Title: Stability Assessment of Statistical Learning Methods
Description: Graphical and computational methods that can be used to assess the
stability of results from supervised statistical learning.
Author: Michel Philipp [aut],
Carolin Strobl [aut],
Achim Zeileis [aut, cre] ,
Thomas Rusch [aut],
Kurt Hornik [aut] ,
Lennart Schneider [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between stablelearner versions 0.1-5 dated 2023-04-13 and 0.1-6 dated 2025-07-24
DESCRIPTION | 16 +++-- MD5 | 20 +++---- NEWS.md | 8 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/forests.R | 96 +++++++++++++++++------------------ inst/doc/forests.html | 123 ++++++++++++++++++++++----------------------- man/LearnerList.Rd | 2 man/accuracy.Rd | 4 - man/stabletree-coercion.Rd | 30 +++++----- man/stabletree.Rd | 22 ++++---- 11 files changed, 166 insertions(+), 155 deletions(-)
Title: Microplots (Sparklines) in 'LaTeX', 'Word', 'HTML', 'Excel'
Description: The microplot function writes a set of R graphics files to be used as
microplots (sparklines) in tables in either 'LaTeX', 'HTML', 'Word',
or 'Excel' files. For 'LaTeX', we provide methods for the
Hmisc::latex() generic function to construct 'latex' tabular
environments which include the graphs. These can be used directly
with the operating system 'pdflatex' or 'latex' command, or by using
one of 'Sweave', 'knitr', 'rmarkdown', or 'Emacs org-mode' as an
intermediary. For 'MS Word', the msWord() function uses the
'flextable' package to construct 'Word' tables which include the
graphs. There are several distinct approaches for constructing HTML
files. The simplest is to use the msWord() function with argument
filetype="html". Alternatively, use either 'Emacs org-mode' or the
htmlTable::htmlTable() function to construct an 'HTML' file
containing tables which include the graphs. See the documentation
for our as.htmlimg() function. For 'Excel' use on 'Windows', the
file examples/iri [...truncated...]
Author: Richard M. Heiberger [aut, cre] ,
Karen Byron [ctb],
Nooreen Dabbish [ctb]
Maintainer: Richard M. Heiberger <rmh@temple.edu>
Diff between microplot versions 1.0-45 dated 2022-01-26 and 1.0-47 dated 2025-07-24
DESCRIPTION | 24 +++++++++++++++++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 1 + NEWS | 19 +++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary demo/AEdotplot.r | 6 ++++-- demo/NTplot.r | 1 + demo/boxplot-ggplot.r | 1 + demo/bwplot-lattice.r | 1 + demo/iris.r | 1 + demo/latex-ggplot.r | 1 + demo/latex.r | 1 + demo/msWord.r | 3 ++- demo/timeseries.r | 1 + demo/xtable.r | 1 + inst/doc/rmhPoster.pdf |binary man/cc176.y.adj.Rd | 2 +- man/latex.AEdotplot.Rd | 2 +- man/msWord.Rd | 2 +- 20 files changed, 75 insertions(+), 30 deletions(-)
Title: Automate Data Exploration and Treatment
Description: Automated data exploration process for analytic tasks and predictive modeling, so
that users could focus on understanding data and extracting insights. The package scans and
analyzes each variable, and visualizes them with typical graphical techniques. Common
data processing methods are also available to treat and format data.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>
Diff between DataExplorer versions 0.8.3 dated 2024-01-23 and 0.8.4 dated 2025-07-24
DataExplorer-0.8.3/DataExplorer/R/DataExplorer-package.r |only DataExplorer-0.8.3/DataExplorer/R/configure_report.r |only DataExplorer-0.8.3/DataExplorer/R/create_report.r |only DataExplorer-0.8.3/DataExplorer/R/drop_columns.r |only DataExplorer-0.8.3/DataExplorer/R/dummify.r |only DataExplorer-0.8.3/DataExplorer/R/group_category.r |only DataExplorer-0.8.3/DataExplorer/R/internal.r |only DataExplorer-0.8.3/DataExplorer/R/introduce.r |only DataExplorer-0.8.3/DataExplorer/R/plot.r |only DataExplorer-0.8.3/DataExplorer/R/plot_bar.r |only DataExplorer-0.8.3/DataExplorer/R/plot_boxplot.r |only DataExplorer-0.8.3/DataExplorer/R/plot_correlation.r |only DataExplorer-0.8.3/DataExplorer/R/plot_density.r |only DataExplorer-0.8.3/DataExplorer/R/plot_histogram.r |only DataExplorer-0.8.3/DataExplorer/R/plot_intro.r |only DataExplorer-0.8.3/DataExplorer/R/plot_missing.r |only DataExplorer-0.8.3/DataExplorer/R/plot_prcomp.r |only DataExplorer-0.8.3/DataExplorer/R/plot_qq.r |only DataExplorer-0.8.3/DataExplorer/R/plot_scatterplot.r |only DataExplorer-0.8.3/DataExplorer/R/plot_str.r |only DataExplorer-0.8.3/DataExplorer/R/profile_missing.r |only DataExplorer-0.8.3/DataExplorer/R/set_missing.r |only DataExplorer-0.8.3/DataExplorer/R/split_columns.r |only DataExplorer-0.8.3/DataExplorer/R/update_columns.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-configure-report.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-create-report.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-drop-columns.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-dummify.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-group-category.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-internal.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-introduce.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-bar.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-boxplot.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-correlation.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-histogram-density.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-intro.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-missing.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-prcomp.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-qq.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-scatterplot.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-plot-str.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-profile-missing.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-set-missing.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-split-columns.r |only DataExplorer-0.8.3/DataExplorer/tests/testthat/test-update-columns.r |only DataExplorer-0.8.4/DataExplorer/DESCRIPTION | 8 DataExplorer-0.8.4/DataExplorer/MD5 | 161 +++++----- DataExplorer-0.8.4/DataExplorer/NEWS.md | 6 DataExplorer-0.8.4/DataExplorer/R/DataExplorer-package.R |only DataExplorer-0.8.4/DataExplorer/R/configure_report.R |only DataExplorer-0.8.4/DataExplorer/R/create_report.R |only DataExplorer-0.8.4/DataExplorer/R/drop_columns.R |only DataExplorer-0.8.4/DataExplorer/R/dummify.R |only DataExplorer-0.8.4/DataExplorer/R/group_category.R |only DataExplorer-0.8.4/DataExplorer/R/internal.R |only DataExplorer-0.8.4/DataExplorer/R/introduce.R |only DataExplorer-0.8.4/DataExplorer/R/plot.R |only DataExplorer-0.8.4/DataExplorer/R/plot_bar.R |only DataExplorer-0.8.4/DataExplorer/R/plot_boxplot.R |only DataExplorer-0.8.4/DataExplorer/R/plot_correlation.R |only DataExplorer-0.8.4/DataExplorer/R/plot_density.R |only DataExplorer-0.8.4/DataExplorer/R/plot_histogram.R |only DataExplorer-0.8.4/DataExplorer/R/plot_intro.R |only DataExplorer-0.8.4/DataExplorer/R/plot_missing.R |only DataExplorer-0.8.4/DataExplorer/R/plot_prcomp.R |only DataExplorer-0.8.4/DataExplorer/R/plot_qq.R |only DataExplorer-0.8.4/DataExplorer/R/plot_scatterplot.R |only DataExplorer-0.8.4/DataExplorer/R/plot_str.R |only DataExplorer-0.8.4/DataExplorer/R/profile_missing.R |only DataExplorer-0.8.4/DataExplorer/R/set_missing.R |only DataExplorer-0.8.4/DataExplorer/R/split_columns.R |only DataExplorer-0.8.4/DataExplorer/R/update_columns.R |only DataExplorer-0.8.4/DataExplorer/build/vignette.rds |binary DataExplorer-0.8.4/DataExplorer/inst/doc/dataexplorer-intro.R | 134 ++++---- DataExplorer-0.8.4/DataExplorer/inst/doc/dataexplorer-intro.html | 63 +-- DataExplorer-0.8.4/DataExplorer/man/DataExplorer-package.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/configure_report.Rd | 6 DataExplorer-0.8.4/DataExplorer/man/create_report.Rd | 12 DataExplorer-0.8.4/DataExplorer/man/dot-getAllMissing.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/dot-getPageLayout.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/dot-ignoreCat.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/dot-lapply.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/drop_columns.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/dummify.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/group_category.Rd | 6 DataExplorer-0.8.4/DataExplorer/man/introduce.Rd | 6 DataExplorer-0.8.4/DataExplorer/man/plotDataExplorer.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/plotDataExplorer.grid.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/plotDataExplorer.multiple.Rd | 6 DataExplorer-0.8.4/DataExplorer/man/plotDataExplorer.single.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/plot_bar.Rd | 8 DataExplorer-0.8.4/DataExplorer/man/plot_boxplot.Rd | 14 DataExplorer-0.8.4/DataExplorer/man/plot_correlation.Rd | 12 DataExplorer-0.8.4/DataExplorer/man/plot_density.Rd | 12 DataExplorer-0.8.4/DataExplorer/man/plot_histogram.Rd | 12 DataExplorer-0.8.4/DataExplorer/man/plot_intro.Rd | 8 DataExplorer-0.8.4/DataExplorer/man/plot_missing.Rd | 8 DataExplorer-0.8.4/DataExplorer/man/plot_prcomp.Rd | 16 DataExplorer-0.8.4/DataExplorer/man/plot_qq.Rd | 10 DataExplorer-0.8.4/DataExplorer/man/plot_scatterplot.Rd | 16 DataExplorer-0.8.4/DataExplorer/man/plot_str.Rd | 8 DataExplorer-0.8.4/DataExplorer/man/profile_missing.Rd | 2 DataExplorer-0.8.4/DataExplorer/man/set_missing.Rd | 6 DataExplorer-0.8.4/DataExplorer/man/split_columns.Rd | 4 DataExplorer-0.8.4/DataExplorer/man/update_columns.Rd | 6 DataExplorer-0.8.4/DataExplorer/tests/testthat/Rplots.pdf |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-configure-report.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-create-report.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-drop-columns.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-dummify.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-group-category.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-internal.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-introduce.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-bar.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-boxplot.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-correlation.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-histogram-density.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-intro.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-missing.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-prcomp.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-qq.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-scatterplot.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-plot-str.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-profile-missing.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-set-missing.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-split-columns.R |only DataExplorer-0.8.4/DataExplorer/tests/testthat/test-update-columns.R |only 127 files changed, 294 insertions(+), 286 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon realms (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.2.0 dated 2025-06-13 and 1.3.0 dated 2025-07-24
DESCRIPTION | 14 - MD5 | 128 +++++++------ NAMESPACE | 7 NEWS.md | 12 + R/calibrate.R | 99 ++++++---- R/marine.R | 78 ++++---- R/plots.R | 234 ++++++++++++++++++++---- R/realms.R | 381 +++++++++++++++++++++++++++------------- R/rice-package.R | 2 R/rice.R | 23 +- R/sets.R | 87 +++++++++ R/sources.R | 299 +++++++++++++++++++++---------- README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rice.R | 11 + inst/doc/rice.Rmd | 23 ++ inst/doc/rice.html | 337 +++++++++++++++++++---------------- man/BCADtoC14.Rd | 5 man/BCADtoD14C.Rd | 4 man/BCADtoF14C.Rd | 4 man/BCADtopMC.Rd | 4 man/C14toBCAD.Rd | 5 man/C14toD14C.Rd | 4 man/C14toF14C.Rd | 6 man/C14tob2k.Rd | 5 man/C14tocalBP.Rd | 7 man/C14topMC.Rd | 4 man/CtoF.Rd |only man/D14CtoC14.Rd | 4 man/D14CtoF14C.Rd | 4 man/D14CtopMC.Rd | 4 man/F14CtoC14.Rd | 11 - man/F14CtoD14C.Rd | 4 man/F14CtopMC.Rd | 4 man/FtoC.Rd |only man/b2ktoC14.Rd | 5 man/b2ktoD14C.Rd | 4 man/b2ktoF14C.Rd | 4 man/b2ktopMC.Rd | 4 man/calBPtoC14.Rd | 5 man/calBPtoD14C.Rd | 4 man/calBPtoF14C.Rd | 4 man/calBPtopMC.Rd | 4 man/caldist.Rd | 10 - man/calibrate.Rd | 23 +- man/clean.Rd | 11 - man/contaminate.Rd | 18 + man/coverage.Rd |only man/draw.CF.Rd |only man/draw.ccurve.Rd | 15 + man/draw.contamination.Rd | 2 man/find.shells.Rd | 2 man/fractions.Rd | 28 +- man/hpd.Rd | 3 man/hpd.overlap.Rd |only man/map.shells.Rd | 2 man/muck.Rd | 22 +- man/pMCtoC14.Rd | 4 man/pMCtoD14C.Rd | 4 man/pMCtoF14C.Rd | 4 man/push.gamma.Rd | 3 man/push.normal.Rd | 3 man/r.calib.Rd | 5 tests/testthat/test-realms.R | 64 +++--- tests/testthat/test-rice.R | 91 --------- vignettes/findshells_browse.png |only vignettes/rice.Rmd | 23 ++ 68 files changed, 1413 insertions(+), 780 deletions(-)
Title: Simulation-Based Regularized Logistic Regression
Description: Regularized (polychotomous) logistic regression
by Gibbs sampling. The package implements subtly different
MCMC schemes with varying efficiency depending on the data type
(binary v. binomial, say) and the desired estimator (regularized maximum
likelihood, or Bayesian maximum a posteriori/posterior mean, etc.) through a
unified interface. For details, see Gramacy & Polson (2012 <doi:10.1214/12-BA719>).
Author: Robert B. Gramacy [cre, aut]
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between reglogit versions 1.2-7 dated 2023-04-25 and 1.2-8 dated 2025-07-24
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- man/pima.Rd | 3 --- man/reglogit.Rd | 2 +- 4 files changed, 13 insertions(+), 12 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.0.1 dated 2025-07-19 and 4.0.2 dated 2025-07-24
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++++------- NAMESPACE | 1 + NEWS.md | 13 +++++++++++++ R/compat.R |only R/nlmixr2.R | 2 +- R/nlmixr2Est.R | 2 +- R/sessioninfo.R | 11 ++++++++++- inst/testfit_nlmixr3.rds |only man/nlmixr2fix.Rd |only tests/testthat.R | 5 ++++- tests/testthat/_snaps |only tests/testthat/test-nlmixr3-load.R |only 13 files changed, 47 insertions(+), 16 deletions(-)
Title: Mathematics PhD Genealogy Data and Plotting
Description: Query, extract, and plot genealogical data from The Mathematics
Genealogy Project <https://mathgenealogy.org/>. Data is gathered from the
'WebSocket' server run by the 'geneagrapher-core' project
<https://github.com/davidalber/geneagrapher-core>.
Author: Louis Aslett [aut, cre]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Diff between maths.genealogy versions 0.1.3 dated 2025-07-07 and 0.1.4 dated 2025-07-24
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ R/disciplines.R | 6 +----- R/get_genealogy.R | 6 +----- R/plot_gg.R | 6 +----- R/plot_gg_path.R | 6 +----- R/plot_grviz.R | 6 +----- R/search_id.R | 9 ++++----- inst/doc/getting-started.html | 8 ++++---- man/disciplines.Rd | 6 ++---- man/get_genealogy.Rd | 6 ++---- man/plot_gg.Rd | 6 ++---- man/plot_gg_path.Rd | 6 ++---- man/plot_grviz.Rd | 6 ++---- man/search_id.Rd | 6 ++---- 16 files changed, 49 insertions(+), 78 deletions(-)
More information about maths.genealogy at CRAN
Permanent link
Title: Export 'grid' Graphics as SVG
Description: Functions to export graphics drawn with package grid to SVG
format. Additional functions provide access to SVG features that
are not available in standard R graphics, such as hyperlinks,
animation, filters, masks, clipping paths, and gradient and pattern fills.
Author: Paul Murrell [cre, aut],
Simon Potter [aut]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gridSVG versions 1.7-5 dated 2023-03-09 and 1.7-6 dated 2025-07-24
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 2 +- inst/doc/animation.pdf |binary inst/doc/extensibility.pdf |binary inst/doc/gridSVG.pdf |binary man/gradients.Rd | 2 +- man/readCoordsJS.Rd | 6 ++++-- man/readMappingsJS.Rd | 6 ++++-- 10 files changed, 22 insertions(+), 18 deletions(-)
Title: Download Flight and Airport Data from Brazil
Description: Download flight and airport data from Brazil’s Civil Aviation Agency
(ANAC) <https://www.gov.br/anac/pt-br>. The data covers detailed
information on aircraft, airports, and airport operations registered
with ANAC. It also includes data on airfares, all international
flights to and from Brazil, and domestic flights within the country.
Author: Rafael H. M. Pereira [aut, cre] ,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2025-05-19
Diff between flightsbr versions 1.1.0 dated 2025-05-19 and 1.1.1 dated 2025-07-24
DESCRIPTION | 6 +- MD5 | 39 +++++++-------- NEWS.md | 5 + R/utils.R | 12 ++-- README.md | 1 build/vignette.rds |binary inst/doc/airports.html | 3 - inst/doc/flights.html | 3 - inst/doc/intro_flightsbr.html | 1 man/altitude_to_numeric.Rd | 36 ++++++------- man/check_input_date_format.Rd | 58 +++++++++++----------- man/download_aircraft_data.Rd | 70 +++++++++++++-------------- man/get_aircraft_dates_available.Rd | 42 ++++++++-------- man/get_aircraft_url.Rd | 52 ++++++++++---------- man/latest_airfares_date.Rd | 62 +++++++++++------------ tests/tests_rafa/test_rafa.R | 1 tests/testthat/test_read_aircraft.R | 2 tests/testthat/test_read_airfares.R | 19 ++++--- tests/testthat/test_read_airport_movements.R | 11 ++-- tests/testthat/test_read_flights.R | 18 +++--- tests/testthat/test_utils.R |only 21 files changed, 229 insertions(+), 212 deletions(-)
Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers
including 'Claude' <https://claude.ai>, 'OpenAI'
<https://chatgpt.com>, and more. Supports streaming, asynchronous
calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] ,
Joe Cheng [aut],
Aaron Jacobs [aut],
Garrick Aden-Buie [aut] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between ellmer versions 0.2.1 dated 2025-06-03 and 0.3.0 dated 2025-07-24
ellmer-0.2.1/ellmer/R/chat-parallel.R |only ellmer-0.2.1/ellmer/R/content-tools.R |only ellmer-0.2.1/ellmer/R/provider-bedrock.R |only ellmer-0.2.1/ellmer/R/provider-claude.R |only ellmer-0.2.1/ellmer/R/provider-cortex.R |only ellmer-0.2.1/ellmer/R/provider-gemini-upload.R |only ellmer-0.2.1/ellmer/R/provider-gemini.R |only ellmer-0.2.1/ellmer/R/provider-huggingface.r |only ellmer-0.2.1/ellmer/R/shiny.R |only ellmer-0.2.1/ellmer/tests/testthat/_snaps/content-tools.md |only ellmer-0.2.1/ellmer/tests/testthat/_snaps/provider-bedrock.md |only ellmer-0.2.1/ellmer/tests/testthat/_snaps/provider-claude.md |only ellmer-0.2.1/ellmer/tests/testthat/_snaps/provider-cortex.md |only ellmer-0.2.1/ellmer/tests/testthat/_snaps/provider-gemini.md |only ellmer-0.2.1/ellmer/tests/testthat/test-chat-parallel.R |only ellmer-0.2.1/ellmer/tests/testthat/test-content-tools.R |only ellmer-0.2.1/ellmer/tests/testthat/test-provider-bedrock.R |only ellmer-0.2.1/ellmer/tests/testthat/test-provider-claude.R |only ellmer-0.2.1/ellmer/tests/testthat/test-provider-cortex.R |only ellmer-0.2.1/ellmer/tests/testthat/test-provider-gemini-upload.R |only ellmer-0.2.1/ellmer/tests/testthat/test-provider-gemini.R |only ellmer-0.3.0/ellmer/DESCRIPTION | 49 ellmer-0.3.0/ellmer/MD5 | 367 +++-- ellmer-0.3.0/ellmer/NAMESPACE | 8 ellmer-0.3.0/ellmer/NEWS.md | 44 ellmer-0.3.0/ellmer/R/batch-chat.R | 34 ellmer-0.3.0/ellmer/R/chat-structured.R | 88 - 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Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.1.4 dated 2025-03-20 and 1.1.5 dated 2025-07-24
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Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
Heather Turner [ctb],
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
David Firth [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.8-5 dated 2023-08-21 and 0.8-6 dated 2025-07-24
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Title: Measuring Agreement Using Sklar's Omega Coefficient
Description: Provides tools for applying Sklar's Omega (Hughes, 2022) <doi:10.1007/s11222-022-10105-2>
methodology to nominal scores, ordinal scores, percentages, counts, amounts (i.e.,
non-negative real numbers), and balances (i.e., any real number). The framework can
accommodate any number of units, any number of coders, and missingness; and
can be used to measure agreement with a gold standard, intra-coder agreement,
and/or inter-coder agreement. Frequentist inference is supported for all levels
of measurement. Bayesian inference is supported for continuous scores only.
