Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-24 0.0-6
2024-09-20 0.0-5
2024-06-27 0.0-4
2024-01-09 0.0-3
2023-09-26 0.0-2
2023-09-10 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-21 0.4.2
2024-07-20 0.4.1
2024-04-03 0.3.12
2022-09-01 0.3.10
2022-03-09 0.3.9
2022-02-27 0.3.8
2021-11-09 0.3.7
2021-09-22 0.3.5
2021-03-01 0.3.4
2020-10-22 0.3.2
2020-04-07 0.2.3
Title: Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Description: Articles in the 'R Journal' were first authored in 'LaTeX', which performs
admirably for 'PDF' files but is less than ideal for modern online interfaces.
The 'texor' package does all the transitional chores and conversions necessary
to move to the online versions.
Author: Abhishek Ulayil [aut, cre, cph] ,
Heather Turner [ctb] ,
Christophe Dervieux [ctb] ,
Mitchell O'Hara-Wild [ctb] ,
Dianne Cook [ctb] ,
Yinxiang Huang [ctb]
Maintainer: Abhishek Ulayil <perricoq@outlook.com>
Diff between texor versions 1.5.6 dated 2025-04-01 and 1.6.0 dated 2025-09-08
DESCRIPTION | 22 ++++++++++++---------- MD5 | 22 +++++++++++----------- NAMESPACE | 8 ++++++++ NEWS.md | 9 +++++++++ R/article-tools.R | 8 ++++---- R/stream-editor.R | 6 +----- R/string-tools.R | 36 ++++++++++++------------------------ build/vignette.rds |binary inst/bookdown_ref.lua | 13 +++++++------ inst/doc/introduction-to-texor.Rmd | 1 - inst/doc/introduction-to-texor.html | 1 - vignettes/introduction-to-texor.Rmd | 1 - 12 files changed, 64 insertions(+), 63 deletions(-)
Title: Data Analyses in Agriculture and Biology
Description: Contains several tools for nonlinear regression analyses and general data analysis in biology and agriculture. Contains also datasets for practicing and teaching purposes. Supports the blog: Onofri (2024) "Fixing the bridge between biologists and statisticians" <https://www.statforbiology.com> and the book: Onofri (2024) "Experimental Methods in Agriculture" <https://www.statforbiology.com/_statbookeng/>. The blog is a collection of short articles aimed at improving the efficiency of communication between biologists and statisticians, as pointed out in Kozak (2016) <doi:10.1590/0103-9016-2015-0399>, spreading a better awareness of the potential usefulness, beauty and limitations of biostatistic.
Author: Andrea Onofri [aut, cre]
Maintainer: Andrea Onofri <andrea.onofri@unipg.it>
Diff between statforbiology versions 0.9.9 dated 2024-10-21 and 1.0.2 dated 2025-09-08
DESCRIPTION | 9 ++-- MD5 | 22 +++++----- NAMESPACE | 4 - NEWS.md | 7 ++- R/SSLL.R | 14 +++--- R/boxcox.nls.R | 21 +++++---- R/getAgroData.R | 4 + R/gnlht.R | 114 +++++++++++++++++++++++++++-------------------------- R/plotRes.R |only R/plotnls.R | 52 +++++++++++++++++------- man/getAgroData.Rd | 5 +- man/plotRes.Rd |only man/plotnls.Rd | 3 - 13 files changed, 149 insertions(+), 106 deletions(-)
More information about statforbiology at CRAN
Permanent link
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.0.1-1 dated 2025-09-01 and 15.0.2-1 dated 2025-09-08
ChangeLog | 18 + DESCRIPTION | 8 MD5 | 27 - configure | 29 - configure.ac | 10 inst/NEWS.Rd | 15 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h.in | 5 inst/include/RcppArmadillo/rng/Alt_R_RNG.h | 49 +- inst/include/armadillo |only inst/include/current/armadillo_bits/arma_version.hpp | 2 inst/include/current/armadillo_bits/mul_gemm.hpp | 167 +++++++++- inst/include/current/armadillo_bits/mul_gemv.hpp | 83 ++++ inst/include/current/armadillo_bits/op_vectorise_meat.hpp | 24 + 15 files changed, 363 insertions(+), 74 deletions(-)
More information about PhoneValidator at CRAN
Permanent link
Title: Permutation Tests for Randomization Model
Description: Perform permutation-based hypothesis testing for randomized
experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470>
and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al.
(2022) <doi:10.1016/j.chemosphere.2022.136736>.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between peramo versions 0.1.3 dated 2023-05-31 and 0.1.5 dated 2025-09-08
DESCRIPTION | 13 ++- MD5 | 38 +++++------ NAMESPACE | 56 ++++++++-------- R/XY.R | 8 +- R/peramo-package.R | 30 +-------- R/tw_complex.R | 83 +++++++++++++++++++++++-- R/zzz.R | 2 build/partial.rdb |binary man/AB.Rd | 82 ++++++++++++------------ man/XY.Rd | 84 ++++++++++++++----------- man/ctm.Rd | 46 ++++++------- man/diffcalc.Rd | 32 ++++----- man/ensulizole.Rd | 68 ++++++++++---------- man/nolesser.Rd | 32 ++++----- man/owl.Rd | 122 ++++++++++++++++++------------------ man/owlStat.Rd | 58 ++++++++--------- man/peramo-package.Rd | 58 ++++++++--------- man/tw_complex.Rd | 143 +++++++++++++++++++++---------------------- man/twl.Rd | 166 +++++++++++++++++++++++++------------------------- man/twlStat.Rd | 76 +++++++++++----------- 20 files changed, 632 insertions(+), 565 deletions(-)
Title: Gene-Level Variant Association Tests for Pedigree Data
Description: Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Visconti Alessia [ctb],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 3.9 dated 2024-04-10 and 4.1 dated 2025-09-08
pedgene-3.9/pedgene/inst/LICENSE.note |only pedgene-4.1/pedgene/DESCRIPTION | 12 - pedgene-4.1/pedgene/MD5 | 26 +- pedgene-4.1/pedgene/NAMESPACE | 2 pedgene-4.1/pedgene/R/pedgene.R | 130 +++++++------- pedgene-4.1/pedgene/R/pedgene.stats.R | 5 pedgene-4.1/pedgene/build/vignette.rds |binary pedgene-4.1/pedgene/inst/COPYRIGHT |only pedgene-4.1/pedgene/inst/NEWS.Rd | 8 pedgene-4.1/pedgene/inst/doc/pedgene.pdf |binary pedgene-4.1/pedgene/tests/test.davies.R |only pedgene-4.1/pedgene/tests/test.davies.Rout.save |only pedgene-4.1/pedgene/tests/test.pedgene.R | 39 ++-- pedgene-4.1/pedgene/tests/test.pedgene.Rout.save | 54 +++-- pedgene-4.1/pedgene/tests/test.pedgene.expanded.R | 24 +- pedgene-4.1/pedgene/tests/test.pedgene.expanded.Rout.save | 55 +++-- 16 files changed, 200 insertions(+), 155 deletions(-)
Title: Green Index Quantification, Analysis and Visualization
Description: Quantification, analysis, and visualization of urban greenness within city networks using data from 'OpenStreetMap' <https://www.openstreetmap.org>.
Author: Sachit Mahajan [aut, cre]
Maintainer: Sachit Mahajan <sachitmahajan90@gmail.com>
Diff between greenR versions 0.0.1.3 dated 2025-06-12 and 0.0.1.4 dated 2025-09-08
greenR-0.0.1.3/greenR/vignettes/hexv.jpg |only greenR-0.0.1.3/greenR/vignettes/nearest_greenspace.png |only greenR-0.0.1.3/greenR/vignettes/zh_access.jpg |only greenR-0.0.1.4/greenR/DESCRIPTION | 6 - greenR-0.0.1.4/greenR/MD5 | 16 ++-- greenR-0.0.1.4/greenR/build/vignette.rds |binary greenR-0.0.1.4/greenR/inst/doc/introduction.html | 4 - greenR-0.0.1.4/greenR/inst/shiny/server.R | 56 +++++++++++++---- greenR-0.0.1.4/greenR/inst/shiny/ui.R | 10 ++- greenR-0.0.1.4/greenR/vignettes/EDU_mit_SGK.svg |only greenR-0.0.1.4/greenR/vignettes/access.jpg |binary 11 files changed, 64 insertions(+), 28 deletions(-)
Title: Methods to Enrich R Objects with Extra Components
Description: Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm', 'glm' and 'betareg'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between enrichwith versions 0.3.1 dated 2020-01-10 and 0.4.0 dated 2025-09-08
DESCRIPTION | 13 MD5 | 86 +-- NEWS.md | 117 ++--- R/data.R | 12 R/enrich-package.R | 8 R/enrich.betareg.R | 13 R/enrich.family.R | 19 R/enrich.glm.R | 28 - R/enrich.link-glm.R | 4 R/enrich.lm.R | 19 R/enriched_glm.R | 11 README.md | 20 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST |only inst/doc/GLMs.R | 64 +- inst/doc/GLMs.Rmd | 16 inst/doc/GLMs.html | 650 +++++++++++++++++----------- inst/doc/bias.R | 18 inst/doc/bias.Rmd | 18 inst/doc/bias.html | 498 ++++++++++++++------- inst/doc/exponential_family.R | 6 inst/doc/exponential_family.Rmd | 2 inst/doc/exponential_family.html | 309 ++++++++----- inst/templates/template_compute_component.R | 1 man/coef.enriched_glm.Rd | 3 man/coef.enriched_lm.Rd | 3 man/create_enrichwith_skeleton.Rd | 11 man/endometrial.Rd | 18 man/enrich.family.Rd | 2 man/enrich.glm.Rd | 2 man/enriched_glm.Rd | 4 man/enrichwith.Rd | 12 man/get_enrichment_options.betareg.Rd | 3 man/get_enrichment_options.family.Rd | 3 man/get_enrichment_options.glm.Rd | 3 man/get_enrichment_options.link-glm.Rd | 3 man/get_enrichment_options.lm.Rd | 3 man/get_information_function.betareg.Rd | 2 man/get_information_function.glm.Rd | 2 man/get_information_function.lm.Rd | 2 vignettes/GLMs.Rmd | 16 vignettes/bias.Rmd | 18 vignettes/enrichwith.bib | 2 vignettes/exponential_family.Rmd | 2 45 files changed, 1248 insertions(+), 798 deletions(-)
Title: State-Space Mass-Balance Model for Marine Ecosystems
Description: Fits a state-space mass-balance model for marine ecosystems,
which implements dynamics derived from
'Ecopath with Ecosim' ('EwE') <https://ecopath.org/>
while fitting to time-series of fishery catch, biomass indices,
age-composition samples, and weight-at-age data.
'Ecostate' fits biological parameters (e.g., equilibrium mass)
and measurement parameters (e.g., catchability coefficients)
jointly with residual variation in process errors, and can include
Bayesian priors for parameters.
Author: James T. Thorson [aut, cre]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between ecostate versions 0.2.0 dated 2024-11-25 and 0.3.0 dated 2025-09-08
ecostate-0.2.0/ecostate/inst/doc/model_of_intermediate_complexity.R |only ecostate-0.2.0/ecostate/inst/doc/model_of_intermediate_complexity.Rmd |only ecostate-0.2.0/ecostate/inst/doc/model_of_intermediate_complexity.html |only ecostate-0.2.0/ecostate/vignettes/model_of_intermediate_complexity.Rmd |only ecostate-0.3.0/ecostate/DESCRIPTION | 17 - ecostate-0.3.0/ecostate/MD5 | 35 +-- ecostate-0.3.0/ecostate/NAMESPACE | 3 ecostate-0.3.0/ecostate/NEWS.md | 10 ecostate-0.3.0/ecostate/R/compute_nll.R | 111 ++++++---- ecostate-0.3.0/ecostate/R/data.R | 85 +++++++ ecostate-0.3.0/ecostate/R/ecostate.R | 37 ++- ecostate-0.3.0/ecostate/R/stanzas.R | 37 +-- ecostate-0.3.0/ecostate/README.md | 24 +- ecostate-0.3.0/ecostate/build/vignette.rds |binary ecostate-0.3.0/ecostate/data/gulf_of_alaska.rda |only ecostate-0.3.0/ecostate/inst/CITATION | 37 ++- ecostate-0.3.0/ecostate/inst/doc/model-description.R |only ecostate-0.3.0/ecostate/inst/doc/model-description.Rmd |only ecostate-0.3.0/ecostate/inst/doc/model-description.html |only ecostate-0.3.0/ecostate/man/compute_nll.Rd | 13 - ecostate-0.3.0/ecostate/man/eastern_bering_sea.Rd | 9 ecostate-0.3.0/ecostate/man/gulf_of_alaska.Rd |only ecostate-0.3.0/ecostate/vignettes/model-description.Rmd |only ecostate-0.3.0/ecostate/vignettes/refs.bib |only 24 files changed, 302 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 0.4.1
2024-02-26 0.4.0
2020-06-02 0.3.1
2018-07-03 0.3.0
2017-04-06 0.2.1
2017-03-31 0.2.0
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 0.1.0 dated 2025-07-18 and 0.1.1 dated 2025-09-08
DESCRIPTION | 41 +++++++++++++++++++++-------------------- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 8 ++++---- man/mcptools-package.Rd | 4 ++-- 5 files changed, 35 insertions(+), 30 deletions(-)
Title: Parsing, Computation, and Diagnostics for Greenhouse Gas
Measurements
Description: Parse static-chamber greenhouse gas measurement
files generated by a variety of instruments; compute flux rates using
multi-observation metadata; and generate diagnostic metrics and plots.
Designed to be easy to integrate into reproducible scientific workflows.
Author: Stephanie Wilson [cre] ,
Ben Bond-Lamberty [aut] ,
Genevieve Noyce [ctb] ,
Roberta Bittencourt Peixoto [ctb] ,
Patrick Megonigal [ctb] ,
Smithsonian Institution [cph, fnd]
Maintainer: Stephanie Wilson <sjw22120@gmail.com>
Diff between fluxfinder versions 1.2.1 dated 2025-09-02 and 1.2.2 dated 2025-09-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++---- R/metadata.R | 4 ++-- R/qaqc.R | 7 ++++++- man/ffi_metadata_match.Rd | 4 ++-- man/ffi_qaqc.Rd | 6 +++++- 7 files changed, 27 insertions(+), 19 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen [aut, cre],
Caitlin K. Frankish [aut],
Axelle Cordier [aut],
Florian G. Weller [aut]
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.6 dated 2025-01-24 and 1.2.8 dated 2025-09-08
DESCRIPTION | 8 MD5 | 25 +- NAMESPACE | 8 R/a-misc.R | 6 R/calibrate_methods.R | 141 ++++++++++++++ R/raster-methods.R | 234 +++++++++++++++++++++++ R/ships_methods.R | 381 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary data/argosmetrics.RData |only man/DEPONS2R.Rd | 1 man/argosmetrics.Rd |only man/as.DeponsRaster.Rd |only man/as.raster.Rd |only man/calib_02.Rd |only man/interpolate.maps.Rd |only man/make.construction.traffic.Rd |only man/plot_calib02.Rd |only man/set.ship.type.Rd |only 18 files changed, 785 insertions(+), 19 deletions(-)
Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations' Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications. For more information see Meier, Mata & Wulff (2025) <doi:10.32614/RJ-2024-005> and Wulff, Meier & Mata (2024) <doi:10.1007/s11625-024-01516-3>.
Author: Dirk U. Wulff [aut] ,
Dominik S. Meier [aut, cre] ,
Rui Mata [ctb]
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>
Diff between text2sdg versions 1.1.1 dated 2023-03-17 and 1.1.2 dated 2025-09-08
DESCRIPTION | 19 +- MD5 | 47 +++--- NEWS.md | 6 R/aurora.R | 4 R/crosstab.R | 6 R/datasets.R | 8 - R/ensemble.R | 11 + R/plot.R | 2 R/sysdata.rda |binary R/text2sdg.R | 5 README.md | 14 -- build/vignette.rds |binary data/aurora_queries.RData |binary inst/CITATION |only inst/doc/text2sdg.R | 10 - inst/doc/text2sdg.Rmd | 6 inst/doc/text2sdg.html | 313 +++++++++++++++++++++++----------------------- man/aurora_queries.Rd | 2 man/detect_sdg.Rd | 6 man/elsevier_queries.Rd | 2 man/plot_sdg.Rd | 2 man/projects.Rd | 2 man/siris_queries.Rd | 2 man/text2sdg.Rd | 24 +++ vignettes/text2sdg.Rmd | 6 25 files changed, 264 insertions(+), 233 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. Also includes
a graphics device for creating drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between magick versions 2.8.7 dated 2025-06-06 and 2.9.0 dated 2025-09-08
DESCRIPTION | 17 +++---- MD5 | 106 +++++++++++++++++++++++----------------------- NAMESPACE | 2 NEWS | 4 + R/RcppExports.R | 4 + R/analysis.R | 4 - R/animation.R | 2 R/coder.R | 2 R/color.R | 28 ++++++++++-- R/composite.R | 6 +- R/defines.R | 2 R/edit.R | 10 ++-- R/effects.R | 2 R/fx.R | 4 - R/geometry.R | 2 R/index.R | 4 - R/options.R | 10 +++- R/paint.R | 8 +-- R/transform.R | 6 +- build/vignette.rds |binary cleanup | 1 inst/WORDLIST | 52 ++++++++-------------- inst/doc/intro.R | 2 inst/doc/intro.Rmd | 8 +-- inst/doc/intro.html | 110 ++++++++++++++++++++++++------------------------ man/analysis.Rd | 4 - man/animation.Rd | 4 - man/color.Rd | 27 +++++++++-- man/composite.Rd | 8 +-- man/config.Rd | 2 man/defines.Rd | 2 man/edges.Rd | 2 man/editing.Rd | 12 ++--- man/effects.Rd | 2 man/fx.Rd | 4 - man/geometry.Rd | 2 man/magick.Rd | 4 - man/options.Rd | 7 ++- man/painting.Rd | 8 +-- man/transform.Rd | 10 ++-- src/Makevars.win | 6 +- src/RcppExports.cpp | 13 +++++ src/attributes.cpp | 2 src/base.cpp | 2 src/color.cpp | 19 +++++++- src/convolve.cpp | 2 src/device.cpp | 6 +- src/edges.cpp | 2 src/edit.cpp | 2 src/magick_types.h | 1 src/options.cpp | 2 src/transformations.cpp | 2 tools/winlibs.R | 12 +++-- vignettes/intro.Rmd | 8 +-- 54 files changed, 326 insertions(+), 247 deletions(-)
Title: Discrete Statistical Distributions
Description: Implementation of new discrete statistical distributions. Each distribution includes the traditional functions as well as an additional function called the family function, which can be used to estimate parameters within the 'gamlss' framework.
Author: Freddy Hernandez-Barajas [aut, cre] ,
Fernando Marmolejo-Ramos [aut] ,
Olga Usuga-Manco [aut]
Maintainer: Freddy Hernandez-Barajas <fhernanb@unal.edu.co>
Diff between DiscreteDists versions 1.0.0 dated 2024-09-13 and 1.1.0 dated 2025-09-08
DiscreteDists-1.0.0/DiscreteDists/build |only DiscreteDists-1.1.0/DiscreteDists/DESCRIPTION | 29 - DiscreteDists-1.1.0/DiscreteDists/MD5 | 144 +++-- DiscreteDists-1.1.0/DiscreteDists/NAMESPACE | 47 + DiscreteDists-1.1.0/DiscreteDists/NEWS.md |only DiscreteDists-1.1.0/DiscreteDists/R/BerG.R |only DiscreteDists-1.1.0/DiscreteDists/R/COMPO.R |only DiscreteDists-1.1.0/DiscreteDists/R/COMPO2.R |only DiscreteDists-1.1.0/DiscreteDists/R/DBH.R | 16 DiscreteDists-1.1.0/DiscreteDists/R/DGEII.R | 13 DiscreteDists-1.1.0/DiscreteDists/R/DIKUM.R | 12 DiscreteDists-1.1.0/DiscreteDists/R/DLD.R | 14 DiscreteDists-1.1.0/DiscreteDists/R/DMOLBE.R | 55 + DiscreteDists-1.1.0/DiscreteDists/R/DPERKS.R |only DiscreteDists-1.1.0/DiscreteDists/R/DsPA.R |only DiscreteDists-1.1.0/DiscreteDists/R/GGEO.R | 11 DiscreteDists-1.1.0/DiscreteDists/R/HYPERPO.R | 18 DiscreteDists-1.1.0/DiscreteDists/R/HYPERPO2.R | 23 DiscreteDists-1.1.0/DiscreteDists/R/POISXL.R | 12 DiscreteDists-1.1.0/DiscreteDists/R/RcppExports.R | 125 ++++ DiscreteDists-1.1.0/DiscreteDists/R/dBerG.R |only DiscreteDists-1.1.0/DiscreteDists/R/dCOMPO.R |only DiscreteDists-1.1.0/DiscreteDists/R/dCOMPO2.R |only DiscreteDists-1.1.0/DiscreteDists/R/dDBH.R | 4 DiscreteDists-1.1.0/DiscreteDists/R/dDGEII.R | 4 DiscreteDists-1.1.0/DiscreteDists/R/dDIKUM.R | 8 DiscreteDists-1.1.0/DiscreteDists/R/dDLD.R | 5 DiscreteDists-1.1.0/DiscreteDists/R/dDMOLBE.R | 35 - 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Title: Canonical Associative Learning Models and their Representations
Description: Implementations of canonical associative learning models,
with tools to run experiment simulations, estimate model parameters,
and compare model representations. Experiments and results are
represented using S4 classes and methods.
Author: Victor Navarro [aut, cre, cph]
Maintainer: Victor Navarro <navarrov@cardiff.ac.uk>
Diff between calmr versions 0.7.0 dated 2025-05-11 and 0.8.1 dated 2025-09-08
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Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann [aut, cre] ,
Jochen Fruend [aut] ,
Bernd Gruber [aut] ,
Tobias Bauer [ctb] ,
Stephen Beckett [ctb] ,
Mariano Devoto [ctb] ,
Gabriel M.F. Felix [ctb] ,
Jose M. Iriondo [ctb] ,
Tore Opsahl [ctb] ,
Rafael B.P. Pinheiro [ctb] ,
Rouven [...truncated...]
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.21 dated 2025-02-20 and 2.22 dated 2025-09-08
bipartite-2.21/bipartite/R/sortweb.r |only bipartite-2.22/bipartite/DESCRIPTION | 35 bipartite-2.22/bipartite/MD5 | 48 bipartite-2.22/bipartite/NAMESPACE | 2 bipartite-2.22/bipartite/R/plotweb.R | 1321 +++++----- bipartite-2.22/bipartite/R/plotweb_deprecated.R |only bipartite-2.22/bipartite/R/sortweb.R |only bipartite-2.22/bipartite/R/versionlog.R | 2 bipartite-2.22/bipartite/build/partial.rdb |binary bipartite-2.22/bipartite/build/vignette.rds |binary bipartite-2.22/bipartite/inst/doc/Intro2bipartite.R | 116 bipartite-2.22/bipartite/inst/doc/Intro2bipartite.Rnw | 142 - bipartite-2.22/bipartite/inst/doc/Intro2bipartite.pdf |binary bipartite-2.22/bipartite/inst/doc/PlottingWithBipartite.R |only bipartite-2.22/bipartite/inst/doc/PlottingWithBipartite.Rmd |only bipartite-2.22/bipartite/inst/doc/PlottingWithBipartite.html |only bipartite-2.22/bipartite/man/bipartite-package.Rd | 11 bipartite-2.22/bipartite/man/networklevel.Rd | 1 bipartite-2.22/bipartite/man/plotweb.Rd | 267 +- bipartite-2.22/bipartite/man/plotweb_deprecated.Rd |only bipartite-2.22/bipartite/man/sortweb.Rd | 31 bipartite-2.22/bipartite/vignettes/Intro2bipartite-concordance.tex |only bipartite-2.22/bipartite/vignettes/Intro2bipartite.Rnw | 142 - bipartite-2.22/bipartite/vignettes/PlottingWithBipartite.Rmd |only bipartite-2.22/bipartite/vignettes/bipartite.bib | 51 bipartite-2.22/bipartite/vignettes/figures/ScreenshotSmall1976LibreOffice.png |only bipartite-2.22/bipartite/vignettes/figures/ScreenshotSmall1976long.png |only bipartite-2.22/bipartite/vignettes/figures/Small1976plot.png |only bipartite-2.22/bipartite/vignettes/figures/motten1982_plotweb.pdf |binary bipartite-2.22/bipartite/vignettes/figures/motten1982_plotweb_old.pdf |only bipartite-2.22/bipartite/vignettes/figures/twocolumn-betweenPlot-1.pdf |binary bipartite-2.22/bipartite/vignettes/small1976.csv |only 32 files changed, 1284 insertions(+), 885 deletions(-)
Title: Wrapper for SQL Server bcp Utility
Description: Provides functions to utilize a command line utility that does bulk inserts and exports from SQL Server databases.
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas.roh@delveds.com>
Diff between bcputility versions 0.4.3 dated 2024-05-08 and 0.4.6 dated 2025-09-08
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NEWS.md | 9 +++++++++ R/bcp.R | 9 +++++++-- README.md | 36 +++++++++++++++++++++++++++++++++--- inst |only man/bcpImport.Rd | 6 +++++- man/figures/logo.png |binary man/makeConnectArgs.Rd | 3 ++- tests/a-init-db.R | 2 +- 10 files changed, 71 insertions(+), 21 deletions(-)
Title: Estimators and Plots for Gamma and Pareto Tail Detection
Description: Estimators for two functionals used to detect Gamma, Pareto or Lognormal distributions, as well as distributions exhibiting similar tail behavior, as introduced by Iwashita and Klar (2023) <doi:10.1111/stan.12316> and
Klar (2024) <doi:10.1080/00031305.2024.2413081>.
One of these functionals, g, originally proposed by Asmussen and Lehtomaa (2017) <doi:10.3390/risks5010010>, distinguishes between log-convex and log-concave tail behavior.
Furthermore the characterization of the lognormal distribution is based on the work of Mosimann (1970) <doi:10.2307/2284599>.
The package also includes methods for visualizing these estimators and their associated confidence intervals across various threshold values.
Author: Bernhard Klar [aut, cre],
Lucas Iglesias [aut]
Maintainer: Bernhard Klar <Bernhard.Klar@kit.edu>
Diff between tailplots versions 0.1.0 dated 2025-04-18 and 0.1.1 dated 2025-09-08
tailplots-0.1.0/tailplots/inst |only tailplots-0.1.1/tailplots/DESCRIPTION | 16 tailplots-0.1.1/tailplots/LICENSE | 4 tailplots-0.1.1/tailplots/MD5 | 36 +- tailplots-0.1.1/tailplots/NAMESPACE | 26 - tailplots-0.1.1/tailplots/R/RcppExports.R |only tailplots-0.1.1/tailplots/R/gamma_estimators.R | 148 +------- tailplots-0.1.1/tailplots/R/gamma_tailplot.R | 385 +++++++++++----------- tailplots-0.1.1/tailplots/R/lnorm_estimators.R |only tailplots-0.1.1/tailplots/R/lnorm_tailplot.R |only tailplots-0.1.1/tailplots/R/pareto_estimators.R | 224 +----------- tailplots-0.1.1/tailplots/R/pareto_tailplot.R | 398 +++++++++++------------ tailplots-0.1.1/tailplots/R/zzz.R |only tailplots-0.1.1/tailplots/README.md |only tailplots-0.1.1/tailplots/build/partial.rdb |binary tailplots-0.1.1/tailplots/man/gamma_tail.Rd | 231 ++++++------- tailplots-0.1.1/tailplots/man/gamma_tailplot.Rd | 96 ++--- tailplots-0.1.1/tailplots/man/lnorm_tail.Rd |only tailplots-0.1.1/tailplots/man/lnorm_tailplot.Rd |only tailplots-0.1.1/tailplots/man/pareto_tail.Rd | 253 +++++++------- tailplots-0.1.1/tailplots/man/pareto_tailplot.Rd | 94 ++--- tailplots-0.1.1/tailplots/src |only 22 files changed, 814 insertions(+), 1097 deletions(-)
Title: Rule-Based Conformance Checking of Business Process Event Data
Description: Check compliance of event-data from (business) processes with respect to specified rules. Rules supported are of three types: frequency (activities that should (not) happen x number of times), order (succession between activities) and exclusiveness (and and exclusive choice between activities).
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between processcheckR versions 0.1.4 dated 2022-10-03 and 0.1.5 dated 2025-09-08
DESCRIPTION | 9 -- MD5 | 26 +++--- R/contains.R | 1 R/processcheckR.R | 1 README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/processcheckr.R | 4 inst/doc/processcheckr.html | 181 +++++++++++++++++++++----------------------- man/absent.Rd | 4 man/contains.Rd | 1 man/contains_between.Rd | 4 man/contains_exactly.Rd | 4 man/processcheckR.Rd | 1 14 files changed, 115 insertions(+), 122 deletions(-)
Title: Multiple Change Point
Description: Nonparametric approach to estimate the location of block boundaries (change-points) of
non-overlapping blocks in a random symmetric matrix which consists of random variables whose
distribution changes from block to block.
BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY-LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>.
Author: Vincent Brault [cre, aut] ,
Cougoulat Glenn [ctb],
Sarah Ouadah [ctb],
Laure Sansonnet [ctb]
Maintainer: Vincent Brault <vincent.brault@univ-grenoble-alpes.fr>
Diff between MuChPoint versions 0.6.3 dated 2022-04-08 and 0.6.4 dated 2025-09-08
DESCRIPTION | 31 ++++++----- MD5 | 20 +++---- NAMESPACE | 24 +++++++++ R/MuChPoint.R | 52 +++----------------- R/MuChPoint_Class.R | 122 ++++++++++++++++++++++++++++------------------- R/RcppExports.R | 2 man/Compute_Cn1n2.Rd | 2 man/MuChPoint-proc.Rd | 5 + man/plot-MuChPoint.Rd | 5 + man/summary-MuChPoint.Rd | 3 - src/MuChPoint_cpp.cpp | 2 11 files changed, 145 insertions(+), 123 deletions(-)
Title: Animated Biplots
Description: Create animated biplots that enables dynamic visualisation of temporal or sequential changes in multivariate data by animating a single biplot across the levels of a time variable. It builds on objects from the 'biplotEZ' package, Lubbe S, le Roux N, Nienkemper-Swanepoel J, Ganey R, Buys R, Adams Z, Manefeldt P (2024) <doi:10.32614/CRAN.package.biplotEZ>, allowing users to create animated biplots that reveal how both samples and variables evolve over time.
Author: Raeesa Ganey [aut, cre, cph] ,
Johane Nienkemper-Swanepoel [aut, cph]
Maintainer: Raeesa Ganey <raeesa.ganey@wits.ac.za>
Diff between moveEZ versions 1.1.0 dated 2025-08-22 and 1.1.1 dated 2025-09-08
DESCRIPTION | 6 ++-- MD5 | 10 +++---- R/globals.R | 3 +- R/plot.R | 72 ++++++++++++++++++++++++++------------------------- inst/doc/moveEZ.html | 10 +++---- man/moveplot.Rd | 12 +++++++- 6 files changed, 64 insertions(+), 49 deletions(-)
Title: 'LuaJIT' Scripting
Description: An interface to 'LuaJIT' <https://luajit.org>, a just-in-time
compiler for the 'Lua' scripting language <https://www.lua.org>. Allows
users to run 'Lua' code from 'R'.
Author: Mike Pall [aut, cph] ,
Lua.org, PUC-Rio [cph] ,
Nicholas Davies [cre, ctb, cph] ,
Scott Lembcke, Howling Moon Software [ctb, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between luajr versions 0.1.9 dated 2025-04-30 and 0.2.0 dated 2025-09-08
luajr-0.1.9/luajr/inst/doc/luajr-module.R |only luajr-0.1.9/luajr/inst/doc/luajr-module.Rmd |only luajr-0.1.9/luajr/inst/doc/luajr-module.html |only luajr-0.1.9/luajr/inst/include/luajr_conf.h |only luajr-0.1.9/luajr/inst/include/luajr_lauxlib.h |only luajr-0.1.9/luajr/inst/include/luajr_lua.h |only luajr-0.1.9/luajr/inst/include/luajr_luajit.h |only luajr-0.1.9/luajr/inst/include/luajr_lualib.h |only luajr-0.1.9/luajr/inst/module |only luajr-0.1.9/luajr/tests/testthat/test-lua_func.R |only luajr-0.1.9/luajr/vignettes/luajr-module.Rmd |only luajr-0.2.0/luajr/DESCRIPTION | 6 luajr-0.2.0/luajr/MD5 | 78 ++++----- luajr-0.2.0/luajr/NAMESPACE | 5 luajr-0.2.0/luajr/NEWS.md | 28 ++- luajr-0.2.0/luajr/R/lua_func.R | 30 ++- luajr-0.2.0/luajr/R/lua_mode.R | 2 luajr-0.2.0/luajr/R/lua_module.R |only luajr-0.2.0/luajr/R/luajr-package.R | 8 luajr-0.2.0/luajr/R/zzz.R | 4 luajr-0.2.0/luajr/build/vignette.rds |binary luajr-0.2.0/luajr/inst/CITATION | 6 luajr-0.2.0/luajr/inst/Lua |only luajr-0.2.0/luajr/inst/doc/luajr.R | 27 +++ luajr-0.2.0/luajr/inst/doc/luajr.Rmd | 148 +++++++++++------ luajr-0.2.0/luajr/inst/doc/luajr.html | 195 ++++++++++++++--------- luajr-0.2.0/luajr/inst/doc/modules.R |only luajr-0.2.0/luajr/inst/doc/modules.Rmd |only luajr-0.2.0/luajr/inst/doc/modules.html |only luajr-0.2.0/luajr/inst/doc/objects.R |only luajr-0.2.0/luajr/inst/doc/objects.Rmd |only luajr-0.2.0/luajr/inst/doc/objects.html |only luajr-0.2.0/luajr/inst/include/luajr.h | 6 luajr-0.2.0/luajr/inst/include/luajr_funcs.h | 5 luajr-0.2.0/luajr/man/lua_func.Rd | 21 ++ luajr-0.2.0/luajr/man/lua_module.Rd |only luajr-0.2.0/luajr/man/lua_profile.Rd | 2 luajr-0.2.0/luajr/man/luajr-package.Rd | 7 luajr-0.2.0/luajr/src/module.cpp |only luajr-0.2.0/luajr/src/push_to.cpp | 11 + luajr-0.2.0/luajr/src/registry_entry.cpp | 23 ++ luajr-0.2.0/luajr/src/registry_entry.h | 16 + luajr-0.2.0/luajr/src/run_func.cpp | 76 ++++---- luajr-0.2.0/luajr/src/setup.cpp | 3 luajr-0.2.0/luajr/src/shared.h | 21 ++ luajr-0.2.0/luajr/src/state.cpp | 3 luajr-0.2.0/luajr/tests/testthat/test-func.R |only luajr-0.2.0/luajr/tests/testthat/test-module.R |only luajr-0.2.0/luajr/vignettes/luajr.Rmd | 148 +++++++++++------ luajr-0.2.0/luajr/vignettes/modules.Rmd |only luajr-0.2.0/luajr/vignettes/objects.Rmd |only 51 files changed, 579 insertions(+), 300 deletions(-)
Title: Performance Spectrum Miner for Event Data
Description: Compute detailed and aggregated performance spectrum for event data. The detailed performance spectrum describes the event data in terms of segments, where the performance of each segment is measured and plotted for any occurrences of this segment over time and can be classified, e.g., regarding the overall population. The aggregated performance spectrum visualises the amount of cases of particular performance over time. Denisov, V., Fahland, D., & van der Aalst, W. M. P. (2018) <doi:10.1007/978-3-319-98648-7_9>.
Author: Greg Van Houdt [aut],
Gert Janssenswillen [ctb, cre],
Gerard van Hulzen [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between psmineR versions 0.1.0 dated 2022-10-10 and 0.1.1 dated 2025-09-08
DESCRIPTION | 13 +++++++------ LICENSE | 2 +- MD5 | 29 +++++++++++++++++------------ R/plot.R | 4 ++-- R/ps_aggregated.R | 4 ++-- R/ps_detailed.R | 4 ++-- R/psmineR.R | 2 +- README.md | 11 ----------- build/partial.rdb |binary build/vignette.rds |only inst |only man/plot.Rd | 2 +- man/ps_aggregated.Rd | 4 ++-- man/ps_detailed.Rd | 4 ++-- man/psmineR.Rd | 1 - vignettes |only 16 files changed, 37 insertions(+), 43 deletions(-)
Title: Numerical Association Rule Mining using Population-Based
Nature-Inspired Algorithms
Description: Framework is devoted to mining numerical association rules through the
utilization of nature-inspired algorithms for optimization. Drawing inspiration
from the 'NiaARM' 'Python' and the 'NiaARM' 'Julia' packages, this repository
introduces the capability to perform numerical association rule mining in
the R programming language.
Fister Jr., Iglesias, Galvez, Del Ser, Osaba and Fister (2018) <doi:10.1007/978-3-030-03493-1_9>.
Author: Iztok Jr. Fister [aut, cre, cph] ,
Gerlinde Emsenhuber [aut] ,
Jan Hendrik Pluemer [aut]
Maintainer: Iztok Jr. Fister <iztok@iztok.space>
Diff between niarules versions 0.2.0 dated 2025-02-20 and 0.3.0 dated 2025-09-08
DESCRIPTION | 29 ++++++++++-------- MD5 | 45 +++++++++++++++++++++++----- NAMESPACE | 33 +++++++++++++++++++-- R/RcppExports.R |only R/build_coral_plots.R |only R/coral_plot_visualization.R |only R/de.R | 4 ++ R/evaluate.R | 13 ++++++++ R/output.R | 7 ++++ R/parse_rules.R |only R/pso.R |only R/visualization |only R/zzz.R |only README.md | 47 ++++++++++++++++++++++++++++++ build |only inst/extdata/abalone_rules.csv |only man/build_coral_plots.Rd |only man/build_layout_cpp.Rd |only man/differential_evolution.Rd | 5 +++ man/evaluate.Rd | 12 +++++++ man/figures |only man/parse_rules.Rd |only man/parse_rules_cpp.Rd |only man/particle_swarm_optimization.Rd |only man/render_coral_rgl.Rd |only src |only tests/testthat/test-build-coral-layout.R |only tests/testthat/test-parse-rules.R |only tests/testthat/test-render-coral-layout.R |only 29 files changed, 172 insertions(+), 23 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.5 dated 2025-03-05 and 0.0.6 dated 2025-09-08
mllrnrs-0.0.5/mllrnrs/tests/testthat/test-glmnet_binary.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-glmnet_multiclass.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-glmnet_regression.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-lightgbm_binary.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-lightgbm_multiclass.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-lightgbm_regression.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-ranger_binary.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-ranger_multiclass.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-ranger_regression.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-xgboost_binary.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-xgboost_multiclass.R |only mllrnrs-0.0.5/mllrnrs/tests/testthat/test-xgboost_regression.R |only mllrnrs-0.0.6/mllrnrs/DESCRIPTION | 14 mllrnrs-0.0.6/mllrnrs/MD5 | 137 +-- mllrnrs-0.0.6/mllrnrs/NAMESPACE | 19 mllrnrs-0.0.6/mllrnrs/R/learner_glmnet.R | 4 mllrnrs-0.0.6/mllrnrs/R/learner_lightgbm.R | 4 mllrnrs-0.0.6/mllrnrs/R/learner_ranger.R | 14 mllrnrs-0.0.6/mllrnrs/R/learner_xgboost.R | 4 mllrnrs-0.0.6/mllrnrs/R/zzz.R | 58 - mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_binary.R | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_binary.html | 25 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_multiclass.R | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_multiclass.html | 35 - mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_regression.R | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_regression.html | 17 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_glmnet_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_binary.R | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_binary.html | 23 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_multiclass.R | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_multiclass.html | 35 - mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_regression.R | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_regression.html | 17 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_lightgbm_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_binary.R | 22 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_binary.html | 25 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_binary.qmd | 22 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_multiclass.R | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_multiclass.html | 35 - mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_regression.R | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_regression.html | 17 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_ranger_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_binary.R | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_binary.html | 23 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_multiclass.R | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_multiclass.html | 35 - mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_regression.R | 14 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_regression.html | 17 mllrnrs-0.0.6/mllrnrs/inst/doc/mllrnrs_xgboost_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/man/LearnerGlmnet.Rd | 296 ++++---- mllrnrs-0.0.6/mllrnrs/man/LearnerLightgbm.Rd | 342 ++++----- mllrnrs-0.0.6/mllrnrs/man/LearnerRanger.Rd | 298 ++++---- mllrnrs-0.0.6/mllrnrs/man/LearnerXgboost.Rd | 344 +++++----- mllrnrs-0.0.6/mllrnrs/tests/testthat.R | 30 mllrnrs-0.0.6/mllrnrs/tests/testthat/test-binary.R |only mllrnrs-0.0.6/mllrnrs/tests/testthat/test-lints.R | 26 mllrnrs-0.0.6/mllrnrs/tests/testthat/test-multiclass.R |only mllrnrs-0.0.6/mllrnrs/tests/testthat/test-regression.R |only mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_glmnet_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_glmnet_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_glmnet_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_lightgbm_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_lightgbm_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_lightgbm_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_ranger_binary.qmd | 22 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_ranger_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_ranger_regression.qmd | 14 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_xgboost_binary.qmd | 20 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_xgboost_multiclass.qmd | 32 mllrnrs-0.0.6/mllrnrs/vignettes/mllrnrs_xgboost_regression.qmd | 14 77 files changed, 1413 insertions(+), 1279 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major
methods
include Gaussian spatial process prediction (known as Kriging), cubic and thin plate splines, and compactly supported
covariance functions for large data sets. The spline and spatial process
methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by maximum likelihood. For spatial process prediction
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. As included are fast approximations for prediction
and conditional simulation for larger data sets.
There are also many useful functions for plotting
and working with spatial data as images. This package also con [...truncated...]
