Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] ,
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-14 dated 2025-04-10 and 1.8-15 dated 2025-12-15
DESCRIPTION | 11 ++++++----- MD5 | 31 ++++++++++++++++--------------- NEWS | 6 ++++++ R/na.fill.R | 4 ++-- build/partial.rdb |only build/vignette.rds |binary inst/doc/zoo-design.Rnw | 4 ++-- inst/doc/zoo-design.pdf |binary inst/doc/zoo-faq.Rnw | 4 ++-- inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.pdf |binary inst/doc/zoo.pdf |binary man/zoo.Rd | 2 +- vignettes/zoo-design.Rnw | 4 ++-- vignettes/zoo-faq.Rnw | 4 ++-- vignettes/zoo.bib | 16 ++++++++-------- 17 files changed, 47 insertions(+), 39 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.3-1 dated 2025-12-04 and 1.3-2 dated 2025-12-15
tram-1.3-1/tram/inst/npnsimulations |only tram-1.3-2/tram/DESCRIPTION | 8 ++--- tram-1.3-2/tram/MD5 | 47 ++++++++++++++++----------------- tram-1.3-2/tram/R/mmlt.R | 2 - tram-1.3-2/tram/inst/NEWS.Rd | 6 ++++ tram-1.3-2/tram/inst/doc/NAMI.pdf |binary tram-1.3-2/tram/inst/doc/mtram.pdf |binary tram-1.3-2/tram/inst/doc/survtram.pdf |binary tram-1.3-2/tram/inst/doc/tram.pdf |binary tram-1.3-2/tram/inst/npn_empeval |only tram-1.3-2/tram/vignettes/mlt.bib | 14 +++++---- tram-1.3-2/tram/vignettes/survtram.bib | 4 +- 12 files changed, 44 insertions(+), 37 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.18 dated 2025-10-13 and 1.9.19 dated 2025-12-15
DESCRIPTION | 8 - MD5 | 20 +-- NEWS | 14 ++ inst/include/TMBad/TMBad.cpp | 96 ++++++++++++---- inst/include/TMBad/TMBad.hpp | 9 + inst/include/TMBad/checkpoint.hpp | 13 +- inst/include/TMBad/compression.hpp | 15 +- inst/include/TMBad/global.hpp | 102 +++++++++++------ inst/include/TMBad/vectorize.hpp | 10 + inst/include/atomic_math.hpp | 12 +- inst/include/tmbutils/newton.hpp | 216 +++++++++++++++++++++++++++++++++---- 11 files changed, 405 insertions(+), 110 deletions(-)
Title: Visualising How Nonlinear Dimension Reduction Warps Your Data
Description: To construct a model in 2-D space from 2-D nonlinear
dimension reduction data and then lift it to the high-dimensional
space. Additionally, provides tools to visualise the model overlay the
data in 2-D and high-dimensional space. Furthermore, provides
summaries and diagnostics to evaluate the nonlinear dimension
reduction layout.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between quollr versions 1.0.1 dated 2025-11-11 and 1.0.4 dated 2025-12-15
quollr-1.0.1/quollr/vignettes/quollr7bestfit_files |only quollr-1.0.4/quollr/DESCRIPTION | 8 quollr-1.0.4/quollr/MD5 | 55 - quollr-1.0.4/quollr/NAMESPACE | 3 quollr-1.0.4/quollr/NEWS.md | 2 quollr-1.0.4/quollr/R/2d.R | 3 quollr-1.0.4/quollr/R/link_plots.R | 236 +++-- quollr-1.0.4/quollr/README.md | 14 quollr-1.0.4/quollr/build/vignette.rds |binary quollr-1.0.4/quollr/inst/doc/quollr1quickstart.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr1quickstart.html | 8 quollr-1.0.4/quollr/inst/doc/quollr2dataprocessing.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr3hexbin.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr4algo.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr4algo.html | 329 ++----- quollr-1.0.4/quollr/inst/doc/quollr5summary.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr6bestbinwidth.Rmd | 4 quollr-1.0.4/quollr/inst/doc/quollr8linkeddetourr.R |only quollr-1.0.4/quollr/inst/doc/quollr8linkeddetourr.Rmd |only quollr-1.0.4/quollr/inst/doc/quollr8linkeddetourr.html |only quollr-1.0.4/quollr/tests/testthat/_snaps/2d.md | 4 quollr-1.0.4/quollr/tests/testthat/_snaps/geom_trimesh/geom-hexgrid-basic-with-all-bin-centroids.svg | 418 +++++----- quollr-1.0.4/quollr/tests/testthat/_snaps/model.md | 30 quollr-1.0.4/quollr/tests/testthat/test-link_plots.R | 12 quollr-1.0.4/quollr/vignettes/quollr1quickstart.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr2dataprocessing.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr3hexbin.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr4algo.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr5summary.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr6bestbinwidth.Rmd | 4 quollr-1.0.4/quollr/vignettes/quollr8linkeddetourr.Rmd |only 31 files changed, 597 insertions(+), 573 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.2.0 dated 2025-10-09 and 1.2.1 dated 2025-12-15
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/arguments.R | 3 +++ R/file_loaders.R | 5 +++-- R/file_openers.R | 4 ++-- R/lamindb.R | 2 +- R/temporary-instance.R | 2 +- build/vignette.rds |binary 8 files changed, 20 insertions(+), 16 deletions(-)
Title: Define and Enforce Contracts for Dataframes as Function
Parameters
Description: A dataframe validation framework for package builders who use
dataframes as function parameters. It performs checks on column names, coerces
data-types, and checks grouping to make sure user inputs conform to a
specification provided by the package author. It provides a mechanism for
package authors to automatically document supported dataframe inputs and
selectively dispatch to functions depending on the format of a dataframe much
like S3 does for classes. It also contains some developer tools to make
working with and documenting dataframe specifications easier. It helps package
developers to improve their documentation and simplifies parameter validation
where dataframes are used as function parameters.
Author: Robert Challen [aut, cre, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between interfacer versions 0.3.3 dated 2025-02-03 and 0.4.0 dated 2025-12-15
DESCRIPTION | 15 MD5 | 104 +++-- NAMESPACE | 7 NEWS.md | 37 + R/devtools.R | 645 +++++++++++++++++++++++++-------- R/globals.R | 7 R/idispatch.R | 196 +++++++--- R/iface-class.R | 427 ++++++++++++++------- R/igroup-process.R | 309 ++++++++++----- R/interfacer-package.R |only R/interfacer.R | 530 ++++++++++++++++++--------- R/utils-dataframe.R | 11 R/utils-functions.R | 145 ++++++- R/zz-demo-functions.R |only README.md | 4 build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/devtools.R | 111 ++--- inst/doc/devtools.Rmd | 29 - inst/doc/devtools.html | 41 +- inst/doc/dispatch.R | 151 ++----- inst/doc/dispatch.Rmd | 194 +++------ inst/doc/dispatch.html | 273 +++++-------- inst/doc/interfacer.R | 25 - inst/doc/interfacer.Rmd | 22 - inst/doc/interfacer.html | 44 +- inst/doc/nesting.html | 2 man/as.list.iface.Rd | 2 man/demo_idispatch.Rd |only man/demo_iparam_tag.Rd |only man/demo_ireturn_tag.Rd |only man/dot-should_run_checks.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/logo.svg | 54 -- man/format.iface.Rd | 2 man/get_iface.Rd |only man/iconvert.Rd | 4 man/idispatch.Rd | 26 - man/iface.Rd | 10 man/igroup_process.Rd | 95 +++- man/imissing.Rd |only man/interfacer-package.Rd |only man/ireturn.Rd | 31 + man/itest.Rd | 10 man/knit_print.iface.Rd | 2 man/print.iface.Rd | 2 man/roxy_tag_parse.roxy_tag_ireturn.Rd |only man/roxy_tag_rd.roxy_tag_iparam.Rd | 6 man/roxy_tag_rd.roxy_tag_ireturn.Rd |only man/use_dataframe.Rd | 8 man/use_iface.Rd | 2 tests/testthat/helper-data.R | 46 +- tests/testthat/test-idispatch.R | 79 +++- tests/testthat/test-roxygen.R | 120 +++++- tests/testthat/test-should-run.R |only vignettes/devtools.Rmd | 29 - vignettes/dispatch.Rmd | 194 +++------ vignettes/interfacer.Rmd | 22 - 61 files changed, 2596 insertions(+), 1480 deletions(-)
Title: 'DataSHIELD' 'Tidyverse' Clientside Package
Description: Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, 'DataSHIELD' contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the clientside package which should be installed locally, and is used in conjuncture with the serverside package 'dsTidyverse' which is installed on the remote server holding the data. For more information, see <https://tidyverse.org/> and <https://datashield.org/>.
Author: Tim Cadman [aut, cre] ,
Mariska Slofstra [aut] ,
Stuart Wheater [aut],
Demetris Avraam [aut]
Maintainer: Tim Cadman <t.j.cadman@umcg.nl>
Diff between dsTidyverseClient versions 1.0.2 dated 2025-02-27 and 1.0.3 dated 2025-12-15
DESCRIPTION | 14 MD5 | 16 - README.md | 26 - inst/doc/dstidyverse.Rmd | 127 ++------ inst/doc/dstidyverse.html | 606 ++++++++++++++++++++--------------------- tests/testthat/test-arrange.R | 2 vignettes/dstidyverse.Rmd | 127 ++------ vignettes/dstidyverse.Rmd.orig | 2 vignettes/pre-render.R | 3 9 files changed, 389 insertions(+), 534 deletions(-)
More information about dsTidyverseClient at CRAN
Permanent link
Title: Creates Define XML Documents
Description: Creates 'define.xml' documents used for regulatory
submissions based on spreadsheet metadata. Can also help
create metadata and generate HTML data explorer.
Author: David Bosak [aut, cre],
Aheer Alvi [aut],
Jonathan Stallings [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between defineR versions 0.0.4 dated 2022-09-20 and 0.0.5 dated 2025-12-15
DESCRIPTION | 12 MD5 | 54 - NEWS.md | 5 R/defineR.R | 5 R/metadata.R | 12 R/write.R | 2 README.md | 5 build/vignette.rds |binary inst/doc/defineR-faq.Rmd | 10 inst/doc/defineR-faq.html | 171 ++--- inst/doc/defineR.R | 2 inst/doc/defineR.Rmd | 15 inst/doc/defineR.html | 191 +++--- man/defineR.Rd | 25 man/write_define.Rd | 2 man/write_metadata.Rd | 2 tests/testthat/data/SDTM_METADATA_JS2.xlsx |only tests/testthat/metadata/demo/SDTM_METADATA.xlsx |binary tests/testthat/metadata/demo/SDTM_METADATA3.xlsx |only tests/testthat/output/check.adam.pdf |only tests/testthat/output/check.sdtm.pdf |only tests/testthat/output/define.adam.html |only tests/testthat/output/define.adam.xml | 4 tests/testthat/output/define.sdtm.html |only tests/testthat/output/define.sdtm.xml | 4 tests/testthat/output/define.sdtm2.html |only tests/testthat/output/define.sdtm2.xml |only tests/testthat/test-checks.R | 2 tests/testthat/test-metadata.R | 5 tests/testthat/test-write.R | 718 ++++++++++++++--------- vignettes/defineR-faq.Rmd | 10 vignettes/defineR.Rmd | 15 32 files changed, 776 insertions(+), 495 deletions(-)
Title: Pacote Para Analise De Experimentos Com Graficos De Superficie
Resposta
Description: Pacote para a analise de experimentos havendo duas variaveis
explicativas quantitativas e uma variavel dependente quantitativa. Os
experimentos podem ser sem repeticoes ou com delineamento estatistico.
Sao ajustados 12 modelos de regressao multipla e plotados graficos de
superficie resposta (Hair JF, 2016) <ISBN:13:978-0138132637>.(Package
for the analysis of experiments having two explanatory quantitative
variables and one quantitative dependent variable. The experiments can
be without repetitions or with a statistical design. Twelve multiple
regression models are fitted and response surface graphs are plotted
(Hair JF, 2016) <ISBN:13:978-0138132637>).