Author: John Hughes [aut, cre]
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between sklarsomega versions 3.0-2 dated 2023-04-04 and 3.0-3 dated 2025-07-24
COPYING | 2 +- DESCRIPTION | 18 +++++++++++------- MD5 | 10 +++++----- R/sklarsomega.R | 10 +++++----- R/zzz.R | 2 +- man/sklars.omega.Rd | 2 +- 6 files changed, 24 insertions(+), 20 deletions(-)
Title: Collecting and Analyzing Mastodon Data
Description: An implementation of calls designed to collect and organize
Mastodon data via its Application Program Interfaces (API), which can
be found at the following URL: <https://docs.joinmastodon.org/>.
Author: David Schoch [aut, cre] ,
Chung-hong Chan [aut] ,
Johannes Gruber [ctb] ,
Tim Schatto-Eckrodt [ctb] ,
Lluis Revilla Sancho [aut]
Maintainer: David Schoch <david@schochastics.net>
Diff between rtoot versions 0.3.5 dated 2024-10-30 and 0.3.6 dated 2025-07-24
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Title: Tandem Clustering with Invariant Coordinate Selection
Description: Implementation of tandem clustering with invariant coordinate
selection with different scatter matrices and several choices for the
selection of components as described in Alfons, A., Archimbaud, A., Nordhausen, K.and Ruiz-Gazen, A. (2024) <doi:10.1016/j.ecosta.2024.03.002>.
Author: Aurore Archimbaud [aut, cre] ,
Andreas Alfons [aut] ,
Klaus Nordhausen [aut] ,
Anne Ruiz-Gazen [aut]
Maintainer: Aurore Archimbaud <aurore.archimbaud@live.fr>
Diff between ICSClust versions 0.1.0 dated 2023-09-21 and 0.1.1 dated 2025-07-24
DESCRIPTION | 21 +++++++++--------- MD5 | 32 ++++++++++++++-------------- R/ICSClust-package.R | 10 +++------ R/ICSClust.R | 13 ++++++----- R/plots.R | 4 ++- R/select_crit.R | 50 +++++++++++++++++++++++++++------------------ R/simulations.R | 10 +++++---- build/partial.rdb |binary man/ICSClust-package.Rd | 13 +++++++++-- man/ICSClust.Rd | 13 ++++++----- man/component_plot.Rd | 2 - man/discriminatory_crit.Rd | 30 ++++++++++++++++++--------- man/med_crit.Rd | 5 ++-- man/mixture_sim.Rd | 5 ++-- man/normal_crit.Rd | 9 ++++---- man/runif_outside_range.Rd | 5 ++-- man/var_crit.Rd | 5 ++-- 17 files changed, 134 insertions(+), 93 deletions(-)
Title: Extra Recipes Steps for Dealing with Omics Data
Description: Omics data (e.g. transcriptomics, proteomics,
metagenomics...) offer a detailed and multi-dimensional perspective
on the molecular components and interactions within complex biological
(eco)systems. Analyzing these data requires adapted procedures, which
are implemented as steps according to the 'recipes' package.
Author: Antoine BICHAT [aut, cre] ,
Julie AUBERT [ctb]
Maintainer: Antoine BICHAT <antoine.bichat@proton.me>
Diff between scimo versions 0.0.2 dated 2024-06-07 and 0.0.3 dated 2025-07-24
DESCRIPTION | 15 - MD5 | 78 ++++---- NEWS.md | 7 R/aggregate.R | 18 + R/aggregate_hclust.R | 124 ++++++++---- R/aggregate_list.R | 111 ++++++----- R/checks.R | 20 +- R/rownormalize_tss.R | 57 +++-- R/select_background.R | 64 +++--- R/select_cv.R | 83 +++++--- R/select_kruskal.R | 94 ++++++--- R/select_wilcoxon.R | 100 ++++++---- R/taxonomy.R | 74 ++++--- R/to_keep.R | 20 -- README.md | 137 +++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/pedcan.R | 22 +- inst/doc/pedcan.Rmd | 22 +- inst/doc/pedcan.html | 77 +++----- man/step_aggregate_hclust.Rd | 6 man/step_aggregate_list.Rd | 6 man/step_rownormalize_tss.Rd | 6 man/step_select_background.Rd | 6 man/step_select_cv.Rd | 6 man/step_select_kruskal.Rd | 6 man/step_select_wilcoxon.Rd | 6 man/step_taxonomy.Rd | 6 tests/testthat/test-aggregate.R | 27 +- tests/testthat/test-aggregate_hclust.R | 91 +++++---- tests/testthat/test-aggregate_list.R | 308 ++++++++++++++++++-------------- tests/testthat/test-checks.R | 19 + tests/testthat/test-rownormalize_tss.R | 4 tests/testthat/test-select_background.R | 112 ++++++----- tests/testthat/test-select_cv.R | 8 tests/testthat/test-select_kruskal.R | 56 +++-- tests/testthat/test-select_wilcoxon.R | 74 ++++--- tests/testthat/test-taxonomy.R | 40 ++-- tests/testthat/test-to_keep.R | 43 ++-- vignettes/pedcan.Rmd | 22 +- 40 files changed, 1124 insertions(+), 851 deletions(-)
Title: Kernel Machine Score Test for Semi-Competing Risks
Description: Kernel Machine Score Test for Pathway Analysis in the Presence of
Semi-Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018)
<doi: 10.1177/0962280216653427>.
Author: Matey Neykov [aut],
Boris P Hejblum [aut, cre],
Jennifer A Sinnot [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between kernscr versions 1.0.6 dated 2023-04-17 and 1.0.7 dated 2025-07-24
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/compute_all_tests.R | 21 +++++++++++---------- R/kernscr-package.R | 6 +++--- R/sim_SCR_data.R | 3 +-- man/compute_all_tests.Rd | 19 +++++++++---------- man/kernscr-package.Rd | 12 ++++++++++-- man/sim_SCR_data.Rd | 3 +-- 9 files changed, 53 insertions(+), 42 deletions(-)
Title: Extract-Transform-Load Framework for Medium Data
Description: A predictable and pipeable framework for performing ETL
(extract-transform-load) operations on publicly-accessible medium-sized data
set. This package sets up the method structure and implements generic
functions. Packages that depend on this package download specific data sets
from the Internet, clean them up, and import them into a local or remote
relational database management system.
Author: Benjamin S. Baumer [aut, cre] ,
Carson Sievert [ctb],
Natalia Iannucci [ctb]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between etl versions 0.4.1 dated 2023-10-12 and 0.4.2 dated 2025-07-24
DESCRIPTION | 15 +++--- MD5 | 68 +++++++++++++++--------------- NEWS.md | 6 ++ R/dbRunScript.R | 14 +++--- R/etl.R | 70 +++++++++++++++---------------- R/etl_cleanup.R | 6 +- R/etl_create.R | 50 +++++++++++----------- R/etl_extract.R | 20 ++++---- R/etl_load.R | 52 +++++++++++------------ R/etl_transform.R | 18 ++++---- R/utils.R | 85 +++++++++++++++++++------------------- README.md | 24 +++++----- build/vignette.rds |binary inst/doc/extending_etl.R | 12 +++-- inst/doc/extending_etl.Rmd | 8 +-- inst/doc/extending_etl.html | 60 ++++++++++++++------------ inst/doc/using_etl.R | 42 +++++++++--------- inst/doc/using_etl.Rmd | 18 ++++---- inst/doc/using_etl.html | 44 +++++++++---------- inst/src/etl_template.R | 2 man/create_etl_package.Rd | 10 ++-- man/dbRunScript.Rd | 12 ++--- man/dbWipe.Rd | 5 -- man/db_type.Rd | 4 - man/etl.Rd | 58 ++++++++++++------------- man/etl_create.Rd | 66 ++++++++++++++--------------- man/etl_init.Rd | 20 ++++---- man/match_files_by_year_months.Rd | 8 +-- man/smart_download.Rd | 4 - man/smart_upload.Rd | 6 +- man/src_mysql_cnf.Rd | 12 ++--- man/valid_year_month.Rd | 4 - tests/testthat/test-etl.R | 39 +++++++++-------- vignettes/extending_etl.Rmd | 8 +-- vignettes/using_etl.Rmd | 18 ++++---- 35 files changed, 454 insertions(+), 434 deletions(-)
Title: Automated Cytometry Gating and Annotation
Description: Given the hypothesis of a bi-modal distribution of cells for
each marker, the algorithm constructs a binary tree, the nodes of which are
subpopulations of cells. At each node, observed cells and markers are modeled
by both a family of normal distributions and a family of bi-modal normal mixture
distributions. Splitting is done according to a normalized difference of AIC
between the two families. Method is detailed in: Commenges, Alkhassim, Gottardo,
Hejblum & Thiebaut (2018) <doi: 10.1002/cyto.a.23601>.
Author: Chariff Alkhassim [aut],
Boris P Hejblum [cre, aut],
Anthony Devaux [aut],
Van Hung Huynh Tran [aut],
Melany Durand [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between cytometree versions 2.0.2 dated 2019-12-04 and 2.0.6 dated 2025-07-24
cytometree-2.0.2/cytometree/R/cytometree-package.R |only cytometree-2.0.2/cytometree/data/datalist |only cytometree-2.0.6/cytometree/DESCRIPTION | 37 cytometree-2.0.6/cytometree/LICENSE | 2 cytometree-2.0.6/cytometree/MD5 | 72 cytometree-2.0.6/cytometree/NAMESPACE | 1 cytometree-2.0.6/cytometree/NEWS.md | 20 cytometree-2.0.6/cytometree/R/CytEM.R | 8 cytometree-2.0.6/cytometree/R/CytofTree.R | 4 cytometree-2.0.6/cytometree/R/CytomeTree.R | 6 cytometree-2.0.6/cytometree/R/DLBCL.r | 2 cytometree-2.0.6/cytometree/R/HIPC.r | 24 cytometree-2.0.6/cytometree/R/IMdata.R | 2 cytometree-2.0.6/cytometree/R/RetrievePops.r | 6 cytometree-2.0.6/cytometree/R/cytometree_package.R |only cytometree-2.0.6/cytometree/R/plot_nodes.R | 9 cytometree-2.0.6/cytometree/README.md | 18 cytometree-2.0.6/cytometree/build/partial.rdb |only cytometree-2.0.6/cytometree/build/vignette.rds |binary cytometree-2.0.6/cytometree/inst/CITATION | 4 cytometree-2.0.6/cytometree/inst/doc/autogating_cytometree.R | 24 cytometree-2.0.6/cytometree/inst/doc/autogating_cytometree.Rmd | 8 cytometree-2.0.6/cytometree/inst/doc/autogating_cytometree.html | 3076 +++++++++- cytometree-2.0.6/cytometree/inst/doc/cytoftree.R | 4 cytometree-2.0.6/cytometree/inst/doc/cytoftree.Rmd | 2 cytometree-2.0.6/cytometree/inst/doc/cytoftree.html | 550 + cytometree-2.0.6/cytometree/man/CytofTree.Rd | 2 cytometree-2.0.6/cytometree/man/CytomeTree.Rd | 6 cytometree-2.0.6/cytometree/man/DLBCL.Rd | 6 cytometree-2.0.6/cytometree/man/HIPC.Rd | 29 cytometree-2.0.6/cytometree/man/IMdata.Rd | 6 cytometree-2.0.6/cytometree/man/RetrievePops.Rd | 4 cytometree-2.0.6/cytometree/man/cytometree-package.Rd | 50 cytometree-2.0.6/cytometree/man/figures |only cytometree-2.0.6/cytometree/man/plot_nodes.Rd | 3 cytometree-2.0.6/cytometree/src/RcppExports.cpp | 5 cytometree-2.0.6/cytometree/tests |only cytometree-2.0.6/cytometree/vignettes/autogating_cytometree.Rmd | 8 cytometree-2.0.6/cytometree/vignettes/cytoftree.Rmd | 2 39 files changed, 3497 insertions(+), 503 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.7.1 dated 2025-01-31 and 1.7.3 dated 2025-07-24
DESCRIPTION | 8 MD5 | 8 R/estimates.R | 1775 +++++++++++++++++++++++++++++++++++---------------- R/utils.R | 24 man/get_estimates.Rd | 2 5 files changed, 1247 insertions(+), 570 deletions(-)
Title: Pseudo-Likelihood Estimation of Log-Multiplicative Association
Models
Description: Log-multiplicative association models (LMA) are
models for cross-classifications of categorical variables
where interactions are represented by products of category
scale values and an association parameter. Maximum
likelihood estimation (MLE) fails for moderate to large
numbers of categorical variables. The 'pleLMA' package
overcomes this limitation of MLE by using pseudo-likelihood
estimation to fit the models to small or large
cross-classifications dichotomous or multi-category variables.
Originally proposed by Besag (1974,
<doi:10.1111/j.2517-6161.1974.tb00999.x>), pseudo-likelihood
estimation takes large complex models and breaks it down
into smaller ones. Rather than maximizing the likelihood
of the joint distribution of all the variables, a
pseudo-likelihood function, which is the product likelihoods
from conditional distributions, is maximized. LMA models can
be derived from a number of different frameworks including
(but not limited to) graphical models and uni-dimension [...truncated...]
Author: Carolyn J. Anderson [aut, cre]
Maintainer: Carolyn J. Anderson <cja@illinois.edu>
Diff between pleLMA versions 0.2.1 dated 2021-10-05 and 0.2.2 dated 2025-07-24
DESCRIPTION | 16 - MD5 | 52 +-- NEWS | 18 - NEWS.md |only R/ItemLoop.R | 2 R/StackData.R | 4 R/StackDataGPCM.R | 6 R/fitStack.R | 2 R/fitStackGPCM.R | 2 R/fit_gpcm.R | 2 R/fit_independence.R | 2 R/fit_nominal.R | 4 R/fit_rasch.R | 4 R/item_gpcm.R | 4 R/ple_lma.R | 20 - R/theta_estimates.R | 8 build/vignette.rds |binary inst/doc/pleLMA_vignette.R | 75 ++--- inst/doc/pleLMA_vignette.Rmd | 22 - inst/doc/pleLMA_vignette.html | 625 +++++++++++++++--------------------------- man/Meta |only man/StackData.Rd | 4 man/StackDataGPCM.Rd | 6 man/fit.rasch.Rd | 2 man/ple.lma.Rd | 2 man/theta.estimates.Rd | 6 tests/testthat/test_nominal.R | 6 vignettes/pleLMA_vignette.Rmd | 22 - 28 files changed, 365 insertions(+), 551 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 3.2 dated 2025-01-13 and 3.3 dated 2025-07-24
tmaptools-3.2/tmaptools/R/deprecated.R |only tmaptools-3.2/tmaptools/R/get_brewer_pal.R |only tmaptools-3.2/tmaptools/R/palette_explorer.R |only tmaptools-3.2/tmaptools/R/xxx_scales.R |only tmaptools-3.2/tmaptools/man/deprecated_functions.Rd |only tmaptools-3.2/tmaptools/man/get_brewer_pal.Rd |only tmaptools-3.2/tmaptools/man/palette_explorer.Rd |only tmaptools-3.2/tmaptools/man/pipe.Rd |only tmaptools-3.3/tmaptools/DESCRIPTION | 13 ++---- tmaptools-3.3/tmaptools/MD5 | 38 ++++++----------- tmaptools-3.3/tmaptools/NAMESPACE | 15 ------ tmaptools-3.3/tmaptools/NEWS.md | 4 + tmaptools-3.3/tmaptools/R/approx_distances.R | 2 tmaptools-3.3/tmaptools/R/bb.R | 19 +++++++- tmaptools-3.3/tmaptools/R/geocode_OSM.R | 5 +- tmaptools-3.3/tmaptools/R/map_coloring.R | 37 ++++------------- tmaptools-3.3/tmaptools/R/tmaptools-package.R | 14 ------ tmaptools-3.3/tmaptools/man/approx_areas.Rd | 12 ++--- tmaptools-3.3/tmaptools/man/approx_distances.Rd | 2 tmaptools-3.3/tmaptools/man/bb.Rd | 18 +++++--- tmaptools-3.3/tmaptools/man/map_coloring.Rd | 43 ++++++++++---------- tmaptools-3.3/tmaptools/man/rev_geocode_OSM.Rd | 5 +- tmaptools-3.3/tmaptools/man/simplify_shape.Rd | 14 +++--- tmaptools-3.3/tmaptools/man/tmaptools-package.Rd | 2 24 files changed, 108 insertions(+), 135 deletions(-)
Title: Several Examined and Concealed States-Dependent Speciation and
Extinction
Description: Simultaneously infers state-dependent diversification across
two or more states of a single or multiple traits while accounting for the
role of a possible concealed trait. See Herrera-Alsina et al. (2019)
<doi:10.1093/sysbio/syy057>.
