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:
2025-07-02 1.0.2
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:
2025-03-22 1.0.0
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:
2025-11-16 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:
2024-09-11 1.0
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:
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:
2019-12-10 0.1.1
2019-05-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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:
2025-09-30 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:
2021-05-06 0.3.1
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:
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:
2023-09-12 0.1.0
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:
2023-05-02 0.3
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:
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:
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:
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:
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:
2023-01-17 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
Title: Non-Parametric Cluster Significance Testing with Reference to a
Unimodal Null Distribution
Description: Assess the significance of identified clusters and estimates the true number of clusters by comparing the explained variation due to the clustering from the original data to that produced by clustering a unimodal reference distribution which preserves the covariance structure in the data. The reference distribution is generated using kernel density estimation and a Gaussian copula framework. A dimension reduction strategy and sparse covariance estimation optimize this method for the high-dimensional, low-sample size setting. This method is described in Helgeson, Vock, and Bair (2021) <doi:10.1111/biom.13376>.
Author: Erika S. Helgeson [aut, cre],
David Vock [aut],
Eric Bair [aut]
Maintainer: Erika S. Helgeson <helge@umn.edu>
Diff between UNPaC versions 1.1.1 dated 2022-06-09 and 1.2.0 dated 2026-01-29
DESCRIPTION | 33 ++++-- LICENSE |only MD5 | 13 +- R/UNPaC_Copula.R | 18 +-- R/UNPaC_null.R | 4 R/UNPaC_num_clust.R | 18 +-- man/UNPaC_Copula.Rd | 252 ++++++++++++++++++++++++------------------------- man/UNPaC_num_clust.Rd | 210 ++++++++++++++++++++-------------------- 8 files changed, 278 insertions(+), 270 deletions(-)
Title: Heatmap-Integrated Decision Tree Visualizations
Description: Creates interpretable decision tree visualizations with the
data represented as a heatmap at the tree's leaf nodes. 'treeheatr'
utilizes the customizable 'ggparty' package for drawing decision
trees.
Author: Trang Le [aut, cre] ,
Jason Moore [aut] ,
University of Pennsylvania [cph]
Maintainer: Trang Le <grixor@gmail.com>
Diff between treeheatr versions 0.2.1 dated 2020-11-19 and 0.2.3 dated 2026-01-29
DESCRIPTION | 45 +-- MD5 | 61 ++-- NEWS.md | 8 R/clust.R | 27 +- R/compute_tree.R | 105 +++----- R/data.R | 2 R/draw_heat.R | 99 ++++--- R/draw_tree.R | 91 +++++-- R/eval_tree.R | 46 +-- R/get_fit.R | 92 +++---- R/globals.R | 14 - R/heat_tree.R | 96 +++++-- R/scale_norm.R | 11 R/treeheatr.R | 9 R/utils.R | 93 +++---- README.md | 59 ++-- build/vignette.rds |binary inst/doc/explore.R | 6 inst/doc/explore.Rmd | 4 inst/doc/explore.html | 489 +++++++++++++++++++++----------------- man/compute_tree.Rd | 4 man/draw_heat.Rd | 6 man/draw_tree.Rd | 8 man/eval_tree.Rd | 2 man/figures/logo.png |only man/figures/unnamed-chunk-4-1.png |binary man/figures/unnamed-chunk-5-1.png |binary man/get_cols.Rd | 2 man/heat_tree.Rd | 18 - man/scale_norm.Rd | 2 tests |only vignettes/explore.Rmd | 4 32 files changed, 808 insertions(+), 595 deletions(-)
Title: Efficient Manipulation of Date-Times
Description: Efficient routines for manipulation of date-time objects while
accounting for time-zones and daylight saving times. The package includes
utilities for updating of date-time components (year, month, day etc.),
modification of time-zones, rounding of date-times, period addition and
subtraction etc. Parts of the 'CCTZ' source code, released under the Apache
2.0 License, are included in this package. See
<https://github.com/google/cctz> for more details.
Author: Vitalie Spinu [aut, cre],
Google Inc. [ctb, cph]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between timechange versions 0.3.0 dated 2024-01-18 and 0.4.0 dated 2026-01-29
DESCRIPTION | 11 ++-- MD5 | 20 ++++---- NEWS.md | 9 +++ R/addition.R | 2 R/utils.R | 6 +- man/time_add.Rd | 2 man/time_update.Rd | 2 src/common.cpp | 59 +++++++++---------------- src/common.h | 7 +-- src/update.cpp | 99 +++++++++++++++++++++++------------------- tests/testthat/test-update.R | 100 +++++++++++++++++++++++++++++++++++++++++++ 11 files changed, 212 insertions(+), 105 deletions(-)
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre] ,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Diff between REDCapCAST versions 25.3.2 dated 2025-03-10 and 26.1.1 dated 2026-01-29
DESCRIPTION | 22 MD5 | 30 NEWS.md | 18 R/ds2dd_detailed.R | 2 R/export_redcap_instrument.R | 19 R/utils.r | 53 - inst/WORDLIST | 2 inst/doc/REDCapCAST.html | 337 ++++------ inst/doc/Shiny-app.html | 98 +- inst/shiny-examples/casting/app.R | 12 inst/shiny-examples/casting/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf | 2 man/clean_redcap_name.Rd | 1 man/create_instrument_meta.Rd | 3 man/cut_string_length.Rd | 2 man/export_redcap_instrument.Rd | 7 man/strsplitx.Rd | 6 16 files changed, 336 insertions(+), 278 deletions(-)
Title: Calculate Crosstab and Topline Tables of Weighted Survey Data
Description: Calculate common types of tables for weighted survey data.
Options include topline and (2-way and 3-way) crosstab tables of
categorical or ordinal data as well as summary tables of weighted
numeric variables. Optionally, include the margin of error at
selected confidence intervals including the design effect. The
design effect is calculated as described by
Kish (1965) <doi:10.1002/bimj.19680100122> beginning
on page 257. Output takes the form of tibbles (simple data frames).
This package conveniently handles labelled data, such as that
commonly used by 'Stata' and 'SPSS.' Complex survey design is
not supported at this time.
Author: John D. Johnson [aut, cre]
Maintainer: John D. Johnson <john.d.johnson@marquette.edu>
This is a re-admission after prior archival of version 0.1.6 dated 2023-05-12
Diff between pollster versions 0.1.6 dated 2023-05-12 and 0.1.7 dated 2026-01-29
DESCRIPTION | 12 +- MD5 | 30 ++--- NEWS.md | 4 R/SummaryStatistics.R | 5 build/vignette.rds |binary inst/doc/crosstab3way.R | 8 - inst/doc/crosstab3way.Rmd | 2 inst/doc/crosstab3way.html | 179 +++++++++++++++++----------------- inst/doc/crosstabs.R | 6 - inst/doc/crosstabs.Rmd | 2 inst/doc/crosstabs.html | 233 ++++++++++++++++++++++----------------------- inst/doc/toplines.R | 4 inst/doc/toplines.html | 67 +++++++----- man/wtd_mean.Rd | 4 vignettes/crosstab3way.Rmd | 2 vignettes/crosstabs.Rmd | 2 16 files changed, 295 insertions(+), 265 deletions(-)
Title: Extract from the Scottish Health and Social Care Open Data
Platform
Description: Extract and interact with data from the Scottish Health and
Social Care Open Data platform <https://www.opendata.nhs.scot>.
Author: Public Health Scotland [cph],
Csilla Scharle [aut],
James Hayes [cre, aut] ,
David Aikman [aut],
Ross Hull [aut]
Maintainer: James Hayes <James.Hayes2@phs.scot>
Diff between phsopendata versions 1.0.1 dated 2025-11-05 and 1.0.2 dated 2026-01-29
DESCRIPTION | 20 +++--- MD5 | 24 +++---- NEWS.md | 6 + R/phs_GET.R | 2 README.md | 88 +++++++++++---------------- inst |only tests/spelling.R |only tests/testthat/test-add_context.R | 88 +++++++++++++++++++++------ tests/testthat/test-get_latest_resource_id.R | 19 +++++ tests/testthat/test-get_resource_sql.R | 5 - tests/testthat/test-list_resources.R | 11 ++- tests/testthat/test-parse_col_select.R | 5 + tests/testthat/test-phs_GET.R | 8 +- tests/testthat/test-request_url.R | 26 +++++++ 14 files changed, 199 insertions(+), 103 deletions(-)
Title: Replicability-Analysis Tools for Meta-Analysis
Description: User-friendly package for reporting replicability-analysis methods, affixed to meta-analyses summary. The replicability-analysis output provides an assessment of the investigated intervention, where it offers quantification of effect replicability and assessment of the consistency of findings.
- Replicability-analysis for fixed-effects and random-effect meta analysis:
- r(u)-value;
- lower bounds on the number of studies with replicated positive and\or negative effect;
- Allows detecting inconsistency of signals;
- forest plots with the summary of replicability analysis results;
- Allows Replicability-analysis with or without the common-effect assumption.
Author: Iman Jaljuli [cre, aut]
Maintainer: Iman Jaljuli <jaljuli.iman@gmail.com>
This is a re-admission after prior archival of version 1.2.0 dated 2023-12-15
Diff between metarep versions 1.2.0 dated 2023-12-15 and 1.2.1 dated 2026-01-29
DESCRIPTION | 11 +-- MD5 | 30 ++++---- R/CD002943_CMP001.R | 2 R/CD003366_CMP005.R | 2 R/CD006823_CMP001.R | 2 R/CD007077_CMP001.r | 2 R/forest.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST |only inst/doc/metarep.R | 4 - inst/doc/metarep.html | 167 +++++++++++++++++++++++++------------------------ man/CD002943_CMP001.Rd | 2 man/CD003366_CMP005.Rd | 2 man/CD006823_CMP001.Rd | 2 man/CD007077_CMP001.Rd | 2 man/forest.metarep.Rd | 2 17 files changed, 121 insertions(+), 111 deletions(-)
Title: Calculate Mass Properties and Uncertainties of Tree Structures
Description: Recursively calculates mass properties (mass, center of mass, moments and products of inertia, and optionally, their uncertainties) for arbitrary decomposition trees. R. L. Zimmerman, J. H. Nakai. (2005) <https://www.sawe.org/product/paper-3360/>).
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between massProps versions 0.3.3 dated 2025-06-20 and 0.3.4 dated 2026-01-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/massProps.Rmd | 4 ++-- inst/doc/massProps.html | 4 ++-- vignettes/massProps.Rmd | 4 ++-- 6 files changed, 18 insertions(+), 14 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through
matching, weighting or subclassification, for example, using propensity scores. Includes
integration with 'MatchIt', 'WeightIt', 'MatchThem', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal',
'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing
functions. Users can also specify data for balance assessment not generated through
the above packages. Also included are methods for assessing balance in clustered or
multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 4.6.1 dated 2025-08-20 and 4.6.2 dated 2026-01-29
DESCRIPTION | 16 MD5 | 176 ++++---- NAMESPACE | 2 NEWS.md | 10 R/bal.compute.R | 75 +-- R/bal.plot.R | 174 ++++---- R/bal.tab.CBPS.R | 9 R/bal.tab.Match.R | 31 - R/bal.tab.cem.match.R | 7 R/bal.tab.designmatch.R | 9 R/bal.tab.ebalance.R | 8 R/bal.tab.matchit.R | 13 R/bal.tab.mimids.R | 11 R/bal.tab.optmatch.R | 9 R/bal.tab.ps.R | 3 R/bal.tab.sbwcau.R | 5 R/bal.tab.time.list.R | 6 R/bal.tab.weightit.R | 28 - R/balance-statistics.R | 4 R/balance-summary.R | 74 +-- R/base.bal.tab.R | 12 R/chk-functions.R | 86 ++-- R/class-bal.tab.cluster.R | 23 - R/class-bal.tab.imp.R | 16 R/class-bal.tab.msm.R | 12 R/class-bal.tab.multi.R | 18 R/class-bal.tab.subclass.R | 18 R/cobalt-package.R | 4 R/f.build.R | 4 R/functions_for_processing.R | 600 +++++++++++++++------------- R/get.w.R | 104 ---- R/love.plot.R | 236 +++++------ R/print.bal.tab.R | 308 +++++++------- R/set.cobalt.options.R | 33 - R/splitfactor.R | 117 ++--- R/utils.R | 93 ++-- R/var.names.R | 25 - R/x2base.R | 581 +++++++++------------------ README.md | 59 +- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/cobalt.Rmd | 155 +++---- inst/doc/cobalt.html | 582 +++++++++++++-------------- inst/doc/faq.Rmd | 78 ++- inst/doc/faq.html | 105 ++--- inst/doc/longitudinal-treat.Rmd | 54 +- inst/doc/longitudinal-treat.html | 107 ++--- inst/doc/love.plot.Rmd | 60 +- inst/doc/love.plot.html | 203 +++++---- inst/doc/optimizing-balance.Rmd | 54 +- inst/doc/optimizing-balance.html | 116 ++--- inst/doc/other-packages.Rmd | 123 +++-- inst/doc/other-packages.html | 645 ++++++++++++++----------------- inst/doc/segmented-data.Rmd | 52 +- inst/doc/segmented-data.html | 228 +++++----- man/bal.compute.Rd | 2 man/bal.plot.Rd | 18 man/bal.tab.CBPS.Rd | 9 man/bal.tab.Match.Rd | 22 - man/bal.tab.cem.match.Rd | 7 man/bal.tab.designmatch.Rd | 6 man/bal.tab.ebalance.Rd | 2 man/bal.tab.matchit.Rd | 12 man/bal.tab.mimids.Rd | 10 man/bal.tab.optmatch.Rd | 2 man/bal.tab.ps.Rd | 2 man/bal.tab.sbwcau.Rd | 2 man/bal.tab.time.list.Rd | 2 man/bal.tab.weightit.Rd | 27 - man/balance-summary.Rd | 3 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/get.w.Rd | 2 man/love.plot.Rd | 24 - man/macros/macros.Rd | 10 man/print.bal.tab.Rd | 9 man/var.names.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test-github-issues.R | 13 tests/testthat/test-s.d.denom.R | 24 - tests/testthat/test-splitfactor.R | 24 - vignettes/cobalt.Rmd | 155 +++---- vignettes/faq.Rmd | 78 ++- vignettes/longitudinal-treat.Rmd | 54 +- vignettes/love.plot.Rmd | 60 +- vignettes/optimizing-balance.Rmd | 54 +- vignettes/other-packages.Rmd | 123 +++-- vignettes/segmented-data.Rmd | 52 +- 89 files changed, 3168 insertions(+), 3224 deletions(-)
More information about LassoHiDFastGibbs at CRAN
Permanent link
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <doi:10.48550/arXiv.1611.09477> or
nonlinear models <doi:10.48550/arXiv.1604.06737> can be used. There
are also functions for dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between embed versions 1.2.1 dated 2025-11-30 and 1.2.2 dated 2026-01-29
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 4 ++ R/umap.R | 14 +++++++-- build/partial.rdb |binary tests/testthat/_snaps/umap.md | 62 +++++++++++++++++++++++++++++++++++++++++- tests/testthat/test-umap.R | 10 +++++- 7 files changed, 93 insertions(+), 15 deletions(-)
Title: Historical and Contemporary Boundaries of the United States of
America
Description: The boundaries for geographical units in the United States of
America contained in this package include state, county, congressional
district, and zip code tabulation area. Contemporary boundaries are provided
by the U.S. Census Bureau (public domain). Historical boundaries for the
years from 1629 to 2000 are provided form the Newberry Library's Atlas of
Historical County Boundaries (licensed CC BY-NC-SA). Additional data is
provided in the USAboundariesData package; this package provides an
interface to access that data.
Author: Lincoln Mullen [aut] ,
Jordan Bratt [aut] ,
United States Census Bureau [cph],
Jacci Ziebert [cre]
Maintainer: Jacci Ziebert <jacciziebert@gmail.com>
This is a re-admission after prior archival of version 0.4.0 dated 2021-10-12
Diff between USAboundaries versions 0.4.0 dated 2021-10-12 and 0.5.1 dated 2026-01-29
USAboundaries-0.4.0/USAboundaries/R/usboundaries-package.r |only USAboundaries-0.4.0/USAboundaries/inst/doc/usaboundaries-sample-analysis.R |only USAboundaries-0.4.0/USAboundaries/inst/doc/usaboundaries-sample-analysis.Rmd |only USAboundaries-0.4.0/USAboundaries/inst/doc/usaboundaries-sample-analysis.html |only USAboundaries-0.4.0/USAboundaries/man/USAboundaries.Rd |only USAboundaries-0.4.0/USAboundaries/man/install_data_package.Rd |only USAboundaries-0.4.0/USAboundaries/vignettes/usaboundaries-sample-analysis.Rmd |only USAboundaries-0.5.1/USAboundaries/DESCRIPTION | 56 - USAboundaries-0.5.1/USAboundaries/LICENSE | 4 USAboundaries-0.5.1/USAboundaries/MD5 | 109 +- USAboundaries-0.5.1/USAboundaries/NAMESPACE | 18 USAboundaries-0.5.1/USAboundaries/NEWS.md | 85 - USAboundaries-0.5.1/USAboundaries/R/data-doc.R | 21 USAboundaries-0.5.1/USAboundaries/R/filters.R | 46 USAboundaries-0.5.1/USAboundaries/R/install-data-pkg.R | 120 +- USAboundaries-0.5.1/USAboundaries/R/state_codes.R | 39 USAboundaries-0.5.1/USAboundaries/R/state_plane.R | 120 +- USAboundaries-0.5.1/USAboundaries/R/state_proj.R | 34 USAboundaries-0.5.1/USAboundaries/R/us_cities.R | 98 +- USAboundaries-0.5.1/USAboundaries/R/us_congressional.R | 70 - USAboundaries-0.5.1/USAboundaries/R/us_counties.R | 160 +-- USAboundaries-0.5.1/USAboundaries/R/us_states.R | 157 +-- USAboundaries-0.5.1/USAboundaries/R/us_zipcodes.R | 44 USAboundaries-0.5.1/USAboundaries/R/usaboundaries-package.R |only USAboundaries-0.5.1/USAboundaries/README.md | 477 +++++----- USAboundaries-0.5.1/USAboundaries/build/vignette.rds |binary USAboundaries-0.5.1/USAboundaries/data/state_codes.rda |binary USAboundaries-0.5.1/USAboundaries/data/states_contemporary_lores.rda |binary USAboundaries-0.5.1/USAboundaries/inst/CITATION | 50 - USAboundaries-0.5.1/USAboundaries/inst/doc/get-started.R |only USAboundaries-0.5.1/USAboundaries/inst/doc/get-started.Rmd |only USAboundaries-0.5.1/USAboundaries/inst/doc/get-started.html |only USAboundaries-0.5.1/USAboundaries/inst/extdata/md-003.csv | 40 USAboundaries-0.5.1/USAboundaries/inst/extdata/md-119.csv |only USAboundaries-0.5.1/USAboundaries/man/USAboundaries-package.Rd |only USAboundaries-0.5.1/USAboundaries/man/check_data_package.Rd |only USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-1.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-2.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-3.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-4.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-5.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-3-6.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-4-1.png |binary USAboundaries-0.5.1/USAboundaries/man/figures/README-unnamed-chunk-4-2.png |binary USAboundaries-0.5.1/USAboundaries/man/install_USAboundariesData.Rd |only USAboundaries-0.5.1/USAboundaries/man/state_codes.Rd | 61 - USAboundaries-0.5.1/USAboundaries/man/state_plane.Rd | 94 - USAboundaries-0.5.1/USAboundaries/man/state_proj.Rd | 54 - USAboundaries-0.5.1/USAboundaries/man/states_contemporary_lores.Rd | 49 - USAboundaries-0.5.1/USAboundaries/man/us_cities.Rd | 84 - USAboundaries-0.5.1/USAboundaries/man/us_congressional.Rd | 71 - USAboundaries-0.5.1/USAboundaries/man/us_counties.Rd | 126 +- USAboundaries-0.5.1/USAboundaries/man/us_states.Rd | 124 +- USAboundaries-0.5.1/USAboundaries/man/us_zipcodes.Rd | 54 - USAboundaries-0.5.1/USAboundaries/tests/testthat.R | 28 USAboundaries-0.5.1/USAboundaries/tests/testthat/test-install-data-pkg.R |only USAboundaries-0.5.1/USAboundaries/tests/testthat/test-state_plane-standalone.R | 50 - USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_cities.R | 51 - USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_congressional.R | 40 USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_counties.R | 62 - USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_states-standalone.R | 39 USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_states.R | 68 - USAboundaries-0.5.1/USAboundaries/tests/testthat/test-us_zipcodes.R | 10 USAboundaries-0.5.1/USAboundaries/vignettes/get-started.Rmd |only 64 files changed, 1499 insertions(+), 1314 deletions(-)
Title: Recursive Non-Additive Emulator for Multi-Fidelity Data
Description: Performs RNA emulation and active learning proposed by Heo and Sung (2025) <doi:10.1080/00401706.2024.2376173> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.
