Title: Markdown-Based Programmable Surveys Using 'Quarto' and 'shiny'
Description: Generate programmable surveys using markdown and R code chunks. Surveys
are composed of two files: a survey.qmd 'Quarto' file defining the
survey content (pages, questions, etc), and an app.R file defining a
'shiny' app with global settings (libraries, database configuration,
etc.) and server configuration options (e.g., conditional skipping /
display, etc.). Survey data collected from respondents is stored in a
'PostgreSQL' database. Features include controls for conditional skip
logic (skip to a page based on an answer to a question), conditional
display logic (display a question based on an answer to a question), a
customizable progress bar, and a wide variety of question types,
including multiple choice (single choice and multiple choices),
select, text, numeric, multiple choice buttons, text area, and dates.
Because the surveys render into a 'shiny' app, designers can also
leverage the reactive capabilities of 'shiny' to create dynamic and
interactive surveys.
Author: John Paul Helveston [aut, cre, cph] ,
Pingfan Hu [aut, cph] ,
Bogdan Bunea [aut, cph] ,
Stefan Munnes [ctb]
Maintainer: John Paul Helveston <john.helveston@gmail.com>
Diff between surveydown versions 0.13.0 dated 2025-08-20 and 0.13.3 dated 2025-09-30
DESCRIPTION | 8 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 19 + R/config.R | 19 - R/server.R | 638 ++++++++++++++++++++++++++++++++-------- R/ui.R | 85 +++-- R/util.R | 389 ++++++++++++++++++++++-- README.md | 42 ++ inst/CITATION | 14 inst/css/surveydown.css | 97 ++++++ inst/js/highlight_unanswered.js | 72 ++++ inst/template/README.md |only inst/template/app.R | 8 inst/template/survey.qmd | 17 + man/sd_create_survey.Rd | 5 man/sd_show_if.Rd | 2 man/sd_skip_forward.Rd | 42 -- man/sd_skip_if.Rd | 47 ++ man/sd_stop_if.Rd |only 20 files changed, 1264 insertions(+), 277 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.4.1 dated 2025-06-07 and 3.4.2 dated 2025-09-30
randomForestSRC-3.4.1/randomForestSRC/R/find.interaction.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/stat.split.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/synthetic.rfsrc.R |only randomForestSRC-3.4.1/randomForestSRC/R/utilities_sgreedy.R |only randomForestSRC-3.4.1/randomForestSRC/R/utilities_tdc.R |only randomForestSRC-3.4.1/randomForestSRC/man/find.interaction.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/man/stat.split.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/man/synthetic.rfsrc.Rd |only randomForestSRC-3.4.1/randomForestSRC/src/Makevars.win |only randomForestSRC-3.4.1/randomForestSRC/src/randomForestSRC.c |only randomForestSRC-3.4.1/randomForestSRC/src/randomForestSRC.h |only randomForestSRC-3.4.2/randomForestSRC/DESCRIPTION | 8 randomForestSRC-3.4.2/randomForestSRC/MD5 | 215 +++- randomForestSRC-3.4.2/randomForestSRC/NAMESPACE | 10 randomForestSRC-3.4.2/randomForestSRC/R/generic.predict.rfsrc.R | 58 - randomForestSRC-3.4.2/randomForestSRC/R/partial.rfsrc.R | 58 - randomForestSRC-3.4.2/randomForestSRC/R/predict.rfsrc.R | 2 randomForestSRC-3.4.2/randomForestSRC/R/print.rfsrc.R | 515 ++++------ randomForestSRC-3.4.2/randomForestSRC/R/quantreg.rfsrc.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.R | 110 -- randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.anonymous.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/rfsrc.fast.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/subsample.rfsrc.R | 1 randomForestSRC-3.4.2/randomForestSRC/R/tune.nodesize.rfsrc.R | 243 +++- randomForestSRC-3.4.2/randomForestSRC/R/tune.rfsrc.R | 463 ++++++-- randomForestSRC-3.4.2/randomForestSRC/R/utilities.R | 140 -- randomForestSRC-3.4.2/randomForestSRC/R/utilities_data.R | 8 randomForestSRC-3.4.2/randomForestSRC/R/utilities_imbalanced.R | 331 ++++-- randomForestSRC-3.4.2/randomForestSRC/configure | 220 +++- randomForestSRC-3.4.2/randomForestSRC/configure.ac | 88 + randomForestSRC-3.4.2/randomForestSRC/data/breast.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/follic.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/hd.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/housing.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/nutrigenomic.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/pbc.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/peakVO2.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/vdv.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/veteran.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/wihs.rda |binary randomForestSRC-3.4.2/randomForestSRC/data/wine.rda |binary randomForestSRC-3.4.2/randomForestSRC/inst/NEWS | 11 randomForestSRC-3.4.2/randomForestSRC/man/breast.Rd | 1 randomForestSRC-3.4.2/randomForestSRC/man/max.subtree.rfsrc.Rd | 3 randomForestSRC-3.4.2/randomForestSRC/man/plot.rfsrc.Rd | 2 randomForestSRC-3.4.2/randomForestSRC/man/plot.variable.rfsrc.Rd | 1 randomForestSRC-3.4.2/randomForestSRC/man/predict.rfsrc.Rd | 7 randomForestSRC-3.4.2/randomForestSRC/man/print.rfsrc.Rd | 2 randomForestSRC-3.4.2/randomForestSRC/man/randomForestSRC_package.Rd | 3 randomForestSRC-3.4.2/randomForestSRC/man/rfsrc.Rd | 7 randomForestSRC-3.4.2/randomForestSRC/man/tune.rfsrc.Rd | 212 ++-- randomForestSRC-3.4.2/randomForestSRC/man/utilities_internal.Rd | 5 randomForestSRC-3.4.2/randomForestSRC/src/R_init_randomForestSRC.c | 28 randomForestSRC-3.4.2/randomForestSRC/src/bootstrap.c |only randomForestSRC-3.4.2/randomForestSRC/src/bootstrap.h |only randomForestSRC-3.4.2/randomForestSRC/src/cindex.c |only randomForestSRC-3.4.2/randomForestSRC/src/cindex.h |only randomForestSRC-3.4.2/randomForestSRC/src/classification.c |only randomForestSRC-3.4.2/randomForestSRC/src/classification.h |only randomForestSRC-3.4.2/randomForestSRC/src/diagnostic.c |only randomForestSRC-3.4.2/randomForestSRC/src/diagnostic.h |only randomForestSRC-3.4.2/randomForestSRC/src/distance.c |only randomForestSRC-3.4.2/randomForestSRC/src/distance.h |only randomForestSRC-3.4.2/randomForestSRC/src/entry.c |only randomForestSRC-3.4.2/randomForestSRC/src/entry.h |only randomForestSRC-3.4.2/randomForestSRC/src/entryGeneric.c |only randomForestSRC-3.4.2/randomForestSRC/src/entryGeneric.h |only randomForestSRC-3.4.2/randomForestSRC/src/error.c |only randomForestSRC-3.4.2/randomForestSRC/src/error.h |only randomForestSRC-3.4.2/randomForestSRC/src/external.h |only randomForestSRC-3.4.2/randomForestSRC/src/factor.h |only randomForestSRC-3.4.2/randomForestSRC/src/factorOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/factorOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/global.h |only randomForestSRC-3.4.2/randomForestSRC/src/importance.c |only randomForestSRC-3.4.2/randomForestSRC/src/importance.h |only randomForestSRC-3.4.2/randomForestSRC/src/importanceAnti.c |only randomForestSRC-3.4.2/randomForestSRC/src/importanceAnti.h |only randomForestSRC-3.4.2/randomForestSRC/src/importancePerm.c |only randomForestSRC-3.4.2/randomForestSRC/src/importancePerm.h |only randomForestSRC-3.4.2/randomForestSRC/src/importanceRand.c |only randomForestSRC-3.4.2/randomForestSRC/src/importanceRand.h |only randomForestSRC-3.4.2/randomForestSRC/src/impute.c |only randomForestSRC-3.4.2/randomForestSRC/src/impute.h |only randomForestSRC-3.4.2/randomForestSRC/src/internal.c |only randomForestSRC-3.4.2/randomForestSRC/src/leafLink.c |only randomForestSRC-3.4.2/randomForestSRC/src/leafLink.h |only randomForestSRC-3.4.2/randomForestSRC/src/marginal.c |only randomForestSRC-3.4.2/randomForestSRC/src/marginal.h |only randomForestSRC-3.4.2/randomForestSRC/src/nativeInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/nativeUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/nativeUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/node.h |only randomForestSRC-3.4.2/randomForestSRC/src/nodeOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/nodeOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/nrutil.c |only randomForestSRC-3.4.2/randomForestSRC/src/nrutil.h |only randomForestSRC-3.4.2/randomForestSRC/src/partial.c |only randomForestSRC-3.4.2/randomForestSRC/src/partial.h |only randomForestSRC-3.4.2/randomForestSRC/src/polarity.c |only randomForestSRC-3.4.2/randomForestSRC/src/polarity.h |only randomForestSRC-3.4.2/randomForestSRC/src/processEnsemble.c |only randomForestSRC-3.4.2/randomForestSRC/src/processEnsemble.h |only randomForestSRC-3.4.2/randomForestSRC/src/quantile.c |only randomForestSRC-3.4.2/randomForestSRC/src/quantile.h |only randomForestSRC-3.4.2/randomForestSRC/src/random.c |only randomForestSRC-3.4.2/randomForestSRC/src/random.h |only randomForestSRC-3.4.2/randomForestSRC/src/regression.c |only randomForestSRC-3.4.2/randomForestSRC/src/regression.h |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrc.c |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrc.h |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrcUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/rfsrcUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/sampling.c |only randomForestSRC-3.4.2/randomForestSRC/src/sampling.h |only randomForestSRC-3.4.2/randomForestSRC/src/sexpOutgoing.c |only randomForestSRC-3.4.2/randomForestSRC/src/sexpOutgoing.h |only randomForestSRC-3.4.2/randomForestSRC/src/snpAuxiliaryInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/sortedLink.c |only randomForestSRC-3.4.2/randomForestSRC/src/sortedLink.h |only randomForestSRC-3.4.2/randomForestSRC/src/sources.list |only randomForestSRC-3.4.2/randomForestSRC/src/split.c |only randomForestSRC-3.4.2/randomForestSRC/src/split.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitClas.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitClas.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitCustom.c | 353 ------ randomForestSRC-3.4.2/randomForestSRC/src/splitCustom.h | 59 - randomForestSRC-3.4.2/randomForestSRC/src/splitCustomDriver.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitCustomDriver.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitGreedy.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitGreedy.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitInfo.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitMahalanobis.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitMahalanobis.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitMult.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitMult.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitQuantile.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitQuantile.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitRegr.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitRegr.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitSurv.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitSurv.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtilSurv.c |only randomForestSRC-3.4.2/randomForestSRC/src/splitUtilSurv.h |only randomForestSRC-3.4.2/randomForestSRC/src/stack.c |only randomForestSRC-3.4.2/randomForestSRC/src/stack.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutput.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutput.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutputQQ.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackOutputQQ.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackParallel.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackParallel.h |only randomForestSRC-3.4.2/randomForestSRC/src/stackPreDefined.c |only randomForestSRC-3.4.2/randomForestSRC/src/stackPreDefined.h |only randomForestSRC-3.4.2/randomForestSRC/src/survival.c |only randomForestSRC-3.4.2/randomForestSRC/src/survival.h |only randomForestSRC-3.4.2/randomForestSRC/src/survivalE.c |only randomForestSRC-3.4.2/randomForestSRC/src/survivalE.h |only randomForestSRC-3.4.2/randomForestSRC/src/svdUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/svdUtil.h |only randomForestSRC-3.4.2/randomForestSRC/src/termOps.c |only randomForestSRC-3.4.2/randomForestSRC/src/termOps.h |only randomForestSRC-3.4.2/randomForestSRC/src/terminal.h |only randomForestSRC-3.4.2/randomForestSRC/src/trace.c |only randomForestSRC-3.4.2/randomForestSRC/src/trace.h |only randomForestSRC-3.4.2/randomForestSRC/src/tree.c |only randomForestSRC-3.4.2/randomForestSRC/src/tree.h |only randomForestSRC-3.4.2/randomForestSRC/src/treeJIT.c |only randomForestSRC-3.4.2/randomForestSRC/src/treeJIT.h |only randomForestSRC-3.4.2/randomForestSRC/src/treeUtil.c |only randomForestSRC-3.4.2/randomForestSRC/src/treeUtil.h |only 173 files changed, 1568 insertions(+), 1599 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Nicely Formatted Contingency Tables and Frequency Tables
Description: Nicely formatted frequency tables and contingency tables (1-way, 2-way, 3-way and 4-way tables), that can easily be exported to HTML or 'Office' documents. Designed to work with pipes.
Author: Mans Thulin [aut, cre],
Kajsa Grind [aut],
Stefan Furne [aut]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between ivo.table versions 0.6 dated 2025-01-15 and 0.7.0 dated 2025-09-30
DESCRIPTION | 12 ++-- MD5 | 29 +++++++--- NAMESPACE | 57 +++++++++++++++++++++ NEWS.md | 3 + R/ivo_table_gt.R |only R/ivo_tables.R | 16 ++--- README.md | 4 + build/vignette.rds |binary inst/doc/ivo_table.R | 8 +- inst/doc/ivo_table.Rmd | 6 +- inst/doc/ivo_table.html | 122 ++++++++++++++++++++++++++------------------- inst/doc/ivo_table_gt.R |only inst/doc/ivo_table_gt.Rmd |only inst/doc/ivo_table_gt.html |only man/figures |only man/ivo_gt_theme.Rd |only man/ivo_table_gt.Rd |only vignettes/ivo_table.Rmd | 6 +- vignettes/ivo_table_gt.Rmd |only vignettes/patchwork.png |only 20 files changed, 181 insertions(+), 82 deletions(-)
Title: Clinical Stroke Research
Description: A collection of tools for clinical trial data management and
analysis in research and teaching.
The package is mainly collected for personal use, but any use beyond that is encouraged.
This package has migrated functions from 'agdamsbo/daDoctoR', and new functions has been added.
Version follows months and year. See NEWS/Changelog for release notes.
This package includes sampled data from the TALOS trial (Kraglund et al (2018) <doi:10.1161/STROKEAHA.117.020067>).
The win_prob() function is based on work by Zou et al (2022) <doi:10.1161/STROKEAHA.121.037744>.
The age_calc() function is based on work by Becker (2020) <doi:10.18637/jss.v093.i02>.
Author: Andreas Gammelgaard Damsbo [aut, cre]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between stRoke versions 25.9.1 dated 2025-09-02 and 25.9.2 dated 2025-09-30
DESCRIPTION | 6 +- MD5 | 11 +++- NEWS.md | 4 + R/trial.R |only data/trial.rda |only inst/WORDLIST | 2 inst/doc/toolbox.html | 114 +++++++++++++++++++++++++------------------------- man/trial.Rd |only 8 files changed, 73 insertions(+), 64 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.9 dated 2025-09-27 and 0.6.10 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 ++++++- inst/doc/vignette.html | 4 ++-- src/cwb/cl/registry.tab.c | 14 +++++++++++++- src/cwb/cqp/context_descriptor.c | 8 ++++++++ 6 files changed, 38 insertions(+), 13 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.3.3 dated 2025-05-26 and 2.3.4 dated 2025-09-30
DESCRIPTION | 6 ++--- MD5 | 22 +++++++++--------- NEWS | 3 ++ build/vignette.rds |binary inst/doc/bignum.html | 32 +++++++++++++------------- inst/doc/crypto_hashing.html | 8 +++--- inst/doc/keys.html | 48 ++++++++++++++++++++-------------------- inst/doc/secure_rng.html | 18 +++++++-------- src/cert.c | 9 ++++--- src/info.c | 5 ++++ tests/testthat/helper-version.R | 2 - tests/testthat/test_ssl_ctx.R | 3 +- 12 files changed, 83 insertions(+), 73 deletions(-)
Title: Visualisation and Analysis of Ocean Data Derived from Satellites
Description: With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University can also be handled previous conversion from HDF4 to HDF5 format. Many other ocean variables can be processed by importing netCDF data files from [...truncated...]
Author: Hector Villalobos [aut, cre] ,
Eduardo Gonzalez-Rodriguez [aut]
Maintainer: Hector Villalobos <hvillalo@ipn.mx>
Diff between satin versions 1.1.0 dated 2022-09-22 and 1.2.0 dated 2025-09-30
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 52 +++++++++++++++++++++++++++------------------------- NEWS | 4 ++++ NEWS.md | 8 +++++++- R/climatology.R | 7 +++++-- R/imageScale.R | 2 +- R/name_ncvars.R |only R/plot.satin.R | 25 +++++++++++++++---------- R/read.cmems.R | 6 ++++-- R/satinDataframe.R | 4 ++-- R/satinMean.R | 4 ++-- README.md | 3 ++- data/dchl.rda |binary data/dcmems.rda |binary data/dmap.rda |binary data/dnpp.rda |binary data/dsst.rda |binary man/crop.Rd | 2 +- man/dchl.Rd | 4 ++-- man/dnpp.Rd | 4 ++-- man/dsst.Rd | 4 ++-- man/isolines.Rd | 4 ++-- man/name_ncvars.Rd |only man/plot.satin.Rd | 9 +++++---- man/read.cmems.Rd | 5 +++-- man/read.ghrsst.Rd | 2 +- man/read.osunpp.Rd | 2 +- man/satinMean.Rd | 4 +++- 28 files changed, 110 insertions(+), 71 deletions(-)
Title: Download Paleoclimate Data from 'PaleoClim'
Description: 'PaleoClim' <http://www.paleoclim.org> (Brown et al. 2019,
<doi:10.1038/sdata.2018.254>) is a set of free, high resolution paleoclimate
surfaces covering the whole globe. It includes data on surface temperature,
precipitation and the standard bioclimatic variables commonly used in
ecological modelling, derived from the 'HadCM3' general circulation model and
downscaled to a spatial resolution of up to 2.5 minutes. Simulations are
available for key time periods from the Late Holocene to mid-Pliocene. Data on
current and Last Glacial Maximum climate is derived from 'CHELSA' (Karger et
al. 2017, <doi:10.1038/sdata.2017.122>) and reprocessed by 'PaleoClim' to
match their format; it is available at up to 30 seconds resolution. This
package provides a simple interface for downloading 'PaleoClim' data in R,
with support for caching and filtering retrieved data by period, resolution,
and geographic extent.
Author: Joe Roe [aut, cre, cph]
Maintainer: Joe Roe <joe@joeroe.io>
Diff between rpaleoclim versions 1.0.1 dated 2023-08-09 and 1.1.0 dated 2025-09-30
rpaleoclim-1.0.1/rpaleoclim/inst/doc/rpaleoclim.R |only rpaleoclim-1.0.1/rpaleoclim/tests/testthat/helper-download.R |only rpaleoclim-1.1.0/rpaleoclim/DESCRIPTION | 12 rpaleoclim-1.1.0/rpaleoclim/MD5 | 30 - rpaleoclim-1.1.0/rpaleoclim/NEWS.md | 7 rpaleoclim-1.1.0/rpaleoclim/R/paleoclim.R | 38 +- rpaleoclim-1.1.0/rpaleoclim/R/rpaleoclim-package.R | 4 rpaleoclim-1.1.0/rpaleoclim/README.md | 4 rpaleoclim-1.1.0/rpaleoclim/build/partial.rdb |binary rpaleoclim-1.1.0/rpaleoclim/build/vignette.rds |binary rpaleoclim-1.1.0/rpaleoclim/inst/CITATION | 6 rpaleoclim-1.1.0/rpaleoclim/inst/doc/rpaleoclim.Rmd | 157 ++++++---- rpaleoclim-1.1.0/rpaleoclim/inst/doc/rpaleoclim.html | 52 +-- rpaleoclim-1.1.0/rpaleoclim/man/figures/README-rpaleoclim-demo-1.png |binary rpaleoclim-1.1.0/rpaleoclim/tests/testthat/test-paleoclim.R | 40 +- rpaleoclim-1.1.0/rpaleoclim/vignettes/eg-paleoclim-crop-1.png |only rpaleoclim-1.1.0/rpaleoclim/vignettes/rpaleoclim.Rmd | 157 ++++++---- rpaleoclim-1.1.0/rpaleoclim/vignettes/rpaleoclim.Rmd.source |only 18 files changed, 309 insertions(+), 198 deletions(-)
Title: Calculate 3D Contour Meshes Using the Marching Cubes Algorithm
Description: A port of the C++ routine for applying the marching cubes algorithm written by
Thomas Lewiner et al. (2012) <doi:10.1080/10867651.2003.10487582> into an R package.
The package supplies the contour3d() function, which takes a 3-dimensional array of voxel
data and calculates the vertices, vertex normals, and faces for a 3d mesh representing
the contour(s) at a given level.
Author: S. H. Wilks [aut, cre],
Thomas Lewiner [aut]
Maintainer: S. H. Wilks <sam.wilks@unimelb.edu.au>
Diff between rmarchingcubes versions 0.1.2 dated 2021-06-16 and 0.1.4 dated 2025-09-30
DESCRIPTION | 25 + MD5 | 31 +- NEWS.md | 11 README.md | 9 build/vignette.rds |binary inst/doc/calculating_3d_contours.R | 48 +-- inst/doc/calculating_3d_contours.Rmd | 2 inst/doc/calculating_3d_contours.html | 442 +++++++++++++++++++++++++--------- src/LookUpTable.h | 96 +++---- src/Makevars | 12 src/Makevars.win | 12 src/MarchingCubes.cpp | 6 src/MarchingCubes.h | 2 src/RcppExports.cpp | 5 tests/testthat/_snaps |only tests/testthat/test-marchingcubes.R | 42 ++- vignettes/calculating_3d_contours.Rmd | 2 17 files changed, 488 insertions(+), 257 deletions(-)
More information about rmarchingcubes at CRAN
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Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data.
Available features include determination of pollen season limits,
replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>),
calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>),
and determination of the base temperature for growing degree days
(Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between pollen versions 0.82.0 dated 2021-12-03 and 0.83.0 dated 2025-09-30
DESCRIPTION | 14 - MD5 | 21 - README.md | 33 +- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 20 - inst/doc/gdd.R | 2 inst/doc/gdd.html | 479 ++++++++++++++++++++++++++--------- inst/doc/intro.R | 12 inst/doc/intro.html | 596 ++++++++++++++++++++++++++++++-------------- man/pollen-package.Rd | 4 tests/testthat/test-zeros.R | 14 - 12 files changed, 831 insertions(+), 364 deletions(-)
Title: Add a Scale Bar to 'OpenStreetMap' Plots
Description: Functionality to handle and project lat-long coordinates, easily download background maps
and add a correct scale bar to 'OpenStreetMap' plots in any map projection.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between OSMscale versions 0.5.22 dated 2025-07-27 and 0.5.23 dated 2025-09-30
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/mapComp.R | 13 ++++++++----- R/pointsMap.R | 7 +++++-- R/projectPoints.R | 2 ++ R/scaleBar.R | 11 +++++++++-- man/mapComp.Rd | 5 +++-- man/pointsMap.Rd | 2 ++ man/projectPoints.Rd | 2 ++ man/scaleBar.Rd | 11 +++++++++-- 10 files changed, 54 insertions(+), 27 deletions(-)
Title: Facilitation of Data Preparation and Plotting Procedures for RDA
and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>
Diff between GABB versions 0.3.9 dated 2025-05-14 and 0.3.10 dated 2025-09-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PCA_RDA_graphics.R | 13 ++++++++++--- 3 files changed, 16 insertions(+), 9 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] ,
AstraZeneca [ctb] ,
Trustees of Columbia University [cph],
Simon Wood [cph] ,
R Core Deveopment Team [cph] ,
Douglas Bates [cph] ,
Martin Maechler [cph] ,
Ben Bolk [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.32.1 dated 2024-01-18 and 2.32.2 dated 2025-09-30
rstanarm-2.32.1/rstanarm/cleanup |only rstanarm-2.32.1/rstanarm/cleanup.win |only rstanarm-2.32.1/rstanarm/inst/include/meta_header.hpp |only rstanarm-2.32.1/rstanarm/src/Makevars.win |only rstanarm-2.32.1/rstanarm/src/rstanarm-win.def |only rstanarm-2.32.1/rstanarm/src/stan_files |only rstanarm-2.32.1/rstanarm/tests/testthat/include |only rstanarm-2.32.1/rstanarm/tests/testthat/stan_files |only rstanarm-2.32.1/rstanarm/tools |only rstanarm-2.32.2/rstanarm/DESCRIPTION | 13 rstanarm-2.32.2/rstanarm/MD5 | 375 - rstanarm-2.32.2/rstanarm/NAMESPACE | 3 rstanarm-2.32.2/rstanarm/R/bayes_R2.R | 4 rstanarm-2.32.2/rstanarm/R/doc-datasets.R | 2 rstanarm-2.32.2/rstanarm/R/doc-rstanarm-package.R | 9 rstanarm-2.32.2/rstanarm/R/jm_data_block.R | 20 rstanarm-2.32.2/rstanarm/R/jm_make_assoc_parts.R | 8 rstanarm-2.32.2/rstanarm/R/jm_make_assoc_terms.R | 3 rstanarm-2.32.2/rstanarm/R/launch_shinystan.R | 2 rstanarm-2.32.2/rstanarm/R/log_lik.R | 6 rstanarm-2.32.2/rstanarm/R/loo-prediction.R | 1 rstanarm-2.32.2/rstanarm/R/loo.R | 56 rstanarm-2.32.2/rstanarm/R/misc.R | 14 rstanarm-2.32.2/rstanarm/R/plots.R | 2 rstanarm-2.32.2/rstanarm/R/pp_check.R | 6 rstanarm-2.32.2/rstanarm/R/pp_data.R | 6 rstanarm-2.32.2/rstanarm/R/predictive_error.R | 1 rstanarm-2.32.2/rstanarm/R/stan_biglm.R | 2 rstanarm-2.32.2/rstanarm/R/stan_clogit.R | 2 rstanarm-2.32.2/rstanarm/R/stan_glm.fit.R | 6 rstanarm-2.32.2/rstanarm/R/stanmodels.R | 63 rstanarm-2.32.2/rstanarm/R/stanmvreg-methods.R | 4 rstanarm-2.32.2/rstanarm/R/stanreg-methods.R | 6 rstanarm-2.32.2/rstanarm/R/stanreg-objects.R | 2 rstanarm-2.32.2/rstanarm/R/stanreg_list.R | 3 rstanarm-2.32.2/rstanarm/R/zzz.R | 11 rstanarm-2.32.2/rstanarm/build/partial.rdb |binary rstanarm-2.32.2/rstanarm/build/vignette.rds |binary rstanarm-2.32.2/rstanarm/configure |only rstanarm-2.32.2/rstanarm/configure.win |only rstanarm-2.32.2/rstanarm/inst/doc/ab-testing.Rmd | 2 rstanarm-2.32.2/rstanarm/inst/doc/ab-testing.html | 1059 +++-- rstanarm-2.32.2/rstanarm/inst/doc/aov.R | 16 rstanarm-2.32.2/rstanarm/inst/doc/aov.html | 227 - rstanarm-2.32.2/rstanarm/inst/doc/betareg.R | 10 rstanarm-2.32.2/rstanarm/inst/doc/betareg.html | 350 + rstanarm-2.32.2/rstanarm/inst/doc/binomial.R | 22 rstanarm-2.32.2/rstanarm/inst/doc/binomial.Rmd | 2 rstanarm-2.32.2/rstanarm/inst/doc/binomial.html | 522 +- rstanarm-2.32.2/rstanarm/inst/doc/continuous.R | 72 rstanarm-2.32.2/rstanarm/inst/doc/continuous.Rmd | 10 rstanarm-2.32.2/rstanarm/inst/doc/continuous.html | 551 +- rstanarm-2.32.2/rstanarm/inst/doc/count.R | 22 rstanarm-2.32.2/rstanarm/inst/doc/count.Rmd | 6 rstanarm-2.32.2/rstanarm/inst/doc/count.html | 346 + rstanarm-2.32.2/rstanarm/inst/doc/glmer.R | 26 rstanarm-2.32.2/rstanarm/inst/doc/glmer.html | 534 ++ rstanarm-2.32.2/rstanarm/inst/doc/jm.R | 20 rstanarm-2.32.2/rstanarm/inst/doc/jm.html | 1918 +++++++--- rstanarm-2.32.2/rstanarm/inst/doc/lm.R | 6 rstanarm-2.32.2/rstanarm/inst/doc/lm.html | 482 +- rstanarm-2.32.2/rstanarm/inst/doc/mrp.R | 274 - rstanarm-2.32.2/rstanarm/inst/doc/mrp.html | 965 +++-- rstanarm-2.32.2/rstanarm/inst/doc/polr.R | 8 rstanarm-2.32.2/rstanarm/inst/doc/polr.html | 327 + rstanarm-2.32.2/rstanarm/inst/doc/pooling.R | 62 rstanarm-2.32.2/rstanarm/inst/doc/pooling.Rmd | 10 rstanarm-2.32.2/rstanarm/inst/doc/pooling.html | 1628 +++++--- rstanarm-2.32.2/rstanarm/inst/doc/priors.R | 30 rstanarm-2.32.2/rstanarm/inst/doc/priors.html | 440 +- rstanarm-2.32.2/rstanarm/inst/doc/rstanarm.R | 24 rstanarm-2.32.2/rstanarm/inst/doc/rstanarm.Rmd | 26 rstanarm-2.32.2/rstanarm/inst/doc/rstanarm.html | 653 ++- rstanarm-2.32.2/rstanarm/inst/include/stan_meta_header.hpp |only rstanarm-2.32.2/rstanarm/inst/stan |only rstanarm-2.32.2/rstanarm/man/bayes_R2.stanreg.Rd | 4 rstanarm-2.32.2/rstanarm/man/launch_shinystan.stanreg.Rd | 2 rstanarm-2.32.2/rstanarm/man/loo.stanreg.Rd | 29 rstanarm-2.32.2/rstanarm/man/loo_predict.stanreg.Rd | 2 rstanarm-2.32.2/rstanarm/man/plot.stanreg.Rd | 2 rstanarm-2.32.2/rstanarm/man/pp_check.stanreg.Rd | 4 rstanarm-2.32.2/rstanarm/man/rstanarm-package.Rd | 29 rstanarm-2.32.2/rstanarm/man/stan_betareg.Rd | 2 rstanarm-2.32.2/rstanarm/man/stan_biglm.Rd | 2 rstanarm-2.32.2/rstanarm/man/stan_glm.Rd | 2 rstanarm-2.32.2/rstanarm/man/stan_lm.Rd | 2 rstanarm-2.32.2/rstanarm/man/stan_polr.Rd | 2 rstanarm-2.32.2/rstanarm/man/stanreg-objects.Rd | 2 rstanarm-2.32.2/rstanarm/src/Makevars | 22 rstanarm-2.32.2/rstanarm/src/stanExports_bernoulli.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_bernoulli.h |only rstanarm-2.32.2/rstanarm/src/stanExports_binomial.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_binomial.h |only rstanarm-2.32.2/rstanarm/src/stanExports_continuous.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_continuous.h |only rstanarm-2.32.2/rstanarm/src/stanExports_count.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_count.h |only rstanarm-2.32.2/rstanarm/src/stanExports_jm.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_jm.h |only rstanarm-2.32.2/rstanarm/src/stanExports_lm.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_lm.h |only rstanarm-2.32.2/rstanarm/src/stanExports_mvmer.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_mvmer.h |only rstanarm-2.32.2/rstanarm/src/stanExports_polr.cc |only rstanarm-2.32.2/rstanarm/src/stanExports_polr.h |only rstanarm-2.32.2/rstanarm/tests/testthat/test_loo.R | 2 rstanarm-2.32.2/rstanarm/tests/testthat/test_methods.R | 3 rstanarm-2.32.2/rstanarm/tests/testthat/test_stan_clogit.R | 7 rstanarm-2.32.2/rstanarm/tests/testthat/test_stan_functions.R | 4 rstanarm-2.32.2/rstanarm/vignettes/ab-testing.Rmd | 2 rstanarm-2.32.2/rstanarm/vignettes/binomial.Rmd | 2 rstanarm-2.32.2/rstanarm/vignettes/continuous.Rmd | 10 rstanarm-2.32.2/rstanarm/vignettes/count.Rmd | 6 rstanarm-2.32.2/rstanarm/vignettes/pooling.Rmd | 10 rstanarm-2.32.2/rstanarm/vignettes/rstanarm.Rmd | 26 115 files changed, 7798 insertions(+), 3660 deletions(-)
More information about OmopConstructor at CRAN
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More information about nonParQuantileCausality at CRAN
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Title: An Analysis Toolbox for Hermitian Positive Definite Matrices
Description: An implementation of data analysis tools for samples of symmetric or
Hermitian positive definite matrices, such as collections of covariance matrices
or spectral density matrices. The tools in this package can be used to perform: (i)
intrinsic wavelet transforms for curves (1D) or surfaces (2D) of Hermitian positive
definite matrices with applications to dimension reduction, denoising and clustering in the
space of Hermitian positive definite matrices; and (ii) exploratory data analysis and inference
for samples of positive definite matrices by means of intrinsic data depth functions and
rank-based hypothesis tests in the space of Hermitian positive definite matrices.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between pdSpecEst versions 1.2.4 dated 2020-01-08 and 1.2.6 dated 2025-09-30
pdSpecEst-1.2.4/pdSpecEst/R/pdSpecEst.R |only pdSpecEst-1.2.4/pdSpecEst/README.md |only pdSpecEst-1.2.4/pdSpecEst/man/pdSpecEst.Rd |only pdSpecEst-1.2.6/pdSpecEst/DESCRIPTION | 10 pdSpecEst-1.2.6/pdSpecEst/MD5 | 63 pdSpecEst-1.2.6/pdSpecEst/NEWS.md | 8 pdSpecEst-1.2.6/pdSpecEst/R/cluster.R | 2 pdSpecEst-1.2.6/pdSpecEst/R/pdSpecEst-package.R |only pdSpecEst-1.2.6/pdSpecEst/build/partial.rdb |binary pdSpecEst-1.2.6/pdSpecEst/build/vignette.rds |binary pdSpecEst-1.2.6/pdSpecEst/inst/doc/depth_ranktests.R | 20 pdSpecEst-1.2.6/pdSpecEst/inst/doc/depth_ranktests.html | 788 +++++++----- pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.R | 34 pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.Rmd | 26 pdSpecEst-1.2.6/pdSpecEst/inst/doc/wavelet_est_clust.html | 919 ++++++++++---- pdSpecEst-1.2.6/pdSpecEst/man/InvWavTransf1D.Rd | 11 pdSpecEst-1.2.6/pdSpecEst/man/InvWavTransf2D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/WavTransf1D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdMean.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdPgram.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdPgram2D.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdRankTests.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecClust1D.Rd | 16 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecClust2D.Rd | 16 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst-package.Rd |only pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst1D.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSpecEst2D.Rd | 10 pdSpecEst-1.2.6/pdSpecEst/man/pdSplineReg.Rd | 3 pdSpecEst-1.2.6/pdSpecEst/man/pdkMeans.Rd | 13 pdSpecEst-1.2.6/pdSpecEst/man/rExamples1D.Rd | 17 pdSpecEst-1.2.6/pdSpecEst/man/rExamples2D.Rd | 12 pdSpecEst-1.2.6/pdSpecEst/src/Makevars | 11 pdSpecEst-1.2.6/pdSpecEst/src/Makevars.win | 11 pdSpecEst-1.2.6/pdSpecEst/src/RcppExports.cpp | 5 pdSpecEst-1.2.6/pdSpecEst/vignettes/wavelet_est_clust.Rmd | 26 35 files changed, 1395 insertions(+), 661 deletions(-)
Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling
and modelling in ecological applications. Functions include models for species
population density, spatial smoothing, multivariate separability, point process
model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and
analysis, auto-logistic modeling, sampling models, cluster optimization, statistical
exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre] ,
Melanie A. Murphy [ctb],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 2.0-2 dated 2023-11-17 and 2.0-3 dated 2025-09-30
spatialEco-2.0-2/spatialEco/man/oli.asw.Rd |only spatialEco-2.0-3/spatialEco/DESCRIPTION | 13 - spatialEco-2.0-3/spatialEco/MD5 | 40 +-- spatialEco-2.0-3/spatialEco/NAMESPACE | 3 spatialEco-2.0-3/spatialEco/R/aspline.downscale.R | 13 - spatialEco-2.0-3/spatialEco/R/cgls_urls.R | 153 +----------- spatialEco-2.0-3/spatialEco/R/crossCorrelation.R | 2 spatialEco-2.0-3/spatialEco/R/dahi.R | 9 spatialEco-2.0-3/spatialEco/R/elev-data.R | 2 spatialEco-2.0-3/spatialEco/R/oli.aws.R | 105 -------- spatialEco-2.0-3/spatialEco/R/raster.gaussian.smooth.R | 69 +++-- spatialEco-2.0-3/spatialEco/R/raster.kendall.R | 2 spatialEco-2.0-3/spatialEco/R/sf.kde.R | 170 +++++--------- spatialEco-2.0-3/spatialEco/R/z_normalization.R |only spatialEco-2.0-3/spatialEco/inst/CITATION | 4 spatialEco-2.0-3/spatialEco/inst/NEWS | 23 + spatialEco-2.0-3/spatialEco/man/cgls_urls.Rd | 79 ------ spatialEco-2.0-3/spatialEco/man/dahi.Rd | 5 spatialEco-2.0-3/spatialEco/man/elev.Rd | 2 spatialEco-2.0-3/spatialEco/man/oli.aws.Rd |only spatialEco-2.0-3/spatialEco/man/raster.gaussian.smooth.Rd | 6 spatialEco-2.0-3/spatialEco/man/sf.kde.Rd | 9 spatialEco-2.0-3/spatialEco/man/z_normalization.Rd |only 23 files changed, 225 insertions(+), 484 deletions(-)
Title: Procrustes Matching for Latent Space Item Response Model
Description: Procrustes matching of the posterior samples of person and item latent positions from latent space item response models. The methods implemented in this package are based on work by Borg, I., Groenen, P. (1997, ISBN:978-0-387-94845-4), Jeon, M., Jin, I. H., Schweinberger, M., Baugh, S. (2021) <doi:10.1007/s11336-021-09762-5>, and Andrew, D. M., Kevin M. Q., Jong Hee Park. (2011) <doi:10.18637/jss.v042.i09>.
Author: Jinwen Luo [aut, cre] ,
Minjeong Jeon [aut]
Maintainer: Jinwen Luo <jevanluo@ucla.edu>
Diff between prolsirm versions 0.1.0 dated 2023-09-20 and 0.1.1 dated 2025-09-30
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/procrustes.R | 6 ++++-- man/procrustes.Rd | 13 ++++++++----- 4 files changed, 20 insertions(+), 15 deletions(-)
Title: Space-Filling Designs
Description: Construct various types of space-filling designs, including Latin hypercube designs, clustering-based designs, maximin designs, maximum projection designs, and uniform designs (Joseph 2016 <doi:10.1080/08982112.2015.1100447>). It also offers the option to optimize designs based on user-defined criteria. This work is supported by U.S. National Science Foundation grant DMS-2310637.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <shangkunwang01@gmail.com>
Diff between SFDesign versions 0.1.2 dated 2025-06-21 and 0.1.3 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/maxpro.R | 4 ++-- R/utils.R | 4 ++-- man/maxpro.crit.Rd | 2 +- src/RcppExports.cpp | 9 +++++---- src/pairwise_design.cpp | 36 +++++++++++++++++------------------- 8 files changed, 40 insertions(+), 41 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.4 dated 2025-06-04 and 3.7.5 dated 2025-09-29
DESCRIPTION | 20 ++-- MD5 | 57 ++++++----- NAMESPACE | 1 NEWS.md | 14 ++ R/ASAP2OM.R | 11 +- R/Class_definitions.R | 47 +++++++-- R/Data_Functions.R | 7 - R/Data_make_update.R | 21 +++- R/Empirical_MP.R | 14 ++ R/MMSE_Object.r | 47 +-------- R/MOM_object.r | 7 + R/Misc_Exported.R | 18 ++- R/Misc_Internal.R | 4 R/OM_functions.R | 4 R/SS2Data.R | 12 +- R/SS2MOM.R | 5 - R/SS2OM.R | 25 ++++- R/SSinternal.R | 125 +++++++++++++++++++++++-- R/SampleOM.R | 41 ++++++-- R/multiMSE.R | 169 +++++++++++++++++++---------------- R/popdyn.R | 236 ++++++++++++++++++++++++++++++++++++++++--------- R/popdyn_MICE.R | 46 +++++---- R/runMSE.R | 117 +++++++++++++++++------- build/partial.rdb |binary man/ASAP2OM.Rd | 3 man/MSEextra.Rd | 4 man/print.multiHist.Rd |only man/show-MSEtool.Rd | 6 + man/tune_MP.Rd | 134 +++++++++++++-------------- src/popddynCPP.cpp | 12 +- 30 files changed, 817 insertions(+), 390 deletions(-)
Title: Access Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Aniruddha Ghosh [ctb],
Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geodata versions 0.6-2 dated 2024-06-10 and 0.6-6 dated 2025-09-29
geodata-0.6-2/geodata/R/helper-functions.R |only geodata-0.6-6/geodata/DESCRIPTION | 25 +++-- geodata-0.6-6/geodata/MD5 | 37 ++++--- geodata-0.6-6/geodata/NAMESPACE | 1 geodata-0.6-6/geodata/R/countries.R | 53 +++++----- geodata-0.6-6/geodata/R/download.R |only geodata-0.6-6/geodata/R/gadm.R | 2 geodata-0.6-6/geodata/R/nasawth.R |only geodata-0.6-6/geodata/R/occurrence.R | 28 ++++- geodata-0.6-6/geodata/R/path.R |only geodata-0.6-6/geodata/R/soil_grids.R | 25 +++-- geodata-0.6-6/geodata/R/soil_isda.R | 70 +++++++++++++- geodata-0.6-6/geodata/R/worldclim.R | 128 +++++++++++++++++--------- geodata-0.6-6/geodata/build/partial.rdb |binary geodata-0.6-6/geodata/man/biooracle.Rd | 2 geodata-0.6-6/geodata/man/cmip6.Rd | 8 - geodata-0.6-6/geodata/man/geodata_path.Rd | 17 +-- geodata-0.6-6/geodata/man/soil_af_isda.Rd | 2 geodata-0.6-6/geodata/man/soil_af_isda_vsi.Rd |only geodata-0.6-6/geodata/man/soil_grids.Rd | 3 geodata-0.6-6/geodata/man/soil_grids_vsi.Rd | 2 geodata-0.6-6/geodata/man/sp_occurrence.Rd | 25 ++--- 22 files changed, 285 insertions(+), 143 deletions(-)
Title: Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and
'base' R Graphics
Description: Theme 'ggplot2', 'lattice', and 'base' graphics based on a
few choices, including foreground color, background color, accent
color, and font family. Fonts that aren't available on the system, but
are available via download on 'Google Fonts', can be automatically
downloaded, cached, and registered for use with the 'showtext' and
'ragg' packages.