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
Rider Johnson [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 16.3.1 dated 2025-03-08 and 17.1 dated 2025-09-08
fields-16.3.1/fields/R/addMarginsGridList.R |only fields-16.3.1/fields/R/makePredictionGrid.R |only fields-17.1/fields/DESCRIPTION | 32 - fields-17.1/fields/MD5 | 133 +++--- fields-17.1/fields/NAMESPACE | 2 fields-17.1/fields/R/Matern.R | 17 fields-17.1/fields/R/Mines.colors.R |only fields-17.1/fields/R/approximateCovariance2D.R |only fields-17.1/fields/R/augmentPredictionGrid.R |only fields-17.1/fields/R/bplot.family.R | 6 fields-17.1/fields/R/circulantEmbedding.R | 5 fields-17.1/fields/R/circulantEmbeddingSetup.R | 58 +- fields-17.1/fields/R/colorBar.R | 27 + fields-17.1/fields/R/divMap.R |only fields-17.1/fields/R/interp.surface.FFT.R | 13 fields-17.1/fields/R/mKrig.R | 13 fields-17.1/fields/R/mKrigFastPredict.R | 90 ++-- fields-17.1/fields/R/mKrigFastPredictSetup.R | 41 +- fields-17.1/fields/R/offGridWeights.R | 61 ++- fields-17.1/fields/R/offGridWeights1D.R | 6 fields-17.1/fields/R/offGridWeights2D.R | 46 +- fields-17.1/fields/R/plotMatrix.R | 6 fields-17.1/fields/R/predictSurface.family.R | 33 - fields-17.1/fields/R/predictSurface.fastTps.R |only fields-17.1/fields/R/predictSurface.mKrig.R | 59 +-- fields-17.1/fields/R/simLocal.spatialProcess.R | 274 +++++++------- fields-17.1/fields/R/spatialProcess.R | 13 fields-17.1/fields/R/spatialProcessSetDefaults.R | 18 fields-17.1/fields/R/stationaryImageCov.R |only fields-17.1/fields/R/summary.spatialProcess.R | 4 fields-17.1/fields/R/test.for.zero.R | 9 fields-17.1/fields/R/unrollZGrid.R | 3 fields-17.1/fields/data/CO2.rda |binary fields-17.1/fields/data/COmonthlyMet.rda |binary fields-17.1/fields/data/LENSExample.rda |only fields-17.1/fields/data/NorthAmericanRainfall.rda |binary fields-17.1/fields/data/NorthAmericanRainfall2.rda |binary fields-17.1/fields/data/PRISMelevation.rda |binary fields-17.1/fields/data/RCMexample.rda |binary fields-17.1/fields/data/RMelevation.rda |binary fields-17.1/fields/data/US.dat.rda |binary fields-17.1/fields/data/WorldBankCO2.rda |binary fields-17.1/fields/data/datalist | 1 fields-17.1/fields/data/glacier.rda |binary fields-17.1/fields/data/lennon.rda |binary fields-17.1/fields/data/ozone2.rda |binary fields-17.1/fields/data/rat.diet.rda |binary fields-17.1/fields/data/world.dat.rda |binary fields-17.1/fields/man/Exponential.Rd | 10 fields-17.1/fields/man/FORTRAN.internal.Rd | 8 fields-17.1/fields/man/LENSExample.Rd |only fields-17.1/fields/man/Tps.Rd | 4 fields-17.1/fields/man/bplot.xy.Rd | 5 fields-17.1/fields/man/fields.tests.Rd | 7 fields-17.1/fields/man/image.cov.Rd | 95 ++-- fields-17.1/fields/man/imagePlot.Rd | 60 ++- fields-17.1/fields/man/mKrig.Rd | 7 fields-17.1/fields/man/offGridWeights.Rd | 88 ++-- fields-17.1/fields/man/predictSurface.Rd | 22 - fields-17.1/fields/man/sim.Krig.Rd | 207 ++++------ fields-17.1/fields/man/sim.rf.Rd | 73 ++- fields-17.1/fields/man/spatialProcess.Rd | 34 + fields-17.1/fields/man/tim.colors.Rd | 61 ++- fields-17.1/fields/man/vgram.Rd | 12 fields-17.1/fields/src/Makevars |only fields-17.1/fields/src/fieldsF77Code.f | 14 fields-17.1/fields/src/init.c | 9 fields-17.1/fields/tests/Likelihood.test.R | 2 fields-17.1/fields/tests/offGridWeights.test.R | 8 fields-17.1/fields/tests/offGridWeights.test.Rout.save | 33 + fields-17.1/fields/tests/offGridWeightsNEW.test.Rout.save | 162 +------- fields-17.1/fields/tests/offGridWeightsNew.test.R | 56 +- fields-17.1/fields/tests/testO3LocalExample.R |only fields-17.1/fields/tests/testO3LocalExample.Rout.save |only 74 files changed, 1097 insertions(+), 850 deletions(-)
Title: Distributional Instrumental Variable (DIV) Model
Description: Distributional instrumental variable (DIV) model
for estimation of the interventional distribution of the outcome Y under a
do intervention on the treatment X. Instruments, predictors and targets can
be univariate or multivariate. Functionality includes estimation of the (conditional)
interventional mean and quantiles, as well as sampling from the fitted (conditional)
interventional distribution.
Author: Anastasiia Holovchak [aut, cre, ctb],
Sorawit Saengkyongam [aut, ctb],
Nicolai Meinshausen [aut, ctb],
Xinwei Shen [aut, ctb]
Maintainer: Anastasiia Holovchak <anastasiia.holovchak@stat.math.ethz.ch>
This is a re-admission after prior archival of version 0.1.2 dated 2025-06-27
Diff between DistributionIV versions 0.1.2 dated 2025-06-27 and 0.1.3 dated 2025-09-08
DESCRIPTION | 18 ++--- MD5 | 24 ++++--- NAMESPACE | 1 NEWS.md | 24 +++++-- R/device.R | 13 +--- R/divfit.R | 120 +++++++++++++++++++------------------ R/energyloss.R | 12 ++- R/energylossbeta.R | 7 +- R/nnmodel.R | 58 +++++++++--------- R/predict.DIV.R | 84 ++++++++++++++------------ R/zzz.R | 5 - inst |only tests/testthat/helper_torch.R |only tests/testthat/test-predict.DIV.R | 121 +++++++++++++++++++++++--------------- 14 files changed, 274 insertions(+), 213 deletions(-)
More information about DistributionIV at CRAN
Permanent link
Title: 'DEXi' Decision Tree Analysis and Visualization
Description: Provides a versatile toolkit for analyzing and visualizing 'DEXi' (Decision EXpert for education)
decision trees, facilitating multi-criteria decision analysis directly within R. Users can
read .dxi files, manipulate decision trees, and evaluate various scenarios. It supports sensitivity
analysis through Monte Carlo simulations, one-at-a-time approaches, and variance-based
methods, helping to discern the impact of input variations. Additionally, it includes functionalities
for generating sampling plans and an array of visualization options for decision trees and
analysis results. A distinctive feature is the synoptic table plot, aiding in the efficient
comparison of scenarios. Whether for in-depth decision modeling or sensitivity analysis, this
package stands as a comprehensive solution. Definition of sensitivity analyses available in
Carpani, Bergez and Monod (2012) <doi:10.1016/j.envsoft.2011.10.002> and detailed description of the package soon available in
Alaphilippe et al. ( [...truncated...]
Author: Roland Allart [aut],
Jacques-Eric Bergez [aut] ,
Marta Carpani [aut],
Herve Monod [aut] ,
Aude Alaphilippe [ctb] ,
Nicolas Cavan [ctb, cre],
INRAE [cph] )
Maintainer: Nicolas Cavan <nicolas.cavan@inrae.fr>
Diff between dexisensitivity versions 1.0.1 dated 2024-10-29 and 1.0.2 dated 2025-09-08
DESCRIPTION | 19 ++++++++++--------- MD5 | 20 ++++++++++---------- NEWS.md | 18 +++++++++++------- R/create_tree.R | 2 +- R/data.R | 2 +- build/partial.rdb |binary man/dexifruits_v1.Rd | 2 +- man/dexisensitivity-package.Rd | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-create_tree.R | 7 +++++-- tests/testthat/test-option.R | 2 ++ 11 files changed, 42 insertions(+), 32 deletions(-)
More information about dexisensitivity at CRAN
Permanent link
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around
the fantastic 'stringi' package. All function and argument names (and
positions) are consistent, all functions deal with "NA"'s and zero
length vectors in the same way, and the output from one function is
easy to feed into the input of another.
Author: Hadley Wickham [aut, cre, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between stringr versions 1.5.1 dated 2023-11-14 and 1.5.2 dated 2025-09-08
DESCRIPTION | 8 - MD5 | 26 ++-- NEWS.md | 4 R/replace.R | 2 R/split.R | 2 build/vignette.rds |binary inst/doc/from-base.R | 2 inst/doc/from-base.html | 245 ++++++++++++++++---------------------- inst/doc/regular-expressions.R | 8 - inst/doc/regular-expressions.html | 3 inst/doc/stringr.html | 3 man/str_glue.Rd | 4 man/str_replace.Rd | 2 man/str_split.Rd | 2 14 files changed, 143 insertions(+), 168 deletions(-)
Title: A Modern K-Means (MKMeans) Clustering Algorithm
Description: It's a Modern K-Means clustering algorithm which works for data of any number of dimensions, has no limit with the number of clusters expected, offers both methods with and without initial cluster centers, and can start with any initial cluster centers for the method with initial cluster centers.
Author: Yarong Yang [aut, cre],
Nader Ebrahimi [ctb],
Yoram Rubin [ctb],
Jacob Zhang [ctb]
Maintainer: Yarong Yang <Yi.YA_yaya@hotmail.com>
Diff between MKMeans versions 3.3 dated 2025-08-26 and 3.4.4 dated 2025-09-08
DESCRIPTION | 12 +- MD5 | 12 +- NAMESPACE | 3 R/MKMeans.R | 211 +++++++++++++++++++++++++++++++++++++++---------- man/MKMean-class.Rd | 4 man/MKMeans-package.Rd | 71 +++++++++------- man/MKMeans.Rd | 63 ++++++++------ 7 files changed, 264 insertions(+), 112 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, ctb] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between bigalgebra versions 2.0.0 dated 2025-08-20 and 2.0.2 dated 2025-09-08
DESCRIPTION | 12 +++---- MD5 | 19 ++++++------ NEWS.md | 8 ++++- R/bigalgebra.R | 64 +++++++++++++++++++++-------------------- README.md | 1 inst/_pkgdown.yml |only man/dgeev.Rd | 6 +-- src/R_init_bigalgebra.c | 3 + src/bigalgebra.cpp | 40 ++++++++++++++++++++++++- src/bigalgebra.h | 1 tests/testthat/test-wrappers.R | 47 ++++++++++++++++++++++++++++++ 11 files changed, 150 insertions(+), 51 deletions(-)
Title: Procedures Based on Item Response Theory Models for the
Development of Short Test Forms
Description: Implement different Item Response Theory (IRT) based procedures for the development of static short test forms (STFs) from a test. Two main procedures are considered, specifically the typical IRT-based procedure for the development of STF, and a recently introduced procedure (Epifania, Anselmi & Robusto, 2022 <doi:10.1007/978-3-031-27781-8_7>).
The procedures differ in how the most informative items are selected for the inclusion in the STF, either by considering their item information functions without considering any specific level of the latent trait (typical procedure) or by considering their informativeness with respect to specific levels of the latent trait, denoted as theta targets (the newly introduced procedure). Regarding the latter procedure, three methods are implemented for the definition of the theta targets: (i) theta targets are defined by segmenting the latent trait in equal intervals and considering the midpoint of each interval (equal interval procedure, ei [...truncated...]
Author: Ottavia M. Epifania [aut, cre],
Pasquale Anselmi [ctb],
Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <ottavia.epifania@unipd.it>
Diff between shortIRT versions 0.1.3 dated 2024-02-16 and 0.1.4 dated 2025-09-08
shortIRT-0.1.3/shortIRT/man/bp.Rd |only shortIRT-0.1.4/shortIRT/DESCRIPTION | 26 +++++++++---- shortIRT-0.1.4/shortIRT/MD5 | 20 +++++----- shortIRT-0.1.4/shortIRT/NAMESPACE | 2 - shortIRT-0.1.4/shortIRT/NEWS.md | 8 +--- shortIRT-0.1.4/shortIRT/R/bp.R | 5 +- shortIRT-0.1.4/shortIRT/R/eip.R | 2 - shortIRT-0.1.4/shortIRT/R/uip.R | 2 - shortIRT-0.1.4/shortIRT/man/bench.Rd |only shortIRT-0.1.4/shortIRT/tests/testthat/test-bp.R | 2 - shortIRT-0.1.4/shortIRT/tests/testthat/test-change_names.R | 2 - shortIRT-0.1.4/shortIRT/tests/testthat/test-diff_theta.R | 3 - 12 files changed, 40 insertions(+), 32 deletions(-)
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits. A paper on this package was published in the Journal of Statistical Software <doi:10.18637/jss.v114.i10>.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 1.2.0 dated 2025-07-16 and 1.3.0 dated 2025-09-08
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NEWS.md | 4 ++++ inst/CITATION |only inst/doc/Multiwave-Estimation.Rmd | 6 +++--- inst/doc/Multiwave-Estimation.html | 12 ++++++------ inst/doc/Multiwave-Object.Rmd | 2 +- inst/doc/Multiwave-Object.html | 4 +++- inst/doc/optimall-vignette.Rmd | 2 +- inst/doc/optimall-vignette.html | 6 ++++-- vignettes/Multiwave-Estimation.Rmd | 6 +++--- vignettes/Multiwave-Object.Rmd | 2 +- vignettes/optimall-vignette.Rmd | 2 +- 13 files changed, 43 insertions(+), 34 deletions(-)
Title: Path-Based Access and Manipulation of Nested Lists
Description: Allows users to list data structures using path-based navigation.
Provides intuitive methods for storing, accessing,
and manipulating nested data through simple path strings.
Key features include strict mode validation, path existence checking, recursive
operations, and automatic parent-level creation. Designed for use cases requiring
organized storage of complex nested data while maintaining simple access patterns.
Particularly useful for configuration management, nested settings, and any
application where data naturally forms a tree-like structure.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between slash versions 0.1.0 dated 2025-04-18 and 0.2.0 dated 2025-09-08
DESCRIPTION | 9 MD5 | 11 NEWS.md |only R/main.R | 100 ++++- README.md | 163 +++++++-- man/slash.Rd | 42 ++ tests/testthat/test-main.R | 804 +++++++++++++++++++++++---------------------- 7 files changed, 678 insertions(+), 451 deletions(-)
Title: Forest Plots for Network Meta-Analysis with Proportion for Paths
and Studies
Description: Provides customized forest plots for network meta-analysis incorporating direct, indirect, and NMA effects. Includes visualizations of evidence contributions through
proportion bars based on the hat matrix and evidence flow decomposition.
Author: Yanqi Zhang [aut, cre]
Maintainer: Yanqi Zhang <zyq1998@iastate.edu>
Diff between NMAforest versions 0.1.0 dated 2025-08-27 and 0.1.1 dated 2025-09-08
DESCRIPTION | 8 - MD5 | 10 - NAMESPACE | 2 R/NMAforest.R | 403 ++++++++++++++++++++++++++++++------------------------- README.md | 6 man/NMAforest.Rd | 21 +- 6 files changed, 251 insertions(+), 199 deletions(-)
Title: Multilevel Functions
Description: Tools used by organizational researchers for the analysis of multilevel data. Includes four broad sets of tools. First, functions for estimating within-group agreement and reliability indices. Second, functions for manipulating multilevel and longitudinal (panel) data. Third, simulations for estimating power and generating multilevel data. Fourth, miscellaneous functions for estimating reliability and performing simple calculations and data transformations.
Author: Paul Bliese [aut, cre],
Gilad Chen [ctb],
Patrick Downes [ctb],
Donald Schepker [ctb],
Jonas Lang [ctb]
Maintainer: Paul Bliese <pdbliese@gmail.com>
Diff between multilevel versions 2.7 dated 2022-03-07 and 2.7.1 dated 2025-09-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/gmeanrel.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Multivariate Regression Association Measure
Description: Implementations of an estimator for the multivariate regression association measure (MRAM) proposed in Shih and Chen (2025) <in revision> and its associated variable selection algorithm. The MRAM quantifies the predictability of a random vector Y from a random vector X given a random vector Z. It takes the maximum value 1 if and only if Y is almost surely a measurable function of X and Z, and the minimum value of 0 if Y is conditionally independent of X given Z. The MRAM generalizes the Kendall's tau copula correlation ratio proposed in Shih and Emura (2021) <doi:10.1016/j.jmva.2020.104708> by employing the spatial sign function. The estimator is based on the nearest neighbor method, and the associated variable selection algorithm is adapted from the feature ordering by conditional independence (FOCI) algorithm of Azadkia and Chatterjee (2021) <doi:10.1214/21-AOS2073>. For further details, see the paper Shih and Chen (2025) <in revision>.
Author: Jia-Han Shih [aut, cre],
Yi-Hau Chen [aut]
Maintainer: Jia-Han Shih <jhshih@math.nsysu.edu.tw>
Diff between MRAM versions 0.1.2 dated 2025-06-06 and 0.2.1 dated 2025-09-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mram.R | 54 ++++++++++++++++++++++++++++++++++++++++-------------- R/vs_mram.R | 40 +++++++++++++++++++++++++++++++++++----- man/mram.Rd | 52 ++++++++++++++++++++++++++++++++++++++-------------- man/vs_mram.Rd | 40 +++++++++++++++++++++++++++++++++++----- 6 files changed, 157 insertions(+), 47 deletions(-)
Title: Locally Stationary Two-Dimensional Wavelet Process Estimation
Scheme
Description: Estimates two-dimensional local wavelet spectra.
Author: Idris Eckley [aut, cre],
Guy Nason [aut],
Sarah Taylor [ctb],
Matthew Nunes [ctb]
Maintainer: Idris Eckley <i.eckley@lancaster.ac.uk>
Diff between LS2W versions 1.3.6 dated 2022-11-01 and 1.3.7 dated 2025-09-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/CITATION | 32 ++++++++++++++------------------ man/AvBasis.wst2D.Rd | 8 ++++---- man/imwr.imwd.rd | 12 ++++++------ 5 files changed, 32 insertions(+), 36 deletions(-)
Title: Sean 'Lahman' Baseball Database
Description: Provides the tables from the 'Sean Lahman Baseball Database' as
a set of R data.frames. It uses the data on pitching, hitting and fielding
performance and other tables from 1871 through 2024, as recorded in the 2025
version of the database. Documentation examples show how many baseball
questions can be investigated.
Author: Michael Friendly [aut],
Chris Dalzell [cre, aut],
Martin Monkman [aut],
Dennis Murphy [aut],
Vanessa Foot [ctb],
Justeena Zaki-Azat [ctb],
Daniel J Eck [ctb],
Sean Lahman [cph]
Maintainer: Chris Dalzell <cdalzell@gmail.com>
Diff between Lahman versions 12.0-0 dated 2024-09-26 and 13.0-0 dated 2025-09-08
Lahman-12.0-0/Lahman/man/figures/Lahman_hex.png |only Lahman-13.0-0/Lahman/DESCRIPTION | 17 +- Lahman-13.0-0/Lahman/MD5 | 152 +++++++++--------- Lahman-13.0-0/Lahman/NEWS.md | 3 Lahman-13.0-0/Lahman/build/vignette.rds |binary Lahman-13.0-0/Lahman/data/AllstarFull.RData |binary Lahman-13.0-0/Lahman/data/Appearances.RData |binary Lahman-13.0-0/Lahman/data/AwardsManagers.RData |binary Lahman-13.0-0/Lahman/data/AwardsPlayers.RData |binary Lahman-13.0-0/Lahman/data/AwardsShareManagers.RData |binary Lahman-13.0-0/Lahman/data/AwardsSharePlayers.RData |binary Lahman-13.0-0/Lahman/data/Batting.RData |binary Lahman-13.0-0/Lahman/data/BattingPost.RData |binary Lahman-13.0-0/Lahman/data/CollegePlaying.RData |binary Lahman-13.0-0/Lahman/data/Fielding.RData |binary Lahman-13.0-0/Lahman/data/FieldingOF.RData |binary Lahman-13.0-0/Lahman/data/FieldingOFsplit.RData |binary Lahman-13.0-0/Lahman/data/FieldingPost.RData |binary Lahman-13.0-0/Lahman/data/HallOfFame.RData |binary Lahman-13.0-0/Lahman/data/HomeGames.RData |binary Lahman-13.0-0/Lahman/data/LahmanData.RData |binary Lahman-13.0-0/Lahman/data/Managers.RData |binary Lahman-13.0-0/Lahman/data/ManagersHalf.RData |binary Lahman-13.0-0/Lahman/data/Parks.RData |binary Lahman-13.0-0/Lahman/data/People.RData |binary Lahman-13.0-0/Lahman/data/Pitching.RData |binary Lahman-13.0-0/Lahman/data/PitchingPost.RData |binary Lahman-13.0-0/Lahman/data/Salaries.RData |binary Lahman-13.0-0/Lahman/data/Schools.RData |binary Lahman-13.0-0/Lahman/data/SeriesPost.RData |binary Lahman-13.0-0/Lahman/data/Teams.RData |binary Lahman-13.0-0/Lahman/data/TeamsFranchises.RData |binary Lahman-13.0-0/Lahman/data/TeamsHalf.RData |binary Lahman-13.0-0/Lahman/data/battingLabels.RData |binary Lahman-13.0-0/Lahman/data/fieldingLabels.RData |binary Lahman-13.0-0/Lahman/data/pitchingLabels.RData |binary Lahman-13.0-0/Lahman/inst/doc/FHM-primer.R |only Lahman-13.0-0/Lahman/inst/doc/FHM-primer.Rmd |only Lahman-13.0-0/Lahman/inst/doc/FHM-primer.html |only Lahman-13.0-0/Lahman/inst/doc/hits-by-type.Rmd | 2 Lahman-13.0-0/Lahman/inst/doc/hits-by-type.html | 10 - Lahman-13.0-0/Lahman/inst/doc/payroll.R | 6 Lahman-13.0-0/Lahman/inst/doc/payroll.html | 86 +++++----- Lahman-13.0-0/Lahman/inst/doc/run-scoring-trends.html | 10 - Lahman-13.0-0/Lahman/inst/doc/strikeoutsandhr.html | 38 ++-- Lahman-13.0-0/Lahman/inst/doc/vignette-intro.Rmd | 8 Lahman-13.0-0/Lahman/inst/doc/vignette-intro.html | 19 +- Lahman-13.0-0/Lahman/inst/scripts/readLahman.R | 15 - Lahman-13.0-0/Lahman/man/AllstarFull.Rd | 4 Lahman-13.0-0/Lahman/man/Appearances.Rd | 4 Lahman-13.0-0/Lahman/man/AwardsManagers.Rd | 4 Lahman-13.0-0/Lahman/man/AwardsPlayers.Rd | 4 Lahman-13.0-0/Lahman/man/AwardsShareManagers.Rd | 4 Lahman-13.0-0/Lahman/man/AwardsSharePlayers.Rd | 4 Lahman-13.0-0/Lahman/man/Batting.Rd | 4 Lahman-13.0-0/Lahman/man/BattingPost.Rd | 4 Lahman-13.0-0/Lahman/man/CollegePlaying.Rd | 2 Lahman-13.0-0/Lahman/man/Fielding.Rd | 4 Lahman-13.0-0/Lahman/man/FieldingOF.Rd | 4 Lahman-13.0-0/Lahman/man/FieldingOFsplit.Rd | 4 Lahman-13.0-0/Lahman/man/FieldingPost.Rd | 4 Lahman-13.0-0/Lahman/man/HallOfFame.Rd | 4 Lahman-13.0-0/Lahman/man/HomeGames.Rd | 4 Lahman-13.0-0/Lahman/man/Lahman-package.Rd | 8 Lahman-13.0-0/Lahman/man/Managers.Rd | 4 Lahman-13.0-0/Lahman/man/ManagersHalf.Rd | 2 Lahman-13.0-0/Lahman/man/Parks.Rd | 4 Lahman-13.0-0/Lahman/man/People.Rd | 4 Lahman-13.0-0/Lahman/man/Pitching.Rd | 4 Lahman-13.0-0/Lahman/man/PitchingPost.Rd | 4 Lahman-13.0-0/Lahman/man/Salaries.Rd | 2 Lahman-13.0-0/Lahman/man/Schools.Rd | 4 Lahman-13.0-0/Lahman/man/SeriesPost.Rd | 4 Lahman-13.0-0/Lahman/man/Teams.Rd | 4 Lahman-13.0-0/Lahman/man/TeamsFranchises.Rd | 2 Lahman-13.0-0/Lahman/man/TeamsHalf.Rd | 2 Lahman-13.0-0/Lahman/man/figures/logo.png |only Lahman-13.0-0/Lahman/vignettes/FHM-primer.Rmd |only Lahman-13.0-0/Lahman/vignettes/hits-by-type.Rmd | 2 Lahman-13.0-0/Lahman/vignettes/vignette-intro.Rmd | 8 80 files changed, 255 insertions(+), 227 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.33 dated 2025-03-21 and 4.34 dated 2025-09-08
DESCRIPTION | 8 +-- MD5 | 42 ++++++++-------- NEWS.md | 50 +++++++++++++++++++- R/distMat.R |only R/distPres.R | 47 +----------------- R/fuzzyRangeChange.R | 10 ++-- R/getRegion.R | 120 +++++++++++++++++++++++++++++------------------- R/gridRecords.R | 46 ++++++++++++------ R/multConvert.R | 16 +++--- R/multTSA.R | 36 ++++++++++---- R/timer.R | 20 +++++--- data/rotif.env.rda |binary data/rotifers.rda |binary man/distMat.Rd |only man/distPres.Rd | 10 ++-- man/fuzzyRangeChange.Rd | 8 +-- man/fuzzySim-package.Rd | 4 - man/getRegion.Rd | 22 +++++--- man/gridRecords.Rd | 45 +++++++++++++++--- man/integerCols.Rd | 4 - man/multConvert.Rd | 36 ++++++++++---- man/multTSA.Rd | 19 ++++--- man/multicol.Rd | 12 ++-- 23 files changed, 342 insertions(+), 213 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre],
Sebastian Krantz [ctb],
Grant McDermott [ctb] ,
Russell Lenth [ctb],
Kyle Butts [ctb]
Maintainer: Laurent Berge <laurent.berge@u-bordeaux.fr>
Diff between fixest versions 0.12.1 dated 2024-06-13 and 0.13.2 dated 2025-09-08
fixest-0.12.1/fixest/src/quf.cpp |only fixest-0.13.2/fixest/DESCRIPTION | 23 fixest-0.13.2/fixest/MD5 | 209 - fixest-0.13.2/fixest/NAMESPACE | 11 fixest-0.13.2/fixest/NEWS.md | 248 ++ fixest-0.13.2/fixest/R/RcppExports.R | 24 fixest-0.13.2/fixest/R/VCOV.R | 824 ++++--- fixest-0.13.2/fixest/R/alias_etable.R | 16 fixest-0.13.2/fixest/R/coefplot.R | 678 +++-- fixest-0.13.2/fixest/R/collinearity.R |only fixest-0.13.2/fixest/R/data_documentation.R |only fixest-0.13.2/fixest/R/data_tools.R | 350 +-- fixest-0.13.2/fixest/R/debug.R |only fixest-0.13.2/fixest/R/did.R | 148 - fixest-0.13.2/fixest/R/estimation.R | 416 ++- fixest-0.13.2/fixest/R/etable.R | 735 +++--- fixest-0.13.2/fixest/R/femlm.R | 4 fixest-0.13.2/fixest/R/fitstats.R | 63 fixest-0.13.2/fixest/R/fixest_env.R | 634 +++-- fixest-0.13.2/fixest/R/fixest_multi.R | 62 fixest-0.13.2/fixest/R/graph_xaxis.R | 40 fixest-0.13.2/fixest/R/iplot.R | 4 fixest-0.13.2/fixest/R/methods.R | 868 +++++-- fixest-0.13.2/fixest/R/miscfuns.R | 1234 ++++------ fixest-0.13.2/fixest/R/onLoad.R | 65 fixest-0.13.2/fixest/R/panel.R | 43 fixest-0.13.2/fixest/R/r-language.R |only fixest-0.13.2/fixest/R/sparse_model_matrix.R |only fixest-0.13.2/fixest/R/startup.R | 125 - fixest-0.13.2/fixest/R/test_fun.R | 293 +- fixest-0.13.2/fixest/README.md | 2 fixest-0.13.2/fixest/build/vignette.rds |binary fixest-0.13.2/fixest/data/base_pub.RData |only fixest-0.13.2/fixest/data/datalist | 2 fixest-0.13.2/fixest/data/fulton.RData |only fixest-0.13.2/fixest/inst/doc/collinearity.R |only fixest-0.13.2/fixest/inst/doc/collinearity.Rmd |only fixest-0.13.2/fixest/inst/doc/collinearity.html |only fixest-0.13.2/fixest/inst/doc/exporting_tables.R | 64 fixest-0.13.2/fixest/inst/doc/exporting_tables.Rmd | 2 fixest-0.13.2/fixest/inst/doc/exporting_tables.html | 273 -- fixest-0.13.2/fixest/inst/doc/fixest_walkthrough.R | 193 - fixest-0.13.2/fixest/inst/doc/fixest_walkthrough.Rmd | 46 fixest-0.13.2/fixest/inst/doc/fixest_walkthrough.html | 1860 +++++++--------- fixest-0.13.2/fixest/inst/doc/multiple_estimations.R | 14 fixest-0.13.2/fixest/inst/doc/multiple_estimations.Rmd | 2 fixest-0.13.2/fixest/inst/doc/multiple_estimations.html | 54 fixest-0.13.2/fixest/inst/doc/standard_errors.R | 278 +- fixest-0.13.2/fixest/inst/doc/standard_errors.Rmd | 58 fixest-0.13.2/fixest/inst/doc/standard_errors.html | 363 +-- fixest-0.13.2/fixest/man/base_did.Rd | 4 fixest-0.13.2/fixest/man/base_pub.Rd |only fixest-0.13.2/fixest/man/base_stagg.Rd | 4 fixest-0.13.2/fixest/man/coefplot.Rd | 220 + fixest-0.13.2/fixest/man/coeftable.fixest.Rd | 22 fixest-0.13.2/fixest/man/coeftable.fixest_multi.Rd | 15 fixest-0.13.2/fixest/man/confint.fixest.Rd | 4 fixest-0.13.2/fixest/man/confint.fixest_multi.Rd | 4 fixest-0.13.2/fixest/man/degrees_freedom.Rd | 4 fixest-0.13.2/fixest/man/demean.Rd | 11 fixest-0.13.2/fixest/man/etable.Rd | 295 +- fixest-0.13.2/fixest/man/feNmlm.Rd | 123 - fixest-0.13.2/fixest/man/feglm.Rd | 151 - fixest-0.13.2/fixest/man/femlm.Rd | 142 - fixest-0.13.2/fixest/man/feols.Rd | 166 - fixest-0.13.2/fixest/man/fitstat.Rd | 34 fixest-0.13.2/fixest/man/fitstat_register.Rd | 2 fixest-0.13.2/fixest/man/fixest-package.Rd | 1 fixest-0.13.2/fixest/man/formula.fixest.Rd | 89 fixest-0.13.2/fixest/man/fulton.Rd |only fixest-0.13.2/fixest/man/hatvalues.fixest.Rd | 25 fixest-0.13.2/fixest/man/lag.formula.Rd | 4 fixest-0.13.2/fixest/man/model.matrix.fixest.Rd | 52 fixest-0.13.2/fixest/man/obs.Rd | 8 fixest-0.13.2/fixest/man/panel.Rd | 2 fixest-0.13.2/fixest/man/predict.fixest.Rd | 4 fixest-0.13.2/fixest/man/print.fixest.Rd | 1 fixest-0.13.2/fixest/man/print.fixest_multi.Rd | 13 fixest-0.13.2/fixest/man/setFixest_coefplot.Rd | 7 fixest-0.13.2/fixest/man/setFixest_estimation.Rd | 52 fixest-0.13.2/fixest/man/setFixest_fml.Rd | 10 fixest-0.13.2/fixest/man/setFixest_vcov.Rd | 26 fixest-0.13.2/fixest/man/sparse_model_matrix.Rd |only fixest-0.13.2/fixest/man/ssc.Rd | 82 fixest-0.13.2/fixest/man/summary.fixest.Rd | 24 fixest-0.13.2/fixest/man/summary.fixest_multi.Rd | 17 fixest-0.13.2/fixest/man/to_integer.Rd | 39 fixest-0.13.2/fixest/man/trade.Rd | 14 fixest-0.13.2/fixest/man/update.fixest.Rd | 57 fixest-0.13.2/fixest/man/vcov.fixest.Rd | 17 fixest-0.13.2/fixest/man/vcov_cluster.Rd | 7 fixest-0.13.2/fixest/man/vcov_conley.Rd | 21 fixest-0.13.2/fixest/man/vcov_hac.Rd | 7 fixest-0.13.2/fixest/man/vcov_hetero.Rd |only fixest-0.13.2/fixest/man/xpd.Rd | 118 - fixest-0.13.2/fixest/src/RcppExports.cpp | 89 fixest-0.13.2/fixest/src/collineairy.cpp |only fixest-0.13.2/fixest/src/convergence.cpp | 48 fixest-0.13.2/fixest/src/demeaning.cpp | 332 -- fixest-0.13.2/fixest/src/dsb.cpp | 5 fixest-0.13.2/fixest/src/fixest_main.cpp |only fixest-0.13.2/fixest/src/fixest_main.h |only fixest-0.13.2/fixest/src/index_fixed_effects.cpp |only fixest-0.13.2/fixest/src/lm_related.cpp | 215 - fixest-0.13.2/fixest/src/misc_funs.cpp | 88 fixest-0.13.2/fixest/src/parallel_funs.cpp | 68 fixest-0.13.2/fixest/src/string_funs.cpp | 5 fixest-0.13.2/fixest/src/to_index.cpp |only fixest-0.13.2/fixest/src/to_index.h |only fixest-0.13.2/fixest/src/util.h |only fixest-0.13.2/fixest/src/vcov_related.cpp | 13 fixest-0.13.2/fixest/tests/fixest_tests.R | 861 ++++++- fixest-0.13.2/fixest/vignettes/collinearity.Rmd |only fixest-0.13.2/fixest/vignettes/exporting_tables.Rmd | 2 fixest-0.13.2/fixest/vignettes/fixest_walkthrough.Rmd | 46 fixest-0.13.2/fixest/vignettes/multiple_estimations.Rmd | 2 fixest-0.13.2/fixest/vignettes/standard_errors.Rmd | 58 117 files changed, 8191 insertions(+), 5867 deletions(-)
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <doi:10.48550/arXiv.1611.09477> or
nonlinear models <doi:10.48550/arXiv.1604.06737> can be used. There
are also functions for dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between embed versions 1.1.5 dated 2025-01-22 and 1.2.0 dated 2025-09-08
DESCRIPTION | 31 +-- LICENSE | 2 MD5 | 149 +++++++------- NAMESPACE | 12 - NEWS.md | 9 R/aaa.R | 42 +++- R/collapse_cart.R | 77 ++++--- R/collapse_stringdist.R | 74 ++++--- R/discretize_cart.R | 73 ++++--- R/discretize_xgb.R | 116 +++++++---- R/embed-package.R | 1 R/embed.R | 235 +++++++++++++---------- R/feature_hash.R | 275 +-------------------------- R/lencode.R |only R/lencode_bayes.R | 64 ++++-- R/lencode_glm.R | 50 ++-- R/lencode_mixed.R | 57 +++-- R/pca_sparse.R | 77 ++++--- R/pca_sparse_bayes.R | 80 ++++--- R/pca_truncated.R | 70 ++++-- R/umap.R | 113 ++++++----- R/woe.R | 161 ++++++++------- build |only man/add_woe.Rd | 2 man/dictionary.Rd | 2 man/embed-package.Rd | 4 man/required_pkgs.embed.Rd | 6 man/rmd/num_comp.Rmd | 5 man/rmd/tunable-args.Rmd | 18 + man/step_collapse_cart.Rd | 4 man/step_collapse_stringdist.Rd | 31 +-- man/step_discretize_cart.Rd | 2 man/step_discretize_xgb.Rd | 4 man/step_embed.Rd | 32 +-- man/step_feature_hash.Rd | 112 ---------- man/step_lencode.Rd |only man/step_lencode_bayes.Rd | 2 man/step_lencode_glm.Rd | 2 man/step_lencode_mixed.Rd | 2 man/step_pca_sparse.Rd | 24 +- man/step_pca_sparse_bayes.Rd | 24 +- man/step_pca_truncated.Rd | 41 +--- man/step_umap.Rd | 37 +-- man/step_woe.Rd | 18 - tests/testthat/_snaps/collapse_cart.md | 6 tests/testthat/_snaps/collapse_stringdist.md | 4 tests/testthat/_snaps/discretize_cart.md | 34 +-- tests/testthat/_snaps/discretize_xgb.md | 36 +-- tests/testthat/_snaps/embed.md | 7 tests/testthat/_snaps/extension_check.md | 2 tests/testthat/_snaps/feature_hash.md | 118 ----------- tests/testthat/_snaps/lencode.md |only tests/testthat/_snaps/lencode_bayes.md | 53 ++--- tests/testthat/_snaps/lencode_glm.md | 18 - tests/testthat/_snaps/lencode_mixed.md | 8 tests/testthat/_snaps/pca_sparse.md | 8 tests/testthat/_snaps/pca_sparse_bayes.md | 16 - tests/testthat/_snaps/pca_truncated.md | 4 tests/testthat/_snaps/umap.md | 26 -- tests/testthat/_snaps/woe.md | 18 - tests/testthat/helper-make_binned_data.R | 6 tests/testthat/test-collapse_cart.R | 82 ++++---- tests/testthat/test-collapse_stringdist.R | 122 ++++++----- tests/testthat/test-discretize_cart.R | 80 +++---- tests/testthat/test-discretize_xgb.R | 235 ++++++++++++----------- tests/testthat/test-embed.R | 272 ++++++++++++++------------ tests/testthat/test-extension_check.R | 1 tests/testthat/test-feature_hash.R | 264 ------------------------- tests/testthat/test-lencode.R |only tests/testthat/test-lencode_bayes.R | 127 ++++++------ tests/testthat/test-lencode_glm.R | 69 +++--- tests/testthat/test-lencode_mixed.R | 86 ++++---- tests/testthat/test-pca_sparse.R | 152 ++++++++------ tests/testthat/test-pca_sparse_bayes.R | 164 ++++++++-------- tests/testthat/test-pca_truncated.R | 142 +++++++------ tests/testthat/test-s3-methods.R | 10 tests/testthat/test-umap.R | 213 ++++++++++++-------- tests/testthat/test-woe.R | 225 +++++++++++++--------- 78 files changed, 2269 insertions(+), 2479 deletions(-)
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.3.8 dated 2025-05-29 and 0.3.9 dated 2025-09-08
DESCRIPTION | 8 +- MD5 | 16 ++--- NAMESPACE | 2 R/DESCRIPTIVES.R |only R/DFA.R | 73 ++++++++++++----------- R/GROUP.DIFFS.R | 18 ++++- R/GROUP.PROFILES.R | 153 ++++++++++++++++++++++++++++---------------------- R/utilities_boc.R | 4 - man/DESCRIPTIVES.Rd |only man/GROUP.PROFILES.Rd | 20 ++++++ 10 files changed, 174 insertions(+), 120 deletions(-)
Title: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size
bitmap arrays using 'librsvg2'. The resulting bitmap can be written to
e.g. png, jpeg or webp format. In addition, the package can convert
images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] ,
Salim Brueggemann [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between rsvg versions 2.6.2 dated 2025-03-23 and 2.7.0 dated 2025-09-08
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NEWS | 3 +++ build/vignette.rds |binary src/Makevars.win | 10 +++++----- src/dummy.cc |only tools/winlibs.R | 6 +++--- 7 files changed, 23 insertions(+), 19 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>. Further discussion on robust mediation analysis can be found in Alfons & Schley (2025) <doi:10.31234/osf.io/2hqdy>.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [dtc]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 1.2.1 dated 2025-02-08 and 1.2.2 dated 2025-09-08
DESCRIPTION | 21 +++++++++-------- MD5 | 50 +++++++++++++++++++++--------------------- NEWS | 7 +++++ R/BSG2014.R | 16 ++++++++----- R/fit_mediation.R | 4 +++ R/robmed-package.R | 8 +++++- R/setup_weight_plot.R | 4 +++ R/summary.R | 4 +++ R/test_mediation.R | 4 +++ R/weight_plot.R | 4 +++ build/partial.rdb |binary build/vignette.rds |binary data/BSG2014.RData |binary inst/CITATION | 8 +++--- inst/doc/robmed-intro.R | 16 ++++++------- inst/doc/robmed-intro.Rnw | 12 +++++----- inst/doc/robmed-intro.pdf |binary man/BSG2014.Rd | 16 ++++++++----- man/fit_mediation.Rd | 4 +++ man/robmed-package.Rd | 8 +++++- man/setup_weight_plot.Rd | 4 +++ man/summary.test_mediation.Rd | 4 +++ man/test_mediation.Rd | 4 +++ man/weight_plot.Rd | 4 +++ vignettes/robmed-intro.Rnw | 12 +++++----- vignettes/robmed.bib | 2 - 26 files changed, 140 insertions(+), 76 deletions(-)
Title: Interactive Viewing of Spatial Data in R
Description: Quickly and conveniently create interactive
visualisations of spatial data with or without background maps.
Attributes of displayed features are fully queryable via pop-up
windows. Additional functionality includes methods to visualise true-
and false-color raster images and bounding boxes.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Michael Sumner [ctb],
Jochen Darley [ctb],
Pierre Roudier [ctb],
[...truncated...]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapview versions 2.11.3 dated 2025-08-28 and 2.11.4 dated 2025-09-08
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS | 2 + NEWS.md | 2 + R/AAAmapviewClasses.R | 1 inst/tinytest/test-mapview.R | 40 ----------------------------------- inst/tinytest/test-mapviewControls.R | 6 ----- man/viewExtent.Rd | 16 ++++++-------- 8 files changed, 23 insertions(+), 64 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file forma [...truncated...]
