Title: Client for the 'World Bank' APIs
Description: Download and search data from the 'World Bank' APIs,
including the 'Indicators' API, the 'Poverty and Inequality Platform
(PIP)' API, the 'Finances One' API, and the 'Projects' API. See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889386-developer-information-overview>
for further details.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between worldbank versions 0.9.1 dated 2026-06-29 and 0.10.0 dated 2026-08-21
DESCRIPTION | 10 ++--- MD5 | 51 +++++++++++++++------------ NAMESPACE | 42 +++++++++++----------- NEWS.md | 18 +++++++++ R/assertions.R | 19 +++++++++- R/fone.R | 16 +++++--- R/httr2.R | 2 - R/indicators.R | 64 +++++++++++++++++++++++++--------- R/pip.R | 58 +++++++++++++++---------------- R/projects.R | 56 +++++++++++++++++++----------- README.md | 8 ++-- man/figures/README-demo-1.png |binary man/pip_aux.Rd | 4 +- man/pip_citation.Rd | 4 +- man/pip_cp.Rd | 10 ++--- man/pip_data.Rd | 15 ++++---- man/pip_group.Rd | 15 ++++---- man/pip_valid_params.Rd | 4 +- man/wb_data.Rd | 18 ++++++++- man/wb_project.Rd | 32 ++++++++++------- tests/testthat/_snaps/pip.md |only tests/testthat/_snaps/projects.md |only tests/testthat/helper-indicators.R |only tests/testthat/test-assertions.R |only tests/testthat/test-fone.R | 27 +++++++++++++- tests/testthat/test-httr2.R |only tests/testthat/test-indicators.R | 68 +++++++++++++++++++++++++++++++++++-- tests/testthat/test-pip.R | 47 +++++++++++++++++++++++++ tests/testthat/test-projects.R | 68 ++++++++++++++++++++++++++++++++++++- 29 files changed, 484 insertions(+), 172 deletions(-)
Title: Curriculum Vitae for R Markdown
Description: Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Rob Hyndman [aut] ,
Yihui Xie [ctb] ,
Albert Krewinkel [cph] ,
JooYoung Seo [ctb] ,
Isabelle Greco [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vitae versions 0.6.0 dated 2024-06-12 and 0.7.0 dated 2026-08-21
DESCRIPTION | 22 ++-- MD5 | 51 +++++----- NEWS.md | 26 +++++ R/awesomecv.R | 49 +++++++++ R/cv_document.R | 3 R/markdowncv.R | 8 + README.md | 14 ++ build/vignette.rds |binary inst/doc/data.html | 3 inst/doc/extending.R | 10 - inst/doc/extending.Rmd | 2 inst/doc/extending.html | 7 - inst/doc/vitae.html | 3 inst/multiple-bibliographies.lua | 1 inst/rmarkdown/templates/hyndman/resources/hyndmantemplate.tex | 11 +- inst/rmarkdown/templates/markdowncv/skeleton/media/davewhipp-print.css | 8 - inst/rmarkdown/templates/markdowncv/skeleton/media/davewhipp-screen.css | 9 - inst/rmarkdown/templates/markdowncv/skeleton/media/kjhealy-print.css | 8 - inst/rmarkdown/templates/markdowncv/skeleton/media/kjhealy-screen.css | 8 - inst/rmarkdown/templates/moderncv/skeleton/moderncv.cls | 11 ++ inst/rmarkdown/templates/twentyseconds/resources/twentysecondstemplate.tex | 2 man/awesomecv.Rd | 6 - man/bibliography_entries.Rd | 2 man/reexports.Rd | 2 man/vitae-package.Rd | 1 tests/testthat/test-font-scale.R |only vignettes/extending.Rmd | 2 27 files changed, 195 insertions(+), 74 deletions(-)
Title: Unsupervised Learning Based Definition of Microbial Rare
Biosphere
Description: A tool to define the rare biosphere. 'ulrb' solves the problem of the
definition of rarity by replacing arbitrary thresholds with an unsupervised machine
learning algorithm (partitioning around medoids, or k-medoids). This algorithm
works for any type of microbiome data, provided there is an abundance table.
This method also works for non-microbiome data.
Author: Francisco Pascoal [aut, cre] ,
Paula Branco [aut] ,
Luis Torgo [aut] ,
Rodrigo Costa [aut] ,
Catarina Magalhaes [aut]
Maintainer: Francisco Pascoal <fpascoal1996@gmail.com>
Diff between ulrb versions 0.1.8 dated 2025-07-07 and 0.1.9 dated 2026-08-21
DESCRIPTION | 10 MD5 | 16 R/define_rb.R | 29 README.md | 11 build/vignette.rds |binary inst/doc/Glossary.html | 107 --- inst/doc/eco-analysis.html | 813 +++++++++++------------ inst/doc/explore-classifications.html | 1177 +++++++++++++++------------------- inst/doc/ulrb-vignet.html | 722 ++++++++------------ 9 files changed, 1270 insertions(+), 1615 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.2.0 dated 2025-07-18 and 0.3.0 dated 2026-08-21
DESCRIPTION | 8 +-- MD5 | 23 ++++---- NEWS.md | 8 +++ R/expect_snapshot_plot.R | 45 ++++++++++++----- R/expect_snapshot_print.R | 18 +++--- R/utils.R | 6 ++ build/partial.rdb |binary inst/tinytest/_tinysnapshot/png-ggplot2_theme_dark.png |only inst/tinytest/helpers.R | 5 + inst/tinytest/test-png.R | 8 +++ inst/tinytest/test-svg.R | 4 - man/expect_snapshot_plot.Rd | 11 +++- man/expect_snapshot_print.Rd | 3 + 13 files changed, 100 insertions(+), 39 deletions(-)
Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette.
'tinycodet' primarily focuses on 4 aspects.
1) Safer decimal (in)equality testing,
standard-evaluated alternatives to with() and aes(),
and other functions for safer coding.
2) A new package import system,
that attempts to combine the benefits of using a package without attaching it,
with the benefits of attaching a package.
3) Extending the string manipulation capabilities of the 'stringi' R package.
4) Reducing repetitive code.
Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tonywilkes.nl@gmail.com>
Diff between tinycodet versions 0.7.0 dated 2026-06-08 and 0.7.1 dated 2026-08-21
DESCRIPTION | 12 ++--- MD5 | 38 ++++++++-------- NEWS.md | 96 ++++++++++++++++++++++++++++++++++------- R/aaa0_tinycodet_help.R | 2 R/import_as.R | 10 ++-- R/pkgs.R | 17 ++----- R/pro.R | 17 ++----- build/partial.rdb |binary inst/tinytest/safer/test-pro.R | 45 +++++++++++++++++-- man/aaa0_tinycodet_help.Rd | 2 man/aaa2_tinycodet_import.Rd | 2 man/import_as.Rd | 12 ++--- man/pkgs.Rd | 19 ++------ man/pro.Rd | 7 +- man/pversion.Rd | 2 man/reexports.Rd | 2 man/safer_partialmatch.Rd | 2 src/C_do_stri_locate_ith0.c | 2 src/C_do_stri_locate_ith1.c | 3 - tests/tinytest.R | 3 + 20 files changed, 189 insertions(+), 104 deletions(-)
Title: Publication-Ready Summary Tables and Forest Plots
Description: A comprehensive framework for descriptive statistics and regression
analysis that produces publication-ready tables and forest plots. Provides a
unified interface from descriptive statistics through multivariable modeling,
with support for linear models, generalized linear models, Cox proportional
hazards, and mixed-effects models. Also includes univariable screening,
multivariate regression, model comparison, and export to multiple formats
including PDF, DOCX, PPTX, 'LaTeX', HTML, and RTF. Built on 'data.table'
for computational efficiency.
Author: Paul Hsin-ti McClelland [aut, cre, cph]
Maintainer: Paul Hsin-ti McClelland <PaulHMcClelland@protonmail.com>
Diff between summata versions 0.11.5 dated 2026-05-07 and 0.12.0 dated 2026-08-21
summata-0.11.5/summata/R/autotable.R |only summata-0.11.5/summata/man/autotable.Rd |only summata-0.11.5/summata/man/format_count_forest.Rd |only summata-0.11.5/summata/tests/testthat/test_compfit.R |only summata-0.11.5/summata/tests/testthat/test_desctable.R |only summata-0.11.5/summata/tests/testthat/test_fit.R |only summata-0.11.5/summata/tests/testthat/test_forest.R |only summata-0.11.5/summata/tests/testthat/test_fullfit.R |only summata-0.11.5/summata/tests/testthat/test_m2dt.R |only summata-0.11.5/summata/tests/testthat/test_multivariate.R |only summata-0.11.5/summata/tests/testthat/test_number_format.R |only summata-0.11.5/summata/tests/testthat/test_survtable.R |only summata-0.11.5/summata/tests/testthat/test_table2.R |only summata-0.12.0/summata/DESCRIPTION | 23 summata-0.12.0/summata/MD5 | 281 +- summata-0.12.0/summata/NAMESPACE | 7 summata-0.12.0/summata/NEWS.md | 25 summata-0.12.0/summata/R/autoforest.R | 14 summata-0.12.0/summata/R/comp_utils.R | 632 ++--- summata-0.12.0/summata/R/compfit.R | 93 summata-0.12.0/summata/R/coxforest.R | 129 - summata-0.12.0/summata/R/desc_utils.R | 21 summata-0.12.0/summata/R/desctable.R | 62 summata-0.12.0/summata/R/fit.R | 94 summata-0.12.0/summata/R/fit_utils.R | 103 summata-0.12.0/summata/R/forest_utils.R | 289 +- summata-0.12.0/summata/R/forestsave.R |only summata-0.12.0/summata/R/fullfit.R | 158 - summata-0.12.0/summata/R/glmforest.R | 149 - summata-0.12.0/summata/R/globals.R | 1 summata-0.12.0/summata/R/imports.R | 7 summata-0.12.0/summata/R/lmforest.R | 100 summata-0.12.0/summata/R/m2dt.R | 164 + summata-0.12.0/summata/R/m2dt_utils.R | 496 +++- summata-0.12.0/summata/R/multifit.R | 403 +-- summata-0.12.0/summata/R/multiforest.R | 62 summata-0.12.0/summata/R/number_utils.R | 306 +- summata-0.12.0/summata/R/recdims.R |only summata-0.12.0/summata/R/surv_utils.R | 320 +- summata-0.12.0/summata/R/survtable.R | 236 + summata-0.12.0/summata/R/table2_utils.R | 869 +++---- summata-0.12.0/summata/R/table2docx.R | 16 summata-0.12.0/summata/R/table2html.R | 31 summata-0.12.0/summata/R/table2pdf.R | 275 +- summata-0.12.0/summata/R/table2pptx.R | 16 summata-0.12.0/summata/R/table2rtf.R | 16 summata-0.12.0/summata/R/table2tex.R | 46 summata-0.12.0/summata/R/tablesave.R |only summata-0.12.0/summata/R/uniforest.R | 77 summata-0.12.0/summata/R/uniscreen.R | 69 summata-0.12.0/summata/README.md | 25 summata-0.12.0/summata/build/vignette.rds |binary summata-0.12.0/summata/inst/WORDLIST | 1 summata-0.12.0/summata/inst/doc/advanced_workflows.R | 64 summata-0.12.0/summata/inst/doc/advanced_workflows.Rmd | 72 summata-0.12.0/summata/inst/doc/advanced_workflows.html | 767 +++--- summata-0.12.0/summata/inst/doc/descriptive_tables.R | 8 summata-0.12.0/summata/inst/doc/descriptive_tables.Rmd | 12 summata-0.12.0/summata/inst/doc/descriptive_tables.html | 20 summata-0.12.0/summata/inst/doc/forest_plots.R | 174 - summata-0.12.0/summata/inst/doc/forest_plots.Rmd | 182 - summata-0.12.0/summata/inst/doc/forest_plots.html | 645 ++--- summata-0.12.0/summata/inst/doc/installation_setup.R | 26 summata-0.12.0/summata/inst/doc/installation_setup.Rmd | 32 summata-0.12.0/summata/inst/doc/installation_setup.html | 34 summata-0.12.0/summata/inst/doc/model_comparison.R | 6 summata-0.12.0/summata/inst/doc/model_comparison.Rmd | 10 summata-0.12.0/summata/inst/doc/model_comparison.html | 32 summata-0.12.0/summata/inst/doc/multivariate_regression.R | 81 summata-0.12.0/summata/inst/doc/multivariate_regression.Rmd | 115 summata-0.12.0/summata/inst/doc/multivariate_regression.html | 527 ++-- summata-0.12.0/summata/inst/doc/regression_modeling.R | 10 summata-0.12.0/summata/inst/doc/regression_modeling.Rmd | 31 summata-0.12.0/summata/inst/doc/regression_modeling.html | 1203 +++++----- summata-0.12.0/summata/inst/doc/survival_tables.R | 15 summata-0.12.0/summata/inst/doc/survival_tables.Rmd | 19 summata-0.12.0/summata/inst/doc/survival_tables.html | 57 summata-0.12.0/summata/inst/doc/table_export.R | 99 summata-0.12.0/summata/inst/doc/table_export.Rmd | 131 - 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summata-0.12.0/summata/vignettes/installation_setup.Rmd | 32 summata-0.12.0/summata/vignettes/model_comparison.Rmd | 10 summata-0.12.0/summata/vignettes/multivariate_regression.Rmd | 115 summata-0.12.0/summata/vignettes/regression_modeling.Rmd | 31 summata-0.12.0/summata/vignettes/survival_tables.Rmd | 19 summata-0.12.0/summata/vignettes/table_export.Rmd | 131 - 169 files changed, 6994 insertions(+), 5046 deletions(-)
Title: Sequential Change-Point Detection via Nonparametric Inference
Description: Detects change points in long univariate time series using the SCAN
framework. The implementation uses a native Rust backend exposed to R via 'extendr'.
Author: Ashoka Prabashwara [aut, cre],
Patricia Menendez [aut],
Liam Hodgkinson [aut],
Stuart Lee [aut]
Maintainer: Ashoka Prabashwara <smashoka123@gmail.com>
Diff between scanr versions 0.1.0 dated 2026-08-20 and 0.1.1 dated 2026-08-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ README.md | 9 ++++++--- inst/doc/scanr-introduction.html | 2 +- src/Makevars | 14 ++++++-------- src/rust/Cargo.lock | 2 +- src/rust/Cargo.toml | 2 +- 7 files changed, 24 insertions(+), 23 deletions(-)
Title: Matched-Null Tests for Cluster-Count Claims
Description: Builds matched nulls for cluster-count claims: synthetic twins of a
dataset that preserve every marginal distribution and the full correlation
matrix while containing no cluster structure by construction. A reported
number of clusters or "types" can then be tested against what the data's own
margins and covariance already produce, using any clustering pipeline. A
t-copula option adds tail dependence to the null, so that an apparent excess
of clusters can be checked against a heavier-tailed alternative before it is
read as evidence of types. Implements the matched-null procedure of Meng
(2026) "Types Without Taxa" <doi:10.17605/OSF.IO/2EKCG>.
Author: Miura Meng [aut, cre]
Maintainer: Miura Meng <haomeng797@gmail.com>
Diff between matchednull versions 0.1.0 dated 2026-07-21 and 0.2.1 dated 2026-08-21
DESCRIPTION | 34 ++++++++-------- MD5 | 28 +++++++------ NEWS.md | 19 ++++++++ R/copula_null.R | 37 ++++++++++++++--- R/matched_null_test.R | 60 ++++++++++++++++++++++++---- README.md | 68 +++++++++++++++++++++++++------- inst/doc/matchednull.R | 4 + inst/doc/matchednull.Rmd | 40 ++++++++++++++++++ inst/doc/matchednull.html | 43 +++++++++++++++++++- man/copula_null.Rd | 34 +++++++++++++--- man/figures |only man/matched_null_test.Rd | 40 ++++++++++++++++-- tests/testthat/test-matched_null_test.R | 38 +++++++++++++++++ tests/testthat/test-t_copula.R |only vignettes/matchednull.Rmd | 40 ++++++++++++++++++ 15 files changed, 417 insertions(+), 68 deletions(-)
Title: Model-Averaged Renewal Process
Description: To implement a model-averaging approach with different renewal
models, with a primary focus on forecasting large earthquakes. Based on
six renewal models (i.e., Poisson, Gamma, Log-Logistics, Weibull,
Log-Normal and BPT), model-averaged point estimates are calculated using
AIC weights. Additionally, both percentile and studentized
bootstrapped model-averaged confidence intervals are constructed. In
comparison, point and interval estimation from the individual or "best"
model (determined via model selection) can be retrieved.
Author: Jie Kang [aut],
Chris Scott [aut],
Vanessa Huang [aut],
Veronica Tsou [aut, cre],
Albert Savary [ctb]
Maintainer: Veronica Tsou <wantungtsou@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2022-08-11
Diff between marp versions 0.1.0 dated 2022-08-11 and 0.1.1 dated 2026-08-21
marp-0.1.0/marp/inst/extdata/large.txt |only marp-0.1.0/marp/inst/extdata/medium.txt |only marp-0.1.0/marp/inst/extdata/small.txt |only marp-0.1.1/marp/DESCRIPTION | 30 - marp-0.1.1/marp/MD5 | 138 +++-- marp-0.1.1/marp/NAMESPACE | 16 marp-0.1.1/marp/NEWS.md | 17 marp-0.1.1/marp/R/bpt_bstrp.R | 57 +- marp-0.1.1/marp/R/bpt_logl.R | 8 marp-0.1.1/marp/R/bpt_rp.R | 99 ++- marp-0.1.1/marp/R/dllog.R | 10 marp-0.1.1/marp/R/gamma_bstrp.R | 39 - marp-0.1.1/marp/R/gamma_logl.R | 7 marp-0.1.1/marp/R/gamma_rp.R | 49 + marp-0.1.1/marp/R/loglogis_bstrp.R | 35 - marp-0.1.1/marp/R/loglogis_logl.R | 7 marp-0.1.1/marp/R/loglogis_rp.R | 47 + marp-0.1.1/marp/R/lognorm_bstrp.R | 34 - marp-0.1.1/marp/R/lognorm_rp.R | 42 - marp-0.1.1/marp/R/lowerT.R | 23 marp-0.1.1/marp/R/marp.R | 96 ++- marp-0.1.1/marp/R/marp_bstrp.R | 39 - marp-0.1.1/marp/R/marp_classes.R |only marp-0.1.1/marp/R/marp_confint.R | 142 +++-- marp-0.1.1/marp/R/marp_methods.R |only marp-0.1.1/marp/R/percent_confint.R | 63 +- marp-0.1.1/marp/R/pllog.R | 22 marp-0.1.1/marp/R/poisson_bstrp.R | 34 - marp-0.1.1/marp/R/poisson_rp.R | 44 - marp-0.1.1/marp/R/student_confint.R | 258 ++++++++-- marp-0.1.1/marp/R/upperT.R | 23 marp-0.1.1/marp/R/weibull_bstrp.R | 35 - marp-0.1.1/marp/R/weibull_logl.R | 7 marp-0.1.1/marp/R/weibull_rp.R | 49 + marp-0.1.1/marp/README.md | 87 +-- marp-0.1.1/marp/build |only marp-0.1.1/marp/inst/doc |only marp-0.1.1/marp/man/bpt_bstrp.Rd | 36 - marp-0.1.1/marp/man/bpt_logl.Rd | 8 marp-0.1.1/marp/man/bpt_rp.Rd | 46 - marp-0.1.1/marp/man/coef.marp_model_fit.Rd |only marp-0.1.1/marp/man/confint.marp_fit.Rd |only marp-0.1.1/marp/man/dllog.Rd | 10 marp-0.1.1/marp/man/gamma_bstrp.Rd | 39 - marp-0.1.1/marp/man/gamma_logl.Rd | 7 marp-0.1.1/marp/man/gamma_rp.Rd | 38 - marp-0.1.1/marp/man/logLik.marp_model_fit.Rd |only marp-0.1.1/marp/man/loglogis_bstrp.Rd | 35 - marp-0.1.1/marp/man/loglogis_logl.Rd | 7 marp-0.1.1/marp/man/loglogis_rp.Rd | 36 - marp-0.1.1/marp/man/lognorm_bstrp.Rd | 34 - marp-0.1.1/marp/man/lognorm_rp.Rd | 31 - marp-0.1.1/marp/man/lowerT.Rd | 23 marp-0.1.1/marp/man/marp.Rd | 56 +- marp-0.1.1/marp/man/marp_bstrp.Rd | 39 - marp-0.1.1/marp/man/marp_confint.Rd | 121 ++-- marp-0.1.1/marp/man/nobs.marp_fit.Rd |only marp-0.1.1/marp/man/nobs.marp_model_fit.Rd |only marp-0.1.1/marp/man/percent_confint.Rd | 51 + marp-0.1.1/marp/man/pllog.Rd | 22 marp-0.1.1/marp/man/poisson_bstrp.Rd | 34 - marp-0.1.1/marp/man/poisson_rp.Rd | 33 - marp-0.1.1/marp/man/print.marp_confint.Rd |only marp-0.1.1/marp/man/print.marp_fit.Rd |only marp-0.1.1/marp/man/print.marp_model_fit.Rd |only marp-0.1.1/marp/man/print.summary_marp_fit.Rd |only marp-0.1.1/marp/man/print.summary_marp_model_fit.Rd |only marp-0.1.1/marp/man/student_confint.Rd | 65 +- marp-0.1.1/marp/man/summary.marp_fit.Rd |only marp-0.1.1/marp/man/summary.marp_model_fit.Rd |only marp-0.1.1/marp/man/upperT.Rd | 23 marp-0.1.1/marp/man/weibull_bstrp.Rd | 35 - marp-0.1.1/marp/man/weibull_logl.Rd | 7 marp-0.1.1/marp/man/weibull_rp.Rd | 40 - marp-0.1.1/marp/tests/testthat/test-bootstrap-orchestration.R |only marp-0.1.1/marp/tests/testthat/test-bpt_bstrp.R | 6 marp-0.1.1/marp/tests/testthat/test-bpt_rp.R | 2 marp-0.1.1/marp/tests/testthat/test-percent_confint.R | 10 marp-0.1.1/marp/tests/testthat/test-s3-interface.R |only marp-0.1.1/marp/vignettes |only 80 files changed, 1462 insertions(+), 989 deletions(-)
Title: Visualize Spatiotemporal Tumor Evolution with Jellyfish Plots
Description: Generates interactive Jellyfish plots to visualize spatiotemporal tumor
evolution by integrating sample and phylogenetic trees into a unified plot.
This approach provides an intuitive way to analyze tumor heterogeneity and
evolution over time and across anatomical locations. The Jellyfish plot
visualization design was first introduced by Lahtinen, Lavikka, et al.
(2023, <doi:10.1016/j.ccell.2023.04.017>).
This package also supports visualizing ClonEvol results, a tool developed
by Dang, et al. (2017, <doi:10.1093/annonc/mdx517>), for analyzing clonal
evolution from multi-sample sequencing data. The 'clonevol' package is not
available on CRAN but can be installed from its GitHub
repository (<https://github.com/hdng/clonevol>).
Author: Kari Lavikka [cph, aut, cre]
Maintainer: Kari Lavikka <kari@karilavikka.fi>
Diff between jellyfisher versions 1.1.1 dated 2025-11-26 and 1.1.2 dated 2026-08-21
DESCRIPTION | 10 +++---- MD5 | 7 ++--- NEWS.md | 4 ++ inst/CITATION |only inst/doc/jellyfisher.html | 64 +++++++++++++++++++++++----------------------- 5 files changed, 45 insertions(+), 40 deletions(-)
Title: A GUI for Dual and Bulk RNA-Sequencing Analysis
Description: A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.
Author: Carmine Fruggiero [aut, cre],
Gaetano Aufiero [aut]
Maintainer: Carmine Fruggiero <fruggierocarmine3@gmail.com>
Diff between inDAGO versions 1.0.3 dated 2025-10-21 and 1.0.4 dated 2026-08-21
DESCRIPTION | 27 +++++++++++----------- MD5 | 14 +++++------ NAMESPACE | 1 R/Saturation.R | 36 +++++++++++++++++++----------- R/app.R | 1 R/globals.R | 1 man/Saturation.Rd | 4 --- tests/testthat/test-inDAGO_shiny.R | 44 ++++++++++++++++++------------------- 8 files changed, 67 insertions(+), 61 deletions(-)
Title: Compute Scores for Different Implicit Measures
Description: A tool for computing the scores for the Implicit Association Test
(IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>)
and the Single Category-IAT (SC-IAT: Karpinski & Steinman
(2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data
(both for the IAT and the SC-IAT), plotting the results, and obtaining a
table with the scores of implicit measures descriptive statistics are
provided.
Author: Ottavia M. Epifania [aut, cre],
Pasquale Anselmi [ctb],
Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2025-08-22
Diff between implicitMeasures versions 0.3.1 dated 2025-08-22 and 1.0.0 dated 2026-08-21
implicitMeasures-0.3.1/implicitMeasures/R/d_density.R |only implicitMeasures-0.3.1/implicitMeasures/R/d_point.R |only implicitMeasures-0.3.1/implicitMeasures/R/descript_d.R |only implicitMeasures-0.3.1/implicitMeasures/R/multi_dsciat.R |only implicitMeasures-0.3.1/implicitMeasures/R/multi_dscore.R |only implicitMeasures-0.3.1/implicitMeasures/man/d_density.Rd |only implicitMeasures-0.3.1/implicitMeasures/man/d_point.Rd |only implicitMeasures-0.3.1/implicitMeasures/man/descript_d.Rd |only implicitMeasures-0.3.1/implicitMeasures/man/multi_dsciat.Rd |only implicitMeasures-0.3.1/implicitMeasures/tests/testthat/test-IAT_rel_descript_d.R |only implicitMeasures-0.3.1/implicitMeasures/tests/testthat/test-compute_iat-replicate.R |only implicitMeasures-0.3.1/implicitMeasures/tests/testthat/test-compute_sciat-replicate.R |only implicitMeasures-0.3.1/implicitMeasures/tests/testthat/test-d_density_d_plot.R |only implicitMeasures-0.3.1/implicitMeasures/tests/testthat/test-multi_dscore_multi_dsciat.R |only implicitMeasures-1.0.0/implicitMeasures/DESCRIPTION | 10 implicitMeasures-1.0.0/implicitMeasures/MD5 | 86 - implicitMeasures-1.0.0/implicitMeasures/NAMESPACE | 14 implicitMeasures-1.0.0/implicitMeasures/NEWS.md | 12 implicitMeasures-1.0.0/implicitMeasures/R/IAT_rel.R | 118 +- implicitMeasures-1.0.0/implicitMeasures/R/clean_iat.R | 7 implicitMeasures-1.0.0/implicitMeasures/R/clean_sciat.R | 23 implicitMeasures-1.0.0/implicitMeasures/R/compute_iat.R | 40 implicitMeasures-1.0.0/implicitMeasures/R/compute_sciat.R | 38 implicitMeasures-1.0.0/implicitMeasures/R/multi-dscore-clean-iat.R |only implicitMeasures-1.0.0/implicitMeasures/R/multi-dscore-clean-sciat.R |only implicitMeasures-1.0.0/implicitMeasures/R/multi-dscore.R |only implicitMeasures-1.0.0/implicitMeasures/R/plot-dsciat.R |only implicitMeasures-1.0.0/implicitMeasures/R/plot-dscore.R |only implicitMeasures-1.0.0/implicitMeasures/R/plot-helpers.R |only implicitMeasures-1.0.0/implicitMeasures/R/plot-multi-dscore.R |only implicitMeasures-1.0.0/implicitMeasures/R/summary-dsciat.R |only implicitMeasures-1.0.0/implicitMeasures/R/summary-dscore.R |only implicitMeasures-1.0.0/implicitMeasures/R/summary-multi-dscore.R |only implicitMeasures-1.0.0/implicitMeasures/build/vignette.rds |binary implicitMeasures-1.0.0/implicitMeasures/inst/doc/IAT-example.R | 32 implicitMeasures-1.0.0/implicitMeasures/inst/doc/IAT-example.Rmd | 72 - implicitMeasures-1.0.0/implicitMeasures/inst/doc/IAT-example.html | 236 +---- implicitMeasures-1.0.0/implicitMeasures/inst/doc/SC-IAT-example.R | 39 implicitMeasures-1.0.0/implicitMeasures/inst/doc/SC-IAT-example.Rmd | 77 - implicitMeasures-1.0.0/implicitMeasures/inst/doc/SC-IAT-example.html | 169 --- implicitMeasures-1.0.0/implicitMeasures/inst/doc/implicitMeasures.Rmd | 3 implicitMeasures-1.0.0/implicitMeasures/inst/doc/implicitMeasures.html | 19 implicitMeasures-1.0.0/implicitMeasures/man/IAT_rel.Rd | 69 - implicitMeasures-1.0.0/implicitMeasures/man/compute_iat.Rd | 2 implicitMeasures-1.0.0/implicitMeasures/man/multi_dscore.Rd | 189 +++- implicitMeasures-1.0.0/implicitMeasures/man/plot.multi_dscore.Rd |only implicitMeasures-1.0.0/implicitMeasures/man/plotScores.Rd |only implicitMeasures-1.0.0/implicitMeasures/man/summary.dsciat.Rd |only implicitMeasures-1.0.0/implicitMeasures/man/summary.dscore.Rd |only implicitMeasures-1.0.0/implicitMeasures/man/summary.multi_dscore.Rd |only implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-IAT_rel.R |only implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-clean_iat.R | 424 +++++---- implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-clean_sciat.R | 458 +++++----- implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-compute_iat.R | 159 +-- implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-compute_sciat.R | 143 +-- implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-multi-dscore-iat.R |only implicitMeasures-1.0.0/implicitMeasures/tests/testthat/test-multi-dscore-sciat.R |only implicitMeasures-1.0.0/implicitMeasures/vignettes/IAT-example.Rmd | 72 - implicitMeasures-1.0.0/implicitMeasures/vignettes/SC-IAT-example.Rmd | 77 - implicitMeasures-1.0.0/implicitMeasures/vignettes/implicitMeasures.Rmd | 3 60 files changed, 1273 insertions(+), 1318 deletions(-)
More information about implicitMeasures at CRAN
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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
visualizations 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 3.5.0 dated 2026-08-04 and 3.5.2 dated 2026-08-21
ggRandomForests-3.5.0/ggRandomForests/tests/testthat/test_lint.R |only ggRandomForests-3.5.2/ggRandomForests/DESCRIPTION | 10 ggRandomForests-3.5.2/ggRandomForests/MD5 | 150 +++++----- ggRandomForests-3.5.2/ggRandomForests/NAMESPACE | 128 ++++---- ggRandomForests-3.5.2/ggRandomForests/NEWS.md | 107 +++++++ ggRandomForests-3.5.2/ggRandomForests/R/calc_roc.R | 32 +- ggRandomForests-3.5.2/ggRandomForests/R/gg_brier.R | 4 ggRandomForests-3.5.2/ggRandomForests/R/gg_error.R | 54 --- ggRandomForests-3.5.2/ggRandomForests/R/gg_isopro.R | 2 ggRandomForests-3.5.2/ggRandomForests/R/gg_partial_rfsrc.R | 11 ggRandomForests-3.5.2/ggRandomForests/R/gg_partial_varpro.R | 68 ++++ ggRandomForests-3.5.2/ggRandomForests/R/gg_roc.R | 20 + ggRandomForests-3.5.2/ggRandomForests/R/gg_vimp.R | 47 --- ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_brier.R | 2 ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_error.R | 47 --- ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_isopro.R | 2 ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_rfsrc.R | 41 -- ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_roc.R | 19 + ggRandomForests-3.5.2/ggRandomForests/R/plot.gg_vimp.R | 4 ggRandomForests-3.5.2/ggRandomForests/R/quantile_pts.R | 2 ggRandomForests-3.5.2/ggRandomForests/README.md | 64 ++++ ggRandomForests-3.5.2/ggRandomForests/build/partial.rdb |binary ggRandomForests-3.5.2/ggRandomForests/build/vignette.rds |binary ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-classification.R | 4 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-classification.html | 58 +-- ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-classification.qmd | 4 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-regression.R | 8 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-regression.html | 60 ++-- ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-regression.qmd | 14 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-survival.R | 6 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-survival.html | 62 ++-- ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests-survival.qmd | 12 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests.R | 4 ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests.html | 20 - ggRandomForests-3.5.2/ggRandomForests/inst/doc/ggRandomForests.qmd | 4 ggRandomForests-3.5.2/ggRandomForests/inst/doc/uvarpro.html | 10 ggRandomForests-3.5.2/ggRandomForests/inst/doc/varpro.html | 30 +- ggRandomForests-3.5.2/ggRandomForests/inst/examples |only ggRandomForests-3.5.2/ggRandomForests/man/calc_auc.Rd | 4 ggRandomForests-3.5.2/ggRandomForests/man/calc_roc.rfsrc.Rd | 8 ggRandomForests-3.5.2/ggRandomForests/man/gg_brier.Rd | 4 ggRandomForests-3.5.2/ggRandomForests/man/gg_error.Rd | 65 ++-- ggRandomForests-3.5.2/ggRandomForests/man/gg_isopro.Rd | 2 ggRandomForests-3.5.2/ggRandomForests/man/gg_partial_rfsrc.Rd | 2 ggRandomForests-3.5.2/ggRandomForests/man/gg_partial_varpro.Rd | 68 ++++ ggRandomForests-3.5.2/ggRandomForests/man/gg_roc.rfsrc.Rd | 22 + ggRandomForests-3.5.2/ggRandomForests/man/gg_vimp.Rd | 20 - ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_brier.Rd | 2 ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_error.Rd | 58 ++- ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_isopro.Rd | 2 ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_rfsrc.Rd | 14 ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_roc.Rd | 19 + ggRandomForests-3.5.2/ggRandomForests/man/plot.gg_vimp.Rd | 4 ggRandomForests-3.5.2/ggRandomForests/man/quantile_pts.Rd | 2 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/helper-varpro-fixtures.R | 21 + ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_autoplot_equivalence.R |only ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_cran_comments.R |only ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_determinism.R |only ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_extractor_contracts.R |only ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_brier.R | 1 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_error.R | 9 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_isopro.R | 16 - ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_partial_rfsrc.R | 14 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_partial_varpro.R | 19 + ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_rfsrc.R | 4 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_roc.R | 26 + ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_shap.R | 18 + ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_udependent.R | 24 + ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_variable.R | 41 ++ ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_varpro.R | 33 ++ ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_varpro_empty_importance.R | 1 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_gg_vimp.R | 61 +--- ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_namespace_hygiene.R | 1 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_quantile_pts.R | 1 ggRandomForests-3.5.2/ggRandomForests/tests/testthat/test_randomForest_helpers.R | 4 ggRandomForests-3.5.2/ggRandomForests/vignettes/ggRandomForests-classification.qmd | 4 ggRandomForests-3.5.2/ggRandomForests/vignettes/ggRandomForests-regression.qmd | 14 ggRandomForests-3.5.2/ggRandomForests/vignettes/ggRandomForests-survival.qmd | 12 ggRandomForests-3.5.2/ggRandomForests/vignettes/ggRandomForests.qmd | 4 79 files changed, 1094 insertions(+), 640 deletions(-)
More information about ggRandomForests at CRAN
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Title: Bayesian Reconciliation in the 'fable' Framework
Description: Implements the 'bayesRecon' probabilistic reconciliation methods
within the 'fable' framework for hierarchical time series forecasting.
Bayesian reconciliation (bayesRecon) methods are accessed via the 'reconcile' verb, following
'fable' conventions. For methodological background, see Corani et al. (2021)
<doi:10.1007/978-3-030-67664-3_13>, Zambon et al. (2024a)
<doi:10.1007/s11222-023-10343-y>, Zambon et al. (2024b)
<https://proceedings.mlr.press/v244/zambon24a.html>, and Carrara et al.
(2026) <doi:10.1016/j.ijforecast.2026.07.003>.
Author: Dario Azzimonti [aut, cre, cph] ,
Stefano Damato [aut] ,
Lorenzo Zambon [aut] ,
Chiara Carrara [aut] ,
Giorgio Corani [aut]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between fable.bayesRecon versions 0.1.0 dated 2026-05-28 and 0.2.0 dated 2026-08-21
DESCRIPTION | 16 - MD5 | 39 +- NAMESPACE | 90 +++--- NEWS.md | 10 R/bayesRecon_BUIS.R | 2 R/bayesRecon_MixCond.R | 84 ++++-- R/bayesRecon_TDcond.R | 13 R/bayesRecon_t.R | 7 README.md | 405 ++++++++++++++++++++++++++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fable.bayesRecon.Rmd | 4 inst/doc/fable.bayesRecon.html | 11 man/bayesRecon_MixCond.Rd | 90 ++++-- man/bayesRecon_t.Rd | 7 man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-18-1.png |only man/figures/README-unnamed-chunk-25-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-7-1.png |only man/figures/hier_large_README.png |only man/figures/hier_small_README.png |only vignettes/fable.bayesRecon.Rmd | 4 vignettes/references.bib | 12 24 files changed, 632 insertions(+), 162 deletions(-)
More information about fable.bayesRecon at CRAN
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Title: Pattern Estimation and Identification for Dyadic Sequences Using
Transition Matrices in R
Description: Provides methods for analyzing categorical dyadic sequences using transition matrices within the Longitudinal Actor-Partner Interdependence Model and Markov-chain framework. The package supports empirical transition counts, maximum likelihood estimation of transition probabilities, and identification of univariate and bivariate patterns of interaction in dyadic sequences.
Author: Mattia Boellenruecher [aut, cre, cph] ,
Megane Bollenruecher [aut] ,
Jean-Philippe Antonietti [aut]
Maintainer: Mattia Boellenruecher <mboellenruec@student.ethz.ch>
Diff between dyadicMarkov versions 0.1.1 dated 2026-06-21 and 0.1.2 dated 2026-08-21
DESCRIPTION | 14 MD5 | 59 NEWS.md | 57 R/apim-bivariate.R | 955 +++++++------- R/apim-univariate.R | 19 R/dyadicMarkov-package.R | 189 +- R/helpers-core.R | 1571 ++++++++++++------------ R/srr-stats-standards.R | 154 +- R/utils-validation.R | 347 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bivariate-workflow.R | 2 inst/doc/bivariate-workflow.Rmd | 302 ++-- inst/doc/bivariate-workflow.html | 149 +- inst/doc/dyadicMarkov-introduction.Rmd | 129 + inst/doc/dyadicMarkov-introduction.html | 141 +- inst/doc/univariate-workflow.Rmd | 242 +-- inst/doc/univariate-workflow.html | 64 man/bivariateCase.Rd | 18 man/completePattern.Rd | 8 man/countEmpBivariate.Rd | 6 man/dyadicMarkov-package.Rd | 31 man/partialPattern.Rd | 8 man/univariatePattern.Rd | 11 tests/testthat/test-bivariate-alpha-boundary.R |only tests/testthat/test-example-data.R | 2 tests/testthat/test-statistic-identity.R |only tests/testthat/test-univariate-alpha-boundary.R |only tests/testthat/test-validation-errors.R | 630 ++++++--- vignettes/bivariate-workflow.Rmd | 302 ++-- vignettes/dyadicMarkov-introduction.Rmd | 129 + vignettes/univariate-workflow.Rmd | 242 +-- 32 files changed, 3186 insertions(+), 2595 deletions(-)
Title: Interactive Clustered Graph for French Scientific Preparatory
Classes
Description: To help French students from scientific preparatory classes for the Grandes Ecoles (CPGE) in their choice of field of study and career options, this package provides an interactive tool and data visualization of a graph clustered by different competitive exams and sectors of activity for French selective engineering schools and selective higher education institutions like Ecoles Normales Superieures (ENS) or specialized university programs (magisteres). Besides, there are two drop-down menus to select on the graph many fields or more than 200 engineering schools or ENS or magisteres. It gives the opportunity to expand, collapse clusters of selective exams interactively too. For more information, see the demonstration video: <https://valerierobert-maths.re/index.php/maths-en-cpge/>. The data was collected via the official French website: <https://www.scei-concours.fr/statistiques.html>.
Author: Valerie Robert [aut, cre]
Maintainer: Valerie Robert <valerie.robert.math@gmail.com>
Diff between cpge versions 1.0.1 dated 2026-08-08 and 1.0.2 dated 2026-08-21
DESCRIPTION | 12 ++-- MD5 | 18 +++--- NEWS.md | 6 +- R/data_graph.R | 104 ++++++++++++++++++++++----------------- R/run_graph.R | 30 ++--------- inst/quarto/cpge_fr.html | 19 +++---- inst/quarto/cpge_fr.qmd | 16 ++---- man/data_graph.Rd | 25 +++++++-- man/run_graph.Rd | 22 +------- tests/testthat/test-data_graph.R | 8 +-- 10 files changed, 130 insertions(+), 130 deletions(-)
Title: Bayesian SVARs with Sign, Zero, and Narrative Restrictions
Description: Implements state-of-the-art algorithms for the Bayesian analysis of Structural Vector Autoregressions (SVARs) identified by sign, zero, and narrative restrictions. The core model is based on a flexible Vector Autoregression with estimated hyper-parameters of the Minnesota prior and the dummy observation priors as in Giannone, Lenza, Primiceri (2015) <doi:10.1162/REST_a_00483> extended by the COVID-specific heteroskedasticity proposed by Lenza, Primiceri (2022) <doi:10.1002/jae.2895>. The sign restrictions are implemented employing the methods proposed by Rubio-Ramírez, Waggoner & Zha (2010) <doi:10.1111/j.1467-937X.2009.00578.x>, while identification through sign and zero restrictions follows the approach developed by Arias, Rubio-Ramírez, & Waggoner (2018) <doi:10.3982/ECTA14468>. Furthermore, our toolset provides algorithms for identification via sign and narrative restrictions, in line with the methods introduced by Antolín-Díaz and Rubio-Ramírez (201 [...truncated...]
Author: Xiaolei Wang [aut, cre] ,
Tomasz Wozniak [aut] ,
Fei Shang [ctb]
Maintainer: Xiaolei Wang <adamwang15@gmail.com>
Diff between bsvarSIGNs versions 2.0 dated 2025-01-29 and 3.0 dated 2026-08-21
bsvarSIGNs-2.0/bsvarSIGNs/src/utils.cpp |only bsvarSIGNs-2.0/bsvarSIGNs/src/utils.h |only bsvarSIGNs-3.0/bsvarSIGNs/DESCRIPTION | 29 bsvarSIGNs-3.0/bsvarSIGNs/MD5 | 76 - bsvarSIGNs-3.0/bsvarSIGNs/NAMESPACE | 8 bsvarSIGNs-3.0/bsvarSIGNs/NEWS.md | 10 bsvarSIGNs-3.0/bsvarSIGNs/R/RcppExports.R | 52 bsvarSIGNs-3.0/bsvarSIGNs/R/bsvarSIGNs-package.R | 52 bsvarSIGNs-3.0/bsvarSIGNs/R/compute.R | 5 bsvarSIGNs-3.0/bsvarSIGNs/R/estimate.R | 175 ++ bsvarSIGNs-3.0/bsvarSIGNs/R/forecast.R | 161 +- bsvarSIGNs-3.0/bsvarSIGNs/R/specify.R | 281 ++- bsvarSIGNs-3.0/bsvarSIGNs/R/utils.R | 16 bsvarSIGNs-3.0/bsvarSIGNs/README.md | 107 + bsvarSIGNs-3.0/bsvarSIGNs/inst/doc/bsvarSIGNs_vignette.pdf |binary bsvarSIGNs-3.0/bsvarSIGNs/inst/include/bsvarSIGNs_RcppExports.h | 411 +++++ bsvarSIGNs-3.0/bsvarSIGNs/inst/tinytest/test_specify.R | 8 bsvarSIGNs-3.0/bsvarSIGNs/man/bsvarSIGNs-package.Rd | 46 bsvarSIGNs-3.0/bsvarSIGNs/man/forecast.PosteriorBSVARSIGN.Rd | 17 bsvarSIGNs-3.0/bsvarSIGNs/man/reexports.Rd |only bsvarSIGNs-3.0/bsvarSIGNs/man/specify_bsvarSIGN.Rd | 119 + bsvarSIGNs-3.0/bsvarSIGNs/man/specify_forecasts.Rd |only bsvarSIGNs-3.0/bsvarSIGNs/man/specify_prior_bsvarSIGN.Rd | 79 - bsvarSIGNs-3.0/bsvarSIGNs/src/Makevars | 4 bsvarSIGNs-3.0/bsvarSIGNs/src/Makevars.win | 4 bsvarSIGNs-3.0/bsvarSIGNs/src/RcppExports.cpp | 710 ++++++++-- bsvarSIGNs-3.0/bsvarSIGNs/src/bsvars_sign.cpp | 299 ++-- bsvarSIGNs-3.0/bsvarSIGNs/src/bsvars_sign.h | 39 bsvarSIGNs-3.0/bsvarSIGNs/src/forecast_bsvarSIGNs.cpp | 54 bsvarSIGNs-3.0/bsvarSIGNs/src/forecast_bsvarSIGNs.h | 3 bsvarSIGNs-3.0/bsvarSIGNs/src/mcmc.cpp | 20 bsvarSIGNs-3.0/bsvarSIGNs/src/restrictions_narrative.cpp | 6 bsvarSIGNs-3.0/bsvarSIGNs/src/restrictions_narrative.h | 2 bsvarSIGNs-3.0/bsvarSIGNs/src/restrictions_zero.cpp | 6 bsvarSIGNs-3.0/bsvarSIGNs/src/restrictions_zero.h | 2 bsvarSIGNs-3.0/bsvarSIGNs/src/sample_NIW.cpp | 8 bsvarSIGNs-3.0/bsvarSIGNs/src/sample_Q.cpp | 26 bsvarSIGNs-3.0/bsvarSIGNs/src/sample_Q.h | 1 bsvarSIGNs-3.0/bsvarSIGNs/src/sample_SOE.cpp |only bsvarSIGNs-3.0/bsvarSIGNs/src/sample_SOE.h |only bsvarSIGNs-3.0/bsvarSIGNs/src/sample_hyper.cpp | 98 + bsvarSIGNs-3.0/bsvarSIGNs/src/utils_bsvarsigns.cpp |only bsvarSIGNs-3.0/bsvarSIGNs/src/utils_bsvarsigns.h |only 43 files changed, 2252 insertions(+), 682 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” (AKA singleton expansion) refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tonywilkes.nl@gmail.com>
Diff between broadcast versions 0.1.9.5 dated 2026-08-20 and 0.1.9.6 dated 2026-08-21
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 6 inst/tinytest/aaa_binary_prep_part1/test-part1-outlen.R | 2 inst/tinytest/aaa_binary_prep_part2/test-drop_dims-drop_ones.R | 120 ++++------ inst/tinytest/aaa_binary_prep_part2/test-mergedims.R | 6 inst/tinytest/aaa_binary_prep_part3/test-PBR.R | 4 inst/tinytest/aaa_binary_prep_part3/test-outdim_simp.R | 4 8 files changed, 81 insertions(+), 81 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-21 0.1.8.8
2026-02-04 0.1.8.6
2024-06-06 0.1.8.4
2023-12-18 0.1.8.1
2023-09-07 0.1.7.9
2023-03-17 0.1.7.7
2023-01-11 0.1.7.6
2022-02-06 0.1.7.4
2021-09-05 0.1.7.3
2021-02-05 0.1.7.2
2020-07-20 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-23 0.5.0
2020-06-08 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-29 1.4
2020-02-17 1.3
2019-12-20 1.2
2019-02-08 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-13 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-08-02 1.2
2026-05-03 1.1
2026-04-29 1.0
2025-12-15 0.5
2025-12-06 0.4
2025-05-23 0.3
2024-07-09 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-23 1.0.0
2026-07-07 0.8.0
2026-05-08 0.7.1
2026-04-30 0.7.0
2025-07-30 0.6.1
2025-06-19 0.6.0
2025-05-23 0.5.0
2025-03-21 0.4.6
2024-12-22 0.4.5
2023-01-06 0.4.4
2022-10-02 0.4.3
2022-09-27 0.4.2
2022-04-24 0.4.1
2022-03-21 0.4.0
2021-03-27 0.3.1
2020-11-04 0.3.0
2020-09-17 0.2.0
2020-07-13 0.1.1
2020-07-07 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-31 11.0.5.2
2024-02-01 11.0.4.1
2023-01-26 11.0.4
2022-03-09 11.0.2
2022-02-21 11.0.0
2020-02-04 10-1.2
2020-01-10 10-1.1
2019-05-26 0.9-48.1
2018-06-03 0.9-48
2018-01-22 0.9-46
2016-05-22 0.9-44
2015-04-24 0.9-43
2014-08-26 0.9-41
2014-03-29 0.9-33
Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut] ),
Tom Palmer [aut, cre] ,
Philipp Lepert [ctb]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between Statamarkdown versions 0.9.7 dated 2026-07-19 and 1.0.0 dated 2026-08-21
Statamarkdown-0.9.7/Statamarkdown/inst/doc/1_Basic_Use_of_Statamarkdown.html |only Statamarkdown-0.9.7/Statamarkdown/inst/doc/2_Linking_Stata_Code_Chunks.html |only Statamarkdown-0.9.7/Statamarkdown/inst/doc/3_Combining_Stata_and_R.html |only Statamarkdown-0.9.7/Statamarkdown/man/Statamarkdown-package.rd |only Statamarkdown-0.9.7/Statamarkdown/man/stata_engine.rd |only Statamarkdown-1.0.0/Statamarkdown/DESCRIPTION | 27 - Statamarkdown-1.0.0/Statamarkdown/MD5 | 53 ++- Statamarkdown-1.0.0/Statamarkdown/NAMESPACE | 8 Statamarkdown-1.0.0/Statamarkdown/NEWS.md | 84 ++++ Statamarkdown-1.0.0/Statamarkdown/R/Statamarkdown-package.R |only Statamarkdown-1.0.0/Statamarkdown/R/engine_output.R | 6 Statamarkdown-1.0.0/Statamarkdown/R/find_stata.r | 70 +++- Statamarkdown-1.0.0/Statamarkdown/R/misc.r | 5 Statamarkdown-1.0.0/Statamarkdown/R/purl_stata.R |only Statamarkdown-1.0.0/Statamarkdown/R/spinstata.R | 111 ++++-- Statamarkdown-1.0.0/Statamarkdown/R/stata_collectcode.r | 83 +++- Statamarkdown-1.0.0/Statamarkdown/R/stata_engine.r | 169 +++++++++- Statamarkdown-1.0.0/Statamarkdown/README.md | 7 Statamarkdown-1.0.0/Statamarkdown/build |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/basicuse.html |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/basicuse.qmd |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/linkblocks.html |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/linkblocks.qmd |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/randstata.html |only Statamarkdown-1.0.0/Statamarkdown/inst/doc/randstata.qmd |only Statamarkdown-1.0.0/Statamarkdown/man/Statamarkdown-package.Rd |only Statamarkdown-1.0.0/Statamarkdown/man/find_stata.Rd | 61 ++- Statamarkdown-1.0.0/Statamarkdown/man/purl_stata.Rd |only Statamarkdown-1.0.0/Statamarkdown/man/spinstata.Rd | 72 ++-- Statamarkdown-1.0.0/Statamarkdown/man/stata_engine.Rd |only Statamarkdown-1.0.0/Statamarkdown/tests |only Statamarkdown-1.0.0/Statamarkdown/vignettes |only 32 files changed, 594 insertions(+), 162 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2 [...truncated...]
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut],
Marc Kery [ctb]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between spOccupancy versions 0.8.0 dated 2024-12-14 and 0.8.1 dated 2026-08-21
DESCRIPTION | 12 MD5 | 174 +- NAMESPACE | 2 NEWS.md | 19 R/generics.R | 306 ++--- R/getSVCSamples.R | 6 R/intPGOcc.R | 2558 ++++++++++++++++++++++---------------------- R/postHocLM.R | 6 R/spIntPGOcc.R | 8 R/stIntPGOcc.R | 6 R/stMsPGOcc.R | 8 R/stPGOcc.R | 6 R/svcTIntPGOcc.R | 10 R/svcTMsPGOcc.R | 8 R/svcTPGBinom.R | 2 R/svcTPGOcc.R | 6 R/tIntPGOcc.R | 6 R/tMsPGOcc.R | 6 R/tPGOcc.R | 6 R/updateMCMC.R | 291 ++++- build/partial.rdb |binary man/PGOcc.Rd | 2 man/getSVCSamples.Rd | 2 man/intMsPGOcc.Rd | 2 man/intPGOcc.Rd | 2 man/lfJSDM.Rd | 2 man/lfMsPGOcc.Rd | 2 man/msPGOcc.Rd | 2 man/postHocLM.Rd | 2 man/ppcOcc.Rd | 2 man/predict.PGOcc.Rd | 2 man/predict.intMsPGOcc.Rd | 2 man/predict.intPGOcc.Rd | 2 man/predict.lfJSDM.Rd | 2 man/predict.lfMsPGOcc.Rd | 2 man/predict.msPGOcc.Rd | 2 man/predict.sfJSDM.Rd | 2 man/predict.sfMsPGOcc.Rd | 2 man/predict.spIntPGOcc.Rd | 2 man/predict.spMsPGOcc.Rd | 2 man/predict.spPGOcc.Rd | 2 man/predict.stIntPGOcc.Rd | 2 man/predict.stMsPGOcc.Rd | 2 man/predict.stPGOcc.Rd | 2 man/predict.svcMsPGOcc.Rd | 2 man/predict.svcPGBinom.Rd | 2 man/predict.svcPGOcc.Rd | 2 man/predict.svcTIntPGOcc.Rd | 2 man/predict.svcTMsPGOcc.Rd | 2 man/predict.svcTPGBinom.Rd | 2 man/predict.svcTPGOcc.Rd | 2 man/predict.tIntPGOcc.Rd | 2 man/predict.tMsPGOcc.Rd | 2 man/predict.tPGOcc.Rd | 2 man/residuals.PGOcc.Rd | 2 man/residuals.spPGOcc.Rd | 2 man/residuals.svcPGOcc.Rd | 2 man/sfJSDM.Rd | 2 man/sfMsPGOcc.Rd | 2 man/simBinom.Rd | 2 man/simIntMsOcc.Rd | 2 man/simIntOcc.Rd | 2 man/simMsOcc.Rd | 2 man/simOcc.Rd | 2 man/simTBinom.Rd | 2 man/simTIntOcc.Rd | 4 man/simTMsOcc.Rd | 2 man/simTOcc.Rd | 6 man/spIntPGOcc.Rd | 2 man/spMsPGOcc.Rd | 2 man/spPGOcc.Rd | 5 man/stIntPGOcc.Rd | 2 man/stMsPGOcc.Rd | 2 man/stPGOcc.Rd | 2 man/svcMsPGOcc.Rd | 2 man/svcPGBinom.Rd | 2 man/svcPGOcc.Rd | 2 man/svcTIntPGOcc.Rd | 2 man/svcTMsPGOcc.Rd | 2 man/svcTPGBinom.Rd | 2 man/svcTPGOcc.Rd | 2 man/tIntPGOcc.Rd | 2 man/tMsPGOcc.Rd | 2 man/tPGOcc.Rd | 2 man/updateMCMC.Rd | 4 man/waicOcc.Rd | 2 src/svcPGOccNNGP.cpp | 91 - src/svcTIntPGOccNNGP.cpp | 6 88 files changed, 1982 insertions(+), 1702 deletions(-)
Title: Calculate vs-SOVs and SOVs for Assemblies with D-Dimensional
Voting
Description: Calculates vote-specific and traditional Shapley-Owen power indices (vs-SOVs and SOVs) for spatial voting games in one to four dimensions. Evaluates voter influence through an a posteriori analysis of relative preferences. Supports weighted voting and various voting thresholds. Compatible with ideal point estimates from NOMINATE, Optimal Classification, and 'MCMCpack'. The method builds on Bibina and Dougherty (2025) <doi:10.2139/ssrn.6324519>.
Author: Keith Dougherty [aut],
Emma Bibina [aut, cre]
Maintainer: Emma Bibina <emma.bibina@uga.edu>
Diff between sov versions 1.0.3 dated 2026-04-04 and 2.0.0 dated 2026-08-21
DESCRIPTION | 6 LICENSE | 2 MD5 | 26 ++- NAMESPACE | 1 NEWS.md | 4 R/plot_sov_geometry.R | 185 ++++++++++++++++++++++++++-- R/utils.R | 8 - R/vs_sov.R | 2 README.md | 21 +-- man/plot_sov_geometry.Rd |only tests/testthat/test_2d_cases.R | 24 +-- tests/testthat/test_estimate_constructors.R | 4 tests/testthat/test_plot_sov_geometry.R |only tests/testthat/test_validation.R | 8 - tests/testthat/test_vs_sov_user.R | 6 15 files changed, 239 insertions(+), 58 deletions(-)
Title: Stochastic Multi-Criteria Acceptability Analysis
Description: Implementation of the Stochastic Multi-Criteria Acceptability Analysis (SMAA) family of Multiple Criteria Decision Analysis (MCDA) methods. Tervonen, T. and Figueira, J. R. (2008) <doi:10.1002/mcda.407>.
Author: Gert van Valkenhoef [aut, cre, cph]
Maintainer: Gert van Valkenhoef <gert@gertvv.nl>
Diff between smaa versions 0.3-3 dated 2024-09-06 and 0.3-4 dated 2026-08-21
smaa-0.3-3/smaa/inst/extdata/thrombo-meas.txt.gz |only smaa-0.3-3/smaa/inst/extdata/thrombo-ranks-nopref.txt.gz |only smaa-0.3-3/smaa/inst/extdata/thrombo-values-nopref.txt.gz |only smaa-0.3-3/smaa/inst/extdata/thrombo-weights-nopref.txt.gz |only smaa-0.3-4/smaa/DESCRIPTION | 10 +- smaa-0.3-4/smaa/MD5 | 32 ++++---- smaa-0.3-4/smaa/build/partial.rdb |binary smaa-0.3-4/smaa/inst/extdata/thrombo-meas.rds |only smaa-0.3-4/smaa/inst/extdata/thrombo-ranks-nopref.rds |only smaa-0.3-4/smaa/inst/extdata/thrombo-values-nopref.rds |only smaa-0.3-4/smaa/inst/extdata/thrombo-weights-nopref.rds |only smaa-0.3-4/smaa/man/smaa-package.Rd | 4 - smaa-0.3-4/smaa/man/smaa.Rd | 4 - smaa-0.3-4/smaa/man/smaa.cf.Rd | 4 - smaa-0.3-4/smaa/man/smaa.cw.Rd | 4 - smaa-0.3-4/smaa/man/smaa.entropy.Rd | 4 - smaa-0.3-4/smaa/man/smaa.pwi.Rd | 4 - smaa-0.3-4/smaa/man/smaa.ra.Rd | 4 - smaa-0.3-4/smaa/man/smaa.ranks.Rd | 6 - smaa-0.3-4/smaa/man/smaa.values.Rd | 6 - smaa-0.3-4/smaa/tests/Examples/smaa-Ex.Rout.save | 48 ++++++------- 21 files changed, 66 insertions(+), 64 deletions(-)
Title: Simplex Regression Models with Parametric or Fixed Mean Link
Functions
Description: Fits and analyzes simplex regression models with either
fixed or parametric mean link functions. Implements the simplex
probability density function, cumulative distribution function,
quantile function, random number generation, and variance evaluation.
