Title: Local Partial Likelihood Estimation and Simultaneous Confidence
Band
Description: Local partial likelihood estimation by Fan, Lin and Zhou(2006)<doi:10.1214/009053605000000796> and simultaneous confidence band is a set of tools to test the covariates-biomarker interaction for survival data. Test for the covariates-biomarker interaction using the bootstrap method and the asymptotic method with simultaneous confidence band (Liu, Jiang and Chen (2015)<doi:10.1002/sim.6563>).
Author: Bingshu E. Chen [aut, cre],
Yicong Liu [aut],
Siwei Zhang [aut],
Teng Wen [aut],
Wenyu Jiang [aut]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Diff between lpl versions 0.15 dated 2026-09-12 and 0.16 dated 2026-09-16
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- R/lpl_basicFunctions.R | 2 +- R/lplb.R | 11 +---------- R/numScoreHess.R | 2 +- R/predict.lple.R | 2 +- R/rSurv.R | 5 +++-- R/rmst.R | 2 +- man/K_func.Rd |only man/asymSCB.Rd |only man/ibs.Rd | 1 + man/lplb.Rd | 3 +-- man/lple.Rd | 2 -- 13 files changed, 26 insertions(+), 34 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] ,
Kosuke Imai [aut] ,
Gary King [aut] ,
Elizabeth Stuart [aut] ,
Alex Whitworth [ctb],
Noah Greifer [cre, aut]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.7.2 dated 2025-05-30 and 4.8.0 dated 2026-09-16
MatchIt-4.7.2/MatchIt/R/zzz.R |only MatchIt-4.7.2/MatchIt/inst/include |only MatchIt-4.7.2/MatchIt/src/Makevars |only MatchIt-4.7.2/MatchIt/src/Makevars.win |only MatchIt-4.8.0/MatchIt/DESCRIPTION | 16 MatchIt-4.8.0/MatchIt/MD5 | 204 +++-- MatchIt-4.8.0/MatchIt/NAMESPACE | 18 MatchIt-4.8.0/MatchIt/NEWS.md | 107 +- MatchIt-4.8.0/MatchIt/R/RcppExports.R | 4 MatchIt-4.8.0/MatchIt/R/add_s.weights.R | 99 +- MatchIt-4.8.0/MatchIt/R/aux_functions.R | 147 ++- MatchIt-4.8.0/MatchIt/R/discard.R | 20 MatchIt-4.8.0/MatchIt/R/dist_functions.R | 29 MatchIt-4.8.0/MatchIt/R/distance2_methods.R | 134 ++- MatchIt-4.8.0/MatchIt/R/get_weights_from_mm.R | 8 MatchIt-4.8.0/MatchIt/R/get_weights_from_subclass.R | 61 - MatchIt-4.8.0/MatchIt/R/input_processing.R | 195 ++--- MatchIt-4.8.0/MatchIt/R/match.qoi.R | 31 MatchIt-4.8.0/MatchIt/R/match_data.R | 143 ++- MatchIt-4.8.0/MatchIt/R/matchit.R | 124 +-- MatchIt-4.8.0/MatchIt/R/matchit2cardinality.R | 311 ++++---- MatchIt-4.8.0/MatchIt/R/matchit2cem.R | 262 +++---- MatchIt-4.8.0/MatchIt/R/matchit2exact.R | 55 - MatchIt-4.8.0/MatchIt/R/matchit2full.R | 131 +-- MatchIt-4.8.0/MatchIt/R/matchit2genetic.R | 177 +--- MatchIt-4.8.0/MatchIt/R/matchit2nearest.R | 194 ++--- MatchIt-4.8.0/MatchIt/R/matchit2optimal.R | 148 +--- MatchIt-4.8.0/MatchIt/R/matchit2quick.R | 104 +- MatchIt-4.8.0/MatchIt/R/matchit2subclass.R | 157 +--- MatchIt-4.8.0/MatchIt/R/plot.matchit.R | 160 +--- MatchIt-4.8.0/MatchIt/R/plot.summary.matchit.R | 22 MatchIt-4.8.0/MatchIt/R/rbind.matchdata.R | 27 MatchIt-4.8.0/MatchIt/R/summary.matchit.R | 370 +++++----- MatchIt-4.8.0/MatchIt/R/utils.R | 295 +++---- MatchIt-4.8.0/MatchIt/build/stage23.rdb |binary MatchIt-4.8.0/MatchIt/build/vignette.rds |binary MatchIt-4.8.0/MatchIt/inst/doc/MatchIt.Rmd | 12 MatchIt-4.8.0/MatchIt/inst/doc/MatchIt.html | 20 MatchIt-4.8.0/MatchIt/inst/doc/assessing-balance.Rmd | 2 MatchIt-4.8.0/MatchIt/inst/doc/assessing-balance.html | 95 +- MatchIt-4.8.0/MatchIt/inst/doc/estimating-effects.Rmd | 10 MatchIt-4.8.0/MatchIt/inst/doc/estimating-effects.html | 88 +- MatchIt-4.8.0/MatchIt/inst/doc/matching-methods.Rmd | 8 MatchIt-4.8.0/MatchIt/inst/doc/matching-methods.html | 213 ++--- MatchIt-4.8.0/MatchIt/inst/doc/sampling-weights.Rmd | 46 - MatchIt-4.8.0/MatchIt/inst/doc/sampling-weights.html | 247 +++--- MatchIt-4.8.0/MatchIt/man/MatchIt-package.Rd | 1 MatchIt-4.8.0/MatchIt/man/add_s.weights.Rd | 6 MatchIt-4.8.0/MatchIt/man/distance.Rd | 16 MatchIt-4.8.0/MatchIt/man/figures/README-unnamed-chunk-5-1.png |binary MatchIt-4.8.0/MatchIt/man/macros/macros.Rd | 3 MatchIt-4.8.0/MatchIt/man/mahalanobis_dist.Rd | 2 MatchIt-4.8.0/MatchIt/man/match_data.Rd | 38 - MatchIt-4.8.0/MatchIt/man/matchit.Rd | 13 MatchIt-4.8.0/MatchIt/man/method_cardinality.Rd | 173 ++-- MatchIt-4.8.0/MatchIt/man/method_cem.Rd | 195 ++--- MatchIt-4.8.0/MatchIt/man/method_exact.Rd | 45 - MatchIt-4.8.0/MatchIt/man/method_full.Rd | 150 +--- MatchIt-4.8.0/MatchIt/man/method_genetic.Rd | 165 +--- MatchIt-4.8.0/MatchIt/man/method_nearest.Rd | 167 +--- MatchIt-4.8.0/MatchIt/man/method_optimal.Rd | 170 +--- MatchIt-4.8.0/MatchIt/man/method_quick.Rd | 100 -- MatchIt-4.8.0/MatchIt/man/method_subclass.Rd | 136 +-- MatchIt-4.8.0/MatchIt/man/plot.matchit.Rd | 5 MatchIt-4.8.0/MatchIt/man/summary.matchit.Rd | 13 MatchIt-4.8.0/MatchIt/src/RcppExports.cpp | 80 -- MatchIt-4.8.0/MatchIt/src/all_equal_to.cpp | 8 MatchIt-4.8.0/MatchIt/src/eucdistC.cpp | 18 MatchIt-4.8.0/MatchIt/src/get_splitsC.cpp | 18 MatchIt-4.8.0/MatchIt/src/has_n_unique.cpp | 21 MatchIt-4.8.0/MatchIt/src/internal.cpp | 325 +++----- MatchIt-4.8.0/MatchIt/src/internal.h | 234 +++--- MatchIt-4.8.0/MatchIt/src/nn_matchC_distmat.cpp | 83 +- MatchIt-4.8.0/MatchIt/src/nn_matchC_distmat_closest.cpp | 84 +- MatchIt-4.8.0/MatchIt/src/nn_matchC_mahcovs.cpp | 174 ++-- MatchIt-4.8.0/MatchIt/src/nn_matchC_mahcovs_closest.cpp | 141 +-- MatchIt-4.8.0/MatchIt/src/nn_matchC_vec.cpp | 134 +-- MatchIt-4.8.0/MatchIt/src/nn_matchC_vec_closest.cpp | 135 +-- MatchIt-4.8.0/MatchIt/src/pairdistC.cpp | 8 MatchIt-4.8.0/MatchIt/src/preprocess_matchC.cpp | 19 MatchIt-4.8.0/MatchIt/src/subclass2mm.cpp | 52 - MatchIt-4.8.0/MatchIt/src/subclass_scootC.cpp | 14 MatchIt-4.8.0/MatchIt/src/tabulateC.cpp | 3 MatchIt-4.8.0/MatchIt/src/weights_matrixC.cpp | 32 MatchIt-4.8.0/MatchIt/tests |only MatchIt-4.8.0/MatchIt/vignettes/MatchIt.Rmd | 12 MatchIt-4.8.0/MatchIt/vignettes/assessing-balance.Rmd | 2 MatchIt-4.8.0/MatchIt/vignettes/estimating-effects.Rmd | 10 MatchIt-4.8.0/MatchIt/vignettes/matching-methods.Rmd | 8 MatchIt-4.8.0/MatchIt/vignettes/sampling-weights.Rmd | 46 - 90 files changed, 3555 insertions(+), 3998 deletions(-)
Title: Generate Predicted Writing Quality Scores
Description: Imports variables from 'ReaderBench' (Dascalu et al.,
2018)<doi:10.1007/978-3-319-66610-5_48>, 'Coh-Metrix' (McNamara et
al., 2014)<doi:10.1017/CBO9780511894664>, and/or 'GAMET' (Crossley et
al., 2019) <doi:10.17239/jowr-2019.11.02.01> output files; downloads
predictive scoring models described in Mercer & Cannon
(2022)<doi:10.31244/jero.2022.01.03> and Mercer et
al.(2021)<doi:10.1177/0829573520987753>; and generates predicted
writing quality and curriculum-based measurement (McMaster & Espin,
2007)<doi:10.1177/00224669070410020301> scores.
Author: Sterett H. Mercer [aut, cre]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Diff between writeAlizer versions 1.7.3 dated 2026-02-17 and 1.7.4 dated 2026-09-16
DESCRIPTION | 14 MD5 | 88 - NAMESPACE | 22 NEWS.md | 20 R/artifact_registry.R | 294 ++--- R/cache.R | 61 - R/download.R | 48 R/file_utilities.R | 94 + R/model_deps.R | 21 R/predict_values.R | 185 ++- R/seed_example_helpers.R | 25 R/writeAlizer.R | 7 README.md | 143 +- build/vignette.rds |binary inst/CITATION | 4 inst/doc/scoring-model-development.Rmd | 71 - inst/doc/scoring-model-development.html | 335 +----- inst/doc/writealizer-getting-started.R | 31 inst/doc/writealizer-getting-started.Rmd | 448 ++++---- inst/doc/writealizer-getting-started.html | 1110 ++++++++++------------ man/import_coh.Rd | 4 man/import_gamet.Rd | 4 man/import_rb.Rd | 4 man/model_deps.Rd | 17 man/predict_quality.Rd | 49 man/preprocess.Rd | 10 man/wa_cache_clear.Rd | 20 man/wa_cache_dir.Rd | 17 man/wa_download.Rd | 49 man/wa_seed_example_models.Rd | 18 man/writeAlizer-package.Rd | 12 tests/testthat/setup-cache.R | 9 tests/testthat/setup-reset-options.R | 5 tests/testthat/test-audit-downloads.R |only tests/testthat/test-audit-inputs.R |only tests/testthat/test-audit-predictions.R |only tests/testthat/test-download-snapshots.R | 3 tests/testthat/test-download.R | 9 tests/testthat/test-helper-urls.R | 16 tests/testthat/test-integration-predict_quality.R | 1 tests/testthat/test-model-deps.R | 20 tests/testthat/test-predict-values-negative.R | 8 tests/testthat/test-preprocess-and-download.R | 4 vignettes/layout.css |only vignettes/references.bib | 5 vignettes/scoring-model-development.Rmd | 71 - vignettes/writealizer-getting-started.Rmd | 448 ++++---- 47 files changed, 1895 insertions(+), 1929 deletions(-)
Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data. Streams vector operations (spatial transforms,
point-in-polygon and nearest-feature joins including a two-sided
grid-partitioned join, select-by-location, clip, erase, dissolve,
'rasterization', 'polygonization', and contouring) through 'sf', and runs
raster operations (zonal statistics, focal windows, terrain derivatives,
resample or 'reproject' warp, polygon masking, map algebra, and 'mosaicking')
in native C or over the tiled '.vec' format, one batch or tile at [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.12.3 dated 2026-09-14 and 0.12.4 dated 2026-09-16
DESCRIPTION | 8 MD5 | 191 ++-- NAMESPACE | 426 ++++----- NEWS.md | 47 + R/index.R | 293 +++--- R/verbs.R | 2 R/write.R | 1013 +++++++++++----------- inst/doc/coverage-topology.html | 4 inst/doc/engine.Rmd | 1618 ++++++++++++++++++------------------ inst/doc/engine.html | 32 inst/doc/formats.html | 8 inst/doc/geometry-expressions.html | 4 inst/doc/indexing.html | 10 inst/doc/joins.html | 4 inst/doc/large-data.html | 4 inst/doc/networks.html | 4 inst/doc/offload.html | 4 inst/doc/quickstart.html | 4 inst/doc/schema.html | 4 inst/doc/sdm.html | 4 inst/doc/spatial.html | 4 inst/doc/streaming-spatial.html | 4 inst/doc/string-ops.html | 4 man/across.Rd | 66 - man/append_vtr.Rd | 199 ++-- man/arrange.Rd | 66 - man/bind_rows.Rd | 86 - man/block_fuzzy_lookup.Rd | 94 +- man/block_lookup.Rd | 78 - man/collect.Rd | 56 - man/count.Rd | 80 - man/create_index.Rd | 138 +-- man/cross_join.Rd | 66 - man/delete_vtr.Rd | 84 - man/desc.Rd | 48 - man/diff_vtr.Rd | 136 +-- man/distinct.Rd | 68 - man/explain.Rd | 52 - man/filter.Rd | 78 - man/floor_time.Rd | 66 - man/fuzzy_join.Rd | 100 +- man/glimpse.Rd | 58 - man/group_by.Rd | 52 - man/has_index.Rd | 62 - man/head.vectra_node.Rd | 42 man/kmer.Rd | 114 +- man/left_join.Rd | 184 ++-- man/link.Rd | 66 - man/lookup.Rd | 130 +- man/materialize.Rd | 66 - man/mutate.Rd | 76 - man/print.vectra_node.Rd | 38 man/pull.Rd | 52 - man/reframe.Rd | 54 - man/relocate.Rd | 60 - man/rename.Rd | 52 - man/rolling.Rd | 112 +- man/select.Rd | 52 - man/slice.Rd | 52 - man/slice_head.Rd | 112 +- man/spatial_overlay.Rd | 384 ++++---- man/summarise.Rd | 94 +- man/tbl.Rd | 52 - man/tbl_csv.Rd | 130 +- man/tbl_fasta.Rd | 98 +- man/tbl_fastq.Rd | 92 +- man/tbl_sqlite.Rd | 68 - man/tbl_tiff.Rd | 78 - man/tbl_xlsx.Rd | 74 - man/tiff_extract_points.Rd | 96 +- man/tiff_metadata.Rd | 56 - man/transmute.Rd | 52 - man/ungroup.Rd | 52 - man/vec_raster_layout.Rd | 38 man/vec_raster_times.Rd | 48 - man/vec_read_pixel_series.Rd | 92 +- man/vec_write_time_cube.Rd | 102 +- man/vectra_mem.Rd | 68 - man/vtr_schema.Rd | 90 +- man/write_csv.Rd | 62 - man/write_sqlite.Rd | 66 - man/write_tiff.Rd | 158 +-- man/write_vtr.Rd | 163 +-- src/init.c | 3 src/r_bridge.h | 3 src/r_bridge_index.c | 68 + src/scan.c | 24 src/tdc/VENDORED_FROM | 2 src/vtr1_tdc.c | 336 +++++-- src/vtr1_tdc.h | 59 + src/vtr_digest.h |only src/vtri.c | 128 +- src/vtri.h | 60 + tests/testthat/test-append-delete.R | 982 ++++++++++----------- tests/testthat/test-audit-tier3.R | 6 tests/testthat/test-index.R | 235 +++++ vignettes/engine.Rmd | 1618 ++++++++++++++++++------------------ 97 files changed, 6561 insertions(+), 5867 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 15. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood estimation" , Hammond (2021, <doi:10.2166/nh.2021.059>). "The FEH 2025 statistical method update", UK Centre for Ecology and Hydrology (2025). "Low flow es [...truncated...]
Author: Anthony Hammond [aut, cre],
Sam Clayton [ctb]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 2.0.2 dated 2026-06-19 and 2.15.0 dated 2026-09-16
DESCRIPTION | 29 ++++-- MD5 | 44 +++++----- R/AMPF.R | 4 R/All.R | 27 +++--- R/FlowAnalysis.R | 61 ++++++++------ R/GetData.R | 24 ++++- R/PeakFlowData.R | 4 R/ReFH.R | 7 - build/vignette.rds |binary data/AMPF.rda |binary data/PeakFlowData.rda |binary inst/doc/Data-input.R | 18 ++-- inst/doc/FEH-statistical-analysis.R | 14 +-- inst/doc/FEH-statistical-analysis.html | 32 +++---- inst/doc/ReFH-analysis.R | 12 +- inst/doc/ReFH-analysis.html | 139 ++++++++++++++++----------------- man/AMPF.Rd | 4 man/HistoricMLE.Rd | 4 man/LowFlows.Rd | 15 ++- man/PeakFlowData.Rd | 4 man/QMED_FEH08.Rd | 84 +++++++++---------- man/ReFH.Rd | 4 man/Seasonality.Rd | 4 23 files changed, 291 insertions(+), 243 deletions(-)
Title: n-Gram Text Regression, aka Concise Comparative Summarization
Description: Function for sparse regression on raw text, regressing a labeling
vector onto a feature space consisting of all possible phrases.
Author: Luke Miratrix [aut, cre]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>
Diff between textreg versions 0.1.5 dated 2018-10-04 and 0.1.6 dated 2026-09-16
textreg-0.1.5/textreg/man/build.corpus.Rd |only textreg-0.1.5/textreg/man/cpp_build.corpus.Rd |only textreg-0.1.5/textreg/man/cpp_textreg.Rd |only textreg-0.1.5/textreg/src/Makevars |only textreg-0.1.5/textreg/src/Makevars.win |only textreg-0.1.5/textreg/src/textreg_init.c |only textreg-0.1.5/textreg/tests/testthat/test-build.corpus.R |only textreg-0.1.6/textreg/DESCRIPTION | 20 textreg-0.1.6/textreg/MD5 | 113 +-- textreg-0.1.6/textreg/NAMESPACE | 4 textreg-0.1.6/textreg/R/RcppExports.R |only textreg-0.1.6/textreg/R/package_and_data_documentation.R | 22 textreg-0.1.6/textreg/R/prediction_code.R | 75 +- textreg-0.1.6/textreg/R/text_searching.R | 8 textreg-0.1.6/textreg/R/textreg.R | 231 ++----- textreg-0.1.6/textreg/build/vignette.rds |binary textreg-0.1.6/textreg/inst/doc/bathtub_vignette.R | 2 textreg-0.1.6/textreg/inst/doc/bathtub_vignette.pdf |binary textreg-0.1.6/textreg/man/bathtub.Rd | 7 textreg-0.1.6/textreg/man/calc.loss.Rd | 8 textreg-0.1.6/textreg/man/clean.text.Rd | 2 textreg-0.1.6/textreg/man/cluster.phrases.Rd | 19 textreg-0.1.6/textreg/man/convert.tm.to.character.Rd | 6 textreg-0.1.6/textreg/man/dirtyBathtub.Rd | 7 textreg-0.1.6/textreg/man/find.CV.C.Rd | 12 textreg-0.1.6/textreg/man/find.threshold.C.Rd | 28 textreg-0.1.6/textreg/man/grab.fragments.Rd | 10 textreg-0.1.6/textreg/man/is.fragment.sample.Rd | 5 textreg-0.1.6/textreg/man/is.textreg.corpus.Rd | 3 textreg-0.1.6/textreg/man/is.textreg.result.Rd | 7 textreg-0.1.6/textreg/man/list.table.chart.Rd | 20 textreg-0.1.6/textreg/man/make.appearance.matrix.Rd | 7 textreg-0.1.6/textreg/man/make.count.table.Rd | 5 textreg-0.1.6/textreg/man/make.list.table.Rd | 11 textreg-0.1.6/textreg/man/make.path.matrix.Rd | 5 textreg-0.1.6/textreg/man/make.phrase.correlation.chart.Rd | 16 textreg-0.1.6/textreg/man/make.phrase.matrix.Rd | 13 textreg-0.1.6/textreg/man/make.similarity.matrix.Rd | 7 textreg-0.1.6/textreg/man/path.matrix.chart.Rd | 8 textreg-0.1.6/textreg/man/phrase.count.Rd | 5 textreg-0.1.6/textreg/man/phrases.Rd | 7 textreg-0.1.6/textreg/man/plot.textreg.result.Rd | 5 textreg-0.1.6/textreg/man/predict.textreg.result.Rd | 7 textreg-0.1.6/textreg/man/print.fragment.sample.Rd | 5 textreg-0.1.6/textreg/man/print.textreg.corpus.Rd | 3 textreg-0.1.6/textreg/man/print.textreg.result.Rd | 7 textreg-0.1.6/textreg/man/refit.model.Rd |only textreg-0.1.6/textreg/man/reformat.textreg.model.Rd | 6 textreg-0.1.6/textreg/man/sample.fragments.Rd | 16 textreg-0.1.6/textreg/man/testCorpora.Rd | 4 textreg-0.1.6/textreg/man/textreg-package.Rd | 12 textreg-0.1.6/textreg/man/textreg.Rd | 31 textreg-0.1.6/textreg/man/tm_gregexpr.Rd | 10 textreg-0.1.6/textreg/src/RcppExports.cpp |only textreg-0.1.6/textreg/src/textreg.cpp | 326 ++-------- textreg-0.1.6/textreg/tests/testthat.R |only textreg-0.1.6/textreg/tests/testthat/Rplots.pdf |binary textreg-0.1.6/textreg/tests/testthat/test-make-word-lists.R | 83 +- textreg-0.1.6/textreg/tests/testthat/test-ngram-call-basics.R | 4 textreg-0.1.6/textreg/tests/testthat/test-prediction.R | 80 +- textreg-0.1.6/textreg/tests/testthat/test-tm-compatability.R | 12 textreg-0.1.6/textreg/tests/testthat/test-various-regressions.R | 4 textreg-0.1.6/textreg/tests/testthat/test-zero-labeling-and-text-files.R | 19 63 files changed, 625 insertions(+), 702 deletions(-)
Title: Structure Parameter Inference Approach
Description: SPINA (Structure Parameter Inference Approach) is a methodology to calculate constant structure parameters of endocrine homeostatic systems from steady-state hormone and metabolite concentrations. Methods and equations for thyroid homeostasis (SPINA Thyr) have been described in Dietrich et al. (2012) <doi:10.1155/2012/351864> and Dietrich et al. (2016) <doi:10.3389/fendo.2016.00057>, and for glucose homeostasis (SPINA Carb) in Dietrich et al. (2022) <doi:10.1038/s41598-022-22531-3> and Dietrich et al. (2024) <doi:10.1111/1753-0407.13525>.
Author: Johannes W. Dietrich [aut, cph, cre] ,
Eleni Karamitrou [ctb] ,
Bernhard O. Boehm [ctb]
Maintainer: Johannes W. Dietrich <johannes.dietrich@ruhr-uni-bochum.de>
Diff between SPINA versions 4.1.0 dated 2018-03-21 and 5.1.0 dated 2026-09-16
SPINA-4.1.0/SPINA/R/SPINA.r |only SPINA-4.1.0/SPINA/data/pilo.csv.gz |only SPINA-4.1.0/SPINA/inst/COPYRIGHTS |only SPINA-4.1.0/SPINA/man/pilo.Rd |only SPINA-5.1.0/SPINA/DESCRIPTION | 36 ++++++++++++----- SPINA-5.1.0/SPINA/LICENSE | 6 +- SPINA-5.1.0/SPINA/MD5 | 62 +++++++++++++++++++---------- SPINA-5.1.0/SPINA/NAMESPACE | 23 ++++++++++ SPINA-5.1.0/SPINA/R/SPINA-package.R |only SPINA-5.1.0/SPINA/R/spina_functions.R |only SPINA-5.1.0/SPINA/README.md |only SPINA-5.1.0/SPINA/build |only SPINA-5.1.0/SPINA/data/Pilo.rda |only SPINA-5.1.0/SPINA/data/Vellore.rda |only SPINA-5.1.0/SPINA/inst/CITATION | 22 ++++------ SPINA-5.1.0/SPINA/inst/doc |only SPINA-5.1.0/SPINA/man/HOMA.Beta.Rd |only SPINA-5.1.0/SPINA/man/HOMA.IR.Rd |only SPINA-5.1.0/SPINA/man/HOMA.IS.Rd |only SPINA-5.1.0/SPINA/man/Pilo.Rd |only SPINA-5.1.0/SPINA/man/QUICKI.Rd |only SPINA-5.1.0/SPINA/man/SPINA-package.Rd |only SPINA-5.1.0/SPINA/man/SPINA.DI.Rd |only SPINA-5.1.0/SPINA/man/SPINA.GBeta.Rd |only SPINA-5.1.0/SPINA/man/SPINA.GD.Rd | 55 ++++++++++++++------------ SPINA-5.1.0/SPINA/man/SPINA.GDTT.Rd | 47 ++++++++++++++-------- SPINA-5.1.0/SPINA/man/SPINA.GR.Rd |only SPINA-5.1.0/SPINA/man/SPINA.GT.Rd | 55 ++++++++++++++------------ SPINA-5.1.0/SPINA/man/SPINA.GTT.Rd | 55 ++++++++++++++------------ SPINA-5.1.0/SPINA/man/SPINA.sGD.Rd | 64 +++++++++++++++++------------- SPINA-5.1.0/SPINA/man/Vellore.Rd |only SPINA-5.1.0/SPINA/man/estimated.GD.Rd | 56 +++++++++++++++----------- SPINA-5.1.0/SPINA/man/estimated.GDTT.Rd | 48 +++++++++++++++------- SPINA-5.1.0/SPINA/man/estimated.GT.Rd | 56 +++++++++++++++----------- SPINA-5.1.0/SPINA/man/estimated.GTT.Rd | 56 +++++++++++++++----------- SPINA-5.1.0/SPINA/man/estimated.TSHI.Rd | 54 +++++++++++++------------ SPINA-5.1.0/SPINA/man/estimated.TTSI.Rd | 58 +++++++++++++++------------ SPINA-5.1.0/SPINA/man/estimated.sGD.Rd | 65 +++++++++++++++++-------------- SPINA-5.1.0/SPINA/man/estimated.sTSHI.Rd | 62 +++++++++++++++-------------- SPINA-5.1.0/SPINA/man/figures |only SPINA-5.1.0/SPINA/tests |only SPINA-5.1.0/SPINA/vignettes |only 42 files changed, 521 insertions(+), 359 deletions(-)
Title: Ensemble Validation and Ranking of Clustering Methods
Description: Provides methods for evaluating and comparing clustering results, with an emphasis on sample-level clustering where observations are treated as the units being clustered and perturbation is performed by removing samples. The package implements internal, stability, and external validation measures and supports the comparison and ranking of clustering procedures across tuning parameter choices. It is conceptually related to the 'clValid' package, which assesses clustering stability by perturbing features; in contrast, this package focuses on perturbing the samples being clustered, making the validation framework suitable for applications such as single-cell clustering where samples or cells are the primary units of interest. Methods are based in part on Visser and Datta (2025) <doi:10.1002/sim.70331>.
Author: Owen Visser [aut, cre],
Somnath Datta [aut, ctb],
Justina Zurauskienė [ctb] ,
Christopher Yau [ctb]
Maintainer: Owen Visser <owviss@gmail.com>
Diff between sclValid versions 0.1.0 dated 2026-09-12 and 0.1.1 dated 2026-09-16
DESCRIPTION | 14 +++++++++---- MD5 | 7 +++--- NEWS.md |only README.md | 49 ++++++++++++++++++++++++++++++++++++++++++++---- man/sclValid-package.Rd | 3 +- 5 files changed, 61 insertions(+), 12 deletions(-)
Title: Fast, Robust Clustering Algorithms for Gene Enrichment Data
Description: Clusters functionally related biological terms from gene set
enrichment results. Terms are compared by the overlap of their gene
sets using Cohen's kappa, the Jaccard index, or the Dice coefficient,
and the resulting similarity matrix is grouped either by agglomerative
hierarchical clustering with single, complete, average, or Ward
linkage, or by the seed-and-merge procedure of the 'DAVID' functional
classification tool. The distance and clustering routines are written
in 'C++' for speed. The methods are described in Huang et al. (2007)
<doi:10.1186/gb-2007-8-9-r183>, Ward (1963)
<doi:10.1080/01621459.1963.10500845>, Cohen (1960)
<doi:10.1177/001316446002000104>, and Jaccard (1912)
<doi:10.1111/j.1469-8137.1912.tb05611.x>.
