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 3.1.0 dated 2024-11-26 and 3.2.0 dated 2025-08-27
usethis-3.1.0/usethis/man/git_branch_default.Rd |only usethis-3.1.0/usethis/man/use_github_actions.Rd |only usethis-3.1.0/usethis/man/use_rscloud_badge.Rd |only usethis-3.1.0/usethis/man/use_tidy_eval.Rd |only usethis-3.2.0/usethis/DESCRIPTION | 30 - usethis-3.2.0/usethis/LICENSE | 2 usethis-3.2.0/usethis/MD5 | 260 ++++----- usethis-3.2.0/usethis/NAMESPACE | 11 usethis-3.2.0/usethis/NEWS.md | 55 + usethis-3.2.0/usethis/R/air.R |only usethis-3.2.0/usethis/R/author.R | 9 usethis-3.2.0/usethis/R/badge.R | 63 +- usethis-3.2.0/usethis/R/block.R | 40 + usethis-3.2.0/usethis/R/browse.R | 29 - usethis-3.2.0/usethis/R/ci.R | 6 usethis-3.2.0/usethis/R/code-of-conduct.R | 9 usethis-3.2.0/usethis/R/course.R | 129 ++-- usethis-3.2.0/usethis/R/coverage.R | 13 usethis-3.2.0/usethis/R/create.R | 155 ++++- usethis-3.2.0/usethis/R/data.R | 35 - usethis-3.2.0/usethis/R/description.R | 18 usethis-3.2.0/usethis/R/directory.R | 7 usethis-3.2.0/usethis/R/edit.R | 29 - usethis-3.2.0/usethis/R/git-default-branch.R | 118 ++-- usethis-3.2.0/usethis/R/git.R | 36 - 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Title: Estimate Rogers-Castro Migration Age Schedules with Bayesian
Models
Description: A collection of functions to estimate Rogers-Castro migration age schedules using 'Stan'. This model which describes the fundamental relationship between migration and age in the form of a flexible multi-exponential migration model was most notably proposed in Rogers and Castro (1978) <doi:10.1068/a100475>.
Author: Jessie Yeung [aut, cre] ,
Monica Alexander [aut] ,
Tim Riffe [aut]
Maintainer: Jessie Yeung <jessieyeung1@gmail.com>
Diff between rcbayes versions 0.2.0 dated 2022-01-17 and 0.3.0 dated 2025-08-27
DESCRIPTION | 21 MD5 | 63 NEWS.md | 7 R/mig_calculate_rc.R | 8 R/rcbayes-package.R | 3 R/stanmodels.R | 2 README.md | 19 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/convergence_issues.R | 152 - inst/doc/convergence_issues.Rmd | 12 inst/doc/convergence_issues.html | 645 ++++- inst/doc/intro_to_rcbayes.R | 34 inst/doc/intro_to_rcbayes.Rmd | 8 inst/doc/intro_to_rcbayes.html | 865 +++++--- inst/shiny-app/RC_app/app.R | 67 inst/stan/rcmodel_normal.stan | 24 inst/stan/rcmodel_normal_sigma_given.stan | 24 inst/stan/rcmodel_poisson.stan | 32 man/mig_calculate_rc.Rd | 8 man/rcbayes-package.Rd | 12 src/Makevars | 5 src/stanExports_lm.cc | 2 src/stanExports_lm.h | 729 +++--- src/stanExports_rcmodel_normal.cc | 2 src/stanExports_rcmodel_normal.h | 2795 +++++++++++++------------ src/stanExports_rcmodel_normal_sigma_given.cc | 2 src/stanExports_rcmodel_normal_sigma_given.h | 2758 +++++++++++++------------ src/stanExports_rcmodel_poisson.cc | 2 src/stanExports_rcmodel_poisson.h | 2799 +++++++++++++------------- vignettes/convergence_issues.Rmd | 12 vignettes/intro_to_rcbayes.Rmd | 8 33 files changed, 6073 insertions(+), 5047 deletions(-)
Title: Statistical Modelling in Action with R
Description: Datasets and functions for the book "Modélisation statistique par la pratique avec R", F. Bertrand, E. Claeys and M. Maumy-Bertrand (2019, ISBN:9782100793525, Dunod, Paris). The first chapter of the book is dedicated to an introduction to the R statistical software. The second chapter deals with correlation analysis: Pearson, Spearman and Kendall simple, multiple and partial correlation coefficients. New wrapper functions for permutation tests or bootstrap of matrices of correlation are provided with the package. The third chapter is dedicated to data exploration with factorial analyses (PCA, CA, MCA, MDA) and clustering. The fourth chapter is dedicated to regression analysis: fitting and model diagnostics are detailed. The exercises focus on covariance analysis, logistic regression, Poisson regression, two-way analysis of variance for fixed or random factors. Various example datasets are shipped with the package: for instance on pokemon, world of warcraft, house tasks or food nutritio [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Emmanuelle Claeys [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between ModStatR versions 1.3.3 dated 2023-03-24 and 1.4.0 dated 2025-08-27
ModStatR-1.3.3/ModStatR/man/ModStatR.Rd |only ModStatR-1.4.0/ModStatR/DESCRIPTION | 27 +++++++++++++++------- ModStatR-1.4.0/ModStatR/MD5 | 29 ++++++++++++++++-------- ModStatR-1.4.0/ModStatR/NEWS.md | 8 ++++++ ModStatR-1.4.0/ModStatR/R/ModStatR-package.R | 17 +++++++------- ModStatR-1.4.0/ModStatR/R/datasets.R | 2 - ModStatR-1.4.0/ModStatR/R/functions.R | 4 +-- ModStatR-1.4.0/ModStatR/demo/Chapitre3.R | 7 +++-- ModStatR-1.4.0/ModStatR/inst/_pkgdown.yml | 5 ++++ ModStatR-1.4.0/ModStatR/man/ModStatR-package.Rd |only ModStatR-1.4.0/ModStatR/man/SidaChat.Rd | 2 - ModStatR-1.4.0/ModStatR/tests |only 12 files changed, 69 insertions(+), 32 deletions(-)
Title: Methods for Handling and Analyzing Time Series of Satellite
Images
Description: Provides functions and methods for: splitting large raster objects
into smaller chunks, transferring images from a binary format into raster
layers, transferring raster layers into an 'RData' file, calculating the
maximum gap (amount of consecutive missing values) of a numeric vector,
and fitting harmonic regression models to periodic time series. The homoscedastic
harmonic regression model is based on G. Roerink, M. Menenti and W. Verhoef (2000) <doi:10.1080/014311600209814>.
Author: Inder Tecuapetla-Gomez [aut, cre]
Maintainer: Inder Tecuapetla-Gomez
<itecuapetla@conabio.gob.mx>
Diff between geoTS versions 0.1.8 dated 2022-11-17 and 0.1.10 dated 2025-08-27
DESCRIPTION | 12 - MD5 | 12 - R/geoTS-package.R | 124 ++++++++--------- R/matrixToRaster.R | 2 R/split_replace.R | 370 +++++++++++++++++++++++++-------------------------- inst/docs/NEWS.txt | 40 +++-- man/geoTS-package.Rd | 21 +- 7 files changed, 293 insertions(+), 288 deletions(-)
Title: Portable and Performant Tour Animations
Description: Provides 2D and 3D tour animations as HTML widgets. The user can interact with the widgets using orbit controls, tooltips, brushing, and timeline controls. Linked brushing is supported using 'crosstalk', and widgets can be embedded in Shiny apps or HTML documents.
Author: Casper Hart [aut, cre],
Earo Wang [aut, ths]
Maintainer: Casper Hart <casperhart93@gmail.com>
Diff between detourr versions 0.1.0 dated 2022-06-20 and 0.2.0 dated 2025-08-27
detourr-0.1.0/detourr/inst/htmlwidgets/lib/04257c7ca672691de31a120d3ea15e4e.wasm |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/2b1202ac2cd1b46a0ba4b94b393d0fcd.wasm |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/efb09fb8bf1b51cb098aa692302e2b7f.wasm |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/long.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/runtime.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/seedrandom.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_sage_2d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_sage_3d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_scatter_2d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_scatter_3d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_slice_2d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/show_slice_3d.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/stdlib.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/stdlib.bundle.js.LICENSE.txt |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/tensorflow.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/tensorflow.bundle.js.LICENSE.txt |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/three.bundle.js |only detourr-0.1.0/detourr/inst/htmlwidgets/lib/three.bundle.js.LICENSE.txt |only detourr-0.1.0/detourr/inst/htmlwidgets/show_sage_2d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_sage_2d.yaml |only detourr-0.1.0/detourr/inst/htmlwidgets/show_sage_3d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_sage_3d.yaml |only detourr-0.1.0/detourr/inst/htmlwidgets/show_scatter_2d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_scatter_2d.yaml |only detourr-0.1.0/detourr/inst/htmlwidgets/show_scatter_3d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_scatter_3d.yaml |only detourr-0.1.0/detourr/inst/htmlwidgets/show_slice_2d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_slice_2d.yaml |only detourr-0.1.0/detourr/inst/htmlwidgets/show_slice_3d.js |only detourr-0.1.0/detourr/inst/htmlwidgets/show_slice_3d.yaml |only detourr-0.2.0/detourr/DESCRIPTION | 16 detourr-0.2.0/detourr/MD5 | 63 --- detourr-0.2.0/detourr/NAMESPACE | 16 detourr-0.2.0/detourr/R/shiny_bindings.r | 209 ++++++++-- detourr-0.2.0/detourr/R/show_sage.R | 4 detourr-0.2.0/detourr/R/show_scatter.R | 15 detourr-0.2.0/detourr/R/show_slice.R | 6 detourr-0.2.0/detourr/R/utils.R | 11 detourr-0.2.0/detourr/inst/htmlwidgets/detourr.js |only detourr-0.2.0/detourr/inst/htmlwidgets/detourr.yaml |only detourr-0.2.0/detourr/inst/htmlwidgets/lib/detourr.bundle.js |only detourr-0.2.0/detourr/inst/htmlwidgets/lib/detourr.bundle.js.LICENSE.txt |only detourr-0.2.0/detourr/man/detour-shiny.Rd | 98 ++++ detourr-0.2.0/detourr/man/reexports.Rd | 2 detourr-0.2.0/detourr/man/show_sage.Rd | 4 detourr-0.2.0/detourr/man/show_scatter.Rd | 4 detourr-0.2.0/detourr/man/show_scatter_internal.Rd | 4 detourr-0.2.0/detourr/man/show_slice.Rd | 4 detourr-0.2.0/detourr/man/tour_aes.Rd | 2 detourr-0.2.0/detourr/tests/testthat/test-add-points.R |only 50 files changed, 347 insertions(+), 111 deletions(-)
Title: Cardiovascular Risk Scores Calculator
Description: A tool to calculate Cardiovascular Risk Scores in large data frames as published in Perez-Vicencio, et al (2024) <doi:10.1136/openhrt-2024-002755>. Cardiovascular risk scores are statistical tools used to assess an individual's likelihood of developing a cardiovascular disease based on various risk factors, such as age, gender, blood pressure, cholesterol levels, and smoking. Here we bring together the six most commonly used in the emergency department. Using 'RiskScorescvd', you can calculate all the risk scores in an extended dataset in seconds. PCE (ASCVD) described in Goff, et al (2013) <doi:10.1161/01.cir.0000437741.48606.98>. EDACS described in Mark DG, et al (2016) <doi:10.1016/j.jacc.2017.11.064>. GRACE described in Fox KA, et al (2006) <doi:10.1136/bmj.38985.646481.55>. HEART is described in Mahler SA, et al (2017) <doi:10.1016/j.clinbiochem.2017.01.003>. SCORE2/OP described in SCORE2 working group and ESC Cardiovascular risk collaboration (2021) [...truncated...]
Author: Daniel Perez-Vicencio [aut, cre] ,
Dimitrios Doudesis [aut],
Alexander JF Thurston [aut],
Jeremy Selva [aut]
Maintainer: Daniel Perez-Vicencio <dvicencio947@gmail.com>
Diff between RiskScorescvd versions 0.2.0 dated 2024-06-27 and 0.3.1 dated 2025-08-27
DESCRIPTION | 24 MD5 | 47 + NAMESPACE | 2 NEWS.md | 45 + R/15_SCORE2-Diabetes_func.R | 586 ++++++++++++------------ R/16_SCORE2-Asia-Pacific_func.R |only R/17_CAD_Consortium_func.R |only README.md | 154 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Calculate_scores.R | 238 +++++++++ inst/doc/Calculate_scores.Rmd | 295 +++++++++++- inst/doc/Calculate_scores.html | 399 +++++++++++++++- man/CAD_Consortium_func.Rd |only man/SCORE2_Asia_Pacific.Rd |only man/SCORE2_Diabetes.Rd | 12 man/figures/README-Plot-1.0.png |only man/figures/README-Plot-1.png |binary man/figures/logo.png |only tests/testthat/test-ASCVD-PCE_func.R |only tests/testthat/test-ASCVD_additional.R |only tests/testthat/test-CAD-Consortium_func.R |only tests/testthat/test-CAD_Consortium_additional.R |only tests/testthat/test-EDACS_func.R |only tests/testthat/test-GRACE_func.R |only tests/testthat/test-HEART_additional.R |only tests/testthat/test-HEART_func.R |only tests/testthat/test-SCORE2-Asia-Pacific_func.R |only tests/testthat/test-SCORE2-Diabetes_func.R | 542 +++++++++++----------- tests/testthat/test-SCORE2_CKD_func.R |only tests/testthat/test-SCORE2_additional.R |only tests/testthat/test-TIMI_func.R |only tests/testthat/test-calc_scores.R |only vignettes/Calculate_scores.Rmd | 295 +++++++++++- 34 files changed, 1954 insertions(+), 685 deletions(-)
Title: Fast 3D Lacunarity for Voxel Data
Description: Calculates 3D lacunarity from voxel data. It is designed for use
with point clouds generated from Light Detection And Ranging (LiDAR) scans
in order to measure the spatial heterogeneity of 3-dimensional structures
such as forest stands. It provides fast 'C++' functions to efficiently bin
point cloud data into voxels and calculate lacunarity using different
variants of the gliding-box algorithm originated by Allain & Cloitre (1991)
<doi:10.1103/PhysRevA.44.3552>.
Author: Elliott Smeds [aut, cre, cph] ,
J. Antonio Guzman Q. [cph]
function)
Maintainer: Elliott Smeds <elliott.alfred93@gmail.com>
Diff between lacunr versions 1.0.1 dated 2024-06-04 and 1.0.2 dated 2025-08-27
DESCRIPTION | 13 ++++--- MD5 | 39 ++++++++++++----------- NEWS.md | 24 ++++++++++---- R/bounding_box.R | 2 - R/voxelize.R | 4 +- README.md | 9 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/lacunr-tutorial.R | 22 ++++++------- inst/doc/lacunr-tutorial.Rmd | 2 - inst/doc/lacunr-tutorial.html | 64 ++++++++++++++++++++------------------- inst/doc/quick-start.html | 6 +-- inst/doc/working-with-lidR.R | 2 + inst/doc/working-with-lidR.Rmd | 2 - inst/doc/working-with-lidR.html | 6 +-- man/bounding_box.Rd | 2 - man/voxelize.Rd | 4 +- tests/testthat/test-lacunarity.R | 7 +++- vignettes/lacunr-tutorial.Rmd | 2 - vignettes/working-with-lidR.Rmd | 2 - 21 files changed, 117 insertions(+), 95 deletions(-)
Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality
assurance and quality control (QA/QC) of eddy covariance flux tower
data processing. It generates data-point removal code via
user-directed selection from a scatterplot, and can export a cleaned
.csv with removed points set to NA plus an R script for
reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>
Diff between fluxtools versions 0.5.0 dated 2025-08-21 and 0.6.0 dated 2025-08-27
DESCRIPTION | 9 MD5 | 34 NEWS.md | 54 - R/prm.R | 1076 +++++++++++------------ R/run_app.R | 70 - R/zzz.R | 20 README.md | 376 ++++---- inst/CITATION | 32 inst/app/app.R | 1607 +++++++++++++++++++++++------------ inst/doc/introduction.R | 144 +-- inst/doc/introduction.Rmd | 381 +++----- inst/doc/introduction.html | 1829 +++++++++++++++++++--------------------- inst/extdata |only man/apply_prm.Rd | 60 - man/get_prm_rules.Rd | 28 man/run_fluxtools.Rd | 40 tests/testthat/test-apply_prm.R | 354 +++---- vignettes/introduction.Rmd | 381 +++----- 18 files changed, 3482 insertions(+), 3013 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.11.2 dated 2025-07-11 and 1.11.2-8 dated 2025-08-27
DESCRIPTION | 12 ++--- MD5 | 56 ++++++++++++------------- NAMESPACE | 2 NEWS.md | 10 ++++ R/MCMC-support.R | 32 +++++++++++--- R/interfacing.R | 80 +++++++++++++++++++------------------ R/ref-grid.R | 3 - R/summary.R | 17 +++++-- R/transformations.R | 2 inst/doc/AQuickStart.html | 4 - inst/doc/FAQs.html | 8 +-- inst/doc/basics.html | 6 +- inst/doc/comparisons.html | 8 +-- inst/doc/confidence-intervals.html | 14 +++--- inst/doc/interactions.html | 16 +++---- inst/doc/messy-data.html | 4 - inst/doc/models.html | 4 - inst/doc/predictions.html | 4 - inst/doc/re-engineering-clds.html | 4 - inst/doc/sophisticated.html | 4 - inst/doc/transformations.html | 6 +- inst/doc/utilities.html | 4 - inst/doc/vignette-topics.html | 4 - inst/doc/xplanations.html | 4 - inst/doc/xtending.Rmd | 7 ++- inst/doc/xtending.html | 17 ++++--- man/extending-emmeans.Rd | 10 ---- man/hpd.summary.Rd | 15 ++++++ vignettes/xtending.Rmd | 7 ++- 29 files changed, 205 insertions(+), 159 deletions(-)
Title: Multivariate Normal Mean Monitoring Through Critical-to-X
Control Chart
Description: A comprehensive set of functions designed for multivariate mean monitoring using the Critical-to-X Control Chart. These functions enable the determination of optimal control limits based on a specified in-control Average Run Length (ARL), the calculation of out-of-control ARL for a given control limit, and post-signal analysis to identify the specific variable responsible for a detected shift in the mean. This suite of tools provides robust support for precise and effective process monitoring and analysis.
Author: Burcu Aytacoglu [aut] ,
Diana Barraza-Barraza [aut, cre] ,
Victor G. Tercero-Gomez [aut] ,
A. Eduardo Cordero-Franco [aut]
Maintainer: Diana Barraza-Barraza <diana.barraza@ujed.mx>
Diff between CTxCC versions 0.3.0 dated 2025-08-25 and 0.4.0 dated 2025-08-27
DESCRIPTION | 6 +- MD5 | 8 ++- R/Functions.R | 114 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/CTXoptim.Rd | 61 ++++++++++++++++------------- man/ms.optim.Rd |only man/ss.optim.Rd |only 6 files changed, 154 insertions(+), 35 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.
Author: Paul Hoffman [aut] ,
Rahul Satija [aut, cre] ,
David Collins [aut] ,
Yuhan Hao [aut] ,
Austin Hartman [aut] ,
Gesmira Molla [aut] ,
Andrew Butler [aut] ,
Tim Stuart [aut] ,
Madeline Kowalski [ctb] ,
Saket Choudhary [ctb] ,
Skylar Li [ctb],
Longda Jia [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between SeuratObject versions 5.1.0 dated 2025-04-22 and 5.2.0 dated 2025-08-27
DESCRIPTION | 41 +++++----- MD5 | 41 +++++----- NAMESPACE | 1 NEWS.md | 13 +++ R/fov.R | 13 ++- R/segmentation.R | 170 ++++++++++++++++++++++++++++++++++++++++++- R/seurat.R | 22 +++++ R/spatial.R | 7 + build/SeuratObject.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary man/Centroids-class.Rd | 3 man/Centroids-methods.Rd | 3 man/CreateFOV.Rd | 14 +++ man/CreateSegmentation.Rd | 3 man/Molecules-class.Rd | 3 man/Molecules-methods.Rd | 3 man/Segmentation-class.Rd | 13 ++- man/Segmentation-methods.Rd | 21 +++++ man/Segmentation-validity.Rd |only man/SeuratObject-package.Rd | 1 man/SpatialImage-class.Rd | 2 22 files changed, 321 insertions(+), 53 deletions(-)
Title: Bayesian Adaptive Trial Simulator Software (BATSS) for
Generalised Linear Models
Description: Defines operating characteristics of Bayesian Adaptive Trials considering a generalised linear model response via Monte Carlo simulations of Bayesian GLM fitted via integrated Laplace approximations (INLA).