Author: Junoh Heo [aut, cre],
Chih-Li Sung [aut]
Maintainer: Junoh Heo <heojunoh@msu.edu>
Diff between RNAmf versions 1.1.2 dated 2025-09-12 and 1.1.3 dated 2026-01-29
RNAmf-1.1.2/RNAmf/R/ALC.R |only RNAmf-1.1.2/RNAmf/R/ALD.R |only RNAmf-1.1.2/RNAmf/R/ALM.R |only RNAmf-1.1.2/RNAmf/R/ALMC.R |only RNAmf-1.1.2/RNAmf/man/ALC_RNAmf.Rd |only RNAmf-1.1.2/RNAmf/man/ALD_RNAmf.Rd |only RNAmf-1.1.2/RNAmf/man/ALMC_RNAmf.Rd |only RNAmf-1.1.2/RNAmf/man/ALM_RNAmf.Rd |only RNAmf-1.1.3/RNAmf/DESCRIPTION | 11 - RNAmf-1.1.3/RNAmf/MD5 | 39 +-- RNAmf-1.1.3/RNAmf/NAMESPACE | 25 +- RNAmf-1.1.3/RNAmf/R/AL_RNAmf.R |only RNAmf-1.1.3/RNAmf/R/GP.R | 137 +++++++------ RNAmf-1.1.3/RNAmf/R/NestedX.R | 2 RNAmf-1.1.3/RNAmf/R/RNAmf.R | 326 ++++++++++++++++++++++++++----- RNAmf-1.1.3/RNAmf/R/functions.R | 66 ++++++ RNAmf-1.1.3/RNAmf/R/imputer_RNA.R |only RNAmf-1.1.3/RNAmf/R/matGP.R | 181 +++++++++-------- RNAmf-1.1.3/RNAmf/R/predict.RNAmf.R | 297 ++++++++++++++++++++-------- RNAmf-1.1.3/RNAmf/R/xifun.R | 2 RNAmf-1.1.3/RNAmf/R/zetafun.R | 2 RNAmf-1.1.3/RNAmf/build/partial.rdb |binary RNAmf-1.1.3/RNAmf/man/AL_RNAmf.Rd |only RNAmf-1.1.3/RNAmf/man/RNAmf.Rd | 24 +- RNAmf-1.1.3/RNAmf/man/closed_form_RNA.Rd |only RNAmf-1.1.3/RNAmf/man/imputer_RNA.Rd |only RNAmf-1.1.3/RNAmf/man/predict.Rd | 19 - 27 files changed, 808 insertions(+), 323 deletions(-)
Title: 3D Rendering Using Obliquely Projected Cubes and Cuboids
Description: Three-dimensional rendering for 'grid' and 'ggplot2' graphics using cubes and cuboids drawn with an oblique projection. As a special case also supports primary view orthographic projections. Can be viewed as an extension to the 'isocubes' package <https://github.com/coolbutuseless/isocubes>.
Author: Trevor L. Davis [aut, cre] ,
Mike FC [aut]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between oblicubes versions 1.0.0 dated 2025-03-10 and 1.0.1 dated 2026-01-29
DESCRIPTION | 15 - MD5 | 44 ++-- NEWS.md | 6 R/aabb_cubes.R | 84 ++++----- R/geom_oblicubes.R | 256 +++++++++++++++------------ R/geom_oblicuboids.R | 256 +++++++++++++++------------ R/hooks.R | 10 - R/light_helpers.R | 58 +++--- R/oblicubesGrob.R | 281 +++++++++++++++++------------- R/oblicuboidsGrob.R | 281 +++++++++++++++++------------- R/utils-cull.R | 129 ++++++------- R/utils-faces.R | 305 ++++++++++++++++----------------- R/utils-misc.R | 86 ++++----- R/utils-transform.R | 36 +-- R/xyz_heightmap.R | 178 ++++++++++--------- build/vignette.rds |binary man/geom_oblicubes.Rd | 10 - man/geom_oblicuboids.Rd | 10 - tests/testthat/test-geom_oblicubes.R | 24 +- tests/testthat/test-geom_oblicuboids.R | 24 +- tests/testthat/test-misc.R | 8 tests/testthat/test-oblicubesGrob.R | 88 +++++---- tests/testthat/test-oblicuboidsGrob.R | 77 ++++---- 23 files changed, 1234 insertions(+), 1032 deletions(-)
Title: Diffusion Non-Additive Model with Tunable Precision
Description: Performs Diffusion Non-Additive (DNA) model proposed by Heo, Boutelet, and Sung (2025+) <doi:10.48550/arXiv.2506.08328> for multi-fidelity computer experiments with tuning parameters. The DNA model captures nonlinear dependencies across fidelity levels using Gaussian process priors and is particularly effective when simulations at different fidelity levels are nonlinearly correlated. The DNA model targets not only interpolation across given fidelity levels but also extrapolation to smaller tuning parameters including the exact solution corresponding to a zero-valued tuning parameter, leveraging a nonseparable covariance kernel structure that models interactions between the tuning parameter and input variables. Closed-form expressions for the predictive mean and variance enable efficient inference and uncertainty quantification. Hyperparameters in the model are estimated via maximum likelihood estimation.
Author: Junoh Heo [aut, cre],
Romain Boutelet [aut],
Chih-Li Sung [aut]
Maintainer: Junoh Heo <heojunoh@msu.edu>
Diff between DNAmf versions 0.1.0 dated 2025-06-23 and 0.1.1 dated 2026-01-29
DNAmf-0.1.0/DNAmf/R/predict.DNAmf_nonsep.R |only DNAmf-0.1.0/DNAmf/man/closed_form.Rd |only DNAmf-0.1.0/DNAmf/man/imputer.Rd |only DNAmf-0.1.1/DNAmf/DESCRIPTION | 8 DNAmf-0.1.1/DNAmf/MD5 | 28 - DNAmf-0.1.1/DNAmf/NAMESPACE | 15 DNAmf-0.1.1/DNAmf/R/DNAmf.R | 294 +++++++++++++++++++ DNAmf-0.1.1/DNAmf/R/DNAmf_internal.R | 16 - DNAmf-0.1.1/DNAmf/R/GP.R | 132 ++++---- DNAmf-0.1.1/DNAmf/R/GP_nonsep.R | 438 ++++++++++++++++------------- DNAmf-0.1.1/DNAmf/R/functions.R | 2 DNAmf-0.1.1/DNAmf/R/imputer.R | 40 -- DNAmf-0.1.1/DNAmf/R/matGP.R | 157 +++++----- DNAmf-0.1.1/DNAmf/R/predict.DNAmf.R |only DNAmf-0.1.1/DNAmf/man/DNAmf.Rd | 2 DNAmf-0.1.1/DNAmf/man/closed_form_DNA.Rd |only DNAmf-0.1.1/DNAmf/man/imputer_DNA.Rd |only DNAmf-0.1.1/DNAmf/man/predict.Rd | 8 18 files changed, 750 insertions(+), 390 deletions(-)
Title: Confidence Intervals for Robust and Classical Linear Mixed Model
Estimators
Description: The main function calculates confidence intervals (CI) for Mixed Models, utilizing both classical estimators from the lmer() function in the 'lme4' package and robust estimators from the rlmer() function in the 'robustlmm' package, as well as the varComprob() function in the 'robustvarComp' package. Three methods are available: the classical Wald method, the wild bootstrap, and the parametric bootstrap. Bootstrap methods offer flexibility in obtaining lower and upper bounds through percentile or BCa methods. More details are given in Mason, F., Cantoni, E., & Ghisletta, P. (2021) <doi:10.5964/meth.6607> and Mason, F., Cantoni, E., & Ghisletta, P. (2024) <doi:10.1037/met0000643>.
Author: Fabio Mason [aut, cre],
Manuel Koller [aut],
Eva Cantoni [ctb, ths],
Paolo Ghisletta [ths]
Maintainer: Fabio Mason <fabio.mason@unige.ch>
Diff between confintROB versions 1.0-2 dated 2025-06-21 and 1.1-1 dated 2026-01-29
confintROB-1.0-2/confintROB/R/medsim-data.R |only confintROB-1.0-2/confintROB/data/medsim.rda |only confintROB-1.0-2/confintROB/inst/medsim |only confintROB-1.0-2/confintROB/man/medsim.Rd |only confintROB-1.0-2/confintROB/tests/confintrob_test.R |only confintROB-1.0-2/confintROB/tests/confintrob_test.Rout.save |only confintROB-1.0-2/confintROB/tests/parallelTest.R |only confintROB-1.0-2/confintROB/tests/varComprob_createParamSampleFunction.R |only confintROB-1.0-2/confintROB/tests/varComprob_createParamSampleFunction.Rout.save |only confintROB-1.1-1/confintROB/DESCRIPTION | 14 - confintROB-1.1-1/confintROB/MD5 | 29 +- confintROB-1.1-1/confintROB/R/BCa.R | 21 + confintROB-1.1-1/confintROB/R/confintrob.R | 6 confintROB-1.1-1/confintROB/R/helpers.R | 119 +++++++++- confintROB-1.1-1/confintROB/R/medication-data.R | 23 + confintROB-1.1-1/confintROB/man/confintROB.Rd | 2 confintROB-1.1-1/confintROB/man/medication.Rd | 23 + confintROB-1.1-1/confintROB/tests/testthat |only confintROB-1.1-1/confintROB/tests/testthat.R |only 19 files changed, 204 insertions(+), 33 deletions(-)
Title: Create Representative Records After Entity Resolution
Description: An implementation of Kaplan, Betancourt, Steorts (2022) <doi:10.1080/00031305.2022.2041482> that creates representative records for use in downstream tasks after entity resolution is performed. Multiple methods for creating the representative records (data sets) are provided.
Author: Andee Kaplan [aut, cre],
Brenda Betancourt [aut],
Rebecca C. Steorts [aut]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>
Diff between representr versions 0.1.5 dated 2023-09-05 and 0.1.6 dated 2026-01-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/emp_kl.R | 2 +- build/vignette.rds |binary inst/doc/representr.R | 12 ++++++------ inst/doc/representr.html | 6 +++--- man/representr.Rd | 2 +- 8 files changed, 26 insertions(+), 22 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.8.3 dated 2026-01-28 and 1.8.4 dated 2026-01-29
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ src/LASlib/lasreader.cpp | 19 ++++++++----------- src/LASlib/lasreader_dtm.cpp | 24 ++++++++++++------------ src/LASlib/lasreader_las.cpp | 10 +++++----- src/LASlib/lastransform.cpp | 4 ++-- src/altrep_compact_replication.cpp | 5 ----- 8 files changed, 41 insertions(+), 45 deletions(-)
Title: Text Analysis Through the 'Receptiviti' API
Description: Sends texts to the <https://www.receptiviti.com> API to be scored,
and facilitates the creation of custom norms and local results databases.
Author: Receptiviti Inc. [fnd, cph],
Kent English [cre],
Micah Iserman [aut, ctr]
Maintainer: Kent English <kenglish@receptiviti.com>
Diff between receptiviti versions 0.2.0 dated 2025-06-07 and 0.2.1 dated 2026-01-29
DESCRIPTION | 8 ++-- MD5 | 12 +++--- NEWS.md | 7 +++ R/manage_request.R | 88 +++++++++++++++++++++---------------------------- R/receptiviti_status.R | 40 +++++++++++++++++++++- README.md | 4 +- man/receptiviti.Rd | 3 + 7 files changed, 98 insertions(+), 64 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of maximally distinct qualitative color palettes,
optionally tailored to color deficiency. A set of colors or a subspace of a
color space is used as input and a final palette of specified size is
generated by picking colors that maximize the minimum pairwise difference
among the chosen colors. Adaptations to color vision deficiency,
background colors, and white points are supported.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johan@jolars.co>
Diff between qualpalr versions 1.0.1 dated 2025-10-17 and 2.0.0 dated 2026-01-29
qualpalr-1.0.1/qualpalr/tests/testthat/test_autopal.R |only qualpalr-2.0.0/qualpalr/DESCRIPTION | 18 - qualpalr-2.0.0/qualpalr/MD5 | 43 +-- qualpalr-2.0.0/qualpalr/NEWS.md | 27 + qualpalr-2.0.0/qualpalr/R/qualpal.R | 10 qualpalr-2.0.0/qualpalr/R/utils.R | 6 qualpalr-2.0.0/qualpalr/README.md | 12 qualpalr-2.0.0/qualpalr/inst/doc/comparisons.html | 6 qualpalr-2.0.0/qualpalr/inst/doc/introduction.html | 54 +-- qualpalr-2.0.0/qualpalr/inst/include/qualpal/color_difference.h | 12 qualpalr-2.0.0/qualpalr/inst/include/qualpal/colors.h | 28 ++ qualpalr-2.0.0/qualpalr/inst/include/qualpal/qualpal.h | 67 ++++ qualpalr-2.0.0/qualpalr/man/figures/README-pairs-1.png |binary qualpalr-2.0.0/qualpalr/man/figures/README-plot-1.png |binary qualpalr-2.0.0/qualpalr/man/qualpal.Rd | 11 qualpalr-2.0.0/qualpalr/man/qualpalr-package.Rd | 4 qualpalr-2.0.0/qualpalr/src/qualpal/color_difference.cpp | 11 qualpalr-2.0.0/qualpalr/src/qualpal/colors.cpp | 19 + qualpalr-2.0.0/qualpalr/src/qualpal/farthest_points.cpp | 45 +++ qualpalr-2.0.0/qualpalr/src/qualpal/farthest_points.h | 8 qualpalr-2.0.0/qualpalr/src/qualpal/qualpal.cpp | 138 ++++++---- qualpalr-2.0.0/qualpalr/src/qualpalr.cpp | 13 qualpalr-2.0.0/qualpalr/tests/testthat/test_qualpal.R | 22 + 23 files changed, 415 insertions(+), 139 deletions(-)
Title: Utilities for Working with R's Operators
Description: Provides a collection of utilities that allow programming with
R's operators. Routines allow classifying operators,
translating to and from an operator and its underlying function, and inverting
some operators (e.g. comparison operators), etc. All methods can be extended
to custom infix operators.
Author: Christopher Brown [aut, cre],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between operator.tools versions 1.6.3 dated 2017-02-28 and 1.6.3.1 dated 2026-01-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-operators.R | 4 ++++ 3 files changed, 9 insertions(+), 5 deletions(-)
More information about operator.tools at CRAN
Permanent link
Title: Toolkit for Data Processing, Quality, and Statistical Models
Description: Offers tools for data formatting, anomaly detection, and classification
of tree-ring data using spatial comparisons and cross-correlation.
Supports flexible detrending and climate–growth modeling via generalized
additive mixed models (Wood 2017, ISBN:978-1498728331) and the 'mgcv'
package (<https://CRAN.R-project.org/package=mgcv>), enabling robust
analysis of non-linear trends and autocorrelated data. Provides
standardized visual reporting, including summaries, diagnostics, and
model performance. Compatible with '.rwl' files and tailored for the
Canadian Forest Service Tree-Ring Data (CFS-TRenD) repository
(Girardin et al. (2021) <doi:10.1139/er-2020-0099>), offering
a comprehensive and adaptable framework for dendrochronologists working
with large and complex datasets.
Author: Xiao Jing Guo [aut, cre],
Martin Girardin [aut],
Juha Metsaranta [aut],
David Gervais [aut],
Elizabeth Campbell [aut]
Maintainer: Xiao Jing Guo <xiaojing.guo@nrcan-rncan.gc.ca>
Diff between growthTrendR versions 0.2.0 dated 2026-01-24 and 0.2.1 dated 2026-01-29
DESCRIPTION | 6 MD5 | 12 R/quality_assessment.R | 24 - inst/doc/demo_vgn3_models.R | 23 - inst/doc/demo_vgn3_models.Rmd | 30 -- inst/doc/demo_vgn3_models.html | 549 ++--------------------------------------- vignettes/demo_vgn3_models.Rmd | 30 -- 7 files changed, 92 insertions(+), 582 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre] ,
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael [...truncated...]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-90 dated 2025-03-31 and 0.8-91 dated 2026-01-29
ChangeLog | 5 +++++ DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ tests/spss.R | 5 ++++- tests/spss.Rout.save | 17 ++++++++++------- tests/stata.R | 5 ++++- tests/stata.Rout.save | 15 +++++++++------ 7 files changed, 43 insertions(+), 26 deletions(-)
Title: Oncology Extension Package for ADaM in 'R' Asset Library
Description: Programming oncology specific Clinical Data Interchange Standards Consortium
(CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a
mandatory part of any New Drug or Biologics License Application submitted to the
United States Food and Drug Administration (FDA). Analysis derivations are
implemented in accordance with the "Analysis Data Model Implementation Guide"
(CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam>).
The package is an extension package of the 'admiral' package.