Author: Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Carson Sievert <carson@posit.co>
Diff between thematic versions 0.1.7 dated 2025-06-19 and 0.1.8 dated 2025-09-29
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 5 +++++ R/ggplot.R | 15 ++++++++------- 4 files changed, 22 insertions(+), 16 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Author: Cody L Marquart [aut, cre] ,
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
This is a re-admission after prior archival of version 0.2.7 dated 2024-02-23
Diff between rENA versions 0.2.7 dated 2024-02-23 and 0.3.0 dated 2025-09-29
rENA-0.2.7/rENA/man/scale.ena.set.Rd |only rENA-0.3.0/rENA/DESCRIPTION | 20 rENA-0.3.0/rENA/MD5 | 188 +- rENA-0.3.0/rENA/NAMESPACE | 43 rENA-0.3.0/rENA/R/ENAdata.R | 14 rENA-0.3.0/rENA/R/ENAplot.R | 86 - rENA-0.3.0/rENA/R/ENAset.R | 2 rENA-0.3.0/rENA/R/RcppExports.R | 53 rENA-0.3.0/rENA/R/accumulate.data.R | 19 rENA-0.3.0/rENA/R/ena.conversations.R | 6 rENA-0.3.0/rENA/R/ena.make.set.R | 20 rENA-0.3.0/rENA/R/ena.plot.R | 24 rENA-0.3.0/rENA/R/ena.plot.group.R | 8 rENA-0.3.0/rENA/R/ena.plot.network.R | 14 rENA-0.3.0/rENA/R/ena.plot.points.R | 2 rENA-0.3.0/rENA/R/ena.plot.trajectory.R | 2 rENA-0.3.0/rENA/R/ena.rotate.by.generalized.R |only rENA-0.3.0/rENA/R/ena.rotate.by.mean.R | 2 rENA-0.3.0/rENA/R/ena.rotate.by.regression.2.R |only rENA-0.3.0/rENA/R/ena.rotate.by.regression.R | 145 +- rENA-0.3.0/rENA/R/ena.set.R | 10 rENA-0.3.0/rENA/R/ena.svd.R | 56 rENA-0.3.0/rENA/R/gmr.R |only rENA-0.3.0/rENA/R/lws.positions.sq.R | 5 rENA-0.3.0/rENA/R/move_nodes.R | 46 rENA-0.3.0/rENA/R/piped.R |only rENA-0.3.0/rENA/R/qedata_classes.R |only rENA-0.3.0/rENA/R/qedata_define.R |only rENA-0.3.0/rENA/R/rENA.R | 8 rENA-0.3.0/rENA/R/utils.R | 75 + rENA-0.3.0/rENA/R/utils.classes.R | 1 rENA-0.3.0/rENA/R/utils.matrix.R | 2 rENA-0.3.0/rENA/R/utils.plot.R | 679 ++++++---- rENA-0.3.0/rENA/R/zzz.R | 4 rENA-0.3.0/rENA/demo/fullExample.R | 6 rENA-0.3.0/rENA/inst/CITATION | 9 rENA-0.3.0/rENA/inst/examples |only rENA-0.3.0/rENA/inst/include/rENA_RcppExports.h | 44 rENA-0.3.0/rENA/inst/rmd/methods.rmd | 21 rENA-0.3.0/rENA/man/ENAplot.Rd | 62 rENA-0.3.0/rENA/man/accumulate.Rd |only rENA-0.3.0/rENA/man/add_group.Rd | 58 rENA-0.3.0/rENA/man/add_network.Rd | 47 rENA-0.3.0/rENA/man/add_nodes.Rd | 60 rENA-0.3.0/rENA/man/add_points.Rd | 66 rENA-0.3.0/rENA/man/add_trajectory.Rd | 60 rENA-0.3.0/rENA/man/as.qe.code.Rd |only rENA-0.3.0/rENA/man/as.qe.data.Rd |only rENA-0.3.0/rENA/man/as.qe.horizon.Rd |only rENA-0.3.0/rENA/man/as.qe.metadata.Rd |only rENA-0.3.0/rENA/man/as.qe.unit.Rd |only rENA-0.3.0/rENA/man/center.Rd |only rENA-0.3.0/rENA/man/check_range.Rd |only rENA-0.3.0/rENA/man/clear.Rd | 49 rENA-0.3.0/rENA/man/codes.Rd |only rENA-0.3.0/rENA/man/compute_SB.Rd |only rENA-0.3.0/rENA/man/define.Rd |only rENA-0.3.0/rENA/man/directed_node_positions.Rd |only rENA-0.3.0/rENA/man/directed_node_positions_with_ground_response_added.Rd |only rENA-0.3.0/rENA/man/ena.plot.Rd | 25 rENA-0.3.0/rENA/man/ena.plot.group.Rd | 3 rENA-0.3.0/rENA/man/ena.plot.network.Rd | 3 rENA-0.3.0/rENA/man/ena.plot.points.Rd | 2 rENA-0.3.0/rENA/man/ena.plot.trajectory.Rd | 2 rENA-0.3.0/rENA/man/ena.rotate.by.generalized.Rd |only rENA-0.3.0/rENA/man/ena.rotate.by.hena.regression.Rd | 10 rENA-0.3.0/rENA/man/ena.rotate.by.hena.regression_2.Rd |only rENA-0.3.0/rENA/man/ena.svd.Rd | 33 rENA-0.3.0/rENA/man/find_binary_cols.Rd |only rENA-0.3.0/rENA/man/fun_skip_sphere_norm.Rd | 17 rENA-0.3.0/rENA/man/fun_sphere_norm.Rd | 17 rENA-0.3.0/rENA/man/get_x1_main_effect.Rd |only rENA-0.3.0/rENA/man/gmr.Rd |only rENA-0.3.0/rENA/man/group.Rd |only rENA-0.3.0/rENA/man/horizon.Rd |only rENA-0.3.0/rENA/man/is.qe.code.Rd |only rENA-0.3.0/rENA/man/is.qe.data.Rd |only rENA-0.3.0/rENA/man/is.qe.horizon.Rd |only rENA-0.3.0/rENA/man/is.qe.metadata.Rd |only rENA-0.3.0/rENA/man/is.qe.unit.Rd |only rENA-0.3.0/rENA/man/merge_columns_c.Rd | 2 rENA-0.3.0/rENA/man/metadata.Rd |only rENA-0.3.0/rENA/man/model.Rd |only rENA-0.3.0/rENA/man/move_nodes_to_unit_circle.Rd | 6 rENA-0.3.0/rENA/man/move_nodes_to_unit_circle_with_equal_space.Rd | 4 rENA-0.3.0/rENA/man/optimize.Rd |only rENA-0.3.0/rENA/man/plot.ena.set.Rd | 61 rENA-0.3.0/rENA/man/prepare_trajectory_data.Rd | 20 rENA-0.3.0/rENA/man/project.Rd |only rENA-0.3.0/rENA/man/reclassify.Rd |only rENA-0.3.0/rENA/man/rotate.Rd |only rENA-0.3.0/rENA/man/scale.ENAplot.Rd |only rENA-0.3.0/rENA/man/show.Rd | 11 rENA-0.3.0/rENA/man/sphere_norm.Rd |only rENA-0.3.0/rENA/man/times-.ena.matrix.Rd |only rENA-0.3.0/rENA/man/units.Rd |only rENA-0.3.0/rENA/man/with.ena.matrix.Rd |only rENA-0.3.0/rENA/man/with_means.Rd | 10 rENA-0.3.0/rENA/man/with_trajectory.Rd | 21 rENA-0.3.0/rENA/src/Makevars.win | 2 rENA-0.3.0/rENA/src/RcppExports.cpp | 78 + rENA-0.3.0/rENA/src/ena.cpp | 166 ++ rENA-0.3.0/rENA/tests/testthat/test-cohens.R | 2 rENA-0.3.0/rENA/tests/testthat/test-convs.R | 10 rENA-0.3.0/rENA/tests/testthat/test-ena_group.R | 4 rENA-0.3.0/rENA/tests/testthat/test-ena_wrapper.R | 2 rENA-0.3.0/rENA/tests/testthat/test-gmr.R |only rENA-0.3.0/rENA/tests/testthat/test-piping.R |only rENA-0.3.0/rENA/tests/testthat/test-set_creator.R | 2 rENA-0.3.0/rENA/tests/testthat/test.connection.matrix.R | 8 rENA-0.3.0/rENA/tests/testthat/test.ena.accumulations.R | 12 rENA-0.3.0/rENA/tests/testthat/test.ena.make.set.R | 28 rENA-0.3.0/rENA/tests/testthat/test.ena.make.set.old.R | 2 rENA-0.3.0/rENA/tests/testthat/test.ena.plot.set.R | 381 ++--- rENA-0.3.0/rENA/tests/testthat/test.ena.use.cases.R | 42 rENA-0.3.0/rENA/tests/testthat/test.util.classes.R | 4 rENA-0.3.0/rENA/tests/testthat/test.util.matrices.R | 4 rENA-0.3.0/rENA/tests/testthat/test.utils.R | 10 118 files changed, 2089 insertions(+), 931 deletions(-)
Title: Test Investment Strategies with English-Like Code
Description: Design, backtest, and analyze portfolio strategies using simple,
English-like function chains. Includes technical indicators, flexible stock
selection, portfolio construction methods (equal weighting, signal weighting,
inverse volatility, hierarchical risk parity), and a compact backtesting
engine for portfolio returns, drawdowns, and summary metrics.
Author: Alberto Pallotta [aut, cre]
Maintainer: Alberto Pallotta <pallottaalberto@gmail.com>
Diff between PortfolioTesteR versions 0.1.1 dated 2025-09-22 and 0.1.2 dated 2025-09-29
DESCRIPTION | 6 MD5 | 87 +- NAMESPACE | 45 + NEWS.md | 65 + R/cross_sectional.R | 4 R/globals.R | 9 R/ml.R |only R/optimization.R | 782 +++++++++++++++++- R/technical_indicators.R | 166 ++- R/utils.R | 25 R/walk_forward.R | 269 ++++++ build/vignette.rds |binary inst/doc/getting-started.R | 79 + inst/doc/getting-started.Rmd | 96 ++ inst/doc/getting-started.html | 127 ++ inst/doc/optimization-walkforward.R |only inst/doc/optimization-walkforward.Rmd |only inst/doc/optimization-walkforward.html |only inst/examples/demo_cci_breakout_biweekly_rank.R |only inst/examples/demo_opt_basic.R |only inst/examples/demo_opt_heatmap.R |only inst/examples/demo_opt_surfaces.R |only inst/examples/demo_quality_momentum_inverse_vol.R |only inst/examples/demo_regime_hrp_momentum.R |only inst/examples/demo_stochrsi_acceleration_riskparity.R |only inst/examples/demo_wf_basic.R |only inst/examples/demo_wf_diagnostics.R |only inst/examples/demo_wf_full_diagnostics.R |only inst/examples/ml_sequence_quickstart.R |only inst/examples/ml_tabular_quickstart.R |only man/bucket_returns.Rd |only man/calc_market_breadth.Rd | 2 man/calc_rolling_correlation.Rd |only man/calc_sector_breadth.Rd | 2 man/calc_stochrsi.Rd |only man/cap_exposure.Rd |only man/cap_turnover.Rd |only man/carry_forward_weights.Rd |only man/combine_scores.Rd |only man/coverage_by_date.Rd |only man/cv_tune_seq.Rd |only man/demo_sector_map.Rd |only man/evaluate_scores.Rd |only man/ic_series.Rd |only man/join_panels.Rd |only man/make_labels.Rd |only man/membership_stability.Rd |only man/ml_backtest.Rd |only man/ml_backtest_seq.Rd |only man/panel_lag.Rd |only man/plot.param_grid_result.Rd |only man/plot.wf_optimization_result.Rd |only man/rebalance_calendar.Rd |only man/roll_fit_predict.Rd |only man/roll_fit_predict_seq.Rd |only man/roll_ic_stats.Rd |only man/run_param_grid.Rd | 7 man/select_top_k_scores.Rd |only man/select_top_k_scores_by_group.Rd |only man/transform_scores.Rd |only man/tune_ml_backtest.Rd |only man/turnover_by_date.Rd |only man/validate_group_map.Rd |only man/validate_no_leakage.Rd |only man/weight_from_scores.Rd |only man/wf_sweep_tabular.Rd |only tests/testthat/test-ml.R |only tests/testthat/test-optimization.R |only tests/testthat/test-walk-forward.R |only vignettes/getting-started.Rmd | 96 ++ vignettes/optimization-walkforward.Rmd |only 71 files changed, 1700 insertions(+), 167 deletions(-)
More information about PortfolioTesteR at CRAN
Permanent link
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap
protocol. Dozens of road, satellite, and topographic map servers are directly
supported. Additionally raster maps
may be constructed using custom tile servers. Maps can be
plotted using either base graphics, or ggplot2. This package is not affiliated
with the OpenStreetMap.org mapping project.
Author: Ian Fellows [aut, cre],
Jan-Peter Stotz [aut]
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.4.0 dated 2023-10-12 and 0.4.1 dated 2025-09-29
DESCRIPTION | 18 +++-- MD5 | 20 ++--- R/osm.R | 34 ++++------ inst/java/JMapViewer.jar |binary inst/java/RTileController.jar |binary java/RTileController.java | 2 java/org/openstreetmap/gui/jmapviewer/tilesources/BingAerialTileSource.java | 4 - man/openmap.Rd | 24 +++---- man/openproj.Rd | 4 - man/plot.OpenStreetMap.Rd | 30 ++++++++ man/raster-OpenStreetMap-method.Rd | 2 11 files changed, 86 insertions(+), 52 deletions(-)
Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that [...truncated...]
Author: Michael Dumelle [aut, cre] ,
Tom Kincaid [aut],
Anthony R. Olsen [aut],
Marc Weber [aut],
Don Stevens [ctb],
Denis White [ctb],
Amanda M. Nahlik [ctb],
Sarah Lehmann [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spsurvey versions 5.5.1 dated 2024-01-09 and 5.6.0 dated 2025-09-29
spsurvey-5.5.1/spsurvey/inst/doc/EDA.R |only spsurvey-5.5.1/spsurvey/inst/doc/EDA.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/EDA.html |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.R |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.html |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.R |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.html |only spsurvey-5.5.1/spsurvey/vignettes/EDA.Rmd |only spsurvey-5.5.1/spsurvey/vignettes/analysis.Rmd |only spsurvey-5.5.1/spsurvey/vignettes/sampling.Rmd |only spsurvey-5.6.0/spsurvey/DESCRIPTION | 30 ++-- spsurvey-5.6.0/spsurvey/MD5 | 43 ++---- spsurvey-5.6.0/spsurvey/NEWS.md | 14 ++ spsurvey-5.6.0/spsurvey/R/adjwgtNR.R | 60 ++++----- spsurvey-5.6.0/spsurvey/R/dsgn_check.R | 16 ++ spsurvey-5.6.0/spsurvey/R/startup.R | 38 ++--- spsurvey-5.6.0/spsurvey/R/utils.R | 3 spsurvey-5.6.0/spsurvey/README.md | 33 ++-- spsurvey-5.6.0/spsurvey/build/vignette.rds |binary spsurvey-5.6.0/spsurvey/inst/doc/start-here.R | 4 spsurvey-5.6.0/spsurvey/inst/doc/start-here.Rmd | 42 +++--- spsurvey-5.6.0/spsurvey/inst/doc/start-here.html | 113 +++++++++-------- spsurvey-5.6.0/spsurvey/man/adjwgtNR.Rd | 24 +-- spsurvey-5.6.0/spsurvey/man/figures |only spsurvey-5.6.0/spsurvey/man/spsurvey-package.Rd | 8 - spsurvey-5.6.0/spsurvey/tests/testthat/test-adjwgtNR.R | 12 + spsurvey-5.6.0/spsurvey/vignettes/start-here.Rmd | 42 +++--- 29 files changed, 262 insertions(+), 220 deletions(-)
Title: Helper Functions for Species Delimitation Analysis
Description: Helpers functions to process, analyse, and visualize the output of
single locus species delimitation methods.
For full functionality, please install suggested software at
<https://legallab.github.io/delimtools/articles/install.html>.
Author: Pedro Bittencourt [aut, cre, cph] ,
Rupert Collins [aut, ctb, cph] ,
Tomas Hrbek [aut, ctb]
Maintainer: Pedro Bittencourt <pedro.sennabittencourt@gmail.com>
Diff between delimtools versions 0.2.0 dated 2025-03-31 and 0.2.1 dated 2025-09-29
DESCRIPTION | 20 +++--- MD5 | 83 +++++++++++++++++++++----- NEWS.md | 14 ++++ R/abgd_tbl.R | 10 ++- R/asap_tbl.R | 10 ++- R/get_delim_cols.R | 55 +++++++---------- R/hap_unite.R | 2 README.md | 43 +++++++++++-- build/vignette.rds |binary inst/doc/install.R | 16 ++--- inst/doc/install.Rmd | 20 ++---- inst/doc/install.html | 37 ++++++----- man/abgd_tbl.Rd | 4 - man/asap_tbl.Rd | 4 - man/figures/README-example-1.png |binary vignettes/geophagus.abgd.svg |only vignettes/geophagus.disthist.svg |only vignettes/geophagus.fasta |only vignettes/geophagus.fasta.Histo.svg |only vignettes/geophagus.fasta.HistoCum.svg |only vignettes/geophagus.fasta.Partition_1.csv |only vignettes/geophagus.fasta.Partition_1.txt |only vignettes/geophagus.fasta.Partition_10.csv |only vignettes/geophagus.fasta.Partition_10.txt |only vignettes/geophagus.fasta.Partition_2.csv |only vignettes/geophagus.fasta.Partition_2.txt |only vignettes/geophagus.fasta.Partition_3.csv |only vignettes/geophagus.fasta.Partition_3.txt |only vignettes/geophagus.fasta.Partition_4.csv |only vignettes/geophagus.fasta.Partition_4.txt |only vignettes/geophagus.fasta.Partition_5.csv |only vignettes/geophagus.fasta.Partition_5.txt |only vignettes/geophagus.fasta.Partition_6.csv |only vignettes/geophagus.fasta.Partition_6.txt |only vignettes/geophagus.fasta.Partition_7.csv |only vignettes/geophagus.fasta.Partition_7.txt |only vignettes/geophagus.fasta.Partition_8.csv |only vignettes/geophagus.fasta.Partition_8.txt |only vignettes/geophagus.fasta.Partition_9.csv |only vignettes/geophagus.fasta.Partition_9.txt |only vignettes/geophagus.fasta.clado.svg |only vignettes/geophagus.fasta.curve.svg |only vignettes/geophagus.fasta.groups.svg |only vignettes/geophagus.fasta.spart |only vignettes/geophagus.fasta.spart.xml |only vignettes/geophagus.fasta.svg |only vignettes/geophagus.part.1.txt |only vignettes/geophagus.part.2.txt |only vignettes/geophagus.part.3.txt |only vignettes/geophagus.part.4.txt |only vignettes/geophagus.part.5.txt |only vignettes/geophagus.part.6.txt |only vignettes/geophagus.part.7.txt |only vignettes/geophagus.part.8.txt |only vignettes/geophagus.partinit.1.txt |only vignettes/geophagus.partinit.2.txt |only vignettes/geophagus.partinit.3.txt |only vignettes/geophagus.partinit.4.txt |only vignettes/geophagus.partinit.5.txt |only vignettes/geophagus.partinit.6.txt |only vignettes/geophagus.partinit.7.txt |only vignettes/geophagus.partinit.8.txt |only vignettes/geophagus.rank.svg |only vignettes/geophagus_raxml.nwk |only vignettes/geophagus_raxml.nwk.mptp.multi.svg |only vignettes/geophagus_raxml.nwk.mptp.multi.txt |only vignettes/geophagus_raxml.nwk.mptp.single.svg |only vignettes/geophagus_raxml.nwk.mptp.single.txt |only vignettes/install.Rmd | 20 ++---- 69 files changed, 220 insertions(+), 118 deletions(-)
Title: Example BGM Files for the Atlantis Ecosystem Model
Description: A collection of box-geometry model (BGM) files for the Atlantis
ecosystem model. Atlantis is a deterministic, biogeochemical,
whole-of-ecosystem model (see <http://atlantis.cmar.csiro.au/> for more information).
Author: Michael D. Sumner [aut, cre],
Hadley Wickham [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between bgmfiles versions 0.0.6 dated 2016-08-10 and 0.1.0 dated 2025-09-29
bgmfiles-0.0.6/bgmfiles/R/bgmfiles-package.r |only bgmfiles-0.1.0/bgmfiles/DESCRIPTION | 18 bgmfiles-0.1.0/bgmfiles/MD5 | 42 bgmfiles-0.1.0/bgmfiles/NAMESPACE | 6 bgmfiles-0.1.0/bgmfiles/NEWS.md | 70 bgmfiles-0.1.0/bgmfiles/R/bgmfiles-package.R |only bgmfiles-0.1.0/bgmfiles/README.md | 179 bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/AEEC_poly_projETRS89_LAEA_snapped0p002.bgm |16134 +++++----- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/CalCurrentV3_utm.bgm | 9558 ++--- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Final_CAM_Boxes_8.bgm | 6568 ++-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/GOM_BGM.bgm | 4974 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Guam_utm1.bgm | 7330 ++-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/JFRE_ll.bgm | 5006 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/JFRE_xy.bgm | 5006 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/NGOM.bgm | 4472 +- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Nordic02.bgm | 6278 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/VMPA_setas.bgm | 898 bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/ams71.bgm | 5512 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/antarctica_28.bgm | 2530 - bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/antarctica_99.bgm | 8778 ++--- bgmfiles-0.1.0/bgmfiles/man/bgmfiles.Rd | 92 bgmfiles-0.1.0/bgmfiles/tests/testthat.R | 8 bgmfiles-0.1.0/bgmfiles/tests/testthat/test-files.R | 16 23 files changed, 41758 insertions(+), 41717 deletions(-)
Title: Integer Sequence Generator
Description: Generates well-known integer sequences. 'gmp' package is adopted for computing with arbitrarily large numbers. Every function has hyperlink to its corresponding item in OEIS (The On-Line Encyclopedia of Integer Sequences) in the function help page. For interested readers, see Sloane and Plouffe (1995, ISBN:978-0125586306).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between Zseq versions 0.2.1 dated 2022-09-07 and 0.2.2 dated 2025-09-29
Zseq-0.2.1/Zseq/man/Zseq-package.Rd |only Zseq-0.2.2/Zseq/DESCRIPTION | 14 +++++++------- Zseq-0.2.2/Zseq/MD5 | 11 +++++------ Zseq-0.2.2/Zseq/R/Factorial.Double.R | 6 ++++-- Zseq-0.2.2/Zseq/R/package-Zseq.R | 3 +-- Zseq-0.2.2/Zseq/R/zzz.R | 2 +- Zseq-0.2.2/Zseq/man/A000165.Rd | 6 ++++-- 7 files changed, 22 insertions(+), 20 deletions(-)
Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] ,
Remi Barillec [aut],
Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>
Diff between psgp versions 0.3-24 dated 2025-09-26 and 0.3-25 dated 2025-09-29
DESCRIPTION | 6 +-- MD5 | 31 ++++++++++--------- src/CovarianceFunction.cpp | 1 src/GaussianProcess.cpp | 8 ++--- src/Makevars | 2 - src/Makevars.win | 6 +++ src/Matern5CF.cpp | 1 src/ModelTrainer.cpp | 8 ++--- src/PSGP.cpp | 65 +++++++++++++++++++++++++++++------------ src/RInterface.cpp | 27 +++++++++++++++-- src/SumCovarianceFunction.cpp | 3 + src/WhiteNoiseCF.cpp | 5 ++- src/psgp_common.h | 9 +++-- src/psgp_estimator.cpp | 64 ++++++++++++++++++++++++++++++---------- src/psgp_estimator.h | 1 src/sensor_metadata_parser.cpp | 7 +++- tests/error_handling.R |only 17 files changed, 171 insertions(+), 73 deletions(-)
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sea surface temperature, chlorophyll, ocean fronts & bathymetry). Recognized classes and formats include netcdf, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer [aut, cre]
Maintainer: Robert K. Bauer <marine.biologging@gmail.com>
This is a re-admission after prior archival of version 0.1.6 dated 2023-11-10
Diff between oceanmap versions 0.1.6 dated 2023-11-10 and 0.1.7 dated 2025-09-29
ChangeLog | 4 ++ DESCRIPTION | 20 ++++++---- MD5 | 30 +++++++-------- NAMESPACE | 1 R/ggplotmaply.r | 19 ++------- R/hidden.r | 23 +++++++++++ R/sysdata.rda |binary data/cmap.RData |binary data/cmap_topo.RData |binary data/parameter_definitions.RData |binary data/region_definitions.RData |binary data/region_definitions_bkp.RData |binary inst/doc/oceanmap.pdf |binary man/ggplotmaply.Rd | 75 +++++++++++++++++++------------------- man/oceanmap.Rd | 2 - man/readbin.Rd | 4 +- 16 files changed, 101 insertions(+), 77 deletions(-)
Title: Functions Based on Entropic Statistics
Description: Methods for data analysis from an entropic perspective. These methods are nonparametric and perform well on non-ordinal data. Currently includes 'HeatMap()' for visualizing distributional characteristics among multiple populations (groups).
Author: Jialin Zhang [aut, cph, cre]
Maintainer: Jialin Zhang <jzhang@math.msstate.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2025-08-25
Diff between EntropicStatistics versions 0.1.1 dated 2025-08-25 and 0.1.3 dated 2025-09-29
DESCRIPTION | 18 ++--- MD5 | 9 +- NAMESPACE | 27 +++++--- R/HeatMap.R | 168 ++++++++++++++++++++++++++++++++++++++++++++---------- build |only man/HeatMap.Rd | 175 ++++++++++++++++++++++++++------------------------------- 6 files changed, 249 insertions(+), 148 deletions(-)
More information about EntropicStatistics at CRAN
Permanent link
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
four different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; 'Nager.Date' for public holidays;
and 'REST Countries API' for general country information. The package enables
users to explore various aspects of Colombia such as geographic locations,
cultural attractions, economic indicators, demographic data, and public
holidays. Additionally, 'ColombiAPI' includes curated datasets covering
Bogota air stations, business and holiday dates, public schools, Colombian
coffee exports, cannabis licenses, Medellin rainfall, malls in Bogota, as
well as datasets on indigenous languages, student admissions and school
statistics, forest liana mortality, municipal and regional data, connectivity
and digital infrastructure, progra [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.2.0 dated 2025-09-17 and 0.3.0 dated 2025-09-29
DESCRIPTION | 24 MD5 | 186 ++++--- NAMESPACE | 12 NEWS.md | 39 + R/colombiapi-package.R | 4 R/data-documentation.R | 444 +++++++++++++++++- R/get_colombia_airports.R | 2 R/get_colombia_attractions.R | 2 R/get_colombia_child_mortality.R | 2 R/get_colombia_cities.R | 2 R/get_colombia_cpi.R | 2 R/get_colombia_departments.R | 2 R/get_colombia_energy_use.R | 2 R/get_colombia_gdp.R | 2 R/get_colombia_holidays.R | 2 R/get_colombia_hospital_beds.R | 2 R/get_colombia_invasive_species.R | 2 R/get_colombia_life_expectancy.R | 2 R/get_colombia_literacy_rate.R | 2 R/get_colombia_native_communities.R | 2 R/get_colombia_natural_areas.R | 2 R/get_colombia_population.R | 2 R/get_colombia_presidents.R | 2 R/get_colombia_radios.R | 2 R/get_colombia_regions.R | 2 R/get_colombia_typical_dishes.R | 2 R/get_colombia_unemployment.R | 2 R/get_country_info_co.R | 2 R/utils.R | 2 R/view_datasets_ColombiAPI.R | 2 README.md | 8 data/Bogota_airstations_df.rda |binary data/Bogota_business_Date.rda |binary data/Bogota_holidays_Date.rda |binary data/Bogota_malls_tbl_df.rda |binary data/Bucaramanga_wifi_tbl_df.rda |only data/Cannabis_Licenses_tbl_df.rda |binary data/Cartagena_wifi_tbl_df.rda |only data/Colombia_coffee_tbl_df.rda |binary data/Medellin_rain_tbl_df.rda |binary data/Tulua_Public_Schools_tbl_df.rda |binary data/admitted_students_df.rda |only data/datalist |only data/dead_lianas_df.rda |only data/digital_centers_tbl_df.rda |only data/digital_graduates_tbl_df.rda |only data/foreign_visitors_tbl_df.rda |only data/gdp_departments_tbl_df.rda |only data/indigenous_vocabulary_df.rda |only data/municipalities_tbl_df.rda |only data/school_levels_df.rda |only data/vehicle_count_tbl_df.rda |only inst/CITATION | 2 inst/doc/colombiAPI_vignette.Rmd | 9 inst/doc/colombiAPI_vignette.html | 88 ++- inst/licenses/LICENSES_DETAILS.md | 52 +- man/Bucaramanga_wifi_tbl_df.Rd |only man/Cartagena_wifi_tbl_df.Rd |only man/ColombiAPI.Rd | 2 man/admitted_students_df.Rd |only man/dead_lianas_df.Rd |only man/digital_centers_tbl_df.Rd |only man/digital_graduates_tbl_df.Rd |only man/foreign_visitors_tbl_df.Rd |only man/gdp_departments_tbl_df.Rd |only man/indigenous_vocabulary_df.Rd |only man/municipalities_tbl_df.Rd |only man/school_levels_df.Rd |only man/vehicle_count_tbl_df.Rd |only tests/testthat/test-Bogota_airstations_df.R | 2 tests/testthat/test-Bogota_business_Date.R | 2 tests/testthat/test-Bogota_holidays_Date.R | 2 tests/testthat/test-Bogota_malls_tbl_df.R | 2 tests/testthat/test-Bucaramanga_wifi_tbl_df.R |only tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 tests/testthat/test-Cartagena_wifi_tbl_df.R |only tests/testthat/test-Colombia_coffee_tbl_df.R | 2 tests/testthat/test-Medellin_rain_tbl_df.R | 2 tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 tests/testthat/test-admitted_students_df.R |only tests/testthat/test-dead_lianas_df.R |only tests/testthat/test-digital_centers_tbl_df.R |only tests/testthat/test-digital_graduates_tbl_df.R |only tests/testthat/test-foreign_visitors_tbl_df.R |only tests/testthat/test-gdp_departments_tbl_df.R |only tests/testthat/test-get_colombia_airports.R | 2 tests/testthat/test-get_colombia_attractions.R | 2 tests/testthat/test-get_colombia_child_mortality.R | 2 tests/testthat/test-get_colombia_cities.R | 2 tests/testthat/test-get_colombia_cpi.R | 2 tests/testthat/test-get_colombia_departments.R | 2 tests/testthat/test-get_colombia_energy_use.R | 2 tests/testthat/test-get_colombia_gdp.R | 2 tests/testthat/test-get_colombia_holidays.R | 2 tests/testthat/test-get_colombia_hospital_beds.R | 2 tests/testthat/test-get_colombia_invasive_species.R | 2 tests/testthat/test-get_colombia_life_expectancy.R | 2 tests/testthat/test-get_colombia_literacy_rate.R | 2 tests/testthat/test-get_colombia_native_communities.R | 2 tests/testthat/test-get_colombia_natural_areas.R | 2 tests/testthat/test-get_colombia_population.R | 2 tests/testthat/test-get_colombia_presidents.R | 2 tests/testthat/test-get_colombia_radios.R | 2 tests/testthat/test-get_colombia_regions.R | 2 tests/testthat/test-get_colombia_typical_dishes.R | 2 tests/testthat/test-get_colombia_unemployment.R | 2 tests/testthat/test-get_country_info_co.R | 2 tests/testthat/test-indigenous_vocabulary_df.R |only tests/testthat/test-municipalities_tbl_df.R |only tests/testthat/test-school_levels_df.R |only tests/testthat/test-vehicle_count_tbl_df.R |only tests/testthat/test-view_datasets_ColombiAPI.R |only vignettes/colombiAPI_vignette.Rmd | 9 113 files changed, 796 insertions(+), 191 deletions(-)
Title: Performs Tests for Cluster Tendency of a Data Set
Description: Test for cluster tendency (clusterability) of a data set.
The methods implemented - reducing the data set to a single dimension using principal component analysis or computing
pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test -
are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms
are appropriate for a data set.
Author: Zachariah Neville [aut, cre],
Naomi Brownstein [aut],
Maya Ackerman [aut],
Andreas Adolfsson [aut]
Maintainer: Zachariah Neville <zachariahneville@outlook.com>
This is a re-admission after prior archival of version 0.1.1.0 dated 2020-03-04
Diff between clusterability versions 0.1.1.0 dated 2020-03-04 and 0.2.1.0 dated 2025-09-29
DESCRIPTION | 14 MD5 | 55 +-- NAMESPACE | 8 NEWS.md | 4 R/clusterability.R | 5 R/clusterabilitytest.R | 42 ++ R/dipsilverman.R | 3 R/normals1.R | 2 R/normals2.R | 2 R/normals3.R | 2 R/normals4.R | 2 R/normals5.R | 2 R/paramchecks.R | 34 +- R/reducestandardize.R | 58 +++ README.md | 11 inst |only man/clusterability.Rd | 263 +++++++--------- man/clusterabilitytest.Rd | 266 +++++++++------- man/normals1.Rd | 56 +-- man/normals2.Rd | 52 +-- man/normals3.Rd | 54 +-- man/normals4.Rd | 54 +-- man/normals5.Rd | 56 +-- man/print.clusterability.Rd | 38 +- tests/testthat.R | 8 tests/testthat/test_printsummary.R | 146 ++++---- tests/testthat/test_reducestandardize.R | 287 ++++++++++------- tests/testthat/test_validateparams.R | 526 ++++++++++++++++---------------- 28 files changed, 1136 insertions(+), 914 deletions(-)
More information about clusterability at CRAN
Permanent link
Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence
via the 'rstan' package, the R interface to the 'Stan' C++ library.
Supported models include single-season occupancy, dynamic occupancy, and
N-mixture abundance models. Covariates on model parameters are specified
using a formula-based interface similar to package 'unmarked', while also
allowing for estimation of random slope and intercept terms. References:
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between ubms versions 1.2.7 dated 2024-10-01 and 1.2.8 dated 2025-09-29
DESCRIPTION | 12 MD5 | 44 - NEWS.md | 6 R/gof.R | 2 R/inputs.R | 1 R/pcount.R | 1 R/spatial.R | 6 R/ubmsFit-methods.R | 10 build/vignette.rds |binary inst/doc/JAGS-comparison.html | 481 +++++++++--------- inst/doc/random-effects.html | 455 ++++++++++------- inst/doc/spatial-models.html | 614 ++++++++++++++--------- inst/doc/ubms.R | 14 inst/doc/ubms.Rmd | 5 inst/doc/ubms.html | 899 +++++++++++++++++++++------------- man/summary-ubmsFit-method.Rd | 4 src/exp_counts_occu.cpp | 4 src/simz.cpp | 10 tests/testthat/test_pcount.R | 7 tests/testthat/test_spatial.R | 19 tests/testthat/test_ubmsFit_methods.R | 4 vignettes/references.bib | 3 vignettes/ubms.Rmd | 5 23 files changed, 1596 insertions(+), 1010 deletions(-)
Title: Spatially Varying Change Points
Description: Implements a spatially varying change point model with
unique intercepts, slopes, variance intercepts and slopes, and
change points at each location. Inference is within the
Bayesian setting using Markov chain Monte Carlo (MCMC). The
response variable can be modeled as Gaussian (no nugget),
probit or Tobit link and the five spatially varying parameter
are modeled jointly using a multivariate conditional
autoregressive (MCAR) prior. The MCAR is a unique process that
allows for a dissimilarity metric to dictate the local spatial
dependencies. Full details of the package can be found in the accompanying vignette.
Furthermore, the details of the package can be found in the corresponding paper published in Spatial Statistics
by Berchuck et al (2019): "A spatially varying change points model for monitoring glaucoma
progression using visual field data", <doi:10.1016/j.spasta.2019.02.001>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>
Diff between spCP versions 1.3 dated 2022-09-05 and 1.4.0 dated 2025-09-29
DESCRIPTION | 16 +- MD5 | 21 +-- NEWS.md |only R/spCP-package.R | 3 build/vignette.rds |binary inst/doc/spCP-example.R | 26 +--- inst/doc/spCP-example.Rmd | 2 inst/doc/spCP-example.html | 288 ++++++++++++++++++++++----------------------- man/spCP.Rd | 3 src/MCMC_Samplers.cpp | 26 ++-- src/PRED_PredictFuture.cpp | 8 - vignettes/spCP-example.Rmd | 2 12 files changed, 200 insertions(+), 195 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.7.4 dated 2024-09-20 and 0.7.5 dated 2025-09-29
DESCRIPTION | 18 MD5 | 158 +- NAMESPACE | 200 +- NEWS.md | 84 - R/RcppExports.R | 38 R/coherence.R | 300 ++-- R/conversions.R | 1798 +++++++++++------------ R/functions.R | 940 ++++++------ R/generators.R | 440 ++--- R/merging.R | 244 +-- R/methods.R | 1726 +++++++++++------------ R/models.R | 596 +++---- R/others.R | 722 ++++----- R/sentopics.R | 301 ++-- R/timeSeries.R | 2550 +++++++++++++++++----------------- R/utils.R | 2224 ++++++++++++++--------------- R/zzz.R | 40 README.md | 308 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Basic_usage.R | 114 - inst/doc/Basic_usage.Rmd | 246 +-- inst/doc/Basic_usage.html | 1317 ++++++++--------- inst/doc/Topical_time_series.R | 140 - inst/doc/Topical_time_series.Rmd | 214 +- inst/doc/Topical_time_series.html | 1139 +++++++-------- man/ECB_press_conferences.Rd | 58 man/ECB_press_conferences_tokens.Rd | 72 man/JST.Rd | 194 +- man/LDA.Rd | 142 - man/LDAvis.Rd | 70 man/LoughranMcDonald.Rd | 72 man/PicaultRenault.Rd | 86 - man/PicaultRenault_data.Rd | 86 - man/as.LDA.Rd | 210 +- man/as.tokens.dfm.Rd | 118 - man/chainsDistances.Rd | 138 - man/chainsScores.Rd | 108 - man/coherence.Rd | 104 - man/compute_PicaultRenault_scores.Rd | 112 - man/get_ECB_press_conferences.Rd | 58 man/get_ECB_speeches.Rd | 74 man/melt.Rd | 52 man/melt.sentopicmodel.Rd | 92 - man/mergeTopics.Rd | 116 - man/plot.multiChains.Rd | 80 - man/plot.sentopicmodel.Rd | 84 - man/print.sentopicmodel.Rd | 66 man/proportion_topics.Rd | 192 +- man/rJST.Rd | 234 +-- man/reexports.Rd | 42 man/reset.Rd | 64 man/sentiment_breakdown.Rd | 208 +- man/sentiment_series.Rd | 162 +- man/sentiment_topics.Rd | 232 +-- man/sentopicmodel.Rd | 172 +- man/sentopics-conversions.Rd | 50 man/sentopics-package.Rd | 110 - man/sentopics_date.Rd | 110 - man/sentopics_labels.Rd | 134 - man/sentopics_sentiment.Rd | 230 +-- man/topWords.Rd | 212 +- tests/testthat.R | 32 tests/testthat/Rplots.pdf |binary tests/testthat/test-JST.R | 184 +- tests/testthat/test-LDA.R | 100 - tests/testthat/test-algorithm.R | 32 tests/testthat/test-basic.R | 166 +- tests/testthat/test-coherence.R | 106 - tests/testthat/test-conversions.R | 450 +++--- tests/testthat/test-generation.R | 150 +- tests/testthat/test-generics.R | 106 - tests/testthat/test-grow.R | 56 tests/testthat/test-others.R | 38 tests/testthat/test-parallel_chains.R | 350 ++-- tests/testthat/test-rJST.R | 186 +- tests/testthat/test-timeSeries.R | 390 ++--- tests/testthat/test-utils.R | 352 ++-- vignettes/Basic_usage.Rmd | 246 +-- vignettes/Topical_time_series.Rmd | 214 +- 80 files changed, 11682 insertions(+), 11677 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written t [...truncated...]
Author: Lucas A. Nell [cph, aut, cre]
Maintainer: Lucas A. Nell <lucnell@gmail.com>
Diff between jackalope versions 1.1.5 dated 2023-11-28 and 1.1.6 dated 2025-09-29
DESCRIPTION | 15 +-- MD5 | 20 ++-- NAMESPACE | 1 NEWS.md | 3 R/jackalope-package.R | 1 README.md | 11 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/jackalope-intro.R | 178 +++++++++++++++++++++--------------------- inst/doc/jackalope-intro.html | 3 src/Makevars.win | 12 -- 11 files changed, 119 insertions(+), 125 deletions(-)
Title: Add Some Van Gogh Colors and Overlay Colors on Your 'ggplot()'
Description: Works with 'ggplot2' to add a Van Gogh color palette to the user’s repertoire.
It also has a function that work alongside 'ggplot2' to create more interesting data visualizations and add contextual information to the user’s plots.
Author: Katelyn Diaz [aut, cre] ,
Silas Weden [aut],
Tess Goldmann [aut],
Aushanae Haller [edt] ,
Kathleen Hablutzel [edt]
Maintainer: Katelyn Diaz <katndiaz@gmail.com>
Diff between ggRtsy versions 0.1.0 dated 2023-09-15 and 1.2.1 dated 2025-09-29
DESCRIPTION | 14 ++++++++------ MD5 | 13 +++++++------ NEWS.md |only R/RectangleFiller.R | 17 +++++++++++++---- README.md | 3 ++- build/vignette.rds |binary inst/doc/Vignette.R | 4 ++-- inst/doc/Vignette.html | 18 +++++++++--------- 8 files changed, 41 insertions(+), 28 deletions(-)
Title: Bayesian Variable Selection using Power-Expected-Posterior Prior
Description: Performs Bayesian variable selection under normal linear
models for the data with the model parameters following as prior distributions either
the power-expected-posterior (PEP) or the intrinsic (a special case of the former)
(Fouskakis and Ntzoufras (2022) <doi: 10.1214/21-BA1288>,
Fouskakis and Ntzoufras (2020) <doi: 10.3390/econometrics8020017>).