Author: Alcinei Mistico Azevedo [aut, cre]
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>
Diff between ExpAnalysis3d versions 0.1.2 dated 2023-09-25 and 0.1.3 dated 2025-12-15
DESCRIPTION | 14 ++-- MD5 | 10 +-- NEWS.md | 4 + R/AjustarRegressao.R | 6 +- R/ExpAnalysis3d-package.R | 9 ++- man/ExpAnalysis3d-package.Rd | 123 +++++++++++++++++++++---------------------- 6 files changed, 87 insertions(+), 79 deletions(-)
Title: Collection of Data Structures
Description: A collection of functions to generate a large variety of
structures in high dimensions. These data structures are useful for
testing, validating, and improving algorithms used in dimensionality
reduction, clustering, machine learning, and visualization.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between cardinalR versions 1.0.1 dated 2025-11-17 and 1.0.4 dated 2025-12-15
cardinalR-1.0.1/cardinalR/R/three_clusters.R |only cardinalR-1.0.1/cardinalR/man/make_three_clust_01.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_02.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_03.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_04.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_05.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_06.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_07.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_08.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_09.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_10.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_11.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_12.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_13.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_14.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_15.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_16.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_17.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_18.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_19.Rd |only cardinalR-1.0.1/cardinalR/man/make_three_clust_20.Rd |only cardinalR-1.0.4/cardinalR/DESCRIPTION | 6 cardinalR-1.0.4/cardinalR/MD5 | 66 - cardinalR-1.0.4/cardinalR/NAMESPACE | 20 cardinalR-1.0.4/cardinalR/NEWS.md | 2 cardinalR-1.0.4/cardinalR/R/cone.R | 2 cardinalR-1.0.4/cardinalR/R/data.R | 120 +++ cardinalR-1.0.4/cardinalR/R/sphere.R | 34 cardinalR-1.0.4/cardinalR/R/util.R | 10 cardinalR-1.0.4/cardinalR/README.md | 21 cardinalR-1.0.4/cardinalR/data/three_clust_01.rda |only cardinalR-1.0.4/cardinalR/data/three_clust_02.rda |only cardinalR-1.0.4/cardinalR/data/three_clust_03.rda |only cardinalR-1.0.4/cardinalR/data/three_clust_04.rda |only cardinalR-1.0.4/cardinalR/data/three_clust_05.rda |only cardinalR-1.0.4/cardinalR/inst/doc/cardinalR01main_function.html | 321 +++------ cardinalR-1.0.4/cardinalR/inst/doc/cardinalR02examples.html | 353 +++------- cardinalR-1.0.4/cardinalR/inst/doc/cardinalR03additionalfun.html | 74 +- cardinalR-1.0.4/cardinalR/inst/scripts/three_clusters.R |only cardinalR-1.0.4/cardinalR/man/figures/README-unnamed-chunk-6-1.png |binary cardinalR-1.0.4/cardinalR/man/gen_clusteredspheres.Rd | 19 cardinalR-1.0.4/cardinalR/man/gen_cone.Rd | 2 cardinalR-1.0.4/cardinalR/man/gen_hole.Rd | 2 cardinalR-1.0.4/cardinalR/man/normalize_data.Rd | 2 cardinalR-1.0.4/cardinalR/man/three_clust_01.Rd |only cardinalR-1.0.4/cardinalR/man/three_clust_02.Rd |only cardinalR-1.0.4/cardinalR/man/three_clust_03.Rd |only cardinalR-1.0.4/cardinalR/man/three_clust_04.Rd |only cardinalR-1.0.4/cardinalR/man/three_clust_05.Rd |only cardinalR-1.0.4/cardinalR/tests/testthat/test-sphere.R | 16 50 files changed, 501 insertions(+), 569 deletions(-)
Title: Bootstrap Inference for Multiple Imputation
Description: Bootstraps and imputes incomplete datasets. Then performs inference on estimates obtained from analysing the imputed datasets as proposed by von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>.
Author: Jonathan Bartlett [aut, cre]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between bootImpute versions 1.2.2 dated 2025-03-25 and 1.3.0 dated 2025-12-15
DESCRIPTION | 8 +- MD5 | 22 +++---- NEWS.md | 3 + R/bootImpute.R | 31 ++++++++-- R/bootMice.R | 7 +- R/bootSmcfcs.R | 7 +- build/partial.rdb |binary man/bootImpute.Rd | 3 + man/bootMice.Rd | 12 +++- man/bootSmcfcs.Rd | 12 +++- tests/testthat/test_bootImpute.r | 115 +++++++++++++++++++++++++++++++++++++++ tests/testthat/test_parallel.R | 29 +++++++++ 12 files changed, 222 insertions(+), 27 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface
for conducting a wide range of factor analysis procedures. 'FAfA'
(Factor Analysis for All) guides users through data uploading,
assumption checking (descriptives, collinearity, multivariate
normality, outliers), data wrangling (variable exclusion, data
splitting), factor retention analysis (e.g., Parallel Analysis, Hull
method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model
testing, Reliability Analysis (e.g., Cronbach's Alpha, McDonald's
Omega), Measurement Invariance testing across groups, and item
weighting techniques. The application leverages established R packages
such as 'lavaan' and 'psych' to perform these analyses, offering an
accessible platform for researchers and students. Results are
presented in user-friendly tables and plots, with options for
downloading outputs.
Author: Abdullah Faruk KILIC [aut, cre],
Ahmet Caliskan [aut]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 0.4 dated 2025-12-06 and 0.5 dated 2025-12-15
DESCRIPTION | 63 ++-- LICENSE |only MD5 | 82 +++-- NAMESPACE | 44 +-- NEWS.md | 14 - R/app_server.R | 211 +++------------ R/app_ui.R | 227 +++++++++++----- R/mod_about_server.r | 225 ++++++++-------- R/mod_about_ui.r | 126 ++++----- R/mod_assumptions_server.r | 264 +++--------------- R/mod_assumptions_ui.R | 133 ++------- R/mod_cfa_server.r | 544 +++++++++++++++----------------------- R/mod_cfa_ui.r | 288 ++++++++++---------- R/mod_data_selection_server.r | 249 +++++------------ R/mod_data_selection_ui.r | 176 +++++------- R/mod_efa_server.r | 574 +++++++++++------------------------------ R/mod_efa_ui.r | 337 ++++-------------------- R/mod_ega_server.r | 350 +++++++++++-------------- R/mod_ega_ui.r | 119 +------- R/mod_inv_server.r | 492 ++++++++--------------------------- R/mod_inv_ui.R | 191 +++++-------- R/mod_item_weighting_server.r | 116 ++------ R/mod_item_weighting_ui.r | 59 ---- R/mod_itemrest_server.r |only R/mod_itemrest_ui.r |only R/mod_missing_server.r |only R/mod_missing_ui.r |only R/mod_reliability_server.r | 191 ++++--------- R/mod_reliability_ui.r | 154 +++-------- R/mod_wrangling_server.r | 419 +++++------------------------ R/mod_wrangling_ui.r | 165 +++-------- R/utils.r | 49 +-- README.md |only inst/WORDLIST | 6 inst/app/www/favicon.ico |binary inst/golem-config.yml | 2 man/about_server.Rd |only man/assumptions_server.Rd |only man/cfa_server.Rd |only man/cfa_ui.Rd |only man/data_selection_server.Rd |only man/efa_server_analysis.Rd |only man/efa_server_fac_ret.Rd |only man/efa_server_report.Rd |only man/figures |only man/inv_server.Rd |only man/item_weighting_server.Rd |only man/mod_itemrest_server.Rd |only man/mod_itemrest_ui.Rd |only man/mod_missing_server.Rd |only man/mod_missing_ui.Rd |only man/op_null_or.Rd |only man/reliability_server.Rd |only man/wrangling_server_ex_var.Rd |only 54 files changed, 2042 insertions(+), 3828 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-02 1.0.4
2024-01-09 1.0.3
2023-09-27 1.0.2
2023-09-14 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-29 0.1.5
2018-01-04 0.1.4
2015-10-31 0.1.3
2015-06-24 0.1.2
2015-06-22 0.1
Title: Analysis of Sex Differences in Omics Data for Complex Diseases
Description: Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.
Author: Enrico Glaab [aut, cre],
Sophie Le Bars [aut],
Mohamed Soudy [aut],
Murodzhon Akhmedov [cph]
Maintainer: Enrico Glaab <enrico.glaab@uni.lu>
Diff between XYomics versions 0.1.1 dated 2025-11-13 and 0.1.2 dated 2025-12-15
DESCRIPTION | 6 MD5 | 36 - R/RcppExports.R | 42 - R/ppi_analysis_sc.R | 639 ++++++++++----------- R/sex_interaction_analysis_sc.R | 2 inst/doc/XYomics_bulk_example.R | 2 inst/doc/XYomics_bulk_example.Rmd | 613 ++++++++++---------- inst/doc/XYomics_bulk_example.html | 504 +++++++---------- inst/doc/XYomics_sc_example.R | 2 inst/doc/XYomics_sc_example.Rmd | 1 inst/doc/XYomics_sc_example.html | 614 +++++++++----------- inst/extdata/Template_report.Rmd | 647 ++++++++++----------- inst/extdata/Template_report_bulk.Rmd | 441 +++++++------- inst/extdata/Template_report_hormonal_network.Rmd | 649 ++++++++++------------ man/XYomics-package.Rd | 2 man/call_sr.Rd | 3 man/construct_ppi_pcsf.Rd | 2 vignettes/XYomics_bulk_example.Rmd | 613 ++++++++++---------- vignettes/XYomics_sc_example.Rmd | 1 19 files changed, 2337 insertions(+), 2482 deletions(-)
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.21 dated 2025-01-14 and 1.0.23 dated 2025-12-15
pmparser-1.0.21/pmparser/tests/testthat/pubmed_sample/open_citation_collection.zip |only pmparser-1.0.23/pmparser/DESCRIPTION | 8 ++--- pmparser-1.0.23/pmparser/MD5 | 16 +++++----- pmparser-1.0.23/pmparser/NEWS.md | 7 ++++ pmparser-1.0.23/pmparser/R/get_citation.R | 4 +- pmparser-1.0.23/pmparser/R/parse_element.R | 3 + pmparser-1.0.23/pmparser/build/vignette.rds |binary pmparser-1.0.23/pmparser/man/getCitation.Rd | 2 - pmparser-1.0.23/pmparser/tests/testthat/pubmed_sample/open_citation_collection.csv |only pmparser-1.0.23/pmparser/tests/testthat/test_get_citation.R | 5 +-- 10 files changed, 27 insertions(+), 18 deletions(-)
Title: 'R' Bindings for the 'Boost' Math Functions
Description: 'R' bindings for the various functions and statistical distributions
provided by the 'Boost' Math library <https://www.boost.org/doc/libs/latest/libs/math/doc/html/index.html>.
Author: Andrew R. Johnson [aut, cre]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between boostmath versions 1.3.0 dated 2025-11-02 and 1.4.0 dated 2025-12-15
DESCRIPTION | 8 LICENSE | 4 MD5 | 544 - NAMESPACE | 1078 +- NEWS.md | 45 R/airy_functions.R | 158 R/anderson_darling_test.R | 30 R/arcsine_distribution.R | 160 R/basic_functions.R | 156 R/bernoulli_distribution.R | 158 R/bessel_functions.R | 304 R/beta_distribution.R | 248 R/beta_functions.R | 218 R/binomial_distribution.R | 248 R/bivariate_statistics.R | 66 R/boostmath-package.R | 16 R/cauchy_distribution.R | 150 R/chatterjee_correlation.R | 32 R/chi_squared_distribution.R | 188 R/constants.R | 38 R/elliptic_integrals.R | 244 R/empirical_cumulative_distribution_function.R |only R/error_functions.R | 82 R/exponential_distribution.R | 158 R/exponential_integrals.R | 50 R/extreme_value_distribution.R | 162 R/factorials_and_binomial_coefficients.R | 134 R/filters.R | 60 R/fisher_f_distribution.R | 162 R/fp_utilities.R |only R/gamma_distribution.R | 162 R/gamma_functions.R | 304 R/geometric_distribution.R | 232 R/hankel_functions.R | 74 R/holtsmark_distribution.R | 156 R/hyperexponential_distribution.R | 162 R/hypergeometric_distribution.R | 166 R/hypergeometric_functions.R | 136 R/interpolators.R | 980 +- R/inverse_chi_squared_distribution.R | 162 R/inverse_gamma_distribution.R | 162 R/inverse_gaussian_distribution.R | 164 R/inverse_hyperbolic_functions.R | 64 R/jacobi_elliptic_functions.R | 208 R/jacobi_theta_functions.R | 196 R/kolmogorov_smirnov_distribution.R | 158 R/lambert_w_function.R | 82 R/landau_distribution.R | 150 R/laplace_distribution.R | 162 R/linear_regression.R | 56 R/ljung_box_test.R | 30 R/logistic_distribution.R | 162 R/logistic_functions.R |only R/lognormal_distribution.R | 162 R/mapairy_distribution.R | 156 R/methods.R | 376 R/negative_binomial_distribution.R | 238 R/non_central_beta_distribution.R | 162 R/non_central_chi_squared_distribution.R | 204 R/non_central_f_distribution.R | 168 R/non_central_t_distribution.R | 162 R/normal_distribution.R | 162 R/number_series.R | 200 R/owens_t_function.R | 34 R/pareto_distribution.R | 162 R/poisson_distribution.R | 158 R/polynomials.R | 644 - R/quadrature_and_differentiation.R | 278 R/rayleigh_distribution.R | 158 R/rootfinding_and_minimisation.R | 248 R/runs_tests.R | 50 R/saspoint5_distribution.R | 150 R/signal_statistics.R | 142 R/sinus_cardinal_hyperbolic_functions.R | 48 R/skew_normal_distribution.R | 166 R/students_t_distribution.R | 186 R/t_tests.R | 90 R/triangular_distribution.R | 166 R/uniform_distribution.R | 162 R/univariate_statistics.R | 242 R/vector_functionals.R | 196 R/weibull_distribution.R | 162 R/z_tests.R | 74 R/zeta_functions.R | 26 R/zzz.R | 16 README.md | 320 build/vignette.rds |binary inst/doc/constants.R | 34 inst/doc/constants.Rmd | 70 inst/doc/constants.html | 1223 +- inst/doc/filters.R | 30 inst/doc/filters.Rmd | 64 inst/doc/filters.html | 756 - inst/doc/fp_utilities.R |only inst/doc/fp_utilities.Rmd |only inst/doc/fp_utilities.html |only inst/doc/interpolation.R | 284 inst/doc/interpolation.Rmd | 384 inst/doc/interpolation.html | 1132 +- inst/doc/quadrature-differentiation.R | 88 inst/doc/quadrature-differentiation.Rmd | 152 inst/doc/quadrature-differentiation.html | 858 - inst/doc/rootfinding-minimisation.R | 104 inst/doc/rootfinding-minimisation.Rmd | 172 inst/doc/rootfinding-minimisation.html | 948 +- inst/doc/special-functions.R | 728 - inst/doc/special-functions.Rmd | 876 - inst/doc/special-functions.html | 1898 ++-- inst/doc/statistical-distributions.R | 2172 ++-- inst/doc/statistical-distributions.Rmd | 2434 ++--- inst/doc/statistical-distributions.html | 4656 +++++----- inst/doc/statistics.R | 210 inst/doc/statistics.Rmd | 292 inst/doc/statistics.html | 1030 +- inst/doc/vector-functionals.R | 66 inst/doc/vector-functionals.Rmd | 92 inst/doc/vector-functionals.html | 796 - inst/tinytest/test_basic_functions.R | 6 inst/tinytest/test_constants.R | 4 man/airy_functions.Rd | 104 man/anderson_darling_test.Rd | 58 man/arcsine_distribution.Rd | 138 man/barycentric_rational.Rd | 68 man/basic_functions.Rd | 128 man/bernoulli_distribution.Rd | 136 man/bessel_functions.Rd | 204 man/beta_distribution.Rd | 182 man/beta_functions.Rd | 176 man/bezier_polynomial.Rd | 64 man/bilinear_uniform.Rd | 78 man/binomial_distribution.Rd | 194 man/bivariate_statistics.Rd | 74 man/boostmath-package.Rd | 50 man/cardinal_cubic_b_spline.Rd | 92 man/cardinal_cubic_hermite.Rd | 74 man/cardinal_quadratic_b_spline.Rd | 88 man/cardinal_quintic_b_spline.Rd | 92 man/cardinal_quintic_hermite.Rd | 88 man/catmull_rom.Rd | 72 man/cauchy_distribution.Rd | 128 man/chatterjee_correlation.Rd | 56 man/chebyshev_polynomials.Rd | 126 man/chi_squared_distribution.Rd | 182 man/condition_numbers.Rd |only man/constants.Rd | 46 man/cubic_hermite.Rd | 76 man/double_exponential_quadrature.Rd | 80 man/elliptic_integrals.Rd | 190 man/empirical_cumulative_distribution_function.Rd |only man/error_functions.Rd | 84 man/exponential_distribution.Rd | 136 man/exponential_integrals.Rd | 64 man/extreme_value_distribution.Rd | 140 man/factorials_and_binomial_coefficients.Rd | 122 man/filters.Rd | 60 man/fisher_f_distribution.Rd | 140 man/fp_utilities.Rd |only man/gamma_distribution.Rd | 140 man/gamma_functions.Rd | 238 man/gegenbauer_polynomials.Rd | 82 man/generic_distribution_functions.Rd | 128 man/geometric_distribution.Rd | 192 man/hankel_functions.Rd | 76 man/hermite_polynomials.Rd | 72 man/holtsmark_distribution.Rd | 134 man/hyperexponential_distribution.Rd | 140 man/hypergeometric_distribution.Rd | 144 man/hypergeometric_functions.Rd | 126 man/inverse_chi_squared_distribution.Rd | 140 man/inverse_gamma_distribution.Rd | 140 man/inverse_gaussian_distribution.Rd | 140 man/inverse_hyperbolic_functions.Rd | 70 man/jacobi_elliptic_functions.Rd | 156 man/jacobi_polynomials.Rd | 96 man/jacobi_theta_functions.Rd | 152 man/kolmogorov_smirnov_distribution.Rd | 136 man/laguerre_polynomials.Rd | 96 man/lambert_w_function.Rd | 82 man/landau_distribution.Rd | 128 man/laplace_distribution.Rd | 140 man/legendre_polynomials.Rd | 126 man/linear_regression.Rd | 70 man/ljung_box_test.Rd | 58 man/logistic_distribution.Rd | 140 man/logistic_functions.Rd |only man/lognormal_distribution.Rd | 140 man/makima.Rd | 74 man/mapairy_distribution.Rd | 134 man/negative_binomial_distribution.Rd | 214 man/non_central_beta_distribution.Rd | 140 man/non_central_chi_squared_distribution.Rd | 172 man/non_central_f_distribution.Rd | 146 man/non_central_t_distribution.Rd | 140 man/normal_distribution.Rd | 140 man/number_series.Rd | 136 man/numerical_differentiation.Rd | 62 man/numerical_integration.Rd | 102 man/ooura_fourier_integrals.Rd | 90 man/owens_t.Rd | 56 man/pareto_distribution.Rd | 140 man/pchip.Rd | 74 man/poisson_distribution.Rd | 136 man/polynomial_root_finding.Rd | 110 man/quintic_hermite.Rd | 86 man/rayleigh_distribution.Rd | 136 man/rootfinding_and_minimisation.Rd | 232 man/runs_tests.Rd | 64 man/saspoint5_distribution.Rd | 128 man/signal_statistics.Rd | 132 man/sinus_cardinal_hyperbolic_functions.Rd | 60 man/skew_normal_distribution.Rd | 144 man/spherical_harmonics.Rd | 82 man/students_t_distribution.Rd | 182 man/t_tests.Rd | 110 man/triangular_distribution.Rd | 144 man/uniform_distribution.Rd | 140 man/univariate_statistics.Rd | 184 man/vector_functionals.Rd | 158 man/weibull_distribution.Rd | 140 man/z_tests.Rd | 100 man/zeta.Rd | 42 src/Makevars | 4 src/bezier_polynomial.cpp |only src/boostmath/macros.hpp | 15 src/boostmath/sexp.hpp | 6 src/constants.cpp | 1 src/cyl_hankel_1.cpp | 3 src/cyl_hankel_2.cpp | 3 src/distribution_member_functions.cpp | 10 src/filters.cpp | 28 src/fp_utilities.cpp |only src/init.cpp | 41 src/interpolators.cpp | 11 src/quadrature_and_differentiation/double_exponential.cpp | 28 src/quadrature_and_differentiation/fourier_integrals.cpp | 58 src/quadrature_and_differentiation/gauss_kronrod.cpp | 25 src/quadrature_and_differentiation/gauss_legendre.cpp | 21 src/quadrature_and_differentiation/numerical_differentiation.cpp | 41 src/quadrature_and_differentiation/trapezoidal.cpp | 17 src/rootfinding_and_minimisation/minima.cpp | 18 src/rootfinding_and_minimisation/polynomial_roots.cpp | 2 src/rootfinding_and_minimisation/with_derivatives.cpp | 65 src/rootfinding_and_minimisation/without_derivatives.cpp | 63 src/special_functions.cpp | 1 src/special_functions/airy_functions.cpp | 2 src/special_functions/basic_functions.cpp | 2 src/special_functions/bessel_functions.cpp | 2 src/special_functions/beta_functions.cpp | 2 src/special_functions/elliptic_integrals.cpp | 2 src/special_functions/error_functions.cpp | 2 src/special_functions/exponential_integrals.cpp | 2 src/special_functions/factorials_and_binomial_coefficients.cpp | 2 src/special_functions/gamma_functions.cpp | 2 src/special_functions/hypergeometric_functions.cpp | 27 src/special_functions/inverse_hyperbolic_functions.cpp | 2 src/special_functions/jacobi_elliptic_functions.cpp | 32 src/special_functions/jacobi_theta_functions.cpp | 2 src/special_functions/lambert_w_function.cpp | 2 src/special_functions/logistic_functions.cpp |only src/special_functions/number_series.cpp | 2 src/special_functions/owens_t_function.cpp | 2 src/special_functions/polynomials.cpp | 64 src/special_functions/sinus_cardinal_hyperbolic_functions.cpp | 2 src/special_functions/zeta_functions.cpp | 2 src/sph_hankel_1.cpp | 3 src/sph_hankel_2.cpp | 3 src/statistical_distributions.cpp | 24 src/statistics.cpp | 2 src/vector_functionals.cpp | 2 tests/tinytest.R | 8 vignettes/constants.Rmd | 70 vignettes/filters.Rmd | 64 vignettes/fp_utilities.Rmd |only vignettes/interpolation.Rmd | 384 vignettes/quadrature-differentiation.Rmd | 152 vignettes/rootfinding-minimisation.Rmd | 172 vignettes/special-functions.Rmd | 876 - vignettes/statistical-distributions.Rmd | 2434 ++--- vignettes/statistics.Rmd | 292 vignettes/vector-functionals.Rmd | 92 280 files changed, 26626 insertions(+), 26626 deletions(-)
Title: Technology Appraisal Toolbox for Health Economic Evaluations in
the Netherlands
Description: Functions to support economic modelling in R based on the methods of the
Dutch guideline for economic evaluations in healthcare <https://www.zorginstituutnederland.nl/documenten/2024/01/16/richtlijn-voor-het-uitvoeren-van-economische-evaluaties-in-de-gezondheidszorg>,
CBS data <https://www.cbs.nl/>, and OECD data <https://www.oecd.org/en.html>.
Author: Stijn Peeters [aut, cre] ,
Eline Krijkamp [aut] ,
Frederick Thielen [aut]
Maintainer: Stijn Peeters <s.b.peeters@eshpm.eur.nl>
Diff between tatooheene versions 0.19.0 dated 2024-12-18 and 1.0.0 dated 2025-12-15
tatooheene-0.19.0/tatooheene/R/data_rp_medical.R |only tatooheene-0.19.0/tatooheene/R/data_rp_patient.R |only tatooheene-0.19.0/tatooheene/R/data_rp_prod.R |only tatooheene-0.19.0/tatooheene/R/discount_value.R |only tatooheene-0.19.0/tatooheene/R/discount_vector.R |only tatooheene-0.19.0/tatooheene/R/nl_med_prices.R |only tatooheene-0.19.0/tatooheene/R/nl_pat_fam_prices.R |only tatooheene-0.19.0/tatooheene/R/nl_prod_oth_prices.R |only tatooheene-0.19.0/tatooheene/data/df_rp_medical.rda |only tatooheene-0.19.0/tatooheene/data/df_rp_patient.rda |only tatooheene-0.19.0/tatooheene/data/df_rp_prod.rda |only tatooheene-0.19.0/tatooheene/man/df_rp_medical.Rd |only tatooheene-0.19.0/tatooheene/man/df_rp_patient.Rd |only tatooheene-0.19.0/tatooheene/man/df_rp_prod.Rd |only tatooheene-0.19.0/tatooheene/man/discount_value.Rd |only tatooheene-0.19.0/tatooheene/man/discount_vector.Rd |only tatooheene-0.19.0/tatooheene/man/nl_med_prices.Rd |only tatooheene-0.19.0/tatooheene/man/nl_pat_fam_prices.Rd |only tatooheene-0.19.0/tatooheene/man/nl_prod_oth_prices.Rd |only tatooheene-1.0.0/tatooheene/DESCRIPTION | 34 +- tatooheene-1.0.0/tatooheene/MD5 | 90 +++-- tatooheene-1.0.0/tatooheene/NAMESPACE | 13 tatooheene-1.0.0/tatooheene/NEWS.md | 33 - tatooheene-1.0.0/tatooheene/R/apply_discounting.R |only tatooheene-1.0.0/tatooheene/R/data_df_ref_prices.R |only tatooheene-1.0.0/tatooheene/R/data_model_output_sick_sicker.R |only tatooheene-1.0.0/tatooheene/R/depreciation_interest.R | 169 +++++----- tatooheene-1.0.0/tatooheene/R/friction_period.R | 143 ++++---- tatooheene-1.0.0/tatooheene/R/globals.R | 11 tatooheene-1.0.0/tatooheene/R/nl_ppp.R | 63 +-- tatooheene-1.0.0/tatooheene/R/nl_price_index.R | 149 +++++--- tatooheene-1.0.0/tatooheene/R/nl_ref_prices.R |only tatooheene-1.0.0/tatooheene/R/pretty_price.R | 46 +- tatooheene-1.0.0/tatooheene/build |only tatooheene-1.0.0/tatooheene/data/data_model_output_sick_sicker.rda |only tatooheene-1.0.0/tatooheene/data/df_cpi_combined.rda |binary tatooheene-1.0.0/tatooheene/data/df_ref_prices.rda |only tatooheene-1.0.0/tatooheene/inst |only tatooheene-1.0.0/tatooheene/man/apply_discounting.Rd |only tatooheene-1.0.0/tatooheene/man/data_model_output_sick_sicker.Rd |only tatooheene-1.0.0/tatooheene/man/depreciation_interest.Rd | 49 +- tatooheene-1.0.0/tatooheene/man/df_cpi_combined.Rd | 64 +-- tatooheene-1.0.0/tatooheene/man/df_fp.Rd | 62 +-- tatooheene-1.0.0/tatooheene/man/df_ref_prices.Rd |only tatooheene-1.0.0/tatooheene/man/friction_period.Rd | 74 ++-- tatooheene-1.0.0/tatooheene/man/nl_ppp.Rd | 2 tatooheene-1.0.0/tatooheene/man/nl_price_index.Rd | 2 tatooheene-1.0.0/tatooheene/man/nl_ref_prices.Rd |only tatooheene-1.0.0/tatooheene/man/pretty_price.Rd | 4 tatooheene-1.0.0/tatooheene/tests |only tatooheene-1.0.0/tatooheene/vignettes |only 51 files changed, 562 insertions(+), 446 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-26 dated 2024-12-12 and 1.3-26.1 dated 2025-12-15
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/RODBC.Rnw | 2 +- inst/doc/RODBC.pdf |binary vignettes/RODBC.Rnw | 2 +- 7 files changed, 17 insertions(+), 13 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour
credibility regions, contour avoiding regions, and simultaneous confidence
bands for latent Gaussian random processes and fields. The package also
contains functions that calculate these quantities for models estimated
with the INLA package. The main references for excursions are Bolin and
Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017)
<doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018)
<doi:10.18637/jss.v086.i05>. These can be generated by the citation
function in R.