Author: Stefan Bundfuss [aut, cre],
Amit Jain [aut],
Vinh Nguyen [aut],
Olga Starostecka [aut],
Kiran Peddamudium [aut],
Tomoyuki Namai [aut],
Ross Farrugia [aut],
Yirong Cao [ctb],
Ashwini Weber [ctb],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@roche.com>
Diff between admiralonco versions 1.3.0 dated 2025-09-01 and 1.4.0 dated 2026-01-29
DESCRIPTION | 16 MD5 | 97 - NAMESPACE | 5 NEWS.md | 58 R/admiralonco-package.R | 12 R/derive_param_bor.R | 56 R/derive_param_clinbenefit.R | 50 R/derive_param_confirmed_bor.R | 50 R/derive_param_confirmed_resp.R | 50 R/derive_param_response.R | 70 - R/filter_pd.R | 86 + README.md | 13 inst/WORDLIST | 6 inst/doc/admiralonco.Rmd | 8 inst/doc/admiralonco.html | 2 inst/doc/adrs.R | 46 inst/doc/adrs.Rmd | 24 inst/doc/adrs.html | 9 inst/doc/adrs_basic.R | 66 - inst/doc/adrs_basic.Rmd | 6 inst/doc/adrs_basic.html | 172 +- inst/doc/adrs_gcig.html | 106 - inst/doc/adrs_imwg.html | 14 inst/doc/adrs_pcwg3.R | 295 ++++- inst/doc/adrs_pcwg3.Rmd | 404 +++++- inst/doc/adrs_pcwg3.html | 1294 +++++++++++++++------- inst/doc/adtte.R | 114 - inst/doc/irecist.R | 14 man/date_source.Rd |only man/derive_param_bor.Rd | 26 man/derive_param_clinbenefit.Rd | 20 man/derive_param_confirmed_bor.Rd | 16 man/derive_param_confirmed_resp.Rd | 17 man/derive_param_response.Rd | 39 man/filter_pd.Rd | 14 man/get_crpr_dataset.Rd | 2 man/signal_crpr.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-derive_param_bor.R | 93 - tests/testthat/test-derive_param_clinbenefit.R | 71 - tests/testthat/test-derive_param_confirmed_bor.R | 79 - tests/testthat/test-derive_param_confirmed_resp.R | 70 - tests/testthat/test-derive_param_response.R | 65 - tests/testthat/test-filter_pd.R | 95 + vignettes/admiralonco.Rmd | 8 vignettes/adrs.Rmd | 24 vignettes/adrs_basic.Rmd | 6 vignettes/adrs_pcwg3.Rmd | 404 +++++- 48 files changed, 2879 insertions(+), 1315 deletions(-)
Title: Access and Process Data and Documents of the Manifesto Project
Description: Provides access to coded election programmes from the Manifesto
Corpus and to the Manifesto Project's Main Dataset and routines to analyse this
data. The Manifesto Project <https://manifesto-project.wzb.eu> collects and
analyses election programmes across time and space to measure the political
preferences of parties. The Manifesto Corpus contains the collected and
annotated election programmes in the Corpus format of the package 'tm' to enable
easy use of text processing and text mining functionality. Specific functions
for scaling of coded political texts are included.
Author: Jirka Lewandowski [aut],
Nicolas Merz [aut],
Sven Regel [aut],
Pola Lehmann [cre, ctb],
Paul Muscat [ctb]
Maintainer: Pola Lehmann <pola.lehmann@wzb.eu>
Diff between manifestoR versions 1.6.1 dated 2025-08-29 and 1.6.2 dated 2026-01-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++++ R/manifestoR-package.r | 2 +- inst/doc/manifestoRworkflow.pdf |binary vignettes/manifestoRworkflow.Rmd | 12 ++++++------ 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Includes implementation of a new [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.8.8 dated 2025-12-05 and 0.9.0 dated 2026-01-29
DESCRIPTION | 7 - MD5 | 52 ++++--- NAMESPACE | 2 NEWS.md | 13 + R/IWP.R | 2 R/calcWO_data_frame.R | 2 R/calcWO_formula.R | 2 R/calcWO_hce.R | 2 R/deltaWO.R |only R/deltaWO_adhce.R |only R/minWO.R | 2 R/simKHCE.R | 40 ++++- R/simTTE.R | 303 +++++++++++++++++++++++++-------------------- inst/doc/Introduction.Rmd | 16 +- inst/doc/Introduction.html | 53 +++++-- inst/doc/Wins.html | 8 - inst/doc/hce.html | 8 - inst/doc/maraca.html | 8 - man/IWP.Rd | 2 man/calcWO.data.frame.Rd | 2 man/calcWO.formula.Rd | 2 man/calcWO.hce.Rd | 2 man/deltaWO.Rd |only man/deltaWO.adhce.Rd |only man/minWO.Rd | 2 man/simKHCE.Rd | 11 + man/simTTE.Rd | 41 +++++- vignettes/Introduction.Rmd | 16 +- vignettes/REFERENCES.bib | 14 +- 29 files changed, 381 insertions(+), 231 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner [aut, cre] ,
Andreas Mayr [aut],
Nora Fenske [aut],
Janek Thomas [aut],
Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between gamboostLSS versions 2.1-0 dated 2025-02-24 and 2.2-0 dated 2026-01-29
ChangeLog | 69 ++++++--- DESCRIPTION | 16 +- MD5 | 36 ++-- NAMESPACE | 1 R/cvrisk.R | 67 -------- build/vignette.rds |binary inst/NEWS.Rd | 18 ++ inst/doc/gamboostLSS_Tutorial.R | 77 +++++----- inst/doc/gamboostLSS_Tutorial.Rnw | 78 +++++----- inst/doc/gamboostLSS_Tutorial.pdf |binary man/as.families.Rd | 14 - man/families.Rd | 3 man/gamboostLSS-package.Rd | 6 tests/bugfixes.R | 39 ++--- tests/regtest-families.R | 282 ++++++++++++++++++------------------- tests/regtest-glmboostLSS.R | 1 tests/regtest-stabilization.R | 19 +- vignettes/bib.bib | 19 +- vignettes/gamboostLSS_Tutorial.Rnw | 78 +++++----- 19 files changed, 410 insertions(+), 413 deletions(-)
Title: Bridge to System Package Manager
Description: Enables binary package installations on Linux distributions.
Provides functions to manage packages via the distribution's package
manager. Also provides transparent integration with R's install.packages()
and a fallback mechanism. When installed as a system package, interacts
with the system's package manager without requiring administrative
privileges via an integrated D-Bus service; otherwise, uses sudo.
Currently, the following backends are supported: DNF, APT, ALPM.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between bspm versions 0.5.7 dated 2024-04-10 and 0.5.8 dated 2026-01-29
DESCRIPTION | 11 +++++----- MD5 | 16 +++++++-------- NEWS.md | 6 +++++ R/bridge.R | 3 -- R/utils.R | 2 - README.md | 43 +++++++++++------------------------------ inst/service/backend/_utils.py | 2 - inst/service/bspm.py | 28 +++++++++++++------------- man/bspm-package.Rd | 1 9 files changed, 50 insertions(+), 62 deletions(-)
Title: Computes Adaptable Radial Axes Mappings
Description: Computes low-dimensional point representations of high-dimensional numerical data according to the data visualization method Adaptable Radial Axes described in: Manuel Rubio-Sánchez, Alberto Sanchez, and Dirk J. Lehmann (2017) "Adaptable radial axes plots for improved multivariate data visualization" <doi:10.1111/cgf.13196>.
Author: Manuel Rubio-Sanchez [aut, cre, cph] ,
Dirk J. Lehmann [ctb] ,
Miguel Angel Munoz Mohedano [ctb] ,
Alberto Sanchez Campos [ctb] ,
Cristina Soguero-Ruiz [ctb]
Maintainer: Manuel Rubio-Sanchez <manuel.rubio@urjc.es>
Diff between aramappings versions 0.1.2 dated 2025-11-25 and 0.1.3 dated 2026-01-29
DESCRIPTION | 11 MD5 | 83 +++--- NEWS.md | 5 R/ara_exact_l1.R | 20 - R/ara_exact_l2.R | 13 - R/ara_exact_linf.R | 19 - R/ara_ordered_l1.R | 13 - R/ara_ordered_l2.R | 13 - R/ara_ordered_linf.R | 13 - R/ara_unconstrained_l1.R | 18 - R/ara_unconstrained_l2.R | 12 R/ara_unconstrained_linf.R | 18 - R/data.R |only R/draw_ara_plot.R | 14 - README.md | 39 --- data |only inst/doc/intro_to_aramappings.R | 23 - inst/doc/intro_to_aramappings.Rmd | 38 +-- inst/doc/intro_to_aramappings.html | 330 ++++++++++++--------------- man/ara_exact_l1.Rd | 294 ++++++++++++------------ man/ara_exact_l2.Rd | 13 - man/ara_exact_linf.Rd | 19 - man/ara_ordered_l1.Rd | 13 - man/ara_ordered_l2.Rd | 13 - man/ara_ordered_linf.Rd | 13 - man/ara_unconstrained_l1.Rd | 18 - man/ara_unconstrained_l2.Rd | 12 man/ara_unconstrained_linf.Rd | 18 - man/auto_mpg.Rd |only man/cereal.Rd |only man/draw_ara_plot_2d_standardized.Rd | 12 man/figures/README-unnamed-chunk-14-1.png |only man/figures/README-unnamed-chunk-15-1.png |only man/wine.Rd |only tests/testthat/test-ara_exact_l1.R | 13 - tests/testthat/test-ara_exact_l2.R | 9 tests/testthat/test-ara_exact_linf.R | 14 - tests/testthat/test-ara_ordered_l1.R | 9 tests/testthat/test-ara_ordered_l2.R | 9 tests/testthat/test-ara_ordered_linf.R | 9 tests/testthat/test-ara_unconstrained_l1.R | 14 - tests/testthat/test-ara_unconstrained_l2.R | 9 tests/testthat/test-ara_unconstrained_linf.R | 14 - tests/testthat/test-draw_ara_plot.R | 53 ---- vignettes/intro_to_aramappings.Rmd | 38 +-- 45 files changed, 607 insertions(+), 691 deletions(-)
Title: Regression Models with Break-Points / Change-Points Estimation
(with Possibly Random Effects)
Description: Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed.
The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and
illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented
in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>).
Estimation of piecewise-constant relationships and changepoints (mean-shift models) is
discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 2.2-0 dated 2026-01-15 and 2.2-1 dated 2026-01-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 6 ++++++ R/stelpmented.R | 10 +++++----- man/segmented-package.Rd | 4 ++-- 5 files changed, 21 insertions(+), 15 deletions(-)
Title: Read Data from Relational Database Management Systems and Health
Information Systems
Description: Import Data from Relational Database Management Systems
(RDBMS) and Health Information Systems ('HIS'). The current version of the
package supports importing data from RDBMS including 'MS SQL', 'MySQL',
'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and
'SORMAS'.
Author: Karim Mane [aut] ,
Emmanuel Kabuga [aut] ,
Bubacarr Bah [aut, cre] ,
Bankole Ahadzie [ctb],
Nuredin Mohammed [ctb],
Abdoelnaser Degoot [ctb],
Hugo Gruson [rev] ,
Pratik Gupte [rev] ,
Andree Valle-Campos [rev] ,
London School of Hygiene and Tropical M [...truncated...]
Maintainer: Bubacarr Bah <Bubacarr.Bah1@lshtm.ac.uk>
Diff between readepi versions 1.0.3 dated 2025-10-29 and 1.0.4 dated 2026-01-29
DESCRIPTION | 8 - MD5 | 30 +++---- NEWS.md | 4 R/read_rdbms.R | 3 R/read_sormas-helpers.R | 4 build/vignette.rds |binary inst/doc/design_principle.html | 160 ++++++++++++++++++++++++++++++++++++++- inst/doc/install_drivers.Rmd | 2 inst/doc/install_drivers.html | 4 inst/doc/query_parameters.Rmd | 2 inst/doc/query_parameters.html | 4 inst/doc/readepi.html | 66 ++++++++-------- man/read_rdbms.Rd | 3 tests/testthat/test-read_rdbms.R | 6 - vignettes/install_drivers.Rmd | 2 vignettes/query_parameters.Rmd | 2 16 files changed, 230 insertions(+), 70 deletions(-)
Title: Extended Tools for Continuous Legends, Polygon Manipulation, and
Visual Display of Categorical Data
Description: Annotate plots with legends for continuous variables and colour
spectra using the base graphics plotting tools; and manipulate irregular
polygons. Includes palettes for colour-blind viewers.
Author: Martin R. Smith [aut, cre, cph] ,
Martin Krzywinski [ctb]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between PlotTools versions 0.3.1 dated 2024-09-03 and 0.4.0 dated 2026-01-29
DESCRIPTION | 33 MD5 | 22 NEWS.md | 6 R/data.R |only data |only inst/CITATION | 3 man/PlotTools-package.Rd | 5 man/cbPalettes.Rd |only tests/testthat/_snaps/SpectrumLegend/spectrumlegend.svg | 694 ++++++++-------- tests/testthat/test-Col2Hex.R | 23 10 files changed, 412 insertions(+), 374 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-18 dated 2024-12-10 and 0.60-19 dated 2026-01-29
CHANGELOG | 10 +++- DESCRIPTION | 10 ++-- MD5 | 53 +++++++++++------------ R/np.copula.R | 1 R/npregiv.R | 4 - R/npregivderiv.R | 4 - R/util.R | 100 +++++++++++++++++++++++++++++++++++++------- R/zzz.R | 2 README.md | 4 - build/partial.rdb |only build/vignette.rds |binary data/cps71.rda |binary inst/doc/entropy_np.Rnw | 13 ++--- inst/doc/entropy_np.pdf |binary inst/doc/np.Rnw | 18 +++---- inst/doc/np.pdf |binary inst/doc/np_faq.Rnw | 37 +++++++++++----- inst/doc/np_faq.pdf |binary man/np.regressioniv.Rd | 4 - man/np.regressionivderiv.Rd | 6 +- man/npuniden.boundary.Rd | 2 man/npuniden.sc.Rd | 2 vignettes/entropy_np.Rnw | 13 ++--- vignettes/entropy_np.bib | 6 +- vignettes/np.Rnw | 18 +++---- vignettes/np.bib | 6 +- vignettes/np_faq.Rnw | 37 +++++++++++----- vignettes/np_faq.bib | 12 ++--- 28 files changed, 233 insertions(+), 129 deletions(-)
Title: Analysis of Longitudinal Data with Irregular Observation Times
Description: Functions to help with analysis of longitudinal data featuring irregular observation times, where the observation times may be associated with the outcome process. There are functions to quantify the degree of irregularity, fit inverse-intensity weighted Generalized Estimating Equations (Lin H, Scharfstein DO, Rosenheck RA (2004) <doi:10.1111/j.1467-9868.2004.b5543.x>), perform multiple outputation (Pullenayegum EM (2016) <doi:10.1002/sim.6829>) and fit semi-parametric joint models (Liang Y (2009) <doi: 10.1111/j.1541-0420.2008.01104.x>).
Author: Eleanor Pullenayegum [aut, cre]
Maintainer: Eleanor Pullenayegum <eleanor.pullenayegum@sickkids.ca>
Diff between IrregLong versions 0.4.0 dated 2024-09-06 and 0.4.1 dated 2026-01-29
DESCRIPTION | 14 +-- MD5 | 38 ++++----- NAMESPACE | 2 NEWS.md | 124 +++++++++++++++--------------- R/IIWcode.R | 49 +++++------ README.md | 2 build/vignette.rds |binary inst/WORDLIST |only inst/doc/Irreglong-vignette.R | 19 ++-- inst/doc/Irreglong-vignette.Rmd | 20 +++- inst/doc/Irreglong-vignette.html | 127 ++++++++++++++++--------------- man/abacus.plot.Rd | 4 man/figures/README-unnamed-chunk-4-1.png |binary man/iiw.Rd | 4 man/iiw.weights.Rd | 8 + man/iiwgee.Rd | 16 ++- man/lagfn.Rd | 2 man/mo.Rd | 7 - man/outputation.Rd | 4 tests |only vignettes/Irreglong-vignette.Rmd | 20 +++- 21 files changed, 251 insertions(+), 209 deletions(-)
Title: Fit Vector Fields and Potential Landscapes from Intensive
Longitudinal Data
Description: A toolbox for estimating vector fields from intensive
longitudinal data, and construct potential landscapes thereafter. The
vector fields can be estimated with two nonparametric methods: the
Multivariate Vector Field Kernel Estimator (MVKE) by Bandi & Moloche
(2018) <doi:10.1017/S0266466617000305> and the Sparse Vector Field
Consensus (SparseVFC) algorithm by Ma et al. (2013)
<doi:10.1016/j.patcog.2013.05.017>. The potential landscapes can be
constructed with a simulation-based approach with the 'simlandr'
package (Cui et al., 2021) <doi:10.31234/osf.io/pzva3>, or the
Bhattacharya et al. (2011) method for path integration
<doi:10.1186/1752-0509-5-85>.