The prior distribution on model space is the uniform over all models
or the uniform on model dimension (a special case of the beta-binomial prior).
The selection is performed by either implementing a full enumeration
and evaluation of all possible models or using the Markov Chain
Monte Carlo Model Composition (MC3) algorithm (Madigan and York (1995) <doi: 10.2307/1403615>).
Complementary functions for hypothesis testing, estimation and
predictions under Bayesian model averaging, as well as, plotting and
printing the results are also provided. The results can be compared to the
ones obtained under other well-known priors on [...truncated...]
Author: Konstantina Charmpi [aut, cre],
Dimitris Fouskakis [aut],
Ioannis Ntzoufras [aut]
Maintainer: Konstantina Charmpi <xarmpi.kon@gmail.com>
Diff between PEPBVS versions 2.1 dated 2024-11-12 and 2.2 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary src/auxiliary_code.cpp | 3 ++- 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.4 dated 2025-03-03 and 0.0.5 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- README.md | 1 + src/Generate.cpp | 10 ++++++++++ 4 files changed, 17 insertions(+), 6 deletions(-)
Title: Optimal Experimental Designs for Dynamic/Functional Models
Description: Optimal experimental designs for functional linear and functional generalised linear models, for scalar responses and profile/dynamic factors. The designs are optimised using the coordinate exchange algorithm. The methods are discussed by Michaelides (2023) <https://eprints.soton.ac.uk/474982/1/Thesis_DamianosMichaelides_Final_pdfa_1_.pdf>.
Author: Damianos Michaelides [aut, cre],
Antony Overstall [aut],
Dave Woods [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>
Diff between fdesigns versions 1.1 dated 2025-06-17 and 1.2 dated 2025-09-29
DESCRIPTION | 16 +++-- MD5 | 39 +++++++------ R/class_functions_all.R | 90 +++++++++---------------------- R/fdesignsR.R | 4 + R/flm_InteractionsPolynomials_mclapply.R | 18 +++--- R/flm_Interactions_mclapply.R | 13 ++-- R/flm_ME_mclapply.R | 10 +-- R/flm_general_Cstarts_mclapply.R | 61 ++++++++------------- R/hidden_functions.R | 49 ++++++++++++++++ build/partial.rdb |binary build/vignette.rds |only inst |only man/fdesigns-package.Rd | 4 - man/pflm.Rd | 33 ++++++----- man/plotfglm.Rd | 27 +++++---- man/plotflm.Rd | 26 +++++--- src/Makevars | 10 ++- src/Makevars.win | 10 ++- src/RcppExports.cpp | 12 ++-- src/fdesignscpp.cpp | 49 ++++++++++++++++ vignettes |only 21 files changed, 282 insertions(+), 189 deletions(-)
Title: Tools for Microscopy Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy.
Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.
Author: Volker Schmid [aut, cre],
Priyanka Kukreja [ctb],
Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between bioimagetools versions 1.1.8 dated 2022-05-28 and 1.1.9 dated 2025-09-29
bioimagetools-1.1.8/bioimagetools/NEWS |only bioimagetools-1.1.9/bioimagetools/DESCRIPTION | 13 +- bioimagetools-1.1.9/bioimagetools/MD5 | 10 - bioimagetools-1.1.9/bioimagetools/NEWS.md |only bioimagetools-1.1.9/bioimagetools/R/writetif.R | 104 ++++++++++--------- bioimagetools-1.1.9/bioimagetools/README.md | 6 - bioimagetools-1.1.9/bioimagetools/build/vignette.rds |binary 7 files changed, 71 insertions(+), 62 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 2.6.1 dated 2022-12-20 and 2.6.3 dated 2025-09-29
RAthena-2.6.1/RAthena/man/Query.Rd |only RAthena-2.6.1/RAthena/man/backend_dbplyr_v2.Rd |only RAthena-2.6.1/RAthena/man/dbClearResult.Rd |only RAthena-2.6.1/RAthena/man/dbColumnInfo.Rd |only RAthena-2.6.1/RAthena/man/dbDataType.Rd |only RAthena-2.6.1/RAthena/man/dbDisconnect.Rd |only RAthena-2.6.1/RAthena/man/dbExistsTable.Rd |only RAthena-2.6.1/RAthena/man/dbFetch.Rd |only RAthena-2.6.1/RAthena/man/dbGetInfo.Rd |only RAthena-2.6.1/RAthena/man/dbGetPartition.Rd |only RAthena-2.6.1/RAthena/man/dbGetQuery.Rd |only RAthena-2.6.1/RAthena/man/dbGetStatement.Rd |only RAthena-2.6.1/RAthena/man/dbGetTables.Rd |only RAthena-2.6.1/RAthena/man/dbHasCompleted.Rd |only RAthena-2.6.1/RAthena/man/dbIsValid.Rd |only RAthena-2.6.1/RAthena/man/dbListFields.Rd |only RAthena-2.6.1/RAthena/man/dbQuote.Rd |only RAthena-2.6.1/RAthena/man/dbRemoveTable.Rd |only RAthena-2.6.1/RAthena/man/dbShow.Rd |only RAthena-2.6.1/RAthena/man/dbStatistics.Rd |only RAthena-2.6.3/RAthena/DESCRIPTION | 13 RAthena-2.6.3/RAthena/MD5 | 154 - RAthena-2.6.3/RAthena/NAMESPACE | 21 RAthena-2.6.3/RAthena/NEWS.md | 15 RAthena-2.6.3/RAthena/R/Connection.R | 1039 ++++------ RAthena-2.6.3/RAthena/R/DataTypes.R | 126 - RAthena-2.6.3/RAthena/R/Driver.R | 345 +-- RAthena-2.6.3/RAthena/R/File_Parser.R | 310 +- RAthena-2.6.3/RAthena/R/Options.R | 297 +- RAthena-2.6.3/RAthena/R/RAthena.R | 3 RAthena-2.6.3/RAthena/R/Result.R | 366 +-- RAthena-2.6.3/RAthena/R/View.R | 393 ++- RAthena-2.6.3/RAthena/R/athena_low_api.R | 383 ++- RAthena-2.6.3/RAthena/R/dplyr_integration.R | 414 ++- RAthena-2.6.3/RAthena/R/fetch_utils.R | 67 RAthena-2.6.3/RAthena/R/install.R | 28 RAthena-2.6.3/RAthena/R/sql_translate_env.R | 338 +-- RAthena-2.6.3/RAthena/R/sql_translate_utils.R | 43 RAthena-2.6.3/RAthena/R/table.R | 949 ++++++--- RAthena-2.6.3/RAthena/R/utils.R | 306 ++ RAthena-2.6.3/RAthena/R/zzz.R | 37 RAthena-2.6.3/RAthena/README.md | 6 RAthena-2.6.3/RAthena/build/vignette.rds |binary RAthena-2.6.3/RAthena/inst/doc/aws_athena_query_caching.html | 123 - RAthena-2.6.3/RAthena/inst/doc/aws_athena_unload.html | 227 +- RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.R | 2 RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.Rmd | 2 RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.html | 15 RAthena-2.6.3/RAthena/inst/doc/changing_backend_file_parser.html | 53 RAthena-2.6.3/RAthena/inst/doc/convert_and_save_cost.Rmd | 2 RAthena-2.6.3/RAthena/inst/doc/convert_and_save_cost.html | 119 - RAthena-2.6.3/RAthena/inst/doc/getting_started.Rmd | 4 RAthena-2.6.3/RAthena/inst/doc/getting_started.html | 225 +- RAthena-2.6.3/RAthena/inst/doc/how_to_retry.html | 37 RAthena-2.6.3/RAthena/man/AthenaConnection.Rd | 140 + RAthena-2.6.3/RAthena/man/AthenaDriver.Rd | 14 RAthena-2.6.3/RAthena/man/AthenaListObjects.Rd |only RAthena-2.6.3/RAthena/man/AthenaPreviewObject.Rd |only RAthena-2.6.3/RAthena/man/AthenaResult.Rd |only RAthena-2.6.3/RAthena/man/AthenaWriteTables.Rd | 36 RAthena-2.6.3/RAthena/man/RAthena-package.Rd | 6 RAthena-2.6.3/RAthena/man/RAthena_options.Rd | 18 RAthena-2.6.3/RAthena/man/assume_role.Rd | 8 RAthena-2.6.3/RAthena/man/athena.Rd | 9 RAthena-2.6.3/RAthena/man/backend_dbplyr.Rd |only RAthena-2.6.3/RAthena/man/backend_dbplyr_v1.Rd | 2 RAthena-2.6.3/RAthena/man/dbConnect-AthenaDriver-method.Rd | 129 - RAthena-2.6.3/RAthena/man/dbConvertTable.Rd | 47 RAthena-2.6.3/RAthena/man/dbListTables.Rd | 8 RAthena-2.6.3/RAthena/man/db_compute.Rd | 90 RAthena-2.6.3/RAthena/man/db_copy_to.Rd | 63 RAthena-2.6.3/RAthena/man/dbplyr_edition.Rd | 2 RAthena-2.6.3/RAthena/man/install_boto.Rd | 10 RAthena-2.6.3/RAthena/man/session_token.Rd | 10 RAthena-2.6.3/RAthena/man/sqlCreateTable.Rd | 22 RAthena-2.6.3/RAthena/man/sqlData.Rd | 4 RAthena-2.6.3/RAthena/man/sql_translate_env.Rd | 12 RAthena-2.6.3/RAthena/man/work_group.Rd | 47 RAthena-2.6.3/RAthena/tests/testthat/helper.R | 138 - RAthena-2.6.3/RAthena/tests/testthat/test-append-data.R | 50 RAthena-2.6.3/RAthena/tests/testthat/test-athena-ddl.R | 90 RAthena-2.6.3/RAthena/tests/testthat/test-dbFetch-n.R | 77 RAthena-2.6.3/RAthena/tests/testthat/test-dplyr-compute.R | 34 RAthena-2.6.3/RAthena/tests/testthat/test-dplyr-copy_to.R | 30 RAthena-2.6.3/RAthena/tests/testthat/test-file-parser.R | 254 +- RAthena-2.6.3/RAthena/tests/testthat/test-metadata.R | 130 - RAthena-2.6.3/RAthena/tests/testthat/test-view.R | 223 +- RAthena-2.6.3/RAthena/vignettes/aws_s3_backend.Rmd | 2 RAthena-2.6.3/RAthena/vignettes/convert_and_save_cost.Rmd | 2 RAthena-2.6.3/RAthena/vignettes/getting_started.Rmd | 4 90 files changed, 4713 insertions(+), 3460 deletions(-)
Title: Optimal Monotone Conditional Error Functions
Description: Design and analysis of confirmatory adaptive clinical trials using the optimal conditional error framework according to Brannath and Bauer (2004) <doi:10.1111/j.0006-341X.2004.00221.x>. An extension to the optimal conditional error function using interim estimates as described in Brannath and Dreher (2024) <doi:10.48550/arXiv.2402.00814> and functions to ensure that the resulting conditional error function is non-increasing are also available.
Author: Morten Dreher [aut, cre],
Werner Brannath [aut, cph] ,
Cornelia Ursula Kunz [ctb] ,
Johanna zur Verth [aut]
Maintainer: Morten Dreher <morten.dreher@outlook.de>
Diff between optconerrf versions 1.0.0 dated 2025-09-09 and 1.0.1 dated 2025-09-29
DESCRIPTION | 6 MD5 | 120 NAMESPACE | 44 NEWS.md | 7 R/classes.R | 886 ++--- R/getDesignOptimalConditionalErrorFunction.R | 356 +- R/getExpectedSecondStageInformation.R | 116 R/getIntegral.R | 108 R/getIntegralWithConstants.R | 106 R/getLevelConstant.R | 168 - R/getLikelihoodRatio.R | 296 - R/getMonotoneFunction.R | 114 R/getMonotonisationConstants.R | 394 +- R/getNu.R | 68 R/getNuPrime.R | 54 R/getOptimalConditionalError.R | 342 +- R/getOverallPower.R | 148 R/getQ.R | 120 R/getSecondStageInformation.R | 170 - R/getSimulationResults.R | 222 - R/integrateExpectedInformation.R | 304 - R/utilities.R | 1664 +++++----- inst/doc/constraints_interim_estimates.Rmd | 602 +-- inst/doc/constraints_interim_estimates.html | 2 inst/doc/introduction.Rmd | 734 ++-- man/PowerResultsOptimalConditionalError.Rd | 20 man/SimulationResultsOptimalConditionalError.Rd | 20 man/TrialDesignOptimalConditionalError.Rd | 26 man/dot-rangeCheck.Rd | 42 man/getExpectedSecondStageInformation.Rd | 138 man/getInnerPsi.Rd | 50 man/getIntegral.Rd | 46 man/getIntegralWithConstants.Rd | 42 man/getLevelConstant.Rd | 66 man/getLikelihoodRatio.Rd | 104 man/getMonotoneFunction.Rd | 100 man/getMonotonisationConstants.Rd | 88 man/getNu.Rd | 68 man/getNuPrime.Rd | 64 man/getOptimalConditionalError.Rd | 90 man/getOverallPower.Rd | 74 man/getPsi.Rd | 58 man/getQ.Rd | 84 man/getSecondStageInformation.Rd | 100 man/getSimulationResults.Rd | 102 man/integrateExpectedInformation.Rd | 74 man/plot.TrialDesignOptimalConditionalError.Rd | 60 man/print.PowerResultsOptimalConditionalError.Rd | 38 man/print.SimulationResultsOptimalConditionalError.Rd | 38 man/print.TrialDesignOptimalConditionalError.Rd | 38 man/summary.TrialDesignOptimalConditionalError.Rd | 38 tests/testthat.R | 24 tests/testthat/test-getDesignOptimalConditionalErrorFunction.R | 104 tests/testthat/test-getExpectedSecondStageInformation.R | 184 - tests/testthat/test-getLevelConstant.R | 120 tests/testthat/test-getNuPrime.R | 16 tests/testthat/test-getOptimalConditionalError.R | 192 - tests/testthat/test-getOverallPower.R | 74 tests/testthat/test-getSecondStageInformation.R | 64 vignettes/constraints_interim_estimates.Rmd | 602 +-- vignettes/introduction.Rmd | 734 ++-- 61 files changed, 5470 insertions(+), 5463 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.3.0 dated 2025-09-05 and 0.3.1 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/coda_statistics.R | 9 ++++----- R/kinesis-package.R | 2 +- R/multivariate.R | 10 +++++++--- README.md | 2 +- inst/po/fr/LC_MESSAGES/R-kinesis.mo |binary man/kinesis-package.Rd | 2 +- po/R-fr.po | 28 ++++++++++++++++------------ po/R-kinesis.pot | 30 +++++++++++++++++------------- 11 files changed, 64 insertions(+), 49 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative,
diverging or sequential), with colors that are distinct for all
people, including color-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018)
<doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
or 'ggplot2'. It provides tools to simulate color-blindness and to
test how well the colors of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Vincent Arel-Bundock [ctb] ,
Ulrik Stervbo [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.16.0 dated 2025-02-25 and 1.17.0 dated 2025-09-29
DESCRIPTION | 31 MD5 | 220 +++--- NAMESPACE | 30 NEWS.md | 4 R/change.R | 2 R/color.R | 4 R/info.R | 54 - R/khroma-deprecated.R | 2 R/khroma-package.R | 32 R/palettes.R | 8 R/scale_colour_crameri.R | 557 ++++++++++++++-- R/scale_colour_picker.R | 2 R/scale_colour_science.R | 4 R/scale_colour_tol.R | 34 - R/sysdata.rda |binary README.md | 150 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/crameri.R | 120 ++- inst/doc/crameri.Rmd | 180 +++-- inst/doc/crameri.html | 558 ++++++++--------- inst/doc/khroma.R |only inst/doc/khroma.Rmd |only inst/doc/khroma.html |only inst/doc/tol.Rmd | 9 inst/doc/tol.html | 335 ++++------ inst/po/fr/LC_MESSAGES/R-khroma.mo |binary inst/tinytest/_snaps/info.rds |binary inst/tinytest/_tinysnapshot/plot_colorblind_bright.svg | 10 inst/tinytest/_tinysnapshot/plot_tiles_bright.svg | 4 inst/tinytest/_tinysnapshot/scheme_muted_FALSETRUE.svg | 18 inst/tinytest/_tinysnapshot/scheme_muted_TRUEFALSE.svg | 20 inst/tinytest/_tinysnapshot/scheme_muted_TRUETRUE.svg | 38 - inst/tinytest/helpers.R |only inst/tinytest/test_ggplot2_crameri.R | 62 + inst/tinytest/test_palettes.R | 2 inst/tinytest/test_plot.R | 76 +- man/change.Rd | 2 man/colour.Rd | 4 man/crameri.Rd | 48 - man/figures/README-usage-colorblind2-1.png |binary man/figures/README-usage-colorblind2-2.png |binary man/figures/README-usage-map-1.png |binary man/figures/README-usage-plot-1.png |binary man/figures/README-usage-plot-2.png |binary man/figures/README-usage-show-1.png |binary man/khroma-deprecated.Rd | 2 man/khroma-package.Rd | 41 - man/scale_crameri_acton.Rd | 40 - man/scale_crameri_bam.Rd | 27 man/scale_crameri_bamO.Rd | 26 man/scale_crameri_bamako.Rd | 40 - man/scale_crameri_batlow.Rd | 40 - man/scale_crameri_batlowK.Rd | 40 - man/scale_crameri_batlowW.Rd | 40 - man/scale_crameri_berlin.Rd | 27 man/scale_crameri_bilbao.Rd | 40 - man/scale_crameri_broc.Rd | 27 man/scale_crameri_brocO.Rd | 26 man/scale_crameri_buda.Rd | 40 - man/scale_crameri_bukavu.Rd | 36 - man/scale_crameri_cork.Rd | 27 man/scale_crameri_corkO.Rd | 26 man/scale_crameri_davos.Rd | 40 - man/scale_crameri_devon.Rd | 40 - man/scale_crameri_fes.Rd | 36 - man/scale_crameri_glasgow.Rd |only man/scale_crameri_grayC.Rd | 40 - man/scale_crameri_hawaii.Rd | 40 - man/scale_crameri_imola.Rd | 40 - man/scale_crameri_lajolla.Rd | 40 - man/scale_crameri_lapaz.Rd | 40 - man/scale_crameri_lipari.Rd |only man/scale_crameri_lisbon.Rd | 27 man/scale_crameri_managua.Rd |only man/scale_crameri_navia.Rd |only man/scale_crameri_naviaW.Rd |only man/scale_crameri_nuuk.Rd | 40 - man/scale_crameri_oleron.Rd | 36 - man/scale_crameri_oslo.Rd | 40 - man/scale_crameri_roma.Rd | 27 man/scale_crameri_romaO.Rd | 26 man/scale_crameri_tofino.Rd | 27 man/scale_crameri_tokyo.Rd | 40 - man/scale_crameri_turku.Rd | 40 - man/scale_crameri_vanimo.Rd | 27 man/scale_crameri_vik.Rd | 27 man/scale_crameri_vikO.Rd | 26 man/scale_land.Rd | 2 man/scale_stratigraphy.Rd | 2 man/scale_tol_BuRd.Rd | 3 man/scale_tol_PRGn.Rd | 3 man/scale_tol_YlOrBr.Rd | 6 man/scale_tol_bright.Rd | 2 man/scale_tol_dark.Rd | 2 man/scale_tol_discreterainbow.Rd | 2 man/scale_tol_highcontrast.Rd | 2 man/scale_tol_incandescent.Rd | 6 man/scale_tol_iridescent.Rd | 6 man/scale_tol_light.Rd | 2 man/scale_tol_mediumcontrast.Rd | 2 man/scale_tol_muted.Rd | 2 man/scale_tol_nightfall.Rd | 3 man/scale_tol_pale.Rd | 2 man/scale_tol_smoothrainbow.Rd | 6 man/scale_tol_sunset.Rd | 3 man/scale_tol_vibrant.Rd | 2 man/science.Rd | 4 man/tol.Rd | 2 po/R-fr.po | 33 - po/R-khroma.pot | 31 tests/tinytest.R | 6 vignettes/bibliography.bib | 12 vignettes/crameri.Rmd | 180 +++-- vignettes/khroma.Rmd |only vignettes/tol.Rmd | 9 116 files changed, 2583 insertions(+), 1616 deletions(-)
Title: Access to the 'DraCor' API
Description: Provide an interface for 'Drama Corpora Project' ('DraCor') API: <https://dracor.org/documentation/api>.
Author: Ivan Pozdniakov [aut, cre]
Maintainer: Ivan Pozdniakov <bucherr@yandex.ru>
Diff between rdracor versions 1.0.5 dated 2025-08-27 and 1.0.6 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 ++++++- R/net.R | 6 +++--- R/text.R | 2 +- build/partial.rdb |binary 6 files changed, 19 insertions(+), 14 deletions(-)
Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph]
Maintainer: Francois Keck <francois.keck@gmail.com>
Diff between bioseq versions 0.1.4 dated 2022-09-06 and 0.1.5 dated 2025-09-29
DESCRIPTION | 11 MD5 | 22 - NEWS.md | 4 R/seq_misc_operations.R | 5 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 - inst/doc/intro-bioseq.R | 8 inst/doc/intro-bioseq.html | 505 +++++++++++++++++++--------------- inst/doc/ref_database.R | 18 - inst/doc/ref_database.html | 668 +++++++++++++++++++++++++-------------------- 12 files changed, 719 insertions(+), 548 deletions(-)
Title: Manage Collections of Datasets and Objects
Description: Create, store, read and manage structured collections of
datasets and other objects using a 'workspace', then bundle it into a
compressed archive. Using open and interoperable formats makes it
possible to exchange bundled data from 'R' to other languages such as
'Python' or 'Julia'. Multiple formats are supported 'Parquet',
'JSON', 'yaml', spatial data and raster data are supported.
Author: Eli Daniels [aut, cre],
David Gohel [aut],
ArData [cph, fnd]
Maintainer: Eli Daniels <eli.daniels@ardata.fr>
Diff between workspace versions 0.1.5 dated 2025-09-11 and 0.1.6 dated 2025-09-29
DESCRIPTION | 9 ++-- MD5 | 11 ++--- NEWS.md | 56 +++++++++++++++++--------- R/readers.R | 11 ++++- R/store.R | 8 +++ man/workspace.Rd | 1 tests/testthat/test-roundtrip-comprehensive.R |only 7 files changed, 67 insertions(+), 29 deletions(-)
Title: Regularized Spatial Maximum Covariance Analysis
Description: Provide regularized maximum covariance analysis incorporating smoothness,
sparseness and orthogonality of couple patterns by using the alternating direction method
of multipliers algorithm. The method can be applied to either regularly or irregularly
spaced data, including 1D, 2D, and 3D (Wang and Huang, 2018 <doi:10.1002/env.2481>).
Author: Wen-Ting Wang [aut, cre] ,
Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatMCA versions 1.0.4 dated 2023-11-21 and 1.0.7 dated 2025-09-29
DESCRIPTION | 24 ++-- MD5 | 32 +++--- NAMESPACE | 23 ++-- NEWS.md | 18 +++ R/SpatMCA-package.R |only R/SpatMCA.R | 185 +++++++++++++++++++------------------- R/helper.R | 33 +++--- R/zzz.R | 7 + man/SpatMCA-package.Rd | 35 ++++--- man/spatmca.Rd | 182 +++++++++++++++++++------------------ src/Makevars | 8 + src/Makevars.win | 6 - src/RcppSpatMCA.cpp | 21 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-RcppExports.R | 5 - tests/testthat/test-SpatMCA.R | 2 tests/testthat/test-helper.R | 13 ++ tools |only 18 files changed, 328 insertions(+), 266 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs, sample sizes in two-phase designs, and a stopping rule for ending data collection. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.6.1 dated 2025-05-11 and 1.7 dated 2025-09-29
DESCRIPTION | 13 ++-- MD5 | 50 +++++++++------- NEWS.md | 4 + R/SampStop.R | 107 ++++++++++++++++-------------------- build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.popA.RData |binary data/TPV.RData |binary data/Test_Data_US.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Design-effects.html | 9 +-- inst/doc/Distance-and-MOS-PSUs.html | 9 +-- inst/doc/SampStop.R |only inst/doc/SampStop.Rmd |only inst/doc/SampStop.html |only inst/doc/Singlestage-samsize.html | 9 +-- inst/doc/Varcomps-multistage.html | 9 +-- man/SampStop.Rd | 71 ++++++++++++++--------- vignettes/SampStop.Rmd |only vignettes/practools.bib | 10 +++ 28 files changed, 159 insertions(+), 132 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.0.2 dated 2025-07-22 and 1.1.0 dated 2025-09-29
DESCRIPTION | 8 MD5 | 55 NAMESPACE | 1 R/R6Model.R | 270 ++- R/RcppExports.R | 4 R/extrafunctions.R | 29 build/partial.rdb |binary inst/include/glmmr/calculator.hpp | 2187 ++++++++++++++++--------------- inst/include/glmmr/covariance.hpp | 233 ++- inst/include/glmmr/formula.hpp | 3 inst/include/glmmr/formulaparse.h | 59 inst/include/glmmr/general.h | 1 inst/include/glmmr/hsgpcovariance.hpp | 7 inst/include/glmmr/interpreter.h | 408 +++-- inst/include/glmmr/maths.h | 109 - inst/include/glmmr/model.hpp | 4 inst/include/glmmr/modeloptim.hpp | 519 ++++--- inst/include/glmmr/optim/lbfgs.h | 15 inst/include/glmmr/optim/lbfgs/BFGSMat.h | 137 + inst/include/glmmr/optim/lbfgs/Param.h | 12 inst/include/glmmr/optim/lbfgsb.h | 2 inst/include/glmmr/optim/optim.h | 15 inst/stan/mcml.stan | 69 man/Model.Rd | 40 man/hsgp_rescale.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 13 src/model_module.cpp | 14 src/stanExports_mcml.h | 588 ++++---- 29 files changed, 2781 insertions(+), 2023 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 2.0.86 dated 2025-08-31 and 2.0.87 dated 2025-09-29
DESCRIPTION | 8 MD5 | 49 ++--- NAMESPACE | 2 NEWS | 10 + R/epi.nomogram.R | 278 +++++++++++++++++++++++++---- R/epi.ssequb.R | 18 - R/epi.ssequc.R | 14 - R/epi.ssninfb.R | 11 - R/epi.ssninfc.R | 10 - R/epi.sssupb.R | 20 +- R/epi.sssupc.R | 22 +- R/zagrestin.R |only R/zclopperpearsonn.R |only R/zexactn.r |only R/zjeffreysn.R |only R/zwilsonn.R |only inst/doc/epiR_descriptive.html | 28 +- inst/doc/epiR_measures_of_association.html | 29 ++- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 14 - man/epi.nomogram.Rd | 92 ++++++--- man/epi.prcc.Rd | 2 man/epi.ssequb.Rd | 62 +++--- man/epi.ssequc.Rd | 37 ++- man/epi.ssninfb.Rd | 25 +- man/epi.ssninfc.Rd | 21 +- man/epi.sssupb.Rd | 25 +- man/epi.sssupc.Rd | 25 +- 28 files changed, 562 insertions(+), 244 deletions(-)
Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps,
in which each region is represented by a single tile of the same shape and
size. The algorithm was first proposed in "Generating Tile Maps" by Graham
McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow
users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>
Diff between tilemaps versions 0.2.0 dated 2020-07-10 and 0.2.1 dated 2025-09-29
DESCRIPTION | 15 - MD5 | 16 - NEWS.md | 4 R/create_island.R | 4 R/generate_map.R | 2 R/many_maps.R | 2 build/vignette.rds |binary inst/doc/tilemaps.R | 6 inst/doc/tilemaps.html | 466 ++++++++++++++++++++++++++++++++++++------------- 9 files changed, 370 insertions(+), 145 deletions(-)
Title: Algorithm Portfolio Selection with Machine Learning
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
Author: Brais Gonzalez-Rodriguez [aut, cre] ,
Ignacio Gomez-Casares [aut] ,
Beatriz Pateiro-Lopez [aut] ,
Julio Gonzalez-Diaz [aut] ,
Maria Caseiro-Arias [ctb],
Antonio Farina-Elorza [ctb],
Manuel Timiraos-Lopez [ctb]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>
Diff between ASML versions 1.0.0 dated 2025-02-19 and 1.1.0 dated 2025-09-29
ASML-1.0.0/ASML/man/figure_comparison.as_data.Rd |only ASML-1.1.0/ASML/DESCRIPTION | 23 ASML-1.1.0/ASML/MD5 | 49 - ASML-1.1.0/ASML/NAMESPACE | 1 ASML-1.1.0/ASML/R/data.R | 39 - ASML-1.1.0/ASML/R/graphics.R | 259 +++++--- ASML-1.1.0/ASML/R/machine_learning.R | 677 ++++++++++++++--------- ASML-1.1.0/ASML/R/partition_and_normalize.R | 361 ++++++------ ASML-1.1.0/ASML/R/tables.R | 417 ++++++++------ ASML-1.1.0/ASML/data/SpMVformat.rda |only ASML-1.1.0/ASML/data/branching.rda |binary ASML-1.1.0/ASML/data/branchingsmall.rda |binary ASML-1.1.0/ASML/man/ASexplainer.Rd |only ASML-1.1.0/ASML/man/ASpredict.Rd | 18 ASML-1.1.0/ASML/man/ASpredict.as_train.Rd | 2 ASML-1.1.0/ASML/man/AStrain.Rd | 18 ASML-1.1.0/ASML/man/AStrain.as_data.Rd | 15 ASML-1.1.0/ASML/man/KPI_summary_table.Rd | 43 - ASML-1.1.0/ASML/man/KPI_summary_table.as_data.Rd |only ASML-1.1.0/ASML/man/KPI_table.Rd | 35 - ASML-1.1.0/ASML/man/KPI_table.as_data.Rd |only ASML-1.1.0/ASML/man/SpMVformat.Rd |only ASML-1.1.0/ASML/man/boxplots.Rd | 18 ASML-1.1.0/ASML/man/figure_comparison.Rd | 20 ASML-1.1.0/ASML/man/ml.Rd | 6 ASML-1.1.0/ASML/man/partition_and_normalize.Rd | 4 ASML-1.1.0/ASML/man/plot.as_data.Rd | 2 ASML-1.1.0/ASML/man/ranking.Rd | 20 ASML-1.1.0/ASML/man/topic-name.Rd |only 29 files changed, 1196 insertions(+), 831 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.13.0 dated 2025-08-19 and 0.14.0 dated 2025-09-29
tinytable-0.13.0/tinytable/R/bootstrap_build.R |only tinytable-0.13.0/tinytable/R/bootstrap_finalize.R |only tinytable-0.13.0/tinytable/R/bootstrap_group.R |only tinytable-0.13.0/tinytable/R/bootstrap_style.R |only tinytable-0.13.0/tinytable/R/strip_tt.R |only tinytable-0.13.0/tinytable/R/theme_html_bootstrap.R |only tinytable-0.13.0/tinytable/R/theme_html_raw.R |only tinytable-0.13.0/tinytable/R/theme_utils.R |only tinytable-0.13.0/tinytable/R/theme_void.R |only tinytable-0.13.0/tinytable/inst/templates/bootstrap.html |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-basic.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-complex.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-empty.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/latex-theme_void.tex |only tinytable-0.13.0/tinytable/man/figures/gallery |only 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Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.19 dated 2025-08-25 and 1.20 dated 2025-09-29
DESCRIPTION | 8 - MD5 | 32 +++---- NAMESPACE | 1 NEWS.md | 15 +++ R/class-workbook-wrappers.R | 117 ++++++++++++++++++++++++-- R/class-workbook.R | 40 ++++++++ R/dates.R | 8 - R/read.R | 4 R/utils.R | 4 inst/WORDLIST | 1 man/convert_date.Rd | 21 +--- man/wbWorkbook.Rd | 9 ++ man/wb_page_setup.Rd | 80 ++++++++++++++++- tests/testthat/test-class-workbook-wrappers.R | 7 + tests/testthat/test-class-worksheet.R | 2 tests/testthat/test-read_from_created_wb.R | 22 ++++ tests/testthat/test-wb_styles.R | 43 +++++++++ 17 files changed, 358 insertions(+), 56 deletions(-)
Title: Conditional Mutual Information Estimation for Multi-Omics Data
Description: The biases introduced in association measures, particularly mutual information,
are influenced by factors such as tumor purity, mutation burden, and hypermethylation.
This package provides the estimation of conditional mutual information (CMI) and its
statistical significance with a focus on its application to multi-omics data. Utilizing
B-spline functions (inspired by Daub et al. (2004) <doi:10.1186/1471-2105-5-118>), the package offers tools to estimate the association between heterogeneous multi-
omics data, while removing the effects of confounding factors. This helps to unravel complex
biological interactions. In addition, it includes methods to evaluate the statistical significance
of these associations, providing a robust framework for multi-omics data integration and
analysis. This package is ideal for researchers in computational biology, bioinformatics,
and systems biology seeking a comprehensive tool for understanding interdependencies in
omics data.
Author: Gaojianyong Wang [aut, cre]
Maintainer: Gaojianyong Wang <gjywang@gmail.com>
Diff between conMItion versions 0.2.0 dated 2025-07-14 and 0.2.1 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ComputePermutation.R | 20 ++++++++++---------- 3 files changed, 15 insertions(+), 15 deletions(-)
Title: Time-Ordered and Time-Aggregated Network Analyses
Description: Approaches for incorporating time into network analysis. Methods include: construction of time-ordered networks (temporal graphs); shortest-time and shortest-path-length analyses; resource spread calculations; data resampling and rarefaction for null model construction; reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks; vector clock latencies; and plotting functionalities. The package supports <doi:10.1371/journal.pone.0020298>.
Author: Benjamin Wong Blonder [aut, cre]
Maintainer: Benjamin Wong Blonder <benjamin.blonder@berkeley.edu>
Diff between timeordered versions 1.0.1 dated 2024-09-15 and 1.0.2 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/transformspreadbyindividual.Rd | 4 +--- 3 files changed, 7 insertions(+), 9 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for audio manipulation and acoustic analysis, including pitch tracking,
spectral analysis, audio segmentation, pitch and formant shifting, etc.
Includes four interactive web apps for synthesizing and annotating audio,
manually correcting pitch contours, and measuring formant frequencies.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>
Diff between soundgen versions 2.7.3 dated 2025-07-17 and 2.7.4 dated 2025-09-29
soundgen-2.7.3/soundgen/man/ERBToHz.Rd |only soundgen-2.7.3/soundgen/man/listDepth.Rd |only soundgen-2.7.3/soundgen/man/notesToHz.Rd |only soundgen-2.7.3/soundgen/man/semitonesToHz.Rd |only soundgen-2.7.4/soundgen/DESCRIPTION | 10 soundgen-2.7.4/soundgen/MD5 | 88 - soundgen-2.7.4/soundgen/NAMESPACE | 2 soundgen-2.7.4/soundgen/NEWS | 17 soundgen-2.7.4/soundgen/R/analyze.R | 35 soundgen-2.7.4/soundgen/R/audSpec.R | 42 soundgen-2.7.4/soundgen/R/formants.R | 2 soundgen-2.7.4/soundgen/R/frequency_scales.R |only soundgen-2.7.4/soundgen/R/math.R | 210 --- soundgen-2.7.4/soundgen/R/modulationSpectrum.R | 2 soundgen-2.7.4/soundgen/R/pitch_postprocessing.R | 25 soundgen-2.7.4/soundgen/R/postprocessing.R | 23 soundgen-2.7.4/soundgen/R/soundgen.R | 18 soundgen-2.7.4/soundgen/R/spectrogram.R | 174 ++- soundgen-2.7.4/soundgen/R/surprisal.R | 533 +++++++--- soundgen-2.7.4/soundgen/R/vtl.R | 30 soundgen-2.7.4/soundgen/README.md | 84 - soundgen-2.7.4/soundgen/inst/shiny/annotation_app/server.R | 12 soundgen-2.7.4/soundgen/inst/shiny/annotation_app/www/nrm66nuk.wav |only soundgen-2.7.4/soundgen/inst/shiny/pitch_app/server.R | 13 soundgen-2.7.4/soundgen/inst/shiny/pitch_app/www/temp.wav |only soundgen-2.7.4/soundgen/man/HzToERB.Rd | 38 soundgen-2.7.4/soundgen/man/HzToNotes.Rd | 20 soundgen-2.7.4/soundgen/man/HzToOther.Rd |only soundgen-2.7.4/soundgen/man/HzToSemitones.Rd | 22 soundgen-2.7.4/soundgen/man/addPitchCands.Rd | 3 soundgen-2.7.4/soundgen/man/analyze.Rd | 13 soundgen-2.7.4/soundgen/man/audSpectrogram.Rd | 25 soundgen-2.7.4/soundgen/man/dot-audSpectrogram.Rd | 23 soundgen-2.7.4/soundgen/man/dot-getSurprisal.Rd | 60 - soundgen-2.7.4/soundgen/man/dot-spectrogram.Rd | 21 soundgen-2.7.4/soundgen/man/estimateVTL.Rd | 24 soundgen-2.7.4/soundgen/man/figures/README-analysis-1.png |binary soundgen-2.7.4/soundgen/man/figures/README-synthsesis-1.png |binary soundgen-2.7.4/soundgen/man/figures/s.mp3 |binary soundgen-2.7.4/soundgen/man/getSurprisal.Rd | 203 ++- soundgen-2.7.4/soundgen/man/getSurprisal_matrix.Rd | 24 soundgen-2.7.4/soundgen/man/getSurprisal_vector.Rd | 14 soundgen-2.7.4/soundgen/man/hz2mel.Rd | 8 soundgen-2.7.4/soundgen/man/modulationSpectrum.Rd | 2 soundgen-2.7.4/soundgen/man/plotSpec.Rd | 14 soundgen-2.7.4/soundgen/man/reverb.Rd | 16 soundgen-2.7.4/soundgen/man/schwa.Rd | 8 soundgen-2.7.4/soundgen/man/soundgen.Rd | 14 soundgen-2.7.4/soundgen/man/spectrogram.Rd | 79 + 49 files changed, 1177 insertions(+), 774 deletions(-)
Title: Read Paradox Database Files into R
Description: Provides a simple and efficient way to read data from Paradox
database files (.db) directly into R as modern 'tibble' data frames.
It uses the underlying 'pxlib' C library, to handle the low-level file format
details and provides a clean, user-friendly R interface.
Author: Daniil Popov [aut, cre]
Maintainer: Daniil Popov <popov.daniil@gmail.com>
Diff between Rparadox versions 0.1.2 dated 2025-09-22 and 0.1.5 dated 2025-09-29
DESCRIPTION | 13 +- MD5 | 38 +++--- NAMESPACE | 3 NEWS.md | 31 ++++ R/pxlib_get_data.R | 29 +++- R/pxlib_metadata.R |only R/pxlib_open_file.R | 41 ++++-- R/read_paradox.R |only R/utils.R | 72 +++++++++-- README.md | 75 +++++++---- inst/doc/Rparadox.R | 33 +++-- inst/doc/Rparadox.Rmd | 54 ++++++-- inst/doc/Rparadox.html | 95 +++++++++------ man/Rparadox-package.Rd | 3 man/pxlib_metadata.Rd |only man/read_paradox.Rd |only src/init.c | 8 - src/interface.c | 232 ++++++++++++++++--------------------- src/paradox.c | 54 +------- tests/testthat/test-get-data.R | 48 +++---- tests/testthat/test-metadata.R |only tests/testthat/test-read_paradox.R |only vignettes/Rparadox.Rmd | 54 ++++++-- 23 files changed, 528 insertions(+), 355 deletions(-)
Title: Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson [...truncated...]
Author: Jeffrey Doser [aut, cre],
Hunter Stanke [aut],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between rFIA versions 1.1.1 dated 2025-03-10 and 1.1.2 dated 2025-09-29
DESCRIPTION | 6 MD5 | 75 +++++------ NEWS.md | 6 R/areaChangeStarter.R | 14 +- R/areaStarter.R | 11 + R/biomass.R | 2 R/biomassStarter.R | 11 + R/carbonStarter.R | 13 + R/diversityStarter.R | 11 + R/dwmStarter.R | 11 + R/fsi.R | 332 +++---------------------------------------------- R/fsiStarter.R |only R/growMortStarter.R | 23 +++ R/invasiveStarter.R | 11 + R/readFIA.R | 2 R/seedlingStarter.R | 11 + R/standStructStarter.R | 10 + R/tpaStarter.R | 10 + R/util.R | 2 R/vegStructStarter.R | 11 + R/vitalRatesStarter.R | 11 + R/volumeStarter.R | 11 + data/fiaRI.rda |binary man/area.Rd | 2 man/areaChange.Rd | 2 man/biomass.Rd | 2 man/carbon.Rd | 2 man/diversity.Rd | 2 man/dwm.Rd | 2 man/fiaRI.Rd | 2 man/fsi.Rd | 2 man/growMort.Rd | 2 man/invasive.Rd | 2 man/seedling.Rd | 2 man/standStruct.Rd | 2 man/tpa.Rd | 2 man/vegStruct.Rd | 2 man/vitalRates.Rd | 2 man/volume.Rd | 2 39 files changed, 239 insertions(+), 387 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
This is a re-admission after prior archival of version 0.6.0 dated 2025-06-16
Diff between occCite versions 0.6.0 dated 2025-06-16 and 0.6.1 dated 2025-09-29
DESCRIPTION | 19 +++++++-------- MD5 | 14 +++++------ NEWS.md | 3 ++ R/occCite_plotting.R | 7 +++++ R/studyTaxonList.R | 2 - inst/doc/a_Simple.html | 14 +++++------ inst/doc/b_Advanced.html | 54 +++++++++++++++++++++---------------------- tests/testthat/test-sumFig.R | 24 +++++++++++-------- 8 files changed, 77 insertions(+), 60 deletions(-)
Title: Draw XmR Charts for NHS 'Making Data Count' Programme
Description: Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHS 'Making Data Count' programme, and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.
