gemma3n-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/graph-context-mamba.cpp |only llamaR-0.2.4/llamaR/src/models/llama-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/mimo2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/openai-moe-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/pangu-embedded.cpp |only llamaR-0.2.4/llamaR/src/models/qwen3vl-moe.cpp |only llamaR-0.2.4/llamaR/src/models/t5-dec.cpp |only llamaR-0.2.4/llamaR/src/models/t5-enc.cpp |only llamaR-0.2.5/llamaR/DESCRIPTION | 22 llamaR-0.2.5/llamaR/MD5 | 463 llamaR-0.2.5/llamaR/NAMESPACE | 11 llamaR-0.2.5/llamaR/NEWS.md | 25 llamaR-0.2.5/llamaR/R/llama.R | 151 llamaR-0.2.5/llamaR/R/mtmd.R |only llamaR-0.2.5/llamaR/R/serve_anthropic.R |only llamaR-0.2.5/llamaR/README.md | 203 llamaR-0.2.5/llamaR/cleanup | 11 llamaR-0.2.5/llamaR/cleanup.win |only llamaR-0.2.5/llamaR/configure.win | 8 llamaR-0.2.5/llamaR/inst/doc/chat-and-agents.Rmd | 107 llamaR-0.2.5/llamaR/inst/doc/chat-and-agents.html | 107 llamaR-0.2.5/llamaR/inst/examples/chat_tools_ministral.R |only llamaR-0.2.5/llamaR/inst/examples/chat_tools_test.R |only llamaR-0.2.5/llamaR/inst/examples/claude_code_launcher.sh |only llamaR-0.2.5/llamaR/inst/examples/diag_qwen35.R |only llamaR-0.2.5/llamaR/inst/examples/dialog_grammar_test.R |only llamaR-0.2.5/llamaR/inst/examples/mcp_web_search.R |only llamaR-0.2.5/llamaR/inst/examples/serve_anthropic_test.sh |only llamaR-0.2.5/llamaR/inst/examples/serve_anthropic_vision.R |only llamaR-0.2.5/llamaR/inst/examples/smoke_chat_tools.R |only llamaR-0.2.5/llamaR/man/llamaR-package.Rd | 2 llamaR-0.2.5/llamaR/man/llama_chat_build.Rd |only llamaR-0.2.5/llamaR/man/llama_chat_parse.Rd |only llamaR-0.2.5/llamaR/man/llama_gen_begin.Rd | 13 llamaR-0.2.5/llamaR/man/llama_gen_begin_at.Rd |only llamaR-0.2.5/llamaR/man/llama_generate.Rd | 13 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llamaR-0.2.5/llamaR/src/common-unicode.h |only llamaR-0.2.5/llamaR/src/common.h |only llamaR-0.2.5/llamaR/src/common_chat_support.cpp |only llamaR-0.2.5/llamaR/src/jinja |only llamaR-0.2.5/llamaR/src/json-partial.cpp |only llamaR-0.2.5/llamaR/src/json-partial.h |only llamaR-0.2.5/llamaR/src/json-schema-to-grammar.cpp |only llamaR-0.2.5/llamaR/src/json-schema-to-grammar.h |only llamaR-0.2.5/llamaR/src/llama-adapter.cpp | 17 llamaR-0.2.5/llamaR/src/llama-adapter.h | 7 llamaR-0.2.5/llamaR/src/llama-arch.cpp | 1987 -- llamaR-0.2.5/llamaR/src/llama-arch.h | 62 llamaR-0.2.5/llamaR/src/llama-batch.cpp | 4 llamaR-0.2.5/llamaR/src/llama-batch.h | 2 llamaR-0.2.5/llamaR/src/llama-chat.cpp | 53 llamaR-0.2.5/llamaR/src/llama-chat.h | 5 llamaR-0.2.5/llamaR/src/llama-context.cpp | 1241 - llamaR-0.2.5/llamaR/src/llama-context.h | 77 llamaR-0.2.5/llamaR/src/llama-cparams.h | 3 llamaR-0.2.5/llamaR/src/llama-ext.h |only llamaR-0.2.5/llamaR/src/llama-grammar.cpp | 84 llamaR-0.2.5/llamaR/src/llama-graph.cpp | 642 llamaR-0.2.5/llamaR/src/llama-graph.h | 86 llamaR-0.2.5/llamaR/src/llama-hparams.cpp | 46 llamaR-0.2.5/llamaR/src/llama-hparams.h | 42 llamaR-0.2.5/llamaR/src/llama-impl.cpp | 10 llamaR-0.2.5/llamaR/src/llama-impl.h | 14 llamaR-0.2.5/llamaR/src/llama-io.cpp | 9 llamaR-0.2.5/llamaR/src/llama-io.h | 6 llamaR-0.2.5/llamaR/src/llama-kv-cache.cpp | 332 llamaR-0.2.5/llamaR/src/llama-kv-cache.h | 36 llamaR-0.2.5/llamaR/src/llama-memory-recurrent.cpp | 56 llamaR-0.2.5/llamaR/src/llama-mmap.cpp | 55 llamaR-0.2.5/llamaR/src/llama-mmap.h | 1 llamaR-0.2.5/llamaR/src/llama-model-loader.cpp | 692 llamaR-0.2.5/llamaR/src/llama-model-loader.h | 41 llamaR-0.2.5/llamaR/src/llama-model-saver.cpp | 218 llamaR-0.2.5/llamaR/src/llama-model-saver.h | 11 llamaR-0.2.5/llamaR/src/llama-model.cpp | 8029 +--------- llamaR-0.2.5/llamaR/src/llama-model.h | 236 llamaR-0.2.5/llamaR/src/llama-quant.cpp | 1074 - llamaR-0.2.5/llamaR/src/llama-vocab.cpp | 266 llamaR-0.2.5/llamaR/src/llama-vocab.h | 6 llamaR-0.2.5/llamaR/src/llama.cpp | 1092 - llamaR-0.2.5/llamaR/src/llama.h | 81 llamaR-0.2.5/llamaR/src/log.cpp |only llamaR-0.2.5/llamaR/src/log.h |only llamaR-0.2.5/llamaR/src/models/afmoe.cpp | 132 llamaR-0.2.5/llamaR/src/models/apertus.cpp | 78 llamaR-0.2.5/llamaR/src/models/arcee.cpp | 80 llamaR-0.2.5/llamaR/src/models/arctic.cpp | 78 llamaR-0.2.5/llamaR/src/models/arwkv7.cpp | 118 llamaR-0.2.5/llamaR/src/models/baichuan.cpp | 67 llamaR-0.2.5/llamaR/src/models/bailingmoe.cpp | 90 llamaR-0.2.5/llamaR/src/models/bailingmoe2.cpp | 114 llamaR-0.2.5/llamaR/src/models/bert.cpp | 133 llamaR-0.2.5/llamaR/src/models/bitnet.cpp | 114 llamaR-0.2.5/llamaR/src/models/bloom.cpp | 90 llamaR-0.2.5/llamaR/src/models/chameleon.cpp | 86 llamaR-0.2.5/llamaR/src/models/chatglm.cpp | 104 llamaR-0.2.5/llamaR/src/models/codeshell.cpp | 71 llamaR-0.2.5/llamaR/src/models/cogvlm.cpp | 67 llamaR-0.2.5/llamaR/src/models/cohere2.cpp |only llamaR-0.2.5/llamaR/src/models/command-r.cpp | 71 llamaR-0.2.5/llamaR/src/models/dbrx.cpp | 71 llamaR-0.2.5/llamaR/src/models/deci.cpp | 107 llamaR-0.2.5/llamaR/src/models/deepseek.cpp | 104 llamaR-0.2.5/llamaR/src/models/deepseek2.cpp | 202 llamaR-0.2.5/llamaR/src/models/deepseek2ocr.cpp |only