Title: Byte Pair Encoding Text Tokenization
Description: Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
VK.com [cph],
Gregory Popovitch [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Ivan Belonogov [ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between tokenizers.bpe versions 0.1.5 dated 2026-05-20 and 0.1.6 dated 2026-06-13
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 src/parallel_hashmap/phmap.h | 279 +++++++++++++++---------------- src/parallel_hashmap/phmap_base.h | 323 ++++++++++++++++++------------------ src/parallel_hashmap/phmap_bits.h | 6 src/parallel_hashmap/phmap_config.h | 8 7 files changed, 328 insertions(+), 310 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Triple-Difference Estimators
Description: Implements triple-difference (DDD) estimators for both average
treatment effects and event-study parameters. Methods include regression
adjustment, inverse-probability weighting, and doubly-robust estimators,
all of which rely on a conditional DDD parallel-trends assumption and
allow covariate adjustment across multiple pre- and post-treatment
periods. The methodology is detailed in Ortiz-Villavicencio and
Sant'Anna (2025) <doi:10.48550/arXiv.2505.09942>.
Author: Marcelo Ortiz-Villavicencio [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Marcelo Ortiz-Villavicencio <marcelo.ortiz@emory.edu>
Diff between triplediff versions 0.2.0 dated 2026-01-15 and 0.2.4 dated 2026-06-13
DESCRIPTION | 8 MD5 | 35 NEWS.md | 21 R/agg_ddd.R | 3 R/att_gt.R | 45 R/compute_aggregations.R | 65 - R/compute_nuisances.R | 224 ++- R/ddd.R | 12 R/mboot.R | 37 R/preprocess.R | 189 ++ README.md | 2 man/agg_ddd.Rd | 3 man/compute_se_agg.Rd | 7 man/ddd.Rd | 10 man/figures/README-unnamed-chunk-10-1.png |binary tests/testthat/test-aggte-clustervars-override.R |only tests/testthat/test-cluster-alignment-correctness.R |only tests/testthat/test-cluster-analytic.R |only tests/testthat/test-cluster-unbalanced-bootstrap.R |only tests/testthat/test-mboot-cluster.R |only tests/testthat/test-preprocess.R | 1295 +++++++++++++++++++- 21 files changed, 1804 insertions(+), 152 deletions(-)
Title: Switzerland's Data Series in One Place
Description: Download and import open Swiss economic time series from
'dataseries.org' <https://dataseries.org>, a comprehensive and
up-to-date collection of public data from Switzerland. Series are
retrieved through the public 'dataseries.org' API and imported as a
'data.frame' or 'ts' object.
Author: Christoph Sax [aut, cre],
Jannes Muenchow [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between dataseries versions 0.2.0 dated 2017-04-29 and 1.0.0 dated 2026-06-13
dataseries-0.2.0/dataseries/NEWS |only dataseries-0.2.0/dataseries/R/as_ts.R |only dataseries-0.2.0/dataseries/R/inventory.R |only dataseries-1.0.0/dataseries/DESCRIPTION | 34 +- dataseries-1.0.0/dataseries/MD5 | 28 + dataseries-1.0.0/dataseries/NAMESPACE | 7 dataseries-1.0.0/dataseries/NEWS.md |only dataseries-1.0.0/dataseries/R/api.R |only dataseries-1.0.0/dataseries/R/catalog.R |only dataseries-1.0.0/dataseries/R/dataseries-package.R |only dataseries-1.0.0/dataseries/R/ds.R | 258 +++++++++++------- dataseries-1.0.0/dataseries/R/utils.R |only dataseries-1.0.0/dataseries/README.md | 89 +++++- dataseries-1.0.0/dataseries/man/cache_ls.Rd |only dataseries-1.0.0/dataseries/man/dataseries-package.Rd |only dataseries-1.0.0/dataseries/man/ds.Rd | 79 +++-- dataseries-1.0.0/dataseries/man/ds_catalog.Rd |only dataseries-1.0.0/dataseries/man/ds_meta.Rd |only dataseries-1.0.0/dataseries/man/ds_search.Rd |only dataseries-1.0.0/dataseries/man/inventory.Rd | 27 - dataseries-1.0.0/dataseries/tests |only 21 files changed, 346 insertions(+), 176 deletions(-)
Title: Model Cumulative Growing Degree-Days for Pest Monitoring
Description: Pest monitoring is crucial, especially during the early season, to understand the distribution and the proliferation of the target pest. Raw count data from pest monitoring/traps can be coupled with environmental variables such as temperature, growing degree-day ('GDD') etc. to get useful insights about the pest phenology. This package pulls temperature data from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), the 'Daymet' application programming interface ('API', <https://daymet.ornl.gov>), or 'Open Meteo' ('API', <https://open-meteo.com/>) sequentially for a user-specified time period and calculates cumulative growing degree-days. Users provide pest development thresholds (lower and upper temperatures), pest of concern, and the geographic coordinates of the trap location to track emergence and phenology.
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 0.1.0 dated 2026-05-20 and 1.0.0 dated 2026-06-13
TrackTrap-0.1.0/TrackTrap/man/plot_phenology_trend.Rd |only TrackTrap-1.0.0/TrackTrap/DESCRIPTION | 26 - TrackTrap-1.0.0/TrackTrap/LICENSE | 2 TrackTrap-1.0.0/TrackTrap/MD5 | 27 - TrackTrap-1.0.0/TrackTrap/NAMESPACE | 8 TrackTrap-1.0.0/TrackTrap/NEWS.md |only TrackTrap-1.0.0/TrackTrap/R/TrackTrap-package.R |only TrackTrap-1.0.0/TrackTrap/R/data.R | 1 TrackTrap-1.0.0/TrackTrap/R/globals.R |only TrackTrap-1.0.0/TrackTrap/R/phenology.R | 350 +++++++++++------- TrackTrap-1.0.0/TrackTrap/R/utils-pipe.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.rda |binary TrackTrap-1.0.0/TrackTrap/man/calc_pest_phenology.Rd | 84 +--- TrackTrap-1.0.0/TrackTrap/man/fetch_open_meteo.Rd |only TrackTrap-1.0.0/TrackTrap/man/pest_thresholds.Rd | 48 +- TrackTrap-1.0.0/TrackTrap/man/pipe.Rd |only TrackTrap-1.0.0/TrackTrap/man/plot_trap_phenology.Rd |only TrackTrap-1.0.0/TrackTrap/tests |only 19 files changed, 333 insertions(+), 213 deletions(-)
Title: Geographically-Conscious Taxonomic Assignment for Metabarcoding
Description: A bioinformatics pipeline for performing taxonomic
assignment of DNA metabarcoding sequence data while considering
geographic location. A detailed tutorial is available at
<https://urodelan.github.io/LocaTT_Tutorial/>.
A manuscript describing these methods is in preparation.
Author: Kenen B Goodwin [aut, cre] ,
Christopher Cousins [ctb],
Taal Levi [ctb],
Tiffany S Garcia [ths]
Maintainer: Kenen B Goodwin <urodelan@gmail.com>
Diff between LocaTT versions 1.2.0 dated 2026-03-27 and 1.3.0 dated 2026-06-13
DESCRIPTION | 9 ++--- MD5 | 55 +++++++++++++++++++++++++++++-- NAMESPACE | 20 +++++++++++ R/cor2cov.R |only R/dcopula.R |only R/ddirmult.R |only R/dissimilarity.R |only R/diversity.R |only R/djsdm.R |only R/dmWAIC.R |only R/dmpredict.R |only R/dmreg.R |only R/dmvlogis.R |only R/mlWAIC.R |only R/mlcoef.R |only R/mlcor.R |only R/mlformat.R |only R/mlpredict.R |only R/mlreg.R |only R/normalize.R |only R/richness.R |only R/softmax.R |only R/waic.R |only inst/CITATION | 4 +- inst/extdata/example_mvlogistic_data.rds |only inst/extdata/example_regression_data.rds |only inst/intdata |only man/cor2cov.Rd |only man/dcopula.Rd |only man/ddirmult.Rd |only man/dissimilarity.Rd |only man/diversity.Rd |only man/djsdm.Rd |only man/dmWAIC.Rd |only man/dmpredict.Rd |only man/dmreg.Rd |only man/dmvlogis.Rd |only man/mlWAIC.Rd |only man/mlcoef.Rd |only man/mlcor.Rd |only man/mlformat.Rd |only man/mlpredict.Rd |only man/mlreg.Rd |only man/normalize.Rd |only man/richness.Rd |only man/softmax.Rd |only man/waic.Rd |only 47 files changed, 79 insertions(+), 9 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.70 dated 2026-02-16 and 1.0 dated 2026-06-13
DESCRIPTION | 6 MD5 | 38 - NAMESPACE | 1 NEWS.md | 21 R/0_globals.R | 3 R/2_1_1_topicsModel_Pred.R | 89 ++- R/2_2_topicsGrams.R | 6 R/4_1_topicsPlot.R | 234 +++++++- README.md | 13 inst/doc/extended_installation_guide.Rmd | 3 inst/doc/extended_installation_guide.html | 2 man/topicsModel.Rd | 12 man/topicsPlot.Rd | 30 - man/topicsPlotOverview.Rd | 53 + tests/testthat/_snaps/1_6_topicsPlot/2-ngram-negative.svg | 44 - tests/testthat/_snaps/1_6_topicsPlot/3-ngram-positive.svg | 66 +- tests/testthat/_snaps/1_6_topicsPlot/topics-overview-plot.svg | 108 +-- tests/testthat/_snaps/1_6_topicsPlot/topics2-overview-plot.svg | 272 +++++----- tests/testthat/test_1_6_topicsPlot.R | 29 - vignettes/extended_installation_guide.Rmd | 3 20 files changed, 687 insertions(+), 346 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Corrections are supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.5 dated 2026-06-04 and 1.0.6 dated 2026-06-13
TmCalculator-1.0.5/TmCalculator/R/plot_circos_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_karyotype_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_linear_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_genome_tracks.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_heatmap.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_interactive.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_linear.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.Rmd |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.html |only TmCalculator-1.0.5/TmCalculator/man/plot_circos_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_karyotype_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_linear_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_genome_tracks.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_heatmap.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_interactive.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_linear.Rd |only TmCalculator-1.0.5/TmCalculator/vignettes/TmCalculator.Rmd |only TmCalculator-1.0.6/TmCalculator/DESCRIPTION | 26 TmCalculator-1.0.6/TmCalculator/MD5 | 58 TmCalculator-1.0.6/TmCalculator/NAMESPACE | 105 - TmCalculator-1.0.6/TmCalculator/R/coor_to_genomic_ranges.R | 3 TmCalculator-1.0.6/TmCalculator/R/ecoli_rep_hotspots.R | 50 TmCalculator-1.0.6/TmCalculator/R/integrate_granges.R | 8 TmCalculator-1.0.6/TmCalculator/R/make_genomiccoord.R | 5 TmCalculator-1.0.6/TmCalculator/R/plot_genome_track.R |only TmCalculator-1.0.6/TmCalculator/R/plot_tm.R |only TmCalculator-1.0.6/TmCalculator/R/to_genomic_ranges.R | 4 TmCalculator-1.0.6/TmCalculator/build/vignette.rds |binary TmCalculator-1.0.6/TmCalculator/data/ecoli_rep_hotspots.rda |binary TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.R | 469 +++-- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.Rmd | 406 ++--- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.html | 782 +++++----- TmCalculator-1.0.6/TmCalculator/inst/scripts |only TmCalculator-1.0.6/TmCalculator/inst/vignette-source |only TmCalculator-1.0.6/TmCalculator/man/TmCalculator-package.Rd | 2 TmCalculator-1.0.6/TmCalculator/man/ecoli_rep_hotspots.Rd | 49 TmCalculator-1.0.6/TmCalculator/man/integrate_granges.Rd | 8 TmCalculator-1.0.6/TmCalculator/man/plot_genome_track.Rd |only TmCalculator-1.0.6/TmCalculator/man/plot_tm.Rd |only TmCalculator-1.0.6/TmCalculator/vignettes/genome_wide_tm_ecoli.Rmd | 406 ++--- 41 files changed, 1267 insertions(+), 1114 deletions(-)
Title: Tidy Intensive Longitudinal Data Analysis
Description: A reproducible, tidyverse-style framework for intensive longitudinal
data analysis in R, with built-in methodological safeguards, provenance
tracking, and reporting tools. Encodes time structure, enforces
within-between decomposition, provides spacing-aware lags, and integrates
diagnostics and visualization. Use ild_prepare(), ild_center(), ild_lag(),
and related functions for a unified pipeline from raw EMA/diary data to
interpretable models.
Author: Alex Litovchenko [aut, cre]
Maintainer: Alex Litovchenko <al4877@columbia.edu>
This is a re-admission after prior archival of version 0.4.0 dated 2026-04-17
Diff between tidyILD versions 0.4.0 dated 2026-04-17 and 0.4.1 dated 2026-06-13
DESCRIPTION | 28 +++-- LICENSE | 2 MD5 | 54 +++++----- NEWS.md | 16 +++ R/ild_prepare.R | 59 +++++++++++ R/ild_prepare_wide.R |only README.md | 2 inst/CITATION | 4 inst/doc/benchmark-simulation-recovery.html | 8 - inst/doc/brms-dynamics-recipes.html | 4 inst/doc/ctsem-continuous-time-dynamics.html | 4 inst/doc/ild-analysis-report.html | 4 inst/doc/ild-decomposition-and-spacing.html | 4 inst/doc/ild-glossary-and-quickstart.R | 17 +++ inst/doc/ild-glossary-and-quickstart.Rmd | 29 +++++ inst/doc/ild-glossary-and-quickstart.html | 133 ++++++++++++++++++++++++++- inst/doc/ild-provenance.html | 34 +++--- inst/doc/ild-specialist-backends.html | 8 - inst/doc/kfas-choosing-backend.html | 4 inst/doc/kfas-irregular-timing-spacing.html | 4 inst/doc/kfas-state-space-modeling.html | 4 inst/doc/temporal-dynamics-model-choice.html | 8 - inst/doc/tidyILD-workflow.html | 4 inst/doc/tsibble-interoperability.html | 4 man/ild_prepare.Rd | 29 +++++ tests/testthat/helper-contract-fixtures.R | 15 ++- tests/testthat/test-heterogeneity-lmer.R | 17 ++- tests/testthat/test-ild_prepare_wide.R |only vignettes/ild-glossary-and-quickstart.Rmd | 29 +++++ 29 files changed, 429 insertions(+), 99 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.8.1 dated 2026-02-16 and 1.9 dated 2026-06-13
DESCRIPTION | 6 ++--- MD5 | 42 ++++++++++++++++++----------------- NAMESPACE | 4 +++ NEWS.md | 6 +++++ R/0_0_text_install.R | 11 +++++---- R/4_4_textWordPrediction.R |only R/7_1_textTopics.R | 31 +++++++++++++++++++++++-- R/7_2_textTopicsAnalysis.R | 16 +++++++++++++ README.md | 7 +++++ inst/doc/LBAM.html | 4 +-- inst/doc/ext_install_guide.Rmd | 2 - inst/doc/ext_install_guide.html | 2 - inst/doc/huggingface_in_r.R | 2 - inst/doc/huggingface_in_r.Rmd | 2 - inst/doc/huggingface_in_r.html | 3 -- inst/python/bert_topic.py | 2 + man/textTopics.Rd | 41 ++++++++++++++++++++++++++++++++-- man/textTopicsWordcloud.Rd | 11 ++++++++- man/textWordPrediction.Rd |only tests/testthat/test_6_textFineTune.R | 2 - tests/testthat/test_7_textTopics.R | 2 - vignettes/ext_install_guide.Rmd | 2 - vignettes/huggingface_in_r.Rmd | 2 - 23 files changed, 154 insertions(+), 46 deletions(-)
Title: Panel VAR Models with Interactive Fixed Effects
Description: Implements the estimator of Tugan (2021) <doi:10.1093/ectj/utaa021>
for panel vector autoregression (VAR) models with interactive fixed effects.
Provides joint estimation of VAR coefficients, latent common factors, and
factor loadings via an iterative algorithm that alternates between principal
component estimation of the factors and least squares estimation of the VAR
coefficients, following the approach of Bai (2009) <doi:10.3982/ECTA6135>.
Supports
impulse response functions under recursive (Cholesky) identification,
parametric confidence bands from the joint asymptotic distribution of the
estimator (Theorem 2.3), and a classical residual bootstrap for robustness
checks.
Author: Binzhi Chen [aut, cre]
Maintainer: Binzhi Chen <Binzhi.Chen9@gmail.com>
Diff between pvarife versions 0.1.1 dated 2026-06-11 and 0.1.2 dated 2026-06-13
DESCRIPTION | 9 +- MD5 | 33 ++++---- R/asymptotic.R | 53 ++++++++++-- R/confidence_bands.R | 143 ++++++++++++++++++++++++----------- R/estimate_pvarife.R | 32 +++++-- R/initial_step.R | 9 ++ R/irf.R | 15 ++- R/simulate.R | 18 ++-- R/utils.R | 7 + man/asymptotic_var.Rd | 18 +++- man/bootstrap_irf_bands.Rd | 38 +++++++-- man/irf_bands.Rd | 15 +++ man/pvarife.Rd | 12 ++ tests/testthat/test-asymptotic.R | 26 ++++++ tests/testthat/test-estimate.R | 18 ++++ tests/testthat/test-generalization.R |only tests/testthat/test-irf.R | 28 ++++++ tests/testthat/test-simulate.R | 18 ++++ 18 files changed, 381 insertions(+), 111 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.8.2 dated 2026-06-12 and 0.8.3 dated 2026-06-13
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 14 R/backends.R | 10 R/join_explain.R | 19 README.md | 2 inst/doc/backends.R | 128 ++ inst/doc/backends.Rmd | 954 ++++++++++++++------ inst/doc/backends.html | 635 ++++++++++--- inst/doc/common-issues.R | 180 +++ inst/doc/common-issues.Rmd | 512 +++++++++-- inst/doc/common-issues.html | 1645 ++++++++++++++++++++++++----------- inst/doc/production.R | 155 +++ inst/doc/production.Rmd | 1306 +++++++++++++++++++--------- inst/doc/production.html | 1206 ++++++++++++++++++-------- inst/doc/quickstart.R | 182 +++ inst/doc/quickstart.Rmd | 1317 +++++++++++++++++----------- inst/doc/quickstart.html | 1748 ++++++++++++++++++++++++++++---------- inst/doc/why-keys-dont-match.R | 67 + inst/doc/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- inst/doc/why-keys-dont-match.html | 785 +++++++++++++---- tests/testthat/Rplots.pdf |binary vignettes/backends.Rmd | 954 ++++++++++++++------ vignettes/common-issues.Rmd | 512 +++++++++-- vignettes/production.Rmd | 1306 +++++++++++++++++++--------- vignettes/quickstart.Rmd | 1317 +++++++++++++++++----------- vignettes/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- 27 files changed, 12128 insertions(+), 5022 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.1.0 dated 2026-06-11 and 3.1.2 dated 2026-06-13
DESCRIPTION | 8 +- MD5 | 32 +++++----- NEWS.md | 40 ++++++++++++ inst/doc/ggRandomForests-regression.html | 34 +++++----- inst/doc/ggRandomForests-survival.html | 40 ++++++------ inst/doc/ggRandomForests.html | 4 - inst/doc/varpro.R | 81 +++++++++++++++++++------ inst/doc/varpro.html | 97 ++++++++++++++++++++++--------- inst/doc/varpro.qmd | 81 +++++++++++++++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/helper-varpro-fixtures.R | 6 + tests/testthat/test_gg_isopro.R | 9 ++ tests/testthat/test_gg_udependent.R | 3 tests/testthat/test_gg_varpro.R | 2 vignettes/precompute_varpro.R | 95 +++++++++++++++++++++++++----- vignettes/varpro.qmd | 81 +++++++++++++++++++------ vignettes/varpro_precomputed.rds |binary 17 files changed, 454 insertions(+), 159 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption [...truncated...]
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.3.0 dated 2025-12-13 and 2.5.0 dated 2026-06-13
did-2.3.0/did/vignettes/TWFE_cache |only did-2.5.0/did/DESCRIPTION | 21 did-2.5.0/did/MD5 | 208 +-- did-2.5.0/did/NAMESPACE | 30 did-2.5.0/did/NEWS.md | 132 + did-2.5.0/did/R/AGGTEobj.R | 8 did-2.5.0/did/R/DIDparams.R | 2 did-2.5.0/did/R/DIDparams2.R | 4 did-2.5.0/did/R/MP.R | 16 did-2.5.0/did/R/aggte.R | 24 did-2.5.0/did/R/att_gt.R | 473 +++++-- did-2.5.0/did/R/compute.aggte.R | 221 ++- did-2.5.0/did/R/compute.att_gt.R | 1067 ++++++++++++---- did-2.5.0/did/R/compute.att_gt2.R | 708 ++++++++-- did-2.5.0/did/R/conditional_did_pretest.R | 224 ++- did-2.5.0/did/R/data.R | 11 did-2.5.0/did/R/ggdid.R | 32 did-2.5.0/did/R/gplot.R | 14 did-2.5.0/did/R/imports.R | 15 did-2.5.0/did/R/mboot.R | 137 +- did-2.5.0/did/R/pre_process_did.R | 298 +++- did-2.5.0/did/R/pre_process_did2.R | 393 +++-- did-2.5.0/did/R/process_attgt.R | 21 did-2.5.0/did/R/simulate_data.R | 15 did-2.5.0/did/R/tidy.R | 130 + did-2.5.0/did/R/utility_functions.R | 116 + did-2.5.0/did/README.md | 56 did-2.5.0/did/build/partial.rdb |binary did-2.5.0/did/build/vignette.rds |binary did-2.5.0/did/inst/CITATION | 2 did-2.5.0/did/inst/doc/TWFE.R | 10 did-2.5.0/did/inst/doc/TWFE.Rmd | 34 did-2.5.0/did/inst/doc/TWFE.html | 59 did-2.5.0/did/inst/doc/did-basics.R | 7 did-2.5.0/did/inst/doc/did-basics.Rmd | 13 did-2.5.0/did/inst/doc/did-basics.html | 82 - did-2.5.0/did/inst/doc/extensions.html | 6 did-2.5.0/did/inst/doc/multi-period-did.Rmd | 2 did-2.5.0/did/inst/doc/multi-period-did.html | 11 did-2.5.0/did/inst/doc/pre-testing.R | 8 did-2.5.0/did/inst/doc/pre-testing.Rmd | 12 did-2.5.0/did/inst/doc/pre-testing.html | 34 did-2.5.0/did/man/AGGTEobj.Rd | 2 did-2.5.0/did/man/DIDparams.Rd | 110 + did-2.5.0/did/man/MP.Rd | 8 did-2.5.0/did/man/aggte.Rd | 24 did-2.5.0/did/man/att_gt.Rd | 150 +- did-2.5.0/did/man/compute.aggte.Rd | 14 did-2.5.0/did/man/compute.att_gt2.Rd | 4 did-2.5.0/did/man/conditional_did_pretest.Rd | 64 did-2.5.0/did/man/did-package.Rd | 3 did-2.5.0/did/man/figures/README-unnamed-chunk-12-1.png |binary did-2.5.0/did/man/figures/README-unnamed-chunk-9-1.png |binary did-2.5.0/did/man/ggdid.AGGTEobj.Rd | 2 did-2.5.0/did/man/ggdid.MP.Rd | 2 did-2.5.0/did/man/ggdid.Rd | 19 did-2.5.0/did/man/mboot.Rd | 9 did-2.5.0/did/man/mpdta.Rd | 11 did-2.5.0/did/man/nobs.AGGTEobj.Rd |only did-2.5.0/did/man/nobs.MP.Rd |only did-2.5.0/did/man/pre_process_did.Rd | 112 + did-2.5.0/did/man/pre_process_did2.Rd | 112 + did-2.5.0/did/man/reexports.Rd | 2 did-2.5.0/did/man/test.mboot.Rd | 8 did-2.5.0/did/man/tidy.AGGTEobj.Rd | 35 did-2.5.0/did/man/tidy.MP.Rd | 25 did-2.5.0/did/man/trimmer.Rd | 4 did-2.5.0/did/tests |only did-2.5.0/did/vignettes/TWFE.Rmd | 34 did-2.5.0/did/vignettes/did-basics.Rmd | 13 did-2.5.0/did/vignettes/multi-period-did.Rmd | 2 did-2.5.0/did/vignettes/pre-testing.Rmd | 12 72 files changed, 4021 insertions(+), 1416 deletions(-)
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding
Description: Methods for analyzing DNA methylation data via Most Recurrent Methylation Patterns (MRMPs). Supports cell-type annotation, spatial deconvolution, unsupervised clustering, and cancer cell-of-origin inference. Includes C-backed summaries for YAME “.cg/.cm” files (overlap counts, log2 odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS deconvolution, and plotting utilities. Scales to large spatial and single-cell methylomes and is robust to extreme sparsity.
Author: Hongxiang Fu [aut, cre] ,
Wanding Zhou [cph, fnd],
The SAMtools/HTSlib authors [ctb, cph] ,
Attractive Chaos [ctb, cph] )
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Diff between MethScope versions 1.0.1 dated 2026-02-26 and 1.0.2 dated 2026-06-13
DESCRIPTION | 11 ++++++----- MD5 | 33 ++++++++++++++++++++------------- NAMESPACE | 2 ++ R/ModelTraining.R | 28 +++++++++++++++++++--------- R/PredictCellType.R | 38 +++++++++++++++++++++++++++++--------- R/PretrainedModels.R |only R/sysdata.rda |binary README.md | 4 +++- inst/doc/MethScope-Tutorial.R | 3 ++- inst/doc/MethScope-Tutorial.Rmd | 5 +++-- inst/doc/MethScope-Tutorial.html | 8 ++++---- inst/extdata/models |only inst/extdata/toy.cm |binary man/Input_training.Rd | 2 +- man/Liu2021_MouseBrain_P1000.Rd |only man/PredictCellType.Rd | 3 ++- man/Zhou2025_HumanAtlas_P1000.Rd |only tests/testthat |only tests/testthat.R |only vignettes/MethScope-Tutorial.Rmd | 5 +++-- 20 files changed, 94 insertions(+), 48 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using STAN
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.0 dated 2026-05-27 and 1.0.1 dated 2026-06-13
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 3 +++ R/bvar.R | 2 ++ R/zzz.R |only README.md | 21 ++++++++++++++++++--- inst/CITATION | 2 +- 7 files changed, 33 insertions(+), 12 deletions(-)
Title: Computes Diversity Indices for Archaeological Data
Description: Companion package of Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>. It computes Diversity Indices, decomposes several of them and computes bootstrap confidence intervals.
Author: Andreu Sanso [aut, cre],
Arnaud Barat [aut],
Jordi Rosell [aut]
Maintainer: Andreu Sanso <andreu.sanso@uib.eu>
Diff between diversityArch versions 0.3.0 dated 2026-05-04 and 0.4.0 dated 2026-06-13
DESCRIPTION | 12 +++---- MD5 | 72 +++++++++++++++++++++---------------------- NEWS.md | 11 ++++++ R/all_indices.R | 87 ++++++++++++++++++++++++++++++++-------------------- R/bs.R | 6 +-- R/bs_dec.R | 10 ++--- R/bs_frag.R | 4 +- R/check_x.R | 11 +----- R/dec_equit.R | 4 +- R/dec_shannon.R | 7 +--- R/dominance.R | 4 +- R/equitability.R | 4 +- R/evenness.R | 4 +- R/margalef.R | 4 +- R/menhinick.R | 4 +- R/shannon.R | 4 +- R/shannon_frag.R | 2 - R/simpson_D.R | 4 +- R/simpson_E.R | 4 +- man/Qesem_f.Rd | 9 ++--- man/Qesem_s.Rd | 9 ++--- man/all_indices.Rd | 8 ++-- man/bs.Rd | 4 +- man/bs_dec.Rd | 4 +- man/bs_frag.Rd | 4 +- man/check_x.Rd | 5 -- man/dec_equit.Rd | 4 +- man/dec_shannon.Rd | 4 +- man/dominance.Rd | 4 +- man/equitability.Rd | 4 +- man/evenness.Rd | 4 +- man/margalef.Rd | 4 +- man/menhinick.Rd | 4 +- man/shannon.Rd | 4 +- man/shannon_frag.Rd | 2 - man/simpson_D.Rd | 4 +- man/simpson_E.Rd | 4 +- 37 files changed, 183 insertions(+), 160 deletions(-)
Title: Canonical Correlation Analysis via Reduced Rank Regression
Description: Canonical correlation analysis (CCA) via reduced-rank regression with support for regularization and cross-validation. Several methods for estimating CCA in high-dimensional settings are implemented. The first set of methods, cca_rrr() (and variants: cca_group_rrr() and cca_graph_rrr()), assumes that one dataset is high-dimensional and the other is low-dimensional, while the second, ecca() (for Efficient CCA) assumes that both datasets are high-dimensional. For both methods, standard l1 regularization as well as group-lasso regularization are available. cca_graph_rrr further supports total variation regularization when there is a known graph structure among the variables of the high-dimensional dataset. In this case, the loadings of the canonical directions of the high-dimensional dataset are assumed to be smooth on the graph. For more details see Donnat and Tuzhilina (2024) <doi:10.48550/arXiv.2405.19539> and Wu, Tuzhilina and Donnat (2025) <doi:10.48550/arXiv.2507.11160> [...truncated...]
Author: Claire Donnat [aut, cre] ,
Elena Tuzhilina [aut] ,
Zixuan Wu [aut]
Maintainer: Claire Donnat <cdonnat@uchicago.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2026-04-29
Diff between ccar3 versions 0.1.1 dated 2026-04-29 and 0.1.2 dated 2026-06-13
DESCRIPTION | 10 ++--- MD5 | 25 ++++++------- R/ecca.r | 1 R/graph_reduced_rank_regression.R | 1 R/group_reduced_rank_regression.R | 15 +++++++ R/reduced_rank_regression.R | 11 +++++ R/utils.R | 62 ++++++++++++++++++++++++++++++++- tests/testthat/helper-cran.R |only tests/testthat/test-cca_graph_rrr_cv.R | 2 + tests/testthat/test-cca_group_rrr.R | 2 - tests/testthat/test-cca_group_rrr_cv.R | 1 tests/testthat/test-cca_rrr.R | 2 - tests/testthat/test-cca_rrr_cv.R | 4 +- tests/testthat/test-ecca.R | 2 - 14 files changed, 114 insertions(+), 24 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.5 dated 2026-04-23 and 0.2.6 dated 2026-06-13
DESCRIPTION | 10 MD5 | 157 +- NAMESPACE | 212 +-- NEWS.md | 128 +- R/BayesERtools-package.R | 12 R/build_spec_coveff.R | 842 ++++++------- R/coveff.R | 903 +++++++------- R/dev_ermod_emax.R | 688 +++++------ R/dev_ermod_lin.R | 1658 +++++++++++++-------------- R/ermod-class.R | 730 ++++++------ R/ermod-methods.R | 750 ++++++------ R/ersim-class.R | 152 +- R/ersim-methods.R | 220 +-- R/eval_ermod.R | 278 ++-- R/loo_kfold.R | 496 ++++---- R/p_direction.R | 164 +- R/plot_ermod.R | 1940 ++++++++++++++++---------------- R/plot_ermod_exp_cov_sel.R | 346 ++--- R/s3_generics.R | 108 - R/sim_ermod.R | 967 ++++++++------- R/utils-draws.R |only R/yyy.R | 356 ++--- README.md | 448 +++---- build/vignette.rds |binary inst/doc/overview_of_the_package.R | 120 - inst/doc/overview_of_the_package.Rmd | 266 ++-- inst/doc/overview_of_the_package.html | 1566 ++++++++++++------------- man/BayesERtools-package.Rd | 72 - man/as_draws.Rd | 104 - man/build_spec_coveff.Rd | 172 +- man/calc_ersim_med_qi.Rd | 40 man/combine_er_components.Rd | 90 - man/d_sim_binom_cov.Rd | 116 - man/d_sim_emax.Rd | 78 - man/d_sim_lin.Rd | 70 - man/d_sim_placebo.Rd | 84 - man/dev_ermod_bin.Rd | 172 +- man/dev_ermod_bin_cov_functions.Rd | 180 +- man/dev_ermod_bin_cov_sel.Rd | 236 +-- man/dev_ermod_bin_exp_sel.Rd | 164 +- man/dev_ermod_emax.Rd | 256 ++-- man/dev_ermod_emax_exp_sel.Rd | 214 +-- man/edit_spec_coveff.Rd | 210 +-- man/ermod_cov_sel_method.Rd | 50 man/ermod_exp_sel_method.Rd | 50 man/ermod_method.Rd | 84 - man/ersim_method.Rd | 56 man/eval_ermod.Rd | 146 +- man/extract_coef_exp_ci.Rd | 54 man/extract_ermod.Rd | 104 - man/extract_ersim.Rd | 104 - man/extract_method.Rd | 104 - man/figures/logo_svg.svg | 1870 +++++++++++++++--------------- man/kfold.Rd | 126 +- man/loo.Rd | 56 man/p_direction.Rd | 146 +- man/plot_cov_sel.Rd | 102 - man/plot_coveff.Rd | 154 +- man/plot_er.Rd | 346 ++--- man/plot_er_exp_sel.Rd | 74 - man/plot_er_gof.Rd | 280 ++-- man/print_coveff.Rd | 150 +- man/prior_summary.Rd | 44 man/sim_coveff.Rd | 142 +- man/sim_er.Rd | 172 +- man/sim_er_new_exp.Rd | 226 +-- man/sim_er_new_exp_marg.Rd | 224 +-- tests/testthat.R | 24 tests/testthat/test-build_spec_coveff.R | 166 +- tests/testthat/test-coveff.R | 346 ++--- tests/testthat/test-dev_ermod_emax.R | 456 +++---- tests/testthat/test-dev_ermod_lin.R | 930 +++++++-------- tests/testthat/test-ermod-methods.R | 298 ++-- tests/testthat/test-eval_ermod.R | 268 ++-- tests/testthat/test-loo_kfold.R | 289 ++-- tests/testthat/test-p_direction.R | 104 - tests/testthat/test-plot_ermod.R | 672 +++++------ tests/testthat/test-sim_ermod.R | 374 +++--- vignettes/data/supported_models.csv | 16 vignettes/overview_of_the_package.Rmd | 266 ++-- 80 files changed, 12438 insertions(+), 12410 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.9 dated 2025-02-17 and 0.1.10 dated 2026-06-13
rstanemax-0.1.10/rstanemax/DESCRIPTION | 16 - rstanemax-0.1.10/rstanemax/MD5 | 19 - rstanemax-0.1.10/rstanemax/NEWS.md | 7 rstanemax-0.1.10/rstanemax/R/posterior_predict.R | 4 rstanemax-0.1.10/rstanemax/build/vignette.rds |binary rstanemax-0.1.10/rstanemax/inst/doc/emaxmodel.html | 117 +++++----- rstanemax-0.1.10/rstanemax/man/posterior_predict.Rd | 4 rstanemax-0.1.10/rstanemax/src/stanExports_emax.cc | 34 +- rstanemax-0.1.10/rstanemax/src/stanExports_emax_binary.cc | 34 +- rstanemax-0.1.10/rstanemax/tests/testthat/test-posterior_integration.R |only rstanemax-0.1.9/rstanemax/src/Makevars.win |only rstanemax-0.1.9/rstanemax/tests/testthat/test-tidybayes_integration.R |only 12 files changed, 121 insertions(+), 114 deletions(-)
Title: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description: An interface to integrate 'igraph' and 'ggplot2' graphics within
a normalized coordinate system. 'RGraphSpace' extends 'ggplot2' with
graph-aware geometries optimized for large networks. The 'GraphSpace' class
integrates directly with 'ggplot2' through specialized 'geoms' and lazy
resolution of node attributes, supporting customization of aesthetics and
visual styles. These 'geoms' use a dual-anchor normalization approach to
align layers, particularly useful for analyses in which network elements
must be spatially aligned with reference maps and images.
Author: Sysbiolab Team [aut],
Flavio Kessler [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.3.0 dated 2026-05-22 and 1.4.0 dated 2026-06-13
RGraphSpace-1.3.0/RGraphSpace/R/inject-nodespace.R |only RGraphSpace-1.4.0/RGraphSpace/DESCRIPTION | 35 - RGraphSpace-1.4.0/RGraphSpace/MD5 | 73 +- RGraphSpace-1.4.0/RGraphSpace/NAMESPACE | 26 RGraphSpace-1.4.0/RGraphSpace/R/annotation-gspace.R |only RGraphSpace-1.4.0/RGraphSpace/R/geom-edgespace.R | 263 ++++--- RGraphSpace-1.4.0/RGraphSpace/R/geom-graphspace.R | 34 RGraphSpace-1.4.0/RGraphSpace/R/geom-nodespace.R | 165 +++- RGraphSpace-1.4.0/RGraphSpace/R/gspace-checks.R | 15 RGraphSpace-1.4.0/RGraphSpace/R/gspace-classes.R | 104 ++ RGraphSpace-1.4.0/RGraphSpace/R/gspace-coercion.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-constructor.R | 18 RGraphSpace-1.4.0/RGraphSpace/R/gspace-features.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-generics.R | 42 + RGraphSpace-1.4.0/RGraphSpace/R/gspace-ggplot-constructor.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-methods.R | 261 +++++-- RGraphSpace-1.4.0/RGraphSpace/R/gspace-normalize.R | 349 +++++----- RGraphSpace-1.4.0/RGraphSpace/R/gspace-supplements.R | 2 RGraphSpace-1.4.0/RGraphSpace/R/gspace-themes.R | 173 ++-- RGraphSpace-1.4.0/RGraphSpace/data/gtoy1.RData |binary RGraphSpace-1.4.0/RGraphSpace/inst/NEWS.Rd | 7 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.R | 10 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.html | 52 - RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-accessors.Rd | 90 +- RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-class.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-methods.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/RGraphSpace-package.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/annotation_gspace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/as.GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/geom_edgespace.Rd | 28 RGraphSpace-1.4.0/RGraphSpace/man/geom_graphspace.Rd | 17 RGraphSpace-1.4.0/RGraphSpace/man/geom_nodespace.Rd | 26 RGraphSpace-1.4.0/RGraphSpace/man/getGraphSpace-methods.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/ggplot-GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/gs_features-utils.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/inject_nodespace.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/normalizeGraphSpace-methods.Rd | 65 + RGraphSpace-1.4.0/RGraphSpace/man/plotGraphSpace-methods.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/theme_gspace.Rd | 42 - RGraphSpace-1.4.0/RGraphSpace/vignettes/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/vignettes/bibliography.bib | 33 42 files changed, 1300 insertions(+), 696 deletions(-)
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Alexander Tedeschi [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael N [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.11.0 dated 2025-08-29 and 0.12.0 dated 2026-06-13
DESCRIPTION | 14 MD5 | 135 ++--- NAMESPACE | 6 NEWS.md | 45 + R/add_param.R |only R/apply_mistnet.R | 6 R/beam.R | 63 +- R/bioRad-deprecated.R | 4 R/calculate_vp.R | 132 ++++- R/clean_mixture.R | 6 R/color_scale.R | 22 R/dbz_eta.R | 2 R/filter_precip.R | 39 + R/integrate_to_ppi.R | 130 ++++ R/project_as_ppi.R | 7 R/read_pvolfile.R | 12 R/s3.R | 2 R/scan_convert.R | 12 R/select.R | 4 R/sunrise_sunset.R | 52 - R/utils.R | 72 ++ R/validate_vpts.R | 18 R/vpts.R | 2 README.md | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/bioRad.Rmd | 2 inst/doc/bioRad.html | 7 inst/doc/rad_aero_22.R | 868 ++++++++++++++++----------------- inst/doc/rad_aero_22.Rmd | 2 inst/doc/rad_aero_22.html | 7 inst/doc/range_correction.html | 41 - man/add_expected_eta_to_scan.Rd | 11 man/add_param.Rd |only man/apply_mistnet.Rd | 4 man/beam_distance.Rd | 14 man/beam_height.Rd | 14 man/beam_profile.Rd | 26 man/beam_profile_overlap.Rd | 26 man/beam_range.Rd | 14 man/beam_width.Rd | 38 - man/bioRad-package.Rd | 1 man/calculate_vp.Rd | 82 ++- man/check_night.Rd | 2 man/clean_mixture.Rd | 4 man/composite_ppi.Rd | 8 man/doy_noy.Rd | 2 man/figures/README-plot_ppi-1.png |binary man/filter_precip.Rd | 10 man/gaussian_beam_profile.Rd | 26 man/integrate_to_ppi.Rd | 63 +- man/is.nan.data.frame.Rd | 20 man/map.Rd | 2 man/min_package_version.Rd |only man/plot.vp.Rd | 2 man/plot.vpi.Rd | 4 man/project_as_ppi.Rd | 4 man/read_pvolfile.Rd | 3 man/scan_to_raster.Rd | 10 man/sunrise_sunset.Rd | 49 - man/tidyverse.Rd | 3 tests/testthat/test-add_param.R |only tests/testthat/test-apply_mistnet.R | 2 tests/testthat/test-beam.R | 31 - tests/testthat/test-filter_precip.R |only tests/testthat/test-integrate_to_ppi.R | 122 ++++ tests/testthat/test-project_as_ppi.R | 11 tests/testthat/test-s3.R | 10 tests/testthat/test-scan_convert.R | 9 vignettes/bioRad.Rmd | 2 vignettes/rad_aero_22.Rmd | 2 71 files changed, 1465 insertions(+), 902 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.10.0 dated 2026-04-08 and 1.10.1 dated 2026-06-13
bbotk-1.10.0/bbotk/inst |only bbotk-1.10.0/bbotk/src/is_dominated.c |only bbotk-1.10.1/bbotk/DESCRIPTION | 10 bbotk-1.10.1/bbotk/MD5 | 173 ++-- bbotk-1.10.1/bbotk/NAMESPACE | 4 bbotk-1.10.1/bbotk/NEWS.md | 7 bbotk-1.10.1/bbotk/R/OptimInstanceAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchFocusSearch.R | 16 bbotk-1.10.1/bbotk/R/OptimizerBatchIrace.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchNLoptr.R | 4 bbotk-1.10.1/bbotk/R/TerminatorStagnationHypervolume.R | 10 bbotk-1.10.1/bbotk/R/helper.R | 6 bbotk-1.10.1/bbotk/R/zzz.R | 2 bbotk-1.10.1/bbotk/build/partial.rdb |binary bbotk-1.10.1/bbotk/man/Archive.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/ArchiveAsync.Rd | 403 +++++----- bbotk-1.10.1/bbotk/man/ArchiveAsyncFrozen.Rd | 313 +++---- bbotk-1.10.1/bbotk/man/ArchiveBatch.Rd | 247 +++--- bbotk-1.10.1/bbotk/man/CallbackAsync.Rd | 79 - bbotk-1.10.1/bbotk/man/CallbackBatch.Rd | 71 - bbotk-1.10.1/bbotk/man/Codomain.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ContextAsync.Rd | 119 +- bbotk-1.10.1/bbotk/man/ContextBatch.Rd | 113 +- bbotk-1.10.1/bbotk/man/EvalInstance.Rd | 185 ++-- bbotk-1.10.1/bbotk/man/Objective.Rd | 307 +++---- bbotk-1.10.1/bbotk/man/ObjectiveRFun.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ObjectiveRFunDt.Rd | 187 ++-- bbotk-1.10.1/bbotk/man/ObjectiveRFunMany.Rd | 162 ++-- bbotk-1.10.1/bbotk/man/ObjectiveTestFunction.Rd | 121 +-- bbotk-1.10.1/bbotk/man/OptimInstance.Rd | 202 ++--- bbotk-1.10.1/bbotk/man/OptimInstanceAsync.Rd | 170 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncMultiCrit.Rd | 154 +-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncSingleCrit.Rd | 153 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatch.Rd | 199 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchMultiCrit.Rd | 152 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchSingleCrit.Rd | 140 +-- bbotk-1.10.1/bbotk/man/OptimInstanceMultiCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/OptimInstanceSingleCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/Optimizer.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/OptimizerAsync.Rd | 91 +- bbotk-1.10.1/bbotk/man/OptimizerBatch.Rd | 88 +- bbotk-1.10.1/bbotk/man/Progressor.Rd | 116 +- bbotk-1.10.1/bbotk/man/Terminator.Rd | 261 +++--- bbotk-1.10.1/bbotk/man/bb_optimize.Rd | 3 bbotk-1.10.1/bbotk/man/bbotk-package.Rd | 1 bbotk-1.10.1/bbotk/man/bbotk_reflections.Rd | 1 bbotk-1.10.1/bbotk/man/branin.Rd | 3 bbotk-1.10.1/bbotk/man/is_dominated.Rd | 5 bbotk-1.10.1/bbotk/man/local_search.Rd | 10 bbotk-1.10.1/bbotk/man/mlr_optimizers.Rd | 5 bbotk-1.10.1/bbotk/man/mlr_optimizers_async_design_points.Rd | 98 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_grid_search.Rd | 101 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_chain.Rd | 88 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_cmaes.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_design_points.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_focus_search.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_gensa.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_grid_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_irace.Rd | 71 - bbotk-1.10.1/bbotk/man/mlr_optimizers_local_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_nloptr.Rd | 69 - bbotk-1.10.1/bbotk/man/mlr_optimizers_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_terminators.Rd | 4 bbotk-1.10.1/bbotk/man/mlr_terminators_clock_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_combo.Rd | 220 ++--- bbotk-1.10.1/bbotk/man/mlr_terminators_evals.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_none.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_perf_reached.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_run_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_batch.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_hypervolume.Rd | 107 +- bbotk-1.10.1/bbotk/man/mlr_test_functions.Rd | 2 bbotk-1.10.1/bbotk/man/reexports.Rd | 2 bbotk-1.10.1/bbotk/man/shrink_ps.Rd | 8 bbotk-1.10.1/bbotk/src/init.c | 4 bbotk-1.10.1/bbotk/src/local_search.c | 2 bbotk-1.10.1/bbotk/tests/testthat/helper.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_Objective.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_OptimInstanceBatchMultiCrit.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchFocusSearch.R | 12 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchLocalSearch.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationBatch.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationHypervolume.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_c_functions.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_helper.R |only bbotk-1.10.1/bbotk/tests/testthat/test_nds_selection.R | 20 89 files changed, 3704 insertions(+), 3561 deletions(-)
Title: Develop Hybridization Probes
Description: Hybridization probes for target sequences can be made based on melting temperature value calculated by R package 'TmCalculator' <https://CRAN.R-project.org/package=TmCalculator> and methods extended from Beliveau, B. J.,(2018) <doi:10.1073/pnas.1714530115>, and those hybridization probes can be used to capture specific target regions in fluorescence in situ hybridization and next generation sequence experiments.
Author: Junhui Li [cre, aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ProbeDeveloper versions 1.1.1 dated 2026-03-23 and 1.1.2 dated 2026-06-13
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- R/ProbeMake.R | 8 ++++---- README.md |only 4 files changed, 12 insertions(+), 11 deletions(-)
More information about ProbeDeveloper at CRAN
Permanent link
Title: An R Interface to the California Academy of Sciences Eschmeyer's
Catalog of Fishes
Description: Accesses the California Academy of Sciences Eschmeyer's Catalog of Fishes in R using web requests. The Catalog of fishes is the leading authority in fish taxonomy. Functions in the package allow users to search for fish taxa and valid names, retrieve taxonomic references, retrieve monthly taxonomic changes, obtain natural history collection information, and see the number of species by taxonomic group. For more information on the Catalog: Fricke, R., Eschmeyer, W. N. & R. van der Laan (eds) 2025. ESCHMEYER'S CATALOG OF FISHES <https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp>.
Author: Samuel R. Borstein [aut, cre],
Brandon Dominy [aut],
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between rcatfish versions 1.0.2 dated 2026-02-19 and 1.0.3 dated 2026-06-12
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 ++--- build/vignette.rds |binary inst/doc/rcatfish-vignette.html | 2 +- tests/testthat/test_rcatfish_updates.R | 2 +- 6 files changed, 14 insertions(+), 15 deletions(-)
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Description: Implementation of the Harmony algorithm for single cell integration, described in Patikas, Yao, et al. <doi:10.64898/2026.03.16.711825>. Package includes a standalone Harmony function and interfaces to external frameworks.
Author: Nikolaos Patikas [aut, ctb] ,
Hongcheng Yao [aut, ctb] ,
Ilya Korsunsky [cre, aut] ,
Martin Hemberg [aut] ,
Nghia Millard [aut] ,
Jean Fan [aut, ctb] ,
Kamil Slowikowski [aut, ctb] ,
Miles Smith [ctb],
Soumya Raychaudhuri [aut]
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>
This is a re-admission after prior archival of version 2.0.4 dated 2026-06-04
Diff between harmony versions 2.0.4 dated 2026-06-04 and 2.0.5 dated 2026-06-12
DESCRIPTION | 6 +- MD5 | 16 ++--- R/zzz.R | 36 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Seurat.html | 108 ++++++++++++++++++------------------- inst/doc/detailedWalkthrough.html | 102 +++++++++++++++++----------------- inst/doc/quickstart.html | 84 ++++++++++++++-------------- tests/testthat/test_two_variable.R | 106 ++++++++++++++++++------------------ 9 files changed, 230 insertions(+), 228 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],
Paul Fearnhead [aut],
Idris A. Eckley [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.6 dated 2026-06-09 and 0.1.7 dated 2026-06-12
DESCRIPTION | 9 +++++---- MD5 | 8 +++++--- src/ChangepointResult.h | 4 ++-- src/Costs.h | 36 +++++++++++++++++++----------------- tests |only 5 files changed, 31 insertions(+), 26 deletions(-)
Title: Utilities for Importing Data from Plain Text Accounting Files
Description: Utilities for querying plain text accounting files from 'Ledger', 'HLedger', and 'Beancount'.
Author: Trevor L. Davis [aut, cre] ,
Jenya Sovetkin [ctb],
Chris Lloyd [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ledger versions 2.0.13 dated 2026-03-30 and 2.1.1 dated 2026-06-12
DESCRIPTION | 11 MD5 | 30 NAMESPACE | 2 NEWS.md | 14 R/net_worth.R | 22 R/prune_coa.R | 6 R/register.R | 85 +- README.md | 969 +++++++++++++++++-------------- man/figures/README-income_chart-1.png |binary man/figures/README-net_worth_chart-1.png |binary man/figures/logo.png |only man/figures/logo.svg |only man/net_worth.Rd | 2 man/prune_coa.Rd | 6 man/register.Rd | 15 tests/testthat/test-net_worth.R | 4 tests/testthat/test-register.R | 18 17 files changed, 686 insertions(+), 498 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.8.0 dated 2026-03-31 and 0.8.2 dated 2026-06-12
DESCRIPTION | 8 MD5 | 182 ++--- NAMESPACE | 76 +- NEWS.md | 23 R/JoinReport.R | 8 R/addin.R | 6 R/advanced_patterns.R | 49 - R/backends.R | 239 +++--- R/join_explain.R | 26 R/join_repair.R | 49 - R/join_spy.R | 41 - R/join_strict.R | 66 - R/joinspy-package.R | 2 R/key_check.R | 36 - R/logging.R | 29 R/string_diagnostics.R | 30 R/utils-keys.R |only README.md | 104 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/backends.Rmd | 612 ++++++++--------- inst/doc/backends.html | 4 inst/doc/common-issues.R | 2 inst/doc/common-issues.Rmd | 983 +++++++++++++-------------- inst/doc/common-issues.html | 25 inst/doc/production.R | 8 inst/doc/production.Rmd | 853 ++++++++++++------------ inst/doc/production.html | 134 +-- inst/doc/quickstart.Rmd | 1029 ++++++++++++++--------------- inst/doc/quickstart.html | 68 + inst/doc/why-keys-dont-match.Rmd | 721 ++++++++++---------- inst/doc/why-keys-dont-match.html | 61 - man/addin_join_inspector.Rd | 32 man/analyze_join_chain.Rd | 84 +- man/check_cartesian.Rd | 72 +- man/detect_cardinality.Rd | 72 +- man/dot-analyze_match.Rd | 44 - man/dot-analyze_multicolumn_keys.Rd | 48 - man/dot-check_cols.Rd |only man/dot-classify_cardinality.Rd |only man/dot-detect_backend.Rd | 40 - man/dot-detect_case_mismatch.Rd | 48 - man/dot-detect_empty_strings.Rd | 36 - man/dot-detect_encoding_issues.Rd | 48 - man/dot-detect_factor_mismatch.Rd | 48 - man/dot-detect_near_matches.Rd | 48 - man/dot-detect_numeric_precision.Rd | 36 - man/dot-detect_type_mismatch.Rd | 48 - man/dot-detect_whitespace.Rd | 48 - man/dot-format_bytes.Rd | 36 - man/dot-join_spy_impl.Rd | 64 - man/dot-json_escape.Rd |only man/dot-levenshtein.Rd | 40 - man/dot-make_key.Rd |only man/dot-perform_join.Rd | 60 - man/dot-predict_row_counts.Rd | 44 - man/dot-report_to_list.Rd | 40 - man/dot-report_to_text.Rd | 40 - man/dot-resolve_by.Rd |only man/dot-summarize_keys.Rd | 40 - man/dot-to_json.Rd | 36 - man/dot-validate_df.Rd |only man/full_join_spy.Rd | 74 +- man/get_log_file.Rd | 34 man/inner_join_spy.Rd | 74 +- man/is_join_report.Rd | 34 man/join_diff.Rd | 66 - man/join_explain.Rd | 86 +- man/join_repair.Rd | 126 +-- man/join_spy.Rd | 136 +-- man/join_strict.Rd | 128 +-- man/joinspy-package.Rd | 53 - man/key_check.Rd | 82 +- man/key_duplicates.Rd | 92 +- man/last_report.Rd | 60 - man/left_join_spy.Rd | 106 +- man/log_report.Rd | 92 +- man/new_join_report.Rd | 70 - man/plot.JoinReport.Rd | 86 +- man/print.JoinReport.Rd | 38 - man/right_join_spy.Rd | 74 +- man/set_log_file.Rd | 66 - man/suggest_repairs.Rd | 56 - man/summary.JoinReport.Rd | 60 - tests/testthat/Rplots.pdf |binary tests/testthat/test-backends-integration.R | 166 ++-- tests/testthat/test-backends.R | 344 ++++----- tests/testthat/test-bugfixes.R |only tests/testthat/test-coverage-boost.R | 24 tests/testthat/test-join_strict.R | 28 tests/testthat/test-phase3-6.R | 12 vignettes/backends.Rmd | 612 ++++++++--------- vignettes/common-issues.Rmd | 983 +++++++++++++-------------- vignettes/production.Rmd | 853 ++++++++++++------------ vignettes/quickstart.Rmd | 1029 ++++++++++++++--------------- vignettes/why-keys-dont-match.Rmd | 721 ++++++++++---------- 96 files changed, 6546 insertions(+), 6545 deletions(-)
Title: Species Distribution Modeling with H3 Grids
Description: Provides tools for species distribution modeling using H3
hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>).
Facilitates retrieval of species occurrence records, generation of H3 grids,
computation of landscape metrics, and preparation of spatial data for modern
species distribution models workflows. Designed for biodiversity and landscape ecology research.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between h3sdm versions 0.1.4 dated 2026-05-29 and 0.1.5 dated 2026-06-12
DESCRIPTION | 16 - MD5 | 42 ++-- NAMESPACE | 2 NEWS.md | 63 ++++++ R/data-doc.R | 122 +++++++++++- R/h3sdm_aoa.R | 16 - R/h3sdm_filter_outliers.R |only R/h3sdm_pa.R | 197 +++++++++++-------- R/h3sdm_pa_from_records.R | 72 ++++++- R/h3sdm_pres.R |only data/cr_outline.rda |only data/cr_outline_c.rda |binary inst/doc/h3sdm.R | 34 ++- inst/doc/h3sdm.Rmd | 103 ++++++---- inst/doc/h3sdm.html | 280 ++++++++++++++-------------- man/bioclim_current.Rd | 2 man/bioclim_future.Rd | 4 man/cr_outline.Rd |only man/cr_outline_c.Rd | 42 +++- man/h3sdm_filter_outliers.Rd |only man/h3sdm_pa.Rd | 77 ++++--- man/h3sdm_pa_from_records.Rd | 17 + man/h3sdm_pres.Rd |only vignettes/articles/multi_model_workflow.Rmd | 248 +++++++++++------------- vignettes/h3sdm.Rmd | 103 ++++++---- 25 files changed, 915 insertions(+), 525 deletions(-)
Title: NASA 'EarthData' Access Utilities
Description: Providing easy, portable access to NASA 'EarthData' products
through the use of bearer tokens. Much of NASA's public data catalogs hosted
and maintained by its 12 Distributed Active Archive Centers ('DAACs') are
now made available on the Amazon Web Services 'S3' storage. However,
accessing this data through the standard 'S3' API is restricted to only to
compute resources running inside 'us-west-2' Data Center in Portland, Oregon,
which allows NASA to avoid being charged data egress rates. This package
provides public access to the data from any networked device by using the
'EarthData' login application programming interface (API),
<https://www.earthdata.nasa.gov/data/earthdata-login>,
providing convenient authentication and access to cloud-hosted NASA 'EarthData'
products. This makes access to a wide range of earth observation data from
any location straight forward and compatible with R packages that are
widely used with cloud native earth observation data (such as 'terra',
's [...truncated...]
Author: Carl Boettiger [aut, cre, cph] ,
Luis Lopez [aut] ,
Yuvi Panda [aut],
Bri Lind [aut] ,
Andy Teucher [ctb] ,
Openscapes [fnd]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between earthdatalogin versions 0.0.3 dated 2025-07-11 and 0.0.4 dated 2026-06-12
earthdatalogin-0.0.3/earthdatalogin/inst/vignette-sources/gdalcubes-stac-cog-explore.Rmd |only earthdatalogin-0.0.4/earthdatalogin/DESCRIPTION | 6 +- earthdatalogin-0.0.4/earthdatalogin/MD5 | 23 ++++------ earthdatalogin-0.0.4/earthdatalogin/NEWS.md | 7 +++ earthdatalogin-0.0.4/earthdatalogin/R/edl_search.R | 3 - earthdatalogin-0.0.4/earthdatalogin/build/vignette.rds |binary earthdatalogin-0.0.4/earthdatalogin/inst/doc/data-formats.html | 4 - earthdatalogin-0.0.4/earthdatalogin/inst/doc/gdalcubes-stac-cog.html | 6 +- earthdatalogin-0.0.4/earthdatalogin/inst/doc/legacy-formats.html | 6 +- earthdatalogin-0.0.4/earthdatalogin/inst/doc/non-egressed.html | 2 earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-edl_netrc.R | 3 + earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-edl_search.R | 15 ++++++ earthdatalogin-0.0.4/earthdatalogin/tests/testthat/test-list-nasa-stacs.R | 10 ++++ 13 files changed, 59 insertions(+), 26 deletions(-)
More information about earthdatalogin at CRAN
Permanent link
Title: A Collection of Tools for Network Analysis
Description: Provides a collection of network analytic (convenience) functions which are missing in other standard packages. This includes triad census with attributes <doi:10.1016/j.socnet.2019.04.003>, core-periphery models <doi:10.1016/S0378-8733(99)00019-2>, and several graph generators. Most functions are build upon 'igraph'.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between netUtils versions 0.8.5 dated 2026-04-14 and 0.8.6 dated 2026-06-12
DESCRIPTION | 6 MD5 | 25 +- NEWS.md | 6 R/dyad_census_attr.R | 11 - R/fast_cliques.R | 4 R/graph_structures.R | 6 R/graphs.R | 8 R/print_igraph.R | 18 +- R/qap.R | 4 R/sample_kcores.R | 4 R/structural_equivalence.R | 2 R/triad_census_attr.R | 316 ++++--------------------------------- R/utils.R | 16 + tests/testthat/test-print_igraph.R |only 14 files changed, 103 insertions(+), 323 deletions(-)
Title: Markov Decision Processes (MDPs)
Description: Create and optimize (semi) MDPs with discrete time steps and
state space. Both hierarchical and ordinary-traditional MDPs can be
modeled.