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.18 dated 2024-02-02 and 1.0.0 dated 2025-09-08
DESCRIPTION | 14 MD5 | 604 ++--- NAMESPACE | 352 +-- R/brainvoyager.R | 880 ++++---- R/cifti.R | 226 +- R/gifti_writer.R | 540 ++--- R/gifti_xml_tools.R | 452 ++-- R/mghheader.R | 1456 +++++++------- R/nifti_common.R | 384 +-- R/nifti_to_mgh.R | 794 +++---- R/optdata.R | 350 +-- R/read_dti_tck.R | 434 ++-- R/read_dti_trk.R | 246 +- R/read_fs_curv.R | 5 R/read_fs_label.R | 400 +-- R/read_fs_mgh.R | 906 ++++---- R/read_fs_patch.R | 332 +-- R/read_fs_surface.R | 2 R/read_fs_volume.R | 98 R/read_fs_weight.R | 138 - R/read_nifti1.R | 438 ++-- R/read_nifti2.R | 314 +-- R/read_nisurface.R | 326 +-- R/rotate3d.R | 404 +-- R/surface_dist.R | 210 +- R/write_fs_curv.R | 4 R/write_fs_mgh.R | 30 R/write_fs_patch.R | 210 +- R/write_fs_surface.R | 9 R/write_fs_weight.R | 186 - R/write_nifti1.R | 488 ++-- R/write_nifti2.R | 448 ++-- build/vignette.rds |binary inst/doc/freesurferformats.R | 32 inst/doc/freesurferformats.Rmd | 624 +++--- inst/doc/freesurferformats.html | 6 inst/doc/freesurferformats_header.R | 36 inst/doc/freesurferformats_header.Rmd | 190 - inst/doc/freesurferformats_header.html | 2 inst/doc/freesurferformats_write.R | 98 inst/doc/freesurferformats_write.Rmd | 314 +-- inst/doc/freesurferformats_write.html | 2 inst/extdata/colorlut.txt | 20 inst/extdata/cube.geo | 36 inst/extdata/cube.gii | 34 inst/extdata/cube.off | 44 inst/extdata/cube.ply | 58 inst/extdata/cube.stl | 172 - inst/extdata/cube.tri | 44 inst/extdata/cube.vtk | 52 inst/extdata/cube.wobj | 40 inst/extdata/cube_quads.byu | 16 inst/extdata/lh.entorhinal_exvivo.label | 2174 ++++++++++----------- inst/extdata/lh.testsurface.asc | 20 inst/extdata/lh.tinysurface.asc | 20 inst/extdata/lh.tinysurface.gii | 126 - inst/extdata/register.dat | 18 inst/extdata/talairach.lta | 60 inst/extdata/talairach.xfm | 16 inst/extdata/tiny_label.gii | 34 inst/extdata/tiny_morph.gii | 26 man/adjust.face.indices.to.Rd | 46 man/annot.max.region.idx.Rd | 40 man/annot.unique.Rd | 82 man/assert.surface.Rd | 40 man/bvsmp.Rd | 46 man/cdata.Rd | 40 man/check.dtype.for.data.Rd | 37 man/check_data_and_settings_consistency.Rd | 60 man/closest.vert.to.point.Rd | 50 man/colortable.from.annot.Rd | 82 man/coord.to.key.Rd | 40 man/delete_all_opt_data.Rd | 28 man/doapply.transform.mtx.Rd | 54 man/download_opt_data.Rd | 28 man/euclidian.dist.Rd | 40 man/faces.quad.to.tris.Rd | 86 man/faces.tris.to.quad.Rd | 40 man/fileopen.gz.or.not.Rd | 30 man/filepath.ends.with.Rd | 40 man/fixed.vec.format.int.Rd | 58 man/flip2D.Rd | 38 man/flip3D.Rd | 52 man/fread3.Rd | 36 man/fs.get.morph.file.ext.for.format.Rd | 80 man/fs.get.morph.file.format.from.filename.Rd | 80 man/fs.patch.Rd | 74 man/fs.surface.to.tmesh3d.Rd | 34 man/fwrite3.Rd | 34 man/get.dti.trk.endianness.Rd | 42 man/get.slice.orientation.Rd | 36 man/get_opt_data_filepath.Rd | 38 man/gifti_writer.Rd | 54 man/gifti_xml.Rd | 116 - man/gifti_xml_add_global_metadata.Rd | 64 man/gifti_xml_write.Rd | 70 man/giftixml_add_labeltable_from_annot.Rd | 38 man/giftixml_add_labeltable_posneg.Rd | 36 man/guess.filename.is.gzipped.Rd | 40 man/int.to.col.brainvoyager.Rd | 36 man/is.bvsmp.Rd | 34 man/is.fs.annot.Rd | 34 man/is.fs.label.Rd | 34 man/is.fs.surface.Rd | 34 man/is.fs.volume.Rd | 34 man/is.mghheader.Rd | 34 man/linesplit.fixed.Rd | 52 man/list_opt_data.Rd | 28 man/mgh.is.conformed.Rd | 40 man/mghheader.Rd | 40 man/mghheader.centervoxelRAS.from.firstvoxelRAS.Rd | 38 man/mghheader.crs.orientation.Rd | 34 man/mghheader.is.conformed.Rd | 34 man/mghheader.is.ras.valid.Rd | 82 man/mghheader.primary.slice.direction.Rd | 34 man/mghheader.ras2vox.Rd | 86 man/mghheader.ras2vox.tkreg.Rd | 86 man/mghheader.scanner2tkreg.Rd | 82 man/mghheader.tkreg2scanner.Rd | 82 man/mghheader.update.from.vox2ras.Rd | 38 man/mghheader.vox2ras.Rd | 86 man/mghheader.vox2ras.tkreg.Rd | 86 man/mghheader.vox2vox.Rd | 38 man/mni152reg.Rd | 40 man/mri_dtype_numbytes.Rd | 36 man/ni1header.for.data.Rd | 38 man/ni1header.template.Rd | 40 man/ni2header.for.data.Rd | 34 man/ni2header.template.Rd | 40 man/nifti.datadim.from.dimfield.Rd | 52 man/nifti.datadim.to.dimfield.Rd | 52 man/nifti.dtype.info.Rd | 40 man/nifti.field.check.length.Rd | 44 man/nifti.field.check.nchar.max.Rd | 44 man/nifti.file.uses.fshack.Rd | 40 man/nifti.file.version.Rd | 34 man/nifti.header.check.Rd | 38 man/nifti.space.info.Rd | 36 man/nifti.time.info.Rd | 36 man/nifti.transform.type.name.Rd | 36 man/parse.stl.ascii.face.Rd | 36 man/parse.transform.matrix.lines.Rd | 40 man/ply.header.lines.Rd | 24 man/polygon.soup.to.indexed.mesh.Rd | 40 man/print.fs.annot.Rd | 32 man/print.fs.label.Rd | 32 man/print.fs.patch.Rd | 32 man/print.fs.surface.Rd | 32 man/print.fs.volume.Rd | 32 man/ras.to.surfaceras.Rd | 48 man/ras.to.talairachras.Rd | 48 man/read.dti.tck.Rd | 48 man/read.dti.trk.Rd | 50 man/read.dti.tsf.Rd | 60 man/read.element.counts.ply.header.Rd | 30 man/read.fixed.char.binary.Rd | 50 man/read.fs.annot.Rd | 2 man/read.fs.colortable.Rd | 78 man/read.fs.curv.Rd | 106 - man/read.fs.gca.Rd | 54 man/read.fs.label.Rd | 66 man/read.fs.label.gii.Rd | 74 man/read.fs.label.native.Rd | 88 man/read.fs.mgh.Rd | 138 - man/read.fs.morph.Rd | 114 - man/read.fs.morph.asc.Rd | 40 man/read.fs.morph.bvsmp.Rd | 38 man/read.fs.morph.cifti.Rd | 104 - man/read.fs.morph.gii.Rd | 102 man/read.fs.morph.ni1.Rd | 40 man/read.fs.morph.ni2.Rd | 34 man/read.fs.morph.nii.Rd | 34 man/read.fs.morph.txt.Rd | 34 man/read.fs.patch.Rd | 52 man/read.fs.patch.asc.Rd | 48 man/read.fs.surface.Rd | 100 man/read.fs.surface.asc.Rd | 94 man/read.fs.surface.bvsrf.Rd | 86 man/read.fs.surface.byu.Rd | 44 man/read.fs.surface.geo.Rd | 86 man/read.fs.surface.gii.Rd | 92 man/read.fs.surface.ico.Rd | 86 man/read.fs.surface.mz3.Rd | 40 man/read.fs.surface.obj.Rd | 86 man/read.fs.surface.off.Rd | 80 man/read.fs.surface.ply.Rd | 86 man/read.fs.surface.stl.Rd | 48 man/read.fs.surface.stl.ascii.Rd | 52 man/read.fs.surface.stl.bin.Rd | 50 man/read.fs.surface.vtk.Rd | 86 man/read.fs.transform.Rd | 92 man/read.fs.transform.dat.Rd | 82 man/read.fs.transform.lta.Rd | 86 man/read.fs.transform.xfm.Rd | 88 man/read.fs.volume.Rd | 140 - man/read.fs.volume.nii.Rd | 112 - man/read.fs.weight.Rd | 84 man/read.fs.weight.asc.Rd | 36 man/read.mesh.brainvoyager.Rd | 86 man/read.nifti1.data.Rd | 48 man/read.nifti1.header.Rd | 40 man/read.nifti1.header.internal.Rd | 40 man/read.nifti2.data.Rd | 42 man/read.nifti2.header.Rd | 34 man/read.nifti2.header.internal.Rd | 46 man/read.smp.brainvoyager.Rd | 70 man/read.smp.brainvoyager.v1or2.Rd | 42 man/read.smp.brainvoyager.v3.Rd | 42 man/read.smp.brainvoyager.v4or5.Rd | 42 man/read_nisurface.Rd | 108 - man/read_nisurfacefile.Rd | 102 man/read_nisurfacefile.fsascii.Rd | 38 man/read_nisurfacefile.fsnative.Rd | 38 man/read_nisurfacefile.gifti.Rd | 38 man/readable.files.Rd | 56 man/readcolortable.Rd | 40 man/readcolortable_oldformat.Rd | 40 man/rotate2D.Rd | 38 man/rotate3D.Rd | 52 man/rotate90.Rd | 38 man/scann.Rd | 44 man/sm0to1.Rd | 70 man/sm1to0.Rd | 70 man/stl.format.file.is.ascii.Rd | 30 man/surfaceras.to.ras.Rd | 62 man/surfaceras.to.talairach.Rd | 56 man/talairachras.to.ras.Rd | 50 man/translate.mri.dtype.Rd | 36 man/vertex.euclid.dist.Rd | 54 man/vertexdists.to.point.Rd | 50 man/write.fs.colortable.Rd | 66 man/write.fs.curv.Rd | 80 man/write.fs.label.Rd | 4 man/write.fs.label.gii.Rd | 112 - man/write.fs.mgh.Rd | 102 man/write.fs.morph.Rd | 92 man/write.fs.morph.asc.Rd | 82 man/write.fs.morph.gii.Rd | 96 man/write.fs.morph.ni1.Rd | 96 man/write.fs.morph.ni2.Rd | 106 - man/write.fs.morph.smp.Rd | 88 man/write.fs.morph.txt.Rd | 78 man/write.fs.patch.Rd | 52 man/write.fs.surface.Rd | 10 man/write.fs.surface.asc.Rd | 8 man/write.fs.surface.bvsrf.Rd | 62 man/write.fs.surface.byu.Rd | 8 man/write.fs.surface.gii.Rd | 8 man/write.fs.surface.mz3.Rd | 8 man/write.fs.surface.obj.Rd | 6 man/write.fs.surface.off.Rd | 4 man/write.fs.surface.off.ply2.Rd | 4 man/write.fs.surface.ply.Rd | 6 man/write.fs.surface.ply2.Rd | 6 man/write.fs.surface.vtk.Rd | 8 man/write.fs.weight.Rd | 86 man/write.fs.weight.asc.Rd | 82 man/write.nifti1.Rd | 50 man/write.nifti2.Rd | 46 man/write.smp.brainvoyager.Rd | 42 man/write.smp.brainvoyager.v2.Rd | 44 man/write.smp.brainvoyager.v3or4or5.Rd | 44 man/xml_node_gifti_MD.Rd | 50 man/xml_node_gifti_coordtransform.Rd | 56 man/xml_node_gifti_label.Rd | 44 man/xml_node_gifti_label_table.Rd | 30 man/xml_node_gifti_label_table_from_annot.Rd | 36 tests/testthat.R | 8 tests/testthat/helper-functions-for-tests.R | 48 tests/testthat/teardown-cran.R | 20 tests/testthat/test-brainvoyager.R | 210 +- tests/testthat/test-cifti.R | 96 tests/testthat/test-gifti_writer.R | 36 tests/testthat/test-gifti_xml_tools.R | 66 tests/testthat/test-helpers.R | 36 tests/testthat/test-mgh2nii.R | 62 tests/testthat/test-mghheader.R | 474 ++-- tests/testthat/test-nifti_to_mgh.R | 90 tests/testthat/test-read_fs_annot.R | 364 +-- tests/testthat/test-read_fs_curv.R | 96 tests/testthat/test-read_fs_label.R | 196 - tests/testthat/test-read_fs_mgh.R | 354 +-- tests/testthat/test-read_fs_patch.R | 96 tests/testthat/test-read_fs_surface.R | 860 ++++---- tests/testthat/test-read_fs_transform.R | 120 - tests/testthat/test-read_fs_weight.R | 16 tests/testthat/test-read_nifti1.R | 202 - tests/testthat/test-read_nifti2.R | 146 - tests/testthat/test-read_nisurface.R | 240 +- tests/testthat/test-rotate3d.R | 186 - tests/testthat/test-surface_dist.R | 72 tests/testthat/test-write_fs_annot.R | 243 +- tests/testthat/test-write_fs_curv.R | 300 +- tests/testthat/test-write_fs_label.R | 116 - tests/testthat/test-write_fs_mgh.R | 376 +-- tests/testthat/test-write_fs_patch.R | 56 tests/testthat/test-write_fs_surface.R | 366 +-- tests/testthat/test-write_fs_weight.R | 90 tests/testthat/test-write_nifti1.R | 158 - tests/testthat/test-write_nifti2.R | 102 vignettes/freesurferformats.Rmd | 624 +++--- vignettes/freesurferformats_header.Rmd | 190 - vignettes/freesurferformats_write.Rmd | 314 +-- 303 files changed, 17001 insertions(+), 16997 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Descriptive Statistical Analysis
Description: Description of statistical associations between variables : measures of local and global association between variables (phi, Cramér V, correlations, eta-squared, Goodman and Kruskal tau, permutation tests, etc.), multiple graphical representations of the associations between variables (using 'ggplot2') and weighted statistics.
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between descriptio versions 1.4.1 dated 2025-05-29 and 1.5 dated 2025-09-08
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++++------ NAMESPACE | 3 ++- NEWS.md | 22 +++++++++++++++++++++- R/agg.wtd.mad.R |only R/agg.wtd.mean.R |only R/agg.wtd.quantile.R |only R/agg.wtd.var.R |only R/assoc.twocat.R | 10 +--------- R/assoc.twocat.by.R | 13 +++++++++---- R/weighted.cramer.R | 4 ++-- man/agg.wtd.mad.Rd |only man/agg.wtd.mean.Rd |only man/agg.wtd.quantile.Rd |only man/agg.wtd.var.Rd |only 15 files changed, 52 insertions(+), 26 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous posterior
distributions with a customizable trajectory length termination criterion.
See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original
Discontinuous Hamiltonian Monte Carlo; Hoffman et al. (2014)
<doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225>
for the definition of possible Hamiltonian Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.6.1 dated 2025-08-24 and 1.6.3 dated 2025-09-07
DESCRIPTION | 34 +++--- MD5 | 52 ++++----- R/interface.R | 7 + build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 8 - inst/doc/Tutorial_for_main_functions.Rmd | 8 - inst/doc/Tutorial_for_main_functions.html | 14 +- src/Makevars | 1 src/Makevars.win | 2 src/dnuts.cpp | 69 ++++++------ src/epsilon_adapt.cpp | 103 +++++++++---------- src/epsilon_adapt.h | 11 ++ src/epsilon_init.cpp | 45 ++++---- src/epsilon_init.h | 3 src/globals_functions.cpp | 6 + src/globals_functions.h | 6 + src/globals_interact.h | 2 src/leapfrog.cpp | 43 ++++---- src/leapfrog.h | 5 src/mcmc.h | 8 + src/recursive_tree.cpp | 161 +++++++++++++++--------------- src/recursive_tree.h | 5 src/single_hmc.cpp | 36 +++--- src/single_hmc.h | 5 src/single_nuts.cpp | 48 ++++---- src/single_nuts.h | 5 vignettes/Tutorial_for_main_functions.Rmd | 8 - 27 files changed, 380 insertions(+), 315 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.8.3 dated 2025-03-22 and 0.8.4 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/nComp.R | 2 +- R/nlr.R | 4 +++- inst/NEWS.Rd | 6 ++++++ 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Articulatory Data Processing in R
Description: A tool for processing Articulate
Assistant Advanced™ (AAA) ultrasound tongue imaging data and Carstens AG500/1 electro-magnetic articulographic data.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between rticulate versions 2.0.1 dated 2025-02-20 and 2.2.0 dated 2025-09-07
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 12 ++++++++++++ R/transform.R | 14 +++++++++++--- build/vignette.rds |binary inst/doc/filter-signals.html | 4 ++-- inst/doc/overview.html | 4 ++-- inst/doc/polar-gams.html | 34 +++++++++++++++++----------------- inst/doc/tongue-imaging.html | 4 ++-- inst/doc/transform-coord.R | 22 +++++++++++++--------- inst/doc/transform-coord.Rmd | 24 ++++++++++++++---------- inst/doc/transform-coord.html | 37 +++++++++++++++++++------------------ vignettes/transform-coord.Rmd | 24 ++++++++++++++---------- 13 files changed, 122 insertions(+), 89 deletions(-)
Title: Use Time Series to Generate and Compare Power Spectral Density
Description: Functions that allow you to generate and compare power spectral density (PSD)
plots given time series data. Fast Fourier Transform (FFT) is used to take a time series
data, analyze the oscillations, and then output the frequencies of these oscillations
in the time series in the form of a PSD plot.Thus given a time series, the dominant
frequencies in the time series can be identified. Additional functions in this package
allow the dominant frequencies of multiple groups of time series to be compared with each other.
To see example usage with the main functions of this package, please visit
this site: <https://yhhc2.github.io/psdr/articles/Introduction.html>.
The mathematical operations used to generate the PSDs are described in these sites:
<https://www.mathworks.com/help/matlab/ref/fft.html>.
<https://www.mathworks.com/help/signal/ug/power-spectral-density-estimates-using-fft.html>.
Author: Yong-Han Hank Cheng [aut, cre]
Maintainer: Yong-Han Hank Cheng <yhhc@uw.edu>
Diff between psdr versions 1.0.1 dated 2021-06-04 and 1.0.3 dated 2025-09-07
DESCRIPTION | 16 LICENSE | 4 MD5 | 24 NEWS.md | 10 README.md | 1 build/vignette.rds |binary inst/doc/Examples.R | 8 inst/doc/Examples.html | 1889 ++++++++++++++++++++++----------------------- inst/doc/Introduction.R | 38 inst/doc/Introduction.html | 600 +++++++------- man/GenerateExampleData.Rd | 28 tests/testthat.R | 8 tests/testthat/test-PSD.R | 145 +-- 13 files changed, 1408 insertions(+), 1363 deletions(-)
Title: Compute Neural Fragility for Ictal iEEG Time Series
Description: Provides tools to compute the neural fragility matrix from intracranial electrocorticographic (iEEG) recordings, enabling the analysis of brain dynamics during seizures. The package implements the method described by Li et al. (2017) <doi:10.23919/ACC.2017.7963378> and includes functions for data preprocessing ('Epoch'), fragility computation ('calcAdjFrag'), and visualization.
Author: Jiefei Wang [aut, cre] ,
Patrick Karas [aut],
Anne-Cecile Lesage [aut] ,
Ioannis Malagaris [aut] ,
Oliver Zhou [aut],
Liliana Camarillo Rodriguez [aut] ,
Sean O'Leary [aut] ,
Yuanyi Zhang [aut]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between EZFragility versions 1.0.3 dated 2025-04-10 and 2.0.1 dated 2025-09-07
EZFragility-1.0.3/EZFragility/R/class_Epoch.r |only EZFragility-1.0.3/EZFragility/man/Epoch-class.Rd |only EZFragility-1.0.3/EZFragility/man/Epoch-method.Rd |only EZFragility-1.0.3/EZFragility/man/Epoch.Rd |only EZFragility-1.0.3/EZFragility/man/visuIEEGData.Rd |only EZFragility-1.0.3/EZFragility/tests/testthat/test-Epoch.R |only EZFragility-1.0.3/EZFragility/tests/testthat/test-truncateTime.R |only EZFragility-2.0.1/EZFragility/DESCRIPTION | 51 +- EZFragility-2.0.1/EZFragility/MD5 | 65 +- EZFragility-2.0.1/EZFragility/NAMESPACE | 32 - EZFragility-2.0.1/EZFragility/R/class_AAA.r | 6 EZFragility-2.0.1/EZFragility/R/class_FragStat.r | 11 EZFragility-2.0.1/EZFragility/R/class_Fragility.r | 8 EZFragility-2.0.1/EZFragility/R/fragStat.r | 83 ++- EZFragility-2.0.1/EZFragility/R/main.r | 31 - EZFragility-2.0.1/EZFragility/R/sysdata.rda |binary EZFragility-2.0.1/EZFragility/R/utils.r | 23 EZFragility-2.0.1/EZFragility/R/visualization.R | 255 ++++------ EZFragility-2.0.1/EZFragility/R/zzz.R | 8 EZFragility-2.0.1/EZFragility/README.md | 7 EZFragility-2.0.1/EZFragility/build/vignette.rds |binary EZFragility-2.0.1/EZFragility/data/pt01EcoG.rda |binary EZFragility-2.0.1/EZFragility/data/pt01Frag.rda |binary EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.R | 36 - EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.Rmd | 58 +- EZFragility-2.0.1/EZFragility/inst/doc/Intro_to_EZFragility.html | 207 ++++---- EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.R |only EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.Rmd |only EZFragility-2.0.1/EZFragility/inst/doc/manuscript_reproducible.html |only EZFragility-2.0.1/EZFragility/man/calcAdjFrag.Rd | 7 EZFragility-2.0.1/EZFragility/man/estimateSOZ.Rd | 9 EZFragility-2.0.1/EZFragility/man/fragStat.Rd | 21 EZFragility-2.0.1/EZFragility/man/plotFragHeatmap.Rd | 57 +- EZFragility-2.0.1/EZFragility/man/show-FragStat-method.Rd | 34 - EZFragility-2.0.1/EZFragility/man/show-Fragility-method.Rd | 34 - EZFragility-2.0.1/EZFragility/tests/testthat/test-fragStat.R | 2 EZFragility-2.0.1/EZFragility/tests/testthat/test-visualization.R | 4 EZFragility-2.0.1/EZFragility/vignettes/Intro_to_EZFragility.Rmd | 58 +- EZFragility-2.0.1/EZFragility/vignettes/manuscript_reproducible.Rmd |only 39 files changed, 604 insertions(+), 503 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.8.1 dated 2024-11-01 and 0.8.2 dated 2025-09-07
DESCRIPTION | 17 ++-- MD5 | 54 ++++++------- NAMESPACE | 2 NEWS.md | 12 +++ R/cross_numeric.R | 5 - R/labels.R | 45 ++++++++--- R/officer.R | 7 - R/options.R | 2 R/utils.R | 37 +++++---- README.md | 24 +----- inst/doc/crosstable-report.R | 2 inst/doc/crosstable-report.html | 9 +- inst/doc/crosstable-selection.html | 48 +++++++----- inst/doc/crosstable.R | 2 inst/doc/crosstable.Rmd | 2 inst/doc/crosstable.html | 44 +++++++---- inst/doc/percent_pattern.html | 28 +++++-- man/apply_labels.Rd | 9 +- tests/testthat/_snaps/by_numeric.md | 141 ++++++++++++++++++++++++++++-------- tests/testthat/_snaps/options.md | 73 +++++++++++++++--- tests/testthat/_snaps/pivot.md | 27 +++++- tests/testthat/_snaps/tests.md | 55 +++++++------- tests/testthat/test-by_factor.R | 1 tests/testthat/test-by_numeric.R | 64 +++++++--------- tests/testthat/test-effects.R | 3 tests/testthat/test-options.R | 24 +++++- tests/testthat/test-tests.R | 25 +++++- vignettes/crosstable.Rmd | 2 28 files changed, 507 insertions(+), 257 deletions(-)
Title: Survey Analysis with Auxiliary Discretized Variables
Description: Probability surveys often use auxiliary continuous data from administrative records, but the utility of this data is diminished when it is discretized for confidentiality. We provide a set of survey estimators to make full use of information from the discretized variables. See Williams, S.Z., Zou, J., Liu, Y., Si, Y., Galea, S. and Chen, Q. (2024), Improving Survey Inference Using Administrative Records Without Releasing Individual-Level Continuous Data. Statistics in Medicine, 43: 5803-5813. <doi:10.1002/sim.10270> for details.
Author: Jungang Zou [aut, cre],
Yutao Liu [aut],
Sharifa Williams [aut],
Qixuan Chen [aut]
Maintainer: Jungang Zou <jungang.zou@gmail.com>
Diff between AuxSurvey versions 1.0 dated 2024-12-20 and 1.1 dated 2025-09-07
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ R/AuxSurvey.R | 45 +++++++++------------------- inst/doc/introduction.html | 6 +-- man/auxsurvey.Rd | 72 +++++++++++++++++++-------------------------- man/postStr_wt.Rd | 20 ++++++------ man/rake_wt.Rd | 20 ++++++------ man/simulate.Rd | 16 ++++------ man/svyBayesmod.Rd | 35 +++++++++------------ man/uwt.Rd | 24 +++++++-------- 10 files changed, 116 insertions(+), 148 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.3.0 dated 2025-01-07 and 1.3.1 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 9 +++++++++ R/load_data.R | 1 + R/plots.R | 21 ++++++++++++++------- R/vaccine-package.R | 7 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vaccine.html | 10 +++++----- man/hvtn505.Rd | 7 +++++-- man/plot_ce.Rd | 10 +++++++++- tests/testthat/test-test-core-functions.R | 2 +- 12 files changed, 63 insertions(+), 32 deletions(-)
Title: Tools for Causal Inference with Possibly Invalid Instrumental
Variables
Description: Two stage curvature identification with machine learning for causal
inference in settings when instrumental variable regression is not suitable
because of potentially invalid instrumental variables. Based on Guo and
Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning:
Causal Inference with Possibly Invalid Instrumental Variables"
<doi:10.48550/arXiv.2203.12808>. The vignette is available in Carl, Emmenegger, Bühlmann and Guo (2025)
"TSCI: Two Stage Curvature Identification for Causal Inference with Invalid Instruments in R" <doi:10.18637/jss.v114.i07>.
Author: David Carl [aut, cre] ,
Corinne Emmenegger [aut] ,
Wei Yuan [aut],
Mengchu Zheng [aut],
Zijian Guo [aut]
Maintainer: David Carl <david.carl@phd.unibocconi.it>
Diff between TSCI versions 3.0.4 dated 2023-10-09 and 3.0.5 dated 2025-09-07
DESCRIPTION | 18 +++++++++--------- MD5 | 20 ++++++++++---------- R/tsci_boosting.R | 6 +++--- R/tsci_forest.R | 6 +++--- R/tsci_poly.R | 6 +++--- R/tsci_secondstage.R | 6 +++--- inst/CITATION | 43 +++++++++++++++++++++---------------------- man/tsci_boosting.Rd | 6 +++--- man/tsci_forest.Rd | 6 +++--- man/tsci_poly.Rd | 6 +++--- man/tsci_secondstage.Rd | 6 +++--- 11 files changed, 64 insertions(+), 65 deletions(-)
Title: Tools for Mapping of Quantitative Traits of Genetically Related
Individuals and Calculating Identity Coefficients from
Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>
Diff between QTLRel versions 1.14 dated 2023-08-08 and 1.15 dated 2025-09-07
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/pedRecode.R | 40 ++++++++++++++++++++++++++++------------ data/miscEx.RData |binary inst/doc/QTLRel_Tutorial.pdf |binary man/ibs.Rd | 2 +- 7 files changed, 40 insertions(+), 23 deletions(-)
Title: A Comprehensive Collection of Neuroscience and Brain-Related
Datasets
Description: Offers a rich and diverse collection of datasets focused on the brain, nervous system, and related disorders.
The package includes clinical, experimental, neuroimaging, behavioral, cognitive, and simulated data on conditions such as Parkinson's disease, Alzheimer's, epilepsy, schizophrenia, gliomas, and mental health.
Datasets cover structural and functional brain data, neurotransmission, gene expression, cognitive performance, and treatment outcomes.
Designed for researchers, neuroscientists, clinicians, psychologists, data scientists, and students, this package facilitates exploratory data analysis, statistical modeling, and hypothesis testing in neuroscience and neuroepidemiology.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between NeuroDataSets versions 0.1.0 dated 2025-05-27 and 0.2.0 dated 2025-09-07
NeuroDataSets-0.1.0/NeuroDataSets/R/view_datasets_neuro.R |only NeuroDataSets-0.1.0/NeuroDataSets/man/view_datasets_neuro.Rd |only NeuroDataSets-0.2.0/NeuroDataSets/DESCRIPTION | 12 NeuroDataSets-0.2.0/NeuroDataSets/MD5 | 96 +++--- NeuroDataSets-0.2.0/NeuroDataSets/NAMESPACE | 2 NeuroDataSets-0.2.0/NeuroDataSets/NEWS.md |only NeuroDataSets-0.2.0/NeuroDataSets/R/data-documentation.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/R/neurodatasets-package.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/R/view_datasets_NeuroDataSets.R |only NeuroDataSets-0.2.0/NeuroDataSets/README.md | 2 NeuroDataSets-0.2.0/NeuroDataSets/build/vignette.rds |binary NeuroDataSets-0.2.0/NeuroDataSets/inst/CITATION | 10 NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.R | 7 NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.Rmd | 17 - NeuroDataSets-0.2.0/NeuroDataSets/inst/doc/introduction_to_neurodatasets.html | 156 +++++----- NeuroDataSets-0.2.0/NeuroDataSets/inst/licenses/LICENSE | 2 NeuroDataSets-0.2.0/NeuroDataSets/man/view_datasets_NeuroDataSets.Rd |only NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-aba_phenotype_data_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-ability_intelligence_list.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-adolescent_mental_health_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-alzheimer_smoking_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-alzheimers_biomarkers_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-bilingual_brains_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-blood_brain_barrier_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_litter_mammals_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_size_iq_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brain_string_players_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-brains_cognitive_matrix.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-cocaine_dopamine_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-dopamine_schizophrenia_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_RCT_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_drug_qol_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-epilepsy_drug_trial_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-gm_expected_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-guineapig_neurotransmission_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-hippocampus_lesions_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-mammals_brain_body_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_human_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-markers_mouse_brain_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-migraine_treatment_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neanderthal_brains_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neuro_pointprocess_matrix.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-neurocognitive_psychiatric_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-oasis_dementia_mri_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-parkinsons_dopamine_list.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-pediatric_glioma_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-sleep_performance_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-subcortical_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-view_datasets_NeuroDataSets.R |only NeuroDataSets-0.2.0/NeuroDataSets/tests/testthat/test-white_matter_patterns_tbl_df.R | 2 NeuroDataSets-0.2.0/NeuroDataSets/vignettes/introduction_to_neurodatasets.Rmd | 17 - 52 files changed, 226 insertions(+), 165 deletions(-)
Title: Ecological Indices Calculator for Nematode Communities
Description: Provides a computational toolkit for analyzing nematode communities in ecological studies.
Includes methods to quantify nematode-based ecological indicators such as metabolic footprints,
energy flow metrics, and community structure. These tools support assessments of soil health,
ecosystem functioning, and trophic interactions, standardizing the use of nematodes as
bioindicators.
Author: Yuxuan He [aut, cre, cph] ,
Dong Wang [ths, cph]
Maintainer: Yuxuan He <heyuxuan@henu.edu.cn>
Diff between Nematode versions 0.2.0 dated 2025-08-20 and 0.2.1 dated 2025-09-07
DESCRIPTION | 17 ++++++------- MD5 | 9 ++++--- NEWS.md |only R/ecological_indices.R | 57 +++++++++++----------------------------------- man/Ecological.Indices.Rd | 41 ++++----------------------------- man/cal.SRI.Rd | 16 ++++-------- 6 files changed, 37 insertions(+), 103 deletions(-)
Title: Correction of Preprocessed MS Data
Description: An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Author: Allison Mason [aut] ,
Gregory Johnson [aut] ,
Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>
Diff between mpactr versions 0.2.1 dated 2025-03-28 and 0.3.0 dated 2025-09-07
DESCRIPTION | 14 - MD5 | 80 +++++---- NEWS.md | 8 R/RcppExports.R | 4 R/data.R | 2 R/filter_pactr-accessors.R | 1 R/filter_pactr-methods.R | 50 +++--- R/filters.R | 21 -- R/import_data.R | 7 R/peak_table_formatter.R | 35 ++-- R/quality_control.R | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/downstream_analyses.R | 2 inst/doc/downstream_analyses.Rmd | 8 inst/doc/downstream_analyses.html | 223 +++++++++++++-------------- inst/doc/mpactr.R | 12 - inst/doc/mpactr.Rmd | 26 +-- inst/doc/mpactr.html | 108 ++++++------- inst/doc/reference_semantics.html | 5 man/cultures_data.Rd | 2 man/filter_cv.Rd | 13 - man/filter_group.Rd | 2 man/filter_mispicked_ions.Rd | 2 man/get_cv_data.Rd | 1 man/import_data.Rd | 6 man/qc_summary.Rd | 8 src/CvFilter.cpp |only src/CvFilter.h |only src/FeatureData.h |only src/IntensityPeaks.h |only src/Makevars |only src/Math.h |only src/RcppExports.cpp | 15 + src/main.cpp | 13 + tests/testthat/test-filter_pactr-accessors.R | 4 tests/testthat/test-filter_pactr-class.R | 4 tests/testthat/test-filter_pactr-methods.R | 13 - tests/testthat/test-filters.R | 65 +++---- tests/testthat/test-import_data.R | 85 ++++++++++ tests/testthat/test-peak_table_formatter.R | 2 tests/testthat/test-quality_control.R | 2 vignettes/downstream_analyses.Rmd | 8 vignettes/mpactr.Rmd | 26 +-- 44 files changed, 489 insertions(+), 396 deletions(-)
Title: Learning from Black-Box Models by Maximum Interpretation
Decomposition
Description: The goal of 'midr' is to provide a model-agnostic method for interpreting and explaining black-box predictive models by creating a globally interpretable surrogate model. The package implements 'Maximum Interpretation Decomposition' (MID), a functional decomposition technique that finds an optimal additive approximation of the original model. This approximation is achieved by minimizing the squared error between the predictions of the black-box model and the surrogate model. The theoretical foundations of MID are described in Iwasawa & Matsumori (2025) [Forthcoming], and the package itself is detailed in Asashiba et al. (2025) <doi:10.48550/arXiv.2506.08338>.
Author: Ryoichi Asashiba [aut, cre],
Hirokazu Iwasawa [aut],
Reiji Kozuma [ctb]
Maintainer: Ryoichi Asashiba <ryoichi.asashiba@gmail.com>
This is a re-admission after prior archival of version 0.5.1 dated 2025-08-27
Diff between midr versions 0.5.1 dated 2025-08-27 and 0.5.2 dated 2025-09-07
DESCRIPTION | 12 +++---- MD5 | 68 +++++++++++++++++++++---------------------- NEWS.md | 10 ++++++ R/color_theme.R | 2 - R/color_theme_info.R | 2 - R/ggmid_mid_breakdown.R | 8 ++--- R/ggmid_mid_conditional.R | 4 +- R/ggmid_mid_importance.R | 12 +++---- R/interpret.R | 4 +- R/mid_conditional.R | 12 +++---- R/mid_effect.R | 2 - R/mid_plots.R | 10 +++--- R/plot_mid_breakdown.R | 6 +-- R/plot_mid_importance.R | 10 +++--- R/scale_color_theme.R | 2 - R/summary_mid.R | 2 - R/weighted_quantile.R | 4 +- R/zzz.R | 1 README.md | 5 +-- man/color.theme.Rd | 2 - man/color.theme.info.Rd | 2 - man/ggmid.mid.breakdown.Rd | 6 +-- man/ggmid.mid.conditional.Rd | 4 +- man/ggmid.mid.importance.Rd | 6 +-- man/interpret.Rd | 4 +- man/mid.conditional.Rd | 8 ++--- man/mid.effect.Rd | 2 - man/mid.plots.Rd | 6 +-- man/midr-package.Rd | 2 - man/plot.mid.breakdown.Rd | 4 +- man/plot.mid.importance.Rd | 6 +-- man/scale_color_theme.Rd | 2 - man/summary.mid.Rd | 2 - man/weighted.quantile.Rd | 2 - man/weighted.tabulate.Rd | 2 - 35 files changed, 123 insertions(+), 113 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.20 dated 2025-08-21 and 1.21 dated 2025-09-07
DESCRIPTION | 10 +++---- MD5 | 40 +++++++++++++++---------------- NEWS.md | 11 -------- README.md | 2 - man/adult.Rd | 8 ++---- man/advertising.Rd | 4 +-- man/bank.Rd | 4 +-- man/caravan.Rd | 2 - man/cereal.Rd | 8 +++--- man/churn.Rd | 13 ++++++++-- man/churnCredit.Rd | 2 - man/churnTel.Rd | 2 - man/corona.Rd | 7 +++-- man/house.Rd | 4 +-- man/housePrice.Rd | 64 +++++++++++++++++++++++++-------------------------- man/insurance.Rd | 4 +-- man/liver-package.Rd | 2 - man/marketing.Rd | 4 +-- man/redWines.Rd | 4 +-- man/risk.Rd | 4 +++ man/whiteWines.Rd | 4 +-- 21 files changed, 103 insertions(+), 100 deletions(-)
Title: Guillem Hurault Functions' Library
Description: Contains various functions for data analysis, notably helpers and diagnostics for Bayesian modelling using Stan.
Author: Guillem Hurault [aut, cre]
Maintainer: Guillem Hurault <ghurault.dev@outlook.com>
Diff between HuraultMisc versions 1.1.1 dated 2021-09-06 and 1.2.1 dated 2025-09-07
HuraultMisc-1.1.1/HuraultMisc/R/illustrations.R |only HuraultMisc-1.1.1/HuraultMisc/man/illustrate_RPS.Rd |only HuraultMisc-1.1.1/HuraultMisc/man/illustrate_forward_chaining.Rd |only HuraultMisc-1.1.1/HuraultMisc/tests/testthat/test-illustrations.R |only HuraultMisc-1.2.1/HuraultMisc/DESCRIPTION | 25 - HuraultMisc-1.2.1/HuraultMisc/MD5 | 115 +++-- HuraultMisc-1.2.1/HuraultMisc/NAMESPACE | 3 HuraultMisc-1.2.1/HuraultMisc/NEWS.md | 16 HuraultMisc-1.2.1/HuraultMisc/R/HuraultMisc-package.R | 2 HuraultMisc-1.2.1/HuraultMisc/R/calibration.R | 66 +-- HuraultMisc-1.2.1/HuraultMisc/R/coverage.R | 64 +-- HuraultMisc-1.2.1/HuraultMisc/R/data.R | 19 HuraultMisc-1.2.1/HuraultMisc/R/deprec-stan.R | 34 - HuraultMisc-1.2.1/HuraultMisc/R/deprec-utils.R |only HuraultMisc-1.2.1/HuraultMisc/R/distribution.R | 103 +++-- HuraultMisc-1.2.1/HuraultMisc/R/draws.R | 38 + HuraultMisc-1.2.1/HuraultMisc/R/misc.R | 26 - HuraultMisc-1.2.1/HuraultMisc/R/predicates.R | 8 HuraultMisc-1.2.1/HuraultMisc/R/prior_post.R | 156 +++++-- HuraultMisc-1.2.1/HuraultMisc/R/pval.R | 34 - HuraultMisc-1.2.1/HuraultMisc/R/stan_misc.R | 63 ++- HuraultMisc-1.2.1/HuraultMisc/R/utility_functions.R | 92 +--- HuraultMisc-1.2.1/HuraultMisc/README.md | 22 - HuraultMisc-1.2.1/HuraultMisc/build |only HuraultMisc-1.2.1/HuraultMisc/inst/WORDLIST |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_config.rds |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_post |only HuraultMisc-1.2.1/HuraultMisc/inst/testdata/stanmodel_prior |only HuraultMisc-1.2.1/HuraultMisc/man/HuraultMisc-package.Rd | 47 +- HuraultMisc-1.2.1/HuraultMisc/man/PPC_group_distribution.Rd | 2 HuraultMisc-1.2.1/HuraultMisc/man/approx_equal.Rd | 58 +- HuraultMisc-1.2.1/HuraultMisc/man/cbbPalette.Rd | 53 +- HuraultMisc-1.2.1/HuraultMisc/man/change_colnames.Rd | 5 HuraultMisc-1.2.1/HuraultMisc/man/compute_calibration.Rd | 27 - HuraultMisc-1.2.1/HuraultMisc/man/compute_rsquared.Rd |only HuraultMisc-1.2.1/HuraultMisc/man/coverage.Rd | 4 HuraultMisc-1.2.1/HuraultMisc/man/extract_ci.Rd | 52 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_distribution.Rd | 13 HuraultMisc-1.2.1/HuraultMisc/man/extract_draws.Rd | 6 HuraultMisc-1.2.1/HuraultMisc/man/extract_index_nd.Rd | 58 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_parameters_from_draw.Rd | 1 HuraultMisc-1.2.1/HuraultMisc/man/extract_pdf.Rd | 48 +- HuraultMisc-1.2.1/HuraultMisc/man/extract_pmf.Rd | 44 +- HuraultMisc-1.2.1/HuraultMisc/man/factor_to_numeric.Rd | 2 HuraultMisc-1.2.1/HuraultMisc/man/is_scalar.Rd | 44 +- HuraultMisc-1.2.1/HuraultMisc/man/is_stanfit.Rd | 34 - HuraultMisc-1.2.1/HuraultMisc/man/is_wholenumber.Rd | 78 +-- HuraultMisc-1.2.1/HuraultMisc/man/logit.Rd | 48 +- HuraultMisc-1.2.1/HuraultMisc/man/pipe.Rd | 24 - HuraultMisc-1.2.1/HuraultMisc/man/post_pred_pval.Rd | 10 HuraultMisc-1.2.1/HuraultMisc/man/prior_posterior.Rd | 206 +++++----- HuraultMisc-1.2.1/HuraultMisc/man/process_replications.Rd | 1 HuraultMisc-1.2.1/HuraultMisc/man/summary_statistics.Rd | 4 HuraultMisc-1.2.1/HuraultMisc/tests/spelling.R |only HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-compute_calibration.R | 3 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-coverage.R | 12 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-draws.R | 48 +- HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-extract_distribution.R | 47 +- HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-misc.R | 4 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-pval.R | 6 HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-stan.R |only HuraultMisc-1.2.1/HuraultMisc/tests/testthat/test-utility.R | 15 62 files changed, 1094 insertions(+), 796 deletions(-)
Title: Goodness-of-Fit for Zero-Inflated Univariate Hidden Markov
Models
Description: Inference, goodness-of-fit tests, and predictions for continuous and discrete univariate Hidden Markov Models (HMM), including zero-inflated distributions. The goodness-of-fit test is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Nasri et al (2020) <doi:10.1029/2019WR025122>.
Author: Bouchra R. Nasri [aut, cre, cph],
Mamadou Yamar Thioub [aut, cph],
Bruno N. Remillard [aut, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GenHMM1d versions 0.2.1 dated 2025-03-13 and 0.2.6 dated 2025-09-07
DESCRIPTION | 6 MD5 | 18 R/EstHMMGen.R | 1963 +++++++++++++++++++++++++++---------------------------- R/GofHMMGen.R | 9 R/PDF.R | 5 R/PDF_unc.R | 378 +++++----- R/bfun.R | 13 man/EstHMMGen.Rd | 6 man/GofHMMGen.Rd | 9 man/bfun.Rd | 14 10 files changed, 1227 insertions(+), 1194 deletions(-)
Title: A Curated Collection of Digestive System and Gastrointestinal
Disease Datasets
Description: Provides an extensive and curated collection of datasets related to the digestive system, stomach, intestines, liver, pancreas, and associated diseases.
This package includes clinical trials, observational studies, experimental datasets, cohort data, and case series involving gastrointestinal disorders such as gastritis, ulcers, pancreatitis, liver cirrhosis, colon cancer, colorectal conditions, Helicobacter pylori infection, irritable bowel syndrome, intestinal infections, and post-surgical outcomes.
The datasets support educational, clinical, and research applications in gastroenterology, public health, epidemiology, and biomedical sciences.
