Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre] ,
Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between proxy versions 0.4-28 dated 2025-12-11 and 0.4-29 dated 2025-12-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/overview.pdf |binary src/apply.c | 12 ++++++------ 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Additional Univariate and Multivariate Distributions
Description: Density, distribution function, quantile function
and random generation for a number of univariate
and multivariate distributions. This package implements the
following distributions: Bernoulli, beta-binomial, beta-negative
binomial, beta prime, Bhattacharjee, Birnbaum-Saunders,
bivariate normal, bivariate Poisson, categorical, Dirichlet,
Dirichlet-multinomial, discrete gamma, discrete Laplace,
discrete normal, discrete uniform, discrete Weibull, Frechet,
gamma-Poisson, generalized extreme value, Gompertz,
generalized Pareto, Gumbel, half-Cauchy, half-normal, half-t,
Huber density, inverse chi-squared, inverse-gamma, Kumaraswamy,
Laplace, location-scale t, logarithmic, Lomax, multivariate
hypergeometric, multinomial, negative hypergeometric,
non-standard beta, normal mixture, Poisson mixture, Pareto,
power, reparametrized beta, Rayleigh, shifted Gompertz, Skellam,
slash, triangular, truncated binomial, truncated normal,
truncated Poisson, Tukey lambda, Wald, zero-inflated binomial,
zer [...truncated...]
Author: Tymoteusz Wolodzko [aut, cre]
Maintainer: ORPHANED
Diff between extraDistr versions 1.10.0 dated 2023-11-30 and 1.10.0.1 dated 2025-12-29
DESCRIPTION | 21 ++++++++++++++------- MD5 | 8 ++++---- R/negative-hypergeometric-distribution.R | 2 +- man/NegHyper.Rd | 2 +- man/extraDistr-package.Rd | 12 +++++++++++- 5 files changed, 31 insertions(+), 14 deletions(-)
Title: Complex Hierarchy Questions in Network Meta-Analysis
Description: Derives the most frequent hierarchies along with their probability of occurrence. One can also define complex hierarchy criteria and calculate their probability. Methodology based on Papakonstantinou et al. (2021) <DOI:10.21203/rs.3.rs-858140/v1>.
Author: Adriani Nikolakopoulou [aut] ,
Guido Schwarzer [aut] ,
Theodoros Papakonstantinou [aut, cre]
Maintainer: Theodoros Papakonstantinou <dev@tpapak.com>
Diff between nmarank versions 0.3-0 dated 2023-02-24 and 0.3-0.1 dated 2025-12-29
DESCRIPTION | 17 +++++++++-------- MD5 | 6 +++--- R/nmarank.R | 4 ++-- man/nmarank.Rd | 4 ++-- 4 files changed, 16 insertions(+), 15 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience
tools for testing and developing your own models.
Author: Ott Toomet [aut, cre],
Arne Henningsen [aut],
Spencer Graves [ctb],
Yves Croissant [ctb],
David Hugh-Jones [ctb],
Luca Scrucca [ctb]
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.5-2.1 dated 2024-03-24 and 1.5-2.2 dated 2025-12-29
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 16 ++++------------ inst/doc/intro-to-maximum-likelihood.pdf |binary inst/doc/stochastic-gradient-maxLik.pdf |binary inst/doc/using-maxlik.pdf |binary man/activePar.Rd | 2 +- man/nObs.Rd | 2 +- man/nParam.Rd | 2 +- 11 files changed, 20 insertions(+), 28 deletions(-)
Title: Automatic Description of Factorial Analysis
Description: Brings a set of tools to help and automatically realise the description of principal component analyses (from 'FactoMineR' functions). Detection of existing outliers, identification of the informative components, graphical views and dimensions description are performed threw dedicated functions. The Investigate() function performs all these functions in one, and returns the result as a report document (Word, PDF or HTML).
Author: Simon Thuleau [aut],
Francois Husson [aut, cre]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoInvestigate versions 1.9 dated 2023-11-27 and 1.9.1 dated 2025-12-29
DESCRIPTION | 18 +++++++++++++----- MD5 | 14 +++++++------- build/partial.rdb |binary man/Investigate.Rd | 8 ++++---- man/classif.Rd | 6 +++--- man/description.Rd | 8 ++++---- man/factoGraph.Rd | 8 ++++---- man/graphHab.Rd | 8 ++++---- 8 files changed, 39 insertions(+), 31 deletions(-)
More information about FactoInvestigate at CRAN
Permanent link
Title: Open Source OCR Engine
Description: Bindings to 'Tesseract':
a powerful optical character recognition (OCR) engine that supports over 100 languages.
The engine is highly configurable in order to tune the detection algorithms and
obtain the best possible results.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between tesseract versions 5.2.3 dated 2025-03-23 and 5.2.4 dated 2025-12-29
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 3 +++ build/vignette.rds |binary configure | 14 ++++---------- inst/doc/intro.html | 32 ++++++++++++++++---------------- 6 files changed, 33 insertions(+), 36 deletions(-)
Title: A Logging Utility for R
Description: Provides a simple yet powerful logging utility. Based loosely on
log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for cat and print statements.
Author: Brian Lee Yung Rowe [aut, cre]
Maintainer: Brian Lee Yung Rowe <r@zatonovo.com>
Diff between futile.logger versions 1.4.3 dated 2016-07-10 and 1.4.9 dated 2025-12-29
futile.logger-1.4.3/futile.logger/tests/testthat |only futile.logger-1.4.3/futile.logger/tests/testthat.R |only futile.logger-1.4.9/futile.logger/DESCRIPTION | 20 - futile.logger-1.4.9/futile.logger/MD5 | 47 +- futile.logger-1.4.9/futile.logger/R/appender.R | 130 +++++++- futile.logger-1.4.9/futile.logger/R/futile.logger-package.R | 5 futile.logger-1.4.9/futile.logger/R/layout.R | 159 ++++++++-- futile.logger-1.4.9/futile.logger/R/logger.R | 133 ++++++-- futile.logger-1.4.9/futile.logger/R/util.R |only futile.logger-1.4.9/futile.logger/README.md | 41 ++ futile.logger-1.4.9/futile.logger/man/flog.appender.Rd | 43 ++ futile.logger-1.4.9/futile.logger/man/flog.carp.Rd | 2 futile.logger-1.4.9/futile.logger/man/flog.layout.Rd | 38 ++ futile.logger-1.4.9/futile.logger/man/flog.logger.Rd | 88 +++-- futile.logger-1.4.9/futile.logger/man/flog.remove.Rd | 2 futile.logger-1.4.9/futile.logger/man/flog.threshold.Rd | 2 futile.logger-1.4.9/futile.logger/man/ftry.Rd | 20 + futile.logger-1.4.9/futile.logger/man/futile.logger-package.Rd | 18 - futile.logger-1.4.9/futile.logger/man/logger.options.Rd | 15 futile.logger-1.4.9/futile.logger/man/prepare_arg.Rd |only futile.logger-1.4.9/futile.logger/man/scat.Rd | 5 futile.logger-1.4.9/futile.logger/tests/test-all.R |only futile.logger-1.4.9/futile.logger/tests/testit |only 23 files changed, 606 insertions(+), 162 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre] ,
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut] ,
Toby Hocking [aut] ,
Benjamin Schwendinger [aut] ,
Ivan Krylov [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduar [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.17.8 dated 2025-07-10 and 1.18.0 dated 2025-12-24
DESCRIPTION | 40 MD5 | 406 - NAMESPACE | 18 NEWS.md | 463 + R/IDateTime.R | 38 R/as.data.table.R | 64 R/between.R | 16 R/bmerge.R | 19 R/cedta.R | 24 R/data.table.R | 413 - R/duplicated.R | 2 R/fcast.R | 88 R/fdroplevels.R | 7 R/fmelt.R | 22 R/foverlaps.R | 33 R/fread.R | 36 R/froll.R | 227 R/frollapply.R |only R/fwrite.R | 17 R/groupingsets.R | 26 R/helpers.R |only R/like.R | 1 R/merge.R | 38 R/mergelist.R |only R/onAttach.R | 4 R/onLoad.R | 55 R/openmp-utils.R | 5 R/print.data.table.R | 43 R/setkey.R | 42 R/setops.R | 16 R/test.data.table.R | 98 R/utils.R | 21 R/wrappers.R | 11 R/xts.R | 6 README.md | 23 build/vignette.rds |binary configure | 1 inst/cc | 4 inst/doc/datatable-benchmarking.R |only inst/doc/datatable-benchmarking.Rmd | 6 inst/doc/datatable-benchmarking.html | 9 inst/doc/datatable-faq.R | 25 inst/doc/datatable-faq.Rmd | 13 inst/doc/datatable-faq.html | 15 inst/doc/datatable-fread-and-fwrite.R |only inst/doc/datatable-fread-and-fwrite.Rmd |only inst/doc/datatable-fread-and-fwrite.html |only inst/doc/datatable-importing.R |only inst/doc/datatable-importing.Rmd | 9 inst/doc/datatable-importing.html | 12 inst/doc/datatable-intro.R | 30 inst/doc/datatable-intro.Rmd | 14 inst/doc/datatable-intro.html | 15 inst/doc/datatable-joins.R | 129 inst/doc/datatable-joins.Rmd | 210 inst/doc/datatable-joins.html | 232 inst/doc/datatable-keys-fast-subset.R | 27 inst/doc/datatable-keys-fast-subset.Rmd | 10 inst/doc/datatable-keys-fast-subset.html | 19 inst/doc/datatable-programming.R | 61 inst/doc/datatable-programming.Rmd | 70 inst/doc/datatable-programming.html | 114 inst/doc/datatable-reference-semantics.R | 41 inst/doc/datatable-reference-semantics.Rmd | 32 inst/doc/datatable-reference-semantics.html | 35 inst/doc/datatable-reshape.R | 53 inst/doc/datatable-reshape.Rmd | 41 inst/doc/datatable-reshape.html | 225 inst/doc/datatable-sd-usage.R | 25 inst/doc/datatable-sd-usage.Rmd | 6 inst/doc/datatable-sd-usage.html | 13 inst/doc/datatable-secondary-indices-and-auto-indexing.R | 38 inst/doc/datatable-secondary-indices-and-auto-indexing.Rmd | 40 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 60 inst/po/es/LC_MESSAGES/R-data.table.mo |binary inst/po/es/LC_MESSAGES/data.table.mo |binary inst/po/fr/LC_MESSAGES/R-data.table.mo |binary inst/po/fr/LC_MESSAGES/data.table.mo |binary inst/po/pt_BR/LC_MESSAGES/R-data.table.mo |binary inst/po/pt_BR/LC_MESSAGES/data.table.mo |binary inst/po/ru/LC_MESSAGES/R-data.table.mo |binary inst/po/ru/LC_MESSAGES/data.table.mo |binary inst/po/zh_CN/LC_MESSAGES/R-data.table.mo |binary inst/po/zh_CN/LC_MESSAGES/data.table.mo |binary inst/tests/benchmark.Rraw.bz2 |binary inst/tests/froll.Rraw.bz2 |binary inst/tests/frollBatch.Rraw.bz2 |only inst/tests/mergelist.Rraw.bz2 |only inst/tests/nafill.Rraw.bz2 |binary inst/tests/other.Rraw.bz2 |binary inst/tests/programming.Rraw.bz2 |binary inst/tests/tests.Rraw.bz2 |binary man/IDateTime.Rd | 38 man/as.data.table.Rd | 2 man/as.matrix.Rd | 2 man/assign.Rd | 11 man/between.Rd | 5 man/cbindlist.Rd |only man/coalesce.Rd | 8 man/data.table-condition-classes.Rd |only man/data.table-options.Rd |only man/data.table.Rd | 14 man/datatable-optimize.Rd | 11 man/fctr.Rd |only man/fdroplevels.Rd | 3 man/foverlaps.Rd | 10 man/fread.Rd | 37 man/frev.Rd |only man/froll.Rd | 278 - man/frolladapt.Rd |only man/frollapply.Rd |only man/fwrite.Rd | 14 man/groupingsets.Rd | 40 man/last.Rd | 3 man/like.Rd | 2 man/measure.Rd | 2 man/melt.data.table.Rd | 11 man/mergelist.Rd |only man/nafill.Rd | 24 man/openmp-utils.Rd | 6 man/print.data.table.Rd | 4 man/rbindlist.Rd | 2 man/selfref.ok.Rd |only man/setDT.Rd | 11 man/setattr.Rd | 4 man/setkey.Rd | 8 man/setorder.Rd | 15 man/subset.data.table.Rd | 2 man/tables.Rd | 2 man/test.Rd | 2 man/test.data.table.Rd | 5 man/transform.data.table.Rd | 6 man/truelength.Rd | 21 src/assign.c | 277 - src/between.c | 17 src/bmerge.c | 70 src/chmatch.c | 102 src/cj.c | 3 src/coalesce.c | 60 src/data.table.h | 158 src/dogroups.c | 109 src/fastmean.c | 25 src/fifelse.c | 4 src/fmelt.c | 102 src/forder.c | 213 src/frank.c | 26 src/fread.c | 2706 +++++----- src/fread.h | 15 src/freadR.c | 482 - src/freadR.h | 11 src/froll.c | 1869 +++++- src/frollR.c | 362 - src/frolladaptive.c | 984 +++ src/frollapply.c |only src/fsort.c | 41 src/fwrite.c | 343 - src/fwrite.h | 6 src/fwriteLookups.h | 3 src/fwriteR.c | 119 src/gsumm.c | 44 src/hash.c |only src/idatetime.c | 88 src/init.c | 463 - src/inrange.c | 17 src/mergelist.c |only src/myomp.h | 1 src/nafill.c | 27 src/negate.c | 10 src/nqrecreateindices.c | 32 src/openmp-utils.c | 93 src/programming.c | 11 src/quickselect.c | 66 src/rbindlist.c | 143 src/reorder.c | 55 src/shellsort.c |only src/shift.c | 8 src/snprintf.c | 2 src/subset.c | 26 src/transpose.c | 97 src/types.c | 38 src/types.h | 2 src/uniqlist.c | 17 src/utils.c | 296 - src/vecseq.c | 19 src/wrappers.c | 2 tests/autoprint.R | 13 tests/autoprint.Rout.save | 14 tests/froll.R | 2 tests/main.R | 1 tests/mergelist.R |only vignettes/_translation_links.R |only vignettes/datatable-benchmarking.Rmd | 6 vignettes/datatable-faq.Rmd | 13 vignettes/datatable-fread-and-fwrite.Rmd |only vignettes/datatable-importing.Rmd | 9 vignettes/datatable-intro.Rmd | 14 vignettes/datatable-joins.Rmd | 210 vignettes/datatable-keys-fast-subset.Rmd | 10 vignettes/datatable-programming.Rmd | 70 vignettes/datatable-reference-semantics.Rmd | 32 vignettes/datatable-reshape.Rmd | 41 vignettes/datatable-sd-usage.Rmd | 6 vignettes/datatable-secondary-indices-and-auto-indexing.Rmd | 40 vignettes/fr/datatable-benchmarking.Rmd | 4 vignettes/fr/datatable-faq.Rmd | 18 vignettes/fr/datatable-fread-and-fwrite.Rmd |only vignettes/fr/datatable-importing.Rmd | 6 vignettes/fr/datatable-intro.Rmd | 37 vignettes/fr/datatable-joins.Rmd |only vignettes/fr/datatable-keys-fast-subset.Rmd | 27 vignettes/fr/datatable-programming.Rmd | 40 vignettes/fr/datatable-reference-semantics.Rmd | 18 vignettes/fr/datatable-reshape.Rmd | 39 vignettes/fr/datatable-sd-usage.Rmd | 15 vignettes/fr/datatable-secondary-indices-and-auto-indexing.Rmd | 48 vignettes/ru/datatable-importing.Rmd | 6 vignettes/ru/datatable-intro.Rmd | 11 vignettes/ru/datatable-reshape.Rmd | 45 218 files changed, 9818 insertions(+), 5200 deletions(-)
Title: Automatic Knowledge Classification
Description: A tidy framework for automatic knowledge classification and visualization. Currently, the core functionality of the framework is mainly supported by modularity-based clustering (community detection) in keyword co-occurrence network, and focuses on co-word analysis of bibliometric research. However, the designed functions in 'akc' are general, and could be extended to solve other tasks in text mining as well.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between akc versions 0.9.9.2 dated 2025-12-16 and 0.9.9.3 dated 2025-12-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/keyword_merge.R | 2 +- inst/doc/akc_vignette.html | 2 +- inst/doc/tutorial_raw_text.html | 8 ++++---- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Low-Rank Methods for MVN and MVT Probabilities
Description: Implementation of the classic Genz algorithm and a novel tile-low-rank algorithm for computing relatively high-dimensional multivariate normal (MVN) and Student-t (MVT) probabilities.
References used for this package:
Foley, James, Andries van Dam, Steven Feiner, and John Hughes.
"Computer Graphics: Principle and Practice". Addison-Wesley
Publishing Company. Reading, Massachusetts (1987, ISBN:0-201-84840-6 1);
Genz, A., "Numerical computation of multivariate
normal probabilities," Journal of Computational and
Graphical Statistics, 1, 141-149 (1992) <doi:10.1080/10618600.1992.10477010>;
Cao, J., Genton, M. G., Keyes, D. E., & Turkiyyah, G. M. "Exploiting Low
Rank Covariance Structures for Computing High-Dimensional Normal and Student-
t Probabilities," Statistics and Computing, 31.1, 1-16 (2021)
<doi:10.1007/s11222-020-09978-y>;
Cao, J., Genton, M. G., Keyes, D. E., & Turkiyyah, G. M. "tlrmvnmvt:
Computing High-Dimensional Multivariate Normal and Student-t Probabilit [...truncated...]
Author: Marc Genton [aut],
David Keyes [aut],
George Turkiyyah [aut],
Jian Cao [aut, cre]
Maintainer: Jian Cao <jian.cao@kaust.edu.sa>
Diff between tlrmvnmvt versions 1.1.2 dated 2022-06-09 and 1.1.2.1 dated 2025-12-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/partial.rdb |binary configure | 4 ++-- configure.ac | 4 ++-- src/Makevars.in | 1 - src/Makevars.win | 1 - 7 files changed, 13 insertions(+), 15 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.4 dated 2025-12-06 and 1.6.4.1 dated 2025-12-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- configure | 17 +++++++++++------ 3 files changed, 16 insertions(+), 11 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.12 dated 2025-03-20 and 1.1.12.1 dated 2025-12-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- configure | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Analyze spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between phylospatial versions 1.2.0 dated 2025-12-20 and 1.2.1 dated 2025-12-23
DESCRIPTION | 6 - MD5 | 41 ++++++----- NAMESPACE | 1 NEWS.md | 6 + R/phylospatial-methods.R | 4 - R/phylospatial-package.R | 1 R/ps_canape.R | 6 + R/ps_dissim.R | 21 +++++- R/ps_diversity.R | 112 ++++++++++++++++++-------------- R/ps_ordinate.R | 47 ++++++++----- R/ps_prioritize.R | 93 +++++++++++++++++++------- R/ps_rand.R | 135 ++++++++++++++++++++++----------------- R/ps_regions.R | 28 ++++++-- R/utils.R | 96 +++++++++++++++++++++++++++ README.md | 37 ++++++---- inst/doc/beta-diversity.html | 2 man/build_tree_ranges_fast.Rd |only man/figures/README-example-1.png |only man/plot.phylospatial.Rd | 2 man/precompute_descendants.Rd |only man/ps_ordinate.Rd | 11 +-- man/ps_rgb.Rd | 2 tests/testthat/Rplots.pdf |binary 23 files changed, 449 insertions(+), 202 deletions(-)
Title: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix
Factorizations to Count Data
Description: Implements fast, scalable optimization algorithms for
fitting topic models ("grade of membership" models) and
non-negative matrix factorizations to count data. The methods
exploit the special relationship between the multinomial topic
model (also, "probabilistic latent semantic indexing") and Poisson
non-negative matrix factorization. The package provides tools to
compare, annotate and visualize model fits, including functions to
efficiently create "structure plots" and identify key features in
topics. The 'fastTopics' package is a successor to the
'CountClust' package. For more information, see
<doi:10.48550/arXiv.2105.13440> and
<doi:10.1186/s13059-023-03067-9>. Please also see the GitHub
repository for additional vignettes not included in the package on
CRAN.
Author: Peter Carbonetto [aut, cre],
Kevin Luo [aut],
Kushal Dey [aut],
Joyce Hsiao [ctb],
Abhishek Sarkar [ctb],
Anthony Hung [ctb],
Xihui Lin [ctb],
Paul C. Boutros [ctb],
Minzhe Wang [ctb],
Tracy Ke [ctb],
Eric Weine [ctb],
Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
This is a re-admission after prior archival of version 0.7-30 dated 2025-10-20
Diff between fastTopics versions 0.7-30 dated 2025-10-20 and 0.7-37 dated 2025-12-23
DESCRIPTION | 14 ++++++------ MD5 | 36 +++++++++++++++---------------- NAMESPACE | 2 - R/annotation_heatmap.R | 11 +++++---- R/embedding_plots.R | 18 ++++++++++----- R/fit_poisson_nmf.R | 2 - R/other_plots.R | 35 +++++++++++++++++++----------- R/structure_plot.R | 7 +++--- R/volcano_plots.R | 9 +++++-- README.md | 2 - inst/doc/relationship.html | 4 +-- inst/doc/single_cell_rnaseq_basic.html | 14 ++++++------ inst/doc/topics_vs_clusters.html | 4 +-- src/RcppExports.cpp | 38 ++++++++++++++++----------------- src/ccd.cpp | 4 ++- src/misc.cpp | 27 ++++++++++++++++++----- src/pnmfem.cpp | 26 ++++++++++++---------- src/scd.cpp | 29 +++++++++++++------------ tests/testthat/test_fit_poisson_nmf.R | 4 +-- 19 files changed, 165 insertions(+), 121 deletions(-)
Title: Electric Vehicle Charging Sessions Profiling and Modelling
Description: Tools for modelling electric vehicle charging sessions into
generic groups with similar connection patterns called "user profiles",
using Gaussian Mixture Models clustering. The clustering and profiling
methodology is described in Cañigueral and Meléndez (2021, ISBN:0142-0615)
<doi:10.1016/j.ijepes.2021.107195>.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marccanyigueral@gmail.com>
Diff between evprof versions 1.1.2 dated 2024-03-14 and 1.2.0 dated 2025-12-23
evprof-1.1.2/evprof/man/plot_model_clusters.Rd |only evprof-1.2.0/evprof/DESCRIPTION | 23 evprof-1.2.0/evprof/MD5 | 108 +-- evprof-1.2.0/evprof/NAMESPACE | 5 evprof-1.2.0/evprof/NEWS.md | 10 evprof-1.2.0/evprof/R/clustering.R | 31 - evprof-1.2.0/evprof/R/data.R | 16 evprof-1.2.0/evprof/R/exploration.R | 73 +- evprof-1.2.0/evprof/R/modelling.R | 271 +++++++--- evprof-1.2.0/evprof/R/preprocessing.R | 48 - evprof-1.2.0/evprof/R/profiling.R | 6 evprof-1.2.0/evprof/README.md | 69 +- evprof-1.2.0/evprof/build/vignette.rds |binary evprof-1.2.0/evprof/data/sessions_feature_names.rda |binary evprof-1.2.0/evprof/data/sessions_summary_feature_names.rda |binary evprof-1.2.0/evprof/inst/doc/evmodel.Rmd | 2 evprof-1.2.0/evprof/inst/doc/evmodel.html | 4 evprof-1.2.0/evprof/inst/doc/sessions-format.html | 4 evprof-1.2.0/evprof/man/california_GMM.Rd | 4 evprof-1.2.0/evprof/man/california_ev_model.Rd | 4 evprof-1.2.0/evprof/man/california_ev_sessions.Rd | 4 evprof-1.2.0/evprof/man/california_ev_sessions_profiles.Rd | 2 evprof-1.2.0/evprof/man/choose_k_GMM.Rd | 5 evprof-1.2.0/evprof/man/cluster_sessions.Rd | 5 evprof-1.2.0/evprof/man/cut_sessions.Rd | 5 evprof-1.2.0/evprof/man/define_clusters.Rd | 2 evprof-1.2.0/evprof/man/detect_outliers.Rd | 5 evprof-1.2.0/evprof/man/divide_by_disconnection.Rd | 3 evprof-1.2.0/evprof/man/divide_by_timecycle.Rd | 3 evprof-1.2.0/evprof/man/drop_outliers.Rd | 3 evprof-1.2.0/evprof/man/get_charging_rates_distribution.Rd | 3 evprof-1.2.0/evprof/man/get_connection_model_mclust_object.Rd | 5 evprof-1.2.0/evprof/man/get_daily_avg_n_sessions.Rd | 3 evprof-1.2.0/evprof/man/get_daily_n_sessions.Rd | 3 evprof-1.2.0/evprof/man/get_dbscan_params.Rd | 5 evprof-1.2.0/evprof/man/get_energy_model_mclust_object.Rd | 2 evprof-1.2.0/evprof/man/get_energy_models.Rd | 8 evprof-1.2.0/evprof/man/mutate_to_log.Rd | 2 evprof-1.2.0/evprof/man/plot_bivarGMM.Rd | 5 evprof-1.2.0/evprof/man/plot_connection_models.Rd |only evprof-1.2.0/evprof/man/plot_density_2D.Rd | 5 evprof-1.2.0/evprof/man/plot_density_3D.Rd | 5 evprof-1.2.0/evprof/man/plot_histogram.Rd | 3 evprof-1.2.0/evprof/man/plot_histogram_grid.Rd | 3 evprof-1.2.0/evprof/man/plot_kNNdist.Rd | 5 evprof-1.2.0/evprof/man/plot_outliers.Rd | 5 evprof-1.2.0/evprof/man/plot_points.Rd | 10 evprof-1.2.0/evprof/man/print.evmodel.Rd | 2 evprof-1.2.0/evprof/man/save_clustering_iterations.Rd | 7 evprof-1.2.0/evprof/man/save_ev_model.Rd | 2 evprof-1.2.0/evprof/man/summarise_sessions.Rd | 4 evprof-1.2.0/evprof/tests/testthat/test-clustering.R | 4 evprof-1.2.0/evprof/tests/testthat/test-exploration.R | 18 evprof-1.2.0/evprof/tests/testthat/test-modelling.R | 8 evprof-1.2.0/evprof/tests/testthat/test-preprocessing.R | 10 evprof-1.2.0/evprof/vignettes/evmodel.Rmd | 2 56 files changed, 499 insertions(+), 345 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <https://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [ctb],
Aaron Robotham [cre],
Rodrigo Tobar [ctb]
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between imager versions 1.0.5 dated 2025-08-03 and 1.0.8 dated 2025-12-23
DESCRIPTION | 8 +- MD5 | 18 +++--- NEWS.md | 2 build/vignette.rds |binary data/boats.rda |binary inst/doc/gettingstarted.Rmd | 4 - inst/doc/gettingstarted.html | 94 ++++++++++++++++----------------- inst/doc/pixsets.html | 58 ++++++++++---------- tests/testthat/test_load_save_videos.R | 2 vignettes/gettingstarted.Rmd | 4 - 10 files changed, 96 insertions(+), 94 deletions(-)
Title: Automatic Generation of Exams in R
Description: Automatic generation of exams based on exercises in Markdown or LaTeX format,
possibly including R code for dynamic generation of exercise elements.
Exercise types include single-choice and multiple-choice questions, arithmetic problems,
string questions, and combinations thereof (cloze). Output formats include standalone
files (PDF, HTML, Docx, ODT, ...), Moodle XML, QTI 1.2, QTI 2.1, Blackboard, Canvas, OpenOlat, ILIAS, TestVision,
Particify, ARSnova, Kahoot!, Grasple, and TCExam. In addition to fully customizable PDF exams, a standardized PDF format
(NOPS) is provided that can be printed, scanned, and automatically evaluated.
Author: Achim Zeileis [aut, cre] ,
Bettina Gruen [aut] ,
Friedrich Leisch [aut] ,
Nikolaus Umlauf [aut] ,
Niels Smits [aut] ,
Mirko Birbaumer [ctb],
Dominik Ernst [ctb] ,
Patrik Keller [ctb],
Reto Stauffer [ctb] ,
Kenji Sato [ctb] ,
Florian Wickelmaier [ctb] [...truncated...]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between exams versions 2.4-2 dated 2025-04-29 and 2.4-3 dated 2025-12-23
exams-2.4-2/exams/inst/xml/nops_fix.html |only exams-2.4-3/exams/DESCRIPTION | 29 exams-2.4-3/exams/MD5 | 93 exams-2.4-3/exams/NAMESPACE | 10 exams-2.4-3/exams/NEWS.md | 3134 +++++++++++++------------- exams-2.4-3/exams/R/add_cloze.R |only exams-2.4-3/exams/R/exams2ans.R | 3 exams-2.4-3/exams/R/exams2blackboard.R | 19 exams-2.4-3/exams/R/exams2moodle.R | 28 exams-2.4-3/exams/R/exams2nops.R | 86 exams-2.4-3/exams/R/exams2pdf.R | 11 exams-2.4-3/exams/R/exams2qti12.R | 4 exams-2.4-3/exams/R/exams2qti21.R | 97 exams-2.4-3/exams/R/exams2wooclap.R |only exams-2.4-3/exams/R/exams_eval.R | 9 exams-2.4-3/exams/R/fileURI.R | 46 exams-2.4-3/exams/R/formatters.R | 44 exams-2.4-3/exams/R/nops_eval.R | 12 exams-2.4-3/exams/R/nops_fix.R | 6 exams-2.4-3/exams/R/nops_scan.R | 7 exams-2.4-3/exams/R/pandoc.R | 26 exams-2.4-3/exams/R/read_metainfo.R | 24 exams-2.4-3/exams/R/search_files.R | 2 exams-2.4-3/exams/R/transformers.R | 16 exams-2.4-3/exams/R/xexams.R | 25 exams-2.4-3/exams/inst/doc/exams.pdf |binary exams-2.4-3/exams/inst/doc/exams2.R | 8 exams-2.4-3/exams/inst/doc/exams2.Rnw | 8 exams-2.4-3/exams/inst/doc/exams2.pdf |binary exams-2.4-3/exams/inst/exercises/penguins.Rmd |only exams-2.4-3/exams/inst/exercises/penguins.Rnw |only exams-2.4-3/exams/inst/nops/de.dcf | 1 exams-2.4-3/exams/inst/nops/eu.dcf |only exams-2.4-3/exams/inst/nops/nops_fix.html |only exams-2.4-3/exams/inst/pandoc/plain.tex | 12 exams-2.4-3/exams/inst/xml/ilias.xml | 15 exams-2.4-3/exams/man/add_cloze.Rd |only exams-2.4-3/exams/man/exams2ans.Rd |only exams-2.4-3/exams/man/exams2blackboard.Rd | 2 exams-2.4-3/exams/man/exams2html.Rd | 2 exams-2.4-3/exams/man/exams2ilias.Rd | 18 exams-2.4-3/exams/man/exams2moodle.Rd | 17 exams-2.4-3/exams/man/exams2nops.Rd | 51 exams-2.4-3/exams/man/exams2pdf.Rd | 2 exams-2.4-3/exams/man/exams2qti12.Rd | 8 exams-2.4-3/exams/man/exams2qti21.Rd | 8 exams-2.4-3/exams/man/exams2wooclap.Rd |only exams-2.4-3/exams/man/match_exams_call.Rd | 13 exams-2.4-3/exams/man/mchoice2string.Rd | 13 exams-2.4-3/exams/man/xexams.Rd | 2 exams-2.4-3/exams/tests/exams2nops.R |only exams-2.4-3/exams/vignettes/exams.bib | 59 exams-2.4-3/exams/vignettes/exams2.Rnw | 8 53 files changed, 2156 insertions(+), 1822 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut],
Ian Cook [aut],
Nic Crane [aut],
Dewey Dunnington [aut] ,
Romain Francois [aut] ,
Jonathan Keane [aut, cre],
Bryce Mecum [aut],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb], [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 22.0.0 dated 2025-10-29 and 22.0.0.1 dated 2025-12-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ inst/build_arrow_static.sh | 3 ++- src/Makevars.in | 2 +- tools/cpp/thirdparty/versions.txt | 7 +++++-- tools/nixlibs.R | 6 ++++++ 7 files changed, 31 insertions(+), 13 deletions(-)
Title: Deep Neural Networks for Survival Analysis using 'torch'
Description: Provides deep learning models for right-censored survival data using the 'torch' backend.
Supports multiple loss functions, including Cox partial likelihood, L2-penalized Cox, time-dependent Cox,
and accelerated failure time (AFT) loss. Offers a formula-based interface, built-in support for cross-validation,
hyperparameter tuning, survival curve plotting, and evaluation metrics such as the C-index, Brier score,
and integrated Brier score. For methodological details, see Kvamme et al. (2019) <https://www.jmlr.org/papers/v20/18-424.html>.
Author: Imad EL BADISY [aut, cre]
Maintainer: Imad EL BADISY <elbadisyimad@gmail.com>
Diff between survdnn versions 0.6.3 dated 2025-10-30 and 0.7.0 dated 2025-12-23
DESCRIPTION | 8 MD5 | 53 +++--- NAMESPACE | 2 NEWS.md | 69 +++++--- R/callbacks.R |only R/evaluation.R | 106 +++++++++--- R/gridsearch_survdnn.R | 77 +++++---- R/losses.R | 2 R/plot_loss.R |only R/predict.survdnn.R | 291 ++++++++++++++++++++++++++++------ R/print.survdnn.R | 7 R/summary.survdnn.R | 17 +- R/survdnn.R | 308 ++++++++++++++++++++++++++----------- R/tune_survdnn.R | 121 +++++++++----- R/zzz.R | 60 +++++++ README.md | 267 +++++++++++++++++++++++--------- man/build_dnn.Rd | 25 +-- man/callback_early_stopping.Rd |only man/cv_survdnn.Rd | 9 + man/evaluate_survdnn.Rd | 21 -- man/gridsearch_survdnn.Rd | 5 man/plot_loss.Rd |only man/predict.survdnn.Rd | 19 +- man/survdnn.Rd | 57 ++++-- man/tune_survdnn.Rd | 11 + tests/testthat/test-callbacks.R |only tests/testthat/test-device.R |only tests/testthat/test-losses.R | 37 +++- tests/testthat/test-missing-data.R |only tests/testthat/test-optimizers.R |only tests/testthat/test-plot-loss.R |only tests/testthat/test-survdnn.R | 68 +++++++- 32 files changed, 1207 insertions(+), 433 deletions(-)
Title: Generate Optimal Designs of Accelerated Life Test using
PSO-Based Algorithm
Description: A computationally efficient solution for generating optimal experimental designs in Accelerated Life Testing (ALT). Leveraging a Particle Swarm Optimization (PSO)-based hybrid algorithm, the package identifies optimal test plans that minimize estimation variance under specified failure models and stress profiles. For more detailed, see Lee et al. (2025), Optimal Robust Strategies for Accelerated Life Tests and Fatigue Testing of Polymer Composite Materials <doi:10.1214/25-AOAS2075>, and Hoang (2025), Model-Robust Minimax Design of Accelerated Life Tests via PSO-based Hybrid Algorithm, Master' Thesis, Unpublished.
Author: Hoai-Linh Hoang [aut, cre],
I-Chen Lee [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut]
Maintainer: Hoai-Linh Hoang <hoailinh.hoang17@gmail.com>
Diff between minimaxALT versions 1.0.2 dated 2025-10-10 and 1.0.3 dated 2025-12-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo, as described
in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>.
The approximation uses Pareto smoothed importance sampling (PSIS), a
new procedure for regularizing importance weights. As a byproduct of
the calculations, we also obtain approximate standard errors for
estimated predictive errors and for the comparison of predictive
errors between models. The package also provides methods for using
stacking and other model weighting techniques to average Bayesian
predictive distributions.
Author: Aki Vehtari [aut],
Jonah Gabry [cre, aut],
Mans Magnusson [aut],
Yuling Yao [aut],
Paul-Christian Buerkner [aut],
Topi Paananen [aut],
Andrew Gelman [aut],
Ben Goodrich [ctb],
Juho Piironen [ctb],
Bruno Nicenboim [ctb],
Leevi Lindgren [ctb],
Visruth S [...truncated...]
Maintainer: Jonah Gabry <jgabry@gmail.com>
Diff between loo versions 2.8.0 dated 2024-07-03 and 2.9.0 dated 2025-12-23
loo-2.8.0/loo/man/figures/stanlogo.png |only loo-2.8.0/loo/tests/testthat/reference-results |only loo-2.9.0/loo/DESCRIPTION | 72 loo-2.9.0/loo/MD5 | 194 loo-2.9.0/loo/NEWS.md | 19 loo-2.9.0/loo/R/E_loo.R | 13 loo-2.9.0/loo/R/crps.R | 12 loo-2.9.0/loo/R/diagnostics.R | 3 loo-2.9.0/loo/R/effective_sample_sizes.R | 85 loo-2.9.0/loo/R/kfold-helpers.R | 7 loo-2.9.0/loo/R/loo.R | 2 loo-2.9.0/loo/R/loo_compare.R | 12 loo-2.9.0/loo/R/loo_model_weights.R | 18 loo-2.9.0/loo/R/loo_moment_matching.R | 2 loo-2.9.0/loo/R/loo_subsample.R | 4 loo-2.9.0/loo/R/psis.R | 104 loo-2.9.0/loo/build/partial.rdb |binary loo-2.9.0/loo/build/vignette.rds |binary loo-2.9.0/loo/inst/CITATION | 85 loo-2.9.0/loo/inst/doc/loo2-elpd.R | 14 loo-2.9.0/loo/inst/doc/loo2-elpd.Rmd | 14 loo-2.9.0/loo/inst/doc/loo2-elpd.html | 432 -- loo-2.9.0/loo/inst/doc/loo2-example.Rmd | 9 loo-2.9.0/loo/inst/doc/loo2-example.html | 463 -- loo-2.9.0/loo/inst/doc/loo2-large-data.R | 398 +- loo-2.9.0/loo/inst/doc/loo2-large-data.html | 741 +-- loo-2.9.0/loo/inst/doc/loo2-lfo.html | 1075 ++--- loo-2.9.0/loo/inst/doc/loo2-mixis.html | 447 -- loo-2.9.0/loo/inst/doc/loo2-moment-matching.R | 48 loo-2.9.0/loo/inst/doc/loo2-moment-matching.Rmd | 48 loo-2.9.0/loo/inst/doc/loo2-moment-matching.html | 630 +-- loo-2.9.0/loo/inst/doc/loo2-non-factorized.R | 190 loo-2.9.0/loo/inst/doc/loo2-non-factorized.html | 990 +--- loo-2.9.0/loo/inst/doc/loo2-weights.html | 570 +- loo-2.9.0/loo/inst/doc/loo2-with-rstan.R | 76 loo-2.9.0/loo/inst/doc/loo2-with-rstan.html | 324 - loo-2.9.0/loo/man/E_loo.Rd | 13 loo-2.9.0/loo/man/crps.Rd | 12 loo-2.9.0/loo/man/figures/logo.svg | 97 loo-2.9.0/loo/man/loo-glossary.Rd | 6 loo-2.9.0/loo/man/loo-package.Rd | 3 loo-2.9.0/loo/man/loo_compare.Rd | 8 loo-2.9.0/loo/man/loo_model_weights.Rd | 3 loo-2.9.0/loo/man/loo_moment_match.Rd | 2 loo-2.9.0/loo/tests/testthat/_snaps |only loo-2.9.0/loo/tests/testthat/test_0_helpers.R | 47 loo-2.9.0/loo/tests/testthat/test_E_loo.R | 92 loo-2.9.0/loo/tests/testthat/test_compare.R | 170 loo-2.9.0/loo/tests/testthat/test_crps.R | 10 loo-2.9.0/loo/tests/testthat/test_deprecated_extractors.R | 121 loo-2.9.0/loo/tests/testthat/test_extract_log_lik.R | 3 loo-2.9.0/loo/tests/testthat/test_gpdfit.R | 18 loo-2.9.0/loo/tests/testthat/test_kfold_helpers.R | 106 loo-2.9.0/loo/tests/testthat/test_loo_and_waic.R | 94 loo-2.9.0/loo/tests/testthat/test_loo_approximate_posterior.R | 153 loo-2.9.0/loo/tests/testthat/test_loo_moment_matching.R | 584 ++ loo-2.9.0/loo/tests/testthat/test_loo_predictive_metric.R | 22 loo-2.9.0/loo/tests/testthat/test_loo_subsampling.R | 1982 +++++----- loo-2.9.0/loo/tests/testthat/test_loo_subsampling_approximations.R |only loo-2.9.0/loo/tests/testthat/test_loo_subsampling_cases.R |only loo-2.9.0/loo/tests/testthat/test_model_weighting.R | 104 loo-2.9.0/loo/tests/testthat/test_pointwise.R | 14 loo-2.9.0/loo/tests/testthat/test_print_plot.R | 75 loo-2.9.0/loo/tests/testthat/test_psis.R | 52 loo-2.9.0/loo/tests/testthat/test_psis_approximate_posterior.R | 166 loo-2.9.0/loo/tests/testthat/test_psislw.R | 39 loo-2.9.0/loo/tests/testthat/test_relative_eff.R | 17 loo-2.9.0/loo/tests/testthat/test_tisis.R | 102 loo-2.9.0/loo/vignettes/logo.svg |only loo-2.9.0/loo/vignettes/loo2-elpd.Rmd | 14 loo-2.9.0/loo/vignettes/loo2-example.Rmd | 9 loo-2.9.0/loo/vignettes/loo2-moment-matching.Rmd | 48 72 files changed, 5454 insertions(+), 5833 deletions(-)
Title: Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Description: Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Author: Chris Reudenbach [cre, aut],
Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Diff between link2GI versions 0.6-2 dated 2024-10-28 and 0.7-2 dated 2025-12-23
link2GI-0.6-2/link2GI/R/linkOTB.R |only link2GI-0.6-2/link2GI/R/otbControls.R |only link2GI-0.6-2/link2GI/R/parseOTB.R |only link2GI-0.6-2/link2GI/man/setenvOTB.Rd |only link2GI-0.7-2/link2GI/DESCRIPTION | 18 link2GI-0.7-2/link2GI/MD5 | 133 - link2GI-0.7-2/link2GI/NAMESPACE | 12 link2GI-0.7-2/link2GI/NEWS | 39 link2GI-0.7-2/link2GI/NEWS.md | 41 link2GI-0.7-2/link2GI/R/gdalControls.R | 245 +- link2GI-0.7-2/link2GI/R/grassControl.R | 1141 ++++++---- link2GI-0.7-2/link2GI/R/initProj.R | 33 link2GI-0.7-2/link2GI/R/link2giKarim.R | 9 link2GI-0.7-2/link2GI/R/linkGDAL.R | 4 link2GI-0.7-2/link2GI/R/linkGRASS.R | 523 ++-- link2GI-0.7-2/link2GI/R/linkSAGA.R | 2 link2GI-0.7-2/link2GI/R/otb_api.R |only link2GI-0.7-2/link2GI/R/otb_link.R |only link2GI-0.7-2/link2GI/R/otb_link_dispatch.R |only link2GI-0.7-2/link2GI/R/otb_link_linux.R |only link2GI-0.7-2/link2GI/R/otb_link_windows.R |only link2GI-0.7-2/link2GI/R/otb_linux_link.R |only link2GI-0.7-2/link2GI/R/otb_linux_run.R |only link2GI-0.7-2/link2GI/R/otb_linux_search.R |only link2GI-0.7-2/link2GI/R/otb_parse.R |only link2GI-0.7-2/link2GI/R/otb_parse_legacy.R |only link2GI-0.7-2/link2GI/R/otb_run.R |only link2GI-0.7-2/link2GI/R/otb_version_select.R |only link2GI-0.7-2/link2GI/R/otb_windows_search.R |only link2GI-0.7-2/link2GI/R/sagaControl.R | 8 link2GI-0.7-2/link2GI/README.md | 90 link2GI-0.7-2/link2GI/build/vignette.rds |binary link2GI-0.7-2/link2GI/inst/doc/link2GI1.Rmd | 62 link2GI-0.7-2/link2GI/inst/doc/link2GI1.html | 183 + link2GI-0.7-2/link2GI/inst/doc/link2GI2.R | 423 ++- link2GI-0.7-2/link2GI/inst/doc/link2GI2.Rmd | 283 +- link2GI-0.7-2/link2GI/inst/doc/link2GI2.html | 474 ++-- link2GI-0.7-2/link2GI/inst/doc/link2GI3.R | 131 - link2GI-0.7-2/link2GI/inst/doc/link2GI3.Rmd | 280 +- link2GI-0.7-2/link2GI/inst/doc/link2GI3.html | 449 ++- link2GI-0.7-2/link2GI/inst/doc/link2GI4.R | 153 - link2GI-0.7-2/link2GI/inst/doc/link2GI4.Rmd | 255 +- link2GI-0.7-2/link2GI/inst/doc/link2GI4.html | 772 +++++- link2GI-0.7-2/link2GI/inst/doc/link2GI5.R |only link2GI-0.7-2/link2GI/inst/doc/link2GI5.Rmd | 331 ++ link2GI-0.7-2/link2GI/inst/doc/link2GI5.html | 445 ++- link2GI-0.7-2/link2GI/inst/doc/link2GI6.R | 1 link2GI-0.7-2/link2GI/inst/doc/link2GI6.Rmd | 211 - link2GI-0.7-2/link2GI/inst/doc/link2GI6.html | 448 +-- link2GI-0.7-2/link2GI/inst/templates/config-default-projects.yml | 126 - link2GI-0.7-2/link2GI/inst/templates/script_setup.brew | 58 link2GI-0.7-2/link2GI/man/findGRASS.Rd | 26 link2GI-0.7-2/link2GI/man/findOTB.Rd | 29 link2GI-0.7-2/link2GI/man/getrowotbVer.Rd |only link2GI-0.7-2/link2GI/man/linkGRASS.Rd | 153 - link2GI-0.7-2/link2GI/man/linkOTB.Rd | 56 link2GI-0.7-2/link2GI/man/linkOTB_linux.Rd |only link2GI-0.7-2/link2GI/man/otb_api.Rd |only link2GI-0.7-2/link2GI/man/parseOTBAlgorithms.Rd | 34 link2GI-0.7-2/link2GI/man/parseOTBFunction.Rd | 38 link2GI-0.7-2/link2GI/man/runOTB.Rd | 103 link2GI-0.7-2/link2GI/man/runOTB_isolated.Rd |only link2GI-0.7-2/link2GI/man/searchGDALX.Rd | 36 link2GI-0.7-2/link2GI/man/searchGRASSW.Rd | 56 link2GI-0.7-2/link2GI/man/searchGRASSX.Rd | 28 link2GI-0.7-2/link2GI/man/searchOTBW.Rd | 53 link2GI-0.7-2/link2GI/man/searchOTBX.Rd | 23 link2GI-0.7-2/link2GI/man/setenvGRASSw.Rd | 5 link2GI-0.7-2/link2GI/tests |only link2GI-0.7-2/link2GI/vignettes/link2GI1.Rmd | 62 link2GI-0.7-2/link2GI/vignettes/link2GI2.Rmd | 283 +- link2GI-0.7-2/link2GI/vignettes/link2GI3.Rmd | 280 +- link2GI-0.7-2/link2GI/vignettes/link2GI4.Rmd | 255 +- link2GI-0.7-2/link2GI/vignettes/link2GI5.Rmd | 331 ++ link2GI-0.7-2/link2GI/vignettes/link2GI6.Rmd | 211 - 75 files changed, 6027 insertions(+), 3418 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu [aut],
Greg Ridgeway [aut],
Dan McCaffrey [aut],
Andrew Morral [aut],
Beth Ann Griffin [aut],
Lane Burgette [aut, cre]
Maintainer: Lane Burgette <burgette@rand.org>
Diff between twang versions 2.6.1 dated 2024-07-22 and 2.6.2 dated 2025-12-23
DESCRIPTION | 34 ++ MD5 | 12 R/ps.fast.R | 710 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.pdf |binary 7 files changed, 390 insertions(+), 366 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.6.0 dated 2025-09-11 and 0.6.1 dated 2025-12-23
DESCRIPTION | 6 MD5 | 39 NEWS.md | 8 R/make_exercise.R | 80 - README.md | 77 - build/vignette.rds |binary inst/doc/ai.html | 537 ++++----- inst/doc/ai.qmd | 51 inst/doc/instructions.html | 4 inst/doc/instructions.qmd | 4 inst/rmarkdown/templates/tutorial_template/skeleton/skeleton.Rmd | 90 + inst/tutorials/getting-started/tutorial.html | 205 +-- inst/tutorials/introduction-to-python |only inst/tutorials/introduction-to-r/tutorial.Rmd | 159 ++ inst/tutorials/introduction-to-r/tutorial.html | 564 +++++++--- tests/testthat/test-make_exercise.R | 61 - tests/testthat/test-render.R | 3 vignettes/ai.qmd | 51 vignettes/instructions.qmd | 4 19 files changed, 1275 insertions(+), 668 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP
API from R functions using the annotations in the R documentation
around your functions.
Author: Barret Schloerke [cre, aut] ,
Jeff Allen [aut, ccp],
Bruno Tremblay [ctb],
Frans van Dunne [ctb],
Sebastiaan Vandewoude [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between plumber versions 1.3.1 dated 2025-12-13 and 1.3.2 dated 2025-12-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++++ tests/testthat/test-zzzz-include.R | 10 ++++++++-- 4 files changed, 21 insertions(+), 8 deletions(-)
Title: Tools for Various R Functions Helpers
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.6 dated 2025-06-16 and 2025.12.22 dated 2025-12-23
DESCRIPTION | 13 +- MD5 | 38 ++++---- NEWS | 7 + R/HelpersMG-package.R | 4 R/IC_clean_data.R | 17 ++- R/MHalgoGen.R | 2 R/MovingWindow.R | 4 R/RandomFromHessianOrMCMC.R | 53 +++++++++-- R/as.parameters.R | 17 ++- R/as.quantiles.R | 21 +++- R/from_min_max.R | 183 ++++++++++++++++++++++++++++++++--------- R/onAttach.R | 4 R/sysdata.rda |binary inst/shiny/cutter/ui.R | 2 man/HelpersMG-package.Rd | 4 man/MovingWindow.Rd | 4 man/RandomFromHessianOrMCMC.Rd | 19 +++- man/as.quantiles.Rd | 4 man/figures/TB.png |binary man/from_min_max.Rd | 6 + 20 files changed, 289 insertions(+), 113 deletions(-)
Title: Routines for Common fMRI Processing Tasks
Description: Supports fMRI (functional magnetic resonance imaging)
analysis tasks including reading in 'CIFTI', 'GIFTI' and
'NIFTI' data, temporal filtering, nuisance regression, and
aCompCor (anatomical Components Correction) (Muschelli et al.
(2014) <doi:10.1016/j.neuroimage.2014.03.028>).
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Mark Fiecas [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRItools versions 0.6.0 dated 2025-05-20 and 0.7.2 dated 2025-12-23
fMRItools-0.6.0/fMRItools/R/dim_reduce.R |only fMRItools-0.6.0/fMRItools/man/dim_reduce.Rd |only fMRItools-0.7.2/fMRItools/DESCRIPTION | 10 - fMRItools-0.7.2/fMRItools/MD5 | 22 +- fMRItools-0.7.2/fMRItools/NAMESPACE | 1 fMRItools-0.7.2/fMRItools/NEWS.md | 7 fMRItools-0.7.2/fMRItools/R/dice_overlap.R |only fMRItools-0.7.2/fMRItools/R/dual_reg_parc.R | 6 fMRItools-0.7.2/fMRItools/R/plot_FC.R | 4 fMRItools-0.7.2/fMRItools/R/plot_FC_gg.R | 143 ++++++++++++------- fMRItools-0.7.2/fMRItools/man/cor_mat.Rd | 4 fMRItools-0.7.2/fMRItools/man/dice_overlap.Rd |only fMRItools-0.7.2/fMRItools/man/plot_FC_gg.Rd | 32 ++-- fMRItools-0.7.2/fMRItools/tests/testthat/test-misc.R | 6 14 files changed, 151 insertions(+), 84 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.6.0 dated 2025-10-31 and 0.6.1 dated 2025-12-23
DESCRIPTION | 20 MD5 | 197 +-- NAMESPACE | 1 R/addIndex.R | 6 R/collapseCohorts.R | 12 R/conceptCohort.R | 13 R/copyCohorts.R | 2 R/deathCohort.R | 5 R/demographicsCohort.R | 2 R/entryAtColumnDate.R | 4 R/exitAtColumnDate.R | 4 R/exitAtDate.R | 4 R/intersectCohorts.R | 2 R/matchCohorts.R | 2 R/measurementCohort.R | 2 R/mockCohortConstructor.R | 31 R/padCohortDate.R | 6 R/renameCohort.R | 2 R/requireCohortIntersect.R | 2 R/requireConceptIntersect.R | 4 R/requireDateRange.R | 38 R/requireDemographics.R | 10 R/requireDuration.R | 4 R/requireIsEntry.R | 6 R/requireMinCohortCount.R | 2 R/requireTableIntersect.R | 2 R/sampleCohorts.R | 2 R/stratifyCohorts.R | 2 R/subsetCohorts.R | 2 R/timeWindowCohorts.R |only R/trimDemographics.R | 2 R/unionCohorts.R | 8 R/yearCohorts.R | 2 README.md | 61 build/vignette.rds |binary inst/doc/a01_building_base_cohorts.html | 17 inst/doc/a02_cohort_table_requirements.R | 248 ++- inst/doc/a02_cohort_table_requirements.Rmd | 12 inst/doc/a02_cohort_table_requirements.html | 1744 ---------------------------- inst/doc/a03_require_demographics.R | 119 - inst/doc/a03_require_demographics.Rmd | 9 inst/doc/a03_require_demographics.html | 1298 -------------------- inst/doc/a04_require_intersections.html | 5 inst/doc/a05_update_cohort_start_end.R | 163 +- inst/doc/a05_update_cohort_start_end.Rmd | 11 inst/doc/a05_update_cohort_start_end.html | 130 -- inst/doc/a06_concatanate_cohorts.html | 5 inst/doc/a07_filter_cohorts.html | 5 inst/doc/a08_split_cohorts.html | 5 inst/doc/a09_combine_cohorts.html | 5 inst/doc/a10_match_cohorts.html | 5 inst/doc/a11_benchmark.html | 5 inst/doc/a12_behind_the_scenes.html | 5 man/addCohortTableIndex.Rd | 7 man/collapseCohorts.Rd | 13 man/conceptCohort.Rd | 2 man/copyCohorts.Rd | 2 man/deathCohort.Rd | 5 man/demographicsCohort.Rd | 2 man/entryAtFirstDate.Rd | 2 man/entryAtLastDate.Rd | 2 man/exitAtDeath.Rd | 2 man/exitAtFirstDate.Rd | 2 man/exitAtLastDate.Rd | 2 man/exitAtObservationEnd.Rd | 2 man/intersectCohorts.Rd | 2 man/matchCohorts.Rd | 2 man/mockCohortConstructor.Rd | 2 man/padCohortDate.Rd | 2 man/padCohortEnd.Rd | 2 man/padCohortStart.Rd | 2 man/renameCohort.Rd | 2 man/requireAge.Rd | 2 man/requireCohortIntersect.Rd | 2 man/requireConceptIntersect.Rd | 4 man/requireDemographics.Rd | 2 man/requireDuration.Rd | 2 man/requireFutureObservation.Rd | 2 man/requireInDateRange.Rd | 18 man/requireIsEntry.Rd | 2 man/requireIsFirstEntry.Rd | 2 man/requireIsLastEntry.Rd | 2 man/requireMinCohortCount.Rd | 2 man/requirePriorObservation.Rd | 2 man/requireSex.Rd | 2 man/requireTableIntersect.Rd | 2 man/sampleCohorts.Rd | 2 man/stratifyCohorts.Rd | 2 man/subsetCohorts.Rd | 2 man/timeWindowCohorts.Rd |only man/trimDemographics.Rd | 2 man/trimDuration.Rd | 2 man/trimToDateRange.Rd | 20 man/unionCohorts.Rd | 2 man/yearCohorts.Rd | 2 tests/testthat/test-conceptCohort.R | 33 tests/testthat/test-unionCohorts.R | 17 tests/testthat/timeWindowCohorts.R |only vignettes/a02_cohort_table_requirements.Rmd | 12 vignettes/a03_require_demographics.Rmd | 9 vignettes/a05_update_cohort_start_end.Rmd | 11 101 files changed, 685 insertions(+), 3787 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform prior [...truncated...]
