Title: Variable Selection using Random Forests
Description: Variable selection from random forests using both
backwards variable elimination (for the selection of small sets
of non-redundant variables) and selection based on the
importance spectrum (somewhat similar to scree plots; for the
selection of large, potentially highly-correlated variables).
Main applications in high-dimensional data (e.g., microarray
data, and other genomics and proteomics applications).
Author: Ramon Diaz-Uriarte [aut, cre]
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
Diff between varSelRF versions 0.7-8 dated 2017-07-10 and 0.7-9 dated 2026-01-30
Changes | 6 + DESCRIPTION | 19 +-- MD5 | 29 ++--- R/varSelRF.R | 246 ++++++++++++++++++++++---------------------- README.md | 6 - build |only inst/CITATION | 10 - man/plot.varSelRF.Rd | 14 +- man/plot.varSelRFBoot.Rd | 19 +-- man/randomVarImpsRF.Rd | 17 +-- man/randomVarImpsRFplot.Rd | 31 ++--- man/selProbPlot.Rd | 17 +-- man/summary.varSelRFBoot.Rd | 17 +-- man/varSelImpSpecRF.Rd | 31 ++--- man/varSelRF.Rd | 15 +- man/varSelRFBoot.Rd | 18 +-- 16 files changed, 247 insertions(+), 248 deletions(-)
Title: Functions for Phylogenetically Based Statistical Analyses
Description: Manipulation and analysis of phylogenetically simulated
data sets and phylogenetically based analyses using GLS.
Author: Ramon Diaz-Uriarte [aut, cre],
Theodore Garland, Jr [aut]
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
Diff between PHYLOGR versions 1.0.11 dated 2020-04-14 and 1.0.12 dated 2026-01-30
PHYLOGR-1.0.11/PHYLOGR/data/GarlandJanis.IC.txt |only PHYLOGR-1.0.11/PHYLOGR/data/GarlandJanis.Original.txt |only PHYLOGR-1.0.11/PHYLOGR/data/GarlandJanis.varcov.txt |only PHYLOGR-1.0.11/PHYLOGR/data/Lacertid.IC.txt |only PHYLOGR-1.0.11/PHYLOGR/data/Lacertid.Original.txt |only PHYLOGR-1.0.11/PHYLOGR/data/Lacertid.varcov.txt |only PHYLOGR-1.0.11/PHYLOGR/data/SimulExample.txt |only PHYLOGR-1.0.12/PHYLOGR/CHANGES | 12 +++++-- PHYLOGR-1.0.12/PHYLOGR/DESCRIPTION | 20 ++++++++---- PHYLOGR-1.0.12/PHYLOGR/MD5 | 24 +++++++-------- PHYLOGR-1.0.12/PHYLOGR/data/GarlandJanis.IC.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/GarlandJanis.Original.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/GarlandJanis.varcov.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/Lacertid.IC.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/Lacertid.Original.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/Lacertid.varcov.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/data/SimulExample.txt.gz |only PHYLOGR-1.0.12/PHYLOGR/man/GarlandJanis.IC.Rd | 8 ++--- PHYLOGR-1.0.12/PHYLOGR/man/GarlandJanis.Original.Rd | 14 ++++---- PHYLOGR-1.0.12/PHYLOGR/man/GarlandJanis.varcov.Rd | 10 +++--- 20 files changed, 51 insertions(+), 37 deletions(-)
Title: 'StreamCatTools'
Description: Tools for using the 'StreamCat' and 'LakeCat' API and
interacting with the 'StreamCat' and 'LakeCat' database.
Convenience functions in the package wrap the API for 'StreamCat'
on <https://api.epa.gov/StreamCat/streams/metrics>.
Author: Marc Weber [aut, cre],
Ryan Hill [ctb],
Selia Markley [ctb],
Travis Hudson [ctb],
Allen Brookes [ctb],
David Rebhuhn [ctb],
Michael Dumelle [ctb],
Zachary Smith [ctb]
Maintainer: Marc Weber <weber.marc@epa.gov>
Diff between StreamCatTools versions 0.9.1 dated 2025-10-25 and 0.10.0 dated 2026-01-30
StreamCatTools-0.10.0/StreamCatTools/DESCRIPTION | 18 StreamCatTools-0.10.0/StreamCatTools/MD5 | 47 +- StreamCatTools-0.10.0/StreamCatTools/NAMESPACE | 9 StreamCatTools-0.10.0/StreamCatTools/NEWS.md | 13 StreamCatTools-0.10.0/StreamCatTools/R/lc_get_data.R | 208 +++++++++ StreamCatTools-0.10.0/StreamCatTools/R/lc_plot.R |only StreamCatTools-0.10.0/StreamCatTools/R/sc_get_data.R | 222 +++++++++- StreamCatTools-0.10.0/StreamCatTools/R/sc_plot.R |only StreamCatTools-0.10.0/StreamCatTools/README.md | 6 StreamCatTools-0.10.0/StreamCatTools/build/vignette.rds |binary StreamCatTools-0.10.0/StreamCatTools/inst/doc/StartHere.Rmd | 2 StreamCatTools-0.10.0/StreamCatTools/inst/doc/StartHere.html | 4 StreamCatTools-0.10.0/StreamCatTools/inst/extdata/JOSS |only StreamCatTools-0.10.0/StreamCatTools/man/lc_get_nlcd.Rd |only StreamCatTools-0.10.0/StreamCatTools/man/lc_get_nni.Rd |only StreamCatTools-0.10.0/StreamCatTools/man/lc_plotnni.Rd |only StreamCatTools-0.10.0/StreamCatTools/man/sc_get_nlcd.Rd |only StreamCatTools-0.10.0/StreamCatTools/man/sc_get_nni.Rd |only StreamCatTools-0.10.0/StreamCatTools/man/sc_plotnni.Rd |only StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-lc_get_nlcd.R |only StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-lc_get_params.R | 2 StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-lc_plot.R |only StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-sc_get_nlcd.R |only StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-sc_get_nni.R |only StreamCatTools-0.10.0/StreamCatTools/tests/testthat/test-sc_plot.R |only StreamCatTools-0.10.0/StreamCatTools/vignettes/Articles/Applications.Rmd | 4 StreamCatTools-0.10.0/StreamCatTools/vignettes/Articles/Introduction.Rmd | 1 StreamCatTools-0.10.0/StreamCatTools/vignettes/Articles/NNI.Rmd |only StreamCatTools-0.10.0/StreamCatTools/vignettes/StartHere.Rmd | 2 StreamCatTools-0.9.1/StreamCatTools/man/lc_nlcd.Rd |only StreamCatTools-0.9.1/StreamCatTools/man/sc_nlcd.Rd |only StreamCatTools-0.9.1/StreamCatTools/tests/testthat/test-lc_nlcd.R |only StreamCatTools-0.9.1/StreamCatTools/tests/testthat/test-sc_nlcd.R |only 33 files changed, 488 insertions(+), 50 deletions(-)
More information about StreamCatTools at CRAN
Permanent link
Title: Gradient-Enhanced Kriging
Description: Gradient-Enhanced Kriging as an emulator for computer experiments based on Maximum-Likelihood estimation.
Author: Carmen van Meegen [aut, cre]
Maintainer: Carmen van Meegen <vanmeegen@statistik.tu-dortmund.de>
Diff between gek versions 1.1.0 dated 2025-03-14 and 1.2.0 dated 2026-01-30
DESCRIPTION | 12 +- MD5 | 96 ++++++++++++-------- NAMESPACE | 31 ++++-- R/blockChol.R | 6 - R/blockCor.R | 2 R/confint.gekm.R |only R/derivModelMatrix.R | 4 R/formula.gekm.R |only R/gekm.R | 231 ------------------------------------------------- R/gekm.fit.R | 19 ++-- R/logLik.gekm.R |only R/logLikFun.R | 76 +++++++++++++--- R/logLikGrad.R | 76 ++++++++++++++-- R/loo.R |only R/plot.gekm.R |only R/predict.gekm.R |only R/print.gekm.R |only R/print.summary.gekm.R |only R/sigma.gekm.R |only R/simulate.gekm.R |only R/summary.gekm.R |only R/tangents.R | 16 +++ R/testfunctions.R | 9 + R/vcov.gekm.R |only R/vcov.summary.gekm.R |only R/vectorfield.R |only build/partial.rdb |binary data |only inst |only man/banana.Rd | 18 +++ man/blockChol.Rd | 2 man/borehole.Rd | 4 man/branin.Rd | 12 ++ man/camel3.Rd | 4 man/camel6.Rd | 4 man/cigar.Rd | 2 man/confint.gekm.Rd |only man/cons.Rd |only man/gekm.Rd | 44 +++++---- man/griewank.Rd | 2 man/himmelblau.Rd | 4 man/logLik.gekm.Rd |only man/logLikFun.Rd |only man/logLikGrad.Rd |only man/loo.Rd |only man/plot.gekm.Rd |only man/predict.gekm.Rd | 113 +++++++++++++++-------- man/qing.Rd | 5 + man/rastrigin.Rd | 2 man/schwefel.Rd | 2 man/short.Rd | 4 man/sigma.gekm.Rd |only man/simulate.gekm.Rd | 88 ++++++++++++++---- man/sphere.Rd | 12 ++ man/steel.Rd | 4 man/styblinski.Rd | 2 man/sulfur.Rd | 4 man/summary.gekm.Rd |only man/tangents.Rd | 4 man/testfunctions.Rd | 42 ++++---- man/vectorfield.Rd |only src/CorFunctions.c | 16 ++- 62 files changed, 542 insertions(+), 430 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of
'amt' includes methods to calculate home ranges, track statistics
(e.g. step lengths, speed, or turning angles), prepare data for
fitting habitat selection analyses, and simulation of space-use from
fitted step-selection functions.
Author: Johannes Signer [aut, cre],
Brian Smith [ctb],
Bjoern Reineking [ctb],
Ulrike Schlaegel [ctb],
John Fieberg [ctb],
Josh O'Brien [ctb],
Bernardo Niebuhr [ctb],
Alec Robitaille [ctb],
Tal Avgar [ctb],
Gerben IJntema [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.3.0.0 dated 2025-08-23 and 0.3.1.0 dated 2026-01-30
DESCRIPTION | 8 - MD5 | 36 +++---- NAMESPACE | 4 NEWS.md | 6 + R/amt.R | 2 R/random_points.R | 5 + R/random_steps.R | 3 R/simulate.R | 8 + R/track.R | 2 build/partial.rdb |binary inst/doc/p1_getting_started.html | 47 ++++----- inst/doc/p2_hr.html | 51 +++++----- inst/doc/p3_rsf.html | 71 +++++++------- inst/doc/p4_SSF.Rmd | 2 inst/doc/p4_SSF.html | 57 +++++------ inst/doc/p5_other_packages.html | 193 +++++++++++++++++++-------------------- inst/doc/p6_uhc_plots.html | 4 man/track.Rd | 2 vignettes/p4_SSF.Rmd | 2 19 files changed, 263 insertions(+), 240 deletions(-)
Title: Tabular Matrix Problems via Pseudoinverse Estimation
Description: The Tabular Matrix Problems via Pseudoinverse Estimation (TMPinv)
is a two-stage estimation method that reformulates structured table-based
systems - such as allocation problems, transaction matrices, and
input-output tables - as structured least-squares problems. Based on the
Convex Least Squares Programming (CLSP) framework, TMPinv solves systems
with row and column constraints, block structure, and optionally reduced
dimensionality by (1) constructing a canonical constraint form and applying
a pseudoinverse-based projection, followed by (2) a convex-programming
refinement stage to improve fit, coherence, and regularization (e.g., via
Lasso, Ridge, or Elastic Net).
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rtmpinv versions 0.1.0 dated 2025-12-03 and 0.2.0 dated 2026-01-30
DESCRIPTION | 8 +-- MD5 | 7 +-- NEWS.md |only R/tmpinv.R | 128 ++++++++++++++++++++++++++++++++++++++++------------------ man/tmpinv.Rd | 2 5 files changed, 100 insertions(+), 45 deletions(-)
Title: Linear Programming via Regularized Least Squares
Description: The Linear Programming via Regularized Least Squares (LPPinv) is a
two-stage estimation method that reformulates linear programs as
structured least-squares problems. Based on the Convex Least
Squares Programming (CLSP) framework, LPPinv solves linear
inequality, equality, and bound constraints by (1) constructing a
canonical constraint system and computing a pseudoinverse
projection, followed by (2) a convex-programming correction stage
to refine the solution under additional regularization (e.g.,
Lasso, Ridge, or Elastic Net). LPPinv is intended for
underdetermined and ill-posed linear problems, for which standard
solvers fail.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rlppinv versions 0.1.0 dated 2025-12-03 and 0.2.0 dated 2026-01-30
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only R/lppinv.R | 54 ++++++++++++++++++++++++++++-------------------------- man/lppinv.Rd | 11 ++++++----- 5 files changed, 42 insertions(+), 38 deletions(-)
Title: Interface to the 'open311' Standard
Description: Access and handle APIs that use the international 'open311'
'GeoReport v2' standard for civic issue tracking
<https://wiki.open311.org/GeoReport_v2/>. Retrieve civic service types
and request data. Select and add available 'open311' endpoints and
jurisdictions. Implicitly supports custom queries and 'open311'
extensions. Requires a minimal number of hard dependencies while
still allowing the integration in common R formats ('xml2', 'tibble',
'sf').
Author: Jonas Lieth [aut, cre, cph]
Maintainer: Jonas Lieth <jslth@outlook.com>
Diff between r311 versions 0.4.3 dated 2025-04-14 and 0.4.4 dated 2026-01-30
DESCRIPTION | 16 +- MD5 | 22 +-- NEWS.md | 6 R/ok.R | 12 + inst/doc/r311.Rmd | 171 ++++++++++++++------------- inst/doc/r311.html | 296 ++++++++++++++++++++++++------------------------ inst/endpoints.json | 7 + man/figures/map-1.png |binary man/o311_endpoints.Rd | 5 man/o311_ok.Rd | 12 + vignettes/r311.Rmd | 171 ++++++++++++++------------- vignettes/r311.Rmd.orig | 7 - 12 files changed, 384 insertions(+), 341 deletions(-)
Title: Download Official Spatial Data from Germany
Description: Provides quick and easy access to official spatial data from
Germany’s Federal Agency for Cartography and Geodesy (BKG) <https://gdz.bkg.bund.de/>.