Author: Lars Relund Nielsen [aut, cre]
Maintainer: Lars Relund Nielsen <lars@relund.dk>
This is a re-admission after prior archival of version 2.1.2 dated 2023-01-31
Diff between MDP2 versions 2.1.2 dated 2023-01-31 and 2.2.2.0 dated 2026-06-12
MDP2-2.1.2/MDP2/R/binary.R |only MDP2-2.1.2/MDP2/R/hmpMDPWriter.R |only MDP2-2.1.2/MDP2/src/matalg.h |only MDP2-2.1.2/MDP2/src/matrix.h |only MDP2-2.2.2.0/MDP2/DESCRIPTION | 26 MDP2-2.2.2.0/MDP2/MD5 | 115 MDP2-2.2.2.0/MDP2/NAMESPACE | 1 MDP2-2.2.2.0/MDP2/NEWS.md | 12 MDP2-2.2.2.0/MDP2/R/convert.R | 3 MDP2-2.2.2.0/MDP2/R/mdp.R | 149 - MDP2-2.2.2.0/MDP2/R/plot.R | 724 ++++- MDP2-2.2.2.0/MDP2/R/writer.R |only MDP2-2.2.2.0/MDP2/build/vignette.rds |binary MDP2-2.2.2.0/MDP2/inst/WORDLIST | 4 MDP2-2.2.2.0/MDP2/inst/doc/building.R | 18 MDP2-2.2.2.0/MDP2/inst/doc/building.Rmd | 16 MDP2-2.2.2.0/MDP2/inst/doc/building.html | 457 +-- MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.R | 10 MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.Rmd | 4 MDP2-2.2.2.0/MDP2/inst/doc/finite-mdp.html | 93 MDP2-2.2.2.0/MDP2/inst/doc/infinite-hmdp.R | 14 MDP2-2.2.2.0/MDP2/inst/doc/infinite-hmdp.html | 189 - MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.R | 8 MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.Rmd | 6 MDP2-2.2.2.0/MDP2/inst/doc/infinite-mdp.html | 113 MDP2-2.2.2.0/MDP2/inst/doc/mdp2.html | 4 MDP2-2.2.2.0/MDP2/inst/examples/convert-ex.R | 13 MDP2-2.2.2.0/MDP2/inst/examples/memoryMDPWriter-ex.R |only MDP2-2.2.2.0/MDP2/inst/examples/plot-ex.R | 76 MDP2-2.2.2.0/MDP2/man/MDP2-package.Rd | 5 MDP2-2.2.2.0/MDP2/man/binaryActionWriter.Rd | 84 MDP2-2.2.2.0/MDP2/man/binaryMDPWriter.Rd | 183 - MDP2-2.2.2.0/MDP2/man/convertBinary2HMP.Rd | 15 MDP2-2.2.2.0/MDP2/man/convertHMP2Binary.Rd | 13 MDP2-2.2.2.0/MDP2/man/getBinInfoActions.Rd | 2 MDP2-2.2.2.0/MDP2/man/getBinInfoStates.Rd | 2 MDP2-2.2.2.0/MDP2/man/getHypergraph.Rd | 83 MDP2-2.2.2.0/MDP2/man/getPolicy.Rd | 4 MDP2-2.2.2.0/MDP2/man/getRPO.Rd | 7 MDP2-2.2.2.0/MDP2/man/hmpMDPWriter.Rd | 59 MDP2-2.2.2.0/MDP2/man/loadMDP.Rd | 3 MDP2-2.2.2.0/MDP2/man/memoryMDPWriter.Rd |only MDP2-2.2.2.0/MDP2/man/plot.HMDP.Rd | 91 MDP2-2.2.2.0/MDP2/man/plotHypergraph.Rd | 145 - MDP2-2.2.2.0/MDP2/man/runCalcWeights.Rd | 2 MDP2-2.2.2.0/MDP2/man/runPolicyIteAve.Rd | 13 MDP2-2.2.2.0/MDP2/man/runPolicyIteDiscount.Rd | 5 MDP2-2.2.2.0/MDP2/man/runValueIte.Rd | 10 MDP2-2.2.2.0/MDP2/src/RcppExports.cpp | 1 MDP2-2.2.2.0/MDP2/src/basicdt.h | 62 MDP2-2.2.2.0/MDP2/src/hmdp.cpp | 2580 +++++++++++++++++-- MDP2-2.2.2.0/MDP2/src/hmdp.h | 1759 +++++++++--- MDP2-2.2.2.0/MDP2/src/modules.cpp | 104 MDP2-2.2.2.0/MDP2/src/timer.h | 172 - MDP2-2.2.2.0/MDP2/tests/testthat/files/cow.csv |only MDP2-2.2.2.0/MDP2/tests/testthat/test_building.R | 519 +++ MDP2-2.2.2.0/MDP2/tests/testthat/test_convert.R | 1 MDP2-2.2.2.0/MDP2/tests/testthat/test_criteria.R | 395 ++ MDP2-2.2.2.0/MDP2/tests/testthat/test_plot.R |only MDP2-2.2.2.0/MDP2/tests/testthat/test_steady.R | 1 MDP2-2.2.2.0/MDP2/vignettes/building.Rmd | 16 MDP2-2.2.2.0/MDP2/vignettes/finite-mdp.Rmd | 4 MDP2-2.2.2.0/MDP2/vignettes/infinite-mdp.Rmd | 6 63 files changed, 6585 insertions(+), 1816 deletions(-)
Title: Computation of the Double-Entry Intraclass Correlation
Description: The functions compute the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). Profiles comprising correlations are automatically transformed according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score prior to computation of the double-entry intraclass correlation (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Author: Christian Bloetner [aut, cre],
Michael Paul Grosz [aut]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between iccde versions 0.3.8 dated 2025-04-23 and 0.3.9 dated 2026-06-12
DESCRIPTION | 6 +- MD5 | 16 ++--- NAMESPACE | 3 - R/iccde.R | 163 +++++++++++++++++++++++++++++++++++++++++++++++++++---- R/iccdeboot.R | 69 +++++++++++++++++------ R/iccdemat.R | 40 +++++++++++-- man/iccde.Rd | 42 ++++++++++++-- man/iccdeboot.Rd | 21 ++++--- man/iccdemat.Rd | 8 ++ 9 files changed, 307 insertions(+), 61 deletions(-)
Title: Temporal Parametric Hazard Modeling
Description: Provides native R implementations of the multiphase parametric
hazard model of Blackstone, Naftel, and Turner (1986)
<doi:10.1080/01621459.1986.10478314> with a focus on behavioral parity,
transparent numerics, and reproducible validation against reference
outputs from the original 'C'/'SAS' HAZARD program, originally developed at
the University of Alabama at Birmingham (UAB). The 'SAS'/'C' code and this R
package are currently developed and maintained at The Cleveland Clinic
Foundation, and the R code was wholly developed at The Cleveland Clinic
Foundation. The generalized temporal
decomposition family extends to longitudinal mixed-effects settings
(Rajeswaran et al. 2018 <doi:10.1177/0962280215623583>). The package is
intentionally implemented in pure R first; performance-critical paths may
later be accelerated with 'Rcpp' without changing the public interface.
Author: John Ehrlinger [aut, cre, cph]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between TemporalHazard versions 1.0.3 dated 2026-05-30 and 1.1.0 dated 2026-06-12
DESCRIPTION | 6 MD5 | 173 ++-- NEWS.md | 359 +++++++++ R/TemporalHazard-package.R |only R/argument_mapping.R | 3 R/decomposition.R | 44 + R/diagnostics.R | 221 +++-- R/hazard_api.R | 266 ++++++- R/hessian-invert.R |only R/hessian-multiphase.R |only R/likelihood-exponential.R | 68 + R/likelihood-loglogistic.R | 77 ++ R/likelihood-lognormal.R | 97 ++ R/likelihood-multiphase.R | 212 +++++ R/likelihood-weibull.R | 183 ++++ R/math_primitives.R | 41 + R/optimizer.R | 67 + R/phase-spec.R | 70 + R/predict-cl.R | 243 ++++-- R/stepwise-formula.R | 43 + R/stepwise.R | 57 + R/weights-fixture.R |only README.md | 8 inst/doc/clinical-analysis-walkthrough.html | 301 +++++--- inst/doc/fitting-hazard-models.R | 145 +++ inst/doc/fitting-hazard-models.html | 371 +++++++++- inst/doc/fitting-hazard-models.qmd | 327 ++++++++ inst/doc/getting-started.html | 36 inst/doc/inference-diagnostics.html | 56 - inst/doc/inference-diagnostics.qmd | 6 inst/doc/mf-mathematical-foundations.html | 2 inst/doc/mf-mathematical-foundations.qmd | 15 inst/doc/prediction-visualization.html | 4 inst/doc/sas-to-r-migration.html | 50 - inst/extdata/stepwise-fixtures/avc-forward-wald.sas |only inst/extdata/stepwise-fixtures/parse-hazard-lst.R |only inst/extdata/stepwise-fixtures/payload |only inst/extdata/weights-fixtures |only inst/fixtures/mp_synthetic_3phase.rds |binary inst/fixtures/stepwise-avc-forward-wald.rds |only man/TemporalHazard-package.Rd |only man/dot-hzr_conserve_events.Rd | 10 man/dot-hzr_free_vcov.Rd |only man/dot-hzr_predict_jacobian_multiphase.Rd | 10 man/dot-hzr_predict_with_se.Rd | 7 man/dot-hzr_predict_with_se_decomposed.Rd |only man/dot-hzr_select_fixmu_phase.Rd | 20 man/figures/readme-hazard-phases.png |binary man/figures/readme-survival.png |binary man/hazard.Rd | 78 ++ man/hzr_argument_mapping.Rd | 5 man/hzr_clamp_prob.Rd | 11 man/hzr_competing_risks.Rd | 16 man/hzr_deciles.Rd | 37 man/hzr_decompos.Rd | 26 man/hzr_kaplan.Rd | 8 man/hzr_log1mexp.Rd | 20 man/hzr_log1pexp.Rd | 18 man/hzr_nelson.Rd | 8 man/hzr_phase.Rd | 74 + man/hzr_stepwise.Rd | 62 + man/predict.hazard.Rd | 31 man/print.summary.hazard.Rd | 5 man/stepwise_trace.Rd | 3 man/vcov.hazard.Rd | 14 tests/testthat/helper-invariants.R |only tests/testthat/helper-sas-parity.R | 333 ++++++++ tests/testthat/test-coe-left-truncation.R |only tests/testthat/test-conservation-of-events.R | 222 +++++ tests/testthat/test-decompos-boundary.R |only tests/testthat/test-diagnostics.R | 158 +++- tests/testthat/test-exponential-hessian.R |only tests/testthat/test-hazard-api.R | 64 + tests/testthat/test-hessian-invert.R |only tests/testthat/test-hessian-stability.R |only tests/testthat/test-interval-censoring-multiphase.R |only tests/testthat/test-interval-censoring-weibull.R | 74 + tests/testthat/test-invariants.R |only tests/testthat/test-loglogistic-hessian.R |only tests/testthat/test-lognormal-hessian.R |only tests/testthat/test-multiphase-api.R | 28 tests/testthat/test-multiphase-gradient.R | 4 tests/testthat/test-multiphase-hessian.R |only tests/testthat/test-multiphase-likelihood.R | 5 tests/testthat/test-phase-specific-covariates.R |only tests/testthat/test-predict-cl.R | 208 +++++ tests/testthat/test-predict-hazard-multiphase.R |only tests/testthat/test-sas-parity.R | 742 +++++++++++++++++++- tests/testthat/test-stepwise-parity.R | 174 ++-- tests/testthat/test-weibull-event-hazard.R |only tests/testthat/test-weibull-hessian.R |only tests/testthat/test-weights-sas-parity.R |only tests/testthat/test-weights.R | 311 ++++++++ vignettes/fitting-hazard-models.qmd | 327 ++++++++ vignettes/inference-diagnostics.qmd | 6 vignettes/mf-mathematical-foundations.qmd | 15 96 files changed, 5924 insertions(+), 761 deletions(-)
More information about TemporalHazard at CRAN
Permanent link
Title: Datasets from the Hello Data Science Book
Description: Provides datasets used for analysis
and visualizations in the open-access Hello Data Science book.
Author: Mine Dogucu [aut, cre] ,
Catalina Medina [aut] ,
Alma Castro [aut]
Maintainer: Mine Dogucu <mdogucu@gmail.com>
Diff between hellodatascience versions 0.1.0 dated 2026-01-19 and 0.1.1 dated 2026-06-12
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++++++++-- NEWS.md | 4 ++++ R/data-confederations.R |only R/data-country-capital.R |only R/data-country-rank.R |only R/data-mx-us-wc-ranks.R |only data/confederations.rda |only data/country_capital.rda |only data/country_rank.rda |only data/mx_us_wc_ranks.rda |only man/confederations.Rd |only man/country_capital.Rd |only man/country_rank.Rd |only man/mx_us_wc_ranks.Rd |only 15 files changed, 22 insertions(+), 6 deletions(-)
More information about hellodatascience at CRAN
Permanent link
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymization methods are included. Note that the package
includes a graphical user interface published in Meindl and Templ (2019) <doi:10.3390/a12090191> that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] ,
Bernhard Meindl [aut],
Alexander Kowarik [aut] ,
Johannes Gussenbauer [aut],
Organisation For Economic Co-Operation And Development [cph] code code for rank swapping,
mdav-microaggregation, suda2 and other risk
measures [...truncated...]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.8.1 dated 2026-03-10 and 5.8.2 dated 2026-06-12
DESCRIPTION | 19 MD5 | 35 - NAMESPACE | 2 NEWS | 13 R/AI_applyAnonymization.R | 33 R/ai_access_utilities.R | 11 R/measure_risk.R | 117 ++- R/recordLinkage.R |only inst/doc/ai_assisted_anonymization.Rmd | 285 ++++---- inst/doc/ai_assisted_anonymization.html | 397 ++++++----- inst/doc/sdcMicro.html | 4 man/AI_applyAnonymization.Rd | 12 man/query_llm.Rd | 3 man/recordLinkage.Rd |only src/Measure_Risk.h | 1081 +++++++++----------------------- tests/testthat/test_ai_early_stopping.R |only tests/testthat/test_ldiversity.R |only tests/testthat/test_pram.R | 490 ++------------ tests/testthat/test_recordLinkage.R |only vignettes/ai_assisted.bib | 93 ++ vignettes/ai_assisted_anonymization.Rmd | 285 ++++---- 21 files changed, 1194 insertions(+), 1686 deletions(-)
Title: Image Processing for Simulated Cameras
Description: Uses convolution-based techniques to generate simulated camera bokeh, depth of field, and other camera effects, using an image and an optional depth map. Accepts both filename inputs and in-memory array representations of images and matrices, including common raster formats such as 'JPEG', 'PNG', 'TIFF', 'TGA', 'BMP', 'PSD', 'GIF', 'HDR', 'PIC', 'PNM', 'DNG', and 'EXR'. Includes functions to perform 2D convolutions, color correction, colorspace conversion, image/matrix reorientation and resizing, image and text overlays, exposure adjustment, camera vignette effects, and image titles.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayimage versions 0.15.1 dated 2025-02-01 and 0.26.1 dated 2026-06-12
rayimage-0.15.1/rayimage/R/run_documentation.R |only rayimage-0.15.1/rayimage/R/save_png.R |only rayimage-0.15.1/rayimage/inst |only rayimage-0.15.1/rayimage/man/add_image_overlay.Rd |only rayimage-0.15.1/rayimage/man/add_title.Rd |only rayimage-0.15.1/rayimage/man/add_vignette.Rd |only rayimage-0.15.1/rayimage/man/run_documentation.Rd |only rayimage-0.15.1/rayimage/man/save_png.Rd |only rayimage-0.26.1/rayimage/DESCRIPTION | 28 rayimage-0.26.1/rayimage/MD5 | 214 ++-- rayimage-0.26.1/rayimage/NAMESPACE | 25 rayimage-0.26.1/rayimage/R/RcppExports.R | 24 rayimage-0.26.1/rayimage/R/add_padding.R | 178 ++- rayimage-0.26.1/rayimage/R/calc_bokeh_size.R | 9 rayimage-0.26.1/rayimage/R/cli_helpers.R |only rayimage-0.26.1/rayimage/R/colorspace_descriptors.R |only rayimage-0.26.1/rayimage/R/colorspace_helpers.R |only rayimage-0.26.1/rayimage/R/convert_color.R | 78 + rayimage-0.26.1/rayimage/R/convert_to_native_raster.R | 44 rayimage-0.26.1/rayimage/R/data.R | 11 rayimage-0.26.1/rayimage/R/flipfunctions.R | 12 rayimage-0.26.1/rayimage/R/generate_2d_disk.R | 37 rayimage-0.26.1/rayimage/R/generate_2d_exponential.R | 44 rayimage-0.26.1/rayimage/R/generate_2d_gaussian.R | 50 rayimage-0.26.1/rayimage/R/get_file_type.R | 55 - rayimage-0.26.1/rayimage/R/get_string_dimensions.R | 26 rayimage-0.26.1/rayimage/R/handle_image_output.R | 8 rayimage-0.26.1/rayimage/R/interpolate_array.R | 62 - rayimage-0.26.1/rayimage/R/linear_png_device.R |only rayimage-0.26.1/rayimage/R/make_vignette_overlay.R | 62 - rayimage-0.26.1/rayimage/R/plot_asp_native_raster.R | 127 +- rayimage-0.26.1/rayimage/R/plot_image.R | 113 +- rayimage-0.26.1/rayimage/R/plot_image_grid.R | 149 +- rayimage-0.26.1/rayimage/R/prepare_native_raster.R |only rayimage-0.26.1/rayimage/R/preview_focus.R | 47 rayimage-0.26.1/rayimage/R/print.R |only rayimage-0.26.1/rayimage/R/ray_read_image.R | 376 +++++-- rayimage-0.26.1/rayimage/R/ray_write_image.R | 159 ++- rayimage-0.26.1/rayimage/R/rayimg.R |only rayimage-0.26.1/rayimage/R/read_image_stb.R |only rayimage-0.26.1/rayimage/R/render_alpha_outline.R |only rayimage-0.26.1/rayimage/R/render_bokeh.R | 146 +- rayimage-0.26.1/rayimage/R/render_bw.R | 54 - rayimage-0.26.1/rayimage/R/render_clamp.R | 76 + rayimage-0.26.1/rayimage/R/render_color_correction.R |only rayimage-0.26.1/rayimage/R/render_convert_colorspace.R |only rayimage-0.26.1/rayimage/R/render_convolution.R | 156 +- rayimage-0.26.1/rayimage/R/render_convolution_fft.R | 187 +-- rayimage-0.26.1/rayimage/R/render_crop.R |only rayimage-0.26.1/rayimage/R/render_distance.R | 16 rayimage-0.26.1/rayimage/R/render_exposure.R |only rayimage-0.26.1/rayimage/R/render_gamma_linear.R |only rayimage-0.26.1/rayimage/R/render_image_overlay.R | 530 +++++++--- rayimage-0.26.1/rayimage/R/render_padding.R |only rayimage-0.26.1/rayimage/R/render_reorient.R | 44 rayimage-0.26.1/rayimage/R/render_resized.R | 135 +- rayimage-0.26.1/rayimage/R/render_stack.R |only rayimage-0.26.1/rayimage/R/render_text_image.R | 273 +++-- rayimage-0.26.1/rayimage/R/render_title.R | 401 ++++--- rayimage-0.26.1/rayimage/R/render_to_display.R |only rayimage-0.26.1/rayimage/R/render_tonemap.R |only rayimage-0.26.1/rayimage/R/render_vibrance.R |only rayimage-0.26.1/rayimage/R/render_vignette.R | 116 -- rayimage-0.26.1/rayimage/R/render_white_balance.R |only rayimage-0.26.1/rayimage/R/rotate_image_array.R |only rayimage-0.26.1/rayimage/data/dragon.rda |binary rayimage-0.26.1/rayimage/data/sunset_image.rda |only rayimage-0.26.1/rayimage/man/add_multi_padding.Rd | 2 rayimage-0.26.1/rayimage/man/add_padding.Rd | 2 rayimage-0.26.1/rayimage/man/apply_color_matrix.Rd |only rayimage-0.26.1/rayimage/man/array_rgb_to_hex_colmajor.Rd |only rayimage-0.26.1/rayimage/man/colorspace_descriptors.Rd |only rayimage-0.26.1/rayimage/man/composite_alpha_outline_image.Rd |only rayimage-0.26.1/rayimage/man/compute_cat_bradford.Rd |only rayimage-0.26.1/rayimage/man/convert_color.Rd | 13 rayimage-0.26.1/rayimage/man/convert_to_native_raster.Rd | 6 rayimage-0.26.1/rayimage/man/dragon.Rd | 4 rayimage-0.26.1/rayimage/man/fill_alpha_gaps.Rd |only rayimage-0.26.1/rayimage/man/find_border_alpha_gaps.Rd |only rayimage-0.26.1/rayimage/man/generate_2d_disk.Rd | 6 rayimage-0.26.1/rayimage/man/generate_2d_exponential.Rd | 6 rayimage-0.26.1/rayimage/man/generate_2d_gaussian.Rd | 6 rayimage-0.26.1/rayimage/man/get_file_type.Rd | 2 rayimage-0.26.1/rayimage/man/get_whitepoint_xyz.Rd |only rayimage-0.26.1/rayimage/man/handle_image_output.Rd | 2 rayimage-0.26.1/rayimage/man/interpolate_array.Rd | 2 rayimage-0.26.1/rayimage/man/linear_png_device.Rd |only rayimage-0.26.1/rayimage/man/make_colorspace.Rd |only rayimage-0.26.1/rayimage/man/make_rgb_xyz_matrices.Rd |only rayimage-0.26.1/rayimage/man/offset_alpha.Rd |only rayimage-0.26.1/rayimage/man/plot_asp_native_raster.Rd | 3 rayimage-0.26.1/rayimage/man/plot_image.Rd | 20 rayimage-0.26.1/rayimage/man/plot_image_grid.Rd | 14 rayimage-0.26.1/rayimage/man/preview_focus.Rd | 2 rayimage-0.26.1/rayimage/man/print.rayimg.Rd |only rayimage-0.26.1/rayimage/man/ray_read_image.Rd | 72 + rayimage-0.26.1/rayimage/man/ray_write_image.Rd | 23 rayimage-0.26.1/rayimage/man/rayimg.Rd |only rayimage-0.26.1/rayimage/man/rayimg_composite_checker.Rd |only rayimage-0.26.1/rayimage/man/rayimg_vertical_ellipsis.Rd |only rayimage-0.26.1/rayimage/man/render_alpha_outline.Rd |only rayimage-0.26.1/rayimage/man/render_bokeh.Rd | 33 rayimage-0.26.1/rayimage/man/render_boolean_distance.Rd | 8 rayimage-0.26.1/rayimage/man/render_bw.Rd | 8 rayimage-0.26.1/rayimage/man/render_clamp.Rd | 29 rayimage-0.26.1/rayimage/man/render_color_correction.Rd |only rayimage-0.26.1/rayimage/man/render_convert_colorspace.Rd |only rayimage-0.26.1/rayimage/man/render_convolution.Rd | 36 rayimage-0.26.1/rayimage/man/render_convolution_fft.Rd | 42 rayimage-0.26.1/rayimage/man/render_crop.Rd |only rayimage-0.26.1/rayimage/man/render_exposure.Rd |only rayimage-0.26.1/rayimage/man/render_gamma_linear.Rd |only rayimage-0.26.1/rayimage/man/render_image_overlay.Rd | 72 + rayimage-0.26.1/rayimage/man/render_padding.Rd |only rayimage-0.26.1/rayimage/man/render_reorient.Rd | 12 rayimage-0.26.1/rayimage/man/render_resized.Rd | 16 rayimage-0.26.1/rayimage/man/render_sprite_overlay.Rd |only rayimage-0.26.1/rayimage/man/render_stack.Rd |only rayimage-0.26.1/rayimage/man/render_text_image.Rd | 32 rayimage-0.26.1/rayimage/man/render_title.Rd | 18 rayimage-0.26.1/rayimage/man/render_to_display.Rd |only rayimage-0.26.1/rayimage/man/render_tonemap.Rd |only rayimage-0.26.1/rayimage/man/render_vibrance.Rd |only rayimage-0.26.1/rayimage/man/render_vignette.Rd | 30 rayimage-0.26.1/rayimage/man/render_white_balance.Rd |only rayimage-0.26.1/rayimage/man/rgb_to_hex.Rd |only rayimage-0.26.1/rayimage/man/rotate_image_array.Rd |only rayimage-0.26.1/rayimage/man/sunset_image.Rd |only rayimage-0.26.1/rayimage/man/to_linear.Rd |only rayimage-0.26.1/rayimage/man/to_srgb.Rd |only rayimage-0.26.1/rayimage/src/Makevars | 2 rayimage-0.26.1/rayimage/src/RcppExports.cpp | 86 + rayimage-0.26.1/rayimage/src/dng_io.cpp |only rayimage-0.26.1/rayimage/src/load_image_stb.cpp |only rayimage-0.26.1/rayimage/src/pointspread.cpp | 23 rayimage-0.26.1/rayimage/tests |only 136 files changed, 3038 insertions(+), 1666 deletions(-)
Title: Sparse Principal Component Analysis with Multiple Principal
Components
Description: Implements an algorithm for computing multiple sparse principal
components of a dataset. The method is based on Cory-Wright and Pauphilet
"Sparse PCA with Multiple Principal Components" (2026)
<doi:10.48550/arXiv.2209.14790>. The algorithm uses an iterative deflation
heuristic with a truncated power method applied at each iteration to compute
sparse principal components with controlled sparsity.
Author: Ryan Cory-Wright [aut, cph] ,
Jean Pauphilet [aut, cre, cph]
Maintainer: Jean Pauphilet <jpauphilet@london.edu>
Diff between msPCA versions 0.4.0 dated 2026-05-22 and 0.4.1 dated 2026-06-12
DESCRIPTION | 10 - MD5 | 28 ++-- NEWS.md | 7 + R/main.R | 50 ++----- README.md | 204 +++++++++++++++++++++---------- build |only inst/CITATION |only inst/doc |only man/feasibility_violation_off.Rd | 3 man/fraction_variance_explained.Rd | 3 man/fraction_variance_explained_perPC.Rd | 2 man/mspca.Rd | 1 man/print_mspca.Rd | 9 - man/tpm.Rd | 1 man/variance_explained_perPC.Rd | 2 vignettes |only 16 files changed, 201 insertions(+), 119 deletions(-)
Title: Estimation and Diagnostics for Many-Facet Measurement Models
Description: Native R implementation of many-facet ordered-response
measurement models with arbitrary facet counts, rating-scale and
partial-credit parameterizations, a bounded generalized partial-credit
extension, and both marginal and joint maximum likelihood estimation.
The package provides a fit / diagnose / report pipeline covering
anchoring, linking, bias and differential-functioning screening, and
publication-oriented reporting summaries, with reproducibility manifests
for replay. See 'Andrich'
(1978) <doi:10.1007/BF02293814>, 'Masters' (1982)
<doi:10.1007/BF02296272>, and 'Muraki' (1992)
<doi:10.1177/014662169201600206> for the underlying ordered-response
models.
Author: Ryuya Komuro [aut, cre, cph]
Maintainer: Ryuya Komuro <ryuya.komuro.c4@tohoku.ac.jp>
Diff between mfrmr versions 0.2.0 dated 2026-05-16 and 0.2.1 dated 2026-06-12
DESCRIPTION | 11 MD5 | 386 +- NAMESPACE | 44 NEWS.md | 445 ++ R/api-advanced.R | 119 R/api-estimation.R | 32 R/api-export-bundles.R | 122 R/api-facet-equivalence.R | 7 R/api-hierarchical-audit.R | 16 R/api-methods.R | 94 R/api-plotting-anchor-qc.R | 7 R/api-plotting-extras.R | 27 R/api-plotting-fit-family.R | 51 R/api-plotting-screening.R | 12 R/api-plotting-secondary.R | 110 R/api-plotting.R | 57 R/api-prediction.R | 46 R/api-reference-benchmark.R | 2 R/api-reporting-checklist.R | 33 R/api-reports.R | 1883 ++++++++++ R/api-resampling.R |only R/api-response-time.R |only R/api-results.R |only R/api-shrinkage.R | 95 R/api-simulation-future-branch.R | 14 R/api-simulation-spec.R | 511 ++ R/api-simulation.R | 3316 +++++++++++++++++- R/api-tables.R | 101 R/api-viewer.R |only R/help_compatibility_layer.R | 2 R/help_gpcm_scope.R | 517 ++ R/help_reporting_and_apa.R | 48 R/help_reports_and_tables.R | 596 +++ R/help_visual_diagnostics.R | 311 + R/help_workflow_methods.R | 67 R/mfrm_core.R | 559 ++- R/mfrmr-package.R | 86 R/reporting.R | 138 README.md | 986 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mfrmr-facets-migration.Rmd | 8 inst/doc/mfrmr-facets-migration.html | 26 inst/doc/mfrmr-gpcm-scope.R | 4 inst/doc/mfrmr-gpcm-scope.Rmd | 151 inst/doc/mfrmr-gpcm-scope.html | 181 inst/doc/mfrmr-mml-and-marginal-fit.Rmd | 33 inst/doc/mfrmr-mml-and-marginal-fit.html | 37 inst/doc/mfrmr-reporting-and-apa.R | 1 inst/doc/mfrmr-reporting-and-apa.Rmd | 7 inst/doc/mfrmr-reporting-and-apa.html | 9 inst/doc/mfrmr-visual-diagnostics.R | 45 inst/doc/mfrmr-visual-diagnostics.Rmd | 87 inst/doc/mfrmr-visual-diagnostics.html | 92 inst/doc/mfrmr-workflow.R | 30 inst/doc/mfrmr-workflow.Rmd | 30 inst/doc/mfrmr-workflow.html | 170 inst/validation/README.md | 45 inst/validation/gpcm-post-0.2.1-roadmap.md |only inst/validation/recovery-validation.R | 485 ++ inst/validation/release-evidence-checklist-0.2.1.csv |only inst/validation/release-evidence-map-0.2.1.md |only inst/validation/release-readiness.R | 357 + man/analyze_dff.Rd | 12 man/analyze_facet_equivalence.Rd | 3 man/analyze_hierarchical_structure.Rd | 3 man/assess_mfrm_recovery.Rd | 86 man/build_apa_outputs.Rd | 9 man/build_conquest_overlap_bundle.Rd | 2 man/build_equating_chain.Rd | 2 man/build_mfrm_manifest.Rd | 10 man/build_mfrm_network_review.Rd |only man/build_mfrm_replay_script.Rd | 10 man/build_mfrm_resampling_spec.Rd |only man/build_mfrm_sim_spec.Rd | 59 man/build_peer_review_design_review.Rd |only man/build_peer_review_sim_spec.Rd |only man/build_summary_table_bundle.Rd | 50 man/build_visual_summaries.Rd | 7 man/compute_facet_icc.Rd | 3 man/diagnose_mfrm.Rd | 11 man/dif_interaction_table.Rd | 10 man/dif_report.Rd | 12 man/draw_mfrm_resamples.Rd |only man/evaluate_mfrm_design.Rd | 59 man/evaluate_mfrm_diagnostic_screening.Rd | 53 man/evaluate_mfrm_recovery.Rd | 38 man/evaluate_mfrm_signal_detection.Rd | 35 man/export_mfrm_bundle.Rd | 15 man/export_mfrm_results.Rd |only man/export_summary_appendix.Rd | 11 man/extract_mfrm_sim_spec.Rd | 5 man/facets_fit_df_guide.Rd | 11 man/facets_fit_review.Rd | 9 man/facets_output_contract_review.Rd | 11 man/facets_output_file_bundle.Rd | 26 man/fair_average_table.Rd | 2 man/fit_measures_table.Rd | 2 man/fit_mfrm.Rd | 21 man/gpcm_capability_matrix.Rd | 52 man/gpcm_runtime_guard_coverage.Rd |only man/gpcm_score_side_contract.Rd |only man/launch_mfrmr_viewer.Rd |only man/mfrm_report.Rd |only man/mfrm_results.Rd |only man/mfrm_results_interactive.Rd |only man/mfrmr-package.Rd | 82 man/mfrmr_compatibility_layer.Rd | 2 man/mfrmr_interval_guide.Rd |only man/mfrmr_output_guide.Rd | 74 man/mfrmr_reporting_and_apa.Rd | 48 man/mfrmr_reports_and_tables.Rd | 20 man/mfrmr_visual_diagnostics.Rd | 24 man/mfrmr_workflow_methods.Rd | 67 man/normalize_conquest_overlap_files.Rd | 2 man/plot.mfrm_bundle.Rd | 3 man/plot.mfrm_design_evaluation.Rd | 7 man/plot.mfrm_diagnostic_screening.Rd |only man/plot.mfrm_facet_nesting.Rd | 2 man/plot.mfrm_facet_sample_review.Rd | 9 man/plot.mfrm_fit.Rd | 16 man/plot_anchor_drift.Rd | 7 man/plot_apa_figure_one.Rd | 5 man/plot_bias_interaction.Rd | 7 man/plot_bubble.Rd | 2 man/plot_data_components.Rd | 10 man/plot_dif_summary.Rd | 5 man/plot_displacement.Rd | 7 man/plot_facet_equivalence.Rd | 3 man/plot_facets_chisq.Rd | 4 man/plot_fair_average.Rd | 7 man/plot_guttman_scalogram.Rd | 2 man/plot_interrater_agreement.Rd | 4 man/plot_local_dependence_heatmap.Rd | 2 man/plot_marginal_fit.Rd | 2 man/plot_marginal_pairwise.Rd | 4 man/plot_qc_dashboard.Rd | 13 man/plot_rater_agreement_heatmap.Rd | 2 man/plot_rater_severity_profile.Rd | 5 man/plot_rater_trajectory.Rd | 5 man/plot_reliability_snapshot.Rd | 2 man/plot_residual_matrix.Rd | 2 man/plot_residual_pca.Rd | 4 man/plot_residual_qq.Rd | 2 man/plot_response_time_review.Rd |only man/plot_shrinkage_funnel.Rd | 15 man/plot_threshold_ladder.Rd | 6 man/plot_unexpected.Rd | 4 man/plot_wright_unified.Rd | 7 man/precision_review_report.Rd | 12 man/predict_mfrm_population.Rd | 16 man/reference_case_review.Rd | 2 man/reporting_checklist.Rd | 4 man/response_time_review.Rd |only man/review_conquest_overlap.Rd | 2 man/run_qc_pipeline.Rd | 8 man/simulate_mfrm_data.Rd | 35 man/summary.mfrm_design_evaluation.Rd | 2 man/summary.mfrm_diagnostic_screening.Rd |only man/summary.mfrm_network_review.Rd |only man/summary.mfrm_peer_review_design_review.Rd |only man/summary.mfrm_population_prediction.Rd | 1 man/summary.mfrm_response_time_review.Rd |only man/summary.mfrm_signal_detection.Rd | 1 man/visual_reporting_template.Rd | 4 tests/testthat/test-anchor-equating.R | 17 tests/testthat/test-api-coverage-gaps.R | 2 tests/testthat/test-api-final-coverage.R | 2 tests/testthat/test-core-coverage-gaps.R | 8 tests/testthat/test-core-coverage.R | 2 tests/testthat/test-core-workflow.R | 4 tests/testthat/test-coverage-push-95.R | 4 tests/testthat/test-diagnostic-screening-validation.R | 130 tests/testthat/test-documentation-terminology.R | 194 - tests/testthat/test-estimation-core.R | 4 tests/testthat/test-export-bundles.R | 480 ++ tests/testthat/test-facets-output-contract-review.R | 2 tests/testthat/test-final-coverage-boost.R | 9 tests/testthat/test-gpcm-capability-matrix.R | 585 +++ tests/testthat/test-gpcm-verification.R | 21 tests/testthat/test-mfrm-results.R |only tests/testthat/test-namespace-contract.R | 42 tests/testthat/test-output-guide.R | 140 tests/testthat/test-output-stability.R | 37 tests/testthat/test-peer-review-simulation.R |only tests/testthat/test-plotting-extras.R | 3 tests/testthat/test-plotting-secondary.R | 15 tests/testthat/test-qc-pipeline.R | 2 tests/testthat/test-recovery-simulation.R | 251 + tests/testthat/test-recovery-validation-protocol.R | 182 tests/testthat/test-reference-benchmark.R | 2 tests/testthat/test-release-readiness-protocol.R | 116 tests/testthat/test-remaining-coverage.R | 2 tests/testthat/test-report-functions.R | 101 tests/testthat/test-reporting-checklist.R | 6 tests/testthat/test-reporting-coverage.R | 2 tests/testthat/test-reporting-gaps.R | 2 tests/testthat/test-resampling-validation.R |only tests/testthat/test-response-time-review.R |only tests/testthat/test-shrinkage.R | 10 tests/testthat/test-simulation-design.R | 110 tests/testthat/test-sparse-simulation.R |only tests/testthat/test-summary-table-bundle.R | 555 ++- tests/testthat/test-visual-reporting-template.R | 91 vignettes/mfrmr-facets-migration.Rmd | 8 vignettes/mfrmr-gpcm-scope.Rmd | 151 vignettes/mfrmr-mml-and-marginal-fit.Rmd | 33 vignettes/mfrmr-reporting-and-apa.Rmd | 7 vignettes/mfrmr-visual-diagnostics.Rmd | 87 vignettes/mfrmr-workflow.Rmd | 30 210 files changed, 15750 insertions(+), 1568 deletions(-)
Title: Fit 'TabNet' Models for Classification and Regression
Description: Implements the 'TabNet' model by Sercan O. Arik et al. (2019)
<doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label
Classification Networks' by Giunchiglia et al. <doi:10.48550/arXiv.2010.10151> and
provides a consistent interface for fitting and creating predictions.
It's also fully compatible with the 'tidymodels' ecosystem.
Author: Daniel Falbel [aut],
RStudio [cph],
Christophe Regouby [cre, ctb],
Egill Fridgeirsson [ctb],
Philipp Haarmeyer [ctb],
Sven Verweij [ctb]
Maintainer: Christophe Regouby <christophe.regouby@free.fr>
Diff between tabnet versions 0.8.0 dated 2026-01-31 and 0.9.0 dated 2026-06-12
tabnet-0.8.0/tabnet/R/explain.R |only tabnet-0.8.0/tabnet/R/model.R |only tabnet-0.8.0/tabnet/R/pretraining.R |only tabnet-0.8.0/tabnet/R/tab-network.R |only tabnet-0.8.0/tabnet/tests/testthat/_snaps/pretraining.md |only tabnet-0.8.0/tabnet/tests/testthat/test-explain.R |only tabnet-0.8.0/tabnet/tests/testthat/test-model.R |only tabnet-0.8.0/tabnet/tests/testthat/test-pretraining.R |only tabnet-0.8.0/tabnet/tests/testthat/test_translations.R |only tabnet-0.9.0/tabnet/DESCRIPTION | 12 tabnet-0.9.0/tabnet/MD5 | 111 ++- tabnet-0.9.0/tabnet/NAMESPACE | 21 tabnet-0.9.0/tabnet/NEWS.md | 12 tabnet-0.9.0/tabnet/R/hardhat.R | 205 ++++++- tabnet-0.9.0/tabnet/R/loss.R | 281 +++++++++- tabnet-0.9.0/tabnet/R/model_explain.R |only tabnet-0.9.0/tabnet/R/model_pretraining.R |only tabnet-0.9.0/tabnet/R/model_training.R |only tabnet-0.9.0/tabnet/R/parsnip.R | 2 tabnet-0.9.0/tabnet/R/plot.R | 2 tabnet-0.9.0/tabnet/R/tabnet_network.R |only tabnet-0.9.0/tabnet/R/utils-pipe.R | 4 tabnet-0.9.0/tabnet/R/utils.R | 14 tabnet-0.9.0/tabnet/README.md | 20 tabnet-0.9.0/tabnet/build/partial.rdb |only tabnet-0.9.0/tabnet/inst/WORDLIST | 6 tabnet-0.9.0/tabnet/inst/doc/Hierarchical_classification.R | 10 tabnet-0.9.0/tabnet/inst/doc/Hierarchical_classification.Rmd | 37 - tabnet-0.9.0/tabnet/inst/doc/Hierarchical_classification.html | 76 +- tabnet-0.9.0/tabnet/inst/doc/Missing_data_predictors.html | 4 tabnet-0.9.0/tabnet/inst/doc/interpretation.html | 4 tabnet-0.9.0/tabnet/inst/doc/selfsupervised_training.R | 10 tabnet-0.9.0/tabnet/inst/doc/selfsupervised_training.Rmd | 10 tabnet-0.9.0/tabnet/inst/doc/selfsupervised_training.html | 14 tabnet-0.9.0/tabnet/man/build_ancestor_matrix_from_outcomes.Rd |only tabnet-0.9.0/tabnet/man/figures/README-model-explain-1.png |binary tabnet-0.9.0/tabnet/man/figures/README-model-fit-1.png |binary tabnet-0.9.0/tabnet/man/figures/README-step-explain-1.png |binary tabnet-0.9.0/tabnet/man/figures/README-step-pretrain-1.png |binary tabnet-0.9.0/tabnet/man/get_constr_output.Rd |only tabnet-0.9.0/tabnet/man/nn_mc_loss.Rd |only tabnet-0.9.0/tabnet/man/nnf_mc_loss.Rd |only tabnet-0.9.0/tabnet/man/nnf_multilabel_one_hot.Rd |only tabnet-0.9.0/tabnet/man/predict.tabnet_fit.Rd |only tabnet-0.9.0/tabnet/man/reexports.Rd |only tabnet-0.9.0/tabnet/man/tabnet-package.Rd |only tabnet-0.9.0/tabnet/man/tabnet_config.Rd | 2 tabnet-0.9.0/tabnet/man/tabnet_explain.Rd | 2 tabnet-0.9.0/tabnet/man/tabnet_nn.Rd | 2 tabnet-0.9.0/tabnet/man/tabnet_pretrain.Rd | 2 tabnet-0.9.0/tabnet/po/R-fr.po | 151 +++-- tabnet-0.9.0/tabnet/po/R-tabnet.pot | 114 ++-- tabnet-0.9.0/tabnet/tests/testthat/Rplots.pdf |binary tabnet-0.9.0/tabnet/tests/testthat/_snaps/model_pretraining.md |only tabnet-0.9.0/tabnet/tests/testthat/helper-tensor.R | 9 tabnet-0.9.0/tabnet/tests/testthat/setup.R | 6 tabnet-0.9.0/tabnet/tests/testthat/test-hardhat_hierarchical.R | 111 --- tabnet-0.9.0/tabnet/tests/testthat/test-hardhat_interfaces.R | 12 tabnet-0.9.0/tabnet/tests/testthat/test-hardhat_multi-outcome.R | 23 tabnet-0.9.0/tabnet/tests/testthat/test-hardhat_scenarios.R | 36 + tabnet-0.9.0/tabnet/tests/testthat/test-hierarchical_utils.R |only tabnet-0.9.0/tabnet/tests/testthat/test-loss.R | 189 ++++++ tabnet-0.9.0/tabnet/tests/testthat/test-model_explain.R |only tabnet-0.9.0/tabnet/tests/testthat/test-model_pretraining.R |only tabnet-0.9.0/tabnet/tests/testthat/test-model_training.R |only tabnet-0.9.0/tabnet/tests/testthat/test-parsnip.R | 11 tabnet-0.9.0/tabnet/tests/testthat/test-translations.R |only tabnet-0.9.0/tabnet/tools |only tabnet-0.9.0/tabnet/vignettes/Hierarchical_classification.Rmd | 37 - tabnet-0.9.0/tabnet/vignettes/selfsupervised_training.Rmd | 10 70 files changed, 1190 insertions(+), 382 deletions(-)
Title: Bayesian Estimation of Multivariate Threshold Autoregressive
Models
Description: Estimation, inference and forecasting using the Bayesian approach for multivariate threshold autoregressive (TAR) models in which the distribution used to describe the noise process belongs to the class of Gaussian variance mixtures.
Author: Luis Hernando Vanegas [aut, cre],
Sergio Alejandro Calderon [aut],
Luz Marina Rondon [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between mtarm versions 0.1.8 dated 2026-01-11 and 0.1.9 dated 2026-06-12
mtarm-0.1.8/mtarm/man/geweke.diagTAR.Rd |only mtarm-0.1.8/mtarm/man/geweke.plotTAR.Rd |only mtarm-0.1.8/mtarm/man/out.of.sample.Rd |only mtarm-0.1.9/mtarm/DESCRIPTION | 11 mtarm-0.1.9/mtarm/MD5 | 54 +- mtarm-0.1.9/mtarm/NAMESPACE | 15 mtarm-0.1.9/mtarm/R/bayesians.R | 514 ++++++++++---------- mtarm-0.1.9/mtarm/R/data.R | 20 mtarm-0.1.9/mtarm/R/estimation.R | 64 +- mtarm-0.1.9/mtarm/R/extractors.R | 108 ++-- mtarm-0.1.9/mtarm/R/forecasting.R | 607 +++++++++++++++--------- mtarm-0.1.9/mtarm/R/simulation.R | 190 ++++--- mtarm-0.1.9/mtarm/R/wrapperfunctions.R | 387 ++++++++++++--- mtarm-0.1.9/mtarm/README.md |only mtarm-0.1.9/mtarm/build |only mtarm-0.1.9/mtarm/data/US.returns.rda |binary mtarm-0.1.9/mtarm/inst |only mtarm-0.1.9/mtarm/man/DIC.mtar.Rd | 48 + mtarm-0.1.9/mtarm/man/HPDinterval.mtar.Rd | 34 + mtarm-0.1.9/mtarm/man/US.returns.Rd | 14 mtarm-0.1.9/mtarm/man/WAIC.mtar.Rd | 48 + mtarm-0.1.9/mtarm/man/as.mcmc.mtar.Rd | 28 - mtarm-0.1.9/mtarm/man/effectiveSize_TAR.Rd |only mtarm-0.1.9/mtarm/man/geweke_diagTAR.Rd |only mtarm-0.1.9/mtarm/man/geweke_plotTAR.Rd |only mtarm-0.1.9/mtarm/man/mtar.Rd | 40 + mtarm-0.1.9/mtarm/man/mtar_grid.Rd | 42 + mtarm-0.1.9/mtarm/man/out_of_sample.Rd |only mtarm-0.1.9/mtarm/man/out_of_sample.listmtar.Rd |only mtarm-0.1.9/mtarm/man/out_of_sample.mtar.Rd |only mtarm-0.1.9/mtarm/man/predict.mtar.Rd | 68 +- mtarm-0.1.9/mtarm/tests |only mtarm-0.1.9/mtarm/vignettes |only 33 files changed, 1475 insertions(+), 817 deletions(-)
Title: Subject-Level Analysis Using 'metalite'
Description: Analyzes subject-level data in clinical trials using the 'metalite'
data structure. The package simplifies the workflow to create
production-ready tables, listings, and figures discussed in the
subject-level analysis chapters of
"R for Clinical Study Reports and Submission"
by Zhang et al. (2022) <https://r4csr.org/>.
Author: Yujie Zhao [aut, cre],
Benjamin Wang [aut],
Hiroaki Fukuda [aut],
PoYao Niu [aut],
Nan Xiao [aut],
Jeetener Chauhan [ctb],
Li Ma [ctb],
Chen Wang [ctb],
Merck Sharp & Dohme Corp [cph]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between metalite.sl versions 0.1.1 dated 2025-05-08 and 0.1.2 dated 2026-06-12
DESCRIPTION | 23 MD5 | 132 ++- NEWS.md | 9 R/collect.R | 13 R/data.R |only R/format_base_char_subgroup.R | 9 R/format_exp_duration.R | 9 R/format_sl_summary.R | 10 R/meta_sl.R | 27 R/plotly_exp_duration.R | 48 - R/prepare_base_char_subgroup.R | 13 R/prepare_sl_summary.R | 9 R/react_base_char.R | 117 +++ R/react_disposition.R | 35 R/react_subgroup_table.R | 11 R/rtf_base_char_subgroup.R | 19 R/rtf_sl_summary.R | 20 R/utils.R | 7 build/vignette.rds |binary data |only inst/doc/baseline-character.html | 13 inst/doc/disposition.R | 25 inst/doc/disposition.Rmd | 25 inst/doc/disposition.html | 355 ++++------ inst/doc/exp_duration.html | 9 inst/doc/exposure-duration-histogram.R |only inst/doc/exposure-duration-histogram.Rmd |only inst/doc/exposure-duration-histogram.html |only inst/doc/interactive-baseline.R | 27 inst/doc/interactive-baseline.Rmd | 35 inst/doc/interactive-baseline.html | 67 + inst/doc/interactive-disposition.R | 56 - inst/doc/interactive-disposition.Rmd | 56 - inst/doc/interactive-disposition.html | 181 +---- inst/doc/metalite.sl.html | 9 inst/doc/trt_compliance.html | 7 man/metalite_sl_adae.Rd |only man/metalite_sl_adexsum.Rd |only man/metalite_sl_adsl.Rd |only man/plotly_exp_duration.Rd | 32 man/react_base_char.Rd | 8 man/react_disposition.Rd | 3 tests/testthat/_snaps |only tests/testthat/helper-rtf-snapshot.R |only tests/testthat/rtf |only tests/testthat/test-independent-testing-disposition.R | 24 tests/testthat/test-independent-testing-plotly_exp_duration.R | 8 tests/testthat/test-independent-testing-prepare_exp_duration.R | 4 tests/testthat/test-independent-testing-react_disposition.R | 12 tests/testthat/test-independent-testing-rtf_base_char_subgroup.R | 76 -- tests/testthat/test-independent-testing-rtf_exp_duration.R | 27 tests/testthat/test-independent-testing-trt_compliance.R | 24 vignettes/disposition.Rmd | 25 vignettes/exposure-duration-histogram.Rmd |only vignettes/interactive-baseline.Rmd | 35 vignettes/interactive-disposition.Rmd | 56 - vignettes/outtable/base0char.rtf | 16 vignettes/outtable/base0charsubgroup.rtf | 16 vignettes/outtable/disposition.rtf | 310 +++----- vignettes/outtable/exp0duration.rtf | 16 vignettes/outtable/treatment0compliance.rtf | 16 vignettes/pdf/disposition.pdf |binary vignettes/pdf/exposure0histogram.pdf |only 63 files changed, 982 insertions(+), 1102 deletions(-)
Title: 'JDemetra+' Quality Report Generator
Description: Tool for generating quality reports from cruncher outputs
(and calculating series scores). The latest version of the cruncher
can be downloaded here:
<https://github.com/jdemetra/jwsacruncher/releases>.
Author: Tanguy Barthelemy [aut, cre, art],
Eulalie Delaune [aut],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between JDCruncheR versions 0.3.6 dated 2025-07-24 and 0.4.0 dated 2026-06-12
JDCruncheR-0.3.6/JDCruncheR/R/QR_export.R |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/WS/ws_ipi |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/WS/ws_ipi.xml |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/data/IPI_nace4.csv |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/data/IPI_nace4_09_2020.csv |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/data/IPI_nace4_09_2021.csv |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/data/world.ods |only JDCruncheR-0.3.6/JDCruncheR/inst/extdata/data/world.xlsx |only JDCruncheR-0.3.6/JDCruncheR/man/export_xlsx.QR_matrix.Rd |only JDCruncheR-0.3.6/JDCruncheR/man/export_xlsx.Rd |only JDCruncheR-0.3.6/JDCruncheR/man/export_xlsx.mQR_matrix.Rd |only JDCruncheR-0.3.6/JDCruncheR/man/fr-export_xlsx.QR_matrix.Rd |only JDCruncheR-0.3.6/JDCruncheR/man/fr-export_xlsx.mQR_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/DESCRIPTION | 21 JDCruncheR-0.4.0/JDCruncheR/MD5 | 128 JDCruncheR-0.4.0/JDCruncheR/NAMESPACE | 126 JDCruncheR-0.4.0/JDCruncheR/NEWS.md | 356 JDCruncheR-0.4.0/JDCruncheR/R/JVS_classes.R |only JDCruncheR-0.4.0/JDCruncheR/R/QR_functions.R | 2742 - JDCruncheR-0.4.0/JDCruncheR/R/QR_matrix_classes.R | 760 JDCruncheR-0.4.0/JDCruncheR/R/deprecated.R |only JDCruncheR-0.4.0/JDCruncheR/R/export.R |only JDCruncheR-0.4.0/JDCruncheR/R/extractQR.R | 1204 JDCruncheR-0.4.0/JDCruncheR/R/extract_JVS.R |only JDCruncheR-0.4.0/JDCruncheR/R/extraction.R |only JDCruncheR-0.4.0/JDCruncheR/R/reading.R |only JDCruncheR-0.4.0/JDCruncheR/R/thresholds.R | 238 JDCruncheR-0.4.0/JDCruncheR/R/zzz.R | 10 JDCruncheR-0.4.0/JDCruncheR/README.md | 990 JDCruncheR-0.4.0/JDCruncheR/build |only JDCruncheR-0.4.0/JDCruncheR/inst/doc |only JDCruncheR-0.4.0/JDCruncheR/inst/extdata/WS/WS_world |only JDCruncheR-0.4.0/JDCruncheR/inst/extdata/WS/WS_world.xml |only JDCruncheR-0.4.0/JDCruncheR/inst/extdata/data/world.csv |only JDCruncheR-0.4.0/JDCruncheR/man/JDCruncheR-package.Rd | 8 JDCruncheR-0.4.0/JDCruncheR/man/JVS_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/QR_matrix.Rd | 124 JDCruncheR-0.4.0/JDCruncheR/man/QR_var_manipulation.Rd | 122 JDCruncheR-0.4.0/JDCruncheR/man/add_indicator.Rd | 102 JDCruncheR-0.4.0/JDCruncheR/man/compute_score.Rd | 284 JDCruncheR-0.4.0/JDCruncheR/man/deprecated-JDCruncheR.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/extract_JVS.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/extract_QR.Rd | 199 JDCruncheR-0.4.0/JDCruncheR/man/extract_score.Rd | 130 JDCruncheR-0.4.0/JDCruncheR/man/figures/logo.svg |23182 +++++----- JDCruncheR-0.4.0/JDCruncheR/man/fr-QR_matrix.Rd | 110 JDCruncheR-0.4.0/JDCruncheR/man/fr-add_indicator.Rd | 88 JDCruncheR-0.4.0/JDCruncheR/man/fr-compute_score.Rd | 252 JDCruncheR-0.4.0/JDCruncheR/man/fr-extract_QR.Rd | 176 JDCruncheR-0.4.0/JDCruncheR/man/fr-extract_score.Rd | 116 JDCruncheR-0.4.0/JDCruncheR/man/fr-print.QR_matrix.Rd | 58 JDCruncheR-0.4.0/JDCruncheR/man/fr-rbind.QR_matrix.Rd | 86 JDCruncheR-0.4.0/JDCruncheR/man/fr-recode_indicator_num.Rd | 58 JDCruncheR-0.4.0/JDCruncheR/man/fr-remove_indicators.Rd | 98 JDCruncheR-0.4.0/JDCruncheR/man/fr-sort.QR_matrix.Rd | 96 JDCruncheR-0.4.0/JDCruncheR/man/fr-weighted_score.Rd | 86 JDCruncheR-0.4.0/JDCruncheR/man/fr-write.QR_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/fr-write.mQR_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/print.QR_matrix.Rd | 74 JDCruncheR-0.4.0/JDCruncheR/man/rbind.QR_matrix.Rd | 113 JDCruncheR-0.4.0/JDCruncheR/man/recode_indicator_num.Rd | 88 JDCruncheR-0.4.0/JDCruncheR/man/sort.Rd | 129 JDCruncheR-0.4.0/JDCruncheR/man/weighted_score.Rd | 111 JDCruncheR-0.4.0/JDCruncheR/man/write.JVS_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/write.QR_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/write.Rd |only JDCruncheR-0.4.0/JDCruncheR/man/write.mQR_matrix.Rd |only JDCruncheR-0.4.0/JDCruncheR/tests/testthat.R | 24 JDCruncheR-0.4.0/JDCruncheR/tests/testthat/data/demetra_m1.csv | 28 JDCruncheR-0.4.0/JDCruncheR/tests/testthat/data/demetra_m2.csv | 28 JDCruncheR-0.4.0/JDCruncheR/tests/testthat/data/demetra_m3.csv | 41 JDCruncheR-0.4.0/JDCruncheR/tests/testthat/test-extractQR.R | 55 JDCruncheR-0.4.0/JDCruncheR/vignettes |only 73 files changed, 15978 insertions(+), 16663 deletions(-)
Title: Interactive Box Plot
Description: Interactive box plot using 'plotly' for clinical trial analysis.