Author: Junguk Hur [aut, cre] ,
Sarah Hong [aut],
Jane Kim [aut]
Maintainer: Junguk Hur <hurlabshared@gmail.com>
Diff between richCluster versions 1.0.2 dated 2025-12-18 and 2.0.0 dated 2026-09-16
DESCRIPTION | 30 MD5 | 134 NEWS.md |only R/RcppExports.R | 26 R/bars.R | 55 R/cluster.R | 276 + R/cluster_correlation.R | 66 R/compare_network_graphs_plotly.R | 16 R/david_cluster.R | 129 R/dots.R | 55 R/export_df.R | 10 R/full_network.R | 16 R/gene_lists.R |only R/hmaps.R | 125 R/merge_enrichment_results.R | 210 R/plot_network_graph.R | 35 build/vignette.rds |binary inst/doc/workflow.R | 124 inst/doc/workflow.html | 4991 ++++++++++------------- inst/extdata/cluster_result.rds |binary man/cluster.Rd | 118 man/cluster_correlation_hmap.Rd | 13 man/cluster_hmap.Rd | 34 man/cluster_network.Rd | 15 man/compare_network_graphs_plotly.Rd | 11 man/david_cluster.Rd | 33 man/export_df.Rd | 11 man/filter_clusters.Rd | 14 man/full_network.Rd | 8 man/merge_enrichment_results.Rd | 37 man/plot_network_graph.Rd | 16 man/richCluster-package.Rd | 1 man/runRichCluster.Rd | 60 man/term_bar.Rd | 5 man/term_dot.Rd | 5 man/term_hmap.Rd | 49 src/ClusterList.cpp | 21 src/ClusterList.h | 13 src/DavidClustering.cpp | 194 src/DavidClustering.h | 26 src/DistanceMatrix.cpp | 35 src/DistanceMatrix.h | 9 src/DistanceMetric.cpp | 105 src/DistanceMetric.h | 2 src/LinkageMethod.cpp | 281 + src/LinkageMethod.h | 4 src/RcppExports.cpp | 37 src/RichCluster.cpp | 248 - src/RichCluster.h | 22 src/StringUtils.cpp | 49 src/StringUtils.h | 11 tests/testthat/helper-artifacts.R |only tests/testthat/helper-characterization.R |only tests/testthat/helper-data.R | 9 tests/testthat/helper-fixture.R |only tests/testthat/helper-oracle.R |only tests/testthat/helper-t3-02.R |only tests/testthat/helper-t3-04a.R |only tests/testthat/review-ledger.csv |only tests/testthat/test-c12-canonical-merge-order.R |only tests/testthat/test-c9-canonical-order.R |only tests/testthat/test-cluster.R | 4 tests/testthat/test-cpp-entry-guards.R |only tests/testthat/test-cpp-units.R |only tests/testthat/test-david-fixed-point.R |only tests/testthat/test-david-kappa-matrix.R |only tests/testthat/test-david-validation.R |only tests/testthat/test-fixture-generation.R |only tests/testthat/test-input-hygiene.R |only tests/testthat/test-instrument-contracts.R |only tests/testthat/test-kappa-oracle.R |only tests/testthat/test-merge-enrichment-results.R |only tests/testthat/test-news-disclosure.R |only tests/testthat/test-od7-na-gene-lists.R |only tests/testthat/test-order-invariance.R |only tests/testthat/test-plot-guards.R |only tests/testthat/test-rc010-plotting.R |only tests/testthat/test-return-doc-contract.R |only tests/testthat/test-review-gate.R |only tests/testthat/test-shipped-numeric-regression.R |only tests/testthat/test-t002-denominator.R |only tests/testthat/test-t006-gene-delim.R |only tests/testthat/test-t107-diagonal.R |only tests/testthat/test-t117-filter-on.R |only tests/testthat/test-verbose-flag.R |only 85 files changed, 4706 insertions(+), 3092 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut],
Milan Bouchet-Valat [aut],
Manuel Munoz-Marquez [aut, cre],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ct [...truncated...]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between Rcmdr versions 2.13.0 dated 2026-06-19 and 2.14.1 dated 2026-09-16
DESCRIPTION | 12 MD5 | 43 +-- NEWS | 5 R/Rcmdr-internal.R | 2 R/Rcmdr-package.R | 4 R/commander.R | 1 R/file-menu.R | 52 +++- R/globals.R | 2 R/startup.R | 14 + inst/doc/Commander-ru.Rnw | 2 inst/doc/Commander-ru.pdf |binary inst/doc/Empezando-con-Rcmdr-es.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr-ko.pdf |binary inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary man/Commander-es.Rd | 11 man/Commander.Rd | 4 man/Options.Rd |only man/Rcmdr-package.Rd | 4 po/R-Rcmdr.pot | 14 - po/R-es.po | 312 ++++++++++--------------- vignettes/Commander-ru.Rnw | 2 23 files changed, 236 insertions(+), 248 deletions(-)
Title: Create a 'Quarto' Blog Post
Description: Provides an interactive 'RStudio' dialog for creating 'Quarto' blog posts with correctly structured YAML front matter. The dialog collects title, author, date, categories, and other metadata, then scaffolds the post directory, creates the 'index.qmd' file, and optionally copies an image. A companion function appends COinS (ContextObjects in Spans) metadata to posts for automatic bibliographic import into reference managers such as 'Zotero'.
Author: Peter Baumgartner [aut, cre, cph]
Maintainer: Peter Baumgartner <petzi53@gmail.com>
Diff between qpost versions 1.0.0 dated 2026-09-12 and 1.1.0 dated 2026-09-16
DESCRIPTION | 6 ++-- MD5 | 30 +++++++++++++---------- NAMESPACE | 1 NEWS.md | 43 +++++++++++++++++++++++++++++++++ R/coins_generation.R | 28 +++++++++++++++++---- R/edit_post.R |only R/get_args.R | 52 +++++++++++++++++++++++++++++++--------- R/utils.R | 32 ++++++++++++++++-------- README.md | 2 - inst/doc/add-coins.html | 4 +-- inst/doc/qpost.html | 4 +-- inst/doc/quarto-blog-posts.html | 4 +-- inst/rstudio/addins.dcf | 5 +++ man/add_coins.Rd | 3 +- man/edit_post.Rd |only man/figures/logo.png |only tests/testthat/test-edit-post.R |only tests/testthat/test-utils.R | 18 +++++++++++++ 18 files changed, 181 insertions(+), 51 deletions(-)
Title: Generalized Principal Component Analysis
Description: Generalized PCA and related matrix decompositions in weighted
inner-product spaces. Methods are based on Allen, G. I., Grosenick, L.,
and Taylor, J. (2014) <doi:10.1080/01621459.2013.852978>, "A generalized
least-square matrix decomposition", Journal of the American Statistical
Association, 109(505), 145-159; and Abdi, H. (2007), "Singular value
decomposition (SVD) and generalized singular value decomposition"
<https://personal.utdallas.edu/~herve/Abdi-SVD2007-pretty.pdf>, in
"Encyclopedia of Measurement and Statistics", 907-912.
Author: Brad Buchsbaum [aut, cre, cph]
Maintainer: Brad Buchsbaum <brad.buchsbaum@gmail.com>
Diff between genpca versions 0.2.0 dated 2026-09-15 and 0.2.1 dated 2026-09-16
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ R/mnpca_mrl.R | 5 ++++- inst/doc/gpca-scale.html | 4 ++-- 5 files changed, 22 insertions(+), 10 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Idris A. Eckley [aut],
Paul Fearnhead [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.9 dated 2026-07-23 and 0.1.10 dated 2026-09-16
DESCRIPTION | 12 - MD5 | 41 +++--- NAMESPACE | 22 +++ R/RcppExports.R | 175 +++++++++++++++------------- R/methods.R |only R/zzz.R |only README.md | 32 ++--- man/detector_candidates.Rd | 10 - man/detector_cands_len.Rd | 4 man/detector_create.Rd | 54 +++++--- man/detector_info_n.Rd | 4 man/detector_info_sn.Rd | 4 man/detector_update.Rd | 27 ++-- man/focus-methods.Rd |only man/focus-package.Rd | 6 man/focus_offline.Rd | 23 +-- man/generate_projection_indexes.Rd | 2 man/get_statistics.Rd | 47 +++---- src/ARpInfo.h | 4 src/CostsArp.h | 6 src/focus_ARp.cpp | 5 src/focus_rcpp_module.cpp | 230 ++++++++++++++++++++----------------- tests/testthat/test-generic.R | 90 ++++++++++++++ 23 files changed, 479 insertions(+), 319 deletions(-)
Title: Nonlinear Least Squares Estimation for Emax Regression Models
Description: Provides estimation and covariate selection tools for Emax
regression models using nonlinear least squares methods. Supported
optimisation algorithms are Gauss-Newton, Levenberg-Marquardt, and
the port library for bounded optimisation. The package also provides
tools to assist in simulation work using Emax regression.
Author: Danielle Navarro [aut, cre]
Maintainer: Danielle Navarro <djnavarro@protonmail.com>
Diff between emaxnls versions 0.1.1 dated 2026-06-30 and 0.2.0 dated 2026-09-16
emaxnls-0.1.1/emaxnls/man/anova.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/deviance.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/df.residual.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/fitted.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/logLik.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/predict.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/print.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/residuals.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/simulate.emaxnls.Rd |only emaxnls-0.1.1/emaxnls/man/summary.emaxnls.Rd |only emaxnls-0.2.0/emaxnls/DESCRIPTION | 24 emaxnls-0.2.0/emaxnls/MD5 | 134 + emaxnls-0.2.0/emaxnls/NAMESPACE | 17 emaxnls-0.2.0/emaxnls/NEWS.md | 244 +++ emaxnls-0.2.0/emaxnls/R/api.R | 599 +++++-- emaxnls-0.2.0/emaxnls/R/data.R | 98 - emaxnls-0.2.0/emaxnls/R/emaxlogistic-class.R |only emaxnls-0.2.0/emaxnls/R/emaxlogistic-init.R |only emaxnls-0.2.0/emaxnls/R/emaxlogistic-methods.R |only emaxnls-0.2.0/emaxnls/R/emaxlogistic-options.R |only emaxnls-0.2.0/emaxnls/R/emaxlogistic-printing.R |only emaxnls-0.2.0/emaxnls/R/emaxnls-class.R | 92 - emaxnls-0.2.0/emaxnls/R/emaxnls-init.R | 34 emaxnls-0.2.0/emaxnls/R/emaxnls-methods.R | 760 +++++++--- emaxnls-0.2.0/emaxnls/R/emaxnls-options.R | 12 emaxnls-0.2.0/emaxnls/R/emaxnls-predict.R | 14 emaxnls-0.2.0/emaxnls/R/emaxnls-printing.R | 360 ++++ emaxnls-0.2.0/emaxnls/R/emaxnls-scm.R | 102 - emaxnls-0.2.0/emaxnls/R/emaxnls-simulate.R | 20 emaxnls-0.2.0/emaxnls/R/emaxnls-update.R | 37 emaxnls-0.2.0/emaxnls/R/er-methods.R |only emaxnls-0.2.0/emaxnls/R/utils-accessors.R | 4 emaxnls-0.2.0/emaxnls/R/utils-adverbs.R | 5 emaxnls-0.2.0/emaxnls/R/utils-globals.R | 3 emaxnls-0.2.0/emaxnls/R/utils-mvtnorm.R |only emaxnls-0.2.0/emaxnls/R/utils-tibble.R | 21 emaxnls-0.2.0/emaxnls/R/utils-validators.R | 52 emaxnls-0.2.0/emaxnls/README.md | 384 +++-- emaxnls-0.2.0/emaxnls/inst/WORDLIST | 67 emaxnls-0.2.0/emaxnls/man/AIC.Rd | 57 emaxnls-0.2.0/emaxnls/man/anova.Rd |only emaxnls-0.2.0/emaxnls/man/coef.emaxnls.Rd | 37 emaxnls-0.2.0/emaxnls/man/confint.emaxnls.Rd | 81 - emaxnls-0.2.0/emaxnls/man/deviance.Rd |only emaxnls-0.2.0/emaxnls/man/df.residual.Rd |only emaxnls-0.2.0/emaxnls/man/emax_converged.Rd | 33 emaxnls-0.2.0/emaxnls/man/emax_df.Rd | 2 emaxnls-0.2.0/emaxnls/man/emax_fun.Rd | 97 - emaxnls-0.2.0/emaxnls/man/emax_logistic.Rd |only emaxnls-0.2.0/emaxnls/man/emax_logistic_init.Rd |only emaxnls-0.2.0/emaxnls/man/emax_logistic_options.Rd |only emaxnls-0.2.0/emaxnls/man/emax_nls.Rd | 81 - emaxnls-0.2.0/emaxnls/man/emax_nls_init.Rd | 33 emaxnls-0.2.0/emaxnls/man/emax_nls_options.Rd | 45 emaxnls-0.2.0/emaxnls/man/emax_scm.Rd | 135 + emaxnls-0.2.0/emaxnls/man/emax_update.Rd | 17 emaxnls-0.2.0/emaxnls/man/fitted.Rd |only emaxnls-0.2.0/emaxnls/man/logLik.Rd |only emaxnls-0.2.0/emaxnls/man/nobs.emaxnls.Rd | 31 emaxnls-0.2.0/emaxnls/man/predict.Rd |only emaxnls-0.2.0/emaxnls/man/print.Rd |only emaxnls-0.2.0/emaxnls/man/residuals.Rd |only emaxnls-0.2.0/emaxnls/man/sigma.emaxnls.Rd | 17 emaxnls-0.2.0/emaxnls/man/simulate.Rd |only emaxnls-0.2.0/emaxnls/man/summary.Rd |only emaxnls-0.2.0/emaxnls/man/vcov.emaxnls.Rd | 30 emaxnls-0.2.0/emaxnls/tests/testthat/helper-platform.R | 72 emaxnls-0.2.0/emaxnls/tests/testthat/test-api.R | 131 + emaxnls-0.2.0/emaxnls/tests/testthat/test-data.R | 6 emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxlogistic-class.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxlogistic-init.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxlogistic-methods.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxlogistic-printing.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxnls-class.R | 12 emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxnls-guess.R | 25 emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxnls-predict.R | 44 emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxnls-printing.R | 142 + emaxnls-0.2.0/emaxnls/tests/testthat/test-emaxnls-simulate.R | 231 ++- emaxnls-0.2.0/emaxnls/tests/testthat/test-er-methods.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-max-time.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-methods.R | 108 + emaxnls-0.2.0/emaxnls/tests/testthat/test-optim-method.R | 210 +- emaxnls-0.2.0/emaxnls/tests/testthat/test-parameter-recovery.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-scm.R | 148 + emaxnls-0.2.0/emaxnls/tests/testthat/test-update.R | 3 emaxnls-0.2.0/emaxnls/tests/testthat/test-utils-mvtnorm.R |only emaxnls-0.2.0/emaxnls/tests/testthat/test-utils-tibble.R | 17 87 files changed, 3671 insertions(+), 1257 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.6.1 dated 2026-08-22 and 1.7.1 dated 2026-09-16
couplr-1.6.1/couplr/R/trace_orlin.R |only couplr-1.6.1/couplr/src/solvers/orlin_ahuja |only couplr-1.6.1/couplr/tests/testthat/test-assignment-orlin.R |only couplr-1.7.1/couplr/DESCRIPTION | 8 couplr-1.7.1/couplr/MD5 | 256 couplr-1.7.1/couplr/NAMESPACE | 54 couplr-1.7.1/couplr/NEWS.md | 3178 +++++----- couplr-1.7.1/couplr/R/RcppExports.R | 56 couplr-1.7.1/couplr/R/flow_model.R | 9 couplr-1.7.1/couplr/R/lap_certify.R | 138 couplr-1.7.1/couplr/R/lap_dispatch.R | 25 couplr-1.7.1/couplr/R/lap_implicit.R | 41 couplr-1.7.1/couplr/R/lap_solve.R | 2750 ++++---- couplr-1.7.1/couplr/R/lap_status.R | 7 couplr-1.7.1/couplr/R/matching_balance_flow.R | 78 couplr-1.7.1/couplr/R/matching_cardinality.R | 24 couplr-1.7.1/couplr/R/matching_cardinality_exact.R | 217 couplr-1.7.1/couplr/R/matching_core.R | 2795 ++++---- couplr-1.7.1/couplr/R/matching_distance.R | 38 couplr-1.7.1/couplr/R/matching_full.R | 301 couplr-1.7.1/couplr/R/matching_lazy.R | 102 couplr-1.7.1/couplr/R/matching_memory.R | 75 couplr-1.7.1/couplr/R/matching_path.R | 37 couplr-1.7.1/couplr/R/trace_auction_scaled.R | 30 couplr-1.7.1/couplr/R/trace_csa.R | 36 couplr-1.7.1/couplr/R/trace_network_simplex.R | 2 couplr-1.7.1/couplr/R/trace_sap_dense.R |only couplr-1.7.1/couplr/R/utils.R | 3 couplr-1.7.1/couplr/build/partial.rdb |binary couplr-1.7.1/couplr/build/vignette.rds |binary couplr-1.7.1/couplr/inst/doc/algorithms.R | 21 couplr-1.7.1/couplr/inst/doc/algorithms.Rmd | 2482 +++---- couplr-1.7.1/couplr/inst/doc/algorithms.html | 188 couplr-1.7.1/couplr/inst/doc/comparison.Rmd | 4 couplr-1.7.1/couplr/inst/doc/comparison.html | 17 couplr-1.7.1/couplr/inst/doc/getting-started.Rmd | 2 couplr-1.7.1/couplr/inst/doc/getting-started.html | 20 couplr-1.7.1/couplr/inst/doc/matching-workflows.html | 28 couplr-1.7.1/couplr/inst/doc/pixel-morphing.html | 4 couplr-1.7.1/couplr/inst/doc/troubleshooting.html | 6 couplr-1.7.1/couplr/man/assignment.Rd | 107 couplr-1.7.1/couplr/man/build_cost_matrix.Rd | 15 couplr-1.7.1/couplr/man/cardinality_match.Rd | 13 couplr-1.7.1/couplr/man/dot-balance_flow_problem.Rd | 4 couplr-1.7.1/couplr/man/dot-couples_from_distance.Rd | 2 couplr-1.7.1/couplr/man/dot-couples_replace.Rd | 4 couplr-1.7.1/couplr/man/estimate_dense_matrix_mb.Rd | 33 couplr-1.7.1/couplr/man/estimate_dense_solve_mb.Rd |only couplr-1.7.1/couplr/man/full_match.Rd | 68 couplr-1.7.1/couplr/man/lazy_cost_spec_inv_cov.Rd | 4 couplr-1.7.1/couplr/man/lazy_pair_distances.Rd | 18 couplr-1.7.1/couplr/man/match_couples.Rd | 40 couplr-1.7.1/couplr/man/match_couples_from_distance.Rd | 3 couplr-1.7.1/couplr/man/match_path.Rd | 4 couplr-1.7.1/couplr/man/resolve_memory_mode.Rd | 4 couplr-1.7.1/couplr/man/solver_status_values.Rd | 2 couplr-1.7.1/couplr/man/verify_assignment.Rd | 113 couplr-1.7.1/couplr/man/verify_flow.Rd | 9 couplr-1.7.1/couplr/src/Makevars | 10 couplr-1.7.1/couplr/src/Makevars.win | 10 couplr-1.7.1/couplr/src/RcppExports.cpp | 230 couplr-1.7.1/couplr/src/core/lap_callback_source.h |only couplr-1.7.1/couplr/src/core/lap_certify.h | 274 couplr-1.7.1/couplr/src/core/lap_certify_rcpp.cpp | 52 couplr-1.7.1/couplr/src/core/lap_eps_repair.h |only couplr-1.7.1/couplr/src/core/lap_exact.h |only couplr-1.7.1/couplr/src/core/lap_hall_rcpp.cpp | 8 couplr-1.7.1/couplr/src/core/lap_internal.h | 8 couplr-1.7.1/couplr/src/core/lap_lazy_types.h | 9 couplr-1.7.1/couplr/src/core/lap_types.h | 46 couplr-1.7.1/couplr/src/core/lap_utils_rcpp.cpp | 142 couplr-1.7.1/couplr/src/core/lap_utils_rcpp.h | 41 couplr-1.7.1/couplr/src/flow/flow_balltree.h | 386 + couplr-1.7.1/couplr/src/flow/flow_compile.cpp | 92 couplr-1.7.1/couplr/src/flow/flow_compile.h | 32 couplr-1.7.1/couplr/src/flow/flow_implicit.h | 840 ++ couplr-1.7.1/couplr/src/flow/flow_implicit_rcpp.cpp | 281 couplr-1.7.1/couplr/src/flow/flow_path.h | 5 couplr-1.7.1/couplr/src/flow/flow_path_rcpp.cpp | 49 couplr-1.7.1/couplr/src/flow/flow_pricing.h | 11 couplr-1.7.1/couplr/src/flow/flow_rcpp.cpp | 190 couplr-1.7.1/couplr/src/flow/flow_row_search.h | 11 couplr-1.7.1/couplr/src/flow/flow_solve.cpp | 121 couplr-1.7.1/couplr/src/flow/flow_tree_nearest.h | 8 couplr-1.7.1/couplr/src/flow/flow_tree_pricing.h | 44 couplr-1.7.1/couplr/src/rcpp_interface.cpp | 157 couplr-1.7.1/couplr/src/solvers/jv_core.cpp | 303 couplr-1.7.1/couplr/src/solvers/jv_core_impl.h |only couplr-1.7.1/couplr/src/solvers/sap_dense |only couplr-1.7.1/couplr/src/solvers/solve_auction.cpp | 299 couplr-1.7.1/couplr/src/solvers/solve_auction.h | 34 couplr-1.7.1/couplr/src/solvers/solve_auction_core.h |only couplr-1.7.1/couplr/src/solvers/solve_auction_lazy_rcpp.cpp | 25 couplr-1.7.1/couplr/src/solvers/solve_csa.cpp | 220 couplr-1.7.1/couplr/src/solvers/solve_csa.h | 22 couplr-1.7.1/couplr/src/solvers/solve_jv_duals.cpp | 82 couplr-1.7.1/couplr/src/solvers/solve_jv_duals_impl.h |only couplr-1.7.1/couplr/src/solvers/solve_jv_duals_lazy_rcpp.cpp | 29 couplr-1.7.1/couplr/src/solvers/solve_jv_lazy_rcpp.cpp | 29 couplr-1.7.1/couplr/tests/testthat/helper-certify.R | 2 couplr-1.7.1/couplr/tests/testthat/test-assignment-auction.R | 194 couplr-1.7.1/couplr/tests/testthat/test-assignment-lapmod.R | 476 - couplr-1.7.1/couplr/tests/testthat/test-assignment-lazy.R | 18 couplr-1.7.1/couplr/tests/testthat/test-assignment-sap-dense.R |only couplr-1.7.1/couplr/tests/testthat/test-cardinality-implicit.R |only couplr-1.7.1/couplr/tests/testthat/test-certificate.R | 70 couplr-1.7.1/couplr/tests/testthat/test-certify-exact.R |only couplr-1.7.1/couplr/tests/testthat/test-certify-row-cover.R |only couplr-1.7.1/couplr/tests/testthat/test-coverage-90-target.R | 4 couplr-1.7.1/couplr/tests/testthat/test-coverage-boost.R | 6 couplr-1.7.1/couplr/tests/testthat/test-coverage-final-push.R | 4 couplr-1.7.1/couplr/tests/testthat/test-coverage-push-90.R | 4 couplr-1.7.1/couplr/tests/testthat/test-cpp-coverage-boost.R | 542 - couplr-1.7.1/couplr/tests/testthat/test-cpp-solvers-coverage.R | 994 +-- couplr-1.7.1/couplr/tests/testthat/test-csa-cost-scaling.R |only couplr-1.7.1/couplr/tests/testthat/test-dispatch-probe.R | 13 couplr-1.7.1/couplr/tests/testthat/test-flow-design.R | 20 couplr-1.7.1/couplr/tests/testthat/test-flow-model.R | 16 couplr-1.7.1/couplr/tests/testthat/test-implicit.R | 64 couplr-1.7.1/couplr/tests/testthat/test-lap-solve-coverage.R | 1202 +-- couplr-1.7.1/couplr/tests/testthat/test-lap-solve-extended-coverage.R | 15 couplr-1.7.1/couplr/tests/testthat/test-lap-solve-final-coverage.R | 4 couplr-1.7.1/couplr/tests/testthat/test-lazy-callback.R |only couplr-1.7.1/couplr/tests/testthat/test-match-couples-lazy.R | 84 couplr-1.7.1/couplr/tests/testthat/test-matching-distance-coverage.R | 47 couplr-1.7.1/couplr/tests/testthat/test-matching-full-implicit.R |only couplr-1.7.1/couplr/tests/testthat/test-matching-full-optimal.R | 91 couplr-1.7.1/couplr/tests/testthat/test-memory-mode.R | 44 couplr-1.7.1/couplr/tests/testthat/test-morph-coverage-final.R | 4 couplr-1.7.1/couplr/tests/testthat/test-rcpp-interface-coverage.R | 2 couplr-1.7.1/couplr/tests/testthat/test-solvers-additional.R | 806 +- couplr-1.7.1/couplr/vignettes/algorithms.Rmd | 2482 +++---- couplr-1.7.1/couplr/vignettes/comparison.Rmd | 4 couplr-1.7.1/couplr/vignettes/getting-started.Rmd | 2 134 files changed, 13985 insertions(+), 10804 deletions(-)
Title: Scalable Statistical Computing with HDF5-Backed Matrices
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, and QR decomposition) written in C++ and R, along with building
blocks from which higher-level multivariate methods such as canonical
correlation analysis can be constructed. These building blocks are designed
not only for direct use, but also as foundational components for developing
new statistical methods that must operate on datasets too large to fit in
memory. The package supports data provided either as 'HDF5' files or
standard R objects, and is intended for high-dimensional applications such
as 'omics' and precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 2.0.5 dated 2026-09-14 and 2.0.6 dated 2026-09-16
DESCRIPTION | 8 +- MD5 | 18 +++--- NEWS.md | 15 +++++ R/S3_core.R | 7 ++ R/hdf5CloseAll.R | 16 ++--- inst/doc/BigDataStatMeth.html | 26 ++++----- inst/include/hdf5Utilities/hdf5Files.hpp | 83 +++++++++++++++++++------------ man/dim.HDF5Matrix.Rd | 3 - src/hdf5_createMatrix.cpp | 16 +++-- src/hdf5_r6_write.cpp | 10 ++- 10 files changed, 123 insertions(+), 79 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Report of Statistical Findings in Quarto
Description: A report of statistical findings (RSF) project template is
generated using a Quarto book.
Author: Derek Chiu [aut, cre]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between rsf versions 0.3.0 dated 2022-09-15 and 1.0.0 dated 2026-09-16
rsf-0.3.0/rsf/R/git_ignore_outputs.R |only rsf-0.3.0/rsf/R/use_references.R |only rsf-0.3.0/rsf/R/write_bookdown_yml.R |only rsf-0.3.0/rsf/R/write_gitignore.R |only rsf-0.3.0/rsf/R/write_index.R |only rsf-0.3.0/rsf/R/write_output_yml.R |only rsf-0.3.0/rsf/R/write_preamble.R |only rsf-0.3.0/rsf/R/write_src.R |only rsf-0.3.0/rsf/inst/extdata/_bookdown.yml |only rsf-0.3.0/rsf/inst/extdata/_output.yml |only rsf-0.3.0/rsf/inst/extdata/gitignore |only rsf-0.3.0/rsf/inst/extdata/index.Rmd |only rsf-0.3.0/rsf/inst/extdata/preamble.tex |only rsf-0.3.0/rsf/inst/rstudio/templates/project/rsf-logo.png |only rsf-0.3.0/rsf/man/git_ignore_outputs.Rd |only rsf-0.3.0/rsf/man/use_references.Rd |only rsf-1.0.0/rsf/DESCRIPTION | 17 ++--- rsf-1.0.0/rsf/LICENSE | 4 - rsf-1.0.0/rsf/MD5 | 44 +++++--------- rsf-1.0.0/rsf/NAMESPACE | 3 rsf-1.0.0/rsf/NEWS.md | 5 + rsf-1.0.0/rsf/R/rsf-package.R | 1 rsf-1.0.0/rsf/R/use_rsf.R | 34 +++++++--- rsf-1.0.0/rsf/README.md | 12 +-- rsf-1.0.0/rsf/inst/extdata/_quarto.yml |only rsf-1.0.0/rsf/inst/extdata/dependencies.R |only rsf-1.0.0/rsf/inst/extdata/index.qmd |only rsf-1.0.0/rsf/inst/extdata/rsf |only rsf-1.0.0/rsf/inst/rstudio/templates/project/logo.png |only rsf-1.0.0/rsf/inst/rstudio/templates/project/skeleton.dcf | 12 --- rsf-1.0.0/rsf/man/figures |only rsf-1.0.0/rsf/man/rsf-package.Rd | 11 ++- rsf-1.0.0/rsf/man/use_rsf.Rd | 18 +++-- 33 files changed, 85 insertions(+), 76 deletions(-)
Title: Reproducible Data Capsules with Provenance and Fallback
Description: Tools for building brick-proof, reproducible, self-contained
data capsules.
Resolves open-data sources through the Comprehensive Knowledge
Archive Network ('CKAN', <https://ckan.org/>) package_show and
package_search endpoints, records and verifies provenance with
Secure Hash Algorithm 256 ('SHA-256') digests and Internet Archive
'Wayback Machine' (<https://web.archive.org/>) snapshots, validates
downloaded data against a pinned schema, and falls back to
schema-driven synthetic data when the real source is unreachable.
Run records are captured in a manifest plus a plain-language summary
so any result can be traced back to its inputs. Distributional drift
between a pinned capsule and a fresh fetch is tested with
Kolmogorov-Smirnov, chi-square, population stability index,
Jensen-Shannon divergence and 'Benford' first-digit screens, because a
re-released extract can be statistically identical yet differ
byte-for-byte, and a column can keep its name and type while having
been s [...truncated...]