Author: Merlise Clyde [aut, cre, cph] ,
Michael Littman [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb],
Betsy Bersson [ctb],
Don van de Bergh [ctb],
Quanli Wang [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 2.0.0 dated 2025-12-16 and 2.0.2 dated 2025-12-23
DESCRIPTION | 6 +- MD5 | 38 ++++++------ NEWS.md | 13 ++++ inst/doc/BAS-vignette.html | 132 ++++++++++++++++++++++----------------------- man/tr.power.prior.Rd | 10 +-- src/glm_deterministic.c | 14 ++++ src/glm_mcmc.c | 10 +++ src/glm_mcmc_grow.c | 9 +++ src/glm_mcmcbas.c | 8 ++ src/glm_sampleworep.c | 12 ++++ src/glm_sampleworep_grow.c | 13 ++++ src/lm_amcmc.c | 13 ++++ src/lm_amcmc_growable.c | 18 ++++-- src/lm_deterministic.c | 10 +++ src/lm_mcmc.c | 14 ++++ src/lm_mcmc_grow.c | 10 +++ src/lm_mcmcbas.c | 14 ++++ src/lm_sampleworep-grow.c | 11 +++ src/lm_sampleworep.c | 11 +++ src/model_probabilities.c | 7 +- 20 files changed, 263 insertions(+), 110 deletions(-)
Title: Hierarchical Methods for Differential Equations
Description: Wrapper for 'Stan' that offers a number of in-built models to implement a hierarchical Bayesian longitudinal model for repeat observation data. Model choice selects the differential equation that is fit to the observations. Single and multi-individual models are available. O'Brien et al. (2024) <doi:10.1111/2041-210X.14463>.
Author: Daniel Falster [aut, ctb] ,
Tess O'Brien [aut, cre, cph] ,
Fonti Kar [ctb] ,
David Warton [aut, ctb]
Maintainer: Tess O'Brien <tess_obrien@fastmail.com>
Diff between hmde versions 1.3 dated 2025-11-26 and 1.3.1 dated 2025-12-22
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 6 - inst/doc/canham.html | 2 inst/doc/constant-growth.html | 180 +++++++++++++++++----------------- inst/doc/here_be_dragons.html | 24 ++-- inst/doc/hmde_for_mathematicians.html | 4 inst/doc/von-bertalanffy.html | 79 +++++++------- 8 files changed, 155 insertions(+), 160 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping
functions to apply a function to each combination of elements in a
list of inputs. Also includes functions for automatically detecting
output type in mapping functions, finding every combination of
elements of lists or rows of data frames, and applying multiple models
to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.4.2 dated 2025-04-25 and 0.4.3 dated 2025-12-22
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/errors.R | 7 +++---- man/cross_fit_robust.Rd | 2 +- man/crossmap-package.Rd | 2 +- 6 files changed, 23 insertions(+), 20 deletions(-)
Title: CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation
Description: Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. [...truncated...]
Author: Xiao Zhang [aut, cre],
Wei Liu [aut],
Jin Liu [aut]
Maintainer: Xiao Zhang <zhangxiao1994@cuhk.edu.cn>
Diff between CAESAR.Suite versions 0.2.3 dated 2025-11-07 and 0.3.0 dated 2025-12-22
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/caesar.R | 6 +++--- R/caesar_annotation.R | 8 ++++---- R/caesar_enrichscore.R | 2 +- R/caesar_image.R | 2 +- R/ruv.R | 4 ++-- R/utilities.r | 1 + README.md | 1 + inst/doc/STMOB.html | 6 +++--- inst/doc/XeniumBC.html | 6 +++--- man/annotation_mat.Rd | 2 +- man/cellembedding_matrix.Rd | 2 +- 13 files changed, 36 insertions(+), 34 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.5.1 dated 2025-03-05 and 2.8.2 dated 2025-12-22
dataquieR-2.5.1/dataquieR/R/util_anytime_installed.R |only dataquieR-2.5.1/dataquieR/man/LONG_LABEL_EXCEPTION.Rd |only dataquieR-2.5.1/dataquieR/man/N_RULES.Rd |only dataquieR-2.5.1/dataquieR/man/UNIVARIATE_OUTLIER_CHECKTYPE.Rd |only dataquieR-2.5.1/dataquieR/man/cash-.dataquieR_result.Rd |only dataquieR-2.5.1/dataquieR/man/dataquieR.progress_fkt.Rd |only dataquieR-2.5.1/dataquieR/man/dataquieR.progress_msg_fkt.Rd |only dataquieR-2.5.1/dataquieR/man/dot-.indicator_or_descriptor.Rd |only dataquieR-2.5.1/dataquieR/man/dot-.manual.Rd |only dataquieR-2.5.1/dataquieR/man/dot-access_dq_rs2-set.Rd |only dataquieR-2.5.1/dataquieR/man/dot-access_dq_rs2.Rd |only dataquieR-2.5.1/dataquieR/man/dot-util_internal_normalize_meta_data.Rd |only dataquieR-2.5.1/dataquieR/man/figures |only dataquieR-2.5.1/dataquieR/man/menu_env.Rd |only dataquieR-2.5.1/dataquieR/man/meta_data_env_criteria.Rd |only dataquieR-2.5.1/dataquieR/man/meta_data_env_group_vars.Rd |only dataquieR-2.5.1/dataquieR/man/meta_data_env_id_vars.Rd |only dataquieR-2.5.1/dataquieR/man/meta_data_env_n_rules.Rd |only dataquieR-2.5.1/dataquieR/man/meta_data_env_time_vars.Rd |only dataquieR-2.5.1/dataquieR/man/sub-.dataquieR_result.Rd |only dataquieR-2.5.1/dataquieR/man/sub-sub-.dataquieR_result.Rd |only dataquieR-2.5.1/dataquieR/man/util_3SD.Rd |only dataquieR-2.5.1/dataquieR/man/util_abbreviate.Rd |only dataquieR-2.5.1/dataquieR/man/util_abbreviate_unique.Rd |only dataquieR-2.5.1/dataquieR/man/util_acc_loess_bin.Rd |only dataquieR-2.5.1/dataquieR/man/util_acc_loess_continuous.Rd |only dataquieR-2.5.1/dataquieR/man/util_acc_varcomp.Rd |only dataquieR-2.5.1/dataquieR/man/util_adjust_data_type.Rd |only dataquieR-2.5.1/dataquieR/man/util_adjust_geom_text_for_plotly.Rd |only dataquieR-2.5.1/dataquieR/man/util_alias2caption.Rd |only dataquieR-2.5.1/dataquieR/man/util_all_ind_functions.Rd |only dataquieR-2.5.1/dataquieR/man/util_all_intro_vars_for_rv.Rd |only dataquieR-2.5.1/dataquieR/man/util_all_is_integer.Rd |only dataquieR-2.5.1/dataquieR/man/util_anytime_installed.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_cd.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_con_contradictions_redcap.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_dc.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_dl.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_ed.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_hl.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_iac.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_iav.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_im.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_loess.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_mar.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_mol.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_ol.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_sl.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_sm.Rd |only dataquieR-2.5.1/dataquieR/man/util_app_sos.Rd |only 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dataquieR-2.5.1/dataquieR/man/util_ensure_suggested.Rd |only dataquieR-2.5.1/dataquieR/man/util_error.Rd |only dataquieR-2.5.1/dataquieR/man/util_eval_rule.Rd |only dataquieR-2.5.1/dataquieR/man/util_eval_to_dataquieR_result.Rd |only dataquieR-2.5.1/dataquieR/man/util_evaluate_calls.Rd |only dataquieR-2.5.1/dataquieR/man/util_expect_data_frame.Rd |only dataquieR-2.5.1/dataquieR/man/util_expect_scalar.Rd |only dataquieR-2.5.1/dataquieR/man/util_extract_all_ids.Rd |only dataquieR-2.5.1/dataquieR/man/util_extract_indicator_metrics.Rd |only dataquieR-2.5.1/dataquieR/man/util_extract_matches.Rd |only dataquieR-2.5.1/dataquieR/man/util_filter_missing_list_table_for_rv.Rd |only dataquieR-2.5.1/dataquieR/man/util_filter_names_by_regexps.Rd |only dataquieR-2.5.1/dataquieR/man/util_finalize_sizing_hints.Rd |only dataquieR-2.5.1/dataquieR/man/util_find_external_functions_in_stacktrace.Rd |only dataquieR-2.5.1/dataquieR/man/util_find_first_externally_called_functions_in_stacktrace.Rd |only 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dataquieR-2.8.2/dataquieR/tests/testthat/test-util_par_pmap.R | 2 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_parallel_futures.R | 20 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_parse_redcap_rule.R | 208 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_plot_categorical_vars.R | 38 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_plot_figure_plotly.R | 1 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_readr_cols_from_metadata.R |only dataquieR-2.8.2/dataquieR/tests/testthat/test-util_remove_na_records.R | 2 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_render_table_dataquieR_summary.R | 35 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_replace_codes_by_na.R | 2 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_validate_known_meta.R | 4 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_varcomp_robust.R | 1 dataquieR-2.8.2/dataquieR/tests/testthat/test-util_warning.R | 4 1071 files changed, 48536 insertions(+), 36315 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.0.0 dated 2025-11-04 and 1.1.0 dated 2025-12-22
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Title: Hardware-Accelerated Rerandomization for Improved Balance
Description: Provides hardware-accelerated tools for performing rerandomization
and randomization testing in experimental research. Using a 'JAX' backend, the
package enables exact rerandomization inference even for large experiments
with hundreds of billions of possible randomizations. Key functionalities
include generating pools of acceptable rerandomizations based on covariate
balance, conducting exact randomization tests, and performing pre-analysis
evaluations to determine optimal rerandomization acceptance thresholds. The
package supports various hardware acceleration frameworks including 'CPU',
'CUDA', and 'METAL', making it versatile across accelerated computing environments. This
allows researchers to efficiently implement stringent rerandomization designs and
conduct valid inference even with large sample sizes. The package is partly based on Jerzak and Goldstein (2023) <doi:10.48550/arXiv.2310.00861>.
Author: Fucheng Warren Zhu [aut] ,
Aniket Sachin Kamat [aut] ,
Connor Jerzak [aut, cre] ,
Rebecca Goldstein [aut]
Maintainer: Connor Jerzak <connor.jerzak@gmail.com>
Diff between fastrerandomize versions 0.2 dated 2025-01-14 and 0.3 dated 2025-12-22
DESCRIPTION | 20 +++-- MD5 | 68 ++++++++++------- NAMESPACE | 14 +++ NEWS.md |only R/FRR_BaseRFxns.R |only R/FRR_BuildBackend.R | 82 ++++++++++++++++---- R/FRR_Diagnostics.R |only R/FRR_Dist.R |only R/FRR_GenerateRandomizations.R | 32 ++++---- R/FRR_GenerateRandomizations_Exact.R | 26 +++--- R/FRR_GenerateRandomizations_MonteCarlo.R | 34 ++++---- R/FRR_HelperFxns.R | 7 + R/FRR_InitializeJAX.R | 110 +++++++++++++++++++++++++++- R/FRR_QJEData.R | 2 R/FRR_RandomizationTest.R | 61 +++++---------- R/FRR_S3Constructors.R | 32 ++++---- build/vignette.rds |binary data/QJEData.RData |binary data/YOPData.RData |binary inst/CITATION | 16 ++-- inst/doc/MainVignette.R | 6 - inst/doc/MainVignette.Rmd | 14 +-- inst/doc/MainVignette.html | 36 ++++----- man/QJEData.Rd | 2 man/build_backend.Rd | 10 +- man/check_jax_availability.Rd | 4 - man/compute_diff_at_tau_for_oneW_R.Rd |only man/diagnose_rerandomization.Rd |only man/diff_in_means_R.Rd |only man/fast_distance.Rd |only man/find_fiducial_interval_R.Rd |only man/generate_randomizations.Rd | 4 - man/generate_randomizations_R.Rd |only man/generate_randomizations_exact.Rd | 4 - man/generate_randomizations_mc.Rd | 4 - man/hotellingT2_R.Rd |only man/plot.fastrerandomize_randomizations.Rd | 7 - man/print.fastrerandomize_randomizations.Rd | 2 man/randomization_test.Rd | 46 +---------- man/randomization_test_R.Rd |only vignettes/MainVignette.Rmd | 14 +-- 41 files changed, 400 insertions(+), 257 deletions(-)
More information about fastrerandomize at CRAN
Permanent link
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between embryogrowth versions 10.4 dated 2025-09-10 and 2025.12.22 dated 2025-12-22
DESCRIPTION | 8 +- MD5 | 44 ++++++------- NEWS | 8 ++ R/HeterogeneityNests.R | 85 +++++++++++++++---------- R/P_TRT.R | 23 ++++-- R/embryogrowth-package.R | 4 - R/modelTSD.R | 9 ++ R/plot.tsd.R | 17 +++-- R/plotR.R | 3 R/tsd.R | 142 +++++++++++++++++++++++-------------------- R/tsd_MHmcmc.R | 1 R/tsd_MHmcmc_p.R | 4 + R/tsd_fit.R | 4 - build/partial.rdb |binary data/DatabaseNestingArea.rda |binary data/DatabaseTSD.rda |binary data/ROSIE.rda |binary data/TSP.list.rda |binary data/stages.rda |binary man/HeterogeneityNests.Rd | 8 +- man/embryogrowth-package.Rd | 4 - man/figures/E.png |binary man/tsd.Rd | 14 +++- 23 files changed, 224 insertions(+), 154 deletions(-)
Title: Spatial Bayesian Methods for Task Functional MRI Studies
Description: Performs a spatial Bayesian general linear model (GLM) for task
functional magnetic resonance imaging (fMRI) data on the cortical surface.
Additional models include group analysis and inference to detect thresholded
areas of activation. Includes direct support for the 'CIFTI' neuroimaging
file format. For more information see A. F. Mejia, Y. R. Yue, D. Bolin, F.
Lindgren, M. A. Lindquist (2020) <doi:10.1080/01621459.2019.1611582> and D.
Spencer, Y. R. Yue, D. Bolin, S. Ryan, A. F. Mejia (2022)
<doi:10.1016/j.neuroimage.2022.118908>.
Author: Amanda Mejia [aut, cre],
Damon Pham [ctb] ,
David Bolin [ctb],
Yu Yue [ctb],
Daniel Spencer [aut] ,
Sarah Ryan [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between BayesfMRI versions 0.10.1 dated 2025-03-07 and 0.11.0 dated 2025-12-22
DESCRIPTION | 12 ++++++------ MD5 | 34 ++++++++++++++++++---------------- NEWS.md | 6 ++++++ R/BayesGLM.R | 4 ++-- R/GLM_est_resid_var_pw.R | 2 +- R/fit_bayesglm.R | 4 +--- R/fit_bayesglm_utils.R | 2 +- R/onAttach.R |only R/rox_args_docs.R | 4 +++- R/scale_BOLD.R | 3 ++- R/util.R | 14 +++++++++++--- README.md | 18 +++++++++++++----- build/partial.rdb |binary man/BayesGLM.Rd | 8 +++++--- man/do_QC.Rd | 8 ++++++-- man/dot-onAttach.Rd |only man/fit_bayesglm.Rd | 6 ++++-- man/mean_var_Tol_Param.Rd | 4 +++- man/scale_BOLD.Rd | 3 ++- 19 files changed, 84 insertions(+), 48 deletions(-)
Title: Quantile-Quantile Plot with Several Gaussian Simulations
Description: Plots a QQ-Norm Plot with several Gaussian simulations.
Author: Matthias Salvisberg [aut, cre]
Maintainer: Matthias Salvisberg <matthias.salvisberg@gmail.com>
Diff between StMoSim versions 3.1.1 dated 2018-11-19 and 3.2.0 dated 2025-12-22
DESCRIPTION | 20 ++++++++++++-------- MD5 | 17 +++++++++-------- R/StMoSim.R | 6 +++++- README.md |only man/StMoSim.Rd | 13 ++++++++++++- man/qqnormSim.Rd | 49 ++++++++++++++++++++++++++++++++++++------------- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ src/qqnormSim.cpp | 1 - 10 files changed, 79 insertions(+), 34 deletions(-)
Title: Date and Time Extensions for the 'rebus' Package
Description: Build regular expressions piece by piece using human readable code.
This package contains date and time functionality, and is primarily intended
to be used by package developers.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus.datetimes versions 0.0-2 dated 2022-11-03 and 0.0-2.1 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/datetime.R | 2 +- man/DateTime.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
More information about rebus.datetimes at CRAN
Permanent link
Title: Kendall Rank Correlation and Mann-Kendall Trend Test
Description: Computes the Kendall rank correlation and Mann-Kendall
trend test. See documentation for use of block bootstrap when
there is autocorrelation.
Author: A.I. McLeod [aut, cre]
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between Kendall versions 2.2.1 dated 2022-03-20 and 2.2.2 dated 2025-12-22
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- data/GuelphP.rda |binary data/PrecipGL.rda |binary man/MannKendall.Rd | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Dyadic Structural Equation Modeling
Description: Scripting of structural equation models via 'lavaan' for
Dyadic Data Analysis, and helper functions for supplemental
calculations, tabling, and model visualization.
Author: John Sakaluk [aut, cre, cph] ,
Omar Camanto [aut] ,
Christopher Quinn-Nilas [ctb] ,
Merissa Prine [ctb],
Robyn Kilshaw [ctb],
Alexandra Fisher [ctb]
Maintainer: John Sakaluk <jksakaluk@gmail.com>
Diff between dySEM versions 1.1.1 dated 2025-01-07 and 1.4.1 dated 2025-12-22
dySEM-1.1.1/dySEM/R/semHelpers.R |only dySEM-1.4.1/dySEM/DESCRIPTION | 34 dySEM-1.4.1/dySEM/MD5 | 152 dySEM-1.4.1/dySEM/NAMESPACE | 5 dySEM-1.4.1/dySEM/NEWS.md | 41 dySEM-1.4.1/dySEM/R/getConstraintTests.R | 6 dySEM-1.4.1/dySEM/R/getDyReliability.R | 4 dySEM-1.4.1/dySEM/R/getDydmacs.R | 2 dySEM-1.4.1/dySEM/R/getIndistFit.R | 95 dySEM-1.4.1/dySEM/R/getInvarCompTable.R | 124 dySEM-1.4.1/dySEM/R/imsM-data.R |only dySEM-1.4.1/dySEM/R/outHelpers.R | 98 dySEM-1.4.1/dySEM/R/outputConstraintTab.R | 157 dySEM-1.4.1/dySEM/R/outputHelpers.R |only dySEM-1.4.1/dySEM/R/outputInvarCompTab.R | 201 - dySEM-1.4.1/dySEM/R/outputModel.R | 4 dySEM-1.4.1/dySEM/R/outputParamFig.R | 123 dySEM-1.4.1/dySEM/R/outputParamTab.R | 1023 +++-- dySEM-1.4.1/dySEM/R/outputUniConstructComp.R |only dySEM-1.4.1/dySEM/R/pnrqM-data.R |only dySEM-1.4.1/dySEM/R/prqcQ-data.R |only dySEM-1.4.1/dySEM/R/scrapeHelpers.R | 62 dySEM-1.4.1/dySEM/R/scrapeVarCross.R | 340 + dySEM-1.4.1/dySEM/R/scriptAPIM.R | 588 +-- dySEM-1.4.1/dySEM/R/scriptBiDy.R | 6 dySEM-1.4.1/dySEM/R/scriptBifac.R |only dySEM-1.4.1/dySEM/R/scriptCFA.R | 440 +- dySEM-1.4.1/dySEM/R/scriptCFM.R | 19 dySEM-1.4.1/dySEM/R/scriptCor.R |only dySEM-1.4.1/dySEM/R/scriptDyEFA.R | 34 dySEM-1.4.1/dySEM/R/scriptHelpers.R | 631 +++ dySEM-1.4.1/dySEM/R/scriptHier.R |only dySEM-1.4.1/dySEM/R/scriptINULL.R | 111 dySEM-1.4.1/dySEM/R/scriptISAT.R | 2 dySEM-1.4.1/dySEM/R/scriptMIM.R | 6 dySEM-1.4.1/dySEM/R/scriptUni.R |only dySEM-1.4.1/dySEM/R/startup.R | 7 dySEM-1.4.1/dySEM/README.md | 68 dySEM-1.4.1/dySEM/build/vignette.rds |binary dySEM-1.4.1/dySEM/data/imsM.rda |only dySEM-1.4.1/dySEM/data/pnrqM.rda |only dySEM-1.4.1/dySEM/data/prqcQ.rda |only dySEM-1.4.1/dySEM/inst/doc/dySEM.R | 10 dySEM-1.4.1/dySEM/inst/doc/dySEM.Rmd | 28 dySEM-1.4.1/dySEM/inst/doc/dySEM.html | 179 - dySEM-1.4.1/dySEM/inst/doc/varnames.html | 5 dySEM-1.4.1/dySEM/man/getConstraintTests.Rd | 2 dySEM-1.4.1/dySEM/man/getDyReliability.Rd | 4 dySEM-1.4.1/dySEM/man/getDydmacs.Rd | 2 dySEM-1.4.1/dySEM/man/getIndistFit.Rd | 28 dySEM-1.4.1/dySEM/man/getInvarCompTable.Rd | 70 dySEM-1.4.1/dySEM/man/imsM.Rd |only dySEM-1.4.1/dySEM/man/outputConstraintTab.Rd | 26 dySEM-1.4.1/dySEM/man/outputInvarCompTab.Rd | 91 dySEM-1.4.1/dySEM/man/outputModel.Rd | 2 dySEM-1.4.1/dySEM/man/outputParamFig.Rd | 60 dySEM-1.4.1/dySEM/man/outputParamTab.Rd | 62 dySEM-1.4.1/dySEM/man/outputUniConstructComp.Rd |only dySEM-1.4.1/dySEM/man/pnrqM.Rd |only dySEM-1.4.1/dySEM/man/prqcQ.Rd |only dySEM-1.4.1/dySEM/man/scrapeVarCross.Rd | 32 dySEM-1.4.1/dySEM/man/scriptAPIM.Rd | 31 dySEM-1.4.1/dySEM/man/scriptBiDy.Rd | 12 dySEM-1.4.1/dySEM/man/scriptBifac.Rd |only dySEM-1.4.1/dySEM/man/scriptCFA.Rd | 151 dySEM-1.4.1/dySEM/man/scriptCFM.Rd | 12 dySEM-1.4.1/dySEM/man/scriptCor.Rd |only dySEM-1.4.1/dySEM/man/scriptDyEFA.Rd | 14 dySEM-1.4.1/dySEM/man/scriptHier.Rd |only dySEM-1.4.1/dySEM/man/scriptINULL.Rd | 12 dySEM-1.4.1/dySEM/man/scriptISAT.Rd | 12 dySEM-1.4.1/dySEM/man/scriptMIM.Rd | 14 dySEM-1.4.1/dySEM/man/scriptUni.Rd |only dySEM-1.4.1/dySEM/tests/testthat/test-getDyReliability.R | 2 dySEM-1.4.1/dySEM/tests/testthat/test-outHelpers.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputConstraintTab.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputInvarCompTab.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputModel-fileIO.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputParamFig.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputParamTab-fileIO.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputParamTab.R |only dySEM-1.4.1/dySEM/tests/testthat/test-outputUniConstructComp.R |only dySEM-1.4.1/dySEM/tests/testthat/test-scrapeVarCross.R | 607 +++ dySEM-1.4.1/dySEM/tests/testthat/test-scriptAPIM.R | 565 ++- dySEM-1.4.1/dySEM/tests/testthat/test-scriptBiDy.R | 292 + dySEM-1.4.1/dySEM/tests/testthat/test-scriptBifac.R |only dySEM-1.4.1/dySEM/tests/testthat/test-scriptCFA.R | 1541 ++++++-- dySEM-1.4.1/dySEM/tests/testthat/test-scriptCFM.R | 366 ++ dySEM-1.4.1/dySEM/tests/testthat/test-scriptCor.R |only dySEM-1.4.1/dySEM/tests/testthat/test-scriptHelpers.R | 1725 ++++++---- dySEM-1.4.1/dySEM/tests/testthat/test-scriptHier.R |only dySEM-1.4.1/dySEM/tests/testthat/test-scriptUni.R |only dySEM-1.4.1/dySEM/tests/testthat/test-semHelpers.R |only dySEM-1.4.1/dySEM/vignettes/dySEM.Rmd | 28 94 files changed, 7389 insertions(+), 2979 deletions(-)
Title: Collection of Correlation and Association Estimators
Description: Compute correlation and other association matrices from
small to high-dimensional datasets with relative simple functions and
sensible defaults. Includes options for shrinkage and robustness to improve
results in noisy or high-dimensional settings (p >= n), plus convenient
print/plot methods for inspection. Implemented with optimised C++ backends
using BLAS/OpenMP and memory-aware symmetric updates. Works with base
matrices and data frames, returning standard R objects via a consistent S3
interface. Useful across genomics, agriculture, and machine-learning
workflows. Supports Pearson, Spearman, Kendall, distance correlation,
partial correlation, and robust biweight mid-correlation; Bland–Altman
analyses and Lin's concordance correlation coefficient (including
repeated-measures extensions). Methods based on Ledoit and Wolf (2004)
<doi:10.1016/S0047-259X(03)00096-4>; Schäfer and Strimmer (2005)
<doi:10.2202/1544-6115.1175>; Lin (1989) <doi:10.2307/2532051>.
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.7.2 dated 2025-12-03 and 0.8.3 dated 2025-12-22
DESCRIPTION | 9 MD5 | 83 +- NAMESPACE | 6 R/biweight_mid_corr.R | 186 +++--- R/bland_altman.R | 128 ++-- R/bland_altman_repeated.R | 76 ++ R/ccc_repeated.R | 865 ++++++++++++++-------------- R/concordance_corr.R | 129 ++-- R/distance_corr.R | 65 +- R/kendall_corr.R | 140 ++-- R/partial_correlation.R | 132 ++-- R/pearson_corr.R | 51 - R/schafer_corr.R | 51 - R/spearman_rho.R | 28 R/validate_corr_input.R | 12 R/view_corr_shiny.R |only man/biweight_mid_corr.Rd | 12 man/ccc.Rd | 5 man/ccc_lmm_reml.Rd | 9 man/ccc_pairwise_u_stat.Rd | 5 man/distance_corr.Rd | 5 man/kendall_tau.Rd | 5 man/partial_correlation.Rd | 9 man/pearson_corr.Rd | 5 man/schafer_corr.Rd | 7 man/spearman_rho.Rd | 4 man/view_corr_shiny.Rd |only src/biweight_mid_corr.cpp | 198 ++++-- src/ccc_repeated.cpp | 4 src/concordance_corr.cpp | 25 src/distance_correlation.cpp | 57 - src/kendall_corr.cpp | 13 src/matrixCorr_detail.h | 9 src/partial_correlation.cpp | 28 tests/testthat/test_biweight_mid_corr.R | 35 - tests/testthat/test_bland_altman.R | 10 tests/testthat/test_bland_altman_repeated.R | 36 + tests/testthat/test_distance_corr.R | 20 tests/testthat/test_kendall.R | 45 - tests/testthat/test_partial_correlation.R |only tests/testthat/test_pearson_corr.R | 22 tests/testthat/test_schafer_corr.R |only tests/testthat/test_spearman_rho.R | 22 tests/testthat/test_view_corr_shiny.R |only tests/testthat/tests_partial_correlation.R | 2 45 files changed, 1539 insertions(+), 1014 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: 'HDF5' (Hierarchical Data Format 5) is a high-performance
library and file format for storing and managing large, complex
data. This package provides the static libraries and headers for
the 'HDF5' 'C' library (release 2.0.0). It is intended for R
package developers to use in the 'LinkingTo' field, which
eliminates the need for users to install system-level 'HDF5'
dependencies. This build is compiled with thread-safety enabled
and supports dynamic loading of external compression filters.
'HDF5' is developed by 'The HDF Group' <https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
The HDF Group [cph] ,
Jean-loup Mark [cph] ,
Gailly Adler [cph]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.0.0.3 dated 2025-12-14 and 2.0.0.4 dated 2025-12-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ configure | 7 +++++-- src/zlib-1.3.1.tar.gz |binary 5 files changed, 18 insertions(+), 9 deletions(-)
Title: Truncated Functional Generalized Linear Models
Description: An implementation of the methodologies described in Xi Liu, Afshin A. Divani, and Alexander Petersen (2022) <doi:10.1016/j.csda.2022.107421>, including
truncated functional linear and truncated functional logistic regression models.
Author: Xi Liu [aut],
Chau Tran [aut, cre],
Alexander Petersen [aut]
Maintainer: Chau Tran <cbtr@ucdavis.edu>
Diff between FGLMtrunc versions 0.1.0 dated 2022-05-26 and 0.2.0 dated 2025-12-22
DESCRIPTION | 12 - MD5 | 12 - build/vignette.rds |binary inst/doc/FGLMtrunc.R | 34 ++--- inst/doc/FGLMtrunc.html | 294 ++++++++++++++++++++++++------------------------ src/Makevars | 1 src/Makevars.win | 1 7 files changed, 180 insertions(+), 174 deletions(-)
Title: Regularization in Cox Frailty Models
Description: Different regularization approaches for Cox Frailty Models by penalization methods are provided.
see Groll et al. (2017) <doi:10.1111/biom.12637> for effects selection.
See also Groll and Hohberg (2024) <doi:10.1002/bimj.202300020> for classical LASSO approach.
Author: Andreas Groll [aut, cre]
Maintainer: Andreas Groll <groll@statistik.tu-dortmund.de>
Diff between PenCoxFrail versions 2.0.0 dated 2024-07-04 and 2.0.1 dated 2025-12-22
DESCRIPTION | 21 +++++++++++++-------- MD5 | 16 ++++++++-------- demo/pencoxfrail-pbc.r | 4 ++-- man/coxFL.Rd | 4 ++-- man/coxlasso.rd | 4 ++-- man/coxridge.rd | 4 ++-- man/pencoxfrail.rd | 15 ++++++++------- src/IntegrMulti.cpp | 1 - src/Makevars.win | 1 - 9 files changed, 37 insertions(+), 33 deletions(-)
Title: Broken Adaptive Ridge Regression with Cyclops
Description: Approximates best-subset selection (L0) regression with
an iteratively adaptive Ridge (L2) penalty for large-scale models.
This package uses Cyclops for an efficient implementation and the
iterative method is described in Kawaguchi et al (2020)
<doi:10.1002/sim.8438> and Li et al (2021)
<doi:10.1016/j.jspi.2020.12.001>.
Author: Marc A. Suchard [aut, cre],
Eric Kawaguchi [aut],
Ning Li [aut],
Gang Li [aut],
Observational Health Data Sciences and Informatics [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between BrokenAdaptiveRidge versions 1.0.1 dated 2025-07-23 and 1.0.2 dated 2025-12-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 8 +++++++- R/Prior.R | 13 ++++++++----- R/fastBarPrior.R | 13 ++++++++----- 5 files changed, 32 insertions(+), 20 deletions(-)
More information about BrokenAdaptiveRidge at CRAN
Permanent link
Title: Tandem Repeat Analysis by Capillary Electrophoresis
Description: A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).
Author: Zachariah McLean [aut, cre, cph] ,
Kevin Correia [aut],
Andrew Jiang [ctb]
Maintainer: Zachariah McLean <zachariah.louis.mclean@gmail.com>
Diff between trace versions 0.6.0 dated 2025-03-14 and 1.0.0 dated 2025-12-22
trace-0.6.0/trace/R/read_fsa.R |only trace-0.6.0/trace/inst/extdata/_extensions |only trace-0.6.0/trace/man/fragments_repeats.Rd |only trace-0.6.0/trace/man/fragments_trace.Rd |only trace-0.6.0/trace/man/generate_trace_template.Rd |only trace-0.6.0/trace/man/peak_table_to_fragments.Rd |only trace-0.6.0/trace/man/repeat_table_to_repeats.Rd |only trace-0.6.0/trace/tests/testthat/test-classes.R |only trace-0.6.0/trace/tests/testthat/test-tidiers.R |only trace-1.0.0/trace/DESCRIPTION | 19 trace-1.0.0/trace/MD5 | 150 - trace-1.0.0/trace/NAMESPACE | 17 trace-1.0.0/trace/NEWS.md | 64 trace-1.0.0/trace/R/add_metadata.R | 161 - trace-1.0.0/trace/R/assign_index_peaks.R | 162 + trace-1.0.0/trace/R/calculate_instability_metrics.R | 937 +++++----- trace-1.0.0/trace/R/call_repeats.R | 386 ++-- trace-1.0.0/trace/R/classes.R | 234 +- trace-1.0.0/trace/R/config.R |only trace-1.0.0/trace/R/constructors.R | 305 +-- trace-1.0.0/trace/R/extract_functions.R | 115 - trace-1.0.0/trace/R/find_alleles.R | 95 - trace-1.0.0/trace/R/find_fragments.R | 140 - trace-1.0.0/trace/R/find_ladders.R | 716 +++++-- trace-1.0.0/trace/R/fix_ladders_shiny_app.R | 39 trace-1.0.0/trace/R/main.R |only trace-1.0.0/trace/R/misc.R | 115 - trace-1.0.0/trace/R/plotting.R | 134 - trace-1.0.0/trace/README.md | 236 -- trace-1.0.0/trace/build/partial.rdb |binary trace-1.0.0/trace/build/vignette.rds |binary trace-1.0.0/trace/data/cell_line_fsa_list.rda |binary trace-1.0.0/trace/data/example_data_repeat_table.rda |binary trace-1.0.0/trace/inst/doc/plotting_traces.R | 46 trace-1.0.0/trace/inst/doc/plotting_traces.Rmd | 51 trace-1.0.0/trace/inst/doc/plotting_traces.html | 172 - trace-1.0.0/trace/inst/extdata/trace_config.yaml |only trace-1.0.0/trace/man/add_metadata.Rd | 55 trace-1.0.0/trace/man/assign_index_peaks.Rd | 61 trace-1.0.0/trace/man/calculate_instability_metrics.Rd | 71 trace-1.0.0/trace/man/call_repeats.Rd | 86 trace-1.0.0/trace/man/extract_alleles.Rd | 18 trace-1.0.0/trace/man/extract_fragments.Rd | 30 trace-1.0.0/trace/man/extract_ladder_summary.Rd | 12 trace-1.0.0/trace/man/extract_repeat_correction_summary.Rd | 33 trace-1.0.0/trace/man/extract_trace_table.Rd | 12 trace-1.0.0/trace/man/figures/README-ggplot-1.png |binary trace-1.0.0/trace/man/figures/README-plot_fragments-1.png |binary trace-1.0.0/trace/man/figures/README-plot_ladders-1.png |binary trace-1.0.0/trace/man/figures/README-plot_traces-1.png |binary trace-1.0.0/trace/man/figures/README-unnamed-chunk-2-1.png |binary trace-1.0.0/trace/man/find_alleles.Rd | 36 trace-1.0.0/trace/man/find_fragments.Rd | 50 trace-1.0.0/trace/man/find_ladders.Rd | 78 trace-1.0.0/trace/man/fix_ladders_interactive.Rd | 17 trace-1.0.0/trace/man/fix_ladders_manual.Rd | 18 trace-1.0.0/trace/man/fragments.Rd | 155 + trace-1.0.0/trace/man/genemapper_table_to_fragments.Rd |only trace-1.0.0/trace/man/load_config.Rd |only trace-1.0.0/trace/man/plot_batch_correction_samples.Rd | 24 trace-1.0.0/trace/man/plot_data_channels.Rd | 2 trace-1.0.0/trace/man/plot_fragments.Rd | 16 trace-1.0.0/trace/man/plot_ladders.Rd | 12 trace-1.0.0/trace/man/plot_repeat_correction_model.Rd | 26 trace-1.0.0/trace/man/plot_traces.Rd | 21 trace-1.0.0/trace/man/read_fsa.Rd | 8 trace-1.0.0/trace/man/remove_fragments.Rd | 6 trace-1.0.0/trace/man/repeat_table_to_fragments.Rd |only trace-1.0.0/trace/man/size_table_to_fragments.Rd |only trace-1.0.0/trace/man/trace-package.Rd | 1 trace-1.0.0/trace/man/trace.Rd |only trace-1.0.0/trace/tests/testthat/fixtures |only trace-1.0.0/trace/tests/testthat/test-add_metadata.R | 124 - trace-1.0.0/trace/tests/testthat/test-assign_index_peaks.R | 58 trace-1.0.0/trace/tests/testthat/test-calculate_instability_metrics.R | 143 + trace-1.0.0/trace/tests/testthat/test-call_repeats.R | 163 + trace-1.0.0/trace/tests/testthat/test-constructors.R | 23 trace-1.0.0/trace/tests/testthat/test-extract_functions.R | 3 trace-1.0.0/trace/tests/testthat/test-find_alleles.R | 39 trace-1.0.0/trace/tests/testthat/test-find_fragments.R | 15 trace-1.0.0/trace/tests/testthat/test-find_ladders.R | 109 - trace-1.0.0/trace/tests/testthat/test-full-pipeline.R | 24 trace-1.0.0/trace/tests/testthat/test-main.R |only trace-1.0.0/trace/tests/testthat/test-shinytest2.R | 143 - trace-1.0.0/trace/tests/testthat/test-trace_output.R |only trace-1.0.0/trace/vignettes/plotting_traces.Rmd | 51 86 files changed, 3057 insertions(+), 2980 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through PyPI.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
This is a re-admission after prior archival of version 1.0.6 dated 2025-11-17
Diff between shapr versions 1.0.6 dated 2025-11-17 and 1.0.7 dated 2025-12-22
DESCRIPTION | 20 LICENSE | 4 MD5 | 622 NAMESPACE | 276 NEWS.md | 554 R/RcppExports.R | 590 R/approach.R | 262 R/approach_categorical.R | 506 R/approach_copula.R | 346 R/approach_ctree.R | 610 R/approach_empirical.R | 1222 - R/approach_gaussian.R | 346 R/approach_independence.R | 256 R/approach_regression_separate.R | 1022 R/approach_regression_surrogate.R | 487 R/approach_timeseries.R | 296 R/approach_vaeac.R | 5843 ++-- R/approach_vaeac_torch_modules.R | 4098 +-- R/asymmetric_and_causal_Shapley.R | 1039 R/check_convergence.R | 180 R/cli.R | 840 R/compute_estimates.R | 723 R/compute_vS.R | 611 R/documentation.R | 172 R/explain.R | 1312 - R/explain_forecast.R | 922 R/finalize_explanation.R | 453 R/get_feature_specs.R | 144 R/get_predict_model.R | 176 R/get_results.R | 258 R/model.R | 348 R/model_ar.R | 69 R/model_arima.R | 184 R/model_glm.R | 70 R/model_lm.R | 64 R/model_mgcv_gam.R | 82 R/model_ranger.R | 172 R/model_workflow.R | 64 R/model_xgboost.R | 172 R/plot.R | 4041 +-- R/prepare_next_iteration.R | 194 R/print.R | 52 R/save_results.R | 50 R/setup.R | 3701 +-- R/shapley_setup.R | 1658 - R/shapr-package.R | 66 R/summary.R | 274 R/testthat-helpers.R | 56 R/timing.R | 162 R/utils.R | 22 R/zzz.R | 346 README.md | 736 build/vignette.rds |binary inst/CITATION | 52 inst/REFERENCES.bib | 482 inst/doc/asymmetric_causal.Rmd | 4682 +-- inst/doc/asymmetric_causal.html | 5384 ++-- inst/doc/general_usage.Rmd | 5948 ++--- inst/doc/general_usage.html | 6932 ++--- inst/doc/regression.Rmd |11421 ++++++--- inst/doc/regression.html |11839 ++++++---- inst/doc/vaeac.Rmd | 2726 +- inst/doc/vaeac.html | 3418 +- man/additional_regression_setup.Rd | 38 man/aicc_full_cpp.Rd | 72 man/aicc_full_single_cpp.Rd | 64 man/append_vS_list.Rd | 44 man/categorical_to_one_hot_layer.Rd | 66 man/check_categorical_valid_MCsamp.Rd | 60 man/check_convergence.Rd | 38 man/check_groups.Rd | 24 man/check_verbose.Rd | 66 man/cli_compute_vS.Rd | 38 man/cli_iter.Rd | 72 man/cli_startup.Rd | 66 man/cli_topline.Rd | 96 man/coalition_matrix_cpp.Rd | 50 man/compute_MSEv_eval_crit.Rd | 168 man/compute_estimates.Rd | 44 man/compute_shapley.Rd | 46 man/compute_time.Rd | 38 man/compute_vS.Rd | 38 man/convert_feature_name_to_idx.Rd | 76 man/correction_matrix_cpp.Rd | 50 man/create_coalition_table.Rd | 194 man/create_ctree.Rd | 82 man/create_marginal_data_cat.Rd | 122 man/create_marginal_data_gaussian.Rd | 50 man/create_marginal_data_training.Rd | 74 man/default_doc_export.Rd | 52 man/default_doc_internal.Rd | 142 man/exact_coalition_table.Rd | 56 man/explain.Rd | 1241 - man/explain_forecast.Rd | 768 man/figures/README-basic_example-1.png |binary man/finalize_explanation.Rd | 38 man/format_convergence_info.Rd | 42 man/format_info_basic.Rd | 36 man/format_info_extra.Rd | 36 man/format_round.Rd | 44 man/format_shapley_info.Rd | 50 man/gauss_cat_loss.Rd | 60 man/gauss_cat_parameters.Rd | 64 man/gauss_cat_sampler_most_likely.Rd | 66 man/gauss_cat_sampler_random.Rd | 60 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Title: Simulation and Inference for Stochastic Differential Equations
Description: Description: Provides functions for simulation and inference for stochastic differential equations (SDEs). It accompanies the book "Simulation and Inference for Stochastic Differential Equations: With R Examples" (Iacus, 2008, Springer; ISBN: 978-0-387-75838-1).
Author: Stefano Maria Iacus [aut, cre]
Maintainer: Stefano Maria Iacus <smiacus@gmail.com>
Diff between sde versions 2.0.18 dated 2022-08-09 and 2.0.21 dated 2025-12-22
DESCRIPTION | 18 +++++++------ MD5 | 10 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sde.errata.pdf |binary src/sde.sim.c | 64 +++++++++++++++++++----------------------------- 6 files changed, 41 insertions(+), 51 deletions(-)
Title: An Imputation Approach to Estimating Path-Specific Causal
Effects
Description: In causal mediation analysis with multiple causally ordered mediators, a set of path-specific
effects are identified under standard ignorability assumptions. This package implements an imputation
approach to estimating these effects along with a set of bias formulas for conducting sensitivity analysis
(Zhou and Yamamoto <doi:10.31235/osf.io/2rx6p>). It contains two main functions: paths() for estimating
path-specific effects and sens() for conducting sensitivity analysis. Estimation uncertainty is quantified
using the nonparametric bootstrap.
Author: Minh Trinh [aut],
Teppei Yamamoto [aut],
Xiang Zhou [cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between paths versions 0.1.1 dated 2021-06-18 and 0.1.2 dated 2025-12-22
paths-0.1.1/paths/ChangeLog |only paths-0.1.2/paths/DESCRIPTION | 28 - paths-0.1.2/paths/MD5 | 35 -- paths-0.1.2/paths/NEWS.md | 24 - paths-0.1.2/paths/R/paths-package.R | 13 paths-0.1.2/paths/R/paths_fit.R | 4 paths-0.1.2/paths/R/plot.sens.R | 2 paths-0.1.2/paths/R/sens.R | 2 paths-0.1.2/paths/README.md | 5 paths-0.1.2/paths/inst/examples/sens.paths-example.R | 2 paths-0.1.2/paths/man/paths-package.Rd | 45 +- paths-0.1.2/paths/man/paths.Rd | 324 +++++++++---------- paths-0.1.2/paths/man/plot.paths.Rd | 174 +++++----- paths-0.1.2/paths/man/plot.sens.Rd | 166 ++++----- paths-0.1.2/paths/man/pred.Rd | 80 ++-- paths-0.1.2/paths/man/sens.Rd | 212 ++++++------ paths-0.1.2/paths/man/summary.paths.Rd | 184 +++++----- paths-0.1.2/paths/man/tatar.Rd | 122 +++---- paths-0.1.2/paths/man/welfare.Rd | 122 +++---- 19 files changed, 775 insertions(+), 769 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.6.0 dated 2025-09-20 and 2.7.0 dated 2025-12-22
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/utility.R | 12 ++++++++++++ R/visualization.R | 11 +++++++++++ build/vignette.rds |binary inst/doc/comparing_results.html | 9 +++++---- inst/doc/intro_vignette.html | 11 ++++++----- inst/doc/manual_execution.html | 9 +++++---- inst/doc/non_hs_analysis.html | 11 ++++++----- inst/doc/obtain_data.html | 9 +++++---- inst/doc/visualization_vignette.html | 17 +++++++++-------- tests/testthat/test-visualization.R | 4 +++- 13 files changed, 86 insertions(+), 51 deletions(-)
Title: Localization Microscopy Data Analysis
Description: Read, register and compare point sets from single molecule localization microscopy.
Author: Jean-Karim Heriche [cre, aut]
Maintainer: Jean-Karim Heriche <heriche@embl.de>
Diff between LOMAR versions 0.5.0 dated 2024-09-26 and 0.5.1 dated 2025-12-22
DESCRIPTION | 15 ++++----- MD5 | 24 +++++++------- NEWS.md | 9 ++++- R/TDA.R | 10 +++--- R/alpha_shape.R | 4 +- R/registration.R | 71 ++++++++++++++++++++++++++++---------------- R/utils.R | 70 ++++++++++++++++++++++--------------------- man/cpd.Rd | 8 +++- man/icp.Rd | 8 +++- man/shape_features_3d.Rd | 1 man/wgmmreg.Rd | 3 + src/diag.cpp | 6 --- tests/testthat/test-utils.R | 2 - 13 files changed, 136 insertions(+), 95 deletions(-)
Title: Plotting Tool for Brain Atlases
Description: Contains 'ggplot2' geom for plotting brain atlases using
simple features. The largest component of the package is the data
for the two built-in atlases. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Ramiro Magno [aut]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 1.6.7 dated 2025-11-14 and 1.6.8 dated 2025-12-22
DESCRIPTION | 10 - MD5 | 72 ++++---- NEWS.md | 2 R/brain_atlas.R | 108 +++++++------ R/brain_join.R | 48 ++--- R/brain_palettes.R | 79 +++++---- R/coord-funcs.R | 97 ++++++----- R/geom-brain.R | 183 ++++++++++++---------- R/ggseg-adapt_scales.R | 104 ++++++------ R/ggseg.R | 69 ++++---- R/layer-brain.R | 232 ++++++++++++++++------------ R/read_freesurfer.R | 46 ++--- R/scale-brain.R | 66 +++++-- README.md | 22 +- inst/doc/externalData.R | 105 ++++++------ inst/doc/externalData.Rmd | 105 ++++++------ inst/doc/externalData.html | 116 +++++++------- inst/doc/freesurfer_files.R | 16 - inst/doc/freesurfer_files.Rmd | 16 - inst/doc/freesurfer_files.html | 18 +- inst/doc/ggseg.R | 100 +++++++----- inst/doc/ggseg.Rmd | 96 +++++++---- inst/doc/ggseg.html | 180 ++++++++++++--------- man/figures/README-unnamed-chunk-5-1.png |binary tests/testthat/test-brain_atlas.R | 73 +++----- tests/testthat/test-brain_join.R | 18 +- tests/testthat/test-brain_palettes.R | 12 - tests/testthat/test-coord-funcs.R | 1 tests/testthat/test-ggseg-adapt_scales.R | 3 tests/testthat/test-ggseg_atlas.R | 92 +++++------ tests/testthat/test-position-brain.R | 16 + tests/testthat/test-read_freesurfer_stats.R | 120 +++++++++++--- tests/testthat/test-scale_brain.R | 55 +++--- tests/testthat/test-theme_brain.R | 21 -- vignettes/externalData.Rmd | 105 ++++++------ vignettes/freesurfer_files.Rmd | 16 - vignettes/ggseg.Rmd | 96 +++++++---- 37 files changed, 1405 insertions(+), 1113 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb] ,
Frederiek - Maarten Kerckhof [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.5 dated 2025-10-18 and 1.3.6 dated 2025-12-22
DESCRIPTION | 10 ++--- MD5 | 28 +++++++------- NEWS.md | 6 +++ R/RcppExports.R | 4 +- R/clustering_functions.R | 13 ++++-- README.md | 2 - inst/doc/the_clusterR_package.html | 18 ++++----- inst/include/ClusterRHeader.h | 21 ++++++++-- inst/include/affinity_propagation.h | 23 ++++++------ man/Optimal_Clusters_GMM.Rd | 7 +++ man/tryCatch_optimal_clust_GMM.Rd | 3 + src/RcppExports.cpp | 7 ++- src/export_inst_folder_headers.cpp | 4 +- src/init.c | 44 +++++++++++----------- tests/testthat/test-gmm.R | 69 ++++++++++++++++++++++++++++++++++++ 15 files changed, 180 insertions(+), 79 deletions(-)
Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jake@agency.fund>
Diff between rsurveycto versions 0.2.2 dated 2025-06-18 and 0.2.4 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md |only R/scto_get_form_definitions.R | 2 +- R/scto_get_form_metadata.R | 28 ++++++++++++++++++++++------ R/scto_meta.R | 2 +- R/scto_write.R | 7 ++++--- man/scto_get_form_metadata.Rd | 6 +++++- man/scto_write.Rd | 7 ++++--- tests/testthat/scto_auth.txt | 2 +- tests/testthat/test-scto-write.R | 2 -- 11 files changed, 52 insertions(+), 31 deletions(-)
Title: Regression Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Author: Oldemar Rodriguez [aut, cre],
Andres Navarro D. [ctb, prg],
Diego Jimenez A. [ctb, prg],
Ariel Arroyo S. [ctb, prg],
Joseline Quiros M. [ctb, prg],
Alejandro Vargas V. [ctb, prg],
Jennifer Lobo V. [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between regressoR versions 4.0.4 dated 2025-05-28 and 4.0.7 dated 2025-12-22
DESCRIPTION | 16 MD5 | 131 +-- NAMESPACE | 154 +-- NEWS.md | 6 R/app_config.R | 70 - R/app_server.R | 374 ++++---- R/app_ui.R | 550 ++++++------- R/cv_utils.R | 780 +++++++++--------- R/general_plots.R | 34 R/generate_code_utils.R | 1162 +++++++++++++-------------- R/golem_utils_server.R | 174 ++-- R/golem_utils_ui.R | 628 +++++++------- R/indices_utils.R | 156 +-- R/mod_Predictive_Power.R | 124 +- R/mod_Predictive_Power_utils.R | 10 R/mod_cross_val.R | 756 ++++++++--------- R/mod_cross_val_utils.R | 186 ++-- R/mod_evaluacion.R | 336 +++---- R/mod_ind_nuevos.R | 1560 +++++++++++++++++++------------------ R/mod_ind_nuevos_utils.R | 114 +- R/mod_information_page.R | 76 - R/mod_model_boost_fct.R | 240 ++--- R/mod_model_boost_utils.R | 2 R/mod_model_nnet_utils.R | 10 R/mod_model_rdim_utils.R | 152 +-- R/mod_model_regp_utils.R | 222 ++--- R/mod_model_rndf_fct.R | 308 +++---- R/mod_model_rndf_utils.R | 114 +- R/mod_model_tree_fct.R | 522 ++++++------ R/mod_model_tree_utils.R | 20 R/mod_models_utils.R | 1128 +++++++++++++------------- R/mod_train_test.R | 1372 ++++++++++++++++---------------- R/mod_varerr.R | 202 ++-- R/regressoR.R | 4 R/run_app.R | 56 - R/string_manipulation.R | 130 +-- R/utils_global.R | 412 ++++----- R/utils_inputs.R | 364 ++++---- R/utils_outputs.R | 292 +++--- inst/app.R |only inst/app/lang/diccionario.csv | 642 +++++++-------- inst/app/www/regressor_inputs.css | 248 ++--- inst/app/www/regressor_inputs.js | 156 +-- inst/app/www/regressor_options.css | 100 +- inst/app/www/regressor_options.js | 26 inst/app/www/script_regressor.js | 74 - inst/app/www/style_regressor.css | 338 ++++---- inst/golem-config.yml | 16 inst/rstudio/addins.dcf | 8 man/as_string_c.Rd | 46 - man/e.rdim.rmse.Rd | 48 - man/e.rdim.vare.Rd | 48 - man/e_JS.Rd | 42 man/e_boost_evol_error.Rd | 56 - man/e_boost_importance.Rd | 52 - man/e_coeff_lambda.Rd | 62 - man/e_posib_lambda.Rd | 64 - man/e_rf_error.Rd | 56 - man/e_rndf_importance.Rd | 54 - man/exe.Rd | 50 - man/extract_code.Rd | 46 - man/general.indices.Rd | 74 - man/mod_ind_nuevos_server.Rd | 24 man/plot_real_prediction.Rd | 48 - man/regressoR.Rd | 68 - man/run_app.Rd | 28 man/summary_indices.Rd | 36 67 files changed, 7793 insertions(+), 7664 deletions(-)
Title: Predictive Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as K-Nearest Neighbors, Decision Trees, ADA Boosting, Extreme Gradient Boosting, Random Forest, Neural Networks, Deep Learning, Support Vector Machines and Bayesian Methods.
Author: Oldemar Rodriguez [aut, cre],
Diego Jimenez [ctb, prg],
Andres Navarro [ctb, prg],
Jennifer Lobo [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between predictoR versions 4.1.5 dated 2025-05-28 and 4.1.6 dated 2025-12-22
DESCRIPTION | 14 MD5 | 19 R/mod_acercade.R | 2 R/mod_evaluacion.R | 17 R/mod_model_xgb_utils.R | 41 - R/mod_models_utils.R | 1124 ++++++++++++++--------------- R/mod_train_test.R | 1824 ++++++++++++++++++++++++------------------------ R/predictoR.R | 4 inst/app.R |only man/e_xgb_importance.Rd | 5 man/predictoR.Rd | 4 11 files changed, 1546 insertions(+), 1508 deletions(-)
Title: Tools for Computational Optimal Transport
Description: Transport theory has seen much success in many fields of statistics and machine learning. We provide a variety of algorithms to compute Wasserstein distance, barycenter, and others. See Peyré and Cuturi (2019) <doi:10.1561/2200000073> for the general exposition to the study of computational optimal transport.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between T4transport versions 0.1.5 dated 2025-11-13 and 0.1.7 dated 2025-12-22
T4transport-0.1.5/T4transport/R/free_median_PF.R |only T4transport-0.1.5/T4transport/man/rmedPF.Rd |only T4transport-0.1.7/T4transport/DESCRIPTION | 8 - T4transport-0.1.7/T4transport/MD5 | 50 +++++--- T4transport-0.1.7/T4transport/NAMESPACE | 15 +- T4transport-0.1.7/T4transport/NEWS.md | 15 ++ T4transport-0.1.7/T4transport/R/RcppExports.R | 16 ++ T4transport-0.1.7/T4transport/R/auxiliary_inputs.R | 59 +++++++++ T4transport-0.1.7/T4transport/R/dist_hdist.R |only T4transport-0.1.7/T4transport/R/free_bary_GradientDescent.R | 4 T4transport-0.1.7/T4transport/R/free_median_Weiszfeld.R |only T4transport-0.1.7/T4transport/R/gromov_barycenter.R |only T4transport-0.1.7/T4transport/R/gromov_distance.R |only T4transport-0.1.7/T4transport/R/hist_bary.R |only T4transport-0.1.7/T4transport/R/hist_bary14C.R | 2 T4transport-0.1.7/T4transport/R/hist_interp.R |only T4transport-0.1.7/T4transport/R/hist_med.R |only T4transport-0.1.7/T4transport/R/other_img2measure.R |only T4transport-0.1.7/T4transport/R/package-T4transport.R | 2 T4transport-0.1.7/T4transport/R/test_time_comparison.R |only T4transport-0.1.7/T4transport/build/partial.rdb |binary T4transport-0.1.7/T4transport/inst/REFERENCES.bib | 13 ++ T4transport-0.1.7/T4transport/man/gwbary.Rd |only T4transport-0.1.7/T4transport/man/gwdist.Rd |only T4transport-0.1.7/T4transport/man/hdist.Rd |only T4transport-0.1.7/T4transport/man/histbary.Rd |only T4transport-0.1.7/T4transport/man/histbary14C.Rd | 2 T4transport-0.1.7/T4transport/man/histinterp.Rd |only T4transport-0.1.7/T4transport/man/histmed.Rd |only T4transport-0.1.7/T4transport/man/img2measure.Rd |only T4transport-0.1.7/T4transport/man/rbaryGD.Rd | 4 T4transport-0.1.7/T4transport/man/rmedWB.Rd |only T4transport-0.1.7/T4transport/src/RcppExports.cpp | 66 +++++++++++ T4transport-0.1.7/T4transport/src/src_gromov.cpp |only T4transport-0.1.7/T4transport/src/utility.cpp | 72 ++++++++++++ T4transport-0.1.7/T4transport/src/utility.h | 1 36 files changed, 289 insertions(+), 40 deletions(-)
Title: Various Functions to Facilitate Visualization of Data and
Analysis
Description: When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.