Author: David Bolin [cre, aut] ,
Finn Lindgren [aut] ,
Suen Man Ho [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.5.8 dated 2023-11-30 and 2.5.11 dated 2025-12-15
DESCRIPTION | 33 ++-- MD5 | 111 +++++++------ NAMESPACE | 6 NEWS.md | 15 + R/contourmap.R | 77 ++++++--- R/contourmap.inla.R | 93 +++++++---- R/contourutil.R | 95 +++++------ R/excursions.R | 129 +++++++++------ R/excursions.inla.R | 153 +++++++++++------- R/exursions-package.R | 57 +++--- R/gaussint.R | 24 +- R/geometry.R | 230 ++++++++++++++++------------ R/inlautils.R | 3 R/interface.mc.R | 141 ++++++++++------- R/local_testthat.R | 3 R/simconf.R | 45 +++-- R/simconf.inla.R | 67 +++++--- R/simconf.mixture.R | 23 +- R/utils.R | 128 +++++++++------ build |only configure | 8 inst/doc |only man/continuous.Rd | 11 - man/contourmap.Rd | 61 ++++--- man/contourmap.inla.Rd | 52 ++++-- man/contourmap.mc.Rd | 42 ++--- man/exc_safe_inla.Rd | 16 - man/excursions-package.Rd | 40 ++-- man/excursions.Rd | 22 +- man/excursions.inla.Rd | 18 +- man/excursions.mc.Rd | 18 +- man/figures |only man/gaussint.Rd | 12 - man/local_exc_testthat.Rd | 14 - man/require.nowarnings.Rd | 2 man/simconf.Rd | 12 - man/simconf.inla.Rd | 17 +- man/simconf.mc.Rd | 4 man/simconf.mixture.Rd | 6 man/submesh.grid.Rd | 2 man/submesh.mesh.Rd | 6 man/summary.excurobj.Rd | 4 man/tricontour.Rd | 46 ++--- src/CAMD/Source/camd_2.c | 6 src/CAMD/Source/camd_dump.c | 2 src/Makevars.in | 2 src/Makevars.win | 2 src/SuiteSparse_config/SuiteSparse_config.h | 4 src/integration.cpp | 2 tests/testthat/_snaps/contourmap_inla.md | 16 + tests/testthat/helper-data.R | 43 +++-- tests/testthat/test-continuous.R | 18 +- vignettes |only 53 files changed, 1166 insertions(+), 775 deletions(-)
Title: 'DataSHIELD' 'Tidyverse' Serverside Package
Description: Implementation of selected 'Tidyverse' functions within 'DataSHIELD', an open-source federated analysis solution in R. Currently, DataSHIELD contains very limited tools for data manipulation, so the aim of this package is to improve the researcher experience by implementing essential functions for data manipulation, including subsetting, filtering, grouping, and renaming variables. This is the serverside package which should be installed on the server holding the data, and is used in conjuncture with the clientside package 'dsTidyverseClient' which is installed in the local R environment of the analyst. For more information, see <https://tidyverse.org/> and <https://datashield.org/>.
Author: Tim Cadman [aut, cre] ,
Mariska Slofstra [aut] ,
Stuart Wheater [aut],
Demetris Avraam [aut]
Maintainer: Tim Cadman <t.j.cadman@umcg.nl>
Diff between dsTidyverse versions 1.0.4 dated 2025-02-27 and 1.1.1 dated 2025-12-15
DESCRIPTION | 19 ++++++++++--------- MD5 | 18 ++++++++++++------ R/utils.R | 21 ++++++++++++--------- README.md | 26 +++----------------------- build |only inst/doc |only tests/testthat/_snaps/utils.md | 6 +++--- tests/testthat/test-distinctDS.R | 3 ++- tests/testthat/test-utils.R | 33 +++++++++++++++++++++++++++++++++ vignettes |only 10 files changed, 75 insertions(+), 51 deletions(-)
Title: Audio Interface for R
Description: Interfaces to audio devices (mainly sample-based) from R to allow recording and playback of audio. Built-in devices include Windows MM, Mac OS X AudioUnits and PortAudio (the last one is very experimental).
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between audio versions 0.1-11 dated 2023-08-17 and 0.1-12 dated 2025-12-15
DESCRIPTION | 13 ++++++++----- MD5 | 14 +++++++------- NEWS | 4 ++++ man/audioSample.Rd | 2 +- src/au.c | 2 +- src/driver.c | 8 ++++++++ src/file.c | 8 ++++---- src/pa.c | 7 ++++++- 8 files changed, 39 insertions(+), 19 deletions(-)
Title: Versatile R Server
Description: Rserve is a versatile, scalable server enabling the
efficient use of R from other applications through
variety of protocols including QAP, WebSockets, HTTP
and HTTPS. It acts as a server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for many popular languages allowing applications
to use facilities of R without the need of linking to
the R binary. Rserve supports remote connections,
user authentication and file transfer. A simple R client
is included in this package as well. It also supports
OCAP mode for secure remote procedure calls,
including support for full event loop, asynchronous
results/graphics and console I/O.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.8-15 dated 2024-12-17 and 1.8-16 dated 2025-12-15
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 21 +++++++++++---------- NEWS | 8 ++++++-- inst/java/REngine.jar |binary inst/java/Rserve.jar |binary src/Rsrv.h | 2 +- src/client/cxx/Rsrv.h | 2 +- src/client/java/Rserve/Rserve.jar |binary src/qap_decode.c | 9 +++++++-- src/qap_decode.h | 1 + src/qap_encode.h | 1 + src/rcompat.h |only 12 files changed, 44 insertions(+), 27 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Omics
Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between PRECAST versions 1.7 dated 2025-10-01 and 1.8 dated 2025-12-15
DESCRIPTION | 9 ++--- MD5 | 25 ++++++++------ R/SetClass.R | 8 ++-- R/Visualization.R | 2 - R/correct_wholegenes.R | 6 +-- R/main.R | 4 +- inst/doc/PRECAST.BreastCancer.html | 4 +- inst/doc/PRECAST.DLPFC.html | 4 +- inst/doc/PRECAST.DLPFC4.html | 4 +- inst/doc/PRECAST.Simu.html | 50 ++++++++++++++--------------- man/chooseColors.Rd | 58 +++++++++++++++++----------------- man/drawFigs.Rd | 62 ++++++++++++++++++------------------- man/getneighborhood_fast.Rd |only man/sp_means_Rcpp.Rd |only man/sp_sums_Rcpp.Rd |only 15 files changed, 120 insertions(+), 116 deletions(-)
Title: Edit and Validate Darwin Core Taxon Data
Description: Edit and validate taxonomic data in compliance with Darwin Core
standards (Darwin Core 'Taxon' class <https://dwc.tdwg.org/terms/#taxon>).
Author: Joel H. Nitta [aut, cre, cph] ,
Wataru Iwasaki [ctb] ,
Collin Schwantes [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/574>),
Stephen Formel [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/57 [...truncated...]
Maintainer: Joel H. Nitta <joelnitta@gmail.com>
Diff between dwctaxon versions 2.0.3 dated 2023-12-13 and 2.0.4 dated 2025-12-15
DESCRIPTION | 15 MD5 | 61 +-- NAMESPACE | 2 NEWS.md | 8 R/check_map_to_parent_accepted.R |only R/dct_add_row.R | 38 +- R/dct_modify_row.R | 191 +++++++++- R/dct_options.R | 19 - R/dct_validate.R | 52 ++ R/globals.R | 3 R/roxygen.R | 47 ++ R/utils.R | 85 ++++ README.md | 55 +- build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/editing.html | 320 ++++++++--------- inst/doc/real-data.R | 38 +- inst/doc/real-data.Rmd | 39 +- inst/doc/real-data.html | 347 +++++++++--------- inst/doc/validation.R | 8 inst/doc/validation.html | 390 ++++++++++----------- inst/doc/what-is-dwc.html | 36 - man/dct_add_row.Rd | 12 man/dct_modify_row.Rd | 24 + man/dct_options.Rd | 12 man/dct_validate.Rd | 3 tests/testthat/_snaps/dct_add_row.md | 24 + tests/testthat/test-check_map_to_parent_accepted.R |only tests/testthat/test-dct_add_row.R | 55 ++ tests/testthat/test-dct_modify_row-remap_parent.R |only tests/testthat/test-dct_modify_row.R | 143 +++++++ tests/testthat/test-utils.R | 186 +++++++++- vignettes/real-data.Rmd | 39 +- 33 files changed, 1566 insertions(+), 689 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-22 0.1.3
2018-03-26 0.1.2
2018-01-08 0.1.1
2017-06-27 0.1.0
Title: Time Series Forecasting Functions
Description: Fundamental time series forecasting models such as autoregressive integrated moving average (ARIMA), exponential smoothing, and simple moving average are included. For ARIMA models, the output follows the traditional parameterisation by Box and Jenkins (1970, ISBN: 0816210942, 9780816210947). Furthermore, there are functions for detailed time series exploration and decomposition, respectively. All data and result visualisations are generated by 'ggplot2' instead of conventional R graphical output. For more details regarding the theoretical background of the models see Hyndman, R.J. and Athanasopoulos, G. (2021) <https://otexts.com/fpp3/>.
Author: Ka Yui Karl Wu [aut, cre]
Maintainer: Ka Yui Karl Wu <karlwuky@suss.edu.sg>
Diff between tsforecast versions 1.1.0 dated 2025-12-12 and 1.2.0 dated 2025-12-15
tsforecast-1.1.0/tsforecast/R/tsforecast_1.1.0.R |only tsforecast-1.2.0/tsforecast/DESCRIPTION | 8 tsforecast-1.2.0/tsforecast/MD5 | 48 - tsforecast-1.2.0/tsforecast/R/tsforecast_1.2.0.R |only tsforecast-1.2.0/tsforecast/inst/examples/tsexplore/tsexplore.R | 2 tsforecast-1.2.0/tsforecast/man/airport.Rd | 54 - tsforecast-1.2.0/tsforecast/man/is.outlier.Rd | 100 +- tsforecast-1.2.0/tsforecast/man/predict.Rd | 168 ++-- tsforecast-1.2.0/tsforecast/man/ts-functions.Rd | 140 +-- tsforecast-1.2.0/tsforecast/man/tsacf.Rd | 250 +++--- tsforecast-1.2.0/tsforecast/man/tsarima.Rd | 410 +++++----- tsforecast-1.2.0/tsforecast/man/tsboxplot.Rd | 90 +- tsforecast-1.2.0/tsforecast/man/tsconvert.Rd | 78 - tsforecast-1.2.0/tsforecast/man/tsdecomp.Rd | 209 ++--- tsforecast-1.2.0/tsforecast/man/tsdiff.Rd | 76 - tsforecast-1.2.0/tsforecast/man/tsesm.Rd | 2 tsforecast-1.2.0/tsforecast/man/tsexplore.Rd | 14 tsforecast-1.2.0/tsforecast/man/tsforecast.Rd | 258 +++--- tsforecast-1.2.0/tsforecast/man/tshistogram.Rd | 98 +- tsforecast-1.2.0/tsforecast/man/tslag.Rd | 2 tsforecast-1.2.0/tsforecast/man/tslineplot.Rd | 2 tsforecast-1.2.0/tsforecast/man/tsmltest.Rd | 66 - tsforecast-1.2.0/tsforecast/man/tsmodeleval.Rd | 88 +- tsforecast-1.2.0/tsforecast/man/tsmovav.Rd | 204 ++-- tsforecast-1.2.0/tsforecast/man/tsqqplot.Rd | 92 +- tsforecast-1.2.0/tsforecast/man/tsscatterplot.Rd | 100 +- 26 files changed, 1291 insertions(+), 1268 deletions(-)
Title: Predictors of Resilience to a Stressor in a Single-Arm Study
Description: Studies of resilience in older adults employ a single-arm design where everyone experiences the stressor. The simplistic approach of regressing change versus baseline yields biased estimates due to regression-to-the-mean. This package provides a method to correct the bias. It also allows covariates to be included. The method implemented in the package is described in Varadhan, R., Zhu, J., and Bandeen-Roche, K (2024), Biostatistics 25(4): 1094-1111.
Author: Ravi Varadhan [aut, cre],
Jiafeng Zhu [ctb]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between resilience versions 2025.1.0 dated 2025-12-11 and 2025.1.1 dated 2025-12-15
resilience-2025.1.0/resilience/man/plot.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/print.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/summary.prepost_resilience_mi_list.Rd |only resilience-2025.1.1/resilience/DESCRIPTION | 8 +- resilience-2025.1.1/resilience/MD5 | 18 ++-- resilience-2025.1.1/resilience/NAMESPACE | 8 +- resilience-2025.1.1/resilience/R/pre-post-regression.R | 6 - resilience-2025.1.1/resilience/R/prepost_mi_list.R | 38 +++++----- resilience-2025.1.1/resilience/man/plot.prepost_mi.Rd |only resilience-2025.1.1/resilience/man/prepost.Rd | 2 resilience-2025.1.1/resilience/man/prepost_mi.Rd |only resilience-2025.1.1/resilience/man/print.prepost_mi.Rd |only resilience-2025.1.1/resilience/man/summary.prepost_mi.Rd |only 14 files changed, 41 insertions(+), 39 deletions(-)
Title: Easily Install and Load Redistricting Software
Description: Easy installation, loading, and control of packages for redistricting
data downloading, spatial data processing, simulation, analysis, and
visualization. This package makes it easy to install and load multiple
'redistverse' packages at once. The 'redistverse' is developed and maintained
by the Algorithm-Assisted Redistricting Methodology (ALARM) Project.