Interfaces various web feature services (WFS) and download servers.
Allows retrieval, caching and filtering with a wide range of open
geodata products, including administrative or non-administrative boundaries,
land cover, elevation models, geographic names, and points of interest
covering Germany. Can be particularly useful for linking regional statistics
to their spatial representations and streamlining workflows that involve
spatial data of Germany.
Author: Jonas Lieth [aut, cre, cph]
Maintainer: Jonas Lieth <jslth@outlook.com>
Diff between ffm versions 0.1.1 dated 2025-11-09 and 0.1.2 dated 2026-01-30
DESCRIPTION | 14 +++++--- MD5 | 72 ++++++++++++++++++++++----------------------- NEWS.md | 8 +++++ R/bkg_admin.R | 4 ++ R/bkg_ags.R | 7 ++++ R/bkg_area_codes.R | 12 +++++++ R/bkg_clc.R | 3 - R/bkg_dem.R | 7 ++++ R/bkg_dlm.R | 2 - R/bkg_quasigeoid.R | 6 +++ R/bkg_wcs.R | 2 - R/bkg_wfs.R | 2 - R/wfs_filter.R | 14 +++++++- R/wfs_xml.R | 3 + man/bkg_admin.Rd | 2 - man/bkg_admin_hierarchy.Rd | 7 +++- man/bkg_ags.Rd | 9 +++++ man/bkg_airports.Rd | 2 - man/bkg_area_codes.Rd | 18 ++++++++++- man/bkg_authorities.Rd | 3 + man/bkg_clc.Rd | 5 +-- man/bkg_crossings.Rd | 2 - man/bkg_dem.Rd | 9 +++++ man/bkg_dlm.Rd | 4 +- man/bkg_geonames.Rd | 2 - man/bkg_grid.Rd | 3 + man/bkg_heliports.Rd | 2 - man/bkg_kfz.Rd | 3 + man/bkg_kilometrage.Rd | 2 - man/bkg_nuts.Rd | 2 - man/bkg_quasigeoid.Rd | 7 +++- man/bkg_ror.Rd | 1 man/bkg_seaports.Rd | 2 - man/bkg_stations.Rd | 2 - man/bkg_trauma_centers.Rd | 2 - man/bkg_wcs.Rd | 2 - man/bkg_wfs.Rd | 2 - 37 files changed, 174 insertions(+), 75 deletions(-)
Title: Interface to 'Rangeland Analysis Platform' (RAP) Products
Description: Provides access to 'Rangeland Analysis Platform' (RAP) products <https://rangelands.app/products> for arbitrary extents via 'GDAL' virtual file system.
Author: Andrew Brown [aut, cre] ,
Georgia Harrison [ctb]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between rapr versions 1.1.1 dated 2025-11-14 and 1.1.2 dated 2026-01-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/get_rap_16day.R | 2 +- build/vignette.rds |binary inst/tinytest/test_rapr.R | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Testing Differences Between Families of Trees
Description: Perform test to detect differences in structure between families of
trees. The method is based on cophenetic distances and aggregated
Student's tests.
Author: Nathalie Vialaneix [aut, cre] ,
Gwendaelle Cardenas [aut],
Marie Chavent [aut] ,
Sylvain Foissac [aut] ,
Pierre Neuvial [aut] ,
Nathanael Randriamihamison [aut]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between treediff versions 0.2.1 dated 2024-02-17 and 0.2.2 dated 2026-01-30
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 9 +++++---- NEWS.md | 6 ++++++ R/HiC2Tree.R | 2 +- R/treediff.R | 8 ++++---- README.md |only 6 files changed, 30 insertions(+), 21 deletions(-)
Title: Rarefaction Tool Kit
Description: Rarefy data, calculate diversity and plot the results.
Author: Paul Saary [aut, cre],
Falk Hildebrand [aut]
Maintainer: Paul Saary <rtk@paulsaary.de>
This is a re-admission after prior archival of version 0.2.6.1 dated 2020-06-13
Diff between rtk versions 0.2.6.1 dated 2020-06-13 and 0.2.7 dated 2026-01-30
DESCRIPTION | 18 +++++++----- MD5 | 14 ++++----- R/rarefaction.R | 16 +++++++++-- build/partial.rdb |binary src/Makevars | 1 src/Makevars.win | 1 src/gzstream.h | 1 tests/testthat/test_rare.R | 64 +++++++++++++++++++++++++++++++++++++++++++++ 8 files changed, 97 insertions(+), 18 deletions(-)
Title: Power Analysis for Differential Expression Studies
Description: Provides a convenient framework to simulate, test, power, and visualize
data for differential expression studies with lognormal or negative binomial
outcomes. Supported designs are two-sample comparisons of independent or
dependent outcomes. Power may be summarized in the context of controlling the
per-family error rate or family-wise error rate. Negative binomial methods are
described in Yu, Fernandez, and Brock (2017) <doi:10.1186/s12859-017-1648-2>
and Yu, Fernandez, and Brock (2020) <doi:10.1186/s12859-020-3541-7>.
Author: Brett Klamer [aut, cre] ,
Lianbo Yu [aut]
Maintainer: Brett Klamer <code@brettklamer.com>
Diff between depower versions 2025.10.21 dated 2025-10-22 and 2026.1.30 dated 2026-01-30
DESCRIPTION | 6 MD5 | 70 +- NAMESPACE | 6 NEWS.md | 15 R/add_power_ci.r |only R/add_power_pi.r |only R/eval_power_ci.r |only R/eval_power_pi.r |only R/glm_nb.r | 14 R/glmm_bnb.r | 2 R/glmm_poisson.r | 2 R/lrt_nb.r | 2 R/mle_bnb.r | 5 R/plot.r | 205 +++++++- R/power.r | 42 + R/sim_bnb.r | 53 +- R/sim_log_lognormal.r | 463 ++++++++++++++---- R/sim_nb.r | 5 R/utils.r | 653 ++++++++++++++++++++++++++ build/partial.rdb |binary inst/REFERENCES.bib | 54 ++ inst/tinytest/test-add_power_ci.r |only inst/tinytest/test-add_power_pi.r |only inst/tinytest/test-binom_ci_clopper_pearson.r |only inst/tinytest/test-binom_ci_wilson.r |only inst/tinytest/test-binom_pi_bayes.r |only inst/tinytest/test-eval_power_ci.r |only inst/tinytest/test-eval_power_pi.r |only inst/tinytest/test-glm_nb.r | 16 inst/tinytest/test-qbetabinom.r |only inst/tinytest/test-qbetabinom_scalar.r |only man/add_power_ci.Rd |only man/add_power_pi.Rd |only man/eval_power_ci.Rd |only man/eval_power_pi.Rd |only man/glm_nb.Rd | 12 man/glmm_bnb.Rd | 2 man/glmm_poisson.Rd | 2 man/lrt_nb.Rd | 2 man/plot.depower.Rd | 4 man/power.Rd | 38 + man/sim_bnb.Rd | 53 +- man/sim_log_lognormal.Rd | 398 ++++++++++++--- man/sim_nb.Rd | 4 tests/manual/verify_ci_pi_coverage.r |only 45 files changed, 1857 insertions(+), 271 deletions(-)
Title: Contextualizing Tests
Description: Dissects a package environment or 'covr' coverage object in order to cross
reference tested code with the lines that are evaluated, as well as linking
those evaluated lines to the documentation that they are described within.
Connecting these three pieces of information provides a mechanism of
linking tests to documented behaviors.
Author: Doug Kelkhoff [aut] ,
Szymon Maksymiuk [aut, cre] ,
Andrew McNeil [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between covtracer versions 0.0.1 dated 2024-07-08 and 0.0.2 dated 2026-01-30
DESCRIPTION | 17 - MD5 | 26 - NEWS.md | 7 R/srcrefs.R | 20 + README.md | 6 build/vignette.rds |binary inst/doc/combining_srcref_data.html | 431 +++++++++++++++++--------------- inst/doc/plotting_test_paths.R | 2 inst/doc/plotting_test_paths.html | 416 +++++++++++++++--------------- inst/doc/working_with_srcrefs.R | 34 +- inst/doc/working_with_srcrefs.html | 374 +++++++++++++++------------ inst/examplepkg/DESCRIPTION | 2 inst/examplepkg/R/rd_sampler.R | 1 inst/examplepkg/man/reexport_example.Rd | 1 14 files changed, 718 insertions(+), 619 deletions(-)
Title: Genome-Wide DNA Methylation Sites Screening by Use of Training
and Testing Samples
Description: A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects. This package also provides two screening functions for screening high-dimensional predictors when the events are rare. The firth method is called 'Rare-Screening' which employs a repeated random sampling with replacement and using linear modeling with Bayes adjustment. The Second method is called 'Firth-ttScreening' which uses 'ttScreening' method with additional Firth correction term in the maximum likelihood for the logistic regression model. These methods handle the high-dimensionality and low event rates.
Author: Meredith Ray [aut, cre],
Mohammad Nahian Ferdous Abrar [aut],
Yu Jiang [aut],
Xin Tong [aut],
Hongmei Zhang [aut]
Maintainer: Meredith Ray <maray@memphis.edu>
Diff between ttScreening versions 1.7 dated 2025-07-03 and 1.8 dated 2026-01-30
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++++--- NAMESPACE | 9 ++++++++- R/Firth_Screening.R |only R/Rare_Screening.R |only man/Rare_Screening.Rd |only man/firth_screening.Rd |only man/ttScreening-package.Rd | 11 ++++++----- 8 files changed, 30 insertions(+), 17 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore [aut, cre],
Pierfrancesco Alaimo Di Loro [ctb],
Marco Mingione [ctb],
Antonio Calcagni' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 2.2 dated 2025-01-07 and 2.3 dated 2026-01-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 6 ++++++ R/boot.overlap.R | 27 ++++++++++++++++++++++----- build/partial.rdb |binary man/ovmult.Rd | 2 +- 7 files changed, 40 insertions(+), 16 deletions(-)
Title: A Modular Two-Step Convex Optimization Estimator for Ill-Posed
Problems
Description: Convex Least Squares Programming (CLSP) is a two-step estimator
for solving underdetermined, ill-posed, or structurally constrained
least-squares problems. It combines pseudoinverse-based estimation with
convex-programming correction methods inspired by Lasso, Ridge, and
Elastic Net to ensure numerical stability, constraint enforcement, and
interpretability. The package also provides numerical stability analysis
and CLSP-specific diagnostics, including partial R^2, normalized RMSE
(NRMSE), Monte Carlo t-tests for mean NRMSE, and condition-number-based
confidence bands.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rclsp versions 0.2.0 dated 2025-11-26 and 0.3.0 dated 2026-01-30
DESCRIPTION | 6 ++-- MD5 | 7 +++-- NEWS.md |only R/clsp.R | 80 +++++++++++++++++++++++++++++++----------------------------- R/utils.R | 50 +++++++++++++++++++++---------------- 5 files changed, 77 insertions(+), 66 deletions(-)
Title: Nested Data Summary, Adverse Events and REDCap
Description: Tools and code snippets for summarizing nested data, adverse events
and REDCap study information.
Author: Lisa Avery [aut] ,
Zeynep Baskurt [aut],
Osvaldo Espin-Garcia [aut],
Katrina Hueniken [aut],
Katherine Lajkosz [aut] ,
Xuan Li [aut],
Tyler Pittman [cre, aut] ,
Anna Santiago [aut] ,
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Tyler Pittman <tyler.pittman@uhn.ca>
Diff between BiostatsUHNplus versions 1.0.3 dated 2025-09-10 and 1.0.4 dated 2026-01-30
DESCRIPTION | 6 MD5 | 70 +++++----- NAMESPACE | 1 NEWS.md | 4 R/ae_timeline_plot.R | 35 ++--- R/covsum_nested.R | 6 R/dsmb_ccru.R | 26 +-- R/dsmb_ddp.R | 26 +-- R/redcap_data_out.R | 2 R/rm_ae_all_g3p.R | 19 +- README.md | 10 - man/dsmb_ccru.Rd | 8 - man/dsmb_ddp.Rd | 2 man/figures/ana10-1.png |binary man/figures/caterpillar_plot_Cows_Model.png |binary man/figures/caterpillar_plot_Yards_Model.png |binary man/figures/caterpillar_plot_ae_category.png |binary man/figures/caterpillar_plot_subject.png |binary man/figures/variance_pie_plot.png |binary man/rm_ae_all_g3p.Rd | 2 man/tables/EXAMPLE_STUDY_AEs_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY__30OCT2020.xlsx |binary 36 files changed, 115 insertions(+), 102 deletions(-)
More information about BiostatsUHNplus at CRAN
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Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Description: Provides plotting utilities supporting packages in the 'easystats'
ecosystem (<https://github.com/easystats/easystats>) and some extra themes,
geoms, and scales for 'ggplot2'. Color scales are based on
<https://materialui.co/>.