Author: Leonel Herrera Alsina [aut] ,
Paul van Els [aut] ,
Thijs Janzen [ctb] ,
Hanno Hildenbrandt [ctb] ,
Pedro Santos Neves [ctb] ,
Rampal S. Etienne [cre, aut]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between secsse versions 3.1.0 dated 2024-04-30 and 3.5.0 dated 2025-07-24
DESCRIPTION | 26 MD5 | 113 NAMESPACE | 2 NEWS.md | 31 R/RcppExports.R | 12 R/default_params_doc.R | 42 R/seccse_multi_loglik.R |only R/secsse_loglik.R | 189 R/secsse_ml.R | 241 R/secsse_ml_func_def_pars.R | 45 R/secsse_prep.R | 70 R/secsse_sim.R | 164 R/secsse_single_branch.R |only R/secsse_utils.R | 246 build/partial.rdb |binary build/vignette.rds |binary inst/doc/complete_tree.html | 2197 +-- inst/doc/plotting_states.html | 223 inst/doc/sim_with_secsse.html | 2 inst/doc/starting_secsse.html |12884 +++++++++------------- man/cla_id_paramPos.Rd | 5 man/cla_secsse_loglik.Rd | 30 man/cla_secsse_ml.Rd | 44 man/cla_secsse_ml_func_def_pars.Rd | 46 man/create_lambda_list.Rd | 18 man/default_params_doc.Rd | 43 man/id_paramPos.Rd | 5 man/plot_idparslist.Rd |only man/plot_state_exact.Rd | 16 man/prepare_full_lambdas.Rd | 5 man/q_doubletrans.Rd | 5 man/secsse_loglik.Rd | 30 man/secsse_loglik_eval.Rd | 16 man/secsse_ml.Rd | 44 man/secsse_ml_func_def_pars.Rd | 50 man/secsse_sim.Rd | 8 man/secsse_single_branch_loglik.Rd |only man/sortingtraits.Rd | 3 src/RcppExports.cpp | 40 src/odeint.h | 65 src/secsse_eval.cpp | 142 src/secsse_loglik.cpp | 71 src/secsse_loglik.h | 53 src/secsse_rhs.h | 22 src/secsse_sim.cpp | 21 src/secsse_sim2.h | 10 src/secsse_single_branch.cpp |only tests/testthat/Rplots.pdf |only tests/testthat/test_cla_secsse_ml.R | 2 tests/testthat/test_cla_secsse_ml_func_def_pars.R | 55 tests/testthat/test_geosse.R | 40 tests/testthat/test_hisse.R | 78 tests/testthat/test_integration_methods.R | 38 tests/testthat/test_ml_func_def_pars.R | 2 tests/testthat/test_ml_par.R | 2 tests/testthat/test_multiphylo.R |only tests/testthat/test_plot_idparslist.R |only tests/testthat/test_plotting.R | 43 tests/testthat/test_secsse_ct.R | 126 tests/testthat/test_secsse_sim.R | 157 tests/testthat/test_secsse_vs_cla_secsse.R | 8 tests/testthat/test_single_branch.R |only 62 files changed, 8269 insertions(+), 9561 deletions(-)
Title: Test of Stationarity and Localized Autocovariance
Description: Provides test of second-order stationarity for time
series (for dyadic and arbitrary-n length data). Provides
localized autocovariance, with confidence intervals,
for locally stationary (nonstationary) time series.
See Nason, G P (2013) "A test for second-order stationarity and
approximate confidence intervals for localized autocovariance
for locally stationary time series." Journal of the Royal Statistical
Society, Series B, 75, 879-904. <doi:10.1111/rssb.12015>.
Author: Guy Nason [aut, cre]
Maintainer: Guy Nason <g.nason@imperial.ac.uk>
Diff between locits versions 1.7.7 dated 2023-09-05 and 1.7.8 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/CHANGES | 4 ++++ man/EstBetaCov.Rd | 4 ++-- man/Rvarlacf.Rd | 2 +- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: Bayesian Instrumental Regression for Disparity Estimation
Description: Bayesian models for accurately estimating conditional
distributions by race, using Bayesian Improved Surname Geocoding (BISG)
probability estimates of individual race. Implements the methods described
in McCartan, Fisher, Goldin, Ho and Imai (2025) <doi:10.1080/01621459.2025.2526695>.
Author: Cory McCartan [aut, cre],
Kosuke Imai [ctb],
Daniel Ho [ctb],
Jacob Goldin [ctb],
Robin Fisher [ctb],
The Stan Development Team [cph]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between birdie versions 0.6.1 dated 2024-06-11 and 0.7.1 dated 2025-07-24
DESCRIPTION | 14 +-- MD5 | 60 +++++++-------- NEWS.md | 7 + R/birdie-package.R | 7 + R/birdie.R | 7 + R/bisg.R | 6 - R/census.R | 36 ++++++++- R/model_cat_dir.R | 7 - R/model_lm.R | 3 R/stanmodels.R | 7 - R/weighted.R | 7 + README.md | 25 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 +- inst/doc/birdie.Rmd | 2 inst/doc/birdie.html | 91 +++++++++++------------ man/birdie-class.Rd | 38 ++++----- man/birdie-family.Rd | 4 - man/birdie-package.Rd | 9 +- man/birdie.Rd | 164 ++++++++++++++++++++++--------------------- man/birdie.ctrl.Rd | 10 +- man/bisg.Rd | 70 +++++++++--------- man/census_race_geo_table.Rd | 33 ++++---- man/disparities.Rd | 10 +- man/est_weighted.Rd | 33 ++++---- man/p_r_natl.Rd | 16 ++-- man/preproc.Rd | 14 +-- man/pseudo_vf.Rd | 8 +- tests/testthat/test-bisg.R | 6 + vignettes/birdie.Rmd | 2 31 files changed, 378 insertions(+), 327 deletions(-)
Title: Reconstructing the Regulatory Programs of Target Genes in
scRNA-Seq Data
Description: Implementation of the scregclust algorithm
described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3>
which reconstructs regulatory programs of target genes in scRNA-seq data.
Target genes are clustered into modules and each module is associated with a linear
model describing the regulatory program.
Author: Felix Held [aut, cre] ,
Ida Larsson [aut] ,
Sven Nelander [aut] ,
Andre Armatowski [ctb]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between scregclust versions 0.2.0 dated 2024-12-06 and 0.2.1 dated 2025-07-24
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++++---------- NEWS.md | 16 +++++++++++++++- R/scregclust.R | 3 ++- README.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/mouse.R |only inst/doc/mouse.Rmd |only inst/doc/mouse.html |only inst/doc/pbmc.Rmd | 8 ++++---- inst/doc/pbmc.html | 33 +++++++++++++++++---------------- src/optim.cpp | 14 ++++++++++++-- vignettes/mouse.Rmd |only vignettes/pbmc.Rmd | 8 ++++---- 15 files changed, 77 insertions(+), 46 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph] ,
Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.45.0 dated 2025-06-02 and 1.45.1 dated 2025-07-24
DESCRIPTION | 6 +-- MD5 | 46 +++++++++++++------------- NEWS.md | 19 ++++++++++ R/RichSOCKcluster.R | 18 +++++++--- R/availableConnections.R | 2 - R/utils,cluster.R | 13 ++++++- build/vignette.rds |binary inst/doc/parallelly-10-local-workers.html | 8 ++-- inst/doc/parallelly-10-local-workers.md | 8 ++-- inst/doc/parallelly-12-remote-workers.html | 32 +++++++++--------- inst/doc/parallelly-12-remote-workers.md | 32 +++++++++--------- inst/doc/parallelly-17-hpc-workers.html | 8 ++-- inst/doc/parallelly-17-hpc-workers.md | 8 ++-- inst/doc/parallelly-21-container-workers.html | 12 +++--- inst/doc/parallelly-21-container-workers.md | 12 +++--- inst/doc/parallelly-22-wine-workers.html | 25 +++++++------- inst/doc/parallelly-22-wine-workers.md | 29 ++++++++++------ man/availableConnections.Rd | 1 man/makeClusterPSOCK.Rd | 10 ++--- vignettes/parallelly-10-local-workers.md | 8 ++-- vignettes/parallelly-12-remote-workers.md | 32 +++++++++--------- vignettes/parallelly-17-hpc-workers.md | 8 ++-- vignettes/parallelly-21-container-workers.md | 12 +++--- vignettes/parallelly-22-wine-workers.md | 29 ++++++++++------ 24 files changed, 216 insertions(+), 162 deletions(-)
Title: Testing Infrastructure for Broom Model Generics
Description: Provides a number of testthat tests that can be
used to verify that tidy(), glance() and augment() methods meet
consistent specifications. This allows methods for the same generic to
be spread across multiple packages, since all of those packages can
make the same guarantees to users about returned objects.
Author: Alex Hayes [aut, cre] ,
Simon Couch [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between modeltests versions 0.1.6 dated 2024-05-03 and 0.1.7 dated 2025-07-24
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/check_arguments.R | 2 +- R/check_glance_outputs.R | 2 +- R/check_single_augment_output.R | 2 +- R/check_tibble.R | 4 ++-- R/utils.R | 1 + man/check_arguments.Rd | 2 +- man/check_glance_outputs.Rd | 2 +- man/check_single_augment_output.Rd | 2 +- man/check_tibble.Rd | 4 ++-- 12 files changed, 31 insertions(+), 26 deletions(-)
Title: Linkage Using Diagnosis Codes
Description: Probabilistic record linkage without direct identifiers using only
diagnosis codes. Method is detailed in: Hejblum, Weber, Liao, Palmer,
Churchill, Szolovits, Murphy, Kohane & Cai (2019) <doi: 10.1038/sdata.2018.298> ;
Zhang, Hejblum, Weber, Palmer, Churchill, Szolovits, Murphy, Liao, Kohane
& Cai (2021) <doi: 10.1093/jamia/ocab187>.
Author: Boris P Hejblum [aut, cre],
Harrison G Zhang [aut],
Tianxi Cai [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between ludic versions 0.2.0 dated 2021-08-18 and 0.2.1 dated 2025-07-24
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NEWS.md | 3 +++ R/atlas.R | 4 ++-- R/ludic-package.R | 14 ++++++-------- README.md | 15 ++++++++------- build/partial.rdb |binary inst/CITATION | 18 +++++++++--------- man/atlas.Rd | 2 +- man/ludic-package.Rd | 16 ++++++++++++---- src/Makevars | 13 +------------ src/Makevars.win | 13 +------------ src/RcppExports.cpp | 5 +++++ 13 files changed, 67 insertions(+), 73 deletions(-)
Title: Fast and Robust Hierarchical Clustering with Noise Point
Detection
Description: The Genie algorithm
(Gagolewski, 2021 <DOI:10.1016/j.softx.2021.100722>) is a robust
and outlier-resistant hierarchical clustering method
(Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>).
This package features its faster and more powerful version.
It allows clustering with respect to mutual reachability distances,
enabling it to act as a noise point detector or a version of
'HDBSCAN*' that can identify a predefined number of
clusters. The package also features an implementation
of the Gini and Bonferroni inequality indices, external cluster validity
measures (e.g., the normalised clustering accuracy, the adjusted Rand index,
the Fowlkes-Mallows index, and normalised mutual information), and internal
cluster validity indices (e.g., the Calinski-Harabasz, Davies-Bouldin,
Ball-Hall, Silhouette, and generalised Dunn indices).
The 'Python' version of 'genieclust' is available via 'PyPI'.
Author: Marek Gagolewski [aut, cre, cph] ,
Maciej Bartoszuk [ctb],
Anna Cena [ctb],
Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between genieclust versions 1.1.6 dated 2024-08-22 and 1.2.0 dated 2025-07-24
genieclust-1.1.6/genieclust/man/emst_mlpack.Rd |only genieclust-1.1.6/genieclust/src/c_distance.h |only genieclust-1.1.6/genieclust/src/c_mst.h |only genieclust-1.1.6/genieclust/src/r_emst.cpp |only genieclust-1.2.0/genieclust/DESCRIPTION | 54 -- genieclust-1.2.0/genieclust/MD5 | 111 ++-- genieclust-1.2.0/genieclust/NAMESPACE | 3 genieclust-1.2.0/genieclust/NEWS | 54 +- genieclust-1.2.0/genieclust/R/RcppExports.R | 105 +--- genieclust-1.2.0/genieclust/R/gclust.R | 219 ++++---- genieclust-1.2.0/genieclust/R/genieclust-package.R | 4 genieclust-1.2.0/genieclust/R/mst.R | 251 ++++------ genieclust-1.2.0/genieclust/man/cluster_validity.Rd | 22 genieclust-1.2.0/genieclust/man/compare_partitions.Rd | 51 +- genieclust-1.2.0/genieclust/man/gclust.Rd | 153 ++---- genieclust-1.2.0/genieclust/man/genieclust-package.Rd | 2 genieclust-1.2.0/genieclust/man/inequality.Rd | 22 genieclust-1.2.0/genieclust/man/mst.Rd | 133 ++--- genieclust-1.2.0/genieclust/src/Makevars | 2 genieclust-1.2.0/genieclust/src/Makevars.win | 2 genieclust-1.2.0/genieclust/src/RcppExports.cpp | 60 +- genieclust-1.2.0/genieclust/src/c_argfuns.h | 24 genieclust-1.2.0/genieclust/src/c_common.h | 133 ++++- genieclust-1.2.0/genieclust/src/c_compare_partitions.h | 20 genieclust-1.2.0/genieclust/src/c_cvi.h | 2 genieclust-1.2.0/genieclust/src/c_disjoint_sets.h | 53 +- genieclust-1.2.0/genieclust/src/c_genie.h | 145 ++--- genieclust-1.2.0/genieclust/src/c_gini_disjoint_sets.h | 35 - genieclust-1.2.0/genieclust/src/c_inequality.h | 6 genieclust-1.2.0/genieclust/src/c_int_dict.h | 4 genieclust-1.2.0/genieclust/src/c_lumbermark.h |only genieclust-1.2.0/genieclust/src/c_matrix.h | 6 genieclust-1.2.0/genieclust/src/c_mst_triple.h |only genieclust-1.2.0/genieclust/src/c_oldmst.h |only genieclust-1.2.0/genieclust/src/c_oldmst_distance.h |only genieclust-1.2.0/genieclust/src/c_postprocess.h | 40 - genieclust-1.2.0/genieclust/src/c_preprocess.h | 103 +++- genieclust-1.2.0/genieclust/src/c_scipy_rectangular_lsap.h | 2 genieclust-1.2.0/genieclust/src/cvi.h | 22 genieclust-1.2.0/genieclust/src/cvi_calinski_harabasz.h | 6 genieclust-1.2.0/genieclust/src/cvi_davies_bouldin.h | 4 genieclust-1.2.0/genieclust/src/cvi_dunnowa.h | 24 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_delta.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d1.h | 10 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d2.h | 6 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d3.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d4.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d5.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_lowercase_d6.h | 14 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_uppercase_d1.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_uppercase_d2.h | 8 genieclust-1.2.0/genieclust/src/cvi_generalized_dunn_uppercase_d3.h | 8 genieclust-1.2.0/genieclust/src/cvi_silhouette.h | 4 genieclust-1.2.0/genieclust/src/cvi_wcnn.h | 6 genieclust-1.2.0/genieclust/src/cvi_wcss.h | 2 genieclust-1.2.0/genieclust/src/r_compare_partitions.cpp | 51 +- genieclust-1.2.0/genieclust/src/r_cvi.cpp | 23 genieclust-1.2.0/genieclust/src/r_gclust.cpp | 165 ------ genieclust-1.2.0/genieclust/src/r_inequality.cpp | 22 genieclust-1.2.0/genieclust/src/r_oldmst.cpp |only 61 files changed, 1135 insertions(+), 1109 deletions(-)
Title: Sample Generalized Random Dot Product Graphs in Linear Time
Description: Samples generalized random product graphs, a generalization of
a broad class of network models. Given matrices X, S, and Y with with
non-negative entries, samples a matrix with expectation X S Y^T and
independent Poisson or Bernoulli entries using the fastRG algorithm of
Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The
algorithm first samples the number of edges and then puts them down
one-by-one. As a result it is O(m) where m is the number of edges, a
dramatic improvement over element-wise algorithms that which require
O(n^2) operations to sample a random graph, where n is the number of
nodes.
Author: Alex Hayes [aut, cre, cph] ,
Karl Rohe [aut, cph],
Jun Tao [aut],
Xintian Han [aut],
Norbert Binkiewicz [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between fastRG versions 0.3.2 dated 2023-08-21 and 0.3.3 dated 2025-07-24
DESCRIPTION | 15 ++- MD5 | 86 +++++++++++----------- NEWS.md | 4 + R/directed_dcsbm.R | 55 +++++--------- R/directed_erdos_renyi.R | 22 ++--- R/directed_factor_model.R | 57 ++++++-------- R/expected-degrees.R | 20 ++--- R/expected-spectra.R | 24 ------ R/plotting.R | 8 +- R/sample_edgelist.R | 38 +++------ R/sample_igraph.R | 25 ++---- R/sample_sparse.R | 25 ++---- R/sample_tidygraph.R | 24 ++---- R/undirected_chung_lu.R | 17 +--- R/undirected_dcsbm.R | 51 +++++-------- R/undirected_erdos_renyi.R | 20 ++--- R/undirected_factor_model.R | 55 ++++++-------- R/undirected_mmsbm.R | 12 --- R/undirected_overlapping_sbm.R | 8 -- R/undirected_planted_partition.R | 27 +++--- R/undirected_sbm.R | 24 ++---- R/utils.R | 2 README.md | 6 - man/chung_lu.Rd | 4 - man/dcsbm.Rd | 8 +- man/directed_dcsbm.Rd | 2 man/directed_erdos_renyi.Rd | 8 +- man/directed_factor_model.Rd | 16 ++-- man/erdos_renyi.Rd | 6 - man/expected_edges.Rd | 14 +-- man/mmsbm.Rd | 4 - man/planted_partition.Rd | 2 man/sample_igraph.Rd | 2 man/sample_sparse.Rd | 2 man/sample_tidygraph.Rd | 2 man/sbm.Rd | 6 - man/undirected_factor_model.Rd | 10 +- tests/testthat/test-allow_self_loops.R | 4 - tests/testthat/test-degree-scaling.R | 28 ++----- tests/testthat/test-directedness.R | 2 tests/testthat/test-poisson_edges.R | 2 tests/testthat/test-retain-isolated-nodes.R | 13 +-- tests/testthat/test-undirected-overlapping-sbms.R | 3 tests/testthat/test-undirected-sbms.R | 4 - 44 files changed, 320 insertions(+), 447 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2023) <doi:10.31234/osf.io/umt57>.