Author: Jingmeng Cui [aut, cre]
Maintainer: Jingmeng Cui <jingmeng.cui@outlook.com>
Diff between fitlandr versions 0.1.0 dated 2023-02-10 and 0.1.1 dated 2026-01-29
DESCRIPTION | 17 ++-- MD5 | 63 +++++++-------- NAMESPACE | 2 NEWS.md | 10 ++ R/2d_landscape.R |only R/Bhattacharya_method.R | 4 R/fit_vectorfield.R | 129 +++++++++++++++---------------- R/fitlandr-package.R | 2 R/kernal_estimator.R | 88 ++++++++++++++------- R/utils-pipe.R | 28 +++--- R/vectorfield_eq.R | 4 R/vectorfield_landscape.R | 7 - R/vectorfield_simulation.R | 5 - README.md | 10 +- build/partial.rdb |binary inst |only man/MVKE.Rd | 6 - man/add_interp_grid.Rd | 42 +++++----- man/align_pot_B.Rd | 76 +++++++++--------- man/fast_bilinear.Rd | 80 +++++++++---------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/find_eqs.Rd | 46 +++++------ man/fit_2d_ld.Rd |only man/fit_2d_vf.Rd | 4 man/fit_3d_vfld.Rd | 121 ++++++++++++++--------------- man/fitlandr-package.Rd | 52 ++++++------ man/normalize_predict_f.Rd | 34 ++++---- man/pathB_options.Rd | 92 +++++++++++----------- man/path_integral_B.Rd | 100 ++++++++++++------------ man/pipe.Rd | 40 ++++----- man/predict.vectorfield.Rd | 56 ++++++------- man/reorder_output.Rd | 38 ++++----- man/sim_vf_options.Rd | 3 34 files changed, 610 insertions(+), 549 deletions(-)
Title: Categorical Regression Splines
Description: Regression splines that handle a mix of continuous and categorical (discrete) data often encountered in applied settings. I would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://www.sharcnet.ca>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Zhenghua Nie [aut],
Brian D. Ripley [ctb]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between crs versions 0.15-38 dated 2024-09-29 and 0.15-39 dated 2026-01-29
CHANGELOG |only DESCRIPTION | 10 MD5 | 55 +-- R/crssigtest.R | 2 R/kernel.R | 125 ++++++-- R/matrix.combns.R | 80 ++++- R/np.regression.glp.R | 17 - R/util.R | 681 ++++++++++++++++++++++++++++++-------------- R/zzz.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/crs.Rnw | 10 inst/doc/crs.pdf |binary inst/doc/crs_faq.Rnw | 34 +- inst/doc/crs_faq.pdf |binary inst/doc/spline_primer.Rnw | 2 inst/doc/spline_primer.pdf |binary man/clsd.Rd | 2 man/crs.Rd | 2 man/crssigtest.Rd | 2 man/data-Engel95.Rd | 200 ++++++------ man/data-wage1.Rd | 2 man/glp.model.matrix.Rd | 3 man/npglpreg.Rd | 10 man/snomadr.Rd | 2 vignettes/crs.Rnw | 10 vignettes/crs.bib | 2 vignettes/crs_faq.Rnw | 34 +- vignettes/spline_primer.Rnw | 2 29 files changed, 864 insertions(+), 427 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyunhwanjeong@icloud.com>
Diff between CB2 versions 1.3.6 dated 2025-10-01 and 1.3.8 dated 2026-01-29
CB2-1.3.6/CB2/src/Makevars.win |only CB2-1.3.8/CB2/DESCRIPTION | 8 - CB2-1.3.8/CB2/MD5 | 11 +- CB2-1.3.8/CB2/R/utils.R | 44 ++++---- CB2-1.3.8/CB2/README.md | 16 ++- CB2-1.3.8/CB2/inst/doc/cb2-input-handling.html | 26 ++--- CB2-1.3.8/CB2/inst/doc/cb2-tutorial.html | 123 ++++++++++--------------- 7 files changed, 107 insertions(+), 121 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-14 1.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-07 0.3.0
2017-11-30 0.2.0
2017-07-09 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-21 2.0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-04 2.5.2
2021-11-06 2.5.1
2021-11-04 2.5.0
2021-01-15 2.4.0
2020-04-22 2.3.1
2020-03-18 2.3.0
2020-01-10 2.2.0
2019-09-13 2.1.0
2019-06-03 2.0.0
2019-01-25 1.5.7
2018-10-08 1.5.6
2018-07-06 1.5.5
2018-01-08 1.5.4
2017-11-27 1.5.3
2017-02-27 1.5.2
2016-09-28 1.5.1
2015-08-05 1.5.0
2014-06-17 1.4.2
2013-10-24 1.4.1
2013-10-18 1.4
2013-08-17 1.3
2013-06-12 1.2.35
2013-01-26 1.2.34
2013-01-20 1.2.33
2012-12-09 1.2.32
2012-04-03 1.2.30
2012-02-19 1.2.29
2012-01-16 1.2.28
2011-01-03 1.2.27
2010-10-09 1.2.26
2010-10-07 1.2.25
2010-09-15 1.2.24
2010-08-05 1.2.23
2010-05-19 1.2.22
2009-12-07 1.2.21
2009-11-04 1.2.20
2009-10-26 1.2.19
2009-08-08 1.2.17
2009-06-24 1.2.15
2009-03-09 1.2.10
2009-03-06 1.2.9
2009-03-03 1.2.8
2009-01-05 1.2.0
2008-07-05 1.1.9
2008-04-22 1.1.7
2008-04-16 1.1.6
2008-03-12 1.1.5
2007-09-30 1.1.3
2007-06-10 1.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-04 0.2.0
2018-03-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-18 0.1.2
2017-07-22 0.1.0
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplemental functions for estimating and analysing structural equation models including Cross Validated Prediction and Testing (CVPAT, Liengaard et al., 2021 <doi:10.1111/deci.12445>).
Author: Nicholas Patrick Danks [aut, cre],
Soumya Ray [aut, ths]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminrExtras versions 0.2.0 dated 2025-09-03 and 0.9.0 dated 2026-01-29
seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap2.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap3.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap4.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap5.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap6.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap7.R |only seminrExtras-0.2.0/seminrExtras/demo/seminr-workbook-v2-chap8.R |only seminrExtras-0.9.0/seminrExtras/DESCRIPTION | 18 seminrExtras-0.9.0/seminrExtras/MD5 | 42 +- seminrExtras-0.9.0/seminrExtras/NAMESPACE | 1 seminrExtras-0.9.0/seminrExtras/R/feature_congruence.R |only seminrExtras-0.9.0/seminrExtras/R/feature_cvpat.R | 110 +++-- seminrExtras-0.9.0/seminrExtras/README.md |only seminrExtras-0.9.0/seminrExtras/demo/00Index | 14 seminrExtras-0.9.0/seminrExtras/demo/seminr-help-debugging.R | 20 - seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap2.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap3.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap4.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap5.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap6.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap7.R |only seminrExtras-0.9.0/seminrExtras/demo/seminr-primer-v2-chap8.R |only seminrExtras-0.9.0/seminrExtras/inst/doc/SEMinRExtras.R | 23 - seminrExtras-0.9.0/seminrExtras/inst/doc/SEMinRExtras.Rmd | 74 ++- seminrExtras-0.9.0/seminrExtras/inst/doc/SEMinRExtras.html | 190 ++++++---- seminrExtras-0.9.0/seminrExtras/man/assess_cvpat.Rd | 4 seminrExtras-0.9.0/seminrExtras/man/assess_cvpat_compare.Rd | 55 ++ seminrExtras-0.9.0/seminrExtras/man/congruence_test.Rd |only seminrExtras-0.9.0/seminrExtras/vignettes/SEMinRExtras.Rmd | 74 ++- seminrExtras-0.9.0/seminrExtras/vignettes/SEMinR_logo.jpg |only seminrExtras-0.9.0/seminrExtras/vignettes/comp_mod.png |only seminrExtras-0.9.0/seminrExtras/vignettes/est_mod.png |only 32 files changed, 401 insertions(+), 224 deletions(-)
Title: Isotope Pattern, Profile and Centroid Calculation for Mass
Spectrometry
Description: Fast and very memory-efficient calculation of isotope patterns,
subsequent convolution to theoretical envelopes (profiles) plus valley
detection and centroidization or intensoid calculation. Batch processing,
resolution interpolation, wrapper, adduct calculations and molecular
formula parsing.
Loos, M., Gerber, C., Corona, F., Hollender, J., Singer, H. (2015)
<doi:10.1021/acs.analchem.5b00941>.
Author: Martin Loos [aut, cre],
Christian Gerber [aut]
Maintainer: Martin Loos <mloos@envibee.ch>
Diff between enviPat versions 2.6 dated 2022-10-21 and 2.8 dated 2026-01-29
DESCRIPTION | 20 ++++++---- MD5 | 23 ++++++----- NEWS |only R/enviPat.R | 6 ++- R/getR.R | 37 ++++++++---------- R/isopattern.R | 2 - R/isowrap.R | 94 ++++++++++++++++++++++++----------------------- data/resolution_list.rda |binary man/getR.Rd | 2 - man/isopattern.Rd | 2 - man/isowrap.Rd | 8 ++-- man/resolution_list.Rd | 8 +++- src/main.c | 13 ++++-- 13 files changed, 117 insertions(+), 98 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 2025.11 dated 2025-12-09 and 2026.1 dated 2026-01-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/bruceR-stats_1_basic.R | 4 ++++ R/bruceR-stats_2_scale.R | 2 +- man/TTEST.Rd | 3 +++ 6 files changed, 21 insertions(+), 10 deletions(-)
Title: A Package for Displaying Visual Scenes as They May Appear to an
Animal with Lower Acuity
Description: This code provides a simple method for representing a visual scene as it may be seen by an animal with less acute vision. When using (or for more information), please cite the original publication.
Author: Eleanor Caves [aut, cre],
Soenke Johnsen [aut]
Maintainer: Eleanor Caves <eleanor.caves@gmail.com>
Diff between AcuityView versions 0.1 dated 2017-05-09 and 1.1.1 dated 2026-01-29
DESCRIPTION | 25 +- MD5 | 11 - NAMESPACE | 1 R/AcuityView.R | 510 +++++++++++++++++------------------------------- R/fft_matrix_shift.R |only man/AcuityView.Rd | 39 ++- man/fft_matrix_shift.Rd | 17 + 7 files changed, 248 insertions(+), 355 deletions(-)
Title: Spatially and Temporally Varying Coefficient Models Using
Generalized Additive Models
Description: A framework for undertaking space and time varying coefficient models (varying parameter models) using a Generalized Additive Model (GAM) with smooths approach. The framework suggests the need to investigate for the presence and nature of any space-time dependencies in the data. It proposes a workflow that creates and refines an initial space-time GAM and includes tools to create and evaluate multiple model forms. The workflow sequence is to: i) Prepare the data by lengthening it to have a single location and time variables for each observation. ii) Create all possible space and/or time models in which each predictor is specified in different ways in smooths. iii) Evaluate each model via their AIC value and pick the best one. iv) Create the final model. v) Calculate the varying coefficient estimates to quantify how the relationships between the target and predictor variables vary over space, time or space-time. vi) Create maps, time series plots etc. The number of knots used in each sm [...truncated...]
Author: Lex Comber [aut, cre],
Paul Harris [ctb],
Gonzalo Irisarri [ctb],
Chris Brunsdon [ctb]
Maintainer: Lex Comber <a.comber@leeds.ac.uk>
Diff between stgam versions 1.1.0 dated 2025-08-27 and 1.2.0 dated 2026-01-29
stgam-1.1.0/stgam/data/hp_data.rda |only stgam-1.1.0/stgam/data/lb.rda |only stgam-1.1.0/stgam/inst/doc/space-time-gam-intro_rev.R |only stgam-1.1.0/stgam/inst/doc/space-time-gam-intro_rev.Rmd |only stgam-1.1.0/stgam/inst/doc/space-time-gam-intro_rev.html |only stgam-1.1.0/stgam/man/hp_data.Rd |only stgam-1.1.0/stgam/man/lb.Rd |only stgam-1.1.0/stgam/vignettes/space-time-gam-intro_rev.Rmd |only stgam-1.2.0/stgam/DESCRIPTION | 16 stgam-1.2.0/stgam/MD5 | 55 + stgam-1.2.0/stgam/NAMESPACE | 14 stgam-1.2.0/stgam/NEWS.md | 11 stgam-1.2.0/stgam/R/calculate_vcs.R | 91 ++- stgam-1.2.0/stgam/R/data.R | 53 - stgam-1.2.0/stgam/R/effect_size.R |only stgam-1.2.0/stgam/R/evaluate_models.R | 420 +++++++++++---- stgam-1.2.0/stgam/R/gam_model_rank.R | 117 +++- stgam-1.2.0/stgam/README.md | 40 - stgam-1.2.0/stgam/build/vignette.rds |binary stgam-1.2.0/stgam/data/chaco.rda |only stgam-1.2.0/stgam/inst/doc/stgam_intro_chaco.R |only stgam-1.2.0/stgam/inst/doc/stgam_intro_chaco.Rmd |only stgam-1.2.0/stgam/inst/doc/stgam_intro_chaco.html |only stgam-1.2.0/stgam/inst/doc/stgam_vc_models_chaco.R |only stgam-1.2.0/stgam/inst/doc/stgam_vc_models_chaco.Rmd |only stgam-1.2.0/stgam/inst/doc/stgam_vc_models_chaco.html |only stgam-1.2.0/stgam/man/calculate_vcs.Rd | 12 stgam-1.2.0/stgam/man/chaco.Rd |only stgam-1.2.0/stgam/man/effect_size.Rd |only stgam-1.2.0/stgam/man/evaluate_models.Rd | 90 ++- stgam-1.2.0/stgam/man/gam_model_rank.Rd | 29 - stgam-1.2.0/stgam/man/stgam-package.Rd | 3 stgam-1.2.0/stgam/vignettes/appraise_plot_1.png |only stgam-1.2.0/stgam/vignettes/appraise_plot_2.png |only stgam-1.2.0/stgam/vignettes/appraise_plot_3.png |only stgam-1.2.0/stgam/vignettes/appraise_plot_4.png |only stgam-1.2.0/stgam/vignettes/model_summaries.RData |only stgam-1.2.0/stgam/vignettes/stgam_intro_chaco.Rmd |only stgam-1.2.0/stgam/vignettes/stgam_vc_models_chaco.Rmd |only stgam-1.2.0/stgam/vignettes/stvc_mods.RData |binary stgam-1.2.0/stgam/vignettes/vignette.bib | 80 ++ 41 files changed, 764 insertions(+), 267 deletions(-)
Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes [aut, cre],
Dwayne Tally [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.2.9 dated 2025-04-08 and 1.2.10 dated 2026-01-29
DESCRIPTION | 8 MD5 | 18 - R/sysdata.rda |binary build/vignette.rds |binary data/cytoData.rda |binary data/cytobandLocations.rda |binary inst/doc/Gallery.html | 409 ++++++++++++++++-------------------- inst/doc/IntroRCytoGPS.html | 437 +++++++++++++++++---------------------- tests/test101-preclean.R | 8 tests/test101-preclean.Rout.save | 20 + 10 files changed, 416 insertions(+), 484 deletions(-)
Title: Statistical Tests for the Production of Reference Materials
Description: The production of certified reference materials (CRMs) requires
various statistical tests depending on the task and recorded data to ensure
that reported values of CRMs are appropriate.
Often these tests are performed according to the procedures described in
'ISO GUIDE 35:2017'. The 'eCerto' package contains a 'Shiny' app which
provides functionality to load, process, report and backup data recorded
during CRM production and facilitates following the recommended procedures.
It is described in Lisec et al (2023) <doi:10.1007/s00216-023-05099-3> and
can also be accessed online <https://apps.bam.de/shn00/eCerto/> without
package installation.
Author: Jan Lisec [cre, aut] ,
Frederik Kress [ctb]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between eCerto versions 0.8.5 dated 2025-03-28 and 0.8.11 dated 2026-01-29
eCerto-0.8.11/eCerto/DESCRIPTION | 22 eCerto-0.8.11/eCerto/MD5 | 119 ++-- eCerto-0.8.11/eCerto/NAMESPACE | 3 eCerto-0.8.11/eCerto/NEWS.md | 20 eCerto-0.8.11/eCerto/R/app_data.R | 7 eCerto-0.8.11/eCerto/R/app_server.R | 1 eCerto-0.8.11/eCerto/R/app_ui.R | 75 +- eCerto-0.8.11/eCerto/R/app_utils.R | 284 +++++++++ eCerto-0.8.11/eCerto/R/fnc_CertValPlot.R | 2 eCerto-0.8.11/eCerto/R/fnc_plot_lts_data.R | 2 eCerto-0.8.11/eCerto/R/fnc_prepFigH1.R | 3 eCerto-0.8.11/eCerto/R/fnc_prepTabH1.R | 4 eCerto-0.8.11/eCerto/R/fnc_prepTabS1.R | 4 eCerto-0.8.11/eCerto/R/fnc_prepTabV1.R | 6 eCerto-0.8.11/eCerto/R/fnc_read_Vdata.R | 2 eCerto-0.8.11/eCerto/R/fnc_read_drmd_xml.R | 36 + eCerto-0.8.11/eCerto/R/fnc_read_lts_input.R | 10 eCerto-0.8.11/eCerto/R/fnc_read_zenodo.R | 116 +++- eCerto-0.8.11/eCerto/R/fnc_scheffe.test.R | 2 eCerto-0.8.11/eCerto/R/fnc_show_help.R | 11 eCerto-0.8.11/eCerto/R/fnc_steyx.R | 2 eCerto-0.8.11/eCerto/R/fnc_styleTabD1.R | 26 eCerto-0.8.11/eCerto/R/fnc_styleTabD2.R | 38 - eCerto-0.8.11/eCerto/R/fnc_styleTabD3.R | 17 eCerto-0.8.11/eCerto/R/m_ExcelUpload.R | 47 + eCerto-0.8.11/eCerto/R/m_check_stability.R | 12 eCerto-0.8.11/eCerto/R/m_report.R | 96 --- eCerto-0.8.11/eCerto/R/m_stability_arrhenius.R | 2 eCerto-0.8.11/eCerto/R/m_xlsx_range_select.R | 89 --- eCerto-0.8.11/eCerto/R/page_DRMD.R | 76 -- eCerto-0.8.11/eCerto/R/page_LTS.R | 127 +--- eCerto-0.8.11/eCerto/R/page_homogeneity.R | 50 - eCerto-0.8.11/eCerto/R/page_stability.R | 51 - eCerto-0.8.11/eCerto/R/page_validation.R | 157 ++--- eCerto-0.8.11/eCerto/R/reactiveClass.R | 2 eCerto-0.8.11/eCerto/R/run_app.R | 2 eCerto-0.8.11/eCerto/R/statistic_helper.R | 4 eCerto-0.8.11/eCerto/R/utils_drmd.R | 287 ++++++---- eCerto-0.8.11/eCerto/data/BAMlogo_raster.rda |only eCerto-0.8.11/eCerto/inst/app/www/reports/report_styles.ccs |only eCerto-0.8.11/eCerto/inst/app/www/reports/report_vorlage_lts.Rmd | 52 - eCerto-0.8.11/eCerto/inst/app/www/rmd/certification_tests.Rmd | 7 eCerto-0.8.11/eCerto/inst/app/www/rmd/help_start.Rmd | 16 eCerto-0.8.11/eCerto/inst/extdata/drmd |only eCerto-0.8.11/eCerto/man/BAMlogo_raster.Rd |only eCerto-0.8.11/eCerto/man/ldply_base.Rd |only eCerto-0.8.11/eCerto/man/run_app.Rd | 2 eCerto-0.8.11/eCerto/man/steyx.Rd | 2 eCerto-0.8.11/eCerto/tests/testthat.R | 5 eCerto-0.8.11/eCerto/tests/testthat/helper-skip.R |only eCerto-0.8.11/eCerto/tests/testthat/test-app_ui.R |only eCerto-0.8.11/eCerto/tests/testthat/test-app_utils.R | 29 + eCerto-0.8.11/eCerto/tests/testthat/test-fnc_CertValPlot.R | 2 eCerto-0.8.11/eCerto/tests/testthat/test-fnc_plot_lts_data.R | 5 eCerto-0.8.11/eCerto/tests/testthat/test-fnc_prepFigV2.R | 2 eCerto-0.8.11/eCerto/tests/testthat/test-fnc_prepFigV3.R | 2 eCerto-0.8.11/eCerto/tests/testthat/test-fnc_read_zenodo.R | 16 eCerto-0.8.11/eCerto/tests/testthat/test-fnc_styleTabDx.R |only eCerto-0.8.11/eCerto/tests/testthat/test-page_DRMD.R |only eCerto-0.8.11/eCerto/tests/testthat/test-page_LTS.R |only eCerto-0.8.11/eCerto/tests/testthat/test-page_validation.R |only eCerto-0.8.11/eCerto/tests/testthat/test-utils_drmd.R |only eCerto-0.8.11/eCerto/tests/testthat/test-validation.R | 4 eCerto-0.8.5/eCerto/R/fnc_xml2df.R |only eCerto-0.8.5/eCerto/tests/testthat/test-page_start.R |only eCerto-0.8.5/eCerto/tests/testthat/test-run_app.R |only 66 files changed, 1078 insertions(+), 880 deletions(-)
Title: Access and Analyse Data from the 'CVD Prevent' API
Description: Provides an R interface to the 'CVD Prevent' application
programming interface (API), allowing users to retrieve and analyse
cardiovascular disease prevention data from primary care records
across England. The Cardiovascular Disease Prevention Audit
(CVDPREVENT) automatically extracts routinely held GP health data to
support national reporting and improvement initiatives. See the API
documentation for details:
<https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Author: Craig Parylo [aut, cre, cph] ,
Cardiovascular Disease Prevention Audit [ant]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between cvdprevent versions 0.2.4 dated 2025-11-11 and 0.2.5 dated 2026-01-29
DESCRIPTION | 10 MD5 | 24 NEWS.md | 13 R/cvd_api_functions.R | 2 R/cvd_api_helpers.R | 17 R/scratchpad.R | 24 R/utils.R | 3 README.md | 8 inst/doc/using_cvdprevent.R | 48 inst/doc/using_cvdprevent.Rmd | 48 inst/doc/using_cvdprevent.html | 4331 ++++++++++++++++++++--------------------- man/cvd_area_system_level.Rd | 2 vignettes/using_cvdprevent.Rmd | 48 13 files changed, 2339 insertions(+), 2239 deletions(-)
Title: Make, Update, and Query Binary Causal Models
Description: Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality (<DOI:10.1017/CBO9780511803161>).