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriebricklayer versions 0.3.9 dated 2026-09-08 and 0.5.0 dated 2026-09-16
DESCRIPTION | 53 - MD5 | 385 +++++++-- NAMESPACE | 266 ++++++ NEWS.md | 1322 +++++++++++++++++++++++++++++++ R/agent_bundle.R | 17 R/areal.R |only R/attest.R |only R/bands.R |only R/bundle.R |only R/chain.R |only R/concentration.R |only R/core.R | 33 R/core_stats.R |only R/crypto_extra.R |only R/custody.R |only R/digest_extra.R |only R/drift.R |only R/eda.R |only R/eda2.R |only R/falsify.R |only R/fetch_native.R | 13 R/fetch_siu.R | 9 R/json_gzip.R |only R/json_native.R | 309 +++++-- R/kem.R |only R/lib_capsule.R | 81 + R/lib_data_loader.R | 276 ++++-- R/lib_helpers.R | 47 - R/lib_manifest.R | 183 +++- R/lib_synthetic.R | 62 - R/mcar.R |only R/nameconstraints.R |only R/parse_siu.R | 56 - R/policy.R |only R/power.R |only R/prereg.R |only R/print_methods.R |only R/profile_extra.R |only R/rate.R |only R/region_map.R |only R/report.R |only R/repro.R |only R/revocation.R |only R/rule_lib.R |only R/rules.R |only R/schema_infer.R |only R/sign.R |only R/sketch.R |only R/timestamp.R |only R/trend.R |only R/x509.R |only R/yoy.R |only R/yoy_labels.R |only R/yoy_output.R |only R/yoy_render.R |only R/yoy_write.R |only README.md | 161 +++ build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 1 inst/WORDLIST |only inst/doc/capsules.html | 2 inst/doc/describe.R |only inst/doc/describe.Rmd |only inst/doc/describe.html |only inst/doc/drift.R |only inst/doc/drift.Rmd |only inst/doc/drift.html |only inst/doc/provenance.R |only inst/doc/provenance.Rmd |only inst/doc/provenance.html |only inst/doc/tables.R |only inst/doc/tables.Rmd |only inst/doc/tables.html |only inst/doc/yoy.R |only inst/doc/yoy.Rmd |only inst/doc/yoy.html |only inst/include/rmoriebricklayer.h | 395 +++++++++ inst/scripts/setup_and_run.R | 3 man/admissions.Rd |only man/adp.Rd |only man/adp_from_counts.Rd |only man/agent_bundle.Rd | 17 man/alos.Rd |only man/apply_schema_validation.Rd | 8 man/ascii_fallback.Rd | 21 man/band_sensitivity.Rd |only man/band_values.Rd |only man/benford_test.Rd |only man/bricklayer_fetch.Rd | 8 man/bricklayer_fetch_parse_siu.Rd | 12 man/bricklayer_fetch_siu.Rd | 9 man/bricklayer_json_from_json.Rd | 6 man/bricklayer_json_to_json.Rd | 42 man/bricklayer_parse_siu.Rd | 13 man/bricklayer_siu_iso_date.Rd | 6 man/bricklayer_siu_resolve_so.Rd | 14 man/bricklayer_siu_schema.Rd | 7 man/capsule_attest.Rd |only man/capsule_bundle.Rd |only man/capsule_drift.Rd |only man/capsule_falsify.Rd |only man/capsule_power.Rd |only man/capsule_report.Rd |only man/capsule_sign.Rd |only man/capsule_verify.Rd |only man/capture_dependencies.Rd |only man/capture_environment.Rd | 15 man/cert_chain_verify.Rd |only man/cert_parse.Rd |only man/chunk_file.Rd |only man/cite_capsule.Rd | 12 man/clean_column_names.Rd |only man/concentration.Rd |only man/core_blake2b.Rd |only man/core_bootstrap_mean.Rd |only man/core_cov.Rd |only man/core_crc32.Rd |only man/core_gamma_cdf.Rd |only man/core_hawkes_nll.Rd |only man/core_ipw_weights.Rd |only man/core_moments.Rd |only man/core_normal_logpdf.Rd |only man/core_normal_pdf.Rd | 3 man/core_sha256.Rd | 6 man/core_sha512.Rd |only man/core_weighted.Rd |only man/correlation_table.Rd |only man/count_trend.Rd |only man/cramers_v.Rd |only man/derive_key.Rd |only man/digest_object.Rd |only man/download_data.Rd | 11 man/drift_chisq.Rd |only man/drift_homogeneity.Rd |only man/drift_ks.Rd |only man/drift_psi.Rd |only man/duplicate_rows.Rd |only man/eb_rates.Rd |only man/environment_diff.Rd |only man/evalue_rr.Rd |only man/expand_bands.Rd |only man/expected_counts.Rd |only man/falsify_family.Rd |only man/fips_key.Rd |only man/fips_keygen.Rd |only man/fips_mu.Rd |only man/fips_sizes.Rd |only man/fiscal_year_label.Rd |only man/frequency_table.Rd |only man/friendly_download.Rd | 23 man/funnel_limits.Rd |only man/hill_tail_index.Rd |only man/hurwitz_zeta.Rd |only man/infer_schema.Rd |only man/inline_hist.Rd |only man/kem_decapsulate.Rd |only man/kem_encapsulate.Rd |only man/kem_keygen.Rd |only man/kem_sizes.Rd |only man/load_provenance.Rd | 11 man/mahalanobis_outliers.Rd |only man/make_manifest.Rd | 18 man/make_synthetic_column.Rd | 32 man/make_synthetic_csv.Rd | 25 man/manifest_canonical.Rd |only man/manifest_recompute.Rd |only man/manifest_record_seed.Rd |only man/mcar_test.Rd |only man/missing_runs.Rd |only man/missingness_map.Rd |only man/missingness_pattern.Rd |only man/missingness_summary.Rd |only man/morans_i.Rd |only man/oqs_keygen.Rd |only man/parse_bands.Rd |only man/period_days.Rd |only man/pqc_backends.Rd |only man/pqc_keygen.Rd |only man/prereg_declare.Rd |only man/profile_columns.Rd |only man/random_bytes.Rd |only man/rate.Rd |only man/rate_change.Rd |only man/record.Rd | 26 man/region_coverage.Rd |only man/region_map_compare.Rd |only man/region_map_from_points.Rd |only man/region_map_integrity.Rd |only man/region_map_second_route.Rd |only man/report_markdown.Rd |only man/resolve_via_arcgis.Rd | 16 man/resolve_via_ckan.Rd | 10 man/resolve_via_ckan_search.Rd | 20 man/resolve_via_socrata.Rd | 10 man/revocation_fetch.Rd |only man/rmbl_base64.Rd |only man/rmbl_chain.Rd |only man/rmbl_core_rank.Rd |only man/rmbl_core_robust.Rd |only man/rmbl_core_spread.Rd |only man/rmbl_core_stats.Rd | 17 man/rmbl_core_trimmed.Rd |only man/rmbl_distinct.Rd |only man/rmbl_drop.Rd |only man/rmbl_file_digest.Rd |only man/rmbl_json_gzip.Rd |only man/rmbl_json_serialize.Rd |only man/rmbl_keyed_digest.Rd |only man/rmbl_merkle.Rd |only man/rmbl_online.Rd |only man/rmbl_print_methods.Rd |only man/rmbl_reservoir.Rd |only man/rmbl_rule_library.Rd |only man/rule.Rd |only man/sha256_file.Rd | 6 man/share.Rd |only man/signing_public_key.Rd |only man/sir.Rd |only man/stay_summary.Rd |only man/step_change.Rd |only man/stock_flow.Rd |only man/timestamp_verify.Rd |only man/to_ascii.Rd | 9 man/top_correlations.Rd |only man/trend_test.Rd |only man/validate_rules.Rd |only man/validate_schema.Rd | 64 + man/verify_capsule.Rd | 41 man/verify_sha256.Rd | 15 man/wayback_snapshot_url.Rd | 9 man/wayback_snapshot_url_native.Rd | 3 man/write_manifest_json.Rd | 20 man/write_summary_txt.Rd | 28 man/write_text_fallback.Rd | 9 man/yoy.Rd |only man/yoy_delim.Rd |only man/yoy_label.Rd |only man/yoy_palettes.Rd |only man/yoy_render.Rd |only man/yoy_summary.Rd |only man/yoy_write.Rd |only src/Makevars | 9 src/Makevars.win | 5 src/init.c | 273 ++++++ src/rmbl_asn1.cpp |only src/rmbl_core.cpp | 210 ++++ src/rmbl_digest.cpp |only src/rmbl_ecdsa.cpp |only src/rmbl_fetch.cpp | 75 + src/rmbl_kdf.cpp |only src/rmbl_keccak.cpp |only src/rmbl_mgf1.cpp |only src/rmbl_mldsa_body.h |only src/rmbl_mldsa_core.h |only src/rmbl_mldsa_ntt.cpp |only src/rmbl_mlkem.cpp |only src/rmbl_mlkem_body.h |only src/rmbl_mlkem_core.h |only src/rmbl_pqc.cpp |only src/rmbl_prehash.h |only src/rmbl_series.cpp |only src/rmbl_sketch.cpp |only src/rmbl_slhdsa.cpp |only src/rmbl_slhdsa_body.h |only src/rmbl_slhdsa_core.h |only src/rmbl_stats.cpp |only src/rmbl_strtod.cpp |only src/siu_parse.cpp | 16 tests/testthat/fips-openssl-vectors.txt |only tests/testthat/fips-self-vectors.txt |only tests/testthat/mlkem-openssl-vectors.txt |only tests/testthat/test-areal.R |only tests/testthat/test-attest.R |only tests/testthat/test-branches.R |only tests/testthat/test-byte-parity.R |only tests/testthat/test-core-stats.R |only tests/testthat/test-crypto-extra.R |only tests/testthat/test-custody.R |only tests/testthat/test-digest-extra.R |only tests/testthat/test-drift.R |only tests/testthat/test-dtoa17.R |only tests/testthat/test-eda.R |only tests/testthat/test-edge-cases.R |only tests/testthat/test-fips-prehash.R |only tests/testthat/test-fips-sig.R |only tests/testthat/test-helper-paths.R |only tests/testthat/test-json-branches.R | 13 tests/testthat/test-json-edges.R |only tests/testthat/test-json-parity.R | 12 tests/testthat/test-kem.R |only tests/testthat/test-last-gaps.R |only tests/testthat/test-linkingto.R |only tests/testthat/test-mcar.R |only tests/testthat/test-nameconstraints.R |only tests/testthat/test-oqs.R |only tests/testthat/test-parity-extra.R |only tests/testthat/test-print-methods.R |only tests/testthat/test-rate.R |only tests/testthat/test-region_map.R |only tests/testthat/test-report.R |only tests/testthat/test-repro.R |only tests/testthat/test-rule-lib.R |only tests/testthat/test-schema-chain.R |only tests/testthat/test-shax.R |only tests/testthat/test-sign-pqc.R |only tests/testthat/test-siu-detectors.R |only tests/testthat/test-sketch.R |only tests/testthat/test-src-hygiene.R |only tests/testthat/test-tables.R |only tests/testthat/test-x509.R |only tests/testthat/test-xmss-kat.R |only tests/testthat/test-yoy.R |only tests/testthat/timestamp-token.txt |only tests/testthat/x509-fixtures.txt |only vignettes/describe.Rmd |only vignettes/drift.Rmd |only vignettes/provenance.Rmd |only vignettes/tables.Rmd |only vignettes/yoy.Rmd |only 320 files changed, 4252 insertions(+), 657 deletions(-)
More information about rmoriebricklayer at CRAN
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Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph] ,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 3.5.2 dated 2025-05-18 and 4.0.0 dated 2026-09-16
rbacon-3.5.2/rbacon/inst/dev |only rbacon-4.0.0/rbacon/DESCRIPTION | 39 - rbacon-4.0.0/rbacon/MD5 | 124 ++-- rbacon-4.0.0/rbacon/NAMESPACE | 152 ++-- rbacon-4.0.0/rbacon/NEWS.md | 210 +++--- rbacon-4.0.0/rbacon/R/MCMC.R | 358 ++++++++++- rbacon-4.0.0/rbacon/R/RcppExports.R | 16 rbacon-4.0.0/rbacon/R/accrate.R | 554 +++++++++--------- rbacon-4.0.0/rbacon/R/agedepth.R | 262 ++++++-- rbacon-4.0.0/rbacon/R/calc.R | 465 +++++++-------- rbacon-4.0.0/rbacon/R/calibrate.R | 53 - rbacon-4.0.0/rbacon/R/forplum.R | 57 + rbacon-4.0.0/rbacon/R/internal_plots.R | 333 +++++++--- rbacon-4.0.0/rbacon/R/plots.R | 100 ++- rbacon-4.0.0/rbacon/R/rbacon-package.R | 10 rbacon-4.0.0/rbacon/R/rbacon.R | 177 +++-- rbacon-4.0.0/rbacon/R/read_write.R | 240 +++++-- rbacon-4.0.0/rbacon/README.md | 8 rbacon-4.0.0/rbacon/build/partial.rdb |binary rbacon-4.0.0/rbacon/build/vignette.rds |binary rbacon-4.0.0/rbacon/inst/doc/rbacon.R | 8 rbacon-4.0.0/rbacon/inst/doc/rbacon.Rmd | 45 - rbacon-4.0.0/rbacon/inst/doc/rbacon.html | 175 +++-- rbacon-4.0.0/rbacon/man/A.modelled.Rd | 2 rbacon-4.0.0/rbacon/man/AgesOfEvents.Rd | 2 rbacon-4.0.0/rbacon/man/Bacon.Age.d.Rd | 2 rbacon-4.0.0/rbacon/man/Bacon.Rd | 39 - rbacon-4.0.0/rbacon/man/Bacon.cleanup.Rd | 2 rbacon-4.0.0/rbacon/man/Bacon.d.Age.Rd | 2 rbacon-4.0.0/rbacon/man/Bacon.hist.Rd | 7 rbacon-4.0.0/rbacon/man/Bacon_runs.Rd |only rbacon-4.0.0/rbacon/man/Baconvergence.Rd | 2 rbacon-4.0.0/rbacon/man/MCMC.diagnostics.Rd | 6 rbacon-4.0.0/rbacon/man/accrate.age.Rd | 2 rbacon-4.0.0/rbacon/man/accrate.age.ghost.Rd | 17 rbacon-4.0.0/rbacon/man/accrate.age.summary.Rd | 2 rbacon-4.0.0/rbacon/man/accrate.depth.Rd | 7 rbacon-4.0.0/rbacon/man/accrate.depth.ghost.Rd | 18 rbacon-4.0.0/rbacon/man/accrate.depth.summary.Rd | 9 rbacon-4.0.0/rbacon/man/accrates.core.Rd | 7 rbacon-4.0.0/rbacon/man/add.dates.Rd | 20 rbacon-4.0.0/rbacon/man/agedepth.Rd | 79 ++ rbacon-4.0.0/rbacon/man/agemodel.it.Rd | 12 rbacon-4.0.0/rbacon/man/ageranges.Rd | 15 rbacon-4.0.0/rbacon/man/bacon2clam.Rd | 2 rbacon-4.0.0/rbacon/man/clam2bacon.Rd | 2 rbacon-4.0.0/rbacon/man/draw.pbmeasured.Rd | 2 rbacon-4.0.0/rbacon/man/draw.pbmodelled.Rd | 7 rbacon-4.0.0/rbacon/man/flux.age.ghost.Rd | 117 +-- rbacon-4.0.0/rbacon/man/proxy.ghost.Rd | 25 rbacon-4.0.0/rbacon/man/rbacon.Rd | 8 rbacon-4.0.0/rbacon/man/scissors.Rd | 2 rbacon-4.0.0/rbacon/man/set.initvals.Rd | 2 rbacon-4.0.0/rbacon/man/squeeze.Rd | 2 rbacon-4.0.0/rbacon/man/stretch.Rd | 2 rbacon-4.0.0/rbacon/man/thinner.Rd | 2 rbacon-4.0.0/rbacon/src/RcppExports.cpp | 80 ++ rbacon-4.0.0/rbacon/src/bacon.cpp | 40 - rbacon-4.0.0/rbacon/src/bacon.h | 73 +- rbacon-4.0.0/rbacon/src/cal.h | 16 rbacon-4.0.0/rbacon/src/hists.cpp |only rbacon-4.0.0/rbacon/src/input.cpp | 2 rbacon-4.0.0/rbacon/vignettes/images/RLGH3_hiatus.png |binary rbacon-4.0.0/rbacon/vignettes/rbacon.Rmd | 45 - 64 files changed, 2579 insertions(+), 1488 deletions(-)
Title: Flexible Argument Parsing for R Scripts
Description: Argument parsing for R scripts, with support for long and short
Unix-style options including option clustering, positional arguments
including those of variable length, and multiple usage patterns which may
take different subsets of options.
Author: Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between arrg versions 0.1.0 dated 2024-09-25 and 0.2.0 dated 2026-09-16
arrg-0.1.0/arrg/R/misc.R |only arrg-0.2.0/arrg/DESCRIPTION | 12 arrg-0.2.0/arrg/MD5 | 24 - arrg-0.2.0/arrg/NAMESPACE | 1 arrg-0.2.0/arrg/NEWS.md | 128 ++++++ arrg-0.2.0/arrg/R/arrg.R | 579 ++++++++++++++++++++++++------ arrg-0.2.0/arrg/R/options.R | 103 +++-- arrg-0.2.0/arrg/R/patterns.R | 249 +++++++++--- arrg-0.2.0/arrg/R/run.R |only arrg-0.2.0/arrg/README.md | 173 +++++--- arrg-0.2.0/arrg/inst/tinytest/test_arrg.R | 479 +++++++++++++++++++++++- arrg-0.2.0/arrg/man/arrg.Rd | 102 ++++- arrg-0.2.0/arrg/man/opt.Rd | 29 - arrg-0.2.0/arrg/man/pat.Rd | 44 +- 14 files changed, 1580 insertions(+), 343 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Estimates rates for continuous character evolution under Brownian motion and Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al. (2012).
Author: Jeremy M. Beaulieu [aut, cre],
Brian O'Meara [aut]
Maintainer: Jeremy M. Beaulieu <jmbeauli@uark.edu>
Diff between OUwie versions 3.0.2 dated 2026-07-01 and 3.0.3 dated 2026-09-16
OUwie-3.0.2/OUwie/R/OUwie.contour.r |only OUwie-3.0.3/OUwie/DESCRIPTION | 14 - OUwie-3.0.3/OUwie/MD5 | 72 ++++-- OUwie-3.0.3/OUwie/NAMESPACE | 9 OUwie-3.0.3/OUwie/R/OUwie.R | 8 OUwie-3.0.3/OUwie/R/OUwie.anc.R | 2 OUwie-3.0.3/OUwie/R/OUwie.contour.R |only OUwie-3.0.3/OUwie/R/OUwie.dredge.R | 2 OUwie-3.0.3/OUwie/R/dentist.R |only OUwie-3.0.3/OUwie/R/hOUwie.R |only OUwie-3.0.3/OUwie/R/hOUwie.bridge.R |only OUwie-3.0.3/OUwie/R/hOUwie.internal.R |only OUwie-3.0.3/OUwie/R/hOUwie.proposal.R |only OUwie-3.0.3/OUwie/R/hOUwie.pruning.R |only OUwie-3.0.3/OUwie/R/varcov.ou.R | 3 OUwie-3.0.3/OUwie/R/vcvbypass.functions.R | 134 ++++++++++- OUwie-3.0.3/OUwie/R/weight.mat.R | 177 ++++++++------- OUwie-3.0.3/OUwie/README.md |only OUwie-3.0.3/OUwie/build/vignette.rds |binary OUwie-3.0.3/OUwie/inst/doc/OUwie_2.1_adds.R | 42 ++- OUwie-3.0.3/OUwie/inst/doc/OUwie_2.1_adds.Rmd | 43 ++- OUwie-3.0.3/OUwie/inst/doc/OUwie_2.1_adds.pdf |binary OUwie-3.0.3/OUwie/inst/doc/calculationUpdate.R | 1 OUwie-3.0.3/OUwie/inst/doc/calculationUpdate.Rmd | 12 - OUwie-3.0.3/OUwie/inst/doc/calculationUpdate.pdf |binary OUwie-3.0.3/OUwie/inst/doc/hOUwiePerformance.R |only OUwie-3.0.3/OUwie/inst/doc/hOUwiePerformance.Rmd |only OUwie-3.0.3/OUwie/inst/doc/hOUwiePerformance.pdf |only OUwie-3.0.3/OUwie/inst/doc/hOUwieStarterGuide.R |only OUwie-3.0.3/OUwie/inst/doc/hOUwieStarterGuide.Rmd |only OUwie-3.0.3/OUwie/inst/doc/hOUwieStarterGuide.pdf |only OUwie-3.0.3/OUwie/man/dent_likelihood.Rd |only OUwie-3.0.3/OUwie/man/dent_propose.Rd |only OUwie-3.0.3/OUwie/man/dent_walk.Rd |only OUwie-3.0.3/OUwie/man/getModelAvgParams.Rd |only OUwie-3.0.3/OUwie/man/getModelTable.Rd |only OUwie-3.0.3/OUwie/man/getOUParamStructure.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.fixed.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.recon.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.sim.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.thorough.Rd |only OUwie-3.0.3/OUwie/man/hOUwie.walk.Rd |only OUwie-3.0.3/OUwie/man/plot.dentist.Rd |only OUwie-3.0.3/OUwie/man/print.dentist.Rd |only OUwie-3.0.3/OUwie/man/summary.dentist.Rd |only OUwie-3.0.3/OUwie/tests/testthat/test-edge-order.R |only OUwie-3.0.3/OUwie/tests/testthat/test-houwie-pruning.R |only OUwie-3.0.3/OUwie/tests/testthat/test-houwie-sampling.R |only OUwie-3.0.3/OUwie/tests/testthat/test-houwie-tree-plan.R |only OUwie-3.0.3/OUwie/tests/testthat/test-houwie.R |only OUwie-3.0.3/OUwie/tests/testthat/test-model-averaging.R |only OUwie-3.0.3/OUwie/vignettes/OUwie_2.1_adds.Rmd | 43 ++- OUwie-3.0.3/OUwie/vignettes/calculationUpdate.Rmd | 12 - OUwie-3.0.3/OUwie/vignettes/hOUwiePerformance.Rmd |only OUwie-3.0.3/OUwie/vignettes/hOUwieStarterGuide.Rmd |only 56 files changed, 395 insertions(+), 179 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs, sample sizes in two-phase designs, and a stopping rule for ending data collection. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.7.5 dated 2026-01-17 and 1.7.6 dated 2026-09-16
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------ NEWS.md | 8 +++++ R/pclass.R | 31 +++++++++++++++---- inst/doc/Design-effects.html | 33 +++++++++----------- inst/doc/Distance-and-MOS-PSUs.html | 14 +++----- inst/doc/SampStop.html | 7 +--- inst/doc/Select-samsize-fcns.html | 30 ++++++++---------- inst/doc/Singlestage-samsize.html | 54 +++++++++++++++------------------- inst/doc/Varcomps-multistage.html | 57 +++++++++++++++++------------------- man/pclass.Rd | 24 ++++++++++++--- 11 files changed, 155 insertions(+), 131 deletions(-)
Title: Add Custom Legends to 'leaflet' Maps
Description: Provides extensions to the 'leaflet' package to
customize legends with images, text styling, orientation, sizing,
and symbology and functions to create symbols to plot on maps.
Author: Thomas Roh [aut, cre],
Ricardo Rodrigo Basa [ctb]
Maintainer: Thomas Roh <thomas.roh@delveds.com>
Diff between leaflegend versions 1.2.8 dated 2026-05-16 and 1.3.0 dated 2026-09-16
DESCRIPTION | 6 MD5 | 16 - NAMESPACE | 6 NEWS.md | 42 +++ R/legend.R | 501 ++++++++++++++++++++++++++++++++++++++----- man/addLeafLegends.Rd | 3 man/legendSymbols.Rd | 97 +++++++- man/mapSymbols.Rd | 110 +++++++++ tests/testthat/test-legend.R | 309 ++++++++++++++++++++++++++ 9 files changed, 1020 insertions(+), 70 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.60 dated 2026-07-09 and 0.61 dated 2026-09-16
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/app.R | 6 +++--- R/browser.R | 12 ++++++++---- R/cran.R | 7 ++++++- R/github.R | 21 ++++++++++++++------- R/markdown.R | 10 ---------- R/paths.R | 8 ++++---- R/string.R | 20 ++++++++++++-------- build/vignette.rds |binary inst/doc/xfun.html | 20 +++++++++----------- man/browser_print.Rd | 4 ++-- man/is_abs_path.Rd | 6 +++--- man/post_release.Rd | 12 +++++++----- tests/test-cran/test-github.R | 16 ++++++++++------ tests/test-cran/test-paths.R | 9 ++++++--- 16 files changed, 103 insertions(+), 86 deletions(-)
Title: Extension Types for Spatial Data for Use with 'Arrow'
Description: Provides extension types and conversions to between R-native
object types and 'Arrow' columnar types. This includes integration among
the 'arrow', 'nanoarrow', 'sf', and 'wk' packages such that spatial
metadata is preserved wherever possible. Extension type implementations
ensure first-class geometry data type support in the 'arrow' and 'nanoarrow'
packages.
Author: Dewey Dunnington [aut, cre] ,
Anthony North [ctb],
Apache Software Foundation [cph],
Ulf Adams [cph],
Daniel Lemire [cph],
Joao Paulo Magalhaes [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between geoarrow versions 0.4.3 dated 2026-06-04 and 0.4.4 dated 2026-09-16
DESCRIPTION | 8 MD5 | 22 - R/pkg-nanoarrow.R | 2 man/geoarrow-package.Rd | 5 man/geoarrow_wkb.Rd | 2 man/na_extension_wkb.Rd | 2 src/geoarrow.c | 631 +++++++++++++++++++++++++++++++++++++++------- src/geoarrow/geoarrow.h | 284 ++++++++++++++++++++ src/geoarrow/geoarrow.hpp | 10 src/nanoarrow.c | 17 + src/nanoarrow/nanoarrow.h | 7 src/r-wk-handle-stream.cc | 1 12 files changed, 865 insertions(+), 126 deletions(-)
Title: Perform a Relative Weights Analysis
Description: Perform a Relative Weights Analysis (RWA) (a.k.a. Key Drivers Analysis) as per the method described
in Tonidandel & LeBreton (2015) <DOI:10.1007/s10869-014-9351-z>, with its original roots in Johnson (2000) <DOI:10.1207/S15327906MBR3501_1>. In essence, RWA decomposes
the total variance predicted in a regression model into weights that accurately reflect the proportional
contribution of the predictor variables, which addresses the issue of multi-collinearity. In typical scenarios,
RWA returns similar results to Shapley regression, but with a significant advantage on computational performance.
Author: Martin Chan [aut, cre]
Maintainer: Martin Chan <martinchan53@gmail.com>
Diff between rwa versions 0.1.1 dated 2026-01-20 and 1.0.0 dated 2026-09-16
DESCRIPTION | 9 MD5 | 66 ++- NAMESPACE | 10 NEWS.md | 172 +++++--- R/bootstrap_rwa.R | 291 ++++++++------- R/globals.R | 3 R/plot_rwa.R | 57 ++ R/rwa.R | 497 ++++++++++++++++---------- R/rwa_calculation.R |only R/rwa_logit.R |only R/rwa_multiregress.R |only README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/bootstrap-confidence-intervals.R | 1 inst/doc/bootstrap-confidence-intervals.Rmd | 51 ++ inst/doc/bootstrap-confidence-intervals.html | 294 +++++++++------ inst/doc/evaluating-rwa-method-reference.html | 4 inst/doc/introduction-to-rwa.R | 23 + inst/doc/introduction-to-rwa.Rmd | 63 +++ inst/doc/introduction-to-rwa.html | 394 +++++++++++--------- inst/doc/regression-methods.R |only inst/doc/regression-methods.Rmd |only inst/doc/regression-methods.html |only inst/doc/weighted-missing-data.R |only inst/doc/weighted-missing-data.Rmd |only inst/doc/weighted-missing-data.html |only man/rwa.Rd | 197 ++++++++-- man/rwa_logit.Rd |only man/rwa_multiregress.Rd |only tests/testthat/test-bootstrap.R | 9 tests/testthat/test-comprehensive-contract.R |only tests/testthat/test-matrix-contract.R |only tests/testthat/test-plot_rwa.R | 91 ++++ tests/testthat/test-rwa.R | 401 ++++++++++++++++++++ tests/testthat/test-significance-contract.R |only tests/testthat/test-usability-contract.R |only tests/testthat/test-weighted-contract.R |only vignettes/bootstrap-confidence-intervals.Rmd | 51 ++ vignettes/introduction-to-rwa.Rmd | 63 +++ vignettes/man |only vignettes/regression-methods.Rmd |only vignettes/weighted-missing-data.Rmd |only 44 files changed, 2015 insertions(+), 741 deletions(-)
Title: Conover-Iman Test of Multiple Comparisons Using Rank Sums
Description: Computes the Conover-Iman test (1979) for stochastic superiority and reports the results among multiple pairwise comparisons after a Kruskal-Wallis omnibus test for stochastic superiority among k groups (Kruskal and Wallis, 1952). conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
Author: Alexis Dinno [aut, cre, cph]
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between conover.test versions 1.1.7 dated 2026-02-12 and 1.2.0 dated 2026-09-16
DESCRIPTION | 12 MD5 | 26 - NAMESPACE | 2 R/all.integers.R |only R/alphabetize.factor.R |only R/centertext.R |only R/conover.test.R | 742 +++++++++++------------------------- R/conovertestheader.R |only R/conovertestptable.R |only R/conovertestttable.R |only R/get_order.R |only R/kwallis.test.R |only R/multiple_comparisons_adjustment.R |only R/pad.left.R | 3 R/pad.spaces.R | 3 R/tformat.R |only R/tiedranks.R |only R/tpad.R |only build/partial.rdb |binary man/conover.test.Rd | 74 ++- 20 files changed, 319 insertions(+), 543 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.18.0 dated 2026-08-20 and 0.19.0 dated 2026-09-16
DESCRIPTION | 6 - MD5 | 36 +++--- NEWS.md | 6 + R/aaa_class.R | 193 +++++++++++++++++++------------------ R/format_tt.R | 29 ++++- R/format_vector_misc.R | 44 +++----- R/theme_tt.R | 4 R/tt.R | 6 - R/typst_finalize.R | 27 +++-- README.md | 2 build/partial.rdb |binary inst/tinytest/test-bugfix.R | 29 +++++ inst/tinytest/test-format.R | 16 +++ inst/tinytest/test-plot_tt.R | 11 ++ man/format_tt.Rd | 18 +++ man/format_vector.Rd | 2 man/initialize-tinytable-method.Rd | 39 ------- man/save_tt.Rd | 16 +++ man/tt.Rd | 16 +++ 19 files changed, 305 insertions(+), 195 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.4.0 dated 2026-03-17 and 0.4.1 dated 2026-09-16
DESCRIPTION | 16 MD5 | 82 +-- NAMESPACE | 362 +++++++------- NEWS.md | 10 R/stat-spikes.R | 74 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/userguide-0-r4p-introduction.html | 2 inst/doc/userguide1-grammar.R | 14 inst/doc/userguide1-grammar.Rmd | 41 + inst/doc/userguide1-grammar.html | 715 ++++++++++++++--------------- inst/doc/userguide2-autoplot-methods.html | 8 man/autoplot.calibration_spct.Rd | 18 man/autoplot.cps_spct.Rd | 18 man/autoplot.filter_spct.Rd | 18 man/autoplot.object_spct.Rd | 18 man/autoplot.raw_spct.Rd | 18 man/autoplot.reflector_spct.Rd | 18 man/autoplot.response_spct.Rd | 18 man/autoplot.source_spct.Rd | 18 man/autoplot.waveband.Rd | 18 man/gg2spectra-ggproto.Rd | 19 man/ggspectra-package.Rd | 5 man/stat_color.Rd | 36 - man/stat_find_qtys.Rd | 36 - man/stat_find_wls.Rd | 36 - man/stat_label_peaks.Rd | 36 - man/stat_peaks.Rd | 36 - man/stat_spikes.Rd | 157 ++++-- man/stat_wb_box.Rd | 36 - man/stat_wb_column.Rd | 36 - man/stat_wb_contribution.Rd | 36 - man/stat_wb_hbar.Rd | 36 - man/stat_wb_irrad.Rd | 36 - man/stat_wb_label.Rd | 36 - man/stat_wb_mean.Rd | 36 - man/stat_wb_relative.Rd | 36 - man/stat_wb_sirrad.Rd | 36 - man/stat_wb_total.Rd | 36 - man/stat_wl_strip.Rd | 36 - man/stat_wl_summary.Rd | 36 - vignettes/userguide1-grammar.Rmd | 41 + 42 files changed, 1232 insertions(+), 1088 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou [aut, cre],
Vivekananda Roy [aut]
Maintainer: Evangelos Evangelou <e.evangelou@maths.bath.ac.uk>
Diff between geoBayes versions 0.7.7 dated 2026-06-17 and 0.7.8 dated 2026-09-16
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS | 4 ++++ R/geobayes-correlation.R | 4 ++-- R/mcsp2.R | 39 +++++++++++++++++++++++++++++++++++++-- R/mcsp_mala.R | 38 ++++++++++++++++++++++++++++++++++++-- man/mcsglmm.Rd | 4 ++++ man/mcsglmm_mala.Rd | 4 ++++ man/mcstrga.Rd | 4 ++++ man/mcstrga_mala.Rd | 4 ++++ src/mcmcfcns.f90 | 19 ++++++++++++------- src/modelfcns_pdfy.f90 | 20 +++++++++++++++++--- 13 files changed, 141 insertions(+), 32 deletions(-)
Title: Fit Bounded Continuous Item Response Theory Models to Data
Description: Bounded continuous data are encountered in many areas of test application.
Examples include visual analogue scales used in the measurement of personality, mood,
depression, and quality of life; item response times from tests with item deadlines;
confidence ratings; and pain intensity ratings. Using this package, item response theory (IRT)
models suitable for bounded continuous item scores can be fitted to data within a Bayesian framework.
The package draws on posterior sampling facilities provided by R-package 'rstan' (Stan Development Team, 2025)<https://mc-stan.org/>.
Available models include the Beta IRT model by Noel and Dauvier (2007)<doi:10.1177/0146621605287691>, the continuous response
model by Samejima (1973)<doi:10.1007/BF03372160>, the unbounded normal model by Mellenbergh (1994)<doi:10.1207/s15327906mbr2903_2>,
and the Simplex IRT model by Flores et al. (2020)<doi:10.1007/978-3-030-43469-4_8>. All models can be
fitted with or without zero-one i [...truncated...]