Author: Jacolien van Rij [aut, cre]
Maintainer: Jacolien van Rij <j.c.van.rij@rug.nl>
Diff between plotfunctions versions 1.4 dated 2020-04-28 and 1.5 dated 2025-12-22
plotfunctions-1.4/plotfunctions/man/plotfunctions.Rd |only plotfunctions-1.5/plotfunctions/DESCRIPTION | 14 plotfunctions-1.5/plotfunctions/MD5 | 94 plotfunctions-1.5/plotfunctions/NAMESPACE | 2 plotfunctions-1.5/plotfunctions/R/plot.R | 195 + plotfunctions-1.5/plotfunctions/R/plotfunctions.R | 16 plotfunctions-1.5/plotfunctions/R/util.R | 74 plotfunctions-1.5/plotfunctions/build/vignette.rds |binary plotfunctions-1.5/plotfunctions/inst/NEWS | 9 plotfunctions-1.5/plotfunctions/inst/doc/plotfunctions.R | 6 plotfunctions-1.5/plotfunctions/inst/doc/plotfunctions.html | 1211 ++++++----- plotfunctions-1.5/plotfunctions/man/addInterval.Rd | 2 plotfunctions-1.5/plotfunctions/man/add_bars.Rd | 6 plotfunctions-1.5/plotfunctions/man/add_n_points.Rd | 2 plotfunctions-1.5/plotfunctions/man/axesLabels.Rd |only plotfunctions-1.5/plotfunctions/man/check_normaldist.Rd | 2 plotfunctions-1.5/plotfunctions/man/color_contour.Rd | 6 plotfunctions-1.5/plotfunctions/man/dotplot_error.Rd | 2 plotfunctions-1.5/plotfunctions/man/drawDevArrows.Rd | 2 plotfunctions-1.5/plotfunctions/man/emptyPlot.Rd | 6 plotfunctions-1.5/plotfunctions/man/errorBars.Rd | 2 plotfunctions-1.5/plotfunctions/man/fill_area.Rd | 2 plotfunctions-1.5/plotfunctions/man/findAbsMin.Rd | 1 plotfunctions-1.5/plotfunctions/man/find_n_neighbors.Rd | 1 plotfunctions-1.5/plotfunctions/man/firstLetterCap.Rd | 1 plotfunctions-1.5/plotfunctions/man/getArrowPos.Rd | 1 plotfunctions-1.5/plotfunctions/man/getCoords.Rd | 2 plotfunctions-1.5/plotfunctions/man/getDec.Rd | 1 plotfunctions-1.5/plotfunctions/man/getFigCoords.Rd | 2 plotfunctions-1.5/plotfunctions/man/getProps.Rd | 2 plotfunctions-1.5/plotfunctions/man/getRange.Rd | 1 plotfunctions-1.5/plotfunctions/man/getRatioCoords.Rd | 1 plotfunctions-1.5/plotfunctions/man/get_palette.Rd | 1 plotfunctions-1.5/plotfunctions/man/gradientLegend.Rd | 8 plotfunctions-1.5/plotfunctions/man/group_sort.Rd | 1 plotfunctions-1.5/plotfunctions/man/inch2coords.Rd | 1 plotfunctions-1.5/plotfunctions/man/isColor.Rd | 1 plotfunctions-1.5/plotfunctions/man/keepFigRatio.Rd |only plotfunctions-1.5/plotfunctions/man/legend_margin.Rd | 2 plotfunctions-1.5/plotfunctions/man/list2str.Rd | 1 plotfunctions-1.5/plotfunctions/man/marginDensityPlot.Rd | 2 plotfunctions-1.5/plotfunctions/man/move_n_point.Rd | 1 plotfunctions-1.5/plotfunctions/man/orderBoxplot.Rd | 1 plotfunctions-1.5/plotfunctions/man/plot_error.Rd | 2 plotfunctions-1.5/plotfunctions/man/plot_image.Rd | 2 plotfunctions-1.5/plotfunctions/man/plotfunctions-package.Rd |only plotfunctions-1.5/plotfunctions/man/plotsurface.Rd | 2 plotfunctions-1.5/plotfunctions/man/se.Rd | 1 plotfunctions-1.5/plotfunctions/man/sortBoxplot.Rd | 2 plotfunctions-1.5/plotfunctions/man/sortGroups.Rd | 1 50 files changed, 1022 insertions(+), 673 deletions(-)
Title: Utilities for Managing a 'Motherduck' Database
Description: Provides helper functions, metadata utilities, and workflows for
administering and managing databases on the 'Motherduck' cloud platform.
Some features require a 'Motherduck' account (<https://motherduck.com/>).
Author: Alejandro Hagan [aut, cre]
Maintainer: Alejandro Hagan <alejandro.hagan@outlook.com>
Diff between motherduck versions 0.2.0 dated 2025-12-02 and 0.2.1 dated 2025-12-22
DESCRIPTION | 6 MD5 | 13 +- NAMESPACE | 3 NEWS.md | 5 R/connection_fns.R | 4 R/utils-db.R | 213 +++++++++++++++++++++++++++------ man/show_information_schema.Rd |only man/validate_database_exists.Rd |only man/validate_database_schema_exists.Rd |only 9 files changed, 199 insertions(+), 45 deletions(-)
Title: Unit Test Add-on for 'testthat'
Description: Enhance package 'testthat' by allowing tests to be attached to the function/object they test.
This allows to keep functional and unit test code together.
Author: Claudia Beleites [aut, cre],
Erick Oduniyi [aut]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.gmbh>
This is a re-admission after prior archival of version 0.2.1 dated 2020-06-24
Diff between hySpc.testthat versions 0.2.1 dated 2020-06-24 and 0.2.2 dated 2025-12-22
hySpc.testthat-0.2.1/hySpc.testthat/README.md |only hySpc.testthat-0.2.2/hySpc.testthat/DESCRIPTION | 11 ++-- hySpc.testthat-0.2.2/hySpc.testthat/LICENSE | 2 hySpc.testthat-0.2.2/hySpc.testthat/MD5 | 13 ++--- hySpc.testthat-0.2.2/hySpc.testthat/R/test-fun.R | 22 --------- hySpc.testthat-0.2.2/hySpc.testthat/R/unittest.R | 23 ---------- hySpc.testthat-0.2.2/hySpc.testthat/man/test_fun.Rd | 2 hySpc.testthat-0.2.2/hySpc.testthat/tests/testthat/test_attached.R | 2 8 files changed, 16 insertions(+), 59 deletions(-)
More information about hySpc.testthat at CRAN
Permanent link
Title: Extract Centerline from Closed Polygons
Description: Generates skeletons of closed 2D polygons using Voronoi diagrams.
It provides methods for 'sf', 'terra', and 'geos' objects to
compute polygon centerlines based on the generated skeletons.
Voronoi, G. (1908) <doi:10.1515/crll.1908.134.198>.
Author: Anatoly Tsyplenkov [aut, cre, cph]
Maintainer: Anatoly Tsyplenkov <atsyplenkov@fastmail.com>
Diff between centerline versions 0.2.4 dated 2025-09-09 and 0.2.5 dated 2025-12-22
DESCRIPTION | 8 MD5 | 28 NEWS.md | 9 R/cnt_path_guess.R | 646 ++++++++++----------- R/geom_cnt.R | 634 ++++++++++----------- R/transformers.R | 102 +-- R/types-check.R | 230 +++---- R/utils.R | 368 ++++++------ README.md | 666 +++++++++++----------- build/partial.rdb |binary man/geom_cnt.Rd | 4 man/geom_cnt_text.Rd | 422 +++++++------- tests/testthat/test-cnt_path.R | 848 ++++++++++++++-------------- tests/testthat/test-cnt_path_guess.R | 1030 +++++++++++++++++------------------ tests/testthat/test-cnt_skeleton.R | 680 +++++++++++------------ 15 files changed, 2848 insertions(+), 2827 deletions(-)
Title: Mander and Thompson Designs
Description: Implements Mander & Thompson's (2010)
<doi:10.1016/j.cct.2010.07.008> methods for two-stage designs
optimal under the alternative hypothesis for phase II [cancer] trials. Also
provides an implementation of Simon's (1989)
<doi:10.1016/0197-2456(89)90015-9> original methodology and
allows exploration of the operating characteristics of sub-optimal designs.
Author: John Kirkpatrick [aut, cre]
Maintainer: John Kirkpatrick <mtdesign@puzzledface.net>
Diff between mtdesign versions 0.1.3 dated 2025-08-23 and 0.1.4 dated 2025-12-22
DESCRIPTION | 11 +--- MD5 | 20 +++---- NEWS.md | 3 + R/functions.R | 75 ++++++++-------------------- README.md | 81 ++++++++++++++----------------- man/createGrid.Rd | 13 +++- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary tests/testthat/test-createGrid.R | 12 ---- tests/testthat/test-obtainDesign.R | 2 11 files changed, 87 insertions(+), 130 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut, cre] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between epiworldR versions 0.10.0.0 dated 2025-11-14 and 0.11.0.0 dated 2025-12-22
epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixing.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesMixingRiskQuarantine.R |only epiworldR-0.10.0.0/epiworldR/R/ModelMeaslesSchool.R |only epiworldR-0.10.0.0/epiworldR/R/global-actions.R |only epiworldR-0.10.0.0/epiworldR/build/partial.rdb |only epiworldR-0.10.0.0/epiworldR/inst/include/epiworld/network-bones.hpp |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measles-quarantine-errors.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measles-quarantine-math.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixing.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixingriskquarantine-multiple.R |only epiworldR-0.10.0.0/epiworldR/inst/tinytest/test-measlesmixingriskquarantine.R |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesMixing.Rd |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesMixingRiskQuarantine.Rd |only epiworldR-0.10.0.0/epiworldR/man/ModelMeaslesSchool.Rd |only epiworldR-0.10.0.0/epiworldR/man/epiworld-data.Rd |only epiworldR-0.10.0.0/epiworldR/src/actions.cpp |only epiworldR-0.11.0.0/epiworldR/DESCRIPTION | 8 epiworldR-0.11.0.0/epiworldR/MD5 | 211 +++-- epiworldR-0.11.0.0/epiworldR/NAMESPACE | 11 epiworldR-0.11.0.0/epiworldR/NEWS.md | 21 epiworldR-0.11.0.0/epiworldR/R/arg-checks.R | 23 epiworldR-0.11.0.0/epiworldR/R/cpp11.R | 84 +- epiworldR-0.11.0.0/epiworldR/R/data.R | 352 ++++++++-- epiworldR-0.11.0.0/epiworldR/R/entity_tools.R |only epiworldR-0.11.0.0/epiworldR/R/events.R |only epiworldR-0.11.0.0/epiworldR/R/functions-renamed.R | 10 epiworldR-0.11.0.0/epiworldR/R/make_saver.R | 47 - epiworldR-0.11.0.0/epiworldR/R/tool.R | 25 epiworldR-0.11.0.0/epiworldR/R/virus.R | 24 epiworldR-0.11.0.0/epiworldR/README.md | 36 - epiworldR-0.11.0.0/epiworldR/inst/doc/advanced-modeling.html | 12 epiworldR-0.11.0.0/epiworldR/inst/doc/getting-started.html | 12 epiworldR-0.11.0.0/epiworldR/inst/doc/likelihood-free-mcmc.html | 8 epiworldR-0.11.0.0/epiworldR/inst/doc/mixing.html | 42 - epiworldR-0.11.0.0/epiworldR/inst/doc/run-multiple.html | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/adjlist-bones.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/agent-events-meat.hpp | 22 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/config.hpp | 12 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/database-bones.hpp | 125 ++- epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/database-meat.hpp | 310 ++++++++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/entity-bones.hpp | 3 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/epiworld.hpp | 6 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/hospitalizationstracker-bones.hpp |only epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/hospitalizationstracker-meat.hpp |only epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/misc.hpp | 54 - epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/model-bones.hpp | 69 + epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/model-meat.hpp | 284 +++++--- epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/modeldiagram-bones.hpp | 9 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/modeldiagram-meat.hpp | 2 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/diffnet.hpp | 2 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/globalevents.hpp | 3 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/init-functions.hpp | 8 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesmixing.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesmixingriskquarantine.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/measlesschool.hpp | 14 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/models.hpp | 102 ++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seir.hpp | 18 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seird.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirdconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirmixing.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/seirmixingquarantine.hpp | 5 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sir.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sird.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirdconnected.hpp | 7 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirlogit.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sirmixing.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sis.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/sisd.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/models/surveillance.hpp | 4 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/randgraph.hpp | 58 - epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/tool-distribute-meat.hpp | 95 ++ epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/userdata-bones.hpp | 16 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/virus-bones.hpp | 8 epiworldR-0.11.0.0/epiworldR/inst/include/epiworld/virus-distribute-meat.hpp | 94 ++ epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-agents-and-dist-virus-tool.R | 42 - epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-data.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-entity_tools.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-globalevents.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-outbreak-active-cases.R |only epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-sir.R | 2 epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-sirconn.R | 2 epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-tool.R | 97 ++ epiworldR-0.11.0.0/epiworldR/inst/tinytest/test-virus.R | 108 +++ epiworldR-0.11.0.0/epiworldR/man/ModelDiffNet.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIR.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRDCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRMixing.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSEIRMixingQuarantine.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIR.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRDCONN.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRLogit.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIRMixing.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSIS.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSISD.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/ModelSURV.Rd | 6 epiworldR-0.11.0.0/epiworldR/man/add_entities_from_dataframe.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-gentime.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-history.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-hospitalizations.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-model-diagram.Rd | 4 epiworldR-0.11.0.0/epiworldR/man/epiworld-repnum.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-summaries.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-transition.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworld-transmissions.Rd |only epiworldR-0.11.0.0/epiworldR/man/epiworldR-deprecated.Rd | 33 epiworldR-0.11.0.0/epiworldR/man/global-events.Rd | 5 epiworldR-0.11.0.0/epiworldR/man/run_multiple.Rd | 31 epiworldR-0.11.0.0/epiworldR/man/tool.Rd | 11 epiworldR-0.11.0.0/epiworldR/man/virus.Rd | 11 epiworldR-0.11.0.0/epiworldR/src/cpp11.cpp | 160 ++-- epiworldR-0.11.0.0/epiworldR/src/db.cpp | 89 ++ epiworldR-0.11.0.0/epiworldR/src/epimodels.cpp | 160 ---- epiworldR-0.11.0.0/epiworldR/src/events.cpp |only epiworldR-0.11.0.0/epiworldR/src/model.cpp | 10 epiworldR-0.11.0.0/epiworldR/src/tool.cpp | 18 epiworldR-0.11.0.0/epiworldR/src/virus.cpp | 19 epiworldR-0.11.0.0/epiworldR/tests/tinytest.R | 7 123 files changed, 2328 insertions(+), 908 deletions(-)
Title: Tools and Infrastructure for Developing 'Scalable' 'HDF5'-Based
Methods
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, QR decomposition, and canonical correlation analysis) written
in C++ and R. These building blocks are designed not only for direct use,
but also as foundational components for developing new statistical methods
that must operate on datasets too large to fit in memory. The package
supports data provided either as 'HDF5' files or standard R objects, and is
intended for high-dimensional applications such as 'omics' and
precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 1.0.2 dated 2025-11-29 and 1.0.3 dated 2025-12-22
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 11 - README.md | 412 +++++++++++++++++++++++++++++++-------- inst/doc/BigDataStatMeth.html | 6 inst/include/BigDataStatMeth.hpp | 10 src/Makevars.in | 5 src/Makevars.win | 5 8 files changed, 359 insertions(+), 110 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Interface to 'Vamp' Audio Analysis Plugins
Description: Provides an interface to the 'Vamp' audio analysis plugin system
<https://www.vamp-plugins.org/> developed by Queen Mary University of London's
Centre for Digital Music. Enables loading and running 'Vamp' plugins for various audio analysis
tasks including tempo detection, onset detection, spectral analysis, and
audio feature extraction. Supports mono and stereo audio with automatic
channel adaptation and domain conversion.
Author: Ed Baker [aut, cre] ,
Authors of vamp-sdk [cph] ,
Mark Borgerding [cph]
Maintainer: Ed Baker <ed@ebaker.me.uk>
Diff between ReVAMP versions 1.0.0 dated 2025-12-19 and 1.0.1 dated 2025-12-22
DESCRIPTION | 8 MD5 | 21 +- NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 4 R/vamp_functions.R | 15 + man/runPlugins.Rd |only src/PluginLoader.cpp | 2 src/R_host.cpp | 377 +++++++++++++++++++++++++++++++++++++ src/RcppExports.cpp | 19 + src/RealTime.cpp | 4 src/RealTime_impl.cpp |only tests/testthat/test-multi-plugin.R |only 13 files changed, 441 insertions(+), 16 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.14 dated 2025-11-18 and 1.0.15 dated 2025-12-22
modsem-1.0.14/modsem/tests/testthat/mplusResults.inp |only modsem-1.0.14/modsem/tests/testthat/mplusResults.out |only modsem-1.0.14/modsem/tests/testthat/mplusResults_1902fe5a594fdff027c6f333f1b42374.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_1d99a51710dbe72680bd2167846dfc39.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_2f55eb38256759e6ebc9b0699ecf1d13.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_3d0f8823f6af05dbc789d0ed60a54090.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_6507283a847451aff127c84c87ebd81b.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_6bb11f99c9f63d831155403fa8debc11.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_ad18af3b9c89a45fac7dc52df3607909.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_c0d691516a85482200cebd668c136807.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_d4fd46d7e74eb5a0b73e2cb1369c4b51.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_d7630a570fe7052efa569a29540ef19e.dat |only modsem-1.0.14/modsem/tests/testthat/mplusResults_e8725a6185cbe0286c28c26f935f24e2.dat |only modsem-1.0.15/modsem/DESCRIPTION | 6 modsem-1.0.15/modsem/MD5 | 92 - modsem-1.0.15/modsem/NAMESPACE | 3 modsem-1.0.15/modsem/R/bootstrap.R | 17 modsem-1.0.15/modsem/R/generics.R | 33 modsem-1.0.15/modsem/R/generics_modsem_da.R | 8 modsem-1.0.15/modsem/R/generics_modsem_pi.R | 8 modsem-1.0.15/modsem/R/model_pi.R | 4 modsem-1.0.15/modsem/R/modsem.R | 2 modsem-1.0.15/modsem/R/modsem_da.R | 5 modsem-1.0.15/modsem/R/modsem_pi.R | 21 modsem-1.0.15/modsem/R/plot_interaction.R | 84 - modsem-1.0.15/modsem/build/partial.rdb |binary modsem-1.0.15/modsem/build/vignette.rds |binary modsem-1.0.15/modsem/inst/doc/customize_plot_interactions.html | 476 +---- modsem-1.0.15/modsem/inst/doc/customizing.html | 434 +---- modsem-1.0.15/modsem/inst/doc/estimation_lms.html | 423 +---- modsem-1.0.15/modsem/inst/doc/fit_measures_da.html | 382 +--- modsem-1.0.15/modsem/inst/doc/higher_order_interactions.html | 519 +----- modsem-1.0.15/modsem/inst/doc/interaction_two_etas.html | 433 +---- modsem-1.0.15/modsem/inst/doc/lavaan.html | 345 ---- modsem-1.0.15/modsem/inst/doc/lms_qml.html | 430 +---- modsem-1.0.15/modsem/inst/doc/meanstructure_lms_qml.html | 382 +--- modsem-1.0.15/modsem/inst/doc/methods.html | 377 +--- modsem-1.0.15/modsem/inst/doc/missing_lms_qml.html | 379 +--- modsem-1.0.15/modsem/inst/doc/modsem.html | 515 +----- modsem-1.0.15/modsem/inst/doc/observed_lms_qml.html | 808 +++------- modsem-1.0.15/modsem/inst/doc/plot_interactions.html | 678 ++------ modsem-1.0.15/modsem/inst/doc/quadratic.html | 399 +--- modsem-1.0.15/modsem/inst/doc/relcorr_items.html | 394 +--- modsem-1.0.15/modsem/inst/doc/simple_slopes.html | 430 +---- modsem-1.0.15/modsem/man/bootstrap_modsem.Rd | 2 modsem-1.0.15/modsem/man/is_interaction_model.Rd |only modsem-1.0.15/modsem/man/plot_jn.Rd | 3 modsem-1.0.15/modsem/man/summary.Rd | 4 modsem-1.0.15/modsem/tests/testthat/test_bootstrap.R | 10 modsem-1.0.15/modsem/tests/testthat/test_linear_da.R | 16 modsem-1.0.15/modsem/tests/testthat/test_multigroup.R | 1 modsem-1.0.15/modsem/tests/testthat/test_sampling_weights_da.R | 1 modsem-1.0.15/modsem/tests/testthat/test_simple_slopes.R | 1 modsem-1.0.15/modsem/vignettes/set_eval_false.bash |only modsem-1.0.15/modsem/vignettes/set_eval_true.bash |only 55 files changed, 2275 insertions(+), 5850 deletions(-)
Title: Generalized Bayesian Optimal Phase II Design (G-BOP2)
Description: Provides functions for implementing the Generalized Bayesian Optimal Phase II (G-BOP2) design using various Particle Swarm Optimization (PSO) algorithms, including:
- PSO-Default, based on Kennedy and Eberhart (1995) <doi:10.1109/ICNN.1995.488968>, "Particle Swarm Optimization";
- PSO-Quantum, based on Sun, Xu, and Feng (2004) <doi:10.1109/ICCIS.2004.1460396>, "A Global Search Strategy of Quantum-Behaved Particle Swarm Optimization";
- PSO-Dexp, based on Stehlík et al. (2024) <doi:10.1016/j.asoc.2024.111913>, "A Double Exponential Particle Swarm Optimization with Non-Uniform Variates as Stochastic Tuning and Guaranteed Convergence to a Global Optimum with Sample Applications to Finding Optimal Exact Designs in Biostatistics";
- and PSO-GO.
Author: Xinying Fang [aut],
Wanni Lei [aut, cre],
Shouhao Zhou [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut],
J. Jack Lee [aut]
Maintainer: Wanni Lei <wanni.lei17@gmail.com>
Diff between GBOP2 versions 0.1.3 dated 2025-04-22 and 0.1.4 dated 2025-12-22
GBOP2-0.1.3/GBOP2/inst/doc/Vignette.html |only GBOP2-0.1.3/GBOP2/inst/doc/Vignette.html.asis |only GBOP2-0.1.3/GBOP2/vignettes/Vignette.Rmd |only GBOP2-0.1.3/GBOP2/vignettes/Vignette.html.asis |only GBOP2-0.1.4/GBOP2/DESCRIPTION | 22 ++- GBOP2-0.1.4/GBOP2/MD5 | 57 +++++---- GBOP2-0.1.4/GBOP2/NAMESPACE | 1 GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_TE.gbop2.R | 24 +--- GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_dualE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_maxP_singleE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_TE.gbop2.R | 23 +-- GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_dualE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/GBOP2_minSS_singleE.gbop2.R | 2 GBOP2-0.1.4/GBOP2/R/PSO_design_TE.gbop2.R | 4 GBOP2-0.1.4/GBOP2/R/PSO_power_TE.gbop2.R | 10 - GBOP2-0.1.4/GBOP2/R/summary.gbop2.R | 8 - GBOP2-0.1.4/GBOP2/build/vignette.rds |binary GBOP2-0.1.4/GBOP2/inst/doc/vignette.html |only GBOP2-0.1.4/GBOP2/inst/doc/vignette.html.asis |only GBOP2-0.1.4/GBOP2/inst/vignette-source |only GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_TE.Rd | 8 - GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_dualE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_maxP_singleE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_TE.Rd | 10 - GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_dualE.Rd | 2 GBOP2-0.1.4/GBOP2/man/GBOP2_minSS_singleE.Rd | 2 GBOP2-0.1.4/GBOP2/src/Calculation2_original.cpp | 4 GBOP2-0.1.4/GBOP2/src/Calculation_minimizeN_twolambda_update.cpp | 30 +++-- GBOP2-0.1.4/GBOP2/src/Calculation_twoboundaries_jsm.cpp | 58 ++++++---- GBOP2-0.1.4/GBOP2/src/GBOP2_types.h | 24 +++- GBOP2-0.1.4/GBOP2/src/Makevars | 2 GBOP2-0.1.4/GBOP2/src/Makevars.win |only GBOP2-0.1.4/GBOP2/src/RcppExports.cpp | 1 GBOP2-0.1.4/GBOP2/vignettes/vignette.html.asis |only 34 files changed, 154 insertions(+), 148 deletions(-)
Title: Guarded Resampling Workflows for Safe and Automated Machine
Learning in R
Description: Provides a guarded resampling workflow for training and evaluating machine‑learning models.
When the guarded resampling path is used, preprocessing and model fitting are re‑estimated within
each resampling split to reduce leakage risk. Supports multiple resampling schemes, integrates
with established engines in the 'tidymodels' ecosystem, and aims to improve evaluation reliability by
coordinating preprocessing, fitting, and evaluation within supported workflows. Offers a lightweight
AutoML‑style workflow by automating model training, resampling, and tuning across multiple algorithms,
while keeping evaluation design explicit and user‑controlled.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.7.0 dated 2025-10-29 and 0.7.5 dated 2025-12-22
fastml-0.7.0/fastml/man/evaluate_models.Rd |only fastml-0.7.5/fastml/DESCRIPTION | 41 fastml-0.7.5/fastml/MD5 | 96 fastml-0.7.5/fastml/NAMESPACE | 87 fastml-0.7.5/fastml/NEWS.md |only fastml-0.7.5/fastml/R/counterfactual_explain.R | 203 - fastml-0.7.5/fastml/R/engine_helpers.R | 15 fastml-0.7.5/fastml/R/evaluate_models.R | 98 fastml-0.7.5/fastml/R/explain_ale.R | 84 fastml-0.7.5/fastml/R/explain_dalex.R | 463 +- fastml-0.7.5/fastml/R/explain_lime.R | 66 fastml-0.7.5/fastml/R/explainer_helpers.R |only fastml-0.7.5/fastml/R/fastexplain.R | 174 fastml-0.7.5/fastml/R/fastexplore.R | 1840 ++------- fastml-0.7.5/fastml/R/fastml.R | 749 ++- fastml-0.7.5/fastml/R/interaction_strength.R | 64 fastml-0.7.5/fastml/R/model_selection_helpers.R | 4 fastml-0.7.5/fastml/R/model_spec_registry.R |only fastml-0.7.5/fastml/R/plot.fastml.R | 83 fastml-0.7.5/fastml/R/plot_ice.R | 35 fastml-0.7.5/fastml/R/predict.fastml.R | 171 fastml-0.7.5/fastml/R/process_model.R | 275 + fastml-0.7.5/fastml/R/resampling_guard.R |only fastml-0.7.5/fastml/R/resampling_utils.R |only fastml-0.7.5/fastml/R/security_guards.R |only fastml-0.7.5/fastml/R/spec_boosting.R | 1 fastml-0.7.5/fastml/R/spec_other.R | 20 fastml-0.7.5/fastml/R/spec_tree.R | 11 fastml-0.7.5/fastml/R/summary.fastml.R | 466 -- fastml-0.7.5/fastml/R/surrogate_tree.R | 64 fastml-0.7.5/fastml/R/train_models.R | 1994 ++++++++-- fastml-0.7.5/fastml/R/xgboost_survival.R | 71 fastml-0.7.5/fastml/R/zzz_globals.R |only fastml-0.7.5/fastml/README.md | 149 fastml-0.7.5/fastml/man/counterfactual_explain.Rd | 41 fastml-0.7.5/fastml/man/explain_dalex.Rd | 3 fastml-0.7.5/fastml/man/explain_lime.Rd | 6 fastml-0.7.5/fastml/man/fastexplain.Rd | 58 fastml-0.7.5/fastml/man/fastexplore.Rd | 136 fastml-0.7.5/fastml/man/fastml.Rd | 68 fastml-0.7.5/fastml/man/fastml_compute_holdout_results.Rd |only fastml-0.7.5/fastml/man/fastml_guard_detect_full_analysis.Rd |only fastml-0.7.5/fastml/man/fastml_prepare_explainer_inputs.Rd |only fastml-0.7.5/fastml/man/plot.fastml.Rd | 3 fastml-0.7.5/fastml/man/plot_ice.Rd | 5 fastml-0.7.5/fastml/man/predict.fastml.Rd | 17 fastml-0.7.5/fastml/man/predict_model.model_fit.Rd |only fastml-0.7.5/fastml/man/process_model.Rd | 10 fastml-0.7.5/fastml/man/train_models.Rd | 67 fastml-0.7.5/fastml/tests/testthat/Rplots.pdf |only fastml-0.7.5/fastml/tests/testthat/test-fastexplain.R | 23 fastml-0.7.5/fastml/tests/testthat/test-fastml-workflows.R |only fastml-0.7.5/fastml/tests/testthat/test-fastml.R | 272 + fastml-0.7.5/fastml/tests/testthat/test-piecewise-exp-utils.R | 3 fastml-0.7.5/fastml/tests/testthat/test-resampling-methods.R |only fastml-0.7.5/fastml/tests/testthat/test-resampling.R |only fastml-0.7.5/fastml/tests/testthat/test-survival.R | 26 57 files changed, 4887 insertions(+), 3175 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.10.1 dated 2025-08-27 and 4.11.0 dated 2025-12-22
ergm-4.10.1/ergm/man/samplk.Rd |only ergm-4.10.1/ergm/src/MHproposals_triadic.c |only ergm-4.11.0/ergm/DESCRIPTION | 24 ergm-4.11.0/ergm/MD5 | 336 ++++---- ergm-4.11.0/ergm/NAMESPACE | 8 ergm-4.11.0/ergm/R/InitErgmConstraint.R | 2 ergm-4.11.0/ergm/R/InitErgmConstraint.operator.R | 120 ++ ergm-4.11.0/ergm/R/InitErgmProposal.R | 17 ergm-4.11.0/ergm/R/InitErgmTerm.R | 50 - ergm-4.11.0/ergm/R/InitErgmTerm.bipartite.R | 4 ergm-4.11.0/ergm/R/InitErgmTerm.dgw_sp.R | 14 ergm-4.11.0/ergm/R/InitErgmTerm.operator.R | 29 ergm-4.11.0/ergm/R/InitErgmTerm.spcache.R | 2 ergm-4.11.0/ergm/R/InitWtErgmTerm.R | 6 ergm-4.11.0/ergm/R/InitWtErgmTerm.operator.R | 24 ergm-4.11.0/ergm/R/approx.hotelling.diff.test.R | 9 ergm-4.11.0/ergm/R/as.network.numeric.R | 5 ergm-4.11.0/ergm/R/control.ergm.R | 35 ergm-4.11.0/ergm/R/data.R | 412 ++++------ ergm-4.11.0/ergm/R/ergm-defunct.R | 6 ergm-4.11.0/ergm/R/ergm-deprecated.R | 8 ergm-4.11.0/ergm/R/ergm-package.R | 220 ----- ergm-4.11.0/ergm/R/ergm.CD.fixed.R | 9 ergm-4.11.0/ergm/R/ergm.MCMLE.R | 20 ergm-4.11.0/ergm/R/ergm.R | 106 -- ergm-4.11.0/ergm/R/ergm.bridge.R | 15 ergm-4.11.0/ergm/R/ergm.eta.R | 14 ergm-4.11.0/ergm/R/ergm.getMCMCsample.R | 37 ergm-4.11.0/ergm/R/ergm.logitreg.R | 2 ergm-4.11.0/ergm/R/ergm.mple.R | 23 ergm-4.11.0/ergm/R/ergm.san.R | 10 ergm-4.11.0/ergm/R/ergm.utility.R | 24 ergm-4.11.0/ergm/R/ergm_estfun.R | 2 ergm-4.11.0/ergm/R/ergm_model.R | 22 ergm-4.11.0/ergm/R/ergm_model.utils.R | 2 ergm-4.11.0/ergm/R/ergm_mplecov.R | 10 ergm-4.11.0/ergm/R/ergm_proposal.R | 12 ergm-4.11.0/ergm/R/get.node.attr.R | 46 - ergm-4.11.0/ergm/R/godfather.R | 50 - ergm-4.11.0/ergm/R/gof.ergm.R | 248 ++++-- ergm-4.11.0/ergm/R/logLik.ergm.R | 5 ergm-4.11.0/ergm/R/mcmc.diagnostics.ergm.R | 8 ergm-4.11.0/ergm/R/nonidentifiability.R | 90 ++ ergm-4.11.0/ergm/R/simulate.ergm.R | 5 ergm-4.11.0/ergm/R/summary.ergm.R | 69 + ergm-4.11.0/ergm/R/zzz.R | 6 ergm-4.11.0/ergm/build/partial.rdb |binary ergm-4.11.0/ergm/build/stage23.rdb |binary ergm-4.11.0/ergm/build/vignette.rds |binary ergm-4.11.0/ergm/data/datalist | 2 ergm-4.11.0/ergm/data/samplk.RData |binary ergm-4.11.0/ergm/data/sampson.RData |binary ergm-4.11.0/ergm/inst/CITATION | 4 ergm-4.11.0/ergm/inst/NEWS.Rd | 125 +++ ergm-4.11.0/ergm/inst/REFERENCES.bib | 385 +++++++++ ergm-4.11.0/ergm/inst/doc/cpp-api.Rmd |only ergm-4.11.0/ergm/inst/doc/cpp-api.html |only ergm-4.11.0/ergm/inst/doc/ergm-term-crossRef.html | 303 +++++-- ergm-4.11.0/ergm/inst/doc/ergm.html | 63 - ergm-4.11.0/ergm/inst/doc/nodal_attributes.html | 4 ergm-4.11.0/ergm/inst/include/cpp |only ergm-4.11.0/ergm/inst/include/ergm_MHproposal_bd.h | 15 ergm-4.11.0/ergm/inst/include/ergm_MHproposal_changestat.h |only ergm-4.11.0/ergm/inst/include/ergm_MHproposals_degree.h | 8 ergm-4.11.0/ergm/inst/include/ergm_Rutil.h | 39 ergm-4.11.0/ergm/inst/include/ergm_changestat.h | 2 ergm-4.11.0/ergm/inst/include/ergm_constants.h | 2 ergm-4.11.0/ergm/inst/include/ergm_dyad_hashmap.h | 16 ergm-4.11.0/ergm/inst/include/ergm_dyadgen.h | 10 ergm-4.11.0/ergm/inst/include/ergm_edgelist.h | 2 ergm-4.11.0/ergm/inst/include/ergm_wtMHproposal_changestat.h |only ergm-4.11.0/ergm/inst/include/ergm_wtchangestat.h | 2 ergm-4.11.0/ergm/inst/include/inc/ergm_MHproposal.h.template.do_not_include_directly.h | 12 ergm-4.11.0/ergm/inst/include/inc/ergm_MHproposal_changestat.h.template.do_not_include_directly.h |only ergm-4.11.0/ergm/inst/include/inc/ergm_changestat.h.template.do_not_include_directly.h | 14 ergm-4.11.0/ergm/inst/include/inc/ergm_changestat_common.do_not_include_directly.h | 1 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree.h.template.do_not_include_directly.h | 16 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree_common.do_not_include_directly.h | 1 ergm-4.11.0/ergm/inst/include/inc/ergm_edgetree_inline_template.do_not_include_directly.h | 18 ergm-4.11.0/ergm/inst/include/inc/ergm_model.h.template.do_not_include_directly.h | 12 ergm-4.11.0/ergm/inst/include/inc/ergm_state.h.template.do_not_include_directly.h | 8 ergm-4.11.0/ergm/man/ChangeStats-ergmConstraint-a69283e7.Rd |only ergm-4.11.0/ergm/man/I-ergmConstraint-ca2567ac.Rd |only ergm-4.11.0/ergm/man/I-ergmTerm-ca2567ac.Rd |only ergm-4.11.0/ergm/man/altkstar-ergmTerm-201bf7a6.Rd | 6 ergm-4.11.0/ergm/man/approx.hotelling.diff.test.Rd | 5 ergm-4.11.0/ergm/man/as.network.numeric.Rd | 5 ergm-4.11.0/ergm/man/b1nodematch-ergmTerm-110b470e.Rd | 2 ergm-4.11.0/ergm/man/b2nodematch-ergmTerm-126ff8a2.Rd | 2 ergm-4.11.0/ergm/man/balance-ergmTerm-9111bd77.Rd | 2 ergm-4.11.0/ergm/man/cdf-ergmTerm-66ced489.Rd |only ergm-4.11.0/ergm/man/cohab.Rd | 10 ergm-4.11.0/ergm/man/control.ergm.Rd | 34 ergm-4.11.0/ergm/man/cyclicalweights-ergmTerm-994a6687.Rd | 2 ergm-4.11.0/ergm/man/degree15-ergmTerm-ea15bf13.Rd | 2 ergm-4.11.0/ergm/man/dsp-ergmTerm-1a10473d.Rd | 7 ergm-4.11.0/ergm/man/dyadnoise-ergmConstraint-03418976.Rd | 2 ergm-4.11.0/ergm/man/ecoli.Rd | 13 ergm-4.11.0/ergm/man/ergm-defunct.Rd | 5 ergm-4.11.0/ergm/man/ergm-deprecated.Rd | 5 ergm-4.11.0/ergm/man/ergm-package.Rd | 73 - ergm-4.11.0/ergm/man/ergm.Rd | 114 -- ergm-4.11.0/ergm/man/ergm.bridge.llr.Rd | 5 ergm-4.11.0/ergm/man/ergm.estfun.Rd | 2 ergm-4.11.0/ergm/man/ergm.eta.Rd | 12 ergm-4.11.0/ergm/man/ergm.godfather.Rd | 18 ergm-4.11.0/ergm/man/ergmConstraint.Rd | 25 ergm-4.11.0/ergm/man/ergmHint.Rd | 25 ergm-4.11.0/ergm/man/ergmProposal.Rd | 19 ergm-4.11.0/ergm/man/ergmReference.Rd | 12 ergm-4.11.0/ergm/man/ergmTerm.Rd | 43 - ergm-4.11.0/ergm/man/ergm_GWDECAY.Rd | 4 ergm-4.11.0/ergm/man/ergm_model.Rd | 16 ergm-4.11.0/ergm/man/esp-ergmTerm-d2e07fc8.Rd | 7 ergm-4.11.0/ergm/man/faux.desert.high.Rd | 11 ergm-4.11.0/ergm/man/faux.dixon.high.Rd | 11 ergm-4.11.0/ergm/man/faux.magnolia.high.Rd | 9 ergm-4.11.0/ergm/man/faux.mesa.high.Rd | 15 ergm-4.11.0/ergm/man/florentine.Rd | 19 ergm-4.11.0/ergm/man/gof.Rd | 58 - ergm-4.11.0/ergm/man/gwdsp-ergmTerm-4e3dfd97.Rd | 7 ergm-4.11.0/ergm/man/gwesp-ergmTerm-3d6fb5a8.Rd | 7 ergm-4.11.0/ergm/man/gwnsp-ergmTerm-6def2a32.Rd | 7 ergm-4.11.0/ergm/man/idegree15-ergmTerm-b83b1a3a.Rd | 2 ergm-4.11.0/ergm/man/intransitive-ergmTerm-4a599cad.Rd | 2 ergm-4.11.0/ergm/man/kapferer.Rd | 7 ergm-4.11.0/ergm/man/logLik.ergm.Rd | 5 ergm-4.11.0/ergm/man/mcmc.diagnostics.Rd | 7 ergm-4.11.0/ergm/man/mutual-ergmTerm-22863009.Rd | 2 ergm-4.11.0/ergm/man/nearsimmelian-ergmTerm-ba85787e.Rd | 2 ergm-4.11.0/ergm/man/nodal_attributes-API.Rd | 11 ergm-4.11.0/ergm/man/nsp-ergmTerm-4586ea4f.Rd | 7 ergm-4.11.0/ergm/man/odegree15-ergmTerm-8ee8801b.Rd | 2 ergm-4.11.0/ergm/man/sampson.Rd | 219 +++-- ergm-4.11.0/ergm/man/san.Rd | 8 ergm-4.11.0/ergm/man/simmelian-ergmTerm-15e60325.Rd | 2 ergm-4.11.0/ergm/man/simmelianties-ergmTerm-3361aef9.Rd | 4 ergm-4.11.0/ergm/man/simulate.ergm.Rd | 5 ergm-4.11.0/ergm/man/spcachenet-ergmAuxiliary-f1950bb3.Rd | 7 ergm-4.11.0/ergm/man/spectrum0.mvar.Rd | 2 ergm-4.11.0/ergm/man/summary.ergm.Rd | 3 ergm-4.11.0/ergm/man/transitive-ergmTerm-838987d1.Rd | 2 ergm-4.11.0/ergm/man/transitiveweights-ergmTerm-7797c57b.Rd | 2 ergm-4.11.0/ergm/man/triadcensus-ergmTerm-6a6bbd87.Rd | 2 ergm-4.11.0/ergm/man/triadic-ergmHint-b01cc436.Rd | 4 ergm-4.11.0/ergm/src/MHproposals.c | 101 +- ergm-4.11.0/ergm/src/MHproposals.h | 22 ergm-4.11.0/ergm/src/MHproposals_triadic.cpp |only ergm-4.11.0/ergm/src/changestats.c | 355 +------- ergm-4.11.0/ergm/src/changestats_auxnet.c | 10 ergm-4.11.0/ergm/src/changestats_dyad_ind.c.template.do_not_include_directly.h | 16 ergm-4.11.0/ergm/src/changestats_experimental.c | 153 +-- ergm-4.11.0/ergm/src/changestats_operator.c | 26 ergm-4.11.0/ergm/src/changestats_operator.c.template.do_not_include_directly.h | 30 ergm-4.11.0/ergm/src/cpp_changestats.cpp |only ergm-4.11.0/ergm/src/cpp_wtchangestats.cpp |only ergm-4.11.0/ergm/src/model.c.template.do_not_include_directly.h | 2 ergm-4.11.0/ergm/src/wtchangestats.c | 159 --- ergm-4.11.0/ergm/src/wtchangestats_auxnet.c | 8 ergm-4.11.0/ergm/tests/testthat.R | 1 ergm-4.11.0/ergm/tests/testthat/helper-htests.R | 4 ergm-4.11.0/ergm/tests/testthat/test-bridge-target.stats.R | 3 ergm-4.11.0/ergm/tests/testthat/test-constrain-blockdiag.R | 8 ergm-4.11.0/ergm/tests/testthat/test-constrain-dind.R | 8 ergm-4.11.0/ergm/tests/testthat/test-constraints.R | 32 ergm-4.11.0/ergm/tests/testthat/test-ergm-term-doc.R | 6 ergm-4.11.0/ergm/tests/testthat/test-gof.R | 27 ergm-4.11.0/ergm/tests/testthat/test-nonident-test.R | 4 ergm-4.11.0/ergm/tests/testthat/test-parallel.R | 1 ergm-4.11.0/ergm/tests/testthat/test-term-Offset.R | 10 ergm-4.11.0/ergm/vignettes/cpp-api.Rmd |only 171 files changed, 2756 insertions(+), 2388 deletions(-)
Title: Helper Functions for Org Files
Description: Helper functions for Org files (<https://orgmode.org/>):
a generic function 'toOrg' for transforming R objects into Org
markup (most useful for data frames; there are also methods for
Dates/POSIXt) and a function to read Org tables into data frames.
Author: Enrico Schumann [aut, cre]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between orgutils versions 0.5-2 dated 2025-12-15 and 0.5-3 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ inst/doc/orgutils_examples.Rnw | 4 ++-- inst/doc/orgutils_examples.pdf |binary vignettes/orgutils_examples.Rnw | 4 ++-- 6 files changed, 18 insertions(+), 13 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks API. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both CPU and GPU devices.
Author: Tomasz Kalinowski [aut, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
Posit Software, PBC [cph, fnd],
Google [cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigri [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between keras3 versions 1.4.0 dated 2025-05-04 and 1.5.0 dated 2025-12-22
DESCRIPTION | 8 MD5 | 1250 +++++----- NAMESPACE | 58 NEWS.md | 102 R/Layer.R | 17 R/activations.R | 26 R/callbacks.R | 12 R/config.R | 79 R/datasets.R | 267 +- R/freeze.R | 7 R/history.R | 2 R/install.R | 181 + R/jax-methods.R | 111 R/layers-backend-wrappers.R | 8 R/layers-convolutional.R | 51 R/layers-core.R | 37 R/layers-merging.R | 16 R/layers-normalization.R | 10 R/layers-pooling.R | 2 R/layers-preprocessing.R | 97 R/layers-regularization.R | 4 R/layers-reshaping.R | 18 R/layers-rnn.R | 3 R/losses.R | 104 R/metrics.R | 12 R/model-persistence.R | 94 R/ops-image.R | 88 R/ops-nn.R | 101 R/ops-numpy.R | 237 + R/ops.R | 119 R/optimizers.R | 176 + R/package.R | 21 R/py-classes.R | 32 R/r-utils.R | 31 R/reexports.R | 21 R/s3-methods.R | 13 R/utils.R | 15 R/variable.R | 11 build/vignette.rds |binary inst/doc/custom_train_step_in_tensorflow.Rmd | 10 inst/doc/custom_train_step_in_tensorflow.html | 10 inst/doc/distributed_training_with_tensorflow.Rmd | 14 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Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: [...truncated...]
Author: Ege Ulgen [aut, cre, cph]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.4.1 dated 2023-08-19 and 0.5.0 dated 2025-12-22
DESCRIPTION | 21 +- MD5 | 46 +++--- NEWS.md | 7 R/core_functions.R | 176 ++++++++++------------- R/data.R | 26 ++- R/utility.R | 228 ++++++++++++++++++++----------- README.md | 2 build/vignette.rds |binary data/example_gene_scna_table.rda |only inst/doc/how_to_use.R | 62 ++++---- inst/doc/how_to_use.html | 1 man/KEGG_cancer_pathways_descriptions.Rd | 4 man/create_SCNA_score_df.Rd | 6 man/create_features_df.Rd | 25 +-- man/create_gene_level_scna_df.Rd | 6 man/create_noncoding_impact_score_df.Rd | 2 man/determine_double_hit_genes.Rd | 4 man/driveR.Rd | 2 man/example_cohort_features_table.Rd | 2 man/example_features_table.Rd | 2 man/example_gene_scna_table.Rd |only man/predict_coding_impact.Rd | 6 man/prioritize_driver_genes.Rd | 4 tests/testthat/test-core_functions.R | 218 ++++++++++++----------------- tests/testthat/test-utility.R | 199 +++++++++++---------------- 25 files changed, 530 insertions(+), 519 deletions(-)
Title: Analysis of Stable Matchings
Description: Implements structural estimators to estimate preferences and correct for
the sample selection bias of observed outcomes in matching
markets. This includes one-sided matching of agents into groups
(Klein, 2015) <doi:10.17863/CAM.5812>
as well as two-sided matching of students to schools
(Klein et al., 2024) <doi:10.1016/j.geb.2024.07.003>.
The package also contains algorithms to find stable matchings
in the three most common matching problems: the stable roommates
problem (Irving, 1985) <doi:10.1016/0196-6774(85)90033-1>,
the college admissions problem (Gale and Shapley, 1962) <doi:10.2307/2312726>,
and the house allocation problem (Shapley and Scarf, 1974) <doi:10.1016/0304-4068(74)90033-0>.
Author: Thilo Klein [aut, cre, cph],
Robert Aue [ctb],
Fahiem Bacchus [cph],
Sven Giegerich [ctb],
Matthias Hericks [ctb],
Alexander Sauer [ctb],
Niklas Sorensson [cph]
Maintainer: Thilo Klein <thilo@klein.uk>
Diff between matchingMarkets versions 1.0-4 dated 2023-08-08 and 1.0-5 dated 2025-12-22
DESCRIPTION | 18 +++++++------- MD5 | 40 ++++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 2 - R/RcppExports.R | 4 +++ R/hri3.R |only R/stabit.R | 37 +++++++++++++++++------------- README.md | 6 ++-- build/partial.rdb |only inst/CITATION | 4 +-- inst/doc/matching.Rnw | 6 ++++ inst/doc/matching.pdf |binary inst/include/System.h | 2 - man/baac00.Rd | 2 - man/hri3.Rd |only man/klein15b.Rd | 2 - man/matchingMarkets-package.Rd | 7 ++--- man/stabit.Rd | 6 +++- src/RcppExports.cpp | 17 ++++++++++++++ src/eadam.cpp |only src/stabitSel2.cpp | 41 +++++++++++++++++++++++++++------- vignettes/Sections/1_Introduction.tex | 6 ++-- vignettes/matching.Rnw | 6 ++++ 23 files changed, 138 insertions(+), 69 deletions(-)
More information about matchingMarkets at CRAN
Permanent link
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.2.0 dated 2025-10-23 and 1.2.1 dated 2025-12-22
DESCRIPTION | 7 +++---- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 6 insertions(+), 7 deletions(-)
Title: R Integration for 'Goose' AI
Description: Seamless integration between R and 'Goose' AI capabilities
including memory management, visualization enhancements, and workflow
automation. Save R objects to 'Goose' memory, apply Block branding to
visualizations, and manage data science project workflows.
For more information about 'Goose' AI, see <https://github.com/block/goose>.
Author: Brandon Theriault [aut, cre]
Maintainer: Brandon Theriault <btheriault@block.xyz>
Diff between gooseR versions 0.1.0 dated 2025-12-17 and 0.1.1 dated 2025-12-22
DESCRIPTION | 6 ++--- MD5 | 33 ++++++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 20 +++++++++++++++++-- R/addins.R | 9 +++----- R/async.R | 6 ----- R/cache.R | 1 R/memory_bulk.R | 45 +++++++++++++++++++++++++++++++------------- R/quarto_integration.R | 1 R/streaming.R | 1 R/ui_components.R | 16 ++++++--------- README.md | 7 ++++-- inst/doc/use-case-demo.html | 4 +-- man/goose_addins.Rd |only man/goose_async.Rd | 4 ++- man/goose_cache.Rd |only man/goose_exists.Rd | 4 +-- man/goose_quarto.Rd |only man/goose_streaming.Rd |only man/goose_ui_components.Rd |only 20 files changed, 99 insertions(+), 59 deletions(-)
Title: Extract Drugs from Differential Expression Data from LINCS
Database
Description: Get Drug information from given differential expression profile. The package search for the bioactive compounds from reference databases such as LINCS containing the genome-wide gene expression signature (GES) from tens of thousands of drug and genetic perturbations (Subramanian et al. (2017) <DOI:10.1016/j.cell.2017.10.049>).
Author: Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between DFD versions 0.3.0 dated 2025-02-11 and 0.4.0 dated 2025-12-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 2 -- R/get_drugs.R | 12 ++++++++++-- 4 files changed, 17 insertions(+), 11 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods Involving Target Trial Emulations
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2025)<Forthcoming>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals. Also, standard computational tools for target trial emulation are included.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.2-1 dated 2025-12-15 and 4.2-2 dated 2025-12-22
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 4 ++++ R/ttemsm.r | 4 ++-- man/rqlm-package.Rd | 4 +++- man/ttemsm.Rd | 18 +++++++++++++++--- 6 files changed, 35 insertions(+), 17 deletions(-)
Title: Czekanowski's Diagrams
Description: Allows for production of Czekanowski's Diagrams with clusters. See K. Bartoszek, A. Vasterlund (2020) <doi:10.2478/bile-2020-0008> and K. Bartoszek, Y. Luo (2023) <doi:10.14708/ma.v51i2.7259>. The suggested 'FuzzyDBScan' package (which allows for fuzzy clustering) can be obtained from
<https://github.com/henrifnk/FuzzyDBScan/> (or from CRAN's Archive <https://cran.r-project.org/src/contrib/Archive/FuzzyDBScan/>).
Author: Albin Vasterlund [aut],
Krzysztof Bartoszek [cre, aut, ths],
Ying Luo [aut],
Piotr Jaskulski [ctb]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
This is a re-admission after prior archival of version 1.6.0 dated 2024-06-23
Diff between RMaCzek versions 1.6.0 dated 2024-06-23 and 1.6.1 dated 2025-12-22
DESCRIPTION | 16 +++--- MD5 | 10 +-- R/czek_matrix.R | 128 +++++++++++++++++++++++++----------------------- R/plot.czek_matrix.R | 11 ++-- man/czek_matrix.Rd | 14 +++-- man/plot.czek_matrix.Rd | 11 ++-- 6 files changed, 103 insertions(+), 87 deletions(-)
Title: Empirical Likelihood Analysis for the Cox Model and
Yang-Prentice (2005) Model
Description: Empirical likelihood ratio tests for the Yang and Prentice (short/long term hazards ratio) model.
Empirical likelihood tests within a Cox model, for parameters defined via
both baseline hazard function and regression parameters.
Author: Mai Zhou [aut, cre]
Maintainer: Mai Zhou <maizhou@gmail.com>
Diff between ELYP versions 0.7-5 dated 2018-08-19 and 0.7-6 dated 2025-12-22
DESCRIPTION | 16 ++++++++++------ MD5 | 4 ++-- man/CoxEL.Rd | 15 +++++++++++---- 3 files changed, 23 insertions(+), 12 deletions(-)
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 4.2-6-2 dated 2025-01-24 and 4.3-4-3 dated 2025-12-22
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Title: A Common Representation of Time Indices of Different Types
Description: Provides an easy-to-use tind class representing time indices
of different types (years, quarters, months, ISO 8601 weeks, dates,
time of day, date-time, and arbitrary integer/numeric indices).
Includes an extensive collection of functions for calendrical computations
(including business applications), index conversions, index parsing,
and other operations. Auxiliary classes representing time differences and
time intervals (with set operations and index matching functionality) are
also provided. All routines have been optimised for speed in order
to facilitate computations on large datasets. More details regarding
calendars in general and calendrical algorithms can be found in
"Calendar FAQ" by Claus Tøndering <https://www.tondering.dk/claus/calendar.html>.