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut] ,
Till Tietz [aut, cre] ,
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut] ,
Julio Solis [ctb],
Georgiy Syunyaev [aut] ,
Moritz Marbach [ctb]
Maintainer: Till Tietz <ttietz2014@gmail.com>
Diff between CausalQueries versions 1.4.4 dated 2025-12-20 and 1.4.5 dated 2026-01-29
DESCRIPTION | 8 MD5 | 12 NEWS.md | 7 inst/stan/simplexes.stan | 71 ++- src/stanExports_simplexes.cc | 34 - src/stanExports_simplexes.h | 860 +++++++++++++++++++++---------------- tests/testthat/test_update_model.R | 15 7 files changed, 598 insertions(+), 409 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization of several non-linear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, Sample Survey Methods And Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coef [...truncated...]
Author: Juris Breidaks [aut],
Martins Liberts [aut],
Jelena Voronova [cre],
Santa Ivanova [aut],
Aleksis Jursevskis [ctb],
Anthony Damico [ctb],
Liliana Roze [ctb],
Central Statistical Bureau of Latvia [cph, fnd]
Maintainer: Jelena Voronova <jelena.voronova@csp.gov.lv>
Diff between vardpoor versions 0.20.1 dated 2020-11-30 and 0.21.0 dated 2026-01-29
vardpoor-0.20.1/vardpoor/LICENSE |only vardpoor-0.21.0/vardpoor/DESCRIPTION | 29 vardpoor-0.21.0/vardpoor/MD5 | 65 vardpoor-0.21.0/vardpoor/NEWS.md | 7 vardpoor-0.21.0/vardpoor/R/domain.R | 2 vardpoor-0.21.0/vardpoor/R/lingini2.R | 2 vardpoor-0.21.0/vardpoor/R/lingpg.R | 2 vardpoor-0.21.0/vardpoor/R/var_srs.R | 4 vardpoor-0.21.0/vardpoor/R/vardannual.R | 333 +- vardpoor-0.21.0/vardpoor/R/vardchanges.R | 6 vardpoor-0.21.0/vardpoor/R/vardchangespoor.R | 6 vardpoor-0.21.0/vardpoor/R/vardchangstrs.R | 78 vardpoor-0.21.0/vardpoor/R/vardcros.R | 1232 +++++----- vardpoor-0.21.0/vardpoor/R/vardcrospoor.R | 84 vardpoor-0.21.0/vardpoor/R/vardom.R | 6 vardpoor-0.21.0/vardpoor/R/vardom_othstr.R | 2 vardpoor-0.21.0/vardpoor/R/vardomh.R | 6 vardpoor-0.21.0/vardpoor/R/variance_est.R | 6 vardpoor-0.21.0/vardpoor/R/varpoord.R | 10 vardpoor-0.21.0/vardpoor/build |only vardpoor-0.21.0/vardpoor/man/lingini2.Rd | 2 vardpoor-0.21.0/vardpoor/man/lingpg.Rd | 2 vardpoor-0.21.0/vardpoor/man/var_srs.Rd | 4 vardpoor-0.21.0/vardpoor/man/vardannual.Rd | 330 +- vardpoor-0.21.0/vardpoor/man/vardchanges.Rd | 6 vardpoor-0.21.0/vardpoor/man/vardchangespoor.Rd | 6 vardpoor-0.21.0/vardpoor/man/vardchangstrs.Rd | 25 vardpoor-0.21.0/vardpoor/man/vardcros.Rd | 47 vardpoor-0.21.0/vardpoor/man/vardcrospoor.Rd | 86 vardpoor-0.21.0/vardpoor/man/vardom.Rd | 6 vardpoor-0.21.0/vardpoor/man/vardom_othstr.Rd | 4 vardpoor-0.21.0/vardpoor/man/vardomh.Rd | 6 vardpoor-0.21.0/vardpoor/man/variance_est.Rd | 6 vardpoor-0.21.0/vardpoor/man/varpoord.Rd | 12 vardpoor-0.21.0/vardpoor/tests/testthat/test_vardom_vardomh_2levels.R |only 35 files changed, 1365 insertions(+), 1057 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible iterators implemented in
C++ for solving problems in combinatorics and computational mathematics.
Handles various combinatorial objects including combinations, permutations,
integer partitions and compositions, Cartesian products, unordered
Cartesian products, and partition of groups. Utilizes the RMatrix class
from 'RcppParallel' for thread safety. The combination and permutation
functions contain constraint parameters that allow for generation of all
results of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is between two bounds). Capable of
ranking/unranking combinatorial objects efficiently (e.g. retrieve only the
nth lexicographical result) which sets up nicely for parallelization as
well as random sampling. Gmp support permits exploration where the total
number of results is large (e.g. comboSample(10000, 500, n = 4)).
Additionally, there are several high performance number theoretic
functions that are [...truncated...]
Author: Joseph Wood [aut, cre]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.9.3 dated 2025-02-03 and 2.9.5 dated 2026-01-29
DESCRIPTION | 9 +++--- MD5 | 45 ++++++++++++++++---------------- NEWS.md | 19 ++++++++++++- README.md | 4 +- build/vignette.rds |binary inst/CITATION |only inst/NEWS.Rd | 25 ++++++++++++++++- inst/doc/CombPermConstraints.html | 5 ++- inst/doc/CombinatorialSampling.html | 5 ++- inst/doc/CombinatoricsIterators.html | 5 ++- inst/doc/ComputationalMathematics.html | 5 ++- inst/doc/GeneralCombinatorics.Rmd | 4 +- inst/doc/GeneralCombinatorics.html | 9 +++--- inst/doc/HighPerformanceBenchmarks.html | 5 ++- inst/doc/OtherCombinatorics.Rmd | 2 - inst/doc/OtherCombinatorics.html | 7 ++-- inst/doc/SubsetSum.html | 5 ++- man/combinatoricsGeneral.Rd | 2 - man/comboGroups.Rd | 2 - man/stdThreadMax.Rd | 2 - src/SetUpUtils.cpp | 11 +++++++ tests/testthat/testErrors.R | 3 +- vignettes/GeneralCombinatorics.Rmd | 4 +- vignettes/OtherCombinatorics.Rmd | 2 - 24 files changed, 118 insertions(+), 62 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.7.3 dated 2025-03-30 and 1.7.4 dated 2026-01-29
ChangeLog | 6 ++- DESCRIPTION | 17 ++++------ MD5 | 36 ++++++++++----------- NAMESPACE | 4 +- NEWS | 4 ++ R/GWASinspector.R | 2 - R/aaa.R | 2 - R/fileFunctions.R | 6 ++- R/headerRelatedFunctions.R | 7 +++- R/loggerFunctions.R | 10 ++--- R/manhattanPlotFunction.R | 8 ++-- R/studyFunctions.R | 7 +++- R/uploadInputFile.R | 14 +++++++- R/variantModifierFunctions.R | 6 ++- inst/doc/GWASinspector.R | 8 ---- inst/doc/GWASinspector.Rmd | 21 ++---------- inst/doc/GWASinspector.html | 73 +++++++++++++++++++------------------------ man/GWASinspector.Rd | 2 - vignettes/GWASinspector.Rmd | 21 ++---------- 19 files changed, 126 insertions(+), 128 deletions(-)
Title: Visualize the Effect of a Continuous Variable on a Time-to-Event
Outcome
Description: Graphically display the (causal) effect of a continuous variable on a time-to-event outcome
using multiple different types of plots based on g-computation. Those functions
include, among others, survival area plots, survival contour plots, survival quantile plots and
3D surface plots. Due to the use of g-computation, all plot allow confounder-adjustment naturally.
For details, see Robin Denz, Nina Timmesfeld (2023) <doi:10.1097/EDE.0000000000001630>.
Author: Robin Denz [aut, cre]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between contsurvplot versions 0.2.2 dated 2025-07-24 and 0.2.3 dated 2026-01-29
DESCRIPTION | 6 MD5 | 90 +++--- NEWS.md | 15 + R/curve_cont_auc.r | 132 +++++++--- R/plot_surv_3Dsurface.r | 7 R/plot_surv_area.r | 6 R/plot_surv_at_t.r | 9 R/plot_surv_lines.r | 5 R/plot_surv_quantiles.r | 8 R/plot_surv_rmst.r | 79 +++-- R/plot_surv_rmtl.r | 81 +++--- inst/doc/introduction.html | 2 man/plot_surv_3Dsurface.Rd | 10 man/plot_surv_quantiles.Rd | 2 man/plot_surv_rmst.Rd | 19 + man/plot_surv_rmtl.Rd | 24 + tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/plot_surv_area/plot-discrete-bins.svg | 16 - tests/testthat/_snaps/plot_surv_area/plot-discrete-round.svg | 16 - tests/testthat/_snaps/plot_surv_area/plot-lots-of-stuff.svg | 118 ++++---- tests/testthat/_snaps/plot_surv_area/plot-sep-lines.svg | 40 +-- tests/testthat/_snaps/plot_surv_area/plot-with-kaplan-meier.svg | 40 +-- tests/testthat/_snaps/plot_surv_at_t/plot-lots-of-stuff.svg | 32 +- tests/testthat/_snaps/plot_surv_at_t/plot-with-ci-multiple-t.svg | 4 tests/testthat/_snaps/plot_surv_contour/plot-at-t.svg | 16 - tests/testthat/_snaps/plot_surv_contour/plot-change-horizon.svg | 20 - tests/testthat/_snaps/plot_surv_contour/plot-cif.svg | 20 - tests/testthat/_snaps/plot_surv_contour/plot-custom-colors.svg | 10 tests/testthat/_snaps/plot_surv_contour/plot-defaults.svg | 20 - tests/testthat/_snaps/plot_surv_contour/plot-lots-of-stuff.svg | 56 ++-- tests/testthat/_snaps/plot_surv_contour/plot-panel-border-axis-dist.svg | 20 - tests/testthat/_snaps/plot_surv_contour/plot-with-group.svg | 20 - tests/testthat/_snaps/plot_surv_heatmap/plot-lots-of-stuff.svg | 36 +- tests/testthat/_snaps/plot_surv_lines/plot-kaplan-meier.svg | 6 tests/testthat/_snaps/plot_surv_lines/plot-lots-of-stuff.svg | 36 +- tests/testthat/_snaps/plot_surv_quantiles/plot-lots-of-stuff.svg | 36 +- tests/testthat/_snaps/plot_surv_rmst/plot-lots-of-stuff.svg | 24 - tests/testthat/_snaps/plot_surv_rmst/plot-multiple-tau-ci.svg |only tests/testthat/_snaps/plot_surv_rmst/plot-multiple-tau.svg |only tests/testthat/_snaps/plot_surv_rmst/plot-with-ci-group.svg |only tests/testthat/_snaps/plot_surv_rmst/plot-with-ci.svg |only tests/testthat/_snaps/plot_surv_rmtl/plot-lots-of-stuff.svg | 36 +- tests/testthat/_snaps/plot_surv_rmtl/plot-multiple-tau-ci.svg |only tests/testthat/_snaps/plot_surv_rmtl/plot-multiple-tau.svg |only tests/testthat/_snaps/plot_surv_rmtl/plot-with-ci.svg |only tests/testthat/_snaps/plot_surv_rmtl/plot-with-group-ci.svg |only tests/testthat/test_plot_surv_3Dsurface.r | 8 tests/testthat/test_plot_surv_lines.r | 2 tests/testthat/test_plot_surv_rmst.r | 33 ++ tests/testthat/test_plot_surv_rmtl.r | 33 ++ 50 files changed, 720 insertions(+), 473 deletions(-)
Title: Continuous Optimization using Memetic Algorithms with Local
Search Chains (MA-LS-Chains)
Description: An implementation of an algorithm family for continuous
optimization called memetic algorithms with local search chains
(MA-LS-Chains), as proposed in Molina et al. (2010) <doi:10.1162/evco.2010.18.1.18102> and Molina et al. (2011) <doi:10.1007/s00500-010-0647-2>. Rmalschains is further discussed in Bergmeir et al. (2016) <doi:10.18637/jss.v075.i04>. Memetic algorithms are hybridizations of genetic
algorithms with local search methods. They are especially suited
for continuous optimization.
Author: Christoph Bergmeir [aut, cre, cph],
Jose M. Benitez [ths],
Daniel Molina [aut, cph],
Robert Davies [ctb, cph] ,
Dirk Eddelbuettel [ctb, cph] ,
Nikolaus Hansen [ctb, cph] ,
Richard J. Wagner [ctb, cph]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between Rmalschains versions 0.2-10 dated 2023-05-24 and 0.2-11 dated 2026-01-29
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/Makevars | 3 ++- src/Makevars.win | 2 +- src/simplex.cc | 7 ++++--- 6 files changed, 21 insertions(+), 14 deletions(-)
Title: Explore Phylogenetic Signals Using Distance-Based Methods
Description: A unified method, called M statistic, is provided for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) <doi:10.1046/j.1420-9101.2002.00472.x> provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic. The M statistic implemented in this package is based on the methodology described in Yao and Yuan (2025) <doi:10.1002/ece3.71106>. [...truncated...]
Author: Liang Yao [aut, cre],
Ye Yuan [aut]
Maintainer: Liang Yao <yaoliang986@ahnu.edu.cn>
Diff between phylosignalDB versions 0.2.2 dated 2025-01-16 and 0.4.2 dated 2026-01-29
DESCRIPTION | 18 +++++++++--------- MD5 | 19 ++++++++++--------- NEWS.md | 9 +++++++++ R/M_statistic.R | 23 ++++++++++++++++------- README.md | 4 +++- build/partial.rdb |binary inst |only man/M_rand_perm.Rd | 3 +++ man/M_stat.Rd | 3 +++ man/phylosignalDB-package.Rd | 6 +++--- man/phylosignal_M.Rd | 3 +++ 11 files changed, 59 insertions(+), 29 deletions(-)
Title: Optimal Binning and Weight of Evidence Framework for Modeling
Description: High-performance implementation of 36 optimal binning algorithms
(16 categorical, 20 numerical) for Weight of Evidence ('WoE') transformation,
credit scoring, and risk modeling. Includes advanced methods such as Mixed
Integer Linear Programming ('MILP'), Genetic Algorithms, Simulated Annealing,
and Monotonic Regression. Features automatic method selection based on
Information Value ('IV') maximization, strict monotonicity enforcement, and
efficient handling of large datasets via 'Rcpp'. Fully integrated with the
'tidymodels' ecosystem for building robust machine learning pipelines.
Based on methods described in Siddiqi (2006) <doi:10.1002/9781119201731>
and Navas-Palencia (2020) <doi:10.48550/arXiv.2001.08025>.