Author: Dylan Molenaar [aut, cre]
Maintainer: Dylan Molenaar <d.molenaar@uva.nl>
Diff between BoundIRT versions 0.6.0 dated 2026-08-21 and 0.8.0 dated 2026-09-16
DESCRIPTION | 12 - MD5 | 72 +++--- NAMESPACE | 20 + R/bridgeBIRT.R | 22 + R/bridgeBIRTinf.R | 6 R/bridgeBIRTno.R | 2 R/coef.latregBIRT.R |only R/dBIRT.R | 2 R/fitBIRT.R | 352 ++++++++++++++---------------- R/latregBIRT.R | 492 ++++++++++++++++++++---------------------- R/loglikBIRT.R | 51 ++-- R/loo.BoundIRT.R |only R/mcmc.BoundIRT.R |only R/plot.bridgeIRT.R |only R/plot.latregBIRT.R |only R/plot.repBIRT.R |only R/print.bridgeBIRT.R | 2 R/print.latregBIRT.R | 2 R/print.repBIRT.R |only R/print.summary.BoundIRT.R |only R/print.summary.bridgeBIRT.R |only R/print.summary.latregBIRT.R |only R/print.summary.repBIRT.R |only R/rBIRT.R | 4 R/repBIRT.R | 31 +- R/rsimpl.R | 2 R/summary.BoundIRT.R | 4 R/summary.bridgeBIRT.R |only R/summary.latregBIRT.R |only R/summary.repBIRT.R |only R/waic.BoundIRT.R |only inst/stan/BetaIRT_inf.stan | 8 inst/stan/NormalIRT_inf.stan | 8 inst/stan/SimplexIRT_inf.stan | 8 man/ACL.Rd | 136 +++++------ man/bridgeBIRT.Rd | 140 ++++++----- man/fitBIRT.Rd | 7 man/latregBIRT.Rd | 19 - man/loglikBIRT.Rd | 141 +++++------- man/loo.Rd |only man/plot.BoundIRT.Rd | 7 man/print.BoundIRT.Rd |only man/print.bridgeBIRT.Rd |only man/print.latregBIRT.Rd |only man/print.repBIRT.Rd |only man/rBIRT.Rd | 4 man/repBIRT.Rd | 28 +- 47 files changed, 836 insertions(+), 746 deletions(-)
Title: Block Diagonal Matrix Approximation
Description: Finds the best block diagonal matrix approximation of a symmetric matrix. This can be exploited for divisive hierarchical clustering using singular vectors, named HC-SVD. The method is described in Bauer (202X) <doi:10.48550/arXiv.2308.06820>.
Author: Jan O. Bauer [aut, cre]
Maintainer: Jan O. Bauer <j.bauer@vu.nl>
Diff between blox versions 0.0.1 dated 2025-09-30 and 0.0.2 dated 2026-09-16
blox-0.0.1/blox/README.md |only blox-0.0.2/blox/DESCRIPTION | 10 blox-0.0.2/blox/MD5 | 21 - blox-0.0.2/blox/R/RcppExports.R | 16 blox-0.0.2/blox/R/hcbeta.R | 10 blox-0.0.2/blox/R/hcsvd.R | 460 +++++++++++++++++++-------- blox-0.0.2/blox/man/bd.approx.Rd | 51 ++- blox-0.0.2/blox/man/hc.beta.Rd | 20 - blox-0.0.2/blox/man/hcsvd.Rd | 60 ++- blox-0.0.2/blox/man/is.ultrametric.Rd | 2 blox-0.0.2/blox/src/RcppExports.cpp | 50 ++ blox-0.0.2/blox/src/utils.cpp | 574 +++++++++++++++++++++++++++++++++- 12 files changed, 1048 insertions(+), 226 deletions(-)
Title: Estimate Brain Networks and Connectivity with ICA and Empirical
Priors
Description: Implements the template ICA (independent components analysis) model
proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the
spatial template ICA model proposed in Mejia et al. (2022)
<doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level
brain as deviations from known population-level networks, which are
estimated using standard ICA algorithms. Both models employ an
expectation-maximization algorithm for estimation of the latent brain
networks and unknown model parameters. Includes direct support for 'CIFTI',
'GIFTI', and 'NIFTI' neuroimaging file formats. Note, this package has been
deprecated and superseded by 'BayesBrainMap', which includes model
improvements and new names for the core functions.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Daniel Spencer [ctb] ,
Mary Beth Nebel [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between templateICAr versions 0.10.0 dated 2025-05-19 and 0.11.3 dated 2026-09-16
DESCRIPTION | 16 ++++---- MD5 | 43 ++++++++++++---------- NAMESPACE | 89 ++++++++++++++++++++++++++--------------------- NEWS.md | 5 ++ R/INLA_check.R | 2 - R/VB_FCtemplateICA.R | 2 - R/activations.R | 1 R/dual_reg.R |only R/dual_reg2.R | 9 ++-- R/dual_reg_parc.R |only R/estimate_template.R | 11 +++++ R/make_mesh.R | 2 - R/norm_BOLD.R | 77 ++++++++++++++++++++++++++-------------- R/rm_nuisIC.R | 4 +- R/templateICA.R | 3 + R/zzz.R |only README.md | 33 +++++++++++++---- man/activations.Rd | 23 ++++++++++++ man/dual_reg.Rd |only man/dual_reg2.Rd | 23 ++++++++++++ man/dual_reg_parc.Rd |only man/estimate_template.Rd | 23 ++++++++++++ man/make_mesh_2D.Rd | 2 - man/norm_BOLD.Rd | 50 ++++++++++++++++++++------ man/templateICA.Rd | 23 ++++++++++++ 25 files changed, 318 insertions(+), 123 deletions(-)
Title: Mann-Kendall Test, Seasonal and Regional Kendall Tests
Description: Contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.
Author: Aldo Marchetto [aut, cre]
Maintainer: Aldo Marchetto <aldo.marchetto@cnr.it>
Diff between rkt versions 1.8 dated 2026-08-25 and 1.9 dated 2026-09-16
DESCRIPTION | 10 ++--- MD5 | 10 +++-- R/pblocks.R |only R/rkt.R | 101 ++++++++++++++++++++++++--------------------------------- R/tauprob.R |only man/pblocks.Rd |only man/rkt.Rd | 22 +++++++++--- man/tauprob.Rd |only 8 files changed, 72 insertions(+), 71 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO (or more generally elastic net), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Artificial Neural Network (ANN), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples.
Note, at the time of this writing, in order to fit gradient boosting machine models one must install the packages 'DiceKriging' and 'rgenoud' using the install.packages() function.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.6-3 dated 2025-12-16 and 0.6-4 dated 2026-09-16
glmnetr-0.6-3/glmnetr/R/calplot_250814.R |only glmnetr-0.6-3/glmnetr/R/nested.cis_250528.R |only glmnetr-0.6-3/glmnetr/R/nested.compare_251212.R |only glmnetr-0.6-3/glmnetr/R/nested.glmnetr_251215.R |only glmnetr-0.6-3/glmnetr/R/plot.cv.glmnetr_0_6_1_250503.R |only glmnetr-0.6-3/glmnetr/R/plot.cv.glmnetr_0_6_2_250525.R |only glmnetr-0.6-3/glmnetr/R/plot.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/plot.nested.glmnetr_250501.R |only glmnetr-0.6-3/glmnetr/R/plot_perf_glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/predict.cv.glmnetr_0_5_5_250404.R |only glmnetr-0.6-3/glmnetr/R/predict.cv.glmnetr_0_6_1_250502.R |only glmnetr-0.6-3/glmnetr/R/predict.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/predict.glmnetr_0_5_5_250404.R |only glmnetr-0.6-3/glmnetr/R/rederive_240508.R |only glmnetr-0.6-3/glmnetr/R/summary.cv.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/summary.nested.glmnetr_251212.R |only glmnetr-0.6-3/glmnetr/R/xgbm_tuned_251215.R |only glmnetr-0.6-3/glmnetr/inst/doc/An_Overview_of_glmnetr_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/An_Overview_of_glmnetr_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/inst/doc/Calibration_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/Calibration_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/inst/doc/Elastic_net_models_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/Elastic_net_models_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/inst/doc/Ridge_and_Lasso_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/Ridge_and_Lasso_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/inst/doc/Using_ann_tab_cv_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/Using_ann_tab_cv_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/inst/doc/Using_stepreg_250818.pdf |only glmnetr-0.6-3/glmnetr/inst/doc/Using_stepreg_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/An_Overview_of_glmnetr_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/An_Overview_of_glmnetr_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/Calibration_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/Calibration_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/Elastic_net_models_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/Elastic_net_models_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/Ridge_and_Lasso_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/Ridge_and_Lasso_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/Using_ann_tab_cv_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/Using_ann_tab_cv_250818.pdf.asis |only glmnetr-0.6-3/glmnetr/vignettes/Using_stepreg_250818.Rmd |only glmnetr-0.6-3/glmnetr/vignettes/Using_stepreg_250818.pdf.asis |only glmnetr-0.6-4/glmnetr/DESCRIPTION | 15 glmnetr-0.6-4/glmnetr/MD5 | 175 ++++----- glmnetr-0.6-4/glmnetr/NAMESPACE | 182 +++++----- glmnetr-0.6-4/glmnetr/R/DiceKriging_260912.R |only glmnetr-0.6-4/glmnetr/R/calplot_260902.R |only glmnetr-0.6-4/glmnetr/R/elastic_tools_250818.R | 6 glmnetr-0.6-4/glmnetr/R/globalVariables_230509.R | 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363 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided. For tutorials, please check Ma and de la Torre (2020) <DOI:10.18637/jss.v093.i14>, Ma and de la Torre (2019) <DOI:10.1111/emip.12262>, Ma (2019) <DOI:10.1007/978-3-030-05584-4_29> and de la Torre and Akbay (2019).
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Samuel Huang [ctb],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb],
Pablo Najera [ctb]
Maintainer: Wenchao Ma <wma@umn.edu>
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Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for a small set of commonly-used,
design-appropriate estimators with robust standard errors and confidence
intervals. Includes estimators for linear regression, instrumental
variables regression, difference-in-means, Horvitz-Thompson estimation,
and regression improving precision of experimental estimates by
interacting treatment with centered pre-treatment covariates introduced by
Lin (2013) <doi:10.1214/12-AOAS583>. Fixed effects are absorbed by
alternating projections rather than by dummy expansion, and
Horvitz-Thompson variance is computed from the randomization declaration.
Author: Alexander Coppock [aut, cre],
Graeme Blair [aut],
Jasper Cooper [aut],
Luke Sonnet [aut],
Macartan Humphreys [ctb],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb],
Molly Offer-Westort [ctb]
Maintainer: Alexander Coppock <acoppock@gmail.com>
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Title: Exact Date and Duration Arithmetic on an Annual Grid
Description: Standardised mapping of dates onto a discrete annual grid,
together with exact date and duration arithmetic. This matters when
the primary unit is years but the input data uses dates. Examples are
actuarial mortality experience analysis and valuation of life
assurance and annuities, for which mortality rates are defined per
year but experience and valuation data are typically defined using
dates.
Author: Tim Gordon [aut, cre]
Maintainer: Tim Gordon <tim.gordon@btinternet.com>
Diff between datey versions 0.1.1 dated 2026-07-14 and 0.1.2 dated 2026-09-16
DESCRIPTION | 6 - MD5 | 41 ++++----- NAMESPACE | 3 NEWS.md | 10 ++ R/common.R | 30 ++++++ R/datey.R | 4 R/ops.R | 2 build/vignette.rds |binary inst/doc/datey.R | 26 ++--- inst/doc/datey.Rmd | 44 ++++----- inst/doc/datey.html | 58 ++++++------ inst/doc/why-datey.R | 26 +++-- inst/doc/why-datey.Rmd | 132 ++++++++++++++--------------- inst/doc/why-datey.html | 195 ++++++++++++++++++++++--------------------- man/NAs.Rd | 2 man/is_NA.Rd | 2 man/ops.Rd | 2 man/replicate.Rd |only src/S_durationy.cpp | 8 + tests/testthat/test-common.R | 88 +++++++++++++++++++ vignettes/datey.Rmd | 44 ++++----- vignettes/why-datey.Rmd | 132 ++++++++++++++--------------- 22 files changed, 503 insertions(+), 352 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves Statistics Canada data
tables, as well as individual vectors, as tidy data frames.
This package enriches the tables with metadata, deals
with encoding issues, allows for bilingual English or French language data retrieval, and bundles
convenience functions to make it easier to work with retrieved table data. For more efficient data
access the package allows for caching data in a local database and database level filtering, data
manipulation and summarizing.
Author: Jens von Bergmann [aut, cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.5.0 dated 2026-08-19 and 0.5.1 dated 2026-09-16
DESCRIPTION | 6 - MD5 | 48 ++++++++------ NEWS.md | 18 +++++ R/cansim_helpers.R | 19 +++-- R/cansim_metadata.R | 11 ++- R/cansim_parquet.R | 4 - R/cansim_vectors.R | 4 - README.md | 4 - build/vignette.rds |binary inst/doc/cansim.Rmd | 2 inst/doc/cansim.html | 37 +++++------ inst/doc/listing_cansim_tables.R |only inst/doc/listing_cansim_tables.Rmd |only inst/doc/listing_cansim_tables.html |only inst/doc/retrieving_cansim_vectors.R |only inst/doc/retrieving_cansim_vectors.Rmd |only inst/doc/retrieving_cansim_vectors.html |only inst/doc/working_with_hierarchies.R |only inst/doc/working_with_hierarchies.Rmd |only inst/doc/working_with_hierarchies.html |only inst/doc/working_with_large_tables.Rmd | 4 - inst/doc/working_with_large_tables.html | 107 +++++++++++++++----------------- man/get_cansim_vector.Rd | 2 man/list_cansim_cached_tables.Rd | 4 - tests/testthat/helper-warnings.R | 6 - tests/testthat/test-character_repair.R | 36 ++++++++++ vignettes/cansim.Rmd | 2 vignettes/listing_cansim_tables.Rmd |only vignettes/retrieving_cansim_vectors.Rmd |only vignettes/working_with_hierarchies.Rmd |only vignettes/working_with_large_tables.Rmd | 4 - 31 files changed, 191 insertions(+), 127 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: The 'leaflet' JavaScript library provides many plugins some of which
are available in the core 'leaflet' package, but there are many more. It is not
possible to support them all in the core 'leaflet' package. This package serves
as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet'
plugins.
Author: Sebastian Gatscha [aut, cre],
Bhaskar Karambelkar [aut],
Barret Schloerke [aut],
Bangyou Zheng [ctb] ,
Robin Cura [ctb] ,
Markus Voge [ctb] ,
Markus Dumke [ctb] ,
Mapbox [ctb, cph] ,
Henry Thasler [ctb, cph] ,
Dennis Wilhelm [ctb, cph] ,
Kirollos Ris [...truncated...]
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Diff between leaflet.extras versions 2.0.2 dated 2026-03-29 and 2.1.0 dated 2026-09-16
DESCRIPTION | 30 LICENSE | 1348 +++---- MD5 | 258 - NAMESPACE | 203 - NEWS.md | 33 R/TileLayer.PouchDBCached.R | 46 R/bounceMarker.R | 138 R/draw.R | 318 - R/drawOptions.R | 918 ++--- R/fullscreen.R | 58 R/geodesic.R | 450 +- R/gps.R | 180 - R/groupedlayercontrol.R | 348 - R/hash.R | 40 R/heatmap.R | 635 ++- R/html_dependencies.R | 86 R/jsFunctions.R | 252 - R/leaflet.extras-package.r | 36 R/leafletDependencies.R | 120 R/mapUtils.R | 153 R/measure-path.R | 271 - R/omnivore.R | 1350 +++---- R/pulseIcon.R | 352 +- R/search.R | 986 ++--- R/sharamov.R | 116 R/sleep.R | 100 R/styleEditor.R | 104 R/utils.R | 28 R/weatherMarkers.R | 399 +- R/webGLHeatmap.R | 704 ++-- R/wms-legend.R | 102 inst/examples/CSV.R | 72 inst/examples/GPX.R | 54 inst/examples/KML.R | 120 inst/examples/TileLayer-Caching.R | 66 inst/examples/TopoJSON.R | 142 inst/examples/data/geojson |only inst/examples/draw.R | 172 inst/examples/geodesic.R | 185 - inst/examples/geojsonv2.R | 544 +-- inst/examples/heatmaps.R | 189 - inst/examples/measurePath.R | 156 inst/examples/pulseIcon.R | 94 inst/examples/search.R | 410 +- inst/examples/shiny/bouncemarkers.R | 54 inst/examples/shiny/choropleth_opacity_app.R |only inst/examples/shiny/draw-events/app.R | 244 - inst/examples/shiny/draw-events/draw_mouse_events.R | 134 inst/examples/shiny/geodesic_app.R | 736 ++-- inst/examples/shiny/groupedlayercontrol_app.R | 222 - inst/examples/shiny/search/app.R | 236 - inst/examples/shiny/search/features_app.R | 122 inst/examples/shiny/search/google_app.R |only inst/examples/shiny/wmslegend.R | 78 inst/examples/sleep.R | 40 inst/examples/styleeditor.R | 62 inst/examples/weatherIcons.R | 120 inst/examples/webglHeatmaps.R | 211 - inst/examples/wmsLegend.R | 46 inst/htmlwidgets/build/lfx-bouncemarker/lfx-bouncemarker-bindings.js | 2 inst/htmlwidgets/build/lfx-choropleth/lfx-choropleth-prod.js | 116 inst/htmlwidgets/build/lfx-choropleth/lfx-choropleth-prod.js.LICENSE.txt | 112 inst/htmlwidgets/build/lfx-draw-drag/lfx-draw-drag-prod.js | 26 inst/htmlwidgets/build/lfx-draw-drag/lfx-draw-drag-prod.js.LICENSE.txt | 24 inst/htmlwidgets/build/lfx-draw/a4e0eb7ad904a4858361.svg | 312 - inst/htmlwidgets/build/lfx-draw/lfx-draw-bindings.js | 2 inst/htmlwidgets/build/lfx-geodesic/lfx-geodesic-bindings.js | 2 inst/htmlwidgets/build/lfx-geodesic/lfx-geodesic-prod.js | 4 inst/htmlwidgets/build/lfx-geodesic/lfx-geodesic-prod.js.LICENSE.txt | 2 inst/htmlwidgets/build/lfx-gps/c1dff5caf910aebd9aca.svg | 494 +- inst/htmlwidgets/build/lfx-gps/lfx-gps-bindings.js | 2 inst/htmlwidgets/build/lfx-groupedlayercontrol/lfx-groupedlayercontrol-prod.js | 4 inst/htmlwidgets/build/lfx-heat/lfx-heat-bindings.js | 2 inst/htmlwidgets/build/lfx-measure-path/lfx-measure-path-bindings.js | 2 inst/htmlwidgets/build/lfx-omnivore/lfx-omnivore-bindings.js | 2 inst/htmlwidgets/build/lfx-pulse-icon/lfx-pulse-icon-bindings.js | 2 inst/htmlwidgets/build/lfx-search/lfx-search-bindings.js | 2 inst/htmlwidgets/build/lfx-styleeditor/887fb08b2baa4a1d3975.svg | 228 - inst/htmlwidgets/build/lfx-styleeditor/lfx-styleeditor-bindings.js | 2 inst/htmlwidgets/build/lfx-weather-markers/86a76ca5e882e8285706.svg | 512 +- inst/htmlwidgets/build/lfx-weather-markers/lfx-weather-markers-prod.css | 84 inst/htmlwidgets/build/lfx-webgl-heatmap/lfx-webgl-heatmap-bindings.js | 2 inst/htmlwidgets/build/map-widget-style/map-widget-style-bindings.js | 2 inst/htmlwidgets/build/tile-bing/tile-bing-bindings.js | 2 man/GroupedLayersControl.Rd | 82 man/TileCaching.Rd | 44 man/addAwesomeMarkersDependencies.Rd | 32 man/addBingTiles.Rd | 76 man/addBootstrapDependency.Rd | 28 man/addBounceMarkers.Rd | 174 man/addGroupedLayersControl.Rd | 162 man/addResetMapButton.Rd | 38 man/debugMap.Rd | 28 man/draw-options.Rd | 368 +- man/draw.Rd | 242 - man/edithandlersOptions.Rd | 40 man/edittoolbarOptions.Rd | 44 man/fullscreen.Rd | 46 man/geodesics.Rd | 379 +- man/gps.Rd | 118 man/groupedLayersControlOptions.Rd | 128 man/handlersOptions.Rd | 112 man/heatmap-legend.Rd |only man/heatmap.Rd | 407 +- man/leaflet.extras-package.Rd | 126 man/leafletExtrasDependencies.Rd | 32 man/leaflethash.Rd | 38 man/measure-path.Rd | 181 - man/omnivore.Rd | 999 ++--- man/pulseMarkers.Rd | 287 - man/search-features.Rd | 74 man/search-geocoding.Rd | 289 - man/search-options.Rd | 236 - man/sleep.Rd | 86 man/style-editor.Rd | 94 man/toolbarOptions.Rd | 96 man/utils.Rd | 125 man/weatherMarkers.Rd | 269 - man/webglheatmap.Rd | 521 +- man/wms-legend.Rd | 116 tests/testthat.R | 26 tests/testthat/test-geodesic.R | 1098 +++--- tests/testthat/test-geojson.R | 690 +-- tests/testthat/test-geojson_mini.R | 706 ++-- tests/testthat/test-groupedlayerscontrol.R | 256 - tests/testthat/test-heatmaps.R | 794 ++-- tests/testthat/test-layers.R | 88 tests/testthat/test-map-controls.R | 1742 +++++----- tests/testthat/test-maputils.R | 93 tests/testthat/test-marker.R | 764 ++-- tests/testthat/testdata |only 131 files changed, 14736 insertions(+), 14253 deletions(-)
More information about leaflet.extras at CRAN
Permanent link
Title: How to Add Two R Tables
Description: Methods to "add" two R tables; also an alternative
interpretation of named vectors as generalized R tables, so that
c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses
'disordR' discipline (Hankin, 2022,
<doi:10.48550/arXiv.2210.03856>). Extraction and replacement
methods are provided. The underlying mathematical structure is
the Free Abelian group, hence the name. To cite in publications
please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between frab versions 0.0-6 dated 2024-07-24 and 0.0-7 dated 2026-09-16
DESCRIPTION | 11 ++-- MD5 | 31 ++++++------ NEWS.md | 41 +++++++++------- R/frab.R | 93 ++++++++++++++++++++----------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/frab.Rmd | 5 ++ inst/doc/frab.html | 23 +++++---- man/Concatenate.Rd |only man/frab.Rd | 8 +-- man/misc.Rd | 8 ++- man/zero.Rd | 2 src/frab.cpp | 64 ++++++++++++------------- src/frab.h | 11 +++- src/sparsetable_ops.cpp | 119 ++++++++++++++++++++---------------------------- vignettes/frab.Rmd | 5 ++ vignettes/frab.bib | 8 +++ 17 files changed, 230 insertions(+), 199 deletions(-)
Title: Clustering with Overlaps
Description: Provide functions for overlaps clustering, fuzzy clustering and interval-valued data manipulation. The package implement the following algorithms:
OKM (Overlapping Kmeans) from Cleuziou, G. (2007) <doi:10.1109/icpr.2008.4761079> ;
NEOKM (Non-exhaustive overlapping Kmeans) from Whang, J. J., Dhillon, I. S., and Gleich, D. F. (2015) <doi:10.1137/1.9781611974010.105> ;
Fuzzy Cmeans from Bezdek, J. C. (1981) <doi:10.1007/978-1-4757-0450-1> ;
Fuzzy I-Cmeans from de A.T. De Carvalho, F. (2005) <doi:10.1016/j.patrec.2006.08.014>.
Author: Guillaume Cleuziou [aut],
Nicolas Hiot [aut, cre] ,
Chengge Shi [ctb]
Maintainer: Nicolas Hiot <nicolas.hiot@univ-orleans.fr>
Diff between COveR versions 1.1.0 dated 2024-11-13 and 1.1.1 dated 2026-09-16
DESCRIPTION | 15 ++++++++++----- MD5 | 6 +++--- README.md | 6 ++++++ src/okm/okm.c | 45 +++++++++++++++++++++++++++++++++------------ 4 files changed, 52 insertions(+), 20 deletions(-)
Title: Access 'umwelt.info' API
Description: Provides an R-based access to the datasets including their
resources from the portal <https://umwelt.info>. The package allows for
an easy integration of those datasets into your R-based workflows. The
functionality of the package mirrors the web-based access as provided
at <https://umwelt.info>. You can use the same queries and get the same
datasets by accessing our API.