Author: Grzegorz Klima [aut, cre, cph]
Maintainer: Grzegorz Klima <dever@post.pl>
This is a re-admission after prior archival of version 0.2.2 dated 2025-11-07
Diff between tind versions 0.2.2 dated 2025-11-07 and 0.2.3 dated 2025-12-22
DESCRIPTION | 8 - MD5 | 80 +++++++------- R/base-parse.R | 2 R/base-th.R | 4 R/base-tz.R | 181 +++++++++++++++++++++++++++++++- R/plot-scales.R | 38 ++++-- build/vignette.rds |binary inst/doc/calendar.html | 176 +++++++++++++++---------------- inst/doc/indices.html | 3 inst/po/en@quot/LC_MESSAGES/R-tind.mo |binary inst/po/pl/LC_MESSAGES/R-tind.mo |binary man/scale_tind.Rd | 38 ++++-- po/R-pl.po | 11 + po/R-tind.pot | 7 - src/parse.c | 80 +++++--------- tests/testthat/test-03-base-tz.R | 27 +++- tests/testthat/test-04-base-th.R | 20 +-- tests/testthat/test-05-base-res.R | 2 tests/testthat/test-06-base-pretty.R | 2 tests/testthat/test-08-base-types.R | 2 tests/testthat/test-09-base-parse.R | 2 tests/testthat/test-10-tind.R | 4 tests/testthat/test-11-format_parse.R | 4 tests/testthat/test-12-coercion.R | 2 tests/testthat/test-13-methods.R | 2 tests/testthat/test-15-tinterval.R | 2 tests/testthat/test-17-ops.R | 2 tests/testthat/test-18-setops_match.R | 2 tests/testthat/test-19-tzone.R | 4 tests/testthat/test-20-tspan.R | 2 tests/testthat/test-21-resolution.R | 2 tests/testthat/test-22-print_summ_str.R | 2 tests/testthat/test-23-round.R | 2 tests/testthat/test-24-cut.R | 2 tests/testthat/test-25-seq.R | 2 tests/testthat/test-26-ord_reg.R | 4 tests/testthat/test-27-calendar.R | 6 - tests/testthat/test-30-other.R | 2 tests/testthat/test-31-merge.R | 2 tests/testthat/test-32-pretty.R | 2 tests/testthat/test-33-plot-scales.R | 2 41 files changed, 467 insertions(+), 268 deletions(-)
Title: Personalized Network-Based Anti-Cancer Therapy Evaluation
Description: Identification of the most appropriate pharmacotherapy for each
patient based on genomic alterations is a major challenge in personalized
oncology. 'PANACEA' is a collection of personalized anti-cancer drug
prioritization approaches utilizing network methods. The methods utilize
personalized "driverness" scores from 'driveR' to rank drugs, mapping these
onto a protein-protein interaction network. The "distance-based" method
scores each drug based on these scores and distances between drugs and genes
to rank given drugs. The "RWR" method propagates these scores via a
random-walk with restart framework to rank the drugs. The methods are
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2023. PANACEA:
network-based methods for pharmacotherapy prioritization in personalized
oncology. Bioinformatics <doi:10.1093/bioinformatics/btad022>.
Author: Ege Ulgen [aut, cre, cph]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between PANACEA versions 1.0.1 dated 2023-08-19 and 1.1.0 dated 2025-12-22
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS.md | 6 +++++- R/utility.R | 9 +++++++++ README.md | 2 +- build/vignette.rds |binary inst/doc/how_to_use.R | 10 +++++----- inst/doc/how_to_use.html | 1 + tests/testthat/test-utility.R | 12 +++++++++--- 9 files changed, 46 insertions(+), 25 deletions(-)
Title: Boundary Line Analysis
Description: Fits boundary line models to datasets as proposed by Webb
(1972) <doi:10.1080/00221589.1972.11514472> and makes statistical
inferences about their parameters. Provides additional tools for
testing datasets for evidence of boundary presence and selecting
initial starting values for model optimization prior to fitting the
boundary line models. It also includes tools for conducting post-hoc
analyses such as predicting boundary values and identifying the most
limiting factor (Miti, Milne, Giller, Lark (2024)
<doi:10.1016/j.fcr.2024.109365>). This ensures a comprehensive
analysis for datasets that exhibit upper boundary structures.
Author: Chawezi Miti [cre, aut, cph] ,
Richard M Lark [aut] ,
Alice E Milne [aut] ,
Ken E Giller [aut] ,
Victor O Sadras [ctb],
University of Nottingham/Rothamsted Research [fnd]
Maintainer: Chawezi Miti <mitichawezi14@gmail.com>
Diff between BLA versions 1.0.1 dated 2024-05-28 and 1.0.2 dated 2025-12-22
DESCRIPTION | 21 +-- MD5 | 38 ++--- NAMESPACE | 2 NEWS.md | 6 R/Perimeter_Area_calc.R |only R/ble_profiling.R | 17 +- R/cbvn.R | 6 R/exp_boundary.R | 175 ++++++++++++++++++++------ README.md | 19 ++ build/partial.rdb |binary build/vignette.rds |binary data/soil.rda |binary inst/doc/BLA.R | 48 +++---- inst/doc/BLA.html | 62 ++++----- inst/doc/Censored_bivariate_normal_model.R | 102 +++++++-------- inst/doc/Censored_bivariate_normal_model.html | 25 +-- inst/doc/Introduction_to_BLA.R | 48 +++---- inst/doc/Introduction_to_BLA.html | 62 ++++----- man/AP.Rd |only man/expl_boundary.Rd | 134 ++++++++++--------- man/figures/README-unnamed-chunk-8-1.png |binary 21 files changed, 453 insertions(+), 312 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)
Author: Philip Leifeld [aut, cre],
Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between texreg versions 1.39.4 dated 2024-07-24 and 1.39.5 dated 2025-12-22
DESCRIPTION | 31 ++++++++------- MD5 | 29 +++++++------- R/extract.R | 75 ++++++++++++++++++++++++++++++++++++-- R/texreg.R | 7 ++- inst/doc/texreg.Rnw | 12 +++--- inst/doc/texreg.pdf |binary man/createTexreg.Rd | 3 - man/extract-oglmx-method.Rd | 4 +- man/extract-prais-method.Rd |only tests/testthat/test-extract.R | 48 ++++++++++++++++++------ tests/testthat/test-huxtablereg.R | 2 - tests/testthat/test-jss.R | 2 + tests/testthat/test-plotreg.R | 15 ++++--- tests/testthat/test-texreg.R | 71 +++++++++++++++++++++-------------- vignettes/texreg.Rnw | 12 +++--- vignettes/texreg.bib | 63 +++++++++++++------------------ 16 files changed, 241 insertions(+), 133 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd] ,
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.9.1 dated 2025-12-01 and 0.9.2 dated 2025-12-22
DESCRIPTION | 6 - MD5 | 41 ++++--- NEWS.md | 4 src/library/pkgdepends/DESCRIPTION | 2 src/library/pkgdepends/R/install-binary.R | 4 src/library/yaml/COPYING | 3 src/library/yaml/DESCRIPTION | 64 +++++++++--- src/library/yaml/LICENSE | 6 - src/library/yaml/NAMESPACE | 9 + src/library/yaml/R/as.yaml.R | 146 ++++++++++++++++++++++++++-- src/library/yaml/R/read_yaml.R | 85 ++++++++++++++-- src/library/yaml/R/verbatim_logical.R | 21 ++++ src/library/yaml/R/write_yaml.R | 42 +++++++- src/library/yaml/R/yaml-package.R |only src/library/yaml/R/yaml.load.R | 154 ++++++++++++++++++++++++++++-- src/library/yaml/R/yaml.load_file.R | 22 ++-- src/library/yaml/src/emitter.c | 18 +-- src/library/yaml/src/r_emit.c | 11 -- src/library/yaml/src/r_ext.c | 8 - src/library/yaml/src/r_ext.h | 4 src/library/yaml/src/r_parse.c | 12 +- tests/testthat/test-repo.R | 2 22 files changed, 549 insertions(+), 115 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.11.0 dated 2025-09-15 and 0.12.0 dated 2025-12-22
DESCRIPTION | 8 +- MD5 | 65 ++++++++++--------- NEWS.md | 8 ++ R/deprecated.R | 4 - R/geom_connector.R | 18 +++++ R/ggcoef_model.R | 3 R/gglikert.R | 17 ++++- R/stat_prop.R | 6 + R/vdiffr-helper.R |only R/weighted_quantile.R | 2 build/vignette.rds |binary inst/doc/ggcoef_model.R | 2 inst/doc/ggcoef_model.Rmd | 2 inst/doc/ggcoef_model.html | 10 --- man/geom_connector.Rd | 8 +- man/geom_stripped_rows.Rd | 10 +-- man/ggcoef_model.Rd | 6 - man/gglikert.Rd | 3 man/ggsurvey.Rd | 2 man/hex_bw.Rd | 2 man/stat_cross.Rd | 6 + man/stat_prop.Rd | 10 +-- man/stat_weighted_mean.Rd | 10 +-- tests/testthat/test-geom_connector.R | 18 ++--- tests/testthat/test-geom_stripped.R | 2 tests/testthat/test-ggcascade.R | 8 +- tests/testthat/test-ggcoef_model.R | 96 ++++++++++++++--------------- tests/testthat/test-gglikert.R | 101 +++++++++++++++++++------------ tests/testthat/test-position_likert.R | 22 +++--- tests/testthat/test-stat_cross.R | 20 +++--- tests/testthat/test-stat_prop.R | 32 ++++----- tests/testthat/test-stat_weighted_mean.R | 14 ++-- tests/testthat/test_ggsurvey.R | 4 - vignettes/ggcoef_model.Rmd | 2 34 files changed, 294 insertions(+), 227 deletions(-)
Title: A 'ggplot2' Extension for Drawing Publication-Ready Sequence
Logos
Description: The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Author: Omar Wagih [aut, cre]
Maintainer: Omar Wagih <omarwagih@gmail.com>
Diff between ggseqlogo versions 0.2 dated 2024-02-08 and 0.2.2 dated 2025-12-22
DESCRIPTION | 16 +++++++++------- MD5 | 12 ++++++------ R/ggseqlogo.r | 4 ++-- inst/doc/ggseqlogo_introduction.html | 4 ++-- man/geom_logo.Rd | 19 +++++++++++++++---- man/ggseqlogo.Rd | 14 ++++++++++---- man/make_col_scheme.Rd | 9 +++++++-- 7 files changed, 51 insertions(+), 27 deletions(-)
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] ,
Vonage Holdings Corp. [ctb, cph] ,
Ian Galpin [ctb, cph] ,
Ben Gertzfield [ctb, cph]
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 9.0.14 dated 2025-09-16 and 9.0.21 dated 2025-12-22
dialrjars-9.0.14/dialrjars/inst/java/carrier-2.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/geocoder-3.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/libphonenumber-9.0.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/prefixmapper-3.14.jar |only dialrjars-9.0.21/dialrjars/DESCRIPTION | 6 dialrjars-9.0.21/dialrjars/MD5 | 26 +-- dialrjars-9.0.21/dialrjars/NAMESPACE | 6 dialrjars-9.0.21/dialrjars/NEWS.md | 70 +++++++++ dialrjars-9.0.21/dialrjars/R/dialrjars.R | 6 dialrjars-9.0.21/dialrjars/inst/COPYRIGHTS | 18 +- dialrjars-9.0.21/dialrjars/inst/java/carrier-2.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/geocoder-3.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/libphonenumber-9.0.21.jar |only dialrjars-9.0.21/dialrjars/inst/java/prefixmapper-3.21.jar |only dialrjars-9.0.21/dialrjars/java/README | 14 - dialrjars-9.0.21/dialrjars/man/dialrjars-package.Rd | 64 ++++---- dialrjars-9.0.21/dialrjars/tests/testthat.R | 8 - dialrjars-9.0.21/dialrjars/tests/testthat/test-dialrjars.R | 76 +++++----- 18 files changed, 182 insertions(+), 112 deletions(-)
Title: Gradient Boosting for Longitudinal Data
Description: Gradient boosting is a powerful statistical learning method known for its ability to model
complex relationships between predictors and outcomes while performing inherent variable selection.
However, traditional gradient boosting methods lack flexibility in handling longitudinal data where
within-subject correlations play a critical role. In this package, we propose a novel approach
Mixed Effect Gradient Boosting ('MEGB'), designed specifically for high-dimensional longitudinal data.
'MEGB' incorporates a flexible semi-parametric model that embeds random effects within the gradient boosting
framework, allowing it to account for within-individual covariance over time. Additionally, the method
efficiently handles scenarios where the number of predictors greatly exceeds the number of observations
(p>>n) making it particularly suitable for genomics data and other large-scale biomedical studies.
Author: Oyebayo Ridwan Olaniran [aut, cre],
Saidat Fehintola Olaniran [aut]
Maintainer: Oyebayo Ridwan Olaniran <olaniran.or@unilorin.edu.ng>
Diff between MEGB versions 0.1 dated 2025-01-29 and 0.2 dated 2025-12-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 4 +--- R/MEGB.R | 3 +-- man/simLong.Rd | 2 +- 5 files changed, 11 insertions(+), 14 deletions(-)
Title: Itrax Data Analysis Tools
Description: Parse, trim, join, visualise and analyse data from Itrax sediment core multi-parameter
scanners manufactured by Cox Analytical Systems, Sweden. Functions are provided for parsing
XRF-peak area files, line-scan optical images, and radiographic images, alongside accompanying metadata.
A variety of data wrangling tasks like trimming, joining and reducing XRF-peak area data are simplified.
Multivariate methods are implemented with appropriate data transformation.
Author: Thomas Bishop [aut, cre]
Maintainer: Thomas Bishop <tombishopemail@gmail.com>
Diff between itraxR versions 1.12.2 dated 2024-05-30 and 1.13.2 dated 2025-12-21
itraxR-1.12.2/itraxR/R/itrax_join.r |only itraxR-1.12.2/itraxR/R/itrax_meta.r |only itraxR-1.13.2/itraxR/DESCRIPTION | 25 ++++--- itraxR-1.13.2/itraxR/MD5 | 42 ++++++------ itraxR-1.13.2/itraxR/NAMESPACE | 5 + itraxR-1.13.2/itraxR/R/itrax_image.R | 4 - itraxR-1.13.2/itraxR/R/itrax_join.R |only itraxR-1.13.2/itraxR/R/itrax_meta.R |only itraxR-1.13.2/itraxR/R/itrax_radiograph.R | 4 - itraxR-1.13.2/itraxR/R/itrax_sumspectra.R |only itraxR-1.13.2/itraxR/man/CD166_19_S1.Rd | 48 ++++++------- itraxR-1.13.2/itraxR/man/itrax_correlation.Rd | 70 ++++++++++---------- itraxR-1.13.2/itraxR/man/itrax_image.Rd | 80 +++++++++++----------- itraxR-1.13.2/itraxR/man/itrax_join.Rd | 2 itraxR-1.13.2/itraxR/man/itrax_meta.Rd | 2 itraxR-1.13.2/itraxR/man/itrax_ordination.Rd | 76 ++++++++++----------- itraxR-1.13.2/itraxR/man/itrax_qspecsettings.Rd | 50 +++++++------- itraxR-1.13.2/itraxR/man/itrax_radiograph.Rd | 82 +++++++++++------------ itraxR-1.13.2/itraxR/man/itrax_reduce.Rd | 84 ++++++++++++------------ itraxR-1.13.2/itraxR/man/itrax_restspectra.Rd | 76 ++++++++++----------- itraxR-1.13.2/itraxR/man/itrax_section.Rd | 82 +++++++++++------------ itraxR-1.13.2/itraxR/man/itrax_spectra.Rd | 70 ++++++++++---------- itraxR-1.13.2/itraxR/man/itrax_sumspectra.Rd |only itraxR-1.13.2/itraxR/man/multivariate_import.Rd | 42 ++++++------ itraxR-1.13.2/itraxR/man/uid_labeller.Rd | 36 +++++----- 25 files changed, 447 insertions(+), 433 deletions(-)
Title: Simplified Access to Brazilian Financial and Macroeconomic Data
Description: It offers simplified access to Brazilian macroeconomic and financial indicators selected from official sources, such as the 'IBGE' (Brazilian Institute of Geography and Statistics) via the 'SIDRA' API and the 'Central Bank of Brazil' via the 'SGS' API. It allows users to quickly retrieve and visualize data series such as the unemployment rate and the Selic interest rate. This package was developed for data access and visualization purposes, without generating forecasts or statistical results. For more information, see the official APIs: <https://sidra.ibge.gov.br/> and <https://dadosabertos.bcb.gov.br/dataset/>.
Author: Joao Paulo dos Santos Pereira Barbosa [aut, cre]
Maintainer: Joao Paulo dos Santos Pereira Barbosa <joao.31582129@gmail.com>
Diff between brfinance versions 0.2.2 dated 2025-10-19 and 0.6.0 dated 2025-12-21
brfinance-0.2.2/brfinance/R/globals.R |only brfinance-0.6.0/brfinance/DESCRIPTION | 11 brfinance-0.6.0/brfinance/MD5 | 57 ++- brfinance-0.6.0/brfinance/NAMESPACE | 20 - brfinance-0.6.0/brfinance/R/download_sgs.R |only brfinance-0.6.0/brfinance/R/get_cdi_rate.R |only brfinance-0.6.0/brfinance/R/get_exchange_rate.R |only brfinance-0.6.0/brfinance/R/get_gdp_growth.R |only brfinance-0.6.0/brfinance/R/get_inflation_rate.R |only brfinance-0.6.0/brfinance/R/get_selic_rate.R | 146 +++++--- brfinance-0.6.0/brfinance/R/get_unemployment.R | 141 ++++++- brfinance-0.6.0/brfinance/R/plot_cdi_rate.R |only brfinance-0.6.0/brfinance/R/plot_exchange_rate.R |only brfinance-0.6.0/brfinance/R/plot_inflation_rate.R |only brfinance-0.6.0/brfinance/R/plot_selic_rate.R | 76 ++-- brfinance-0.6.0/brfinance/R/plot_series_comparison.R |only brfinance-0.6.0/brfinance/R/plot_time_series.R |only brfinance-0.6.0/brfinance/R/plot_unemployment.R | 73 ++-- brfinance-0.6.0/brfinance/R/zzz.R | 32 + brfinance-0.6.0/brfinance/README.md | 288 +++++++++++----- brfinance-0.6.0/brfinance/build |only brfinance-0.6.0/brfinance/inst |only brfinance-0.6.0/brfinance/man/dot-get_sgs_series.Rd |only brfinance-0.6.0/brfinance/man/get_cdi_rate.Rd |only brfinance-0.6.0/brfinance/man/get_exchange_rate.Rd |only brfinance-0.6.0/brfinance/man/get_gdp_growth.Rd |only brfinance-0.6.0/brfinance/man/get_inflation_rate.Rd |only brfinance-0.6.0/brfinance/man/get_selic_rate.Rd | 69 +++ brfinance-0.6.0/brfinance/man/get_unemployment.Rd | 83 ++++ brfinance-0.6.0/brfinance/man/plot_cdi_rate.Rd |only brfinance-0.6.0/brfinance/man/plot_exchange_rate.Rd |only brfinance-0.6.0/brfinance/man/plot_inflation_rate.Rd |only brfinance-0.6.0/brfinance/man/plot_series_comparison.Rd |only brfinance-0.6.0/brfinance/vignettes |only 34 files changed, 735 insertions(+), 261 deletions(-)
Title: Descriptive Statistics and Data Management Tools
Description: Extracts and summarizes metadata from data frames, including variable names, labels, types, and missing values. Computes compact descriptive statistics, frequency tables, and cross-tabulations to assist with efficient data exploration. Includes an interactive and exportable codebook generator for documenting variable metadata. Facilitates the identification of missing data patterns and structural issues in datasets. Designed to streamline initial data management and exploratory analysis workflows within 'R'.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.3.0 dated 2025-10-22 and 0.4.1 dated 2025-12-21
spicy-0.3.0/spicy/R/print_spicy.R |only spicy-0.3.0/spicy/man/print.spicy.Rd |only spicy-0.3.0/spicy/tests/testthat/test-print_spicy.R |only spicy-0.4.1/spicy/DESCRIPTION | 10 spicy-0.4.1/spicy/MD5 | 40 spicy-0.4.1/spicy/NAMESPACE | 10 spicy-0.4.1/spicy/NEWS.md | 31 spicy-0.4.1/spicy/R/cross_tab.R | 1006 ++++++++++--------- spicy-0.4.1/spicy/R/freq.R | 554 +++++----- spicy-0.4.1/spicy/R/freq_print.R |only spicy-0.4.1/spicy/R/globals.R |only spicy-0.4.1/spicy/R/spicy_tables.R |only spicy-0.4.1/spicy/R/tables_ascii.R |only spicy-0.4.1/spicy/R/varlist.R | 32 spicy-0.4.1/spicy/README.md | 207 ++- spicy-0.4.1/spicy/man/build_ascii_table.Rd |only spicy-0.4.1/spicy/man/cross_tab.Rd | 157 +- spicy-0.4.1/spicy/man/freq.Rd | 172 ++- spicy-0.4.1/spicy/man/print.spicy_cross_table.Rd |only spicy-0.4.1/spicy/man/print.spicy_freq_table.Rd |only spicy-0.4.1/spicy/man/spicy_print_table.Rd |only spicy-0.4.1/spicy/man/spicy_tables.Rd |only spicy-0.4.1/spicy/man/varlist.Rd | 6 spicy-0.4.1/spicy/tests/testthat/test-cross_tab.R | 145 +- spicy-0.4.1/spicy/tests/testthat/test-freq.R | 218 ++-- spicy-0.4.1/spicy/tests/testthat/test-freq_print.R |only spicy-0.4.1/spicy/tests/testthat/test-tables_ascii.R |only spicy-0.4.1/spicy/tests/testthat/test-varlist.R | 78 - 28 files changed, 1509 insertions(+), 1157 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre] ,
Daniel Schuch [ctb] ,
Joao Bazzo [ctb] ,
Mario Gavidia-Calderon [ctb] ,
Karl Ropkins [ctb]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Diff between vein versions 1.5.0 dated 2025-10-04 and 1.6.0 dated 2025-12-21
vein-1.5.0/vein/man/inventory.Rd |only vein-1.6.0/vein/DESCRIPTION | 10 vein-1.6.0/vein/MD5 | 25 vein-1.6.0/vein/NAMESPACE | 1 vein-1.6.0/vein/NEWS.md | 10 vein-1.6.0/vein/R/get_project.R | 244 ++++----- vein-1.6.0/vein/R/inventory.R | 622 ++++++++++++------------ vein-1.6.0/vein/R/vein-deprecated.R | 6 vein-1.6.0/vein/inst/doc/basics.html | 4 vein-1.6.0/vein/man/get_project.Rd | 1 vein-1.6.0/vein/man/vein-deprecated.Rd | 3 vein-1.6.0/vein/tests/testthat/Rplots.pdf |binary vein-1.6.0/vein/tests/testthat/test-inventory.R | 76 +- vein-1.6.0/vein/tests/testthat/test-make_grid.R | 18 14 files changed, 513 insertions(+), 507 deletions(-)
Title: Perform Analysis and Create Visualizations of Proteins
Description: Read Protein Data Bank (PDB) files, performs its analysis, and
presents the result using different visualization types including 3D. The
package also has additional capability for handling Virus Report data from
the National Center for Biotechnology Information (NCBI) database.
Nature Structural Biology 10, 980 (2003) <doi:10.1038/nsb1203-980>.
US National Library of Medicine (2021) <https://www.ncbi.nlm.nih.gov/datasets/docs/reference-docs/data-reports/virus/>.
Author: Simon Liles [aut, cre]
Maintainer: Simon Liles <simon@quantknot.com>
Diff between protein8k versions 0.0.1 dated 2021-08-16 and 0.0.2 dated 2025-12-21
DESCRIPTION | 18 + MD5 | 34 +-- R/Data.R | 46 ++-- R/getAtomicRecord.R | 52 ++-- R/getTitleSection.R | 14 - R/proteinClassDefinition.R | 46 ++-- R/read.pdb.R | 46 ++-- R/summary.Protein.R | 22 +- R/write_viz.R | 8 build/vignette.rds |binary inst/doc/intro_protein8k.R | 4 inst/doc/intro_protein8k.html | 419 +++++++++++++++++++++++++++++++-------- inst/doc/using_plot3D.R | 4 inst/doc/using_plot3D.html | 446 ++++++++++++++++++++++++++++++++---------- man/Protein-class.Rd | 46 ++-- man/getAtomicRecord.Rd | 32 +-- man/p53_tetramerization.Rd | 46 ++-- man/read.pdb.Rd | 46 ++-- 18 files changed, 924 insertions(+), 405 deletions(-)
Title: Structural Scenario Analysis for Bayesian Structural Vector
Autoregression Models
Description: Implements the scenario analysis proposed by Antolin-Diaz,
Petrella and Rubio-Ramirez (2021)
"Structural scenario analysis with SVARs" <doi:10.1016/j.jmoneco.2020.06.001>.
Author: Giovanni Lombardo [aut, cre]
Maintainer: Giovanni Lombardo <giannilmbd@gmail.com>
Diff between APRScenario versions 0.0.3.0 dated 2025-07-24 and 0.0.3.1 dated 2025-12-21
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++++-------------- R/KL.r | 5 ++--- R/forc_h.r | 8 ++++---- R/gen_mats.r | 8 ++++---- R/mat_forc.r | 8 ++++---- R/scenarios.r | 3 ++- inst/doc/APRScenario.R | 2 +- inst/doc/APRScenario.Rmd | 2 +- inst/doc/APRScenario.html | 2 +- man/forc_h.Rd | 11 ++++++++++- man/gen_mats.Rd | 4 +++- man/mat_forc.Rd | 12 +++++++++++- man/scenarios.Rd | 3 ++- vignettes/APRScenario.Rmd | 2 +- vignettes/APRScenario_files |only 16 files changed, 67 insertions(+), 41 deletions(-)
Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a
library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre],
Erin LeDell [aut],
Chris Kennedy [aut],
Sam Lendle [ctb],
Mark van der Laan [aut, ths]
Maintainer: Eric Polley <epolley@uchicago.edu>
Diff between SuperLearner versions 2.0-29 dated 2024-02-20 and 2.0-40 dated 2025-12-21
SuperLearner-2.0-29/SuperLearner/tests/cran |only SuperLearner-2.0-29/SuperLearner/tests/testthat/test-SampleSplitSuperLearner.R |only SuperLearner-2.0-29/SuperLearner/tests/testthat/test-createLearner.R |only SuperLearner-2.0-29/SuperLearner/tests/testthat/test-randomForest.R |only SuperLearner-2.0-40/SuperLearner/DESCRIPTION | 8 SuperLearner-2.0-40/SuperLearner/MD5 | 40 SuperLearner-2.0-40/SuperLearner/NAMESPACE | 1 SuperLearner-2.0-40/SuperLearner/R/SL.bartMachine.R | 2 SuperLearner-2.0-40/SuperLearner/R/SL.cforest.R | 2 SuperLearner-2.0-40/SuperLearner/R/SL.gam.R | 2 SuperLearner-2.0-40/SuperLearner/R/SL.xgboost.R | 51 SuperLearner-2.0-40/SuperLearner/R/create.Learner.R | 2 SuperLearner-2.0-40/SuperLearner/build/vignette.rds |binary SuperLearner-2.0-40/SuperLearner/inst/NEWS | 9 SuperLearner-2.0-40/SuperLearner/inst/doc/Guide-to-SuperLearner.R | 59 SuperLearner-2.0-40/SuperLearner/inst/doc/Guide-to-SuperLearner.Rmd | 70 SuperLearner-2.0-40/SuperLearner/inst/doc/Guide-to-SuperLearner.html | 860 ++++------ SuperLearner-2.0-40/SuperLearner/man/CV.SuperLearner.Rd | 4 SuperLearner-2.0-40/SuperLearner/man/CVFolds.Rd | 2 SuperLearner-2.0-40/SuperLearner/man/SL.cforest.Rd | 2 SuperLearner-2.0-40/SuperLearner/man/create.SL.xgboost.Rd | 2 SuperLearner-2.0-40/SuperLearner/tests/testthat/test-SuperLearner.R | 4 SuperLearner-2.0-40/SuperLearner/vignettes/Guide-to-SuperLearner.Rmd | 70 23 files changed, 458 insertions(+), 732 deletions(-)
Title: Necessary Condition Analysis
Description: Performs a Necessary Condition Analysis (NCA). (Dul, J. 2016. Necessary Condition Analysis (NCA). ''Logic and Methodology of 'Necessary but not Sufficient' causality." Organizational Research Methods 19(1), 10-52) <doi:10.1177/1094428115584005>.
NCA identifies necessary (but not sufficient) conditions in datasets, where x causes (e.g. precedes) y. Instead of drawing a regression line ''through the middle of the data'' in an xy-plot, NCA draws the ceiling line. The ceiling line y = f(x) separates the area with observations from the area without observations.
(Nearly) all observations are below the ceiling line: y <= f(x). The empty zone is in the upper left hand corner of the xy-plot (with the convention that the x-axis is ''horizontal'' and the y-axis is ''vertical'' and that values increase ''upwards'' and ''to the right''). The ceiling line is a (piecewise) linear non-decreasing line: a linear step function or a straight line. It indicates which level of x (e.g. an effort or [...truncated...]
Author: Jan Dul [aut],
Govert Buijs [cre]
Maintainer: Govert Buijs <buijs@rsm.nl>
Diff between NCA versions 4.0.4 dated 2025-11-14 and 4.0.5 dated 2025-12-21
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 4 R/nca_bottleneck.R | 297 +++++++++++++++++++---------------------------------- R/nca_output.R | 124 +++++++++++----------- R/p_bottleneck.R | 7 - man/NCA-package.Rd | 4 7 files changed, 193 insertions(+), 263 deletions(-)
Title: Generalized Additive Latent and Mixed Models
Description: Estimates generalized additive latent and
mixed models using maximum marginal likelihood,
as defined in Sorensen et al. (2023)
<doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
Skrondal (2004)'s unifying framework for multilevel latent variable
modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse
matrix methods, Laplace approximation, and automatic differentiation. The
framework includes generalized multilevel models with heteroscedastic
residuals, mixed response types, factor loadings, smoothing splines,
crossed random effects, and combinations thereof. Syntax for model
formulation is close to 'lme4' (Bates et al. (2015)
<doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019)
<doi:10.1080/00273171.2018.1516541>).
Author: Oeystein Soerensen [aut, cre] ,
Douglas Bates [ctb],
Ben Bolker [ctb],
Martin Maechler [ctb],
Allan Leal [ctb],
Fabian Scheipl [ctb],
Steven Walker [ctb],
Simon Wood [ctb]
Maintainer: Oeystein Soerensen <oystein.sorensen@psykologi.uio.no>
Diff between galamm versions 0.3.0 dated 2025-11-26 and 0.4.0 dated 2025-12-21
DESCRIPTION | 13 MD5 | 166 +++++++----- NAMESPACE | 13 R/galamm.R | 8 R/gratia_appraise.R |only R/gratia_derivatives.R |only R/gratia_draw.R |only R/misc.R | 4 R/model_frame.R |only R/plot.galamm.R | 168 +++++++++++- R/predict.galamm.R | 23 + R/qqmath.R |only R/residuals.galamm.R | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/glmm_factor.Rmd | 38 ++ inst/doc/glmm_factor.html | 196 ++++++++------- inst/doc/latent_observed_interaction.Rmd | 18 + inst/doc/latent_observed_interaction.html | 13 inst/doc/lmm_factor.Rmd | 60 +++- inst/doc/lmm_factor.html | 114 +++++--- inst/doc/lmm_heteroscedastic.Rmd | 12 inst/doc/lmm_heteroscedastic.html | 38 +- inst/doc/mixed_response.Rmd | 9 inst/doc/mixed_response.html | 22 - inst/doc/posterior_sampling.Rmd |only inst/doc/posterior_sampling.html |only inst/doc/scaling.html | 10 inst/doc/semiparametric.Rmd | 10 inst/doc/semiparametric.html | 20 - man/VarCorr.Rd | 3 man/anova.galamm.Rd | 2 man/appraise.galamm.Rd |only man/coef.galamm.Rd | 3 man/confint.galamm.Rd | 3 man/derivatives.galamm.Rd |only man/deviance.galamm.Rd | 3 man/draw.galamm.Rd |only man/factor_loadings.galamm.Rd | 3 man/family.galamm.Rd | 3 man/fitted.galamm.Rd | 3 man/fixef.Rd | 3 man/formula.galamm.Rd | 3 man/llikAIC.Rd | 3 man/logLik.galamm.Rd | 3 man/model.frame.galamm.Rd |only man/nobs.galamm.Rd | 3 man/plot.galamm.Rd | 90 +++++- man/plot_smooth.galamm.Rd | 2 man/predict.galamm.Rd | 18 + man/print.VarCorr.galamm.Rd | 3 man/print.galamm.Rd | 2 man/print.summary.galamm.Rd | 2 man/qqmath.galamm.Rd |only man/ranef.galamm.Rd | 3 man/residuals.galamm.Rd | 8 man/response.Rd | 3 man/sigma.galamm.Rd | 3 man/summary.galamm.Rd | 2 man/vcov.galamm.Rd | 3 tests/testthat/test-galamm-glmm.R | 47 +++ tests/testthat/test-galamm-lmm.R | 29 +- tests/testthat/test-galamm-semiparametric.R | 36 ++ tests/testthat/test-gratia-functions.R |only vignettes/glmm_factor.Rmd | 38 ++ vignettes/glmm_factor_binomial_diagnostic-1.png |binary vignettes/glmm_factor_poisson_diagnostic-1.png |binary vignettes/glmm_factor_poisson_diagnostic_lme4-1.png |binary vignettes/latent_observed_interaction.Rmd | 18 + vignettes/lmm_factor.Rmd | 60 +++- vignettes/lmm_factor_diagnostic_plot-1.png |binary vignettes/lmm_heteroscedastic.Rmd | 12 vignettes/lmm_heteroscedastic_diagnostic-1.png |binary vignettes/mixed_response.Rmd | 9 vignettes/posterior_sampling.Rmd |only vignettes/scaling-glmm-plot-1.png |binary vignettes/scaling-hsced-plot-1.png |binary vignettes/scaling-lmm-plot-1.png |binary vignettes/scaling-semiparametric-binomial-plot-1.png |binary vignettes/scaling-semiparametric-gaussian-plot-1.png |binary vignettes/semiparametric-gamm4-binomial-1.png |binary vignettes/semiparametric-gaussian-gamm-diagnostic-1.png |binary vignettes/semiparametric-gaussian-gamm4-diagnostic-1.png |binary vignettes/semiparametric-gaussian-gamm4-smooth-1.png |binary vignettes/semiparametric.Rmd | 10 vignettes/unnamed-chunk-10-1.png |only vignettes/unnamed-chunk-12-1.png |only vignettes/unnamed-chunk-15-1.png |only vignettes/unnamed-chunk-19-1.png |only vignettes/unnamed-chunk-20-1.png |only vignettes/unnamed-chunk-28-1.png |only vignettes/unnamed-chunk-29-1.png |only vignettes/unnamed-chunk-3-1.png |only vignettes/unnamed-chunk-6-1.png |only vignettes/unnamed-chunk-66-1.png |only vignettes/unnamed-chunk-73-1.png |only vignettes/unnamed-chunk-75-1.png |only 97 files changed, 1026 insertions(+), 379 deletions(-)
Title: Epigenome-Wide Mediation Analysis Study
Description: DNA methylation is essential for human, and environment can change the DNA methylation
and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find
potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide.
For more information on the methods we used, please see the following references:
Tingley, D. (2014) <doi:10.18637/jss.v059.i05>,
Turner, S. D. (2018) <doi:10.21105/joss.00731>,
Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.
Author: Xiuquan Nie [aut, cph, cre],
Mengyi Wang [ctb, rev]
Maintainer: Xiuquan Nie <niexiuquan1995@foxmail.com>
Diff between EMAS versions 0.2.3 dated 2025-09-04 and 0.2.4 dated 2025-12-21
EMAS-0.2.3/EMAS/R/EMAS.manhattan.R |only EMAS-0.2.3/EMAS/man/EMAS.manhattan.Rd |only EMAS-0.2.4/EMAS/DESCRIPTION | 12 +++++------- EMAS-0.2.4/EMAS/MD5 | 8 +++----- EMAS-0.2.4/EMAS/NAMESPACE | 5 ----- EMAS-0.2.4/EMAS/R/open.R | 2 +- 6 files changed, 9 insertions(+), 18 deletions(-)
Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling
Japanese iteration marks, Japanese character type conversions,
segmentation by phrase, and text normalization which is based on rules
for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism
dictionary for 'MeCab'). These features are specific to Japanese and
are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut],
Koki Takahashi [cph] ,
Shuhei Iitsuka [cph] ,
Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>
Diff between audubon versions 0.5.2 dated 2024-04-26 and 0.6.1 dated 2025-12-21
audubon-0.5.2/audubon/R/bind_lr.R |only audubon-0.5.2/audubon/R/bind_tf_idf2.R |only audubon-0.5.2/audubon/R/collapse_tokens.R |only audubon-0.5.2/audubon/R/lexical_density.R |only audubon-0.5.2/audubon/R/mute_tokens.R |only audubon-0.5.2/audubon/R/pack.R |only audubon-0.5.2/audubon/R/prettify.R |only audubon-0.5.2/audubon/build |only audubon-0.5.2/audubon/inst/testdata |only audubon-0.5.2/audubon/man/bind_lr.Rd |only audubon-0.5.2/audubon/man/bind_tf_idf2.Rd |only audubon-0.5.2/audubon/man/collapse_tokens.Rd |only audubon-0.5.2/audubon/man/get_dict_features.Rd |only audubon-0.5.2/audubon/man/lex_density.Rd |only audubon-0.5.2/audubon/man/mute_tokens.Rd |only audubon-0.5.2/audubon/man/ngram_tokenizer.Rd |only audubon-0.5.2/audubon/man/pack.Rd |only audubon-0.5.2/audubon/man/prettify.Rd |only audubon-0.5.2/audubon/man/strj_hiraganize.Rd |only audubon-0.5.2/audubon/man/strj_katakanize.Rd |only audubon-0.5.2/audubon/man/strj_segment.Rd |only audubon-0.5.2/audubon/man/strj_tinyseg.Rd |only audubon-0.5.2/audubon/tests/spelling.R |only audubon-0.5.2/audubon/tests/testthat/_snaps/bind_lr.md |only audubon-0.5.2/audubon/tests/testthat/_snaps/collapse_tokens.md |only audubon-0.5.2/audubon/tests/testthat/_snaps/lex_density.md |only audubon-0.5.2/audubon/tests/testthat/_snaps/mute_tokens.md |only audubon-0.5.2/audubon/tests/testthat/test-bind_lr.R |only audubon-0.5.2/audubon/tests/testthat/test-bind_tf_idf2.R |only audubon-0.5.2/audubon/tests/testthat/test-collapse_tokens.R |only audubon-0.5.2/audubon/tests/testthat/test-lex_density.R |only audubon-0.5.2/audubon/tests/testthat/test-mute_tokens.R |only audubon-0.5.2/audubon/tests/testthat/test-other-utils.R |only audubon-0.5.2/audubon/tests/testthat/test-strj-tokenize_1.R |only audubon-0.5.2/audubon/tests/testthat/test-strj-tokenize_2.R |only audubon-0.6.1/audubon/DESCRIPTION | 16 - audubon-0.6.1/audubon/MD5 | 96 ++---- audubon-0.6.1/audubon/NAMESPACE | 16 - audubon-0.6.1/audubon/NEWS.md | 17 + audubon-0.6.1/audubon/R/audubon-package.R | 20 + audubon-0.6.1/audubon/R/labellers.R |only audubon-0.6.1/audubon/R/strj-date.R |only audubon-0.6.1/audubon/R/strj-fill.R | 102 ++++-- audubon-0.6.1/audubon/R/strj-japanese.R | 154 +++++---- audubon-0.6.1/audubon/R/strj-normalize.R | 34 +- audubon-0.6.1/audubon/R/strj-rewrite.R | 108 ++++-- audubon-0.6.1/audubon/R/strj-tokenize.R | 160 ++++------ audubon-0.6.1/audubon/R/tokenize-impl.R | 144 +-------- audubon-0.6.1/audubon/R/zzz.R | 7 audubon-0.6.1/audubon/README.md | 100 ++---- audubon-0.6.1/audubon/inst/packer/audubon.bundle.js | 2 audubon-0.6.1/audubon/inst/packer/audubon.bundle.js.LICENSE.txt | 18 - audubon-0.6.1/audubon/man/default_format.Rd |only audubon-0.6.1/audubon/man/figures/README-demo_date-1.png |only audubon-0.6.1/audubon/man/figures/README-demo_wrap-1.png |only audubon-0.6.1/audubon/man/label_date_jp.Rd |only audubon-0.6.1/audubon/man/label_wrap_jp.Rd |only audubon-0.6.1/audubon/man/read_rewrite_def.Rd | 12 audubon-0.6.1/audubon/man/strj-hira-kana.Rd |only audubon-0.6.1/audubon/man/strj_fill_iter_mark.Rd | 18 - audubon-0.6.1/audubon/man/strj_normalize.Rd | 4 audubon-0.6.1/audubon/man/strj_parse_date.Rd |only audubon-0.6.1/audubon/man/strj_rewrite_as_def.Rd | 20 - audubon-0.6.1/audubon/man/strj_romanize.Rd | 28 - audubon-0.6.1/audubon/man/strj_tokenize.Rd | 59 ++- audubon-0.6.1/audubon/man/strj_transcribe_num.Rd | 17 - audubon-0.6.1/audubon/tests/testthat/_snaps/labellers.md |only audubon-0.6.1/audubon/tests/testthat/_snaps/strj-tokenize.md |only audubon-0.6.1/audubon/tests/testthat/test-labellers.R |only audubon-0.6.1/audubon/tests/testthat/test-strj-fill.R | 4 audubon-0.6.1/audubon/tests/testthat/test-strj-japanese.R | 15 audubon-0.6.1/audubon/tests/testthat/test-strj-rewrite-and-normalize.R | 4 audubon-0.6.1/audubon/tests/testthat/test-strj-tokenize.R |only 73 files changed, 579 insertions(+), 596 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). The pair
correlation function describes the spatial distribution of objects, e.g.
random, aggregated or regularly spaced. This is a reimplementation of the
method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050>
using the library 'GEOS' <doi:10.5281/zenodo.11396894>.
Author: Robert Nuske [aut, cre]
Maintainer: Robert Nuske <robert.nuske@mailbox.org>
Diff between apcf versions 0.3.2 dated 2025-02-28 and 0.3.3 dated 2025-12-21
DESCRIPTION | 13 +- MD5 | 17 +- NEWS.md | 4 README.md | 2 build/vignette.rds |binary inst/CITATION | 29 ++-- inst/doc/intro.html | 334 ++++++++++++++++++++++++++++++---------------------- src/Makevars.in | 1 src/Makevars.ucrt |only src/Makevars.win | 2 10 files changed, 236 insertions(+), 166 deletions(-)
Title: Statistical Inference for Weighted Data
Description: Analyzes and models data subject to sampling biases.
Provides functions to estimate the density and cumulative distribution
functions from biased samples of continuous distributions. Includes
the estimators proposed by Bhattacharyya et al. (1988)
<doi:10.1080/03610928808829825> and Jones (1991) <doi:10.2307/2337020>
for density, and by Cox (2005, ISBN:052184939X) and Bose and Dutta
(2022) <doi:10.1007/s00184-021-00824-3> for distribution, with
different bandwidth selectors. Also includes a real length-biased
dataset on shrub width from Muttlak (1988)
<https://www.proquest.com/openview/3dd74592e623cdbcfa6176e85bd3d390/1?cbl=18750&diss=y&pq-origsite=gscholar>.
Author: Sanchez Martinez Noelia [cre, aut] ,
Borrajo Garcia Maria Isabel [aut] ,
Conde Amboage Mercedes [aut]
Maintainer: Sanchez Martinez Noelia <noelia.sanchez.martinez@rai.usc.es>
Diff between WData versions 0.1.0 dated 2025-08-18 and 0.1.1 dated 2025-12-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 - build/partial.rdb |binary 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] ,
Terrence D. Jorgensen [aut] ,
Luc De Wilde [aut],
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsika [...truncated...]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-20 dated 2025-09-21 and 0.6-21 dated 2025-12-21
lavaan-0.6-20/lavaan/R/ctr_estfun.R |only lavaan-0.6-20/lavaan/R/ctr_informative_testing.R |only lavaan-0.6-20/lavaan/R/ctr_mplus2lavaan.R |only lavaan-0.6-20/lavaan/R/ctr_pml_plrt.R |only lavaan-0.6-20/lavaan/R/ctr_pml_plrt2.R |only lavaan-0.6-20/lavaan/R/ctr_pml_plrt_nested.R |only lavaan-0.6-20/lavaan/R/ctr_pml_utils.R |only lavaan-0.6-20/lavaan/R/lav_bootstrap_lrt.R |only lavaan-0.6-20/lavaan/R/lav_norm.R |only lavaan-0.6-20/lavaan/R/ldw_trace.R |only lavaan-0.6-20/lavaan/man/InformativeTesting.Rd |only lavaan-0.6-20/lavaan/man/estfun.Rd |only lavaan-0.6-20/lavaan/man/lavExport.Rd |only lavaan-0.6-20/lavaan/man/plot.InformativeTesting.Rd |only lavaan-0.6-21/lavaan/DESCRIPTION | 6 lavaan-0.6-21/lavaan/MD5 | 362 +++--- lavaan-0.6-21/lavaan/NAMESPACE | 105 - lavaan-0.6-21/lavaan/R/00generic.R | 8 lavaan-0.6-21/lavaan/R/ctr_modelcov.R | 4 lavaan-0.6-21/lavaan/R/ctr_pairwise_fit.R | 10 lavaan-0.6-21/lavaan/R/ctr_pml_doubly_robust_utils.R | 44 lavaan-0.6-21/lavaan/R/lav_bootstrap.R | 150 ++ lavaan-0.6-21/lavaan/R/lav_bvmix.R | 8 lavaan-0.6-21/lavaan/R/lav_bvord.R | 24 lavaan-0.6-21/lavaan/R/lav_bvreg.R | 10 lavaan-0.6-21/lavaan/R/lav_cfa_bentler1982.R | 3 lavaan-0.6-21/lavaan/R/lav_cfa_guttman1952.R | 20 lavaan-0.6-21/lavaan/R/lav_cor.R | 23 lavaan-0.6-21/lavaan/R/lav_data.R | 44 lavaan-0.6-21/lavaan/R/lav_data_patterns.R | 2 lavaan-0.6-21/lavaan/R/lav_data_print.R | 17 lavaan-0.6-21/lavaan/R/lav_efa_extraction.R | 36 lavaan-0.6-21/lavaan/R/lav_efa_print.R | 10 lavaan-0.6-21/lavaan/R/lav_efa_summary.R | 6 lavaan-0.6-21/lavaan/R/lav_export.R | 47 lavaan-0.6-21/lavaan/R/lav_export_bugs.R | 4 lavaan-0.6-21/lavaan/R/lav_export_estimation.R | 4 lavaan-0.6-21/lavaan/R/lav_export_mplus.R | 10 lavaan-0.6-21/lavaan/R/lav_fit_aic.R | 16 lavaan-0.6-21/lavaan/R/lav_fit_cfi.R | 5 lavaan-0.6-21/lavaan/R/lav_fit_measures.R | 64 - lavaan-0.6-21/lavaan/R/lav_fit_other.R | 2 lavaan-0.6-21/lavaan/R/lav_fit_rmsea.R | 2 lavaan-0.6-21/lavaan/R/lav_fit_srmr.R | 11 lavaan-0.6-21/lavaan/R/lav_fit_utils.R | 1 lavaan-0.6-21/lavaan/R/lav_graph.R |only lavaan-0.6-21/lavaan/R/lav_graphics.R | 2 lavaan-0.6-21/lavaan/R/lav_h1.R | 2 lavaan-0.6-21/lavaan/R/lav_label_code.R |only lavaan-0.6-21/lavaan/R/lav_lavaanList_inspect.R | 22 lavaan-0.6-21/lavaan/R/lav_lavaanList_methods.R | 47 lavaan-0.6-21/lavaan/R/lav_lavaanList_simulate.R | 4 lavaan-0.6-21/lavaan/R/lav_lavaan_step00_init.R | 2 lavaan-0.6-21/lavaan/R/lav_lavaan_step01_ovnames.R | 22 lavaan-0.6-21/lavaan/R/lav_lavaan_step02_options.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step03_data.R | 4 lavaan-0.6-21/lavaan/R/lav_lavaan_step04_partable.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step08_start.R | 24 lavaan-0.6-21/lavaan/R/lav_lavaan_step09_model.R | 27 lavaan-0.6-21/lavaan/R/lav_lavaan_step10_cache.R | 8 lavaan-0.6-21/lavaan/R/lav_lavaan_step11_optim.R | 3 lavaan-0.6-21/lavaan/R/lav_lavaan_step12_implied.R | 9 lavaan-0.6-21/lavaan/R/lav_lavaan_step13_vcov.R | 10 lavaan-0.6-21/lavaan/R/lav_lavaan_step16_rotation.R | 5 lavaan-0.6-21/lavaan/R/lav_lavaan_step17_lavaan.R | 2 lavaan-0.6-21/lavaan/R/lav_matrix.R | 108 - lavaan-0.6-21/lavaan/R/lav_model.R | 8 lavaan-0.6-21/lavaan/R/lav_model_compute.R | 174 +- lavaan-0.6-21/lavaan/R/lav_model_efa.R | 8 lavaan-0.6-21/lavaan/R/lav_model_estimate.R | 6 lavaan-0.6-21/lavaan/R/lav_model_gradient.R | 233 +-- lavaan-0.6-21/lavaan/R/lav_model_gradient_mml.R | 16 lavaan-0.6-21/lavaan/R/lav_model_gradient_pml.R | 100 - lavaan-0.6-21/lavaan/R/lav_model_h1_information.R | 69 - lavaan-0.6-21/lavaan/R/lav_model_h1_omega.R | 10 lavaan-0.6-21/lavaan/R/lav_model_hessian.R | 16 lavaan-0.6-21/lavaan/R/lav_model_implied.R | 8 lavaan-0.6-21/lavaan/R/lav_model_information.R | 28 lavaan-0.6-21/lavaan/R/lav_model_lik.R | 12 lavaan-0.6-21/lavaan/R/lav_model_loglik.R | 22 lavaan-0.6-21/lavaan/R/lav_model_objective.R | 75 - lavaan-0.6-21/lavaan/R/lav_model_plotinfo.R |only lavaan-0.6-21/lavaan/R/lav_model_utils.R | 35 lavaan-0.6-21/lavaan/R/lav_model_vcov.R | 20 lavaan-0.6-21/lavaan/R/lav_model_wls.R | 6 lavaan-0.6-21/lavaan/R/lav_modification.R | 3 lavaan-0.6-21/lavaan/R/lav_mplus_lavaan.R |only lavaan-0.6-21/lavaan/R/lav_msg.R | 20 lavaan-0.6-21/lavaan/R/lav_muthen1984.R | 4 lavaan-0.6-21/lavaan/R/lav_mvnorm_missing_h1.R | 9 lavaan-0.6-21/lavaan/R/lav_object_check_version.R |only lavaan-0.6-21/lavaan/R/lav_object_generate.R | 61 - 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Title: Visualization of BART and BARP using SHAP
Description: Complex machine learning models are often difficult to interpret. Shapley values serve as a powerful tool to understand and explain why a model makes a particular prediction. This package computes variable contributions using permutation-based Shapley values for Bayesian Additive Regression Trees (BART) and its extension with Post-Stratification (BARP). The permutation-based SHAP method proposed by Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> is grounded in data obtained via MCMC sampling. Similar to the BART model introduced by Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>, this package leverages Bayesian posterior samples generated during model estimation, allowing variable contributions to be computed without requiring additional sampling. The BART model is designed to work with the following R packages: 'BART' <doi:10.18637/jss.v097.i01>, 'bartMachine' <doi:10.18637/jss.v070.i04>, and 'dbarts' <https://CRAN.R-project.org/ [...truncated...]
Author: Dong-eun Lee [aut, cre],
Eun-Kyung Lee [aut]
Maintainer: Dong-eun Lee <ldongeun.leel@gmail.com>
Diff between bartXViz versions 1.0.8 dated 2025-07-28 and 1.0.9 dated 2025-12-21
DESCRIPTION | 11 - MD5 | 44 ++--- NAMESPACE | 233 +++++++++++++-------------- R/Explain_stats.R |only R/plot.explainbarp.R | 53 ++++-- R/plot_default.R | 73 +++++--- R/plot_explainBART.R | 60 ++++--- R/plot_explainbartMachine.R | 16 + R/plot_func.R | 15 - R/waterfall_plot.R | 2 man/Explain.barp.Rd | 104 ++++++------ man/Explain.bart.Rd | 148 ++++++++--------- man/Explain.bartMachine.Rd | 150 ++++++++--------- man/Explain.default.Rd | 350 ++++++++++++++++++++--------------------- man/Explain.wbart.Rd | 148 ++++++++--------- man/Explain_stats.Rd |only man/barps.Rd | 140 ++++++++-------- man/decision_plot.Rd | 130 +++++++-------- man/one_hot.Rd | 114 ++++++------- man/plot.Explain.Rd | 117 +++++++------ man/plot.ExplainBART.Rd | 201 ++++++++++++----------- man/plot.Explainbarp.Rd | 137 ++++++++-------- man/plot.ExplainbartMachine.Rd | 119 +++++++------ man/waterfall_plot.Rd | 126 +++++++------- 24 files changed, 1304 insertions(+), 1187 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.13.0 dated 2025-11-18 and 0.15.0 dated 2025-12-21
vapour-0.13.0/vapour/src/Makevars.win |only vapour-0.15.0/vapour/DESCRIPTION | 8 vapour-0.15.0/vapour/MD5 | 15 vapour-0.15.0/vapour/NEWS.md | 8 vapour-0.15.0/vapour/configure | 2691 +++++++------- vapour-0.15.0/vapour/inst/doc/vapour.html | 6 vapour-0.15.0/vapour/inst/include/gdalapplib/gdalapplib.h | 3 vapour-0.15.0/vapour/src/Makevars.in | 3 vapour-0.15.0/vapour/src/Makevars.ucrt | 1 9 files changed, 1383 insertions(+), 1352 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.15.1 dated 2025-11-02 and 0.15.2 dated 2025-12-21
DESCRIPTION | 6 MD5 | 148 +++++----- NEWS.md | 31 +- R/expand_style.R | 4 R/grid_colspan.R | 2 R/html_finalize.R | 72 +++- R/html_style.R | 37 ++ R/print.R | 2 R/rbind2.R | 8 R/sanity.R | 42 +- R/style_tt.R | 19 - R/tabularray_style.R | 71 ++-- R/tabulator_data.R | 6 R/tabulator_style.R | 2 R/theme_default.R | 3 R/theme_html.R | 12 R/theme_latex.R | 13 README.md | 56 +-- build/partial.rdb |binary inst/tinytable.css | 51 ++- inst/tinytable_dark.css |only inst/tinytest/_tinysnapshot/escape-issue150_caption.html | 4 inst/tinytest/_tinysnapshot/escape-issue150_caption_02.html | 10 inst/tinytest/_tinysnapshot/escape-issue150_caption_03.html | 10 inst/tinytest/_tinysnapshot/escape-latex.html | 4 inst/tinytest/_tinysnapshot/escape-latex_colnames.html | 4 inst/tinytest/_tinysnapshot/escape-simple.html | 4 inst/tinytest/_tinysnapshot/format_tt-conditional_output.html | 4 inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 4 inst/tinytest/_tinysnapshot/group-html_tutorial_01.html | 36 +- inst/tinytest/_tinysnapshot/group-issue165_extra_row.html | 14 inst/tinytest/_tinysnapshot/group-issue165_html_centering_style.html | 18 - inst/tinytest/_tinysnapshot/group-issue258_01_html.html | 18 - inst/tinytest/_tinysnapshot/group-issue258_02_html.html | 20 - inst/tinytest/_tinysnapshot/group-multilevel-basic.html | 10 inst/tinytest/_tinysnapshot/group-multilevel-empty.html | 14 inst/tinytest/_tinysnapshot/group-nse.html | 4 inst/tinytest/_tinysnapshot/group_matrix-multiple_positions_multiple_rows.html | 4 inst/tinytest/_tinysnapshot/group_matrix-row_duplication.html | 4 inst/tinytest/_tinysnapshot/group_matrix-single_column_with_styling.html | 4 inst/tinytest/_tinysnapshot/group_matrix-single_position_single_row.html | 4 inst/tinytest/_tinysnapshot/html-alignment.html | 12 inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 4 inst/tinytest/_tinysnapshot/html-caption.html | 4 inst/tinytest/_tinysnapshot/html-conditional_styling.html | 4 inst/tinytest/_tinysnapshot/html-font_size.html | 8 inst/tinytest/_tinysnapshot/html-footnote.html | 4 inst/tinytest/_tinysnapshot/html-formatting.html | 4 inst/tinytest/_tinysnapshot/html-images.html | 4 inst/tinytest/_tinysnapshot/html-individual_cells.html | 4 inst/tinytest/_tinysnapshot/html-issue297.html | 4 inst/tinytest/_tinysnapshot/html-issue355a.html | 72 ++-- inst/tinytest/_tinysnapshot/html-issue355b.html | 42 +- inst/tinytest/_tinysnapshot/html-issue575.html | 54 +-- inst/tinytest/_tinysnapshot/html-issue58.html | 12 inst/tinytest/_tinysnapshot/html-issue88.html | 4 inst/tinytest/_tinysnapshot/html-issue92.html | 8 inst/tinytest/_tinysnapshot/html-line_break.html | 4 inst/tinytest/_tinysnapshot/html-merge_cells.html | 4 inst/tinytest/_tinysnapshot/html-missing_value.html | 4 inst/tinytest/_tinysnapshot/html-omit_headers.html | 4 inst/tinytest/_tinysnapshot/html-spanning_cells.html | 4 inst/tinytest/_tinysnapshot/html-vectorized_color_j.html | 12 inst/tinytest/_tinysnapshot/latex-tabular_caption.tex |only inst/tinytest/_tinysnapshot/style-align_partial.html | 40 +- inst/tinytest/_tinysnapshot/style-issue507_markdown_styles.html | 44 +- inst/tinytest/_tinysnapshot/style-issue514_white_blue.html | 12 inst/tinytest/_tinysnapshot/style-smallcap.html | 20 - inst/tinytest/_tinysnapshot/theme-issue531_style_colors_override_stripes.html | 24 - inst/tinytest/test-latex.R | 7 inst/tinytest/test-misc.R | 1 inst/tinytest/test-tabulator.R | 7 man/rbind2-tinytable-tinytable-method.Rd | 8 man/style_tt.Rd | 6 man/theme_html.Rd | 8 man/tt.Rd | 18 - 76 files changed, 716 insertions(+), 534 deletions(-)
Title: Support Functions for Wrangling and Visualization
Description: Suite of helper functions for data wrangling and visualization.