References: Lüdecke et al. (2021) <doi:10.21105/joss.03393>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, inv] ,
Indrajeet Patil [aut] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Jeffrey R. Stevens [ctb] ,
Matthew Smith [ [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between see versions 0.12.0 dated 2025-09-14 and 0.13.0 dated 2026-01-30
DESCRIPTION | 25 LICENSE | 4 MD5 | 314 +-- NAMESPACE | 404 ++-- NEWS.md | 1490 +++++++-------- R/coord_radar.R | 78 R/data_plot.R | 420 ++-- R/geom_binomdensity.R | 236 +- R/geom_point2.R | 204 +- R/geom_poolpoint.R | 128 - R/geom_violindot.R | 218 +- R/geom_violinhalf.R | 298 +-- R/golden_ratio.R | 32 R/plot.bayesfactor_models.R | 306 +-- R/plot.binned_residuals.R | 32 R/plot.check_collinearity.R | 21 R/plot.check_distribution.R | 404 ++-- R/plot.check_heteroscedasticity.R | 7 R/plot.check_homogeneity.R | 29 R/plot.check_model.R | 115 - R/plot.check_normality.R | 117 - R/plot.check_outliers.R | 11 R/plot.check_outliers.dots.R | 87 R/plot.check_outliers.scree.R | 25 R/plot.check_overdisp.R | 30 R/plot.check_predictions.R | 48 R/plot.compare_parameters.R | 592 +++--- R/plot.describe_distribution.R | 436 ++-- R/plot.effectsize_table.R | 202 +- R/plot.estimate_density.R | 643 +++--- R/plot.hdi.R | 618 +++--- R/plot.p_direction.R | 532 ++--- R/plot.p_function.R | 4 R/plot.p_significance.R | 628 +++--- R/plot.parameters_brms_meta.R | 526 ++--- R/plot.parameters_model.R | 1928 ++++++++++---------- R/plot.parameters_sem.R | 418 ++-- R/plot.performance_roc.R | 110 - R/plot.performance_simres.R | 348 +-- R/plot.point_estimates.R | 572 ++--- R/plot.rope.R | 330 +-- R/print.check_model.R | 2 R/print.data_plot.R | 12 R/reshape_to_long.R | 60 R/scale_color_colorhex.R | 496 ++--- R/see-package.R | 68 R/utils.R | 75 R/utils_add_prior_layer.R | 318 +-- build/partial.rdb |binary inst/CITATION | 26 inst/WORDLIST | 192 - man/add_plot_attributes.Rd | 88 man/bluebrown_colors.Rd | 46 man/coord_radar.Rd | 72 man/data_plot.Rd | 200 +- man/flat_colors.Rd | 46 man/geom_binomdensity.Rd | 112 - man/geom_from_list.Rd | 252 +- man/geom_point2.Rd | 148 - man/geom_poolpoint.Rd | 110 - man/geom_violindot.Rd | 238 +- man/geom_violinhalf.Rd | 292 +-- man/ggplot2-ggproto.Rd | 20 man/golden_ratio.Rd | 42 man/material_colors.Rd | 46 man/metro_colors.Rd | 46 man/okabeito_colors.Rd | 82 man/palette_bluebrown.Rd | 58 man/palette_colorhex.Rd | 60 man/palette_flat.Rd | 58 man/palette_material.Rd | 58 man/palette_metro.Rd | 58 man/palette_okabeito.Rd | 80 man/palette_pizza.Rd | 46 man/palette_see.Rd | 58 man/palette_social.Rd | 58 man/pizza_colors.Rd | 34 man/plot.datawizard_table.Rd | 128 - man/plot.see_bayesfactor_models.Rd | 136 - man/plot.see_bayesfactor_parameters.Rd | 76 man/plot.see_check_collinearity.Rd | 104 - man/plot.see_check_dag.Rd | 162 - man/plot.see_check_distribution.Rd | 68 man/plot.see_check_heteroscedasticity.Rd | 100 - man/plot.see_check_homogeneity.Rd | 64 man/plot.see_check_model.Rd | 109 - man/plot.see_check_normality.Rd | 164 - man/plot.see_check_outliers.Rd | 222 +- man/plot.see_compare_parameters.Rd | 136 - man/plot.see_compare_performance.Rd | 64 man/plot.see_effectsize_table.Rd | 50 man/plot.see_equivalence_test.Rd | 126 - man/plot.see_estimate_contrasts.Rd | 70 man/plot.see_estimate_density.Rd | 150 - man/plot.see_hdi.Rd | 114 - man/plot.see_n_factors.Rd | 86 man/plot.see_p_direction.Rd | 114 - man/plot.see_p_function.Rd | 128 - man/plot.see_p_significance.Rd | 114 - man/plot.see_parameters_brms_meta.Rd | 192 - man/plot.see_parameters_distribution.Rd | 114 - man/plot.see_parameters_model.Rd | 254 +- man/plot.see_parameters_pca.Rd | 96 man/plot.see_parameters_simulate.Rd | 144 - man/plot.see_performance_roc.Rd | 70 man/plot.see_performance_simres.Rd | 155 - man/plot.see_point_estimate.Rd | 138 - man/plot.see_rope.Rd | 110 - man/plot.see_si.Rd | 102 - man/plots.Rd | 172 - man/print.see_performance_pp_check.Rd | 189 - man/scale_color_bluebrown.Rd | 238 +- man/scale_color_colorhex.Rd | 266 +- man/scale_color_flat.Rd | 260 +- man/scale_color_material.Rd | 260 +- man/scale_color_metro.Rd | 260 +- man/scale_color_okabeito.Rd | 268 +- man/scale_color_pizza.Rd | 236 +- man/scale_color_see.Rd | 258 +- man/scale_color_social.Rd | 260 +- man/see-package.Rd | 96 man/see_colors.Rd | 46 man/social_colors.Rd | 46 man/theme_abyss.Rd | 178 - man/theme_azurelight.Rd | 184 - man/theme_blackboard.Rd | 178 - man/theme_lucid.Rd | 180 - man/theme_modern.Rd | 200 +- man/theme_radar.Rd | 224 +- tests/testthat.R | 16 tests/testthat/helper.R | 32 tests/testthat/test-check_model.R | 24 tests/testthat/test-geom_binomdensity.R | 234 +- tests/testthat/test-golden_ratio.R | 6 tests/testthat/test-performance_large_datasets.R |only tests/testthat/test-plot.check_distribution.R | 16 tests/testthat/test-plot.check_heteroscedasticity.R | 12 tests/testthat/test-plot.check_homogeneity.R | 12 tests/testthat/test-plot.check_normality.R | 154 - tests/testthat/test-plot.cluster_analysis.R | 8 tests/testthat/test-plot.compare_performance.R | 16 tests/testthat/test-plot.easycormatrix.R | 10 tests/testthat/test-plot.equivalence_test.R | 12 tests/testthat/test-plot.estimate_contrasts.R | 22 tests/testthat/test-plot.estimate_density.R | 78 tests/testthat/test-plot.hdi.R | 18 tests/testthat/test-plot.parameters_model.R | 28 tests/testthat/test-plot.parameters_pca.R | 16 tests/testthat/test-plot.parameters_simulate.R | 12 tests/testthat/test-plot.performance_roc.R | 36 tests/testthat/test-plot.rope.R | 16 tests/testthat/test-plot.si.R | 18 tests/testthat/test-plot.simulate_parameters.R | 92 tests/testthat/test-plots.R | 137 - tests/testthat/test-scale_color_colorhex_c.R | 40 tests/testthat/test-scale_color_okabeito.R | 190 - tests/testthat/test-scale_color_values.R | 72 tests/testthat/test-vdiffr_bayestestr_plots.R | 46 tests/testthat/test-vdiffr_check_model.R |only 159 files changed, 13149 insertions(+), 12710 deletions(-)
Title: Estimate Chla Concentrations of Phytoplankton Groups
Description: Determine the chlorophyll a (Chl a) concentrations of different
phytoplankton groups based on their pigment biomarkers. The method uses
non-negative matrix factorisation and simulated annealing to minimise error
between the observed and estimated values of pigment concentrations
(Hayward et al. (2023) <doi:10.1002/lom3.10541>).
The approach is similar to the widely used 'CHEMTAX' program
(Mackey et al. 1996) <doi:10.3354/meps144265>, but is more straightforward,
accurate, and not reliant on initial guesses for the pigment to Chl a
ratios for phytoplankton groups.
Author: Alexander Hayward [aut, cre, cph],
Tylar Murray [aut],
Sebastian Di Geronimo [aut],
Mohd Aasim Maqsood Khan [aut],
Andy McKenzie [aut]
Maintainer: Alexander Hayward <phytoclass@outlook.com>
Diff between phytoclass versions 2.0.0 dated 2024-11-14 and 2.3.1 dated 2026-01-30
phytoclass-2.0.0/phytoclass/R/Bounded_weights.R |only phytoclass-2.0.0/phytoclass/R/Condition_test.R |only phytoclass-2.0.0/phytoclass/R/Conduit_1.R |only phytoclass-2.0.0/phytoclass/R/Conduit_2.R |only phytoclass-2.0.0/phytoclass/R/Conduit_3.R |only phytoclass-2.0.0/phytoclass/R/Fac_F_RR1.R |only phytoclass-2.0.0/phytoclass/R/Fac_F_RR2.R |only phytoclass-2.0.0/phytoclass/R/Fac_F_RR3.R |only phytoclass-2.0.0/phytoclass/R/Minimise_elements.R |only phytoclass-2.0.0/phytoclass/R/Minimise_elements1.R |only phytoclass-2.0.0/phytoclass/R/Minimise_elements2.R |only phytoclass-2.0.0/phytoclass/R/NNLS_MF_Final.R |only phytoclass-2.0.0/phytoclass/R/Normalise_F.R |only phytoclass-2.0.0/phytoclass/R/Normalise_S.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_NNLS_MF_Final.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_Normalise_F.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_Random_Neighbour.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_Random_Neighbour2.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_Sim_Anneal.R |only phytoclass-2.0.0/phytoclass/R/Prochloro_wrangling.R |only phytoclass-2.0.0/phytoclass/R/Random_neighbour2.R |only phytoclass-2.0.0/phytoclass/R/Randomise_elements.R |only phytoclass-2.0.0/phytoclass/R/Steepest_Desc.R |only phytoclass-2.0.0/phytoclass/R/Weight_error.R |only phytoclass-2.0.0/phytoclass/R/Wrangling.R |only phytoclass-2.0.0/phytoclass/R/target.R |only phytoclass-2.0.0/phytoclass/R/vectorise.R |only phytoclass-2.0.0/phytoclass/man/Conduit_1.Rd |only phytoclass-2.0.0/phytoclass/man/Conduit_2.Rd |only phytoclass-2.0.0/phytoclass/man/Conduit_3.Rd |only phytoclass-2.0.0/phytoclass/man/Fac_F_RR1.Rd |only phytoclass-2.0.0/phytoclass/man/Fac_F_RR2.Rd |only phytoclass-2.0.0/phytoclass/man/Fac_F_RR3.Rd |only phytoclass-2.0.0/phytoclass/man/Minimise_elements.Rd |only phytoclass-2.0.0/phytoclass/man/Minimise_elements1.Rd |only phytoclass-2.0.0/phytoclass/man/Minimise_elements2.Rd |only phytoclass-2.0.0/phytoclass/man/Prochloro_NNLS_MF_Final.Rd |only phytoclass-2.0.0/phytoclass/man/Prochloro_Random_Neighbour_2.Rd |only phytoclass-2.0.0/phytoclass/man/Random_neighbour2.Rd |only phytoclass-2.0.0/phytoclass/man/target.Rd |only phytoclass-2.0.0/phytoclass/tests/testthat/test-simulated_annealing.R |only phytoclass-2.3.1/phytoclass/DESCRIPTION | 29 phytoclass-2.3.1/phytoclass/MD5 | 169 phytoclass-2.3.1/phytoclass/NAMESPACE | 1 phytoclass-2.3.1/phytoclass/NEWS.md | 35 phytoclass-2.3.1/phytoclass/R/Cluster.R | 164 phytoclass-2.3.1/phytoclass/R/Conduit.R |only phytoclass-2.3.1/phytoclass/R/Default_min_max.R | 74 phytoclass-2.3.1/phytoclass/R/Fac_F_RR.R |only phytoclass-2.3.1/phytoclass/R/Matrix_checks.R | 230 phytoclass-2.3.1/phytoclass/R/Minimise_elements_comb.R |only phytoclass-2.3.1/phytoclass/R/NNLS_MF.R | 264 phytoclass-2.3.1/phytoclass/R/Random_neighbour.R | 335 phytoclass-2.3.1/phytoclass/R/Replace_Rand.R | 81 phytoclass-2.3.1/phytoclass/R/SAALS.R | 29 phytoclass-2.3.1/phytoclass/R/Steepest_Descent.R | 108 phytoclass-2.3.1/phytoclass/R/data.R | 2 phytoclass-2.3.1/phytoclass/R/figures.R |only phytoclass-2.3.1/phytoclass/R/simulated_annealing.R | 390 phytoclass-2.3.1/phytoclass/R/simulated_annealing_prochloro.R | 705 - 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Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 3.9.1 dated 2025-12-16 and 3.9.2 dated 2026-01-30
DESCRIPTION | 9 MD5 | 20 NEWS.md | 5 R/ML_BARTMachineModel.R | 15 R/TrainingParams.R | 12 inst/doc/UserGuide.html | 40 man/BARTMachineModel.Rd | 15 man/set_optim-methods.Rd | 12 tests/testthat/Rplots.pdf |binary tests/testthat/helper-parallel.R | 11 tests/testthat/test-survival.txt | 3974 +++++++++++++++++++-------------------- 11 files changed, 2076 insertions(+), 2037 deletions(-)
Title: HIC diffeREntial Analysis Method
Description: Perform Hi-C data differential analysis based on pixel-level
differential analysis and a post hoc inference strategy to quantify
signal in clusters of pixels. Clusters of pixels are obtained through
a connectivity-constrained two-dimensional hierarchical clustering.
Author: Elise Jorge [aut, cre],
Sylvain Foissac [aut] ,
Toby Hocking [aut] ,
Pierre Neuvial [aut] ,
Nathalie Vialaneix [aut] ,
Gilles Blanchard [ctb],
Guillermo Durand [ctb] ,
Nicolas Enjalbert-Courrech [ctb],
Etienne Roquain [ctb]
Maintainer: Elise Jorge <elise.jorge@inrae.fr>
Diff between hicream versions 0.0.3 dated 2026-01-12 and 0.0.4 dated 2026-01-30
DESCRIPTION | 11 +- MD5 | 14 +-- NEWS.md | 6 + R/AggloClust2D.R | 2 README.md | 198 +++++++++++++++++-------------------------- inst/doc/A-Installation.html | 8 - inst/doc/B-Introduction.html | 54 +++++------ inst/python/2Dclust.py | 3 8 files changed, 134 insertions(+), 162 deletions(-)
Title: Companion to Applied Regression Data Sets
Description: Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage (2019).