Author: Dominique-Laurent Couturier [aut, cre] ,
Liz Ryan [aut] ,
Rainer Puhr [aut],
Thomas Jaki [aut] ,
Stephane Heritier [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Diff between BATSS versions 1.0.0 dated 2024-10-02 and 1.0.1 dated 2025-08-27
DESCRIPTION | 21 +++++++++++---------- MD5 | 2 +- 2 files changed, 12 insertions(+), 11 deletions(-)
Title: Continuous Time Stochastic Modelling using Template Model
Builder
Description: Perform state and parameter inference, and forecasting, in
stochastic state-space systems using the 'ctsmTMB' class. This class,
built with the 'R6' package, provides a user-friendly interface for
defining and handling state-space models. Inference is based on
maximum likelihood estimation, with derivatives efficiently computed
through automatic differentiation enabled by the 'TMB'/'RTMB' packages
(Kristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The available
inference methods include Kalman filters, in addition to a Laplace
approximation-based smoothing method. For further details of these
methods refer to the documentation of the 'CTSMR' package
<https://ctsm.info/ctsmr-reference.pdf> and Thygesen (2025)
<doi:10.48550/arXiv.2503.21358>. Forecasting capabilities include
moment predictions and stochastic path simulations, both implemented
in 'C++' using 'Rcpp' (Eddelbuettel et al., 2018)
<doi:10.1080/00031305.2017.1375990> for computational efficiency.
Author: Phillip Vetter [aut, cre, cph],
Jan Moeller [ctb],
Uffe Thygesen [ctb],
Peder Bacher [ctb],
Henrik Madsen [ctb]
Maintainer: Phillip Vetter <pbrve@dtu.dk>
Diff between ctsmTMB versions 1.0.0 dated 2025-04-08 and 1.0.1 dated 2025-08-27
ctsmTMB-1.0.0/ctsmTMB/R/EKF_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/LAPLACE2_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/LAPLACE_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/LKF_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/UKF_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/backup.R |only ctsmTMB-1.0.0/ctsmTMB/R/build_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/check_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/compile_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/data.R |only ctsmTMB-1.0.0/ctsmTMB/R/data_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/deriv_funs.R |only ctsmTMB-1.0.0/ctsmTMB/R/estimate_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/flags_and_rebuild.R |only ctsmTMB-1.0.0/ctsmTMB/R/methods.R |only ctsmTMB-1.0.0/ctsmTMB/R/model_function_strings.R |only ctsmTMB-1.0.0/ctsmTMB/R/new_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/predict_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/rcpp_estimate_test.R |only ctsmTMB-1.0.0/ctsmTMB/R/simulate_functions.R |only ctsmTMB-1.0.0/ctsmTMB/R/utils.R |only ctsmTMB-1.0.0/ctsmTMB/R/zzz_hacks.R |only ctsmTMB-1.0.0/ctsmTMB/inst/include/ctsmTMB_customfuns.hpp |only ctsmTMB-1.0.0/ctsmTMB/man/ctsm.Rd |only ctsmTMB-1.0.1/ctsmTMB/DESCRIPTION | 60 ctsmTMB-1.0.1/ctsmTMB/MD5 | 126 - ctsmTMB-1.0.1/ctsmTMB/NAMESPACE | 7 ctsmTMB-1.0.1/ctsmTMB/NEWS.md | 14 ctsmTMB-1.0.1/ctsmTMB/R/RcppExports.R | 8 ctsmTMB-1.0.1/ctsmTMB/R/S3methods.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_estimate_RTMB.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_estimate_TMB.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_filter.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_predict.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_returns.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_simulate.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_kalman_funs.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_misc_funs.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_strings.R |only ctsmTMB-1.0.1/ctsmTMB/R/ctsmTMB.R | 1030 +++++++----- ctsmTMB-1.0.1/ctsmTMB/R/method_estimate.R |only ctsmTMB-1.0.1/ctsmTMB/R/method_filter.R |only ctsmTMB-1.0.1/ctsmTMB/R/method_predict.R |only ctsmTMB-1.0.1/ctsmTMB/R/method_simulate.R |only ctsmTMB-1.0.1/ctsmTMB/R/method_smooth.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_builders.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_checkers.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_cpp_compilers.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_cpp_writers.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_data_setters.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_drules_and_extrafuns.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_flags.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_rebuilders.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_transformations.R |only ctsmTMB-1.0.1/ctsmTMB/R/model_utils.R |only ctsmTMB-1.0.1/ctsmTMB/R/zzz_data.R |only ctsmTMB-1.0.1/ctsmTMB/R/zzz_globalvariables.R |only ctsmTMB-1.0.1/ctsmTMB/R/zzz_imports.R | 14 ctsmTMB-1.0.1/ctsmTMB/R/zzzz_test_rcpp_estimate.R |only ctsmTMB-1.0.1/ctsmTMB/README.md | 86 - ctsmTMB-1.0.1/ctsmTMB/build/vignette.rds |binary ctsmTMB-1.0.1/ctsmTMB/inst/doc/ctsmTMB.R | 31 ctsmTMB-1.0.1/ctsmTMB/inst/doc/ctsmTMB.Rmd | 38 ctsmTMB-1.0.1/ctsmTMB/inst/doc/ctsmTMB.html | 152 - ctsmTMB-1.0.1/ctsmTMB/inst/doc/estimate.Rmd | 4 ctsmTMB-1.0.1/ctsmTMB/inst/doc/estimate.html | 8 ctsmTMB-1.0.1/ctsmTMB/inst/doc/predict.html | 46 ctsmTMB-1.0.1/ctsmTMB/inst/doc/using_another_optimizer.Rmd | 1 ctsmTMB-1.0.1/ctsmTMB/inst/doc/using_another_optimizer.html | 73 ctsmTMB-1.0.1/ctsmTMB/inst/include/ctsmTMB.h | 10 ctsmTMB-1.0.1/ctsmTMB/inst/include/template_ekf.h |only ctsmTMB-1.0.1/ctsmTMB/inst/include/template_lkf.h |only ctsmTMB-1.0.1/ctsmTMB/inst/include/template_ukf.h |only ctsmTMB-1.0.1/ctsmTMB/man/Ornstein.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/ctsmTMB.Rd | 284 +++ ctsmTMB-1.0.1/ctsmTMB/man/plot.ctsmTMB.fit.Rd | 16 ctsmTMB-1.0.1/ctsmTMB/man/plot.ctsmTMB.pred.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/plot.ctsmTMB.profile.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/print.ctsmTMB.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/print.ctsmTMB.fit.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/profile.ctsmTMB.fit.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/man/summary.ctsmTMB.fit.Rd | 2 ctsmTMB-1.0.1/ctsmTMB/src/Makevars.win | 8 ctsmTMB-1.0.1/ctsmTMB/src/RcppExports.cpp | 40 ctsmTMB-1.0.1/ctsmTMB/src/ekf_filter.cpp |only ctsmTMB-1.0.1/ctsmTMB/src/ekf_predict.cpp | 30 ctsmTMB-1.0.1/ctsmTMB/src/ekf_simulate.cpp | 10 ctsmTMB-1.0.1/ctsmTMB/src/helper_funs2.h | 65 ctsmTMB-1.0.1/ctsmTMB/tests/testthat/test-first.R | 6 ctsmTMB-1.0.1/ctsmTMB/vignettes/ctsmTMB.Rmd | 38 ctsmTMB-1.0.1/ctsmTMB/vignettes/estimate.Rmd | 4 ctsmTMB-1.0.1/ctsmTMB/vignettes/using_another_optimizer.Rmd | 1 92 files changed, 1455 insertions(+), 769 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] ,
Arnaud Barras [aut] ,
Veronika Braunisch [aut] ,
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sdmtune@gmail.com>
Diff between SDMtune versions 1.3.2 dated 2024-12-16 and 1.3.3 dated 2025-08-27
DESCRIPTION | 16 MD5 | 96 ++--- NEWS.md | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/basic-use.R | 414 +++++++++++------------ inst/doc/basic-use.html | 2 inst/doc/hyper-tuning.R | 266 +++++++------- inst/doc/presence-absence.R | 114 +++--- inst/doc/var-selection.R | 290 ++++++++-------- tests/testthat/_snaps/ANN-class.md | 32 - tests/testthat/_snaps/BRT-class.md | 34 - tests/testthat/_snaps/Maxent-class.md | 30 - tests/testthat/_snaps/Maxnet-class.md | 28 - tests/testthat/_snaps/RF-class.md | 30 - tests/testthat/_snaps/SDMmodel-class.md | 194 +++++----- tests/testthat/_snaps/SDMmodel2MaxEnt.md | 10 tests/testthat/_snaps/SDMmodelCV-class.md | 202 +++++------ tests/testthat/_snaps/SDMtune-class.md | 28 - tests/testthat/_snaps/SWD-class.md | 104 ++--- tests/testthat/_snaps/addSamplesToBg.md | 10 tests/testthat/_snaps/aicc.md | 30 - tests/testthat/_snaps/auc.md | 20 - tests/testthat/_snaps/checkMaxentInstallation.md | 22 - tests/testthat/_snaps/confMatrix.md | 20 - tests/testthat/_snaps/convertFolds.md | 8 tests/testthat/_snaps/corVar.md | 10 tests/testthat/_snaps/doJk.md | 20 - tests/testthat/_snaps/gridSearch.md | 20 - tests/testthat/_snaps/maxentTh.md | 10 tests/testthat/_snaps/maxentVarImp.md | 10 tests/testthat/_snaps/mergeSWD.md | 24 - tests/testthat/_snaps/modelReport.md | 146 ++++---- tests/testthat/_snaps/optimizeModel.md | 74 ++-- tests/testthat/_snaps/plotJk.md | 8 tests/testthat/_snaps/plotPA.md | 28 - tests/testthat/_snaps/plotPred.md | 20 - tests/testthat/_snaps/predict-SDMmodel.md | 58 +-- tests/testthat/_snaps/predict-SDMmodelCV.md | 58 +-- tests/testthat/_snaps/prepareSWD.md | 36 +- tests/testthat/_snaps/randomFolds.md | 10 tests/testthat/_snaps/reduceVar.md | 28 - tests/testthat/_snaps/swd2csv.md | 8 tests/testthat/_snaps/trainMaxent.md | 10 tests/testthat/_snaps/trainValTest.md | 10 tests/testthat/_snaps/tss.md | 20 - tests/testthat/_snaps/utils.md | 134 +++---- tests/testthat/_snaps/varSel.md | 28 - tests/testthat/test-plotCor.R | 9 49 files changed, 1398 insertions(+), 1387 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>.
Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case
study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
Author: Clara Happ-Kurz [aut, cre]
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between MFPCA versions 1.3-10 dated 2022-09-15 and 1.3-11 dated 2025-08-27
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- R/MFPCAfit_methods.R | 1 - R/univariateExpansions.R | 6 +++--- README.md | 3 --- build/partial.rdb |binary configure.ac | 2 +- inst/CITATION | 8 ++++---- man/findAlphaVopt.Rd | 4 ++-- man/splineFunction1D.Rd | 2 +- man/splineFunction2D.Rd | 2 +- man/univExpansion.Rd | 2 +- 12 files changed, 31 insertions(+), 34 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 Asasihba [aut, cre],
Hirokazu Iwasawa [aut],
Reiji Kozuma [ctb]
Maintainer: Ryoichi Asasihba <ryoichi.asashiba@gmail.com>
Diff between midr versions 0.5.0 dated 2025-06-23 and 0.5.1 dated 2025-08-27
midr-0.5.0/midr/R/mid_extract.R |only midr-0.5.0/midr/R/weighted.R |only midr-0.5.0/midr/man/mid.extract.Rd |only midr-0.5.0/midr/man/weighted.Rd |only midr-0.5.0/midr/man/weighted.mse.Rd |only midr-0.5.1/midr/DESCRIPTION | 11 midr-0.5.1/midr/MD5 | 147 +- midr-0.5.1/midr/NAMESPACE | 24 midr-0.5.1/midr/NEWS.md | 116 +- midr-0.5.1/midr/R/RcppExports.R |only midr-0.5.1/midr/R/color_theme.R | 868 +++++++-------- midr-0.5.1/midr/R/color_theme_info.R |only midr-0.5.1/midr/R/factor_encoder.R | 75 - midr-0.5.1/midr/R/get_yhat.R | 142 +- midr-0.5.1/midr/R/ggmid.R | 68 - midr-0.5.1/midr/R/ggmid_mid_breakdown.R | 51 midr-0.5.1/midr/R/ggmid_mid_conditional.R | 53 midr-0.5.1/midr/R/ggmid_mid_importance.R | 51 midr-0.5.1/midr/R/interpret.R | 407 +++---- midr-0.5.1/midr/R/mid_breakdown.R | 68 - midr-0.5.1/midr/R/mid_conditional.R | 57 midr-0.5.1/midr/R/mid_effect.R |only midr-0.5.1/midr/R/mid_importance.R | 43 midr-0.5.1/midr/R/mid_plots.R | 33 midr-0.5.1/midr/R/mid_terms.R |only midr-0.5.1/midr/R/midr-package.R | 15 midr-0.5.1/midr/R/misc_functions.R | 361 ------ midr-0.5.1/midr/R/numeric_encoder.R | 115 + midr-0.5.1/midr/R/plot_mid.R | 62 - midr-0.5.1/midr/R/plot_mid_breakdown.R | 52 midr-0.5.1/midr/R/plot_mid_conditional.R | 55 midr-0.5.1/midr/R/plot_mid_importance.R | 52 midr-0.5.1/midr/R/predict_mid.R | 101 - midr-0.5.1/midr/R/print_mid.R | 27 midr-0.5.1/midr/R/scale_color_theme.R |only midr-0.5.1/midr/R/set_color_theme.R |only midr-0.5.1/midr/R/shapviz_mid.R | 18 midr-0.5.1/midr/R/summary_mid.R | 48 midr-0.5.1/midr/R/theme_midr.R |only midr-0.5.1/midr/R/weighted_loss.R |only midr-0.5.1/midr/R/weighted_quantile.R |only midr-0.5.1/midr/R/zzz.R |only midr-0.5.1/midr/README.md | 29 midr-0.5.1/midr/build/partial.rdb |binary midr-0.5.1/midr/man/color.theme.Rd | 108 + midr-0.5.1/midr/man/color.theme.info.Rd |only midr-0.5.1/midr/man/factor.encoder.Rd | 50 midr-0.5.1/midr/man/figures/README-ggmid-1.png |binary midr-0.5.1/midr/man/figures/README-mid_breakdown-1.png |binary midr-0.5.1/midr/man/figures/README-mid_conditional-1.png |binary midr-0.5.1/midr/man/figures/README-mid_importance-1.png |binary midr-0.5.1/midr/man/figures/logo.png |binary midr-0.5.1/midr/man/get.yhat.Rd | 61 - midr-0.5.1/midr/man/ggmid.Rd | 52 midr-0.5.1/midr/man/ggmid.mid.breakdown.Rd | 42 midr-0.5.1/midr/man/ggmid.mid.conditional.Rd | 39 midr-0.5.1/midr/man/ggmid.mid.importance.Rd | 40 midr-0.5.1/midr/man/interpret.Rd | 92 - midr-0.5.1/midr/man/mid.breakdown.Rd | 58 - midr-0.5.1/midr/man/mid.conditional.Rd | 57 midr-0.5.1/midr/man/mid.effect.Rd |only midr-0.5.1/midr/man/mid.importance.Rd | 39 midr-0.5.1/midr/man/mid.plots.Rd | 29 midr-0.5.1/midr/man/mid.terms.Rd |only midr-0.5.1/midr/man/numeric.encoder.Rd | 69 - midr-0.5.1/midr/man/plot.mid.Rd | 51 midr-0.5.1/midr/man/plot.mid.breakdown.Rd | 43 midr-0.5.1/midr/man/plot.mid.conditional.Rd | 45 midr-0.5.1/midr/man/plot.mid.importance.Rd | 43 midr-0.5.1/midr/man/predict.mid.Rd | 56 midr-0.5.1/midr/man/print.mid.Rd | 24 midr-0.5.1/midr/man/scale_color_theme.Rd | 37 midr-0.5.1/midr/man/set.color.theme.Rd |only midr-0.5.1/midr/man/shapviz.mid.Rd | 10 midr-0.5.1/midr/man/summary.mid.Rd | 27 midr-0.5.1/midr/man/theme_midr.Rd | 21 midr-0.5.1/midr/man/weighted.loss.Rd |only midr-0.5.1/midr/man/weighted.quantile.Rd | 9 midr-0.5.1/midr/man/weighted.tabulate.Rd | 9 midr-0.5.1/midr/src |only midr-0.5.1/midr/tests/testthat/test-color_theme.R |only midr-0.5.1/midr/tests/testthat/test-fittedvalues.R |only midr-0.5.1/midr/tests/testthat/test-getyhat.R |only midr-0.5.1/midr/tests/testthat/test-infunction.R |only midr-0.5.1/midr/tests/testthat/test-interpret.R | 22 midr-0.5.1/midr/tests/testthat/test-mid_f.R | 4 midr-0.5.1/midr/tests/testthat/test-modelframe.R |only 87 files changed, 2299 insertions(+), 1987 deletions(-)
Title: Calculate Carbon-Equivalent Emissions
Description: Provides a flexible tool for calculating carbon-equivalent emissions. Mostly using data from the UK Government's Greenhouse Gas Conversion Factors report <https://www.gov.uk/government/publications/greenhouse-gas-reporting-conversion-factors-2024>, it facilitates transparent emissions calculations for various sectors, including travel, accommodation, and clinical activities. The package is designed for easy integration into R workflows, with additional support for 'shiny' applications and community-driven extensions.
Author: Lily Clements [aut, cre]
Maintainer: Lily Clements <lily@idems.international>
Diff between carbonr versions 0.2.1 dated 2024-10-16 and 0.2.7 dated 2025-08-27
carbonr-0.2.1/carbonr/tests/testthat/test-household_emissions.R |only carbonr-0.2.1/carbonr/tests/testthat/test-industrial_emissions.R |only carbonr-0.2.7/carbonr/DESCRIPTION | 19 carbonr-0.2.7/carbonr/MD5 | 106 +- carbonr-0.2.7/carbonr/R/airplane_emissions.R | 11 carbonr-0.2.7/carbonr/R/airport_finder.R | 4 carbonr-0.2.7/carbonr/R/building_emissions.R | 253 +++--- carbonr-0.2.7/carbonr/R/clinical_emissions.R | 222 ++++- carbonr-0.2.7/carbonr/R/clinical_theatre_data.R | 339 ++++++-- carbonr-0.2.7/carbonr/R/construction_emissions.R | 348 +++++--- carbonr-0.2.7/carbonr/R/electrical_emissions.R | 315 ++++++- carbonr-0.2.7/carbonr/R/global.R | 2 carbonr-0.2.7/carbonr/R/hotel_emissions.R | 22 carbonr-0.2.7/carbonr/R/household_emissions.R | 398 ++++++---- carbonr-0.2.7/carbonr/R/land_emissions.R | 1 carbonr-0.2.7/carbonr/R/material_emissions.R | 351 +++++--- carbonr-0.2.7/carbonr/R/metal_emissions.R | 285 +++++-- carbonr-0.2.7/carbonr/R/office_emissions.R | 157 ++- carbonr-0.2.7/carbonr/R/paper_emissions.R | 262 +++++- carbonr-0.2.7/carbonr/R/plastic_emissions.R | 284 ++++--- carbonr-0.2.7/carbonr/R/rail_emissions.R | 102 +- carbonr-0.2.7/carbonr/R/stations.R | 2 carbonr-0.2.7/carbonr/R/sysdata.rda |binary carbonr-0.2.7/carbonr/R/vehicle_emissions.R | 9 carbonr-0.2.7/carbonr/README.md | 18 carbonr-0.2.7/carbonr/build/vignette.rds |binary carbonr-0.2.7/carbonr/inst/carbonr_0.2.2.pdf |only carbonr-0.2.7/carbonr/inst/doc/introduction-to-carbonr.R | 160 ++-- carbonr-0.2.7/carbonr/inst/doc/introduction-to-carbonr.Rmd | 56 - carbonr-0.2.7/carbonr/inst/doc/introduction-to-carbonr.html | 121 +-- carbonr-0.2.7/carbonr/inst/sysdata_update.R |only carbonr-0.2.7/carbonr/inst/uk_gov_data.xlsx |only carbonr-0.2.7/carbonr/inst/uk_gov_data_2024.xlsx |only carbonr-0.2.7/carbonr/inst/uk_gov_data_2025.xlsx |only carbonr-0.2.7/carbonr/man/building_emissions.Rd | 66 + carbonr-0.2.7/carbonr/man/carbonr.Rd | 2 carbonr-0.2.7/carbonr/man/clinical_theatre_data.Rd | 252 ++---- carbonr-0.2.7/carbonr/man/clinical_theatre_emissions.Rd | 217 ++--- carbonr-0.2.7/carbonr/man/construction_emissions.Rd | 207 ++--- carbonr-0.2.7/carbonr/man/electrical_emissions.Rd | 102 +- carbonr-0.2.7/carbonr/man/hotel_emissions.Rd | 8 carbonr-0.2.7/carbonr/man/household_emissions.Rd | 283 +------ carbonr-0.2.7/carbonr/man/material_emissions.Rd | 367 +-------- carbonr-0.2.7/carbonr/man/metal_emissions.Rd | 92 +- carbonr-0.2.7/carbonr/man/office_emissions.Rd | 67 + carbonr-0.2.7/carbonr/man/paper_emissions.Rd | 70 + carbonr-0.2.7/carbonr/man/plastic_emissions.Rd | 159 ++- carbonr-0.2.7/carbonr/man/rail_emissions.Rd | 10 carbonr-0.2.7/carbonr/man/stations.Rd | 2 carbonr-0.2.7/carbonr/man/vehicle_emissions.Rd | 8 carbonr-0.2.7/carbonr/tests/testthat/test-building_emissions.R | 71 + carbonr-0.2.7/carbonr/tests/testthat/test-clinical_theatre_data.R | 81 +- carbonr-0.2.7/carbonr/tests/testthat/test-land_emissions.R | 2 carbonr-0.2.7/carbonr/tests/testthat/test-material_emissions.R |only carbonr-0.2.7/carbonr/tests/testthat/test-office_emissions.R | 2 carbonr-0.2.7/carbonr/tests/testthat/test-output_display.R | 14 carbonr-0.2.7/carbonr/tests/testthat/test-z_household_emissions.R |only carbonr-0.2.7/carbonr/tests/testthat/test-z_industrial_emissions.R |only carbonr-0.2.7/carbonr/vignettes/introduction-to-carbonr.Rmd | 56 - 59 files changed, 3503 insertions(+), 2482 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression or any other function. Also includes a comprehensive framework for discrete-time
simulation, and networks-based simulation which can generate even more complex longitudinal and dependent data.