Designed for researchers, clinicians, data scientists, students, and educators interested in digestive diseases, the package facilitates reproducible analysis, modeling, and hypothesis testing using real-world and historical data.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between DigestiveDataSets versions 0.1.0 dated 2025-06-03 and 0.2.0 dated 2025-09-07
DigestiveDataSets-0.1.0/DigestiveDataSets/R/view_datasets_digestive.R |only DigestiveDataSets-0.1.0/DigestiveDataSets/man/view_datasets_digestive.Rd |only DigestiveDataSets-0.1.0/DigestiveDataSets/tests/testthat/test-view_datasets_digestive.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/DESCRIPTION | 12 - DigestiveDataSets-0.2.0/DigestiveDataSets/MD5 | 79 +++--- DigestiveDataSets-0.2.0/DigestiveDataSets/NAMESPACE | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/NEWS.md |only DigestiveDataSets-0.2.0/DigestiveDataSets/R/data-documentation.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/R/digestivedatasets-package.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/R/view_datasets_DigestiveDataSets.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/README.md | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/build/vignette.rds |binary DigestiveDataSets-0.2.0/DigestiveDataSets/inst/CITATION | 9 DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.R | 7 DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.Rmd | 15 + DigestiveDataSets-0.2.0/DigestiveDataSets/inst/doc/introduction_to_digestivedatasets.html | 116 +++++----- DigestiveDataSets-0.2.0/DigestiveDataSets/man/view_datasets_DigestiveDataSets.Rd |only DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-anorexia_weight_change_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-bleeding_ulcers_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-campylobacter_infections_ts.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-cholera_deaths_1849_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-colon_stageBC_chemo_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-colonoscopy_features_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-crc_mirnas_pubmed_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-cystic_fibrosis_snps_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-digestive_cancer_survival_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ecoli_infections_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-gastric_cancer_trial_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-gi_damage_prevention_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-helicobacter_children_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-horse_colic_surgery_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ibs_cam_trials_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-intestinal_smartpill_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-intestinal_surgery_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-liver_cirrhosis_prednisone_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-lynch_ontario_families_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-norovirus_derbyshire_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-pancreatic_cancer_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-pbc_mayo_survival_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-post_ercp_pancreatitis_tbl_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-ugi_bleeding_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-view_datasets_DigestiveDataSets.R |only DigestiveDataSets-0.2.0/DigestiveDataSets/tests/testthat/test-weight_loss_df.R | 2 DigestiveDataSets-0.2.0/DigestiveDataSets/vignettes/introduction_to_digestivedatasets.Rmd | 15 + 44 files changed, 183 insertions(+), 128 deletions(-)
More information about DigestiveDataSets at CRAN
Permanent link
Title: Multivariate Random Forest with Compositional Responses
Description: Multivariate random forests with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, or the alpha-transformation of Tsagris, Preston and Wood (2011), <doi:10.48550/arXiv.1106.1451>, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalRF versions 1.3 dated 2025-07-10 and 1.4 dated 2025-09-07
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ man/CompositionalRF-package.Rd | 9 +++++++-- man/comp.rf.Rd | 5 ++--- man/cv.alfacomprf.Rd | 5 +++++ man/cv.comprf.Rd | 2 +- man/mrf.Rd | 3 +-- 7 files changed, 27 insertions(+), 19 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: Extract, Format, and Print Statistical Output
Description: Provides functions that format statistical output in a way that
can be inserted into R Markdown documents. This is analogous to the
apa_print() functions in the 'papaja' package but prints Markdown
or LaTeX syntax.
Author: Jeffrey R. Stevens [aut, cre, cph]
Maintainer: Jeffrey R. Stevens <jeffrey.r.stevens@protonmail.com>
Diff between cocoon versions 0.2.0 dated 2025-01-29 and 0.2.1 dated 2025-09-07
DESCRIPTION | 10 ++--- MD5 | 36 ++++++++++----------- NEWS.md | 8 +++- R/format_stats.R | 5 +- R/format_stats_BFBayesFactor.R | 17 ++++----- R/format_stats_easycorrelation.R | 32 +++++++++--------- R/import-standalone-types-check.R | 1 README.md | 2 - build/vignette.rds |binary inst/CITATION | 2 - inst/doc/cocoon.html | 6 +-- tests/testthat/helper.R | 18 +++++----- tests/testthat/test-format_stats.R | 1 tests/testthat/test-format_stats_BFBayesFactor.R | 1 tests/testthat/test-format_stats_aov.R | 1 tests/testthat/test-format_stats_easycorrelation.R | 1 tests/testthat/test-format_stats_htest.R | 1 tests/testthat/test-format_stats_lm.R | 1 tests/testthat/test-format_stats_lmerModLmerTest.R | 1 19 files changed, 71 insertions(+), 73 deletions(-)
Title: Behavioral Insight Design: A Toolkit for Integrating Behavioral
Science in UI/UX Design
Description: Provides a framework and toolkit to guide 'shiny' developers in
implementing the Behavioral Insight Design (BID) framework. The package offers
functions for documenting each of the five stages (Notice, Interpret,
Structure, Anticipate, and Validate), along with a comprehensive concept
dictionary.
Author: Jeremy Winget [aut, cre]
Maintainer: Jeremy Winget <contact@jrwinget.com>
Diff between bidux versions 0.3.0 dated 2025-08-29 and 0.3.1 dated 2025-09-07
DESCRIPTION | 14 MD5 | 165 ++-- NAMESPACE | 10 NEWS.md | 95 ++ R/bid-concepts.R | 3 R/bid_anticipate.R | 102 +- R/bid_interpret.R | 111 +- R/bid_notice.R | 77 +- R/bid_structure.R | 60 + R/bid_validate.R | 108 +- R/mappings.R | 51 + R/structure_suggest.R | 610 +++++++++++++++- R/suggest_rules.R |only R/telemetry.R | 691 +++++++++++++++++- R/utils.R | 269 +++---- README.md | 229 ++++-- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/advanced-workflows.R |only inst/doc/advanced-workflows.Rmd |only inst/doc/advanced-workflows.html |only inst/doc/behavioral-science-primer.R |only inst/doc/behavioral-science-primer.Rmd |only inst/doc/behavioral-science-primer.html |only inst/doc/concepts-reference.Rmd | 2 inst/doc/concepts-reference.html | 2 inst/doc/getting-started.R | 71 + inst/doc/getting-started.Rmd | 103 +- inst/doc/getting-started.html | 138 ++- inst/doc/introduction-to-bid.Rmd | 6 inst/doc/introduction-to-bid.html | 6 inst/doc/practical-examples.R |only inst/doc/practical-examples.Rmd |only inst/doc/practical-examples.html |only inst/doc/telemetry-integration.R | 385 +++++++++- inst/doc/telemetry-integration.Rmd | 447 +++++++++++ inst/doc/telemetry-integration.html | 835 ++++++++++++++++------ man/adjust_suggestion_score.Rd | 6 man/apply_suggestion_rules.Rd |only man/as_tibble.bid_issues.Rd |only man/bid_address.Rd |only man/bid_anticipate.Rd | 46 - man/bid_concept.Rd | 3 man/bid_flags.Rd |only man/bid_ingest_telemetry.Rd | 19 man/bid_interpret.Rd | 43 - man/bid_notice.Rd | 43 - man/bid_notice_issue.Rd |only man/bid_notices.Rd |only man/bid_pipeline.Rd |only man/bid_structure.Rd | 35 man/bid_telemetry.Rd |only man/bid_validate.Rd | 60 - man/bidux-package.Rd | 4 man/build_concept_group.Rd | 8 man/build_groups_with_suggestions.Rd | 8 man/deduplicate_warnings_suggestions.Rd |only man/dot-calculate_severity_metrics.Rd |only man/dot-classify_issue_type.Rd |only man/dot-create_issues_tibble.Rd |only man/dot-flags_from_issues.Rd |only man/dot-suggest_theory_from_text.Rd |only man/extract_stage1_theory.Rd | 8 man/figures/logo.png |binary man/get_cognitive_load_suggestions.Rd | 6 man/get_consolidated_suggestion_rules.Rd |only man/get_dual_processing_suggestions.Rd | 6 man/get_fallback_suggestion.Rd |only man/get_generic_suggestions.Rd | 6 man/get_information_scent_suggestions.Rd | 6 man/get_onboarding_suggestions.Rd | 6 man/get_progressive_disclosure_suggestions.Rd | 6 man/get_proximity_suggestions.Rd | 6 man/get_visual_hierarchy_suggestions.Rd | 6 man/infer_concepts_from_story.Rd | 8 man/print.bid_issues.Rd |only man/rank_and_sort_suggestions.Rd | 8 man/structure_suggestions.Rd | 26 man/suggest_layout_from_previous.Rd | 5 tests/testthat/test-bid_anticipate.R | 985 ++++++++++++++++++++++---- tests/testthat/test-bid_concepts.R | 227 +++++ tests/testthat/test-bid_ingest_telemetry.R | 13 tests/testthat/test-bid_interpret.R | 377 ++++++++- tests/testthat/test-bid_issues.R |only tests/testthat/test-bid_notice.R | 171 +++- tests/testthat/test-bid_report.R | 65 - tests/testthat/test-bid_structure.R | 16 tests/testthat/test-bid_suggest_components.R | 82 +- tests/testthat/test-bid_validate.R | 430 +++++++---- tests/testthat/test-bridges.R |only tests/testthat/test-structure_suggest.R |only tests/testthat/test-suggest_rules.R |only tests/testthat/test-telemetry_helpers.R |only tests/testthat/test-utils.R | 561 ++++++++++++++ vignettes/advanced-workflows.Rmd |only vignettes/behavioral-science-primer.Rmd |only vignettes/concepts-reference.Rmd | 2 vignettes/getting-started.Rmd | 103 +- vignettes/introduction-to-bid.Rmd | 6 vignettes/practical-examples.Rmd |only vignettes/telemetry-integration.Rmd | 447 +++++++++++ 101 files changed, 6971 insertions(+), 1486 deletions(-)
Title: Datasets from the Survival TV Series Alone
Description: A collection of datasets on the Alone survival TV series in tidy format.
Included in the package are 4 datasets detailing the survivors, their loadouts,
episode details and season information.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between alone versions 0.6 dated 2025-06-12 and 0.7 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ data/episodes.rda |binary data/loadouts.rda |binary data/seasons.rda |binary data/survivalists.rda |binary 7 files changed, 15 insertions(+), 9 deletions(-)
Title: Analysis of Visual Meteor Data
Description: Provides a suite of analytical functionalities to process and analyze
visual meteor observations from the Visual Meteor Database
of the International Meteor Organization <https://www.imo.net/>.
Author: Janko Richter [aut, cre]
Maintainer: Janko Richter <janko@richtej.de>
Diff between vismeteor versions 1.8.5 dated 2024-01-16 and 2.0.0 dated 2025-09-07
vismeteor-1.8.5/vismeteor/man/vmperception.l.Rd |only vismeteor-1.8.5/vismeteor/tests/testthat/test_vmperception.l.R |only vismeteor-2.0.0/vismeteor/DESCRIPTION | 10 vismeteor-2.0.0/vismeteor/LICENSE | 2 vismeteor-2.0.0/vismeteor/MD5 | 64 + vismeteor-2.0.0/vismeteor/NAMESPACE | 5 vismeteor-2.0.0/vismeteor/NEWS.md |only vismeteor-2.0.0/vismeteor/R/mideal.R | 14 vismeteor-2.0.0/vismeteor/R/perception.R | 134 --- vismeteor-2.0.0/vismeteor/R/vmgeom.R | 59 - vismeteor-2.0.0/vismeteor/R/vmgeom_vst.R |only vismeteor-2.0.0/vismeteor/R/vmideal.R | 61 - vismeteor-2.0.0/vismeteor/R/vmideal_vst.R |only vismeteor-2.0.0/vismeteor/build/vignette.rds |binary vismeteor-2.0.0/vismeteor/inst/derivation |only vismeteor-2.0.0/vismeteor/inst/doc/vismeteor.Rmd | 50 - vismeteor-2.0.0/vismeteor/inst/doc/vismeteor.html | 82 +- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.R | 135 ++- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.Rmd | 207 ++++- vismeteor-2.0.0/vismeteor/inst/doc/vmgeom.html | 354 ++++++---- vismeteor-2.0.0/vismeteor/inst/doc/vmideal.R | 84 ++ vismeteor-2.0.0/vismeteor/inst/doc/vmideal.Rmd | 181 ++++- vismeteor-2.0.0/vismeteor/inst/doc/vmideal.html | 312 ++++++-- vismeteor-2.0.0/vismeteor/man/mideal.Rd | 14 vismeteor-2.0.0/vismeteor/man/vmgeom.Rd | 56 - vismeteor-2.0.0/vismeteor/man/vmgeomVst.Rd |only vismeteor-2.0.0/vismeteor/man/vmideal.Rd | 59 - vismeteor-2.0.0/vismeteor/man/vmidealVst.Rd |only vismeteor-2.0.0/vismeteor/man/vmperception.Rd | 25 vismeteor-2.0.0/vismeteor/tests/testthat/test_dvmgeom.R | 12 vismeteor-2.0.0/vismeteor/tests/testthat/test_pvmideal.R | 2 vismeteor-2.0.0/vismeteor/tests/testthat/test_vmgeomVst.R |only vismeteor-2.0.0/vismeteor/tests/testthat/test_vmidealVst.R |only vismeteor-2.0.0/vismeteor/tests/testthat/test_vmperception.R | 325 --------- vismeteor-2.0.0/vismeteor/vignettes/vismeteor.Rmd | 50 - vismeteor-2.0.0/vismeteor/vignettes/vmgeom.Rmd | 207 ++++- vismeteor-2.0.0/vismeteor/vignettes/vmideal.Rmd | 181 ++++- 37 files changed, 1570 insertions(+), 1115 deletions(-)
Title: Extraction and Management of Clinical Practice Research Datalink
Data
Description: Simplify the process of extracting and processing Clinical Practice
Research Datalink (CPRD) data in order to build datasets ready for statistical
analysis. This process is difficult in 'R', as the raw data is very large and
cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create
'SQLite' databases which are stored on the hard disk. These are then queried
to extract the required information for a cohort of interest, and create
datasets ready for statistical analysis. The processes follow closely that
from the 'rEHR' package, see Springate et al., (2017)
<doi:10.1371/journal.pone.0171784>.
Author: Alexander Pate [aut, cre, cph]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Diff between rcprd versions 0.0.1 dated 2024-11-13 and 0.0.2 dated 2025-09-07
DESCRIPTION | 14 MD5 | 128 - NAMESPACE | 1 NEWS.md | 4 R/extract_bmi.R | 23 R/extract_cholhdl_ratio.R | 23 R/extract_diabetes.R | 17 R/extract_ho.R | 23 R/extract_impotence.R | 17 R/extract_smoking.R | 67 R/extract_test_data.R | 41 R/extract_test_data_var.R | 18 R/extract_test_recent.R | 38 R/extract_time_until.R | 43 R/functions_read_txt.R | 553 ++-- R/misc_functions.R | 279 +- R/rcprd-misc.R | 6 README.md | 16 inst/aurum_data/aurum_allpatid_extract_practice_001.txt |only inst/aurum_data/aurum_allpatid_extract_practice_002.txt |only inst/aurum_data/aurum_allpatid_set1_extract_drugissue_001.txt | 202 - inst/aurum_data/aurum_allpatid_set1_extract_drugissue_002.txt | 202 - inst/aurum_data/aurum_allpatid_set1_extract_drugissue_003.txt | 202 - inst/doc/Details-on-algorithms-for-extracting-specific-variables.R | 2 inst/doc/Details-on-algorithms-for-extracting-specific-variables.Rmd | 294 +- inst/doc/Details-on-algorithms-for-extracting-specific-variables.html | 325 ++ inst/doc/rcprd.R | 82 inst/doc/rcprd.Rmd | 1058 ++++----- inst/doc/rcprd.html | 1116 +++++----- man/add_to_database.Rd | 9 man/combine_query.aurum.Rd | 2 man/cprd_extract.Rd | 9 man/db_query.Rd | 27 man/extract_bmi.Rd | 15 man/extract_cholhdl_ratio.Rd | 15 man/extract_cohort.Rd | 2 man/extract_diabetes.Rd | 12 man/extract_ho.Rd | 19 man/extract_practices.Rd |only man/extract_smoking.Rd | 21 man/extract_test_data.Rd | 23 man/extract_test_data_var.Rd | 13 man/extract_test_recent.Rd | 22 man/extract_time_until.Rd | 19 man/extract_txt_char.Rd | 2 man/extract_txt_cons.Rd | 2 man/extract_txt_death.Rd | 2 man/extract_txt_drug.Rd | 2 man/extract_txt_hes_primary.Rd | 2 man/extract_txt_linkage.Rd | 2 man/extract_txt_obs.Rd | 2 man/extract_txt_pat.Rd | 2 man/extract_txt_prac.Rd |only man/extract_txt_prob.Rd | 2 man/extract_txt_ref.Rd | 2 tests/testthat/test-extract_vars.R | 38 tests/testthat/test-misc_functions.R | 6 vignettes/Details-on-algorithms-for-extracting-specific-variables.Rmd | 294 +- vignettes/identify_numunits_bmi.csv | 18 vignettes/identify_numunits_chol.csv | 6 vignettes/identify_numunits_cholhdl_ratio.csv | 34 vignettes/identify_numunits_hdl.csv | 8 vignettes/identify_numunits_height.csv | 9 vignettes/identify_numunits_sbp.csv | 11 vignettes/identify_numunits_weight.csv | 7 vignettes/rcprd.Rmd | 1058 ++++----- vignettes/refs.bib | 62 67 files changed, 3774 insertions(+), 2799 deletions(-)
Title: Interactive Overlays on 'shiny' Plots
Description: Provides rectangular elements that can be dragged and resized over
plots in 'shiny' apps. This may be useful in applications where users need
to mark regions on the plot for further input or processing.
Author: Nick Davies [aut, cre, cph]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between overshiny versions 0.1.1 dated 2025-08-28 and 0.2.0 dated 2025-09-07
overshiny-0.1.1/overshiny/tests/testthat/Rplots.pdf |only overshiny-0.2.0/overshiny/DESCRIPTION | 18 overshiny-0.2.0/overshiny/MD5 | 46 - overshiny-0.2.0/overshiny/NAMESPACE | 3 overshiny-0.2.0/overshiny/NEWS.md | 10 overshiny-0.2.0/overshiny/R/bounds.R |only overshiny-0.2.0/overshiny/R/heading.R |only overshiny-0.2.0/overshiny/R/script.R | 41 - overshiny-0.2.0/overshiny/R/server.R | 488 +++++++------ overshiny-0.2.0/overshiny/R/snap.R |only overshiny-0.2.0/overshiny/R/ui.R | 11 overshiny-0.2.0/overshiny/README.md | 64 - overshiny-0.2.0/overshiny/build/vignette.rds |binary overshiny-0.2.0/overshiny/inst/doc/epidemics.R |only overshiny-0.2.0/overshiny/inst/doc/epidemics.Rmd |only overshiny-0.2.0/overshiny/inst/doc/epidemics.html |only overshiny-0.2.0/overshiny/inst/doc/overshiny.R | 59 - overshiny-0.2.0/overshiny/inst/doc/overshiny.Rmd | 156 +--- overshiny-0.2.0/overshiny/inst/doc/overshiny.html | 237 +++--- overshiny-0.2.0/overshiny/inst/www/overshiny/overshiny.css | 3 overshiny-0.2.0/overshiny/man/overlayBounds.Rd | 2 overshiny-0.2.0/overshiny/man/overlayPlotOutput.Rd | 1 overshiny-0.2.0/overshiny/man/overlayServer.Rd | 171 +++- overshiny-0.2.0/overshiny/man/overlayToken.Rd | 8 overshiny-0.2.0/overshiny/man/rangeHeading.Rd |only overshiny-0.2.0/overshiny/man/snapGrid.Rd |only overshiny-0.2.0/overshiny/tests/testthat/test-panel.R | 3 overshiny-0.2.0/overshiny/vignettes/epidemics.Rmd |only overshiny-0.2.0/overshiny/vignettes/overshiny.Rmd | 156 +--- 29 files changed, 730 insertions(+), 747 deletions(-)
Title: Multilevel and Mixed Effects Model Diagnostics and Effect Sizes
Description: Effect sizes, diagnostics and performance metrics for
multilevel and mixed effects models.
Includes marginal and conditional 'R2' estimates for linear mixed effects models
based on Johnson (2014) <doi:10.1111/2041-210X.12225>.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between multilevelTools versions 0.2.0 dated 2025-04-13 and 0.2.1 dated 2025-09-07
DESCRIPTION | 11 MD5 | 60 NAMESPACE | 4 NEWS.md | 5 R/descriptives.R | 10 R/diagnostics.R | 23 R/models.R | 58 R/plotting.R | 352 +- R/ranef.r | 614 +-- R/styler.R | 4 build/vignette.rds |binary inst/doc/lmer-vignette.R | 502 +- inst/doc/lmer-vignette.html | 6316 ++++++++++++++++++------------------ man/APAStyler.modelTest.merMod.Rd | 4 man/acfByID.Rd | 4 man/evaluateLags.Rd | 2 man/meanDecompose.Rd | 74 man/modelCompare.merMod.Rd | 4 man/modelDiagnostics.lme.Rd | 4 man/modelDiagnostics.merMod.Rd | 8 man/modelPerformance.merMod.Rd | 28 man/modelTest.merMod.Rd | 18 man/nEffective.Rd | 2 man/omegaSEM.Rd | 3 man/plot.modelDiagnostics.lme.Rd | 6 man/plot.modelDiagnostics.merMod.Rd | 8 man/ranef2long.Rd | 56 man/ranefdata.Rd | 184 - man/residualDiagnostics.lme.Rd | 6 man/residualDiagnostics.merMod.Rd | 6 man/weighted.sma.Rd | 2 31 files changed, 4189 insertions(+), 4189 deletions(-)
More information about multilevelTools at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-27 0.5.1
2025-06-23 0.5.0
Title: Translation of Logit Regression Coefficients into Percentages
Description: Translation of logit models coefficients into percentages, following Deauvieau (2010) <doi:10.1177/0759106309352586>.
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between translate.logit versions 1.0 dated 2023-02-23 and 1.0.2 dated 2025-09-07
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NEWS.md |only R/translate.logit.R | 3 +++ README.md |only man/translate.logit.Rd | 4 ++-- 6 files changed, 13 insertions(+), 8 deletions(-)
More information about translate.logit at CRAN
Permanent link
Title: Miscellaneous Tools for Sequence Analysis
Description: It provides miscellaneous sequence analysis functions for describing episodes in individual sequences, measuring association between domains in multidimensional sequence analysis (see Piccarreta (2017) <doi:10.1177/0049124115591013>), heat maps of sequence data, Globally Interdependent Multidimensional Sequence Analysis (see Robette et al (2015) <doi:10.1177/0081175015570976>), smoothing sequences for index plots (see Piccarreta (2012) <doi:10.1177/0049124112452394>), coding sequences for Qualitative Harmonic Analysis (see Deville (1982)), measuring stress from multidimensional scaling factors (see Piccarreta and Lior (2010) <doi:10.1111/j.1467-985X.2009.00606.x>), symmetrical (or canonical) Partial Least Squares (see Bry (1996)).
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between seqhandbook versions 0.1.1 dated 2023-04-02 and 0.1.2 dated 2025-09-07
seqhandbook-0.1.1/seqhandbook/build |only seqhandbook-0.1.1/seqhandbook/inst |only seqhandbook-0.1.1/seqhandbook/vignettes |only seqhandbook-0.1.2/seqhandbook/DESCRIPTION | 25 +++++++++++++---------- seqhandbook-0.1.2/seqhandbook/MD5 | 23 ++++++++------------- seqhandbook-0.1.2/seqhandbook/NEWS.md | 5 ++++ seqhandbook-0.1.2/seqhandbook/README.md | 19 +++++++++++++++-- seqhandbook-0.1.2/seqhandbook/man/seq2qha.Rd | 2 - seqhandbook-0.1.2/seqhandbook/man/seq_heatmap.Rd | 6 ++--- seqhandbook-0.1.2/seqhandbook/man/seqi1epi.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqifpos.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqinepi.Rd | 4 +-- seqhandbook-0.1.2/seqhandbook/man/seqsmooth.Rd | 4 +-- 13 files changed, 58 insertions(+), 38 deletions(-)
Title: A Curated Collection of Pulmonary and Respiratory Disease
Datasets
Description: Provides a comprehensive and curated collection of datasets related to the lungs, respiratory system, and associated diseases.
This package includes epidemiological, clinical, experimental, and simulated datasets on conditions such as lung cancer, asthma,
Chronic Obstructive Pulmonary Disease (COPD), tuberculosis, whooping cough, pneumonia, influenza, and other respiratory illnesses.
It is designed to support data exploration, statistical modeling, teaching, and research in pulmonary medicine, public health,
environmental epidemiology, and respiratory disease surveillance.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between PulmoDataSets versions 0.1.0 dated 2025-06-03 and 0.2.0 dated 2025-09-07
PulmoDataSets-0.1.0/PulmoDataSets/R/view_datasets_pulmo.R |only PulmoDataSets-0.1.0/PulmoDataSets/man/view_datasets_pulmo.Rd |only PulmoDataSets-0.1.0/PulmoDataSets/tests/testthat/test-view_datasets_pulmo.R |only PulmoDataSets-0.2.0/PulmoDataSets/DESCRIPTION | 12 PulmoDataSets-0.2.0/PulmoDataSets/MD5 | 101 +++--- PulmoDataSets-0.2.0/PulmoDataSets/NAMESPACE | 2 PulmoDataSets-0.2.0/PulmoDataSets/NEWS.md |only PulmoDataSets-0.2.0/PulmoDataSets/R/data-documentation.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/R/pulmodatasets-package.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/R/view_datasets_PulmoDataSets.R |only PulmoDataSets-0.2.0/PulmoDataSets/README.md | 2 PulmoDataSets-0.2.0/PulmoDataSets/build/vignette.rds |binary PulmoDataSets-0.2.0/PulmoDataSets/inst/CITATION | 8 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.R | 7 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.Rmd | 14 PulmoDataSets-0.2.0/PulmoDataSets/inst/doc/introduction_to_pulmodatasets.html | 147 +++++----- PulmoDataSets-0.2.0/PulmoDataSets/man/view_datasets_PulmoDataSets.Rd |only PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-UK_female_lung_deaths_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-UK_male_lung_deaths_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-USMortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-USRegionalMortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-ai_ipn_performance_dt.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-air_polution_mortality_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-asthma_patients_tbl_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-bronchitis_Cardiff_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-chicago_pollution_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-child_wheeze_pollution_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-children_respiratory_rates_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-danish_lung_incidence_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-engwales_cancer_mortality_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-influenza_us_1975_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lung_cancer_survival_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lung_nodules_detection_dt.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-lungca_cancer_deaths_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-neonatal_intubation_times_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-nicotine_gum_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-ohio_children_wheeze_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-patients_lung_diseases_tbl_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-pneumonia_influenza_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_clinical_trial_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_infections_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_trial_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-respiratory_trial_outcomes_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_UK_tbl_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_doctors_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_lung_cancer_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-smoking_youth_tbl_df.R | 2 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-tlc_lung_capacity_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-tuberculosis_vaccine_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-veterans_lung_cancer_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-view_datasets_PulmoDataSets.R |only PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_dk_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_phila_df.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/tests/testthat/test-whooping_cough_ts.R | 3 PulmoDataSets-0.2.0/PulmoDataSets/vignettes/introduction_to_pulmodatasets.Rmd | 14 55 files changed, 251 insertions(+), 162 deletions(-)
Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.3.0 dated 2025-04-12 and 0.3.1 dated 2025-09-07
DESCRIPTION | 6 MD5 | 12 NEWS.md | 6 R/utils_nonmem.R | 5 inst/doc/covariates.html | 572 ++++++++++----------------------------------- inst/doc/library.html | 429 +++++++++++---------------------- inst/resources/rv_lib.json | 8 7 files changed, 304 insertions(+), 734 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Author: Thong Pham [aut, cre],
Paul Sheridan [aut],
Hidetoshi Shimodaira [aut]
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.2.10 dated 2024-03-28 and 1.2.11 dated 2025-09-07
DESCRIPTION | 22 +++++++++--- MD5 | 8 ++-- man/PAFit-package.Rd | 4 +- man/plot.PAFit_net.Rd | 2 - man/test_linear_PA.rd | 90 +++++++++++++++++++++++++------------------------- 5 files changed, 69 insertions(+), 57 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-22 0.3.1
2025-07-10 0.3.0
2022-02-16 0.2.1
2020-07-27 0.2.0
2020-05-28 0.1.3
2020-04-05 0.1.2
2020-02-28 0.1.1
2019-08-20 0.1.0
Title: Acesso aos Dados do 'SIDRA' do IBGE
Description: Functions for accessing and manipulating data from Brazilian
Institute of Geography and Statistics (IBGE)'s API 'SIDRA' (acronym for IBGE
System of Automatic Retrieval) from the new endpoints
at <https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Ferramentas para acessar
e manipular dados via API do Sistema IBGE De Recuperação Automática 'SIDRA'
do Instituto Brasileiro de Geografia e Estatística (IBGE).
Author: Rodrigo Emmanuel Santana Borges [cre, aut, cph]
Maintainer: Rodrigo Emmanuel Santana Borges <rodrigo@borges.net.br>
Diff between sidra versions 0.1.7 dated 2025-08-27 and 0.1.9 dated 2025-09-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/call_Ibge.R | 7 ++++--- R/sidra.R | 9 +++++---- man/sidra.Rd | 2 +- tests/testthat/test-sidra.R | 9 +++++---- tests/testthat/test-tab_agr.R | 7 ++++--- 8 files changed, 37 insertions(+), 25 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-27 1.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-05 1.2.2
2013-11-20 1.2.1
2013-05-13 1.2
2011-09-07 1.1
2011-06-04 1.0
Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following
Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
The primary objective of this package is to perform a variance component analysis (VCA)
according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
Procedures" (2014). There are plotting methods for visualization of an experimental design,
plotting random effects and residuals. For ANOVA type estimation two methods for computing
ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of
variance components can be derived, which is used in estimating confidence intervals. Linear
hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
more comprehensive description of the features.
Author: Andre Schuetzenmeister [aut, cre] ,
Florian Dufey [aut]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.5.1 dated 2024-03-07 and 1.5.2 dated 2025-09-06
DESCRIPTION | 20 MD5 | 24 R/model_check.R | 2 R/reml.R | 24 R/utils.R | 5887 +++++++++++++++++++++++------------------------ data/LSMeans_Data2.RData |only inst/ChangeLog.txt | 7 man/SattDF.Rd | 7 man/VCA-Package.Rd | 4 man/combineVC.Rd |only man/lmerMatrices.Rd | 2 man/lmerSummary.Rd | 8 man/remlMM.Rd | 6 man/remlVCA.Rd | 4 14 files changed, 3058 insertions(+), 2937 deletions(-)
Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise
performed manually. This includes setting up unit testing, test
coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp',
'RStudio' projects, and more.
Author: Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Malcolm Barrett [aut] ,
Andy Teucher [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between usethis versions 3.2.0 dated 2025-08-27 and 3.2.1 dated 2025-09-06
DESCRIPTION | 17 +++++++++-------- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/create.R | 7 +++++++ R/proj.R | 3 +-- R/release.R | 2 +- tests/testthat/_snaps/release.md | 1 - tests/testthat/test-create.R | 1 + 8 files changed, 31 insertions(+), 19 deletions(-)
Title: Tools for Trade Practitioners
Description: A collection of tools for trade practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of tariffs and quotas under different competitive regimes. These tools are derived from Anderson et al. (2001) <doi:10.1016/S0047-2727(00)00085-2> and Froeb et al. (2003) <doi:10.1016/S0304-4076(02)00166-5>.
Author: Charles Taragin [aut, cre]
Maintainer: Charles Taragin <ctaragin+trader@gmail.com>
Diff between trade versions 0.8.1 dated 2022-08-24 and 0.8.3 dated 2025-09-06
DESCRIPTION | 18 +-- MD5 | 14 +- R/SimFunctions.R | 22 ++-- R/cournot_tariff.R | 2 build/vignette.rds |binary inst/doc/Reference.html | 241 +++++++++++++++++++++--------------------------- man/Sim-Functions.Rd | 22 ++-- man/cournot_tariff.Rd | 2 8 files changed, 150 insertions(+), 171 deletions(-)
Title: Functions for Tidy Analysis and Generation of Random Data
Description: To make it easy to generate random numbers based upon the underlying stats
distribution functions. All data is returned in a tidy and structured
format making working with the data simple and straight forward. Given that the
data is returned in a tidy 'tibble' it lends itself to working with the rest of the
'tidyverse'.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between TidyDensity versions 1.5.1 dated 2025-07-23 and 1.5.2 dated 2025-09-06
DESCRIPTION | 6 MD5 | 74 +-- NEWS.md | 14 R/autoplot-triangular.R | 288 ++++++------- R/est-param-triangular.R | 226 +++++----- R/helper-dist-type-extract.R | 84 ++-- R/random-tidy-geom.R | 274 ++++++------- R/random-tidy-mixture.R | 414 ++++++++++++-------- R/stats-triangular-tbl.R | 190 ++++----- R/tidy_distribution_summary_tbl.R | 170 ++++---- R/utils-convert-to-ts.R | 224 +++++----- R/utils-quantile-normalize.R | 170 +++----- README.md | 26 - build/vignette.rds |binary inst/doc/getting-started.html | 45 +- man/bootstrap_p_vec.Rd | 110 ++--- man/bootstrap_q_vec.Rd | 112 ++--- man/cgmean.Rd | 92 ++-- man/chmean.Rd | 92 ++-- man/ckurtosis.Rd | 90 ++-- man/cmean.Rd | 92 ++-- man/cmedian.Rd | 90 ++-- man/csd.Rd | 92 ++-- man/cskewness.Rd | 90 ++-- man/cvar.Rd | 94 ++-- man/dist_type_extractor.Rd | 72 +-- man/figures/README-more_than_nine_simulations-1.png |binary man/figures/README-more_than_nine_simulations-2.png |binary man/figures/README-more_than_nine_simulations-3.png |binary man/figures/README-more_than_nine_simulations-4.png |binary man/figures/README-plot_density-1.png |binary man/figures/README-plot_density-2.png |binary man/figures/README-plot_density-3.png |binary man/figures/README-plot_density-4.png |binary man/quantile_normalize.Rd | 12 man/tidy_mixture_density.Rd | 35 + man/tidy_stat_tbl.Rd | 182 ++++---- man/triangle_plot.Rd | 70 +-- 38 files changed, 1839 insertions(+), 1691 deletions(-)
Title: Applies Display Metadata to Analysis Results Datasets
Description: Creates a framework to store and apply display metadata to
Analysis Results Datasets (ARDs). The use of 'tfrmt' allows users to
define table format and styling without the data, and later apply the
format to the data.
Author: Becca Krouse [aut, cre],
Christina Fillmore [aut] ,
Ellis Hughes [aut] ,
Karima Ahmad [aut] ,
Shannon Haughton [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd],
Atorus Research LLC [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between tfrmt versions 0.1.3 dated 2024-10-15 and 0.2.0 dated 2025-09-06
tfrmt-0.1.3/tfrmt/R/display_row_frmts.R |only tfrmt-0.1.3/tfrmt/tests/testthat/test-display_row_frmts.R |only tfrmt-0.2.0/tfrmt/DESCRIPTION | 87 +--- tfrmt-0.2.0/tfrmt/MD5 | 55 +- tfrmt-0.2.0/tfrmt/NAMESPACE | 5 tfrmt-0.2.0/tfrmt/NEWS.md | 51 ++ tfrmt-0.2.0/tfrmt/R/apply_col_plan.R | 3 tfrmt-0.2.0/tfrmt/R/apply_row_grp_plan.R | 2 tfrmt-0.2.0/tfrmt/R/apply_tfrmt.R | 11 tfrmt-0.2.0/tfrmt/R/big_n.R | 55 ++ tfrmt-0.2.0/tfrmt/R/prep_card.R |only tfrmt-0.2.0/tfrmt/R/print_to_ggplot.R | 2 tfrmt-0.2.0/tfrmt/R/print_to_gt.R | 1 tfrmt-0.2.0/tfrmt/R/shuffle_card.R |only tfrmt-0.2.0/tfrmt/R/struct_utils.R | 6 tfrmt-0.2.0/tfrmt/R/tfrmt_checks.R | 4 tfrmt-0.2.0/tfrmt/README.md | 16 tfrmt-0.2.0/tfrmt/man/display_row_frmts.Rd | 34 - tfrmt-0.2.0/tfrmt/man/prep_big_n.Rd |only tfrmt-0.2.0/tfrmt/man/prep_combine_vars.Rd |only tfrmt-0.2.0/tfrmt/man/prep_hierarchical_fill.Rd |only tfrmt-0.2.0/tfrmt/man/prep_label.Rd |only tfrmt-0.2.0/tfrmt/man/print_to_ggplot.Rd | 2 tfrmt-0.2.0/tfrmt/man/shuffle_card.Rd |only tfrmt-0.2.0/tfrmt/tests/testthat/_snaps/prep_card.md |only tfrmt-0.2.0/tfrmt/tests/testthat/_snaps/shuffle_card.md |only tfrmt-0.2.0/tfrmt/tests/testthat/helper_transform_gt_html.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-apply_page_plan.R | 49 ++ tfrmt-0.2.0/tfrmt/tests/testthat/test-big_ns.R | 255 ++++++++++++ tfrmt-0.2.0/tfrmt/tests/testthat/test-col_style_structure.R | 26 - tfrmt-0.2.0/tfrmt/tests/testthat/test-display_insights.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-expr_to_filter.R | 28 + tfrmt-0.2.0/tfrmt/tests/testthat/test-make_mock_data.R | 24 - tfrmt-0.2.0/tfrmt/tests/testthat/test-prep_card.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-shuffle_card.R |only tfrmt-0.2.0/tfrmt/tests/testthat/test-utils_tfrmt.R | 54 ++ 36 files changed, 603 insertions(+), 167 deletions(-)
Title: Spatial Predictive Modeling
Description: Introduction to some novel accurate hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. It contains two commonly used geostatistical methods, two machine learning methods, four hybrid methods and two averaging methods. For each method, two functions are provided. One function is for assessing the predictive errors and accuracy of the method based on cross-validation. The other one is for generating spatial predictions using the method. For details please see: Li, J., Potter, A., Huang, Z., Daniell, J. J. and Heap, A. (2010) <https://ecat.ga.gov.au/geonetwork/srv/eng/catalog.search#/metadata/71407>
Li, J., Heap, A. D., Potter, A., Huang, Z. and Daniell, J. (2011) <doi:10.1016/j.csr.2011.05.015>
Li, J., Heap, A. D., Potter, A. and Daniell, J. (2011) <doi:10.1016/j.envsoft.2011.07.004>
Li, J., Potter, A., Huang, Z. and Heap, A. (2012) <https://ecat.ga.gov.au/geonetwork/srv/eng/catalog.search#/metadata/74030>.
Author: Jin Li [aut, cre]
Maintainer: Jin Li <jinli68@gmail.com>
Diff between spm versions 1.2.2 dated 2022-05-06 and 1.2.3 dated 2025-09-06
DESCRIPTION | 17 - MD5 | 22 +- R/gbmcv.R | 6 R/gbmidwcv.R | 4 R/gbmokgbmidwcv.R | 4 build/vignette.rds |binary inst/doc/spm.R | 176 ++++++++--------- inst/doc/spm.Rmd | 2 inst/doc/spm.html | 527 +++++++++++++++++++++++++++++++-------------------- man/gbmidwcv.Rd | 4 man/gbmokgbmidwcv.Rd | 4 vignettes/spm.Rmd | 2 12 files changed, 446 insertions(+), 322 deletions(-)
Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximu [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb],
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb],
Virgilio Gomez-Rubio [ctb],
Daniel Griffith [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
James LeSage [ctb],
Ange [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.4-1 dated 2025-09-04 and 1.4-2 dated 2025-09-06
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 6 +++++- R/sarlm_tests.R | 2 +- inst/tinytest/test_Durbin_factor.R | 16 ---------------- 5 files changed, 15 insertions(+), 27 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon timescales (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 1.3.0 dated 2025-07-24 and 1.4.0 dated 2025-09-06
rice-1.3.0/rice/R/realms.R |only rice-1.3.0/rice/man/BCADtoD14C.Rd |only rice-1.3.0/rice/man/C14toD14C.Rd |only rice-1.3.0/rice/man/D14CtoC14.Rd |only rice-1.3.0/rice/man/D14CtoF14C.Rd |only rice-1.3.0/rice/man/D14CtopMC.Rd |only rice-1.3.0/rice/man/F14CtoD14C.Rd |only rice-1.3.0/rice/man/b2ktoD14C.Rd |only rice-1.3.0/rice/man/calBPtoD14C.Rd |only rice-1.3.0/rice/man/draw.D14C.Rd |only rice-1.3.0/rice/man/pMCtoD14C.Rd |only rice-1.3.0/rice/tests/testthat/test-realms.R |only rice-1.4.0/rice/DESCRIPTION | 10 - rice-1.4.0/rice/MD5 | 176 +++++++++++------------ rice-1.4.0/rice/NAMESPACE | 20 +- rice-1.4.0/rice/NEWS.md | 22 +- rice-1.4.0/rice/R/calibrate.R | 36 ++-- rice-1.4.0/rice/R/marine.R | 21 ++ rice-1.4.0/rice/R/plots.R | 149 +++++++++---------- rice-1.4.0/rice/R/rice-package.R | 2 rice-1.4.0/rice/R/rice.R | 34 ++-- rice-1.4.0/rice/R/sets.R | 24 +-- rice-1.4.0/rice/R/shroud.R | 2 rice-1.4.0/rice/R/sources.R | 50 +++--- rice-1.4.0/rice/R/timescales.R |only rice-1.4.0/rice/README.md | 2 rice-1.4.0/rice/inst/CITATION | 74 ++------- rice-1.4.0/rice/inst/doc/rice.R | 14 - rice-1.4.0/rice/inst/doc/rice.Rmd | 46 +++--- rice-1.4.0/rice/inst/doc/rice.html | 157 ++++++++++---------- rice-1.4.0/rice/man/BCADtoC14.Rd | 6 rice-1.4.0/rice/man/BCADtoDelta14C.Rd |only rice-1.4.0/rice/man/BCADtoF14C.Rd | 6 rice-1.4.0/rice/man/BCADtob2k.Rd | 8 - rice-1.4.0/rice/man/BCADtocalBP.Rd | 10 - rice-1.4.0/rice/man/BCADtopMC.Rd | 8 - rice-1.4.0/rice/man/C14toBCAD.Rd | 8 - rice-1.4.0/rice/man/C14toDelta14C.Rd |only rice-1.4.0/rice/man/C14toF14C.Rd | 2 rice-1.4.0/rice/man/C14tob2k.Rd | 2 rice-1.4.0/rice/man/C14tocalBP.Rd | 2 rice-1.4.0/rice/man/C14topMC.Rd | 2 rice-1.4.0/rice/man/CtoF.Rd | 2 rice-1.4.0/rice/man/Delta14CtoC14.Rd |only rice-1.4.0/rice/man/Delta14CtoF14C.Rd |only rice-1.4.0/rice/man/Delta14CtopMC.Rd |only rice-1.4.0/rice/man/F14C.age.Rd | 2 rice-1.4.0/rice/man/F14CtoC14.Rd | 2 rice-1.4.0/rice/man/F14CtoDelta14C.Rd |only rice-1.4.0/rice/man/F14CtopMC.Rd | 2 rice-1.4.0/rice/man/FtoC.Rd | 2 rice-1.4.0/rice/man/adjust.background.Rd | 8 - rice-1.4.0/rice/man/adjust.fractionation.Rd | 4 rice-1.4.0/rice/man/age.F14C.Rd | 2 rice-1.4.0/rice/man/age.pMC.Rd | 2 rice-1.4.0/rice/man/as.bin.Rd | 4 rice-1.4.0/rice/man/as.one.Rd | 8 - rice-1.4.0/rice/man/b2ktoBCAD.Rd | 12 - rice-1.4.0/rice/man/b2ktoC14.Rd | 2 rice-1.4.0/rice/man/b2ktoDelta14C.Rd |only rice-1.4.0/rice/man/b2ktoF14C.Rd | 2 rice-1.4.0/rice/man/b2ktocalBP.Rd | 2 rice-1.4.0/rice/man/b2ktopMC.Rd | 2 rice-1.4.0/rice/man/calBPtoBCAD.Rd | 12 - rice-1.4.0/rice/man/calBPtoC14.Rd | 2 rice-1.4.0/rice/man/calBPtoDelta14C.Rd |only rice-1.4.0/rice/man/calBPtoF14C.Rd | 2 rice-1.4.0/rice/man/calBPtob2k.Rd | 2 rice-1.4.0/rice/man/calBPtopMC.Rd | 2 rice-1.4.0/rice/man/caldist.Rd | 6 rice-1.4.0/rice/man/calib.t.Rd | 4 rice-1.4.0/rice/man/calibrate.Rd | 4 rice-1.4.0/rice/man/clean.Rd | 2 rice-1.4.0/rice/man/contaminate.Rd | 2 rice-1.4.0/rice/man/draw.Delta14C.Rd |only rice-1.4.0/rice/man/draw.ccurve.Rd | 16 +- rice-1.4.0/rice/man/draw.dates.Rd | 6 rice-1.4.0/rice/man/find.shells.Rd | 3 rice-1.4.0/rice/man/fromto.Rd | 18 +- rice-1.4.0/rice/man/l.calib.Rd | 4 rice-1.4.0/rice/man/map.shells.Rd | 3 rice-1.4.0/rice/man/muck.Rd | 2 rice-1.4.0/rice/man/older.Rd | 4 rice-1.4.0/rice/man/overlap.Rd | 2 rice-1.4.0/rice/man/p.range.Rd | 4 rice-1.4.0/rice/man/pMC.age.Rd | 2 rice-1.4.0/rice/man/pMCtoC14.Rd | 2 rice-1.4.0/rice/man/pMCtoDelta14C.Rd |only rice-1.4.0/rice/man/pMCtoF14C.Rd | 2 rice-1.4.0/rice/man/push.gamma.Rd | 7 rice-1.4.0/rice/man/push.normal.Rd | 5 rice-1.4.0/rice/man/r.calib.Rd | 4 rice-1.4.0/rice/man/rice-package.Rd | 2 rice-1.4.0/rice/man/rice.Rd | 4 rice-1.4.0/rice/man/shroud.Rd | 2 rice-1.4.0/rice/man/span.Rd | 2 rice-1.4.0/rice/man/spread.Rd | 2 rice-1.4.0/rice/man/younger.Rd | 4 rice-1.4.0/rice/tests/testthat/test-rice.R | 2 rice-1.4.0/rice/tests/testthat/test-timescales.R |only rice-1.4.0/rice/vignettes/rice.Rmd | 46 +++--- 101 files changed, 568 insertions(+), 569 deletions(-)
Title: Record Linkage Toolkit
Description: Functions to assist in performing probabilistic record linkage and
deduplication: generating pairs, comparing records, em-algorithm for
estimating m- and u-probabilities
(I. Fellegi & A. Sunter (1969) <doi:10.1080/01621459.1969.10501049>,
T.N. Herzog, F.J. Scheuren, & W.E. Winkler (2007),
"Data Quality and Record Linkage Techniques", ISBN:978-0-387-69502-0),
forcing one-to-one matching. Can also be
used for pre- and post-processing for machine learning methods for record
linkage. Focus is on memory, CPU performance and flexibility.