Author: Tom Smith [cre, aut],
Christopher Reading [aut],
Simon Wellesley-Miller [aut],
Zoe Turner [aut] ,
Tom Jemmett [aut] ,
Chris Mainey [aut] ,
John MacKintosh [aut],
Marcos Fabietti [aut],
Fran Barton [aut] ,
NHS-R community [cph]
Maintainer: Tom Smith <thomas.smith103@nhs.net>
Diff between NHSRplotthedots versions 0.1.0 dated 2021-11-03 and 0.2.2 dated 2025-09-29
NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.R |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.Rmd |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.html |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/logo.png |only NHSRplotthedots-0.1.0/NHSRplotthedots/man/figures/logo.png |only NHSRplotthedots-0.1.0/NHSRplotthedots/vignettes/intro.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/DESCRIPTION | 64 - NHSRplotthedots-0.2.2/NHSRplotthedots/MD5 | 148 +- NHSRplotthedots-0.2.2/NHSRplotthedots/NAMESPACE | 23 NHSRplotthedots-0.2.2/NHSRplotthedots/NEWS.md | 15 NHSRplotthedots-0.2.2/NHSRplotthedots/R/NHSRplotthedots-package.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/R/ZZZ.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/R/geom_ptd_icon.R | 267 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_rebase_column.R | 20 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_short_group_warnings.R | 27 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_target_column.R | 2 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_calculate_assurance_type.R | 19 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_calculate_point_type.R | 97 + NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_create_ggplot.R | 299 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_create_plotly.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_rebase.R | 43 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc.R | 176 ++- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_colours.R | 23 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_options.R | 36 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_standard.R | 60 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_target.R | 61 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_validate_plot_options.R | 52 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_validate_spc_options.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/R/to_datetime.R | 4 NHSRplotthedots-0.2.2/NHSRplotthedots/README.md | 251 +++- NHSRplotthedots-0.2.2/NHSRplotthedots/build/vignette.rds |binary NHSRplotthedots-0.2.2/NHSRplotthedots/inst/WORDLIST | 56 - NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.html |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.R | 41 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.Rmd | 126 +- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.html | 514 +++++++--- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.R | 2 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.Rmd | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.html | 270 ++++- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/other-spc-tools.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/other-spc-tools.html |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/hex-logo.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/icons |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/images |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/test-hex-logo.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/GeomPTDIcon.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/NHSRplotthedots-package.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-1.png |binary NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-ptd-create-ggplot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-ptd_create_ggplot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-with-plot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example1-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example2-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-limits-example-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-2-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-3-1.png |binary NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-5-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/geom_ptd_icon.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_create_ggplot.Rd | 65 - NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_create_plotly.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_rebase.Rd | 37 NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_spc.Rd | 74 - NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_spc_colours.Rd | 18 NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_target.Rd | 54 - NHSRplotthedots-0.2.2/NHSRplotthedots/tests/spelling.R | 9 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/geom_ptd_icon.md | 20 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/ptd_spc.md | 225 ++-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/ptd_spc_standard.md | 120 +- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-geom_ptd_icon.R | 174 ++- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_add_rebase_column.R | 25 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_add_short_group_warnings.R | 22 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_calculate_assurance_type.R | 56 - NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_calculate_point_type.R | 147 +- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_create_ggplot.R | 158 +-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_create_plotly.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc.R | 282 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc_options.R | 32 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc_standard.R | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_validate_plot_options.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_validate_spc_options.R | 25 NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/NHSRplotthedots.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/deviations.Rmd | 126 +- NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/number-of-points-required.Rmd | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/other-spc-tools.Rmd |only 86 files changed, 2958 insertions(+), 1536 deletions(-)
More information about NHSRplotthedots at CRAN
Permanent link
Title: Causal Inference in Spatiotemporal Event Data
Description: Implementation of Matched Wake Analysis (mwa) for studying causal relationships in spatiotemporal event data, introduced by Schutte and Donnay (2014) <doi:10.1016/j.polgeo.2014.03.001>.
Author: Sebastian Schutte [aut],
Karsten Donnay [aut, cre]
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between mwa versions 0.4.4 dated 2022-04-26 and 0.5.0 dated 2025-09-29
DESCRIPTION | 19 ++++++++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- NEWS | 5 +++++ R/mwa.R | 35 ++++++++++++++++++++++++++++------- README.md | 4 ++-- man/matchedwake.Rd | 15 ++++++++++++--- man/plot.matchedwake.Rd | 8 +++++++- man/slideWakeMatch.Rd | 19 ++++++++++++++----- 9 files changed, 87 insertions(+), 36 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-85 dated 2020-01-08 and 0.9-0 dated 2025-09-29
DESCRIPTION | 14 ++++++---- MD5 | 58 +++++++++++++++++++++--------------------- NAMESPACE | 2 + R/JMbayes_plot_survfitJM2.R |only R/MCMCfit.R | 2 - R/chol.transf.R | 2 - R/confint.JMbayes.R | 2 - R/dynInfo.R | 16 +++++------ R/dynPred_lme.R | 2 - R/format.perc.R | 2 - R/format.pval2.R | 2 - R/initSurvival.R | 2 - R/log.posterior.b.R | 2 - R/marglogLik.R | 6 ++-- R/methods_mvJointModelBayes.R | 5 ++- R/mvJointModelBayes.R | 25 +++++++++++++----- R/plot_survfit_mvJMbayes_hp.R |only R/predict.JMbayes.R | 8 ++--- R/predict_eventTime.R | 2 - R/print.summary.JMbayes.R | 4 +- R/survfitJM.JMbayes.R | 8 ++--- R/survfitJM.mvJMbayes.R | 11 +++++-- R/td_effect.R | 2 - R/xtable.JMbayes.R | 4 +- README.md | 8 ++--- man/JMbayes.Rd | 4 +- man/plot-survfitJM.Rd | 20 +++++++------- man/xtable.Rd | 6 ++-- src/Makevars | 5 +-- src/Makevars.win | 5 +-- src/RcppExports.cpp | 5 +++ 31 files changed, 132 insertions(+), 102 deletions(-)
Title: Intervention in Prediction Measure for Random Forests
Description: Computes intervention in prediction measure for assessing variable importance for random forests. See details at I. Epifanio (2017) <DOI:10.1186/s12859-017-1650-8>.
Author: Irene Epifanio [aut, cre],
Stefano Nembrini [aut],
Aleix Alcacer [aut],
Vicente Bolos [aut]
Maintainer: Irene Epifanio <epifanio@uji.es>
This is a re-admission after prior archival of version 1.2 dated 2017-08-09
Diff between IPMRF versions 1.2 dated 2017-08-09 and 1.3 dated 2025-09-29
IPMRF-1.2/IPMRF/R/getTreeranger.R |only IPMRF-1.2/IPMRF/R/ipmranger.R |only IPMRF-1.2/IPMRF/R/ipmrangernew.R |only IPMRF-1.2/IPMRF/man/IPMRF-internal-ranger.Rd |only IPMRF-1.2/IPMRF/man/ipmranger.Rd |only IPMRF-1.2/IPMRF/man/ipmrangernew.Rd |only IPMRF-1.3/IPMRF/DESCRIPTION | 34 ++++++++++---- IPMRF-1.3/IPMRF/MD5 | 32 +++++-------- IPMRF-1.3/IPMRF/NAMESPACE | 2 IPMRF-1.3/IPMRF/NEWS | 3 + IPMRF-1.3/IPMRF/R/prevtree.R | 2 IPMRF-1.3/IPMRF/inst/CITATION | 19 ++++--- IPMRF-1.3/IPMRF/man/IPMRF-internal-gbm.Rd | 1 IPMRF-1.3/IPMRF/man/IPMRF-internal.Rd | 1 IPMRF-1.3/IPMRF/man/IPMRF-package.Rd | 14 ++--- IPMRF-1.3/IPMRF/man/ipmgbmnew.Rd | 14 ++--- IPMRF-1.3/IPMRF/man/ipmparty.Rd | 65 +++++---------------------- IPMRF-1.3/IPMRF/man/ipmpartynew.Rd | 30 +++++------- IPMRF-1.3/IPMRF/man/ipmrf.Rd | 56 +++++++++++------------ IPMRF-1.3/IPMRF/man/ipmrfnew.Rd | 24 ++++----- 20 files changed, 139 insertions(+), 158 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.1 dated 2025-08-25 and 0.2.2 dated 2025-09-29
DESCRIPTION | 6 +-- MD5 | 33 +++++++++-------- NEWS.md | 8 ++++ R/get_pvol.R | 1 R/get_pvol_dk.R | 6 +-- R/get_pvol_sk.R |only R/get_pvol_us.R | 4 +- R/get_weather_radars.R | 1 R/zzz.R | 2 - inst/doc/supported_sources.R | 5 +- inst/doc/supported_sources.Rmd | 5 +- inst/doc/supported_sources.html | 59 +++++++++++++++---------------- tests/testthat/teardown_remove_cache.R |only tests/testthat/test-get_pvol_dk.R | 6 ++- tests/testthat/test-get_pvol_nl.R | 34 +++++++++-------- tests/testthat/test-get_pvol_sk.R |only tests/testthat/test-get_pvol_us.R | 8 ++-- tests/testthat/test-get_weather_radars.R | 8 ---- vignettes/supported_sources.Rmd | 5 +- 19 files changed, 104 insertions(+), 87 deletions(-)
Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.5.1 dated 2022-08-15 and 0.6.0 dated 2025-09-29
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- build/partial.rdb |binary man/find_critical_pos.Rd | 2 +- src/Makevars | 13 +------------ src/Makevars.win | 15 ++------------- src/RcppExports.cpp | 4 ++-- src/rcpparma.cpp | 15 +++++++++------ 9 files changed, 35 insertions(+), 49 deletions(-)
Title: Modular Differential Evolution for Experimenting with Operators
Description: Modular implementation of the Differential Evolution algorithm for
experimenting with different types of operators.
Author: Felipe Campelo [aut, cre],
Moises Botelho [aut]
Maintainer: Felipe Campelo <f.campelo@bristol.ac.uk>
Diff between ExpDE versions 0.1.4 dated 2018-01-10 and 0.2.0 dated 2025-09-29
ExpDE-0.1.4/ExpDE/R/rastrigin.R |only ExpDE-0.1.4/ExpDE/R/sphere.R |only ExpDE-0.1.4/ExpDE/man/mutation_current_to_pbest.Rd |only ExpDE-0.2.0/ExpDE/DESCRIPTION | 21 ExpDE-0.2.0/ExpDE/MD5 | 139 +- ExpDE-0.2.0/ExpDE/NAMESPACE | 65 - ExpDE-0.2.0/ExpDE/R/ExpDE.R | 582 +++++----- ExpDE-0.2.0/ExpDE/R/ExpDE2.R |only ExpDE-0.2.0/ExpDE/R/check_stop_criteria.R | 90 - ExpDE-0.2.0/ExpDE/R/create_population.R | 56 ExpDE-0.2.0/ExpDE/R/evaluate_population.R | 126 +- ExpDE-0.2.0/ExpDE/R/function_rastrigin.R |only ExpDE-0.2.0/ExpDE/R/function_rosenbrock.R |only ExpDE-0.2.0/ExpDE/R/function_sphere.R |only ExpDE-0.2.0/ExpDE/R/gen_methods.R |only ExpDE-0.2.0/ExpDE/R/gen_problems.R |only ExpDE-0.2.0/ExpDE/R/get_exp_params_1.R |only ExpDE-0.2.0/ExpDE/R/mutation_best.R | 182 +-- ExpDE-0.2.0/ExpDE/R/mutation_current_to_pbest.R | 193 +-- ExpDE-0.2.0/ExpDE/R/mutation_mean.R | 162 +- ExpDE-0.2.0/ExpDE/R/mutation_none.R | 36 ExpDE-0.2.0/ExpDE/R/mutation_operators.R | 30 ExpDE-0.2.0/ExpDE/R/mutation_rand.R | 148 +- ExpDE-0.2.0/ExpDE/R/mutation_wgi.R | 196 +-- ExpDE-0.2.0/ExpDE/R/print_progress.R | 106 - ExpDE-0.2.0/ExpDE/R/recombination_arith.R | 68 - ExpDE-0.2.0/ExpDE/R/recombination_bin.R | 120 +- ExpDE-0.2.0/ExpDE/R/recombination_blxAlphaBeta.R | 184 +-- ExpDE-0.2.0/ExpDE/R/recombination_eigen.R | 128 +- ExpDE-0.2.0/ExpDE/R/recombination_exp.R | 142 +- ExpDE-0.2.0/ExpDE/R/recombination_geo.R | 130 +- ExpDE-0.2.0/ExpDE/R/recombination_lbga.R | 164 +- ExpDE-0.2.0/ExpDE/R/recombination_linear.R | 142 +- ExpDE-0.2.0/ExpDE/R/recombination_mmax.R | 208 +-- ExpDE-0.2.0/ExpDE/R/recombination_none.R | 48 ExpDE-0.2.0/ExpDE/R/recombination_npoint.R | 176 +-- ExpDE-0.2.0/ExpDE/R/recombination_onepoint.R | 154 +- ExpDE-0.2.0/ExpDE/R/recombination_operators.R | 50 ExpDE-0.2.0/ExpDE/R/recombination_pbest.R | 146 +- ExpDE-0.2.0/ExpDE/R/recombination_sbx.R | 112 - ExpDE-0.2.0/ExpDE/R/recombination_wright.R | 120 +- ExpDE-0.2.0/ExpDE/R/selection_standard.R | 64 - ExpDE-0.2.0/ExpDE/R/utils.R | 58 ExpDE-0.2.0/ExpDE/R/zz_get_experimental_parameters_2.R |only ExpDE-0.2.0/ExpDE/R/zz_get_experimental_parameters_vB.R |only ExpDE-0.2.0/ExpDE/R/zz_get_random_recmutpars.R |only ExpDE-0.2.0/ExpDE/man/ExpDE.Rd | 470 ++++---- ExpDE-0.2.0/ExpDE/man/ExpDE2.Rd |only ExpDE-0.2.0/ExpDE/man/check_stop_criteria.Rd | 44 ExpDE-0.2.0/ExpDE/man/create_population.Rd | 38 ExpDE-0.2.0/ExpDE/man/evaluate_population.Rd | 42 ExpDE-0.2.0/ExpDE/man/gen_methods.Rd |only ExpDE-0.2.0/ExpDE/man/gen_problems.Rd |only ExpDE-0.2.0/ExpDE/man/get_exp_params_1.Rd |only ExpDE-0.2.0/ExpDE/man/get_experimental_parameters_activity2.Rd |only ExpDE-0.2.0/ExpDE/man/get_experimental_parameters_activity_versionB.Rd |only ExpDE-0.2.0/ExpDE/man/mutation_best.Rd | 100 - ExpDE-0.2.0/ExpDE/man/mutation_mean.Rd | 84 - ExpDE-0.2.0/ExpDE/man/mutation_none.Rd | 52 ExpDE-0.2.0/ExpDE/man/mutation_operators.Rd | 28 ExpDE-0.2.0/ExpDE/man/mutation_rand.Rd | 84 - ExpDE-0.2.0/ExpDE/man/mutation_wgi.Rd | 104 - ExpDE-0.2.0/ExpDE/man/print_progress.Rd | 64 - ExpDE-0.2.0/ExpDE/man/recombination_arith.Rd | 56 ExpDE-0.2.0/ExpDE/man/recombination_bin.Rd | 88 - ExpDE-0.2.0/ExpDE/man/recombination_blxAlphaBeta.Rd | 112 - ExpDE-0.2.0/ExpDE/man/recombination_eigen.Rd | 86 - ExpDE-0.2.0/ExpDE/man/recombination_exp.Rd | 80 - ExpDE-0.2.0/ExpDE/man/recombination_geo.Rd | 82 - ExpDE-0.2.0/ExpDE/man/recombination_lbga.Rd | 76 - ExpDE-0.2.0/ExpDE/man/recombination_linear.Rd | 74 - ExpDE-0.2.0/ExpDE/man/recombination_mmax.Rd | 110 - ExpDE-0.2.0/ExpDE/man/recombination_none.Rd | 44 ExpDE-0.2.0/ExpDE/man/recombination_npoint.Rd | 88 - ExpDE-0.2.0/ExpDE/man/recombination_onepoint.Rd | 86 - ExpDE-0.2.0/ExpDE/man/recombination_operators.Rd | 30 ExpDE-0.2.0/ExpDE/man/recombination_pbest.Rd | 102 - ExpDE-0.2.0/ExpDE/man/recombination_sbx.Rd | 90 - ExpDE-0.2.0/ExpDE/man/recombination_wright.Rd | 74 - ExpDE-0.2.0/ExpDE/man/selection_standard.Rd | 48 80 files changed, 3403 insertions(+), 3379 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.8 dated 2025-06-27 and 2.2.9 dated 2025-09-29
DESCRIPTION | 27 ++-- MD5 | 97 ++++++++++------- NAMESPACE | 11 +- NEWS | 52 +++++++++ R/GHcop.R | 70 +++++++++++- R/HAIRPINcop.R |only R/JOcop.R | 52 +++++++-- R/M.R | 2 R/MOcop.R |only R/N4220cop.R |only R/NORMcop.R |only R/PSP.R | 5 R/Tcop.R |only R/W.R | 2 R/kfuncCOP_Pd.R |only R/lcomCOP.R | 63 +++++++++-- R/rmseCOP.R | 4 man/CIRCcop.Rd | 38 ++++-- man/EMPIRcop.Rd | 8 - man/FGMcop.Rd | 29 +++++ man/FRcop.Rd | 2 man/GHcop.Rd | 218 ++++++++++++++++++--------------------- man/HAIRPINcop.Rd |only man/HRcop.Rd | 6 - man/JOcopB5.Rd | 21 +++ man/LCOMDIA_GH2cop.Rd |only man/LCOMDIA_GH3cop.Rd |only man/LCOMDIA_GHcop.Rd |only man/LCOMDIA_ManyCops.Rd |only man/LzCOPpermsym.Rd | 23 ++++ man/MOcop.Rd |only man/N4220cop.Rd |only man/NORMcop.Rd |only man/ORDSUMcop.Rd | 264 +++++++++++++++++++++++++++++++++++++++++++++--- man/ORDSUWcop.Rd | 16 +- man/P.Rd | 42 ++++--- man/RAYcop.Rd | 2 man/RFcop.Rd | 2 man/Tcop.Rd |only man/W.Rd | 38 ++++++ man/breveCOP.Rd | 10 - man/composite1COP.Rd | 23 ++-- man/composite2COP.Rd | 16 ++ man/composite3COP.Rd | 4 man/copBasic-package.Rd | 148 ++++++++++++++------------ man/footCOP.Rd | 85 ++++++++++----- man/gEVcop.Rd | 39 +++---- man/glueCOP.Rd | 85 +++++++++------ man/isCOP.permsym.Rd | 6 - man/isCOP.radsym.Rd | 164 ++++++++++++++++++----------- man/kfuncCOP.Rd | 85 ++++++++------- man/kfuncCOP_Pd.Rd |only man/lcomCOP.Rd | 104 ++++++++++-------- man/rN4220cop.Rd |only man/rhoCOP.Rd | 12 +- man/spectralmeas.Rd | 100 +++++++++--------- man/tEVcop.Rd | 13 +- man/taildepCOP.Rd | 90 ++++++++-------- 58 files changed, 1378 insertions(+), 700 deletions(-)
Title: Bayesian Hierarchical Poisson Models for Multiple Grouped
Outcomes with Clustering
Description: Bayesian hierarchical methods for the detection of differences in rates of related outcomes for multiple treatments for clustered observations (Carragher et al. (2020) <doi:10.1002/sim.8563>). This software was developed for the Precision Drug Theraputics: Risk Prediction in Pharmacoepidemiology project as part of a Rutherford Fund Fellowship at Health Data Research (UK), Medical Research Council (UK) award reference MR/S003967/1 (<https://gtr.ukri.org/>). Principal Investigator: Raymond Carragher.
Author: Raymond Carragher [aut, cre]
Maintainer: Raymond Carragher <rcarragh@gmail.com>
This is a re-admission after prior archival of version 1.7 dated 2020-04-01
Diff between bhpm versions 1.7 dated 2020-04-01 and 1.8.1 dated 2025-09-29
DESCRIPTION | 24 MD5 | 181 +- NAMESPACE | 64 R/bhpm.cluster.1a.hier2.R | 76 R/bhpm.cluster.1a.hier2.lev0.R | 724 ++++----- R/bhpm.cluster.1a.hier2.lev0.convergence.R | 940 +++++------ R/bhpm.cluster.1a.hier2.lev0.summary.stats.R | 470 ++--- R/bhpm.cluster.1a.hier2.lev1.R | 664 ++++---- R/bhpm.cluster.1a.hier2.lev1.convergence.R | 960 ++++++------ R/bhpm.cluster.1a.hier2.lev1.summary.stats.R | 478 +++--- R/bhpm.cluster.1a.hier3.R | 88 - R/bhpm.cluster.1a.hier3.lev0.R | 822 +++++----- R/bhpm.cluster.1a.hier3.lev0.convergence.R | 1346 ++++++++--------- R/bhpm.cluster.1a.hier3.lev0.summary.stats.R | 700 ++++---- R/bhpm.cluster.1a.hier3.lev1.R | 800 +++++----- R/bhpm.cluster.1a.hier3.lev1.convergence.R | 1346 ++++++++--------- R/bhpm.cluster.1a.hier3.lev1.summary.stats.R | 700 ++++---- R/bhpm.cluster.1a.hier3.lev2.R | 784 ++++----- R/bhpm.cluster.1a.hier3.lev2.convergence.R | 1330 ++++++++-------- R/bhpm.cluster.1a.hier3.lev2.summary.stats.R | 686 ++++---- R/bhpm.cluster.BB.hier2.R | 92 - R/bhpm.cluster.BB.hier2.lev0.R | 764 ++++----- R/bhpm.cluster.BB.hier2.lev0.convergence.R | 758 ++++----- R/bhpm.cluster.BB.hier2.lev0.summary.stats.R | 348 ++-- R/bhpm.cluster.BB.hier2.lev1.R | 760 ++++----- R/bhpm.cluster.BB.hier2.lev1.convergence.R | 746 ++++----- R/bhpm.cluster.BB.hier2.lev1.summary.stats.R | 322 ++-- R/bhpm.cluster.BB.hier3.R | 110 - R/bhpm.cluster.BB.hier3.lev0.R | 1032 ++++++------- R/bhpm.cluster.BB.hier3.lev0.convergence.R | 1336 ++++++++-------- R/bhpm.cluster.BB.hier3.lev0.summary.stats.R | 576 +++---- R/bhpm.cluster.BB.hier3.lev1.R | 986 ++++++------ R/bhpm.cluster.BB.hier3.lev1.convergence.R | 1272 ++++++++-------- R/bhpm.cluster.BB.hier3.lev1.summary.stats.R | 546 +++--- R/bhpm.cluster.BB.hier3.lev2.R | 1004 ++++++------ R/bhpm.cluster.BB.hier3.lev2.convergence.R | 1310 ++++++++-------- R/bhpm.cluster.BB.hier3.lev2.summary.stats.R | 542 +++--- R/bhpm.cluster.ptheta.R | 174 +- R/bhpm.convergence.R | 178 +- R/bhpm.gen.initial.values.R | 878 +++++------ R/bhpm.global.sim.param.defaults.R | 72 R/bhpm.hyper.params.defaults.R | 80 - R/bhpm.monitor.defaults.R | 86 - R/bhpm.monitor.samples.R | 52 R/bhpm.npm.R | 124 - R/bhpm.params.R | 354 ++-- R/bhpm.pm.R | 146 - R/bhpm.pm.weights.R | 72 R/bhpm.ptheta.R | 50 R/bhpm.summary.stats.R | 162 +- R/global.R | 1978 ++++++++++++------------- data/bhpm.cluster.data1.txt.gz |binary data/bhpm.cluster.data2.txt.gz |binary data/bhpm.multi.treatments.random.order.txt.gz |binary data/bhpm.multi.treatments.txt.gz |binary data/demo.cluster.data.txt.gz |only man/bhpm.Package.rd | 66 man/bhpm.cluster.1a.hier2.rd | 344 ++-- man/bhpm.cluster.1a.hier3.rd | 364 ++-- man/bhpm.cluster.BB.hier2.rd | 370 ++-- man/bhpm.cluster.BB.hier3.rd | 412 ++--- man/bhpm.cluster.data1.rd | 22 man/bhpm.cluster.data2.rd | 22 man/bhpm.convergence.diag.rd | 144 - man/bhpm.gen.initial.values.rd | 122 - man/bhpm.global.sim.param.defaults.rd | 100 - man/bhpm.hyper.params.defaults.rd | 100 - man/bhpm.monitor.defaults.rd | 100 - man/bhpm.monitor.samples.rd | 98 - man/bhpm.multi.treatments.random.order.rd | 22 man/bhpm.multi.treatments.rd | 32 man/bhpm.npm.rd | 356 ++-- man/bhpm.pm.rd | 396 ++--- man/bhpm.pointmass.weights.rd | 90 - man/bhpm.print.convergence.summary.rd | 106 - man/bhpm.print.summary.stats.rd | 94 - man/bhpm.ptheta.rd | 98 - man/bhpm.sim.control.params.rd | 104 - man/bhpm.summary.stats.rd | 116 - man/demo.cluster.data.rd |only src/bhpm1a_poisson_mc_hier2_lev0.cpp | 47 src/bhpm1a_poisson_mc_hier2_lev1.cpp | 16 src/bhpm1a_poisson_mc_hier3_lev0.cpp | 19 src/bhpm1a_poisson_mc_hier3_lev1.cpp | 24 src/bhpm1a_poisson_mc_hier3_lev2.cpp | 16 src/bhpmBB_poisson_mc_hier2_lev0.cpp | 20 src/bhpmBB_poisson_mc_hier2_lev1.cpp | 16 src/bhpmBB_poisson_mc_hier3_lev0.cpp | 32 src/bhpmBB_poisson_mc_hier3_lev1.cpp | 28 src/bhpmBB_poisson_mc_hier3_lev2.cpp | 54 src/bhpm_Rdefines.h |only src/bhpm_exec.cpp | 3 src/register.cpp | 3 93 files changed, 17034 insertions(+), 17015 deletions(-)
Title: Read, Manipulate, and Write Profiler Data
Description: Defines a data structure for profiler data, and methods to read and
write from the 'Rprof' and 'pprof' file formats.
Author: Kirill Mueller [aut, cre] ,
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between profile versions 1.0.3 dated 2022-08-22 and 1.0.4 dated 2025-09-29
DESCRIPTION | 17 ++++++++++------- MD5 | 22 ++++++++++++---------- NEWS.md | 13 ++++++++++++- R/api.R | 14 +++++++------- man/validate_profile.Rd | 15 +++++++++------ tests/testthat.R | 8 ++++++++ tests/testthat/_snaps |only tests/testthat/test-dm.R |only tests/testthat/test-pprof-from-ds.R | 2 -- tests/testthat/test-pprof-write.R | 2 -- tests/testthat/test-rprof-from-ds.R | 2 -- tests/testthat/test-rprof-read.R | 2 -- tests/testthat/test-rprof-write.R | 2 -- 13 files changed, 58 insertions(+), 41 deletions(-)
Title: Encuesta Nacional de Hogares (Peruvian Home National Survey)
Description: Descarga, lee y analiza bases de la Encuesta Nacional de Hogares (ENAHO) y otras encuestas del Instituto Nacional de Estadística e Informática (INEI) del Perú. (Downloads, reads, and combines data from the Peruvian Home National Survey and other surveys from the National Institute for Statistics (INEI).)
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between enaho versions 0.2.0 dated 2025-07-23 and 0.2.5 dated 2025-09-29
DESCRIPTION | 12 - MD5 | 56 ++++- NAMESPACE | 3 NEWS.md |only R/combinar.inei.R | 19 + R/descargar.inei.R | 2 R/internal.R |only R/leer.inei.R | 162 ++++++++++++++-- R/leer.inei.web.R | 4 R/media.inei.R |only R/proporcion.inei.R |only R/variablesxperiodo.R |only README.md | 261 ++------------------------- build |only inst/doc |only inst/extdata/UBIGEOS_2022_1891_distritos.csv |only inst/extdata/codigosencuesta.rds |binary inst/extdata/enaho_2024_Modulo37_t1 |only inst/extdata/modulosdata.rds |binary inst/extdata/tildes.csv |only man/combinar.inei.Rd | 4 man/descargar.inei.Rd | 2 man/leer.inei.Rd | 12 - man/leer.inei.web.Rd | 6 man/media.inei.Rd |only man/modulos.Rd | 2 man/proporcion.inei.Rd |only man/variablesxperiodo.Rd |only vignettes |only 29 files changed, 245 insertions(+), 300 deletions(-)
Title: Integrative Survival Modeling
Description: Contains implementations of
the integrative Cox model with uncertain event times
proposed by Wang, et al. (2020) <doi:10.1214/19-AOAS1287>,
the regularized Cox cure rate model with uncertain event status
proposed by Wang, et al. (2023) <doi:10.1007/s12561-023-09374-w>,
and other survival analysis routines including
the Cox cure rate model proposed by
Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531>
via an EM algorithm proposed by
Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>,
the regularized Cox cure rate model with elastic net penalty following
Masud et al. (2018) <doi:10.1177/0962280216677748>.
Author: Wenjie Wang [aut, cre] ,
Kun Chen [ths] ,
Jun Yan [ths]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between intsurv versions 0.2.2 dated 2021-01-08 and 0.3.0 dated 2025-09-28
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Title: Working with Rotation Data
Description: Tools for working with rotational data, including
simulation from the most commonly used distributions on SO(3),
methods for different Bayes, mean and median type estimators for
the central orientation of a sample, confidence/credible
regions for the central orientation based on those estimators and
a novel visualization technique for rotation data. Most recently,
functions to identify potentially discordant (outlying) values
have been added. References: Bingham, Melissa A. and Nordman, Dan J. and Vardeman, Steve B. (2009),
Bingham, Melissa A and Vardeman, Stephen B and Nordman, Daniel J (2009),
Bingham, Melissa A and Nordman, Daniel J and Vardeman, Stephen B (2010),
Leon, C.A. and Masse, J.C. and Rivest, L.P. (2006),
Hartley, R and Aftab, K and Trumpf, J. (2011),
Stanfill, Bryan and Genschel, Ulrike and Hofmann, Heike (2013),
Maonton, Jonathan (2004),
Mardia, KV and Jupp, PE (2000, ISBN:9780471953333),
Rancourt, D. and Rivest, L.P. and Asselin, J. (2000),
Chang, Ted and Rivest, Loui [...truncated...]
Author: Bryan Stanfill [aut, cre],
Heike Hofmann [aut],
Ulrike Genschel [aut],
Aymeric Stamm [ctb] ,
Luciano Selzer [ctb]
Maintainer: Bryan Stanfill <bstanfill2003@gmail.com>
Diff between rotations versions 1.6.5 dated 2023-12-07 and 1.6.6 dated 2025-09-28
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS | 31 +++++++++------ R/data.R | 2 R/help.R | 13 ++---- build/vignette.rds |binary inst/doc/rotations-intro.pdf |binary man/drill.Rd | 2 man/rotations.Rd | 31 +++++++++++++-- src/Makevars | 4 - src/Makevars.win | 5 -- src/RcppExports.cpp | 88 +++++++++++++++++++++---------------------- 12 files changed, 118 insertions(+), 90 deletions(-)
Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
Mark Clements [aut],
R Core Team [ctb]
Maintainer: Devin Incerti <devin.incerti@gmail.com>
Diff between hesim versions 0.5.5 dated 2024-09-18 and 0.5.6 dated 2025-09-28
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Title: Reference on Constants, Units and Uncertainty
Description: CODATA internationally recommended values of the fundamental
physical constants, provided as symbols for direct use within the R language.
Optionally, the values with uncertainties and/or units are also provided if
the 'errors', 'units' and/or 'quantities' packages are installed.
The Committee on Data for Science and Technology (CODATA) is an
interdisciplinary committee of the International Council for Science which
periodically provides the internationally accepted set of values of the
fundamental physical constants. This package contains the "2022 CODATA"
version, published on May 2024:
Eite Tiesinga, Peter J. Mohr, David B. Newell, and Barry N. Taylor (2024)
<https://physics.nist.gov/cuu/Constants/>.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between constants versions 1.0.1 dated 2021-02-25 and 2022.0 dated 2025-09-28
DESCRIPTION | 17 +++++++++-------- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/constants.R | 23 +++++++++++------------ README.md | 24 +++++++++++++----------- data/codata.cor.rda |binary data/codata.rda |binary man/codata.Rd | 12 ++++++------ man/constants-package.Rd | 9 +++++---- 9 files changed, 57 insertions(+), 49 deletions(-)
Title: Shiny Module for Taking Free-Form Notes
Description: An enterprise-targeted scalable and customizable 'shiny' module providing an easy way to incorporate free-form note taking or discussion boards into applications.
The package includes a 'shiny' module that can be included in any 'shiny' application to create a panel containing searchable, editable text broken down by section headers.
Can be used with a local 'SQLite' database, or a compatible remote database of choice.
Author: Daniel Kovtun [cre, aut]
Maintainer: Daniel Kovtun <quantumfusetrader@gmail.com>
Diff between shinyNotes versions 0.0.2 dated 2023-02-19 and 0.0.3 dated 2025-09-28
DESCRIPTION | 8 +- MD5 | 36 ++++++------ NEWS.md | 4 + R/data.R | 10 +-- R/note_crud.R | 4 - R/runExample.R | 2 R/sqlite_db.R | 24 ++++---- build/vignette.rds |binary inst/doc/shinyNotes.R | 18 +++--- inst/doc/shinyNotes.html | 139 ++++++++++++++++++++++++----------------------- man/connect_sqlite.Rd | 8 +- man/create_schema.Rd | 4 - man/db.read_table.Rd | 8 +- man/db.write_table.Rd | 4 - man/demo_notes.Rd | 4 - man/emojis.Rd | 2 man/markdown_notes.Rd | 4 - man/runExample.Rd | 2 man/shinynotes.Rd | 4 - 19 files changed, 148 insertions(+), 137 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.4.2 dated 2025-01-07 and 1.4.3 dated 2025-09-28
DESCRIPTION | 12 +++++------ MD5 | 31 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 8 ++++++- R/lda.R | 6 +++-- R/seededlda.R | 22 ++++++++++++--------- R/utils.R | 23 ++++++++++++++++++++++ inst/WORDLIST | 3 -- man/as.dictionary.textmodel_lda.Rd |only man/print.textmodel_lda.Rd | 4 +-- man/terms.Rd | 10 ++++----- man/textmodel_lda.Rd | 5 ++-- src/Makevars.in | 2 - src/Makevars.win | 2 - tests/testthat/test-textmodel_lda.R | 3 +- tests/testthat/test-textmodel_seededlda.R | 2 - tests/testthat/test-utils.R | 11 ++++++++++ 17 files changed, 97 insertions(+), 48 deletions(-)
Title: Structures for Preference Data
Description: Convenient structures for creating, sourcing, reading, writing
and manipulating ordinal preference data. Methods for writing to/from PrefLib
formats. See Nicholas Mattei and Toby Walsh "PrefLib: A Library of Preference
Data" (2013) <doi:10.1007/978-3-642-41575-3_20>.
Author: Floyd Everest [aut, cre] ,
Heather Turner [aut] ,
Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>
This is a re-admission after prior archival of version 0.1.1 dated 2023-09-07
Diff between prefio versions 0.1.1 dated 2023-09-07 and 0.2.0 dated 2025-09-28
prefio-0.1.1/prefio/R/aggregate.preferences.R |only prefio-0.1.1/prefio/R/choices.R |only prefio-0.1.1/prefio/R/group.preferences.R |only prefio-0.1.1/prefio/R/utils-pipe.R |only prefio-0.1.1/prefio/man/aggregate.preferences.Rd |only prefio-0.1.1/prefio/man/choices.Rd |only prefio-0.1.1/prefio/man/group.Rd |only prefio-0.1.1/prefio/man/pipe.Rd |only prefio-0.1.1/prefio/man/reexports.Rd |only prefio-0.1.1/prefio/tests/testthat/test-aggregated_preferences.R |only prefio-0.1.1/prefio/tests/testthat/test-choices.R |only prefio-0.1.1/prefio/tests/testthat/test-group.R |only prefio-0.2.0/prefio/DESCRIPTION | 21 prefio-0.2.0/prefio/MD5 | 67 prefio-0.2.0/prefio/NAMESPACE | 65 prefio-0.2.0/prefio/NEWS.md | 12 prefio-0.2.0/prefio/R/adjacency.R | 110 prefio-0.2.0/prefio/R/pref_summaries.R |only prefio-0.2.0/prefio/R/pref_tools.R |only prefio-0.2.0/prefio/R/preferences.R | 1573 ++++------ prefio-0.2.0/prefio/R/prefio-package.R | 3 prefio-0.2.0/prefio/R/preflib.R | 152 prefio-0.2.0/prefio/R/ranking_matrix.R |only prefio-0.2.0/prefio/build/partial.rdb |binary prefio-0.2.0/prefio/inst/WORDLIST | 60 prefio-0.2.0/prefio/man/adjacency.Rd | 45 prefio-0.2.0/prefio/man/figures |only prefio-0.2.0/prefio/man/pref_add_unranked.Rd |only prefio-0.2.0/prefio/man/pref_blank.Rd |only prefio-0.2.0/prefio/man/pref_cov.Rd |only prefio-0.2.0/prefio/man/pref_get_items.Rd |only prefio-0.2.0/prefio/man/pref_get_rank.Rd |only prefio-0.2.0/prefio/man/pref_irv.Rd |only prefio-0.2.0/prefio/man/pref_keep.Rd |only prefio-0.2.0/prefio/man/pref_length.Rd |only prefio-0.2.0/prefio/man/pref_omit.Rd |only prefio-0.2.0/prefio/man/pref_pop.Rd |only prefio-0.2.0/prefio/man/pref_rev.Rd |only prefio-0.2.0/prefio/man/pref_trunc.Rd |only prefio-0.2.0/prefio/man/pref_type.Rd |only prefio-0.2.0/prefio/man/preferences.Rd | 319 -- prefio-0.2.0/prefio/man/ranking_matrix.Rd |only prefio-0.2.0/prefio/man/read_preflib.Rd | 24 prefio-0.2.0/prefio/man/write_preflib.Rd | 17 prefio-0.2.0/prefio/tests/data/sydney_2023.tsv |only prefio-0.2.0/prefio/tests/testthat/_snaps |only prefio-0.2.0/prefio/tests/testthat/test-adjacency.R | 49 prefio-0.2.0/prefio/tests/testthat/test-preferences.R | 1046 +++++- prefio-0.2.0/prefio/tests/testthat/test-preflib.R | 48 prefio-0.2.0/prefio/tests/testthat/test-rankingmatrix.R |only prefio-0.2.0/prefio/tests/testthat/test-summaries.R |only prefio-0.2.0/prefio/tests/testthat/test-tools.R |only 52 files changed, 2058 insertions(+), 1553 deletions(-)
Title: Holding the Database for the 'extrafont' Package
Description: It is meant to be used with the 'extrafont' package. The 'extrafont' package contains the code to install and use fonts, while the 'extrafontdb' package contains the font database.
Author: Winston Chang [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between extrafontdb versions 1.0 dated 2012-06-11 and 1.1 dated 2025-09-28
extrafontdb-1.0/extrafontdb/man/extrafontdb.Rd |only extrafontdb-1.1/extrafontdb/DESCRIPTION | 31 ++++++++++++----- extrafontdb-1.1/extrafontdb/MD5 | 17 ++++++--- extrafontdb-1.1/extrafontdb/NAMESPACE | 2 + extrafontdb-1.1/extrafontdb/NEWS |only extrafontdb-1.1/extrafontdb/R/extrafontdb.r | 15 +------- extrafontdb-1.1/extrafontdb/README.md | 24 +++++++++++++ extrafontdb-1.1/extrafontdb/inst/CITATION |only extrafontdb-1.1/extrafontdb/man/extrafontdb-package.Rd |only extrafontdb-1.1/extrafontdb/tests |only 10 files changed, 64 insertions(+), 25 deletions(-)
Title: 'systemPipeShiny' Utility Functions
Description: The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>
Diff between spsUtil versions 0.2.2 dated 2021-10-30 and 0.2.2.1 dated 2025-09-28
DESCRIPTION | 8 ++-- MD5 | 26 ++++++------- R/spsUtil.R | 2 - man/checkNameSpace.Rd | 8 ++-- man/checkUrl.Rd | 2 - man/historyStack.Rd | 94 ++++++++++++++++++++++++-------------------------- man/inc.Rd | 16 ++++---- man/msg.Rd | 43 ++++++++++------------ man/notFalsy.Rd | 23 +++++------- man/quiet.Rd | 8 ++-- man/simepleStack.Rd | 48 ++++++++++++------------- man/spsOption.Rd | 14 +++---- man/strUniquefy.Rd | 2 - man/timeout.Rd | 15 ++++--- 14 files changed, 153 insertions(+), 156 deletions(-)
Title: Sparse Latent Class Model for Cognitive Diagnosis
Description: Perform a Bayesian estimation of the exploratory
Sparse Latent Class Model for Binary Data
described by Chen, Y., Culpepper, S. A., and Liang, F. (2020)
<doi:10.1007/s11336-019-09693-2>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between slcm versions 0.1.0 dated 2023-08-12 and 0.1.1 dated 2025-09-28
DESCRIPTION | 27 ++++++++++++------------ MD5 | 20 +++++++++-------- NAMESPACE | 1 R/slcm-wrapper.R | 38 +++++++++++++++++++++++++++------- R/utils.R |only README.md | 1 build/partial.rdb |binary man/attribute_pattern_table_header.Rd |only man/slcm-package.Rd | 3 -- man/slcm.Rd | 17 ++++++++------- src/Makevars | 3 ++ src/Makevars.win | 3 ++ 12 files changed, 74 insertions(+), 39 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.4.1 dated 2025-01-17 and 1.4.2 dated 2025-09-28
DESCRIPTION | 10 MD5 | 14 NEWS.md | 8 R/nls.R | 4 R/nls_methods.R | 669 ++++++++++++++++++------------------ configure | 18 configure.ac | 2 inst/unit_tests/unit_tests_gslnls.R | 195 +++++----- 8 files changed, 489 insertions(+), 431 deletions(-)
Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.