For more details, see Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.3.2 dated 2025-06-24 and 0.4.0 dated 2025-08-27
DESCRIPTION | 12 - MD5 | 124 +++++++++------- NAMESPACE | 6 NEWS.md | 23 +++ R/dag.r | 82 +++++++---- R/dag2matrix.r | 42 +++-- R/dag_from_data.r | 2 R/formula_interface.r | 45 +++++- R/input_checks.r | 72 ++++++++- R/network.r |only R/node.r | 53 ++++--- R/node_identity.r | 68 ++++++++- R/node_lmer.r | 5 R/node_time_to_event.r | 10 + R/sim_discrete_time.r | 127 +++++++++++++---- R/sim_dt_helpers.r | 9 - R/sim_from_dag.r | 80 ++++++++-- R/sim_n_datasets.r | 6 build/vignette.rds |binary inst/doc/simDAG.R | 2 inst/doc/simDAG.Rmd | 8 - inst/doc/simDAG.html | 34 ++-- inst/doc/v_covid_example.Rmd | 3 inst/doc/v_covid_example.html | 5 inst/doc/v_custom_nodes.R | 4 inst/doc/v_custom_nodes.Rmd | 15 +- inst/doc/v_custom_nodes.html | 84 ++++++----- inst/doc/v_sim_from_dag.Rmd | 34 ++-- inst/doc/v_sim_from_dag.html | 113 ++++++++++----- inst/doc/v_sim_networks.R |only inst/doc/v_sim_networks.Rmd |only inst/doc/v_sim_networks.html |only man/add_node.Rd | 12 - man/as.igraph.DAG.Rd | 5 man/dag2matrix.Rd | 6 man/net.Rd |only man/network.Rd |only man/node_identity.Rd | 82 ++++++++++- man/node_time_to_event.Rd | 5 man/node_zeroinfl.Rd | 2 man/plot.DAG.Rd | 5 man/simDAG.Rd | 7 man/sim_discrete_time.Rd | 11 + man/sim_from_dag.Rd | 22 ++ tests/testthat/_snaps/DAG.network_S3.md |only tests/testthat/_snaps/dag.md | 2 tests/testthat/test_DAG.network_S3.r |only tests/testthat/test_dag.r | 3 tests/testthat/test_dag2matrix.r | 31 ++++ tests/testthat/test_input_checks_node.r | 12 + tests/testthat/test_input_checks_sim2data.r | 15 ++ tests/testthat/test_input_checks_sim_discrete_time.r | 13 + tests/testthat/test_network.r |only tests/testthat/test_node.r | 11 + tests/testthat/test_node_cox.r | 14 + tests/testthat/test_node_identity.r | 140 +++++++++++++++++++ tests/testthat/test_node_lmer.r | 29 +++ tests/testthat/test_node_time_to_event.r | 57 +++++++ tests/testthat/test_sim2data.r | 4 tests/testthat/test_sim_discrete_time.r | 71 +++++++++ tests/testthat/test_sim_from_dag.r | 32 +++- tests/testthat/test_sim_n_datasets.r | 4 vignettes/images_v_joss/disc_time_sim.bib | 49 ++++++ vignettes/simDAG.Rmd | 8 - vignettes/v_covid_example.Rmd | 3 vignettes/v_custom_nodes.Rmd | 15 +- vignettes/v_sim_from_dag.Rmd | 34 ++-- vignettes/v_sim_networks.Rmd |only 68 files changed, 1411 insertions(+), 361 deletions(-)
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.9 dated 2025-07-25 and 1.7.0 dated 2025-08-27
DESCRIPTION | 6 +++--- MD5 | 31 ++++++++++++++++--------------- NEWS.md | 6 ++++++ R/inline.R |only R/pm2-3.R | 29 ++++++++++++++++++++++------- inst/doc/Introduction.R | 30 +++++++++++++++--------------- inst/doc/Introduction.Rnw | 7 ++++++- inst/doc/Introduction.pdf |binary inst/doc/SimpleGuide.pdf |binary inst/doc/multistate.pdf |binary inst/doc/predictnl.pdf |binary man/gsm.control.Rd | 6 +++++- src/test-nmmin.cpp | 32 ++++++++++++++++++++++++-------- tests/testthat/test_base.R | 15 +++++++-------- tests/testthat/test_delayed.R | 6 ++++++ tests/testthat/test_missing.R | 12 ++++++------ vignettes/Introduction.Rnw | 7 ++++++- 17 files changed, 122 insertions(+), 65 deletions(-)
Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.0 dated 2025-04-24 and 0.1.1 dated 2025-08-27
hdMTD-0.1.0/hdMTD/LICENSE |only hdMTD-0.1.0/hdMTD/README.md |only hdMTD-0.1.1/hdMTD/DESCRIPTION | 8 ++++---- hdMTD-0.1.1/hdMTD/MD5 | 5 ++--- hdMTD-0.1.1/hdMTD/NEWS.md |only 5 files changed, 6 insertions(+), 7 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations, (3) calculating confidence intervals and the associated
actual coverage for binomial proportions, (4) calculating the support values and the
probability mass function of the Kaplan-Meier product-limit estimator, and (5) plotting
the actual coverage function associated with a confidence interval for the survivor
function from a randomly right-censored data set. Each is given in greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif,
weibull) corresponding to a user-given complete or right-censored dataset and level of
significance. The crplot() algorithm plots more points in areas of greater curvature to
ensure a smooth appearance throughout the confidence region boundary. An alternative
heuristic plots a specified number of poin [...truncated...]
Author: Christopher Weld [aut, cre] ,
Kexin Feng [aut],
Hayeon Park [aut],
Yuxin Qin [aut],
Xingyu Wang [aut],
Heather Sasinowska [aut],
Lawrence Leemis [aut],
Yuan Chang [ctb],
Brock Crook [ctb],
Chris Kuebler [ctb],
Andrew Loh [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld241@gmail.com>
Diff between conf versions 1.9.1 dated 2024-05-05 and 1.9.2 dated 2025-08-27
conf-1.9.1/conf/tests |only conf-1.9.2/conf/DESCRIPTION | 13 +- conf-1.9.2/conf/MD5 | 51 ++++----- conf-1.9.2/conf/NAMESPACE | 2 conf-1.9.2/conf/R/STAR_package_functions.R | 3 conf-1.9.2/conf/R/conf-package.R | 1 conf-1.9.2/conf/build/vignette.rds |binary conf-1.9.2/conf/inst/CITATION | 2 conf-1.9.2/conf/inst/doc/coversim.R | 84 +++++++-------- conf-1.9.2/conf/inst/doc/coversim.html | 113 +++++++++----------- conf-1.9.2/conf/inst/doc/crplot.R | 30 ++--- conf-1.9.2/conf/inst/doc/crplot.html | 4 conf-1.9.2/conf/inst/doc/crplot_advanced.R | 144 +++++++++++++------------- conf-1.9.2/conf/inst/doc/crplot_advanced.html | 4 conf-1.9.2/conf/inst/doc/km.outcomes.R | 2 conf-1.9.2/conf/inst/doc/km.outcomes.html | 4 conf-1.9.2/conf/inst/doc/km.pmf.R | 10 - conf-1.9.2/conf/inst/doc/km.pmf.html | 4 conf-1.9.2/conf/inst/doc/km.support.R | 2 conf-1.9.2/conf/inst/doc/km.support.html | 4 conf-1.9.2/conf/inst/doc/km.surv.R | 12 +- conf-1.9.2/conf/inst/doc/km.surv.html | 4 conf-1.9.2/conf/man/conf.Rd | 1 conf-1.9.2/conf/man/km.outcomes.Rd | 12 +- conf-1.9.2/conf/man/km.pmf.Rd | 20 +-- conf-1.9.2/conf/man/km.support.Rd | 2 conf-1.9.2/conf/man/km.surv.Rd | 2 27 files changed, 264 insertions(+), 266 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
treespaceServer().
For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
Author: Thibaut Jombart [aut] ,
Michelle Kendall [aut, cre] ,
Jacob Almagro-Garcia [aut] ,
Caroline Colijn [aut]
Maintainer: Michelle Kendall <michelle.kendall@ndm.ox.ac.uk>
Diff between treespace versions 1.1.4.3 dated 2023-09-07 and 1.1.4.4 dated 2025-08-27
DESCRIPTION | 24 +++++++++++++----------- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/plotGroves.R | 4 ++-- R/plotTreeDiff.R | 2 +- build/vignette.rds |binary inst/doc/DengueVignette.html | 4 ++-- inst/doc/TransmissionTreesVignette.html | 4 ++-- inst/doc/introduction.html | 4 ++-- inst/doc/tipCategories.html | 4 ++-- man/plotGroves.Rd | 2 +- man/plotGrovesD3.Rd | 2 +- man/plotTreeDiff.Rd | 2 +- 13 files changed, 44 insertions(+), 37 deletions(-)
More information about SampleSizeCalculator at CRAN
Permanent link
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around by Pascal Have of 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@asnr.fr>
This is a re-admission after prior archival of version 0.9-2.1 dated 2025-07-23
Diff between rlibkriging versions 0.9-2.1 dated 2025-07-23 and 0.9-2.2 dated 2025-08-27
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- src/libK/lbfgsb_cpp/Lbfgsb.3.0/include/lbfgsb/lbfgsb.h | 2 +- tools/setup.sh | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Renewal Method for Extreme Values Extrapolation
Description: Peaks Over Threshold (POT) or 'methode du renouvellement'. The
distribution for the excesses can be chosen, and heterogeneous data
(including historical data or block data) can be used in a
Maximum-Likelihood framework.
Author: Yves Deville [aut] ,
Bardet [aut],
Nathan Bengaouer [cre]
Maintainer: Nathan Bengaouer <nathan.bengaouer@asnr.fr>
Diff between Renext versions 3.1-4 dated 2023-08-29 and 3.1-5 dated 2025-08-27
ChangeLog | 17 +++++++++++++++++ DESCRIPTION | 29 ++++++++++++++++++++++------- MD5 | 14 +++++++------- R/anova.Renouv.R | 22 ++++++++++++---------- R/interevt.R | 3 ++- R/plot.Renouv.R | 2 +- build/partial.rdb |binary man/NBlevy.Rd | 2 +- 8 files changed, 62 insertions(+), 27 deletions(-)
Title: Fast and Efficient Processing of PAM Data
Description: Processing Chlorophyll Fluorescence & P700 Absorbance data generated by WALZ hardware. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.
Author: Julien Boehm [cre, aut] ,
Philipp Schrag [aut]
Maintainer: Julien Boehm <julien.boehm@uni-rostock.de>
Diff between pam versions 1.0.4 dated 2025-07-29 and 1.0.6 dated 2025-08-27
DESCRIPTION | 6 MD5 | 17 R/read_pam_data.R | 458 ++++++++++---------- build/partial.rdb |binary inst/CITATION | 16 man/read_dual_pam_data.Rd | 2 man/read_junior_pam_data.Rd | 96 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/results/20240925_model_result.csv |only tests/testthat/results/20240925_raw_data.csv |only tests/testthat/results/20240925_regression_data.csv |only 11 files changed, 299 insertions(+), 296 deletions(-)
Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: Francois Rousset [aut, cre, cph] ,
Jimmy Lopez [ctb],
Alexandre Genin [ctb],
Khalid Belkhir [ctb]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between genepop versions 1.2.2 dated 2023-01-19 and 1.2.11 dated 2025-08-27
genepop-1.2.11/genepop/DESCRIPTION | 14 genepop-1.2.11/genepop/MD5 | 76 - genepop-1.2.11/genepop/NAMESPACE | 3 genepop-1.2.11/genepop/R/Genepop.R | 6 genepop-1.2.11/genepop/inst/CITATION | 16 genepop-1.2.11/genepop/inst/NEWS.Rd | 23 genepop-1.2.11/genepop/inst/doc/404.html | 84 - genepop-1.2.11/genepop/inst/doc/GenepopS.Rmd | 34 genepop-1.2.11/genepop/inst/doc/GenepopS.pdf |binary genepop-1.2.11/genepop/inst/doc/GenepopS.tex | 538 ++++----- genepop-1.2.11/genepop/inst/doc/all-menu-options.html | 90 - genepop-1.2.11/genepop/inst/doc/bibliography.html | 88 - genepop-1.2.11/genepop/inst/doc/code-maintenance-credits-contact-etc..html | 84 - genepop-1.2.11/genepop/inst/doc/copyright.html | 84 - genepop-1.2.11/genepop/inst/doc/evaluating-the-performance-of-inferences-for-isolation-by-distance.html | 84 - genepop-1.2.11/genepop/inst/doc/genepop.bib | 2 genepop-1.2.11/genepop/inst/doc/installing-genepop-and-session-examples.html | 106 + genepop-1.2.11/genepop/inst/doc/introduction.html | 96 - genepop-1.2.11/genepop/inst/doc/libs/gitbook-2.6.7/css/plugin-highlight.css | 2 genepop-1.2.11/genepop/inst/doc/libs/gitbook-2.6.7/js/plugin-fontsettings.js | 25 genepop-1.2.11/genepop/inst/doc/methods.html | 88 - genepop-1.2.11/genepop/inst/doc/opt74.md | 2 genepop-1.2.11/genepop/inst/doc/sec-settings.html | 84 - genepop-1.2.11/genepop/inst/doc/the-input-file.html | 84 - genepop-1.2.11/genepop/inst/genepop-shiny/pages/pages_def_optsMOAO.R | 9 genepop-1.2.11/genepop/inst/make-exe/make_exe.bat | 2 genepop-1.2.11/genepop/man/GUI.Rd | 28 genepop-1.2.11/genepop/src/F_est.cpp | 542 +++++----- genepop-1.2.11/genepop/src/F_est.h | 2 genepop-1.2.11/genepop/src/GenepopS.cpp | 7 genepop-1.2.11/genepop/src/Makevars | 2 genepop-1.2.11/genepop/src/Makevars.win | 6 genepop-1.2.11/genepop/src/RGenepop.cpp | 13 genepop-1.2.11/genepop/src/bootstrap.cpp | 4 genepop-1.2.11/genepop/src/genepop.cpp | 57 - genepop-1.2.11/genepop/src/multimig.cpp | 10 genepop-1.2.11/genepop/tests/test-all.R | 22 genepop-1.2.11/genepop/tests/testthat/test_IBD.R | 6 genepop-1.2.2/genepop/inst/genepop-shiny/cmdline.old |only genepop-1.2.2/genepop/inst/genepop-shiny/fichier.in |only 40 files changed, 1271 insertions(+), 1152 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate
the command line behaviour of R.
Author: Hadley Wickham [aut, cre],
Yihui Xie [aut] ,
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevicius [ctb],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between evaluate versions 1.0.4 dated 2025-06-18 and 1.0.5 dated 2025-08-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/evaluation.R | 2 ++ R/watchout.R | 27 +++++++++++++++++---------- 5 files changed, 30 insertions(+), 17 deletions(-)
Title: Causal Decomposition Analysis
Description: We implement causal decomposition analysis using methods proposed by Park, Lee, and Qin (2022) and Park, Kang, and Lee (2023), which provide researchers with multiple-mediator imputation, single-mediator imputation, and product-of-coefficients regression approaches to estimate the initial disparity, disparity reduction, and disparity remaining (<doi:10.1177/00491241211067516>; <doi:10.1177/00811750231183711>). We also implement sensitivity analysis for causal decomposition using R-squared values as sensitivity parameters (Park, Kang, Lee, and Ma, 2023 <doi:10.1515/jci-2022-0031>). Finally, we include individualized causal decomposition and sensitivity analyses proposed by Park, Kang, and Lee (2025+) <doi:10.48550/arXiv.2506.19010>.
Author: Suyeon Kang [aut, cre],
Soojin Park [aut],
Karen Xu [ctb]
Maintainer: Suyeon Kang <suyeon.kang@ucf.edu>
Diff between causal.decomp versions 0.1.0 dated 2023-03-03 and 0.2.0 dated 2025-08-27
causal.decomp-0.1.0/causal.decomp/R/select.treat.R |only causal.decomp-0.1.0/causal.decomp/R/select.treat.pocr.R |only causal.decomp-0.1.0/causal.decomp/man/causal.decomp.Rd |only causal.decomp-0.2.0/causal.decomp/DESCRIPTION | 39 causal.decomp-0.2.0/causal.decomp/MD5 | 67 causal.decomp-0.2.0/causal.decomp/NAMESPACE | 25 causal.decomp-0.2.0/causal.decomp/R/aaa-rpart-compat.R |only causal.decomp-0.2.0/causal.decomp/R/causal.decomp.R | 48 causal.decomp-0.2.0/causal.decomp/R/combine.R | 126 - causal.decomp-0.2.0/causal.decomp/R/combine.b.R | 144 - causal.decomp-0.2.0/causal.decomp/R/data.R | 159 + causal.decomp-0.2.0/causal.decomp/R/genU.R |only causal.decomp-0.2.0/causal.decomp/R/globals.R | 18 causal.decomp-0.2.0/causal.decomp/R/ind.decomp.R |only causal.decomp-0.2.0/causal.decomp/R/ind.sens.R |only causal.decomp-0.2.0/causal.decomp/R/mmi.R | 815 ++++----- causal.decomp-0.2.0/causal.decomp/R/pocr.R | 796 ++++----- causal.decomp-0.2.0/causal.decomp/R/print.R | 154 + causal.decomp-0.2.0/causal.decomp/R/reg1_no_int.R |only causal.decomp-0.2.0/causal.decomp/R/select_group.R |only causal.decomp-0.2.0/causal.decomp/R/select_group_pocr.R |only causal.decomp-0.2.0/causal.decomp/R/sensitivity.R | 702 +++---- causal.decomp-0.2.0/causal.decomp/R/smi.R | 882 +++++----- causal.decomp-0.2.0/causal.decomp/R/zzz-globals.R |only causal.decomp-0.2.0/causal.decomp/R/zzz-imports.R |only causal.decomp-0.2.0/causal.decomp/build/vignette.rds |binary causal.decomp-0.2.0/causal.decomp/data/idata.rda |only causal.decomp-0.2.0/causal.decomp/data/sMIDUS.rda |binary causal.decomp-0.2.0/causal.decomp/data/sdata.rda |binary causal.decomp-0.2.0/causal.decomp/inst/doc/Releases.R | 18 causal.decomp-0.2.0/causal.decomp/inst/doc/Releases.Rmd | 73 causal.decomp-0.2.0/causal.decomp/inst/doc/Releases.html | 617 +++--- causal.decomp-0.2.0/causal.decomp/man/causal.decomp-package.Rd |only causal.decomp-0.2.0/causal.decomp/man/idata.Rd |only causal.decomp-0.2.0/causal.decomp/man/ind.decomp.Rd |only causal.decomp-0.2.0/causal.decomp/man/ind.sens.Rd |only causal.decomp-0.2.0/causal.decomp/man/mmi.Rd | 86 causal.decomp-0.2.0/causal.decomp/man/pocr.Rd | 26 causal.decomp-0.2.0/causal.decomp/man/sMIDUS.Rd | 6 causal.decomp-0.2.0/causal.decomp/man/sdata.Rd | 8 causal.decomp-0.2.0/causal.decomp/man/sensitivity.Rd | 26 causal.decomp-0.2.0/causal.decomp/man/smi.Rd | 60 causal.decomp-0.2.0/causal.decomp/vignettes/Releases.Rmd | 73 43 files changed, 2574 insertions(+), 2394 deletions(-)
Title: Download and Process Data from the Paleobiology Database
Description: Includes functions to wrap most endpoints of the
'PaleobioDB' API and to visualize and process the obtained fossil
data. The API documentation for the Paleobiology Database can be
found at <https://paleobiodb.org/data1.2/>.