Author: Yujie Zhao [aut, cre],
Benjamin Wang [aut],
Yilong Zhang [ctb],
Nan Xiao [ctb],
Hiroaki Fukuda [ctb],
Sarad Nepal [ctb],
Madhusudhan Ginnaram [ctb],
Venkatesh Burla [ctb],
Merck Sharp & Dohme Corp [cph]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between boxly versions 0.1.1 dated 2023-10-23 and 0.1.2 dated 2026-06-12
DESCRIPTION | 18 +-- MD5 | 34 +++--- NEWS.md | 9 + R/boxly.R | 49 +++++++-- R/meta_boxly.R | 15 +- R/prepare_boxly.R | 84 ++++++++++++---- README.md | 18 +++ build/vignette.rds |binary inst/doc/boxly-cran.R | 24 ++-- inst/doc/boxly-cran.html | 23 ++-- inst/doc/hover-label.R |only inst/doc/hover-label.Rmd |only inst/doc/hover-label.html |only man/boxly.Rd | 5 man/prepare_boxly.Rd | 14 ++ tests/testthat.R | 8 - tests/testthat/test-independant-testing-prepare_boxly.R | 21 ++-- tests/testthat/test-independent-testing-boxly.R | 30 +++-- tests/testthat/test-independent-testing-meta_boxly.R | 16 +-- vignettes/hover-label.Rmd |only 20 files changed, 248 insertions(+), 120 deletions(-)
Title: ADaM in R Asset Library - Ophthalmology
Description: Aids the programming of Clinical Data Standards Interchange
Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM)
datasets in R. ADaM datasets are a mandatory part of any New Drug or
Biologics License Application submitted to the United States Food and
Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Edoardo Mancini [aut, cre] ,
Yuki Matsunaga [aut],
F. Hoffmann-La Roche AG [cph, fnd],
Novartis AG [cph, fnd]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiralophtha versions 1.4.0 dated 2026-01-16 and 1.5.0 dated 2026-06-12
admiralophtha-1.4.0/admiralophtha/R/convert_etdrs_to_logmar.R |only admiralophtha-1.4.0/admiralophtha/R/convert_logmar_to_etdrs.R |only admiralophtha-1.5.0/admiralophtha/DESCRIPTION | 39 admiralophtha-1.5.0/admiralophtha/MD5 | 72 - admiralophtha-1.5.0/admiralophtha/NEWS.md | 174 ++- admiralophtha-1.5.0/admiralophtha/R/admiralophtha-package.R | 32 admiralophtha-1.5.0/admiralophtha/R/derive_var_bcvacritxfl.R | 12 admiralophtha-1.5.0/admiralophtha/R/logmar_etdrs.R |only admiralophtha-1.5.0/admiralophtha/README.md | 14 admiralophtha-1.5.0/admiralophtha/build/vignette.rds |binary admiralophtha-1.5.0/admiralophtha/inst/WORDLIST | 10 admiralophtha-1.5.0/admiralophtha/inst/doc/adbcva.Rmd | 6 admiralophtha-1.5.0/admiralophtha/inst/doc/adbcva.html | 67 - admiralophtha-1.5.0/admiralophtha/inst/doc/admiralophtha.Rmd | 2 admiralophtha-1.5.0/admiralophtha/inst/doc/admiralophtha.html | 2 admiralophtha-1.5.0/admiralophtha/inst/doc/adoe.Rmd | 10 admiralophtha-1.5.0/admiralophtha/inst/doc/adoe.html | 67 - admiralophtha-1.5.0/admiralophtha/inst/doc/advfq.R | 28 admiralophtha-1.5.0/admiralophtha/inst/doc/advfq.Rmd | 8 admiralophtha-1.5.0/admiralophtha/inst/doc/advfq.html | 551 ++++------ admiralophtha-1.5.0/admiralophtha/inst/doc/standards.Rmd | 2 admiralophtha-1.5.0/admiralophtha/inst/doc/standards.html | 2 admiralophtha-1.5.0/admiralophtha/man/admiralophtha-package.Rd | 12 admiralophtha-1.5.0/admiralophtha/man/admiralophtha_adbcva.Rd | 2 admiralophtha-1.5.0/admiralophtha/man/admiralophtha_adoe.Rd | 2 admiralophtha-1.5.0/admiralophtha/man/admiralophtha_advfq.Rd | 2 admiralophtha-1.5.0/admiralophtha/man/convert_etdrs_to_logmar.Rd | 24 admiralophtha-1.5.0/admiralophtha/man/convert_logmar_to_etdrs.Rd | 7 admiralophtha-1.5.0/admiralophtha/man/derive_var_bcvacritxfl.Rd | 7 admiralophtha-1.5.0/admiralophtha/man/derive_var_bcvacritxfl_util.Rd | 7 admiralophtha-1.5.0/admiralophtha/man/figures/novartis_logo.png |binary admiralophtha-1.5.0/admiralophtha/man/figures/roche_logo.png |binary admiralophtha-1.5.0/admiralophtha/tests/testthat/_snaps/derive_var_bcvacritxfl.md | 28 admiralophtha-1.5.0/admiralophtha/vignettes/adbcva.Rmd | 6 admiralophtha-1.5.0/admiralophtha/vignettes/admiralophtha.Rmd | 2 admiralophtha-1.5.0/admiralophtha/vignettes/adoe.Rmd | 10 admiralophtha-1.5.0/admiralophtha/vignettes/advfq.Rmd | 8 admiralophtha-1.5.0/admiralophtha/vignettes/articles/templates.Rmd |only admiralophtha-1.5.0/admiralophtha/vignettes/standards.Rmd | 2 39 files changed, 612 insertions(+), 605 deletions(-)
Title: Parallelize Common Functions via One Magic Function
Description: The futurize() function turns sequential map-reduce functions such as base::lapply(), purrr::map(), 'foreach::foreach() %do% { ... }' into concurrent alternatives, providing you with a simple, straightforward path to scalable parallel computing via the 'future' ecosystem <doi:10.32614/RJ-2021-048>. By combining this transpiler function with R's native pipe operator, you have a convenient way for speeding up iterative computations with minimal refactoring, e.g. 'lapply(xs, fcn) |> futurize()', 'purrr::map(xs, fcn) |> futurize()', and 'foreach::foreach(x = xs) %do% { fcn(x) } |> futurize()'. Other map-reduce packages that can be "futurized" are 'BiocParallel', 'plyr', 'crossmap', 'pbapply' packages. There is also support for a growing set of domain-specific packages on CRAN (e.g. 'boot', 'caret', 'DiceKriging', 'ez', 'fgsea', 'fwb', 'gamlss', 'glmmTMB', 'glmnet', 'kernelshap', 'lme4', 'metafor', 'mgcv', 'modelsummary', 'parameters', 'partykit', 'pls', 'pvclust', 'riskRegre [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between futurize versions 0.3.0 dated 2026-04-01 and 1.0.0 dated 2026-06-12
.aspell/WORDLIST.rds |binary DESCRIPTION | 31 MD5 | 357 ++++++----- NEWS.md | 69 ++ R/addons-DiceKriging.R |only R/addons-Sim.DiffProc.R |only R/addons-SuperLearner.R |only R/addons-boot.R | 25 R/addons-ez.R |only R/addons-foreach.R | 12 R/addons-gamlss.R | 1 R/addons-modelsummary.R |only R/addons-parameters.R |only R/addons-pls.R |only R/addons-pvclust.R |only R/addons-rugarch.R |only R/addons-sandwich.R |only R/addons-stars.R |only R/futurize.R | 6 R/futurize_options.R | 20 R/register_all_transpilers.R | 36 - R/transpile.R | 2 R/utils-options.R | 11 README.md | 70 +- build/vignette.rds |binary inst/doc/futurize-11-apply.html | 25 inst/doc/futurize-11-apply.md | 27 inst/doc/futurize-21-purrr.html | 4 inst/doc/futurize-21-purrr.md | 5 inst/doc/futurize-22-crossmap.html | 2 inst/doc/futurize-22-crossmap.md | 1 inst/doc/futurize-31-plyr.html | 4 inst/doc/futurize-31-plyr.md | 5 inst/doc/futurize-51-foreach.html | 4 inst/doc/futurize-51-foreach.md | 5 inst/doc/futurize-55-pbapply.html | 4 inst/doc/futurize-55-pbapply.md | 6 inst/doc/futurize-61-BiocParallel.html | 4 inst/doc/futurize-61-BiocParallel.md | 5 inst/doc/futurize-81-DiceKriging.html |only inst/doc/futurize-81-DiceKriging.md |only inst/doc/futurize-81-Sim.DiffProc.html |only inst/doc/futurize-81-Sim.DiffProc.md |only inst/doc/futurize-81-SingleCellExperiment.html | 53 - 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vignettes/futurize-81-SuperLearner.md |only vignettes/futurize-81-TSP.md | 2 vignettes/futurize-81-boot.md | 33 - vignettes/futurize-81-caret.md | 14 vignettes/futurize-81-ez.md |only vignettes/futurize-81-gamlss.md | 2 vignettes/futurize-81-kernelshap.md | 4 vignettes/futurize-81-modelsummary.md |only vignettes/futurize-81-parameters.md |only vignettes/futurize-81-partykit.md | 8 vignettes/futurize-81-pls.md |only vignettes/futurize-81-pvclust.md |only vignettes/futurize-81-riskRegression.md | 2 vignettes/futurize-81-rugarch.md |only vignettes/futurize-81-sandwich.md |only vignettes/futurize-81-scater.md | 17 vignettes/futurize-81-scuttle.md | 61 - vignettes/futurize-81-seriation.md | 4 vignettes/futurize-81-shapr.md | 4 vignettes/futurize-81-stars.md |only vignettes/futurize-81-vegan.md | 10 215 files changed, 1569 insertions(+), 1767 deletions(-)
Title: Fast Conversion and Querying of Danish Registers with 'Parquet'
Description: Converts large Danish register files ('sas7bdat') into 'Parquet'
format with year-based 'Hive' partitioning and chunked reading for
larger-than-memory files. Supports parallel conversion with a 'targets'
pipeline and reading those registers into 'DuckDB' tables for faster
querying and analyses.
Author: Signe Kirk Broedbaek [aut, cre] ,
Luke Johnston [aut] ,
Steno Diabetes Center Aarhus [cph],
Aarhus University [cph]
Maintainer: Signe Kirk Broedbaek <signekb@clin.au.dk>
Diff between fastreg versions 0.13.0 dated 2026-06-04 and 0.13.8 dated 2026-06-12
DESCRIPTION | 6 +- MD5 | 20 ++++---- NEWS.md | 50 ++++++++++++++++++++ R/convert.R | 20 ++++++-- R/log.R | 19 +++++-- R/use.R | 2 inst/doc/fastreg.html | 94 +++++++++++++++++++-------------------- inst/template-conversion-log.qmd | 6 +- inst/template-targets.R | 2 tests/testthat/test-convert.R | 40 ++++++++++++++++ tests/testthat/test-log.R | 16 +++--- 11 files changed, 196 insertions(+), 79 deletions(-)
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.6.13 dated 2026-06-05 and 1.6.14 dated 2026-06-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/rrepest.R | 11 +++++++++-- 3 files changed, 14 insertions(+), 7 deletions(-)
Title: 'ICESat-2' Altimeter Data using R
Description: Programmatic connection to the 'OpenAltimetry' API <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global 'Geolocated' Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice 'Freeboard'), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects 'altimetry' data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice 'freeboard', and vegetation canopy hei [...truncated...]
Author: Lampros Mouselimis [aut, cre] ,
OpenAltimetry.org [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between IceSat2R versions 1.0.9 dated 2026-03-05 and 1.1.0 dated 2026-06-12
DESCRIPTION | 11 MD5 | 52 NAMESPACE | 1 NEWS.md | 6 R/API_utils.R | 42 R/mission_orbits.R | 1570 +++++++++---------- README.md | 2 inst/data_files/technical_specs_urls.csv | 3 inst/doc/IceSat-2_Atlas_products_PDF.R | 3 inst/doc/IceSat-2_Atlas_products_PDF.Rmd | 3 inst/doc/IceSat-2_Atlas_products_PDF.pdf |binary inst/doc/IceSat-2_Mission_Orbits_PDF.pdf |binary inst/doc/IceSat-2_Virtual_File_System_Orbits_PDF.pdf |binary man/available_RGTs.Rd | 22 man/available_nominal_orbits.Rd | 16 man/latest_orbits.Rd | 4 man/overall_mission_orbits.Rd | 11 man/revisit_time_RGTs.Rd | 22 man/time_specific_orbits.Rd | 71 man/vsi_kml_from_zip.Rd | 32 man/vsi_nominal_orbits_wkt.Rd | 67 man/vsi_time_specific_orbits_wkt.Rd | 78 tests/testthat/test-API_utils.R | 81 tests/testthat/test-get_Atlas_data.R | 319 ++- tests/testthat/test-get_Tracks_data.R | 53 tests/testthat/test-mission_orbits.R | 235 +- vignettes/IceSat-2_Atlas_products_PDF.Rmd | 3 27 files changed, 1433 insertions(+), 1274 deletions(-)
Title: Header-Only 'C++' and 'R' Interface
Description: Provides a header only, 'C++' interface to 'R' with enhancements
over 'cpp11'. Enforces copy-on-write semantics consistent with 'R'
behavior. Offers native support for ALTREP objects, 'UTF-8' string
handling, modern 'C++' features and idioms, and reduced memory
requirements. Allows for vendoring, making it useful for restricted
environments. Compared to 'cpp11', it adds support for converting 'C++'
maps to 'R' lists, 'Roxygen' documentation directly in 'C++' code, proper
handling of matrix attributes, support for nullable external pointers,
bidirectional copy of complex number types, flexibility in type
conversions, use of nullable pointers, and various performance
optimizations.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Posit Software, PBC [aut]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between cpp4r versions 0.6.0 dated 2026-05-17 and 1.0.0 dated 2026-06-12
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Title: An 'Armadillo' Interface
Description: Provides function declarations and inline function definitions
that facilitate communication between R and the 'Armadillo' 'C++' library
for linear algebra and scientific computing. This implementation is derived
from Vargas Sepulveda and Schneider Malamud (2024)
<doi:10.1016/j.softx.2025.102087>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Jonathan Schneider Malamud [ctb],
Conrad Sanderson [aut] )
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between armadillo4r versions 0.9.0 dated 2026-05-20 and 1.0.0 dated 2026-06-12
armadillo4r-0.9.0/armadillo4r/inst/extdata/NAMESPACE |only armadillo4r-0.9.0/armadillo4r/inst/extdata/README.md |only armadillo4r-0.9.0/armadillo4r/inst/extdata/cleanup |only armadillo4r-0.9.0/armadillo4r/inst/extdata/configure |only armadillo4r-0.9.0/armadillo4r/inst/extdata/configure.win |only armadillo4r-0.9.0/armadillo4r/inst/extdata/dev |only armadillo4r-0.9.0/armadillo4r/inst/extdata/src |only armadillo4r-0.9.0/armadillo4r/tests/testthat |only armadillo4r-0.9.0/armadillo4r/tests/testthat.R |only armadillo4r-1.0.0/armadillo4r/DESCRIPTION | 41 ++----- armadillo4r-1.0.0/armadillo4r/MD5 | 52 +++++----- armadillo4r-1.0.0/armadillo4r/R/template.R | 26 +++-- armadillo4r-1.0.0/armadillo4r/README.md | 7 + armadillo4r-1.0.0/armadillo4r/inst/extdata/pkgtemplate |only armadillo4r-1.0.0/armadillo4r/inst/include/armadillo4r/wrappers/sparse_matrices.hpp | 14 +- armadillo4r-1.0.0/armadillo4r/inst/tinytest |only armadillo4r-1.0.0/armadillo4r/man/pkg_template.Rd | 4 armadillo4r-1.0.0/armadillo4r/man/unvendor.Rd | 4 armadillo4r-1.0.0/armadillo4r/man/vendor.Rd | 12 +- armadillo4r-1.0.0/armadillo4r/tests/tinytest.R |only 20 files changed, 85 insertions(+), 75 deletions(-)
Title: ADaM in R Asset Library
Description: A toolbox for programming Clinical Data Interchange Standards
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>).
Author: Edoardo Mancini [aut, cre] ,
Stefan Bundfuss [aut] ,
Arianna Cascone [aut] ,
Kristin Dahnert [aut],
Jeffrey Dickinson [aut],
Ross Farrugia [aut],
Fanny Gautier [aut] ,
Liam Hobby [aut],
Gordon Miller [aut],
Lina Patil [aut],
Ben Straub [aut],
F. Hoff [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiral versions 1.4.2 dated 2026-05-28 and 1.5.0 dated 2026-06-12
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Title: Bayesian Exploratory Factor Analysis
Description: Exploratory Bayesian factor analysis of continuous, mixed-type, and bounded continuous variables using the mode-jumping algorithm of Man and Culpepper (2020) <doi:10.1080/01621459.2020.1773833>.
Author: Albert Man [aut],
Steven Andrew Culpepper [aut, cre]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
This is a re-admission after prior archival of version 0.0.0.4 dated 2021-02-10
Diff between bayesefa versions 0.0.0.4 dated 2021-02-10 and 0.0.0.6 dated 2026-06-12
DESCRIPTION | 19 +++--- MD5 | 28 +++++----- NAMESPACE | 20 +++---- R/RcppExports.R | 64 +++++------------------ build |only inst/CITATION |only inst/WORDLIST |only man/IFA_Mode_Jumper.Rd | 51 ------------------ man/bayesefa-package.Rd | 5 + src/EFA_mode_jumper4.cpp | 43 +++++++++++++-- src/IFA_mode_jumper_mixedresponses_v4bounded.cpp | 2 src/IFA_mode_jumper_v5.cpp | 55 ------------------- src/Makevars | 2 src/Makevars.win | 10 ++- src/RcppExports.cpp | 20 +++++++ src/commonEFAfunctions.cpp | 5 + src/commonEFAfunctions.h |only 17 files changed, 126 insertions(+), 198 deletions(-)
Title: Ebrahim-Farrington Goodness-of-Fit Test for Logistic Regression
Description: Implements the Ebrahim-Farrington goodness-of-fit test for logistic
regression models, particularly effective for sparse data and binary outcomes.
This test provides an improved alternative to the traditional Hosmer-Lemeshow
test by using a modified Pearson chi-square statistic with data-dependent
grouping. The test is based on Farrington (1996) theoretical framework but
simplified for practical implementation with binary data. Includes functions
for both the original Farrington test (for grouped data) and the new
Ebrahim-Farrington test (for binary data with automatic grouping), the
Directed Ebrahim-Farrington (DEF) test that targets calibration-shape
departures, and an ensemble that combines the DEF bases via the Cauchy
combination test. For more details see Hosmer (1980) <doi:10.1080/03610928008827941> and Farrington (1996) <doi:10.1111/j.2517-6161.1996.tb02086.x>.
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 1.0.0 dated 2025-09-01 and 2.0.0 dated 2026-06-12
DESCRIPTION | 27 +- MD5 | 32 +- NAMESPACE | 17 + NEWS.md | 80 +++++++ R/def_ensemble_gof.R |only R/def_gof.R |only R/ebrahim_farrington_test.R | 39 ++- R/run_all_gof.R |only README.md | 192 +++++++++++++++-- inst/WORDLIST |only inst/doc/ebrahim-farrington-intro.R | 12 + inst/doc/ebrahim-farrington-intro.Rmd | 62 +++++ inst/doc/ebrahim-farrington-intro.html | 370 +++++++++++++++++++++++---------- man/def.ensemble.gof.Rd |only man/def.gof.Rd |only man/ef.gof.Rd | 22 + man/run.all.gof.Rd |only tests/testthat/test-def-ensemble-gof.R |only tests/testthat/test-def-gof.R |only tests/testthat/test-ef-method.R |only tests/testthat/test-run-all-gof.R |only vignettes/ebrahim-farrington-intro.Rmd | 62 +++++ vignettes/power_size_def.png |only 23 files changed, 761 insertions(+), 154 deletions(-)
Title: Cryptographic Hash Functions and Data Encoding
Description: Fast and memory-efficient streaming hash functions,
binary/text encoding and serialization. Hashes strings and raw vectors
directly. Stream hashes files which can be larger than memory, as
well as in-memory objects through R's serialization mechanism.
Implements the SHA-256, SHA-3 and 'Keccak' cryptographic hash
functions, SHAKE256 extendable-output function (XOF), 'SipHash'
pseudo-random function, base64 (including the URL-safe variant) and
base58 encoding, 'CBOR' and 'JSON' serialization.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
The Mbed TLS Contributors [cph] ,
Red Hat, Inc. [cph] ,
Luke Dashjr [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between secretbase versions 1.2.2 dated 2026-05-01 and 1.3.0 dated 2026-06-12
DESCRIPTION | 13 ++-- MD5 | 24 ++++---- NEWS.md | 4 + R/base.R | 20 ++++++- README.md | 31 +++++++--- build/partial.rdb |binary man/base64dec.Rd | 11 +++ man/base64enc.Rd | 10 +++ man/secretbase-package.Rd | 7 ++ src/base64.c | 130 +++++++++++++++++++++++++++------------------- src/init.c | 4 - src/secret.h | 6 +- tests/tests.R | 12 ++++ 13 files changed, 184 insertions(+), 88 deletions(-)
Title: Fast and Scalable Cellwise-Robust Ensemble
Description: Functions to perform robust variable selection and regression using the Fast and Scalable
Cellwise-Robust Ensemble (FSCRE) algorithm. The approach establishes a robust foundation
using the Detect Deviating Cells (DDC) algorithm and robust correlation estimates. It then
employs a competitive ensemble architecture where a robust Least Angle Regression (LARS)
engine proposes candidate variables and cross-validation arbitrates their assignment. A final
robust MM-estimator is applied to the selected predictors.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between srlars versions 2.0.1 dated 2026-03-30 and 3.0.0 dated 2026-06-12
DESCRIPTION | 8 - MD5 | 38 +++---- NAMESPACE | 2 NEWS.md | 8 + R/checkInputData.R | 48 +++++--- R/coef.srlars.R | 10 + R/computeCVError.R | 190 ++++++++++++++++++++++------------- R/computeRobustFoundation.R | 93 +++++++++-------- R/performSelectionLoop.R | 222 ++++++++++++++++++++++++++++++++--------- R/predict.srlars.R | 32 +++-- R/srlars.R | 91 +++++++++++++--- README.md | 26 +++- man/checkInputData.Rd | 30 +++++ man/coef.srlars.Rd | 10 + man/computeCVError.Rd | 17 +-- man/computeRobustFoundation.Rd | 13 +- man/performSelectionLoop.Rd | 79 ++++++++++++-- man/predict.srlars.Rd | 30 +++-- man/srlars.Rd | 32 +++++ tests/testthat/test-srlars.R | 134 ++++++++++++++---------- 20 files changed, 778 insertions(+), 335 deletions(-)
Title: Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).
Author: Dominic Gruen [aut, cre]
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
This is a re-admission after prior archival of version 0.4.0 dated 2026-02-23
Diff between RaceID versions 0.4.0 dated 2026-02-23 and 0.4.1 dated 2026-06-12
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 1 - R/VarID_functions.R | 17 +++++++---------- inst/doc/RaceID.html | 4 ++-- man/pruneKnn.Rd | 2 +- 6 files changed, 21 insertions(+), 25 deletions(-)
Title: Spatial and Environmental Data Tools for Landscape Ecology
Description: Provides functions for landscape analysis and data retrieval.
The package allows users to download environmental variables from global
datasets (e.g., WorldClim, CHELSA, ESA WorldCover, Nighttime Lights), and
to compute spatial and landscape metrics using a hexagonal grid system
based on the H3 spatial index. It is useful for ecological modeling,
biodiversity studies, and spatial data processing in landscape ecology.
Fick and Hijmans (2017) <doi:10.1002/joc.5086>.
Zanaga et al. (2022) <doi:10.5281/zenodo.7254221>.
Uber Technologies Inc. (2022) "H3: Hexagonal hierarchical spatial index".
Román et al. (2018) <doi:10.1016/j.rse.2018.03.017>.
Karger et al. (2017) <doi:10.1038/sdata.2017.122>.
Brun et al. (2022) <doi:10.5194/essd-14-5573-2022>.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between paisaje versions 0.2.0 dated 2026-01-07 and 0.3.0 dated 2026-06-12
paisaje-0.2.0/paisaje/man/reexports.Rd |only paisaje-0.3.0/paisaje/DESCRIPTION | 34 +- paisaje-0.3.0/paisaje/MD5 | 39 +-- paisaje-0.3.0/paisaje/NAMESPACE | 22 + paisaje-0.3.0/paisaje/NEWS.md | 72 +++++ paisaje-0.3.0/paisaje/R/cr_outline_c.R |only paisaje-0.3.0/paisaje/R/extract_cat_raster.R | 51 +--- paisaje-0.3.0/paisaje/R/get_chelsa_future.R |only paisaje-0.3.0/paisaje/R/get_chelsa_historic.R |only paisaje-0.3.0/paisaje/R/get_cr_outline.R |only paisaje-0.3.0/paisaje/R/get_nightlight_data.R | 285 +++++++++++++++++------ paisaje-0.3.0/paisaje/R/get_records_by_hexagon.R | 18 - paisaje-0.3.0/paisaje/R/utils_globals.R | 9 paisaje-0.3.0/paisaje/build/partial.rdb |binary paisaje-0.3.0/paisaje/build/vignette.rds |binary paisaje-0.3.0/paisaje/data/cr_outline.rda |only paisaje-0.3.0/paisaje/data/cr_outline_c.rda |binary paisaje-0.3.0/paisaje/inst/WORDLIST |only paisaje-0.3.0/paisaje/inst/doc/paisaje.html | 4 paisaje-0.3.0/paisaje/man/cr_outline.Rd |only paisaje-0.3.0/paisaje/man/cr_outline_c.Rd | 47 +++ paisaje-0.3.0/paisaje/man/get_chelsa_future.Rd |only paisaje-0.3.0/paisaje/man/get_chelsa_historic.Rd |only paisaje-0.3.0/paisaje/man/get_cr_outline.Rd |only paisaje-0.3.0/paisaje/man/get_nightlight_data.Rd | 169 +++++++++++-- paisaje-0.3.0/paisaje/man/paisaje-package.Rd | 7 26 files changed, 582 insertions(+), 175 deletions(-)
Title: Generates Dense and Sparse Graphs using Graphon Extensions
Description: Generates dense or sparse graphs using graphon mixtures and graphettes. Graphon mixtures uses two graphons U and W to generate graphs. Sparse graphs are generated in this case using the inverse line graph (root) operation. Graphettes have 3 components, the graphon W, a real-valued sequence and a graph edit function. Both techniques can generate dense or sparse graphs. Kandanaarachchi and Ong (2026) <doi:10.48550/arXiv.2505.13864>, Wijesinghe et al (2026) <doi:10.48550/arXiv.2602.23566>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between graphonmix versions 0.0.1.0 dated 2025-10-09 and 0.1.1 dated 2026-06-12
DESCRIPTION | 12 +-- MD5 | 51 +++++++++---- NAMESPACE | 11 ++ R/autoplot_separate_dense_sparse.R |only R/graph_separation.R |only R/graphettes.R |only R/utils.R | 64 ++++++++++++++++- README.md | 111 +++++++++++++++++------------- build/vignette.rds |binary inst/doc/graphette.R |only inst/doc/graphette.Rmd |only inst/doc/graphette.html |only inst/doc/graphonmix.Rmd | 8 +- inst/doc/graphonmix.html | 69 +++++++++--------- inst/doc/linegraphons.html | 16 ++-- man/autoplot.separate_dense_and_sparse.Rd |only man/create_exp_matrix.Rd | 2 man/figures/README-example-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-2-3.png |binary man/figures/README-unnamed-chunk-3-1.png |only man/graphonmix-package.Rd | 4 - man/ring_graphon.Rd |only man/sample_graphette.Rd |only man/sample_sparse_graphon.Rd |only man/sbm_graphon.Rd |only man/separate_dense_and_sparse.Rd |only man/star_f1.Rd |only man/star_f2.Rd |only man/star_f3.Rd |only man/star_f4.Rd |only man/star_f5.Rd |only vignettes/bibliography.bib | 11 ++ vignettes/graphette.Rmd |only vignettes/graphonmix.Rmd | 8 +- 36 files changed, 239 insertions(+), 128 deletions(-)
Title: Generalized Linear Models Extended
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses,
including parametric links and heteroscedastic latent variables.
Author: Achim Zeileis [aut, cre] ,
Roger Koenker [aut] ,
Philipp Doebler [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glmx versions 0.2-1 dated 2024-09-03 and 0.2-2 dated 2026-06-12
DESCRIPTION | 17 ++++++++++------- MD5 | 9 +++++---- NEWS.md | 9 +++++++++ README.md |only build/partial.rdb |binary man/plinks.Rd | 5 +---- 6 files changed, 25 insertions(+), 15 deletions(-)
Title: Interactive Forest Plot
Description: Interactive forest plot for clinical trial safety analysis
using 'metalite', 'reactable', 'plotly', and Analysis Data Model (ADaM)
datasets. Includes functionality for adverse event filtering,
incidence-based group filtering, hover-over reveals, and search and sort
operations. The workflow allows for metadata construction, data preparation,
output formatting, and interactive plot generation.
Author: Yilong Zhang [aut],
Benjamin Wang [aut],
Yujie Zhao [aut, cre],
Nan Xiao [ctb],
Hiroaki Fukuda [aut],
Yulia Sidi [ctb],
Xuan Deng [ctb],
Jeetener Chauhan [ctb],
Li Ma [ctb],
Chen Wang [ctb],
Madhusudhan Ginnaram [ctb],
Merck & Co., Inc., Rahway, NJ, [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between forestly versions 0.1.4 dated 2026-02-18 and 0.1.5 dated 2026-06-12
DESCRIPTION | 16 +- MD5 | 44 +++---- NEWS.md | 8 + R/ae_forestly.R | 126 +++++++++++--------- R/ae_listing.R | 107 +++++++++++------ R/format_ae_forestly.R | 8 + R/prepare_ae_forestly.R | 33 ++++- build/vignette.rds |binary inst/doc/customize-ae-specific-columns.html | 16 +- inst/doc/customize-color.html | 16 +- inst/doc/customize-diff-label.html | 16 +- inst/doc/customize-digits.html | 16 +- inst/doc/customize-display-only-soc.html | 16 +- inst/doc/customize-listing-columns.html | 16 +- inst/doc/customize-toggle-buttons.html | 18 +- inst/doc/customize-width.R | 82 +++++++++++++ inst/doc/customize-width.Rmd | 100 +++++++++++++++- inst/doc/customize-width.html | 174 +++++++++++++++++++++++++--- inst/doc/customize-xlimit.html | 16 +- inst/doc/forest-plot-static.html | 2 man/ae_forestly.Rd | 2 man/prepare_ae_forestly.Rd | 10 + vignettes/customize-width.Rmd | 100 +++++++++++++++- 23 files changed, 729 insertions(+), 213 deletions(-)
Title: Datasets and Basic Statistics for Symbolic Data Analysis
Description: Provides benchmark datasets and foundational tools for Symbolic Data Analysis (SDA). The package includes functions for constructing symbolic data objects from classical data, converting among different interval-valued data formats, managing interval-valued, histogram-valued, modal-valued, and multi-valued data, and performing basic descriptive statistics. It is designed to support teaching, methodological research, and the development of SDA techniques.
Author: Po-Wei Chen [aut],
Chun-houh Chen [aut],
Han-Ming Wu [cre]
Maintainer: Han-Ming Wu <wuhm@g.nccu.edu.tw>
Diff between dataSDA versions 0.2.5 dated 2026-03-14 and 0.2.6 dated 2026-06-12
dataSDA-0.2.5/dataSDA/inst/doc/dataSDA_intro_files |only dataSDA-0.2.6/dataSDA/DESCRIPTION | 20 dataSDA-0.2.6/dataSDA/MD5 | 55 dataSDA-0.2.6/dataSDA/NAMESPACE | 1 dataSDA-0.2.6/dataSDA/NEWS.md | 33 dataSDA-0.2.6/dataSDA/R/data.R | 9157 +++++----- dataSDA-0.2.6/dataSDA/R/interval_dist.R | 764 dataSDA-0.2.6/dataSDA/R/interval_utils.R | 119 dataSDA-0.2.6/dataSDA/R/utilities.R | 198 dataSDA-0.2.6/dataSDA/README.md | 13 dataSDA-0.2.6/dataSDA/build/vignette.rds |binary dataSDA-0.2.6/dataSDA/data/environment.mix.rda |binary dataSDA-0.2.6/dataSDA/inst/doc/dataSDA_intro.R | 904 dataSDA-0.2.6/dataSDA/inst/doc/dataSDA_intro.Rmd | 923 - dataSDA-0.2.6/dataSDA/inst/doc/dataSDA_intro.html | 1059 - dataSDA-0.2.6/dataSDA/man/abalone.iGAP.Rd | 108 dataSDA-0.2.6/dataSDA/man/abalone.int.Rd | 106 dataSDA-0.2.6/dataSDA/man/aggregate_to_symbolic.Rd | 263 dataSDA-0.2.6/dataSDA/man/bats.int.Rd | 103 dataSDA-0.2.6/dataSDA/man/check_zero_width_intervals.Rd |only dataSDA-0.2.6/dataSDA/man/china_temp.int.Rd | 111 dataSDA-0.2.6/dataSDA/man/environment.mix.Rd | 129 dataSDA-0.2.6/dataSDA/man/face.iGAP.Rd | 98 dataSDA-0.2.6/dataSDA/man/interval_distance.Rd | 210 dataSDA-0.2.6/dataSDA/man/lisbon_air_quality.int.Rd | 114 dataSDA-0.2.6/dataSDA/man/mtcars.mix.Rd | 116 dataSDA-0.2.6/dataSDA/tests/testthat/test-aggregate_to_symbolic_zero_width.R |only dataSDA-0.2.6/dataSDA/tests/testthat/test-check_zero_width_intervals.R |only dataSDA-0.2.6/dataSDA/vignettes/dataSDA_intro.Rmd | 923 - 29 files changed, 8270 insertions(+), 7257 deletions(-)
Title: Downloading and Cleaning U.S. Macroeconomic Data
Description: Utilities to retrieve and tidy U.S. macroeconomic data series
from public government data providers. Functions streamline access to series
from the Federal Reserve Bank of St. Louis Federal Reserve Economic Data (FRED),
the Bureau of Labor Statistics flat files, and the Bureau of Economic
Analysis National Income and Product Accounts tables, then return
consistent, tidy data frames ready for modeling and graphics. The package includes
helpers for date alignment, log-linear projections, and common macro diagnostics,
along with convenience plot builders for quick publication-quality charts.
Author: Mike Konczal [aut, cre]
Maintainer: Mike Konczal <konczal@gmail.com>
Diff between tidyusmacro versions 0.1.0 dated 2025-09-30 and 0.2.0 dated 2026-06-12
DESCRIPTION | 16 +- MD5 | 41 +++--- NAMESPACE | 13 ++ NEWS.md | 42 ++++++ R/data-dallasTrimPCEcomponents.R |only R/getBLSFiles.R | 253 +++++++++++++++++++++++++++++---------- R/getDallasTrimPCE.R |only R/getFRED.R | 17 ++ R/getNIPAFiles.R | 2 R/getPCEInflation.R | 25 ++- R/getUnrateFRED.R | 2 R/logLinearProjection.R | 33 ++++- R/theme_esp.R | 51 ++++++- README.md | 171 +++++++++++++++++++++----- data/dallasTrimPCEcomponents.rda |only man/dallasTrimPCEcomponents.Rd |only man/getBLSFiles.Rd | 56 ++++++-- man/getDallasTrimPCE.Rd |only man/getFRED.Rd | 2 man/getNIPAFiles.Rd | 2 man/getPCEInflation.Rd | 25 ++- man/getUnrateFRED.Rd | 2 man/logLinearProjection.Rd | 5 tests |only 24 files changed, 579 insertions(+), 179 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Synthesize Bio [aut, cre]
Maintainer: Synthesize Bio <candace@synthesize.bio>
Diff between rsynthbio versions 4.1.0 dated 2026-02-25 and 4.2.0 dated 2026-06-12
rsynthbio-4.1.0/rsynthbio/man/OUTPUT_TRANSFORMERS.Rd |only rsynthbio-4.1.0/rsynthbio/man/get_json.Rd |only rsynthbio-4.1.0/rsynthbio/man/get_output_transformer.Rd |only rsynthbio-4.1.0/rsynthbio/man/make_api_request.Rd |only rsynthbio-4.1.0/rsynthbio/man/poll_model_query.Rd |only rsynthbio-4.1.0/rsynthbio/man/start_model_query.Rd |only rsynthbio-4.1.0/rsynthbio/man/transform_baseline_output.Rd |only rsynthbio-4.1.0/rsynthbio/man/transform_metadata_output.Rd |only rsynthbio-4.2.0/rsynthbio/DESCRIPTION | 8 rsynthbio-4.2.0/rsynthbio/MD5 | 48 +-- rsynthbio-4.2.0/rsynthbio/NAMESPACE | 1 rsynthbio-4.2.0/rsynthbio/NEWS.md | 19 + rsynthbio-4.2.0/rsynthbio/R/call_model_api.R | 143 ++++++++-- rsynthbio-4.2.0/rsynthbio/R/output-transformers.R | 8 rsynthbio-4.2.0/rsynthbio/R/self-hosted.R |only rsynthbio-4.2.0/rsynthbio/R/utils.R | 96 ++++++ rsynthbio-4.2.0/rsynthbio/README.md | 102 +++++-- rsynthbio-4.2.0/rsynthbio/build/vignette.rds |binary rsynthbio-4.2.0/rsynthbio/inst/doc/available-metadata.Rmd |only rsynthbio-4.2.0/rsynthbio/inst/doc/available-metadata.html |only rsynthbio-4.2.0/rsynthbio/inst/doc/getting-started.Rmd | 6 rsynthbio-4.2.0/rsynthbio/inst/doc/getting-started.html | 8 rsynthbio-4.2.0/rsynthbio/inst/doc/self-hosted.R |only rsynthbio-4.2.0/rsynthbio/inst/doc/self-hosted.Rmd |only rsynthbio-4.2.0/rsynthbio/inst/doc/self-hosted.html |only rsynthbio-4.2.0/rsynthbio/man/SELF_HOSTED_TIMEOUT.Rd |only rsynthbio-4.2.0/rsynthbio/man/get_example_query.Rd | 19 + rsynthbio-4.2.0/rsynthbio/man/list_models.Rd | 18 + rsynthbio-4.2.0/rsynthbio/man/predict_query.Rd | 43 ++- rsynthbio-4.2.0/rsynthbio/tests/testthat/test-call_model_api.R | 4 rsynthbio-4.2.0/rsynthbio/tests/testthat/test-self-hosted.R |only rsynthbio-4.2.0/rsynthbio/vignettes/available-metadata.Rmd |only rsynthbio-4.2.0/rsynthbio/vignettes/getting-started.Rmd | 6 rsynthbio-4.2.0/rsynthbio/vignettes/self-hosted.Rmd |only 34 files changed, 442 insertions(+), 87 deletions(-)
Title: Compact Package Representations
Description: A tool, grammar, and standard to represent and exchange
R package source code as text files. Converts one or more source
packages to a text file and restores the package structures from the file.
Author: Nan Xiao [aut] ,
Yilong Zhang [aut],
Keaven Anderson [aut],
Amin Shirazi [ctb],
Jeff Cheng [ctb],
Danfeng Fu [ctb],
Benjamin Wang [aut],
Dickson Wanjau [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Dickson Wanjau <dickson.wanjau@merck.com>
Diff between pkglite versions 0.2.5 dated 2026-02-24 and 0.2.6 dated 2026-06-12
DESCRIPTION | 14 MD5 | 204 NAMESPACE | 82 NEWS.md | 150 R/collate.R | 444 - R/collection.R | 516 - R/dictionary.R | 444 - R/pack.R | 654 - R/pkglite-package.R | 38 R/spec.R | 266 R/templates.R | 514 - R/unpack.R | 660 - R/utils-cli.R | 486 - R/utils.R | 262 README.md | 172 build/vignette.rds |binary inst/CITATION | 24 inst/doc/filecollection.R | 64 inst/doc/filecollection.Rmd | 164 inst/doc/filecollection.html | 600 - inst/doc/filespec.R | 90 inst/doc/filespec.Rmd | 244 inst/doc/filespec.html | 712 - inst/doc/format.R | 12 inst/doc/format.Rmd | 184 inst/doc/format.html | 374 inst/doc/pkglite.R | 150 inst/doc/pkglite.Rmd | 344 inst/doc/pkglite.html | 696 - inst/examples/pkg1/DESCRIPTION | 32 inst/examples/pkg1/NAMESPACE | 6 inst/examples/pkg1/NEWS.md | 10 inst/examples/pkg1/R/data.R | 12 inst/examples/pkg1/R/hello.R | 22 inst/examples/pkg1/R/pkg1-package.R | 4 inst/examples/pkg1/README.md | 6 inst/examples/pkg1/inst/extdata/dataset.tsv | 202 inst/examples/pkg1/man/dataset.Rd | 32 inst/examples/pkg1/man/hello_world.Rd | 34 inst/examples/pkg1/man/pkg1-package.Rd | 36 inst/examples/pkg1/vignettes/example.bib | 16 inst/examples/pkg1/vignettes/pkg1.Rmd | 44 inst/examples/pkg2/DESCRIPTION | 32 inst/examples/pkg2/NAMESPACE | 6 inst/examples/pkg2/NEWS.md | 10 inst/examples/pkg2/R/data.R | 12 inst/examples/pkg2/R/hello.R | 22 inst/examples/pkg2/R/pkg2-package.R | 4 inst/examples/pkg2/README.md | 6 inst/examples/pkg2/inst/extdata/dataset.tsv | 202 inst/examples/pkg2/man/dataset.Rd | 32 inst/examples/pkg2/man/hello_world.Rd | 34 inst/examples/pkg2/man/pkg2-package.Rd | 36 inst/examples/pkg2/vignettes/example.bib | 16 inst/examples/pkg2/vignettes/pkg2.Rmd | 44 inst/logo/logo.R | 26 man/collate.Rd | 80 man/ext_binary.Rd | 60 man/ext_text.Rd | 60 man/file_auto.Rd | 72 man/file_default.Rd | 58 man/file_ectd.Rd | 60 man/file_name_patterns.Rd | 68 man/file_spec.Rd | 114 man/file_spec_templates.Rd | 114 man/is_file_collection.Rd | 66 man/is_file_spec.Rd | 72 man/merge.file_collection.Rd | 84 man/pack.Rd | 118 man/pipe.Rd | 34 man/pkglite-package.Rd | 83 man/print.file_collection.Rd | 68 man/print.file_spec.Rd | 74 man/prune.Rd | 78 man/remove_content.Rd | 96 man/sanitize.Rd | 72 man/sanitize_file_collection.Rd | 66 man/unpack.Rd | 138 man/verify_ascii.Rd | 84 tests/testthat.R | 8 tests/testthat/_snaps/independent_test_pack/fc_to_text1.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/fc_to_text2.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/file_to_vec.txt | 2156 ++-- tests/testthat/_snaps/independent_test_pack/pack.txt | 4318 +++++----- tests/testthat/_snaps/independent_test_pack/read_file_text1.txt | 32 tests/testthat/_snaps/independent_test_pack/read_file_text2.txt | 6 tests/testthat/_snaps/independent_test_pack/read_file_text3.txt | 10 tests/testthat/_snaps/independent_test_pack/read_file_text4.txt | 6 tests/testthat/_snaps/independent_test_pack/read_file_text5.txt | 12 tests/testthat/helper.R | 216 tests/testthat/test-independent-test_dictionary.R | 324 tests/testthat/test-independent-test_file_spec.R | 122 tests/testthat/test-independent-test_templates.R | 1134 +- tests/testthat/test-independent-test_utils.R | 122 tests/testthat/test-independent_test_collate.R | 238 tests/testthat/test-independent_test_collection.R | 296 tests/testthat/test-independent_test_pack.R | 152 tests/testthat/test-independent_test_unpack.R | 186 vignettes/custom.css | 80 vignettes/filecollection.Rmd | 164 vignettes/filespec.Rmd | 244 vignettes/format.Rmd | 184 vignettes/pkglite.Rmd | 344 103 files changed, 13065 insertions(+), 12922 deletions(-)
Title: Marker-Based Estimation of Heritability Using Individual Plant
or Plot Data
Description: Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author: Willem Kruijer [aut],
Ian White [ctb] ,
Padraic Flood [dtc],
Rik Kooke [dtc],
Bart-Jan van Rossum [cre, aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between heritability versions 1.4 dated 2023-08-24 and 1.5 dated 2026-06-12
DESCRIPTION | 37 ++- MD5 | 24 +- R/AI_algorithm.R | 498 ++++++++++++++++++++++---------------------- R/AI_algorithm_weights.r | 434 +++++++++++++++++++------------------- R/GINV.R | 2 R/KinshipTransform.R | 2 R/marker_h2_means.r | 2 man/BT_LW_H.Rd | 2 man/heritability-package.Rd | 4 man/leafArea.Rd | 2 man/marker_h2.Rd | 2 man/marker_h2_means.Rd | 2 man/repeatability.Rd | 4 13 files changed, 516 insertions(+), 499 deletions(-)
Title: Automated Mendelian Randomization Workflows and Visualizations
Description: Provides tools to summarize, analyze, and visualize results
from Mendelian randomization studies using summarized genetic
association data. The package includes functions for generating forest
plots and scatter plots at the single-nucleotide polymorphism
and Mendelian randomization method levels, and for fitting multiple
estimators in a unified workflow, including inverse-variance weighted
estimation, Mendelian randomization Egger regression,
the weighted median estimator, the robust adjusted
profile score, Mendelian randomization pleiotropy residual sum
and outlier, Mendelian randomization with the genotype
recoding invariance property, and a Bayesian horseshoe
method. Related methods are described by Burgess (2013)
<doi:10.1002/gepi.21758>, Bowden (2015) <doi:10.1093/ije/dyv080>,
Bowden (2016) <doi:10.1002/gepi.21965>, Zhao (2020)
<doi:10.1214/19-AOS1866>, Verbanck (2018)
<doi:10.1038/s41588-018-0099-7>, Dudbridge (2025)
<doi:10.1371/journal.pgen.1011 [...truncated...]
Author: Kelin Zhong [aut, cre],
Chia-Ling Kuo [aut]
Maintainer: Kelin Zhong <kelinzhonguconn@gmail.com>
Diff between autoMR versions 1.1.2 dated 2026-05-02 and 1.2.0 dated 2026-06-12
DESCRIPTION | 6 MD5 | 23 +-- NAMESPACE | 2 R/copied_functions.R | 104 ++++++++++----- R/global_Variables.R | 2 R/mr_forest.R | 15 -- R/mr_scatter_class.R | 3 R/mr_workflows.R | 299 ++++++++++++++++++++++++++++++++++---------- man/GWAS_forest.Rd | 2 man/export_scatter_plots.Rd | 3 man/mr_grip.Rd |only man/plot_mr_scatter.Rd | 11 + man/run_mr_analysis.Rd | 3 13 files changed, 341 insertions(+), 132 deletions(-)
Title: Monte Carlo Confidence Intervals in Structural Equation Modeling
Description: Monte Carlo confidence intervals for free and defined parameters
in models fitted in the structural equation modeling package 'lavaan'
can be generated using the 'semmcci' package.
'semmcci' has three main functions, namely, MC(), MCMI(), and MCStd().
The output of 'lavaan' is passed as the first argument
to the MC() function or the MCMI() function to generate Monte Carlo confidence intervals.
Monte Carlo confidence intervals for the standardized estimates
can also be generated by passing the output of the MC() function or the MCMI() function
to the MCStd() function.
A description of the package and code examples
are presented in Pesigan and Cheung (2024) <doi:10.3758/s13428-023-02114-4>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Shu Fai Cheung [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between semmcci versions 1.1.5 dated 2025-10-19 and 1.1.6 dated 2026-06-11
semmcci-1.1.5/semmcci/tests/testthat/test-semmcci.R |only semmcci-1.1.6/semmcci/DESCRIPTION | 8 - semmcci-1.1.6/semmcci/LICENSE | 2 semmcci-1.1.6/semmcci/MD5 | 41 ++++------ semmcci-1.1.6/semmcci/NEWS.md | 6 + semmcci-1.1.6/semmcci/R/lavHelper-std-lav-dot.R | 2 semmcci-1.1.6/semmcci/R/miHelper-ariv-dot.R | 2 semmcci-1.1.6/semmcci/R/miHelper-mi-combine-dot.R | 2 semmcci-1.1.6/semmcci/R/miHelper-total-adj-dot.R | 2 semmcci-1.1.6/semmcci/R/semmcci-func.R | 2 semmcci-1.1.6/semmcci/R/semmcci-mc-func.R | 2 semmcci-1.1.6/semmcci/R/semmcci-mc-generic.R | 2 semmcci-1.1.6/semmcci/R/semmcci-mc.R | 2 semmcci-1.1.6/semmcci/build/partial.rdb |binary semmcci-1.1.6/semmcci/man/Func.Rd | 14 +-- semmcci-1.1.6/semmcci/man/MC.Rd | 14 +-- semmcci-1.1.6/semmcci/man/MCFunc.Rd | 14 +-- semmcci-1.1.6/semmcci/man/MCGeneric.Rd | 14 +-- semmcci-1.1.6/semmcci/man/MCMI.Rd | 12 +- semmcci-1.1.6/semmcci/man/MCStd.Rd | 12 +- semmcci-1.1.6/semmcci/man/semmcci-package.Rd | 5 + semmcci-1.1.6/semmcci/tests/testthat/test-semmcci-mc-moment.R | 2 22 files changed, 85 insertions(+), 75 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.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.6.2 dated 2026-05-08 and 0.7.1 dated 2026-06-11
DESCRIPTION | 12 MD5 | 66 +++-- NAMESPACE | 12 NEWS.md | 70 +++++ R/chunk.R |only R/explain.R | 2 R/offload.R |only R/print.R | 1 R/verbs_grouping.R | 13 - README.md | 437 +++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/engine.html | 4 inst/doc/formats.html | 8 inst/doc/indexing.html | 130 ++++++++-- inst/doc/joins.html | 4 inst/doc/large-data.html | 12 inst/doc/offload.R |only inst/doc/offload.Rmd |only inst/doc/offload.html |only inst/doc/quickstart.html | 20 + inst/doc/schema.html | 4 inst/doc/sdm.R |only inst/doc/sdm.Rmd |only inst/doc/sdm.html |only inst/doc/string-ops.html | 4 man/chunk_feeder.Rd |only man/collect_chunked.Rd |only man/group_map.Rd |only man/offload.Rd |only src/collect.c | 58 ++++ src/collect.h | 6 src/fuzzy_join.c | 5 src/init.c | 4 src/r_bridge.c | 18 + src/r_bridge.h | 2 src/tdc/VENDORED_FROM | 2 src/vec_omp.h | 21 + tests/testthat/test-collect-chunked.R |only tests/testthat/test-groupby.R | 23 + tests/testthat/test-offload.R |only vignettes/offload.Rmd |only vignettes/sdm.Rmd |only 42 files changed, 675 insertions(+), 263 deletions(-)
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
Hadley Wickham [aut],
Gary Ritchie [aut],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between rstudioapi versions 0.18.0 dated 2026-01-16 and 0.19.0 dated 2026-06-11
DESCRIPTION | 10 +- MD5 | 63 +++++++------ NAMESPACE | 1 NEWS.md | 19 ++++ R/auth.R | 168 +++++++++++++++++++++++++++++++++---- R/code.R | 14 ++- R/document-api.R | 76 ++++++++++++++++ build/vignette.rds |binary man/getDelegatedAzureToken.Rd | 24 ++++- man/jobAdd.Rd | 20 ++-- man/jobAddOutput.Rd | 20 ++-- man/jobAddProgress.Rd | 20 ++-- man/jobGetState.Rd | 20 ++-- man/jobList.Rd | 20 ++-- man/jobRemove.Rd | 20 ++-- man/jobRunScript.Rd | 20 ++-- man/jobSetProgress.Rd | 20 ++-- man/jobSetState.Rd | 20 ++-- man/jobSetStatus.Rd | 20 ++-- man/launcherAvailable.Rd | 26 ++--- man/launcherConfig.Rd | 26 ++--- man/launcherContainer.Rd | 26 ++--- man/launcherControlJob.Rd | 26 ++--- man/launcherGetInfo.Rd | 26 ++--- man/launcherGetJob.Rd | 26 ++--- man/launcherGetJobs.Rd | 26 ++--- man/launcherHostMount.Rd | 26 ++--- man/launcherNfsMount.Rd | 26 ++--- man/launcherPlacementConstraint.Rd | 26 ++--- man/launcherResourceLimit.Rd | 26 ++--- man/launcherSubmitJob.Rd | 26 ++--- man/launcherSubmitR.Rd | 26 ++--- man/showEditSuggestion.Rd |only 33 files changed, 588 insertions(+), 325 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 2.3.0 dated 2026-01-16 and 2.4.0 dated 2026-06-11
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 4 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/include/RcppThread/quickpool.hpp | 355 ++++++++++++++++++++++++++-------- man/RcppThread.Rd | 5 8 files changed, 295 insertions(+), 95 deletions(-)
Title: Bootstrap for Regression Effect Sizes
Description: Generates nonparametric bootstrap confidence intervals
(Efron and Tibshirani, 1993: <doi:10.1201/9780429246593>)
for standardized regression coefficients (beta) and other effect sizes,
including multiple correlation, semipartial correlations,
improvement in R-squared, squared partial correlations,
and differences in standardized regression coefficients,
for models fitted by lm().
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaNB versions 1.0.6 dated 2025-10-19 and 1.0.7 dated 2026-06-11
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 28 ++++++++++++++-------------- NEWS.md | 6 ++++++ R/betaNB-methods-beta-nb.R | 6 ++---- build/partial.rdb |binary data/nas1982.rda |binary man/BetaNB.Rd | 14 +++++++------- man/DeltaRSqNB.Rd | 14 +++++++------- man/DiffBetaNB.Rd | 14 +++++++------- man/NB.Rd | 14 +++++++------- man/PCorNB.Rd | 14 +++++++------- man/RSqNB.Rd | 14 +++++++------- man/SCorNB.Rd | 14 +++++++------- man/betaNB-package.Rd | 5 +++++ 15 files changed, 82 insertions(+), 73 deletions(-)
Title: Monte Carlo for Regression Effect Sizes
Description: Generates Monte Carlo confidence intervals
for standardized regression coefficients (beta) and other effect sizes,
including multiple correlation, semipartial correlations,
improvement in R-squared, squared partial correlations,
and differences in standardized regression coefficients,
for models fitted by lm().
'betaMC' combines ideas from Monte Carlo confidence intervals for the indirect effect
(Pesigan and Cheung, 2024 <doi:10.3758/s13428-023-02114-4>)
and the sampling covariance matrix of regression coefficients
(Dudgeon, 2017 <doi:10.1007/s11336-017-9563-z>)
to generate confidence intervals effect sizes in regression.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaMC versions 1.3.3 dated 2025-10-19 and 1.3.4 dated 2026-06-11
DESCRIPTION | 11 ++++++----- LICENSE | 2 +- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/betaMC-methods-beta-mc.R | 6 ++---- build/partial.rdb |binary data/nas1982.rda |binary man/BetaMC.Rd | 16 ++++++++-------- man/DeltaRSqMC.Rd | 16 ++++++++-------- man/DiffBetaMC.Rd | 16 ++++++++-------- man/MC.Rd | 16 ++++++++-------- man/MCMI.Rd | 16 ++++++++-------- man/PCorMC.Rd | 16 ++++++++-------- man/RSqMC.Rd | 16 ++++++++-------- man/SCorMC.Rd | 16 ++++++++-------- man/betaMC-package.Rd | 5 +++++ 16 files changed, 99 insertions(+), 89 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.0.4 dated 2026-05-03 and 0.1.0 dated 2026-06-11
colleyRstats-0.0.4/colleyRstats/inst/WORDLIST.txt |only colleyRstats-0.1.0/colleyRstats/DESCRIPTION | 29 colleyRstats-0.1.0/colleyRstats/MD5 | 82 colleyRstats-0.1.0/colleyRstats/NAMESPACE | 35 colleyRstats-0.1.0/colleyRstats/NEWS.md | 57 colleyRstats-0.1.0/colleyRstats/R/globals.R | 10 colleyRstats-0.1.0/colleyRstats/R/imports.R | 36 colleyRstats-0.1.0/colleyRstats/R/paper.R |only colleyRstats-0.1.0/colleyRstats/R/pipeline.R |only colleyRstats-0.1.0/colleyRstats/R/plotting.R | 154 colleyRstats-0.1.0/colleyRstats/R/reporting.R | 2618 ++++++---- colleyRstats-0.1.0/colleyRstats/R/utils.R | 363 - colleyRstats-0.1.0/colleyRstats/R/zzz-aliases.R |only colleyRstats-0.1.0/colleyRstats/inst/WORDLIST | 340 - colleyRstats-0.1.0/colleyRstats/inst/doc/getting-started.html | 18 colleyRstats-0.1.0/colleyRstats/man/add_pareto_emoa_column.Rd | 4 colleyRstats-0.1.0/colleyRstats/man/add_pareto_moocore_column.Rd |only colleyRstats-0.1.0/colleyRstats/man/analyze_and_report.Rd |only colleyRstats-0.1.0/colleyRstats/man/assumption_methods_text.Rd |only colleyRstats-0.1.0/colleyRstats/man/checkAssumptionsForAnova.Rd | 5 colleyRstats-0.1.0/colleyRstats/man/check_homogeneity_by_group.Rd | 5 colleyRstats-0.1.0/colleyRstats/man/check_normality_by_group.Rd | 10 colleyRstats-0.1.0/colleyRstats/man/cite_methods.Rd |only colleyRstats-0.1.0/colleyRstats/man/generateEffectPlot.Rd | 20 colleyRstats-0.1.0/colleyRstats/man/generateMoboPlot.Rd | 15 colleyRstats-0.1.0/colleyRstats/man/generateMoboPlot2.Rd | 19 colleyRstats-0.1.0/colleyRstats/man/ggbetweenstatsWithPriorNormalityCheck.Rd | 13 colleyRstats-0.1.0/colleyRstats/man/ggbetweenstatsWithPriorNormalityCheckAsterisk.Rd | 5 colleyRstats-0.1.0/colleyRstats/man/ggwithinstatsWithPriorNormalityCheck.Rd | 13 colleyRstats-0.1.0/colleyRstats/man/ggwithinstatsWithPriorNormalityCheckAsterisk.Rd | 5 colleyRstats-0.1.0/colleyRstats/man/latex_preamble.Rd |only colleyRstats-0.1.0/colleyRstats/man/remove_outliers_REI.Rd | 12 colleyRstats-0.1.0/colleyRstats/man/reportART.Rd | 23 colleyRstats-0.1.0/colleyRstats/man/reportArtCon.Rd |only colleyRstats-0.1.0/colleyRstats/man/reportArtConTable.Rd |only colleyRstats-0.1.0/colleyRstats/man/reportDunnTest.Rd | 13 colleyRstats-0.1.0/colleyRstats/man/reportDunnTestTable.Rd | 26 colleyRstats-0.1.0/colleyRstats/man/reportMeanAndSD.Rd | 13 colleyRstats-0.1.0/colleyRstats/man/reportNPAV.Rd | 15 colleyRstats-0.1.0/colleyRstats/man/reportNparLD.Rd | 24 colleyRstats-0.1.0/colleyRstats/man/report_all.Rd |only colleyRstats-0.1.0/colleyRstats/man/reportggstatsplot.Rd | 20 colleyRstats-0.1.0/colleyRstats/man/reportggstatsplotPostHoc.Rd | 21 colleyRstats-0.1.0/colleyRstats/man/reshape_data.Rd | 1 colleyRstats-0.1.0/colleyRstats/man/save_paper_figure.Rd |only colleyRstats-0.1.0/colleyRstats/tests/testthat/test-paper.R |only colleyRstats-0.1.0/colleyRstats/tests/testthat/test-plotting.R | 15 colleyRstats-0.1.0/colleyRstats/tests/testthat/test-reporting.R | 172 colleyRstats-0.1.0/colleyRstats/tests/testthat/test-utils.R | 116 49 files changed, 2811 insertions(+), 1516 deletions(-)
Title: Robust Confidence Intervals for Standardized Regression
Coefficients
Description: Generates robust confidence intervals for standardized regression coefficients
using heteroskedasticity-consistent standard errors for models fitted by lm()
as described in Dudgeon (2017) <doi:10.1007/s11336-017-9563-z>.
The package can also be used to generate confidence intervals for R-squared,
adjusted R-squared, and differences of standardized regression coefficients.