Author: John Fox [aut],
Sanford Weisberg [aut],
Brad Price [aut, cre]
Maintainer: Brad Price <brad.price@mail.wvu.edu>
Diff between carData versions 3.0-5 dated 2022-01-05 and 3.0-6 dated 2026-01-30
DESCRIPTION | 25 +++----- MD5 | 16 ++--- build/partial.rdb |binary man/AMSsurvey.Rd | 4 - man/States.Rd | 142 ++++++++++++++++++++++++------------------------- man/TitanicSurvival.Rd | 2 man/UN.Rd | 2 man/Vocab.Rd | 2 man/Wells.Rd | 98 ++++++++++++++++----------------- 9 files changed, 144 insertions(+), 147 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph]
,
Milan Straka [aut, cph] ,
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.15 dated 2025-11-28 and 0.8.16 dated 2026-01-30
DESCRIPTION | 6 MD5 | 250 - NAMESPACE | 242 - NEWS.md | 494 +- R/RcppExports.R | 70 R/datasets.R | 254 - R/nlp_collocation.R | 230 - R/nlp_cooccurrence.R | 472 +- R/nlp_dependency_parsing.R | 304 - R/nlp_dependency_utlities.R | 862 ++--- R/nlp_flow.R | 3004 +++++++++--------- R/nlp_morphological.R | 254 - R/nlp_phrase_sequences.R | 360 +- R/nlp_rake.R | 186 - R/pkg.R | 20 R/sentiment.R | 382 +- R/topicmodels.R | 288 - R/udpipe_models.R | 996 ++--- R/udpipe_parse.R | 1034 +++--- R/udpipe_reconstruct.R | 352 +- R/udpipe_train.R | 738 ++-- R/utils.R | 1808 +++++----- README.md | 200 - build/vignette.rds |binary inst/doc/udpipe-annotation.R | 158 inst/doc/udpipe-annotation.Rmd | 366 +- inst/doc/udpipe-annotation.html | 1009 ++---- inst/doc/udpipe-parallel.R | 84 inst/doc/udpipe-parallel.Rmd | 224 - inst/doc/udpipe-parallel.html | 744 +--- inst/doc/udpipe-train.R | 318 - inst/doc/udpipe-train.Rmd | 1108 +++--- inst/doc/udpipe-train.html | 2337 ++++++-------- inst/doc/udpipe-tryitout.R | 62 inst/doc/udpipe-tryitout.Rmd | 144 inst/doc/udpipe-tryitout.html | 737 +--- inst/doc/udpipe-universe.R | 8 inst/doc/udpipe-universe.Rmd | 82 inst/doc/udpipe-universe.html | 493 +- inst/doc/udpipe-usecase-postagging-lemmatisation.R | 236 - inst/doc/udpipe-usecase-postagging-lemmatisation.Rmd | 446 +- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 1077 ++---- inst/doc/udpipe-usecase-topicmodelling.R | 292 - inst/doc/udpipe-usecase-topicmodelling.Rmd | 530 +-- inst/doc/udpipe-usecase-topicmodelling.html | 1242 +++---- inst/dummydata/traindata.conllu | 80 inst/models-ud-2.0/params_parser | 136 inst/models-ud-2.0/params_tagger | 136 inst/models-ud-2.0/params_tokenizer | 136 man/as.data.frame.udpipe_connlu.Rd | 92 man/as.matrix.cooccurrence.Rd | 64 man/as_conllu.Rd | 112 man/as_cooccurrence.Rd | 60 man/as_fasttext.Rd | 56 man/as_phrasemachine.Rd | 100 man/as_word2vec.Rd | 64 man/brussels_listings.Rd | 44 man/brussels_reviews.Rd | 52 man/brussels_reviews_anno.Rd | 120 man/brussels_reviews_w2v_embeddings_lemma_nl.Rd | 28 man/cbind_dependencies.Rd | 136 man/cbind_morphological.Rd | 118 man/cooccurrence.Rd | 248 - man/document_term_frequencies.Rd | 200 - man/document_term_frequencies_statistics.Rd | 76 man/document_term_matrix.Rd | 354 +- man/dtm_align.Rd | 172 - man/dtm_bind.Rd | 156 man/dtm_chisq.Rd | 118 man/dtm_colsums.Rd | 132 man/dtm_conform.Rd | 178 - man/dtm_cor.Rd | 60 man/dtm_remove_lowfreq.Rd | 80 man/dtm_remove_sparseterms.Rd | 74 man/dtm_remove_terms.Rd | 70 man/dtm_remove_tfidf.Rd | 104 man/dtm_reverse.Rd | 60 man/dtm_sample.Rd | 72 man/dtm_svd_similarity.Rd | 230 - man/dtm_tfidf.Rd | 62 man/keywords_collocation.Rd | 164 man/keywords_phrases.Rd | 220 - man/keywords_rake.Rd | 152 man/paste.data.frame.Rd | 90 man/predict.LDA.Rd | 218 - man/strsplit.data.frame.Rd | 102 man/syntaxpatterns.Rd | 22 man/syntaxrelation.Rd | 58 man/txt_collapse.Rd | 58 man/txt_contains.Rd | 88 man/txt_context.Rd | 132 man/txt_count.Rd | 58 man/txt_freq.Rd | 56 man/txt_grepl.Rd | 116 man/txt_highlight.Rd | 56 man/txt_next.Rd | 62 man/txt_nextgram.Rd | 90 man/txt_overlap.Rd | 50 man/txt_paste.Rd | 78 man/txt_previous.Rd | 62 man/txt_previousgram.Rd | 90 man/txt_recode.Rd | 88 man/txt_recode_ngram.Rd | 100 man/txt_sample.Rd | 54 man/txt_sentiment.Rd | 234 - man/txt_show.Rd | 46 man/txt_tagsequence.Rd | 132 man/udpipe.Rd | 212 - man/udpipe_accuracy.Rd | 132 man/udpipe_annotate.Rd | 228 - man/udpipe_annotation_params.Rd | 64 man/udpipe_download_model.Rd | 386 +- man/udpipe_load_model.Rd | 104 man/udpipe_read_conllu.Rd | 46 man/udpipe_train.Rd | 258 - man/unique_identifier.Rd | 70 man/unlist_tokens.Rd | 50 src/RcppExports.cpp | 5 src/udpipe.cpp | 4 vignettes/udpipe-annotation.Rmd | 366 +- vignettes/udpipe-parallel.Rmd | 224 - vignettes/udpipe-train.Rmd | 1108 +++--- vignettes/udpipe-tryitout.Rmd | 144 vignettes/udpipe-universe.Rmd | 82 vignettes/udpipe-usecase-postagging-lemmatisation.Rmd | 446 +- vignettes/udpipe-usecase-topicmodelling.Rmd | 530 +-- 126 files changed, 17146 insertions(+), 18472 deletions(-)
Title: Simulate and Analyse Social Interaction Data
Description: Provides tools to simulate and analyse datasets of social interactions
between individuals using hierarchical Bayesian models implemented in Stan.
Model fitting is performed via the 'rstan' package. Users can generate
realistic interaction data where individual phenotypes influence and respond
to those of their partners, with control over sampling design parameters such
as the number of individuals, partners, and repeated dyads. The simulation
framework allows flexible control over variation and correlation in mean trait
values, social responsiveness, and social impact, making it suitable for
research on interacting phenotypes and on direct and indirect genetic effects
('DGEs' and 'IGEs'). The package also includes functions to fit and compare
alternative models of social effects, including impact–responsiveness,
variance–partitioning, and trait-based models, and to summarise model
performance in terms of bias and dispersion. For a more detailed description
of the available models and [...truncated...]
Author: Rori Efrain Wijnhorst [aut, cre]
Maintainer: Rori Efrain Wijnhorst <roriwijnhorst@gmail.com>
Diff between socialSim versions 0.1.6 dated 2025-10-30 and 0.1.8 dated 2026-01-30
DESCRIPTION | 34 +-- MD5 | 26 +-- NEWS.md | 4 R/run_model.R | 140 ++++++---------- R/simulate_data.R | 361 +++++++++++++++++++++--------------------- R/summarise_results.R | 17 - README.md | 12 - inst/doc/getting-started.Rmd | 199 +++++++++++------------ inst/doc/getting-started.html | 6 inst/stan/Trait.stan | 247 ++++++++++++++-------------- man/run_model.Rd | 13 - man/simulate_data.Rd | 3 man/summarise_results.Rd | 11 - vignettes/getting-started.Rmd | 199 +++++++++++------------ 14 files changed, 620 insertions(+), 652 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting
text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering
of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further
processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.6.0 dated 2025-09-10 and 3.7.0 dated 2026-01-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ src/bindings.cpp | 7 +++++++ 4 files changed, 16 insertions(+), 6 deletions(-)
Title: Efficient Outlier Detection for Large Time Series Databases
Description: Programs for detecting and cleaning outliers in single time series and in time series from homogeneous and heterogeneous databases using an Orthogonal Greedy Algorithm (OGA) for saturated linear regression models. The programs implement the procedures presented in the paper entitled "Efficient Outlier Detection for Large Time Series Databases" by Pedro Galeano, Daniel Peña and Ruey S. Tsay (2026), working paper, Universidad Carlos III de Madrid. Version 1.1.2 fixes one bug.
Author: Pedro Galeano [aut, cre] ,
Daniel Pena [aut] ,
Ruey S. Tsay [aut]
Maintainer: Pedro Galeano <pedro.galeano@uc3m.es>
This is a re-admission after prior archival of version 1.1.1 dated 2025-09-03
Diff between outliers.ts.oga versions 1.1.1 dated 2025-09-03 and 1.1.2 dated 2026-01-30
DESCRIPTION | 12 +- MD5 | 16 ++- NAMESPACE | 7 - R/FRED_MD.R |only R/outliers.ts.oga.R | 235 +++++++++++++++++++++++++++++++++++++++++++++++++--- data |only man/FRED_MD.Rd |only man/db_het_oga.Rd | 6 - man/db_hom_oga.Rd | 6 - man/single_oga.Rd | 6 - 10 files changed, 251 insertions(+), 37 deletions(-)
More information about outliers.ts.oga at CRAN
Permanent link
Title: Descriptive Analysis on Three Glioblastoma EHRs Datasets
Description: Provides functions to load and analyze three open Electronic
Health Records (EHRs) datasets of patients diagnosed with
glioblastoma, previously released under the Creative Common
Attribution 4.0 International (CC BY 4.0) license. Users can generate
basic descriptive statistics, frequency tables and save descriptive
summary tables, as well as create and export univariate or bivariate
plots. The package is designed to work with the included datasets and
to facilitate quick exploratory data analysis and reporting. More
information about these three datasets of EHRs of patients with
glioblastoma can be found in this article: Gabriel Cerono, Ombretta
Melaiu, and Davide Chicco, 'Clinical feature ranking based on ensemble
machine learning reveals top survival factors for glioblastoma
multiforme', Journal of Healthcare Informatics Research 8, 1-18 (March
2024). <doi:10.1007/s41666-023-00138-1>.
Author: Samuele Marelli [aut, cre],
Davide Chicco [aut]
Maintainer: Samuele Marelli <samu2003.marelli@gmail.com>
Diff between glioblastomaEHRsData versions 0.1.0 dated 2025-09-21 and 1.1.0 dated 2026-01-30
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- NEWS.md | 8 +++++++- R/Utrecht2019datasetDescriptiveStatistics.R | 16 +++++++++++----- R/descriptiveTableUtrecht2019dataset.R | 3 ++- R/saveTable.R | 2 +- README.md | 16 ++++++++++++++++ man/glioblastomaEHRsData-package.Rd | 7 +++++++ man/saveTable.Rd | 2 +- 9 files changed, 59 insertions(+), 22 deletions(-)
More information about glioblastomaEHRsData at CRAN
Permanent link
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and evaluation,
ensemble of models, ensemble forecasting and visualization. The package permits to run
consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences)
dataset and to combine them in ensemble models and ensemble projections. Some bench of other
evaluation and visualisation tools are also available within the package.
Author: Maya Gueguen [aut, cre],
Helene Blancheteau [aut],
Remi Lemaire-Patin [aut],
Wilfried Thuiller [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.3-4-4 dated 2026-01-26 and 4.3-4-5 dated 2026-01-30
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/BIOMOD_Report.R | 4 ++-- R/biomod2_classes_1.R | 2 +- inst/doc/news.Rmd | 4 ++++ inst/doc/news.html | 34 +++++++++++++++++++--------------- man/BIOMOD_Report.Rd | 4 ++-- man/OptionsBigboss.Rd | 2 +- vignettes/news.Rmd | 4 ++++ 9 files changed, 45 insertions(+), 33 deletions(-)
Title: Superlatively Fast Fuzzy Joins
Description: Empowers users to fuzzily-merge data frames with millions or tens of millions of rows in minutes with low memory usage. The package uses the locality sensitive hashing algorithms developed by Datar, Immorlica, Indyk and Mirrokni (2004) <doi:10.1145/997817.997857>, and Broder (1998) <doi:10.1109/SEQUEN.1997.666900> to avoid having to compare every pair of records in each dataset, resulting in fuzzy-merges that finish in linear time.