llamaR-0.2.5/llamaR/src/models/delta-net-base.cpp |only llamaR-0.2.5/llamaR/src/models/dots1.cpp | 94 llamaR-0.2.5/llamaR/src/models/dream.cpp | 76 llamaR-0.2.5/llamaR/src/models/ernie4-5-moe.cpp | 39 llamaR-0.2.5/llamaR/src/models/ernie4-5.cpp | 106 llamaR-0.2.5/llamaR/src/models/eurobert.cpp |only llamaR-0.2.5/llamaR/src/models/exaone-moe.cpp | 136 llamaR-0.2.5/llamaR/src/models/exaone.cpp | 74 llamaR-0.2.5/llamaR/src/models/exaone4.cpp | 91 llamaR-0.2.5/llamaR/src/models/falcon-h1.cpp | 134 llamaR-0.2.5/llamaR/src/models/falcon.cpp | 65 llamaR-0.2.5/llamaR/src/models/gemma-embedding.cpp | 94 llamaR-0.2.5/llamaR/src/models/gemma.cpp | 57 llamaR-0.2.5/llamaR/src/models/gemma2.cpp |only llamaR-0.2.5/llamaR/src/models/gemma3.cpp | 106 llamaR-0.2.5/llamaR/src/models/gemma3n.cpp |only llamaR-0.2.5/llamaR/src/models/gemma4.cpp |only llamaR-0.2.5/llamaR/src/models/glm-dsa.cpp |only llamaR-0.2.5/llamaR/src/models/glm4-moe.cpp | 166 llamaR-0.2.5/llamaR/src/models/glm4.cpp | 132 llamaR-0.2.5/llamaR/src/models/gpt2.cpp | 78 llamaR-0.2.5/llamaR/src/models/gptneox.cpp | 102 llamaR-0.2.5/llamaR/src/models/granite-hybrid.cpp | 172 llamaR-0.2.5/llamaR/src/models/granite-moe.cpp |only llamaR-0.2.5/llamaR/src/models/granite.cpp | 129 llamaR-0.2.5/llamaR/src/models/grok.cpp | 118 llamaR-0.2.5/llamaR/src/models/grovemoe.cpp | 90 llamaR-0.2.5/llamaR/src/models/hunyuan-dense.cpp | 132 llamaR-0.2.5/llamaR/src/models/hunyuan-moe.cpp | 89 llamaR-0.2.5/llamaR/src/models/hunyuan-vl.cpp |only llamaR-0.2.5/llamaR/src/models/internlm2.cpp | 70 llamaR-0.2.5/llamaR/src/models/jais.cpp | 86 llamaR-0.2.5/llamaR/src/models/jais2.cpp |only llamaR-0.2.5/llamaR/src/models/jamba.cpp | 130 llamaR-0.2.5/llamaR/src/models/jina-bert-v2.cpp |only llamaR-0.2.5/llamaR/src/models/jina-bert-v3.cpp |only llamaR-0.2.5/llamaR/src/models/kimi-linear.cpp |only llamaR-0.2.5/llamaR/src/models/lfm2.cpp | 348 llamaR-0.2.5/llamaR/src/models/lfm2moe.cpp |only llamaR-0.2.5/llamaR/src/models/llada-moe.cpp | 76 llamaR-0.2.5/llamaR/src/models/llada.cpp | 89 llamaR-0.2.5/llamaR/src/models/llama-embed.cpp |only llamaR-0.2.5/llamaR/src/models/llama.cpp | 146 llamaR-0.2.5/llamaR/src/models/llama4.cpp |only llamaR-0.2.5/llamaR/src/models/maincoder.cpp | 67 llamaR-0.2.5/llamaR/src/models/mamba-base.cpp |only llamaR-0.2.5/llamaR/src/models/mamba.cpp | 86 llamaR-0.2.5/llamaR/src/models/mamba2.cpp |only llamaR-0.2.5/llamaR/src/models/mimo2.cpp |only llamaR-0.2.5/llamaR/src/models/minicpm.cpp |only llamaR-0.2.5/llamaR/src/models/minicpm3.cpp | 90 llamaR-0.2.5/llamaR/src/models/minimax-m2.cpp | 57 llamaR-0.2.5/llamaR/src/models/mistral3.cpp | 125 llamaR-0.2.5/llamaR/src/models/mistral4.cpp |only llamaR-0.2.5/llamaR/src/models/models.h | 1903 +- llamaR-0.2.5/llamaR/src/models/modern-bert.cpp | 93 llamaR-0.2.5/llamaR/src/models/mpt.cpp | 92 llamaR-0.2.5/llamaR/src/models/nemotron-h-moe.cpp |only llamaR-0.2.5/llamaR/src/models/nemotron-h.cpp | 204 llamaR-0.2.5/llamaR/src/models/nemotron.cpp | 79 llamaR-0.2.5/llamaR/src/models/neo-bert.cpp | 62 llamaR-0.2.5/llamaR/src/models/nomic-bert-moe.cpp |only llamaR-0.2.5/llamaR/src/models/nomic-bert.cpp |only llamaR-0.2.5/llamaR/src/models/olmo.cpp | 73 llamaR-0.2.5/llamaR/src/models/olmo2.cpp | 75 llamaR-0.2.5/llamaR/src/models/olmoe.cpp | 61 llamaR-0.2.5/llamaR/src/models/openai-moe.cpp |only llamaR-0.2.5/llamaR/src/models/openelm.cpp | 57 llamaR-0.2.5/llamaR/src/models/orion.cpp | 76 llamaR-0.2.5/llamaR/src/models/paddleocr.cpp |only llamaR-0.2.5/llamaR/src/models/pangu-embed.cpp |only llamaR-0.2.5/llamaR/src/models/phi2.cpp | 77 llamaR-0.2.5/llamaR/src/models/phi3.cpp | 102 llamaR-0.2.5/llamaR/src/models/phimoe.cpp |only llamaR-0.2.5/llamaR/src/models/plamo.cpp | 60 llamaR-0.2.5/llamaR/src/models/plamo2.cpp | 124 llamaR-0.2.5/llamaR/src/models/plamo3.cpp | 81 llamaR-0.2.5/llamaR/src/models/plm.cpp | 76 llamaR-0.2.5/llamaR/src/models/qwen.cpp | 58 llamaR-0.2.5/llamaR/src/models/qwen2.cpp | 85 llamaR-0.2.5/llamaR/src/models/qwen2moe.cpp | 96 llamaR-0.2.5/llamaR/src/models/qwen2vl.cpp | 66 llamaR-0.2.5/llamaR/src/models/qwen3.cpp | 79 llamaR-0.2.5/llamaR/src/models/qwen35.cpp |only llamaR-0.2.5/llamaR/src/models/qwen35moe.cpp |only llamaR-0.2.5/llamaR/src/models/qwen3moe.cpp | 91 llamaR-0.2.5/llamaR/src/models/qwen3next.cpp | 656 llamaR-0.2.5/llamaR/src/models/qwen3vl.cpp | 74 llamaR-0.2.5/llamaR/src/models/qwen3vlmoe.cpp |only llamaR-0.2.5/llamaR/src/models/refact.cpp | 97 llamaR-0.2.5/llamaR/src/models/rnd1.cpp | 86 llamaR-0.2.5/llamaR/src/models/rwkv6-base.cpp | 2 llamaR-0.2.5/llamaR/src/models/rwkv6.cpp | 95 llamaR-0.2.5/llamaR/src/models/rwkv6qwen2.cpp | 83 llamaR-0.2.5/llamaR/src/models/rwkv7-base.cpp | 2 llamaR-0.2.5/llamaR/src/models/rwkv7.cpp | 125 llamaR-0.2.5/llamaR/src/models/seed-oss.cpp | 78 llamaR-0.2.5/llamaR/src/models/smallthinker.cpp | 104 llamaR-0.2.5/llamaR/src/models/smollm3.cpp | 76 llamaR-0.2.5/llamaR/src/models/stablelm.cpp | 82 llamaR-0.2.5/llamaR/src/models/starcoder.cpp | 80 llamaR-0.2.5/llamaR/src/models/starcoder2.cpp | 88 llamaR-0.2.5/llamaR/src/models/step35.cpp |only llamaR-0.2.5/llamaR/src/models/t5.cpp |only llamaR-0.2.5/llamaR/src/models/t5encoder.cpp |only llamaR-0.2.5/llamaR/src/models/wavtokenizer-dec.cpp | 119 llamaR-0.2.5/llamaR/src/models/xverse.cpp | 61 llamaR-0.2.5/llamaR/src/mtmd |only llamaR-0.2.5/llamaR/src/nlohmann |only llamaR-0.2.5/llamaR/src/peg-parser.cpp |only llamaR-0.2.5/llamaR/src/peg-parser.h |only llamaR-0.2.5/llamaR/src/r_chat_interface.cpp |only llamaR-0.2.5/llamaR/src/r_llama_compat.h | 26 llamaR-0.2.5/llamaR/src/r_llama_interface.cpp | 254 llamaR-0.2.5/llamaR/src/r_mtmd_interface.cpp |only llamaR-0.2.5/llamaR/src/regex-partial.cpp |only llamaR-0.2.5/llamaR/src/regex-partial.h |only llamaR-0.2.5/llamaR/src/unicode.cpp | 290 llamaR-0.2.5/llamaR/src/unicode.h | 2 llamaR-0.2.5/llamaR/src/vendor |only llamaR-0.2.5/llamaR/tests/testthat.R | 28 llamaR-0.2.5/llamaR/tests/testthat/test-chat-build-roundtrip.R |only llamaR-0.2.5/llamaR/tests/testthat/test-chat-build.R |only llamaR-0.2.5/llamaR/tests/testthat/test-core-extra.R |only llamaR-0.2.5/llamaR/tests/testthat/test-hf.R | 12 llamaR-0.2.5/llamaR/tests/testthat/test-lora-multi.R |only llamaR-0.2.5/llamaR/tests/testthat/test-mtmd.R |only llamaR-0.2.5/llamaR/tests/testthat/test-serve-anthropic-e2e.R |only llamaR-0.2.5/llamaR/tests/testthat/test-serve-anthropic.R |only llamaR-0.2.5/llamaR/vignettes/chat-and-agents.Rmd | 107 259 files changed, 15564 insertions(+), 14350 deletions(-)
Title: Time-to-Event Landmark Analysis using an Array of Longitudinal
and Survival Sub-Models
Description: Provides a modular end-to-end framework for dynamic risk prediction
based on time-to-event and longitudinal data. This allows flexible specifications
for the longitudinal and survival sub-models. The 'landmaRk' package enables
reproducible benchmarks of different model choices, including cross-validation
to assess out-of-sample predictive performance. Methods are described in
Velasco-Pardo, Constantine-Cooke, Lees and Vallejos (2026, manuscript under
preparation) 'Landmarking with Latent Class Mixed Models for Dynamic Prediction
of Time-to-event Data with Heterogeneous Biomarker Trajectories'.
Author: Victor Velasco-Pardo [aut, cre] ,
Nathan Constantine-Cooke [aut] ,
Charlie Lees [aut] ,
Catalina Vallejos [aut]
Maintainer: Victor Velasco-Pardo <vvelasco@ed.ac.uk>
Diff between landmaRk versions 0.1.2 dated 2026-06-26 and 0.1.3 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 8 +++++++- 3 files changed, 12 insertions(+), 6 deletions(-)
Title: Asymmetric Smoothed-Association Matrices via GAM Fits
Description: Render a pairwise, asymmetric smoothed-association matrix
of continuous variables. Each cell shows the fitted spline from an
'mgcv' generalised additive model, with the upper triangle
displaying 'gam(x_j ~ s(x_i))' and the lower triangle
'gam(x_i ~ s(x_j))'. Unlike Pearson's correlation matrix, the
visualisation is intentionally asymmetric, revealing
heteroscedasticity, leverage, and directional non-linearity that
a single scalar correlation hides. An asymmetry index and a
24-category shape taxonomy quantify the directional difference
and qualitative form of each fitted smooth.
Author: Max Moldovan [aut, cre, cph]
Maintainer: Max Moldovan <max.moldovan@adelaide.edu.au>
Diff between janusplot versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-07-02
DESCRIPTION | 7 MD5 | 48 +-- NEWS.md | 180 ++++++++++++- R/internal-assemble.R | 18 + R/internal-cell.R | 361 ++++++++++++++++++++++++-- R/internal-fit.R | 347 +++++++++++++++++++++++++ R/janusplot.R | 382 +++++++++++++++++++++++++--- R/shape-metrics.R | 2 README.md | 13 inst/CITATION | 13 inst/doc/janusplot.Rmd | 2 inst/doc/janusplot.html | 67 ++-- inst/doc/shape-recognition-sensitivity.html | 10 man/janusplot.Rd | 171 ++++++++++++ man/janusplot_data.Rd | 69 ++++- tests/testthat/test-axes.R |only tests/testthat/test-compact.R |only tests/testthat/test-derivatives.R | 30 ++ tests/testthat/test-engine.R |only tests/testthat/test-focus.R |only tests/testthat/test-integration.R | 2 tests/testthat/test-k-check.R |only tests/testthat/test-shape-sensitivity.R | 2 tests/testthat/test-validate.R | 46 +++ tests/testthat/test-validation-linear.R | 2 tests/testthat/test-vdiffr.R | 19 + vignettes/janusplot.Rmd | 2 vignettes/mathjax-config.html |only 28 files changed, 1624 insertions(+), 169 deletions(-)
Title: Recursive Partitioning for Graded Response Models
Description: Provides methods for recursive partitioning based on the
'Graded Response Model' ('GRM'), extending the 'MOB' algorithm from the
'partykit' package. The package allows for fitting
'GRM' trees that partition the population into homogeneous
subgroups based on item response patterns and covariates.
Includes specialized plotting functions for visualizing 'GRM' trees
with different terminal node displays (threshold regions,
parameter profiles, and factor score distributions). The package also implements the Longitudinal GRMTree for detecting response shift in PROMs measured at two time points, embedding a constrained two-factor longitudinal GRM within recursive partitioning, with post-hoc characterization of recalibration and reprioritization.