The only theme for these functions is that they tend towards simple, short, and narrowly-scoped.
These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Author: Nicholas J Lyon [aut, cre, cph]
Maintainer: Nicholas J Lyon <njlyon@alumni.iastate.edu>
Diff between supportR versions 1.5.0 dated 2025-06-03 and 1.6.0 dated 2025-12-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 10 +++++++++- R/count_diff.R | 6 +++++- R/diff_check.R | 11 +++++++---- R/num_check.R | 10 +++++----- README.md | 6 +++--- inst/doc/supportr_01_wrangle.html | 5 +++-- inst/doc/supportr_02_quality-control.html | 5 +++-- inst/doc/supportr_03_visualizations.html | 7 ++++--- inst/doc/supportr_04_outside-of-r.html | 5 +++-- man/count_diff.Rd | 2 +- man/num_check.Rd | 8 ++++---- 13 files changed, 63 insertions(+), 44 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc_node_en.html> for more information).
Choose observational time series from meteorological stations with 'selectDWD()'.
Find raster data from radar and interpolation according to <https://brry.github.io/rdwd/raster-data.html>.
Download (multiple) data sets with progress bars and no re-downloads through 'dataDWD()'.
Read both tabular observational data and binary gridded datasets with 'readDWD()'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.9.3 dated 2025-08-18 and 1.9.8 dated 2025-12-21
DESCRIPTION | 14 MD5 | 112 +++---- NAMESPACE | 143 ++++----- NEWS.md | 5 R/addBorders.R | 2 R/checkUpdates.R | 2 R/createIndex.R | 2 R/dataDWD.R | 21 + R/dirDWD.R | 11 R/fileType.R | 4 R/index.R | 4 R/indexFTP.R | 2 R/locdir.R | 21 - R/metaInfo.R | 2 R/nearbyStations.R | 6 R/plotRadar.R | 4 R/projectRasterDWD.R | 2 R/rdwd-package.R | 4 R/readDWD.R | 10 R/readVars.R | 2 R/runLocalTests.R | 2 R/selectDWD.R | 8 R/updateIndexes.R | 4 R/zzz.R | 6 README.md | 16 - build/vignette.rds |binary data/datalist | 10 data/fileIndex.rda |binary data/formatIndex.rda |binary data/geoIndex.rda |binary data/gridIndex.rda |binary data/metaIndex.rda |binary inst/doc/rdwd.Rmd | 60 +-- inst/doc/rdwd.html | 562 ++++++++++++++++++------------------- inst/shinyapps/compare_years/app.R | 2 man/addBorders.Rd | 2 man/checkIndex.Rd | 112 +++---- man/checkUpdates.Rd | 2 man/createIndex.Rd | 2 man/dataDWD.Rd | 15 man/dirDWD.Rd | 4 man/dwdbase.Rd | 6 man/fileType.Rd | 4 man/index.Rd | 4 man/indexFTP.Rd | 2 man/locdir.Rd | 15 man/nearbyStations.Rd | 6 man/plotRadar.Rd | 4 man/projectRasterDWD.Rd | 2 man/rdwd.Rd | 4 man/readDWD.Rd | 2 man/readDWD.data.Rd | 2 man/readDWD.deriv.Rd | 2 man/readVars.Rd | 2 man/selectDWD.Rd | 8 man/updateIndexes.Rd | 4 vignettes/rdwd.Rmd | 60 +-- 57 files changed, 662 insertions(+), 645 deletions(-)
Title: Spatial and Spatio-Temporal Models using 'INLA'
Description: Prepare objects to implement models over spatial and
spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
These objects contain data to for the 'cgeneric' interface in
'INLA', enabling fast parallel computations.
We implemented the spatial barrier model, see Bakka et. al. (2019)
<doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal
models proposed in Lindgren et. al. (2024)
<https://raco.cat/index.php/SORT/article/view/428665>.
Details are provided in the available vignettes and from the URL bellow.
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAspacetime versions 0.1.12 dated 2025-03-14 and 0.1.13 dated 2025-12-21
INLAspacetime-0.1.12/INLAspacetime/R/upperPadding.R |only INLAspacetime-0.1.12/INLAspacetime/R/utils.R |only INLAspacetime-0.1.12/INLAspacetime/README.md |only INLAspacetime-0.1.12/INLAspacetime/inst/examples |only INLAspacetime-0.1.12/INLAspacetime/man/check_package_version_and_load.Rd |only INLAspacetime-0.1.12/INLAspacetime/man/upperPadding.Rd |only INLAspacetime-0.1.12/INLAspacetime/vignettes/web/result_barrier.R |only INLAspacetime-0.1.13/INLAspacetime/DESCRIPTION | 26 +- INLAspacetime-0.1.13/INLAspacetime/MD5 | 92 ++++---- INLAspacetime-0.1.13/INLAspacetime/NAMESPACE | 4 INLAspacetime-0.1.13/INLAspacetime/R/INLAspacetime.R | 2 INLAspacetime-0.1.13/INLAspacetime/R/ar2cov.R | 5 INLAspacetime-0.1.13/INLAspacetime/R/ar2precision.R | 51 ++-- INLAspacetime-0.1.13/INLAspacetime/R/barrierModel.define.R | 46 ++-- INLAspacetime-0.1.13/INLAspacetime/R/cgeneric_sspde.R | 99 ++++---- INLAspacetime-0.1.13/INLAspacetime/R/inlabru.R | 6 INLAspacetime-0.1.13/INLAspacetime/R/mesh2d.R | 7 INLAspacetime-0.1.13/INLAspacetime/R/mesh2fem.R | 2 INLAspacetime-0.1.13/INLAspacetime/R/mesh2projector.R | 6 INLAspacetime-0.1.13/INLAspacetime/R/paramsUtils.R | 36 ++- INLAspacetime-0.1.13/INLAspacetime/R/stModel.define.R | 65 ++++- INLAspacetime-0.1.13/INLAspacetime/R/stModel.matrices.R | 112 ++++------ INLAspacetime-0.1.13/INLAspacetime/build/partial.rdb |binary INLAspacetime-0.1.13/INLAspacetime/build/vignette.rds |binary INLAspacetime-0.1.13/INLAspacetime/demo |only INLAspacetime-0.1.13/INLAspacetime/inst/doc/transparent_barriers.Rmd | 16 - INLAspacetime-0.1.13/INLAspacetime/inst/doc/transparent_barriers.html | 15 - INLAspacetime-0.1.13/INLAspacetime/inst/doc/website_examples.html | 2 INLAspacetime-0.1.13/INLAspacetime/man/Jmatrices.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/ar2cov.Rd | 3 INLAspacetime-0.1.13/INLAspacetime/man/ar2precision.Rd | 21 - INLAspacetime-0.1.13/INLAspacetime/man/barrierModel.define.Rd | 20 - INLAspacetime-0.1.13/INLAspacetime/man/bru_get_mapper.stModel_cgeneric.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/cgeneric_sspde.Rd | 32 -- INLAspacetime-0.1.13/INLAspacetime/man/mesh2d.Rd | 5 INLAspacetime-0.1.13/INLAspacetime/man/mesh2projector.Rd | 4 INLAspacetime-0.1.13/INLAspacetime/man/paramsUtils.Rd | 11 INLAspacetime-0.1.13/INLAspacetime/man/pcrange.Rd |only INLAspacetime-0.1.13/INLAspacetime/man/stModel.define.Rd | 28 +- INLAspacetime-0.1.13/INLAspacetime/man/stModel.matrices.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/man/stModel.precision.Rd | 2 INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime.c | 27 +- INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime.h | 24 -- INLAspacetime-0.1.13/INLAspacetime/src/INLAspacetime_init.c |only INLAspacetime-0.1.13/INLAspacetime/src/cgeneric_ast.c |only INLAspacetime-0.1.13/INLAspacetime/src/cgeneric_vrst.c |only INLAspacetime-0.1.13/INLAspacetime/vignettes/transparent_barriers.Rmd | 16 - INLAspacetime-0.1.13/INLAspacetime/vignettes/web/INLAspacetime.bib | 13 - INLAspacetime-0.1.13/INLAspacetime/vignettes/web/barrierExample.Rmd | 23 +- INLAspacetime-0.1.13/INLAspacetime/vignettes/web/barrier_global.Rmd |only INLAspacetime-0.1.13/INLAspacetime/vignettes/web/piemonte.Rmd | 18 - 51 files changed, 463 insertions(+), 382 deletions(-)
Title: Network Reconstruction and Changepoint Detection
Description: Package EDISON (Estimation of Directed Interactions from
Sequences Of Non-homogeneous gene expression) runs an MCMC
simulation to reconstruct networks from time series data, using
a non-homogeneous, time-varying dynamic Bayesian network.
Networks segments and changepoints are inferred concurrently,
and information sharing priors provide a reduction of the
inference uncertainty.
Author: Frank Dondelinger [aut, cre],
Sophie Lebre [aut]
Maintainer: Frank Dondelinger <fdondelinger.work@gmail.com>
Diff between EDISON versions 1.1.1 dated 2016-03-30 and 1.1.2 dated 2025-12-21
DESCRIPTION | 24 MD5 | 251 +++++----- NAMESPACE | 130 ++--- NEWS | 30 - R/BinoHyperMove.R | 174 +++---- R/BinoHyperRatio.R | 166 +++--- R/CalculateChanges.R | 160 +++--- R/CalculateLikelihoodRatio.R | 110 ++-- R/CalculatePriorRatio.R | 126 ++--- R/CollectNetworkInfo.R | 184 +++---- R/EDISON-package.R | 86 +-- R/EDISON.run.R | 196 ++++---- R/ExpHyperMove.R | 352 +++++++------- R/ExpHyperRatioTarget.R | 130 ++--- R/HyperParms.R | 158 +++--- R/HyperparameterMove.R | 150 +++--- R/NetworkProbBino.R | 148 +++--- R/NetworkProbExp.R | 100 ++-- R/NetworkRatioBino.R | 102 ++-- R/NetworkRatioExp.R | 92 +-- R/PriorRatioPoisson.R | 142 ++--- R/ProposeDiscrete.R | 104 ++-- R/addProposalNetworkInfo.R | 62 +- R/bp.computeAlpha.R | 126 ++--- R/buildXY.R | 80 +-- R/calculateCPPGlobal.R | 48 - R/calculateCPProbabilities.R | 104 ++-- R/calculateEdgeProbabilities.R | 102 ++-- R/calculateEdgeProbabilitiesSegs.R | 80 +-- R/calculateEdgeProbabilitiesTimePoints.R | 136 ++--- R/computePx.R | 74 +-- R/computeRho4.R | 82 +-- R/convert_nets.R | 120 ++-- R/cp.birth.R | 558 +++++++++++------------ R/cp.death.R | 404 ++++++++-------- R/cp.shift.R | 426 ++++++++--------- R/defaultOptions.R | 196 ++++---- R/dinvgamma.R | 68 +- R/fix_eigenvalues.R | 94 +-- R/generateNetwork.R | 402 ++++++++-------- R/imports.R |only R/init.R | 224 ++++----- R/main.R | 402 ++++++++-------- R/make_structure_move.R | 402 ++++++++-------- R/output.R | 172 +++---- R/phase.update.R | 272 +++++------ R/proposalTuning.R | 56 +- R/proposeContinuous.R | 74 +-- R/psrf.R | 176 +++---- R/psrf_check.R | 94 +-- R/psrf_check_hyper.R | 80 +-- R/readDataTS.R | 80 +-- R/rinvgamma.R | 52 +- R/runDBN.R | 382 +++++++-------- R/sampleBinit.R | 68 +- R/sampleBxy.R | 54 +- R/sampleDelta2.R | 86 +-- R/sampleK.R | 58 +- R/sampleParms.R | 374 +++++++-------- R/sampleSig2.R | 50 +- R/simulateNetwork.R | 298 ++++++------ R/updateNetworkInfo.R | 38 - R/updateSigMulti.R | 92 +-- R/updateSigSolo.R | 112 ++-- inst/CITATION | 24 man/AcceptableMove.Rd | 77 +-- man/BinoHyperMove.Rd | 93 +-- man/BinoHyperRatio.Rd | 93 +-- man/CalculateChanges.Rd | 63 +- man/CalculateLikelihoodRatio.Rd | 93 +-- man/CalculatePriorRatio.Rd | 97 +--- man/CollectNetworkInfo.Rd | 104 ++-- man/EDISON-package.Rd | 103 ++-- man/EDISON.run.Rd | 175 +++---- man/ExpHyperMove.Rd | 101 ++-- man/ExpHyperRatioTarget.Rd | 89 +-- man/HyperParms.Rd | 65 +- man/HyperparameterMove.Rd | 99 ++-- man/NetworkProbBino.Rd | 83 +-- man/NetworkProbExp.Rd | 73 +-- man/NetworkRatioBino.Rd | 73 +-- man/NetworkRatioExp.Rd | 75 +-- man/PriorRatioPoisson.Rd | 73 +-- man/ProposeDiscrete.Rd | 81 +-- man/addProposalNetworkInfo.Rd | 55 +- man/bp.computeAlpha.Rd | 156 +++--- man/buildXY.Rd | 53 +- man/calculateCPPGlobal.Rd | 53 +- man/calculateCPProbabilities.Rd | 75 +-- man/calculateEdgeProbabilities.Rd | 103 ++-- man/calculateEdgeProbabilitiesSegs.Rd | 73 +-- man/calculateEdgeProbabilitiesTimePoints.Rd | 69 +- man/computePx.Rd | 73 +-- man/computeRho4.Rd | 79 +-- man/convert_nets.Rd | 59 +- man/cp.birth.Rd | 123 ++--- man/cp.death.Rd | 127 ++--- man/cp.shift.Rd | 119 ++-- man/defaultOptions.Rd | 107 ++-- man/dinvgamma.Rd | 73 +-- man/fix_eigenvalues.Rd | 65 +- man/generateNetwork.Rd | 168 +++--- man/init.Rd | 81 +-- man/main.Rd | 91 +-- man/make_structure_move.Rd | 140 +++-- man/output.Rd | 77 +-- man/phase.update.Rd | 125 ++--- man/proposalTuning.Rd | 49 -- man/proposeContinuous.Rd | 77 +-- man/psrf.Rd | 123 ++--- man/psrf_check.Rd | 69 +- man/psrf_check_hyper.Rd | 61 +- man/readDataTS.Rd | 67 +- man/rinvgamma.Rd | 75 +-- man/runDBN.Rd | 176 +++---- man/sampleBinit.Rd | 71 +- man/sampleBxy.Rd | 69 +- man/sampleDelta2.Rd | 83 +-- man/sampleK.Rd | 69 +- man/sampleParms.Rd | 95 +-- man/sampleSig2.Rd | 69 +- man/simulateNetwork.Rd | 216 ++++---- man/updateSigMulti.Rd | 121 ++--- man/updateSigSolo.Rd | 103 ++-- tests/test-all.R | 2 tests/testthat/test-fixed-edges.r | 100 ++-- tests/testthat/test-structure-moves.r | 674 ++++++++++++++-------------- 127 files changed, 8132 insertions(+), 8088 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 1.4.3 dated 2025-07-22 and 1.4.4 dated 2025-12-20
CausalQueries-1.4.3/CausalQueries/man/CausalQueries.Rd |only CausalQueries-1.4.4/CausalQueries/DESCRIPTION | 24 CausalQueries-1.4.4/CausalQueries/LICENSE | 4 CausalQueries-1.4.4/CausalQueries/MD5 | 86 CausalQueries-1.4.4/CausalQueries/NAMESPACE | 1 CausalQueries-1.4.4/CausalQueries/NEWS.md | 42 CausalQueries-1.4.4/CausalQueries/R/CausalQueries-package.R | 6 CausalQueries-1.4.4/CausalQueries/R/build_vignettes.R | 3 CausalQueries-1.4.4/CausalQueries/R/data.R | 2 CausalQueries-1.4.4/CausalQueries/R/map_query_to_causal_type.R | 16 CausalQueries-1.4.4/CausalQueries/R/methods.R | 4 CausalQueries-1.4.4/CausalQueries/R/plot_dag.R | 36 CausalQueries-1.4.4/CausalQueries/R/prep_stan_data.R | 54 CausalQueries-1.4.4/CausalQueries/R/query_model.R | 6 CausalQueries-1.4.4/CausalQueries/R/update_model.R | 4 CausalQueries-1.4.4/CausalQueries/R/zzz.R | 35 CausalQueries-1.4.4/CausalQueries/README.md | 4 CausalQueries-1.4.4/CausalQueries/build/vignette.rds |binary CausalQueries-1.4.4/CausalQueries/inst/doc/a-getting-started.Rmd | 61 CausalQueries-1.4.4/CausalQueries/inst/doc/a-getting-started.html | 176 - CausalQueries-1.4.4/CausalQueries/inst/doc/b-plotting.html | 21 CausalQueries-1.4.4/CausalQueries/inst/doc/c-canonical-models.html | 39 CausalQueries-1.4.4/CausalQueries/inst/doc/d-front-door.html | 5 CausalQueries-1.4.4/CausalQueries/inst/doc/e-posteriors.Rmd | 10 CausalQueries-1.4.4/CausalQueries/inst/doc/e-posteriors.html | 19 CausalQueries-1.4.4/CausalQueries/inst/doc/f-complier-profiling.Rmd |only CausalQueries-1.4.4/CausalQueries/inst/doc/f-complier-profiling.html |only CausalQueries-1.4.4/CausalQueries/inst/stan/simplexes.stan | 136 - CausalQueries-1.4.4/CausalQueries/man/CausalQueries-package.Rd |only CausalQueries-1.4.4/CausalQueries/man/institutions_data.Rd | 2 CausalQueries-1.4.4/CausalQueries/man/plot_model.Rd | 30 CausalQueries-1.4.4/CausalQueries/src/stanExports_simplexes.h | 896 ++++------ CausalQueries-1.4.4/CausalQueries/tests/testthat/test_prep_stan_data_validation.R |only CausalQueries-1.4.4/CausalQueries/tests/testthat/test_query_error_messages.R |only CausalQueries-1.4.4/CausalQueries/vignettes/a-getting-started.Rmd | 61 CausalQueries-1.4.4/CausalQueries/vignettes/a1batchplot-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cchainq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cconfoundedq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/civq1-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/civq2-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cmbiasq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cmed2q-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cmedq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/cnapq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/csimpleq-1.png |binary CausalQueries-1.4.4/CausalQueries/vignettes/e-posteriors.Rmd | 10 CausalQueries-1.4.4/CausalQueries/vignettes/f-complier-profiling.Rmd |only CausalQueries-1.4.4/CausalQueries/vignettes/f-complier-profiling.Rmd.orig |only 48 files changed, 963 insertions(+), 830 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Shejuty Devnath [aut],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.11 dated 2025-08-20 and 0.1.12 dated 2025-12-20
DESCRIPTION | 12 - MD5 | 42 +++-- NEWS.md | 4 R/LONBGLSS.R | 14 - R/LONBGLSS_1.R |only R/LONRBGLSS.R | 14 - R/LONRBGLSS_1.R |only R/RcppExports.R | 64 ++++++-- R/mixedBayes.R | 8 - build/partial.rdb |binary src/BGL.cpp | 90 ++++++----- src/BGL2.cpp |only src/BGLSS.cpp | 99 ++++++------ src/BGLSS2.cpp |only src/BL.cpp | 86 ++++++---- src/BL2.cpp |only src/BLSS.cpp | 92 ++++++----- src/BLSS2.cpp |only src/RBGL.cpp | 90 ++++++----- src/RBGL2.cpp |only src/RBGLSS.cpp | 103 +++++++----- src/RBGLSS2.cpp |only src/RBL.cpp | 91 ++++++----- src/RBL2.cpp |only src/RBLSS.cpp | 92 ++++++----- src/RBLSS2.cpp |only src/RcppExports.cpp | 414 +++++++++++++++++++++++++++++++++++++++++++++++----- 27 files changed, 907 insertions(+), 408 deletions(-)
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.3.0 dated 2025-09-13 and 1.4.0 dated 2025-12-20
DESCRIPTION | 8 MD5 | 70 ++-- NAMESPACE | 3 NEWS.md | 9 R/data.R | 13 R/family.R | 4 R/fit.R | 60 ++- R/internal.R | 6 R/methods.R | 12 R/predict.R | 2 R/project.R | 3 R/utility.R | 78 ++++ data/atlantic_yellowtail.rda |only inst/doc/dsem.Rmd | 5 inst/doc/dsem.html | 131 +++++--- inst/doc/mgcv.html | 21 - inst/doc/model-description.html | 112 +++--- inst/doc/multiple_data.Rmd | 5 inst/doc/multiple_data.html | 55 ++- inst/doc/spatial.html | 17 - inst/doc/spatial_factor_analysis.Rmd | 5 inst/doc/spatial_factor_analysis.html | 52 ++- man/alaska_sponge_coral_fish.Rd | 40 +- man/atlantic_yellowtail.Rd |only man/bering_sea_capelin_forecasts.Rd | 36 +- man/deviance_explained.Rd | 6 man/red_grouper_diet.Rd | 36 +- man/reexports.Rd | 3 man/sample_variable.Rd | 6 man/tinyVAST.Rd | 2 src/tinyVAST.cpp | 43 ++ tests/testthat/test-deviance-residuals.R | 77 ++++ tests/testthat/test-smooths.R | 24 + vignettes/dsem.Rmd | 5 vignettes/multiple_data.Rmd | 5 vignettes/spatial_factor_analysis.Rmd | 5 vignettes/tinyVAST_vignettes.bib | 502 +++++++++++++++++++++---------- 37 files changed, 1017 insertions(+), 444 deletions(-)
Title: Multistage MCMC Method for Detecting DMRs
Description: Implements differential methylation region (DMR) detection using a
multistage Markov chain Monte Carlo (MCMC) algorithm based on the
alpha-skew generalized normal (ASGN) distribution. Version 0.2.0 removes
the Anderson-Darling test stage, improves computational efficiency of the
core ASGN and multistage MCMC routines, and adds convenience functions for
summarizing and visualizing detected DMRs. The methodology is based on
Yang (2025) <https://www.proquest.com/docview/3218878972>.
Author: Zhexuan Yang [aut, cre],
Duchwan Ryu [aut],
Feng Luan [aut]
Maintainer: Zhexuan Yang <zky5198@psu.edu>
Diff between mmcmcBayes versions 0.1.0 dated 2025-11-24 and 0.2.0 dated 2025-12-20
mmcmcBayes-0.1.0/mmcmcBayes/R/traceplot_asgn.R |only mmcmcBayes-0.1.0/mmcmcBayes/man/traceplot_asgn.Rd |only mmcmcBayes-0.2.0/mmcmcBayes/DESCRIPTION | 21 mmcmcBayes-0.2.0/mmcmcBayes/MD5 | 28 - mmcmcBayes-0.2.0/mmcmcBayes/NAMESPACE | 9 mmcmcBayes-0.2.0/mmcmcBayes/NEWS.md |only mmcmcBayes-0.2.0/mmcmcBayes/R/asgn_func.R | 297 +++++------ mmcmcBayes-0.2.0/mmcmcBayes/R/compare_dmrs.R | 99 ++- mmcmcBayes-0.2.0/mmcmcBayes/R/data.R | 3 mmcmcBayes-0.2.0/mmcmcBayes/R/mmcmcBayes.R | 533 +++++++-------------- mmcmcBayes-0.2.0/mmcmcBayes/R/plot_dmr_region.R |only mmcmcBayes-0.2.0/mmcmcBayes/R/summarize_dmrs.R |only mmcmcBayes-0.2.0/mmcmcBayes/inst |only mmcmcBayes-0.2.0/mmcmcBayes/man/asgn_func.Rd | 61 +- mmcmcBayes-0.2.0/mmcmcBayes/man/compare_dmrs.Rd | 58 +- mmcmcBayes-0.2.0/mmcmcBayes/man/mmcmcBayes.Rd | 152 +++-- mmcmcBayes-0.2.0/mmcmcBayes/man/normal_demo.Rd | 3 mmcmcBayes-0.2.0/mmcmcBayes/man/plot_dmr_region.Rd |only mmcmcBayes-0.2.0/mmcmcBayes/man/summarize_dmrs.Rd |only 19 files changed, 591 insertions(+), 673 deletions(-)
Title: Clustering of Sites with Species Data
Description: Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Author: Sebastian Schmidtlein [aut, cre] ,
Jason Collison [aut],
Robin Pfannendoerfer [aut],
Lubomir Tichy [ctb]
Maintainer: Sebastian Schmidtlein <schmidtlein@kit.edu>
Diff between isopam versions 3.2 dated 2025-01-16 and 3.3 dated 2025-12-20
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 2 R/clusters.R | 17 R/isopam.R | 986 +++++++++++++++++++++++++++----------------------------- man/clusters.Rd | 10 man/isopam.Rd | 86 +++- 7 files changed, 579 insertions(+), 544 deletions(-)
Title: Install 'Futureverse' in One Go
Description: The 'Futureverse' is a set of packages for parallel and distributed process 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 0.1.0 dated 2024-06-07 and 0.1.1 dated 2025-12-20
DESCRIPTION | 14 ++++---- MD5 | 14 ++++---- NEWS.md | 7 ++++ R/futureverse.R | 2 - README.md | 75 ++++++++++++++++++++++++++++++++++++--------- build/partial.rdb |binary inst |only man/figures |only man/futureverse-package.Rd | 4 +- 9 files changed, 87 insertions(+), 29 deletions(-)
Title: Durability of Vaccine Efficacy
Description: Implements maximum likelihood methods for
evaluating the durability of vaccine efficacy in a randomized,
placebo-controlled clinical trial with staggered enrollment of participants
and potential crossover of placebo recipients before the end of the trial.
Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab226>
and
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
Author: Danyu Lin [aut],
Yu Gu [aut],
Donglin Zeng [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DOVE versions 1.10 dated 2023-12-13 and 1.11 dated 2025-12-20
DESCRIPTION | 8 - MD5 | 12 +- NEWS | 165 ++++++++++++++++--------------- R/print.DOVE.R | 138 +++++++++++++------------- build/vignette.rds |binary inst/doc/dove-vignette.R | 236 ++++++++++++++++++++++----------------------- inst/doc/dove-vignette.pdf |binary 7 files changed, 284 insertions(+), 275 deletions(-)
Title: Tidy Population Genetics
Description: We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.
Author: Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica [aut, cre, cph] ,
Chang Christopher [ctb] ),
Shaun Purcell [ctb] ),
Bengtsson Henrik [ctb] )
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidypopgen versions 0.4.0 dated 2025-10-24 and 0.4.1 dated 2025-12-20
DESCRIPTION | 8 MD5 | 73 +-- NEWS.md | 4 R/filter_high_relatedness.R | 9 R/gen_tibble_packedancestry.R | 1 R/gt_as_plink.R | 2 R/gt_dapc_tidiers.R | 2 R/gt_load.R | 10 R/gt_order_loci.R | 5 R/gt_pca_tidiers.R | 2 R/gt_update_backingfile.R | 35 + R/is_loci_table_ordered.R | 18 R/local_reimplementations.R | 9 R/qc_report_indiv.R | 93 ++++ R/qc_report_loci.R | 122 ++++-- R/windows_pop_tajimas_d.R | 2 README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 3 inst/doc/a01_overview.R | 84 +++- inst/doc/a01_overview.Rmd | 170 ++++++-- inst/doc/a01_overview.html | 587 ++++++++++++++++++----------- inst/doc/a02_qc.html | 57 +- inst/doc/tidypopgen.html | 102 ++--- man/autoplot.qc_report_indiv.Rd | 6 man/gt_order_loci.Rd | 5 man/gt_update_backingfile.Rd | 21 - man/qc_report_indiv.Rd | 5 man/qc_report_loci.Rd | 9 man/tidypopgen-package.Rd | 2 tests/testthat/test_gen_tibble_save_load.R | 13 tests/testthat/test_gt_order_loci.R | 102 ----- tests/testthat/test_qc_report_indiv.R | 111 +++++ tests/testthat/test_qc_report_loci.R | 53 ++ vignettes/a01_overview.Rmd | 170 ++++++-- vignettes/img/gt_save.jpg |only vignettes/img/update_backingfile.jpg |only 39 files changed, 1298 insertions(+), 602 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal . Details refer to (Peter Wittek, et al (2017)) <doi:10.18637/jss.v078.i09>.
Author: Peter Wittek [aut],
Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.7.6 dated 2022-09-26 and 1.7.7 dated 2025-12-20
DESCRIPTION | 11 ++++------ LICENSE |only MD5 | 23 +++++++++++---------- data/rgbs.txt.gz |binary src/Makevars | 1 src/Makevars.win | 1 src/Rsomoclu.cpp | 2 - src/denseCpuKernels.cpp | 38 ++++++++++++++++++++--------------- src/io.h | 2 - src/mapDistanceFunctions.cpp | 38 ++++++++++++++++++++--------------- src/somoclu.h | 40 +++++++++++++++++++++---------------- src/sparseCpuKernels.cpp | 38 ++++++++++++++++++++--------------- src/training.cpp | 46 ++++++++++++++++++++++++++----------------- 13 files changed, 136 insertions(+), 104 deletions(-)
Title: Preprocessing Pupil Size Data
Description: Pupillometric data collected using SR Research Eyelink eye trackers
requires significant preprocessing. This package contains functions for
preparing pupil dilation data for visualization and statistical analysis.
Specifically, it provides a pipeline of functions which aid in data validation,
the removal of blinks/artifacts, downsampling, and baselining, among others.
Additionally, plotting functions for creating grand average and conditional
average plots are provided. See the vignette for samples of the functionality.
The package is designed for handling data collected with SR Research
Eyelink eye trackers using Sample Reports created in SR Research Data
Viewer.
Author: Aki-Juhani Kyroelaeinen [aut, cre],
Vincent Porretta [aut],
Jacolien van Rij [ctb],
Juhani Jaervikivi [ctb]
Maintainer: Aki-Juhani Kyroelaeinen <akkyro@gmail.com>
This is a re-admission after prior archival of version 0.6.2 dated 2020-03-10
Diff between PupilPre versions 0.6.2 dated 2020-03-10 and 0.6.3 dated 2025-12-20
DESCRIPTION | 10 MD5 | 96 +- R/PupilPre.R | 6 R/interactive.R | 5 R/plotting.R | 11 R/process.R | 34 R/utilities.R | 10 build/vignette.rds |binary inst/NEWS | 30 inst/doc/PupilPre_Basic_Preprocessing.R | 98 +- inst/doc/PupilPre_Basic_Preprocessing.Rmd | 8 inst/doc/PupilPre_Basic_Preprocessing.html | 755 +++++++++++++++------ inst/doc/PupilPre_Cleanup.R | 48 - inst/doc/PupilPre_Cleanup.html | 453 +++++++++--- inst/doc/PupilPre_Interpolation_and_Filtering.R | 20 inst/doc/PupilPre_Interpolation_and_Filtering.Rmd | 2 inst/doc/PupilPre_Interpolation_and_Filtering.html | 238 ++++-- inst/doc/PupilPre_Message_Alignment.R | 24 inst/doc/PupilPre_Message_Alignment.html | 299 +++++--- inst/doc/PupilPre_Plotting.R | 44 - inst/doc/PupilPre_Plotting.Rmd | 4 inst/doc/PupilPre_Plotting.html | 457 ++++++++---- man/NA_summary.Rd | 5 man/PupilPre.Rd | 7 man/apply_butter.Rd | 6 man/baseline.Rd | 8 man/blink_summary.Rd | 2 man/butter_filter_app.Rd | 3 man/check_baseline.Rd | 5 man/clean_artifact.Rd | 17 man/clean_blink.Rd | 10 man/compare_summary.Rd | 2 man/downsample.Rd | 4 man/interpolate_NAs.Rd | 3 man/plot_compare_app.Rd | 3 man/plot_events.Rd | 11 man/plot_summary_app.Rd | 3 man/ppl_check_eye_recording.Rd | 2 man/ppl_plot_avg.Rd | 28 man/ppl_plot_avg_cdiff.Rd | 21 man/ppl_plot_avg_contour.Rd | 20 man/ppl_prep_data.Rd | 8 man/ppl_select_recorded_eye.Rd | 2 man/rm_sparse_events.Rd | 10 man/user_cleanup_app.Rd | 3 man/verify_cleanup_app.Rd | 3 vignettes/PupilPre_Basic_Preprocessing.Rmd | 8 vignettes/PupilPre_Interpolation_and_Filtering.Rmd | 2 vignettes/PupilPre_Plotting.Rmd | 4 49 files changed, 1959 insertions(+), 893 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Analyze spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
This is a re-admission after prior archival of version 1.1.1 dated 2025-05-02
Diff between phylospatial versions 1.1.1 dated 2025-05-02 and 1.2.0 dated 2025-12-20
phylospatial-1.1.1/phylospatial/R/quantize.R |only phylospatial-1.1.1/phylospatial/tests/testthat/test-quantize.R |only phylospatial-1.2.0/phylospatial/DESCRIPTION | 10 - phylospatial-1.2.0/phylospatial/MD5 | 67 +++--- phylospatial-1.2.0/phylospatial/NAMESPACE | 2 phylospatial-1.2.0/phylospatial/NEWS.md | 12 + phylospatial-1.2.0/phylospatial/R/phylospatial-package.R | 1 phylospatial-1.2.0/phylospatial/R/phylospatial.R | 2 phylospatial-1.2.0/phylospatial/R/ps_canape.R | 2 phylospatial-1.2.0/phylospatial/R/ps_diversity.R | 11 - phylospatial-1.2.0/phylospatial/R/ps_quantize.R |only phylospatial-1.2.0/phylospatial/R/ps_rand.R | 78 +++++--- phylospatial-1.2.0/phylospatial/R/utils.R | 96 ++++++++-- phylospatial-1.2.0/phylospatial/README.md | 8 phylospatial-1.2.0/phylospatial/inst/doc/alpha-diversity.R | 16 + phylospatial-1.2.0/phylospatial/inst/doc/alpha-diversity.Rmd | 22 +- phylospatial-1.2.0/phylospatial/inst/doc/alpha-diversity.html | 40 ++-- phylospatial-1.2.0/phylospatial/inst/doc/beta-diversity.R | 5 phylospatial-1.2.0/phylospatial/inst/doc/beta-diversity.Rmd | 5 phylospatial-1.2.0/phylospatial/inst/doc/prioritization.R | 5 phylospatial-1.2.0/phylospatial/inst/doc/prioritization.Rmd | 5 phylospatial-1.2.0/phylospatial/inst/extdata/alpha-diversity-rand.tif |binary phylospatial-1.2.0/phylospatial/man/clade_dist.Rd | 6 phylospatial-1.2.0/phylospatial/man/ps_canaper.Rd | 2 phylospatial-1.2.0/phylospatial/man/ps_quantize.Rd |only phylospatial-1.2.0/phylospatial/man/ps_rand.Rd | 39 ++-- phylospatial-1.2.0/phylospatial/man/quantize.Rd | 58 ++---- phylospatial-1.2.0/phylospatial/tests/testthat/Rplots.pdf |binary phylospatial-1.2.0/phylospatial/tests/testthat/test-phylospatial.R | 5 phylospatial-1.2.0/phylospatial/tests/testthat/test-ps_canape.R | 11 - phylospatial-1.2.0/phylospatial/tests/testthat/test-ps_dissim.R | 4 phylospatial-1.2.0/phylospatial/tests/testthat/test-ps_diversity.R | 15 + phylospatial-1.2.0/phylospatial/tests/testthat/test-ps_quantize.R |only phylospatial-1.2.0/phylospatial/tests/testthat/test-ps_rand.R | 28 ++ phylospatial-1.2.0/phylospatial/vignettes/alpha-diversity.Rmd | 22 +- phylospatial-1.2.0/phylospatial/vignettes/beta-diversity.Rmd | 5 phylospatial-1.2.0/phylospatial/vignettes/prioritization.Rmd | 5 37 files changed, 398 insertions(+), 189 deletions(-)
Title: Nonparametric ANCOVA Methods
Description: Nonparametric methods for analysis of covariance (ANCOVA) are
distribution-free and provide a flexible statistical framework for
situations where the assumptions of parametric ANCOVA are violated
or when the response variable is ordinal. This package implements
several well-known nonparametric ANCOVA procedures, including Quade,
Puri and Sen, McSweeney and Porter, Burnett and Barr, Hettmansperger
and McKean, Shirley, and Puri-Sen-Harwell-Serlin. The package provides
user-friendly functions to apply these methods in practice.
These methods are described in Olejnik et al. (1985)
<doi:10.1177/0193841X8500900104> and Harwell et al. (1988)
<doi:10.1037/0033-2909.104.2.268>.
Author: Mina Jahangiri [aut, cre] ,
Ali Taghavi Rad [aut] ,
Anoshirvan Kazemnejad [aut] ,
Keith Goldfeld [ctb] ,
Shayan Mostafaei [ctb]
Maintainer: Mina Jahangiri <minajahangiri984@gmail.com>
Diff between npANCOVA versions 0.1.0 dated 2025-11-09 and 0.1.1 dated 2025-12-20
npANCOVA-0.1.0/npANCOVA/R/Burnet_Barr.r |only npANCOVA-0.1.1/npANCOVA/DESCRIPTION | 27 +++++++++++++++------------ npANCOVA-0.1.1/npANCOVA/MD5 | 11 ++++++----- npANCOVA-0.1.1/npANCOVA/NEWS.md |only npANCOVA-0.1.1/npANCOVA/R/Burnett_Barr.r |only npANCOVA-0.1.1/npANCOVA/inst/WORDLIST | 5 ++++- npANCOVA-0.1.1/npANCOVA/man/Burnett_Barr.Rd | 2 +- npANCOVA-0.1.1/npANCOVA/man/npANCOVA.Rd | 8 ++++---- 8 files changed, 30 insertions(+), 23 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] ,
Abhraneel Sarma [ctb],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Amar Al-Zubaidi [ctb],
Andre Simon [ctb] ,
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] ,
Ben Baumer [ctb], [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.50 dated 2025-03-16 and 1.51 dated 2025-12-20
DESCRIPTION | 43 +++++---- MD5 | 54 ++++++------ R/block.R | 7 + R/hooks-extra.R | 7 - R/hooks-html.R | 7 - R/hooks.R | 5 + R/otel.R |only R/output.R | 38 +++++--- R/parser.R | 2 R/plot.R | 10 +- R/utils-vignettes.R | 2 R/utils.R | 25 +++++ R/zzz.R | 11 ++ build/vignette.rds |binary inst/doc/datatables.html | 14 +-- inst/doc/docco-classic.html | 26 +++-- inst/doc/docco-linear.html | 20 ++-- inst/doc/knit_expand.html | 16 +-- inst/doc/knit_print.html | 178 +++++++---------------------------------- inst/doc/knitr-intro.html | 28 +++--- inst/doc/knitr-markdown.html | 22 ++--- inst/doc/knitr-refcard.html | 12 +- inst/examples/knitr-manual.Rnw | 2 inst/examples/knitr-manual.lyx | 4 inst/examples/knitr-themes.Rnw | 3 inst/examples/knitr-themes.lyx | 7 - man/download_image.Rd | 4 tests/testit/test-hooks-md.R | 7 + tests/testit/test-otel.R |only 29 files changed, 251 insertions(+), 303 deletions(-)
Title: Create Common Tables and Listings Used in Clinical Trials
Description: Structure and formatting requirements for clinical trial table and listing outputs
vary between pharmaceutical companies. 'junco' provides additional tooling for use alongside
the 'rtables', 'rlistings' and 'tern' packages when creating table and listing outputs. While
motivated by the specifics of Johnson and Johnson Clinical and Statistical Programming's
table and listing shells, 'junco' provides functionality that is general and reusable.
Major features include a) alternative and extended statistical analyses beyond what 'tern'
supports for use in standard safety and efficacy tables, b) a robust production-grade
Rich Text Format (RTF) exporter for both tables and listings, c) structural support
for spanning column headers and risk difference columns in tables, and d) robust
font-aware automatic column width algorithms for both listings and tables.
Author: Gabriel Becker [cre, aut] ,
Ilse Augustyns [aut],
Paul Jenkins [aut],
Daniel Hofstaedter [aut],
Joseph Kovach [aut],
David Munoz Tord [aut],
Daniel Sabanes Bove [aut],
Ezequiel Anokian [ctb],
Renfei Mao [ctb],
Mrinal Das [ctb],
Wojciech Wojciak [ctb] [...truncated...]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2025-07-11
Diff between junco versions 0.1.1 dated 2025-07-11 and 0.1.2 dated 2025-12-20
junco-0.1.1/junco/R/unicodify.R |only junco-0.1.1/junco/man/count_denom_fraction.Rd |only junco-0.1.1/junco/man/d_test_proportion_diff_j.Rd |only junco-0.1.1/junco/man/format_xx_fct.Rd |only junco-0.1.1/junco/man/fraction_count_denom.Rd |only junco-0.1.1/junco/man/h_a_freq_dataprep.Rd |only junco-0.1.1/junco/man/h_a_freq_prepinrows.Rd |only junco-0.1.1/junco/man/h_colexpr_substr.Rd |only junco-0.1.1/junco/man/h_create_altdf.Rd |only junco-0.1.1/junco/man/h_denom_parentdf.Rd |only junco-0.1.1/junco/man/h_df_add_newlevels.Rd |only junco-0.1.1/junco/man/h_get_label_map.Rd |only junco-0.1.1/junco/man/h_prop_diff_test.Rd |only junco-0.1.1/junco/man/h_subset_combo.Rd |only junco-0.1.1/junco/man/h_upd_dfrow.Rd |only junco-0.1.1/junco/man/h_update_factor.Rd |only junco-0.1.1/junco/man/jj_uc_map.Rd |only junco-0.1.1/junco/man/jjcsformat_pval_fct.Rd |only junco-0.1.1/junco/man/jjcsformat_range_fct.Rd |only junco-0.1.1/junco/man/non_blank_sentinel.Rd |only junco-0.1.1/junco/man/null_fn.Rd |only junco-0.1.1/junco/tests/testthat/test-unicodify.R |only junco-0.1.1/junco/tests/testthat/test_markup_unicodify.R |only junco-0.1.2/junco/DESCRIPTION | 33 junco-0.1.2/junco/MD5 | 446 ++++---- junco-0.1.2/junco/NAMESPACE | 27 junco-0.1.2/junco/NEWS.md | 38 junco-0.1.2/junco/R/a_eair_j.R | 72 - junco-0.1.2/junco/R/a_freq_combos_j.R | 74 + junco-0.1.2/junco/R/a_freq_j.R | 254 ++--- junco-0.1.2/junco/R/a_freq_resp_var_j.R | 25 junco-0.1.2/junco/R/a_freq_subcol_j.R | 52 - junco-0.1.2/junco/R/a_maxlev.R |only junco-0.1.2/junco/R/a_summarize_aval_chg_diff.R | 19 junco-0.1.2/junco/R/a_summarize_ex_j.R | 77 - junco-0.1.2/junco/R/a_two_tier.R |only junco-0.1.2/junco/R/analyze_values.R | 1 junco-0.1.2/junco/R/ancova.R | 2 junco-0.1.2/junco/R/ancova_rbmi.R | 36 junco-0.1.2/junco/R/cmhrms.R |only junco-0.1.2/junco/R/cmp_functions.R | 7 junco-0.1.2/junco/R/column_stats.R | 184 --- junco-0.1.2/junco/R/colwidths.R | 59 - junco-0.1.2/junco/R/count_denom_fraction.R | 20 junco-0.1.2/junco/R/coxph_hr.R | 11 junco-0.1.2/junco/R/docx_exporter_functions.R |only junco-0.1.2/junco/R/estimate_proportion_diff.R | 43 junco-0.1.2/junco/R/event_free.R | 6 junco-0.1.2/junco/R/get_ref_info.R | 6 junco-0.1.2/junco/R/h_freq_funs.R | 210 ++-- junco-0.1.2/junco/R/jjcs_num_formats.R | 9 junco-0.1.2/junco/R/jjcsformats.R | 503 ++++------ junco-0.1.2/junco/R/junco_utils_default_stats_formats_labels.R | 32 junco-0.1.2/junco/R/lsmeans.R | 3 junco-0.1.2/junco/R/mmrm.R | 5 junco-0.1.2/junco/R/mmrm_rbmi.R | 24 junco-0.1.2/junco/R/odds_ratio.R | 1 junco-0.1.2/junco/R/pool_rbmi.R | 35 junco-0.1.2/junco/R/proportions.R | 14 junco-0.1.2/junco/R/proposal_argument_convention.R | 7 junco-0.1.2/junco/R/pruning_functions.R | 60 - junco-0.1.2/junco/R/rbmi.R | 236 ++-- junco-0.1.2/junco/R/relative_risk.R | 2 junco-0.1.2/junco/R/remove_col_count.R | 14 junco-0.1.2/junco/R/resp01_functions.R | 4 junco-0.1.2/junco/R/sorting_functions.R | 48 junco-0.1.2/junco/R/span_var_map.R | 24 junco-0.1.2/junco/R/split_functions.R | 164 +-- junco-0.1.2/junco/R/summarize_ancova.R | 13 junco-0.1.2/junco/R/summarize_row_counts.R | 4 junco-0.1.2/junco/R/tabulate_lsmeans.R | 8 junco-0.1.2/junco/R/tabulate_lsmeans_wide.R | 77 - junco-0.1.2/junco/R/tabulate_rbmi.R | 6 junco-0.1.2/junco/R/test_proportion_diff.R | 165 --- junco-0.1.2/junco/R/title_footers.R | 16 junco-0.1.2/junco/R/tt_to_tblfile.R | 253 +++-- junco-0.1.2/junco/R/utils.R | 50 junco-0.1.2/junco/README.md | 16 junco-0.1.2/junco/build/vignette.rds |binary junco-0.1.2/junco/inst/WORDLIST | 187 +-- junco-0.1.2/junco/inst/doc/auto_colwidths.R | 6 junco-0.1.2/junco/inst/doc/auto_colwidths.Rmd | 6 junco-0.1.2/junco/inst/doc/auto_colwidths.html | 219 ++-- junco-0.1.2/junco/inst/doc/junco.html | 4 junco-0.1.2/junco/inst/doc/table_and_listing_customizations.R |only junco-0.1.2/junco/inst/doc/table_and_listing_customizations.html |only junco-0.1.2/junco/inst/doc/table_and_listing_customizations.rmd |only junco-0.1.2/junco/inst/template_file.docx |only junco-0.1.2/junco/inst/template_file_watermark_landscape.docx |only junco-0.1.2/junco/inst/template_file_watermark_landscape_pagenum.docx |only junco-0.1.2/junco/inst/template_file_watermark_portrait.docx |only junco-0.1.2/junco/inst/template_file_watermark_portrait_pagenum.docx |only junco-0.1.2/junco/man/a_eair100_j.Rd | 106 -- junco-0.1.2/junco/man/a_freq_combos_j.Rd | 79 + junco-0.1.2/junco/man/a_freq_j.Rd | 38 junco-0.1.2/junco/man/a_freq_resp_var_j.Rd | 25 junco-0.1.2/junco/man/a_freq_subcol_j.Rd | 57 - 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Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/en-us>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Tyler Littlefield [ctb],
httr development team [ctb] ,
Scott Holden [ctb] ,
Chris Stone [ctb] ,
Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between AzureAuth versions 1.3.3 dated 2021-09-13 and 1.3.4 dated 2025-12-20
DESCRIPTION | 10 MD5 | 42 +- NAMESPACE | 2 NEWS.md | 4 R/AzureAuth.R | 2 R/cert_creds.R | 2 R/normalize.R | 2 R/token.R | 8 R/token_manual.R |only README.md | 2 build/vignette.rds |binary inst/doc/scenarios.Rmd | 8 inst/doc/scenarios.html | 305 ++++++++++++++------- inst/doc/shiny.html | 303 ++++++++++++--------- inst/doc/token.Rmd | 4 inst/doc/token.html | 504 ++++++++++++++++++++++------------- man/AzureManualToken.Rd |only man/AzureR_dir.Rd | 2 man/get_azure_token.Rd | 8 man/get_manual_token.Rd |only man/guid.Rd | 2 tests/testthat/test03_manual_token.R |only vignettes/scenarios.Rmd | 8 vignettes/token.Rmd | 4 24 files changed, 774 insertions(+), 448 deletions(-)
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.2 dated 2025-11-27 and 1.1.3 dated 2025-12-20
wbids-1.1.2/wbids/inst/doc/data-model.R |only wbids-1.1.2/wbids/inst/doc/data-model.qmd |only wbids-1.1.2/wbids/vignettes/data-model.qmd |only wbids-1.1.3/wbids/DESCRIPTION | 22 wbids-1.1.3/wbids/LICENSE | 4 wbids-1.1.3/wbids/MD5 | 107 wbids-1.1.3/wbids/NAMESPACE | 50 wbids-1.1.3/wbids/NEWS.md | 4 wbids-1.1.3/wbids/R/global-variables.R | 24 wbids-1.1.3/wbids/R/ids_bulk.R | 582 - wbids-1.1.3/wbids/R/ids_bulk_files.R | 80 wbids-1.1.3/wbids/R/ids_bulk_series.R | 84 wbids-1.1.3/wbids/R/ids_get.R | 1088 +- wbids-1.1.3/wbids/R/ids_get_ed.R | 82 wbids-1.1.3/wbids/R/ids_list_counterparts.R | 58 wbids-1.1.3/wbids/R/ids_list_entities.R | 130 wbids-1.1.3/wbids/R/ids_list_series.R | 56 wbids-1.1.3/wbids/R/ids_list_series_topics.R | 48 wbids-1.1.3/wbids/R/perform_request.R | 208 wbids-1.1.3/wbids/R/read_bulk_info.R | 42 wbids-1.1.3/wbids/R/sysdata.R | 54 wbids-1.1.3/wbids/R/wbids-package.R | 28 wbids-1.1.3/wbids/README.md | 378 wbids-1.1.3/wbids/build/vignette.rds |binary wbids-1.1.3/wbids/inst/doc/data-model.Rmd |only wbids-1.1.3/wbids/inst/doc/data-model.html | 3786 +--------- wbids-1.1.3/wbids/inst/doc/downloading-the-full-ids-data.R |only wbids-1.1.3/wbids/inst/doc/downloading-the-full-ids-data.Rmd |only wbids-1.1.3/wbids/inst/doc/downloading-the-full-ids-data.html |only wbids-1.1.3/wbids/man/counterparts.Rd | 32 wbids-1.1.3/wbids/man/entities.Rd | 32 wbids-1.1.3/wbids/man/ids_bulk.Rd | 116 wbids-1.1.3/wbids/man/ids_bulk_files.Rd | 58 wbids-1.1.3/wbids/man/ids_bulk_series.Rd | 68 wbids-1.1.3/wbids/man/ids_get.Rd | 288 wbids-1.1.3/wbids/man/ids_get_ed.Rd | 82 wbids-1.1.3/wbids/man/ids_list_counterparts.Rd | 66 wbids-1.1.3/wbids/man/ids_list_entities.Rd | 88 wbids-1.1.3/wbids/man/ids_list_geographies.Rd | 90 wbids-1.1.3/wbids/man/ids_list_series.Rd | 64 wbids-1.1.3/wbids/man/ids_list_series_topics.Rd | 56 wbids-1.1.3/wbids/man/read_bulk_info.Rd | 32 wbids-1.1.3/wbids/man/series.Rd | 32 wbids-1.1.3/wbids/man/series_topics.Rd | 32 wbids-1.1.3/wbids/man/wbids-package.Rd | 70 wbids-1.1.3/wbids/tests/testthat.R | 24 wbids-1.1.3/wbids/tests/testthat/test-ids_bulk.R | 808 +- wbids-1.1.3/wbids/tests/testthat/test-ids_bulk_files.R | 30 wbids-1.1.3/wbids/tests/testthat/test-ids_bulk_series.R | 36 wbids-1.1.3/wbids/tests/testthat/test-ids_get.R | 1311 +-- wbids-1.1.3/wbids/tests/testthat/test-ids_get_ed.R | 16 wbids-1.1.3/wbids/tests/testthat/test-ids_list_counterparts.R | 20 wbids-1.1.3/wbids/tests/testthat/test-ids_list_entities.R | 48 wbids-1.1.3/wbids/tests/testthat/test-ids_list_series.R | 18 wbids-1.1.3/wbids/tests/testthat/test-ids_list_series_topics.R | 16 wbids-1.1.3/wbids/tests/testthat/test-perform_request.R | 230 wbids-1.1.3/wbids/tests/testthat/test-read_bulk_info.R | 28 wbids-1.1.3/wbids/vignettes/data-model.Rmd |only wbids-1.1.3/wbids/vignettes/downloading-the-full-ids-data.Rmd |only 59 files changed, 4045 insertions(+), 6661 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: Provide the EMU Speech Database Management System (EMU-SDMS) with
database management, data extraction, data preparation and data
visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/>
for more details.
Author: Markus Jochim [aut, cre] ,
Raphael Winkelmann [aut],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Markus Jochim <markusjochim@phonetik.uni-muenchen.de>
Diff between emuR versions 2.5.2 dated 2025-09-02 and 2.6.0 dated 2025-12-20
emuR-2.5.2/emuR/R/emuR-packageDocs.R |only emuR-2.6.0/emuR/DESCRIPTION | 12 +- emuR-2.6.0/emuR/MD5 | 17 ++- emuR-2.6.0/emuR/NEWS.md | 10 ++ emuR-2.6.0/emuR/R/buildtrack.R | 2 emuR-2.6.0/emuR/R/emuR-package.R |only emuR-2.6.0/emuR/R/emuR-server.R | 147 +++++++++++++++++++++++++++------- emuR-2.6.0/emuR/README.md | 33 ++++++- emuR-2.6.0/emuR/man/buildtrack.Rd | 2 emuR-2.6.0/emuR/man/emuR-package.Rd | 4 emuR-2.6.0/emuR/man/rdaTrackToSsff.Rd |only 11 files changed, 172 insertions(+), 55 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.17.4 dated 2025-01-23 and 0.18.0 dated 2025-12-20
DESCRIPTION | 12 ++++----- MD5 | 41 +++++++++++++++++-------------- NEWS.md | 12 +++++++++ R/Tfmat_qform_conversion.R |only R/load_surf.R | 3 ++ R/replace_NA_with_label.R |only R/resample_gifti.R | 6 +++- R/rox_args_docs.R | 2 - R/sysdata.rda |binary R/view_xifti_surface.R | 2 - R/write_cifti.R | 7 +++-- R/write_nifti.R | 16 +++++++++++- README.md | 31 +++++++++++++++++++---- build/vignette.rds |binary inst/doc/ciftiTools_vignette_mini.html | 41 +++++++++++++++---------------- man/Tfmat_from_qform.Rd |only man/qform_from_Tfmat.Rd |only man/replace_NA_with_label.Rd |only man/rgl_interactive_plots_Description.Rd | 2 - man/view_surf.Rd | 2 - man/view_xifti_surface.Rd | 2 - tests/testthat/test-misc.R | 4 +++ tests/testthat/test-plotting_surf.R | 2 - tests/testthat/test-writing.R | 15 +++++++++++ 24 files changed, 139 insertions(+), 61 deletions(-)
Title: Single Cell Poisson Probability Paradigm
Description: Useful to visualize the Poissoneity (an independent Poisson statistical framework,
where each RNA measurement for each cell comes from its own independent Poisson distribution) of
Unique Molecular Identifier (UMI) based single cell RNA sequencing (scRNA-seq) data, and explore
cell clustering based on model departure as a novel data representation.