Author: Beniamino Green [aut, cre, cph],
Etienne Bacher [ctb] ,
The authors of the dependency Rust crates [ctb, cph]
Maintainer: Beniamino Green <beniamino.green@yale.edu>
Diff between zoomerjoin versions 0.2.1 dated 2025-04-13 and 0.2.2 dated 2026-01-30
zoomerjoin-0.2.1/zoomerjoin/tests/testthat/_snaps |only zoomerjoin-0.2.2/zoomerjoin/DESCRIPTION | 24 zoomerjoin-0.2.2/zoomerjoin/LICENSE |only zoomerjoin-0.2.2/zoomerjoin/MD5 | 86 +-- zoomerjoin-0.2.2/zoomerjoin/NAMESPACE | 1 zoomerjoin-0.2.2/zoomerjoin/NEWS.md | 2 zoomerjoin-0.2.2/zoomerjoin/R/euclidean_join_core.R | 5 zoomerjoin-0.2.2/zoomerjoin/R/euclidean_logical_joins.R | 29 - zoomerjoin-0.2.2/zoomerjoin/R/extendr-wrappers.R | 12 zoomerjoin-0.2.2/zoomerjoin/R/hamming_join_core.R | 9 zoomerjoin-0.2.2/zoomerjoin/R/hamming_logical_joins.R | 86 +-- zoomerjoin-0.2.2/zoomerjoin/R/jaccard_join_core.R | 11 zoomerjoin-0.2.2/zoomerjoin/R/jaccard_logical_joins.R | 107 ++-- zoomerjoin-0.2.2/zoomerjoin/R/join_core.R | 15 zoomerjoin-0.2.2/zoomerjoin/R/string_group.R | 28 - zoomerjoin-0.2.2/zoomerjoin/R/string_similarities.R | 15 zoomerjoin-0.2.2/zoomerjoin/README.md | 46 - zoomerjoin-0.2.2/zoomerjoin/build/partial.rdb |binary zoomerjoin-0.2.2/zoomerjoin/build/vignette.rds |binary zoomerjoin-0.2.2/zoomerjoin/inst/doc/benchmarks.R | 260 +++++----- zoomerjoin-0.2.2/zoomerjoin/inst/doc/benchmarks.html | 7 zoomerjoin-0.2.2/zoomerjoin/inst/doc/guided_tour.R | 1 zoomerjoin-0.2.2/zoomerjoin/inst/doc/guided_tour.Rmd | 1 zoomerjoin-0.2.2/zoomerjoin/inst/doc/guided_tour.html | 36 - zoomerjoin-0.2.2/zoomerjoin/inst/doc/matching_vectors.html | 7 zoomerjoin-0.2.2/zoomerjoin/man/euclidean-joins.Rd | 19 zoomerjoin-0.2.2/zoomerjoin/man/hamming-joins.Rd | 77 +- zoomerjoin-0.2.2/zoomerjoin/man/hamming_distance.Rd | 6 zoomerjoin-0.2.2/zoomerjoin/man/jaccard-joins.Rd | 91 ++- zoomerjoin-0.2.2/zoomerjoin/man/jaccard_similarity.Rd | 6 zoomerjoin-0.2.2/zoomerjoin/man/jaccard_string_group.Rd | 26 - zoomerjoin-0.2.2/zoomerjoin/src/Makevars.in | 8 zoomerjoin-0.2.2/zoomerjoin/src/rust/Cargo.lock |only zoomerjoin-0.2.2/zoomerjoin/src/rust/Cargo.toml | 8 zoomerjoin-0.2.2/zoomerjoin/src/rust/prepare_vendors.sh | 14 zoomerjoin-0.2.2/zoomerjoin/src/rust/src/lib.rs | 236 +++++---- zoomerjoin-0.2.2/zoomerjoin/src/rust/src/minhashjoiner.rs | 117 ++-- zoomerjoin-0.2.2/zoomerjoin/src/rust/vendor.tar.xz |binary zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-hamming_dist.R | 14 zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-test_input_validation.R | 29 + zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-test_jaccard_sim.R | 18 zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-test_logical_euclid_join.R | 30 + zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-test_logical_lsh_join.R | 43 + zoomerjoin-0.2.2/zoomerjoin/tests/testthat/test-test_string_group.R | 11 zoomerjoin-0.2.2/zoomerjoin/vignettes/guided_tour.Rmd | 1 45 files changed, 933 insertions(+), 609 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to
Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>,
Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>,
Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>,
Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>,
Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and
Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Author: Romain Leroux [aut, cre] ,
France Mentre [aut] ,
Jeremy Seurat [ctb]
Maintainer: Romain Leroux <romainlerouxPFIM@gmail.com>
Diff between PFIM versions 7.0.1 dated 2025-11-26 and 7.0.2 dated 2026-01-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/BayesianFim.R | 12 ++++++------ R/FedorovWynnAlgorithm.R | 6 +++--- R/IndividualFim.R | 12 ++++++------ R/MultiplicativeAlgorithm.R | 31 ++++++++++++++++++++----------- R/PopulationFim.R | 14 +++++++------- 7 files changed, 52 insertions(+), 43 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut] ,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 4.0.0 dated 2025-07-30 and 4.2.1 dated 2026-01-30
OBIC-4.0.0/OBIC/tests/testthat/test-precipitation_surpluss.R |only OBIC-4.2.1/OBIC/DESCRIPTION | 10 OBIC-4.2.1/OBIC/MD5 | 99 ++--- OBIC-4.2.1/OBIC/NAMESPACE | 1 OBIC-4.2.1/OBIC/NEWS.md | 56 ++ OBIC-4.2.1/OBIC/R/groundwater_recharge.R | 163 +++++++- OBIC-4.2.1/OBIC/R/management_defaults.R | 11 OBIC-4.2.1/OBIC/R/nitrogen_efficiency.R | 5 OBIC-4.2.1/OBIC/R/obic.R | 171 ++++++--- OBIC-4.2.1/OBIC/R/obic_format_inputs.R | 2 OBIC-4.2.1/OBIC/R/obic_recommendations.R | 2 OBIC-4.2.1/OBIC/R/precipitation_surplus.R | 146 +++---- OBIC-4.2.1/OBIC/R/tables.R | 11 OBIC-4.2.1/OBIC/build/vignette.rds |binary OBIC-4.2.1/OBIC/data/binnenveld.rda |binary OBIC-4.2.1/OBIC/data/column_description.obic.rda |binary OBIC-4.2.1/OBIC/data/crops.obic.rda |binary OBIC-4.2.1/OBIC/data/recom.obic.rda |binary OBIC-4.2.1/OBIC/data/recom.obic_bkp.rda |binary OBIC-4.2.1/OBIC/data/weight.obic.rda |binary OBIC-4.2.1/OBIC/inst/doc/description-of-the-columns.html | 83 +++- OBIC-4.2.1/OBIC/inst/doc/obic_introduction.R | 12 OBIC-4.2.1/OBIC/inst/doc/obic_introduction.Rmd | 12 OBIC-4.2.1/OBIC/inst/doc/obic_introduction.html | 31 - OBIC-4.2.1/OBIC/inst/doc/obic_score_aggregation.R | 4 OBIC-4.2.1/OBIC/inst/doc/obic_score_aggregation.Rmd | 6 OBIC-4.2.1/OBIC/inst/doc/obic_score_aggregation.html | 9 OBIC-4.2.1/OBIC/inst/doc/obic_water_functions.html | 16 OBIC-4.2.1/OBIC/inst/doc/obic_workability.html | 17 OBIC-4.2.1/OBIC/man/add_management.Rd | 4 OBIC-4.2.1/OBIC/man/binnenveld.Rd | 2 OBIC-4.2.1/OBIC/man/calc_n_efficiency.Rd | 4 OBIC-4.2.1/OBIC/man/calc_psp.Rd | 21 + OBIC-4.2.1/OBIC/man/column_description.obic.Rd | 2 OBIC-4.2.1/OBIC/man/crops.obic.Rd | 2 OBIC-4.2.1/OBIC/man/format_soilcompaction.Rd | 2 OBIC-4.2.1/OBIC/man/ind_gw_recharge.Rd | 39 +- OBIC-4.2.1/OBIC/man/ind_gw_target.Rd |only OBIC-4.2.1/OBIC/man/obic_farm.Rd | 10 OBIC-4.2.1/OBIC/man/obic_field.Rd | 16 OBIC-4.2.1/OBIC/man/obic_field_dt.Rd | 10 OBIC-4.2.1/OBIC/man/weight.obic.Rd | 11 OBIC-4.2.1/OBIC/tests/testthat/test-groundwater_recharge.R | 207 +++++++++-- OBIC-4.2.1/OBIC/tests/testthat/test-management.R | 39 ++ OBIC-4.2.1/OBIC/tests/testthat/test-obic_farm.R | 96 ++++- OBIC-4.2.1/OBIC/tests/testthat/test-obic_field_dt.R | 142 ++++++- OBIC-4.2.1/OBIC/tests/testthat/test-precipitation_surplus.R | 75 +++ OBIC-4.2.1/OBIC/tests/testthat/test-recommendations.R | 15 OBIC-4.2.1/OBIC/tests/testthat/test_obic_field.R |only OBIC-4.2.1/OBIC/vignettes/obic_introduction.Rmd | 12 OBIC-4.2.1/OBIC/vignettes/obic_score_aggregation.Rmd | 6 OBIC-4.2.1/OBIC/vignettes/water_funs_references.bib | 2 52 files changed, 1220 insertions(+), 364 deletions(-)
Title: Provider-Agnostic OAuth Authentication for 'shiny' Applications
Description: Provides a simple, configurable, provider-agnostic 'OAuth 2.0' and
'OpenID Connect' (OIDC) authentication framework for 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval, asynchronous
flows, and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.2.0 dated 2026-01-13 and 0.3.0 dated 2026-01-30
DESCRIPTION | 9 - MD5 | 60 ++++---- NEWS.md | 10 + R/methods__token.R | 162 +++++++++++++--------- R/oauth_module_server.R | 147 +++++++++++++------ R/utils__shiny.R | 97 +++++++++++++ inst/doc/usage.Rmd | 38 ++++- inst/doc/usage.html | 70 ++++++--- man/introspect_token.Rd | 7 man/oauth_module_server.Rd | 13 - man/refresh_token.Rd | 8 - man/revoke_token.Rd | 7 tests/testthat/helper-login.R | 27 ++- tests/testthat/test-audit-async-options.R | 93 ++++++------ tests/testthat/test-audit-async-session-context.R | 12 - tests/testthat/test-client-bearer-req-headers.R | 4 tests/testthat/test-client-bearer-req.R | 5 tests/testthat/test-discovery-auth-methods.R | 5 tests/testthat/test-discovery-hardened.R | 5 tests/testthat/test-errors-and-audit.R | 8 - tests/testthat/test-introspect-token.R | 16 -- tests/testthat/test-jwks-malformed-and-pinning.R | 2 tests/testthat/test-module-server-async.R | 117 ++++++++++++--- tests/testthat/test-module-server.R | 72 +++++++-- tests/testthat/test-redirect-following-disabled.R | 8 + tests/testthat/test-refresh-races.R | 106 +++++++------- tests/testthat/test-revoke-on-session-end.R | 14 - tests/testthat/test-revoke-token.R | 16 -- tests/testthat/test-state-fail-delay.R | 4 tests/testthat/test-utils-http-helpers.R | 4 vignettes/usage.Rmd | 38 ++++- 31 files changed, 794 insertions(+), 390 deletions(-)
Title: Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide
Polymorphisms' (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH),
introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
at differential selection between two populations.
Various plotting functions are included to facilitate
visualization and interpretation of these statistics.
Author: Alexander Klassmann [aut, cre],
Mathieu Gautier [aut],
Renaud Vitalis [aut]
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>
Diff between rehh versions 3.2.2 dated 2021-09-15 and 3.2.3 dated 2026-01-30
DESCRIPTION | 9 MD5 | 77 +- NAMESPACE | 2 NEWS.md | 7 R/calc_candidate_regions.R | 151 ++- R/calc_ehh.R | 5 R/calc_ehhs.R | 5 R/calc_furcation.R | 8 R/calc_pairwise_haplen.R | 14 R/make.example.files.R | 6 R/plot.ehh.R | 2 R/plot.ehhs.R | 2 R/rehh.R | 5 R/scan_hh.R | 5 R/scan_hh_full.R | 17 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 13 inst/doc/examples.R | 12 inst/doc/examples.Rmd | 10 inst/doc/examples.html | 652 ++++++++-------- inst/doc/rehh.R | 70 - inst/doc/rehh.Rmd | 22 inst/doc/rehh.html | 1038 +++++++++++++-------------- man/calc_candidate_regions.Rd | 53 + man/calc_ehh.Rd | 5 man/calc_ehhs.Rd | 5 man/calc_pairwise_haplen.Rd | 14 man/make.example.files.Rd | 5 man/plot.ehh.Rd | 2 man/plot.ehhs.Rd | 2 man/rehh-package.Rd | 24 man/scan_hh.Rd | 5 man/scan_hh_full.Rd | 17 src/CALL_FURCATION.c | 15 tests/testthat/test_calc_candidate_regions.R | 2 tests/testthat/test_scan_full.R | 13 vignettes/examples.Rmd | 10 vignettes/rehh.Rmd | 22 vignettes/vignette.bib | 21 40 files changed, 1279 insertions(+), 1068 deletions(-)
Title: A Fully Featured Logging Framework
Description: A flexible, light-weight logging
framework based on 'R6' classes. It supports hierarchical loggers,
structured logging, output to plaintext, 'JSON', (rotating) files,
and memory buffers. Additional appenders for 'Elasticsearch', 'Dynatrace',
databases, email and push notifications, and more are available
in the 'lgrExtra' package.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgr versions 0.5.0 dated 2025-07-23 and 0.5.2 dated 2026-01-30
DESCRIPTION | 18 ++++---- MD5 | 16 +++---- NEWS.md | 10 ++++ R/Appender.R | 9 +++- R/Filter.R | 2 build/vignette.rds |binary inst/doc/lgr.html | 89 ++++++++++++++++++++-------------------- man/AppenderFileRotatingDate.Rd | 14 +++--- man/AppenderFileRotatingTime.Rd | 55 +++++++++++++----------- 9 files changed, 117 insertions(+), 96 deletions(-)
Title: R Analyzer for Large-Scale Assessments
Description: Download, prepare and analyze data from large-scale assessments and
surveys with complex sampling and assessment design (see 'Rutkowski',
2010 <doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of
the package, see 'Mirazchiyski', 2021b (< [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.6.0 dated 2025-11-26 and 1.6.2 dated 2026-01-30
DESCRIPTION | 8 MD5 | 40 NEWS.md | 518 - R/RALSA.r | 2 R/common.r | 7076 ++++++++-------- R/lsa.bench.r | 12 R/lsa.bin.log.reg.r | 12 R/lsa.convert.data.r | 168 R/lsa.corr.r | 230 R/lsa.crosstabs.r | 747 - R/lsa.data.diag.r | 389 R/lsa.download.data.r | 470 - R/lsa.lin.reg.r | 83 R/lsa.merge.data.r | 446 - R/lsa.pcts.means.r | 32 R/lsa.prctls.r | 32 R/lsa.vars.dict.r | 157 inst/shiny/GUI/server.r |20223 ++++++++++++++++++++++++------------------------ inst/shiny/GUI/ui.r | 5007 +++++------ man/lsa.corr.Rd | 16 man/lsa.lin.reg.Rd | 15 21 files changed, 17992 insertions(+), 17691 deletions(-)
Title: Named Entity Recognition in Texts using 'NameTag'
Description: Wraps the 'nametag' library <https://github.com/ufal/nametag>, allowing users to find and extract entities (names, persons, locations, addresses, ...) in raw text and build your own entity recognition models.