Author: Sara Varela [aut] ,
Javier Gonzalez Hernandez [aut],
Luciano Fabris Sgarbi [aut] ,
Adrian Castro Insua [cre, ctb]
Maintainer: Adrian Castro Insua <adrian.castro.insua@uvigo.gal>
Diff between paleobioDB versions 1.0.0 dated 2024-02-29 and 1.0.1 dated 2025-08-27
DESCRIPTION | 27 +-- MD5 | 50 +++--- R/network.R | 49 ------ R/pbdb_geographic_functions.R | 12 - R/pbdb_queries.R | 21 +- README.md | 177 +++++++--------------- build |only man/figures/README-pbdb_map-1.png |binary man/figures/README-pbdb_map_occur-1.png |binary man/figures/README-pbdb_map_richness-1.png |binary man/figures/README-pbdb_orig_ext_1-1.png |binary man/figures/README-pbdb_orig_ext_2-1.png |binary man/figures/README-pbdb_richness-1.png |binary man/figures/README-pbdb_subtaxa-1.png |binary man/figures/README-pbdb_temp_range-1.png |binary man/figures/README-pbdb_temporal_resolution-1.png |binary man/pbdb_map.Rd | 4 man/pbdb_map_occur.Rd | 4 man/pbdb_map_richness.Rd | 4 man/pbdb_ref_collections.Rd | 2 man/pbdb_scale.Rd | 2 man/pbdb_scales.Rd | 10 - tests/testthat/fixtures/no_records_resp.rds |only tests/testthat/test-network.R | 17 -- tests/testthat/test-queries_collections.R | 2 tests/testthat/test-queries_intervals_scales.R | 9 - tests/testthat/test-queries_references.R | 7 27 files changed, 159 insertions(+), 238 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] ,
Matthieu Resche-Rigon [aut] ,
Johanna Munoz Avila [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.10.0 dated 2023-11-17 and 1.10.1 dated 2025-08-27
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- build/partial.rdb |binary man/find.defaultMethod.Rd | 2 +- man/mice.impute.2l.2stage.bin.Rd | 2 +- man/mice.impute.2l.2stage.heckman.Rd | 2 +- man/mice.impute.2l.2stage.norm.Rd | 2 +- man/mice.impute.2l.2stage.pois.Rd | 2 +- man/mice.impute.2l.glm.bin.Rd | 2 +- man/mice.impute.2l.glm.norm.Rd | 2 +- man/mice.impute.2l.glm.pois.Rd | 2 +- man/mice.impute.2l.jomo.Rd | 2 +- man/mice.par.Rd | 4 ++-- man/micemd-package.Rd | 2 +- man/overimpute.Rd | 2 +- man/plot.mira.Rd | 2 +- 16 files changed, 33 insertions(+), 33 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph] ,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Arsene Druel [aut] ,
Julien Ruffault [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Francois Pimont [ctb] ,
Herve Cochar [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.8.1 dated 2025-04-23 and 4.8.3 dated 2025-08-27
DESCRIPTION | 39 - MD5 | 77 +- R/RcppExports.R | 20 R/defaultControl.R | 25 R/extract.R | 14 R/plot_internals.R | 4 R/soil_retentionCurvePlot.R | 95 +++ build/partial.rdb |binary inst/include/medfate_RcppExports.h | 8 man/defaultControl.Rd | 19 man/soil.Rd | 2 man/soil_retentionCurvePlot.Rd |only man/soil_texture.Rd | 29 man/transp_modes.Rd | 3 src/RcppExports.cpp | 22 src/communication_structures.cpp | 242 ++++--- src/communication_structures.h | 112 ++- src/growth.cpp | 3 src/hydrology.cpp | 101 +-- src/inner_sureau.cpp | 1146 ++++++++++++++++++++++++------------- src/inner_sureau.h | 17 src/modelInput.cpp | 4 src/numerical_solving.cpp | 8 src/numerical_solving.h | 4 src/photosynthesis.cpp | 22 src/photosynthesis.h | 3 src/soil.cpp | 19 src/soil.h | 2 src/soil_thermodynamics.cpp | 73 +- src/soil_thermodynamics.h | 8 src/spwb.cpp | 73 ++ src/spwb_day.cpp | 3 src/struct_photosynthesis.h |only src/struct_sureau.h |only src/transpiration.h | 12 src/transpiration_advanced.cpp | 76 +- src/transpiration_basic.cpp | 71 +- tests/testthat/Rplots.pdf |binary tests/testthat/test_fordyn.R | 21 tests/testthat/test_growth.R | 53 + tests/testthat/test_spwb.R | 59 + 41 files changed, 1630 insertions(+), 859 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.1 dated 2025-03-05 and 1.3.2 dated 2025-08-27
DESCRIPTION | 10 MD5 | 124 +++++---- NAMESPACE | 5 NEWS.md | 129 +++++----- R/geosearch.R |only R/layergroupconditional.R | 24 + R/leaflet.extras2-package.R | 2 R/openweather.R | 10 R/reachability.R | 7 R/sidebar.R | 2 inst/examples/antpath_app.R | 4 inst/examples/arrowhead_app.R | 3 inst/examples/buildings_app.R | 20 - inst/examples/clusterCharts_app.R | 39 +-- inst/examples/clustercharts_sum.R | 29 +- inst/examples/conditional_app.R | 6 inst/examples/contextmenu_app.R | 10 inst/examples/divicons_app.R | 26 +- inst/examples/divicons_html_app.R | 37 +- inst/examples/easyprint_app.R | 39 +-- inst/examples/geosearch_app.R |only inst/examples/gibs_app.R | 6 inst/examples/heightgraph_app.R | 54 ++-- inst/examples/hexbin_app.R | 14 - inst/examples/history_app.R | 2 inst/examples/labelgun_app.R | 28 +- inst/examples/layergroupcollision_app.R | 26 +- inst/examples/leafletsync/sync_basic.R | 25 - inst/examples/leafletsync/sync_offsetHelper.R | 16 - inst/examples/leafletsync/sync_offset_continuous.R | 28 -- inst/examples/leafletsync/sync_with_synclist.R | 26 -- inst/examples/mapkeyIcons_app.R | 4 inst/examples/movingmarker_app.R | 18 - inst/examples/multi_sidebar_app.R | 2 inst/examples/openweather_app.R | 21 - inst/examples/playback_app.R | 35 +- inst/examples/playback_app_awesomemarkers.R | 16 - inst/examples/playback_app_divicon.R | 18 - inst/examples/reachability_app.R | 73 ++++- inst/examples/side_by_side_app.R | 10 inst/examples/sidebar_app.R | 8 inst/examples/tangram/tangram_app.R | 2 inst/examples/timeslider_app.R | 13 - inst/examples/wms_app.R | 6 inst/htmlwidgets/lfx-geosearch |only inst/htmlwidgets/lfx-heightgraph/img |only inst/htmlwidgets/lfx-openweather/leaflet-openweathermap-bindings.js | 6 inst/htmlwidgets/lfx-openweather/owmloading.gif |only inst/htmlwidgets/lfx-reachability/leaflet.reachability-bindings.js | 21 + man/addGeosearch.Rd |only man/addLayerGroupConditional.Rd | 24 + man/geosearchOptions.Rd |only man/geosearchProvider.Rd |only man/openweatherCurrentOptions.Rd | 13 - man/removeGeosearch.Rd |only tests/testthat/test-divicon.R | 4 tests/testthat/test-geosearch.R |only tests/testthat/test-heightgraph.R | 4 tests/testthat/test-history.R | 17 + tests/testthat/test-labelgun.R | 2 tests/testthat/test-layergroupcollision.R | 4 tests/testthat/test-layergroupconditional.R |only tests/testthat/test-movingmarker.R | 20 + tests/testthat/test-playback.R | 66 ++++- tests/testthat/test-reachability.R | 42 +++ tests/testthat/test-timeslider.R | 28 ++ tests/testthat/test-velocity.R | 18 + 67 files changed, 769 insertions(+), 477 deletions(-)
More information about leaflet.extras2 at CRAN
Permanent link
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.1 dated 2025-07-23 and 1.6.2 dated 2025-08-27
DESCRIPTION | 8 MD5 | 36 R/GPModel.R | 41 configure.ac | 2 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 1 man/GPModel.Rd | 33 man/GPModel_shared_params.Rd | 33 man/fitGPModel.Rd | 33 src/DF_utils.cpp | 54 src/Vecchia_utils.cpp | 19 src/c_api.cpp | 10 src/include/GPBoost/DF_utils.h | 107 src/include/GPBoost/cov_fcts.h | 133 - src/include/GPBoost/likelihoods.h | 1263 +++++++--- src/include/GPBoost/re_comp.h | 30 src/include/GPBoost/re_model_template.h | 683 +++-- src/include/GPBoost/utils.h | 37 tests/testthat/test_GPModel_non_Gaussian_data.R | 541 ++++ tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 411 +-- 19 files changed, 2453 insertions(+), 1022 deletions(-)
Title: Pre- And Postprocessing of Morphological Data from Relaxed Clock
Bayesian Phylogenetics
Description: Performs automated morphological character partitioning for
phylogenetic analyses and analyze macroevolutionary parameter
outputs from clock (time-calibrated) Bayesian inference analyses, following
concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Author: Tiago Simoes [cre, aut] ,
Noah Greifer [aut] ,
Joelle Barido-Sottani [aut] ,
Stephanie Pierce [aut]
Maintainer: Tiago Simoes <trsimoes87@gmail.com>
Diff between EvoPhylo versions 0.3.2 dated 2022-11-03 and 0.3.5 dated 2025-08-27
DESCRIPTION | 23 +-- MD5 | 83 ++++++----- NAMESPACE | 17 +- NEWS.md | 14 + R/CharPart.R | 118 +++++++++++++++- R/ST&P_FBD.R | 28 ++- R/ST&P_Rates.R | 122 ++++++++++++++++ R/SelectionStrength.R | 242 ++++++++++++++++++--------------- R/helpers.R | 17 ++ build/vignette.rds |binary inst/CITATION | 26 ++- inst/doc/char-part.R | 26 +-- inst/doc/char-part.Rmd | 18 +- inst/doc/char-part.html | 12 - inst/doc/data_treatment.Rmd | 1 inst/doc/data_treatment.html | 4 inst/doc/fbd-params.R | 78 +++++----- inst/doc/fbd-params.Rmd | 1 inst/doc/fbd-params.html | 20 +- inst/doc/offset_handling.R | 10 - inst/doc/offset_handling.Rmd | 1 inst/doc/offset_handling.html | 37 ++--- inst/doc/rates-selection_BEAST2.R | 42 ++--- inst/doc/rates-selection_BEAST2.Rmd | 1 inst/doc/rates-selection_BEAST2.html | 18 +- inst/doc/rates-selection_MrBayes.R | 58 +++---- inst/doc/rates-selection_MrBayes.Rmd | 78 ++++------ inst/doc/rates-selection_MrBayes.html | 121 +++++++--------- inst/extdata/iguania_50genes.phy |only inst/extdata/iguania_partitions.txt |only man/clade_membership.Rd |only man/clockrate_dens_plot.Rd | 6 man/clockrate_reg_plot.Rd | 6 man/combine_log.Rd | 4 man/plot_back_rates.Rd | 8 - man/plot_treerates_sgn.Rd | 4 man/write_partitioned_alignments.Rd | 6 man/write_partitioned_alignments2.Rd |only vignettes/Sum_RateTable_Medians_4p.csv |only vignettes/char-part.Rmd | 18 +- vignettes/data_treatment.Rmd | 1 vignettes/fbd-params.Rmd | 1 vignettes/offset_handling.Rmd | 1 vignettes/rates-selection_BEAST2.Rmd | 1 vignettes/rates-selection_MrBayes.Rmd | 78 ++++------ 45 files changed, 830 insertions(+), 520 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
Malcolm Barrett [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.5 dated 2025-07-03 and 0.3.0 dated 2025-08-27
cardx-0.2.5/cardx/R/ard_categorical.survey.design.R |only cardx-0.2.5/cardx/R/ard_categorical_max.R |only cardx-0.2.5/cardx/R/ard_dichotomous.survey.design.R |only cardx-0.2.5/cardx/man/ard_categorical.survey.design.Rd |only cardx-0.2.5/cardx/man/ard_categorical_max.Rd |only cardx-0.2.5/cardx/man/ard_continuous.survey.design.Rd |only cardx-0.2.5/cardx/man/ard_dichotomous.survey.design.Rd |only cardx-0.2.5/cardx/tests/testthat/_snaps/ard_categorical.survey.design.md |only cardx-0.2.5/cardx/tests/testthat/_snaps/ard_categorical_max.md |only cardx-0.2.5/cardx/tests/testthat/_snaps/ard_continuous.survey.design.md |only cardx-0.2.5/cardx/tests/testthat/_snaps/ard_dichotomous.survey.design.md |only cardx-0.2.5/cardx/tests/testthat/test-ard_categorical.survey.design.R |only cardx-0.2.5/cardx/tests/testthat/test-ard_categorical_max.R |only cardx-0.2.5/cardx/tests/testthat/test-ard_continuous.survey.design.R |only cardx-0.2.5/cardx/tests/testthat/test-ard_dichotomous.survey.design.R |only cardx-0.3.0/cardx/DESCRIPTION | 11 - cardx-0.3.0/cardx/MD5 | 78 +++++----- cardx-0.3.0/cardx/NAMESPACE | 11 + cardx-0.3.0/cardx/NEWS.md | 20 ++ cardx-0.3.0/cardx/R/add_total_n.survey.design.R | 4 cardx-0.3.0/cardx/R/ard_categorical_ci.R | 4 cardx-0.3.0/cardx/R/ard_categorical_ci.survey.design.R | 2 cardx-0.3.0/cardx/R/ard_continuous.survey.design.R | 24 +-- cardx-0.3.0/cardx/R/ard_continuous_ci.survey.design.R | 2 cardx-0.3.0/cardx/R/ard_incidence_rate.R | 2 cardx-0.3.0/cardx/R/ard_missing.survey.design.R | 4 cardx-0.3.0/cardx/R/ard_stats_t_test_onesample.R | 4 cardx-0.3.0/cardx/R/ard_stats_wilcox_test_onesample.R | 4 cardx-0.3.0/cardx/R/ard_tabulate.survey.design.R |only cardx-0.3.0/cardx/R/ard_tabulate_abnormal.R |only cardx-0.3.0/cardx/R/ard_tabulate_max.R |only cardx-0.3.0/cardx/R/ard_tabulate_value.survey.design.R |only cardx-0.3.0/cardx/R/deprecated.R |only cardx-0.3.0/cardx/R/import-standalone-forcats.R | 67 ++++++++ cardx-0.3.0/cardx/R/reexports.R | 12 - cardx-0.3.0/cardx/man/ard_categorical_ci.Rd | 2 cardx-0.3.0/cardx/man/ard_summary.survey.design.Rd |only cardx-0.3.0/cardx/man/ard_tabulate.survey.design.Rd |only cardx-0.3.0/cardx/man/ard_tabulate_abnormal.Rd |only cardx-0.3.0/cardx/man/ard_tabulate_max.Rd |only cardx-0.3.0/cardx/man/ard_tabulate_value.survey.design.Rd |only cardx-0.3.0/cardx/man/cardx-package.Rd | 1 cardx-0.3.0/cardx/man/deprecated.Rd |only cardx-0.3.0/cardx/man/dot-check_dichotomous_value.Rd | 4 cardx-0.3.0/cardx/man/dot-process_nested_list_as_df.Rd | 4 cardx-0.3.0/cardx/man/dot-unique_and_sorted.Rd | 2 cardx-0.3.0/cardx/man/reexports.Rd | 7 cardx-0.3.0/cardx/tests/testthat/_snaps/ard_summary.survey.design.md |only cardx-0.3.0/cardx/tests/testthat/_snaps/ard_tabulate.survey.design.md |only cardx-0.3.0/cardx/tests/testthat/_snaps/ard_tabulate_abnormal.md |only cardx-0.3.0/cardx/tests/testthat/_snaps/ard_tabulate_max.md |only cardx-0.3.0/cardx/tests/testthat/_snaps/ard_tabulate_value.survey.design.md |only cardx-0.3.0/cardx/tests/testthat/test-ard_categorical_ci.data.frame.R | 16 +- cardx-0.3.0/cardx/tests/testthat/test-ard_summary.survey.design.R |only cardx-0.3.0/cardx/tests/testthat/test-ard_tabulate.survey.design.R |only cardx-0.3.0/cardx/tests/testthat/test-ard_tabulate_abnormal.R |only cardx-0.3.0/cardx/tests/testthat/test-ard_tabulate_max.R |only cardx-0.3.0/cardx/tests/testthat/test-ard_tabulate_value.survey.design.R |only 58 files changed, 195 insertions(+), 90 deletions(-)
Title: Binned Data Analysis
Description: Algorithms developed for binned data analysis,
gene expression data analysis and
measurement error models for ordinal data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between bda versions 18.3.2 dated 2024-08-25 and 19.0.0 dated 2025-08-27
DESCRIPTION | 8 ++-- MD5 | 10 +++--- PORTING | 1 R/blinding.R |only man/blinding.Rd |only src/ckernel.c | 91 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ src/init.c | 4 +- 7 files changed, 105 insertions(+), 9 deletions(-)
Title: Spatially and Temporally Varying Coefficient Models Using
Generalized Additive Models
Description: A framework for specifying spatially, temporally and spatially-and-temporally varying coefficient models using Generalized Additive Models with smooths. The smooths are parameterised with location, time and predictor variables. The framework supports the investigation of the presence and nature of any space-time dependencies in the data by evaluating multiple model forms (specifications) using a Generalized Cross-Validation score. The workflow sequence is to: i) Prepare the data by lengthening it to have a single location and time variables for each observation. ii) Evaluate all possible spatial and/or temporal models in which each predictor is specified in different ways. iii) Evaluate each model and pick the best one. iv) Create the final model. v) Calculate the varying coefficient estimates to quantify how the relationships between the target and predictor variables vary over space, time or space-time. vi) Create maps, time series plots etc. For more details see: Comber et al (2023) [...truncated...]