Author: Yue Pan [aut, cre],
Justin Landis [aut] ,
Dirk Dittmer [aut],
James S. Marron [aut],
Di Wu [aut]
Maintainer: Yue Pan <yuep027@gmail.com>
Diff between scpoisson versions 0.0.1 dated 2022-08-17 and 0.0.2 dated 2025-12-19
scpoisson-0.0.1/scpoisson/README.md |only scpoisson-0.0.1/scpoisson/inst/WORDLIST |only scpoisson-0.0.2/scpoisson/DESCRIPTION | 10 scpoisson-0.0.2/scpoisson/MD5 | 60 scpoisson-0.0.2/scpoisson/NAMESPACE | 5 scpoisson-0.0.2/scpoisson/NEWS.md | 4 scpoisson-0.0.2/scpoisson/R/LouvainDepart.R | 110 scpoisson-0.0.2/scpoisson/R/Object_representation.R | 12 scpoisson-0.0.2/scpoisson/R/data_representation.R | 24 scpoisson-0.0.2/scpoisson/R/differential_expression.R | 4 scpoisson-0.0.2/scpoisson/R/hclustDepart.R | 38 scpoisson-0.0.2/scpoisson/R/print.R | 16 scpoisson-0.0.2/scpoisson/R/qq_env_small.R | 17 scpoisson-0.0.2/scpoisson/build/partial.rdb |binary scpoisson-0.0.2/scpoisson/build/vignette.rds |binary scpoisson-0.0.2/scpoisson/inst/doc/scpoissonmodel.Rmd | 12 scpoisson-0.0.2/scpoisson/inst/doc/scpoissonmodel.html | 1808 ++++++++-- scpoisson-0.0.2/scpoisson/man/HclustDepart.Rd | 22 scpoisson-0.0.2/scpoisson/man/LouvainDepart.Rd | 52 scpoisson-0.0.2/scpoisson/man/adj_CDF_logit.Rd | 6 scpoisson-0.0.2/scpoisson/man/diff_gene_list.Rd | 20 scpoisson-0.0.2/scpoisson/man/new_scppp.Rd |only scpoisson-0.0.2/scpoisson/man/print.scppp.Rd |only scpoisson-0.0.2/scpoisson/man/qqplot_env_pois.Rd | 24 scpoisson-0.0.2/scpoisson/man/sigp.Rd | 18 scpoisson-0.0.2/scpoisson/tests/testthat.R | 2 scpoisson-0.0.2/scpoisson/tests/testthat/_snaps/qqplot/qq-env-plot-matrix.svg | 280 - scpoisson-0.0.2/scpoisson/tests/testthat/test_differential_expression.R | 6 scpoisson-0.0.2/scpoisson/tests/testthat/test_hclustDepart.R | 2 scpoisson-0.0.2/scpoisson/tests/testthat/test_model_departure.R | 2 scpoisson-0.0.2/scpoisson/tests/testthat/test_qqplot.R | 7 scpoisson-0.0.2/scpoisson/tests/testthat/test_scppp_constructor.R | 1 scpoisson-0.0.2/scpoisson/vignettes/scpoissonmodel.Rmd | 12 33 files changed, 1944 insertions(+), 630 deletions(-)
Title: Easy Spatial Modeling with Random Forest
Description: Automatic generation and selection of spatial predictors for Random Forest models fitted to spatially structured data. Spatial predictors are constructed from a distance matrix among training samples using Moran's Eigenvector Maps (MEMs; Dray, Legendre, and Peres-Neto 2006 <DOI:10.1016/j.ecolmodel.2006.02.015>) or the RFsp approach (Hengl et al. <DOI:10.7717/peerj.5518>). These predictors are used alongside user-supplied explanatory variables in Random Forest models. The package provides functions for model fitting, multicollinearity reduction, interaction identification, hyperparameter tuning, evaluation via spatial cross-validation, and result visualization using partial dependence and interaction plots. Model fitting relies on the 'ranger' package (Wright and Ziegler 2017 <DOI:10.18637/jss.v077.i01>).
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between spatialRF versions 1.1.4 dated 2022-08-19 and 1.1.5 dated 2025-12-19
spatialRF-1.1.4/spatialRF/R/distance_matrix.R |only spatialRF-1.1.4/spatialRF/R/plant_richness_df.R |only spatialRF-1.1.4/spatialRF/R/vif.R |only spatialRF-1.1.4/spatialRF/data/distance_matrix.rda |only spatialRF-1.1.4/spatialRF/data/plant_richness_df.rda |only spatialRF-1.1.4/spatialRF/man/distance_matrix.Rd |only spatialRF-1.1.4/spatialRF/man/plant_richness_df.Rd |only spatialRF-1.1.4/spatialRF/man/vif.Rd |only spatialRF-1.1.5/spatialRF/DESCRIPTION | 21 spatialRF-1.1.5/spatialRF/LICENSE |only spatialRF-1.1.5/spatialRF/MD5 | 320 ++-- spatialRF-1.1.5/spatialRF/NAMESPACE | 11 spatialRF-1.1.5/spatialRF/NEWS.md | 30 spatialRF-1.1.5/spatialRF/R/auc.R | 25 spatialRF-1.1.5/spatialRF/R/auto_cor.R | 189 +- spatialRF-1.1.5/spatialRF/R/auto_vif.R | 281 +--- spatialRF-1.1.5/spatialRF/R/beowulf_cluster.R | 96 - spatialRF-1.1.5/spatialRF/R/case_weights.R | 46 spatialRF-1.1.5/spatialRF/R/data.R |only spatialRF-1.1.5/spatialRF/R/default_distance_thresholds.R | 32 spatialRF-1.1.5/spatialRF/R/double_center_distance_matrix.R | 53 spatialRF-1.1.5/spatialRF/R/filter_spatial_predictors.R | 84 - spatialRF-1.1.5/spatialRF/R/get_evaluation.R | 59 spatialRF-1.1.5/spatialRF/R/get_importance.R | 65 spatialRF-1.1.5/spatialRF/R/get_importance_local.R | 43 spatialRF-1.1.5/spatialRF/R/get_moran.R | 42 spatialRF-1.1.5/spatialRF/R/get_performance.R | 57 spatialRF-1.1.5/spatialRF/R/get_predictions.R | 39 spatialRF-1.1.5/spatialRF/R/get_residuals.R | 41 spatialRF-1.1.5/spatialRF/R/get_response_curves.R | 152 +- spatialRF-1.1.5/spatialRF/R/get_spatial_predictors.R | 44 spatialRF-1.1.5/spatialRF/R/is_binary.R | 67 spatialRF-1.1.5/spatialRF/R/make_spatial_fold.R | 147 +- spatialRF-1.1.5/spatialRF/R/make_spatial_folds.R | 168 +- spatialRF-1.1.5/spatialRF/R/mem.R | 65 spatialRF-1.1.5/spatialRF/R/mem_multithreshold.R | 83 - spatialRF-1.1.5/spatialRF/R/moran.R | 127 + spatialRF-1.1.5/spatialRF/R/moran_multithreshold.R | 107 + spatialRF-1.1.5/spatialRF/R/objects_size.R | 85 - spatialRF-1.1.5/spatialRF/R/optimization_function.R | 111 + spatialRF-1.1.5/spatialRF/R/pca.R | 69 - spatialRF-1.1.5/spatialRF/R/pca_multithreshold.R | 95 - spatialRF-1.1.5/spatialRF/R/plot_evaluation.R | 118 - spatialRF-1.1.5/spatialRF/R/plot_importance.R | 184 +- spatialRF-1.1.5/spatialRF/R/plot_moran.R | 190 +- spatialRF-1.1.5/spatialRF/R/plot_optimization.R | 97 - spatialRF-1.1.5/spatialRF/R/plot_residuals_diagnostics.R | 66 spatialRF-1.1.5/spatialRF/R/plot_response_curves.R | 218 +-- spatialRF-1.1.5/spatialRF/R/plot_response_surface.R | 107 - spatialRF-1.1.5/spatialRF/R/plot_training_df.R | 55 spatialRF-1.1.5/spatialRF/R/plot_training_df_moran.R | 76 - spatialRF-1.1.5/spatialRF/R/plot_tuning.R | 77 - spatialRF-1.1.5/spatialRF/R/prepare_importance_spatial.R | 44 spatialRF-1.1.5/spatialRF/R/print.R | 178 +- spatialRF-1.1.5/spatialRF/R/print_evaluation.R | 102 - spatialRF-1.1.5/spatialRF/R/print_importance.R | 51 spatialRF-1.1.5/spatialRF/R/print_moran.R | 140 -- spatialRF-1.1.5/spatialRF/R/print_performance.R | 104 + spatialRF-1.1.5/spatialRF/R/rank_spatial_predictors.R | 252 +-- spatialRF-1.1.5/spatialRF/R/rescale_vector.R | 43 spatialRF-1.1.5/spatialRF/R/residuals_diagnostics.R | 52 spatialRF-1.1.5/spatialRF/R/residuals_test.R | 12 spatialRF-1.1.5/spatialRF/R/rf.R | 233 +-- spatialRF-1.1.5/spatialRF/R/rf_compare.R | 112 - spatialRF-1.1.5/spatialRF/R/rf_evaluate.R | 395 ++--- spatialRF-1.1.5/spatialRF/R/rf_importance.R | 145 +- spatialRF-1.1.5/spatialRF/R/rf_repeat.R | 356 ++--- spatialRF-1.1.5/spatialRF/R/rf_spatial.R | 408 ++---- spatialRF-1.1.5/spatialRF/R/rf_tuning.R | 401 ++--- spatialRF-1.1.5/spatialRF/R/root_mean_squared_error.R | 37 spatialRF-1.1.5/spatialRF/R/select_spatial_predictors_recursive.R | 232 ++- spatialRF-1.1.5/spatialRF/R/select_spatial_predictors_sequential.R | 234 +-- spatialRF-1.1.5/spatialRF/R/setup_parallel_execution.R |only spatialRF-1.1.5/spatialRF/R/standard_error.R | 9 spatialRF-1.1.5/spatialRF/R/statistical_mode.R | 9 spatialRF-1.1.5/spatialRF/R/the_feature_engineer.R | 672 +++++----- spatialRF-1.1.5/spatialRF/R/thinning.R | 60 spatialRF-1.1.5/spatialRF/R/thinning_til_n.R | 54 spatialRF-1.1.5/spatialRF/R/utils-pipe.R |only spatialRF-1.1.5/spatialRF/R/weights_from_distance_matrix.R | 27 spatialRF-1.1.5/spatialRF/data/plants_df.rda |only spatialRF-1.1.5/spatialRF/data/plants_distance.rda |only spatialRF-1.1.5/spatialRF/data/plants_predictors.rda |only spatialRF-1.1.5/spatialRF/data/plants_response.rda |only spatialRF-1.1.5/spatialRF/data/plants_rf.rda |only spatialRF-1.1.5/spatialRF/data/plants_rf_spatial.rda |only spatialRF-1.1.5/spatialRF/data/plants_xy.rda |only spatialRF-1.1.5/spatialRF/inst/CITATION | 16 spatialRF-1.1.5/spatialRF/man/auc.Rd | 32 spatialRF-1.1.5/spatialRF/man/auto_cor.Rd | 80 - spatialRF-1.1.5/spatialRF/man/auto_vif.Rd | 87 - spatialRF-1.1.5/spatialRF/man/beowulf_cluster.Rd | 71 - spatialRF-1.1.5/spatialRF/man/case_weights.Rd | 51 spatialRF-1.1.5/spatialRF/man/default_distance_thresholds.Rd | 37 spatialRF-1.1.5/spatialRF/man/dot-vif_to_df.Rd |only spatialRF-1.1.5/spatialRF/man/double_center_distance_matrix.Rd | 53 spatialRF-1.1.5/spatialRF/man/figures |only spatialRF-1.1.5/spatialRF/man/filter_spatial_predictors.Rd | 75 - spatialRF-1.1.5/spatialRF/man/get_evaluation.Rd | 69 - spatialRF-1.1.5/spatialRF/man/get_importance.Rd | 51 spatialRF-1.1.5/spatialRF/man/get_importance_local.Rd | 55 spatialRF-1.1.5/spatialRF/man/get_moran.Rd | 54 spatialRF-1.1.5/spatialRF/man/get_performance.Rd | 59 spatialRF-1.1.5/spatialRF/man/get_predictions.Rd | 51 spatialRF-1.1.5/spatialRF/man/get_residuals.Rd | 51 spatialRF-1.1.5/spatialRF/man/get_response_curves.Rd | 85 - spatialRF-1.1.5/spatialRF/man/get_spatial_predictors.Rd | 54 spatialRF-1.1.5/spatialRF/man/is_binary.Rd | 61 spatialRF-1.1.5/spatialRF/man/make_spatial_fold.Rd | 96 - spatialRF-1.1.5/spatialRF/man/make_spatial_folds.Rd | 116 + spatialRF-1.1.5/spatialRF/man/mem.Rd | 63 spatialRF-1.1.5/spatialRF/man/mem_multithreshold.Rd | 73 - spatialRF-1.1.5/spatialRF/man/moran.Rd | 87 - spatialRF-1.1.5/spatialRF/man/moran_multithreshold.Rd | 94 - spatialRF-1.1.5/spatialRF/man/normality.Rd | 19 spatialRF-1.1.5/spatialRF/man/objects_size.Rd | 55 spatialRF-1.1.5/spatialRF/man/optimization_function.Rd | 94 + spatialRF-1.1.5/spatialRF/man/pca.Rd | 68 - spatialRF-1.1.5/spatialRF/man/pca_multithreshold.Rd | 81 - spatialRF-1.1.5/spatialRF/man/pipe.Rd |only spatialRF-1.1.5/spatialRF/man/plants_df.Rd |only spatialRF-1.1.5/spatialRF/man/plants_distance.Rd |only spatialRF-1.1.5/spatialRF/man/plants_predictors.Rd |only spatialRF-1.1.5/spatialRF/man/plants_response.Rd |only spatialRF-1.1.5/spatialRF/man/plants_rf.Rd |only spatialRF-1.1.5/spatialRF/man/plants_rf_spatial.Rd |only spatialRF-1.1.5/spatialRF/man/plants_xy.Rd |only spatialRF-1.1.5/spatialRF/man/plot_evaluation.Rd | 110 + spatialRF-1.1.5/spatialRF/man/plot_importance.Rd | 95 - spatialRF-1.1.5/spatialRF/man/plot_moran.Rd | 35 spatialRF-1.1.5/spatialRF/man/plot_optimization.Rd | 46 spatialRF-1.1.5/spatialRF/man/plot_residuals_diagnostics.Rd | 29 spatialRF-1.1.5/spatialRF/man/plot_response_curves.Rd | 34 spatialRF-1.1.5/spatialRF/man/plot_response_surface.Rd | 33 spatialRF-1.1.5/spatialRF/man/plot_training_df.Rd | 34 spatialRF-1.1.5/spatialRF/man/plot_training_df_moran.Rd | 44 spatialRF-1.1.5/spatialRF/man/plot_tuning.Rd | 52 spatialRF-1.1.5/spatialRF/man/prepare_importance_spatial.Rd | 35 spatialRF-1.1.5/spatialRF/man/print.Rd | 37 spatialRF-1.1.5/spatialRF/man/print_evaluation.Rd | 45 spatialRF-1.1.5/spatialRF/man/print_importance.Rd | 36 spatialRF-1.1.5/spatialRF/man/print_moran.Rd | 36 spatialRF-1.1.5/spatialRF/man/print_performance.Rd | 36 spatialRF-1.1.5/spatialRF/man/rank_spatial_predictors.Rd | 71 - spatialRF-1.1.5/spatialRF/man/rescale_vector.Rd | 30 spatialRF-1.1.5/spatialRF/man/residuals_diagnostics.Rd | 27 spatialRF-1.1.5/spatialRF/man/rf.Rd | 159 +- spatialRF-1.1.5/spatialRF/man/rf_compare.Rd | 55 spatialRF-1.1.5/spatialRF/man/rf_evaluate.Rd | 43 spatialRF-1.1.5/spatialRF/man/rf_importance.Rd | 34 spatialRF-1.1.5/spatialRF/man/rf_repeat.Rd | 80 - spatialRF-1.1.5/spatialRF/man/rf_spatial.Rd | 87 - spatialRF-1.1.5/spatialRF/man/rf_tuning.Rd | 46 spatialRF-1.1.5/spatialRF/man/root_mean_squared_error.Rd | 24 spatialRF-1.1.5/spatialRF/man/select_spatial_predictors_recursive.Rd | 117 - spatialRF-1.1.5/spatialRF/man/select_spatial_predictors_sequential.Rd | 85 - spatialRF-1.1.5/spatialRF/man/setup_parallel_execution.Rd |only spatialRF-1.1.5/spatialRF/man/standard_error.Rd | 18 spatialRF-1.1.5/spatialRF/man/statistical_mode.Rd | 18 spatialRF-1.1.5/spatialRF/man/the_feature_engineer.Rd | 65 spatialRF-1.1.5/spatialRF/man/thinning.Rd | 41 spatialRF-1.1.5/spatialRF/man/thinning_til_n.Rd | 42 spatialRF-1.1.5/spatialRF/man/weights_from_distance_matrix.Rd | 25 163 files changed, 6568 insertions(+), 5578 deletions(-)
Title: Exponential Random Graph Models for Small Networks
Description: Simulation and estimation of Exponential Random Graph Models (ERGMs)
for small networks using exact statistics as shown in Vega Yon et al. (2020)
<DOI:10.1016/j.socnet.2020.07.005>. As a difference from the 'ergm'
package, 'ergmito' circumvents using Markov-Chain Maximum Likelihood Estimator
(MC-MLE) and instead uses Maximum Likelihood Estimator (MLE) to fit ERGMs
for small networks. As exhaustive enumeration is computationally feasible for
small networks, this R package takes advantage of this and provides tools for
calculating likelihood functions, and other relevant functions, directly,
meaning that in many cases both estimation and simulation of ERGMs for
small networks can be faster and more accurate than simulation-based
algorithms.
Author: George Vega Yon [cre, aut] ,
Kayla de la Haye [ths] ,
Army Research Laboratory and the U.S. Army Research Office [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.3-1 dated 2023-06-14
Diff between ergmito versions 0.3-1 dated 2023-06-14 and 0.3-2 dated 2025-12-19
ergmito-0.3-1/ergmito/build/ergmito.pdf |only ergmito-0.3-1/ergmito/inst/NEWS |only ergmito-0.3-2/ergmito/DESCRIPTION | 13 ++- ergmito-0.3-2/ergmito/MD5 | 24 +++--- ergmito-0.3-2/ergmito/NEWS.md | 4 + ergmito-0.3-2/ergmito/R/utils.R | 2 ergmito-0.3-2/ergmito/build/stage23.rdb |binary ergmito-0.3-2/ergmito/build/vignette.rds |binary ergmito-0.3-2/ergmito/inst/doc/ergm-equations.html | 6 - ergmito-0.3-2/ergmito/inst/doc/extending-ergmito.html | 42 ++++++------ ergmito-0.3-2/ergmito/man/exact_loglik.Rd | 2 ergmito-0.3-2/ergmito/man/figures/README-fivenets-gof-1.png |binary ergmito-0.3-2/ergmito/man/figures/README-net2-1.png |binary ergmito-0.3-2/ergmito/man/nvertex.Rd | 2 14 files changed, 49 insertions(+), 46 deletions(-)
Title: A DNA Reference Library Manager
Description: Reference database manager offering a set of functions
to import, organize, clean, filter, audit and export reference genetic
data. Provide functions to download sequence data from
NCBI GenBank <https://www.ncbi.nlm.nih.gov/genbank/>.
Designed as an environment for semi-automatic and assisted
construction of reference databases and to improve standardization
and repeatability in barcoding and metabarcoding studies.
Author: Francois Keck [aut, cre, cph]
Maintainer: Francois Keck <francois.keck@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2022-09-22
Diff between refdb versions 0.1.1 dated 2022-09-22 and 0.1.2 dated 2025-12-19
refdb-0.1.1/refdb/man/refdb_import_BOLD.Rd |only refdb-0.1.2/refdb/DESCRIPTION | 18 refdb-0.1.2/refdb/MD5 | 34 refdb-0.1.2/refdb/NAMESPACE | 2 refdb-0.1.2/refdb/R/fields.R | 10 refdb-0.1.2/refdb/R/import_BOLD.R | 167 ++-- refdb-0.1.2/refdb/R/import_NCBI.R | 28 refdb-0.1.2/refdb/R/refdb_export.R | 57 + refdb-0.1.2/refdb/R/refdb_ncbi_taxonomy.R | 4 refdb-0.1.2/refdb/README.md | 11 refdb-0.1.2/refdb/build/vignette.rds |binary refdb-0.1.2/refdb/inst/doc/intro_refdb.R | 40 - refdb-0.1.2/refdb/inst/doc/intro_refdb.html | 795 ++++++++++++--------- refdb-0.1.2/refdb/inst/doc/ncbi_bold.html | 490 +++++++----- refdb-0.1.2/refdb/man/refdb-package.Rd | 2 refdb-0.1.2/refdb/man/refdb_export_utax.Rd |only refdb-0.1.2/refdb/man/refdb_import_NCBI.Rd | 10 refdb-0.1.2/refdb/man/refdb_set_ncbitax.Rd | 4 refdb-0.1.2/refdb/tests/testthat/test_import_web.R | 10 19 files changed, 967 insertions(+), 715 deletions(-)
Title: Ternary Plots for Trinomial Regression Models
Description: An implementation of the ternary plot for interpreting regression
coefficients of trinomial regression models, as proposed in Santi, Dickson
and Espa (2019) <doi:10.1080/00031305.2018.1442368>. Ternary plots can be
drawn using either 'ggtern' package (based on 'ggplot2') or 'Ternary'
package (based on standard graphics). The package and its features are
illustrated in Santi, Dickson, Espa and Giuliani (2022)
<doi:10.18637/jss.v103.c01>.
Author: Flavio Santi [cre, aut] ,
Maria Michela Dickson [aut] ,
Giuseppe Espa [aut] ,
Diego Giuliani [aut]
Maintainer: Flavio Santi <flavio.santi@unitn.it>
This is a re-admission after prior archival of version 3.1.4 dated 2023-12-10
Diff between plot3logit versions 3.1.4 dated 2023-12-10 and 3.2.0 dated 2025-12-19
plot3logit-3.1.4/plot3logit/vignettes/plot3logit-jss.asis |only plot3logit-3.1.4/plot3logit/vignettes/plot3logit-jss.pdf |only plot3logit-3.2.0/plot3logit/DESCRIPTION | 26 +- plot3logit-3.2.0/plot3logit/MD5 | 48 +++-- plot3logit-3.2.0/plot3logit/NEWS.md | 12 + plot3logit-3.2.0/plot3logit/R/field3logit.R | 7 plot3logit-3.2.0/plot3logit/R/plot3logit-package.R | 11 - plot3logit-3.2.0/plot3logit/README.md | 7 plot3logit-3.2.0/plot3logit/build/partial.rdb |binary plot3logit-3.2.0/plot3logit/build/vignette.rds |binary plot3logit-3.2.0/plot3logit/inst/REFERENCES.bib | 91 +++++++++- plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-main.R |only plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-main.Rnw |only plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-main.pdf |only plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-overview.R |only plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-overview.Rmd | 20 +- plot3logit-3.2.0/plot3logit/inst/doc/plot3logit-overview.html | 51 +++-- plot3logit-3.2.0/plot3logit/man/autoplot.Hfield3logit.Rd | 4 plot3logit-3.2.0/plot3logit/man/field3logit.Rd | 7 plot3logit-3.2.0/plot3logit/man/plot3logit-package.Rd | 15 + plot3logit-3.2.0/plot3logit/man/stat_3logit.Rd | 6 plot3logit-3.2.0/plot3logit/man/stat_conf3logit.Rd | 37 +++- plot3logit-3.2.0/plot3logit/man/stat_field3logit.Rd | 37 +++- plot3logit-3.2.0/plot3logit/vignettes/figures |only plot3logit-3.2.0/plot3logit/vignettes/plot3logit-main.Rnw |only plot3logit-3.2.0/plot3logit/vignettes/plot3logit-overview.Rmd | 20 +- plot3logit-3.2.0/plot3logit/vignettes/tables |only 27 files changed, 292 insertions(+), 107 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.1.7 dated 2025-12-04 and 0.1.8 dated 2025-12-19
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 13 ++++++ R/Ganttify.R | 115 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- README.md | 20 +++++++++ man/Ganttify.Rd | 35 ++++++++++++++++- 6 files changed, 189 insertions(+), 10 deletions(-)
Title: Working with Ethiopian Dates
Description: A robust and efficient solution for working with Ethiopian dates. It can seamlessly convert to and from Gregorian dates.
It is designed to be compatible with the 'tidyverse' data workflow, including plotting with 'ggplot2'.
It ensures lightning-fast computations by integrating high-performance 'C++' code through 'Rcpp' package.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between ethiodate versions 0.2.0 dated 2025-05-28 and 0.3.0 dated 2025-12-19
DESCRIPTION | 17 +++-- MD5 | 57 +++++++++-------- NAMESPACE | 3 NEWS.md | 10 +++ R/Ops-date.R | 20 +++--- R/date-components.R | 45 +++++++------- R/dates.R | 69 ++++++++++----------- R/formats.R | 76 ++++++++++++++++------- R/utils.R | 44 +++++-------- R/vctrs-date.R | 49 +++++++-------- R/vctrs-difftime.R | 35 +++++------ R/zzz.R |only build/vignette.rds |binary inst/CITATION | 22 ++++-- inst/doc/ethiodate.Rmd | 8 +- inst/doc/ethiodate.html | 24 +++---- inst/doc/ggplot.R | 12 ++- inst/doc/ggplot.Rmd | 17 +++-- inst/doc/ggplot.html | 43 +++++++------ inst/doc/parsing.html | 29 ++++----- man/eth_date.Rd | 11 ++- man/is_eth_date.Rd | 17 +++-- src/RcppExports.cpp | 4 - src/dates.cpp | 81 ++++++++++++++++--------- tests/testthat/_snaps/snaps.md | 110 +++++++++++++++++++++++++++------- tests/testthat/test-dates.R | 130 ++++++++++++++++++++++++++--------------- tests/testthat/test-snaps.R | 30 +++++---- tests/testthat/test-vctrs.R | 41 +++++++++--- vignettes/ethiodate.Rmd | 8 +- vignettes/ggplot.Rmd | 17 +++-- 30 files changed, 630 insertions(+), 399 deletions(-)
Title: Generate Mind Maps
Description: Convert Markdown ('.md') or R Markdown ('.Rmd') texts, R scripts, directory structures, and other hierarchical structured documents into mind map widgets or 'Freemind' codes or 'Mermaid' mind map codes, and vice versa. 'Freemind' mind map ('.mm') files can be opened by or imported to common mind map software such as 'Freemind' (<https://freemind.sourceforge.io/wiki/index.php/Main_Page>). 'Mermaid' mind map codes (<https://mermaid.js.org/>) can be directly embedded in documents.
Author: Peng Zhao [aut, cre]
Maintainer: Peng Zhao <pengzhao20@outlook.com>
This is a re-admission after prior archival of version 1.3.2 dated 2021-11-22
Diff between mindr versions 1.3.2 dated 2021-11-22 and 1.4.1 dated 2025-12-19
DESCRIPTION | 32 +++-- MD5 | 52 ++++---- NAMESPACE | 19 --- R/experimental.R |only R/individual.R | 168 +++++---------------------- R/internal.R | 31 +++- R/wrapper.R | 317 ++++----------------------------------------------- build |only inst/doc |only man/dir2md.Rd | 11 - man/dir2mm.Rd | 12 - man/dir2r.Rd | 12 - man/get_mmdshape.Rd |only man/markmap.Rd | 32 ----- man/markmapOption.Rd | 18 -- man/md2dir.Rd | 18 -- man/md2mm.Rd | 13 -- man/md2mmd.Rd |only man/md2r.Rd | 11 - man/mm.Rd | 220 ++--------------------------------- man/mm2dir.Rd | 10 - man/mm2md.Rd | 11 - man/mm2r.Rd | 11 - man/mmm.Rd |only man/outline.Rd | 7 - man/outline_pdf.Rd |only man/r2dir.Rd | 10 - man/r2md.Rd | 11 - man/r2mm.Rd | 11 - vignettes |only 30 files changed, 162 insertions(+), 875 deletions(-)
Title: Calculate Estimates in Models with Interaction
Description: A tool to calculate and plot estimates from models
in which an interaction between the main predictor and a continuous covariate has been specified.
Methods used in the package refer to Harrell Jr FE (2015, ISBN:9783319330396);
Durrleman S, Simon R. (1989) <doi:10.1002/sim.4780080504>; Greenland S. (1995) <doi:10.1097/00001648-199507000-00005>.
Author: Giorgio Melloni [aut, cre] ,
Andrea Bellavia [aut] ,
Hong Xiong [aut]
Maintainer: Giorgio Melloni <melloni.giorgio@gmail.com>
Diff between interactionRCS versions 0.1.1 dated 2023-11-21 and 0.1.2 dated 2025-12-19
interactionRCS-0.1.1/interactionRCS/inst/extdata/vignette_files |only interactionRCS-0.1.2/interactionRCS/DESCRIPTION | 19 interactionRCS-0.1.2/interactionRCS/MD5 | 40 interactionRCS-0.1.2/interactionRCS/NAMESPACE | 3 interactionRCS-0.1.2/interactionRCS/R/hrcubspline.R | 5 interactionRCS-0.1.2/interactionRCS/R/hrspline.R | 5 interactionRCS-0.1.2/interactionRCS/R/lincubspline.R | 5 interactionRCS-0.1.2/interactionRCS/R/lininter.R | 5 interactionRCS-0.1.2/interactionRCS/R/orcubspline.R | 5 interactionRCS-0.1.2/interactionRCS/R/orspline.R | 5 interactionRCS-0.1.2/interactionRCS/R/umaru.R | 2 interactionRCS-0.1.2/interactionRCS/R/wrapper_int.R | 4 interactionRCS-0.1.2/interactionRCS/README.md | 4 interactionRCS-0.1.2/interactionRCS/build/vignette.rds |binary interactionRCS-0.1.2/interactionRCS/inst/doc/vignette.R | 10 interactionRCS-0.1.2/interactionRCS/inst/doc/vignette.html | 28 interactionRCS-0.1.2/interactionRCS/inst/extdata/vignette.html | 1753 +++++++++- interactionRCS-0.1.2/interactionRCS/man/umaru.Rd | 2 18 files changed, 1657 insertions(+), 238 deletions(-)
More information about interactionRCS at CRAN
Permanent link
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sev-in.ru>
Diff between ursa versions 3.11.4 dated 2025-02-20 and 3.11.5 dated 2025-12-19
DESCRIPTION | 21 +- MD5 | 258 ++++++++++++++++----------------- NAMESPACE | 3 NEWS.md | 24 ++- R/chunk.R | 25 +-- R/classCRS.R | 77 ++++++++- R/classColorTable.R | 14 + R/classConnection.R | 3 R/classGrid.R | 10 + R/classRaster.R | 8 - R/classRaster.Replace.R | 2 R/classRaster_GroupGeneric.R | 2 R/classRaster_as.table.R | 40 ++++- R/classRaster_close.R | 70 +++++++- R/classRaster_head.R | 5 R/classStack.R | 12 + R/colorize.R | 24 ++- R/compose_close.R | 20 ++ R/compose_design.R | 21 ++ R/compose_open.R | 69 ++++++-- R/compose_panel.R | 46 +++++ R/conn.open_envi.R | 72 ++++++++- R/conn.open_gdal.R | 2 R/conn.write_gdal.R | 7 R/cubehelix.R | 35 +++- R/display.R | 1 R/envi_files.R | 27 ++- R/get_earthdata.R | 20 +- R/glance.R | 27 ++- R/identify.R | 96 +++++++----- R/package_raster.R | 4 R/package_sf.R | 1 R/panel_coastline.R | 20 +- R/panel_graticule.R | 44 ++++- R/panel_new.R | 13 + R/panel_plot.R | 26 ++- R/panel_raster.R | 43 +++++ R/regrid.R | 60 +++++-- R/session.R | 7 R/spatial_engine.R | 159 +++++++++++++++++--- R/spatial_write.R | 155 +++++++++++++++---- R/trackline.R | 36 +++- R/ursa_000.R | 2 R/ursa_as.R | 2 R/ursa_blank.R | 14 - R/ursa_cache.R | 2 R/ursa_crop.R | 2 R/ursa_crs.R | 12 + R/ursa_grid.R | 7 R/ursa_match.R |only R/ursa_new.R | 12 + R/xxx.gdal_rasterize.R | 41 +++-- R/xxx.gdalwarp.R | 3 R/xxx.geomap.R | 59 +++++-- R/xxx.ncdf.R | 63 +++++--- R/xxx.panel_basemap.R | 2 R/xxx.panel_cluster.R | 33 +++- R/xxx.spatialize.R | 304 +++++++++++++++++++++++++++++---------- R/yyy.cache.R | 13 + R/yyy.connection.R | 10 + R/yyy.plot.R | 7 R/yyy.project.R | 43 +++++ R/yyy.syno.R | 6 R/yyy.tile.R | 26 ++- R/yyy.util.R | 31 +++ inst/requisite/browseURL.html | 14 + inst/requisite/coast-l.rds |binary man/00ursa-package.Rd | 2 man/Ops.band_group.Rd | 2 man/Ops.focal_extrem.Rd | 2 man/Ops.focal_median.Rd | 2 man/Ops.local_stat.Rd | 2 man/Ops.zonal_stat.Rd | 2 man/chunk.Rd | 9 - man/classColorTable.Rd | 9 + man/classRaster.Rd | 2 man/classRaster.Replace.Rd | 2 man/classRaster_as.array.Rd | 2 man/classRaster_as.integer.Rd | 2 man/classRaster_as.matrix.Rd | 2 man/classRaster_as.raster.Rd | 2 man/classRaster_close.Rd | 2 man/classRaster_commonGeneric.Rd | 2 man/classRaster_dim.Rd | 2 man/classRaster_head.Rd | 2 man/classRaster_hist.Rd | 2 man/classRaster_na.omit.Rd | 2 man/classRaster_plot.Rd | 2 man/classRaster_rep.Rd | 2 man/classRaster_seq.Rd | 2 man/classValue.Rd | 2 man/colorize.Rd | 2 man/compose_legend.Rd | 2 man/compose_plot.Rd | 2 man/conn.open_envi.Rd | 2 man/conn.read_envi.Rd | 2 man/conn.read_gdal.Rd | 2 man/conn.write_gdal.Rd | 2 man/cubehelix.Rd | 7 man/discolor.Rd | 2 man/display.Rd | 2 man/display_brick.Rd | 2 man/envi_files.Rd | 2 man/glance.Rd | 2 man/ignorevalue.Rd | 2 man/legend_colorbar.Rd | 2 man/legend_mtext.Rd | 2 man/panel_annotation.Rd | 2 man/panel_graticule.Rd | 2 man/panel_plot.Rd | 2 man/panel_shading.Rd | 2 man/pixelsize.Rd | 2 man/polygonize.Rd | 2 man/reclass.Rd | 2 man/regrid.Rd | 5 man/spatial_engine.Rd | 6 man/spatial_levelsplit.Rd | 2 man/spatial_read.Rd | 2 man/spatial_write.Rd | 16 +- man/temporal_interpolate.Rd | 2 man/ursa_000.Rd | 2 man/ursa_cache.Rd | 4 man/ursa_crop.Rd | 2 man/ursa_dummy.Rd | 2 man/ursa_grid.Rd | 2 man/ursa_info.Rd | 2 man/ursa_match.Rd |only man/whiteboxing.Rd | 2 src/init.c | 268 +++++++++++++++++----------------- src/ursa.c | 29 +++ src/ursa.h | 126 ++++++++-------- 131 files changed, 2066 insertions(+), 836 deletions(-)
Title: Fast Data Summary Reports
Description: Generates an RMarkdown data report with two components:
a summary of an input dataset and a diff of the dataset relative to an old version.
Author: Bryant Cong [aut, cre],
Alex Gordon [aut]
Maintainer: Bryant Cong <bryant.bcp@gmail.com>
Diff between datareportR versions 0.1.1 dated 2025-10-20 and 0.1.2 dated 2025-12-19
DESCRIPTION | 19 ++++++++++++------- MD5 | 11 ++++++++--- NAMESPACE | 13 +++++++------ README.md | 2 +- build |only inst |only vignettes |only 7 files changed, 28 insertions(+), 17 deletions(-)
Title: Clinical Trial Simulator
Description: Simulate phase II and/or phase III clinical trials. It supports various types of endpoints and adaptive strategies. Tools for carrying out graphical testing procedure and combination test under group sequential design are also provided.
Author: Han Zhang [cre, aut]
Maintainer: Han Zhang <zhangh.ustc@gmail.com>
Diff between TrialSimulator versions 1.3.0 dated 2025-09-26 and 1.7.0 dated 2025-12-19
TrialSimulator-1.3.0/TrialSimulator/R/arm.R |only TrialSimulator-1.3.0/TrialSimulator/R/controller.R |only TrialSimulator-1.3.0/TrialSimulator/R/endpoint.R |only TrialSimulator-1.3.0/TrialSimulator/R/listener.R |only TrialSimulator-1.3.0/TrialSimulator/R/trial.R |only TrialSimulator-1.7.0/TrialSimulator/DESCRIPTION | 6 TrialSimulator-1.7.0/TrialSimulator/MD5 | 82 ++-- TrialSimulator-1.7.0/TrialSimulator/NEWS.md | 28 + TrialSimulator-1.7.0/TrialSimulator/R/Arm.R |only TrialSimulator-1.7.0/TrialSimulator/R/Arms.R | 14 TrialSimulator-1.7.0/TrialSimulator/R/Controller.R |only TrialSimulator-1.7.0/TrialSimulator/R/Controllers.R | 30 + TrialSimulator-1.7.0/TrialSimulator/R/Endpoint.R |only TrialSimulator-1.7.0/TrialSimulator/R/Endpoints.R | 16 TrialSimulator-1.7.0/TrialSimulator/R/Listener.R |only TrialSimulator-1.7.0/TrialSimulator/R/Trial.R |only TrialSimulator-1.7.0/TrialSimulator/R/Trials.R | 103 +++++ TrialSimulator-1.7.0/TrialSimulator/README.md | 22 - TrialSimulator-1.7.0/TrialSimulator/build/vignette.rds |binary TrialSimulator-1.7.0/TrialSimulator/inst/doc/actionFunctions.Rmd | 41 +- TrialSimulator-1.7.0/TrialSimulator/inst/doc/actionFunctions.html | 20 - TrialSimulator-1.7.0/TrialSimulator/inst/doc/adaptiveDesign.html | 4 TrialSimulator-1.7.0/TrialSimulator/inst/doc/defineLongitudinalEndpoints.Rmd | 2 TrialSimulator-1.7.0/TrialSimulator/inst/doc/defineLongitudinalEndpoints.html | 5 TrialSimulator-1.7.0/TrialSimulator/inst/doc/defineNonTimeToEventEndpoints.html | 4 TrialSimulator-1.7.0/TrialSimulator/inst/doc/defineTimeToEventEndpoints.html | 19 - TrialSimulator-1.7.0/TrialSimulator/inst/doc/doseRanging.R |only TrialSimulator-1.7.0/TrialSimulator/inst/doc/doseRanging.Rmd |only TrialSimulator-1.7.0/TrialSimulator/inst/doc/doseRanging.html |only TrialSimulator-1.7.0/TrialSimulator/inst/doc/responseAdaptive.R | 87 ++-- TrialSimulator-1.7.0/TrialSimulator/inst/doc/responseAdaptive.Rmd | 83 ---- TrialSimulator-1.7.0/TrialSimulator/inst/doc/responseAdaptive.html | 33 - TrialSimulator-1.7.0/TrialSimulator/inst/doc/simulatePfsAndOs.Rmd | 2 TrialSimulator-1.7.0/TrialSimulator/inst/doc/simulatePfsAndOs.html | 6 TrialSimulator-1.7.0/TrialSimulator/man/Arms.Rd | 24 + TrialSimulator-1.7.0/TrialSimulator/man/Controllers.Rd | 24 + TrialSimulator-1.7.0/TrialSimulator/man/Endpoints.Rd | 21 + TrialSimulator-1.7.0/TrialSimulator/man/Trials.Rd | 50 ++ TrialSimulator-1.7.0/TrialSimulator/man/arm.Rd | 2 TrialSimulator-1.7.0/TrialSimulator/man/controller.Rd | 2 TrialSimulator-1.7.0/TrialSimulator/man/endpoint.Rd | 2 TrialSimulator-1.7.0/TrialSimulator/man/listener.Rd | 2 TrialSimulator-1.7.0/TrialSimulator/man/trial.Rd | 2 TrialSimulator-1.7.0/TrialSimulator/tests/testthat/test-trial.R | 180 ++++++++++ TrialSimulator-1.7.0/TrialSimulator/vignettes/actionFunctions.Rmd | 41 +- TrialSimulator-1.7.0/TrialSimulator/vignettes/defineLongitudinalEndpoints.Rmd | 2 TrialSimulator-1.7.0/TrialSimulator/vignettes/doseRanging.Rmd |only TrialSimulator-1.7.0/TrialSimulator/vignettes/responseAdaptive.Rmd | 83 ---- TrialSimulator-1.7.0/TrialSimulator/vignettes/simulatePfsAndOs.Rmd | 2 49 files changed, 709 insertions(+), 335 deletions(-)
More information about TrialSimulator at CRAN
Permanent link
Title: Identify Mutually Exclusive Mutations
Description: An optimized method for identifying mutually
exclusive genomic events. Its main contribution is a
statistical analysis based on the Poisson-Binomial
distribution that takes into account that some samples
are more mutated than others. See [Canisius, Sander, John WM Martens,
and Lodewyk FA Wessels. (2016) "A novel independence test for
somatic alterations in cancer shows that
biology drives mutual exclusivity but chance explains
most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>].
The mutations matrices are sparse matrices. The method developed takes
advantage of the advantages of this type of matrix to save
time and computing resources.
Author: Juan A. Ferrer-Bonsoms [aut, cre],
Laura Jareno [aut],
Angel Rubio [aut]
Maintainer: Juan A. Ferrer-Bonsoms <jafhernandez@tecnun.es>
This is a re-admission after prior archival of version 0.3.2 dated 2023-04-14
Diff between Rediscover versions 0.3.2 dated 2023-04-14 and 0.3.3 dated 2025-12-19
Rediscover-0.3.2/Rediscover/tests/runTests.R |only Rediscover-0.3.3/Rediscover/DESCRIPTION | 26 ++ Rediscover-0.3.3/Rediscover/MD5 | 23 +- Rediscover-0.3.3/Rediscover/NEWS.md | 4 Rediscover-0.3.3/Rediscover/R/discoversomaticInteractions.R | 7 Rediscover-0.3.3/Rediscover/R/getMutex.R | 3 Rediscover-0.3.3/Rediscover/R/getMutexAB.R | 2 Rediscover-0.3.3/Rediscover/build/vignette.rds |binary Rediscover-0.3.3/Rediscover/inst/doc/Rediscover.R | 16 - Rediscover-0.3.3/Rediscover/inst/doc/Rediscover.html | 105 ++++++++---- Rediscover-0.3.3/Rediscover/tests/testthat |only Rediscover-0.3.3/Rediscover/tests/testthat.R |only 12 files changed, 125 insertions(+), 61 deletions(-)
Title: Generates Raven-Like Matrices According to Rules
Description: Generates Raven like matrices according to different rules and the response list associated to the matrix.
The package can generate matrices composed of 4 or 9 cells, along with a response list of 11 elements (the correct response + 10 incorrect responses). The matrices can be generated according to both logical rules (i.e., the relationships between the elements in the matrix are manipulated to create the matrix) and visual-spatial rules (i.e., the visual or spatial characteristics of the elements are manipulated to generate the matrix).
The graphical elements of this package are based on the 'DescTools' package.
This package has been developed within the PRIN2020 Project (Prot. 20209WKCLL) titled "Computerized, Adaptive and Personalized Assessment of Executive Functions and Fluid Intelligence" and founded by the Italian Ministry of Education and Research.
Author: Andrea Brancaccio [aut, ctb, cph, cre],
Ottavia M. Epifania [aut, ctb, com],
Debora de Chiusole [ctb]
Maintainer: Andrea Brancaccio <andreabrancaccio01@gmail.com>
Diff between matRiks versions 0.1.4 dated 2025-12-19 and 0.1.5 dated 2025-12-19
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/draw.R | 13 ++++++++----- inst/doc/generate_matriks.html | 8 ++++---- man/draw.Rd | 3 +++ 6 files changed, 27 insertions(+), 20 deletions(-)
Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using Gaussian models, together with time-series power demand calculations.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marccanyigueral@gmail.com>
Diff between evsim versions 1.7.0 dated 2025-10-08 and 1.7.1 dated 2025-12-19
evsim-1.7.0/evsim/inst |only evsim-1.7.0/evsim/man/plot_ts.Rd |only evsim-1.7.1/evsim/DESCRIPTION | 10 +- evsim-1.7.1/evsim/MD5 | 20 ++-- evsim-1.7.1/evsim/NAMESPACE | 5 - evsim-1.7.1/evsim/NEWS.md | 8 + evsim-1.7.1/evsim/R/demand.R | 65 +-------------- evsim-1.7.1/evsim/R/simulation.R | 4 evsim-1.7.1/evsim/man/estimate_connection.Rd | 2 evsim-1.7.1/evsim/man/get_charging_rates_distribution.Rd | 2 evsim-1.7.1/evsim/man/get_demand.Rd | 4 evsim-1.7.1/evsim/man/get_occupancy.Rd | 6 - 12 files changed, 35 insertions(+), 91 deletions(-)
Title: Exploration and Visualisation of Skeletal Transcriptomics Data
Description: Allows search and visualisation of a collection of uniformly processed skeletal transcriptomic datasets. Includes methods to identify datasets where genes of interest are differentially expressed and find datasets with a similar gene expression pattern to a query dataset Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM (2019) <doi:10.1093/bioinformatics/bty947>.
Author: Jamie Soul [aut, cre, cph]
Maintainer: Jamie Soul <jamie.soul@liverpool.ac.uk>
Diff between SkeletalVis versions 0.1.1 dated 2025-05-06 and 0.1.2 dated 2025-12-19
DESCRIPTION | 6 - MD5 | 21 +++--- NEWS.md | 5 + R/load_skeletalvis.R | 108 ++++++++++++++++++++++++++------- README.md | 29 +++++--- build/partial.rdb |only build/vignette.rds |binary inst/doc/SkeletalVis.R | 10 +-- man/SkeletalVis-package.Rd | 2 man/figures/README-plotting-1.png |binary man/load_skeletalvis.Rd | 9 ++ tests/testthat/test-load_skeletalvis.R | 33 ++++++++++ 12 files changed, 170 insertions(+), 53 deletions(-)
Title: Fast Algorithms for Robust Slopes
Description: Fast algorithms for the Theil-Sen estimator,
Siegel's repeated median slope estimator, and Passing-Bablok regression.
The implementation is based on algorithms by
Dillencourt et. al (1992) <doi:10.1142/S0218195992000020> and Matousek et. al (1998) <doi:10.1007/PL00009190>.
The implementations are detailed in
Raymaekers (2023) <doi:10.32614/RJ-2023-012> and
Raymaekers J., Dufey F. (2022) <doi:10.48550/arXiv.2202.08060>.
All algorithms run in quasilinear time.
Author: Jakob Raymaekers [aut, cre]
Maintainer: Jakob Raymaekers <jakob.raymaekers@uantwerpen.be>
Diff between robslopes versions 1.1.3 dated 2023-04-27 and 1.1.4 dated 2025-12-19
DESCRIPTION | 19 ++++++++++++------- MD5 | 10 +++++----- src/HelpFunctions.cpp | 6 +++--- src/rcpparma_Passing_Bablok.cpp | 2 +- src/rcpparma_Theil_Sen.cpp | 2 +- src/rcpparma_repeated_median.cpp | 6 +++--- 6 files changed, 25 insertions(+), 20 deletions(-)
Title: Time Series Forecasting Functions
Description: Fundamental time series forecasting models such as autoregressive integrated moving average (ARIMA), exponential smoothing, and simple moving average are included. For ARIMA models, the output follows the traditional parameterisation by Box and Jenkins (1970, ISBN: 0816210942, 9780816210947). Furthermore, there are functions for detailed time series exploration and decomposition, respectively. All data and result visualisations are generated by 'ggplot2' instead of conventional R graphical output. For more details regarding the theoretical background of the models see Hyndman, R.J. and Athanasopoulos, G. (2021) <https://otexts.com/fpp3/>.
Author: Ka Yui Karl Wu [aut, cre]
Maintainer: Ka Yui Karl Wu <karlwuky@suss.edu.sg>
Diff between tsforecast versions 1.2.0 dated 2025-12-15 and 1.2.1 dated 2025-12-19
tsforecast-1.2.0/tsforecast/R/tsforecast_1.2.0.R |only tsforecast-1.2.1/tsforecast/DESCRIPTION | 6 +-- tsforecast-1.2.1/tsforecast/MD5 | 46 +++++++++++------------ tsforecast-1.2.1/tsforecast/R/tsforecast_1.2.1.R |only tsforecast-1.2.1/tsforecast/man/airport.Rd | 2 - tsforecast-1.2.1/tsforecast/man/is.outlier.Rd | 2 - tsforecast-1.2.1/tsforecast/man/predict.Rd | 2 - tsforecast-1.2.1/tsforecast/man/ts-functions.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsacf.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsarima.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsboxplot.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsconvert.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsdecomp.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsdiff.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsesm.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsexplore.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsforecast.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tshistogram.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tslag.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tslineplot.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsmltest.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsmodeleval.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsmovav.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsqqplot.Rd | 2 - tsforecast-1.2.1/tsforecast/man/tsscatterplot.Rd | 2 - 25 files changed, 47 insertions(+), 47 deletions(-)
Title: Density, Distribution, and Sampling Functions for Evidence
Accumulation Models
Description: Calculate the probability density functions (PDFs) for two threshold evidence
accumulation models (EAMs). These are defined using the following Stochastic
Differential Equation (SDE), dx(t) = v(x(t),t)*dt+D(x(t),t)*dW, where x(t) is
the accumulated evidence at time t, v(x(t),t) is the drift rate, D(x(t),t) is
the noise scale, and W is the standard Wiener process. The boundary conditions
of this process are the upper and lower decision thresholds, represented by b_u(t)
and b_l(t), respectively. Upper threshold b_u(t) > 0, while lower threshold b_l(t) < 0.
The initial condition of this process x(0) = z where b_l(t) < z < b_u(t). We
represent this as the relative start point w = z/(b_u(0)-b_l(0)), defined as
a ratio of the initial threshold location. This package generates the PDF using
the same approach as the 'python' package it is based upon, 'PyBEAM' by Murrow and Holmes
(2023) <doi:10.3758/s13428-023-02162-w>. First, it converts the SDE model into the
forwards Fokke [...truncated...]
Author: Raphael Hartmann [aut, cre] ,
Matthew Murrow [aut]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between ream versions 1.0-9 dated 2025-12-18 and 1.0-10 dated 2025-12-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/guideline.html | 4 ++-- src/R_wrapper.cpp | 4 ++-- src/ream_init.c | 6 +++--- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Panel Evaluation in Forensic Kinship Analysis
Description: Evaluate specific panels in different aspects: i) Simulation tools related to pedigree researches; ii) calculation for systemic effectiveness indicators, such as probability of exclusion (PE).
Author: Guanju Ma [aut, cre],
Shujin Li [ctb]
Maintainer: Guanju Ma <guanjuma@hebmu.edu.cn>
Diff between KINSIMU versions 0.1.2-2 dated 2024-06-13 and 0.1.3 dated 2025-12-19
DESCRIPTION | 14 ++-- MD5 | 42 ++++++------ NEWS.md | 10 ++ R/EvaluatePanel.R | 2 R/IICAL.R | 5 + R/LRgpgcam.R | 5 + R/LRhsip.R | 5 + R/LRparas.R | 6 + R/logLR.R | 11 ++- R/pedisimu.R | 2 R/testsimulation.R | 2 R/trioPI.R | 2 build/vignette.rds |binary inst/doc/Instruction_of_functions_of_R_package_KINSIMU.Rnw | 7 +- inst/doc/Instruction_of_functions_of_R_package_KINSIMU.pdf |binary man/IICAL.Rd | 2 man/LRgpgcam.Rd | 2 man/LRhsip.Rd | 2 man/LRparas.Rd | 3 man/logLR.Rd | 2 man/testsimulation.Rd | 2 vignettes/Instruction_of_functions_of_R_package_KINSIMU.Rnw | 7 +- 22 files changed, 83 insertions(+), 50 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.7.0 dated 2025-11-21 and 1.7.1 dated 2025-12-19
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/period-class.R | 2 +- tests/testthat/test-period.R | 2 -- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Rmetrics - Modelling Trends and Unit Roots
Description: Provides four addons for analyzing trends and
unit roots in financial time series: (i) functions for the density
and probability of the augmented Dickey-Fuller Test, (ii) functions
for the density and probability of MacKinnon's unit root test
statistics, (iii) reimplementations for the ADF and MacKinnon
Test, and (iv) an 'urca' Unit Root Test Interface for Pfaff's
unit root test suite.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fUnitRoots versions 4040.81 dated 2024-05-15 and 4052.82 dated 2025-12-19
DESCRIPTION | 22 +-- MD5 | 14 +- NEWS.md | 9 + inst/_pkgdown.yml |only inst/pkgdown.yml |only man/DickeyFullerPValues.Rd | 137 ++++++++++----------- man/MacKinnonPValues.Rd | 160 +++++++++++------------- man/UnitrootTests.Rd | 182 +++++++++++----------------- man/UnitrootUrcaInterface.Rd | 276 +++++++++++++++++++------------------------ 9 files changed, 366 insertions(+), 434 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.1.0 dated 2025-10-30 and 1.1.1 dated 2025-12-19
DESCRIPTION | 13 MD5 | 62 +- NAMESPACE | 4 NEWS.md | 18 R/baseline_table.R | 41 - R/check_nonnum.R | 3 R/classif_model_compare.R | 4 R/extract_num.R | 9 R/initial_cleaning.R | 12 R/misc.R | 14 R/regressions.R | 2 R/subject_standardize.R | 2 R/time_roc.R |only R/unit_standardize.R | 33 + R/utils.R | 4 README.md | 10 man/baseline_table.Rd | 2 man/calc_cindex.Rd |only man/df_view_nonnum.Rd | 2 man/figures/README-example_3.7-2.png |binary man/figures/README-example_3.7-3.png |binary man/figures/README-example_3.7-4.png |only man/time_roc_plot.Rd |only man/unit_standardize.Rd | 32 - man/value_initial_cleaning.Rd | 5 man/vec2code.Rd | 10 tests/testthat/_snaps/classif_model_compare.md | 20 tests/testthat/_snaps/classif_model_compare/pr-plot.svg | 5 tests/testthat/_snaps/interactions.md | 54 +- tests/testthat/_snaps/rcs_plot.md | 80 +-- tests/testthat/_snaps/regressions.md | 372 ++++++++-------- tests/testthat/_snaps/time_roc |only tests/testthat/test-misc.R | 8 tests/testthat/test-time_roc.R |only 34 files changed, 466 insertions(+), 355 deletions(-)
Title: Causal Inference with Continuous (Multiple Time Point)
Interventions
Description: Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.
