Title: A Numerical Implementation of Interval-Valued Kriging
Description: An interval-valued extension of ordinary and simple kriging.
Optimization of the function is based on a generalized interval distance.
This creates a non-differentiable cost function that requires a
differentiable approximation to the absolute value function. This
differentiable approximation is optimized using a Newton-Raphson algorithm
with a penalty function to impose the constraints. Analyses in the package
are driven by the 'intsp' and 'intgrd'
classes,
which are interval-valued extensions of
'SpatialPointsDataFrame' and 'SpatialPixelsDataFrame' respectively.
The package includes several wrappers to functions in the
'gstat' and 'sp' packages.
Author: Brennan Bean [aut, cre]
Maintainer: Brennan Bean <brennan.bean@usu.edu>
Diff between intkrige versions 1.0.1 dated 2020-02-07 and 1.0.2 dated 2025-09-20
DESCRIPTION | 12 MD5 | 104 ++-- NAMESPACE | 3 R/generics.R | 6 R/intKrigeDriver.R | 143 ++---- R/intgrd-class.R | 25 - R/intsp-class.R | 24 - R/supportFunctions.R | 68 +-- README.md | 86 +-- build/partial.rdb |binary build/vignette.rds |binary data/ohMap.rda |binary inst/REFERENCES.bib | 25 - inst/doc/intkriging-workflow.R | 91 ++-- inst/doc/intkriging-workflow.Rmd | 21 inst/doc/intkriging-workflow.html | 763 +++++++++++++++++++++++----------- man/dist_cpp.Rd | 78 +-- man/extract-methods.Rd | 100 ++-- man/figures/README-varioCheck2-1.png |binary man/fit.intvariogram.Rd | 48 +- man/head.intgrd.Rd | 54 +- man/head.intsp.Rd | 56 +- man/interval-methods-assign.Rd | 60 +- man/interval-methods.Rd | 46 +- man/interval.as.data.frame-methods.Rd | 42 - man/intgrd-class.Rd | 32 - man/intkrige-package.Rd | 118 ++--- man/intkrige.Rd | 310 ++++++------- man/intsp-class.Rd | 32 - man/intvCheck.Rd | 44 - man/intvariogram-methods.Rd | 58 +- man/ohMap.Rd | 32 - man/ohtemp.Rd | 68 +-- man/plot-intgrd-missing-method.Rd | 62 +- man/plot-intsp-missing-method.Rd | 86 +-- man/print.intgrd.Rd | 50 +- man/print.intsp.Rd | 52 +- man/print.summary.intgrd.Rd | 42 - man/print.summary.intsp.Rd | 42 - man/show-intgrd-method.Rd | 26 - man/show-intsp-method.Rd | 26 - man/summary.intgrd.Rd | 46 +- man/summary.intsp.Rd | 46 +- man/tail.intgrd.Rd | 54 +- man/tail.intsp.Rd | 54 +- man/utsnow.Rd | 80 +-- man/utsnow_dtl.Rd | 84 +-- man/utsnow_dtl2.Rd | 92 ++-- src/Makevars | 6 src/Makevars.win | 6 src/RcppExports.cpp | 5 tests/testthat/test_intkrige.R | 22 vignettes/intkriging-workflow.Rmd | 21 53 files changed, 1865 insertions(+), 1586 deletions(-)
Title: A Future API for Parallel and Distributed Processing using
'batchtools'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'batchtools' package.
This allows you to process futures, as defined by the 'future' package,
in parallel out of the box, not only on your local machine or ad-hoc
cluster of machines, but also via high-performance compute ('HPC') job
schedulers such as 'LSF', 'OpenLava', 'Slurm', 'SGE', and 'TORQUE' / 'PBS',
e.g. 'y <- future.apply::future_lapply(files, FUN = process)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.batchtools versions 0.20.0 dated 2025-08-25 and 0.21.0 dated 2025-09-20
DESCRIPTION | 10 +- MD5 | 59 ++++++------- NAMESPACE | 7 + NEWS.md | 50 +++++++++++ R/BatchtoolsFutureBackend-class.R | 117 +++++++++++++++++++++----- R/BatchtoolsTemplateFutureBackend-class.R | 2 R/batchtools_bash.R | 20 +++- R/batchtools_lsf.R | 9 +- R/batchtools_openlava.R | 9 +- R/batchtools_sge.R | 9 +- R/batchtools_slurm.R | 61 +++++++++++-- R/batchtools_torque.R | 8 + R/makeClusterFutureSlurm2.R |only R/runOSCommand.R |only inst/WORDLIST | 9 ++ inst/templates/bash.tmpl | 57 ++++++++++-- inst/templates/lsf.tmpl | 51 +++++++++-- inst/templates/openlava.tmpl | 51 +++++++++-- inst/templates/sge.tmpl | 55 +++++++++--- inst/templates/slurm.tmpl | 53 +++++++++-- inst/templates/torque.tmpl | 51 +++++++++-- man/BatchtoolsFutureBackend.Rd | 18 ++-- man/BatchtoolsTemplateFutureBackend.Rd | 18 ++-- man/batchtools_bash.Rd | 77 +++++++++++++---- man/batchtools_lsf.Rd | 80 +++++++++++++---- man/batchtools_multicore.Rd | 2 man/batchtools_openlava.Rd | 80 +++++++++++++---- man/batchtools_sge.Rd | 84 +++++++++++++----- man/batchtools_slurm.Rd | 134 +++++++++++++++++++++++------- man/batchtools_torque.Rd | 79 +++++++++++++---- man/future.batchtools.Rd | 2 man/makeClusterFunctionsSlurm2.Rd |only 32 files changed, 969 insertions(+), 293 deletions(-)
More information about future.batchtools at CRAN
Permanent link
Title: Outlier Detection and Influence Diagnostics for Meta-Analysis
Description: Computational tools for outlier detection and influence diagnostics in meta-analysis (Noma et al. (2025) <doi:10.1101/2025.09.18.25336125>). Bootstrap distributions of influence statistics are computed, and explicit thresholds for identifying outliers are provided. These methods can also be applied to the analysis of influential centers or regions in multicenter or multiregional clinical trials (Aoki and Noma (2021) <doi:10.1080/24709360.2021.1921944>, Nakamura and Noma (2021) <doi:10.5691/jjb.41.117>).
Author: Hisashi Noma [aut, cre],
Kazushi Maruo [aut],
Masahiko Gosho [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between boutliers versions 1.1-2 dated 2023-05-22 and 2.1-1 dated 2025-09-20
boutliers-1.1-2/boutliers/R/LRT_FE.r |only boutliers-1.1-2/boutliers/R/STR_FE.r |only boutliers-1.1-2/boutliers/man/LRT_FE.Rd |only boutliers-1.1-2/boutliers/man/STR_FE.Rd |only boutliers-2.1-1/boutliers/DESCRIPTION | 13 - boutliers-2.1-1/boutliers/MD5 | 28 +-- boutliers-2.1-1/boutliers/NAMESPACE | 2 boutliers-2.1-1/boutliers/NEWS.md | 4 boutliers-2.1-1/boutliers/R/LRT.r | 164 ++++++++++++++++----- boutliers-2.1-1/boutliers/R/STR.r | 60 ++++--- boutliers-2.1-1/boutliers/R/VRATIO.r | 61 +++---- boutliers-2.1-1/boutliers/build/partial.rdb |binary boutliers-2.1-1/boutliers/man/LRT.Rd | 18 +- boutliers-2.1-1/boutliers/man/STR.Rd | 20 ++ boutliers-2.1-1/boutliers/man/VRATIO.Rd | 13 + boutliers-2.1-1/boutliers/man/boutliers-package.Rd | 19 ++ boutliers-2.1-1/boutliers/man/finasteride.Rd | 6 17 files changed, 286 insertions(+), 122 deletions(-)
Title: Download and Analyze Crash Data
Description: Download crash data from the National Highway Traffic Safety Administration and prepare it for research.
Author: Steve Jackson [aut, cre]
Maintainer: Steve Jackson <steve.jackson@toxcel.com>
This is a re-admission after prior archival of version 1.2.0 dated 2024-04-06
Diff between rfars versions 1.2.0 dated 2024-04-06 and 2.0.0 dated 2025-09-20
rfars-1.2.0/rfars/R/read_basic_sas_nocat.R |only rfars-1.2.0/rfars/man/auto_label_unlabeled_values.Rd |only rfars-1.2.0/rfars/man/read_basic_sas_nocat.Rd |only rfars-2.0.0/rfars/DESCRIPTION | 20 rfars-2.0.0/rfars/MD5 | 92 rfars-2.0.0/rfars/NAMESPACE | 6 rfars-2.0.0/rfars/NEWS.md | 14 rfars-2.0.0/rfars/R/compare_counts.R | 33 rfars-2.0.0/rfars/R/counts.R | 229 rfars-2.0.0/rfars/R/data.R | 156 rfars-2.0.0/rfars/R/download_fars.R | 25 rfars-2.0.0/rfars/R/download_gescrss.R | 10 rfars-2.0.0/rfars/R/find_cases.R | 193 rfars-2.0.0/rfars/R/get_fars.R | 272 rfars-2.0.0/rfars/R/get_gescrss.R | 141 rfars-2.0.0/rfars/R/helpers.R | 139 rfars-2.0.0/rfars/R/prep_fars.R | 111 rfars-2.0.0/rfars/R/prep_gescrss.R | 62 rfars-2.0.0/rfars/R/read_basic_sas.R | 195 rfars-2.0.0/rfars/R/use_fars.R | 29 rfars-2.0.0/rfars/R/use_gescrss.R | 20 rfars-2.0.0/rfars/README.md | 868 rfars-2.0.0/rfars/build/vignette.rds |binary rfars-2.0.0/rfars/data/annual_counts.rda |only rfars-2.0.0/rfars/data/fars_codebook.rda |binary rfars-2.0.0/rfars/data/gescrss_codebook.rda |binary rfars-2.0.0/rfars/inst/doc/Alcohol_Counts.R |only rfars-2.0.0/rfars/inst/doc/Alcohol_Counts.Rmd |only rfars-2.0.0/rfars/inst/doc/Alcohol_Counts.html |only rfars-2.0.0/rfars/inst/doc/Counts.R | 129 rfars-2.0.0/rfars/inst/doc/Counts.Rmd | 168 rfars-2.0.0/rfars/inst/doc/Counts.html | 1420 rfars-2.0.0/rfars/inst/doc/Crash_sequence_of_events.R | 17 rfars-2.0.0/rfars/inst/doc/Crash_sequence_of_events.Rmd | 20 rfars-2.0.0/rfars/inst/doc/Crash_sequence_of_events.html | 171 rfars-2.0.0/rfars/inst/doc/Searchable_Codebooks.R | 38 rfars-2.0.0/rfars/inst/doc/Searchable_Codebooks.Rmd | 60 rfars-2.0.0/rfars/inst/doc/Searchable_Codebooks.html |29977 +-------------- rfars-2.0.0/rfars/man/annual_counts.Rd |only rfars-2.0.0/rfars/man/counts.Rd | 15 rfars-2.0.0/rfars/man/download_fars.Rd | 2 rfars-2.0.0/rfars/man/fars_codebook.Rd | 36 rfars-2.0.0/rfars/man/gescrss_codebook.Rd | 37 rfars-2.0.0/rfars/man/get_fars.Rd | 36 rfars-2.0.0/rfars/man/get_gescrss.Rd | 34 rfars-2.0.0/rfars/man/get_sas_attrs.Rd |only rfars-2.0.0/rfars/man/parse_sas_format.Rd |only rfars-2.0.0/rfars/man/read_basic_sas.Rd | 9 rfars-2.0.0/rfars/vignettes/Alcohol_Counts.Rmd |only rfars-2.0.0/rfars/vignettes/Counts.Rmd | 168 rfars-2.0.0/rfars/vignettes/Crash_sequence_of_events.Rmd | 20 rfars-2.0.0/rfars/vignettes/Searchable_Codebooks.Rmd | 60 rfars-2.0.0/rfars/vignettes/images |only 53 files changed, 5958 insertions(+), 29074 deletions(-)
Title: Partial Least Squares Regression for Beta Regression Models
Description: Provides Partial least squares Regression for (weighted) beta regression models (Bertrand 2013, <https://ojs-test.apps.ocp.math.cnrs.fr/index.php/J-SFdS/article/view/215>) and k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsRbeta versions 0.3.1 dated 2025-08-18 and 0.3.2 dated 2025-09-20
DESCRIPTION | 19 +++--- MD5 | 107 ++++++++++++++++++++----------------- R/PLS_beta.R | 2 R/PLS_beta_formula.R | 2 R/PLS_beta_kfoldcv.R | 2 R/PLS_beta_kfoldcv_formula.R | 2 R/PLS_beta_wvc.R | 2 R/bootplsbeta.R | 2 R/coefs.plsRbeta.R | 2 R/coefs.plsRbeta.raw.R | 2 R/coefs.plsRbetanp.R | 2 R/kfolds2CVinfos_beta.R | 2 R/kfolds2Chisq.R | 2 R/kfolds2Chisqind.R | 2 R/permcoefs.plsRbeta.R | 2 R/permcoefs.plsRbeta.raw.R | 2 R/permcoefs.plsRbetanp.R | 2 R/plsRbeta.R | 2 R/print.plsRbetamodel.R | 2 R/print.summary.plsRbetamodel.R | 2 R/simul_data_UniYX_beta.R | 2 R/summary.plsRbetamodel.R | 2 R/tilt.bootplsbeta.R | 2 README.md | 90 ++++++++++++++++++++----------- inst/CITATION | 6 +- inst/_pkgdown.yml |only inst/doc/tn_Insights.Rmd | 4 - inst/doc/tn_Insights.html | 10 +-- man/PLS_beta.Rd | 2 man/PLS_beta_formula.Rd | 2 man/PLS_beta_kfoldcv.Rd | 2 man/PLS_beta_kfoldcv_formula.Rd | 2 man/PLS_beta_wvc.Rd | 2 man/bootplsbeta.Rd | 2 man/coefs.plsRbeta.Rd | 2 man/coefs.plsRbeta.raw.Rd | 2 man/coefs.plsRbetanp.Rd | 2 man/kfolds2CVinfos_beta.Rd | 2 man/kfolds2Chisq.Rd | 2 man/kfolds2Chisqind.Rd | 2 man/permcoefs.plsRbeta.Rd | 2 man/permcoefs.plsRbeta.raw.Rd | 2 man/permcoefs.plsRbetanp.Rd | 2 man/plsRbeta-package.Rd | 4 - man/plsRbeta.Rd | 2 man/print.plsRbetamodel.Rd | 2 man/print.summary.plsRbetamodel.Rd | 2 man/simul_data_UniYX_beta.Rd | 2 man/summary.plsRbetamodel.Rd | 2 man/tilt.bootplsbeta.Rd | 2 tests |only vignettes/tn_Insights.Rmd | 4 - 52 files changed, 184 insertions(+), 144 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.5.1 dated 2025-07-15 and 2.6.0 dated 2025-09-20
DESCRIPTION | 6 - MD5 | 23 +++---- NAMESPACE | 6 + NEWS.md | 6 + R/data_generation.R | 76 ++++++++++++++++++++++--- inst/doc/comparing_results.html | 2 inst/doc/intro_vignette.html | 4 - inst/doc/manual_execution.html | 4 - inst/doc/non_hs_analysis.html | 4 - inst/doc/obtain_data.html | 4 - inst/doc/visualization_vignette.html | 4 - man/safe_get_content.Rd |only tests/testthat/test-data_generation.R | 103 +++++++++++++++++++++++++++++++--- 13 files changed, 201 insertions(+), 41 deletions(-)
Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
Description: A generalised data structure for fast and efficient loading and data munching of sparse omics data. The 'OmicFlow' requires an up-front validated metadata template from the user,
which serves as a guide to connect all the pieces together by aligning them into a single object that is defined as an 'omics' class.