Author: Luise Quoss [aut, cre],
Johannes Vogel [aut],
Maximilian Berthold [aut],
Nationales Zentrum fuer Umwelt- und Naturschutzinformationen [cph]
Maintainer: Luise Quoss <luise.quoss@uba.de>
Diff between umweltapir versions 0.2.2 dated 2026-08-24 and 0.2.3 dated 2026-09-16
DESCRIPTION | 6 ++--- MD5 | 16 +++++++------- NEWS.md | 4 +++ R/download_resources.R | 7 ++++-- R/fetch_api.R | 34 +++++++++++++++++++++++------- man/download_resources.Rd | 4 +-- man/fetch_data.Rd | 4 +-- man/umweltapir-package.Rd | 4 +-- tests/testthat/test-fetch_api.R | 44 +++++++++++++++++++++++++++++++++++----- 9 files changed, 91 insertions(+), 32 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Brent Pedersen [cph] ,
Giulio Genovese [cph] ,
Nicola Asuni [cph] ,
Devon Ryan [cph] ,
Duc [...truncated...]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 1.5.1-0.1.3 dated 2026-07-28 and 1.5.2-0.1.5 dated 2026-09-16
Rduckhts-1.5.1-0.1.3/Rduckhts/inst/duckhts_extension/bcftools_shim.c |only Rduckhts-1.5.1-0.1.3/Rduckhts/inst/duckhts_extension/duckvep/duckvep_variant_tile.c |only Rduckhts-1.5.1-0.1.3/Rduckhts/inst/duckhts_extension/duckvep/duckvep_variant_tile.h |only Rduckhts-1.5.1-0.1.3/Rduckhts/inst/duckhts_extension/include/vcf_types.h |only Rduckhts-1.5.1-0.1.3/Rduckhts/inst/extdata/samples_s1.txt |only Rduckhts-1.5.1-0.1.3/Rduckhts/man/duckhts_append_metadata.Rd |only Rduckhts-1.5.1-0.1.3/Rduckhts/man/duckhts_detect_platform.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/DESCRIPTION | 12 Rduckhts-1.5.2-0.1.5/Rduckhts/MD5 | 464 Rduckhts-1.5.2-0.1.5/Rduckhts/NAMESPACE | 11 Rduckhts-1.5.2-0.1.5/Rduckhts/NEWS.md | 178 Rduckhts-1.5.2-0.1.5/Rduckhts/R/bootstrap.R | 525 Rduckhts-1.5.2-0.1.5/Rduckhts/R/build.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/catalog.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/connection.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/convert_parquet.R | 387 Rduckhts-1.5.2-0.1.5/Rduckhts/R/duckhts.R | 2552 ++-- Rduckhts-1.5.2-0.1.5/Rduckhts/R/extension_metadata.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/geno.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/haplotypes.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/htslib.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/load_compat.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/package.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/package_paths.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/simd.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/somalier.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/source_manifest.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/sql_helpers.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/R/type_helpers.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/configure | 46 Rduckhts-1.5.2-0.1.5/Rduckhts/configure.win | 46 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/COPYRIGHT | 7 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bam_reader.c | 448 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bam_site_counts.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_field_vector.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_filter_vector.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_format.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_genotypes.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_reader.c | 4341 +------ Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcf_scan.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcftools_filter.c | 424 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/bcftools_norm_udf.c | 275 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckhts.c | 496 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckhts_sources.tsv |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_annotate.c | 1247 +- Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_ensembl.c | 7 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_haplotype_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_model.c | 89 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_model.h | 10 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_phase_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_reference.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_reference.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/duckvep_sql.c | 350 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/include/duckvep_kernel.h | 23 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_annotation_internal.h | 18 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_carriers.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_carriers.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_coding.c | 11 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_coding.h | 14 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_codon.c | 132 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_codon.h | 51 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_compat.h | 26 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_delta.c | 2612 ++-- Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_delta.h | 278 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_effect.c | 92 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_effect.h | 7 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_event.h | 44 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_haplotype.c | 559 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_haplotype.h | 121 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_haplotype_stream.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_haplotype_stream.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_hgvs.c | 1578 ++ Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_hgvs.h | 145 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_kernel.c | 231 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_model_internal.h | 19 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_phase.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_phase.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_projection.c | 225 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_projection.h | 38 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_sequence_diff.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_sequence_diff.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_sv.c | 76 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_sv.h | 30 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_transcript_edit.c | 264 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/duckvep/kernel/src/duckvep_transcript_edit.h | 52 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/geno_reader.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/cram/cram_io.c | 16 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/cram/cram_structs.h | 1 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/faidx.c | 118 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/hts.c | 4 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/htslib.map | 1 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/htslib/faidx.h | 15 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/htslib/hts.h | 5 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/htslib/sam.h | 3 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/htslib/vcf.h | 1 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/htslib/vcf.c | 55 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bam_format.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bam_site_counts.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_field_vector.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_filter_vector.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_format.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_genotypes.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_index_snapshot.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcf_scan.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/bcftools_shim.h | 26 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/duckdb_alloc.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/duckdb_list.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/duckhts_somalier.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/duckvep_sql.h | 1 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/liftover_nw_limit.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/reference_cache.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/region_list.h |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/include/vep_parser.h | 4 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/interval_udf.c | 9 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/liftover_udf.c | 126 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/munge_udf.c | 145 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/reference_cache.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/region_list.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/score_udf.c | 20 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/seq_reader.c | 134 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier_bam_extract_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier_contamination_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier_matched_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/somalier_vcf_extract_sql.c |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/tabix_reader.c | 84 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/duckhts_extension/vep_parser.c | 56 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_materialize.sam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_offset.sam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_offset.sam.bgz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_offset.sam.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_offset_gzip.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_offset_uncompressed.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_read_groups.sam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_record_ends.tsv |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.bam.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.bam.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.bam.legacy.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.bam.legacy.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.cram |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_all_unplaced.cram.crai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.bam.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.bam.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.bam.legacy.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.bam.legacy.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.cram |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_empty.cram.crai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_malformed.sam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.bam.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.bam.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.bam.legacy.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.bam.legacy.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.cram |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_mixed.cram.crai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.bam.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.bam.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.bam.legacy.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.bam.legacy.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.cram |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bam_scan_single.cram.crai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_cache_lifecycle.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_filter_list_regression.vcf | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_literal_contigs.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_literal_contigs.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_literal_contigs.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_literal_contigs.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_literal_contigs.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scalar_counts.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scalar_counts.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scalar_counts.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scalar_counts.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scalar_counts.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.empty.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.empty.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.empty.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.empty.vcf.gz.index.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.empty.vcf.gz.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.full.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.full.vcf.gz.index.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.full.vcf.gz.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.none.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.none.vcf.gz.index.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.none.vcf.gz.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.partial.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.partial.vcf.gz.index.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.partial.vcf.gz.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.shifted.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.shifted.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.shifted.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.shifted.vcf.gz.index.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.shifted.vcf.gz.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/bcf_scan_contigs.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_hgvs_anchor.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_hgvs_anchor.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_indel_translation.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_indel_translation.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_minimal.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_minimal.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_n_indel.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_n_indel.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_repeat.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/duckvep_repeat.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/faidx_invalid.bed |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/faidx_invalid.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/faidx_invalid.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_calls.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_calls.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_calls.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_calls.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_calls.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format_case.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format_case.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format_case.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format_case.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_format_case.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_gt_allele.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_gt_allele.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_gt_allele.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_phase_partial.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_number.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_number.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_number.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_payload.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_type.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_type.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_type.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_width.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_width.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_ps_width.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_raw_gt.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/geno_vcf44.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/liftover_nw_limit.chain |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/liftover_nw_limit_dst.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/liftover_nw_limit_dst.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/liftover_nw_limit_src.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/liftover_nw_limit_src.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_names.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_names.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_names.fa.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_names.fa.gz.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_names.fa.gz.gzi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union.bcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union.bcf.csi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union.vcf.gz.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union_no_contig.index.tbi |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/region_union_no_contig.vcf.gz |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/somalier_brace.bam |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/somalier_brace.bam.bai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/somalier_brace.fa |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/somalier_brace.fa.fai |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/somalier_sites.vcf |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/tidy_chunk_boundary.vcf | 3 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/extdata/vcfpp_manifest.tsv | 18 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/function_catalog/functions.md | 342 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/function_catalog/functions.tsv | 73 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/function_catalog/functions.yaml | 498 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/function_catalog/reference.md |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bam_bed_coverage.R | 19 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bam_file_offset.R | 82 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bam_materialize.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bam_scan.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_basic.R | 580 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bcf.R | 762 - Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bcf_regression.R | 272 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bcftools_norm.R | 142 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bigwig.R | 18 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_bin_counts.R | 33 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_cgranges_api.R | 110 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_cigar_utils.R | 9 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_connection.R | 41 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_convert_parquet.R | 109 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_duckvep.R | 5860 +++++----- Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_duckvep_haplotypes.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_duckvep_phase.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_fastq_qc.R | 186 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_geno.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_htslib_contract.R | 171 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_indexes_bgzip.R | 31 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_integration.R | 274 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_intervals.R | 84 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_liftover.R | 332 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_liftover_stress.R | 81 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_mosdepth.R | 113 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_multi.R | 42 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_munge.R | 59 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_munge_threading.R | 27 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_native_marker.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_parallel_empty_contigs.R | 83 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_pileup.R | 95 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_quality_encoding.R | 67 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_reference_cache.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_region_lists.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_samtools_idxstats.R | 20 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_score.R | 411 Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_seq_ops.R | 591 - Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_somalier.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_somalier_extraction.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_sql_quoting.R |only Rduckhts-1.5.2-0.1.5/Rduckhts/inst/tinytest/test_variantkey_regionkey.R | 18 Rduckhts-1.5.2-0.1.5/Rduckhts/man/Rduckhts.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/detect_complex_types.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/duckdb_type_mappings.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/duckhts_build.Rd | 23 Rduckhts-1.5.2-0.1.5/Rduckhts/man/duckhts_load.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/extract_array_element.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/extract_map_data.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_bcf.Rd | 15 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_bcf_multi.Rd | 5 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_bcf_samples.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_connect.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_functions.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_geno.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_haplotypes.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_htslib_config.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_htslib_info.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_htslib_version.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_load.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_simd_backend.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_bam_counts.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_charr.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_import_sites.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_matched_contamination.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_relatedness.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_sketches.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/rduckhts_somalier_vcf_counts.Rd |only Rduckhts-1.5.2-0.1.5/Rduckhts/man/setup_hts_env.Rd | 2 Rduckhts-1.5.2-0.1.5/Rduckhts/src |only Rduckhts-1.5.2-0.1.5/Rduckhts/tests/tinytest.R | 4 Rduckhts-1.5.2-0.1.5/Rduckhts/tools/append_extension_metadata.R | 109 Rduckhts-1.5.2-0.1.5/Rduckhts/tools/bootstrap.R | 1 Rduckhts-1.5.2-0.1.5/Rduckhts/tools/write_htslib_config.R |only 345 files changed, 17748 insertions(+), 13480 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.7.0 dated 2026-08-31 and 3.8.0 dated 2026-09-16
randomForestSRC-3.7.0/randomForestSRC/man/utilities_internal.Rd |only randomForestSRC-3.8.0/randomForestSRC/DESCRIPTION | 8 randomForestSRC-3.8.0/randomForestSRC/MD5 | 92 - randomForestSRC-3.8.0/randomForestSRC/NAMESPACE | 5 randomForestSRC-3.8.0/randomForestSRC/NEWS.md | 101 + randomForestSRC-3.8.0/randomForestSRC/R/generic.predict.rfsrc.R | 10 randomForestSRC-3.8.0/randomForestSRC/R/imbalanced.rfsrc.R | 4 randomForestSRC-3.8.0/randomForestSRC/R/impute.learn.rfsrc.R | 391 +++- randomForestSRC-3.8.0/randomForestSRC/R/impute.rfsrc.R | 164 + randomForestSRC-3.8.0/randomForestSRC/R/partial.rfsrc.R | 279 +-- randomForestSRC-3.8.0/randomForestSRC/R/plot.quantreg.rfsrc.R | 355 ++- randomForestSRC-3.8.0/randomForestSRC/R/plot.subsample.rfsrc.R | 204 +- randomForestSRC-3.8.0/randomForestSRC/R/plot.survival.rfsrc.R | 33 randomForestSRC-3.8.0/randomForestSRC/R/plot.variable.rfsrc.R | 792 ++++---- randomForestSRC-3.8.0/randomForestSRC/R/print.rfsrc.R | 130 - randomForestSRC-3.8.0/randomForestSRC/R/quantreg.rfsrc.R | 495 ++--- randomForestSRC-3.8.0/randomForestSRC/R/rfsrc.R | 14 randomForestSRC-3.8.0/randomForestSRC/R/rfsrc.anonymous.R | 4 randomForestSRC-3.8.0/randomForestSRC/R/sidClustering.rfsrc.R | 6 randomForestSRC-3.8.0/randomForestSRC/R/subsample.rfsrc.R | 123 - randomForestSRC-3.8.0/randomForestSRC/R/utilities_data.R | 23 randomForestSRC-3.8.0/randomForestSRC/R/utilities_imbalanced.R | 419 ++-- randomForestSRC-3.8.0/randomForestSRC/R/utilities_impute.R | 202 ++ randomForestSRC-3.8.0/randomForestSRC/R/utilities_impute_learn.R | 830 +++++++-- randomForestSRC-3.8.0/randomForestSRC/R/utilities_multivariate.R | 9 randomForestSRC-3.8.0/randomForestSRC/R/utilities_performance.R | 11 randomForestSRC-3.8.0/randomForestSRC/R/utilities_predict.R | 360 ++- randomForestSRC-3.8.0/randomForestSRC/R/utilities_quantreg.R | 718 ++++++- randomForestSRC-3.8.0/randomForestSRC/R/utilities_subsample.R | 306 ++- randomForestSRC-3.8.0/randomForestSRC/R/utilities_subsample_bootstrap.R | 49 randomForestSRC-3.8.0/randomForestSRC/R/utilities_survival.R | 105 + randomForestSRC-3.8.0/randomForestSRC/man/classification.performance.Rd |only randomForestSRC-3.8.0/randomForestSRC/man/fast.saveload.Rd |only randomForestSRC-3.8.0/randomForestSRC/man/imbalanced.rfsrc.Rd | 733 ++++---- randomForestSRC-3.8.0/randomForestSRC/man/impute.learn.rfsrc.Rd | 218 +- randomForestSRC-3.8.0/randomForestSRC/man/impute.rfsrc.Rd | 65 randomForestSRC-3.8.0/randomForestSRC/man/multivariate.values.Rd |only randomForestSRC-3.8.0/randomForestSRC/man/nutrigenomic.Rd | 20 randomForestSRC-3.8.0/randomForestSRC/man/partial.rfsrc.Rd | 528 +++-- randomForestSRC-3.8.0/randomForestSRC/man/plot.quantreg.rfsrc.Rd | 191 +- randomForestSRC-3.8.0/randomForestSRC/man/plot.subsample.rfsrc.Rd | 220 +- randomForestSRC-3.8.0/randomForestSRC/man/plot.survival.rfsrc.Rd | 171 + randomForestSRC-3.8.0/randomForestSRC/man/plot.variable.rfsrc.Rd | 461 +++-- randomForestSRC-3.8.0/randomForestSRC/man/predict.rfsrc.Rd | 69 randomForestSRC-3.8.0/randomForestSRC/man/print.rfsrc.Rd | 11 randomForestSRC-3.8.0/randomForestSRC/man/quantreg.rfsrc.Rd | 904 ++++++---- randomForestSRC-3.8.0/randomForestSRC/man/rfsrc.Rd | 92 - randomForestSRC-3.8.0/randomForestSRC/man/sidClustering.rfsrc.Rd | 118 + randomForestSRC-3.8.0/randomForestSRC/man/subsample.rfsrc.Rd | 615 ++++-- 49 files changed, 7101 insertions(+), 3557 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.3 dated 2026-09-09 and 1.3.4 dated 2026-09-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 - NEWS.md | 5 +++++ R/clusterCharts.R | 2 +- R/leaflet.extras2-package.R | 1 - 6 files changed, 15 insertions(+), 12 deletions(-)
More information about leaflet.extras2 at CRAN
Permanent link
Title: Make Symmetric and Asymmetric ARDL Estimations
Description: Implements estimation procedures for Autoregressive Distributed Lag (ARDL)
and Nonlinear ARDL (NARDL) models, which allow researchers to investigate both
short- and long-run relationships in time series data under mixed orders of integration.
The package supports simultaneous modeling of symmetric and asymmetric regressors,
flexible treatment of short-run and long-run asymmetries, and automated equation handling.
It includes several cointegration testing approaches such as the Pesaran-Shin-Smith F
and t bounds tests, and narayan test.
Methodological foundations are provided in Pesaran, Shin, and Smith (2001)
<doi:10.1016/S0304-4076(01)00049-5> and Shin, Yu, and Greenwood-Nimmo (2014, ISBN:9780123855079).
Author: Huseyin karamelikli [aut, cre] ,
Huseyin Utku Demir [aut]
Maintainer: Huseyin karamelikli <hakperest@gmail.com>
Diff between kardl versions 2.0.5 dated 2026-07-22 and 2.0.6 dated 2026-09-16
kardl-2.0.5/kardl/build/partial.rdb |only kardl-2.0.6/kardl/DESCRIPTION | 11 ++++++---- kardl-2.0.6/kardl/MD5 | 9 +++++--- kardl-2.0.6/kardl/R/old_versions_data.R |only kardl-2.0.6/kardl/build/stage23.rdb |only kardl-2.0.6/kardl/data |only kardl-2.0.6/kardl/inst/doc/intro.html | 32 +++++++++++++++--------------- kardl-2.0.6/kardl/man/imf_example_data.Rd |only 8 files changed, 29 insertions(+), 23 deletions(-)
Title: R Interface to the 'COIN-OR' 'Clp' Linear Programming Solver
Description: Solves linear programs with 'Clp', the simplex and interior
point code of the 'COIN-OR' project <https://github.com/coin-or/Clp>.
Provides a one-call solver interface for dense and sparse constraint
matrices, and complete low level bindings to the 'Clp' callable library
covering problem construction, warm starts, presolve options, basis
access and 'MPS' files. A compatibility layer reproduces the interface
of the archived 'clpAPI' package so that existing code keeps working.
'Clp' itself is not bundled and must be installed on the system; the
'Rtools' toolchain supplies it on 'Windows', from 'Rtools' 4.3 on.
Author: Sam Lovick [aut, cre]
Maintainer: Sam Lovick <sam@lovickconsulting.com>
Diff between coinclp versions 0.1.0 dated 2026-09-15 and 0.1.1 dated 2026-09-16
DESCRIPTION | 11 ++++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 25 +++++++++++++++++++++++++ R/coinclp-package.R | 5 ++++- R/names-io.R | 11 +++++++++++ README.md | 24 +++++++++++++++++++++++- inst/doc/coinclp.Rmd | 6 ++++-- inst/doc/coinclp.html | 5 ++++- man/clp_save_model.Rd | 12 ++++++++++++ man/coinclp-package.Rd | 5 ++++- src/Makevars.win | 26 +++++++++++++++++++------- tests/test-compat-clpAPI.R | 16 +++++++++++----- vignettes/coinclp.Rmd | 6 ++++-- 13 files changed, 139 insertions(+), 37 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2025) <doi:10.3758/s13428-025-02643-0>.
Author: Vencislav Popov [aut, cph] ,
Gidon T. Frischkorn [aut, cre, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Gidon T. Frischkorn <gfrischkorn@icloud.com>
Diff between bmm versions 1.3.1 dated 2026-06-05 and 1.3.2 dated 2026-09-16
DESCRIPTION | 20 - MD5 | 88 +++---- NAMESPACE | 3 NEWS.md | 27 ++ R/bmm.R | 1 R/bmmformula.R | 27 ++ R/distributions.R | 24 + R/helpers-data.R | 14 - R/helpers-inits.R | 30 +- R/helpers-model.R | 235 +++++++++++++++---- R/helpers-parameters.R | 4 R/helpers-prior.R | 11 R/model_cswald.R | 7 R/model_ddm.R | 8 R/model_ezdm.R | 8 R/model_imm.R | 3 R/model_m3.R | 44 +-- R/model_mixture2p.R | 3 R/model_mixture3p.R | 3 R/model_sdm.R | 77 +++++- R/summary.R | 15 - R/update.R | 8 R/utils.R | 26 +- README.md | 12 build/partial.rdb |binary inst/stan_chunks/sdm_simple_funs.stan | 27 ++ inst/stan_chunks/sdm_simple_likelihood.stan | 10 inst/stan_chunks/sdm_simple_likelihood_threaded.stan |only inst/stan_chunks/sdm_simple_tdata.stan | 24 + man/bmm-package.Rd | 8 man/cswald.Rd | 4 man/ddm.Rd | 5 man/ezdm.Rd | 5 man/m3.Rd | 6 man/use_model_template.Rd | 7 tests/testthat/test-distributions.R | 20 + tests/testthat/test-helpers-formula.R | 33 ++ tests/testthat/test-helpers-init.R | 111 ++++++++ tests/testthat/test-helpers-model.R | 85 ++++++ tests/testthat/test-helpers-parameters.R | 14 + tests/testthat/test-helpers-prior.R | 37 ++ tests/testthat/test-model_ezdm.R | 5 tests/testthat/test-model_m3.R | 64 +++++ tests/testthat/test-model_sdm-stancode.R |only tests/testthat/test-parameters.R | 54 ++++ tests/testthat/test-summary.R | 66 +++++ 46 files changed, 1081 insertions(+), 202 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.8.0 dated 2025-11-12 and 1.9.0 dated 2026-09-16
DESCRIPTION | 10 - MD5 | 266 +++++++++++++++++++++-------------------- NEWS.md | 15 ++ R/rd-AJR5.R | 3 R/rd-Arca.R | 4 R/rd-EUCC.R |only R/rd-Presidents.R | 2 R/rd-TV16.R | 8 - R/rd-african_coups.R | 3 R/rd-eurouhi.R |only R/rd-natodefspend.R |only R/rd-postcol_growth.R | 31 +++- R/rd-shuparks.R |only README.md | 4 build/partial.rdb |binary data/AJR5.rda |binary data/Arca.rda |binary data/CFT15.rda |binary data/CP77.rda |binary data/DAPO.rda |binary data/DCE12.rda |binary data/DJIA.rda |binary data/DST.rda |binary data/Datasaurus.rda |binary data/Dee04.rda |binary data/EBJ.rda |binary data/ESS10NO.rda |binary data/ESS9GB.rda |binary data/ESSBE5.rda |binary data/EUCC.rda |only data/GHR04.rda |binary data/Guber99.rda |binary data/LOTI.rda |binary data/LTPT.rda |binary data/LTWT.rda |binary data/Lipset59.rda |binary data/Mitchell68.rda |binary data/Newhouse77.rda |binary data/ODGI.rda |binary data/OODTPT.rda |binary data/PPGE.rda |binary data/PRDEG.rda |binary data/Parvin73.rda |binary data/Presidents.rda |binary data/Russett64.rda |binary data/SBCD.rda |binary data/SCP16.rda |binary data/TV16.rda |binary data/USFAHR.rda |binary data/Weede84.rda |binary data/af_crime93.rda |binary data/african_coups.rda |binary data/aluminum_premiums.rda |binary data/anes_partytherms.rda |binary data/anes_prochoice.rda |binary data/anes_vote84.rda |binary data/arcticseaice.rda |binary data/arg_tariff.rda |binary data/asn_stats.rda |binary data/chile88.rda |binary data/china_peace.rda |binary data/clemson_temps.rda |binary data/co2emissions.rda |binary data/coffee_imports.rda |binary data/coffee_price.rda |binary data/commodity_prices.rda |binary data/country_isocodes.rda |binary data/eight_schools.rda |binary data/election_turnout.rda |binary data/epl_odds.rda |binary data/eq_passengercars.rda |binary data/eu_ua_fta24.rda |binary data/eurostat_codes.rda |binary data/eurouhi.rda |only data/eustates.rda |binary data/fakeAPI.rda |binary data/fakeHappiness.rda |binary data/fakeLogit.rda |binary data/fakeTSCS.rda |binary data/fakeTSD.rda |binary data/gas_demand.rda |binary data/gatt_members.rda |binary data/ghp100k.rda |binary data/gss_abortion.rda |binary data/gss_spending.rda |binary data/gss_wages.rda |binary data/illiteracy30.rda |binary data/inglehart03.rda |binary data/min_wage.rda |binary data/mm_mlda.rda |binary data/mm_nhis.rda |binary data/mm_randhie.rda |binary data/mmb_war.rda |binary data/mvprod.rda |binary data/natodefspend.rda |only data/nesarc_drinkspd.rda |binary data/postcol_growth.rda |binary data/pwt_sample.rda |binary data/quartets.rda |binary data/recessions.rda |binary data/rok_unga.rda |binary data/scb_regions.rda |binary data/sealevels.rda |binary data/shuparks.rda |only data/so2concentrations.rda |binary data/states_war.rda |binary data/steves_clothes.rda |binary data/stevesteps.rda |binary data/sugar_price.rda |binary data/sweden_counties.rda |binary data/thatcher_approval.rda |binary data/therms.rda |binary data/turnips.rda |binary data/ukg_eeri.rda |binary data/uniondensity.rda |binary data/usa_chn_gdp_forecasts.rda |binary data/usa_computers.rda |binary data/usa_migration.rda |binary data/usa_states.rda |binary data/usa_tradegdp.rda |binary data/voteincome.rda |binary data/wb_groups.rda |binary data/wbd_example.rda |binary data/wvs_ccodes.rda |binary data/wvs_immig.rda |binary data/wvs_justifbribe.rda |binary data/wvs_usa_abortion.rda |binary data/wvs_usa_educat.rda |binary data/wvs_usa_regions.rda |binary data/yugo_sales.rda |binary man/AJR5.Rd | 3 man/Arca.Rd | 4 man/EUCC.Rd |only man/Presidents.Rd | 2 man/TV16.Rd | 6 man/african_coups.Rd | 3 man/eurouhi.Rd |only man/natodefspend.Rd |only man/postcol_growth.Rd | 29 +++- man/shuparks.Rd |only 140 files changed, 227 insertions(+), 166 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.4.4 dated 2026-05-07 and 2.5.0 dated 2026-09-16
DESCRIPTION | 15 MD5 | 171 ++-- NAMESPACE | 7 NEWS.md | 101 ++ R/RcppExports.R | 8 R/align-fpca.R | 4 R/boxplot.R | 40 - R/curve_boxplot.R | 5 R/curve_functions.R | 28 R/elastic.depth.R | 8 R/elastic.distance.R | 10 R/elastic_changepoint.R | 30 R/elastic_logistic.R | 2 R/elastic_prediction.R | 2 R/elastic_regression.R | 7 R/gauss_model.R | 8 R/geometry.R | 126 --- R/image_funcs.R | 138 --- R/interparc.R |only R/jointfPCA.R | 3 R/kmeans.R | 41 - R/multiple_align_functions.R | 11 R/multivariate_karcher_mean.R | 8 R/optimum.reparam.R | 32 R/pair_align_functions.R | 15 R/pair_align_image.R | 47 - R/pns.R | 7 R/ppd.R | 21 R/predict.curve_pca.R | 56 - R/predict.hfpca.R | 2 R/predict.jfpca.R | 2 R/predict.jfpcah.R | 6 R/predict.lpcr.R | 8 R/predict.mlpcr.R | 8 R/predict.pcr.R | 8 R/predict.vfpca.R | 2 R/refactoring.R | 4 R/regression_functions.R | 4 R/reparam_curve.R | 6 R/reparam_image.R | 5 R/sample_shapes.R | 27 R/time-warping.R | 24 R/tolerance.R | 2 R/utils.R | 22 README.md | 3 man/beta.Rd | 2 man/elastic.depth.Rd | 8 man/elastic.distance.Rd | 8 man/figures/README-1d_aligned_plot-2.png |binary man/figures/README-1d_aligned_plot-3.png |binary man/figures/README-1d_aligned_plot-5.png |binary man/figures/README-1d_aligned_plot-6.png |binary man/gam_to_psi.Rd | 9 man/growth_vel.Rd | 2 man/im.Rd | 2 man/interparc.Rd |only man/multiple_align_functions.Rd | 10 man/optimum.reparam.Rd | 7 man/pair_align_functions.Rd | 14 man/ppd.Rd | 14 man/psi_to_gam.Rd | 9 man/simu_data.Rd | 2 man/simu_warp.Rd | 2 man/simu_warp_median.Rd | 2 man/time_warping.Rd | 15 man/toy_data.Rd | 2 man/toy_warp.Rd | 2 src/RcppExports.cpp | 26 src/fdaqmap/incl/UnitSquareImage.h | 2 src/fdaqmap/src/UnitSquareImage.cpp | 40 + src/fdasrsf/DP.cpp | 107 +- src/fdasrsf/DP.h | 6 src/fdasrsf/DynamicProgrammingQ2.cpp | 58 - src/fdasrsf/DynamicProgrammingQ2.h | 13 src/fdasrsf/dp_grid.cpp | 32 src/fdasrsf/dp_grid.h | 62 - src/fdasrsf/dp_nbhd.cpp | 31 src/fdasrsf/mlogit_warp_grad.cpp | 2 src/fdasrsf/rbfgs.h | 1207 +++++++++++++++++-------------- src/wrapperQMAP.cpp | 15 src/wrapperSRSF.cpp | 41 - tests/testthat/_snaps/boxplot.md | 530 ++++++------- tests/testthat/_snaps/time-warping.md | 2 tests/testthat/test-boxplot.R | 4 tests/testthat/test-image-registration.R |only tests/testthat/test-norm-penalty.R |only tests/testthat/test-optimum-reparam.R |only tests/testthat/test-predict-pcr.R |only tests/testthat/test-regressions.R |only tests/testthat/test-time-warping.R | 56 + 90 files changed, 1886 insertions(+), 1542 deletions(-)
Title: Multiple Unobserved Sources of Error State Space Models
Description: Implements the Power / Trend / Seasonal (PTS) model, a unified
state-space framework based on the Multiple Source of Error (MSOE) model. It brings
the trend, seasonal and irregular component models of Harvey (1989)
<doi:10.1017/CBO9781107049994>, Durbin and Koopman (2012)
<doi:10.1093/acprof:oso/9780199641178.001.0001>, Proietti (2000)
<doi:10.1016/S0169-2070(00)00037-6>, Sbrana and Silvestrini (2023)
<doi:10.1016/j.ijforecast.2022.03.003> and others together under a single
estimation, selection and forecasting interface, with an optional Box-Cox power
transformation. Models are estimated by maximum likelihood through the
Kalman filter and smoother, with automatic component selection by
information criteria.
Author: Diego J. Pedregal [aut, ctb] ,
Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between muse versions 0.1.1 dated 2026-07-30 and 0.1.2 dated 2026-09-16
DESCRIPTION | 17 ++++++++--------- MD5 | 12 ++++++------ NEWS | 10 ++++++++++ README.md | 4 ++++ inst/doc/pts.html | 8 ++++---- man/figures/muse-purple-light-web.png |binary tests/testthat/test_pts_methods.R | 5 ++++- 7 files changed, 36 insertions(+), 20 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the embedded
'libxls' C library <https://github.com/libxls/libxls> and '.xlsx' via
the embedded 'RapidXML' C++ library
<https://rapidxml.sourceforge.net/>. Works on Windows, Mac and Linux
without external dependencies.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Posit, PBC [cph, fnd] ,
Marcin Kalicinski [ctb, cph] ,
Komarov Valery [ctb, cph] ,
Christophe Leitienne [ctb, cph] ,
Bob Colbert [ctb, cph] ,
David Hoerl [ctb, cph] ,
Evan Miller [ctb, cph]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between readxl versions 1.5.0 dated 2026-05-16 and 1.5.0.1 dated 2026-09-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 +++++- src/cran.h | 6 +++--- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: 'LimeSurvey' '.lss' Questionnaires to and from Word Documents
Description: Turn a 'LimeSurvey' '.lss' survey export into a
publication-quality questionnaire document in Word ('.docx') or PDF,
with up to four of the survey's own languages side by side. Every
label the package adds around that content -- column headers, type
names, the audit section -- is written in English, French, German,
Spanish or Italian, whatever the survey languages are. A rule-based
audit flags missing translations, forward filter references,
duplicate codes, array-scale inconsistencies and orphan structural
references. Questionnaires travel the other way too: describe one in
R, or fill in a Word form, and write a '.lss' file ready to import.
Meant for the people who work on questionnaires -- researchers,
methodologists, ethics committees, translators and reviewers -- and
fully local: the source file is the only input, and no questionnaire
content is uploaded to a third-party service.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between lssdoc versions 0.2.0 dated 2026-09-13 and 0.3.0 dated 2026-09-16
DESCRIPTION | 34 MD5 | 99 + NAMESPACE | 6 NEWS.md | 29 R/as_lss_spec.R |only R/chrome_strings.R | 1684 ++++++++++++++++------------- R/lss_defaults.R | 212 +-- R/lss_spec.R | 594 ++++++++-- R/read_form_docx.R |only R/read_lss.R | 196 +++ R/write_form_docx.R |only R/write_lss.R | 435 +++++-- README.md | 58 build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 10 inst/doc/lssdoc.html | 2 inst/doc/write-in-word.R |only inst/doc/write-in-word.Rmd |only inst/doc/write-in-word.html |only man/as_lss_spec.Rd |only man/check_form_docx.Rd |only man/lss_spec.Rd | 64 - man/lss_template_docx.Rd |only man/lssdoc-package.Rd | 4 man/read_form_docx.Rd |only man/read_lss.Rd | 5 man/write_form_docx.Rd |only man/write_lss.Rd | 67 - tests/testthat/_snaps |only tests/testthat/helper-fixtures.R |only tests/testthat/test-as_lss_spec.R |only tests/testthat/test-audit-fixture.R | 4 tests/testthat/test-audit_lss.R | 26 tests/testthat/test-chrome_strings.R | 61 - tests/testthat/test-coverage-boost.R | 4 tests/testthat/test-coverage-boost3.R | 2 tests/testthat/test-coverage-boost5.R | 6 tests/testthat/test-coverage-boost6.R | 10 tests/testthat/test-coverage-full.R | 10 tests/testthat/test-coverage-full2.R | 10 tests/testthat/test-coverage-full3.R | 17 tests/testthat/test-coverage-full4.R | 22 tests/testthat/test-lss_model.R | 14 tests/testthat/test-page-width.R | 4 tests/testthat/test-question_types.R | 2 tests/testthat/test-quotas.R | 4 tests/testthat/test-read_form_docx.R |only tests/testthat/test-read_lss.R | 91 + tests/testthat/test-render-types.R | 6 tests/testthat/test-render_audit.R | 6 tests/testthat/test-render_coverage.R | 36 tests/testthat/test-render_questionnaire.R | 18 tests/testthat/test-render_snapshot.R | 28 tests/testthat/test-variable-names.R | 4 tests/testthat/test-write_form_docx.R |only tests/testthat/test-write_lss.R | 921 +++++++++++---- tests/testthat/test-write_lss_multilang.R |only vignettes/write-in-word.Rmd |only 59 files changed, 3228 insertions(+), 1579 deletions(-)
Title: An R Client to Retrieve Data from DHIS2
Description: Provides a user-friendly interface for interacting with the District Health
Information Software 2 ('DHIS2', <https://dhis2.org>) instance. It streamlines
data retrieval, empowering researchers, analysts, and healthcare professionals
to obtain and utilize data efficiently.