A description of the package and code examples
are presented in Pesigan, Sun, and Cheung (2023) <doi:10.1080/00273171.2023.2201277>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaSandwich versions 1.0.8 dated 2025-10-19 and 1.0.9 dated 2026-06-11
DESCRIPTION | 10 ++++----- LICENSE | 2 - MD5 | 30 ++++++++++++++-------------- NEWS.md | 6 +++++ R/betaSandwich-beta-adf.R | 4 +-- R/betaSandwich-beta-hc.R | 2 - R/betaSandwich-beta-mvn.R | 2 - R/betaSandwich-methods-diff-beta-sandwich.R | 4 +-- build/partial.rdb |binary data/nas1982.rda |binary man/BetaADF.Rd | 14 ++++++------- man/BetaHC.Rd | 12 +++++------ man/BetaN.Rd | 12 +++++------ man/DiffBetaSandwich.Rd | 10 ++++----- man/RSqBetaSandwich.Rd | 10 ++++----- man/betaSandwich-package.Rd | 5 ++++ 16 files changed, 67 insertions(+), 56 deletions(-)
Title: Confidence Intervals for Standardized Regression Coefficients
Description: Generates confidence intervals for standardized regression coefficients
using delta method standard errors for models fitted by lm()
as described in Yuan and Chan (2011) <doi:10.1007/s11336-011-9224-6>
and Jones and Waller (2015) <doi:10.1007/s11336-013-9380-y>.
The package can also be used to generate confidence intervals for
differences of standardized regression coefficients
and as a general approach to performing the delta method.
A description of the package and code examples
are presented in Pesigan, Sun, and Cheung (2023) <doi:10.1080/00273171.2023.2201277>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between betaDelta versions 1.0.6 dated 2025-10-19 and 1.0.7 dated 2026-06-11
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/betaDelta-beta-delta-dot.R | 4 ++-- R/betaDelta-beta-delta.R | 4 ++-- R/betaDelta-methods-beta-delta.R | 4 ++-- R/betaDelta-methods-diff-beta-delta.R | 4 ++-- R/deltaMethod-methods.R | 4 ++-- build/partial.rdb |binary data/nas1982.rda |binary man/BetaDelta.Rd | 8 ++++---- man/Delta.Rd | 4 ++-- man/DeltaGeneric.Rd | 4 ++-- man/DiffBetaDelta.Rd | 4 ++-- man/betaDelta-package.Rd | 5 +++++ 16 files changed, 52 insertions(+), 41 deletions(-)
Title: Survey Standard Error Estimation for Cumulated Estimates and
their Differences in Complex Panel Designs
Description: Calculate point estimates and their standard errors in complex household surveys using bootstrap replicates. Bootstrapping considers survey design with a rotating panel. A comprehensive description of the methodology can be found under <https://statistikat.github.io/surveysd/articles/methodology.html>.
Author: Johannes Gussenbauer [aut, cre],
Alexander Kowarik [aut] ,
Eileen Vattheuer [aut],
Gregor de Cillia [aut],
Matthias Till [ctb]
Maintainer: Johannes Gussenbauer <Johannes.Gussenbauer@statistik.gv.at>
Diff between surveysd versions 2.0.2 dated 2026-04-27 and 2.0.3 dated 2026-06-11
DESCRIPTION | 6 MD5 | 50 +-- R/calc.stError.R | 8 inst/doc/error_estimation.R | 3 inst/doc/error_estimation.Rmd | 4 inst/doc/error_estimation.html | 546 +++++++++++++++++++------------------- inst/doc/ipf.R | 3 inst/doc/ipf.Rmd | 3 inst/doc/ipf.html | 28 - inst/doc/methodology.R | 3 inst/doc/methodology.Rmd | 3 inst/doc/methodology.html | 16 - inst/doc/raowu.R | 3 inst/doc/raowu.Rmd | 3 inst/doc/raowu.html | 7 inst/doc/surveysd.R | 3 inst/doc/surveysd.Rmd | 3 tests/testthat.R | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test_calcstError.R | 374 ++++++++++++++++++++------ vignettes/error_estimation.Rmd | 4 vignettes/ipf.Rmd | 3 vignettes/methodology.Rmd | 3 vignettes/raowu.Rmd | 3 vignettes/surveysd.Rmd | 3 vignettes/surveysd.html | 68 ++-- 26 files changed, 700 insertions(+), 453 deletions(-)
Title: Robust Trend-Cycle Decomposition for Macroeconomic Time Series
Description: Provides high-performance tools for macroeconomic trend
extraction and filtering, specifically designed to solve the end-point
problem in real-time. Implements the MacroBoost Hybrid (MBH) filter
using penalized P-splines and gradient boosting. Unlike the standard
Hodrick-Prescott filter, 'MacroFilters' utilizes component-wise
L2-boosting with robust loss functions (Huber) to handle extreme
transient shocks (e.g., COVID-19) without inducing spurious trend
shifts. The algorithm includes an automated two-layer diagnostic stage
for unit roots and structural breaks, optimized via corrected AICc for
computational efficiency. Methodology detailed in Kinel (2026)
<doi:10.2139/ssrn.6371138>.
Author: Michal Kinel [aut, cre]
Maintainer: Michal Kinel <michal.kinel@gmail.com>
Diff between MacroFilters versions 0.1.0 dated 2026-05-27 and 0.2.1 dated 2026-06-11
DESCRIPTION | 17 +- MD5 | 72 ++++++--- NAMESPACE | 19 ++ NEWS.md |only R/00_class_system.R | 4 R/02_algo_hp.R | 42 ++++- R/03_algo_hamilton.R | 66 +++++++-- R/04_algo_bhp.R | 64 ++++++-- R/05_algo_mbh.R | 176 ++++++++++++++++-------- R/autoplot.R |only R/data.R | 64 ++++++++ R/internals.R |only R/zzz.R |only README.md | 23 ++- build/vignette.rds |binary data/es_gdp.rda |only data/fr_gdp.rda |only inst/CITATION | 15 +- inst/doc/introduction.R | 93 ++++++------ inst/doc/introduction.Rmd | 123 +++++++++------- inst/doc/introduction.html | 276 ++++++++++++++++++++++---------------- inst/doc/real_time_revisions.R | 2 inst/doc/real_time_revisions.Rmd | 7 inst/doc/real_time_revisions.html | 54 +++---- inst/doc/tuning_mbh.R | 26 ++- inst/doc/tuning_mbh.Rmd | 37 +++-- inst/doc/tuning_mbh.html | 138 ++++++++++--------- inst/doc/uncertainty_bands.R |only inst/doc/uncertainty_bands.Rmd |only inst/doc/uncertainty_bands.html |only man/autoplot.macrofilter.Rd |only man/bhp_filter.Rd | 29 +++ man/es_gdp.Rd |only man/fr_gdp.Rd |only man/hamilton_filter.Rd | 37 ++++- man/hp_filter.Rd | 25 ++- man/mbh_filter.Rd | 103 +++++++++----- man/reexports.Rd |only tests/testthat/test-autoplot.R |only tests/testthat/test-bootstrap.R |only tests/testthat/test-mbh_filter.R | 24 +++ vignettes/introduction.Rmd | 123 +++++++++------- vignettes/real_time_revisions.Rmd | 7 vignettes/tuning_mbh.Rmd | 37 +++-- vignettes/uncertainty_bands.Rmd |only 45 files changed, 1142 insertions(+), 561 deletions(-)
Title: Parametric Mortality Curve Fitting and Mortality Forecasting
Tools
Description: Provides tools for fitting parametric mortality curves. Implements multiple optimisation strategies to enhance robustness and stability of parameter estimation. Offers tools for forecasting mortality rates guided by mortality curves.
For modelling details see:
Tabeau (2001) <doi:10.1007/0-306-47562-6_1>,
Renshaw and Haberman (2006) <doi:10.1016/j.insmatheco.2005.12.001>,
Cairns et al. (2009) <doi:10.1080/10920277.2009.10597538>,
Li and Lee (2005) <doi: 10.1353/dem.2005.0021>.
Author: Jackie Li [aut, cre, cph]
Maintainer: Jackie Li <jackieli@smu.edu.sg>
Diff between demofit versions 0.1.3 dated 2026-04-28 and 0.1.4 dated 2026-06-11
DESCRIPTION | 6 +-- MD5 | 82 +++++++++++++++++++++++++++++++------------------- NAMESPACE | 51 +++++++++++++++++++++++++++++++ NEWS | 7 +++- R/APCS.R | 16 +++++---- R/CAES.R | 22 +++++++------ R/CBDCS.R | 16 +++++---- R/CBDQCS.R | 18 ++++++---- R/CBDS.R | 14 ++++---- R/CFM2S.R | 26 ++++++++------- R/CFMS.R | 28 +++++++++-------- R/ENI.R | 4 +- R/ENS.R | 6 ++- R/LCLS.R |only R/LCS.R | 16 +++++---- R/PAPCS.R |only R/PCAES.R |only R/PCBDCS.R |only R/PCBDQCS.R |only R/PCBDS.R |only R/PCFM2S.R |only R/PCFMS.R |only R/PLCS.R |only R/PRHS.R |only R/RHS.R | 18 ++++++---- R/STARS.R | 10 +++--- R/modelS3.R | 49 +++++++++++++++++++++++++++-- inst/CITATION | 2 - inst/doc/demofit.Rmd | 8 ++-- inst/doc/demofit.html | 21 ++++++------ man/APCS.Rd | 2 - man/CAES.Rd | 2 - man/CBDCS.Rd | 2 - man/CBDQCS.Rd | 2 - man/CBDS.Rd | 2 - man/CFM2S.Rd | 2 - man/CFMS.Rd | 2 - man/LCLS.Rd |only man/LCS.Rd | 2 - man/PAPCS.Rd |only man/PCAES.Rd |only man/PCBDCS.Rd |only man/PCBDQCS.Rd |only man/PCBDS.Rd |only man/PCFM2S.Rd |only man/PCFMS.Rd |only man/PLCS.Rd |only man/PRHS.Rd |only man/RHS.Rd | 2 - man/STARS.Rd | 2 - man/modelS3.Rd | 8 ++-- vignettes/demofit.Rmd | 8 ++-- 52 files changed, 298 insertions(+), 158 deletions(-)
Title: Calculates Composite Index
Description: It uses the first-order sensitivity index to measure whether the weights assigned by the creator of the composite indicator match the actual importance of the variables. Moreover, the variance inflation factor is used to reduce the set of correlated variables. In the case of a discrepancy between the importance and the assigned weight, the script determines weights that allow adjustment of the weights to the intended impact of variables. If the optimised weights are unable to reflect the desired importance, the highly correlated variables are reduced, taking into account variance inflation factor. The final outcome of the script is the calculated value of the composite indicator based on optimal weights and a reduced set of variables, and the linear ordering of the analysed objects.
Author: Olgun Aydin [cre] ,
Marta Kuc-Czarnecka [aut] ,
Michal Pietrzak [aut]
Maintainer: Olgun Aydin <olgun.aydin@pg.edu.pl>
Diff between compindexR versions 0.1.3 dated 2023-11-25 and 0.1.4 dated 2026-06-11
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- R/scaling.R | 9 +-------- R/si_linear_exc_vif.R | 4 ++-- README.md | 4 ++-- 5 files changed, 18 insertions(+), 24 deletions(-)
Title: Extract and Tidy Canadian 'Hydrometric' Data
Description: Provides functions to access historical and real-time national 'hydrometric'
data from Water Survey of Canada data sources and then applies tidy data principles.
Author: Sam Albers [aut, cre, cph] ,
Province of British Columbia [cph] ,
Tula Foundation [cph] ,
David Hutchinson [ctb],
Dewey Dunnington [ctb],
Ryan Whaley [ctb],
Government of Canada [dtc],
Luke Winslow [rev] ,
Laura DeCicco [rev]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between tidyhydat versions 1.0.0 dated 2026-02-03 and 1.0.1 dated 2026-06-11
DESCRIPTION | 8 MD5 | 119 ++++---- NEWS.md | 5 R/available.R | 146 ++++++---- R/realtime-webservice.R | 16 - R/realtime.R | 2 R/utils-realtime.R | 6 R/utils.R | 102 +++++- build/partial.rdb |binary build/vignette.rds |binary data/allstations.rda |binary data/hy_data_symbols.rda |binary data/hy_data_types.rda |binary inst/doc/tidyhydat_an_introduction.Rmd | 60 ++-- inst/doc/tidyhydat_an_introduction.html | 64 ++-- inst/doc/tidyhydat_example_analysis.Rmd | 32 -- inst/doc/tidyhydat_example_analysis.html | 60 +--- inst/doc/tidyhydat_hydat_db.Rmd | 16 - inst/doc/tidyhydat_hydat_db.html | 18 - man/available_flows.Rd | 4 man/available_levels.Rd | 4 man/hy_agency_list.Rd | 44 +-- man/hy_annual_instant_peaks.Rd | 44 +-- man/hy_annual_stats.Rd | 44 +-- man/hy_daily.Rd | 44 +-- man/hy_daily_flows.Rd | 44 +-- man/hy_daily_levels.Rd | 44 +-- man/hy_data_symbols.Rd | 46 +-- man/hy_data_types.Rd | 46 +-- man/hy_datum_list.Rd | 44 +-- man/hy_monthly_flows.Rd | 44 +-- man/hy_monthly_levels.Rd | 44 +-- man/hy_reg_office_list.Rd | 44 +-- man/hy_sed_daily_loads.Rd | 44 +-- man/hy_sed_daily_suscon.Rd | 44 +-- man/hy_sed_monthly_loads.Rd | 44 +-- man/hy_sed_monthly_suscon.Rd | 44 +-- man/hy_sed_samples.Rd | 44 +-- man/hy_sed_samples_psd.Rd | 44 +-- man/hy_src.Rd | 2 man/hy_stations.Rd | 46 +-- man/hy_stn_data_coll.Rd | 44 +-- man/hy_stn_data_range.Rd | 44 +-- man/hy_stn_op_schedule.Rd | 44 +-- man/hy_stn_regulation.Rd | 44 +-- man/hy_version.Rd | 44 +-- man/realtime_dd.Rd | 6 man/realtime_stations.Rd | 6 man/realtime_ws.Rd | 6 man/tidyhydat-package.Rd | 5 tests/testthat/fixtures/wateroffice.ec.gc.ca/services/real_time_data/csv/inline-7f58b3.R |only tests/testthat/test-available-classes.R | 80 +++++ tests/testthat/test-realtime-webservice.R | 16 + vignettes/tidyhydat_an_introduction.Rmd | 60 ++-- vignettes/tidyhydat_example_analysis.Rmd | 32 -- vignettes/tidyhydat_hydat_db.Rmd | 16 - vignettes/vignette-fig-old_rec-1.png |binary vignettes/vignette-fig-old_rec_yr-1.png |binary vignettes/vignette-fig-pcrtile_plt-1.png |binary vignettes/vignette-fig-tile_plt-1.png |binary vignettes/vignette-fig-unnamed-chunk-15-1.png |binary 61 files changed, 1067 insertions(+), 886 deletions(-)
Title: Flexible Non-Linear Least Square Model Fitting
Description: Provides tools for flexible non-linear least squares model fitting using general-purpose optimization techniques. The package supports a variety of optimization algorithms, including those provided by the 'optimx' package, making it suitable for handling complex non-linear models. Features include parallel processing support via the 'future' and 'foreach' packages, comprehensive model diagnostics, and visualization capabilities. Implements methods described in Nash and Varadhan (2011, <doi:10.18637/jss.v043.i09>).
Author: Johan Aparicio [cre, aut],
Jeffrey Endelman [aut],
University of Wisconsin Madison [cph]
Maintainer: Johan Aparicio <aparicioarce@wisc.edu>
Diff between flexFitR versions 1.2.2 dated 2026-01-27 and 1.2.3 dated 2026-06-11
DESCRIPTION | 6 - MD5 | 36 +++--- NEWS.md | 13 ++ R/00_dt_potato.R | 23 +++- R/02_modeler.R | 226 ----------------------------------------- R/03_metrics.R | 3 R/04_predict.R | 9 - R/08_comparison.R | 4 R/11_influence.R | 8 - R/12_update.R | 4 R/99_growth_curves.R | 9 - data/dt_potato_22.rda |only inst/doc/canopy-model.html | 7 - inst/doc/how_to_start.html | 13 +- inst/doc/maturity-model.html | 7 - inst/doc/plotting.html | 5 inst/doc/predicted_values.html | 9 - man/dt_potato.Rd | 4 man/dt_potato_22.Rd |only man/fn_lll.Rd | 2 20 files changed, 101 insertions(+), 287 deletions(-)
Title: Easily Build Command Line Applications
Description: Run simple 'R' scripts as command line applications, with
automatic robust and convenient support for command line arguments.
This package provides 'Rapp', an alternative 'R' front-end similar to
'Rscript', that enables this.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between Rapp versions 0.3.0 dated 2025-12-14 and 0.4.0 dated 2026-06-11
DESCRIPTION | 10 MD5 | 61 ++- NAMESPACE | 4 NEWS.md | 74 +++- R/app.R | 25 + R/args.R | 186 +++++++++-- R/help.R | 247 +++++++++++++-- R/install.R | 269 ++++++++++++++-- R/utils.R | 53 +++ R/yaml.R | 64 ---- README.md | 125 +++++-- inst/add-path-entry.ps1 | 36 ++ inst/examples/flip-coin.R | 2 inst/examples/todo.R | 15 inst/notes |only man/install_pkg_cli_apps.Rd | 29 + tests/testthat/_snaps/basics.md | 6 tests/testthat/_snaps/help-snapshots.md | 99 ++++-- tests/testthat/_snaps/multi-options.md | 22 - tests/testthat/_snaps/regressions.md |only tests/testthat/_snaps/subcommands.md |only tests/testthat/_snaps/todo.md | 10 tests/testthat/apps/kitchen-sink.R | 1 tests/testthat/apps/ls.R | 4 tests/testthat/apps/nested-commands.R | 1 tests/testthat/apps/simple-commands.R | 3 tests/testthat/test-help-annotations.R | 176 ++++++++++- tests/testthat/test-help-snapshots.R | 36 -- tests/testthat/test-install.R | 500 +++++++++++++++++++++++++++++++ tests/testthat/test-multi-options.R | 7 tests/testthat/test-regressions.R | 509 ++++++++++++++++++++++++++++++++ tests/testthat/test-subcommands.R | 267 ++++++++++++++++ tests/testthat/test-todo.R | 25 + 33 files changed, 2508 insertions(+), 358 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 2.7.3 dated 2026-05-12 and 3.1.0 dated 2026-06-11
ggRandomForests-2.7.3/ggRandomForests/man/gg_partialpro.Rd |only ggRandomForests-2.7.3/ggRandomForests/man/plot.gg_partialpro.Rd |only ggRandomForests-3.1.0/ggRandomForests/DESCRIPTION | 18 ggRandomForests-3.1.0/ggRandomForests/MD5 | 247 - ggRandomForests-3.1.0/ggRandomForests/NAMESPACE | 62 ggRandomForests-3.1.0/ggRandomForests/NEWS.md | 270 + ggRandomForests-3.1.0/ggRandomForests/R/autoplot_methods.R | 40 ggRandomForests-3.1.0/ggRandomForests/R/calc_roc.R | 169 ggRandomForests-3.1.0/ggRandomForests/R/gg_beta_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_brier.R | 54 ggRandomForests-3.1.0/ggRandomForests/R/gg_error.R | 10 ggRandomForests-3.1.0/ggRandomForests/R/gg_isopro.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_ivarpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_partial.R | 31 ggRandomForests-3.1.0/ggRandomForests/R/gg_partial_rfsrc.R | 50 ggRandomForests-3.1.0/ggRandomForests/R/gg_partial_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_partialpro.R | 175 ggRandomForests-3.1.0/ggRandomForests/R/gg_rfsrc.R | 39 ggRandomForests-3.1.0/ggRandomForests/R/gg_roc.R | 110 ggRandomForests-3.1.0/ggRandomForests/R/gg_survival.R | 33 ggRandomForests-3.1.0/ggRandomForests/R/gg_udependent.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_variable.R | 77 ggRandomForests-3.1.0/ggRandomForests/R/gg_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/gg_vimp.R | 50 ggRandomForests-3.1.0/ggRandomForests/R/help.R | 4 ggRandomForests-3.1.0/ggRandomForests/R/kaplan.R | 2 ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_beta_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_brier.R | 20 ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_error.R | 33 ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_isopro.R |only ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_ivarpro.R |only ggRandomForests-3.1.0/ggRandomForests/R/plot.gg_partial.R | 170 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|only ggRandomForests-3.1.0/ggRandomForests/build/vignette.rds |binary ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-regression.R | 42 ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-regression.html | 2006 --------- ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-regression.qmd | 128 ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-survival.R | 36 ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-survival.html | 2171 ---------- ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests-survival.qmd | 194 ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests.html | 71 ggRandomForests-3.1.0/ggRandomForests/inst/doc/ggRandomForests.qmd | 77 ggRandomForests-3.1.0/ggRandomForests/inst/doc/varpro.R |only ggRandomForests-3.1.0/ggRandomForests/inst/doc/varpro.html |only ggRandomForests-3.1.0/ggRandomForests/inst/doc/varpro.qmd |only ggRandomForests-3.1.0/ggRandomForests/man/autoplot.gg.Rd | 44 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ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_partial_varpro.Rd |only ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_rfsrc.Rd | 69 ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_roc.Rd | 42 ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_survival.Rd | 24 ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_udependent.Rd |only ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_variable.Rd | 27 ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_varpro.Rd |only ggRandomForests-3.1.0/ggRandomForests/man/plot.gg_vimp.Rd | 19 ggRandomForests-3.1.0/ggRandomForests/man/print.gg.Rd | 33 ggRandomForests-3.1.0/ggRandomForests/man/quantile_pts.Rd | 4 ggRandomForests-3.1.0/ggRandomForests/man/summary.gg.Rd | 34 ggRandomForests-3.1.0/ggRandomForests/man/surv_partial.rfsrc.Rd | 50 ggRandomForests-3.1.0/ggRandomForests/man/varpro_feature_names.Rd | 6 ggRandomForests-3.1.0/ggRandomForests/tests/testthat/Rplots.pdf |binary ggRandomForests-3.1.0/ggRandomForests/tests/testthat/_snaps |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/helper-varpro-fixtures.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/setup.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_beta_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_isopro.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_ivarpro.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_partial_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_partialpro.R | 55 ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_roc.R | 154 ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_udependent.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_variable.R | 265 + ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_gg_vimp.R | 26 ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_namespace_hygiene.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_plot_conventions.R |only ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_plot_layer_data.R | 107 ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_snapshots.R | 299 + ggRandomForests-3.1.0/ggRandomForests/tests/testthat/test_surv_partial.R | 10 ggRandomForests-3.1.0/ggRandomForests/vignettes/ggRandomForests-regression.qmd | 128 ggRandomForests-3.1.0/ggRandomForests/vignettes/ggRandomForests-survival.qmd | 194 ggRandomForests-3.1.0/ggRandomForests/vignettes/ggRandomForests.bib | 19 ggRandomForests-3.1.0/ggRandomForests/vignettes/ggRandomForests.qmd | 77 ggRandomForests-3.1.0/ggRandomForests/vignettes/precompute_varpro.R |only ggRandomForests-3.1.0/ggRandomForests/vignettes/varpro.qmd |only ggRandomForests-3.1.0/ggRandomForests/vignettes/varpro_precomputed.rds |only 130 files changed, 3917 insertions(+), 5493 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.4 dated 2025-12-10 and 0.3.0 dated 2026-06-11
getRad-0.2.4/getRad/man/get_vpts_aloft.Rd |only getRad-0.2.4/getRad/man/get_vpts_rmi.Rd |only getRad-0.2.4/getRad/man/req_cache_getrad.Rd |only getRad-0.3.0/getRad/DESCRIPTION | 10 getRad-0.3.0/getRad/MD5 | 91 +++--- getRad-0.3.0/getRad/NAMESPACE | 1 getRad-0.3.0/getRad/NEWS.md | 12 getRad-0.3.0/getRad/R/getRad-package.R | 1 getRad-0.3.0/getRad/R/get_pvol.R | 14 - getRad-0.3.0/getRad/R/get_pvol_at.R |only getRad-0.3.0/getRad/R/get_pvol_cz.R | 57 +++- getRad-0.3.0/getRad/R/get_pvol_ee.R | 5 getRad-0.3.0/getRad/R/get_pvol_nl.R | 13 getRad-0.3.0/getRad/R/get_pvol_ro.R | 16 + getRad-0.3.0/getRad/R/get_vpts.R | 134 +++++++--- getRad-0.3.0/getRad/R/get_vpts_aloft.R | 15 - getRad-0.3.0/getRad/R/get_vpts_birdcast.R |only getRad-0.3.0/getRad/R/get_vpts_coverage.R | 7 getRad-0.3.0/getRad/R/get_vpts_coverage_aloft.R | 1 getRad-0.3.0/getRad/R/get_vpts_coverage_birdcast.R |only getRad-0.3.0/getRad/R/get_vpts_local.R |only getRad-0.3.0/getRad/R/get_vpts_local_aloft.R |only getRad-0.3.0/getRad/R/get_vpts_local_dark_ecology.R |only getRad-0.3.0/getRad/R/get_vpts_rmi.R | 2 getRad-0.3.0/getRad/R/get_weather_radars.R | 4 getRad-0.3.0/getRad/R/utils.R | 57 +++- getRad-0.3.0/getRad/R/utils_pvol.R | 11 getRad-0.3.0/getRad/R/utils_vpts_aloft.R | 29 -- getRad-0.3.0/getRad/R/zzz.R | 37 ++ getRad-0.3.0/getRad/README.md | 25 - getRad-0.3.0/getRad/inst/doc/supported_sources.R | 1 getRad-0.3.0/getRad/inst/doc/supported_sources.Rmd | 1 getRad-0.3.0/getRad/inst/doc/supported_sources.html | 4 getRad-0.3.0/getRad/man/getRad-package.Rd | 17 - getRad-0.3.0/getRad/man/get_pvol.Rd | 2 getRad-0.3.0/getRad/man/get_vpts.Rd | 47 ++- getRad-0.3.0/getRad/man/get_vpts_coverage.Rd | 9 getRad-0.3.0/getRad/man/get_weather_radars.Rd | 2 getRad-0.3.0/getRad/tests/testthat/test-get_pvol.R | 30 ++ getRad-0.3.0/getRad/tests/testthat/test-get_pvol_at.R |only getRad-0.3.0/getRad/tests/testthat/test-get_pvol_cz.R | 21 + getRad-0.3.0/getRad/tests/testthat/test-get_pvol_dk.R | 1 getRad-0.3.0/getRad/tests/testthat/test-get_pvol_ee.R | 26 + getRad-0.3.0/getRad/tests/testthat/test-get_pvol_nl.R | 53 ++- getRad-0.3.0/getRad/tests/testthat/test-get_pvol_ro.R | 7 getRad-0.3.0/getRad/tests/testthat/test-get_pvol_se.R | 2 getRad-0.3.0/getRad/tests/testthat/test-get_vpts_birdcast.R |only getRad-0.3.0/getRad/tests/testthat/test-get_vpts_coverage.R | 22 + getRad-0.3.0/getRad/tests/testthat/test-get_vpts_coverage_birdcast.R |only getRad-0.3.0/getRad/tests/testthat/test-get_vpts_coverage_rmi.R | 2 getRad-0.3.0/getRad/tests/testthat/test-get_vpts_local.R |only getRad-0.3.0/getRad/tests/testthat/test-get_vpts_local_aloft.R |only getRad-0.3.0/getRad/tests/testthat/test-get_vpts_local_dark_ecology.R |only getRad-0.3.0/getRad/vignettes/supported_sources.Rmd | 1 54 files changed, 589 insertions(+), 201 deletions(-)
Title: Staggered DiD Tools: Event Studies and ATT Aggregation
Description: Provides tools for difference-in-differences (DiD) estimation and
visualization with staggered adoption. Includes run_es() for event-study
curves (dynamic effects by relative time) and calc_att() for aggregated
ATT estimation (overall, by cohort, by calendar time). Supports multiple
modern estimators: Callaway-Sant'Anna (2021), Sun-Abraham (2021),
Borusyak-Jaravel-Spiess (2024), Wooldridge TWM, and Deb et al. FLEX.
Author: Yosuke Abe [aut, cre]
Maintainer: Yosuke Abe <yosuke.abe0507@gmail.com>
Diff between fixes versions 0.8.1 dated 2026-05-10 and 0.11.2 dated 2026-06-11
DESCRIPTION | 29 MD5 | 85 + NAMESPACE | 34 NEWS.md | 316 ++++++ R/RcppExports.R | 132 ++ R/autoplot-es_result.R | 22 R/bootstrap_cs.R | 226 ++-- R/calc_att.R |only R/contamination_weights_sa.R |only R/estimators_bjs.R | 32 R/estimators_cs.R | 144 +-- R/estimators_flex.R |only R/estimators_sa.R | 156 --- R/estimators_twm.R |only R/honest_did.R |only R/plot_att_gt.R | 242 +++-- R/plot_es.R | 168 ++- R/plot_es_interactive.R | 176 ++- R/plot_honest.R |only R/run_did.R |only R/run_es.R | 1277 +++++++++++++++++----------- R/tidy-did_result.R |only R/utils-internal.R |only README.md | 482 ++++++---- inst/doc/fixes-intro.html | 8 inst/profile |only man/autoplot.es_result.Rd | 14 man/calc_att.Rd |only man/compute_contamination_weights.Rd |only man/figures/README-twm-plot-1.png |only man/glance.did_result.Rd |only man/honest_sensitivity.Rd |only man/plot_att_gt.Rd | 29 man/plot_contamination_weights.Rd |only man/plot_es.Rd | 4 man/plot_es_interactive.Rd | 16 man/plot_honest.Rd |only man/run_did.Rd |only man/run_es.Rd | 47 - man/tidy.did_result.Rd |only src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 66 + src/bootstrap_cs.cpp |only src/compute_att_gt.cpp | 17 src/cov_demeaning.cpp |only src/indicator_matrix.cpp |only src/iw_aggregation.cpp |only tests/testthat/test-att.R |only tests/testthat/test-contamination-weights.R |only tests/testthat/test-cs.R | 4 tests/testthat/test-did.R |only tests/testthat/test-flex.R |only tests/testthat/test-honest.R |only tests/testthat/test-rcpp-bootstrap.R |only tests/testthat/test-rcpp-covdemeaning.R |only tests/testthat/test-rcpp-indicator.R |only tests/testthat/test-rcpp-iw.R |only tests/testthat/test-robustness.R |only tests/testthat/test-sa.R | 44 tests/testthat/test-twm.R |only tests/testthat/test-utils-internal.R |only 62 files changed, 2448 insertions(+), 1322 deletions(-)
Title: Streamlined Analysis of Wild Pedigree Data
Description: Analyzing pedigree data of wild
populations. While primarily designed to process outputs from the
'COLONY' (Jones & Wang (2010) <doi:10.1111/j.1755-0998.2009.02787.x>)
pedigree reconstruction software, it can also accommodate
data from other sources. By linking reconstructed pedigrees with
genetic sample metadata, 'wpeR' produces spatial and temporal
visualizations as well as tabular summaries that support
interpretation of family structures and dynamics. The main goal of the
package is to provide a solution for the analysis of
complex wild pedigree data and to help the user to gain insights
into genetic relationships within wild animal populations.
Author: Tomaz Skrbinsek [aut],
Gregor Simcic [aut, cre]
Maintainer: Gregor Simcic <grega0simcic@gmail.com>
Diff between wpeR versions 0.1.0 dated 2025-07-14 and 0.2.0 dated 2026-06-11
DESCRIPTION | 8 MD5 | 64 +- NAMESPACE | 1 NEWS.md | 17 R/anim_timespan.R | 36 - R/check_sampledata.R | 41 + R/data.R | 7 R/org_fams.R | 17 R/ped_satplot.R | 49 +- R/ped_spatial.R | 16 R/plot_table.R | 158 ++++--- R/pps_subfunctions.R | 265 +++++------ README.md | 15 build/vignette.rds |binary data/wolf_samples.rda |binary inst/doc/wpeR.R | 123 +++-- inst/doc/wpeR.Rmd | 133 ++++- inst/doc/wpeR.html | 738 +++++++++++++++++---------------- man/anim_timespan.Rd | 21 man/check_sampledata.Rd | 24 - man/org_fams.Rd | 13 man/ped_satplot.Rd | 30 - man/ped_spatial.Rd | 10 man/plot_table.Rd | 61 +- man/wolf_samples.Rd | 5 tests/testthat/test-anim_timespan.R | 10 tests/testthat/test-check_sampledata.R | 47 ++ tests/testthat/test-org_fams.R | 3 tests/testthat/test-ped_satplot.R | 10 tests/testthat/test-ped_spatial.R | 10 tests/testthat/test-plot_table.R | 29 - tests/testthat/test-pps_subfunctions.R | 10 vignettes/wpeR.Rmd | 133 ++++- 33 files changed, 1275 insertions(+), 829 deletions(-)
Title: Interactive Tabular Matrix Problems via Pseudoinverse Estimation
Description: Provides an interactive wrapper for the 'tmpinv()' function from
the 'rtmpinv' package with options extending its functionality to pre-
and post-estimation processing and streamlined incorporation of prior cell
information. The Tabular Matrix Problems via Pseudoinverse Estimation
(TMPinv) is a two-stage estimation method that reformulates structured
table-based systems - such as allocation problems, transaction matrices,
and input-output tables - as structured least-squares problems. Based
on the Convex Least Squares Programming (CLSP) framework, TMPinv solves
systems with row and column constraints, block structure, and optionally
reduced dimensionality by (1) constructing a canonical constraint form
and applying a pseudoinverse-based projection, followed by (2) a
convex-programming refinement stage to improve fit, coherence, and
regularization (e.g., via Lasso, Ridge, or Elastic Net).
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rtmpinvi versions 1.1.0 dated 2026-06-07 and 2.0.0 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 11 insertions(+), 6 deletions(-)
Title: Linear Programming via Regularized Least Squares
Description: The Linear Programming via Regularized Least Squares (LPPinv) is a
two-stage estimation method that reformulates linear programs as
structured least-squares problems. Based on the Convex Least
Squares Programming (CLSP) framework, LPPinv solves linear
inequality, equality, and bound constraints by (1) constructing a
canonical constraint system and computing a pseudoinverse
projection, followed by (2) a convex-programming correction stage
to refine the solution under additional regularization (e.g.,
Lasso, Ridge, or Elastic Net). LPPinv is intended for
underdetermined and ill-posed linear problems, for which standard
solvers fail.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rlppinv versions 1.1.0 dated 2026-06-07 and 2.0.0 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 8 +++++++- 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Assessing Package Risk Metrics
Description: A reliable and validated tool that captures detailed risk metrics
such as R 'CMD' check, test coverage, traceability matrix, documentation, dependencies,
reverse dependencies, suggested dependency analysis, repository data,
and enhanced reporting for R packages that are local or stored
on remote repositories such as GitHub, CRAN, and Bioconductor.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between risk.assessr versions 3.1.1 dated 2026-04-08 and 4.1.0 dated 2026-06-11
risk.assessr-3.1.1/risk.assessr/R/get_tests_long_sum_stf.R |only risk.assessr-3.1.1/risk.assessr/R/get_tests_skip_stf.R |only risk.assessr-3.1.1/risk.assessr/R/map_tests_stf.R |only risk.assessr-3.1.1/risk.assessr/R/run_covr_modes.R |only risk.assessr-3.1.1/risk.assessr/R/run_covr_skip_nstf.R |only risk.assessr-3.1.1/risk.assessr/R/run_covr_skip_stf.R |only risk.assessr-3.1.1/risk.assessr/R/unittest_methods.R |only risk.assessr-3.1.1/risk.assessr/man/check_covr_skip_nstf.Rd |only risk.assessr-3.1.1/risk.assessr/man/check_pkg_tests_and_snaps.Rd |only risk.assessr-3.1.1/risk.assessr/man/cleanup_and_return_null.Rd |only risk.assessr-3.1.1/risk.assessr/man/coverage_skip.Rd |only risk.assessr-3.1.1/risk.assessr/man/create_covr_list_no_skip.Rd |only risk.assessr-3.1.1/risk.assessr/man/create_results_summary.Rd |only risk.assessr-3.1.1/risk.assessr/man/filter_symbol_functions.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_expect.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_function_no_tests.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_source_test_mapping_nstf.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_test_path.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_tests_long_sum_stf.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_tests_skip_stf.Rd |only risk.assessr-3.1.1/risk.assessr/man/get_toplevel_assignments.Rd |only risk.assessr-3.1.1/risk.assessr/man/load_package_datasets.Rd |only risk.assessr-3.1.1/risk.assessr/man/map_functions_to_docs.Rd |only risk.assessr-3.1.1/risk.assessr/man/map_functions_to_scripts.Rd |only risk.assessr-3.1.1/risk.assessr/man/map_test.Rd |only risk.assessr-3.1.1/risk.assessr/man/map_testthat.Rd |only risk.assessr-3.1.1/risk.assessr/man/nest_expect.Rd |only risk.assessr-3.1.1/risk.assessr/man/nest_test.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_coverage.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_covr.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_covr_modes.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_covr_safe_stf.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_covr_skip_nstf.Rd |only risk.assessr-3.1.1/risk.assessr/man/run_covr_skip_stf.Rd |only risk.assessr-3.1.1/risk.assessr/man/unrowname.Rd |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-get_tests_long_sum_stf.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-get_tests_skip_stf.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-get_toplevel_assignments.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-map_functions_to_scripts.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-map_tests_stf.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-run_coverage.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-run_covr.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-run_covr_modes.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-run_covr_skip_nstf.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-run_covr_skip_stf.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test-unittest_methods.R |only risk.assessr-3.1.1/risk.assessr/tests/testthat/test_get_package_tarfile.R |only risk.assessr-4.1.0/risk.assessr/DESCRIPTION | 26 risk.assessr-4.1.0/risk.assessr/MD5 | 187 - 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Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Rebecca Kuiper [aut],
Yves Rosseel [ctb],
Aleksandra Dacko [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>
Diff between restriktor versions 0.6-30 dated 2026-02-05 and 0.6-50 dated 2026-06-11
DESCRIPTION | 7 MD5 | 55 +-- NAMESPACE | 7 R/compute_chiBarSquare_weights.R | 113 +++--- R/conLM.R | 4 R/con_constraints.R | 14 R/con_loglik.R | 6 R/con_pvalue.R | 2 R/ext_ic_infer.R | 172 +++++++--- R/goric.R | 76 ++++ R/goric_benchmark.R | 1 R/goric_benchmark_plot.R | 38 -- R/goric_benchmark_print.R | 4 R/goric_evSyn.R | 338 +++++++++++++------ R/goric_evSyn_leave1studyout.R |only R/goric_evSyn_plot.R | 80 +++- R/goric_evSyn_print.R | 51 +- R/goric_evSyn_summary.R | 200 ++++++----- R/goric_evSyn_utilities.R | 33 + R/goric_print.R | 8 R/goric_utilities.R | 2 R/utilities.R | 20 - inst/doc/Guidelines_GORIC-benchmarks.html | 411 ++++++++++++------------ inst/doc/Guidelines_GORIC_output.html | 49 +- inst/doc/Tutorial_GORICA_restriktor_lavaan.html | 23 - inst/doc/Tutorial_GORIC_restriktor_evSyn.html | 59 ++- man/evSyn.Rd | 108 +++++- man/goric.Rd | 8 man/restriktor-package.rd | 4 29 files changed, 1173 insertions(+), 720 deletions(-)
Title: Conservation Planning Datasets
Description: Conservation planning datasets for learning how to use the
'prioritizr' package <https://CRAN.R-project.org/package=prioritizr>.
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Kristine Camille V Buenafe [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph R Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizrdata versions 0.3.2 dated 2023-04-06 and 0.3.3 dated 2026-06-11
DESCRIPTION | 31 - MD5 | 42 + NAMESPACE | 27 - R/deprecated.R |only R/package.R | 65 +- R/salt_data.R | 232 +++++----- R/tas_data.R | 282 ++++++------ R/wa_data.R | 376 ++++++++++------- README.md | 130 ++--- build/partial.rdb |binary inst/extdata/wa_attr_data.rds |only inst/extdata/wa_carbon.tif |only inst/extdata/wa_features_names.txt | 792 ++++++++++++++++++------------------ inst/scripts |only man/prioritizrdata-deprecated.Rd |only man/prioritizrdata.Rd | 87 ++- man/salt_data.Rd | 194 ++++---- man/tas_data.Rd | 168 +++---- man/wa_data.Rd | 306 ++++++++----- tests/testthat.R | 6 tests/testthat/helper_nonNA_cells.R | 6 tests/testthat/test_deprecated.R |only tests/testthat/test_salt_data.R | 82 +-- tests/testthat/test_tas_data.R | 44 +- tests/testthat/test_wa_data.R | 179 ++++---- 25 files changed, 1636 insertions(+), 1413 deletions(-)
More information about prioritizrdata at CRAN
Permanent link
Title: Test for Discretized Normality in Ordinal Data
Description: Tests whether multivariate ordinal data may stem from discretizing a multivariate normal distribution.
The test is described by Foldnes and Grønneberg (2019) <doi:10.1080/10705511.2019.1673168>.
In addition, an adjusted polychoric correlation estimator is provided that takes marginal knowledge into account,
as described by Grønneberg and Foldnes (2022) <doi:10.1037/met0000495>.
Author: Njal Foldnes [aut, cre],
Steffen Groenneberg [aut]
Maintainer: Njal Foldnes <njal.foldnes@gmail.com>
Diff between discnorm versions 0.2.1 dated 2022-05-25 and 0.2.2 dated 2026-06-11
DESCRIPTION | 11 +- MD5 | 25 +++--- NEWS.md | 24 +++++- R/bootTest.R | 20 +++-- R/catLSadj.R | 48 +++++++----- R/computeT.R | 2 R/pc_th.R | 2 build/vignette.rds |binary inst/CITATION | 43 +++++++---- inst/doc/discnormvignette.R | 2 inst/doc/discnormvignette.html | 156 +++++++++++++++++++++-------------------- tests |only 12 files changed, 197 insertions(+), 136 deletions(-)
Title: Tabular Matrix Problems via Pseudoinverse Estimation
Description: The Tabular Matrix Problems via Pseudoinverse Estimation (TMPinv)
is a two-stage estimation method that reformulates structured table-based
systems - such as allocation problems, transaction matrices, and
input-output tables - as structured least-squares problems. Based on the
Convex Least Squares Programming (CLSP) framework, TMPinv solves systems
with row and column constraints, block structure, and optionally reduced
dimensionality by (1) constructing a canonical constraint form and applying
a pseudoinverse-based projection, followed by (2) a convex-programming
refinement stage to improve fit, coherence, and regularization (e.g., via
Lasso, Ridge, or Elastic Net).
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rtmpinv versions 1.1.0 dated 2026-06-07 and 2.0.0 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 11 insertions(+), 6 deletions(-)
Title: A Modular Two-Step Convex Optimization Estimator for Ill-Posed
Problems
Description: Convex Least Squares Programming (CLSP) is a two-step estimator
for solving underdetermined, ill-posed, or structurally constrained
least-squares problems. It combines pseudoinverse-based estimation with
convex-programming correction methods inspired by Lasso, Ridge, and
Elastic Net to ensure numerical stability, constraint enforcement, and
interpretability. The package also provides numerical stability analysis
and CLSP-specific diagnostics, including partial R^2, normalized RMSE
(NRMSE), Monte Carlo t-tests for mean NRMSE, and condition-number-based
confidence bands.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rclsp versions 2.0.0 dated 2026-06-08 and 2.0.1 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Prepare and Explore Data for Palaeobiological Analyses
Description: Provides functionality to support data preparation and exploration for
palaeobiological analyses, improving code reproducibility and accessibility. The
wider aim of 'palaeoverse' is to bring the palaeobiological community together
to establish agreed standards. The package currently includes functionality for
data cleaning, binning (time and space), exploration, summarisation and
visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart/>)
and auxiliary functions are also provided. Details can be found in:
Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.
Author: Lewis A. Jones [aut, cre] ,
William Gearty [aut] ,
Bethany J. Allen [aut] ,
Kilian Eichenseer [aut] ,
Christopher D. Dean [aut] ,
Etienne Bacher [aut] ,
Joseph T. Flannery-Sutherland [aut] ,
Sofia Galvan [ctb] ,
Miranta Kouvari [ctb] ,
Pedro L. Godoy [...truncated...]
Maintainer: Lewis A. Jones <LewisA.Jones@outlook.com>
Diff between palaeoverse versions 1.4.0 dated 2024-10-14 and 1.5.0 dated 2026-06-11
DESCRIPTION | 64 MD5 | 196 NAMESPACE | 11 NEWS.md | 129 R/axis_geo.R | 736 R/bin_lat.R | 38 R/bin_space.R | 127 R/bin_time.R | 538 R/data.R | 6 R/group_apply.R | 110 R/lat_bins_area.R | 43 R/lat_bins_degrees.R | 62 R/look_up.R | 317 R/palaeorotate.R | 216 R/phylo_check.R | 50 R/release.R | 1 R/tax_certainty.R |only R/tax_check.R | 151 R/tax_expand_lat.R | 22 R/tax_expand_time.R | 39 R/tax_range_space.R | 106 R/tax_range_strat.R | 342 R/tax_range_time.R | 316 R/tax_unique.R | 122 R/time_bins.R | 378 README.md | 212 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 18 inst/WORDLIST |only inst/doc/phanerozoic-reefs.Rmd | 4 inst/doc/phanerozoic-reefs.html | 15 inst/doc/structure-and-standards.R | 146 inst/doc/structure-and-standards.Rmd | 6 inst/doc/structure-and-standards.html | 15 inst/doc/tetrapod-biodiversity.Rmd | 32 inst/doc/tetrapod-biodiversity.html | 41 man/GTS2012.Rd | 2 man/GTS2020.Rd | 2 man/axis_geo.Rd | 64 man/group_apply.Rd | 16 man/interval_key.Rd | 2 man/palaeoverse-package.Rd | 10 man/phylo_check.Rd | 2 man/tax_certainty.Rd |only man/tax_range_strat.Rd | 22 man/tax_range_time.Rd | 20 man/time_bins.Rd | 27 tests/testthat.R | 8 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/axis_geo.md |only tests/testthat/_snaps/axis_geo/axis-geo-on-multiple-sides.svg | 306 tests/testthat/_snaps/axis_geo/axis-geo-with-autofit.svg |only tests/testthat/_snaps/axis_geo/axis-geo-with-autofit2.svg |only tests/testthat/_snaps/axis_geo/axis-geo-with-backwards-ultrametric-tree.svg | 63 tests/testthat/_snaps/axis_geo/axis-geo-with-downwards-fossil-tree.svg | 69 tests/testthat/_snaps/axis_geo/axis-geo-with-fossil-tree.svg | 69 tests/testthat/_snaps/axis_geo/axis-geo-with-multiple-scales.svg | 20 tests/testthat/_snaps/axis_geo/axis-geo-with-negative-axis.svg |only tests/testthat/_snaps/axis_geo/axis-geo-with-time-bins-scale.svg | 8814 +++++----- tests/testthat/_snaps/axis_geo/axis-geo-with-title.svg |only tests/testthat/_snaps/axis_geo/axis-geo-with-ultrametric-tree.svg | 60 tests/testthat/_snaps/axis_geo/axis-geo.svg | 20 tests/testthat/_snaps/bin_lat.md |only tests/testthat/_snaps/bin_space.md |only tests/testthat/_snaps/bin_time.md |only tests/testthat/_snaps/group_apply.md |only tests/testthat/_snaps/lat_bins_area.md |only tests/testthat/_snaps/lat_bins_degrees.md |only tests/testthat/_snaps/look_up.md |only tests/testthat/_snaps/palaeorotate.md |only tests/testthat/_snaps/phylo_check.md |only tests/testthat/_snaps/tax_check.md |only tests/testthat/_snaps/tax_expand_lat.md |only tests/testthat/_snaps/tax_expand_time.md |only tests/testthat/_snaps/tax_range_space.md |only tests/testthat/_snaps/tax_range_strat.md |only tests/testthat/_snaps/tax_range_strat/tax-range-strat-does-uncertainty.svg | 52 tests/testthat/_snaps/tax_range_strat/tax-range-strat-labels.svg | 44 tests/testthat/_snaps/tax_range_strat/tax-range-strat-plots-groups.svg |only tests/testthat/_snaps/tax_range_strat/tax-range-strat-plots.svg | 44 tests/testthat/_snaps/tax_range_strat/tax-range-strat-sorts.svg | 44 tests/testthat/_snaps/tax_range_strat/tax-range-strat-stops-some-plot-args.svg |only tests/testthat/_snaps/tax_range_time.md |only tests/testthat/_snaps/tax_unique.md |only tests/testthat/_snaps/time_bins.md |only tests/testthat/helper-vdiffr.R | 6 tests/testthat/setup-data.R | 8 tests/testthat/test-axis_geo.R | 253 tests/testthat/test-bin_lat.R | 80 tests/testthat/test-bin_space.R | 118 tests/testthat/test-bin_time.R | 239 tests/testthat/test-group_apply.R | 191 tests/testthat/test-lat_bins_area.R | 17 tests/testthat/test-lat_bins_degrees.R | 16 tests/testthat/test-look_up.R | 159 tests/testthat/test-palaeorotate.R | 206 tests/testthat/test-phylo_check.R | 41 tests/testthat/test-tax_certainty.R |only tests/testthat/test-tax_check.R | 77 tests/testthat/test-tax_expand_lat.R | 108 tests/testthat/test-tax_expand_time.R | 120 tests/testthat/test-tax_range_space.R | 141 tests/testthat/test-tax_range_strat.R | 204 tests/testthat/test-tax_range_time.R | 42 tests/testthat/test-tax_unique.R | 432 tests/testthat/test-time_bins.R | 283 vignettes/alpha-div-plot-2-1.png |binary vignettes/phanerozoic-reefs.Rmd | 4 vignettes/source/_phanerozoic-reefs.Rmd | 2 vignettes/source/_tetrapod-biodiversity.Rmd | 14 vignettes/structure-and-standards.Rmd | 6 vignettes/tetrapod-biodiversity.Rmd | 32 113 files changed, 9698 insertions(+), 7490 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.7.0 dated 2026-06-10 and 1.7.1 dated 2026-06-11
DESCRIPTION | 6 +-- MD5 | 23 ++++++------ NEWS.md | 8 ++++ R/Learner.R | 11 +++-- R/LearnerClassif.R | 19 ++++++++- R/LearnerRegr.R | 16 +++++++- man/benchmark.Rd | 4 +- man/figures/block.png |only man/figures/block.svg |only man/figures/mlr3verse.svg |only man/resample.Rd | 4 +- tests/testthat/test_Learner.R | 28 ++++++++++++++ tests/testthat/test_LearnerClassif.R | 67 +++++++++++++++++++++++++++++++++++ tests/testthat/test_LearnerRegr.R | 48 +++++++++++++++++++++++++ 14 files changed, 208 insertions(+), 26 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.15 dated 2026-04-29 and 1.3.16 dated 2026-06-11
DESCRIPTION | 8 MD5 | 46 +-- R/MAplotW.R | 131 +++++---- R/VolcanoPlotW.R | 552 ++++++++++++++--------------------------- R/addBagPlot.R | 70 ++--- R/cumFrqPlot.R | 12 R/foldChangeArrow.R | 13 R/legendHist.R | 8 R/mouseOverHtmlFile.R | 43 +-- R/plotPCAw.R | 110 +++++--- R/profileAsClu.R | 28 +- build/vignette.rds |binary inst/doc/wrGraphVignette1.R | 6 inst/doc/wrGraphVignette1.Rmd | 41 +-- inst/doc/wrGraphVignette1.html | 163 ++++++------ man/MAplotW.Rd | 11 man/VolcanoPlotW.Rd | 36 +- man/addBagPlot.Rd | 39 +- man/cumFrqPlot.Rd | 13 man/foldChangeArrow.Rd | 2 man/mouseOverHtmlFile.Rd | 10 man/plotPCAw.Rd | 29 +- man/profileAsClu.Rd | 10 vignettes/wrGraphVignette1.Rmd | 41 +-- 24 files changed, 671 insertions(+), 751 deletions(-)
Title: Read and Play Digital Music (MIDI)
Description: Bindings to 'libfluidsynth' to parse and synthesize MIDI files. It can
read MIDI into a data frame, play it on the local audio device, or convert into
an audio file.
Author: Jeroen Ooms [aut, cre] ,
S. Christian Collins [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between fluidsynth versions 1.0.2 dated 2024-10-04 and 1.0.3 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 6 ++++++ src/init.c | 14 ++++++++++++-- 4 files changed, 25 insertions(+), 9 deletions(-)
Title: Client for Central Bank APIs
Description: A client for retrieving data and metadata from central bank
APIs including 'Banco de España' (BdE), 'Banco de Portugal' (BdP),
'Bank for International Settlements' (BIS), 'Bank of Canada' (BoC),
'Bank of England' (BoE), 'Bank of Japan' (BoJ), 'Banque de France'
(BdF), 'Czech National Bank' (CNB), 'Deutsche Bundesbank' (BBk),
'European Central Bank' (ECB), 'National Bank of Poland' (NBP),
'Norges Bank' (NoB), 'Oesterreichische Nationalbank' (OeNB), 'Sveriges
Riksbank' (SRb), and 'Swiss National Bank' (SNB).
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between bbk versions 0.10.0 dated 2026-05-16 and 0.11.0 dated 2026-06-11
DESCRIPTION | 17 +- MD5 | 188 +++++++++++++----------- NAMESPACE | 12 + NEWS.md | 22 ++ R/assertions.R | 18 +- R/bbk-package.R | 4 R/bbk.R | 150 +++++++++---------- R/bde.R | 51 +++--- R/bdf.R | 133 ++++++++++------- R/bdp.R | 114 +++++++------- R/bis.R | 68 ++++---- R/boc.R | 94 ++++++------ R/boe.R | 38 ++-- R/boj.R | 93 ++++++----- R/cache.R | 12 - R/cnb.R |only R/ecb.R | 84 +++++----- R/fx-rates.R | 34 ++-- R/nbp.R | 60 +++---- R/nob.R | 68 ++++---- R/onb.R | 109 +++++++------ R/purrr.R | 14 - R/sdmx.R | 28 ++- R/snb.R | 195 ++++++++++++++++++++----- R/srb.R | 88 +++++------ R/utils.R | 46 +++++ README.md | 10 - man/bbk-package.Rd | 2 man/bbk_data.Rd | 15 + man/bbk_dimension.Rd | 7 man/bbk_metadata.Rd | 7 man/bbk_series.Rd | 5 man/bde_data.Rd | 5 man/bde_latest.Rd | 5 man/bdf_codelist.Rd | 5 man/bdf_data.Rd | 5 man/bdf_dataset.Rd | 5 man/bdf_dimension.Rd |only man/bdp_data.Rd | 5 man/bdp_dataset.Rd | 7 man/bdp_dimension.Rd | 7 man/bdp_domain.Rd | 7 man/bdp_series.Rd | 7 man/bis_data.Rd | 5 man/bis_dimension.Rd | 7 man/bis_metadata.Rd | 7 man/boc_catalog.Rd | 4 man/boc_data.Rd | 9 - man/boe_data.Rd | 5 man/boj_data.Rd | 5 man/boj_metadata.Rd | 7 man/cnb_czeonia.Rd |only man/cnb_data.Rd |only man/cnb_dimension.Rd |only man/cnb_fx_other_rates.Rd |only man/cnb_fx_rates.Rd |only man/cnb_indicators.Rd |only man/cnb_pribor.Rd |only man/cnb_snapshots.Rd |only man/cnb_tree.Rd |only man/ecb_data.Rd | 5 man/ecb_dimension.Rd | 7 man/ecb_metadata.Rd | 7 man/figures/README-plotting-1.png |binary man/nbp_fx_rates.Rd | 5 man/nbp_gold.Rd | 5 man/nob_data.Rd | 5 man/nob_dimension.Rd | 7 man/nob_metadata.Rd | 7 man/onb_data.Rd | 5 man/onb_dimension.Rd | 7 man/onb_frequency.Rd | 7 man/onb_hierarchy.Rd | 7 man/onb_metadata.Rd | 7 man/onb_toc.Rd | 7 man/snb_data.Rd | 5 man/snb_dimension.Rd | 7 man/snb_metadata.Rd |only man/snb_toc.Rd |only man/srb_calendar.Rd | 7 man/srb_cross_rates.Rd | 5 man/srb_data.Rd | 5 man/srb_series.Rd | 7 tests/testthat/fixtures/bdf-dimension.rds |only tests/testthat/fixtures/cnb-arad-data.rds |only tests/testthat/fixtures/cnb-arad-dimension.rds |only tests/testthat/fixtures/cnb-fx-rates.rds |only tests/testthat/fixtures/cnb-pribor.rds |only tests/testthat/fixtures/snb-metadata.rds |only tests/testthat/fixtures/snb-toc.rds |only tests/testthat/test-bbk.R | 41 ++++- tests/testthat/test-bde.R | 12 - tests/testthat/test-bdf.R |only tests/testthat/test-bdp.R | 41 +++-- tests/testthat/test-bis.R | 36 +++- tests/testthat/test-boc.R |only tests/testthat/test-boe.R | 4 tests/testthat/test-boj.R | 22 +- tests/testthat/test-cnb.R |only tests/testthat/test-ecb.R | 32 +++- tests/testthat/test-exchange-rates.R | 4 tests/testthat/test-nbp.R | 16 +- tests/testthat/test-nob.R | 10 - tests/testthat/test-onb.R |only tests/testthat/test-sdmx.R | 19 ++ tests/testthat/test-snb.R | 61 +++++++ tests/testthat/test-srb.R | 22 +- 107 files changed, 1504 insertions(+), 833 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.1 dated 2026-06-04 and 1.5.2 dated 2026-06-11
DESCRIPTION | 8 ++-- MD5 | 26 ++++++------- NEWS | 6 +++ R/do_add_adv_stats.R | 14 ++++--- R/do_stats.R | 84 ++++++++++++++++++++++++++++++++---------- R/get_donut_usage.R | 15 +++++-- R/get_donut_usage_action.R | 4 +- R/get_net_rtg_on_off.R | 20 ++++++++-- inst/doc/BAwiR.html | 4 +- inst/doc/BAwiR_pbp.html | 4 +- inst/doc/BAwiR_sc.html | 4 +- man/get_donut_usage.Rd | 8 +++- man/get_donut_usage_action.Rd | 2 - man/get_net_rtg_on_off.Rd | 1 14 files changed, 139 insertions(+), 61 deletions(-)
Title: A 'shiny' Package for Data Analysis
Description: Provides a 'shiny' application with a user-friendly interface
for interactive data analysis. It supports exploratory data analysis
through descriptive statistics, data visualization, statistical
tests (e.g., normality assessment), linear modeling, data
import, transformation and reporting. For more details see Shapiro and Wilk
(1965) <doi:10.2307/2333709>.