Once this unified structure is established, users can perform manual subsetting, visualisation, and statistical analysis, or leverage the automated 'autoFlow' method to generate a comprehensive report.
Author: Alem Gusinac [aut, cre] ,
Thomas Ederveen [aut] ,
Annemarie Boleij [aut, fnd]
Maintainer: Alem Gusinac <alem.gusinac@gmail.com>
Diff between OmicFlow versions 1.3.1 dated 2025-09-04 and 1.3.2 dated 2025-09-20
DESCRIPTION | 10 LICENSE | 4 MD5 | 92 NAMESPACE | 126 R/colormap.R | 98 R/composition_plot.R | 310 - R/diversity.R | 184 - R/diversity_plot.R | 286 - R/foldchange.R | 378 +- R/hill_taxa.R | 164 - R/metagenomics-class.R | 914 ++--- R/omics-class.R | 3115 +++++++++---------- R/ordination_plot.R | 224 - R/pairwise_adonis.R | 194 - R/pairwise_anosim.R | 158 R/plot_pairwise_stats.R | 220 - R/proteomics-class.R | 270 - R/utils.R | 262 - R/volcano_plot.R | 334 +- exec/autoFlow.R | 182 - inst/extdata/counts.tsv | 486 +- inst/extdata/features.tsv | 486 +- inst/extdata/metadata.tsv | 10 inst/report.Rmd | 474 +- inst/styles.css | 74 man/composition_plot.Rd | 176 - man/diversity_plot.Rd | 164 - man/metagenomics.Rd | 572 +-- man/omics.Rd | 1714 +++++----- man/ordination_plot.Rd | 122 man/pairwise_adonis.Rd | 110 man/pairwise_anosim.Rd | 104 man/proteomics.Rd | 446 +- man/volcano_plot.Rd | 166 - tests/testthat.R | 28 tests/testthat/input/metagenomics/rooted_tree.newick | 2 tests/testthat/test-alpha_diversity.R | 76 tests/testthat/test-autoflow.R | 32 tests/testthat/test-composition.R | 32 tests/testthat/test-dfe.R | 36 tests/testthat/test-hill.R | 28 tests/testthat/test-metagenomics.R | 32 tests/testthat/test-ordination.R | 38 tests/testthat/test-subsetting.R | 34 tests/testthat/test-transformations.R | 34 tests/testthat/test-utils.R | 62 tests/testthat/test-write_biom.R | 42 47 files changed, 6551 insertions(+), 6554 deletions(-)
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format or
'KEGG' KGML format into 'igraph' objects. Includes tools to find all
cycles in the resulting graphs and determine which ones involve
negative feedback (inhibition).
Author: Kevin R. Coombes [aut, cre],
Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between WayFindR versions 0.3.1 dated 2025-04-09 and 0.4.1 dated 2025-09-20
DESCRIPTION | 8 MD5 | 34 +- NAMESPACE | 5 R/06-cycles.R | 74 ++++++ R/sysdata.rda |binary build/vignette.rds |binary data/edgeColors.rda |binary data/edgeTypes.rda |binary data/nodeColors.rda |binary data/nodeShapes.rda |binary inst/doc/WayFindR_getStarted.R | 2 inst/doc/WayFindR_getStarted.Rmd | 2 inst/doc/WayFindR_getStarted.html | 439 ++++++++++++++------------------------ inst/doc/WayFindR_metrics.html | 354 +++++++++++++----------------- inst/doc/WayFindR_plots.html | 280 ++++++++++-------------- man/04-cycles.Rd | 17 + tests/06-testCycle.R | 2 vignettes/WayFindR_getStarted.Rmd | 2 18 files changed, 571 insertions(+), 648 deletions(-)
Title: Robust Singular Value Decomposition using Density Power
Divergence
Description: Computing singular value decomposition with robustness is a challenging task.
This package provides an implementation of computing robust SVD using density power
divergence (<doi:10.48550/arXiv.2109.10680>). It combines the idea of robustness and efficiency in estimation
based on a tuning parameter. It also provides utility functions to simulate various
scenarios to compare performances of different algorithms.
Author: Subhrajyoty Roy [aut, cre]
Maintainer: Subhrajyoty Roy <subhrajyotyroy@gmail.com>
Diff between rsvddpd versions 1.0.0 dated 2021-10-27 and 1.0.1 dated 2025-09-20
DESCRIPTION | 18 LICENSE | 4 MD5 | 33 - NAMESPACE | 7 NEWS.md | 18 R/RcppExports.R | 14 R/rSVDdpd.R | 346 +++++++----- R/simulation.R | 500 +++++++++--------- README.md | 286 +++++----- build/vignette.rds |binary inst/doc/rSVDdpd-intro.R | 150 ++--- inst/doc/rSVDdpd-intro.Rmd | 378 +++++++------- inst/doc/rSVDdpd-intro.html | 1182 +++++++++++++++++++++++++++----------------- man/rSVDdpd.Rd | 8 man/rank.rSVDdpd.Rd |only src/Makevars | 1 src/Makevars.win | 1 vignettes/rSVDdpd-intro.Rmd | 378 +++++++------- 18 files changed, 1859 insertions(+), 1465 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.8.0 dated 2025-05-18 and 0.9.0 dated 2025-09-20
svrep-0.8.0/svrep/man/rescale_reps.Rd |only svrep-0.9.0/svrep/DESCRIPTION | 15 svrep-0.9.0/svrep/MD5 | 193 svrep-0.9.0/svrep/NAMESPACE | 162 svrep-0.9.0/svrep/NEWS.md | 19 svrep-0.9.0/svrep/R/accessor-functions.R |only svrep-0.9.0/svrep/R/add_inactive_replicates.R | 415 - svrep-0.9.0/svrep/R/as_bootstrap_design.R | 651 +- svrep-0.9.0/svrep/R/as_data_frame_with_weights.R | 263 svrep-0.9.0/svrep/R/as_jackknife_design.R | 1137 +-- svrep-0.9.0/svrep/R/bootstrap_helpers.R | 714 +- svrep-0.9.0/svrep/R/calibrate_to_estimate.R | 790 +- svrep-0.9.0/svrep/R/calibrate_to_sample.R | 925 +- svrep-0.9.0/svrep/R/fays_generalized_replication.R | 1383 ++-- svrep-0.9.0/svrep/R/generalized_bootstrap.R | 1628 ++--- svrep-0.9.0/svrep/R/libraries_data.R | 188 svrep-0.9.0/svrep/R/lou_vax_data.R | 213 svrep-0.9.0/svrep/R/make_bootstrap_weights.R | 1439 ++-- svrep-0.9.0/svrep/R/quadratic_forms.R | 3099 ++++----- svrep-0.9.0/svrep/R/quadratic_forms_of_survey_design_objects.R | 1015 +-- svrep-0.9.0/svrep/R/redistribute_weights.R | 542 - svrep-0.9.0/svrep/R/rescale_replicates.R | 637 -- svrep-0.9.0/svrep/R/shuffle_replicates.R | 170 svrep-0.9.0/svrep/R/stack_replicate_designs.R | 496 - svrep-0.9.0/svrep/R/subsample_replicates.R | 256 svrep-0.9.0/svrep/R/successive-difference-replication.R | 1100 +-- svrep-0.9.0/svrep/R/summarize_rep_weights.R | 659 +- svrep-0.9.0/svrep/R/svrep-package-options.R | 136 svrep-0.9.0/svrep/R/svrep-package.R | 72 svrep-0.9.0/svrep/R/svyby_repwts.R | 313 svrep-0.9.0/svrep/R/variance-estimators.R | 466 - svrep-0.9.0/svrep/README.md | 1036 +-- svrep-0.9.0/svrep/build/partial.rdb |binary svrep-0.9.0/svrep/build/vignette.rds |binary svrep-0.9.0/svrep/inst/CITATION | 20 svrep-0.9.0/svrep/inst/doc/bootstrap-replicates.R | 700 +- svrep-0.9.0/svrep/inst/doc/bootstrap-replicates.Rmd | 1432 ++-- svrep-0.9.0/svrep/inst/doc/bootstrap-replicates.html | 2700 ++++---- svrep-0.9.0/svrep/inst/doc/nonresponse-adjustments.R | 320 - svrep-0.9.0/svrep/inst/doc/nonresponse-adjustments.html | 1277 ++-- svrep-0.9.0/svrep/inst/doc/sample-based-calibration.R | 598 - svrep-0.9.0/svrep/inst/doc/sample-based-calibration.html | 2655 ++++---- svrep-0.9.0/svrep/inst/doc/two-phase-sampling.R | 834 +- svrep-0.9.0/svrep/inst/doc/two-phase-sampling.Rmd | 1928 +++--- svrep-0.9.0/svrep/inst/doc/two-phase-sampling.html | 3181 +++++----- svrep-0.9.0/svrep/man/add_inactive_replicates.Rd | 229 svrep-0.9.0/svrep/man/as_bootstrap_design.Rd | 369 - svrep-0.9.0/svrep/man/as_data_frame_with_weights.Rd | 131 svrep-0.9.0/svrep/man/as_fays_gen_rep_design.Rd | 422 - svrep-0.9.0/svrep/man/as_gen_boot_design.Rd | 661 +- svrep-0.9.0/svrep/man/as_random_group_jackknife_design.Rd | 463 - svrep-0.9.0/svrep/man/as_sdr_design.Rd | 347 - svrep-0.9.0/svrep/man/assign_hadamard_rows.Rd | 164 svrep-0.9.0/svrep/man/calibrate_to_estimate.Rd | 346 - svrep-0.9.0/svrep/man/calibrate_to_sample.Rd | 349 - svrep-0.9.0/svrep/man/draw_antal_tille_resample.Rd | 58 svrep-0.9.0/svrep/man/draw_doubled_half_sample.Rd | 52 svrep-0.9.0/svrep/man/estimate_boot_reps_for_target_cv.Rd | 258 svrep-0.9.0/svrep/man/estimate_boot_sim_cv.Rd | 208 svrep-0.9.0/svrep/man/get_design_quad_form.Rd | 413 - svrep-0.9.0/svrep/man/get_nearest_psd_matrix.Rd | 85 svrep-0.9.0/svrep/man/get_rep_scale_coefs.Rd |only svrep-0.9.0/svrep/man/get_rep_type.Rd |only svrep-0.9.0/svrep/man/ht_matrix_to_joint_probs.Rd | 52 svrep-0.9.0/svrep/man/is_psd_matrix.Rd | 86 svrep-0.9.0/svrep/man/libraries.Rd | 198 svrep-0.9.0/svrep/man/lou_pums_microdata.Rd | 106 svrep-0.9.0/svrep/man/lou_vax_survey.Rd | 62 svrep-0.9.0/svrep/man/lou_vax_survey_control_totals.Rd | 76 svrep-0.9.0/svrep/man/make_deville_tille_matrix.Rd | 124 svrep-0.9.0/svrep/man/make_doubled_half_bootstrap_weights.Rd | 249 svrep-0.9.0/svrep/man/make_fays_gen_rep_factors.Rd | 375 - svrep-0.9.0/svrep/man/make_gen_boot_factors.Rd | 389 - svrep-0.9.0/svrep/man/make_kernel_var_matrix.Rd | 177 svrep-0.9.0/svrep/man/make_ppswor_approx_matrix.Rd | 184 svrep-0.9.0/svrep/man/make_quad_form_matrix.Rd | 422 - svrep-0.9.0/svrep/man/make_rwyb_bootstrap_weights.Rd | 424 - svrep-0.9.0/svrep/man/make_sd_matrix.Rd | 78 svrep-0.9.0/svrep/man/make_sdr_replicate_factors.Rd | 132 svrep-0.9.0/svrep/man/make_twophase_quad_form.Rd | 619 - svrep-0.9.0/svrep/man/redistribute_weights.Rd | 136 svrep-0.9.0/svrep/man/rescale_replicates.Rd | 287 svrep-0.9.0/svrep/man/shuffle_replicates.Rd | 100 svrep-0.9.0/svrep/man/stack_replicate_designs.Rd | 140 svrep-0.9.0/svrep/man/subsample_replicates.Rd | 162 svrep-0.9.0/svrep/man/summarize_rep_weights.Rd | 195 svrep-0.9.0/svrep/man/svrep-package-options.Rd | 154 svrep-0.9.0/svrep/man/svrep-package.Rd | 52 svrep-0.9.0/svrep/man/svyby_repwts.Rd | 271 svrep-0.9.0/svrep/man/variance-estimators.Rd | 534 - svrep-0.9.0/svrep/tests/testthat/test-accessor-functions.R |only svrep-0.9.0/svrep/tests/testthat/test-add_inactive_replicates.R | 46 svrep-0.9.0/svrep/tests/testthat/test-bootstrap-helpers.R | 225 svrep-0.9.0/svrep/tests/testthat/test-doubled_half_bootstrap.R | 624 - svrep-0.9.0/svrep/tests/testthat/test-fays-generalized-replication.R | 1 svrep-0.9.0/svrep/tests/testthat/test-quadratic-forms.R | 1692 ++--- svrep-0.9.0/svrep/tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 61 svrep-0.9.0/svrep/tests/testthat/test-rwyb_bootstrap.R | 796 +- svrep-0.9.0/svrep/vignettes/bootstrap-replicates.Rmd | 1432 ++-- svrep-0.9.0/svrep/vignettes/two-phase-sampling.Rmd | 1928 +++--- 100 files changed, 26504 insertions(+), 26417 deletions(-)
Title: Extra Additive Terms for Generalized Additive Models for
Location Scale and Shape
Description: Interface for extra smooth functions including tensor products,
neural networks and decision trees.