Author: David Kariuki [aut, cre, cph]
Maintainer: David Kariuki <hello@damurka.com>
This is a re-admission after prior archival of version 1.0.6 dated 2024-10-06
Diff between khisr versions 1.0.6 dated 2024-10-06 and 1.0.8 dated 2026-09-16
khisr-1.0.6/khisr/inst/secret/secret.json |only khisr-1.0.8/khisr/DESCRIPTION | 22 khisr-1.0.8/khisr/LICENSE | 2 khisr-1.0.8/khisr/MD5 | 183 + khisr-1.0.8/khisr/NAMESPACE | 38 khisr-1.0.8/khisr/NEWS.md | 182 + khisr-1.0.8/khisr/R/AuthCred-class.R | 55 khisr-1.0.8/khisr/R/analytics-dimension.R | 2 khisr-1.0.8/khisr/R/api_get.R | 250 +- khisr-1.0.8/khisr/R/get_analytics.R | 125 - khisr-1.0.8/khisr/R/get_analytics_by_level.R | 208 - khisr-1.0.8/khisr/R/get_analytics_outliers.R |only khisr-1.0.8/khisr/R/get_complete_data_set_registrations.R |only khisr-1.0.8/khisr/R/get_data_elements_with_category_options.R | 113 khisr-1.0.8/khisr/R/get_data_store.R |only khisr-1.0.8/khisr/R/get_data_value_audits.R |only khisr-1.0.8/khisr/R/get_data_value_sets.R |only khisr-1.0.8/khisr/R/get_datasets_by_level.R | 204 - khisr-1.0.8/khisr/R/get_enrollment_analytics.R |only khisr-1.0.8/khisr/R/get_enrollment_analytics_aggregate.R |only khisr-1.0.8/khisr/R/get_enrollments.R |only khisr-1.0.8/khisr/R/get_event_analytics.R |only khisr-1.0.8/khisr/R/get_event_analytics_aggregate.R |only khisr-1.0.8/khisr/R/get_events.R |only khisr-1.0.8/khisr/R/get_file_resources.R |only khisr-1.0.8/khisr/R/get_geo_features.R |only khisr-1.0.8/khisr/R/get_metadata.R | 150 - khisr-1.0.8/khisr/R/get_metadata_helpers.R | 438 +-- khisr-1.0.8/khisr/R/get_organisations_by_level.R | 110 khisr-1.0.8/khisr/R/get_relationships.R |only khisr-1.0.8/khisr/R/get_sql_views.R |only khisr-1.0.8/khisr/R/get_system_info.R |only khisr-1.0.8/khisr/R/get_tracked_entities.R |only khisr-1.0.8/khisr/R/get_tracker.R |only khisr-1.0.8/khisr/R/get_tracker_analytics.R |only khisr-1.0.8/khisr/R/get_validation_results.R |only khisr-1.0.8/khisr/R/khis_cred.R | 1221 +++++----- khisr-1.0.8/khisr/R/khisr-package.R | 108 khisr-1.0.8/khisr/R/metadata-filter.R | 3 khisr-1.0.8/khisr/R/tracker-filter.R |only khisr-1.0.8/khisr/R/utils-ui.R | 436 +-- khisr-1.0.8/khisr/R/utils.R | 383 +-- khisr-1.0.8/khisr/README.md | 198 + khisr-1.0.8/khisr/build/vignette.rds |binary khisr-1.0.8/khisr/inst/WORDLIST |only khisr-1.0.8/khisr/inst/doc/khisr.R | 75 khisr-1.0.8/khisr/inst/doc/khisr.Rmd | 535 ++-- khisr-1.0.8/khisr/inst/doc/khisr.html | 657 +---- khisr-1.0.8/khisr/inst/extdata/blank_cred_conf.json | 2 khisr-1.0.8/khisr/inst/extdata/valid_cred_conf.json | 14 khisr-1.0.8/khisr/inst/secret/khisr-docs.json |binary khisr-1.0.8/khisr/inst/secret/khisr-testing.json |binary khisr-1.0.8/khisr/man/analytics-dimension.Rd | 2 khisr-1.0.8/khisr/man/get_analytics.Rd | 12 khisr-1.0.8/khisr/man/get_analytics_by_level.Rd | 16 khisr-1.0.8/khisr/man/get_analytics_outliers.Rd |only khisr-1.0.8/khisr/man/get_complete_data_set_registrations.Rd |only khisr-1.0.8/khisr/man/get_data_elements_with_category_options.Rd | 2 khisr-1.0.8/khisr/man/get_data_sets_by_level.Rd | 12 khisr-1.0.8/khisr/man/get_data_store_keys.Rd |only khisr-1.0.8/khisr/man/get_data_store_namespaces.Rd |only khisr-1.0.8/khisr/man/get_data_store_value.Rd |only khisr-1.0.8/khisr/man/get_data_value_audits.Rd |only khisr-1.0.8/khisr/man/get_data_value_sets.Rd |only khisr-1.0.8/khisr/man/get_enrollment_analytics.Rd |only khisr-1.0.8/khisr/man/get_enrollment_analytics_aggregate.Rd |only khisr-1.0.8/khisr/man/get_enrollments.Rd |only khisr-1.0.8/khisr/man/get_event_analytics.Rd |only khisr-1.0.8/khisr/man/get_event_analytics_aggregate.Rd |only khisr-1.0.8/khisr/man/get_events.Rd |only khisr-1.0.8/khisr/man/get_file_resources.Rd |only khisr-1.0.8/khisr/man/get_geo_features.Rd |only khisr-1.0.8/khisr/man/get_metadata.Rd | 6 khisr-1.0.8/khisr/man/get_organisations_by_level.Rd | 6 khisr-1.0.8/khisr/man/get_relationships.Rd |only khisr-1.0.8/khisr/man/get_sql_view_data.Rd |only khisr-1.0.8/khisr/man/get_sql_views.Rd |only khisr-1.0.8/khisr/man/get_system_info.Rd |only khisr-1.0.8/khisr/man/get_tracked_entities.Rd |only khisr-1.0.8/khisr/man/get_validation_results.Rd |only khisr-1.0.8/khisr/man/khis_api_version.Rd |only khisr-1.0.8/khisr/man/khis_base_url.Rd | 5 khisr-1.0.8/khisr/man/khis_cred.Rd | 47 khisr-1.0.8/khisr/man/khis_cred_clear.Rd | 1 khisr-1.0.8/khisr/man/khis_display_name.Rd | 93 khisr-1.0.8/khisr/man/khis_has_cred.Rd | 3 khisr-1.0.8/khisr/man/khis_username.Rd | 7 khisr-1.0.8/khisr/man/khisr-configuration.Rd | 14 khisr-1.0.8/khisr/man/khisr-package.Rd | 2 khisr-1.0.8/khisr/man/metadata-filter.Rd | 2 khisr-1.0.8/khisr/man/metadata-helpers.Rd | 29 khisr-1.0.8/khisr/man/tracked_entity_filter.Rd |only khisr-1.0.8/khisr/tests/testthat/_snaps/AuthCred-class.md | 16 khisr-1.0.8/khisr/tests/testthat/helper.R | 46 khisr-1.0.8/khisr/tests/testthat/test-AuthCred-class.R | 48 khisr-1.0.8/khisr/tests/testthat/test-get_analytics.R | 4 khisr-1.0.8/khisr/tests/testthat/test-get_analytics_by_level.R | 12 khisr-1.0.8/khisr/tests/testthat/test-get_analytics_outliers.R |only khisr-1.0.8/khisr/tests/testthat/test-get_complete_data_set_registrations.R |only khisr-1.0.8/khisr/tests/testthat/test-get_data_elements_with_category_options.R | 8 khisr-1.0.8/khisr/tests/testthat/test-get_data_sets_by_level.R | 14 khisr-1.0.8/khisr/tests/testthat/test-get_data_store.R |only khisr-1.0.8/khisr/tests/testthat/test-get_data_value_audits.R |only khisr-1.0.8/khisr/tests/testthat/test-get_data_value_sets.R |only khisr-1.0.8/khisr/tests/testthat/test-get_enrollment_analytics.R |only khisr-1.0.8/khisr/tests/testthat/test-get_enrollment_analytics_aggregate.R |only khisr-1.0.8/khisr/tests/testthat/test-get_enrollments.R |only khisr-1.0.8/khisr/tests/testthat/test-get_event_analytics.R |only khisr-1.0.8/khisr/tests/testthat/test-get_event_analytics_aggregate.R |only khisr-1.0.8/khisr/tests/testthat/test-get_events.R |only khisr-1.0.8/khisr/tests/testthat/test-get_file_resources.R |only khisr-1.0.8/khisr/tests/testthat/test-get_geo_features.R |only khisr-1.0.8/khisr/tests/testthat/test-get_metadata.R | 25 khisr-1.0.8/khisr/tests/testthat/test-get_metadata_helpers.R | 67 khisr-1.0.8/khisr/tests/testthat/test-get_organisations_by_level.R | 52 khisr-1.0.8/khisr/tests/testthat/test-get_relationships.R |only khisr-1.0.8/khisr/tests/testthat/test-get_sql_views.R |only khisr-1.0.8/khisr/tests/testthat/test-get_system_info.R |only khisr-1.0.8/khisr/tests/testthat/test-get_tracked_entities.R |only khisr-1.0.8/khisr/tests/testthat/test-get_tracker.R |only khisr-1.0.8/khisr/tests/testthat/test-get_tracker_analytics.R |only khisr-1.0.8/khisr/tests/testthat/test-get_validation_results.R |only khisr-1.0.8/khisr/tests/testthat/test-khis_accessors.R |only khisr-1.0.8/khisr/tests/testthat/test-khis_cred.R | 250 +- khisr-1.0.8/khisr/tests/testthat/test-tracker-filter.R |only khisr-1.0.8/khisr/tests/testthat/test-utils.R |only khisr-1.0.8/khisr/vignettes/khisr.Rmd | 535 ++-- 127 files changed, 3790 insertions(+), 3260 deletions(-)
Title: Integrative Bayesian Multiple Regression for Multi-Platform
Biomarkers
Description: A Bayesian framework that integrates several regression models to
identify a parsimonious set of biomarkers shared across disparate data
platforms (for example genomic, transcriptomic and proteomic assays).
Subjects are partitioned into subgroups defined by their pattern of
platform availability, so that no subject with partially missing platform
data is excluded, and information is borrowed across subgroups through a
Markov random field prior on the variable-selection indicators together
with non-local (product moment) priors on the regression effects. The
methodology was introduced for time-to-event outcomes by Chekouo,
Stingo, Doecke and Do (2017) <doi:10.1111/biom.12587>; this package
additionally supports continuous (Gaussian) and binary (probit) outcomes.
Posterior inference is carried out by a Markov chain Monte Carlo sampler
implemented in C for computational efficiency.
Author: Sinian Zhang [aut],
Jianfeng Wang [aut],
Thierry Chekouo [aut, cre]
Maintainer: Thierry Chekouo <tchekouo@umn.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2026-08-22
Diff between IntegMultiReg versions 0.1.1 dated 2026-08-22 and 0.1.3 dated 2026-09-16
DESCRIPTION | 6 MD5 | 68 ++++++--- NAMESPACE | 21 +++ NEWS.md | 64 ++++++--- R/diagnostics.R |only R/fit.R | 211 ++++++++++++++++++++++++------- R/imr-data.R |only R/methods.R | 68 +++++++++ R/posterior-draws.R |only R/posterior-kernel.R |only R/predict.R | 211 ++++++++++++++++++++++--------- README.md | 40 +++++ build/partial.rdb |binary build/vignette.rds |binary configure | 18 +- configure.ac | 2 inst/doc/IntegMultiReg.html | 24 +-- man/IntegMultiReg-package.Rd | 1 man/as.data.frame.imr_data.Rd |only man/compare_imr.Rd |only man/confint.imr.Rd |only man/imr.Rd | 50 ++++++- man/imr_data.Rd |only man/imr_posterior_methods.Rd |only man/plot.imr.Rd | 22 ++- man/posterior_draws.Rd |only man/posterior_summary.Rd |only man/predict.imr.Rd | 18 ++ man/predict.imr_posterior.Rd |only man/validate_imr.Rd |only man/validate_imr_data.Rd |only src/initial.c | 4 src/main_function_final.c | 31 +++- src/main_prediction.c | 34 +++- src/main_prediction_test.c | 4 src/prediction_cv.c | 21 ++- src/sample_gam.c | 9 + src/sample_latent_binary_outcome.c | 8 - src/truncate.c | 8 - tests/testthat/test-data-interface.R |only tests/testthat/test-diagnostics.R |only tests/testthat/test-formula-prediction.R |only tests/testthat/test-gc-safety.R |only tests/testthat/test-posterior-draws.R |only tests/testthat/test-survival-scale.R |only 45 files changed, 723 insertions(+), 220 deletions(-)
Title: Statistical Mediation Analysis for SEMs
Description: Conducts mediation analysis for structural equation models (SEM)
estimated with 'lavaan', 'blavaan', 'cSEM', or 'modsem'. Implements
the Baron and Kenny (1986) <doi:10.1037/0022-3514.51.6.1173> and
Zhao, Lynch & Chen (2010) <doi:10.1086/651257>
approaches to determine the presence and type of mediation. Supports
covariance-based SEM, partial least squares SEM, Bayesian SEM, and
moderated mediation and mediated moderation models. Tests indirect
effects with the Sobel, Delta, Monte-Carlo, and bootstrap methods or,
for Bayesian models, with posterior summaries and equal-tailed or highest
density credible intervals. Reports the effect size measures RIT, RID,
and Upsilon of Lachowicz, Preacher and Kelley (2018)
<doi:10.1037/met0000165>. Results can be summarized, extracted with
standard methods such as summary(), coef() and confint(), and plotted.
Author: Mehmet Mehmetoglu [aut] ,
Matthias Mittner [aut, cre] ,
Kjell Slupphaug [aut]
Maintainer: Matthias Mittner <matthias.mittner@uit.no>
Diff between rmedsem versions 1.0.0 dated 2026-03-16 and 1.1.0 dated 2026-09-16
rmedsem-1.0.0/rmedsem/man/RID.Rd |only rmedsem-1.0.0/rmedsem/man/RIT.Rd |only rmedsem-1.0.0/rmedsem/man/Upsilon.Rd |only rmedsem-1.0.0/rmedsem/man/as.data.frame.rmedsem.Rd |only rmedsem-1.0.0/rmedsem/man/figures/README-unnamed-chunk-2-1.png |only rmedsem-1.0.0/rmedsem/man/figures/README-unnamed-chunk-3-1.png |only rmedsem-1.0.0/rmedsem/man/figures/README-unnamed-chunk-8-1.png |only rmedsem-1.0.0/rmedsem/man/figures/README-unnamed-chunk-9-1.png |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation.pdf |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation.png |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation.svg |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation2.png |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation2.svg |only rmedsem-1.0.0/rmedsem/man/figures/logo_mediation2.svg.2023_06_15_15_26_32.0.svg |only rmedsem-1.0.0/rmedsem/man/figures/make-logo.R |only rmedsem-1.0.0/rmedsem/man/plot_coef.Rd |only rmedsem-1.0.0/rmedsem/man/plot_effect.Rd |only rmedsem-1.0.0/rmedsem/man/pre_indent_merge.Rd |only rmedsem-1.0.0/rmedsem/man/print.rmedsem.Rd |only rmedsem-1.0.0/rmedsem/man/print.rmedsem.blavaan.Rd |only rmedsem-1.0.0/rmedsem/man/print.rmedsem.lavaan.csem.modsem.Rd |only rmedsem-1.0.0/rmedsem/man/print_effectsize.Rd |only rmedsem-1.0.0/rmedsem/man/rmedsem.blavaan.Rd |only rmedsem-1.0.0/rmedsem/man/rmedsem.cSEMResults.Rd |only rmedsem-1.0.0/rmedsem/man/rmedsem.lavaan.Rd |only rmedsem-1.0.0/rmedsem/man/rmedsem.modsem.Rd |only rmedsem-1.0.0/rmedsem/man/summary.rmedsem.Rd |only rmedsem-1.0.0/rmedsem/man/validate_rmedsem_args.Rd |only rmedsem-1.1.0/rmedsem/DESCRIPTION | 24 rmedsem-1.1.0/rmedsem/MD5 | 80 - rmedsem-1.1.0/rmedsem/NAMESPACE | 15 rmedsem-1.1.0/rmedsem/NEWS.md | 53 rmedsem-1.1.0/rmedsem/R/accessors.R | 486 ++++++- rmedsem-1.1.0/rmedsem/R/data.R | 121 + rmedsem-1.1.0/rmedsem/R/plotting.R | 84 - rmedsem-1.1.0/rmedsem/R/printing.R | 614 +++++----- rmedsem-1.1.0/rmedsem/R/rmedsem.R | 338 +++++ rmedsem-1.1.0/rmedsem/R/rmedsem_blavaan.R | 80 - rmedsem-1.1.0/rmedsem/R/rmedsem_csem.R | 71 - rmedsem-1.1.0/rmedsem/R/rmedsem_lavaan.R | 93 - rmedsem-1.1.0/rmedsem/R/rmedsem_modsem.R | 145 -- rmedsem-1.1.0/rmedsem/README.md | 163 +- rmedsem-1.1.0/rmedsem/build |only rmedsem-1.1.0/rmedsem/man/effect-sizes.Rd |only rmedsem-1.1.0/rmedsem/man/figures/README-unnamed-chunk-11-1.png |only rmedsem-1.1.0/rmedsem/man/hsbdemo.Rd | 29 rmedsem-1.1.0/rmedsem/man/mchoice.Rd | 51 rmedsem-1.1.0/rmedsem/man/plot.rmedsem.Rd | 45 rmedsem-1.1.0/rmedsem/man/rmedsem-methods.Rd |only rmedsem-1.1.0/rmedsem/man/rmedsem.Rd | 272 ++++ rmedsem-1.1.0/rmedsem/man/workout.Rd | 44 rmedsem-1.1.0/rmedsem/tests/testthat/test-accessors.R | 94 + rmedsem-1.1.0/rmedsem/tests/testthat/test-argcheck.R |only rmedsem-1.1.0/rmedsem/tests/testthat/test-blavaan.R | 98 + rmedsem-1.1.0/rmedsem/tests/testthat/test-csem.R | 44 rmedsem-1.1.0/rmedsem/tests/testthat/test-modsem.R | 58 rmedsem-1.1.0/rmedsem/tests/testthat/test-printing.R |only rmedsem-1.1.0/rmedsem/tests/testthat/test-upsilon.R | 89 - 58 files changed, 2276 insertions(+), 915 deletions(-)
Title: Universal Design-Oriented Enhancements for 'ggplot2'
Description: A collection of enhancements to 'ggplot2', with a focus on creating Universally Designed, accessible graphs easily and quickly.
Author: Alex Bajcz [aut, cre]
Maintainer: Alex Bajcz <bajcz003@umn.edu>
Diff between ggplotplus versions 0.5.6 dated 2026-07-27 and 0.5.7 dated 2026-09-16
DESCRIPTION | 8 MD5 | 42 - NAMESPACE | 52 - R/UserFacingCoreFunctions.R | 1060 +++++++++++++++++++++++++++++---- R/middleware.R | 286 ++++++++ R/s7methods.R | 11 README.md | 77 ++ man/GeomPointPlus.Rd | 4 man/add_alttext_plus.Rd |only man/direct_labels_plus.Rd | 8 man/dot-directlabel_lines.Rd | 2 man/dot-directlabel_points.Rd | 2 man/dot-is_between.Rd | 5 man/geom_point_plus.Rd | 6 man/ggplotplus-package.Rd | 5 man/icon_array_plus.Rd |only man/scale_continuous_plus.Rd | 4 man/scale_focus_plus.Rd | 179 ++++- man/theme_plus.Rd | 7 tests/testthat/Rplots.pdf |binary tests/testthat/test-Coaching.R | 95 ++ tests/testthat/test-alttext-plus.R |only tests/testthat/test-icon_array_plus.R |only tests/testthat/test-scale_focus_plus.R | 253 +++++++ 24 files changed, 1837 insertions(+), 269 deletions(-)
Title: Deep Compositional Spatial Models
Description: Deep compositional spatial models are standard spatial covariance
models coupled with an injective warping function of the spatial
domain. The warping function is constructed through a composition
of multiple elemental injective functions in a deep-learning
framework. The package implements two cases for the univariate setting; first,
when these warping functions are known up to some weights that
need to be estimated, and, second, when the weights in each layer are random.
In the multivariate setting only the former case is available.
Estimation and inference is done using `tensorflow`, which makes use of
graphics processing units.
For more details see Zammit-Mangion et al. (2022) <doi:10.1080/01621459.2021.1887741>,
Vu et al. (2022) <doi:10.5705/ss.202020.0156>,
Vu et al. (2023) <doi:10.1016/j.spasta.2023.100742>, and
Shao et al. (2025) <doi:10.48550/arXiv.2505.12548>.
Author: Andrew Zammit-Mangion [aut],
Quan Vu [aut, cre],
Xuanjie Shao [aut]
Maintainer: Quan Vu <quanvustats@gmail.com>
Diff between deepspat versions 0.3.2 dated 2026-08-28 and 0.3.3 dated 2026-09-16
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 1 NEWS.md | 36 +++--- R/bisquare_basis.R | 202 +++++++++++++++++---------------- R/deepspat.R | 1 R/summary.deepspat.R | 305 ++++++++++++++++++++++++++------------------------- README.md | 36 ++++-- man/bisquares1D.Rd | 1 man/bisquares2D.Rd | 1 10 files changed, 323 insertions(+), 288 deletions(-)
Title: Canadian Hydrological Analyses
Description: A collection of user-submitted functions to aid in the analysis of hydrological data, particularly for users in Canada. The functions focus on the use of Canadian data sets, and are suited to Canadian hydrology, such as the important cold region hydrological processes and will work with Canadian hydrological models. The functions are grouped into several themes, currently including Statistical hydrology, Basic data manipulations, Visualization, and Spatial hydrology. Functions developed by the Floodnet project are also included. CSHShydRology has been developed with the assistance of the Canadian Society for Hydrological Sciences (CSHS) which is an affiliated society of the Canadian Water Resources Association (CWRA). As of version 1.2.6, functions now fail gracefully when attempting to download data from a url which is unavailable.
Author: Kevin Shook [cre, aut],
Paul Whitfield [aut],
Robert Chlumsky [aut],
Daniel Moore [aut],
Martin Durocher [aut],
Matthew Lemieux [ctb],
Jason Chiang [ctb],
Joel Trubilowicz [aut],
SJ Kim [ctb],
Billy Browning [aut],
Vincenzo Coia [aut],
Jad Saade [ctb [...truncated...]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between CSHShydRology versions 1.5.0 dated 2026-04-20 and 1.6 dated 2026-09-16
DESCRIPTION | 33 +++-- MD5 | 97 +++++++++------- NAMESPACE | 191 +++++++++++++++------------------ NEWS.md | 15 ++ R/ch_annual_plot.R |only R/ch_catchment_hyps.R | 4 R/ch_checkcatchment.R | 19 +-- R/ch_checkchannels.R | 13 +- R/ch_col_transparent.R | 2 R/ch_contours.R | 15 +- R/ch_get_url_data.R | 6 - R/ch_gg_hydrographs.R | 7 - R/ch_read_AHCCD_monthly.R | 4 R/ch_regime_plot.R | 200 +++++++++++++++++++++++++++-------- R/ch_tidyhydat_ECDE_meta.R | 25 ++-- R/ch_volcano_pourpoints.R | 6 - R/ch_volcano_raster.R | 7 - R/ch_wbt_catchment.R | 15 +- R/ch_wbt_catchment_onestep.R | 26 ++-- R/ch_wbt_channels.R | 19 +-- R/ch_wbt_check_whitebox.R | 10 + R/ch_wbt_flow_accumulation.R | 14 +- R/ch_wbt_flow_direction.R | 12 +- R/ch_wbt_pourpoints.R | 11 - R/ch_wbt_removesinks.R | 58 ++++------ R/scale_gumbel.R |only R/utils.R | 23 ++-- README.md | 4 inst/doc/ch_model_hydrograph.html | 14 +- man/CSHShydRology-package.Rd | 5 man/ch_annual_plot.Rd |only man/ch_catchment_hyps.Rd | 2 man/ch_checkcatchment.Rd | 2 man/ch_checkchannels.Rd | 2 man/ch_col_transparent.Rd | 2 man/ch_contours.Rd | 2 man/ch_get_url_data.Rd | 3 man/ch_gumbel_trans.Rd |only man/ch_regime_plot.Rd | 68 ++++++++++- man/ch_test_url_file.Rd | 2 man/ch_volcano_pourpoints.Rd | 2 man/ch_volcano_raster.Rd | 2 man/ch_wbt_catchment.Rd | 2 man/ch_wbt_catchment_onestep.Rd | 2 man/ch_wbt_channels.Rd | 2 man/ch_wbt_check_whitebox.Rd | 2 man/ch_wbt_flow_accumulation.Rd | 2 man/ch_wbt_flow_direction.Rd | 2 man/ch_wbt_pourpoints.Rd | 2 man/gumbel_spacing.Rd |only tests/testthat/test_assert_pkg.R |only tests/testthat/test_ch_annual_plot.R |only tests/testthat/test_ch_regime_plot.R |only tests/testthat/test_scale_gumbel.R |only 54 files changed, 597 insertions(+), 359 deletions(-)
Title: Accessing the 'CHILDES' Database
Description: Tools for connecting to 'CHILDES', an open repository for
transcripts of parent-child interaction. For more information on the
underlying data, see <https://langcog.github.io/childes-db-website/>.
Author: Michael C. Frank [aut, cre, cph],
Mika Braginsky [aut],
Alessandro Sanchez [aut, ctb],
Daniel Yurovsky [aut],
Kyle MacDonald [ctb],
Stephan Meylan [ctb],
Jessica Mankewitz [ctb]
Maintainer: Michael C. Frank <mcfrank@stanford.edu>
Diff between childesr versions 0.2.3 dated 2022-01-26 and 0.3.0 dated 2026-09-16
childesr-0.2.3/childesr/R/childesr.R |only childesr-0.2.3/childesr/man/get_table.Rd |only childesr-0.3.0/childesr/DESCRIPTION | 32 childesr-0.3.0/childesr/MD5 | 85 + childesr-0.3.0/childesr/NAMESPACE | 2 childesr-0.3.0/childesr/NEWS.md | 23 childesr-0.3.0/childesr/R/childesr-package.R |only childesr-0.3.0/childesr/R/connect.R |only childesr-0.3.0/childesr/R/get.R |only childesr-0.3.0/childesr/README.md | 21 childesr-0.3.0/childesr/build/vignette.rds |binary childesr-0.3.0/childesr/inst/doc/access_childes_db.R | 125 +- childesr-0.3.0/childesr/inst/doc/access_childes_db.Rmd | 25 childesr-0.3.0/childesr/inst/doc/access_childes_db.html | 737 +++++++++------- childesr-0.3.0/childesr/man/childesr-package.Rd |only childesr-0.3.0/childesr/man/clear_connections.Rd | 9 childesr-0.3.0/childesr/man/connect_to_childes.Rd | 17 childesr-0.3.0/childesr/man/get_collections.Rd | 10 childesr-0.3.0/childesr/man/get_content.Rd | 15 childesr-0.3.0/childesr/man/get_contexts.Rd | 19 childesr-0.3.0/childesr/man/get_corpora.Rd | 10 childesr-0.3.0/childesr/man/get_db_info.Rd | 12 childesr-0.3.0/childesr/man/get_participants.Rd | 23 childesr-0.3.0/childesr/man/get_speaker_statistics.Rd | 23 childesr-0.3.0/childesr/man/get_sql_query.Rd | 20 childesr-0.3.0/childesr/man/get_tokens.Rd | 23 childesr-0.3.0/childesr/man/get_transcripts.Rd | 23 childesr-0.3.0/childesr/man/get_types.Rd | 23 childesr-0.3.0/childesr/man/get_utterances.Rd | 23 childesr-0.3.0/childesr/tests |only childesr-0.3.0/childesr/vignettes/access_childes_db.Rmd | 25 31 files changed, 840 insertions(+), 485 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, for meta-analysis
across studies. 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 0.2.0 dated 2026-07-02 and 0.4.1 dated 2026-09-16
admixr2-0.2.0/admixr2/man/admClearCache.Rd |only admixr2-0.2.0/admixr2/tests/manual/test-fork-psock.R |only admixr2-0.4.1/admixr2/DESCRIPTION | 21 admixr2-0.4.1/admixr2/MD5 | 166 admixr2-0.4.1/admixr2/NAMESPACE | 3 admixr2-0.4.1/admixr2/NEWS.md | 1702 +++++++ admixr2-0.4.1/admixr2/R/RcppExports.R | 12 admixr2-0.4.1/admixr2/R/adfo.R | 1304 ++++- admixr2-0.4.1/admixr2/R/adfweight.R |only admixr2-0.4.1/admixr2/R/adgh.R | 1294 ++++- admixr2-0.4.1/admixr2/R/adirmc.R | 723 ++- admixr2-0.4.1/admixr2/R/admc.R | 2232 +++++++--- admixr2-0.4.1/admixr2/R/covreport.R |only admixr2-0.4.1/admixr2/R/data.R | 62 admixr2-0.4.1/admixr2/R/datagen.R | 273 - admixr2-0.4.1/admixr2/R/driver.R |only admixr2-0.4.1/admixr2/R/errmodel.R |only admixr2-0.4.1/admixr2/R/estType.R |only admixr2-0.4.1/admixr2/R/examplomycin.R | 88 admixr2-0.4.1/admixr2/R/inference.R |only admixr2-0.4.1/admixr2/R/model.R | 1652 +++++++ admixr2-0.4.1/admixr2/R/optim-steps.R |only admixr2-0.4.1/admixr2/R/parse.R | 342 + admixr2-0.4.1/admixr2/R/plot.R | 419 + admixr2-0.4.1/admixr2/R/simulate.R | 357 + admixr2-0.4.1/admixr2/R/studies.R |only admixr2-0.4.1/admixr2/R/utils.R | 150 admixr2-0.4.1/admixr2/R/zzz.R | 234 - 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admixr2-0.4.1/admixr2/tests/testthat/test-errmodel-rxode2-oracle.R |only admixr2-0.4.1/admixr2/tests/testthat/test-errmodel.R |only admixr2-0.4.1/admixr2/tests/testthat/test-fo-nll.R | 74 admixr2-0.4.1/admixr2/tests/testthat/test-inference.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-adfo.R | 38 admixr2-0.4.1/admixr2/tests/testthat/test-integration-adgh-unpaired.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-adgh.R | 16 admixr2-0.4.1/admixr2/tests/testthat/test-integration-beta.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-cache-hit.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-cold-session.R | 27 admixr2-0.4.1/admixr2/tests/testthat/test-integration-cov.R | 170 admixr2-0.4.1/admixr2/tests/testthat/test-integration-daemon-patch.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-daemon-wipe.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-datagen-roundtrip.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-edge-cases.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-errmodel.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-fixed-theta.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-grad-branches.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-grad.R | 46 admixr2-0.4.1/admixr2/tests/testthat/test-integration-gradbatch-multi.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-irmc.R | 99 admixr2-0.4.1/admixr2/tests/testthat/test-integration-model-constant.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-multi-output.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-ordinal.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-parallel.R | 45 admixr2-0.4.1/admixr2/tests/testthat/test-integration-pipeline.R | 68 admixr2-0.4.1/admixr2/tests/testthat/test-integration-plot.R | 213 admixr2-0.4.1/admixr2/tests/testthat/test-integration-realdata.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-resid-moments.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-roundtrip.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-sandwich.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-sens-columns.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-sens2.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-shi21.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-simulate.R | 341 - admixr2-0.4.1/admixr2/tests/testthat/test-integration-t-errmodel.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-tbs-exact.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-theta-sens.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-worker-load.R |only admixr2-0.4.1/admixr2/tests/testthat/test-integration-xsession-cache.R |only admixr2-0.4.1/admixr2/tests/testthat/test-irmc-kernels.R | 24 admixr2-0.4.1/admixr2/tests/testthat/test-model.R | 358 + admixr2-0.4.1/admixr2/tests/testthat/test-multi-output.R |only admixr2-0.4.1/admixr2/tests/testthat/test-nll-from-samples.R | 45 admixr2-0.4.1/admixr2/tests/testthat/test-normalise-study.R | 259 + admixr2-0.4.1/admixr2/tests/testthat/test-optim-steps-shi.R |only admixr2-0.4.1/admixr2/tests/testthat/test-parse.R | 168 admixr2-0.4.1/admixr2/tests/testthat/test-restart-output-var.R | 7 admixr2-0.4.1/admixr2/tests/testthat/test-sens-ui.R |only admixr2-0.4.1/admixr2/tests/testthat/test-traceplot.R | 62 admixr2-0.4.1/admixr2/tests/testthat/test-transform-vs-rxode2.R |only admixr2-0.4.1/admixr2/tests/testthat/test-utils.R | 131 admixr2-0.4.1/admixr2/vignettes/_common.R |only admixr2-0.4.1/admixr2/vignettes/admixr2.Rmd | 44 110 files changed, 12763 insertions(+), 2969 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-30 0.1.12
2026-05-11 0.1.11
2025-11-05 0.1.10
2024-09-09 0.1.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-06 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-22 0.0.2
2025-01-16 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-08-31 0.12.0
2026-02-04 0.11.3
2024-10-10 0.11.2
2024-01-08 0.11.1
2022-12-13 0.11.0
2021-09-21 0.10.3
2018-07-26 0.10.2
2018-07-09 0.10.1
2016-04-24 0.9.4
2015-02-03 0.9.3
2014-11-15 0.9.2
2014-10-09 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-29 0.2.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-23 1.4.7
2025-12-16 1.4.6
2021-02-01 1.4.5
2020-10-26 1.4.4
2020-09-03 1.4.3
2020-08-03 1.4.2
2020-07-27 1.4.1
2020-07-21 1.4.0
2020-06-29 1.3.9
2020-01-15 1.3.8
2019-01-22 1.3.7
2019-01-15 1.3.6
2018-09-10 1.3.5
2018-07-22 1.3.4
2018-07-18 1.3.3
2018-03-16 1.3.2
2018-03-15 1.3.1
2018-03-13 1.3.0
2018-03-12 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-12 1.5.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-02 0.1-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-29 0.7.4
2026-01-18 0.7.3
2025-12-02 0.7.2
2025-03-19 0.7.1
2024-03-06 0.7.0
2023-04-14 0.6.4
2023-01-19 0.6.3
2022-10-10 0.6.2
2022-03-22 0.6.1
2022-03-08 0.6.0
2021-12-03 0.5.1
2021-10-28 0.5.0
2021-07-29 0.4.1
2021-07-13 0.4.0
2020-08-27 0.3.1
Title: Vertical Profiles of Biological Signals in Weather Radar Data
Description: 'R' implementation of the 'vol2bird' software for generating vertical profiles
of birds and other biological signals in weather radar data. See Dokter et al.