For more details see <https://alarm-redist.org>.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [aut] ,
tidyverse contributors [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
This is a re-admission after prior archival of version 0.1.1 dated 2025-10-27
Diff between redistverse versions 0.1.1 dated 2025-10-27 and 0.1.2 dated 2025-12-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ man/redistverse-package.Rd | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of Machine Learning
(ML) techniques as easy and accessible as possible, particularly within the framework of
the Knowledge Discovery in Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive or classification
modeling workflow, aligning closely with the fundamental steps of the KDD methodology,
from data selection and preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis. The 'MLwrap' workflow
is organized into four core steps; preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). It also includes global and pairwise interaction analysis based on
Friedman’s H-statistic to support a more detailed interpretation of complex feature
relationships.These steps correspond, respectively, to data preparation and transformation,
model construction, hyperparameter optimizat [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.2.3 dated 2025-11-11 and 0.3.0 dated 2025-12-15
DESCRIPTION | 48 MD5 | 60 - NAMESPACE | 4 R/Hstats.R |only R/Integrated_Gradients.R | 8 R/InterpretableML.R | 1512 +++++++++++++------------ R/MulticlassPlots.R |only R/Objects.R | 137 +- R/Tuners.R | 88 - R/ale.R |only R/check_arguments.R | 3 R/evaluate_model.R | 28 R/fine_tuning.R | 6 R/metrics.R | 30 R/partial_dependence_plot.R |only R/permutation_feature_importance.R | 22 R/plotting_utils.R | 1986 +++++++++++++++++++--------------- R/results_binary_classification.R | 6 R/results_multiclass_classification.R | 6 R/results_regression.R | 6 R/shap_values.R | 46 R/table_utils.R | 1150 +++++++++++-------- R/tutorial.R | 112 - R/zzz.R | 6 README.md | 2 man/plot_ale.Rd |only man/plot_pdp.Rd |only man/sensitivity_analysis.Rd | 28 man/table_h2_total.Rd |only man/table_pairwise_interaction.Rd |only man/table_pfi_results.Rd | 26 man/table_shap_results.Rd | 23 man/tutorial.Rd | 4 tests/testthat/test-Tuners.R | 34 tests/testthat/test-model_tuning.R | 4 35 files changed, 2936 insertions(+), 2449 deletions(-)
Title: Inferential Statistics
Description: Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3), intersection-union (Sozu et al. (2015), ISBN:978-3-319-22005-5) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test; furthermore, computation of intersection-union z-test as well as multiple imputation Wilcoxon tests. Graphical visualizations: volcano plot, Bland-Altman plots (Bland and Altman (1986), <doi:10.1016/S0140-6736(86)90837-8>; Shieh (2018), <doi:10.1186/s12874-018-0505-y>), mean difference plot (Boehning et al. (2008), <doi:10.1177/0962280207081867>), plot of test statistic for permutation [...truncated...]
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKinfer versions 1.2 dated 2024-04-06 and 1.3 dated 2025-12-15
DESCRIPTION | 15 MD5 | 42 - NAMESPACE | 16 NEWS | 16 R/boot.t.test.R | 11 R/h0plot.R |only R/md2sens.R |only R/md2zfactor.R |only R/mdplot.R |only R/pairwiseFun.R | 2 R/perm.t.test.R | 13 R/rm.oneway.test.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/fingsys.RData |binary inst/doc/MKinfer.R | 80 ++ inst/doc/MKinfer.Rmd | 149 ++++ inst/doc/MKinfer.html | 1550 ++++++++++++++++++++++++++++---------------------- man/boot.t.test.Rd | 6 man/h0plot.Rd |only man/md2sens.Rd |only man/md2zfactor.Rd |only man/mdplot.Rd |only man/perm.t.test.Rd | 6 vignettes/MKinfer.Rmd | 149 ++++ vignettes/MKinfer.bib | 34 + 26 files changed, 1380 insertions(+), 711 deletions(-)
Title: Bayesian Logistic Regression with Heavy-Tailed Priors
Description: Efficient Bayesian multinomial logistic regression based on heavy-tailed
(hyper-LASSO, non-convex) priors. The posterior of coefficients and hyper-parameters
is sampled with restricted Gibbs sampling for leveraging the high-dimensionality and
Hamiltonian Monte Carlo for handling the high-correlation among coefficients. A detailed
description of the method: Li and Yao (2018),
Journal of Statistical Computation and Simulation, 88:14, 2827-2851, <doi:10.48550/arXiv.1405.3319>.
Author: Longhai Li [aut] ,
Steven Liu [aut, cre]
Maintainer: Steven Liu <shinyu.lieu@gmail.com>
Diff between HTLR versions 0.4-4 dated 2022-10-22 and 1.0 dated 2025-12-15
HTLR-0.4-4/HTLR/R/HTLR-package.R |only HTLR-0.4-4/HTLR/man/HTLR-package.Rd |only HTLR-0.4-4/HTLR/tests/testthat/bplrhmc_expect.rda |only HTLR-1.0/HTLR/DESCRIPTION | 32 - HTLR-1.0/HTLR/MD5 | 35 - HTLR-1.0/HTLR/NAMESPACE | 1 HTLR-1.0/HTLR/R/htlr.R | 2 HTLR-1.0/HTLR/R/initial-state.R | 5 HTLR-1.0/HTLR/README.md | 8 HTLR-1.0/HTLR/build/vignette.rds |binary HTLR-1.0/HTLR/inst/CITATION | 4 HTLR-1.0/HTLR/inst/doc/simu.R | 4 HTLR-1.0/HTLR/inst/doc/simu.Rmd | 3 HTLR-1.0/HTLR/inst/doc/simu.html | 485 +++++++++++++++------- HTLR-1.0/HTLR/inst/install_old_htlr.R | 2 HTLR-1.0/HTLR/src/Makevars | 11 HTLR-1.0/HTLR/src/Makevars.win | 11 HTLR-1.0/HTLR/tests/testthat/test-bplrhmc.r | 2 HTLR-1.0/HTLR/tests/testthat/test-gendata.r | 2 HTLR-1.0/HTLR/vignettes/simu.Rmd | 3 20 files changed, 386 insertions(+), 224 deletions(-)
Title: Causal Modeling in Epidemiology
Description: Create causal models for use in epidemiological studies,
including sufficient-component cause models as introduced by
Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
Author: Felix Forster [aut, cre, cph]
Maintainer: Felix Forster <forsterepi@gmail.com>
Diff between epicmodel versions 0.2.0 dated 2024-12-11 and 0.2.1 dated 2025-12-15
epicmodel-0.2.0/epicmodel/R/utils.R |only epicmodel-0.2.0/epicmodel/tests/testthat/test-utils.R |only epicmodel-0.2.1/epicmodel/DESCRIPTION | 15 epicmodel-0.2.1/epicmodel/MD5 | 56 epicmodel-0.2.1/epicmodel/NEWS.md | 12 epicmodel-0.2.1/epicmodel/R/check_steplist.R | 92 epicmodel-0.2.1/epicmodel/R/create_scc.R | 43 epicmodel-0.2.1/epicmodel/R/dag.R | 29 epicmodel-0.2.1/epicmodel/R/intervention.R | 114 epicmodel-0.2.1/epicmodel/R/mechanism.R | 10 epicmodel-0.2.1/epicmodel/R/prevent.R | 29 epicmodel-0.2.1/epicmodel/R/process_steplist.R | 12 epicmodel-0.2.1/epicmodel/R/process_steplist_user.R | 15 epicmodel-0.2.1/epicmodel/R/scc_class.R | 25 epicmodel-0.2.1/epicmodel/R/scc_utils.R | 204 - epicmodel-0.2.1/epicmodel/R/steplist.R | 8 epicmodel-0.2.1/epicmodel/build/partial.rdb |binary epicmodel-0.2.1/epicmodel/build/vignette.rds |binary epicmodel-0.2.1/epicmodel/inst/doc/epicmodel.html | 3 epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/delete.R | 134 epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/does.R | 224 - epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/icc.R | 290 - epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/module.R | 210 - epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/server_utils.R | 1420 ++++----- epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/ui_utils.R | 738 ++-- epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/what.R | 206 - epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/R/where.R | 200 - epicmodel-0.2.1/epicmodel/inst/shiny/steplist_creator/server.R | 1528 +++++----- epicmodel-0.2.1/epicmodel/man/epicmodel-package.Rd | 2 epicmodel-0.2.1/epicmodel/man/plot_dag.Rd | 2 30 files changed, 2759 insertions(+), 2862 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 1.0.4 dated 2025-09-27 and 1.0.5 dated 2025-12-15
comtradr-1.0.4/comtradr/tests/testthat/ref_table |only comtradr-1.0.5/comtradr/DESCRIPTION | 8 comtradr-1.0.5/comtradr/MD5 | 128 +- comtradr-1.0.5/comtradr/NEWS.md | 18 comtradr-1.0.5/comtradr/R/utils.R | 27 comtradr-1.0.5/comtradr/R/zzz.R | 6 comtradr-1.0.5/comtradr/README.md | 24 comtradr-1.0.5/comtradr/build/vignette.rds |binary comtradr-1.0.5/comtradr/data/country_codes.rda |binary comtradr-1.0.5/comtradr/data/ct_pretty_cols.rda |binary comtradr-1.0.5/comtradr/inst/doc/bulk_files.R | 40 comtradr-1.0.5/comtradr/inst/doc/caching.R | 28 comtradr-1.0.5/comtradr/inst/doc/comtradr.R | 166 +- comtradr-1.0.5/comtradr/inst/doc/comtradr.html | 2 comtradr-1.0.5/comtradr/inst/doc/large_data.R | 90 - comtradr-1.0.5/comtradr/inst/doc/large_data.html | 10 comtradr-1.0.5/comtradr/inst/doc/transition.R | 196 +-- comtradr-1.0.5/comtradr/inst/doc/transition.html | 2 comtradr-1.0.5/comtradr/inst/extdata/cmd_b4.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_b5.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_eb.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_eb02.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_eb10.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_eb10s.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h0.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h1.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h2.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h3.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h4.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h5.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_h6.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_hs.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_s1.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_s2.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_s3.