Author: Lex Comber [aut, cre],
Paul Harris [ctb],
Chris Brunsdon [ctb]
Maintainer: Lex Comber <a.comber@leeds.ac.uk>
Diff between stgam versions 1.0.2 dated 2025-06-12 and 1.1.0 dated 2025-08-27
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 4 R/calculate_vcs.R | 12 - R/evaluate_models.R | 22 +- R/gam_model_rank.R | 25 +-- README.md | 3 inst/doc/space-time-gam-intro_rev.R | 20 +- inst/doc/space-time-gam-intro_rev.Rmd | 39 ++--- inst/doc/space-time-gam-intro_rev.html | 247 +++++++++++++++++---------------- man/calculate_vcs.Rd | 4 man/gam_model_rank.Rd | 2 vignettes/space-time-gam-intro_rev.Rmd | 39 ++--- vignettes/stvc_mods.RData |binary 14 files changed, 234 insertions(+), 215 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 1.1.0 dated 2025-08-19 and 1.1.1 dated 2025-08-27
marquee-1.1.0/marquee/man/figures/README-pressure-1.png |only marquee-1.1.0/marquee/tests/testthat/Rplots.pdf |only marquee-1.1.1/marquee/DESCRIPTION | 8 marquee-1.1.1/marquee/MD5 | 37 +-- marquee-1.1.1/marquee/NEWS.md | 10 marquee-1.1.1/marquee/R/aaa.R |only marquee-1.1.1/marquee/R/element_marquee.R | 65 +++++- marquee-1.1.1/marquee/R/geom_marquee.R | 4 marquee-1.1.1/marquee/R/grob.R | 29 +- marquee-1.1.1/marquee/R/images.R | 43 +++ marquee-1.1.1/marquee/R/style.R | 108 +++++++--- marquee-1.1.1/marquee/R/style_helpers.R | 8 marquee-1.1.1/marquee/README.md | 4 marquee-1.1.1/marquee/man/element_marquee.Rd | 9 marquee-1.1.1/marquee/man/figures/README-unnamed-chunk-2-1.png |binary marquee-1.1.1/marquee/man/geom_marquee.Rd | 4 marquee-1.1.1/marquee/tests/testthat/test-element_marquee.R | 2 marquee-1.1.1/marquee/tests/testthat/test-geom_marquee.R | 2 marquee-1.1.1/marquee/tests/testthat/test-grob.R | 2 marquee-1.1.1/marquee/tests/testthat/test-guide_marquee.R | 7 marquee-1.1.1/marquee/tests/testthat/test-images.R | 2 21 files changed, 251 insertions(+), 93 deletions(-)
Title: Gene Set Analysis Using the Gene Set Ordinal Association Test
Description: Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.
Author: Frank Koopmans [aut, cre]
Maintainer: Frank Koopmans <ftwkoopmans@gmail.com>
This is a re-admission after prior archival of version 1.1.2 dated 2025-02-22
Diff between goat versions 1.1.2 dated 2025-02-22 and 1.1.3 dated 2025-08-27
DESCRIPTION | 9 MD5 | 38 - NEWS.md | 4 R/download_data.R | 391 ++++++++-------- R/partition_genes.R | 172 +++---- R/plot_volcano.R | 242 +++++---- R/simplify_ontology.R | 830 +++++++++++++++++----------------- R/simplify_similarity.R | 8 R/test_genesets.R | 250 +++++----- R/test_genesets_fisherexact.R | 154 +++--- R/test_genesets_goat.R | 740 +++++++++++++++--------------- man/download_genesets_goatrepo.Rd | 2 man/partition_genes.Rd | 2 man/plot_heatmap.Rd | 4 man/plot_lollipop.Rd | 4 man/plot_volcano.Rd | 4 man/test_genesets.Rd | 4 man/test_genesets_fisherexact.Rd | 4 man/test_genesets_goat_precomputed.Rd | 4 man/treemap_plot.Rd | 4 20 files changed, 1476 insertions(+), 1394 deletions(-)
Title: User-Friendly 'shiny' App for Bayesian Species Distribution
Models
Description: A user-friendly 'shiny' application for Bayesian machine
learning analysis of marine species distributions. GLOSSA (Global
Ocean Species Spatio-temporal Analysis) uses Bayesian Additive
Regression Trees (BART; Chipman, George, and McCulloch (2010)
<doi:10.1214/09-AOAS285>) to model species distributions with
intuitive workflows for data upload, processing, model fitting, and
result visualization. It supports presence-absence and presence-only
data (with pseudo-absence generation), spatial thinning,
cross-validation, and scenario-based projections. GLOSSA is designed
to facilitate ecological research by providing easy-to-use tools for
analyzing and visualizing marine species distributions across
different spatial and temporal scales. Optionally, pseudo-absences can
be generated within the environmental space using the external package
'flexsdm' (not on CRAN), which can be downloaded from
<https://github.com/sjevelazco/flexsdm>; this functionality is used
conditionally when a [...truncated...]
Author: Jorge Mestre-Tomas [aut, cre] ,
Alba Fuster-Alonso [aut]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
This is a re-admission after prior archival of version 1.2.2 dated 2025-07-15
Diff between glossa versions 1.2.2 dated 2025-07-15 and 1.2.3 dated 2025-08-27
glossa-1.2.2/glossa/tests/testthat/Rplots.pdf |only glossa-1.2.3/glossa/DESCRIPTION | 16 glossa-1.2.3/glossa/MD5 | 114 - glossa-1.2.3/glossa/NEWS.md | 10 glossa-1.2.3/glossa/R/generate_pseudo_absences.R | 109 + glossa-1.2.3/glossa/R/glossa_analysis.R | 9 glossa-1.2.3/glossa/inst/app/server.R | 22 glossa-1.2.3/glossa/inst/app/ui.R | 2 glossa-1.2.3/glossa/inst/extdata/sp1.txt | 1002 +++++----- glossa-1.2.3/glossa/inst/extdata/sp2.csv | 1002 +++++----- glossa-1.2.3/glossa/inst/extdata/testthat_coords.csv | 6 glossa-1.2.3/glossa/man/buffer_polygon.Rd | 38 glossa-1.2.3/glossa/man/clean_coordinates.Rd | 86 glossa-1.2.3/glossa/man/contBoyce.Rd | 122 - glossa-1.2.3/glossa/man/create_coords_layer.Rd | 44 glossa-1.2.3/glossa/man/cross_validate_model.Rd | 58 glossa-1.2.3/glossa/man/downloadActionButton.Rd | 76 glossa-1.2.3/glossa/man/evaluation_metrics.Rd | 42 glossa-1.2.3/glossa/man/export_plot_server.Rd | 32 glossa-1.2.3/glossa/man/export_plot_ui.Rd | 32 glossa-1.2.3/glossa/man/extract_noNA_cov_values.Rd | 48 glossa-1.2.3/glossa/man/file_input_area_server.Rd | 30 glossa-1.2.3/glossa/man/file_input_area_ui.Rd | 46 glossa-1.2.3/glossa/man/fit_bart_model.Rd | 48 glossa-1.2.3/glossa/man/generate_cv_folds.Rd | 94 glossa-1.2.3/glossa/man/generate_pa_buffer_out.Rd | 82 glossa-1.2.3/glossa/man/generate_pa_env_space_flexsdm.Rd |only glossa-1.2.3/glossa/man/generate_pa_random.Rd | 82 glossa-1.2.3/glossa/man/generate_pa_target_group.Rd | 86 glossa-1.2.3/glossa/man/generate_prediction_plot.Rd | 60 glossa-1.2.3/glossa/man/generate_pseudo_absences.Rd | 100 glossa-1.2.3/glossa/man/getFprTpr.Rd | 50 glossa-1.2.3/glossa/man/get_covariate_names.Rd | 42 glossa-1.2.3/glossa/man/glossa_analysis.Rd | 174 - glossa-1.2.3/glossa/man/glossa_export.Rd | 122 - glossa-1.2.3/glossa/man/invert_polygon.Rd | 38 glossa-1.2.3/glossa/man/layer_mask.Rd | 40 glossa-1.2.3/glossa/man/misClassError.Rd | 50 glossa-1.2.3/glossa/man/optimalCutoff.Rd | 64 glossa-1.2.3/glossa/man/pa_optimal_cutoff.Rd | 46 glossa-1.2.3/glossa/man/plot_cv_folds_points.Rd | 38 glossa-1.2.3/glossa/man/plot_cv_metrics.Rd | 36 glossa-1.2.3/glossa/man/predict_bart.Rd | 46 glossa-1.2.3/glossa/man/read_extent_polygon.Rd | 40 glossa-1.2.3/glossa/man/read_layers_zip.Rd | 58 glossa-1.2.3/glossa/man/read_presences_absences_csv.Rd | 78 glossa-1.2.3/glossa/man/remove_duplicate_points.Rd | 38 glossa-1.2.3/glossa/man/remove_points_polygon.Rd | 56 glossa-1.2.3/glossa/man/response_curve_bart.Rd | 42 glossa-1.2.3/glossa/man/run_glossa.Rd | 80 glossa-1.2.3/glossa/man/sensitivity.Rd | 50 glossa-1.2.3/glossa/man/sparkvalueBox.Rd | 82 glossa-1.2.3/glossa/man/specificity.Rd | 50 glossa-1.2.3/glossa/man/validate_fit_projection_layers.Rd | 52 glossa-1.2.3/glossa/man/validate_layers_zip.Rd | 44 glossa-1.2.3/glossa/man/validate_pa_fit_time.Rd | 44 glossa-1.2.3/glossa/man/variable_importance.Rd | 58 glossa-1.2.3/glossa/man/youdensIndex.Rd | 50 glossa-1.2.3/glossa/tests/testthat/test-generate_pseudo_absences.R | 20 59 files changed, 2621 insertions(+), 2465 deletions(-)
Title: Fast and Memory Efficient Fitting of Linear Models with
High-Dimensional Fixed Effects
Description: Fast and user-friendly estimation of generalized linear models with
multiple fixed effects and cluster the standard errors. The method to obtain
the estimated fixed-effects coefficients is based on Stammann (2018)
<doi:10.48550/arXiv.1707.01815>, Gaure (2013)
<doi:10.1016/j.csda.2013.03.024>, Berge (2018)
<https://ideas.repec.org/p/luc/wpaper/18-13.html>, and Correia et al. (2020)
<doi: 10.1177/1536867X20909691>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Yoto Yotov [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between capybara versions 1.0.1 dated 2025-05-22 and 1.8.0 dated 2025-08-27
capybara-1.0.1/capybara/R/feglm_control.R |only capybara-1.0.1/capybara/R/fixed_effects.R |only capybara-1.0.1/capybara/man/feglm_control.Rd |only capybara-1.0.1/capybara/man/fixed_effects.Rd |only capybara-1.0.1/capybara/src/00_main.h |only capybara-1.0.1/capybara/src/01_linear_algebra.cpp |only capybara-1.0.1/capybara/src/02_center_variables.cpp |only capybara-1.0.1/capybara/src/03_lm_fit.cpp |only capybara-1.0.1/capybara/src/04_glm_fit.cpp |only capybara-1.0.1/capybara/src/05_glm_offset_fit.cpp |only capybara-1.0.1/capybara/src/06_get_alpha.cpp |only capybara-1.0.1/capybara/src/07_group_sums.cpp |only capybara-1.0.1/capybara/tests/testthat/test-group-sums.R |only capybara-1.0.1/capybara/tests/testthat/test-predict.R |only capybara-1.0.1/capybara/tests/testthat/test-weights.R |only capybara-1.8.0/capybara/DESCRIPTION | 17 capybara-1.8.0/capybara/MD5 | 109 - capybara-1.8.0/capybara/NAMESPACE | 6 capybara-1.8.0/capybara/NEWS.md | 54 capybara-1.8.0/capybara/R/apes.R | 66 capybara-1.8.0/capybara/R/bias_corr.R | 77 capybara-1.8.0/capybara/R/capybara-package.R | 5 capybara-1.8.0/capybara/R/cpp11.R | 16 capybara-1.8.0/capybara/R/feglm.R | 73 capybara-1.8.0/capybara/R/feglm_helpers.R | 202 -- capybara-1.8.0/capybara/R/feglm_offset.R | 6 capybara-1.8.0/capybara/R/felm.R | 66 capybara-1.8.0/capybara/R/felm_helpers.R | 35 capybara-1.8.0/capybara/R/fenegbin.R | 179 - capybara-1.8.0/capybara/R/fit_control.R |only capybara-1.8.0/capybara/R/fit_helpers.R |only capybara-1.8.0/capybara/R/generics_fitted.R | 2 capybara-1.8.0/capybara/R/generics_predict.R | 56 capybara-1.8.0/capybara/R/generics_summary.R | 10 capybara-1.8.0/capybara/R/summary_table.R | 22 capybara-1.8.0/capybara/README.md | 217 +- capybara-1.8.0/capybara/build/vignette.rds |binary capybara-1.8.0/capybara/configure | 287 ++- capybara-1.8.0/capybara/inst/Makevars.example |only capybara-1.8.0/capybara/inst/doc/intro.html | 321 +-- capybara-1.8.0/capybara/man/capybara-package.Rd | 2 capybara-1.8.0/capybara/man/feglm.Rd | 8 capybara-1.8.0/capybara/man/felm.Rd | 10 capybara-1.8.0/capybara/man/fenegbin.Rd | 12 capybara-1.8.0/capybara/man/fepoisson.Rd | 6 capybara-1.8.0/capybara/man/figures/logo.svg | 906 +++++----- capybara-1.8.0/capybara/man/fit_control.Rd |only capybara-1.8.0/capybara/src/01_center.h |only capybara-1.8.0/capybara/src/02_beta.h |only capybara-1.8.0/capybara/src/03_alpha.h |only capybara-1.8.0/capybara/src/04_lm.h |only capybara-1.8.0/capybara/src/05_glm_helpers.h |only capybara-1.8.0/capybara/src/06_glm.h |only capybara-1.8.0/capybara/src/07_negbin.h |only capybara-1.8.0/capybara/src/08_sums.h |only capybara-1.8.0/capybara/src/Makevars.in | 2 capybara-1.8.0/capybara/src/capybara.cpp |only capybara-1.8.0/capybara/src/cpp11.cpp | 62 capybara-1.8.0/capybara/tests/testthat/test-apes-bias.R | 7 capybara-1.8.0/capybara/tests/testthat/test-deterministic.R | 11 capybara-1.8.0/capybara/tests/testthat/test-errors.R | 35 capybara-1.8.0/capybara/tests/testthat/test-feglm-atypical-columns.R | 11 capybara-1.8.0/capybara/tests/testthat/test-feglm.R | 190 +- capybara-1.8.0/capybara/tests/testthat/test-felm.R | 130 + capybara-1.8.0/capybara/tests/testthat/test-fenegbin.R | 18 capybara-1.8.0/capybara/tests/testthat/test-fepoisson.R | 147 + capybara-1.8.0/capybara/tests/testthat/test-fixed-effects.R | 125 + capybara-1.8.0/capybara/tests/testthat/test-model-formulas.R |only capybara-1.8.0/capybara/tests/testthat/test-no-fixed-effects.R | 24 capybara-1.8.0/capybara/tests/testthat/test-vcov.R | 2 70 files changed, 2035 insertions(+), 1499 deletions(-)
Title: Data Modification and Analysis for Communication Research
Description: Provides convenience functions for common data modification
and analysis tasks in communication research. This includes functions
for univariate and bivariate data analysis, index generation and
reliability computation, and intercoder reliability tests. All
functions follow the style and syntax of the tidyverse, and are
construed to perform their computations on multiple variables at once.
Functions for univariate and bivariate data analysis comprise summary
statistics for continuous and categorical variables, as well as
several tests of bivariate association including effect sizes.
Functions for data modification comprise index generation and
automated reliability analysis of index variables. Functions for
intercoder reliability comprise tests of several intercoder
reliability estimates, including simple and mean pairwise percent
agreement, Krippendorff's Alpha (Krippendorff 2004, ISBN:
9780761915454), and various Kappa coefficients (Brennan & Prediger
1981 <doi: 10.1177/001316 [...truncated...]
Author: Julian Unkel [aut, cre] ,
Mario Haim [aut] ,
Lara Kobilke [aut]
Maintainer: Julian Unkel <julian.unkel@gmail.com>
This is a re-admission after prior archival of version 0.4.1 dated 2024-02-22
Diff between tidycomm versions 0.4.1 dated 2024-02-22 and 0.4.2 dated 2025-08-27
DESCRIPTION | 42 ++++++++-------- MD5 | 81 +++++++++++++++---------------- NEWS.md | 14 +++++ R/tdcmm_class.R | 17 +++--- R/utils-designs.R | 6 +- R/utils-pipe.R | 2 R/utils.R | 2 README.md | 52 ++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/v01_univariate.html | 10 +-- inst/doc/v02_bivariate.html | 29 ++++------- inst/doc/v03_reliability.html | 4 - inst/doc/v04_icr.R | 2 inst/doc/v04_icr.html | 4 - inst/doc/v05_scales.html | 4 - man/design_gray.Rd | 2 man/design_grey.Rd | 2 man/design_lmu.Rd | 2 man/figures/README-unnamed-chunk-8-1.png |only man/model.Rd | 1 man/new_tdcmm.Rd | 5 + man/pipe.Rd | 2 man/tab_percentiles.Rd | 4 - man/tdcmm-class.Rd | 1 man/visualize.Rd | 10 +-- tests/testthat/test-add_index.R | 2 tests/testthat/test-categorical.R | 4 - tests/testthat/test-correlate_partial.R | 2 tests/testthat/test-correlation.R | 2 tests/testthat/test-describe.R | 2 tests/testthat/test-icr.R | 2 tests/testthat/test-icr_agreement.R | 2 tests/testthat/test-icr_kappa.R | 10 +-- tests/testthat/test-icr_kripp_alpha.R | 10 +-- tests/testthat/test-regression.R | 2 tests/testthat/test-reliability.R | 2 tests/testthat/test-scaling.R | 2 tests/testthat/test-tab_percentiles.R | 2 tests/testthat/test-tdcmm_visualize.R | 8 +-- tests/testthat/test-ttest.R | 4 - tests/testthat/test-unianova.R | 2 42 files changed, 186 insertions(+), 170 deletions(-)
Title: Automatically Set the Width Option on Terminal Emulators
Description: Automatically sets the value of options("width") when the
terminal emulator is resized. The functions of this package only work if R is compiled for Unix systems and it is running interactively in a terminal emulator.
Author: Jakson Aquino [aut] ,
Dominique-Laurent Couturier [aut, cre]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
This is a re-admission after prior archival of version 1.0-4 dated 2015-07-07
Diff between setwidth versions 1.0-4 dated 2015-07-07 and 1.1.0 dated 2025-08-27
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS | 6 ++++++ man/setwidth-package.Rd | 20 +++++++++++--------- src/registerDynamicSymbol.c |only src/setwidth.c | 26 +++++++++++++------------- 7 files changed, 52 insertions(+), 36 deletions(-)
Title: A Comprehensive Package for Sediment Source Unmixing
Description: "This package quantifies the provenance of sediments in a catchment or study area. Based on a characterization of the sediment sources and the end sediment mixtures, a mixing model algorithm is applied to the sediment mixtures to estimate the relative contribution of each potential source. The package includes several graphs to help users in their data understanding, such as box plots, correlation, PCA, and LDA graphs. In addition, new developments such as the Consensus Ranking (CR), Consistent Tracer Selection (CTS), and Linear Variability Propagation (LVP) methods are included to correctly apply the fingerprinting technique and increase dataset and model understanding. A new method based on Conservative Balance (CB) method has also been included to enable the use of isotopic tracers."