(2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Author: Anders Henja [aut] ,
Adriaan M. Dokter [aut, cre] ,
Alexander Tedeschi [ctb] ,
Tsung-Yu Lin [ctb] ,
Subranshu Maji [ctb] ,
Daniel Sheldon [ctb] ,
Bart Kranstauber [ctb] ,
Jurriaan H. Spaaks [ctb] ,
Lourens Veen [ctb] ,
Iwan Holleman [ctb] ,
Hidde Lei [...truncated...]
Maintainer: Adriaan M. Dokter <vol2birdr@cornell.edu>
Diff between vol2birdR versions 1.3.1 dated 2026-07-27 and 1.3.2 dated 2026-09-16
DESCRIPTION | 10 MD5 | 34 NAMESPACE | 6 NEWS.md | 13 R/install.R | 211 +++ configure | 1354 ++++++++++++++----------- configure.ac | 50 man/assert_version_available.Rd |only man/default_pytorch_version.Rd |only man/get_install_urls.Rd | 5 man/install_config.Rd | 14 man/install_mistnet.Rd | 4 man/install_mistnet_from_file.Rd | 18 man/install_platform.Rd |only man/supported_pytorch_versions_for_platform.Rd |only src/Makevars.win | 14 src/RaveIO.cpp | 12 src/includes/libvol2bird/constants.h | 6 src/libvol2bird/libvol2bird.c | 17 tools/m4/ax_lib_hdf5.m4 | 17 20 files changed, 1110 insertions(+), 675 deletions(-)
Title: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets
Description: The accumulation of single-cell RNA sequencing (scRNA-seq) studies
highlights the potential benefits of integrating multiple datasets. By
augmenting sample sizes and enhancing analytical robustness, integration
can lead to more insightful biological conclusions. However, challenges
arise due to the inherent diversity and batch discrepancies within and
across studies. 'SCIntRuler' addresses these challenges by guiding the
integration of multiple scRNA-seq datasets.
Author: Yue Lyu [aut, cre]
Maintainer: Yue Lyu <yuelyu0521@gmail.com>
This is a re-admission after prior archival of version 0.99.6 dated 2024-07-12
Diff between SCIntRuler versions 0.99.6 dated 2024-07-12 and 0.99.8 dated 2026-09-16
DESCRIPTION | 29 ++- MD5 | 78 +++++----- NAMESPACE | 3 NEWS.md |only R/CalcuSCIR.R | 5 R/FindCell.R | 21 +- R/FindNNDist.R | 20 +- R/FindNNDistC.R | 21 +- R/GetCluster.R | 4 R/NormData.R | 38 ++++- R/PermTest.R | 55 +++++-- R/PlotSCIR.R | 5 R/RcppExports.R | 12 - R/SCEtoSeurat.R | 3 R/SummCluster.R | 3 R/crossdist.R |only R/data.R | 2 R/sim_result_data.R | 2 README.md | 26 ++- build/vignette.rds |binary inst/CITATION |only inst/doc/SCIntRuler.R | 28 +-- inst/doc/SCIntRuler.Rmd | 30 +-- inst/doc/SCIntRuler.html | 288 ++++++++++++++++++-------------------- man/CalcuSCIR.Rd | 5 man/FindCell.Rd | 11 - man/FindNNDist.Rd | 7 man/FindNNDistC.Rd | 7 man/GetCluster.Rd | 4 man/NormData.Rd | 3 man/PermTest.Rd | 12 + man/PlotSCIR.Rd | 5 man/SCEtoSeurat.Rd | 2 man/SummCluster.Rd | 3 man/crossdist.Rd | 6 man/sim_data_sce.Rd | 1 man/sim_result.Rd | 2 tests/testthat/test-FindNNDist.R | 17 ++ tests/testthat/test-NormData.R | 4 tests/testthat/test-PermTest.R |only tests/testthat/test-SCEtoSeurat.R | 9 + vignettes/SCIntRuler.Rmd | 30 +-- 42 files changed, 459 insertions(+), 342 deletions(-)
Title: Verified Interval Arithmetic with Correctly Rounded Kernels
Description: Verified interval arithmetic for R, in the inf-sup (endpoint)
representation of the set-based flavor of the interval standard. Every
operation returns an enclosure that provably contains the exact result:
outward rounding is obtained from the predecessor and successor formulas of
Rump, Zimmermann, Boldo and Melquiond (2009)
<doi:10.1007/s10543-009-0218-z>, which are valid under round-to-nearest and
therefore need no change to the floating-point rounding mode. That mode is
not reachable from R, and changing it would not be a local act: it is
per-thread state of the processor, so it would govern every floating-point
operation executed afterwards on that thread, in this package or anywhere
else. Elementary functions are provided at two levels: a fast level over
the included correctly rounded binary64 implementation, comprising fifteen
kernels from CORE-MATH <doi:10.1109/ARITH54963.2022.00014> and the hardware
square root, widened by the pre-registered slack of two outward step [...truncated...]
Author: Jose Mauricio Gomez Julian [aut, cre] ,
Alexei Sibidanov [ctb, cph],
Paul Zimmermann [ctb, cph],
Tom Hubrecht [ctb, cph],
Cyprien Peignier [ctb, cph],
CERN [cph],
INRIA [cph],
Szabolcs Nagy [ctb, cph]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between RobustArithmetic versions 0.1.0 dated 2026-09-12 and 0.2.0 dated 2026-09-16
RobustArithmetic-0.1.0/RobustArithmetic/man/ra_environment_anchor.Rd |only RobustArithmetic-0.2.0/RobustArithmetic/DESCRIPTION | 57 - RobustArithmetic-0.2.0/RobustArithmetic/MD5 | 97 +- RobustArithmetic-0.2.0/RobustArithmetic/NAMESPACE | 3 RobustArithmetic-0.2.0/RobustArithmetic/NEWS.md |only RobustArithmetic-0.2.0/RobustArithmetic/R/RobustArithmetic-package.R | 30 RobustArithmetic-0.2.0/RobustArithmetic/R/core-math.R |only RobustArithmetic-0.2.0/RobustArithmetic/R/decimal.R | 94 +- RobustArithmetic-0.2.0/RobustArithmetic/R/elementary.R | 134 +-- RobustArithmetic-0.2.0/RobustArithmetic/R/interval-class.R | 6 RobustArithmetic-0.2.0/RobustArithmetic/R/newton.R | 92 +- RobustArithmetic-0.2.0/RobustArithmetic/R/operator-table.R | 126 +- RobustArithmetic-0.2.0/RobustArithmetic/R/safeguards.R | 435 +++++----- RobustArithmetic-0.2.0/RobustArithmetic/R/sysdata.rda |binary RobustArithmetic-0.2.0/RobustArithmetic/R/zzz.R | 18 RobustArithmetic-0.2.0/RobustArithmetic/build/vignette.rds |binary RobustArithmetic-0.2.0/RobustArithmetic/inst/COPYRIGHTS |only RobustArithmetic-0.2.0/RobustArithmetic/inst/doc/robustarithmetic.R | 3 RobustArithmetic-0.2.0/RobustArithmetic/inst/doc/robustarithmetic.Rmd | 42 RobustArithmetic-0.2.0/RobustArithmetic/inst/doc/robustarithmetic.html | 119 +- RobustArithmetic-0.2.0/RobustArithmetic/man/RobustArithmetic-package.Rd | 42 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_check_sentinels.Rd | 63 - RobustArithmetic-0.2.0/RobustArithmetic/man/ra_elem.Rd | 29 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_fast_level_status.Rd |only RobustArithmetic-0.2.0/RobustArithmetic/man/ra_measure_library_error.Rd | 42 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_operator_table.Rd | 55 - RobustArithmetic-0.2.0/RobustArithmetic/man/ra_paving_show.Rd | 14 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_sentinels.Rd | 63 - RobustArithmetic-0.2.0/RobustArithmetic/man/ra_show.Rd | 6 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_slack.Rd | 20 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_solve.Rd | 27 RobustArithmetic-0.2.0/RobustArithmetic/man/ra_verify_operator_table.Rd | 18 RobustArithmetic-0.2.0/RobustArithmetic/src |only RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/core-math-cases.csv |only RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/helper-fast-level.R |only RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-core-math.R |only RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-decimal.R | 148 +++ RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-elementary.R | 101 +- RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-expression.R | 2 RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-gate-elementary-vs-mpfr.R | 141 +-- RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-newton.R | 56 + RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-operator-table.R | 28 RobustArithmetic-0.2.0/RobustArithmetic/tests/testthat/test-safeguards.R | 361 ++++---- RobustArithmetic-0.2.0/RobustArithmetic/vignettes/robustarithmetic.Rmd | 42 44 files changed, 1479 insertions(+), 1035 deletions(-)
More information about RobustArithmetic at CRAN
Permanent link
Title: Multiscale Change Point Detection via Gradual Bandwidth
Adjustment in Moving Sum Processes
Description: Multiscale moving sum procedure for the detection of changes in expectation in univariate sequences. References - Multiscale change point detection via gradual bandwidth adjustment in moving sum processes, Tijana Levajkovic and Michael Messer (2023) <doi:10.1214/22-EJS2101>.
Author: Tijana Levajkovic [aut],
Michael Messer [aut, cre]
Maintainer: Michael Messer <michaelmessermath@gmail.com>
Diff between mscp versions 1.0 dated 2021-02-24 and 2.0 dated 2026-09-16
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- R/mscp.r | 8 ++++---- R/plot.mscp.r | 2 +- man/mscp.Rd | 8 ++++---- 5 files changed, 22 insertions(+), 21 deletions(-)
Title: The Multiple Filter Test for Change Point Detection
Description: Provides statistical tests and algorithms for the detection of change points in time series and point processes - particularly for changes in the mean in time series and for changes in the rate and in the variance in point processes. References - Michael Messer, Marietta Kirchner, Julia Schiemann, Jochen Roeper, Ralph Neininger and Gaby Schneider (2014), A multiple filter test for the detection of rate changes in renewal processes with varying variance <doi:10.1214/14-AOAS782>. Stefan Albert, Michael Messer, Julia Schiemann, Jochen Roeper, Gaby Schneider (2017), Multi-scale detection of variance changes in renewal processes in the presence of rate change points <doi:10.1111/jtsa.12254>. Michael Messer, Kaue M. Costa, Jochen Roeper and Gaby Schneider (2017), Multi-scale detection of rate changes in spike trains with weak dependencies <doi:10.1007/s10827-016-0635-3>. Michael Messer, Stefan Albert and Gaby Schneider (2018), The multiple filter test for change point detec [...truncated...]
Author: Michael Messer [aut, cre],
Stefan Albert [aut],
Solveig Plomer [aut],
Gaby Schneider [aut]
Maintainer: Michael Messer <michaelmessermath@gmail.com>
This is a re-admission after prior archival of version 2.0 dated 2019-03-11
Diff between MFT versions 2.0 dated 2019-03-11 and 3.1 dated 2026-09-16
DESCRIPTION | 33 +++++++++++++++++++++++++-------- MD5 | 12 ++++++------ man/MFT.mean.Rd | 17 ++++++++++++++--- man/MFT.peaks.Rd | 19 +++++++++++++++---- man/MFT.rate.Rd | 22 ++++++++++++++++++---- man/MFT.variance.Rd | 19 +++++++++++++++---- man/plot.MFT.Rd | 18 +++++++++++++++--- 7 files changed, 108 insertions(+), 32 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph] ,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.3.3 dated 2026-08-27 and 0.3.4 dated 2026-09-16
DESCRIPTION | 8 +- MD5 | 20 +++---- NEWS.md | 8 ++ R/afstemningsomraader.R | 6 -- R/available_sections.R | 21 +++++-- R/status_check.R | 59 +++++---------------- inst/doc/status.html | 21 +++---- tests/testthat/_snaps/status_check.md | 16 ++--- tests/testthat/test-available_sections.R | 24 ++++++-- tests/testthat/test-reverse.R | 12 ++-- tests/testthat/test-status_check.R | 86 +++++++++++++++++++++++++------ 11 files changed, 167 insertions(+), 114 deletions(-)
Title: Standard TLGs for Clinical Trials Reporting
Description: Provide standard tables, listings, and graphs (TLGs)
libraries used in clinical trials. This package implements a structure
to reformat the data with 'dunlin', create reporting tables using
'rtables' and 'tern' with standardized input arguments to enable quick
generation of standard outputs. In addition, it also provides
comprehensive data checks and script generation functionality.
Author: Liming Li [aut] ,
Benoit Falquet [aut] ,
Xiaoli Duan [aut],
Adrian Waddell [ctb],
Chenkai Lv [ctb],
Pawel Rucki [ctb],
Tim Barnett [ctb],
Tian Fang [ctb],
Joe Zhu [cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between chevron versions 0.2.13 dated 2026-07-17 and 0.2.14 dated 2026-09-16
DESCRIPTION | 10 MD5 | 191 NAMESPACE | 58 NEWS.md | 308 R/assertions.R | 420 R/cmt01a.R | 299 R/gen_args.R | 73 R/lbt01.R | 224 R/lbt05.R | 503 R/mng01.R | 434 R/rtables_utils.R | 1236 - README.md | 280 build/vignette.rds |binary inst/WORDLIST | 59 inst/doc/chevron.html | 427 inst/doc/chevron_catalog.html | 7933 ++++------ inst/doc/chevron_catalog.rmd | 2858 +-- inst/doc/script_generator.html | 240 man/ael01_nollt.Rd | 150 man/ael02.Rd | 118 man/ael03.Rd | 114 man/aet01.Rd | 158 man/aet01_aesi.Rd | 192 man/aet02.Rd | 174 man/aet03.Rd | 136 man/aet04.Rd | 166 man/aet05.Rd | 170 man/aet05_all.Rd | 80 man/aet10.Rd | 138 man/cfbt01.Rd | 220 man/chevron-package.Rd | 84 man/chevron_tlg-class.Rd | 248 man/cml02a_gl.Rd | 126 man/cmt01a.Rd | 214 man/cmt02_pt.Rd | 190 man/coxt01.Rd | 206 man/coxt02.Rd | 166 man/dmt01.Rd | 176 man/dose_change_rule.Rd | 22 man/dst01.Rd | 190 man/dtht01.Rd | 158 man/dummy_template.Rd | 28 man/egt01.Rd | 182 man/egt02_1.Rd | 142 man/egt02_2.Rd | 118 man/egt03.Rd | 178 man/egt05_qtcat.Rd | 182 man/empty_rule.Rd | 22 man/ext01.Rd | 226 man/fstg01.Rd | 176 man/fstg02.Rd | 168 man/kmg01.Rd | 156 man/lbt01.Rd | 206 man/lbt04.Rd | 164 man/lbt04_lyt.Rd | 78 man/lbt05.Rd | 178 man/lbt06.Rd | 150 man/lbt07.Rd | 164 man/lbt14.Rd | 176 man/lbt15.Rd | 66 man/mht01.Rd | 172 man/missing_rule.Rd | 22 man/mng01.Rd | 238 man/nocoding.Rd | 22 man/outcome_rule.Rd | 22 man/pdt01.Rd | 176 man/pdt02.Rd | 172 man/reexports.Rd | 40 man/rmpt01.Rd | 160 man/rmpt03.Rd | 130 man/rmpt04.Rd | 128 man/rmpt05.Rd | 128 man/rmpt06.Rd | 156 man/rspt01.Rd | 202 man/std_listing.Rd | 78 man/ttet01.Rd | 184 man/vst01.Rd | 198 man/vst02_1.Rd | 146 man/vst02_2.Rd | 118 man/yes_no_rule.Rd | 22 tests/testthat/_snaps/mng01/mng01-with-custom-theme.new.svg |only tests/testthat/_snaps/mng01/mng01-with-custom-theme.svg | 612 tests/testthat/_snaps/mng01/mng01-with-default-value.new.svg |only tests/testthat/_snaps/mng01/mng01-with-default-value.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-combination-of-x-variables.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-combination-of-x-variables.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-custom-color-set.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-custom-color-set.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-custom-line-type-set.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-custom-line-type-set.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-custom-unnamed-color-set.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-custom-unnamed-color-set.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-custom-unnamed-line-type-set.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-custom-unnamed-line-type-set.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-jitter.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-jitter.svg | 592 tests/testthat/_snaps/mng01/run-mng01-with-numeric-x-variables.new.svg |only tests/testthat/_snaps/mng01/run-mng01-with-numeric-x-variables.svg | 656 tests/testthat/test-fstg01.R | 16 tests/testthat/test-fstg02.R | 20 vignettes/chevron_catalog.rmd | 2858 +-- 101 files changed, 16083 insertions(+), 16646 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott [aut, cre] ,
NEWUOA , and a
modified version of the R math libraries .
Original copyright notices have been maintained in all source
files. In these cases, copyright claimed by Steven L. Scott is
limited to modifications made to the [...truncated...]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.9.16 dated 2025-09-02 and 0.9.17 dated 2026-09-16
Boom-0.9.16/Boom/inst/include/LinAlg/stack_columns.hpp |only Boom-0.9.16/Boom/inst/include/Models/FactorModels/PosteriorSamplers/PoissonFactorModelPosteriorSampler.hpp |only Boom-0.9.16/Boom/inst/include/cpputil/Split.hpp |only Boom-0.9.16/Boom/src/LinAlg/stack_columns.cpp |only Boom-0.9.16/Boom/src/Models/FactorModels/PosteriorSamplers/PoissonFactorModelPosteriorSampler.cpp |only Boom-0.9.16/Boom/src/cpputil/split.cpp |only Boom-0.9.16/Boom/src/numopt/simulated_annealing.cpp |only Boom-0.9.17/Boom/DESCRIPTION | 43 Boom-0.9.17/Boom/MD5 | 473 +++--- Boom-0.9.17/Boom/NAMESPACE | 7 Boom-0.9.17/Boom/R/detect_posixct.R |only Boom-0.9.17/Boom/R/histabunch.R | 72 Boom-0.9.17/Boom/R/intensity.R |only Boom-0.9.17/Boom/R/plot.unit.test.output.R |only Boom-0.9.17/Boom/inst/include/LinAlg/Array.hpp | 443 +++++ Boom-0.9.17/Boom/inst/include/LinAlg/ArrayIterator.hpp | 18 Boom-0.9.17/Boom/inst/include/LinAlg/Matrix.hpp | 18 Boom-0.9.17/Boom/inst/include/LinAlg/Selector.hpp | 25 Boom-0.9.17/Boom/inst/include/LinAlg/Vector.hpp | 2 Boom-0.9.17/Boom/inst/include/LinAlg/VectorViewIterator.hpp | 17 Boom-0.9.17/Boom/inst/include/Models/CategoricalData.hpp | 41 Boom-0.9.17/Boom/inst/include/Models/CompositeModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/DirichletModel.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/DoubleModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/ExponentialModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/FactorModels/MultinomialFactorModel.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/PoissonFactorModel.hpp | 165 +- Boom-0.9.17/Boom/inst/include/Models/FactorModels/PosteriorSamplers/MultinomialFactorModelPosteriorSampler.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/PosteriorSamplers/PFMIGPS.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/PosteriorSamplers/PoissonFactorHierarchicalSampler.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/PosteriorSamplers/PoissonFactorPosteriorSamplerBase.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/PosteriorSamplers/VisitorPriorManager.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/SiteBase.hpp |only Boom-0.9.17/Boom/inst/include/Models/FactorModels/VisitorBase.hpp |only Boom-0.9.17/Boom/inst/include/Models/FiniteMixtureModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/GP/GaussianProcessRegressionModel.hpp | 13 Boom-0.9.17/Boom/inst/include/Models/GP/GpMeanFunction.hpp | 10 Boom-0.9.17/Boom/inst/include/Models/GammaModel.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/GaussianModelBase.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/Glm/BinomialLogitModel.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/Glm/BinomialProbitModel.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/Glm/ChoiceData.hpp | 132 + Boom-0.9.17/Boom/inst/include/Models/Glm/GlmCoefs.hpp | 9 Boom-0.9.17/Boom/inst/include/Models/Glm/GlmMvnPriorBase.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/Glm/LogisticRegressionModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/Glm/LoglinearModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp | 151 +- Boom-0.9.17/Boom/inst/include/Models/Glm/MultinomialProbitModel.hpp | 8 Boom-0.9.17/Boom/inst/include/Models/Glm/MultivariateRegression.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/Glm/MvtRegModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/Glm/OrdinalCutpointModel.hpp | 8 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.hpp | 6 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.hpp | 13 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/LoglinearModelBipfSampler.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/MLVS.hpp | 64 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.hpp | 52 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.hpp | 6 Boom-0.9.17/Boom/inst/include/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.hpp | 6 Boom-0.9.17/Boom/inst/include/Models/Glm/ProbitRegression.hpp | 10 Boom-0.9.17/Boom/inst/include/Models/Glm/RegressionModel.hpp | 23 Boom-0.9.17/Boom/inst/include/Models/Glm/TRegression.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp | 21 Boom-0.9.17/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/Graphical |only Boom-0.9.17/Boom/inst/include/Models/HMM/Clickstream/NestedHmm.hpp | 21 Boom-0.9.17/Boom/inst/include/Models/HMM/HMM2.hpp | 103 + Boom-0.9.17/Boom/inst/include/Models/HMM/HmmFilter.hpp | 83 - Boom-0.9.17/Boom/inst/include/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.hpp | 8 Boom-0.9.17/Boom/inst/include/Models/IRT/PcrNid.hpp | 9 Boom-0.9.17/Boom/inst/include/Models/MarginallyUniformCorrelationModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/MarkovModel.hpp | 31 Boom-0.9.17/Boom/inst/include/Models/ModelTypes.hpp | 7 Boom-0.9.17/Boom/inst/include/Models/MultilevelCategoricalData.hpp |only Boom-0.9.17/Boom/inst/include/Models/MultilevelMultinomialModel.hpp |only Boom-0.9.17/Boom/inst/include/Models/MultinomialModel.hpp | 8 Boom-0.9.17/Boom/inst/include/Models/MvnGivenScalarSigma.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/MvnGivenSigma.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/MvnModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/MvtModel.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/PoissonModel.hpp | 3 Boom-0.9.17/Boom/inst/include/Models/Policies/CompositeParamPolicy.hpp | 5 Boom-0.9.17/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/Policies/MultivariateDataPolicy.hpp |only Boom-0.9.17/Boom/inst/include/Models/PosteriorSamplers/Imputer.hpp | 51 Boom-0.9.17/Boom/inst/include/Models/PosteriorSamplers/MultilevelMultinomialPosteriorSampler.hpp |only Boom-0.9.17/Boom/inst/include/Models/PosteriorSamplers/MvnConjSampler.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/ProductDirichletModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/StateSpace/Multivariate/AdjustedDataWorkspace.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/TimeSeries/ArmaPriors.hpp | 18 Boom-0.9.17/Boom/inst/include/Models/TimeSeries/NonzeroMeanAr1Model.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/TimeSeries/TimeSeries.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/TimeSeries/TimeSeriesDataPolicy.hpp | 32 Boom-0.9.17/Boom/inst/include/Models/TimeSeries/TimeSeriesSufstatDataPolicy.hpp | 20 Boom-0.9.17/Boom/inst/include/Models/UniformCorrelationModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Models/WeightedMvnModel.hpp | 4 Boom-0.9.17/Boom/inst/include/Models/WishartModel.hpp | 6 Boom-0.9.17/Boom/inst/include/Models/ZeroInflatedGammaModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/ZeroInflatedLognormalModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 1 Boom-0.9.17/Boom/inst/include/Models/ZeroMeanMvnModel.hpp | 2 Boom-0.9.17/Boom/inst/include/Samplers/MoveAccounting.hpp | 1 Boom-0.9.17/Boom/inst/include/TargetFun/JacobianChecker.hpp | 12 Boom-0.9.17/Boom/inst/include/TargetFun/MultinomialLogitTransform.hpp | 11 Boom-0.9.17/Boom/inst/include/TargetFun/SumMultinomialLogitTransform.hpp |only Boom-0.9.17/Boom/inst/include/TargetFun/Transformation.hpp | 10 Boom-0.9.17/Boom/inst/include/cpputil/Date.hpp | 6 Boom-0.9.17/Boom/inst/include/cpputil/DateTime.hpp | 28 Boom-0.9.17/Boom/inst/include/cpputil/DefaultMap.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/ParamFileIoManager.hpp | 5 Boom-0.9.17/Boom/inst/include/cpputil/ProgressTracker.hpp | 22 Boom-0.9.17/Boom/inst/include/cpputil/Ptr.hpp | 3 Boom-0.9.17/Boom/inst/include/cpputil/SortedVector.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/StringSplitter.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/ThreadTools.hpp | 3 Boom-0.9.17/Boom/inst/include/cpputil/ToString.hpp | 2 Boom-0.9.17/Boom/inst/include/cpputil/apply_permutation.hpp | 14 Boom-0.9.17/Boom/inst/include/cpputil/data_checking.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/file_utils.hpp | 6 Boom-0.9.17/Boom/inst/include/cpputil/find.