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_s4.rds |binary comtradr-1.0.5/comtradr/inst/extdata/cmd_ss.rds |binary comtradr-1.0.5/comtradr/inst/extdata/customs.rds |binary comtradr-1.0.5/comtradr/inst/extdata/dataitem.rds |only comtradr-1.0.5/comtradr/inst/extdata/flow.rds |binary comtradr-1.0.5/comtradr/inst/extdata/freq.rds |only comtradr-1.0.5/comtradr/inst/extdata/list_of_datasets.rda |binary comtradr-1.0.5/comtradr/inst/extdata/mos.rds |only comtradr-1.0.5/comtradr/inst/extdata/mot.rds |binary comtradr-1.0.5/comtradr/inst/extdata/partner.rds |binary comtradr-1.0.5/comtradr/inst/extdata/qtyunit.rds |only comtradr-1.0.5/comtradr/inst/extdata/reporter.rds |binary comtradr-1.0.5/comtradr/man/ct_commodity_db_type.Rd | 2 comtradr-1.0.5/comtradr/man/ct_commodity_lookup.Rd | 2 comtradr-1.0.5/comtradr/man/ct_country_lookup.Rd | 2 comtradr-1.0.5/comtradr/man/ct_get_data.Rd | 2 comtradr-1.0.5/comtradr/man/ct_get_ref_table.Rd | 6 comtradr-1.0.5/comtradr/man/ct_get_remaining_hourly_queries.Rd | 2 comtradr-1.0.5/comtradr/man/ct_get_reset_time.Rd | 2 comtradr-1.0.5/comtradr/man/ct_migrate_cache.Rd | 2 comtradr-1.0.5/comtradr/man/ct_register_token.Rd | 2 comtradr-1.0.5/comtradr/man/ct_search.Rd | 2 comtradr-1.0.5/comtradr/man/ct_update_databases.Rd | 2 comtradr-1.0.5/comtradr/man/ct_use_pretty_cols.Rd | 2 comtradr-1.0.5/comtradr/man/get_primary_comtrade_key.Rd | 2 comtradr-1.0.5/comtradr/man/set_primary_comtrade_key.Rd | 2 comtradr-1.0.5/comtradr/tests/testthat/httpbin |only comtradr-1.0.5/comtradr/tests/testthat/re_tb1 |only comtradr-1.0.5/comtradr/tests/testthat/re_tb2 |only comtradr-1.0.5/comtradr/tests/testthat/re_tb3 |only comtradr-1.0.5/comtradr/tests/testthat/test-.onload.R | 19 comtradr-1.0.5/comtradr/tests/testthat/test-ct_perform_request.R |only comtradr-1.0.5/comtradr/tests/testthat/test-utils.R | 578 +++++++++- 68 files changed, 995 insertions(+), 379 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 0.1.5 dated 2025-11-13 and 0.2.1 dated 2025-12-15
BayesSIM-0.1.5/BayesSIM/R/options_gp.R |only BayesSIM-0.1.5/BayesSIM/R/options_spline.R |only BayesSIM-0.1.5/BayesSIM/man/Xlinear.Rd |only BayesSIM-0.1.5/BayesSIM/man/alphaTheta.Rd |only BayesSIM-0.1.5/BayesSIM/man/expcov_gpPolar.Rd |only BayesSIM-0.1.5/BayesSIM/man/expcov_gpSphere.Rd |only BayesSIM-0.1.5/BayesSIM/man/expcov_gpSpike.Rd |only BayesSIM-0.1.5/BayesSIM/man/knotsSimple.Rd |only BayesSIM-0.1.5/BayesSIM/man/plot.bsimGp.Rd |only BayesSIM-0.1.5/BayesSIM/man/plot.bsimSpline.Rd |only BayesSIM-0.1.5/BayesSIM/man/predict.bsimGp.Rd |only BayesSIM-0.1.5/BayesSIM/man/predict.bsimSpline.Rd |only BayesSIM-0.1.5/BayesSIM/man/summary.bsimGp.Rd |only BayesSIM-0.1.5/BayesSIM/man/summary.bsimSpline.Rd |only BayesSIM-0.1.5/BayesSIM/man/transX_fisher.Rd |only BayesSIM-0.1.5/BayesSIM/man/transX_sp.Rd |only BayesSIM-0.1.5/BayesSIM/man/unitSphere.Rd |only BayesSIM-0.1.5/BayesSIM/man/vMF.Rd |only BayesSIM-0.1.5/BayesSIM/tests/testthat/test-options-plot.R |only BayesSIM-0.1.5/BayesSIM/tests/testthat/test-options-predict.R |only BayesSIM-0.1.5/BayesSIM/tests/testthat/test-options-summary.R |only BayesSIM-0.2.1/BayesSIM/DESCRIPTION | 40 BayesSIM-0.2.1/BayesSIM/MD5 | 112 +- BayesSIM-0.2.1/BayesSIM/NAMESPACE | 59 - BayesSIM-0.2.1/BayesSIM/R/a_common.R | 107 -- BayesSIM-0.2.1/BayesSIM/R/aa_bspline_ver3.R | 5 BayesSIM-0.2.1/BayesSIM/R/bayesSIM.R | 244 +++-- BayesSIM-0.2.1/BayesSIM/R/bsFisher-functions.R | 109 -- BayesSIM-0.2.1/BayesSIM/R/bsFisher.R | 422 ++++---- BayesSIM-0.2.1/BayesSIM/R/bsPolar.R | 373 ++++--- BayesSIM-0.2.1/BayesSIM/R/bsSphere-functions.R | 149 --- BayesSIM-0.2.1/BayesSIM/R/bsSphere.R | 423 ++++---- BayesSIM-0.2.1/BayesSIM/R/bsSpike.R | 381 ++++--- BayesSIM-0.2.1/BayesSIM/R/generics.R |only BayesSIM-0.2.1/BayesSIM/R/gpFisher.R | 360 +++---- BayesSIM-0.2.1/BayesSIM/R/gpPolar-functions.R | 179 --- BayesSIM-0.2.1/BayesSIM/R/gpPolar-sampler.R | 82 - BayesSIM-0.2.1/BayesSIM/R/gpPolar.R | 418 ++++---- BayesSIM-0.2.1/BayesSIM/R/gpPolarTemp.R | 244 ++--- BayesSIM-0.2.1/BayesSIM/R/gpSphere-functions.R | 53 - BayesSIM-0.2.1/BayesSIM/R/gpSphere-united.R | 486 +++++----- BayesSIM-0.2.1/BayesSIM/R/gpspike-functions.R | 50 - BayesSIM-0.2.1/BayesSIM/R/gpspike.R | 352 +++---- BayesSIM-0.2.1/BayesSIM/R/initial-params.R |only BayesSIM-0.2.1/BayesSIM/R/prior-params.R |only BayesSIM-0.2.1/BayesSIM/R/utils.R | 453 +++++---- BayesSIM-0.2.1/BayesSIM/R/zzz.R | 39 BayesSIM-0.2.1/BayesSIM/man/BayesSIM-package.Rd | 4 BayesSIM-0.2.1/BayesSIM/man/BayesSIM.Rd | 120 +- BayesSIM-0.2.1/BayesSIM/man/DATA1.Rd | 2 BayesSIM-0.2.1/BayesSIM/man/SplineState.Rd | 4 BayesSIM-0.2.1/BayesSIM/man/as_bsim.Rd |only BayesSIM-0.2.1/BayesSIM/man/bsFisher.Rd | 164 +-- BayesSIM-0.2.1/BayesSIM/man/bsPolar.Rd | 168 ++- BayesSIM-0.2.1/BayesSIM/man/bsSphere.Rd | 175 ++- BayesSIM-0.2.1/BayesSIM/man/bsSpike.Rd | 161 +-- BayesSIM-0.2.1/BayesSIM/man/coef.bsim.Rd |only BayesSIM-0.2.1/BayesSIM/man/compileModelAndMCMC.Rd | 39 BayesSIM-0.2.1/BayesSIM/man/fitted.bsim.Rd |only BayesSIM-0.2.1/BayesSIM/man/genBasic.Rd |only BayesSIM-0.2.1/BayesSIM/man/getFunction.Rd |only BayesSIM-0.2.1/BayesSIM/man/getInit.Rd |only BayesSIM-0.2.1/BayesSIM/man/getModelDef.Rd |only BayesSIM-0.2.1/BayesSIM/man/getVarMonitor.Rd |only BayesSIM-0.2.1/BayesSIM/man/gof.Rd |only BayesSIM-0.2.1/BayesSIM/man/gpFisher.Rd | 155 +-- BayesSIM-0.2.1/BayesSIM/man/gpPolar.Rd | 204 ++-- BayesSIM-0.2.1/BayesSIM/man/gpSphere.Rd | 169 ++- BayesSIM-0.2.1/BayesSIM/man/gpSpike.Rd | 148 +-- BayesSIM-0.2.1/BayesSIM/man/init_param.Rd |only BayesSIM-0.2.1/BayesSIM/man/nimTraceplot.Rd |only BayesSIM-0.2.1/BayesSIM/man/plot.Rd |only BayesSIM-0.2.1/BayesSIM/man/predict.bsim.Rd |only BayesSIM-0.2.1/BayesSIM/man/prior_param.Rd |only BayesSIM-0.2.1/BayesSIM/man/summary.bsim.Rd |only BayesSIM-0.2.1/BayesSIM/tests/testthat/test-BayesSIM.R | 218 ++-- BayesSIM-0.2.1/BayesSIM/tests/testthat/test-generic.R |only 77 files changed, 3518 insertions(+), 3353 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.2.2 dated 2025-12-01 and 0.2.3 dated 2025-12-15
yulab.utils-0.2.2/yulab.utils/man/check_pkg.Rd |only yulab.utils-0.2.2/yulab.utils/man/yulab_abort.Rd |only yulab.utils-0.2.2/yulab.utils/man/yulab_inform.Rd |only yulab.utils-0.2.2/yulab.utils/man/yulab_warn.Rd |only yulab.utils-0.2.3/yulab.utils/DESCRIPTION | 11 - yulab.utils-0.2.3/yulab.utils/MD5 | 104 ++++++----- yulab.utils-0.2.3/yulab.utils/NAMESPACE | 12 + yulab.utils-0.2.3/yulab.utils/NEWS.md | 18 + yulab.utils-0.2.3/yulab.utils/R/cache.R | 137 ++++++++++++--- yulab.utils-0.2.3/yulab.utils/R/download.R | 77 +++++++- yulab.utils-0.2.3/yulab.utils/R/error-utils.r | 105 +++++------ yulab.utils-0.2.3/yulab.utils/R/file.R | 7 yulab.utils-0.2.3/yulab.utils/R/list.R | 14 - yulab.utils-0.2.3/yulab.utils/R/load-orgdb.r |only yulab.utils-0.2.3/yulab.utils/R/os.R | 5 yulab.utils-0.2.3/yulab.utils/R/parse_ratio.R |only yulab.utils-0.2.3/yulab.utils/R/pkg-utils.R | 87 ++++----- yulab.utils-0.2.3/yulab.utils/R/quiet.r | 26 +- yulab.utils-0.2.3/yulab.utils/R/regexpr.R | 26 +- yulab.utils-0.2.3/yulab.utils/R/scihub-dl.R | 8 yulab.utils-0.2.3/yulab.utils/R/str-utils.R | 48 ++--- yulab.utils-0.2.3/yulab.utils/R/utilities.R | 21 +- yulab.utils-0.2.3/yulab.utils/R/yulab-msg.R | 10 - yulab.utils-0.2.3/yulab.utils/man/check_directory.Rd | 8 yulab.utils-0.2.3/yulab.utils/man/check_file.Rd | 8 yulab.utils-0.2.3/yulab.utils/man/check_input.Rd | 26 +- yulab.utils-0.2.3/yulab.utils/man/check_packages.Rd | 11 + yulab.utils-0.2.3/yulab.utils/man/check_range.Rd | 8 yulab.utils-0.2.3/yulab.utils/man/cran-bioc-pkg.Rd | 15 + yulab.utils-0.2.3/yulab.utils/man/download_yulab_file.Rd |only yulab.utils-0.2.3/yulab.utils/man/exec.Rd | 6 yulab.utils-0.2.3/yulab.utils/man/get_dependencies.Rd | 13 + yulab.utils-0.2.3/yulab.utils/man/get_fun_from_pkg.Rd | 11 + yulab.utils-0.2.3/yulab.utils/man/github-pkg.Rd | 15 + yulab.utils-0.2.3/yulab.utils/man/has_internet.Rd | 6 yulab.utils-0.2.3/yulab.utils/man/is.installed.Rd | 16 + yulab.utils-0.2.3/yulab.utils/man/load_OrgDb.Rd |only yulab.utils-0.2.3/yulab.utils/man/ls2df.Rd | 8 yulab.utils-0.2.3/yulab.utils/man/mypkg.Rd | 13 + yulab.utils-0.2.3/yulab.utils/man/o.Rd | 7 yulab.utils-0.2.3/yulab.utils/man/packageTitle.Rd | 11 + yulab.utils-0.2.3/yulab.utils/man/parse_ratio.Rd |only yulab.utils-0.2.3/yulab.utils/man/pload.Rd | 20 +- yulab.utils-0.2.3/yulab.utils/man/rbindlist.Rd | 6 yulab.utils-0.2.3/yulab.utils/man/read.cb.Rd | 7 yulab.utils-0.2.3/yulab.utils/man/regexpr-style.Rd | 23 +- yulab.utils-0.2.3/yulab.utils/man/show_in_excel.Rd | 7 yulab.utils-0.2.3/yulab.utils/man/str-detect.Rd | 17 + yulab.utils-0.2.3/yulab.utils/man/str-extract.Rd | 13 + yulab.utils-0.2.3/yulab.utils/man/str-starts-ends.Rd | 15 + yulab.utils-0.2.3/yulab.utils/man/str_wrap.Rd | 15 + yulab.utils-0.2.3/yulab.utils/man/user_dir.Rd | 6 yulab.utils-0.2.3/yulab.utils/man/yread.Rd | 12 + yulab.utils-0.2.3/yulab.utils/man/yulab-cache.Rd | 49 ++++- yulab.utils-0.2.3/yulab.utils/man/yulab-message.Rd |only yulab.utils-0.2.3/yulab.utils/man/yulab_msg.Rd | 8 yulab.utils-0.2.3/yulab.utils/tests |only 57 files changed, 777 insertions(+), 319 deletions(-)
Title: Processing Force-Plate Data
Description: Process raw force-plate data (txt-files) by segmenting them into trials and, if needed, calculating (user-defined) descriptive
statistics of variables for user-defined time bins (relative to trigger onsets) for each trial. When segmenting the data a baseline
correction, a filter, and a data imputation can be applied if needed. Experimental data can also be processed and combined with the
segmented force-plate data. This procedure is suggested by Johannsen et al. (2023) <doi:10.6084/m9.figshare.22190155> and some of the
options (e.g., choice of low-pass filter) are also suggested by Winter (2009) <doi:10.1002/9780470549148>.