Author: Luis Gustavo Schuck [aut, cre]
Maintainer: Luis Gustavo Schuck <luisgustavoschuck@yahoo.com.br>
Diff between spada versions 0.1.5 dated 2026-04-21 and 0.1.6 dated 2026-06-11
spada-0.1.5/spada/man/figures/articles |only spada-0.1.5/spada/man/figures/install_release.png |only spada-0.1.5/spada/man/figures/install_release_old.png |only spada-0.1.5/spada/man/figures/spada_loading.png |only spada-0.1.5/spada/man/figures/spada_logo.png |only spada-0.1.6/spada/DESCRIPTION | 21 spada-0.1.6/spada/MD5 | 148 ++-- spada-0.1.6/spada/NAMESPACE | 20 spada-0.1.6/spada/NEWS.md | 64 + spada-0.1.6/spada/R/about_spada_module.R | 8 spada-0.1.6/spada/R/calculate_cols_module.R | 16 spada-0.1.6/spada/R/config_module.R | 23 spada-0.1.6/spada/R/convert_cols_module.R | 42 - spada-0.1.6/spada/R/cor_matrix_module.R |only spada-0.1.6/spada/R/correlation_module.R | 35 spada-0.1.6/spada/R/data_highlights_module.R | 1 spada-0.1.6/spada/R/data_module.R | 11 spada-0.1.6/spada/R/duplicates_module.R |only spada-0.1.6/spada/R/exploratory_module.R | 14 spada-0.1.6/spada/R/export_file_module.R | 42 - spada-0.1.6/spada/R/filter_rows_module.R | 57 - spada-0.1.6/spada/R/frequencies_module.R |only spada-0.1.6/spada/R/groupby_module.R | 23 spada-0.1.6/spada/R/import_file_module.R | 7 spada-0.1.6/spada/R/insert_output_module.R | 21 spada-0.1.6/spada/R/join_module.R | 6 spada-0.1.6/spada/R/lm_module.R | 7 spada-0.1.6/spada/R/navbar_df_info_module.R | 3 spada-0.1.6/spada/R/normality_test_module.R | 90 -- spada-0.1.6/spada/R/order_cols_module.R | 2 spada-0.1.6/spada/R/order_rows_module.R | 2 spada-0.1.6/spada/R/output_module.R | 77 +- spada-0.1.6/spada/R/rename_cols_module.R | 10 spada-0.1.6/spada/R/restore_session_module.R | 14 spada-0.1.6/spada/R/sidebar_module.R | 78 +- spada-0.1.6/spada/R/spada.R | 55 - spada-0.1.6/spada/R/spada_server.R | 40 - spada-0.1.6/spada/R/spada_themes.R | 123 ++- spada-0.1.6/spada/R/spada_ui.R | 9 spada-0.1.6/spada/R/stats_table_module.R | 18 spada-0.1.6/spada/R/summarise_module.R | 7 spada-0.1.6/spada/R/table_values_module.R | 98 +- spada-0.1.6/spada/R/utils.R | 370 ++++++++-- spada-0.1.6/spada/R/z_test_module.R | 53 - spada-0.1.6/spada/R/zzz.R | 52 - spada-0.1.6/spada/README.md | 94 +- spada-0.1.6/spada/inst/doc/spada.Rmd | 22 spada-0.1.6/spada/inst/doc/spada.html | 63 + spada-0.1.6/spada/inst/www |only spada-0.1.6/spada/man/figures/data.png |only spada-0.1.6/spada/man/figures/export.png |only spada-0.1.6/spada/man/figures/highlights.png |only spada-0.1.6/spada/man/figures/import.png |only spada-0.1.6/spada/man/figures/logo.png |binary spada-0.1.6/spada/man/figures/metadata.png |only spada-0.1.6/spada/man/figures/navbar_active_dataset.png |only spada-0.1.6/spada/man/figures/overview.png |only spada-0.1.6/spada/man/spada.Rd | 2 spada-0.1.6/spada/tests/testthat/test-about_spada_module.R | 2 spada-0.1.6/spada/tests/testthat/test-calculate_cols_module.R | 9 spada-0.1.6/spada/tests/testthat/test-config_module.R | 24 spada-0.1.6/spada/tests/testthat/test-convert_cols_module.R | 46 - spada-0.1.6/spada/tests/testthat/test-cor_matrix_module.R |only spada-0.1.6/spada/tests/testthat/test-data_module.R | 27 spada-0.1.6/spada/tests/testthat/test-duplicates_module.R |only spada-0.1.6/spada/tests/testthat/test-export_file_module.R | 61 + spada-0.1.6/spada/tests/testthat/test-filter_rows_module.R | 18 spada-0.1.6/spada/tests/testthat/test-frequencies_module.R |only spada-0.1.6/spada/tests/testthat/test-join_module.R | 2 spada-0.1.6/spada/tests/testthat/test-navbar_df_info_module.R | 20 spada-0.1.6/spada/tests/testthat/test-order_cols_module.R | 2 spada-0.1.6/spada/tests/testthat/test-order_rows_module.R | 2 spada-0.1.6/spada/tests/testthat/test-output_module.R | 9 spada-0.1.6/spada/tests/testthat/test-restore_session_module.R | 2 spada-0.1.6/spada/tests/testthat/test-sidebar_module.R | 34 spada-0.1.6/spada/tests/testthat/test-table_values_module.R | 10 spada-0.1.6/spada/tests/testthat/test-utils.R | 11 spada-0.1.6/spada/vignettes/spada.Rmd | 22 78 files changed, 1389 insertions(+), 760 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.3.0 dated 2026-03-01 and 0.4.0 dated 2026-06-11
mlr3cluster-0.3.0/mlr3cluster/R/MeasureClustInternal.R |only mlr3cluster-0.4.0/mlr3cluster/DESCRIPTION | 38 - mlr3cluster-0.4.0/mlr3cluster/MD5 | 230 +++--- mlr3cluster-0.4.0/mlr3cluster/NAMESPACE | 9 mlr3cluster-0.4.0/mlr3cluster/NEWS.md | 42 + mlr3cluster-0.4.0/mlr3cluster/R/LearnerClust.R | 18 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustAffinityPropagation.R | 24 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustAgnes.R | 33 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustBICO.R | 3 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustBIRCH.R | 3 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustCLARA.R | 19 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustCMeans.R | 31 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustCobweb.R | 10 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustDBSCAN.R | 5 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustDBSCANfpc.R | 9 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustDiana.R | 38 - mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustEM.R | 13 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustFanny.R | 26 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustFarthestFirst.R | 11 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustFeatureless.R | 25 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustFlexmix.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustGenie.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustHDBSCAN.R | 8 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustHclust.R | 16 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustKCCA.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustKKMeans.R | 48 - mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustKMeans.R | 15 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustKProto.R | 20 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustMclust.R | 16 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustMeanShift.R | 16 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustMiniBatchKMeans.R | 29 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustMovMF.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustOPTICS.R | 5 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustPAM.R | 31 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustProtoclust.R | 18 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustSKMeans.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustSOM.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustSTDBSCAN.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustSimpleKMeans.R | 11 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustSpectral.R | 19 mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustTclust.R |only mlr3cluster-0.4.0/mlr3cluster/R/LearnerClustXMeans.R | 11 mlr3cluster-0.4.0/mlr3cluster/R/MeasureClust.R | 5 mlr3cluster-0.4.0/mlr3cluster/R/MeasureClustSimple.R |only mlr3cluster-0.4.0/mlr3cluster/R/PredictionClust.R | 5 mlr3cluster-0.4.0/mlr3cluster/R/PredictionDataClust.R | 8 mlr3cluster-0.4.0/mlr3cluster/R/TaskClust.R | 3 mlr3cluster-0.4.0/mlr3cluster/R/as_prediction_clust.R | 15 mlr3cluster-0.4.0/mlr3cluster/R/as_task_clust.R | 8 mlr3cluster-0.4.0/mlr3cluster/R/bibentries.R | 338 ++++++++-- mlr3cluster-0.4.0/mlr3cluster/R/cluster_stats.R |only mlr3cluster-0.4.0/mlr3cluster/R/helper.R | 19 mlr3cluster-0.4.0/mlr3cluster/R/measures.R | 22 mlr3cluster-0.4.0/mlr3cluster/R/zzz.R | 44 - mlr3cluster-0.4.0/mlr3cluster/README.md | 5 mlr3cluster-0.4.0/mlr3cluster/build/partial.rdb |binary mlr3cluster-0.4.0/mlr3cluster/man/LearnerClust.Rd | 165 ++-- mlr3cluster-0.4.0/mlr3cluster/man/MeasureClust.Rd | 107 +-- mlr3cluster-0.4.0/mlr3cluster/man/PredictionClust.Rd | 110 +-- mlr3cluster-0.4.0/mlr3cluster/man/TaskClust.Rd | 119 +-- mlr3cluster-0.4.0/mlr3cluster/man/mlr3cluster-package.Rd | 1 mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.MBatchKMeans.Rd | 103 +-- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.SimpleKMeans.Rd | 98 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.agnes.Rd | 120 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.ap.Rd | 114 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.bico.Rd | 93 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.birch.Rd | 93 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.clara.Rd | 113 +-- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.cmeans.Rd | 99 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.cobweb.Rd | 98 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.dbscan.Rd | 93 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.dbscan_fpc.Rd | 93 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.diana.Rd | 121 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.em.Rd | 96 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.fanny.Rd | 120 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.featureless.Rd | 96 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.ff.Rd | 98 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.flexmix.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.genie.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.hclust.Rd | 95 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.hdbscan.Rd | 96 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.kcca.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.kkmeans.Rd | 101 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.kmeans.Rd | 99 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.kproto.Rd | 116 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.mclust.Rd | 114 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.meanshift.Rd | 108 +-- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.movMF.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.optics.Rd | 93 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.pam.Rd | 119 ++- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.protoclust.Rd | 99 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.skmeans.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.som.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.specc.Rd | 101 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.stdbscan.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.tclust.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_learners_clust.xmeans.Rd | 100 +- mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.avg_between.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.avg_within.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.ch.Rd | 39 - mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.davies_bouldin.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.dunn.Rd | 43 - mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.dunn2.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.entropy.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.pearsongamma.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.silhouette.Rd | 45 + mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.wb_ratio.Rd |only mlr3cluster-0.4.0/mlr3cluster/man/mlr_measures_clust.wss.Rd | 34 - mlr3cluster-0.4.0/mlr3cluster/man/mlr_tasks_ruspini.Rd | 4 mlr3cluster-0.4.0/mlr3cluster/man/mlr_tasks_usarrests.Rd | 4 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/_snaps |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/helper.R | 15 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/helper_expectations.R | 6 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_LearnerClust.R | 9 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_MeasureClust.R | 59 + mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_PredictionClust.R | 28 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_cluster_stats.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_cmeans.R | 1 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan.R | 2 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan_fpc.R | 2 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_featureless.R | 9 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_flexmix.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_genie.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kcca.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kkmeans.R | 3 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmeans.R | 1 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_kproto.R | 2 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_movMF.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_optics.R | 2 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_skmeans.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_som.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_spectral.R | 2 mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_stdbscan.R |only mlr3cluster-0.4.0/mlr3cluster/tests/testthat/test_mlr_learners_clust_tclust.R |only 134 files changed, 3092 insertions(+), 1931 deletions(-)
Title: Calculate Urinary Saturation with the EQUIL2 Algorithm
Description: Saturation of ionic substances in urine is calculated based on
sodium, potassium, calcium, magnesium, ammonia, chloride, phosphate, sulfate,
oxalate, citrate, ph, and urate. This program is intended for research use,
only. The code within is translated from EQUIL2 Visual Basic code based on
Werness, et al (1985) "EQUIL2: a BASIC computer program for the calculation
of urinary saturation" <doi:10.1016/s0022-5347(17)47703-2> to R. The Visual
Basic code was kindly provided by Dr. John Lieske of the Mayo Clinic.
Author: Bill Denney [aut, cre, cph] ,
John Lieske [cph]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between equil2 versions 1.0.0 dated 2022-12-20 and 1.1.0 dated 2026-06-11
DESCRIPTION | 13 +-- MD5 | 36 ++++++---- NAMESPACE | 1 NEWS.md | 37 ++++++++++ R/equil2.R | 28 +++++-- R/equil2_v1.R |only R/unit_setup.R | 12 ++- README.md | 24 +++--- build/vignette.rds |binary inst/CITATION | 54 ++++++++------- inst/WORDLIST | 48 +++++++++++++ inst/clsEquil2.bas.txt |only inst/doc/original-source-v1.R |only inst/doc/original-source-v1.Rmd |only inst/doc/original-source-v1.html |only inst/doc/original-source.Rmd | 103 ++++++++++++++++++++++++++++ inst/doc/original-source.html | 140 ++++++++++++++++++++++++++++++++++++++- man/equil2.Rd | 16 +++- man/equil2_v1.Rd |only tests/testthat/test-equil2.R | 84 ++++++++++++++++++++++- tests/testthat/test-equil2_v1.R |only vignettes/original-source-v1.Rmd |only vignettes/original-source.Rmd | 103 ++++++++++++++++++++++++++++ 23 files changed, 623 insertions(+), 76 deletions(-)
Title: BDEW Standard Load Profiles for Electricity and Gas
Description: Provides representative standard load profiles (SLPs) for
electricity and gas published by the German Association of Energy and Water
Industries (BDEW Bundesverband der Energie- und Wasserwirtschaft e.V.)
in a tidy format. The electricity profiles cover the 1999 profiles —
households (H0), commercial (G0–G6), and agriculture (L0–L2) — and the
updated 2025 profiles (H25, G25, L25, P25, S25), which additionally
represent households with photovoltaic systems and battery storage. An
interface generates an electricity load profile over a user-defined date
range. A second interface generates daily gas load profiles using the
BDEW/VKU/GEODE synthetic 'SigLinDe' procedure from daily temperatures and a
customer value ('Kundenwert'). The 1999 data and methodology are described
in VDEW (1999), "Repräsentative VDEW-Lastprofile",
<https://www.bdew.de/media/documents/1999_Repraesentative-VDEW-Lastprofile.pdf>.
The electricity generation algorithm is described in VDEW (2000), "Anwendung
der Rep [...truncated...]
Author: Markus Doering [aut, cre, cph]
Maintainer: Markus Doering <m4rkus.doering@gmail.com>
Diff between standardlastprofile versions 1.1.0 dated 2026-03-16 and 2.0.0 dated 2026-06-11
standardlastprofile-1.1.0/standardlastprofile/build |only standardlastprofile-1.1.0/standardlastprofile/data/slp.rda |only standardlastprofile-1.1.0/standardlastprofile/inst/doc |only standardlastprofile-1.1.0/standardlastprofile/tests/testthat/test-standardise_state_names.R |only standardlastprofile-1.1.0/standardlastprofile/vignettes |only standardlastprofile-2.0.0/standardlastprofile/DESCRIPTION | 44 standardlastprofile-2.0.0/standardlastprofile/MD5 | 96 standardlastprofile-2.0.0/standardlastprofile/NAMESPACE | 6 standardlastprofile-2.0.0/standardlastprofile/NEWS.md | 79 standardlastprofile-2.0.0/standardlastprofile/R/data.R | 21 standardlastprofile-2.0.0/standardlastprofile/R/plots.R | 1001 +++++++++- standardlastprofile-2.0.0/standardlastprofile/R/siglinde.R |only standardlastprofile-2.0.0/standardlastprofile/R/slp_electricity.R |only standardlastprofile-2.0.0/standardlastprofile/R/slp_gas.R |only standardlastprofile-2.0.0/standardlastprofile/R/slp_gas_kundenwert.R |only standardlastprofile-2.0.0/standardlastprofile/R/slp_gas_reference.R |only standardlastprofile-2.0.0/standardlastprofile/R/slp_generate.R | 378 --- standardlastprofile-2.0.0/standardlastprofile/R/slp_info.R | 128 + standardlastprofile-2.0.0/standardlastprofile/R/sysdata.rda |binary standardlastprofile-2.0.0/standardlastprofile/R/utils.R | 837 ++++++-- standardlastprofile-2.0.0/standardlastprofile/R/zzz.R |only standardlastprofile-2.0.0/standardlastprofile/README.md | 381 +-- standardlastprofile-2.0.0/standardlastprofile/data/slp_electricity_profiles.rda |only standardlastprofile-2.0.0/standardlastprofile/inst/WORDLIST | 123 + standardlastprofile-2.0.0/standardlastprofile/man/figures/README-H0_vs_2025-1.png |binary standardlastprofile-2.0.0/standardlastprofile/man/figures/README-bdew-1999-small_multiples-1.png |binary standardlastprofile-2.0.0/standardlastprofile/man/figures/README-bdew-2025-small_multiples-1.png |binary standardlastprofile-2.0.0/standardlastprofile/man/figures/README-slp_gas_cities-1.png |only standardlastprofile-2.0.0/standardlastprofile/man/figures/README-slp_gas_readme_plot-1.png |only standardlastprofile-2.0.0/standardlastprofile/man/slp.Rd | 99 standardlastprofile-2.0.0/standardlastprofile/man/slp_electricity.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_electricity_profiles.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_gas.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_gas_coefficients.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_gas_kundenwert.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_gas_siglinde.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_gas_weekday_factors.Rd |only standardlastprofile-2.0.0/standardlastprofile/man/slp_generate.Rd | 195 - standardlastprofile-2.0.0/standardlastprofile/man/slp_info.Rd | 37 standardlastprofile-2.0.0/standardlastprofile/man/standardlastprofile-package.Rd | 9 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-as_date.R | 12 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-dynamization_fun.R | 4 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-format_helpers.R | 18 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_15min_seq.R | 4 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_daily_sequence.R | 14 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_holidays.R | 62 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_period.R | 16 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_weekday.R | 12 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-get_wkday_period.R | 8 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-is_date.R | 8 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-match_profile.R | 33 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-paste_helpers.R | 8 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-readme.R | 6 standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_electricity.R |only standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_gas.R |only standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_gas_kundenwert.R |only standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_gas_reference.R |only standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_gas_siglinde.R |only standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_generate.R | 257 -- standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-slp_info.R | 130 - standardlastprofile-2.0.0/standardlastprofile/tests/testthat/test-vignette_examples.R | 8 61 files changed, 2522 insertions(+), 1512 deletions(-)
More information about standardlastprofile at CRAN
Permanent link
Title: Analyze Results Generated by the 'SqueezeMeta' Pipeline
Description: 'SqueezeMeta' is a versatile pipeline for the automated analysis of metagenomics/metatranscriptomics data (<https://github.com/jtamames/SqueezeMeta>). This package provides functions loading 'SqueezeMeta' results into R, filtering them based on different criteria, and visualizing the results using basic plots. The 'SqueezeMeta' project (and any subsets of it generated by the different filtering functions) is parsed into a single object, whose different components (e.g. tables with the taxonomic or functional composition across samples, contig/gene abundance profiles) can be easily analyzed using other R packages such as 'vegan' or 'DESeq2'. The methods in this package are further described in Puente-Sánchez et al., (2020) <doi:10.1186/s12859-020-03703-2>.
Author: Fernando Puente-Sanchez [aut, cre],
Natalia Garcia-Garcia [aut]
Maintainer: Fernando Puente-Sanchez <fernando.puente.sanchez@slu.se>
This is a re-admission after prior archival of version 1.7.2 dated 2025-06-14
Diff between SQMtools versions 1.7.2 dated 2025-06-14 and 1.8.0 dated 2026-06-11
DESCRIPTION | 9 MD5 | 68 ++- NAMESPACE | 3 R/RecA.R | 2 R/aggregate_methods.R | 37 +- R/bin_methods.R | 25 - R/combineSQM.R | 277 +++++++--------- R/combineSQMlite.R | 32 + R/exportPathway.R | 2 R/exportSeqs.R | 2 R/ext_bindings.R | 14 R/extra_methods.R | 20 + R/figures.R | 265 +++++---------- R/loadSQM.R | 751 +++++++++++++++++++++++++++----------------- R/loadSQMlite.R | 31 - R/mostAbundant.R | 31 + R/subset_methods.R | 644 ++++++++++++++++++++++--------------- R/tax_methods.R |only data/CheckMProkaryote.RData |binary data/Hadza.RData |binary data/MGKOs.RData |binary data/MGOGs.RData |binary data/RecA.RData |binary data/USiCGs.RData |binary man/RecA.Rd | 3 man/combineSQM.Rd | 2 man/loadSQM.Rd | 13 man/mostAbundant.Rd | 8 man/plotBins.Rd | 19 - man/plotTaxonomy.Rd | 6 man/renameSamples.Rd |only man/subsetBins.Rd | 29 + man/subsetContigs.Rd | 3 man/subsetORFs.Rd | 2 man/subsetSamples.Rd | 10 man/subsetTax.Rd | 5 36 files changed, 1344 insertions(+), 969 deletions(-)
Title: Stochastic Data Envelopment Analysis
Description: Set of functions for Stochastic Data Envelopment Analysis. Chance constrained versions of radial, directional and additive DEA models are implemented, as long as super-efficiency models. See: Cooper, W.W.; Deng, H.; Huang, Z.; Li, S.X. (2002). <doi:10.1057/palgrave.jors.2601433>, Bolós, V.J.; Benítez, R.; Coll-Serrano, V. (2024) <doi:10.1016/j.orp.2024.100307>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between SdeaR versions 1.0.2 dated 2025-12-12 and 1.1.0 dated 2026-06-11
DESCRIPTION | 13 MD5 | 38 - NAMESPACE | 2 R/make_deadata_stoch.R | 27 - R/modelstoch_additive.R | 364 +++++++++++----- R/modelstoch_additive_p.R | 382 +++++++++++------ R/modelstoch_addsupereff.R | 470 ++++++++++++++------- R/modelstoch_dir.R | 847 ++++++++++++++++++++++++++------------ R/modelstoch_dir_dd.R | 751 +++++++++++++++++++++++---------- R/modelstoch_radial.R | 827 +++++++++++++++++++++++++------------ R/modelstoch_radial_supereff.R | 95 +++- build/partial.rdb |binary man/make_deadata_stoch.Rd | 24 - man/modelstoch_additive.Rd | 32 - man/modelstoch_additive_p.Rd | 34 - man/modelstoch_addsupereff.Rd | 32 - man/modelstoch_dir.Rd | 42 + man/modelstoch_dir_dd.Rd | 42 + man/modelstoch_radial.Rd | 84 ++- man/modelstoch_radial_supereff.Rd | 41 + 20 files changed, 2852 insertions(+), 1295 deletions(-)
Title: Insulin Sensitivity Indices Calculator
Description: Facilitates the calculation of 40 different insulin sensitivity
indices based on fasting, oral glucose tolerance test (OGTT), lipid
(adipose), tracer (palmitate and glycerol rate), and DXA (fat mass)
measurement values. Enables easy and accurate assessment of insulin
sensitivity, critical for understanding and managing metabolic disorders
like diabetes and obesity. Indices calculated are described in
Gastaldelli (2022) <doi:10.1002/oby.23503>,
Suleman (2024) <doi:10.1210/clinem/dgae275>, and
Lorenzo (2010) <doi:10.1210/jc.2010-1144>.
Author: Sufyan Suleman [aut, cre]
Maintainer: Sufyan Suleman <sufyansuleman@hotmail.com>
Diff between InsuSensCalc versions 0.0.1 dated 2024-04-04 and 0.1.0 dated 2026-06-11
DESCRIPTION | 27 ++- LICENSE | 2 MD5 | 29 +-- NEWS.md | 45 +++++ R/calc_indices.R | 55 ++---- R/example_data.R | 2 README.md | 225 +++++++++++++++++++++++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 9 - man/example_data.Rd | 86 +++++----- man/isi_calculator.Rd | 287 +++++++++++++++++------------------ tests/testthat/test-isi_calculator.R | 57 ++---- tests/testthat/test-isi_na.R |only tests/testthat/test-isi_values.R |only vignettes/introduction.Rmd | 2 17 files changed, 545 insertions(+), 283 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.2-3 dated 2026-04-13 and 0.2-4 dated 2026-06-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/w3c.R | 15 ++++++++++++--- 3 files changed, 17 insertions(+), 8 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation (Rue et al., 2009)
<doi:10.1111/j.1467-9868.2008.00700.x> as described in Jamil and Rue
(2026a) <doi:10.48550/arXiv.2603.25690>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax. See also the companion paper on implementation and
workflows, Jamil and Rue (2026b) <doi:10.48550/arXiv.2604.00671>.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.4 dated 2026-04-02 and 0.2.5 dated 2026-06-11
DESCRIPTION | 11 +-- MD5 | 51 +++++++------- NAMESPACE | 1 NEWS.md | 17 ++++ R/INLAvaan-package.R | 1 R/inlavaan.R | 23 +++--- R/lavaan-unexported.R | 97 +++++++++++++++++++++------- R/log-likelihood-and-grad.R | 8 +- R/method-diagnostics.R | 6 - R/method-fitmeasures.R | 51 ++++++++------ R/method-predict.R | 46 ++++++------- R/qsnorm_fast.R | 2 R/utils-compare_mcmc.R | 6 - R/zzz.R | 8 ++ README.md | 47 +++++-------- demo/00Index | 1 demo/acfa.R |only inst/CITATION | 6 - inst/doc/INLAvaan.html | 22 +++--- inst/doc/mediation.html | 8 +- man/acfa.Rd | 26 +++---- man/agrowth.Rd | 26 +++---- man/asem.Rd | 26 +++---- man/figures/README-fig-compare-poldem-1.png |binary man/inlavaan.Rd | 26 +++---- man/qsnorm_fast.Rd | 2 tests/testthat/test-priors.R | 16 ++-- 27 files changed, 295 insertions(+), 239 deletions(-)
Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing
Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas. Additional utilities support staggered treatment adoption [...truncated...]
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between BMisc versions 1.4.8 dated 2025-02-04 and 1.4.9 dated 2026-06-11
BMisc-1.4.8/BMisc/R/utils-data-table.R |only BMisc-1.4.8/BMisc/R/zzz.R |only BMisc-1.4.9/BMisc/DESCRIPTION | 18 BMisc-1.4.9/BMisc/MD5 | 85 +-- BMisc-1.4.9/BMisc/NAMESPACE | 5 BMisc-1.4.9/BMisc/NEWS.md | 27 + BMisc-1.4.9/BMisc/R/BMisc.R | 413 +++++++++++------- BMisc-1.4.9/BMisc/R/imports.R | 4 BMisc-1.4.9/BMisc/README.md | 128 ++++- BMisc-1.4.9/BMisc/inst/CITATION | 2 BMisc-1.4.9/BMisc/man/BMisc.Rd | 5 BMisc-1.4.9/BMisc/man/TorF.Rd | 4 BMisc-1.4.9/BMisc/man/check_staggered.Rd | 10 BMisc-1.4.9/BMisc/man/combineDfs.Rd | 2 BMisc-1.4.9/BMisc/man/combine_ecdfs.Rd | 6 BMisc-1.4.9/BMisc/man/compare_binary.Rd | 5 BMisc-1.4.9/BMisc/man/cs2panel.Rd | 7 BMisc-1.4.9/BMisc/man/drop_collinear.Rd | 9 BMisc-1.4.9/BMisc/man/get_Yi1.Rd | 9 BMisc-1.4.9/BMisc/man/get_YiGmin1.Rd | 11 BMisc-1.4.9/BMisc/man/get_Yibar.Rd | 8 BMisc-1.4.9/BMisc/man/get_Yibar_pre.Rd | 10 BMisc-1.4.9/BMisc/man/get_Yit.Rd | 10 BMisc-1.4.9/BMisc/man/get_first_difference.Rd | 8 BMisc-1.4.9/BMisc/man/get_group.Rd | 10 BMisc-1.4.9/BMisc/man/get_lagYi.Rd | 8 BMisc-1.4.9/BMisc/man/get_list_element.Rd | 4 BMisc-1.4.9/BMisc/man/get_principal_components.Rd | 10 BMisc-1.4.9/BMisc/man/invert_ecdf.Rd | 7 BMisc-1.4.9/BMisc/man/lhs_vars.Rd | 2 BMisc-1.4.9/BMisc/man/orig2t.Rd | 5 BMisc-1.4.9/BMisc/man/panel2cs.Rd | 9 BMisc-1.4.9/BMisc/man/panel2cs2.Rd | 9 BMisc-1.4.9/BMisc/man/t2orig.Rd | 5 BMisc-1.4.9/BMisc/man/time_invariant_to_panel.Rd | 10 BMisc-1.4.9/BMisc/man/toformula.Rd | 2 BMisc-1.4.9/BMisc/man/weighted_checkfun.Rd | 5 BMisc-1.4.9/BMisc/man/weighted_combine_list.Rd | 5 BMisc-1.4.9/BMisc/man/weighted_ecdf.Rd | 7 BMisc-1.4.9/BMisc/man/weighted_mean.Rd | 6 BMisc-1.4.9/BMisc/man/weighted_quantile.Rd | 6 BMisc-1.4.9/BMisc/tests/testthat/helper-skip.R |only BMisc-1.4.9/BMisc/tests/testthat/test-BMisc.R | 47 +- BMisc-1.4.9/BMisc/tests/testthat/test-distributions.R |only BMisc-1.4.9/BMisc/tests/testthat/test-formula.R |only BMisc-1.4.9/BMisc/tests/testthat/test-panel.R |only BMisc-1.4.9/BMisc/tests/testthat/test-utils.R |only 47 files changed, 703 insertions(+), 240 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson [aut, cre] ,
Julie Josse [aut],
Sebastien Le [aut],
Jeremy Mazet [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.14 dated 2026-04-08 and 2.15 dated 2026-06-11
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 1 R/CA.R | 57 +++-- R/FAMD.R | 8 R/HCPC.R | 21 +- R/MCA.R | 216 ++++++++++++++-------- R/MFA.R | 189 +++++++++++++------ R/PCA.R | 407 ++++++++++++++++++++++++++++------------- R/catdes.r | 447 ++++++++++++++++++++++++++++++++++------------ R/condes.r | 231 +++++++++++++---------- R/dimdesc.r | 3 R/print.CA.R | 13 - R/svd.triplet.R | 30 ++- build/vignette.rds |binary data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/clustering.html | 2 man/HCPC.Rd | 4 vignettes/FactoMineR.html | 2 21 files changed, 1133 insertions(+), 546 deletions(-)
Title: Tree Guided Machine Learning for Personalized Predictions and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.4.0 dated 2026-01-22 and 0.5.0 dated 2026-06-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/03c.rootML_bs.R | 1 - R/08b.continuousML.R | 4 ++++ 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Yujing Lu [aut],
Oscar A. Rysavy [aut] ,
Patrick J. Breheny [aut, cre]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.2.3 dated 2026-01-26 and 4.3.0 dated 2026-06-11
plmmr-4.2.3/plmmr/R/fbm2bm.R |only plmmr-4.2.3/plmmr/R/get_hostname.R |only plmmr-4.2.3/plmmr/R/penalties.R |only plmmr-4.2.3/plmmr/R/standardize_matrix.R |only plmmr-4.2.3/plmmr/R/subset_bigsnp.R |only plmmr-4.2.3/plmmr/inst/tinytest/_debug_standardization.R |only plmmr-4.2.3/plmmr/inst/tinytest/_penncath_mid_test.R |only plmmr-4.2.3/plmmr/inst/tinytest/_sign_flip_issue.R |only plmmr-4.2.3/plmmr/inst/tinytest/_test_big_cbind.R |only plmmr-4.2.3/plmmr/inst/tinytest/_test_fbm.R |only plmmr-4.2.3/plmmr/inst/tinytest/_test_process_plink.R |only plmmr-4.2.3/plmmr/inst/tinytest/_test_rotation_approach.R |only plmmr-4.2.3/plmmr/man/MCP.Rd |only plmmr-4.2.3/plmmr/man/SCAD.Rd |only plmmr-4.2.3/plmmr/man/fbm2bm.Rd |only plmmr-4.2.3/plmmr/man/get_hostname.Rd |only plmmr-4.2.3/plmmr/man/lasso.Rd |only plmmr-4.3.0/plmmr/DESCRIPTION | 19 plmmr-4.3.0/plmmr/MD5 | 271 ++++++------ plmmr-4.3.0/plmmr/NAMESPACE | 1 plmmr-4.3.0/plmmr/NEWS.md | 28 + plmmr-4.3.0/plmmr/R/add_predictors.R | 29 - plmmr-4.3.0/plmmr/R/align_ids.R | 25 - plmmr-4.3.0/plmmr/R/big_cbind.R | 9 plmmr-4.3.0/plmmr/R/coef-cv-plmm.R | 11 plmmr-4.3.0/plmmr/R/coef-plmm.R | 16 plmmr-4.3.0/plmmr/R/compute_blup.R |only plmmr-4.3.0/plmmr/R/construct_variance.R | 38 - plmmr-4.3.0/plmmr/R/count_constant_features.R | 10 plmmr-4.3.0/plmmr/R/count_cores.R | 3 plmmr-4.3.0/plmmr/R/create_design.R | 32 - plmmr-4.3.0/plmmr/R/create_design_filebacked.R | 90 ++-- plmmr-4.3.0/plmmr/R/create_design_in_memory.R | 8 plmmr-4.3.0/plmmr/R/create_log.R | 29 - plmmr-4.3.0/plmmr/R/cv-plmm.R | 165 +++---- plmmr-4.3.0/plmmr/R/cvf.R | 67 +-- plmmr-4.3.0/plmmr/R/data.R | 10 plmmr-4.3.0/plmmr/R/eigen_K.R | 27 - plmmr-4.3.0/plmmr/R/estimate_eta.R | 24 - plmmr-4.3.0/plmmr/R/find_example_data.R | 56 +- plmmr-4.3.0/plmmr/R/get_data.R | 25 - plmmr-4.3.0/plmmr/R/impute_snp_data.R | 106 ++--- plmmr-4.3.0/plmmr/R/index_samples.R | 27 - plmmr-4.3.0/plmmr/R/lam_names.R | 5 plmmr-4.3.0/plmmr/R/log_lik.R | 45 +- plmmr-4.3.0/plmmr/R/loss-plmm.R | 11 plmmr-4.3.0/plmmr/R/name_and_count_bigsnp.R | 45 +- plmmr-4.3.0/plmmr/R/plmm.R | 143 ++---- plmmr-4.3.0/plmmr/R/plmm_checks.R | 104 ++-- plmmr-4.3.0/plmmr/R/plmm_fit.R | 111 +++-- plmmr-4.3.0/plmmr/R/plmm_format.R | 40 + plmmr-4.3.0/plmmr/R/plmm_prep.R | 132 ++---- plmmr-4.3.0/plmmr/R/plot-cv-plmm.R | 40 + plmmr-4.3.0/plmmr/R/plot-plmm.R | 25 - plmmr-4.3.0/plmmr/R/predict-cv-plmm.R |only plmmr-4.3.0/plmmr/R/predict-plmm.R | 53 -- plmmr-4.3.0/plmmr/R/predict_within_cv.R | 48 -- plmmr-4.3.0/plmmr/R/pretty_time.R | 7 plmmr-4.3.0/plmmr/R/print-summary-cv-plmm.R | 8 plmmr-4.3.0/plmmr/R/print-summary-plmm.R | 8 plmmr-4.3.0/plmmr/R/process_delim.R | 56 -- plmmr-4.3.0/plmmr/R/process_plink.R | 139 ++---- plmmr-4.3.0/plmmr/R/read_data_files.R | 66 +-- plmmr-4.3.0/plmmr/R/read_plink_files.R | 42 -- plmmr-4.3.0/plmmr/R/relatedness_mat.R | 64 +-- plmmr-4.3.0/plmmr/R/rotate_filebacked.R | 29 - plmmr-4.3.0/plmmr/R/setup_lambda.R | 23 - plmmr-4.3.0/plmmr/R/standardize_filebacked.R | 48 +- plmmr-4.3.0/plmmr/R/standardize_in_memory.R |only plmmr-4.3.0/plmmr/R/subset_filebacked.R |only plmmr-4.3.0/plmmr/R/summary-cv-plmm.R | 38 - plmmr-4.3.0/plmmr/R/summary-plmm.R | 20 plmmr-4.3.0/plmmr/R/untransform.R | 20 plmmr-4.3.0/plmmr/R/untransform_delim.R | 23 - plmmr-4.3.0/plmmr/R/untransform_in_memory.R | 21 - plmmr-4.3.0/plmmr/R/untransform_plink.R | 23 - plmmr-4.3.0/plmmr/R/zzz.R | 2 plmmr-4.3.0/plmmr/README.md | 4 plmmr-4.3.0/plmmr/build/partial.rdb |binary plmmr-4.3.0/plmmr/build/vignette.rds |binary plmmr-4.3.0/plmmr/inst/CITATION | 20 plmmr-4.3.0/plmmr/inst/doc/getting-started.Rmd | 10 plmmr-4.3.0/plmmr/inst/doc/getting-started.html | 36 - plmmr-4.3.0/plmmr/inst/tinytest/test_cv.R | 65 ++- plmmr-4.3.0/plmmr/inst/tinytest/test_data.R |only plmmr-4.3.0/plmmr/inst/tinytest/test_plink.R |only plmmr-4.3.0/plmmr/inst/tinytest/test_plmm.R | 292 ++++++++------ plmmr-4.3.0/plmmr/man/add_predictors.Rd | 12 plmmr-4.3.0/plmmr/man/admix.Rd | 10 plmmr-4.3.0/plmmr/man/align_ids.Rd | 16 plmmr-4.3.0/plmmr/man/big_cbind.Rd | 6 plmmr-4.3.0/plmmr/man/coef.cv_plmm.Rd | 11 plmmr-4.3.0/plmmr/man/coef.plmm.Rd | 10 plmmr-4.3.0/plmmr/man/compute_blup.Rd |only plmmr-4.3.0/plmmr/man/construct_variance.Rd | 4 plmmr-4.3.0/plmmr/man/count_constant_features.Rd | 4 plmmr-4.3.0/plmmr/man/create_design.Rd | 27 - plmmr-4.3.0/plmmr/man/create_design_filebacked.Rd | 33 - plmmr-4.3.0/plmmr/man/create_design_in_memory.Rd | 2 plmmr-4.3.0/plmmr/man/create_log.Rd | 11 plmmr-4.3.0/plmmr/man/cv_plmm.Rd | 74 +-- plmmr-4.3.0/plmmr/man/cvf.Rd | 17 plmmr-4.3.0/plmmr/man/eigen_K.Rd | 17 plmmr-4.3.0/plmmr/man/estimate_eta.Rd | 14 plmmr-4.3.0/plmmr/man/find_example_data.Rd | 13 plmmr-4.3.0/plmmr/man/get_data.Rd | 22 - plmmr-4.3.0/plmmr/man/impute_snp_data.Rd | 27 - plmmr-4.3.0/plmmr/man/index_samples.Rd | 14 plmmr-4.3.0/plmmr/man/lam_names.Rd | 4 plmmr-4.3.0/plmmr/man/log_lik.Rd | 12 plmmr-4.3.0/plmmr/man/name_and_count_bigsnp.Rd | 20 plmmr-4.3.0/plmmr/man/plmm.Rd | 93 ++-- plmmr-4.3.0/plmmr/man/plmm_checks.Rd | 44 +- plmmr-4.3.0/plmmr/man/plmm_fit.Rd | 50 +- plmmr-4.3.0/plmmr/man/plmm_format.Rd | 43 +- plmmr-4.3.0/plmmr/man/plmm_loss.Rd | 7 plmmr-4.3.0/plmmr/man/plmm_prep.Rd | 48 +- plmmr-4.3.0/plmmr/man/plmmr-package.Rd | 5 plmmr-4.3.0/plmmr/man/plot.cv_plmm.Rd | 26 - plmmr-4.3.0/plmmr/man/plot.plmm.Rd | 9 plmmr-4.3.0/plmmr/man/predict.cv_plmm.Rd |only plmmr-4.3.0/plmmr/man/predict.plmm.Rd | 33 - plmmr-4.3.0/plmmr/man/predict_within_cv.Rd | 34 - plmmr-4.3.0/plmmr/man/pretty_time.Rd | 4 plmmr-4.3.0/plmmr/man/print.summary.cv_plmm.Rd | 5 plmmr-4.3.0/plmmr/man/process_delim.Rd | 28 - plmmr-4.3.0/plmmr/man/process_plink.Rd | 46 +- plmmr-4.3.0/plmmr/man/read_data_files.Rd | 22 - plmmr-4.3.0/plmmr/man/read_plink_files.Rd | 10 plmmr-4.3.0/plmmr/man/relatedness_mat.Rd | 19 plmmr-4.3.0/plmmr/man/rotate_filebacked.Rd | 15 plmmr-4.3.0/plmmr/man/setup_lambda.Rd | 26 - plmmr-4.3.0/plmmr/man/standardize_filebacked.Rd | 29 - plmmr-4.3.0/plmmr/man/standardize_in_memory.Rd | 10 plmmr-4.3.0/plmmr/man/subset_filebacked.Rd | 24 - plmmr-4.3.0/plmmr/man/summary.cv_plmm.Rd | 12 plmmr-4.3.0/plmmr/man/summary.plmm.Rd | 10 plmmr-4.3.0/plmmr/man/untransform.Rd | 8 plmmr-4.3.0/plmmr/man/untransform_delim.Rd | 16 plmmr-4.3.0/plmmr/man/untransform_in_memory.Rd | 10 plmmr-4.3.0/plmmr/man/untransform_plink.Rd | 16 plmmr-4.3.0/plmmr/man/unzip_example_data.Rd | 9 plmmr-4.3.0/plmmr/src/Makevars | 2 plmmr-4.3.0/plmmr/src/big_standardize.cpp | 4 plmmr-4.3.0/plmmr/src/plmm_init.c | 4 plmmr-4.3.0/plmmr/src/standardize.cpp | 2 plmmr-4.3.0/plmmr/src/utilities.cpp | 129 ------ plmmr-4.3.0/plmmr/src/utilities.h | 2 plmmr-4.3.0/plmmr/vignettes/getting-started.Rmd | 10 149 files changed, 2108 insertions(+), 2128 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 1.2.0 dated 2025-10-29 and 1.2.1 dated 2026-06-11
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/Andromeda.R | 2 +- R/Indices.R | 2 +- R/LoadingSaving.R | 2 +- R/Object.R | 2 +- R/Operations.R | 13 ++++++++++--- inst/doc/UsingAndromeda.html | 6 +++--- man/Andromeda-package.Rd | 1 + 10 files changed, 41 insertions(+), 24 deletions(-)
Title: R Interface to the 'Uno' Nonlinear Optimization Solver
Description: Bindings to 'Uno' (Unifying Nonlinear Optimization), a C++ solver
for smooth nonlinearly constrained optimization. 'Uno' unifies Lagrange-Newton
methods, including sequential quadratic programming and interior-point
methods, by decomposing them into interacting building blocks
(constraint-relaxation, inequality-handling, Hessian, and globalization
strategies) that can be freely combined, either through options or through
presets that reproduce established solvers such as 'filterSQP' and 'IPOPT'.
The framework is described in Vanaret and Leyffer (2024)
<doi:10.48550/arXiv.2406.13454>.
Author: Balasubramanian Narasimhan [aut, cre],
Charlie Vanaret [aut, cph] ,
Sven Leyffer [aut, cph] ,
HiGHS development team [cph] ; see
inst/COPYRIGHTS)
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between Uno versions 2.7.3 dated 2026-06-08 and 2.7.3-1 dated 2026-06-11
.Rinstignore |only DESCRIPTION | 7 ++++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ configure | 23 ++++++++--------------- configure.win | 8 ++------ inst/build_highs.sh | 13 +++++++++---- inst/build_uno.sh | 20 ++++++++++++++++---- 8 files changed, 51 insertions(+), 38 deletions(-)
Title: A Unified Framework for Machine Learning Ensembles in Survival
Analysis
Description: Implements a Super Learner framework for right-censored survival data.
The package fits convex combinations of parametric, semiparametric, and machine
learning survival learners by minimizing cross-validated risk using inverse
probability of censoring weighting (IPCW). It provides tools for automated
hyperparameter grid search, high-dimensional variable screening, and evaluation
of prediction performance using metrics such as the Brier score, Uno's C-index,
and time-dependent area under the curve (AUC). Additional utilities support
model interpretation for survival ensembles, including Shapley additive
explanations (SHAP), and estimation of covariate-adjusted restricted mean
survival time (RMST) contrasts. The methodology is related to treatment-specific
survival curve estimation using machine learning described by Westling et al.
(2024) <doi:10.1080/01621459.2023.2205060>, and the unified
ensemble framework described in Lyu et al. (2026) <doi:10.64898/2026.03.11.711010>.
Author: Yue Lyu [aut, cre]
Maintainer: Yue Lyu <yuelyu0521@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2026-05-04
Diff between SuperSurv versions 0.1.2 dated 2026-05-04 and 0.1.7 dated 2026-06-11
SuperSurv-0.1.2/SuperSurv/inst/doc/scaleup-parallel.R |only SuperSurv-0.1.2/SuperSurv/inst/doc/scaleup-parallel.Rmd |only SuperSurv-0.1.2/SuperSurv/inst/doc/scaleup-parallel.html |only SuperSurv-0.1.2/SuperSurv/vignettes/scaleup-parallel.Rmd |only SuperSurv-0.1.7/SuperSurv/DESCRIPTION | 12 - SuperSurv-0.1.7/SuperSurv/MD5 | 102 +++++------- SuperSurv-0.1.7/SuperSurv/R/explainability.R | 30 +-- SuperSurv-0.1.7/SuperSurv/R/rmst.R | 8 SuperSurv-0.1.7/SuperSurv/R/wrapper.R | 12 - SuperSurv-0.1.7/SuperSurv/README.md | 23 +- SuperSurv-0.1.7/SuperSurv/build/vignette.rds |binary SuperSurv-0.1.7/SuperSurv/inst/doc/base-learner-rfsrc.R | 11 - SuperSurv-0.1.7/SuperSurv/inst/doc/base-learner-rfsrc.Rmd | 13 - SuperSurv-0.1.7/SuperSurv/inst/doc/causal-rmst.R | 8 SuperSurv-0.1.7/SuperSurv/inst/doc/causal-rmst.Rmd | 8 SuperSurv-0.1.7/SuperSurv/inst/doc/causal-rmst.html | 25 +- SuperSurv-0.1.7/SuperSurv/inst/doc/extending-supersurv.Rmd | 4 SuperSurv-0.1.7/SuperSurv/inst/doc/extending-supersurv.html | 4 SuperSurv-0.1.7/SuperSurv/inst/doc/installation.R | 3 SuperSurv-0.1.7/SuperSurv/inst/doc/installation.Rmd | 3 SuperSurv-0.1.7/SuperSurv/inst/doc/installation.html | 17 -- SuperSurv-0.1.7/SuperSurv/inst/doc/model-performance.R | 6 SuperSurv-0.1.7/SuperSurv/inst/doc/model-performance.Rmd | 7 SuperSurv-0.1.7/SuperSurv/inst/doc/model-performance.html | 31 ++- SuperSurv-0.1.7/SuperSurv/inst/doc/parametric-models.html | 2 SuperSurv-0.1.7/SuperSurv/inst/doc/screening-methods.R | 16 + SuperSurv-0.1.7/SuperSurv/inst/doc/screening-methods.Rmd | 16 + SuperSurv-0.1.7/SuperSurv/inst/doc/screening-methods.html | 24 +- SuperSurv-0.1.7/SuperSurv/inst/doc/shap-explanations.R | 65 ++++--- SuperSurv-0.1.7/SuperSurv/inst/doc/shap-explanations.Rmd | 37 ++-- SuperSurv-0.1.7/SuperSurv/inst/doc/shap-explanations.html | 63 +++---- SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-best.R | 6 SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-best.Rmd | 6 SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-best.html | 5 SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-ensemble.R | 6 SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-ensemble.Rmd | 6 SuperSurv-0.1.7/SuperSurv/inst/doc/supersurv-ensemble.html | 11 - SuperSurv-0.1.7/SuperSurv/man/explain_kernel.Rd | 3 SuperSurv-0.1.7/SuperSurv/man/plot_beeswarm.Rd | 4 SuperSurv-0.1.7/SuperSurv/man/plot_dependence.Rd | 3 SuperSurv-0.1.7/SuperSurv/man/plot_global_importance.Rd | 3 SuperSurv-0.1.7/SuperSurv/man/plot_marginal_rmst_curve.Rd | 4 SuperSurv-0.1.7/SuperSurv/man/plot_patient_waterfall.Rd | 3 SuperSurv-0.1.7/SuperSurv/man/plot_rmst_vs_obs.Rd | 4 SuperSurv-0.1.7/SuperSurv/man/surv.xgboost.Rd | 5 SuperSurv-0.1.7/SuperSurv/vignettes/base-learner-rfsrc.Rmd | 13 - SuperSurv-0.1.7/SuperSurv/vignettes/causal-rmst.Rmd | 8 SuperSurv-0.1.7/SuperSurv/vignettes/extending-supersurv.Rmd | 4 SuperSurv-0.1.7/SuperSurv/vignettes/installation.Rmd | 3 SuperSurv-0.1.7/SuperSurv/vignettes/model-performance.Rmd | 7 SuperSurv-0.1.7/SuperSurv/vignettes/screening-methods.Rmd | 16 + SuperSurv-0.1.7/SuperSurv/vignettes/shap-explanations.Rmd | 37 ++-- SuperSurv-0.1.7/SuperSurv/vignettes/supersurv-best.Rmd | 6 SuperSurv-0.1.7/SuperSurv/vignettes/supersurv-ensemble.Rmd | 6 54 files changed, 406 insertions(+), 313 deletions(-)
Title: NASCAR Race Data
Description: A collection of NASCAR race, driver, owner and manufacturer
data across the three major NASCAR divisions: NASCAR Cup Series, NXS,
and NASCAR Craftsman Truck Series. The curated
data begins with the 1949 season and is updated weekly during the
racing season. Explore race, season, or career performance for drivers,
teams, and manufacturers throughout NASCAR's history. Data was sourced
with permission from DriverAverages.com.
Author: Kyle Grealis [aut, cre] ,
Nick Triplett [ctb],
Gabriel Odom [ctb]
Maintainer: Kyle Grealis <kyle@kylegrealis.com>
Diff between nascaR.data versions 3.0.1 dated 2026-02-16 and 3.1.0 dated 2026-06-11
DESCRIPTION | 10 ++-- MD5 | 32 +++++++------ NAMESPACE | 1 NEWS.md | 15 ++++++ R/export.R |only R/r2_upload.R | 41 +++++++++++++---- README.md | 57 ++++++++++++++++++++++- build/vignette.rds |binary inst/CITATION | 2 inst/doc/a-race-winning-strategy.html | 22 ++++----- inst/doc/ingesting-nascar-data.R |only inst/doc/ingesting-nascar-data.Rmd |only inst/doc/ingesting-nascar-data.html |only inst/updates/cup_track_info.rda |binary inst/updates/nxs_track_info.rda |binary inst/updates/scraper.R | 81 ++++++++++++++++++++++++---------- inst/updates/truck_track_info.rda |binary man/export_series.Rd |only tests/testthat/test-data.R | 36 +++++++++++++++ vignettes/ingesting-nascar-data.Rmd |only 20 files changed, 232 insertions(+), 65 deletions(-)
Title: Translates R Help Documentation using Large Language Models
Description: Translates R help documentation on the fly by using a Large
Language model of your choice. If you are using 'RStudio' or
'Positron' the translated help will appear in the help pane.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between lang versions 0.1.1 dated 2026-06-05 and 0.1.2 dated 2026-06-11
DESCRIPTION | 6 MD5 | 21 ++- NEWS.md | 6 R/lang-help.R | 8 + R/rd-translate.R | 10 + README.md | 233 ++++++++++++++++++----------------- man/lang_help.Rd | 8 + tests/testthat/_snaps/aaa-nosetup.md |only tests/testthat/_snaps/zzz-local.md |only tests/testthat/helper-utils.R | 10 + tests/testthat/rd |only tests/testthat/test-aaa-nosetup.R |only tests/testthat/test-zzz-local.R |only 13 files changed, 183 insertions(+), 119 deletions(-)
Title: R Client for the Interactive Brokers Client Portal API
Description: Provides a lightweight R interface to the Interactive Brokers (IBKR)
Client Portal REST API. Functions cover session management, account and portfolio
queries, market data retrieval, and order placement and cancellation. Requires a
locally running IBKR Client Portal Gateway.
Author: Nagappan Karuppiah [aut, cre]
Maintainer: Nagappan Karuppiah <ibkrcp@gmail.com>
Diff between ibkrcp versions 0.1.1 dated 2026-05-07 and 0.1.2 dated 2026-06-11
DESCRIPTION | 10 +- MD5 | 44 ++++----- NAMESPACE | 1 NEWS.md | 11 ++ R/orders.R | 14 +- R/portfolio.R | 25 ++--- R/session.R | 15 +++ R/utils.R | 14 ++ README.md | 48 ++++++---- man/ibkr_auth_status.Rd | 2 man/ibkr_cancel_order.Rd | 2 man/ibkr_get_price_history.Rd | 2 man/ibkr_live_orders.Rd | 2 man/ibkr_logout.Rd |only man/ibkr_ping.Rd | 2 man/ibkr_place_order.Rd | 2 man/ibkr_portfolio_accounts.Rd | 2 man/ibkr_portfolio_positions.Rd | 9 + man/ibkr_portfolio_summary.Rd | 2 tests/testthat/localhost-5000/v1/api/iserver/secdef/search-82afae-POST.json | 6 - tests/testthat/localhost-5000/v1/api/logout.json |only tests/testthat/localhost-5000/v1/api/portfolio2/U1234567/positions-c39a17.json | 8 + tests/testthat/test_portfolio.R | 8 + tests/testthat/test_session.R | 8 + 24 files changed, 155 insertions(+), 82 deletions(-)
Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>,
a standalone 'C++' library for fast symbolic manipulation. The package has functionalities
for symbolic computation like calculating exact mathematical expressions, solving
systems of linear equations and code generation.
Author: Jialin Ma [cre, aut],
Isuru Fernando [aut],
Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>
Diff between symengine versions 0.2.11 dated 2026-03-04 and 0.2.13 dated 2026-06-11
DESCRIPTION | 6 - MD5 | 12 +-- src/rbinding.cpp | 148 +++++++++++++++++++-------------------- src/upstream.tar |binary tools/bundle_symengine_source.sh | 2 tools/release_procedure.md | 52 +++++++++++-- tools/symengine_patch.diff | 14 +++ 7 files changed, 141 insertions(+), 93 deletions(-)
Title: R Interface to RESTful Web Services
Description: Models a RESTful service as if it were a nested R list.
Author: Michael Lawrence [aut, cre]
Maintainer: Michael Lawrence <lawremi@gmail.com>
Diff between restfulr versions 0.0.16 dated 2025-06-27 and 0.0.17 dated 2026-06-11
DESCRIPTION | 14 +++++++------- MD5 | 5 +++-- R/HTTP-class.R | 16 ++++++++++++---- inst/unitTests/test_HTTP.R |only 4 files changed, 22 insertions(+), 13 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 5.0.1 dated 2026-02-28 and 5.0.2 dated 2026-06-11
DESCRIPTION | 8 +- MD5 | 68 +++++++++++----------- NEWS.md | 4 + R/plot.nlmixr2.R | 2 README.md | 117 +++++++++++++++++++++++--------------- man/figures/README-example-1.png |binary man/figures/README-example-10.png |binary man/figures/README-example-11.png |binary man/figures/README-example-12.png |binary man/figures/README-example-13.png |binary man/figures/README-example-14.png |binary man/figures/README-example-15.png |binary man/figures/README-example-16.png |binary man/figures/README-example-17.png |binary man/figures/README-example-18.png |binary man/figures/README-example-19.png |binary man/figures/README-example-2.png |binary man/figures/README-example-20.png |binary man/figures/README-example-21.png |binary man/figures/README-example-22.png |binary man/figures/README-example-23.png |binary man/figures/README-example-24.png |binary man/figures/README-example-25.png |binary man/figures/README-example-26.png |binary man/figures/README-example-27.png |binary man/figures/README-example-28.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/figures/README-example-6.png |binary man/figures/README-example-7.png |binary man/figures/README-example-8.png |binary man/figures/README-example-9.png |binary man/reexports.Rd | 2 tests/testthat/test-plots.R | 34 +++++++++++ 35 files changed, 149 insertions(+), 86 deletions(-)
Title: Vectorised Probability Distributions
Description: Vectorised distribution objects with tools for manipulating,
visualising, and using probability distributions. Designed to allow model
prediction outputs to return distributions rather than their parameters,
allowing users to directly interact with predictive distributions in a
data-oriented workflow. In addition to providing generic replacements for
p/d/q/r functions, other useful statistics can be computed including means,
variances, intervals, and highest density regions.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Matthew Kay [aut] ,
Alex Hayes [aut] ,
Rob Hyndman [aut] ,
Earo Wang [ctb] ,
Vencislav Popov [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between distributional versions 0.7.0 dated 2026-03-17 and 0.7.1 dated 2026-06-11
DESCRIPTION | 8 +- MD5 | 56 +++++++++---------- NEWS.md | 11 +++ R/dist_inflated.R | 22 +++++-- R/dist_truncated.R | 9 ++- R/distribution.R | 1 R/utils.R | 2 man/dist_categorical.Rd | 2 man/dist_dirichlet.Rd | 2 man/dist_f.Rd | 2 man/dist_gev.Rd | 2 man/dist_gh.Rd | 2 man/dist_gk.Rd | 2 man/dist_gpd.Rd | 2 man/dist_gumbel.Rd | 4 - man/dist_horseshoe.Rd | 2 man/dist_mixture.Rd | 2 man/dist_multinomial.Rd | 2 man/dist_multivariate_normal.Rd | 4 - man/dist_multivariate_t.Rd | 2 man/dist_poisson_inverse_gaussian.Rd | 4 - man/dist_sample.Rd | 2 man/dist_student_t.Rd | 8 +- man/dist_studentized_range.Rd | 2 man/distributional-package.Rd | 1 man/reexports.Rd | 2 man/variance.Rd | 6 +- tests/testthat/test-dist-multivariate-normal.R | 12 ++++ tests/testthat/test-inflated.R | 72 ++++++++++++++++++++++++- 29 files changed, 180 insertions(+), 68 deletions(-)
More information about distributional at CRAN
Permanent link
Title: Dynamic Relational Event Analysis and Modeling
Description: A set of tools for relational and event analysis, including two- and one-mode network brokerage and structural measures, and helper functions optimized for relational event analysis with large datasets, including creating relational risk sets, computing network statistics, estimating relational event models, and simulating relational event sequences. For more information on relational event models, see Butts (2008) <doi:10.1111/j.1467-9531.2008.00203.x>, Lerner and Lomi (2020) <doi:10.1017/nws.2019.57>, Bianchi et al. (2024) <doi:10.1146/annurev-statistics-040722-060248>, and Butts et al. (2023) <doi:10.1017/nws.2023.9>. In terms of the structural measures in this package, see Leal (2025) <doi:10.1177/00491241251322517>, Burchard and Cornwell (2018) <doi:10.1016/j.socnet.2018.04.001>, and Fujimoto et al. (2018) <doi:10.1017/nws.2018.11>. This package was developed with support from the National Science Foundation’s (NSF) Human Networks and Data [...truncated...]