Author: Borja Latorre [aut, cre],
Ivan Lizaga [aut],
Leticia Gaspar [aut],
Leticia Palazon [aut],
Ana Navas [aut],
Vince Q Vu [ctb]
Maintainer: Borja Latorre <borja.latorre@csic.es>
Diff between fingerPro versions 1.1 dated 2018-08-28 and 2.0 dated 2025-08-27
fingerPro-1.1/fingerPro/R/DFATest.R |only fingerPro-1.1/fingerPro/R/KWTest.R |only fingerPro-1.1/fingerPro/R/LDAPlot.R |only fingerPro-1.1/fingerPro/R/PCAPlot.R |only fingerPro-1.1/fingerPro/R/boxPlot.R |only fingerPro-1.1/fingerPro/R/correlationPlot.R |only fingerPro-1.1/fingerPro/R/data.R |only fingerPro-1.1/fingerPro/R/inputSample.R |only fingerPro-1.1/fingerPro/R/plotResults.R |only fingerPro-1.1/fingerPro/R/rangeTest.R |only fingerPro-1.1/fingerPro/R/writeResults.R |only fingerPro-1.1/fingerPro/data |only fingerPro-1.1/fingerPro/man/DFATest.Rd |only fingerPro-1.1/fingerPro/man/KWTest.Rd |only fingerPro-1.1/fingerPro/man/LDAPlot.Rd |only fingerPro-1.1/fingerPro/man/PCAPlot.Rd |only fingerPro-1.1/fingerPro/man/boxPlot.Rd |only fingerPro-1.1/fingerPro/man/catchment.Rd |only fingerPro-1.1/fingerPro/man/correlationPlot.Rd |only fingerPro-1.1/fingerPro/man/fingerPro-package.Rd |only fingerPro-1.1/fingerPro/man/inputSample.Rd |only fingerPro-1.1/fingerPro/man/plotResults.Rd |only fingerPro-1.1/fingerPro/man/rangeTest.Rd |only fingerPro-1.1/fingerPro/man/unmixing_c.Rd |only fingerPro-1.1/fingerPro/man/writeResults.Rd |only fingerPro-2.0/fingerPro/DESCRIPTION | 44 fingerPro-2.0/fingerPro/MD5 | 104 fingerPro-2.0/fingerPro/NAMESPACE | 56 fingerPro-2.0/fingerPro/R/CB_method.R |only fingerPro-2.0/fingerPro/R/CI.R |only fingerPro-2.0/fingerPro/R/CR.R |only fingerPro-2.0/fingerPro/R/CTS_error.R |only fingerPro-2.0/fingerPro/R/CTS_error_2s.R |only fingerPro-2.0/fingerPro/R/CTS_error_3s.R |only fingerPro-2.0/fingerPro/R/CTS_error_4s.R |only fingerPro-2.0/fingerPro/R/CTS_error_5s.R |only fingerPro-2.0/fingerPro/R/CTS_seeds.R |only fingerPro-2.0/fingerPro/R/CTS_seeds_pairs.R |only fingerPro-2.0/fingerPro/R/CTS_seeds_quartets.R |only fingerPro-2.0/fingerPro/R/CTS_seeds_singles.R |only fingerPro-2.0/fingerPro/R/CTS_seeds_triplets.R |only fingerPro-2.0/fingerPro/R/DFA_test.R |only fingerPro-2.0/fingerPro/R/KW_test.R |only fingerPro-2.0/fingerPro/R/LDA_plot.R |only fingerPro-2.0/fingerPro/R/PCA_plot.R |only fingerPro-2.0/fingerPro/R/RcppExports.R | 73 fingerPro-2.0/fingerPro/R/box_plot.R |only fingerPro-2.0/fingerPro/R/correlation_plot.R |only fingerPro-2.0/fingerPro/R/fingerPro-package.R |only fingerPro-2.0/fingerPro/R/functions.R |only fingerPro-2.0/fingerPro/R/ggbiplot.r | 9 fingerPro-2.0/fingerPro/R/globals.R |only fingerPro-2.0/fingerPro/R/individual_tracer_analysis.R |only fingerPro-2.0/fingerPro/R/inputMixture.R |only fingerPro-2.0/fingerPro/R/inputSource.R | 37 fingerPro-2.0/fingerPro/R/least_squares.R |only fingerPro-2.0/fingerPro/R/plot_results.R |only fingerPro-2.0/fingerPro/R/range_test.R |only fingerPro-2.0/fingerPro/R/ternary_diagram.R |only fingerPro-2.0/fingerPro/R/unmix.R | 265 +- fingerPro-2.0/fingerPro/R/unmix_unconstrained.R |only fingerPro-2.0/fingerPro/R/unmix_unconstrained_lvp.R |only fingerPro-2.0/fingerPro/R/write_results.R |only fingerPro-2.0/fingerPro/inst |only fingerPro-2.0/fingerPro/man/CB_method.Rd |only fingerPro-2.0/fingerPro/man/CI.Rd |only fingerPro-2.0/fingerPro/man/CR.Rd |only fingerPro-2.0/fingerPro/man/CTS_error.Rd |only fingerPro-2.0/fingerPro/man/CTS_seeds.Rd |only fingerPro-2.0/fingerPro/man/DFA_test.Rd |only fingerPro-2.0/fingerPro/man/KW_test.Rd |only fingerPro-2.0/fingerPro/man/LDA_plot.Rd |only fingerPro-2.0/fingerPro/man/PCA_plot.Rd |only fingerPro-2.0/fingerPro/man/box_plot.Rd |only fingerPro-2.0/fingerPro/man/check_database.Rd |only fingerPro-2.0/fingerPro/man/correlation_plot.Rd |only fingerPro-2.0/fingerPro/man/fingerPro.Rd |only fingerPro-2.0/fingerPro/man/ggbiplot.Rd | 128 - fingerPro-2.0/fingerPro/man/individual_tracer_analysis.Rd |only fingerPro-2.0/fingerPro/man/inputMixture.Rd |only fingerPro-2.0/fingerPro/man/inputSource.Rd | 30 fingerPro-2.0/fingerPro/man/plot_results.Rd |only fingerPro-2.0/fingerPro/man/range_test.Rd |only fingerPro-2.0/fingerPro/man/raw_dataset.Rd |only fingerPro-2.0/fingerPro/man/select_tracers.Rd |only fingerPro-2.0/fingerPro/man/ternary_diagram.Rd |only fingerPro-2.0/fingerPro/man/unmix.Rd | 63 fingerPro-2.0/fingerPro/man/virtual_mixture.Rd |only fingerPro-2.0/fingerPro/man/write_results.Rd |only fingerPro-2.0/fingerPro/src/RcppExports.cpp | 83 fingerPro-2.0/fingerPro/src/fingerprinting.cpp | 1710 +++++++++++++- 91 files changed, 2298 insertions(+), 304 deletions(-)
Title: A Set of Tools for Calculating Spatial Synchrony Between
Tree-Ring Chronologies
Description: Provides functions for the calculation and plotting of synchrony in
tree growth from tree-ring width chronologies (TRW index). It combines
variance-covariance (VCOV) mixed modelling with functions that quantify
the degree to which the TRW chronologies contain a common temporal
signal. It also implements temporal trends in spatial synchrony using a
moving window. These methods can also be used with other kind of ecological
variables that have temporal autocorrelation corrected.
Author: Josu G. Alday [aut, cre] ,
Tatiana A. Shestakova [aut] ,
Victor Resco de Dios [aut] ,
Jordi Voltas [aut]
Maintainer: Josu G. Alday <josucham@gmail.com>
Diff between DendroSync versions 0.1.4 dated 2022-05-26 and 0.1.5 dated 2025-08-27
DESCRIPTION | 41 +++++++++++++++++++++++++++++++---------- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/conifersIP.R | 4 ++-- R/dendro.varcov.R | 18 +++++++++--------- R/sync.R | 14 +++++++------- man/conifersIP.Rd | 4 ++-- man/dendro.varcov.Rd | 18 +++++++++--------- man/sync.Rd | 14 +++++++------- 9 files changed, 84 insertions(+), 54 deletions(-)
Title: Interface to the 'Azure Maps' API
Description: Provides a wrapper for the Microsoft 'Azure Maps' REST APIs <https://learn.microsoft.com/en-us/rest/api/maps/route?view=rest-maps-2025-01-01>,
enabling users to access mapping and geospatial services directly from R.
This package simplifies authenticating, building, and sending requests for
services like route directions. It handles conversions between R objects
(such as 'sf' objects) and the GeoJSON+JSON format required by the API,
making it easier to integrate 'Azure Maps' into R-based data analysis workflows.
Author: Juan P. Fonseca-Zamora [aut, cre]
Maintainer: Juan P. Fonseca-Zamora <ts18jpf@leeds.ac.uk>
Diff between azuremapsr versions 0.0.1 dated 2025-08-26 and 0.0.2 dated 2025-08-27
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 7 - R/bodyBuilder.R | 2 R/data.R | 8 + README.md | 204 +++++++++++++++++++++-------------------- data/sample_response_leeds.rda |only man/sample_response_leeds.Rd |only 8 files changed, 130 insertions(+), 109 deletions(-)
Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance, phylogenetic trees), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution, biostratigraphy or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.5.0 dated 2025-05-21 and 0.6.0 dated 2025-08-27
DESCRIPTION | 8 +-- MD5 | 76 ++++++++++++++++++----------- NAMESPACE | 7 ++ NEWS.md | 6 ++ R/all_preserved.R |only R/apply_niche.R | 2 R/apply_taphonomy.R | 1 R/bounded_niche.R | 1 R/gradient_from_data.R |only R/last_occ.R |only R/perfect_preservation.R |only R/range_offset.R |only R/snd_niche.R | 1 R/trivial_gradient.R |only R/trivial_niche.R |only README.md | 6 +- inst/CITATION | 4 - inst/WORDLIST | 8 ++- inst/doc/FossilSim_integration.R | 2 inst/doc/FossilSim_integration.Rmd | 4 - inst/doc/FossilSim_integration.html | 25 ++++----- inst/doc/StratPal.html | 14 ++--- inst/doc/event_data.Rmd | 12 ++++ inst/doc/event_data.html | 52 +++++++++++++------ inst/doc/paleoTS_functionality.html | 17 +++--- inst/doc/phenotypic_evolution.html | 14 ++--- man/StratPal-package.Rd | 2 man/all_preserved.Rd |only man/apply_niche.Rd | 2 man/apply_taphonomy.Rd | 1 man/bounded_niche.Rd | 1 man/gradient_from_data.Rd |only man/last_occ.Rd |only man/perfect_preservation.Rd |only man/range_offset.Rd |only man/snd_niche.Rd | 1 man/trivial_gradient.Rd |only man/trivial_niche.Rd |only tests/testthat/test_all_preserved.R |only tests/testthat/test_apply_niche.R | 9 +++ tests/testthat/test_apply_taphonomy.R | 10 +++ tests/testthat/test_gradient_from_data.R |only tests/testthat/test_last_occ.R |only tests/testthat/test_perfect_preservation.R |only tests/testthat/test_plot.pre_paleoTS.R |only tests/testthat/test_range_offset.R |only tests/testthat/test_trivial_gradient.R |only tests/testthat/test_trivial_niche.R |only vignettes/FossilSim_integration.Rmd | 4 - vignettes/event_data.Rmd | 12 ++++ 50 files changed, 206 insertions(+), 96 deletions(-)
Title: Fast Text Tokenization
Description: Interfaces with the 'Hugging Face' tokenizers library to provide implementations
of today's most used tokenizers such as the 'Byte-Pair Encoding' algorithm
<https://huggingface.co/docs/tokenizers/index>. It's extremely fast for both
training new vocabularies and tokenizing texts.
Author: Daniel Falbel [aut, cre],
Regouby Christophe [ctb],
Posit [cph]
Maintainer: Daniel Falbel <daniel@posit.co>
This is a re-admission after prior archival of version 0.1.4 dated 2024-09-04
Diff between tok versions 0.1.4 dated 2024-09-04 and 0.2.0 dated 2025-08-27
tok-0.1.4/tok/man/tok-package.Rd |only tok-0.1.4/tok/src/Makevars |only tok-0.1.4/tok/src/Makevars.win |only tok-0.1.4/tok/src/rust/config |only tok-0.2.0/tok/DESCRIPTION | 14 tok-0.2.0/tok/MD5 | 45 - tok-0.2.0/tok/NEWS.md | 9 tok-0.2.0/tok/R/encoding.R | 2 tok-0.2.0/tok/R/extendr-wrappers.R | 1 tok-0.2.0/tok/R/tokenizer.R | 10 tok-0.2.0/tok/configure |only tok-0.2.0/tok/configure.win |only tok-0.2.0/tok/inst/po |only tok-0.2.0/tok/po |only tok-0.2.0/tok/src/Makevars.in |only tok-0.2.0/tok/src/Makevars.win.in |only tok-0.2.0/tok/src/rust/Cargo.lock | 411 ++++++++------- tok-0.2.0/tok/src/rust/Cargo.toml | 12 tok-0.2.0/tok/src/rust/src/decoders.rs | 8 tok-0.2.0/tok/src/rust/src/models.rs | 34 - tok-0.2.0/tok/src/rust/src/normalizers.rs | 18 tok-0.2.0/tok/src/rust/src/post_processors.rs | 9 tok-0.2.0/tok/src/rust/src/pre_tokenizers.rs | 17 tok-0.2.0/tok/src/rust/src/tokenizer.rs | 12 tok-0.2.0/tok/src/rust/src/trainers.rs | 35 - tok-0.2.0/tok/src/rust/vendor-config.toml |only tok-0.2.0/tok/src/rust/vendor.tar.xz |binary tok-0.2.0/tok/tests/testthat/test-message-translations.R |only tok-0.2.0/tok/tools/config.R |only tok-0.2.0/tok/tools/msrv.R |only 30 files changed, 358 insertions(+), 279 deletions(-)
Title: Interpolation of Data with Variable Spatial Support
Description: Data with irregular spatial support, such as runoff related data or data from administrative units, can with 'rtop' be interpolated to locations without observations with the top-kriging method. A description of the package is given by Skøien et al (2014) <doi:10.1016/j.cageo.2014.02.009>.
Author: Jon Olav Skoeien [aut, cre],
Qingyun Duan [ctb]
Maintainer: Jon Olav Skoeien <jon.skoien@gmail.com>
Diff between rtop versions 0.6-9 dated 2024-01-30 and 0.6-17 dated 2025-08-27
rtop-0.6-17/rtop/DESCRIPTION | 7 +++---- rtop-0.6-17/rtop/MD5 | 10 +++++----- rtop-0.6-17/rtop/man/getRtopParams.Rd | 2 +- rtop-0.6-17/rtop/man/useRtopWithIntamap.Rd | 3 +-- rtop-0.6-17/rtop/tests/rtop.R | 12 +++++++----- rtop-0.6-17/rtop/tests/rtop.rout.save |only rtop-0.6-9/rtop/tests/rtop.Rout.save |only 7 files changed, 17 insertions(+), 17 deletions(-)
Title: Automatic Scoring of the Cognitive Reflection Test
Description: Automatic coding of open-ended responses to the Cognitive Reflection Test (CRT), a widely used class of tests in cognitive science and psychology that assess the tendency to override an initial intuitive (but incorrect) answer and engage in reflection to reach a correct solution. The package standardizes CRT response coding across datasets in cognitive psychology, decision-making, and related fields. Automated coding reduces manual effort and improves reproducibility by limiting variability from subjective interpretation of open-ended responses. The package supports automatic coding and machine scoring for the original English-language CRT (Frederick, 2005) <doi:10.1257/089533005775196732>, CRT4 and CRT7 (Toplak et al., 2014) <doi:10.1080/13546783.2013.844729>, CRT-long (Primi et al., 2016) <doi:10.1002/bdm.1883>, and CRT-2 (Thomson & Oppenheimer, 2016) <doi:10.1017/s1930297500007622>.
Author: Giuseppe Corbelli [aut, cre]
Maintainer: Giuseppe Corbelli <giuseppe.corbelli@uninettunouniversity.net>
Diff between reflectR versions 2.1.3 dated 2024-05-15 and 2.1.4 dated 2025-08-27
reflectR-2.1.3/reflectR/tests |only reflectR-2.1.4/reflectR/DESCRIPTION | 27 ++++++----- reflectR-2.1.4/reflectR/MD5 | 11 ++-- reflectR-2.1.4/reflectR/NEWS.md | 63 +++++++++++---------------- reflectR-2.1.4/reflectR/R/reflectR-package.R | 26 ++++++----- reflectR-2.1.4/reflectR/inst/WORDLIST | 4 - reflectR-2.1.4/reflectR/man/reflectR.Rd | 26 ++++++----- 7 files changed, 77 insertions(+), 80 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 1.3.0 dated 2025-07-16 and 1.3.1 dated 2025-08-27
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 4 build/vignette.rds |binary inst/doc/ggPMX-guide.R | 3 inst/doc/ggPMX-guide.Rmd | 17 - inst/doc/ggPMX-guide.pdf |binary man/ggPMX.Rd | 2 tests/testthat/test-param_table.R | 62 ++--- tests/testthat/test-plot-individual.R | 5 tests/testthat/test-pmx-report.R | 388 +++++++++++++++++----------------- vignettes/ggPMX-guide.Rmd | 17 - 12 files changed, 268 insertions(+), 258 deletions(-)
Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The
goal of 'workflows' is to streamline this process by bundling the
model alongside the preprocessor, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut] ,
Hannah Frick [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hannah Frick <hannah@posit.co>
Diff between workflows versions 1.2.0 dated 2025-02-18 and 1.3.0 dated 2025-08-27
DESCRIPTION | 41 +-- LICENSE | 2 MD5 | 144 +++++------ NAMESPACE | 12 NEWS.md | 13 - R/action.R | 26 +- R/broom.R | 57 ++-- R/butcher.R | 19 + R/compat-purrr.R | 16 - R/extract.R | 64 ++++- R/fit-action-model.R | 34 ++ R/fit.R | 110 +++++++- R/generics.R | 42 +++ R/post-action-tailor.R |only R/pre-action-case-weights.R | 8 R/pre-action-formula.R | 7 R/pre-action-recipe.R | 14 - R/pre-action-variables.R | 52 ++-- R/predict.R | 47 +++ R/pull.R | 30 +- R/reexports.R | 8 R/sparsevctrs.R | 67 +++-- R/stage.R | 18 - R/survival-censoring-weights.R | 20 + R/utils.R | 25 + R/workflow.R | 89 +++++-- README.md | 25 + build/vignette.rds |binary inst/doc/stages.R | 2 inst/doc/stages.Rmd | 12 inst/doc/stages.html | 15 - man/add_case_weights.Rd | 8 man/add_formula.Rd | 30 +- man/add_model.Rd | 16 - man/add_recipe.Rd | 4 man/add_tailor.Rd |only man/augment.workflow.Rd | 6 man/extract-workflow.Rd | 19 + man/fit-workflow.Rd | 42 +-- man/glance.workflow.Rd | 6 man/is_trained_workflow.Rd | 4 man/predict-workflow.Rd | 6 man/reexports.Rd | 4 man/required_pkgs.workflow.Rd |only man/rmd/add-formula.Rmd | 24 - man/rmd/indicators.Rmd | 16 - man/tidy.workflow.Rd | 13 - man/workflow-extractors.Rd | 6 man/workflow.Rd | 31 +- man/workflows-internals.Rd | 22 + man/workflows-package.Rd | 7 tests/testthat/_snaps/extract.md | 34 ++ tests/testthat/_snaps/fit-action-model.md | 8 tests/testthat/_snaps/fit.md | 16 + tests/testthat/_snaps/post-action-tailor.md |only tests/testthat/_snaps/predict.md | 8 tests/testthat/_snaps/printing.md | 20 + tests/testthat/_snaps/workflow.md | 16 + tests/testthat/helper-extract_parameter_set.R | 10 tests/testthat/helper-tunable.R |only tests/testthat/test-broom.R | 55 ++++ tests/testthat/test-extract.R | 326 ++++++++++++++++++++------ tests/testthat/test-fit-action-model.R | 28 ++ tests/testthat/test-fit.R | 75 +++++ tests/testthat/test-generics.R | 181 ++++++++++++++ tests/testthat/test-post-action-tailor.R |only tests/testthat/test-pre-action-case-weights.R | 21 + tests/testthat/test-pre-action-formula.R | 5 tests/testthat/test-pre-action-recipe.R | 7 tests/testthat/test-pre-action-variables.R | 20 + tests/testthat/test-predict.R | 42 +++ tests/testthat/test-printing.R | 10 tests/testthat/test-sparsevctrs.R | 304 +++++++++++++++++++----- tests/testthat/test-workflow.R | 40 +++ vignettes/extras/getting-started.Rmd | 125 ++++++--- vignettes/stages.Rmd | 12 76 files changed, 2051 insertions(+), 595 deletions(-)
Title: Basic Statistics
Description: Basic statistical analyses. The package has been developed
to be used in statistics courses at Bocconi University (Milan, Italy).
Currently, the package includes some exploratory and inferential analyses
usually presented in introductory statistics courses.
Author: Raffaella Piccarreta [aut],
Sergio Venturini [cre]
Maintainer: Sergio Venturini <sergio.venturini@unicatt.it>
Diff between UBStats versions 0.2.2 dated 2024-08-26 and 0.3.0 dated 2025-08-27
UBStats-0.2.2/UBStats/R/UBStats_Main_Visible_ALL_202406.R |only UBStats-0.2.2/UBStats/R/UBStats_Utility_Invisible_NEW_202406.R |only UBStats-0.3.0/UBStats/DESCRIPTION | 8 UBStats-0.3.0/UBStats/MD5 | 54 +- UBStats-0.3.0/UBStats/R/UBStats_Main_Visible_ALL_202508.R |only UBStats-0.3.0/UBStats/R/UBStats_Utility_Invisible_202508.R |only UBStats-0.3.0/UBStats/R/zz_datasets.R | 221 ++++++++++ UBStats-0.3.0/UBStats/README.md | 10 UBStats-0.3.0/UBStats/data/Banner.RData |only UBStats-0.3.0/UBStats/data/CallCentre_KPI.RData |only UBStats-0.3.0/UBStats/data/Grocery_NE.RData |only UBStats-0.3.0/UBStats/data/Marketing_Mix.RData |only UBStats-0.3.0/UBStats/data/Time_Social.RData |only UBStats-0.3.0/UBStats/data/Transition.RData |only UBStats-0.3.0/UBStats/man/Banner.Rd |only UBStats-0.3.0/UBStats/man/CI.diffmean.Rd | 2 UBStats-0.3.0/UBStats/man/CI.diffprop.Rd | 2 UBStats-0.3.0/UBStats/man/CI.mean.Rd | 2 UBStats-0.3.0/UBStats/man/CI.prop.Rd | 2 UBStats-0.3.0/UBStats/man/CallCentre_KPI.Rd |only UBStats-0.3.0/UBStats/man/Grocery_NE.Rd |only UBStats-0.3.0/UBStats/man/LM.output.Rd | 2 UBStats-0.3.0/UBStats/man/Marketing_Mix.Rd |only UBStats-0.3.0/UBStats/man/TEST.diffmean.Rd | 2 UBStats-0.3.0/UBStats/man/TEST.diffprop.Rd | 2 UBStats-0.3.0/UBStats/man/TEST.diffvar.Rd | 2 UBStats-0.3.0/UBStats/man/TEST.mean.Rd | 2 UBStats-0.3.0/UBStats/man/TEST.prop.Rd | 2 UBStats-0.3.0/UBStats/man/Time_Social.Rd |only UBStats-0.3.0/UBStats/man/Transition.Rd |only UBStats-0.3.0/UBStats/man/distr.plot.x.Rd | 2 UBStats-0.3.0/UBStats/man/distr.plot.xy.Rd | 2 UBStats-0.3.0/UBStats/man/distr.summary.x.Rd | 2 UBStats-0.3.0/UBStats/man/distr.table.x.Rd | 2 UBStats-0.3.0/UBStats/man/distr.table.xy.Rd | 2 UBStats-0.3.0/UBStats/man/summaries.plot.x.Rd | 2 36 files changed, 278 insertions(+), 47 deletions(-)
Title: Ready-to-Use Omics Formatting, Analysis, and Visualization
Pipeline
Description: Provides a flexible and streamlined pipeline for formatting, analyzing, and
visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics,
metabolomics). The package includes tools for shaping input data into analysis-ready
structures, fitting linear or mixed-effect models, extracting key contrasts, and
generating a rich variety of ready-to-use publication-quality plots.