Author: Raphael Hartmann [aut, cre] ,
Anton Koger [aut, ctb] ,
Leif Johannsen [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between forceplate versions 1.1-4 dated 2025-03-19 and 1.1-5 dated 2025-12-15
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- R/segment_fp_data.R | 3 ++- man/segment_fp_data.Rd | 3 ++- 4 files changed, 14 insertions(+), 11 deletions(-)
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch [aut, cre]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.9.31 dated 2024-08-29 and 0.9.33 dated 2025-12-15
DESCRIPTION | 8 MD5 | 41 - NEWS.md | 10 R/All.R | 2 R/escapes.R |only R/html.tabular.R | 164 ++-- R/latex.tabular.R | 26 R/options.R | 151 ++- R/tabular.R | 1764 ++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/HTML.R |only inst/doc/HTML.Rmd |only inst/doc/HTML.html |only inst/doc/knitrTables.R |only inst/doc/knitrTables.Rmd |only inst/doc/knitrTables.pdf |only inst/doc/tables.R | 34 inst/doc/tables.Rnw | 4 inst/doc/tables.pdf |binary man/html.tabular.Rd | 3 man/latex.tabular.Rd | 3 man/table_options.Rd | 12 vignettes/tables.Rnw | 4 vignettes/tables.Rout.save | 11 vignettes/tables.bib | 2 25 files changed, 1235 insertions(+), 1004 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2025)<Forthcoming>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.1-1 dated 2025-12-06 and 4.2-1 dated 2025-12-15
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++++---- NAMESPACE | 5 +++++ NEWS.md | 4 ++++ R/stabwt.r |only R/stabwtlong.r |only R/stabwtmulti.r |only data/exdata04.RData |binary man/stabwt.Rd |only man/stabwtlong.Rd |only man/stabwtmulti.Rd |only 11 files changed, 24 insertions(+), 9 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.4.0 dated 2025-09-06 and 1.5.0 dated 2025-12-15
rice-1.4.0/rice/man/coverage.Rd |only rice-1.4.0/rice/man/howmanyC14.Rd |only rice-1.5.0/rice/DESCRIPTION | 16 - rice-1.5.0/rice/MD5 | 129 ++++---- rice-1.5.0/rice/NAMESPACE | 8 rice-1.5.0/rice/NEWS.md | 11 rice-1.5.0/rice/R/calibrate.R | 251 +++++++++++++++- rice-1.5.0/rice/R/plots.R | 113 ++++--- rice-1.5.0/rice/R/rice-package.R | 4 rice-1.5.0/rice/R/rice.R | 12 rice-1.5.0/rice/R/sets.R | 74 ---- rice-1.5.0/rice/R/sources.R | 26 + rice-1.5.0/rice/R/timescales.R | 357 ++++++++++------------- rice-1.5.0/rice/build/partial.rdb |binary rice-1.5.0/rice/build/vignette.rds |binary rice-1.5.0/rice/inst/doc/rice.R | 17 - rice-1.5.0/rice/inst/doc/rice.Rmd | 23 + rice-1.5.0/rice/inst/doc/rice.html | 264 ++++++++++------- rice-1.5.0/rice/man/BCADtoC14.Rd | 8 rice-1.5.0/rice/man/BCADtoDelta14C.Rd | 8 rice-1.5.0/rice/man/BCADtoF14C.Rd | 8 rice-1.5.0/rice/man/BCADtob2k.Rd | 4 rice-1.5.0/rice/man/BCADtocalBP.Rd | 6 rice-1.5.0/rice/man/BCADtopMC.Rd | 8 rice-1.5.0/rice/man/C14toBCAD.Rd | 10 rice-1.5.0/rice/man/C14toDelta14C.Rd | 4 rice-1.5.0/rice/man/C14toF14C.Rd | 4 rice-1.5.0/rice/man/C14tob2k.Rd | 6 rice-1.5.0/rice/man/C14tocalBP.Rd | 6 rice-1.5.0/rice/man/C14topMC.Rd | 4 rice-1.5.0/rice/man/CtoF.Rd | 4 rice-1.5.0/rice/man/Delta14CtoC14.Rd | 4 rice-1.5.0/rice/man/Delta14CtoF14C.Rd | 4 rice-1.5.0/rice/man/Delta14CtopMC.Rd | 4 rice-1.5.0/rice/man/F14CtoC14.Rd | 4 rice-1.5.0/rice/man/F14CtoDelta14C.Rd | 4 rice-1.5.0/rice/man/F14CtopMC.Rd | 4 rice-1.5.0/rice/man/FtoC.Rd | 4 rice-1.5.0/rice/man/age.range.Rd |only rice-1.5.0/rice/man/b2ktoBCAD.Rd | 4 rice-1.5.0/rice/man/b2ktoC14.Rd | 4 rice-1.5.0/rice/man/b2ktoDelta14C.Rd | 4 rice-1.5.0/rice/man/b2ktoF14C.Rd | 4 rice-1.5.0/rice/man/b2ktopMC.Rd | 4 rice-1.5.0/rice/man/calBPtoBCAD.Rd | 6 rice-1.5.0/rice/man/calBPtoC14.Rd | 4 rice-1.5.0/rice/man/calBPtoDelta14C.Rd | 4 rice-1.5.0/rice/man/calBPtoF14C.Rd | 4 rice-1.5.0/rice/man/calBPtopMC.Rd | 4 rice-1.5.0/rice/man/calib.t.Rd | 3 rice-1.5.0/rice/man/calibrate.Rd | 4 rice-1.5.0/rice/man/calibrate.table.Rd |only rice-1.5.0/rice/man/draw.ccurve.Rd | 2 rice-1.5.0/rice/man/draw.dates.Rd | 15 rice-1.5.0/rice/man/fromto.Rd | 7 rice-1.5.0/rice/man/howmuchC14.Rd |only rice-1.5.0/rice/man/hpd.Rd | 2 rice-1.5.0/rice/man/overlap.Rd | 3 rice-1.5.0/rice/man/pMCtoC14.Rd | 4 rice-1.5.0/rice/man/pMCtoDelta14C.Rd | 6 rice-1.5.0/rice/man/pMCtoF14C.Rd | 4 rice-1.5.0/rice/man/push.gamma.Rd | 3 rice-1.5.0/rice/man/push.normal.Rd | 3 rice-1.5.0/rice/man/rice-package.Rd | 2 rice-1.5.0/rice/man/rice.Rd | 2 rice-1.5.0/rice/tests/testthat/test-rice.R | 4 rice-1.5.0/rice/tests/testthat/test-timescales.R | 9 rice-1.5.0/rice/vignettes/rice.Rmd | 23 + 68 files changed, 922 insertions(+), 629 deletions(-)
Title: Effect Size and Confidence Interval Calculator
Description: Measure of the Effect ('MOTE') is an effect size calculator, including a
wide variety of effect sizes in the mean differences family (all versions of d) and
the variance overlap family (eta, omega, epsilon, r). 'MOTE' provides non-central
confidence intervals for each effect size, relevant test statistics, and output
for reporting in APA Style (American Psychological Association, 2010,
<ISBN:1433805618>) with 'LaTeX'. In research, an over-reliance on p-values
may conceal the fact that a study is under-powered (Halsey, Curran-Everett,
Vowler, & Drummond, 2015 <doi:10.1038/nmeth.3288>). A test may be statistically
significant, yet practically inconsequential (Fritz, Scherndl, & Kühberger, 2012
<doi:10.1177/0959354312436870>). Although the American Psychological Association
has long advocated for the inclusion of effect sizes (Wilkinson & American
Psychological Association Task Force on Statistical Inference, 1999
<doi:10.1037/0003-066X.54.8.594>), the [...truncated...]
Author: Erin M. Buchanan [aut, cre] ,
Amber M Gillenwaters [aut] ,
John E. Scofield [aut] ,
K. D. Valentine [aut]
Maintainer: Erin M. Buchanan <buchananlab@gmail.com>
Diff between MOTE versions 1.0.2 dated 2019-04-10 and 1.2.2 dated 2025-12-15
MOTE-1.0.2/MOTE/R/d.dep.t.avg.R |only MOTE-1.0.2/MOTE/R/d.dep.t.diff.R |only MOTE-1.0.2/MOTE/R/d.dep.t.diff.t.R |only MOTE-1.0.2/MOTE/R/d.dep.t.rm.R |only MOTE-1.0.2/MOTE/R/d.ind.t.R |only MOTE-1.0.2/MOTE/R/d.ind.t.t.R |only MOTE-1.0.2/MOTE/R/d.prop.R |only MOTE-1.0.2/MOTE/R/d.single.t.R |only MOTE-1.0.2/MOTE/R/d.single.t.t.R |only MOTE-1.0.2/MOTE/R/d.to.r.R |only MOTE-1.0.2/MOTE/R/d.z.mean.R |only MOTE-1.0.2/MOTE/R/d.z.z.R |only MOTE-1.0.2/MOTE/R/delta.ind.t.R |only MOTE-1.0.2/MOTE/R/epsilon.full.SS.R |only MOTE-1.0.2/MOTE/R/eta.F.R |only MOTE-1.0.2/MOTE/R/eta.full.SS.R |only MOTE-1.0.2/MOTE/R/eta.partial.SS.R |only MOTE-1.0.2/MOTE/R/g.ind.t.R |only MOTE-1.0.2/MOTE/R/ges.partial.SS.mix.R |only MOTE-1.0.2/MOTE/R/ges.partial.SS.rm.R |only MOTE-1.0.2/MOTE/R/omega.F.R |only MOTE-1.0.2/MOTE/R/omega.full.SS.R |only MOTE-1.0.2/MOTE/R/omega.gen.SS.rm.R |only MOTE-1.0.2/MOTE/R/omega.partial.SS.bn.R |only MOTE-1.0.2/MOTE/R/omega.partial.SS.rm.R |only MOTE-1.0.2/MOTE/R/r.correl.R |only MOTE-1.0.2/MOTE/R/v.chi.sq.R |only MOTE-1.0.2/MOTE/man/d.dep.t.avg.Rd |only MOTE-1.0.2/MOTE/man/d.dep.t.diff.Rd |only MOTE-1.0.2/MOTE/man/d.dep.t.diff.t.Rd |only MOTE-1.0.2/MOTE/man/d.dep.t.rm.Rd |only MOTE-1.0.2/MOTE/man/d.ind.t.Rd |only MOTE-1.0.2/MOTE/man/d.ind.t.t.Rd |only MOTE-1.0.2/MOTE/man/d.prop.Rd |only MOTE-1.0.2/MOTE/man/d.single.t.Rd |only MOTE-1.0.2/MOTE/man/d.single.t.t.Rd |only MOTE-1.0.2/MOTE/man/d.to.r.Rd |only MOTE-1.0.2/MOTE/man/d.z.mean.Rd |only MOTE-1.0.2/MOTE/man/d.z.z.Rd |only MOTE-1.0.2/MOTE/man/delta.ind.t.Rd |only MOTE-1.0.2/MOTE/man/epsilon.full.SS.Rd |only MOTE-1.0.2/MOTE/man/eta.F.Rd |only MOTE-1.0.2/MOTE/man/eta.full.SS.Rd |only MOTE-1.0.2/MOTE/man/eta.partial.SS.Rd |only MOTE-1.0.2/MOTE/man/g.ind.t.Rd |only MOTE-1.0.2/MOTE/man/ges.partial.SS.mix.Rd |only MOTE-1.0.2/MOTE/man/ges.partial.SS.rm.Rd |only MOTE-1.0.2/MOTE/man/odds.Rd |only MOTE-1.0.2/MOTE/man/omega.F.Rd |only MOTE-1.0.2/MOTE/man/omega.full.SS.Rd |only MOTE-1.0.2/MOTE/man/omega.gen.SS.rm.Rd |only MOTE-1.0.2/MOTE/man/omega.partial.SS.bn.Rd |only MOTE-1.0.2/MOTE/man/omega.partial.SS.rm.Rd |only MOTE-1.0.2/MOTE/man/r.correl.Rd |only MOTE-1.0.2/MOTE/man/v.chi.sq.Rd |only MOTE-1.2.2/MOTE/DESCRIPTION | 30 ++-- MOTE-1.2.2/MOTE/MD5 | 211 ++++++++++++++++++----------- MOTE-1.2.2/MOTE/NAMESPACE | 41 ++++- MOTE-1.2.2/MOTE/NEWS.md |only MOTE-1.2.2/MOTE/R/apa.R | 101 ++++++++++--- MOTE-1.2.2/MOTE/R/bn1-data.R | 34 ++-- MOTE-1.2.2/MOTE/R/bn2-data.R | 32 ++-- MOTE-1.2.2/MOTE/R/chisq-data.R | 38 +++-- MOTE-1.2.2/MOTE/R/ci_r.R |only MOTE-1.2.2/MOTE/R/ci_r2.R |only MOTE-1.2.2/MOTE/R/d_dep_t_avg.R |only MOTE-1.2.2/MOTE/R/d_dep_t_diff.R |only MOTE-1.2.2/MOTE/R/d_dep_t_diff_t.R |only MOTE-1.2.2/MOTE/R/d_dep_t_rm.R |only MOTE-1.2.2/MOTE/R/d_effect.R |only MOTE-1.2.2/MOTE/R/d_ind_t.R |only MOTE-1.2.2/MOTE/R/d_ind_t_t.R |only MOTE-1.2.2/MOTE/R/d_prop.R |only MOTE-1.2.2/MOTE/R/d_single_t.R |only MOTE-1.2.2/MOTE/R/d_single_t_t.R |only MOTE-1.2.2/MOTE/R/d_to_r.R |only MOTE-1.2.2/MOTE/R/d_z_mean.R |only MOTE-1.2.2/MOTE/R/d_z_z.R |only MOTE-1.2.2/MOTE/R/delta_ind_t.R |only MOTE-1.2.2/MOTE/R/dept-data.R | 5 MOTE-1.2.2/MOTE/R/epsilon_full_ss.R |only MOTE-1.2.2/MOTE/R/eta_f.R |only MOTE-1.2.2/MOTE/R/eta_full_ss.R |only MOTE-1.2.2/MOTE/R/eta_partial_ss.R |only MOTE-1.2.2/MOTE/R/f_r_square.R |only MOTE-1.2.2/MOTE/R/g_ind_t.R |only MOTE-1.2.2/MOTE/R/ges_partial_ss_mix.R |only MOTE-1.2.2/MOTE/R/ges_partial_ss_rm.R |only MOTE-1.2.2/MOTE/R/h_prop.R |only MOTE-1.2.2/MOTE/R/indt-data.R | 20 +- MOTE-1.2.2/MOTE/R/lambda_to_r2.R |only MOTE-1.2.2/MOTE/R/mix2-data.R | 36 ++-- MOTE-1.2.2/MOTE/R/noncentral_f.R |only MOTE-1.2.2/MOTE/R/noncentral_t.R |only MOTE-1.2.2/MOTE/R/noncentral_x.R |only MOTE-1.2.2/MOTE/R/odds.R | 128 ++++++++++------- MOTE-1.2.2/MOTE/R/omega_f.R |only MOTE-1.2.2/MOTE/R/omega_full_ss.R |only MOTE-1.2.2/MOTE/R/omega_g_ss_rm.R |only MOTE-1.2.2/MOTE/R/omega_partial_ss_bn.R |only MOTE-1.2.2/MOTE/R/omega_partial_ss_rm.R |only MOTE-1.2.2/MOTE/R/r_correl.R |only MOTE-1.2.2/MOTE/R/r_effect.R |only MOTE-1.2.2/MOTE/R/r_square_f.R |only MOTE-1.2.2/MOTE/R/rm1-data.R | 28 +-- MOTE-1.2.2/MOTE/R/rm2-data.R | 40 +++-- MOTE-1.2.2/MOTE/R/singt-data.R | 18 +- MOTE-1.2.2/MOTE/R/v_chi_sq.R |only MOTE-1.2.2/MOTE/README.md | 23 +-- MOTE-1.2.2/MOTE/inst/CITATION | 2 MOTE-1.2.2/MOTE/man/apa.Rd | 42 +++-- MOTE-1.2.2/MOTE/man/bn1_data.Rd | 34 +++- MOTE-1.2.2/MOTE/man/bn2_data.Rd | 34 +++- MOTE-1.2.2/MOTE/man/chisq_data.Rd | 38 +++-- MOTE-1.2.2/MOTE/man/ci_r2.Rd |only MOTE-1.2.2/MOTE/man/d_dep_t_avg.Rd |only MOTE-1.2.2/MOTE/man/d_dep_t_diff.Rd |only MOTE-1.2.2/MOTE/man/d_dep_t_diff_t.Rd |only MOTE-1.2.2/MOTE/man/d_dep_t_rm.Rd |only MOTE-1.2.2/MOTE/man/d_effect.Rd |only MOTE-1.2.2/MOTE/man/d_ind_t.Rd |only MOTE-1.2.2/MOTE/man/d_ind_t_t.Rd |only MOTE-1.2.2/MOTE/man/d_prop.Rd |only MOTE-1.2.2/MOTE/man/d_single_t.Rd |only MOTE-1.2.2/MOTE/man/d_single_t_t.Rd |only MOTE-1.2.2/MOTE/man/d_to_r.Rd |only MOTE-1.2.2/MOTE/man/d_z_mean.Rd |only MOTE-1.2.2/MOTE/man/d_z_z.Rd |only MOTE-1.2.2/MOTE/man/delta_ind_t.Rd |only MOTE-1.2.2/MOTE/man/dept_data.Rd | 11 - MOTE-1.2.2/MOTE/man/epsilon_full_ss.Rd |only MOTE-1.2.2/MOTE/man/eta_f.Rd |only MOTE-1.2.2/MOTE/man/eta_full_ss.Rd |only MOTE-1.2.2/MOTE/man/eta_partial_ss.Rd |only MOTE-1.2.2/MOTE/man/g_ind_t.Rd |only MOTE-1.2.2/MOTE/man/ges_partial_ss_mix.Rd |only MOTE-1.2.2/MOTE/man/ges_partial_ss_rm.Rd |only MOTE-1.2.2/MOTE/man/h_prop.Rd |only MOTE-1.2.2/MOTE/man/indt_data.Rd | 20 +- MOTE-1.2.2/MOTE/man/mix2_data.Rd | 35 ++-- MOTE-1.2.2/MOTE/man/odds_ratio.Rd |only MOTE-1.2.2/MOTE/man/omega_f.Rd |only MOTE-1.2.2/MOTE/man/omega_full_ss.Rd |only MOTE-1.2.2/MOTE/man/omega_g_ss_rm.Rd |only MOTE-1.2.2/MOTE/man/omega_partial_ss_bn.Rd |only MOTE-1.2.2/MOTE/man/omega_partial_ss_rm.Rd |only MOTE-1.2.2/MOTE/man/r_correl.Rd |only MOTE-1.2.2/MOTE/man/r_effect.Rd |only MOTE-1.2.2/MOTE/man/rm1_data.Rd | 29 ++- MOTE-1.2.2/MOTE/man/rm2_data.Rd | 41 +++-- MOTE-1.2.2/MOTE/man/singt_data.Rd | 19 +- MOTE-1.2.2/MOTE/man/v_chi_sq.Rd |only MOTE-1.2.2/MOTE/tests |only 153 files changed, 674 insertions(+), 416 deletions(-)
Title: The Fill-Mask Association Test
Description: The Fill-Mask Association Test ('FMAT')
<doi:10.1037/pspa0000396>
is an integrative and probability-based method using
Masked Language Models to measure conceptual associations
(e.g., attitudes, biases, stereotypes, social norms, cultural values)
as propositions in natural language.