For more details on the methods, see Samejima (1969) <doi:10.1002/J.2333-8504.1968.TB00153.X>, Komboz et al. (2018) <doi:10.1177/0013164416664394> and Arimoro et al. (2025) <doi:10.1007/s11136-025-04018-6>.
Author: Olayinka I. Arimoro [aut, cre] ,
Tolulope T. Sajobi [aut],
Lisa M. Lix [aut],
Matthew T. James [ctb],
Maria Santana [ctb],
Emmanuel Ugochukwu [ctb]
Maintainer: Olayinka I. Arimoro <olayinka.arimoro@ucalgary.ca>
Diff between grmtree versions 0.1.0 dated 2026-01-14 and 0.2.0 dated 2026-07-02
DESCRIPTION | 17 +- MD5 | 61 ++++++++-- NAMESPACE | 24 +++- NEWS.md | 63 ++++++++-- R/generate_nodescores_dataset.R |only R/grmtree-control.R | 73 +++++++++--- R/grmtree-fscores.R | 124 --------------------- R/grmtree_long_data.R |only R/long-grmtree-discrpar.R |only R/long-grmtree-fscores.R |only R/long-grmtree-itempar.R |only R/long-grmtree-latentpar.R |only R/long-grmtree-plot.R |only R/long-grmtree-threshpar.R |only R/longitudinal_grmtree.R |only R/rs_characterize.R |only R/rs_characterize_plots.R |only README.md | 58 ++++++++- build/partial.rdb |only build/vignette.rds |binary data/grmtree_long_data.rda |only inst/doc/getting-started-with-grmtree-package.html | 4 inst/doc/longitudinal-grmtree.R |only inst/doc/longitudinal-grmtree.Rmd |only inst/doc/longitudinal-grmtree.html |only man/discrpar_longitudinal_grmtree.Rd |only man/fscores_longitudinal_grmtree.Rd |only man/generate_node_scores_dataset.Rd | 69 ++++++++--- man/grmforest.Rd | 2 man/grmtree_long_data.Rd |only man/itempar_longitudinal_grmtree.Rd |only man/latentpar_longitudinal_grmtree.Rd |only man/longitudinal_grmfit.Rd |only man/longitudinal_grmtree.Rd |only man/node_regionplot_longitudinal.Rd |only man/plot.longitudinal_grmtree.Rd |only man/plot_rs_heatmap.Rd |only man/plot_rs_tree.Rd |only man/prepare_longitudinal_data.Rd |only man/print.rs_characterization.Rd |only man/rs_characterize.Rd |only man/threshpar_longitudinal_grmtree.Rd |only tests/testthat/helper-longitudinal.R |only tests/testthat/test-all-long-grmtree.R |only tests/testthat/test-extraction-functions.R |only tests/testthat/test-fscores.R | 84 -------------- tests/testthat/test-generate_node_scores_dataset.R |only tests/testthat/test-long-grmtree.R |only tests/testthat/test-prep_long_data.R |only tests/testthat/test-rs-characterize.R |only vignettes/longitudinal-grmtree.Rmd |only 51 files changed, 288 insertions(+), 291 deletions(-)
Title: Geographic and Taxonomic Occurrence R-Based Scrubbing
Description: Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Author: Natalie N. Patten [aut] ,
Michelle L. Gaynor [aut, cre] ,
Douglas E. Soltis [ctb] ,
Pamela S. Soltis [ctb]
Maintainer: Michelle L. Gaynor <shellyleegaynor@gmail.com>
Diff between gatoRs versions 1.0.2 dated 2024-05-17 and 2.0.0 dated 2026-07-02
gatoRs-1.0.2/gatoRs/R/get_idigbio.R |only gatoRs-1.0.2/gatoRs/man/get_idigbio.Rd |only gatoRs-2.0.0/gatoRs/DESCRIPTION | 33 gatoRs-2.0.0/gatoRs/MD5 | 140 ++-- gatoRs-2.0.0/gatoRs/NAMESPACE | 129 +-- gatoRs-2.0.0/gatoRs/R/basic_locality_clean.R | 158 ++-- gatoRs-2.0.0/gatoRs/R/basis_clean.R | 126 +-- gatoRs-2.0.0/gatoRs/R/citation_bellow.R | 64 - gatoRs-2.0.0/gatoRs/R/correct_class.R | 180 ++--- gatoRs-2.0.0/gatoRs/R/data.R | 10 gatoRs-2.0.0/gatoRs/R/data_chomp.R | 66 - gatoRs-2.0.0/gatoRs/R/filter_fix_names.R | 130 +-- gatoRs-2.0.0/gatoRs/R/fixAfterPeriod.R | 58 - gatoRs-2.0.0/gatoRs/R/fix_columns.R | 122 +-- gatoRs-2.0.0/gatoRs/R/fix_names.R | 260 +++---- gatoRs-2.0.0/gatoRs/R/full_clean.R | 204 ++--- gatoRs-2.0.0/gatoRs/R/gators_download.R | 329 +++++---- gatoRs-2.0.0/gatoRs/R/gators_merge.R | 70 +- gatoRs-2.0.0/gatoRs/R/get_gbif.R | 404 +++++------ gatoRs-2.0.0/gatoRs/R/get_idigbio_arc.R |only gatoRs-2.0.0/gatoRs/R/global_vars.R | 2 gatoRs-2.0.0/gatoRs/R/matchColClasses.R | 36 - gatoRs-2.0.0/gatoRs/R/need_to_georeference.R | 72 +- gatoRs-2.0.0/gatoRs/R/needed_records.R | 52 - gatoRs-2.0.0/gatoRs/R/one_point_per_pixel.R | 110 +-- gatoRs-2.0.0/gatoRs/R/process_flagged.R | 460 ++++++------- gatoRs-2.0.0/gatoRs/R/remove_duplicates.R | 318 ++++----- gatoRs-2.0.0/gatoRs/R/remove_missing.R | 90 +- gatoRs-2.0.0/gatoRs/R/remove_skewed.R | 48 - gatoRs-2.0.0/gatoRs/R/removed_redacted.R | 50 - gatoRs-2.0.0/gatoRs/R/setupduckDB.R |only gatoRs-2.0.0/gatoRs/R/suppress_output.R | 40 - gatoRs-2.0.0/gatoRs/R/taxa_clean.R | 178 ++--- gatoRs-2.0.0/gatoRs/R/thin_points.R | 96 +- gatoRs-2.0.0/gatoRs/R/utils-pipe.R | 28 gatoRs-2.0.0/gatoRs/README.md | 116 +-- gatoRs-2.0.0/gatoRs/build/vignette.rds |binary gatoRs-2.0.0/gatoRs/inst/CITATION | 38 - gatoRs-2.0.0/gatoRs/inst/doc/Introduction.R | 12 gatoRs-2.0.0/gatoRs/inst/doc/Introduction.Rmd | 546 +++++++-------- gatoRs-2.0.0/gatoRs/inst/doc/Introduction.html | 837 ++++++++++++++++-------- gatoRs-2.0.0/gatoRs/inst/doc/ManyDownloads.Rmd | 170 ++-- gatoRs-2.0.0/gatoRs/inst/doc/ManyDownloads.html | 461 +++++++++---- gatoRs-2.0.0/gatoRs/man/basic_locality_clean.Rd | 110 +-- gatoRs-2.0.0/gatoRs/man/basis_clean.Rd | 64 - gatoRs-2.0.0/gatoRs/man/citation_bellow.Rd | 64 - gatoRs-2.0.0/gatoRs/man/correct_class.Rd | 190 ++--- gatoRs-2.0.0/gatoRs/man/data.Rd | 36 - gatoRs-2.0.0/gatoRs/man/data_chomp.Rd | 74 +- gatoRs-2.0.0/gatoRs/man/filter_fix_names.Rd | 88 +- gatoRs-2.0.0/gatoRs/man/fixAfterPeriod.Rd | 42 - gatoRs-2.0.0/gatoRs/man/fix_columns.Rd | 80 +- gatoRs-2.0.0/gatoRs/man/fix_names.Rd | 54 - gatoRs-2.0.0/gatoRs/man/full_clean.Rd | 246 +++---- gatoRs-2.0.0/gatoRs/man/gators_download.Rd | 198 +++-- gatoRs-2.0.0/gatoRs/man/gators_merge.Rd | 64 - gatoRs-2.0.0/gatoRs/man/get_gbif.Rd | 70 +- gatoRs-2.0.0/gatoRs/man/get_idigbio_arc.Rd |only gatoRs-2.0.0/gatoRs/man/matchColClasses.Rd | 44 - gatoRs-2.0.0/gatoRs/man/need_to_georeference.Rd | 74 +- gatoRs-2.0.0/gatoRs/man/needed_records.Rd | 58 - gatoRs-2.0.0/gatoRs/man/one_point_per_pixel.Rd | 92 +- gatoRs-2.0.0/gatoRs/man/pipe.Rd | 40 - gatoRs-2.0.0/gatoRs/man/process_flagged.Rd | 100 +- gatoRs-2.0.0/gatoRs/man/remove_duplicates.Rd | 162 ++-- gatoRs-2.0.0/gatoRs/man/remove_missing.Rd | 98 +- gatoRs-2.0.0/gatoRs/man/remove_redacted.Rd | 56 - gatoRs-2.0.0/gatoRs/man/remove_skewed.Rd | 52 - gatoRs-2.0.0/gatoRs/man/setupduckDB.Rd |only gatoRs-2.0.0/gatoRs/man/suppress_output.Rd | 44 - gatoRs-2.0.0/gatoRs/man/taxa_clean.Rd | 98 +- gatoRs-2.0.0/gatoRs/man/thin_points.Rd | 92 +- gatoRs-2.0.0/gatoRs/vignettes/Introduction.Rmd | 546 +++++++-------- gatoRs-2.0.0/gatoRs/vignettes/ManyDownloads.Rmd | 170 ++-- 74 files changed, 4957 insertions(+), 4392 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Fetches, harmonizes, and analyses data from the Spanish National
Forest Inventory for reproducible, design-aware forest inventory workflows.
Computes tree- and stand-level metrics, applies sampling-based expansion
factors, estimates volume, and supports extensible processing for external
inventory designs with custom sampling schemes and volume equations. Spatial
extensions can attach plot geometries, preserve geometry sidecars through
metric workflows, and return georeferenced sf outputs for mapping and
remote-sensing integration.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Aitor Vazquez-Veloso [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.7.7 dated 2026-04-09 and 0.7.8 dated 2026-07-02
basifoR-0.7.7/basifoR/man/get_snfi_iavc.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vcc.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vle.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vsc.Rd |only basifoR-0.7.8/basifoR/DESCRIPTION | 17 basifoR-0.7.8/basifoR/MD5 | 150 + basifoR-0.7.8/basifoR/NAMESPACE | 52 basifoR-0.7.8/basifoR/NEWS | 74 basifoR-0.7.8/basifoR/R/dbhMetric.R | 6 basifoR-0.7.8/basifoR/R/default_snfi_volume_equations.R | 868 ----------- basifoR-0.7.8/basifoR/R/dendroMetrics.R | 171 +- basifoR-0.7.8/basifoR/R/dominant_height_method_registry.R |only basifoR-0.7.8/basifoR/R/externalMetrics.R | 156 + basifoR-0.7.8/basifoR/R/externalMetrics2Vol.R | 50 basifoR-0.7.8/basifoR/R/external_dendroMetrics.R | 101 - basifoR-0.7.8/basifoR/R/external_volume_method_registry.R | 58 basifoR-0.7.8/basifoR/R/internal.R | 506 ------ basifoR-0.7.8/basifoR/R/inventoryMetrics.R | 292 ++- basifoR-0.7.8/basifoR/R/inventoryMetrics_spatial.R |only basifoR-0.7.8/basifoR/R/listNFI_tables.R |only basifoR-0.7.8/basifoR/R/metrics2Vol.R | 119 + basifoR-0.7.8/basifoR/R/metrics2Vol_spatial.R |only basifoR-0.7.8/basifoR/R/new_concentric_design.R | 20 basifoR-0.7.8/basifoR/R/new_external_schema.R | 24 basifoR-0.7.8/basifoR/R/new_inventory_design.R | 24 basifoR-0.7.8/basifoR/R/new_volume_method.R | 6 basifoR-0.7.8/basifoR/R/nfiMetrics.R | 183 +- basifoR-0.7.8/basifoR/R/nfiMetrics_spatial.R |only basifoR-0.7.8/basifoR/R/plotNFI_spatial.R |only basifoR-0.7.8/basifoR/R/print.concentric_design.R | 4 basifoR-0.7.8/basifoR/R/print.inventory_design.R | 2 basifoR-0.7.8/basifoR/R/readNFI.R | 5 basifoR-0.7.8/basifoR/R/readNFI_spatial.R |only basifoR-0.7.8/basifoR/R/readNFIsf.R |only basifoR-0.7.8/basifoR/R/snfi_volume_equations.R | 110 - basifoR-0.7.8/basifoR/R/snfi_volume_method_registry.R | 34 basifoR-0.7.8/basifoR/R/sysdata.rda |binary basifoR-0.7.8/basifoR/R/trees_per_ha.R | 13 basifoR-0.7.8/basifoR/R/update.external_dendroMetrics.R | 25 basifoR-0.7.8/basifoR/man/addNFIcoords.Rd |only basifoR-0.7.8/basifoR/man/addNFIsf.Rd |only basifoR-0.7.8/basifoR/man/asNFI_spatial_sf.Rd |only basifoR-0.7.8/basifoR/man/copyNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/copyNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/copyNFIspatial_sidecars.Rd |only basifoR-0.7.8/basifoR/man/dbhMetric.Rd | 9 basifoR-0.7.8/basifoR/man/default_dominant_height_methods.Rd |only basifoR-0.7.8/basifoR/man/default_external_volume_methods.Rd | 7 basifoR-0.7.8/basifoR/man/default_snfi_volume_equations.Rd | 26 basifoR-0.7.8/basifoR/man/dendroMetrics.Rd | 52 basifoR-0.7.8/basifoR/man/dominant_height_method_registry.Rd |only basifoR-0.7.8/basifoR/man/externalMetrics.Rd | 46 basifoR-0.7.8/basifoR/man/externalMetrics2Vol.Rd | 22 basifoR-0.7.8/basifoR/man/external_dendroMetrics.Rd | 47 basifoR-0.7.8/basifoR/man/external_volume_method_registry.Rd | 55 basifoR-0.7.8/basifoR/man/fetchNFI.Rd | 8 basifoR-0.7.8/basifoR/man/filter_gadm_province_spatial.Rd |only basifoR-0.7.8/basifoR/man/gadm_spatial.Rd |only basifoR-0.7.8/basifoR/man/getNFI.Rd | 7 basifoR-0.7.8/basifoR/man/getNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/getNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/hasNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/hasNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/inventoryMetrics.Rd | 136 - basifoR-0.7.8/basifoR/man/inventoryMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/listNFI_tables.Rd |only basifoR-0.7.8/basifoR/man/metrics2Vol.Rd | 105 + basifoR-0.7.8/basifoR/man/metrics2Vol_spatial.Rd |only basifoR-0.7.8/basifoR/man/new_concentric_design.Rd | 27 basifoR-0.7.8/basifoR/man/new_dominant_height_method.Rd |only basifoR-0.7.8/basifoR/man/new_external_schema.Rd | 20 basifoR-0.7.8/basifoR/man/new_inventory_design.Rd | 42 basifoR-0.7.8/basifoR/man/new_volume_method.Rd | 18 basifoR-0.7.8/basifoR/man/nfiMetrics.Rd | 100 - basifoR-0.7.8/basifoR/man/nfiMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.inventoryMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.metrics2Vol_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.nfiMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.readNFI_spatial.Rd |only basifoR-0.7.8/basifoR/man/print.concentric_design.Rd | 15 basifoR-0.7.8/basifoR/man/print.external_schema.Rd | 18 basifoR-0.7.8/basifoR/man/print.inventory_design.Rd | 14 basifoR-0.7.8/basifoR/man/readNFI.Rd | 38 basifoR-0.7.8/basifoR/man/readNFI_spatial.Rd |only basifoR-0.7.8/basifoR/man/readNFIcoords.Rd |only basifoR-0.7.8/basifoR/man/readNFIsf.Rd |only basifoR-0.7.8/basifoR/man/snfi_design.Rd | 7 basifoR-0.7.8/basifoR/man/snfi_volume_method_registry.Rd | 50 basifoR-0.7.8/basifoR/man/trees_per_ha.Rd | 14 basifoR-0.7.8/basifoR/man/trees_per_ha.concentric_design.Rd | 17 basifoR-0.7.8/basifoR/man/trees_per_ha.inventory_design.Rd | 17 basifoR-0.7.8/basifoR/man/update.dendroMetrics.Rd | 7 basifoR-0.7.8/basifoR/man/update.external_dendroMetrics.Rd | 32 basifoR-0.7.8/basifoR/man/update.inventoryMetrics.Rd | 20 basifoR-0.7.8/basifoR/man/update.list.Rd | 10 95 files changed, 1760 insertions(+), 2296 deletions(-)
Title: Estimate Survival Data with Data Integration
Description: Provides flexible and efficient tools for integrating external risk scores into Cox proportional hazards models while accounting for population heterogeneity. Enables robust estimation, improved predictive accuracy, and user-friendly workflows for modern survival analysis. For more information, see Wang et al. (2023) <doi:10.48550/arXiv.2302.11123>.
Author: Yubo Shao [aut, cre],
Lingfeng Luo [aut],
Xiaohan Liu [aut],
Junyi Qiu [aut],
Di Wang [aut],
Kevin He [aut]
Maintainer: Yubo Shao <ybshao@umich.edu>
Diff between survkl versions 1.0.0 dated 2026-04-21 and 1.0.2 dated 2026-07-02
DESCRIPTION | 8 MD5 | 22 - R/plot.R | 8 inst/doc/Methods.Rmd | 202 ++++++++++ inst/doc/Methods.html | 192 +++++++++ inst/doc/survkl.Rmd | 914 +++++++++++++++++++++++------------------------ man/plot.coxkl_enet.Rd | 4 src/Makevars | 16 src/Makevars.win | 19 vignettes/Methods.Rmd | 202 ++++++++++ vignettes/references.bib | 12 vignettes/survkl.Rmd | 914 +++++++++++++++++++++++------------------------ 12 files changed, 1537 insertions(+), 976 deletions(-)
Title: ROBust INference for Covariate Adjustment in Randomized Clinical
Trials
Description: Performs robust estimation and inference when using covariate adjustment
and/or covariate-adaptive randomization in randomized controlled trials.
This package is trimmed to reduce the dependencies and validated to be used across industry.
See "FDA's final guidance on covariate adjustment"<https://www.regulations.gov/docket/FDA-2019-D-0934>, Tsiatis (2008) <doi:10.1002/sim.3113>,
Bugni et al. (2018) <doi:10.1080/01621459.2017.1375934>, Ye, Shao, Yi, and Zhao (2023)<doi:10.1080/01621459.2022.2049278>,
Ye, Shao, and Yi (2022)<doi:10.1093/biomet/asab015>, Rosenblum and van der Laan (2010)<doi:10.2202/1557-4679.1138>,
Wang et al. (2021)<doi:10.1080/01621459.2021.1981338>, Ye, Bannick, Yi, and Shao (2023)<doi:10.1080/24754269.2023.2205802>,
and Bannick, Shao, Liu, Du, Yi, and Ye (2024)<doi:10.48550/arXiv.2306.10213>.
Author: Liming Li [aut, cre] ,
Marlena Bannick [aut] ,
Daniel Sabanes Bove [aut] ,
Dong Xi [aut],
Ting Ye [aut],
Yanyao Yi [aut],
Gregory Chen [ctb],
Gilead Sciences, Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
Merck Sharp & Dohme, Inc. [cph, fnd],
[...truncated...]
Maintainer: Liming Li <liming.li1@astrazeneca.com>
Diff between RobinCar2 versions 0.2.2 dated 2026-01-09 and 0.2.3 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/predict_couterfactual.R | 2 +- inst/WORDLIST | 23 +++++++++++++++++++++++ inst/doc/intro.html | 14 +++++++------- tests/testthat/test-predict_counterfactual.R | 13 +++++++++++++ 7 files changed, 64 insertions(+), 18 deletions(-)
Title: Higher-Level Interface of 'torch' Package to Auto-Train Neural
Networks
Description: Provides a higher-level interface to the 'torch' package for defining,
training, and fine-tuning neural networks through code generation.
The package supports several architectures, including feedforward
(multi-layer perceptron) and recurrent neural networks (RNN, LSTM,
GRU), while reducing boilerplate 'torch' code. Model training
methods also bridge to machine learning frameworks in R,
particularly the 'tidymodels' ecosystem, including 'parsnip' model
specifications, workflows, recipes, and tuning tools.