Author: Vencislav Popov [aut, cre, cph] ,
Gidon T. Frischkorn [aut, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Vencislav Popov <vencislav.popov@gmail.com>
Diff between bmm versions 1.0.1 dated 2024-05-27 and 1.2.0 dated 2025-07-24
bmm-1.0.1/bmm/man/pipe.Rd |only bmm-1.0.1/bmm/tests/testthat/test-bmmformula.R |only bmm-1.2.0/bmm/DESCRIPTION | 32 bmm-1.2.0/bmm/MD5 | 130 +-- bmm-1.2.0/bmm/NAMESPACE | 28 bmm-1.2.0/bmm/NEWS.md | 31 bmm-1.2.0/bmm/R/bmm.R | 74 +- bmm-1.2.0/bmm/R/bmmformula.R | 465 ++++++------ bmm-1.2.0/bmm/R/brms-misc.R | 73 + bmm-1.2.0/bmm/R/data.R | 24 bmm-1.2.0/bmm/R/distributions.R | 423 +++++++---- bmm-1.2.0/bmm/R/helpers-data.R | 73 - bmm-1.2.0/bmm/R/helpers-model.R | 329 ++++---- bmm-1.2.0/bmm/R/helpers-parameters.R | 23 bmm-1.2.0/bmm/R/helpers-postprocess.R | 16 bmm-1.2.0/bmm/R/helpers-prior.R | 374 +++++----- bmm-1.2.0/bmm/R/model_imm.R | 589 ++++++---------- bmm-1.2.0/bmm/R/model_m3.R |only bmm-1.2.0/bmm/R/model_mixture2p.R | 29 bmm-1.2.0/bmm/R/model_mixture3p.R | 111 +-- bmm-1.2.0/bmm/R/model_sdm.R | 76 -- bmm-1.2.0/bmm/R/restructure.R | 77 +- bmm-1.2.0/bmm/R/summary.R | 143 +-- bmm-1.2.0/bmm/R/update.R | 54 - bmm-1.2.0/bmm/R/utils.R | 368 +++++---- bmm-1.2.0/bmm/R/zzz.R | 17 bmm-1.2.0/bmm/README.md | 199 +++-- bmm-1.2.0/bmm/build/partial.rdb |binary bmm-1.2.0/bmm/data/oberauer_lewandowsky_2019_e1.rda |only bmm-1.2.0/bmm/inst/CITATION | 6 bmm-1.2.0/bmm/man/IMMdist.Rd | 18 bmm-1.2.0/bmm/man/SDMdist.Rd | 33 bmm-1.2.0/bmm/man/apply_links.Rd |only bmm-1.2.0/bmm/man/bmf2bf.Rd | 12 bmm-1.2.0/bmm/man/bmm-package.Rd | 1 bmm-1.2.0/bmm/man/bmm.Rd | 31 bmm-1.2.0/bmm/man/bmmformula.Rd | 10 bmm-1.2.0/bmm/man/construct_m3_act_funs.Rd |only bmm-1.2.0/bmm/man/imm.Rd | 70 + bmm-1.2.0/bmm/man/k2sd.Rd | 5 bmm-1.2.0/bmm/man/m3.Rd |only bmm-1.2.0/bmm/man/m3dist.Rd |only bmm-1.2.0/bmm/man/mixture2p.Rd | 16 bmm-1.2.0/bmm/man/mixture2p_dist.Rd | 6 bmm-1.2.0/bmm/man/mixture3p.Rd | 32 bmm-1.2.0/bmm/man/mixture3p_dist.Rd | 6 bmm-1.2.0/bmm/man/oberauer_lewandowsky_2019_e1.Rd |only bmm-1.2.0/bmm/man/postprocess_brm.Rd | 2 bmm-1.2.0/bmm/man/rejection_sampling.Rd |only bmm-1.2.0/bmm/man/revert_postprocess_brm.Rd | 2 bmm-1.2.0/bmm/man/sdm.Rd | 18 bmm-1.2.0/bmm/man/softmax.Rd | 2 bmm-1.2.0/bmm/man/standata.bmmformula.Rd | 7 bmm-1.2.0/bmm/man/summary.bmmfit.Rd | 2 bmm-1.2.0/bmm/man/update.bmmfit.Rd | 12 bmm-1.2.0/bmm/man/use_model_template.Rd | 2 bmm-1.2.0/bmm/tests/testthat/test-bmm.R | 91 +- bmm-1.2.0/bmm/tests/testthat/test-default-priors.R | 104 +- bmm-1.2.0/bmm/tests/testthat/test-distributions.R | 113 +++ bmm-1.2.0/bmm/tests/testthat/test-helpers-data.R | 307 +++----- bmm-1.2.0/bmm/tests/testthat/test-helpers-formula.R | 307 +++++++- bmm-1.2.0/bmm/tests/testthat/test-helpers-model.R | 26 bmm-1.2.0/bmm/tests/testthat/test-helpers-parameters.R |only bmm-1.2.0/bmm/tests/testthat/test-helpers-postprocess.R | 21 bmm-1.2.0/bmm/tests/testthat/test-helpers-prior.R | 23 bmm-1.2.0/bmm/tests/testthat/test-model_imm.R | 276 +++++-- bmm-1.2.0/bmm/tests/testthat/test-model_m3.R |only bmm-1.2.0/bmm/tests/testthat/test-model_mixture3p.R | 60 - bmm-1.2.0/bmm/tests/testthat/test-restructure.R | 3 bmm-1.2.0/bmm/tests/testthat/test-summary.R | 14 bmm-1.2.0/bmm/tests/testthat/test-update.R | 20 bmm-1.2.0/bmm/tests/testthat/test-utils.R | 137 ++- 72 files changed, 3103 insertions(+), 2450 deletions(-)
Title: Generalized and Classical Blockmodeling of Valued Networks
Description: This is primarily meant as an implementation of generalized blockmodeling for valued networks.
In addition, measures of similarity or dissimilarity based on structural equivalence and
regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted:
Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>,
Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>.
Author: Ales Ziberna [aut, cre],
Marjan Cugmas [ctb]
Maintainer: Ales Ziberna <ales.ziberna@gmail.com>
Diff between blockmodeling versions 1.1.5 dated 2023-08-23 and 1.1.7 dated 2025-07-24
CHANGES | 14 ++ DESCRIPTION | 9 - MD5 | 20 +-- NAMESPACE | 2 R/critFunC.R | 10 - R/encodeToZeroIndexed.R |only R/numClust.R |only R/unlistClu.R | 4 man/critFunC.Rd | 8 + man/encodeToZeroIndexed.Rd |only man/numClust.Rd |only man/unlistClu.Rd | 2 src/blockmodelingC.c | 293 +++++++++++++++++++++------------------------ 13 files changed, 189 insertions(+), 173 deletions(-)
Title: Partitioning Beta Diversity into Turnover and Nestedness
Components
Description: Functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.
Author: Andres Baselga [aut, cre],
David Orme [aut],
Sebastien Villeger [aut],
Julien De Bortoli [aut],
Fabien Leprieur [aut],
Maxime Logez [aut],
Sara Martinez-Santalla [aut],
Ramiro Martin-Devasa [aut],
Carola Gomez-Rodriguez [aut],
Rosa M. Crujeiras [aut] [...truncated...]
Maintainer: Andres Baselga <andres.baselga@usc.es>
Diff between betapart versions 1.6 dated 2023-03-13 and 1.6.1 dated 2025-07-24
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------ man/beta.pair.Rd | 2 - man/betapart-package.Rd | 2 - man/decay.model.Rd | 10 +++---- man/functional.betapart.core.Rd | 2 - man/functional.betapart.core.pairwise.Rd | 40 ++++++++++++++++--------------- man/inter_geom.Rd | 2 - man/qhull.opt.Rd | 2 - 9 files changed, 43 insertions(+), 41 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.6.2 dated 2025-05-28 and 0.7.0 dated 2025-07-24
DESCRIPTION | 13 MD5 | 219 ++++---- NAMESPACE | 4 NEWS.md | 177 +++--- R/afterhours_line.R | 6 R/calculate_distribution_summary.R |only R/collaboration_area.R | 2 R/collaboration_line.R | 6 R/create_boxplot.R | 18 R/create_bubble.R | 4 R/create_density.R | 31 - R/create_hist.R | 32 - R/create_inc.R | 33 + R/create_line.R | 26 R/create_line_asis.R | 28 - R/create_period_scatter.R | 8 R/create_rogers.R |only R/create_scatter.R | 8 R/create_stacked.R | 4 R/email_line.R | 6 R/external_line.R | 6 R/extract_hr.R | 8 R/flag_ch_ratio.R | 2 R/flag_em_ratio.R | 2 R/flag_extreme.R | 2 R/flag_outlooktime.R | 4 R/globals.R | 21 R/hrvar_count_all.R | 6 R/identify_habit.R | 9 R/identify_outlier.R | 2 R/identify_usage_segments.R | 496 +++++++++++++++---- R/keymetrics_scan.R | 4 R/meeting_line.R | 6 R/network_g2g.R | 2 R/one2one_line.R | 6 R/p2p_data_sim.R | 4 R/prep_query.R | 2 README.md | 1 man/afterhours_dist.Rd | 1 man/afterhours_fizz.Rd | 1 man/afterhours_line.Rd | 17 man/afterhours_rank.Rd | 1 man/afterhours_summary.Rd | 1 man/afterhours_trend.Rd | 1 man/calculate_distribution_summary.Rd |only man/collaboration_area.Rd | 1 man/collaboration_dist.Rd | 1 man/collaboration_fizz.Rd | 1 man/collaboration_line.Rd | 27 - man/collaboration_rank.Rd | 1 man/collaboration_sum.Rd | 1 man/collaboration_trend.Rd | 1 man/create_bar.Rd | 1 man/create_bar_asis.Rd | 1 man/create_boxplot.Rd | 1 man/create_bubble.Rd | 1 man/create_density.Rd | 17 man/create_dist.Rd | 1 man/create_fizz.Rd | 1 man/create_hist.Rd | 17 man/create_inc.Rd | 13 man/create_line.Rd | 13 man/create_line_asis.Rd | 20 man/create_period_scatter.Rd | 1 man/create_rank.Rd | 1 man/create_rogers.Rd |only man/create_sankey.Rd | 1 man/create_scatter.Rd | 1 man/create_stacked.Rd | 1 man/create_tracking.Rd | 1 man/create_trend.Rd | 1 man/email_dist.Rd | 1 man/email_fizz.Rd | 1 man/email_line.Rd | 17 man/email_rank.Rd | 1 man/email_summary.Rd | 1 man/email_trend.Rd | 1 man/external_dist.Rd | 1 man/external_fizz.Rd | 1 man/external_line.Rd | 17 man/external_rank.Rd | 1 man/external_sum.Rd | 1 man/hr_trend.Rd | 1 man/hrvar_count.Rd | 1 man/hrvar_trend.Rd | 1 man/identify_habit.Rd | 2 man/identify_inactiveweeks.Rd | 3 man/identify_nkw.Rd | 3 man/identify_usage_segments.Rd | 102 +++ man/keymetrics_scan.Rd | 1 man/meeting_dist.Rd | 1 man/meeting_fizz.Rd | 1 man/meeting_line.Rd | 17 man/meeting_rank.Rd | 1 man/meeting_summary.Rd | 1 man/meeting_trend.Rd | 1 man/network_p2p.Rd | 4 man/one2one_dist.Rd | 1 man/one2one_fizz.Rd | 1 man/one2one_freq.Rd | 1 man/one2one_line.Rd | 17 man/one2one_rank.Rd | 1 man/one2one_sum.Rd | 1 man/one2one_trend.Rd | 1 man/plot_ts_us.Rd | 48 + tests/testthat/test_calculate_distribution_summary.R |only tests/testthat/test_create_boxplot.R | 11 tests/testthat/test_create_density.R | 11 tests/testthat/test_create_hist.R | 11 tests/testthat/test_create_inc.R | 52 + tests/testthat/test_create_line.R | 26 tests/testthat/test_create_line_asis.R | 48 + tests/testthat/test_identify_usage_segments.R |only tests/testthat/test_max_window_truncation.R |only 114 files changed, 1340 insertions(+), 429 deletions(-)
Title: Covariance Inference and Decompositions for Tensor Datasets
Description: A collection of functions for Kronecker structured covariance
estimation and testing under the array normal model. For estimation,
maximum likelihood and Bayesian equivariant estimation procedures are
implemented. For testing, a likelihood ratio testing procedure is
available. This package also contains additional functions for manipulating
and decomposing tensor data sets. This work was partially supported by NSF
grant DMS-1505136. Details of the methods are described in
Gerard and Hoff (2015) <doi:10.1016/j.jmva.2015.01.020> and
Gerard and Hoff (2016) <doi:10.1016/j.laa.2016.04.033>.
Author: David Gerard [aut, cre] ,
Peter Hoff [aut]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between tensr versions 1.0.1 dated 2018-08-15 and 1.0.2 dated 2025-07-24
tensr-1.0.1/tensr/man/tensr.Rd |only tensr-1.0.2/tensr/DESCRIPTION | 17 tensr-1.0.2/tensr/MD5 | 139 - tensr-1.0.2/tensr/NAMESPACE | 76 - tensr-1.0.2/tensr/NEWS.md |only tensr-1.0.2/tensr/R/basic_tensor.R | 892 +++++------ tensr-1.0.2/tensr/R/equi_mcmc.R | 521 +++--- tensr-1.0.2/tensr/R/hoff_functions.R | 670 ++++---- tensr-1.0.2/tensr/R/like_inference.R | 563 +++---- tensr-1.0.2/tensr/R/loss_functions.R | 210 +- tensr-1.0.2/tensr/R/post_equi_mcmc.R | 633 ++++---- tensr-1.0.2/tensr/R/starting_values.R | 281 +-- tensr-1.0.2/tensr/R/tensor_decompositions.R | 1287 ++++++++--------- tensr-1.0.2/tensr/R/tensr.R | 136 - tensr-1.0.2/tensr/README.md | 185 +- tensr-1.0.2/tensr/build/partial.rdb |only tensr-1.0.2/tensr/build/vignette.rds |binary tensr-1.0.2/tensr/inst/CITATION | 62 tensr-1.0.2/tensr/inst/doc/equivariant_estimation.R | 360 ++-- tensr-1.0.2/tensr/inst/doc/equivariant_estimation.Rmd | 468 +++--- tensr-1.0.2/tensr/inst/doc/equivariant_estimation.html | 1096 +++++++------- tensr-1.0.2/tensr/inst/doc/maximum_likelihood.R | 160 +- tensr-1.0.2/tensr/inst/doc/maximum_likelihood.Rmd | 238 +-- tensr-1.0.2/tensr/inst/doc/maximum_likelihood.html | 883 ++++++----- tensr-1.0.2/tensr/man/Kom.Rd | 83 - tensr-1.0.2/tensr/man/amprod.Rd | 103 - tensr-1.0.2/tensr/man/anorm_cd.Rd | 105 - tensr-1.0.2/tensr/man/arrIndices.Rd | 56 tensr-1.0.2/tensr/man/array_bic_aic.Rd | 157 +- tensr-1.0.2/tensr/man/atrans.Rd | 93 - tensr-1.0.2/tensr/man/collapse_mode.Rd | 84 - tensr-1.0.2/tensr/man/convert_cov.Rd | 154 +- tensr-1.0.2/tensr/man/demean_tensor.Rd | 92 - tensr-1.0.2/tensr/man/equi_mcmc.Rd | 165 +- tensr-1.0.2/tensr/man/figures |only tensr-1.0.2/tensr/man/fnorm.Rd | 68 tensr-1.0.2/tensr/man/get_equi_bayes.Rd | 144 - tensr-1.0.2/tensr/man/get_isvd.Rd | 137 - tensr-1.0.2/tensr/man/holq.Rd | 294 +-- tensr-1.0.2/tensr/man/hooi.Rd | 129 - tensr-1.0.2/tensr/man/hosvd.Rd | 117 - tensr-1.0.2/tensr/man/ihop.Rd | 185 +- tensr-1.0.2/tensr/man/kendalltau.Rd | 62 tensr-1.0.2/tensr/man/ldan.Rd | 42 tensr-1.0.2/tensr/man/listprod.Rd | 48 tensr-1.0.2/tensr/man/lq.Rd | 92 - tensr-1.0.2/tensr/man/lrt_null_dist_dim_same.Rd | 241 +-- tensr-1.0.2/tensr/man/lrt_stat.Rd | 92 - tensr-1.0.2/tensr/man/mat.Rd | 83 - tensr-1.0.2/tensr/man/mhalf.Rd | 58 tensr-1.0.2/tensr/man/mle_from_holq.Rd | 86 - tensr-1.0.2/tensr/man/multi_stein_loss.Rd | 115 - tensr-1.0.2/tensr/man/multi_stein_loss_cov.Rd | 109 - tensr-1.0.2/tensr/man/multiway_takemura.Rd | 146 - tensr-1.0.2/tensr/man/polar.Rd | 84 - tensr-1.0.2/tensr/man/qr2.Rd | 74 tensr-1.0.2/tensr/man/random_ortho.Rd | 68 tensr-1.0.2/tensr/man/rmirror_wishart.Rd | 87 - tensr-1.0.2/tensr/man/rmvnorm.Rd | 68 tensr-1.0.2/tensr/man/rsan.Rd | 52 tensr-1.0.2/tensr/man/rwish.Rd | 62 tensr-1.0.2/tensr/man/sample_right_wishart.Rd | 86 - tensr-1.0.2/tensr/man/sample_sig.Rd | 96 - tensr-1.0.2/tensr/man/start_ident.Rd | 72 tensr-1.0.2/tensr/man/start_resids.Rd | 96 - tensr-1.0.2/tensr/man/tensr-package.Rd |only tensr-1.0.2/tensr/man/topK.Rd | 64 tensr-1.0.2/tensr/man/tr.Rd | 58 tensr-1.0.2/tensr/man/trim.Rd | 58 tensr-1.0.2/tensr/man/tsum.Rd | 32 tensr-1.0.2/tensr/man/zscores.Rd | 66 tensr-1.0.2/tensr/vignettes/equivariant_estimation.Rmd | 468 +++--- tensr-1.0.2/tensr/vignettes/maximum_likelihood.Rmd | 238 +-- 73 files changed, 7046 insertions(+), 7000 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.0.2 dated 2025-07-21 and 4.0.3 dated 2025-07-24
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ R/rxode2_md5.R | 2 +- R/utils.R | 21 ++++++++++++++++++++- inst/doc/rxode2-syntax.html | 27 ++++++++++++++------------- inst/include/rxode2parseVer.h | 4 ++-- man/rxUnloadAll.Rd | 7 ++++++- 8 files changed, 62 insertions(+), 28 deletions(-)
Title: Format Output of Various Routines in a Suitable Way for Reports
and Publication
Description: A bunch of convenience functions that transform the results of some basic statistical analyses
into table format nearly ready for publication. This includes descriptive tables, tables of
logistic regression and Cox regression results as well as forest plots.
Author: Thomas A. Gerds [aut, cre],
Christian Torp-Pedersen [ctb],
Klaus K Holst [ctb],
Brice Ozenne [aut]
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between Publish versions 2023.01.17 dated 2023-01-17 and 2025.07.24 dated 2025-07-24
Publish-2023.01.17/Publish/R/ci.mean.data.frame.R |only Publish-2023.01.17/Publish/tests/TestBaselineTable.pdf |only Publish-2023.01.17/Publish/tests/TestBaselineTable.tex |only Publish-2023.01.17/Publish/tests/test-glmSeries.R |only Publish-2023.01.17/Publish/tests/test-publish-gls.R |only Publish-2023.01.17/Publish/tests/test-publish-mi.R |only Publish-2023.01.17/Publish/tests/test-publish.R |only Publish-2023.01.17/Publish/tests/test-regressionTable.R |only Publish-2023.01.17/Publish/tests/test-univariateTable.R |only Publish-2025.07.24/Publish/DESCRIPTION | 8 - Publish-2025.07.24/Publish/MD5 | 60 +++----- Publish-2025.07.24/Publish/NAMESPACE | 2 Publish-2025.07.24/Publish/R/followupTable.R | 9 - Publish-2025.07.24/Publish/R/plotConfidence.R | 6 Publish-2025.07.24/Publish/R/print.regressionTable.R | 8 - Publish-2025.07.24/Publish/R/publish-package.R | 4 Publish-2025.07.24/Publish/R/publish.ci.R | 6 Publish-2025.07.24/Publish/R/publish.prodlim.R | 75 ++-------- Publish-2025.07.24/Publish/R/publish.riskReclassification.R | 32 ++-- Publish-2025.07.24/Publish/R/publish.riskRegression.R | 2 Publish-2025.07.24/Publish/R/regressionTable.R | 13 - Publish-2025.07.24/Publish/R/specialFrame.R | 22 +- Publish-2025.07.24/Publish/R/stripes.R | 6 Publish-2025.07.24/Publish/R/summary.ci.R | 2 Publish-2025.07.24/Publish/man/Publish-package.Rd | 17 ++ Publish-2025.07.24/Publish/man/followupTable.Rd | 5 Publish-2025.07.24/Publish/man/plotConfidence.Rd | 2 Publish-2025.07.24/Publish/man/print.regressionTable.Rd |only Publish-2025.07.24/Publish/man/publish.ci.Rd | 2 Publish-2025.07.24/Publish/man/publish.riskReclassification.Rd |only Publish-2025.07.24/Publish/man/publish.riskRegression.Rd | 2 Publish-2025.07.24/Publish/man/specialFrame.Rd | 22 +- Publish-2025.07.24/Publish/man/stripes.Rd | 2 Publish-2025.07.24/Publish/man/summary.ci.Rd | 2 Publish-2025.07.24/Publish/tests/testthat |only Publish-2025.07.24/Publish/tests/testthat.R |only 36 files changed, 156 insertions(+), 153 deletions(-)
Title: Prediction Error Curves for Risk Prediction Models in Survival
Analysis
Description: Validation of risk predictions obtained from survival models and
competing risk models based on censored data using inverse weighting and
cross-validation. Most of the 'pec' functionality has been moved to 'riskRegression'.