Author: Juergen Niedballa [aut, cre] ,
Alexandre Courtiol [aut] ,
Rahel Sollmann [aut] ,
John Mathai [ctb],
Seth Timothy Wong [ctb] ,
An The Truong Nguyen [ctb] ,
Azlan bin Mohamed [ctb] ,
Andrew Tilker [ctb] ,
Roshan Guharajan [ctb] ,
Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 2.3.1 dated 2025-09-02 and 3.0.0 dated 2025-09-28
DESCRIPTION | 31 MD5 | 75 NAMESPACE | 141 NEWS.md | 156 R/PPC.residuals.R |only R/aggregateStations.R |only R/cameraOperation.R | 30 R/camtrapR-package.R | 4 R/communityModel.R | 326 R/createCovariates.R |only R/detectionHistory.R | 256 R/detectionMaps.R | 2 R/imageRename.R | 151 R/plot.R | 71 R/predict.R | 738 +- R/readWildlifeInsights.R |only R/readcamtrapDP.R |only R/recordTable.R | 15 R/recordTableIndividual.R | 16 R/speciesAccum.R |only R/surveyDashboard.R |11743 ++++++++++++++++++++++++++++++--- R/variousOtherHelperFunctions.R | 80 R/zzz.R |only README.md | 12 inst/dashboard_help |only inst/doc/camtrapr5.html | 3468 ++++++--- man/PPC.community.Rd |only man/PPC.residuals.Rd |only man/aggregateStations.Rd |only man/camtrapR-package.Rd | 3 man/communityModel.Rd | 24 man/createCovariates.Rd |only man/detectionHistory.Rd | 180 man/imageRename.Rd | 28 man/plot_coef-commOccu-method.Rd | 3 man/plot_effects-commOccu-method.Rd | 3 man/predict-commOccu-method.Rd | 10 man/readWildlifeInsights.Rd |only man/readcamtrapDP.Rd |only man/speciesAccum.Rd |only man/surveyDashboard.Rd | 123 tests/testthat/test_cameraOperation.R | 23 tests/testthat/test_detectionHistory.R | 15 43 files changed, 14859 insertions(+), 2868 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-26 1.0.5
2013-12-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 1.1.1
2020-09-30 1.1.0
2020-05-06 1.0.1
2019-10-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-16 0.3.11
2021-12-08 0.3.10
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.29 dated 2024-11-04 and 2.30 dated 2025-09-28
DESCRIPTION | 28 - MD5 | 47 +- NEWS.md | 14 R/html_document.R | 592 ++++++++++++++++++--------------- R/html_document_base.R | 22 - R/jupyter.R | 4 R/pandoc.R | 23 - R/render.R | 3 R/slidy_presentation.R | 2 R/util.R | 4 build/vignette.rds |binary inst/doc/lua-filters.html | 5 inst/doc/rmarkdown.R | 22 - inst/doc/rmarkdown.Rmd | 2 inst/doc/rmarkdown.html | 4 man/html_document.Rd | 86 ++-- man/html_document_base.Rd | 4 man/html_fragment.Rd | 4 man/html_notebook.Rd | 5 man/html_vignette.Rd | 10 man/ioslides_presentation.Rd | 4 man/slidy_presentation.Rd | 4 tests/testthat/resources/template.html |only tests/testthat/test-pandoc.R | 2 vignettes/rmarkdown.Rmd | 2 25 files changed, 476 insertions(+), 417 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.23 dated 2025-08-18 and 1.1.24 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 7 +++++-- R/lang.aff.R | 9 ++++++++- inst/doc/lingtypology_creating_maps.html | 9 +++++---- inst/doc/lingtypology_db_API.html | 9 +++++---- inst/doc/lingtypology_dplyr.html | 11 ++++++----- inst/doc/lingtypology_glottolog_functions.Rmd | 4 ++-- inst/doc/lingtypology_glottolog_functions.html | 11 ++++++----- inst/doc/lingtypology_intro.html | 9 +++++---- tests/testthat/test-lang-aff.R | 4 ++-- vignettes/lingtypology_glottolog_functions.Rmd | 4 ++-- 12 files changed, 62 insertions(+), 47 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.10.1 dated 2025-08-25 and 2.11.0 dated 2025-09-28
DESCRIPTION | 10 MD5 | 104 NAMESPACE | 25 NEWS.md | 12 R/HPart.R |only R/RcppExports.R | 32 R/VisualizeMatching.R | 10 R/hierarchical_mutual_information.R |only R/spectral_clustering.R | 2 R/tree_distance.R | 15 R/zzz.R | 56 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 22 inst/WORDLIST | 31 inst/doc/Generalized-RF.html | 5 inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.html | 13 inst/doc/compare-treesets.html | 5 inst/doc/different-leaves.html | 5 inst/doc/information.html | 5 inst/doc/landscapes.html | 1954 ---------- inst/doc/treespace.html | 7 inst/doc/using-distances.html | 162 man/GeneralizedRF.Rd | 7 man/HH.Rd |only man/HPart.Rd |only man/HierarchicalMutualInfo.Rd |only man/HierarchicalMutualInformation.Rd |only man/JaccardRobinsonFoulds.Rd | 1 man/KendallColijn.Rd | 1 man/MASTSize.Rd | 161 man/MatchingSplitDistance.Rd | 1 man/NNIDist.Rd | 239 - man/NyeSimilarity.Rd | 1 man/PathDist.Rd | 1 man/Robinson-Foulds.Rd | 1 man/SPRDist.Rd | 1 man/TreeDistance.Rd | 1 man/VisualizeMatching.Rd | 3 man/clone.Rd |only src/RcppExports.cpp | 109 src/day_1985.cpp | 3 src/hmi.cpp |only src/hpart.cpp |only src/hpart.h |only src/hpart_relabel.cpp |only src/ints.h | 8 src/li_diameters.h |only src/nni_distance.cpp | 531 +- src/tree_distances.cpp | 58 src/tree_distances.h | 6 tests/testthat/_snaps/HPart |only tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 20 tests/testthat/test-HPart.R |only tests/testthat/test-hierarchical_mutual_information.R |only tests/testthat/test-hmi.cpp.R |only tests/testthat/test-information.R | 8 tests/testthat/test-spectral_clustering.R | 3 tests/testthat/test-tree_distance.R | 53 tests/testthat/test-tree_distance_nni.R | 73 61 files changed, 1081 insertions(+), 2689 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.4-0 dated 2025-07-25 and 3.4-1 dated 2025-09-28
DESCRIPTION | 18 ++--- MD5 | 38 ++++++----- NEWS | 7 ++ build/vignette.rds |binary inst/doc/NAobjects.R |only inst/doc/NAobjects.Rnw |only inst/doc/NAobjects.pdf |only inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 148 ++++++++++++++++++++++----------------------- inst/doc/datasets.Rnw | 32 ++++----- inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 106 ++++++++++++++++++++++++++++---- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 vignettes/NAobjects.Rnw |only vignettes/datasets.Rnw | 32 ++++----- vignettes/updates.Rnw | 106 ++++++++++++++++++++++++++++---- 22 files changed, 335 insertions(+), 156 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions
by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The
method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Author: Wen-Ting Wang [aut, cre] ,
Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.3.5 dated 2023-11-13 and 1.3.8 dated 2025-09-28
DESCRIPTION | 26 +-- MD5 | 59 ++++---- NAMESPACE | 3 NEWS.md | 13 + R/SpatPCA.R | 86 ++++++----- R/helper.R | 21 +- R/zzz.R | 4 README.md | 102 ++++++++++--- build/vignette.rds |binary inst/doc/demo-one-dim-location.R | 78 ++++++---- inst/doc/demo-one-dim-location.Rmd | 80 ++++++---- inst/doc/demo-one-dim-location.html | 82 ++++++----- inst/doc/demo-two-dim-location.R | 78 +++++----- inst/doc/demo-two-dim-location.Rmd | 81 ++++++----- inst/doc/demo-two-dim-location.html | 145 +++++++++---------- man/plot.spatpca.Rd | 2 man/predict.Rd | 2 man/predictEigenfunction.Rd | 2 man/setCores.Rd | 8 - man/spatpca.Rd | 80 +++++----- src/Makevars | 3 src/Makevars.win | 5 src/RcppExports.cpp | 36 ++-- src/RcppSpatPCA.cpp | 263 ++++++++++++++++++------------------ tests/testthat.R | 1 tests/testthat/test-SpatPCA.R | 8 - tests/testthat/test-helper.R | 12 - tests/testthat/test-zzz.R | 54 +------ tools |only vignettes/demo-one-dim-location.Rmd | 80 ++++++---- vignettes/demo-two-dim-location.Rmd | 81 ++++++----- 31 files changed, 804 insertions(+), 691 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 1.0.1 dated 2025-07-04 and 1.0.2 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/doc/litteR-installation.html | 10 +++++----- inst/doc/litteR-manual.html | 36 ++++++++++++++++++------------------ tests/testthat/test-stats.R | 18 +++++++++--------- 6 files changed, 49 insertions(+), 42 deletions(-)
Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.1 dated 2025-08-27 and 0.1.2 dated 2025-09-28
hdMTD-0.1.1/hdMTD/R/raindata.R |only hdMTD-0.1.1/hdMTD/R/sleepscoring.R |only hdMTD-0.1.1/hdMTD/R/testChains.R |only hdMTD-0.1.1/hdMTD/build |only hdMTD-0.1.1/hdMTD/data/raindata.rda |only hdMTD-0.1.1/hdMTD/data/sleepscoring.rda |only hdMTD-0.1.1/hdMTD/data/testChains.rda |only hdMTD-0.1.1/hdMTD/man/checkSample.Rd |only hdMTD-0.1.1/hdMTD/man/raindata.Rd |only hdMTD-0.1.1/hdMTD/man/sleepscoring.Rd |only hdMTD-0.1.1/hdMTD/man/testChains.Rd |only hdMTD-0.1.2/hdMTD/DESCRIPTION | 6 hdMTD-0.1.2/hdMTD/MD5 | 97 ++--- hdMTD-0.1.2/hdMTD/NAMESPACE | 41 ++ hdMTD-0.1.2/hdMTD/NEWS.md | 31 + hdMTD-0.1.2/hdMTD/R/MTDest-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDest.R | 392 ++++++++++++---------- hdMTD-0.1.2/hdMTD/R/MTDmodel-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDmodel.R | 32 + hdMTD-0.1.2/hdMTD/R/accessors.R |only hdMTD-0.1.2/hdMTD/R/as-MTD.R |only hdMTD-0.1.2/hdMTD/R/checkSample.R | 4 hdMTD-0.1.2/hdMTD/R/countsTab.R | 9 hdMTD-0.1.2/hdMTD/R/dTV_sample.R | 53 ++ hdMTD-0.1.2/hdMTD/R/empirical_probs.R |only hdMTD-0.1.2/hdMTD/R/freqTab.R | 26 + hdMTD-0.1.2/hdMTD/R/hdMTD-methods.R |only hdMTD-0.1.2/hdMTD/R/hdMTD.R | 175 ++++++++- hdMTD-0.1.2/hdMTD/R/hdMTD_BIC.R | 68 +++ hdMTD-0.1.2/hdMTD/R/hdMTD_CUT.R | 23 - hdMTD-0.1.2/hdMTD/R/hdMTD_FS.R | 21 - hdMTD-0.1.2/hdMTD/R/hdMTD_FSC.R | 11 hdMTD-0.1.2/hdMTD/R/oscillation.R | 78 ++-- hdMTD-0.1.2/hdMTD/R/probs.R | 290 ++++++++++++---- hdMTD-0.1.2/hdMTD/R/utils.R | 50 +- hdMTD-0.1.2/hdMTD/R/validation.R | 75 ++-- hdMTD-0.1.2/hdMTD/man/MTD-accessors.Rd |only hdMTD-0.1.2/hdMTD/man/MTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest.Rd | 105 +++-- hdMTD-0.1.2/hdMTD/man/MTDmodel.Rd | 11 hdMTD-0.1.2/hdMTD/man/as.MTD.Rd |only hdMTD-0.1.2/hdMTD/man/countsTab.Rd | 9 hdMTD-0.1.2/hdMTD/man/dTV_sample.Rd | 55 ++- hdMTD-0.1.2/hdMTD/man/empirical_probs.Rd |only hdMTD-0.1.2/hdMTD/man/freqTab.Rd | 18 - hdMTD-0.1.2/hdMTD/man/hdMTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/hdMTD.Rd | 50 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_BIC.Rd | 44 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_CUT.Rd | 19 - hdMTD-0.1.2/hdMTD/man/hdMTD_FS.Rd | 17 hdMTD-0.1.2/hdMTD/man/hdMTD_FSC.Rd | 11 hdMTD-0.1.2/hdMTD/man/oscillation.Rd | 64 ++- hdMTD-0.1.2/hdMTD/man/probs.Rd | 95 +++-- hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDest.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDmodel.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD.R | 46 +- hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_BIC.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_CUT.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_FS.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-probs.R | 4 61 files changed, 1397 insertions(+), 679 deletions(-)
Title: Changepoint Detection via Modified Genetic Algorithm
Description: The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package [...truncated...]
Author: Mo Li [aut, cre],
QiQi Lu [aut]
Maintainer: Mo Li <mo.li@louisiana.edu>
Diff between changepointGA versions 0.1.1 dated 2025-05-22 and 0.1.3 dated 2025-09-28
changepointGA-0.1.1/changepointGA/R/GA.R |only changepointGA-0.1.1/changepointGA/R/IslandGA.R |only changepointGA-0.1.1/changepointGA/R/datasimulation.R |only changepointGA-0.1.1/changepointGA/R/defaultsetting.R |only changepointGA-0.1.1/changepointGA/man/GA.Rd |only changepointGA-0.1.1/changepointGA/man/GA_param.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA_param.Rd |only changepointGA-0.1.1/changepointGA/man/TsPlotCheck.Rd |only changepointGA-0.1.1/changepointGA/man/operators.Rd |only changepointGA-0.1.3/changepointGA/DESCRIPTION | 11 changepointGA-0.1.3/changepointGA/MD5 | 84 changepointGA-0.1.3/changepointGA/NAMESPACE | 18 changepointGA-0.1.3/changepointGA/R/AMOCfunc.R | 57 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.Order.R | 82 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.R | 73 changepointGA-0.1.3/changepointGA/R/GAfunc.R | 164 changepointGA-0.1.3/changepointGA/R/RcppExports.R | 56 changepointGA-0.1.3/changepointGA/R/cptDist.R | 60 changepointGA-0.1.3/changepointGA/R/cptga-class.R |only changepointGA-0.1.3/changepointGA/R/cptga.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl-class.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl.R |only changepointGA-0.1.3/changepointGA/R/ts.sim.R |only changepointGA-0.1.3/changepointGA/R/utils.R |only changepointGA-0.1.3/changepointGA/README.md | 209 changepointGA-0.1.3/changepointGA/build/vignette.rds |binary changepointGA-0.1.3/changepointGA/inst/doc/vignette.R | 223 changepointGA-0.1.3/changepointGA/inst/doc/vignette.Rmd | 271 changepointGA-0.1.3/changepointGA/inst/doc/vignette.html | 6808 +++++++++- changepointGA-0.1.3/changepointGA/man/AMOCcrossover.Rd | 4 changepointGA-0.1.3/changepointGA/man/AMOCmutation.Rd | 8 changepointGA-0.1.3/changepointGA/man/AMOCpopulation.Rd | 12 changepointGA-0.1.3/changepointGA/man/AMOCselection.Rd | 2 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Order.Rd | 23 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Rd | 30 changepointGA-0.1.3/changepointGA/man/changepointGA-package.Rd |only changepointGA-0.1.3/changepointGA/man/cptDist.Rd | 14 changepointGA-0.1.3/changepointGA/man/cptga-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptga.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/mutation.Rd | 18 changepointGA-0.1.3/changepointGA/man/plot.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/plot.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/random_population.Rd | 36 changepointGA-0.1.3/changepointGA/man/selectTau.Rd | 4 changepointGA-0.1.3/changepointGA/man/selection_linearrank.Rd | 2 changepointGA-0.1.3/changepointGA/man/ts.sim.Rd | 118 changepointGA-0.1.3/changepointGA/src/ARIMA_BIC.cpp |only changepointGA-0.1.3/changepointGA/src/Makevars |only changepointGA-0.1.3/changepointGA/src/Makevars.win |only changepointGA-0.1.3/changepointGA/src/PopInitia.cpp | 60 changepointGA-0.1.3/changepointGA/src/RcppExports.cpp | 32 changepointGA-0.1.3/changepointGA/vignettes/vignette.Rmd | 271 57 files changed, 7544 insertions(+), 1206 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.9 dated 2025-06-07 and 1.4.10 dated 2025-09-28
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md |only R/grid.hexagontile.R | 2 +- R/hexDensity.R | 4 ++-- R/hexbinFull.R | 3 ++- R/plotHexDensity.R | 25 +++++++++++++++++++------ R/xy2hcell.R | 2 +- man/hexbinFull.Rd | 2 +- src/hbin.f | 4 ++-- src/hbin_frac.f | 6 ++++-- 11 files changed, 45 insertions(+), 28 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.4-0 dated 2025-07-23 and 3.4-2 dated 2025-09-28
DESCRIPTION | 14 - MD5 | 52 ++--- NEWS | 45 ++++ R/intensity.ppm.R | 383 +++++++++++++++++++++++++---------------- R/kppm.R | 9 R/mppm.R | 50 +++-- R/ppm.R | 4 R/predictmppm.R | 105 ++++++----- R/rmh.ppm.R | 9 R/rmhmodel.ppm.R | 60 +++++- R/simulatekppm.R | 10 - R/slrm.R | 5 R/subfits.R | 28 ++ R/sysdata.rda |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/intensity.ppm.Rd | 17 + man/rmh.ppm.Rd | 28 ++ man/rmhmodel.ppm.Rd | 21 ++ man/simulate.kppm.Rd | 20 +- man/simulate.ppm.Rd | 28 ++ man/spatstat.model-internal.Rd | 14 - tests/testsD.R | 9 tests/testsK.R | 16 + tests/testsM.R | 10 - tests/testsP2.R | 14 + tests/testsR2.R | 20 +- 27 files changed, 684 insertions(+), 291 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre],
Richard Harris [aut],
Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.6-1 dated 2024-11-16 and 0.6-2 dated 2025-09-28
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ NEWS.md | 4 +++ R/hgwr.R | 59 ++++++++++++++++++++++------------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/hgwrr.html | 7 +++--- src/hetero_test.cpp | 6 ++++- 8 files changed, 50 insertions(+), 48 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.6 dated 2025-07-23 and 0.10.7 dated 2025-09-27
sasLM-0.10.6/sasLM/inst/doc/Report-Different-Simplest2410021412.pdf |only sasLM-0.10.6/sasLM/inst/doc/Report-NOT-OKs2410021413.pdf |only sasLM-0.10.6/sasLM/inst/doc/Validation-Report-GLM-2410021413.pdf |only sasLM-0.10.7/sasLM/DESCRIPTION | 6 +- sasLM-0.10.7/sasLM/MD5 | 22 +++++---- sasLM-0.10.7/sasLM/R/CumAlpha.R | 23 +++++----- sasLM-0.10.7/sasLM/R/OBFBound.R |only sasLM-0.10.7/sasLM/R/PocockBound.R | 11 ++-- sasLM-0.10.7/sasLM/inst/NEWS.Rd | 9 +++ sasLM-0.10.7/sasLM/inst/doc/Report-Different-Simplest2509281051.pdf |only sasLM-0.10.7/sasLM/inst/doc/Report-NOT-OKs2509281052.pdf |only sasLM-0.10.7/sasLM/inst/doc/Validation-Report-GLM-2509281053.pdf |only sasLM-0.10.7/sasLM/man/CumAlpha.Rd | 18 ++++--- sasLM-0.10.7/sasLM/man/OBFBound.Rd |only sasLM-0.10.7/sasLM/man/PocockBound.Rd | 6 ++ sasLM-0.10.7/sasLM/man/seqBound.Rd | 6 ++ 16 files changed, 62 insertions(+), 39 deletions(-)
Title: Bayesian Estimation of DINA Model
Description: Estimate the Deterministic Input, Noisy "And" Gate (DINA)
cognitive diagnostic model parameters using the Gibbs sampler described
by Culpepper (2015) <doi:10.3102/1076998615595403>.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between dina versions 2.0.0 dated 2019-02-01 and 2.0.2 dated 2025-09-27
DESCRIPTION | 24 ++++++++++++------------ MD5 | 23 ++++++++++++----------- NEWS.md | 24 ++++++++++++++++++++++++ R/dina-est.R | 4 ++-- README.md | 28 ++++++++++------------------ build |only inst/CITATION | 15 ++++++++------- man/dina-package.Rd | 10 ++++------ man/dina.Rd | 4 ++-- src/Makevars | 3 --- src/Makevars.win | 3 --- src/RcppExports.cpp | 5 +++++ src/dina-estimation-routine.cpp | 6 +++--- 13 files changed, 82 insertions(+), 67 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, and push the image to
DockerHub.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.1 dated 2024-12-17 and 0.1.3 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 15 +++++++++++++++ R/create.R | 8 ++++++-- R/dockerfile.R | 10 +++++----- README.md | 4 ++-- man/create.Rd | 6 +++++- tests/testthat/test-build.R | 29 +++++++++++++++++++++++------ tests/testthat/test-create.R | 7 ++++--- 9 files changed, 72 insertions(+), 31 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming
to complement existing R packages. The functionality includes among others
multidimensional compensatory and noncompensatory IRT models
(Reckase, 2009, <doi:10.1007/978-0-387-89976-3>),
MCMC for hierarchical IRT models and testlet models
(Fox, 2010, <doi:10.1007/978-1-4419-0742-4>),
NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>),
Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>;
Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>),
faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011,
<doi:10.1111/j.1745-3984.2011.00143.x>),
ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>),
DETECT statistic (Stout, Habing, Douglas & Kim, 1996,
<doi:10.1177/014662169602000403>), local structural equation modeling
(LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016,
<doi:10.1080/00273171.20 [...truncated...]
Author: Alexander Robitzsch [aut, cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 4.1-15 dated 2024-02-05 and 4.2-133 dated 2025-09-27
DESCRIPTION | 16 MD5 | 539 +++++++++--------- NAMESPACE | 3 R/IRT.anova.sirt.R |only R/IRT.expectedCounts.mirt.R | 8 R/IRT.mle.R | 4 R/RcppExports.R | 26 R/amh_plot.R | 9 R/anova_sirt.R | 42 - R/attach.environment.sirt.R | 18 R/automatic.recode.R | 4 R/brm.irf.R | 4 R/brm.sim.R | 7 R/btm.R | 16 R/categorize.R | 6 R/ccov.np.R | 15 R/ccov_np_compute_ccov_sum_score.R | 4 R/cfa_meas_inv.R | 4 R/class.accuracy.rasch.R | 8 R/conf.detect.R | 4 R/create.ccov.R | 4 R/data.prep.R | 16 R/data.recode.sirt.R | 4 R/data.wide2long.R | 18 R/decategorize.R | 6 R/detect.index.R | 14 R/dexppow.R | 3 R/dif.logisticregression.R | 67 +- R/dif.strata.variance.R | 9 R/dirichlet.simul.R | 4 R/dmlavaan_est_model.R | 5 R/dmlavaan_est_model_bread_matrix_score_derivatives.R | 9 R/dmlavaan_est_model_parameterTable.R | 7 R/dmlavaan_joint_parameterTable.R | 4 R/dmlavaan_se_bootstrap.R | 11 R/dmlavaan_se_sandwich.R | 6 R/eigenvalues.manymatrices.R | 14 R/equating.rasch.jackknife.R | 10 R/expl.detect.R | 22 R/f1d.irt.R | 4 R/fit.adisop.R | 16 R/fit.gradedresponse.R | 23 R/fit.gradedresponse_alg.R | 6 R/gom_em_calc_theta.R | 6 R/gom_em_est_b.R | 10 R/gom_em_est_covariance.R | 4 R/gom_em_est_lambda.R | 14 R/invariance.alignment.R | 150 ++++- R/invariance_alignment_cfa_config.R | 10 R/invariance_alignment_cfa_config_estimate.R | 10 R/invariance_alignment_proc_labels.R | 6 R/invariance_alignment_simulate.R | 18 R/likelihood_adjustment.R | 50 - R/likelihood_adjustment_aux.R | 6 R/linking.haberman.R | 6 R/linking.haberman.lq.R | 87 ++ R/linking.haebara.R | 10 R/linking.robust.R | 4 R/linking_2groups.R |only R/linking_2groups_haebara_fun.R |only R/linking_2groups_haebara_grad.R |only R/linking_2groups_numerical_gradient.R |only R/linking_2groups_power_loss.R |only R/linking_2groups_stocking_lord_fun.R |only R/linking_2groups_stocking_lord_grad.R |only R/linking_2groups_vector_with_names.R |only R/linking_haberman_als.R | 8 R/linking_haberman_als_residual_weights.R | 10 R/linking_haberman_als_vcov.R | 9 R/linking_haberman_compute_lts_mean.R | 8 R/linking_haberman_itempars_prepare.R | 6 R/linking_haberman_lq_pw_create_design.R |only R/linking_haberman_lq_pw_le.R |only R/linking_haberman_lq_pw_le_arrange_Vgamma.R |only R/linking_haberman_lq_pw_le_grad.R |only R/linking_haberman_lq_pw_le_hess_delta.R |only R/linking_haberman_lq_pw_le_hess_gamma.R |only R/linking_haebara_gradient_function_R.R | 6 R/linking_haebara_optim_function_R.R | 9 R/locpolycor.R |only R/locpolycor_est_polycor_itempair.R |only R/locpolycor_est_polycor_opt_fun.R |only R/locpolycor_est_thresh_grad_fun.R |only R/locpolycor_est_thresh_item.R |only R/locpolycor_est_thresh_opt_fun.R |only R/lq_fit.R | 49 + R/lsdm.R | 6 R/lsdm_est_logist_quant.R | 12 R/lsem.MGM.stepfunctions.R | 4 R/lsem.bootstrap.R | 9 R/lsem.estimate.R | 57 + R/lsem.permutationTest.R | 11 R/lsem.test.R | 32 - R/lsem_aggregate_statistics.R |only R/lsem_bootstrap_draw_bootstrap_sample.R | 22 R/lsem_estimate_proc_args.R | 12 R/lsem_fit_initial_model.R | 7 R/lsem_fit_initial_model_sufficient_statistics.R | 36 - R/lsem_fitsem.R | 42 - R/lsem_fitsem_compute_sufficient_statistics.R | 61 +- R/lsem_fitsem_joint_estimation_prepare_partable.R | 14 R/lsem_fitsem_raw_data_define_pseudo_weights.R | 4 R/lsem_group_moderator.R | 32 - R/lsem_local_weights.R | 94 ++- R/lsem_parameter_summary.R | 4 R/lsem_residualize.R | 134 +++- R/m_est.R | 12 R/mcmc.2pno.R | 4 R/mcmc.2pno_alg.R | 5 R/mcmc.2pnoh.R | 64 +- R/mcmc_3pno_testlet_draw_itempars.R | 27 R/mcmc_Rhat.R | 9 R/mcmc_WaldTest.R | 8 R/mcmc_as_formula.R | 6 R/mcmc_confint.R | 11 R/mcmc_derivedPars.R | 6 R/mcmc_plot.R | 9 R/mcmc_rename_define_symbols.R | 6 R/mcmc_rename_helper.R | 8 R/mcmc_rename_parameter_names.R | 6 R/mcmc_rename_undo_parameter_names.R | 4 R/mcmc_summary.R | 21 R/mcmc_summary_print_information_criteria.R | 18 R/mcmclist2coda.R | 4 R/mgsem.R | 4 R/mgsem_bdiag.R | 6 R/mgsem_cd_opt.R | 4 R/mgsem_create_index.R | 6 R/mgsem_duplication_matrix.R | 6 R/mgsem_evaluate_penalties.R | 6 R/mgsem_grad_fun.R | 6 R/mgsem_list_elements_est_total_implied.R | 4 R/mgsem_loglike_suffstat_derivative.R | 16 R/mgsem_opt_fun.R | 4 R/mgsem_output_proc_casewise_likelihood.R | 4 R/mgsem_output_proc_residuals.R | 4 R/mgsem_partable2model.R | 4 R/mgsem_proc_data.R | 4 R/mgsem_proc_model.R | 12 R/mgsem_proc_model_is_B.R | 4 R/mgsem_proc_model_partable_define_index.R | 6 R/mgsem_proc_model_update_penalties_matrix.R | 4 R/mgsem_proc_suffstat.R | 4 R/mgsem_suffstat_covariance_matrix.R | 13 R/mgsem_vcov_me.R | 8 R/mirt.specify.partable.R | 7 R/nedelsky.irf.R | 6 R/nedelsky.sim.R | 6 R/noharm.sirt.R | 4 R/noharm_sirt_efa_rotated_solution.R | 4 R/noharm_sirt_optim_function.R | 19 R/noharm_sirt_optim_function_R.R | 9 R/noharm_sirt_optim_gradient.R | 32 - R/noharm_sirt_optim_gradient_R.R | 11 R/noharm_sirt_optim_gradient_R_der_gamma_item.R | 21 R/noharm_sirt_optim_gradient_R_der_gamma_item_pair.R | 21 R/noharm_sirt_partable_extract_par.R | 4 R/noharm_sirt_partable_include_par.R | 6 R/noharm_sirt_preproc.R | 65 +- R/noharm_sirt_preproc_parameter_table_matrix.R | 9 R/noharm_sirt_preproc_pattern_matrix.R | 4 R/normal2.cw.R | 2 R/package_version_date.R | 6 R/parmsummary_extend.R | 17 R/pbivnorm2.R | 34 - R/rasch.copula3.R | 10 R/rasch.pairwise.itemcluster.R | 11 R/rasch_jml_update_b.R | 7 R/rasch_mirtlc_est_a.R | 11 R/rasch_pairwise_iterations.R | 4 R/rasch_pairwise_optimize.R | 7 R/rasch_pairwise_optimize_opt_fun_terms2.R | 10 R/resp_groupwise.R | 4 R/rexppow.R | 10 R/rm.facets.R | 37 - R/rm_determine_fixed_tau_parameters.R | 4 R/rm_facets_center_value_aggregate.R | 4 R/rm_facets_pp_mle.R | 5 R/rm_facets_pp_mle_calc_ll.R | 5 R/rm_numdiff_index.R | 14 R/rm_pcm_calcprobs.R | 8 R/rm_posterior.R | 4 R/rm_proc_create_pseudoraters.R | 8 R/rm_proc_data.R | 22 R/rm_smooth_distribution.R | 4 R/rm_trim_increments_mstep.R | 5 R/rmvn.R | 4 R/sia.sirt.R | 24 R/sia_sirt_remove_transitive.R | 6 R/sim.rasch.dep.R | 8 R/sim.raschtype.R | 6 R/sirt_EAP.R | 4 R/sirt_MAP.R | 4 R/sirt_add_list_elements.R | 4 R/sirt_logit_to_probs.R | 4 R/sirt_matrix_lower_to_upper.R | 4 R/sirt_max.R |only R/sirt_optimizer.R | 4 R/sirt_pem_collect_parameters.R | 4 R/sirt_pem_create_parameter_index.R | 4 R/sirt_rbind_fill.R | 6 R/sirt_rename_list_entry.R | 6 R/smirt_postproc.R | 33 - R/sqrt_diag.R | 13 R/sqrt_diag_positive.R |only R/summary.gom.em.R | 5 R/summary.lsem.R | 5 R/summary.lsem.permutationTest.R | 4 R/summary_round_helper.R | 4 R/tam2mirt_fix.R | 58 - R/tam2mirt_freed.R | 78 +- R/testlet.marginalized.R | 6 R/tetrachoric2.R | 44 - R/truescore.irt.R | 10 R/truescore_irt_irf.R | 6 R/unidim.csn.R | 8 R/wle.rasch.jackknife.R | 8 R/write.format2.R | 15 R/write.fwf2.R | 10 R/xxirt.R | 76 +- R/xxirt_EAP.R | 8 R/xxirt_classprobs_lca.R | 4 R/xxirt_classprobs_lca_init_par.R | 8 R/xxirt_compute_casewise_likelihood.R | 14 R/xxirt_compute_itemprobs.R | 28 R/xxirt_compute_likelihood.R | 20 R/xxirt_compute_posterior.R | 18 R/xxirt_compute_priorDistribution.R | 7 R/xxirt_compute_prior_Theta_from_x.R | 3 R/xxirt_compute_prob_item_from_x.R | 7 R/xxirt_createDiscItem.R | 11 R/xxirt_createItemList.R | 13 R/xxirt_createParTable.R | 19 R/xxirt_createThetaDistribution.R | 11 R/xxirt_data_proc.R | 10 R/xxirt_em_algorithm.R | 38 - R/xxirt_em_args_extract.R |only R/xxirt_hessian.R | 8 R/xxirt_ic.R | 13 R/xxirt_ic_compute_criteria.R | 16 R/xxirt_irf_lca_init_par.R | 6 R/xxirt_mstep_ThetaParameters.R | 32 - R/xxirt_mstep_itemParameters.R | 63 +- R/xxirt_mstep_itemParameters_evalPrior.R | 4 R/xxirt_newton_raphson.R | 68 +- R/xxirt_nr_grad_fun_R.R | 6 R/xxirt_nr_grad_fun_Rcpp.R | 52 + R/xxirt_nr_grad_fun_numapprox.R | 14 R/xxirt_nr_grad_fun_pml_casewise.R |only R/xxirt_nr_opt_fun_pml_casewise.R |only R/xxirt_nr_optim_fun.R | 27 R/xxirt_nr_pml_grad_fun.R |only R/xxirt_nr_pml_more_arguments.R |only R/xxirt_nr_pml_opt_fun.R |only R/xxirt_nr_pml_opt_fun_R.R |only R/xxirt_nr_pml_preproc_data.R |only R/xxirt_partable_extract_freeParameters.R | 2 R/xxirt_postproc_parameters.R | 16 R/xxirt_prepare_response_data.R | 6 R/xxirt_proc_ParTable.R | 10 R/xxirt_sandwich_pml.R |only R/xxirt_simulate.R | 10 R/xxirt_summary_parts.R | 24 build/partial.rdb |binary data/data.pisa2006Read.rda |only data/datalist | 1 inst/CITATION | 3 inst/NEWS | 40 + man/R2conquest.Rd | 4 man/data.pisa2006Read.Rd |only man/data.pisaMath.Rd | 4 man/invariance.alignment.Rd | 33 + man/linking.haberman.Rd | 48 + man/linking_2groups.Rd |only man/locpolycor.Rd |only man/lq_fit.Rd | 5 man/lsem.estimate.Rd | 15 man/lsem.test.Rd | 8 man/matrixfunctions.sirt.Rd | 5 man/xxirt.Rd | 275 +++++++++ man/xxirt_createParTable.Rd | 5 man/xxirt_createThetaDistribution.Rd | 5 src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 123 +++- src/sirt_rcpp_invariance_alignment.cpp | 18 src/sirt_rcpp_polychoric2.cpp | 8 src/sirt_rcpp_rm_sdt.cpp | 27 src/sirt_rcpp_xxirt.cpp | 369 ++++++++++++ 289 files changed, 3292 insertions(+), 1725 deletions(-)
Title: Utility Functions for Forest Inventory and Silviculture
Description: Perform common dendrometry operations such as inventory preparing, and inventory data analysis.
Author: Adrian Cidre Gonzalez [aut, cre],
Aitor Vazquez Veloso [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between silviculture versions 0.1.0 dated 2025-05-29 and 0.2.0 dated 2025-09-27
silviculture-0.1.0/silviculture/R/biomass.R |only silviculture-0.1.0/silviculture/R/dendrometry-summary.R |only silviculture-0.1.0/silviculture/R/dendrometry.R |only silviculture-0.1.0/silviculture/R/globals.R |only silviculture-0.1.0/silviculture/R/inventory.R |only silviculture-0.1.0/silviculture/R/lidar.R |only silviculture-0.1.0/silviculture/R/volume.R |only silviculture-0.1.0/silviculture/man/Inventory.Rd |only silviculture-0.1.0/silviculture/man/SampleSize.Rd |only silviculture-0.1.0/silviculture/man/calc_dominant_height.Rd |only silviculture-0.2.0/silviculture/DESCRIPTION | 27 + silviculture-0.2.0/silviculture/MD5 | 156 +++++++--- silviculture-0.2.0/silviculture/NAMESPACE | 63 ++-- silviculture-0.2.0/silviculture/NEWS.md | 66 ++++ silviculture-0.2.0/silviculture/R/deprecated-funs.R |only silviculture-0.2.0/silviculture/R/inventory-summary.R |only silviculture-0.2.0/silviculture/R/metrics-lidar.R |only silviculture-0.2.0/silviculture/R/metrics-stand-density.R |only silviculture-0.2.0/silviculture/R/metrics-stand-level.R |only silviculture-0.2.0/silviculture/R/metrics-tree-level.R |only silviculture-0.2.0/silviculture/R/predict-biomass.R |only silviculture-0.2.0/silviculture/R/predict-height.R |only silviculture-0.2.0/silviculture/R/sample-size.R |only silviculture-0.2.0/silviculture/R/silviculture-package.R |only silviculture-0.2.0/silviculture/R/sysdata.rda |binary silviculture-0.2.0/silviculture/R/treatment-thinning.R |only silviculture-0.2.0/silviculture/R/utils-not-exported.R | 133 ++++++++ silviculture-0.2.0/silviculture/R/zzz.R | 25 + silviculture-0.2.0/silviculture/README.md | 5 silviculture-0.2.0/silviculture/build/partial.rdb |binary silviculture-0.2.0/silviculture/data/biomass_models.rda |binary silviculture-0.2.0/silviculture/data/inventory_samples.rda |binary silviculture-0.2.0/silviculture/inst |only silviculture-0.2.0/silviculture/man/calc_accumulated_trees.Rd |only silviculture-0.2.0/silviculture/man/calc_dominant_metric.Rd |only silviculture-0.2.0/silviculture/man/calc_n_cost.Rd |only silviculture-0.2.0/silviculture/man/calc_n_optimal.Rd |only silviculture-0.2.0/silviculture/man/calc_n_prop.Rd |only silviculture-0.2.0/silviculture/man/calc_n_simple.Rd | 48 +-- silviculture-0.2.0/silviculture/man/eq_biomass_cudjoe_2024.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_dieguez_aranda_2009.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_manrique_2017.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_menendez_2022.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_montero_2005.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2011.Rd |only silviculture-0.2.0/silviculture/man/eq_biomass_ruiz_peinado_2012.Rd |only silviculture-0.2.0/silviculture/man/eq_hd_vazquez_veloso_2025.Rd |only silviculture-0.2.0/silviculture/man/figures/lifecycle-deprecated.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-experimental.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-stable.svg |only silviculture-0.2.0/silviculture/man/figures/lifecycle-superseded.svg |only silviculture-0.2.0/silviculture/man/figures/logo.png |binary silviculture-0.2.0/silviculture/man/lid_fcov.Rd | 66 ++-- silviculture-0.2.0/silviculture/man/lid_lhdi.Rd | 58 +-- silviculture-0.2.0/silviculture/man/plot.Rd | 38 +- silviculture-0.2.0/silviculture/man/silv_basal_area.Rd | 108 +++--- silviculture-0.2.0/silviculture/man/silv_biomass.Rd | 142 ++++----- silviculture-0.2.0/silviculture/man/silv_density_hart.Rd |only silviculture-0.2.0/silviculture/man/silv_density_ntrees_ha.Rd |only silviculture-0.2.0/silviculture/man/silv_density_sdi.Rd |only silviculture-0.2.0/silviculture/man/silv_diametric_class.Rd | 90 ++--- silviculture-0.2.0/silviculture/man/silv_dominant_height.Rd | 118 +++---- silviculture-0.2.0/silviculture/man/silv_lorey_height.Rd | 87 ++--- silviculture-0.2.0/silviculture/man/silv_ntrees_ha.Rd | 85 ++--- silviculture-0.2.0/silviculture/man/silv_predict_biomass.Rd |only silviculture-0.2.0/silviculture/man/silv_predict_height.Rd |only silviculture-0.2.0/silviculture/man/silv_sample_size.Rd | 103 +++--- silviculture-0.2.0/silviculture/man/silv_sample_size_simple.Rd |only silviculture-0.2.0/silviculture/man/silv_sample_size_stratified.Rd |only silviculture-0.2.0/silviculture/man/silv_spacing_index.Rd | 98 +++--- silviculture-0.2.0/silviculture/man/silv_sqrmean_diameter.Rd | 84 ++--- silviculture-0.2.0/silviculture/man/silv_stand_basal_area.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_dominant_diameter.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_dominant_height.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_lorey_height.Rd |only silviculture-0.2.0/silviculture/man/silv_stand_qmean_diameter.Rd |only silviculture-0.2.0/silviculture/man/silv_summary.Rd | 148 ++++----- silviculture-0.2.0/silviculture/man/silv_treatment_thinning.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_basal_area.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_dclass.Rd |only silviculture-0.2.0/silviculture/man/silv_tree_volume.Rd |only silviculture-0.2.0/silviculture/man/silv_volume.Rd | 104 +++--- silviculture-0.2.0/silviculture/man/silviculture-package.Rd |only 83 files changed, 1097 insertions(+), 755 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.8 dated 2025-07-17 and 0.6.9 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/vignette.html | 9 +++++---- src/cwb/cqp/parser.tab.c | 8 ++++---- 6 files changed, 22 insertions(+), 17 deletions(-)
Title: Spectral Data for Light-Emitting-Diodes
Description: Spectral emission data for some frequently used light emitting
diodes available as electronic components. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Shafiuddin Ahmed [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyLEDs versions 0.5.2 dated 2023-11-01 and 0.5.3 dated 2025-09-27
DESCRIPTION | 21 MD5 | 46 - NEWS.md | 10 R/led_brands.r | 5 R/leds-mspct.r | 46 + R/oo-maya-leds.r | 2 README.md | 294 +++-------- build/partial.rdb |binary build/vignette.rds |binary data/COB-dimming-mspct.rda |binary data/COB-reflectors-mspct.rda |binary data/leds-mspct.rda |binary inst/doc/userguide-0-r4p-introduction.Rmd | 158 +++--- inst/doc/userguide-0-r4p-introduction.html | 157 +++--- inst/doc/userguide-1-data-use.R | 12 inst/doc/userguide-1-data-use.Rmd | 50 + inst/doc/userguide-1-data-use.html | 748 ++++++++++++++--------------- man/figures/README-unnamed-chunk-1-1.png |binary man/led_brands.Rd | 12 man/led_colors.Rd | 20 man/leds.mspct.Rd | 47 + man/oo_maya_leds.Rd | 2 vignettes/userguide-0-r4p-introduction.Rmd | 158 +++--- vignettes/userguide-1-data-use.Rmd | 50 + 24 files changed, 936 insertions(+), 902 deletions(-)
More information about photobiologyLEDs at CRAN
Permanent link
Title: Correction of Preprocessed MS Data
Description: An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Author: Allison Mason [aut] ,
Gregory Johnson [aut] ,
Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>
This is a re-admission after prior archival of version 0.3.0 dated 2025-09-07
Diff between mpactr versions 0.3.0 dated 2025-09-07 and 0.3.1 dated 2025-09-27
DESCRIPTION | 9 - MD5 | 106 ++++++++++---------- NAMESPACE | 5 NEWS.md | 10 + R/filter_pactr-accessors.R | 12 ++ R/filters.R | 15 ++ R/import_data.R | 5 R/mpactR-package.R | 4 R/mpactr-accessors.R | 9 + R/peak_table_formatter.R | 20 ++- R/quality_control.R | 3 R/utils.R |only inst/doc/downstream_analyses.R | 3 inst/doc/downstream_analyses.Rmd | 4 inst/doc/downstream_analyses.html | 16 +-- inst/doc/mpactr.R | 10 + inst/doc/mpactr.Rmd | 14 +- inst/doc/mpactr.html | 63 +++--------- inst/doc/reference_semantics.R | 3 inst/doc/reference_semantics.Rmd | 5 man/filter_cv.Rd | 6 - man/filter_group.Rd | 3 man/filter_insource_ions.Rd | 3 man/filter_mispicked_ions.Rd | 3 man/filter_summary.Rd | 3 man/get_cv_data.Rd | 3 man/get_group_averages.Rd | 3 man/get_meta_data.Rd | 3 man/get_peak_table.Rd | 3 man/get_raw_data.Rd | 3 man/get_similar_ions.Rd | 3 man/import_data.Rd | 3 man/limit_cores.Rd |only man/qc_summary.Rd | 3 src/CvFilter.cpp | 18 +-- tests/testthat.R | 1 tests/testthat/exttestdata/cut_ions.csv | 138 +++++++++++++-------------- tests/testthat/test-data.R | 1 tests/testthat/test-filter_pactr-accessors.R | 14 +- tests/testthat/test-filter_pactr-class.R | 113 ++++++++-------------- tests/testthat/test-filter_pactr-methods.R | 101 ++++++++----------- tests/testthat/test-filters.R | 13 +- tests/testthat/test-import_data.R | 21 +--- tests/testthat/test-mpactr-accessors.R | 4 tests/testthat/test-mpactr-class.R | 9 - tests/testthat/test-mpactr-methods.R | 4 tests/testthat/test-pactr-class_cloning.R | 1 tests/testthat/test-peak_table_formatter.R | 9 + tests/testthat/test-qc_graph_pactr-class.R | 10 - tests/testthat/test-quality_control.R | 2 tests/testthat/test-statistics.R | 1 tests/testthat/test-summary-class.R | 1 vignettes/downstream_analyses.Rmd | 4 vignettes/mpactr.Rmd | 14 +- vignettes/reference_semantics.Rmd | 5 55 files changed, 467 insertions(+), 375 deletions(-)
Title: Exploratory Reduced Reparameterized Unified Model Estimation
Description: Perform a Bayesian estimation of the exploratory reduced
reparameterized unified model (ErRUM) described by Culpepper and Chen (2018)
<doi:10.3102/1076998618791306>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph] ,
Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between errum versions 0.0.3 dated 2020-03-20 and 0.0.4 dated 2025-09-27
DESCRIPTION | 25 ++++++++++++------------- MD5 | 17 +++++++++-------- NEWS.md | 12 ++++++++++++ README.md | 10 +++++----- build |only inst/CITATION | 16 ++++++++-------- man/errum-package.Rd | 6 ++---- src/Makevars | 4 +++- src/Makevars.win | 4 +++- src/RcppExports.cpp | 5 +++++ 10 files changed, 59 insertions(+), 40 deletions(-)
Title: DiSTATIS Three Way Metric Multidimensional Scaling
Description: Implement DiSTATIS and CovSTATIS (three-way multidimensional scaling). DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.