Supported language models include 'BERT'
<doi:10.48550/arXiv.1810.04805> and its variants available at 'Hugging Face'
<https://huggingface.co/models?pipeline_tag=fill-mask>.
Methodological references and installation guidance are provided at
<https://psychbruce.github.io/FMAT/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between FMAT versions 2025.8 dated 2025-08-19 and 2025.12 dated 2025-12-15
DESCRIPTION | 10 - MD5 | 16 +- NEWS.md | 4 R/FMAT.R | 88 ++++++++------ README.md | 292 +++++++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary man/BERT_vocab.Rd | 4 man/FMAT_run.Rd | 7 - man/set_cache_folder.Rd | 4 9 files changed, 339 insertions(+), 86 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 2.0.88 dated 2025-10-21 and 2.0.89 dated 2025-12-15
epiR-2.0.88/epiR/inst/doc/epiR_descriptive.R |only epiR-2.0.88/epiR/inst/doc/epiR_descriptive.Rmd |only epiR-2.0.88/epiR/inst/doc/epiR_descriptive.html |only epiR-2.0.88/epiR/inst/doc/epiR_measures_of_association.R |only epiR-2.0.88/epiR/inst/doc/epiR_measures_of_association.Rmd |only epiR-2.0.88/epiR/inst/doc/epiR_measures_of_association.html |only epiR-2.0.88/epiR/vignettes/attributable_fraction.png |only epiR-2.0.88/epiR/vignettes/attributable_risk.png |only epiR-2.0.88/epiR/vignettes/epiR_descriptive.Rmd |only epiR-2.0.88/epiR/vignettes/epiR_descriptive.bib |only epiR-2.0.88/epiR/vignettes/epiR_measures_of_association.Rmd |only epiR-2.0.88/epiR/vignettes/epiR_measures_of_association.bib |only epiR-2.0.88/epiR/vignettes/epidemic_curve-01.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-02.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-03.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-04.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-05.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-06.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-07.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-08.png |only epiR-2.0.88/epiR/vignettes/epidemic_curve-09.png |only epiR-2.0.88/epiR/vignettes/low_bw_adjusted_or.png |only epiR-2.0.88/epiR/vignettes/low_bw_unadjusted_or.png |only epiR-2.0.88/epiR/vignettes/map-01.png |only epiR-2.0.88/epiR/vignettes/map-02.png |only epiR-2.0.88/epiR/vignettes/population_attributable_fraction.png |only epiR-2.0.88/epiR/vignettes/population_attributable_risk.png |only epiR-2.0.88/epiR/vignettes/prob_dis_freedom.png |only epiR-2.0.88/epiR/vignettes/ranked_error_bar-01.png |only epiR-2.0.88/epiR/vignettes/ranked_error_bar-02.png |only epiR-2.0.88/epiR/vignettes/risk_ratio.png |only epiR-2.0.89/epiR/DESCRIPTION | 12 epiR-2.0.89/epiR/MD5 | 105 ++- epiR-2.0.89/epiR/NEWS | 16 epiR-2.0.89/epiR/R/epi.kappa.R | 265 ++++------ epiR-2.0.89/epiR/R/epi.nomogram.R | 4 epiR-2.0.89/epiR/R/zRRkoopman.R | 10 epiR-2.0.89/epiR/build/vignette.rds |binary epiR-2.0.89/epiR/inst/doc/epiR_descriptive_epi.R |only epiR-2.0.89/epiR/inst/doc/epiR_descriptive_epi.Rmd |only epiR-2.0.89/epiR/inst/doc/epiR_descriptive_epi.html |only epiR-2.0.89/epiR/inst/doc/epiR_diagnostic_tests.R |only epiR-2.0.89/epiR/inst/doc/epiR_diagnostic_tests.Rmd |only epiR-2.0.89/epiR/inst/doc/epiR_diagnostic_tests.html |only epiR-2.0.89/epiR/inst/doc/epiR_measures_of_assoc.R |only epiR-2.0.89/epiR/inst/doc/epiR_measures_of_assoc.Rmd |only epiR-2.0.89/epiR/inst/doc/epiR_measures_of_assoc.html |only epiR-2.0.89/epiR/inst/doc/epiR_sample_size.R | 15 epiR-2.0.89/epiR/inst/doc/epiR_sample_size.Rmd | 23 epiR-2.0.89/epiR/inst/doc/epiR_sample_size.html | 33 - epiR-2.0.89/epiR/inst/doc/epiR_surveillance.R | 199 +++---- epiR-2.0.89/epiR/inst/doc/epiR_surveillance.Rmd | 242 +++------ epiR-2.0.89/epiR/inst/doc/epiR_surveillance.html | 67 +- epiR-2.0.89/epiR/man/epi.2by2.Rd | 2 epiR-2.0.89/epiR/man/epi.kappa.Rd | 33 - epiR-2.0.89/epiR/man/rsu.dxtest.Rd | 4 epiR-2.0.89/epiR/vignettes/epiR_descriptive_epi.Rmd |only epiR-2.0.89/epiR/vignettes/epiR_descriptive_epi.bib |only epiR-2.0.89/epiR/vignettes/epiR_diagnostic_tests.Rmd |only epiR-2.0.89/epiR/vignettes/epiR_diagnostic_tests.bib |only epiR-2.0.89/epiR/vignettes/epiR_measures_of_assoc.Rmd |only epiR-2.0.89/epiR/vignettes/epiR_measures_of_assoc.bib |only epiR-2.0.89/epiR/vignettes/epiR_sample_size.Rmd | 23 epiR-2.0.89/epiR/vignettes/epiR_sample_size.bib | 6 epiR-2.0.89/epiR/vignettes/epiR_surveillance.Rmd | 242 +++------ epiR-2.0.89/epiR/vignettes/epiR_surveillance.bib | 6 epiR-2.0.89/epiR/vignettes/figures |only 67 files changed, 599 insertions(+), 708 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] ,
Unicode, Inc. [dtc, cph]
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.6-5 dated 2025-04-01 and 0.6-6 dated 2025-12-15
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- NEWS | 6 ++++++ build/partial.rdb |binary build/vignette.rds |binary data/tznames.RData |binary inst/doc/datetimeutils_examples.Rnw | 4 ++-- inst/doc/datetimeutils_examples.pdf |binary inst/tinytest/test.R | 6 ++++++ vignettes/auto |only vignettes/datetimeutils_examples.Rnw | 4 ++-- 11 files changed, 32 insertions(+), 18 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <DOI:10.1007/978-3-031-70584-7>, and Time Series: A Data Analysis Approach Using R (2nd ed). Chapman-Hall, 2026, <https://www.routledge.com/Time-Series-A-Data-Analysis-Approach-Using-R/Shumway-Stoffer/p/book/9781041031642>. Most scripts are designed to require minimal input to produce aesthetically pleasing output for ease of use in live demonstrations and course work.
Author: David Stoffer [aut, cre],
Nicky Poison [ctb, mus, spy]
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 2.3 dated 2025-08-21 and 2.4 dated 2025-12-15
DESCRIPTION | 8 +- MD5 | 152 ++++++++++++++++++++++++++------------------------- NAMESPACE | 11 +-- R/SigExtract.R | 43 +++++--------- R/arma.check.R |only R/arma.spec.R | 19 +++++- R/lag1.plot.R | 13 +++- R/lag2.plot.R | 14 +++- R/mvspec.R | 6 +- R/sarima.R | 13 +++- R/sarima.sim.R | 33 ++++++++++- R/timex.R |only R/tsplot.R | 51 +++++++++-------- R/zzz.R | 30 ---------- README.md | 46 ++++++++------- data/MEI2.rda |only man/ARMAtoAR.Rd | 5 + man/EBV.Rd | 5 + man/EM.Rd | 23 +++++-- man/ENSO.Rd | 13 ++++ man/ESS.Rd | 3 - man/Grid.Rd | 2 man/Hare.Rd | 8 +- man/Kfilter.Rd | 4 - man/Ksmooth.Rd | 3 - man/Lynx.Rd | 6 +- man/MEI.Rd | 15 ++++- man/MEI2.Rd |only man/SV.mcmc.Rd | 12 ++-- man/SigExtract.Rd | 16 ++++- man/USpop20.Rd | 23 ++++--- man/acf1.Rd | 1 man/acf2.Rd | 6 +- man/ar.boot.Rd | 3 - man/ar.mcmc.Rd | 3 - man/ar1miss.Rd | 7 ++ man/arf.Rd | 7 ++ man/arma.check.Rd |only man/arma.spec.Rd | 33 +++++++---- man/astsa-package.Rd | 21 ++++--- man/autoSpec.Rd | 2 man/blood.Rd | 1 man/bnrf1ebv.Rd | 4 + man/bnrf1hvs.Rd | 4 + man/cardox.Rd | 3 + man/ccf2.Rd | 2 man/climhyd.Rd | 3 + man/cpg.Rd | 3 + man/djia.Rd | 13 ++++ man/dna2vector.Rd | 1 man/econ5.Rd | 7 ++ man/eqexp.Rd | 39 +++++++++++-- man/fmri1.Rd | 3 + man/gas.Rd | 4 + man/gtemp.month.Rd | 6 -- man/lag1.plot.Rd | 18 ++++-- man/lag2.plot.Rd | 12 +++- man/lap.xts.Rd | 13 ++++ man/matrixpwr.Rd | 7 +- man/mvspec.Rd | 8 +- man/nyse.Rd | 2 man/oil.Rd | 4 + man/polyMul.Rd | 1 man/sarima.Rd | 11 ++- man/sarima.sim.Rd | 22 +++++-- man/sleep1.Rd | 9 +-- man/sleep2.Rd | 8 -- man/soi.Rd | 4 - man/soiltemp.Rd | 11 +++ man/sp500.gr.Rd | 48 ++++++++-------- man/sp500w.Rd | 8 ++ man/spec.ic.Rd | 14 +--- man/specenv.Rd | 22 +++---- man/star.Rd | 8 +- man/sunspotz.Rd | 5 + man/test.linear.Rd | 2 man/timex.Rd |only man/trend.Rd | 7 +- man/tspairs.Rd | 8 +- man/tsplot.Rd | 81 +++++++++++++-------------- 80 files changed, 659 insertions(+), 427 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.4 dated 2025-12-04 and 1.4.5 dated 2025-12-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/model_formula_reader.R | 16 +++++++++++++--- R/other_functions.R | 4 ++-- 5 files changed, 31 insertions(+), 13 deletions(-)