Author: Kevin A. Carson [aut, cre] ,
Diego F. Leal [aut]
Maintainer: Kevin A. Carson <kacarson@arizona.edu>
Diff between dream versions 2.1.2 dated 2026-06-03 and 2.1.3 dated 2026-06-10
DESCRIPTION | 6 - MD5 | 73 ++++++------- NAMESPACE | 1 NEWS.md | 7 + R/RcppExports.R | 8 + R/dream_estimate.R | 58 ++++++---- R/dream_process.R | 198 +++++++++++++++++++++--------------- R/dream_remstats.R | 38 ++++-- man/as.data.frame.dream_sequence.Rd | 3 man/coef.dream_rem.Rd | 3 man/create_res.Rd | 102 ++++++++++-------- man/dream_sequence.Rd | 3 man/dreamstats_actor.Rd | 3 man/dreamstats_actorfe.Rd | 3 man/dreamstats_degree.Rd | 3 man/dreamstats_dyadfe.Rd | 2 man/dreamstats_dyadic.Rd | 3 man/dreamstats_event.Rd | 3 man/dreamstats_fourcycles.Rd | 3 man/dreamstats_persistence.Rd | 3 man/dreamstats_prefattachment.Rd | 3 man/dreamstats_recency.Rd | 3 man/dreamstats_reciprocity.Rd | 3 man/dreamstats_repetition.Rd | 3 man/dreamstats_triads.Rd | 3 man/estimate_rem.Rd | 5 man/gof_rem.Rd | 3 man/logLik.dream_rem.Rd | 3 man/new_dream_sequence.Rd | 3 man/plot.dream_rem.Rd | 7 - man/predict.dream_rem.Rd | 3 man/residuals.dream_rem.Rd | 3 man/vcov.dream_rem.Rd | 3 src/RcppExports.cpp | 36 ++++++ src/actorvarying_risksets.cpp | 41 ++++--- src/cumulative_full_riskset.cpp |only src/fullriskset.cpp | 34 +++--- src/onemoderiskset_temporal.cpp | 21 ++- 38 files changed, 444 insertions(+), 256 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph] ,
David Lawson [ctb, cph],
Ivan Marin-Franch [ctb, cph],
Matthias Muller [ctb],
Jonathan Denniss [ctb, cph],
Astrid Zeman [ctb],
Giovanni Montesano [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 3.1.0 dated 2026-03-03 and 3.1.1 dated 2026-06-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-opiPresent.r | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Likelihood Based Inference
Description: Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between LBI versions 0.2.4 dated 2026-05-22 and 0.2.5 dated 2026-06-10
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/LIvRatio.R | 85 +++++++++++++++++++++++++++++++++-------------------------- R/LIvtest.R | 80 +++++++++++++++++++++++++++++++------------------------ inst/NEWS.Rd | 6 ++++ 5 files changed, 106 insertions(+), 79 deletions(-)
Title: Item Response Theory Modeling and Scoring for Judgment Data
Description: Psychometric analysis and scoring of judgment data using polytomous Item-Response Theory (IRT) models, as described in Myszkowski and Storme (2019) <doi:10.1037/aca0000225> and Myszkowski (2021) <doi:10.1037/aca0000287>. A function is used to automatically compare and select models, as well as to present a variety of model-based statistics. Plotting functions are used to present category curves, as well as information, reliability and standard error functions.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between jrt versions 1.1.3 dated 2025-07-31 and 1.2.0 dated 2026-06-10
DESCRIPTION | 14 - MD5 | 24 +- NEWS.md | 7 R/info.plot.R | 11 - R/jcc.plot.R | 3 R/jrt.R | 38 --- build/partial.rdb |binary build/vignette.rds |binary inst/doc/my-vignette.R | 14 - inst/doc/my-vignette.Rmd | 40 --- inst/doc/my-vignette.html | 477 +++++++++++++++++++++------------------------- man/jrt.Rd | 6 vignettes/my-vignette.Rmd | 40 --- 13 files changed, 281 insertions(+), 393 deletions(-)
Title: Fit Zeta Distributions to Forensic Data
Description: Fits Zeta distributions (discrete power laws) to data that arises
from forensic surveys of clothing on the presence of glass and paint in
various populations. The general method is described to some extent in
Coulson, S.A., Buckleton, J.S., Gummer, A.B., and Triggs, C.M. (2001)
<doi:10.1016/S1355-0306(01)71847-3>, although the implementation differs.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between fitPS versions 1.0.1 dated 2024-03-19 and 1.0.6 dated 2026-06-10
fitPS-1.0.1/fitPS/inst/doc/examples.Rnw |only fitPS-1.0.1/fitPS/inst/doc/simple_P_fit.Rnw |only fitPS-1.0.1/fitPS/vignettes/bootconfregion.pdf |only fitPS-1.0.1/fitPS/vignettes/examples.Rnw |only fitPS-1.0.1/fitPS/vignettes/simple_P_fit.Rnw |only fitPS-1.0.6/fitPS/DESCRIPTION | 18 fitPS-1.0.6/fitPS/MD5 | 94 ++- fitPS-1.0.6/fitPS/NAMESPACE | 21 fitPS-1.0.6/fitPS/NEWS.md |only fitPS-1.0.6/fitPS/R/add.R |only fitPS-1.0.6/fitPS/R/bayesOptions.R |only fitPS-1.0.6/fitPS/R/confint.psFit.R | 22 fitPS-1.0.6/fitPS/R/credint.R |only fitPS-1.0.6/fitPS/R/fitDist.R | 422 +++++++++------ fitPS-1.0.6/fitPS/R/fitDistBayes.R |only fitPS-1.0.6/fitPS/R/fitDistBayesIntegrate.R |only fitPS-1.0.6/fitPS/R/fitZIDist.R | 666 ++++++++++++++----------- fitPS-1.0.6/fitPS/R/fitZIDistBayes.R |only fitPS-1.0.6/fitPS/R/fitdistLaplace.R |only fitPS-1.0.6/fitPS/R/internalfunctions.R |only fitPS-1.0.6/fitPS/R/logLik.psFit.R |only fitPS-1.0.6/fitPS/R/makePrior.R |only fitPS-1.0.6/fitPS/R/plot.psFit.R | 8 fitPS-1.0.6/fitPS/R/plotPosterior.R |only fitPS-1.0.6/fitPS/R/predict.psFit.R | 20 fitPS-1.0.6/fitPS/R/print.psData.R | 58 +- fitPS-1.0.6/fitPS/R/print.psFit.R | 119 ++-- fitPS-1.0.6/fitPS/R/probfun.R | 92 +-- fitPS-1.0.6/fitPS/R/profileLikelihoodZIZ.R | 84 +-- fitPS-1.0.6/fitPS/R/rZIzeta.R | 10 fitPS-1.0.6/fitPS/R/rzeta.R | 22 fitPS-1.0.6/fitPS/R/zetaParameterisation.R |only fitPS-1.0.6/fitPS/R/zizPosteriorGrid.R |only fitPS-1.0.6/fitPS/R/zizPosteriorImportance.R |only fitPS-1.0.6/fitPS/R/zizPosteriorLaplace.R |only fitPS-1.0.6/fitPS/README.md |only fitPS-1.0.6/fitPS/build/partial.rdb |binary fitPS-1.0.6/fitPS/build/vignette.rds |binary fitPS-1.0.6/fitPS/inst/doc/examples.R | 119 +--- fitPS-1.0.6/fitPS/inst/doc/examples.Rmd |only fitPS-1.0.6/fitPS/inst/doc/examples.pdf |binary fitPS-1.0.6/fitPS/inst/doc/simple_P_fit.R | 41 - fitPS-1.0.6/fitPS/inst/doc/simple_P_fit.Rmd |only fitPS-1.0.6/fitPS/inst/doc/simple_P_fit.pdf |binary fitPS-1.0.6/fitPS/man/add.Rd |only fitPS-1.0.6/fitPS/man/confint.psFit.Rd | 14 fitPS-1.0.6/fitPS/man/credint.Rd |only fitPS-1.0.6/fitPS/man/fitDist.Rd | 153 ++++- fitPS-1.0.6/fitPS/man/fitZIDist.Rd | 146 +++-- fitPS-1.0.6/fitPS/man/logLik.psFit.Rd |only fitPS-1.0.6/fitPS/man/makePrior.Rd |only fitPS-1.0.6/fitPS/man/plotPosterior.Rd |only fitPS-1.0.6/fitPS/man/predict.psFit.Rd | 8 fitPS-1.0.6/fitPS/man/rZIzeta.Rd | 8 fitPS-1.0.6/fitPS/man/rzeta.Rd | 2 fitPS-1.0.6/fitPS/tests |only fitPS-1.0.6/fitPS/vignettes/examples.Rmd |only fitPS-1.0.6/fitPS/vignettes/simple_P_fit.Rmd |only 58 files changed, 1261 insertions(+), 886 deletions(-)
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.3.9 dated 2025-09-08 and 0.4.3 dated 2026-06-10
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/DESCRIPTIVES.R | 4 ++-- R/GROUP.DIFFS.R | 6 +++--- R/GROUP.PROFILES.R | 50 ++++++++++++++++++++++++++++++++------------------ R/umvn.R | 4 +++- R/utilities_boc.R | 13 +++++++++++++ man/GROUP.PROFILES.Rd | 10 ++++------ 8 files changed, 68 insertions(+), 41 deletions(-)
Title: Approximate Bayesian Regularization for Parsimonious Estimates
Description: Approximate Bayesian regularization using Gaussian approximations. The input is a vector of estimates
and a Gaussian error covariance matrix of the key parameters. Bayesian shrinkage is then applied
to obtain parsimonious solutions. The method is described on
Karimova, van Erp, Leenders, and Mulder (2025) <DOI:10.1016/j.jmp.2025.102925>. Gibbs samplers are used
for model fitting. The shrinkage priors that are supported are Gaussian (ridge) priors, Laplace
(lasso) priors (Park and Casella, 2008 <DOI:10.1198/016214508000000337>), and horseshoe priors
(Carvalho, et al., 2010; <DOI:10.1093/biomet/asq017>). These priors include an option
for grouped regularization of different subsets of parameters (Meier et al., 2008;
<DOI:10.1111/j.1467-9868.2007.00627.x>). F priors are used for the penalty
parameters lambda^2 (Mulder and Pericchi, 2018 <DOI:10.1214/17-BA1092>). This correspond to
half-Cauchy priors on lambda (Carvalho, Polson, Scott, 2010 <DOI:10.1093/bio [...truncated...]
Author: Joris Mulder [aut, cre],
Diana Karimova [aut, ctb],
Sara van Erp [ctb],
Roger Leenders [ctb]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between shrinkem versions 0.2.0 dated 2024-10-05 and 0.3.0 dated 2026-06-10
DESCRIPTION | 28 +- MD5 | 15 - NAMESPACE | 7 R/RcppExports.R |only R/shrinkem_main_functions.R | 508 +++++++++----------------------------------- inst |only man/shrinkem.Rd | 6 src |only tests |only 9 files changed, 144 insertions(+), 420 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-10 dated 2025-12-02 and 0.3-11 dated 2026-06-10
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/tbm_supplement.Rnw | 5 ++--- inst/doc/tbm_supplement.pdf |binary vignettes/mlt.bib | 8 ++++---- vignettes/tbm_supplement.Rnw | 5 ++--- 8 files changed, 27 insertions(+), 22 deletions(-)
Title: Minimal Matrix Client-Server API
Description: A minimal-dependency client for the 'Matrix' Client-Server
HTTP API <https://spec.matrix.org/>, suitable for talking to a
'Synapse' <https://element-hq.github.io/synapse/> or 'Conduit'
<https://conduit.rs/> homeserver. Covers login, room management,
message send and history, media upload or download, and the
transport endpoints needed to coordinate end-to-end encryption
(device-key and one-time-key publication, key query and claim,
to-device events). Encryption itself is out of scope;
pair with a separate crypto package.
Author: Troy Hernandez [aut, cre] ,
cornball.ai [cph]
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between mx.api versions 0.2.0 dated 2026-05-13 and 0.3.0 dated 2026-06-10
DESCRIPTION | 8 - MD5 | 46 +++++++-- NAMESPACE | 20 ++++ NEWS.md | 30 ++++++ R/account.R |only R/devices.R |only R/http.R | 28 +++++ R/media.R | 167 ++++++++++++++++++++++++++++++++-- R/messages.R | 165 +++++++++++++++++++++++++++++++++ R/profile.R |only R/rooms.R | 25 +++++ README.md | 87 ++++++++++++++--- build |only inst/tinytest/test_devices.R |only inst/tinytest/test_errors.R |only inst/tinytest/test_media.R | 20 ++++ inst/tinytest/test_profile_room_ops.R |only inst/tinytest/test_state_account.R |only man/mx.api-package.Rd | 15 +-- man/mx_canonical_json.Rd | 3 man/mx_delete_device.Rd |only man/mx_devices.Rd |only man/mx_get_account_data.Rd |only man/mx_get_state.Rd |only man/mx_guess_mime.Rd |only man/mx_media_config.Rd |only man/mx_profile.Rd |only man/mx_redact.Rd |only man/mx_room_invite.Rd |only man/mx_send_event.Rd |only man/mx_send_media.Rd |only man/mx_set_account_data.Rd |only man/mx_set_avatar_url.Rd |only man/mx_set_displayname.Rd |only man/mx_set_state.Rd |only man/mx_typing.Rd |only 36 files changed, 564 insertions(+), 50 deletions(-)
Title: Tidy Tools for Joinpoint Regression Models
Description: Provides tools to fit joinpoint regression models with a log-linear
specification by levels of a categorical variable. The package acts as a
wrapper around the 'segmented' package, facilitating model fitting, selection,
and interpretation. It includes functions to estimate the Annual Percent Change
(APC) and the Average Annual Percent Change (AAPC), along with their 95%
confidence intervals, and to generate formatted summary tables and plots of results.
Author: Tamara Ricardo [aut, cre]
Maintainer: Tamara Ricardo <tamararicardo83@gmail.com>
Diff between joinpointR versions 0.6.2 dated 2026-05-28 and 1.0.0 dated 2026-06-10
DESCRIPTION | 14 +- MD5 | 40 ++++--- NAMESPACE | 1 NEWS.md | 10 + R/as_ft_jp.R |only R/get_aapc.R | 129 +++++++++++++++---------- R/get_apc.R | 113 +++++++++++++++------- R/gg_jpoint.R | 277 +++++++++++++++++++++++++++++++++++++++++++----------- R/hiv_data.R |only R/model_jp.R | 213 ++++++++++++++++++++++++++++------------- R/summary_jp.R | 220 ++++++++++++++++++------------------------ R/utils.R | 17 ++- README.md | 4 build |only data |only inst |only man/get_aapc.Rd | 49 ++++++--- man/get_apc.Rd | 42 +++++--- man/gg_jpoint.Rd | 97 ++++++++++++++++-- man/hiv_data.Rd |only man/jp_to_ft.Rd |only man/model_jp.Rd | 68 ++++++++----- man/summary_jp.Rd | 49 ++++----- vignettes |only 24 files changed, 887 insertions(+), 456 deletions(-)
Title: A Magical Framework for Collaborative & Reproducible Data
Analysis
Description: A comprehensive data analysis framework for NIH-funded research that streamlines workflows for both data cleaning and preparing NIH Data Archive ('NDA') submission templates. Provides unified access to multiple data sources ('REDCap', 'MongoDB', 'Qualtrics', 'SQL', 'ORACLE') through interfaces to their APIs, with specialized functions for data cleaning, filtering, merging, and parsing. Features automatic validation, field harmonization, and memory-aware processing to enhance reproducibility in multi-site collaborative research as described in Mittal et al. (2021) <doi:10.20900/jpbs.20210011>.
Author: Joshua G. Kenney [aut, cre],
Trevor F. Williams [aut],
Minerva K. Pappu [aut],
Michael J. Spilka [aut],
Danielle N. Pratt [ctb],
Victor J. Pokorny [ctb],
Santiago Castiello de Obeso [ctb],
Praveen Suthaharan [ctb],
Christian R. Horgan [ctb]
Maintainer: Joshua G. Kenney <joshua.kenney@yale.edu>
Diff between wizaRdry versions 0.6.8 dated 2026-05-12 and 0.6.16 dated 2026-06-10
DESCRIPTION | 6 MD5 | 45 ++--- R/checkQualtricsDuplicates.R | 4 R/createCsv.R | 11 + R/createNdaSubmissionTemplate.R | 11 + R/dataRequest.R | 38 ++-- R/getMongo.R | 359 ++++++++++++++++++++++++---------------- R/getOracle.R | 17 + R/getQualtrics.R | 15 + R/getRedcap.R | 60 ++++++ R/getSql.R | 12 + R/indexFilter.R |only R/ndaRequest.R | 337 +++++++++++++++++++++---------------- R/ndaTransformations.R | 242 ++++++++++++++++++++++---- R/ndaValidationHelpers.R | 8 R/ndaValidator.R | 134 +++++++------- R/testSuite.R | 10 - R/zzz.R | 10 + man/mongo.index.Rd | 5 man/nda.Rd | 16 - man/oracle.index.Rd | 5 man/qualtrics.index.Rd | 5 man/redcap.index.Rd | 6 man/sql.index.Rd | 5 24 files changed, 897 insertions(+), 464 deletions(-)
Title: Headless Venn Diagram Analysis and Rendering
Description: Headless companion to the 'Venn Diagram Lab' web tool
(<https://www.venndiagramlab.org/>). Build, render, and statistically
analyze Venn / 'UpSet' diagrams from 'CSV' / 'TSV' / 'GMT' / 'GMX'
inputs. Provides the same 44 SVG models, intersection / 'Jaccard' /
hypergeometric statistics, and PDF report layout as the web tool,
with byte-equivalent 'TSV' exports (parity-tested against the
published Python package). Integrates with 'ggplot2', 'tidygraph',
and 'broom'.
Author: Zoltan Dul [aut, cre] ,
Marton Oelbei [aut] ,
N. Shaun B. Thomas [aut],
Azeddine Si Ammour [aut] ,
Attila Csikasz-Nagy [aut]
Maintainer: Zoltan Dul <zoltan.dul@gmail.com>
Diff between vennDiagramLab versions 2.0.5 dated 2026-05-18 and 2.4.2 dated 2026-06-10
vennDiagramLab-2.0.5/vennDiagramLab/tests/testthat/fixtures |only vennDiagramLab-2.4.2/vennDiagramLab/DESCRIPTION | 20 vennDiagramLab-2.4.2/vennDiagramLab/MD5 | 103 vennDiagramLab-2.4.2/vennDiagramLab/NAMESPACE | 23 vennDiagramLab-2.4.2/vennDiagramLab/NEWS.md | 118 vennDiagramLab-2.4.2/vennDiagramLab/R/classes.R | 22 vennDiagramLab-2.4.2/vennDiagramLab/R/cluster.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/enrichment-plot-helpers.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/excel-workbook.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/io.R | 128 vennDiagramLab-2.4.2/vennDiagramLab/R/region-accessors.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/region-expression.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/render-enrichment-bar.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/render-enrichment-lollipop.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/render-pdf.R | 685 ++++ vennDiagramLab-2.4.2/vennDiagramLab/R/render-share-distribution.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/render-svg-items.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/render-svg.R | 33 vennDiagramLab-2.4.2/vennDiagramLab/R/render-upset.R | 105 vennDiagramLab-2.4.2/vennDiagramLab/R/share-distribution.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/zip-report.R |only vennDiagramLab-2.4.2/vennDiagramLab/R/zzz.R | 3 vennDiagramLab-2.4.2/vennDiagramLab/README.md | 128 vennDiagramLab-2.4.2/vennDiagramLab/inst/CITATION | 7 vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v01_quickstart.html | 356 +- vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v02_real_cancer_drivers.html | 429 ++ vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v03_proportional_diagrams.html | 437 ++ vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v04_upset_vs_venn_vs_network.html | 361 +- vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v05_statistics_deep_dive.html | 420 ++ vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v06_pipeline_integration.html | 390 +- vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v07_pdf_reports.html | 361 +- vennDiagramLab-2.4.2/vennDiagramLab/inst/doc/v08_custom_styling_and_export.html | 419 +- vennDiagramLab-2.4.2/vennDiagramLab/inst/extdata/samples/dataset_mock_gene_sets.csv | 551 --- vennDiagramLab-2.4.2/vennDiagramLab/inst/extdata/samples/dataset_mock_streaming_platforms.csv | 1602 +++++----- vennDiagramLab-2.4.2/vennDiagramLab/man/SvgImage-class.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/cluster_set_order.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/exclusive_items.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/intersection_items.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/item_share_distribution.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/parse_region_expression.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/render_cluster_heatmap.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/render_enrichment_bar.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/render_enrichment_lollipop.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/render_share_distribution.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/render_venn_svg.Rd | 22 vennDiagramLab-2.4.2/vennDiagramLab/man/to_excel_workbook.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/to_pdf_report.Rd | 10 vennDiagramLab-2.4.2/vennDiagramLab/man/to_zip_report.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/man/union_items.Rd |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-cluster.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-enrichment-plot-helpers.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-excel-workbook.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-parity-with-webtool-v222.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-phase11-integration.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-region-accessors.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-region-expression.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-enrichment-bar.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-enrichment-lollipop.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-pdf.R | 124 vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-share-distribution.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-svg-highlight.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-svg-items.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-render-upset.R | 4 vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-share-distribution.R |only vennDiagramLab-2.4.2/vennDiagramLab/tests/testthat/test-zip-report.R |only 65 files changed, 4605 insertions(+), 2256 deletions(-)
More information about vennDiagramLab at CRAN
Permanent link
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.2.0 dated 2026-03-11 and 2.2.1 dated 2026-06-10
DESCRIPTION | 11 MD5 | 50 +- NAMESPACE | 2 NEWS.md | 7 R/geom_diamond.R | 123 ++++-- R/is_subset.R | 2 R/nuggets-package.R | 2 R/partition.R | 454 ++++++++++++++++++------- R/testers.R | 11 R/ui-conditionFilterModule.R | 13 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/data-preparation.html | 16 inst/doc/nuggets.html | 2 man/association_matrix.Rd | 10 man/dig_ancestors.Rd | 3 man/is_subset.Rd | 2 man/nuggets-package.Rd | 5 man/partition.Rd | 409 ++++++++++++++++------ man/reexports.Rd | 2 tests/testthat/test-dig_complement_contrasts.R | 11 tests/testthat/test-geom_diamond.R | 48 +- tests/testthat/test-partition.R | 136 +++++++ tests/testthat/test-testers.R | 14 tests/testthat/test-wilcox_test.R | 8 26 files changed, 983 insertions(+), 360 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed
outputs from commonly used statistical and psychometric functions into
compact, single-row tables and simple graphs, with utilities to export
results to CSV, Word, and Excel formats. The package does not implement
new statistical methods or estimation procedures; instead, it organises
and presents results obtained from existing packages such as 'psych',
'stats', 'gtsummary', and 'lavaan' to streamline reporting workflows in
clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.2.6 dated 2026-04-25 and 0.2.7 dated 2026-06-10
DESCRIPTION | 17 ++++++++++++----- MD5 | 12 +++++++----- NAMESPACE | 2 ++ NEWS.md | 14 ++++++++++++++ R/make_dataframe_to_output.R | 2 +- R/make_lavaan_mediation_tables.R |only inst/CITATION | 25 +++++++++++++------------ man/make_lavaan_mediation_tables.Rd |only 8 files changed, 49 insertions(+), 23 deletions(-)
Title: OPTICS K-Xi Density-Based Clustering
Description: Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in nois [...truncated...]
Author: Thomas Charlon [aut, cre]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between opticskxi versions 1.2.1 dated 2025-03-09 and 1.2.2 dated 2026-06-10
DESCRIPTION | 9 +++---- MD5 | 26 +++++++++++--------- NEWS.md | 4 +++ R/dist_matrix.R | 12 +++++---- build/vignette.rds |binary inst/doc/ensemble_metrics.R | 2 - inst/doc/ensemble_metrics.pdf |binary inst/doc/opticskxi.R | 26 +++++++++----------- inst/doc/opticskxi.Rnw | 48 +++++++++++++++++++------------------- inst/doc/opticskxi.pdf |binary man/normalize.Rd | 2 - tests/testthat/Rplots.pdf |only tests/testthat/test-cosine_simi.R |only tests/testthat/test-opticskxi.R | 2 - vignettes/opticskxi.Rnw | 48 +++++++++++++++++++------------------- 15 files changed, 92 insertions(+), 87 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Danielle Newby [aut, cre] ,
Xihang Chen [aut] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Danielle Newby <danielle.newby@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.2.4 dated 2025-03-24 and 0.3.0 dated 2026-06-10
DESCRIPTION | 41 MD5 | 102 - NAMESPACE | 28 R/CohortSymmetry-package.R | 22 R/crudeSequenceRatio.R | 30 R/generateSequenceCohortSet.R | 770 +++++----- R/getConfidenceInterval.R | 78 - R/getSummarisedResult.R | 134 - R/helpers.R | 338 ++-- R/mockCohortSymmetry.R | 186 +- R/nullSequenceRatio.R | 188 +- R/tableSequenceratios.R | 128 - README.md | 362 ++-- build/vignette.rds |binary inst/WORDLIST | 132 - inst/doc/a01_Introduction.R | 150 +- inst/doc/a01_Introduction.Rmd | 260 +-- inst/doc/a01_Introduction.html | 941 ++++++------ inst/doc/a02_Generate_a_sequence_cohort.R | 296 ++-- inst/doc/a02_Generate_a_sequence_cohort.Rmd | 562 +++---- inst/doc/a02_Generate_a_sequence_cohort.html | 1297 ++++++++--------- inst/doc/a03_Summarise_sequence_ratios.R | 126 - inst/doc/a03_Summarise_sequence_ratios.Rmd | 174 +- inst/doc/a03_Summarise_sequence_ratios.html | 821 +++++------ inst/doc/a04_Visualise_sequence_ratios.R | 166 +- inst/doc/a04_Visualise_sequence_ratios.Rmd | 260 +-- inst/doc/a04_Visualise_sequence_ratios.html | 851 +++++------ inst/doc/a05_Summarise_temporal_symmetry.R | 152 +- inst/doc/a05_Summarise_temporal_symmetry.Rmd | 224 +-- inst/doc/a05_Summarise_temporal_symmetry.html | 961 ++++++------- inst/doc/a06_Visualise_temporal_symmetry.R | 132 - inst/doc/a06_Visualise_temporal_symmetry.Rmd | 190 +- inst/doc/a06_Visualise_temporal_symmetry.html | 787 +++++----- man/CohortSymmetry-package.Rd | 80 - man/generateSequenceCohortSet.Rd | 148 +- man/mockCohortSymmetry.Rd | 86 - man/plotSequenceRatios.Rd | 96 - man/plotTemporalSymmetry.Rd | 98 - man/summariseSequenceRatios.Rd | 70 man/summariseTemporalSymmetry.Rd | 72 man/tableSequenceRatios.Rd | 96 - man/tableTemporalSymmetry.Rd | 96 - tests/testthat.R | 24 tests/testthat/test-attrition.R | 1886 +++++++++++++------------- tests/testthat/test-dbs.R | 182 +- tests/testthat/test-eunomia.R | 138 - vignettes/a01_Introduction.Rmd | 260 +-- vignettes/a02_Generate_a_sequence_cohort.Rmd | 562 +++---- vignettes/a03_Summarise_sequence_ratios.Rmd | 174 +- vignettes/a04_Visualise_sequence_ratios.Rmd | 260 +-- vignettes/a05_Summarise_temporal_symmetry.Rmd | 224 +-- vignettes/a06_Visualise_temporal_symmetry.Rmd | 190 +- 52 files changed, 7820 insertions(+), 7811 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for
the 'zip' function, that does not require any additional external
tools on any platform.
Author: Gabor Csardi [aut, cre],
Kuba Podgorski [ctb],
Rich Geldreich [ctb],
Arm Limited [ctb, cph] ),
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zip versions 2.3.3 dated 2025-05-13 and 3.0.0 dated 2026-06-10
DESCRIPTION | 18 MD5 | 176 NEWS.md | 68 R/compat-vctrs.R | 2 R/http.R |only R/inflate.R | 18 R/process.R | 181 R/threaded.R |only R/utils.R | 168 R/zip.R | 269 README.md | 86 man/inflate.Rd | 8 man/internal |only man/unzip.Rd | 47 man/unzip_process.Rd | 25 man/zip-package.Rd | 6 man/zip.Rd | 54 man/zip_list.Rd | 21 man/zip_process.Rd | 5 src/Makevars | 22 src/Makevars.win | 29 src/cleancall.c |only src/cleancall.h |only src/cmdunzip_lib.c |only src/crypto.c |only src/crypto.h |only src/errors.c |only src/errors.h |only src/init.c | 42 src/install.libs.R | 2 src/mbedtls |only src/miniz.c |11477 ++++++++++----------- src/miniz.h | 1946 +-- src/rzip.c | 358 src/tools/cmdunzip.c | 57 src/tools/cmdzip.c | 57 src/zip.c | 1229 ++ src/zip.h | 69 tests/testthat/_snaps/errors.md | 26 tests/testthat/_snaps/http.md |only tests/testthat/_snaps/threaded-unzip.md |only tests/testthat/_snaps/unzip.md | 2 tests/testthat/_snaps/weird-paths.md | 2 tests/testthat/fixtures/aes128.zip |only tests/testthat/fixtures/aes192.zip |only tests/testthat/fixtures/aes256.zip |only tests/testthat/fixtures/cp437.zip |only tests/testthat/fixtures/cp932.zip |only tests/testthat/fixtures/http-nodirs.zip |only tests/testthat/fixtures/http.zip |only tests/testthat/fixtures/make-encrypted-fixtures.sh |only tests/testthat/fixtures/make-zip64-fixtures.sh |only tests/testthat/fixtures/stored-zero-compsize.zip |only tests/testthat/fixtures/zip64-extra.zip |only tests/testthat/fixtures/zip64.zip |only tests/testthat/fixtures/zipcrypto.zip |only tests/testthat/helper-encryption.R |only tests/testthat/helper.R | 243 tests/testthat/test-crypto.R |only tests/testthat/test-errors.R | 40 tests/testthat/test-http.R |only tests/testthat/test-keys.R |only tests/testthat/test-large-files.R | 4 tests/testthat/test-threaded-unzip.R |only tests/testthat/test-unzip-process.R | 34 tests/testthat/test-unzip.R | 126 tests/testthat/test-zip-encrypt.R |only tests/testthat/test-zip-list.R | 59 tests/testthat/test-zip.R | 194 tests/testthat/test-zip64.R |only tools/extra |only tools/getzipexe.R | 4 tools/valgrind.supp |only 73 files changed, 10482 insertions(+), 6692 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph] ,
Yong Yang [ctb, cph] ,
Yi Cao [ctb, cph] ,
Neil Kaye [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.14.0 dated 2026-05-09 and 2.14.1 dated 2026-06-10
DESCRIPTION | 6 MD5 | 355 NAMESPACE | 464 - NEWS.md | 101 R/3Dplot.R | 202 R/HPart.R | 352 R/Information.R | 760 - R/Islands.R | 156 R/MSTSegments.R | 158 R/Plot3.R | 168 R/RcppExports.R | 618 - R/Reduce.R | 134 R/TreeDist-package.R | 286 R/VisualizeMatching.R | 450 R/cluster_stats.R | 548 - R/hierarchical_mutual_information.R | 374 R/kmeanspp.R | 52 R/lap.R | 130 R/median.R | 172 R/parallel.R | 238 R/plot.R | 150 R/shiny.R | 258 R/spectral_clustering.R | 162 R/transfer_consensus.R | 1161 +- R/tree_distance.R | 592 - R/tree_distance_info.R | 882 - R/tree_distance_kendall-colijn.R | 432 R/tree_distance_mast.R | 232 R/tree_distance_msd.R | 126 R/tree_distance_msi.R | 158 R/tree_distance_nni.R | 342 R/tree_distance_nye.R | 416 R/tree_distance_path.R | 216 R/tree_distance_rf.R | 446 R/tree_distance_spr.R | 1050 +- R/tree_distance_transfer.R | 8 R/tree_distance_utilities.R | 1554 +-- R/tree_information.R | 946 +- R/trustworthiness.R | 154 R/zzz.R | 56 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 148 inst/REFERENCES.bib | 1496 +-- inst/TreeDist.svg | 88 inst/WORDLIST | 275 inst/apa-old-doi-prefix.csl | 4546 +++++----- inst/doc/Generalized-RF.Rmd | 586 - inst/doc/Robinson-Foulds.Rmd | 718 - inst/doc/Using-TreeDist.Rmd | 304 inst/doc/Using-TreeDist.html | 6 inst/doc/compare-treesets.Rmd | 354 inst/doc/different-leaves.Rmd | 194 inst/doc/information.Rmd | 580 - inst/doc/landscapes.Rmd | 256 inst/doc/treespace.Rmd | 942 +- inst/doc/using-distances.Rmd | 856 - inst/include/TreeDist/lap_impl.h | 13 inst/treespace/app.R | 57 man/AllSplitPairings.Rd | 78 man/CalculateTreeDistance.Rd | 60 man/CompareAll.Rd | 106 man/Entropy.Rd | 66 man/GeneralizedRF.Rd | 128 man/HH.Rd | 24 man/HPart.Rd | 130 man/HierarchicalMutualInfo.Rd | 280 man/HierarchicalMutualInformation.Rd | 24 man/Islands.Rd | 158 man/JaccardRobinsonFoulds.Rd | 292 man/KMeansPP.Rd | 110 man/KendallColijn.Rd | 290 man/LAPJV.Rd | 126 man/MASTSize.Rd | 164 man/MCITree.Rd | 114 man/MSTSegments.Rd | 170 man/MapTrees.Rd | 250 man/MappingQuality.Rd | 112 man/MatchingSplitDistance.Rd | 208 man/MeilaVariationOfInformation.Rd | 118 man/NNIDist.Rd | 242 man/NormalizeInfo.Rd | 192 man/NyeSimilarity.Rd | 284 man/PathDist.Rd | 176 man/ReduceTrees.Rd | 102 man/ReportMatching.Rd | 54 man/Robinson-Foulds.Rd | 328 man/SPRDist.Rd | 188 man/SpectralEigens.Rd | 102 man/SplitEntropy.Rd | 102 man/SplitSharedInformation.Rd | 196 man/StartParallel.Rd | 210 man/TransferConsensus.Rd | 132 man/TransferDist.Rd | 236 man/TreeDist-package.Rd | 302 man/TreeDistance.Rd | 676 - man/TreeInfo.Rd | 432 man/VisualizeMatching.Rd | 178 man/clone.Rd | 66 man/cluster-statistics.Rd | 212 man/cpp_mutual_clustering_all_pairs.Rd | 54 man/cpp_transfer_consensus.Rd | 70 man/cpp_transfer_dist.Rd | 52 man/cpp_transfer_dist_all_pairs.Rd | 48 man/cpp_transfer_dist_cross_pairs.Rd | 48 man/dot-SPRPairDeO.Rd | 44 man/dot-ThreeDPlotServer.Rd | 50 man/dot-TreeDistance.Rd | 46 man/entropy_int.Rd | 40 man/median.multiPhylo.Rd | 188 src/lap.cpp | 295 src/pairwise_distances.cpp | 4 src/tree_distances.cpp | 2 src/tree_distances.h | 6 tests/benchmark/benchmark.R | 36 tests/benchmark/kmeanspp_streaming.R |only tests/testthat.R | 8 tests/testthat/_snaps/HPart/plot-hpart.svg | 96 tests/testthat/_snaps/MSTSegments/mst-example-plot.svg | 622 - tests/testthat/_snaps/Plot3/plotting-order.svg | 134 tests/testthat/_snaps/Plot3/simple-plot.svg | 134 tests/testthat/_snaps/VisualizeMatching/hidden-edge-labels.svg | 500 - tests/testthat/_snaps/VisualizeMatching/jrf-vm-matchzeros-false.svg | 348 tests/testthat/_snaps/VisualizeMatching/rf-collapse-a-node.svg | 566 - tests/testthat/_snaps/VisualizeMatching/rf-collapse-and-change.svg | 554 - tests/testthat/_snaps/VisualizeMatching/rf-vm-single-splits-plainedges.svg | 352 tests/testthat/_snaps/VisualizeMatching/test-vm.svg | 396 tests/testthat/_snaps/VisualizeMatching/test-vmr.svg | 368 tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 566 - tests/testthat/_snaps/VisualizeMatching/vm-one-rooted.svg | 196 tests/testthat/_snaps/VisualizeMatching/vm-unrooted.svg | 182 tests/testthat/_snaps/plot/test-lc-letters.svg | 162 tests/testthat/_snaps/plot/test-uc-letters.svg | 162 tests/testthat/_snaps/plot/test-with-space.svg | 162 tests/testthat/_snaps/plot/test-without-space.svg | 162 tests/testthat/setup.R | 14 tests/testthat/test-HPart.R | 150 tests/testthat/test-Islands.R | 38 tests/testthat/test-MCITree.R | 104 tests/testthat/test-MSTSegments.R | 94 tests/testthat/test-Plot3.R | 56 tests/testthat/test-Reduce.R | 132 tests/testthat/test-VisualizeMatching.R | 310 tests/testthat/test-batch_coverage.R | 892 - tests/testthat/test-binary_entropy_counts.R | 12 tests/testthat/test-cluster_stats.R | 170 tests/testthat/test-day_1985.cpp.r | 154 tests/testthat/test-different-tips.R | 166 tests/testthat/test-hierarchical_mutual_information.R | 124 tests/testthat/test-hmi.cpp.R | 318 tests/testthat/test-information.R | 196 tests/testthat/test-kmeanspp.R | 35 tests/testthat/test-lap.R | 720 - tests/testthat/test-large-trees.R | 254 tests/testthat/test-mast.R | 158 tests/testthat/test-mci_impl.R | 106 tests/testthat/test-pairwise_distances.R | 606 - tests/testthat/test-parallel.R | 50 tests/testthat/test-plot.R | 74 tests/testthat/test-spectral_clustering.R | 36 tests/testthat/test-split_info.R | 142 tests/testthat/test-transfer_consensus.R | 1428 +-- tests/testthat/test-tree_distance.R | 2044 ++-- tests/testthat/test-tree_distance_kc.R | 120 tests/testthat/test-tree_distance_nni.R | 416 tests/testthat/test-tree_distance_path.R | 66 tests/testthat/test-tree_distance_spr.R | 860 - tests/testthat/test-tree_distance_transfer.R | 1014 +- tests/testthat/test-tree_distance_utilities.R | 838 - tests/testthat/test-tree_information.R | 316 vignettes/Generalized-RF.Rmd | 586 - vignettes/Robinson-Foulds.Rmd | 718 - vignettes/Using-TreeDist.Rmd | 304 vignettes/compare-treesets.Rmd | 354 vignettes/different-leaves.Rmd | 194 vignettes/information.Rmd | 580 - vignettes/landscapes.Rmd | 256 vignettes/treespace.Rmd | 942 +- vignettes/using-distances.Rmd | 856 - 179 files changed, 28653 insertions(+), 28905 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Jakub Nowicki [aut, cre],
Kamil Zyla [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Rodrigo Basa [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Jakub Nowicki <opensource+kuba@appsilon.com>
Diff between rhino versions 1.11.0 dated 2025-04-02 and 1.12.0 dated 2026-06-10
DESCRIPTION | 28 MD5 | 61 NAMESPACE | 5 NEWS.md | 16 R/init.R | 113 R/rhino.R | 57 R/tools.R | 76 inst/WORDLIST | 3 inst/rstudio/templates/project/init.dcf | 10 inst/templates/agents_md |only inst/templates/app_structure/app/main.R | 7 inst/templates/node/package-lock.json |13781 ++++++++----------------- inst/templates/node/package.json | 26 man/covr_r.Rd |only man/covr_report.Rd |only man/init.Rd | 7 man/log.Rd | 5 man/use_agents_md.Rd |only man/use_e2e_tests.Rd |only man/use_github_actions_ci.Rd |only tests/e2e/app-files/hello.cy.js | 4 tests/e2e/app-files/main.R | 2 tests/e2e/app-files/say_hello_module.R |only tests/e2e/app-files/test-say_hello_module.R |only tests/e2e/test-build-js.R | 71 tests/e2e/test-build-sass.R | 52 tests/e2e/test-covr_r.R |only tests/e2e/test-format-js.R | 51 tests/e2e/test-format-sass.R | 50 tests/e2e/test-lint-js.R | 42 tests/e2e/test-lint-sass.R | 42 tests/testthat/helpers/hello.R |only tests/testthat/helpers/main.R |only tests/testthat/helpers/say_hello_module.R |only tests/testthat/helpers/test-hello.R |only tests/testthat/helpers/test-say_hello_module.R |only tests/testthat/test-init.R |only tests/testthat/test-rhino.R | 97 tests/testthat/test-tools.R | 42 39 files changed, 5266 insertions(+), 9382 deletions(-)
Title: Neutrosophic Analysis of Row Column Designs
Description: Description: Provides methods for Neutrosophic Analysis of Variance (NANOVA)
and Neutrosophic Analysis of Covariance (NANCOVA) for row-column designs,
including Latin square designs and Youden square designs, using
interval-valued observations. The package computes neutrosophic sums of
squares, mean squares, interval-valued F-statistics, significance tests,
and multiple comparisons using Least Significant Difference (LSD)
procedures. For crisp data, users may enter identical lower and upper
values of responses to obtain classical Analysis of Variance (ANOVA)
results. Similarly, users may enter identical lower and upper values for
both responses and covariates to obtain classical Analysis of Covariance
(ANCOVA) results.
Author: Neethu R.S. [aut, ctb],
Boyina Devi Priyanka [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Vinaykumar L.N. [aut, cre]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between NeutroRCDsAnalysis versions 0.1.0 dated 2026-06-08 and 0.1.1 dated 2026-06-10
DESCRIPTION | 10 +++++++--- MD5 | 2 +- 2 files changed, 8 insertions(+), 4 deletions(-)
More information about NeutroRCDsAnalysis at CRAN
Permanent link
Title: Tidy and Streamlined Metabolomics Data Workflows
Description: Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>, Stekhoven et al. (2012) <doi:10.1093/bioinformatics/btr597>, Tibshirani et al. (2017) <doi:10.18129/B9.BIOC.IMPUTE>, Troyanskaya et al. (2001) <doi:10.1093/bioinformatics/17.6.520>), normalization (Bolstad et al. (2003) <doi:10.1093/bioinformatics/19.2.185>, Dieterle et al. (2006) <doi:10.1021/ac051632c>, Zhao et al. (2020) <doi:10.1038/s41598-020-72664-6>) transformation, centering and scaling (Van Den Berg et al. (2006) <doi:10.1186/1471-2164-7-142>) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) <doi:10.21105/joss.01686>) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and [...truncated...]
Author: Yannik Schermer [aut, cre, cph]
Maintainer: Yannik Schermer <yannik.schermer@chem.rptu.de>
Diff between metamorphr versions 0.4.0 dated 2026-06-09 and 0.4.1 dated 2026-06-10
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 5 R/io.R | 8 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/conjugate-screening.html | 4 man/figures/README-example-dplyr-1-1.svg | 614 ++++++++++++------------- man/figures/README-example-dplyr-2-1.svg | 512 ++++++++++---------- man/figures/README-example-workflow-1.svg | 300 ++++++------ man/metamorphr-package.Rd | 5 tests/testthat/test-read_featuretable.R | 10 tests/testthat/test-read_featuretable_mzmine.R | 3 14 files changed, 772 insertions(+), 729 deletions(-)
Title: Laplace Factor Model Analysis and Evaluation
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
This is a re-admission after prior archival of version 0.3.3 dated 2025-12-06
Diff between LFM versions 0.3.3 dated 2025-12-06 and 0.3.4 dated 2026-06-10
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- NAMESPACE | 1 + R/rlaplace.R |only man/rlaplace.Rd |only 5 files changed, 9 insertions(+), 6 deletions(-)
Title: Estimate Functional and Stochastic Parameters of Linear Models
with Correlated Residuals and Missing Data
Description: Implements the Generalized Method of Wavelet Moments with Exogenous Inputs estimator (GMWMX) presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L., Molinari, R. and Guerrier, S. (2024) <doi:10.48550/arXiv.2409.05160>.
The GMWMX estimator allows to estimate functional and stochastic parameters of linear models with correlated residuals in presence of missing data.
The 'gmwmx2' package provides functions to load and plot Global Navigation Satellite System (GNSS) data from the Nevada Geodetic Laboratory and functions to estimate linear model model with correlated residuals in presence of missing data.
Author: Lionel Voirol [aut, cre] ,
Haotian Xu [aut] ,
Yuming Zhang [aut] ,
Luca Insolia [aut] ,
Roberto Molinari [aut] ,
Stephane Guerrier [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between gmwmx2 versions 0.0.4 dated 2026-01-07 and 0.0.5 dated 2026-06-10
gmwmx2-0.0.4/gmwmx2/inst/doc/fit_model.R |only gmwmx2-0.0.4/gmwmx2/inst/doc/fit_model.Rmd |only gmwmx2-0.0.4/gmwmx2/inst/doc/fit_model.html |only gmwmx2-0.0.4/gmwmx2/man/plot.fit_gnss_ts_ngl.Rd |only gmwmx2-0.0.4/gmwmx2/man/summary.fit_gnss_ts_ngl.Rd |only gmwmx2-0.0.4/gmwmx2/vignettes/fit_model.Rmd |only gmwmx2-0.0.5/gmwmx2/DESCRIPTION | 12 gmwmx2-0.0.5/gmwmx2/MD5 | 136 gmwmx2-0.0.5/gmwmx2/NAMESPACE | 42 gmwmx2-0.0.5/gmwmx2/NEWS.md | 30 gmwmx2-0.0.5/gmwmx2/R/RcppExports.R | 8 gmwmx2-0.0.5/gmwmx2/R/constructor_time_series_model.R |only gmwmx2-0.0.5/gmwmx2/R/create_X_matrix.R |only gmwmx2-0.0.5/gmwmx2/R/fill_missing_parameters.R |only gmwmx2-0.0.5/gmwmx2/R/find_initial_values_wn_fl.R | 20 gmwmx2-0.0.5/gmwmx2/R/find_initial_values_wn_pl.R | 102 gmwmx2-0.0.5/gmwmx2/R/generate.R |only gmwmx2-0.0.5/gmwmx2/R/get_autocovariance.R |only gmwmx2-0.0.5/gmwmx2/R/get_variance_covariance_matrix.R |only gmwmx2-0.0.5/gmwmx2/R/gmwm2.R |only gmwmx2-0.0.5/gmwmx2/R/gmwmx2.R | 1546 +++++----- gmwmx2-0.0.5/gmwmx2/R/loss_functions_gmwmx.R |only gmwmx2-0.0.5/gmwmx2/R/misc.R |only gmwmx2-0.0.5/gmwmx2/R/ngl.R | 10 gmwmx2-0.0.5/gmwmx2/R/old_implementation_gmwmx2.R |only gmwmx2-0.0.5/gmwmx2/R/prepare_optim_layout.R |only gmwmx2-0.0.5/gmwmx2/R/time_series_model.R |only gmwmx2-0.0.5/gmwmx2/R/transformation_functions.R |only gmwmx2-0.0.5/gmwmx2/README.md | 4 gmwmx2-0.0.5/gmwmx2/build/vignette.rds |binary gmwmx2-0.0.5/gmwmx2/inst/doc/data_generation.R |only gmwmx2-0.0.5/gmwmx2/inst/doc/data_generation.Rmd |only gmwmx2-0.0.5/gmwmx2/inst/doc/data_generation.html |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_composite_stochastic_models.R |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_composite_stochastic_models.Rmd |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_composite_stochastic_models.html |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_geodetic_time_series_from_ngl.R |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_geodetic_time_series_from_ngl.Rmd |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_geodetic_time_series_from_ngl.html |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors.R |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors.Rmd |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors.html |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors_and_missing_observations.R |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors_and_missing_observations.Rmd |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_linear_models_with_dependent_errors_and_missing_observations.html |only gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_small_network.R | 548 +-- gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_small_network.Rmd | 17 gmwmx2-0.0.5/gmwmx2/inst/doc/estimate_small_network.html | 522 +-- gmwmx2-0.0.5/gmwmx2/inst/doc/load_plot_data_ngl.R | 3 gmwmx2-0.0.5/gmwmx2/inst/doc/load_plot_data_ngl.Rmd | 11 gmwmx2-0.0.5/gmwmx2/inst/doc/load_plot_data_ngl.html | 48 gmwmx2-0.0.5/gmwmx2/inst/doc/plot_large_network.R | 349 +- gmwmx2-0.0.5/gmwmx2/inst/doc/plot_large_network.Rmd | 12 gmwmx2-0.0.5/gmwmx2/inst/doc/plot_large_network.html | 281 - gmwmx2-0.0.5/gmwmx2/inst/papers |only gmwmx2-0.0.5/gmwmx2/man/Ma.Rd |only gmwmx2-0.0.5/gmwmx2/man/ar1.Rd |only gmwmx2-0.0.5/gmwmx2/man/as_model_list.Rd |only gmwmx2-0.0.5/gmwmx2/man/dot-comp_prefix.Rd |only gmwmx2-0.0.5/gmwmx2/man/dot-gmwmx2_get_plot_colors.Rd |only gmwmx2-0.0.5/gmwmx2/man/download_estimated_velocities_ngl.Rd | 4 gmwmx2-0.0.5/gmwmx2/man/fill_missing_parameters.Rd |only gmwmx2-0.0.5/gmwmx2/man/flicker.Rd |only gmwmx2-0.0.5/gmwmx2/man/format_model_text.Rd |only gmwmx2-0.0.5/gmwmx2/man/format_params.Rd |only gmwmx2-0.0.5/gmwmx2/man/generate.Rd |only gmwmx2-0.0.5/gmwmx2/man/get_autocovariance.Rd |only gmwmx2-0.0.5/gmwmx2/man/get_theoretical_wv.Rd |only gmwmx2-0.0.5/gmwmx2/man/get_variance_covariance_matrix_model.Rd |only gmwmx2-0.0.5/gmwmx2/man/gmwm2.Rd |only gmwmx2-0.0.5/gmwmx2/man/gmwmx2.Rd | 58 gmwmx2-0.0.5/gmwmx2/man/gmwmx2_new_no_missing.Rd |only gmwmx2-0.0.5/gmwmx2/man/gmwmx2_new_with_missing.Rd |only gmwmx2-0.0.5/gmwmx2/man/gmwmx2_plot_colors.Rd |only gmwmx2-0.0.5/gmwmx2/man/inv_trans_alpha_matern.Rd |only gmwmx2-0.0.5/gmwmx2/man/inv_trans_from_real_to_minus_1_and_1.Rd |only gmwmx2-0.0.5/gmwmx2/man/loss_fn_gmwm.Rd |only gmwmx2-0.0.5/gmwmx2/man/loss_fn_gmwmx_no_missing.Rd |only gmwmx2-0.0.5/gmwmx2/man/loss_fn_gmwmx_with_missing.Rd |only gmwmx2-0.0.5/gmwmx2/man/markov_two_states.Rd |only gmwmx2-0.0.5/gmwmx2/man/matern.Rd |only gmwmx2-0.0.5/gmwmx2/man/pl.Rd |only gmwmx2-0.0.5/gmwmx2/man/plot.generated_composite_model_time_series.Rd |only gmwmx2-0.0.5/gmwmx2/man/plot.generated_missingness.Rd |only gmwmx2-0.0.5/gmwmx2/man/plot.generated_time_series.Rd |only gmwmx2-0.0.5/gmwmx2/man/plot.gmwm2_fit.Rd |only gmwmx2-0.0.5/gmwmx2/man/plot.gmwmx2_fit_gnss_ts_ngl.Rd |only gmwmx2-0.0.5/gmwmx2/man/plus-.sum_model.Rd |only gmwmx2-0.0.5/gmwmx2/man/plus-.time_series_model.Rd |only gmwmx2-0.0.5/gmwmx2/man/prepare_optim_layout.Rd |only gmwmx2-0.0.5/gmwmx2/man/print.gmwm2_fit.Rd |only gmwmx2-0.0.5/gmwmx2/man/print.gmwmx2_fit.Rd |only gmwmx2-0.0.5/gmwmx2/man/print.gmwmx2_fit_gnss_ts_ngl.Rd |only gmwmx2-0.0.5/gmwmx2/man/rw.Rd |only gmwmx2-0.0.5/gmwmx2/man/sum_model.Rd |only gmwmx2-0.0.5/gmwmx2/man/theta_to_domain.Rd |only gmwmx2-0.0.5/gmwmx2/man/trans_alpha_matern.Rd |only gmwmx2-0.0.5/gmwmx2/man/trans_from_real_to_minus_1_and_1.Rd |only gmwmx2-0.0.5/gmwmx2/man/wn.Rd |only gmwmx2-0.0.5/gmwmx2/src/RcppExports.cpp | 26 gmwmx2-0.0.5/gmwmx2/src/rw.cpp |only gmwmx2-0.0.5/gmwmx2/vignettes/REFERENCES.bib | 47 gmwmx2-0.0.5/gmwmx2/vignettes/data_generation.Rmd |only gmwmx2-0.0.5/gmwmx2/vignettes/estimate_composite_stochastic_models.Rmd |only gmwmx2-0.0.5/gmwmx2/vignettes/estimate_geodetic_time_series_from_ngl.Rmd |only gmwmx2-0.0.5/gmwmx2/vignettes/estimate_linear_models_with_dependent_errors.Rmd |only gmwmx2-0.0.5/gmwmx2/vignettes/estimate_linear_models_with_dependent_errors_and_missing_observations.Rmd |only gmwmx2-0.0.5/gmwmx2/vignettes/estimate_small_network.Rmd | 17 gmwmx2-0.0.5/gmwmx2/vignettes/load_plot_data_ngl.Rmd | 11 gmwmx2-0.0.5/gmwmx2/vignettes/plot_large_network.Rmd | 12 110 files changed, 2083 insertions(+), 1793 deletions(-)
Title: Assessing Package Test Reliability and Quality
Description: A reliable and validated tool that calculates unit test coverage for R packages with standard testing frameworks and non-standard testing frameworks.
Author: Edward Gillian [cre, aut] ,
Hugo Bottois [aut] ,
Paulin Charliquart [aut],
Andre Couturier [aut],
Sanofi [cph, fnd]
Maintainer: Edward Gillian <edward.gillian-ext@sanofi.com>
Diff between test.assessr versions 2.1.0 dated 2026-04-30 and 2.1.2 dated 2026-06-10
DESCRIPTION | 22 +- MD5 | 22 +- NEWS.md | 15 + R/install_package_local.R | 8 R/set_up_pkg.R | 4 R/unpack_tarball.R | 99 ++++++++-- README.md | 8 tests/testthat/helper-skip_conditions.R |only tests/testthat/test-install_package_local.R | 31 +++ tests/testthat/test-set_up_pkg.R | 28 ++ tests/testthat/test-skip_conditions.R |only tests/testthat/test-unpack_tarball.R | 276 ++++++++++++++++++++++++++-- tests/testthat/test-utils.R | 66 ++++++ 13 files changed, 507 insertions(+), 72 deletions(-)
Title: Synthetic Control Methods
Description: Implementation of prediction and inference procedures for Synthetic Control methods using least square, lasso, ridge, or simplex-type constraints. Uncertainty is quantified with prediction intervals as developed in Cattaneo, Feng, and Titiunik (2021) <doi:10.1080/01621459.2021.1979561> for a single treated unit and in Cattaneo, Feng, Palomba, and Titiunik (2027) <doi:10.1162/rest_a_01588> for multiple treated units and staggered adoption. More details about the software implementation can be found in Cattaneo, Feng, Palomba, and Titiunik (2025) <doi:10.18637/jss.v113.i01>.
Author: Matias D. Cattaneo [aut, cre],
Yingjie Feng [aut],
Filippo Palomba [aut],
Rocio Titiunik [aut]
Maintainer: Matias D. Cattaneo <matias.d.cattaneo@gmail.com>
Diff between scpi versions 4.0.0 dated 2026-06-03 and 4.0.1 dated 2026-06-10
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 2 +- R/scpi-package.R | 2 +- build/partial.rdb |binary 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Utility Functions and Development Tools for the Admiral Package
Family
Description: Utility functions to check data, variables and conditions for
functions used in 'admiral' and 'admiral' extension packages.
Additional utility helper functions to assist developers with
maintaining documentation, testing and general upkeep of 'admiral' and
'admiral' extension packages.
Author: Edoardo Mancini [aut, cre] ,
Stefan Bundfuss [aut] ,
Arianna Cascone [aut] ,
Kristin Dahnert [aut],
Jeffrey Dickinson [aut],
Ross Farrugia [aut],
Fanny Gautier [aut] ,
Liam Hobby [aut],
Gordon Miller [aut],
Lina Patil [aut],
Ben Straub [aut],
F. Hoff [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiraldev versions 1.4.1 dated 2026-05-27 and 1.5.0 dated 2026-06-10
DESCRIPTION | 29 - MD5 | 167 +++--- NAMESPACE | 6 NEWS.md | 47 + R/admiraldev-package.R | 63 +- R/assertions.R | 12 R/is.R | 51 + R/roclet_rdx.R | 9 R/roxygen_helpers.R |only inst/WORDLIST | 4 inst/doc/package_extensions.Rmd | 2 inst/doc/package_extensions.html | 4 inst/doc/writing_custom_examples.R | 2 inst/doc/writing_custom_examples.Rmd | 4 inst/doc/writing_custom_examples.html | 4 man/add_suffix_to_vars.Rd | 6 man/admiraldev-package.Rd | 8 man/arg_name.Rd | 12 man/assert_atomic_vector.Rd | 44 - man/assert_character_scalar.Rd | 44 - man/assert_character_vector.Rd | 44 - man/assert_data_frame.Rd | 44 - man/assert_date_vector.Rd | 44 - man/assert_expr.Rd | 44 - man/assert_expr_list.Rd | 44 - man/assert_filter_cond.Rd | 44 - man/assert_function.Rd | 44 - man/assert_integer_scalar.Rd | 44 - man/assert_list_element.Rd | 44 - man/assert_list_of.Rd | 44 - man/assert_logical_scalar.Rd | 44 - man/assert_named.Rd | 44 - man/assert_numeric_vector.Rd | 44 - man/assert_one_to_one.Rd | 44 - man/assert_param_does_not_exist.Rd | 44 - man/assert_s3_class.Rd | 44 - man/assert_same_type.Rd | 44 - man/assert_symbol.Rd | 44 - man/assert_unit.Rd | 44 - man/assert_vars.Rd | 44 - man/assert_varval_list.Rd | 44 - man/backquote.Rd | 4 man/capture_output.Rd | 4 man/contains_vars.Rd | 10 man/convert_dtm_to_dtc.Rd | 10 man/dquote.Rd | 4 man/enumerate.Rd | 12 man/execute_example.Rd | 4 man/expr_c.Rd | 6 man/extract_vars.Rd | 10 man/figures/gsk_logo.png |binary man/figures/roche_logo.png |binary man/filter_if.Rd | 10 man/friendly_type_of.Rd | 12 man/get_constant_vars.Rd | 6 man/get_dataset.Rd | 6 man/get_duplicates.Rd | 6 man/get_source_vars.Rd | 6 man/grapes-notin-grapes.Rd | 10 man/grapes-or-grapes.Rd | 12 man/is_auto.Rd | 4 man/is_order_vars.Rd | 4 man/is_valid_dtc.Rd | 44 + man/replace_symbol_in_expr.Rd | 6 man/replace_values_by_names.Rd | 6 man/roxygen/rdx_meta.R | 1 man/roxygen_order_na_handling.Rd |only man/roxygen_param_by_vars.Rd |only man/roxygen_param_dataset.Rd |only man/roxygen_save_memory.Rd |only man/squote.Rd | 4 man/suppress_warning.Rd | 10 man/valid_time_units.Rd | 12 man/vars2chr.Rd | 10 man/warn_if_incomplete_dtc.Rd | 10 man/warn_if_inconsistent_list.Rd | 10 man/warn_if_invalid_dtc.Rd | 10 man/warn_if_vars_exist.Rd | 10 man/what_is_it.Rd | 12 tests/testthat/_snaps/assertions.md | 186 +++--- tests/testthat/_snaps/roclet_rdx/test_class.Rd | 68 +- tests/testthat/_snaps/roxygen2.md |only tests/testthat/test-assertions.R | 667 +++++++++---------------- tests/testthat/test-is.R | 23 tests/testthat/test-roclet_rdx.R | 2 tests/testthat/test-roxygen2.R |only vignettes/package_extensions.Rmd | 2 vignettes/writing_custom_examples.Rmd | 4 88 files changed, 1360 insertions(+), 1319 deletions(-)
Title: Simultaneous Selection by Trait and WAASB Index
Description: This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot generated by the 'metan'. The aim of the current package is to effectively distinguish the top-ranked genotypes in MET (Multi-Environmental Trials). For a detailed explanation of the process of obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the manual included in this package as well as the study by Olivoto & Lúcio (2020) <doi:10.1111/2041-210X.13384>. In this context, "WAASB" refers to the "Weighted Average of Absolute Scores" provided by Olivoto et al. (2019) <doi:10.2134/agronj2019.03.0220>, which quantifies the stability of genotypes across different environments using linear mixed-effect models. To run the package, you need to extract the "WAASB" and "WAASBY" coefficients using the 'metan' and apply them. This tool utilizes PCA (Principal Component Analysis) and differentiates the entries which may be genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a c [...truncated...]