Based on a maximum entropy Markov model which is described in Strakova J., Straka M. and Hajic J. (2013) <https://ufal.mff.cuni.cz/~straka/papers/2013-tsd_ner.pdf>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph] ,
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between nametagger versions 0.1.5 dated 2025-08-31 and 0.1.6 dated 2026-01-30
DESCRIPTION | 22 +++++------ MD5 | 10 ++--- NEWS.md | 6 +++ R/datasets.R | 2 - man/europeananews.Rd | 2 - src/nametag/src/morphodita/morpho/persistent_unordered_map.h | 4 +- 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Test the Kronecker Product Structure in Tensor Factor Models
Description: To test if a tensor time series following a Tucker-decomposition factor model has a Kronecker product structure. Supplementary functions for tensor reshape and its reversal are also included.
Author: Zetai Cen [aut, cre]
Maintainer: Zetai Cen <z.cen@lse.ac.uk>
Diff between KOFM versions 0.1.1 dated 2025-01-08 and 1.1.1 dated 2026-01-30
DESCRIPTION | 8 +-- MD5 | 15 +++--- NEWS.md |only R/testKron_auto.R | 2 inst/doc/A-short-introduction-to-KOFM.R | 2 inst/doc/A-short-introduction-to-KOFM.Rmd | 8 ++- inst/doc/A-short-introduction-to-KOFM.html | 64 +++++++++++++++-------------- vignettes/A-short-introduction-to-KOFM.Rmd | 8 ++- vignettes/ref.bib | 27 +++++++++--- 9 files changed, 82 insertions(+), 52 deletions(-)
Title: Intraclass Correlation Coefficient for Count Data
Description: Estimates the intraclass correlation coefficient (ICC) for count data to assess repeatability (intra-methods concordance) and concordance (between-method concordance). In the concordance setting, the ICC is equivalent to the concordance correlation coefficient estimated by variance components. The ICC is estimated using the estimates from generalized linear mixed models. The within-subjects distributions considered are: Poisson; Negative Binomial with additive and proportional extradispersion; Zero-Inflated Poisson; and Zero-Inflated Negative Binomial with additive and proportional extradispersion. The statistical methodology used to estimate the ICC with count data can be found in Carrasco (2010) <doi:10.1111/j.1541-0420.2009.01335.x>.
Author: Josep L. Carrasco [aut, cre]
Maintainer: Josep L. Carrasco <jlcarrasco@ub.edu>
Diff between iccCounts versions 1.1.2 dated 2024-02-28 and 1.1.4 dated 2026-01-30
DESCRIPTION | 16 ++- MD5 | 18 ++-- NAMESPACE | 1 R/core_functions.R | 6 - R/gof_functions.R | 160 ++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/iccCounts_examples.R | 4 inst/doc/iccCounts_examples.Rmd | 2 inst/doc/iccCounts_examples.html | 40 ++++----- vignettes/iccCounts_examples.Rmd | 2 10 files changed, 148 insertions(+), 101 deletions(-)
Title: Shiny Application for Latent Structure Analysis with a Graphical
User Interface
Description: Provides an interactive Shiny-based toolkit for conducting latent structure analyses, including Latent Profile Analysis (LPA), Latent Class Analysis (LCA), Latent Trait Analysis (LTA/IRT), Exploratory Factor Analysis (EFA), Confirmatory Factor Analysis (CFA), and Structural Equation Modeling (SEM). The implementation is grounded in established methodological frameworks: LPA is supported through 'tidyLPA' (Rosenberg et al., 2018) <doi:10.21105/joss.00978>, LCA through 'poLCA' (Linzer & Lewis, 2011) <doi:10.32614/CRAN.package.poLCA> & 'glca' (Kim & Kim, 2024) <doi:10.32614/CRAN.package.glca>, LTA/IRT via 'mirt' (Chalmers, 2012) <doi:10.18637/jss.v048.i06>, and EFA via 'psych' (Revelle, 2025). SEM and CFA functionalities build upon the 'lavaan' framework (Rosseel, 2012) <doi:10.18637/jss.v048.i02>. Users can upload datasets or use built-in examples, fit models, compare fit indices, visualize results, and export outputs without programming.
Author: Hasan Djidu [aut, cre] ,
Heri Retnawati [ctb] ,
Samsul Hadi [ctb] ,
Haryanto [ctb]
Maintainer: Hasan Djidu <hasandjidu@gmail.com>
Diff between projectLSA versions 0.0.6 dated 2026-01-16 and 0.0.7 dated 2026-01-30
projectLSA-0.0.6/projectLSA/inst/app/www/styleCSS.R |only projectLSA-0.0.6/projectLSA/man/figures/CFA4.png |only projectLSA-0.0.6/projectLSA/man/figures/CFA7.png |only projectLSA-0.0.6/projectLSA/man/figures/Homepage.png |only projectLSA-0.0.6/projectLSA/man/figures/LCA2.png |only projectLSA-0.0.6/projectLSA/man/figures/LCA3.png |only projectLSA-0.0.6/projectLSA/man/figures/LPA3.png |only projectLSA-0.0.6/projectLSA/man/figures/LPA4.png |only projectLSA-0.0.6/projectLSA/man/figures/LTA3.png |only projectLSA-0.0.6/projectLSA/man/figures/LTA6.png |only projectLSA-0.0.6/projectLSA/man/figures/SEM.png |only projectLSA-0.0.7/projectLSA/DESCRIPTION | 16 - projectLSA-0.0.7/projectLSA/MD5 | 40 +--- projectLSA-0.0.7/projectLSA/NEWS.md | 3 projectLSA-0.0.7/projectLSA/README.md | 42 +---- projectLSA-0.0.7/projectLSA/inst/app/app.R | 34 ++++ projectLSA-0.0.7/projectLSA/inst/app/homepage_ui.R | 23 -- projectLSA-0.0.7/projectLSA/inst/app/lca_ui.R | 3 projectLSA-0.0.7/projectLSA/inst/app/lpa_ui.R | 2 projectLSA-0.0.7/projectLSA/inst/app/rsconnect |only projectLSA-0.0.7/projectLSA/inst/app/serverCFA.R | 2 projectLSA-0.0.7/projectLSA/inst/app/serverLCA.R | 2 projectLSA-0.0.7/projectLSA/inst/app/serverLPA.R | 2 projectLSA-0.0.7/projectLSA/inst/app/styleCSS.R | 98 +++++++++--- projectLSA-0.0.7/projectLSA/inst/app/www/logoProjectLSA.png |binary projectLSA-0.0.7/projectLSA/man/figures/logoProjectLSA.png |binary projectLSA-0.0.7/projectLSA/man/projectLSA-package.Rd | 8 27 files changed, 173 insertions(+), 102 deletions(-)
Title: Joint Analysis and Imputation of Incomplete Data
Description: Joint analysis and imputation of incomplete data in the Bayesian
framework, using (generalized) linear (mixed) models and extensions there of,
survival models, or joint models for longitudinal and survival data, as
described in Erler, Rizopoulos and Lesaffre (2021) <doi:10.18637/jss.v100.i20>.
Incomplete covariates, if present, are automatically imputed.
The package performs some preprocessing of the data and creates a 'JAGS'
model, which will then automatically be passed to 'JAGS'
<https://mcmc-jags.sourceforge.io/> with the help of
the package 'rjags'.
Author: Nicole S. Erler [aut, cre]
Maintainer: Nicole S. Erler <n.s.erler@umcutrecht.nl>
Diff between JointAI versions 1.0.6 dated 2024-04-02 and 1.1.0 dated 2026-01-30
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JointAI-1.1.0/JointAI/NAMESPACE | 154 JointAI-1.1.0/JointAI/NEWS.md | 33 JointAI-1.1.0/JointAI/R/JAGSmodel_clm.R | 298 JointAI-1.1.0/JointAI/R/JAGSmodel_clmm.R | 360 - JointAI-1.1.0/JointAI/R/JAGSmodel_glm.R | 208 JointAI-1.1.0/JointAI/R/JAGSmodel_glmm.R | 344 - JointAI-1.1.0/JointAI/R/JAGSmodel_mlogit.R | 140 JointAI-1.1.0/JointAI/R/JAGSmodel_mlogitmm.R | 158 JointAI-1.1.0/JointAI/R/JAGSmodel_surv.R | 892 +- JointAI-1.1.0/JointAI/R/JointAI.R | 617 +- JointAI-1.1.0/JointAI/R/build_model.R | 26 JointAI-1.1.0/JointAI/R/convergence_criteria.R | 508 - JointAI-1.1.0/JointAI/R/crosscorr.R |only JointAI-1.1.0/JointAI/R/datasets.R | 580 - JointAI-1.1.0/JointAI/R/deprecated.R | 417 + JointAI-1.1.0/JointAI/R/divide_matrices.R | 360 - JointAI-1.1.0/JointAI/R/extract_state.R | 82 JointAI-1.1.0/JointAI/R/get_MIdat.R | 408 - JointAI-1.1.0/JointAI/R/get_data_list.R | 1006 +-- JointAI-1.1.0/JointAI/R/get_model_dimensions.R | 106 JointAI-1.1.0/JointAI/R/get_model_info.R | 1214 ++- JointAI-1.1.0/JointAI/R/get_modeltypes.R | 157 JointAI-1.1.0/JointAI/R/get_refs.R | 390 - 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Title: Access the 'Gmail' 'RESTful' API
Description: An interface to the 'Gmail' 'RESTful' API. Allows access to
your 'Gmail' messages, threads, drafts and labels.
Author: Jim Hester [aut],
Jennifer Bryan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between gmailr versions 2.0.0 dated 2023-06-30 and 3.0.0 dated 2026-01-30
gmailr-2.0.0/gmailr/R/deprecated.R |only gmailr-2.0.0/gmailr/cleanup |only gmailr-2.0.0/gmailr/configure |only gmailr-2.0.0/gmailr/configure.win |only gmailr-2.0.0/gmailr/man/gmailr-deprecated-auth.Rd |only gmailr-2.0.0/gmailr/man/gmailr-deprecated.Rd |only gmailr-2.0.0/gmailr/tools |only gmailr-3.0.0/gmailr/DESCRIPTION | 20 gmailr-3.0.0/gmailr/LICENSE | 2 gmailr-3.0.0/gmailr/MD5 | 142 +++---- gmailr-3.0.0/gmailr/NAMESPACE | 45 -- gmailr-3.0.0/gmailr/NEWS.md | 23 + gmailr-3.0.0/gmailr/R/aaa.R | 4 gmailr-3.0.0/gmailr/R/gm_auth.R | 163 ++++---- gmailr-3.0.0/gmailr/R/gm_draft.R | 25 - gmailr-3.0.0/gmailr/R/gm_history.R | 17 gmailr-3.0.0/gmailr/R/gm_label.R | 14 gmailr-3.0.0/gmailr/R/gm_message.R | 157 ++++--- gmailr-3.0.0/gmailr/R/gm_mime.R | 264 ++++++++++--- gmailr-3.0.0/gmailr/R/gm_thread.R | 44 +- gmailr-3.0.0/gmailr/R/gmailr.R | 193 ++++++--- gmailr-3.0.0/gmailr/R/quoted_printable.R | 8 gmailr-3.0.0/gmailr/R/utils.R | 24 - gmailr-3.0.0/gmailr/README.md | 10 gmailr-3.0.0/gmailr/build/vignette.rds |binary gmailr-3.0.0/gmailr/inst/doc/deploy-a-token.R | 34 - gmailr-3.0.0/gmailr/inst/doc/deploy-a-token.Rmd | 23 - gmailr-3.0.0/gmailr/inst/doc/deploy-a-token.html | 11 gmailr-3.0.0/gmailr/inst/doc/gmailr.R | 56 +- gmailr-3.0.0/gmailr/inst/doc/gmailr.Rmd | 44 +- gmailr-3.0.0/gmailr/inst/doc/gmailr.html | 24 - gmailr-3.0.0/gmailr/inst/doc/sending_messages.R | 45 +- gmailr-3.0.0/gmailr/inst/doc/sending_messages.Rmd | 56 +- gmailr-3.0.0/gmailr/inst/doc/sending_messages.html | 15 gmailr-3.0.0/gmailr/inst/secret/gmailr-dev-token |binary gmailr-3.0.0/gmailr/man/gm_attachment.Rd | 4 gmailr-3.0.0/gmailr/man/gm_auth.Rd | 4 gmailr-3.0.0/gmailr/man/gm_auth_configure.Rd | 2 gmailr-3.0.0/gmailr/man/gm_create_label.Rd | 2 gmailr-3.0.0/gmailr/man/gm_deauth.Rd | 4 gmailr-3.0.0/gmailr/man/gm_delete_draft.Rd | 2 gmailr-3.0.0/gmailr/man/gm_delete_label.Rd | 2 gmailr-3.0.0/gmailr/man/gm_delete_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_delete_thread.Rd | 2 gmailr-3.0.0/gmailr/man/gm_import_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_insert_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_last_response.Rd | 9 gmailr-3.0.0/gmailr/man/gm_message.Rd | 2 gmailr-3.0.0/gmailr/man/gm_messages.Rd | 2 gmailr-3.0.0/gmailr/man/gm_mime.Rd | 6 gmailr-3.0.0/gmailr/man/gm_modify_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_modify_thread.Rd | 2 gmailr-3.0.0/gmailr/man/gm_save_attachment.Rd | 2 gmailr-3.0.0/gmailr/man/gm_save_attachments.Rd | 2 gmailr-3.0.0/gmailr/man/gm_scopes.Rd | 2 gmailr-3.0.0/gmailr/man/gm_send_draft.Rd | 4 gmailr-3.0.0/gmailr/man/gm_send_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_token.Rd | 2 gmailr-3.0.0/gmailr/man/gm_trash_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_trash_thread.Rd | 2 gmailr-3.0.0/gmailr/man/gm_untrash_message.Rd | 4 gmailr-3.0.0/gmailr/man/gm_untrash_thread.Rd | 2 gmailr-3.0.0/gmailr/man/gm_update_label.Rd | 8 gmailr-3.0.0/gmailr/man/gmailr-configuration.Rd | 2 gmailr-3.0.0/gmailr/man/gmailr-package.Rd | 2 gmailr-3.0.0/gmailr/man/quoted_printable_encode.Rd | 2 gmailr-3.0.0/gmailr/tests/testthat/_snaps/gm_auth.md | 23 + gmailr-3.0.0/gmailr/tests/testthat/_snaps/gm_label.md |only gmailr-3.0.0/gmailr/tests/testthat/test-gm_auth.R | 20 gmailr-3.0.0/gmailr/tests/testthat/test-gm_label.R | 2 gmailr-3.0.0/gmailr/tests/testthat/test-gm_message.R | 36 + gmailr-3.0.0/gmailr/tests/testthat/test-gm_mime.R | 302 +++++++++++---- gmailr-3.0.0/gmailr/tests/testthat/test-gmailr-package.R | 9 gmailr-3.0.0/gmailr/vignettes/deploy-a-token.Rmd | 23 - gmailr-3.0.0/gmailr/vignettes/gmailr.Rmd | 44 +- gmailr-3.0.0/gmailr/vignettes/sending_messages.Rmd | 56 +- 76 files changed, 1357 insertions(+), 722 deletions(-)
Title: Genetic Association Analysis
Description: This is a companion to Henry-Stewart talk by Zhao (2026, <doi:10.69645/FRFQ9519>),
which gathers information, metadata and scripts to showcase modern genetic analysis -- ranging from testing
of polymorphic variant(s) for Hardy-Weinberg equilibrium, association with traits using genetic and statistical
models, Bayesian implementation, power calculation in study design, and genetic annotation. It also covers
R integration with the Linux environment, GitHub, package creation and web applications. The earlier version
by Zhao (2009, <doi:10.69645/DCRY5578>) provides an brief introduction to these topics.