Author: Derek Beaton [aut, ctb],
Ju-Chi Yu [aut, ctb],
Vincent Guillemot [aut, ctb],
Herve Abdi [aut, cre]
Maintainer: Herve Abdi <herve@utdallas.edu>
Diff between DistatisR versions 1.1.1 dated 2022-12-05 and 1.1.2 dated 2025-09-27
DistatisR-1.1.1/DistatisR/README.md |only DistatisR-1.1.2/DistatisR/DESCRIPTION | 21 ++- DistatisR-1.1.2/DistatisR/MD5 | 57 ++++------ DistatisR-1.1.2/DistatisR/R/BeersProjectiveMapping.R | 2 DistatisR-1.1.2/DistatisR/R/DistatisR-package.R | 7 - DistatisR-1.1.2/DistatisR/R/GraphDistatisRv.R | 2 DistatisR-1.1.2/DistatisR/R/WinesRankingRawData.R | 2 DistatisR-1.1.2/DistatisR/R/amariSorting.R | 4 DistatisR-1.1.2/DistatisR/R/computePartial4Groups.R | 9 - DistatisR-1.1.2/DistatisR/R/createCubeOfCovDis.R | 4 DistatisR-1.1.2/DistatisR/R/distatis.R | 26 ++++ DistatisR-1.1.2/DistatisR/R/list2CubeOfCov.R | 2 DistatisR-1.1.2/DistatisR/R/multiculturalSortingSpices.R | 2 DistatisR-1.1.2/DistatisR/R/projectVoc.R | 2 DistatisR-1.1.2/DistatisR/R/sortingWines.R | 6 - DistatisR-1.1.2/DistatisR/man/DistatisR-package.Rd | 4 DistatisR-1.1.2/DistatisR/man/GraphDistatisRv.Rd | 2 DistatisR-1.1.2/DistatisR/man/WinesRankingRawData.Rd | 2 DistatisR-1.1.2/DistatisR/man/amariSorting.Rd | 2 DistatisR-1.1.2/DistatisR/man/computePartial4Groups.Rd | 8 - DistatisR-1.1.2/DistatisR/man/createCubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/distatis.Rd | 6 + DistatisR-1.1.2/DistatisR/man/list2CubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.F4voc.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.cubeOfCovDis.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataAmari.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataSortingSpices.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.dataSortingWines.Rd | 2 DistatisR-1.1.2/DistatisR/man/print.str_BeersProjectiveMapping.Rd | 2 DistatisR-1.1.2/DistatisR/man/sortingWines.Rd | 4 30 files changed, 110 insertions(+), 80 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.3.0 dated 2025-09-11 and 0.3.1 dated 2025-09-27
DESCRIPTION | 13 - MD5 | 60 +++--- NAMESPACE | 46 ++-- NEWS.md | 9 R/CopernicusMarine-package.r | 4 R/cms_cite_product.r | 48 ++-- R/cms_download_subset.r | 189 +++++++++++-------- R/cms_login.r | 250 ++++++++++++------------- R/cms_products_list.r | 216 ++++++++++----------- R/generics.r | 127 ++++++------ R/import.r | 2 README.md | 396 ++++++++++++++++++++-------------------- man/CopernicusMarine-package.Rd | 52 ++--- man/account.Rd | 88 ++++---- man/cms_cite_product.Rd | 66 +++--- man/cms_download_native.Rd | 166 ++++++++-------- man/cms_download_subset.Rd | 190 ++++++++++--------- man/cms_get_client_info.Rd | 56 ++--- man/cms_login.Rd | 68 +++--- man/cms_product_details.Rd | 70 +++---- man/cms_product_metadata.Rd | 60 +++--- man/cms_product_services.Rd | 74 +++---- man/cms_products_list.Rd | 90 ++++----- man/cms_wmts.Rd | 158 +++++++-------- tests/testthat.R | 10 - tests/testthat/helper.r | 38 +-- tests/testthat/test_dev.r | 52 ++--- tests/testthat/test_login.r | 74 +++---- tests/testthat/test_product.r | 146 +++++++------- tests/testthat/test_subset.r | 3 tests/testthat/test_wmts.r | 112 +++++------ 31 files changed, 1502 insertions(+), 1431 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Bayesian Mode Inference
Description: A two-step Bayesian approach for mode inference following
Cross, Hoogerheide, Labonne and van Dijk (2024) <doi:10.1016/j.econlet.2024.111579>).
First, a mixture distribution is fitted on the data using a sparse finite
mixture (SFM) Markov chain Monte Carlo (MCMC) algorithm. The number of
mixture components does not have to be known; the size of the mixture is
estimated endogenously through the SFM approach. Second, the modes of the
estimated mixture at each MCMC draw are retrieved using algorithms
specifically tailored for mode detection. These estimates are then used to
construct posterior probabilities for the number of modes, their locations
and uncertainties, providing a powerful tool for mode inference.
Author: Nalan Bastuerk [aut],
Jamie Cross [aut],
Peter de Knijff [aut],
Lennart Hoogerheide [aut],
Paul Labonne [aut, cre],
Herman van Dijk [aut]
Maintainer: Paul Labonne <labonnepaul@gmail.com>
Diff between BayesMultiMode versions 0.7.3 dated 2024-10-31 and 0.7.4 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/plot_methods.R | 42 +++++++++++++++++++++++++----------------- build/partial.rdb |binary 5 files changed, 36 insertions(+), 25 deletions(-)
More information about BayesMultiMode at CRAN
Permanent link
Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This
package intends to handle many file formats that were native to the
antiquated Commodore Amiga machine. This package focuses on file types from
the older Amiga operating systems (<= 3.0). It will read and write specific
file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between AmigaFFH versions 0.4.7 dated 2025-01-08 and 0.4.8 dated 2025-09-27
DESCRIPTION | 10 ++-- MD5 | 94 ++++++++++++++++++++--------------------- NAMESPACE | 1 NEWS.md | 5 ++ R/iff.0.r | 1 man/AmigaBasic.Rd | 6 +- man/AmigaBasic.reserved.Rd | 8 +-- man/AmigaBasicBMAP-io.Rd | 12 ++--- man/AmigaBasicBMAP.Rd | 8 +-- man/AmigaBitmapFont.Rd | 4 - man/ExtractBasic.Rd | 8 +-- man/as.AmigaBasic.Rd | 10 ++-- man/as.AmigaBasicBMAP.Rd | 6 +- man/as.character.Rd | 8 +-- man/as.raw.Rd | 4 - man/availableFontSizes.Rd | 4 - man/c.Rd | 4 - man/check.names.AmigaBasic.Rd | 8 +-- man/colourToAmigaRaw.Rd | 4 - man/fontName.Rd | 4 - man/font_example.Rd | 4 - man/getAmigaBitmapFont.Rd | 4 - man/names.AmigaBasic.Rd | 8 +-- man/packBitmap.Rd | 4 - man/rasterToAmigaBitmapFont.Rd | 4 - man/rawToAmigaBasic.Rd | 8 +-- man/rawToAmigaBasicBMAP.Rd | 10 ++-- man/rawToAmigaBasicShape.Rd | 4 - man/rawToAmigaBitmapFont.Rd | 4 - man/rawToAmigaBitmapFontSet.Rd | 4 - man/rawToAmigaIcon.Rd | 4 - man/rawToHWSprite.Rd | 4 - man/rawToIFFChunk.Rd | 4 - man/rawToSysConfig.Rd | 4 - man/read.AmigaBasic.Rd | 10 ++-- man/read.AmigaBasicShape.Rd | 6 +- man/read.AmigaBitmapFont.Rd | 6 +- man/read.AmigaBitmapFontSet.Rd | 6 +- man/read.AmigaIcon.Rd | 6 +- man/read.SysConfig.Rd | 6 +- man/read.iff.Rd | 6 +- man/simpleAmigaIcon.Rd | 4 - man/write.AmigaBasic.Rd | 14 +++--- man/write.AmigaBasicShape.Rd | 4 - man/write.AmigaBitmapFont.Rd | 12 ++--- man/write.AmigaIcon.Rd | 6 +- man/write.SysConfig.Rd | 6 +- man/write.iff.Rd | 6 +- 48 files changed, 192 insertions(+), 185 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 5.2.4 dated 2025-06-13 and 5.3.0 dated 2025-09-27
secr-5.2.4/secr/R/movemat.R |only secr-5.2.4/secr/R/pxi.R |only secr-5.3.0/secr/DESCRIPTION | 8 secr-5.3.0/secr/MD5 | 226 +- secr-5.3.0/secr/NAMESPACE | 18 secr-5.3.0/secr/NEWS | 41 secr-5.3.0/secr/R/AIC.R | 12 secr-5.3.0/secr/R/CV.R | 6 secr-5.3.0/secr/R/D.designdata.R | 14 secr-5.3.0/secr/R/DENSITY.R | 8 secr-5.3.0/secr/R/Dsurface.R | 350 ++-- secr-5.3.0/secr/R/Enk.R | 17 secr-5.3.0/secr/R/MCgof.R | 60 secr-5.3.0/secr/R/RMarkInput.R | 2 secr-5.3.0/secr/R/RcppExports.R | 4 secr-5.3.0/secr/R/Rsurface.R | 2 secr-5.3.0/secr/R/addSightings.R | 2 secr-5.3.0/secr/R/addTelemetry.R | 6 secr-5.3.0/secr/R/autoini.R | 17 secr-5.3.0/secr/R/circular.R | 16 secr-5.3.0/secr/R/clone.R | 10 secr-5.3.0/secr/R/collate.R | 28 secr-5.3.0/secr/R/confint.secr.R | 111 - secr-5.3.0/secr/R/derivedDcoef.R |only secr-5.3.0/secr/R/derivedDsurface.R | 250 +- secr-5.3.0/secr/R/derivedMS.R | 13 secr-5.3.0/secr/R/detectpar.R | 62 secr-5.3.0/secr/R/deviance.R | 2 secr-5.3.0/secr/R/discretize.R | 4 secr-5.3.0/secr/R/empirical.R | 2 secr-5.3.0/secr/R/esa.R | 75 secr-5.3.0/secr/R/esaPlot.R | 8 secr-5.3.0/secr/R/exportedutility.R | 270 +++ secr-5.3.0/secr/R/fastsecrloglik.R | 85 secr-5.3.0/secr/R/fxi.R | 54 secr-5.3.0/secr/R/generalsecrloglik.R | 175 +- secr-5.3.0/secr/R/homerange.R | 115 + secr-5.3.0/secr/R/join2.R | 30 secr-5.3.0/secr/R/loglikhelperfn.R | 67 secr-5.3.0/secr/R/make.capthist.R | 34 secr-5.3.0/secr/R/make.grid.R | 10 secr-5.3.0/secr/R/make.mask.R | 2 secr-5.3.0/secr/R/makeNewData.R | 18 secr-5.3.0/secr/R/makeStart.R | 53 secr-5.3.0/secr/R/mask.check.R | 13 secr-5.3.0/secr/R/methods.R | 57 secr-5.3.0/secr/R/modelAverage.R | 10 secr-5.3.0/secr/R/par.secr.fit.R | 1 secr-5.3.0/secr/R/pdot.R | 24 secr-5.3.0/secr/R/plot.capthist.r | 33 secr-5.3.0/secr/R/plot.secr.R | 16 secr-5.3.0/secr/R/plot.traps.R | 4 secr-5.3.0/secr/R/pmixProfileLL.R | 6 secr-5.3.0/secr/R/predict.secr.R | 17 secr-5.3.0/secr/R/preparedata.R | 86 - secr-5.3.0/secr/R/reduce.R | 10 secr-5.3.0/secr/R/regionN.R | 166 - secr-5.3.0/secr/R/reparameterize.R | 9 secr-5.3.0/secr/R/score.test.R | 155 + secr-5.3.0/secr/R/secr.design.MS.R | 133 - secr-5.3.0/secr/R/secr.fit.R | 288 ++- secr-5.3.0/secr/R/secr.refit.R | 14 secr-5.3.0/secr/R/sim.capthist.R | 36 secr-5.3.0/secr/R/sim.detect.R | 112 - secr-5.3.0/secr/R/sim.popn.R | 30 secr-5.3.0/secr/R/sim.secr.R | 10 secr-5.3.0/secr/R/simOU.capthist.R |only secr-5.3.0/secr/R/simulate.R | 4 secr-5.3.0/secr/R/snip.R | 2 secr-5.3.0/secr/R/split.capthist.R | 4 secr-5.3.0/secr/R/split.traps.R | 4 secr-5.3.0/secr/R/suggest.buffer.R | 36 secr-5.3.0/secr/R/summary.capthist.R | 8 secr-5.3.0/secr/R/summary.secr.R | 6 secr-5.3.0/secr/R/summary.traps.R | 14 secr-5.3.0/secr/R/telemetry.R | 14 secr-5.3.0/secr/R/trap.builder.R | 120 - secr-5.3.0/secr/R/trend.R | 29 secr-5.3.0/secr/R/utility.R | 1873 ++++++++++------------ secr-5.3.0/secr/R/verify.R | 34 secr-5.3.0/secr/R/write.captures.R | 8 secr-5.3.0/secr/R/write.mask.R | 4 secr-5.3.0/secr/R/write.traps.R | 5 secr-5.3.0/secr/R/xy2CH.R | 2 secr-5.3.0/secr/build/partial.rdb |binary secr-5.3.0/secr/build/vignette.rds |binary secr-5.3.0/secr/inst/doc/secr-datainput.R | 16 secr-5.3.0/secr/inst/doc/secr-datainput.pdf |binary secr-5.3.0/secr/inst/doc/secr-overview.R | 5 secr-5.3.0/secr/inst/doc/secr-overview.Rmd | 753 ++------ secr-5.3.0/secr/inst/doc/secr-overview.pdf |binary secr-5.3.0/secr/man/OVpossum.Rd | 6 secr-5.3.0/secr/man/derivedDsurface.Rd | 31 secr-5.3.0/secr/man/details.Rd | 2 secr-5.3.0/secr/man/detectfn.Rd | 13 secr-5.3.0/secr/man/homerange.Rd | 32 secr-5.3.0/secr/man/make.spcosa.Rd | 4 secr-5.3.0/secr/man/predict.secr.Rd | 4 secr-5.3.0/secr/man/predictDsurface.Rd | 5 secr-5.3.0/secr/man/secr-internal.Rd | 6 secr-5.3.0/secr/man/secr-package.Rd | 34 secr-5.3.0/secr/man/secr.fit.Rd | 10 secr-5.3.0/secr/man/secr.refit.Rd | 10 secr-5.3.0/secr/man/sim.capthist.Rd | 3 secr-5.3.0/secr/man/sim.secr.Rd | 7 secr-5.3.0/secr/man/simOU.capthist.Rd |only secr-5.3.0/secr/man/suggest.buffer.Rd | 10 secr-5.3.0/secr/man/userdist.Rd | 2 secr-5.3.0/secr/src/RcppExports.cpp | 13 secr-5.3.0/secr/src/autils.cpp | 11 secr-5.3.0/secr/tests/testthat.R | 2 secr-5.3.0/secr/tests/testthat/test-derived.R | 4 secr-5.3.0/secr/tests/testthat/test-groups.R |only secr-5.3.0/secr/tests/testthat/test-initial.R | 40 secr-5.3.0/secr/tests/testthat/test-relativeD.R | 2 secr-5.3.0/secr/tests/testthat/test-trapbuilder.R | 6 secr-5.3.0/secr/vignettes/secr-overview.Rmd | 753 ++------ 117 files changed, 3819 insertions(+), 3649 deletions(-)
Title: Target Controlled Infusion (TCI)
Description: Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.
Author: Ryan Jarrett [aut, cre]
Maintainer: Ryan Jarrett <ryantjarrett@gmail.com>
Diff between tci versions 0.2.0 dated 2022-08-15 and 0.2.1 dated 2025-09-27
DESCRIPTION | 15 ++-- MD5 | 29 ++++---- R/poppk_mods.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/custom.R | 2 inst/doc/custom.html | 148 +++++++++++++++++++++++---------------------- inst/doc/overview.R | 14 ++-- inst/doc/overview.html | 154 ++++++++++++++++++++++++----------------------- inst/doc/poppk.R | 12 +-- inst/doc/poppk.html | 150 +++++++++++++++++++++++---------------------- man/eleveld_pd.Rd | 4 - man/eleveld_pk.Rd | 4 - src/Makevars | 18 +++-- src/Makevars.win | 17 ++--- src/pk_cpp_functions.cpp | 2 16 files changed, 297 insertions(+), 274 deletions(-)
Title: Distances and Routes on Geographical Grids
Description: Provides classes and functions to calculate various
distance measures and routes in heterogeneous geographic
spaces represented as grids. The package implements measures
to model dispersal histories first presented by van Etten and
Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost
distances as well as more complex distances based on (constrained)
random walks can be calculated. The distances implemented in
the package are used in geographical genetics, accessibility
indicators, and may also have applications in other fields of
geospatial analysis.
Author: Jacob van Etten [aut] ,
Kaue de Sousa [ctb] ,
Andrew Marx [cre, ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>
Diff between gdistance versions 1.6.4 dated 2023-06-19 and 1.6.5 dated 2025-09-27
DESCRIPTION | 14 - MD5 | 20 +- NEWS.md | 5 R/AAATransition-class.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.R | 10 - inst/doc/Overview.html | 420 ++++++++++++++++++++++++++++------------------ man/Transition-classes.Rd | 2 man/gdistance.Rd | 2 vignettes/gdistance1.bib | 5 11 files changed, 289 insertions(+), 191 deletions(-)
Title: Bayesian Analysis of Networks of Binary and/or Ordinal Variables
Description: Bayesian variable selection methods for analyzing the structure of a Markov random field model for a network of binary and/or ordinal variables.
Author: Maarten Marsman [aut, cre] ,
Giuseppe Arena [ctb] ,
Karoline Huth [ctb] ,
Nikola Sekulovski [ctb] ,
Don van den Bergh [ctb]
Maintainer: Maarten Marsman <m.marsman@uva.nl>
Diff between bgms versions 0.1.4.2 dated 2024-12-05 and 0.1.6.0 dated 2025-09-27
bgms-0.1.4.2/bgms/R/print.bgms.R |only bgms-0.1.4.2/bgms/R/utility_functions.R |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.R |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.Rmd |only bgms-0.1.4.2/bgms/inst/doc/bgmcompare.html |only bgms-0.1.4.2/bgms/inst/doc/introduction.R |only bgms-0.1.4.2/bgms/inst/doc/introduction.Rmd |only bgms-0.1.4.2/bgms/inst/doc/introduction.html |only bgms-0.1.4.2/bgms/src/gibbs_functions.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions.h |only bgms-0.1.4.2/bgms/src/gibbs_functions_compare.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions_edge_prior.cpp |only bgms-0.1.4.2/bgms/src/gibbs_functions_edge_prior.h |only bgms-0.1.4.2/bgms/vignettes/bgmcompare.Rmd |only bgms-0.1.4.2/bgms/vignettes/introduction.Rmd |only bgms-0.1.6.0/bgms/DESCRIPTION | 43 bgms-0.1.6.0/bgms/MD5 | 145 +- bgms-0.1.6.0/bgms/NAMESPACE | 26 bgms-0.1.6.0/bgms/NEWS.md | 82 + bgms-0.1.6.0/bgms/R/RcppExports.R | 28 bgms-0.1.6.0/bgms/R/bgm.R | 1019 +++++++++-------- bgms-0.1.6.0/bgms/R/bgmCompare.R | 1132 ++++++++----------- bgms-0.1.6.0/bgms/R/bgmcompare-methods.r |only bgms-0.1.6.0/bgms/R/bgms-methods.R |only bgms-0.1.6.0/bgms/R/bgms-package.R | 85 - 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Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to
calculate distance matrices for continuous, binary, and multi-dimensional
input matrices, which supports a broad variety of 41 predefined distance
functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user-
defined functions written in C++. For ease of use, the 'parDist' function
extends the signature of the 'dist' function and uses the same parameter
naming conventions as distance methods of existing R packages. The package
is mainly implemented in C++ and leverages the 'RcppParallel' package to
parallelize the distance computations with the help of the 'TinyThread'
library. Furthermore, the 'Armadillo' linear algebra library is used for
optimized matrix operations during distance calculations. The curiously
recurring template pattern (CRTP) technique is applied to avoid virtual
functions, which improves the Dynamic Time Warping calculations while
the implementation stays flexible enough to support differe [...truncated...]
Author: Alexander Eckert [aut, cre],
Lucas Godoy [ctb],
Srikanth KS [ctb]
Maintainer: Alexander Eckert <info@alexandereckert.com>
Diff between parallelDist versions 0.2.6 dated 2022-02-03 and 0.2.7 dated 2025-09-27
DESCRIPTION | 7 +++---- MD5 | 28 ++++++++++++++-------------- R/parDist.R | 2 +- README.md | 38 +++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ inst/doc/parallelDist.R | 2 +- inst/doc/parallelDist.Rnw | 12 ++++++------ inst/doc/parallelDist.pdf |binary man/parDist.Rd | 4 ++-- src/DistanceDTWGeneric.h | 2 +- src/Makevars | 2 -- src/Makevars.win | 2 -- vignettes/parallelDist.Rnw | 12 ++++++------ vignettes/parallelDist.bib | 6 +++--- 15 files changed, 75 insertions(+), 47 deletions(-)
Title: Data for Sunlight Spectra
Description: Data for the extraterrestrial solar spectral irradiance and ground
level solar spectral irradiance and irradiance. In addition data for
shade light under vegetation and irradiance time series from different
broadband sensors. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, trl, cre] ,
T. Matthew Robson [ctb] ,
Saara M. Hartiakinen [ctb] ,
Anders Lindfors [ctb],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySun versions 0.5.0 dated 2024-04-01 and 0.5.1 dated 2025-09-27
DESCRIPTION | 31 +- MD5 | 55 ++-- NEWS.md | 16 + R/example.solar.irrad.data.r | 159 +++++++++++--- R/example.solar.spectra.data.r | 85 +++++++ README.md | 10 build/partial.rdb |binary build/vignette.rds |binary data/broad-band.rda |binary data/gap-mspct.rda |binary data/sun-elevation-spct.rda |only data/sun-hourly-ozone-spct.rda |only data/sun-hourly-spct.rda |binary data/sun-may-morning-spct.rda |binary data/sun-reference-mspct.rda |binary inst/doc/r4p-introduction.Rmd | 162 +++++++------- inst/doc/r4p-introduction.html | 164 +++++++------- inst/doc/user-guide.R | 16 - inst/doc/user-guide.Rmd | 21 + inst/doc/user-guide.html | 342 ++++++++++++++++--------------- man/figures/README-unnamed-chunk-1-1.png |binary man/four_days_1min.data.Rd |only man/gap.mspct.Rd | 7 man/irrad_Kipp.data.Rd | 33 ++ man/photobiologySun-package.Rd | 2 man/ppfd_BF.data.Rd | 40 ++- man/ppfd_LICOR.data.Rd | 37 ++- man/sun_elevation.spct.Rd |only man/sun_hourly_ozone.spct.Rd |only vignettes/r4p-introduction.Rmd | 162 +++++++------- vignettes/user-guide.Rmd | 21 + 31 files changed, 834 insertions(+), 529 deletions(-)
More information about photobiologySun at CRAN
Permanent link
Title: Cone Constrained Convex Problems
Description: Routines for solving convex optimization problems with cone constraints by means of interior-point methods. The implemented algorithms are partially ported from CVXOPT, a Python module for convex optimization (see <https://cvxopt.org> for more information).
Author: Bernhard Pfaff [aut, cre],
Lieven Vandenberghe [cph] ,
Martin Andersen [cph] ,
Joachim Dahl [cph]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between cccp versions 0.3-2 dated 2025-07-30 and 0.3-3 dated 2025-09-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/DCP.cpp | 2 +- src/DNL.cpp | 2 +- src/GPP.cpp | 2 +- src/RPP.cpp | 2 +- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Interface with the United Nations Comtrade API
Description: Interface with and extract data from the United Nations 'Comtrade'
API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping
data for a variety of commodities, these functions allow for easy API query
and data returned as a tidy data frame.
Author: Paul Bochtler [aut, cre, cph] ,
Harriet Goers [aut],
Chris Muir [aut],
Alicia Schep [rev] ,
Rafael Hellwig [rev] ,
Ernest Guevarra [rev] ,
Nicholas Potter [rev] ,
Juergen Amann [ctb]
Maintainer: Paul Bochtler <paulbochtler.gh@gmail.com>
Diff between comtradr versions 1.0.3 dated 2024-11-15 and 1.0.4 dated 2025-09-27
DESCRIPTION | 23 +++++---- MD5 | 90 +++++++++++++++++++------------------- NEWS.md | 7 ++ R/data.R | 2 R/utils.R | 11 +++- R/zzz.R | 2 build/vignette.rds |binary data/country_codes.rda |binary data/ct_pretty_cols.rda |binary inst/WORDLIST | 6 ++ inst/doc/bulk_files.html | 5 +- inst/doc/caching.html | 5 +- inst/doc/comtradr.R | 4 - inst/doc/comtradr.Rmd | 4 - inst/doc/comtradr.html | 13 ++--- inst/doc/large_data.html | 5 +- inst/doc/transition.html | 7 +- inst/extdata/cmd_b4.rds |binary inst/extdata/cmd_b5.rds |binary inst/extdata/cmd_eb.rds |binary inst/extdata/cmd_eb02.rds |binary inst/extdata/cmd_eb10.rds |binary inst/extdata/cmd_eb10s.rds |binary inst/extdata/cmd_h0.rds |binary inst/extdata/cmd_h1.rds |binary inst/extdata/cmd_h2.rds |binary inst/extdata/cmd_h3.rds |binary inst/extdata/cmd_h4.rds |binary inst/extdata/cmd_h5.rds |binary inst/extdata/cmd_h6.rds |binary inst/extdata/cmd_hs.rds |binary inst/extdata/cmd_s1.rds |binary inst/extdata/cmd_s2.rds |binary inst/extdata/cmd_s3.rds |binary inst/extdata/cmd_s4.rds |binary inst/extdata/cmd_ss.rds |binary inst/extdata/customs.rds |binary inst/extdata/flow.rds |binary inst/extdata/list_of_datasets.rda |binary inst/extdata/mot.rds |binary inst/extdata/partner.rds |binary inst/extdata/reporter.rds |binary man/country_codes.Rd | 2 tests/testthat/test-.onload.R | 3 + tests/testthat/test-utils.R | 11 ++-- vignettes/comtradr.Rmd | 4 - 46 files changed, 116 insertions(+), 88 deletions(-)
Title: Continuous Norming
Description: A comprehensive toolkit for generating continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers both
distribution-free modeling using Taylor polynomials and parametric modeling
using the beta-binomial and the 'Sinh-Arcsinh' distribution. Originally developed
for achievement tests, it is applicable to a wide range of mental, physical, or
other test scores dependent on continuous or discrete explanatory variables. The
package provides several advantages: It minimizes deviations from representativeness
in subsamples, interpolates between discrete levels of explanatory variables,
and significantly reduces the required sample size compared to conventional
norming per age group. cNORM enables graphical and analytical evaluation of
model fit, accommodates a wide range of scales including those with negative
and descending values, and even supports conventional norming. It generates
norm tables including confidence intervals. It also includes methods f [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.4.1 dated 2025-05-11 and 3.5.0 dated 2025-09-27
DESCRIPTION | 14 +-- MD5 | 62 +++++++++----- NAMESPACE | 20 ++-- NEWS.md | 11 +- R/plot.R | 161 +++++++++++++++++++++++++++++++------- R/predict.R | 4 R/shash.R |only README.md | 25 +++++ build/vignette.rds |binary inst/doc/BetaBinomial.Rmd | 2 inst/doc/BetaBinomial.html | 17 ++-- inst/doc/ShaSh.R |only inst/doc/ShaSh.Rmd |only inst/doc/ShaSh.html |only inst/doc/WeightedRegression.html | 9 +- inst/doc/cNORM-Demo.html | 11 +- man/cnorm.shash.Rd |only man/compare.Rd | 16 ++- man/derivationTable.Rd | 1 man/diagnostics.shash.Rd |only man/dshash.Rd |only man/getNormCurve.Rd | 1 man/log_likelihood_shash.Rd |only man/normTable.Rd | 1 man/normTable.shash.Rd |only man/plot.cnormShaSh.Rd |only man/plotDensity.Rd | 3 man/predict.cnormBetaBinomial.Rd | 1 man/predict.cnormBetaBinomial2.Rd | 1 man/predict.cnormShaSh.Rd |only man/predictCoefficients_shash.Rd |only man/predictNorm.Rd | 1 man/predictRaw.Rd | 1 man/print.cnormShaSh.Rd |only man/pshash.Rd |only man/qshash.Rd |only man/rawTable.Rd | 1 man/rshash.Rd |only man/summary.cnormShaSh.Rd |only vignettes/BetaBinomial.Rmd | 2 vignettes/ShaSh.Rmd |only 41 files changed, 269 insertions(+), 96 deletions(-)
Title: Ordinal Relations
Description: Functions to handle ordinal relations reflected within the feature space. Those function allow to search for ordinal relations in multi-class datasets. One can check whether proposed relations are reflected in a specific feature representation. Furthermore, it provides functions to filter, organize and further analyze those ordinal relations.
Author: L Lausser [aut],
LM Schaefer [aut],
R Szekely [aut],
HA Kestler [aut, cre]
Maintainer: HA Kestler <hans.kestler@uni-ulm.de>
Diff between ORION versions 1.0.3 dated 2022-02-07 and 1.0.4 dated 2025-09-27
DESCRIPTION | 27 - MD5 | 50 - NAMESPACE | 103 ++- R/as.edgedataframe.R | 1 R/conf.R | 4 R/confusionTable.R | 4 R/dropSets.R | 3 R/dropSize.R | 1 R/dropThreshold.R | 2 R/esl_org-data.R | 2 R/groupwise.R | 4 R/keepSets.R | 1 R/keepSize.R | 3 R/keepThreshold.R | 3 R/package.R |only R/plot.R | 7 R/predictionMap.R | 12 R/print.R | 5 R/subcascades.R | 6 R/summary.R | 5 R/tunePareto.occ.R | 11 build/vignette.rds |binary inst/doc/ORION.R | 2 inst/doc/ORION.html | 1322 +++++++++++++++++++++++++++++++++----------------- man/ORION-package.Rd |only man/predictionMap.Rd | 4 man/tunePareto.occ.Rd | 6 27 files changed, 1044 insertions(+), 544 deletions(-)
Title: Detect Population Structure Within Phylogenetic Trees
Description: Algorithms for detecting population structure from the history of
coalescent events recorded in phylogenetic trees. This method classifies each
tip and internal node of a tree into disjoint sets characterized by similar
coalescent patterns.
Author: Erik Volz [aut, cre] ,
Fabricia F. Nascimento [ctb] ,
Vinicius B. Franceschi [ctb]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treestructure versions 0.1.0 dated 2020-02-17 and 0.7.0 dated 2025-09-27
treestructure-0.1.0/treestructure/R/treestructure.R |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.R |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.Rmd |only treestructure-0.1.0/treestructure/inst/doc/structuredCoalescent.html |only treestructure-0.1.0/treestructure/vignettes/structuredCoalescent.Rmd |only treestructure-0.7.0/treestructure/DESCRIPTION | 48 treestructure-0.7.0/treestructure/MD5 | 49 treestructure-0.7.0/treestructure/NAMESPACE | 4 treestructure-0.7.0/treestructure/R/addtips.R |only treestructure-0.7.0/treestructure/R/m13.R | 1067 ++++++---- treestructure-0.7.0/treestructure/R/treestructure-package.R |only treestructure-0.7.0/treestructure/build/vignette.rds |binary treestructure-0.7.0/treestructure/inst/Ebola_down_sampled_tree.rds |only treestructure-0.7.0/treestructure/inst/Makona_1610_genomes_2016-06-23.ml.tree |only treestructure-0.7.0/treestructure/inst/doc/supportValues.R |only treestructure-0.7.0/treestructure/inst/doc/supportValues.Rmd |only treestructure-0.7.0/treestructure/inst/doc/supportValues.html |only treestructure-0.7.0/treestructure/inst/doc/treestructure.R |only treestructure-0.7.0/treestructure/inst/doc/treestructure.Rmd |only treestructure-0.7.0/treestructure/inst/doc/treestructure.html |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.R |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.Rmd |only treestructure-0.7.0/treestructure/inst/doc/updating_treestructure.html |only treestructure-0.7.0/treestructure/inst/downsampled_tree_struc.rds |only treestructure-0.7.0/treestructure/inst/struc_plot_example.rds |only treestructure-0.7.0/treestructure/inst/treestructure.Rmd | 2 treestructure-0.7.0/treestructure/inst/trestruct_chindex.rds |only treestructure-0.7.0/treestructure/inst/trestruct_res.rds |only treestructure-0.7.0/treestructure/inst/trestruct_res_nobt.rds |only treestructure-0.7.0/treestructure/inst/tscl | 4 treestructure-0.7.0/treestructure/man/addtips.Rd |only treestructure-0.7.0/treestructure/man/plot.TreeStructure.Rd | 14 treestructure-0.7.0/treestructure/man/treestructure-package.Rd | 31 treestructure-0.7.0/treestructure/man/treestructure.test.Rd |only treestructure-0.7.0/treestructure/man/trestruct.Rd | 83 treestructure-0.7.0/treestructure/src/RcppExports.cpp | 5 treestructure-0.7.0/treestructure/vignettes/bib |only treestructure-0.7.0/treestructure/vignettes/supportValues.Rmd |only treestructure-0.7.0/treestructure/vignettes/treestructure.Rmd |only treestructure-0.7.0/treestructure/vignettes/updating_treestructure.Rmd |only 40 files changed, 883 insertions(+), 424 deletions(-)
Title: A Simple Author Handler for Scientific Writing
Description: Handles and formats author information in scientific writing
in 'R Markdown' and 'Quarto'. 'plume' provides easy-to-use and
flexible tools for inserting author data in 'YAML' as well as
generating author and contribution lists (among others) as strings
from tabular data.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between plume versions 0.2.5 dated 2024-09-02 and 0.3.0 dated 2025-09-27
DESCRIPTION | 13 MD5 | 178 +-- NAMESPACE | 30 NEWS.md | 64 + R/aaa.R | 85 - R/als.R | 19 R/as-lines.R |only R/checkers.R | 335 +++--- R/context-binder.R | 3 R/context-selectors.R | 26 R/credit-roles.R | 31 R/data-encyclopedists.R | 17 R/enumerate.R | 11 R/icon.R | 48 R/name-handler.R | 5 R/plm-symbols.R |only R/plm-template.R | 21 R/plume-handler.R | 195 +-- R/plume-package.R | 24 R/plume-quarto.R | 96 + R/plume.R | 205 ++- R/sequential.R | 10 R/set-default-names.R | 22 R/status-setter.R | 62 - R/utils-doc.R |only R/utils-list.R | 5 R/utils-plm.R | 8 R/utils-tbl.R | 41 R/utils.R | 112 +- R/yaml.R | 26 README.md | 34 inst/doc/comprehensive-affiliation-schema.R | 4 inst/doc/plume-workflow.R | 27 inst/doc/plume-workflow.Rmd | 18 inst/doc/plume-workflow.html | 88 - inst/doc/plume.R | 137 -- inst/doc/plume.Rmd | 163 +-- inst/doc/plume.html | 1289 ++++++++----------------- inst/doc/working-in-other-languages.R | 51 inst/doc/working-in-other-languages.Rmd | 55 - inst/doc/working-in-other-languages.html | 78 - man/Plume.Rd | 102 + man/PlumeHandler.Rd | 45 man/PlumeQuarto.Rd | 50 man/StatusSetter.Rd | 10 man/StatusSetterPlume.Rd | 11 man/StatusSetterPlumeQuarto.Rd | 24 man/as_lines.Rd |only man/credit_roles.Rd | 4 man/encyclopedists.Rd | 6 man/enumerate.Rd | 6 man/everyone.Rd | 17 man/icn_orcid.Rd |only man/orcid.Rd | 11 man/plm_symbols.Rd |only man/plm_template.Rd | 5 man/plume-package.Rd | 2 man/sequential.Rd | 5 man/set_default_names.Rd | 13 tests/testthat/_snaps/as-lines.md |only tests/testthat/_snaps/credit-roles.md | 2 tests/testthat/_snaps/defunct.md |only tests/testthat/_snaps/deprecated.md |only tests/testthat/_snaps/get-author-list.md | 21 tests/testthat/_snaps/get-contact-details.md | 22 tests/testthat/_snaps/get-contributions.md | 48 tests/testthat/_snaps/get-footnotes.md | 28 tests/testthat/_snaps/get-orcids.md | 24 tests/testthat/_snaps/icon.md | 24 tests/testthat/_snaps/initialize.md | 92 - tests/testthat/_snaps/plm-symbols.md |only tests/testthat/_snaps/plm-template.md | 21 tests/testthat/_snaps/sequential.md | 2 tests/testthat/_snaps/set-default-names.md | 69 - tests/testthat/_snaps/set-main-contributors.md | 8 tests/testthat/_snaps/set-status.md | 56 - tests/testthat/_snaps/to-yaml.md | 14 tests/testthat/helper-plume.R | 4 tests/testthat/test-as-lines.R |only tests/testthat/test-defunct.R |only tests/testthat/test-deprecated.R |only tests/testthat/test-get-author-list.R | 31 tests/testthat/test-get-contact-details.R | 4 tests/testthat/test-get-contributions.R | 37 tests/testthat/test-get-footnotes.R | 20 tests/testthat/test-get-orcids.R | 7 tests/testthat/test-icon.R | 18 tests/testthat/test-initialize.R | 124 +- tests/testthat/test-plm-symbols.R |only tests/testthat/test-plm-template.R | 15 tests/testthat/test-sequential.R | 4 tests/testthat/test-set-main-contributors.R | 12 tests/testthat/test-set-status.R | 53 - tests/testthat/test-to-yaml.R | 14 vignettes/plume-workflow.Rmd | 18 vignettes/plume.Rmd | 163 +-- vignettes/working-in-other-languages.Rmd | 55 - 97 files changed, 2283 insertions(+), 2674 deletions(-)
Title: Analysis of Elliptical Tubes Under the Relative Curvature
Condition
Description: Analysis of elliptical tubes with applications in biological modeling. The package is based on the references: Taheri, M., Pizer, S. M., & Schulz, J. (2024) "The Mean Shape under the Relative Curvature Condition." Journal of Computational and Graphical Statistics <doi:10.1080/10618600.2025.2535600> and arXiv <doi:10.48550/arXiv.2404.01043>. Mohsen Taheri Shalmani (2024) "Shape Statistics via Skeletal Structures", PhD Thesis, University of Stavanger, Norway <doi:10.13140/RG.2.2.34500.23685>. Key features include constructing discrete elliptical tubes, calculating transformations, validating structures under the Relative Curvature Condition (RCC), computing means, and generating simulations. Supports intrinsic and non-intrinsic mean calculations and transformations, size estimation, plotting, and random sample generation based on a reference tube. The intrinsic approach relies on the interior path of the original non-convex space, incorporating the RCC, while the no [...truncated...]