Designed for transparency and reproducibility across a wide range of study designs,
with customizable components for statistical modeling.
Author: Laura Martinez-Gili [cre, aut, cph]
Maintainer: Laura Martinez-Gili <martinez.gili.laura@gmail.com>
Diff between readyomics versions 0.1.0 dated 2025-08-20 and 0.1.1 dated 2025-08-27
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/build_phyloseq.R | 2 ++ R/mva.R | 2 ++ R/process_ngs.R | 2 ++ inst/doc/readyomics.R | 8 ++++++-- inst/doc/readyomics.Rmd | 20 +++++++++++++------- inst/doc/readyomics.html | 13 +++++++------ man/build_phyloseq.Rd | 2 ++ man/mva.Rd | 2 ++ man/process_ngs.Rd | 2 ++ vignettes/readyomics.Rmd | 20 +++++++++++++------- 13 files changed, 70 insertions(+), 37 deletions(-)
Title: Data Visualisation on 'Lifemap' Tree
Description: Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.
Author: Cassandra Bompard [aut],
Damien M. de Vienne [aut] ,
Julien Barnier [aut] ,
Aurelie Siberchicot [ctb, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
This is a re-admission after prior archival of version 1.1.5 dated 2025-03-06
Diff between LifemapR versions 1.1.5 dated 2025-03-06 and 1.1.6 dated 2025-08-27
DESCRIPTION | 15 - MD5 | 16 - R/display_map.R | 4 README.md | 2 build/vignette.rds |binary inst/doc/runLifemapR.R | 10 - inst/doc/runLifemapR.Rmd | 15 - inst/doc/runLifemapR.html | 373 +++++++++++++++++++++++++--------------------- vignettes/runLifemapR.Rmd | 15 - 9 files changed, 234 insertions(+), 216 deletions(-)
Title: Utilities for Scheduling Functions to Execute Later with Event
Loops
Description: Executes arbitrary R or C functions some time after the
current time, after the R execution stack has emptied. The functions
are scheduled in an event loop.
Author: Winston Chang [aut],
Joe Cheng [aut],
Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Marcus Geelnard [ctb, cph] ,
Evan Nemerson [ctb, cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between later versions 1.4.3 dated 2025-08-20 and 1.4.4 dated 2025-08-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/later-cpp.html | 9 ++++----- tests/testthat/test-private-loops.R | 2 +- tests/testthat/test-run_now.R | 11 ++++------- 6 files changed, 21 insertions(+), 21 deletions(-)
Title: Interactive Add-on Functionality for 'intamap'
Description: The methods in this package adds to the functionality of the 'intamap' package, such as bias correction and network optimization. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.
Author: Edzer Pebesma [aut],
Jon Skoien [aut, cre],
Olivier Baume [ctb],
A Chorti [ctb],
Dionisis Hristopulos [ctb],
Stepahnie Melles [ctb],
Giannis Spiliopoulos [ctb]
Maintainer: Jon Skoien <jon.skoien@gmail.com>
This is a re-admission after prior archival of version 1.2-6 dated 2023-10-30
Diff between intamapInteractive versions 1.2-6 dated 2023-10-30 and 1.2-7 dated 2025-08-27
DESCRIPTION | 7 +++---- MD5 | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-)
More information about intamapInteractive at CRAN
Permanent link
Title: Goodness-of-Fit Tests for Copulae
Description: Several Goodness-of-Fit (GoF) tests for Copulae are provided. A new hybrid test, Zhang et al. (2016) <doi:10.1016/j.jeconom.2016.02.017> is implemented which supports all of the individual tests in the package, e.g. Genest et al. (2009) <doi:10.1016/j.insmatheco.2007.10.005>. Estimation methods for the margins are provided and all the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau. For reproducibility of results, the functions support the definition of seeds. Also all the tests support automatized parallelization of the bootstrapping tasks. The package provides an interface to perform new GoF tests by submitting the test statistic.
Author: Simon Trimborn [aut, cre],
Ostap Okhrin [aut],
Martin Waltz [aut]
Maintainer: Simon Trimborn <trimborn.econometrics@gmail.com>
This is a re-admission after prior archival of version 0.4-2 dated 2025-05-09
Diff between gofCopula versions 0.4-2 dated 2025-05-09 and 0.4-3 dated 2025-08-27
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.9.0.1 dated 2025-08-26 and 4.10.1 dated 2025-08-27
DESCRIPTION | 10 MD5 | 153 ++-- NAMESPACE | 12 R/InitErgmConstraint.R | 6 R/InitErgmConstraint.blockdiag.R | 4 R/InitErgmTerm.R | 85 +- R/InitErgmTerm.bipartite.R | 4 R/InitErgmTerm.bipartite.degree.R | 4 R/InitErgmTerm.coincidence.R | 4 R/InitErgmTerm.dgw_sp.R | 42 - R/InitErgmTerm.operator.R | 17 R/InitErgmTerm.projection.R | 2 R/InitErgmTerm.spcache.R | 6 R/InitWtErgmTerm.R | 17 R/InitWtErgmTerm.auxnet.R | 4 R/InitWtErgmTerm.operator.R | 31 R/check.ErgmTerm.R | 13 R/ergm-terms-index.R | 19 R/ergm.R | 142 ++- R/ergm.bridge.R | 33 R/ergm.errors.R | 3 R/ergm.geodistn.R | 7 R/ergm.initialfit.R | 8 R/ergm.logitreg.R | 28 R/ergm.mple.R | 8 R/ergm.pl.R | 6 R/ergm.san.R | 2 R/ergm.utility.R | 70 + R/ergmMPLE.R | 2 R/ergm_model.R | 3 R/ergm_model.utils.R | 2 R/ergm_state.R | 4 R/get.node.attr.R | 23 R/gof.ergm.R | 375 +++++----- R/rlebdm.R | 4 R/simulate.ergm.R | 8 R/to_ergm_Cdouble.R | 2 R/zzz.R | 4 build/partial.rdb |binary build/stage23.rdb |binary inst/CITATION | 4 inst/NEWS.Rd | 94 ++ inst/doc/Terms-API.Rmd | 1 inst/doc/Terms-API.html | 3 inst/doc/ergm-term-crossRef.html | 141 +-- inst/doc/ergm.html | 280 +++---- inst/doc/nodal_attributes.html | 9 inst/include/ergm_MHstorage.h | 6 inst/include/ergm_constants.h | 4 inst/include/ergm_simple_Matrix.h |only inst/include/ergm_storage.h | 6 inst/include/ergm_stubs.c | 10 inst/include/ergm_util.h | 10 inst/include/ergm_wtchangestats_auxnet.h | 44 - inst/include/inc/ergm_MHproposal.h.template.do_not_include_directly.h | 1 inst/include/inc/ergm_edgetree_inline_template.do_not_include_directly.h | 2 inst/include/inc/ergm_model.h.template.do_not_include_directly.h | 2 man/ergm.Rd | 124 ++- man/gof.Rd | 52 - man/macros/ergm-spec.Rd | 2 man/macros/uid-algo.Rd | 2 man/mutual-ergmTerm-22863009.Rd | 22 man/nodecovar-ergmTerm-35c93a8b.Rd | 2 man/simulate.ergm.Rd | 23 src/MCMC.c.template.do_not_include_directly.h | 32 src/MHproposals_triadic.c | 37 src/changestats_dgw_sp.c | 148 +-- src/changestats_dgw_sp.h | 9 src/changestats_operator.c | 216 ----- src/changestats_operator.c.template.do_not_include_directly.h |only src/ergm_Rutil.c | 47 + src/geodist.c | 51 + src/init.c | 2 src/model.c.template.do_not_include_directly.h | 27 src/wtchangestats_auxnet.c | 68 - src/wtchangestats_operator.c | 242 ------ tests/testthat/test-gof.R | 10 tests/testthat/test-skip.R |only vignettes/Terms-API.Rmd | 1 79 files changed, 1425 insertions(+), 1476 deletions(-)
Title: A 'Shiny' Tool to Create Interactive Catalogues for Geospatial
Data
Description: Seamlessly create interactive online catalogues for geospatial data. Items can be mapped as points or areas and retrieved using either a map or a dynamic table with search form and optional column filters.
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between spatialCatalogueViewer versions 0.1.2 dated 2025-08-26 and 0.1.3 dated 2025-08-27
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 9 ++++++++- R/app_server.R | 7 ++++--- R/app_ui.R | 14 +++++++++++++- 5 files changed, 33 insertions(+), 13 deletions(-)
More information about spatialCatalogueViewer at CRAN
Permanent link
Title: Access to the 'DraCor' API
Description: Provide an interface for 'Drama Corpora Project' ('DraCor') API: <https://dracor.org/documentation/api>.
Author: Ivan Pozdniakov [aut, cre]
Maintainer: Ivan Pozdniakov <bucherr@yandex.ru>
This is a re-admission after prior archival of version 1.0.4 dated 2024-09-26
Diff between rdracor versions 1.0.4 dated 2024-09-26 and 1.0.5 dated 2025-08-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NEWS.md | 7 ++++++- R/net.R | 2 ++ build/partial.rdb |binary 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Posit, PBC [cph],
Intel [aut, cph] ,
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.11 dated 2025-08-27 and 5.1.11-1 dated 2025-08-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/include/RcppParallel/TBB.h | 11 ++++++++++- 3 files changed, 15 insertions(+), 6 deletions(-)
Title: Calculating Topological Properties of Phylogenies
Description: Tools for calculating and viewing topological properties of phylogenetic trees.
Author: Michelle Kendall [aut, cre] ,
Michael Boyd [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <michelle.kendall@ndm.ox.ac.uk>
Diff between phyloTop versions 2.1.2 dated 2023-01-24 and 2.1.3 dated 2025-08-27
DESCRIPTION | 17 +++++++++-------- MD5 | 13 +++++++------ NEWS.md | 6 ++++++ R/makeEpiRecord.R | 2 +- README.md | 4 ++-- build/partial.rdb |binary man/figures |only man/makeEpiRecord.Rd | 2 +- 8 files changed, 26 insertions(+), 18 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.4.2 dated 2025-06-05 and 3.5.0 dated 2025-08-27
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/Cluster.R | 28 +++++++++++++++++++++++++++- inst/doc/Logging.pdf |binary inst/doc/Parallel.pdf |binary man/makeCluster.Rd | 6 +++++- tests/testthat/test-cluster.R | 21 +++++++++++++++++++++ 8 files changed, 73 insertions(+), 14 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.11 dated 2025-07-22 and 1.0.12 dated 2025-08-27
modsem-1.0.11/modsem/tests/testthat/mplusResults.inp |only modsem-1.0.11/modsem/tests/testthat/mplusResults.out |only modsem-1.0.11/modsem/tests/testthat/mplusResults_2f55eb38256759e6ebc9b0699ecf1d13.dat |only modsem-1.0.11/modsem/tests/testthat/mplusResults_6507283a847451aff127c84c87ebd81b.dat |only modsem-1.0.11/modsem/tests/testthat/mplusResults_6bb11f99c9f63d831155403fa8debc11.dat |only modsem-1.0.11/modsem/tests/testthat/mplusResults_ad18af3b9c89a45fac7dc52df3607909.dat |only modsem-1.0.11/modsem/tests/testthat/mplusResults_e8725a6185cbe0286c28c26f935f24e2.dat |only modsem-1.0.12/modsem/DESCRIPTION | 8 modsem-1.0.12/modsem/MD5 | 342 ++-- modsem-1.0.12/modsem/NAMESPACE | 9 modsem-1.0.12/modsem/R/RcppExports.R | 32 modsem-1.0.12/modsem/R/bootstrap.R | 52 modsem-1.0.12/modsem/R/calc_se_da.R | 206 +- modsem-1.0.12/modsem/R/check_model_da.R | 61 modsem-1.0.12/modsem/R/colorize_output.R | 48 modsem-1.0.12/modsem/R/compare_fit.R | 14 modsem-1.0.12/modsem/R/constraints_pi_ca.R | 8 modsem-1.0.12/modsem/R/construct_matrices_da.R | 49 modsem-1.0.12/modsem/R/cov_model.R | 6 modsem-1.0.12/modsem/R/datasets.R | 20 modsem-1.0.12/modsem/R/equations_lms.R | 379 +++- modsem-1.0.12/modsem/R/equations_qml.R | 39 modsem-1.0.12/modsem/R/est_h0.R | 46 modsem-1.0.12/modsem/R/est_lms.R | 561 +++---- modsem-1.0.12/modsem/R/est_qml.R | 131 - modsem-1.0.12/modsem/R/fit_modsem_da.R | 127 + modsem-1.0.12/modsem/R/formatted_objects.R | 2 modsem-1.0.12/modsem/R/generics.R | 100 - modsem-1.0.12/modsem/R/generics_lavaan.R | 32 modsem-1.0.12/modsem/R/generics_modsem_da.R | 359 ++-- modsem-1.0.12/modsem/R/generics_modsem_mplus.R | 52 modsem-1.0.12/modsem/R/generics_modsem_pi.R | 86 - modsem-1.0.12/modsem/R/inspect_da.R | 30 modsem-1.0.12/modsem/R/labelled_params_da.R | 2 modsem-1.0.12/modsem/R/lavaan_labels.R | 4 modsem-1.0.12/modsem/R/method_settings_da.R | 12 modsem-1.0.12/modsem/R/method_settings_pi.R | 2 modsem-1.0.12/modsem/R/model_da.R | 229 ++ modsem-1.0.12/modsem/R/model_parameters_da.R | 90 - modsem-1.0.12/modsem/R/model_pi.R | 16 modsem-1.0.12/modsem/R/modsem_da.R | 195 +- modsem-1.0.12/modsem/R/modsem_mplus.R | 375 +++- modsem-1.0.12/modsem/R/modsem_pi.R | 68 modsem-1.0.12/modsem/R/multiple_imputation_da.R | 92 - modsem-1.0.12/modsem/R/optimize_da.R | 96 - modsem-1.0.12/modsem/R/parser.R | 14 modsem-1.0.12/modsem/R/plot_interaction.R | 257 +-- modsem-1.0.12/modsem/R/print_partable.R | 85 - 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Title: Estimate Migratory Connectivity for Migratory Animals
Description: Allows the user to estimate transition probabilities for
migratory animals between any two phases of the annual cycle, using a
variety of different data types. Also quantifies the strength of
migratory connectivity (MC), a standardized metric to quantify the
extent to which populations co-occur between two phases of the annual
cycle. Includes functions to estimate MC and the more traditional
metric of migratory connectivity strength (Mantel correlation)
incorporating uncertainty from multiple sources of sampling error. For
cross-species comparisons, methods are provided to estimate
differences in migratory connectivity strength, incorporating
uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>,
Cohen et al. (2019) <doi:10.1111/ecog.03974>, Roberts et al. (2023)
<doi:10.1002/eap.2788>, and Hostetler et al. (2025)
<doi:10.1111/2041-210X.14467> for details on some of these methods.
Author: Jeffrey A. Hostetler [cre, aut],
Michael T. Hallworth [aut],
Clark S. Rushing [ctb],
Emily B. Cohen [ctb],
Valentine Herrmann [ctb],
Henry Stevens [ctb]
Maintainer: Jeffrey A. Hostetler <jhostetler@usgs.gov>
Diff between MigConnectivity versions 0.4.7 dated 2024-03-26 and 0.5.0 dated 2025-08-27
DESCRIPTION | 21 MD5 | 64 NAMESPACE | 2 R/MigConnectivity.R | 2 R/calcConnectivity.R | 62 R/estConnectivity.R | 341 +++++ R/instrinsicIsotopes.R | 8 R/outputConnectivity.R | 474 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 12 inst/doc/MigConnectivity.Rmd | 2 inst/doc/MigConnectivity.html | 30 inst/doc/olderFunctionality.R | 2524 +++++++++++++++++++-------------------- inst/doc/olderFunctionality.html | 56 inst/doc/simulateIsoMC.R | 686 +++++----- inst/doc/simulateIsoMC.html | 8 inst/examples/estNMCExamples.R |only man/MigConnectivity.Rd | 3 man/calcNMC.Rd |only man/calcTransition.Rd | 2 man/diffMC.Rd | 4 man/diffMantel.Rd | 4 man/estMC.Rd | 2 man/estNMC.Rd |only man/estTransition.Rd | 7 man/isoAssign.Rd | 2 man/plot.estMigConnectivity.Rd | 7 man/weightAssign.Rd | 6 vignettes/MigConnectivity.Rmd | 2 vignettes/WorkedExample.RMD | 125 - vignettes/WorkedExample.html |only vignettes/estStrength.html |only vignettes/estTransition.RMD | 2 vignettes/estTransition.html |only vignettes/mc_library.bib | 20 36 files changed, 2565 insertions(+), 1913 deletions(-)
More information about MigConnectivity at CRAN
Permanent link
Title: Fitting and Assessing Neighborhood Models of the Effect of
Interspecific Competition on the Growth of Trees
Description: Code for fitting and assessing models for the growth of trees. In
particular for the Bayesian neighborhood competition linear regression model
of Allen (2020): methods for model fitting and generating fitted/predicted
values, evaluating the effect of competitor species identity using
permutation tests, and evaluating model performance using spatial
cross-validation.
Author: Albert Y. Kim [aut, cre] ,
David Allen [aut] ,
Simon Couch [aut]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
This is a re-admission after prior archival of version 0.2.0 dated 2021-10-02
Diff between forestecology versions 0.2.0 dated 2021-10-02 and 0.2.1 dated 2025-08-27
DESCRIPTION | 20 MD5 | 28 NEWS.md | 46 - R/bw_datasets.R | 2 R/forestecology.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 27 inst/doc/forestecology.html | 730 +++++++++++++------- man/forestecology.Rd | 19 man/species_bw.Rd | 2 vignettes/man/figures/README-unnamed-chunk-13-1.png |binary vignettes/man/figures/README-unnamed-chunk-3-1.png |binary vignettes/man/figures/README-unnamed-chunk-6-1.png |binary vignettes/man/figures/README-unnamed-chunk-9-1.png |binary 15 files changed, 588 insertions(+), 289 deletions(-)
Title: Fast and Exact Computation of Gaussian Stochastic Process
Description: Implements fast and exact computation of Gaussian stochastic process with the Matern kernel using forward filtering and backward smoothing algorithm. It includes efficient implementations of the inverse Kalman filter, with applications such as estimating particle interaction functions. These tools support models with or without noise. Additionally, the package offers algorithms for fast parameter estimation in latent factor models, where the factor loading matrix is orthogonal, and latent processes are modeled by Gaussian processes. See the references: 1) Mengyang Gu and Yanxun Xu (2020), Journal of Computational and Graphical Statistics; 2) Xinyi Fang and Mengyang Gu (2024), <doi:10.48550/arXiv.2407.10089>; 3) Mengyang Gu and Weining Shen (2020), Journal of Machine Learning Research; 4) Yizi Lin, Xubo Liu, Paul Segall and Mengyang Gu (2025), <doi:10.48550/arXiv.2501.01324>.