Author: Jan van der Laan [aut, cre]
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between reclin2 versions 0.5.0 dated 2024-02-09 and 0.6.0 dated 2025-09-06
DESCRIPTION | 15 +- MD5 | 120 +++++++++--------- NAMESPACE | 2 NEWS | 15 ++ R/RcppExports.R | 8 + R/add_from_x.R | 2 R/comparators.R | 2 R/compare_pairs.R | 2 R/compare_vars.R | 2 R/get_comparators.R | 1 R/get_inspect_pairs.R | 2 R/greedy.R | 18 ++ R/pair.R | 4 R/pair_blocking.R | 4 R/pair_minsim.R | 4 R/problink_em.R | 2 R/select_greedy.R | 5 R/select_n_to_m.R | 9 + R/select_preprocess.R | 4 R/utils.R |only README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/deduplication.R | 1 inst/doc/deduplication.html | 23 +-- inst/doc/deduplication.md | 1 inst/doc/record_linkage_using_machine_learning.R | 1 inst/doc/record_linkage_using_machine_learning.html | 91 +++++++------- inst/doc/record_linkage_using_machine_learning.md | 1 inst/doc/using_a_cluster_for_record_linkage.html | 128 ++++++++++---------- man/add_from_x.Rd | 2 man/comparators.Rd | 2 man/compare_pairs.Rd | 2 man/compare_vars.Rd | 2 man/get_inspect_pairs.Rd | 2 man/greedy.Rd | 13 +- man/pair.Rd | 4 man/pair_blocking.Rd | 4 man/pair_minsim.Rd | 4 man/select_n_to_m.Rd | 7 + man/val_or.Rd |only src/RcppExports.cpp | 30 ++++ src/greedy.cpp | 54 ++++++++ tests/test_cluster_compare_vars.R | 1 tests/test_cluster_pair.R | 1 tests/test_cluster_pair_blocking.R | 1 tests/test_cluster_pair_minsim.R | 1 tests/test_compare_vars.R | 1 tests/test_distribute_over_cluster.R | 1 tests/test_greedy.R | 58 +++++++++ tests/test_merge_pairs.R | 1 tests/test_pair.R | 1 tests/test_pair_blocking.R | 1 tests/test_pair_minsim.R | 1 tests/test_problink_em.R | 1 tests/test_score_simple.R | 1 tests/test_select_greedy.R | 18 ++ tests/test_select_preprocess.R | 1 tests/test_select_unique.R | 1 tests/test_set_seed.R | 1 vignettes/deduplication.md | 1 vignettes/record_linkage_using_machine_learning.md | 1 62 files changed, 471 insertions(+), 220 deletions(-)
Title: Prediction Rule Ensembles
Description: Derives prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with adjustments and improvements described in
Fokkema (2020; <DOI:10.18637/jss.v092.i12>) and Fokkema & Strobl
(2020; <DOI:10.1037/met0000256>). The main function pre() derives
prediction rule ensembles consisting of rules and/or linear terms for
continuous, binary, count, multinomial, survival and multivariate
continuous responses. Function gpe() derives generalized prediction
ensembles, consisting of rules, hinge and linear functions of the
predictor variables.
Author: Marjolein Fokkema [aut, cre],
Benjamin Christoffersen [aut]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 1.0.7 dated 2024-01-12 and 1.0.8 dated 2025-09-06
pre-1.0.7/pre/NEWS |only pre-1.0.7/pre/inst/doc/missingness.R |only pre-1.0.7/pre/inst/doc/missingness.Rmd |only pre-1.0.7/pre/inst/doc/missingness.html |only pre-1.0.7/pre/inst/doc/tuning.R |only pre-1.0.7/pre/inst/doc/tuning.Rmd |only pre-1.0.7/pre/inst/doc/tuning.html |only pre-1.0.7/pre/vignettes/missingness.Rmd |only pre-1.0.7/pre/vignettes/tuning.Rmd |only pre-1.0.8/pre/DESCRIPTION | 26 pre-1.0.8/pre/MD5 | 65 pre-1.0.8/pre/NEWS.md |only pre-1.0.8/pre/R/gpe.R | 22 pre-1.0.8/pre/R/mi_pre.R | 2 pre-1.0.8/pre/R/pre.R | 801 ++++++---- pre-1.0.8/pre/build/partial.rdb |binary pre-1.0.8/pre/build/vignette.rds |binary pre-1.0.8/pre/inst/doc/Missingness.R |only pre-1.0.8/pre/inst/doc/Missingness.Rmd |only pre-1.0.8/pre/inst/doc/Missingness.html |only pre-1.0.8/pre/inst/doc/Tuning.R |only pre-1.0.8/pre/inst/doc/Tuning.Rmd |only pre-1.0.8/pre/inst/doc/Tuning.html |only pre-1.0.8/pre/inst/doc/relaxed.Rmd | 40 pre-1.0.8/pre/inst/doc/relaxed.html | 221 +- pre-1.0.8/pre/inst/doc/speed.R | 20 pre-1.0.8/pre/inst/doc/speed.Rmd | 40 pre-1.0.8/pre/inst/doc/speed.html | 82 - pre-1.0.8/pre/man/gpe.Rd | 2 pre-1.0.8/pre/man/gpe_cv.glmnet.Rd | 4 pre-1.0.8/pre/man/gpe_rules_pre.Rd | 8 pre-1.0.8/pre/man/gpe_trees.Rd | 14 pre-1.0.8/pre/man/pairplot.Rd | 10 pre-1.0.8/pre/man/pre.Rd | 39 pre-1.0.8/pre/man/rTerm.Rd | 2 pre-1.0.8/pre/man/singleplot.Rd | 9 pre-1.0.8/pre/tests/testthat/previous_results/airquality_w_pre_with_glmtree_w_offset.RDS |only pre-1.0.8/pre/tests/testthat/tests_pre.R | 14 pre-1.0.8/pre/vignettes/Missingness.Rmd |only pre-1.0.8/pre/vignettes/Tuning.Rmd |only pre-1.0.8/pre/vignettes/bib.bib | 190 ++ pre-1.0.8/pre/vignettes/relaxed.Rmd | 40 pre-1.0.8/pre/vignettes/speed.Rmd | 40 43 files changed, 1104 insertions(+), 587 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.3.0 dated 2024-06-11 and 1.3.1 dated 2025-09-06
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md | 5 +++++ R/internal.R | 3 --- R/print_and_plot.R | 4 ++-- build/vignette.rds |binary inst/doc/binary_models.html | 14 +++++++------- inst/doc/intro_to_phylopath.R | 12 ++++++------ inst/doc/intro_to_phylopath.html | 18 +++++++++--------- man/plot.DAG.Rd | 2 +- tests/testthat/test-check_models_data_tree.R |only 11 files changed, 44 insertions(+), 41 deletions(-)
Title: ADaM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Analysis Data Model (ADaM) datasets constructed
using the Study Data Tabulation Model (SDTM) datasets contained in the
'pharmaversesdtm' package and the template scripts from the 'admiral'
family of packages. ADaM dataset specifications are described in the
CDISC ADaM implementation guide, accessible by creating a free account
on <https://www.cdisc.org/>.
Author: Fanny Gautier [aut, cre] ,
Stefan Bundfuss [aut] ,
Edoardo Mancini [aut] ,
Lina Patil [aut],
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline LLC [cph, fnd]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between pharmaverseadam versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-09-06
DESCRIPTION | 68 ++++--- MD5 | 167 +++++++++--------- NAMESPACE | 1 NEWS.md | 58 +++++- R/adae.R | 21 +- R/adbcva_ophtha.R | 82 ++------ R/adce_vaccine.R | 7 R/adcm.R | 19 +- R/adcoeq_metabolic.R |only R/adeg.R | 29 ++- R/adex.R | 40 +++- R/adface_vaccine.R | 43 ++++ R/adis_vaccine.R | 37 +++- R/adlb.R | 68 ++++++- R/adlb_metabolic.R |only R/adlbhy.R | 17 + R/admh.R | 17 - R/adoe_ophtha.R | 32 ++- R/adpc.R | 25 +- R/adpp.R | 17 - R/adppk.R | 13 + R/adrs_onco.R | 26 ++ R/adsl.R | 15 - R/adsl_vaccine.R | 7 R/adtr_onco.R | 24 ++ R/adtte_onco.R | 14 + R/advfq_ophtha.R | 32 ++- R/advs.R | 30 ++- R/advs_metabolic.R |only R/advs_peds.R | 25 ++ R/pharmaverseadam-package.R | 1 README.md | 101 +++++++---- data/adae.rda |binary data/adbcva_ophtha.rda |binary data/adce_vaccine.rda |binary data/adcm.rda |binary data/adcoeq_metabolic.rda |only data/adeg.rda |binary data/adex.rda |binary data/adface_vaccine.rda |binary data/adis_vaccine.rda |binary data/adlb.rda |binary data/adlb_metabolic.rda |only data/adlbhy.rda |binary data/admh.rda |binary data/adoe_ophtha.rda |binary data/adpc.rda |binary data/adpp.rda |binary data/adppk.rda |binary data/adrs_onco.rda |binary data/adsl.rda |binary data/adsl_vaccine.rda |binary data/adtr_onco.rda |binary data/adtte_onco.rda |binary data/advfq_ophtha.rda |binary data/advs.rda |binary data/advs_metabolic.rda |only data/advs_peds.rda |binary inst/WORDLIST | 374 +++++++++++++++++++++++++---------------- inst/extdata/adams-specs.json |only inst/extdata/adams-specs.xlsx |binary man/adae.Rd | 16 - man/adbcva_ophtha.Rd | 78 ++------ man/adce_vaccine.Rd | 2 man/adcm.Rd | 14 - man/adcoeq_metabolic.Rd |only man/adeg.Rd | 25 ++ man/adex.Rd | 36 +++ man/adface_vaccine.Rd | 39 ++++ man/adis_vaccine.Rd | 33 +++ man/adlb.Rd | 64 ++++++- man/adlb_metabolic.Rd |only man/adlbhy.Rd | 13 + man/admh.Rd | 12 - man/adoe_ophtha.Rd | 28 ++- man/adpc.Rd | 21 +- man/adpp.Rd | 12 - man/adppk.Rd | 9 man/adrs_onco.Rd | 22 ++ man/adsl.Rd | 10 - man/adsl_vaccine.Rd | 2 man/adtr_onco.Rd | 20 +- man/adtte_onco.Rd | 10 - man/advfq_ophtha.Rd | 28 ++- man/advs.Rd | 26 ++ man/advs_metabolic.Rd |only man/advs_peds.Rd | 21 ++ man/figures/cytel_logo.png |only man/figures/gsk_logo.png |only man/figures/roche_logo.png |only man/pharmaverseadam-package.Rd | 17 + 91 files changed, 1323 insertions(+), 645 deletions(-)
More information about pharmaverseadam at CRAN
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Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data handling (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and resid [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.7.4 dated 2025-08-18 and 0.7.5 dated 2025-09-06
DESCRIPTION | 12 MD5 | 198 ++++++------ NAMESPACE | 1 NEWS.md | 28 + R/aov.b.R | 7 R/aov.w.R | 7 R/blimp.R | 10 R/blimp.bayes.R | 7 R/blimp.plot.R | 7 R/blimp.print.R | 7 R/blimp.update.R | 10 R/center.R | 7 R/check.collin.R | 7 R/check.outlier.R | 7 R/check.resid.R | 9 R/chr.color.R | 7 R/chr.grep.R | 14 R/chr.gsub.R | 12 R/chr.omit.R | 10 R/chr.trim.R | 7 R/chr.trunc.R | 17 - R/ci.cor.R | 7 R/ci.mean.R | 7 R/ci.mean.diff.R | 7 R/ci.mean.w.R | 7 R/ci.prop.R | 7 R/ci.prop.diff.R | 7 R/ci.var.R | 7 R/cluster.rwg.R | 10 R/cluster.scores.R | 10 R/coding.R | 5 R/coeff.robust.R | 326 ++++++++++++++++---- R/coeff.std.R | 9 R/cohens.d.R | 16 R/cor.matrix.R | 7 R/crosstab.R | 7 R/descript.R | 138 ++++---- R/df.check.R | 7 R/df.duplicated.R | 7 R/df.head.R | 7 R/df.long.R | 14 R/df.move.R | 12 R/df.rbind.R | 5 R/df.rename.R | 4 R/df.subset.R | 5 R/dominance.R | 7 R/dominance.manual.R | 7 R/effsize.R | 5 R/freq.R | 309 ++++++++---------- R/item.alpha.R | 7 R/item.cfa.R | 7 R/item.invar.R | 7 R/item.omega.R | 7 R/item.reverse.R | 7 R/item.scores.R | 7 R/lagged.R | 7 R/mplus.R | 10 R/mplus.bayes.R | 7 R/mplus.lca.R | 7 R/mplus.plot.R | 7 R/mplus.print.R | 7 R/mplus.update.R | 10 R/multilevel.cfa.R | 12 R/multilevel.cor.R | 12 R/multilevel.descript.R | 12 R/multilevel.fit.R | 5 R/multilevel.icc.R | 12 R/multilevel.invar.R | 10 R/multilevel.omega.R | 12 R/multilevel.r2.manual.R | 21 - R/na.as.R | 14 R/na.auxiliary.R | 7 R/na.coverage.R | 7 R/na.descript.R | 7 R/na.indicator.R | 7 R/na.pattern.R | 7 R/na.prop.R | 7 R/na.test.R | 7 R/plot.misty.object.R | 7 R/print.misty.object.R | 766 ++++++++++++++++++++++++++++++++++++++++------- R/rec.R | 12 R/robust.lmer.R |only R/script.open.R | 7 R/setsource.R | 5 R/skewness.R | 14 R/summa.R | 294 +++++++++++++----- R/test.levene.R | 7 R/test.t.R | 14 R/test.welch.R | 7 R/test.z.R | 16 R/uniq.R | 14 R/utils.R | 6 R/write.result.R | 254 ++++++++++++--- R/write.sav.R | 7 R/write.xlsx.R | 5 man/check.resid.Rd | 2 man/coeff.robust.Rd | 225 ++++++++++--- man/descript.Rd | 9 man/freq.Rd | 23 - man/robust.lmer.Rd |only man/summa.Rd | 97 ++++- 101 files changed, 2169 insertions(+), 1235 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.44.0 dated 2025-01-28 and 1.45.1 dated 2025-09-06
DESCRIPTION | 9 - MD5 | 288 ++++++++++++++++++------------------ NEWS.md | 15 + R/03-estimation.R | 40 +++-- R/04-PrepData.R | 5 R/05-model.elements.R | 2 R/DIF.R | 2 R/DRF.R | 6 R/DTF.R | 2 R/DeltaMethod.R | 8 - R/EMstep.group.R | 11 + R/M2.R | 2 R/MDIFF.R | 2 R/MDISC.R | 2 R/MHRM.utils.R | 2 R/PLCI.mirt.R | 14 - R/RCI.R | 135 ++++++++++++---- R/RMSD_DIF.R | 26 ++- R/SIBTEST.R | 13 + R/SingleGroup-methods.R | 20 +- R/areainfo.R | 2 R/averageMI.R | 2 R/bfactor.R | 2 R/boot.LR.R | 2 R/boot.mirt.R | 4 R/createItem.R | 2 R/empirical_ES.R | 2 R/empirical_plot.R | 2 R/empirical_rxx.R | 2 R/estfun.R | 2 R/expand.table.R | 2 R/expected.test.R | 2 R/extract.group.R | 17 +- R/extract.item.R | 13 - R/extract.mirt.R | 2 R/fixedCalib.R | 2 R/fixef.R | 2 R/fscores.R | 18 +- R/fscores.internal.R | 4 R/gen.difficulty.R | 2 R/imputeMissing.R | 2 R/itemGAM.R | 6 R/itemfit.R | 2 R/iteminfo.R | 2 R/itemplot.R | 2 R/itemstats.R | 47 +++-- R/lagrange.R | 2 R/likert2int.R | 2 R/marginal_rxx.R | 32 +++- R/mdirt.R | 2 R/mirt-package.R | 18 +- R/mirt.R | 4 R/mirt.model.R | 2 R/mixedmirt.R | 4 R/mod2values.R | 2 R/multipleGroup.R | 5 R/numerical_deriv.R | 2 R/personfit.R | 2 R/poly2dich.R | 2 R/randef.R | 17 +- R/read.mirt.R | 2 R/reverse.score.R | 4 R/simdata.R | 4 R/testinfo.R | 2 R/utils.R | 11 + R/wald.R | 2 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mirt-vignettes.html | 124 +++++++++------ man/Attitude.Rd | 2 man/Bock1997.Rd | 2 man/DIF.Rd | 2 man/DRF.Rd | 4 man/DTF.Rd | 2 man/DeltaMethod.Rd | 8 - man/LSAT6.Rd | 2 man/LSAT7.Rd | 4 man/M2.Rd | 2 man/MDIFF.Rd | 2 man/MDISC.Rd | 2 man/PLCI.mirt.Rd | 8 - man/RCI.Rd | 77 +++++++++ man/RMSD_DIF.Rd | 22 ++ man/SAT12.Rd | 2 man/SIBTEST.Rd | 8 - man/SLF.Rd | 2 man/Science.Rd | 2 man/anova-method.Rd | 2 man/areainfo.Rd | 2 man/averageMI.Rd | 2 man/bfactor.Rd | 2 man/boot.LR.Rd | 2 man/boot.mirt.Rd | 4 man/coef-method.Rd | 2 man/createItem.Rd | 2 man/deAyala.Rd | 2 man/draw_parameters.Rd | 2 man/empirical_ES.Rd | 2 man/empirical_plot.Rd | 2 man/empirical_rxx.Rd | 2 man/estfun.AllModelClass.Rd | 2 man/expand.table.Rd | 2 man/expected.test.Rd | 2 man/extract.group.Rd | 7 man/extract.item.Rd | 11 - man/extract.mirt.Rd | 2 man/fixedCalib.Rd | 2 man/fixef.Rd | 2 man/fscores.Rd | 11 + man/gen.difficulty.Rd | 2 man/imputeMissing.Rd | 2 man/itemGAM.Rd | 6 man/itemfit.Rd | 2 man/iteminfo.Rd | 2 man/itemplot.Rd | 2 man/itemstats.Rd | 16 +- man/lagrange.Rd | 2 man/likert2int.Rd | 2 man/logLik-method.Rd | 2 man/marginal_rxx.Rd | 32 +++- man/mdirt.Rd | 2 man/mirt.Rd | 4 man/mirt.model.Rd | 2 man/mixedmirt.Rd | 4 man/mod2values.Rd | 2 man/multipleGroup.Rd | 5 man/numerical_deriv.Rd | 2 man/personfit.Rd | 2 man/plot-method.Rd | 2 man/poly2dich.Rd | 2 man/print-method.Rd | 2 man/randef.Rd | 10 + man/read.mirt.Rd | 2 man/residuals-method.Rd | 2 man/reverse.score.Rd | 4 man/secondOrderTest.Rd | 2 man/show-method.Rd | 2 man/simdata.Rd | 2 man/summary-method.Rd | 2 man/testinfo.Rd | 2 man/vcov-method.Rd | 2 man/wald.Rd | 2 src/Makevars | 2 tests/testthat/test-09-mirt.model.R | 9 + 145 files changed, 885 insertions(+), 481 deletions(-)
Title: Miscellaneous Utilities and Functions
Description: Miscellaneous tools and functions,
including: generate descriptive statistics tables,
format output, visualize relations among variables or check
distributions, and generic functions for residual and
model diagnostics.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between JWileymisc versions 1.4.3 dated 2025-04-13 and 1.4.4 dated 2025-09-06
DESCRIPTION | 9 MD5 | 57 NAMESPACE | 502 +++---- NEWS.md | 14 R/data.R | 2 R/descriptives.R | 2 R/descriptives_helpers.R | 505 +++---- R/diagnostics.R | 2 R/geoms_themes.R | 130 - R/plotting.R | 1866 +++++++++++++-------------- R/scoring.R | 2 R/styler.R | 1654 ++++++++++++------------ R/utils.R | 1147 ++++++++-------- R/visual_acuity.R | 9 build/partial.rdb |binary build/vignette.rds |binary inst/doc/diagnostics-vignette.R | 240 +-- inst/doc/diagnostics-vignette.html | 1322 +++++++++---------- inst/doc/exploratory-vignette.R | 476 +++--- inst/doc/exploratory-vignette.html | 1996 ++++++++++++++--------------- inst/doc/model-test-vignette.R | 84 - inst/doc/model-test-vignette.html | 1004 +++++++------- man/VAObject-class.Rd | 10 man/aces_daily.Rd | 2 man/density_inversion.Rd |only man/styletests.Rd | 4 man/testDistribution.Rd | 338 ++-- tests/testthat/test-SEMSummary.R | 1 tests/testthat/test-descriptives-helpers.R | 170 +- tests/testthat/test-descriptives.R | 16 30 files changed, 5841 insertions(+), 5723 deletions(-)
Title: Fitting Deep Distributional Regression
Description: Allows for the specification of semi-structured deep distributional regression models which are fitted in a neural network as
proposed by Ruegamer et al. (2023) <doi:10.18637/jss.v105.i02>.
Predictors can be modeled using structured (penalized) linear effects, structured non-linear effects or using an unstructured deep network model.
Author: David Ruegamer [aut, cre],
Christopher Marquardt [ctb],
Laetitia Frost [ctb],
Florian Pfisterer [ctb],
Philipp Baumann [ctb],
Chris Kolb [ctb],
Lucas Kook [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between deepregression versions 2.3.1 dated 2025-09-01 and 2.3.2 dated 2025-09-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/python/utils/types.py | 7 ++++++- 3 files changed, 11 insertions(+), 6 deletions(-)
More information about deepregression at CRAN
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Title: A Comprehensive Collection of Cardiovascular and Heart Disease
Datasets
Description: Offers a diverse collection of datasets focused on cardiovascular and heart disease research, including heart failure, myocardial infarction, aortic dissection, transplant outcomes, cardiovascular risk factors, drug efficacy, and mortality trends.
Designed for researchers, clinicians, epidemiologists, and data scientists, the package features clinical, epidemiological, and simulated datasets covering a wide range of conditions and treatments such as statins, anticoagulants, and beta blockers.
It supports analyses related to disease progression, treatment effects, rehospitalization, and public health outcomes across various cardiovascular patient populations.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between CardioDataSets versions 0.1.0 dated 2025-05-13 and 0.2.0 dated 2025-09-05
CardioDataSets-0.1.0/CardioDataSets/R/view_datasets.R |only CardioDataSets-0.1.0/CardioDataSets/man/view_datasets.Rd |only CardioDataSets-0.1.0/CardioDataSets/tests/testthat/test-view_datasets.R |only CardioDataSets-0.2.0/CardioDataSets/DESCRIPTION | 15 - CardioDataSets-0.2.0/CardioDataSets/MD5 | 25 +- CardioDataSets-0.2.0/CardioDataSets/NAMESPACE | 2 CardioDataSets-0.2.0/CardioDataSets/NEWS.md |only CardioDataSets-0.2.0/CardioDataSets/R/view_datasets_CardioDataSets.R |only CardioDataSets-0.2.0/CardioDataSets/README.md | 10 - CardioDataSets-0.2.0/CardioDataSets/build/vignette.rds |binary CardioDataSets-0.2.0/CardioDataSets/inst/CITATION | 6 CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.R | 7 CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.Rmd | 14 + CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.html | 96 ++++++---- CardioDataSets-0.2.0/CardioDataSets/man/view_datasets_CardioDataSets.Rd |only CardioDataSets-0.2.0/CardioDataSets/tests/testthat/test-view_datasets_CardioDataSets.R |only CardioDataSets-0.2.0/CardioDataSets/vignettes/Introduction_to_CardioDataSets.Rmd | 14 + 17 files changed, 126 insertions(+), 63 deletions(-)
More information about CardioDataSets at CRAN
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Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.2.4 dated 2025-07-15 and 0.2.5 dated 2025-09-05
NMsim-0.2.4/NMsim/R/dtapply.R |only NMsim-0.2.4/NMsim/man/dtapply.Rd |only NMsim-0.2.5/NMsim/DESCRIPTION | 6 NMsim-0.2.5/NMsim/MD5 | 101 +++-- NMsim-0.2.5/NMsim/NAMESPACE | 1 NMsim-0.2.5/NMsim/NEWS.md | 31 + NMsim-0.2.5/NMsim/R/NMcreateDoses.R | 23 + NMsim-0.2.5/NMsim/R/NMexec.R | 9 NMsim-0.2.5/NMsim/R/NMextractText.R | 11 NMsim-0.2.5/NMsim/R/NMreadInits.R | 63 +-- NMsim-0.2.5/NMsim/R/NMreadSection.R | 8 NMsim-0.2.5/NMsim/R/NMreadSim.R | 8 NMsim-0.2.5/NMsim/R/NMreadSimOne.R | 4 NMsim-0.2.5/NMsim/R/NMsim.R | 95 +++-- NMsim-0.2.5/NMsim/R/NMsimRes_utils.R | 3 NMsim-0.2.5/NMsim/R/NMsim_helpers.R | 2 NMsim-0.2.5/NMsim/R/NMwriteInits.R | 162 +++++++- NMsim-0.2.5/NMsim/R/NMwriteInitsOne.R | 39 +- NMsim-0.2.5/NMsim/R/NMwriteSectionOne.R | 13 NMsim-0.2.5/NMsim/R/addParType.R | 142 ++++++- NMsim-0.2.5/NMsim/R/checkTimes.R | 10 NMsim-0.2.5/NMsim/R/deleteTmpDirs.R |only NMsim-0.2.5/NMsim/R/fnAppend.R | 60 ++- NMsim-0.2.5/NMsim/R/sampleCovs.R | 10 NMsim-0.2.5/NMsim/R/seedFunDefault.R | 1 NMsim-0.2.5/NMsim/R/typicalize.R | 84 ++-- NMsim-0.2.5/NMsim/README.md | 10 NMsim-0.2.5/NMsim/man/NMcreateDoses.Rd | 10 NMsim-0.2.5/NMsim/man/NMreadInits.Rd | 1 NMsim-0.2.5/NMsim/man/NMsim.Rd | 70 ++- NMsim-0.2.5/NMsim/man/NMwriteInits.Rd | 11 NMsim-0.2.5/NMsim/man/addParType.Rd |only NMsim-0.2.5/NMsim/man/addParameter.Rd |only NMsim-0.2.5/NMsim/man/count_ij.Rd | 2 NMsim-0.2.5/NMsim/man/deleteTmpDirs.Rd |only NMsim-0.2.5/NMsim/man/fnAppend.Rd | 16 NMsim-0.2.5/NMsim/man/initsToExt.Rd |only NMsim-0.2.5/NMsim/man/triagSize.Rd | 4 NMsim-0.2.5/NMsim/man/typicalize.Rd |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.ext |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.lst |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.mod |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.phi |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011_fo1.txt |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr032_sd1_NWPRI.mod |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMcreateDoses_17.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_04.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_04b.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03_OMEGAP.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03_OMEGAPD.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMwriteInits_07.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_01.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_02.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_03.rds |only NMsim-0.2.5/NMsim/tests/testthat/test_NMcreateDoses.R | 9 NMsim-0.2.5/NMsim/tests/testthat/test_NMsim.R | 67 ++- NMsim-0.2.5/NMsim/tests/testthat/test_NMsim_NWPRI.R | 189 ++++++---- NMsim-0.2.5/NMsim/tests/testthat/test_NMsim_default.R | 2 NMsim-0.2.5/NMsim/tests/testthat/test_NMwriteInits.R | 17 NMsim-0.2.5/NMsim/tests/testthat/test_typicalize.R |only 63 files changed, 924 insertions(+), 372 deletions(-)
Title: Optimal Estimation of Function Parameters by Iterated
Linearization
Description: Package for estimating the parameters of a nonlinear function using iterated linearization via Taylor series. Method is based on Kubáček (2000) ISBN: 80-244-0093-6. The algorithm is a generalization of the procedure given in Köning, R., Wimmer, G.
and Witkovský, V. (2014) <doi:10.1088/0957-0233/25/11/115001>.
Author: Stanislav Zamecnik [aut, cre],
Vojtech Sindlar [aut] ,
Zdenka Gerslova [aut] ,
Gejza Wimmer [aut] ,
Technology Agency of the Czech Republic [fnd] ,
Masaryk University, a public university, ID: 00216224 [cph]
Maintainer: Stanislav Zamecnik <zamecnik@math.muni.cz>
This is a re-admission after prior archival of version 0.1.1 dated 2021-11-04
Diff between OEFPIL versions 0.1.1 dated 2021-11-04 and 0.1.2 dated 2025-09-05
DESCRIPTION | 8 MD5 | 66 +- NAMESPACE | 46 - NEWS.md | 24 R/NanoIndent.OEFPIL.R | 488 +++++++-------- R/OEFPIL.R | 1460 ++++++++++++++++++++++----------------------- R/coef.OEFPIL.R | 80 +- R/confBands.OEFPIL.R | 238 +++---- R/confInt.OEFPIL.R | 162 ++-- R/curvplot.OEFPIL.R | 238 +++---- R/ortresiduals.OEFPIL.R | 210 +++--- R/paramplot.OEFPIL.R | 194 ++--- R/plot.OEFPIL.R | 226 +++--- R/print.OEFPIL.R | 72 +- R/silica2098-data.R | 60 - R/silicaBerk-data.R | 54 - R/summary.OEFPIL.R | 202 +++--- R/vcov.OEFPIL.R | 52 - README.md | 240 +++---- build/partial.rdb |binary man/NanoIndent.OEFPIL.Rd | 200 +++--- man/OEFPIL.Rd | 240 +++---- man/coef.OEFPIL.Rd | 78 +- man/confBands.OEFPIL.Rd | 104 +-- man/confInt.OEFPIL.Rd | 86 +- man/curvplot.OEFPIL.Rd | 106 +-- man/ortresiduals.OEFPIL.Rd | 86 +- man/paramplot.OEFPIL.Rd | 88 +- man/plot.OEFPIL.Rd | 130 ++-- man/print.OEFPIL.Rd | 62 - man/silica2098.Rd | 72 +- man/silicaBerk.Rd | 64 - man/summary.OEFPIL.Rd | 88 +- man/vcov.OEFPIL.Rd | 62 - 34 files changed, 2793 insertions(+), 2793 deletions(-)
Title: Identify Text Written by Large Language Models using 'GPTZero'
Description: An R interface to the 'GPTZero' API (<https://gptzero.me/docs>). Allows
users to classify text into human and computer written with probabilities. Formats
the data into data frames where each sentence is an observation. Paragraph-level
and document-level predictions are organized to align with the sentences.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between gptzeror versions 0.0.1 dated 2023-06-05 and 0.0.2 dated 2025-09-05
gptzeror-0.0.1/gptzeror/R/gptzeror-package.R |only gptzeror-0.0.2/gptzeror/DESCRIPTION | 17 gptzeror-0.0.2/gptzeror/MD5 | 34 - gptzeror-0.0.2/gptzeror/NAMESPACE | 18 gptzeror-0.0.2/gptzeror/NEWS.md | 4 gptzeror-0.0.2/gptzeror/R/GPTZeroR-package.R |only gptzeror-0.0.2/gptzeror/R/api_url.R | 6 gptzeror-0.0.2/gptzeror/R/key.R | 180 +++--- gptzeror-0.0.2/gptzeror/R/predict.R | 276 +++++----- gptzeror-0.0.2/gptzeror/R/utils.R | 38 - gptzeror-0.0.2/gptzeror/inst/httptest2/redact.R | 8 gptzeror-0.0.2/gptzeror/man/gptzero_set_key.Rd | 56 +- gptzeror-0.0.2/gptzeror/man/gptzeror-package.Rd | 4 gptzeror-0.0.2/gptzeror/man/key.Rd | 44 - gptzeror-0.0.2/gptzeror/tests/testthat.R | 24 gptzeror-0.0.2/gptzeror/tests/testthat/httptest2/predict/api.gptzero.me/v2/predict/files-8c5839-POST.json | 86 +-- gptzeror-0.0.2/gptzeror/tests/testthat/httptest2/predict/api.gptzero.me/v2/predict/text-6834ac-POST.json | 86 +-- gptzeror-0.0.2/gptzeror/tests/testthat/setup.R | 72 +- gptzeror-0.0.2/gptzeror/tests/testthat/test-predict.R | 26 19 files changed, 492 insertions(+), 487 deletions(-)
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP
<doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors'
package in the 'Monolix' installation, as described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>.
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
Chart Data instead of exporting it from the 'Monolix' gui.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [aut] ,
Seid Hamzic [aut],
Benjamin Gui [...truncated...]
Maintainer: Aleksandr Pogodaev <alex.pogodaev@novartis.com>
Diff between ggPMX versions 1.3.1 dated 2025-08-27 and 1.3.2 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 4 ++++ R/plot-individual.R | 16 ++++++++-------- R/pmx-reader.R | 24 +++++++++++++++++++++--- R/pmxClass.R | 2 +- inst/doc/ggPMX-guide.pdf |binary tests/testthat/setup.R |only tests/testthat/test-reader.R | 40 ++++++++++++++++++++++++++++++++++++++++ 9 files changed, 85 insertions(+), 22 deletions(-)
Title: Accesses Brazilian Public Security Data from SINESP Since 2015
Description: Allows access to data from the Brazilian Public Security Information System (SINESP) by state and municipality. It should be emphasized that the package only extracts the data and facilitates its manipulation in R. Therefore, its sole purpose is to support empirical research. All data credits belong to SINESP, an integrated information platform developed and maintained by the National Secretariat of Public Security (SENASP) of the Ministry of Justice and Public Security. <https://www.gov.br/mj/pt-br/assuntos/sua-seguranca/seguranca-publica/sinesp-1>.
Author: Giovanni Vargette [aut, cre] ,
Igor Laltuf [aut] ,
Marcelo Justus [aut]
Maintainer: Giovanni Vargette <g216978@dac.unicamp.br>
Diff between BrazilCrime versions 0.2.1 dated 2024-09-14 and 0.3.0 dated 2025-09-05
BrazilCrime-0.2.1/BrazilCrime/R/get_sinesp_data.R |only BrazilCrime-0.2.1/BrazilCrime/man/get_sinesp_data.Rd |only BrazilCrime-0.3.0/BrazilCrime/DESCRIPTION | 23 BrazilCrime-0.3.0/BrazilCrime/LICENSE | 4 BrazilCrime-0.3.0/BrazilCrime/MD5 | 37 BrazilCrime-0.3.0/BrazilCrime/NAMESPACE | 10 BrazilCrime-0.3.0/BrazilCrime/R/br_crime_predict.R |only BrazilCrime-0.3.0/BrazilCrime/R/get_sinesp_vde_data.R | 166 +-- BrazilCrime-0.3.0/BrazilCrime/R/sysdata.rda |binary BrazilCrime-0.3.0/BrazilCrime/README.md | 454 +++++----- BrazilCrime-0.3.0/BrazilCrime/build |only BrazilCrime-0.3.0/BrazilCrime/inst/THANKS |only BrazilCrime-0.3.0/BrazilCrime/inst/doc |only BrazilCrime-0.3.0/BrazilCrime/inst/extdata/ufs.csv | 56 - BrazilCrime-0.3.0/BrazilCrime/man/br_crime_predict.Rd |only BrazilCrime-0.3.0/BrazilCrime/man/get_sinesp_vde_data.Rd | 85 - BrazilCrime-0.3.0/BrazilCrime/tests/testthat.R | 24 BrazilCrime-0.3.0/BrazilCrime/tests/testthat/test-get_sinesp_data.R | 68 - BrazilCrime-0.3.0/BrazilCrime/tests/testthat/test-get_sinesp_vde_data.R | 94 +- BrazilCrime-0.3.0/BrazilCrime/vignettes |only 20 files changed, 506 insertions(+), 515 deletions(-)
Title: Markdown Parser and Renderer for R Graphics
Description: Provides the mean to parse and render markdown text with grid
along with facilities to define the styling of the text.
Author: Thomas Lin Pedersen [aut, cre] ,
Martin Mitas [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between marquee versions 1.1.1 dated 2025-08-27 and 1.2.0 dated 2025-09-05
DESCRIPTION | 11 - MD5 | 54 +++--- NAMESPACE | 3 NEWS.md | 9 + R/classic_style.R | 238 ++++++++++++++++------------ R/geom_marquee.R | 13 - R/grob.R | 82 ++++++--- R/guide_marquee.R | 2 R/marquee-package.R | 5 R/style.R | 106 ++++++++++-- R/style_set.R | 77 +++++---- inst/doc/marquee.html | 18 +- inst/doc/marquee_style.Rmd | 2 inst/doc/marquee_style.html | 25 +- man/classic_style.Rd | 10 + man/figures/README-unnamed-chunk-2-1.png |binary 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/geom_marquee.Rd | 2 man/guide_marquee.Rd | 2 man/marquee_grob.Rd | 7 man/style.Rd | 27 ++- tests/testthat/_snaps/grob/marquee_grob.png |binary tests/testthat/_snaps/parse/parsed.csv | 122 +++++++------- tests/testthat/_snaps/style.md | 4 tests/testthat/_snaps/style_set.md | 2 tests/testthat/test-style.R | 14 - vignettes/marquee_style.Rmd | 2 30 files changed, 512 insertions(+), 325 deletions(-)
Title: Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.
Author: Diogo Melo [aut, cre] ,
Ana Paula Assis [aut],
Edgar Zanella [ctb],
Fabio Andrade Machado [aut] ,
Guilherme Garcia [aut],
Alex Hubbe [rev] ,
Gabriel Marroig [ths]
Maintainer: Diogo Melo <diogro@gmail.com>
Diff between evolqg versions 0.3-4 dated 2023-12-05 and 0.3-6 dated 2025-09-05
DESCRIPTION | 19 ++++++++++--------- MD5 | 24 ++++++++++++------------ R/EigenTensorDecomposition.R | 2 +- R/EvolQG.R | 4 ++-- R/MantelCor.R | 2 +- R/MantelModTest.R | 2 +- man/MantelCor.Rd | 2 +- man/MantelModTest.Rd | 2 +- man/evolqg.Rd | 25 +++++++++++++++++++++++++ man/ratones.Rd | 2 +- src/Makevars | 1 + src/Makevars.win | 1 + tests/testthat/test.TestModularity.r | 3 ++- 13 files changed, 59 insertions(+), 30 deletions(-)
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.3.1 dated 2025-07-17 and 0.4.0 dated 2025-09-05
Spower-0.3.1/Spower/man/SpowerCurve.Rd |only Spower-0.4.0/Spower/DESCRIPTION | 10 Spower-0.4.0/Spower/MD5 | 28 + Spower-0.4.0/Spower/NAMESPACE | 4 Spower-0.4.0/Spower/R/Spower.R | 114 ++++-- Spower-0.4.0/Spower/R/SpowerBatch.R |only Spower-0.4.0/Spower/R/SpowerCurve.R | 170 ++++----- Spower-0.4.0/Spower/R/util.R | 19 - Spower-0.4.0/Spower/build/vignette.rds |binary Spower-0.4.0/Spower/inst/doc/SpowerIntro.R |only Spower-0.4.0/Spower/inst/doc/SpowerIntro.Rmd |only Spower-0.4.0/Spower/inst/doc/SpowerIntro.html |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.R |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.Rmd |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.html |only Spower-0.4.0/Spower/inst/intro.rds |only Spower-0.4.0/Spower/inst/intro2.rds |only Spower-0.4.0/Spower/man/Spower.Rd | 306 ++++++++++++++--- Spower-0.4.0/Spower/man/getLastSpower.Rd | 7 Spower-0.4.0/Spower/vignettes/SpowerIntro.Rmd |only Spower-0.4.0/Spower/vignettes/SpowerIntro_logicals.Rmd |only 21 files changed, 462 insertions(+), 196 deletions(-)
Title: Sensitivity Analysis for Irregular Assessment Times
Description: Sensitivity analysis for trials with irregular and informative
assessment times, based on a new influence function-based, augmented
inverse intensity-weighted estimator.