Offers several fixed and parametric link functions for the mean
submodel, tools for residual analysis and diagnostic plotting,
hypothesis testing procedures, and influence measures such as Cook's
distance and leverage (hat values). Includes the Scout Score (SS)
criterion for model selection, enabling comprehensive inference and
diagnostic analysis within the simplex regression framework.
For more details see Barndorff-Nielsen and Jorgensen (1991)
<doi:10.1016/0047-259X(91)90008-P> and Justino and Cribari-Neto (2026)
<doi:10.1016/j.apm.2025.116713>.
Author: Maria Eduarda da Cruz Justino [aut, cre] ,
Francisco Cribari-Neto [ctb, ths]
Maintainer: Maria Eduarda da Cruz Justino <eueduardacruz@gmail.com>
Diff between SimplexRegression versions 0.1.5 dated 2026-07-19 and 0.1.6 dated 2026-08-21
SimplexRegression-0.1.5/SimplexRegression/man/penalized.ic.Rd |only SimplexRegression-0.1.5/SimplexRegression/man/penalized.ss.Rd |only SimplexRegression-0.1.6/SimplexRegression/DESCRIPTION | 6 SimplexRegression-0.1.6/SimplexRegression/MD5 | 41 +- SimplexRegression-0.1.6/SimplexRegression/NAMESPACE | 21 - SimplexRegression-0.1.6/SimplexRegression/NEWS.md | 18 + SimplexRegression-0.1.6/SimplexRegression/R/simplexreg_fit.R | 2 SimplexRegression-0.1.6/SimplexRegression/R/simplexreg_ic.R |only SimplexRegression-0.1.6/SimplexRegression/R/simplexreg_methods.R | 141 ---------- SimplexRegression-0.1.6/SimplexRegression/R/simplexreg_penalized_ic.R | 26 - SimplexRegression-0.1.6/SimplexRegression/R/simplexreg_sscriteria.R | 10 SimplexRegression-0.1.6/SimplexRegression/inst/WORDLIST | 10 SimplexRegression-0.1.6/SimplexRegression/inst/doc/relative-humidity.R | 11 SimplexRegression-0.1.6/SimplexRegression/inst/doc/relative-humidity.Rmd | 26 - SimplexRegression-0.1.6/SimplexRegression/inst/doc/relative-humidity.html | 72 ++--- SimplexRegression-0.1.6/SimplexRegression/man/ic.Rd |only SimplexRegression-0.1.6/SimplexRegression/man/ic.penalized.Rd |only SimplexRegression-0.1.6/SimplexRegression/man/simplexreg.fit.Rd | 2 SimplexRegression-0.1.6/SimplexRegression/man/simplexreg.methods.Rd | 47 --- SimplexRegression-0.1.6/SimplexRegression/man/ss.penalized.Rd |only SimplexRegression-0.1.6/SimplexRegression/tests/testthat/test-simplexreg_ic.R |only SimplexRegression-0.1.6/SimplexRegression/tests/testthat/test-simplexreg_methods.R | 100 ------- SimplexRegression-0.1.6/SimplexRegression/tests/testthat/test-simplexreg_penalized_ic.R | 54 +-- SimplexRegression-0.1.6/SimplexRegression/tests/testthat/test-simplexreg_sscriteria.R | 50 +-- SimplexRegression-0.1.6/SimplexRegression/vignettes/relative-humidity.Rmd | 26 - 25 files changed, 202 insertions(+), 461 deletions(-)
More information about SimplexRegression at CRAN
Permanent link
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted
(glass_intensity_slider()), and options for accent color, blur,
corner radius, and motion or tint behavior.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.1.1 dated 2026-08-02 and 0.2.0 dated 2026-08-21
shinyglass-0.1.1/shinyglass/man/figures |only shinyglass-0.2.0/shinyglass/DESCRIPTION | 34 shinyglass-0.2.0/shinyglass/MD5 | 54 shinyglass-0.2.0/shinyglass/NAMESPACE | 8 shinyglass-0.2.0/shinyglass/NEWS.md | 138 shinyglass-0.2.0/shinyglass/R/glass-intensity.R |only shinyglass-0.2.0/shinyglass/R/glass-theme.R | 584 ++ shinyglass-0.2.0/shinyglass/R/shinyglass-package.R | 25 shinyglass-0.2.0/shinyglass/README.md | 116 shinyglass-0.2.0/shinyglass/build |only shinyglass-0.2.0/shinyglass/inst/WORDLIST | 66 shinyglass-0.2.0/shinyglass/inst/doc |only shinyglass-0.2.0/shinyglass/inst/examples/apple-glass-reference.R | 26 shinyglass-0.2.0/shinyglass/inst/examples/bslib-dashboard.R | 115 shinyglass-0.2.0/shinyglass/inst/examples/chrome-kitchen-sink.R |only shinyglass-0.2.0/shinyglass/inst/examples/demo-app.R | 46 shinyglass-0.2.0/shinyglass/inst/examples/inputs-gallery.R | 199 shinyglass-0.2.0/shinyglass/inst/examples/intensity-slider-demo.R |only shinyglass-0.2.0/shinyglass/inst/examples/plotly-gt-demo.R |only shinyglass-0.2.0/shinyglass/inst/js/shiny-glass.js | 1063 ++++ shinyglass-0.2.0/shinyglass/inst/scss/glass.scss | 2399 +++++++++- shinyglass-0.2.0/shinyglass/man/glass_intensity_slider.Rd |only shinyglass-0.2.0/shinyglass/man/glass_preset_input.Rd |only shinyglass-0.2.0/shinyglass/man/glass_resolved_preset.Rd |only shinyglass-0.2.0/shinyglass/man/glass_theme.Rd | 56 shinyglass-0.2.0/shinyglass/man/glass_theme_toggle.Rd |only shinyglass-0.2.0/shinyglass/man/observe_glass_intensity.Rd |only shinyglass-0.2.0/shinyglass/man/observe_glass_preset_input.Rd |only shinyglass-0.2.0/shinyglass/man/observe_glass_theme_toggle.Rd |only shinyglass-0.2.0/shinyglass/man/shinyglass-package.Rd | 29 shinyglass-0.2.0/shinyglass/man/update_glass_theme.Rd |only shinyglass-0.2.0/shinyglass/tests/testthat/test-glass-theme.R | 408 + shinyglass-0.2.0/shinyglass/vignettes |only 33 files changed, 4923 insertions(+), 443 deletions(-)
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-test, Wilcoxon-test, ANOVA models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <mirzaghaderi@gmail.com>
Diff between rtpcr versions 2.1.8 dated 2026-05-21 and 2.1.9 dated 2026-08-21
rtpcr-2.1.8/rtpcr/man/figures/shiny_rtpcr.png |only rtpcr-2.1.8/rtpcr/vignettes/--find-assets.html |only rtpcr-2.1.9/rtpcr/DESCRIPTION | 9 rtpcr-2.1.9/rtpcr/MD5 | 31 rtpcr-2.1.9/rtpcr/NEWS.md | 5 rtpcr-2.1.9/rtpcr/R/ANOVA_DCt.R | 12 rtpcr-2.1.9/rtpcr/R/ANOVA_DDCt.R | 52 rtpcr-2.1.9/rtpcr/R/globalVariables.R | 3 rtpcr-2.1.9/rtpcr/inst/doc/Method.Rmd | 8 rtpcr-2.1.9/rtpcr/inst/doc/Method.html | 5 rtpcr-2.1.9/rtpcr/inst/doc/manual.R | 16 rtpcr-2.1.9/rtpcr/inst/doc/manual.Rmd | 70 - rtpcr-2.1.9/rtpcr/inst/doc/manual.html | 667 +++++----- rtpcr-2.1.9/rtpcr/inst/shinyapp/app.R | 285 +++- rtpcr-2.1.9/rtpcr/inst/shinyapp/rsconnect/shinyapps.io/mirzaghaderi/rtpcr.dcf | 4 rtpcr-2.1.9/rtpcr/inst/shinyapp/www/qPCR_Plot.jpg |only rtpcr-2.1.9/rtpcr/vignettes/Method.Rmd | 8 rtpcr-2.1.9/rtpcr/vignettes/manual.Rmd | 70 - 18 files changed, 698 insertions(+), 547 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between RTMBdist versions 1.0.5 dated 2026-07-22 and 1.0.6 dated 2026-08-21
DESCRIPTION | 8 +++--- MD5 | 31 +++++++++++++---------- NAMESPACE | 7 +++++ NEWS.md | 2 + R/aaa_utils.R | 36 +++++++++++++-------------- R/combinom.R |only R/exgauss.R | 2 - R/laplace_check.R |only README.md | 5 +++ inst/doc/Examples.R | 21 +++------------ inst/doc/Examples.Rmd | 24 ++++-------------- inst/doc/Examples.html | 54 ++++++++++++++++------------------------- inst/doc/distlist.Rmd | 4 +++ inst/doc/distlist.html | 7 +++++ man/combinom.Rd |only man/laplace_check.Rd |only tests/testthat/test-combinom.R |only vignettes/Examples.Rmd | 24 ++++-------------- vignettes/distlist.Rmd | 4 +++ 19 files changed, 109 insertions(+), 120 deletions(-)
Title: A Comprehensive Interface for Accessing the Protein Data Bank
Description: Provides an R interface to the 'RCSB' Protein Data Bank ('PDB') Search
and Data APIs (<https://www.rcsb.org/>). Supports full-text, attribute,
sequence, motif, structure, and chemical searches; retrieval of entry-,
assembly-, polymer-entity-, and chemical-component-level metadata; and
conversion of API responses into analysis-ready tables and typed R objects for
reproducible structural bioinformatics workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between rPDBapi versions 3.0.1 dated 2026-03-07 and 3.0.2 dated 2026-08-21
DESCRIPTION | 6 MD5 | 46 NEWS.md | 13 R/data_fetcher.R | 3 R/find_papers.R | 2 R/find_results.R | 3 R/get_fasta_from_rcsb_entry.R | 3 R/get_info.R | 2 R/get_pdb_file.R | 2 R/perform_search.R | 3 R/query_search.R | 2 build/vignette.rds |binary inst/doc/rPDBapi-structural-bioinformatics.R | 1251 +++---- inst/doc/rPDBapi-structural-bioinformatics.Rmd | 125 inst/doc/rPDBapi-structural-bioinformatics.html | 3952 ------------------------ man/data_fetcher.Rd | 2 man/find_papers.Rd | 2 man/find_results.Rd | 2 man/get_fasta_from_rcsb_entry.Rd | 2 man/get_info.Rd | 2 man/get_pdb_file.Rd | 2 man/perform_search.Rd | 2 man/query_search.Rd | 2 vignettes/rPDBapi-structural-bioinformatics.Rmd | 125 24 files changed, 927 insertions(+), 4627 deletions(-)
Title: Robust Effect Size Index (RESI) Estimation
Description: Summarize model output using a robust effect size index. The index is introduced in Vandekar, Tao, & Blume (2020, <doi:10.1007/s11336-020-09698-2>). Software paper available at <doi:10.18637/jss.v112.i03>.
Author: Megan Jones [aut],
Kaidi Kang [aut],
Simon Vandekar [aut, cre],
Gina Yu [ctb],
Xinyu Zhang [ctb]
Maintainer: Simon Vandekar <simon.vandekar@vumc.org>
Diff between RESI versions 1.4.2 dated 2026-07-24 and 1.5.1 dated 2026-08-21
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 13 + R/resi_asymptotic.R | 255 ++++++++++++++++++++++++++++++---- R/simulations.R | 55 ++++--- tests/testthat/test-resi.R | 10 - tests/testthat/test-resi_asymptotic.R | 174 +++++++++++++++++++++++ 7 files changed, 462 insertions(+), 63 deletions(-)
Title: Adds Subtotals to Data Reports
Description: Adds subtotal rows / sections (a la the 'SAS' 'Proc Tabulate' All option) to a Group By output by running a series of Group By functions with partial sets of the same variables and combining the results with the original. Can be used to add comprehensive information to a data report or to quickly aggregate Group By outputs used to gain a greater understanding of data.
Author: Yoni Aboody [aut, cre, cph]
Maintainer: Yoni Aboody <yoniaboody@gmail.com>
Diff between ReportSubtotal versions 0.1.2 dated 2024-12-02 and 0.2.1 dated 2026-08-21
DESCRIPTION | 12 +-- MD5 | 34 +++++--- NAMESPACE | 40 ++++++---- NEWS.md | 9 ++ R/ReportSubtotal-package.R | 54 +++++++------ R/subtotal_dupe_removal.R | 55 +++++++------- R/subtotal_row.R | 164 +++++++++++++----------------------------- R/subtotal_section.R | 140 +++++++++++++---------------------- R/utils.R |only README.md |only man/ReportSubtotal-package.Rd | 5 + man/subtotal_dupe_removal.Rd | 26 +++--- man/subtotal_row.Rd | 35 ++++---- man/subtotal_section.Rd | 38 +++++---- tests |only 15 files changed, 287 insertions(+), 325 deletions(-)
More information about ReportSubtotal at CRAN
Permanent link
Title: Relational Data Modeler
Description: The aim of this package is to manipulate relational
data models in R.
It provides functions to create, modify and export data models
in json format.
It also allows importing models created
with 'MySQL Workbench' (<https://www.mysql.com/products/workbench/>).
These functions are accessible through a graphical user
interface made with 'shiny'.
Constraints such as types, keys, uniqueness and mandatory fields are
automatically checked and corrected when editing a model.
Finally, real data can be confronted to a model to check their compatibility.
Author: Patrice Godard [aut, cre, cph],
Kai Lin [ctb]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between ReDaMoR versions 1.0.0 dated 2026-05-19 and 1.0.1 dated 2026-08-21
DESCRIPTION | 8 ++--- MD5 | 22 ++++++++-------- NAMESPACE | 62 +++++++++++++++++++++++++++------------------- R/RelDataModel.R | 2 - R/RelTableModel.R | 2 - R/model_relational_data.R | 14 +++++----- build/vignette.rds |binary inst/doc/ReDaMoR.R | 41 +++++++++++++++++------------- inst/doc/ReDaMoR.Rmd | 41 +++++++++++++++++------------- inst/doc/ReDaMoR.html | 53 ++++++++++++++++++++------------------- inst/pkgdown.yml | 6 ++-- vignettes/ReDaMoR.Rmd | 41 +++++++++++++++++------------- 12 files changed, 161 insertions(+), 131 deletions(-)
Title: Access your Coletum's Data from API
Description: Get your data (forms, structures, answers) from Coletum
<https://coletum.com> to handle and analyse.
Author: Andre Smaniotto [aut, cre],
Marcelo Magnani [aut],
Rodrigo Sant'Ana [aut],
GeoSapiens [cph, fnd]
Maintainer: Andre Smaniotto <smaniotto@geosapiens.com.br>
Diff between RColetum versions 1.0.0 dated 2026-04-16 and 1.1.0 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 8 ++++++++ R/GetAnswers.R | 5 ++++- R/GetForm.R | 3 ++- R/GetForms.R | 4 ++-- R/utils.R | 2 +- man/GetAnswers.Rd | 2 +- man/GetForm.Rd | 3 ++- man/GetForms.Rd | 4 ++-- man/RColetum-package.Rd | 1 + tests/testthat/test-FlattenAnswers.R | 5 +++++ tests/testthat/test-GetAnswers.R | 6 ++++++ tests/testthat/test-GetAnswersComplexForm.R | 2 ++ tests/testthat/test-GetForms.R | 2 ++ 15 files changed, 56 insertions(+), 27 deletions(-)
Title: Bayesian Geostatistical Modeling with RAMPS
Description: Bayesian geostatistical modeling of Gaussian processes using a
reparameterized and marginalized posterior sampling (RAMPS) algorithm
designed to lower autocorrelation in MCMC samples. Package performance is
tuned for large spatial datasets.
Author: Brian J Smith [aut, cre],
Jun Yan [aut],
Mary Kathryn Cowles [aut]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between ramps versions 0.6.18 dated 2023-03-13 and 0.6.19 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/DIC.R | 2 +- R/engine.R | 2 +- R/georamps.R | 4 ++-- R/predict.R | 4 ++-- R/utils.R | 2 +- data/NURE.R | 4 ++-- data/simJSS.R | 6 +++--- 9 files changed, 24 insertions(+), 24 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.3.3 dated 2026-07-16 and 1.3.4 dated 2026-08-21
qol-1.3.3/qol/man/get_integer_length.Rd |only qol-1.3.4/qol/DESCRIPTION | 12 qol-1.3.4/qol/MD5 | 117 qol-1.3.4/qol/NAMESPACE | 7 qol-1.3.4/qol/NEWS.md | 92 qol-1.3.4/qol/R/any_table.R | 655 +++- qol-1.3.4/qol/R/apply_format.R | 23 qol-1.3.4/qol/R/build_master.R | 904 ++++- qol-1.3.4/qol/R/compute.R | 6 qol-1.3.4/qol/R/conversion.R | 6 qol-1.3.4/qol/R/crosstabs.R | 219 + qol-1.3.4/qol/R/dummy_data.R | 3 qol-1.3.4/qol/R/excel_helpers.R | 1291 +++++--- qol-1.3.4/qol/R/export_with_style.R | 62 qol-1.3.4/qol/R/frequencies.R | 314 + qol-1.3.4/qol/R/globals.R | 192 - qol-1.3.4/qol/R/html_helpers.R |only qol-1.3.4/qol/R/if_else.R | 3478 +++++++++++----------- qol-1.3.4/qol/R/import_export.R | 66 qol-1.3.4/qol/R/loading.R | 309 + qol-1.3.4/qol/R/multi_join.R | 46 qol-1.3.4/qol/R/options.R | 37 qol-1.3.4/qol/R/qol.R | 5 qol-1.3.4/qol/R/recode.R | 253 - qol-1.3.4/qol/R/renaming.R | 32 qol-1.3.4/qol/R/retain.R | 32 qol-1.3.4/qol/R/small_helpers.R | 90 qol-1.3.4/qol/R/split_by.R | 2 qol-1.3.4/qol/R/strings.R | 2 qol-1.3.4/qol/R/summarise_plus.R | 53 qol-1.3.4/qol/R/transpose_plus.R | 4 qol-1.3.4/qol/README.md | 4 qol-1.3.4/qol/inst/extdata/qol_table.min.css.txt |only qol-1.3.4/qol/inst/extdata/qol_table.min.js.txt |only qol-1.3.4/qol/inst/tinytest/test-any_table.R | 707 ++++ qol-1.3.4/qol/inst/tinytest/test-crosstabs.R | 84 qol-1.3.4/qol/inst/tinytest/test-frequencies.R | 17 qol-1.3.4/qol/inst/tinytest/test-if_else.R | 1261 ++++--- qol-1.3.4/qol/inst/tinytest/test-import_export.R | 22 qol-1.3.4/qol/inst/tinytest/test-loading.R | 123 qol-1.3.4/qol/inst/tinytest/test-multi_join.R | 18 qol-1.3.4/qol/inst/tinytest/test-options.R | 9 qol-1.3.4/qol/inst/tinytest/test-recode.R | 48 qol-1.3.4/qol/inst/tinytest/test-renaming.R | 14 qol-1.3.4/qol/inst/tinytest/test-retain.R | 4 qol-1.3.4/qol/inst/tinytest/test-small_helpers.R | 32 qol-1.3.4/qol/inst/tinytest/test-summarise_plus.R | 55 qol-1.3.4/qol/inst/tinytest/test-transpose_plus.R | 18 qol-1.3.4/qol/man/any_table.Rd | 56 qol-1.3.4/qol/man/build_master.Rd | 47 qol-1.3.4/qol/man/check_required_package.Rd |only qol-1.3.4/qol/man/combine_into_workbook.Rd | 96 qol-1.3.4/qol/man/create_table_of_contents.Rd |only qol-1.3.4/qol/man/crosstabs.Rd | 40 qol-1.3.4/qol/man/excel_output_style.Rd | 54 qol-1.3.4/qol/man/export_with_style.Rd | 27 qol-1.3.4/qol/man/frequencies.Rd | 40 qol-1.3.4/qol/man/import_export.Rd | 10 qol-1.3.4/qol/man/qol-package.Rd | 6 qol-1.3.4/qol/man/qol_options.Rd | 2 qol-1.3.4/qol/man/recode.Rd | 24 qol-1.3.4/qol/man/run_scripts.Rd |only qol-1.3.4/qol/man/save_load.Rd | 44 63 files changed, 7410 insertions(+), 3764 deletions(-)
Title: PubMed Pairwise Co-Occurrence Matrix Construction and
Visualization
Description: Queries the 'NCBI' (National Center for Biotechnology Information)
Entrez 'E-utilities' API to count pairwise co-occurrences between two sets
of terms in 'PubMed' or 'PubMed Central'. It returns a matrix-like data
frame of publication counts and can export hyperlink-enabled results in
CSV or ODS format. The package also provides heatmap helpers for
exploratory visualization of overlap patterns. Based on the method described
in Becker et al. (2003) "PubMatrix: a tool for multiplex literature mining"
<doi:10.1186/1471-2105-4-61>.
Author: Tyler Laird [aut],
Enrique Toledo [aut, cre]
Maintainer: Enrique Toledo <enriquetoledo@gmail.com>
Diff between PubMatrixR versions 1.0.0 dated 2026-03-12 and 1.0.1 dated 2026-08-21
DESCRIPTION | 16 +-- MD5 | 41 ++++--- NAMESPACE | 24 ++-- NEWS.md | 26 ++++ R/PubMatrix.R | 139 +++++++++++++++++++++----- R/heatmap_functions.R | 143 ++++++++++++++++++--------- README.md | 41 ++++--- build/vignette.rds |binary inst/WORDLIST | 23 ++++ inst/doc/WntExample.R |only inst/doc/WntExample.Rmd |only inst/doc/WntExample.html |only inst/doc/vignette.R | 15 +- inst/doc/vignette.Rmd | 18 ++- inst/doc/vignette.html | 104 +++++++++---------- man/PubMatrix.Rd | 17 +++ man/PubMatrixR-package.Rd | 2 man/plot_pubmatrix_heatmap.Rd | 42 ++++++-- man/pubmatrix_heatmap.Rd | 9 + tests/testthat/setup.R |only tests/testthat/test-heatmap.R | 130 ++++++++++++++++++++++++ tests/testthat/test-pubmatrix.R | 209 +++++++++++++++++++++++++++++++++++++--- vignettes/WntExample.Rmd |only vignettes/vignette.Rmd | 18 ++- 24 files changed, 788 insertions(+), 229 deletions(-)
Title: PS-Integrated Methods for Incorporating Real-World Evidence in
Clinical Studies
Description: High-quality real-world data can be transformed into scientific
real-world evidence for regulatory and healthcare decision-making
using proven analytical methods and techniques. For example, propensity
score (PS) methodology can be applied to select a subset of real-world
data containing patients that are similar to those in the current clinical
study in terms of baseline covariates, and to stratify the selected
patients together with those in the current study into more homogeneous
strata. Then, statistical methods such as the power prior approach or
composite likelihood approach can be applied in each stratum to draw
inference for the parameters of interest. This package provides
functions that implement the PS-integrated real-world
evidence analysis methods such as
Wang et al. (2019) <doi:10.1080/10543406.2019.1657133>,
Wang et al. (2020) <doi:10.1080/10543406.2019.1684309>, and
Chen et al. (2020) <doi:10.1080/10543406.2020.1730877>.
Author: Chenguang Wang [aut],
Trustees of Columbia University [cph] ,
Wei-Chen Chen [aut, cre]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between psrwe versions 3.2-1 dated 2026-02-18 and 3.2-2 dated 2026-08-21
DESCRIPTION | 8 +- MD5 | 35 ++++++------ NAMESPACE | 114 ++++++++++++++++++++++------------------- NEWS.md | 7 ++ R/psrwe_powerprior.R | 18 +++++- R/psrwe_powerprior_watt.R | 26 ++++++--- R/stanmodels.R | 4 - build/partial.rdb |binary demo/00Index | 2 demo/sec_7_1_ex.r |only demo/sec_7_2_ex.r |only inst/stan/powerp.stan | 8 ++ inst/stan/powerps.stan | 7 ++ inst/stan/powerps_wattcon.stan | 7 ++ inst/stan/powerpsbinary.stan | 7 ++ man/psrwe-package.Rd | 1 man/psrwe_powerp.Rd | 4 + man/psrwe_powerp_watt.Rd | 4 + man/rwe_stan.Rd | 1 src/RcppExports.cpp |only 20 files changed, 163 insertions(+), 90 deletions(-)
Title: Quantifying Animal Movement and Space-Use Patterns with
Statistical Physics
Description: Provides tools to analyse animal movement and space-use patterns from
telemetry data using methods derived from statistical physics. Methods
span displacement-based approaches, distribution fitting, space-use
metrics (including the influence of correlations on space-use), network-based
community detection, and measures of entropy and predictability.
The package enables characterisation of these patterns across spatial
and temporal scales, including variation within and among individuals
(inter- and intraspecific analyses). Outputs include interpretable
metrics and visualisations to support ecological analysis and the
investigation of fundamental movement processes. For applications of
these methods in ecological studies see Rodríguez et al. (2017)
<doi:10.1038/s41598-017-00165-0> and Sequeira et al. (2018)
<doi:10.1073/pnas.1716137115>.
Author: Hannah J. Calich [aut, cre, cph] ,
Jorge Rodriguez [aut] ,
Victor Eguiluz [aut] ,
Ana M. M. Sequeira [aut]
Maintainer: Hannah J. Calich <hannah.calich@gmail.com>
Diff between PhysMove versions 1.2.4 dated 2026-08-04 and 1.2.5 dated 2026-08-21
DESCRIPTION | 8 ++-- MD5 | 50 +++++++++++++++--------------- NEWS.md | 11 +++++- R/infomapCommunities.R | 2 - R/plotDispPDF.R | 8 ++-- R/randomise.R | 8 ++-- R/turningAngles.R | 2 - README.md | 13 +++---- inst/WORDLIST | 4 +- inst/doc/pt1_introduction.R | 7 ++-- inst/doc/pt1_introduction.Rmd | 13 ++++--- inst/doc/pt1_introduction.html | 24 ++++++++------ inst/doc/pt2_movement_patterns.R | 4 +- inst/doc/pt2_movement_patterns.Rmd | 16 ++++----- inst/doc/pt2_movement_patterns.html | 22 ++++++------- inst/doc/pt3_space_use_patterns.Rmd | 2 - inst/doc/pt3_space_use_patterns.html | 4 +- inst/doc/pt4_intraspecific_movements.Rmd | 2 - inst/doc/pt4_intraspecific_movements.html | 4 +- man/plotDispPDF.Rd | 4 +- man/randomise.Rd | 6 +-- man/turningAngles.Rd | 2 - vignettes/pt1_introduction.Rmd | 13 ++++--- vignettes/pt2_movement_patterns.Rmd | 16 ++++----- vignettes/pt3_space_use_patterns.Rmd | 2 - vignettes/pt4_intraspecific_movements.Rmd | 2 - 26 files changed, 131 insertions(+), 118 deletions(-)
Title: Parallel Factor Analysis Modelling of Longitudinal Microbiome
Data
Description: Creation and selection of PARAllel FACtor Analysis (PARAFAC)
models of longitudinal microbiome data. You can import your own data with
our import functions or use one of the example datasets to create your own
PARAFAC models. Selection of the optimal number of components can be done
using assessModelQuality() and assessModelStability(). The selected model can
then be plotted using plotPARAFACmodel(). The Parallel Factor
Analysis method was originally described by Caroll and Chang (1970)
<doi:10.1007/BF02310791> and Harshman (1970)
<https://www.psychology.uwo.ca/faculty/harshman/wpppfac0.pdf>.
Author: Geert Roelof van der Ploeg [aut, cre] ,
Johan Westerhuis [ctb] ,
Anna Heintz-Buschart [ctb] ,
Age Smilde [ctb] ,
University of Amsterdam [cph, fnd]
Maintainer: Geert Roelof van der Ploeg <roel@simula.no>
Diff between parafac4microbiome versions 1.3.2 dated 2025-07-31 and 1.3.3 dated 2026-08-21
DESCRIPTION | 12 MD5 | 62 ++-- NEWS.md | 5 R/multiwayCLR.R | 46 +-- R/multiwayCenter.R | 42 +-- R/multiwayScale.R | 44 +-- R/parafac4microbiome-package.R | 14 - R/plotModelMetric.R | 104 ++++---- R/plotModelStability.R | 236 +++++++++---------- R/plotModelTCCs.R | 112 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Fujita2023.html | 17 - inst/doc/Introduction.html | 7 inst/doc/Shao2019.html | 19 - inst/doc/vanderPloeg2024.html | 11 man/corcondia.Rd | 48 +-- man/figures/lifecycle-deprecated.svg | 42 +-- man/figures/lifecycle-experimental.svg | 42 +-- man/figures/lifecycle-stable.svg | 58 ++-- man/figures/lifecycle-superseded.svg | 42 +-- man/importTreeSummarizedExperiment.Rd | 104 ++++---- man/parafac_core_als.Rd | 66 ++--- man/plotModelStability.Rd | 108 ++++---- man/plotModelTCCs.Rd | 44 +-- tests/testthat/test-importTreeSummarizedExperiment.R | 208 ++++++++-------- tests/testthat/test-initializePARAFAC.R | 172 ++++++------- tests/testthat/test-multiwayCLR.R | 30 +- tests/testthat/test-multiwayScale.R | 48 +-- tests/testthat/test-plotModelMetric.R | 8 tests/testthat/test-plotModelStability.R | 10 tests/testthat/test-plotModelTCCs.R | 22 - 32 files changed, 896 insertions(+), 887 deletions(-)
More information about parafac4microbiome at CRAN
Permanent link
Title: Helper Functions for Org Files
Description: Helper functions for Org files (<https://orgmode.org/>):
a generic function 'toOrg' for transforming R objects into Org
markup (most useful for data frames; there are also methods for
Dates/POSIXt) and a function to read Org tables into data frames.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between orgutils versions 0.5-3 dated 2025-12-22 and 0.5-4 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS | 6 ++++++ R/toOrg.R | 4 ++-- build/vignette.rds |binary inst/doc/orgutils_examples.R | 18 +++++++++--------- inst/doc/orgutils_examples.Rnw | 11 +++++++---- inst/doc/orgutils_examples.pdf |binary inst/tinytest/orgtable4.org | 2 ++ inst/tinytest/orgtable4b.org |only inst/tinytest/test_readOrg.R | 30 ++++++++++++++++++++++++++++++ vignettes/orgutils_examples.Rnw | 11 +++++++---- 12 files changed, 78 insertions(+), 33 deletions(-)
Title: Automated Analysis of Phenotypic Data
Description: Provides functions to analyze and visualize meristic, mensural, and categorical
phenotypic data in a comparative framework. The package implements an
automated pipeline that summarizes traits, identifies diagnostic variables
among groups, performs multivariate and univariate statistical analyses, and
produces publication-ready graphics. Earlier implementation are
described in Torres (2025) <doi:10.64898/2025.12.18.695244> (v1.0.0)
and Torres (2026) <doi:10.1002/ece3.73111> (v2.0.0).
Author: Javier Torres [aut, cre]
Maintainer: Javier Torres <metalofis@gmail.com>
Diff between Orangutan versions 2.1.0 dated 2026-03-31 and 2.2.0 dated 2026-08-21
DESCRIPTION | 8 - MD5 | 14 - NAMESPACE | 2 R/Orangutan.R | 360 ++++++++++++++++++++++++++++++++++++++++++++++++--- R/html_report.R | 105 ++++++++++++-- R/imports.R | 4 README.md | 53 +++++-- man/run_orangutan.Rd | 16 +- 8 files changed, 494 insertions(+), 68 deletions(-)
Title: N-Way Partial Least Squares Modelling of Multi-Way Data
Description: Creation and selection of N-way Partial Least Squares (NPLS) models. Selection of the optimal number of components can be done using ncrossreg(). NPLS was originally described by Rasmus Bro, see <doi:10.1002/%28SICI%291099-128X%28199601%2910%3A1%3C47%3A%3AAID-CEM400%3E3.0.CO%3B2-C>.
Author: Geert Roelof van der Ploeg [aut, cre] ,
Johan Westerhuis [ctb] ,
Anna Heintz-Buschart [ctb] ,
Age Smilde [ctb] ,
University of Amsterdam [cph, fnd]
Maintainer: Geert Roelof van der Ploeg <roel@simula.no>
Diff between NPLStoolbox versions 1.1.0 dated 2025-07-31 and 1.1.1 dated 2026-08-21
DESCRIPTION | 13 ++++---- MD5 | 10 +++--- NEWS.md | 5 +++ R/data.R | 66 ++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/Introduction.html | 5 ++- 6 files changed, 53 insertions(+), 46 deletions(-)
Title: Derivation of Regression-Based Normative Data
Description: Normative data are often used to estimate the relative position of a raw test score in the population. This package allows for deriving regression-based normative data. It includes functions that enable the fitting of regression models for the mean and residual (or variance) structures, test the model assumptions, derive the normative data in the form of normative tables or automatic scoring sheets, and estimate confidence intervals for the norms. This package accompanies the book Van der Elst, W. (2024). Regression-based normative data for psychological assessment. A hands-on approach using R. Springer Nature.
Author: Wim Van der Elst [aut, cre]
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between NormData versions 1.1 dated 2024-04-12 and 1.2 dated 2026-08-21
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/Bootstrap.Stage.2.NormScore.R | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Tools for Creating Publication-Ready Regression Tables
Description: Simplifies regression modeling in R by integrating multiple modeling and summarization
tools into a cohesive, user-friendly interface. Designed to be accessible for researchers,
particularly those in Low- and Middle-Income Countries (LMIC). Built upon widely accepted
statistical methods, including logistic regression (Hosmer et al. 2013, ISBN:9781118548429),
log-binomial regression (Spiegelman and Hertzmark 2005 <doi:10.1093/aje/kwi188>),
Firth penalized logistic regression (Firth 1993 <doi:10.1093/biomet/80.1.27>),
Poisson and robust Poisson regression (Zou 2004 <doi:10.1093/aje/kwh090>),
negative binomial regression (Hilbe 2011, ISBN:9780521179515), Cox proportional
hazards regression, parametric survival regression, causal mediation analysis,
and linear regression
(Kutner et al. 2005, ISBN:9780071122214). Leverages multiple dependencies to ensure
high-quality output and generate reproducible, publication-ready tables in alignment with
best practices in epidemiology [...truncated...]
Author: Rubeshkumar Polani [aut, cre] ,
Salin K Eliyas [aut] ,
Manikandanesan Sakthivel [aut] ,
Mogan Kaviprawin [aut] ,
Yuvaraj Krishnamoorthy [aut] ,
Marie Gilbert Majella [aut]
Maintainer: Rubeshkumar Polani <rubesh@thinkdenominator.com>
Diff between gtregression versions 1.0.0 dated 2025-08-18 and 1.1.0 dated 2026-08-21
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gtregression-1.1.0/gtregression/man/uni_reg.Rd | 106 gtregression-1.1.0/gtregression/tests/testthat/test-app-reference-levels.R |only gtregression-1.1.0/gtregression/tests/testthat/test-check_collinearity.R | 320 ++ gtregression-1.1.0/gtregression/tests/testthat/test-check_convergence.R | 365 ++- gtregression-1.1.0/gtregression/tests/testthat/test-check_ph.R |only gtregression-1.1.0/gtregression/tests/testthat/test-compare_models.R |only gtregression-1.1.0/gtregression/tests/testthat/test-cox_reg.R |only gtregression-1.1.0/gtregression/tests/testthat/test-data-prep-operations.R |only gtregression-1.1.0/gtregression/tests/testthat/test-data_diabetes_mediation.R |only gtregression-1.1.0/gtregression/tests/testthat/test-data_endometrial.R |only gtregression-1.1.0/gtregression/tests/testthat/test-descriptive_table.R | 539 ++-- gtregression-1.1.0/gtregression/tests/testthat/test-dissect.R | 161 - gtregression-1.1.0/gtregression/tests/testthat/test-fit_multi_model.R | 153 - gtregression-1.1.0/gtregression/tests/testthat/test-fit_uni_model.R | 140 - gtregression-1.1.0/gtregression/tests/testthat/test-forest_reg.R |only gtregression-1.1.0/gtregression/tests/testthat/test-gtregression_app.R |only gtregression-1.1.0/gtregression/tests/testthat/test-helper_labels.R | 50 gtregression-1.1.0/gtregression/tests/testthat/test-helpers_validation.R | 195 + gtregression-1.1.0/gtregression/tests/testthat/test-identify_confounder.R | 446 +++ gtregression-1.1.0/gtregression/tests/testthat/test-interaction_models.R | 425 ++- gtregression-1.1.0/gtregression/tests/testthat/test-km_plot.R |only gtregression-1.1.0/gtregression/tests/testthat/test-km_risk_table.R |only gtregression-1.1.0/gtregression/tests/testthat/test-logrank_test.R |only gtregression-1.1.0/gtregression/tests/testthat/test-mediation_analysis.R |only gtregression-1.1.0/gtregression/tests/testthat/test-merge_tables.R | 492 +++- gtregression-1.1.0/gtregression/tests/testthat/test-modify_table.R | 459 +++ gtregression-1.1.0/gtregression/tests/testthat/test-multi_reg.R | 567 +++- gtregression-1.1.0/gtregression/tests/testthat/test-option_args.R |only gtregression-1.1.0/gtregression/tests/testthat/test-plot_mediation.R |only gtregression-1.1.0/gtregression/tests/testthat/test-plot_model_fit.R |only gtregression-1.1.0/gtregression/tests/testthat/test-plot_reg.R | 536 +++- gtregression-1.1.0/gtregression/tests/testthat/test-plot_reg_combine.R | 283 +- gtregression-1.1.0/gtregression/tests/testthat/test-plot_surv_fit.R |only gtregression-1.1.0/gtregression/tests/testthat/test-reg_check_linear.R | 74 gtregression-1.1.0/gtregression/tests/testthat/test-rmst_table.R |only gtregression-1.1.0/gtregression/tests/testthat/test-save_functions.R | 399 ++- gtregression-1.1.0/gtregression/tests/testthat/test-select_models.R | 407 ++- gtregression-1.1.0/gtregression/tests/testthat/test-stratified_multi_reg.R | 532 ++-- gtregression-1.1.0/gtregression/tests/testthat/test-stratified_uni_reg.R | 410 +-- gtregression-1.1.0/gtregression/tests/testthat/test-surv_model_compare.R |only gtregression-1.1.0/gtregression/tests/testthat/test-surv_predict.R |only gtregression-1.1.0/gtregression/tests/testthat/test-surv_reg.R |only gtregression-1.1.0/gtregression/tests/testthat/test-survival_prob.R |only gtregression-1.1.0/gtregression/tests/testthat/test-survival_quantiles.R |only gtregression-1.1.0/gtregression/tests/testthat/test-survival_summary.R |only gtregression-1.1.0/gtregression/tests/testthat/test-uni_reg.R | 395 ++- gtregression-1.1.0/gtregression/tests/testthat/test-variable_labels.R |only gtregression-1.1.0/gtregression/vignettes/causal-mediation.Rmd |only gtregression-1.1.0/gtregression/vignettes/confounding-interaction.Rmd |only gtregression-1.1.0/gtregression/vignettes/customize-export.Rmd |only gtregression-1.1.0/gtregression/vignettes/descriptive-tables.Rmd |only gtregression-1.1.0/gtregression/vignettes/diagnostics-selection.Rmd |only gtregression-1.1.0/gtregression/vignettes/function-options.Rmd |only gtregression-1.1.0/gtregression/vignettes/gtregression-app.Rmd |only gtregression-1.1.0/gtregression/vignettes/gtregression-intro.Rmd | 507 +--- gtregression-1.1.0/gtregression/vignettes/regression-tables.Rmd |only gtregression-1.1.0/gtregression/vignettes/stratified-analysis.Rmd |only gtregression-1.1.0/gtregression/vignettes/survival-analysis.Rmd |only gtregression-1.1.0/gtregression/vignettes/visualise-results.Rmd |only 232 files changed, 17081 insertions(+), 6895 deletions(-)
Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including:
- bivariate generalized linear mixed models for synthesizing odds ratios, relative risks,
and risk differences
(Chu et al., 2012 <doi:10.1177/0962280210393712>)
- tests and measures for between-study heterogeneity
(Lin et al., 2017 <doi:10.1111/biom.12543>;
Wang et al., 2022 <doi:10.1002/sim.9261>;
Yu et al., 2025 <doi:10.1186/s12874-025-02719-7>);
- measures, tests, and visualization tools for publication bias, small-study effects, or related bias
(Lin and Chu, 2018 <doi:10.1111/biom.12817>;
Lin, 2019 <doi:10.1002/jrsm.1340>;
Lin, 2020 <doi:10.1177/0962280220910172>;
Shi et al., 2020 <doi:10.1002/jrsm.1415>);
- meta-analysis of combining standardized mean differences and odds ratios
(Jing et al., 2023 <doi:10.1080/10543406.2022.2105345>);
- meta-analysis of diagnostic tests for synthesizing sensitivities, specificities, etc.
(Reitsma et al., 2005 <doi:10.1016 [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Yaqi Jing [ctb],
Kristine J. Rosenberger [ctb],
Linyu Shi [ctb],
Yipeng Wang [ctb],
Xing Xing [ctb] ,
Zhiyuan Yu [ctb],
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between altmeta versions 4.3.1 dated 2026-04-30 and 4.4 dated 2026-08-21
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++------ NAMESPACE | 2 +- R/meta.or.smd.R | 2 +- R/pb.timelag.R |only data/dat.sherrington.rda |only man/dat.sherrington.Rd |only man/pb.bayesian.binary.Rd | 2 +- man/pb.hybrid.binary.Rd | 6 +++--- man/pb.hybrid.generic.Rd | 6 +++--- man/pb.timelag.Rd |only 11 files changed, 24 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-11 1.1.9
2016-02-18 1.1.5
2015-10-22 1.1.4
2013-11-05 1.1.2
2013-04-01 1.1.1
2012-09-17 1.1.0
2010-07-24 1.0.13
2010-06-09 1.0.11
2010-05-10 1.0.10
2010-05-06 1.0.8
Title: Understanding Nonlinear Mixed Effects Modeling for Population
Pharmacokinetics
Description: This shows how 'NONMEM' (Beal SL, Sheiner LB, Boeckmann AJ,
Bauer RJ. NONMEM 7.5 Users Guides. Icon plc, 2020) software works.
'NONMEM' classical estimation methods such as 'First Order (FO)
approximation', 'First Order Conditional Estimation (FOCE)', and
'Laplacian approximation' are explained. Functions are also provided
for post-run processing of NONMEM output files, generating PDF
diagnostic reports including objective function value analysis,
parameter estimates, prediction and residual diagnostics, empirical
Bayes estimate (EBE) analysis, input data summary, and individual
pharmacokinetic parameter distributions. Helper utilities for
building NONMEM-ready datasets from SDTM-style source tables are
also included.
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between nmw versions 0.3.1 dated 2026-06-09 and 0.5.1 dated 2026-08-21
nmw-0.3.1/nmw/man/AddPage.Rd |only nmw-0.3.1/nmw/man/ClosePDF.Rd |only nmw-0.3.1/nmw/man/PrepPDF.Rd |only nmw-0.3.1/nmw/man/PrinMTxt.Rd |only nmw-0.3.1/nmw/man/PrinTxt.Rd |only nmw-0.5.1/nmw/DESCRIPTION | 14 nmw-0.5.1/nmw/MD5 | 90 +-- nmw-0.5.1/nmw/NAMESPACE | 16 nmw-0.5.1/nmw/R/AddCox.R | 4 nmw-0.5.1/nmw/R/CombDmExPc.R | 6 nmw-0.5.1/nmw/R/CovStep.R | 1 nmw-0.5.1/nmw/R/InitStep.R | 14 nmw-0.5.1/nmw/R/TabStep.R | 2 nmw-0.5.1/nmw/R/ctl2nmw.R |only nmw-0.5.1/nmw/R/nm_parse.R | 36 - nmw-0.5.1/nmw/R/nm_read.R | 9 nmw-0.5.1/nmw/R/nm_stats.R | 4 nmw-0.5.1/nmw/R/nm_summary.R | 71 -- nmw-0.5.1/nmw/R/pdf_report.R | 221 +------ nmw-0.5.1/nmw/R/plot_pairs.R | 2 nmw-0.5.1/nmw/R/report_ebe.R | 908 +++++++++++++++----------------- nmw-0.5.1/nmw/R/report_indipk.R | 109 ++- nmw-0.5.1/nmw/R/report_input.R | 183 ++++-- nmw-0.5.1/nmw/R/report_ofv.R | 396 +++++++------ nmw-0.5.1/nmw/R/report_output.R | 61 +- nmw-0.5.1/nmw/R/report_param.R | 267 +++------ nmw-0.5.1/nmw/R/report_pred.R | 438 ++++++++------- nmw-0.5.1/nmw/R/report_resid.R | 710 ++++++++++++++++--------- nmw-0.5.1/nmw/R/utils_data.R | 18 nmw-0.5.1/nmw/R/utils_report.R | 58 +- nmw-0.5.1/nmw/inst/NEWS.Rd | 119 ++++ nmw-0.5.1/nmw/man/ClassifyCovariates.Rd |only nmw-0.5.1/nmw/man/GetNRecFromXML.Rd |only nmw-0.5.1/nmw/man/OFV_SCREEN_LAYOUT.Rd | 4 nmw-0.5.1/nmw/man/ReadLastTable.Rd |only nmw-0.5.1/nmw/man/SumOut.Rd | 14 nmw-0.5.1/nmw/man/TrimOut.Rd | 5 nmw-0.5.1/nmw/man/ctl2nmw.Rd |only nmw-0.5.1/nmw/man/e.Rd | 27 nmw-0.5.1/nmw/man/nmw_report_ebe.Rd | 10 nmw-0.5.1/nmw/man/nmw_report_indipk.Rd | 11 nmw-0.5.1/nmw/man/nmw_report_input.Rd | 10 nmw-0.5.1/nmw/man/nmw_report_ofv.Rd | 10 nmw-0.5.1/nmw/man/nmw_report_output.Rd | 11 nmw-0.5.1/nmw/man/nmw_report_param.Rd | 10 nmw-0.5.1/nmw/man/nmw_report_pred.Rd | 10 nmw-0.5.1/nmw/man/nmw_report_resid.Rd | 10 nmw-0.5.1/nmw/tests |only 48 files changed, 2174 insertions(+), 1715 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.21 dated 2026-07-02 and 1.0.22 dated 2026-08-21
modsem-1.0.21/modsem/tests/testthat/mplusResults_a38cc9c25f40845079c9955f90f260f0.dat |only modsem-1.0.21/modsem/tests/testthat/mplusResults_f3bccb91f6126be98dccff864043cccd.dat |only modsem-1.0.21/modsem/vignettes/set_eval_false.bash |only modsem-1.0.21/modsem/vignettes/set_eval_true.bash |only modsem-1.0.22/modsem/DESCRIPTION | 9 modsem-1.0.22/modsem/MD5 | 123 - modsem-1.0.22/modsem/NAMESPACE | 10 modsem-1.0.22/modsem/R/RcppExports.R | 4 modsem-1.0.22/modsem/R/bootstrap.R | 32 modsem-1.0.22/modsem/R/calc_se_da.R | 4 modsem-1.0.22/modsem/R/construct_matrices_da.R | 17 modsem-1.0.22/modsem/R/cov_model.R | 134 - modsem-1.0.22/modsem/R/equations_lms.R | 250 ++ modsem-1.0.22/modsem/R/est_lms.R | 697 +++++-- modsem-1.0.22/modsem/R/generics_modsem_da.R | 1 modsem-1.0.22/modsem/R/inspect_da.R | 8 modsem-1.0.22/modsem/R/lavaan_labels.R | 12 modsem-1.0.22/modsem/R/model_da.R | 35 modsem-1.0.22/modsem/R/model_parameters_da.R | 94 modsem-1.0.22/modsem/R/optimize_da.R | 20 modsem-1.0.22/modsem/R/plot_interaction.R | 21 modsem-1.0.22/modsem/R/quadrature.R | 120 - modsem-1.0.22/modsem/R/reliablity_single_item.R | 29 modsem-1.0.22/modsem/R/simulate_partable.R | 184 - modsem-1.0.22/modsem/R/utils_da.R | 20 modsem-1.0.22/modsem/build/partial.rdb |binary modsem-1.0.22/modsem/build/vignette.rds |binary modsem-1.0.22/modsem/inst/doc/composites.html | 357 ++- modsem-1.0.22/modsem/inst/doc/customize_plot_interactions.html | 476 +++- modsem-1.0.22/modsem/inst/doc/customizing.html | 434 +++- modsem-1.0.22/modsem/inst/doc/estimation_lms.html | 423 +++- modsem-1.0.22/modsem/inst/doc/fit_measures_da.html | 382 +++ modsem-1.0.22/modsem/inst/doc/higher_order_interactions.html | 519 +++-- modsem-1.0.22/modsem/inst/doc/interaction_two_etas.html | 433 +++- modsem-1.0.22/modsem/inst/doc/lavaan.html | 345 ++- modsem-1.0.22/modsem/inst/doc/lms_qml.html | 430 +++- modsem-1.0.22/modsem/inst/doc/mc-lms-ord.html | 379 ++- modsem-1.0.22/modsem/inst/doc/meanstructure_lms_qml.html | 382 +++ modsem-1.0.22/modsem/inst/doc/methods.html | 377 ++- modsem-1.0.22/modsem/inst/doc/missing_lms_qml.html | 379 +++ modsem-1.0.22/modsem/inst/doc/modsem.html | 515 +++-- modsem-1.0.22/modsem/inst/doc/observed_lms_qml.html | 955 ++++++--- modsem-1.0.22/modsem/inst/doc/plot_interactions.html | 686 ++++--- modsem-1.0.22/modsem/inst/doc/quadratic.html | 399 +++- modsem-1.0.22/modsem/inst/doc/relcorr_items.html | 394 +++- modsem-1.0.22/modsem/inst/doc/simple_slopes.html | 430 +++- modsem-1.0.22/modsem/man/bootstrap_modsem.Rd | 10 modsem-1.0.22/modsem/man/modsem-package.Rd | 5 modsem-1.0.22/modsem/man/modsem_inspect.Rd | 1 modsem-1.0.22/modsem/man/relcorr_single_item.Rd | 3 modsem-1.0.22/modsem/src/RcppExports.cpp | 22 modsem-1.0.22/modsem/src/equations_lms.cpp | 365 +++ modsem-1.0.22/modsem/tests/testthat/mplusResults.inp | 49 modsem-1.0.22/modsem/tests/testthat/mplusResults.out | 974 ---------- modsem-1.0.22/modsem/tests/testthat/mplusResults_034950db9f6a046dcbf4348715ec98cb.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_1902fe5a594fdff027c6f333f1b42374.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_1d99a51710dbe72680bd2167846dfc39.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_3d0f8823f6af05dbc789d0ed60a54090.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_6507283a847451aff127c84c87ebd81b.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_6bb11f99c9f63d831155403fa8debc11.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_ad18af3b9c89a45fac7dc52df3607909.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_c0d691516a85482200cebd668c136807.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_cef7da5bcf84a819ec0f66c18d6ea355.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_d4fd46d7e74eb5a0b73e2cb1369c4b51.dat |only modsem-1.0.22/modsem/tests/testthat/mplusResults_e8725a6185cbe0286c28c26f935f24e2.dat |only modsem-1.0.22/modsem/tests/testthat/test_grad_lms.R | 12 modsem-1.0.22/modsem/tests/testthat/test_labels_h0_pi.R | 2 modsem-1.0.22/modsem/tests/testthat/test_lms.R | 3 modsem-1.0.22/modsem/tests/testthat/test_ordered_da.R | 6 modsem-1.0.22/modsem/tests/testthat/test_rescov_eta_xi_lms.R | 46 70 files changed, 8049 insertions(+), 3968 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 0.22.0 dated 2026-06-10 and 0.23.0 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NAMESPACE | 34 ++++++++++++++++++++++------------ NEWS.md | 5 +++++ R/calculate_hash.R | 24 ++++++++++++++++++++---- R/leanify.R | 2 +- R/zzz.R | 2 +- man/calculate_hash.Rd | 2 +- man/figures/logo.png |binary man/hash_input.Rd | 11 +++++++++-- man/leanify_r6.Rd | 2 +- tests/testthat/test_calculate_hash.R |only tests/testthat/test_map.R | 2 +- 13 files changed, 77 insertions(+), 38 deletions(-)
Title: Inference on the Generalization Error
Description: Confidence interval and resampling methods for inference on
the generalization error.
Author: Sebastian Fischer [cre, aut] ,
Hannah Schulz-Kuempel [aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3inferr versions 0.2.1 dated 2025-11-26 and 0.2.2 dated 2026-08-21
DESCRIPTION | 8 - MD5 | 26 ++--- NEWS.md | 4 man/mlr3inferr-package.Rd | 3 man/mlr_measures_abstract_ci.Rd | 152 ++++++++++++++---------------- man/mlr_measures_ci.Rd | 119 ++++++++++++----------- man/mlr_measures_ci.con_z.Rd | 85 ++++++++-------- man/mlr_measures_ci.cor_t.Rd | 87 ++++++++--------- man/mlr_measures_ci.holdout.Rd | 85 ++++++++-------- man/mlr_measures_ci.ncv.Rd | 85 ++++++++-------- man/mlr_measures_ci.wald_cv.Rd | 85 ++++++++-------- man/mlr_resamplings_ncv.Rd | 114 +++++++++++----------- man/mlr_resamplings_paired_subsampling.Rd | 116 +++++++++++----------- tests/testthat/test_MeasureCiWaldCV.R | 9 + 14 files changed, 506 insertions(+), 472 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 0.2.2 dated 2026-07-27 and 0.2.3 dated 2026-08-21
mfrmr-0.2.2/mfrmr/R/utils-file-integrity.R |only mfrmr-0.2.3/mfrmr/DESCRIPTION | 18 mfrmr-0.2.3/mfrmr/MD5 | 395 +-- mfrmr-0.2.3/mfrmr/NAMESPACE | 171 - mfrmr-0.2.3/mfrmr/NEWS.md | 110 mfrmr-0.2.3/mfrmr/R/api-advanced.R | 568 ++++ mfrmr-0.2.3/mfrmr/R/api-as-ggplot.R | 76 mfrmr-0.2.3/mfrmr/R/api-bias-collection.R | 63 mfrmr-0.2.3/mfrmr/R/api-estimation.R | 1219 ++++++++- mfrmr-0.2.3/mfrmr/R/api-export-bundles.R | 489 +++ mfrmr-0.2.3/mfrmr/R/api-import.R | 176 + mfrmr-0.2.3/mfrmr/R/api-methods.R | 1181 ++++++++- mfrmr-0.2.3/mfrmr/R/api-plotting-extras.R | 13 mfrmr-0.2.3/mfrmr/R/api-plotting-fit-family.R | 672 ++++- mfrmr-0.2.3/mfrmr/R/api-plotting-wright-facets.R | 11 mfrmr-0.2.3/mfrmr/R/api-plotting.R | 123 mfrmr-0.2.3/mfrmr/R/api-prediction.R | 16 mfrmr-0.2.3/mfrmr/R/api-q3.R | 2 mfrmr-0.2.3/mfrmr/R/api-quadrature-sensitivity.R |only mfrmr-0.2.3/mfrmr/R/api-reporting-checklist.R | 69 mfrmr-0.2.3/mfrmr/R/api-reports.R | 409 +++ mfrmr-0.2.3/mfrmr/R/api-results.R | 269 +- 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Title: A Set of Tools for Sound Localization
Description: A set of functions and tools to conduct acoustic source localization, as well as organize and check localization data and results. The localization functions implement the modified steered response power algorithm described by Cobos et al. (2011) <doi:10.1109/LSP.2010.2091502>.