Author: Michael Schomaker [aut, cre],
Leo Fuhrhop [ctb],
Han Bao [ctb]
Maintainer: Michael Schomaker <michael.schomaker@stat.uni-muenchen.de>
Diff between CICI versions 0.9.6 dated 2025-07-21 and 0.9.7 dated 2025-12-19
CICI-0.9.6/CICI/R/contrast.R |only CICI-0.9.6/CICI/R/print.contrastResult.R |only CICI-0.9.7/CICI/DESCRIPTION | 19 - CICI-0.9.7/CICI/MD5 | 34 +- CICI-0.9.7/CICI/NAMESPACE | 23 + CICI-0.9.7/CICI/R/contrast.r |only CICI-0.9.7/CICI/R/custom.measure.r | 67 ++-- CICI-0.9.7/CICI/R/feasible.r |only CICI-0.9.7/CICI/R/gformula.r | 97 +++--- CICI-0.9.7/CICI/R/helper.r | 470 ++++++++++++++++++++++++++++++- CICI-0.9.7/CICI/R/mi.boot.r | 108 +++++-- CICI-0.9.7/CICI/R/plot.feasible.r |only CICI-0.9.7/CICI/R/plot.gformula.r | 26 - CICI-0.9.7/CICI/R/print.contrastResult.r |only CICI-0.9.7/CICI/R/print.feasible.R |only CICI-0.9.7/CICI/R/summary.feasible.R |only CICI-0.9.7/CICI/man/CICI-package.Rd | 7 CICI-0.9.7/CICI/man/custom.measure.Rd | 4 CICI-0.9.7/CICI/man/feasible.Rd |only CICI-0.9.7/CICI/man/gformula.Rd | 5 CICI-0.9.7/CICI/man/mi.boot.Rd | 3 CICI-0.9.7/CICI/man/plot.feasible.Rd |only CICI-0.9.7/CICI/man/print.feasible.Rd |only CICI-0.9.7/CICI/man/summary.feasible.Rd |only 24 files changed, 716 insertions(+), 147 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.8.0 dated 2025-12-10 and 0.8.1 dated 2025-12-19
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 12 ++++++++++++ R/combine_answers.R | 17 +++++++++++++++++ R/gtsummary_themes.R | 8 ++++---- R/plot_multiple_answers.R | 6 ++++-- R/plot_trajectories.R | 3 ++- man/combine_answers.Rd | 5 +++++ tests/testthat/test-plot_multiple_answers.R | 28 +++++++++++++++++++++++++++- 9 files changed, 82 insertions(+), 19 deletions(-)
Title: Build a Metric Subspaces Data Model for a Data Source
Description: Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.
Author: Werner Mueller [aut, cre]
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganDataModel versions 1.1.7 dated 2024-07-21 and 2.0.1 dated 2025-12-19
DESCRIPTION | 13 - MD5 | 37 ++-- R/RcppExports.R | 26 ++ R/dmBuildMetricSubspaces.R | 51 ++--- R/dmEvaluate.R | 118 +++++------- R/dmPlotMetricSubspaces.R | 86 ++++----- R/dmTrain.R | 230 +++++++++++++++--------- R/keras_zip_lists.R |only man/dmBuildMetricSubspaces.Rd | 2 man/dmCalculateDensityValue.Rd | 2 man/dmGetContainedInMetricSubspaces.Rd | 2 man/dmPlotMetricSubspaceParameters.Rd | 2 man/dmPlotMetricSubspaces.Rd | 4 man/dmRemoveMetricSubspaces.Rd | 2 man/dmTrain.Rd | 7 man/ganDataModel-package.Rd | 37 ++-- src/RcppExports.cpp | 73 +++++++ src/dataModel.h | 107 +++++++---- src/dmInt.cpp | 273 +++++++++++++++++++---------- src/volumeElementGraph.h | 305 ++++++++++++++++++--------------- 20 files changed, 834 insertions(+), 543 deletions(-)
Title: qPCR Data Analysis
Description: Amplification efficiency estimation, statistical analysis, and graphical representation of quantitative real-time PCR (qPCR) data using one or more specified reference genes is handled by 'rtpcr' package. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to analyse the relative expression (Delta Delta Ct method or Delta Ct method). The functions further provide standard errors and confidence intervals for means, apply statistical mean comparisons and present significance.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 2.0.5 dated 2025-12-12 and 2.1.0 dated 2025-12-19
rtpcr-2.0.5/rtpcr/data/Taylor_etal2019.rda |only rtpcr-2.0.5/rtpcr/data/data_ttest.rda |only rtpcr-2.0.5/rtpcr/inst/extdata/Taylor_etal2019.csv |only rtpcr-2.0.5/rtpcr/inst/extdata/data_ttest.csv |only rtpcr-2.0.5/rtpcr/man/Taylor_etal2019.Rd |only rtpcr-2.0.5/rtpcr/man/data_ttest.Rd |only rtpcr-2.1.0/rtpcr/DESCRIPTION | 8 rtpcr-2.1.0/rtpcr/MD5 | 108 - rtpcr-2.1.0/rtpcr/R/ANOVA_DCt.r | 266 +-- rtpcr-2.1.0/rtpcr/R/ANOVA_DDCt.r | 383 ++--- rtpcr-2.1.0/rtpcr/R/Means_DDCt.r | 96 - rtpcr-2.1.0/rtpcr/R/REPEATED_DDCt.r | 349 ++-- rtpcr-2.1.0/rtpcr/R/TTEST_DDCt.r | 527 ++++--- rtpcr-2.1.0/rtpcr/R/efficiency.r | 50 rtpcr-2.1.0/rtpcr/R/globalVariables.r | 5 rtpcr-2.1.0/rtpcr/R/meanTech.r | 48 rtpcr-2.1.0/rtpcr/R/multiplot.r | 77 - rtpcr-2.1.0/rtpcr/R/package_data.r | 112 + rtpcr-2.1.0/rtpcr/R/plotOneFactor.r | 174 +- rtpcr-2.1.0/rtpcr/R/plotThreeFactor.r | 256 ++- rtpcr-2.1.0/rtpcr/R/plotTwoFactor.r | 264 ++- rtpcr-2.1.0/rtpcr/R/qpcrhlpr.r | 216 ++ rtpcr-2.1.0/rtpcr/data/data_1factor_Two_ref.rda |only rtpcr-2.1.0/rtpcr/data/data_1factor_one_ref.rda |only rtpcr-2.1.0/rtpcr/data/data_1factor_one_ref_Eff.rda |only rtpcr-2.1.0/rtpcr/data/data_2factor3ref.rda |only rtpcr-2.1.0/rtpcr/data/data_2factorBlock.rda |binary rtpcr-2.1.0/rtpcr/data/data_2factorBlock3ref.rda |only rtpcr-2.1.0/rtpcr/inst/doc/vignette.R | 308 +++- rtpcr-2.1.0/rtpcr/inst/doc/vignette.Rmd | 401 ++++- rtpcr-2.1.0/rtpcr/inst/doc/vignette.html | 865 +++++++++--- rtpcr-2.1.0/rtpcr/inst/extdata/data_1factor_Two_ref.csv |only rtpcr-2.1.0/rtpcr/inst/extdata/data_1factor_one_ref.csv |only rtpcr-2.1.0/rtpcr/inst/extdata/data_1factor_one_ref_Eff.csv |only rtpcr-2.1.0/rtpcr/inst/extdata/data_2factor3ref.csv |only rtpcr-2.1.0/rtpcr/inst/extdata/data_2factorBlock.csv | 36 rtpcr-2.1.0/rtpcr/inst/extdata/data_2factorBlock3ref.csv |only rtpcr-2.1.0/rtpcr/man/ANOVA_DCt.Rd | 115 - rtpcr-2.1.0/rtpcr/man/ANOVA_DDCt.Rd | 201 +- rtpcr-2.1.0/rtpcr/man/Means_DDCt.Rd | 59 rtpcr-2.1.0/rtpcr/man/REPEATED_DDCt.Rd | 98 - rtpcr-2.1.0/rtpcr/man/TTEST_DDCt.Rd | 127 + rtpcr-2.1.0/rtpcr/man/data_1factor.Rd | 2 rtpcr-2.1.0/rtpcr/man/data_1factor_Two_ref.Rd |only rtpcr-2.1.0/rtpcr/man/data_1factor_one_ref.Rd |only rtpcr-2.1.0/rtpcr/man/data_1factor_one_ref_Eff.Rd |only rtpcr-2.1.0/rtpcr/man/data_2factor.Rd | 2 rtpcr-2.1.0/rtpcr/man/data_2factor3ref.Rd |only rtpcr-2.1.0/rtpcr/man/data_2factorBlock.Rd | 2 rtpcr-2.1.0/rtpcr/man/data_2factorBlock3ref.Rd |only rtpcr-2.1.0/rtpcr/man/data_3factor.Rd | 2 rtpcr-2.1.0/rtpcr/man/efficiency.Rd | 34 rtpcr-2.1.0/rtpcr/man/meanTech.Rd | 27 rtpcr-2.1.0/rtpcr/man/multiplot.Rd | 55 rtpcr-2.1.0/rtpcr/man/plotOneFactor.Rd | 78 - rtpcr-2.1.0/rtpcr/man/plotThreeFactor.Rd | 113 + rtpcr-2.1.0/rtpcr/man/plotTwoFactor.Rd | 121 + rtpcr-2.1.0/rtpcr/vignettes/vignette.Rmd | 401 ++++- rtpcr-2.1.0/rtpcr/vignettes/vignette_files |only 59 files changed, 4133 insertions(+), 1853 deletions(-)
Title: Gamma and Exponential Generalized Linear Models with Elastic Net
Penalty
Description: Implements the fast iterative shrinkage-thresholding algorithm
(FISTA) algorithm to fit a Gamma distribution with an elastic net
penalty as described in Chen, Arakvin and Martin (2018)
<doi:10.48550/arXiv.1804.07780>. An implementation for the case of the
exponential distribution is also available, with details available
in Chen and Martin (2018) <doi:10.2139/ssrn.3085672>.
Author: Anthony Christidis [aut, cre],
Xin Chen [aut],
Daniel Hanson [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
This is a re-admission after prior archival of version 1.1.3 dated 2025-03-30
Diff between RPEGLMEN versions 1.1.3 dated 2025-03-30 and 1.1.4 dated 2025-12-19
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 8 +++++++- R/glmGammaNet.R | 27 +++++++++++++++------------ R/glmnet_exp.R | 27 +++++++++++++++------------ man/fit.glmGammaNet.Rd | 26 +++++++++++++++----------- man/glmnet_exp.Rd | 26 +++++++++++++++----------- 7 files changed, 78 insertions(+), 58 deletions(-)
Title: A 'Shiny' App for Reliability Analysis
Description: An interactive web application for reliability analysis using the 'shiny' <https://shiny.posit.co/> framework. The app provides an easy-to-use interface for performing reliability analysis using 'WeibullR' <https://cran.r-project.org/package=WeibullR> and 'ReliaGrowR' <https://cran.r-project.org/package=ReliaGrowR>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
This is a re-admission after prior archival of version 0.4 dated 2025-11-11
Diff between ReliaShiny versions 0.4 dated 2025-11-11 and 0.4.1 dated 2025-12-19
DESCRIPTION | 9 ++++----- MD5 | 3 ++- inst/paper |only 3 files changed, 6 insertions(+), 6 deletions(-)
Title: A Unified Pipeline for Pupillometry Data
Description: Provides a unified pipeline to clean, prepare, plot,
and run basic analyses on pupillometry experiments.
Author: Samuel Forbes [aut, cre],
David Robinson [ctb]
Maintainer: Samuel Forbes <samuel.h.forbes@gmail.com>
This is a re-admission after prior archival of version 0.0.6 dated 2025-11-10
Diff between PupillometryR versions 0.0.6 dated 2025-11-10 and 0.0.7 dated 2025-12-19
DESCRIPTION | 8 - MD5 | 12 +- README.md | 11 ++ inst/doc/PupillometryR.R | 44 +++++----- inst/doc/PupillometryR.Rmd | 48 ++++++----- inst/doc/PupillometryR.html | 180 +++++++++++++++++++++----------------------- vignettes/PupillometryR.Rmd | 48 ++++++----- 7 files changed, 178 insertions(+), 173 deletions(-)
Title: Data Language Engine for 'knitr' / 'rmarkdown'
Description: Implements a data language engine for incorporating data directly in
'rmarkdown' documents so that they can be made completely standalone.
Author: David M. Kaplan [aut, cre, cph]
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>
This is a re-admission after prior archival of version 0.6.1 dated 2020-12-08
Diff between knitrdata versions 0.6.1 dated 2020-12-08 and 0.6.2 dated 2025-12-19
DESCRIPTION | 17 MD5 | 26 NEWS.md | 6 R/data_engine.R | 88 + README.md | 5 build/vignette.rds |binary inst/doc/data_language_engine_vignette.Rmd | 2 inst/doc/data_language_engine_vignette.html | 1542 +++++++++++++++++----------- man/create_chunk.Rd | 6 man/create_data_chunk_dialog.Rd | 6 man/data_decode.Rd | 6 man/is.file.binary.Rd | 6 man/list_rmd_chunks.Rd | 12 vignettes/data_language_engine_vignette.Rmd | 2 14 files changed, 1079 insertions(+), 645 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short
cgeneric, to define a Gaussian Markov random (GMRF) model.
The cgeneric contain code to specify GMRF elements such as
the graph and the precision matrix, and also the initial and
prior for its parameters, useful for model inference.
It can be accessed from a C program and is the recommended
way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>).
The 'INLAtools' implement functions to evaluate
each one of the model specifications from R.
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
A very useful functionality is the Kronecker product method
that creates a new model from multiple cgeneric models.
It also works with the rgeneric, the R version of the
cgeneric intended to easy try implementation of new GMRF models.
The Kronecker between two cgeneric models was used in
Sterr [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.0.5 dated 2025-11-20 and 0.0.6 dated 2025-12-19
DESCRIPTION | 6 ++--- MD5 | 13 ++++++------ R/cgeneric.R | 16 ++++++++------- R/cgeneric_utils.R | 56 ++++++++++++++++++++++++++--------------------------- demo/00Index | 1 demo/cgeneric.R | 9 ++++++-- demo/kronecker.R | 6 +++-- demo/minimal.R |only 8 files changed, 59 insertions(+), 48 deletions(-)
Title: Estimate Latent Classes on a Mixture of Continuous and
Dichotomous Data
Description: EQ-5D value set estimation can be done using the hybrid model likelihood as described by
Oppe and van Hout (2010) <doi:10.1002/hec.3560> and Ramos-Goñi et al. (2017) <doi:10.1097/MLR.0000000000000283>.
The package is based on 'flexmix' and among others contains an M-step-driver as described by Leisch (2004) <doi:10.18637/jss.v011.i08>.
Users can estimate latent classes and address preference heterogeneity. Both uncensored and censored data are supported.
Furthermore, heteroscedasticity can be taken into account. It is possible to control for different covariates on the continuous and dichotomous parts of the data and start values can differ
between the expected latent classes.
Author: Svenja Elkenkamp [aut, cre],
Kim Rand [aut],
John Grosser [aut],
EuroQol [fnd]
Maintainer: Svenja Elkenkamp <svenja.elkenkamp@uni-bielefeld.de>
Diff between hyreg2 versions 1.0.0 dated 2025-10-06 and 1.1.0 dated 2025-12-19
hyreg2-1.0.0/hyreg2/man/give_id.Rd |only hyreg2-1.1.0/hyreg2/DESCRIPTION | 13 hyreg2-1.1.0/hyreg2/MD5 | 49 + hyreg2-1.1.0/hyreg2/NAMESPACE | 2 hyreg2-1.1.0/hyreg2/NEWS.md |only hyreg2-1.1.0/hyreg2/R/FLXMRhyreg.R | 202 +++++-- hyreg2-1.1.0/hyreg2/R/FLXMRhyreg_het.R | 82 +-- hyreg2-1.1.0/hyreg2/R/data.R | 35 - hyreg2-1.1.0/hyreg2/R/helper_functions.R |only hyreg2-1.1.0/hyreg2/R/hyreg2.R | 584 +++++++++++++---------- hyreg2-1.1.0/hyreg2/R/hyreg2_het.R | 59 -- hyreg2-1.1.0/hyreg2/R/plot_hyreg2.R | 50 - hyreg2-1.1.0/hyreg2/build |only hyreg2-1.1.0/hyreg2/data/simulated_data_norm.rda |binary hyreg2-1.1.0/hyreg2/inst |only hyreg2-1.1.0/hyreg2/man/FLXMRhyreg.Rd | 6 hyreg2-1.1.0/hyreg2/man/get_stv.Rd | 2 hyreg2-1.1.0/hyreg2/man/give_class.Rd |only hyreg2-1.1.0/hyreg2/man/hyreg2.Rd | 28 - hyreg2-1.1.0/hyreg2/man/hyreg2_het.Rd | 8 hyreg2-1.1.0/hyreg2/man/plot_hyreg2.Rd | 23 hyreg2-1.1.0/hyreg2/man/simulated_data.Rd | 86 +-- hyreg2-1.1.0/hyreg2/man/simulated_data_mo.Rd | 66 +- hyreg2-1.1.0/hyreg2/man/simulated_data_norm.Rd | 67 +- hyreg2-1.1.0/hyreg2/man/summary_hyreg2.Rd | 7 hyreg2-1.1.0/hyreg2/vignettes |only 26 files changed, 785 insertions(+), 584 deletions(-)
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for
number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/>
and GNU 'MP' <https://gmplib.org/> with support for operations on
standard rings (the integers, the integers modulo n, finite
fields, the rational, p-adic, real, and complex numbers) as well
as matrices and polynomials over rings. 'FLINT' implements
midpoint-radius interval arithmetic, also known as ball
arithmetic, in the real and complex numbers, enabling computation
in arbitrary precision with rigorous propagation of rounding and
other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>.
Finally, 'FLINT' provides ball arithmetic implementations of many
special mathematical functions, with high coverage of reference
works such as the NIST Digital Library of Mathematical Functions
<https://dlmf.nist.gov/>. The R interface defines S4 classes,
generic functions, and methods for representation and basic
operations as [...truncated...]
Author: Mikael Jagan [aut, cre] ,
Martin Maechler [ctb]
Maintainer: Mikael Jagan <jaganmn2@gmail.com>
Diff between flint versions 0.1.3 dated 2025-12-18 and 0.1.4 dated 2025-12-19
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS.Rd | 14 ++++++++++++++ src/acb.c | 7 +++++++ src/acf.c | 10 ++++++++++ src/arb.c | 6 ++++++ src/arf.c | 8 ++++++++ src/flint.h | 5 +++-- src/fmpq.c | 6 ++++++ src/fmpz.c | 8 ++++++++ src/mag.c | 7 +++++++ src/slong.c | 8 ++++++++ src/ulong.c | 8 ++++++++ src/utils.c | 20 +++++++++++++------- 16 files changed, 127 insertions(+), 38 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: The 'abn' R package facilitates Bayesian network analysis, a
probabilistic graphical model that derives from empirical data a
directed acyclic graph (DAG). This DAG describes the dependency
structure between random variables. The R package 'abn' provides
routines to help determine optimal Bayesian network models for a given
data set. These models are used to identify statistical dependencies
in messy, complex data. Their additive formulation is equivalent to
multivariate generalised linear modelling, including mixed models with
independent and identically distributed (iid) random effects. The core
functionality of the 'abn' package revolves around model selection,
also known as structure discovery. It supports both exact and
heuristic structure learning algorithms and does not restrict the data
distribution of parent-child combinations, providing flexibility in
model creation and analysis. The 'abn' package uses Laplace
approximations for metric estimation and includes wrappers to the
[...truncated...]
Author: Matteo Delucchi [aut, cre] ,
Reinhard Furrer [aut] ,
Gilles Kratzer [aut] ,
Fraser Iain Lewis [aut] ,
Jonas I. Liechti [ctb] ,
Marta Pittavino [ctb] ,
Kalina Cherneva [ctb]
Maintainer: Matteo Delucchi <matteo.delucchi@math.uzh.ch>
Diff between abn versions 3.1.12 dated 2025-11-25 and 3.1.13 dated 2025-12-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 2 +- configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/mixed_effect_BN_model.html | 2 +- src/mostprobable.c | 1 - 7 files changed, 22 insertions(+), 23 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single
value. 'tidyr' contains tools for changing the shape (pivoting) and
hierarchy (nesting and 'unnesting') of a dataset, turning deeply
nested lists into rectangular data frames ('rectangling'), and
extracting values out of string columns. It also includes tools for
working with missing values (both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Davis Vaughan [aut],
Maximilian Girlich [aut],
Kevin Ushey [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between tidyr versions 1.3.1 dated 2024-01-24 and 1.3.2 dated 2025-12-19
tidyr-1.3.1/tidyr/R/compat-lazyeval.R |only tidyr-1.3.1/tidyr/R/compat-obj-type.R |only tidyr-1.3.1/tidyr/R/compat-types-check.R |only tidyr-1.3.1/tidyr/vignettes/classroom.csv |only tidyr-1.3.1/tidyr/vignettes/classroom2.csv |only tidyr-1.3.2/tidyr/DESCRIPTION | 17 tidyr-1.3.2/tidyr/MD5 | 302 +++++------ tidyr-1.3.2/tidyr/NEWS.md | 309 ++++++----- tidyr-1.3.2/tidyr/R/append.R | 3 tidyr-1.3.2/tidyr/R/chop.R | 60 +- tidyr-1.3.2/tidyr/R/complete.R | 79 --- tidyr-1.3.2/tidyr/R/data.R | 13 tidyr-1.3.2/tidyr/R/dep-extract.R | 4 tidyr-1.3.2/tidyr/R/dep-lazyeval.R | 128 +++- tidyr-1.3.2/tidyr/R/doc-params.R | 29 - tidyr-1.3.2/tidyr/R/drop-na.R | 12 tidyr-1.3.2/tidyr/R/expand.R | 101 +-- tidyr-1.3.2/tidyr/R/extract.R | 38 + tidyr-1.3.2/tidyr/R/fill.R | 54 +- tidyr-1.3.2/tidyr/R/gather.R | 29 - tidyr-1.3.2/tidyr/R/hoist.R | 20 tidyr-1.3.2/tidyr/R/id.R | 1 tidyr-1.3.2/tidyr/R/import-standalone-lazyeval.R |only tidyr-1.3.2/tidyr/R/import-standalone-obj-type.R |only tidyr-1.3.2/tidyr/R/import-standalone-types-check.R |only tidyr-1.3.2/tidyr/R/nest-legacy.R | 41 + tidyr-1.3.2/tidyr/R/nest.R | 112 ++-- tidyr-1.3.2/tidyr/R/pack.R | 34 - tidyr-1.3.2/tidyr/R/pivot-long.R | 192 ++++--- tidyr-1.3.2/tidyr/R/pivot-wide.R | 240 +++++---- tidyr-1.3.2/tidyr/R/replace_na.R | 22 tidyr-1.3.2/tidyr/R/separate-longer.R | 29 - tidyr-1.3.2/tidyr/R/separate-rows.R | 17 tidyr-1.3.2/tidyr/R/separate-wider.R | 335 +++++++------ tidyr-1.3.2/tidyr/R/separate.R | 82 ++- tidyr-1.3.2/tidyr/R/seq.R | 8 tidyr-1.3.2/tidyr/R/spread.R | 40 + tidyr-1.3.2/tidyr/R/tidyr.R | 1 tidyr-1.3.2/tidyr/R/uncount.R | 7 tidyr-1.3.2/tidyr/R/unite.R | 61 +- tidyr-1.3.2/tidyr/R/unnest-auto.R | 3 tidyr-1.3.2/tidyr/R/unnest-helper.R | 29 - tidyr-1.3.2/tidyr/R/unnest-longer.R | 77 +- tidyr-1.3.2/tidyr/R/unnest-wider.R | 63 +- tidyr-1.3.2/tidyr/R/unnest.R | 97 ++- tidyr-1.3.2/tidyr/R/utils.R | 69 ++ tidyr-1.3.2/tidyr/README.md | 4 tidyr-1.3.2/tidyr/build/vignette.rds |binary tidyr-1.3.2/tidyr/inst/doc/in-packages.R | 178 +++--- tidyr-1.3.2/tidyr/inst/doc/in-packages.Rmd | 90 +-- tidyr-1.3.2/tidyr/inst/doc/in-packages.html | 59 +- tidyr-1.3.2/tidyr/inst/doc/nest.R | 18 tidyr-1.3.2/tidyr/inst/doc/nest.Rmd | 20 tidyr-1.3.2/tidyr/inst/doc/nest.html | 33 - tidyr-1.3.2/tidyr/inst/doc/pivot.R | 264 +++++----- tidyr-1.3.2/tidyr/inst/doc/pivot.Rmd | 255 ++++----- tidyr-1.3.2/tidyr/inst/doc/pivot.html | 327 ++++++------ tidyr-1.3.2/tidyr/inst/doc/programming.R | 2 tidyr-1.3.2/tidyr/inst/doc/programming.Rmd | 30 - tidyr-1.3.2/tidyr/inst/doc/programming.html | 7 tidyr-1.3.2/tidyr/inst/doc/rectangle.R | 110 ++-- tidyr-1.3.2/tidyr/inst/doc/rectangle.Rmd | 126 ++-- tidyr-1.3.2/tidyr/inst/doc/rectangle.html | 117 ++-- tidyr-1.3.2/tidyr/inst/doc/tidy-data.R | 77 +- tidyr-1.3.2/tidyr/inst/doc/tidy-data.Rmd | 87 +-- tidyr-1.3.2/tidyr/inst/doc/tidy-data.html | 155 +++--- tidyr-1.3.2/tidyr/man/chop.Rd | 14 tidyr-1.3.2/tidyr/man/cms_patient_experience.Rd | 10 tidyr-1.3.2/tidyr/man/complete.Rd | 12 tidyr-1.3.2/tidyr/man/drop_na.Rd | 6 tidyr-1.3.2/tidyr/man/expand.Rd | 48 - tidyr-1.3.2/tidyr/man/expand_grid.Rd | 44 - tidyr-1.3.2/tidyr/man/extract.Rd | 8 tidyr-1.3.2/tidyr/man/fill.Rd | 33 - tidyr-1.3.2/tidyr/man/gather.Rd | 6 tidyr-1.3.2/tidyr/man/hoist.Rd | 6 tidyr-1.3.2/tidyr/man/nest.Rd | 40 - tidyr-1.3.2/tidyr/man/nest_legacy.Rd | 14 tidyr-1.3.2/tidyr/man/pack.Rd | 14 tidyr-1.3.2/tidyr/man/pivot_longer.Rd | 10 tidyr-1.3.2/tidyr/man/pivot_longer_spec.Rd | 6 tidyr-1.3.2/tidyr/man/pivot_wider.Rd | 16 tidyr-1.3.2/tidyr/man/pivot_wider_spec.Rd | 8 tidyr-1.3.2/tidyr/man/relig_income.Rd | 2 tidyr-1.3.2/tidyr/man/replace_na.Rd | 10 tidyr-1.3.2/tidyr/man/separate.Rd | 22 tidyr-1.3.2/tidyr/man/separate_longer_delim.Rd | 10 tidyr-1.3.2/tidyr/man/separate_rows.Rd | 2 tidyr-1.3.2/tidyr/man/separate_wider_delim.Rd | 24 tidyr-1.3.2/tidyr/man/spread.Rd | 18 tidyr-1.3.2/tidyr/man/tidyr_data_masking.Rd | 24 tidyr-1.3.2/tidyr/man/tidyr_tidy_select.Rd | 4 tidyr-1.3.2/tidyr/man/unite.Rd | 8 tidyr-1.3.2/tidyr/man/unnest.Rd | 20 tidyr-1.3.2/tidyr/man/unnest_longer.Rd | 16 tidyr-1.3.2/tidyr/man/unnest_wider.Rd | 16 tidyr-1.3.2/tidyr/src/melt.cpp | 48 - tidyr-1.3.2/tidyr/tests/testthat/_snaps/append.md | 5 tidyr-1.3.2/tidyr/tests/testthat/_snaps/chop.md | 30 - tidyr-1.3.2/tidyr/tests/testthat/_snaps/drop-na.md | 14 tidyr-1.3.2/tidyr/tests/testthat/_snaps/expand.md | 25 tidyr-1.3.2/tidyr/tests/testthat/_snaps/extract.md | 35 - tidyr-1.3.2/tidyr/tests/testthat/_snaps/fill.md | 29 + tidyr-1.3.2/tidyr/tests/testthat/_snaps/gather.md | 45 + tidyr-1.3.2/tidyr/tests/testthat/_snaps/hoist.md | 51 + tidyr-1.3.2/tidyr/tests/testthat/_snaps/nest-legacy.md | 15 tidyr-1.3.2/tidyr/tests/testthat/_snaps/pack.md | 6 tidyr-1.3.2/tidyr/tests/testthat/_snaps/pivot-long.md | 169 +++--- tidyr-1.3.2/tidyr/tests/testthat/_snaps/pivot-wide.md | 192 ++++--- tidyr-1.3.2/tidyr/tests/testthat/_snaps/pivot.md | 25 tidyr-1.3.2/tidyr/tests/testthat/_snaps/replace_na.md | 15 tidyr-1.3.2/tidyr/tests/testthat/_snaps/separate-longer.md | 21 tidyr-1.3.2/tidyr/tests/testthat/_snaps/separate-rows.md | 3 tidyr-1.3.2/tidyr/tests/testthat/_snaps/separate-wider.md | 92 ++- tidyr-1.3.2/tidyr/tests/testthat/_snaps/separate.md | 17 tidyr-1.3.2/tidyr/tests/testthat/_snaps/seq.md | 10 tidyr-1.3.2/tidyr/tests/testthat/_snaps/spread.md | 5 tidyr-1.3.2/tidyr/tests/testthat/_snaps/unnest-helper.md | 66 +- tidyr-1.3.2/tidyr/tests/testthat/_snaps/unnest-longer.md | 51 - tidyr-1.3.2/tidyr/tests/testthat/_snaps/unnest-wider.md | 14 tidyr-1.3.2/tidyr/tests/testthat/_snaps/unnest.md | 34 - tidyr-1.3.2/tidyr/tests/testthat/test-append.R | 2 tidyr-1.3.2/tidyr/tests/testthat/test-chop.R | 64 +- tidyr-1.3.2/tidyr/tests/testthat/test-complete.R | 3 tidyr-1.3.2/tidyr/tests/testthat/test-drop-na.R | 13 tidyr-1.3.2/tidyr/tests/testthat/test-expand.R | 60 +- tidyr-1.3.2/tidyr/tests/testthat/test-extract.R | 39 - tidyr-1.3.2/tidyr/tests/testthat/test-fill.R | 48 + tidyr-1.3.2/tidyr/tests/testthat/test-gather.R | 39 - tidyr-1.3.2/tidyr/tests/testthat/test-hoist.R | 98 ++- tidyr-1.3.2/tidyr/tests/testthat/test-nest-legacy.R | 95 ++- tidyr-1.3.2/tidyr/tests/testthat/test-nest.R | 11 tidyr-1.3.2/tidyr/tests/testthat/test-pack.R | 24 tidyr-1.3.2/tidyr/tests/testthat/test-pivot-long.R | 196 ++++--- tidyr-1.3.2/tidyr/tests/testthat/test-pivot-wide.R | 263 +++++++--- tidyr-1.3.2/tidyr/tests/testthat/test-pivot.R | 12 tidyr-1.3.2/tidyr/tests/testthat/test-replace_na.R | 6 tidyr-1.3.2/tidyr/tests/testthat/test-separate-longer.R | 16 tidyr-1.3.2/tidyr/tests/testthat/test-separate-rows.R | 18 tidyr-1.3.2/tidyr/tests/testthat/test-separate-wider.R | 192 ++++--- tidyr-1.3.2/tidyr/tests/testthat/test-separate.R | 20 tidyr-1.3.2/tidyr/tests/testthat/test-seq.R | 6 tidyr-1.3.2/tidyr/tests/testthat/test-spread.R | 63 +- tidyr-1.3.2/tidyr/tests/testthat/test-uncount.R | 5 tidyr-1.3.2/tidyr/tests/testthat/test-unite.R | 36 + tidyr-1.3.2/tidyr/tests/testthat/test-unnest-auto.R | 13 tidyr-1.3.2/tidyr/tests/testthat/test-unnest-helper.R | 34 - tidyr-1.3.2/tidyr/tests/testthat/test-unnest-longer.R | 88 ++- tidyr-1.3.2/tidyr/tests/testthat/test-unnest-wider.R | 59 +- tidyr-1.3.2/tidyr/tests/testthat/test-unnest.R | 38 - tidyr-1.3.2/tidyr/vignettes/in-packages.Rmd | 90 +-- tidyr-1.3.2/tidyr/vignettes/nest.Rmd | 20 tidyr-1.3.2/tidyr/vignettes/pivot.Rmd | 255 ++++----- tidyr-1.3.2/tidyr/vignettes/programming.Rmd | 30 - tidyr-1.3.2/tidyr/vignettes/rectangle.Rmd | 126 ++-- tidyr-1.3.2/tidyr/vignettes/tidy-data.Rmd | 87 +-- 156 files changed, 4769 insertions(+), 3605 deletions(-)
Title: Generates Raven-Like Matrices According to Rules
Description: Generates Raven like matrices according to different rules and the response list associated to the matrix. The package can generate matrices composed of 4 or 9 cells, along with a response list of 11 elements (the correct response + 10 incorrect responses). The matrices can be generated according to both logical rules (i.e., the relationships between the elements in the matrix are manipulated to create the matrix) and visual-spatial rules (i.e., the visual or spatial characteristics of the elements are manipulated to generate the matrix).
The graphical elements of this package are based on the 'DescTools' package.
This package has been developed within the PRIN2020 Project (Prot. 20209WKCLL) titled "Computerized, Adaptive and Personalized Assessment of Executive Functions and Fluid Intelligence" and founded by the Italian Ministry of Education and Research.
Author: Andrea Brancaccio [aut, ctb, cph, cre],
Ottavia M. Epifania [aut, ctb, com],
Debora de Chiusole [ctb]
Maintainer: Andrea Brancaccio <andreabrancaccio01@gmail.com>
Diff between matRiks versions 0.1.3 dated 2024-02-16 and 0.1.4 dated 2025-12-19
DESCRIPTION | 26 ++++++++++++++++++-------- MD5 | 33 +++++++++++++++++---------------- NEWS.md | 8 +++----- R/draw.R | 20 +++++++++++++------- build/vignette.rds |binary inst/CITATION |only inst/doc/black-figures.html | 12 ++++++------ inst/doc/circle-sections.html | 18 +++++++++--------- inst/doc/closed-figures.html | 14 +++++++------- inst/doc/eight-shapes-figures.html | 4 ++-- inst/doc/flowers-figures.html | 12 ++++++------ inst/doc/generate_matriks.R | 7 +++++++ inst/doc/generate_matriks.Rmd | 10 ++++++++++ inst/doc/generate_matriks.html | 21 ++++++++++++--------- inst/doc/lines.html | 16 ++++++++-------- inst/doc/other-figures.html | 10 +++++----- man/draw.Rd | 7 +++++-- vignettes/generate_matriks.Rmd | 10 ++++++++++ 18 files changed, 138 insertions(+), 90 deletions(-)
Title: Formatting Tools for Scientific Journal Writing
Description: Scientific journal numeric formatting policies implemented in
code. Emphasis on formatting mean/upper/lower sets of values to pasteable
text for journal submission. For example c(2e6, 1e6, 3e6) becomes
"2.00 million (1.00--3.00)". Lancet and Nature have built-in
styles for rounding and punctuation marks. Users may extend
journal styles arbitrarily. Four metrics are supported;
proportions, percentage points, counts and rates. Magnitudes for
all metrics are discovered automatically.
Author: Sam Byrne [aut, cre, cph]
Maintainer: Sam Byrne <ssbyrne@uw.edu>
Diff between journalR versions 0.2.1 dated 2025-12-14 and 0.6.0 dated 2025-12-19
journalR-0.2.1/journalR/R/data_types.R |only journalR-0.2.1/journalR/man/assert_data_type.Rd |only journalR-0.2.1/journalR/man/format_means_df.Rd |only journalR-0.2.1/journalR/man/fround_count.Rd |only journalR-0.2.1/journalR/man/fround_dtype.Rd |only journalR-0.2.1/journalR/man/fround_dtype_lancet.Rd |only journalR-0.2.1/journalR/man/get_data_type_labels.Rd |only journalR-0.2.1/journalR/man/get_data_types.Rd |only journalR-0.2.1/journalR/man/get_style_item_by_data_type.Rd |only journalR-0.6.0/journalR/DESCRIPTION | 22 journalR-0.6.0/journalR/MD5 | 101 - journalR-0.6.0/journalR/NAMESPACE | 10 journalR-0.6.0/journalR/NEWS.md | 30 journalR-0.6.0/journalR/R/assertions.R | 41 journalR-0.6.0/journalR/R/bindings.R | 1 journalR-0.6.0/journalR/R/format_vectors.R | 969 ++++++---- journalR-0.6.0/journalR/R/metrics.R |only journalR-0.6.0/journalR/R/pretty_print_journal.R | 468 ++-- journalR-0.6.0/journalR/R/set_magnitude.R | 334 ++- journalR-0.6.0/journalR/R/styles.R | 253 +- journalR-0.6.0/journalR/R/switch_strict.R | 11 journalR-0.6.0/journalR/R/zzz.R | 6 journalR-0.6.0/journalR/README.md | 423 ++-- journalR-0.6.0/journalR/man/add_epsilon.Rd |only journalR-0.6.0/journalR/man/apply_sigfig_zero_padding.Rd |only journalR-0.6.0/journalR/man/assert_clu_relationship.Rd | 4 journalR-0.6.0/journalR/man/assert_fround_return_schema.Rd |only journalR-0.6.0/journalR/man/assert_metric.Rd |only journalR-0.6.0/journalR/man/assert_rate_unit.Rd |only journalR-0.6.0/journalR/man/assert_set_choice.Rd | 4 journalR-0.6.0/journalR/man/assert_style_schema.Rd | 4 journalR-0.6.0/journalR/man/assert_x_gte_y.Rd | 4 journalR-0.6.0/journalR/man/assert_x_in_y.Rd | 4 journalR-0.6.0/journalR/man/assert_x_not_in_y.Rd | 4 journalR-0.6.0/journalR/man/fmt_magnitude.Rd | 37 journalR-0.6.0/journalR/man/format_decimal.Rd |only journalR-0.6.0/journalR/man/format_int.Rd |only journalR-0.6.0/journalR/man/format_journal_clu.Rd | 42 journalR-0.6.0/journalR/man/format_journal_df.Rd | 46 journalR-0.6.0/journalR/man/format_lancet_clu.Rd | 26 journalR-0.6.0/journalR/man/format_lancet_df.Rd | 27 journalR-0.6.0/journalR/man/format_metric_cols.Rd |only journalR-0.6.0/journalR/man/format_nature_clu.Rd | 26 journalR-0.6.0/journalR/man/format_nature_df.Rd | 24 journalR-0.6.0/journalR/man/format_oxford_comma.Rd | 7 journalR-0.6.0/journalR/man/fround.Rd | 7 journalR-0.6.0/journalR/man/fround_clu_triplet.Rd | 34 journalR-0.6.0/journalR/man/fround_count_rate.Rd |only journalR-0.6.0/journalR/man/fround_metric.Rd |only journalR-0.6.0/journalR/man/fround_metric_lancet.Rd |only journalR-0.6.0/journalR/man/fround_props.Rd | 23 journalR-0.6.0/journalR/man/get_metric_labels.Rd |only journalR-0.6.0/journalR/man/get_metrics.Rd |only journalR-0.6.0/journalR/man/get_style_item_by_metric.Rd |only journalR-0.6.0/journalR/man/new_style.Rd | 20 journalR-0.6.0/journalR/man/set_magnitude.Rd | 53 journalR-0.6.0/journalR/man/set_magnitude_count.Rd |only journalR-0.6.0/journalR/man/set_magnitude_prop.Rd |only journalR-0.6.0/journalR/man/set_magnitude_rate.Rd |only journalR-0.6.0/journalR/man/set_style.Rd | 37 journalR-0.6.0/journalR/tests/testthat/test-format_vectors.R | 226 ++ journalR-0.6.0/journalR/tests/testthat/test-pretty_print_journal.R | 250 ++ journalR-0.6.0/journalR/tests/testthat/test-rates.R |only journalR-0.6.0/journalR/tests/testthat/test-set_magnitude.R | 235 ++ journalR-0.6.0/journalR/tests/testthat/test-set_magnitude_deprec.R |only journalR-0.6.0/journalR/tests/testthat/test-switch_strict.R | 4 66 files changed, 2697 insertions(+), 1120 deletions(-)
Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine
('GEOS') library (<https://libgeos.org/>) and a vector format
with which to efficiently store 'GEOS' geometries. High-performance functions
to extract information from, calculate relationships between, and
transform geometries are provided. Finally, facilities to import
and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] ,
Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between geos versions 0.2.4 dated 2023-11-30 and 0.2.5 dated 2025-12-19
DESCRIPTION | 19 +++++++------ MD5 | 26 ++++++++++-------- NAMESPACE | 1 NEWS.md | 8 +++++ R/compat-terra.R |only R/geos-binary-geometry.R | 13 +++++++-- R/geos-geometry.R | 51 +++++++++++++++++++++++++++++++++---- R/geos-plot.R | 11 ++++++- R/zzz.R | 41 +++++++++++++++++++++++++++++ README.md | 2 - man/as_geos_geometry.Rd | 3 ++ man/geos-package.Rd | 2 - man/geos_intersection.Rd | 13 +++++++-- src/geos-strtree.c | 6 ++-- tests/testthat/test-compat-terra.R |only 15 files changed, 159 insertions(+), 37 deletions(-)
Title: Bayesian Change-Point Detection and Time Series Decomposition
Description: BEAST is a Bayesian estimator of abrupt change, seasonality, and trend for decomposing univariate time series and 1D sequential data. Interpretation of time series depends on model choice; different models can yield contrasting or contradicting estimates of patterns, trends, and mechanisms. BEAST alleviates this by abandoning the single-best-model paradigm and instead using Bayesian model averaging over many competing decompositions. It detects and characterizes abrupt changes (changepoints, breakpoints, structural breaks, joinpoints), cyclic or seasonal variation, and nonlinear trends. BEAST not only detects when changes occur but also quantifies how likely the changes are true. It estimates not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is generically applicable to any real-valued time series, such as those from remote sensing, economics, climate science, ecology, hydrology, and other environmental and biological systems. Example applications include iden [...truncated...]
Author: Tongxi Hu [aut],
Yang Li [aut],
Xuesong Zhang [aut],
Kaiguang Zhao [aut, cre],
Jack Dongarra [ctb],
Cleve Moler [ctb]
Maintainer: Kaiguang Zhao <zhao.1423@osu.edu>
Diff between Rbeast versions 1.0.1 dated 2024-08-30 and 1.0.2 dated 2025-12-19
DESCRIPTION | 10 MD5 | 75 +- NEWS.md | 7 R/beast.R | 11 R/beast.irreg.R | 8 R/zzz.R | 25 README.md | 79 ++ build |only man/beast.Rd | 809 ++++++++++++++----------- man/beast.irreg.Rd | 865 ++++++++++++++++----------- man/beast123.Rd | 1281 +++++++++++++++++++++------------------- man/minesweeper.Rd | 15 man/tetris.Rd | 15 src/abc_000_macro.h | 191 +++-- src/abc_001_config.h | 26 src/abc_datatype.h | 19 src/abc_ide_util_R.c | 16 src/abc_mat.h | 3 src/abc_mem.h | 2 src/abc_pthread.h | 230 +++---- src/abc_sort.c | 68 ++ src/abc_sort.h | 8 src/abc_sort_template.h | 7 src/abc_ts_func.c | 27 src/abc_ts_func.h | 1 src/beastv2_COREV4.c | 18 src/beastv2_COREV4_bic.c | 14 src/beastv2_COREV4_bic_mthrd.c | 19 src/beastv2_COREV4_gui.c | 16 src/beastv2_COREV4_mthrd.c | 35 - src/beastv2_date.c | 2 src/beastv2_func_q.c | 2 src/beastv2_header.h | 5 src/beastv2_header_solaris.h | 5 src/beastv2_io_in_args.c | 19 src/beastv2_io_out_printargs.c | 44 - src/beastv2_model_allocinit_q.c | 80 -- src/beastv2_prior_model.c | 377 ++++++++--- src/glue_code.c | 66 -- 39 files changed, 2578 insertions(+), 1922 deletions(-)
Title: Software Citation Tools
Description: A collection of functions to extract citation information from 'R' packages and to deal with files in 'citation file format' (<https://citation-file-format.github.io/>), extending the functionality already provided by the citation() function in the 'utils' package.
Author: Jan Philipp Dietrich [aut, cre] ,
Waldir Leoncio [aut]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between citation versions 0.8.2 dated 2023-03-30 and 0.12.2 dated 2025-12-19
DESCRIPTION | 23 ++++++++++++++--------- MD5 | 18 +++++++++--------- R/cff2bibentry.R | 35 +++++++++++++++++++---------------- R/cff2md.R | 19 ++++++++++++++++++- R/r2cff.R | 32 +++++++++++++++++++++++++++++--- README.md | 11 ++++++----- build/partial.rdb |binary man/citation-package.Rd | 4 ++-- tests/testthat/test-cff2r.R | 39 ++++++++++++++++++++------------------- tests/testthat/test-r2cff.R | 2 -- 10 files changed, 117 insertions(+), 66 deletions(-)
Title: Create TLGs using the 'tidyverse'
Description: Generate tables, listings, and graphs (TLG) using 'tidyverse'.
Tables can be created functionally, using a standard TLG process, or by
specifying table and column metadata to create generic analysis summaries.
The 'envsetup' package can also be leveraged to create environments for table
creation.
Author: Nicholas Masel [aut],
Steven Haesendonckx [aut],
Pelagia Alexandra Papadopoulou [aut],
Sheng-Wei Wang [aut],
Eli Miller [aut] ,
Nathan Kosiba [aut] ,
Aidan Ceney [aut] ,
Janssen R&D [cph, fnd],
David Hugh-Jones [cph] ,
Konrad Pagacz [aut, cre]
Maintainer: Konrad Pagacz <kpagacz@its.jnj.com>
Diff between tidytlg versions 0.10.0 dated 2025-07-02 and 0.11.0 dated 2025-12-19
tidytlg-0.10.0/tidytlg/tests/testthat/_snaps/png/png1.rtf |only tidytlg-0.10.0/tidytlg/tests/testthat/_snaps/png/png2.rtf |only tidytlg-0.10.0/tidytlg/tests/testthat/test-getFileName.R |only tidytlg-0.10.0/tidytlg/tests/testthat/test-snapshot-Listing01.R |only tidytlg-0.11.0/tidytlg/DESCRIPTION | 17 tidytlg-0.11.0/tidytlg/MD5 | 306 - tidytlg-0.11.0/tidytlg/NEWS.md | 28 tidytlg-0.11.0/tidytlg/R/add_bottom_borders.R | 16 tidytlg-0.11.0/tidytlg/R/add_format.R | 20 tidytlg-0.11.0/tidytlg/R/add_indent.R | 6 tidytlg-0.11.0/tidytlg/R/add_newrows.R | 24 tidytlg-0.11.0/tidytlg/R/bind_table.R | 45 tidytlg-0.11.0/tidytlg/R/check_args.R | 42 tidytlg-0.11.0/tidytlg/R/data.R | 426 - tidytlg-0.11.0/tidytlg/R/freq.R | 134 tidytlg-0.11.0/tidytlg/R/generate_results.R | 29 tidytlg-0.11.0/tidytlg/R/gentlg.R | 94 tidytlg-0.11.0/tidytlg/R/gentlg_single.R | 169 tidytlg-0.11.0/tidytlg/R/getFileName.R | 18 tidytlg-0.11.0/tidytlg/R/nested_freq.R | 30 tidytlg-0.11.0/tidytlg/R/quick_rtf_jnj.R | 90 tidytlg-0.11.0/tidytlg/R/remove_zero_padding.R | 6 tidytlg-0.11.0/tidytlg/R/rmdpstitle.R | 22 tidytlg-0.11.0/tidytlg/R/roundSAS.R | 17 tidytlg-0.11.0/tidytlg/R/statlist.R | 101 tidytlg-0.11.0/tidytlg/R/tidytlg-package.R | 142 tidytlg-0.11.0/tidytlg/R/tlgsetup.R | 20 tidytlg-0.11.0/tidytlg/R/univar.R | 46 tidytlg-0.11.0/tidytlg/R/utility.R | 4 tidytlg-0.11.0/tidytlg/build/vignette.rds |binary tidytlg-0.11.0/tidytlg/data/cdisc_adae.rda |binary tidytlg-0.11.0/tidytlg/data/cdisc_adsl.rda |binary tidytlg-0.11.0/tidytlg/inst/WORDLIST |only tidytlg-0.11.0/tidytlg/inst/doc/freq.R | 19 tidytlg-0.11.0/tidytlg/inst/doc/freq.Rmd | 142 tidytlg-0.11.0/tidytlg/inst/doc/freq.html | 236 tidytlg-0.11.0/tidytlg/inst/doc/symbols.Rmd | 17 tidytlg-0.11.0/tidytlg/inst/doc/symbols.html | 54 tidytlg-0.11.0/tidytlg/inst/doc/tbl_manipulation.Rmd | 52 tidytlg-0.11.0/tidytlg/inst/doc/tbl_manipulation.html | 110 tidytlg-0.11.0/tidytlg/inst/doc/tidytlg.R | 90 tidytlg-0.11.0/tidytlg/inst/doc/tidytlg.Rmd | 261 - tidytlg-0.11.0/tidytlg/inst/doc/tidytlg.html | 626 +- tidytlg-0.11.0/tidytlg/inst/doc/tlgsetup.R | 4 tidytlg-0.11.0/tidytlg/inst/doc/tlgsetup.Rmd | 32 tidytlg-0.11.0/tidytlg/inst/doc/tlgsetup.html | 57 tidytlg-0.11.0/tidytlg/inst/doc/univar.R | 16 tidytlg-0.11.0/tidytlg/inst/doc/univar.Rmd | 109 tidytlg-0.11.0/tidytlg/inst/doc/univar.html | 115 tidytlg-0.11.0/tidytlg/man/add_bottom_borders.Rd | 16 tidytlg-0.11.0/tidytlg/man/add_format.Rd | 32 tidytlg-0.11.0/tidytlg/man/add_indent.Rd | 18 tidytlg-0.11.0/tidytlg/man/add_newrows.Rd | 93 tidytlg-0.11.0/tidytlg/man/bind_table.Rd | 113 tidytlg-0.11.0/tidytlg/man/cdisc-adae.Rd | 116 tidytlg-0.11.0/tidytlg/man/cdisc-adlb.Rd | 92 tidytlg-0.11.0/tidytlg/man/cdisc-adsl.Rd | 102 tidytlg-0.11.0/tidytlg/man/cdisc-advs.Rd | 74 tidytlg-0.11.0/tidytlg/man/char2factor.Rd | 6 tidytlg-0.11.0/tidytlg/man/column_metadata.Rd | 18 tidytlg-0.11.0/tidytlg/man/files.Rd | 4 tidytlg-0.11.0/tidytlg/man/freq.Rd | 191 tidytlg-0.11.0/tidytlg/man/generate_results.Rd | 21 tidytlg-0.11.0/tidytlg/man/gentlg.Rd | 94 tidytlg-0.11.0/tidytlg/man/nested_freq.Rd | 192 tidytlg-0.11.0/tidytlg/man/old_format.Rd | 2 tidytlg-0.11.0/tidytlg/man/remove_zero_padding.Rd | 8 tidytlg-0.11.0/tidytlg/man/replace_na_with_blank.Rd | 2 tidytlg-0.11.0/tidytlg/man/rmdpstitle.Rd | 22 tidytlg-0.11.0/tidytlg/man/roundSAS.Rd | 11 tidytlg-0.11.0/tidytlg/man/statlist.Rd | 110 tidytlg-0.11.0/tidytlg/man/table_metadata.Rd | 32 tidytlg-0.11.0/tidytlg/man/tidytlg.Rd | 136 tidytlg-0.11.0/tidytlg/man/tlgsetup.Rd | 28 tidytlg-0.11.0/tidytlg/man/univar.Rd | 109 tidytlg-0.11.0/tidytlg/tests/testthat.R | 3 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/borders/noborders.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/borders/oldformat.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/borders/oldformatlisting.rtf | 54 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/borders/spanningbordersrow1.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/borders/stubborntest.rtf | 30 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/colheader/colheader1.rtf | 34 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/colheader/colheader2.rtf | 34 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/colspan/colspan1.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/colspan/colspan2.rtf | 40 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/colspan/colspan3.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/insert_empty_rows/inserts.rtf | 38 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/multiple-tables-in-rtf/multipletabs.rtf | 88 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/page_numbers/pagenumbers.rtf | 56 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/page_numbers/pagenumberstable.rtf | 56 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/png/test2plots.rtf | 12 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/titles/gsvit01a.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/_snaps/tlgsetup/testtlgsetup.rtf | 40 tidytlg-0.11.0/tidytlg/tests/testthat/freq_rowtext_row_header.R | 137 tidytlg-0.11.0/tidytlg/tests/testthat/test-bind_table.R | 66 tidytlg-0.11.0/tidytlg/tests/testthat/test-borders.R | 281 - tidytlg-0.11.0/tidytlg/tests/testthat/test-check_args.R | 698 +- tidytlg-0.11.0/tidytlg/tests/testthat/test-colheader.R | 55 tidytlg-0.11.0/tidytlg/tests/testthat/test-colspan.R | 115 tidytlg-0.11.0/tidytlg/tests/testthat/test-freq.R | 2386 ++++++++-- tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_cutoff.R | 49 tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_descending_by.R | 29 tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_ord.R | 610 ++ tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_pad.R | 146 tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_sparse.R | 209 tidytlg-0.11.0/tidytlg/tests/testthat/test-freq_subset.R | 18 tidytlg-0.11.0/tidytlg/tests/testthat/test-gentlg.R | 30 tidytlg-0.11.0/tidytlg/tests/testthat/test-get_file_name.R |only tidytlg-0.11.0/tidytlg/tests/testthat/test-insert_empty_rows.R | 101 tidytlg-0.11.0/tidytlg/tests/testthat/test-metadata.R | 151 tidytlg-0.11.0/tidytlg/tests/testthat/test-multiple-tables-in-rtf.R | 78 tidytlg-0.11.0/tidytlg/tests/testthat/test-nested.R | 1582 +++++- tidytlg-0.11.0/tidytlg/tests/testthat/test-nested_cutoff.R | 826 +++ tidytlg-0.11.0/tidytlg/tests/testthat/test-nested_freq.R | 118 tidytlg-0.11.0/tidytlg/tests/testthat/test-nested_ord.R | 356 + tidytlg-0.11.0/tidytlg/tests/testthat/test-page_numbers.R | 93 tidytlg-0.11.0/tidytlg/tests/testthat/test-png.R | 72 tidytlg-0.11.0/tidytlg/tests/testthat/test-quick_rtf_jnj.R | 8 tidytlg-0.11.0/tidytlg/tests/testthat/test-roundSAS.R | 34 tidytlg-0.11.0/tidytlg/tests/testthat/test-spanning_headers.R | 108 tidytlg-0.11.0/tidytlg/tests/testthat/test-titles.R | 60 tidytlg-0.11.0/tidytlg/tests/testthat/test-tlgsetup.R | 74 tidytlg-0.11.0/tidytlg/tests/testthat/test-univar.R | 627 +- tidytlg-0.11.0/tidytlg/tests/testthat/test-univar_keep.R | 161 tidytlg-0.11.0/tidytlg/tests/testthat/test-univar_ord.R | 719 ++- tidytlg-0.11.0/tidytlg/tests/testthat/test-univar_precision.R | 464 + tidytlg-0.11.0/tidytlg/tests/testthat/test-univar_rowbyvar.R | 771 ++- tidytlg-0.11.0/tidytlg/tests/testthat/test-univar_rowtext.R | 100 tidytlg-0.11.0/tidytlg/tests/testthat/test-utility.R | 55 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/borders/noborders.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/borders/oldformat.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/borders/oldformatlisting.rtf | 54 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/borders/spanningbordersrow1.rtf | 52 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/borders/stubborntest.rtf | 30 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/colheader1.rtf | 34 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/colheader2.rtf | 34 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/colspan1.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/colspan2.rtf | 40 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/colspan3.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/emptyrowsinsertions/inserts.rtf | 38 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/gsvit01a.rtf | 28 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/multiple_tables_in_one_file/multipletabs.rtf | 88 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/pagenumbers.rtf | 56 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/pagenumberstable.rtf | 56 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/png1.png |binary tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/png1.rtf | 10 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/png2.png |binary tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/png2.rtf | 10 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/test2plots.rtf | 12 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/testtlgsetup.rtf | 40 tidytlg-0.11.0/tidytlg/tests/testthat/test_outputs/tsidem01.rtf | 44 tidytlg-0.11.0/tidytlg/vignettes/freq.Rmd | 142 tidytlg-0.11.0/tidytlg/vignettes/symbols.Rmd | 17 tidytlg-0.11.0/tidytlg/vignettes/tbl_manipulation.Rmd | 52 tidytlg-0.11.0/tidytlg/vignettes/tidytlg.Rmd | 261 - tidytlg-0.11.0/tidytlg/vignettes/tlgsetup.Rmd | 32 tidytlg-0.11.0/tidytlg/vignettes/univar.Rmd | 109 157 files changed, 13261 insertions(+), 5684 deletions(-)
Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to
facilitate testing R packages.