Author: Joshua Marie [aut, cre],
Antoine Soetewey [aut]
Maintainer: Joshua Marie <joshua.marie.k@gmail.com>
Diff between kindling versions 0.3.0 dated 2026-03-03 and 0.3.1 dated 2026-07-02
DESCRIPTION | 26 MD5 | 40 - NAMESPACE | 8 NEWS.md | 20 R/generalized-nn-fit.R | 1014 +++++++++++++++++++------------------ R/kindling-package.R | 17 R/plot.R |only R/utils.R | 8 R/variable-imp.R | 18 R/zzz.R | 1 README.md | 45 - inst/doc/custom-act-fn.html | 5 inst/doc/kindling.html | 5 inst/doc/special-cases.html | 5 inst/doc/tuning-capabilities.html | 5 man/autoplot.nn_fit.Rd |only man/autoplot_diagnostics.Rd |only man/kindling-varimp.Rd | 14 man/kindling.Rd | 15 man/reexports.Rd | 3 tests/testthat/test-plot.R |only tests/testthat/test-train-nn.R | 38 - tests/testthat/test-variable-imp.R | 6 23 files changed, 677 insertions(+), 616 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, and convenience clients for the World
Health Organization Global Health Observatory (GHO) OData API
<https://ghoapi.azureedge.net/api/> and the United Nations
Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between DSIR versions 0.7.1 dated 2026-05-23 and 0.8.0 dated 2026-07-02
DESCRIPTION | 11 ++-- MD5 | 42 ++++++++++------- NAMESPACE | 1 NEWS.md | 46 +++++++++++++++++++ R/aarr.R |only R/gho.R | 76 ++++++++++++++++++++++++++++---- README.md | 25 ++++++++++ build/vignette.rds |binary inst/WORDLIST | 3 + inst/doc/DSIR.html | 67 ++++++++++++++-------------- inst/doc/visualizing-indicators.R |only inst/doc/visualizing-indicators.Rmd |only inst/doc/visualizing-indicators.html |only man/aarr.Rd |only man/gho_count.Rd | 15 +++++- man/gho_coverage.Rd | 15 +++++- man/gho_data.Rd | 18 +++++++ man/gho_dimensions.Rd | 11 ++++ man/gho_has_data.Rd | 15 +++++- tests/testthat/test-aarr.R |only tests/testthat/test-gho-availability.R | 19 ++++++++ tests/testthat/test-gho-catalog-cache.R |only tests/testthat/test-gho-dimensions.R | 23 +++++++++ tests/testthat/test-gho-get-mock.R | 48 ++++++++++++++++++++ tests/testthat/test-gho.R | 34 ++++++++++++++ vignettes/visualizing-indicators.Rmd |only 26 files changed, 401 insertions(+), 68 deletions(-)
Title: Access Chinese Data via Public APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including 'Nager.Date'
and 'World Bank API', retrieving real-time or historical data related to China, such
as holidays and economic indicators. Additionally, the package includes one of the
largest curated collections of open datasets focused on China and Hong Kong, covering
topics such as air quality, demographics, input-output tables, epidemiology, political
structure, names, and social indicators. The package supports reproducible research
and teaching by integrating reliable international APIs and structured datasets from
public, academic, and government sources.
For more information on the APIs, see:
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ChinAPIs versions 0.1.1 dated 2026-02-12 and 0.2.0 dated 2026-07-02
ChinAPIs-0.1.1/ChinAPIs/R/get_country_info_cn.R |only ChinAPIs-0.1.1/ChinAPIs/man/get_country_info_cn.Rd |only ChinAPIs-0.1.1/ChinAPIs/tests/testthat/test-get_country_info_cn.R |only ChinAPIs-0.2.0/ChinAPIs/DESCRIPTION | 22 - ChinAPIs-0.2.0/ChinAPIs/MD5 | 143 ++++------ ChinAPIs-0.2.0/ChinAPIs/NAMESPACE | 2 ChinAPIs-0.2.0/ChinAPIs/NEWS.md | 17 + ChinAPIs-0.2.0/ChinAPIs/R/chinapis-package.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/data-documentation.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_child_mortality.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_cpi.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_energy_use.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_gdp.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_holidays.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_hospital_beds.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_life_expectancy.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_literacy_rate.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_population.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_unemployment.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/utils.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/view_datasets_ChinAPIs.R | 4 ChinAPIs-0.2.0/ChinAPIs/README.md | 11 ChinAPIs-0.2.0/ChinAPIs/build/vignette.rds |binary ChinAPIs-0.2.0/ChinAPIs/inst/CITATION | 2 ChinAPIs-0.2.0/ChinAPIs/inst/doc/ChinAPIs_vignette.Rmd | 10 ChinAPIs-0.2.0/ChinAPIs/inst/doc/ChinAPIs_vignette.html | 18 - ChinAPIs-0.2.0/ChinAPIs/inst/licenses/LICENSE-APIs.txt | 9 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-COVID19_HongKong_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-bj_air_quality_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_admin_divisions_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_cars_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_corruption_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2002_122_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2005_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2007_135_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2010_41_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2012_139_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2015_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2017_149_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2017_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2018_153_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2018_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2020_153_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2020_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-chinese_cities_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-chinese_dams_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-family_name_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_child_mortality.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_cpi.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_energy_use.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_gdp.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_holidays.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_hospital_beds.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_life_expectancy.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_literacy_rate.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_population.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_unemployment.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-given_name_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-health_family_life_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_councillors_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_districts_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_population_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_street_names_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-panda_locations_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-population_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-sars_hong_kong_list.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-shanghai_factories_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-shanghai_pm25_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top1000name_prov_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top100name_year_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top50char_year_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-view_datasets_ChinAPIs.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-wenchuan_ptsd_matrix.R | 4 ChinAPIs-0.2.0/ChinAPIs/vignettes/ChinAPIs_vignette.Rmd | 10 74 files changed, 239 insertions(+), 245 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). The package and its workflows are described in Karl (2026) <doi:10.1016/j.chemolab.2026.105660>. Package code was drafted with assistance from generative [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.2.1 dated 2026-06-02 and 3.2.3 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 52 +++---- NEWS | 43 ++++- R/SVEMnet.R | 143 ++++++++++++++++++- R/bigexp.R | 51 ++++++- R/coef.R | 4 R/export_candidates_csv.R | 9 - R/glmnet_compat.R | 40 +++++ R/glmnet_with_cv.R | 223 +++++++++++++++---------------- R/select_candidates.R | 6 R/svem_random_table_multi.R | 26 ++- R/svem_score_random.R | 56 ++++++- R/svem_select_score_from_table.R | 28 +++ R/svem_significance_test_parallel.R | 79 +++++++++- inst/CITATION | 20 ++ man/SVEMnet-package.Rd | 4 man/SVEMnet.Rd | 66 ++++++++- man/bigexp_terms.Rd | 9 - man/glmnet_with_cv.Rd | 41 +++-- man/lipid_screen.Rd | 4 man/svem_nonzero.Rd | 4 man/svem_random_table_multi.Rd | 2 man/svem_score_random.Rd | 27 +++ man/svem_select_from_score_table.Rd | 22 ++- man/svem_significance_test_parallel.Rd | 21 +- tests/testthat/test-audit-fixes.R |only tests/testthat/test-complexity-edf.R |only tests/testthat/test-significance-tests.R | 50 +++++- 28 files changed, 779 insertions(+), 261 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently for maximum likelihood estimation and Bayesian posterior sampling. Users should preserve sufficient numerical precision when loading astronomical observation times; see the manual for details. Also see Hu and Tak (2020) <doi:10.48550/arXiv.2005.08049>.