Author: Mohsen Taheri Shalmani [aut, cre] ,
Joern Schulz [aut],
Stephen M. Pizer [aut]
Maintainer: Mohsen Taheri Shalmani <MohsenTaheriShalmani@gmail.com>
Diff between ETRep versions 1.2.0 dated 2025-06-05 and 1.2.1 dated 2025-09-27
DESCRIPTION | 12 - MD5 | 29 ++-- NEWS | 15 +- R/ETRep_Display.R |only R/ETRep_Functions.R | 122 ++++++++++++++------ R/OnLoadFile.R |only build/partial.rdb |binary man/create_Elliptical_Tube.Rd | 9 - man/dot-etrep_open3d.Rd |only man/dot-etrep_show3d.Rd |only man/dot-onLoad.Rd |only man/intrinsic_Transformation_Elliptical_Tubes.Rd | 2 man/intrinsic_mean_tube.Rd | 4 man/nonIntrinsic_Transformation_Elliptical_Tubes.Rd | 2 man/nonIntrinsic_mean_tube.Rd | 4 man/plot_Elliptical_Tube.Rd | 5 man/simulate_etube.Rd | 17 +- man/tube_Surface_Mesh.Rd | 11 + 18 files changed, 160 insertions(+), 72 deletions(-)
Title: Multiple Testing for Hypotheses with Hierarchical or Group
Structure
Description: Performs multiple testing corrections that take specific structure
of hypotheses into account, as described in Sankaran & Holmes (2014)
<doi:10.18637/jss.v059.i13>.
Author: Kris Sankaran [aut, cre]
Maintainer: Kris Sankaran <ksankaran@wisc.edu>
This is a re-admission after prior archival of version 1.1.1 dated 2015-05-05
Diff between structSSI versions 1.1.1 dated 2015-05-05 and 1.2.0 dated 2025-09-27
structSSI-1.1.1/structSSI/R/Adaptive.GBH.R |only structSSI-1.1.1/structSSI/R/BuildEdgelist.R |only structSSI-1.1.1/structSSI/R/EstimatedHFDRControl.R |only structSSI-1.1.1/structSSI/R/FindRoot.R |only structSSI-1.1.1/structSSI/R/HypTreeJSON.R |only structSSI-1.1.1/structSSI/R/ListTreePval.R |only structSSI-1.1.1/structSSI/R/Oracle.GBH.R |only structSSI-1.1.1/structSSI/R/PlotHypTree.R |only structSSI-1.1.1/structSSI/R/SignificanceStars.R |only structSSI-1.1.1/structSSI/R/estimate.pi0.R |only structSSI-1.1.1/structSSI/R/gbh_definition.R |only structSSI-1.1.1/structSSI/R/hFDR.adjust.R |only structSSI-1.1.1/structSSI/R/hFDR.internal.R |only structSSI-1.1.1/structSSI/R/pi0.lsl.R |only structSSI-1.1.1/structSSI/R/pi0.tail.p.R |only structSSI-1.1.1/structSSI/R/pi0.tst.R |only structSSI-1.1.1/structSSI/R/stepUp.R |only structSSI-1.1.1/structSSI/R/treePValues.R |only structSSI-1.1.1/structSSI/R/tree_definition.R |only structSSI-1.1.1/structSSI/R/validHypothesesTree.R |only structSSI-1.1.1/structSSI/data/gtemp.txt |only structSSI-1.1.1/structSSI/man/GBH-class.Rd |only structSSI-1.1.1/structSSI/man/hypothesesTree.Rd |only structSSI-1.1.1/structSSI/man/structSSI-internal.Rd |only structSSI-1.1.1/structSSI/tests/testGBHProcedures.R |only structSSI-1.1.1/structSSI/tests/testHierarchicalMethods.R |only structSSI-1.2.0/structSSI/DESCRIPTION | 31 +- structSSI-1.2.0/structSSI/MD5 | 65 +--- structSSI-1.2.0/structSSI/NAMESPACE | 57 +-- structSSI-1.2.0/structSSI/R/chlamydiae.R |only structSSI-1.2.0/structSSI/R/gbh.R |only structSSI-1.2.0/structSSI/R/gbh_class.R |only structSSI-1.2.0/structSSI/R/hfdr.R |only structSSI-1.2.0/structSSI/R/hfdr_class.R |only structSSI-1.2.0/structSSI/R/hfdr_plot.R |only structSSI-1.2.0/structSSI/data/chlamydiae.rda |binary structSSI-1.2.0/structSSI/data/gtemp.txt.gz |only structSSI-1.2.0/structSSI/inst/CITATION | 17 - structSSI-1.2.0/structSSI/man/Adaptive.GBH.Rd | 176 +++++------- structSSI-1.2.0/structSSI/man/EstimatedHFDRControl.Rd | 76 +---- structSSI-1.2.0/structSSI/man/Oracle.GBH.Rd | 175 +++++------- structSSI-1.2.0/structSSI/man/PlotHypTree.Rd |only structSSI-1.2.0/structSSI/man/chlamydiae.Rd | 67 ++-- structSSI-1.2.0/structSSI/man/estimate.pi0.Rd | 201 +++++-------- structSSI-1.2.0/structSSI/man/gbh-class.Rd |only structSSI-1.2.0/structSSI/man/gtemp.Rd | 10 structSSI-1.2.0/structSSI/man/hFDR.adjust.Rd | 204 ++++++-------- structSSI-1.2.0/structSSI/man/hypothesisTree-class.Rd |only structSSI-1.2.0/structSSI/man/structSSI-package.Rd | 4 structSSI-1.2.0/structSSI/man/treePValues.Rd | 74 +---- structSSI-1.2.0/structSSI/tests/testthat |only structSSI-1.2.0/structSSI/tests/testthat.R |only 52 files changed, 506 insertions(+), 651 deletions(-)
More information about spuriouscorrelations at CRAN
Permanent link
Title: Configuration of Jupiter's Four Largest Satellites
Description: Calculate, plot and animate the configuration of Jupiter's four
largest satellites (known as Galilean satellites) for a given date and time
(UTC - Coordinated Universal Time).
The galsat() function returns numerical values of the satellites’ positions.
x – the apparent rectangular coordinate of the satellite with respect to the
center of Jupiter’s disk in the equatorial plane in the units of Jupiter’s
equatorial radius; X is positive toward the west,
y – the apparent rectangular coordinate of the satellite with respect to the
center of Jupiter’s disk from the equatorial plane in the units of Jupiter’s
equatorial radius; Y is positive toward the north.
For more details see Meeus (1988, ISBN 0-943396-22-0) "Astronomical Formulae
for Calculators".
The galsat_animate() function creates an animation of the Galilean
satellites' positions. You provide the starting time, duration, the time
step between frames, and the pause between frames.
The function delta_t() returns the value of delta-T in [...truncated...]
Author: Lech Jaszowski [aut, cre, cph]
Maintainer: Lech Jaszowski <lech.jaszowski@interia.pl>
Diff between galisats versions 2.0.2 dated 2025-09-11 and 2.2.0 dated 2025-09-27
DESCRIPTION | 13 +- MD5 | 27 ++++- NAMESPACE | 1 NEWS.md | 12 ++ R/galilean_satellites.R | 177 ++++++++++++++++++++++++++++++++++++-- README.md | 71 ++++++++++++--- man/figures/README-example-1.png |binary man/figures/README-example-10.png |only man/figures/README-example-11.png |only man/figures/README-example-12.png |only man/figures/README-example-13.png |only man/figures/README-example-2.png |only man/figures/README-example-3.png |only man/figures/README-example-4.png |only man/figures/README-example-5.png |only man/figures/README-example-6.png |only man/figures/README-example-7.png |only man/figures/README-example-8.png |only man/figures/README-example-9.png |only man/galsat.Rd | 20 +++- man/galsat_animate.Rd |only 21 files changed, 282 insertions(+), 39 deletions(-)
Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto-grading check-fields and check-boxes for 'rmarkdown'
or 'quarto' HTML. It can be used in class, when teacher share materials
and tasks, so students can solve some problems and check their work. In
contrast to the 'learnr' package, the 'checkdown' package works serverlessly
without 'shiny'.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between checkdown versions 0.0.12 dated 2023-10-27 and 0.0.13 dated 2025-09-27
DESCRIPTION | 13 - MD5 | 16 - NEWS | 7 R/check_question.R | 18 +- build/vignette.rds |binary inst/doc/start_checkdown.R | 32 +-- inst/doc/start_checkdown.Rmd | 11 - inst/doc/start_checkdown.html | 348 ++++++++++++++++++++++++------------------ vignettes/start_checkdown.Rmd | 11 - 9 files changed, 258 insertions(+), 198 deletions(-)
Title: Choice Item Response Theory
Description: Jointly model the accuracy of cognitive responses and item choices
within a Bayesian hierarchical framework as described by Culpepper and
Balamuta (2015) <doi:10.1007/s11336-015-9484-7>. In addition, the package
contains the datasets used within the analysis of the paper.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between cIRT versions 1.3.2 dated 2022-02-21 and 1.3.3 dated 2025-09-27
DESCRIPTION | 22 MD5 | 25 - NEWS.md | 14 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 8 inst/doc/Estimating-the-Model-in-the-Paper.html | 453 +++++++++--------- inst/doc/Package-Overview.html | 66 +- inst/doc/Simulation-Study-with-cIRT.R | 442 ++++++++--------- inst/doc/Simulation-Study-with-cIRT.html | 595 ++++++++++++------------ man/cIRT-package.Rd | 3 src/Makevars | 3 src/Makevars.win | 3 src/project_source.cpp | 6 14 files changed, 862 insertions(+), 778 deletions(-)
Title: Bayesian Estimation of the Reduced Reparameterized Unified Model
with Gibbs Sampling
Description: Implementation of Gibbs sampling algorithm for Bayesian Estimation
of the Reduced Reparameterized Unified Model ('rrum'), described by
Culpepper and Hudson (2017) <doi: 10.1177/0146621617707511>.
Author: Steven Andrew Culpepper [aut, cph] ,
Aaron Hudson [aut, cph] ,
James Joseph Balamuta [aut, cph, cre]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between rrum versions 0.2.1 dated 2023-11-29 and 0.2.2 dated 2025-09-27
DESCRIPTION | 25 +++++++++++++------------ MD5 | 12 ++++++------ NEWS.md | 18 ++++++++++++------ README.md | 12 ++---------- build/partial.rdb |binary man/rrum-package.Rd | 1 - src/rRUM_Gibbs.cpp | 10 +++++----- 7 files changed, 38 insertions(+), 40 deletions(-)
Title: Ordinal Higher-Order Exploratory General Diagnostic Model for
Polytomous Data
Description: Perform a Bayesian estimation of the ordinal exploratory
Higher-order General Diagnostic Model (OHOEGDM) for Polytomous Data
described by Culpepper, S. A. and Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>.
Author: Steven Andrew Culpepper [aut, cph] ,
James Joseph Balamuta [aut, cre, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between ohoegdm versions 0.1.0 dated 2022-02-24 and 0.1.1 dated 2025-09-27
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 15 ++++++++------- NEWS.md | 13 +++++++++++++ README.md | 10 +++++----- build |only inst/CITATION | 4 ++-- man/ohoegdm-package.Rd | 3 +-- src/Makevars | 8 +++++--- src/Makevars.win | 8 +++++--- 9 files changed, 53 insertions(+), 34 deletions(-)
Title: Bayesian Estimation of an Exploratory Deterministic Input, Noisy
and Gate Model
Description: Perform a Bayesian estimation of the exploratory
deterministic input, noisy and gate (EDINA)
cognitive diagnostic model described by Chen et al. (2018)
<doi:10.1007/s11336-017-9579-4>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph] ,
Jeffrey A. Douglas [aut]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between edina versions 0.1.1 dated 2020-03-25 and 0.1.2 dated 2025-09-27
DESCRIPTION | 25 ++++++++++++------------- MD5 | 17 +++++++++-------- NEWS.md | 13 +++++++++++++ README.md | 19 +++++-------------- build |only inst/CITATION | 16 ++++++++-------- man/edina-package.Rd | 7 ++----- src/Makevars | 8 +++++--- src/Makevars.win | 8 +++++--- src/RcppExports.cpp | 5 +++++ 10 files changed, 64 insertions(+), 54 deletions(-)
Title: R Wrapper for 'agena.ai' API
Description: An R wrapper for 'agena.ai' <https://www.agena.ai> which provides users capabilities to work with 'agena.ai' using the R environment. Users can create Bayesian network models from scratch or import existing models in R and export to 'agena.ai' cloud or local API for calculations. Note: running calculations requires a valid 'agena.ai' API license (past the initial trial period of the local API).
Author: Erhan Pisirir [aut],
Eugene Dementiev [aut, cre],
Martin Neil [aut, cph]
Maintainer: Eugene Dementiev <support@agenarisk.com>
Diff between agena.ai versions 1.1.1 dated 2023-09-26 and 1.1.2 dated 2025-09-27
DESCRIPTION | 6 LICENSE | 4 MD5 | 90 NAMESPACE | 46 NEWS.md | 42 R/RAgena.R | 109 - README.md | 2886 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/batch-calculate.Rmd | 132 - inst/doc/batch-calculate.html | 129 - inst/doc/calculate-cloud.Rmd | 148 - inst/doc/calculate-cloud.html | 151 - inst/doc/calculate-local.Rmd | 154 - inst/doc/calculate-local.html | 155 - inst/doc/create-model.html | 203 +- inst/doc/sensitivity-cloud.Rmd | 116 - inst/doc/sensitivity-cloud.html | 139 - inst/doc/sensitivity-local.Rmd | 112 - inst/doc/sensitivity-local.html | 135 - inst/doc/setup-local-calculation.Rmd | 68 inst/doc/setup-local-calculation.html | 121 - man/Dataset-class.Rd | 42 man/Model-class.Rd | 230 +- man/Network-class.Rd | 86 man/Node-class.Rd | 178 - man/calculate.Rd | 52 man/create_batch_cases.Rd | 42 man/create_csv_template.Rd | 36 man/create_sensitivity_config.Rd | 62 man/from_cmpx.Rd | 38 man/generate_cmpx.Rd | 36 man/local_api_activate_license.Rd | 34 man/local_api_batch_calculate.Rd | 34 man/local_api_calculate.Rd | 42 man/local_api_clone.Rd | 28 man/local_api_compile.Rd | 30 man/local_api_sensitivity.Rd | 42 man/login.Rd | 38 man/sensitivity_analysis.Rd | 46 vignettes/CarCosts_DataSet_Modified.csv | 12 vignettes/batch-calculate.Rmd | 132 - vignettes/calculate-cloud.Rmd | 148 - vignettes/calculate-local.Rmd | 154 - vignettes/sensitivity-cloud.Rmd | 116 - vignettes/sensitivity-local.Rmd | 112 - vignettes/setup-local-calculation.Rmd | 68 46 files changed, 3392 insertions(+), 3392 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Roger Bivand [ctb] ,
Andrew Brown [ctb] ,
Michael Chirico [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-60 dated 2025-07-21 and 1.8-70 dated 2025-09-26
DESCRIPTION | 8 +-- MD5 | 106 ++++++++++++++++++++--------------------- NEWS.md | 32 +++++++++++- R/SpatVectorCollection.R | 4 + R/aggregate.R | 3 + R/colors.R | 10 +++ R/generics.R | 53 +++++++++++++++++--- R/plot_2rasters.R | 6 +- R/plot_add.R | 1 R/plot_axes.R | 8 +-- R/plot_legend_classes.R | 7 +- R/plot_legend_continuous.R | 20 ++++--- R/plot_vector.R | 13 +++-- R/rast.R | 16 ++++-- R/tapp.R | 11 ++-- R/tiles.R | 13 ++++- R/time.R | 24 +++++---- R/values.R | 49 ++++++++++++++++++ R/vect.R | 19 ++++--- inst/tinytest/test_vect-geom.R | 4 + man/aggregate.Rd | 10 +++ man/all.equal.Rd | 19 +++++-- man/app.Rd | 2 man/colors.Rd | 5 + man/distance.Rd | 4 - man/divide.Rd | 2 man/global.Rd | 2 man/identical.Rd | 16 +++--- man/makeTiles.Rd | 8 +-- man/north.Rd | 2 man/plet.Rd | 2 man/plot.Rd | 7 +- man/resample.Rd | 7 +- man/scatter.Rd | 2 man/terra-package.Rd | 2 man/vect.Rd | 4 - src/RcppModule.cpp | 18 ++++++ src/distValueRaster.cpp | 3 - src/distVector.cpp | 2 src/gdal_algs.cpp | 10 +++ src/gdal_multidimensional.cpp | 32 +++++++++++- src/geos_methods.cpp | 1 src/geos_spat.h | 7 ++ src/geosphere.cpp | 2 src/ncdf.cpp | 1 src/raster_methods.cpp | 25 +++++++++ src/read_ogr.cpp | 91 ++++++++++++++++++++++++++++++++--- src/spatRaster.h | 2 src/spatRasterMultiple.cpp | 2 src/spatVector.cpp | 13 +++-- src/spatVector.h | 2 src/vector_methods.cpp | 2 src/write_gdal.cpp | 2 src/write_ogr.cpp | 9 ++- 54 files changed, 542 insertions(+), 183 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut] ,
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.12 dated 2025-08-29 and 2.8.13 dated 2025-09-26
DESCRIPTION | 10 - MD5 | 38 ++-- NAMESPACE | 1 NEWS.md | 7 R/SDA-spatial.R | 88 ++++++++--- R/SDA_query.R | 21 +- R/fetchEDIT_tools.R | 6 R/get_OSD.R | 6 R/get_SDA_NASIS_keys.R |only R/get_SDA_property.R | 50 +++--- inst/doc/local-ssurgo.R | 97 +++++------- inst/doc/local-ssurgo.Rmd | 202 +++++++++++++++----------- inst/doc/local-ssurgo.html | 302 +++++++++++++++++++++++---------------- man/SDA_spatialQuery.Rd | 81 +++++++--- man/get_OSD.Rd | 2 man/get_SDA_NASIS_key.Rd |only man/make_EDIT_service_URL.Rd | 6 tests/testthat/test-SDA_query.R | 97 +++++++++++- tests/testthat/test-fetchLDM.R | 2 tests/testthat/test-fetchNASIS.R | 20 +- vignettes/local-ssurgo.Rmd | 202 +++++++++++++++----------- 21 files changed, 764 insertions(+), 474 deletions(-)
Title: Multi-Reader Multi-Case Analysis of Variance
Description: Estimation and comparison of the performances of diagnostic tests
in multi-reader multi-case studies where true case statuses (or ground
truths) are known and one or more readers provide test ratings for multiple
cases. Reader performance metrics are provided for area under and expected
utility of ROC curves, likelihood ratio of positive or negative tests, and
sensitivity and specificity. ROC curves can be estimated empirically or
with binormal or binormal likelihood-ratio models. Statistical comparisons
of diagnostic tests are based on the ANOVA model of Obuchowski-Rockette and
the unified framework of Hillis (2005) <doi:10.1002/sim.2024>. The ANOVA
can be conducted with data from a full factorial, nested, or partially
paired study design; with random or fixed readers or cases; and covariances
estimated with the DeLong method, jackknifing, or an unbiased method. Smith
and Hillis (2020) <doi:10.1117/12.2549075>.
Author: Brian J Smith [aut, cre],
Stephen L Hillis [aut],
Lorenzo L Pesce [ctb]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MRMCaov versions 0.3.0 dated 2023-01-10 and 0.3.1 dated 2025-09-26
DESCRIPTION | 12 MD5 | 34 - NAMESPACE | 2 NEWS.md | 6 R/data.R | 26 R/jackknife.R | 2 R/print.R | 14 R/roc.R | 2 R/summary.R | 19 R/utils.R | 4 README.md | 15 build/partial.rdb |binary build/vignette.rds |binary data/Kundel.RData |binary data/Soh.RData |only inst/CITATION | 2 inst/doc/UserGuide.R | 4 inst/doc/UserGuide.html | 1448 +++++++++++++++++++++++++++++++----------------- man/Soh.Rd |only 19 files changed, 1023 insertions(+), 567 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.21 dated 2025-09-07 and 1.22 dated 2025-09-26
DESCRIPTION | 6 +++--- MD5 | 48 +++++++++++++++++++++++++----------------------- NEWS.md | 4 ++++ data/datalist | 1 + data/drug.RData |only man/adult.Rd | 9 +++------ man/advertising.Rd | 6 ++---- man/bank.Rd | 6 ++---- man/caravan.Rd | 15 +++++++++------ man/cereal.Rd | 17 +++-------------- man/churn.Rd | 16 ++++++++-------- man/churnCredit.Rd | 6 ++---- man/churnTel.Rd | 6 ++---- man/corona.Rd | 6 ++---- man/drug.Rd |only man/fertilizer.Rd | 1 - man/figures/logo.png |binary man/house.Rd | 6 ++---- man/housePrice.Rd | 6 ++---- man/insurance.Rd | 6 ++---- man/kNN.Rd | 3 +-- man/kNN.plot.Rd | 7 ++----- man/marketing.Rd | 6 ++---- man/redWines.Rd | 6 ++---- man/risk.Rd | 1 - man/whiteWines.Rd | 6 ++---- 26 files changed, 81 insertions(+), 113 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, visualise, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. A series of published empirical datasets is included. Documentation about 'archeofrag' is provided by a vignette and by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by the 'archeofrag.gui' R package, a companion GUI application available at <https://analytics.huma-num.fr/Sebast [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 1.2.0 dated 2025-03-27 and 1.2.3 dated 2025-09-26
archeofrag-1.2.0/archeofrag/data/GrandeRivoire.RData |only archeofrag-1.2.0/archeofrag/man/GrandeRivoire.Rd |only archeofrag-1.2.3/archeofrag/DESCRIPTION | 13 archeofrag-1.2.3/archeofrag/MD5 | 54 archeofrag-1.2.3/archeofrag/NEWS.md | 16 archeofrag-1.2.3/archeofrag/R/frag.edges.weighting.R | 2 archeofrag-1.2.3/archeofrag/R/frag.get.parameters.R | 13 archeofrag-1.2.3/archeofrag/R/frag.graph.reduce.R | 16 archeofrag-1.2.3/archeofrag/R/frag.simul.process.R | 1 archeofrag-1.2.3/archeofrag/R/make_frag_object.R | 4 archeofrag-1.2.3/archeofrag/R/utils.R | 24 archeofrag-1.2.3/archeofrag/TODO | 10 archeofrag-1.2.3/archeofrag/build/vignette.rds |binary archeofrag-1.2.3/archeofrag/data/BoutDesVergnes.RData |binary archeofrag-1.2.3/archeofrag/data/Chauzeys.RData |binary archeofrag-1.2.3/archeofrag/data/Fumane.RData |binary archeofrag-1.2.3/archeofrag/data/Geelbek.RData |only archeofrag-1.2.3/archeofrag/data/GrandeRivoire1stMeso.RData |only archeofrag-1.2.3/archeofrag/data/GrandeRivoire2ndMeso.RData |only archeofrag-1.2.3/archeofrag/data/Grotte16.RData |only archeofrag-1.2.3/archeofrag/data/StCesaire1987.RData |only archeofrag-1.2.3/archeofrag/data/StCesaire2024.RData |only archeofrag-1.2.3/archeofrag/inst/doc/archeofrag-vignette.html | 902 ++++------ archeofrag-1.2.3/archeofrag/man/BoutDesVergnes.Rd | 4 archeofrag-1.2.3/archeofrag/man/Chauzeys.Rd | 4 archeofrag-1.2.3/archeofrag/man/Fumane.Rd | 2 archeofrag-1.2.3/archeofrag/man/Geelbek.Rd |only archeofrag-1.2.3/archeofrag/man/GrandeRivoire1stMeso.Rd |only archeofrag-1.2.3/archeofrag/man/GrandeRivoire2ndMeso.Rd |only archeofrag-1.2.3/archeofrag/man/Grotte16.Rd |only archeofrag-1.2.3/archeofrag/man/StCesaire1987.Rd |only archeofrag-1.2.3/archeofrag/man/StCesaire2024.Rd |only archeofrag-1.2.3/archeofrag/man/frag.graph.reduce.Rd | 8 archeofrag-1.2.3/archeofrag/man/frag.simul.process.Rd | 7 archeofrag-1.2.3/archeofrag/tests/testthat/test-frag.simul.compare.R | 1 35 files changed, 475 insertions(+), 606 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
George Stagg [ctb] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 7.0.0 dated 2025-09-01 and 8.0.0 dated 2025-09-26
DESCRIPTION | 8 +++++--- MD5 | 24 +++++++++++++----------- NEWS | 4 ++++ R/wasm.R | 4 ++-- build/partial.rdb |binary configure | 6 ++++++ inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- src/Makevars.win | 2 +- src/V8_types.h | 8 +++++++- src/bindings.cpp | 8 ++++++++ src/emscripten |only tools/winlibs.R | 6 +++--- 13 files changed, 54 insertions(+), 26 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.3 dated 2025-08-19 and 1.19.4 dated 2025-09-26
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/csv/replacementPatterns.csv | 5 +++-- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-spark.R | 9 +++++++-- 6 files changed, 27 insertions(+), 14 deletions(-)
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models. There is also a function for partial and semipartial
correlations and a function for conducting Cohen's
set correlation analyses.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.2.6 dated 2025-06-20 and 0.2.7 dated 2025-09-26
DESCRIPTION | 11 +++--- MD5 | 18 +++++------ NAMESPACE | 2 - R/COUNT_REGRESSION.R | 71 ++++++++++++++++++++++--------------------- R/LOGISTIC_REGRESSION.R | 72 ++++++++++++++++++++++---------------------- R/utilities_boc.R | 4 +- man/COUNT_REGRESSION.Rd | 22 ------------- man/LOGISTIC_REGRESSION.Rd | 21 ------------ man/MODERATED_REGRESSION.Rd | 6 --- man/OLS_REGRESSION.Rd | 6 --- 10 files changed, 89 insertions(+), 144 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: 'ttf2pt1' Program
Description: Contains the program 'ttf2pt1', for use with the
'extrafont' package. This product includes software developed by the 'TTF2PT1'
Project and its contributors.
Author: Winston Chang [aut],
Andrew Weeks [aut],
Frank M. Siegert [aut],
Mark Heath [aut],
Thomas Henlick [aut],
Sergey Babkin [aut],
Turgut Uyar [aut],
Rihardas Hepas [aut],
Szalay Tamas [aut],
Johan Vromans [aut],
Petr Titera [aut],
Lei Wang [aut],
Chen Xi [...truncated...]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Rttf2pt1 versions 1.3.13 dated 2025-09-24 and 1.3.14 dated 2025-09-26
DESCRIPTION | 15 +++++++++------ MD5 | 9 +++++---- NEWS.md | 5 +++++ README.md | 18 ++++++++++++++---- inst |only src/ttf2pt1/t1asm.c | 27 ++++++++++++++++++++++----- 6 files changed, 55 insertions(+), 19 deletions(-)
Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full second- or
third-order polynomial, shifted and rotated squared difference model,
rising ridge surfaces, basic squared difference model, asymmetric or
level-dependent congruence effect models). The package provides plotting
functions for 3d wireframe surfaces, interactive 3d plots, and contour plots.
Calculates many surface parameters (a1 to a5, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schoenbrodt [cre, aut],
Sarah Humberg [aut]
Maintainer: Felix Schoenbrodt <felix@nicebread.de>
Diff between RSA versions 0.10.6 dated 2023-01-12 and 0.10.8 dated 2025-09-26
DESCRIPTION | 12 MD5 | 21 R/RSA.R | 2076 ++++++++++++++++++++++++++++----------------------------- R/RSA.ST.R | 8 R/aictab.R | 2 R/globals.R |only R/plot.RSA.R | 94 +- inst/CITATION | 8 inst/News.Rd | 24 man/RSA.Rd | 6 man/RSA.ST.Rd | 6 man/plotRSA.Rd | 8 12 files changed, 1168 insertions(+), 1097 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] ,
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remify versions 3.2.8 dated 2025-01-29 and 3.2.9 dated 2025-09-26
DESCRIPTION | 11 ++++++----- MD5 | 34 +++++++++++++++++----------------- R/rehshape.R | 6 +++--- R/remify.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rehshape.Rmd | 1 - inst/doc/rehshape.html | 1 - inst/doc/remify.R | 2 +- inst/doc/remify.Rmd | 3 +-- inst/doc/remify.html | 11 +++++------ inst/doc/riskset.R | 17 ++++++++--------- inst/doc/riskset.Rmd | 18 ++++++++---------- inst/doc/riskset.html | 17 ++++++++--------- src/remify.cpp | 16 +++++++++------- vignettes/rehshape.Rmd | 1 - vignettes/remify.Rmd | 3 +-- vignettes/riskset.Rmd | 18 ++++++++---------- 18 files changed, 77 insertions(+), 86 deletions(-)
Title: Prepare American Psychological Association Journal Articles with
R Markdown
Description: Tools to create dynamic, submission-ready manuscripts, which
conform to American Psychological Association manuscript guidelines. We
provide R Markdown document formats for manuscripts (PDF and Word) and
revision letters (PDF). Helper functions facilitate reporting statistical
analyses or create publication-ready tables and plots.
Author: Frederik Aust [aut, cre] ,
Marius Barth [aut] ,
Birk Diedenhofen [ctb],
Christoph Stahl [ctb],
Joseph V. Casillas [ctb],
Rudolf Siegel [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between papaja versions 0.1.3 dated 2024-10-24 and 0.1.4 dated 2025-09-26
papaja-0.1.3/papaja/inst/rmarkdown/templates/apa6/resources/apa6_man__.docx |only papaja-0.1.4/papaja/DESCRIPTION | 19 +++--- papaja-0.1.4/papaja/MD5 | 31 +++++----- papaja-0.1.4/papaja/R/apa_print_emm_lsm.R | 15 +--- papaja-0.1.4/papaja/R/apa_print_glm.R | 10 +-- papaja-0.1.4/papaja/R/cite_r.R | 10 +-- papaja-0.1.4/papaja/R/lookup_tables.R | 2 papaja-0.1.4/papaja/R/mbess-ci-r2.R |only papaja-0.1.4/papaja/R/utils.R | 6 + papaja-0.1.4/papaja/README.md | 12 ++- papaja-0.1.4/papaja/build/partial.rdb |binary papaja-0.1.4/papaja/build/vignette.rds |binary papaja-0.1.4/papaja/inst/NEWS.md | 9 ++ papaja-0.1.4/papaja/inst/WORDLIST | 1 papaja-0.1.4/papaja/inst/doc/extending_apa_print.html | 19 +++--- papaja-0.1.4/papaja/tests/testthat/test_apa_print_emm_lsm.R | 2 papaja-0.1.4/papaja/tests/testthat/test_apa_print_htest.R | 23 ++++++- papaja-0.1.4/papaja/tests/testthat/test_apa_table.log |only 18 files changed, 99 insertions(+), 60 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.34 dated 2025-09-08 and 4.36 dated 2025-09-26
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 219 +++++++++++++++++++++++++++--------------------- R/fuzzyRangeChange.R | 4 R/getRegion.R | 20 ++-- R/gridRecords.R | 4 man/fuzzySim-package.Rd | 4 man/getRegion.Rd | 25 +++-- 8 files changed, 171 insertions(+), 127 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen [aut],
Alain Hauser [aut, cre]
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.3.0 dated 2022-11-09 and 1.4.1 dated 2025-09-26
DESCRIPTION | 25 + MD5 | 32 +- R/impact_analysis.R | 2 R/impact_inference.R | 16 + R/impact_plot.R | 8 README.md | 14 - build/vignette.rds |binary inst/CITATION | 4 inst/doc/CausalImpact.R | 82 +++--- inst/doc/CausalImpact.Rmd | 4 inst/doc/CausalImpact.html | 426 +++++++++++++++++++++++---------- tests/testthat/test-impact-analysis.R | 6 tests/testthat/test-impact-inference.R | 4 tests/testthat/test-impact-misc.R | 10 tests/testthat/test-impact-model.R | 11 tests/testthat/test-impact-plot.R | 57 ++-- vignettes/CausalImpact.Rmd | 4 17 files changed, 462 insertions(+), 243 deletions(-)
Title: Compress and Decompress Data Using the 'BLOSC' Library
Description: Arrays of structured data types can require large volumes of disk
space to store. 'Blosc' is a library that provides a fast and efficient way
to compress such data. It is often applied in storage of n-dimensional
arrays, such as in the case of the geo-spatial 'zarr' file format. This
package can be used to compress and decompress data using 'Blosc'.
Author: Pepijn de Vries [aut, cre] ,
Chris Maiwald [cph],
Alexander Gessler [cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between blosc versions 0.1.1 dated 2025-09-11 and 0.1.2 dated 2025-09-26
DESCRIPTION | 6 MD5 | 34 - NAMESPACE | 16 NEWS.md | 4 R/blosc-package.R | 20 R/r2dtype.R | 174 +++--- README.md | 174 +++--- configure | 911 +++++++++++++++++++++++++++++++++- configure.ac | 71 +- inst/doc/dtypes.Rmd | 342 ++++++------ man/blosc-package.Rd | 64 +- man/blosc.Rd | 122 ++-- man/dtype.Rd | 186 +++--- man/figures/logo.svg | 200 +++---- src/umHalf.inl | 1228 +++++++++++++++++++++++----------------------- tests/testthat.R | 24 tests/testthat/test_dev.R | 50 - vignettes/dtypes.Rmd | 342 ++++++------ 18 files changed, 2432 insertions(+), 1536 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison
methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others.
This version introduces two new procedures: the Jonckheere-Terpstra trend test
and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in
teaching, applied statistical analysis, and reproducible research.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 1.8.5 dated 2025-06-27 and 2.0.0 dated 2025-09-26
DESCRIPTION | 8 - MD5 | 50 +++++----- NAMESPACE | 5 + R/BonferroniTest.R | 173 ++++++++++++++++++++++++++----------- R/DuncanTest.R | 183 +++++++++++++++++++++++++-------------- R/GabrielTest.R | 177 +++++++++++++++++++++++++------------- R/HolmTest.R | 168 ++++++++++++++++++++++++------------ R/LSDTest.R | 163 +++++++++++++++++++++++++---------- R/SNKTest.R | 194 +++++++++++++++++++++++++++--------------- R/ScheffeTest.R | 180 +++++++++++++++++++++++++------------- R/SidakTest.R |only R/TukeyTest.R | 153 ++++++++++++++++++++++++--------- R/plot_comparations.R | 153 ++++++++++++++++++++++----------- R/posthoc_planner.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Analitica-intro.html | 10 +- man/BonferroniTest.Rd | 42 ++++++--- man/DuncanTest.Rd | 44 ++++++--- man/GabrielTest.Rd | 41 ++++++-- man/HolmTest.Rd | 38 +++++--- man/LSDTest.Rd | 34 ++++++- man/Posthoc_planner.Rd |only man/SNKTest.Rd | 40 ++++++-- man/ScheffeTest.Rd | 41 ++++++-- man/SidakTest.Rd |only man/TukeyTest.Rd | 54 +++++++++-- man/plot.comparaciones.Rd | 46 ++++++--- 28 files changed, 1372 insertions(+), 625 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Richard Chandler [aut],
Ken Kellner [cre, aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Lea Pautrel [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
A [...truncated...]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between unmarked versions 1.5.0 dated 2025-02-10 and 1.5.1 dated 2025-09-26
unmarked-1.5.0/unmarked/R/classes.R |only unmarked-1.5.0/unmarked/R/deprecated_sim_power.R |only unmarked-1.5.0/unmarked/R/zzz.R |only unmarked-1.5.0/unmarked/inst/shinyPower |only unmarked-1.5.0/unmarked/man/imputeMissing.Rd |only unmarked-1.5.0/unmarked/man/sight2perpdist.Rd |only unmarked-1.5.0/unmarked/src/hmm.c |only unmarked-1.5.0/unmarked/tests/testthat/test_powerAnalysis_deprecated.R |only unmarked-1.5.0/unmarked/tests/testthat/test_simulate_deprecated.R |only unmarked-1.5.1/unmarked/DESCRIPTION | 25 unmarked-1.5.1/unmarked/MD5 | 235 - unmarked-1.5.1/unmarked/NAMESPACE | 8 unmarked-1.5.1/unmarked/NEWS.md | 10 unmarked-1.5.1/unmarked/R/All_classes.R |only unmarked-1.5.1/unmarked/R/All_generics.R |only unmarked-1.5.1/unmarked/R/IDS.R | 176 unmarked-1.5.1/unmarked/R/RcppExports.R | 36 unmarked-1.5.1/unmarked/R/colext.R | 532 +- unmarked-1.5.1/unmarked/R/distsamp.R | 54 unmarked-1.5.1/unmarked/R/distsampOpen.R | 52 unmarked-1.5.1/unmarked/R/fitted.R | 164 unmarked-1.5.1/unmarked/R/gdistremoval.R | 304 - unmarked-1.5.1/unmarked/R/gdistsamp.R | 72 unmarked-1.5.1/unmarked/R/getDesign.R | 1987 +++------- unmarked-1.5.1/unmarked/R/getP.R | 9 unmarked-1.5.1/unmarked/R/gmultmix.R | 50 unmarked-1.5.1/unmarked/R/goccu.R | 117 unmarked-1.5.1/unmarked/R/gpcount.R | 50 unmarked-1.5.1/unmarked/R/mixedModelTools.R | 25 unmarked-1.5.1/unmarked/R/multinomPois.R | 47 unmarked-1.5.1/unmarked/R/multmixOpen.R | 46 unmarked-1.5.1/unmarked/R/nmixTTD.R | 27 unmarked-1.5.1/unmarked/R/nonparboot.R | 10 unmarked-1.5.1/unmarked/R/occu.R | 45 unmarked-1.5.1/unmarked/R/occuCOP.R | 340 - unmarked-1.5.1/unmarked/R/occuComm.R | 133 unmarked-1.5.1/unmarked/R/occuFP.R | 56 unmarked-1.5.1/unmarked/R/occuMS.R | 9 unmarked-1.5.1/unmarked/R/occuMulti.R | 39 unmarked-1.5.1/unmarked/R/occuPEN.R | 92 unmarked-1.5.1/unmarked/R/occuRN.R | 42 unmarked-1.5.1/unmarked/R/occuTTD.R | 46 unmarked-1.5.1/unmarked/R/parboot.R | 14 unmarked-1.5.1/unmarked/R/pcount.R | 41 unmarked-1.5.1/unmarked/R/pcount.spHDS.R | 33 unmarked-1.5.1/unmarked/R/pcountOpen.R | 52 unmarked-1.5.1/unmarked/R/plotEffects.R | 7 unmarked-1.5.1/unmarked/R/posteriorSamples.R | 11 unmarked-1.5.1/unmarked/R/power.R | 15 unmarked-1.5.1/unmarked/R/predict.R | 560 -- unmarked-1.5.1/unmarked/R/ranef.R | 43 unmarked-1.5.1/unmarked/R/removed_functions.R |only unmarked-1.5.1/unmarked/R/residuals.R | 39 unmarked-1.5.1/unmarked/R/simulate.R | 37 unmarked-1.5.1/unmarked/R/square_brackets.R |only unmarked-1.5.1/unmarked/R/unmarkedCrossVal.R | 32 unmarked-1.5.1/unmarked/R/unmarkedEstimate.R | 48 unmarked-1.5.1/unmarked/R/unmarkedFit.R | 233 - unmarked-1.5.1/unmarked/R/unmarkedFitList.R | 54 unmarked-1.5.1/unmarked/R/unmarkedFrame.R | 667 --- unmarked-1.5.1/unmarked/R/unmarkedLinComb.R | 17 unmarked-1.5.1/unmarked/R/update.R | 63 unmarked-1.5.1/unmarked/R/utils.R | 262 - unmarked-1.5.1/unmarked/build/partial.rdb |binary unmarked-1.5.1/unmarked/build/vignette.rds |binary unmarked-1.5.1/unmarked/inst/doc/colext.Rmd | 108 unmarked-1.5.1/unmarked/inst/doc/colext.html | 116 unmarked-1.5.1/unmarked/inst/doc/contributing_to_unmarked.Rmd | 104 unmarked-1.5.1/unmarked/inst/doc/contributing_to_unmarked.html | 139 unmarked-1.5.1/unmarked/inst/doc/distsamp.html | 140 unmarked-1.5.1/unmarked/inst/doc/occuMulti.html | 58 unmarked-1.5.1/unmarked/inst/doc/simulate.html | 144 unmarked-1.5.1/unmarked/inst/doc/spp-dist.html | 40 unmarked-1.5.1/unmarked/inst/doc/unmarked.R | 28 unmarked-1.5.1/unmarked/inst/doc/unmarked.Rmd | 46 unmarked-1.5.1/unmarked/inst/doc/unmarked.html | 188 unmarked-1.5.1/unmarked/man/distsamp.Rd | 2 unmarked-1.5.1/unmarked/man/extract-methods.Rd | 59 unmarked-1.5.1/unmarked/man/unmarkedFrame-class.Rd | 15 unmarked-1.5.1/unmarked/src/RcppExports.cpp | 183 unmarked-1.5.1/unmarked/src/TMB/tmb_colext.hpp |only unmarked-1.5.1/unmarked/src/TMB/tmb_goccu.hpp | 14 unmarked-1.5.1/unmarked/src/TMB/unmarked_TMBExports.cpp | 3 unmarked-1.5.1/unmarked/src/nll_distsampOpen.cpp | 18 unmarked-1.5.1/unmarked/src/nll_gdistremoval.cpp | 16 unmarked-1.5.1/unmarked/src/nll_gdistsamp.cpp | 14 unmarked-1.5.1/unmarked/src/nll_gmultmix.cpp | 45 unmarked-1.5.1/unmarked/src/nll_gpcount.cpp | 16 unmarked-1.5.1/unmarked/src/nll_multmixOpen.cpp | 18 unmarked-1.5.1/unmarked/src/nll_nmixTTD.cpp | 6 unmarked-1.5.1/unmarked/src/nll_occuCOP.cpp | 4 unmarked-1.5.1/unmarked/src/nll_occuTTD.cpp | 10 unmarked-1.5.1/unmarked/src/nll_pcountOpen.cpp | 20 unmarked-1.5.1/unmarked/tests/testthat/data |only unmarked-1.5.1/unmarked/tests/testthat/test_IDS.R | 209 - 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Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight
important informations (differences from totals, comparisons between lines or
columns, contributions to variance, confidence intervals, odds ratios, etc.).