Author: Mikis Stasinopoulos [aut, cre] ,
Robert Rigby [aut] ,
Vlasios Voudouris [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss.add versions 5.1-13 dated 2024-03-28 and 5.1-14 dated 2025-09-20
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- build/partial.rdb |binary man/centilesTwo.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: The Directed Prediction Index for Quasi-Causal Inference with
Cross-Sectional Data
Description: The Directed Prediction Index ('DPI') is
a quasi-causal inference method for cross-sectional data
designed to quantify the relative endogeneity (relative dependence)
of outcome (Y) versus predictor (X) variables in regression models.
By comparing the proportion of variance explained (R-squared)
between the Y-as-outcome model and the X-as-outcome model
while controlling for a sufficient number of possible confounders,
it suggests a plausible (admissible) direction of influence
from a more exogenous variable (X) to a more endogenous variable (Y).
Methodological details are provided at
<https://psychbruce.github.io/DPI/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between DPI versions 2025.8 dated 2025-08-19 and 2025.9 dated 2025-09-20
DPI-2025.8/DPI/man/data_random.Rd |only DPI-2025.9/DPI/DESCRIPTION | 29 +- DPI-2025.9/DPI/MD5 | 24 + DPI-2025.9/DPI/NAMESPACE | 7 DPI-2025.9/DPI/NEWS.md | 18 + DPI-2025.9/DPI/R/DPI.R | 456 +++++++++++++++++++++++++------------ DPI-2025.9/DPI/README.md | 80 +++++- DPI-2025.9/DPI/man/DPI-package.Rd | 4 DPI-2025.9/DPI/man/DPI.Rd | 92 +++---- DPI-2025.9/DPI/man/DPI_curve.Rd | 24 - DPI-2025.9/DPI/man/S3method.dpi.Rd | 6 DPI-2025.9/DPI/man/dag_network.Rd | 29 +- DPI-2025.9/DPI/man/matrix_cor.Rd |only DPI-2025.9/DPI/man/sim_data.Rd |only DPI-2025.9/DPI/man/sim_data_exp.Rd |only 15 files changed, 517 insertions(+), 252 deletions(-)
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP (Lundberg and Lee,
2017, <doi:10.48550/arXiv.1705.07874>) permutation SHAP, and additive
SHAP for model interpretability. For Kernel SHAP and permutation
SHAP, if the number of features is too large for exact calculations,
the algorithms iterate until the SHAP values are sufficiently precise
in terms of their standard errors. The package integrates smoothly
with meta-learning packages such as 'tidymodels', 'caret' or 'mlr3'.
It supports multi-output models, case weights, and parallel
computations. Visualizations can be done using the R package
'shapviz'.
Author: Michael Mayer [aut, cre] ,
David Watson [aut] ,
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.9.0 dated 2025-07-25 and 0.9.1 dated 2025-09-20
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 12 +++ R/kernelshap.R | 20 +++-- R/permshap.R | 30 +++++--- R/utils.R | 26 +++---- R/utils_kernelshap.R | 37 +++++++--- R/utils_permshap.R | 35 ++++++---- tests/testthat/test-basic.R | 154 ++++++++++++++++++++++++++++++-------------- 9 files changed, 222 insertions(+), 114 deletions(-)
Title: Interface for the 'QuickJS-NG' Lightweight 'JavaScript' Engine
Description: An 'R' interface to the 'QuickJS' portable 'JavaScript'
engine. The engine and all 'R' to 'JavaScript' interoperability is bundled
within the package, requiring no dependencies beyond a 'C' compiler.
Author: Andrew R. Johnson [aut, cre] ,
QuickJS Authors [cph] ,
QuickJS-NG Authors [cph]
Maintainer: Andrew R. Johnson <andrew.johnson@arjohnsonau.com>
Diff between QuickJSR versions 1.8.0 dated 2025-06-09 and 1.8.1 dated 2025-09-20
DESCRIPTION | 8 LICENSE | 4 MD5 | 100 NAMESPACE | 16 NEWS.md | 175 - R/JSContext.R | 336 +- R/qjs.R | 158 - R/quickjsr-package.R | 20 R/utils.R | 6 R/zzz.R | 8 README.md | 272 +- build/vignette.rds |binary inst/doc/working_with_js_types.R | 80 inst/doc/working_with_js_types.Rmd | 224 - inst/doc/working_with_js_types.html | 1044 ++++----- inst/include/quickjs_helpers.hpp | 3 inst/tinytest/test_JSContext.R | 94 inst/tinytest/test_data_conversion.R | 144 - inst/tinytest/test_qjs_eval.R | 16 inst/tinytest/test_to_json_asis.R | 20 inst/tinytest/test_to_json_dataframe.R | 32 inst/tinytest/test_to_json_date.R | 28 inst/tinytest/test_to_json_factor.R | 12 inst/tinytest/test_to_json_matrix.R | 22 man/JSContext-method-assign.Rd | 64 man/JSContext-method-call.Rd | 66 man/JSContext-method-get.Rd | 60 man/JSContext-method-source.Rd | 70 man/JSContext-method-validate.Rd | 58 man/JSContext.Rd | 42 man/QuickJSR-package.Rd | 58 man/from_json.Rd | 34 man/qjs_eval.Rd | 56 man/quickjs_version.Rd | 28 man/to_json.Rd | 38 src/quickjs/CMakeLists.txt | 888 +++---- src/quickjs/LICENSE | 48 src/quickjs/README.md | 48 src/quickjs/amalgam.js | 98 src/quickjs/builtin-array-fromasync.js | 72 src/quickjs/meson.build | 1042 ++++----- src/quickjs/meson_options.txt | 12 src/quickjs/repl.js | 3782 ++++++++++++++++----------------- src/quickjs/standalone.js | 258 +- src/quickjs/test262-fast.conf | 264 +- src/quickjs/test262.conf | 788 +++--- src/quickjs/test262_errors.txt | 354 +-- src/quickjs/tests.conf | 20 src/quickjs/unicode_download.sh | 38 tests/tinytest.R | 10 vignettes/working_with_js_types.Rmd | 224 - 51 files changed, 5666 insertions(+), 5676 deletions(-)
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Author: Matthijs S. Berends [aut, cre] ,
Dennis Souverein [aut, ctb] ,
Erwin E. A. Hassing [aut, ctb],
Aislinn Cook [ctb] ,
Andrew P. Norgan [ctb] ,
Anita Williams [ctb] ,
Annick Lenglet [ctb] ,
Anthony Underwood [ctb] ,
Anton Mymrikov [ctb],
Bart C. Meijer [...truncated...]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 3.0.0 dated 2025-06-02 and 3.0.1 dated 2025-09-20
DESCRIPTION | 14 - MD5 | 132 ++++++------ NAMESPACE | 3 NEWS.md | 33 +++ R/aa_globals.R | 1 R/aa_helper_functions.R | 128 ++++-------- R/aa_helper_pm_functions.R | 14 + R/ab.R | 28 ++ R/ab_property.R | 2 R/age.R | 14 + R/amr_selectors.R | 4 R/antibiogram.R | 19 + R/av_property.R | 2 R/count.R | 18 - R/custom_mdro_guideline.R | 4 R/data.R | 12 + R/disk.R | 12 - R/eucast_rules.R | 40 +-- R/first_isolate.R | 22 +- R/ggplot_sir.R | 5 R/mdro.R | 85 +++----- R/mean_amr_distance.R | 2 R/mic.R | 20 + R/mo.R | 18 + R/mo_property.R | 2 R/pca.R | 2 R/plotting.R | 392 +++++++++++++++++++++++--------------- R/proportion.R | 20 - R/random.R | 156 ++++++++------- R/sir.R | 133 ++++++------ R/sir_calc.R | 14 - R/sir_df.R | 2 R/sysdata.rda |binary R/translate.R | 5 R/vctrs.R | 1 R/zzz.R | 4 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary data/antibiotics.rda |binary data/antimicrobials.rda |binary data/microorganisms.rda |binary inst/doc/welcome_to_AMR.Rmd | 2 inst/doc/welcome_to_AMR.html | 5 man/age_groups.Rd | 8 man/antibiogram.Rd | 1 man/antimicrobial_selectors.Rd | 2 man/antimicrobials.Rd | 6 man/as.sir.Rd | 9 man/custom_eucast_rules.Rd | 2 man/custom_mdro_guideline.Rd | 2 man/first_isolate.Rd | 24 +- man/ggplot_sir.Rd | 8 man/mdro.Rd | 2 man/mean_amr_distance.Rd | 2 man/microorganisms.Rd | 4 man/plot.Rd | 100 ++++----- man/random.Rd | 28 ++ tests/testthat/test-_misc.R | 12 - tests/testthat/test-ab.R | 8 tests/testthat/test-disk.R | 8 tests/testthat/test-mic.R | 8 tests/testthat/test-mo.R | 8 tests/testthat/test-mo_property.R | 2 tests/testthat/test-sir.R | 19 - tests/testthat/test-zzz.R | 20 + vignettes/welcome_to_AMR.Rmd | 2 67 files changed, 962 insertions(+), 699 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.5-0 dated 2025-07-20 and 3.6-0 dated 2025-09-20
DESCRIPTION | 12 +++--- MD5 | 66 ++++++++++++++++++------------------ NAMESPACE | 25 +++++++++++++ NEWS | 64 ++++++++++++++++++++++++++++++++++ R/NAobjects.R | 22 ++++++++++-- R/as.im.R | 4 +- R/clickpoly.R | 16 +++++++- R/disc.R | 50 +++++++++++++++++---------- R/hyperframe.R | 77 +++++++++++++++++++++++++++--------------- R/images.R | 40 +++++++++++++-------- R/marks.R | 6 ++- R/persp.im.R | 67 ++++++++++++++++++++++++------------ R/plot.im.R | 45 ++++++++++++++---------- R/plot.owin.R | 60 +++++++++++++++++++------------- R/plot.ppp.R | 37 ++++++++++++-------- R/plot.psp.R | 74 ++++++++++++++++++++++++++++++++-------- R/pp3.R | 6 ++- R/ppp.R | 5 ++ R/ppx.R | 7 ++- R/quadclass.R | 2 + R/solist.R | 34 ++++++++++++++++-- R/window.R | 7 +++ inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/clickpoly.Rd | 16 ++++++++ man/disc.Rd | 23 ++++++++++++ man/macros/defns.Rd | 2 - man/padimage.Rd | 13 ++----- man/persp.im.Rd | 7 +++ man/plot.owin.Rd | 20 ++++++++++ man/plot.ppp.Rd | 6 ++- man/plot.psp.Rd | 21 ++++++++++- man/spatstat.geom-internal.Rd | 28 ++++++++++++++- tests/testsGtoJ.R | 18 +++++++++ 34 files changed, 659 insertions(+), 223 deletions(-)
Title: Robust Econometric Inference
Description: Drawing statistical inference on the coefficients
of a short- or long-horizon predictive regression with persistent
regressors by using the IVX method of Magdalinos and Phillips (2009)
<doi:10.1017/S0266466608090154> and Kostakis, Magdalinos and
Stamatogiannis (2015) <doi:10.1093/rfs/hhu139>.
Author: Kostas Vasilopoulos [cre, aut],
Efthymios Pavlidis [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between ivx versions 1.1.0 dated 2020-11-24 and 1.1.1 dated 2025-09-20
ivx-1.1.0/ivx/R/ivx_ar.R |only ivx-1.1.0/ivx/R/step-methods.R |only ivx-1.1.0/ivx/build |only ivx-1.1.1/ivx/DESCRIPTION | 8 - ivx-1.1.1/ivx/MD5 | 51 ++++---- ivx-1.1.1/ivx/NAMESPACE | 4 ivx-1.1.1/ivx/NEWS.md | 34 +++-- ivx-1.1.1/ivx/R/ac_test.R | 39 ++++-- ivx-1.1.1/ivx/R/data.R | 60 +++++----- ivx-1.1.1/ivx/R/extract-texreg-methods.R | 22 ++- ivx-1.1.1/ivx/R/ivx-ar.R |only ivx-1.1.1/ivx/R/ivx-package.R | 10 - ivx-1.1.1/ivx/R/ivx.R | 165 ++++++++++++++--------------- ivx-1.1.1/ivx/R/methods-step.R |only ivx-1.1.1/ivx/R/methods.R | 111 ++++++++++++++----- ivx-1.1.1/ivx/README.md | 18 +-- ivx-1.1.1/ivx/inst/CITATION | 35 +++--- ivx-1.1.1/ivx/inst/WORDLIST | 1 ivx-1.1.1/ivx/man/ac_test_.Rd | 4 ivx-1.1.1/ivx/man/ivx-package.Rd | 5 ivx-1.1.1/ivx/man/ivx_ar.Rd | 5 ivx-1.1.1/ivx/man/ivx_ar_fit.Rd | 2 ivx-1.1.1/ivx/man/summary.ivx_ar.Rd | 2 ivx-1.1.1/ivx/man/ylpc.Rd | 5 ivx-1.1.1/ivx/src/Makevars | 12 -- ivx-1.1.1/ivx/src/Makevars.win | 12 -- ivx-1.1.1/ivx/src/RcppExports.cpp | 5 ivx-1.1.1/ivx/src/ivx_fit_cpp.cpp | 49 +++++++- ivx-1.1.1/ivx/tests/testthat/test-ivx-ar.R | 11 + 29 files changed, 393 insertions(+), 277 deletions(-)
Title: Stream Suitable Online Support Vector Machines
Description: Soft-margin support vector machines (SVMs) are a common class of classification models. The training of SVMs usually requires that the data be available all at once in a single batch, however the Stochastic majorization-minimization (SMM) algorithm framework allows for the training of SVMs on streamed data instead Nguyen, Jones & McLachlan(2018)<doi:10.1007/s42081-018-0001-y>. This package utilizes the SMM framework to provide functions for training SVMs with hinge loss, squared-hinge loss, and logistic loss.
Author: Andrew Thomas Jones [aut, cre],
Hien Duy Nguyen [aut],
Geoffrey J. McLachlan [aut]
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between SSOSVM versions 0.2.1 dated 2019-05-06 and 0.2.2 dated 2025-09-20
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 5 ++++- R/RcppExports.R | 2 +- R/Utility_functions.R | 2 +- README.md | 12 ++++++++---- src/Makevars | 8 ++------ src/Makevars.win | 4 ---- src/RcppExports.cpp | 5 +++++ src/main.cpp | 2 +- 10 files changed, 50 insertions(+), 34 deletions(-)
Title: Clustering via Stochastic Approximation and Gaussian Mixture
Models
Description: Computes clustering by fitting Gaussian mixture models (GMM) via stochastic approximation following the methods of Nguyen and Jones (2018) <doi:10.1201/9780429446177>. It also provides some test data generation and plotting functionality to assist with this process.