Author: Jose Evandeilton Lopes [aut, cre, cph]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between OptimalBinningWoE versions 1.0.3 dated 2026-01-23 and 1.0.8 dated 2026-01-29
DESCRIPTION | 8 MD5 | 41 NEWS.md | 219 + R/obwoe.R | 4696 +++++++++++++++++----------------- R/step_obwoe.R | 3596 +++++++++++++------------- README.md | 1198 ++++++-- inst/doc/introduction.R | 122 inst/doc/introduction.Rmd | 1456 +++++----- inst/doc/introduction.html | 222 - src/Makevars | 39 src/Makevars.win | 39 src/OBC_GMB_v5.cpp | 2 src/OBC_IVB_v5.cpp | 719 ++--- src/OBC_JEDI_v5.cpp | 603 ++-- src/OBC_MBA_v5.cpp | 651 ++-- src/OBC_Sketch_v5.cpp | 895 ++---- src/OBN_CM_v5.cpp | 1070 ++++--- src/OBN_MOB_v5.cpp | 8 src/OBN_UBSD_v5.cpp | 6 src/common/cutpoints_validator.h |only tests/testthat/test-categorical-all.R | 26 vignettes/introduction.Rmd | 1456 +++++----- 22 files changed, 8919 insertions(+), 8153 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-12 1.0.1
2020-09-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-14 0.1.7
2020-08-10 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-20 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-29 2025.7.29
2023-03-24 2023.3.8
2021-05-13 2021.5.4
2020-03-08 2020.3.4
2019-09-18 2019.9.18
2019-09-11 2019.9.11
2019-07-11 2019.7.9
2017-03-02 2017.03
2015-06-08 2015.5
2013-07-31 2013.8
2012-08-03 0.7.9
2011-10-08 0.7.8
2011-09-23 0.7.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-02 9.7
2024-02-03 9.4
2023-11-28 9.3
2023-09-02 9.1
2023-04-07 8.9
2023-01-26 8.6
2022-11-15 8.5
2022-02-07 8.4
2021-11-09 8.2
2020-03-02 8.0
2019-01-08 7.1
2019-01-06 7.0
2018-12-06 6.7
2018-08-02 6.1
2017-05-05 6.0
2017-04-18 5.9
2017-01-13 5.7
2016-05-07 5.3
2016-05-03 5.2
2015-10-22 5.0
2015-09-16 4.9
2015-08-18 4.7
2015-06-29 4.5
2015-06-10 4.2
2015-05-21 3.9
2015-05-16 3.7
2014-12-08 3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-19 0.3.0
2021-01-22 0.2.0
2020-08-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-15 0.1.15
2025-04-27 0.1.12
2025-04-19 0.1.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-02 0.2.0
2022-11-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-12-21 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-07 1.2.5
2022-03-25 1.2.4
2022-03-09 1.2.3
2021-10-19 1.2.2
2021-02-28 1.2.1
2020-12-16 1.2.0
2018-11-15 1.1.0
2018-01-17 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-27 0.1
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.5-0 dated 2025-11-28 and 3.6-1 dated 2026-01-29
DESCRIPTION | 16 MD5 | 152 ++- NAMESPACE | 12 NEWS | 108 ++ R/Gcom.R | 6 R/Kcom.R | 6 R/aaaa.R | 2 R/as.tess.rppm.R |only R/augment.msr.R | 8 R/cdftest.R | 2 R/dppm.R | 4 R/eem.R | 2 R/effectfun.R | 108 ++ R/evidenceslrm.R | 2 R/fiksel.R | 6 R/kppm.R | 1655 +---------------------------------------- R/kppmCLadap.R |only R/kppmComLik.R |only R/kppmMinCon.R |only R/kppmPalmLik.R |only R/kppmWaagLik.R |only R/leverage.R | 24 R/lurking.R | 99 +- R/lurkmppm.R | 15 R/makepspace.R | 5 R/measures.R | 16 R/mincontrast.R | 19 R/mpl.R | 75 + R/objsurf.R | 8 R/penttinen.R | 56 + R/poissonfitsbetter.R | 3 R/predict.ppm.R | 100 +- R/profilepl.R | 201 +++- R/psst.R | 6 R/psstA.R | 6 R/psstG.R | 6 R/qqplotppm.R | 2 R/resid4plot.R | 29 R/rhohat.R | 2 R/rppm.R | 11 R/simulatekppm.R | 2 R/strauss.R | 8 R/strausshard.R | 7 R/summary.dppm.R | 11 R/summary.kppm.R | 22 R/summary.mppm.R | 2 R/summary.ppm.R | 8 R/triplets.R | 10 R/update.ppm.R | 50 - inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/Gcom.Rd | 6 man/Kcom.Rd | 6 man/as.fv.kppm.Rd | 23 man/as.tess.rppm.Rd |only man/clusterstrength.Rd |only man/dppm.Rd | 33 man/effectfun.Rd | 8 man/kppm.Rd | 165 ++-- man/logLik.kppm.Rd | 14 man/lurking.Rd | 64 - man/macros/defns.Rd | 2 man/panysib.Rd | 25 man/persist.Rd |only man/profilepl.Rd | 71 + man/psib.Rd | 5 man/psst.Rd | 6 man/psstA.Rd | 6 man/psstG.Rd | 6 man/repul.Rd | 3 man/rppm.Rd | 33 man/spatstat.model-internal.Rd | 14 man/spatstat.model-package.Rd | 2 src/Epent.c |only src/init.c | 1 src/proto.h | 1 tests/testsD.R | 28 tests/testsEtoF.R | 80 + tests/testsK.R | 32 tests/testsP2.R | 22 tests/testsS.R | 48 + tests/testsUtoZ.R | 17 82 files changed, 1465 insertions(+), 2152 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.4.4 dated 2025-09-18 and 3.4.5 dated 2026-01-29
DESCRIPTION | 8 - MD5 | 54 ++++----- NEWS | 5 R/labkey.defaults.R | 29 +++++ R/labkey.deleteRows.R | 11 -- R/labkey.domain.R | 28 +---- R/labkey.executeSql.R | 5 R/labkey.experiment.R | 15 -- R/labkey.getFolders.R | 30 +++-- R/labkey.getQueryInfo.R | 16 -- R/labkey.getQueryLists.R | 18 +-- R/labkey.getSchemas.R | 6 - R/labkey.importRows.R | 5 R/labkey.insertRows.R | 5 R/labkey.moduleProperty.R | 10 - R/labkey.moveRows.R | 5 R/labkey.pipeline.R | 20 --- R/labkey.provenance.R | 15 -- R/labkey.query.import.R | 5 R/labkey.rstudio.R | 15 -- R/labkey.saveBatch.R | 7 - R/labkey.security.R | 27 +--- R/labkey.selectRows.R | 164 +++++++++++++++++------------ R/labkey.storage.R | 15 -- R/labkey.updateRows.R | 6 - R/makeFilter.R | 252 ++++++++++++++++++++++++---------------------- man/Rlabkey-package.Rd | 4 man/makeFilter.Rd | 11 +- 28 files changed, 382 insertions(+), 409 deletions(-)
Title: Utilities for Working with Google APIs
Description: Provides utilities for working with Google APIs
<https://developers.google.com/apis-explorer>. This includes
functions and classes for handling common credential types and for
preparing, executing, and processing HTTP requests.
Author: Jennifer Bryan [aut, cre] ,
Craig Citro [aut],
Hadley Wickham [aut] ,
Google Inc [cph],
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between gargle versions 1.6.0 dated 2025-09-03 and 1.6.1 dated 2026-01-29
DESCRIPTION | 10 - MD5 | 105 +++++++------- NAMESPACE | 2 NEWS.md | 8 - R/AuthState-class.R | 4 R/aaa.R | 17 ++ R/credentials_app_default.R | 6 R/credentials_gce.R | 10 - R/request_retry.R | 4 R/response_process.R | 20 +- README.md | 6 build/vignette.rds |binary inst/discovery-doc-ingest/discover-discovery.R | 60 ++++---- inst/discovery-doc-ingest/drive-example.R | 6 inst/discovery-doc-ingest/ingest-functions.R | 14 - inst/doc/auth-from-web.R | 10 - inst/doc/auth-from-web.Rmd | 28 ++- inst/doc/auth-from-web.html | 16 -- inst/doc/gargle-auth-in-client-package.R | 26 +-- inst/doc/gargle-auth-in-client-package.Rmd | 39 +++-- inst/doc/get-api-credentials.R | 12 - inst/doc/get-api-credentials.Rmd | 16 +- inst/doc/get-api-credentials.html | 4 inst/doc/how-gargle-gets-tokens.R | 32 ++-- inst/doc/how-gargle-gets-tokens.Rmd | 54 ++++--- inst/doc/how-gargle-gets-tokens.html | 12 - inst/doc/non-interactive-auth.R | 6 inst/doc/non-interactive-auth.Rmd | 86 ++++++----- inst/doc/non-interactive-auth.html | 32 ++-- inst/doc/oauth-client-not-app.R | 10 - inst/doc/oauth-client-not-app.Rmd | 15 +- inst/doc/oauth-client-not-app.html | 4 inst/doc/request-helper-functions.R | 18 +- inst/doc/request-helper-functions.Rmd | 33 +++- inst/doc/request-helper-functions.html | 182 ++++++++++++------------- inst/doc/troubleshooting.R | 16 +- inst/doc/troubleshooting.Rmd | 39 +++-- inst/doc/troubleshooting.html | 21 +- man/AuthState-class.Rd | 4 man/credentials_app_default.Rd | 6 man/credentials_gce.Rd | 10 - man/gargle_last_response.Rd |only man/request_retry.Rd | 4 man/response_process.Rd | 14 + tests/testthat/test-aaa.R | 38 +++++ tests/testthat/test-response_process.R | 36 ++++ vignettes/auth-from-web.Rmd | 28 ++- vignettes/gargle-auth-in-client-package.Rmd | 39 +++-- vignettes/get-api-credentials.Rmd | 16 +- vignettes/how-gargle-gets-tokens.Rmd | 54 ++++--- vignettes/non-interactive-auth.Rmd | 86 ++++++----- vignettes/oauth-client-not-app.Rmd | 15 +- vignettes/request-helper-functions.Rmd | 33 +++- vignettes/troubleshooting.Rmd | 39 +++-- 54 files changed, 828 insertions(+), 577 deletions(-)
Title: Bitmap Tools
Description: Provides functions for creating, modifying, and displaying bitmaps including printing them in the terminal. There is a special emphasis on monochrome bitmap fonts and their glyphs as well as colored pixel art/sprites. Provides native read/write support for the 'hex' and 'yaff' bitmap font formats and if 'monobit' <https://github.com/robhagemans/monobit> is installed can also read/write several additional bitmap font formats.
Author: Trevor L. Davis [aut, cre] ,
Frederic Cambus [tyg] ,
Markus Kuhn [tyg] ,
josehzz [art]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between bittermelon versions 2.1.1 dated 2025-01-16 and 2.2.1 dated 2026-01-29
DESCRIPTION | 16 MD5 | 187 ++++----- NAMESPACE | 8 NEWS.md | 15 R/Extract.bm_matrix.R | 27 - R/Ops.bm_object.R | 116 +++-- R/Summary.bm_list.R | 15 R/as.data.frame.bm_matrix.R | 64 +-- R/as.matrix.bm_matrix.R | 65 +-- R/as_bm_bitmap.R | 587 +++++++++++++++++------------ R/as_bm_list.R | 44 +- R/as_bm_pixmap.R | 187 ++++----- R/bind.R | 104 ++--- R/bm_bitmap.R | 2 R/bm_call.R | 9 R/bm_clamp.R | 107 ++--- R/bm_compose.R | 40 +- R/bm_compress.R | 201 +++++----- R/bm_distort.R | 107 ++--- R/bm_edit.R | 14 R/bm_expand.R | 110 ++--- R/bm_extend.R | 571 +++++++++++++++++----------- R/bm_extract.R |only R/bm_flip.R | 98 ++-- R/bm_font.R | 56 +- R/bm_gray.R | 27 - R/bm_invert.R | 35 - R/bm_list.R | 33 - R/bm_mask.R | 320 +++++++++------- R/bm_options.R | 46 +- R/bm_outline.R | 68 +-- R/bm_overlay.R | 245 +++++++----- R/bm_pad.R | 327 +++++++++++----- R/bm_padding_lengths.R | 64 +-- R/bm_pixel_picker.R | 175 ++++---- R/bm_pixmap.R | 2 R/bm_print.R | 32 - R/bm_replace.R | 73 +-- R/bm_resize.R | 157 ++++--- R/bm_rotate.R | 50 +- R/bm_shadow.R | 616 ++++++++++++++++++++----------- R/bm_shift.R | 142 ++++--- R/bm_trim.R | 270 ++++++++----- R/combine.R | 170 ++++---- R/farming_crops_16x16.R | 134 ++++-- R/hex.R | 250 ++++++------ R/lengths.R | 46 +- R/monobit.R | 59 +- R/plot.bm_matrix.R | 105 ++--- R/print.bm_bitmap.R | 229 ++++++----- R/print.bm_pixmap.R | 369 ++++++++++-------- R/sprites.R | 1 R/ucp.R | 46 +- R/utils-color.R | 102 ++--- R/utils-unicode.R | 12 R/yaff.R | 359 +++++++++--------- README.md | 162 ++++---- build/vignette.rds |binary inst/doc/bittermelon.html | 197 +++++---- man/bm_compress.Rd | 2 man/bm_distort.Rd | 2 man/bm_extract.Rd |only man/bm_mask.Rd | 2 man/bm_options.Rd | 2 man/bm_print.Rd | 6 man/is_supported_bitmap.Rd |only man/print.bm_pixmap.Rd | 2 tests/testthat/test-bm_bitmap.R | 144 +++---- tests/testthat/test-bm_clamp.R | 113 ++--- tests/testthat/test-bm_distort.R | 165 ++++---- tests/testthat/test-bm_expand.R | 57 +- tests/testthat/test-bm_extend.R | 323 +++++++++------- tests/testthat/test-bm_extract.R |only tests/testthat/test-bm_flip.R | 86 ++-- tests/testthat/test-bm_font.R | 17 tests/testthat/test-bm_gray.R | 42 +- tests/testthat/test-bm_invert.R | 41 +- tests/testthat/test-bm_list.R | 285 +++++++------- tests/testthat/test-bm_mask.R | 83 ++-- tests/testthat/test-bm_options.R | 7 tests/testthat/test-bm_outline.R | 52 +- tests/testthat/test-bm_overlay.R | 200 +++++----- tests/testthat/test-bm_pad.R | 107 ++--- tests/testthat/test-bm_pixmap.R | 134 +++--- tests/testthat/test-bm_replace.R | 49 +- tests/testthat/test-bm_shift.R | 47 +- tests/testthat/test-bm_trim.R | 345 ++++++++--------- tests/testthat/test-bm_widths.R | 40 +- tests/testthat/test-gridpattern.R | 33 - tests/testthat/test-hex.R | 75 +-- tests/testthat/test-monobit.R | 28 - tests/testthat/test-plot.R | 74 ++- tests/testthat/test-print.bm_bitmap.R | 116 +++-- tests/testthat/test-print.bm_pixmap.R | 358 ++++++++---------- tests/testthat/test-unicode.R | 26 - tests/testthat/test-yaff.R | 43 +- tests/testthat/txt/bm_extract_pixmap.txt |only 97 files changed, 6021 insertions(+), 4758 deletions(-)
Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js',
a re-usable easy interface JavaScript chart library, based on D3 v4+.
Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts.
All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
NAVER Corp [cph] ,
Mike Bostock [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between billboarder versions 0.5.0 dated 2024-09-09 and 0.5.1 dated 2026-01-29
DESCRIPTION | 6 MD5 | 44 NEWS.md | 273 - R/billboarder-shiny.R | 2 R/billboarder.R | 184 build/vignette.rds |binary inst/doc/billboarder-intro.R | 184 inst/doc/billboarder-intro.html | 3969 ++++++++-------- inst/doc/billboarder-mapping.R | 120 inst/doc/billboarder-mapping.html | 3843 +++++++-------- inst/doc/billboarder-options.R | 330 - inst/doc/billboarder-options.html | 4103 ++++++++-------- inst/doc/billboarder.R | 761 +-- inst/doc/billboarder.Rmd | 1043 ++-- inst/doc/billboarder.html | 4590 +++++++++---------- inst/htmlwidgets/lib/billboard/billboard.min.css | 18 inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js | 118 inst/htmlwidgets/lib/billboard/datalab.min.css | 18 inst/htmlwidgets/lib/billboard/graph.min.css | 18 inst/htmlwidgets/lib/billboard/insight.min.css | 18 inst/htmlwidgets/lib/billboard/modern.min.css | 18 man/bb_proxy_focus.Rd | 2 vignettes/billboarder.Rmd | 1043 ++-- 23 files changed, 10398 insertions(+), 10307 deletions(-)
Title: Computation of the WHO Child Growth Standards
Description: Provides WHO Child Growth Standards (z-scores) with
confidence intervals and standard errors around the
prevalence estimates, taking into account complex sample designs.
More information on the methods is
available online:
<https://www.who.int/tools/child-growth-standards>.
Author: Dirk Schumacher [aut],
Elaine Borghi [ctb, cre],
Jonathan Polonsky [ctb],
Giovanna Gatica Dominguez [ctb],
World Health Organization [cph]
Maintainer: Elaine Borghi <nfsdata@who.int>
Diff between anthro versions 1.0.1 dated 2023-09-17 and 1.1.0 dated 2026-01-29
DESCRIPTION | 30 - MD5 | 59 +- NAMESPACE | 19 NEWS.md | 28 R/assertions.R | 30 - R/prevalence-compute-api.R |only R/prevalence-hybrid-sw.R |only R/prevalence-simple.R |only R/prevalence-survey.R |only R/prevalence.R | 648 ++++++++++++---------- R/sysdata.rda |binary R/utils.R | 14 R/z-score-arm-circumference-for-age.R | 10 R/z-score-bmi-for-age.R | 14 R/z-score-head-circumference-for-age.R | 10 R/z-score-helper.R | 52 + R/z-score-length-for-age.R | 10 R/z-score-subscapular-skinfold-for-age.R | 10 R/z-score-triceps-skinfold-for-age.R | 10 R/z-score-weight-for-age.R | 22 R/z-score-weight-for-lenhei.R | 87 +- R/z-score.R | 65 +- README.md | 20 man/anthro-package.Rd | 13 man/anthro_prevalence.Rd | 17 man/anthro_zscores.Rd | 17 tests/testthat/test-age-groups.R | 8 tests/testthat/test-prevalence-simple-estimates.R |only tests/testthat/test-prevalence.R | 104 ++- tests/testthat/test-zscore-bmi-for-age.R | 76 +- tests/testthat/test-zscore-length-for-age.R | 6 tests/testthat/test-zscore-weight-for-age.R | 34 - tests/testthat/test-zscores.R | 103 ++- 33 files changed, 981 insertions(+), 535 deletions(-)
Title: Spot R Functions & Packages
Description: Helpers for parsing out the R functions
and packages used in R scripts and notebooks.
Author: Bryan Shalloway [aut, cre]
Maintainer: Bryan Shalloway <brshallodev@gmail.com>
Diff between funspotr versions 0.0.4 dated 2023-11-21 and 0.0.5 dated 2026-01-29
funspotr-0.0.4/funspotr/man/list_files_github_gists.Rd |only funspotr-0.0.5/funspotr/DESCRIPTION | 8 funspotr-0.0.5/funspotr/LICENSE | 4 funspotr-0.0.5/funspotr/MD5 | 53 - funspotr-0.0.5/funspotr/NAMESPACE | 1 funspotr-0.0.5/funspotr/NEWS.md | 5 funspotr-0.0.5/funspotr/R/copy-to-local-tempfile.R | 100 +- funspotr-0.0.5/funspotr/R/helpers.R | 108 +- funspotr-0.0.5/funspotr/R/list-files-gh-gists.R | 168 +--- funspotr-0.0.5/funspotr/R/list-files-gh-repo.R | 482 +++++------ funspotr-0.0.5/funspotr/R/list-files-wd.R | 86 +- funspotr-0.0.5/funspotr/R/network-plot.R | 204 ++-- funspotr-0.0.5/funspotr/R/spot-files.R | 232 ++--- funspotr-0.0.5/funspotr/R/spot-funs.R | 704 ++++++++--------- funspotr-0.0.5/funspotr/R/spot-pkgs.R | 556 ++++++------- funspotr-0.0.5/funspotr/R/spot-tags.R | 214 ++--- funspotr-0.0.5/funspotr/inst/ex-rmd-tags.Rmd | 14 funspotr-0.0.5/funspotr/inst/header.md | 10 funspotr-0.0.5/funspotr/man/check_pkgs_availability.Rd | 92 +- funspotr-0.0.5/funspotr/man/install_missing_pkgs.Rd | 94 +- funspotr-0.0.5/funspotr/man/list_files_github_repo.Rd | 4 funspotr-0.0.5/funspotr/man/list_files_wd.Rd | 4 funspotr-0.0.5/funspotr/man/network_plot.Rd | 2 funspotr-0.0.5/funspotr/man/spot_funs_files.Rd | 108 +- funspotr-0.0.5/funspotr/man/spot_pkgs_used.Rd | 64 - funspotr-0.0.5/funspotr/man/spot_tags.Rd | 162 +-- funspotr-0.0.5/funspotr/man/str_detect_r_docs.Rd | 66 - funspotr-0.0.5/funspotr/man/unnest_results.Rd | 2 28 files changed, 1762 insertions(+), 1785 deletions(-)
Title: System Identification in R
Description: Provides functions for constructing mathematical models of dynamical systems from measured input-output data.