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/index_table.hpp | 81 - Boom-0.9.17/Boom/inst/include/cpputil/make_unique.hpp |only Boom-0.9.17/Boom/inst/include/cpputil/portable_math.hpp | 2 Boom-0.9.17/Boom/inst/include/cpputil/random_element.hpp | 8 Boom-0.9.17/Boom/inst/include/cpputil/report_error.hpp | 4 Boom-0.9.17/Boom/inst/include/cpputil/string_utils.hpp | 2 Boom-0.9.17/Boom/inst/include/cpputil/timer.hpp | 94 + Boom-0.9.17/Boom/inst/include/distributions.hpp | 6 Boom-0.9.17/Boom/inst/include/math/Permutation.hpp |only Boom-0.9.17/Boom/inst/include/numopt.hpp | 21 Boom-0.9.17/Boom/inst/include/numopt/ClassAssigner.hpp |only Boom-0.9.17/Boom/inst/include/numopt/SimulatedAnnealingOptimizer.hpp |only Boom-0.9.17/Boom/inst/include/stats/DataTable.hpp | 297 +++ Boom-0.9.17/Boom/inst/include/stats/Design.hpp | 26 Boom-0.9.17/Boom/inst/include/stats/Encoders.hpp | 186 ++ Boom-0.9.17/Boom/inst/include/stats/FreqDist.hpp | 28 Boom-0.9.17/Boom/inst/include/stats/classifier_metrics.hpp |only Boom-0.9.17/Boom/inst/include/stats/fake_data_table.hpp |only Boom-0.9.17/Boom/inst/include/stats/kl_divergence.hpp |only Boom-0.9.17/Boom/inst/include/stats/logit.hpp | 23 Boom-0.9.17/Boom/inst/include/stats/moments.hpp | 15 Boom-0.9.17/Boom/inst/include/stats/optimal_arm_probabilities.hpp |only Boom-0.9.17/Boom/man/DetectPosixct.Rd |only Boom-0.9.17/Boom/man/Intensity.Rd |only Boom-0.9.17/Boom/man/histabunch.Rd | 7 Boom-0.9.17/Boom/man/unit.testing.Rd |only Boom-0.9.17/Boom/src/LinAlg/Array.cpp | 252 ++- Boom-0.9.17/Boom/src/LinAlg/ArrayIterator.cpp | 8 Boom-0.9.17/Boom/src/LinAlg/Givens.cpp | 1 Boom-0.9.17/Boom/src/LinAlg/Matrix.cpp | 22 Boom-0.9.17/Boom/src/LinAlg/Selector.cpp | 3 Boom-0.9.17/Boom/src/LinAlg/SubMatrix.cpp | 1 Boom-0.9.17/Boom/src/LinAlg/Vector.cpp | 20 Boom-0.9.17/Boom/src/Makevars | 9 Boom-0.9.17/Boom/src/Models/BinomialModel.cpp | 16 Boom-0.9.17/Boom/src/Models/CategoricalData.cpp | 72 Boom-0.9.17/Boom/src/Models/CompositeModel.cpp | 4 Boom-0.9.17/Boom/src/Models/DirichletModel.cpp | 9 Boom-0.9.17/Boom/src/Models/ExponentialModel.cpp | 5 Boom-0.9.17/Boom/src/Models/FactorModels/MultinomialFactorModel.cpp |only Boom-0.9.17/Boom/src/Models/FactorModels/PoissonFactorModel.cpp | 96 - Boom-0.9.17/Boom/src/Models/FactorModels/PosteriorSamplers/MultinomialFactorModelPosteriorSampler.cpp |only Boom-0.9.17/Boom/src/Models/FactorModels/PosteriorSamplers/PFMIGPS.hpp |only Boom-0.9.17/Boom/src/Models/FactorModels/PosteriorSamplers/PoissonFactorHierarchicalSampler.cpp |only Boom-0.9.17/Boom/src/Models/FactorModels/PosteriorSamplers/PoissonFactorPosteriorSamplerBase.cpp |only Boom-0.9.17/Boom/src/Models/FactorModels/PosteriorSamplers/VisitorPriorManager.cpp |only Boom-0.9.17/Boom/src/Models/FiniteMixtureModel.cpp | 4 Boom-0.9.17/Boom/src/Models/GammaModel.cpp | 5 Boom-0.9.17/Boom/src/Models/GaussianModelBase.cpp | 5 Boom-0.9.17/Boom/src/Models/Glm/BinomialLogitModel.cpp | 6 Boom-0.9.17/Boom/src/Models/Glm/BinomialProbitModel.cpp | 6 Boom-0.9.17/Boom/src/Models/Glm/ChoiceData.cpp | 73 Boom-0.9.17/Boom/src/Models/Glm/GlmCoefs.cpp | 17 Boom-0.9.17/Boom/src/Models/Glm/LogisticRegressionModel.cpp | 6 Boom-0.9.17/Boom/src/Models/Glm/LoglinearModel.cpp | 11 Boom-0.9.17/Boom/src/Models/Glm/MultinomialLogitModel.cpp | 249 +-- Boom-0.9.17/Boom/src/Models/Glm/MultinomialProbitModel.cpp | 7 Boom-0.9.17/Boom/src/Models/Glm/MultivariateRegression.cpp | 4 Boom-0.9.17/Boom/src/Models/Glm/MvtRegModel.cpp | 4 Boom-0.9.17/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 50 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.cpp | 10 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 2 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/LoglinearModelBipfSampler.cpp | 4 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/MLVS.cpp | 62 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/MultinomialLogitCompositeSpikeSlabSampler.cpp | 205 ++ Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.cpp | 14 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.cpp | 8 Boom-0.9.17/Boom/src/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.cpp | 8 Boom-0.9.17/Boom/src/Models/Glm/ProbitRegression.cpp | 4 Boom-0.9.17/Boom/src/Models/Glm/RegressionModel.cpp | 21 Boom-0.9.17/Boom/src/Models/Glm/TRegression.cpp | 6 Boom-0.9.17/Boom/src/Models/Glm/VariableSelectionPrior.cpp | 16 Boom-0.9.17/Boom/src/Models/Glm/WeightedRegressionModel.cpp | 12 Boom-0.9.17/Boom/src/Models/Graphical |only Boom-0.9.17/Boom/src/Models/HMM/Clickstream/NestedHmm.cpp | 19 Boom-0.9.17/Boom/src/Models/HMM/HMM2.cpp | 93 - Boom-0.9.17/Boom/src/Models/HMM/HmmFilter.cpp | 176 -- Boom-0.9.17/Boom/src/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.cpp | 4 Boom-0.9.17/Boom/src/Models/HMM/hmm_tools.cpp | 2 Boom-0.9.17/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.cpp | 1 Boom-0.9.17/Boom/src/Models/IRT/SubjectPrior.cpp | 2 Boom-0.9.17/Boom/src/Models/Impute/MixedDataImputer.cpp | 7 Boom-0.9.17/Boom/src/Models/Impute/MixedDataImputerWithErrorCorrection.cpp | 4 Boom-0.9.17/Boom/src/Models/MarginallyUniformCorrelationModel.cpp | 4 Boom-0.9.17/Boom/src/Models/MarkovModel.cpp | 121 + Boom-0.9.17/Boom/src/Models/ModelTypes.cpp | 8 Boom-0.9.17/Boom/src/Models/MultilevelCategoricalData.cpp |only Boom-0.9.17/Boom/src/Models/MultilevelMultinomialModel.cpp |only Boom-0.9.17/Boom/src/Models/MultinomialModel.cpp | 55 Boom-0.9.17/Boom/src/Models/MvnGivenScalarSigma.cpp | 2 Boom-0.9.17/Boom/src/Models/MvnGivenSigma.cpp | 4 Boom-0.9.17/Boom/src/Models/MvnModel.cpp | 7 Boom-0.9.17/Boom/src/Models/MvtModel.cpp | 3 Boom-0.9.17/Boom/src/Models/PointProcess/MarkovModulatedPoissonProcess.cpp | 2 Boom-0.9.17/Boom/src/Models/PointProcess/PoissonClusterProcess.cpp | 1 Boom-0.9.17/Boom/src/Models/PoissonModel.cpp | 3 Boom-0.9.17/Boom/src/Models/Policies/MultivariateDataPolicy.cpp |only Boom-0.9.17/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 1 Boom-0.9.17/Boom/src/Models/PosteriorSamplers/MultilevelMultinomialPosteriorSampler.cpp |only Boom-0.9.17/Boom/src/Models/PosteriorSamplers/MvnConjSampler.cpp | 24 Boom-0.9.17/Boom/src/Models/ProductDirichletModel.cpp | 2 Boom-0.9.17/Boom/src/Models/TimeSeries/NonzeroMeanAr1Model.cpp | 2 Boom-0.9.17/Boom/src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp | 1 Boom-0.9.17/Boom/src/Models/UniformCorrelationModel.cpp | 2 Boom-0.9.17/Boom/src/Models/WeightedMvnModel.cpp | 4 Boom-0.9.17/Boom/src/Models/ZeroInflatedGammaModel.cpp | 5 Boom-0.9.17/Boom/src/Models/ZeroInflatedLognormalModel.cpp | 5 Boom-0.9.17/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 6 Boom-0.9.17/Boom/src/Models/ZeroMeanMvnModel.cpp | 4 Boom-0.9.17/Boom/src/TargetFun/JacobianChecker.cpp | 33 Boom-0.9.17/Boom/src/TargetFun/MultinomialLogitTransform.cpp | 14 Boom-0.9.17/Boom/src/TargetFun/SumMultinomialLogitTransform.cpp |only Boom-0.9.17/Boom/src/cpputil/Date.cpp | 10 Boom-0.9.17/Boom/src/cpputil/DateTime.cpp | 34 Boom-0.9.17/Boom/src/cpputil/StringSplitter.cpp |only Boom-0.9.17/Boom/src/cpputil/ThreadTools.cpp | 1 Boom-0.9.17/Boom/src/cpputil/apply_permutation.cpp | 40 Boom-0.9.17/Boom/src/cpputil/check_probabilities.cpp |only Boom-0.9.17/Boom/src/cpputil/parse_range.cpp | 3 Boom-0.9.17/Boom/src/cpputil/rep.cpp | 1 Boom-0.9.17/Boom/src/distributions/dirichlet.cpp | 2 Boom-0.9.17/Boom/src/distributions/rng.cpp | 2 Boom-0.9.17/Boom/src/distributions/trun_gamma.cpp | 1 Boom-0.9.17/Boom/src/distributions/trun_norm.cpp | 1 Boom-0.9.17/Boom/src/math/kissfft/kiss_fft.cpp | 2 Boom-0.9.17/Boom/src/numopt/ClassAssigner.cpp |only Boom-0.9.17/Boom/src/numopt/SimulatedAnnealingOptimizer.cpp |only Boom-0.9.17/Boom/src/numopt/newton.cpp | 3 Boom-0.9.17/Boom/src/stats/DataTable.cpp | 743 ++++++++-- Boom-0.9.17/Boom/src/stats/Design.cpp | 28 Boom-0.9.17/Boom/src/stats/Encoders.cpp | 296 +++ Boom-0.9.17/Boom/src/stats/FreqDist.cpp | 31 Boom-0.9.17/Boom/src/stats/IQagent.cpp | 8 Boom-0.9.17/Boom/src/stats/classifier_metrics.cpp |only Boom-0.9.17/Boom/src/stats/fake_data_table.cpp |only Boom-0.9.17/Boom/src/stats/hexbin.cpp | 1 Boom-0.9.17/Boom/src/stats/kl_divergence.cpp |only Boom-0.9.17/Boom/src/stats/moments.cpp | 8 Boom-0.9.17/Boom/src/stats/optimal_arm_probabilities.cpp |only 260 files changed, 4811 insertions(+), 1633 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
This is a re-admission after prior archival of version 0.24.0-1 dated 2026-07-29
Diff between adbcpostgresql versions 0.24.0-1 dated 2026-07-29 and 0.24.0-2 dated 2026-09-16
DESCRIPTION | 6 - MD5 | 8 +- src/c/driver_manager/adbc_driver_manager.cc | 3 src/c/driver_manager/adbc_driver_manager_internal.h | 6 + src/c/driver_manager/adbc_driver_manager_profiles.cc | 58 ++++++++++++------- 5 files changed, 49 insertions(+), 32 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and
'SubCortexMesh' subcortical outputs for a given sample by
restructuring the data values into a single file. The single file can
then be used by the package for analyses independently from its base
dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.5.3 dated 2026-09-02 and 1.5.4 dated 2026-09-16
VertexWiseR-1.5.3/VertexWiseR/man/figures/Flowchart.JPG |only VertexWiseR-1.5.4/VertexWiseR/DESCRIPTION | 10 VertexWiseR-1.5.4/VertexWiseR/MD5 | 70 +-- VertexWiseR-1.5.4/VertexWiseR/NEWS.md | 9 VertexWiseR-1.5.4/VertexWiseR/R/CAT12vextract.R | 2 VertexWiseR-1.5.4/VertexWiseR/R/DTSERIESvextract.R | 2 VertexWiseR-1.5.4/VertexWiseR/R/FSLRvextract.R | 2 VertexWiseR-1.5.4/VertexWiseR/R/HIPvextract.R | 2 VertexWiseR-1.5.4/VertexWiseR/R/RFT_vertex_analysis.R | 6 VertexWiseR-1.5.4/VertexWiseR/R/SCMvextract.R | 30 - VertexWiseR-1.5.4/VertexWiseR/R/SURFvextract.R | 4 VertexWiseR-1.5.4/VertexWiseR/R/TFCE_vertex_analysis.R | 21 VertexWiseR-1.5.4/VertexWiseR/R/TFCE_vertex_analysis_mixed.R | 13 VertexWiseR-1.5.4/VertexWiseR/R/classes.r | 2 VertexWiseR-1.5.4/VertexWiseR/R/conversion_functions.R | 4 VertexWiseR-1.5.4/VertexWiseR/R/other_functions_scm.R | 2 VertexWiseR-1.5.4/VertexWiseR/R/plot_overlay_surf.r | 2 VertexWiseR-1.5.4/VertexWiseR/R/plot_surf3d.R | 65 ++ VertexWiseR-1.5.4/VertexWiseR/R/smooth_surf.R | 2 VertexWiseR-1.5.4/VertexWiseR/inst/doc/VertexWiseR_Example_3.html | 136 +++--- VertexWiseR-1.5.4/VertexWiseR/man/CAT12vextract.Rd | 90 ++-- VertexWiseR-1.5.4/VertexWiseR/man/DTSERIESvextract.Rd | 96 ++-- VertexWiseR-1.5.4/VertexWiseR/man/FSLRvextract.Rd | 2 VertexWiseR-1.5.4/VertexWiseR/man/HIPvextract.Rd | 2 VertexWiseR-1.5.4/VertexWiseR/man/RFT_vertex_analysis.Rd | 6 VertexWiseR-1.5.4/VertexWiseR/man/ROImap-class.Rd | 2 VertexWiseR-1.5.4/VertexWiseR/man/SCMvextract.Rd | 126 ++--- VertexWiseR-1.5.4/VertexWiseR/man/SURFvextract.Rd | 4 VertexWiseR-1.5.4/VertexWiseR/man/TFCE_threshold.Rd | 2 VertexWiseR-1.5.4/VertexWiseR/man/TFCE_vertex_analysis.Rd | 10 VertexWiseR-1.5.4/VertexWiseR/man/TFCE_vertex_analysis_mixed.Rd | 10 VertexWiseR-1.5.4/VertexWiseR/man/figures/Flowchart.jpg |only VertexWiseR-1.5.4/VertexWiseR/man/fslr_to_fs5_map.Rd | 44 +- VertexWiseR-1.5.4/VertexWiseR/man/plot_overlay_surf.Rd | 220 +++++----- VertexWiseR-1.5.4/VertexWiseR/man/smooth_surf.Rd | 2 VertexWiseR-1.5.4/VertexWiseR/man/surf_to_atlas.Rd | 4 VertexWiseR-1.5.4/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd | 4 37 files changed, 533 insertions(+), 475 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features an API for
extending these templates to address novel scientific research aims. Full
methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Adrien Le Guillou [aut],
Chad Klumb [aut],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 2.6.1 dated 2026-05-12 and 2.6.2 dated 2026-09-16
DESCRIPTION | 14 MD5 | 178 +++++---- NAMESPACE | 121 +++--- NEWS.md | 44 ++ R/EpiModel-package.R | 253 ++++++++----- R/as.data.frame.R | 24 - R/dcm.R | 45 ++ R/degree.dist.R |only R/edgelists.R | 203 ++++++++--- R/icm.R | 18 R/icm.inputs.R | 13 R/net.fn.accessor.R | 58 ++- R/net.fn.modules.R | 11 R/net.fn.scenarios.R | 26 - R/net.inputs.R | 176 ++++++++- R/net.mod.infection.R | 2 R/net.mod.simnet.R | 103 +++++ R/netdx.R | 14 R/netest.R | 62 ++- R/netsim.R | 34 + R/plot.R | 20 + R/plot.comp_plot.R | 15 R/plot.dcm.R | 6 R/plot.degree.dist.R |only R/plot.icm.R | 13 R/plot.netdx.R | 125 ++++++ R/plot.netsim.R | 15 R/plot.stat_table.R | 34 + R/print.R | 2 R/reachable.R | 92 ++++- R/summary.R | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Intro.Rmd | 4 inst/doc/Intro.html | 18 inst/doc/attributes-and-summary-statistics.html | 8 inst/doc/model-parameters.html | 8 inst/doc/network-objects.R | 16 inst/doc/network-objects.Rmd | 60 ++- inst/doc/network-objects.html | 128 +++++- man/EpiModel-package.Rd | 251 ++++++++----- man/as_cumulative_edgelist.Rd | 47 ++ man/check_attr_lengths.Rd | 9 man/comp_plot.Rd | 3 man/control.net.Rd | 70 +++ man/dedup_cumulative_edgelist.Rd | 34 + man/edges_correct.Rd | 19 + man/edges_correct_eligible.Rd |only man/get_cumulative_degree.Rd | 37 +- man/get_cumulative_edgelist.Rd | 62 ++- man/get_cumulative_edgelists_df.Rd | 41 +- man/get_degree_dist.Rd |only man/get_partners.Rd | 54 ++ man/icm.Rd | 18 man/infection.2g.net.Rd | 2 man/init.icm.Rd | 3 man/multilayer.Rd | 6 man/net-accessor.Rd | 11 man/netdx.Rd | 12 man/netest.Rd | 45 +- man/netsim.Rd | 22 + man/param.icm.Rd | 10 man/param.net.Rd | 7 man/plot.dcm.Rd | 2 man/plot.epi.data.frame.Rd | 6 man/plot.icm.Rd | 6 man/plot.netdx.Rd | 91 ++++ man/plot.netsim.Rd | 6 man/reachable-nodes.Rd | 41 +- man/summary.dcm.Rd | 5 man/tedgelist_cumulative_degree.Rd |only man/tedgelist_momentary_degree.Rd |only man/update_cumulative_edgelist.Rd | 47 ++ man/update_dissolution.Rd | 7 tests/testthat/Rplots.pdf |binary tests/testthat/test-accessors.R | 59 +++ tests/testthat/test-comp-plot.R |only tests/testthat/test-cumulative_edgelist.R | 93 +++++ tests/testthat/test-dcm.R | 65 +++ tests/testthat/test-edges-correct.R |only tests/testthat/test-ergm.ego.R | 27 + tests/testthat/test-geom_bands.R |only tests/testthat/test-get.R | 35 + tests/testthat/test-net-inputs-validation.R |only tests/testthat/test-net-tergmLite.R | 42 +- tests/testthat/test-netdx.R | 167 +++++++++ tests/testthat/test-netest.R | 34 + tests/testthat/test-newmodules.R | 440 +++++++++++++++++++++++- tests/testthat/test-plot-dcm.R |only tests/testthat/test-plot-epi-dataframe.R |only tests/testthat/test-plot-sims.R |only tests/testthat/test-print.R | 29 + tests/testthat/test-transmat-dendo.R | 4 tests/testthat/test-truncate-restart.R |only tests/testthat/test-utils.R | 27 + vignettes/Intro.Rmd | 4 vignettes/network-objects.Rmd | 60 ++- 97 files changed, 3295 insertions(+), 743 deletions(-)
Title: Implement Descriptive Studies Using the Common Data Model
Description: An end-to-end framework that enables users to implement various descriptive studies for a given set of target and outcome cohorts for data mapped to the Observational Medical Outcomes Partnership Common Data Model.
Author: Jenna Reps [aut, cre],
Patrick Ryan [aut],
Chris Knoll [aut]
Maintainer: Jenna Reps <jreps@its.jnj.com>
Diff between Characterization versions 3.0.1 dated 2026-05-15 and 4.1.0 dated 2026-09-16
Characterization-3.0.1/Characterization/inst/sql/sql_server/TargetCounts.sql |only Characterization-3.0.1/Characterization/man/computeDechallengeRechallengeAnalyses.Rd |only Characterization-3.0.1/Characterization/man/computeRechallengeFailCaseSeriesAnalyses.Rd |only Characterization-3.0.1/Characterization/man/computeTimeToEventAnalyses.Rd |only Characterization-4.1.0/Characterization/DESCRIPTION | 15 Characterization-4.1.0/Characterization/MD5 | 156 +-- Characterization-4.1.0/Characterization/NAMESPACE | 5 Characterization-4.1.0/Characterization/R/CaseSeries.R | 105 +- Characterization-4.1.0/Characterization/R/CohortGeneration.R | 325 ++++-- Characterization-4.1.0/Characterization/R/CohortIncidence.R |only Characterization-4.1.0/Characterization/R/Database.R | 9 Characterization-4.1.0/Characterization/R/DechallengeRechallenge.R | 266 ++--- Characterization-4.1.0/Characterization/R/ExportingCsvFiles.R | 281 ++--- Characterization-4.1.0/Characterization/R/HelperFunctions.R | 40 Characterization-4.1.0/Characterization/R/LookupCohortSettings.R | 104 +- Characterization-4.1.0/Characterization/R/RiskFactorAnalysis.R | 125 +- Characterization-4.1.0/Characterization/R/RunCharacterization.R | 392 +++++++- Characterization-4.1.0/Characterization/R/StudyPopulation.R |only Characterization-4.1.0/Characterization/R/TargetAnalysis.R | 95 - Characterization-4.1.0/Characterization/R/TimeToEvent.R | 101 -- Characterization-4.1.0/Characterization/R/ViewShiny.R | 113 +- Characterization-4.1.0/Characterization/build/vignette.rds |binary Characterization-4.1.0/Characterization/inst/doc/Specification.R | 24 Characterization-4.1.0/Characterization/inst/doc/Specification.Rmd | 34 Characterization-4.1.0/Characterization/inst/doc/Specification.html | 58 - Characterization-4.1.0/Characterization/inst/doc/UsingPackage.R | 77 + Characterization-4.1.0/Characterization/inst/doc/UsingPackage.Rmd | 126 ++ Characterization-4.1.0/Characterization/inst/doc/UsingPackage.html | 147 ++- Characterization-4.1.0/Characterization/inst/settings/resultsDataModelSpecification.csv | 482 ++++++---- Characterization-4.1.0/Characterization/inst/shinyConfigUpdate.json | 6 Characterization-4.1.0/Characterization/inst/sql/sql_server/CaseCohorts.sql | 50 - Characterization-4.1.0/Characterization/inst/sql/sql_server/CaseSeriesBinaryExtraction.sql | 6 Characterization-4.1.0/Characterization/inst/sql/sql_server/CreateTargetCohortTable.sql | 47 Characterization-4.1.0/Characterization/inst/sql/sql_server/DechallengeRechallenge.sql | 6 Characterization-4.1.0/Characterization/inst/sql/sql_server/DropTargetCohortTable.sql | 26 Characterization-4.1.0/Characterization/inst/sql/sql_server/DropTimeToEvent.sql | 6 Characterization-4.1.0/Characterization/inst/sql/sql_server/NonCaseCohorts.sql | 181 ++- Characterization-4.1.0/Characterization/inst/sql/sql_server/OutcomeEras.sql |only Characterization-4.1.0/Characterization/inst/sql/sql_server/RechallengeFailCaseSeries.sql | 76 + Characterization-4.1.0/Characterization/inst/sql/sql_server/ResultTables.sql | 14 Characterization-4.1.0/Characterization/inst/sql/sql_server/RiskFactorBinaryExtraction.sql | 45 Characterization-4.1.0/Characterization/inst/sql/sql_server/RiskFactorContinuousExtraction.sql | 81 + Characterization-4.1.0/Characterization/inst/sql/sql_server/TargetCohorts.sql | 358 +++++++ Characterization-4.1.0/Characterization/inst/sql/sql_server/TimeToEvent.sql | 59 - Characterization-4.1.0/Characterization/inst/sql/sql_server/UpdateVersionNumber.sql | 2 Characterization-4.1.0/Characterization/inst/sql/sql_server/migrations/Migration_2-v4_0_0_table_change.sql |only Characterization-4.1.0/Characterization/inst/sql/sql_server/migrations/Migration_3-v4_1_0_cohort_incidence.sql |only Characterization-4.1.0/Characterization/man/Characterization-package.Rd | 1 Characterization-4.1.0/Characterization/man/cleanIncremental.Rd | 4 Characterization-4.1.0/Characterization/man/cleanNonIncremental.Rd | 4 Characterization-4.1.0/Characterization/man/createCaseSeriesSettings.Rd | 30 Characterization-4.1.0/Characterization/man/createCharacterizationSettings.Rd | 19 Characterization-4.1.0/Characterization/man/createCharacterizationTables.Rd | 6 Characterization-4.1.0/Characterization/man/createCohortIncidenceSettings.Rd |only Characterization-4.1.0/Characterization/man/createDechallengeRechallengeSettings.Rd | 15 Characterization-4.1.0/Characterization/man/createDuringCovariateSettings.Rd | 4 Characterization-4.1.0/Characterization/man/createRiskFactorSettings.Rd | 33 Characterization-4.1.0/Characterization/man/createSqliteDatabase.Rd | 6 Characterization-4.1.0/Characterization/man/createStudyPopulationSettings.Rd |only Characterization-4.1.0/Characterization/man/createTargetBaselineSettings.Rd | 20 Characterization-4.1.0/Characterization/man/createTimeToEventSettings.Rd | 14 Characterization-4.1.0/Characterization/man/exampleOmopConnectionDetails.Rd | 4 Characterization-4.1.0/Characterization/man/getDbDuringCovariateData.Rd | 4 Characterization-4.1.0/Characterization/man/insertResultsToDatabase.Rd | 12 Characterization-4.1.0/Characterization/man/loadCharacterizationSettings.Rd | 14 Characterization-4.1.0/Characterization/man/runCharacterizationAnalyses.Rd | 28 Characterization-4.1.0/Characterization/man/saveCharacterizationSettings.Rd | 14 Characterization-4.1.0/Characterization/man/viewCharacterization.Rd | 4 Characterization-4.1.0/Characterization/tests/testthat/setup.R | 26 Characterization-4.1.0/Characterization/tests/testthat/test-CaseSeries.R | 116 +- Characterization-4.1.0/Characterization/tests/testthat/test-CohortGeneration.R | 171 +++ Characterization-4.1.0/Characterization/tests/testthat/test-CohortIncidence.R |only Characterization-4.1.0/Characterization/tests/testthat/test-ExportingCsvFiles.R | 213 +--- Characterization-4.1.0/Characterization/tests/testthat/test-HelperFunctions.R |only Characterization-4.1.0/Characterization/tests/testthat/test-Incremental.R | 15 Characterization-4.1.0/Characterization/tests/testthat/test-RiskFactor.R | 94 + Characterization-4.1.0/Characterization/tests/testthat/test-StudyPopulation.R |only Characterization-4.1.0/Characterization/tests/testthat/test-dbs.R | 22 Characterization-4.1.0/Characterization/tests/testthat/test-dechallengeRechallenge.R | 287 ++++- Characterization-4.1.0/Characterization/tests/testthat/test-manualData.R | 84 + Characterization-4.1.0/Characterization/tests/testthat/test-runCharacterization.R | 174 +-- Characterization-4.1.0/Characterization/tests/testthat/test-targetAnalysis.R | 101 +- Characterization-4.1.0/Characterization/tests/testthat/test-timeToEvent.R | 61 + Characterization-4.1.0/Characterization/tests/testthat/test-viewShiny.R | 35 Characterization-4.1.0/Characterization/vignettes/Specification.Rmd | 34 Characterization-4.1.0/Characterization/vignettes/UsingPackage.Rmd | 126 ++ 86 files changed, 3799 insertions(+), 2039 deletions(-)
More information about Characterization at CRAN
Permanent link
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.7.0 dated 2026-05-09 and 1.7.1 dated 2026-09-16
odbc-1.7.0/odbc/src/cctz/WORKSPACE |only odbc-1.7.0/odbc/src/cctz/include/civil_time.h |only odbc-1.7.0/odbc/src/cctz/include/civil_time_detail.h |only odbc-1.7.0/odbc/src/cctz/include/time_zone.h |only odbc-1.7.0/odbc/src/cctz/src/cctz.h |only odbc-1.7.0/odbc/src/cctz/src/cctz_v1_test.cc |only odbc-1.7.1/odbc/DESCRIPTION | 16 odbc-1.7.1/odbc/MD5 | 205 +- odbc-1.7.1/odbc/NAMESPACE | 5 odbc-1.7.1/odbc/NEWS.md | 18 odbc-1.7.1/odbc/R/aaa-odbc-data-type.R | 40 odbc-1.7.1/odbc/R/connection-pane.R | 132 - odbc-1.7.1/odbc/R/db.R | 27 odbc-1.7.1/odbc/R/dbi-connection.R | 207 +- odbc-1.7.1/odbc/R/dbi-driver.R | 115 - odbc-1.7.1/odbc/R/dbi-result.R | 114 - odbc-1.7.1/odbc/R/dbi-table.R | 213 +- odbc-1.7.1/odbc/R/dbi.R | 2 odbc-1.7.1/odbc/R/driver-access.R | 36 odbc-1.7.1/odbc/R/driver-bigquery.R | 34 odbc-1.7.1/odbc/R/driver-databricks.R | 85 odbc-1.7.1/odbc/R/driver-db2.R | 81 odbc-1.7.1/odbc/R/driver-hana.R | 30 odbc-1.7.1/odbc/R/driver-hive.R | 62 odbc-1.7.1/odbc/R/driver-impala.R | 34 odbc-1.7.1/odbc/R/driver-mysql.R | 36 odbc-1.7.1/odbc/R/driver-netezza.R | 18 odbc-1.7.1/odbc/R/driver-oracle.R | 142 + odbc-1.7.1/odbc/R/driver-postgres.R | 36 odbc-1.7.1/odbc/R/driver-snowflake.R | 235 +- odbc-1.7.1/odbc/R/driver-spark.R | 40 odbc-1.7.1/odbc/R/driver-sql-server.R | 174 + odbc-1.7.1/odbc/R/driver-sqlite.R | 34 odbc-1.7.1/odbc/R/driver-teradata.R | 89 odbc-1.7.1/odbc/R/driver-vertica.R | 36 odbc-1.7.1/odbc/R/odbc-config.R | 6 odbc-1.7.1/odbc/R/odbc-connection.R | 156 + odbc-1.7.1/odbc/R/odbc-drivers.R | 5 odbc-1.7.1/odbc/R/odbc-package.R | 3 odbc-1.7.1/odbc/R/odbc.R | 6 odbc-1.7.1/odbc/R/utils.R | 145 + odbc-1.7.1/odbc/R/zzz.R | 4 odbc-1.7.1/odbc/README.md | 24 odbc-1.7.1/odbc/inst/doc/develop.Rmd | 2 odbc-1.7.1/odbc/inst/doc/develop.html | 7 odbc-1.7.1/odbc/man/ConnectionAttributes.Rd | 1 odbc-1.7.1/odbc/man/Oracle.Rd | 6 odbc-1.7.1/odbc/man/databricks.Rd | 16 odbc-1.7.1/odbc/man/dbConnect-OdbcDriver-method.Rd | 2 odbc-1.7.1/odbc/man/driver-Snowflake.Rd | 1 odbc-1.7.1/odbc/man/odbc-package.Rd | 1 odbc-1.7.1/odbc/man/snowflake.Rd | 9 odbc-1.7.1/odbc/src/cctz/CMakeLists.txt |only odbc-1.7.1/odbc/src/cctz/LICENSE.txt | 5 odbc-1.7.1/odbc/src/cctz/MODULE.bazel |only odbc-1.7.1/odbc/src/cctz/Makefile | 97 - odbc-1.7.1/odbc/src/cctz/cmake |only odbc-1.7.1/odbc/src/cctz/examples/CMakeLists.txt |only odbc-1.7.1/odbc/src/cctz/examples/classic.cc | 17 odbc-1.7.1/odbc/src/cctz/examples/epoch_shift.cc | 11 odbc-1.7.1/odbc/src/cctz/examples/example1.cc | 10 odbc-1.7.1/odbc/src/cctz/examples/example2.cc | 4 odbc-1.7.1/odbc/src/cctz/examples/example3.cc | 11 odbc-1.7.1/odbc/src/cctz/examples/example4.cc | 15 odbc-1.7.1/odbc/src/cctz/examples/hello.cc | 10 odbc-1.7.1/odbc/src/cctz/include/cctz |only odbc-1.7.1/odbc/src/cctz/src/cctz_benchmark.cc |only odbc-1.7.1/odbc/src/cctz/src/civil_time_detail.cc |only odbc-1.7.1/odbc/src/cctz/src/civil_time_test.cc | 218 +- odbc-1.7.1/odbc/src/cctz/src/test_time_zone_names.cc |only odbc-1.7.1/odbc/src/cctz/src/test_time_zone_names.h |only odbc-1.7.1/odbc/src/cctz/src/time_tool.cc | 388 +++- odbc-1.7.1/odbc/src/cctz/src/time_zone_fixed.cc | 5 odbc-1.7.1/odbc/src/cctz/src/time_zone_fixed.h | 2 odbc-1.7.1/odbc/src/cctz/src/time_zone_format.cc | 753 +++++--- odbc-1.7.1/odbc/src/cctz/src/time_zone_format_test.cc | 1357 +++++++++++--- odbc-1.7.1/odbc/src/cctz/src/time_zone_fuzz_test.cc |only odbc-1.7.1/odbc/src/cctz/src/time_zone_if.cc | 21 odbc-1.7.1/odbc/src/cctz/src/time_zone_if.h | 89 odbc-1.7.1/odbc/src/cctz/src/time_zone_impl.cc | 128 - odbc-1.7.1/odbc/src/cctz/src/time_zone_impl.h | 49 odbc-1.7.1/odbc/src/cctz/src/time_zone_info.cc | 1460 ++++++++-------- odbc-1.7.1/odbc/src/cctz/src/time_zone_info.h | 135 - odbc-1.7.1/odbc/src/cctz/src/time_zone_libc.cc | 427 +++- odbc-1.7.1/odbc/src/cctz/src/time_zone_libc.h | 32 odbc-1.7.1/odbc/src/cctz/src/time_zone_lookup.cc | 205 +- odbc-1.7.1/odbc/src/cctz/src/time_zone_lookup_test.cc | 1354 ++++++-------- odbc-1.7.1/odbc/src/cctz/src/time_zone_name_win.cc |only odbc-1.7.1/odbc/src/cctz/src/time_zone_name_win.h |only odbc-1.7.1/odbc/src/cctz/src/time_zone_posix.cc | 20 odbc-1.7.1/odbc/src/cctz/src/time_zone_posix.h | 52 odbc-1.7.1/odbc/src/cctz/src/tzfile.h | 124 - odbc-1.7.1/odbc/src/cctz/src/zone_info_source.cc |only odbc-1.7.1/odbc/src/nanodbc/nanodbc.cpp | 12 odbc-1.7.1/odbc/src/odbc_connection.h | 2 odbc-1.7.1/odbc/src/odbc_result.cpp | 13 odbc-1.7.1/odbc/tests/testthat/_snaps/utils.md | 4 odbc-1.7.1/odbc/tests/testthat/helper.R | 51 odbc-1.7.1/odbc/tests/testthat/test-dbi-connection.R | 40 odbc-1.7.1/odbc/tests/testthat/test-driver-databricks.R | 19 odbc-1.7.1/odbc/tests/testthat/test-driver-mysql.R | 11 odbc-1.7.1/odbc/tests/testthat/test-driver-oracle.R | 16 odbc-1.7.1/odbc/tests/testthat/test-driver-postgres.R | 8 odbc-1.7.1/odbc/tests/testthat/test-driver-redshift.R | 1 odbc-1.7.1/odbc/tests/testthat/test-driver-snowflake.R | 32 odbc-1.7.1/odbc/tests/testthat/test-driver-sql-server.R | 294 ++- odbc-1.7.1/odbc/tests/testthat/test-driver-sqlite.R | 8 odbc-1.7.1/odbc/tests/testthat/test-odbc-config.R | 38 odbc-1.7.1/odbc/tests/testthat/test-odbc-connection.R | 27 odbc-1.7.1/odbc/tests/testthat/test-utils.R | 197 +- odbc-1.7.1/odbc/vignettes/develop.Rmd | 2 111 files changed, 6559 insertions(+), 3905 deletions(-)