Author: Thomas A. Gerds [aut, cre]
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between pec versions 2023.04.12 dated 2023-04-11 and 2025.06.24 dated 2025-07-24
pec-2023.04.12/pec/R/marginal.prodlim.R |only pec-2023.04.12/pec/R/plot.CiCindex.R |only pec-2023.04.12/pec/R/predictLandmark.R |only pec-2025.06.24/pec/DESCRIPTION | 14 +- pec-2025.06.24/pec/MD5 | 74 ++++++------ pec-2025.06.24/pec/NAMESPACE | 1 pec-2025.06.24/pec/R/R2.R | 2 pec-2025.06.24/pec/R/Special.R | 2 pec-2025.06.24/pec/R/calPlot.R | 16 +- pec-2025.06.24/pec/R/crps.R | 2 pec-2025.06.24/pec/R/ipcw.R | 2 pec-2025.06.24/pec/R/pec.R | 3 pec-2025.06.24/pec/R/plot.pec.R | 6 - pec-2025.06.24/pec/R/plotPredictEventProb.R | 8 - pec-2025.06.24/pec/R/plotPredictSurvProb.R | 8 - pec-2025.06.24/pec/R/predictEventProb.R | 4 pec-2025.06.24/pec/R/predictEventProb.coxboost.R | 2 pec-2025.06.24/pec/R/predictLifeYearsLost.R | 4 pec-2025.06.24/pec/R/predictRestrictedMeanTime.R | 113 +++++++++---------- pec-2025.06.24/pec/R/predictSurvProb.R | 112 +++++++++--------- pec-2025.06.24/pec/R/print.pec.R | 2 pec-2025.06.24/pec/R/print.riskReclassification.R | 14 ++ pec-2025.06.24/pec/R/selectCox.R | 2 pec-2025.06.24/pec/man/R2.Rd | 2 pec-2025.06.24/pec/man/Special.Rd | 2 pec-2025.06.24/pec/man/calPlot.Rd | 16 +- pec-2025.06.24/pec/man/coxboost.Rd | 2 pec-2025.06.24/pec/man/crps.Rd | 2 pec-2025.06.24/pec/man/ipcw.Rd | 2 pec-2025.06.24/pec/man/pec.Rd | 3 pec-2025.06.24/pec/man/plot.pec.Rd | 6 - pec-2025.06.24/pec/man/plotPredictEventProb.Rd | 8 - pec-2025.06.24/pec/man/plotPredictSurvProb.Rd | 8 - pec-2025.06.24/pec/man/predictEventProb.Rd | 4 pec-2025.06.24/pec/man/predictLifeYearsLost.Rd | 4 pec-2025.06.24/pec/man/predictRestrictedMeanTime.Rd | 7 - pec-2025.06.24/pec/man/predictSurvProb.Rd | 2 pec-2025.06.24/pec/man/print.pec.Rd | 2 pec-2025.06.24/pec/man/print.riskReclassification.Rd |only pec-2025.06.24/pec/man/selectCox.Rd | 2 40 files changed, 229 insertions(+), 234 deletions(-)
Title: Parametric Frailty Models
Description: Fits Parametric Frailty Models by maximum marginal likelihood.
Possible baseline hazards:
exponential, Weibull, inverse Weibull (Fréchet),
Gompertz, lognormal, log-skew-normal, and loglogistic.
Possible Frailty distributions:
gamma, positive stable, inverse Gaussian and lognormal.
Author: Federico Rotolo [aut, cre],
Marco Munda [aut],
Andrea Callegaro [ctb]
Maintainer: Federico Rotolo <federico.rotolo@sanofi.com>
Diff between parfm versions 2.7.7 dated 2023-01-17 and 2.7.8 dated 2025-07-24
DESCRIPTION | 6 MD5 | 10 - build/partial.rdb |binary inst/CITATION | 8 man/parfm.Rd | 434 ++++++++++++++++++++++++++-------------------------- man/select.parfm.Rd | 184 +++++++++++----------- 6 files changed, 321 insertions(+), 321 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F. Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005> and K. Bartoszek, and J. Tredgett Clarke, J. Fuentes-Gonzalez, V. Mitov, J. Pienaar, M. Piwczynski, R. Puchalka, K. Spalik, K. L. Voje (2024) <doi:10.1111/2041-210X.14376>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Author: Krzysztof Bartoszek [cre, aut],
John Clarke [ctb],
Jesualdo Fuentes-Gonzalez [ctb],
Jason Pienaar [ctb]
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between mvSLOUCH versions 2.7.6 dated 2023-11-20 and 2.7.7 dated 2025-07-24
DESCRIPTION | 10 ++++----- MD5 | 38 ++++++++++++++++++------------------- man/BrownianMotionModel.Rd | 5 ++++ man/OU_RSS.Rd | 8 +++++++ man/OU_phylreg.Rd | 7 +++++- man/OU_xVz.Rd | 8 +++++++ man/SummarizeBM.Rd | 11 ++++++++++ man/SummarizeMVSLOUCH.Rd | 5 ++++ man/SummarizeOUCH.Rd | 5 ++++ man/estimate.evolutionary.model.Rd | 5 ++++ man/generate.model.setups.Rd | 10 +++++++++ man/mvSLOUCH-package.Rd | 14 +++++++++++-- man/mvslouchModel.Rd | 5 ++++ man/ouchModel.Rd | 5 ++++ man/parametric.bootstrap.Rd | 14 +++++++++++++ man/phyltree_paths.Rd | 2 - man/plot.clustered_phylo.Rd | 6 +++++ man/simulBMProcPhylTree.Rd | 16 +++++++++++++++ man/simulMVSLOUCHProcPhylTree.Rd | 16 +++++++++++++++ man/simulOUCHProcPhylTree.Rd | 16 +++++++++++++++ 20 files changed, 178 insertions(+), 28 deletions(-)
Title: k-Means Like Blockmodeling of One-Mode and Linked Networks
Description: Implements k-means like blockmodeling of one-mode and linked networks as presented in Žiberna (2020) <doi:10.1016/j.socnet.2019.10.006>. The development of this package is financially supported by the Slovenian Research Agency (<https://www.arrs.si/>) within the research programs P5-0168 and the research projects J7-8279 (Blockmodeling multilevel and temporal networks) and J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Ales Ziberna [aut, cre]
Maintainer: Ales Ziberna <ales.ziberna@fdv.uni-lj.si>
Diff between kmBlock versions 0.1.2 dated 2023-09-18 and 0.1.4 dated 2025-07-24
CHANGES | 10 +++ DESCRIPTION | 8 +- MD5 | 10 +-- R/kmBlock.r | 12 +--- man/kmBlock-package.Rd | 132 ++++++++++++++++++++++++------------------------- man/kmBlockORPC.Rd | 4 - 6 files changed, 92 insertions(+), 84 deletions(-)
Title: Interface Between the 'JDemetra+' Cruncher and R, and Quality
Report Generator
Description: Tool for generating quality reports from cruncher outputs
(and calculating series scores). The latest version of the cruncher
can be downloaded here:
<https://github.com/jdemetra/jwsacruncher/releases>.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between JDCruncheR versions 0.3.5 dated 2025-04-15 and 0.3.6 dated 2025-07-24
DESCRIPTION | 9 MD5 | 26 +- NEWS.md | 20 +- R/QR_export.R | 111 ++++++----- R/QR_functions.R | 356 ++++++++++++++++++++++--------------- R/QR_matrix_classes.R | 56 +++-- R/extractQR.R | 304 +++++++++++++++++++------------ R/thresholds.R | 4 R/zzz.R | 1 man/compute_score.Rd | 4 tests/testthat/data/demetra_m1.csv | 244 +------------------------ tests/testthat/data/demetra_m2.csv | 28 +- tests/testthat/data/demetra_m3.csv | 28 +- tests/testthat/test-extractQR.R | 41 +--- 14 files changed, 593 insertions(+), 639 deletions(-)
Title: Fast Machine Learning Model Training and Evaluation
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing
comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning.
It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut] ,
Eda Karaismailoglu [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between fastml versions 0.6.0 dated 2025-06-10 and 0.6.2 dated 2025-07-24
fastml-0.6.0/fastml/R/helper_functions.R |only fastml-0.6.0/fastml/R/models.R |only fastml-0.6.2/fastml/DESCRIPTION | 6 fastml-0.6.2/fastml/MD5 | 56 ++--- fastml-0.6.2/fastml/R/engine_helpers.R |only fastml-0.6.2/fastml/R/fastml.R | 88 ++++++-- fastml-0.6.2/fastml/R/model_selection_helpers.R |only fastml-0.6.2/fastml/R/params_helpers.R |only fastml-0.6.2/fastml/R/plot.fastml.R | 123 ++++++----- fastml-0.6.2/fastml/R/predict.fastml.R | 207 ++++++++----------- fastml-0.6.2/fastml/R/process_model.R |only fastml-0.6.2/fastml/R/spec_boosting.R |only fastml-0.6.2/fastml/R/spec_linear.R |only fastml-0.6.2/fastml/R/spec_other.R |only fastml-0.6.2/fastml/R/spec_tree.R |only fastml-0.6.2/fastml/R/summary.fastml.R | 2 fastml-0.6.2/fastml/R/train_models.R | 106 +++++++-- fastml-0.6.2/fastml/README.md | 14 + fastml-0.6.2/fastml/man/availableMethods.Rd | 2 fastml-0.6.2/fastml/man/fastml.Rd | 47 +++- fastml-0.6.2/fastml/man/flatten_and_rename_models.Rd | 2 fastml-0.6.2/fastml/man/get_best_model_idx.Rd | 2 fastml-0.6.2/fastml/man/get_best_model_names.Rd | 2 fastml-0.6.2/fastml/man/get_best_workflows.Rd | 2 fastml-0.6.2/fastml/man/get_default_engine.Rd | 2 fastml-0.6.2/fastml/man/get_default_params.Rd | 2 fastml-0.6.2/fastml/man/get_default_tune_params.Rd | 2 fastml-0.6.2/fastml/man/get_engine_names.Rd | 2 fastml-0.6.2/fastml/man/get_model_engine_names.Rd | 2 fastml-0.6.2/fastml/man/plot.fastml.Rd | 38 +++ fastml-0.6.2/fastml/man/predict.fastml.Rd | 10 fastml-0.6.2/fastml/man/process_model.Rd | 56 ++--- fastml-0.6.2/fastml/man/train_models.Rd | 23 +- fastml-0.6.2/fastml/tests/testthat/test-fastml.R | 159 ++++++++++++++ 34 files changed, 666 insertions(+), 289 deletions(-)
Title: Expectation-Maximization Algorithm for Multivariate Normal
(Gaussian) with Missing Data
Description: Initially designed to distribute code for estimating the Gaussian
graphical model with Lasso regularization, also known as the graphical lasso
(glasso), using an Expectation-Maximization (EM) algorithm based on work by
Städler and Bühlmann (2012) <doi:10.1007/s11222-010-9219-7>. As a byproduct,
code for estimating means and covariances (or the precision matrix) under a
multivariate normal (Gaussian) distribution is also available.
Author: Carl F. Falk [cre, aut]
Maintainer: Carl F. Falk <carl.falk@mcgill.ca>
Diff between EMgaussian versions 0.2.1 dated 2024-03-04 and 0.2.2 dated 2025-07-24
DESCRIPTION | 10 MD5 | 22 R/emcov.R | 7 R/emprec.R | 7 R/ggm.R | 38 - build/partial.rdb |binary man/EMggm.Rd | 38 - man/em.cov.Rd | 7 man/em.prec.Rd | 7 src/rcpp_EMcov.cpp | 5 src/rcpp_EMprec.cpp | 5 tests/testthat/_snaps/glasso.md | 1308 ++++++++++++++++++++-------------------- 12 files changed, 740 insertions(+), 714 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],
Dragoș Moldovan-Gruenfeld [aut],
Jeroen Ooms [aut],
Jacob Wujciak-Jens [aut],
Javier Luraschi [ctb],
Karl Dunkle Werner [...truncated...]
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between arrow versions 20.0.0.2 dated 2025-05-26 and 21.0.0 dated 2025-07-24
arrow-20.0.0.2/arrow/tools/cpp/CMakeLists.txt-e |only arrow-20.0.0.2/arrow/tools/cpp/build-support/cpplint.py |only arrow-20.0.0.2/arrow/tools/cpp/build-support/iwyu |only arrow-20.0.0.2/arrow/tools/cpp/build-support/lint_cpp_cli.py |only arrow-20.0.0.2/arrow/tools/cpp/build-support/lint_exclusions.txt |only arrow-20.0.0.2/arrow/tools/cpp/build-support/lintutils.py |only arrow-20.0.0.2/arrow/tools/cpp/build-support/run-infer.sh |only arrow-20.0.0.2/arrow/tools/cpp/build-support/run_clang_format.py |only arrow-20.0.0.2/arrow/tools/cpp/build-support/run_clang_tidy.py |only arrow-20.0.0.2/arrow/tools/cpp/build-support/run_cpplint.py |only arrow-20.0.0.2/arrow/tools/cpp/cmake_modules/AWSSDKVariables.cmake |only arrow-20.0.0.2/arrow/tools/cpp/cmake_modules/aws_sdk_cpp_generate_variables.sh |only arrow-20.0.0.2/arrow/tools/cpp/cmake_modules/thrift-cstdint.patch |only arrow-20.0.0.2/arrow/tools/cpp/src/arrow/acero/doc |only arrow-20.0.0.2/arrow/tools/cpp/src/arrow/acero/pch.h |only 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arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/reader_internal.cc | 16 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/reader_writer_benchmark.cc | 123 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/schema.cc | 185 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/schema_internal.cc | 88 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/schema_internal.h | 12 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/variant_internal.cc |only arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/variant_internal.h |only arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/writer.cc | 11 arrow-21.0.0/arrow/tools/cpp/src/parquet/arrow/writer.h | 7 arrow-21.0.0/arrow/tools/cpp/src/parquet/bloom_filter.cc | 2 arrow-21.0.0/arrow/tools/cpp/src/parquet/chunker_internal.cc |only arrow-21.0.0/arrow/tools/cpp/src/parquet/chunker_internal.h |only arrow-21.0.0/arrow/tools/cpp/src/parquet/chunker_internal_codegen.py |only arrow-21.0.0/arrow/tools/cpp/src/parquet/chunker_internal_generated.h |only 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|only arrow-21.0.0/arrow/tools/cpp/subprojects/zstd.wrap |only arrow-21.0.0/arrow/tools/cpp/thirdparty/README.md | 16 arrow-21.0.0/arrow/tools/cpp/thirdparty/update.rb |only arrow-21.0.0/arrow/tools/cpp/thirdparty/versions.txt | 95 arrow-21.0.0/arrow/tools/cpp/vcpkg.json | 8 arrow-21.0.0/arrow/tools/dotenv | 6 arrow-21.0.0/arrow/tools/nixlibs.R | 3 arrow-21.0.0/arrow/tools/ubsan.supp | 8 650 files changed, 12577 insertions(+), 7424 deletions(-)
Title: Phylogenetic Methods for Multiple Gene Data
Description: Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>.
'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Author: Klaus Schliep [aut, cre] ,
Thibaut Jombart [aut],
Zhian Namir Kamvar [aut],
Eric Archer [aut],
Rebecca Harris [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between apex versions 1.0.6 dated 2024-01-31 and 1.0.7 dated 2025-07-24
apex-1.0.6/apex/vignettes/apex.md |only apex-1.0.7/apex/DESCRIPTION | 11 - apex-1.0.7/apex/MD5 | 33 +-- apex-1.0.7/apex/NEWS | 7 apex-1.0.7/apex/R/concatenate.R | 3 apex-1.0.7/apex/R/exports.R | 10 - apex-1.0.7/apex/R/plot.R | 4 apex-1.0.7/apex/build/partial.rdb |binary apex-1.0.7/apex/build/vignette.rds |binary apex-1.0.7/apex/inst/doc/apex.R | 31 +-- apex-1.0.7/apex/inst/doc/apex.Rmd | 5 apex-1.0.7/apex/inst/doc/apex.html | 239 ++++++++++++++-------------- apex-1.0.7/apex/man/multidna2alignment.Rd | 2 apex-1.0.7/apex/man/multidna2genind.Rd | 6 apex-1.0.7/apex/man/multidna2multiphyDat.Rd | 2 apex-1.0.7/apex/man/plot-multidna-method.Rd | 2 apex-1.0.7/apex/vignettes/apex.Rmd | 5 apex-1.0.7/apex/vignettes/figs/concat-2.png |binary 18 files changed, 192 insertions(+), 168 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 1.0.0 dated 2025-05-07 and 1.1.0 dated 2025-07-24
DESCRIPTION | 10 ++-- MD5 | 21 ++++----- NAMESPACE | 1 NEWS.md | 18 +++++++ R/LoadingSaving.R | 2 R/Object.R | 82 ++++++++++++++++++++++++++++++------ R/Operations.R | 29 ++++++++++++ inst/doc/UsingAndromeda.html | 6 +- man/andromeda_constructor.Rd | 3 + man/flushAndromeda.Rd |only tests/testthat/test-loadingSaving.R | 10 ++-- tests/testthat/test-object.R | 8 +++ 12 files changed, 152 insertions(+), 38 deletions(-)
Title: Access and Analyse 'VALD' Data via Our External 'APIs'
Description: Provides helper functions and wrappers to simplify authentication,
data retrieval, and result processing from the 'VALD' 'APIs'.
Designed to streamline integration for analysts and researchers working
with 'VALD's external 'APIs'.
For further documentation on integrating with 'VALD' 'APIs', see:
<https://support.vald.com/hc/en-au/articles/23415335574553-How-to-integrate-with-VALD-APIs>.
For a step-by-step guide to using this package, see:
<https://support.vald.com/hc/en-au/articles/48730811824281-A-guide-to-using-the-valdr-R-package>.
Author: Kieran Harrison [aut, cre],
VALD Support [ctb],
VALD [cph]
Maintainer: Kieran Harrison <k.harrison@vald.com>
Diff between valdr versions 1.0.0 dated 2025-07-19 and 1.0.1 dated 2025-07-24
DESCRIPTION | 12 + MD5 | 34 ++-- R/auth.R | 4 R/config.R | 141 ++++++++++++++---- R/forcedecks_result_definitions.R | 3 R/zzz.R |only man/dot-onAttach.Rd |only man/dot-onLoad.Rd |only man/dot-retry_key_get.Rd |only man/get_access_token.Rd | 2 man/get_config.Rd | 8 - man/load_credentials.Rd | 14 - man/set_credentials.Rd | 10 - tests/testthat/helper-env.R | 24 ++- tests/testthat/test-2-set_credentials.R | 10 + tests/testthat/test-4-start_date_not_set.R | 12 + tests/testthat/test-5-start_date_set.R | 101 ++++++++---- tests/testthat/test-6-credential_region_handling.R | 12 - tests/testthat/test-7a-start_date_persistence_write.R | 13 - tests/testthat/test-7b-start_date_persistence_read.R | 11 - 20 files changed, 278 insertions(+), 133 deletions(-)
Title: Estimation of Smooth Hazard Models for Interval-Censored Data
Description: Estimation of two-state (survival) models and irreversible illness-
death models with possibly interval-censored, left-truncated and right-censored
data. Proportional intensities regression models can be specified to allow for
covariates effects separately for each transition. We use either a parametric
approach with Weibull baseline intensities or a semi-parametric approach with
M-splines approximation of baseline intensities in order to obtain smooth
estimates of the hazard functions. Parameter estimates are obtained by maximum
likelihood in the parametric approach and by penalized maximum likelihood in the
semi-parametric approach.