Author: Richard Hedley [cre, aut] ,
Marcus Becker [aut],
Tim Huang [aut]
Maintainer: Richard Hedley <rwhedley@gmail.com>
Diff between locaR versions 0.2.0 dated 2026-02-23 and 0.3.0 dated 2026-08-21
DESCRIPTION | 13 ++-- MD5 | 22 +++---- NAMESPACE | 1 NEWS.md | 34 ++++++---- R/spatialEntropy.R |only README.md | 21 ++++++ inst/doc/V2_Detecting_sound_sources.html | 2 inst/doc/V3_Intro_to_localize.R | 9 ++ inst/doc/V3_Intro_to_localize.Rmd | 13 ++++ inst/doc/V3_Intro_to_localize.html | 96 ++++++++++++++++++------------- man/locaR-package.Rd | 4 - man/spatialEntropy.Rd |only vignettes/V3_Intro_to_localize.Rmd | 13 ++++ 13 files changed, 154 insertions(+), 74 deletions(-)
Title: Estimation of Marginal Treatment Effects using Local
Instrumental Variables
Description: In the generalized Roy model, the marginal treatment effect (MTE) can be used as
a building block for constructing conventional causal parameters such as the average treatment
effect (ATE) and the average treatment effect on the treated (ATT). Given a treatment selection
equation and an outcome equation, the function mte() estimates the MTE via the semiparametric
local instrumental variables method or the normal selection model. The function mte_at() evaluates
MTE at different values of the latent resistance u with a given X = x, and the function mte_tilde_at()
evaluates MTE projected onto the estimated propensity score. The function ace() estimates
population-level average causal effects such as ATE, ATT, or the marginal policy relevant
treatment effect.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between localIV versions 0.3.1 dated 2020-06-26 and 0.3.2 dated 2026-08-21
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- NEWS.md | 6 ++++++ R/mte_tilde_at.R | 17 ++++++++--------- man/figures/README-mte_tilde_at-1.png |binary man/mte_tilde_at.Rd | 17 ++++++++--------- man/toydata.Rd | 32 +++++++++++++++++--------------- 8 files changed, 52 insertions(+), 46 deletions(-)
Title: L-Infinity Normalization and Dominant Community State Types
Description: Implements L-infinity normalization for compositional matrices,
assigns samples to dominant features, constructs truncated and
hierarchically refined dominant community state types, and computes
representative landmark profiles. The methods are described in the
accompanying publication <doi:10.48550/arXiv.2503.21543>. Bundled vaginal
and gut microbiome data support reproducible demonstrations of the package
interface; phenotype fields in the stratified gut subset are illustrative
and are not suitable for population-level inference.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between linf versions 0.1.0 dated 2026-08-05 and 0.2.0 dated 2026-08-21
linf-0.1.0/linf/man/collapse.rare.Rd |only linf-0.1.0/linf/man/expand.rare.Rd |only linf-0.1.0/linf/man/linf.cells.Rd |only linf-0.2.0/linf/DESCRIPTION | 6 linf-0.2.0/linf/MD5 | 71 - linf-0.2.0/linf/NAMESPACE | 5 linf-0.2.0/linf/NEWS.md |only linf-0.2.0/linf/R/backend_helpers.R | 16 linf-0.2.0/linf/R/dcst_landmark_pipeline.R | 16 linf-0.2.0/linf/R/landmarks.R | 100 - linf-0.2.0/linf/R/linf.R | 619 ++++------- linf-0.2.0/linf/R/transfer_dcsts.R | 10 linf-0.2.0/linf/README.md | 109 - linf-0.2.0/linf/build/partial.rdb |binary linf-0.2.0/linf/build/vignette.rds |binary linf-0.2.0/linf/inst/doc/linf-intro.R | 14 linf-0.2.0/linf/inst/doc/linf-intro.Rmd | 14 linf-0.2.0/linf/inst/doc/linf-intro.html | 16 linf-0.2.0/linf/inst/doc/linf-vaginal.R | 24 linf-0.2.0/linf/inst/doc/linf-vaginal.Rmd | 26 linf-0.2.0/linf/inst/doc/linf-vaginal.html | 28 linf-0.2.0/linf/man/dcst.view.Rd |only linf-0.2.0/linf/man/figures/readme-dcst-barplot.png |binary linf-0.2.0/linf/man/latex.linf.csts.Rd | 8 linf-0.2.0/linf/man/linf.csts.Rd | 22 linf-0.2.0/linf/man/linf.dcst.landmark.pipeline.Rd | 11 linf-0.2.0/linf/man/linf.dominant.features.Rd |only linf-0.2.0/linf/man/linf.landmarks.Rd | 10 linf-0.2.0/linf/man/refine.linf.csts.Rd | 9 linf-0.2.0/linf/man/refine.linf.csts.iter.Rd | 12 linf-0.2.0/linf/man/transfer.dcsts.Rd | 6 linf-0.2.0/linf/tests/testthat/test-dcst-landmark-pipeline.R | 24 linf-0.2.0/linf/tests/testthat/test-filter.asv.R | 32 linf-0.2.0/linf/tests/testthat/test-label-formatting.R | 18 linf-0.2.0/linf/tests/testthat/test-landmarks.R | 35 linf-0.2.0/linf/tests/testthat/test-public-terminology.R |only linf-0.2.0/linf/tests/testthat/test-sparse-backend.R | 18 linf-0.2.0/linf/tests/testthat/test-transfer-dcsts.R | 6 linf-0.2.0/linf/vignettes/linf-intro.Rmd | 14 linf-0.2.0/linf/vignettes/linf-vaginal.Rmd | 26 40 files changed, 621 insertions(+), 704 deletions(-)
Title: Post-Estimation Utilities for 'lavaan' Fitted Models
Description: Companion toolbox for structural equation models fitted with 'lavaan'. Provides post-estimation diagnostics and graphics that operate directly on a fitted object using its estimates and covariance, and refits auxiliary models when needed. The package relies on 'lavaan' (Rosseel, 2012) <doi:10.18637/jss.v048.i02>.
Author: Giuseppe Corbelli [aut, cre]
Maintainer: Giuseppe Corbelli <giuseppe.corbelli@uninettunouniversity.net>
Diff between lavinteract versions 0.5.1 dated 2026-04-28 and 0.5.3 dated 2026-08-21
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 13 +++ R/lav_cv.R | 221 +++++++++++++++++++++++++++++++++++++--------------------- inst/WORDLIST | 2 man/lav_cv.Rd | 54 +++++++++++--- 6 files changed, 209 insertions(+), 97 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre, art, cph]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.4.1 dated 2026-07-31 and 1.5.0 dated 2026-08-21
IssueTrackeR-1.4.1/IssueTrackeR/man/format_issues.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/format_labels.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/format_milestones.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/generate_age_mat.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/github_errors.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/plot.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/print.Rd |only IssueTrackeR-1.4.1/IssueTrackeR/man/rbind.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/DESCRIPTION | 13 IssueTrackeR-1.5.0/IssueTrackeR/MD5 | 105 - IssueTrackeR-1.5.0/IssueTrackeR/NAMESPACE | 98 - IssueTrackeR-1.5.0/IssueTrackeR/NEWS.md | 29 IssueTrackeR-1.5.0/IssueTrackeR/R/check.R | 34 IssueTrackeR-1.5.0/IssueTrackeR/R/contributor.R |only IssueTrackeR-1.5.0/IssueTrackeR/R/finding-objects.R | 95 + IssueTrackeR-1.5.0/IssueTrackeR/R/format.R | 107 + IssueTrackeR-1.5.0/IssueTrackeR/R/options.R | 21 IssueTrackeR-1.5.0/IssueTrackeR/R/plot.R | 411 ++++ IssueTrackeR-1.5.0/IssueTrackeR/R/print.R | 24 IssueTrackeR-1.5.0/IssueTrackeR/R/summary.R | 8 IssueTrackeR-1.5.0/IssueTrackeR/R/update_database.R | 10 IssueTrackeR-1.5.0/IssueTrackeR/R/utils.R | 9 IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_issues.R | 152 - IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_labels.R | 27 IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_dataset_milestones.R | 65 IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_issues.R | 145 + IssueTrackeR-1.5.0/IssueTrackeR/R/wrangling_repo.R | 10 IssueTrackeR-1.5.0/IssueTrackeR/R/write.R | 14 IssueTrackeR-1.5.0/IssueTrackeR/R/zzz.R | 2 IssueTrackeR-1.5.0/IssueTrackeR/inst/WORDLIST | 1 IssueTrackeR-1.5.0/IssueTrackeR/inst/data_issues/closed_issues.yaml | 846 ++++++---- IssueTrackeR-1.5.0/IssueTrackeR/inst/data_issues/list_milestones.yaml | 14 IssueTrackeR-1.5.0/IssueTrackeR/inst/data_issues/open_issues.yaml | 634 +++++-- IssueTrackeR-1.5.0/IssueTrackeR/man/author_last_comment.Rd | 11 IssueTrackeR-1.5.0/IssueTrackeR/man/count_issues.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/man/extract_nth.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/man/get.Rd | 27 IssueTrackeR-1.5.0/IssueTrackeR/man/get_all_repos.Rd | 8 IssueTrackeR-1.5.0/IssueTrackeR/man/new_issue.Rd | 8 IssueTrackeR-1.5.0/IssueTrackeR/man/new_issues.Rd | 12 IssueTrackeR-1.5.0/IssueTrackeR/man/plot-issues.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/man/print-issues.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/man/rbind-issues.Rd |only IssueTrackeR-1.5.0/IssueTrackeR/man/reset_options.Rd | 8 IssueTrackeR-1.5.0/IssueTrackeR/man/summary.Rd | 2 IssueTrackeR-1.5.0/IssueTrackeR/man/update_database.Rd | 8 IssueTrackeR-1.5.0/IssueTrackeR/man/with_comments.Rd | 6 IssueTrackeR-1.5.0/IssueTrackeR/man/with_labels.Rd | 2 IssueTrackeR-1.5.0/IssueTrackeR/man/with_text.Rd | 2 IssueTrackeR-1.5.0/IssueTrackeR/man/write.Rd | 13 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/data/closed_issues.yaml | 31 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/helper.R | 58 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-add_n_years.R | 4 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-bin_count.R | 34 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-count_issues.R |only IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-extract.R | 10 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-finding.R | 37 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-get.R | 21 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-isDark.R | 4 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-plot.R | 10 IssueTrackeR-1.5.0/IssueTrackeR/tests/testthat/test-summary.R | 24 61 files changed, 2203 insertions(+), 1011 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 6.8 dated 2025-10-27 and 7.0 dated 2026-08-21
DESCRIPTION | 8 - MD5 | 77 +++++++-------- R/LRisochron.R |only R/ThU.R | 14 ++ R/UPb.R | 15 +- R/age.R | 2 R/agespectrum.R | 51 +++++---- R/bayes.R | 20 +-- R/cad.R | 46 ++++++-- R/central.R | 13 ++ R/ci.R | 1 R/concordia.R | 266 ++++++++++++++++++++++++++++++++++++++++------------ R/discordia.R | 134 ++++++++++++++------------ R/diseq.R | 21 ++-- R/errorellipse.R | 14 +- R/evolution.R | 36 ++++--- R/flipper.R | 41 ++++++-- R/helioplot.R | 13 +- R/io.R | 8 - R/isochron.R | 236 +++++++++++++++++++++------------------------- R/ludwig.R | 4 R/mds.R | 7 - R/peakfit.R | 7 - R/radialplot.R | 135 ++++++++++++++++---------- R/regression.R | 7 + R/toolbox.R | 15 +- R/weightedmean.R | 99 ++++++++++++------- R/york.R | 54 ++++------ R/york2ludwig.R | 64 ++++++++---- man/agespectrum.Rd | 12 ++ man/cad.Rd | 32 ++++-- man/concordia.Rd | 28 +++++ man/data2york.Rd | 30 ++--- man/diss.Rd | 3 man/evolution.Rd | 6 - man/helioplot.Rd | 7 + man/isochron.Rd | 14 +- man/radialplot.Rd | 17 +++ man/scatterplot.Rd | 10 + man/weightedmean.Rd | 17 +++ 40 files changed, 1014 insertions(+), 570 deletions(-)
Title: ISO 3166-1 Country Codes
Description: ISO 3166-1 country codes and ISO 4217 currency codes provided
by the International Organization for Standardization.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between isocountry versions 0.6.1 dated 2026-06-29 and 0.7.0 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/data.R | 11 ++++++++--- data/isocurrency.rda |binary man/isocountry.Rd | 7 +++++-- man/isocurrency.Rd | 5 ++++- 7 files changed, 31 insertions(+), 16 deletions(-)
Title: Interpretable Contextual-Accountable and Responsible Machine
Learning
Description: A general-purpose framework for Interpretable Contextual-Accountable
and Responsible Machine Learning (ICARM) that works with any clean tabular
data across any application domain including healthcare, finance, social
science, business, and education. Automatically detects whether a prediction
task is binary classification, multi-class classification, or regression
from the target variable type. Provides a unified entry point icarm_fit()
supporting both interpretable learners (Classification and Regression Trees
(CART), logistic regression, linear regression, Generalized Additive Models
(GAM)) and extended learners (random forest, 'XGBoost', Support Vector
Machines (SVM)) with consistent interfaces for global and local model
explanation including approximate SHapley Additive exPlanations (SHAP)
values and Partial Dependence Profiles (PDPs), learning curve diagnostics,
group-level fairness auditing across protected attributes, probability
calibration, threshold analysis, multi-model comp [...truncated...]
Author: Olushina Olawale Awe [aut, cre],
Ludwigsburg University of Education [fnd]
Maintainer: Olushina Olawale Awe <olawaleawe@gmail.com>
Diff between icarm versions 0.2.0 dated 2026-07-09 and 0.3.0 dated 2026-08-21
DESCRIPTION | 13 +- MD5 | 26 ++-- NAMESPACE | 9 + R/data.R | 2 R/icarm_ale.R |only R/icarm_core.R | 4 R/icarm_cv.R |only R/icarm_drift.R |only R/icarm_fit.R | 300 ++++++++++++++++++++++++++++++++++++++++++------ R/icarm_shap.R | 2 R/plots.R | 164 ++++++++++++++++++++++++-- R/utils_internal.R | 266 +++++++++++++++++++++--------------------- build |only man/icarm_ale.Rd |only man/icarm_cv.Rd |only man/icarm_drift.Rd |only man/icarm_plot_ale.Rd |only man/icarm_plot_cv.Rd |only man/icarm_plot_drift.Rd |only 19 files changed, 592 insertions(+), 194 deletions(-)
Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Victor-Hugo Baldera-Chaponan [aut] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between huito versions 0.2.6 dated 2025-10-18 and 0.2.7 dated 2026-08-21
huito-0.2.6/huito/inst/doc/germinar.R |only huito-0.2.6/huito/inst/doc/germinar.Rmd |only huito-0.2.6/huito/inst/doc/germinar.html |only huito-0.2.6/huito/inst/doc/huito.Rmd |only huito-0.2.6/huito/inst/doc/labels.R |only huito-0.2.6/huito/inst/doc/labels.html |only huito-0.2.6/huito/inst/doc/labels.qmd |only huito-0.2.6/huito/inst/doc/stickers.R |only huito-0.2.6/huito/inst/doc/stickers.Rmd |only huito-0.2.6/huito/inst/doc/stickers.html |only huito-0.2.6/huito/vignettes/germinar.Rmd |only huito-0.2.6/huito/vignettes/huito |only huito-0.2.6/huito/vignettes/huito.Rmd |only huito-0.2.6/huito/vignettes/huito.zip |only huito-0.2.6/huito/vignettes/labels.qmd |only huito-0.2.6/huito/vignettes/stickers.Rmd |only huito-0.2.7/huito/DESCRIPTION | 14 - huito-0.2.7/huito/MD5 | 69 +++--- huito-0.2.7/huito/NEWS.md | 7 huito-0.2.7/huito/R/image_import.R | 43 ++-- huito-0.2.7/huito/R/include_image.R | 64 +++--- huito-0.2.7/huito/R/label_print.R | 192 +++++++++++------- huito-0.2.7/huito/README.md | 41 ++- huito-0.2.7/huito/build/vignette.rds |binary huito-0.2.7/huito/inst/doc/GerminaR.R |only huito-0.2.7/huito/inst/doc/GerminaR.html |only huito-0.2.7/huito/inst/doc/GerminaR.qmd |only huito-0.2.7/huito/inst/doc/horizontal.R |only huito-0.2.7/huito/inst/doc/horizontal.html |only huito-0.2.7/huito/inst/doc/horizontal.qmd |only huito-0.2.7/huito/inst/doc/huito.R | 97 +++++++-- huito-0.2.7/huito/inst/doc/huito.html | 260 +++++++++++++++---------- huito-0.2.7/huito/inst/doc/huito.qmd |only huito-0.2.7/huito/inst/doc/inkaverse.R |only huito-0.2.7/huito/inst/doc/inkaverse.html |only huito-0.2.7/huito/inst/doc/inkaverse.qmd |only huito-0.2.7/huito/inst/doc/package.R |only huito-0.2.7/huito/inst/doc/package.html |only huito-0.2.7/huito/inst/doc/package.qmd |only huito-0.2.7/huito/inst/doc/vertical.R |only huito-0.2.7/huito/inst/doc/vertical.html |only huito-0.2.7/huito/inst/doc/vertical.qmd |only huito-0.2.7/huito/man/image_import.Rd | 4 huito-0.2.7/huito/man/include_image.Rd | 14 + huito-0.2.7/huito/man/label_print.Rd | 11 - huito-0.2.7/huito/man/reexports.Rd | 2 huito-0.2.7/huito/vignettes/GerminaR.qmd |only huito-0.2.7/huito/vignettes/horizontal.qmd |only huito-0.2.7/huito/vignettes/huito-package.md |only huito-0.2.7/huito/vignettes/huito.qmd |only huito-0.2.7/huito/vignettes/inkaverse.qmd |only huito-0.2.7/huito/vignettes/logo_inkaverse.jpg |only huito-0.2.7/huito/vignettes/package.qmd |only huito-0.2.7/huito/vignettes/vertical.qmd |only 54 files changed, 520 insertions(+), 298 deletions(-)
Title: Fit the Meta-D' Model of Confidence Ratings Using 'brms'
Description: Implementation of Bayesian regressions over the meta-d' model of
psychological data from two alternative forced choice tasks with
ordinal confidence ratings. For more information, see
Maniscalco & Lau (2012) <doi:10.1016/j.concog.2011.09.021>.
The package is a front-end to the 'brms' package, which facilitates a wide
range of regression designs, as well as tools for efficiently extracting
posterior estimates, plotting, and significance testing.
Author: Kevin O'Neill [aut, cre, cph] ,
Stephen Fleming [aut, cph]
Maintainer: Kevin O'Neill <kevin.o'neill@ucl.ac.uk>
Diff between hmetad versions 0.1.2 dated 2026-05-15 and 0.2.0 dated 2026-08-21
hmetad-0.1.2/hmetad/R/roc_draws.R |only hmetad-0.1.2/hmetad/man/response_probabilities.Rd |only hmetad-0.2.0/hmetad/DESCRIPTION | 8 hmetad-0.2.0/hmetad/MD5 | 108 +-- hmetad-0.2.0/hmetad/NAMESPACE | 60 + hmetad-0.2.0/hmetad/NEWS.md | 14 hmetad-0.2.0/hmetad/R/auroc1_draws.R |only hmetad-0.2.0/hmetad/R/auroc2_draws.R |only hmetad-0.2.0/hmetad/R/epred_draws_metad.R | 142 +++- hmetad-0.2.0/hmetad/R/hmetad-package.R | 1 hmetad-0.2.0/hmetad/R/hmetad.R | 288 ++++---- hmetad-0.2.0/hmetad/R/linpred_draws_metad.R | 1 hmetad-0.2.0/hmetad/R/mean_confidence_draws.R | 114 ++- hmetad-0.2.0/hmetad/R/metacognitive_bias_draws.R | 23 hmetad-0.2.0/hmetad/R/metad_family.R | 26 hmetad-0.2.0/hmetad/R/predicted_draws_metad.R | 91 +- hmetad-0.2.0/hmetad/R/roc1_draws.R |only hmetad-0.2.0/hmetad/R/roc2_draws.R |only hmetad-0.2.0/hmetad/R/simulate.R | 205 +++--- hmetad-0.2.0/hmetad/R/type1_draws.R |only hmetad-0.2.0/hmetad/R/type2_draws.R |only hmetad-0.2.0/hmetad/README.md | 288 ++++---- hmetad-0.2.0/hmetad/inst/doc/alternative_distributions.R | 8 hmetad-0.2.0/hmetad/inst/doc/alternative_distributions.Rmd | 8 hmetad-0.2.0/hmetad/inst/doc/alternative_distributions.html | 46 - hmetad-0.2.0/hmetad/inst/doc/categorical.Rmd | 244 +++---- hmetad-0.2.0/hmetad/inst/doc/categorical.html | 248 +++---- hmetad-0.2.0/hmetad/inst/doc/hmetad.R | 45 - hmetad-0.2.0/hmetad/inst/doc/hmetad.Rmd | 49 - hmetad-0.2.0/hmetad/inst/doc/hmetad.html | 385 ++++++------ hmetad-0.2.0/hmetad/inst/doc/parameterization.Rmd | 9 hmetad-0.2.0/hmetad/inst/doc/parameterization.html | 20 hmetad-0.2.0/hmetad/man/aggregate_metad.Rd | 8 hmetad-0.2.0/hmetad/man/auroc1.Rd |only hmetad-0.2.0/hmetad/man/auroc1_draws.Rd |only hmetad-0.2.0/hmetad/man/auroc2.Rd |only hmetad-0.2.0/hmetad/man/auroc2_draws.Rd |only hmetad-0.2.0/hmetad/man/bias_draws.Rd | 20 hmetad-0.2.0/hmetad/man/epred_draws_metad.Rd | 33 - hmetad-0.2.0/hmetad/man/fit_metad.Rd | 7 hmetad-0.2.0/hmetad/man/hmetad-package.Rd | 2 hmetad-0.2.0/hmetad/man/joint_probabilities.Rd |only hmetad-0.2.0/hmetad/man/mean_conf_draws.Rd | 14 hmetad-0.2.0/hmetad/man/mean_confidence.Rd |only hmetad-0.2.0/hmetad/man/metad.Rd | 12 hmetad-0.2.0/hmetad/man/predicted_draws_metad.Rd | 30 hmetad-0.2.0/hmetad/man/roc1.Rd |only hmetad-0.2.0/hmetad/man/roc1_draws.Rd | 36 - hmetad-0.2.0/hmetad/man/roc2.Rd |only hmetad-0.2.0/hmetad/man/roc2_draws.Rd | 56 + hmetad-0.2.0/hmetad/man/sim_metad.Rd | 24 hmetad-0.2.0/hmetad/man/sim_metad_condition.Rd | 20 hmetad-0.2.0/hmetad/man/sim_metad_participant.Rd | 51 - hmetad-0.2.0/hmetad/man/sim_metad_participant_condition.Rd | 48 - hmetad-0.2.0/hmetad/man/type1_draws.Rd |only hmetad-0.2.0/hmetad/man/type1_probabilities.Rd |only hmetad-0.2.0/hmetad/man/type2_draws.Rd |only hmetad-0.2.0/hmetad/man/type2_probabilities.Rd |only hmetad-0.2.0/hmetad/tests/testthat/test-draws.R | 272 +++++++- hmetad-0.2.0/hmetad/tests/testthat/test-hmetad.R | 9 hmetad-0.2.0/hmetad/vignettes/alternative_distributions.Rmd | 8 hmetad-0.2.0/hmetad/vignettes/categorical.Rmd | 244 +++---- hmetad-0.2.0/hmetad/vignettes/hmetad.Rmd | 49 - hmetad-0.2.0/hmetad/vignettes/parameterization.Rmd | 9 hmetad-0.2.0/hmetad/vignettes/src/_categorical.Rmd | 4 65 files changed, 2023 insertions(+), 1364 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.5.1 dated 2025-11-11 and 0.5.2 dated 2026-08-21
healthyAddress-0.5.1/healthyAddress/inst/extdata/street-names.txt |only healthyAddress-0.5.2/healthyAddress/DESCRIPTION | 8 healthyAddress-0.5.2/healthyAddress/MD5 | 135 - healthyAddress-0.5.2/healthyAddress/NAMESPACE | 84 healthyAddress-0.5.2/healthyAddress/NEWS.md | 7 healthyAddress-0.5.2/healthyAddress/R/HashStreetName.R | 94 - healthyAddress-0.5.2/healthyAddress/R/NumberSuffix2raw.R | 44 healthyAddress-0.5.2/healthyAddress/R/anyComma.R | 20 healthyAddress-0.5.2/healthyAddress/R/check_address_input.R | 6 healthyAddress-0.5.2/healthyAddress/R/concat_upper.R | 28 healthyAddress-0.5.2/healthyAddress/R/download_latlon_data.R | 2 healthyAddress-0.5.2/healthyAddress/R/encode_address.R | 106 - healthyAddress-0.5.2/healthyAddress/R/extract_flatNumberFirstLast.R | 64 healthyAddress-0.5.2/healthyAddress/R/extract_postcode.R | 50 healthyAddress-0.5.2/healthyAddress/R/extract_standard_address.R | 76 healthyAddress-0.5.2/healthyAddress/R/followed_by_STE_POSTCODE.R | 8 healthyAddress-0.5.2/healthyAddress/R/get_StreetType.R | 52 healthyAddress-0.5.2/healthyAddress/R/has_SaintName.R | 12 healthyAddress-0.5.2/healthyAddress/R/healthyAddress-package.R | 54 healthyAddress-0.5.2/healthyAddress/R/isPostcode.R | 14 healthyAddress-0.5.2/healthyAddress/R/latlon.R | 116 - healthyAddress-0.5.2/healthyAddress/R/match_StreetType.R | 76 healthyAddress-0.5.2/healthyAddress/R/match_word.R | 38 healthyAddress-0.5.2/healthyAddress/R/max_nchar.R | 12 healthyAddress-0.5.2/healthyAddress/R/multistate_postcodes.R | 6 healthyAddress-0.5.2/healthyAddress/R/mutate_latlon.R | 80 healthyAddress-0.5.2/healthyAddress/R/n_words.R | 8 healthyAddress-0.5.2/healthyAddress/R/nany_lowercase.R | 62 healthyAddress-0.5.2/healthyAddress/R/postcode2ste.R | 106 - healthyAddress-0.5.2/healthyAddress/R/read_locality_by_postcode.R | 10 healthyAddress-0.5.2/healthyAddress/R/standardize_address.R | 384 ++-- healthyAddress-0.5.2/healthyAddress/R/street-types.R | 908 +++++----- healthyAddress-0.5.2/healthyAddress/R/the_XXX.R | 78 healthyAddress-0.5.2/healthyAddress/R/toupper_basic.R | 24 healthyAddress-0.5.2/healthyAddress/R/unique_Postcodes.R | 64 healthyAddress-0.5.2/healthyAddress/README.md | 78 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_000_valgrind_esplanade.R | 12 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_HashStreetName.R | 16 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_NumberSuffix2Raw.R | 18 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_THE.R | 34 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_WordData.R | 22 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_anyComma.R | 14 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_check_address_input.R | 12 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_compress_latlon.R | 40 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_concat_upper.R | 24 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_extract_flatNumberFirstLast.R | 56 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_extract_postcode.R | 12 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_followed_by_STE_POSTCODE.R | 20 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_healthyAddress.R | 880 ++++----- healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_is_postcode.R | 8 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_match_word.R | 16 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_max_nchar.R | 8 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_multistate_postcodes.R | 2 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_n_words.R | 10 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_toupper_basic.R | 8 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_unique_Postcodes.R | 32 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_which_first_strstr.R | 6 healthyAddress-0.5.2/healthyAddress/inst/tinytest/test_xnumber.R | 20 healthyAddress-0.5.2/healthyAddress/man/HashStreetName.Rd | 58 healthyAddress-0.5.2/healthyAddress/man/compress_latlon.Rd | 96 - healthyAddress-0.5.2/healthyAddress/man/download_latlon_data.Rd | 64 healthyAddress-0.5.2/healthyAddress/man/healthyAddress-package.Rd | 51 healthyAddress-0.5.2/healthyAddress/man/match_StreetType.Rd | 56 healthyAddress-0.5.2/healthyAddress/man/mutate_latlon.Rd | 42 healthyAddress-0.5.2/healthyAddress/man/nany_lowercase.Rd | 56 healthyAddress-0.5.2/healthyAddress/man/standardize_address.Rd | 206 +- healthyAddress-0.5.2/healthyAddress/man/toupper_basic.Rd | 36 healthyAddress-0.5.2/healthyAddress/man/unique_Postcodes.Rd | 54 healthyAddress-0.5.2/healthyAddress/src/StandardAddress.c | 11 69 files changed, 2462 insertions(+), 2452 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: Explore and Import 'Metopio' Health Atlas Data and Spatial
Layers
Description: Allows for painless use of the 'Metopio' health atlas APIs
<https://metopio.com/health-atlas> to explore and import data.
'Metopio' health atlases store open public health data. See what topics
(or indicators) are available among specific populations, periods, and
geographic layers. Download relevant data along with geographic
boundaries or point datasets. Spatial datasets are returned as 'sf'
objects.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between healthatlas versions 0.2.2 dated 2025-07-22 and 0.2.3 dated 2026-08-21
healthatlas-0.2.2/healthatlas/tests/testthat/_snaps |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_coverage |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_data |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_layer |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_point |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_subcategories |only healthatlas-0.2.2/healthatlas/tests/testthat/ha_topics |only healthatlas-0.2.2/healthatlas/tests/testthat/helpers.R |only healthatlas-0.2.2/healthatlas/tests/testthat/setup.R |only healthatlas-0.2.2/healthatlas/tests/testthat/test-ha_subcategories.R |only healthatlas-0.2.2/healthatlas/vignettes/healthatlas |only healthatlas-0.2.3/healthatlas/DESCRIPTION | 11 healthatlas-0.2.3/healthatlas/MD5 | 72 -- healthatlas-0.2.3/healthatlas/NEWS.md | 4 healthatlas-0.2.3/healthatlas/R/ha_layer.R | 30 healthatlas-0.2.3/healthatlas/R/helpers.R | 8 healthatlas-0.2.3/healthatlas/README.md | 71 +- healthatlas-0.2.3/healthatlas/build/vignette.rds |binary healthatlas-0.2.3/healthatlas/inst/doc/healthatlas.R | 182 ++--- healthatlas-0.2.3/healthatlas/inst/doc/healthatlas.Rmd | 32 healthatlas-0.2.3/healthatlas/inst/doc/healthatlas.html | 346 ---------- healthatlas-0.2.3/healthatlas/man/figures/README-unnamed-chunk-9-1.png |binary healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_coverage.R | 79 -- healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_data.R | 101 +- healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_layer.R | 44 - healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_point_layer.R | 38 - healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_subcategory.R |only healthatlas-0.2.3/healthatlas/tests/testthat/test-ha_topics.R | 54 - healthatlas-0.2.3/healthatlas/vignettes/healthatlas.Rmd | 32 29 files changed, 334 insertions(+), 770 deletions(-)
Title: Graph Drawing with Intelligent Placement (GRIP)
Description: Implements GRIP multiscale graph layout with a unified choice
between hop-count and geometry-aware edge-length graph metrics in 2D and
3D. Provides layout scoring, candidate
comparison, multiscale trace diagnostics, synthetic graph families,
and advanced experimental geodesic-KK utilities for weighted-layout
evaluation and polish. Based on Gajer and Kobourov (2002)
<doi:10.7155/jgaa.00052> and Gajer, Goodrich and Kobourov (2004)
<doi:10.1016/j.comgeo.2004.03.014>.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between grip versions 0.1.2 dated 2026-08-05 and 0.1.3 dated 2026-08-21
grip-0.1.2/grip/man/trace.weighted.grip.Rd |only grip-0.1.2/grip/man/weighted.grip.Rd |only grip-0.1.3/grip/DESCRIPTION | 12 grip-0.1.3/grip/MD5 | 92 +-- grip-0.1.3/grip/NAMESPACE | 2 grip-0.1.3/grip/NEWS.md | 11 grip-0.1.3/grip/R/deprecated_api.R | 8 grip-0.1.3/grip/R/gmds_layout_interface.R | 19 grip-0.1.3/grip/R/grip-package.R | 10 grip-0.1.3/grip/R/grip_geodesic_misf_kk.R | 22 grip-0.1.3/grip/R/grip_layout.R | 240 +++++++++- grip-0.1.3/grip/R/grip_layout_weighted.R | 106 +--- grip-0.1.3/grip/R/grip_quality.R | 3 grip-0.1.3/grip/README.md | 51 +- grip-0.1.3/grip/inst/doc/grip-examples.Rmd | 14 grip-0.1.3/grip/inst/doc/grip-examples.html | 25 - grip-0.1.3/grip/inst/doc/grip-real-data.R | 4 grip-0.1.3/grip/inst/doc/grip-real-data.Rmd | 14 grip-0.1.3/grip/inst/doc/grip-real-data.html | 33 - grip-0.1.3/grip/inst/doc/grip-trace-and-diagnostics.R | 2 grip-0.1.3/grip/inst/doc/grip-trace-and-diagnostics.Rmd | 14 grip-0.1.3/grip/inst/doc/grip-trace-and-diagnostics.html | 20 grip-0.1.3/grip/inst/doc/weighted-grip-intro.R | 10 grip-0.1.3/grip/inst/doc/weighted-grip-intro.Rmd | 40 - grip-0.1.3/grip/inst/doc/weighted-grip-intro.html | 58 +- grip-0.1.3/grip/man/edge.kk.Rd | 7 grip-0.1.3/grip/man/globalrep.grip.Rd | 18 grip-0.1.3/grip/man/globalrep.weighted.grip.Rd | 19 grip-0.1.3/grip/man/grip-package.Rd | 10 grip-0.1.3/grip/man/grip.Rd | 90 +++ grip-0.1.3/grip/man/misf.geodesic.kk.Rd | 14 grip-0.1.3/grip/man/prepare.edge.kk.Rd | 3 grip-0.1.3/grip/man/score.misf.geodesic.kk.Rd | 8 grip-0.1.3/grip/man/trace.grip.Rd | 98 ++-- grip-0.1.3/grip/src/DrawGraph.h | 3 grip-0.1.3/grip/src/MishEngine.cpp | 2 grip-0.1.3/grip/src/MishSupport.cpp | 10 grip-0.1.3/grip/src/MishWeighted.cpp | 6 grip-0.1.3/grip/src/Point.h | 3 grip-0.1.3/grip/src/Rounding.h |only grip-0.1.3/grip/tests/testthat/helper-weighted-nd-trace-parity.R | 3 grip-0.1.3/grip/tests/testthat/test-edge-isometric-gkk.R | 7 grip-0.1.3/grip/tests/testthat/test-layout-metric-dispatch.R |only grip-0.1.3/grip/tests/testthat/test-layout-weighted-globalrep.R | 42 - grip-0.1.3/grip/tests/testthat/test-layout-weighted-trace.R | 40 - grip-0.1.3/grip/vignettes/grip-examples.Rmd | 14 grip-0.1.3/grip/vignettes/grip-real-data.Rmd | 14 grip-0.1.3/grip/vignettes/grip-trace-and-diagnostics.Rmd | 14 grip-0.1.3/grip/vignettes/weighted-grip-intro.Rmd | 40 - 49 files changed, 779 insertions(+), 496 deletions(-)
Title: Import, Inspect, Analyse, and Report Gazepoint GP3 Exports
Description: Tools for importing, inspecting, cleaning, summarising,
modelling, and reporting Gazepoint GP3 and Gazepoint Analysis CSV
exports. The package supports offline workflows for all-gaze,
fixation, pupil, area-of-interest, transition, time-course, quality-audit, and
manuscript-reporting analyses.
The package methodology is described in the peer-reviewed
software paper <doi:10.3390/jemr19040076>.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3tools versions 2.0.1 dated 2026-07-14 and 2.3.0 dated 2026-08-21
DESCRIPTION | 10 - MD5 | 100 ++++++++++ NAMESPACE | 59 ++++++ NEWS.md | 169 ++++++++++++++++++ R/advanced_aoi_assignment.R |only R/binocular_pupil_reconstruction.R |only R/binocular_pupil_validation.R |only R/event_detection_extensions.R |only R/event_detector_benchmarking.R |only R/event_detector_comparison.R |only R/gpbiometrics_bridge.R |only R/high_priority_signal_helpers.R |only R/naming_compatibility_aliases.R |only R/naming_policy.R |only R/performance_benchmarking.R |only R/plot_gazepoint_binocular_diagnostics.R |only R/pupil_signal_extensions.R |only R/scanpath_cluster_stability.R |only R/scanpath_clustering.R |only R/scanpath_clustering_workflow.R |only R/signal_preprocessing_workflow.R |only R/window_aoi_extensions.R |only README.md | 83 ++++++++ build/partial.rdb |only inst/CITATION | 2 inst/benchmarks |only man/add_gazepoint_aoi.Rd |only man/add_gazepoint_dynamic_aoi.Rd |only man/add_gazepoint_polygon_aoi.Rd |only man/analyse_gazepoint_binocular_sensitivity.Rd |only man/analyze_gazepoint_window.Rd |only man/audit_gazepoint_binocular_reconstruction.Rd |only man/audit_gazepoint_dynamic_aoi_coverage.Rd |only man/audit_gazepoint_naming_consistency.Rd |only man/benchmark_gazepoint_event_detectors.Rd |only man/benchmark_gazepoint_export_performance.Rd |only man/bootstrap_gazepoint_scanpath_clusters.Rd |only man/check_gazepoint_performance_regression.Rd |only man/cluster_gazepoint_scanpaths.Rd |only man/compare_gazepoint_event_detectors.Rd |only man/construct_gazepoint_combined_pupil.Rd |only man/create_gazepoint_cross_package_report.Rd |only man/create_gazepoint_event_review_template.Rd |only man/detect_gazepoint_blinks.Rd |only man/detect_gazepoint_fixations_velocity.Rd |only man/diagnose_gazepoint_binocular_pupil.Rd |only man/downsample_gazepoint_pupil.Rd |only man/extract_gazepoint_representative_scanpaths.Rd |only man/fit_gazepoint_binocular_calibration.Rd |only man/gp3tools_naming_policy.Rd |only man/gp3tools_performance_limits.Rd |only man/interpolate_gazepoint_blinks.Rd |only man/mean_gazepoint_pupil.Rd |only man/plot_gazepoint_binocular_diagnostics.Rd |only man/plot_gazepoint_event_detector_agreement.Rd |only man/plot_gazepoint_event_detector_benchmark.Rd |only man/plot_gazepoint_scanpath_cluster_stability.Rd |only man/plot_gazepoint_scanpath_clusters.Rd |only man/prepare_gazepoint_gpbiometrics_bridge.Rd |only man/preprocess_gazepoint_signals.Rd |only man/reconstruct_gazepoint_binocular_pupil.Rd |only man/regress_gazepoint_pupils.Rd |only man/run_gazepoint_gpbiometrics_workflow.Rd |only man/select_gazepoint_scanpath_clusters.Rd |only man/simulate_gazepoint_fixations.Rd |only man/smooth_gazepoint_coordinate.Rd |only man/stress_test_gazepoint_binocular_reconstruction.Rd |only man/summarise_gazepoint_binocular_reporting.Rd |only man/summarise_gazepoint_coordinate_coverage.Rd |only man/summarise_gazepoint_event_detector_agreement.Rd |only man/summarise_gazepoint_event_detector_benchmark.Rd |only man/summarise_gazepoint_face_reactivity.Rd |only man/summarise_gazepoint_face_windows.Rd |only man/summarise_gazepoint_pupil_response_features.Rd |only man/summarise_gazepoint_scanpath_cluster_stability.Rd |only man/summarise_gazepoint_time_clusters.Rd |only man/validate_gazepoint_binocular_reconstruction.Rd |only man/write_gazepoint_naming_audit.Rd |only man/write_gazepoint_performance_benchmark.Rd |only tests/testthat/helper-binocular.R |only tests/testthat/test-advanced-aoi-assignment.R |only tests/testthat/test-binocular-pupil-plots.R |only tests/testthat/test-binocular-pupil-reconstruction.R |only tests/testthat/test-binocular-pupil-validation.R |only tests/testthat/test-event-detector-benchmarking.R |only tests/testthat/test-event-detector-comparison.R |only tests/testthat/test-gpbiometrics-bridge.R |only tests/testthat/test-high-priority-signal-extensions.R |only tests/testthat/test-naming-compatibility-aliases.R |only tests/testthat/test-naming-policy.R |only tests/testthat/test-performance-benchmarking.R |only tests/testthat/test-scanpath-cluster-stability.R |only tests/testthat/test-scanpath-clustering-workflow.R |only tests/testthat/test-scanpath-clustering.R |only tests/testthat/test-signal-preprocessing-workflow.R |only 95 files changed, 405 insertions(+), 18 deletions(-)
Title: Generalized Least Squares with Measurement Error
Description: Performs linear regression with correlated predictors, responses and correlated measurement errors in predictors and responses, correcting for biased caused by these.
Author: Krzysztof Bartoszek [cre, aut, ths]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between GLSME versions 1.0.5 dated 2019-09-15 and 1.0.6 dated 2026-08-21
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ NAMESPACE | 6 +++++- inst/CITATION | 37 +++++++++++++------------------------ man/GLSME-package.Rd | 4 ++-- man/GLSME.Rd | 19 ++++++++++--------- man/GLSME.predict.Rd | 8 ++++---- 7 files changed, 46 insertions(+), 51 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
van Valkenhoef et al. (2012) <doi:10.1002/jrsm.1054>;
van Valkenhoef et al. (2015) <doi:10.1002/jrsm.1167>.
Author: Gert van Valkenhoef [aut, cre],
Joel Kuiper [aut]
Maintainer: Gert van Valkenhoef <gert@gertvv.nl>
Diff between gemtc versions 1.1-1 dated 2026-03-26 and 1.1-2 dated 2026-08-21
DESCRIPTION | 32 ++++++++++++++--------------- MD5 | 8 ++++--- R/inits.R | 10 ++++----- R/rtruncnorm.R |only tests/testthat/test-rturncnorm.R |only tests/testthat/test-unit-relative.effect.R | 11 +++------ 6 files changed, 30 insertions(+), 31 deletions(-)
Title: Create, Optimize, and Refine Data Nuggets
Description: Creating, optimizing and refining data nuggets.
Data nuggets reduce a large dataset into a small collection of nuggets of
data, each containing a center (location), weight (importance), and scale
(variability) parameter. Data nugget centers are selected based on a
space-filling maximum-entropy scheme. Data nugget weights are created by
counting the number observations closest to a given data nugget center.
We then say the data nugget 'contains' these observations and the data
nugget center is recalculated as the mean of these observations. Data nugget
scales are created by calculating the trace of the covariance matrix of the
observations contained within a data nugget divided by the dimension of the
dataset. The optimal number of data nuggets is determined data-driven based
on the relative second-order differences of propensity score indices. Data
nuggets are refined by 'splitting' data nuggets which have high scales or
elongated shapes (defined as the ratio of the two largest eigenva [...truncated...]
Author: Rituparna Dey [aut, cre],
Yajie Duan [aut],
Traymon Beavers [aut],
Javier Cabrera [aut],
Ge Cheng [aut],
Kunting Qi [aut],
Mariusz Lubomirski [aut]
Maintainer: Rituparna Dey <rituparnadey525@gmail.com>
Diff between datanugget versions 1.4.0 dated 2025-12-04 and 1.5.0 dated 2026-08-21
datanugget-1.4.0/datanugget/R/createDN.R |only datanugget-1.4.0/datanugget/R/create_refine.DN.R |only datanugget-1.4.0/datanugget/R/refineDN.R |only datanugget-1.4.0/datanugget/man/create_refine.DN.Rd |only datanugget-1.5.0/datanugget/DESCRIPTION | 44 +++-- datanugget-1.5.0/datanugget/MD5 | 26 +-- datanugget-1.5.0/datanugget/NAMESPACE | 6 datanugget-1.5.0/datanugget/R/create.DN.R |only datanugget-1.5.0/datanugget/R/create.DNcenters.R | 144 ++++++++++++------ datanugget-1.5.0/datanugget/R/getDN.means.R | 10 - datanugget-1.5.0/datanugget/R/optimal.DN.R |only datanugget-1.5.0/datanugget/R/refine.DN.R |only datanugget-1.5.0/datanugget/man/create.DN.Rd | 18 +- datanugget-1.5.0/datanugget/man/create.DNcenters.Rd | 2 datanugget-1.5.0/datanugget/man/datanugget-package.Rd | 4 datanugget-1.5.0/datanugget/man/getDN.means.Rd | 2 datanugget-1.5.0/datanugget/man/optimal.DN.Rd |only datanugget-1.5.0/datanugget/man/refine.DN.Rd | 71 ++++---- 18 files changed, 194 insertions(+), 133 deletions(-)
Title: Analysis of Semi-Competing Risks Data Using Copula-Based Models
Description: Simulate and analyze Semi-competing Risks Data using
copula-based models. The Semi-competing Risks Data consist of a
terminal event time and single or multiple intermediate event times.
The marginal survival functions of these event times are estimated
without parametric assumptions. The association parameters measuring dependency
among these event times involving the copula model are yielded from
solving a concordance estimating equations or maximizing a
pseudo-likelihood function. Details can be found in the article by
Tonghui Yu and Liming Xiang (2026) <doi:10.1093/biomtc/ujag087>.
Author: Tonghui Yu [aut, cre],
Binhui Zhang [aut]
Maintainer: Tonghui Yu <tonghui_yu@126.com>
Diff between CopulaSCR versions 1.0.1 dated 2026-06-12 and 1.0.2 dated 2026-08-21
DESCRIPTION | 14 +- MD5 | 86 ++++++++++------- NAMESPACE | 22 ++++ R/CalCopula.R | 2 R/CopulaSCR-package.R | 2 R/accessors.R |only R/data-doc.R | 32 +++++- R/mscr.R | 16 ++- R/plot.R | 210 +++++++++++++++++++++++++++++++++++++++++- R/plotBS.R | 29 +++-- R/predict.R | 75 +++++++++++---- R/predictscr.R | 122 ++++++++++++++++-------- R/print.R | 6 - R/scrasso.R | 20 ++-- R/scrsurv.R | 41 +++++--- R/simSCRnp.R | 4 R/simmulSCR.R | 3 R/summary.R | 191 +++++++++++++++++++++++++++++++++++++- build |only data/mimiv_demo.rda |only man/CopulaSCR-package.Rd | 2 man/SCRdata.Rd | 2 man/SCRdata_by_tr.Rd | 2 man/association_estimates.Rd |only man/brier_scores.Rd |only man/dyBS.Rd | 18 ++- man/integrated_brier_score.Rd |only man/logLik.mscr.Rd |only man/mSCRdata.Rd | 2 man/marginal_fit.Rd |only man/mimiv_demo.Rd |only man/mscr.Rd | 14 +- man/plot.mscr.Rd | 4 man/plot.scrassonp.Rd |only man/plot.scrsurv.Rd | 4 man/predict.mscr.Rd | 17 +-- man/predict.scrsurv.Rd | 12 +- man/predicted_values.Rd |only man/predictscr.Rd | 31 +++--- man/print.mscr.Rd | 2 man/print.scrassonp.Rd | 2 man/print.scrsurv.Rd | 2 man/scrassonp.Rd | 16 +-- man/scrsurv.Rd | 18 +-- man/simSCR.Rd | 2 man/simSCRmul.Rd | 2 man/simSCRtr.Rd | 2 man/summary.mscr.Rd |only man/summary.scrassonp.Rd | 2 man/summary.scrsurv.Rd |only man/terminal_survival.Rd |only 51 files changed, 799 insertions(+), 232 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data--based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k--NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv. [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 8.2 dated 2026-05-23 and 8.3 dated 2026-08-21
DESCRIPTION | 12 ++++++------ MD5 | 38 ++++++++++++++++++++++---------------- NAMESPACE | 2 +- R/bic.mixcompnorm.R | 4 +++- R/bic.mixdiri.R |only R/diri.reg.R | 2 +- R/diri.reg.irls.R |only R/fd.contour.R | 5 ----- R/mix.diri.R |only R/ternary.R | 4 ++-- R/zadr.R | 13 +++++++++---- R/zadr.irls.R |only man/Compositional-package.Rd | 4 ++-- man/bic.alfamixnorm.Rd | 2 +- man/bic.mixcompnorm.Rd | 9 ++++++--- man/bic.mixdiri.Rd |only man/diri.reg.Rd | 18 +++++++++++++++--- man/mix.diri.Rd |only man/probout.Rd | 13 ++++++------- man/tflr.Rd | 4 ++-- man/tflr.betest.Rd | 4 ++-- man/tflr.indeptest.Rd | 4 ++-- man/zadr.Rd | 12 ++++++++++++ 23 files changed, 92 insertions(+), 58 deletions(-)
Title: Oncology Extension Package for ADaM in 'R' Asset Library
Description: Programming oncology specific 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>). The package is
an extension package of the 'admiral' package.
Author: Stefan Bundfuss [aut, cre],
Amit Jain [aut],
Vinh Nguyen [aut],
Olga Starostecka [aut],
Kiran Peddamudium [aut],
Tomoyuki Namai [aut],
Ross Farrugia [aut],
Yirong Cao [ctb],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [cph, fnd],
Bristol [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@external.roche.com>
Diff between admiralonco versions 1.4.1 dated 2026-05-21 and 1.5.0 dated 2026-08-21
DESCRIPTION | 16 - MD5 | 64 ++-- NAMESPACE | 140 ++++---- NEWS.md | 14 R/admiralonco-package.R | 25 - R/tte_sources.R | 2 README.md | 12 build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/admiralonco.html | 8 inst/doc/adrs_basic.html | 34 +- inst/doc/adrs_gcig.Rmd | 2 inst/doc/adrs_gcig.html | 114 +++---- inst/doc/adrs_imwg.R | 2 inst/doc/adrs_imwg.Rmd | 2 inst/doc/adrs_imwg.html | 20 - inst/doc/adrs_lymphoma.R |only inst/doc/adrs_lymphoma.Rmd |only inst/doc/adrs_lymphoma.html |only inst/doc/adrs_pcwg3.Rmd | 2 inst/doc/adrs_pcwg3.html | 112 +++---- inst/doc/adtr.R | 4 inst/doc/adtr.Rmd | 6 inst/doc/adtr.html | 12 inst/doc/adtte.R | 127 +++++--- inst/doc/adtte.Rmd | 158 ++++++--- inst/doc/adtte.html | 696 ++++++++++++++++++++++++++++---------------- inst/templates/ad_adtr.R | 4 man/admiralonco-package.Rd | 2 vignettes/adrs_gcig.Rmd | 2 vignettes/adrs_imwg.Rmd | 2 vignettes/adrs_lymphoma.Rmd |only vignettes/adrs_pcwg3.Rmd | 2 vignettes/adtr.Rmd | 6 vignettes/adtte.Rmd | 158 ++++++--- 35 files changed, 1058 insertions(+), 696 deletions(-)
Title: Tidy, 'ggplot2'-Native Visualization for Genomic Variants
Description: A simple, opinionated toolkit for visualizing genomic variant
data using a 'ggplot2'-native grammar. Accepts VCF files or plain data
frames and produces lollipop plots, consequence summaries, mutational
spectrum charts, and cohort-level comparisons as standard 'ggplot2'
objects. Designed for both wet-lab biologists and experienced
bioinformaticians.
Author: Joash Joshua Ayo [aut, cre]
Maintainer: Joash Joshua Ayo <joashjoshua789@gmail.com>
Diff between ggvariant versions 0.1.0 dated 2026-02-27 and 0.2.0 dated 2026-08-21
ggvariant-0.1.0/ggvariant/inst/doc/introduction-to-ggvariant.R |only ggvariant-0.1.0/ggvariant/inst/doc/introduction-to-ggvariant.Rmd |only ggvariant-0.1.0/ggvariant/inst/doc/introduction-to-ggvariant.html |only ggvariant-0.1.0/ggvariant/vignettes/introduction-to-ggvariant.Rmd |only ggvariant-0.2.0/ggvariant/DESCRIPTION | 23 ggvariant-0.2.0/ggvariant/MD5 | 74 - ggvariant-0.2.0/ggvariant/NAMESPACE | 11 ggvariant-0.2.0/ggvariant/NEWS.md |only ggvariant-0.2.0/ggvariant/R/ggvariant-package.R | 19 ggvariant-0.2.0/ggvariant/R/gvf-methods.R |only ggvariant-0.2.0/ggvariant/R/plot_functions.R | 545 ++++---- ggvariant-0.2.0/ggvariant/R/plot_lollipop.R | 395 +++--- ggvariant-0.2.0/ggvariant/R/plot_oncoprint.R |only ggvariant-0.2.0/ggvariant/R/plot_tmb.R |only ggvariant-0.2.0/ggvariant/R/read_vcf.R | 653 +++++----- ggvariant-0.2.0/ggvariant/R/utils.R | 34 ggvariant-0.2.0/ggvariant/README.md | 232 +-- ggvariant-0.2.0/ggvariant/build/partial.rdb |only ggvariant-0.2.0/ggvariant/build/vignette.rds |binary ggvariant-0.2.0/ggvariant/inst/CITATION |only ggvariant-0.2.0/ggvariant/inst/REFERENCES.bib |only ggvariant-0.2.0/ggvariant/inst/doc/ggvariant.R |only ggvariant-0.2.0/ggvariant/inst/doc/ggvariant.Rmd |only ggvariant-0.2.0/ggvariant/inst/doc/ggvariant.html |only ggvariant-0.2.0/ggvariant/man/coerce_variants.Rd | 139 +- ggvariant-0.2.0/ggvariant/man/figures |only ggvariant-0.2.0/ggvariant/man/ggvariant-package.Rd | 56 ggvariant-0.2.0/ggvariant/man/gv_palette.Rd | 54 ggvariant-0.2.0/ggvariant/man/gvf-methods.Rd |only ggvariant-0.2.0/ggvariant/man/plot_consequence_summary.Rd | 134 +- ggvariant-0.2.0/ggvariant/man/plot_lollipop.Rd | 172 +- ggvariant-0.2.0/ggvariant/man/plot_oncoprint.Rd |only ggvariant-0.2.0/ggvariant/man/plot_tmb.Rd |only ggvariant-0.2.0/ggvariant/man/plot_variant_spectrum.Rd | 148 +- ggvariant-0.2.0/ggvariant/man/read_vcf.Rd | 118 + ggvariant-0.2.0/ggvariant/tests/testthat/_snaps |only ggvariant-0.2.0/ggvariant/tests/testthat/test-coerce-variants.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-core.R | 29 ggvariant-0.2.0/ggvariant/tests/testthat/test-gvf-methods.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-parse-ann-csq.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-pivot-samples-genotype.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-plot-consequence-summary.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-plot-lollipop.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-plot-oncoprint.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-plot-tmb.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-plot-variant-spectrum.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-read-vcf-malformed.R |only ggvariant-0.2.0/ggvariant/tests/testthat/test-utils.R |only ggvariant-0.2.0/ggvariant/vignettes/ggvariant.Rmd |only 49 files changed, 1570 insertions(+), 1266 deletions(-)
Title: Visualization of 'exametrika' Output Using 'ggplot2'
Description: Provides 'ggplot2'-based visualization functions for output objects
from the 'exametrika' package, which implements test data engineering methods
described in Shojima (2022, ISBN:978-981-16-9547-1). Supports a wide range of
psychometric models including Item Response Theory, Latent Class Analysis,
Latent Rank Analysis, Biclustering (binary, ordinal, and nominal),
Bayesian Network Models, and related network models. All plot functions
return 'ggplot2' objects that can be further customized by the user.