Author: Suraj Yerramilli [aut, cre],
Arun Tangirala [aut]
Maintainer: Suraj Yerramilli <surajyerramilli@gmail.com>
Diff between sysid versions 1.0.4 dated 2017-01-07 and 1.0.5 dated 2026-01-28
DESCRIPTION | 19 MD5 | 126 ++-- NAMESPACE | 193 +++--- R/data.R | 232 ++++---- R/estUtil.R | 462 +++++++-------- R/estpoly.R | 1272 ++++++++++++++++++++++---------------------- R/idframe.R | 560 +++++++++---------- R/idinput.R | 310 +++++----- R/imports.R | 8 R/ioNamesData.R | 258 ++++---- R/iv.R | 312 +++++----- R/nonparam.R | 540 +++++++++--------- R/poly.R | 390 ++++++------- R/predict.R | 238 ++++---- R/preprocess.R | 382 ++++++------- R/rarx.R | 156 ++--- R/readData.R | 145 ++--- R/sim.R | 172 ++--- R/util.R | 104 +-- README.md | 77 ++ man/armax.Rd | 142 ++-- man/armaxsim.Rd | 48 - man/arx.Rd | 140 ++-- man/arxsim.Rd | 48 - man/bj.Rd | 172 ++--- man/bjsim.Rd | 48 - man/compare.Rd | 62 +- man/cstr.Rd | 52 - man/cstrData.Rd | 58 +- man/cstr_mis.Rd | 42 - man/dataSlice.Rd | 86 +- man/detrend.Rd | 84 +- man/estpoly.Rd | 74 +- man/etfe.Rd | 66 +- man/fitch.Rd | 56 - man/frd.Rd | 30 - man/getcov.Rd | 32 - man/grapes-equals-grapes.Rd | 36 - man/idframe.Rd | 76 +- man/idfrd.Rd | 78 +- man/idinput.Rd | 72 +- man/idpoly.Rd | 108 +-- man/impulseest.Rd | 92 +-- man/impulseplot.Rd | 42 - man/inputData.Rd | 40 - man/inputNames-set.Rd | 44 - man/iv.Rd | 104 +-- man/iv4.Rd | 110 +-- man/misdata.Rd | 58 +- man/nInputSeries.Rd | 32 - man/oe.Rd | 140 ++-- man/oesim.Rd | 46 - man/optimOptions.Rd | 54 - man/plot.idframe.Rd | 62 +- man/plot.idfrd.Rd | 62 +- man/predict.estpoly.Rd | 76 +- man/rarx.Rd | 110 +-- man/read.idframe.Rd | 60 +- man/read.table.idframe.Rd | 101 +-- man/residplot.Rd | 40 - man/sim.Rd | 84 +- man/spa.Rd | 70 +- man/step.Rd | 52 - man/time.Rd | 46 - 64 files changed, 4577 insertions(+), 4514 deletions(-)
Title: Install 'Futureverse' in One Go
Description: The 'Futureverse' is a set of packages for parallel and distributed processing with the 'future' package at its core, cf. Bengtsson (2021) <doi:10.32614/RJ-2021-048>. This package is designed to make it easy to install common 'Futureverse' packages in a single step. This package is intended for end-users, interactive use, and R scripts. Packages must not list it as a dependency - instead, explicitly declare each 'Futureverse' package as a dependency as needed.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between futureverse versions 0.1.1 dated 2025-12-20 and 0.2.0 dated 2026-01-28
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 9 ++++++++- R/futureverse.R | 5 +++-- R/futureverse_deps.R | 2 +- README.md | 35 +++++++++++++++++++---------------- inst/CITATION | 28 ++++++++++++++++++++++++++++ man/futureverse-package.Rd | 4 ++-- man/futureverse_deps.Rd | 2 +- man/futureverse_update.Rd | 2 +- 10 files changed, 77 insertions(+), 38 deletions(-)
Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent,
plant, ant, and weather data from the Portal Project. Portal is a
long-term (and ongoing) experimental monitoring site in the Chihuahuan
desert. The raw data files can be found at
<https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] ,
Hao Ye [aut] ,
Erica M. Christensen [aut] ,
Juniper L. Simonis [aut] ,
Ellen K. Bledsoe [aut] ,
Renata M. Diaz [aut] ,
Shawn D. Taylor [aut] ,
Ethan P, White [aut] ,
S.K. Morgan Ernest [aut] ,
Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.4.4 dated 2025-06-30 and 0.4.5 dated 2026-01-28
DESCRIPTION | 8 MD5 | 23 +- NEWS.md | 9 + R/NDVI.R | 20 ++ R/download_data.R | 6 README.md | 6 build/vignette.rds |binary inst/doc/portal_researcher_examples.html | 27 +-- inst/doc/rodent-abundance-demo.html | 49 ++--- man/load_datafile.Rd | 2 man/ndvi.Rd | 3 tests/testthat/_snaps/99-regression.md |only tests/testthat/test-99-regression.R | 269 +++++++++++++------------------ 13 files changed, 205 insertions(+), 217 deletions(-)
Title: Scraper for National Hockey League Data
Description: Scrapes and cleans data from the 'NHL' and 'ESPN' APIs into data.frames and lists. Wraps 125+ endpoints documented in <https://github.com/RentoSaijo/nhlscraper/wiki> from high-level multi-season summaries and award winners to low-level decisecond replays and bookmakers' odds, making them more accessible. Features cleaning and visualization tools, primarily for play-by-plays.
Author: Rento Saijo [aut, cre, cph] ,
Lars Skytte [ctb]
Maintainer: Rento Saijo <rentosaijo0527@gmail.com>
Diff between nhlscraper versions 0.4.1 dated 2025-12-17 and 0.4.2 dated 2026-01-28
nhlscraper-0.4.1/nhlscraper/tests/testthat/test-shifts.R |only nhlscraper-0.4.2/nhlscraper/DESCRIPTION | 8 nhlscraper-0.4.2/nhlscraper/MD5 | 55 nhlscraper-0.4.2/nhlscraper/NAMESPACE | 13 nhlscraper-0.4.2/nhlscraper/NEWS.md | 12 nhlscraper-0.4.2/nhlscraper/R/Clean.R | 1308 +++------- nhlscraper-0.4.2/nhlscraper/R/Game.R | 132 - nhlscraper-0.4.2/nhlscraper/R/GameOld.R | 28 nhlscraper-0.4.2/nhlscraper/R/Load.R | 73 nhlscraper-0.4.2/nhlscraper/README.md | 4 nhlscraper-0.4.2/nhlscraper/build/vignette.rds |binary nhlscraper-0.4.2/nhlscraper/inst/doc/example.Rmd | 2 nhlscraper-0.4.2/nhlscraper/inst/doc/example.html | 2 nhlscraper-0.4.2/nhlscraper/man/add_on_ice_players.Rd |only nhlscraper-0.4.2/nhlscraper/man/boxscore.Rd | 3 nhlscraper-0.4.2/nhlscraper/man/calculate_angle.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/calculate_distance.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/count_goals_shots.Rd | 28 nhlscraper-0.4.2/nhlscraper/man/flag_is_home.Rd | 18 nhlscraper-0.4.2/nhlscraper/man/flag_is_rebound.Rd | 24 nhlscraper-0.4.2/nhlscraper/man/flag_is_rush.Rd | 22 nhlscraper-0.4.2/nhlscraper/man/get_shift_charts.Rd | 2 nhlscraper-0.4.2/nhlscraper/man/normalize_coordinates.Rd | 26 nhlscraper-0.4.2/nhlscraper/man/shift_chart.Rd |only nhlscraper-0.4.2/nhlscraper/man/shift_charts.Rd |only nhlscraper-0.4.2/nhlscraper/man/shifts.Rd | 7 nhlscraper-0.4.2/nhlscraper/man/strip_game_id.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/strip_situation_code.Rd | 27 nhlscraper-0.4.2/nhlscraper/man/strip_time_period.Rd | 23 nhlscraper-0.4.2/nhlscraper/tests/testthat/test-shift_chart.R |only nhlscraper-0.4.2/nhlscraper/vignettes/example.Rmd | 2 31 files changed, 785 insertions(+), 1097 deletions(-)
Title: Latent Class Discriminant Analysis
Description: Providing a method for Local Discrimination via Latent Class Models. The approach is described in <https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Bucker.pdf>.
Author: Michael Buecker [aut, cre]
Maintainer: Michael Buecker <michael.buecker@fh-muenster.de>
Diff between lcda versions 0.3.2 dated 2024-02-15 and 0.3.3 dated 2026-01-28
DESCRIPTION | 20 ++++++++++++++------ MD5 | 23 ++++++++++++++++------- R/cclcda.default.R | 3 +++ R/cclcda2.default.R | 9 +++++---- R/lcda.default.R | 4 +++- R/validate_inputs.R |only README.md |only build |only inst |only man/cclcda.Rd | 6 +++--- man/cclcda2.Rd | 6 +++--- man/lcda.Rd | 2 +- tests |only vignettes |only 14 files changed, 48 insertions(+), 25 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, and streaming responses in real-time. Supports local
inference without requiring cloud APIs or internet connectivity, ensuring complete
data privacy and control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb, rev]
Maintainer: Pawan Rama Mali <prm@outlook.in>
Diff between edgemodelr versions 0.1.4 dated 2026-01-22 and 0.1.5 dated 2026-01-28
DESCRIPTION | 28 ++++----- MD5 | 26 ++++---- R/api.R | 36 +++++------ R/ollama.R | 6 - inst/CITATION | 2 man/edge_benchmark.Rd | 2 man/edge_clean_cache.Rd | 2 man/edge_find_gguf_models.Rd | 2 man/edge_find_ollama_models.Rd | 2 man/edge_load_ollama_model.Rd | 2 man/edge_small_model_config.Rd | 102 ++++++++++++++++----------------- man/test_ollama_model_compatibility.Rd | 2 src/bindings.cpp | 20 +++--- src/ggml/ggml-backend-reg.cpp | 16 ++--- 14 files changed, 124 insertions(+), 124 deletions(-)
Title: MCMC Estimation of Bayesian Vectorautoregressions
Description: Efficient Markov Chain Monte Carlo (MCMC) algorithms for the
fully Bayesian estimation of vectorautoregressions (VARs) featuring
stochastic volatility (SV). Implements state-of-the-art shrinkage
priors following Gruber & Kastner (2025) <doi:10.1016/j.ijforecast.2025.02.001>.
Efficient equation-per-equation estimation following Kastner & Huber
(2020) <doi:10.1002/for.2680> and Carrerio et al. (2021)
<doi:10.1016/j.jeconom.2021.11.010>.
Author: Luis Gruber [cph, aut, cre] ,
Stefan Haan [aut],
Gregor Kastner [aut, ths]
Maintainer: Luis Gruber <Luis.Gruber@aau.at>
Diff between bayesianVARs versions 0.1.5 dated 2024-11-13 and 0.1.6 dated 2026-01-28
DESCRIPTION | 30 MD5 | 78 NAMESPACE | 7 NEWS.md | 10 R/RcppExports.R | 20 R/bvar_wrapper.R | 1486 ++++----- R/data.R | 8 R/irf.R |only R/plots.R | 1511 +++++----- R/utility_functions.R | 4974 ++++++++++++++++++--------------- README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/bayesianVARs-vignette.R | 7 inst/doc/bayesianVARs-vignette.Rmd | 377 +- inst/doc/bayesianVARs-vignette.pdf |binary inst/doc/irf-vignette.R |only inst/doc/irf-vignette.Rmd |only inst/doc/irf-vignette.html |only inst/doc/scalability-vignette.R |only inst/doc/scalability-vignette.html |only inst/doc/scalability-vignette.qmd |only man/bvar.Rd | 63 man/extractB0.Rd |only man/irf.Rd |only man/plot.bayesianVARs_irf.Rd |only man/plot.bayesianVARs_residuals.Rd |only man/posterior_heatmap.Rd | 61 man/residuals.bayesianVARs_bvar.Rd |only man/specify_prior_phi.Rd | 8 man/specify_prior_sigma.Rd | 2 man/specify_structural_restrictions.Rd |only man/summary.bayesianVARs_bvar.Rd | 5 man/usmacro_growth.Rd | 8 src/RcppExports.cpp | 80 src/bvar_cpp.cpp | 83 src/irf.cpp |only src/sample_coefficients.h | 33 src/utilities_cpp.cpp | 44 src/utilities_cpp.h |only tests/testthat/setup-all.R | 144 tests/testthat/test-bvar.R | 681 +++- tests/testthat/test-irf.R |only vignettes/bayesianVARs-vignette.Rmd | 377 +- vignettes/huge.bib |only vignettes/huge_all_combinations.RData |only vignettes/irf-vignette.Rmd |only vignettes/irfs.bib |only vignettes/ref.bib | 728 ++-- vignettes/scalability-vignette.qmd |only 51 files changed, 6083 insertions(+), 4755 deletions(-)
Title: Excess Hazard Modelling Considering Inappropriate Mortality
Rates
Description: Fits relative survival regression models with or without proportional excess hazards and with the additional possibility to correct for background mortality by one or more parameter(s). These models are relevant when the observed mortality in the studied group is not comparable to that of the general population or in population-based studies where the available life tables used for net survival estimation are insufficiently stratified. In the latter case, the proposed model by Touraine et al. (2020) <doi:10.1177/0962280218823234> can be used. The user can also fit a model that relaxes the proportional expected hazards assumption considered in the Touraine et al. excess hazard model. This extension was proposed by Mba et al. (2020) <doi:10.1186/s12874-020-01139-z> to allow non-proportional effects of the additional variable on the general population mortality. In non-population-based studies, researchers can identify non-comparability source of bias in terms of expected mort [...truncated...]
Author: Juste Goungounga [aut, cre] ,
Hadrien Charvat [aut] ,
Darlin Mba [aut] ,
Nathalie Graffeo [aut] ,
Roch Giorgi [aut]
Maintainer: Juste Goungounga <juste.goungounga@ehesp.fr>
Diff between xhaz versions 2.0.2 dated 2024-06-29 and 2.1.0 dated 2026-01-28
DESCRIPTION | 45 - MD5 | 110 +- NAMESPACE | 13 R/AIC.bsplines.R | 5 R/AIC.constant.R | 5 R/AIC.mexhazLT.R | 4 R/BIC.bsplines.R | 4 R/BIC.constant.R | 6 R/BIC.mexhazLT.R | 4 R/alpha_stripper.R |only R/as.predxhaz_list.R |only R/as_predxhaz.R |only R/ccr.mevents.R | 1 R/coercion_as_xhaz.R |only R/duplicate.R | 7 R/esteve_ph_optim_maxim_function.R | 10 R/exphaz.R | 209 +---- R/exphaz_years.R | 773 +++++++------------- R/formulaLT.R | 3 R/giorgi.tdph.maxim.R | 4 R/imports.R |only R/mexhazLT.R | 6 R/plot.predxhaz.R | 59 - R/pred_list.R |only R/predict.xhaz.bsplines.R | 226 +----- R/predict.xhaz.constant.R | 259 +----- R/predxhaz_list.R |only R/print.xhaz.predxhaz.R | 2 R/utils-predxhaz.R |only R/without_breakpoint_without_cut.R | 1010 +++++++-------------------- R/xhaz.R | 8 build/vignette.rds |binary data/ccr.mevents.rda |binary inst/doc/introduction.R | 4 inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 851 +++++++++++----------- inst/doc/rescaling_excess_hazard_models.R | 176 +++- inst/doc/rescaling_excess_hazard_models.Rmd | 195 +++-- inst/doc/rescaling_excess_hazard_models.html | 884 +++++++++++++---------- man/AIC.bsplines.Rd | 5 man/AIC.constant.Rd | 5 man/AIC.mexhazLT.Rd | 4 man/BIC.bsplines.Rd | 4 man/BIC.constant.Rd | 6 man/BIC.mexhazLT.Rd | 4 man/as.predxhaz.Rd |only man/as.predxhaz_list.Rd |only man/as.xhaz.Rd |only man/ccr.mevents.Rd | 1 man/duplicate.Rd | 7 man/exphaz.Rd | 6 man/mexhazLT.Rd | 2 man/plot.predxhaz.Rd | 13 man/plot.predxhaz_list.Rd |only man/pred_list.Rd |only man/predict.bsplines.Rd | 2 man/print.predxhaz.Rd | 2 man/xhaz-package.Rd | 12 man/xhaz.Rd | 6 tests/testthat/test-as-xhaz.R |only vignettes/README_files |only vignettes/introduction.Rmd | 8 vignettes/rescaling_excess_hazard_models.Rmd | 195 +++-- 63 files changed, 2296 insertions(+), 2877 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation as described in Rue et al. (2009)
<doi:10.1111/j.1467-9868.2008.00700.x>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.2 dated 2026-01-27 and 0.2.3 dated 2026-01-28
INLAvaan-0.2.2/INLAvaan/R/qsn.R |only INLAvaan-0.2.2/INLAvaan/tests/testthat/test-qsn.R |only INLAvaan-0.2.3/INLAvaan/DESCRIPTION | 6 INLAvaan-0.2.3/INLAvaan/MD5 | 28 INLAvaan-0.2.3/INLAvaan/NEWS.md | 7 INLAvaan-0.2.3/INLAvaan/R/create_lav_from_inlavaan_internal.R | 2 INLAvaan-0.2.3/INLAvaan/R/inlavaan.R | 5 INLAvaan-0.2.3/INLAvaan/R/qsnorm_fast.R |only INLAvaan-0.2.3/INLAvaan/README.md | 381 ++-------- INLAvaan-0.2.3/INLAvaan/inst/doc/INLAvaan.html | 109 +- INLAvaan-0.2.3/INLAvaan/inst/doc/mediation.html | 38 INLAvaan-0.2.3/INLAvaan/inst/doc/mediation.qmd | 3 INLAvaan-0.2.3/INLAvaan/man/figures/README-fig-compare-poldem-1.png |binary INLAvaan-0.2.3/INLAvaan/tests/testthat/test-mvn_loglik.R | 4 INLAvaan-0.2.3/INLAvaan/tests/testthat/test-qsnorm_fast.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-variance_estimation.R | 2 INLAvaan-0.2.3/INLAvaan/vignettes/mediation.qmd | 3 17 files changed, 188 insertions(+), 400 deletions(-)
Title: Feature-Based Clustering of Longitudinal Trajectories
Description: Identifies clusters of individual longitudinal trajectories. In the spirit of Leffondre et al. (2004), the procedure involves identifying each trajectory to a point in the space of measures. In this context, a measure is a quantity meant to capture a certain characteristic feature of the trajectory. The points in the space of measures are then clustered using a version of spectral clustering.