Author: Mengyang Gu [aut, cre],
Xinyi Fang [aut],
Yizi Lin [aut]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between FastGaSP versions 0.6.1 dated 2025-06-05 and 0.6.2 dated 2025-08-27
CHANGELOG | 3 DESCRIPTION | 8 - MD5 | 27 +++--- NAMESPACE | 2 R/RcppExports.R | 14 ++- R/functions.R | 4 build/partial.rdb |binary man/Construct_G_matern_3_2.Rd |only man/Construct_W0_matern_3_2.Rd |only man/Construct_W_matern_3_2.Rd |only man/Sample_KF.Rd | 2 man/Sample_KF_post.Rd | 2 man/fgasp-class.Rd | 2 man/fgasp.Rd | 2 src/RcppExports.cpp | 38 +++++++++ src/functions.cpp | 165 +++++++++++++++++++++++++++++++++++++---- 16 files changed, 229 insertions(+), 40 deletions(-)
Title: Tools to Easily Read/Write NetCDF Files into/from
Multidimensional R Arrays
Description: Set of wrappers for the 'ncdf4' package to simplify and extend its
reading/writing capabilities into/from multidimensional R arrays.
Author: BSC-CNS [aut, cph],
Nicolau Manubens [aut],
Nuria Perez-Zanon [ctb] ,
An-Chi Ho [ctb],
Ariadna Batalla [cre],
Victoria Agudetse [ctb]
Maintainer: Ariadna Batalla <ariadna.batalla@bsc.es>
Diff between easyNCDF versions 0.1.3 dated 2025-06-04 and 0.1.4 dated 2025-08-27
DESCRIPTION | 13 ++++++++----- MD5 | 8 +++++--- NEWS.md | 3 +++ R/ArrayToNc.R | 21 +++++++++++++++++---- tests |only 5 files changed, 33 insertions(+), 12 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut] ,
Malan Bosman [aut] ,
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.6.1 dated 2025-07-03 and 0.7.0 dated 2025-08-27
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cards-0.7.0/cards/NEWS.md | 38 cards-0.7.0/cards/R/add_calculated_row.R | 4 cards-0.7.0/cards/R/apply_fmt_fun.R | 2 cards-0.7.0/cards/R/ard_hierarchical.R | 6 cards-0.7.0/cards/R/ard_identity.R | 2 cards-0.7.0/cards/R/ard_missing.R | 4 cards-0.7.0/cards/R/ard_mvsummary.R |only cards-0.7.0/cards/R/ard_pairwise.R | 2 cards-0.7.0/cards/R/ard_stack.R | 38 cards-0.7.0/cards/R/ard_stack_hierarchical.R | 45 cards-0.7.0/cards/R/ard_strata.R | 33 cards-0.7.0/cards/R/ard_summary.R |only cards-0.7.0/cards/R/ard_tabulate.R |only cards-0.7.0/cards/R/ard_tabulate_value.R |only cards-0.7.0/cards/R/ard_total_n.R | 8 cards-0.7.0/cards/R/as_card_fn.R | 8 cards-0.7.0/cards/R/as_nested_list.R | 4 cards-0.7.0/cards/R/bind_ard.R | 4 cards-0.7.0/cards/R/check_ard_structure.R | 2 cards-0.7.0/cards/R/data.R | 3 cards-0.7.0/cards/R/deprecated.R | 94 +- cards-0.7.0/cards/R/filter_ard_hierarchical.R | 314 +++++- cards-0.7.0/cards/R/get_ard_statistics.R | 4 cards-0.7.0/cards/R/maximum_variable_value.R |only cards-0.7.0/cards/R/nest_for_ard.R | 16 cards-0.7.0/cards/R/print.R | 2 cards-0.7.0/cards/R/print_ard_conditions.R | 6 cards-0.7.0/cards/R/rename_ard_columns.R | 4 cards-0.7.0/cards/R/rename_ard_groups.R | 2 cards-0.7.0/cards/R/replace_null_statistic.R | 2 cards-0.7.0/cards/R/selectors.R | 2 cards-0.7.0/cards/R/shuffle_ard.R | 146 ++- cards-0.7.0/cards/R/sort_ard_hierarchical.R | 452 ++++------ cards-0.7.0/cards/R/summary_functions.R | 2 cards-0.7.0/cards/R/syntax.R | 16 cards-0.7.0/cards/R/tidy_ard_order.R | 4 cards-0.7.0/cards/R/tidy_as_ard.R | 2 cards-0.7.0/cards/R/unlist_ard_columns.R | 4 cards-0.7.0/cards/R/update_ard.R | 4 cards-0.7.0/cards/README.md | 4 cards-0.7.0/cards/data/ADLB.rda |only cards-0.7.0/cards/inst/WORDLIST | 2 cards-0.7.0/cards/man/adam.Rd | 5 cards-0.7.0/cards/man/add_calculated_row.Rd | 4 cards-0.7.0/cards/man/apply_fmt_fun.Rd | 2 cards-0.7.0/cards/man/ard_mvsummary.Rd |only cards-0.7.0/cards/man/ard_pairwise.Rd | 2 cards-0.7.0/cards/man/ard_stack.Rd | 20 cards-0.7.0/cards/man/ard_stack_hierarchical.Rd | 16 cards-0.7.0/cards/man/ard_strata.Rd | 31 cards-0.7.0/cards/man/ard_summary.Rd |only cards-0.7.0/cards/man/ard_tabulate.Rd |only cards-0.7.0/cards/man/ard_tabulate_value.Rd |only cards-0.7.0/cards/man/as_cards_fn.Rd | 8 cards-0.7.0/cards/man/as_nested_list.Rd | 2 cards-0.7.0/cards/man/bind_ard.Rd | 4 cards-0.7.0/cards/man/cards-package.Rd | 5 cards-0.7.0/cards/man/check_ard_structure.Rd | 2 cards-0.7.0/cards/man/deprecated.Rd | 41 cards-0.7.0/cards/man/dot-calculate_stats_as_ard.Rd | 2 cards-0.7.0/cards/man/dot-calculate_tabulation_statistics.Rd | 2 cards-0.7.0/cards/man/dot-check_dichotomous_value.Rd | 4 cards-0.7.0/cards/man/dot-check_for_missing_combos_in_denom.Rd | 2 cards-0.7.0/cards/man/dot-check_no_ard_columns.Rd | 2 cards-0.7.0/cards/man/dot-cli_condition_messaging.Rd | 2 cards-0.7.0/cards/man/dot-cli_groups_and_variable.Rd | 2 cards-0.7.0/cards/man/dot-create_list_for_attributes.Rd | 2 cards-0.7.0/cards/man/dot-default_fmt_fun.Rd | 4 cards-0.7.0/cards/man/dot-derive_overall_labels.Rd |only cards-0.7.0/cards/man/dot-detect_msgs.Rd | 2 cards-0.7.0/cards/man/dot-eval_ard_calls.Rd | 4 cards-0.7.0/cards/man/dot-fill_overall_grp_values.Rd | 15 cards-0.7.0/cards/man/dot-lst_results_as_df.Rd | 2 cards-0.7.0/cards/man/dot-one_row_ard_to_nested_list.Rd | 2 cards-0.7.0/cards/man/dot-process_denominator.Rd | 4 cards-0.7.0/cards/man/dot-process_nested_list_as_df.Rd | 4 cards-0.7.0/cards/man/dot-table_as_df.Rd | 2 cards-0.7.0/cards/man/dot-trim_ard.Rd | 4 cards-0.7.0/cards/man/filter_ard_hierarchical.Rd | 73 + cards-0.7.0/cards/man/get_ard_statistics.Rd | 2 cards-0.7.0/cards/man/maximum_variable_value.Rd | 4 cards-0.7.0/cards/man/nest_for_ard.Rd | 7 cards-0.7.0/cards/man/print.card.Rd | 2 cards-0.7.0/cards/man/print_ard_conditions.Rd | 2 cards-0.7.0/cards/man/rename_ard_columns.Rd | 4 cards-0.7.0/cards/man/rename_ard_groups.Rd | 2 cards-0.7.0/cards/man/replace_null_statistic.Rd | 2 cards-0.7.0/cards/man/selectors.Rd | 2 cards-0.7.0/cards/man/shuffle_ard.Rd | 4 cards-0.7.0/cards/man/sort_ard_hierarchical.Rd | 28 cards-0.7.0/cards/man/summary_functions.Rd | 2 cards-0.7.0/cards/man/syntax.Rd | 16 cards-0.7.0/cards/man/tidy_ard_order.Rd | 4 cards-0.7.0/cards/man/tidy_as_ard.Rd | 2 cards-0.7.0/cards/man/unlist_ard_columns.Rd | 4 cards-0.7.0/cards/man/update_ard.Rd | 4 cards-0.7.0/cards/tests/testthat/_snaps/add_calculated_row.md | 50 - cards-0.7.0/cards/tests/testthat/_snaps/apply_fmt_fun.md | 9 cards-0.7.0/cards/tests/testthat/_snaps/ard_mvsummary.md |only cards-0.7.0/cards/tests/testthat/_snaps/ard_pairwise.md | 14 cards-0.7.0/cards/tests/testthat/_snaps/ard_stack.md | 18 cards-0.7.0/cards/tests/testthat/_snaps/ard_strata.md | 67 + cards-0.7.0/cards/tests/testthat/_snaps/ard_summary.md |only cards-0.7.0/cards/tests/testthat/_snaps/ard_tabulate.md |only cards-0.7.0/cards/tests/testthat/_snaps/ard_tabulate_value.md |only cards-0.7.0/cards/tests/testthat/_snaps/as_nested_list.md | 50 - cards-0.7.0/cards/tests/testthat/_snaps/bind_ard.md | 24 cards-0.7.0/cards/tests/testthat/_snaps/check_ard_structure.md | 2 cards-0.7.0/cards/tests/testthat/_snaps/filter_ard_hierarchical.md | 53 + cards-0.7.0/cards/tests/testthat/_snaps/options.md | 4 cards-0.7.0/cards/tests/testthat/_snaps/print.md | 42 cards-0.7.0/cards/tests/testthat/_snaps/print_ard_conditions.md | 22 cards-0.7.0/cards/tests/testthat/_snaps/rename_ard_columns.md | 5 cards-0.7.0/cards/tests/testthat/_snaps/rename_ard_groups.md | 8 cards-0.7.0/cards/tests/testthat/_snaps/shuffle_ard.md | 256 ++++- cards-0.7.0/cards/tests/testthat/_snaps/sort_ard_hierarchical.md | 6 cards-0.7.0/cards/tests/testthat/_snaps/tidy_ard_row_order.md | 2 cards-0.7.0/cards/tests/testthat/_snaps/update_ard.md | 27 cards-0.7.0/cards/tests/testthat/test-add_calculated_row.R | 8 cards-0.7.0/cards/tests/testthat/test-apply_fmt_fun.R | 6 cards-0.7.0/cards/tests/testthat/test-ard_mvsummary.R |only cards-0.7.0/cards/tests/testthat/test-ard_pairwise.R | 18 cards-0.7.0/cards/tests/testthat/test-ard_stack.R | 272 ++++-- cards-0.7.0/cards/tests/testthat/test-ard_stack_hierarchical.R | 72 + cards-0.7.0/cards/tests/testthat/test-ard_strata.R | 55 + cards-0.7.0/cards/tests/testthat/test-ard_summary.R |only cards-0.7.0/cards/tests/testthat/test-ard_tabulate.R |only cards-0.7.0/cards/tests/testthat/test-ard_tabulate_value.R |only cards-0.7.0/cards/tests/testthat/test-as_card.R | 2 cards-0.7.0/cards/tests/testthat/test-as_nested_list.R | 2 cards-0.7.0/cards/tests/testthat/test-bind_ard.R | 12 cards-0.7.0/cards/tests/testthat/test-check_ard_structure.R | 2 cards-0.7.0/cards/tests/testthat/test-filter_ard_hierarchical.R | 173 +++ cards-0.7.0/cards/tests/testthat/test-get_ard_statistics.R | 2 cards-0.7.0/cards/tests/testthat/test-options.R | 6 cards-0.7.0/cards/tests/testthat/test-print.R | 10 cards-0.7.0/cards/tests/testthat/test-print_ard_conditions.R | 18 cards-0.7.0/cards/tests/testthat/test-rename_ard_columns.R | 12 cards-0.7.0/cards/tests/testthat/test-rename_ard_groups.R | 14 cards-0.7.0/cards/tests/testthat/test-replace_null_statistic.R | 2 cards-0.7.0/cards/tests/testthat/test-selectors.R | 12 cards-0.7.0/cards/tests/testthat/test-shuffle_ard.R | 342 +++++++ cards-0.7.0/cards/tests/testthat/test-sort_ard_hierarchical.R | 81 + cards-0.7.0/cards/tests/testthat/test-tidy_ard_column_order.R | 2 cards-0.7.0/cards/tests/testthat/test-tidy_ard_row_order.R | 2 cards-0.7.0/cards/tests/testthat/test-unlist_ard_columns.R | 12 cards-0.7.0/cards/tests/testthat/test-update_ard.R | 18 167 files changed, 2674 insertions(+), 1116 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Author: Eric Marcon [aut, cre] ,
Florence Puech [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between divent versions 0.5-2 dated 2025-02-09 and 0.5-3 dated 2025-08-27
DESCRIPTION | 14 MD5 | 34 - NEWS.md | 7 R/abd_freq_count.R | 4 R/accum_sp.R | 2 R/accum_sp_hill.R | 6 R/species_distribution.R | 10 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 1292 ++++++++++++++++++++++----------------------- man/abd_freq_count.Rd | 5 man/accum_sp.Rd | 2 man/accum_sp_hill.Rd | 4 man/alphahull.Rd | 86 +- man/div_gen_simpson.Rd | 142 ++-- man/divent-package.Rd | 5 man/ent_gen_simpson.Rd | 168 ++--- man/non_species_columns.Rd | 42 - 18 files changed, 920 insertions(+), 903 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Posit, PBC [cph],
Intel [aut, cph] ,
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.10 dated 2025-01-23 and 5.1.11 dated 2025-08-27
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/include/RcppParallel/Common.h | 5 +++++ inst/include/RcppParallel/TBB.h | 4 +--- src/options.cpp | 4 ++++ src/tbb.cpp | 4 ++++ src/tbb/include/tbb/task.h | 8 ++++---- 8 files changed, 33 insertions(+), 18 deletions(-)
Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggridges versions 0.5.6 dated 2024-01-23 and 0.5.7 dated 2025-08-27
ggridges-0.5.6/ggridges/tests/figs |only ggridges-0.5.7/ggridges/DESCRIPTION | 13 ggridges-0.5.7/ggridges/MD5 | 108 +-- ggridges-0.5.7/ggridges/NAMESPACE | 1 ggridges-0.5.7/ggridges/NEWS.md | 10 ggridges-0.5.7/ggridges/R/geom-density-line.R | 4 ggridges-0.5.7/ggridges/R/geoms-gradient.R | 11 ggridges-0.5.7/ggridges/R/geoms.R | 24 ggridges-0.5.7/ggridges/R/geomsv.R | 10 ggridges-0.5.7/ggridges/R/position.R | 2 ggridges-0.5.7/ggridges/R/scale-cyclical.R | 15 ggridges-0.5.7/ggridges/R/scale-point.R | 32 - ggridges-0.5.7/ggridges/R/scale-vline.R | 26 ggridges-0.5.7/ggridges/R/stats.R | 15 ggridges-0.5.7/ggridges/build/vignette.rds |binary ggridges-0.5.7/ggridges/inst/doc/gallery.R | 6 ggridges-0.5.7/ggridges/inst/doc/gallery.Rmd | 6 ggridges-0.5.7/ggridges/inst/doc/gallery.html | 82 +- ggridges-0.5.7/ggridges/inst/doc/introduction.R | 10 ggridges-0.5.7/ggridges/inst/doc/introduction.Rmd | 14 ggridges-0.5.7/ggridges/inst/doc/introduction.html | 305 ++++------ ggridges-0.5.7/ggridges/man/geom_density_line.Rd | 71 +- ggridges-0.5.7/ggridges/man/geom_density_ridges.Rd | 12 ggridges-0.5.7/ggridges/man/geom_ridgeline.Rd | 8 ggridges-0.5.7/ggridges/man/geom_ridgeline_gradient.Rd | 7 ggridges-0.5.7/ggridges/man/geom_vridgeline.Rd | 8 ggridges-0.5.7/ggridges/man/position_points_jitter.Rd | 2 ggridges-0.5.7/ggridges/man/scale_cyclical.Rd | 9 ggridges-0.5.7/ggridges/man/scale_point.Rd | 2 ggridges-0.5.7/ggridges/man/scale_vline.Rd | 2 ggridges-0.5.7/ggridges/man/stat_binline.Rd | 47 + ggridges-0.5.7/ggridges/man/stat_density_ridges.Rd | 12 ggridges-0.5.7/ggridges/tests/testthat/Rplots.pdf |only ggridges-0.5.7/ggridges/tests/testthat/_snaps |only ggridges-0.5.7/ggridges/tests/testthat/test_geom_gradient.R | 4 ggridges-0.5.7/ggridges/tests/testthat/test_scale_cyclical.R | 2 ggridges-0.5.7/ggridges/tests/testthat/test_stat_density_ridges.R | 20 ggridges-0.5.7/ggridges/vignettes/gallery.Rmd | 6 ggridges-0.5.7/ggridges/vignettes/introduction.Rmd | 14 39 files changed, 518 insertions(+), 402 deletions(-)
Title: 'ggplot2' Pattern Geoms
Description: Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.
Author: Mike FC [aut],
Trevor L. Davis [aut, cre] ,
ggplot2 authors [aut]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ggpattern versions 1.1.4 dated 2025-01-28 and 1.2.1 dated 2025-08-27
DESCRIPTION | 11 ++++----- MD5 | 24 +++++++++---------- NEWS.md | 12 +++++++++ R/geom-sf.R | 2 - R/scale-pattern-auto.R | 48 +++++++++++++++++++-------------------- README.md | 6 +++- build/vignette.rds |binary inst/doc/patterns-noise.html | 8 +++--- inst/doc/patterns-stripes.R | 36 +++++++++++++++-------------- inst/doc/patterns-stripes.Rmd | 50 +++++++++++++++++++++-------------------- inst/doc/patterns-stripes.html | 50 ++++++++++++++++++++--------------------- man/scale_continuous.Rd | 28 +++++++++++++--------- vignettes/patterns-stripes.Rmd | 50 +++++++++++++++++++++-------------------- 13 files changed, 175 insertions(+), 150 deletions(-)
Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods,
statistical summaries and graphics functions for the analysing tidy time
series data. The package name 'feasts' is an acronym comprising of its key
features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Di Cook [ctb],
Thiyanga Talagala [ctb] ,
Leanne Chhay [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between feasts versions 0.4.1 dated 2024-09-25 and 0.4.2 dated 2025-08-27
feasts-0.4.1/feasts/R/gg_geom.R |only feasts-0.4.1/feasts/tests/testthat/Rplots.pdf |only feasts-0.4.2/feasts/DESCRIPTION | 8 +- feasts-0.4.2/feasts/MD5 | 42 ++++++------- feasts-0.4.2/feasts/NAMESPACE | 9 ++ feasts-0.4.2/feasts/NEWS.md | 18 +++++ feasts-0.4.2/feasts/R/acf.R | 15 ++++ feasts-0.4.2/feasts/R/features.R | 1 feasts-0.4.2/feasts/R/graphics.R | 80 +++++++++++++++++++++++++- feasts-0.4.2/feasts/R/guerrero.R | 2 feasts-0.4.2/feasts/R/utils.R | 5 + feasts-0.4.2/feasts/R/x13arimaseats.R | 4 - feasts-0.4.2/feasts/build/vignette.rds |binary feasts-0.4.2/feasts/inst/doc/feasts.html | 69 +++++++++++++--------- feasts-0.4.2/feasts/man/X_13ARIMA_SEATS.Rd | 4 - feasts-0.4.2/feasts/man/autoplot.tbl_cf.Rd | 7 ++ feasts-0.4.2/feasts/man/gg_arma.Rd | 8 +- feasts-0.4.2/feasts/man/gg_irf.Rd | 4 + feasts-0.4.2/feasts/man/gg_lag.Rd | 5 + feasts-0.4.2/feasts/man/gg_season.Rd | 5 + feasts-0.4.2/feasts/man/gg_subseries.Rd | 8 +- feasts-0.4.2/feasts/man/gg_tsdisplay.Rd | 5 + feasts-0.4.2/feasts/man/gg_tsresiduals.Rd | 12 +++ 23 files changed, 240 insertions(+), 71 deletions(-)