Author: Ali Arminian [aut, cre, cph]
Maintainer: Ali Arminian <abeyran@gmail.com>
Diff between rYWAASB versions 0.3 dated 2025-05-23 and 0.4 dated 2026-06-10
DESCRIPTION | 10 +-- MD5 | 14 ++--- NEWS.md | 4 + R/ranki.R | 2 build/stage23.rdb |binary inst/doc/rYWAASB_manual.html | 114 +++++++++++++++++++++---------------------- inst/extdata/dm.xls |binary inst/extdata/maize.xls |binary 8 files changed, 74 insertions(+), 70 deletions(-)
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] ,
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between rtdists versions 0.11-5 dated 2022-01-07 and 0.11-6 dated 2026-06-10
DESCRIPTION | 11 MD5 | 85 - NAMESPACE | 94 - NEWS | 354 ++-- R/RcppExports.R | 38 R/deprecated.R | 54 R/diffusion.R | 992 +++++------ R/lba.r | 1246 +++++++------- R/lba_race.R | 872 +++++----- R/rr98-data.R | 182 +- R/rtdists-package.R | 50 R/single-lba.r | 1374 ++++++++-------- R/speed_acc-data.R | 64 build/vignette.rds |binary inst/doc/reanalysis_rr98.R | 1406 ++++++++-------- inst/doc/reanalysis_rr98.Rmd | 1870 +++++++++++----------- inst/doc/reanalysis_rr98.html | 2924 ++++++++++++++++++++--------------- inst/extdata/AUTHORS | 44 inst/extdata/lba-math.R | 344 ++-- man/Diffusion.Rd | 578 +++--- man/LBA-race.Rd | 334 ++- man/LBA.Rd | 693 ++++---- man/deprecated.Rd | 50 man/rr98.Rd | 222 +- man/rtdists-package.Rd | 69 man/single-LBA.Rd | 236 +- man/speed_acc.Rd | 122 - src/Sampling.h | 7 tests/testthat.R | 6 tests/testthat/test-diffusion-bugs.R | 224 +- tests/testthat/test-diffusion-math.R | 222 +- tests/testthat/test-diffusion-rcpp.R | 268 +-- tests/testthat/test-diffusion.R | 340 ++-- tests/testthat/test-lba-bugs.R | 1360 ++++++++-------- tests/testthat/test-lba-math.R | 258 +-- tests/testthat/test-lba_basics.R | 1096 ++++++------- tests/testthat/test-lba_input.R | 498 ++--- tests/testthat/test-lba_race-basic.R | 110 - tests/testthat/test-lba_race.R | 668 +++---- tests/testthat/test-lba_race_input.R | 650 +++---- tests/testthat/test-pdiffusion_rng.R | 288 +-- tests/testthat/test-rdiffusion.R |only tests/testthat/test-rrd.R | 84 - vignettes/reanalysis_rr98.Rmd | 1870 +++++++++++----------- 44 files changed, 11436 insertions(+), 10821 deletions(-)
Title: Model-Based Standardisation for Indirect Treatment Comparison
with Limited Subject-Level Data
Description: For the problem of indirect treatment comparison with limited subject-level data, this
package provides tools for model-based standardisation with several different computation approaches.
See Remiro‐Azócar A, Heath A, Baio G (2022) ``Parametric G‐computation for compatible
indirect treatment comparisons with limited individual patient data'',
Res. Synth. Methods, 1–31. ISSN 1759-2879, <doi:10.1002/jrsm.1565>.
Author: Nathan Green [aut, cre, cph] ,
Chengyang Gao [aut],
Antonio Remiro-Azocar [aut]
Maintainer: Nathan Green <n.green@ucl.ac.uk>
Diff between outstandR versions 1.0.0 dated 2026-01-21 and 2.0.0 dated 2026-06-10
DESCRIPTION | 17 - MD5 | 105 +++---- NAMESPACE | 12 NEWS.md | 164 ++++++++++- R/calc_ALD_stats.R | 2 R/calc_IPD_stats.R | 14 R/calc_stc.R | 37 +- R/check_formula.R | 88 ++++-- R/estimate_var_sandwich.R | 12 R/gcomp_bayes.R | 170 +++-------- R/gcomp_ml.R | 239 +++++++++------- R/get_var_method.R | 9 R/maic.R | 344 ++++++++++++++++++------ R/mim.R | 81 +++-- R/outstandR.R | 51 +++ R/parse_formula.R | 2 R/prep_data.R | 10 R/print-strategies.R | 15 - R/result_stats.R | 2 R/simulate_ALD_pseudo_pop.R |only R/strategy_.R | 180 ++++++++++-- R/validate_outstandr.R | 1 README.md | 81 +++-- build/partial.rdb |binary man/AC_IPD_binY_contX.Rd | 68 ++-- man/AC_IPD_contY_mixedX.Rd | 70 ++-- man/BC_ALD_binY_contX.Rd | 60 ++-- man/BC_ALD_contY_mixedX.Rd | 62 ++-- man/IPD_stat_factory.Rd | 36 +- man/calc_ALD_stats.Rd | 2 man/calc_IPD_stats.Rd | 8 man/calc_gcomp_bayes.Rd | 23 - man/calc_gcomp_ml.Rd | 6 man/calc_mim.Rd | 8 man/check_balance_formula.Rd |only man/check_formula.Rd | 6 man/check_formula_base.Rd |only man/figures |only man/gcomp_ml.boot.Rd | 9 man/gcomp_ml_means.Rd | 7 man/maic.boot.Rd | 112 ++++--- man/maic_weights.Rd | 46 +-- man/outstandR-package.Rd | 5 man/outstandR.Rd | 3 man/prep_ipd.Rd | 3 man/result_stats.Rd | 2 man/simulate_ALD_pseudo_pop.Rd | 85 +++++ man/strategy.Rd | 35 ++ tests/testthat/test-IPD_stats.R | 18 - tests/testthat/test-auto_marginals.R | 4 tests/testthat/test-copula_userdefined_distns.R | 9 tests/testthat/test-gcomp.R | 76 +++-- tests/testthat/test-maic_moments.R |only tests/testthat/test-maicstc.R | 116 +++++--- tests/testthat/test-mim.R | 33 +- tests/testthat/test-sandwich_estimator.R | 26 + 56 files changed, 1719 insertions(+), 855 deletions(-)
Title: Factor Model Estimation with Latent Variables
Description: A flexible framework for estimating factor models with multiple
latent variables. Supports linear, probit, ordered probit, and multinomial
logit model components. Features include multi-stage estimation, automatic
parameter initialization, analytical gradients and Hessians, and parallel
estimation. Methods are described in Heckman, Humphries, and Veramendi
(2016) <doi:10.1016/j.jeconom.2015.12.001>, Heckman, Humphries, and
Veramendi (2018) <doi:10.1086/698760>, and Humphries, Joensen, and
Veramendi (2024) <doi:10.1257/pandp.20241026>.
Author: Greg Veramendi [aut, cre],
Jess Xiong [aut]
Maintainer: Greg Veramendi <greg.veramendi@gmail.com>
Diff between factorana versions 1.3.4 dated 2026-05-12 and 1.7.1 dated 2026-06-10
DESCRIPTION | 8 MD5 | 156 +++ NAMESPACE | 11 NEWS.md | 167 ++++ R/RcppExports.R | 18 R/bootstrap_factorana.R |only R/define_factor_model.R | 72 + R/define_model_component.R | 92 ++ R/define_model_system.R | 5 R/fix_factor_param.R | 16 R/initialize_parameters.R | 176 +--- R/optimize_model.R | 56 + R/simulate_factor_model.R |only R/vcov_factorana.R |only inst/doc/dynamic_structural.R | 36 inst/doc/dynamic_structural.Rmd | 76 + inst/doc/dynamic_structural.html | 76 + inst/doc/measurement_system.R | 26 inst/doc/measurement_system.Rmd | 70 + inst/doc/measurement_system.html | 148 +++ inst/doc/roy_model.R | 11 inst/doc/roy_model.Rmd | 22 inst/doc/roy_model.html | 94 +- man/bootstrap_factorana.Rd |only man/bootstrap_factorana_multistage.Rd |only man/bootstrap_fit_sample.Rd |only man/collect_bootstrap.Rd |only man/define_factor_model.Rd | 16 man/define_model_component.Rd | 38 man/estimate_model_rcpp.Rd | 6 man/evaluate_obs_scores_cpp.Rd |only man/generate_bootstrap_samples.Rd |only man/robust_se.Rd |only man/simulate_factor_model.Rd |only man/vcov_factorana.Rd |only src/FactorModel.cpp | 393 +++++++--- src/FactorModel.h | 65 + src/RcppExports.cpp | 13 src/rcpp_interface.cpp | 132 ++- tests/testthat/test-bootstrap.R |only tests/testthat/test-component-ergonomics.R |only tests/testthat/test-mlogit-category-coding.R |only tests/testthat/test-oprobit-category-coding.R |only tests/testthat/test-se-interactions.R |only tests/testthat/test-simulate-factor-model.R |only tests/testthat/test-vcov-robust.R |only tests/testthat/test_logs/test_A_measurement_system_20260529_092814.txt |only tests/testthat/test_logs/test_A_measurement_system_20260529_152148.txt |only tests/testthat/test_logs/test_A_measurement_system_20260531_153721.txt |only tests/testthat/test_logs/test_A_measurement_system_20260605_080051.txt |only tests/testthat/test_logs/test_A_measurement_system_20260605_085754.txt |only tests/testthat/test_logs/test_A_measurement_system_20260605_100223.txt |only 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tests/testthat/test_logs/test_H_se_quadratic_20260610_081615.txt |only tests/testthat/test_logs/test_parallelization_roy_20260529_085705.txt |only tests/testthat/test_logs/test_parallelization_roy_20260531_145249.txt |only tests/testthat/test_logs/test_parallelization_roy_20260605_072924.txt |only tests/testthat/test_logs/test_parallelization_roy_20260605_093125.txt |only tests/testthat/test_logs/test_parallelization_roy_20260606_133933.txt |only tests/testthat/test_logs/test_parallelization_roy_20260608_063824.txt |only tests/testthat/test_logs/test_parallelization_roy_20260610_073853.txt |only vignettes/dynamic_structural.Rmd | 76 + vignettes/measurement_system.Rmd | 70 + vignettes/roy_model.Rmd | 22 128 files changed, 1779 insertions(+), 388 deletions(-)
Title: Neutrosophic Analysis Crossover Designs
Description: Provides methods for Neutrosophic Analysis of Variance
(NANOVA) for crossover designs and multi-session designs with
direct and residual effects using interval-valued observations.
The package computes neutrosophic sums of squares, mean squares,
interval-valued F-statistics, significance tests, and multiple
comparisons using Least Significant Difference (LSD) procedures.
For crisp data, users may enter identical lower and upper response
values to obtain classical Analysis of Variance (ANOVA) results.
The basic idea of neutrosophic statistics is obtained from
Smarandache (2014) <https://fs.unm.edu/NeutrosophicStatistics.pdf>,
while the analysis procedures implemented in this package are newly developed.
Author: Boyina Devi Priyanka [aut, ctb],
Neethu R.S [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Vinaykumar L.N. [aut, cre]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between NeutroCODsAnalysis versions 0.0.1 dated 2026-06-09 and 0.1.0 dated 2026-06-10
DESCRIPTION | 18 +++++++++--------- MD5 | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-)
More information about NeutroCODsAnalysis at CRAN
Permanent link
Title: Goldilocks Adaptive Trial Designs for Time-to-Event Endpoints
Description: Implements the Goldilocks adaptive trial design for a time to event
outcome using a piecewise exponential model and conjugate Gamma prior
distributions. The method closely follows the article by Broglio and
colleagues <doi:10.1080/10543406.2014.888569>, which allows users to explore
the operating characteristics of different trial designs.
Author: Graeme L. Hickey [aut, cre] ,
Ying Wan [aut],
Thevaa Chandereng [aut] ,
Becton, Dickinson and Company [cph],
Tim Kacprowski [ctb]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between goldilocks versions 0.4.0 dated 2025-01-08 and 0.5.0 dated 2026-06-10
DESCRIPTION | 24 ++- MD5 | 78 +++++++---- NAMESPACE | 2 NEWS.md | 52 +++++++ R/analyse_data.R | 37 ++++- R/enrollment.R | 2 R/impute_data.R | 3 R/posterior.R | 62 +++++++-- R/randomization.R | 2 R/sim_comp_data.R | 7 - R/summarise_sims.R | 4 R/survival_adapt.R | 103 +++++++++++---- R/test_final.R | 9 + README.md | 17 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/architecture.R |only inst/doc/architecture.Rmd |only inst/doc/architecture.html |only inst/doc/bayes-piecewise.R |only inst/doc/bayes-piecewise.Rmd |only inst/doc/bayes-piecewise.html |only inst/doc/broglio.R | 21 ++- inst/doc/broglio.Rmd | 43 +++++- inst/doc/broglio.html | 234 +++++++++++++++++++++++++++------- inst/doc/single-arm.R |only inst/doc/single-arm.Rmd |only inst/doc/single-arm.html |only man/goldilocks-package.Rd | 2 man/sim_comp_data.Rd | 7 - man/sim_trials.Rd | 31 +++- man/survival_adapt.Rd | 77 ++++++++--- src/logrank_r.cpp | 17 -- tests/testthat/test-analyse_data.R |only tests/testthat/test-enrollment.R |only tests/testthat/test-posterior.R |only tests/testthat/test-prop_to_haz.R |only tests/testthat/test-pwe.R |only tests/testthat/test-randomization.R |only tests/testthat/test-sim_comp_data.R |only tests/testthat/test-summarise_sims.R |only tests/testthat/test-survival_adapt.R | 236 ++++++++++++++++++++++++++++++++++- vignettes/architecture.Rmd |only vignettes/bayes-piecewise.Rmd |only vignettes/bayes-piecewise_cache |only vignettes/broglio.Rmd | 43 +++++- vignettes/single-arm.Rmd |only vignettes/single-arm_cache |only 48 files changed, 908 insertions(+), 205 deletions(-)
Title: Ab Initio Uncertainty Quantification
Description: Uncertainty quantification and inverse estimation by probabilistic generative models from the beginning of the data analysis. An example is a Fourier basis method for inverse estimation in scattering analysis of microscopy videos. It does not require specifying a certain range of Fourier bases and it substantially reduces computational cost via the generalized Schur algorithm. See the reference: Mengyang Gu, Yue He, Xubo Liu and Yimin Luo (2023), <doi:10.48550/arXiv.2309.02468>, and Tong Lin, Jinseok Lee, Matt Helgeson, Megan T Valentine, Yimin Luo, Mengyang Gu (2026), <doi:10.48550/arXiv.2605.29424>.
Author: Yue He [aut],
Xubo Liu [aut],
Tong Lin [aut],
Mengyang Gu [aut, cre]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between AIUQ versions 0.5.4 dated 2026-05-25 and 0.5.5 dated 2026-06-10
AIUQ-0.5.4/AIUQ/inst/extdata |only AIUQ-0.5.5/AIUQ/CHANGELOG | 4 + AIUQ-0.5.5/AIUQ/DESCRIPTION | 10 ++-- AIUQ-0.5.5/AIUQ/MD5 | 25 +++++------- AIUQ-0.5.5/AIUQ/R/SAM_model_free_workflow.R | 2 AIUQ-0.5.5/AIUQ/R/functions_model_free.R | 2 AIUQ-0.5.5/AIUQ/build/partial.rdb |binary AIUQ-0.5.5/AIUQ/build/vignette.rds |binary AIUQ-0.5.5/AIUQ/inst/doc/AIUQ.R | 58 ++++++++++++---------------- AIUQ-0.5.5/AIUQ/inst/doc/AIUQ.Rmd | 14 +----- AIUQ-0.5.5/AIUQ/inst/doc/AIUQ.html | 50 ++++++++++-------------- AIUQ-0.5.5/AIUQ/man/SAM.Rd | 2 AIUQ-0.5.5/AIUQ/man/l2_fixedAB.Rd | 5 +- AIUQ-0.5.5/AIUQ/vignettes/AIUQ.Rmd | 14 +----- 14 files changed, 83 insertions(+), 103 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.12.0 dated 2026-01-24 and 0.13.0 dated 2026-06-10
DESCRIPTION | 6 MD5 | 44 NEWS.md | 20 R/cov_initial_search.R | 2282 ++++++++++++++++++------------------- R/covmatrix.R | 20 R/get_model_stats.R | 5 R/get_optim_dotlist.R | 3 R/laploglik_products.R | 1057 ++++++++--------- R/loocv.R | 21 R/predict.R | 35 R/predict_glm.R | 23 R/spcov_matrix.R | 426 +++--- R/spcov_vector.R | 308 ++-- R/sprnorm.R | 726 +++++------ R/tidy.R | 4 R/tidy_glm.R | 4 R/transform_anis.R | 60 inst/doc/introduction.html | 155 +- tests/testthat/test-extras-spglm.R | 278 ++-- tests/testthat/test-extras-splm.R | 16 tests/testthat/test-extras.R | 4 tests/testthat/test-spglm.R | 4 tests/testthat/test-splm.R | 4 23 files changed, 2827 insertions(+), 2678 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Tables and
Figures
Description: Create production-ready Rich Text Format (RTF) tables and figures
with flexible format.
Author: Yilong Zhang [aut],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Benjamin Wang [aut],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [aut, cre],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [c [...truncated...]
Maintainer: Ruchitbhai Patel <ruchitbhai.patel@merck.com>
Diff between r2rtf versions 1.3.0 dated 2026-01-09 and 1.3.1 dated 2026-06-10
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- NEWS.md | 6 ++++++ 3 files changed, 16 insertions(+), 10 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.12.0 dated 2026-04-28 and 0.12.1 dated 2026-06-10
plotthis-0.12.0/plotthis/man/gggrob.Rd |only plotthis-0.12.0/plotthis/tests/testthat/Rplots.pdf |only plotthis-0.12.1/plotthis/DESCRIPTION | 6 plotthis-0.12.1/plotthis/MD5 | 236 - plotthis-0.12.1/plotthis/R/areaplot.R | 8 plotthis-0.12.1/plotthis/R/barplot.R | 30 plotthis-0.12.1/plotthis/R/boxviolinplot.R | 62 plotthis-0.12.1/plotthis/R/chordplot.R | 8 plotthis-0.12.1/plotthis/R/clustreeplot.R | 14 plotthis-0.12.1/plotthis/R/common_args.R | 1 plotthis-0.12.1/plotthis/R/corplot.R | 18 plotthis-0.12.1/plotthis/R/densityplot.R | 22 plotthis-0.12.1/plotthis/R/dimplot.R | 30 plotthis-0.12.1/plotthis/R/dotplot.R | 30 plotthis-0.12.1/plotthis/R/enrich.R | 16 plotthis-0.12.1/plotthis/R/gsea.R | 4 plotthis-0.12.1/plotthis/R/heatmap-utils.R |only plotthis-0.12.1/plotthis/R/heatmap.R | 1541 ++--------- plotthis-0.12.1/plotthis/R/jitterplot.R | 8 plotthis-0.12.1/plotthis/R/lineplot.R | 18 plotthis-0.12.1/plotthis/R/manhattanplot.R | 1 plotthis-0.12.1/plotthis/R/network.R | 22 plotthis-0.12.1/plotthis/R/piechart.R | 8 plotthis-0.12.1/plotthis/R/qqplot.R | 8 plotthis-0.12.1/plotthis/R/radarplot.R | 12 plotthis-0.12.1/plotthis/R/rarefractionplot.R | 10 plotthis-0.12.1/plotthis/R/ringplot.R | 8 plotthis-0.12.1/plotthis/R/roccurve.R | 8 plotthis-0.12.1/plotthis/R/sankeyplot.R | 16 plotthis-0.12.1/plotthis/R/scatterplot.R | 19 plotthis-0.12.1/plotthis/R/spatialplot.R | 47 plotthis-0.12.1/plotthis/R/theming.R | 11 plotthis-0.12.1/plotthis/R/trendplot.R | 8 plotthis-0.12.1/plotthis/R/upsetplot.R | 8 plotthis-0.12.1/plotthis/R/utils.R | 3 plotthis-0.12.1/plotthis/R/velocityplot.R | 14 plotthis-0.12.1/plotthis/R/venndiagram.R | 10 plotthis-0.12.1/plotthis/R/volcanoplot.R | 10 plotthis-0.12.1/plotthis/R/wordcloudplot.R | 5 plotthis-0.12.1/plotthis/man/AreaPlot.Rd | 3 plotthis-0.12.1/plotthis/man/AreaPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/BarPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/BarPlotGrouped.Rd | 3 plotthis-0.12.1/plotthis/man/BarPlotSingle.Rd | 3 plotthis-0.12.1/plotthis/man/BoxViolinPlot-internal.Rd | 7 plotthis-0.12.1/plotthis/man/BoxViolinPlotAtomic.Rd | 7 plotthis-0.12.1/plotthis/man/ChordPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/ClustreePlot.Rd | 3 plotthis-0.12.1/plotthis/man/ClustreePlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/CorPairsPlot.Rd | 3 plotthis-0.12.1/plotthis/man/CorPairsPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/CorPlot.Rd | 5 plotthis-0.12.1/plotthis/man/CorPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/DensityHistoPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/DimPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/DimPlotAtomic3D.Rd | 1 plotthis-0.12.1/plotthis/man/DotPlotAtomic.Rd | 14 plotthis-0.12.1/plotthis/man/EnrichMapAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/EnrichNetworkAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/Heatmap.Rd | 154 - plotthis-0.12.1/plotthis/man/HeatmapAtomic.Rd | 77 plotthis-0.12.1/plotthis/man/JitterPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/LinePlot.Rd | 3 plotthis-0.12.1/plotthis/man/LinePlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/LinePlotGrouped.Rd | 3 plotthis-0.12.1/plotthis/man/LinePlotSingle.Rd | 3 plotthis-0.12.1/plotthis/man/ManhattanPlot.Rd | 2 plotthis-0.12.1/plotthis/man/ManhattanPlotAtomic.Rd | 2 plotthis-0.12.1/plotthis/man/Network.Rd | 3 plotthis-0.12.1/plotthis/man/NetworkAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/PieChart.Rd | 3 plotthis-0.12.1/plotthis/man/PieChartAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/QQPlot.Rd | 3 plotthis-0.12.1/plotthis/man/QQPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/ROCCurve.Rd | 3 plotthis-0.12.1/plotthis/man/ROCCurveAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/RadarPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/RarefactionPlot.Rd | 3 plotthis-0.12.1/plotthis/man/RarefactionPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/RidgePlot.Rd | 3 plotthis-0.12.1/plotthis/man/RidgePlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/RingPlot.Rd | 3 plotthis-0.12.1/plotthis/man/RingPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/SankeyPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/ScatterPlot.Rd | 4 plotthis-0.12.1/plotthis/man/ScatterPlotAtomic.Rd | 4 plotthis-0.12.1/plotthis/man/SplitBarPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/TrendPlot.Rd | 3 plotthis-0.12.1/plotthis/man/TrendPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/UpsetPlot.Rd | 3 plotthis-0.12.1/plotthis/man/UpsetPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/VelocityPlot.Rd | 3 plotthis-0.12.1/plotthis/man/VennDiagram.Rd | 3 plotthis-0.12.1/plotthis/man/VennDiagramAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/VolcanoPlot.Rd | 3 plotthis-0.12.1/plotthis/man/VolcanoPlotAtomic.Rd | 3 plotthis-0.12.1/plotthis/man/WordCloudPlot.Rd | 2 plotthis-0.12.1/plotthis/man/WordCloudPlotAtomic.Rd | 2 plotthis-0.12.1/plotthis/man/barplot.Rd | 5 plotthis-0.12.1/plotthis/man/boxviolinplot.Rd | 13 plotthis-0.12.1/plotthis/man/chordplot.Rd | 4 plotthis-0.12.1/plotthis/man/common_args.Rd | 2 plotthis-0.12.1/plotthis/man/densityhistoplot.Rd | 6 plotthis-0.12.1/plotthis/man/dimplot.Rd | 4 plotthis-0.12.1/plotthis/man/dot-anno_ggcat.Rd | 5 plotthis-0.12.1/plotthis/man/dot-check_annotation.Rd |only plotthis-0.12.1/plotthis/man/dot-gggrob.Rd |only plotthis-0.12.1/plotthis/man/dot-reorder_anno_side.Rd |only plotthis-0.12.1/plotthis/man/dot-resolve_anno_aliases.Rd |only plotthis-0.12.1/plotthis/man/dot-setup_annos.Rd |only plotthis-0.12.1/plotthis/man/dotplot.Rd | 18 plotthis-0.12.1/plotthis/man/enrichmap1.Rd | 4 plotthis-0.12.1/plotthis/man/gsea.Rd | 3 plotthis-0.12.1/plotthis/man/heatmap-anno.Rd | 50 plotthis-0.12.1/plotthis/man/heatmap-layer.Rd | 2 plotthis-0.12.1/plotthis/man/jitterplot.Rd | 3 plotthis-0.12.1/plotthis/man/join_heatmap_meta.Rd | 2 plotthis-0.12.1/plotthis/man/process_heatmap_data.Rd | 2 plotthis-0.12.1/plotthis/man/radarplot.Rd | 4 plotthis-0.12.1/plotthis/man/sankeyplot.Rd | 4 plotthis-0.12.1/plotthis/man/spatialplots.Rd | 16 plotthis-0.12.1/plotthis/tests/testthat/test-dotplot.R | 22 plotthis-0.12.1/plotthis/tests/testthat/test-manhattanplot.R | 2 123 files changed, 1177 insertions(+), 1693 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut] ,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-adjoa Kwarteng [ctb] ,
Guido Schwarzer [aut, [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.5-0 dated 2026-05-28 and 3.6-0 dated 2026-06-10
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 27 +++++++++++++++++++++++++++ R/crossnma2netmeta.R | 6 +++--- R/netgraph.netmeta.R | 18 +++++++++--------- R/netmeta.R | 14 +++++++++++++- R/nma.ruecker.R | 32 +++++++++++++++++++------------- R/print.netimpact.R | 15 +++++++++++++-- R/textmeth.R | 8 ++++++++ inst/doc/netmeta-workflow.pdf |binary inst/doc/netmeta.pdf |binary man/netmeta.Rd | 7 +++++++ man/print.netimpact.Rd | 3 +++ 13 files changed, 118 insertions(+), 44 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in
'mlr3' and its companion packages. Comes with helper functions for
functional programming, for printing, to work with 'data.table', as
well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3misc versions 0.21.0 dated 2026-02-26 and 0.22.0 dated 2026-06-10
mlr3misc-0.21.0/mlr3misc/tests/testthat/test_set_pars.R |only mlr3misc-0.22.0/mlr3misc/DESCRIPTION | 8 mlr3misc-0.22.0/mlr3misc/MD5 | 153 ++-- mlr3misc-0.22.0/mlr3misc/NEWS.md | 11 mlr3misc-0.22.0/mlr3misc/R/Callback.R | 30 mlr3misc-0.22.0/mlr3misc/R/Context.R | 11 mlr3misc-0.22.0/mlr3misc/R/Dictionary.R | 18 mlr3misc-0.22.0/mlr3misc/R/as_short_string.R | 5 mlr3misc-0.22.0/mlr3misc/R/calculate_hash.R | 1 mlr3misc-0.22.0/mlr3misc/R/check_operators.R | 10 mlr3misc-0.22.0/mlr3misc/R/check_packages_installed.R | 12 mlr3misc-0.22.0/mlr3misc/R/chunk.R | 1 mlr3misc-0.22.0/mlr3misc/R/crate.R | 13 mlr3misc-0.22.0/mlr3misc/R/dictionary_sugar.R | 24 mlr3misc-0.22.0/mlr3misc/R/did_you_mean.R | 4 mlr3misc-0.22.0/mlr3misc/R/encapsulate.R | 122 ++- mlr3misc-0.22.0/mlr3misc/R/formulate.R | 4 mlr3misc-0.22.0/mlr3misc/R/get_seed.R | 2 mlr3misc-0.22.0/mlr3misc/R/has_element.R | 2 mlr3misc-0.22.0/mlr3misc/R/insert_named.R | 14 mlr3misc-0.22.0/mlr3misc/R/leanify.R | 14 mlr3misc-0.22.0/mlr3misc/R/load_dataset.R | 1 mlr3misc-0.22.0/mlr3misc/R/named_list.R | 2 mlr3misc-0.22.0/mlr3misc/R/purrr_map.R | 26 mlr3misc-0.22.0/mlr3misc/R/rcbind.R | 9 mlr3misc-0.22.0/mlr3misc/R/rd_info.R | 34 mlr3misc-0.22.0/mlr3misc/R/register_namespace_callback.R | 18 mlr3misc-0.22.0/mlr3misc/R/remove_named.R | 8 mlr3misc-0.22.0/mlr3misc/R/require_namespaces.R | 5 mlr3misc-0.22.0/mlr3misc/R/rowwise_table.R | 1 mlr3misc-0.22.0/mlr3misc/R/set_class.R | 2 mlr3misc-0.22.0/mlr3misc/R/set_params.R | 2 mlr3misc-0.22.0/mlr3misc/R/strip_srcrefs.R | 4 mlr3misc-0.22.0/mlr3misc/R/to_decimal.R | 2 mlr3misc-0.22.0/mlr3misc/R/topo_sort.R | 9 mlr3misc-0.22.0/mlr3misc/R/unnest.R | 29 mlr3misc-0.22.0/mlr3misc/R/warn_deprecated.R | 3 mlr3misc-0.22.0/mlr3misc/man/Callback.Rd | 195 ++--- mlr3misc-0.22.0/mlr3misc/man/Context.Rd | 123 +-- mlr3misc-0.22.0/mlr3misc/man/Dictionary.Rd | 376 +++++----- mlr3misc-0.22.0/mlr3misc/man/catn.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/check_operators.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/compat-map.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/cross_join.Rd | 6 mlr3misc-0.22.0/mlr3misc/man/encapsulate.Rd | 8 mlr3misc-0.22.0/mlr3misc/man/get_seed.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/leanify_r6.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/map_values.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/mlr3misc-package.Rd | 1 mlr3misc-0.22.0/mlr3misc/man/mlr_callbacks.Rd | 5 mlr3misc-0.22.0/mlr3misc/man/register_namespace_callback.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/require_namespaces.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/rowwise_table.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/sequence_helpers.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/set_class.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/shuffle.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/strip_srcrefs.Rd | 4 mlr3misc-0.22.0/mlr3misc/man/to_decimal.Rd | 2 mlr3misc-0.22.0/mlr3misc/man/which_min.Rd | 2 mlr3misc-0.22.0/mlr3misc/src/keep_in_bounds.c | 15 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_Callback.R | 21 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_Context.R | 4 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_Dictionary.R | 42 - mlr3misc-0.22.0/mlr3misc/tests/testthat/test_as_short_string.R | 10 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_check_packages_installed.R | 6 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_chunk.R | 40 - mlr3misc-0.22.0/mlr3misc/tests/testthat/test_crate.R | 10 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_distinct_values.R | 1 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_encapsulate.R | 27 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_formulate.R | 4 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_get_private.R | 6 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_has_element.R | 3 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_leanify.R | 21 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_reorder_vector.R | 1 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_require_namespaces.R | 15 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_topo_sort.R | 72 + mlr3misc-0.22.0/mlr3misc/tests/testthat/test_warn_deprecated.R | 4 mlr3misc-0.22.0/mlr3misc/tests/testthat/test_with_package.R | 10 78 files changed, 979 insertions(+), 703 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.6.0 dated 2026-04-02 and 1.7.0 dated 2026-06-10
DESCRIPTION | 14 MD5 | 357 ++++----- NEWS.md | 24 R/Learner.R | 33 R/LearnerClassif.R | 7 R/LearnerClassifDebug.R | 4 R/LearnerClassifRpart.R | 8 R/LearnerRegr.R | 6 R/LearnerRegrDebug.R | 4 R/LearnerRegrFeatureless.R | 4 R/LearnerRegrRpart.R | 6 R/Measure.R | 17 R/MeasureAIC.R | 4 R/MeasureClassifCosts.R | 4 R/MeasureElapsedTime.R | 5 R/MeasureRegrPinball.R | 7 R/MeasureRegrRQR.R | 15 R/MeasureRegrRSQ.R | 14 R/MeasureSimilarity.R | 2 R/MeasureSimple.R | 13 R/PredictionDataClassif.R | 2 R/PredictionDataRegr.R | 4 R/ResampleResult.R | 4 R/ResamplingCustom.R | 1 R/ResamplingCustomCV.R | 3 R/Task.R | 85 -- R/TaskClassif.R | 45 - R/TaskClassif_german_credit.R | 2 R/TaskGeneratorPeak.R | 4 R/TaskRegr_mtcars.R | 2 R/TaskUnsupervised.R | 2 R/as_measure.R | 2 R/as_task_classif.R | 2 R/as_task_regr.R | 2 R/as_task_unsupervised.R | 4 R/helper.R | 7 R/mlr_reflections.R | 5 R/worker.R | 13 build/partial.rdb |binary man/BenchmarkResult.Rd | 679 +++++++++--------- man/CallbackResample.Rd | 64 - man/ContextResample.Rd | 105 +- man/DataBackend.Rd | 109 +- man/DataBackendDataTable.Rd | 233 +++--- man/HotstartStack.Rd | 210 ++--- man/Learner.Rd | 592 ++++++++-------- man/LearnerClassif.Rd | 165 ++-- man/LearnerRegr.Rd | 179 ++-- man/Measure.Rd | 386 +++++----- man/MeasureClassif.Rd | 126 +-- man/MeasureRegr.Rd | 126 +-- man/MeasureSimilarity.Rd | 136 +-- man/Prediction.Rd | 255 +++--- man/PredictionClassif.Rd | 167 ++-- man/PredictionRegr.Rd | 136 +-- man/ResampleResult.Rd | 643 ++++++++--------- man/Resampling.Rd | 334 ++++----- man/ResultData.Rd | 802 ++++++++++----------- man/Task.Rd | 1068 ++++++++++++++--------------- man/TaskClassif.Rd | 233 +++--- man/TaskGenerator.Rd | 197 ++--- man/TaskRegr.Rd | 163 ++-- man/TaskSupervised.Rd | 162 ++-- man/TaskUnsupervised.Rd | 131 +-- man/as_data_backend.Rd | 2 man/benchmark.Rd | 9 man/benchmark_grid.Rd | 4 man/california_housing.Rd | 2 man/mlr3-package.Rd | 7 man/mlr_learners.Rd | 6 man/mlr_learners_classif.debug.Rd | 198 ++--- man/mlr_learners_classif.featureless.Rd | 122 +-- man/mlr_learners_classif.rpart.Rd | 122 +-- man/mlr_learners_regr.debug.Rd | 122 +-- man/mlr_learners_regr.featureless.Rd | 122 +-- man/mlr_learners_regr.rpart.Rd | 122 +-- man/mlr_measures.Rd | 6 man/mlr_measures_aic.Rd | 74 +- man/mlr_measures_bic.Rd | 74 +- man/mlr_measures_classif.acc.Rd | 4 man/mlr_measures_classif.auc.Rd | 23 man/mlr_measures_classif.bacc.Rd | 4 man/mlr_measures_classif.bbrier.Rd | 4 man/mlr_measures_classif.ce.Rd | 4 man/mlr_measures_classif.costs.Rd | 86 +- man/mlr_measures_classif.dor.Rd | 4 man/mlr_measures_classif.fbeta.Rd | 4 man/mlr_measures_classif.fdr.Rd | 4 man/mlr_measures_classif.fn.Rd | 4 man/mlr_measures_classif.fnr.Rd | 4 man/mlr_measures_classif.fomr.Rd | 4 man/mlr_measures_classif.fp.Rd | 4 man/mlr_measures_classif.fpr.Rd | 4 man/mlr_measures_classif.logloss.Rd | 9 man/mlr_measures_classif.mauc_au1p.Rd | 6 man/mlr_measures_classif.mauc_au1u.Rd | 6 man/mlr_measures_classif.mauc_aunp.Rd | 6 man/mlr_measures_classif.mauc_aunu.Rd | 4 man/mlr_measures_classif.mauc_mu.Rd | 6 man/mlr_measures_classif.mbrier.Rd | 4 man/mlr_measures_classif.mcc.Rd | 19 man/mlr_measures_classif.npv.Rd | 4 man/mlr_measures_classif.ppv.Rd | 4 man/mlr_measures_classif.prauc.Rd | 4 man/mlr_measures_classif.precision.Rd | 6 man/mlr_measures_classif.recall.Rd | 6 man/mlr_measures_classif.sensitivity.Rd | 6 man/mlr_measures_classif.specificity.Rd | 6 man/mlr_measures_classif.tn.Rd | 4 man/mlr_measures_classif.tnr.Rd | 4 man/mlr_measures_classif.tp.Rd | 4 man/mlr_measures_classif.tpr.Rd | 4 man/mlr_measures_debug_classif.Rd | 72 + man/mlr_measures_elapsed_time.Rd | 101 +- man/mlr_measures_internal_valid_score.Rd | 91 +- man/mlr_measures_oob_error.Rd | 72 + man/mlr_measures_regr.bias.Rd | 2 man/mlr_measures_regr.ktau.Rd | 5 man/mlr_measures_regr.mae.Rd | 2 man/mlr_measures_regr.mape.Rd | 2 man/mlr_measures_regr.maxae.Rd | 2 man/mlr_measures_regr.medae.Rd | 2 man/mlr_measures_regr.medse.Rd | 2 man/mlr_measures_regr.mse.Rd | 2 man/mlr_measures_regr.msle.Rd | 2 man/mlr_measures_regr.pbias.Rd | 2 man/mlr_measures_regr.pinball.Rd | 88 +- man/mlr_measures_regr.rmse.Rd | 2 man/mlr_measures_regr.rmsle.Rd | 2 man/mlr_measures_regr.rqr.Rd | 104 +- man/mlr_measures_regr.rsq.Rd | 101 +- man/mlr_measures_regr.sae.Rd | 2 man/mlr_measures_regr.smape.Rd | 4 man/mlr_measures_regr.srho.Rd | 2 man/mlr_measures_regr.sse.Rd | 2 man/mlr_measures_selected_features.Rd | 72 + man/mlr_measures_sim.jaccard.Rd | 2 man/mlr_measures_sim.phi.Rd | 2 man/mlr_reflections.Rd | 5 man/mlr_resamplings.Rd | 6 man/mlr_resamplings_bootstrap.Rd | 82 +- man/mlr_resamplings_custom.Rd | 116 +-- man/mlr_resamplings_custom_cv.Rd | 116 +-- man/mlr_resamplings_cv.Rd | 82 +- man/mlr_resamplings_holdout.Rd | 82 +- man/mlr_resamplings_insample.Rd | 82 +- man/mlr_resamplings_loo.Rd | 82 +- man/mlr_resamplings_repeated_cv.Rd | 154 ++-- man/mlr_resamplings_subsampling.Rd | 82 +- man/mlr_task_generators.Rd | 6 man/mlr_task_generators_2dnormals.Rd | 102 +- man/mlr_task_generators_cassini.Rd | 102 +- man/mlr_task_generators_circle.Rd | 102 +- man/mlr_task_generators_friedman1.Rd | 66 - man/mlr_task_generators_moons.Rd | 102 +- man/mlr_task_generators_peak.Rd | 66 - man/mlr_task_generators_simplex.Rd | 102 +- man/mlr_task_generators_smiley.Rd | 102 +- man/mlr_task_generators_spirals.Rd | 102 +- man/mlr_task_generators_xor.Rd | 102 +- man/mlr_tasks.Rd | 6 man/mlr_tasks_breast_cancer.Rd | 2 man/mlr_tasks_german_credit.Rd | 4 man/mlr_tasks_iris.Rd | 2 man/mlr_tasks_mtcars.Rd | 4 man/mlr_tasks_penguins.Rd | 2 man/mlr_tasks_pima.Rd | 4 man/mlr_tasks_sonar.Rd | 2 man/mlr_tasks_spam.Rd | 2 man/mlr_tasks_wine.Rd | 2 man/mlr_tasks_zoo.Rd | 2 man/reexports.Rd | 4 man/resample.Rd | 7 man/uhash.Rd | 2 tests/testthat/_snaps/Task.md | 2 tests/testthat/test_Learner.R | 159 ++++ tests/testthat/test_MeasureRegrPinball.R | 2 tests/testthat/test_PredictionDataRegr.R | 18 tests/testthat/test_as_task_unsupervised.R |only tests/testthat/test_convert_task.R | 22 180 files changed, 6281 insertions(+), 5951 deletions(-)
Title: Exact Post Selection Inference with Applications to the Lasso
Description: Implements the conditional estimation procedure of
Lee, Sun, Sun and Taylor (2016) <doi:10.1214/15-AOS1371>.
This procedure allows hypothesis testing on the mean of
a normal random vector subject to linear constraints.
Also supports computation of the MLE of the mean subject to the
same constraints.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between epsiwal versions 0.1.0 dated 2019-07-02 and 0.2.0 dated 2026-06-10
ChangeLog | 6 + DESCRIPTION | 19 ++-- MD5 | 43 ++++++--- NAMESPACE | 5 + R/ci_connorm.r | 156 ++++++++++++++++++++++++------------ R/epsiwal.r | 9 +- R/mle_connorm.r |only R/pconnorm.r | 53 ++++++++++-- R/ptruncnorm.r | 31 ++++--- R/utils.r | 134 ++++++++++++++++++++++++++---- README.md | 133 +++++++++++++++++++++++++++--- inst/CITATION | 21 ++-- man/NEWS.Rd | 9 ++ man/ci_connorm.Rd | 15 ++- man/ci_connorm_max.Rd |only man/epsiwal.Rd | 18 +++- man/mle_connorm.Rd |only man/mle_connorm_max.Rd |only man/pconnorm.Rd | 23 +++-- man/pconnorm_max.Rd |only man/ptruncnorm.Rd | 18 ++-- tests/testthat/test-issue-tail.r |only tests/testthat/test-max_functions.r |only tests/testthat/test-mle_connorm.r |only tests/testthat/test-pconnorm.r | 34 +++++++ tests/testthat/test-utils.r |only tools/figure/under_null_pvals-1.png |binary 27 files changed, 572 insertions(+), 155 deletions(-)
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre, cph],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedrohcgs@gmail.com>
Diff between DRDID versions 1.2.3 dated 2025-12-04 and 1.3.0 dated 2026-06-10
DESCRIPTION | 8 +- MD5 | 58 ++++++++--------- NEWS.md | 43 ++++++++++++ R/drdid_imp_rc.R | 20 ++--- R/drdid_panel.R | 55 +++++----------- R/drdid_rc.R | 115 ++++++++++++++++------------------ R/drdid_rc1.R | 28 +++----- R/fastglm_fit.R |only R/ipw_did_panel.R | 18 ++--- R/ipw_did_rc.R | 22 ++---- R/pre_process_drdid.R | 12 ++- R/pscore.cal.R | 9 -- R/reg_did_panel.R | 12 +-- R/reg_did_rc.R | 22 ++---- R/std_ipw_did_panel.R | 29 ++++---- R/std_ipw_did_rc.R | 47 +++++++------ R/wboot.dr.tr.panel.R | 17 +---- R/wboot.ipw.panel.R | 7 -- R/wboot.reg.panel.R | 10 +- R/wboot.std.ipw.panel.R | 7 -- R/wboot_drdid_imp_rc.R | 20 ++--- R/wboot_drdid_rc.R | 47 +++++-------- R/wboot_drdid_rc1.R | 27 ++----- R/wboot_ipw_rc.R | 7 -- R/wboot_reg_rc.R | 20 ++--- R/wboot_std_ipw_rc.R | 7 -- R/wols.br.panel.R | 10 +- R/wols_rc.R | 10 +- build/partial.rdb |binary inst/WORDLIST | 5 + tests/testthat/test_regression_lock.R |only 31 files changed, 321 insertions(+), 371 deletions(-)
Title: Automatic Toolkit for Construction, Optimization, Scoring and
Simulation of Forced-Choice Tests
Description: Forced-choice (FC) response has gained increasing popularity
and interest for its resistance to faking when well-designed (Cao &
Drasgow, 2019 <doi:10.1037/apl0000414>). To established well-designed
FC scales, typically each item within a block should measure different
trait and have similar level of social desirability (Zhang et al.,
2020 <doi:10.1177/1094428119836486>). Recent study also suggests the
importance of high inter-item agreement of social desirability between
items within a block (Pavlov et al., 2021
<doi:10.31234/osf.io/hmnrc>). In addition to this, FC developers may
also need to maximize factor loading differences (Brown &
Maydeu-Olivares, 2011 <doi:10.1177/0013164410375112>) or minimize item
location differences (Cao & Drasgow, 2019 <doi:10.1037/apl0000414>)
depending on scoring models. Decision of which items should be
assigned to the same block, also called as item pairing, is thus critical
to the quality of an FC test. Becau [...truncated...]
Author: Mengtong Li [cre, aut] ,
Tianjun Sun [aut] ,
Bo Zhang [aut]
Maintainer: Mengtong Li <mt_li@fudan.edu.cn>
Diff between autoFC versions 1.0.0.1000 dated 2026-05-27 and 1.0.0.1001 dated 2026-06-10
DESCRIPTION | 6 MD5 | 12 NEWS.md |only R/generate_tirt_mplus_syntax.R | 548 ++++++++++++++++++++--------------------- R/prepare_tirt_stan_data.R | 218 ++++++++-------- R/zzz.R |only inst/doc/intro-to-autoFC.html | 4 man/prepare_tirt_stan_data.Rd | 2 8 files changed, 396 insertions(+), 394 deletions(-)
Title: Betas-Select in Structural Equation Models and Linear Models
Description: It computes betas-select, coefficients after standardization in
structural equation models and regression models, standardizing only selected
variables. Supports models with moderation, with product terms formed after
standardization. It also offers confidence intervals that account for
standardization, including bootstrap confidence intervals as proposed by
Cheung et al. (2022) <doi:10.1037/hea0001188>. An introduction to the package
can be found in Sun et al. (2026) <doi:10.1080/00273171.2026.2672692>.
Author: Shu Fai Cheung [aut, cre] ,
Rong Wei Sun [aut] ,
Florbela Chang [aut] ,
Wendie Yang [aut] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between betaselectr versions 0.1.4 dated 2026-04-07 and 0.2.1 dated 2026-06-09
DESCRIPTION | 11 MD5 | 142 NEWS.md | 7 R/lav_betaselect.R | 1372 ++--- R/lm_betaselect.R | 1567 +++--- R/lm_betaselect_methods.R | 5144 ++++++++++----------- README.md | 34 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/betaselectr_glm.Rmd | 3 inst/doc/betaselectr_glm.html | 17 inst/doc/betaselectr_lav.Rmd | 7 inst/doc/betaselectr_lav.html | 20 inst/doc/betaselectr_lm.Rmd | 3 inst/doc/betaselectr_lm.html | 15 man/anova.lm_betaselect.Rd | 194 man/coef.lav_betaselect.Rd | 120 man/coef.lm_betaselect.Rd | 190 man/confint.lav_betaselect.Rd | 134 man/confint.lm_betaselect.Rd | 356 - man/data_test_medmod.Rd | 86 man/data_test_mod_cat.Rd | 70 man/data_test_mod_cat2.Rd | 76 man/data_test_mod_cat_binary.Rd | 68 man/figures |only man/getCall.lm_betaselect.Rd | 156 man/lav_betaselect.Rd | 811 +-- man/lm_betaselect.Rd | 969 +-- man/predict.glm_betaselect.Rd | 182 man/predict.lm_betaselect.Rd | 174 man/print.lav_betaselect.Rd | 298 - man/std_data.Rd | 90 man/summary.glm_betaselect.Rd | 524 +- man/summary.lm_betaselect.Rd | 444 - man/vcov.lm_betaselect.Rd | 282 - tests/testthat/test-lav_betaselect.R | 264 - tests/testthat/test-lav_betaselect_check.R | 96 tests/testthat/test-lav_betaselect_coef.R | 140 tests/testthat/test-lav_betaselect_confint.R | 84 tests/testthat/test-lav_betaselect_mg.R | 296 - tests/testthat/test-lav_betaselect_mg_eq.R | 288 - tests/testthat/test-lav_betaselect_mod.R | 200 tests/testthat/test-lav_betaselect_mod_Intercept.R | 180 tests/testthat/test-lav_betaselect_mod_boot_1.R | 140 tests/testthat/test-lav_betaselect_mod_boot_2.R | 114 tests/testthat/test-lav_betaselect_mod_boot_3.R | 104 tests/testthat/test-lav_betaselect_mod_boot_4.R | 110 tests/testthat/test-lav_betaselect_mod_colon.R | 200 tests/testthat/test-lav_betaselect_mod_mg.R | 240 tests/testthat/test-lav_betaselect_mod_no_center.R | 168 tests/testthat/test-lav_betaselect_one_iv.R | 204 tests/testthat/test-lav_betaselect_ord.R | 136 tests/testthat/test-lav_betaselect_parallel.R | 122 tests/testthat/test-lav_betaselect_print_ustd.R | 82 tests/testthat/test-lav_betaselect_tmp.R | 136 tests/testthat/test-lav_betaselect_user_1.R | 136 tests/testthat/test-lav_betaselect_user_2.R | 83 tests/testthat/test-lav_betaselect_user_boot_1.R | 168 tests/testthat/test_find_all_products_cats.R | 102 tests/testthat/test_glm_betaselect_skip_def.R | 28 vignettes/apa.csl | 3832 +++++++-------- vignettes/articles/apa.csl | 3832 +++++++-------- vignettes/articles/lav_betaselect_technical.Rmd | 495 +- vignettes/articles/lm_betaselect_technical.Rmd | 207 vignettes/articles/references.bib | 16 vignettes/betaselectr_glm.Rmd | 3 vignettes/betaselectr_glm.Rmd.original | 821 +-- vignettes/betaselectr_lav.Rmd | 7 vignettes/betaselectr_lav.Rmd.original | 811 +-- vignettes/betaselectr_lm.Rmd | 3 vignettes/betaselectr_lm.Rmd.original | 845 +-- vignettes/references.bib | 362 - 73 files changed, 14375 insertions(+), 14246 deletions(-)
Title: Soil Health Assessment Models for Assessing Soil Conditions and
Suitability
Description: Soil health assessment builds information to improve decision in
soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO
<https://www.fao.org/land-water/databases-and-software/crop-information/en/>],
groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>],
carbon sequestration, irrigation potential, and status of soil resources.
Author: Christian Thine Omuto [aut, cre]
Maintainer: Christian Thine Omuto <thineomuto@yahoo.com>
Diff between soilassessment versions 1.3.0 dated 2026-04-22 and 1.3.1 dated 2026-06-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/imageIndices.R | 21 ++++----------------- 3 files changed, 10 insertions(+), 23 deletions(-)
More information about soilassessment at CRAN
Permanent link
Title: Twin Support Vector Machines
Description: Provides twin support vector machine classifiers and visualization
tools for small to moderate classification problems. Includes one-vs-one
multi-class classification and a standard support vector machine baseline
for comparison.
Author: Shamika Tissera [aut, cre]
Maintainer: Shamika Tissera <nimeshshamika@gmail.com>
Diff between twinsvm versions 0.0.1 dated 2026-06-08 and 0.0.2 dated 2026-06-09
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only README.md | 2 +- inst/doc/twinsvm.html | 6 +++--- tests/testthat/test-multiclass.R | 8 +++----- 6 files changed, 15 insertions(+), 16 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis and meta-analysis functions (e.g., to
calculate effect sizes and 95% Confidence Intervals (CI) on Standardised
Effect Sizes (d) for AB/BA cross-over repeated-measures experimental
designs), data presentation functions (e.g., density curve overlaid on
histogram),and the data sets analyzed in different research papers in
software engineering (e.g., related to software defect prediction or multi-
site experiment concerning the extent to which structured abstracts were
clearer and more complete than conventional abstracts) to streamline
reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] ,
Barbara Kitchenham [aut, ctb] ,
Tomasz Lewowski [aut, ctb] ,
Marian Jureczko [ctb] ,
David Budgen [ctb] ,
Pearl Brereton [ctb] ,
Jacky Keung [ctb] ,
Stuart Charters [ctb] ,
Shirley Gibbs [ctb] ,
Amnart Pohthong [ctb] , [...truncated...]
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.5.3 dated 2023-10-18 and 0.6.0 dated 2026-06-09
DESCRIPTION | 20 +- MD5 | 24 +-- NAMESPACE | 3 NEWS.md | 11 + R/MetaAnalysisForFamiliesOfExperimentsSR.R | 4 R/MunzelBrunnerPairedRankTest.R |only R/rPaperFunctions.R | 2 R/reproducer.R | 10 - README.md | 168 +++++++++++++++++++++- data/MunzelBrunner02.PGI.rda |only inst/CITATION | 38 +--- man/MunzelBrunner02.PGI.Rd |only man/pairedRankTest.Rd |only man/pairedSignTest.Rd |only man/rSimulations.Rd | 6 tests/testthat/test-MunzelBrunnerPairedRankTest.R |only 16 files changed, 221 insertions(+), 65 deletions(-)
Title: Distance-Based Learning for Mixed-Type Data
Description: Provides tools for constructing, computing, and using distance
measures for numerical, categorical, and mixed-type data. The package
implements a flexible framework in which continuous and categorical
components can be combined under additive, commensurable, and
association-aware specifications. Supported methods include classical
distances such as Gower, Euclidean, Manhattan, and Mahalanobis-type
distances; categorical dissimilarities such as simple matching,
occurrence-frequency, and association-based measures; and mixed-type
presets designed to reduce biases due to variable type, scale,
distribution, redundancy, and number of categories. The package also
provides scaling options, supervised and unsupervised distance
constructions, leave-one-variable-out tools for distance-based variable
importance, and integration with distance-based learning workflows such
as nearest-neighbour prediction, partitioning around medoids, and
spectral clustering. Methods are motivated by van de Velden,
[...truncated...]
Author: Alfonso Iodice D'Enza [aut, cre],
Angelos Markos [aut],
Michel van de Velden [aut],
Carlo Cavicchia [aut]
Maintainer: Alfonso Iodice D'Enza <iodicede@unina.it>
Diff between manydist versions 0.4.9 dated 2026-02-04 and 0.5.0 dated 2026-06-09
manydist-0.4.9/manydist/man/cdist.Rd |only manydist-0.4.9/manydist/man/ndist.Rd |only manydist-0.5.0/manydist/DESCRIPTION | 67 manydist-0.5.0/manydist/MD5 | 85 manydist-0.5.0/manydist/NAMESPACE | 159 + manydist-0.5.0/manydist/NEWS.md |only manydist-0.5.0/manydist/R/all_dist_methods_specs.R |only manydist-0.5.0/manydist/R/benchmark_mdist.R |only manydist-0.5.0/manydist/R/cat_custom_delta.R | 363 +-- manydist-0.5.0/manydist/R/cat_delta.R | 474 ++-- manydist-0.5.0/manydist/R/cdist.R | 467 ++-- manydist-0.5.0/manydist/R/compare_lovo_mdist.R |only manydist-0.5.0/manydist/R/compare_lovo_mdist_methods.R |only manydist-0.5.0/manydist/R/congruence_coeff.R |only manydist-0.5.0/manydist/R/daisy_gower_dist.R |only manydist-0.5.0/manydist/R/delta_int_knn.R |only manydist-0.5.0/manydist/R/delta_knn_ba.R |only manydist-0.5.0/manydist/R/dist_methods_tbl.R |only manydist-0.5.0/manydist/R/dist_model_helpers.R |only manydist-0.5.0/manydist/R/dist_to_affinity.R |only manydist-0.5.0/manydist/R/dkss_preprocessing.R |only manydist-0.5.0/manydist/R/gen_mixed.R |only manydist-0.5.0/manydist/R/generate_dataset.R |only manydist-0.5.0/manydist/R/getCall_methods.R |only manydist-0.5.0/manydist/R/gower_recipe.R | 27 manydist-0.5.0/manydist/R/gudmm_calculate_R_MI.R |only manydist-0.5.0/manydist/R/gudmm_distance_categorical_exact.R |only manydist-0.5.0/manydist/R/gudmm_distance_dependency_mixed_matrix.R |only manydist-0.5.0/manydist/R/gudmm_jensen_shannon.R |only manydist-0.5.0/manydist/R/gudmm_mutual_info_classif.R |only manydist-0.5.0/manydist/R/gudmm_mutual_info_regression.R |only manydist-0.5.0/manydist/R/gudmm_mutual_info_score.R |only manydist-0.5.0/manydist/R/gudmm_preprocessing.R |only manydist-0.5.0/manydist/R/idist.R |only manydist-0.5.0/manydist/R/indicator_based.R | 904 ++----- manydist-0.5.0/manydist/R/knn_dist_functions.R |only manydist-0.5.0/manydist/R/knn_dist_parsnip_registration.R |only manydist-0.5.0/manydist/R/lovo_mdist.R |only manydist-0.5.0/manydist/R/lovo_mdist_methods.R |only manydist-0.5.0/manydist/R/lovo_method_spec.R |only manydist-0.5.0/manydist/R/make_mdist_recipe.R |only manydist-0.5.0/manydist/R/mdist.R | 1146 +++++++--- manydist-0.5.0/manydist/R/mdist_class.R |only manydist-0.5.0/manydist/R/mdist_summary_impl.R |only manydist-0.5.0/manydist/R/mg_gower_dist_modify.R |only manydist-0.5.0/manydist/R/mg_gower_fcn.R |only manydist-0.5.0/manydist/R/mg_gower_mod_matrix.R |only manydist-0.5.0/manydist/R/mg_normalized_MI.R |only manydist-0.5.0/manydist/R/mg_self_adaptive_distance.R |only manydist-0.5.0/manydist/R/ndist.R | 153 - manydist-0.5.0/manydist/R/nearest_neighbor_dist_tunable.R |only manydist-0.5.0/manydist/R/pam_dist_functions.R |only manydist-0.5.0/manydist/R/spectral_cluster.R |only manydist-0.5.0/manydist/R/spectral_dist_functions.R |only manydist-0.5.0/manydist/R/spectral_from_dist.R |only manydist-0.5.0/manydist/R/step_mdist_functions.R |only manydist-0.5.0/manydist/R/summary.MDist.R |only manydist-0.5.0/manydist/R/sysdata.rda |only manydist-0.5.0/manydist/R/z_preproc.R | 2 manydist-0.5.0/manydist/R/zzz.R |only manydist-0.5.0/manydist/R/zzz_imports.R |only manydist-0.5.0/manydist/man/compare_lovo_mdist.Rd |only manydist-0.5.0/manydist/man/congruence_coeff.Rd |only manydist-0.5.0/manydist/man/gen_mixed.Rd |only manydist-0.5.0/manydist/man/generate_dataset.Rd |only manydist-0.5.0/manydist/man/lovo_mdist.Rd |only manydist-0.5.0/manydist/man/lovo_method_spec.Rd |only manydist-0.5.0/manydist/man/make_mdist_recipe.Rd |only manydist-0.5.0/manydist/man/mdist.Rd | 245 +- manydist-0.5.0/manydist/man/mdist_summary_impl.Rd |only manydist-0.5.0/manydist/man/nearest_neighbor_dist.Rd |only manydist-0.5.0/manydist/man/pam_dist.Rd |only manydist-0.5.0/manydist/man/spectral_dist.Rd |only manydist-0.5.0/manydist/man/spectral_from_dist.Rd |only manydist-0.5.0/manydist/man/step_mdist.Rd |only 75 files changed, 2301 insertions(+), 1791 deletions(-)
Title: Confidence Curves and P-Value Functions for Meta-Analysis
Description: Provides tools for the combination of individual study results in
meta-analyses using 'p-value' functions. Implements various combination methods
including those by Fisher, Stouffer, Tippett, Edgington along with
weighted generalizations. Contains functionality for the visualization
and calculation of confidence curves and drapery plots to summarize
evidence across studies.