Author: Koji Kosugi [aut, cre] ,
Daichi Kamimura [aut]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between ggExametrika versions 1.1.1 dated 2026-06-15 and 1.1.2 dated 2026-08-21
ggExametrika-1.1.1/ggExametrika/tests/testthat/Rplots.pdf |only ggExametrika-1.1.1/ggExametrika/tools |only ggExametrika-1.1.2/ggExametrika/DESCRIPTION | 8 ggExametrika-1.1.2/ggExametrika/MD5 | 75 - ggExametrika-1.1.2/ggExametrika/NAMESPACE | 3 ggExametrika-1.1.2/ggExametrika/NEWS.md | 170 ++ ggExametrika-1.1.2/ggExametrika/R/Biclustering.R | 352 +---- ggExametrika-1.1.2/ggExametrika/R/GRM.R | 67 ggExametrika-1.1.2/ggExametrika/R/ICCtoTIC.R | 167 -- ggExametrika-1.1.2/ggExametrika/R/IRPtoCMPRMP.R | 693 ++-------- ggExametrika-1.1.2/ggExametrika/R/LRAordinal.R | 369 +---- ggExametrika-1.1.2/ggExametrika/R/PolyBiclustering.R | 52 ggExametrika-1.1.2/ggExametrika/R/ScoreField.R | 21 ggExametrika-1.1.2/ggExametrika/R/ScoreRank.R | 27 ggExametrika-1.1.2/ggExametrika/R/arraytoLDPSR.R | 65 ggExametrika-1.1.2/ggExametrika/R/option.R | 14 ggExametrika-1.1.2/ggExametrika/R/plotDistractor_gg.R | 21 ggExametrika-1.1.2/ggExametrika/R/plotFCBR_gg.R | 18 ggExametrika-1.1.2/ggExametrika/R/plotGraph_gg.R | 11 ggExametrika-1.1.2/ggExametrika/R/plotLDPSR_gg.R | 10 ggExametrika-1.1.2/ggExametrika/R/utils-internal.R |only ggExametrika-1.1.2/ggExametrika/R/zzz.R | 8 ggExametrika-1.1.2/ggExametrika/README.md | 158 +- ggExametrika-1.1.2/ggExametrika/man/ItemInformationFunc_GRM.Rd | 15 ggExametrika-1.1.2/ggExametrika/man/dot-apply_legend.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-axis_scaler.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-plot_item_category.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-plot_membership_profile.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-plot_reference_vector.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-plot_student_distribution.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-resolve_colors.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-resolve_title.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-validate_exametrika.Rd |only ggExametrika-1.1.2/ggExametrika/man/dot-variable_scaler.Rd |only ggExametrika-1.1.2/ggExametrika/man/plotArray_gg.Rd | 6 ggExametrika-1.1.2/ggExametrika/man/plotCRV_gg.Rd | 7 ggExametrika-1.1.2/ggExametrika/man/plotICBR_gg.Rd | 8 ggExametrika-1.1.2/ggExametrika/man/plotICRF_gg.Rd | 2 ggExametrika-1.1.2/ggExametrika/man/plotICRP_gg.Rd | 6 ggExametrika-1.1.2/ggExametrika/man/plotRRV_gg.Rd | 7 ggExametrika-1.1.2/ggExametrika/man/plotScoreFreq_gg.Rd | 2 ggExametrika-1.1.2/ggExametrika/man/plotScoreRank_gg.Rd | 2 ggExametrika-1.1.2/ggExametrika/tests/testthat/helper-setup.R | 29 ggExametrika-1.1.2/ggExametrika/tests/testthat/test-DAG-plots.R | 6 ggExametrika-1.1.2/ggExametrika/tests/testthat/test-fixtures.R |only ggExametrika-1.1.2/ggExametrika/tests/testthat/test-utility-functions.R |only 46 files changed, 957 insertions(+), 1442 deletions(-)
Title: G-Functions
Description: Modified versions of the lag() and summary() functions: glag() and gsummary(). The prefix 'g' is a reminder of who to blame if things do not work as they should.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between gfunctions versions 1.1 dated 2025-07-23 and 1.2 dated 2026-08-21
DESCRIPTION | 8 - MD5 | 10 +- NEWS | 16 +++ R/gfunctions-source-code.R | 189 +++++++++++++++++++-------------------------- man/gfunctions-package.Rd | 4 man/gsummary.Rd | 8 + 6 files changed, 114 insertions(+), 121 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.2.7 dated 2026-07-29 and 2.2.8 dated 2026-08-21
DESCRIPTION | 17 MD5 | 241 - NAMESPACE | 15 R/BivariateUtils.R |only R/BuildInfo.R |only R/CVUtils.R |only R/CoordinateValidation.R |only R/Geo3DUtils.R |only R/GeoAniso.R | 125 R/GeoCV.R | 967 +++--- R/GeoCompositeLik.r | 37 R/GeoCompositeLik2.R | 333 +- R/GeoCorrFct.r | 526 +-- R/GeoCorrFct_Cop.R | 388 -- R/GeoCovDisplay.R | 493 +++ R/GeoCovariogram.r | 933 ++++-- R/GeoCovmatrix.r | 387 +- R/GeoDistances.R | 216 + R/GeoDoScores.R | 144 R/GeoFit.R | 591 +++ R/GeoFit2.R | 101 R/GeoIndCompositeLik2.R | 28 R/GeoKrig.r | 2243 ++++++++------ R/GeoKrigWeights.R | 147 R/GeoKrigloc.R | 609 ++- R/GeoKriglocWeights.R | 996 ++++-- R/GeoLik.r | 103 R/GeoNA.R | 18 R/GeoNeighIndex.R | 241 + R/GeoNeighbSelect.R | 578 ++- R/GeoNeighborhood.R | 1157 +++++-- R/GeoPit.R | 523 +-- R/GeoQQ.R | 212 - R/GeoResiduals.r | 189 - R/GeoScatterplot.R | 2444 +++++++++++++++ R/GeoScores.R | 373 +- R/GeoSim.r | 896 +---- R/GeoSimCopula.R | 421 +- R/GeoSimapprox.r | 966 +++--- R/GeoSimcond.R | 2384 ++++----------- R/GeoSpoutlier.R | 209 - R/GeoTest.r | 501 ++- R/GeoTestIndependence.R | 231 - R/GeoTestIsotropy.R | 779 ++--- R/GeoTestsupp_space.R | 247 - R/GeoVarest.R | 1166 +++++-- R/GeoVarestbootstrap.R | 942 +++--- R/GeoVariogram.r | 1565 ++++++---- R/GeoVariogramDir.R | 23 R/GeoWls.r | 663 ++-- R/KrigUtils.R |only R/MarginalUtils.R |only R/MeanUtils.R |only R/Optimize1D.R |only R/ParallelUtils.R |only R/SimCE.R | 543 ++- R/SimcondUtils.R |only R/SimulationUtils.R |only R/TB.R | 107 R/TestUtils.R |only R/Utility.r | 611 +++ R/Utility_cov.R | 2124 +++++++++++++ R/VarestUtils.R |only R/sp2Geo.R | 4 man/CkInput.Rd | 6 man/CkType.Rd | 6 man/CompIndLik2.Rd | 4 man/CompLik.Rd | 3 man/CompLik2.Rd | 4 man/GeoCV.Rd | 77 man/GeoCorrFct.Rd | 9 man/GeoCorrFct_Cop.Rd | 136 man/GeoCovariogram.Rd | 127 man/GeoCovmatrix.Rd | 69 man/GeoDosocores.Rd | 19 man/GeoFit.Rd | 124 man/GeoFit2.Rd | 74 man/GeoKrig.Rd | 239 + man/GeoKrigWeights.Rd | 93 man/GeoKrigloc.Rd | 183 - man/GeoKriglocWeights.Rd | 114 man/GeoModels-3D.Rd |only man/GeoModels-spacetime-ordering.Rd |only man/GeoNA.Rd | 20 man/GeoNeighIndex.Rd | 252 - man/GeoNeighbSelect.Rd | 146 man/GeoNeighborhood.Rd | 21 man/GeoOutlier.Rd | 37 man/GeoPit.Rd | 132 man/GeoQQ.Rd | 12 man/GeoResiduals.Rd | 42 man/GeoScatterplot.Rd | 489 ++- man/GeoScores.Rd | 215 - man/GeoSim.Rd | 130 man/GeoSimCopula.Rd | 102 man/GeoSimapprox.Rd | 153 man/GeoSimcond.Rd | 256 + man/GeoTestIndependence.Rd | 11 man/GeoTestIsotropy.Rd | 233 - man/GeoTestsupp_space.Rd | 11 man/GeoVarest.Rd | 39 man/GeoVarestbootstrap.Rd | 54 man/GeoVariogram.Rd | 158 - man/GeoWls.Rd | 50 man/GeovariogramDir.Rd | 7 man/Lik.Rd | 4 man/SimCE.Rd | 54 man/StartParam.Rd | 6 man/WlsStart.Rd | 6 man/plot.GeoVariogram.Rd | 12 man/sp2Geo.Rd | 11 src/2gammainc.c | 17 src/2kummer.c | 156 - src/CompositeLikelihood2.c | 899 +---- src/CompositeLikelihood2_ani.c | 382 +- src/CompositeLikelihoodCond2.c | 439 +- src/CompositeLikelihoodCond2_ani.c | 197 - src/CorrelationFunction.c | 1432 ++++++--- src/Distributions.c | 5578 +++++++++++++++++++++++------------- src/DuplicateCoordinates.c |only src/GeoBivDensity.c |only src/GeoModels_init.c | 200 + src/KrigSolve.c |only src/PairCache.c |only src/TB.c | 162 - src/Utility.c | 503 --- src/clayton_gibbs.c |only src/count_conditional_gibbs.c |only src/covariance_series.c |only src/gamma_gibbs.c | 34 src/header.h | 166 - src/skewgaussian_gibbs.c | 28 src/weightedleastsquare.c | 546 ++- 133 files changed, 28381 insertions(+), 16065 deletions(-)
Title: Exact Tree
Description: Grows optimally global trees based on the algorithm defined in the thesis by van Os, B.J. (2001, ISBN:9789090144795). It is possible to obtain both classification and regression trees depending on the measurement level of the outcome variable. The algorithm is based on the dynamic programming principle and guarantees that the resulting tree is optimal with respect to the chosen impurity measure. The package also includes a function to visualize the resulting trees, a function that summarizes the tree with its splitting information and leaf information, and a predict function that provides estimates for a new dataset given a model fit.
Author: Juan Claramunt Gonzalez [aut, cre, cph],
Bart Jan van Os [aut],
Elise Dusseldorp [aut]
Maintainer: Juan Claramunt Gonzalez <j.claramunt.gonzalez@fsw.leidenuniv.nl>
Diff between ExactTree versions 0.1.1 dated 2026-08-07 and 0.1.2 dated 2026-08-21
ExactTree-0.1.1/ExactTree/src/Timer.f95 |only ExactTree-0.1.2/ExactTree/DESCRIPTION | 10 +++++----- ExactTree-0.1.2/ExactTree/MD5 | 17 ++++++++--------- ExactTree-0.1.2/ExactTree/R/ETree.R | 1 + ExactTree-0.1.2/ExactTree/R/SelectVar.R | 4 ++++ ExactTree-0.1.2/ExactTree/R/plot.ETree.R | 6 ++---- ExactTree-0.1.2/ExactTree/src/Makevars | 7 +++---- ExactTree-0.1.2/ExactTree/src/Makevars.win | 7 +++---- ExactTree-0.1.2/ExactTree/src/OptimalTrees.f95 | 10 +++++----- ExactTree-0.1.2/ExactTree/src/init.c | 4 ++-- 10 files changed, 33 insertions(+), 33 deletions(-)
Title: Download and Process Environmental Variables
Description: Provides a unified interface to download, harmonise and extract a
wide range of environmental and socio-economic variables from established
open data web services (such as 'WorldClim' <https://www.worldclim.org/>,
'CHELSA' <https://chelsa-climate.org/> and 'Bio-ORACLE'
<https://www.bio-oracle.org/>, among others) for use in macroecology and
biogeography. The package handles
spatial subsetting to a study area, reprojection to a common coordinate
reference system, and extraction of values at sampling points, so that
predictors from heterogeneous sources can be assembled within a single
reproducible workflow. Helper functions for collinearity checking and
variable exploration are also included.
Author: Andrea Simoncini [aut, cre] ,
Michele Bertoncini [aut] ,
Andrea Cerofolini [aut] ,
Andrea Dalpasso [aut] ,
Mattia Falaschi [aut] ,
Gentile Francesco Ficetola [aut] ,
Elia Lo Parrino [aut]
Maintainer: Andrea Simoncini <simonciniandre@gmail.com>
Diff between envar versions 0.1.0 dated 2026-07-31 and 0.1.1 dated 2026-08-21
DESCRIPTION | 6 MD5 | 320 - NAMESPACE | 72 NEWS.md | 50 R/accessibility.R | 820 +-- R/aridity.R | 926 +-- R/biooracle.R | 638 +- R/cache_utils.R | 196 R/chelsa.R | 1496 +++--- R/cleanup_temp.R | 16 R/climatezones.R | 880 +-- R/cloudcover.R | 818 +-- R/corr_check.R | 693 +- R/create_target_grid.R | 80 R/data.R | 82 R/download_file.R | 178 R/download_file_figshare.R | 215 R/earthenvlandcover.R | 768 +-- R/envar-package.R | 23 R/extr_check.R | 1022 ++-- R/extract_layer_name.R | 38 R/freshwater.R | 972 ++-- R/gcamlandcover.R | 796 +-- R/gdppast.R | 908 +-- R/geososlandcover.R | 810 +-- R/get_par.R | 454 - R/habitat.R | 1118 ++-- R/heterogeneity.R | 832 +-- R/hybridlandcover.R | 772 +-- R/melc.R | 840 +-- R/metadata.R |only R/par_set.R | 983 ++-- R/pftlandcover.R | 946 ++-- R/population.R | 812 +-- R/process_extent.R | 2560 +++++----- R/process_points.R | 92 R/process_raster_layer.R | 560 +- R/protection.R | 768 +-- R/provenance.R |only R/roads.R |only R/soil.R | 806 +-- R/soilclimate.R | 914 +-- R/spectre.R | 822 +-- R/ssp_rcp.R | 122 R/topography.R | 828 +-- R/utils-pipe.R | 32 R/validate_helpers.R | 150 R/worldclim.R | 1042 ++-- R/zzz.R | 12 README.md | 314 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 inst/doc/intro.Rmd | 406 - inst/doc/intro.html | 1381 ++--- inst/doc/package_overview.Rmd | 2136 ++++----- inst/doc/package_overview.html | 3097 ++++++------- inst/doc/sdm.Rmd | 646 +- inst/doc/sdm.html | 1615 +++--- inst/doc/variables.Rmd | 2490 +++++----- inst/doc/variables.html | 4016 ++++++++--------- man/Alps.Rd | 50 man/Apollo.Rd | 50 man/Europe.Rd | 46 man/accessibility.Rd | 132 man/aridity.Rd | 114 man/biooracle.Rd | 196 man/chelsa.Rd | 438 - man/clear_cache.Rd | 43 man/climatezones.Rd | 154 man/cloudcover.Rd | 146 man/corr_check.Rd | 197 man/earthenvlandcover.Rd | 120 man/envar-package.Rd | 72 man/extr_check.Rd | 208 man/figures/Fig1.png |binary man/figures/logo.png |binary man/freshwater.Rd | 220 man/gcamlandcover.Rd | 150 man/gdppast.Rd | 124 man/geososlandcover.Rd | 124 man/habitat.Rd | 160 man/heterogeneity.Rd | 130 man/hybridlandcover.Rd | 94 man/melc.Rd | 132 man/metadata.Rd |only man/par_set.Rd | 587 +- man/pftlandcover.Rd | 104 man/pipe.Rd | 44 man/population.Rd | 100 man/protection.Rd | 112 man/roads.Rd |only man/soil.Rd | 90 man/soilclimate.Rd | 150 man/spectre.Rd | 162 man/topography.Rd | 138 man/worldclim.Rd | 186 vignettes/figs/intro-unnamed-chunk-11-1.png |binary vignettes/figs/intro-unnamed-chunk-6-1.png |binary vignettes/figs/package_overview-unnamed-chunk-12-1.png |binary vignettes/figs/package_overview-unnamed-chunk-14-1.png |binary vignettes/figs/package_overview-unnamed-chunk-16-1.png |binary vignettes/figs/package_overview-unnamed-chunk-18-1.png |binary vignettes/figs/package_overview-unnamed-chunk-20-1.png |binary vignettes/figs/package_overview-unnamed-chunk-22-1.png |binary vignettes/figs/package_overview-unnamed-chunk-24-1.png |binary vignettes/figs/package_overview-unnamed-chunk-26-1.png |binary vignettes/figs/package_overview-unnamed-chunk-28-1.png |binary vignettes/figs/package_overview-unnamed-chunk-30-1.png |binary vignettes/figs/package_overview-unnamed-chunk-32-1.png |binary vignettes/figs/package_overview-unnamed-chunk-34-1.png |binary vignettes/figs/package_overview-unnamed-chunk-36-1.png |binary vignettes/figs/package_overview-unnamed-chunk-38-1.png |binary vignettes/figs/package_overview-unnamed-chunk-40-1.png |binary vignettes/figs/package_overview-unnamed-chunk-42-1.png |binary vignettes/figs/package_overview-unnamed-chunk-46-1.png |binary vignettes/figs/package_overview-unnamed-chunk-5-1.png |binary vignettes/figs/package_overview-unnamed-chunk-51-1.png |binary vignettes/figs/package_overview-unnamed-chunk-53-1.png |binary vignettes/figs/package_overview-unnamed-chunk-56-1.png |binary vignettes/figs/package_overview-unnamed-chunk-58-1.png |binary vignettes/figs/package_overview-unnamed-chunk-60-1.png |binary vignettes/figs/package_overview-unnamed-chunk-62-1.png |binary vignettes/figs/package_overview-unnamed-chunk-64-1.png |binary vignettes/figs/package_overview-unnamed-chunk-66-1.png |binary vignettes/figs/package_overview-unnamed-chunk-7-1.png |binary vignettes/figs/package_overview-unnamed-chunk-76-1.png |binary vignettes/figs/package_overview-unnamed-chunk-80-1.png |binary vignettes/figs/package_overview-unnamed-chunk-82-1.png |binary vignettes/figs/package_overview-unnamed-chunk-9-1.png |binary vignettes/figs/sdm-unnamed-chunk-16-1.png |binary vignettes/figs/sdm-unnamed-chunk-7-1.png |binary vignettes/figs/variables-roads-plot-1.png |only vignettes/figs/variables-unnamed-chunk-10-1.png |binary vignettes/figs/variables-unnamed-chunk-12-1.png |binary vignettes/figs/variables-unnamed-chunk-14-1.png |binary vignettes/figs/variables-unnamed-chunk-16-1.png |binary vignettes/figs/variables-unnamed-chunk-18-1.png |binary vignettes/figs/variables-unnamed-chunk-20-1.png |binary vignettes/figs/variables-unnamed-chunk-22-1.png |binary vignettes/figs/variables-unnamed-chunk-24-1.png |binary vignettes/figs/variables-unnamed-chunk-26-1.png |binary vignettes/figs/variables-unnamed-chunk-28-1.png |binary vignettes/figs/variables-unnamed-chunk-30-1.png |binary vignettes/figs/variables-unnamed-chunk-32-1.png |binary vignettes/figs/variables-unnamed-chunk-34-1.png |binary vignettes/figs/variables-unnamed-chunk-36-1.png |binary vignettes/figs/variables-unnamed-chunk-38-1.png |binary vignettes/figs/variables-unnamed-chunk-40-1.png |binary vignettes/figs/variables-unnamed-chunk-42-1.png |binary vignettes/figs/variables-unnamed-chunk-44-1.png |binary vignettes/figs/variables-unnamed-chunk-48-1.png |binary vignettes/figs/variables-unnamed-chunk-5-1.png |binary vignettes/figs/variables-unnamed-chunk-50-1.png |binary vignettes/figs/variables-unnamed-chunk-8-1.png |binary vignettes/images/Corr_plot_apollo.png |binary vignettes/images/Corr_plot_example.png |binary vignettes/images/Prediction.png |binary vignettes/intro.Rmd | 406 - vignettes/package_overview.Rmd | 2136 ++++----- vignettes/reference-style.csl | 402 - vignettes/references.bib | 870 +-- vignettes/sdm.Rmd | 646 +- vignettes/variables.Rmd | 2490 +++++----- 164 files changed, 28365 insertions(+), 27785 deletions(-)
Title: Objects for Predicting Energy Expenditure
Description: This is a data-only package containing model objects that predict
human energy expenditure from wearable sensor data. Supported methods include
the neural networks of Montoye et al. (2017) <doi:10.1080/1091367X.2017.1337638>
and the models of Staudenmayer et al. (2015) <doi:10.1152/japplphysiol.00026.2015>,
one a linear model and the other a random forest. The package is intended as
a spoke for the hub-package 'accelEE', which brings together the above methods
and others from packages such as 'Sojourn' and 'TwoRegression.'
Author: Paul R. Hibbing [aut, cre],
Alexander H.K. Montoye [ctb],
John Staudenmayer [ctb],
Children's Mercy Kansas City [cph]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between EE.Data versions 0.1.1 dated 2026-04-01 and 0.2.0 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/data_doc.R | 2 +- data/montoye_lw.rda |binary data/montoye_rw.rda |binary man/montoye.Rd | 4 ++-- 7 files changed, 20 insertions(+), 13 deletions(-)
Title: Tools for Dyadic Multilevel Models
Description: Provides tools for dyadic multilevel modeling with linear and
generalized linear mixed-effects models. It validates and prepares
long-format cross-sectional and intensive longitudinal data, including
ecological momentary assessment designs, for distinguishable and
exchangeable dyads. It also supports datasets containing multiple observed
dyad compositions. It constructs composition-aware,
model-ready variables for Actor-Partner Interdependence Models (APIMs),
Dyadic Score Models (DSMs), and Dyad-Individual Models (DIMs). Prepared data
can be used with model engines such as 'glmmTMB' and 'brms' for Gaussian and
non-Gaussian outcomes, including counts, proportions, and skewed continuous
responses. Post-estimation tools compare compatible fitted models and
back-transform exchangeable sum-and-difference random-effect covariance
structures into member-level quantities. The APIM and DSM specifications
and their relationships follow Iida et al. (2018)
<doi:10.1177/0265407517725407>; the [...truncated...]
Author: Pascal Kueng [aut, cre, cph]
Maintainer: Pascal Kueng <kueng.pascal@gmail.com>
Diff between dyadMLM versions 0.1.0 dated 2026-07-30 and 0.2.0 dated 2026-08-21
dyadMLM-0.1.0/dyadMLM/R/compare_dyad_models.R |only dyadMLM-0.1.0/dyadMLM/man/compare_nested_glmmTMB_models.Rd |only dyadMLM-0.1.0/dyadMLM/man/print.exchangeable_rescov.Rd |only dyadMLM-0.1.0/dyadMLM/tests/testthat/test-compare_dyad_models.R |only dyadMLM-0.2.0/dyadMLM/DESCRIPTION | 7 dyadMLM-0.2.0/dyadMLM/MD5 | 151 dyadMLM-0.2.0/dyadMLM/NAMESPACE | 5 dyadMLM-0.2.0/dyadMLM/NEWS.md | 64 dyadMLM-0.2.0/dyadMLM/R/add_actor_partner_columns.R | 15 dyadMLM-0.2.0/dyadMLM/R/add_dyad_individual_columns.R | 30 dyadMLM-0.2.0/dyadMLM/R/add_dyadic_score_columns.R | 25 dyadMLM-0.2.0/dyadMLM/R/add_temporal_lag_columns.R | 26 dyadMLM-0.2.0/dyadMLM/R/backtransform_residual_covariance.R | 167 - dyadMLM-0.2.0/dyadMLM/R/center_predictors.R | 66 dyadMLM-0.2.0/dyadMLM/R/compare_nested_models.R |only dyadMLM-0.2.0/dyadMLM/R/data.R | 22 dyadMLM-0.2.0/dyadMLM/R/dyad-generated-columns.R | 331 -- dyadMLM-0.2.0/dyadMLM/R/dyadMLM-package.R |only dyadMLM-0.2.0/dyadMLM/R/infer_dyad_compositions.R | 240 + dyadMLM-0.2.0/dyadMLM/R/prepare_dyad_data.R | 145 dyadMLM-0.2.0/dyadMLM/R/print_dyadMLM_data.R | 84 dyadMLM-0.2.0/dyadMLM/R/summary_dyadMLM_data.R |only dyadMLM-0.2.0/dyadMLM/R/temporary_dyad_occasion_completion.R |only dyadMLM-0.2.0/dyadMLM/R/utils-compositions.R | 49 dyadMLM-0.2.0/dyadMLM/R/validate_dyad_data.R | 39 dyadMLM-0.2.0/dyadMLM/README.md | 172 - dyadMLM-0.2.0/dyadMLM/data/dyads_cross.rda |binary dyadMLM-0.2.0/dyadMLM/data/dyads_ild.rda |binary dyadMLM-0.2.0/dyadMLM/data/dyads_nbinom_cross.rda |binary dyadMLM-0.2.0/dyadMLM/data/dyads_nbinom_ild.rda |binary dyadMLM-0.2.0/dyadMLM/inst/CITATION | 10 dyadMLM-0.2.0/dyadMLM/inst/WORDLIST | 9 dyadMLM-0.2.0/dyadMLM/inst/doc/apim.R | 337 +- dyadMLM-0.2.0/dyadMLM/inst/doc/apim.Rmd | 508 +-- dyadMLM-0.2.0/dyadMLM/inst/doc/apim.html | 1516 +++++----- dyadMLM-0.2.0/dyadMLM/inst/doc/dim.R | 71 dyadMLM-0.2.0/dyadMLM/inst/doc/dim.Rmd | 160 - dyadMLM-0.2.0/dyadMLM/inst/doc/dim.html | 634 ++-- dyadMLM-0.2.0/dyadMLM/inst/doc/dsm.R | 119 dyadMLM-0.2.0/dyadMLM/inst/doc/dsm.Rmd | 195 - dyadMLM-0.2.0/dyadMLM/inst/doc/dsm.html | 542 +-- dyadMLM-0.2.0/dyadMLM/inst/doc/getting-started.R | 41 dyadMLM-0.2.0/dyadMLM/inst/doc/getting-started.Rmd | 235 - dyadMLM-0.2.0/dyadMLM/inst/doc/getting-started.html | 1422 ++++----- dyadMLM-0.2.0/dyadMLM/man/add_actor_partner_columns.Rd | 4 dyadMLM-0.2.0/dyadMLM/man/add_temporal_lag_columns.Rd | 7 dyadMLM-0.2.0/dyadMLM/man/center_predictors.Rd | 5 dyadMLM-0.2.0/dyadMLM/man/compare_nested_models.Rd |only dyadMLM-0.2.0/dyadMLM/man/dyadMLM-package.Rd |only dyadMLM-0.2.0/dyadMLM/man/dyad_generated_columns.Rd | 12 dyadMLM-0.2.0/dyadMLM/man/dyads_cross.Rd | 4 dyadMLM-0.2.0/dyadMLM/man/dyads_ild.Rd | 10 dyadMLM-0.2.0/dyadMLM/man/dyads_nbinom_cross.Rd | 4 dyadMLM-0.2.0/dyadMLM/man/dyads_nbinom_ild.Rd | 4 dyadMLM-0.2.0/dyadMLM/man/infer_dyad_compositions.Rd | 23 dyadMLM-0.2.0/dyadMLM/man/prepare_dyad_data.Rd | 66 dyadMLM-0.2.0/dyadMLM/man/print.exchangeable_covariance.Rd |only dyadMLM-0.2.0/dyadMLM/man/recover_exchangeable_covariance.Rd | 33 dyadMLM-0.2.0/dyadMLM/man/restore_observed_dyad_rows.Rd |only dyadMLM-0.2.0/dyadMLM/man/summary.dyadMLM_data.Rd |only dyadMLM-0.2.0/dyadMLM/man/temporarily_complete_dyad_occasions.Rd |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-add_actor_partner_columns.R | 70 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-add_dyad_individual_columns.R | 67 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-add_dyadic_score_columns.R | 123 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-add_temporal_lag_columns.R | 108 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-apim-gmc-predictors.R |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-assign_arbitrary_member_roles.R | 26 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-backtransform-residual-covariance.R | 259 + dyadMLM-0.2.0/dyadMLM/tests/testthat/test-center_predictors.R | 28 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-compare_nested_models.R |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-dsm-model-equivalence.R |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-dyad_generated_columns.R | 205 + dyadMLM-0.2.0/dyadMLM/tests/testthat/test-example-data.R | 21 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-infer_dyad_compositions.R | 205 - dyadMLM-0.2.0/dyadMLM/tests/testthat/test-prepare_dyad_data.R | 315 +- dyadMLM-0.2.0/dyadMLM/tests/testthat/test-print-dyadMLM_data.R | 257 + dyadMLM-0.2.0/dyadMLM/tests/testthat/test-public-api-cleanup.R | 132 dyadMLM-0.2.0/dyadMLM/tests/testthat/test-summary-dyadMLM_data.R |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-temporary_dyad_occasion_completion.R |only dyadMLM-0.2.0/dyadMLM/tests/testthat/test-validate_dyad_data.R | 73 dyadMLM-0.2.0/dyadMLM/vignettes/apim.Rmd | 508 +-- dyadMLM-0.2.0/dyadMLM/vignettes/diagram-helpers.Rinc | 144 dyadMLM-0.2.0/dyadMLM/vignettes/dim.Rmd | 160 - dyadMLM-0.2.0/dyadMLM/vignettes/dsm.Rmd | 195 - dyadMLM-0.2.0/dyadMLM/vignettes/getting-started.Rmd | 235 - dyadMLM-0.2.0/dyadMLM/vignettes/references.bib | 440 ++ 86 files changed, 6833 insertions(+), 4347 deletions(-)
Title: Dynamic and Interactive EEG Graphics
Description: Allows to visualize high-density electroencephalography (HD-EEG) data through interactive plots and animations, enabling exploratory and communicative analysis of temporal-spatial brain signals. Funder: Masaryk University (Grant No. MUNI/A/1457/2023).
Author: Zdeňka Gerslova [aut, cre] ,
Stanislav Katina [rev] ,
Martin Lamos [ctb]
Maintainer: Zdeňka Gerslova <gerslovaz@math.muni.cz>
Diff between diegr versions 0.2.0 dated 2026-01-24 and 0.3.1 dated 2026-08-21
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Title: Toolkit for Analyzing Curricular Complexity
Description: Enables educational researchers and practitioners to calculate the curricular complexity of a plan of study, visualize its prerequisite structure at scale, and conduct customizable analyses. The original tool can be found at <https://curricularanalytics.org>. Additional functions to explore curriculum complexity from the literature are also included.
Author: David Reeping [aut, cre]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexity versions 1.0.3 dated 2026-07-08 and 1.1.0 dated 2026-08-21
DESCRIPTION | 6 MD5 | 18 + NEWS.md | 31 +++ R/generate_curricular_complexity_scorecard.R |only R/topic_cruciality.R |only build/vignette.rds |binary inst/doc/CurricularComplexity-demo.R | 45 ++++ inst/doc/CurricularComplexity-demo.Rmd | 87 +++++++++ inst/doc/CurricularComplexity-demo.html | 229 ++++++++++++++++++------ man/generate_curricular_complexity_scorecard.Rd |only man/topic_cruciality.Rd |only vignettes/CurricularComplexity-demo.Rmd | 87 +++++++++ 12 files changed, 435 insertions(+), 68 deletions(-)
More information about CurricularComplexity at CRAN
Permanent link
Title: R Interface for the RAPIDS cuML Suite of Libraries
Description: R interface for RAPIDS cuML (<https://github.com/NVIDIA/cuml>),
a suite of GPU-accelerated machine learning libraries powered by CUDA
(<https://en.wikipedia.org/wiki/CUDA>).
Author: Yitao Li [aut, cph] ,
Tomasz Kalinowski [aut, cre, cph],
Daniel Falbel [aut, cph],
RStudio [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between cuda.ml versions 0.3.3 dated 2026-04-29 and 0.4.0 dated 2026-08-21
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cuda.ml-0.4.0/cuda.ml/tests/testthat/test-runtime-functional.R |only cuda.ml-0.4.0/cuda.ml/tests/testthat/test-runtime-loader.R |only cuda.ml-0.4.0/cuda.ml/tests/testthat/test-sgd.R | 37 cuda.ml-0.4.0/cuda.ml/tests/testthat/test-source-install.R |only cuda.ml-0.4.0/cuda.ml/tests/testthat/test-svm-serde.R | 38 cuda.ml-0.4.0/cuda.ml/tests/testthat/test-svm.R | 113 - cuda.ml-0.4.0/cuda.ml/tests/testthat/test-tsne.R | 23 cuda.ml-0.4.0/cuda.ml/tests/testthat/test-tsvd.R | 110 + cuda.ml-0.4.0/cuda.ml/tests/testthat/test-umap.R | 14 cuda.ml-0.4.0/cuda.ml/tools/audit-backend.R |only cuda.ml-0.4.0/cuda.ml/tools/audit-nvforest-cpu-backend.R |only cuda.ml-0.4.0/cuda.ml/tools/config.R | 6 cuda.ml-0.4.0/cuda.ml/tools/config/Makefile.cmake.in |only cuda.ml-0.4.0/cuda.ml/tools/config/cleanup.R | 20 cuda.ml-0.4.0/cuda.ml/tools/config/configure.R | 302 ++- cuda.ml-0.4.0/cuda.ml/tools/config/utils/native-symbols.R |only cuda.ml-0.4.0/cuda.ml/tools/diff-api.R |only cuda.ml-0.4.0/cuda.ml/tools/merge-backend-lock.R |only cuda.ml-0.4.0/cuda.ml/tools/nvrtc-probe.c |only cuda.ml-0.4.0/cuda.ml/tools/package-backend.R |only cuda.ml-0.4.0/cuda.ml/tools/package-nvforest-cpu-backend.R |only cuda.ml-0.4.0/cuda.ml/vignettes |only 143 files changed, 5229 insertions(+), 3509 deletions(-)
Title: Statistical Tools for Ranks
Description: Account for uncertainty when working with ranks. Estimate
standard errors consistently in linear regression with ranked
variables. Construct confidence sets of various kinds for positions
of populations in a ranking based on values of a certain feature and
their estimation errors. Theory based on Mogstad, Romano, Shaikh, and
Wilhelm (2023)<doi:10.1093/restud/rdad006> and Chetverikov and Wilhelm
(2023) <doi:10.48550/arXiv.2310.15512>.
Author: Daniel Wilhelm [aut, cre],
Pawel Morgen [aut]
Maintainer: Daniel Wilhelm <d.wilhelm@lmu.de>
Diff between csranks versions 1.2.3 dated 2024-09-12 and 1.3.0 dated 2026-08-21
csranks-1.2.3/csranks/tests/testthat/testdata/generate_testdata.R |only csranks-1.3.0/csranks/DESCRIPTION | 36 csranks-1.3.0/csranks/MD5 | 144 ++- csranks-1.3.0/csranks/NAMESPACE | 16 csranks-1.3.0/csranks/NEWS.md | 7 csranks-1.3.0/csranks/R/argument_checks.R | 311 ++++-- csranks-1.3.0/csranks/R/data.R | 12 csranks-1.3.0/csranks/R/diffmeans.R | 91 +- csranks-1.3.0/csranks/R/formula_checks.R |only csranks-1.3.0/csranks/R/formula_parsing.R |only csranks-1.3.0/csranks/R/formula_processing.R |only csranks-1.3.0/csranks/R/ivregranks.R |only csranks-1.3.0/csranks/R/ivregranks_model_usage.R |only csranks-1.3.0/csranks/R/ivregranks_summary.R |only csranks-1.3.0/csranks/R/ivregranks_vcov.R |only csranks-1.3.0/csranks/R/lmranks.R | 383 +++----- csranks-1.3.0/csranks/R/lmranks_env.R |only csranks-1.3.0/csranks/R/lmranks_model_selection.R | 23 csranks-1.3.0/csranks/R/lmranks_model_usage.R | 20 csranks-1.3.0/csranks/R/lmranks_obs_influence.R | 32 csranks-1.3.0/csranks/R/lmranks_summary.R | 454 ++-------- csranks-1.3.0/csranks/R/plotranking.R | 41 csranks-1.3.0/csranks/R/rank_utils.R | 203 ++-- csranks-1.3.0/csranks/R/ranks.R | 113 +- csranks-1.3.0/csranks/R/ranks_multinom.R | 90 + csranks-1.3.0/csranks/R/utilityfunctions.R | 2 csranks-1.3.0/csranks/R/vcov_utils.R |only csranks-1.3.0/csranks/README.md | 1 csranks-1.3.0/csranks/build/partial.rdb |binary csranks-1.3.0/csranks/build/vignette.rds |binary csranks-1.3.0/csranks/inst/WORDLIST | 3 csranks-1.3.0/csranks/inst/doc/Inference-for-Ranks.R | 38 csranks-1.3.0/csranks/inst/doc/Inference-for-Ranks.html | 58 - csranks-1.3.0/csranks/inst/doc/Inference-for-Ranks.rmd | 40 csranks-1.3.0/csranks/inst/doc/Rank-Rank-Reg.R | 127 +- csranks-1.3.0/csranks/inst/doc/Rank-Rank-Reg.html | 347 +++---- csranks-1.3.0/csranks/inst/doc/Rank-Rank-Reg.rmd | 131 +- csranks-1.3.0/csranks/inst/vcov_edit.R |only csranks-1.3.0/csranks/man/csranks.Rd | 6 csranks-1.3.0/csranks/man/cstaubest.Rd | 10 csranks-1.3.0/csranks/man/irank.Rd | 35 csranks-1.3.0/csranks/man/irank_against.Rd | 24 csranks-1.3.0/csranks/man/ivregranks.Rd |only csranks-1.3.0/csranks/man/lmranks.Rd | 13 csranks-1.3.0/csranks/man/plotranking.Rd | 2 csranks-1.3.0/csranks/tests/setup.R | 4 csranks-1.3.0/csranks/tests/spelling.R | 9 csranks-1.3.0/csranks/tests/testthat/_problems |only csranks-1.3.0/csranks/tests/testthat/test_argument_checks.R | 260 +++-- csranks-1.3.0/csranks/tests/testthat/test_csranks_compare.R | 74 + csranks-1.3.0/csranks/tests/testthat/test_csranks_marg.R | 4 csranks-1.3.0/csranks/tests/testthat/test_csranks_multinom.R | 4 csranks-1.3.0/csranks/tests/testthat/test_diffmeans.R | 175 ++- csranks-1.3.0/csranks/tests/testthat/test_env.R |only csranks-1.3.0/csranks/tests/testthat/test_formula_processing.R |only csranks-1.3.0/csranks/tests/testthat/test_grouped_lmranks.R | 91 +- csranks-1.3.0/csranks/tests/testthat/test_grouped_lmranks_vcov.R | 322 +++---- csranks-1.3.0/csranks/tests/testthat/test_ivregranks.R |only csranks-1.3.0/csranks/tests/testthat/test_ivregranks_vcov.R |only csranks-1.3.0/csranks/tests/testthat/test_lmranks.R | 322 ++----- csranks-1.3.0/csranks/tests/testthat/test_lmranks_predict.R | 105 +- csranks-1.3.0/csranks/tests/testthat/test_lmranks_vcov.R | 392 +++----- csranks-1.3.0/csranks/tests/testthat/test_multinom_lowlevel.R | 254 +++-- csranks-1.3.0/csranks/tests/testthat/test_plotranking.R | 2 csranks-1.3.0/csranks/tests/testthat/test_rank_utils.R | 208 ++-- csranks-1.3.0/csranks/tests/testthat/test_utility_functions.R | 100 +- csranks-1.3.0/csranks/tests/testthat/test_vcov_utils.R |only csranks-1.3.0/csranks/tests/testthat/testdata/Markdown_vcov_sims.Rmd |only csranks-1.3.0/csranks/tests/testthat/testdata/generate_testdata_ivregranks.R |only csranks-1.3.0/csranks/tests/testthat/testdata/generate_testdata_ivregranks_empirical.R |only csranks-1.3.0/csranks/tests/testthat/testdata/generate_testdata_lmranks.R |only csranks-1.3.0/csranks/tests/testthat/testdata/generate_testdata_weights.R |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_covariates_FALSE.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_covariates_TRUE.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_increasing_FALSE.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_n_10.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_n_100.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_n_50.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_cov_sigmahat_regressor_1.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/ivregranks_vcov_sims.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/lmranks_cov_sigmahat_weighted.rda |only csranks-1.3.0/csranks/tests/testthat/testdata/vcov_sims_code_extracted.R |only csranks-1.3.0/csranks/tests/testthat/testthat-problems.rds |binary csranks-1.3.0/csranks/vignettes/Inference-for-Ranks.rmd | 40 csranks-1.3.0/csranks/vignettes/Rank-Rank-Reg.rmd | 131 +- 85 files changed, 2746 insertions(+), 2564 deletions(-)
Title: Flexible Modeling of Count Data
Description: For Bayesian and classical inference and prediction with count-valued data,
Simultaneous Transformation and Rounding (STAR) Models provide a flexible, interpretable,
and easy-to-use approach. STAR models the observed count data using a rounded
continuous data model and incorporates a transformation for greater flexibility.
Implicitly, STAR formalizes the commonly-applied yet incoherent procedure of
(i) transforming count-valued data and subsequently
(ii) modeling the transformed data using Gaussian models.
STAR is well-defined for count-valued data, which is reflected in predictive accuracy,
and is designed to account for zero-inflation, bounded or censored data, and over- or underdispersion.
Importantly, STAR is easy to combine with existing MCMC or point estimation
methods for continuous data, which allows seamless adaptation of continuous data
models (such as linear regressions, additive models, BART, random forests,
and gradient boosting machines) for count-valued data. The package [...truncated...]
Author: Brian King [aut, cre],
Dan Kowal [aut]
Maintainer: Brian King <brianking387@gmail.com>
Diff between countSTAR versions 1.2.0 dated 2026-04-03 and 1.2.1 dated 2026-08-21
DESCRIPTION | 8 MD5 | 178 NAMESPACE | 104 NEWS.md | 44 R/RcppExports.R | 466 +- R/STAR_Bayesian.R | 3054 +++++++-------- R/STAR_frequentist.R | 3488 ++++++++--------- R/data.R | 30 R/helper_functions.R | 1617 ++++---- R/internal_functions.R | 8420 +++++++++++++++++++++---------------------- R/warpDLM.R | 486 +- README.md | 144 build/partial.rdb |binary build/vignette.rds |binary inst/doc/countSTAR.R | 256 - inst/doc/countSTAR.Rmd | 676 +-- inst/doc/countSTAR.html | 1813 ++++----- man/BrentMethod.Rd | 62 man/HPDregion.Rd | 58 man/a_j.Rd | 64 man/bam_star.Rd | 282 - man/bart_star.Rd | 384 - man/bart_star_ispline.Rd | 216 - man/blm_star.Rd | 290 - man/blm_star_exact.Rd | 164 man/blm_star_exact_bnp.Rd | 184 man/blm_star_gibbs_bnp.Rd | 204 - man/computeTimeRemaining.Rd | 48 man/confint.lmstar.Rd | 86 man/credBands.Rd | 48 man/ergMean.Rd | 56 man/expectation2_gRcpp.Rd | 60 man/expectation_gRcpp.Rd | 60 man/expectation_identity.Rd | 60 man/expectation_log.Rd | 60 man/expectation_sqrt.Rd | 60 man/g_bc.Rd | 70 man/g_cdf.Rd | 96 man/g_inv.Rd | 64 man/g_inv_approx.Rd | 76 man/g_inv_bc.Rd | 64 man/gbm_star.Rd | 278 - man/genEM_star.Rd | 281 - man/genMCMC_star.Rd | 306 - man/genMCMC_star_ispline.Rd | 222 - man/getEffSize.Rd | 58 man/init_bam_orthog.Rd | 84 man/init_bam_thin.Rd | 84 man/init_lm_gprior.Rd | 94 man/init_lm_hs.Rd | 86 man/init_lm_ridge.Rd | 78 man/init_params_mean.Rd | 56 man/interval_gRcpp.Rd | 64 man/invlogit.Rd | 36 man/lm_star.Rd | 214 - man/logLikePointRcpp.Rd | 58 man/logLikeRcpp.Rd | 58 man/logit.Rd | 36 man/plot_coef.Rd | 62 man/plot_fitted.Rd | 54 man/plot_pmf.Rd | 54 man/pmaxRcpp.Rd | 46 man/pminRcpp.Rd | 46 man/predict.lmstar.Rd | 134 man/pvals.Rd | 72 man/randomForest_star.Rd | 277 - man/rdir.Rd | 54 man/roaches.Rd | 58 man/round_floor.Rd | 62 man/rtruncnormRcpp.Rd | 64 man/sampleFastGaussian.Rd | 52 man/sample_bam_orthog.Rd | 128 man/sample_bam_thin.Rd | 128 man/sample_lm_gprior.Rd | 110 man/sample_lm_hs.Rd | 94 man/sample_lm_ridge.Rd | 90 man/sample_params_mean.Rd | 62 man/simBaS.Rd | 58 man/simulate_nb_friedman.Rd | 116 man/simulate_nb_lm.Rd | 128 man/splineBasis.Rd | 62 man/spline_star.Rd | 260 - man/spline_star_exact.Rd | 166 man/spline_star_gibbs_bnp.Rd | 196 - man/truncnorm_mom.Rd | 54 man/uni.slice.Rd | 72 man/update_struct.Rd | 52 man/warpDLM.Rd | 128 vignettes/countSTAR.Rmd | 676 +-- vignettes/refs.bib | 144 90 files changed, 14748 insertions(+), 14704 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb],
Hugo Tovar [ctb],
Hualin Wang [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.2.4 dated 2023-12-06 and 1.3.1 dated 2026-08-21
DESCRIPTION | 21 +++-- MD5 | 35 ++++---- NAMESPACE | 25 +++--- NEWS.md |only R/corto.R | 175 ++++++++++++++++--------------------------- R/functions.R | 145 +++++++++++++++++++++++++++++++---- R/gsea.R | 30 +++---- R/mra.R | 100 +++++++++++++++++++----- build/vignette.rds |binary inst/doc/corto_vignette.R | 16 +-- inst/doc/corto_vignette.Rmd | 14 +-- inst/doc/corto_vignette.html | 18 ++-- man/filter_regulon.Rd |only man/getregulon.Rd |only man/mra.Rd | 5 - man/plot_gsea2.Rd | 3 man/scatter.Rd | 2 man/textrepel.Rd | 4 man/val2col.Rd | 2 vignettes/corto_vignette.Rmd | 14 +-- 20 files changed, 376 insertions(+), 233 deletions(-)
Title: Contrast Analyses for Factorial Designs
Description: Contrast analysis for factorial designs provides an
alternative to the traditional ANOVA approach, offering the distinct
advantage of testing targeted hypotheses. The foundation of this
package is primarily rooted in the works of Rosenthal, Rosnow, and
Rubin (2000, ISBN: 978-0521659802) as well as Sedlmeier and Renkewitz
(2018, ISBN: 978-3868943214).
Author: Johannes Titz [aut, cre],
Markus Burkhardt [aut],
Mirka Henninger [ctb],
Simone Malejka [ctb]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between cofad versions 0.3.3 dated 2025-05-15 and 0.4.0 dated 2026-08-21
DESCRIPTION | 17 MD5 | 100 +- NAMESPACE | 7 NEWS.md | 66 + R/calc_contrast.R | 184 ++-- R/calc_contrast_aggregated.R | 26 R/cofad-package.R | 1 R/data.R | 48 + R/design_detection.R |only R/examples.R |only R/helper.R | 1135 +++++++++++++++++++++++++-- R/print_methods.R | 75 + R/run_app.R | 7 R/server.R | 994 +++++++++++++++++++---- R/summary_methods.R | 5 R/ui.R | 277 +++++- R/utils-pipe.R | 4 README.md | 985 +++++++++++++++-------- build/partial.rdb |binary data/rosenthal_tbl54.rda |only data/rosenthal_tbl68_mixed.rda |only inst/CITATION |only inst/extdata/citation.txt | 14 inst/extdata/cofad-copy.js |only inst/extdata/intro.html | 11 inst/shinylive |only man/calc_contrast.Rd | 18 man/calc_contrast_aggregated.Rd | 18 man/cofad-package.Rd | 2 man/detect_design.Rd |only man/figures |only man/lambda_diff.Rd | 31 man/pipe.Rd | 11 man/print.cofad_mx.Rd | 2 man/print.cofad_wi.Rd | 2 man/rosenthal_tbl54.Rd |only man/rosenthal_tbl68.Rd | 2 man/rosenthal_tbl68_mixed.Rd |only man/run_app.Rd | 4 man/sedlmeier_p525.Rd | 5 man/summary.cofad_wi.Rd | 2 man/testing_effect.Rd | 4 tests/testthat/test-citation-formats.R |only tests/testthat/test-competing-ui.R |only tests/testthat/test-copy-button-layout.R |only tests/testthat/test-copyable-output.R |only tests/testthat/test-coverage-additions.R |only tests/testthat/test-design-detection.R |only tests/testthat/test-example-datasets.R |only tests/testthat/test-example-presets.R |only tests/testthat/test-export-controls.R |only tests/testthat/test-gui.R | 11 tests/testthat/test-mixed-choice-tooltips.R |only tests/testthat/test-partial-eta.R |only tests/testthat/test-r-code-panel.R |only tests/testthat/test-server-in-process.R |only tests/testthat/test-server-manual-fallback.R |only tests/testthat/test-variance-display.R |only tests/testthat/test-within-r-scores.R |only tools |only 60 files changed, 3243 insertions(+), 825 deletions(-)
Title: Diagnostic Tools for Logistic and Conditional Logistic
Regression
Description: Provides tools for fitting, assessing, and comparing logistic
and conditional logistic regression models. Includes residual diagnostics
and goodness of fit measures for model development and evaluation in
matched case control studies.
Author: Brenda Contla Hernandez [aut, cre],
Matthieu Vignes [ctb] ,
Chris Compton [ctb]
Maintainer: Brenda Contla Hernandez <B.Hernandez@massey.ac.nz>
Diff between CLRtools versions 0.1.1 dated 2026-03-16 and 0.1.2 dated 2026-08-21
DESCRIPTION | 8 MD5 | 135 +-- NAMESPACE | 178 ++- NEWS.md | 17 R/CLRtools-package.R | 68 - R/DRtest.R | 196 ++-- R/check_coef_change.R | 222 ++-- R/check_coef_significant.R | 202 ++-- R/check_interactions.R | 240 ++--- R/coeff.OR.R | 220 ++-- R/compare_models_loo.R | 136 +-- R/confidence.interval.R | 134 +-- R/cov.patterns.R | 138 +-- R/cutpoints.R | 238 ++--- R/delta.coefficient.R | 122 +- R/diagnostic_bayes.R | 94 +- R/diagnosticplots_class.R | 190 ++-- R/discordant.pairs.R | 176 +-- R/glow11m.R | 50 - R/glow500.R | 48 - R/helpers_functions.R | 176 +-- R/osius_rojek.R | 202 ++-- R/r_measures.R | 224 ++--- R/rcv_measures.R | 214 ++-- R/residuals_clog.R | 370 ++++---- R/residuals_logistic.R | 362 ++++---- R/stukels_test.R | 156 +-- R/summarize_results.R | 190 ++-- R/univariable.clogmodels.R | 234 ++--- R/univariable.models.R | 200 ++-- README.md |only build/vignette.rds |binary inst/doc/Bayesian_Logistic_regression.R | 8 inst/doc/Bayesian_Logistic_regression.Rmd | 1159 ++++++++++++-------------- inst/doc/Bayesian_Logistic_regression.html | 106 +- inst/doc/Conditional_Logistic_Regression.Rmd | 342 +++---- inst/doc/Logistic_Regression.Rmd | 478 +++++----- inst/doc/Logistic_Regression.html | 2 man/CLRtools-package.Rd | 63 - man/DRtest.Rd | 122 +- man/check_coef_change.Rd | 112 +- man/check_coef_significant.Rd | 96 +- man/check_interactions.Rd | 106 +- man/coeff.OR.Rd | 124 +- man/compare_bayesm.Rd | 84 - man/compare_bayesm_by_predictor.Rd | 110 +- man/compare_models_loo.Rd | 62 - man/confidence.interval.Rd | 96 +- man/cov.patterns.Rd | 110 +- man/cutpoints.Rd | 126 +- man/delta.coefficient.Rd | 82 - man/diagnostic_bayes.Rd | 62 - man/diagnosticplots_class.Rd | 120 +- man/discordant.pairs.Rd | 72 - man/glow11m.Rd | 74 - man/glow500.Rd | 72 - man/logit_prob_plot.Rd | 92 +- man/osius_rojek.Rd | 124 +- man/r_measures.Rd | 108 +- man/rcv_measures.Rd | 114 +- man/residuals_clog.Rd | 150 +-- man/residuals_logistic.Rd | 158 +-- man/stukels_test.Rd | 100 +- man/summarize_results.Rd | 108 +- man/univariable.clogmodels.Rd | 138 +-- man/univariable.models.Rd | 102 +- vignettes/Bayesian_Logistic_regression.Rmd | 1159 ++++++++++++-------------- vignettes/Conditional_Logistic_Regression.Rmd | 342 +++---- vignettes/Logistic_Regression.Rmd | 478 +++++----- 69 files changed, 6062 insertions(+), 6039 deletions(-)
Title: Interpretable Civic-Accountable and Responsible Machine Learning
Description: A general-purpose framework for Interpretable Civic-Accountable
and Responsible Machine Learning (ICARM). Works with any clean tabular
data and automatically detects whether a task is binary classification,
multi-class classification, or regression from the target variable type.
Provides a single unified entry point civic_fit() alongside tidy interfaces
for global and local model explanations, group-level fairness auditing,
probability calibration, multi-model comparison, threshold analysis, and
reproducible audit trails. Designed to support the DataCitizen-Pro research
agenda at Ludwigsburg University of Education: developing data literacy,
statistical reasoning, and democratic judgment formation in civic and
political teacher education.
References: Biecek (2018) <doi:10.18637/jss.v085.i04>,
Kuhn (2008) <doi:10.18637/jss.v028.i05>,
Awe (2025) <https://github.com/Olawaleawe/civic.icarm>.
Author: Olushina Olawale Awe [aut, cre],
Ludwigsburg University of Education [fnd]
Maintainer: Olushina Olawale Awe <olawaleawe@gmail.com>
Diff between civic.icarm versions 0.3.0 dated 2026-06-22 and 0.4.0 dated 2026-08-21
DESCRIPTION | 9 MD5 | 42 - NAMESPACE | 63 - R/civic.icarm-package.R | 42 - R/civic_data_utils.R | 480 ++++++------- R/civic_explain.R | 388 +++++------ R/civic_fairness.R | 538 +++++++-------- R/civic_fit.R | 825 +++++++++++++---------- R/civic_scorecard.R | 800 +++++++++++----------- R/data.R | 176 ++--- R/plots.R | 1568 ++++++++++++++++++++++----------------------- R/predict.R | 142 ++-- R/utils_internal.R | 148 ++-- README.md | 262 +++---- build |only inst/WORDLIST | 18 man/civic_dashboard.Rd | 70 +- man/civic_explain_local.Rd | 50 - man/civic_fit.Rd | 2 man/civic_plots.Rd | 28 man/plot.civic_model.Rd |only man/predict.civic_model.Rd | 64 - tests/testthat/test-all.R | 438 ++++++------ 23 files changed, 3125 insertions(+), 3028 deletions(-)
Title: Access and Harmonize Childfree Demographic Data
Description: Reads demographic data from a variety of public data sources, extracting and harmonizing variables useful for the study of childfree individuals. The identification of childfree individuals and those with other family statuses uses Neal & Neal's (2024) "A Framework for Studying Adults who Neither have Nor Want Children" <doi:10.1177/10664807231198869>; A pre-print is available at <doi:10.31234/osf.io/fa89m>.
Author: Zachary Neal [aut, cre] ,
Jennifer Watling Neal [aut]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between childfree versions 0.0.5 dated 2026-02-26 and 0.0.6 dated 2026-08-21
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 4 + R/nsfg.R | 118 +++++++++++++++++++++++++++++++++++++----------- R/soss.R | 55 +++++++++++++--------- inst/doc/childfree.R | 5 ++ inst/doc/childfree.Rmd | 6 ++ inst/doc/childfree.html | 26 ++++++++-- man/soss.Rd | 12 ++-- vignettes/childfree.Rmd | 6 ++ 10 files changed, 185 insertions(+), 71 deletions(-)
Title: Advanced Continuous Glucose Monitoring Analysis with
High-Performance C++ Backend
Description: Tools for advanced analysis of continuous glucose monitoring (CGM)
time-series, implementing GRID (Glucose Rate Increase Detector) and GRID-based
algorithms for postprandial peak detection, and detection of hypoglycemic and
hyperglycemic episodes (Levels 1/2/Extended) aligned with international consensus
CGM metrics. Core algorithms are implemented in optimized C++ using 'Rcpp' to
provide accurate and fast analysis on large datasets.
Author: Sang Ho Park [aut, cre],
Rosa Oh [aut, ctb],
Sang-Man Jin [aut, ctb]
Maintainer: Sang Ho Park <shstat1729@gmail.com>
Diff between cgmguru versions 1.2.0 dated 2026-07-08 and 1.3.0 dated 2026-08-21
cgmguru-1.2.0/cgmguru/LICENSE |only cgmguru-1.3.0/cgmguru/DESCRIPTION | 8 cgmguru-1.3.0/cgmguru/LICENSE.note |only cgmguru-1.3.0/cgmguru/MD5 | 66 +-- cgmguru-1.3.0/cgmguru/NAMESPACE | 1 cgmguru-1.3.0/cgmguru/NEWS.md | 29 + cgmguru-1.3.0/cgmguru/R/RcppExports.R | 4 cgmguru-1.3.0/cgmguru/R/cgmguru-functions-docs.R | 16 cgmguru-1.3.0/cgmguru/R/cgmguru-package.R | 12 cgmguru-1.3.0/cgmguru/R/interval_down.R |only cgmguru-1.3.0/cgmguru/inst/doc/detect_all_events.Rmd | 10 cgmguru-1.3.0/cgmguru/inst/doc/detect_all_events.html | 35 - cgmguru-1.3.0/cgmguru/inst/doc/examples.R | 7 cgmguru-1.3.0/cgmguru/inst/doc/examples.Rmd | 12 cgmguru-1.3.0/cgmguru/inst/doc/examples.html | 10 cgmguru-1.3.0/cgmguru/inst/doc/grid.html | 4 cgmguru-1.3.0/cgmguru/inst/doc/intro.Rmd | 4 cgmguru-1.3.0/cgmguru/inst/doc/intro.html | 4 cgmguru-1.3.0/cgmguru/man/cgmguru-package.Rd | 12 cgmguru-1.3.0/cgmguru/man/detect_all_events.Rd | 8 cgmguru-1.3.0/cgmguru/man/detect_hyperglycemic_events.Rd | 4 cgmguru-1.3.0/cgmguru/man/detect_hypoglycemic_events.Rd | 4 cgmguru-1.3.0/cgmguru/man/interval_down.Rd |only cgmguru-1.3.0/cgmguru/src/RcppExports.cpp | 13 cgmguru-1.3.0/cgmguru/src/detect_all_events.cpp | 109 +---- cgmguru-1.3.0/cgmguru/src/detect_hyperglycemic_events.cpp | 194 +--------- cgmguru-1.3.0/cgmguru/src/detect_hypoglycemic_events.cpp | 151 ++----- cgmguru-1.3.0/cgmguru/src/event_preprocessing.h | 123 ++++++ cgmguru-1.3.0/cgmguru/src/interpolate_cgm.cpp | 6 cgmguru-1.3.0/cgmguru/src/interval_down.cpp |only cgmguru-1.3.0/cgmguru/src/rebound_events.cpp | 7 cgmguru-1.3.0/cgmguru/src/variability_metrics.cpp | 6 cgmguru-1.3.0/cgmguru/tests/testthat/test-iglu-episode-parity.R | 61 +++ cgmguru-1.3.0/cgmguru/tests/testthat/test-interval_down.R |only cgmguru-1.3.0/cgmguru/vignettes/detect_all_events.Rmd | 10 cgmguru-1.3.0/cgmguru/vignettes/examples.Rmd | 12 cgmguru-1.3.0/cgmguru/vignettes/intro.Rmd | 4 37 files changed, 483 insertions(+), 463 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.59.5 dated 2026-01-14 and 1.65.2 dated 2026-08-21
DESCRIPTION | 8 MD5 | 50 NEWS.md | 5 R/ggplot_as_list.R | 1404 ++++- R/html_functionality.R | 211 README.md | 2 inst/README-known_issues.md | 2 inst/doc/additional_examples.html | 4 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 10 inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 4422 ++++++++++-------- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 285 - inst/shiny-examples/example2/ui.R | 10 inst/shiny-examples/example3/ui.R | 7 inst/shiny-examples/example4/server.R | 11 inst/shiny-examples/example4/ui.R | 59 inst/ui-examples/cX-function.R.gz |binary tests/testthat/test-other-cxHtmlPage.R | 216 tests/testthat/test-other-ggplot_as_list.R | 981 +++ tests/testthat/test-ui-bar.R | 14 tests/testthat/test-ui-bullet.R | 4 tests/testthat/test-ui-meter.R | 44 tests/testthat/test-ui-pie.R | 4 tests/testthat/test-ui-scatter3D.R | 12 vignettes/getting_started.Rmd | 2 26 files changed, 5268 insertions(+), 2503 deletions(-)
Title: Fit Bounded Continuous Item Response Theory Models to Data
Description: Bounded continuous data are encountered in many areas of test application.
Examples include visual analogue scales used in the measurement of personality, mood,
depression, and quality of life; item response times from tests with item deadlines;
confidence ratings; and pain intensity ratings. Using this package, item response theory (IRT)
models suitable for bounded continuous item scores can be fitted to data within a Bayesian framework.
The package draws on posterior sampling facilities provided by R-package 'rstan' (Stan Development Team, 2025)<https://mc-stan.org/>.
Available models include the Beta IRT model by Noel and Dauvier (2007)<doi:10.1177/0146621605287691>, the continuous response
model by Samejima (1973)<doi:10.1007/BF03372160>, the unbounded normal model by Mellenbergh (1994)<doi:10.1207/s15327906mbr2903_2>,
and the Simplex IRT model by Flores et al. (2020)<doi:10.1007/978-3-030-43469-4_8>. All models can be
fitted with or without zero-one i [...truncated...]