Author: Jing Hua Zhao [aut, cre] ,
Benjamin Altmann [ctb],
Brian Ripley [ctb]
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>
Diff between gaawr2 versions 0.0.3 dated 2025-03-24 and 0.0.5 dated 2026-01-30
DESCRIPTION | 26 +++++++++++--------- MD5 | 38 +++++++++++++++--------------- NEWS.md | 14 +++++++++++ README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary data/DiaHealth.rda |binary data/diabetes.rda |binary inst/REFERENCES.bib | 10 +++++++ inst/doc/gaawr2.R | 11 ++++++++ inst/doc/gaawr2.Rmd | 18 +++++++++----- inst/doc/gaawr2.html | 64 +++++++++++++++++++++++---------------------------- inst/doc/web.R | 2 - inst/doc/web.Rmd | 12 +++++++-- inst/doc/web.html | 10 ++++++- inst/scripts/cran.sh | 3 ++ inst/scripts/docs.sh | 1 man/gaawr2.Rd | 2 - vignettes/gaawr2.Rmd | 18 +++++++++----- vignettes/web.Rmd | 12 +++++++-- 20 files changed, 154 insertions(+), 89 deletions(-)
Title: Tools for Data Manipulation
Description: An implementation of common higher order functions with syntactic
sugar for anonymous function. Provides also a link to 'dplyr' and
'data.table' for common transformations on data frames to work around non
standard evaluation by default.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between dat versions 0.5.0 dated 2020-05-15 and 0.7.0 dated 2026-01-30
dat-0.5.0/dat/tests/testthat/test-lintr.R |only dat-0.7.0/dat/DESCRIPTION | 10 dat-0.7.0/dat/MD5 | 21 dat-0.7.0/dat/NEWS | 91 +- dat-0.7.0/dat/R/DataFrame.R | 19 dat-0.7.0/dat/R/dataTableBackend.R | 5 dat-0.7.0/dat/build/vignette.rds |binary dat-0.7.0/dat/inst/doc/Introduction.R | 78 - dat-0.7.0/dat/inst/doc/Introduction.html | 783 ++++++++++--------- dat-0.7.0/dat/inst/doc/performance.R | 160 +-- dat-0.7.0/dat/inst/doc/performance.html | 678 ++++++++++------ dat-0.7.0/dat/tests/testthat/test-mutar-data-table.R | 12 12 files changed, 1082 insertions(+), 775 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.0.2 dated 2026-01-08 and 2.1.0 dated 2026-01-30
DESCRIPTION | 43 MD5 | 210 + NAMESPACE | 64 NEWS.md | 147 - R/Backfill-class.R |only R/Backfill-methods.R |only R/Backfill-validity.R |only R/Data-class.R | 30 R/Data-methods.R | 279 ++ R/Data-validity.R | 14 R/Design-class.R | 14 R/Design-methods.R | 64 R/Rules-class.R | 65 R/Rules-methods.R | 50 R/Rules-validity.R | 19 R/Simulations-class.R | 8 R/Simulations-methods.R | 84 R/helpers_backfill.R |only R/helpers_data.R | 68 R/helpers_design.R | 233 + R/helpers_knitr.R | 27 R/helpers_knitr_Backfill.R |only R/helpers_knitr_CohortSize.R | 57 R/helpers_knitr_Design.R | 11 R/helpers_knitr_Increments.R | 59 R/helpers_knitr_Opening.R |only R/helpers_knitr_Recruitment.R |only R/helpers_knitr_Stopping.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 12 inst/doc/crmPack-jss-paper.html | 4 inst/doc/example.Rmd | 2 inst/doc/example.html | 4 inst/doc/ordinal-crm.html | 106 inst/doc/parallel_computing_with_extensions.html | 4 inst/doc/rolling-crm.Rmd | 2 inst/doc/rolling-crm.html | 4 inst/doc/simulations.Rmd | 2 inst/doc/simulations.html | 4 inst/doc/tidy_method.html | 48 inst/doc/trial_analysis.R | 18 inst/doc/trial_analysis.Rmd | 32 inst/doc/trial_analysis.html | 1194 +++++----- inst/doc/trial_backfill.R |only inst/doc/trial_backfill.Rmd |only inst/doc/trial_backfill.pdf |only inst/doc/trial_definition.html | 2 inst/doc/upgrading_from_the_old_crmPack.html | 16 man/Backfill-class.Rd |only man/CohortSizeRandom-class.Rd |only man/DADesign-class.Rd | 1 man/Data-class.Rd | 14 man/Design-class.Rd | 14 man/DualDesign-class.Rd | 1 man/GeneralSimulationsSummary-class.Rd | 6 man/Opening-class.Rd |only man/OpeningAll-class.Rd |only man/OpeningAny-class.Rd |only man/OpeningList-class.Rd |only man/OpeningMinCohorts-class.Rd |only man/OpeningMinDose-class.Rd |only man/OpeningMinResponses-class.Rd |only man/OpeningNone-class.Rd |only man/Recruitment-class.Rd |only man/RecruitmentRatio-class.Rd |only man/RecruitmentUnlimited-class.Rd |only man/StoppingPatientsNearDose-class.Rd | 13 man/and-Opening-Opening-method.Rd |only man/crmPack.Rd | 2 man/h_determine_dlts.Rd | 14 man/h_enroll_backfill_patients.Rd |only man/h_kable_param_default.Rd |only man/h_update_backfill_queue.Rd |only man/knit_print.Rd | 264 ++ man/maxRecruits.Rd |only man/openCohort.Rd |only man/or-Opening-Opening-method.Rd |only man/plot-Data.Rd | 57 man/show-GeneralSimulations-method.Rd |only man/simulate-DADesign-method.Rd | 4 man/simulate-Design-method.Rd | 4 man/simulate-DualDesign-method.Rd | 4 man/size.Rd | 13 man/subset-Data.Rd |only man/tidy.Rd | 25 man/update-Data-method.Rd | 13 man/v_backfill.Rd |only man/v_cohort_size.Rd | 6 man/v_opening.Rd |only man/v_recruitment.Rd |only tests/testthat/fixtures/default_da_simulations.Rds |binary tests/testthat/fixtures/default_dual_simulations.Rds |binary tests/testthat/fixtures/default_pseudo_dual_flexi_simulations.Rds |binary tests/testthat/fixtures/default_pseudo_dual_simulations.Rds |binary tests/testthat/fixtures/default_pseudo_simulations.Rds |binary tests/testthat/fixtures/default_simulations.Rds |binary tests/testthat/helper-data.R | 17 tests/testthat/helper-design.R | 58 tests/testthat/test-Backfill-class.R |only tests/testthat/test-Backfill-methods.R |only tests/testthat/test-Backfill-validity.R |only tests/testthat/test-CrmPackClass-class.R | 2 tests/testthat/test-CrmPackClass-methods.R | 5 tests/testthat/test-Data-class.R | 47 tests/testthat/test-Data-methods.R | 81 tests/testthat/test-Data-validity.R | 24 tests/testthat/test-Design-class.R | 25 tests/testthat/test-Design-methods.R | 22 tests/testthat/test-Rules-class.R | 34 tests/testthat/test-Rules-methods.R | 64 tests/testthat/test-Rules-validity.R | 36 tests/testthat/test-Simulations-class.R | 5 tests/testthat/test-Simulations-methods.R | 26 tests/testthat/test-helpers_data.R |only tests/testthat/test-helpers_design.R | 16 tests/testthat/test-helpers_knitr.R | 116 tests/testthat/test-helpers_knitr_Backfill.R |only tests/testthat/test-helpers_knitr_Design.R | 50 tests/testthat/test-helpers_knitr_Opening.R |only tests/testthat/test-helpers_knitr_Recruitment.R |only vignettes/example.Rmd | 2 vignettes/rolling-crm.Rmd | 2 vignettes/simulations.Rmd | 2 vignettes/trial_analysis.Rmd | 32 vignettes/trial_backfill.Rmd |only vignettes/trial_backfill.html |only vignettes/vignettes.bib | 15 128 files changed, 3069 insertions(+), 1071 deletions(-)
Title: Monthly Climate Data for Germany, Usable for Heating and Cooling
Calculations
Description: This data package contains monthly climate data in Germany, it can be used for heating and
cooling calculations (external temperature, heating / cooling days, solar radiation).
Author: Tobias Loga [aut] ,
Guillaume Behem [aut],
Jens Calisti [cre]
Maintainer: Jens Calisti <jens@tangled.de>
Diff between clidamonger versions 1.4.0 dated 2025-07-10 and 1.5.0 dated 2026-01-30
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ data/data.sol.rda |binary data/data.ta.hd.rda |binary data/list.station.ta.rda |binary man/data.sol.Rd | 2 +- man/data.ta.hd.Rd | 2 +- 8 files changed, 16 insertions(+), 12 deletions(-)
Title: Grammar of Graphics for 'base' Plot
Description: A grammar of graphics framework built on 'base' graphics. It
provides a 'bbplot' object and a '+' operator to incrementally compose plots
from data, aesthetic mappings and layers, then render them using the base
plotting system. The package includes common geometric layers (points, lines,
segments, bars, histograms, boxplots and tiles), scales for color and other
aesthetics, legends, faceting, themes, and significance annotations.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between plotbb versions 0.1.0 dated 2026-01-15 and 0.1.1 dated 2026-01-30
DESCRIPTION | 15 +- MD5 | 31 ++-- NAMESPACE | 7 + NEWS.md | 10 + R/bb-bar.R | 23 ++- R/bb-boxplot.R |only R/bb-hist.R |only R/bb-signif.R |only R/bbplot.R | 51 ++++--- R/theme.R | 24 +++ R/utilities.R | 118 +++++++++++++++++ inst/doc/plotbb.R | 70 ++++++++-- inst/doc/plotbb.html | 352 ++++++++++++++++++++++++++++++++------------------- inst/doc/plotbb.qmd | 103 ++++++++++++-- man/bb-theme.Rd | 6 man/layer.Rd | 28 +++- tests |only vignettes/plotbb.qmd | 103 ++++++++++++-- 18 files changed, 712 insertions(+), 229 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability of linear structural
equation models and factor analysis models. The routines are based on the
graphical representation of structural equation models.