Author: Celia Touraine [aut],
Thomas Alexander Gerds [aut, cre],
Pierre Joly [aut] ,
Cecile Proust-Lima [aut] ,
Helene Jacqmin-Gadda [aut] ,
Amadou Diakite [aut] ,
W.D. Cody [aut] ,
A.H. Morris [aut] ,
B.W. Brown [aut] ,
Robin Genuer [ctb]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between SmoothHazard versions 2024.04.10 dated 2024-04-10 and 2025.07.24 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 50 +++++++++++++++++++++++++------------------------- R/idm.R | 8 ++++---- R/intensity.R | 6 +++--- R/plot.idm.R | 8 ++++---- R/plot.shr.R | 4 ++-- R/predict.idm.R | 4 ++-- R/print.idm.R | 4 ++-- R/print.shr.R | 4 ++-- R/shr.R | 6 +++--- R/simSurvIC.R | 2 +- R/simulateIDM.R | 2 +- R/summary.idm.R | 6 +++--- R/summary.shr.R | 6 +++--- man/idm.Rd | 8 ++++---- man/idmModel.Rd | 2 +- man/intensity.Rd | 2 +- man/plot.idm.Rd | 8 ++++---- man/plot.shr.Rd | 4 ++-- man/predict.idm.Rd | 4 ++-- man/print.idm.Rd | 4 ++-- man/print.shr.Rd | 4 ++-- man/shr.Rd | 6 +++--- man/summary.idm.Rd | 6 +++--- man/summary.shr.Rd | 6 +++--- man/survIC.Rd | 2 +- 26 files changed, 87 insertions(+), 87 deletions(-)
Title: Parse Messy Geographic Coordinates
Description: Parse messy geographic coordinates from various character formats
to decimal degree numeric values. Parse coordinates into
their parts (degree, minutes, seconds); calculate hemisphere
from coordinates; pull out individually degrees,
minutes, or seconds; add and subtract degrees, minutes,
and seconds. C++ code herein originally inspired from code
written by Jeffrey D. Bogan, but then completely re-written.
Author: Scott Chamberlain [aut] ,
Alban Sagouis [aut, cre] ,
Alec L. Robitaille [ctb] ,
Maelle Salmon [ctb] ,
Hiroaki Yutani [ctb],
Jeffrey Bogan [ctb] ,
Julien Brun [rev] ,
Maria Munafo [rev] ,
rOpenSci [fnd] ,
German Centre for Integrative Biodiversity Res [...truncated...]
Maintainer: Alban Sagouis <sagouis@pm.me>
This is a re-admission after prior archival of version 0.4.3 dated 2025-05-29
Diff between parzer versions 0.4.3 dated 2025-05-29 and 0.4.4 dated 2025-07-24
DESCRIPTION | 6 +-- MD5 | 37 +++++++++++----------- NEWS.md | 8 ++++ R/dms-fxns.R | 24 ++------------ R/parzer-package.R | 2 - R/zzz.R | 4 +- inst/doc/parzer.html | 47 +++++----------------------- inst/doc/use_cases.html | 55 +++++++-------------------------- src/RcppExports.cpp | 2 - src/latlong.cpp | 6 +-- src/pz_parse_parts.cpp | 19 ++++++----- tests/testthat/setup.R |only tests/testthat/test-dms.R | 3 + tests/testthat/test-parse_hemisphere.R | 17 +++++++--- tests/testthat/test-parse_lat.R | 24 ++++++++++++-- tests/testthat/test-parse_lat_lon.R | 22 +++++++++++++ tests/testthat/test-parse_llstr.R | 9 +++++ tests/testthat/test-parse_lon.R | 34 ++++++++++++++++++-- tests/testthat/test-parse_parts.R | 26 +++++++++++++++ tests/testthat/test-utils.R | 6 ++- 20 files changed, 201 insertions(+), 150 deletions(-)
Title: Map User-Created Functions
Description: Create an interactive function map by analyzing a specified
R script. It uses the find_dependencies() function from the
'functiondepends' package to recursively trace all user-defined
function dependencies.
Author: Antonio Fratamico [aut, cre]
Maintainer: Antonio Fratamico <fratamicoa@outlook.com>
Diff between funcMapper versions 1.0.0 dated 2025-07-22 and 1.0.1 dated 2025-07-24
DESCRIPTION | 8 +++++--- MD5 | 4 ++-- NEWS.md | 6 +++++- 3 files changed, 12 insertions(+), 6 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.0 dated 2025-07-15 and 1.5.2 dated 2025-07-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/repeated_twoway_generation.R | 2 +- inst/doc/eSp_balanced_design_powertest.html | 8 ++++---- tests/testthat/test-repeated_twoway_generation.R | 11 +++++++++++ 6 files changed, 30 insertions(+), 13 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Visualize the Effect of a Continuous Variable on a Time-to-Event
Outcome
Description: Graphically display the (causal) effect of a continuous variable on a time-to-event outcome
using multiple different types of plots based on g-computation. Those functions
include, among others, survival area plots, survival contour plots, survival quantile plots and
3D surface plots. Due to the use of g-computation, all plot allow confounder-adjustment naturally.
For details, see Robin Denz, Nina Timmesfeld (2023) <doi:10.1097/EDE.0000000000001630>.
Author: Robin Denz [aut, cre]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between contsurvplot versions 0.2.1 dated 2023-08-15 and 0.2.2 dated 2025-07-24
DESCRIPTION | 8 MD5 | 101 - NEWS.md | 25 R/curve_cont.r | 10 R/curve_cont_auc.r |only R/plot_surv_3Dsurface.r | 4 R/plot_surv_animated.r | 10 R/plot_surv_lines.r | 7 R/plot_surv_rmst.r | 51 R/plot_surv_rmtl.r | 10 build/vignette.rds |binary inst/doc/introduction.R | 48 inst/doc/introduction.html | 555 ++++------ man/curve_cont.Rd | 6 man/plot_surv_3Dsurface.Rd | 4 man/plot_surv_animated.Rd | 4 man/plot_surv_area.Rd | 4 man/plot_surv_at_t.Rd | 4 man/plot_surv_contour.Rd | 14 man/plot_surv_heatmap.Rd | 4 man/plot_surv_lines.Rd | 4 man/plot_surv_matrix.Rd | 4 man/plot_surv_quantiles.Rd | 4 man/plot_surv_rmst.Rd | 4 man/plot_surv_rmtl.Rd | 4 tests/testthat/_snaps/plot_surv_area/plot-at-t.svg | 14 tests/testthat/_snaps/plot_surv_area/plot-change-horizon.svg | 18 tests/testthat/_snaps/plot_surv_area/plot-cif.svg | 14 tests/testthat/_snaps/plot_surv_area/plot-custom-colors.svg | 16 tests/testthat/_snaps/plot_surv_area/plot-defaults.svg | 14 tests/testthat/_snaps/plot_surv_area/plot-lots-of-stuff.svg | 4 tests/testthat/_snaps/plot_surv_area/plot-with-group.svg | 14 tests/testthat/_snaps/plot_surv_area/plot-with-nonmonotonic.svg | 20 tests/testthat/_snaps/plot_surv_contour/plot-at-t.svg | 37 tests/testthat/_snaps/plot_surv_contour/plot-change-horizon.svg | 60 - tests/testthat/_snaps/plot_surv_contour/plot-defaults.svg | 60 - tests/testthat/_snaps/plot_surv_contour/plot-lots-of-stuff.svg | 102 + tests/testthat/_snaps/plot_surv_contour/plot-panel-border-axis-dist.svg | 50 tests/testthat/_snaps/plot_surv_contour/plot-with-group.svg | 120 +- tests/testthat/_snaps/plot_surv_heatmap/plot-at-t.svg | 18 tests/testthat/_snaps/plot_surv_heatmap/plot-change-horizon.svg | 18 tests/testthat/_snaps/plot_surv_heatmap/plot-cif.svg | 18 tests/testthat/_snaps/plot_surv_heatmap/plot-contour-lines.svg | 19 tests/testthat/_snaps/plot_surv_heatmap/plot-custom-colors.svg | 22 tests/testthat/_snaps/plot_surv_heatmap/plot-defaults.svg | 18 tests/testthat/_snaps/plot_surv_heatmap/plot-lots-of-stuff.svg | 22 tests/testthat/_snaps/plot_surv_heatmap/plot-panel-border-axis-dist.svg | 18 tests/testthat/_snaps/plot_surv_heatmap/plot-with-group.svg | 20 tests/testthat/_snaps/plot_surv_lines/plot-change-horizon.svg | 8 tests/testthat/_snaps/plot_surv_lines/plot-cont-color.svg | 14 tests/testthat/_snaps/plot_surv_lines/plot-lots-of-stuff.svg | 12 tests/testthat/_snaps/plot_surv_rmst/plot-lots-of-stuff.svg | 3 52 files changed, 820 insertions(+), 822 deletions(-)
Title: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
'NIFTI' Format
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or 'NIFTI' format. Note that the latest version of 'XQuartz' seems to be necessary under MacOS.
Author: Pierre Lafaye De Micheaux [aut, cre],
Jonathan L Marchini [aut],
Cleve Moler [cph] ,
Jack Dongarra [cph] ,
Richard Hanson [cph] ,
Sven Hammarling [cph] ,
Jeremy Du Croz [cph]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
This is a re-admission after prior archival of version 1.1-24 dated 2021-10-05
Diff between AnalyzeFMRI versions 1.1-24 dated 2021-10-05 and 1.1-25 dated 2025-07-24
DESCRIPTION | 14 MD5 | 134 ++-- R/analyzeFMRI.R | 64 +- R/niftiFMRI.R | 164 +++-- R/with_dir.R |only TODO | 30 + inst/AnalyzeFMRI.gui.R | 20 inst/CITATION | 8 inst/HISTORY | 51 + inst/ICA.gui.R | 16 inst/ICAst.gui.R | 9 inst/plot.volume.gui.R | 170 ++++-- inst/smoothing.examples.R | 7 man/ICAspat.Rd | 11 man/ICAtemp.Rd | 4 man/N2G.Rd | 2 man/N2G.Spatial.Mixture.Rd | 6 man/NonLinearSmoothArray.Rd | 5 man/SmoothEst.Rd | 4 man/analyze2nifti.Rd | 11 man/centering.Rd | 4 man/eigenvalues.Rd | 8 man/f.analyze.file.summary.Rd | 2 man/f.basic.hdr.list.create.Rd | 4 man/f.basic.hdr.nifti.list.create.Rd | 8 man/f.complete.hdr.nifti.list.create.Rd | 6 man/f.icast.fmri.Rd | 5 man/f.nifti.file.summary.Rd | 2 man/f.plot.ica.fmri.Rd | 1 man/f.plot.ica.fmri.jpg.Rd | 5 man/f.plot.volume.gui.Rd | 8 man/f.read.analyze.slice.Rd | 2 man/f.read.analyze.slice.at.all.timepoints.Rd | 2 man/f.read.analyze.tpt.Rd | 2 man/f.read.analyze.ts.Rd | 2 man/f.read.analyze.volume.Rd | 2 man/f.read.header.Rd | 4 man/f.read.nifti.header.Rd | 4 man/f.read.nifti.slice.Rd | 2 man/f.read.nifti.slice.at.all.timepoints.Rd | 3 man/f.read.nifti.tpt.Rd | 2 man/f.read.nifti.ts.Rd | 2 man/f.read.nifti.volume.Rd | 2 man/f.read.volume.Rd | 2 man/f.spectral.summary.nifti.Rd | 3 man/f.write.analyze.Rd | 16 man/f.write.array.to.img.2bytes.Rd | 3 man/f.write.array.to.img.8bit.Rd | 3 man/f.write.array.to.img.float.Rd | 6 man/f.write.list.to.hdr.Rd | 17 man/f.write.list.to.hdr.nifti.Rd | 17 man/f.write.nifti.Rd | 9 man/f.write.nii.array.to.img.2bytes.Rd | 3 man/f.write.nii.array.to.img.8bit.Rd | 3 man/f.write.nii.array.to.img.float.Rd | 6 man/fourDto2D.Rd | 8 man/magicfield.Rd | 7 man/reduction.Rd | 6 man/threeDto4D.Rd | 28 - man/twoDto4D.Rd | 13 man/with_dir.Rd |only man/xyzt2st.Rd | 7 src/analyzeFMRI.c | 413 ++++++++++---- src/niftiFMRI.c | 14 src/slapack.unused | 719 +++++++++++++------------- src/spatial.c | 56 +- src/spatial.filters.non.linear.c | 22 tests/test.R | 8 tests/test.Rout.save | 21 69 files changed, 1298 insertions(+), 924 deletions(-)
Title: Robust Beta Regression
Description: Robust estimators for the beta regression, useful for modeling
bounded continuous data. Currently, four types of robust estimators are supported.
They depend on a tuning constant which may be fixed or selected by a
data-driven algorithm also implemented in the package. Diagnostic tools
associated with the fitted model, such as the residuals and goodness-of-fit
statistics, are implemented. Robust Wald-type tests are available. More details
about robust beta regression are described in Maluf et al. (2025)
<doi:10.1007/s00184-024-00949-1>.
Author: Felipe Queiroz [aut, cre],
Yuri Maluf [aut],
Silvia Ferrari [ctb]
Maintainer: Felipe Queiroz <ffelipeq@outlook.com>
Diff between robustbetareg versions 0.3.0 dated 2022-10-28 and 0.3.1 dated 2025-07-24
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- R/robustbetareg.R | 18 +++++++++--------- man/EGB.Rd | 2 +- man/plotenvelope.Rd | 2 +- man/residuals.robustbetareg.Rd | 4 ++-- man/robustbetareg.Rd | 4 ++-- man/robustbetareg.control.Rd | 2 +- man/waldtypetest.Rd | 4 ++-- 9 files changed, 32 insertions(+), 31 deletions(-)
Title: Store Data About Rows
Description: Tools for keeping track of information, named
"keys", about rows of data frame like objects. This is done by
creating special attribute "keys" which is updated after every change
in rows (subsetting, ordering, etc.). This package is designed to
work tightly with 'dplyr' package.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between keyholder versions 0.1.7 dated 2023-03-11 and 0.1.8 dated 2025-07-24
DESCRIPTION | 11 + MD5 | 44 +++---- NAMESPACE | 2 NEWS.md | 4 R/id.R | 6 - R/keyed-df-one-tbl.R | 2 R/keyed-df-two-tbl.R | 102 +++++++++++++---- R/keys-manip.R | 20 ++- R/keys-set.R | 9 + R/scoped.R | 194 +++++++++++++++++++++++---------- R/utils.R | 2 README.md | 36 ++---- build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 63 +++++----- man/keyed-df-one-tbl.Rd | 2 man/keyed-df-two-tbl.Rd | 2 tests/testthat/test-id.R | 8 - tests/testthat/test-keyed-df-one-tbl.R | 79 ++++++++----- tests/testthat/test-keyed-df-two-tbl.R | 83 +++++++++----- tests/testthat/test-keys-manip.R | 32 ++++- tests/testthat/test-scoped.R | 110 ++++++++++++------ tests/testthat/test-utils.R | 27 ++-- 23 files changed, 555 insertions(+), 285 deletions(-)
Title: Flexible Segment Geoms with Arrows for 'ggplot2'
Description: Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.
Author: Matthew Hall [aut, cre]
Maintainer: Matthew Hall <matthew.hall@lshtm.ac.uk>
Diff between ggarchery versions 0.4.3 dated 2024-03-28 and 0.4.4 dated 2025-07-24
DESCRIPTION | 12 ++++---- MD5 | 6 ++-- R/geom-arrowsegment.R | 2 - man/geom_arrowsegment.Rd | 69 ++++++++++++++++++++++++++++++++++++----------- 4 files changed, 64 insertions(+), 25 deletions(-)
Title: Dose Titration Algorithm Tuning
Description: Dose Titration Algorithm Tuning (DTAT) is a methodologic framework
allowing dose individualization to be conceived as a continuous
learning process that begins in early-phase clinical trials and
continues throughout drug development, on into clinical practice.
This package includes code that researchers may use to reproduce
or extend key results of the DTAT research programme, plus tools
for trialists to design and simulate a '3+3/PC' dose-finding study.
Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and
Norris (2017c) <doi:10.1101/240846>.
Author: David C. Norris [aut, cre]
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between DTAT versions 0.3-7 dated 2024-05-24 and 0.3-8 dated 2025-07-24
DESCRIPTION | 10 MD5 | 26 +- R/DTAT-package.R | 6 R/Onoue.Friberg.R | 38 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DTAT-package.bib | 4 inst/doc/Designing-33PC.R | 2 inst/doc/Designing-33PC.html | 450 ++++++++++++++++++++++++++++++------------- inst/doc/dtat.R | 26 +- inst/doc/dtat.pdf |binary man/DTAT-package.Rd | 10 man/Onoue.Friberg.Rd | 2 vignettes/DTAT-package.bib | 4 14 files changed, 386 insertions(+), 192 deletions(-)
Title: Building and Estimating Structural Equation Models
Description: A powerful, easy to use syntax for specifying and estimating complex
Structural Equation Models. Models can be estimated using Partial
Least Squares Path Modeling or Covariance-Based Structural Equation
Modeling or covariance based Confirmatory Factor Analysis. Methods described in Ray, Danks, and Valdez (2021).