Author: Dylan Molenaar [aut, cre]
Maintainer: Dylan Molenaar <d.molenaar@uva.nl>
Diff between BoundIRT versions 0.5.0 dated 2026-05-05 and 0.6.0 dated 2026-08-21
BoundIRT-0.5.0/BoundIRT/data/female.rda |only BoundIRT-0.5.0/BoundIRT/man/Abasement.Rd |only BoundIRT-0.5.0/BoundIRT/man/out_beta.Rd |only BoundIRT-0.6.0/BoundIRT/DESCRIPTION | 6 BoundIRT-0.6.0/BoundIRT/MD5 | 11 - BoundIRT-0.6.0/BoundIRT/R/latregBIRT.R | 293 +++++++++++++++++++++++------- BoundIRT-0.6.0/BoundIRT/data/ACL.rda |only BoundIRT-0.6.0/BoundIRT/man/ACL.Rd |only BoundIRT-0.6.0/BoundIRT/man/latregBIRT.Rd | 197 ++++++++++++-------- 9 files changed, 353 insertions(+), 154 deletions(-)
Title: Binscatter Estimation and Inference
Description: Provides tools for statistical analysis using the binscatter methods developed by Cattaneo, Crump, Farrell and Feng (2024) <https://nppackages.github.io/references/Cattaneo-Crump-Farrell-Feng_2024_AER.pdf>, Cattaneo, Crump, Farrell and Feng (2025) <https://nppackages.github.io/references/Cattaneo-Crump-Farrell-Feng_2025_Stata.pdf> and Cattaneo, Crump, Farrell and Feng (2026) <https://nppackages.github.io/references/Cattaneo-Crump-Farrell-Feng_2026_RESTAT.pdf>. Binscatter provides a flexible way of describing the relationship between two variables based on partitioning/binning of the independent variable of interest. binsreg(), binsqreg() and binsglm() implement binscatter least squares regression, quantile regression and generalized linear regression respectively, with particular focus on constructing binned scatter plots. They also implement robust (pointwise and uniform) inference of regression functions and derivatives thereof. binstest() implements hypothesis test [...truncated...]
Author: Matias D. Cattaneo [aut, cre],
Richard K. Crump [aut],
Max H. Farrell [aut],
Yingjie Feng [aut]
Maintainer: Matias D. Cattaneo <matias.d.cattaneo@gmail.com>
Diff between binsreg versions 2.1 dated 2026-05-22 and 2.2 dated 2026-08-21
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- R/binstest.R | 12 +++++++++++- tests/testthat |only tests/testthat.R |only 5 files changed, 19 insertions(+), 7 deletions(-)
Title: Bayesian Quantile Regression Models for Complex Survey Data
Analysis
Description: Provides Bayesian quantile regression models for complex survey data
under informative sampling using survey-weighted estimators. Both single- and
multiple-output models are supported. To accelerate computation, all algorithms
are implemented in 'C++' using 'Rcpp', 'RcppArmadillo', and 'RcppEigen', and
are called from 'R'. See Nascimento and Gonçalves (2024) <doi:10.1093/jssam/smae015>
and Nascimento and Gonçalves (2026) <doi:10.1093/jssam/smaf040>.
Author: Tomas Rodriguez Taborda [aut, cre],
Johnatan Cardona Jimenez [aut],
Marcus L. Nascimento [aut],
Kelly Cristina Mota Goncalves [aut]
Maintainer: Tomas Rodriguez Taborda <torodriguezt@unal.edu.co>
Diff between bayesQRsurvey versions 0.3.0 dated 2026-07-07 and 0.3.1 dated 2026-08-21
DESCRIPTION | 9 - MD5 | 27 ++- NAMESPACE | 1 R/bqr.svy.R | 20 +- R/mo.bqr.svy.R | 2 R/plot_quantile.R | 312 +++++++++++++++++++++++++++------------------- R/plot_quantile_region.R | 184 +++++++++++---------------- R/summary_bqr_svy.R | 81 ++++++++++- build/vignette.rds |only data/Anthro.rda |binary inst/doc |only man/figures |only man/plot.bqr.svy.Rd | 35 +++-- man/plotQuantileRegion.Rd | 26 ++- vignettes |only 15 files changed, 417 insertions(+), 280 deletions(-)
Title: Automated Functions for Basic Statistical Tests
Description: Provides simple and intuitive functions for basic statistical analyses.
Methods include the t-test (Student 1908 <doi:10.1093/biomet/6.1.1>),
the Mann-Whitney U test (Mann and Whitney 1947 <doi:10.1214/aoms/1177730491>),
Pearson's correlation (Pearson 1895 <doi:10.1098/rspl.1895.0041>),
and analysis of variance (Fisher 1925, <doi:10.1007/978-1-4612-4380-9_5>).
Functions are compatible with 'ggplot2' and 'dplyr'.
Author: Luiz Garcia [aut, cre]
Maintainer: Luiz Garcia <luiz.cardoso@ufpr.br>
Diff between autotestR versions 1.2.15 dated 2026-04-28 and 1.2.16 dated 2026-08-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/utils_stats.R | 2 +- R/zzz.R | 14 ++++++++++++-- README.md | 8 +++++--- 5 files changed, 25 insertions(+), 13 deletions(-)
Title: Estimate Sleep from 'Accelerometry' Data
Description: Interfaces the 'asleep' python
module <https://github.com/OxWearables/asleep> from
Yuan (2024) <doi:10.1038/s41746-024-01148-y> to estimate
sleep from 'accelerometry' data.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between asleep versions 0.1.0 dated 2026-08-04 and 0.3.0 dated 2026-08-21
asleep-0.1.0/asleep/R/utils-pipe.R |only asleep-0.1.0/asleep/man/pipe.Rd |only asleep-0.3.0/asleep/DESCRIPTION | 13 asleep-0.3.0/asleep/MD5 | 25 - asleep-0.3.0/asleep/NAMESPACE | 4 asleep-0.3.0/asleep/NEWS.md | 10 asleep-0.3.0/asleep/R/asleep.R | 116 +++--- asleep-0.3.0/asleep/R/py_asleep.R |only asleep-0.3.0/asleep/R/py_require_asleep.R |only asleep-0.3.0/asleep/R/sl_load_model.R | 21 - asleep-0.3.0/asleep/R/zzz.R | 10 asleep-0.3.0/asleep/man/asleep.Rd | 101 +++-- asleep-0.3.0/asleep/man/py_require_asleep.Rd |only asleep-0.3.0/asleep/tests/testthat/test-asleep.R | 192 +++++++++- asleep-0.3.0/asleep/tests/testthat/test-model-and-read.R | 29 + asleep-0.3.0/asleep/tests/testthat/test-reticulate-wrappers.R | 25 + 16 files changed, 426 insertions(+), 120 deletions(-)
Title: Statistical Framework for in Vivo Drug Combination Studies
Description: A framework for evaluating drug combination effects in preclinical in vivo studies.
'SynergyLMM' provides functions to analyze longitudinal tumor growth experiments using mixed-effects models,
perform time-resolved analyses of synergy and antagonism, evaluate model diagnostics and performance,
and assess both post-hoc and a priori statistical power.
The calculation of drug combination synergy follows the statistical framework provided by Demidenko and Miller (2019, <doi:10.1371/journal.pone.0224137>).
The implementation and analysis of linear mixed-effect models is based on the methods described by Pinheiro and Bates (2000, <doi:10.1007/b98882>),
and Gałecki and Burzykowski (2013, <doi:10.1007/978-1-4614-3900-4>).
Author: Rafael Romero-Becerra [aut, cre] ,
Zhi Zhao [ctb],
Tero Aittokallio [ctb]
Maintainer: Rafael Romero-Becerra <rafrombec@gmail.com>
Diff between SynergyLMM versions 1.1.3 dated 2026-05-12 and 1.1.4 dated 2026-08-20
DESCRIPTION | 8 +- MD5 | 32 ++++----- NEWS.md | 19 +++++ R/getRTV.R | 10 +- R/lmmModel.R | 8 +- R/lmmSynergy.R | 16 ---- R/plot_lmmSynergy.R | 67 +++++++++--------- R/utils.R | 42 +++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/SynergyLMM.html | 7 - tests/testthat/test-lmmDiagnostics.R | 39 +++++++---- tests/testthat/test-lmmModel.R | 20 +++-- tests/testthat/test-lmmPower.R | 67 +++++++++++------- tests/testthat/test-lmmSynergy.R | 120 ++++++++++++++++++++-------------- tests/testthat/test-plot_SynergyLMM.R | 21 ++++- tests/testthat/test-utils.R | 59 ++++++++++++++++ 17 files changed, 353 insertions(+), 182 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting. This release adds three capability themes: multi-criteria
decision analysis (AHP, ANP, DEMATEL, TOPSIS, VIKOR, MOORA, SMART,
WASPAS, PROMETHEE II, ELECTRE I), small-sample survey helpers, and
text and open-ended response analysis (term and n-gram frequency,
keyword in context, co-occurrence and co-occurrence networks, sentiment,
document-feature matrices, and topic modelling via LDA or structural
topic models).
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.4 dated 2026-07-24 and 0.4.0 dated 2026-08-20
DESCRIPTION | 26 MD5 | 265 +++++-- NAMESPACE | 139 +++ NEWS.md | 339 +++++++++ R/accessors.R |only R/amendments.R |only R/analysis_plan.R | 182 ++++- R/as_data_frame.R |only R/conditions.R | 57 + R/conjoint_design.R |only R/dashboard.R | 2 R/decision_data.R |only R/decision_dematel.R |only R/decision_methods.R |only R/decision_preference.R |only R/decision_ranking.R |only R/decision_sensitivity.R |only R/demo_helpers.R | 4 R/git_link.R |only R/google_sheets.R | 31 R/model_layer.R | 128 ++- R/plots.R | 819 ++++++++++++++++++++++- R/psychometrics.R | 13 R/quality_report.R | 12 R/read_responses.R | 55 - R/read_write_sframe.R | 145 +++- R/render_survey.R | 210 +++++ R/reporting.R | 150 +--- R/rstudio_addins.R |only R/sf_instrument.R | 7 R/sf_item.R | 109 +++ R/sf_scale.R | 4 R/sframe_methods.R | 21 R/statistics_reports.R | 239 ++++++ R/surveyframe-package.R | 17 R/text_analysis.R |only R/utils.R | 16 R/validate_sframe.R | 237 +++++- R/validation_result.R |only README.md | 57 + build/vignette.rds |binary inst/CITATION | 30 inst/WORDLIST |only inst/builder/survey_builder.html | 573 +++++++++++++++- inst/doc/analysing-survey-responses.R | 10 inst/doc/analysing-survey-responses.Rmd | 10 inst/doc/analysing-survey-responses.html | 154 ---- inst/doc/building-survey-instrument.R | 15 inst/doc/building-survey-instrument.Rmd | 24 inst/doc/building-survey-instrument.html | 56 - inst/doc/efa-cfa-sem-pls-syntax.Rmd | 4 inst/doc/efa-cfa-sem-pls-syntax.html | 66 - inst/doc/mcdm-analysis.R |only inst/doc/mcdm-analysis.Rmd |only inst/doc/mcdm-analysis.html |only inst/doc/scale-reliability-validity.R | 20 inst/doc/scale-reliability-validity.Rmd | 20 inst/doc/scale-reliability-validity.html | 34 inst/doc/small-sample.R |only inst/doc/small-sample.Rmd |only inst/doc/small-sample.html |only inst/doc/surveybuilder-gui-overview.Rmd | 9 inst/doc/surveybuilder-gui-overview.html | 10 inst/doc/surveyframe.R | 73 +- inst/doc/surveyframe.Rmd | 179 ++++- inst/doc/surveyframe.html | 818 +++++++++++++--------- inst/doc/text-analysis.R |only inst/doc/text-analysis.Rmd |only inst/doc/text-analysis.html |only inst/extdata/hotel_supplier_mcdm.sframe |only inst/extdata/hotel_supplier_mcdm_responses.csv |only inst/extdata/surveyframe_input_types_demo.sframe | 35 inst/extdata/tourism_services_demo.sframe | 62 + inst/rstudio |only inst/schema |only inst/shiny/app.R | 372 ++++++++++ inst/static_survey/template.html | 253 +++++++ man/amend_sframe.Rd |only man/amendment_log.Rd |only man/as_sframe.Rd |only man/cfa_syntax.Rd | 4 man/clean_text_responses.Rd |only man/codebook_report.Rd | 4 man/extract_quotes.Rd |only man/launch_builder_demo.Rd | 4 man/launch_dashboard.Rd | 2 man/link_git_commit.Rd |only man/ngram_frequency.Rd |only man/outlier_report.Rd | 2 man/read_responses.Rd | 4 man/render_report.Rd | 2 man/sensitivity_analysis.Rd |only man/sf_accessors.Rd |only man/sf_component_list.Rd |only man/sf_conjoint_design.Rd |only man/sf_identity.Rd |only man/sf_instrument.Rd | 2 man/sf_item.Rd | 21 man/sf_plan-set.Rd |only man/sf_report_accessors.Rd |only man/sf_scale.Rd | 4 man/sf_validation_accessors.Rd |only man/sframe_aggregate_judgements.Rd |only man/sframe_as_data_frame.Rd |only man/sframe_assemble_pairwise.Rd |only man/sframe_codebook_items_display.Rd | 10 man/sframe_collected_weights.Rd |only man/sframe_decision_options.Rd |only man/sframe_dematel_compute.Rd |only man/sframe_draw_likert_diverging.Rd | 4 man/sframe_draw_mosaic.Rd | 4 man/sframe_plot_cooccurrence.Rd |only man/sframe_plot_cooccurrence_network.Rd |only man/sframe_plot_decision_ranking.Rd |only man/sframe_plot_dematel_influence.Rd |only man/sframe_plot_descriptives.Rd | 2 man/sframe_plot_efa_loadings.Rd | 4 man/sframe_plot_group_comparison.Rd | 2 man/sframe_plot_likert_scale.Rd | 2 man/sframe_plot_ngram_frequency.Rd |only man/sframe_plot_sentiment.Rd |only man/sframe_plot_term_frequency.Rd |only man/sframe_plot_topics.Rd |only man/sframe_rated_matrix.Rd |only man/sframe_run_stm_topics.Rd |only man/sframe_run_topic_model_lda.Rd |only man/sframe_small_sample_advisory.Rd |only man/sframe_subset.Rd |only man/sframe_validation.Rd |only man/sframe_warn_design.Rd |only man/surveyframe-package.Rd | 17 man/term_context.Rd |only man/term_frequency.Rd |only man/validate_model.Rd | 18 man/validate_sframe.Rd | 46 - man/validity_report.Rd | 2 tests/testthat/test-accessors.R |only tests/testthat/test-amendments.R |only tests/testthat/test-builder-analysis.R | 8 tests/testthat/test-builder-text-options.R |only tests/testthat/test-chrome-detritus.R |only tests/testthat/test-conjoint-design.R |only tests/testthat/test-core.R | 49 + tests/testthat/test-decision-ahp-anp.R |only tests/testthat/test-decision-data.R |only tests/testthat/test-decision-dematel.R |only tests/testthat/test-decision-item-types.R |only tests/testthat/test-decision-preference.R |only tests/testthat/test-decision-ranking.R |only tests/testthat/test-decision-scale-guards.R |only tests/testthat/test-decision-sensitivity.R |only tests/testthat/test-decision-topsis.R |only tests/testthat/test-git-link.R |only tests/testthat/test-item-rest-correlation.R |only tests/testthat/test-known-vars-expansion.R |only tests/testthat/test-mcdm-fixture.R |only tests/testthat/test-model-type-guards.R |only tests/testthat/test-quality-decision-columns.R |only tests/testthat/test-read-responses-name-repair.R |only tests/testthat/test-repeated-anova-strata.R |only tests/testthat/test-rstudio-addins.R |only tests/testthat/test-serialisation-fixed-point.R |only tests/testthat/test-sframe-schema.R |only tests/testthat/test-shiny-decision-render.R |only tests/testthat/test-shiny-export-shape.R |only tests/testthat/test-studio-decision-roles.R |only tests/testthat/test-text-analysis.R |only tests/testthat/test-text-cooccurrence-network.R |only tests/testthat/test-text-cooccurrence.R |only tests/testthat/test-text-ngram-context.R |only tests/testthat/test-text-sentiment.R |only tests/testthat/test-text-topics.R |only tests/testthat/test-v03-analysis-models.R | 76 ++ tests/testthat/test-v034-effect-cis.R | 36 + tests/testthat/test-v034-family-plots.R | 41 + tests/testthat/test-v034-stats-reporting.R | 2 vignettes/analysing-survey-responses.Rmd | 10 vignettes/building-survey-instrument.Rmd | 24 vignettes/efa-cfa-sem-pls-syntax.Rmd | 4 vignettes/mcdm-analysis.Rmd |only vignettes/scale-reliability-validity.Rmd | 20 vignettes/small-sample.Rmd |only vignettes/surveybuilder-gui-overview.Rmd | 9 vignettes/surveyframe.Rmd | 179 ++++- vignettes/text-analysis.Rmd |only 185 files changed, 5548 insertions(+), 1181 deletions(-)
Title: Robust Latent Profile Analysis
Description: Provides a comprehensive toolset for estimating Latent Profile
Analysis (LPA) models that are robust to multivariate outliers and missing
data. By integrating a high-performance 'C++' engine via 'RcppArmadillo',
it reliably extracts latent profiles using both Expectation-Maximization (EM)
and Markov Chain Monte Carlo (MCMC) Bayesian estimation. The EM engine
implements a Full Information Maximum Likelihood (FIML) approach, Huber
weighting, and LASSO regularization with k-fold cross-validation for optimal
penalty tuning. The MCMC engine utilizes a Bayesian Lasso approach with
Laplace priors, the same Huber down-weighting available in the EM engine,
multiple chains (4 by default), and classic Gelman-Rubin/effective sample
size convergence diagnostics. It supports multiple geometric variance-covariance
models, along with functions for bootstrapped likelihood ratio tests (BLRT), BCH
auxiliary variable analysis, and plotting.
For methodological details on the Bootstrapped Likelihood Ratio T [...truncated...]
Author: Valerio Riccardo Aquila [aut, cre]
Maintainer: Valerio Riccardo Aquila <valerio_aquila@hotmail.it>
Diff between RobustLPA versions 0.1.0 dated 2026-07-05 and 1.0.0 dated 2026-08-20
DESCRIPTION | 29 - MD5 | 59 +- NAMESPACE | 7 NEWS.md | 111 ++++ R/RcppExports.R | 12 R/RobustLPA-package.R | 1 R/bch_robust.R |only R/blrt_robust.R | 179 +++++-- R/data.R |only R/estimate_profiles_robust.R | 188 ++++++- R/label_utils.R |only R/mcmc_diagnostics.R |only R/parallel_utils.R |only R/plot_mcmc_chains.R |only R/plot_robust_lpa.R | 104 +++- R/print_summary_robust_lpa.R |only R/robust_lpa.R | 958 +++++++++++++++++++++++++++++++------ R/robust_m_step.R | 164 ++++-- R/robust_mean.R | 48 + build/vignette.rds |only data |only inst |only man/RobustLPA-package.Rd | 2 man/bch_robust.Rd |only man/blrt_robust.Rd | 81 ++- man/estimate_profiles_robust.Rd | 53 +- man/neuro_data.Rd |only man/plot_mcmc_chains.Rd |only man/plot_robust_lpa.Rd | 22 man/print.robust_lpa.Rd |only man/print.summary.robust_lpa.Rd |only man/robust_lpa.Rd | 243 ++++++++- man/robust_m_step.Rd | 61 +- man/robust_mean.Rd | 32 + man/summary.robust_lpa.Rd |only src/RcppExports.cpp | 36 + src/robust_engine.cpp | 1019 ++++++++++++++++++++++++++++++---------- vignettes |only 38 files changed, 2732 insertions(+), 677 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.9.0 dated 2026-01-13 and 1.10.0 dated 2026-08-20
DESCRIPTION | 10 - MD5 | 113 ++++++++++--- NAMESPACE | 2 NEWS | 57 +++++++ R/attribs.R | 17 +- R/extensions.R | 8 R/foreign.R |only R/image.R | 4 R/nifti.R | 74 +++++---- R/viewer.R | 72 ++++++++ R/xform.R | 22 -- build/partial.rdb |binary inst/doxygen |only inst/include/RNifti.h | 2 inst/include/RNifti/NiftiImage.h | 42 ++--- inst/include/RNifti/NiftiImage_impl.h | 276 ++++++++-------------------------- inst/tinytest/test-35-viewer.R | 40 ++++ inst/tinytest/test-40-foreign.R | 57 ++++++- inst/tinytest/test-55-fuzz.R | 9 + man/ExtensionCodes.Rd | 5 man/asNifti.Rd | 61 ++++--- man/extensions.Rd | 9 - man/readNifti.Rd | 8 man/view.Rd | 49 +++++- man/writeNifti.Rd | 14 + src/main.cpp | 138 +++++++++++------ tools/figures/unnamed-chunk-12-1.png |binary tools/figures/unnamed-chunk-15-1.png |binary tools/figures/unnamed-chunk-5-1.png |binary 29 files changed, 663 insertions(+), 426 deletions(-)
Title: Reality Check and Predictive Ability Tests for Forecast
Evaluation
Description: Implements a comprehensive suite of statistical tests for
evaluating the accuracy of forecasting models against a benchmark.
The package is grounded in the reality check framework of White
(2000) <doi:10.1111/1468-0262.00152>, extended by Hansen (2005)
<doi:10.1198/073500105000000063> for Superior Predictive Ability
(SPA), Giacomini & White (2006) <doi:10.1111/j.1468-0262.2006.00718.x>
for Conditional Predictive Ability (CPA), and Corradi & Swanson
(2006) <doi:10.1016/j.jeconom.2005.07.026> for predictive density
evaluation via the Kullback-Leibler Information Criterion (KLIC) and
ZP Quantile Loss test, the Continuous Ranked Probability
Score (CRPS) (Gneiting & Raftery, 2007)
<doi:10.1198/016214506000001437>, coverage tests (Kupiec, 1995)
<doi:10.3905/jod.1995.407942>, HAC covariance estimation (Newey &
West, 1987) <doi:10.2307/1913610>, and Moving Block Bootstrap
resampling (Kunsch, 1989) <doi:10.1214/aos/1176347265>.
Author: Joanna Jedrzejewska [aut, cre] ,
Krzysztof Drachal [ctb]
Maintainer: Joanna Jedrzejewska <j.jedrzejewska3@uw.edu.pl>
Diff between RCtest versions 1.0 dated 2026-06-02 and 1.1 dated 2026-08-20
DESCRIPTION | 23 ++-- MD5 | 26 ++--- NEWS.md | 16 ++- R/analysis_helpers.R | 93 ++++++++++++++---- R/statistical_tests.R | 175 ++++++++++++++++++++++------------ R/workflow_functions.R | 12 +- man/compute_klic.Rd | 3 man/compute_kupiec.Rd | 3 man/compute_zp.Rd | 3 man/estimate_forecast_variance.Rd | 58 +++++++++-- man/kullback_leibler_test.Rd | 5 man/reality_check_zp_test.Rd | 5 man/run_comprehensive_erc_analysis.Rd | 22 ++++ man/white_reality_check_cdf_approx.Rd | 120 ++++++++++++++++------- 14 files changed, 401 insertions(+), 163 deletions(-)
Title: Nonparametric Probabilistic-Statistical Variate Analysis
Description: Calculate posterior joint and conditional probabilities, probability distributions of population frequencies, information-theoretic measures, and expected utilities, by means of Bayesian nonparametrics. Data can be any combination of nominal, ordinal, continuous, censored, rounded types. Data imputation is automatic and done in a principled way. Markov-chain Monte Carlo calculations are automatically handled and do not require user supervision. Applications range from statistical estimation and probabilistic hypothesis testing to evidence-based inference and decision making, in a wide range of disciplines from astrophysics to medicine. For more details and examples see for instance Porta Mana & al. (2026) <doi:10.31219/osf.io/8nr56>, Dunson & Bhattacharya (2011) <doi:10.1093/acprof:oso/9780199694587.003.0005>, Lindley & Novick (1981) <doi:10.1214/aos/1176345331>, Bernardo & Smith (2000) <doi:10.1002/9780470316870>, Müller et al. (2015) <doi:10 [...truncated...]
Author: PierGianLuca Porta Mana [aut, cre, cph] ,
Aurora Grefsrud [ctb] ,
Hakon Mydland [ctb] ,
Maksim Ohvrill [ctb],
Simen Hesthamar Hauge [ctb]
Maintainer: PierGianLuca Porta Mana <pgl@portamana.org>
Diff between prova versions 1.0.0 dated 2026-07-16 and 2.3.0 dated 2026-08-20
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Title: Generalized Linear Models Adjusting for Misrepresentation
Description: Fit Generalized Linear Models to continuous and count outcomes, as well as estimate the prevalence of misrepresentation of an important binary predictor. Misrepresentation typically arises when there is an incentive for the binary factor to be misclassified in one direction (e.g., in insurance settings where policy holders may purposely deny a risk status in order to lower the insurance premium). This is accomplished by treating a subset of the response variable as resulting from a mixture distribution. Model parameters are estimated via the Expectation Maximization algorithm and standard errors of the estimates are obtained from closed forms of the Observed Fisher Information. For an introduction to the models and the misrepresentation framework, see Xia et. al., (2023) <https://variancejournal.org/article/73151-maximum-likelihood-approaches-to-misrepresentation-models-in-glm-ratemaking-model-comparisons>.
Author: Patrick Rafael [cre, aut],
Xia Michelle [aut],
Rexford Akakpo [aut]
Maintainer: Patrick Rafael <pbr2608@vt.edu>
Diff between glmMisrep versions 0.1.1 dated 2024-04-18 and 0.1.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- NEWS | 6 ++++++ man/LnRegMisrepEM.Rd | 4 ++-- man/MEPS14.Rd | 2 +- man/NormRegMisrepEM.Rd | 4 ++-- man/gammaRegMisrepEM.Rd | 4 ++-- man/nbRegMisrepEM.Rd | 4 ++-- man/poisRegMisrepEM.Rd | 4 ++-- man/predict.misrepEM.Rd | 3 ++- tests/LN-testing.R | 6 +++--- tests/NB-testing.R | 6 +++--- tests/Norm-testing.R | 2 +- tests/Pois-testing.R | 35 +++++++++++++++++++---------------- tests/gamma-testing.R | 6 +++--- 15 files changed, 65 insertions(+), 55 deletions(-)
Title: Bioinformatic Distances
Description: Provides a unified interface for computing, comparing, and
examining distances, dissimilarities, divergences, and selected
similarities for bioinformatics data. The core installation exposes 60
canonical named routes for numerical data and more than 90 when the
suggested 'philentropy' backend is installed; aliases, user-defined
functions, and mixed-data combinations are not included in these counts.
Weighted Minkowski distances can be computed through 'parallelDist', an
internal multicore implementation, or optional 'OpenCL' kernels, while the
established weighted Euclidean GPU implementation is retained as the
optimized p = 2 route. The package also supports theory-guided comparison
of distance distributions for clustering, explicit mathematical property
classifications, mixed-data constructions through 'manydist', and a
specialized Gene Ontology-derived TF-IDF distance.
Author: Quirin Stier [aut, rev, ctb] ,
Michael Thrun [aut, cre] ,
Luca Brinkmann [ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between BIDistances versions 1.0.0 dated 2026-08-19 and 1.0.1 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 2 +- tests/testthat/test-fast-dip-pvalues.R | 17 ++++++++++++----- 4 files changed, 20 insertions(+), 13 deletions(-)
Title: Access Argentine WFS and WMS Geospatial Web Services
Description: Discovers and reads geospatial layers published by Argentine
public organizations through the Open Geospatial Consortium standards
Web Feature Service (WFS) and Web Map Service (WMS). Provides a cached
catalogue of endpoints, capability parsing with version negotiation,
paginated vector downloads returned as 'sf' objects, and raster map
retrieval returned as 'terra' objects. For the underlying standards see
<https://www.ogc.org/standards/wfs/> and <https://www.ogc.org/standards/wms/>.
Author: Thomas Artopoulos [aut, cre]
Maintainer: Thomas Artopoulos <thomas.artopoulos@gmail.com>
Diff between Argentum versions 1.0.0 dated 2025-02-12 and 2.1.0 dated 2026-08-20
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Title: A Comprehensive Collection of Agricultural and Agronomic
Datasets
Description: Offers a rich and diverse collection of datasets focused on agriculture, agronomy, animal science,
and related fields. The package includes experimental, observational, and field-trial data on crops such as rice,
wheat, corn, soybean, cotton, coffee, avocado, and orange, as well as forestry species including bamboo, eucalyptus,
and timber. Datasets cover plant breeding and genetics, factorial and randomized block experiments, herbicide and
insecticide efficacy trials, pest and disease infestation, soil characteristics and land suitability, plant growth
regulators, seed germination, and crop yield modeling. Additional datasets address animal science topics such as
cattle insemination and conception, pig and broiler growth, lamb births, and toxicology studies on aquatic and
non-target species. Data sources include peer-reviewed agronomic studies, uniformity and Latin square field trials,
glasshouse experiments, and international agricultural surveys.
Designed for agronomists, researchers [...truncated...]
Author: Renzo Caceres Rossi [aut, cre] ,
Prabhanjan Tattar [ctb] ,
A.P. Gore [ctb] ,
S.A. Paranjape [ctb] ,
M.B. Kulkarni [ctb] ,
Gabriel Danilo Shimizu [ctb] ,
Rodrigo Yudi Palhaci Marubayashi [ctb] ,
Leandro Simoes Azeredo Goncalves [ctb] ,
Al-Ahmadgaid B. [...truncated...]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between agridatasets versions 0.1.0 dated 2026-08-08 and 0.1.1 dated 2026-08-20
DESCRIPTION | 643 ++++++++++++++++++++++- MD5 | 161 ++--- NEWS.md |only R/agridatasets-package.R | 2 R/data-documentation.R | 2 R/view_datasets_agridatasets.R | 2 README.md | 11 inst/CITATION | 6 inst/licenses/LICENSE.md | 27 inst/licenses/LICENSES_DETAILS.md | 10 tests/testthat/test-alfalfa_soil.R | 2 tests/testthat/test-apple_canker.R | 2 tests/testthat/test-apple_uniformity.R | 2 tests/testthat/test-arabica_soil.R | 2 tests/testthat/test-arabica_temp.R | 2 tests/testthat/test-arabica_terrain.R | 2 tests/testthat/test-arabica_water.R | 2 tests/testthat/test-avocado_us_sale.R | 2 tests/testthat/test-bamboo_growth.R | 2 tests/testthat/test-biological_control.R | 2 tests/testthat/test-bird_grazing.R | 2 tests/testthat/test-black_duck_survival.R | 2 tests/testthat/test-blackgrass_herbicide.R | 2 tests/testthat/test-broiler_growth.R | 2 tests/testthat/test-budworm_pyrethroid.R | 2 tests/testthat/test-carrot_fly_infestation.R | 2 tests/testthat/test-carrot_insecticide.R | 2 tests/testthat/test-cattle_butterfat.R | 2 tests/testthat/test-cauliflower_growth.R | 2 tests/testthat/test-coffee_composition.R | 2 tests/testthat/test-coffee_production.R | 2 tests/testthat/test-cork_tree_direction.R | 2 tests/testthat/test-corn_hybrid_density.R | 2 tests/testthat/test-cotton_pesticide.R | 2 tests/testthat/test-cowpea_maize_yield.R | 2 tests/testthat/test-cows_insemination.R | 2 tests/testthat/test-earthworm_crop_soils.R | 2 tests/testthat/test-earthworm_population.R | 2 tests/testthat/test-eelworm_fumigation.R | 2 tests/testthat/test-egg_weight_daily.R | 2 tests/testthat/test-eucalyptus_progenies.R | 2 tests/testthat/test-fish_feeding.R | 2 tests/testthat/test-fungicide_latin_square.R | 2 tests/testthat/test-grape_uniformity.R | 2 tests/testthat/test-guinea_pig_sleep.R | 2 tests/testthat/test-hawaii_plant_size.R | 2 tests/testthat/test-hawaii_tree_growth.R | 2 tests/testthat/test-idn_rice_farms.R | 2 tests/testthat/test-kiwi_crop_design.R | 2 tests/testthat/test-ladybird_fungus.R | 2 tests/testthat/test-lamb_births.R | 2 tests/testthat/test-nitrofen_toxicity.R | 2 tests/testthat/test-orange_rootstocks.R | 2 tests/testthat/test-peach_uniformity.R | 2 tests/testthat/test-pig_weight_gain.R | 2 tests/testthat/test-plant_growth_regulator.R | 2 tests/testthat/test-pollen_removal.R | 2 tests/testthat/test-potato_scab_sulfur.R | 2 tests/testthat/test-rabbit_body_mass.R | 2 tests/testthat/test-red_wine_quality.R | 2 tests/testthat/test-rice_wheat_production.R | 2 tests/testthat/test-river_deforestation.R | 2 tests/testthat/test-robusta_soil.R | 2 tests/testthat/test-robusta_temp.R | 2 tests/testthat/test-robusta_terrain.R | 2 tests/testthat/test-robusta_water.R | 2 tests/testthat/test-seed_germination.R | 2 tests/testthat/test-soil_munsell_colors.R | 2 tests/testthat/test-soil_munsell_minerals.R | 2 tests/testthat/test-soybean_cultivars.R | 2 tests/testthat/test-strawberry_cross_disease.R | 2 tests/testthat/test-strawberry_yield.R | 2 tests/testthat/test-timber_genetics.R | 2 tests/testthat/test-tomato_insecticides.R | 2 tests/testthat/test-tomato_uniformity.R | 2 tests/testthat/test-toxin_lethal_dose.R | 2 tests/testthat/test-turnip_density.R | 2 tests/testthat/test-us_state_soils.R | 2 tests/testthat/test-view_datasets_agridatasets.R | 2 tests/testthat/test-wheat_bunt.R | 2 tests/testthat/test-wheat_splitsplit.R | 2 tests/testthat/test-willow_cutting_yield.R | 2 82 files changed, 824 insertions(+), 184 deletions(-)
Title: High-Dimensional Mediation Analysis via Transfer Learning
Description: Provides a framework for high-dimensional mediation analysis using transfer learning. The main function TransHDM() integrates large-scale source data to improve the detection power of potential mediators in small-sample target studies. It addresses data heterogeneity via transfer regularization and debiased estimation while controlling the false discovery rate. The package also includes utilities for data generation (gen_simData_homo(), gen_simData_hetero()), baseline methods such as lasso() and dblasso(), sure independence screening via SIS(), and model diagnostics through source_detection(). The methodology is described in Pan et al. (2025) <doi:10.1093/bib/bbaf460>.
Author: Huer Gao [aut, cre, cph],
Lulu Pan [aut, cph],
Yongfu Yu [ctb, cph],
Guoyou Qin [ctb, cph]
Maintainer: Huer Gao <26111020050@m.fudan.edu.cn>
Diff between TransHDM versions 1.0.1 dated 2026-03-17 and 1.1.3 dated 2026-08-20
TransHDM-1.0.1/TransHDM/vignettes/dblasso.png |only TransHDM-1.0.1/TransHDM/vignettes/model.png |only TransHDM-1.1.3/TransHDM/DESCRIPTION | 19 TransHDM-1.1.3/TransHDM/MD5 | 85 TransHDM-1.1.3/TransHDM/NAMESPACE | 14 TransHDM-1.1.3/TransHDM/R/10_mediation_inference.R |only TransHDM-1.1.3/TransHDM/R/11_joint_test.R |only TransHDM-1.1.3/TransHDM/R/1_generate_simulationData_homogeneous_design.R | 20 TransHDM-1.1.3/TransHDM/R/2_generate_simulationData_heterogeneous_design.R | 22 TransHDM-1.1.3/TransHDM/R/4_lasso.R | 21 TransHDM-1.1.3/TransHDM/R/5_dblasso.R | 19 TransHDM-1.1.3/TransHDM/R/7_source_detect.R | 8 TransHDM-1.1.3/TransHDM/R/8_SIS.R | 26 TransHDM-1.1.3/TransHDM/R/9_TransHDM.R | 781 ++-- TransHDM-1.1.3/TransHDM/R/data_inflam.R |only TransHDM-1.1.3/TransHDM/R/plot_TransHDM.R |only TransHDM-1.1.3/TransHDM/R/plot_source_detect.R |only TransHDM-1.1.3/TransHDM/R/summary_10.R |only TransHDM-1.1.3/TransHDM/R/summary_4.R | 16 TransHDM-1.1.3/TransHDM/R/summary_5.R | 152 TransHDM-1.1.3/TransHDM/R/summary_7.R | 17 TransHDM-1.1.3/TransHDM/R/summary_8.R | 33 TransHDM-1.1.3/TransHDM/R/summary_9.R | 23 TransHDM-1.1.3/TransHDM/build/partial.rdb |binary TransHDM-1.1.3/TransHDM/build/vignette.rds |binary TransHDM-1.1.3/TransHDM/data |only TransHDM-1.1.3/TransHDM/inst/WORDLIST | 63 TransHDM-1.1.3/TransHDM/inst/doc/tutorial.R | 326 -- TransHDM-1.1.3/TransHDM/inst/doc/tutorial.Rmd | 361 -- TransHDM-1.1.3/TransHDM/inst/doc/tutorial.html | 1577 ++++------ TransHDM-1.1.3/TransHDM/man/SIS.Rd | 23 TransHDM-1.1.3/TransHDM/man/TransHDM.Rd | 35 TransHDM-1.1.3/TransHDM/man/dblasso.Rd | 16 TransHDM-1.1.3/TransHDM/man/gen_simData_hetero.Rd | 2 TransHDM-1.1.3/TransHDM/man/gen_simData_homo.Rd | 2 TransHDM-1.1.3/TransHDM/man/inflam_effect.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_external1.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_external2.Rd |only TransHDM-1.1.3/TransHDM/man/inflam_target.Rd |only TransHDM-1.1.3/TransHDM/man/joint_test.Rd |only TransHDM-1.1.3/TransHDM/man/lasso.Rd | 17 TransHDM-1.1.3/TransHDM/man/mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/man/plot.TransHDM.Rd |only TransHDM-1.1.3/TransHDM/man/plot.source_detection.Rd |only TransHDM-1.1.3/TransHDM/man/print.SIS.Rd |only TransHDM-1.1.3/TransHDM/man/print.TransHDM.Rd |only TransHDM-1.1.3/TransHDM/man/print.dblasso.Rd |only TransHDM-1.1.3/TransHDM/man/print.lasso.Rd |only TransHDM-1.1.3/TransHDM/man/print.mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/man/print.source_detection.Rd |only TransHDM-1.1.3/TransHDM/man/print.summary.dblasso.Rd |only TransHDM-1.1.3/TransHDM/man/source_detection.Rd | 6 TransHDM-1.1.3/TransHDM/man/summary.mediation_inference.Rd |only TransHDM-1.1.3/TransHDM/tests/test_pipeline.R |only TransHDM-1.1.3/TransHDM/vignettes/tutorial.Rmd | 361 -- 55 files changed, 1857 insertions(+), 2188 deletions(-)
Title: Interface to 'JDemetra+ 3.x' Time Series Analysis Software
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to decompose a time series, including
high-frequency data with multiple periodicities.
Author: Jean Palate [aut],
Tanguy Barthelemy [aut, cre, cph]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3xjars versions 0.1.1 dated 2026-07-08 and 0.1.2 dated 2026-08-20
rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-advancedsa-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-advancedsa-base-core-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-highfreq-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-highfreq-base-core-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-sts-base-api-2.4.1.jar |only rjd3xjars-0.1.1/rjd3xjars/inst/java/jdplus-sts-base-core-2.4.1.jar |only rjd3xjars-0.1.2/rjd3xjars/DESCRIPTION | 14 +++--- rjd3xjars-0.1.2/rjd3xjars/MD5 | 22 +++++----- rjd3xjars-0.1.2/rjd3xjars/NEWS.md | 19 ++++++++ rjd3xjars-0.1.2/rjd3xjars/R/zzz.R | 6 +- rjd3xjars-0.1.2/rjd3xjars/README.md | 4 - rjd3xjars-0.1.2/rjd3xjars/inst/WORDLIST |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-advancedsa-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-advancedsa-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-highfreq-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-highfreq-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-sts-base-api-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/inst/java/jdplus-sts-base-core-2.5.2.jar |only rjd3xjars-0.1.2/rjd3xjars/tests |only 19 files changed, 44 insertions(+), 21 deletions(-)
Title: Neuroscience Extension Package for ADaM in 'R' Asset Library
Description: Programming neuroscience specific Clinical Data Standards
Interchange 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>). This package
extends the 'admiral' package.
Author: Jian Wang [aut] ,
Meilin Jiang [aut, cre] ,
Miles Almond [aut] ,
Xiao Chen [aut] ,
Fanny Gautier [aut] ,
Gayatri G. [aut],
Leena Khatri [aut] ,
Edoardo Mancini [aut] ,
Eric Nantz [aut],
Lina Patil [aut],
Chris Pelentrides [aut],
Katie Withycombe [aut [...truncated...]
Maintainer: Meilin Jiang <meilin.jiang@lilly.com>
Diff between admiralneuro versions 0.2.0 dated 2026-02-04 and 0.3.0 dated 2026-08-20
DESCRIPTION | 34 +-- MD5 | 54 ++--- NAMESPACE | 310 +++++++++++++++-------------- NEWS.md | 31 ++ R/admiralneuro-package.R | 39 +-- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/adlb.R |only inst/doc/adlb.Rmd |only inst/doc/adlb.html |only inst/doc/admiralneuro.Rmd | 6 inst/doc/admiralneuro.html | 11 - inst/doc/adnv.Rmd | 8 inst/doc/adnv.html | 12 - inst/doc/adpet.Rmd | 10 inst/doc/adpet.html | 10 inst/templates/ad_adlb.R |only man/admiralneuro-package.Rd | 6 man/admiralneuro_adapet.Rd | 2 man/admiralneuro_adtpet.Rd | 2 man/adsl_neuro.Rd | 2 man/compute_centiloid.Rd | 4 man/compute_upsit_percentile.Rd | 4 man/figures/eli_lilly_and_company_logo.png |binary man/figures/roche_logo.png |binary vignettes/adlb.Rmd |only vignettes/admiralneuro.Rmd | 6 vignettes/adnv.Rmd | 8 vignettes/adpet.Rmd | 10 vignettes/articles |only 31 files changed, 330 insertions(+), 246 deletions(-)
Title: Solvers for Boundary Value Problems of Differential Equations
Description: Functions that solve boundary value problems ('BVP') of systems of ordinary
differential equations ('ODE') and differential algebraic equations ('DAE').
The functions provide an interface to the FORTRAN functions
'twpbvpC', 'colnew/colsys', and an R-implementation of the shooting method.
Mazzia, F., J.R. Cash and K. Soetaert (2014),
"Solving Boundary Value Problems in the Open Source Software R:
Package bvpSolve" <doi:10.7494/OpMath.2014.34.2.387>.
Author: Karline Soetaert [aut] ,
Jeff Cash [aut],
Francesca Mazzia [aut],
Uri M. Ascher [ctb] ,
G. Bader [ctb] ,
J. Christiansen [ctb] ,
Robert R. Russell [ctb] ,
George Helffrich [cre, ctb]
Maintainer: George Helffrich <ghfbsd@gmail.com>
This is a re-admission after prior archival of version 1.4.4.1 dated 2023-09-21
Diff between bvpSolve versions 1.4.4.1 dated 2023-09-21 and 1.4.4.2 dated 2026-08-20
DESCRIPTION | 37 MD5 | 50 R/Utilities.R | 4 R/bvpsolver.R | 14 build/vignette.rds |binary inst/doc/bvpSolve.R | 1596 ++++++++++++------------- inst/doc/bvpSolve.Rnw | 56 inst/doc/bvpSolve.pdf |binary inst/doc/bvpTests.R | 3114 ++++++++++++++++++++++++------------------------- inst/doc/bvpTests.Rnw | 57 inst/doc/bvpTests.pdf |binary man/bvpSolve.Rd | 8 man/bvpcol.Rd | 12 man/bvptwp.Rd | 6 man/diagnostics.Rd | 12 man/plot.bvpSolve.Rd | 5 src/acdcR.f | 4 src/colnewR.f | 6 src/errmsg.f | 4 src/forcings.c | 2 src/rprintf.c | 36 src/twpbvpa.f | 2 src/twpbvplc.f | 2 vignettes/bvpSolve.Rnw | 56 vignettes/bvpTests.Rnw | 57 vignettes/docs.bib | 4 26 files changed, 2586 insertions(+), 2558 deletions(-)
Title: Gene Operations for Real-Coded Genes
Description: Representation-dependent gene-level operations
for genetic and evolutionary algorithms with real-coded genes
used in the R-package 'xega' <https://CRAN.R-project.org/package=xega>
are collected in this package. The common feature of the gene
operations is that all of them are useful for derivation-free
optimization algorithms. At the moment the package
implements initialization, mutation, crossover, and replication
operations for differential evolution as described in
Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>. In addition, several (more recent)
methods for determining the scale factor are provided.
For 'xega''s architecture,
see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaDfGene versions 1.0.0.9 dated 2026-02-16 and 1.0.0.10 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/xegaDfReplicate.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Construct Mixed Type Data Structures with Vectors of Vectors
Description: Mixed type vectors are useful for combining semantically similar
classes. Some examples of semantically related classes include time across
different granularities (e.g. daily, monthly, annual) and probability
distributions (e.g. Normal, Uniform, Poisson). These groups of vector types
typically share common statistical operations which vary in results with the
attributes of each vector. The 'vecvec' data structure facilitates efficient
storage and computation across multiple vectors within the same object.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vecvec versions 1.2.0 dated 2026-06-23 and 1.3.0 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 54 ++++++++------ NAMESPACE | 2 NEWS.md | 42 +++++++++++ R/apply.R | 121 +++++++++++++++++++++++++++++++++ R/coercion.R | 13 +++ R/compare.R | 59 +++++++++++++++- R/group-methods.R | 54 ++++++++------ R/hook.R | 24 ++++-- R/predicates.R | 41 +++++++++-- R/replacement.R | 87 +++++++++++++++++++++-- R/utils.R | 97 ++++++++++++++++++++++++-- R/vctrs.R | 102 +++++++++++++++++++++++---- R/vecvec-package.R | 1 R/vecvec.R | 105 ++++++++++++++++------------ README.md | 6 - man/vecvec_mapply.Rd |only src |only tests/testthat/_snaps/format.md | 54 ++++++++++++++ tests/testthat/test-apply.R |only tests/testthat/test-arith.R | 13 +++ tests/testthat/test-coercion.R |only tests/testthat/test-compare.R | 42 +++++++++++ tests/testthat/test-format.R | 21 +++++ tests/testthat/test-math.R | 22 ++++++ tests/testthat/test-predicates.R | 77 +++++++++++++++++++++ tests/testthat/test-replacement.R | 44 ++++++++++++ tests/testthat/test-utils.R |only tests/testthat/test-vctrs.R | 139 ++++++++++++++++++++++++++++++++++++++ tests/testthat/test-vecvec.R | 19 +++++ 30 files changed, 1095 insertions(+), 154 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.16.0 dated 2025-10-22 and 2.16.1 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 46 +++--- NAMESPACE | 28 ++- NEWS.md | 12 + R/dictionary_to_labels.R | 14 + R/lookfor.R | 11 - R/na_values.R | 4 R/recode.R | 15 + R/retrocompatibility.R | 2 R/to_character.R | 58 ++++--- R/to_factor.R | 104 +++++++------ R/val_labels.R | 193 +++++++++++++++---------- R/var_label.R | 11 - README.md | 3 build/vignette.rds |binary inst/doc/look_for.html | 220 ++++++++++++++--------------- inst/doc/missing_values.html | 3 man/dictionary_to_variable_labels.Rd | 6 man/na_values.Rd | 4 man/reexports.Rd | 4 man/to_character.Rd | 2 man/to_factor.Rd | 6 tests/testthat/test-dictionary_to_labels.R | 15 + tests/testthat/test-labelled.r | 70 ++++++++- 24 files changed, 497 insertions(+), 342 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.11.0 dated 2026-08-03 and 0.12.0 dated 2026-08-20
DESCRIPTION | 16 MD5 | 41 - NAMESPACE | 19 NEWS.md | 26 R/contributions.R | 4 R/deprecated.R |only R/plot_categorical.R | 63 ++ R/plot_continuous.R | 42 + R/plot_means.R | 29 + R/tbl_maihda.R | 874 +++++++++++++++++++++++++++------ README.md | 2 inst/extdata |only man/contributions.Rd | 4 man/da.svyglm.fit.Rd | 40 - man/deprecated.Rd |only man/plot_categorical.Rd | 11 man/plot_continuous.Rd | 19 man/plot_means.Rd | 8 man/tbl_maihda.Rd | 216 ++++++-- tests/testthat/test-maihda.R | 48 + tests/testthat/test-plot_categorical.R | 13 tests/testthat/test-plot_continuous.R | 22 tests/testthat/test-plot_means.R | 7 23 files changed, 1253 insertions(+), 251 deletions(-)
Title: Quiver Plots for 'ggplot2'
Description: An extension of 'ggplot2' to provide quiver plots to visualise vector fields.
This functionality is implemented using a geom to produce a new graphical layer, which
allows aesthetic options. This layer can be overlaid on a map to improve visualisation
of mapped data.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggquiver versions 0.4.0 dated 2025-12-18 and 0.5.0 dated 2026-08-20
ggquiver-0.4.0/ggquiver/R/ggquiver.R |only ggquiver-0.5.0/ggquiver/DESCRIPTION | 8 ggquiver-0.5.0/ggquiver/MD5 | 36 - ggquiver-0.5.0/ggquiver/NAMESPACE | 5 ggquiver-0.5.0/ggquiver/NEWS.md | 10 ggquiver-0.5.0/ggquiver/R/geom-quiver.r | 64 + ggquiver-0.5.0/ggquiver/R/ggquiver-package.R |only ggquiver-0.5.0/ggquiver/R/stat-quiver.r | 37 - ggquiver-0.5.0/ggquiver/README.md | 13 ggquiver-0.5.0/ggquiver/man/figures/README-sealplot-custom-1.png |binary ggquiver-0.5.0/ggquiver/man/geom_quiver.Rd | 14 ggquiver-0.5.0/ggquiver/man/ggquiver-package.Rd | 2 ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/basic-quiver-plot.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-center.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-closed-arrow.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-legend-arrowhead.svg |only ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-random-data.svg | 20 ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-rescale.svg | 338 +++++----- ggquiver-0.5.0/ggquiver/tests/testthat/_snaps/geom_quiver/quiver-plot-with-vecsize-0.svg | 334 ++++----- ggquiver-0.5.0/ggquiver/tests/testthat/test-geom_quiver.R | 43 + ggquiver-0.5.0/ggquiver/tests/testthat/test-stat_quiver.R |only 21 files changed, 1038 insertions(+), 888 deletions(-)
Title: Schema-Based Validation of 'R' Objects with User-Defined Rules
Description: A schema-based validation framework for 'R' objects using user-defined rules. Provides three 'S7' classes 'Registry', 'Schema', and 'Validator' to manage rules, define list-based schemas, and validate data in a flexible and extensible manner.
Author: Luke Jenkins [aut, cre, cph]
Maintainer: Luke Jenkins <luke-jenkins-dev@outlook.com>
Diff between fluffy versions 1.0.0 dated 2026-06-10 and 1.0.1 dated 2026-08-20
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 16 R/aaa_Schema.r | 7 R/abb_add_rule_generics.r | 5 R/registry_defaults.r | 404 ++++++---- R/utils.r | 2 README.md | 11 inst/doc/custom-rules.Rmd | 2 inst/doc/custom-rules.html | 17 inst/doc/validating-data.R | 4 inst/doc/validating-data.Rmd | 4 inst/doc/validating-data.html | 16 inst/doc/validation-rules.Rmd | 2 inst/doc/validation-rules.html | 47 - man/Schema.Rd | 8 man/add_rule.Rd | 5 man/show_builtins.Rd | 2 tests/testthat/test-cross_rule_allowed_forbidden_type_mismatch.r | 44 + tests/testthat/test-cross_rule_length_min_max_length.r |only tests/testthat/test-rule_coerce.r | 5 tests/testthat/test-rule_coerce_last.r | 134 +-- tests/testthat/test-rule_length.r |only tests/testthat/test-rule_min_max_length.r | 2 tests/testthat/test-rule_type.r | 3 vignettes/custom-rules.Rmd | 2 vignettes/validating-data.Rmd | 4 vignettes/validation-rules.Rmd | 2 28 files changed, 539 insertions(+), 267 deletions(-)
Title: Function Argument Validation
Description: Validate function arguments succinctly with informative error messages.
Author: Luke Jenkins [aut, cre, cph]
Maintainer: Luke Jenkins <luke-jenkins-dev@outlook.com>
Diff between favr versions 1.0.0 dated 2025-12-15 and 2.0.0 dated 2026-08-20
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Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson [aut, cre],
Dan Reuman [aut],
Rob Emerson [ctb]
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-639 dated 2024-07-24 and 0.1-640 dated 2026-08-20
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 28 ++++++++++++++-------------- inst/doc/CheddarQuickstart.R | 2 -- inst/doc/CheddarQuickstart.pdf |binary inst/doc/Collections.R | 2 -- inst/doc/Collections.pdf |binary inst/doc/Community.R | 2 -- inst/doc/Community.pdf |binary inst/doc/ImportExport.R | 2 -- inst/doc/ImportExport.pdf |binary inst/doc/PlotsAndStats.R | 2 -- inst/doc/PlotsAndStats.pdf |binary man/cheddar.Rd | 4 ++-- tests/util_test.R | 21 ++++++++++----------- vignettes/cheddar.bib | 16 +++++++++++++++- 15 files changed, 59 insertions(+), 44 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.22.0 dated 2025-09-17 and 1.23.0 dated 2026-08-20
DESCRIPTION | 8 MD5 | 163 ++++++------- NAMESPACE | 46 ++- NEWS.md | 18 + R/assert_package.R | 14 - R/custom_tidiers.R | 123 ++++++++-- R/helpers.R | 7 R/model_get_coefficients_type.R | 86 +++++++ R/model_get_pairwise_contrasts.R | 39 +-- R/model_list_terms_levels.R | 16 - R/model_list_variables.R | 4 R/tidy_add_coefficients_type.R | 6 R/tidy_add_estimate_to_reference_rows.R | 11 R/tidy_add_pairwise_contrasts.R | 19 - R/tidy_add_reference_rows.R | 8 R/tidy_and_attach.R | 11 R/tidy_disambiguate_terms.R | 3 R/tidy_group_by.R | 9 R/tidy_select_variables.R | 5 README.md | 6 build/vignette.rds |binary data/supported_models.rda |binary inst/doc/broom-helpers.html | 353 ++++++++++++++--------------- man/dot-clean_backticks.Rd | 4 man/dot-escape_regex.Rd | 4 man/model_compute_terms_contributions.Rd | 42 +-- man/model_get_assign.Rd | 42 +-- man/model_get_coefficients_type.Rd | 45 +-- man/model_get_contrasts.Rd | 42 +-- man/model_get_model.Rd | 42 +-- man/model_get_model_frame.Rd | 42 +-- man/model_get_model_matrix.Rd | 44 +-- man/model_get_n.Rd | 42 +-- man/model_get_nlevels.Rd | 42 +-- man/model_get_offset.Rd | 42 +-- man/model_get_pairwise_contrasts.Rd | 42 +-- man/model_get_response.Rd | 42 +-- man/model_get_response_variable.Rd | 42 +-- man/model_get_terms.Rd | 42 +-- man/model_get_weights.Rd | 42 +-- man/model_get_xlevels.Rd | 42 +-- man/model_identify_variables.Rd | 44 +-- man/model_list_contrasts.Rd | 42 +-- man/model_list_higher_order_variables.Rd | 42 +-- man/model_list_terms_levels.Rd | 42 +-- man/model_list_variables.Rd | 44 +-- man/reexports.Rd | 2 man/select_helpers.Rd | 2 man/supported_models.Rd | 1 man/tidy_add_coefficients_type.Rd | 34 +- man/tidy_add_contrasts.Rd | 32 +- man/tidy_add_estimate_to_reference_rows.Rd | 38 +-- man/tidy_add_header_rows.Rd | 32 +- man/tidy_add_n.Rd | 34 +- man/tidy_add_pairwise_contrasts.Rd | 32 +- man/tidy_add_reference_rows.Rd | 36 +- man/tidy_add_term_labels.Rd | 32 +- man/tidy_add_variable_labels.Rd | 32 +- man/tidy_all_effects.Rd | 14 - man/tidy_attach_model.Rd | 34 +- man/tidy_avg_comparisons.Rd | 14 - man/tidy_avg_slopes.Rd | 14 - man/tidy_broom.Rd | 15 - man/tidy_coxphms.Rd |only man/tidy_disambiguate_terms.Rd | 32 +- man/tidy_ggpredict.Rd | 14 - man/tidy_group_by.Rd | 32 +- man/tidy_identify_variables.Rd | 32 +- man/tidy_marginal_contrasts.Rd | 14 - man/tidy_marginal_predictions.Rd | 14 - man/tidy_margins.Rd | 14 - man/tidy_multgee.Rd | 15 - man/tidy_parameters.Rd | 17 - man/tidy_plus_plus.Rd | 34 +- man/tidy_remove_intercept.Rd | 32 +- man/tidy_select_variables.Rd | 32 +- man/tidy_svy_vglm.Rd | 15 - man/tidy_vgam.Rd | 15 - man/tidy_with_broom_or_parameters.Rd | 15 - man/tidy_zeroinfl.Rd | 15 - tests/testthat/test-disambiguate_terms.R | 14 - tests/testthat/test-select_helpers.R | 9 tests/testthat/test-tidy_plus_plus.R | 42 +++ 83 files changed, 1468 insertions(+), 1191 deletions(-)
Title: Bayesian Estimation of Mixtures of Multivariate Bernoulli
Distributions
Description: Fully Bayesian inference for estimating the number of clusters and related parameters to heterogeneous binary data.