Author: Andrew Redd [aut, cre] ,
Yujing Gao [aut],
Shu Yang [aut],
Bonnie Smith [aut],
Ravi Varadhan [aut],
Agatha Mallett [ctb, ctr],
Daniel Scharfstein [pdr, aut] ,
University of Utah [cph]
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between SensIAT versions 0.2.0 dated 2025-08-18 and 0.3.0 dated 2025-09-05
SensIAT-0.2.0/SensIAT/R/Cond_mean_fn.R |only SensIAT-0.2.0/SensIAT/R/PCORI_example_data.R |only SensIAT-0.2.0/SensIAT/R/PCORI_fulldata_model.R |only SensIAT-0.2.0/SensIAT/R/PCORI_within_group_model.R |only SensIAT-0.2.0/SensIAT/R/SensIAT_prepare_data.R |only SensIAT-0.2.0/SensIAT/R/Y_draw_fn.R |only SensIAT-0.2.0/SensIAT/R/compute_influence_term_2_quadv.R |only SensIAT-0.2.0/SensIAT/R/data_transform.R |only SensIAT-0.2.0/SensIAT/man/Cond_mean_fn.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_fit_marginal_model.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_jackknife.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_prepare_data.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler_mave.Rd |only SensIAT-0.2.0/SensIAT/man/sensitivity_expected_values.Rd |only SensIAT-0.3.0/SensIAT/DESCRIPTION | 6 SensIAT-0.3.0/SensIAT/MD5 | 92 +-- SensIAT-0.3.0/SensIAT/NAMESPACE | 22 SensIAT-0.3.0/SensIAT/NEWS.md | 10 SensIAT-0.3.0/SensIAT/R/RcppExports.R | 4 SensIAT-0.3.0/SensIAT/R/SensIAT_sim_outcome_modeler_mave.R | 242 +++++----- SensIAT-0.3.0/SensIAT/R/add_class.R | 3 SensIAT-0.3.0/SensIAT/R/autoplot.R | 18 SensIAT-0.3.0/SensIAT/R/compute_influence_for_one_alpha_and_one_patient.R | 4 SensIAT-0.3.0/SensIAT/R/compute_influence_term_2_quadv_sim.R | 174 +++---- SensIAT-0.3.0/SensIAT/R/example_data.R |only SensIAT-0.3.0/SensIAT/R/fit_marginal_model.R | 8 SensIAT-0.3.0/SensIAT/R/fulldata_model.R |only SensIAT-0.3.0/SensIAT/R/jackknife.R | 67 +- SensIAT-0.3.0/SensIAT/R/predict_within_group.R | 7 SensIAT-0.3.0/SensIAT/R/prepare_data.R |only SensIAT-0.3.0/SensIAT/R/sensitivity_expected_values.R | 42 - SensIAT-0.3.0/SensIAT/R/sim_outcome_modeler.R | 14 SensIAT-0.3.0/SensIAT/R/within_group_model.R |only SensIAT-0.3.0/SensIAT/inst/examples/basic.R | 4 SensIAT-0.3.0/SensIAT/inst/examples/recreate_original.R | 2 SensIAT-0.3.0/SensIAT/man/SensIAT_example_data.Rd | 8 SensIAT-0.3.0/SensIAT/man/add_class.Rd | 2 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_fulldata_jackknife_results.Rd | 4 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_fulldata_model.Rd | 4 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_within_group_model.Rd | 6 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_withingroup_jackknife_results.Rd | 4 SensIAT-0.3.0/SensIAT/man/compute_SensIAT_expected_values.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_marginal_mean_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_single_index_fixed_coef_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_single_index_norm1coef_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_within_group_model.Rd | 10 SensIAT-0.3.0/SensIAT/man/jackknife.Rd | 34 + SensIAT-0.3.0/SensIAT/man/pcoriaccel_estimate_pmf.Rd | 1 SensIAT-0.3.0/SensIAT/man/pcoriaccel_evaluate_basis.Rd | 1 SensIAT-0.3.0/SensIAT/man/pcoriaccel_evaluate_basis_mat.Rd | 1 SensIAT-0.3.0/SensIAT/man/predict.SensIAT_within_group_model.Rd | 9 SensIAT-0.3.0/SensIAT/man/prepare_SensIAT_data.Rd |only SensIAT-0.3.0/SensIAT/src/estimate_pmf.cpp | 1 SensIAT-0.3.0/SensIAT/src/spline_basis.h | 3 SensIAT-0.3.0/SensIAT/tests/testthat/test-PCORI_within_group_model.R | 10 SensIAT-0.3.0/SensIAT/tests/testthat/test-SensIAT_sim_outcome_modeler_mave.R | 140 ++++- SensIAT-0.3.0/SensIAT/tests/testthat/test-influence_term1.R | 2 SensIAT-0.3.0/SensIAT/tests/testthat/test-influence_term2.R | 2 59 files changed, 521 insertions(+), 440 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
This method draws from the simulation framework used in the Gelman and Hill (2007) textbook:
Data Analysis Using Regression and Multilevel/Hierarchical Models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut],
Alex Whitworth [ctb]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between merTools versions 0.6.2 dated 2024-02-08 and 0.6.3 dated 2025-09-05
DESCRIPTION | 10 +- MD5 | 45 +++++------ NEWS.md | 4 + R/helpers.R | 2 R/merList.R | 17 +++- R/merPlots.R | 6 - R/subBoot.R | 4 - build/vignette.rds |binary inst/doc/Using_predictInterval.html | 16 ++-- inst/doc/imputation.html | 4 - inst/doc/marginal_effects.html | 6 - inst/doc/merToolsIntro.html | 22 ++--- man/VarCorr.merModList.Rd | 4 - man/merModList-class.Rd |only man/merTools-package.Rd | 142 ++++++++++++++++++------------------ man/mkNewReTrms.Rd | 66 ++++++++-------- man/modelFixedEff.Rd | 66 ++++++++-------- man/plotFEsim.Rd | 94 +++++++++++------------ man/plotREsim.Rd | 118 ++++++++++++++--------------- man/ranef.merModList.Rd | 72 ++++++++---------- man/thetaExtract.Rd | 50 ++++++------ tests/testthat/_snaps/predict2.md | 20 ++--- tests/testthat/test-predict1.R | 8 +- tests/testthat/test-predict2.R | 8 +- 24 files changed, 399 insertions(+), 385 deletions(-)
Title: Process and Report 'GreenFeed' Data
Description: Provides tools for downloading, processing, and reporting daily and finalized 'GreenFeed' data.
Author: Guillermo Martinez-Boggio [cre, aut, cph] ,
Meredith Harrison [ctb],
Patrick Lutz [ctb]
Maintainer: Guillermo Martinez-Boggio <gmartinezboggio@ucdavis.edu>
Diff between greenfeedr versions 1.3.0 dated 2025-08-18 and 1.3.1 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/viseat.R | 8 ++++++++ README.md | 7 +------ inst/doc/greenfeedr.html | 2 +- inst/shinyapp/app_server.R | 2 +- 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Fairness Evaluation Metrics with Confidence Intervals for Binary
Protected Attributes
Description: A collection of functions for computing fairness metrics for machine learning and statistical models, including confidence intervals for each metric. The package supports the evaluation of group-level fairness criterion commonly used in fairness research, particularly in healthcare for binary protected attributes. It is based on the overview of fairness in machine learning written by Gao et al (2024) <doi:10.48550/arXiv.2406.09307>.
Author: Jianhui Gao [aut] ,
Benjamin Smith [aut, cre] ,
Benson Chou [aut] ,
Jessica Gronsbell [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between fairmetrics versions 1.0.4 dated 2025-07-22 and 1.0.5 dated 2025-09-05
fairmetrics-1.0.4/fairmetrics/R/Fairness.R |only fairmetrics-1.0.4/fairmetrics/R/Helper.R |only fairmetrics-1.0.4/fairmetrics/man/eval_cond_stats_parity.Rd |only fairmetrics-1.0.5/fairmetrics/DESCRIPTION | 11 fairmetrics-1.0.5/fairmetrics/MD5 | 61 fairmetrics-1.0.5/fairmetrics/NAMESPACE | 1 fairmetrics-1.0.5/fairmetrics/R/ModelPerformance.R | 76 fairmetrics-1.0.5/fairmetrics/R/eval_acc_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_bs_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_cond_acc_equality.R |only fairmetrics-1.0.5/fairmetrics/R/eval_eq_odds.R |only fairmetrics-1.0.5/fairmetrics/R/eval_eq_opp.R |only fairmetrics-1.0.5/fairmetrics/R/eval_neg_class_bal.R |only fairmetrics-1.0.5/fairmetrics/R/eval_neg_pred_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pos_class_bal.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pos_pred_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pred_equality.R |only fairmetrics-1.0.5/fairmetrics/R/eval_stats_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_treatment_equality.R |only fairmetrics-1.0.5/fairmetrics/R/get_fairness_metrics.R | 469 ++- fairmetrics-1.0.5/fairmetrics/build/vignette.rds |binary fairmetrics-1.0.5/fairmetrics/inst/CITATION | 2 fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.R | 144 - fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.Rmd | 465 +-- fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.html | 1434 +---------- fairmetrics-1.0.5/fairmetrics/man/eval_acc_parity.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_bs_parity.Rd | 12 fairmetrics-1.0.5/fairmetrics/man/eval_cond_acc_equality.Rd | 12 fairmetrics-1.0.5/fairmetrics/man/eval_eq_odds.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_eq_opp.Rd | 15 fairmetrics-1.0.5/fairmetrics/man/eval_neg_class_bal.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_neg_pred_parity.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_pos_class_bal.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_pos_pred_parity.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_pred_equality.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_stats_parity.Rd | 13 fairmetrics-1.0.5/fairmetrics/man/eval_treatment_equality.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/get_fairness_metrics.Rd | 28 fairmetrics-1.0.5/fairmetrics/vignettes/fairmetrics.Rmd | 465 +-- 39 files changed, 1104 insertions(+), 2188 deletions(-)
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.4.2 dated 2025-06-01 and 0.4.3 dated 2025-09-05
DESCRIPTION | 6 - MD5 | 27 ++-- NEWS.md | 7 + R/create_template.R | 11 + R/custom_modules.R | 8 + README.md | 206 ++++++++++++++++++++++++++---------- inst/app_skeleton/load.Rmd | 6 - inst/app_skeleton/save.Rmd | 25 +++- inst/app_skeleton/testthat.Rmd |only inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/core_load.R | 6 - inst/shiny/modules/core_save.R | 33 +++-- inst/shiny/modules/rep_markdown.R | 4 tests/testthat/test-save_load.R | 13 +- 15 files changed, 257 insertions(+), 99 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.2.1 dated 2025-07-15 and 0.3.0 dated 2025-09-05
kinesis-0.2.1/kinesis/inst/tinytest/_tinysnapshot |only kinesis-0.2.1/kinesis/inst/tinytest/helpers.R |only kinesis-0.2.1/kinesis/man/update_selectize_values.Rd |only kinesis-0.2.1/kinesis/man/update_selectize_variables.Rd |only kinesis-0.3.0/kinesis/DESCRIPTION | 19 kinesis-0.3.0/kinesis/MD5 | 181 +-- kinesis-0.3.0/kinesis/NAMESPACE | 6 kinesis-0.3.0/kinesis/NEWS.md | 8 kinesis-0.3.0/kinesis/R/bertin.R | 16 kinesis-0.3.0/kinesis/R/ca.R | 16 kinesis-0.3.0/kinesis/R/coda.R | 104 - kinesis-0.3.0/kinesis/R/coda_barplot.R | 2 kinesis-0.3.0/kinesis/R/coda_hist.R | 2 kinesis-0.3.0/kinesis/R/coda_statistics.R | 3 kinesis-0.3.0/kinesis/R/count.R |only kinesis-0.3.0/kinesis/R/count_diversity_alpha.R | 26 kinesis-0.3.0/kinesis/R/count_diversity_beta.R | 69 - kinesis-0.3.0/kinesis/R/count_occurrence.R | 29 kinesis-0.3.0/kinesis/R/diversity.R |only kinesis-0.3.0/kinesis/R/graphics.R | 3 kinesis-0.3.0/kinesis/R/help.R | 4 kinesis-0.3.0/kinesis/R/home.R | 49 kinesis-0.3.0/kinesis/R/import.R | 117 +- kinesis-0.3.0/kinesis/R/kinesis-internal.R | 177 --- kinesis-0.3.0/kinesis/R/kinesis-package.R | 6 kinesis-0.3.0/kinesis/R/lm.R |only kinesis-0.3.0/kinesis/R/multivariate.R | 79 - kinesis-0.3.0/kinesis/R/pca.R | 14 kinesis-0.3.0/kinesis/R/plot.R | 2 kinesis-0.3.0/kinesis/R/prepare.R | 213 +--- kinesis-0.3.0/kinesis/R/run.R | 12 kinesis-0.3.0/kinesis/R/scatter.R | 111 -- kinesis-0.3.0/kinesis/R/table.R | 2 kinesis-0.3.0/kinesis/R/ternary.R | 110 +- kinesis-0.3.0/kinesis/R/time_interval.R | 46 kinesis-0.3.0/kinesis/R/variables.R |only kinesis-0.3.0/kinesis/README.md | 5 kinesis-0.3.0/kinesis/build/partial.rdb |binary kinesis-0.3.0/kinesis/inst/app/aoristic/server.R | 1 kinesis-0.3.0/kinesis/inst/app/aoristic/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/ca/server.R | 3 kinesis-0.3.0/kinesis/inst/app/ca/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/diversity/server.R | 10 kinesis-0.3.0/kinesis/inst/app/diversity/ui.R | 7 kinesis-0.3.0/kinesis/inst/app/mcd/server.R | 3 kinesis-0.3.0/kinesis/inst/app/mcd/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/pca/server.R | 1 kinesis-0.3.0/kinesis/inst/app/pca/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/scatter/config.yml | 4 kinesis-0.3.0/kinesis/inst/app/scatter/server.R | 6 kinesis-0.3.0/kinesis/inst/app/scatter/ui.R | 3 kinesis-0.3.0/kinesis/inst/app/seriation/server.R | 3 kinesis-0.3.0/kinesis/inst/app/seriation/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/source/server.R | 1 kinesis-0.3.0/kinesis/inst/app/source/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/ternary/server.R | 1 kinesis-0.3.0/kinesis/inst/app/ternary/ui.R | 2 kinesis-0.3.0/kinesis/inst/extdata |only kinesis-0.3.0/kinesis/inst/po/fr/LC_MESSAGES/R-kinesis.mo |binary kinesis-0.3.0/kinesis/inst/tinytest/bronze.csv | 740 +++++++------- kinesis-0.3.0/kinesis/inst/tinytest/fake.csv |only kinesis-0.3.0/kinesis/inst/tinytest/test_coda.R | 33 kinesis-0.3.0/kinesis/inst/tinytest/test_coda_logratio.R | 15 kinesis-0.3.0/kinesis/inst/tinytest/test_coda_plot.R | 44 kinesis-0.3.0/kinesis/inst/tinytest/test_import.R | 20 kinesis-0.3.0/kinesis/inst/tinytest/test_inputs.R | 25 kinesis-0.3.0/kinesis/inst/tinytest/test_prepare.R | 45 kinesis-0.3.0/kinesis/inst/tinytest/test_ternary.R | 52 kinesis-0.3.0/kinesis/man/bertin_server.Rd | 4 kinesis-0.3.0/kinesis/man/bertin_ui.Rd | 4 kinesis-0.3.0/kinesis/man/checkbox_ui.Rd |only kinesis-0.3.0/kinesis/man/count_server.Rd |only kinesis-0.3.0/kinesis/man/count_ui.Rd |only kinesis-0.3.0/kinesis/man/diversity_alpha_server.Rd | 6 kinesis-0.3.0/kinesis/man/diversity_alpha_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_beta_server.Rd | 13 kinesis-0.3.0/kinesis/man/diversity_beta_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_docs_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_server.Rd |only kinesis-0.3.0/kinesis/man/diversity_ui.Rd |only kinesis-0.3.0/kinesis/man/falsy.Rd |only kinesis-0.3.0/kinesis/man/home_ui.Rd | 2 kinesis-0.3.0/kinesis/man/kinesis-package.Rd | 4 kinesis-0.3.0/kinesis/man/lm_server.Rd |only kinesis-0.3.0/kinesis/man/lm_ui.Rd |only kinesis-0.3.0/kinesis/man/occurrence_server.Rd | 6 kinesis-0.3.0/kinesis/man/occurrence_ui.Rd | 4 kinesis-0.3.0/kinesis/man/prepare_server.Rd | 11 kinesis-0.3.0/kinesis/man/run_app.Rd | 4 kinesis-0.3.0/kinesis/man/selectize_ui.Rd | 5 kinesis-0.3.0/kinesis/man/update_checkbox_colnames.Rd |only kinesis-0.3.0/kinesis/man/update_input.Rd |only kinesis-0.3.0/kinesis/man/update_selectize_colnames.Rd |only kinesis-0.3.0/kinesis/man/update_selectize_rownames.Rd |only kinesis-0.3.0/kinesis/po/R-fr.po | 479 +++++---- kinesis-0.3.0/kinesis/po/R-kinesis.pot | 462 ++++---- kinesis-0.3.0/kinesis/tests/tinytest.R | 6 97 files changed, 1619 insertions(+), 1871 deletions(-)
Title: Supervised Feature Selection
Description: Interfaces for choosing important predictors in supervised
regression, classification, and censored regression models. Permuted
importance scores (Biecek and Burzykowski (2021)
<doi:10.1201/9780429027192>) can be computed for 'tidymodels' model
fits.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between important versions 0.0.1 dated 2025-08-20 and 0.2.0 dated 2025-09-05
DESCRIPTION | 15 +- MD5 | 37 +++++- NAMESPACE | 25 ++++ NEWS.md | 10 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/importance_perm.R | 18 ++- R/important-package.R | 26 +++- R/recipe_utils.R |only R/step_predictor_best.R |only R/step_predictor_desirability.R |only R/step_predictor_retain.R |only README.md | 103 ++++++++++++++++++- build/partial.rdb |binary inst/WORDLIST | 3 man/required_pkgs.important.Rd |only man/rmd |only man/step_predictor_best.Rd |only man/step_predictor_desirability.Rd |only man/step_predictor_retain.Rd |only tests/testthat/_snaps/recipes_utils.md |only tests/testthat/_snaps/step_predictor_best.md |only tests/testthat/_snaps/step_predictor_desirability.md |only tests/testthat/_snaps/step_predictor_retain.md |only tests/testthat/helper-objects.R | 49 ++++++--- tests/testthat/test-recipes_utils.R |only tests/testthat/test-step_predictor_best.R |only tests/testthat/test-step_predictor_desirability.R |only tests/testthat/test-step_predictor_retain.R |only 29 files changed, 242 insertions(+), 44 deletions(-)
Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational
Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database.
Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or
SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Author: Anthony Sena [aut, cre],
Jamie Gilbert [aut],
Gowtham Rao [aut],
Freddy Avila Cruz [aut],
Martijn Schuemie [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between CohortGenerator versions 0.12.0 dated 2025-07-31 and 0.12.1 dated 2025-09-05
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 6 + R/SubsetQueryBuilders.R | 2 build/vignette.rds |binary inst/doc/CreatingCohortSubsetDefinitions.R | 18 ++--- inst/doc/CreatingCohortSubsetDefinitions.html | 4 - inst/doc/GeneratingCohorts.pdf |binary inst/doc/SamplingCohorts.R | 92 +++++++++++++------------- inst/doc/SamplingCohorts.pdf |binary 10 files changed, 77 insertions(+), 71 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.4.3 dated 2025-08-21 and 2.5.1 dated 2025-09-05
DESCRIPTION | 6 MD5 | 45 ++-- NAMESPACE | 15 + R/IBM_k_samples_test.R | 92 +++++--- R/admix_estim.R | 24 +- R/admix_test.R | 10 R/decontaminated_dist.R | 51 +++- R/extractors.R | 309 +++++++++++++++++++++++----- R/gaussianity_test.R | 14 - R/orthobasis_test.R | 13 - R/utils.R | 88 +++++-- build/partial.rdb |binary inst/doc/admixture-weight-estimation.html | 18 - man/admix_estim.Rd | 21 + man/decontaminated_density.Rd | 13 - man/get_cluster_members.admix_cluster.Rd |only man/get_cluster_sizes.admix_cluster.Rd |only man/get_discrepancy_id.IBM_test.Rd |only man/get_discrepancy_matrix.IBM_test.Rd |only man/get_discrepancy_matrix.admix_cluster.Rd |only man/get_discrepancy_rank.IBM_test.Rd |only man/get_known_component.admix_cluster.Rd |only man/get_known_component.admix_estim.Rd |only man/get_known_component.htest.Rd |only man/get_mixing_weights.admix_estim.Rd |only man/get_mixing_weights.htest.Rd |only man/get_statistic_components.IBM_test.Rd |only man/get_tabulated_dist.IBM_test.Rd |only man/plot.decontaminated_density.Rd | 14 - man/reject_nullHyp.htest.Rd |only man/which_rank.htest.Rd |only 31 files changed, 550 insertions(+), 183 deletions(-)
Title: 'Canvas' LMS API Integration
Description: Allow R users to interact with the 'Canvas' Learning Management System (LMS) API (see
<https://canvas.instructure.com/doc/api/all_resources.html> for details).
It provides a set of functions to access and manipulate course data, assignments, grades, users,
and other resources available through the 'Canvas' API.
Author: Tomer Iwan [aut, cre],
Niels Smits [ctb] ,
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvcanvas versions 0.0.5 dated 2025-03-31 and 0.0.6 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 144 ++++++++++++++++------------ NAMESPACE | 16 +++ NEWS.md | 5 R/create_assignment_group.R | 7 - R/create_conversation.R |only R/create_course_section.R | 7 - R/create_folder.R | 7 - R/create_group_category.R | 7 - R/create_module.R | 15 +- R/create_module_item.R | 20 +-- R/create_page.R | 7 - R/delete_course_section.R | 6 - R/delete_page.R | 19 +-- R/edit_section.R | 7 - R/get_all_courses.R | 49 ++------- R/get_assignment_details.R | 6 - R/get_assignment_groups.R | 18 +-- R/get_assignment_submissions.R | 17 +-- R/get_assignments.R | 17 +-- R/get_calendar_events.R | 20 ++- R/get_conversations.R |only R/get_course_enrollments.R | 16 +-- R/get_course_files.R | 17 +-- R/get_course_folders.R | 21 ++-- R/get_course_gradebook.R |only R/get_course_groups.R | 16 +-- R/get_course_media_objects.R | 18 +-- R/get_course_pages.R | 18 +-- R/get_course_quizzes.R | 17 +-- R/get_course_root_folder.R |only R/get_course_sections.R | 16 +-- R/get_course_students.R | 17 +-- R/get_course_users.R | 17 +-- R/get_courses.R | 2 R/get_department_statistics.R | 16 +-- R/get_department_statistics_by_subaccount.R | 16 +-- R/get_discussions.R | 17 +-- R/get_favorite_courses.R | 6 - R/get_folder_files.R |only R/get_group_categories.R | 16 +-- R/get_group_memberships.R | 16 +-- R/get_group_users.R | 16 +-- R/get_module_items.R | 16 +-- R/get_modules.R | 17 +-- R/get_quiz_submissions.R |only R/get_roles.R | 1 R/get_section_information.R | 6 - R/get_single_conversation.R |only R/get_user_folders.R |only R/paginate.R |only R/post_new_discussion.R | 7 - R/query_progress.R |only R/update_course_grades.R |only R/update_page.R | 25 ++-- R/update_quiz.R | 9 - R/update_section_grades.R |only R/upload_file.R | 21 ++-- R/upload_folder_file.R |only R/upload_qti_file_with_migration.R | 49 +++++---- inst/doc/QTI_quiz.R | 7 - inst/doc/QTI_quiz.Rmd | 7 - inst/doc/QTI_quiz.html | 6 - inst/doc/getting_started.R | 3 inst/doc/getting_started.Rmd | 3 inst/doc/groups_use_case.R | 15 +- inst/doc/groups_use_case.Rmd | 21 +--- inst/doc/groups_use_case.html | 37 +++---- man/append_access_token.Rd |only man/create_conversation.Rd |only man/extract_next_url.Rd |only man/get_conversations.Rd |only man/get_course_folders.Rd | 7 + man/get_course_gradebook.Rd |only man/get_course_root_folder.Rd |only man/get_folder_files.Rd |only man/get_quiz_submissions.Rd |only man/get_single_conversation.Rd |only man/get_user_folders.Rd |only man/paginate.Rd |only man/query_progress.Rd |only man/update_course_grades.Rd |only man/update_section_grades.Rd |only man/upload_folder_file.Rd |only vignettes/QTI_quiz.Rmd | 7 - vignettes/getting_started.Rmd | 3 vignettes/groups_use_case.Rmd | 21 +--- 87 files changed, 519 insertions(+), 449 deletions(-)
Title: Byte Pair Encoding Text Tokenization
Description: Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
VK.com [cph],
Gregory Popovitch [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Ivan Belonogov [ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between tokenizers.bpe versions 0.1.3 dated 2023-09-15 and 0.1.4 dated 2025-09-05
DESCRIPTION | 8 LICENSE.note | 2 MD5 | 20 - NEWS.md | 4 src/parallel_hashmap/btree.h | 52 +-- src/parallel_hashmap/phmap.h | 522 +++++++++++++++++++++--------------- src/parallel_hashmap/phmap_base.h | 476 +++++++++++++++----------------- src/parallel_hashmap/phmap_bits.h | 83 ++--- src/parallel_hashmap/phmap_config.h | 66 +++- src/parallel_hashmap/phmap_dump.h | 67 +++- src/parallel_hashmap/phmap_utils.h | 2 11 files changed, 724 insertions(+), 578 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 1.0.2 dated 2025-08-22 and 1.0.3 dated 2025-09-05
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 3 R/tidysdm-package.R | 1 R/zzz.R | 5 + inst/doc/a0_tidysdm_overview.html | 112 ++++++++++++++++---------------- inst/doc/a1_palaeodata_application.html | 26 +++---- inst/doc/a2_tidymodels_additions.html | 81 ++++++++++++++--------- inst/doc/a3_troubleshooting.html | 67 ++++++++----------- man/geom_split_violin.Rd | 10 +- tests/spelling.R | 9 +- tests/testthat/Rplots.pdf |binary 12 files changed, 185 insertions(+), 159 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.8.1 dated 2025-04-28 and 1.8.2 dated 2025-09-05
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 6 +++++- R/RCM_est.R | 7 +++++-- R/RCM_int.R | 12 ++++++++---- R/RCM_rmd.R | 4 ++-- R/define_S4_class_RCModel.R | 6 +++++- build/partial.rdb |binary 8 files changed, 37 insertions(+), 22 deletions(-)
Title: Exploratory Analysis of Temporal and Spatio-Temporal Health Data
Description: A collection of commonly used visualizations of temporal and
spatio-temporal health data including case counts, incidence rates, and
covariates. The available plot types include time series, heatmaps,
seasonality plots, maps and more. The package supports standard data
transformations such as temporal and spatial aggregations, while
offering extensive customization options for the resulting figures.
Author: Carles Mila [aut, cre] ,
Giovenale Moirano [aut] ,
Anna B. Kawiecki [aut] ,
Rachel Lowe [aut, cph]
Maintainer: Carles Mila <carles.milagarcia@bsc.es>
Diff between GHRexplore versions 0.1.1 dated 2025-07-10 and 0.2.0 dated 2025-09-05
DESCRIPTION | 6 - MD5 | 45 ++++---- NAMESPACE | 1 NEWS.md | 8 + R/dengue_MS.R | 19 ++- R/dengue_SP.R | 4 R/map_MS.R | 6 - R/plot_compare.R | 2 R/plot_map.R | 79 +++++++++------ R/plot_timeseries.R | 4 R/plot_timeseries2.R |only README.md | 2 inst/doc/GHRexplore.R | 47 ++++++++- inst/doc/GHRexplore.Rmd | 65 +++++++++++- inst/doc/GHRexplore.html | 166 ++++++++++++++++++++------------- man/dengue_MS.Rd | 16 +-- man/dengue_SP.Rd | 2 man/map_MS.Rd | 2 man/plot_compare.Rd | 2 man/plot_map.Rd | 19 ++- man/plot_timeseries.Rd | 3 man/plot_timeseries2.Rd |only tests/testthat/test-plot_map.R | 6 - tests/testthat/test-plot_timeseries2.R |only vignettes/GHRexplore.Rmd | 65 +++++++++++- 25 files changed, 402 insertions(+), 167 deletions(-)
Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.6 dated 2025-08-28 and 0.1.7 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/speakeasyR.html | 10 +++++----- src/se2/src/speakeasy2/se2_core.c | 5 +++-- 7 files changed, 33 insertions(+), 26 deletions(-)
Title: Nearest Neighbor Descent Method for Approximate Nearest
Neighbors
Description: The Nearest Neighbor Descent method for finding approximate
nearest neighbors by Dong and co-workers (2010)
<doi:10.1145/1963405.1963487>. Based on the 'Python' package
'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Author: James Melville [aut, cre, cph],
Vitalie Spinu [ctb],
Ralf Stubner [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between rnndescent versions 0.1.6 dated 2024-05-14 and 0.1.8 dated 2025-09-05
DESCRIPTION | 8 +++--- MD5 | 30 ++++++++++++------------ NEWS.md | 5 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/brute-force.html | 2 - inst/doc/hubness.html | 40 ++++++++++++++++---------------- inst/doc/metrics.html | 2 - inst/doc/nearest-neighbor-descent.html | 2 - inst/doc/querying-data.html | 4 +-- inst/doc/random-partition-forests.html | 2 - inst/doc/rnndescent.html | 2 - tests/testthat/test_brute_force.R | 4 +-- tests/testthat/test_descent_euclidean.R | 2 - tests/testthat/test_random_nbrs.R | 4 +-- tests/testthat/test_rptree.R | 8 +++--- 16 files changed, 60 insertions(+), 55 deletions(-)
Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Author: Alexandre Almeida [aut],
Adam Loy [aut, cre],
Heike Hofmann [aut]
Maintainer: Adam Loy <loyad01@gmail.com>
Diff between qqplotr versions 0.0.6 dated 2023-01-25 and 0.0.7 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 69 +++++----- NEWS.md | 4 R/data.R | 2 R/geom_qq_band.R | 4 R/qqplotr.R | 3 R/stat_pp_band.R | 8 - R/stat_pp_line.R | 6 R/stat_pp_point.R | 5 R/stat_qq_band.R | 8 - R/stat_qq_line.R | 4 R/stat_qq_point.R | 4 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 28 +--- inst/doc/introduction.R | 10 - inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 196 +++++++++++++++--------------- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/longjump.Rd | 2 man/qqplotr.Rd | 19 ++ man/stat_pp_band.Rd | 82 +++++++++--- man/stat_pp_line.Rd | 78 +++++++++-- man/stat_pp_point.Rd | 78 +++++++++-- man/stat_qq_band.Rd | 82 +++++++++--- man/stat_qq_line.Rd | 78 +++++++++-- man/stat_qq_point.Rd | 78 +++++++++-- vignettes/introduction.Rmd | 2 36 files changed, 572 insertions(+), 288 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.2 dated 2025-08-28 and 1.6.3 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/nanodbc/nanodbc.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Neighborhood Deprivation Indices
Description: Computes various geospatial indices of socioeconomic deprivation and disparity
in the United States. Some indices are considered "spatial" because they
consider the values of neighboring (i.e., adjacent) census geographies in
their computation, while other indices are "aspatial" because they only
consider the value within each census geography. Two types of aspatial
neighborhood deprivation indices (NDI) are available: including:
(1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x>
and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066>
and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002>
who use variables chosen by Roux and Mair (2010)
<doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple
demographic characteristics from the U.S. Census Bureau American Community
Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5
(2005-2009 onward), the package can also compute indices of racia [...truncated...]
Author: Ian D. Buller [aut, cre, cph] ,
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between ndi versions 0.1.5 dated 2024-01-23 and 0.2.1 dated 2025-09-05
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Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2023) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] ,
KANK Karunarathna [ctb] ,
Sarah Heaps [ctb] ,
Scott Pease [ctb] ,
Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.51 dated 2025-03-14 and 1.1.593 dated 2025-09-05
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mvgam-1.1.593/mvgam/tests/testthat/test-backends.R | 56 mvgam-1.1.593/mvgam/tests/testthat/test-dynamic.R | 405 mvgam-1.1.593/mvgam/tests/testthat/test-example_processing.R | 39 mvgam-1.1.593/mvgam/tests/testthat/test-gp.R | 972 - mvgam-1.1.593/mvgam/tests/testthat/test-jsdgam.R | 6777 +++++------ mvgam-1.1.593/mvgam/tests/testthat/test-mvgam_priors.R | 866 - mvgam-1.1.593/mvgam/tests/testthat/test-summary-structure.R |only mvgam-1.1.593/mvgam/tests/testthat/test-tidier_methods.R | 80 mvgam-1.1.593/mvgam/vignettes/data_in_mvgam.Rmd | 872 - mvgam-1.1.593/mvgam/vignettes/mvgam_overview.Rmd | 1215 - mvgam-1.1.593/mvgam/vignettes/trend_formulas.Rmd | 70 176 files changed, 31565 insertions(+), 27038 deletions(-)
Title: Power Analysis and Sample Size Calculation
Description: Power analysis and sample size calculation for Welch and Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>), comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>), ANCOVA (Shieh (2020), <doi:10.1007/s11336-019-09692-3>), reference ranges (Jennen-Steinmetz and Wellek (2005), <doi:10.1002/sim.2177>), multiple primary endpoints (Sozu et al. (2015), ISBN:978 [...truncated...]
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKpower versions 1.0 dated 2024-09-23 and 1.1 dated 2025-09-05
DESCRIPTION | 15 ++- MD5 | 24 +++--- NAMESPACE | 3 NEWS | 8 ++ R/histSimPower.R | 24 +++--- R/powerDiagnosticTest.R | 4 - R/qqunifSimPower.R | 18 ++-- R/ssizeAUCCI.R | 2 R/volcanoSimPower.R | 40 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MKpower.html | 183 +++++++++++++++++++++++------------------------- man/ssize.auc.ci.Rd | 13 +-- 13 files changed, 168 insertions(+), 166 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with
meteorological data in the tidy data framework. Extends 'ggplot2' for
better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.18.1 dated 2025-05-13 and 0.18.2 dated 2025-09-05
DESCRIPTION | 38 +- MD5 | 75 ++-- NAMESPACE | 2 NEWS.md | 24 + R/Derivate.R | 2 R/FitLm.R | 4 R/GetTopography.R | 4 R/MaskLand.R | 2 R/ReadNetCDF.R | 104 +++++- R/Smooth2D.R | 2 R/WriteNetCDF.R | 8 R/arrowGrob.R | 12 R/geom_contour_tanaka.R | 1 R/geom_text_contour.R | 3 R/guide_colorstrip.R | 10 R/helpfunctions.R | 23 - R/scale-unbinned.R | 18 - R/scale_vector.R | 1 R/standard_atmosphere.R | 2 R/stat_contour2.r | 479 +++++++++++++++-------------- R/stat_contour_fill.R | 11 R/textContourGrob.R | 2 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/Visualization-tools.html | 298 +++++++++--------- inst/doc/Working-with-data.html | 239 ++++++++------ man/ReadNetCDF.Rd | 28 + man/figures/field-1.png |binary man/figures/timeseries-1.png |binary man/metR.Rd | 1 man/standard_atmosphere.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/era5 |only tests/testthat/test-ReadNetCDF.R | 25 + tests/testthat/test-fitlm.R | 4 tests/testthat/test-vis-guide_colorstrip.R | 17 - 38 files changed, 835 insertions(+), 616 deletions(-)
Title: Individual-Level, Summary-Level and Single-Step Bayesian
Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
(1) fixed effects and coefficients of covariates,
(2) environmental random effects, and its corresponding variance,
(3) genetic variance,
(4) residual variance,
(5) heritability,
(6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
(7) SNP effect size,
(8) phenotype/genetic variance explained (PVE) for single or multiple SNPs,
(9) posterior probability of association of the genomic window (WPPA),
(10) posterior inclusive probability (PIP).
The functions are not limited, we will keep on going in enriching it with more features.
References: Lilin Yin et al. (2025) <doi:10.18637/jss [...truncated...]
Author: Lilin Yin [aut, cre, cph] ,
Haohao Zhang [aut, cph] ,
Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>
Diff between hibayes versions 3.0.3 dated 2024-02-20 and 3.1.0 dated 2025-09-05
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 13 +++++++------ inst/CITATION |only src/Makevars | 2 +- src/Makevars.win | 2 +- src/omp_set.h | 2 -- src/rm.cpp | 4 ++-- src/solver.cpp | 28 ++++++++++++++-------------- 8 files changed, 41 insertions(+), 37 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.2.3 dated 2024-05-19 and 0.2.5 dated 2025-09-05
DESCRIPTION | 10 - MD5 | 54 +++++---- NAMESPACE | 10 + R/cox.tcdca.R | 47 +++++++- R/getplot.R | 27 ++-- R/modeldata.R | 9 + R/netdata.R | 251 ++++++++++++++++++++++++++++++++++++++++++++- R/randomForest.R | 9 + R/scidca.R | 23 ---- R/scidca.coxph.R | 11 + R/scidca.glm.R | 11 + R/scidca.scixgboot.R |only R/scidca.svm.R | 7 - R/scidcacrr.R | 11 + R/scidcaksvm.R | 7 - R/tcdca.R | 27 +++- man/cox.tcdca.Rd | 42 +++++++ man/netdata.coxph.Rd |only man/netdata.crr.Rd |only man/netdata.glm.Rd |only man/netdata.randomFores.Rd |only man/netdata.scixgboot.Rd |only man/netdata.svm.Rd |only man/scidca.Rd | 24 ---- man/scidca.coxph.Rd | 5 man/scidca.crr.Rd | 5 man/scidca.glm.Rd | 5 man/scidca.ksvm.Rd | 5 man/scidca.randomForest.Rd | 5 man/scidca.scixgboot.Rd |only man/scidca.svm.Rd | 5 man/tcdca.Rd | 41 ++++++- 32 files changed, 533 insertions(+), 118 deletions(-)
Title: More Miscellaneous Steps for the 'recipes' Package
Description: Contains additional miscellaneous steps for the 'recipes' package.
These steps are useful, but doesn't have a good home in other 'recipes'
packages or its extensions.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between extrasteps versions 0.1.0 dated 2024-10-03 and 0.3.0 dated 2025-09-05
extrasteps-0.1.0/extrasteps/tests/testthat/_snaps/combine_stringdist.md |only extrasteps-0.1.0/extrasteps/tests/testthat/_snaps/yeet.md |only extrasteps-0.3.0/extrasteps/DESCRIPTION | 9 extrasteps-0.3.0/extrasteps/MD5 | 92 ++++------ extrasteps-0.3.0/extrasteps/NAMESPACE | 2 extrasteps-0.3.0/extrasteps/NEWS.md | 6 extrasteps-0.3.0/extrasteps/R/0_imports.R | 2 extrasteps-0.3.0/extrasteps/R/aaa.R | 6 extrasteps-0.3.0/extrasteps/R/date_after.R | 82 +++++--- extrasteps-0.3.0/extrasteps/R/date_before.R | 80 +++++--- extrasteps-0.3.0/extrasteps/R/date_nearest.R | 88 ++++++--- extrasteps-0.3.0/extrasteps/R/difftime.R | 44 ++-- extrasteps-0.3.0/extrasteps/R/encoding_binary.R | 30 +-- extrasteps-0.3.0/extrasteps/R/encoding_frequency.R | 22 +- extrasteps-0.3.0/extrasteps/R/maxabs.R | 22 +- extrasteps-0.3.0/extrasteps/R/minmax.R | 22 +- extrasteps-0.3.0/extrasteps/R/robust.R | 24 +- extrasteps-0.3.0/extrasteps/R/time_event.R | 47 ++--- extrasteps-0.3.0/extrasteps/R/unit_normalize.R | 24 +- extrasteps-0.3.0/extrasteps/README.md | 4 extrasteps-0.3.0/extrasteps/man/step_date_after.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_date_before.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_date_nearest.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_difftime.Rd | 19 -- extrasteps-0.3.0/extrasteps/man/step_encoding_binary.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_encoding_frequency.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_maxabs.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_minmax.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_robust.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_time_event.Rd | 34 +-- extrasteps-0.3.0/extrasteps/man/step_unit_normalize.Rd | 22 +- extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_after.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_before.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_nearest.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/difftime.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/maxabs.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/minmax.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/robust.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/time_event.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/unit_normalize.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/test-date_after.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-date_before.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-date_nearest.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-maxabs.R | 4 extrasteps-0.3.0/extrasteps/tests/testthat/test-minmax.R | 4 extrasteps-0.3.0/extrasteps/tests/testthat/test-robust.R | 53 ++++- extrasteps-0.3.0/extrasteps/tests/testthat/test-time_event.R | 25 +- extrasteps-0.3.0/extrasteps/tests/testthat/test-unit_normalize.R | 36 ++- 48 files changed, 676 insertions(+), 549 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using
MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many
other sources.
Author: Steven L. Scott [aut, cre]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between bsts versions 0.9.10 dated 2024-01-17 and 0.9.11 dated 2025-09-05
DESCRIPTION | 23 ++++--- MD5 | 58 ++++++++++---------- inst/tests/tests/testthat/test-dirm.R | 4 - inst/tests/tests/testthat/test-dynamic-regression.R | 14 +++- inst/tests/tests/testthat/test-goog.R | 4 - inst/tests/tests/testthat/test-multivariate.R | 2 inst/tests/tests/testthat/test-plot-components.R | 3 - inst/tests/tests/testthat/test-poisson.R | 14 ++-- inst/tests/tests/testthat/test-prediction.R | 6 +- inst/tests/tests/testthat/test-regressionholiday.R | 6 +- inst/tests/tests/testthat/test-student.R | 10 +-- inst/tests/tests/testthat/test-trig.R | 2 inst/tests/testthat/test-dirm.R | 4 - inst/tests/testthat/test-dynamic-regression.R | 14 +++- inst/tests/testthat/test-goog.R | 4 - inst/tests/testthat/test-multivariate.R | 2 inst/tests/testthat/test-plot-components.R | 3 - inst/tests/testthat/test-poisson.R | 14 ++-- inst/tests/testthat/test-prediction.R | 6 +- inst/tests/testthat/test-regressionholiday.R | 6 +- inst/tests/testthat/test-student.R | 10 +-- inst/tests/testthat/test-trig.R | 2 man/add.dynamic.regression.Rd | 21 +++---- man/add.monthly.annual.cycle.Rd | 2 man/bsts.Rd | 4 - man/descriptive-plots.Rd | 12 ++-- man/mbsts.Rd | 9 +-- man/plot.bsts.mixed.Rd | 3 - man/to.posixt.Rd | 6 +- man/wide.to.long.Rd | 7 +- 30 files changed, 142 insertions(+), 133 deletions(-)
Title: A Minimalist Web Framework for R
Description: A minimalist web framework for developing application programming
interfaces in R that provides a flexible framework for handling common
HTTP-requests, errors, logging, and an ability to integrate any R code as
server middle-ware.