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
Andre Calero Valdez [aut],
Juan Manuel Velasquez Estrada [ctb],
James Uanhoro [ctb],
Johannes Nakayama [ctb],
Lilian Koyan [ctb],
Laura Burbach [ctb],
Arturo Heynar Cano Bejar [ctb],
Susanne A [...truncated...]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminr versions 2.3.4 dated 2024-10-13 and 2.3.6 dated 2025-07-24
DESCRIPTION | 16 MD5 | 68 NAMESPACE | 5 R/estimate_bootstrap.R | 3 R/estimate_pls.R | 14 R/estimate_simplePLS.R | 2 R/evaluate_measurement_model.R | 2 R/evaluate_model.R | 139 R/evaluate_reliability.R | 402 - R/evaluate_validity.R | 190 R/feature_consistent.R | 2 R/feature_plspredict.R | 292 - R/import_lavaan_syntax.R | 15 R/inspect_mmMatrix.R | 4 R/inspect_smMatrix.R | 4 R/library.R | 777 +- R/plot_dot.R | 3348 +++++------- R/report_cbsem.R | 2 R/report_cfa.R | 2 R/report_paths_and_intervals.R | 53 R/report_summary.R | 8 build/vignette.rds |binary demo/seminr-primer-chap2.R | 6 inst/doc/SEMinR.R | 322 - inst/doc/SEMinR.html | 28 man/csem2seminr.Rd | 15 man/estimate_pls.Rd | 6 man/rhoC_AVE.Rd |only tests/fixtures/V_3_6_0/boot_report_total_indirect_paths.csv |only tests/fixtures/V_3_6_0/loadings1.csv | 28 tests/fixtures/V_3_6_0/path_coef1.csv | 10 tests/fixtures/V_3_6_0/predict_pls_DA.csv |only tests/fixtures/V_3_6_0/predict_pls_EA.csv |only tests/fixtures/V_3_6_0/rho1.csv | 10 tests/fixtures/V_3_6_0/two_stage_predict.csv |only tests/fixtures/V_3_6_0/two_stage_predict_pls.csv |only tests/testthat/test-assess-model.R |only tests/testthat/test-plspredict.R |only tests/testthat/test-summary.R | 22 39 files changed, 3093 insertions(+), 2702 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut] ,
Friedrich Pahlke [aut, cre] ,
Till Jensen [ctb],
Daniel Sabanes Bove [ctb] ,
Stephen Schueuerhuis [ctb] ,
Tobias Muetze [ctb]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 4.2.0 dated 2025-03-24 and 4.2.1 dated 2025-07-24
DESCRIPTION | 21 MD5 | 146 +- NAMESPACE | 4 NEWS.md | 18 R/RcppExports.R | 6 R/class_analysis_dataset.R | 75 + R/class_analysis_results.R | 16 R/class_core_parameter_set.R | 28 R/class_design.R | 18 R/class_design_plan.R | 6 R/class_simulation_results.R | 1143 +++++++++++---------- R/class_summary.R | 26 R/f_analysis_base.R | 297 +++-- R/f_analysis_base_means.R | 1469 ++++++++++++++++----------- R/f_analysis_base_rates.R | 1405 ++++++++++++++++--------- R/f_analysis_base_survival.R | 1091 +++++++++++--------- R/f_analysis_boundary_recalculation.R | 4 R/f_analysis_enrichment_means.R | 6 R/f_analysis_multiarm.R | 212 +-- R/f_analysis_multiarm_survival.R | 15 R/f_core_assertions.R | 102 - R/f_core_constants.R | 35 R/f_core_plot.R | 4 R/f_core_utilities.R | 259 ++-- R/f_design_group_sequential.R | 589 ++++++++-- R/f_design_plan_counts.R | 434 ++++++- R/f_design_plan_means.R | 10 R/f_design_plan_survival.R | 1 R/f_design_plan_utilities.R | 6 R/f_object_r_code.R | 356 ++++-- R/f_quality_assurance.R | 524 +++++++-- R/f_simulation_base_counts.R | 322 +++-- R/f_simulation_base_survival.R | 100 - R/f_simulation_enrichment.R | 577 +++++++--- R/f_simulation_enrichment_means.R | 404 ++++--- R/f_simulation_enrichment_rates.R | 608 +++++++---- R/f_simulation_enrichment_survival.R | 522 ++++++--- R/f_simulation_multiarm.R | 657 ++++++++---- R/f_simulation_multiarm_means.R | 10 R/f_simulation_multiarm_rates.R | 10 R/f_simulation_multiarm_survival.R | 35 R/pkgname.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rpact_getting_started.html | 4 inst/tests/META | 2 man/InstallationQualificationResult.Rd |only man/SimulationResultsCountData.Rd | 28 man/SimulationResultsEnrichmentMeans.Rd | 66 - man/SimulationResultsEnrichmentRates.Rd | 60 - man/SimulationResultsEnrichmentSurvival.Rd | 84 - man/SimulationResultsMeans.Rd | 48 man/SimulationResultsMultiArmMeans.Rd | 72 - man/SimulationResultsMultiArmRates.Rd | 68 - man/SimulationResultsMultiArmSurvival.Rd | 78 - man/SimulationResultsRates.Rd | 48 man/SimulationResultsSurvival.Rd | 88 - man/TrialDesignGroupSequential.Rd | 4 man/TrialDesignInverseNormal.Rd | 4 man/checkInstallationQualificationStatus.Rd |only man/disableStartupMessages.Rd |only man/enableStartupMessages.Rd |only man/getAnalysisResults.Rd | 2 man/getDesignGroupSequential.Rd | 6 man/getDesignInverseNormal.Rd | 6 man/getFinalConfidenceInterval.Rd | 2 man/getSimulationMultiArmMeans.Rd | 2 man/getSimulationMultiArmRates.Rd | 2 man/getSimulationMultiArmSurvival.Rd | 2 man/print.InstallationQualificationResult.Rd |only man/testPackage.Rd | 2 src/RcppExports.cpp | 14 src/f_design_group_sequential.cpp | 1164 +++++++-------------- src/f_utilities.cpp | 135 +- tests/rpact_test_result_report.html |only tests/rpact_test_result_report.pdf |binary tests/testthat.Rout | 36 77 files changed, 8336 insertions(+), 5270 deletions(-)
Title: Provides a Function to Calculate Prize Winner Indices Based on
Bibliometric Data
Description: A function 'PWI()' that calculates prize winner indices based on bibliometric data is provided. The default is the 'Derek de Solla Price Memorial Medal'. Users can provide recipients of other prizes.
Author: Robin Haunschild [aut, cre]
Maintainer: Robin Haunschild <R.Haunschild@fkf.mpg.de>
Diff between PWIR versions 0.0.3 dated 2023-10-20 and 0.0.3.1 dated 2025-07-24
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- man/PWI.Rd | 8 ++++---- man/PWI2.Rd | 4 ++-- man/countries.Rd | 2 +- 5 files changed, 16 insertions(+), 15 deletions(-)
Title: Convolution-Closed Models for Count Time Series
Description: Useful tools for fitting, validating, and forecasting of practical convolution-closed time series models for low counts are provided. Marginal distributions of the data can be modelled via Poisson and Generalized Poisson innovations. Regression effects can be incorporated through time varying innovation rates. The models are described in Jung and Tremayne (2011) <doi:10.1111/j.1467-9892.2010.00697.x> and the model assessment tools are presented in Czado et al. (2009) <doi:10.1111/j.1541-0420.2009.01191.x> and, Tsay (1992) <doi:10.2307/2347612>.
Author: Manuel Huth [aut, cre],
Robert C. Jung [aut],
Andy Tremayne [aut]
Maintainer: Manuel Huth <manuel.huth@yahoo.com>
Diff between coconots versions 2.0.0 dated 2025-03-22 and 2.0.1 dated 2025-07-24
coconots-2.0.0/coconots/R/plot.cocoBoot.R |only coconots-2.0.0/coconots/R/plot.cocoForecast.R |only coconots-2.0.0/coconots/R/plot.cocoForecastCollection.R |only coconots-2.0.0/coconots/R/plot.cocoPit.R |only coconots-2.0.0/coconots/R/plot.cocoResid.R |only coconots-2.0.0/coconots/R/print.summary.coco.R |only coconots-2.0.0/coconots/R/print.summary.cocoSoc.R |only coconots-2.0.0/coconots/R/summary.cocoReg.R |only coconots-2.0.0/coconots/R/summary.cocoSoc.R |only coconots-2.0.1/coconots/DESCRIPTION | 12 coconots-2.0.1/coconots/MD5 | 55 +- coconots-2.0.1/coconots/NAMESPACE | 29 + coconots-2.0.1/coconots/NEWS.md |only coconots-2.0.1/coconots/R/cocoBoot.R | 82 +++- coconots-2.0.1/coconots/R/cocoPit.R | 91 ++++ coconots-2.0.1/coconots/R/cocoReg.R | 327 +++++++++++++++- coconots-2.0.1/coconots/R/cocoResid.R | 110 +++++ coconots-2.0.1/coconots/R/cocoSoc.R | 13 coconots-2.0.1/coconots/R/installJuliaPackages.R | 13 coconots-2.0.1/coconots/R/predict.coco.R | 95 ++++ coconots-2.0.1/coconots/R/utils.R |only coconots-2.0.1/coconots/build/partial.rdb |binary coconots-2.0.1/coconots/man/cocoReg.Rd | 23 - coconots-2.0.1/coconots/man/cocoResid.Rd | 2 coconots-2.0.1/coconots/man/cocoScore.Rd | 6 coconots-2.0.1/coconots/man/cocoSim.Rd | 6 coconots-2.0.1/coconots/man/cocoSoc.Rd | 18 coconots-2.0.1/coconots/man/cuts.Rd | 16 coconots-2.0.1/coconots/man/downloads.Rd | 12 coconots-2.0.1/coconots/man/goldparticle.Rd | 16 coconots-2.0.1/coconots/man/predict.coco.Rd | 9 coconots-2.0.1/coconots/man/reexports.Rd | 4 coconots-2.0.1/coconots/man/setJuliaSeed.Rd | 2 coconots-2.0.1/coconots/tests/testthat/test-coconots.R | 2 34 files changed, 832 insertions(+), 111 deletions(-)
Title: CITation ANalysis Toolpack
Description: Supports quantitative research in scientometrics and bibliometrics.
Provides various tools for preprocessing bibliographic
data retrieved, e.g., from Elsevier's Scopus,
computing bibliometric impact of individuals,
or modelling phenomena encountered in the social sciences.
This package is deprecated; see 'agop' instead.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between CITAN versions 2022.1.1 dated 2022-03-21 and 2025.7.1 dated 2025-07-24
DESCRIPTION | 34 ++++++++++---------- MD5 | 52 +++++++++++++++---------------- NAMESPACE | 1 NEWS | 5 +++ R/CITAN-package.R | 51 ++++--------------------------- R/biblio.assess.R | 8 ++-- R/biblio.clear.R | 8 ++-- R/biblio.connect.R | 2 - R/biblio.create.R | 2 - R/biblio.getcitations.R | 2 - R/biblio.import.R | 10 +++--- R/biblio.info.R | 8 +--- R/biblio.internal.R | 4 +- R/biblio.search.R | 18 +++++----- R/biblio.stats.R | 2 - R/biblio.tidy.R | 4 +- R/execquery.R | 4 +- R/scopus.data.R | 2 - R/scopus.importsources.R | 2 - R/scopus.readcsv.R | 2 - R/string.R | 2 - inst/CITATION | 2 - man/CITAN-package.Rd | 59 +++++++++--------------------------- man/dbExecQuery.Rd | 2 - man/lbsClear.Rd | 2 - man/lbsDeleteAllAuthorsDocuments.Rd | 4 +- man/lbsTidy.Rd | 2 - 27 files changed, 117 insertions(+), 177 deletions(-)
Title: Modelling of Soil Water Retention and Hydraulic Conductivity
Data
Description: Provides functions for efficiently estimating properties of
the Van Genuchten-Mualem model for soil hydraulic parameters from
possibly sparse soil water retention and hydraulic conductivity data
by multi-response parameter estimation methods
(Stewart, W.E., Caracotsios, M. Soerensen, J.P. (1992)
"Parameter estimation from multi-response data"
<doi:10.1002/aic.690380502>). Parameter estimation is simplified
by exploiting the fact that residual and saturated water contents
and saturated conductivity are conditionally linear parameters
(Bates, D. M. and Watts, D. G. (1988)
"Nonlinear Regression Analysis and Its Applications"
<doi:10.1002/9780470316757>).
Estimated parameters are optionally constrained by the evaporation
characteristic length (Lehmann, P., Bickel, S., Wei, Z. and Or, D. (2020)
"Physical Constraints for Improved Soil Hydraulic Parameter
Estimation by Pedotransfer Functions" <doi:10.1029/2019WR025963>)
to ensure that the estimated parameters are physically [...truncated...]
Author: Andreas Papritz [aut, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between soilhypfit versions 0.1-7 dated 2022-08-31 and 0.1-8 dated 2025-07-24
ChangeLog | 9 +++++++++ DESCRIPTION | 34 ++++++++++++++++++++++++++-------- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 16 ++++++++++++++++ man/soilhypfit_control_fit_wrc_hcc.Rd | 2 +- man/soilhypfit_fit_wrc_hcc.Rd | 4 ++-- man/soilhypfit_prfloglik.Rd | 23 +++++++++++++---------- man/soilhypfit_sim_wrc_hcc.Rd | 13 +++++++++---- 10 files changed, 86 insertions(+), 35 deletions(-)
Title: Estimation of Number of Clusters and Identification of Atypical
Units
Description: It is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.
Author: Itziar Irigoien [aut, cre],
Concepcion Arenas [aut]
Maintainer: Itziar Irigoien <itziar.irigoien@ehu.eus>
Diff between ICGE versions 0.4.2 dated 2022-10-17 and 0.4.3 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/INCAnumclu.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Pixel Filters for 'ggplot2' and 'grid'
Description: Provides a range of filters that can be applied to layers from the
'ggplot2' package and its extensions, along with other graphic elements such
as guides and theme elements. The filters are applied at render time and
thus uses the exact pixel dimensions needed.
Author: Thomas Lin Pedersen [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggfx versions 1.0.1 dated 2022-08-22 and 1.0.2 dated 2025-07-24
DESCRIPTION | 12 - MD5 | 40 +-- NEWS.md | 4 R/doc-object-support.R | 5 R/ggplot.R | 2 R/raster-helpers.R | 2 README.md | 22 +- build/vignette.rds |binary inst/doc/custom_filters.R | 2 inst/doc/custom_filters.html | 413 +++++++++++++++++++-------------------- inst/doc/geoms.R | 2 inst/doc/geoms.html | 265 +++++++++++++------------ inst/doc/ggfx.R | 4 inst/doc/ggfx.Rmd | 2 inst/doc/ggfx.html | 281 +++++++++++++------------- man/figures/README-example-1.png |binary man/object_support.Rd | 5 man/render_context.Rd | 2 man/with_interpolate.Rd | 2 man/with_mask.Rd | 2 vignettes/ggfx.Rmd | 2 21 files changed, 552 insertions(+), 517 deletions(-)
Title: Fast Estimation of CUB Models via Louis' Identity
Description: For ordinal rating data, consider the accelerated EM algorithm to estimate and test models within the family of
CUB models (where CUB stands for Combination of a
discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix. Best-subset variable selection is then implemented since it becomes more feasible from the computational point of view.
Author: Rosaria Simone [aut, cre]
Maintainer: Rosaria Simone <rosaria.simone@unina.it>
Diff between FastCUB versions 0.0.3 dated 2024-03-08 and 0.0.4 dated 2025-07-24
DESCRIPTION | 6 MD5 | 18 +- NAMESPACE | 1 R/bestcub.R | 225 +++++++++++++++++++++++++--------- R/fastCUB.R | 217 +++++++++++++++++---------------- R/parnames.R | 116 +++++++++-------- R/print.R | 22 --- R/summary.R | 369 +++++++++++++++++++++++++++++---------------------------- R/vcov.R | 11 + man/fastCUB.Rd | 4 10 files changed, 558 insertions(+), 431 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] ,
Eva Cantagallo [aut],
William Anderson [aut],
Julien Peron [ctb],
Johan Verbeeck [ctb]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 3.3.1 dated 2025-07-07 and 3.3.3 dated 2025-07-24
DESCRIPTION | 8 MD5 | 111 ++++---- NEWS | 12 R/BuyseMultComp.R | 94 ++++-- R/BuyseTest-check.R | 14 - R/BuyseTest-initialization.R | 4 R/BuyseTest-print.R | 2 R/BuyseTest.R | 1 R/CasinoTest.R | 208 +++++++++------ R/S4-BuysePower-summary.R | 8 R/S4-BuyseTest-coef.R | 42 +-- R/S4-BuyseTest-confint.R | 27 - R/S4-BuyseTest-get.R | 9 R/S4-BuyseTest-model.tables.R | 9 R/S4-BuyseTest-sensitivity.R | 71 ++--- R/S4-BuyseTest-summary.R | 35 +- R/S4-BuyseTest.R | 4 R/S4-BuyseTest.vcov.R | 8 R/doc-data.R | 86 ++++-- data/profil.rda |only inst/doc-paired/bibliography.bib | 19 + inst/doc-paired/figures |only inst/doc-paired/paired-compress.pdf |binary inst/doc-paired/paired.R | 2 inst/doc-paired/paired.aux | 34 +- inst/doc-paired/paired.bbl | 11 inst/doc-paired/paired.blg | 60 ++-- inst/doc-paired/paired.fdb_latexmk | 19 - inst/doc-paired/paired.fls | 8 inst/doc-paired/paired.log | 68 ++-- inst/doc-paired/paired.org | 361 +++++++++++++++++++++++++- inst/doc-paired/paired.out | 11 inst/doc-paired/paired.pdf |binary inst/doc-paired/paired.synctex.gz |only inst/doc-paired/paired.tex | 386 ++++++++++++++++++++++++++-- inst/doc/overview.pdf |binary inst/doc/overview.pdf.asis | 10 inst/doc/paired.pdf |binary inst/doc/paired.pdf.asis | 117 ++++++++ inst/doc/wilcoxonTest.pdf |binary inst/doc/wilcoxonTest.pdf.asis | 6 man/BuyseMultComp.Rd | 7 man/BuyseTest.Rd | 1 man/CasinoTest.Rd | 36 +- man/S4BuysePower-summary.Rd | 6 man/S4BuyseTest-coef.Rd | 38 +- man/S4BuyseTest-confint.Rd | 21 - man/S4BuyseTest-model.tables.Rd | 7 man/S4BuyseTest-summary.Rd | 12 man/S4BuyseTest-vcov.Rd | 4 man/data-profil.Rd |only man/getIid.Rd | 4 man/getPseudovalue.Rd | 5 man/sensitivity.Rd | 7 src/FCT_calcStatistic.h | 96 ++++-- tests/testthat/test-BuyseTest-sensitivity.R |only vignettes/overview.pdf.asis | 10 vignettes/paired.pdf.asis | 117 ++++++++ vignettes/wilcoxonTest.pdf.asis | 6 59 files changed, 1662 insertions(+), 580 deletions(-)
Title: Biological Geometries
Description: Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. [...truncated...]
Author: Peijian Shi [aut, cre],
Johan Gielis [aut],
Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between biogeom versions 1.4.3 dated 2024-03-29 and 1.4.4 dated 2025-07-24
DESCRIPTION | 8 +++--- MD5 | 64 ++++++++++++++++++++++++------------------------- build/partial.rdb |binary man/DEPE.Rd | 4 +++ man/DETE.Rd | 4 +++ man/DNRGE.Rd | 4 +++ man/EPE.Rd | 4 +++ man/ETE.Rd | 4 +++ man/NRGE.Rd | 4 +++ man/SurfaceAreaEPE.Rd | 12 ++++----- man/SurfaceAreaETE.Rd | 12 ++++----- man/SurfaceAreaNRGE.Rd | 12 ++++----- man/SurfaceAreaSGE.Rd | 12 ++++----- man/TE.Rd | 4 +++ man/TSE.Rd | 4 +++ man/VolumeETE.Rd | 12 ++++----- man/VolumeNRGE.Rd | 12 ++++----- man/VolumeSGE.Rd | 12 ++++----- man/adjdata.Rd | 4 +-- man/areaGE.Rd | 12 ++++----- man/areaovate.Rd | 12 ++++----- man/bilat.Rd | 10 +++---- man/fitEPE.Rd | 8 ++++-- man/fitETE.Rd | 8 ++++-- man/fitGE.Rd | 4 +-- man/fitLorenz.Rd | 16 ++++++------ man/fitNRGE.Rd | 5 +++ man/fitSuper.Rd | 4 +-- man/fitovate.Rd | 4 +-- man/fitsigmoid.Rd | 16 ++++++------ man/lmPE.Rd | 4 +++ man/lmTE.Rd | 4 +++ man/sigmoid.Rd | 12 ++++----- 33 files changed, 181 insertions(+), 130 deletions(-)
Title: Monte Carlo Simulations Made Easy and Tidy
Description: Framework to run Monte Carlo simulations over a parameter grid.
Allows to parallelize the simulations.
Generates plots and 'LaTeX' tables
summarizing the results from the simulation.