Author: Panagiotis Papastamoulis [aut, cre]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between BayesBinMix versions 1.4.1 dated 2017-07-04 and 1.4.2 dated 2026-08-20
DESCRIPTION | 18 +++++++++++++----- MD5 | 6 +++--- inst/CITATION | 2 +- man/coupledMetropolis.Rd | 2 +- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Operations on Permutation Genes
Description: An implementation of
representation-dependent gene level operations for
genetic algorithms with genes representing permutations:
Initialization of genes, mutation, and crossover.
The crossover operation provided is position-based crossover
(Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8).
For mutation, several variants are included: Order-based mutation
(Syswerda, G., Chap. 21 in Davis, L. (1991, ISBN:0-442-00173-8),
randomized Lin-Kernighan heuristics
(Croes, G. A. (1958) <doi:10.1287/opre.6.6.791> and
Lin, S. and Kernighan. B. W. (1973)
<doi:10.1287/opre.21.2.498>),
and randomized greedy operators.
A random mix operator for mutation selects a mutation variant
randomly.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPermGene versions 1.0.0.1 dated 2025-04-16 and 1.0.0.2 dated 2026-08-20
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS | 6 ++++++ R/xegaPermMutate.R | 8 ++++---- 4 files changed, 19 insertions(+), 13 deletions(-)
Title: Binary Gene Operations for Genetic Algorithms
Description: Representation-dependent gene level operations of a
genetic algorithm with binary coded genes
for the R-package 'xega' <https://CRAN.R-project.org/package=xega>:
Initialization of random binary genes, several gene maps for
binary genes, several mutation operators, several crossover
operators with 1 and 2 kids, replication
pipelines for 1 and 2 kids, and, last but not least, function
factories for configuration.
See Goldberg, D. E. (1989, ISBN:0-201-15767-5).
For crossover operators, see
Syswerda, G. (1989, ISBN:1-55860-066-3),
Spears, W. and De Jong, K. (1991, ISBN:1-55860-208-9).
For mutation operators, see
Stanhope, S. A. and Daida, J. M. (1996, ISBN:0-18-201-031-7).
For 'xega''s architecture,
see Geyer-Schulz, A. (2025) <doi:10.5445/IR/1000187255>.
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaGaGene versions 1.0.0.6 dated 2026-02-16 and 1.0.0.7 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/xegaOperatorPipelinesInGene.R | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>),
and grammatical differential evolution (O'Neill, M. and Brabazon, A. (2006) in
Arabinia, H. (2006, ISBN:978-193-241596-3).
All algorithms reuse basic adaptive mechanisms for performance optimization.
For the architecture, see Geyer-Sc [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.23 dated 2026-02-17 and 0.9.1.0 dated 2026-08-20
DESCRIPTION | 20 +- MD5 | 24 +- NAMESPACE | 8 NEWS | 52 +++++ R/xega-package.R | 47 ++++- R/xegaImproved.R |only R/xegaRerun.R | 42 +++- R/xegaResult.R | 5 R/xegaRun.R | 473 ++++++++++++++++++++++++++++++++++++++++++++++++---- R/xegaVersion.R | 4 man/xega.Rd | 49 +++++ man/xegaImproved.Rd |only man/xegaReRun.Rd | 9 man/xegaRun.Rd | 262 ++++++++++++++++++++++++++-- 14 files changed, 901 insertions(+), 94 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detailed data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored and shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.2.2 dated 2026-06-29 and 1.2.3 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 24 ++--- NAMESPACE | 80 ++++++++++------- R/ClickHouse.R | 2 R/chMDB.R | 12 ++ R/chTKCat.R | 10 +- R/fileMDB.R | 18 +-- R/shiny-helpers.R | 4 build/vignette.rds |binary inst/ClickHouse/Data-Model/chTKCat-MDB-data-model.json | 61 ++++++++---- inst/doc/TKCat-KMR-POK.html | 6 - inst/doc/TKCat.html | 64 ++++++------- inst/pkgdown.yml | 6 - 13 files changed, 175 insertions(+), 120 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Includes functionality to estimate latent class analyses, and to plot
'dagitty' and 'igraph' objects.
Author: Caspar J. van Lissa [aut, cre] ,
Mauricio Garnier-Villarreal [ctb] ,
Frank C Gootjes [ctb]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between tidySEM versions 0.2.10 dated 2026-01-11 and 0.2.11 dated 2026-08-20
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Title: Outlier Robust Two-Stage Least Squares Inference and Testing
Description: An implementation of easy tools for outlier robust inference in
two-stage least squares (2SLS) models. The user specifies a reference
distribution against which observations are classified as outliers or not.
After removing the outliers, adjusted standard errors are automatically
provided. Furthermore, several statistical tests for the false outlier
detection rate can be calculated. The outlier removing algorithm can be
iterated a fixed number of times or until the procedure converges. The
algorithms and robust inference are described in more detail in Jiao (2019)
<https://drive.google.com/file/d/1qPxDJnLlzLqdk94X9wwVASptf1MPpI2w/view>.
Author: Jonas Kurle [aut, cre]
Maintainer: Jonas Kurle <mail@jonaskurle.com>
Diff between robust2sls versions 0.2.3 dated 2025-05-20 and 0.2.4 dated 2026-08-20
robust2sls-0.2.3/robust2sls/tests/testthat/_snaps/monte_carlo |only robust2sls-0.2.3/robust2sls/tests/testthat/_snaps/monte_carlo.md |only robust2sls-0.2.3/robust2sls/tests/testthat/test-monte_carlo.R |only robust2sls-0.2.4/robust2sls/DESCRIPTION | 12 robust2sls-0.2.4/robust2sls/MD5 | 111 robust2sls-0.2.4/robust2sls/NEWS.md | 29 robust2sls-0.2.4/robust2sls/R/class.R | 6 robust2sls-0.2.4/robust2sls/README.md | 32 robust2sls-0.2.4/robust2sls/build/robust2sls.pdf |only robust2sls-0.2.4/robust2sls/build/stage23.rdb |binary robust2sls-0.2.4/robust2sls/build/vignette.rds |binary robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.R | 54 robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.Rmd | 249 - robust2sls-0.2.4/robust2sls/inst/doc/monte-carlo.html | 498 -- robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.R | 5 robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.Rmd | 5 robust2sls-0.2.4/robust2sls/inst/doc/outlier-testing.html | 61 robust2sls-0.2.4/robust2sls/inst/doc/overview.Rmd | 4 robust2sls-0.2.4/robust2sls/inst/doc/overview.html | 31 robust2sls-0.2.4/robust2sls/man/beta_hausman.Rd | 76 robust2sls-0.2.4/robust2sls/man/beta_inf.Rd | 88 robust2sls-0.2.4/robust2sls/man/beta_inf_correction.Rd | 92 robust2sls-0.2.4/robust2sls/man/beta_t.Rd | 68 robust2sls-0.2.4/robust2sls/man/beta_test_avar.Rd | 64 robust2sls-0.2.4/robust2sls/man/conv_diff.Rd | 48 robust2sls-0.2.4/robust2sls/man/new_robust2sls.Rd | 54 robust2sls-0.2.4/robust2sls/man/outliers.Rd | 44 robust2sls-0.2.4/robust2sls/man/outliers_prop.Rd | 46 robust2sls-0.2.4/robust2sls/man/plot.robust2sls.Rd | 52 robust2sls-0.2.4/robust2sls/man/print.robust2sls.Rd | 68 robust2sls-0.2.4/robust2sls/man/validate_robust2sls.Rd | 38 robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/beta_inf_test.md | 518 +-- robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/bootstrap.md | 290 - robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_m0.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test1_m4.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test2_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/class/test3_default.png |binary robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/initial_estimators.md | 1240 +++---- robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/monte_carlo_fixtures |only robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/monte_carlo_fixtures.md |only robust2sls-0.2.4/robust2sls/tests/testthat/_snaps/outlier_tests.md | 1708 +++++----- robust2sls-0.2.4/robust2sls/tests/testthat/create-testdata.R |only robust2sls-0.2.4/robust2sls/tests/testthat/helper-normalise-for-snapshot.R |only robust2sls-0.2.4/robust2sls/tests/testthat/test-beta_inf_test.R | 16 robust2sls-0.2.4/robust2sls/tests/testthat/test-bootstrap.R | 71 robust2sls-0.2.4/robust2sls/tests/testthat/test-initial_estimators.R | 21 robust2sls-0.2.4/robust2sls/tests/testthat/test-iterative_estimators2.R | 9 robust2sls-0.2.4/robust2sls/tests/testthat/test-monte_carlo_fixtures.R |only robust2sls-0.2.4/robust2sls/tests/testthat/test-outlier_tests.R | 115 robust2sls-0.2.4/robust2sls/tests/testthat/test-utility.R | 6 robust2sls-0.2.4/robust2sls/tests/testthat/testdata |only robust2sls-0.2.4/robust2sls/vignettes/monte-carlo.Rmd | 249 - robust2sls-0.2.4/robust2sls/vignettes/outlier-testing.Rmd | 5 robust2sls-0.2.4/robust2sls/vignettes/overview.Rmd | 4 55 files changed, 2884 insertions(+), 3203 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.17.1 dated 2025-11-10 and 2.17.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- R/EMMIX.R | 4 ++-- R/RCLRMIX.R | 2 +- R/RCLSMIX.R | 4 ++-- R/REBMIX.R | 2 +- R/RNGMIX.R | 2 +- R/defaults.R | 31 ++++++++++++------------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ inst/doc/rebmix.R | 2 -- inst/doc/rebmix.Rnw | 12 +++++++----- inst/doc/rebmix.pdf |binary src/emf.cpp | 2 +- src/rebmixf.cpp | 2 +- src/rngmixf.cpp | 2 +- vignettes/rebmix.Rnw | 12 +++++++----- 18 files changed, 61 insertions(+), 61 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.28 dated 2026-07-02 and 1.29 dated 2026-08-20
DESCRIPTION | 8 - MD5 | 48 +++++------ NAMESPACE | 70 +++++++++-------- NEWS.md | 21 +++++ R/class-workbook.R | 29 ++++++- R/converters.R | 19 ++-- R/read.R | 74 +++++++++++++++--- R/wb_load.R | 34 +++++--- R/wb_styles.R | 4 inst/AUTHORS | 1 inst/WORDLIST | 2 man/col2int.Rd | 17 ++-- man/create_font.Rd | 4 man/wb_to_df.Rd | 7 + src/load_workbook.cpp | 46 +++++++---- src/xlsb.cpp | 8 + src/xlsb_funs.h | 117 +++++++++++++++++++++-------- tests/testthat/test-base_font.R | 2 tests/testthat/test-class-workbook.R | 21 ++++- tests/testthat/test-converters.R | 4 tests/testthat/test-loading_workbook.R | 39 +++++++++ tests/testthat/test-read_from_created_wb.R | 12 ++ tests/testthat/test-read_xlsb.R | 2 tests/testthat/test-wb_functions.R | 2 tests/testthat/test-wb_styles.R | 3 25 files changed, 439 insertions(+), 155 deletions(-)
Title: Fast and Extensible Pattern Discovery in Tabular Data
Description: Fast and extensible framework for discovering interesting patterns
in tabular data. The package searches combinations of fuzzy or Boolean
predicates and evaluates the resulting subgroups using statistical, logical,
or structural measures. It supports a broad range of pattern-discovery
tasks, including
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 be supplied to guide custom pattern searches,
making the framework applicable beyond traditional association-rule mining.
Efficient implementation enables pattern discovery on large and dense data
sets. Package includes methods for visualization and supports interactive
explo [...truncated...]
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.2.2 dated 2026-07-22 and 2.2.3 dated 2026-08-20
DESCRIPTION | 37 +- MD5 | 148 +++++----- NAMESPACE | 181 ++++++------ NEWS.md | 9 R/dig.R | 15 - R/dig_associations.R | 8 R/dig_baseline_contrasts.R | 3 R/dig_complement_contrasts.R | 3 R/dig_correlations.R | 3 R/dig_grid.R | 3 R/dig_paired_baseline_contrasts.R | 3 R/dig_tautologies.R | 4 R/is_almost_constant.R | 2 R/permute.R |only R/ui-aboutTable.R | 6 R/ui-exploreApp.R | 3 R/ui-searchStatsTable.R |only README.md | 125 +++++--- build/vignette.rds |binary inst/doc/association-rules.Rmd | 5 inst/doc/association-rules.html | 6 inst/doc/comparison-with-arules.R |only inst/doc/comparison-with-arules.Rmd |only inst/doc/comparison-with-arules.html |only inst/doc/conditional-correlations.R |only inst/doc/conditional-correlations.Rmd |only inst/doc/conditional-correlations.html |only inst/doc/contrast-patterns.R |only inst/doc/contrast-patterns.Rmd |only inst/doc/contrast-patterns.html |only inst/doc/custom-patterns.R |only inst/doc/custom-patterns.Rmd |only inst/doc/custom-patterns.html |only inst/doc/data-preparation.Rmd | 16 - inst/doc/data-preparation.html | 41 +- inst/doc/nuggets.Rmd | 12 inst/doc/nuggets.html | 17 + man/dig.Rd | 13 man/dig_associations.Rd | 6 man/dig_baseline_contrasts.Rd | 3 man/dig_complement_contrasts.Rd | 3 man/dig_correlations.Rd | 3 man/dig_grid.Rd | 3 man/dig_paired_baseline_contrasts.Rd | 3 man/dig_tautologies.Rd | 4 man/is_almost_constant.Rd | 2 man/nuggets-package.Rd | 4 man/permute.Rd |only src/dig.cpp | 4 src/dig/AssocStorage.h | 157 +++++++--- src/dig/BaseChain.h | 171 +++++++++-- src/dig/BinomialCoefficients.h | 54 +++ src/dig/BitChain.h | 89 ++++++ src/dig/Bitset.h | 165 +++++++++-- src/dig/Cache.h | 209 +++++--------- src/dig/CallbackCaller.h | 209 +++++++++++++- src/dig/ChainCollection.h | 103 ++++++- src/dig/Clause.h | 49 +++ src/dig/CombinatorialProgress.h | 80 +++++ src/dig/Config.h | 285 +++++++++++++++++++ src/dig/DeductionEngine.h | 228 ++++++++++----- src/dig/Digger.h | 484 +++++++++++++++++++++++++++++---- src/dig/FloatChain.h | 114 ++++++- src/dig/FubitChain.h | 169 ++++++++++- src/dig/SearchStats.h |only src/dig/Selector.h | 52 +++ src/dig/SimdChain.h | 90 ++++++ src/dig/SparseBitChain.h | 118 +++++++- src/test-dig-BaseChain.cpp | 16 - src/test-dig-BitChain.cpp | 20 - src/test-dig-Cache.cpp | 71 ++-- src/test-dig-ChainCollection.cpp | 24 - src/test-dig-DeductionEngine.cpp | 10 src/test-dig-FloatChain.cpp | 24 - src/test-dig-FubitChain.cpp | 24 - src/test-dig-SparseBitChain.cpp | 20 - tests/testthat/test-dig.R | 213 +++++++++++++- tests/testthat/test-permute.R |only vignettes/association-rules.Rmd | 5 vignettes/comparison-with-arules.Rmd |only vignettes/comparison-with-arules.rds |only vignettes/conditional-correlations.Rmd |only vignettes/contrast-patterns.Rmd |only vignettes/custom-patterns.Rmd |only vignettes/data-preparation.Rmd | 16 - vignettes/nuggets.Rmd | 12 86 files changed, 3183 insertions(+), 796 deletions(-)
Title: Fractional Response Regressions
Description: Provides routines for the estimation and specification analysis of fractional response models. Includes univariate one-part, two-part, and double-inflated three-part fractional models. Further incorporates estimators for panel data settings and addresses unobserved heterogeneity and endogeneity via correlated random effects and control function approaches. Extends fractional methodology to multivariate data via fractional multinomial logit models and handles high-dimensional multicollinear data via fractional ridge regression. Calculates analytical partial effects across all model types and includes generalised goodness-of-functional-form (GGOFF) and Regression Equation Specification Error Test (RESET) hypothesis tests. Methods are described in Papke and Wooldridge (1996) <doi:10.1002/(SICI)1099-1255(199611)11:6%3C619::AID-JAE418%3E3.0.CO;2-1>, Papke and Wooldridge (2008) <doi:10.1016/j.jeconom.2008.05.009>, Buis (2008) <http://maartenbuis.nl/software/likelihoodFmlogit.p [...truncated...]
Author: Sulman Olieko Owili [aut, cre]
Maintainer: Sulman Olieko Owili <oliekosulman@gmail.com>
Diff between fracreg versions 1.0.1 dated 2026-08-05 and 1.1.0 dated 2026-08-20
DESCRIPTION | 12 MD5 | 66 - NAMESPACE | 63 + NEWS.md | 24 R/fracreg-package.R | 4 R/fracreg.R | 8 R/fracreg.pe.R | 18 R/fracreg.pe.table.R | 61 - R/fracreg.table.R | 43 R/fracreg.tests.table.R | 28 R/fracreghet.R | 8 R/fracreghet.extractors.R | 2 R/fracreghet.pe.table.R | 41 R/fracreghet.table.R | 42 R/fracreghet.tests.table.R | 26 R/fracregmlogit.R | 23 R/fracregmlogit.pe.R | 169 ++- R/fracregmlogit.plot.R | 4 R/fracregmlogit.wtp.R | 27 R/fracregpd.R | 3 R/fracregpd.pe.R | 28 R/fracregpd.table.R | 53 R/fracregridge.R | 1 R/fracregridge.pe.R | 3 R/utils.R | 1074 ++++++++++++++++--- R/zzz.R | 6 README.md | 1365 +++++++++++------------- inst/doc/fracreg_tutorial.html | 1595 +++++++++++++++-------------- man/figures/README-fracregmlogit_wtp-1.png |binary man/fracreg-package.Rd | 4 man/fracreghet.Rd | 2 man/fracregmlogit.pe.Rd | 8 man/fracregpd.pe.Rd | 24 man/summary.fracregmlogit.Rd | 7 34 files changed, 2979 insertions(+), 1863 deletions(-)
Title: Calculate AZTI’s Marine Biotic Index
Description: Calculate AZTI’s Marine Biotic Index - AMBI. The included list of
benthic fauna species according to their sensitivity
to pollution. Matching species in sample data to the list allows the
calculation of fractions of individuals in the different sensitivity
categories and thereafter the AMBI index. The Shannon Diversity Index H'
and the Danish benthic fauna quality index DKI (Dansk Kvalitetsindeks) can
also be calculated, as well as the multivariate M-AMBI index.
Borja, A., Franco, J. ,Pérez, V. (2000) "A marine biotic index to
establish the ecological quality of soft bottom benthos within European
estuarine and coastal environments" <doi:10.1016/S0025-326X(00)00061-8>.
Author: Ciaran J. Murray [aut, cre, cph] ,
Angel Borja [aut] ,
Sarai Pouso [aut] ,
Inigo Muxika [aut] ,
Joxe Mikel Garmendia [aut] ,
Steen Knudsen [ctb] ,
GES4SEAS [fnd]
Maintainer: Ciaran J. Murray <cjm@niva-dk.dk>
Diff between ambiR versions 0.1.1 dated 2025-12-19 and 0.2.0 dated 2026-08-20
DESCRIPTION | 12 ++++----- MD5 | 40 ++++++++++++++++++--------------- NAMESPACE | 13 ++++++---- NEWS.md | 24 ++++++++++++++----- R/AMBI.R | 17 ++++++++------ R/AMBIr-package.R | 1 R/MAMBI.R | 2 - R/test_data.R | 2 - R/utils-pipe.R | 2 - README.md | 2 + inst/doc/ambi-figures.html | 26 +++++++++++---------- inst/doc/ambiR.html | 7 ++--- inst/doc/background.Rmd | 2 - inst/doc/background.html | 10 ++++---- man/ambiR-package.Rd | 1 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/pipe.Rd | 2 - man/test_data.Rd | 2 - tests/testthat/test-calc_ambi.R | 12 +++++++++ vignettes/background.Rmd | 2 - 23 files changed, 108 insertions(+), 71 deletions(-)
Title: Semi-Supervised Learning with Mixed Missingness in Finite
Mixture Models
Description: Semi-supervised Gaussian finite mixture models for partially labelled data
under complete-case, missing completely at random (MCAR), entropy-dependent missing
at random (MAR), and mixed MCAR/MAR label-missingness formulations. For the mixed
formulation, the source of a missing label may be observed or latent. The package
supports equal and component-specific covariance matrices, model fitting, simulation,
initialization, prediction, classification performance assessment, and entropy-based
diagnostics. A semi-synthetic Blood Transfusion data set is included to illustrate the
applied workflow.
Author: Geoffrey J. McLachlan [aut] ,
Jinran Wu [aut, cre]
Maintainer: Jinran Wu <jinran.wu@uq.edu.au>
Diff between SSLfmm versions 0.1.0 dated 2025-12-09 and 0.2.0 dated 2026-08-20
SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised.R |only SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised_Complete_Initial.R |only SSLfmm-0.1.0/SSLfmm/R/EM_FMM_SemiSupervised_Initial.R |only SSLfmm-0.1.0/SSLfmm/R/bayesclassifier.R |only SSLfmm-0.1.0/SSLfmm/R/compute_d2.R |only SSLfmm-0.1.0/SSLfmm/R/error_beta_classification.R |only SSLfmm-0.1.0/SSLfmm/R/get_clusterprobs.R |only SSLfmm-0.1.0/SSLfmm/R/get_entropy.R |only SSLfmm-0.1.0/SSLfmm/R/initialestimate.R |only SSLfmm-0.1.0/SSLfmm/R/logsumexp.R |only SSLfmm-0.1.0/SSLfmm/R/neg_loglik.R |only SSLfmm-0.1.0/SSLfmm/R/normalise_logprob.R |only SSLfmm-0.1.0/SSLfmm/R/pack_theta.R |only SSLfmm-0.1.0/SSLfmm/R/rmix.R |only SSLfmm-0.1.0/SSLfmm/R/simulate_mixed_missingness.R |only SSLfmm-0.1.0/SSLfmm/R/unpack_theta.R |only SSLfmm-0.1.0/SSLfmm/R/zzz_imports.R |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised.Rd |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised_Complete_Initial.Rd |only SSLfmm-0.1.0/SSLfmm/man/EM_FMM_SemiSupervised_Initial.Rd |only SSLfmm-0.1.0/SSLfmm/man/bayesclassifier.Rd |only SSLfmm-0.1.0/SSLfmm/man/compute_d2.Rd |only SSLfmm-0.1.0/SSLfmm/man/error_beta_classification.Rd |only SSLfmm-0.1.0/SSLfmm/man/get_clusterprobs.Rd |only SSLfmm-0.1.0/SSLfmm/man/get_entropy.Rd |only SSLfmm-0.1.0/SSLfmm/man/initialestimate.Rd |only SSLfmm-0.1.0/SSLfmm/man/logsumexp.Rd |only SSLfmm-0.1.0/SSLfmm/man/neg_loglik.Rd |only SSLfmm-0.1.0/SSLfmm/man/normalise_logprob.Rd |only SSLfmm-0.1.0/SSLfmm/man/pack_theta.Rd |only SSLfmm-0.1.0/SSLfmm/man/unpack_theta.Rd |only SSLfmm-0.2.0/SSLfmm/DESCRIPTION | 56 +++--- SSLfmm-0.2.0/SSLfmm/MD5 | 62 +++---- SSLfmm-0.2.0/SSLfmm/NAMESPACE | 36 +--- SSLfmm-0.2.0/SSLfmm/R/00_utils.R |only SSLfmm-0.2.0/SSLfmm/R/01_model.R |only SSLfmm-0.2.0/SSLfmm/R/02_initialization.R |only SSLfmm-0.2.0/SSLfmm/R/03_likelihoods.R |only SSLfmm-0.2.0/SSLfmm/R/04_fit.R |only SSLfmm-0.2.0/SSLfmm/R/05_simulation.R |only SSLfmm-0.2.0/SSLfmm/R/06_metrics_plot.R |only SSLfmm-0.2.0/SSLfmm/README.md |only SSLfmm-0.2.0/SSLfmm/data |only SSLfmm-0.2.0/SSLfmm/man/SSLfmm-package.Rd |only SSLfmm-0.2.0/SSLfmm/man/blood_transfusion.Rd |only SSLfmm-0.2.0/SSLfmm/man/classification_performance.Rd |only SSLfmm-0.2.0/SSLfmm/man/fit_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/initialize_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/plot_entropy_labels.Rd |only SSLfmm-0.2.0/SSLfmm/man/predict.SSLfmm.Rd |only SSLfmm-0.2.0/SSLfmm/man/rmix.Rd | 50 ++--- SSLfmm-0.2.0/SSLfmm/man/simulate_mixed_missingness.Rd | 84 ++++------ SSLfmm-0.2.0/SSLfmm/man/simulate_sslfmm.Rd |only SSLfmm-0.2.0/SSLfmm/tests |only 54 files changed, 122 insertions(+), 166 deletions(-)
Title: Fishing Effort Standardization
Description: Marine fisheries governance and management rely heavily on reliable
indicators of stock abundance and fishing pressure to ensure the sustainable
utilization of marine resources. Catch Per Unit Effort (CPUE) is widely used
as an index of relative abundance, but direct comparison of catch rates is
often affected by differences in fishing effort, vessel characteristics,
gear efficiency, and operational practices. The FESta package provides
methods for fishing effort and CPUE standardization, including vessel-based,
gear-based, relative effort, derived effort, generalized linear models,
generalized additive models, generalized linear mixed models, ordered
quantile transformation models, and multi-gear standardization techniques
for fisheries stock assessment and monitoring.
To cite our package run this command, citation("FESta").
Author: Eldho Varghese [aut, cre],
Jayasankar J [aut],
Ashutosh Dalal [aut, ctb],
Sathianandan T V [aut],
Sreepriya V [aut, ctb],
Reshma Gills [ctb],
Grinson George [ctb]
Maintainer: Eldho Varghese <eldhoiasri@gmail.com>
Diff between FESta versions 1.0.1 dated 2026-08-03 and 1.0.2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/MGMSstd.R | 40 ++++++++++++++++++++++++++++++++++++++-- R/StdEffort.R | 14 +++++++++----- 4 files changed, 53 insertions(+), 13 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.2.4 dated 2026-07-24 and 0.3.0 dated 2026-08-20
DESCRIPTION | 6 MD5 | 164 - NAMESPACE | 8 NEWS.md | 51 R/Base_Fit.R | 81 R/RTMB_Model.R | 7 R/RTMB_Model_impl_classic.R | 31 R/RTMB_Model_impl_optimize.R | 7 R/RTMB_Model_impl_sampling.R | 4 R/centering.R |only R/classic.R | 20 R/model.R | 32 R/parameters.R | 62 R/posterior_predict.R |only R/summary_mcmc.R |only R/wrapper_corr.R | 163 - R/wrapper_fa.R | 66 R/wrapper_glmer.R | 319 +- R/wrapper_irt.R | 34 R/wrapper_lm_glm_lmer.R | 12 R/wrapper_lrt.R | 66 R/wrapper_mdu.R | 198 - R/wrapper_mediation.R | 495 ++- R/wrapper_mixture.R | 70 R/wrapper_table.R | 90 R/wrapper_ttest.R | 42 build/vignette.rds |binary inst/doc/analysis_reference.R | 10 inst/doc/analysis_reference.Rmd | 42 inst/doc/analysis_reference.html | 440 +- inst/doc/introduction.Rmd | 9 inst/doc/introduction.html | 9 inst/doc/ja-analysis_reference.R | 16 inst/doc/ja-analysis_reference.Rmd | 3413 +++++++++++----------- inst/doc/ja-analysis_reference.html | 1048 +++--- inst/doc/ja-introduction.Rmd | 9 inst/doc/ja-introduction.html | 9 inst/doc/ja-rtmb_internals.Rmd | 6 inst/doc/ja-rtmb_internals.html | 26 inst/doc/ja-wrapper_functions.R | 23 inst/doc/ja-wrapper_functions.Rmd | 52 inst/doc/ja-wrapper_functions.html | 146 inst/doc/ja-writing_models.R | 37 inst/doc/ja-writing_models.Rmd | 52 inst/doc/ja-writing_models.html | 785 ++--- inst/doc/rtmb_internals.Rmd | 6 inst/doc/rtmb_internals.html | 23 inst/doc/wrapper_functions.R | 25 inst/doc/wrapper_functions.Rmd | 85 inst/doc/wrapper_functions.html | 310 + inst/doc/writing_models.R | 41 inst/doc/writing_models.Rmd | 61 inst/doc/writing_models.html | 258 - man/Classic_Fit.Rd | 2 man/MAP_Fit.Rd | 4 man/MCMC_Fit.Rd | 4 man/RTMB_Fit_Base.Rd | 112 man/VB_Fit.Rd | 2 man/center_grand_mean.Rd |only man/center_within_cluster.Rd |only man/make_glmer_re_terms.Rd | 11 man/posterior_predict.Rd |only man/pp_check.Rd |only man/rtmb_corr.Rd | 6 man/rtmb_glm.Rd | 4 man/rtmb_glmer.Rd | 8 man/rtmb_lm.Rd | 4 man/rtmb_lmer.Rd | 4 man/rtmb_mediation.Rd | 33 man/rtmb_model.Rd | 10 man/rtmb_table.Rd | 1 man/summary_mcmc.Rd |only tests/testthat/test-centering.R |only tests/testthat/test-fixed-jacobian.R |only tests/testthat/test-formula-data-environment.R | 6 tests/testthat/test-mediation-random-intercepts.R |only tests/testthat/test-posterior-predict.R |only tests/testthat/test-setup-data.R |only tests/testthat/test-summary-mcmc.R |only tests/testthat/test-wrappers.R | 502 +++ vignettes/analysis_reference.Rmd | 42 vignettes/introduction.Rmd | 9 vignettes/ja-analysis_reference.Rmd | 3413 +++++++++++----------- vignettes/ja-introduction.Rmd | 9 vignettes/ja-rtmb_internals.Rmd | 6 vignettes/ja-wrapper_functions.Rmd | 52 vignettes/ja-writing_models.Rmd | 52 vignettes/rtmb_internals.Rmd | 6 vignettes/wrapper_functions.Rmd | 85 vignettes/writing_models.Rmd | 61 90 files changed, 8005 insertions(+), 5412 deletions(-)
Title: R Client for the 'VirusTotal' API
Description: Provides a comprehensive R interface to the 'VirusTotal' API v3.0
<https://docs.virustotal.com/>, a Google service that analyzes files and
URLs for viruses, worms, trojans and other malware. Features include
file/URL scanning, domain categorization, passive DNS information, IP
reputation analysis, IoC relationships, sandbox analysis, and
comment/voting systems. Implements rate limiting, error handling, and
response validation for robust security analysis workflows.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between virustotal versions 0.6.0 dated 2026-04-13 and 0.7.0 dated 2026-08-20
virustotal-0.6.0/virustotal/man/rate_limit.Rd |only virustotal-0.6.0/virustotal/tests/README.html |only virustotal-0.6.0/virustotal/tests/README.md |only virustotal-0.6.0/virustotal/tests/_covrpage.Rmd |only virustotal-0.6.0/virustotal/tests/testthat/test-data-structures.R |only virustotal-0.6.0/virustotal/tests/testthat/test-pkg-style.R |only virustotal-0.7.0/virustotal/DESCRIPTION | 16 virustotal-0.7.0/virustotal/MD5 | 301 +++++---- virustotal-0.7.0/virustotal/NAMESPACE | 41 - virustotal-0.7.0/virustotal/NEWS.md | 81 ++ virustotal-0.7.0/virustotal/R/domain_report.R | 57 - virustotal-0.7.0/virustotal/R/download_file.R | 23 virustotal-0.7.0/virustotal/R/errors.R | 18 virustotal-0.7.0/virustotal/R/file_report.R | 90 +- virustotal-0.7.0/virustotal/R/get_analysis.R | 4 virustotal-0.7.0/virustotal/R/get_behaviour_evtx.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_html.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_memdump.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_pcap.R | 25 virustotal-0.7.0/virustotal/R/get_behaviour_report.R | 4 virustotal-0.7.0/virustotal/R/get_domain_comments.R | 16 virustotal-0.7.0/virustotal/R/get_domain_info.R | 40 - virustotal-0.7.0/virustotal/R/get_domain_relationship.R | 39 - virustotal-0.7.0/virustotal/R/get_domain_votes.R | 36 - virustotal-0.7.0/virustotal/R/get_file_behaviour_mitre_trees.R | 4 virustotal-0.7.0/virustotal/R/get_file_behaviour_summary.R | 4 virustotal-0.7.0/virustotal/R/get_file_behaviours.R | 6 virustotal-0.7.0/virustotal/R/get_file_comments.R | 22 virustotal-0.7.0/virustotal/R/get_file_download_url.R | 16 virustotal-0.7.0/virustotal/R/get_file_relationships.R | 48 - virustotal-0.7.0/virustotal/R/get_file_upload_url.R | 19 virustotal-0.7.0/virustotal/R/get_file_votes.R | 22 virustotal-0.7.0/virustotal/R/get_ip_comments.R | 12 virustotal-0.7.0/virustotal/R/get_ip_info.R | 12 virustotal-0.7.0/virustotal/R/get_ip_votes.R | 12 virustotal-0.7.0/virustotal/R/get_url_comments.R | 13 virustotal-0.7.0/virustotal/R/get_url_relationships.R | 25 virustotal-0.7.0/virustotal/R/get_url_votes.R | 13 virustotal-0.7.0/virustotal/R/ip_report.R | 21 virustotal-0.7.0/virustotal/R/post_domain_comments.R | 26 virustotal-0.7.0/virustotal/R/post_domain_votes.R | 26 virustotal-0.7.0/virustotal/R/post_file_comments.R | 20 virustotal-0.7.0/virustotal/R/post_file_votes.R | 16 virustotal-0.7.0/virustotal/R/post_ip_comments.R | 24 virustotal-0.7.0/virustotal/R/post_ip_votes.R | 24 virustotal-0.7.0/virustotal/R/post_url_comments.R | 23 virustotal-0.7.0/virustotal/R/post_url_votes.R | 19 virustotal-0.7.0/virustotal/R/rate_limiting.R | 99 --- virustotal-0.7.0/virustotal/R/rescan_domain.R | 4 virustotal-0.7.0/virustotal/R/rescan_file.R | 10 virustotal-0.7.0/virustotal/R/rescan_ip.R | 4 virustotal-0.7.0/virustotal/R/rescan_url.R | 11 virustotal-0.7.0/virustotal/R/s3_classes.R | 26 virustotal-0.7.0/virustotal/R/scan_file.R | 37 - virustotal-0.7.0/virustotal/R/scan_url.R | 7 virustotal-0.7.0/virustotal/R/security.R | 26 virustotal-0.7.0/virustotal/R/set_key.R | 31 virustotal-0.7.0/virustotal/R/url_report.R | 5 virustotal-0.7.0/virustotal/R/utils.R | 78 +- virustotal-0.7.0/virustotal/R/virustotal.R | 314 +++++++--- virustotal-0.7.0/virustotal/R/vt_key.R |only virustotal-0.7.0/virustotal/R/zzz.R | 8 virustotal-0.7.0/virustotal/README.md | 92 ++ virustotal-0.7.0/virustotal/build/vignette.rds |binary virustotal-0.7.0/virustotal/inst/CITATION | 30 virustotal-0.7.0/virustotal/inst/WORDLIST |only virustotal-0.7.0/virustotal/inst/doc/using_virustotal.R | 71 +- virustotal-0.7.0/virustotal/inst/doc/using_virustotal.Rmd | 122 ++- virustotal-0.7.0/virustotal/inst/doc/using_virustotal.html | 105 +-- virustotal-0.7.0/virustotal/man/cleanup_temp_files.Rd | 14 virustotal-0.7.0/virustotal/man/create_safe_temp_dir.Rd | 14 virustotal-0.7.0/virustotal/man/download_file.Rd | 9 virustotal-0.7.0/virustotal/man/file_report.Rd | 3 virustotal-0.7.0/virustotal/man/format_file_size.Rd | 14 virustotal-0.7.0/virustotal/man/get_analysis.Rd | 2 virustotal-0.7.0/virustotal/man/get_behaviour_evtx.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_html.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_memdump.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_pcap.Rd | 11 virustotal-0.7.0/virustotal/man/get_behaviour_report.Rd | 2 virustotal-0.7.0/virustotal/man/get_domain_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_domain_info.Rd | 4 virustotal-0.7.0/virustotal/man/get_domain_relationship.Rd | 4 virustotal-0.7.0/virustotal/man/get_domain_votes.Rd | 4 virustotal-0.7.0/virustotal/man/get_file_behaviour_mitre_trees.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_behaviour_summary.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_behaviours.Rd | 4 virustotal-0.7.0/virustotal/man/get_file_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_download_url.Rd | 2 virustotal-0.7.0/virustotal/man/get_file_relationships.Rd | 12 virustotal-0.7.0/virustotal/man/get_file_upload_url.Rd | 3 virustotal-0.7.0/virustotal/man/get_file_votes.Rd | 2 virustotal-0.7.0/virustotal/man/get_rate_limit_status.Rd | 6 virustotal-0.7.0/virustotal/man/get_url_comments.Rd | 2 virustotal-0.7.0/virustotal/man/get_url_relationships.Rd | 6 virustotal-0.7.0/virustotal/man/get_url_votes.Rd | 2 virustotal-0.7.0/virustotal/man/has_vt_key.Rd |only virustotal-0.7.0/virustotal/man/init_rate_limit.Rd | 4 virustotal-0.7.0/virustotal/man/ip_report.Rd | 4 virustotal-0.7.0/virustotal/man/is_api_key_configured.Rd | 12 virustotal-0.7.0/virustotal/man/is_rate_limit_initialized.Rd | 4 virustotal-0.7.0/virustotal/man/is_safe_environment.Rd | 14 virustotal-0.7.0/virustotal/man/post_file_comments.Rd | 6 virustotal-0.7.0/virustotal/man/post_file_votes.Rd | 2 virustotal-0.7.0/virustotal/man/post_url_comments.Rd | 6 virustotal-0.7.0/virustotal/man/post_url_votes.Rd | 2 virustotal-0.7.0/virustotal/man/print.virustotal_domain_report.Rd | 4 virustotal-0.7.0/virustotal/man/print.virustotal_error.Rd | 3 virustotal-0.7.0/virustotal/man/print.virustotal_file_report.Rd | 4 virustotal-0.7.0/virustotal/man/print.virustotal_response.Rd | 4 virustotal-0.7.0/virustotal/man/rate-limiting.Rd | 16 virustotal-0.7.0/virustotal/man/record_request.Rd |only virustotal-0.7.0/virustotal/man/rescan_file.Rd | 2 virustotal-0.7.0/virustotal/man/reset_rate_limit.Rd | 10 virustotal-0.7.0/virustotal/man/sanitize_domain.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_file_path.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_hash.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_ip.Rd | 12 virustotal-0.7.0/virustotal/man/sanitize_url.Rd | 12 virustotal-0.7.0/virustotal/man/security-utilities.Rd | 14 virustotal-0.7.0/virustotal/man/set_key.Rd | 13 virustotal-0.7.0/virustotal/man/summary.virustotal_response.Rd | 4 virustotal-0.7.0/virustotal/man/utilities.Rd | 16 virustotal-0.7.0/virustotal/man/validate_vt_response.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal-classes.Rd | 12 virustotal-0.7.0/virustotal/man/virustotal-errors.Rd | 12 virustotal-0.7.0/virustotal/man/virustotal-package.Rd | 13 virustotal-0.7.0/virustotal/man/virustotal_GET.Rd | 13 virustotal-0.7.0/virustotal/man/virustotal_GET_raw.Rd |only virustotal-0.7.0/virustotal/man/virustotal_POST.Rd | 15 virustotal-0.7.0/virustotal/man/virustotal_auth_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_check.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal_domain_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_file_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_file_scan.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_info.Rd | 14 virustotal-0.7.0/virustotal/man/virustotal_ip_report.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_rate_limit_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_url_scan.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_validation_error.Rd | 10 virustotal-0.7.0/virustotal/man/virustotal_version.Rd | 14 virustotal-0.7.0/virustotal/man/vt_key.Rd |only virustotal-0.7.0/virustotal/man/vt_request.Rd |only virustotal-0.7.0/virustotal/man/vt_url_id.Rd |only virustotal-0.7.0/virustotal/tests/spelling.R |only virustotal-0.7.0/virustotal/tests/testthat/_snaps |only virustotal-0.7.0/virustotal/tests/testthat/helper-capture.R |only virustotal-0.7.0/virustotal/tests/testthat/helper-fixtures.R |only virustotal-0.7.0/virustotal/tests/testthat/setup.R |only virustotal-0.7.0/virustotal/tests/testthat/test-audit-v3-conformance.R |only virustotal-0.7.0/virustotal/tests/testthat/test-auth.R | 46 - virustotal-0.7.0/virustotal/tests/testthat/test-domain-operations.R | 74 +- virustotal-0.7.0/virustotal/tests/testthat/test-error-handling.R | 89 ++ virustotal-0.7.0/virustotal/tests/testthat/test-file-operations.R | 116 ++- virustotal-0.7.0/virustotal/tests/testthat/test-fixture-hygiene.R |only virustotal-0.7.0/virustotal/tests/testthat/test-fixtures.R |only virustotal-0.7.0/virustotal/tests/testthat/test-integration.R |only virustotal-0.7.0/virustotal/tests/testthat/test-ip-operations.R | 33 - virustotal-0.7.0/virustotal/tests/testthat/test-rate-limiting.R | 138 +++- virustotal-0.7.0/virustotal/tests/testthat/test-s3-print.R |only virustotal-0.7.0/virustotal/tests/testthat/test-url-operations.R | 28 virustotal-0.7.0/virustotal/tests/testthat/test-utils.R |only virustotal-0.7.0/virustotal/vignettes/using_virustotal.Rmd | 122 ++- 164 files changed, 2164 insertions(+), 1431 deletions(-)
Title: Client for the YouTube Data API
Description: Search public YouTube data and retrieve channels, videos,
playlists, comments, captions, live broadcasts, and reference data.
Authenticated methods support common uploads, playlist changes, comment
moderation, and media updates. See the YouTube Data API documentation at
<https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb],
John Muschelli [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 1.4.1 dated 2026-08-02 and 2.0.0 dated 2026-08-20
tuber-1.4.1/tuber/R/delete_captions.R |only tuber-1.4.1/tuber/R/delete_channel_sections.R |only tuber-1.4.1/tuber/R/delete_comments.R |only tuber-1.4.1/tuber/R/delete_playlist_items.R |only tuber-1.4.1/tuber/R/delete_playlists.R |only tuber-1.4.1/tuber/R/delete_videos.R |only tuber-1.4.1/tuber/R/get_captions.R |only tuber-1.4.1/tuber/R/get_channel_stats.R |only tuber-1.4.1/tuber/R/get_comment_threads.R |only tuber-1.4.1/tuber/R/get_comments.R |only tuber-1.4.1/tuber/R/get_live_chat_messages.R |only tuber-1.4.1/tuber/R/get_playlist_item_videoids.R |only tuber-1.4.1/tuber/R/get_playlist_items.R |only tuber-1.4.1/tuber/R/get_playlists.R |only tuber-1.4.1/tuber/R/get_related_videos.R |only tuber-1.4.1/tuber/R/get_subscriptions.R |only tuber-1.4.1/tuber/R/get_super_chat_events.R |only tuber-1.4.1/tuber/R/list_caption_tracks.R |only tuber-1.4.1/tuber/R/list_channel_resources.R |only tuber-1.4.1/tuber/R/list_guidecats.R |only tuber-1.4.1/tuber/R/list_langs.R |only tuber-1.4.1/tuber/R/list_videocats.R |only tuber-1.4.1/tuber/R/list_videos.R |only tuber-1.4.1/tuber/R/yt_topic_search.R |only tuber-1.4.1/tuber/man/delete_captions.Rd |only tuber-1.4.1/tuber/man/delete_channel_sections.Rd |only tuber-1.4.1/tuber/man/delete_comments.Rd |only tuber-1.4.1/tuber/man/delete_playlist_items.Rd |only tuber-1.4.1/tuber/man/delete_playlists.Rd |only tuber-1.4.1/tuber/man/delete_videos.Rd |only tuber-1.4.1/tuber/man/get_captions.Rd |only tuber-1.4.1/tuber/man/get_channel_info_cached.Rd |only tuber-1.4.1/tuber/man/get_channel_sections.Rd |only tuber-1.4.1/tuber/man/get_channel_stats.Rd |only tuber-1.4.1/tuber/man/get_comment_threads.Rd |only tuber-1.4.1/tuber/man/get_comments.Rd |only tuber-1.4.1/tuber/man/get_live_chat_messages.Rd |only tuber-1.4.1/tuber/man/get_live_streams.Rd |only tuber-1.4.1/tuber/man/get_playlist_item_videoids.Rd |only tuber-1.4.1/tuber/man/get_playlist_items.Rd |only tuber-1.4.1/tuber/man/get_playlists.Rd |only tuber-1.4.1/tuber/man/get_premiere_info.Rd |only tuber-1.4.1/tuber/man/get_related_videos.Rd |only tuber-1.4.1/tuber/man/get_stats.Rd |only tuber-1.4.1/tuber/man/get_subscriptions.Rd |only tuber-1.4.1/tuber/man/get_super_chat_events.Rd |only tuber-1.4.1/tuber/man/list_caption_tracks.Rd |only tuber-1.4.1/tuber/man/list_channel_resources.Rd |only tuber-1.4.1/tuber/man/list_guidecats.Rd |only tuber-1.4.1/tuber/man/list_langs.Rd |only tuber-1.4.1/tuber/man/list_langs_cached.Rd |only tuber-1.4.1/tuber/man/list_regions_cached.Rd |only tuber-1.4.1/tuber/man/list_videocats.Rd |only tuber-1.4.1/tuber/man/list_videocats_cached.Rd |only tuber-1.4.1/tuber/man/list_videos.Rd |only tuber-1.4.1/tuber/man/search_shorts.Rd |only tuber-1.4.1/tuber/man/track_quota_usage.Rd |only tuber-1.4.1/tuber/man/tuber_GET_cached.Rd |only tuber-1.4.1/tuber/man/yt_topic_search.Rd |only tuber-1.4.1/tuber/tests/testthat/_problems |only tuber-1.4.1/tuber/tests/testthat/test-get-related-videos.R |only tuber-2.0.0/tuber/DESCRIPTION | 18 tuber-2.0.0/tuber/MD5 | 359 +++--- tuber-2.0.0/tuber/NAMESPACE | 63 - tuber-2.0.0/tuber/NEWS.md | 47 tuber-2.0.0/tuber/R/caching.R | 309 ++--- tuber-2.0.0/tuber/R/change_playlist_title.R | 88 + tuber-2.0.0/tuber/R/delete_caption.R |only tuber-2.0.0/tuber/R/delete_channel_section.R |only tuber-2.0.0/tuber/R/delete_comment.R |only tuber-2.0.0/tuber/R/delete_playlist.R |only tuber-2.0.0/tuber/R/delete_playlist_item.R |only tuber-2.0.0/tuber/R/delete_video.R |only tuber-2.0.0/tuber/R/download_caption.R |only tuber-2.0.0/tuber/R/error_handling.R | 42 tuber-2.0.0/tuber/R/extended_endpoints.R | 561 +++------- tuber-2.0.0/tuber/R/get_all_channel_video_stats.R | 39 tuber-2.0.0/tuber/R/get_all_comments.R | 243 +--- tuber-2.0.0/tuber/R/get_channel_details.R |only tuber-2.0.0/tuber/R/get_playlist_item_ids.R | 99 - tuber-2.0.0/tuber/R/get_playlist_video_ids.R |only tuber-2.0.0/tuber/R/get_stats.R | 148 +- tuber-2.0.0/tuber/R/get_video_details.R | 30 tuber-2.0.0/tuber/R/helper_functions.R | 133 +- tuber-2.0.0/tuber/R/insert_channel_banner.R | 34 tuber-2.0.0/tuber/R/list_abuse_report_reasons.R | 100 - tuber-2.0.0/tuber/R/list_captions.R | 104 + tuber-2.0.0/tuber/R/list_channel_activities.R | 201 +-- tuber-2.0.0/tuber/R/list_channel_members.R | 79 - tuber-2.0.0/tuber/R/list_channel_sections.R | 125 +- tuber-2.0.0/tuber/R/list_channel_videos.R | 33 tuber-2.0.0/tuber/R/list_comment_threads.R |only tuber-2.0.0/tuber/R/list_comments.R |only tuber-2.0.0/tuber/R/list_languages.R |only tuber-2.0.0/tuber/R/list_live_chat_messages.R |only tuber-2.0.0/tuber/R/list_my_videos.R | 41 tuber-2.0.0/tuber/R/list_playlist_items.R |only tuber-2.0.0/tuber/R/list_playlists.R |only tuber-2.0.0/tuber/R/list_popular_videos.R |only tuber-2.0.0/tuber/R/list_regions.R | 72 - tuber-2.0.0/tuber/R/list_subscriptions.R |only tuber-2.0.0/tuber/R/list_super_chat_events.R |only tuber-2.0.0/tuber/R/list_video_categories.R |only tuber-2.0.0/tuber/R/quota_management.R | 193 +-- tuber-2.0.0/tuber/R/read_sbv.R | 4 tuber-2.0.0/tuber/R/set_video_thumbnail.R | 14 tuber-2.0.0/tuber/R/tuber.R | 232 ++-- tuber-2.0.0/tuber/R/unicode_utils.R | 1 tuber-2.0.0/tuber/R/update_video_metadata.R | 205 ++- tuber-2.0.0/tuber/R/upload_caption.R | 206 ++- tuber-2.0.0/tuber/R/upload_video.R | 136 +- tuber-2.0.0/tuber/R/utils.R | 42 tuber-2.0.0/tuber/R/yt_oauth.R | 44 tuber-2.0.0/tuber/R/yt_search.R | 218 ++- tuber-2.0.0/tuber/README.md | 140 +- tuber-2.0.0/tuber/build/vignette.rds |binary tuber-2.0.0/tuber/inst/doc/api-conventions.R |only tuber-2.0.0/tuber/inst/doc/api-conventions.Rmd |only tuber-2.0.0/tuber/inst/doc/api-conventions.html |only tuber-2.0.0/tuber/inst/doc/batch-processing-quota.R | 49 tuber-2.0.0/tuber/inst/doc/batch-processing-quota.Rmd | 74 - tuber-2.0.0/tuber/inst/doc/batch-processing-quota.html | 166 +- tuber-2.0.0/tuber/inst/doc/emoji-analysis.R | 24 tuber-2.0.0/tuber/inst/doc/emoji-analysis.Rmd | 24 tuber-2.0.0/tuber/inst/doc/emoji-analysis.html | 24 tuber-2.0.0/tuber/inst/doc/emoji-handling.R | 10 tuber-2.0.0/tuber/inst/doc/emoji-handling.Rmd | 10 tuber-2.0.0/tuber/inst/doc/emoji-handling.html | 10 tuber-2.0.0/tuber/inst/doc/troubleshooting.Rmd | 56 tuber-2.0.0/tuber/inst/doc/troubleshooting.html | 96 - tuber-2.0.0/tuber/inst/doc/tuber-ex.R | 33 tuber-2.0.0/tuber/inst/doc/tuber-ex.Rmd | 35 tuber-2.0.0/tuber/inst/doc/tuber-ex.html | 60 - tuber-2.0.0/tuber/man/add_tuber_attributes.Rd | 3 tuber-2.0.0/tuber/man/change_playlist_title.Rd | 32 tuber-2.0.0/tuber/man/delete_caption.Rd |only tuber-2.0.0/tuber/man/delete_channel_section.Rd |only tuber-2.0.0/tuber/man/delete_comment.Rd |only tuber-2.0.0/tuber/man/delete_playlist.Rd |only tuber-2.0.0/tuber/man/delete_playlist_item.Rd |only tuber-2.0.0/tuber/man/delete_video.Rd |only tuber-2.0.0/tuber/man/download_caption.Rd |only tuber-2.0.0/tuber/man/get_all_channel_video_stats.Rd | 10 tuber-2.0.0/tuber/man/get_all_comments.Rd | 34 tuber-2.0.0/tuber/man/get_cached_response.Rd | 1 tuber-2.0.0/tuber/man/get_channel_details.Rd |only tuber-2.0.0/tuber/man/get_playlist_item_ids.Rd | 51 tuber-2.0.0/tuber/man/get_playlist_video_ids.Rd |only tuber-2.0.0/tuber/man/get_video_broadcast_timing.Rd |only tuber-2.0.0/tuber/man/get_video_details.Rd | 14 tuber-2.0.0/tuber/man/get_video_stats.Rd |only tuber-2.0.0/tuber/man/get_video_thumbnails.Rd | 13 tuber-2.0.0/tuber/man/handle_api_error.Rd | 1 tuber-2.0.0/tuber/man/handle_network_error.Rd | 1 tuber-2.0.0/tuber/man/insert_channel_banner.Rd | 7 tuber-2.0.0/tuber/man/is_cacheable_endpoint.Rd | 1 tuber-2.0.0/tuber/man/is_static_query.Rd | 1 tuber-2.0.0/tuber/man/list_abuse_report_reasons.Rd | 33 tuber-2.0.0/tuber/man/list_captions.Rd | 34 tuber-2.0.0/tuber/man/list_channel_activities.Rd | 62 - tuber-2.0.0/tuber/man/list_channel_members.Rd | 11 tuber-2.0.0/tuber/man/list_channel_sections.Rd | 50 tuber-2.0.0/tuber/man/list_channel_videos.Rd | 21 tuber-2.0.0/tuber/man/list_comment_threads.Rd |only tuber-2.0.0/tuber/man/list_comments.Rd |only tuber-2.0.0/tuber/man/list_languages.Rd |only tuber-2.0.0/tuber/man/list_live_broadcasts.Rd |only tuber-2.0.0/tuber/man/list_live_chat_messages.Rd |only tuber-2.0.0/tuber/man/list_my_videos.Rd | 22 tuber-2.0.0/tuber/man/list_playlist_items.Rd |only tuber-2.0.0/tuber/man/list_playlists.Rd |only tuber-2.0.0/tuber/man/list_popular_videos.Rd |only tuber-2.0.0/tuber/man/list_regions.Rd | 19 tuber-2.0.0/tuber/man/list_subscriptions.Rd |only tuber-2.0.0/tuber/man/list_super_chat_events.Rd |only tuber-2.0.0/tuber/man/list_video_categories.Rd |only tuber-2.0.0/tuber/man/print.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/quota_cost.Rd |only tuber-2.0.0/tuber/man/read_sbv.Rd | 4 tuber-2.0.0/tuber/man/search_short_videos.Rd |only tuber-2.0.0/tuber/man/store_cached_response.Rd | 1 tuber-2.0.0/tuber/man/sub-.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/suggest_solution.Rd | 1 tuber-2.0.0/tuber/man/summary.tuber_result.Rd | 1 tuber-2.0.0/tuber/man/tuber-package.Rd | 4 tuber-2.0.0/tuber/man/tuber_DELETE.Rd | 5 tuber-2.0.0/tuber/man/tuber_GET.Rd | 18 tuber-2.0.0/tuber/man/tuber_POST.Rd | 5 tuber-2.0.0/tuber/man/tuber_POST_json.Rd | 1 tuber-2.0.0/tuber/man/tuber_PUT.Rd | 5 tuber-2.0.0/tuber/man/tuber_check.Rd | 1 tuber-2.0.0/tuber/man/unicode_utils.Rd | 1 tuber-2.0.0/tuber/man/update_video_metadata.Rd | 76 - tuber-2.0.0/tuber/man/upload_caption.Rd | 51 tuber-2.0.0/tuber/man/upload_video.Rd | 13 tuber-2.0.0/tuber/man/validate_channel_id.Rd | 1 tuber-2.0.0/tuber/man/validate_language_code.Rd | 1 tuber-2.0.0/tuber/man/validate_part_parameter.Rd | 1 tuber-2.0.0/tuber/man/validate_playlist_id.Rd | 1 tuber-2.0.0/tuber/man/validate_region_code.Rd | 1 tuber-2.0.0/tuber/man/validate_rfc3339_date.Rd | 1 tuber-2.0.0/tuber/man/validate_video_id.Rd | 1 tuber-2.0.0/tuber/man/warn_deprecated.Rd | 1 tuber-2.0.0/tuber/man/yt_get_quota_usage.Rd | 8 tuber-2.0.0/tuber/man/yt_key.Rd | 15 tuber-2.0.0/tuber/man/yt_oauth.Rd | 30 tuber-2.0.0/tuber/man/yt_reset_quota.Rd | 3 tuber-2.0.0/tuber/man/yt_search.Rd | 24 tuber-2.0.0/tuber/man/yt_set_quota_limit.Rd | 8 tuber-2.0.0/tuber/tests/testthat/test-auth.R | 33 tuber-2.0.0/tuber/tests/testthat/test-basic-functionality.R | 18 tuber-2.0.0/tuber/tests/testthat/test-captions.R | 2 tuber-2.0.0/tuber/tests/testthat/test-channel-members.R | 4 tuber-2.0.0/tuber/tests/testthat/test-channels.R | 24 tuber-2.0.0/tuber/tests/testthat/test-comment-threads.R | 8 tuber-2.0.0/tuber/tests/testthat/test-comments.R | 15 tuber-2.0.0/tuber/tests/testthat/test-integration-ready.R | 73 - tuber-2.0.0/tuber/tests/testthat/test-list-channel-activities.R | 5 tuber-2.0.0/tuber/tests/testthat/test-list-channel-sections.R | 4 tuber-2.0.0/tuber/tests/testthat/test-live-chat.R | 12 tuber-2.0.0/tuber/tests/testthat/test-pagination-mocks.R | 36 tuber-2.0.0/tuber/tests/testthat/test-playlist-items.R | 9 tuber-2.0.0/tuber/tests/testthat/test-playlists.R | 8 tuber-2.0.0/tuber/tests/testthat/test-release-correctness.R |only tuber-2.0.0/tuber/tests/testthat/test-request-assembly.R | 93 - tuber-2.0.0/tuber/tests/testthat/test-super-chat.R | 12 tuber-2.0.0/tuber/tests/testthat/test-thumbnails.R | 10 tuber-2.0.0/tuber/tests/testthat/test-videos.R | 2 tuber-2.0.0/tuber/tests/testthat/test-write-operations.R | 128 +- tuber-2.0.0/tuber/vignettes/api-conventions.Rmd |only tuber-2.0.0/tuber/vignettes/batch-processing-quota.Rmd | 74 - tuber-2.0.0/tuber/vignettes/emoji-analysis.Rmd | 24 tuber-2.0.0/tuber/vignettes/emoji-handling.Rmd | 10 tuber-2.0.0/tuber/vignettes/troubleshooting.Rmd | 56 tuber-2.0.0/tuber/vignettes/tuber-ex.Rmd | 35 235 files changed, 3451 insertions(+), 3024 deletions(-)
Title: Partially Replicated Test-Control Designs for Early Generation
Varietal Trials
Description: Provides functions for generating partially replicated (p-rep)
test-control designs for early generation varietal trials conducted
across multiple environments. The package implements three
construction methods for obtaining p-rep test-control designs with
one or more control treatments. The package extends the partially
replicated design framework of Vinaykumar et al. (2026)
<doi:10.1007/s12355-025-01684-1> to accommodate test-control
comparisons in breeding trials. Functions are provided for
generating randomized and non-randomized layouts and for displaying
the design parameters and treatment allocations for each
environment. The proposed designs are useful for large-scale
varietal evaluation trials where a large number of test lines are
assessed under limited experimental resources.