Author: Marie-Pierre Sylvestre [aut],
Laurence Boulanger [aut, cre],
Gillis Delmas Tchouangue Dinkou [ctb],
Dan Vatnik [ctb]
Maintainer: Laurence Boulanger <laurence.boulanger@umontreal.ca>
Diff between traj versions 2.2.1 dated 2025-02-01 and 3.0.0 dated 2026-01-28
traj-2.2.1/traj/R/CalinskiHarabasz.R |only traj-2.2.1/traj/R/CheckCorrelation.R |only traj-2.2.1/traj/R/Step1Measures.R |only traj-2.2.1/traj/R/Step2Selection.R |only traj-2.2.1/traj/R/Step3Clusters.R |only traj-2.2.1/traj/build |only traj-2.2.1/traj/inst |only traj-2.2.1/traj/man/Step1Measures.Rd |only traj-2.2.1/traj/man/Step2Selection.Rd |only traj-2.2.1/traj/man/Step3Clusters.Rd |only traj-2.2.1/traj/vignettes |only traj-3.0.0/traj/DESCRIPTION | 13 traj-3.0.0/traj/MD5 | 33 -- traj-3.0.0/traj/NAMESPACE | 25 - traj-3.0.0/traj/NEWS.md | 11 traj-3.0.0/traj/R/plot.trajClusters.R | 453 +++++-------------------------- traj-3.0.0/traj/R/quiet.R |only traj-3.0.0/traj/R/spect.R |only traj-3.0.0/traj/R/trajClusters.R |only traj-3.0.0/traj/R/trajMeasures.R |only traj-3.0.0/traj/R/trajReduce.R |only traj-3.0.0/traj/man/plot.trajClusters.Rd | 116 +++---- traj-3.0.0/traj/man/traj-package.Rd | 4 traj-3.0.0/traj/man/trajClusters.Rd |only traj-3.0.0/traj/man/trajMeasures.Rd |only traj-3.0.0/traj/man/trajReduce.Rd |only 26 files changed, 182 insertions(+), 473 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.13 dated 2025-12-11 and 1.1.14 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/plotmulti.R | 35 ++++++++++++++++++++--------------- inst/doc/tepr.html | 4 ++-- 5 files changed, 32 insertions(+), 24 deletions(-)
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits. A paper on this package was published in the Journal of Statistical Software <doi:10.18637/jss.v114.i10>.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 1.3.0 dated 2025-09-08 and 1.3.1 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/Multiwave-Estimation.R | 4 ++-- inst/doc/Multiwave-Estimation.Rmd | 4 ++-- inst/doc/Multiwave-Estimation.html | 4 ++-- inst/doc/optimall-vignette.html | 2 +- vignettes/Multiwave-Estimation.Rmd | 4 ++-- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Multi-Fidelity Computer Experiments Using the Tuo-Wu-Yu Model
Description: This R function implements the nonstationary Kriging model
proposed by Tuo, Wu and Yu (2014) <DOI:10.1080/00401706.2013.842935>
for analyzing multi-fidelity computer outputs. This function computes
the maximum likelihood estimates for the model parameters as well
as the predictive means and variances of the exact solution.
Author: Wenjia Wang [aut, cre],
Rui Tuo [aut],
C. F. Jeff Wu [aut]
Maintainer: Wenjia Wang <1992wangwenjia@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2017-05-12
Diff between diffMeshGP versions 0.1.0 dated 2017-05-12 and 0.1.1 dated 2026-01-28
DESCRIPTION | 27 ++-- MD5 | 7 - NAMESPACE | 2 R/GPdiffMesh.R | 379 +++++++++++++++++++++++++++++++++++---------------------- tests |only 5 files changed, 262 insertions(+), 153 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Implements the Robust Scoring Equations estimator to fit linear
mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller [aut, cre]
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between robustlmm versions 3.3-3 dated 2025-05-26 and 3.4-2 dated 2026-01-28
DESCRIPTION | 15 ++++++----- MD5 | 37 ++++++++++++++++------------ NAMESPACE | 2 + R/AllClass.R | 35 ++++++++++++++++++++++++++ R/accessors.R | 28 ++++++++++++++++----- R/asymptoticEfficiency.R | 2 - R/generateLongitudinalDatasets.R |only R/plotLongitudinalBySubject.R |only R/processFile.R | 12 ++++++--- R/rlmer.R | 39 +++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/rlmer.Rnw | 8 +++--- inst/doc/rlmer.pdf |binary inst/doc/simulationStudies.pdf |binary man/generateLongitudinalDatasets.Rd |only man/partialMoment_standardNormal.Rd | 2 - man/plotLongitudinalBySubject.Rd |only tests/test_generateLongitudinalDatasets.R |only vignettes/rlmer.Rnw | 8 +++--- vignettes/rlmer.bib | 20 +++++++-------- vignettes/rlmer.sty | 2 - vignettes/simulationStudies.bib | 5 +-- 22 files changed, 157 insertions(+), 58 deletions(-)
Title: Robust Survey Statistics Estimation
Description: Robust (outlier-resistant) estimators of finite population
characteristics like of means, totals, ratios, regression, etc. Available
methods are M- and GM-estimators of regression, weight reduction,
trimming, and winsorization. The package extends the 'survey'
<https://CRAN.R-project.org/package=survey> package.
Author: Beat Hulliger [aut] ,
Tobias Schoch [aut, cre] ,
Martin Sterchi [ctr, com],
R-core [ctb, cph]
Maintainer: Tobias Schoch <tobias.schoch@fhnw.ch>
Diff between robsurvey versions 0.7 dated 2024-08-22 and 0.7-1 dated 2026-01-28
DESCRIPTION | 11 +-- MD5 | 76 ++++++++++++----------- NAMESPACE | 10 ++- NEWS.md | 14 ++++ R/class_svyreg_rob.R | 4 - R/class_svystat_rob.R | 43 +++++++++++-- R/mer.R | 2 R/robsurvey-internal.R | 107 ++++++++++++++++++++------------- R/svymean_dalen.R | 40 ++++-------- R/svymean_huber.R | 39 +++--------- R/svymean_trimmed.R | 33 ++-------- R/svymean_tukey.R | 48 +++++--------- R/svymean_winsorized.R | 68 ++++++-------------- R/within_tolerance.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Handling_of_NA_and_domains.md |only inst/doc/basic.R | 8 +- inst/doc/basic.html | 8 +- inst/doc/doc_comparison.pdf |binary inst/doc/doc_greg.pdf |binary inst/doc/doc_regression_covariance.pdf |binary inst/doc/greg.R | 10 +-- inst/doc/regression.R | 10 +-- inst/doc/rht.R | 8 +- inst/doc/rht.html | 4 - man/class_svystat_rob.Rd | 13 +++- man/sampling.Rd | 8 +- man/within_tolerance.Rd |only src/huber2.c | 2 src/mallows.c | 2 src/psifunctions.c | 2 src/regression.c | 2 src/regression_cov.c | 4 - src/regression_scale.c | 2 src/robsurvey_error.c | 2 src/sampling.c | 2 src/trimmedwinsorized.c | 2 src/wquantile.c | 2 tests/check_functions.R | 10 ++- tests/domain.R |only 41 files changed, 306 insertions(+), 290 deletions(-)
Title: Build Reproducible Analytical Pipelines with 'Nix'
Description: Streamlines the creation of reproducible analytical pipelines using
'default.nix' expressions generated via the 'rix' package for reproducibility. Define
derivations in 'R', 'Python' or 'Julia', chain them into a composition of pure
functions and build the resulting pipeline using 'Nix' as the underlying
end-to-end build tool. Functions to plot the pipeline as a directed acyclic
graph are included, as well as functions to load and inspect intermediary results
for interactive analysis. User experience heavily inspired by the 'targets' package.
Author: Bruno Rodrigues [aut, cre] ,
William Michael Landau [rev]
for rOpenSci, see
<https://github.com/ropensci/software-review/issues/706>),
Anthony Martinez [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>)
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rixpress versions 0.10.1 dated 2025-10-14 and 0.11.2 dated 2026-01-28
rixpress-0.10.1/rixpress/man/build_env_exports.Rd |only rixpress-0.10.1/rixpress/man/build_hybrid_src.Rd |only rixpress-0.10.1/rixpress/man/build_language_commands.Rd |only rixpress-0.10.1/rixpress/man/build_local_src.Rd |only rixpress-0.10.1/rixpress/man/build_phase.Rd |only rixpress-0.10.1/rixpress/man/build_remote_src.Rd |only rixpress-0.10.1/rixpress/man/build_reticulate_phase.Rd |only rixpress-0.10.1/rixpress/man/build_src_part.Rd |only rixpress-0.10.1/rixpress/man/build_transfer_command.Rd |only rixpress-0.10.1/rixpress/man/build_user_code_cmd.Rd |only rixpress-0.10.1/rixpress/man/clean_user_functions.Rd |only rixpress-0.10.1/rixpress/man/create_rxp_derivation.Rd |only rixpress-0.10.1/rixpress/man/extract_dependencies.Rd |only rixpress-0.10.1/rixpress/man/extract_julia_dependencies.Rd |only rixpress-0.10.1/rixpress/man/extract_markdown_dependencies.Rd |only rixpress-0.10.1/rixpress/man/extract_python_dependencies.Rd |only rixpress-0.10.1/rixpress/man/extract_r_dependencies.Rd |only rixpress-0.10.1/rixpress/man/figures |only rixpress-0.10.1/rixpress/man/is_remote_url.Rd |only rixpress-0.10.1/rixpress/man/make_derivation_snippet.Rd |only rixpress-0.10.1/rixpress/man/process_encoder.Rd |only rixpress-0.10.1/rixpress/man/process_read_function.Rd |only rixpress-0.10.1/rixpress/man/propagate_noop_builds.Rd |only rixpress-0.10.1/rixpress/man/rxp_common_setup.Rd |only rixpress-0.10.1/rixpress/man/sanitize_nix_env.Rd |only rixpress-0.11.2/rixpress/DESCRIPTION | 8 rixpress-0.11.2/rixpress/MD5 | 142 +- rixpress-0.11.2/rixpress/NAMESPACE | 2 rixpress-0.11.2/rixpress/NEWS.md | 53 rixpress-0.11.2/rixpress/R/derivs.R | 22 rixpress-0.11.2/rixpress/R/parse_pkgs.R | 31 rixpress-0.11.2/rixpress/R/plot_dag.R | 554 ++++++++-- rixpress-0.11.2/rixpress/R/rxp_copy.R | 2 rixpress-0.11.2/rixpress/R/rxp_ga.R | 2 rixpress-0.11.2/rixpress/R/rxp_init.R | 2 rixpress-0.11.2/rixpress/R/rxp_inspect.R | 4 rixpress-0.11.2/rixpress/R/rxp_io.R | 47 rixpress-0.11.2/rixpress/R/rxp_make.R | 2 rixpress-0.11.2/rixpress/R/rxp_pipeline.R |only rixpress-0.11.2/rixpress/R/rxp_populate.R | 5 rixpress-0.11.2/rixpress/R/rxp_read_load.R | 4 rixpress-0.11.2/rixpress/R/rxp_trace.R | 48 rixpress-0.11.2/rixpress/R/rxp_write_dag.R | 26 rixpress-0.11.2/rixpress/README.md | 33 rixpress-0.11.2/rixpress/build/vignette.rds |binary rixpress-0.11.2/rixpress/inst/doc/ci.Rmd | 6 rixpress-0.11.2/rixpress/inst/doc/ci.html | 6 rixpress-0.11.2/rixpress/inst/doc/cmdstanr.Rmd | 2 rixpress-0.11.2/rixpress/inst/doc/core-functions.Rmd | 2 rixpress-0.11.2/rixpress/inst/doc/debugging.Rmd | 4 rixpress-0.11.2/rixpress/inst/doc/debugging.html | 4 rixpress-0.11.2/rixpress/inst/doc/encoding-decoding.Rmd | 2 rixpress-0.11.2/rixpress/inst/doc/importing-data.Rmd | 2 rixpress-0.11.2/rixpress/inst/doc/intro-concepts.Rmd | 4 rixpress-0.11.2/rixpress/inst/doc/intro-concepts.html | 4 rixpress-0.11.2/rixpress/inst/doc/polyglot-julia.Rmd | 4 rixpress-0.11.2/rixpress/inst/doc/polyglot-julia.html | 4 rixpress-0.11.2/rixpress/inst/doc/polyglot.Rmd | 6 rixpress-0.11.2/rixpress/inst/doc/polyglot.html | 8 rixpress-0.11.2/rixpress/inst/doc/scope.Rmd | 2 rixpress-0.11.2/rixpress/inst/doc/sub-pipelines.R |only rixpress-0.11.2/rixpress/inst/doc/sub-pipelines.Rmd |only rixpress-0.11.2/rixpress/inst/doc/sub-pipelines.html |only rixpress-0.11.2/rixpress/inst/doc/tutorial.Rmd | 8 rixpress-0.11.2/rixpress/inst/doc/tutorial.html | 9 rixpress-0.11.2/rixpress/man/flatten_derivations.Rd |only rixpress-0.11.2/rixpress/man/print.rxp_pipeline.Rd |only rixpress-0.11.2/rixpress/man/rxp_ggdag.Rd | 20 rixpress-0.11.2/rixpress/man/rxp_make.Rd | 1 rixpress-0.11.2/rixpress/man/rxp_pipeline.Rd |only rixpress-0.11.2/rixpress/man/rxp_populate.Rd | 3 rixpress-0.11.2/rixpress/man/rxp_trace.Rd | 2 rixpress-0.11.2/rixpress/man/rxp_visnetwork.Rd | 17 rixpress-0.11.2/rixpress/tests/testthat/test-parse-pkgs.R | 159 ++ rixpress-0.11.2/rixpress/tests/testthat/test-plot_dag.R | 2 rixpress-0.11.2/rixpress/tests/testthat/test-rxp_pipeline.R |only rixpress-0.11.2/rixpress/vignettes/ci.Rmd | 6 rixpress-0.11.2/rixpress/vignettes/cmdstanr.Rmd | 2 rixpress-0.11.2/rixpress/vignettes/core-functions.Rmd | 2 rixpress-0.11.2/rixpress/vignettes/debugging.Rmd | 4 rixpress-0.11.2/rixpress/vignettes/encoding-decoding.Rmd | 2 rixpress-0.11.2/rixpress/vignettes/importing-data.Rmd | 2 rixpress-0.11.2/rixpress/vignettes/intro-concepts.Rmd | 4 rixpress-0.11.2/rixpress/vignettes/polyglot-julia.Rmd | 4 rixpress-0.11.2/rixpress/vignettes/polyglot.Rmd | 6 rixpress-0.11.2/rixpress/vignettes/scope.Rmd | 2 rixpress-0.11.2/rixpress/vignettes/sub-pipelines.Rmd |only rixpress-0.11.2/rixpress/vignettes/subpipelines.png |only rixpress-0.11.2/rixpress/vignettes/subpipelines_trace.png |only rixpress-0.11.2/rixpress/vignettes/tutorial.Rmd | 8 90 files changed, 997 insertions(+), 313 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools or programming languages such
as Python or Julia. Additional helpers make it easy to run R code in
'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.17.4 dated 2026-01-16 and 0.18.1 dated 2026-01-28
rix-0.17.4/rix/man/read_renv_lock.Rd |only rix-0.17.4/rix/man/renv_lock_r_ver.Rd |only rix-0.17.4/rix/man/renv_remote_pkgs.Rd |only rix-0.18.1/rix/DESCRIPTION | 6 rix-0.18.1/rix/MD5 | 89 +- rix-0.18.1/rix/NEWS.md | 56 + rix-0.18.1/rix/R/available_r.R | 12 rix-0.18.1/rix/R/fetchers.R | 416 ++++++++-- rix-0.18.1/rix/R/ga_cachix.R | 2 rix-0.18.1/rix/R/make_launcher.R | 2 rix-0.18.1/rix/R/nix_build.R | 2 rix-0.18.1/rix/R/nix_hash.R | 223 ++++- rix-0.18.1/rix/R/renv_helpers.R | 32 rix-0.18.1/rix/R/rix.R | 43 - rix-0.18.1/rix/R/rix_helpers.R | 42 - rix-0.18.1/rix/R/setup_cachix.R | 4 rix-0.18.1/rix/R/tar_nix_ga.R | 2 rix-0.18.1/rix/R/with_nix.R | 2 rix-0.18.1/rix/README.md | 1 rix-0.18.1/rix/inst/doc/installing-r-packages.Rmd | 6 rix-0.18.1/rix/inst/doc/installing-r-packages.html | 8 rix-0.18.1/rix/inst/doc/packaging-your-code.html | 4 rix-0.18.1/rix/inst/doc/remote-dependencies.R | 18 rix-0.18.1/rix/inst/doc/remote-dependencies.Rmd | 122 ++ rix-0.18.1/rix/inst/doc/remote-dependencies.html | 117 ++ rix-0.18.1/rix/inst/extdata/available_df.csv | 2 rix-0.18.1/rix/inst/extdata/default.nix | 12 rix-0.18.1/rix/man/available_dates.Rd | 4 rix-0.18.1/rix/man/available_df.Rd | 14 rix-0.18.1/rix/man/ga_cachix.Rd | 4 rix-0.18.1/rix/man/renv2nix.Rd | 4 rix-0.18.1/rix/man/rix.Rd | 33 rix-0.18.1/rix/man/rix_init.Rd | 2 rix-0.18.1/rix/man/setup_cachix.Rd | 6 rix-0.18.1/rix/man/tar_nix_ga.Rd | 4 rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_combined_default.nix | 1 rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_default.nix | 1 rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_git_default.nix |only rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_pypi_default.nix |only rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_simple_default.nix | 1 rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_src_default.nix | 1 rix-0.18.1/rix/tests/testthat/_snaps/rix-python/python_uv_default.nix | 1 rix-0.18.1/rix/tests/testthat/_snaps/rix/multiple_forges_default.nix |only rix-0.18.1/rix/tests/testthat/result |only rix-0.18.1/rix/tests/testthat/test-fetchers.R | 26 rix-0.18.1/rix/tests/testthat/test-rix-python.R | 86 ++ rix-0.18.1/rix/tests/testthat/test-rix.R | 58 + rix-0.18.1/rix/vignettes/installing-r-packages.Rmd | 6 rix-0.18.1/rix/vignettes/remote-dependencies.Rmd | 122 ++ 49 files changed, 1304 insertions(+), 293 deletions(-)
Title: Kernel Functions and Tools for Machine Learning Applications
Description: Kernel functions for diverse types of data (including, but not
restricted to: nonnegative and real vectors, real matrices, categorical
and ordinal variables, sets, strings), plus other utilities like kernel
similarity, kernel Principal Components Analysis (PCA) and features'
importance for Support Vector Machines (SVMs), which expand other 'R'
packages like 'kernlab'.
Author: Elies Ramon [aut, cre, cph]
Maintainer: Elies Ramon <eramon@everlyrusher.com>
Diff between kerntools versions 1.2.0 dated 2025-02-19 and 1.2.1 dated 2026-01-28
DESCRIPTION | 9 +++-- MD5 | 32 ++++++++++---------- NAMESPACE | 1 NEWS.md | 6 +++ R/importancies.R | 2 - R/kernel_functions.R | 4 +- R/kernel_study.R | 2 - README.md | 14 +++++++-- inst/WORDLIST | 4 ++ inst/doc/Kernel-PCA-and-CIA.html | 14 ++++----- inst/doc/Kernel-functions.Rmd | 4 +- inst/doc/Kernel-functions.html | 60 +++++++++++++++++++-------------------- inst/doc/kerntools.Rmd | 2 - inst/doc/kerntools.html | 46 ++++++++++++++--------------- man/vonNeumann.Rd | 2 - vignettes/Kernel-functions.Rmd | 4 +- vignettes/kerntools.Rmd | 2 - 17 files changed, 113 insertions(+), 95 deletions(-)
More information about EQUALPrognosis at CRAN
Permanent link
More information about DataQualityDashboard at CRAN
Permanent link
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'ewtp', 'rewtp', 'ewtpr', 'rewtpr', 'max', 'wtr', 'rwtr', 'pwt', and 'rpwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 0.4.2 dated 2025-12-17 and 0.4.3 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/ewt.R | 2 +- R/ewtp.R | 15 +++++++++++++++ R/km.R | 18 ++++++++++++------ R/rmt.R | 18 ++++++++++++++++-- R/wintime.R | 32 +++++++++++++++++++++++++------- inst/doc/wintime_vignette.html | 36 ++++++++++++++++++------------------ 8 files changed, 97 insertions(+), 44 deletions(-)