Author: Yihui Xie [aut, cre] ,
Tomas Kalibera [ctb],
Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 0.14 dated 2025-12-06 and 0.15 dated 2025-12-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/testit.R | 17 +++++++++++++---- 3 files changed, 18 insertions(+), 9 deletions(-)
Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph] ,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.14.0 dated 2025-11-03 and 1.0.1 dated 2025-12-19
surveydown-0.14.0/surveydown/R/translation.R |only surveydown-0.14.0/surveydown/inst/examples |only surveydown-0.14.0/surveydown/inst/js/after_body.js |only surveydown-0.14.0/surveydown/inst/js/enter_key.js |only surveydown-0.14.0/surveydown/inst/js/highlight_unanswered.js |only surveydown-0.14.0/surveydown/inst/js/update_progress.js |only surveydown-0.14.0/surveydown/man/sd_create_translations.Rd |only surveydown-1.0.1/surveydown/DESCRIPTION | 10 surveydown-1.0.1/surveydown/MD5 | 75 surveydown-1.0.1/surveydown/NAMESPACE | 5 surveydown-1.0.1/surveydown/NEWS.md | 19 surveydown-1.0.1/surveydown/R/config.R | 1020 ++++++-- surveydown-1.0.1/surveydown/R/messages.R |only surveydown-1.0.1/surveydown/R/server.R | 1075 +++++++- surveydown-1.0.1/surveydown/R/ui.R | 1390 +++++------ surveydown-1.0.1/surveydown/R/util.R | 138 - surveydown-1.0.1/surveydown/README.md | 12 surveydown-1.0.1/surveydown/inst/css/surveydown.css | 35 surveydown-1.0.1/surveydown/inst/js/clipboard.js |only surveydown-1.0.1/surveydown/inst/js/cookies.js | 127 - surveydown-1.0.1/surveydown/inst/js/highlighting.js |only surveydown-1.0.1/surveydown/inst/js/interaction.js |only surveydown-1.0.1/surveydown/inst/js/progressbar.js |only surveydown-1.0.1/surveydown/inst/lua/include-resources.lua | 7 surveydown-1.0.1/surveydown/inst/template/app.R | 2 surveydown-1.0.1/surveydown/inst/template/survey.qmd | 72 surveydown-1.0.1/surveydown/man/sd_close.Rd | 41 surveydown-1.0.1/surveydown/man/sd_copy_value.Rd | 35 surveydown-1.0.1/surveydown/man/sd_create_messages.Rd |only surveydown-1.0.1/surveydown/man/sd_get_url_pars.Rd | 61 surveydown-1.0.1/surveydown/man/sd_is_answered.Rd | 39 surveydown-1.0.1/surveydown/man/sd_nav.Rd |only surveydown-1.0.1/surveydown/man/sd_next.Rd | 30 surveydown-1.0.1/surveydown/man/sd_output.Rd | 34 surveydown-1.0.1/surveydown/man/sd_question.Rd | 66 surveydown-1.0.1/surveydown/man/sd_redirect.Rd | 55 surveydown-1.0.1/surveydown/man/sd_server.Rd | 62 surveydown-1.0.1/surveydown/man/sd_show_if.Rd | 41 surveydown-1.0.1/surveydown/man/sd_skip_if.Rd | 41 surveydown-1.0.1/surveydown/man/sd_store_value.Rd | 54 surveydown-1.0.1/surveydown/man/sd_ui.Rd | 36 41 files changed, 2981 insertions(+), 1601 deletions(-)
Title: 'Shiny' Applications for the R Package 'Luminescence'
Description: A collection of 'shiny' applications for the R package
'Luminescence'. These mainly, but not exclusively, include applications for
plotting chronometric data from e.g. luminescence or radiocarbon dating. It
further provides access to bootstraps tooltip and popover functionality and
contains the 'jscolor.js' library with a custom 'shiny' output binding.
Author: Christoph Burow [aut, cre] ,
Urs Tilmann Wolpert [aut],
Sebastian Kreutzer [aut] ,
Marco Colombo [aut] ,
R Luminescence Package Team [ctb],
Jan Odvarko [cph] ,
AnalytixWare [cph] ,
RStudio [cph]
Maintainer: Christoph Burow <christoph.burow@gmx.net>
Diff between RLumShiny versions 0.2.5 dated 2025-07-12 and 0.2.6 dated 2025-12-19
RLumShiny-0.2.5/RLumShiny/inst/shiny/KDE/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/abanico/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/cosmicdose/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/doserecovery/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/fastratio/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/fastratio/Server.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/fastratio/UI.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/histogram/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/radialplot/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/transformCW/Global.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/transformCW/Server.R |only RLumShiny-0.2.5/RLumShiny/inst/shiny/transformCW/UI.R |only RLumShiny-0.2.6/RLumShiny/DESCRIPTION | 18 RLumShiny-0.2.6/RLumShiny/LICENSE | 164 ++++---- RLumShiny-0.2.6/RLumShiny/MD5 | 153 ++++--- RLumShiny-0.2.6/RLumShiny/NEWS.md | 24 + RLumShiny-0.2.6/RLumShiny/R/addin.R | 15 RLumShiny-0.2.6/RLumShiny/R/app_RLum.R | 13 RLumShiny-0.2.6/RLumShiny/R/helpers-server.R |only RLumShiny-0.2.6/RLumShiny/R/helpers-ui.R |only RLumShiny-0.2.6/RLumShiny/R/module_importTab.R |only RLumShiny-0.2.6/RLumShiny/R/module_printCode.R | 102 +++-- RLumShiny-0.2.6/RLumShiny/inst/shiny/KDE/global.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/KDE/server.R | 181 +++------ RLumShiny-0.2.6/RLumShiny/inst/shiny/KDE/ui.R | 39 + RLumShiny-0.2.6/RLumShiny/inst/shiny/KDE/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/abanico/global.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/abanico/server.R | 88 +--- RLumShiny-0.2.6/RLumShiny/inst/shiny/abanico/ui.R | 70 --- RLumShiny-0.2.6/RLumShiny/inst/shiny/abanico/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/aliquotsize/server.R | 12 RLumShiny-0.2.6/RLumShiny/inst/shiny/aliquotsize/ui.R | 16 RLumShiny-0.2.6/RLumShiny/inst/shiny/aliquotsize/www/style.css | 4 RLumShiny-0.2.6/RLumShiny/inst/shiny/convert/server.R | 72 ++- RLumShiny-0.2.6/RLumShiny/inst/shiny/convert/ui.R | 42 -- RLumShiny-0.2.6/RLumShiny/inst/shiny/convert/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/cosmicdose/global.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/cosmicdose/server.R | 58 +- RLumShiny-0.2.6/RLumShiny/inst/shiny/cosmicdose/ui.R | 12 RLumShiny-0.2.6/RLumShiny/inst/shiny/cosmicdose/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/doserecovery/global.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/doserecovery/server.R | 105 ++--- RLumShiny-0.2.6/RLumShiny/inst/shiny/doserecovery/ui.R | 72 --- RLumShiny-0.2.6/RLumShiny/inst/shiny/doserecovery/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/doseresponsecurve |only RLumShiny-0.2.6/RLumShiny/inst/shiny/fading/server.R | 148 +++---- RLumShiny-0.2.6/RLumShiny/inst/shiny/fading/ui.R | 14 RLumShiny-0.2.6/RLumShiny/inst/shiny/fading/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/fastratio/global.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/fastratio/server.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/fastratio/ui.R |only RLumShiny-0.2.6/RLumShiny/inst/shiny/fastratio/www/style.css | 3 RLumShiny-0.2.6/RLumShiny/inst/shiny/finitemixture/server.R | 34 - 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Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2.3 dated 2025-08-20 and 1.2.4 dated 2025-12-19
DESCRIPTION | 10 ++++----- MD5 | 41 +++++++++++++++++++++------------------- NEWS.md | 8 +++++++ R/AAA_definitions.R | 12 ++++++++++- R/extractFOSC.R | 2 - README.md | 19 ++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/README_files/hdbscan-1.png |binary inst/doc/dbscan.R | 20 +++++++++---------- inst/doc/dbscan.Rnw | 11 ++++------ inst/doc/dbscan.pdf |binary man/dbscan_tidiers.Rd | 2 - man/extractFOSC.Rd | 2 - src/ANN/ANN.h | 19 +++++++----------- src/ANN/ANNperf.h | 27 +++++++++++--------------- src/ANN/ANNx.h | 27 +++++++++++--------------- src/ANN/Copyright.txt |only src/ANN/License.txt |only src/ANN/ReadMe.txt |only tests/testthat/test-dbscan.R | 6 +++++ vignettes/dbscan.Rnw | 11 ++++------ vignettes/dbscan.bib | 21 +++++++++++--------- 23 files changed, 130 insertions(+), 108 deletions(-)
Title: Thresholded Partial Least Squares Model for Neuroimaging Data
Description: Uses thresholded partial least squares algorithm to create a regression or classification model. For more information, see Lee, Bradlow, and Kable <doi:10.1016/j.crmeth.2022.100227>.
Author: Sangil Lee [aut, cre]
Maintainer: Sangil Lee <sangillee3rd@gmail.com>
Diff between TPLSr versions 1.0.4 dated 2022-06-10 and 1.0.5 dated 2025-12-19
DESCRIPTION | 8 MD5 | 18 - NEWS.md | 9 R/evalTuningParam.R | 3 README.md | 4 build/vignette.rds |binary inst/doc/TPLS_example1.R | 2 inst/doc/TPLS_example1.html | 397 +++++++++++++------------- inst/doc/TPLS_example2.R | 2 inst/doc/TPLS_example2.html | 651 ++++++++++++++++++++++---------------------- 10 files changed, 558 insertions(+), 536 deletions(-)
Title: Dataset of the 'Contoso' Company
Description: A collection of synthetic datasets simulating sales transactions from a fictional company. The dataset includes various related tables that contain essential business and operational data, useful for analyzing sales performance and other business insights. Key tables included in the package are:
- "sales": Contains data on individual sales transactions, including order details, pricing, quantities, and customer information.
- "customer": Stores customer-specific details such as demographics, geographic location, occupation, and birthday.
- "store": Provides information about stores, including location, size, status, and operational dates.
- "orders": Contains details about customer orders, including order and delivery dates, store, and customer data.
- "product": Contains data on products, including attributes such as product name, category, price, cost, and weight.
- "date": A time-based table that includes date-related attributes like year, month, quarter, day, and working day indica [...truncated...]
Author: Alejandro Hagan [aut, cre]
Maintainer: Alejandro Hagan <alejandro.hagan@outlook.com>
Diff between contoso versions 1.2.1 dated 2025-11-24 and 1.2.2 dated 2025-12-19
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/database.R | 6 ++++++ README.md | 10 +++++++--- man/figures/contoso_water_color.jpg |only 6 files changed, 26 insertions(+), 11 deletions(-)
Title: A Deep Learning for Statistical Classification and Regression
Analysis with Random Effects
Description: Statistical classification and regression have been popular among various fields and stayed in the limelight of scientists of those fields. Examples of the fields include clinical trials where the statistical classification of patients is indispensable to predict the clinical courses of diseases. Considering the negative impact of diseases on performing daily tasks, correctly classifying patients based on the clinical information is vital in that we need to identify patients of the high-risk group to develop a severe state and arrange medical treatment for them at an opportune moment. Deep learning - a part of artificial intelligence - has gained much attention, and research on it burgeons during past decades: see, e.g, Kazemi and Mirroshandel (2018) <DOI:10.1016/j.artmed.2017.12.001>. It is a veritable technique which was originally designed for the classification, and hence, the Buddle package can provide sublime solutions to various challenging classification and regression pr [...truncated...]
Author: Jiwoong Kim [aut, cre]
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Diff between Buddle versions 2.0.1 dated 2020-02-13 and 2.0.2 dated 2025-12-19
DESCRIPTION | 25 ++++--- MD5 | 16 ++--- R/BuddleMain.R | 165 +++++++++++++++++++--------------------------------- man/TrainBuddle.Rd | 3 src/Buddle.h | 1 src/Common.h | 2 src/Makevars | 19 +++++ src/Makevars.win | 17 ++++- src/RcppExports.cpp | 5 + 9 files changed, 121 insertions(+), 132 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models with the possibility of non-informative random right or left censoring.
Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value and standard normal distributions as important special cases. Inference is based on likelihood, penalized likelihood and bootstrap methods.
Lastly, some numerical and graphical devices for diagnostic of the fitted models are offered.
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph] ,
Gilberto Paula [aut],
Luis Vanegas [aut]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.2.4 dated 2025-12-09 and 0.2.5 dated 2025-12-18
DESCRIPTION | 6 MD5 | 60 ++++---- NAMESPACE | 3 R/aux_fs.R | 8 - R/bootglg.R | 8 - R/coef.sglg.R |only R/fitted.sglg.R |only R/glg.R | 84 +++++++----- R/influence.sglg.R | 6 R/kmpar.R | 19 +- R/logLik.sglg.R | 2 R/plot.npc.R | 22 ++- R/response_scheme.R | 6 R/rglg.R | 5 R/sglg.R | 14 -- R/shape.R | 27 +--- R/smooth_parameters.R | 2 R/summary.sglg.R | 2 R/survglg.R | 282 ++++++++++++++++++------------------------ R/vcov.sglg.R |only man/bootglg.Rd | 8 - man/coef.sglg.Rd |only man/fitted.sglg.Rd |only man/glg.Rd | 50 ++++--- man/plotnpc.Rd | 22 ++- man/plotsurv.sglg.Rd | 19 +- man/rglg.Rd | 2 man/sglg.Rd | 4 man/shape.Rd | 21 +-- man/smoothp.Rd | 2 man/survglg.Rd | 24 +-- man/vcov.sglg.Rd |only tests/testthat/test_glg.R | 2 tests/testthat/test_survglg.R | 2 34 files changed, 347 insertions(+), 365 deletions(-)
Title: 'Ping' 'URLs' to Time 'Requests'
Description: A suite of functions to ping 'URLs' and to time
'HTTP' 'requests'. Designed to work with 'httr'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between httping versions 0.2.0 dated 2018-01-02 and 0.3.0 dated 2025-12-18
DESCRIPTION | 17 +++--- LICENSE | 2 MD5 | 22 ++++---- NAMESPACE | 1 R/httping-package.R | 21 ++++--- R/ping.R | 17 +++--- R/time.R | 121 ++++++++++++++++++++++++++++++++++----------- README.md | 88 +++++++++++++++++--------------- man/httping-package.Rd | 17 ++++-- man/time.Rd | 3 - tests/testthat/test-ping.R | 42 +++++++++------ tests/testthat/test-time.R | 8 -- 12 files changed, 222 insertions(+), 137 deletions(-)
Title: Post-Estimation Functions for Generalized Linear Mixed Models
Description: Several functions for working with mixed effects regression models for limited dependent variables. The functions facilitate post-estimation of model predictions or margins, and comparisons between model predictions for assessing or probing moderation. Additional helper functions facilitate model comparisons and implements simulation-based inference for model predictions of alternative-specific outcome models. See also, Melamed and Doan (2024, ISBN: 978-1032509518).
Author: David Melamed [aut, cre]
Maintainer: David Melamed <dmmelamed@gmail.com>
Diff between catregs versions 1.2.4 dated 2025-11-06 and 1.3 dated 2025-12-18
DESCRIPTION | 6 ++-- MD5 | 4 +-- R/functions.R | 76 ++++++++++++++++++++++++++++++++++++++++++++++++---------- 3 files changed, 68 insertions(+), 18 deletions(-)
Title: Work with Data from High-Resolution Biologging Tags
Description: High-resolution movement-sensor tags typically include accelerometers
to measure body posture and sudden movements or changes in speed,
magnetometers to measure direction of travel, and pressure sensors
to measure dive depth in aquatic or marine animals. The sensors in these tags usually sample many times per second. Some tags include sensors for speed, turning rate (gyroscopes), and sound. This package provides software tools to facilitate calibration, processing, and analysis of such data. Tools are provided for: data import/export;
calibration (from raw data to calibrated data in scientific units);
visualization (for example, multi-panel time-series plots);
data processing (such as event detection, calculation of derived metrics like jerk and
dynamic acceleration, dive detection, and dive parameter calculation); and statistical analysis (for example, track reconstruction, a rotation test, and Mahalanobis distance analysis).
Author: Stacy DeRuiter [aut, cre, cph] ,
Mark Johnson [aut, cph],
David Sweeney [aut],
Ye Joo McNamara-Oh [aut],
Samuel Fynewever [aut],
Racheal Tejevbo [aut],
Tiago Marques [aut],
Yuqian Wang [aut],
Su Ogedegbe [aut]
Maintainer: Stacy DeRuiter <stacy.deruiter@calvin.edu>
Diff between tagtools versions 0.2.0 dated 2024-06-28 and 0.3.0 dated 2025-12-18
tagtools-0.2.0/tagtools/inst/shiny |only tagtools-0.3.0/tagtools/DESCRIPTION | 27 tagtools-0.3.0/tagtools/MD5 | 167 ++- tagtools-0.3.0/tagtools/NAMESPACE | 4 tagtools-0.3.0/tagtools/NEWS.md | 41 tagtools-0.3.0/tagtools/R/RcppExports.R |only tagtools-0.3.0/tagtools/R/add_nc.R | 15 tagtools-0.3.0/tagtools/R/body_axes.R | 243 ++--- tagtools-0.3.0/tagtools/R/decdc.R | 12 tagtools-0.3.0/tagtools/R/decz.R | 2 tagtools-0.3.0/tagtools/R/fir_nodelay.R | 10 tagtools-0.3.0/tagtools/R/fix_offset_3d.R | 6 tagtools-0.3.0/tagtools/R/fix_pressure.R | 6 tagtools-0.3.0/tagtools/R/hilbert_env.R | 2 tagtools-0.3.0/tagtools/R/interp2length.R | 9 tagtools-0.3.0/tagtools/R/m_dist.R | 138 +-- tagtools-0.3.0/tagtools/R/make_specgram.R | 15 tagtools-0.3.0/tagtools/R/mean_absorption.R | 8 tagtools-0.3.0/tagtools/R/norm2.R | 2 tagtools-0.3.0/tagtools/R/odba.R | 2 tagtools-0.3.0/tagtools/R/plot_prh_fig2.R | 4 tagtools-0.3.0/tagtools/R/plot_prh_fig2_m2.R | 4 tagtools-0.3.0/tagtools/R/prh_predictor1.R | 342 ++++---- tagtools-0.3.0/tagtools/R/prh_predictor2.R | 346 ++++---- tagtools-0.3.0/tagtools/R/read_cats.R | 427 +++++++--- tagtools-0.3.0/tagtools/R/read_cats_csv.R | 100 +- tagtools-0.3.0/tagtools/R/rough_cal_3d.R | 10 tagtools-0.3.0/tagtools/R/save_nc.R | 14 tagtools-0.3.0/tagtools/R/sens_struct.R | 35 tagtools-0.3.0/tagtools/R/spectrum_level.R | 60 - tagtools-0.3.0/tagtools/R/spherical_cal.R | 57 - tagtools-0.3.0/tagtools/R/tag2animal.R | 87 +- tagtools-0.3.0/tagtools/R/tagtools-package.R |only tagtools-0.3.0/tagtools/R/tortuosity.R | 8 tagtools-0.3.0/tagtools/R/undo_cal.R | 9 tagtools-0.3.0/tagtools/README.md | 9 tagtools-0.3.0/tagtools/man/add_nc.Rd | 4 tagtools-0.3.0/tagtools/man/conv_cpp.Rd |only tagtools-0.3.0/tagtools/man/decdc.Rd | 4 tagtools-0.3.0/tagtools/man/fir_nodelay.Rd | 4 tagtools-0.3.0/tagtools/man/m_dist.Rd | 38 tagtools-0.3.0/tagtools/man/make_specgram.Rd | 11 tagtools-0.3.0/tagtools/man/mean_absorption.Rd | 2 tagtools-0.3.0/tagtools/man/prh_predictor1.Rd | 11 tagtools-0.3.0/tagtools/man/prh_predictor2.Rd | 4 tagtools-0.3.0/tagtools/man/read_cats.Rd | 64 + tagtools-0.3.0/tagtools/man/read_cats_csv.Rd | 8 tagtools-0.3.0/tagtools/man/rough_cal_3d.Rd | 5 tagtools-0.3.0/tagtools/man/sens_struct.Rd | 7 tagtools-0.3.0/tagtools/man/spectrum_level.Rd | 6 tagtools-0.3.0/tagtools/man/spherical_cal.Rd | 10 tagtools-0.3.0/tagtools/man/tagtools-package.Rd |only tagtools-0.3.0/tagtools/man/tortuosity.Rd | 2 tagtools-0.3.0/tagtools/src |only tagtools-0.3.0/tagtools/tests/testthat/Rplots.pdf |binary tagtools-0.3.0/tagtools/tests/testthat/test-comp_filt.R | 22 tagtools-0.3.0/tagtools/tests/testthat/test-decdc.R | 25 tagtools-0.3.0/tagtools/tests/testthat/test-depth_rate.R | 19 tagtools-0.3.0/tagtools/tests/testthat/test-fir_nodelay.R | 24 tagtools-0.3.0/tagtools/tests/testthat/test-h_track.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-hilbert_transform.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-inclination.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-interp2length.R | 17 tagtools-0.3.0/tagtools/tests/testthat/test-interp_nan.R | 2 tagtools-0.3.0/tagtools/tests/testthat/test-inv_axis.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-julian_day.R | 2 tagtools-0.3.0/tagtools/tests/testthat/test-lalo2llf.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-m_dist.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-mean_absorption.R | 2 tagtools-0.3.0/tagtools/tests/testthat/test-median_filter.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-msa.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-njerk.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-norm2.R | 6 tagtools-0.3.0/tagtools/tests/testthat/test-ocdr.R | 28 tagtools-0.3.0/tagtools/tests/testthat/test-odba.R | 25 tagtools-0.3.0/tagtools/tests/testthat/test-ptrack.R | 23 tagtools-0.3.0/tagtools/tests/testthat/test-rotate_data.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-rotate_vecs.R | 2 tagtools-0.3.0/tagtools/tests/testthat/test-rotation_test.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-rotmat2euler.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-sound_speed.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-spectrum_level.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-speed_from_depth.R | 14 tagtools-0.3.0/tagtools/tests/testthat/test-spherical_cal.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-tortuosity.R | 4 tagtools-0.3.0/tagtools/tests/testthat/test-zero-crossing.R | 2 86 files changed, 1545 insertions(+), 1133 deletions(-)
Title: Khmaladze Martingale Transformation Goodness-of-Fit Test
Description: Consider a goodness-of-fit (GOF) problem of
testing whether a random sample comes from one
sample location-scale model where location and
scale parameters are unknown. It is well known
that Khmaladze martingale transformation method
proposed by Khmaladze (1981) <doi:10.1137/1126027>
provides asymptotic distribution free test for the GOF problem.
This package provides test statistic and critical
value of GOF test for normal, Cauchy, and logistic
distributions. This package used the main algorithm
proposed by Kim (2020) <doi:10.1007/s00180-020-00971-7>
and tests for other distributions will be available
at the later version.
Author: Jiwoong Kim [aut, cre]
Maintainer: Jiwoong Kim <jwboys26@gmail.com>
Diff between GofKmt versions 2.2.0 dated 2020-10-20 and 2.3.1 dated 2025-12-18
GofKmt-2.2.0/GofKmt/R/KmtFunc.R |only GofKmt-2.2.0/GofKmt/R/tbl_data.R |only GofKmt-2.2.0/GofKmt/data |only GofKmt-2.2.0/GofKmt/man/GetCV.Rd |only GofKmt-2.2.0/GofKmt/man/KhmaladzeTrans.Rd |only GofKmt-2.2.0/GofKmt/man/Tables.Rd |only GofKmt-2.2.0/GofKmt/src/Cauchy.h |only GofKmt-2.2.0/GofKmt/src/Kmt.h |only GofKmt-2.2.0/GofKmt/src/KmtMain.cpp |only GofKmt-2.2.0/GofKmt/src/Logistic.h |only GofKmt-2.2.0/GofKmt/src/Normal.h |only GofKmt-2.3.1/GofKmt/DESCRIPTION | 37 +++++++--- GofKmt-2.3.1/GofKmt/MD5 | 33 ++++----- GofKmt-2.3.1/GofKmt/NAMESPACE | 14 ++-- GofKmt-2.3.1/GofKmt/R/RFuncLib.R |only GofKmt-2.3.1/GofKmt/R/RcppExports.R | 20 +++++ GofKmt-2.3.1/GofKmt/R/sysdata.rda |binary GofKmt-2.3.1/GofKmt/man/Run_KMT.Rd |only GofKmt-2.3.1/GofKmt/src/Common.h | 62 +++++++----------- GofKmt-2.3.1/GofKmt/src/Distr.h |only GofKmt-2.3.1/GofKmt/src/FuncLib.cpp |only GofKmt-2.3.1/GofKmt/src/Makevars | 19 ++++- GofKmt-2.3.1/GofKmt/src/Makevars.win | 17 ++++- GofKmt-2.3.1/GofKmt/src/Optimal_Main.h |only GofKmt-2.3.1/GofKmt/src/Optimal_Side.h |only GofKmt-2.3.1/GofKmt/src/RcppExports.cpp | 102 ++++++++++++++++++++++++++---- 26 files changed, 212 insertions(+), 92 deletions(-)
Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.3 dated 2025-11-01 and 0.1.4 dated 2025-12-18
DESCRIPTION | 6 - MD5 | 72 ++++++++-------- NAMESPACE | 13 -- NEWS.md | 11 ++ R/MTD-plot.R | 10 +- R/MTDest-methods.R | 122 ++++++++++++--------------- R/MTDest-plot.R | 42 ++++----- R/MTDest.R | 39 ++++++-- R/MTDmodel-methods.R | 113 ++++++++++++------------- R/MTDmodel.R | 82 +++++++++--------- R/accessors.R | 95 ++++++++++----------- R/as-MTD.R | 25 +---- R/hdMTD-methods.R | 62 +++++++------ R/hdMTD.R | 17 +++ R/hdMTD_BIC.R | 4 R/hdMTD_CUT.R | 44 +++++++++ R/hdMTD_FS.R | 44 +++++++++ R/oscillation.R | 46 +++++----- R/perfectSample.R | 11 +- R/probs.R | 136 +++++------------------------- R/utils.R | 170 ++++++++++++++++++------------------- R/validation.R | 155 ++++++++++++++++++++-------------- man/MTD-accessors.Rd | 45 ++++++---- man/MTD-methods.Rd | 45 ++++------ man/MTDest-methods.Rd | 48 ++++------ man/MTDest.Rd | 37 +++++++- man/MTDmodel.Rd | 51 +++++++++-- man/as.MTD.Rd | 10 +- man/hdMTD-methods.Rd | 21 ++-- man/hdMTD.Rd | 20 +++- man/hdMTD_FS.Rd | 2 man/oscillation.Rd | 41 ++++----- man/perfectSample.Rd | 72 +++++++--------- man/plot.MTD.Rd | 166 ++++++++++++++++++------------------ man/plot.MTDest.Rd | 193 +++++++++++++++++++++---------------------- man/probs.Rd | 44 ++++----- tests/testthat/test-MTDest.R | 6 - 37 files changed, 1111 insertions(+), 1009 deletions(-)
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload and download of files.
Author: Emmanuel Blondel [aut, cre] ,
Julien Barde [ctb] ,
Stephen Eglen [ctb] ,
Hans Van Calster [ctb] ,
Floris Vanderhaeghe [ctb] ,
Jemma Stachelek [ctb] ,
Collin Schwantes [ctb] ,
Nicholas Tierney [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.10.3 dated 2025-11-24 and 0.10.4 dated 2025-12-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 19 ++++++++++++++----- R/ZenodoManager.R | 16 +++++++++------- R/ZenodoRecord.R | 2 +- README.md | 2 +- 6 files changed, 34 insertions(+), 23 deletions(-)
Title: 'Dang' Associated New Goodies
Description: A collection of utility functions.
Author: Dirk Eddelbuettel [aut, cre] ,
Petr Pikal [ctb] ),
David Hinds [ctb] ),
Brodie Gaslam [ctb] '),
Kevin Denny [ctb] ,
Kabira Namit [ctb] ,
R Core [ctb] ,
Joshua Ulrich [ctb] ,
Jordan Mark Barbone [ctb] ,
Charlie Gao [ctb] ,
Andrew Uhl [ctb] ,
Dewey Dun [...truncated...]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dang versions 0.0.16 dated 2023-12-02 and 0.0.17 dated 2025-12-18
dang-0.0.16/dang/R/googleFinanceData.R |only dang-0.0.16/dang/R/muteTweets.R |only dang-0.0.16/dang/man/googleFinanceData.Rd |only dang-0.0.16/dang/man/muteTweeters.Rd |only dang-0.0.17/dang/ChangeLog | 70 +++++++++++++++++++ dang-0.0.17/dang/DESCRIPTION | 57 +++++++++++++-- dang-0.0.17/dang/MD5 | 22 ++--- dang-0.0.17/dang/R/checkCRANStatus.R | 2 dang-0.0.17/dang/R/cranORCIDs.R |only dang-0.0.17/dang/R/reorderMicrobenchmarkResults.R |only dang-0.0.17/dang/R/rollMinMax.R | 3 dang-0.0.17/dang/README.md | 12 +-- dang-0.0.17/dang/inst/NEWS.Rd | 17 ++++ dang-0.0.17/dang/man/cranORCIDs.Rd |only dang-0.0.17/dang/man/reorderMicrobenchmarkResults.Rd |only dang-0.0.17/dang/man/rollMinMax.Rd | 3 16 files changed, 157 insertions(+), 29 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] ,
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 1.0.6 dated 2025-03-17 and 1.0.8 dated 2025-12-18
DESCRIPTION | 12 MD5 | 80 +-- NAMESPACE | 532 +++++++++++---------- NEWS.md | 13 R/FitCoupledGrowth_class.R | 9 R/FitDynamicGrowth_class.R | 9 R/FitIsoGrowth_class.R | 10 R/FitMultipleDynamicGrowth_class.R | 674 +++++++++++++-------------- R/FitSecondaryGrowth_class.R | 10 R/FitSerial_class.R |only R/GlobalGrowthFit_class.R | 812 ++++++++++++++++----------------- R/GrowthFit_class.R | 9 R/MCMCcoupled_class.R |only R/data.R | 10 R/fit_coupled_growth.R | 55 ++ R/fit_iso_growth.R | 2 R/guess_coupled.R |only R/predictMCMC.R | 324 ++++++------- R/predictMCMC_coupled.R |only R/top_fit.R | 2 R/twofold_dilution.R |only build/vignette.rds |binary data/example_od.rda |only inst/doc/v01_growth_predictions.html | 58 +- inst/doc/v02_growth_fitting.html | 72 ++ inst/doc/v03_growth_uncertainty.html | 35 + inst/doc/v04_model_comparison.html | 26 - inst/doc/v05_custom_stochastic.html | 8 inst/doc/v06_coupledmodels.html | 29 - inst/doc/v07_serial_dilution.R |only inst/doc/v07_serial_dilution.Rmd |only inst/doc/v07_serial_dilution.html |only inst/doc/v21_math_models.html | 9 inst/doc/v22_datasets.html | 8 inst/doc/v23_units-dilemma.html | 32 - inst/doc/v24_publication_figures.html | 17 inst/doc/v31_secondary_for_static.html | 11 inst/doc/v99_deprecated.html | 100 +++- man/FitCoupledGrowth.Rd | 256 +++++----- man/FitSerial.Rd |only man/MCMCcoupled.Rd |only man/cost_coupled_twosteps.Rd | 52 +- man/example_od.Rd |only man/fit_coupled_growth.Rd | 316 ++++++------ man/fit_serial_dilution.Rd |only man/get_TTDs.Rd |only man/make_guess_coupled.Rd |only man/predictMCMC_coupled.Rd |only man/show_guess_coupled.Rd |only vignettes/v07_serial_dilution.Rmd |only 50 files changed, 1996 insertions(+), 1596 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.8 dated 2025-11-25 and 0.1.9 dated 2025-12-18
DESCRIPTION | 6 - MD5 | 6 - data/bullet.rda |binary inst/doc/jpinfect.html | 204 ++++++++++++++++++++++++------------------------- 4 files changed, 108 insertions(+), 108 deletions(-)
Title: Presenting Statistical Results Effectively
Description: Includes functions and data used in the book "Presenting Statistical Results Effectively", Andersen and Armstrong (2022, ISBN: 978-1446269800). Several functions aid in data visualization - creating compact letter displays for simple slopes, kernel density estimates with normal density overlay. Other functions aid in post-model evaluation heatmap fit statistics for binary predictors, several variable importance measures, compact letter displays and simple-slope calculation. Finally, the package makes available the example datasets used in the book.
Author: Dave Armstrong [aut, cre],
Robert Andersen [aut],
Justin Esarey [cph],
John Fox [cph],
Michael Friendly [cph],
Adrian Bowman [cph],
Adelchi Azzalini [cph],
Dewey Michael [cph]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between psre versions 0.3 dated 2025-12-04 and 0.4 dated 2025-12-18
DESCRIPTION | 18 ++++--- MD5 | 6 +- NAMESPACE | 2 R/effective_functions.r | 118 +++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 132 insertions(+), 12 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre] ,
Alexa A. Sochaniwsky [aut]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.1.2 dated 2025-05-06 and 2.2.0 dated 2025-12-18
ChangeLog | 4 ++ DESCRIPTION | 15 ++++++---- MD5 | 43 +++++++++++++++++------------- NAMESPACE | 5 ++- R/RcppExports.R | 16 +++++++++++ R/gh_mixture.R | 7 ++--- R/mixture.R | 7 ++--- R/pcm.R | 2 - R/st_mixture.R | 7 ++--- R/t_mixture.R | 7 ++--- R/vg_mixture.R | 9 +++--- man/ARI.Rd | 3 ++ man/dmg.Rd |only man/dmgh.Rd |only man/dmst.Rd |only man/dmvg.Rd |only man/ghpcm.Rd | 2 - man/mixture.Rd | 6 ++-- man/pcm.Rd | 2 - man/stpcm.Rd | 2 - man/tpcm.Rd | 2 - man/vgpcm.Rd | 2 - src/RcppExports.cpp | 67 ++++++++++++++++++++++++++++++++++++++++++++++++ src/VG_Model/VG_EEE.hpp | 1 src/density.cpp |only 25 files changed, 157 insertions(+), 52 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and routines for graphical display.
Author: Michael Dewey [aut, cre]
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.12 dated 2025-03-15 and 1.13 dated 2025-12-18
DESCRIPTION | 11 +++--- MD5 | 36 +++++++++++---------- NEWS | 8 ++++ R/albatros.R | 81 +++++++++++++++++++++++------------------------- R/docontours.R | 5 ++ R/makescale.R |only build/metap.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 2 - inst/doc/compare.pdf |binary inst/doc/metap.pdf |binary inst/doc/plotmetap.R | 9 ++++- inst/doc/plotmetap.Rnw | 18 ++++++++-- inst/doc/plotmetap.pdf |binary man/albatros.Rd | 38 ++++++++++++++++++---- man/details.Rd |only man/metap-internal.Rd | 4 ++ vignettes/plotmetap.Rnw | 18 ++++++++-- 20 files changed, 147 insertions(+), 83 deletions(-)
Title: A Lightweight Version of R Markdown
Description: Render R Markdown to Markdown (without using 'knitr'), and Markdown
to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead
of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts,
subscripts, footnotes, element attributes, and appendices,
but not all 'Pandoc' Markdown features are (or will be) supported. With
additional JavaScript and CSS, you can also create HTML slides and articles.
This package can be viewed as a trimmed-down version of R Markdown and
'knitr'. It does not aim at rich Markdown features or a large variety of
output formats (the primary formats are HTML and 'LaTeX'). Book and website
projects of multiple input documents are also supported.
Author: Yihui Xie [aut, cre] ,
Tim Taylor [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between litedown versions 0.8 dated 2025-11-02 and 0.9 dated 2025-12-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 14 ++++++++++++++ R/fuse.R | 44 +++++++++++++++++++++++++++++++++++++------- R/mark.R | 8 ++++---- R/package.R | 23 +++++++++++++++-------- R/utils.R | 44 ++++++++++++++++++++++++-------------------- inst/doc/slides.html | 30 +++++++++++++++--------------- man/fuse_book.Rd | 8 ++++---- man/mark.Rd | 22 ++++++++++++++-------- man/pkg_desc.Rd | 5 ++++- 11 files changed, 145 insertions(+), 81 deletions(-)
Title: Utilities for Simulation, Plots, Quantile Functions and
Programming
Description: Plot density and distribution functions with automatic selection of
suitable regions. Numerically invert (compute quantiles) distribution
functions. Simulate real and complex numbers from distributions of their
magnitude and arguments. Optionally, the magnitudes and/or arguments may
be fixed in almost arbitrary ways. Create polynomials from roots given in
Cartesian or polar form. Small programming utilities: check if an object
is identical to NA, count positional arguments in a call, set
intersection of more than two sets, check if an argument is unnamed,
compute the graph of S4 classes in packages.
Author: Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between gbutils versions 0.5 dated 2022-05-27 and 0.5.1 dated 2025-12-18
DESCRIPTION | 17 +++++++++-------- MD5 | 27 ++++++++++++++------------- NEWS.md | 21 +++++++++++++-------- README.md | 3 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Plot_pdf.pdf |binary inst/pkgdown.yml |only man/adjacencyOfClasses.Rd | 8 ++++---- man/cdf2quantile.Rd | 6 +++--- man/isNA.Rd | 3 +-- man/isargunnamed.Rd | 3 ++- man/mintersect.Rd | 2 +- man/parse_text.Rd | 4 +--- man/sim_numbers.Rd | 10 +++++----- 15 files changed, 54 insertions(+), 50 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.1-0 dated 2025-11-21 and 2.2-0 dated 2025-12-18
kstMatrix-2.1-0/kstMatrix/R/kmsf2basis.R |only kstMatrix-2.1-0/kstMatrix/man/kmsf2basis.Rd |only kstMatrix-2.2-0/kstMatrix/Changelog | 8 kstMatrix-2.2-0/kstMatrix/DESCRIPTION | 8 kstMatrix-2.2-0/kstMatrix/MD5 | 58 - kstMatrix-2.2-0/kstMatrix/NAMESPACE | 6 kstMatrix-2.2-0/kstMatrix/R/kmSF2basis.R |only kstMatrix-2.2-0/kstMatrix/R/kmbasisfringe.R |only kstMatrix-2.2-0/kstMatrix/R/kmbasisneighbourhood.R |only kstMatrix-2.2-0/kstMatrix/R/kmfringe.R | 96 - kstMatrix-2.2-0/kstMatrix/R/kmgradations.R | 2 kstMatrix-2.2-0/kstMatrix/R/kmlearningpaths.R | 174 +-- kstMatrix-2.2-0/kstMatrix/R/kmneighbourhood.R | 184 +-- kstMatrix-2.2-0/kstMatrix/R/plot.R | 685 ++++++------- kstMatrix-2.2-0/kstMatrix/inst/doc/kstMatrix.R | 4 kstMatrix-2.2-0/kstMatrix/inst/doc/kstMatrix.Rmd | 20 kstMatrix-2.2-0/kstMatrix/inst/doc/kstMatrix.html | 50 kstMatrix-2.2-0/kstMatrix/man/kmSF2basis.Rd |only kstMatrix-2.2-0/kstMatrix/man/kmSR2basis.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmbasis.kmsurmisefunction.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmbasis.kmsurmiserelation.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmbasis.matrix.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmbasisfringe.Rd |only kstMatrix-2.2-0/kstMatrix/man/kmbasisneighbourhood.Rd |only kstMatrix-2.2-0/kstMatrix/man/kmfringe.Rd | 6 kstMatrix-2.2-0/kstMatrix/man/kmgradations.Rd | 6 kstMatrix-2.2-0/kstMatrix/man/kmlearningpaths.Rd | 6 kstMatrix-2.2-0/kstMatrix/man/kmneighbourhood.Rd | 6 kstMatrix-2.2-0/kstMatrix/man/kmnneighbourhood.Rd | 6 kstMatrix-2.2-0/kstMatrix/man/kmsurmisefunction.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmsurmiserelation.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/kmunionclosure.Rd | 2 kstMatrix-2.2-0/kstMatrix/man/plot.Rd | 17 kstMatrix-2.2-0/kstMatrix/vignettes/kstMatrix.Rmd | 20 34 files changed, 745 insertions(+), 631 deletions(-)
Title: Rmetrics - Importing Economic and Financial Data
Description: Provides a collection of utility functions
to download and manage data sets from the Internet or from other
sources.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fImport versions 4041.88 dated 2024-09-20 and 4052.89 dated 2025-12-18
DESCRIPTION | 20 +++---- MD5 | 32 +++++------ NAMESPACE | 6 +- NEWS.md | 6 +- R/import-fred.R | 131 ++++++++++++++++++++++------------------------ data/amexListing.csv.gz |binary data/h15Listing.csv.gz |binary data/nasdaqListing.csv.gz |binary data/nyseListing.csv.gz |binary data/oandaListing.csv.gz |binary data/stoxxListing.csv.gz |binary data/swxListing.csv.gz |binary inst/_pkgdown.yml | 2 man/00fImport-package.Rd | 24 +------- man/class-fWEBDATA.Rd | 88 ++++++++++++------------------ man/import-fred.Rd | 116 ++++++++++++++++++++-------------------- man/methods-show.Rd | 37 +++--------- 17 files changed, 209 insertions(+), 253 deletions(-)
Title: Sample and Precomputed Data for Use with 'exams.forge'
Description: Provides a small collection of datasets supporting Pearson correlation
and linear regression analysis. It includes the precomputed dataset 'sos100',
with integer values summing to zero and squared sum equal to 100. For other
values of 'n' and user-defined parameters, the 'sos()' function from the
'exams.forge' package can be used to generate datasets on the fly. In addition,
the package contains around 500 german R Markdown exercises that illustrate the usage
of 'exams.forge' commands.
Author: Sigbert Klinke [aut, cre]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between exams.forge.data versions 0.1.2 dated 2025-09-11 and 0.1.3 dated 2025-12-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/exams.forge.data.R | 14 ++++++++++---- inst/doc/exams.forge.data.Rmd | 14 ++++++++++---- inst/doc/exams.forge.data.html | 20 +++++++++++++------- vignettes/exams.forge.data.Rmd | 14 ++++++++++---- 6 files changed, 52 insertions(+), 28 deletions(-)
More information about exams.forge.data at CRAN
Permanent link
Title: Efficient Approximate Bayesian Computation Sampling Schemes
Description: Enables launching a series of simulations of a computer code from the R session, and to retrieve the simulation outputs in an appropriate format for post-processing treatments. Five sequential sampling schemes and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot [aut],
Nicolas Dumoulin [aut, cre],
Thierry Faure [aut],
Carlo Albert. [aut]
Maintainer: Nicolas Dumoulin <nicolas.dumoulin@inrae.fr>
Diff between EasyABC versions 1.5.2 dated 2023-01-05 and 1.6 dated 2025-12-18
EasyABC-1.5.2/EasyABC/man/EasyABC-internal.Rd |only EasyABC-1.6/EasyABC/CHANGELOG | 11 EasyABC-1.6/EasyABC/DESCRIPTION | 41 - EasyABC-1.6/EasyABC/MD5 | 49 - EasyABC-1.6/EasyABC/NAMESPACE | 46 + EasyABC-1.6/EasyABC/R/ABC_emulation.R | 120 +++ EasyABC-1.6/EasyABC/R/ABC_mcmc.R | 243 +++++++ EasyABC-1.6/EasyABC/R/ABC_rejection.R | 195 ++++++ EasyABC-1.6/EasyABC/R/ABC_sequential.R | 374 ++++++++++++ EasyABC-1.6/EasyABC/R/EasyABC-package.R |only EasyABC-1.6/EasyABC/R/RcppExports.R |only EasyABC-1.6/EasyABC/R/SABC.R | 107 +++ EasyABC-1.6/EasyABC/R/binary_model.R | 41 + EasyABC-1.6/EasyABC/R/binary_model_cluster.R | 48 + EasyABC-1.6/EasyABC/R/traitmodel.R |only EasyABC-1.6/EasyABC/build |only EasyABC-1.6/EasyABC/inst |only EasyABC-1.6/EasyABC/man/ABC_emulation.Rd | 267 +++++--- EasyABC-1.6/EasyABC/man/ABC_mcmc.Rd | 518 +++++++++------- EasyABC-1.6/EasyABC/man/ABC_rejection.Rd | 412 +++++++------ EasyABC-1.6/EasyABC/man/ABC_sequential.Rd | 747 +++++++++++++----------- EasyABC-1.6/EasyABC/man/EasyABC-package.Rd | 63 +- EasyABC-1.6/EasyABC/man/SABC.Rd | 175 +++-- EasyABC-1.6/EasyABC/man/binary_model.Rd | 102 +-- EasyABC-1.6/EasyABC/man/binary_model_cluster.Rd | 115 ++- EasyABC-1.6/EasyABC/man/trait_model.Rd |only EasyABC-1.6/EasyABC/man/trait_model_internal.Rd |only EasyABC-1.6/EasyABC/src |only EasyABC-1.6/EasyABC/vignettes |only 29 files changed, 2619 insertions(+), 1055 deletions(-)
Title: Quality Evaluation of Core Collections
Description: Implements various quality evaluation statistics to assess the
value of plant germplasm core collections using qualitative and
quantitative phenotypic trait data according to Odong et al. (2015)
<doi:10.1007/s00122-012-1971-y>.
Author: J. Aravind [aut, cre] ,
Vikender Kaur [aut] ,
Dhammaprakash Pandhari Wankhede [aut] ,
Joghee Nanjundan [aut] ,
ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.org.in>
This is a re-admission after prior archival of version 0.1.3 dated 2022-07-03
Diff between EvaluateCore versions 0.1.3 dated 2022-07-03 and 0.1.4 dated 2025-12-18
EvaluateCore-0.1.3/EvaluateCore/build/EvaluateCore.pdf |only EvaluateCore-0.1.4/EvaluateCore/DESCRIPTION | 38 EvaluateCore-0.1.4/EvaluateCore/MD5 | 125 EvaluateCore-0.1.4/EvaluateCore/NAMESPACE | 9 EvaluateCore-0.1.4/EvaluateCore/NEWS.md | 14 EvaluateCore-0.1.4/EvaluateCore/R/EvaluateCore-deprecated.R | 2 EvaluateCore-0.1.4/EvaluateCore/R/bar.evaluate.core.R | 52 EvaluateCore-0.1.4/EvaluateCore/R/box.evaluate.core.R | 39 EvaluateCore-0.1.4/EvaluateCore/R/cassava_CC.R | 8 EvaluateCore-0.1.4/EvaluateCore/R/cassava_EC.R | 12 EvaluateCore-0.1.4/EvaluateCore/R/checks.evaluate.core.R | 35 EvaluateCore-0.1.4/EvaluateCore/R/chisquare.evalueate.core.R | 49 EvaluateCore-0.1.4/EvaluateCore/R/corr.evaluate.core.R | 16 EvaluateCore-0.1.4/EvaluateCore/R/coverage.evaluate.core.R | 22 EvaluateCore-0.1.4/EvaluateCore/R/cr.evaluate.core.R | 56 EvaluateCore-0.1.4/EvaluateCore/R/dist.evaluate.core.R | 14 EvaluateCore-0.1.4/EvaluateCore/R/diversity.evaluate.core.R | 20 EvaluateCore-0.1.4/EvaluateCore/R/freqdist.evaluate.core.R | 88 EvaluateCore-0.1.4/EvaluateCore/R/globals.R | 6 EvaluateCore-0.1.4/EvaluateCore/R/iqr.evaluate.core.R | 19 EvaluateCore-0.1.4/EvaluateCore/R/levene.evaluate.core.R | 57 EvaluateCore-0.1.4/EvaluateCore/R/pca.evaluate.core.R | 20 EvaluateCore-0.1.4/EvaluateCore/R/pdfdist.evaluate.core.R | 86 EvaluateCore-0.1.4/EvaluateCore/R/percentdiff.evaluate.core.R | 38 EvaluateCore-0.1.4/EvaluateCore/R/qq.evaluate.core.R | 157 + EvaluateCore-0.1.4/EvaluateCore/R/rpr.evaluate.core.R |only EvaluateCore-0.1.4/EvaluateCore/R/scv.evaluate.core.R |only EvaluateCore-0.1.4/EvaluateCore/R/shannon.evaluate.core.R | 4 EvaluateCore-0.1.4/EvaluateCore/R/signtest.evaluate.core.R | 3 EvaluateCore-0.1.4/EvaluateCore/R/snk.evaluate.core.R | 72 EvaluateCore-0.1.4/EvaluateCore/R/ttest.evaluate.core.R | 78 EvaluateCore-0.1.4/EvaluateCore/R/vpf.evaluate.core.R |only EvaluateCore-0.1.4/EvaluateCore/R/vr.evaluate.core.R | 4 EvaluateCore-0.1.4/EvaluateCore/R/wilcox.evaluate.core.R | 24 EvaluateCore-0.1.4/EvaluateCore/R/xtra.R | 2 EvaluateCore-0.1.4/EvaluateCore/README.md | 233 - EvaluateCore-0.1.4/EvaluateCore/build/partial.rdb |binary EvaluateCore-0.1.4/EvaluateCore/build/stage23.rdb |only EvaluateCore-0.1.4/EvaluateCore/inst/CITATION | 43 EvaluateCore-0.1.4/EvaluateCore/inst/REFERENCES.bib | 1280 +++++----- EvaluateCore-0.1.4/EvaluateCore/inst/pkgdown.yml |only EvaluateCore-0.1.4/EvaluateCore/man/bar.evaluate.core.Rd | 23 EvaluateCore-0.1.4/EvaluateCore/man/box.evaluate.core.Rd | 12 EvaluateCore-0.1.4/EvaluateCore/man/cassava_CC.Rd | 6 EvaluateCore-0.1.4/EvaluateCore/man/cassava_EC.Rd | 10 EvaluateCore-0.1.4/EvaluateCore/man/checks.evaluate.core.Rd | 2 EvaluateCore-0.1.4/EvaluateCore/man/chisquare.evaluate.core.Rd | 8 EvaluateCore-0.1.4/EvaluateCore/man/corr.evaluate.core.Rd | 8 EvaluateCore-0.1.4/EvaluateCore/man/coverage.evaluate.core.Rd | 23 EvaluateCore-0.1.4/EvaluateCore/man/cr.evaluate.core.Rd | 47 EvaluateCore-0.1.4/EvaluateCore/man/dist.evaluate.core.Rd | 7 EvaluateCore-0.1.4/EvaluateCore/man/diversity.evaluate.core.Rd | 667 ++--- EvaluateCore-0.1.4/EvaluateCore/man/freqdist.evaluate.core.Rd | 14 EvaluateCore-0.1.4/EvaluateCore/man/iqr.evaluate.core.Rd | 7 EvaluateCore-0.1.4/EvaluateCore/man/levene.evaluate.core.Rd | 19 EvaluateCore-0.1.4/EvaluateCore/man/pca.evaluate.core.Rd | 7 EvaluateCore-0.1.4/EvaluateCore/man/pdfdist.evaluate.core.Rd | 6 EvaluateCore-0.1.4/EvaluateCore/man/percentdiff.evaluate.core.Rd | 35 EvaluateCore-0.1.4/EvaluateCore/man/qq.evaluate.core.Rd | 37 EvaluateCore-0.1.4/EvaluateCore/man/rpr.evaluate.core.Rd |only EvaluateCore-0.1.4/EvaluateCore/man/scv.evaluate.core.Rd |only EvaluateCore-0.1.4/EvaluateCore/man/shannon.evaluate.core-deprecated.Rd | 2 EvaluateCore-0.1.4/EvaluateCore/man/signtest.evaluate.core.Rd | 1 EvaluateCore-0.1.4/EvaluateCore/man/snk.evaluate.core.Rd | 23 EvaluateCore-0.1.4/EvaluateCore/man/ttest.evaluate.core.Rd | 31 EvaluateCore-0.1.4/EvaluateCore/man/vpf.evaluate.core.Rd |only EvaluateCore-0.1.4/EvaluateCore/man/vr.evaluate.core.Rd | 4 EvaluateCore-0.1.4/EvaluateCore/man/wilcox.evaluate.core.Rd | 7 68 files changed, 2173 insertions(+), 1558 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre] ,
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut] ,
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] ,
Chih-Chen Lin [ctb, cph]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-16 dated 2024-09-16 and 1.7-17 dated 2025-12-18
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ inst/doc/svmdoc.R | 14 +++++++------- inst/doc/svmdoc.Rnw | 32 +++++++++++++++++++++++--------- inst/doc/svmdoc.pdf |binary inst/doc/svminternals.Rnw | 2 +- inst/doc/svminternals.pdf |binary man/bclust.Rd | 3 ++- vignettes/svmdoc.Rnw | 32 +++++++++++++++++++++++--------- vignettes/svminternals.Rnw | 2 +- 13 files changed, 79 insertions(+), 44 deletions(-)
Title: A Simple Router for HTTP and WebSocket Requests
Description: In order to make sure that web request ends up in the correct
handler function a router is often used. 'routr' is a package implementing a
simple but powerful routing functionality for R based servers. It is a fully
functional 'fiery' plugin, but can also be used with other 'httpuv' based
servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between routr versions 1.1.0 dated 2025-11-18 and 2.0.0 dated 2025-12-18
DESCRIPTION | 10 MD5 | 32 +-- NAMESPACE | 3 NEWS.md | 10 R/openapi_route.R | 6 R/otel.R | 32 --- R/redirector.R | 22 -- R/route.R | 314 ++++++++++++++---------------- R/routestack.R | 38 ++- man/Route-class.Rd | 83 +++++-- tests/testthat/_snaps/redirector.md | 4 tests/testthat/_snaps/route.md | 14 - tests/testthat/test-openapi_route.R | 12 - tests/testthat/test-redirector.R | 3 tests/testthat/test-route.R | 16 - tests/testthat/test-shared_secret_route.R | 2 tests/testthat/test-tidy_api.R | 4 17 files changed, 304 insertions(+), 301 deletions(-)