Author: Vinaykumar L.N. [aut, cre],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Sayantani Karmakar [aut, ctb],
Vinayaka [aut, ctb]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between TCpRepDesigns versions 0.0.1 dated 2026-06-25 and 0.0.2 dated 2026-08-20
DESCRIPTION | 41 +-- MD5 | 24 - R/TCpRep1.R | 625 +++++++++++++++++++++++++---------------------- R/TCpRep2.R | 633 +++++++++++++++++++++++++----------------------- R/TCpRep3.R | 633 +++++++++++++++++++++++++----------------------- R/TCpRepEfficiency.R | 355 ++++++++++++++++---------- man/TCpRep1.Rd | 22 - man/TCpRep2.Rd | 20 - man/TCpRep3.Rd | 21 - man/TCpRepEfficiency.Rd | 70 +++-- man/print.TCpRep.Rd | 3 man/print.TCpRep2.Rd | 4 man/print.pRep3.Rd | 4 13 files changed, 1328 insertions(+), 1127 deletions(-)
Title: Simplified Statistical Analysis with Plain-English
Interpretation
Description: A toolkit for common statistical analyses including descriptive statistics, Student's t-tests (one-sample, independent, and paired), one-way and two-way Analysis of Variance (ANOVA), Multivariate Analysis of Variance (MANOVA), chi-square tests, Fisher's Exact Test, McNemar's Test, correlation analysis, simple and multiple linear regression, logistic regression, Friedman Test, and non-parametric tests (Mann-Whitney U, Wilcoxon Signed Rank, and Kruskal-Wallis). Each function automatically interprets results in plain English, reporting effect sizes, confidence intervals, and p-value interpretations, and prints relevant assumption checks by default. A context argument allows users to describe their study design, echoed back alongside the interpretation as a reminder to read results in that context. Post-hoc tests are automatically applied following significant results. A master function automatically detects the appropriate test based on the structure of the input data. Methods are based o [...truncated...]
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between statease versions 1.3.0 dated 2026-07-02 and 1.4.0 dated 2026-08-20
DESCRIPTION | 8 MD5 | 73 - NEWS.md | 2 R/analyze.R | 50 R/anova2_interpret.R | 55 R/anova_interpret.R | 47 R/check_assumptions.R | 55 R/chisq_interpret.R | 47 R/cor_interpret.R | 47 R/fisher_interpret.R | 39 R/friedman_interpret.R | 39 R/logistic_interpret.R | 53 R/mcnemar_interpret.R | 40 R/mlr_interpret.R | 67 + R/nonparam_interpret.R | 106 + R/power_interpret.R | 4 R/reg_interpret.R | 55 R/ttest_interpret.R | 63 - R/utils-assumptions.R |only README.md | 111 + inst/doc/statease.html | 730 ++++++++----- inst/shiny/app.R | 565 ++++++++++ inst/shiny/rsconnect/shinyapps.io/devwebwacky/statease.dcf | 4 man/analyze.Rd | 6 man/anova2_interpret.Rd | 5 man/anova_interpret.Rd | 5 man/chisq_interpret.Rd | 5 man/cor_interpret.Rd | 6 man/fisher_interpret.Rd | 11 man/friedman_interpret.Rd | 5 man/kruskal_interpret.Rd | 5 man/logistic_interpret.Rd | 5 man/mannwhitney_interpret.Rd | 11 man/mcnemar_interpret.Rd | 5 man/mlr_interpret.Rd | 5 man/reg_interpret.Rd | 5 man/ttest_interpret.Rd | 6 man/wilcoxon_interpret.Rd | 11 38 files changed, 1884 insertions(+), 472 deletions(-)
Title: Hash Table and Hash Set
Description: It provides three implementations of hash tables and hash maps: 1. using
'std::unordered_map' and 'std::unordered_set' C++ libraries, 2. wrapping around
the 'fastmatch' package, 3. using R environment.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <guzuguang@suat-sz.edu.cn>
Diff between hashtable versions 1.0.0 dated 2026-07-27 and 1.0.1 dated 2026-08-20
DESCRIPTION | 8 MD5 | 45 +-- NEWS |only R/RcppExports.R | 168 ++++++++++++ R/hash_env.R | 17 + R/hash_fm.R | 7 R/hash_set.R | 1 R/hash_table.R | 33 ++ build/vignette.rds |binary inst/doc/benchmark2.html | 4 inst/doc/hashtable.R | 8 inst/doc/hashtable.html | 72 ++--- man/hash_env.Rd | 2 man/hash_fm.Rd | 4 man/hash_set.Rd | 2 man/hash_table.Rd | 2 src/RcppExports.cpp | 522 +++++++++++++++++++++++++++++++++++++++ src/hash.h | 3 src/hash_env.cpp | 275 +++++++++++++++++++- src/hash_fm.cpp | 12 src/hash_table.cpp | 161 ++++++++++++ tests/testthat/test_hash_env.R | 21 + tests/testthat/test_hash_fm.R | 19 + tests/testthat/test_hash_table.R | 20 + 24 files changed, 1321 insertions(+), 85 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Cole Jensen [aut],
Jessie Fielding [aut],
Hunter Melton [aut],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Erick Matsen [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>
Diff between dowser versions 2.4.1 dated 2026-03-26 and 2.5.1 dated 2026-08-20
dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Discrete-Trait-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Germlines-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.R |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.Rmd |only dowser-2.4.1/dowser/inst/doc/Measurable-Evolution.pdf |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.R |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.Rmd |only dowser-2.4.1/dowser/inst/doc/NonB-Cell-Data.html |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.R |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.Rmd |only dowser-2.4.1/dowser/inst/doc/Resolve-Light-Chains-Vignette.pdf |only dowser-2.4.1/dowser/inst/doc/Sequences-Vignette.R |only 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dowser-2.5.1/dowser/R/Plotting.R | 149 dowser-2.5.1/dowser/R/Statistics.R | 44 dowser-2.5.1/dowser/R/TimeTreesFunctions.R | 605 ++ dowser-2.5.1/dowser/R/TreeFunctions.R | 907 +-- dowser-2.5.1/dowser/README.md | 30 dowser-2.5.1/dowser/build/partial.rdb |binary dowser-2.5.1/dowser/build/vignette.rds |binary dowser-2.5.1/dowser/data/BiopsyTrees.rda |binary dowser-2.5.1/dowser/data/ExampleClones.rda |binary dowser-2.5.1/dowser/data/ExampleMixedClones.rda |binary dowser-2.5.1/dowser/data/IsotypeTrees.rda |binary dowser-2.5.1/dowser/data/TimeTrees.rda |binary dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.R | 30 dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.Rmd | 6 dowser-2.5.1/dowser/inst/doc/Building-Time-Trees-Vignette.pdf |binary dowser-2.5.1/dowser/inst/doc/Building-Trees-Vignette.pdf |binary dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.R |only dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.Rmd |only dowser-2.5.1/dowser/inst/doc/Input-Output-Vignette.pdf 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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 0.2.6 dated 2026-06-12 and 0.2.7 dated 2026-08-20
DESCRIPTION | 8 MD5 | 197 ++++---- NEWS.md | 17 R/data.R | 904 ++++++++++++++++++++------------------ README.md | 8 build/partial.rdb |only inst/doc/dataSDA_intro.Rmd | 4 inst/doc/dataSDA_intro.html | 4 man/abalone.iGAP.Rd | 7 man/abalone.int.Rd | 7 man/acid_rain.int.Rd | 3 man/age_cholesterol_weight.int.Rd | 3 man/age_pyramids.hist.Rd | 10 man/airline_flights.hist.Rd | 3 man/airline_flights2.modal.Rd | 3 man/bank_rates.Rd | 3 man/baseball.int.Rd | 3 man/bats.int.Rd | 10 man/bird.mix.Rd | 3 man/bird_color_taxonomy.hist.Rd | 6 man/bird_species.mix.Rd | 3 man/bird_species_extended.mix.Rd | 3 man/blood.hist.Rd | 6 man/blood_pressure.int.Rd | 3 man/car.int.Rd | 3 man/car_models.int.Rd | 5 man/cardiological.int.Rd | 7 man/cars.int.Rd | 8 man/china_climate_month.hist.Rd | 11 man/china_climate_season.hist.Rd | 11 man/china_temp.int.Rd | 8 man/credit_card.int.Rd | 3 man/crime.modal.Rd | 3 man/crime2.modal.Rd | 3 man/crude_oil_wti.its.Rd | 12 man/djia.its.Rd | 19 man/employment.int.Rd | 3 man/energy_consumption.distr.Rd | 3 man/environment.mix.Rd | 9 man/euro_usd.its.Rd | 7 man/exchange_rate_returns.hist.Rd | 15 man/face.iGAP.Rd | 4 man/finance.int.Rd | 3 man/french_agriculture.hist.Rd | 11 man/freshwater_fish.int.Rd | 5 man/fuel_consumption.modal.Rd | 3 man/fungi.int.Rd | 5 man/hardwood.hist.Rd | 9 man/hdi_gender.int.Rd | 7 man/health_insurance.mix.Rd | 3 man/health_insurance2.modal.Rd | 3 man/hierarchy.Rd | 3 man/hierarchy.hist.Rd | 6 man/hierarchy.int.Rd | 3 man/horses.int.Rd | 3 man/ibovespa.its.Rd | 13 man/iris.int.Rd | 5 man/irish_wind.its.Rd | 3 man/judge1.int.Rd | 15 man/judge2.int.Rd | 15 man/judge3.int.Rd | 15 man/lackinfo.int.Rd | 9 man/lisbon_air_quality.int.Rd | 16 man/loans_by_purpose.int.Rd | 14 man/loans_by_risk.int.Rd | 12 man/loans_by_risk_quantile.int.Rd | 13 man/lung_cancer.hist.Rd | 3 man/lynne1.int.Rd | 4 man/merval.its.Rd | 7 man/mushroom.int.Rd | 3 man/mushroom_fuzzy.mix.Rd | 3 man/nycflights.int.Rd | 9 man/occupations.modal.Rd | 3 man/occupations2.modal.Rd | 3 man/ohtemp.int.Rd | 8 man/oils.int.Rd | 4 man/ozone.hist.Rd | 20 man/petrobras.its.Rd | 13 man/polish_cars.mix.Rd | 9 man/polish_voivodships.int.Rd | 13 man/profession.int.Rd | 3 man/shanghai_stock.its.Rd | 18 man/soccer_bivar.int.Rd | 6 man/sp500.its.Rd | 12 man/synthetic_clusters.int.Rd | 7 man/teams.int.Rd | 3 man/temperature_city.int.Rd | 7 man/tennis.int.Rd | 3 man/town_services.mix.Rd | 3 man/trivial_intervals.int.Rd | 3 man/uscrime.int.Rd | 8 man/utsnow.int.Rd | 15 man/veterinary.int.Rd | 4 man/video1.int.Rd | 12 man/video2.int.Rd | 12 man/video3.int.Rd | 12 man/water_flow.int.Rd | 5 man/wine.int.Rd | 5 man/world_cup.int.Rd | 3 vignettes/dataSDA_intro.Rmd | 4 100 files changed, 1029 insertions(+), 764 deletions(-)
Title: Spatial and Environmental Blocking for Cross-Validation
Description: Creates spatially or environmentally separated, or
group-preserving, training and testing folds for k-fold,
leave-group-out, and leave-one-out cross-validation. Provides spatial
blocking, clustering, buffering, and nearest-neighbour distance-matching
methods, together with tools to visualise folds, summarise fold sizes and class balance,
and assess train–test separation and environmental novelty. Also estimates spatial
autocorrelation ranges in point samples and continuous raster covariates
to provide an initial distance scale for designing spatial folds. Methods
are described in Valavi, R. et al. (2019)
<doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre] ,
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 3.2-0 dated 2025-08-21 and 4.0-0 dated 2026-08-20
blockCV-3.2-0/blockCV/R/v2_buffering.R |only blockCV-3.2-0/blockCV/R/v2_environBlock.R |only blockCV-3.2-0/blockCV/R/v2_explorer.R |only blockCV-3.2-0/blockCV/R/v2_spatialAutoRange.R |only blockCV-3.2-0/blockCV/R/v2_spatialBlock.R |only blockCV-3.2-0/blockCV/man/buffering.Rd |only blockCV-3.2-0/blockCV/man/envBlock.Rd |only blockCV-3.2-0/blockCV/man/foldExplorer.Rd |only blockCV-3.2-0/blockCV/man/rangeExplorer.Rd |only blockCV-3.2-0/blockCV/man/spatialAutoRange.Rd |only blockCV-3.2-0/blockCV/man/spatialBlock.Rd |only blockCV-3.2-0/blockCV/tests/testthat/test-v2-functions.R |only blockCV-4.0-0/blockCV/DESCRIPTION | 30 blockCV-4.0-0/blockCV/MD5 | 123 blockCV-4.0-0/blockCV/NAMESPACE | 31 blockCV-4.0-0/blockCV/NEWS.md |only blockCV-4.0-0/blockCV/R/RcppExports.R | 22 blockCV-4.0-0/blockCV/R/blockCV.R | 37 blockCV-4.0-0/blockCV/R/checks.R | 350 + blockCV-4.0-0/blockCV/R/cv_block_size.R | 6 blockCV-4.0-0/blockCV/R/cv_buffer.R | 89 blockCV-4.0-0/blockCV/R/cv_cluster.R | 285 + blockCV-4.0-0/blockCV/R/cv_distance.R |only blockCV-4.0-0/blockCV/R/cv_group.R |only blockCV-4.0-0/blockCV/R/cv_knndm.R |only blockCV-4.0-0/blockCV/R/cv_nndm.R | 532 +- blockCV-4.0-0/blockCV/R/cv_plot.R | 186 - blockCV-4.0-0/blockCV/R/cv_similarity.R | 364 + blockCV-4.0-0/blockCV/R/cv_spatial.R | 247 - blockCV-4.0-0/blockCV/R/cv_spatial_autocor.R | 97 blockCV-4.0-0/blockCV/R/cv_summary.R |only blockCV-4.0-0/blockCV/R/utils.R | 332 + blockCV-4.0-0/blockCV/README.md |only blockCV-4.0-0/blockCV/build/vignette.rds |binary blockCV-4.0-0/blockCV/inst/doc/tutorial_1.R | 481 +- blockCV-4.0-0/blockCV/inst/doc/tutorial_1.Rmd | 868 ++-- blockCV-4.0-0/blockCV/inst/doc/tutorial_1.html | 1822 +++++----- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.R | 387 +- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.Rmd | 593 +-- blockCV-4.0-0/blockCV/inst/doc/tutorial_2.html | 1437 ++++--- blockCV-4.0-0/blockCV/inst/doc/tutorial_3.R |only blockCV-4.0-0/blockCV/inst/doc/tutorial_3.Rmd |only blockCV-4.0-0/blockCV/inst/doc/tutorial_3.html |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.R |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.Rmd |only blockCV-4.0-0/blockCV/inst/doc/tutorial_4.html |only blockCV-4.0-0/blockCV/inst/extdata/species_pb.csv |only blockCV-4.0-0/blockCV/man/blockCV.Rd | 33 blockCV-4.0-0/blockCV/man/cv_block_size.Rd | 4 blockCV-4.0-0/blockCV/man/cv_buffer.Rd | 45 blockCV-4.0-0/blockCV/man/cv_cluster.Rd | 115 blockCV-4.0-0/blockCV/man/cv_distance.Rd |only blockCV-4.0-0/blockCV/man/cv_group.Rd |only blockCV-4.0-0/blockCV/man/cv_knndm.Rd |only blockCV-4.0-0/blockCV/man/cv_nndm.Rd | 56 blockCV-4.0-0/blockCV/man/cv_plot.Rd | 42 blockCV-4.0-0/blockCV/man/cv_similarity.Rd | 72 blockCV-4.0-0/blockCV/man/cv_spatial.Rd | 62 blockCV-4.0-0/blockCV/man/cv_spatial_autocor.Rd | 23 blockCV-4.0-0/blockCV/man/cv_summary.Rd |only blockCV-4.0-0/blockCV/man/figures/cv_clust.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_sim.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_spat.jpg |only blockCV-4.0-0/blockCV/man/figures/cv_spat_folds.jpg |only blockCV-4.0-0/blockCV/tests/testthat/test-balance-folds.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_buffer.R | 45 blockCV-4.0-0/blockCV/tests/testthat/test-cv_cluster.R | 185 - blockCV-4.0-0/blockCV/tests/testthat/test-cv_distance.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_group.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_knndm.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_nndm-leakage.R |only blockCV-4.0-0/blockCV/tests/testthat/test-cv_nndm.R | 87 blockCV-4.0-0/blockCV/tests/testthat/test-cv_plot.R | 122 blockCV-4.0-0/blockCV/tests/testthat/test-cv_similarity.R | 158 blockCV-4.0-0/blockCV/tests/testthat/test-cv_spatial.R | 153 blockCV-4.0-0/blockCV/tests/testthat/test-cv_spatial_autocor.R | 24 blockCV-4.0-0/blockCV/tests/testthat/test-cv_summary.R |only blockCV-4.0-0/blockCV/tests/testthat/test-data.R | 6 blockCV-4.0-0/blockCV/tests/testthat/test-interactive-defaults.R |only blockCV-4.0-0/blockCV/tests/testthat/test-presence-bg-validation.R |only blockCV-4.0-0/blockCV/vignettes/tutorial_1.Rmd | 868 ++-- blockCV-4.0-0/blockCV/vignettes/tutorial_2.Rmd | 593 +-- blockCV-4.0-0/blockCV/vignettes/tutorial_3.Rmd |only blockCV-4.0-0/blockCV/vignettes/tutorial_4.Rmd |only 84 files changed, 6685 insertions(+), 4327 deletions(-)
Title: Blinded Sample Size Re-Estimation for Binary Endpoints
Description: Tools for blinded sample size re-estimation (BSSR) in two-arm clinical
trials with binary endpoints, together with the exact power and sample size
calculations that the re-estimation relies on. Five exact statistical tests are
implemented: Pearson chi-squared, Fisher exact, Fisher mid-p, Z-pooled exact
unconditional, and Boschloo exact unconditional. Each test is available with a
one-sided or a two-sided alternative, and the exact unconditional tests can be
combined with the Berger-Boos procedure. Sample sizes can be re-estimated either at
the planning stage, to study the operating characteristics of a design, or from the
blinded data of a trial that is under way. Statistical methods based on Mehrotra et
al. (2003) <doi:10.1111/1541-0420.00051>, Berger and Boos (1994)
<doi:10.1080/01621459.1994.10476836> and Kieser (2020)
<doi:10.1007/978-3-030-49528-2_21>.
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between bbssr versions 1.0.2 dated 2025-06-18 and 2.0.0 dated 2026-08-20
DESCRIPTION | 40 - LICENSE | 2 MD5 | 103 +- NAMESPACE | 55 + NEWS.md | 221 +++-- R/BinaryBSSR.R |only R/BinaryPower.R | 146 ++- R/BinaryPowerBSSR.R | 356 +++++---- R/BinaryRR.R | 239 +++--- R/BinarySampleSize.R | 225 +++-- R/RcppExports.R |only R/bbssr-package.R |only R/cp_bounds.R |only R/fisher_pvalue.R |only R/integer_breaks.R |only R/plot.bbssr_power.R |only R/plot.bbssr_powerbssr.R |only R/plot.bbssr_rr.R |only R/plot.bbssr_samplesize.R |only R/print.bbssr_bssr.R |only R/print.bbssr_power.R |only R/print.bbssr_powerbssr.R |only R/print.bbssr_rr.R |only R/print.bbssr_samplesize.R |only R/resolve_label.R |only R/tie_groups.R |only R/unconditional_pvalue.R |only R/zstat.R |only build/vignette.rds |binary inst/WORDLIST | 82 +- inst/doc/bbssr-interim-reestimation.R |only inst/doc/bbssr-interim-reestimation.Rmd |only inst/doc/bbssr-interim-reestimation.html |only inst/doc/bbssr-introduction.R | 209 ++--- inst/doc/bbssr-introduction.Rmd | 445 ++++------- inst/doc/bbssr-introduction.html | 669 ++++++++--------- inst/doc/bbssr-statistical-methods.R | 337 ++------ inst/doc/bbssr-statistical-methods.Rmd | 779 ++++++-------------- inst/doc/bbssr-statistical-methods.html | 1007 ++++++++----------------- inst/doc/bbssr-validation.R | 587 +++++---------- inst/doc/bbssr-validation.Rmd | 811 +++++++------------- inst/doc/bbssr-validation.html | 1203 ++++++++----------------------- man/BinaryBSSR.Rd |only man/BinaryPower.Rd | 92 +- man/BinaryPowerBSSR.Rd | 127 +-- man/BinaryRR.Rd | 80 +- man/BinarySampleSize.Rd | 85 +- man/bbssr-package.Rd |only man/figures/bssr_comparison.png |binary man/plot.bbssr_power.Rd |only man/plot.bbssr_powerbssr.Rd |only man/plot.bbssr_rr.Rd |only man/plot.bbssr_samplesize.Rd |only man/print.bbssr_bssr.Rd |only man/print.bbssr_power.Rd |only man/print.bbssr_powerbssr.Rd |only man/print.bbssr_rr.Rd |only man/print.bbssr_samplesize.Rd |only src |only tests/testthat/helper-reference.R |only tests/testthat/test-binary-bssr.R |only tests/testthat/test-binary-power-bssr.R | 280 +++---- tests/testthat/test-binary-power.R | 159 +--- tests/testthat/test-binary-rr.R | 249 ++++-- tests/testthat/test-binary-sample-size.R | 99 +- tests/testthat/test-external-reference.R |only tests/testthat/test-internal.R |only tests/testthat/test-s3-methods.R |only vignettes/bbssr-interim-reestimation.Rmd |only vignettes/bbssr-introduction.Rmd | 445 ++++------- vignettes/bbssr-statistical-methods.Rmd | 779 ++++++-------------- vignettes/bbssr-validation.Rmd | 811 +++++++------------- 72 files changed, 4396 insertions(+), 6326 deletions(-)
Title: Analysis the Weather Data for Agriculture
Description: Functions are collected to analyse weather data for agriculture
purposes including to read weather records in multiple formats,
calculate extreme climate index. Demonstration data are included the
SILO daily climate data (licensed under CC BY 4.0, <https://www.longpaddock.qld.gov.au/silo/>).
Author: Bangou Zheng [aut, cre]
Maintainer: Bangou Zheng <zheng.bangyou@gmail.com>
Diff between tidyweather versions 0.2.0 dated 2026-02-19 and 0.3.0 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 16 ++- NAMESPACE | 10 +- R/spherical_distance.R |only R/thermal_time.R | 137 +++++++++++++++++++++++++++++- man/interpolate_hourly_sin_pp_adjusted.Rd |only man/spherical_distance.Rd |only man/thermal_time.Rd | 12 ++ man/weather_options.Rd | 5 - tests/testthat/test-spherical_distance.R |only tests/testthat/test-thermal_time.R | 77 ++++++++++++++++ 11 files changed, 242 insertions(+), 25 deletions(-)
Title: Management Strategy Evaluation for Salmon Species
Description: Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and
habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across
early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of
hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models
fitted to data.
Author: Quang Huynh [aut, cre]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between salmonMSE versions 2.1.0 dated 2026-04-25 and 3.0.0 dated 2026-08-20
salmonMSE-2.1.0/salmonMSE/R/Harvest_MMP.R |only salmonMSE-2.1.0/salmonMSE/R/MMSE2SMSE.R |only salmonMSE-2.1.0/salmonMSE/R/Rel.R |only salmonMSE-2.1.0/salmonMSE/R/SOM2MOM.R |only salmonMSE-2.1.0/salmonMSE/R/SOM2MOM_int.R |only salmonMSE-2.1.0/salmonMSE/R/multiHist2SHist.R |only salmonMSE-2.1.0/salmonMSE/man/Harvest_MMP.Rd |only salmonMSE-2.1.0/salmonMSE/man/PNI50.Rd |only salmonMSE-2.1.0/salmonMSE/man/SAR_fitness.Rd |only salmonMSE-2.1.0/salmonMSE/man/SHist-class.Rd |only salmonMSE-2.1.0/salmonMSE/man/salmonMSE-int.Rd |only salmonMSE-2.1.0/salmonMSE/man/smolt_func.Rd |only salmonMSE-3.0.0/salmonMSE/DESCRIPTION | 18 salmonMSE-3.0.0/salmonMSE/MD5 | 107 - salmonMSE-3.0.0/salmonMSE/NAMESPACE | 34 salmonMSE-3.0.0/salmonMSE/NEWS.md | 20 salmonMSE-3.0.0/salmonMSE/R/AHA.R | 61 salmonMSE-3.0.0/salmonMSE/R/CM.R | 6 salmonMSE-3.0.0/salmonMSE/R/CM_int.R | 47 salmonMSE-3.0.0/salmonMSE/R/CMfun.R | 672 ++++++---- salmonMSE-3.0.0/salmonMSE/R/brood_func.R |only salmonMSE-3.0.0/salmonMSE/R/catch_func.R |only salmonMSE-3.0.0/salmonMSE/R/check_SOM.R |only salmonMSE-3.0.0/salmonMSE/R/data_obj.R | 8 salmonMSE-3.0.0/salmonMSE/R/define-SOM.R | 1182 ++++++++---------- salmonMSE-3.0.0/salmonMSE/R/fitness.R | 85 + salmonMSE-3.0.0/salmonMSE/R/hatchery.R | 421 ++++-- salmonMSE-3.0.0/salmonMSE/R/plot-LHG.R | 36 salmonMSE-3.0.0/salmonMSE/R/plot-SOM.R | 391 ++--- salmonMSE-3.0.0/salmonMSE/R/plot-statevar.R | 32 salmonMSE-3.0.0/salmonMSE/R/pm.R | 169 +- salmonMSE-3.0.0/salmonMSE/R/ref.R | 707 +++++----- salmonMSE-3.0.0/salmonMSE/R/salmonMSE.R | 1041 +++++++++++---- salmonMSE-3.0.0/salmonMSE/R/simpleSOM.R |only salmonMSE-3.0.0/salmonMSE/R/zzz.R | 15 salmonMSE-3.0.0/salmonMSE/README.md | 4 salmonMSE-3.0.0/salmonMSE/build/partial.rdb |binary salmonMSE-3.0.0/salmonMSE/data/glossary.rda |binary salmonMSE-3.0.0/salmonMSE/data/multi_SOM.rda |binary salmonMSE-3.0.0/salmonMSE/data/simple_SOM.rda |binary salmonMSE-3.0.0/salmonMSE/inst/include/CMreport.Rmd | 594 ++++----- salmonMSE-3.0.0/salmonMSE/man/CM_MSY.Rd |only salmonMSE-3.0.0/salmonMSE/man/CMfigures.Rd | 49 salmonMSE-3.0.0/salmonMSE/man/Deprecated.Rd |only salmonMSE-3.0.0/salmonMSE/man/Effort_solver.Rd |only salmonMSE-3.0.0/salmonMSE/man/Harvest-class.Rd | 21 salmonMSE-3.0.0/salmonMSE/man/Hatchery-class.Rd | 4 salmonMSE-3.0.0/salmonMSE/man/P_PNI50.Rd |only salmonMSE-3.0.0/salmonMSE/man/SMSE-class.Rd | 27 salmonMSE-3.0.0/salmonMSE/man/brood_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_broodtake.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_phi.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/calc_pwild_age.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/calc_ref.Rd | 5 salmonMSE-3.0.0/salmonMSE/man/calc_spawners.Rd |only salmonMSE-3.0.0/salmonMSE/man/calc_yearling.Rd |only salmonMSE-3.0.0/salmonMSE/man/catch_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/check_SOM.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/define_hatchery_args.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-CM_ER.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-CM_prod.Rd |only salmonMSE-3.0.0/salmonMSE/man/dot-egg_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/fit_CM.Rd | 3 salmonMSE-3.0.0/salmonMSE/man/fitness_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/get_F.Rd | 4 salmonMSE-3.0.0/salmonMSE/man/glossary.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/nextgen_SRR_func.Rd |only salmonMSE-3.0.0/salmonMSE/man/salmonMSE.Rd | 40 salmonMSE-3.0.0/salmonMSE/man/salmonMSE_env.Rd | 2 salmonMSE-3.0.0/salmonMSE/man/simpleSOM-class.Rd |only salmonMSE-3.0.0/salmonMSE/man/stray_func.Rd |only 71 files changed, 3426 insertions(+), 2387 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently. Polynomial mean coefficients are handled conditionally within the Kalman recursion, reducing the dimension of numerical maximum likelihood optimization and permitting exact Gaussian conditional updates during Bayesian posterior sampling. Maximum likelihood estimation is computationally efficient and suitable for large-scale data analysis, while Bayesian posterior sampling is better suited to small-scale analyses requiring more careful uncertainty qua [...truncated...]
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.3 dated 2026-07-02 and 1.0.4 dated 2026-08-20
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 4 R/drw.R | 729 +++++++++++++++++++++++++++++---------------------- man/Rdrw-internal.Rd | 6 man/Rdrw-package.Rd | 8 man/drw.Rd | 10 man/drw.sim.Rd | 2 8 files changed, 457 insertions(+), 326 deletions(-)
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 1.0.4 dated 2026-07-07 and 1.0.5 dated 2026-08-20
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS.md | 2 inst/doc/rcatfish-vignette.html | 2 man/rcatfish_classification.Rd | 62 +++++++-------- man/rcatfish_glossary.Rd | 62 +++++++-------- man/rcatfish_updates.Rd | 130 ++++++++++++++++----------------- tests/testthat/test_rcatfish_updates.R | 6 + 8 files changed, 146 insertions(+), 142 deletions(-)
Title: Macros Generating 'nimble' Code
Description: Macros to generate 'nimble' code from a concise syntax. Included are macros for generating linear modeling code using a formula-based syntax and for building for() loops. For more details review the 'nimble' manual: <https://r-nimble.org/manual/cha-user-defined.html#sec:user-macros>.
Author: Ken Kellner [cre, aut],
Perry de Valpine [aut],
Christopher Paciorek [aut],
Daniel Turek [aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between nimbleMacros versions 0.1.1 dated 2025-03-11 and 0.1.3 dated 2026-08-20
DESCRIPTION | 12 +- MD5 | 37 ++++---- NAMESPACE | 1 NEWS.md |only R/FORLOOP.R | 52 ++++++++--- R/LINPRED.R | 92 ++++++++++++-------- R/LM.R | 39 ++++---- R/utilities.R | 151 +++++++++++++++++++++++++++++++++ R/zzz.R | 1 build/vignette.rds |binary inst/doc/nimbleMacros.Rmd | 4 inst/doc/nimbleMacros.html | 4 man/FORLOOP.Rd | 30 ++++-- man/LINPRED.Rd | 80 +++++++++-------- man/LINPRED_PRIORS.Rd | 74 ++++++++-------- man/LM.Rd | 56 ++++++------ man/simplifyForLoops.Rd |only tests/testthat/test_FORLOOP.R | 84 ++++++++++++++++++ tests/testthat/test_formulaHandlers.R | 2 tests/testthat/test_simplifyForLoops.R |only vignettes/nimbleMacros.Rmd | 4 21 files changed, 519 insertions(+), 204 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Yoel Diaz-Saucedo [aut] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.7.2 dated 2026-07-28 and 0.7.3 dated 2026-08-20
inti-0.7.2/inti/R/outliers_remove.R |only inti-0.7.2/inti/R/plot_diag.R |only inti-0.7.2/inti/inst/doc/heritability.Rmd |only inti-0.7.2/inti/inst/doc/yupana.Rmd |only inti-0.7.2/inti/man/outliers_remove.Rd |only inti-0.7.2/inti/man/plot_diag.Rd |only inti-0.7.2/inti/vignettes/heritability.Rmd |only inti-0.7.2/inti/vignettes/yupana.Rmd |only inti-0.7.3/inti/DESCRIPTION | 12 inti-0.7.3/inti/MD5 | 117 inti-0.7.3/inti/NAMESPACE | 172 inti-0.7.3/inti/NEWS.md | 4 inti-0.7.3/inti/R/H2cal.R | 50 inti-0.7.3/inti/R/design_augmented.R | 839 ++-- inti-0.7.3/inti/R/design_repblock.R | 656 +++ inti-0.7.3/inti/R/design_split_rcbd.R | 843 +++- inti-0.7.3/inti/R/plot_augmented_design.R | 801 ++-- inti-0.7.3/inti/R/plot_split_rcbd_design.R | 668 ++- inti-0.7.3/inti/R/plot_standard_design.R | 475 +- inti-0.7.3/inti/R/remove_outliers.R | 31 inti-0.7.3/inti/R/rticle.R | 29 inti-0.7.3/inti/R/tarpuy.R | 77 inti-0.7.3/inti/R/tarpuy_design.R | 651 ++- inti-0.7.3/inti/R/tarpuy_plex.R | 796 ++-- inti-0.7.3/inti/R/tarpuy_plotdesign.R | 622 ++- inti-0.7.3/inti/R/tarpuy_traits.R | 684 ++- inti-0.7.3/inti/README.md | 12 inti-0.7.3/inti/build/vignette.rds |binary inti-0.7.3/inti/inst/doc/apps.html | 2 inti-0.7.3/inti/inst/doc/apps.qmd | 7 inti-0.7.3/inti/inst/doc/heritability.R | 15 inti-0.7.3/inti/inst/doc/heritability.html | 1096 ++---- inti-0.7.3/inti/inst/doc/heritability.qmd |only inti-0.7.3/inti/inst/doc/policy.qmd | 7 inti-0.7.3/inti/inst/doc/rticles.qmd | 9 inti-0.7.3/inti/inst/doc/tarpuy.html | 2 inti-0.7.3/inti/inst/doc/tarpuy.qmd | 11 inti-0.7.3/inti/inst/doc/yupana.R | 16 inti-0.7.3/inti/inst/doc/yupana.html | 408 -- inti-0.7.3/inti/inst/doc/yupana.qmd |only inti-0.7.3/inti/inst/tarpuy/helpers.R |only inti-0.7.3/inti/inst/tarpuy/pkgs.R | 94 inti-0.7.3/inti/inst/tarpuy/server.R | 4500 +++++++++++++++++--------- inti-0.7.3/inti/inst/tarpuy/ui.R | 341 - inti-0.7.3/inti/inst/tarpuy/www/msgs.R | 33 inti-0.7.3/inti/inst/tarpuy/www/tarpuy.css |only inti-0.7.3/inti/inst/tarpuy/www/tarpuy.js |only inti-0.7.3/inti/man/H2cal.Rd | 2 inti-0.7.3/inti/man/design_augmented.Rd | 32 inti-0.7.3/inti/man/design_repblock.Rd | 163 inti-0.7.3/inti/man/design_split_rcbd.Rd | 134 inti-0.7.3/inti/man/plot_augmented_design.Rd | 66 inti-0.7.3/inti/man/plot_split_rcbd_design.Rd | 65 inti-0.7.3/inti/man/plot_standard_design.Rd | 68 inti-0.7.3/inti/man/remove_outliers.Rd | 13 inti-0.7.3/inti/man/rticle.Rd | 2 inti-0.7.3/inti/man/tarpuy.Rd | 59 inti-0.7.3/inti/man/tarpuy_design.Rd | 165 inti-0.7.3/inti/man/tarpuy_plex.Rd | 5 inti-0.7.3/inti/man/tarpuy_plotdesign.Rd | 79 inti-0.7.3/inti/man/tarpuy_traits.Rd | 212 - inti-0.7.3/inti/vignettes/apps.qmd | 7 inti-0.7.3/inti/vignettes/heritability.qmd |only inti-0.7.3/inti/vignettes/policy.qmd | 7 inti-0.7.3/inti/vignettes/rticles.qmd | 9 inti-0.7.3/inti/vignettes/tarpuy.qmd | 11 inti-0.7.3/inti/vignettes/yupana.qmd |only 67 files changed, 9296 insertions(+), 5883 deletions(-)
Title: Test Data Engineering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 1.15.0 dated 2026-07-15 and 2.0.0 dated 2026-08-20
exametrika-1.15.0/exametrika/man/IRM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningGA_BNM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningPBIL_BNM.Rd |only exametrika-1.15.0/exametrika/man/StrLearningPBIL_LDLRA.Rd |only exametrika-2.0.0/exametrika/DESCRIPTION | 11 exametrika-2.0.0/exametrika/MD5 | 255 +- exametrika-2.0.0/exametrika/NAMESPACE | 22 exametrika-2.0.0/exametrika/NEWS.md | 642 ++++++ exametrika-2.0.0/exametrika/R/00_EMclus.R | 46 exametrika-2.0.0/exametrika/R/00_EMclus_nominal.R |only exametrika-2.0.0/exametrika/R/00_ModelFitModule.R | 74 exametrika-2.0.0/exametrika/R/00_exametrikaPlot.R | 12 exametrika-2.0.0/exametrika/R/00_exametrikaPrint.R | 30 exametrika-2.0.0/exametrika/R/00_isotonic_CORE.R |only exametrika-2.0.0/exametrika/R/00_plot_irt.R | 2 exametrika-2.0.0/exametrika/R/00_plot_lca_lra.R | 76 exametrika-2.0.0/exametrika/R/00_print_biclustering.R | 88 exametrika-2.0.0/exametrika/R/00_print_lca_lra.R | 136 + exametrika-2.0.0/exametrika/R/00_print_network.R | 14 exametrika-2.0.0/exametrika/R/04C_ParameterEstimation.R | 73 exametrika-2.0.0/exametrika/R/05_LCA.R | 293 ++ exametrika-2.0.0/exametrika/R/06_LRA.R | 53 exametrika-2.0.0/exametrika/R/07_Biclustering.R | 93 exametrika-2.0.0/exametrika/R/07_IRM.R | 18 exametrika-2.0.0/exametrika/R/08A_BNM.R | 179 + exametrika-2.0.0/exametrika/R/08C_BNM_GA.R | 56 exametrika-2.0.0/exametrika/R/09B_LDLRA_GA.R | 30 exametrika-2.0.0/exametrika/R/09_LDLRA.R | 56 exametrika-2.0.0/exametrika/R/10_LDB.R | 19 exametrika-2.0.0/exametrika/R/11_BINET.R | 6 exametrika-2.0.0/exametrika/R/12_LRA_ordinal.R | 180 - exametrika-2.0.0/exametrika/R/13_LRA_rated.R | 45 exametrika-2.0.0/exametrika/R/14_grm.R | 78 exametrika-2.0.0/exametrika/R/15_Biclustering_nominal.R | 33 exametrika-2.0.0/exametrika/R/16_Biclustering_ordinal.R | 162 + exametrika-2.0.0/exametrika/R/17_Biclustering_nominal_IRM.R | 7 exametrika-2.0.0/exametrika/R/18_Biclustering_ordinal_IRM.R | 19 exametrika-2.0.0/exametrika/R/19_Biclustering_rated.R | 7 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Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic heuristic algorithms for
global optimization of problems with and without general constraints.
The aim is to curate a collection of its variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it provides implementations of the algorithms 'jDE' by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133> for single-objective
optimization and 'NCDE' by Qu et al. (2012) <doi:10.1109/TEVC.2011.2161873>
for multimodal optimization (single-objective problems with
multiple solutions).
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.2-0 dated 2026-06-07 and 1.2-1 dated 2026-08-20
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/JDEoptim.R | 11 +++++++---- R/NCDEoptim.R | 15 +++++++++------ R/SPJDEoptim.R | 4 ++-- build/partial.rdb |binary inst/NEWS.Rd | 7 +++++++ man/SPJDEoptim.Rd | 2 +- 8 files changed, 39 insertions(+), 26 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines is now augmented with splines
of degree 1 to 4. Constraints for degrees 3 (monotone) and 4
(monotone and convex) use the Karlin-Studden SOCP characterization
for the sign of the polynomial, while other constraints applied
at the knots are added as linear problems. The method for cubic
splines is described in 'Abbes (2026)' <doi:10.5281/zenodo.17427913>.
Other formulations are simple consequences of the other given
references. All B-spline and polynomial functions have been
rewritten for consistency. This package provides an original
B-spline library for conversion between PP-form and B-spline
representation, evaluation, differentiation, callable and
non-callable objects, print human readable pp forms, view basis,
all based on "De Boor\'s" theory. It also
extends to multiple knots to catch up singularities. This feature is
robust in the package including for constrained regression.
T [...truncated...]
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.2.2 dated 2026-07-28 and 0.2.5 dated 2026-08-20
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More information about BsplineQuantReg at CRAN
Permanent link
Title: Add Bio Tooltips to HTML Reports
Description: Provides lightweight helpers for adding gene and chemical
tooltips to 'R Markdown', 'Quarto', 'shiny', 'pkgdown', and other HTML outputs.
The package emits small HTML spans with module-specific data attributes
and attaches the browser-side 'bio-tooltips' JavaScript and CSS assets
through 'htmltools'. Entity lookup and rendering are handled in the
browser by 'bio-tooltips'; this package does not query biological
databases from R during package checks.
Author: Matthew J. Meier [aut, cre]
Maintainer: Matthew J. Meier <matthew.meier@hc-sc.gc.ca>
Diff between BioTooltipR versions 0.1.0 dated 2026-06-30 and 0.1.1 dated 2026-08-20
DESCRIPTION | 11 LICENSE | 4 MD5 | 108 +- NAMESPACE | 36 NEWS.md | 35 R/auto.R | 188 +-- R/columns.R | 244 ++-- R/dependencies.R | 530 +++++----- R/package.R | 16 R/plotly.R | 428 ++++---- R/spans.R | 228 ++-- R/tables.R | 266 ++--- R/utils.R | 226 ++-- README.md | 180 +-- build/vignette.rds |binary inst/WORDLIST | 60 - inst/doc/BioTooltipR.R | 58 - inst/doc/BioTooltipR.Rmd | 426 ++++---- inst/doc/BioTooltipR.html | 417 ++++--- inst/htmltools/bio-tooltips/LICENSE | 12 inst/htmltools/bio-tooltips/README.md | 34 inst/htmltools/bio-tooltips/SOURCE | 44 inst/htmltools/bio-tooltips/bio-tooltips.css | 2 inst/htmltools/bio-tooltips/bio-tooltips.global.js | 478 ++++----- inst/htmltools/d3/LICENSE | 26 inst/htmltools/d3/README.md | 8 inst/htmltools/d3/SOURCE | 34 inst/htmltools/d3/d3.min.js | 4 inst/htmltools/ideogram/LICENSE | 274 ++--- inst/htmltools/ideogram/README.md | 8 inst/htmltools/ideogram/SOURCE | 34 inst/htmltools/ideogram/ideogram.min.js | 4 inst/rmarkdown/templates/biotooltipr-report/skeleton/skeleton.Rmd | 54 - inst/rmarkdown/templates/biotooltipr-report/template.yaml | 4 man/BioTooltipR-package.Rd | 55 - man/auto_gene_tooltips.Rd | 80 - man/bio_tooltip_span.Rd | 92 - man/bio_tooltips_dependency.Rd | 50 man/bt_datatable.Rd | 66 - man/bt_deg_table.Rd | 76 - man/bt_kable.Rd | 82 - man/bt_plotly_gene_hover.Rd | 110 +- man/chem_column.Rd | 82 - man/chem_tt.Rd | 76 - man/gene_column.Rd | 54 - man/gene_tt.Rd | 60 - man/tooltip_column.Rd | 98 - man/use_bio_tooltips.Rd | 142 +- tests/testthat.R | 8 tests/testthat/test-columns.R | 36 tests/testthat/test-dependencies.R | 202 +-- tests/testthat/test-plotly.R | 145 +- tests/testthat/test-spans.R | 50 tests/testthat/test-tables.R | 24 vignettes/BioTooltipR.Rmd | 426 ++++---- 55 files changed, 3316 insertions(+), 3179 deletions(-)
Title: Bayesian Q Methodology: Exact Rank-Order Likelihood for Forced Q
Sorts
Description: A Bayesian analysis for Q methodology, alongside the classical
one. Models the forced Q sort as an ordered partition of the statements
through an exact rank-order likelihood (the design quotas fix the
partition margins, so the likelihood of the observed sorting event is
exact), fits it by a parameter-expanded Gibbs sampler in R with no
compiled code and a
convergence gate on rotation-invariant functionals, resolves
rotational ambiguity via the MatchAlign post-processing of Poworoznek
et al. (2025) <doi:10.1214/25-BA1544>, and returns the familiar Q
tables as posterior summaries: credible intervals for bounded
participant loadings, flag probabilities with an explicit unclassified
state, quota-respecting factor arrays, distinguishing and consensus
statements judged against a posterior critical difference and a
grid-width equivalence region, one posterior false-discovery rule for
all published claims, and a two-signal posterior-predictive workflow
for the number of factors.
Author: Raymond Dacosta Azadda [aut, cre] ,
Henry Ofoe Agbi-Kaiser [aut] ,
Hannah D. Robinson [aut] ,
AK-ACE Team [aut],
Karsten Hueffer [aut],
Taa'aii Peter [aut],
Stacy Rasmus [aut]
Maintainer: Raymond Dacosta Azadda <rdazadda@alaska.edu>
Diff between bayesqm versions 0.1.0 dated 2026-06-17 and 0.2.0 dated 2026-08-20
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Title: Treatment Effect Estimation for Time-to-Event Data with
Intercurrent Events
Description: Analysis of treatment effects in clinical trials with time-to-event outcomes is complicated by intercurrent events. This package implements methods for estimating and inferring the cumulative incidence functions for time-to-event (TTE) outcomes with intercurrent events (ICE) under the five strategies outlined in the ICH E9 (R1) addendum, see Deng (2025) <doi:10.1002/sim.70091>. This package can be used for analyzing data from both randomized controlled trials and observational studies. In general, the data involve a primary outcome event and, potentially, an intercurrent event. Two data structures are allowed: competing risks, where only the time to the first event is recorded, and semicompeting risks, where the times to both the primary outcome event and intercurrent event (or censoring) are recorded. For estimation methods, users can choose nonparametric estimation (which does not use covariates) and semiparametrically efficient estimation.
Author: Yuhao Deng [aut],
Yi Zhou [cre]
Maintainer: Yi Zhou <yzhou@pku.edu.cn>
Diff between tteICE versions 1.1.4 dated 2026-03-16 and 1.1.5 dated 2026-08-20
DESCRIPTION | 12 - MD5 | 102 ++++++------ NAMESPACE | 61 ++++--- R/basic.R | 2 R/bshaz_tteICE.R | 2 R/coef_tteICE.R | 2 R/plot_ate.R | 2 R/plot_tteICE.R | 3 R/predict_tteICE.R | 2 R/print_tteICE.R | 2 R/scr_composite.R | 2 R/scr_natural_eff.R | 67 +++++--- R/scr_principal.R | 2 R/scr_removed.R | 2 R/scr_tteICE.R | 4 R/scr_whileon.R | 2 R/summary_tteICE.R | 2 R/surv_boot.R | 11 - R/surv_composite_eff.R | 33 ++-- R/surv_natural_eff.R | 49 ++++-- R/surv_principal_eff.R | 48 ++++-- R/surv_removed_eff.R | 48 ++++-- R/surv_treatment_eff.R | 33 ++-- R/surv_tteICE.R | 8 - R/surv_whileon_eff.R | 48 ++++-- R/tteICE.R | 5 R/zph_tteICE.R | 4 build/partial.rdb |binary inst/shiny/server_s1.R | 32 +++- inst/shiny/server_s2.R | 19 +- inst/shiny/server_s3.R | 18 +- inst/shiny/server_s4.R | 14 + inst/shiny/server_s5.R | 18 +- inst/shiny/server_s6.R | 17 +- inst/shiny/ui_data.R | 241 ++++++++++++++++++++++++++---- inst/shiny/www/style_cn_causal.css | 29 +-- inst/tteICE.pdf |binary man/bshaz.Rd | 36 ++-- man/bshaz.tteICE.Rd | 64 ++++---- man/coef.tteICE.Rd | 82 +++++----- man/plot.tteICE.Rd | 3 man/predict.tteICE.Rd | 124 +++++++-------- man/print.summary.tteICE.Rd | 42 ++--- man/print.tteICE.Rd | 2 man/scr.tteICE.Rd | 2 man/summary.tteICE.Rd | 100 ++++++------ man/surv.boot.Rd | 2 man/surv.tteICE.Rd | 6 man/tteICE-package.Rd | 116 +++++++------- man/tteICE.Rd | 295 ++++++++++++++++++------------------- man/zph.Rd | 40 ++--- man/zph.tteICE.Rd | 90 +++++------ 52 files changed, 1164 insertions(+), 786 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.6.0 dated 2025-10-08 and 1.7.0 dated 2026-08-20
REDCapR-1.6.0/REDCapR/inst/misc/coph.credentials |only REDCapR-1.6.0/REDCapR/inst/misc/dev-2.credentials |only REDCapR-1.7.0/REDCapR/DESCRIPTION | 8 REDCapR-1.7.0/REDCapR/LICENSE | 4 REDCapR-1.7.0/REDCapR/MD5 | 775 +- REDCapR-1.7.0/REDCapR/NAMESPACE | 113 REDCapR-1.7.0/REDCapR/NEWS.md | 28 REDCapR-1.7.0/REDCapR/R/REDCapR-package.R | 132 REDCapR-1.7.0/REDCapR/R/constant.R | 461 - REDCapR-1.7.0/REDCapR/R/create-batch-glossary.R | 208 REDCapR-1.7.0/REDCapR/R/helpers-testing.R | 266 REDCapR-1.7.0/REDCapR/R/kernel-api.R | 241 REDCapR-1.7.0/REDCapR/R/metadata-utilities.R | 270 REDCapR-1.7.0/REDCapR/R/project-dag-write.R | 359 - REDCapR-1.7.0/REDCapR/R/project-delete-multiple-arm.R | 215 REDCapR-1.7.0/REDCapR/R/project-delete-single-arm.R | 219 REDCapR-1.7.0/REDCapR/R/project-simple.R | 327 - REDCapR-1.7.0/REDCapR/R/redcap-arm-export.R | 372 - REDCapR-1.7.0/REDCapR/R/redcap-column-sanitize.R | 128 REDCapR-1.7.0/REDCapR/R/redcap-dag-read.R | 335 - REDCapR-1.7.0/REDCapR/R/redcap-delete.R | 476 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REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-dag/before.R | 14 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/default.R | 96 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/one-field.R | 92 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/overwrite-true.R | 90 REDCapR-1.7.0/REDCapR/inst/test-data/specific-redcapr/write-oneshot/two-fields.R | 92 REDCapR-1.7.0/REDCapR/man/REDCapR-package.Rd | 217 REDCapR-1.7.0/REDCapR/man/collapse_vector.Rd | 60 REDCapR-1.7.0/REDCapR/man/constant.Rd | 234 REDCapR-1.7.0/REDCapR/man/create_batch_glossary.Rd | 122 REDCapR-1.7.0/REDCapR/man/figures/logo.svg | 278 REDCapR-1.7.0/REDCapR/man/kernel_api.Rd | 152 REDCapR-1.7.0/REDCapR/man/metadata_utilities.Rd | 188 REDCapR-1.7.0/REDCapR/man/redcap_arm_export.Rd | 178 REDCapR-1.7.0/REDCapR/man/redcap_column_sanitize.Rd | 112 REDCapR-1.7.0/REDCapR/man/redcap_dag_read.Rd | 169 REDCapR-1.7.0/REDCapR/man/redcap_delete.Rd | 271 REDCapR-1.7.0/REDCapR/man/redcap_event_instruments.Rd | 216 REDCapR-1.7.0/REDCapR/man/redcap_event_read.Rd | 194 REDCapR-1.7.0/REDCapR/man/redcap_file_download_oneshot.Rd | 292 REDCapR-1.7.0/REDCapR/man/redcap_file_repo_list_oneshot.Rd | 212 REDCapR-1.7.0/REDCapR/man/redcap_file_upload_oneshot.Rd | 266 REDCapR-1.7.0/REDCapR/man/redcap_instrument_download.Rd | 276 REDCapR-1.7.0/REDCapR/man/redcap_instrument_repeating.Rd |only REDCapR-1.7.0/REDCapR/man/redcap_instruments.Rd | 186 REDCapR-1.7.0/REDCapR/man/redcap_log_read.Rd | 259 REDCapR-1.7.0/REDCapR/man/redcap_metadata_coltypes.Rd | 346 - REDCapR-1.7.0/REDCapR/man/redcap_metadata_read.Rd | 194 REDCapR-1.7.0/REDCapR/man/redcap_metadata_write.Rd | 200 REDCapR-1.7.0/REDCapR/man/redcap_next_free_record_name.Rd | 172 REDCapR-1.7.0/REDCapR/man/redcap_project.Rd | 170 REDCapR-1.7.0/REDCapR/man/redcap_project_info_read.Rd | 329 - REDCapR-1.7.0/REDCapR/man/redcap_read.Rd | 651 +- REDCapR-1.7.0/REDCapR/man/redcap_read_eav_oneshot.Rd | 350 - 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REDCapR-1.7.0/REDCapR/tests/test-all.R | 32 REDCapR-1.7.0/REDCapR/tests/testthat/test-arm-export.R | 260 REDCapR-1.7.0/REDCapR/tests/testthat/test-column-sanitize.R | 70 REDCapR-1.7.0/REDCapR/tests/testthat/test-constant.R | 196 REDCapR-1.7.0/REDCapR/tests/testthat/test-create-batch-glossary.R | 198 REDCapR-1.7.0/REDCapR/tests/testthat/test-create-credential-local.R | 74 REDCapR-1.7.0/REDCapR/tests/testthat/test-dag-read.R | 162 REDCapR-1.7.0/REDCapR/tests/testthat/test-delete.R | 406 - REDCapR-1.7.0/REDCapR/tests/testthat/test-event-instruments.R | 372 - REDCapR-1.7.0/REDCapR/tests/testthat/test-event-read.R | 356 - REDCapR-1.7.0/REDCapR/tests/testthat/test-file-oneshot.R | 1166 +-- REDCapR-1.7.0/REDCapR/tests/testthat/test-file-repo-list-oneshot.R | 328 - REDCapR-1.7.0/REDCapR/tests/testthat/test-instrument-repeating.R |only REDCapR-1.7.0/REDCapR/tests/testthat/test-instruments-metadata.R | 164 REDCapR-1.7.0/REDCapR/tests/testthat/test-instruments.R | 188 REDCapR-1.7.0/REDCapR/tests/testthat/test-log-read.R | 100 REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-coltypes.R | 460 - REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-read.R | 642 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-utilities.R | 380 - REDCapR-1.7.0/REDCapR/tests/testthat/test-metadata-write.R | 110 REDCapR-1.7.0/REDCapR/tests/testthat/test-next-free-record-name.R | 188 REDCapR-1.7.0/REDCapR/tests/testthat/test-project-info-read.R | 236 REDCapR-1.7.0/REDCapR/tests/testthat/test-project.R | 158 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 390 - REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-plumbing.R | 190 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-repeating-sparse.R | 246 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-simple.R | 1800 ++--- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-batch-survey.R | 228 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-clinical-trial.R | 86 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-dag.R | 90 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-decimal-comma.R | 232 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-decimal-dot.R | 176 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-eav-oneshot.R | 706 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-errors.R | 184 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-oneshot-eav.R | 698 +- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-oneshot.R | 1542 ++--- REDCapR-1.7.0/REDCapR/tests/testthat/test-read-russian.R | 88 REDCapR-1.7.0/REDCapR/tests/testthat/test-read-superwide.R | 294 REDCapR-1.7.0/REDCapR/tests/testthat/test-report.R | 346 - REDCapR-1.7.0/REDCapR/tests/testthat/test-retrieve-credential-local.R | 346 - REDCapR-1.7.0/REDCapR/tests/testthat/test-retrieve-credential-mssql.R | 332 - REDCapR-1.7.0/REDCapR/tests/testthat/test-sanitize.R | 146 REDCapR-1.7.0/REDCapR/tests/testthat/test-skippers.R | 22 REDCapR-1.7.0/REDCapR/tests/testthat/test-survey-link-export-oneshot.R | 134 REDCapR-1.7.0/REDCapR/tests/testthat/test-users-export.R | 286 REDCapR-1.7.0/REDCapR/tests/testthat/test-utilities-collapse_vector.R | 40 REDCapR-1.7.0/REDCapR/tests/testthat/test-utilities-replace_nas_with_explicit.R | 160 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-field-names.R | 105 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-no-logical.R | 160 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-record-id-name.R | 78 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-repeat.R | 66 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate-uniqueness.R | 220 REDCapR-1.7.0/REDCapR/tests/testthat/test-validate.R | 192 REDCapR-1.7.0/REDCapR/tests/testthat/test-variables.R | 186 REDCapR-1.7.0/REDCapR/tests/testthat/test-version.R | 90 REDCapR-1.7.0/REDCapR/tests/testthat/test-write-batch.R | 416 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-dag.R | 428 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-error.R | 298 REDCapR-1.7.0/REDCapR/tests/testthat/test-write-oneshot.R | 564 - REDCapR-1.7.0/REDCapR/tests/testthat/test-write-serialization.R |only REDCapR-1.7.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 344 - REDCapR-1.7.0/REDCapR/vignettes/SecurityDatabase.Rmd | 694 +- REDCapR-1.7.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 1068 +-- REDCapR-1.7.0/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 540 - REDCapR-1.7.0/REDCapR/vignettes/longitudinal-and-repeating.Rmd | 852 +- REDCapR-1.7.0/REDCapR/vignettes/workflow-read.Rmd | 866 +- REDCapR-1.7.0/REDCapR/vignettes/workflow-write.Rmd | 838 +- 391 files changed, 42356 insertions(+), 42029 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>. Note that the required
package 'ggm' depends on 'graph' from Bioconductor, which is not installed
automatically; the simplest route is install.packages("BiocManager");
BiocManager::install("phylopath").