Author: Andrew Thomas Jones [aut, cre],
Hien Duy Nguyen [aut]
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between SAGMM versions 0.2.4 dated 2019-06-29 and 0.2.5 dated 2025-09-20
SAGMM-0.2.4/SAGMM/tests/testthat/Rplots.pdf |only SAGMM-0.2.5/SAGMM/DESCRIPTION | 22 +++++++++++++++------- SAGMM-0.2.5/SAGMM/MD5 | 23 +++++++++++------------ SAGMM-0.2.5/SAGMM/NAMESPACE | 2 +- SAGMM-0.2.5/SAGMM/NEWS.md | 4 ++++ SAGMM-0.2.5/SAGMM/R/RcppExports.R | 8 ++++---- SAGMM-0.2.5/SAGMM/R/main.R | 6 +++--- SAGMM-0.2.5/SAGMM/man/SAGMM.Rd | 2 +- SAGMM-0.2.5/SAGMM/man/SAGMMFit.Rd | 3 +-- SAGMM-0.2.5/SAGMM/src/Makevars | 8 ++------ SAGMM-0.2.5/SAGMM/src/Makevars.win | 4 ---- SAGMM-0.2.5/SAGMM/src/RcppExports.cpp | 5 +++++ SAGMM-0.2.5/SAGMM/src/SAGMM.cpp | 2 +- 13 files changed, 48 insertions(+), 41 deletions(-)
Title: Low Memory Use Trimmed K-Means
Description: Performs the trimmed k-means clustering algorithm with lower memory use. It also provides a number of utility functions such as BIC calculations.
Author: Andrew Thomas Jones [aut, cre],
Hien Duy Nguyen [aut]
Maintainer: Andrew Thomas Jones <andrewthomasjones@gmail.com>
Diff between lowmemtkmeans versions 0.1.2 dated 2017-01-08 and 0.1.4 dated 2025-09-20
lowmemtkmeans-0.1.2/lowmemtkmeans/R/wrapper.R |only lowmemtkmeans-0.1.4/lowmemtkmeans/DESCRIPTION | 23 ++-- lowmemtkmeans-0.1.4/lowmemtkmeans/MD5 | 29 ++--- lowmemtkmeans-0.1.4/lowmemtkmeans/NAMESPACE | 2 lowmemtkmeans-0.1.4/lowmemtkmeans/NEWS.md | 5 lowmemtkmeans-0.1.4/lowmemtkmeans/R/RcppExports.R | 46 ++++++-- lowmemtkmeans-0.1.4/lowmemtkmeans/README.md | 48 +++++--- lowmemtkmeans-0.1.4/lowmemtkmeans/man/cluster_BIC.Rd | 1 lowmemtkmeans-0.1.4/lowmemtkmeans/man/nearest_cluster.Rd | 3 lowmemtkmeans-0.1.4/lowmemtkmeans/man/scale_mat_inplace.Rd | 5 lowmemtkmeans-0.1.4/lowmemtkmeans/man/tkmeans.Rd | 15 +- lowmemtkmeans-0.1.4/lowmemtkmeans/src/Makevars | 4 lowmemtkmeans-0.1.4/lowmemtkmeans/src/Makevars.win | 4 lowmemtkmeans-0.1.4/lowmemtkmeans/src/RcppExports.cpp | 26 +++- lowmemtkmeans-0.1.4/lowmemtkmeans/src/tkmeans.cpp | 63 ++++++++--- lowmemtkmeans-0.1.4/lowmemtkmeans/tests/testthat/test_iris.R | 2 16 files changed, 198 insertions(+), 78 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.39 dated 2025-07-18 and 3.40 dated 2025-09-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 17 ++++++++++++++++- R/Boyce.R | 8 +++++--- R/evaluate.R | 11 +++++++++-- R/varImp.R | 46 +++++++++++++++++++++++++++++----------------- man/modEvA-package.Rd | 4 ++-- 7 files changed, 71 insertions(+), 35 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' family of packages
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 3.1-5 dated 2025-07-17 and 3.2-0 dated 2025-09-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS | 18 ++++++++++++++++++ R/locator.R | 17 +++++++++++++++-- R/utilseq.R | 2 +- inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/macros/defns.Rd | 2 +- man/revcumsum.Rd | 5 +++-- man/spatstat.utils-internal.Rd | 2 ++ man/spatstatLocator.Rd | 16 +++++++++++++++- 12 files changed, 73 insertions(+), 22 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Convert Plot to 'grob' or 'ggplot' Object
Description: Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggplotify versions 0.1.2 dated 2023-08-09 and 0.1.3 dated 2025-09-20
DESCRIPTION | 14 ++++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 4 +++- NEWS.md | 5 +++++ R/as-ggplot.R | 6 +++--- R/as-grob.R | 6 ++++++ R/ggplotify-package.R |only build/vignette.rds |binary inst/doc/ggplotify.html | 26 ++++++++++++++++---------- man/as-grob.Rd | 3 +++ man/ggplotify-package.Rd |only 11 files changed, 54 insertions(+), 28 deletions(-)
Title: High Dimensional Bayesian Mediation Analysis
Description: Perform mediation analysis in the presence of high-dimensional
mediators based on the potential outcome framework. Bayesian Mediation
Analysis (BAMA), developed by Song et al (2019) <doi:10.1111/biom.13189> and
Song et al (2020) <doi:10.48550/arXiv.2009.11409>,
relies on two Bayesian sparse linear mixed models to simultaneously analyze
a relatively large number of mediators for a continuous exposure and outcome
assuming a small number of mediators are truly active. This sparsity
assumption also allows the extension of univariate mediator analysis by
casting the identification of active mediators as a variable selection
problem and applying Bayesian methods with continuous shrinkage priors on
the effects.
Author: Alexander Rix [aut],
Mike Kleinsasser [aut, cre],
Yanyi Song [aut]
Maintainer: Mike Kleinsasser <mkleinsa@umich.edu>
Diff between bama versions 1.3.0 dated 2023-01-24 and 1.3.1 dated 2025-09-20
DESCRIPTION | 10 ++-- MD5 | 12 ++--- R/bama.R | 10 ++-- inst/doc/bama.html | 111 ++++++++++++++++++++++++++--------------------------- man/bama.Rd | 10 ++-- src/Makevars | 1 src/Makevars.win | 1 7 files changed, 76 insertions(+), 79 deletions(-)
Title: Network Reverse Engineering with Approximate Bayesian
Computation
Description: We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as a scale-free structure and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-eng [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Khadija Musayeva [ctb],
Nicolas Jung [ctb],
Universite de Strasbourg [cph],
CNRS [cph]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between networkABC versions 0.9-0 dated 2025-08-28 and 0.9-1 dated 2025-09-19
DESCRIPTION | 16 ++++++++-------- MD5 | 42 +++++++++++++++++++++--------------------- NEWS.md | 5 +++++ README.md | 5 ++++- inst/CITATION | 4 +++- inst/doc/vignette.html | 8 ++++---- man/networkABC-package.Rd | 4 ++-- src/R_init_networkABC.c | 2 +- src/abc_R.c | 2 +- src/abc_R.h | 2 +- src/graph.c | 2 +- src/graph.h | 2 +- src/graph_adjacency_list.h | 2 +- src/motif.c | 2 +- src/motif.h | 2 +- src/network.h | 2 +- src/network_random_R.c | 2 +- src/network_random_R.h | 2 +- src/pool.c | 2 +- src/pool.h | 2 +- src/utils.c | 2 +- src/utils.h | 2 +- 22 files changed, 62 insertions(+), 52 deletions(-)
Title: Classification Models with Copula Functions
Description: Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Angelica Hernandez Quintero [aut, cph] ,
Pedro Abraham Montoya Calzada [aut, cph] ,
Carlos Alberto Lopez Hernandez [aut, cph] ,
Juan Manuel Marquez Romero [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rsalinas@correo.uaa.mx>
This is a re-admission after prior archival of version 1.0.1 dated 2024-10-23
Diff between MLCOPULA versions 1.0.1 dated 2024-10-23 and 1.1.0 dated 2025-09-19
DESCRIPTION | 28 +++---- MD5 | 42 +++++----- NAMESPACE | 22 +++-- R/aux_mi_report.R | 20 ++--- R/classification_report.R | 24 +++--- R/copulaClassifier.R | 5 + R/copulaPredict.R | 13 --- R/density_estimation.R | 24 ++++-- R/f_aux2.R | 32 ++++---- R/faux.R | 44 +++++------ R/join_marginal.R |only R/kernel_estimation.R | 18 +--- R/mi_gaussian.R | 10 +- R/mi_report.R | 20 ++--- R/norm_test.R |only R/normal_estimation.R | 7 - R/sfmx.R | 8 +- R/train_independent.R | 28 +++---- README.md | 166 +++++++++++++++++++++---------------------- build/partial.rdb |binary man/classification_report.Rd | 94 ++++++++++++------------ man/copulaClassifier.Rd | 154 +++++++++++++++++++-------------------- man/copulaPredict.Rd | 78 ++++++++++---------- 23 files changed, 420 insertions(+), 417 deletions(-)
Title: Multiple Imputation for Proteomics
Description: A framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) <doi:10.1371/journal.pcbi.1010420>. It is dedicated to dealing with multiple imputation for proteomics.
Author: Marie Chion [aut] ,
Christine Carapito [aut] ,
Frederic Bertrand [cre, aut] ,
Gordon Smyth [ctb],
Davis McCarthy [ctb],
Helene Borges [ctb],
Thomas Burger [ctb],
Quentin Giai-Gianetto [ctb],
Samuel Wieczorek [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between mi4p versions 1.2 dated 2024-10-02 and 1.3 dated 2025-09-19
DESCRIPTION | 28 ++++++++++++++++------------ MD5 | 27 +++++++++++++++++---------- NEWS.md | 6 ++++++ README.md | 37 ++++++++++--------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 +++++- inst/_pkgdown.yml |only inst/doc/Intromi4p.Rmd | 2 +- inst/doc/Intromi4p.html | 8 ++++---- man/mi4p-package.Rd | 2 +- tests |only vignettes/Intromi4p.Rmd | 2 +- 13 files changed, 61 insertions(+), 57 deletions(-)
Title: Database Queries Using 'data.table' Syntax
Description: Query database tables over a 'DBI' connection using 'data.table' syntax.
Attach database schemas to the search path. Automatically merge using foreign
key constraints.
Author: Kjell P. Konis [aut, cre],
Luis Rocha [ctb]
Maintainer: Kjell P. Konis <kjellk@gmail.com>
Diff between dbi.table versions 1.0.4 dated 2025-06-28 and 1.0.5 dated 2025-09-19
dbi.table-1.0.4/dbi.table/vignettes/introduction_to_dbi_table.md |only dbi.table-1.0.5/dbi.table/DESCRIPTION | 8 dbi.table-1.0.5/dbi.table/MD5 | 163 dbi.table-1.0.5/dbi.table/NAMESPACE | 186 dbi.table-1.0.5/dbi.table/NEWS.md | 60 dbi.table-1.0.5/dbi.table/R/DBI_methods.R | 1848 - dbi.table-1.0.5/dbi.table/R/as.data.table.R | 24 dbi.table-1.0.5/dbi.table/R/attach.R | 244 dbi.table-1.0.5/dbi.table/R/calls.R | 390 dbi.table-1.0.5/dbi.table/R/catalog.R | 354 dbi.table-1.0.5/dbi.table/R/connection.R | 118 dbi.table-1.0.5/dbi.table/R/cte.R | 158 dbi.table-1.0.5/dbi.table/R/dbi.table.R | 1612 dbi.table-1.0.5/dbi.table/R/examples.R | 162 dbi.table-1.0.5/dbi.table/R/extract.R | 710 dbi.table-1.0.5/dbi.table/R/merge.R | 848 dbi.table-1.0.5/dbi.table/R/onLoad.R | 74 dbi.table-1.0.5/dbi.table/R/reference.test.R | 176 dbi.table-1.0.5/dbi.table/R/relational.R | 266 dbi.table-1.0.5/dbi.table/R/s3_methods_duckdb.R | 144 dbi.table-1.0.5/dbi.table/R/s3_methods_mariadb.R | 102 dbi.table-1.0.5/dbi.table/R/s3_methods_postgres.R | 50 dbi.table-1.0.5/dbi.table/R/s3_methods_sql_server.R | 204 dbi.table-1.0.5/dbi.table/R/s3_methods_sqlite.R | 56 dbi.table-1.0.5/dbi.table/R/specials.R | 216 dbi.table-1.0.5/dbi.table/R/sql.join.R | 450 dbi.table-1.0.5/dbi.table/R/sql_statement.R | 10 dbi.table-1.0.5/dbi.table/R/sql_translation.R | 42 dbi.table-1.0.5/dbi.table/R/tables_schema.R | 146 dbi.table-1.0.5/dbi.table/R/utilities.R | 370 dbi.table-1.0.5/dbi.table/R/write_sql.R | 372 dbi.table-1.0.5/dbi.table/build/vignette.rds |binary dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.R | 252 dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.Rmd | 756 dbi.table-1.0.5/dbi.table/inst/doc/introduction_to_dbi_table.html | 1703 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/LICENSE | 40 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/album.csv | 696 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/artist.csv | 552 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/customer.csv | 120 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/employee.csv | 18 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/genre.csv | 52 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/invoice.csv | 826 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/invoiceline.csv | 4482 +- dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/mediatype.csv | 12 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/playlist.csv | 38 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/playlisttrack.csv |17432 +++++----- dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/schema.sql | 56 dbi.table-1.0.5/dbi.table/inst/example_files/chinook_export/track.csv | 7008 ++-- dbi.table-1.0.5/dbi.table/inst/sql_statements/foreign_keys_postgres.sql | 106 dbi.table-1.0.5/dbi.table/inst/sql_statements/foreign_keys_sqlite.sql | 4 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_Microsoft_SQL_Server.sql | 64 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_default.sql | 4 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_duckdb.sql | 44 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_mariadb.sql | 52 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_postgres.sql | 60 dbi.table-1.0.5/dbi.table/inst/sql_statements/tables_schema_sqlite.sql | 24 dbi.table-1.0.5/dbi.table/man/DBI-methods.Rd | 454 dbi.table-1.0.5/dbi.table/man/as.data.frame.Rd | 114 dbi.table-1.0.5/dbi.table/man/as.dbi.table.Rd | 102 dbi.table-1.0.5/dbi.table/man/csql.Rd | 46 dbi.table-1.0.5/dbi.table/man/dbi.attach.Rd | 94 dbi.table-1.0.5/dbi.table/man/dbi.catalog.Rd | 66 dbi.table-1.0.5/dbi.table/man/dbi.table-package.Rd | 386 dbi.table-1.0.5/dbi.table/man/example_databases.Rd | 40 dbi.table-1.0.5/dbi.table/man/merge.Rd | 240 dbi.table-1.0.5/dbi.table/man/reference.test.Rd | 120 dbi.table-1.0.5/dbi.table/man/sql.join.Rd | 92 dbi.table-1.0.5/dbi.table/tests/testthat.R | 24 dbi.table-1.0.5/dbi.table/tests/testthat/setup.R | 68 dbi.table-1.0.5/dbi.table/tests/testthat/test-DBI-methods.R | 560 dbi.table-1.0.5/dbi.table/tests/testthat/test-as.dbi.table.R | 94 dbi.table-1.0.5/dbi.table/tests/testthat/test-assumptions.R | 42 dbi.table-1.0.5/dbi.table/tests/testthat/test-attach.R | 98 dbi.table-1.0.5/dbi.table/tests/testthat/test-data.table-examples.R | 684 dbi.table-1.0.5/dbi.table/tests/testthat/test-data.table-set-functions.R | 42 dbi.table-1.0.5/dbi.table/tests/testthat/test-dbi.catalog.R | 30 dbi.table-1.0.5/dbi.table/tests/testthat/test-dbi.table.R | 352 dbi.table-1.0.5/dbi.table/tests/testthat/test-mariadb.R | 74 dbi.table-1.0.5/dbi.table/tests/testthat/test-merge.R | 478 dbi.table-1.0.5/dbi.table/tests/testthat/test-postgres.R | 34 dbi.table-1.0.5/dbi.table/tests/testthat/test-relational.R | 180 dbi.table-1.0.5/dbi.table/tests/testthat/test-sql.join.R | 128 dbi.table-1.0.5/dbi.table/vignettes/introduction_to_dbi_table.Rmd | 756 83 files changed, 24686 insertions(+), 24676 deletions(-)
Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in Greifer, et al. (2025) <doi:10.32614/RJ-2024-015>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] ,
Steven Worthington [aut] ,
Stefano Iacus [aut] ,
Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between clarify versions 0.2.1 dated 2024-05-30 and 0.2.2 dated 2025-09-19
clarify-0.2.1/clarify/inst/doc/Zelig.R |only clarify-0.2.1/clarify/inst/doc/clarify.R |only clarify-0.2.1/clarify/tests/testthat/helper.R |only clarify-0.2.2/clarify/DESCRIPTION | 35 clarify-0.2.2/clarify/MD5 | 100 clarify-0.2.2/clarify/NAMESPACE | 2 clarify-0.2.2/clarify/NEWS.md | 23 clarify-0.2.2/clarify/R/checks.R | 163 - clarify-0.2.2/clarify/R/clarify-package.R | 5 clarify-0.2.2/clarify/R/clarify_est_methods.R | 80 clarify-0.2.2/clarify/R/clarify_predict.R | 70 clarify-0.2.2/clarify/R/get_model_components.R | 38 clarify-0.2.2/clarify/R/misim.R | 88 clarify-0.2.2/clarify/R/plot.clarify_adrf.R | 75 clarify-0.2.2/clarify/R/plot.clarify_est.R | 42 clarify-0.2.2/clarify/R/plot.clarify_setx.R | 157 - clarify-0.2.2/clarify/R/sim.R | 116 clarify-0.2.2/clarify/R/sim_adrf.R | 144 - clarify-0.2.2/clarify/R/sim_ame.R | 264 + clarify-0.2.2/clarify/R/sim_apply.R | 113 clarify-0.2.2/clarify/R/sim_setx.R | 171 - clarify-0.2.2/clarify/R/summary.clarify_est.R | 144 - clarify-0.2.2/clarify/R/transform.clarify_est.R | 78 clarify-0.2.2/clarify/R/utils.R | 401 ++ clarify-0.2.2/clarify/README.md | 204 - clarify-0.2.2/clarify/build/partial.rdb |binary clarify-0.2.2/clarify/build/vignette.rds |binary clarify-0.2.2/clarify/inst/CITATION |only clarify-0.2.2/clarify/inst/doc/Zelig.Rmd | 2 clarify-0.2.2/clarify/inst/doc/Zelig.html | 49 clarify-0.2.2/clarify/inst/doc/clarify.Rmd | 397 +- clarify-0.2.2/clarify/inst/doc/clarify.html | 1380 ++++++---- clarify-0.2.2/clarify/man/clarify-package.Rd | 5 clarify-0.2.2/clarify/man/figures/README-example-1.png |binary clarify-0.2.2/clarify/man/figures/README-example2-1.png |binary clarify-0.2.2/clarify/man/figures/README-unnamed-chunk-6-1.png |binary clarify-0.2.2/clarify/man/misim.Rd | 2 clarify-0.2.2/clarify/man/plot.clarify_adrf.Rd | 8 clarify-0.2.2/clarify/man/plot.clarify_setx.Rd | 4 clarify-0.2.2/clarify/man/sim.Rd | 11 clarify-0.2.2/clarify/man/sim_adrf.Rd | 26 clarify-0.2.2/clarify/man/sim_ame.Rd | 42 clarify-0.2.2/clarify/man/sim_apply.Rd | 42 clarify-0.2.2/clarify/man/sim_setx.Rd | 38 clarify-0.2.2/clarify/man/summary.clarify_est.Rd | 31 clarify-0.2.2/clarify/man/transform.clarify_est.Rd | 6 clarify-0.2.2/clarify/tests/testthat/helpers.R |only clarify-0.2.2/clarify/tests/testthat/setup.R |only clarify-0.2.2/clarify/tests/testthat/test-misim.R | 14 clarify-0.2.2/clarify/tests/testthat/test-sim.R | 5 clarify-0.2.2/clarify/tests/testthat/test-sim_ame.R | 569 +++- clarify-0.2.2/clarify/vignettes/Zelig.Rmd | 2 clarify-0.2.2/clarify/vignettes/clarify.Rmd | 397 +- clarify-0.2.2/clarify/vignettes/references.bib | 303 ++ 54 files changed, 3701 insertions(+), 2145 deletions(-)
Title: A Cepstral Model for Covariate-Dependent Time Series
Description: Modeling associations between covariates and power spectra of replicated time series using a cepstral-based semiparametric framework. Implements a fast two-stage estimation procedure via Whittle likelihood and multivariate regression.The methodology is based on Li and Dong (2025) <doi:10.1080/10618600.2025.2473936>.
Author: Qi Xia [aut, cre],
Zeda Li [aut, ctb]
Maintainer: Qi Xia <xiaqi1010@gmail.com>
Diff between CepReg versions 0.1.0 dated 2025-09-10 and 0.1.2 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/cepstral.R | 30 ++++++++++++++++-------------- man/CepReg.Rd | 14 ++++++-------- man/boot_effect.Rd | 12 ++++++++---- man/env_get.Rd | 4 ++-- 6 files changed, 40 insertions(+), 36 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2021) <doi:10.1016/j.insmatheco.2020.11.010> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] ,
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens.r@gmail.com>
Diff between smurf versions 1.1.7 dated 2025-02-23 and 1.1.8 dated 2025-09-19
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/smurf.html | 4 ++-- src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 25 insertions(+), 17 deletions(-)
Title: Motion Trajectory Analysis
Description: Methods for analyzing (cell) motion in two or three dimensions.
Available measures include displacement, confinement ratio, autocorrelation,
straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks,
steps, or subtracks with varying length. While the methodology has been developed for
cell trajectory analysis, it is applicable to anything that moves including animals,
people, or vehicles.
Some of the methodology implemented in this packages was described by:
Beauchemin, Dixit, and Perelson (2007) <doi:10.4049/jimmunol.178.9.5505>,
Beltman, Maree, and de Boer (2009) <doi:10.1038/nri2638>,
Gneiting and Schlather (2004) <doi:10.1137/S0036144501394387>,
Mokhtari, Mech, Zitzmann, Hasenberg, Gunzer, and Figge (2013) <doi:10.1371/journal.pone.0080808>,
Moreau, Lemaitre, Terriac, Azar, Piel, Lennon-Dumenil, and Bousso (2012) <doi:10.1016/j.immuni.2012.05.014>,
Textor, Peixoto, Henrickson, Sinn, von Andrian, and Westermann (2011) [...truncated...]
Author: Johannes Textor [aut, cre],
Katharina Dannenberg [aut],
Jeffrey Berry [aut],
Gerhard Burger [aut],
Annie Liu [aut],
Mark Miller [aut],
Inge Wortel [aut]
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between celltrackR versions 1.2.1 dated 2024-08-26 and 1.2.2 dated 2025-09-19
DESCRIPTION | 8 ++-- MD5 | 26 +++++++-------- NEWS.md | 6 +++ build/vignette.rds |binary inst/doc/QC.Rmd | 2 - inst/doc/QC.html | 11 +++--- inst/doc/ana-methods.R | 2 - inst/doc/ana-methods.html | 9 +++-- inst/doc/clustering.html | 11 +++--- inst/doc/data-QC.R | 56 +++++++++++++++++----------------- inst/doc/data-QC.html | 9 +++-- inst/doc/reading-converting-data.html | 9 +++-- inst/doc/simulation.html | 9 +++-- vignettes/QC.Rmd | 2 - 14 files changed, 86 insertions(+), 74 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide [...truncated...]
Author: Jarrett D. Phillips [aut, cre],
Steven H. French [ctb],
Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.6-1 dated 2022-06-13 and 1.0.7-1 dated 2025-09-19
HACSim-1.0.6-1/HACSim/R/launchApp.R |only HACSim-1.0.6-1/HACSim/inst |only HACSim-1.0.6-1/HACSim/man/launchApp.Rd |only HACSim-1.0.7-1/HACSim/DESCRIPTION | 25 ++++++++++++++------ HACSim-1.0.7-1/HACSim/MD5 | 38 +++++++------------------------ HACSim-1.0.7-1/HACSim/NAMESPACE | 6 +++- HACSim-1.0.7-1/HACSim/R/HAC.sim.R | 3 +- HACSim-1.0.7-1/HACSim/R/sim.seqs.R | 2 - HACSim-1.0.7-1/HACSim/R/zzz.R | 2 - HACSim-1.0.7-1/HACSim/build/partial.rdb |binary HACSim-1.0.7-1/HACSim/src/Makevars | 4 --- HACSim-1.0.7-1/HACSim/src/Makevars.win | 1 HACSim-1.0.7-1/HACSim/src/accumulate.cpp | 21 +++++++++-------- 13 files changed, 48 insertions(+), 54 deletions(-)
Title: Import and Process Data from the 'Lattes' Curriculum Platform
Description: Tool for import and process data from 'Lattes' curriculum platform (<http://lattes.cnpq.br/>). The Brazilian government keeps an extensive base of curricula for academics from all over the country, with over 5 million registrations. The academic life of the Brazilian researcher, or related to Brazilian universities, is documented in 'Lattes'. Some information that can be obtained: professional formation, research area, publications, academics advisories, projects, etc. 'getLattes' package allows work with 'Lattes' data exported to XML format.
Author: Roney Fraga Souza [aut, cre, cph] ,
Winicius Sabino [aut],
Luis Felipe de Souza Rodrigues [aut]
Maintainer: Roney Fraga Souza <roneyfraga@gmail.com>
Diff between getLattes versions 0.2.0 dated 2021-06-11 and 1.0.0 dated 2025-09-19
getLattes-0.2.0/getLattes/man/figures/README-pressure-1.png |only getLattes-1.0.0/getLattes/DESCRIPTION | 38 getLattes-1.0.0/getLattes/MD5 | 28 getLattes-1.0.0/getLattes/NAMESPACE | 3 getLattes-1.0.0/getLattes/NEWS.md | 6 getLattes-1.0.0/getLattes/R/getArtigosAceitos.R |only getLattes-1.0.0/getLattes/R/getTrabalhoEmEventos.R |only getLattes-1.0.0/getLattes/R/writePublicationsRis.R |only getLattes-1.0.0/getLattes/README.md | 56 getLattes-1.0.0/getLattes/build/vignette.rds |binary getLattes-1.0.0/getLattes/inst/CITATION | 35 getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.R | 127 - getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.Rmd | 84 - getLattes-1.0.0/getLattes/inst/doc/introduction_getLattes.html | 819 ++++++---- getLattes-1.0.0/getLattes/man/figures/logo.png |only getLattes-1.0.0/getLattes/man/getArtigosAceitos.Rd |only getLattes-1.0.0/getLattes/man/getTrabalhosEmEventos.Rd |only getLattes-1.0.0/getLattes/man/writePublicationsRis.Rd |only getLattes-1.0.0/getLattes/vignettes/introduction_getLattes.Rmd | 84 - 19 files changed, 873 insertions(+), 407 deletions(-)
Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect
to see as the first table (i.e. "Table 1") in a medical/epidemiological journal
article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between table1 versions 1.5.0 dated 2025-09-12 and 1.5.1 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/table1.R | 2 +- inst/doc/table1-examples.html | 4 ++-- inst/doc/table1-latex.pdf |binary inst/doc/table1-weighted.html | 4 ++-- 7 files changed, 19 insertions(+), 15 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>
Diff between glossa versions 1.2.3 dated 2025-08-27 and 1.2.4 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/glossa_analysis.R | 5 +++-- R/read_validate_files.R | 34 ++++++++++++++++++++++++---------- man/read_layers_zip.Rd | 5 ++++- 6 files changed, 47 insertions(+), 21 deletions(-)
Title: R Wrapper for 'pikchr' (PIC) Diagram Language
Description: An 'R' interface to 'pikchr' (<https://pikchr.org>, pronounced “picture”), a 'PIC'-like markup language for creating diagrams within technical documentation. Originally developed by Brian Kernighan, 'PIC' has been adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. 'pikchr' is designed to be embedded in fenced code blocks of Markdown or other documentation markup languages, making it ideal for generating diagrams in text-based formats. This package allows R users to seamlessly integrate the descriptive syntax of 'pikchr' for diagram creation directly within the 'R' environment.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Richard Hipp [ctb],
Brian Kernighan [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pikchr versions 1.0.1 dated 2025-03-31 and 1.0.3 dated 2025-09-19
DESCRIPTION | 10 +-- MD5 | 14 ++-- NEWS.md | 12 +++ R/engine.R | 108 +++++++++++++++++++++++++++------- R/pikchrWrappers.R | 34 ++++++---- build/vignette.rds |binary inst/doc/Examples.html | 152 +------------------------------------------------ src/pikchr.c | 10 +-- 8 files changed, 141 insertions(+), 199 deletions(-)
Title: Multivariable Fractional Polynomials
Description: Multivariable Fractional Polynomial algorithm for model-building. Fractional polynomials are used to represent curvature in regression models. A key reference is Royston and Altman, 1994.
Author: Georg Heinze [cre],
Gareth Ambler [aut],
Axel Benner [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between mfp versions 1.5.4.1 dated 2024-05-14 and 1.5.5.1 dated 2025-09-19
DESCRIPTION | 12 MD5 | 23 NEWS.md | 4 R/predict.mfp.R | 10 build/vignette.rds |binary data/GBSG.rda |binary data/bodyfat.rda |binary inst/doc/mfp_vignette.R | 94 +- inst/doc/mfp_vignette.html | 1655 ++++++++++++++++++++++----------------------- man/bodyfat.Rd | 2 man/mfp.Rd | 2 man/predict.mfp.Rd | 11 vignettes/jointfp_model.R |only 13 files changed, 908 insertions(+), 905 deletions(-)
Title: Event Classification, Visualization and Analysis of Eye Tracking
Data
Description: Functions for analysing eye tracking data, including event detection, visualizations and area of interest (AOI) based analyses.