Author: Rina Foygel Barber [aut],
Mathias Drton [aut],
Miriam Kranzlmueller [aut],
Nils Sturma [cre, aut],
Luca Weihs [aut]
Maintainer: Nils Sturma <nils.sturma@epfl.ch>
Diff between SEMID versions 0.4.2 dated 2025-10-21 and 0.5.0 dated 2026-01-30
DESCRIPTION | 31 +- MD5 | 23 + NAMESPACE | 8 NEWS.md | 16 - R/factor_analysis_ZUTA.R |only R/factor_analysis_extmID.R |only R/factor_analysis_graphFunctions.R |only R/factor_analysis_localBBCriterion.R |only R/factor_analysis_mID.R |only R/factor_analysis_matchingCriterion.R |only README.md | 442 ++++++++++++++++++++-------------- man/ZUTA.Rd |only man/checkLocalBBCriterion.Rd |only man/checkMatchingCriterion.Rd |only man/extmID.Rd |only man/findColumnsWithSumOne.Rd |only man/mID.Rd |only man/print.ZUTAresult.Rd |only man/print.extmIDresult.Rd |only man/print.mIDresult.Rd |only 20 files changed, 320 insertions(+), 200 deletions(-)
Title: Fast Truncated Singular Value Decomposition and Principal
Components Analysis for Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular value
decomposition and principal components analysis of large sparse and dense
matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.3.5.1 dated 2022-10-03 and 2.3.7 dated 2026-01-30
DESCRIPTION | 11 ++++++----- MD5 | 27 ++++++++++++++------------- R/eigen.R | 9 +++------ R/prcomp.R | 14 ++++++-------- R/ssvd.R | 22 ++++++++++------------ README |only README.md | 8 +++++++- build/vignette.rds |binary inst/doc/irlba.pdf |binary man/irlba.Rd | 25 ++++++++++++++++++++----- man/partial_eigen.Rd | 7 ++----- man/prcomp_irlba.Rd | 12 +++++------- man/ssvd.Rd | 34 +++++++++++++++++++++------------- man/summary.irlba_prcomp.Rd | 1 - man/svdr.Rd | 13 ++++++++++--- 15 files changed, 104 insertions(+), 79 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-16 0.4.1
2025-08-26 0.4.0
2025-05-25 0.3.9
2024-12-23 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-17 0.1.31
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-14 0.2.7
2021-11-02 0.2.0
2021-06-27 0.1.17
2020-09-21 0.1.13
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-02 1.0.2
Title: Weighted Correlation Network Analysis
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Author: Peter Langfelder [aut, cre],
Steve Horvath [aut],
Chaochao Cai [aut],
Jun Dong [aut],
Jeremy Miller [aut],
Lin Song [aut],
Andy Yip [aut],
Bin Zhang [aut]
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between WGCNA versions 1.73 dated 2024-09-18 and 1.74 dated 2026-01-30
WGCNA-1.73/WGCNA/R/GOenrichmentAnalysis.R |only WGCNA-1.74/WGCNA/Changelog | 24 +++ WGCNA-1.74/WGCNA/DESCRIPTION | 12 - WGCNA-1.74/WGCNA/MD5 | 24 +-- WGCNA-1.74/WGCNA/NAMESPACE | 5 WGCNA-1.74/WGCNA/R/Functions.R | 25 ++- WGCNA-1.74/WGCNA/R/GOenrichmentAnalysis-stub.R |only WGCNA-1.74/WGCNA/R/heatmapWithLegend.R | 62 +++++-- WGCNA-1.74/WGCNA/R/modulePreservation.R | 5 WGCNA-1.74/WGCNA/build/partial.rdb |binary WGCNA-1.74/WGCNA/inst/CITATION | 3 WGCNA-1.74/WGCNA/man/GOenrichmentAnalysis.Rd | 194 ------------------------- WGCNA-1.74/WGCNA/man/formatLabels.Rd | 6 WGCNA-1.74/WGCNA/man/plotColorUnderTree.Rd | 8 + 14 files changed, 128 insertions(+), 240 deletions(-)
Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors of
parameter terms. Parameter terms are the labels used to reference
values in vectors, matrices and arrays. They represent the names in
coefficient tables and the column names in 'mcmc' and 'mcmc.list'
objects.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Ayla Pearson [ctb] ,
Evan Amies-Galonski [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between term versions 0.3.6 dated 2025-01-21 and 0.3.7 dated 2026-01-30
term-0.3.6/term/man/figures/lifecycle-archived.svg |only term-0.3.6/term/man/figures/lifecycle-defunct.svg |only term-0.3.6/term/man/figures/lifecycle-maturing.svg |only term-0.3.6/term/man/figures/lifecycle-questioning.svg |only term-0.3.6/term/man/figures/lifecycle-retired.svg |only term-0.3.6/term/man/figures/lifecycle-soft-deprecated.svg |only term-0.3.7/term/DESCRIPTION | 21 ++--- term-0.3.7/term/MD5 | 56 ++++++-------- term-0.3.7/term/NAMESPACE | 1 term-0.3.7/term/NEWS.md | 12 +++ term-0.3.7/term/R/as-term.R | 4 - term-0.3.7/term/R/deprecated.R | 14 +-- term-0.3.7/term/R/npdims.R | 10 -- term-0.3.7/term/R/params.R | 3 term-0.3.7/term/R/pars-terms.R | 4 - term-0.3.7/term/R/subset.R | 4 - term-0.3.7/term/R/term-package.R |only term-0.3.7/term/R/term.R | 8 +- term-0.3.7/term/R/tindex.R | 4 - term-0.3.7/term/R/vld.R | 2 term-0.3.7/term/inst/WORDLIST | 5 + term-0.3.7/term/man/as_term.Rd | 2 term-0.3.7/term/man/deprecated.Rd | 14 +-- term-0.3.7/term/man/figures/lifecycle-deprecated.svg | 22 +++++ term-0.3.7/term/man/figures/lifecycle-experimental.svg | 22 +++++ term-0.3.7/term/man/figures/lifecycle-stable.svg | 30 +++++++ term-0.3.7/term/man/figures/lifecycle-superseded.svg | 22 +++++ term-0.3.7/term/man/npdims.term.Rd | 9 +- term-0.3.7/term/man/params.Rd | 2 term-0.3.7/term/man/pars_terms.Rd | 2 term-0.3.7/term/man/term-package.Rd |only term-0.3.7/term/tests/testthat/test-npdims.R | 2 term-0.3.7/term/tests/testthat/test-summary.R | 12 ++- 33 files changed, 196 insertions(+), 91 deletions(-)
Title: Manipulate R Data Frames Using SQL
Description: The sqldf() function is typically passed a single argument which
is an SQL select statement where the table names are ordinary R data
frame names. sqldf() transparently sets up a database, imports the
data frames into that database, performs the SQL select or other
statement and returns the result using a heuristic to determine which
class to assign to each column of the returned data frame. The sqldf()
or read.csv.sql() functions can also be used to read filtered files
into R even if the original files are larger than R itself can handle.
'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.
Author: G. Grothendieck [aut, cre]
Maintainer: G. Grothendieck <ggrothendieck@gmail.com>
Diff between sqldf versions 0.4-11 dated 2017-06-28 and 0.4-12 dated 2026-01-30
DESCRIPTION | 19 +- INSTALL | 8 - MD5 | 14 - R/sqldf.R | 2 README.md | 440 +++++++++++++++++++++++++---------------------------------- inst/NEWS | 8 - inst/csv.awk | 2 man/sqldf.Rd | 79 +++++----- 8 files changed, 255 insertions(+), 317 deletions(-)
Title: Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks. This
package wraps the SNNS functionality to make it available from
within R. Using the 'RSNNS' low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be accessed.
Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and
learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph],
Jose M. Benitez [ths],
Andreas Zell [ctb] ,
Niels Mache [ctb] ,
Guenter Mamier [ctb] ,
Michael Vogt [ctb] ,
Sven Doering [ctb] ,
Ralf Huebner [ctb] ,
Kai-Uwe Herrmann [ctb] ,
Tobias Soyez [ctb] ,
Michael Schmalzl [ctb [...truncated...]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RSNNS versions 0.4-17 dated 2023-11-30 and 0.4-18 dated 2026-01-30
ChangeLog | 5 +++++ DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/RSNNS-package.R | 4 ++-- man/RSNNS-package.Rd | 2 -- src/Makevars | 2 +- src/Makevars.win | 2 +- src/scaled_conj_grad.cpp | 4 +++- 8 files changed, 25 insertions(+), 20 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types
of resampling objects (e.g. bootstrap, cross-validation).
Author: Hannah Frick [aut, cre] ,
Fanny Chow [aut],
Max Kuhn [aut],
Michael Mahoney [aut] ,
Julia Silge [aut] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between rsample versions 1.3.1 dated 2025-07-29 and 1.3.2 dated 2026-01-30
DESCRIPTION | 8 ++-- MD5 | 66 ++++++++++++++++----------------- NEWS.md | 9 ++++ R/bootci.R | 2 - R/initial_split.R | 33 +++++++++++----- R/initial_validation_split.R | 8 +++- R/internal_calibration_split.R | 5 ++ R/make_groups.R | 4 +- R/mc.R | 8 +++- R/misc.R | 29 ++++++++++++++ R/tidy.R | 4 +- R/validation_split.R | 11 ++++- R/vfold.R | 8 ++-- build/vignette.rds |binary man/bootstraps.Rd | 2 - man/clustering_cv.Rd | 2 - man/group_bootstraps.Rd | 2 - man/group_mc_cv.Rd | 2 - man/group_vfold_cv.Rd | 6 +-- man/initial_split.Rd | 20 ++++------ man/initial_validation_split.Rd | 2 - man/int_pctl.Rd | 2 - man/mc_cv.Rd | 2 - man/reg_intervals.Rd | 2 - man/rolling_origin.Rd | 2 - man/rsample-package.Rd | 2 - man/slide-resampling.Rd | 2 - man/tidy.rsplit.Rd | 2 - man/validation_split.Rd | 8 ++-- man/vfold_cv.Rd | 2 - tests/testthat/_snaps/initial_split.md | 12 ++++++ tests/testthat/test-initial_split.R | 10 +++++ tests/testthat/test-reshuffle_rset.R | 6 ++- tests/testthat/test-rolling_origin.R | 18 ++++++--- 34 files changed, 200 insertions(+), 101 deletions(-)
Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between rollupTree versions 0.3.2 dated 2025-06-18 and 0.4.0 dated 2026-01-30
DESCRIPTION | 6 +- MD5 | 20 +++++---- NAMESPACE | 4 + NEWS.md | 4 + R/update_prop.R | 80 +++++++++++++++++++++++++++++++------- inst/doc/rollupTree.html | 2 man/df_get_by_key.Rd | 2 man/df_get_row_by_id.Rd |only man/df_get_row_by_key.Rd |only man/df_set_by_id.Rd | 2 man/df_set_row_by_id.Rd |only man/df_set_row_by_key.Rd |only tests/testthat/test-update_prop.R | 24 +++++++++++ 13 files changed, 117 insertions(+), 27 deletions(-)
Title: An Implementation of Matrix Mathematics that Respects Row and
Column Names
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.6.13 dated 2025-05-14 and 0.6.14 dated 2026-01-30
DESCRIPTION | 10 - LICENSE | 2 MD5 | 47 ++++---- NAMESPACE | 1 NEWS.md | 20 +++ R/Utilities.R | 159 +++++++++++++++++++++++++++- R/complete_and_sort.R | 17 +- README.md | 6 - build/vignette.rds |binary inst/CITATION | 8 - inst/WORDLIST | 4 inst/doc/about-vector-arguments.html | 5 inst/doc/aggregation-vignette.R | 4 inst/doc/aggregation-vignette.Rmd | 9 + inst/doc/aggregation-vignette.html | 96 +++++++--------- inst/doc/applybyname-vignette.html | 9 - inst/doc/matsbyname.Rmd | 8 - inst/doc/matsbyname.html | 17 +- inst/doc/using-summarise-in-matsbyname.html | 5 man/complete_and_sort.Rd | 17 +- man/rename_to_pref_suff_byname.Rd | 2 man/rename_via_pattern_byname.Rd |only tests/testthat/test-Utilities.R | 123 +++++++++++++++++++++ vignettes/aggregation-vignette.Rmd | 9 + vignettes/matsbyname.Rmd | 8 - 25 files changed, 441 insertions(+), 145 deletions(-)
Title: Conformal Time Series Forecasting Using State of Art Machine
Learning Algorithms
Description: Conformal time series forecasting using the caret infrastructure.
It provides access to state-of-the-art machine learning models for forecasting
applications. The hyperparameter of each model is selected based on time
series cross-validation, and forecasting is done recursively.
Author: Resul Akay [aut, cre]
Maintainer: Resul Akay <resulakay1@gmail.com>
Diff between caretForecast versions 0.1.1 dated 2022-10-24 and 0.1.2 dated 2026-01-30
DESCRIPTION | 11 - MD5 | 46 ++-- NAMESPACE | 2 NEWS.md | 8 R/arml.R | 90 +++++++++ R/fit_conformal_reg.R | 54 +++++ R/forecast.R | 80 ++++++-- R/predict_conformal.R | 101 ++++++++++ R/utils.R | 267 ++++++++++++++++++++++++++++- README.md | 79 +++++++- man/ARml.Rd | 20 +- man/calibrate_horizon_scores.Rd |only man/conformalRegressor.Rd | 1 man/conformalRegressorByHorizon.Rd |only man/figures/README-example2-1.png |binary man/figures/README-example3-1.png |binary man/figures/README-example4-1.png |binary man/figures/README-example4-2.png |binary man/figures/README-example5-1.png |binary man/figures/README-example5-2.png |binary man/figures/README-example6-1.png |binary man/figures/README-example6-2.png |binary man/figures/README-example_conformal-1.png |only man/forecast_loop_cal.Rd |only man/predict.conformalRegressorByHorizon.Rd |only tests/testthat/test-short_series.R |only tests/testthat/test-suggested_method.R | 2 27 files changed, 692 insertions(+), 69 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-10 0.1.1
2019-05-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-27 1.0.1
2018-07-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-18 0.8.1
2019-12-17 0.7.6
2019-12-17 0.7.7
2019-12-15 0.7.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-16 1.0.5
2024-01-26 1.0.3
2022-06-02 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-26 0.3.0
2019-06-13 0.2.0
2018-09-16 0.1.3
2017-08-01 0.1.2
2017-07-24 0.1.1
2017-07-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-06 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-30 2.1.2
2025-05-16 1.1.4
2025-05-16 1.1.5
2024-01-26 1.1.2
2022-06-07 1.1.0
2020-06-24 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-17 0.1.6
2021-07-26 0.1.5
2018-02-17 0.1.4
2017-10-30 0.1.3
2015-06-19 0.1.2
2015-05-26 0.1.1
2014-07-25 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-11 1.0.1
2016-07-31 1.0.0
2016-07-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-13 1.0.2
2021-05-03 1.0.1
2021-04-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-29 0.2.1
2026-01-24 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-24 0.8.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-21 1.5.1
2024-09-20 1.4.2
2024-02-23 1.4.0
2023-06-17 1.3.2-1
2023-06-06 1.3.2
2023-04-02 1.3.0
2023-02-14 1.2.2
2023-01-10 1.2.1
2022-11-29 1.1.0
2022-09-15 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-02 0.1.3
2024-05-01 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-09 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-02 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-21 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-09 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-12 0.1.0