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.3.1 dated 2025-09-06 and 1.4.0 dated 2026-08-20
DESCRIPTION | 20 - MD5 | 74 +++-- NAMESPACE | 5 NEWS.md | 235 +++++++++++++---- R/DAG.R | 205 ++++++++++++++ R/internal.R | 373 +++++++++++++++++++++++---- R/phylopath.R | 99 ++++--- R/print_and_plot.R | 219 ++++++++++----- build/vignette.rds |binary inst/doc/binary_models.R | 8 inst/doc/binary_models.Rmd | 29 +- inst/doc/binary_models.html | 120 +++++--- inst/doc/intro_to_phylopath.R | 24 - inst/doc/intro_to_phylopath.Rmd | 30 +- inst/doc/intro_to_phylopath.html | 79 ++--- man/as.data.frame.fitted_DAG.Rd |only man/average.Rd | 3 man/average_DAGs.Rd | 3 man/best.Rd | 3 man/choice.Rd | 3 man/coef.fitted_DAG.Rd |only man/est_DAG.Rd | 52 +++ man/figures/unnamed-chunk-2-1.png |binary man/figures/unnamed-chunk-3-1.png |binary man/plot.DAG.Rd | 2 man/plot.fitted_DAG.Rd | 2 man/plot.phylopath_summary.Rd |only man/plot_model_set.Rd | 2 tests/testthat/helper-fixtures.R |only tests/testthat/test-as_data_frame.R |only tests/testthat/test-average_DAGs.R |only tests/testthat/test-basis_set.R |only tests/testthat/test-check_models_data_tree.R | 286 ++++++++++++-------- tests/testthat/test-consensus_order.R |only tests/testthat/test-dag.R | 76 +++-- tests/testthat/test-define_model_set.R | 69 +++- tests/testthat/test-est_DAG.R |only tests/testthat/test-extractors.R |only tests/testthat/test-internals.R |only tests/testthat/test-phylo_path.R |only tests/testthat/test-plots.R |only tests/testthat/test-print_fitted_DAG.R |only tests/testthat/test-statistics.R |only tests/testthat/test-summary.R |only vignettes/binary_models.Rmd | 29 +- vignettes/intro_to_phylopath.Rmd | 30 +- 46 files changed, 1498 insertions(+), 582 deletions(-)
Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Outlier detection method that flags suspicious values within observations,
constrasting them against the normal values in a user-readable format, potentially
describing conditions within the data that make a given outlier more rare.
Full procedure is described in Cortes (2020) <doi:10.48550/arXiv.2001.00636>.
Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes [aut, cre]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between outliertree versions 1.10.0-1 dated 2026-03-05 and 1.10.0-2 dated 2026-08-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- configure | 26 +++++++++++++------------- configure.ac | 2 +- inst/doc/Introducing_OutlierTree.html | 4 ++-- src/fit_model.cpp | 4 ++-- 6 files changed, 26 insertions(+), 26 deletions(-)
Title: Unified Algorithm for Non-Convex Penalized Estimation for
Generalized Linear Models
Description: An efficient unified nonconvex penalized estimation algorithm for
Gaussian (linear), binomial Logit (logistic), Poisson, multinomial Logit,
and Cox proportional hazard regression models.
The unified algorithm is implemented based on the convex concave procedure and
the algorithm can be applied to most of the existing nonconvex penalties.
The algorithm also supports convex penalty:
least absolute shrinkage and selection operator (LASSO).
Supported nonconvex penalties include
smoothly clipped absolute deviation (SCAD),
minimax concave penalty (MCP), truncated LASSO penalty (TLP),
clipped LASSO (CLASSO), sparse ridge (SRIDGE),
modified bridge (MBRIDGE) and modified log (MLOG).
For high-dimensional data (data set with many variables),
the algorithm selects relevant variables producing a parsimonious regression model.
Kim, D., Lee, S. and Kwon, S. (2021) <doi:10.32614/RJ-2021-003>,
Lee, S., Kwon, S. and Kim, Y. (2016) <doi:10.1016/j.csda.2015.08.019>,
Kwon, S., Lee, S. and Kim, [...truncated...]
Author: Dongshin Kim [aut, cre, cph],
Sunghoon Kwon [aut, cph],
Sangin Lee [aut, cph]
Maintainer: Dongshin Kim <dongshin.kim@outlook.com>
This is a re-admission after prior archival of version 1.0.0 dated 2018-11-17
Diff between ncpen versions 1.0.0 dated 2018-11-17 and 1.0.1 dated 2026-08-20
DESCRIPTION | 20 +- MD5 | 79 ++++---- NAMESPACE | 30 +-- NEWS.md | 23 -- R/ncpen_cpp_wrap.R | 7 R/ncpen_package.R | 5 R/ncpen_util.R | 5 R/ncpen_ux.R | 2 README.md | 8 build |only man/coef.cv.ncpen.Rd | 104 +++++------ man/coef.ncpen.Rd | 82 ++++---- man/control.ncpen.Rd | 282 ++++++++++++++++-------------- man/cv.ncpen.Rd | 323 ++++++++++++++++++----------------- man/cv.ncpen.reg.Rd | 333 +++++++++++++++++++----------------- man/excluded.Rd | 42 ++-- man/fold.cv.ncpen.Rd | 131 +++++++------- man/gic.ncpen.Rd | 134 +++++++------- man/interact.data.Rd | 74 ++++---- man/make.ncpen.data.Rd | 60 +++--- man/native_cpp_ncpen_fun_.Rd | 143 ++++++++------- man/native_cpp_nr_fun_.Rd | 50 ++--- man/native_cpp_obj_fun_.Rd | 46 ++--- man/native_cpp_obj_grad_fun_.Rd | 46 ++--- man/native_cpp_obj_hess_fun_.Rd | 46 ++--- man/native_cpp_p_ncpen_fun_.Rd | 123 +++++++------ man/native_cpp_pen_fun_.Rd | 50 ++--- man/native_cpp_pen_grad_fun_.Rd | 50 ++--- man/native_cpp_qlasso_fun_.Rd | 97 +++++----- man/native_cpp_set_dev_mode_.Rd | 34 +-- man/ncpen-package.Rd | 99 +++++----- man/ncpen.Rd | 367 +++++++++++++++++++++------------------- man/ncpen.reg.Rd | 356 ++++++++++++++++++++------------------ man/plot.cv.ncpen.Rd | 81 ++++---- man/plot.ncpen.Rd | 89 ++++----- man/power.data.Rd | 56 +++--- man/predict.ncpen.Rd | 138 +++++++-------- man/sam.gen.ncpen.Rd | 135 +++++++------- man/same.base.Rd | 42 ++-- man/to.indicators.Rd | 86 ++++----- man/to.ncpen.x.mat.Rd | 105 +++++------ 41 files changed, 2077 insertions(+), 1906 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb],
Samuel [...truncated...]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.46.1 dated 2026-03-07 and 1.47 dated 2026-08-20
DESCRIPTION | 8 MD5 | 317 ++++++++++++++++++------------------- NAMESPACE | 25 +- NEWS.md | 28 +++ R/00-classes.R | 10 - R/02b-item_methods.R | 238 ++++++++++++++++++++++++++- R/03-estimation.R | 29 +-- R/04-PrepData.R | 2 R/05-model.elements.R | 6 R/06-LoadPars.R | 72 ++++++-- R/DIF.R | 41 +++- R/DTF.R | 2 R/EMstep.group.R | 9 - R/EMstep.utils.R | 7 R/M2.R | 2 R/MDIFF.R | 2 R/MDISC.R | 2 R/Mixture-methods.R | 2 R/PLCI.mirt.R | 2 R/RCI.R | 92 ++++++++++ R/SIBTEST.R | 2 R/SingleGroup-methods.R | 54 +++--- R/areainfo.R | 2 R/averageMI.R | 2 R/bfactor.R | 120 ++++++++++++-- R/boot.LR.R | 2 R/boot.mirt.R | 2 R/createGroup.R | 2 R/createItem.R | 2 R/empirical_ES.R | 2 R/empirical_plot.R | 2 R/empirical_rxx.R | 2 R/estfun.R | 2 R/expand.table.R | 2 R/expected.item.R | 2 R/expected.test.R | 2 R/extract.group.R | 2 R/extract.item.R | 2 R/extract.mirt.R | 3 R/fixef.R | 2 R/fscores.R | 36 +++- R/fscores.internal.R | 305 ++++++++++++++++++++++++++++------- R/gen.difficulty.R | 2 R/imputeMissing.R | 2 R/itemGAM.R | 2 R/itemfit.R | 2 R/iteminfo.R | 2 R/itemplot.R | 19 +- R/itemplot.internal.R | 29 ++- R/itemstats.R | 28 ++- R/key2binary.R | 2 R/lagrange.R | 50 +++++ R/likert2int.R | 2 R/marginal_moments.R | 2 R/marginal_rxx.R | 2 R/mdirt.R | 2 R/mirt-package.R | 25 ++ R/mirt.R | 14 + R/mirt.model.R | 2 R/mirtCluster.R | 4 R/mixedmirt.R | 2 R/mod2values.R | 2 R/multipleGroup.R | 14 + R/personfit.R | 2 R/pirt.R |only R/poly2dich.R | 2 R/probtrace.R | 2 R/randef.R | 2 R/remap.distance.R | 2 R/reverse.score.R | 2 R/simdata.R | 2 R/testinfo.R | 2 R/utils.R | 23 +- R/wald.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/pirt_DIF.RData |only inst/doc/mirt-vignettes.html | 18 +- man/DIF.Rd | 5 man/DTF.Rd | 2 man/DiscreteClass-class.Rd | 2 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/MixedClass-class.Rd | 2 man/MixtureClass-class.Rd | 2 man/MultipleGroupClass-class.Rd | 2 man/PLCI.mirt.Rd | 2 man/RCI.Rd | 92 ++++++++++ man/SIBTEST.Rd | 2 man/SingleGroupClass-class.Rd | 2 man/anova-method.Rd | 2 man/areainfo.Rd | 2 man/averageMI.Rd | 2 man/bfactor.Rd | 119 ++++++++++++- man/boot.LR.Rd | 2 man/boot.mirt.Rd | 2 man/coef-method.Rd | 2 man/createGroup.Rd | 2 man/createItem.Rd | 2 man/empirical_ES.Rd | 2 man/empirical_plot.Rd | 2 man/empirical_rxx.Rd | 2 man/expand.table.Rd | 2 man/expected.item.Rd | 2 man/expected.test.Rd | 2 man/extract.group.Rd | 2 man/extract.item.Rd | 2 man/extract.mirt.Rd | 2 man/fixef.Rd | 2 man/fscores.Rd | 27 ++- man/gen.difficulty.Rd | 2 man/imputeMissing.Rd | 2 man/itemGAM.Rd | 2 man/itemfit.Rd | 2 man/iteminfo.Rd | 2 man/itemplot.Rd | 14 + man/itemstats.Rd | 2 man/key2binary.Rd | 2 man/lagrange.Rd | 48 +++++ man/likert2int.Rd | 2 man/logLik-method.Rd | 2 man/marginal_moments.Rd | 2 man/marginal_rxx.Rd | 2 man/mdirt.Rd | 2 man/mirt-package.Rd | 2 man/mirt.Rd | 14 + man/mirt.model.Rd | 2 man/mirtCluster.Rd | 4 man/mixedmirt.Rd | 2 man/mod2values.Rd | 2 man/multipleGroup.Rd | 14 + man/personfit.Rd | 2 man/pirt.Rd |only man/pirt_DIF.Rd |only man/plot-method.Rd | 2 man/poly2dich.Rd | 2 man/print-method.Rd | 2 man/probtrace.Rd | 2 man/randef.Rd | 2 man/remap.distance.Rd | 2 man/residuals-method.Rd | 2 man/reverse.score.Rd | 2 man/secondOrderTest.Rd | 2 man/show-method.Rd | 2 man/simdata.Rd | 2 man/summary-method.Rd | 2 man/testinfo.Rd | 2 man/thetaComb.Rd | 2 man/vcov-method.Rd | 2 man/wald.Rd | 2 src/Estep.cpp | 6 src/Misc.cpp | 10 + src/Misc.h | 2 src/traceLinePts.cpp | 169 ++++++++++++++++--- src/traceLinePts.h | 21 ++ tests/testthat/test-02-mirtTwo.R | 8 tests/testthat/test-07-mixedmirt.R | 13 - tests/testthat/test-10-extras.R | 7 tests/testthat/test-13-grsmIRT.R | 4 tests/testthat/test-14-unfolding.R | 2 tests/testthat/test-19-PIRT.R |only 162 files changed, 1822 insertions(+), 597 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [ctb],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.9.2 dated 2026-06-30 and 1.9.3 dated 2026-08-20
lava-1.9.2/lava/R/measurement.error.R |only lava-1.9.2/lava/R/zcolorbar.R |only lava-1.9.2/lava/inst/doc/correlation.Rmd |only lava-1.9.2/lava/inst/doc/influencefunction.Rmd |only lava-1.9.2/lava/inst/doc/nonlinear.Rmd |only lava-1.9.2/lava/man/measurement.error.Rd |only lava-1.9.2/lava/vignettes/correlation.Rmd |only lava-1.9.2/lava/vignettes/influencefunction.Rmd |only lava-1.9.2/lava/vignettes/nonlinear.Rmd |only lava-1.9.3/lava/DESCRIPTION | 16 lava-1.9.3/lava/INDEX | 86 lava-1.9.3/lava/MD5 | 153 lava-1.9.3/lava/NAMESPACE | 263 - lava-1.9.3/lava/NEWS.md | 11 lava-1.9.3/lava/R/IC.R | 2 lava-1.9.3/lava/R/Missing.R | 4 lava-1.9.3/lava/R/binomial.rrw.R | 16 lava-1.9.3/lava/R/bootstrap.R | 2 lava-1.9.3/lava/R/colorbar.R |only lava-1.9.3/lava/R/confint.R | 2 lava-1.9.3/lava/R/constrain.R | 2 lava-1.9.3/lava/R/contr.R | 18 lava-1.9.3/lava/R/distribution.R | 87 lava-1.9.3/lava/R/effects.R | 7 lava-1.9.3/lava/R/estimate.array.R | 27 lava-1.9.3/lava/R/estimate.default.R | 18 lava-1.9.3/lava/R/estimate_calculus.R | 91 lava-1.9.3/lava/R/eventTime.R | 99 lava-1.9.3/lava/R/intervention.R | 6 lava-1.9.3/lava/R/measurement_error.R |only lava-1.9.3/lava/R/mixture.R | 4 lava-1.9.3/lava/R/napass0.R | 90 lava-1.9.3/lava/R/sim.default.R | 2 lava-1.9.3/lava/R/sim.lvm.R | 98 lava-1.9.3/lava/R/stack.R |binary lava-1.9.3/lava/R/summary.estimate.R | 5 lava-1.9.3/lava/R/timedep.R | 8 lava-1.9.3/lava/R/twostage.R | 8 lava-1.9.3/lava/R/z_dist_old.R |only lava-1.9.3/lava/README.md | 27 lava-1.9.3/lava/build/vignette.rds |binary lava-1.9.3/lava/inst/doc/correlation.R | 51 lava-1.9.3/lava/inst/doc/correlation.html | 1161 +++---- lava-1.9.3/lava/inst/doc/correlation.qmd |only lava-1.9.3/lava/inst/doc/influencefunction.R | 116 lava-1.9.3/lava/inst/doc/influencefunction.html | 3106 ++++++++----------- lava-1.9.3/lava/inst/doc/influencefunction.qmd |only lava-1.9.3/lava/inst/doc/nonlinear.R | 72 lava-1.9.3/lava/inst/doc/nonlinear.html | 1267 +++---- lava-1.9.3/lava/inst/doc/nonlinear.qmd |only lava-1.9.3/lava/man/IC.default.Rd | 2 lava-1.9.3/lava/man/Missing.Rd | 2 lava-1.9.3/lava/man/binomial.rd.Rd | 10 lava-1.9.3/lava/man/bootstrap.lvm.Rd | 2 lava-1.9.3/lava/man/colorbar.Rd | 2 lava-1.9.3/lava/man/confint.lvmfit.Rd | 2 lava-1.9.3/lava/man/constrain-set.Rd | 2 lava-1.9.3/lava/man/contr.Rd | 1 lava-1.9.3/lava/man/estimate.array.Rd | 4 lava-1.9.3/lava/man/estimate.default.Rd | 4 lava-1.9.3/lava/man/eventTime.Rd | 55 lava-1.9.3/lava/man/figures/estimate-contrast-1.svg | 216 - lava-1.9.3/lava/man/figures/gof1-1.svg | 235 - lava-1.9.3/lava/man/figures/lvm1-1.svg | 48 lava-1.9.3/lava/man/figures/mediation1-1.svg | 42 lava-1.9.3/lava/man/figures/nlin1-1.svg | 108 lava-1.9.3/lava/man/figures/simres1-1.svg | 470 +- lava-1.9.3/lava/man/intervention.lvm.Rd | 4 lava-1.9.3/lava/man/measurement_error.Rd |only lava-1.9.3/lava/man/merge.estimate.Rd | 6 lava-1.9.3/lava/man/mixture.Rd | 4 lava-1.9.3/lava/man/na.pass0.Rd | 7 lava-1.9.3/lava/man/sim.default.Rd | 2 lava-1.9.3/lava/man/sim.lvm.Rd | 83 lava-1.9.3/lava/man/stack.estimate.Rd | 2 lava-1.9.3/lava/man/timedep.Rd | 8 lava-1.9.3/lava/man/twostage.lvmfit.Rd | 2 lava-1.9.3/lava/man/twostageCV.Rd | 6 lava-1.9.3/lava/tests/testthat/test-estimate-array.R | 44 lava-1.9.3/lava/tests/testthat/test-estimate-id.R | 58 lava-1.9.3/lava/tests/testthat/test-merge-estimate.R | 45 lava-1.9.3/lava/tests/testthat/test-misc.R | 27 lava-1.9.3/lava/tests/testthat/test-sim.R | 8 lava-1.9.3/lava/vignettes/correlation.qmd |only lava-1.9.3/lava/vignettes/influencefunction.qmd |only lava-1.9.3/lava/vignettes/nonlinear.qmd |only lava-1.9.3/lava/vignettes/ref.bib | 2 87 files changed, 4285 insertions(+), 4153 deletions(-)
Title: Testlet Item Response Theory
Description: Implementation of Testlet and Item Response Theory.
A light-version yet comprehensive and streamlined framework for psychometric analysis using
unidimensional and multidimensional Item Response Theory
(IRT; Baker & Kim (2004) <doi:10.1201/9781482276725>) and Testlet Response Theory
(TRT; Wainer et al., (2007) <doi:10.1017/CBO9780511618765>).
Designed for researchers, this package supports the estimation of item and person
parameters for a wide variety of models, including binary (i.e., Rasch, 2-Parameter Logistic, 3-Parameter Logistic)
and polytomous (Partial Credit Model, Generalized Partial Credit Model, Graded Response Model) formats. It also supports the estimation of Testlet models (Rasch Testlet, 2-Parameter Logistic Testlet, 3-Parameter Logistic Testlet, Bifactor, Partial Credit Model Testlet, Graded Response), allowing users to account for local item dependence in bundled items. A key feature is the specialized support for combination use and joint estimation of [...truncated...]
Author: Jiawei Xiong [aut, cre],
Cheng Tang [ctb],
Qidi Liu [ctb]
Maintainer: Jiawei Xiong <jiawei.xiong@uga.edu>
Diff between tirt versions 0.3.1 dated 2026-03-24 and 0.4.0 dated 2026-08-20
DESCRIPTION | 22 +++++++++------- MD5 | 52 ++++++++++++++++++++++++++++++--------- NAMESPACE | 12 +++++++++ R/dif.R |only R/information.R |only R/irt_engine.R |only R/irt_trt.R | 25 ++++++++++++++++++ R/item_fit.R |only R/ld_stats.R |only R/mixture_irt.R |only R/person_fit.R |only R/polytomousirt.R | 15 +++++++++-- R/reliability.R |only R/score_table.R |only R/sim_mirt.R |only R/sim_tirt.R |only R/tcc.R |only R/trt_binary.R | 26 ++++++++++++++++++- build/vignette.rds |binary inst/doc/intro_tirt.Rmd | 2 + inst/doc/intro_tirt.html | 6 ++++ inst/doc/psychometric_tools.R |only inst/doc/psychometric_tools.Rmd |only inst/doc/psychometric_tools.html |only man/dif.Rd |only man/irt_trt.Rd | 25 ++++++++++++++++++ man/item_fit.Rd |only man/item_info.Rd |only man/ld_stats.Rd |only man/mixture_irt.Rd |only man/person_fit.Rd |only man/polytomous_irt.Rd | 15 +++++++++-- man/reliability.Rd |only man/score_table.Rd |only man/sim_mirt.Rd |only man/sim_tirt.Rd |only man/tcc.Rd |only man/test_info.Rd |only man/trt_binary.Rd | 26 ++++++++++++++++++- vignettes/intro_tirt.Rmd | 2 + vignettes/psychometric_tools.Rmd |only 41 files changed, 199 insertions(+), 29 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions, and a batch sequential-design proposer based on Thompson sampling from the bootstrap ensemble (Thompson (1933) <doi:10.1093/biomet/25.3-4.285>; Kandasamy et al. (2018) <doi:10.48550/arXiv.1705.09236>). Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl ( [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.2.3 dated 2026-07-02 and 3.5.0 dated 2026-08-20
DESCRIPTION | 17 MD5 | 98 - NAMESPACE | 12 NEWS | 198 +- R/SVEMnet-package.R | 16 R/SVEMnet.R | 572 +++++-- R/bigexp.R | 172 +- R/coef.R | 111 - R/export_candidates_csv.R | 173 -- R/forward_selection.R |only R/glmnet_compat.R | 230 ++ R/glmnet_with_cv.R | 826 ++++++---- R/ij_diagnostic.R |only R/lipid_screen.R | 29 R/plot.svemnet.R | 174 +- R/predict.cv.R | 37 R/predict.svem_lasso.R | 88 - R/select_candidates.R | 83 - R/spec_limit_utility.R | 65 R/svem_random_table_multi.R | 34 R/svem_score_random.R | 456 +++-- R/svem_select_score_from_table.R | 59 R/svem_significance_test_parallel.R | 2064 +++++++++++++++----------- R/svem_thompson_batch.R |only R/svem_wmt_multi.R | 51 R/validation.R |only inst/CITATION | 2 man/SVEMnet-package.Rd | 16 man/SVEMnet.Rd | 62 man/bigexp_terms.Rd | 37 man/coef.svem_model.Rd | 24 man/forward_aicc.Rd |only man/glmnet_with_cv.Rd | 72 man/lipid_screen.Rd | 15 man/plot.svem_binomial.Rd | 10 man/plot.svem_model.Rd | 10 man/predict.svem_model.Rd | 14 man/predict_cv.Rd | 8 man/print.bigexp_formula.Rd |only man/print.svem_thompson_batch.Rd |only man/svem_export_candidates_csv.Rd | 149 - man/svem_forward.Rd |only man/svem_ij_variance.Rd |only man/svem_nonzero.Rd | 29 man/svem_score_random.Rd | 73 man/svem_significance_test_parallel.Rd | 79 man/svem_thompson_batch.Rd |only man/svem_wmt_multi.Rd | 52 tests/testthat/test-audit-fixes.R | 8 tests/testthat/test-bugfixes-3.3.1.R |only tests/testthat/test-complexity-edf.R | 5 tests/testthat/test-fitter-hardening-3.4.0.R |only tests/testthat/test-forward-selection.R |only tests/testthat/test-member-diagnostics-ij.R |only tests/testthat/test-release-hardening-3.4.0.R |only tests/testthat/test-scoring-hardening-3.4.0.R |only tests/testthat/test-thompson-batch.R |only tests/testthat/test-wmt-hardening-3.4.0.R |only tests/testthat/test_extras.R | 18 59 files changed, 3787 insertions(+), 2461 deletions(-)
Title: Relative Importance Factor Analysis
Description: Tools for estimating, comparing, and visualizing Relative
Importance Factor (RIF) indices based on rank-frequency distributions
and discrete power-law models. The package provides reproducible
workflows for data preparation, model fitting, goodness-of-fit
assessment, bootstrap inference, and publication-ready outputs.
The implemented methodology is described in Llinas et al. (2026)
<doi:10.3390/math14060966>.
Author: Humberto J. Llinas M. [aut, cre],
Humberto J. Llinas S. [aut],
Javier A. De la Hoz M. [aut],
Brian J. Llinas M. [aut],
Jose J. Padilla [aut]
Maintainer: Humberto J. Llinas M. <lhumberto@uninorte.edu.co>
Diff between RIFanalysis versions 0.9.1 dated 2026-08-08 and 0.9.2 dated 2026-08-20
DESCRIPTION | 6 MD5 | 75 +-- NEWS.md |only R/export_rif_excel.R | 65 ++ R/export_rif_plots.R | 2 R/export_rif_visuals.R | 2 R/rif_analysis.R | 6 R/rif_fit_bootstrap.R | 225 +++++++-- R/rif_fit_powerlaw.R | 6 R/rif_workflow_z1.R | 29 + R/rif_workflow_z2.R | 7 R/rif_workflow_z3.R | 55 +- build/partial.rdb |only data/data_by_type.rda |binary inst/doc/Vignette1.R | 13 inst/doc/Vignette1.Rmd | 1057 ++++++++++++++++++++++----------------------- inst/doc/Vignette1.html | 69 +- inst/doc/Vignette2.R | 11 inst/doc/Vignette2.Rmd | 710 +++++++++++++++--------------- inst/doc/Vignette2.html | 65 +- inst/doc/Vignette3.R | 12 inst/doc/Vignette3.Rmd | 757 ++++++++++++++++---------------- inst/doc/Vignette3.html | 59 +- man/RIFanalysis-package.Rd | 2 man/export_rif_excel.Rd | 10 man/export_rif_plots.Rd | 2 man/export_rif_visuals.Rd | 2 man/rif_analysis.Rd | 6 man/rif_fit_bootstrap.Rd | 6 man/rif_fit_powerlaw.Rd | 6 man/rif_workflow_z1.Rd | 11 man/rif_workflow_z2.Rd | 7 man/rif_workflow_z3.Rd | 22 tests |only vignettes/Vignette1.Rmd | 1057 ++++++++++++++++++++++----------------------- vignettes/Vignette2.Rmd | 710 +++++++++++++++--------------- vignettes/Vignette3.Rmd | 757 ++++++++++++++++---------------- 37 files changed, 3055 insertions(+), 2774 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 12.0.0 dated 2025-11-11 and 13.0.0 dated 2026-08-20
praznik-12.0.0/praznik/inst/tinytest |only praznik-12.0.0/praznik/tests/tinytest.R |only praznik-13.0.0/praznik/DESCRIPTION | 10 +-- praznik-13.0.0/praznik/MD5 | 84 +++++++++++--------------- praznik-13.0.0/praznik/NAMESPACE | 2 praznik-13.0.0/praznik/R/algorithms.R | 50 ++++++++++++--- praznik-13.0.0/praznik/R/scorers.R | 38 +++++++++++ praznik-13.0.0/praznik/inst/NEWS | 3 praznik-13.0.0/praznik/man/CMI.Rd | 2 praznik-13.0.0/praznik/man/CMIM.Rd | 2 praznik-13.0.0/praznik/man/DISR.Rd | 2 praznik-13.0.0/praznik/man/JIM.Rd | 2 praznik-13.0.0/praznik/man/JMI.Rd | 2 praznik-13.0.0/praznik/man/JMI3.Rd | 2 praznik-13.0.0/praznik/man/JMIM.Rd | 2 praznik-13.0.0/praznik/man/MIM.Rd | 2 praznik-13.0.0/praznik/man/MRMR.Rd | 2 praznik-13.0.0/praznik/man/NJMIM.Rd | 2 praznik-13.0.0/praznik/man/cmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/cmiScores.Rd | 2 praznik-13.0.0/praznik/man/dnmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/hScores.Rd | 2 praznik-13.0.0/praznik/man/icmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/impScores.Rd | 2 praznik-13.0.0/praznik/man/jhScores.Rd | 2 praznik-13.0.0/praznik/man/jmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/jmiScores.Rd | 2 praznik-13.0.0/praznik/man/maxCmiScores.Rd | 2 praznik-13.0.0/praznik/man/maxJmiScores.Rd | 2 praznik-13.0.0/praznik/man/miMatrix.Rd | 2 praznik-13.0.0/praznik/man/miScores.Rd | 2 praznik-13.0.0/praznik/man/minCmiScores.Rd | 2 praznik-13.0.0/praznik/man/minMaxCmiScores.Rd | 2 praznik-13.0.0/praznik/man/njmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/njmiScores.Rd | 2 praznik-13.0.0/praznik/man/nmiMatrix.Rd | 2 praznik-13.0.0/praznik/man/praznik-package.Rd | 6 + praznik-13.0.0/praznik/man/triScores.Rd | 2 praznik-13.0.0/praznik/src/jmi3.h | 2 praznik-13.0.0/praznik/src/trips.h | 2 praznik-13.0.0/praznik/tests/cran.R |only 41 files changed, 188 insertions(+), 67 deletions(-)
Title: Isotonic Distributional Regression (IDR)
Description: Distributional regression under stochastic order restrictions for
numeric and binary response variables and partially ordered covariates,
including right-censored responses via Survival-IDR. See Henzi, Ziegel,
Gneiting (2021) <doi:10.1111/rssb.12450> and Bladt, Henzi, van den Heuvel,
Ziegel (2026) <doi:10.48550/arXiv.2608.02914>.
Author: Bram van den Heuvel [aut, cre],
Alexander Henzi [aut],
Martin Bladt [aut],
Johanna Ziegel [ths]
Maintainer: Bram van den Heuvel <bram.vandenheuvel@stat.math.ethz.ch>
Diff between isodistrreg versions 0.1.0 dated 2021-03-22 and 0.5.2 dated 2026-08-20
isodistrreg-0.1.0/isodistrreg/R/RcppExports.R |only isodistrreg-0.1.0/isodistrreg/R/multivHazardLoop.R |only isodistrreg-0.1.0/isodistrreg/R/partialOrders.R |only isodistrreg-0.1.0/isodistrreg/man/compOrd.Rd |only isodistrreg-0.1.0/isodistrreg/man/multivHazardLoop.Rd |only isodistrreg-0.1.0/isodistrreg/man/neighborPoints.Rd |only isodistrreg-0.1.0/isodistrreg/man/prepareData.Rd |only isodistrreg-0.1.0/isodistrreg/man/reexports.Rd |only isodistrreg-0.1.0/isodistrreg/man/trReduc.Rd |only isodistrreg-0.1.0/isodistrreg/src/RcppExports.cpp |only isodistrreg-0.1.0/isodistrreg/src/idrHazard.cpp |only isodistrreg-0.1.0/isodistrreg/src/isoCdf_sequential.cpp |only isodistrreg-0.1.0/isodistrreg/src/pavaMatrix.cpp |only isodistrreg-0.5.2/isodistrreg/DESCRIPTION | 57 isodistrreg-0.5.2/isodistrreg/MD5 | 156 - isodistrreg-0.5.2/isodistrreg/NAMESPACE | 78 isodistrreg-0.5.2/isodistrreg/R/bagging.R | 304 +- isodistrreg-0.5.2/isodistrreg/R/data.R | 66 isodistrreg-0.5.2/isodistrreg/R/dindexm.R | 303 +- isodistrreg-0.5.2/isodistrreg/R/evaluation.R | 1373 +++++----- isodistrreg-0.5.2/isodistrreg/R/extendr-wrappers.R |only isodistrreg-0.5.2/isodistrreg/R/modeling.R | 1340 +++++---- isodistrreg-0.5.2/isodistrreg/R/package.R | 271 + isodistrreg-0.5.2/isodistrreg/build/partial.rdb |only isodistrreg-0.5.2/isodistrreg/build/vignette.rds |binary isodistrreg-0.5.2/isodistrreg/cleanup |only isodistrreg-0.5.2/isodistrreg/cleanup.win |only isodistrreg-0.5.2/isodistrreg/configure |only isodistrreg-0.5.2/isodistrreg/configure.win |only isodistrreg-0.5.2/isodistrreg/inst/CITATION | 68 isodistrreg-0.5.2/isodistrreg/inst/doc/IDR_arXiv_preprint.Rnw | 14 isodistrreg-0.5.2/isodistrreg/inst/doc/IDR_arXiv_preprint.pdf |binary isodistrreg-0.5.2/isodistrreg/man/bscore.Rd | 6 isodistrreg-0.5.2/isodistrreg/man/crps.Rd | 10 isodistrreg-0.5.2/isodistrreg/man/dindexm.Rd | 29 isodistrreg-0.5.2/isodistrreg/man/dot-onUnload.Rd | 30 isodistrreg-0.5.2/isodistrreg/man/idr.Rd | 111 isodistrreg-0.5.2/isodistrreg/man/idrbag.Rd | 56 isodistrreg-0.5.2/isodistrreg/man/isodistrreg-package.Rd | 60 isodistrreg-0.5.2/isodistrreg/man/isotonic_regression.Rd |only isodistrreg-0.5.2/isodistrreg/man/isotonic_regression_impl.Rd |only isodistrreg-0.5.2/isodistrreg/man/pit.Rd | 20 isodistrreg-0.5.2/isodistrreg/man/plain_survival_isotonic_distributional_regression.Rd |only isodistrreg-0.5.2/isodistrreg/man/plain_survival_isotonic_distributional_regression_threshold.Rd |only isodistrreg-0.5.2/isodistrreg/man/plot.idr.Rd | 15 isodistrreg-0.5.2/isodistrreg/man/predict.dindexfit.Rd | 21 isodistrreg-0.5.2/isodistrreg/man/predict.idrfit.Rd | 31 isodistrreg-0.5.2/isodistrreg/man/qpred.Rd | 9 isodistrreg-0.5.2/isodistrreg/man/qscore.Rd | 6 isodistrreg-0.5.2/isodistrreg/man/rain.Rd | 4 isodistrreg-0.5.2/isodistrreg/man/survival_isotonic_distributional_regression_threshold.Rd |only isodistrreg-0.5.2/isodistrreg/man/warn_once.Rd |only isodistrreg-0.5.2/isodistrreg/src/Makevars.in |only isodistrreg-0.5.2/isodistrreg/src/Makevars.win.in |only isodistrreg-0.5.2/isodistrreg/src/entrypoint.c |only isodistrreg-0.5.2/isodistrreg/src/isodistrreg-win.def |only isodistrreg-0.5.2/isodistrreg/src/rust |only isodistrreg-0.5.2/isodistrreg/tests |only isodistrreg-0.5.2/isodistrreg/tools |only isodistrreg-0.5.2/isodistrreg/vignettes/IDR_arXiv_preprint.Rnw | 14 isodistrreg-0.5.2/isodistrreg/vignettes/arXiv_preprint.pdf |binary 61 files changed, 2504 insertions(+), 1948 deletions(-)
Title: A Blazing Fast Implementation of Random Forest
Description: Yet another implementation of the Random Forest method by Breiman (2001) <doi:10.1023/A:1010933404324>, written in Rust and tailored towards stability, correctness, efficiency and scalability on modern multi-core machines.
Handles both classification and regression, as well as provides permutation feature importance via a novel, highly optimised algorithm.
Author: Miron Bartosz Kursa [aut, cre] ,
Krzysztof Piotr Piwonski [aut]
Maintainer: Miron Bartosz Kursa <m@mbq.me>
Diff between fru versions 0.0.7 dated 2026-05-07 and 1.0.0 dated 2026-08-20
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/a.R | 4 +++- inst/CITATION |only inst/NEWS | 4 ++++ man/fru.Rd | 4 +++- src/fru/Cargo.lock | 6 +++--- src/fru/Cargo.toml | 2 +- src/xrf/Cargo.lock | 2 +- src/xrf/Cargo.toml | 2 +- src/xrf/src/lib.rs | 9 +++++++++ 11 files changed, 39 insertions(+), 21 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.4.0 dated 2026-07-15 and 1.4.1 dated 2026-08-20
DESCRIPTION | 10 MD5 | 88 ++--- NAMESPACE | 208 ++++++------ R/APclustering.R | 2 R/AgglomerativeNestingClustering.R | 2 R/AutomaticProjectionBasedClustering.R | 2 R/ClusterAccuracy.R | 219 +++++++------ R/ClusterAlignLabels.R |only R/ClusterApply.R | 2 R/ClusterDendrogram.R | 17 - R/ClusterDistances.R | 2 R/ClusterDunnIndex.R | 4 R/ClusterNoEstimation.R | 2 R/ClusterPlotMDS.R | 2 R/ClusterabilityMDplot.R | 10 R/DatabionicSwarmClustering.R | 4 R/DensityPeakClustering.R | 2 R/DivisiveAnalysisClustering.R | 2 R/FannyClustering.R | 2 R/GenieClustering.R | 137 ++++---- R/HierarchicalClusterData.R | 86 +++-- R/HierarchicalClusterDists.R | 535 ++++++++++++++++++++++++++++++--- R/HierarchicalClustering.R | 286 +++++++++++++---- R/HierarchicalDBSCAN.R | 2 R/IsDissimilarity.R |only R/MSTclustering.R | 2 R/MarkovClustering.R | 2 R/MinimalEnergyClustering.R | 149 ++++----- R/MinimaxLinkageClustering.R | 140 ++++---- R/NetworkClustering.R | 2 R/PAMclustering.R | 2 R/SparseClustering.R | 189 ++++++----- R/kmeansClustering.R | 2 build/partial.rdb |binary inst/doc/FCPS.html | 16 man/ClusterAccuracy.Rd | 10 man/ClusterAlignLabels.Rd |only man/ClusterDendrogram.Rd | 7 man/GenieClustering.Rd | 11 man/HierarchicalClusterData.Rd | 20 - man/HierarchicalClusterDists.Rd | 293 ++++++++++++++++-- man/HierarchicalClustering.Rd | 256 +++++++++++++-- man/IsDissimilarity.Rd |only man/MinimalEnergyClustering.Rd | 106 +++--- man/MinimaxLinkageClustering.Rd | 106 +++--- man/ProjectionPursuitClustering.Rd | 151 ++++----- man/SparseClustering.Rd | 165 +++++----- 47 files changed, 2248 insertions(+), 1007 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” (AKA singleton expansion) refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tonywilkes.nl@gmail.com>
Diff between broadcast versions 0.1.9 dated 2026-05-29 and 0.1.9.5 dated 2026-08-20
broadcast-0.1.9.5/broadcast/DESCRIPTION | 12 broadcast-0.1.9.5/broadcast/MD5 | 212 ++++--- broadcast-0.1.9.5/broadcast/NAMESPACE | 2 broadcast-0.1.9.5/broadcast/NEWS.md | 35 + broadcast-0.1.9.5/broadcast/R/RcppExports.R | 102 +++ broadcast-0.1.9.5/broadcast/R/aaa00_broadcast_help.R | 6 broadcast-0.1.9.5/broadcast/R/aaa01_broadcast_operators.R | 14 broadcast-0.1.9.5/broadcast/R/aaa02_broadcast_casting.R | 5 broadcast-0.1.9.5/broadcast/R/aaa04_broadcast_linearalgebra.R | 3 broadcast-0.1.9.5/broadcast/R/bc_b.R | 22 broadcast-0.1.9.5/broadcast/R/bc_bit.R | 14 broadcast-0.1.9.5/broadcast/R/bc_cplx.R | 4 broadcast-0.1.9.5/broadcast/R/bc_d.R | 6 broadcast-0.1.9.5/broadcast/R/bc_dim.R | 2 broadcast-0.1.9.5/broadcast/R/bc_i.R | 6 broadcast-0.1.9.5/broadcast/R/bc_ifelse.R | 5 broadcast-0.1.9.5/broadcast/R/bc_list.R | 2 broadcast-0.1.9.5/broadcast/R/bc_raw.R | 2 broadcast-0.1.9.5/broadcast/R/bc_rel.R | 2 broadcast-0.1.9.5/broadcast/R/bc_str.R | 12 broadcast-0.1.9.5/broadcast/R/bc_strrep.R | 2 broadcast-0.1.9.5/broadcast/R/bcapply.R | 2 broadcast-0.1.9.5/broadcast/R/bind_array.R | 3 broadcast-0.1.9.5/broadcast/R/broadcastWrappers.R | 49 - broadcast-0.1.9.5/broadcast/R/broadcaster.R | 46 + broadcast-0.1.9.5/broadcast/R/cast_shallow2atomic.R | 17 broadcast-0.1.9.5/broadcast/R/class_methods.R | 4 broadcast-0.1.9.5/broadcast/R/internal_binary.R | 158 ----- broadcast-0.1.9.5/broadcast/R/internal_bind.R | 9 broadcast-0.1.9.5/broadcast/R/internal_functions.R | 23 broadcast-0.1.9.5/broadcast/R/internal_typefuns.R | 11 broadcast-0.1.9.5/broadcast/R/meta_functions.R | 90 +++ broadcast-0.1.9.5/broadcast/R/reorient_vector.R |only broadcast-0.1.9.5/broadcast/R/vector2array.R | 27 broadcast-0.1.9.5/broadcast/build/partial.rdb |binary broadcast-0.1.9.5/broadcast/inst/examples/bind_array.R | 2 broadcast-0.1.9.5/broadcast/inst/examples/reorient_vector.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part1 |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part2 |only broadcast-0.1.9.5/broadcast/inst/tinytest/aaa_binary_prep_part3 |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_b/logic_gates.csv |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_b/test-logic.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/bc_bytes/test-bc_bit_int.R | 45 + broadcast-0.1.9.5/broadcast/inst/tinytest/bc_general/test-binaryerrors.R | 4 broadcast-0.1.9.5/broadcast/inst/tinytest/bc_str/test-bc_str_dist.R | 17 broadcast-0.1.9.5/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-broadcaster.R | 114 ++-- broadcast-0.1.9.5/broadcast/inst/tinytest/cast_lists |only broadcast-0.1.9.5/broadcast/inst/tinytest/class/test-eval.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/class/test-mbroadcasters.R | 21 broadcast-0.1.9.5/broadcast/inst/tinytest/helper/test-vector2array.R | 11 broadcast-0.1.9.5/broadcast/inst/tinytest/internal/test-return_missing.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/overload/test-method_dispatch.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/reorient_vector |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-coercion-special.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-coercion-zerolen.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-names-1dnames.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/shallow2atomic/test-names-dimnames.R |only broadcast-0.1.9.5/broadcast/inst/tinytest/test-binary1d.R | 4 broadcast-0.1.9.5/broadcast/inst/tinytest/test-binary_errors.R | 4 broadcast-0.1.9.5/broadcast/man/aaa00_broadcast_help.Rd | 8 broadcast-0.1.9.5/broadcast/man/aaa01_broadcast_operators.Rd | 10 broadcast-0.1.9.5/broadcast/man/aaa02_broadcast_casting.Rd | 5 broadcast-0.1.9.5/broadcast/man/bc.b.Rd | 19 broadcast-0.1.9.5/broadcast/man/bc.bit.Rd | 10 broadcast-0.1.9.5/broadcast/man/bc.str.Rd | 6 broadcast-0.1.9.5/broadcast/man/bind_array.Rd | 2 broadcast-0.1.9.5/broadcast/man/broadcaster.Rd | 6 broadcast-0.1.9.5/broadcast/man/cast_shallow2atomic.Rd | 17 broadcast-0.1.9.5/broadcast/man/linear_algebra_stats.Rd | 3 broadcast-0.1.9.5/broadcast/man/reorient_vector.Rd |only broadcast-0.1.9.5/broadcast/man/vector2array.Rd | 14 broadcast-0.1.9.5/broadcast/src/C_arraysize_overflow.c | 2 broadcast-0.1.9.5/broadcast/src/C_max_type.c |only broadcast-0.1.9.5/broadcast/src/RcppExports.cpp | 282 +++++++--- broadcast-0.1.9.5/broadcast/src/broadcast.h | 185 ++++-- broadcast-0.1.9.5/broadcast/src/rcpp_bcRel_bit.cpp | 21 broadcast-0.1.9.5/broadcast/src/rcpp_bc_b.cpp | 17 broadcast-0.1.9.5/broadcast/src/rcpp_bc_bind.cpp | 26 broadcast-0.1.9.5/broadcast/src/rcpp_bindhelpers.cpp | 80 ++ broadcast-0.1.9.5/broadcast/src/rcpp_virt_binary_prep.cpp |only broadcast-0.1.9.5/broadcast/tests/tinytest.R | 17 broadcast-0.1.9/broadcast/inst/examples/recast_dirvector.R |only broadcast-0.1.9/broadcast/inst/tinytest/bc_b/test-bc_b_equivalences.R |only broadcast-0.1.9/broadcast/inst/tinytest/binary_prep |only broadcast-0.1.9/broadcast/inst/tinytest/cast |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-1dnames.R |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-dimnames.R |only broadcast-0.1.9/broadcast/inst/tinytest/shallow2atomic/test-specialcoercion.R |only broadcast-0.1.9/broadcast/inst/tinytest/test-S4error-callerenv.R |only broadcast-0.1.9/broadcast/src/C_bindhelper_get_alongdims.c |only broadcast-0.1.9/broadcast/src/C_bindhelper_max_type.c |only broadcast-0.1.9/broadcast/src/C_bindhelper_sum_along.c |only broadcast-0.1.9/broadcast/src/C_check_conf_dim.c |only broadcast-0.1.9/broadcast/src/C_chunkify_dims.c |only broadcast-0.1.9/broadcast/src/C_determine_dimmode.c |only broadcast-0.1.9/broadcast/src/C_make_outdim.c |only broadcast-0.1.9/broadcast/src/C_pmax.c |only broadcast-0.1.9/broadcast/src/rcpp_classes.cpp |only broadcast-0.1.9/broadcast/src/rcpp_mergedims.cpp |only 99 files changed, 1056 insertions(+), 805 deletions(-)
Title: Content Analysis in R: Integrated Qualitative (LLMs) and
Quantitative Pipeline
Description: Provides an integrated pipeline for content analysis
combining qualitative coding assisted by large language models (LLMs)
with classical quantitative text analysis. Includes modules for
pre-processing (tokenization, stopwords for Brazilian Portuguese),
descriptive statistics, keyness, co-occurrence networks, word clouds
(including comparative and X-ray variants), sentiment analysis via
OpLexicon, Latent Dirichlet Allocation (LDA), inter-coder
reliability metrics (Krippendorff, Gwet), and modern visualizations
based on ggplot2. Special focus on Brazilian corpora and
political-institutional codebooks. Inspired by Maerz and Benoit (2025)
<https://quallmer.github.io/quallmer/>.
Author: Anderson Henrique [aut, cre]
Maintainer: Anderson Henrique <anderson.henrique@usp.br>
Diff between acR versions 0.3.2 dated 2026-08-07 and 0.3.3 dated 2026-08-20
DESCRIPTION | 6 MD5 | 59 ++--- NAMESPACE | 1 NEWS.md | 92 ++++++++ R/ac_ellmer_chat.R | 2 R/ac_qual_code.R | 96 ++++++++ R/ac_qual_codebook.R | 9 R/ac_qual_live.R | 12 - R/ac_qual_models.R | 8 R/ac_qual_report.R | 259 +++++++++++++++++++++++- R/ac_qual_search_literature.R | 4 README.md | 30 ++ inst/doc/analise-proposicoes.R | 4 inst/doc/analise-proposicoes.Rmd | 6 inst/doc/analise-proposicoes.html | 8 inst/doc/qualitativo-llm.R | 4 inst/doc/qualitativo-llm.Rmd | 12 - inst/doc/qualitativo-llm.html | 62 +++-- inst/doc/replicabilidade.html | 14 - man/ac_qual_code.Rd | 9 man/ac_qual_codebook.Rd | 5 man/ac_qual_report_full.Rd |only man/ac_qual_search_literature.Rd | 2 tests/testthat/test-ac_qual_code.R | 134 ++++++++++++ tests/testthat/test-ac_qual_codebook.R | 6 tests/testthat/test-ac_qual_live.R | 28 ++ tests/testthat/test-ac_qual_report.R | 86 +++++++ tests/testthat/test-ac_qual_search_literature.R | 4 tests/testthat/test-plots-snapshot.R | 5 vignettes/analise-proposicoes.Rmd | 6 vignettes/qualitativo-llm.Rmd | 12 - 31 files changed, 862 insertions(+), 123 deletions(-)
Title: Regression Modeling Using Vasicek Distribution
Description: Provides density, cumulative distribution, quantile, and
random generation functions for Vasicek distributions with standard
normal and standard logistic kernels. The normal-kernel distribution is
parameterized by either its mean or a fixed quantile, whereas the
logistic-kernel distribution uses a fixed-quantile parameterization.
Zero-adjusted, one-adjusted, and zero-and-one-adjusted extensions of the
normal-kernel mean parameterization are also provided for responses that
include boundary values. The corresponding 'NVASIM', 'NVASIQ', 'LVASIQ',
'ZANVASIM', 'OANVASIM', and 'ZOANVASIM' families are available for fitting
Generalized Additive Models for Location, Scale and Shape,
as introduced by Rigby and Stasinopoulos (2005,
<doi:10.1111/j.1467-9876.2005.00510.x>). Some functions are written in
'C++' using 'Rcpp', developed by Eddelbuettel and Francois (2011,
<doi:10.18637/jss.v040.i08>).
Author: Josmar Mazucheli [aut, cre],
Bruna Alves [ctb]
Maintainer: Josmar Mazucheli <jmazucheli@gmail.com>
Diff between vasicekreg versions 1.0.2 dated 2026-01-12 and 1.1.0 dated 2026-08-20
vasicekreg-1.0.2/vasicekreg/R/dpqr-vasicekmean.R |only vasicekreg-1.0.2/vasicekreg/R/dpqr-vasicekquant.R |only vasicekreg-1.0.2/vasicekreg/man/VASIM.Rd |only vasicekreg-1.0.2/vasicekreg/man/VASIQ.Rd |only vasicekreg-1.0.2/vasicekreg/src/vasicekmean.cpp |only vasicekreg-1.0.2/vasicekreg/src/vasicekquant.cpp |only vasicekreg-1.1.0/vasicekreg/DESCRIPTION | 29 vasicekreg-1.1.0/vasicekreg/MD5 | 47 vasicekreg-1.1.0/vasicekreg/NAMESPACE | 64 + vasicekreg-1.1.0/vasicekreg/NEWS.md | 94 + vasicekreg-1.1.0/vasicekreg/R/RcppExports.R | 60 - vasicekreg-1.1.0/vasicekreg/R/bodyfat.R | 34 vasicekreg-1.1.0/vasicekreg/R/dpqr-01NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-0NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-1NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-LvasicekQ.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-NvasicekM.R |only vasicekreg-1.1.0/vasicekreg/R/dpqr-NvasicekQ.R |only vasicekreg-1.1.0/vasicekreg/R/utils.R |only vasicekreg-1.1.0/vasicekreg/R/vasicekreg-package.R | 143 ++ vasicekreg-1.1.0/vasicekreg/README.md |only vasicekreg-1.1.0/vasicekreg/man/LVASIQ.Rd |only vasicekreg-1.1.0/vasicekreg/man/NVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/NVASIQ.Rd |only vasicekreg-1.1.0/vasicekreg/man/OANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/ZANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/ZOANVASIM.Rd |only vasicekreg-1.1.0/vasicekreg/man/bodyfat.Rd | 34 vasicekreg-1.1.0/vasicekreg/man/vasicekreg-package.Rd | 144 ++ vasicekreg-1.1.0/vasicekreg/src/LvasicekQ.cpp |only vasicekreg-1.1.0/vasicekreg/src/NvasicekM.cpp |only vasicekreg-1.1.0/vasicekreg/src/NvasicekQ.cpp |only vasicekreg-1.1.0/vasicekreg/src/RcppExports.cpp | 200 +++- vasicekreg-1.1.0/vasicekreg/tests/testthat/helper-global-tau.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-derivatives.R | 481 ++++++++-- vasicekreg-1.1.0/vasicekreg/tests/testthat/test-dpqr.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-families.R |only vasicekreg-1.1.0/vasicekreg/tests/testthat/test-rqres-augmented.R |only 38 files changed, 1148 insertions(+), 182 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 derived environmental variables such as growing degree-day ('GDD') to get useful insights about the pest phenology. This package pulls temperature data from the 'Daymet' application programming interface ('API', <https://daymet.ornl.gov>), or 'Open-Meteo' ('API', <https://open-meteo.com/>) or manual user-supplied CSV file from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), for a user-specified time period and calculates cumulative growing degree-days. Users provide intended date range, pest of concern, and the geographic coordinates of the trap location to track pest emergence and phenology throughout the growing season.
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 1.0.0 dated 2026-06-13 and 1.0.1 dated 2026-08-20
TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.R |only TrackTrap-1.0.0/TrackTrap/tests/testthat/test-phenology.R |only TrackTrap-1.0.1/TrackTrap/DESCRIPTION | 17 TrackTrap-1.0.1/TrackTrap/LICENSE | 2 TrackTrap-1.0.1/TrackTrap/MD5 | 33 TrackTrap-1.0.1/TrackTrap/NEWS.md | 26 TrackTrap-1.0.1/TrackTrap/R/TrackTrap-package.R | 1 TrackTrap-1.0.1/TrackTrap/R/data.R | 25 TrackTrap-1.0.1/TrackTrap/R/phenology.R | 428 +++++----- TrackTrap-1.0.1/TrackTrap/build |only TrackTrap-1.0.1/TrackTrap/data/pest_thresholds.rda |binary TrackTrap-1.0.1/TrackTrap/inst |only TrackTrap-1.0.1/TrackTrap/man/TrackTrap-package.Rd |only TrackTrap-1.0.1/TrackTrap/man/calc_pest_phenology.Rd | 31 TrackTrap-1.0.1/TrackTrap/man/fetch_open_meteo.Rd | 12 TrackTrap-1.0.1/TrackTrap/man/pest_thresholds.Rd | 22 TrackTrap-1.0.1/TrackTrap/man/plot_trap_phenology.Rd | 31 TrackTrap-1.0.1/TrackTrap/tests/testthat/test-calc_pest_phenology.R |only TrackTrap-1.0.1/TrackTrap/tests/testthat/test-pest_thresholds.R |only TrackTrap-1.0.1/TrackTrap/vignettes |only 20 files changed, 375 insertions(+), 253 deletions(-)
Title: World Development Indicators and Other World Bank Data
Description: Search and download data from over 40 databases hosted by the World Bank, including the World Development Indicators ('WDI'), International Debt Statistics, Doing Business, Human Capital Index, and Sub-national Poverty indicators.
Author: Vincent Arel-Bundock [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between WDI versions 2.7.10 dated 2026-04-05 and 2.8.0 dated 2026-08-20
DESCRIPTION | 7 ++--- MD5 | 14 +++++----- NEWS.md | 12 ++++++-- R/WDI.R | 51 ++++++++++++++++++++++++++++--------- README.md | 16 +++++++---- data/WDI_data.RData |binary man/WDIcache.Rd | 7 ++--- tests/testthat/helper-pagination.R |only tests/testthat/test-pagination.R |only 9 files changed, 74 insertions(+), 33 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut],
Ken Kellner [cre, aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Lea Pautrel [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between unmarked versions 1.5.1 dated 2025-09-26 and 1.5.2 dated 2026-08-20
DESCRIPTION | 8 +- MD5 | 81 ++++++++++---------- NAMESPACE | 2 NEWS.md | 6 + R/gdistremoval.R | 4 + R/occuComm.R | 1 R/occuPEN.R | 8 +- R/plotEffects.R | 2 R/ranef.R | 4 - R/simulate.R | 4 - R/square_brackets.R | 1 R/unmarkedFit.R | 25 ++++-- R/unmarkedFrame.R | 17 ++++ R/utils.R | 17 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/cap-recap.html | 2 inst/doc/distsamp.html | 10 +- inst/doc/occuMulti.html | 58 +++++++-------- inst/doc/spp-dist.html | 10 +- inst/doc/unmarked.html | 16 ++-- man/detFuns.Rd | 5 + man/getStarts.Rd |only man/modSel.Rd | 5 + man/pcountOpen.Rd | 139 ++++++++++++++++++------------------ man/predict.Rd | 5 - man/unmarkedFitList-class.rd | 1 man/unmarkedMultFrame.Rd | 1 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_distsamp.R | 4 - tests/testthat/test_formatInputs.R | 22 ++--- tests/testthat/test_makePiFun.R | 6 - tests/testthat/test_occu.R | 6 - tests/testthat/test_occuFP.R | 14 +++ tests/testthat/test_occuPEN.R | 27 ++++++ tests/testthat/test_pcount.R | 2 tests/testthat/test_pcount.spHDS.R | 2 tests/testthat/test_pcountOpen.R | 2 tests/testthat/test_plotEffects.R | 32 ++++++++ tests/testthat/test_unmarkedFrame.R | 28 +++++++ tests/testthat/test_utils.R | 27 ++++++ 42 files changed, 401 insertions(+), 207 deletions(-)
Title: Tweedie Distribution
Description: Provides density, distribution function, quantile function, and random
generation for the Tweedie distribution under the compound Poisson-Gamma
parameterisation with power parameter in (1, 2). The density is evaluated
using the series expansion of Dunn and Smyth (2005) <doi:10.1007/s11222-005-4070-y>,
implemented in C++ via 'Rcpp' and 'RcppArmadillo' for performance. A constructor
compatible with the 'distributional' package is also provided for use in tidy
modelling workflows.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between tweedieDistr versions 0.1.1 dated 2026-07-23 and 0.2.0 dated 2026-08-20
DESCRIPTION | 6 +- MD5 | 14 ++--- NEWS.md | 4 + src/dtweedie.cpp | 142 +++++++++++++++++++++++++++++++++++-------------------- src/ptweedie.cpp | 10 ++- src/qtweedie.cpp | 42 ++++++++++------ src/utils.cpp | 14 ++++- src/utils.h | 2 8 files changed, 150 insertions(+), 84 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.17.0 dated 2026-06-26 and 0.18.0 dated 2026-08-20
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