The package includes implementations of the IV-T, I-DT, adaptive velocity threshold, and Identification by two means clustering (I2MC) algorithms.
See separate documentation for each function. The principles underlying I-VT and I-DT algorithms are described in Salvucci & Goldberg (2000,\doi{10.1145/355017.355028}).
Two-means clustering is described in Hessels et al. (2017, \doi{10.3758/s13428-016-0822-1}).
The adaptive velocity threshold algorithm is described in Nyström & Holmqvist (2010,\doi{10.3758/BRM.42.1.188}).
See a demonstration in the URL.
Author: Johan Lundin Kleberg [aut, cre]
Maintainer: Johan Lundin Kleberg <johan.lundin.kleberg@su.se>
Diff between kollaR versions 1.1.0 dated 2025-05-07 and 1.1.2 dated 2025-09-19
DESCRIPTION | 6 +-- MD5 | 24 ++++++++------- R/FixationFilterFunctions.R | 32 ++++++++++++++------ R/PreprocessingFunctions.R | 68 +++++++++++++++++++++++++++++++++++++++++--- R/VisualizationFunctions.R | 7 ++-- man/algorithm_adaptive.Rd | 3 + man/algorithm_ivt.Rd | 6 +++ man/calculate_rms.Rd |only man/ivt_filter.Rd | 3 + man/kollaR-package.Rd | 2 - man/movmean.filter.Rd |only man/plot_sample_velocity.Rd | 3 + man/preprocess_gaze.Rd | 5 ++- man/trim_fixations.Rd | 2 - 14 files changed, 127 insertions(+), 34 deletions(-)
Title: Analysis of Visual Meteor Data
Description: Provides a suite of analytical functionalities to process and analyze
visual meteor observations from the Visual Meteor Database
of the International Meteor Organization <https://www.imo.net/>.
Author: Janko Richter [aut, cre]
Maintainer: Janko Richter <janko@richtej.de>
Diff between vismeteor versions 2.0.0 dated 2025-09-07 and 2.0.1 dated 2025-09-19
DESCRIPTION | 8 - MD5 | 61 ++++++------ NEWS.md | 11 ++ R/data.R | 4 R/freq.R | 85 +++++++++-------- R/perception.R | 2 R/vmgeom.R | 13 +- R/vmgeom_vst.R | 36 ++++--- R/vmideal.R | 10 +- R/vmideal_vst.R | 55 ++++++----- README.md | 16 +++ inst/derivation/vmgeom_vst.R | 94 +++++++++++++++++++ inst/derivation/vmideal_vst.R | 116 ++++++++++++++++++++++- inst/derivation/vmperceptions.R | 94 +++++++++++++++++-- inst/doc/vismeteor.R | 10 ++ inst/doc/vismeteor.Rmd | 24 +++- inst/doc/vismeteor.html | 196 ++++++++++++++++++++-------------------- inst/doc/vmgeom.R | 2 inst/doc/vmgeom.Rmd | 2 inst/doc/vmgeom.html | 15 +-- inst/doc/vmideal.html | 11 +- man/PER_2015_magn.Rd | 3 man/PER_2015_rates.Rd | 5 - man/vmgeom.Rd | 3 man/vmgeomVst.Rd | 16 +++ man/vmideal.Rd | 10 +- man/vmidealVst.Rd | 18 +++ man/vmperception.Rd | 2 man/vmtable.Rd | 14 ++ tests/testthat/test_load_vmdb.R |only vignettes/vismeteor.Rmd | 24 +++- vignettes/vmgeom.Rmd | 2 32 files changed, 690 insertions(+), 272 deletions(-)
Title: Transmodal Analysis (TMA)
Description: A robust computational framework for analyzing complex multimodal data. Extends existing state-dependent models to account for diverse data streams, addressing challenges such as varying temporal scales and learner characteristics to improve the robustness and interpretability of findings. For methodological details, see Shaffer, Wang, and Ruis (2025) "Transmodal Analysis" <doi:10.18608/jla.2025.8423>.
Author: Cody L Marquart [aut, cre] ,
Muhammad Hasnat Ashiq [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between tma versions 0.3.0 dated 2025-08-25 and 0.3.1 dated 2025-09-19
DESCRIPTION | 10 +- MD5 | 41 ++++++---- NAMESPACE | 12 ++ NEWS.md | 11 ++ R/accum_multidim_c.R | 8 + R/qedata_classes.R |only R/temp_accum_multidim.R | 8 + R/utils.R | 14 +-- R/view.R | 5 + R/zzz.R | 15 +++ man/ATTR_NAMES.Rd |only man/accumulate.Rd | 4 man/adjacency_key.Rd |only man/as.qe.code.Rd |only man/as.qe.data.Rd |only man/as.qe.horizon.Rd |only man/as.qe.metadata.Rd |only man/as.qe.unit.Rd |only man/is.qe.code.Rd |only man/is.qe.data.Rd |only man/is.qe.horizon.Rd |only man/is.qe.metadata.Rd |only man/is.qe.unit.Rd |only src/Makevars | 2 src/code.cpp | 78 ++++++++++--------- tests/testthat/test-accum-multidim.R | 117 +++++++++++++++------------- tests/testthat/test-multidim-cpp.R | 123 ++++++++++++++++-------------- tests/testthat/test-simple-conversation.R | 33 ++++++-- 28 files changed, 297 insertions(+), 184 deletions(-)
Title: Robust and User-Friendly Analysis of Growth and Fluorescence
Curves
Description: High-throughput analysis of growth curves and fluorescence
data using three methods: linear regression, growth model fitting, and
smooth spline fit. Analysis of dose-response relationships via
smoothing splines or dose-response models. Complete data analysis
workflows can be executed in a single step via user-friendly wrapper
functions. The results of these workflows are summarized in detailed
reports as well as intuitively navigable 'R' data containers. A 'shiny'
application provides access to all features without
requiring any programming knowledge. The package is described in further
detail in Wirth et al. (2023) <doi:10.1038/s41596-023-00850-7>.
Author: Nicolas T. Wirth [aut, cre, cph] ,
Jonathan Funk [aut] ,
Matthias Kahm [ctb] ,
Maik Kschischo [ctb] ,
Thomas Petzoldt [ctb] ,
Andrew Stein [ctb] ,
Michael W. Kearney [ctb] ,
Santiago I. Hurtado [ctb] ,
Mark Heckmann [ctb] ,
Nicholas Hamilton [ctb] ,
[...truncated...]
Maintainer: Nicolas T. Wirth <mail.nicowirth@gmail.com>
Diff between QurvE versions 1.1.1 dated 2024-01-26 and 1.1.2 dated 2025-09-19
DESCRIPTION | 69 ++-- MD5 | 52 +-- NAMESPACE | 2 NEWS.md | 21 + R/data_parsers.R | 70 ++++ R/dose-response-analysis.R | 2 R/fluorescence_plots.R | 122 +++++-- R/fluorescence_workflows.R | 31 + R/group_tables.R | 24 + R/growth_plots.R | 600 ++++++++++++++++++++++-------------- R/growth_workflows.R | 36 +- R/utils.R | 10 build/partial.rdb |binary build/vignette.rds |binary inst/doc/shiny_app_manual.html | 14 inst/doc/vignette_fluorescence.html | 23 - inst/doc/vignette_growth.html | 31 + inst/shiny_app/app.R | 119 +++++-- man/big_palette.Rd |only man/fl.drFitModel.Rd | 2 man/flBootSpline.Rd | 4 man/growth.drFit.Rd | 2 man/growth.gcBootSpline.Rd | 2 man/growth.gcFitLinear.Rd | 2 man/growth.gcFitModel.Rd | 2 man/growth.gcFitSpline.Rd | 2 man/growth.workflow.Rd | 4 man/single_hue_palettes.Rd |only 28 files changed, 848 insertions(+), 398 deletions(-)
Title: Conducts Analyses Informing Ecosystem Restoration Decisions
Description: Three sets of data and functions for informing ecosystem restoration
decisions, particularly in the context of the U.S. Army Corps of Engineers.
First, model parameters are compiled as a data set and associated metadata
for over 300 habitat suitability models developed by the U.S. Fish and
Wildlife Service (USFWS 1980, <https://www.fws.gov/policy-library/870fw1>).
Second, functions for conducting habitat suitability analyses both for the
models described above as well as generic user-specified model parameterizations.
Third, a suite of decision support tools for conducting cost-effectiveness and
incremental cost analyses (Robinson et al. 1995, IWR Report 95-R-1, U.S.
Army Corps of Engineers).
Author: S. Kyle McKay [aut, cre] ,
Darixa D. Hernandez-Abrams [aut],
Kiara C. Cushway [aut]
Maintainer: S. Kyle McKay <skmckay@gmail.com>
Diff between ecorest versions 2.0.0 dated 2024-09-12 and 2.0.1 dated 2025-09-19
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- data/HSImetadata.RData |binary data/HSImodels.RData |binary man/HSImodels.Rd | 2 +- 5 files changed, 12 insertions(+), 11 deletions(-)
Title: Dynamic Models for Confidence and Response Time Distributions
Description: Provides density functions for the joint distribution of
choice, response time and confidence for discrete confidence judgments
as well as functions for parameter fitting, prediction and simulation
for various dynamical models of decision confidence. All models are
explained in detail by Hellmann et al. (2023;
Preprint available at <https://osf.io/9jfqr/>, published version: <doi:10.1037/rev0000411>). Implemented models are the dynaViTE model,
dynWEV model, the 2DSD model (Pleskac & Busemeyer, 2010, <doi:10.1037/a0019737>),
and various race models. C++ code for dynWEV and 2DSD is based on the
'rtdists' package by Henrik Singmann.
Author: Sebastian Hellmann [aut, cre] ,
Manuel Rausch [aut, fnd]
Maintainer: Sebastian Hellmann <sebastian.hellmann@tum.de>
Diff between dynConfiR versions 1.0.0 dated 2025-05-08 and 1.1.0 dated 2025-09-19
DESCRIPTION | 12 - MD5 | 85 ++++++----- NAMESPACE | 7 NEWS.md | 4 R/RaceModels.R | 11 - R/RcppExports.R | 8 + R/d2DSD.R | 2 R/dDDConf.R | 8 - R/dMTLNR.R |only R/dWEV.R | 10 - R/ddynaViTE.R | 10 - R/fitRTConf.R | 32 +++- R/fitRTConfModels.R | 14 + R/int_fill_thresholds.R | 2 R/int_find_start_thetas_MTLNR_simulation.R |only R/int_fitting_MTLNR.R |only R/int_fitting_RMs_simulate_start_thetas.R | 2 R/likelihood_MTLNR.R |only R/predictRTConf.R | 18 +- R/predictRTConfModels.R | 25 +-- R/predictratingdist_DDConf.R | 2 R/predictratingdist_MTLNR.R |only R/predictratingdist_RM.R | 2 R/predictratingdist_WEV.R | 2 R/rLCA.R | 11 - R/simulateConfModel.R | 15 + R/simulateMTLNR.R |only inst/doc/dynConfiR.html | 5 man/LogLikMTLNR.Rd |only man/MTLNR.Rd |only man/RaceModels.Rd | 11 - man/d2DSD.Rd | 2 man/dDDConf.Rd | 8 - man/dynaViTE.Rd | 20 +- man/fitRTConf.Rd | 20 ++ man/fitRTConfModels.Rd | 4 man/predictDDConf.Rd | 2 man/predictMTLNR.Rd |only man/predictRM.Rd | 2 man/predictRTConf.Rd | 14 - man/predictRTConfModels.Rd | 17 +- man/predictWEV.Rd | 2 man/rLCA.Rd | 11 - man/simulateMTLNR.Rd |only man/simulateRTConf.Rd | 13 - src/Density_MTLNR.h |only src/RcppExports.cpp | 31 ++++ src/SeqSampConf.cpp | 220 +++++++++++++++++++++++++++++ src/SeqSampConf.h | 1 49 files changed, 497 insertions(+), 168 deletions(-)
Title: Display Idiomatic Code to Construct Most R Objects
Description: Prints code that can be used to recreate R objects. In a
sense it is similar to 'base::dput()' or 'base::deparse()' but
'constructive' strives to use idiomatic constructors.
Author: Antoine Fabri [aut, cre],
Kirill Mueller [ctb] ,
Jacob Scott [ctb],
cynkra GmbH [fnd]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Diff between constructive versions 1.2.0 dated 2025-08-28 and 1.3.0 dated 2025-09-19
DESCRIPTION | 10 +++--- MD5 | 48 ++++++++++++++++--------------- NAMESPACE | 3 + NEWS.md | 14 ++++++++- R/C_wrappers.R | 6 +++ R/construct_idiomatic.R | 9 ++++- R/s3-externalptr.R | 8 ++++- R/s3-ggplot2-CoordCartesian.R | 5 +-- R/s3-xml_document.R |only R/templates.R | 2 + R/zzz.R | 2 + inst/doc/extend-constructive.html | 10 +++--- man/construct.Rd | 1 man/constructive-package.Rd | 2 - man/opts_xml_document.Rd |only src/constructive.cpp | 46 +++++++++-------------------- tests/testthat/_snaps/s3-data.table.md | 47 ++++++++++++++++-------------- tests/testthat/_snaps/s3-externalptr.md | 10 +----- tests/testthat/_snaps/s3-xml_document.md |only tests/testthat/_snaps/s3-xts.md | 13 +++----- tests/testthat/test-construct_diff.R | 2 - tests/testthat/test-s3-data.table.R | 44 ++++++++++++++-------------- tests/testthat/test-s3-externalptr.R | 4 +- tests/testthat/test-s3-xml_document.R |only tests/testthat/test-s7-S7_S3_class.R | 2 - tests/testthat/test-s7-S7_generic.R | 2 - tests/testthat/test-s7-S7_union.R | 2 - 27 files changed, 155 insertions(+), 137 deletions(-)
Title: Tools to Use and Explore the 'BioTIME' Database
Description: The 'BioTIME' database was first published in
2018 and inspired ideas, questions, project and research
article. To make it even more accessible, an R package
was created.
The 'BioTIMEr' package provides tools designed to interact with the
'BioTIME' database. The functions provided include the 'BioTIME' recommended
methods for preparing (gridding and rarefaction) time series data, a
selection of standard biodiversity metrics (including species richness,
numerical abundance and exponential Shannon) alongside examples on how to
display change over time. It also includes a sample subset of both the query
and meta data, the full versions of which are freely available on the 'BioTIME'
website <https://biotime.st-andrews.ac.uk/home.php>.