All functions are pipe-friendly and render data frames which can be easily
manipulated. In the same time, time-taking operations are done with 'data.table'
to go faster with big dataframes. Tables can be exported with formats and colors
to 'Excel', plot and html.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between tabxplor versions 1.3.0 dated 2025-03-09 and 1.3.1 dated 2025-09-26
DESCRIPTION | 8 MD5 | 24 NEWS.md | 7 R/jmvtab.b.R | 428 ++-- R/jmvtab.h.R | 67 R/tab.R | 8 R/tab_classes.R | 12 R/utils.R | 90 README.md | 12 build/vignette.rds |binary inst/doc/tabxplor.html | 5144 ++++++++++++++++++------------------------------- inst/i18n/fr.json | 107 - man/jmvtab.Rd | 23 13 files changed, 2392 insertions(+), 3538 deletions(-)
Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
Author: Sergej Potapov [aut],
Werner Adler [aut],
Matthias Schmid [aut],
Frederic Bertrand [cre, aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between survAUC versions 1.3-0 dated 2024-09-09 and 1.4-0 dated 2025-09-26
survAUC-1.3-0/survAUC/R/BaggC.R |only survAUC-1.3-0/survAUC/R/survAUC_Song_Zhou.R |only survAUC-1.3-0/survAUC/man/AUC.ChamDiao.Rd |only survAUC-1.3-0/survAUC/man/AUC.HungChiang.Rd |only survAUC-1.3-0/survAUC/man/AUC.Song_Zhou.Rd |only survAUC-1.3-0/survAUC/man/AUC.uno.Rd |only survAUC-1.3-0/survAUC/man/IntegratedAUC.Rd |only survAUC-1.3-0/survAUC/man/OXS.Rd |only survAUC-1.3-0/survAUC/man/plot.survAUC.Rd |only survAUC-1.3-0/survAUC/man/schemper.Err.Rd |only survAUC-1.4-0/survAUC/DESCRIPTION | 32 ++- survAUC-1.4-0/survAUC/MD5 | 88 +++++---- survAUC-1.4-0/survAUC/NAMESPACE | 39 ++-- survAUC-1.4-0/survAUC/NEWS.md | 10 + survAUC-1.4-0/survAUC/R/BeggC.R |only survAUC-1.4-0/survAUC/R/IntegratedAUC.R | 66 +++++++ survAUC-1.4-0/survAUC/R/UnoC.R | 63 ++++++ survAUC-1.4-0/survAUC/R/plot.survAUC.R | 61 ++++++ survAUC-1.4-0/survAUC/R/schemper.R | 62 ++++++ survAUC-1.4-0/survAUC/R/survAUC-package.R |only survAUC-1.4-0/survAUC/R/survAUC_ChamDiao.R | 61 ++++++ survAUC-1.4-0/survAUC/R/survAUC_HungChiang.R | 61 ++++++ survAUC-1.4-0/survAUC/R/survAUC_SongZhou.R |only survAUC-1.4-0/survAUC/R/survAUC_Uno.R | 79 ++++++++ survAUC-1.4-0/survAUC/R/surv_measures.R | 199 +++++++++++++++++++++- survAUC-1.4-0/survAUC/R/zzz.R | 15 - survAUC-1.4-0/survAUC/README.md |only survAUC-1.4-0/survAUC/inst |only survAUC-1.4-0/survAUC/man/BeggC.Rd | 62 +++--- survAUC-1.4-0/survAUC/man/GHCI.Rd | 79 ++++---- survAUC-1.4-0/survAUC/man/IntAUC.Rd |only survAUC-1.4-0/survAUC/man/R2_type_Coef.Rd |only survAUC-1.4-0/survAUC/man/UnoC.Rd | 88 +++++---- survAUC-1.4-0/survAUC/man/figures |only survAUC-1.4-0/survAUC/man/plot_survAUC_survErr.Rd |only survAUC-1.4-0/survAUC/man/predErr.Rd | 121 +++++++------ survAUC-1.4-0/survAUC/man/schemper.Rd |only survAUC-1.4-0/survAUC/man/survAUC-package.Rd |only survAUC-1.4-0/survAUC/man/survAUC_ChamDiao.Rd |only survAUC-1.4-0/survAUC/man/survAUC_HungChiang.Rd |only survAUC-1.4-0/survAUC/man/survAUC_SongZhou.Rd |only survAUC-1.4-0/survAUC/man/survAUC_Uno.Rd |only survAUC-1.4-0/survAUC/src/R_init_survAUC.c | 2 survAUC-1.4-0/survAUC/src/survAUC_Cham_Diao.c | 2 survAUC-1.4-0/survAUC/src/survAUC_HZ.c | 2 survAUC-1.4-0/survAUC/src/survAUC_Hung_Chiang.c | 2 survAUC-1.4-0/survAUC/src/survAUC_SongZhou.c | 2 survAUC-1.4-0/survAUC/src/survAUC_UNO.c | 2 survAUC-1.4-0/survAUC/src/surv_measures.c | 2 survAUC-1.4-0/survAUC/src/utils.c | 2 survAUC-1.4-0/survAUC/tests |only 51 files changed, 952 insertions(+), 250 deletions(-)
Title: Testing, Monitoring, and Dating Structural Changes: C++ Version
Description: A fast implementation with additional experimental features for
testing, monitoring and dating structural changes in (linear)
regression models. 'strucchangeRcpp' features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g. cumulative/moving
sum, recursive/moving estimates) and F statistics, respectively.
These methods are described in Zeileis et al. (2002)
<doi:10.18637/jss.v007.i02>.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals,
and their magnitude as well as the model fit can be evaluated
using a variety of statistical measures.
Author: Dainius Masiliunas [aut, cre] ,
Achim Zeileis [aut] ,
Marius Appel [aut],
Friedrich Leisch [aut],
Kurt Hornik [aut],
Christian Kleiber [aut],
Andrei Mirt [ctb] ,
Bruce Hansen [ctb],
Edgar C. Merkle [ctb],
Nikolaus Umlauf [ctb]
Maintainer: Dainius Masiliunas <pastas4@gmail.com>
Diff between strucchangeRcpp versions 1.5-4-1.0.0 dated 2024-10-17 and 1.5-4-1.0.1 dated 2025-09-26
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NEWS | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/strucchange-intro.pdf |binary src/recresid.cpp | 4 ++-- 7 files changed, 20 insertions(+), 14 deletions(-)
More information about strucchangeRcpp at CRAN
Permanent link
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.10 dated 2025-03-29 and 1.2.11 dated 2025-09-26
simStateSpace-1.2.10/simStateSpace/R/simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.10/simStateSpace/R/simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.10/simStateSpace/man/LinSDECov.Rd |only simStateSpace-1.2.10/simStateSpace/man/LinSDEMean.Rd |only simStateSpace-1.2.10/simStateSpace/tests/testthat/Rplots.pdf |only simStateSpace-1.2.10/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov.R |only simStateSpace-1.2.10/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean.R |only simStateSpace-1.2.11/simStateSpace/DESCRIPTION | 12 simStateSpace-1.2.11/simStateSpace/MD5 | 142 - simStateSpace-1.2.11/simStateSpace/NAMESPACE | 22 simStateSpace-1.2.11/simStateSpace/NEWS.md | 12 simStateSpace-1.2.11/simStateSpace/R/RcppExports.R | 582 +++++ simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-cov-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-lin-sde-mean-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-long-dot.R | 35 simStateSpace-1.2.11/simStateSpace/R/simStateSpace-methods-simstatespace.R | 33 simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-cov-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-ssm-mean-y.R |only simStateSpace-1.2.11/simStateSpace/R/simStateSpace-wide-dot.R | 9 simStateSpace-1.2.11/simStateSpace/build/partial.rdb |binary simStateSpace-1.2.11/simStateSpace/man/LinSDE2SSM.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/LinSDECovEta.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDECovY.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDEMeanEta.Rd |only simStateSpace-1.2.11/simStateSpace/man/LinSDEMeanY.Rd |only simStateSpace-1.2.11/simStateSpace/man/ProjectToHurwitz.Rd |only 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simStateSpace-1.2.11/simStateSpace/man/SimSSMLinGrowthIVary.Rd | 42 simStateSpace-1.2.11/simStateSpace/man/SimSSMLinSDEFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMLinSDEIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMOUFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMOUIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMVARFixed.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SimSSMVARIVary.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/SpectralAbscissa.Rd |only simStateSpace-1.2.11/simStateSpace/man/SpectralRadius.Rd |only simStateSpace-1.2.11/simStateSpace/man/TestPhi.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/TestPhiHurwitz.Rd |only simStateSpace-1.2.11/simStateSpace/man/TestStability.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/TestStationarity.Rd | 21 simStateSpace-1.2.11/simStateSpace/man/as.data.frame.simstatespace.Rd | 9 simStateSpace-1.2.11/simStateSpace/man/as.matrix.simstatespace.Rd | 9 simStateSpace-1.2.11/simStateSpace/man/plot.simstatespace.Rd | 18 simStateSpace-1.2.11/simStateSpace/src/Makevars | 2 simStateSpace-1.2.11/simStateSpace/src/Makevars.win | 2 simStateSpace-1.2.11/simStateSpace/src/RcppExports.cpp | 311 ++ simStateSpace-1.2.11/simStateSpace/src/source.cpp | 1122 +++++++++- simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-cov-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-lin-sde-mean-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-project-to-hurwitz.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-project-to-stability.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-alpha-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-beta-n-2.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-beta-n.R | 79 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-cov-diag-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-cov-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-iota-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-nu-n.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-phi-n-2.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-phi-n.R | 62 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-fixed.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-i-vary.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth-i-vary.R | 27 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-growth.R | 24 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-fixed.R | 29 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-lin-sde-i-vary.R | 28 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-fixed.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-ou-i-vary.R | 22 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-fixed.R | 17 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-sim-ssm-var-i-vary.R | 17 simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-spectral-abscissa.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-spectral-radius.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-cov-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-cov-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-mean-eta.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-ssm-mean-y.R |only simStateSpace-1.2.11/simStateSpace/tests/testthat/test-simStateSpace-tests.R | 29 99 files changed, 2926 insertions(+), 205 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.3 dated 2024-09-25 and 1.2.4 dated 2025-09-26
DESCRIPTION | 28 +++---- MD5 | 44 ++++++----- NAMESPACE | 3 NEWS.md | 10 ++ R/export.R | 5 - R/export_methods.R | 6 + R/extensions.R | 6 - R/import.R | 3 R/import_list.R | 21 ++++- R/import_methods.R | 9 ++ R/sysdata.rda |binary R/utils.R | 8 -- README.md | 143 +++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/labelled.html | 22 ++--- inst/doc/rio.html | 94 ++++++++++++++---------- man/export.Rd | 1 man/import.Rd | 1 man/rio.Rd | 1 tests/testdata/example.xlsm |only tests/testthat/test_extensions.R | 21 +++-- tests/testthat/test_format_qs2.R |only tests/testthat/test_format_xls.R | 27 +++++++ tests/testthat/test_import_list.R | 33 ++++++++ 24 files changed, 305 insertions(+), 181 deletions(-)
Title: Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM), Tenenhaus, Esposito Vinzi, Chatelin, Lauro (2005) <doi:10.1016/j.csda.2004.03.005>,
analysis for both metric and non-metric data, as well as REBUS analysis, Esposito Vinzi, Trinchera, Squillacciotti, and Tenenhaus (2008) <doi:10.1002/asmb.728>.
Author: Gaston Sanchez [aut],
Laura Trinchera [aut],
Giorgio Russolillo [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plspm versions 0.5.2 dated 2025-08-18 and 0.6.0 dated 2025-09-26
DESCRIPTION | 38 +++++++------ MD5 | 53 ++++++++++-------- NAMESPACE | 36 ++++++++---- NEWS | 29 +++++++++- R/check_arguments.R | 6 +- R/check_specifications.R | 4 - R/plot.plspm.R | 3 - R/plspm-package.R | 41 +++++++++----- R/plspm.R | 2 R/plspm.groups.R | 2 R/print.rebus.R | 2 R/rebus.test.R | 2 R/summary_plspm.R | 4 - README.md |only build/partial.rdb |only inst/CITATION |only inst/_pkgdown.yml |only inst/doc/plspm_introduction.R | 50 ++++++++++++++++- inst/doc/plspm_introduction.Rnw | 94 +++++++++++++++++++++++++++++++-- inst/doc/plspm_introduction.pdf |binary man/plspm-package.Rd |only man/plspm.Rd | 1 tests/testthat/test-check-blocks.r | 20 +++---- tests/testthat/test-check-data.r | 20 +++---- tests/testthat/test-check-modes.r | 24 +++----- tests/testthat/test-check-path.r | 8 +- tests/testthat/test-check-scheme.r | 38 ++++++------- tests/testthat/test-get-metric.r | 8 +- tests/testthat/test-manifest-scaling.r | 13 ++-- vignettes/plspm_introduction.Rnw | 94 +++++++++++++++++++++++++++++++-- 30 files changed, 426 insertions(+), 166 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.13.2 dated 2025-07-31 and 0.14.0 dated 2025-09-26
DESCRIPTION | 14 MD5 | 138 ++++----- NAMESPACE | 1 NEWS.md | 39 ++ R/insert.hinges.r | 52 +++ R/interpolate.spectrum.r | 64 ++-- R/make-var-labels.R | 11 R/mspct.quantile.r | 23 + R/mspct.row.funs.r | 2 R/rbindspct.r | 46 +-- R/spct-conversion-qty-unit.R | 434 +++++++++++++--------------- R/spct.classes.r | 11 R/spct.clean.r | 13 R/spct.integrate.r | 46 +-- R/spct.irrad.r | 4 R/spct.metadata.r | 440 +++++++++++++++++++---------- R/spct.new.r | 83 +++++ R/spct.normalize.r | 104 +++++- R/spct.peaks.r | 37 +- R/spct.spikes.R | 32 +- R/spct.summaries.r | 57 ++- R/spct.trim.r | 16 - R/spct.utils.r | 42 +- R/trim.waveband.r | 34 +- R/zmspct.classes.R | 57 +++ README.md | 32 +- data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D50.illuminant.spct.rda |binary data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear_body.spct.rda |binary data/cone_fundamentals10.spct.rda |binary data/filter-cps-mspct.rda |binary data/filter-data.rda |binary data/green_leaf.spct.rda |binary data/r4p-pkgs.rda |binary data/response-data.rda |binary data/solutes.rda |binary data/sun.data.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary inst/doc/userguide-0-r4p-introduction.html | 7 inst/doc/userguide-1-radiation.Rmd | 7 inst/doc/userguide-1-radiation.html | 66 +++- man/add_attr2tb.Rd | 23 + man/as.generic_spct.Rd | 10 man/as.response_spct.Rd | 29 + man/check_wl_stepsize.Rd | 8 man/getWhereMeasured.Rd | 41 +- man/interpolate_spct.Rd | 39 +- man/interpolate_spectrum.Rd | 33 +- man/interpolate_wl.Rd | 46 ++- man/normalize.Rd | 47 +-- man/print.generic_spct.Rd | 19 + man/s_quantile.Rd | 11 man/setWhereMeasured.Rd | 77 ++++- man/spct_metadata.Rd | 9 man/thin_wl.Rd | 60 +-- man/trim_waveband.Rd | 10 man/v_replace_hinges.Rd | 38 ++ vignettes/userguide-1-radiation.Rmd | 7 70 files changed, 1590 insertions(+), 829 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.5 dated 2025-08-20 and 11.6 dated 2025-09-26
NNS-11.5/NNS/R/Internal_Functions.R |only NNS-11.6/NNS/DESCRIPTION | 8 NNS-11.6/NNS/MD5 | 147 +- NNS-11.6/NNS/R/ANOVA.R | 208 ++-- NNS-11.6/NNS/R/ARMA.R | 7 NNS-11.6/NNS/R/ARMA_optim.R | 15 NNS-11.6/NNS/R/Boost.R | 392 +++---- NNS-11.6/NNS/R/Central_tendencies.R | 7 NNS-11.6/NNS/R/Copula.R | 38 NNS-11.6/NNS/R/Dependence.R | 28 NNS-11.6/NNS/R/FSD.R | 2 NNS-11.6/NNS/R/NNS_Distance.R | 104 -- NNS-11.6/NNS/R/NNS_Distance_bulk.R |only NNS-11.6/NNS/R/NNS_VAR.R | 239 +++- NNS-11.6/NNS/R/NNS_meboot.R | 300 ++--- NNS-11.6/NNS/R/Normalization.R | 4 NNS-11.6/NNS/R/Partition_Map.R | 129 -- NNS-11.6/NNS/R/RcppExports.R | 68 + NNS-11.6/NNS/R/Regression.R | 134 +- NNS-11.6/NNS/R/SSD.R | 2 NNS-11.6/NNS/R/Seasonality_Test.R | 2 NNS-11.6/NNS/R/Stack.R | 506 ++++++---- NNS-11.6/NNS/R/TSD.R | 2 NNS-11.6/NNS/R/Uni_Causation.R | 10 NNS-11.6/NNS/R/Uni_SD_Routines.R | 6 NNS-11.6/NNS/R/dy_d_wrt.R | 2 NNS-11.6/NNS/R/dy_dx.R | 2 NNS-11.6/NNS/R/gvload.R | 3 NNS-11.6/NNS/README.md | 4 NNS-11.6/NNS/inst/doc/NNSvignette_Classification.R | 139 +- NNS-11.6/NNS/inst/doc/NNSvignette_Classification.Rmd | 21 NNS-11.6/NNS/inst/doc/NNSvignette_Classification.html | 87 - NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.R | 212 +++- NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 153 ++- NNS-11.6/NNS/inst/doc/NNSvignette_Clustering_and_Regression.html | 318 ++++-- NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.R | 3 NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.Rmd | 3 NNS-11.6/NNS/inst/doc/NNSvignette_Comparing_Distributions.html | 31 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.R | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.html | 15 NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.R | 174 +-- NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.Rmd | 48 NNS-11.6/NNS/inst/doc/NNSvignette_Forecasting.html | 109 +- NNS-11.6/NNS/inst/doc/NNSvignette_Overview.R | 77 - NNS-11.6/NNS/inst/doc/NNSvignette_Overview.Rmd | 68 + NNS-11.6/NNS/inst/doc/NNSvignette_Overview.html | 136 +- NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.R | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.Rmd | 5 NNS-11.6/NNS/inst/doc/NNSvignette_Partial_Moments.html | 9 NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.R | 411 ++++---- NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.Rmd | 15 NNS-11.6/NNS/inst/doc/NNSvignette_Sampling.html | 23 NNS-11.6/NNS/man/NNS.boost.Rd | 2 NNS-11.6/NNS/man/NNS.distance.Rd | 2 NNS-11.6/NNS/man/NNS.meboot.Rd | 2 NNS-11.6/NNS/man/NNS.reg.Rd | 372 +++---- NNS-11.6/NNS/man/NNS.stack.Rd | 9 NNS-11.6/NNS/src/NNS_distance.cpp |only NNS-11.6/NNS/src/NNS_part.cpp |only NNS-11.6/NNS/src/RcppExports.cpp | 246 ++++ NNS-11.6/NNS/src/SD.cpp | 43 NNS-11.6/NNS/src/central_tendencies.cpp | 57 - NNS-11.6/NNS/src/fast_lm.cpp | 5 NNS-11.6/NNS/src/internal_functions.cpp |only NNS-11.6/NNS/tests/testthat/Rplots.pdf |binary NNS-11.6/NNS/vignettes/NNSvignette_Classification.Rmd | 21 NNS-11.6/NNS/vignettes/NNSvignette_Clustering_and_Regression.Rmd | 153 ++- NNS-11.6/NNS/vignettes/NNSvignette_Comparing_Distributions.Rmd | 3 NNS-11.6/NNS/vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 5 NNS-11.6/NNS/vignettes/NNSvignette_Forecasting.Rmd | 48 NNS-11.6/NNS/vignettes/NNSvignette_Overview.Rmd | 68 + NNS-11.6/NNS/vignettes/NNSvignette_Partial_Moments.Rmd | 5 NNS-11.6/NNS/vignettes/NNSvignette_Sampling.Rmd | 15 NNS-11.6/NNS/vignettes/images/NNSmc_1_tgt_drift.png |binary NNS-11.6/NNS/vignettes/images/multi_impute.png |only NNS-11.6/NNS/vignettes/images/overview_arma.png |only NNS-11.6/NNS/vignettes/images/overview_reg.png |only NNS-11.6/NNS/vignettes/images/uni_impute.png |only 79 files changed, 3312 insertions(+), 2185 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 3.0.1 dated 2025-08-28 and 3.0.2 dated 2025-09-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 12 ++++++++++++ R/datasetQuery.R | 9 ++++++++- R/stackDataFilesArrow.R | 10 +++++----- README.md | 8 ++++++++ 6 files changed, 42 insertions(+), 15 deletions(-)
Title: A Collection of Graphon Estimation Methods
Description: Provides a not-so-comprehensive list of methods for estimating graphon,
a symmetric measurable function, from a single or multiple of observed networks.
For a detailed introduction on graphon and popular estimation techniques,
see the paper by Orbanz, P. and Roy, D.M.(2014) <doi:10.1109/TPAMI.2014.2334607>.
It also contains several auxiliary functions for generating sample networks
using various network models and graphons.
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between graphon versions 0.3.5 dated 2021-08-13 and 0.3.6 dated 2025-09-26
graphon-0.3.5/graphon/man/graphon-package.Rd |only graphon-0.3.6/graphon/DESCRIPTION | 14 +++++++------- graphon-0.3.6/graphon/MD5 | 11 +++++------ graphon-0.3.6/graphon/R/graphon-package.R | 3 +-- graphon-0.3.6/graphon/R/init.R | 2 +- graphon-0.3.6/graphon/README.md | 4 +--- graphon-0.3.6/graphon/build/partial.rdb |binary 7 files changed, 15 insertions(+), 19 deletions(-)
Title: Causal Effect Identification from Multiple Incomplete Data
Sources
Description: Identification of causal effects from arbitrary observational and
experimental probability distributions via do-calculus and standard
probability manipulations using a search-based algorithm by
Tikka, Hyttinen and Karvanen (2021) <doi:10.18637/jss.v099.i05>.
Allows for the presence of mechanisms related to selection bias
(Bareinboim and Tian, 2015) <doi:10.1609/aaai.v29i1.9679>,
transportability (Bareinboim and Pearl, 2014)
<http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>,
missing data (Mohan, Pearl, and Tian, 2013)
<http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations
of these. Also supports identification in the presence of context-specific
independence (CSI) relations through labeled directed acyclic graphs
(LDAG). For details on CSIs see (Corander et al., 2019)
<doi:10.1016/j.apal.2019.04.004>.
Author: Santtu Tikka [aut, cre] ,
Antti Hyttinen [ctb] ,
Juha Karvanen [ctb]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dosearch versions 1.0.11 dated 2024-07-16 and 1.0.12 dated 2025-09-26
dosearch-1.0.11/dosearch/R/srr-stats-standards.R |only dosearch-1.0.12/dosearch/DESCRIPTION | 15 +++-- dosearch-1.0.12/dosearch/MD5 | 35 ++++++------- dosearch-1.0.12/dosearch/NEWS.md | 4 + dosearch-1.0.12/dosearch/R/dosearch-package.R | 38 --------------- dosearch-1.0.12/dosearch/R/dosearch.R | 33 ------------- dosearch-1.0.12/dosearch/R/internal.R | 13 ++--- dosearch-1.0.12/dosearch/R/internal_dag.R | 6 -- dosearch-1.0.12/dosearch/R/internal_ldag.R | 6 -- dosearch-1.0.12/dosearch/build/vignette.rds |binary dosearch-1.0.12/dosearch/inst/CITATION | 29 +++++++---- dosearch-1.0.12/dosearch/inst/doc/dosearch.R | 12 ++-- dosearch-1.0.12/dosearch/inst/doc/dosearch.Rmd | 2 dosearch-1.0.12/dosearch/inst/doc/dosearch.html | 2 dosearch-1.0.12/dosearch/man/dosearch.Rd | 3 - dosearch-1.0.12/dosearch/tests/testthat.R | 20 ------- dosearch-1.0.12/dosearch/tests/testthat/test-errors.R | 2 dosearch-1.0.12/dosearch/tests/testthat/test-interface.R | 4 - dosearch-1.0.12/dosearch/vignettes/dosearch.Rmd | 2 19 files changed, 69 insertions(+), 157 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.6.2 dated 2025-06-10 and 1.7.0 dated 2025-09-26
DESCRIPTION | 10 - MD5 | 75 ++++---- NAMESPACE | 4 NEWS.md | 10 + R/RcppExports.R | 4 R/ability.R | 4 R/database.R | 12 + R/dexter.R | 2 R/dif.R | 19 ++ R/equating.R | 8 R/fit_enorm.R | 19 +- R/individual_differences.R | 25 -- R/interaction_model.R | 10 - R/latent_cor.R | 260 ++++++++++++++++++++++-------- R/misc.R | 34 +++ R/misc_anon.R | 2 R/oplike.R | 74 ++++---- R/plausible_values.R | 7 R/plots.R | 8 R/suf_stats.R | 19 +- R/theta_functions.R | 2 R/tia.R | 33 ++- build/vignette.rds |binary inst/doc/DIF_vignette.html | 15 - inst/doc/Equating.html | 25 +- inst/doc/Plausible_Values.html | 21 +- inst/doc/Test_Individual_differences.html | 19 +- inst/doc/dexter.html | 85 +++++---- inst/doc/profile-plots.html | 20 +- man/coef.latent_cor.Rd |only man/latent_cor.Rd | 21 +- man/start_new_project_from_oplm.Rd | 12 - man/tia_tables.Rd | 7 src/RcppExports.cpp | 13 - src/ability.cpp | 16 + src/data.cpp | 28 ++- src/pv.cpp | 39 +++- tests/testthat/test_database.R | 1 tests/testthat/test_tia.R | 2 39 files changed, 626 insertions(+), 339 deletions(-)
Title: Spatiotemporal Boundary Detection Model for Areal Unit Data
Description: Implements a spatiotemporal boundary detection model with a dissimilarity
metric for areal data with inference in a Bayesian setting using Markov chain
Monte Carlo (MCMC). The response variable can be modeled as Gaussian (no nugget),
probit or Tobit link and spatial correlation is introduced at each time point
through a conditional autoregressive (CAR) prior. Temporal correlation is introduced
through a hierarchical structure and can be specified as exponential or first-order
autoregressive. Full details of the package can be found in the accompanying vignette.
Furthermore, the details of the package can be found in "Diagnosing Glaucoma
Progression with Visual Field Data Using a Spatiotemporal Boundary Detection Method",
by Berchuck et al (2019) <doi:10.1080/01621459.2018.1537911>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>
Diff between womblR versions 1.0.5 dated 2022-09-05 and 1.0.6 dated 2025-09-26
DESCRIPTION | 16 +- MD5 | 14 - R/womblR-package.R | 3 build/vignette.rds |binary inst/doc/womblR-example.R | 28 +-- inst/doc/womblR-example.html | 313 +++++++++++++++++++++---------------------- man/womblR.Rd | 1 src/MCMC_Samplers.cpp | 19 +- 8 files changed, 203 insertions(+), 191 deletions(-)
Title: Tools to Create Formal Language Parser
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph],
David M. Beazley [aut, cph],
Yasutaka Tanaka [ctb],
Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.7.4 dated 2022-05-08 and 1.7.7 dated 2025-09-26
DESCRIPTION | 8 MD5 | 26 - R/lex.R | 6 R/logger.R | 4 R/yacc.R | 16 build/vignette.rds |binary inst/doc/intro-to-rly.R | 2 inst/doc/intro-to-rly.html | 938 +++++++++++++++++++++++---------------------- man/LRParser.Rd | 2 man/LexToken.Rd | 2 man/Lexer.Rd | 2 man/NullLogger.Rd | 2 man/RlyLogger.Rd | 2 man/YaccProduction.Rd | 2 14 files changed, 522 insertions(+), 490 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] ,
Maximillian H.K. Hesselbarth [ctb] , get_unique_values, and rcpp_get_coma
functions),
Marco Sciaini [ctb] , get_unique_values, and rcpp_get_coma
functions),
Sebastian Hanss [ctb] , get_unique_values, and rcpp_get_coma
funct [...truncated...]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.9.5 dated 2023-11-28 and 0.9.6 dated 2025-09-26
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/coma.html | 7 ++++--- inst/doc/incoma.html | 9 +++++---- inst/doc/wecoma.html | 9 +++++---- src/create_neighborhood.cpp | 5 +++++ src/rcpp_get_wecoma.cpp | 4 ++-- 10 files changed, 41 insertions(+), 28 deletions(-)
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds
for numerical data, with special functions for thresholding images.
Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R
users. See <https://imagej.net/plugins/auto-threshold> and Landini et
al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] ,
Luis Alvarez [ctb] ,
Sergi Padilla-Parra [ctb, ths] ,
Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.4.2 dated 2023-12-13 and 1.4.3 dated 2025-09-26
DESCRIPTION | 24 ++++++----- MD5 | 18 ++++---- NEWS.md | 6 ++ build/vignette.rds |binary inst/doc/finding-thresholds.R | 2 inst/doc/finding-thresholds.Rmd | 2 inst/doc/finding-thresholds.html | 65 +++++++++++++++----------------- inst/doc/thresholding-image-stacks.html | 36 +++++++---------- inst/doc/thresholding-images.html | 24 +++++------ vignettes/finding-thresholds.Rmd | 2 10 files changed, 90 insertions(+), 89 deletions(-)
More information about autothresholdr at CRAN
Permanent link
Title: Post-Processing of Markov Chain Monte Carlo Simulations for
Chronological Modelling
Description: Statistical analysis of archaeological dates and groups of
dates. This package allows to post-process Markov Chain Monte Carlo
(MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>,
'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal'
<https://bcal.shef.ac.uk/>. It provides functions for the study of
rhythms of the long term from the posterior distribution of a series
of dates (tempo and activity plot). It also allows the estimation and
visualization of time ranges from the posterior distribution of groups
of dates (e.g. duration, transition and hiatus between successive
phases) as described in Philippe and Vibet (2020)
<doi:10.18637/jss.v093.c01>.
Author: Anne Philippe [aut, cre] ,
Marie-Anne Vibet [aut] ,
Nicolas Frerebeau [aut] ,
Thomas S. Dye [ctb] ,
Nantes Universite [fnd] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between ArchaeoPhases versions 2.0 dated 2024-06-16 and 2.1.0 dated 2025-09-26
ArchaeoPhases-2.0/ArchaeoPhases/R/reexport.R |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.R |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.Rmd |only ArchaeoPhases-2.0/ArchaeoPhases/inst/doc/bibliography.html |only ArchaeoPhases-2.0/ArchaeoPhases/man/reexports.Rd |only ArchaeoPhases-2.0/ArchaeoPhases/vignettes/bibliography.Rmd |only ArchaeoPhases-2.1.0/ArchaeoPhases/DESCRIPTION | 63 +- ArchaeoPhases-2.1.0/ArchaeoPhases/MD5 | 302 +++++----- ArchaeoPhases-2.1.0/ArchaeoPhases/NAMESPACE | 25 ArchaeoPhases-2.1.0/ArchaeoPhases/NEWS.md | 38 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/AllClasses.R | 66 +- ArchaeoPhases-2.1.0/ArchaeoPhases/R/AllGenerics.R | 105 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/R/ArchaeoPhases-internal.R | 5 ArchaeoPhases-2.1.0/ArchaeoPhases/R/ArchaeoPhases-package.R | 41 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/activity.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/allen-mcmc.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/allen-relations.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/bind.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/R/boundaries.R | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/R/coerce.R | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/depth.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/R/hiatus.R | 31 - ArchaeoPhases-2.1.0/ArchaeoPhases/R/interval.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/R/occurrence.R | 5 ArchaeoPhases-2.1.0/ArchaeoPhases/R/phases.R | 27 ArchaeoPhases-2.1.0/ArchaeoPhases/R/plot.R | 95 --- ArchaeoPhases-2.1.0/ArchaeoPhases/R/read.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/show.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/R/summary.R | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/R/transition.R | 18 ArchaeoPhases-2.1.0/ArchaeoPhases/R/validate.R | 25 ArchaeoPhases-2.1.0/ArchaeoPhases/R/zzz.R | 7 ArchaeoPhases-2.1.0/ArchaeoPhases/README.md | 174 +++++ ArchaeoPhases-2.1.0/ArchaeoPhases/build/partial.rdb |binary ArchaeoPhases-2.1.0/ArchaeoPhases/build/vignette.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/CITATION | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/ArchaeoPhases.Rmd | 76 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/ArchaeoPhases.html | 77 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/allen.Rmd | 85 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/allen.html | 101 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/import.Rmd | 59 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/doc/import.html | 104 +-- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-phases.R | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_bcal.R | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_chronomodel.R | 12 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-read_oxcal.R | 7 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/examples/ex-tempo.R | 1 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/po |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/events_hiatus.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/occurrence.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_boundaries.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_hiatus.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_snaps/phases_transition.rds |binary ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_activity.svg | 28 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_cred.svg | 60 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_decr.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_hdr.svg | 66 +- ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_incr.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_event_inter.svg | 36 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_occurrence.svg | 48 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_decr.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_hiatus.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_inc.svg | 52 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_succession.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_phase_transition.svg | 56 + ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_tempo_cred.svg | 34 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/_tinysnapshot/plot_tempo_gauss.svg | 34 - ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/helpers.R |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_activity.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_allen.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_boundaries.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_events.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_hiatus.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_interval.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_occurrence.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_older.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_phases.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_read.R |only ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_summary.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_tempo.R | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/inst/tinytest/test_transition.R | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/man/ActivityEvents-class.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/ArchaeoPhases-package.Rd | 48 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/CumulativeEvents-class.Rd | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/man/EventsMCMC-class.Rd | 2 ArchaeoPhases-2.1.0/ArchaeoPhases/man/MCMC-class.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/OccurrenceEvents-class.Rd | 20 ArchaeoPhases-2.1.0/ArchaeoPhases/man/PhasesMCMC-class.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/TimeRange-class.Rd | 21 ArchaeoPhases-2.1.0/ArchaeoPhases/man/activity.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_analyze.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_analyze_relations.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_complement.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_composition.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_converse.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_count.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_illustrate.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_illustrate_relations.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_intersect.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_joint_concurrency.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_observe.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_observe_frequency.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_plot.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relate_intervals.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relation.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_relation_code.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_table.Rd |only ArchaeoPhases-2.1.0/ArchaeoPhases/man/allen_union.Rd | 3 ArchaeoPhases-2.1.0/ArchaeoPhases/man/as_events.Rd | 4 ArchaeoPhases-2.1.0/ArchaeoPhases/man/as_phases.Rd | 18 ArchaeoPhases-2.1.0/ArchaeoPhases/man/bury.Rd | 14 ArchaeoPhases-2.1.0/ArchaeoPhases/man/data.frame.Rd | 12 ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-events-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-events-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-phases-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-succession-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-succession-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-tempo-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/figures/README-tempo-plot-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/man/interval_credible.Rd | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/man/interval_hdr.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/man/occurrence.Rd | 50 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/phases.Rd | 10 ArchaeoPhases-2.1.0/ArchaeoPhases/man/plot_events.Rd | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/man/plot_phases.Rd | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_bcal.Rd | 32 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_chronomodel.Rd | 49 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/read_oxcal.Rd | 35 - ArchaeoPhases-2.1.0/ArchaeoPhases/man/summary.Rd | 8 ArchaeoPhases-2.1.0/ArchaeoPhases/man/tempo.Rd | 11 ArchaeoPhases-2.1.0/ArchaeoPhases/po |only ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/ArchaeoPhases.Rmd | 76 +- ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/ArchaeoPhases.Rmd.orig | 6 ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/allen.Rmd | 85 +- ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/allen.Rmd.orig | 54 - ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/activity-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/analyze_stratigraphy-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/basic_relations-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/bcal-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-autocor-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-autocor-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/coda-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/event-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/identity_relation-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/illustrate_stratigraphy-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/occurrence-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/oxcal-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/phases-1.png |only ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/phases-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-chronomodel-events-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-chronomodel-phases-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/read-oxcal-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/relation_and_converse-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/relation_and_converse-2.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/succession-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/figures/tempo-plot-1.png |binary ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/import.Rmd | 59 + ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/import.Rmd.orig | 43 - ArchaeoPhases-2.1.0/ArchaeoPhases/vignettes/precompile.R | 4 160 files changed, 1642 insertions(+), 1515 deletions(-)
Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] ,
Remi Barillec [aut],
Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>
Diff between psgp versions 0.3-23 dated 2025-07-17 and 0.3-24 dated 2025-09-26
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/PSGP.cpp | 12 ++++-------- 4 files changed, 14 insertions(+), 15 deletions(-)
Title: A Soil Survey Toolkit
Description: A collection of data processing, visualization, and export functions to support soil survey operations. Many of the functions build on the `SoilProfileCollection` S4 class provided by the aqp package, extending baseline visualization to more elaborate depictions in the context of spatial and taxonomic data. While this package is primarily developed by and for the USDA-NRCS, in support of the National Cooperative Soil Survey, the authors strive for generalization sufficient to support any soil survey operation. Many of the included functions are used by the SoilWeb suite of websites and movile applications. These functions are provided here, with additional documentation, to enable others to replicate high quality versions of these figures for their own purposes.
Author: Dylan Beaudette [cre, aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 2.3.3 dated 2025-04-17 and 2.4 dated 2025-09-26
DESCRIPTION | 6 - MD5 | 34 +++--- NAMESPACE | 2 NEWS.md | 12 ++ R/PLSS2LL.R | 176 +++++++++++++++++++++------------ R/huePositionPlot.R | 20 +-- R/samplingStability.R | 4 R/vizAnnualClimate.R | 4 build/vignette.rds |binary data/OSDexamples.rda |binary data/table5.2.rda |binary man/PLSS2LL.Rd | 10 - man/formatPLSS.Rd | 42 ++++--- man/huePositionPlot.Rd | 20 +-- man/vizAnnualClimate.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-PLSS2LL.R | 66 ++++++++++++ tests/testthat/test-vizAnnualClimate.R | 5 18 files changed, 274 insertions(+), 131 deletions(-)
Title: Analysis of Eye Data
Description: There is no ophthalmic researcher who has not had headaches from
the handling of visual acuity entries. Different notations, untidy entries.
This shall now be a matter of the past. Eye makes it as easy as pie to work
with VA data - easy cleaning, easy conversion between
Snellen, logMAR, ETDRS letters, and qualitative visual acuity
shall never pester you again. The eye
package automates the pesky task to count number of patients and eyes,
and can help to clean data with easy re-coding for right and left eyes.
It also contains functions to help reshaping eye side specific variables
between wide and long format. Visual acuity conversion is based on
Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>,
Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>,
Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and
Bach (2007) <https://michaelbach.de/sci/acuity.html>.
Author: Tjebo Heeren [aut, cre] ,
Antoine Fabri [ctb]
Maintainer: Tjebo Heeren <tjebo@gmx.de>
Diff between eye versions 1.2.1 dated 2021-09-04 and 1.3.0 dated 2025-09-26
eye-1.2.1/eye/build/partial.rdb |only eye-1.3.0/eye/DESCRIPTION | 27 eye-1.3.0/eye/MD5 | 68 - eye-1.3.0/eye/NAMESPACE | 6 eye-1.3.0/eye/NEWS.md | 33 eye-1.3.0/eye/R/eye.R | 2 eye-1.3.0/eye/R/reveal.R | 6 eye-1.3.0/eye/R/str_helper.R | 26 eye-1.3.0/eye/R/va.R | 145 +- eye-1.3.0/eye/R/va_cleaner.R | 64 - eye-1.3.0/eye/R/va_methods.R | 15 eye-1.3.0/eye/README.md | 215 ++- eye-1.3.0/eye/build/vignette.rds |binary eye-1.3.0/eye/inst/CITATION | 6 eye-1.3.0/eye/inst/doc/eye.R | 20 eye-1.3.0/eye/inst/doc/eye.Rmd | 27 eye-1.3.0/eye/inst/doc/eye.html | 1573 ++++++++++++++++++---------- eye-1.3.0/eye/man/VAwrapper.Rd | 2 eye-1.3.0/eye/man/clean_va.Rd | 7 eye-1.3.0/eye/man/convertQuali.Rd | 18 eye-1.3.0/eye/man/eye.Rd | 6 eye-1.3.0/eye/man/eye_codes.Rd | 2 eye-1.3.0/eye/man/plausibility_methods.Rd | 2 eye-1.3.0/eye/man/reveal_methods.Rd | 5 eye-1.3.0/eye/man/reveal_split.Rd | 4 eye-1.3.0/eye/man/set_eye_strings.Rd | 23 eye-1.3.0/eye/man/snellen_steps.Rd | 2 eye-1.3.0/eye/man/va.Rd | 80 - eye-1.3.0/eye/man/va_methods.Rd | 2 eye-1.3.0/eye/man/va_mixed.Rd | 25 eye-1.3.0/eye/man/which_va.Rd | 4 eye-1.3.0/eye/tests/testthat/test-eyes.R | 1 eye-1.3.0/eye/tests/testthat/test-reveal.R | 2 eye-1.3.0/eye/tests/testthat/test-va.R | 54 eye-1.3.0/eye/tests/testthat/test_cleanVA.r |only eye-1.3.0/eye/vignettes/eye.Rmd | 27 36 files changed, 1671 insertions(+), 828 deletions(-)
Title: 'rbi' Helper Functions
Description: Contains a collection of helper functions to use with 'rbi', the R
interface to 'LibBi', described in
Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to
adapt the proposal distribution and number of particles in
particle Markov-Chain Monte Carlo, as well as calculating the
Deviance Information Criterion (DIC) and converting between times in 'LibBi'
results and R time/dates.
Author: Sebastian Funk [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi.helpers versions 0.4.0 dated 2023-08-24 and 0.4.1 dated 2025-09-26
DESCRIPTION | 20 +++++++--- MD5 | 38 ++++++++++---------- NEWS.md | 4 ++ R/acceptance_rate.R | 6 +-- R/adapt_particles.R | 6 +-- R/adapt_proposal.R | 11 +++-- R/get_mvn_params.r | 4 +- R/times.r | 10 ++--- R/update_proposal.r | 6 +-- build/vignette.rds |binary inst/doc/rbi.helpers.R | 76 ++++++++++++++++++++--------------------- inst/doc/rbi.helpers.html | 1 man/acceptance_rate.Rd | 4 +- man/adapt_particles.Rd | 6 +-- man/adapt_proposal.Rd | 6 +-- man/get_mvn_params.Rd | 4 +- man/numeric_to_time.Rd | 2 - man/update_proposal.Rd | 4 +- tests/testthat/test-adapt.r | 4 -- tests/testthat/test-proposal.r | 2 - 20 files changed, 111 insertions(+), 103 deletions(-)