Author: Hans Martin [aut],
Jonathan Callahan [aut, cre]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between beakr versions 0.4.3 dated 2021-04-06 and 0.4.4 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 36 ++++---- NEWS.md | 6 + R/Beakr.R | 102 +++++++++--------------- R/Error.R | 45 ++++------ R/Listener.R | 50 +++++------- R/Middleware.R | 68 ++++++---------- R/Request.R | 125 +++++++++++------------------- R/Response.R | 134 +++++++++++++++----------------- R/Router.R | 146 ++++++++++++++--------------------- README.md | 31 ++++--- man/Beakr.Rd | 105 +++++++++++-------------- man/Error.Rd | 63 ++++++++------- man/Listener.Rd | 65 ++++++++------- man/Middleware.Rd | 73 +++++++++-------- man/Request.Rd | 162 +++++++++++++++++++++------------------ man/Response.Rd | 210 ++++++++++++++++++++++++++++++--------------------- man/Router.Rd | 120 ++++++++++++++++------------- man/beakr-package.Rd | 21 ++++- 19 files changed, 778 insertions(+), 792 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.
Author: Charles Taragin [aut, cre],
Michael Sandfort [aut],
Shlok Goyal [ctb]
Maintainer: Charles Taragin <ctaragin+antitrustr@gmail.com>
Diff between antitrust versions 0.99.26 dated 2022-08-24 and 0.99.29 dated 2025-09-05
DESCRIPTION | 13 MD5 | 112 NAMESPACE | 202 R/AIDSFunctions.R | 918 ++-- R/AggregateGamesMethods.R |only R/AntitrustClasses.R | 230 - R/Auction2ndLogitFunctions.R | 706 +-- R/AuctionClasses.R | 662 +-- R/BargainingLogitFunctions.R | 463 +- R/BertrandClasses.R | 720 +-- R/BertrandRUMClasses.R | 1096 ++--- R/CESFunctions.R | 786 +-- R/CMCRBertrandFunctions.R | 618 +- R/CMCRMethods.R | 514 +- R/CVMethods.R | 787 +-- R/CostMethods.R | 805 +-- R/CournotFunctions.R | 821 +-- R/HypoMonMethods.R | 1274 +++-- R/LogitFunctions.R | 1458 +++--- R/MarginsMethods.R | 1272 +++-- R/OutputMethods.R | 1872 ++++---- R/OwnershipMethods.R | 410 - R/PSMethods.R | 630 +- R/ParamsMethods.R | 5872 ++++++++++++++------------- R/PlotMethods.R | 254 - R/PriceDeltaMethods.R | 642 +- R/PricesMethods.R | 1680 ++++--- R/SimFunctions.R | 1062 ++-- R/SummaryMethods.R | 1299 +++--- R/UPPMethods.R | 242 - R/VerticalClasses.R | 200 R/VerticalFunctions.R | 727 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Reference.R | 8 inst/doc/Reference.Rmd | 4639 ++++++++++----------- inst/doc/Reference.html | 8428 +++++++++++++++++++-------------------- man/Antitrust-Class.Rd | 3 man/Auction2ndLogit-Functions.Rd | 4 man/Bargaining-Classes.Rd | 76 man/BargainingLogit-Functions.Rd | 4 man/BertrandRUM-Classes.Rd | 3 man/CES-Functions.Rd | 4 man/CMCRBertrand-Functions.Rd | 7 man/Cournot-Functions.Rd | 5 man/Logit-Functions.Rd | 36 man/Margins-Methods.Rd | 8 man/MarginsAG-Methods.Rd |only man/Output-Methods.Rd | 2 man/PS-methods.Rd | 2 man/Params-Methods.Rd | 3 man/PriceDelta-Methods.Rd | 36 man/Sim-Functions.Rd | 53 man/SupplyChain-Functions.Rd | 28 man/Vertical-Classes.Rd | 3 man/defineMarketTools-methods.Rd | 34 man/summary-methods.Rd | 13 vignettes/Reference.Rmd | 4639 ++++++++++----------- 58 files changed, 23671 insertions(+), 22714 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-10 0.1.0
Title: Collinearity Detection using Redefined Variance Inflation Factor
and Graphical Methods
Description: The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. The objective of this package is to detect it using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation. For more details see Salmerón R., García C.B. and García J. (2018) <doi:10.1080/00949655.2018.1463376>, Salmerón, R., Rodríguez, A. and García C. (2020) <doi:10.1007/s00180-019-00922-x>, Salmerón, R., García, C.B, Rodríguez, A. and García, C. (2022) <doi:10.32614/RJ-2023-010>, Salmerón, R., García, C.B. and García, J. (2025) <doi:10.1007/s10614-024-10575-8> and Salmerón, R., García, C.B, García J. (2023, working paper) <doi:10.48550/arXiv.2005.02245>. You can also view the package vignette using 'browseVignettes("rvif")', the package website using 'browseURL(system.file("docs/index.html", package = "rvif"))' or version control on GitHub (<https: [...truncated...]
Author: R. Salmeron [aut, cre],
C.B. Garcia [aut]
Maintainer: R. Salmeron <romansg@ugr.es>
This is a re-admission after prior archival of version 3.0 dated 2025-07-29
Diff between rvif versions 3.0 dated 2025-07-29 and 3.1 dated 2025-09-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/docs/index.html | 6 +++--- inst/docs/pkgdown.yml | 2 +- tests/testthat/test-cv_vif.R | 23 ++++++----------------- tests/testthat/test-cv_vif_plot.R | 6 ++---- tests/testthat/test-multicollinearity.R | 13 ------------- tests/testthat/test-rvifs.R | 20 ++++++++------------ 8 files changed, 31 insertions(+), 61 deletions(-)
Title: Visualization of Patient Profiles
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
as demography, concomitant medication.
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
or can be embedded in custom report(s).
Author: Laure Cougnaud [aut, cre],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between patientProfilesVis versions 2.0.9 dated 2024-06-18 and 2.0.10 dated 2025-09-05
DESCRIPTION | 10 MD5 | 18 R/report_combineVerticallyGGplot.R | 2 R/subjectProfileTextPlot.R | 4 build/vignette.rds |binary inst/NEWS | 2 inst/doc/patientProfiles-template-SDTM.R | 94 +- inst/doc/patientProfiles-template-SDTM.html | 261 ++++--- inst/doc/patientProfilesVis-introduction.R | 504 +++++++------- inst/doc/patientProfilesVis-introduction.html | 921 ++++++++++++++++---------- 10 files changed, 1063 insertions(+), 753 deletions(-)
More information about patientProfilesVis at CRAN
Permanent link
Title: Mosquito Gene Drive Explorer
Description: Provides a model designed to be a reliable testbed where various gene
drive interventions for mosquito-borne diseases control. It is being developed to
accommodate the use of various mosquito-specific gene drive systems within a
population dynamics framework that allows migration of individuals between patches
in landscape. Previous work developing the population dynamics can be found in Deredec et al.
(2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>,
and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017)
<doi:10.1038/s41598-017-02744-7>.
Author: Hector Manuel Sanchez Castellanos [aut, cre],
Jared Bennett [aut],
Sean Wu [aut],
John M. Marshall [aut]
Maintainer: Hector Manuel Sanchez Castellanos <sanchez.hmsc@berkeley.edu>
This is a re-admission after prior archival of version 1.6.0 dated 2020-10-05
Diff between MGDrivE versions 1.6.0 dated 2020-10-05 and 1.6.2 dated 2025-09-05
MGDrivE-1.6.0/MGDrivE/R/Cube-SplitDrive.R |only MGDrivE-1.6.2/MGDrivE/DESCRIPTION | 14 MGDrivE-1.6.2/MGDrivE/MD5 | 265 MGDrivE-1.6.2/MGDrivE/NAMESPACE | 16 MGDrivE-1.6.2/MGDrivE/NEWS.md | 35 MGDrivE-1.6.2/MGDrivE/R/Cube-ASmidler.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-AlleleSail.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-Auxiliary.R | 26 MGDrivE-1.6.2/MGDrivE/R/Cube-CLEAVRMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CLEAVRX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CRISPR2MF_SM.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CRISPR2X.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ClvR.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ClvR2.R | 18 MGDrivE-1.6.2/MGDrivE/R/Cube-ConfinableHoming.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ConfinableHomingX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ECHACR.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ECHACRX.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ImmunizingReversalMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ImmunizingReversalX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-JOHNConfineableHomingWithRandB.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ShredderMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ShredderY.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveY.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-tGD.R | 11 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Auxiliary.R | 36 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Graphics.R | 2 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Releases.R | 3 MGDrivE-1.6.2/MGDrivE/R/MGDrivE.R | 4 MGDrivE-1.6.2/MGDrivE/R/Network-Class.R | 42 MGDrivE-1.6.2/MGDrivE/R/Network-Migration.R | 4 MGDrivE-1.6.2/MGDrivE/R/Network-Parameters.R | 12 MGDrivE-1.6.2/MGDrivE/R/Network-Simulation.R | 2 MGDrivE-1.6.2/MGDrivE/R/Patch-Class.R | 8 MGDrivE-1.6.2/MGDrivE/R/Patch-Methods.R | 14 MGDrivE-1.6.2/MGDrivE/R/Patch-Migration.R | 2 MGDrivE-1.6.2/MGDrivE/R/Patch-Simulation.R | 122 MGDrivE-1.6.2/MGDrivE/R/RcppExports.R | 11 MGDrivE-1.6.2/MGDrivE/README.md | 2 MGDrivE-1.6.2/MGDrivE/build/partial.rdb |binary MGDrivE-1.6.2/MGDrivE/build/vignette.rds |binary MGDrivE-1.6.2/MGDrivE/inst/CITATION | 4 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.R | 86 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.Rmd | 71 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.html | 3555 +++++----- MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.R | 6 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.Rmd | 56 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.html | 784 +- MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.R | 296 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.Rmd | 12 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.html | 1554 ++-- MGDrivE-1.6.2/MGDrivE/man/MGDrivE-Cube.Rd | 21 MGDrivE-1.6.2/MGDrivE/man/MGDrivE-Model.Rd | 3 MGDrivE-1.6.2/MGDrivE/man/Network.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/Patch.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/basicRepeatedReleases.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcAquaticStageSurvivalProbability.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcAverageGenerationTime.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcDensityDependentDeathRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcHurdleExpKernel.Rd | 4 MGDrivE-1.6.2/MGDrivE/man/calcLarvalDist.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcLarvalPopEquilibrium.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcLarvalStageMortalityRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcPopulationGrowthRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcQuantiles.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeASmidler.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeAlleleSail.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeCLEAVRMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeCLEAVRX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeClvR.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeClvR2.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHoming.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHomingJOHN.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHomingX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeECHACR.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeECHACRX.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeHomingDriveSM.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeImmunizingReversalMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeImmunizingReversalX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeModifiers.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/cubeSplitDrive.Rd | 4 MGDrivE-1.6.2/MGDrivE/man/cubeSplitDriveX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeSplitDriveY.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXHomingDeposition.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXShredderMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXShredderY.Rd |only MGDrivE-1.6.2/MGDrivE/man/get_alpha_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_beta_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_conF_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_conM_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_drivecubeindex_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_eta_Network.Rd | 9 MGDrivE-1.6.2/MGDrivE/man/get_femalePop_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_genotypesID_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_genotypesN_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_malePop_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_muAd_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_muAq_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_nPatch_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_omega_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_patchReleases_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_phi_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_s_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_tNow_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_tau_Network.Rd | 7 MGDrivE-1.6.2/MGDrivE/man/get_timeAq_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_xiF_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_xiM_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/ggColUtility.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/normalise.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Migration_Deterministic_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Migration_Stochastic_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_PopDynamics_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_adultDeath_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_adultDeath_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggReleases_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_initOutput_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_larvaDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_larvaDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_mating_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_mating_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_migrationIn_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_oviposit_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_oviposit_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupaDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupaDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupation_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupation_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_releases_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_writeOutput_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/quantileC.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/rDirichlet.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/reset_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_NetworkPointer_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_initialPopulation_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_population_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_population_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-Auxilary.cpp | 8 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-DistanceFunctions.cpp | 1 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-Kernels.cpp | 130 MGDrivE-1.6.2/MGDrivE/src/RcppExports.cpp | 14 MGDrivE-1.6.2/MGDrivE/vignettes/diagram.png |only MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_examples.Rmd | 71 MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_math.Rmd | 56 MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_run.Rmd | 12 150 files changed, 4139 insertions(+), 3355 deletions(-)
Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, and identify cut points. Also includes three example data
sets of administrative education records for learning how to process records
with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between eeptools versions 1.2.5 dated 2023-06-01 and 1.2.7 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 47 +++--- NEWS.md | 9 + R/eeptools-data.R |only R/eeptools-package.r | 121 ---------------- R/eeptools.R | 2 R/modsims.R | 4 R/moves_calc.R | 2 R/proficiency_tools.R | 6 R/theme_dpi.R | 16 +- build/vignette.rds |binary inst/doc/intro.html | 357 +++++++++++++++++++++++------------------------- man/crosstabplot.Rd | 2 man/eeptools.Rd | 19 +- man/gelmansim.Rd | 4 man/midsch.Rd | 2 man/moves_calc.Rd | 2 man/profpoly.Rd | 2 man/profpoly.data.Rd | 2 man/stuatt.Rd | 2 man/stulevel.Rd | 2 man/theme_dpi.Rd | 4 man/theme_dpi_map.Rd | 4 man/theme_dpi_map2.Rd | 4 man/theme_dpi_mapPNG.Rd | 4 25 files changed, 262 insertions(+), 363 deletions(-)
Title: Solve the Empirical Bayes Normal Means Problem
Description: Provides simple, fast, and stable functions to fit the normal
means model using empirical Bayes. For available models and details, see
function ebnm(). Our JSS article,
Willwerscheid, Carbonetto, and Stephens (2025) <doi:10.18637/jss.v114.i03>,
provides a detailed introduction to the package.
Author: Jason Willwerscheid [aut],
Matthew Stephens [aut],
Peter Carbonetto [aut, cre],
Andrew Goldstein [ctb],
Yusha Liu [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between ebnm versions 1.1-2 dated 2023-10-12 and 1.1-38 dated 2025-09-05
ebnm-1.1-2/ebnm/inst/doc/ebnm.R |only ebnm-1.1-2/ebnm/inst/doc/ebnm.Rmd |only ebnm-1.1-2/ebnm/inst/doc/ebnm.html |only ebnm-1.1-2/ebnm/vignettes/ebnm.Rmd |only ebnm-1.1-38/ebnm/DESCRIPTION | 17 - ebnm-1.1-38/ebnm/MD5 | 86 +++-- ebnm-1.1-38/ebnm/NAMESPACE | 3 ebnm-1.1-38/ebnm/R/check_fn.R |only ebnm-1.1-38/ebnm/R/ebnm.R | 159 +++++++--- ebnm-1.1-38/ebnm/R/ebnm_fns.R | 90 +++-- ebnm-1.1-38/ebnm/R/ebnm_methods.R | 45 +- ebnm-1.1-38/ebnm/R/generalized_binary.R | 34 +- ebnm-1.1-38/ebnm/R/grid_selection.R | 2 ebnm-1.1-38/ebnm/R/infer_prior_family.R | 1 ebnm-1.1-38/ebnm/R/point_exponential.R | 1 ebnm-1.1-38/ebnm/R/point_laplace.R | 3 ebnm-1.1-38/ebnm/R/point_normal.R | 1 ebnm-1.1-38/ebnm/R/rebayes.R | 13 ebnm-1.1-38/ebnm/R/workhorse_parametric.R | 7 ebnm-1.1-38/ebnm/build/partial.rdb |only ebnm-1.1-38/ebnm/build/vignette.rds |binary ebnm-1.1-38/ebnm/inst/CITATION | 35 +- ebnm-1.1-38/ebnm/inst/code |only ebnm-1.1-38/ebnm/inst/doc/baseball.R |only ebnm-1.1-38/ebnm/inst/doc/baseball.Rmd |only ebnm-1.1-38/ebnm/inst/doc/baseball.html |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.R |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.Rmd |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.html |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.R |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.Rmd |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.html |only ebnm-1.1-38/ebnm/man/confint.ebnm.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm.Rd | 76 +++- ebnm-1.1-38/ebnm/man/ebnm_check_fn.Rd |only ebnm-1.1-38/ebnm/man/ebnm_generalized_binary.Rd | 12 ebnm-1.1-38/ebnm/man/ebnm_normal.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_normal_scale_mixture.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_npmle.Rd | 16 - ebnm-1.1-38/ebnm/man/ebnm_point_exponential.Rd | 33 +- ebnm-1.1-38/ebnm/man/ebnm_point_laplace.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_point_mass.Rd | 6 ebnm-1.1-38/ebnm/man/ebnm_point_normal.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_unimodal.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_nonnegative.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_nonpositive.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_symmetric.Rd | 11 ebnm-1.1-38/ebnm/tests/testthat/test_optmethod.R | 108 ++++-- ebnm-1.1-38/ebnm/tests/testthat/test_point_mass.R | 4 ebnm-1.1-38/ebnm/tests/testthat/test_prior_family_inference.R | 3 ebnm-1.1-38/ebnm/vignettes/baseball.Rmd |only ebnm-1.1-38/ebnm/vignettes/ebnm.bib | 18 + ebnm-1.1-38/ebnm/vignettes/extending_ebnm.Rmd |only ebnm-1.1-38/ebnm/vignettes/shrink_intro.Rmd |only 54 files changed, 588 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-18 1.1.0
2019-05-08 1.0.0
More information about connector.databricks at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-18 1.0.0
2023-10-15 0.1.8
2023-09-05 0.1.7
2023-07-04 0.1.6
2023-05-08 0.1.5
2022-03-30 0.1.4
2021-10-24 0.1.3
2021-10-17 0.1.3
2021-10-08 0.1.2
2020-11-24 0.1.1
2020-09-29 0.1.0
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the density, EM, and censored EM version (Bartoš & Schimmack, 2022,
<doi:10.15626/MP.2021.2720>; Schimmack & Bartoš, 2023, <doi: 10.1371/journal.pone.0290084>),
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.4.4 dated 2025-08-20 and 2.4.5 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/tools.R | 4 +++- build/partial.rdb |binary tests/testthat/test-zcurve.R | 6 +++--- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Easily Install and Load the 'Tidymodels' Packages
Description: The tidy modeling "verse" is a collection of packages for
modeling and statistical analysis that share the underlying design
philosophy, grammar, and data structures of the tidyverse.
Author: Max Kuhn [aut, cre] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tidymodels versions 1.3.0 dated 2025-02-21 and 1.4.0 dated 2025-09-05
DESCRIPTION | 30 +- LICENSE | 2 MD5 | 36 +- NAMESPACE | 2 NEWS.md | 8 R/attach.R | 28 +- R/conflicts.R | 44 +-- R/emails.R | 9 R/imports.R | 1 R/tags.R | 23 + R/tidymodels_prefer.R | 138 ++++++---- R/update.R | 54 +++ README.md | 18 - build/vignette.rds |binary inst/doc/Tags.R | 4 inst/doc/Tags.Rmd | 7 inst/rmarkdown/templates/model-analysis/skeleton/skeleton.Rmd | 22 - man/tidymodels-package.Rd | 2 vignettes/Tags.Rmd | 7 19 files changed, 288 insertions(+), 147 deletions(-)
Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of
stepped wedge cluster randomized trials (SW CRT) based on a repeated
cross-sectional or cohort sampling scheme (Hussey MA and Hughes JP (2007)
Contemporary Clinical Trials 28:182-191).
Author: Jim Hughes [aut, cre],
Navneet R. Hakhu [aut],
Emily Voldal [aut],
Fan Xia [aut]
Maintainer: Jim Hughes <jphughes@uw.edu>
Diff between swCRTdesign versions 4.0 dated 2023-08-25 and 4.1 dated 2025-09-04
DESCRIPTION | 36 +++++- MD5 | 41 ++++--- NAMESPACE | 4 R/swGlmPwr.R | 192 +++++++++++++++++++++-------------- R/swGlmSiz.R |only R/swPlot.R | 48 +++++--- R/swPwr.r | 132 +++++++++++++++++------- R/swSim.R | 6 - R/swSim2.R |only R/swSimPwr.R | 244 ++++++++++++++++++++++++++++++--------------- R/swSiz.R |only R/swSummary.R | 53 +++++++-- README.md |only man/ReleaseNotes.Rd | 46 +++----- man/blkDiag.Rd | 2 man/swCRTdesign-package.Rd | 75 +++++++++++++ man/swDsn.Rd | 10 - man/swGlmPwr.Rd | 63 ++++++++++- man/swGlmSiz.Rd |only man/swPlot.Rd | 13 +- man/swPwr.Rd | 88 +++++++++++----- man/swSim2.Rd |only man/swSimPwr.Rd | 17 ++- man/swSiz.Rd |only man/swSummary.Rd | 14 ++ 25 files changed, 759 insertions(+), 325 deletions(-)
Title: General Effect Modelling
Description: Two-step modeling with separation of sources of variation through analysis of variance and subsequent multivariate
modeling through a range of unsupervised and supervised statistical methods. Separation can focus on removal of interfering
effects or isolation of effects of interest. EF Mosleth et al. (2021) <doi:10.1038/s41598-021-82388-w> and EF Mosleth et al.
(2020) <doi:10.1016/B978-0-12-409547-2.14882-6>.
Author: Kristian Hovde Liland [aut, cre],
Ellen Faergestad Mosleth [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between gemR versions 1.2.1 dated 2025-06-27 and 1.2.2 dated 2025-09-04
gemR-1.2.1/gemR/man/pls.Rd |only gemR-1.2.2/gemR/DESCRIPTION | 13 ++++++------ gemR-1.2.2/gemR/MD5 | 26 ++++++++++++------------ gemR-1.2.2/gemR/NAMESPACE | 2 - gemR-1.2.2/gemR/NEWS | 22 ++++++++++++++++---- gemR-1.2.2/gemR/R/elastic.R | 8 ++++--- gemR-1.2.2/gemR/R/knock.in.R | 4 +++ gemR-1.2.2/gemR/R/neuralnet.R | 3 ++ gemR-1.2.2/gemR/R/pls.R | 41 +++++++++++++++++---------------------- gemR-1.2.2/gemR/R/sca.R | 2 - gemR-1.2.2/gemR/README.md | 3 +- gemR-1.2.2/gemR/man/knock.in.Rd | 4 +++ gemR-1.2.2/gemR/man/pls.GEM.Rd |only gemR-1.2.2/gemR/man/reexports.Rd | 5 ++-- gemR-1.2.2/gemR/man/sca.Rd | 2 - 15 files changed, 79 insertions(+), 56 deletions(-)
Title: Manipulate ACLED Data
Description: Tools working with data from ACLED (Armed Conflict Location and Event Data). Functions include simplified access to ACLED's API (<https://apidocs.acleddata.com/>), methods for keeping local versions of ACLED data up-to-date, and functions for common ACLED data transformations.
Author: Armed Conflict Location and Event Data ACLED [cph],
Trey Billing [aut, cre],
Lucas Fagliano [aut],
Katayoun Kishi [ctb]
Maintainer: Trey Billing <t.billing@acleddata.com>
Diff between acledR versions 0.1.0 dated 2025-02-24 and 1.0.0 dated 2025-09-04
acledR-0.1.0/acledR/vignettes/workflow.png |only acledR-1.0.0/acledR/DESCRIPTION | 10 acledR-1.0.0/acledR/MD5 | 67 +- acledR-1.0.0/acledR/NAMESPACE | 2 acledR-1.0.0/acledR/NEWS.md | 5 acledR-1.0.0/acledR/R/acled_access.R | 5 acledR-1.0.0/acledR/R/acled_api.R | 246 ++++++---- acledR-1.0.0/acledR/R/acled_auth.R |only acledR-1.0.0/acledR/R/acled_deletions_api.R | 180 ++++++- acledR-1.0.0/acledR/R/acled_transform_interaction.R | 5 acledR-1.0.0/acledR/R/acled_transform_longer.R | 6 acledR-1.0.0/acledR/R/acled_transform_wider.R | 6 acledR-1.0.0/acledR/R/acled_update.R | 98 ++- acledR-1.0.0/acledR/README.md | 7 acledR-1.0.0/acledR/inst/doc/get_started.R | 16 acledR-1.0.0/acledR/inst/doc/get_started.Rmd | 32 - acledR-1.0.0/acledR/inst/doc/get_started.html | 174 +++---- acledR-1.0.0/acledR/man/acled_access.Rd | 8 acledR-1.0.0/acledR/man/acled_api.Rd | 23 acledR-1.0.0/acledR/man/acled_auth.Rd |only acledR-1.0.0/acledR/man/acled_deletions_api.Rd | 9 acledR-1.0.0/acledR/man/acled_transform_interaction.Rd | 5 acledR-1.0.0/acledR/man/acled_transform_longer.Rd | 6 acledR-1.0.0/acledR/man/acled_transform_wider.Rd | 6 acledR-1.0.0/acledR/man/acled_update.Rd | 20 acledR-1.0.0/acledR/tests/testthat/setup-acled_api.R | 84 ++- acledR-1.0.0/acledR/tests/testthat/setup-acled_deletions_api.R | 18 acledR-1.0.0/acledR/tests/testthat/setup-acled_transform_interaction.R | 8 acledR-1.0.0/acledR/tests/testthat/setup-acled_update.R | 18 acledR-1.0.0/acledR/tests/testthat/test-acled_access.R | 2 acledR-1.0.0/acledR/tests/testthat/test-acled_api.R | 237 +++------ acledR-1.0.0/acledR/tests/testthat/test-acled_deletions_api.R | 80 --- acledR-1.0.0/acledR/tests/testthat/test-acled_transform_longer.R | 13 acledR-1.0.0/acledR/tests/testthat/test-acled_transform_wider.R | 26 - acledR-1.0.0/acledR/tests/testthat/test-acled_update.R | 45 - acledR-1.0.0/acledR/vignettes/get_started.Rmd | 32 - 36 files changed, 815 insertions(+), 684 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Franziska Eidloth [aut],
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.8 dated 2025-07-10 and 0.9.9 dated 2025-09-04
wrappedtools-0.9.8/wrappedtools/tests/testthat/compare2numvars_out.rda |only wrappedtools-0.9.8/wrappedtools/tests/testthat/test-compare_2_numvars.R |only wrappedtools-0.9.9/wrappedtools/DESCRIPTION | 10 wrappedtools-0.9.9/wrappedtools/MD5 | 24 wrappedtools-0.9.9/wrappedtools/NEWS.md | 4 wrappedtools-0.9.9/wrappedtools/R/basefunctions.R | 244 wrappedtools-0.9.9/wrappedtools/R/pkgstart.R | 115 wrappedtools-0.9.9/wrappedtools/R/tests.R | 2741 +++++----- wrappedtools-0.9.9/wrappedtools/inst/doc/wrappedtools.html | 6 wrappedtools-0.9.9/wrappedtools/man/ColSeeker.Rd | 8 wrappedtools-0.9.9/wrappedtools/man/bt.Rd | 2 wrappedtools-0.9.9/wrappedtools/man/compare_n_numvars.Rd | 1 wrappedtools-0.9.9/wrappedtools/man/flex2rmd.Rd | 4 wrappedtools-0.9.9/wrappedtools/man/identical_cols.Rd | 2 14 files changed, 1588 insertions(+), 1573 deletions(-)
Title: Connect to the 'nettskjema.no' API of the University of Oslo
Description: Enables users to retrieve data, meta-data, and codebooks from
<https://nettskjema.no/>. The data from the API is richer than from
the online data portal. This package is not developed
by the University of Oslo IT. Mowinckel (2021) <doi:10.5281/zenodo.4745481>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Trym Nohr Fjoertoft [ctb]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between nettskjemar versions 1.0.2 dated 2025-06-06 and 1.0.3 dated 2025-09-04
nettskjemar-1.0.2/nettskjemar/README.md |only nettskjemar-1.0.2/nettskjemar/inst/Nettskjema_api.png |only nettskjemar-1.0.2/nettskjemar/inst/Nettskjema_api.svg |only nettskjemar-1.0.2/nettskjemar/tests/fixtures |only nettskjemar-1.0.2/nettskjemar/vignettes/attachments.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/authentication.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/forms.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/labelled_data.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/metadata.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/nettskjemar.Rmd.orig |only nettskjemar-1.0.2/nettskjemar/vignettes/submissions.Rmd.orig |only nettskjemar-1.0.3/nettskjemar/DESCRIPTION | 13 nettskjemar-1.0.3/nettskjemar/MD5 | 190 ++- nettskjemar-1.0.3/nettskjemar/NAMESPACE | 1 nettskjemar-1.0.3/nettskjemar/NEWS.md | 8 nettskjemar-1.0.3/nettskjemar/R/nettskjemar-package.R | 4 nettskjemar-1.0.3/nettskjemar/R/ns-auth.R | 10 nettskjemar-1.0.3/nettskjemar/R/ns-data.R | 13 nettskjemar-1.0.3/nettskjemar/R/ns-data_labels.R | 24 nettskjemar-1.0.3/nettskjemar/R/ns-form.R | 29 nettskjemar-1.0.3/nettskjemar/R/ns-me.R | 7 nettskjemar-1.0.3/nettskjemar/R/ns-meta.R | 12 nettskjemar-1.0.3/nettskjemar/R/ns-sitrep.R |only nettskjemar-1.0.3/nettskjemar/R/ns-submission.R | 9 nettskjemar-1.0.3/nettskjemar/R/utils.R | 22 nettskjemar-1.0.3/nettskjemar/build/partial.rdb |binary nettskjemar-1.0.3/nettskjemar/build/vignette.rds |binary nettskjemar-1.0.3/nettskjemar/inst/WORDLIST | 121 +- nettskjemar-1.0.3/nettskjemar/inst/_vcr |only nettskjemar-1.0.3/nettskjemar/inst/doc/attachments.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/attachments.Rmd | 98 - nettskjemar-1.0.3/nettskjemar/inst/doc/attachments.html | 122 +- nettskjemar-1.0.3/nettskjemar/inst/doc/authentication.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/authentication.Rmd | 73 - nettskjemar-1.0.3/nettskjemar/inst/doc/authentication.html | 106 -- nettskjemar-1.0.3/nettskjemar/inst/doc/custom_requests.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/custom_requests.Rmd |only nettskjemar-1.0.3/nettskjemar/inst/doc/custom_requests.html |only nettskjemar-1.0.3/nettskjemar/inst/doc/forms.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/forms.Rmd | 59 - nettskjemar-1.0.3/nettskjemar/inst/doc/forms.html | 135 +- nettskjemar-1.0.3/nettskjemar/inst/doc/labelled_data.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/labelled_data.Rmd | 344 ------ nettskjemar-1.0.3/nettskjemar/inst/doc/labelled_data.html | 247 +--- nettskjemar-1.0.3/nettskjemar/inst/doc/metadata.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/metadata.Rmd | 123 -- nettskjemar-1.0.3/nettskjemar/inst/doc/metadata.html | 33 nettskjemar-1.0.3/nettskjemar/inst/doc/nettskjemar.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/nettskjemar.Rmd | 295 ----- nettskjemar-1.0.3/nettskjemar/inst/doc/nettskjemar.html | 427 ++------ nettskjemar-1.0.3/nettskjemar/inst/doc/submissions.R |only nettskjemar-1.0.3/nettskjemar/inst/doc/submissions.Rmd | 22 nettskjemar-1.0.3/nettskjemar/inst/doc/submissions.html | 529 +++++++++- nettskjemar-1.0.3/nettskjemar/inst/nettskjemar.png |only nettskjemar-1.0.3/nettskjemar/inst/nettskjemar.svg |only nettskjemar-1.0.3/nettskjemar/man/figures/logo.png |binary nettskjemar-1.0.3/nettskjemar/man/nettskjemar-package.Rd | 2 nettskjemar-1.0.3/nettskjemar/man/ns_client.Rd | 3 nettskjemar-1.0.3/nettskjemar/man/ns_get_data.Rd | 13 nettskjemar-1.0.3/nettskjemar/man/ns_get_form_reports.Rd | 11 nettskjemar-1.0.3/nettskjemar/man/ns_get_forms.Rd | 10 nettskjemar-1.0.3/nettskjemar/man/ns_get_me.Rd | 7 nettskjemar-1.0.3/nettskjemar/man/ns_get_meta.Rd | 10 nettskjemar-1.0.3/nettskjemar/man/ns_get_submission.Rd | 9 nettskjemar-1.0.3/nettskjemar/man/ns_sitrep.Rd |only nettskjemar-1.0.3/nettskjemar/tests/_vcr |only nettskjemar-1.0.3/nettskjemar/tests/testthat/helpers.R | 18 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-data_labels.R | 6 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-ns-attachment.R | 11 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-ns-auth.R | 20 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-ns-codebook.R | 7 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-ns-me.R | 4 nettskjemar-1.0.3/nettskjemar/tests/testthat/test-ns-meta.R | 12 nettskjemar-1.0.3/nettskjemar/vignettes/_vcr |only nettskjemar-1.0.3/nettskjemar/vignettes/attachments.Rmd | 98 - nettskjemar-1.0.3/nettskjemar/vignettes/authentication.Rmd | 73 - nettskjemar-1.0.3/nettskjemar/vignettes/custom_requests.Rmd |only nettskjemar-1.0.3/nettskjemar/vignettes/forms.Rmd | 59 - nettskjemar-1.0.3/nettskjemar/vignettes/labelled_data.Rmd | 344 ------ nettskjemar-1.0.3/nettskjemar/vignettes/metadata.Rmd | 123 -- nettskjemar-1.0.3/nettskjemar/vignettes/nettskjemar.Rmd | 295 ----- nettskjemar-1.0.3/nettskjemar/vignettes/submissions.Rmd | 22 82 files changed, 1800 insertions(+), 2433 deletions(-)
Title: Accessing 'SimFin' Data
Description: Through simfinapi, you can intuitively access the 'SimFin'
Web-API (<https://www.simfin.com/>) to make 'SimFin' data easily
available in R. To obtain an 'SimFin' API key (and thus to use this
package), you need to register at <https://app.simfin.com/login>.
Author: Matthias Gomolka [aut, cre]
Maintainer: Matthias Gomolka <matthias.gomolka@posteo.de>
Diff between simfinapi versions 1.0.0 dated 2024-02-27 and 1.0.1 dated 2025-09-04
simfinapi-1.0.0/simfinapi/tests/testthat/test-sfa_load_statement.R |only simfinapi-1.0.1/simfinapi/DESCRIPTION | 10 simfinapi-1.0.1/simfinapi/MD5 | 56 +- simfinapi-1.0.1/simfinapi/NEWS.md | 4 simfinapi-1.0.1/simfinapi/R/call_api.R | 3 simfinapi-1.0.1/simfinapi/R/check_inputs.R | 204 +++++----- simfinapi-1.0.1/simfinapi/R/sfa_load__shares_outstanding.R | 22 - simfinapi-1.0.1/simfinapi/R/sfa_load_companies.R | 7 simfinapi-1.0.1/simfinapi/R/sfa_load_shareprices.R | 5 simfinapi-1.0.1/simfinapi/R/sfa_load_statement.R | 13 simfinapi-1.0.1/simfinapi/R/sfa_set_api_key.R | 4 simfinapi-1.0.1/simfinapi/R/utils.R | 5 simfinapi-1.0.1/simfinapi/R/zzz.R | 6 simfinapi-1.0.1/simfinapi/README.md | 107 +---- simfinapi-1.0.1/simfinapi/build/vignette.rds |binary simfinapi-1.0.1/simfinapi/inst/doc/simfinapi.R | 4 simfinapi-1.0.1/simfinapi/inst/doc/simfinapi.Rmd | 4 simfinapi-1.0.1/simfinapi/inst/doc/simfinapi.html | 1 simfinapi-1.0.1/simfinapi/man/figures/README-plot_data-1.png |binary simfinapi-1.0.1/simfinapi/man/sfa_load_common_shares_outstanding.Rd | 2 simfinapi-1.0.1/simfinapi/man/sfa_load_shareprices.Rd | 2 simfinapi-1.0.1/simfinapi/man/sfa_load_statements.Rd | 2 simfinapi-1.0.1/simfinapi/man/sfa_load_weighted_shares_outstanding.Rd | 2 simfinapi-1.0.1/simfinapi/man/sfa_set_api_key.Rd | 4 simfinapi-1.0.1/simfinapi/tests/testthat/test-call_api.R | 3 simfinapi-1.0.1/simfinapi/tests/testthat/test-sfa_load_companies.R | 19 simfinapi-1.0.1/simfinapi/tests/testthat/test-sfa_load_statements.R |only simfinapi-1.0.1/simfinapi/tests/testthat/test-sfa_set_cache_dir.R | 6 simfinapi-1.0.1/simfinapi/tests/testthat/test-sfa_set_key.R | 6 simfinapi-1.0.1/simfinapi/vignettes/simfinapi.Rmd | 4 30 files changed, 234 insertions(+), 271 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.12 dated 2023-12-06 and 2.13 dated 2025-09-04
DESCRIPTION | 16 +++++++-------- MD5 | 48 +++++++++++++++++++++++++++------------------- NAMESPACE | 11 ++++++++++ R/ILDS.r |only R/Morpho-package.R | 6 ++--- R/computeArea.r | 4 ++- R/icpmat.r | 29 +++++++++++++++++++++++++-- R/inscribeEllipse.r |only R/meshDist.r | 10 ++++----- R/meshDistMatrix.r | 2 - R/prcompfast.r | 2 - R/virtualMeshScan.r | 2 - R/warpmovie.matrix.r | 2 - inst/NEWS.Rd | 17 ++++++++++++++++ man/ILDS.Rd |only man/ILDSR2.Rd |only man/Morpho-package.Rd | 30 ++++++++++++++-------------- man/getOuterViewpoints.Rd | 2 - man/icpmat.Rd | 10 +++++++-- man/inscribeEllipse.Rd |only man/inscribeEllipseRot.Rd |only man/meshDist.Rd | 6 ++--- man/plot.ILDSR2.Rd |only man/render.Rd | 4 +-- man/visualize.Rd |only man/warpmovie3d.Rd | 2 - src/Makevars | 3 +- src/init.c | 4 +++ src/inscribeEllipse.cpp |only src/inscribeEllipse.h |only 30 files changed, 143 insertions(+), 67 deletions(-)
Title: Gradient-Based Recognition of Spatial Patterns in Environmental
Data
Description: Provides algorithms for detection of spatial patterns from oceanographic data using image processing methods based on Gradient Recognition.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between grec versions 1.6.1 dated 2025-01-23 and 1.6.2 dated 2025-09-04
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 3 +++ R/SpatRaster-class.R | 26 ++++++++------------------ R/grec-main.R | 8 ++++---- R/grec-package.R | 2 +- build/partial.rdb |binary man/getGradients.Rd | 8 ++++---- 9 files changed, 33 insertions(+), 39 deletions(-)
Title: Generalized Linear Models for Categorical Responses
Description: In statistical modeling, there is a wide variety of regression models for categorical dependent variables (nominal or ordinal data); yet, there is no software embracing all these models together in a uniform and generalized format. Following the methodology proposed by Peyhardi, Trottier, and Guédon (2015) <doi:10.1093/biomet/asv042>, we introduce 'GLMcat', an R package to estimate generalized linear models implemented under the unified specification (r, F, Z). Where r represents the ratio of probabilities (reference, cumulative, adjacent, or sequential), F the cumulative cdf function for the linkage, and Z, the design matrix. The package accompanies the paper "GLMcat: An R Package for Generalized Linear Models for Categorical Responses" in the Journal of Statistical Software, Volume 114, Issue 9 (see <doi:10.18637/jss.v114.i09>).
Author: Lorena Leon [aut, cre],
Jean Peyhardi [aut],
Catherine Trottier [aut]
Maintainer: Lorena Leon <ylorenaleonv@gmail.com>
Diff between GLMcat versions 0.2.7 dated 2024-09-20 and 1.0.0 dated 2025-09-04
DESCRIPTION | 10 - MD5 | 19 +-- NEWS.md | 7 + build/vignette.rds |binary inst/CITATION |only inst/doc/Discrete_CM_examples.pdf |binary inst/doc/GLMcat_tutorial.R | 4 inst/doc/GLMcat_tutorial.pdf |binary inst/doc/Var_sel_ex.pdf |binary man/discrete_cm.Rd | 207 +++++++++++++++++++------------------- man/glmcat.Rd | 175 ++++++++++++++++---------------- 11 files changed, 217 insertions(+), 205 deletions(-)
Title: Microsoft Finance Time Series Forecasting Framework
Description: Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time
Series Forecasting Framework, aka Finn, can be used to forecast any component of the income
statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time,
Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built
to meet the needs of financial analysts to better forecast their businesses within a company, and has
a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!
Author: Mike Tokic [aut, cre] ,
Aadharsh Kannan [aut]
Maintainer: Mike Tokic <mftokic@gmail.com>
Diff between finnts versions 0.5.0 dated 2024-10-25 and 0.6.0 dated 2025-09-04
DESCRIPTION | 10 +-- MD5 | 42 ++++++------- NEWS.md | 16 +++++ R/ensemble_models.R | 2 R/feature_selection.R | 14 +++- R/final_models.R | 25 +++++--- R/forecast_time_series.R | 3 R/hierarchy.R | 6 + R/models.R | 41 ++++++++++--- R/multistep_helper.R | 2 R/prep_data.R | 25 -------- R/prep_models.R | 37 +++++++++--- R/train_models.R | 58 ++++++++++++++++++- R/utility.R | 2 inst/doc/back-testing-and-hyperparameter-tuning.html | 10 +-- inst/doc/models-used-in-finnts.R | 10 +-- inst/doc/models-used-in-finnts.Rmd | 10 +-- inst/doc/models-used-in-finnts.html | 2 man/forecast_time_series.Rd | 3 man/prep_data.Rd | 3 man/prep_models.Rd | 7 +- vignettes/models-used-in-finnts.Rmd | 10 +-- 22 files changed, 222 insertions(+), 116 deletions(-)
Title: Epigenome-Wide Mediation Analysis Study
Description: DNA methylation is essential for human, and environment can change the DNA methylation
and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find
potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide.
For more information on the methods we used, please see the following references:
Tingley, D. (2014) <doi:10.18637/jss.v059.i05>,
Turner, S. D. (2018) <doi:10.21105/joss.00731>,
Rosseel, D. (2012) <doi:10.18637/jss.v048.i02>.