Author: Alban Sagouis [aut, cre] ,
Faye Moyes [aut] ,
Ines S. Martins [aut, rev] ,
Shane A. Blowes [ctb] ,
Viviana Brambilla [ctb] ,
Cher F. Y. Chow [ctb] ,
Ada Fontrodona-Eslava [ctb] ,
Laura Antao [ctb, rev] ,
Jonathan M. Chase [fnd] ,
Maria Dornelas [fnd, [...truncated...]
Maintainer: Alban Sagouis <alban.sagouis@idiv.de>
Diff between BioTIMEr versions 0.2.4 dated 2025-06-06 and 0.2.5 dated 2025-09-19
DESCRIPTION | 8 MD5 | 24 NEWS.md | 4 README.md | 5 inst/doc/vignette1.html | 4 tests/testthat/_snaps/runResampling.md |32652 ++++++++++++++++++++++++++++++++- tests/testthat/test-gridding.R | 3 tests/testthat/test-metrics.R | 10 tests/testthat/test-runResampling.R | 80 tests/testthat/test-scales.R | 3 tests/testthat/test-slopes.R | 2 tests/testthat/test-workflow_alpha.R | 1 tests/testthat/test-workflow_beta.R | 1 13 files changed, 32719 insertions(+), 78 deletions(-)
Title: Manipulate ACLED Data
Description: Tools working with data from ACLED (Armed Conflict Location and Event Data). Functions include simplified access to ACLED's API (<https://apidocs.acleddata.com/>), methods for keeping local versions of ACLED data up-to-date, and functions for common ACLED data transformations.
Author: Armed Conflict Location and Event Data ACLED [cph],
Trey Billing [aut, cre],
Lucas Fagliano [aut],
Katayoun Kishi [ctb]
Maintainer: Trey Billing <t.billing@acleddata.com>
Diff between acledR versions 1.0.0 dated 2025-09-04 and 1.0.1 dated 2025-09-19
acledR-1.0.0/acledR/R/acled_access.R |only acledR-1.0.0/acledR/man/acled_access.Rd |only acledR-1.0.0/acledR/tests/testthat/setup-acled_access.R |only acledR-1.0.0/acledR/tests/testthat/test-acled_access.R |only acledR-1.0.1/acledR/DESCRIPTION | 6 acledR-1.0.1/acledR/MD5 | 34 - acledR-1.0.1/acledR/NAMESPACE | 1 acledR-1.0.1/acledR/NEWS.md | 5 acledR-1.0.1/acledR/R/acled_api.R | 209 +--------- acledR-1.0.1/acledR/R/acled_deletions_api.R | 162 ------- acledR-1.0.1/acledR/R/acled_update.R | 88 ---- acledR-1.0.1/acledR/man/acled_api.Rd | 15 acledR-1.0.1/acledR/man/acled_auth.Rd | 1 acledR-1.0.1/acledR/man/acled_deletions_api.Rd | 18 acledR-1.0.1/acledR/man/acled_update.Rd | 12 acledR-1.0.1/acledR/tests/testthat/setup-acled_api.R | 10 acledR-1.0.1/acledR/tests/testthat/setup-acled_deletions_api.R | 6 acledR-1.0.1/acledR/tests/testthat/test-acled_api.R | 59 +- acledR-1.0.1/acledR/tests/testthat/test-acled_deletions_api.R | 6 acledR-1.0.1/acledR/tests/testthat/test-acled_update.R | 12 20 files changed, 136 insertions(+), 508 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalized,
and standard 'IB' clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2024) <doi:10.48550/arXiv.2407.03389>. The standard 'IB' method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
and the generalized 'IB' from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>.
Author: Efthymios Costa [aut],
Ioanna Papatsouma [aut],
Angelos Markos [aut, cre]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.2 dated 2025-07-10 and 1.2.1 dated 2025-09-19
IBclust-1.2.1/IBclust/DESCRIPTION | 15 + IBclust-1.2.1/IBclust/MD5 | 70 +++----- IBclust-1.2.1/IBclust/NAMESPACE | 13 + IBclust-1.2.1/IBclust/R/AIB.R | 8 - IBclust-1.2.1/IBclust/R/AIBmix.R | 137 +++++++++-------- IBclust-1.2.1/IBclust/R/DIBmix.R | 123 +++++++-------- IBclust-1.2.1/IBclust/R/DIBmix_iterate.R | 188 +++++++++++++++--------- IBclust-1.2.1/IBclust/R/GIBmix.R | 161 +++++++++----------- IBclust-1.2.1/IBclust/R/GIBmix_iterate.R | 192 +++++++++++++++--------- IBclust-1.2.1/IBclust/R/IBmix.R | 130 +++++++--------- IBclust-1.2.1/IBclust/R/IBmix_iterate.R | 186 +++++++++++++++-------- IBclust-1.2.1/IBclust/R/aibclust-class.R |only IBclust-1.2.1/IBclust/R/aibclust-methods.R |only IBclust-1.2.1/IBclust/R/bw_select.R | 147 ++++++++++++------ IBclust-1.2.1/IBclust/R/calc_metrics.R | 3 IBclust-1.2.1/IBclust/R/coord_to_pxy_R.R | 20 +- IBclust-1.2.1/IBclust/R/gibclust-class.R |only IBclust-1.2.1/IBclust/R/gibclust-methods.R |only IBclust-1.2.1/IBclust/R/input_checks.R |only IBclust-1.2.1/IBclust/README.md | 12 - IBclust-1.2.1/IBclust/build/partial.rdb |binary IBclust-1.2.1/IBclust/inst/CITATION | 4 IBclust-1.2.1/IBclust/inst/REFERENCES.bib | 30 +++ IBclust-1.2.1/IBclust/man/AIBmix.Rd | 167 +++++++++++++++++---- IBclust-1.2.1/IBclust/man/DIBmix.Rd | 226 ++++++++++++++++++++++------- IBclust-1.2.1/IBclust/man/GIBmix.Rd | 203 ++++++++++++++++++-------- IBclust-1.2.1/IBclust/man/IBmix.Rd | 192 ++++++++++++++++++------ IBclust-1.2.1/IBclust/man/figures/logo.png |binary IBclust-1.2.1/IBclust/src/Makevars.win | 4 IBclust-1.2.1/IBclust/src/qt_x_step.cpp | 5 IBclust-1.2/IBclust/LICENSE |only IBclust-1.2/IBclust/R/AIBcat.R |only IBclust-1.2/IBclust/R/AIBcont.R |only IBclust-1.2/IBclust/R/DIBcat.R |only IBclust-1.2/IBclust/R/DIBcont.R |only IBclust-1.2/IBclust/R/GIBcat.R |only IBclust-1.2/IBclust/R/GIBcont.R |only IBclust-1.2/IBclust/R/IBcat.R |only IBclust-1.2/IBclust/R/IBcont.R |only IBclust-1.2/IBclust/man/AIBcat.Rd |only IBclust-1.2/IBclust/man/AIBcont.Rd |only IBclust-1.2/IBclust/man/DIBcat.Rd |only IBclust-1.2/IBclust/man/DIBcont.Rd |only IBclust-1.2/IBclust/man/GIBcat.Rd |only IBclust-1.2/IBclust/man/GIBcont.Rd |only IBclust-1.2/IBclust/man/IBcat.Rd |only IBclust-1.2/IBclust/man/IBcont.Rd |only 47 files changed, 1435 insertions(+), 801 deletions(-)
Title: Dynamic Model Averaging
Description: Dynamic model averaging for binary and continuous
outcomes.
Author: Tyler H. McCormick [aut],
Adrian Raftery [aut],
David Madigan [aut],
Sevvandi Kandanaarachchi [ctb, aut],
Hana Sevcikova [ctb, aut, cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between dma versions 1.4-1 dated 2025-07-29 and 1.4-2 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-logistic-dma.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.5 dated 2025-03-12 and 0.3.6 dated 2025-09-19
DESCRIPTION | 14 +- MD5 | 176 ++++++++++++++------------- NAMESPACE | 2 R/apollo_avgInterDraws.R | 4 R/apollo_avgIntraDraws.R | 4 R/apollo_classAlloc.R | 9 + R/apollo_cnl.R | 10 + R/apollo_cnl2.R | 10 + R/apollo_combineModels.R | 4 R/apollo_dft.R | 2 R/apollo_drugChoiceData.R | 2 R/apollo_el.R | 10 + R/apollo_emdc.R | 2 R/apollo_emdc1.R | 8 - R/apollo_emdc2.R | 13 -- R/apollo_estimate.R | 125 +++++++++++++++++-- R/apollo_estimateHB.R | 3 R/apollo_expandLoop.R | 28 +++- R/apollo_fmnl.R | 10 + R/apollo_fnl.R | 10 + R/apollo_initialise.R | 2 R/apollo_lc.R | 13 +- R/apollo_lcEM_new.R |only R/apollo_makeCluster.R | 76 +++++------ R/apollo_makeGrad.R | 4 R/apollo_makeHessian.R | 2 R/apollo_mixUnconditionals.R | 14 +- R/apollo_mnl.R | 12 + R/apollo_modeChoiceData.R | 2 R/apollo_modelOutput.R | 49 ++++++- R/apollo_modifyUserDefFunc.R | 2 R/apollo_nl.R | 17 ++ R/apollo_normalDensity.R | 10 + R/apollo_ol.R | 13 +- R/apollo_op.R | 13 +- R/apollo_panelProd.R | 4 R/apollo_preEstimate.R |only R/apollo_prediction.R | 59 ++++++++- R/apollo_prepareProb.R | 6 R/apollo_preprocess.R | 2 R/apollo_print.R | 4 R/apollo_rrm.R | 12 + R/apollo_saveOutput.R | 14 +- R/apollo_sharesTest.R | 18 ++ R/apollo_swissRouteChoiceData.R | 14 +- R/apollo_timeUseData.R | 2 R/apollo_tobit.R | 10 + R/apollo_unconditionals.R | 5 R/apollo_validateInputs.R | 2 R/apollo_varcov.R | 12 - R/onAttach.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/apollofirstexample.html | 237 ++++++++++++++++++------------------- man/apollo_avgInterDraws.Rd | 2 man/apollo_avgIntraDraws.Rd | 2 man/apollo_classAlloc.Rd | 1 man/apollo_cnl.Rd | 2 man/apollo_cnl2.Rd | 2 man/apollo_combineModels.Rd | 2 man/apollo_dft.Rd | 2 man/apollo_drugChoiceData.Rd | 2 man/apollo_el.Rd | 2 man/apollo_emdc.Rd | 2 man/apollo_emdc1.Rd | 2 man/apollo_emdc2.Rd | 11 - man/apollo_estimate.Rd | 2 man/apollo_fmnl.Rd | 2 man/apollo_fnl.Rd | 2 man/apollo_lc.Rd | 2 man/apollo_lcEM_new.Rd |only man/apollo_mixUnconditionals.Rd | 9 + man/apollo_mnl.Rd | 2 man/apollo_modeChoiceData.Rd | 2 man/apollo_modelOutput.Rd | 1 man/apollo_nl.Rd | 2 man/apollo_normalDensity.Rd | 2 man/apollo_ol.Rd | 5 man/apollo_op.Rd | 4 man/apollo_panelProd.Rd | 2 man/apollo_preEstimate.Rd |only man/apollo_prediction.Rd | 2 man/apollo_prepareProb.Rd | 2 man/apollo_rrm.Rd | 2 man/apollo_saveOutput.Rd | 2 man/apollo_swissRouteChoiceData.Rd | 14 +- man/apollo_timeUseData.Rd | 2 man/apollo_tobit.Rd | 2 man/apollo_unconditionals.Rd | 9 + man/apollo_validateInputs.Rd | 2 man/apollo_varcov.Rd | 2 91 files changed, 811 insertions(+), 377 deletions(-)
Title: Package Documentation Websites with 'Quarto', 'Docsify',
'Docute', or 'MkDocs'
Description: This is a simple and powerful package to create, render, preview,
and deploy documentation websites for 'R' packages. It is a lightweight and
flexible alternative to 'pkgdown', with support for many documentation
generators, including 'Quarto', 'Docute', 'Docsify', and 'MkDocs'.