Author: Stefan Linner [aut, cre, cph],
Ignacio Moreira Lara [aut],
Konstantin Lehmann [aut]
Maintainer: Stefan Linner <stefan.linner97@gmail.com>
Diff between tidyMC versions 1.0.0 dated 2024-01-11 and 1.0.1 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++++--------- R/latex_table.R | 2 +- R/mc.R | 2 +- R/methods.R | 4 ++-- README.md | 29 +++++++++++++++++------------ inst/doc/tidyMC.html | 23 ++++++++++++----------- man/figures/README-unnamed-chunk-9-1.png |only man/figures/README-unnamed-chunk-9-2.png |only man/figures/README-unnamed-chunk-9-3.png |only man/figures/README-unnamed-chunk-9-4.png |only man/figures/README-unnamed-chunk-9-5.png |only man/figures/README-unnamed-chunk-9-6.png |only man/plot.mc.Rd | 2 +- man/plot.summary.mc.Rd | 2 +- man/tidy_mc_latex.Rd | 2 +- 16 files changed, 55 insertions(+), 43 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.2-6 dated 2025-05-22 and 3.3-1 dated 2025-07-24
DESCRIPTION | 16 ++--- MD5 | 46 +++++++++------- NAMESPACE | 8 ++ NEWS | 69 +++++++++++++++++++++++++ R/auclpp.R | 88 ++++++++++++++++---------------- R/evidencelppm.R | 11 ++-- R/linfun.R | 11 ++++ R/linim.R | 9 ++- R/linnet.R | 15 +++++ R/lintess.R | 110 ++++++++++++++++++++++++++++++++++++++-- R/lintessmakers.R | 17 ++++-- R/roclpp.R |only build |only inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/as.linfun.Rd | 17 +++++- man/auc.lpp.Rd | 60 +++++++++++++-------- man/identify.linnet.Rd |only man/identify.lintess.Rd |only man/lintess.Rd | 4 + man/macros/defns.Rd | 25 +++++---- man/marks.linnet.Rd | 12 +++- man/roc.lpp.Rd | 76 ++++++++++++++++++++++++--- man/spatstat.linnet-internal.Rd | 4 - tests/testsAtoK.R | 25 ++++++--- tests/testsMtoZ.R | 2 26 files changed, 488 insertions(+), 141 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to fourth-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of the package can be found in Puy et al. (2022) <doi:10.18637/jss.v102.i05>.
Author: Arnald Puy [aut, cre] ,
Bertrand Ioos [ctb] ,
Gilles Pujol [ctb] ,
RStudio [cph]
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 1.1.5 dated 2024-02-21 and 1.1.6 dated 2025-07-24
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 5 +++++ R/sensobol-package.R | 3 +-- R/sobol_indices.R | 14 +++++++------- R/sobol_matrices.R | 6 +++--- R/sobol_ode.R | 8 ++++---- R/vars_matrices.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sensobol.pdf |binary man/sensobol-package.Rd | 8 ++++++++ man/sobol_dummy.Rd | 6 +++--- man/sobol_indices.Rd | 8 ++++---- man/sobol_matrices.Rd | 6 +++--- man/sobol_ode.Rd | 8 ++++---- man/vars_matrices.Rd | 4 ++-- 17 files changed, 67 insertions(+), 55 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and download
machine learning data, tasks and experiments. The 'OpenML' objects can
be automatically converted to 'mlr3' objects. For a more
sophisticated interface with more upload options, see
the 'OpenML' package.
Author: Michel Lang [aut] ,
Sebastian Fischer [cre, aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3oml versions 0.10.0 dated 2024-06-04 and 0.10.1 dated 2025-07-24
DESCRIPTION | 13 ++--- MD5 | 24 ++++----- NEWS.md | 6 +- R/publish_collection.R | 2 R/publish_data.R | 2 R/publish_task.R | 2 R/read_arff.R | 6 +- README.md | 117 ++++++++++++++++++++++++++++------------------ build/partial.rdb |binary man/publish_collection.Rd | 2 man/publish_data.Rd | 2 man/publish_task.Rd | 2 man/read_arff.Rd | 6 +- 13 files changed, 108 insertions(+), 76 deletions(-)
Title: Ensemble Sampler for Affine-Invariant MCMC
Description: Provides ensemble samplers for
affine-invariant Monte Carlo Markov Chain, which allow a faster
convergence for badly scaled estimation problems. Two samplers are
proposed: the 'differential.evolution' sampler from ter Braak and
Vrugt (2008) <doi:10.1007/s11222-008-9104-9> and the 'stretch' sampler
from Goodman and Weare (2010) <doi:10.2140/camcos.2010.5.65>.
Author: Hugo Gruson [cre, aut, cph] ,
Sanda Dejanic [aut, cph],
Andreas Scheidegger [aut, cph]
Maintainer: Hugo Gruson <hugo.gruson+R@normalesup.org>
Diff between mcmcensemble versions 3.1.0 dated 2024-03-20 and 3.2.0 dated 2025-07-24
DESCRIPTION | 19 MD5 | 49 NAMESPACE | 1 NEWS.md | 27 R/MCMCEnsemble.R | 57 R/d.e.mcmc.R | 99 - R/mcmcensemble-package.R | 1 R/s.m.mcmc.R | 79 - R/utils.R |only README.md | 33 build/partial.rdb |binary build/vignette.rds |binary inst/doc/diagnostic-pkgs.R | 12 inst/doc/diagnostic-pkgs.Rmd | 10 inst/doc/diagnostic-pkgs.html | 43 inst/doc/faq.R | 12 inst/doc/faq.Rmd | 12 inst/doc/faq.html | 45 man/MCMCEnsemble.Rd | 11 man/figures/README-example-de-1.svg | 2233 +++++++++++++++---------------- man/figures/README-example-stretch-1.svg | 2222 +++++++++++++++--------------- tests/testthat/test-MCMCEnsemble.R | 170 +- tests/testthat/test-convergence.R | 60 vignettes/blog/blog_v3.Rmd | 38 vignettes/diagnostic-pkgs.Rmd | 10 vignettes/faq.Rmd | 12 26 files changed, 2719 insertions(+), 2536 deletions(-)
Title: Multi-Calibration Boosting
Description: Implements 'Multi-Calibration Boosting' (2018) <https://proceedings.mlr.press/v80/hebert-johnson18a.html> and
'Multi-Accuracy Boosting' (2019) <doi:10.48550/arXiv.1805.12317> for the multi-calibration of a machine learning model's prediction.
'MCBoost' updates predictions for sub-groups in an iterative fashion in order to mitigate biases like poor calibration or large accuracy differences across subgroups.
Multi-Calibration works best in scenarios where the underlying data & labels are unbiased, but resulting models are.
This is often the case, e.g. when an algorithm fits a majority population while ignoring or under-fitting minority populations.
Author: Florian Pfisterer [aut] ,
Susanne Dandl [ctb] ,
Christoph Kern [ctb] ,
Carolin Becker [ctb],
Bernd Bischl [ctb] ,
Sebastian Fischer [ctb, cre]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mcboost versions 0.4.3 dated 2024-04-12 and 0.4.4 dated 2025-07-24
DESCRIPTION | 17 ++++++----- MD5 | 48 ++++++++++++++++---------------- NEWS.md | 6 ++++ R/MCBoost.R | 5 +-- R/PipeOpLearnerPred.R | 10 +++--- R/PipeOpMCBoost.R | 4 +- R/PipelineMCBoost.R | 2 - R/Predictor.R | 14 ++++----- README.md | 6 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mcboost_basics_extensions.R | 2 - inst/doc/mcboost_basics_extensions.Rmd | 2 - inst/doc/mcboost_basics_extensions.html | 4 +- inst/doc/mcboost_example.R | 2 - inst/doc/mcboost_example.html | 2 - man/AuditorFitter.Rd | 4 +- man/CVLearnerAuditorFitter.Rd | 2 - man/LearnerAuditorFitter.Rd | 2 - man/MCBoost.Rd | 6 ++-- man/SubgroupAuditorFitter.Rd | 2 - man/SubpopAuditorFitter.Rd | 2 - man/mlr_pipeops_mcboost.Rd | 14 ++++----- man/ppl_mcboost.Rd | 2 - vignettes/mcboost_basics_extensions.Rmd | 2 - 25 files changed, 83 insertions(+), 77 deletions(-)
Title: Generalized Entropy Calibration
Description: Generalized Entropy Calibration produces calibration weights
using generalized entropy as the objective function for optimization.
This approach, as implemented in the 'GECal' package, is based on
Kwon, Kim, and Qiu (2024) <doi:10.48550/arXiv.2404.01076>. 'GECal' incorporates design weights into the constraints to maintain design consistency, rather than including
them in the objective function itself.
Author: Yonghyun Kwon [aut, cre] ,
Jae Kwang Kim [aut] ,
Yumou Qiu [aut]
Maintainer: Yonghyun Kwon <yhkwon@kma.ac.kr>
Diff between GECal versions 0.1.5 dated 2024-09-25 and 0.1.7 dated 2025-07-24
DESCRIPTION | 17 ++++++++--------- MD5 | 19 ++++++++++++------- NAMESPACE | 1 + R/G.R | 2 +- R/GEcalib.R | 30 +++++++++++++++++++----------- R/estimate.R | 19 ++++++++++--------- R/targetftn.R | 7 +++++-- inst |only man/GEcalib.Rd | 19 ++++++++++++++----- 9 files changed, 70 insertions(+), 44 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
MOLGENIS org [cph, fnd]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between DSMolgenisArmadillo versions 2.0.9 dated 2024-07-09 and 3.0.0 dated 2025-07-24
DESCRIPTION | 21 MD5 | 36 NAMESPACE | 8 NEWS.md | 6 R/ArmadilloConnection.R | 55 + R/ArmadilloOAuth.R | 415 ++++++++++ R/ArmadilloResult.R | 1 R/utils.R | 4 build/vignette.rds |binary inst/doc/DSMolgenisArmadillo.Rmd | 240 ++++-- inst/doc/DSMolgenisArmadillo.html | 627 +++++++++------ inst/doc/development.html | 4 inst/doc/workspaces.html | 4 man/ArmadilloCredentials-class.Rd |only man/armadillo.get_credentials.Rd |only tests/testthat/test-ArmadilloConnection.R | 30 tests/testthat/test-ArmadilloOAuth.R | 1188 +++++++++++++++++++++++++++++- tests/testthat/test-utils.R | 4 vignettes/DSMolgenisArmadillo.Rmd | 240 ++++-- vignettes/DSMolgenisArmadillo.Rmd.orig | 49 + 20 files changed, 2452 insertions(+), 480 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Working with 'Sapfluxnet' Project Data
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project,
the first global database of sap flow measurements.
Author: Victor Granda [aut, cre] ,
Rafael Poyatos [aut] ,
Victor Flo [aut] ,
Jacob Nelson [ctb] ,
Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between sapfluxnetr versions 0.1.4 dated 2023-01-25 and 0.1.5 dated 2025-07-24
DESCRIPTION | 21 MD5 | 52 - NEWS.md | 5 R/getters.R | 46 + R/metrics.R | 38 + R/visualizations.R | 8 README.md | 11 build/vignette.rds |binary inst/doc/custom-aggregation.html | 498 +++++++------- inst/doc/data-flags.html | 4 inst/doc/memory-and-parallelization.R | 160 ++-- inst/doc/memory-and-parallelization.Rmd | 4 inst/doc/memory-and-parallelization.html | 169 ++-- inst/doc/metadata-and-data-units.html | 98 +- inst/doc/sapfluxnetr-quick-guide.R | 88 +- inst/doc/sapfluxnetr-quick-guide.Rmd | 3 inst/doc/sapfluxnetr-quick-guide.html | 981 ++++++++++++++-------------- inst/doc/sfn-data-classes.html | 1080 +++++++++++++++---------------- man/figures/README-example_multi-1.png |binary man/figures/README-example_multi-2.png |binary man/figures/README-example_single-1.png |binary man/figures/README-example_single-2.png |binary man/sfn_plot.Rd | 8 tests/testthat/test-getters.R | 36 - tests/testthat/test-metrics.R | 18 vignettes/memory-and-parallelization.Rmd | 4 vignettes/sapfluxnetr-quick-guide.Rmd | 3 27 files changed, 1735 insertions(+), 1600 deletions(-)
Title: Decipher Microbial Turnover along a Gradient
Description: Two pipelines are provided to study microbial turnover along a gradient, including the beta diversity and microbial abundance change. The 'betaturn' class consists of the steps of community dissimilarity matrix generation, matrix conversion, differential test and visualization. The workflow of 'taxaturn' class includes the taxonomic abundance calculation, abundance transformation, abundance change summary, statistical analysis and visualization. Multiple statistical approaches can contribute to the analysis of microbial turnover.
Author: Chi Liu [aut, cre],
Xiangzhen Li [ctb],
Minjie Yao [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between mecoturn versions 0.3.0 dated 2023-09-10 and 0.3.1 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/betaturn.R | 6 +++--- R/taxaturn.R | 2 +- man/betaturn.Rd | 6 +++--- man/taxaturn.Rd | 2 +- 6 files changed, 17 insertions(+), 17 deletions(-)
Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert [aut, cre] ,
Martin Maechler [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between simsalapar versions 1.0-12 dated 2023-04-27 and 1.0-13 dated 2025-07-24
DESCRIPTION | 20 +++++++++--- MD5 | 10 +++--- R/graphics.R | 84 ++++++++++++++++++++++++++++++++---------------------- build/partial.rdb |binary man/device.Rd | 2 - man/mayplot.Rd | 33 +++++++++++++-------- 6 files changed, 92 insertions(+), 57 deletions(-)
Title: Polygons with Holes for the Grammar of Graphics
Description: Tools for working with polygons with holes in 'ggplot2', with a
new 'geom' for drawing a 'polypath' applying the 'evenodd' or 'winding'
rules.
Author: Michael D. Sumner [aut, cre],
Kohske Takahashi [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between ggpolypath versions 0.3.0 dated 2023-09-25 and 0.4.0 dated 2025-07-24
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- NEWS.md | 4 ++ R/geom_polypath.R | 10 +++--- build/vignette.rds |binary inst/doc/ggpolypath.R | 4 +- inst/doc/ggpolypath.html | 32 ++++++++++---------- man/geom_polypath.Rd | 75 +++++++++++++++++++++++++++++++++++------------ 8 files changed, 95 insertions(+), 52 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.84 dated 2025-05-26 and 2.0.85 dated 2025-07-24
DESCRIPTION | 8 MD5 | 57 +- NEWS | 14 R/epi.2by2.R | 258 +++++++-- R/zORwald.R | 10 R/zRRwald.R | 6 build/vignette.rds |binary inst/doc/epiR_descriptive.R | 37 - inst/doc/epiR_descriptive.Rmd | 60 +- inst/doc/epiR_descriptive.html | 519 ++++++++++++++---- inst/doc/epiR_measures_of_association.R | 106 +++ inst/doc/epiR_measures_of_association.Rmd | 203 ++++--- inst/doc/epiR_measures_of_association.html | 695 +++++++++++++++++++------ inst/doc/epiR_sample_size.Rmd | 38 - inst/doc/epiR_sample_size.html | 405 +++++++++++++- inst/doc/epiR_surveillance.R | 16 inst/doc/epiR_surveillance.Rmd | 55 + inst/doc/epiR_surveillance.html | 450 +++++++++++++--- man/epi.2by2.Rd | 18 man/epi.indirectadj.Rd | 52 + vignettes/attributable_fraction.png |binary vignettes/attributable_risk.png |binary vignettes/epiR_descriptive.Rmd | 60 +- vignettes/epiR_measures_of_association.Rmd | 203 ++++--- vignettes/epiR_sample_size.Rmd | 38 - vignettes/epiR_surveillance.Rmd | 55 + vignettes/population_attributable_fraction.png |binary vignettes/population_attributable_risk.png |binary vignettes/risk_ratio.png |binary vignettes/styles.css |only 30 files changed, 2547 insertions(+), 816 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-08 0.5.3
2019-07-10 0.5.2
2019-02-14 0.5.1
2018-08-25 0.5.0
2018-08-07 0.4.3
2018-07-15 0.4.2
2018-07-08 0.4.1
2018-03-31 0.4.0
2016-05-08 0.3.2
2016-03-29 0.3.1
2016-03-11 0.3
2016-02-26 0.2
Title: Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment
policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment,
and traditional longitudinal effects. Continuous, binary, categorical treatments, and multivariate treatments are allowed as well are
censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure
irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects
can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Supports survival outcomes with competing risks (Diaz, Hoffman, and Hejazi; <doi:10.1007/s10985-023-09606-7>).
Author: Nicholas Williams [aut, cre, cph] ,
Ivan Diaz [aut, cph] ,
Beaudan Campbell-Brown [ctb]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between lmtp versions 1.5.2 dated 2025-06-13 and 1.5.3 dated 2025-07-24
DESCRIPTION | 17 ++++++++++++----- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/checks.R | 2 +- R/lmtp_survival.R | 2 +- R/utils.R | 11 ++++++++++- man/lmtp-package.Rd | 5 +++++ tests/testthat/test-shifted.R | 28 +++++++++++++++++++++++++++- 8 files changed, 74 insertions(+), 16 deletions(-)
Title: Pipe-Friendly Vector Replacement with Case Statements
Description: Offers a pipe-friendly alternative to the 'dplyr' functions
case_when() and if_else(), as well as a number of user-friendly
simplifications for common use cases. These functions accept a vector
as an optional first argument, allowing conditional statements to be
built using the 'magrittr' dot operator. The functions also coerce
all outputs to the same type, meaning you no longer have to worry
about using specific typed variants of NA or explicitly declaring
integer outputs, and evaluate outputs somewhat lazily, so you don't
waste time on long operations that won't be used.
Author: Alexander Rossell Hayes [aut, cre, cph] ,
Patrice Kiener [ctb] , ORCID:
<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between incase versions 0.3.2 dated 2023-08-21 and 0.4.0 dated 2025-07-24
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Title: Distributed Linear Regression Models with Response Missing
Variables
Description: As a distributed imputation strategy, the Distributed full
information Multiple Imputation method is developed to impute
missing response variables in distributed linear regression.
The philosophy of the package is described in 'Guo' (2025)
<doi:10.1038/s41598-025-93333-6>.
Author: Guangbao Guo [aut, cre] ,
Limin Song [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between DLMRMV versions 0.2.0 dated 2025-06-24 and 1.0.0 dated 2025-07-24
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++++++++---- NAMESPACE | 12 +++++++++++- R/CSLMI.R | 2 +- R/DERLS.R |only R/DERLS_InfoFilter.R |only R/DERLS_Woodbury.R |only R/DMCEM.R |only R/DfiMI.R |only R/DfiMI_lasso.R |only R/MCEM.R |only man/CSLMI.Rd | 16 +++++++++------- man/DERLS.Rd |only man/DERLS_InfoFilter.Rd |only man/DERLS_Woodbury.Rd |only man/DMCEM.Rd |only man/DfiMI.Rd |only man/DfiMI_lasso.Rd |only man/MCEM.Rd |only 19 files changed, 43 insertions(+), 17 deletions(-)
Title: Tools for Working with Data During Statistical Analysis
Description: Contains tools for working with data during statistical analysis, promoting flexible, intuitive, and reproducible workflows. There are functions designated for specific statistical tasks such building a custom univariate descriptive table, computing pairwise association statistics, etc. These are built on a collection of data manipulation tools designed for general use that are motivated by the functional programming concept.
Author: Alex Zajichek [aut, cre]
Maintainer: Alex Zajichek <alexzajichek@gmail.com>
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