Author: Xiuquan Nie [aut, cph, cre],
Mengyi Wang [ctb, rev]
Maintainer: Xiuquan Nie <niexiuquan1995@foxmail.com>
Diff between EMAS versions 0.2.2 dated 2022-08-11 and 0.2.3 dated 2025-09-04
DESCRIPTION | 22 +++++++++------------- MD5 | 16 ++++++++-------- R/EMAS.manhattan.R | 2 +- R/Emas.R | 4 +--- R/Emas.parallel.R | 2 +- build/partial.rdb |binary man/EMAS.manhattan.Rd | 2 +- man/Emas.Rd | 4 +--- man/Emas.parallel.Rd | 2 +- 9 files changed, 23 insertions(+), 31 deletions(-)
Title: Ensemble Learning Framework for Diagnostic and Prognostic
Modeling
Description: Provides a framework to build and evaluate diagnosis or
prognosis models using stacking, voting, and bagging ensemble
techniques with various base learners. The package also includes
tools for visualization and interpretation of models. The development
version of the package is available on 'GitHub' at
<https://github.com/xiaojie0519/E2E>. The methods
are based on the foundational work of Breiman (1996) <doi:10.1007/BF00058655>
on bagging and Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1>
on stacking.
Author: Shanjie Luan [aut, cre]
Maintainer: Shanjie Luan <Luan20050519@163.com>
Diff between E2E versions 0.0.3 dated 2025-08-26 and 0.1.0 dated 2025-09-04
E2E-0.0.3/E2E/vignettes/Dia_SHAP_Example.pdf |only E2E-0.0.3/E2E/vignettes/Diagnostic_Matrix.pdf |only E2E-0.0.3/E2E/vignettes/Diagnostic_PRC.png |only E2E-0.0.3/E2E/vignettes/Diagnostic_ROC.pdf |only E2E-0.0.3/E2E/vignettes/Pro_SHAP_Example.pdf |only E2E-0.0.3/E2E/vignettes/Prognostic_KM.pdf |only E2E-0.0.3/E2E/vignettes/Prognostic_TDROC.pdf |only E2E-0.1.0/E2E/DESCRIPTION | 6 E2E-0.1.0/E2E/MD5 | 51 +- E2E-0.1.0/E2E/NAMESPACE | 3 E2E-0.1.0/E2E/R/Figure.R | 47 +- E2E-0.1.0/E2E/R/diagnosis.R | 513 +++++++++++++++--------- E2E-0.1.0/E2E/README.md | 4 E2E-0.1.0/E2E/build/vignette.rds |binary E2E-0.1.0/E2E/inst/doc/diagnostic-workflow.R | 23 - E2E-0.1.0/E2E/inst/doc/diagnostic-workflow.Rmd | 23 - E2E-0.1.0/E2E/inst/doc/diagnostic-workflow.html | 110 +---- E2E-0.1.0/E2E/inst/doc/getting-started.Rmd | 6 E2E-0.1.0/E2E/inst/doc/getting-started.html | 14 E2E-0.1.0/E2E/inst/doc/parameter-reference.Rmd |only E2E-0.1.0/E2E/inst/doc/parameter-reference.html |only E2E-0.1.0/E2E/inst/doc/prognostic-workflow.R | 2 E2E-0.1.0/E2E/inst/doc/prognostic-workflow.Rmd | 2 E2E-0.1.0/E2E/inst/doc/prognostic-workflow.html | 2 E2E-0.1.0/E2E/man/apply_dia.Rd | 85 ++- E2E-0.1.0/E2E/man/bagging_dia.Rd | 10 E2E-0.1.0/E2E/man/evaluate_model_dia.Rd | 13 E2E-0.1.0/E2E/man/evaluate_predictions_dia.Rd |only E2E-0.1.0/E2E/vignettes/diagnostic-workflow.Rmd | 23 - E2E-0.1.0/E2E/vignettes/getting-started.Rmd | 6 E2E-0.1.0/E2E/vignettes/parameter-reference.Rmd |only E2E-0.1.0/E2E/vignettes/prognostic-workflow.Rmd | 2 32 files changed, 499 insertions(+), 446 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.11 dated 2023-01-06 and 0.8.12 dated 2025-09-04
DESCRIPTION | 6 - MD5 | 60 +++++++++--------- NEWS.md | 8 ++ R/datasets.R | 10 +-- R/topicmodels.R | 8 +- R/udpipe_models.R | 58 ++++++++--------- R/udpipe_parse.R | 48 +++++++------- R/udpipe_train.R | 16 ++-- R/utils.R | 13 +-- build/vignette.rds |binary inst/doc/udpipe-annotation.Rmd | 2 inst/doc/udpipe-annotation.html | 6 - inst/doc/udpipe-parallel.html | 6 - inst/doc/udpipe-train.html | 6 - inst/doc/udpipe-tryitout.html | 4 - inst/doc/udpipe-universe.html | 4 - inst/doc/udpipe-usecase-postagging-lemmatisation.html | 4 - inst/doc/udpipe-usecase-topicmodelling.html | 4 - man/brussels_listings.Rd | 4 - man/brussels_reviews.Rd | 4 - man/brussels_reviews_anno.Rd | 2 man/predict.LDA.Rd | 8 +- man/txt_tagsequence.Rd | 13 +-- man/udpipe.Rd | 40 ++++++------ man/udpipe_accuracy.Rd | 4 - man/udpipe_annotate.Rd | 8 +- man/udpipe_download_model.Rd | 54 ++++++++-------- man/udpipe_load_model.Rd | 4 - man/udpipe_train.Rd | 12 +-- src/udpipe.cpp | 6 - vignettes/udpipe-annotation.Rmd | 2 31 files changed, 215 insertions(+), 209 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Author: Nicolas Frerebeau [aut, cre] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Jean-Baptiste Fourvel [ctb] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 3.3.1 dated 2025-05-15 and 3.3.2 dated 2025-09-04
DESCRIPTION | 11 ++++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/plot_ford.R | 5 ++++- R/tabula-package.R | 2 +- README.md | 17 ++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alpha.html | 2 +- inst/doc/beta.html | 2 +- inst/po/fr/LC_MESSAGES/R-tabula.mo |binary man/tabula-package.Rd | 3 ++- po/R-fr.po | 4 ++-- 13 files changed, 45 insertions(+), 29 deletions(-)
Title: R Interface to 'Quarto' Markdown Publishing System
Description: Convert R Markdown documents and 'Jupyter' notebooks to a
variety of output formats using 'Quarto'.
Author: JJ Allaire [aut] ,
Christophe Dervieux [cre, aut] ,
Posit Software, PBC [cph, fnd],
Gordon Woodhull [ctb]
Maintainer: Christophe Dervieux <cderv@posit.co>
Diff between quarto versions 1.5.0 dated 2025-07-28 and 1.5.1 dated 2025-09-04
DESCRIPTION | 6 MD5 | 26 - NEWS.md | 467 +++++++++++++++++----------------- R/render.R | 459 ++++++++++++++++----------------- inst/doc/advanced-vignettes.html | 2 inst/doc/dynamic-metadata.html | 6 inst/doc/hello-pdf.pdf |binary inst/doc/hello.html | 2 inst/doc/publishing.html | 2 inst/doc/r-scripts.html | 6 man/quarto_render.Rd | 251 +++++++++--------- tests/testthat/helpers.R | 4 tests/testthat/test-utils-extract.R | 2 tests/testthat/test-utils.R | 494 ++++++++++++++++++------------------ 14 files changed, 867 insertions(+), 860 deletions(-)
Title: Khattree-Bahuguna's Univariate and Multivariate Skewness
Description: Computes Khattree-Bahuguna's univariate and multivariate skewness, principal-component-based Khattree-Bahuguna's multivariate skewness. It also provides several measures of univariate or multivariate skewnesses including, Pearson’s coefficient of skewness, Bowley’s univariate skewness and Mardia's multivariate skewness. See Khattree, R. and Bahuguna, M. (2019) <doi: 10.1007/s41060-018-0106-1>.
Author: Zhixin Lun [aut, cre] ,
Ravindra Khattree [aut]
Maintainer: Zhixin Lun <zhixin.lun@cuanschutz.edu>
Diff between KbMvtSkew versions 1.0.2 dated 2020-03-23 and 1.1.0 dated 2025-09-04
DESCRIPTION | 22 +++++++++++----------- MD5 | 18 +++++++++--------- NAMESPACE | 22 +++++++++++----------- R/KbSkewness.R | 12 ++++++++---- man/data-Chatterjee.Rd | 4 +++- man/data-OlymWomen.Rd | 4 +++- man/data-SwissHead.Rd | 4 +++- man/kbMvtSkew.Rd | 6 ++++-- man/kbSkew.Rd | 2 ++ man/pcKbSkew.Rd | 4 ++-- 10 files changed, 56 insertions(+), 42 deletions(-)
Title: A Unified Data Layer for Large-Scale Single-Cell, Spatial and
Bulk Immunomics
Description: Provides a unified data layer for single-cell, spatial and bulk
T-cell and B-cell immune receptor repertoire data. Think AnnData or SeuratObject,
but for AIRR data.
Author: Vadim I. Nazarov [aut, cre]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Diff between immundata versions 0.0.1 dated 2025-04-08 and 0.0.3 dated 2025-09-04
immundata-0.0.1/immundata/R/immundata.R |only immundata-0.0.1/immundata/R/load_immundata.R |only immundata-0.0.1/immundata/R/load_metadata.R |only immundata-0.0.1/immundata/R/load_repertoires.R |only immundata-0.0.1/immundata/R/load_repertoires_utils.R |only immundata-0.0.1/immundata/R/mouse-ici.R |only immundata-0.0.1/immundata/R/receptor_schema.R |only immundata-0.0.1/immundata/R/utils.R |only immundata-0.0.1/immundata/inst/extdata/metadata_samples.tsv |only immundata-0.0.1/immundata/inst/extdata/sample_0_1k.tsv |only immundata-0.0.1/immundata/inst/extdata/sample_1k_2k.tsv |only immundata-0.0.1/immundata/man/imd_files.Rd |only immundata-0.0.1/immundata/man/load_immundata.Rd |only immundata-0.0.1/immundata/man/load_metadata.Rd |only immundata-0.0.1/immundata/man/load_repertoires.Rd |only immundata-0.0.1/immundata/tests/testthat/test-data-manipulation.R |only immundata-0.0.3/immundata/DESCRIPTION | 31 immundata-0.0.3/immundata/MD5 | 96 immundata-0.0.3/immundata/NAMESPACE | 67 immundata-0.0.3/immundata/R/core_immundata.R |only immundata-0.0.3/immundata/R/globals.R | 181 + immundata-0.0.3/immundata/R/immundata-package.R | 53 immundata-0.0.3/immundata/R/io_annotations_write.R |only immundata-0.0.3/immundata/R/io_immundata_conversion.R |only immundata-0.0.3/immundata/R/io_immundata_read.R |only immundata-0.0.3/immundata/R/io_immundata_write.R |only immundata-0.0.3/immundata/R/io_metadata_read.R |only immundata-0.0.3/immundata/R/io_repertoires_processing.R |only immundata-0.0.3/immundata/R/io_repertoires_read.R |only immundata-0.0.3/immundata/R/io_repertoires_utils.R |only immundata-0.0.3/immundata/R/operations_agg.R |only immundata-0.0.3/immundata/R/operations_annotate.R |only immundata-0.0.3/immundata/R/operations_count.R |only immundata-0.0.3/immundata/R/operations_filter.R |only immundata-0.0.3/immundata/R/operations_mutate.R |only immundata-0.0.3/immundata/R/operations_print.R |only immundata-0.0.3/immundata/R/operations_utils.R |only immundata-0.0.3/immundata/R/operations_utils_levenshtein.R |only immundata-0.0.3/immundata/R/test_utils.R |only immundata-0.0.3/immundata/R/zzz.R | 1 immundata-0.0.3/immundata/README.md | 1360 +++++++++- immundata-0.0.3/immundata/inst/extdata/single_cell |only immundata-0.0.3/immundata/inst/extdata/tsv |only immundata-0.0.3/immundata/man/IMD_GLOBALS.Rd | 4 immundata-0.0.3/immundata/man/ImmunData.Rd | 124 immundata-0.0.3/immundata/man/agg_receptors.Rd |only immundata-0.0.3/immundata/man/agg_repertoires.Rd |only immundata-0.0.3/immundata/man/annotate_immundata.Rd |only immundata-0.0.3/immundata/man/count.ImmunData.Rd |only immundata-0.0.3/immundata/man/filter_immundata.Rd |only immundata-0.0.3/immundata/man/from_immunarch.Rd |only immundata-0.0.3/immundata/man/get_test_idata.Rd |only immundata-0.0.3/immundata/man/imd_schema.Rd | 39 immundata-0.0.3/immundata/man/immundata-package.Rd | 14 immundata-0.0.3/immundata/man/make_receptor_schema.Rd |only immundata-0.0.3/immundata/man/make_seq_options.Rd |only immundata-0.0.3/immundata/man/mutate_immundata.Rd |only immundata-0.0.3/immundata/man/preprocess_postprocess.Rd |only immundata-0.0.3/immundata/man/read_immundata.Rd |only immundata-0.0.3/immundata/man/read_metadata.Rd |only immundata-0.0.3/immundata/man/read_repertoires.Rd |only immundata-0.0.3/immundata/man/write_immundata.Rd |only immundata-0.0.3/immundata/tests/testthat/test-annotate-barcodes.R |only immundata-0.0.3/immundata/tests/testthat/test-annotate-immundata.R |only immundata-0.0.3/immundata/tests/testthat/test-annotate-receptors.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-barcodes.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-immundata-exact.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-immundata-hamm.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-immundata-lev.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-immundata-regex.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-immundata.R |only immundata-0.0.3/immundata/tests/testthat/test-filter-receptors.R |only immundata-0.0.3/immundata/tests/testthat/test-io-immundata-read.R |only immundata-0.0.3/immundata/tests/testthat/test-io-immundata-write.R |only immundata-0.0.3/immundata/tests/testthat/test-io-repertoires.R |only 75 files changed, 1662 insertions(+), 308 deletions(-)
Title: Cytokine Profiling Analysis Tool
Description: Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.
Author: Shubh Saraswat [cre, aut, cph] ,
Xiaohua Douglas Zhang [aut]
Maintainer: Shubh Saraswat <shubh.saraswat00@gmail.com>
Diff between CytoProfile versions 0.2.1 dated 2025-05-19 and 0.2.2 dated 2025-09-04
DESCRIPTION | 8 MD5 | 123 ++-- NAMESPACE | 6 NEWS.md | 21 R/cyt_anova.R | 39 - R/cyt_bp.R | 39 - R/cyt_bp2.R | 44 - R/cyt_dualflashplot.R | 71 +- R/cyt_errbp.R | 443 ++++++++------ R/cyt_heatmap.R | 204 ++++-- R/cyt_mint_splsda.R |only R/cyt_pca.R | 460 ++++++++++----- R/cyt_rf.R | 187 +++++- R/cyt_skku.R | 79 +- R/cyt_splsda.R | 966 +++++++++++++++++++++----------- R/cyt_ttest.R | 7 R/cyt_volc.R | 81 +- R/cyt_xgb.R | 162 +++-- R/data.R | 54 + README.md | 45 + data/ExampleData5.rda |only inst/WORDLIST | 14 inst/doc/getting_started.R | 23 inst/doc/getting_started.Rmd | 38 - inst/doc/getting_started.html | 291 +++++---- man/ExampleData5.Rd |only man/cyt_anova.Rd | 3 man/cyt_bp.Rd | 3 man/cyt_bp2.Rd | 3 man/cyt_dualflashplot.Rd | 3 man/cyt_errbp.Rd | 7 man/cyt_heatmap.Rd | 30 man/cyt_mint_splsda.Rd |only man/cyt_pca.Rd | 3 man/cyt_rf.Rd | 3 man/cyt_skku.Rd | 3 man/cyt_splsda.Rd | 29 man/cyt_ttest.Rd | 3 man/cyt_volc.Rd | 3 man/cyt_xgb.Rd | 3 man/figures/logo.png |binary man/figures/readme-EDA2-1.png |binary man/figures/readme-EDA2-2.png |binary man/figures/readme-EDA2-3.png |binary man/figures/readme-EDA2-4.png |binary man/figures/readme-EDA6-1.png |binary man/figures/readme-EDA7-1.png |binary man/figures/readme-Multivariate1-10.png |binary man/figures/readme-Multivariate1-4.png |binary man/figures/readme-Multivariate1-5.png |binary man/figures/readme-Multivariate1-6.png |binary man/figures/readme-Multivariate1-7.png |binary man/figures/readme-Multivariate1-9.png |binary man/figures/readme-Multivariate2-1.png |binary man/figures/readme-Multivariate2-2.png |binary man/figures/readme-Multivariate2-3.png |binary man/figures/readme-Multivariate2-4.png |binary man/figures/readme-Multivariate2-5.png |binary man/figures/readme-Multivariate2-6.png |binary man/figures/readme-Multivariate2-7.png |only man/figures/readme-Multivariate2-8.png |only man/figures/readme-Multivariate2-9.png |only man/figures/readme-Multivariate3-1.png |only man/figures/readme-Multivariate3-2.png |only man/figures/readme-Multivariate3-3.png |only man/figures/readme-Multivariate3-4.png |only man/figures/readme-Multivariate3-5.png |only man/figures/readme-Multivariate3-6.png |only vignettes/getting_started.Rmd | 38 - 69 files changed, 2372 insertions(+), 1167 deletions(-)
Title: Conditional Multivariate t Distribution, Expectation
Maximization Algorithm, and Its Stochastic Variants
Description: Computes conditional multivariate t probabilities, random deviates, and densities. It can also be used to create missing values at random in a dataset, resulting in a missing at random (MAR) mechanism. Inbuilt in the package are the Expectation-Maximization (EM), Monte Carlo EM, and Stochastic EM algorithms for imputation of missing values in datasets assuming the multivariate t distribution. See Kinyanjui, Tamba, Orawo, and Okenye (2020)<doi:10.3233/mas-200493>, and Kinyanjui, Tamba, and Okenye(2021)<http://www.ceser.in/ceserp/index.php/ijamas/article/view/6726/0> for more details.
Author: Paul Kinyanjui [aut, cre],
Cox Tamba [aut],
Justin Okenye [aut],
Luke Orawo [ctb]
Maintainer: Paul Kinyanjui <kinyanjui.access@gmail.com>
Diff between CondMVT versions 0.1.0 dated 2022-06-28 and 0.1.1 dated 2025-09-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SMCEM_Uonestep.R | 3 ++- man/pcmvt.Rd | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Transformation Discriminant Analysis
Description: Performs transformation discrimination analysis and non-transformation discrimination analysis. It also includes functions for Linear Discriminant Analysis, Quadratic Discriminant Analysis, and Mixture Discriminant Analysis. In the context of mixture discriminant analysis, it offers options for both common covariance matrix (common sigma) and individual covariance matrices (uncommon sigma) for the mixture components.
Author: Jing Li [aut, cre],
Yana Melnykov [aut]
Maintainer: Jing Li <jli178@crimson.ua.edu>
Diff between transDA versions 1.0.1 dated 2025-06-09 and 1.0.2 dated 2025-09-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/tda.R | 2 +- demo/demotda.R | 8 ++++---- man/predict.tda.Rd | 2 +- man/summary.tda.Rd | 2 +- man/tda.Rd | 10 +++++----- man/transDA-package.Rd | 9 ++++----- 8 files changed, 27 insertions(+), 28 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility (GBIF;
<https://www.gbif.org/developer/summary>). GBIF is a database
of species occurrence records from sources all over the globe.
rgbif includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the GBIF
tile map service to make rasters summarizing huge amounts of data.
Author: Scott Chamberlain [aut] ,
Damiano Oldoni [aut] ,
Vijay Barve [ctb] ,
Peter Desmet [ctb] ,
Laurens Geffert [ctb],
Dan Mcglinn [ctb] ,
Karthik Ram [ctb] ,
rOpenSci [fnd] ,
John Waller [aut, cre]
Maintainer: John Waller <jwaller@gbif.org>
Diff between rgbif versions 3.8.2 dated 2025-06-12 and 3.8.3 dated 2025-09-04
rgbif-3.8.2/rgbif/tests/fixtures/name_parse.yml |only rgbif-3.8.3/rgbif/DESCRIPTION | 8 rgbif-3.8.3/rgbif/MD5 | 492 rgbif-3.8.3/rgbif/NAMESPACE | 13 rgbif-3.8.3/rgbif/NEWS.md | 12 rgbif-3.8.3/rgbif/R/collection_search.R |only rgbif-3.8.3/rgbif/R/dataset.R | 4 rgbif-3.8.3/rgbif/R/dataset_doi.R | 5 rgbif-3.8.3/rgbif/R/dataset_list_funs.R | 4 rgbif-3.8.3/rgbif/R/dataset_search.r | 22 rgbif-3.8.3/rgbif/R/dataset_suggest.r | 2 rgbif-3.8.3/rgbif/R/dataset_uuid_funs.R | 22 rgbif-3.8.3/rgbif/R/datasets.r | 2 rgbif-3.8.3/rgbif/R/derived_dataset.R | 4 rgbif-3.8.3/rgbif/R/elevation.r | 2 rgbif-3.8.3/rgbif/R/enumeration.R | 70 rgbif-3.8.3/rgbif/R/gbif_geocode.R | 6 rgbif-3.8.3/rgbif/R/installation_search.R |only rgbif-3.8.3/rgbif/R/installation_uuid_funs.R |only rgbif-3.8.3/rgbif/R/installations.r | 144 rgbif-3.8.3/rgbif/R/institution_search.R |only rgbif-3.8.3/rgbif/R/lit_search.R | 106 rgbif-3.8.3/rgbif/R/name_backbone.r | 4 rgbif-3.8.3/rgbif/R/name_backbone_checklist.R | 4 rgbif-3.8.3/rgbif/R/name_lookup.r | 2 rgbif-3.8.3/rgbif/R/name_parse.R | 2 rgbif-3.8.3/rgbif/R/name_suggest.r | 3 rgbif-3.8.3/rgbif/R/name_usage.r | 5 rgbif-3.8.3/rgbif/R/network.R | 2 rgbif-3.8.3/rgbif/R/networks.r | 2 rgbif-3.8.3/rgbif/R/nodes.r | 194 rgbif-3.8.3/rgbif/R/occ_count.r | 6 rgbif-3.8.3/rgbif/R/occ_count_.R | 2 rgbif-3.8.3/rgbif/R/occ_download.R | 7 rgbif-3.8.3/rgbif/R/occ_download_cached.R | 2 rgbif-3.8.3/rgbif/R/occ_download_cancel.R | 116 rgbif-3.8.3/rgbif/R/occ_download_dataset_activity.R | 94 rgbif-3.8.3/rgbif/R/occ_download_datasets.R | 82 rgbif-3.8.3/rgbif/R/occ_download_describe.R | 6 rgbif-3.8.3/rgbif/R/occ_download_doi.R | 7 rgbif-3.8.3/rgbif/R/occ_download_list.R | 116 rgbif-3.8.3/rgbif/R/occ_download_meta.R | 4 rgbif-3.8.3/rgbif/R/occ_download_sql.R | 4 rgbif-3.8.3/rgbif/R/occ_facet.R | 7 rgbif-3.8.3/rgbif/R/occ_get.r | 11 rgbif-3.8.3/rgbif/R/occ_metadata.r | 112 rgbif-3.8.3/rgbif/R/organizations.r | 7 rgbif-3.8.3/rgbif/R/print_gbif.R | 232 rgbif-3.8.3/rgbif/R/zzz.r | 65 rgbif-3.8.3/rgbif/man/collection_search.Rd |only rgbif-3.8.3/rgbif/man/dataset.Rd | 2 rgbif-3.8.3/rgbif/man/dataset_doi.Rd | 7 rgbif-3.8.3/rgbif/man/dataset_list_funs.Rd | 4 rgbif-3.8.3/rgbif/man/dataset_search.Rd | 14 rgbif-3.8.3/rgbif/man/dataset_uuid_funs.Rd | 37 rgbif-3.8.3/rgbif/man/datasets.Rd | 2 rgbif-3.8.3/rgbif/man/derived_dataset.Rd | 4 rgbif-3.8.3/rgbif/man/elevation.Rd | 2 rgbif-3.8.3/rgbif/man/enumeration.Rd | 4 rgbif-3.8.3/rgbif/man/gbif_geocode.Rd | 8 rgbif-3.8.3/rgbif/man/installation_search.Rd |only rgbif-3.8.3/rgbif/man/installation_uuid_funs.Rd |only rgbif-3.8.3/rgbif/man/installations.Rd | 2 rgbif-3.8.3/rgbif/man/institution_search.Rd |only rgbif-3.8.3/rgbif/man/lit_search.Rd | 31 rgbif-3.8.3/rgbif/man/name_backbone.Rd | 4 rgbif-3.8.3/rgbif/man/name_backbone_checklist.Rd | 2 rgbif-3.8.3/rgbif/man/name_lookup.Rd | 2 rgbif-3.8.3/rgbif/man/name_parse.Rd | 2 rgbif-3.8.3/rgbif/man/name_suggest.Rd | 2 rgbif-3.8.3/rgbif/man/name_usage.Rd | 2 rgbif-3.8.3/rgbif/man/network.Rd | 2 rgbif-3.8.3/rgbif/man/networks.Rd | 2 rgbif-3.8.3/rgbif/man/nodes.Rd | 2 rgbif-3.8.3/rgbif/man/occ_count.Rd | 2 rgbif-3.8.3/rgbif/man/occ_count_.Rd | 2 rgbif-3.8.3/rgbif/man/occ_download.Rd | 4 rgbif-3.8.3/rgbif/man/occ_download_cached.Rd | 2 rgbif-3.8.3/rgbif/man/occ_download_cancel.Rd | 9 rgbif-3.8.3/rgbif/man/occ_download_dataset_activity.Rd | 2 rgbif-3.8.3/rgbif/man/occ_download_datasets.Rd | 7 rgbif-3.8.3/rgbif/man/occ_download_describe.Rd | 5 rgbif-3.8.3/rgbif/man/occ_download_doi.Rd | 4 rgbif-3.8.3/rgbif/man/occ_download_list.Rd | 2 rgbif-3.8.3/rgbif/man/occ_download_meta.Rd | 2 rgbif-3.8.3/rgbif/man/occ_download_sql.Rd | 4 rgbif-3.8.3/rgbif/man/occ_facet.Rd | 2 rgbif-3.8.3/rgbif/man/occ_get.Rd | 4 rgbif-3.8.3/rgbif/man/occ_metadata.Rd | 2 rgbif-3.8.3/rgbif/man/organizations.Rd | 5 rgbif-3.8.3/rgbif/tests/fixtures/collection_search.yml |only rgbif-3.8.3/rgbif/tests/fixtures/dataset.yml | 1838 rgbif-3.8.3/rgbif/tests/fixtures/dataset_doi.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/dataset_list_funs.yml | 45 rgbif-3.8.3/rgbif/tests/fixtures/dataset_search.yml | 9738 rgbif-3.8.3/rgbif/tests/fixtures/dataset_search_facet.yml | 121 rgbif-3.8.3/rgbif/tests/fixtures/dataset_suggest.yml | 7363 rgbif-3.8.3/rgbif/tests/fixtures/dataset_suggest_description.yml | 2927 rgbif-3.8.3/rgbif/tests/fixtures/dataset_uuid_funs.yml |122958 +++++++++- rgbif-3.8.3/rgbif/tests/fixtures/derived_dataset_1.yml | 25 rgbif-3.8.3/rgbif/tests/fixtures/derived_dataset_2.yml | 23 rgbif-3.8.3/rgbif/tests/fixtures/elevation.yml | 61 rgbif-3.8.3/rgbif/tests/fixtures/elevation_geonames_conn.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/elevation_geonames_conn_unauthorized.yml | 47 rgbif-3.8.3/rgbif/tests/fixtures/elevation_models.yml | 161 rgbif-3.8.3/rgbif/tests/fixtures/elevation_unauthorized.yml | 24 rgbif-3.8.3/rgbif/tests/fixtures/elevation_warning_zero_zero.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/enumeration.yml | 888 rgbif-3.8.3/rgbif/tests/fixtures/enumeration_fails_well.yml | 19 rgbif-3.8.3/rgbif/tests/fixtures/gbif_citation_downloadkey.yml | 47 rgbif-3.8.3/rgbif/tests/fixtures/gbif_citation_occ_download_meta.yml | 47 rgbif-3.8.3/rgbif/tests/fixtures/gbif_get_wait.yml |only rgbif-3.8.3/rgbif/tests/fixtures/gbif_oai_get_records.yml | 103 rgbif-3.8.3/rgbif/tests/fixtures/gbif_oai_identify.yml | 68 rgbif-3.8.3/rgbif/tests/fixtures/gbif_oai_list_identifiers.yml | 22 rgbif-3.8.3/rgbif/tests/fixtures/gbif_oai_list_metadataformats.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/gbif_oai_list_sets.yml | 2054 rgbif-3.8.3/rgbif/tests/fixtures/installation_search.yml |only rgbif-3.8.3/rgbif/tests/fixtures/installation_uuid_funs.yml |only rgbif-3.8.3/rgbif/tests/fixtures/installations.yml | 2675 rgbif-3.8.3/rgbif/tests/fixtures/installations_deleted.yml | 59 rgbif-3.8.3/rgbif/tests/fixtures/installations_uuid.yml | 19 rgbif-3.8.3/rgbif/tests/fixtures/installations_uuid_data.yml | 19 rgbif-3.8.3/rgbif/tests/fixtures/institution_search.yml |only rgbif-3.8.3/rgbif/tests/fixtures/map_fetch_png.yml | 5631 rgbif-3.8.3/rgbif/tests/fixtures/map_fetch_terra.yml |17593 - rgbif-3.8.3/rgbif/tests/fixtures/name_backbone.yml | 47 rgbif-3.8.3/rgbif/tests/fixtures/name_backbone_verbose_true.yml | 183 rgbif-3.8.3/rgbif/tests/fixtures/name_issues.yml | 168 rgbif-3.8.3/rgbif/tests/fixtures/name_lookup_constituentKey.yml | 3774 rgbif-3.8.3/rgbif/tests/fixtures/name_lookup_habitat.yml |10713 rgbif-3.8.3/rgbif/tests/fixtures/name_lookup_no_results.yml | 25 rgbif-3.8.3/rgbif/tests/fixtures/name_suggest.yml | 1905 rgbif-3.8.3/rgbif/tests/fixtures/name_suggest_many_args.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/name_usage.yml | 285 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_children.yml | 558 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_descriptions.yml | 283 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_distributions.yml | 1043 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_iucnRedListCategory.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_media.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_name.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_parents.yml | 270 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_references.yml | 487 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_related.yml | 1900 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_speciesProfiles.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_synonyms.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_typeSpecimens.yml | 37 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_data_vernacularNames.yml | 363 rgbif-3.8.3/rgbif/tests/fixtures/name_usage_fails_well.yml | 21 rgbif-3.8.3/rgbif/tests/fixtures/network.yml | 44 rgbif-3.8.3/rgbif/tests/fixtures/network_constituents.yml |10327 rgbif-3.8.3/rgbif/tests/fixtures/nodes.yml | 4457 rgbif-3.8.3/rgbif/tests/fixtures/occ_count.yml | 159 rgbif-3.8.3/rgbif/tests/fixtures/occ_count_.yml | 175 rgbif-3.8.3/rgbif/tests/fixtures/occ_count_facet.yml | 196 rgbif-3.8.3/rgbif/tests/fixtures/occ_count_legacy_params.yml | 105 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_args_with_many_inputs.yml | 2389 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_catalog_number.yml | 504 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_coordinateUncertaintyInMeters.yml | 678 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_degreeOfEstablishment.yml | 1008 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_depth.yml | 201 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_distanceFromCentroidInMeters.yml | 720 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_dropped_fields.yml | 335 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_elevation.yml | 210 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_eventId.yml | 1386 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_fails_well.yml | 41 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_gadmGid.yml | 699 rgbif-3.8.3/rgbif/tests/fixtures/occ_data_identifiedBy.yml | 1483 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rgbif-3.8.3/rgbif/tests/testthat/test-dataset_search.r | 11 rgbif-3.8.3/rgbif/tests/testthat/test-gbif_photos.R | 60 rgbif-3.8.3/rgbif/tests/testthat/test-installation_search.R |only rgbif-3.8.3/rgbif/tests/testthat/test-installation_uuid_funs.R |only rgbif-3.8.3/rgbif/tests/testthat/test-institution_search.R |only rgbif-3.8.3/rgbif/tests/testthat/test-lit_search.R | 35 rgbif-3.8.3/rgbif/tests/testthat/test-name_backbone_checklist.R | 190 rgbif-3.8.3/rgbif/tests/testthat/test-name_parse.R | 14 rgbif-3.8.3/rgbif/tests/testthat/test-occ_data.R | 2 rgbif-3.8.3/rgbif/tests/testthat/test-occ_download.R | 9 rgbif-3.8.3/rgbif/tests/testthat/test-occ_download_meta.R | 2 rgbif-3.8.3/rgbif/tests/testthat/test-occ_download_queue.R | 2 rgbif-3.8.3/rgbif/tests/testthat/test-occ_download_sql.R | 1 rgbif-3.8.3/rgbif/tests/testthat/test-occ_search.r | 2 rgbif-3.8.3/rgbif/tests/testthat/test-utils.R | 18 256 files changed, 184446 insertions(+), 102985 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Ben Wilson [aut, cre],
Matei Zaharia [aut],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Ben Wilson <benjamin.wilson@databricks.com>
Diff between mlflow versions 3.2.0 dated 2025-08-21 and 3.3.2 dated 2025-09-04
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Facilitate Citation of R Packages
Description: Facilitates the citation of R packages used in analysis
projects. Scans project for packages used, gets their citations, and
produces a document with citations in the preferred bibliography
format, ready to be pasted into reports or manuscripts. Alternatively,
'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.
Author: Francisco Rodriguez-Sanchez [aut, cre, cph] ,
Connor P. Jackson [aut] ,
Shaurita D. Hutchins [ctb],
James M. Clawson [ctb]
Maintainer: Francisco Rodriguez-Sanchez <f.rodriguez.sanc@gmail.com>
Diff between grateful versions 0.2.12 dated 2025-04-30 and 0.3.0 dated 2025-09-04
DESCRIPTION | 17 +- MD5 | 51 ++++---- NEWS.md | 13 ++ R/cite_packages.R | 65 +++++++++- R/create_rmd.R | 8 + R/get_citations.R | 20 ++- R/get_pkgs_info.R | 14 ++ R/render_citations.R | 3 R/scan_packages.R | 123 ++++++++++++++++++- R/utils_citations.R | 28 ++++ R/write_citation_paragraph.R | 76 +++++++----- README.md | 133 ++++++++++++++++----- inst/CITATION | 2 man/cite_packages.Rd | 55 +++++++- man/figures/logo.png |only man/get_citations.Rd | 9 + man/get_pkgs_info.Rd | 27 +++- man/grateful-package.Rd | 2 man/scan_packages.Rd | 27 +++- tests/testthat/test-cite_packages.R | 57 ++++++++- tests/testthat/test-create_rmd.R | 4 tests/testthat/test-get_citations.R | 14 ++ tests/testthat/test-get_csl.R | 2 tests/testthat/test-get_pkgs_info.R | 10 + tests/testthat/test-render_citations.R | 14 +- tests/testthat/test-scan_packages.R | 207 ++++++++++++++++++++++++++++----- tests/testthat/test-utils_citations.R | 25 +++ 27 files changed, 829 insertions(+), 177 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 1.0.2 dated 2025-07-31 and 1.1.0 dated 2025-09-04
boostmath-1.0.2/boostmath/src/boostmath/complex_interop.hpp |only boostmath-1.0.2/boostmath/vignettes/boost-math.html |only boostmath-1.1.0/boostmath/DESCRIPTION | 6 boostmath-1.1.0/boostmath/MD5 | 125 +++- boostmath-1.1.0/boostmath/NAMESPACE | 52 + boostmath-1.1.0/boostmath/NEWS.md | 3 boostmath-1.1.0/boostmath/R/anderson_darling_test.R |only boostmath-1.1.0/boostmath/R/bivariate_statistics.R |only boostmath-1.1.0/boostmath/R/chatterjee_correlation.R |only boostmath-1.1.0/boostmath/R/constants.R |only boostmath-1.1.0/boostmath/R/interpolators.R |only boostmath-1.1.0/boostmath/R/linear_regression.R |only boostmath-1.1.0/boostmath/R/ljung_box_test.R |only boostmath-1.1.0/boostmath/R/quadrature_and_differentiation.R | 2 boostmath-1.1.0/boostmath/R/runs_tests.R |only boostmath-1.1.0/boostmath/R/signal_statistics.R |only boostmath-1.1.0/boostmath/R/t_tests.R |only boostmath-1.1.0/boostmath/R/univariate_statistics.R |only boostmath-1.1.0/boostmath/R/z_tests.R |only boostmath-1.1.0/boostmath/R/zzz.R | 4 boostmath-1.1.0/boostmath/build/vignette.rds |binary boostmath-1.1.0/boostmath/inst/doc/constants.R |only boostmath-1.1.0/boostmath/inst/doc/constants.Rmd |only boostmath-1.1.0/boostmath/inst/doc/constants.html |only boostmath-1.1.0/boostmath/inst/doc/interpolation.R |only boostmath-1.1.0/boostmath/inst/doc/interpolation.Rmd |only boostmath-1.1.0/boostmath/inst/doc/interpolation.html |only boostmath-1.1.0/boostmath/inst/doc/quadrature-differentiation.R | 4 boostmath-1.1.0/boostmath/inst/doc/quadrature-differentiation.Rmd | 4 boostmath-1.1.0/boostmath/inst/doc/quadrature-differentiation.html | 12 boostmath-1.1.0/boostmath/inst/doc/statistics.R |only boostmath-1.1.0/boostmath/inst/doc/statistics.Rmd |only boostmath-1.1.0/boostmath/inst/doc/statistics.html |only boostmath-1.1.0/boostmath/inst/doc/vector-functionals.R | 44 - boostmath-1.1.0/boostmath/inst/doc/vector-functionals.Rmd | 44 - boostmath-1.1.0/boostmath/inst/doc/vector-functionals.html | 55 +- boostmath-1.1.0/boostmath/inst/tinytest/test_constants.R |only boostmath-1.1.0/boostmath/man/anderson_darling_test.Rd |only boostmath-1.1.0/boostmath/man/barycentric_rational.Rd |only boostmath-1.1.0/boostmath/man/bezier_polynomial.Rd |only boostmath-1.1.0/boostmath/man/bilinear_uniform.Rd |only boostmath-1.1.0/boostmath/man/bivariate_statistics.Rd |only boostmath-1.1.0/boostmath/man/cardinal_cubic_b_spline.Rd |only boostmath-1.1.0/boostmath/man/cardinal_cubic_hermite.Rd |only boostmath-1.1.0/boostmath/man/cardinal_quadratic_b_spline.Rd |only boostmath-1.1.0/boostmath/man/cardinal_quintic_b_spline.Rd |only boostmath-1.1.0/boostmath/man/cardinal_quintic_hermite.Rd |only boostmath-1.1.0/boostmath/man/catmull_rom.Rd |only boostmath-1.1.0/boostmath/man/chatterjee_correlation.Rd |only boostmath-1.1.0/boostmath/man/constants.Rd |only boostmath-1.1.0/boostmath/man/cubic_hermite.Rd |only boostmath-1.1.0/boostmath/man/linear_regression.Rd |only boostmath-1.1.0/boostmath/man/ljung_box_test.Rd |only boostmath-1.1.0/boostmath/man/makima.Rd |only boostmath-1.1.0/boostmath/man/ooura_fourier_integrals.Rd | 2 boostmath-1.1.0/boostmath/man/pchip.Rd |only boostmath-1.1.0/boostmath/man/quintic_hermite.Rd |only boostmath-1.1.0/boostmath/man/runs_tests.Rd |only boostmath-1.1.0/boostmath/man/signal_statistics.Rd |only boostmath-1.1.0/boostmath/man/t_tests.Rd |only boostmath-1.1.0/boostmath/man/univariate_statistics.Rd |only boostmath-1.1.0/boostmath/man/z_tests.Rd |only boostmath-1.1.0/boostmath/src/Makevars | 26 boostmath-1.1.0/boostmath/src/boostmath/macros.hpp | 56 ++ boostmath-1.1.0/boostmath/src/boostmath/sexp.hpp |only boostmath-1.1.0/boostmath/src/constants.cpp |only boostmath-1.1.0/boostmath/src/cyl_hankel_1.cpp | 2 boostmath-1.1.0/boostmath/src/cyl_hankel_2.cpp | 2 boostmath-1.1.0/boostmath/src/init.cpp | 272 ++++++++++ boostmath-1.1.0/boostmath/src/interpolators |only boostmath-1.1.0/boostmath/src/interpolators.cpp |only boostmath-1.1.0/boostmath/src/quadrature_and_differentiation/fourier_integrals.cpp | 8 boostmath-1.1.0/boostmath/src/quadrature_and_differentiation/numerical_differentiation.cpp | 2 boostmath-1.1.0/boostmath/src/sph_hankel_1.cpp | 2 boostmath-1.1.0/boostmath/src/sph_hankel_2.cpp | 2 boostmath-1.1.0/boostmath/src/statistics |only boostmath-1.1.0/boostmath/src/statistics.cpp |only boostmath-1.1.0/boostmath/vignettes/constants.Rmd |only boostmath-1.1.0/boostmath/vignettes/interpolation.Rmd |only boostmath-1.1.0/boostmath/vignettes/quadrature-differentiation.Rmd | 4 boostmath-1.1.0/boostmath/vignettes/statistics.Rmd |only boostmath-1.1.0/boostmath/vignettes/vector-functionals.Rmd | 44 - 82 files changed, 635 insertions(+), 142 deletions(-)
Title: Bias Correction via Iterative Bootstrap
Description: An implementation of the iterative bootstrap procedure of
Kuk (1995) <doi:10.1111/j.2517-6161.1995.tb02035.x> to correct the estimation bias of a fitted model object. This
procedure has better bias correction properties than the
bootstrap bias correction technique.
Author: Samuel Orso [aut, cre],
Stephane Guerrier [ctb],
Yuming Zhang [ctb]
Maintainer: Samuel Orso <Samuel.Orso@unige.ch>
Diff between ib versions 0.2.0 dated 2022-04-04 and 0.2.1 dated 2025-09-04
DESCRIPTION | 11 - MD5 | 52 ++++---- NAMESPACE | 8 + NEWS.md | 5 R/AllClass.R | 243 +++++++++++++++++++++----------------- R/AllGeneric.R | 1 R/ib_betareg.R | 4 R/ib_glm.R | 8 - R/ib_glmer.R |only R/ib_lm.R | 4 R/ib_lmer.R | 4 R/ib_nls.R | 4 R/ib_vglm.R | 4 R/summary.R | 23 +++ build/partial.rdb |binary inst/examples/eg_glmer.R |only inst/examples/eg_lmer.R | 2 man/Ib-class.Rd | 50 +++---- man/SummaryIb-class.Rd | 42 ++---- man/ib.Rd | 27 +++- man/simulation-betareg-method.Rd | 4 man/simulation-glm-method.Rd | 4 man/simulation-glmerMod-method.Rd |only man/simulation-lm-method.Rd | 4 man/simulation-lmerMod-method.Rd | 4 man/simulation-negbin-method.Rd | 4 man/simulation-nls-method.Rd | 4 man/simulation-vglm-method.Rd | 4 man/summary-IbGlmer-method.Rd |only 29 files changed, 303 insertions(+), 217 deletions(-)