Author: Saverio Fontana [aut, cre] ,
Felix Hofmann [aut] ,
Leonhard Held [aut] ,
Samuel Pawel [aut]
Maintainer: Saverio Fontana <savefontana@gmail.com>
Diff between confMeta versions 0.1.0 dated 2026-04-20 and 0.1.1 dated 2026-06-09
DESCRIPTION | 6 +- MD5 | 16 +++---- NAMESPACE | 1 NEWS.md | 9 +++- R/autoplot_pfun.R | 96 ++++++++++++++++++++++++++++++++----------- R/confMeta.R | 62 +++++++++++++++------------ inst/doc/confMeta-usage.html | 8 +-- man/autoplot.confMeta.Rd | 5 ++ man/confMeta.Rd | 24 +++++++--- 9 files changed, 154 insertions(+), 73 deletions(-)
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 1.2.0 dated 2025-09-02 and 1.3.0 dated 2026-06-09
DESCRIPTION | 18 MD5 | 38 NEWS.md | 40 R/rsl2odim.R | 4 R/vol2bird_config.R | 4 README.md | 4 inst/COPYRIGHTS | 22 inst/librsl/wsr88d_locations.dat | 377 +++--- man/rsl2odim.Rd | 4 man/vol2birdR-package.Rd | 4 man/vol2bird_config.Rd | 4 src/RaveIO.cpp | 39 src/includes/libvol2bird/constants.h | 4 src/includes/libvol2bird/libvol2bird.h | 15 src/librsl/wsr88d.c | 6 src/librsl/wsr88d_m31.c | 17 src/libvol2bird/librsl.c | 7 src/libvol2bird/libvol2bird.c | 1764 +++++++++++++++-------------- src/mistnet.cpp | 8 tests/testthat/test-class_vol2birdconfig.R | 27 20 files changed, 1350 insertions(+), 1056 deletions(-)
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data
in Brazil. Implements water quality indices including the Water Quality Index
('WQI'/'IQA') using the weighted geometric mean following 'CETESB' methodology,
the Trophic State Index ('TSI'/'IET') after Carlson (1977)
<doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004)
<https://teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index ('NSF WQI', Brown
(1970)). The package also checks compliance with Brazilian standard 'CONAMA'
Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
including the legal frequency rule (Art. 15, 80% conformity over six or more
samples per year), and provides seasonal analysis with regional flow-season
calendars, pollutant load computation, exceedance probability estimation, 'IET'
visualization, and multivariate 'PCA' tools f [...truncated...]
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.8.2 dated 2026-01-16 and 0.9.0 dated 2026-06-09
DESCRIPTION | 26 +++ MD5 | 66 +++++++--- NAMESPACE | 40 ++++++ NEWS.md | 67 ++++++++++ R/balnear.R |only R/conama_freq.R |only R/iqa.R | 171 +++++++++++++++----------- R/load_exceedance.R |only R/mk_seasonal.R |only R/nsfwqi.R | 217 ++++++++++++++++++--------------- R/plot_iet.R |only R/plot_map_quality.R |only R/seasonal.R |only R/testando.R | 5 R/tikatuwq-package.R | 2 R/wq_buranhem.R | 18 ++ R/wq_pca.R |only README.md | 105 ++++++++++++--- build/partial.rdb |only inst/ANALISE_TECNICA_TIKATUWQ.md |only inst/CRAN-SUBMISSION |only inst/README_install.md |only inst/doc/tikatuwq-methods.html | 39 +++-- inst/doc/tikatuwq-workflow.html | 92 ++++++------- inst/doc/tikatuwq.html | 11 - inst/extdata/conama_limits.csv | 110 ++++++++++++++-- inst/run_check_cran.R |only man/assign_season.Rd |only man/balnear_check.Rd |only man/compare_seasons.Rd |only man/compute_load.Rd |only man/conama_freq_check.Rd |only man/exceedance_prob.Rd |only man/iqa.Rd | 75 +++++++---- man/mk_seasonal.Rd |only man/nsfwqi.Rd | 90 ++++++++----- man/plot_iet.Rd |only man/plot_map_quality.Rd |only man/tikatuwq-package.Rd | 2 man/wq_demo.Rd | 13 + man/wq_pca.Rd |only tests/testthat/test-balnear.R |only tests/testthat/test-conama_freq.R |only tests/testthat/test-iqa-geometric.R |only tests/testthat/test-load_exceedance.R |only tests/testthat/test-mk_seasonal.R |only tests/testthat/test-plot_iet.R |only tests/testthat/test-plot_map_quality.R |only tests/testthat/test-seasonal.R |only tests/testthat/test-wq_pca.R |only 50 files changed, 782 insertions(+), 367 deletions(-)
Title: Savvy Parity Regression Model Estimation with 'savvyPR'
Description: Implements the Savvy Parity Regression 'savvyPR' methodology
for multivariate linear regression analysis. The package solves an
optimization problem that balances the contribution of each predictor
variable to ensure estimation stability in the presence of
multicollinearity. It supports two distinct parameterization methods,
a Budget-based approach that allocates a fixed loss contribution to
each predictor, and a Target-based approach (t-tuning) that utilizes
a relative elasticity weight for the response variable. The package
provides comprehensive tools for model estimation, risk distribution
analysis, and parameter tuning via cross-validation (PR1, PR2, and
PR3 model types) to optimize predictive accuracy. Methods are based
on Asimit, Chen, Ichim and Millossovich (2026)
<https://openaccess.city.ac.uk/id/eprint/37017/>.
Author: Ziwei Chen [aut, cre] ,
Vali Asimit [aut] ,
Pietro Millossovich [aut]
Maintainer: Ziwei Chen <Ziwei.Chen.3@citystgeorges.ac.uk>
Diff between savvyPR versions 0.1.1 dated 2026-04-07 and 0.1.2 dated 2026-06-09
savvyPR-0.1.1/savvyPR/tests/testthat/Rplots.pdf |only savvyPR-0.1.2/savvyPR/DESCRIPTION | 6 savvyPR-0.1.2/savvyPR/MD5 | 21 savvyPR-0.1.2/savvyPR/R/cv.savvyPR.R | 616 ++-- savvyPR-0.1.2/savvyPR/R/savvyPR.R | 582 ++-- savvyPR-0.1.2/savvyPR/build/vignette.rds |binary savvyPR-0.1.2/savvyPR/inst/doc/savvyPR_example.R | 302 +- savvyPR-0.1.2/savvyPR/inst/doc/savvyPR_example.html | 1620 ++++++------- savvyPR-0.1.2/savvyPR/man/cv.savvyPR.Rd | 16 savvyPR-0.1.2/savvyPR/man/savvyPR.Rd | 7 savvyPR-0.1.2/savvyPR/tests/testthat/test-plot_functions.R | 579 ++-- savvyPR-0.1.2/savvyPR/tests/testthat/test-savvyPR.R | 396 +-- 12 files changed, 2103 insertions(+), 2042 deletions(-)
Title: Personal Themes and Formatting Preferences
Description: A collection of utility functions, themes, and templates to
support personal data analysis workflows. Includes functions for
formatting numeric values as text, custom themes and color scales for
'ggplot2', and automatic formatting for tables created with 'gt'.
Author: W. Jake Thompson [aut, cre, cph]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between wjake versions 1.0.0 dated 2026-05-20 and 1.0.1 dated 2026-06-09
DESCRIPTION | 6 +- MD5 | 10 +-- NEWS.md | 4 + README.md | 110 ++++++++++++++++++++--------------------- build/partial.rdb |binary tests/testthat/test-fmt-text.R | 22 ++++---- 6 files changed, 79 insertions(+), 73 deletions(-)
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://api-docs.serpstat.com/docs/serpstat-public-api/jenasqbwtxdlr-introduction-to-serpstat-api>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.4.1 dated 2026-05-25 and 0.4.2 dated 2026-06-09
DESCRIPTION | 6 ++--- MD5 | 15 +++++++------- NAMESPACE | 1 NEWS.md | 4 +++ R/search_analytics.R | 46 +++++++++++++++++++++++++++++++++++++++++++ R/serpstatr.R | 18 +++------------- README.md | 1 man/serpstatr.Rd | 20 +++--------------- man/sst_sa_keyword_trends.Rd |only 9 files changed, 71 insertions(+), 40 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2.4 dated 2025-12-19 and 1.2.5 dated 2026-06-09
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/dbscan.R | 8 ++++---- R/kNN.R | 7 ++++--- R/optics.R | 33 ++++++++++++++++----------------- R/reachability.R | 47 +++++++++++++++++++++++++---------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dbscan.pdf |binary inst/doc/hdbscan.html | 24 ++++++++++++------------ man/dbscan.Rd | 13 ++++++++----- man/kNN.Rd | 8 +++++--- man/optics.Rd | 36 +++++++++++++++++++----------------- man/reachability.Rd | 49 +++++++++++++++++++++++++++---------------------- vignettes/dbscan.bib | 5 +---- 16 files changed, 146 insertions(+), 128 deletions(-)
Title: Clustering-Based K-Nearest Neighbor Regression for Longitudinal
Data
Description: Implements the 'CKNNRLD' algorithm (Clustering-Based K-Nearest
Neighbor Regression for Longitudinal Data) for improving K-Nearest
Neighbor ('KNN') regression on longitudinal data through cluster-based
partitioning and localized prediction. Offers enhanced computational
efficiency and accuracy for high-volume longitudinal datasets. The
acronym 'KNN' stands for K-Nearest Neighbor. References: Loeloe MS,
Tabatabaei SM, Sefidkar R, Mehrparvar AH, Jambarsang S (2025).
"Boosting K-nearest neighbor regression performance for longitudinal
data through a novel learning approach." BMC Bioinformatics, 26, 232.
<doi:10.1186/s12859-025-06205-1>.
Author: Mohammad Sadegh Loeloe [aut, cre],
Seyyed Mohammad Tabatabaei [aut],
Reyhane Sefidkar [aut],
Amir Houshang Mehrparvar [aut],
Sara Jambarsang [aut, ths]
Maintainer: Mohammad Sadegh Loeloe <mslbiostat@gmail.com>
Diff between CKNNRLD versions 0.1.2 dated 2026-05-28 and 0.1.4 dated 2026-06-09
DESCRIPTION | 25 +++------ MD5 | 24 ++++---- NAMESPACE | 8 -- R/BestC.R | 127 +++++++++++------------------------------------ R/CKNNRLD.R | 52 +++++-------------- R/KNNRLD.R | 22 +++++--- R/Tuning_CKNNRLD.R | 140 +++++++++++----------------------------------------- R/Tuning_KNNRLD.R | 55 +++++++++++++------- man/BestC.Rd | 19 ++----- man/CKNNRLD.Rd | 24 +++----- man/CKNNRLD.tune.Rd | 30 ++++------- man/KNNRLD.Rd | 10 +-- man/KNNRLD.tune.Rd | 23 +++----- 13 files changed, 192 insertions(+), 367 deletions(-)
Title: Weighted Meta-Analysis with Pseudo-Populations
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
Author: Subharup Guha [aut, cre],
Mengqi Xu [aut],
Chayce Reed [aut],
Kashish Priyam [aut],
Yi Li [aut]
Maintainer: Subharup Guha <Subharup.Guha@dartmouth.edu>
Diff between WMAP versions 1.3.0 dated 2026-06-05 and 1.3.1 dated 2026-06-09
DESCRIPTION | 6 - MD5 | 18 ++--- R/stage-1.R | 14 +++ R/stage-2.R | 48 ++++++++----- inst/doc/WMAP.R | 23 +----- inst/doc/WMAP.Rmd | 31 +------- inst/doc/WMAP.html | 166 +++++++++++++++++++++-------------------------- man/balancing.weights.Rd | 14 +++ man/causal.estimate.Rd | 47 +++++++------ vignettes/WMAP.Rmd | 31 +------- 10 files changed, 186 insertions(+), 212 deletions(-)
Title: Encapsulated 'REDCap' Projects for Synchronized Data Pipelines
Description: Wraps dozens of 'REDCap' API endpoints into a standardized R6
object. Research Electronic Data Capture ('REDCap') is a survey and
database web application software maintained by Vanderbilt University.
It has a robust application programming interface (API) utilized by
several R packages. 'REDCapSync' uses 'redcapAPI' and 'REDCapR'
behind-the-scenes to retrieve all metadata, data, and log details for
a project. To minimize unnecessary server calls, the interim 'REDCap'
log is analyzed and used to only update necessary records.
Furthermore, the user can define custom datasets that save to a
directory. Those datasets continue to refresh when projects are
synced. Having a secure, standardized, API-efficient,
project-agnostic R object for 'REDCap' projects, streamlines
downstream use in scripts, functions, and shiny applications.
Author: Brandon Rose [cre, aut, cph] ,
Natalie Goulett [ctb]
Maintainer: Brandon Rose <thecodingdocs@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2026-05-21
Diff between REDCapSync versions 0.1.0 dated 2026-05-21 and 0.1.1 dated 2026-06-09
REDCapSync-0.1.0/REDCapSync/R/REDCap_API.R |only REDCapSync-0.1.0/REDCapSync/R/REDCap_log.R |only REDCapSync-0.1.0/REDCapSync/R/zzz.R |only REDCapSync-0.1.0/REDCapSync/tests/testthat/test-zzz.R |only REDCapSync-0.1.1/REDCapSync/DESCRIPTION | 10 REDCapSync-0.1.1/REDCapSync/MD5 | 80 ++-- REDCapSync-0.1.1/REDCapSync/NAMESPACE | 7 REDCapSync-0.1.1/REDCapSync/NEWS.md | 36 + REDCapSync-0.1.1/REDCapSync/R/REDCapSync-package.R | 7 REDCapSync-0.1.1/REDCapSync/R/REDCapSyncDataset.R | 15 REDCapSync-0.1.1/REDCapSync/R/cache.R | 11 REDCapSync-0.1.1/REDCapSync/R/config.R | 174 +++++++-- REDCapSync-0.1.1/REDCapSync/R/datasets.R | 9 REDCapSync-0.1.1/REDCapSync/R/project_helpers.R | 2 REDCapSync-0.1.1/REDCapSync/R/redcap_api.R |only REDCapSync-0.1.1/REDCapSync/R/redcap_log.R |only REDCapSync-0.1.1/REDCapSync/R/sync.R | 47 ++ REDCapSync-0.1.1/REDCapSync/R/tokens.R | 3 REDCapSync-0.1.1/REDCapSync/R/utils-assert.R | 4 REDCapSync-0.1.1/REDCapSync/R/utils-xlsx-csv.R | 208 ++++++----- REDCapSync-0.1.1/REDCapSync/R/utils.R | 6 REDCapSync-0.1.1/REDCapSync/README.md | 6 REDCapSync-0.1.1/REDCapSync/inst/WORDLIST | 2 REDCapSync-0.1.1/REDCapSync/inst/doc/Cache.R | 5 REDCapSync-0.1.1/REDCapSync/inst/doc/Cache.Rmd | 7 REDCapSync-0.1.1/REDCapSync/inst/doc/Cache.html | 21 - REDCapSync-0.1.1/REDCapSync/inst/doc/Datasets.R | 6 REDCapSync-0.1.1/REDCapSync/inst/doc/Datasets.Rmd | 6 REDCapSync-0.1.1/REDCapSync/inst/doc/Datasets.html | 24 - REDCapSync-0.1.1/REDCapSync/inst/doc/Projects.html | 40 +- REDCapSync-0.1.1/REDCapSync/inst/doc/REDCapSync.R | 4 REDCapSync-0.1.1/REDCapSync/inst/doc/REDCapSync.Rmd | 6 REDCapSync-0.1.1/REDCapSync/inst/doc/REDCapSync.html | 6 REDCapSync-0.1.1/REDCapSync/man/config.Rd | 135 +++++-- REDCapSync-0.1.1/REDCapSync/man/dataset.Rd | 21 + REDCapSync-0.1.1/REDCapSync/tests/testthat/test-cache.R | 2 REDCapSync-0.1.1/REDCapSync/tests/testthat/test-config.R | 130 +++++- REDCapSync-0.1.1/REDCapSync/tests/testthat/test-redcap_log.R | 42 +- REDCapSync-0.1.1/REDCapSync/tests/testthat/test-sync.R | 9 REDCapSync-0.1.1/REDCapSync/tests/testthat/test-tokens.R | 20 + REDCapSync-0.1.1/REDCapSync/tests/testthat/test-utils.R | 10 REDCapSync-0.1.1/REDCapSync/vignettes/Cache.Rmd | 7 REDCapSync-0.1.1/REDCapSync/vignettes/Datasets.Rmd | 6 REDCapSync-0.1.1/REDCapSync/vignettes/REDCapSync.Rmd | 6 44 files changed, 809 insertions(+), 331 deletions(-)
Title: LLM-Assisted Data Cleaning with Multi-Provider Support
Description: Detects and suggests fixes for semantic inconsistencies in data
frames by calling large language models (LLMs) through a unified,
provider-agnostic interface. Supported providers include 'OpenAI'
('GPT-4o', 'GPT-4o-mini') <https://platform.openai.com>,
'Anthropic' ('Claude') <https://www.anthropic.com>,
'Google' ('Gemini') <https://ai.google.dev>,
'Groq' (free-tier 'LLaMA' and 'Mixtral') <https://groq.com>,
and local 'Ollama' models <https://ollama.com>.
The package identifies issues that rule-based tools cannot detect:
abbreviation variants, typographic errors, case inconsistencies, and
malformed values. Results are returned as tidy data frames with column,
row index, detected value, issue type, suggested fix, and confidence
score. An offline fallback using statistical and fuzzy-matching methods
is provided for use without any application programming interface (API)
key. Interactive fix application with human review is supported via
'apply_fixes()'. Metho [...truncated...]
Author: Sadikul Islam [aut, cre] ,
Rajesh Kaushal [aut]
Maintainer: Sadikul Islam <sadikul.islamiasri@gmail.com>
Diff between llmclean versions 0.1.0 dated 2026-04-22 and 0.1.1 dated 2026-06-09
DESCRIPTION | 43 +++++++++++++++++++++++-------------------- MD5 | 6 +++--- inst/doc/llmclean-intro.html | 6 +++--- man/llmclean-package.Rd | 5 +++++ 4 files changed, 34 insertions(+), 26 deletions(-)
Title: Access Brazilian National Treasury Open Data APIs
Description: Provides a unified interface to access open data from the
Brazilian National Treasury ('Tesouro Nacional') and related government
APIs. Covers six data sources: 'SICONFI'
<https://apidatalake.tesouro.gov.br/docs/siconfi/> for fiscal reports
('RREO', 'RGF', 'DCA', 'MSC') and entity information; 'CUSTOS'
<https://apidatalake.tesouro.gov.br/docs/custos/> for federal
government cost data; 'SADIPEM'
<https://apidatalake.tesouro.gov.br/docs/sadipem/> for public debt and
credit operations; 'Transferencias Constitucionais'
<https://apiapex.tesouro.gov.br/aria/v1/transferencias_constitucionais/docs>
for constitutional transfers to states and municipalities; 'SIORG'
<https://estruturaorganizacional.dados.gov.br> for federal
organizational structure; and 'SIOPE' ('FNDE'/'MEC') for education
spending data. Features automatic pagination, in-memory caching,
retry logic, and tidy output.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorin [aut],
Diogo Bezerra [aut],
Tiago Pereira [aut],
Fernando Barbalho [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between tesouror versions 0.2.2 dated 2026-05-06 and 0.2.3 dated 2026-06-09
DESCRIPTION | 6 ++-- MD5 | 22 +++++++------- NEWS.md | 10 ++++++ R/siconfi.R | 23 +++++++++------ build/vignette.rds |binary inst/doc/siconfi.R | 10 ++++++ inst/doc/siconfi.Rmd | 19 ++++++++++++ inst/doc/siconfi.html | 48 ++++++++++++++++++++++---------- inst/doc/transferencias_pernambuco.html | 4 +- man/get_rreo.Rd | 17 +++++++---- tests/testthat/test-url-construction.R | 22 ++++++++++++++ vignettes/siconfi.Rmd | 19 ++++++++++++ 12 files changed, 153 insertions(+), 47 deletions(-)
Title: Robust Test Statistics for Structural Equation Models
Description: Supports penalized eigenvalue block-averaging and penalized
regression p-values (Foldnes, Moss, Grønneberg, 2024)
<doi:10.1080/10705511.2024.2372028>, including their extension to nested
model comparison (Foldnes, Grønneberg, Moss, 2026)
<doi:10.3758/s13428-026-02968-4>, as well as traditional p-values such as
Satorra-Bentler. All p-values can be calculated using unbiased or biased
gamma estimates (Du, Bentler, 2022) <doi:10.1080/10705511.2022.2063870> and
two choices of chi square statistics. The tests apply to any
minimum-discrepancy estimator -- ML, GLS, ULS, and categorical WLSMV/DWLS --
with experimental support for full-information maximum-likelihood (FIML) fits
under missing data.
Author: Jonas Moss [aut, cre] ,
Njal Foldnes [ctb] ,
Steffen Groenneberg [ctb]
Maintainer: Jonas Moss <jonas.moss.statistics@gmail.com>
Diff between semTests versions 0.7.1 dated 2025-10-09 and 0.9.0 dated 2026-06-09
semTests-0.7.1/semTests/R/derivatives.R |only semTests-0.7.1/semTests/man/laavan_tests.Rd |only semTests-0.7.1/semTests/man/sparsify.Rd |only semTests-0.9.0/semTests/DESCRIPTION | 32 semTests-0.9.0/semTests/MD5 | 112 - semTests-0.9.0/semTests/NAMESPACE | 9 semTests-0.9.0/semTests/NEWS.md |only semTests-0.9.0/semTests/R/checks.R |only semTests-0.9.0/semTests/R/fiml_fmg.R |only semTests-0.9.0/semTests/R/gamma.R | 451 +++--- semTests-0.9.0/semTests/R/get_a_matrix.R | 244 --- semTests-0.9.0/semTests/R/imhof.R |only semTests-0.9.0/semTests/R/lavaan_helper.R | 277 --- semTests-0.9.0/semTests/R/pvalues.R | 742 ++++++---- semTests-0.9.0/semTests/R/support.R |only semTests-0.9.0/semTests/R/tests.R | 194 +- semTests-0.9.0/semTests/R/utility.R | 193 +- semTests-0.9.0/semTests/README.md | 210 +- semTests-0.9.0/semTests/build |only semTests-0.9.0/semTests/inst |only semTests-0.9.0/semTests/man/check_lavaan.Rd |only semTests-0.9.0/semTests/man/check_supported.Rd |only semTests-0.9.0/semTests/man/check_supported_nested.Rd |only semTests-0.9.0/semTests/man/default.Rd | 24 semTests-0.9.0/semTests/man/eba_pvalue.Rd | 24 semTests-0.9.0/semTests/man/fiml_lambdas.Rd |only semTests-0.9.0/semTests/man/fiml_lambdas_nested.Rd |only semTests-0.9.0/semTests/man/fiml_saturated_moments.Rd |only semTests-0.9.0/semTests/man/fit_provenance.Rd |only semTests-0.9.0/semTests/man/gamma.Rd | 44 semTests-0.9.0/semTests/man/gamma_to_gamma_unbiased.Rd | 40 semTests-0.9.0/semTests/man/imhof_pvalue.Rd |only semTests-0.9.0/semTests/man/is_classic_nt.Rd |only semTests-0.9.0/semTests/man/is_fiml.Rd |only semTests-0.9.0/semTests/man/lambdas_nested.Rd |only semTests-0.9.0/semTests/man/lav_ugamma_nested_2000.Rd | 50 semTests-0.9.0/semTests/man/lavaan_tests.Rd |only semTests-0.9.0/semTests/man/nanull.Rd | 24 semTests-0.9.0/semTests/man/nested_factor_2000.Rd |only semTests-0.9.0/semTests/man/pall.Rd | 24 semTests-0.9.0/semTests/man/peba_pvalue.Rd | 24 semTests-0.9.0/semTests/man/pols_pvalue.Rd | 24 semTests-0.9.0/semTests/man/print.semTests_pvalues.Rd |only semTests-0.9.0/semTests/man/pvalue_all.Rd | 24 semTests-0.9.0/semTests/man/pvalue_internal.Rd | 55 semTests-0.9.0/semTests/man/pvalues.Rd | 273 ++- semTests-0.9.0/semTests/man/rescale_missing.Rd |only semTests-0.9.0/semTests/man/scaled_f.Rd | 40 semTests-0.9.0/semTests/man/semTests-support.Rd |only semTests-0.9.0/semTests/man/split_input.Rd | 30 semTests-0.9.0/semTests/man/trad_pvalue.Rd | 46 semTests-0.9.0/semTests/man/ugamma.Rd | 24 semTests-0.9.0/semTests/man/ugamma_nested.Rd | 24 semTests-0.9.0/semTests/man/warn_fiml_information.Rd |only semTests-0.9.0/semTests/tests/testthat.R | 8 semTests-0.9.0/semTests/tests/testthat/setup.R | 93 - semTests-0.9.0/semTests/tests/testthat/test-checks.R |only semTests-0.9.0/semTests/tests/testthat/test-errors.R |only semTests-0.9.0/semTests/tests/testthat/test-estimators.R |only semTests-0.9.0/semTests/tests/testthat/test-imhof.R |only semTests-0.9.0/semTests/tests/testthat/test-internals.R |only semTests-0.9.0/semTests/tests/testthat/test-methods.R |only semTests-0.9.0/semTests/tests/testthat/test-nested-reduction.R |only semTests-0.9.0/semTests/tests/testthat/test-one-lambda.R | 17 semTests-0.9.0/semTests/tests/testthat/test-pvalues.R | 17 semTests-0.9.0/semTests/tests/testthat/test-split-input.R |only semTests-0.9.0/semTests/tests/testthat/test-support.R |only semTests-0.9.0/semTests/tests/testthat/test-unbiased-new.R | 54 semTests-0.9.0/semTests/tests/testthat/test-utility.R | 166 +- semTests-0.9.0/semTests/tests/testthat/values_groups.Rds |binary semTests-0.9.0/semTests/tests/testthat/values_nested_groups.Rds |binary semTests-0.9.0/semTests/tests/testthat/values_nested_no_groups.Rds |binary semTests-0.9.0/semTests/tests/testthat/values_no_groups.Rds |binary semTests-0.9.0/semTests/vignettes |only 74 files changed, 1830 insertions(+), 1783 deletions(-)
Title: Convert Data among QTL Mapping Packages
Description: Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2convert versions 0.32 dated 2026-04-30 and 0.34 dated 2026-06-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ R/probs_qtl_to_qtl2.R | 6 +++++- README.md | 20 +++++++++++++++++++- man/qtl2convert-package.Rd | 5 +++++ 6 files changed, 48 insertions(+), 12 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.4.1 dated 2026-05-14 and 2.4.2 dated 2026-06-09
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- NAMESPACE | 2 + NEWS | 3 ++ R/rsa.R | 14 +++++++++++ inst/doc/bignum.html | 32 +++++++++++++-------------- inst/doc/crypto_hashing.html | 4 +-- inst/doc/keys.html | 48 ++++++++++++++++++++--------------------- inst/doc/secure_rng.html | 18 +++++++-------- man/rsa_encrypt.Rd | 9 +++++++ src/rsa.c | 27 +++++++++++++++++++++++ tests/testthat/test_keys_rsa.R | 9 ++++++- 12 files changed, 129 insertions(+), 67 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut] ,
John Zobolas [aut] ,
Alexander Winterstetter [ctb],
Toby Hocking [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.14.0 dated 2025-12-13 and 0.15.0 dated 2026-06-09
DESCRIPTION | 24 + MD5 | 189 +++++++------- NEWS.md | 15 + R/LearnerClassifCVGlmnet.R | 142 ++++++---- R/LearnerClassifGlmnet.R | 112 ++++---- R/LearnerClassifKKNN.R | 30 +- R/LearnerClassifLDA.R | 12 R/LearnerClassifLogReg.R | 50 ++- R/LearnerClassifMultinom.R | 19 + R/LearnerClassifNaiveBayes.R | 27 +- R/LearnerClassifNnet.R | 16 - R/LearnerClassifQDA.R | 16 - R/LearnerClassifRanger.R | 40 ++- R/LearnerClassifSVM.R | 36 +- R/LearnerClassifXgboost.R | 261 ++++++++------------ R/LearnerRegrCVGlmnet.R | 117 +++++--- R/LearnerRegrGlmnet.R | 102 +++---- R/LearnerRegrKKNN.R | 29 +- R/LearnerRegrKM.R | 21 + R/LearnerRegrLM.R | 28 +- R/LearnerRegrNnet.R | 11 R/LearnerRegrRanger.R | 92 +++++-- R/LearnerRegrSVM.R | 32 +- R/LearnerRegrXgboost.R | 144 +++++------ R/bibentries.R | 5 R/helpers.R | 3 R/helpers_glmnet.R | 37 +- R/helpers_ranger.R | 4 R/helpers_xgboost.R |only R/zzz.R | 6 README.md | 2 build/partial.rdb |binary inst/paramtest/helper.R | 3 inst/paramtest/test_paramtest_classif.cv_glmnet.R | 46 ++- inst/paramtest/test_paramtest_classif.glmnet.R | 43 +-- inst/paramtest/test_paramtest_classif.kknn.R | 13 inst/paramtest/test_paramtest_classif.lda.R | 26 + inst/paramtest/test_paramtest_classif.logreg.R | 29 +- inst/paramtest/test_paramtest_classif.multinom.R | 13 inst/paramtest/test_paramtest_classif.naive_bayes.R | 26 + inst/paramtest/test_paramtest_classif.nnet.R | 13 inst/paramtest/test_paramtest_classif.qda.R | 26 + inst/paramtest/test_paramtest_classif.ranger.R | 27 +- inst/paramtest/test_paramtest_classif.svm.R | 26 + inst/paramtest/test_paramtest_classif.xgboost.R | 37 +- inst/paramtest/test_paramtest_regr.cv_glmnet.R | 46 ++- inst/paramtest/test_paramtest_regr.glmnet.R | 43 +-- inst/paramtest/test_paramtest_regr.kknn.R | 13 inst/paramtest/test_paramtest_regr.km.R | 26 + inst/paramtest/test_paramtest_regr.lm.R | 26 + inst/paramtest/test_paramtest_regr.nnet.R | 13 inst/paramtest/test_paramtest_regr.ranger.R | 27 +- inst/paramtest/test_paramtest_regr.svm.R | 26 + inst/paramtest/test_paramtest_regr.xgboost.R | 37 +- man/mlr3learners-package.Rd | 6 man/mlr_learners_classif.cv_glmnet.Rd | 216 +++++++++------- man/mlr_learners_classif.glmnet.Rd | 194 +++++++------- man/mlr_learners_classif.kknn.Rd | 90 +++--- man/mlr_learners_classif.lda.Rd | 90 +++--- man/mlr_learners_classif.log_reg.Rd | 102 ++++--- man/mlr_learners_classif.multinom.Rd | 90 +++--- man/mlr_learners_classif.naive_bayes.Rd | 90 +++--- man/mlr_learners_classif.nnet.Rd | 92 +++---- man/mlr_learners_classif.qda.Rd | 90 +++--- man/mlr_learners_classif.ranger.Rd | 153 ++++++----- man/mlr_learners_classif.svm.Rd | 90 +++--- man/mlr_learners_classif.xgboost.Rd | 175 ++++++------- man/mlr_learners_regr.cv_glmnet.Rd | 220 +++++++++------- man/mlr_learners_regr.glmnet.Rd | 199 +++++++-------- man/mlr_learners_regr.kknn.Rd | 90 +++--- man/mlr_learners_regr.km.Rd | 90 +++--- man/mlr_learners_regr.lm.Rd | 96 +++---- man/mlr_learners_regr.nnet.Rd | 92 +++---- man/mlr_learners_regr.ranger.Rd | 176 +++++++------ man/mlr_learners_regr.svm.Rd | 90 +++--- man/mlr_learners_regr.xgboost.Rd | 176 ++++++------- tests/testthat/helper.R | 16 - tests/testthat/setup.R | 1 tests/testthat/teardown.R | 1 tests/testthat/test_classif_cv_glmnet.R | 56 ++++ tests/testthat/test_classif_glmnet.R | 39 ++ tests/testthat/test_classif_log_reg.R | 19 - tests/testthat/test_classif_multinom.R | 11 tests/testthat/test_classif_naive_bayes.R | 4 tests/testthat/test_classif_nnet.R | 4 tests/testthat/test_classif_qda.R | 1 tests/testthat/test_classif_ranger.R | 2 tests/testthat/test_classif_svm.R | 2 tests/testthat/test_classif_xgboost.R | 137 ++++++---- tests/testthat/test_regr_cv_glmnet.R | 29 ++ tests/testthat/test_regr_glmnet.R | 28 ++ tests/testthat/test_regr_km.R | 8 tests/testthat/test_regr_nnet.R | 4 tests/testthat/test_regr_ranger.R | 21 - tests/testthat/test_regr_svm.R | 2 tests/testthat/test_regr_xgboost.R | 152 ++++++++--- 96 files changed, 3122 insertions(+), 2329 deletions(-)
Title: Roadmap Footers for 'Reveal.js' Slides in 'Quarto' and 'R
Markdown'
Description: Adds section-aware roadmap footers to 'Reveal.js' slide decks
created with 'Quarto' or 'R Markdown'. The footer highlights completed,
current, and upcoming sections as slides advance. Supports multiple
visual styles, inherited section tags, roadmap-free slides, and
configurable colors, size, and positioning options.
Author: Tiger Tang [aut, cre]
Maintainer: Tiger Tang <tigerloveslobsters@gmail.com>
Diff between deckroadmap versions 0.1.4 dated 2026-04-21 and 0.1.5 dated 2026-06-09
DESCRIPTION | 9 +- MD5 | 19 +++--- NEWS.md | 12 +++ R/use_roadmap.R | 8 ++ README.md | 74 +++++++++++++++++++---- inst/assets/roadmap.js | 72 ++++++++++++++++++++-- inst/doc/get-started.Rmd | 53 +++++++++++++--- inst/doc/get-started.html | 129 +++++++++++++++++++++++++---------------- man/figures/slide_example4.gif |only man/use_roadmap.Rd | 7 +- vignettes/get-started.Rmd | 53 +++++++++++++--- 11 files changed, 329 insertions(+), 107 deletions(-)
Title: Computed ABC Analysis
Description: Identify the most relative data points by dividing a numeric data set into three classes A, B, and C, where class A items are the "import few", class C items are the "trivial many" with class B items being something in between, resembling the idea of the Pareto principle.
This ABC classification is done using an ABC curve, which plots cumulative "Yield" against "Effort", similar to a Lorenz curve. Class borders are then precisely mathematically defined on that curve, aiding in interpretation. Based on: Ultsch A, Lotsch J (2015) "Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data". PLoS ONE 10(6): e0129767. <doi:10.1371/journal.pone.0129767>.
Author: Jorn Lotsch [aut] ,
Andre Himmelspach [aut, cre]
Maintainer: Andre Himmelspach <himmelspach@med.uni-frankfurt.de>
Diff between cABCanalysis versions 1.0 dated 2026-04-28 and 1.0.1 dated 2026-06-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cABC_analysis.R | 2 +- R/cABC_special_cases.R | 2 +- README.md | 19 +++++++++++++++---- tests/testthat/test-cABC_analysis.R | 18 ++++++++++++++++++ 6 files changed, 44 insertions(+), 15 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-12 dated 2025-12-08 and 1.1-13 dated 2026-06-09
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.Rnw | 2 +- inst/doc/mlt.pdf |binary tests/AFT-Ex.R | 5 +++-- tests/AFT-Ex.Rout.save | 16 +++++++--------- vignettes/mlt.Rnw | 2 +- vignettes/mlt.bib | 27 +++++++++++++++------------ 10 files changed, 47 insertions(+), 38 deletions(-)
Title: Dynamic Time Warping Algorithms
Description: A comprehensive implementation of dynamic time warping
(DTW) algorithms in R. DTW computes the optimal (least cumulative
distance) alignment between points of two time series. Common DTW
variants covered include local (slope) and global (window)
constraints, subsequence matches, arbitrary distance definitions,
normalizations, minimum variance matching, and so on. Provides
cumulative distances, alignments, specialized plot styles, etc.,
as described in Giorgino (2009) <doi:10.18637/jss.v031.i07>.
Author: Toni Giorgino [aut, cre]
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>
Diff between dtw versions 1.23-2 dated 2026-04-09 and 1.23-3 dated 2026-06-09
DESCRIPTION | 10 +++--- MD5 | 30 +++++++++--------- R/mvm.R | 1 R/stepPattern.R | 65 ++++++++++++++++++++++++++++++++++----- R/window.R | 5 --- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dtw.R | 2 - inst/doc/dtw.pdf |binary man/dtwPlot.Rd | 8 ++-- man/dtwPlotDensity.Rd | 8 ++-- man/dtwPlotThreeWay.Rd | 8 ++-- man/dtwPlotTwoWay.Rd | 8 ++-- man/dtwWindowingFunctions.Rd | 5 +-- man/mvm.Rd | 4 ++ man/stepPattern.Rd | 70 +++++++++++++++++++++++++++++++++++++++---- 16 files changed, 165 insertions(+), 59 deletions(-)
Title: Global Value Chain Decomposition
Description: Four global value chain (GVC) decompositions are implemented.
The Leontief decomposition derives the value added origin of exports by
country and industry as in Hummels, Ishii and Yi (2001). The Koopman,
Wang and Wei (2014) decomposition splits country-level exports into 9
value added components, and the Wang, Wei and Zhu (2013) decomposition
splits bilateral exports into 16 value added components. The Borin and
Mancini (2019) decomposition splits country-, sector- or bilateral-level
exports into up to 13 value added and GVC components. Various GVC
indicators based on these decompositions are computed in the
complimentary 'gvc' package.
--- References: ---
Hummels, D., Ishii, J., & Yi, K. M. (2001). The nature and growth of
vertical specialization in world trade. Journal of international
Economics, 54(1), 75-96.
Koopman, R., Wang, Z., & Wei, S. J. (2014). Tracing value-added and double
counting in gross exports. American Economic Review, 104(2), 459-94.
Wang, Z., Wei, S. J., &a [...truncated...]
Author: Bastiaan Quast [aut, cre] ,
Fei Wang [aut],
Victor Stolzenburg [aut],
Oliver Reiter [ctb],
Sebastian Krantz [ctb]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between decompr versions 6.4.0 dated 2022-06-19 and 6.9.0 dated 2026-06-09
DESCRIPTION | 44 +++++++------- MD5 | 41 +++++++------ NAMESPACE | 1 NEWS.md | 12 +++ R/bm.R |only R/decomp.R | 19 +++--- R/decompr.R | 17 +++-- R/kww.R | 14 ++++ R/leontief.R | 2 R/load_tables_vectors.R | 2 R/wwz.R | 2 README.md | 4 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/decompr.html | 141 +++++++++++++++++++++++---------------------- man/bm.Rd |only man/decomp.Rd | 12 ++- man/decompr-package.Rd | 16 +++-- man/kww.Rd | 16 ++++- man/leontief.Rd | 2 man/load_tables_vectors.Rd | 2 man/wwz.Rd | 2 tests/testthat/test_bm.R |only 23 files changed, 213 insertions(+), 138 deletions(-)
Title: Reinforcement Learning Tools for Multi-Armed Bandit
Description: A flexible general-purpose toolbox for implementing Rescorla-Wagner models
in multi-armed bandit tasks.
As the successor and functional extension of the 'binaryRL' package,
'multiRL' modularizes the Markov Decision Process (MDP) into six core
components. This framework enables users to construct custom models via
intuitive if-else syntax and define latent learning rules for agents.
For parameter estimation, it provides both likelihood-based
inference (MLE and MAP) and simulation-based inference (ABC and
RNN), with full support for parallel processing across subjects.
The workflow is highly standardized, featuring four main functions
that strictly follow the four-step protocol (and ten rules)
proposed by Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Beyond the three built-in models (TD, RSTD, and Utility), users
can easily derive new variants by declaring which variables are
treated as free parameters.
Author: YuKi [aut, cre] ,
Xinyu [aut]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between multiRL versions 0.3.7 dated 2026-03-31 and 0.4.5 dated 2026-06-09
DESCRIPTION | 6 MD5 | 135 ++--- R/base_setClass.R | 4 R/base_summary.R | 4 R/document_behrule.R | 19 R/document_control.R | 30 + R/document_params.R | 35 + R/document_priors.R | 6 R/engine_RNN.R | 62 +- R/engine_RNN3.R | 62 +- R/estimate_2_RNN.R | 65 ++ R/func_alpha.R | 87 ++- R/func_beta.R | 48 + R/func_delta.R | 47 + R/func_epsilon.R | 30 + R/func_gamma.R | 35 + R/func_zeta.R | 63 ++ R/process_1_input.R | 9 R/process_2_behrule.R | 13 R/process_3_record.R | 13 R/process_4_output.R | 145 +++-- R/process_5_metric.R | 5 R/step_1_run_m.R | 4 R/tool_fake_block.R |only data/WMT.rda |only man/RSTD.Rd | 118 ++-- man/TD.Rd | 116 ++-- man/Utility.Rd | 124 ++--- man/WMT.Rd |only man/algorithm.Rd | 82 +-- man/behrule.Rd | 151 +++--- man/colnames.Rd | 180 +++---- man/control.Rd | 892 ++++++++++++++++++------------------ man/data.Rd | 160 +++--- man/engine_ABC.Rd | 110 ++-- man/engine_RNN.Rd | 158 +++--- man/estimate_0_ENV.Rd | 102 ++-- man/estimate_1_LBI.Rd | 72 +- man/estimate_1_MAP.Rd | 134 ++--- man/estimate_1_MLE.Rd | 126 ++--- man/estimate_2_ABC.Rd | 124 ++--- man/estimate_2_RNN.Rd | 124 ++--- man/estimate_2_SBI.Rd | 68 +- man/estimation_methods.Rd | 136 ++--- man/fit_p.Rd | 184 +++---- man/func_alpha.Rd | 71 ++ man/func_beta.Rd | 38 + man/func_delta.Rd | 37 + man/func_epsilon.Rd | 25 - man/func_gamma.Rd | 31 + man/func_zeta.Rd | 60 ++ man/layer.Rd | 196 +++---- man/params.Rd | 769 +++++++++++++++---------------- man/plot.multiRL.replay.Rd | 56 +- man/policy.Rd | 122 ++-- man/priors.Rd | 6 man/process_1_input.Rd | 182 +++---- man/process_2_behrule.Rd | 68 +- man/process_3_record.Rd | 78 +-- man/process_4_output_cpp.Rd | 74 +- man/process_4_output_r.Rd | 74 +- man/process_5_metric.Rd | 82 +-- man/rcv_d.Rd | 240 ++++----- man/reduction.Rd | 120 ++-- man/rpl_e.Rd | 204 ++++---- man/run_m.Rd | 260 +++++----- man/settings.Rd | 194 +++---- man/summary-multiRL.model-method.Rd | 38 - man/system.Rd | 154 +++--- src/process_4_output.cpp | 319 +++++++----- 70 files changed, 4176 insertions(+), 3410 deletions(-)
Title: Tidy and Streamlined Metabolomics Data Workflows
Description: Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>, Stekhoven et al. (2012) <doi:10.1093/bioinformatics/btr597>, Tibshirani et al. (2017) <doi:10.18129/B9.BIOC.IMPUTE>, Troyanskaya et al. (2001) <doi:10.1093/bioinformatics/17.6.520>), normalization (Bolstad et al. (2003) <doi:10.1093/bioinformatics/19.2.185>, Dieterle et al. (2006) <doi:10.1021/ac051632c>, Zhao et al. (2020) <doi:10.1038/s41598-020-72664-6>) transformation, centering and scaling (Van Den Berg et al. (2006) <doi:10.1186/1471-2164-7-142>) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) <doi:10.21105/joss.01686>) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and [...truncated...]
Author: Yannik Schermer [aut, cre, cph]
Maintainer: Yannik Schermer <yannik.schermer@chem.rptu.de>
Diff between metamorphr versions 0.3.0 dated 2026-03-04 and 0.4.0 dated 2026-06-09
DESCRIPTION | 6 MD5 | 38 +- NAMESPACE | 4 NEWS.md | 9 R/convert.R |only R/internal_functions.R | 8 R/io.R | 148 ++++++-- R/misc.R | 55 +++ R/sysdata.rda |binary README.md | 10 inst/doc/conjugate-screening.html | 4 inst/extdata/toy_mzmine.csv |only man/calc_kmd.Rd | 2 man/convert_from_matrix.Rd |only man/convert_from_wide.Rd |only man/figures/functions.svg | 2 man/read_featuretable.Rd | 16 man/read_featuretable_mzmine.Rd |only man/remove_empty_cols.Rd |only tests/testthat/data/test_read_featuretable_empty_cols.csv |only tests/testthat/data/test_read_featuretable_mzmine_no_empty_cols.csv |only tests/testthat/test-convert_from_matrix.R |only tests/testthat/test-convert_from_wide.R |only tests/testthat/test-read_featuretable.R | 167 ++++++---- tests/testthat/test-read_featuretable_mzmine.R |only tests/testthat/test-remove_empty_cols.R |only 26 files changed, 345 insertions(+), 124 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],
Paul Fearnhead [aut],
Idris A. Eckley [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.5 dated 2026-05-06 and 0.1.6 dated 2026-06-09
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- R/RcppExports.R | 7 ++++-- README.md | 21 ++++++++++--------- man/detector_update.Rd | 6 ++++- src/ARpInfo.h | 6 ++--- src/Candidate.h | 8 +++---- src/Info.h | 50 +++++++++++++++++++++++----------------------- src/MultivariateInfo.h | 2 - src/NonparametricInfo.h | 4 +-- src/RcppExports.cpp | 9 ++++---- src/focus_ARp.cpp | 4 +-- src/focus_rcpp_module.cpp | 10 ++++++--- 13 files changed, 86 insertions(+), 73 deletions(-)
Title: Cross-Validating Regression Models
Description: Cross-validation methods of regression models that exploit features of various
modeling functions to improve speed. Some of the methods implemented in the package are
novel, as described in Fox and Monette (2026) <doi:10.18637/jss.v116.i08>,
and the package vignettes. For general introductions to cross-validation,
see, for example, Gareth James, Daniela Witten, Trevor Hastie, and Robert Tibshirani
(2021, ISBN 978-1-0716-1417-4, Secs. 5.1, 5.3), "An Introduction to Statistical Learning with
Applications in R, Second Edition", and Trevor Hastie, Robert Tibshirani,
and Jerome Friedman (2009, ISBN 978-0-387-84857-0, Sec. 7.10), "The Elements of Statistical
Learning, Second Edition".
Author: John Fox [aut] ,
Georges Monette [aut, cre]
Maintainer: Georges Monette <georges+cv@yorku.ca>
Diff between cv versions 2.0.4 dated 2025-06-16 and 2.0.6 dated 2026-06-09
DESCRIPTION | 29 +-- MD5 | 86 ++++++---- NEWS.md | 4 R/Pigs.R | 5 R/cv-select.R | 56 +++--- R/cv.R | 11 - R/cv.modList.R | 49 ++--- build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 14 + inst/doc/cv-extend.html | 60 +++--- inst/doc/cv-mixed.html | 47 ++--- inst/doc/cv-notes.html | 38 +--- inst/doc/cv-selection.html | 29 +-- inst/doc/cv.Rmd | 4 inst/doc/cv.html | 66 +++---- man/Pigs.Rd | 5 man/cv.Rd | 4 man/cv.function.Rd | 55 +++--- man/cv.modList.Rd | 48 ++--- vignettes/cv-notes_cache/html/__packages | 10 - vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.RData |binary vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.rdb |binary vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.rdx |binary vignettes/cv-notes_cache/html/glm.timings_2b7c8d05fe831884caced4b0ec3053df.RData |binary vignettes/cv-notes_cache/html/glm.timings_2b7c8d05fe831884caced4b0ec3053df.rdx |binary vignettes/cv-selection_cache/html/__packages | 11 - vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.RData |binary vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdb |binary vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdx |binary vignettes/cv.Rmd | 4 vignettes/fig |only 32 files changed, 339 insertions(+), 296 deletions(-)
Title: Multidimensional Penalized Splines for (Excess) Hazard Models,
Relative Mortality Ratio Models and Marginal Intensity Models
Description: Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (than [...truncated...]
Author: Mathieu Fauvernier [aut, cre],
Laurent Roche [aut],
Laurent Remontet [aut],
Zoe Uhry [ctb],
Nadine Bossard [ctb],
Elsa Coz [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 2.0.4 dated 2026-05-09 and 2.0.5 dated 2026-06-09
survPen-2.0.4/survPen/R/survPenV2_04.r |only survPen-2.0.5/survPen/DESCRIPTION | 6 survPen-2.0.5/survPen/MD5 | 88 - survPen-2.0.5/survPen/NEWS | 11 survPen-2.0.5/survPen/R/survPenV2_05.r |only survPen-2.0.5/survPen/build/vignette.rds |binary survPen-2.0.5/survPen/inst/doc/survival_analysis_with_survPen.R | 29 survPen-2.0.5/survPen/inst/doc/survival_analysis_with_survPen.Rmd | 40 survPen-2.0.5/survPen/inst/doc/survival_analysis_with_survPen.html | 564 +++++++--- survPen-2.0.5/survPen/man/HeartFailure.Rd | 2 survPen-2.0.5/survPen/man/NR.beta.Rd | 2 survPen-2.0.5/survPen/man/NR.rho.Rd | 2 survPen-2.0.5/survPen/man/constraint.Rd | 2 survPen-2.0.5/survPen/man/cor.var.Rd | 2 survPen-2.0.5/survPen/man/crs.FP.Rd | 2 survPen-2.0.5/survPen/man/crs.Rd | 2 survPen-2.0.5/survPen/man/datCancer.Rd | 2 survPen-2.0.5/survPen/man/design.matrix.Rd | 2 survPen-2.0.5/survPen/man/expected.table.Rd | 2 survPen-2.0.5/survPen/man/instr.Rd | 2 survPen-2.0.5/survPen/man/inv.repam.Rd | 2 survPen-2.0.5/survPen/man/list.wicss.Rd | 2 survPen-2.0.5/survPen/man/model.cons.Rd | 2 survPen-2.0.5/survPen/man/predSNS.Rd | 2 survPen-2.0.5/survPen/man/predict.survPen.Rd | 2 survPen-2.0.5/survPen/man/print.summary.survPen.Rd | 2 survPen-2.0.5/survPen/man/pwcst.Rd | 2 survPen-2.0.5/survPen/man/rd.Rd | 2 survPen-2.0.5/survPen/man/repam.Rd | 2 survPen-2.0.5/survPen/man/robust.var.Rd | 2 survPen-2.0.5/survPen/man/smf.Rd | 2 survPen-2.0.5/survPen/man/smooth.cons.Rd | 2 survPen-2.0.5/survPen/man/smooth.cons.integral.Rd | 2 survPen-2.0.5/survPen/man/smooth.spec.Rd | 2 survPen-2.0.5/survPen/man/splitmult.Rd | 2 survPen-2.0.5/survPen/man/summary.survPen.Rd | 2 survPen-2.0.5/survPen/man/survPen.Rd | 2 survPen-2.0.5/survPen/man/survPen.fit.Rd | 2 survPen-2.0.5/survPen/man/survPenObject.Rd | 2 survPen-2.0.5/survPen/man/tensor.in.Rd | 2 survPen-2.0.5/survPen/man/tensor.prod.S.Rd | 2 survPen-2.0.5/survPen/man/tensor.prod.X.Rd | 2 survPen-2.0.5/survPen/vignettes/survival_analysis_with_survPen.Rmd | 40 survPen-2.0.5/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-55-1.png |binary survPen-2.0.5/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-56-1.png |binary survPen-2.0.5/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-57-1.png |only survPen-2.0.5/survPen/vignettes/survival_analysis_with_survPen_files/figure-html/unnamed-chunk-58-1.png |only 47 files changed, 594 insertions(+), 250 deletions(-)
Title: Prediction Rule Ensembles
Description: Derives prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with adjustments and improvements described in
Fokkema (2020; <DOI:10.18637/jss.v092.i12>) and Fokkema & Strobl
(2020; <DOI:10.1037/met0000256>). The main function pre() derives
prediction rule ensembles consisting of rules and/or linear terms for
continuous, binary, count, multinomial, survival and multivariate
continuous responses. Function gpe() derives generalized prediction
ensembles, consisting of rules, hinge and linear functions of the
predictor variables.
Author: Marjolein Fokkema [aut, cre],
Benjamin Christoffersen [aut]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 1.0.8 dated 2025-09-06 and 1.0.9 dated 2026-06-09
DESCRIPTION | 8 MD5 | 40 +- NEWS.md | 305 +++++++++----------- R/pre.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Missingness.R | 112 +++---- inst/doc/Missingness.html | 44 +- inst/doc/Tuning.R | 24 - inst/doc/Tuning.Rmd | 2 inst/doc/Tuning.html | 4 inst/doc/relaxed.R | 2 inst/doc/relaxed.Rmd | 2 inst/doc/relaxed.html | 75 ++-- inst/doc/speed.R | 16 - inst/doc/speed.html | 12 man/caret_pre_model.Rd | 5 tests/testthat/previous_results/lung_w_pre_surv.RDS |binary tests/testthat/tests_pre.R | 3 vignettes/Tuning.Rmd | 2 vignettes/relaxed.Rmd | 2 21 files changed, 319 insertions(+), 343 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation as documented by Broatch and Karl (2018) <doi:10.48550/arXiv.1710.05284>,
Karl, Yang, and Lohr (2014) <doi:10.1016/j.csda.2013.11.019>, and by
Karl (2012) <doi:10.1515/1559-0410.1471>. Karl and Zimmerman <doi:10.1016/j.jspi.2020.06.004> use this package to illustrate how the home field effect estimator from a mixed model can be biased under nonrandom scheduling.
Author: Andrew T. Karl [cre, aut] ,
Jennifer Broatch [aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.2-4 dated 2023-01-07 and 1.2-5 dated 2026-06-09
DESCRIPTION | 13 + MD5 | 27 ++- NAMESPACE | 25 +-- NEWS | 29 +++ NEWS.md |only R/NB_mov.r | 29 +-- R/N_mov.r | 34 +--- R/PB_cre.R | 20 +- R/game.pred.R | 57 +++++++ R/mvglmmRank-package.R |only R/mvglmmRank.R | 163 +++++++++++++++++++++ build |only inst |only man/game.pred.Rd | 126 ++++++++-------- man/mvglmmRank-package.Rd | 94 ++++++------ man/mvglmmRank.Rd | 350 +++++++++++++++++++++++++--------------------- tests |only 17 files changed, 621 insertions(+), 346 deletions(-)
Title: 'Fish Bioenergetics 4.0' Model Implementation with
High-Performance 'TMB' Backend
Description: An implementation of the 'Fish Bioenergetics 4.0' framework
described in Deslauriers et al. (2017)
<doi:10.1080/03632415.2017.1377558>. Provides automated parameter
optimization, multi-prey diet modeling, and comprehensive energy budget
simulations for fisheries research and aquaculture applications. An
optional 'TMB' (Template Model Builder) backend delivers 10-50x speedup
in maximum likelihood estimation while maintaining full backward
compatibility. Includes species-specific parameter databases and tools
for modeling fish growth, consumption, and metabolism under varying
environmental conditions.
Author: Hans Ttito [aut, cre]
Maintainer: Hans Ttito <kvttitos@gmail.com>
Diff between fb4package versions 2.0.0 dated 2026-05-07 and 2.1.0 dated 2026-06-09
DESCRIPTION | 9 - MD5 | 49 ++++--- NEWS.md | 40 +++++ R/10-data-processing.R | 190 ++++++++++++++++++++++++++-- R/11.3-data-validators.R | 5 R/12-simulation-engine.R | 209 ++++++++++++++++++++++++------- R/13.0-bioenergetic-classes.R | 29 ++++ R/14.0-tmb-shared.R | 2 R/14.1-strategy-interface.R | 20 +- R/14.3-result-builders.R | 9 + README.md | 6 build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/fb4-case-study-chinook.html | 6 inst/doc/fb4-introduction.html | 6 inst/doc/fb4-shiny-validation.R |only inst/doc/fb4-shiny-validation.Rmd |only inst/doc/fb4-shiny-validation.html |only inst/doc/fb4-species-database.html | 4 inst/doc/fb4-statistical-estimation.html | 4 inst/doc/fb4-temperature-climate.html | 4 man/Bioenergetic.Rd | 13 + man/execute_daily_simulation.Rd | 6 man/figures/logo.png |only man/process_contaminant_data.Rd |only man/process_nutrient_data.Rd |only tests/testthat/test-12-simulation.R | 4 tests/testthat/test-13-nutrients.R |only tests/testthat/test-14c-contaminants.R |only vignettes/fb4-shiny-validation.Rmd |only 30 files changed, 513 insertions(+), 108 deletions(-)