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.2 dated 2020-09-08 and 1.0.3 dated 2026-07-02
DESCRIPTION | 20 - MD5 | 14 NAMESPACE | 4 R/drw.R | 961 +++++++++++++++++++++++---------------------------- man/Rdrw-internal.Rd | 2 man/Rdrw-package.Rd | 8 man/drw.Rd | 201 +++------- man/drw.sim.Rd | 49 +- 8 files changed, 544 insertions(+), 715 deletions(-)
Title: Degree-Day Phenology Calculator ('shiny' Application)
Description: Provides a 'shiny' application to compute daily and cumulative degree-days from minimum and maximum temperatures using average, single triangle, and single sine methods, with optional upper temperature thresholds. The application maps cumulative thermal accumulation to user-defined developmental stage thresholds and supports exporting tabular and graphical outputs. The degree-day approach follows assumptions described by Higley et al. (1986) <doi:10.1093/ee/15.5.999>.
Author: Victor Manuel Almaraz Valle [aut, cre] ,
J. Concepcion Rodriguez Maciel [aut],
Gustavo Ramirez Valverde [aut],
Jaime Alfredo Urzua Gutierrez [aut],
Manuel Alejandro Tejeda Reyes [aut]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between DegreeDayCalc versions 0.1.0 dated 2026-02-17 and 0.1.1 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 1 R/degree_days.R | 171 +++++++++++------------ R/zzz.R | 7 README.md | 16 -- inst/CITATION | 69 ++++----- inst/app/app.R | 245 +++++++++++++++++++++++---------- tests/testthat/test-degree-days-core.R | 32 ++++ 9 files changed, 350 insertions(+), 217 deletions(-)
Title: Store and Transfer Amplicon Sequence Data
Description: Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.
Author: Sarah Westcott [aut] ,
Gregory Johnson [aut] ,
Pat Schloss [cph, cre]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between strollur versions 0.1.2 dated 2026-06-24 and 0.1.3 dated 2026-07-02
DESCRIPTION | 8 MD5 | 106 +-- NAMESPACE | 1 NEWS.md | 13 R/RcppExports.R | 18 R/add.R | 40 - R/error_messages.R | 10 R/import_dataset.R | 20 R/load_dataset.R | 6 R/r6_strollur.R | 58 - R/read_mothur_oligos.R |only R/read_phyloseq.R | 2 R/read_qiime2.R | 6 R/report.R | 4 R/utils.R | 24 R/write_mothur.R | 13 README.md | 5 inst/doc/Accessing_Dataset.html | 17 inst/doc/Data_Transfers.html | 232 +++---- inst/doc/Example_Analysis_Across_Software_Tools.R | 2 inst/doc/Example_Analysis_Across_Software_Tools.Rmd | 2 inst/doc/Example_Analysis_Across_Software_Tools.html | 6 inst/doc/Functions_for_Package_Developers.html | 556 +++++++++---------- inst/doc/General_Importing.R | 3 inst/doc/General_Importing.Rmd | 5 inst/doc/General_Importing.html | 20 inst/doc/Importing_from_phyloseq.html | 8 inst/doc/Importing_from_qiime2.R | 2 inst/doc/Importing_from_qiime2.Rmd | 2 inst/doc/Importing_from_qiime2.html | 10 inst/extdata/miseq_sop.010.rds |only inst/extdata/miseq_sop.rds |binary inst/extdata/miseq_sop_table.010.rds |only inst/extdata/paired_read.oligos |only inst/include/strollur.h | 6 man/add.Rd | 11 man/read_mothur_oligos.Rd |only man/report.Rd | 4 man/strollur.Rd | 12 man/xdev_add_report.Rd | 13 man/xdev_report.Rd | 4 src/bintable.cpp | 2 src/dataset.cpp | 38 - src/rcpp_xint_xdev_functions.cpp | 55 + src/rcpp_xint_xdev_functions.h | 20 tests/testthat/_snaps/r6_strollur.md | 6 tests/testthat/test-import.R | 17 tests/testthat/test-is_equal.R | 2 tests/testthat/test-names.R | 2 tests/testthat/test-r6_strollur.R | 6 tests/testthat/test-read_mothur_oligos.R |only tests/testthat/test-save_load.R | 20 tests/testthat/test-write_mothur.R | 2 tests/testthat/test-xint-xdev.R | 2 vignettes/Example_Analysis_Across_Software_Tools.Rmd | 2 vignettes/General_Importing.Rmd | 5 vignettes/Importing_from_qiime2.Rmd | 2 57 files changed, 720 insertions(+), 710 deletions(-)
Title: 'shiny' Application for Life Table and Fertility Analysis
Description: Provides a 'shiny' application to construct age-specific life tables and fertility schedules from individual female daily egg records. The application computes age-specific survival and fertility functions and estimates key demographic parameters including the net reproductive rate, mean generation time, intrinsic rate of increase, finite rate of increase and doubling time. Optional confidence intervals can be obtained using percentile bootstrap or delete-1 jackknife resampling at the female level. Methods and definitions follow Stevens (2009) <doi:10.1007/978-0-387-89882-7> and Rossini et al. (2024) <doi:10.1371/journal.pone.0299598>.
Author: Victor Manuel Almaraz Valle [aut, cre]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between LifeTableFertility versions 0.1.0 dated 2026-02-17 and 0.1.1 dated 2026-07-02
DESCRIPTION | 12 +-- MD5 | 9 +- NAMESPACE | 3 R/imports.R |only inst/CITATION | 35 +++++------ inst/app/app.R | 181 +++++++++++++++++++++++++++------------------------------ 6 files changed, 116 insertions(+), 124 deletions(-)
More information about LifeTableFertility at CRAN
Permanent link
Title: Interactive 'shiny' Application for Constructing Life Tables
Description: Provides an interactive 'shiny' application to construct stage-structured life tables from tabular input data. The application includes input validation, demographic calculations, visualization tools, and export of tables and figures to support reproducible workflows in ecological and entomological studies. Methods for life table construction follow classical demographic approaches described in Martinez (2015) <doi:10.13140/RG.2.2.21333.65760>.
Author: Victor Manuel Almaraz Valle [aut, cre],
J. Concepcion Rodriguez Maciel [aut],
Gustavo Ramirez Valverde [aut],
Carlos Eduardo Aguilar Castillo [aut],
Alejandro Perez Panduro [aut]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between LifeTableBuilder versions 0.1.2 dated 2026-02-20 and 0.1.3 dated 2026-07-02
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- README.md | 2 +- inst/CITATION | 17 +++++++++-------- inst/shiny/app.R | 17 +++++++++++------ 5 files changed, 32 insertions(+), 26 deletions(-)
More information about LifeTableBuilder at CRAN
Permanent link
Title: Forest Many-Objective Robust Decision Making ('FoRDM')
Description: Forest Many-Objective Robust Decision Making ('FoRDM') is a R toolkit for supporting robust forest management under deep uncertainty.
It provides a forestry-focused application of Many-Objective Robust Decision Making ('MORDM') to forest simulation outputs,
enabling users to evaluate robustness using regret- and 'satisficing'-based measures. 'FoRDM' identifies robust solutions,
generates Pareto fronts, and offers interactive 2D, 3D, and parallel-coordinate visualizations.
Author: Marc Djahangard [aut, cre],
Rasoul Yousefpour [aut]
Maintainer: Marc Djahangard <marc.djahangard@ife.uni-freiburg.de>
Diff between FoRDM versions 1.0.2 dated 2026-04-07 and 1.0.3 dated 2026-07-02
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 8 +++----- R/FoRDM.R | 35 ++++++++++++++++++----------------- README.md | 2 +- inst/CITATION | 23 +++++++++++++++-------- 7 files changed, 50 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-19 1.0.0
2023-06-11 0.1.1
2023-05-30 0.1.0