Author: Etienne Bacher [aut, cre, cph],
Vincent Arel-Bundock [aut]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between altdoc versions 0.5.0 dated 2025-01-23 and 0.6.0 dated 2025-09-19
DESCRIPTION | 9 LICENSE | 4 MD5 | 207 + NAMESPACE | 12 NEWS.md | 357 +-- R/altdoc_variables.R | 136 - R/check.R | 117 - R/freeze.R | 130 - R/import_man.R | 479 ++-- R/import_misc.R | 354 +-- R/import_readme.R | 169 - R/import_vignettes.R | 496 ++-- R/preview_docs.R | 60 R/qmd2md.R | 113 R/rd2qmd.R | 249 +- R/render_docs.R | 286 +- R/settings.R | 134 - R/settings_docsify.R | 196 - R/settings_docute.R | 195 - R/settings_mkdocs.R | 352 +-- R/settings_quarto_website.R | 264 +- R/setup_docs.R | 391 +-- R/setup_github_actions.R | 92 R/utils.R | 436 ++- README.md | 488 ++-- build/vignette.rds |binary inst/WORDLIST | 75 inst/doc/get-started.R | 6 inst/doc/get-started.Rmd | 390 +-- inst/doc/get-started.html | 1133 +++++----- inst/docsify/docsify.html | 90 inst/docsify/docsify.md | 18 inst/docute/docute.html | 104 inst/gha/altdoc.yaml | 146 - inst/mkdocs/mkdocs.yml | 80 inst/preamble/preamble_man_qmd.yml | 12 inst/preamble/preamble_vignettes_qmd.yml | 12 inst/preamble/preamble_vignettes_rmd.yml | 8 inst/quarto_website/quarto_website.yml | 84 man/preview_docs.Rd | 62 man/render_docs.Rd | 244 +- man/setup_docs.Rd | 168 - man/setup_github_actions.Rd | 50 tests/spelling.R | 13 tests/testthat.R | 8 tests/testthat/_snaps/docsify/render_docs.md | 373 +-- tests/testthat/_snaps/docute/render_docs.md | 284 +- tests/testthat/_snaps/mkdocs/render_docs.md | 498 ++-- tests/testthat/_snaps/rd2qmd.md |only tests/testthat/examples/examples-man/between.Rd | 36 tests/testthat/examples/examples-man/between.md | 80 tests/testthat/examples/examples-man/is-internal.Rd | 36 tests/testthat/examples/examples-man/long_title.Rd |only tests/testthat/examples/examples-man/should-fail.Rd | 34 tests/testthat/examples/examples-qmd/with-preamble.qmd | 26 tests/testthat/examples/examples-qmd/without-preamble.qmd | 16 tests/testthat/examples/examples-vignettes/basic.Rmd | 36 tests/testthat/examples/examples-vignettes/several-outputs.Rmd | 48 tests/testthat/examples/examples-vignettes/with-figure.Rmd | 50 tests/testthat/examples/examples-yaml/basic.Rmd | 20 tests/testthat/examples/examples-yaml/options.Rmd | 28 tests/testthat/examples/examples-yaml/several-outputs.Rmd | 32 tests/testthat/examples/testpkg.altdoc.noURL |only tests/testthat/examples/testpkg.altdoc.nonGithubURL |only tests/testthat/examples/testpkg.altdoc/DESCRIPTION | 32 tests/testthat/examples/testpkg.altdoc/NAMESPACE | 14 tests/testthat/examples/testpkg.altdoc/NEWS.md | 18 tests/testthat/examples/testpkg.altdoc/R/examplesIf_false.R | 24 tests/testthat/examples/testpkg.altdoc/R/examplesIf_true.R | 24 tests/testthat/examples/testpkg.altdoc/R/hello_base.R | 56 tests/testthat/examples/testpkg.altdoc/R/hello_r6.R | 59 tests/testthat/examples/testpkg.altdoc/README.Rmd | 82 tests/testthat/examples/testpkg.altdoc/README.md | 72 tests/testthat/examples/testpkg.altdoc/man/examplesIf_false.Rd | 44 tests/testthat/examples/testpkg.altdoc/man/examplesIf_true.Rd | 44 tests/testthat/examples/testpkg.altdoc/man/hello_base.Rd | 74 tests/testthat/examples/testpkg.altdoc/man/hello_r6.Rd | 178 - tests/testthat/examples/testpkg.altdoc/vignettes/test.Rmd | 42 tests/testthat/examples/testpkg.lifecycle |only tests/testthat/helper.R | 183 - tests/testthat/test-check_md_structure.R | 62 tests/testthat/test-freeze.R | 46 tests/testthat/test-import_man.R | 141 - tests/testthat/test-parallel.R | 19 tests/testthat/test-preview_docs.R | 26 tests/testthat/test-qmd2md.R | 89 tests/testthat/test-rd2qmd.R | 81 tests/testthat/test-render_docs.R | 517 ++-- tests/testthat/test-settings.R | 38 tests/testthat/test-setup_docs.R | 130 - tests/testthat/test-setup_github_actions.R | 62 tests/testthat/test-update.R | 247 +- tests/testthat/test-utils.R | 116 - vignettes/customize.qmd | 546 ++-- vignettes/deploy.qmd | 176 - vignettes/get-started.Rmd | 390 +-- 96 files changed, 7142 insertions(+), 6516 deletions(-)
Title: Simulate Non-Proportional Hazards
Description: A toolkit for simulation studies concerning time-to-event endpoints
with non-proportional hazards. 'SimNPH' encompasses functions for simulating
time-to-event data in various scenarios, simulating different trial designs
like fixed-followup, event-driven, and group sequential designs. The package
provides functions to calculate the true values of common summary statistics
for the implemented scenarios and offers common analysis methods for
time-to-event data. Helper functions for running simulations with the
'SimDesign' package and for aggregating and presenting the results are also
included. Results of the conducted simulation study are available in the
paper: "A Comparison of Statistical Methods for Time-To-Event Analyses in
Randomized Controlled Trials Under Non-Proportional Hazards",
Klinglmüller et al. (2025) <doi:10.1002/sim.70019>.
Author: Tobias Fellinger [aut, cre] ,
Florian Klinglmueller [aut]
Maintainer: Tobias Fellinger <tobias.fellinger@ages.at>
Diff between SimNPH versions 0.5.7 dated 2025-04-08 and 0.5.8 dated 2025-09-19
DESCRIPTION | 16 +- MD5 | 32 +++-- NEWS.md | 7 + R/report_plots.R | 2 R/shhr_gg.R | 25 +--- build/vignette.rds |binary inst/doc/simple_example.Rmd | 81 ++++++++------ inst/doc/simple_example.html | 180 +++++++++++++++++---------------- man/results_pivot_longer.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-analyse_describe.R | 28 ++--- tests/testthat/test-report_plots.R | 72 ++----------- tests/testthat/test-shhr_gg.R | 9 - tests/testthat/test-summarise.R | 35 +++--- vignettes/simple_example.Rmd | 81 ++++++++------ 15 files changed, 280 insertions(+), 290 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 2.0.1 dated 2024-11-22 and 2.1.0 dated 2025-09-19
DESCRIPTION | 8 LICENSE | 4 MD5 | 75 NAMESPACE | 197 NEWS.md | 16 R/DiveR-package.R | 12 R/concat_conserved_kmer.R | 8 R/metadata_extraction.R | 316 R/plot_conservation_level.R | 435 R/plot_correlation.R | 96 R/plot_dynamics_protein.R | 402 R/plot_dynamics_proteome.R | 380 R/plot_entropy.R | 390 R/plot_time.R | 116 R/plot_world_map.R | 272 R/sample_data.R | 146 README.md | 66 inst/extdata/GISAID_EpiCoV.faa | 230 inst/extdata/NCBI_Protein.faa | 114 inst/extdata/city_mapper.csv |84914 +++++++++++++++++++-------------------- man/JSON_sample.Rd | 32 man/concat_conserved_kmer.Rd | 72 man/extract_from_GISAID.Rd | 28 man/extract_from_NCBI.Rd | 28 man/json2csv.Rd | 58 man/match_region_to_target.Rd |only man/metadata.Rd | 42 man/metadata_extraction.Rd | 52 man/plot_correlation.Rd | 96 man/plot_dynamics_protein.Rd | 88 man/plot_dynamics_proteome.Rd | 82 man/plot_entropy.Rd | 98 man/plot_time.Rd | 74 man/protein_2hosts.Rd | 70 man/proteins_1host.Rd | 70 man/vDiveR-package.Rd | 46 tests/testthat.R | 24 tests/testthat/test-concat-seq.R | 154 tests/testthat/test-json2csv.R | 108 39 files changed, 44716 insertions(+), 44703 deletions(-)
Title: Variable Selection for Model-Based Clustering of Mixed-Type Data
Set with Missing Values
Description: Full model selection (detection of the relevant features and estimation of the number of clusters) for model-based clustering (see reference here <doi:10.1007/s11222-016-9670-1>). Data to analyze can be continuous, categorical, integer or mixed. Moreover, missing values can occur and do not necessitate any pre-processing. Shiny application permits an easy interpretation of the results.
Author: Matthieu Marbac [aut],
Mohammed Sedki [aut, cre]
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 2.1.3.1 dated 2020-10-14 and 2.1.3.2 dated 2025-09-19
VarSelLCM-2.1.3.1/VarSelLCM/inst/doc/VarSelLCM.pdf |only VarSelLCM-2.1.3.2/VarSelLCM/DESCRIPTION | 23 ++++++++---- VarSelLCM-2.1.3.2/VarSelLCM/MD5 | 36 +++++++++---------- VarSelLCM-2.1.3.2/VarSelLCM/R/Plot.R | 31 +++++++++------- VarSelLCM-2.1.3.2/VarSelLCM/R/VarSelLCM.R | 10 ++--- VarSelLCM-2.1.3.2/VarSelLCM/R/model.R | 2 - VarSelLCM-2.1.3.2/VarSelLCM/build/vignette.rds |binary VarSelLCM-2.1.3.2/VarSelLCM/inst/CITATION | 10 ++--- VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.R | 34 ++++++++--------- VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.Rmd | 2 - VarSelLCM-2.1.3.2/VarSelLCM/inst/doc/VarSelLCM.html |only VarSelLCM-2.1.3.2/VarSelLCM/man/VarSelCluster.Rd | 17 +++++++- VarSelLCM-2.1.3.2/VarSelLCM/man/VarSelLCM-package.Rd | 13 +++++- VarSelLCM-2.1.3.2/VarSelLCM/man/plot-methods.Rd | 3 - VarSelLCM-2.1.3.2/VarSelLCM/src/Makevars | 2 - VarSelLCM-2.1.3.2/VarSelLCM/src/Makevars.win | 2 - VarSelLCM-2.1.3.2/VarSelLCM/src/RcppExports.cpp | 5 ++ VarSelLCM-2.1.3.2/VarSelLCM/src/XEM.cpp | 6 +-- VarSelLCM-2.1.3.2/VarSelLCM/src/XEMPen.cpp | 6 ++- VarSelLCM-2.1.3.2/VarSelLCM/vignettes/VarSelLCM.Rmd | 2 - 20 files changed, 121 insertions(+), 83 deletions(-)
Title: Algorithms and Tools for Tabular Statistics and Hierarchical
Computations
Description: Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.8.1 dated 2025-08-18 and 1.8.2 dated 2025-09-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 3 +++ NEWS.md | 8 ++++++++ R/DummyDuplicated.R | 23 ----------------------- R/get_colnames.R |only R/zero_col.R |only man/get_colnames.Rd |only man/zero_col.Rd |only 9 files changed, 23 insertions(+), 31 deletions(-)
Title: Monte-Carlo Methods for Simulating Luminescence Phenomena
Description: A collection of functions to simulate luminescence production in
dosimetric materials using Monte Carlo methods. Implemented are models for
delocalised transitions (e.g., Chen and McKeever (1997) <doi:10.1142/2781>),
localised transitions (e.g., Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>)
and tunnelling transitions (Jain et al. (2012) <doi:10.1088/0953-8984/24/38/385402>
and Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>).
Supported stimulation methods are thermal luminescence (TL),
continuous-wave optically stimulated luminescence (CW-OSL),
linearly-modulated optically stimulated luminescence (LM-OSL),
linearly-modulated infrared stimulated luminescence (LM-IRSL),
and isothermal luminescence (ITL or ISO-TL).
Author: Johannes Friedrich [aut, trl] ,
Sebastian Kreutzer [aut, trl, cre] ,
Vasilis Pagonis [aut] ,
Christoph Schmidt [aut] ,
Christian Laag [ctb] ,
Ena Rajovic [ctb],
Alex Roy Duncan [ctb]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between RLumCarlo versions 0.1.9 dated 2022-08-08 and 0.1.10 dated 2025-09-19
DESCRIPTION | 43 ++++---- MD5 | 78 +++++++-------- NEWS.md | 5 R/RLumCarlo-package.R | 10 + README.md | 60 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/RLumCarlo_-_Getting_started_with_RLumCarlo.pdf |binary man/RLumCarlo-package.Rd | 14 ++ man/create_ClusterSystem.Rd | 2 man/figures/README-unnamed-chunk-2-1.png |binary man/methods_RLumCarlo.Rd | 2 man/plot_RLumCarlo.Rd | 2 man/run_MC_CW_IRSL_LOC.Rd | 2 man/run_MC_CW_IRSL_TUN.Rd | 2 man/run_MC_CW_OSL_DELOC.Rd | 2 man/run_MC_ISO_DELOC.Rd | 2 man/run_MC_ISO_LOC.Rd | 2 man/run_MC_ISO_TUN.Rd | 2 man/run_MC_LM_OSL_DELOC.Rd | 2 man/run_MC_LM_OSL_LOC.Rd | 2 man/run_MC_LM_OSL_TUN.Rd | 2 man/run_MC_TL_DELOC.Rd | 2 man/run_MC_TL_LOC.Rd | 2 man/run_MC_TL_TUN.Rd | 2 src/Makevars | 4 src/Makevars.win | 4 tests/testthat/test_run_MC_CW_IRSL_LOC.R | 9 + tests/testthat/test_run_MC_CW_IRSL_TUN.R | 3 tests/testthat/test_run_MC_CW_OSL_DELOC.R | 3 tests/testthat/test_run_MC_ISO_DELOC.R | 3 tests/testthat/test_run_MC_ISO_LOC.R | 3 tests/testthat/test_run_MC_ISO_TUN.R | 4 tests/testthat/test_run_MC_LM_OSL_DELOC.R | 3 tests/testthat/test_run_MC_LM_OSL_LOC.R | 3 tests/testthat/test_run_MC_LM_OSL_TUN.R | 3 tests/testthat/test_run_MC_TL_DELOC.R | 3 tests/testthat/test_run_MC_TL_LOC.R | 3 tests/testthat/test_run_MC_TL_TUN.R | 1 vignettes/RLumCarlo_-_Getting_started_with_RLumCarlo.Rmd | 2 40 files changed, 159 insertions(+), 132 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv',
'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut] ,
Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Shelby Bearrows [ctb],
https://github.com/mandreyel/ [cph] ,
Jukka Jylaenki [cph] ,
Mikkel Joergensen [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between vroom versions 1.6.5 dated 2023-12-05 and 1.6.6 dated 2025-09-19
vroom-1.6.5/vroom/build/vroom.pdf |only vroom-1.6.6/vroom/DESCRIPTION | 17 +++++++++-------- vroom-1.6.6/vroom/MD5 | 21 ++++++++++----------- vroom-1.6.6/vroom/NEWS.md | 4 ++++ vroom-1.6.6/vroom/README.md | 4 +++- vroom-1.6.6/vroom/build/stage23.rdb |binary vroom-1.6.6/vroom/build/vignette.rds |binary vroom-1.6.6/vroom/inst/doc/benchmarks.html | 16 ++++++++-------- vroom-1.6.6/vroom/inst/doc/vroom.R | 18 +++++++++--------- vroom-1.6.6/vroom/inst/doc/vroom.html | 11 ++++++----- vroom-1.6.6/vroom/man/vroom_fwf.Rd | 8 +++++--- vroom-1.6.6/vroom/src/iconv_file.cc | 5 +++-- 12 files changed, 57 insertions(+), 47 deletions(-)
Title: A GUI for Dual and Bulk RNA-Sequencing Analysis
Description: A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.
Author: Carmine Fruggiero [aut, cre],
Gaetano Aufiero [aut]
Maintainer: Carmine Fruggiero <fruggierocarmine3@gmail.com>
Diff between inDAGO versions 1.0.1 dated 2025-09-13 and 1.0.2 dated 2025-09-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/CombinedAlignment.R | 48 +++++++++++++++++++++++++++++++++++++++++++++--- 3 files changed, 50 insertions(+), 8 deletions(-)
Title: A Fast and Scalable Exhaustive Feature Selection Framework
Description: The goal of this package is to provide an easy to use, fast and
scalable exhaustive search framework. Exhaustive feature selections
typically require a very large number of models to be fitted and evaluated.
Execution speed and memory management are crucial factors here. This package
provides solutions for both. Execution speed is optimized by using a
multi-threaded C++ backend, and memory issues are solved by by only storing
the best results during execution and thus keeping memory usage constant.
Author: Rudolf Jagdhuber [aut, cre],
Jorge Nocedal [cph] ,
Naoaki Okazaki [cph]
Maintainer: Rudolf Jagdhuber <r.jagdhuber@gmail.com>
Diff between ExhaustiveSearch versions 1.0.1 dated 2021-01-18 and 1.0.2 dated 2025-09-19
DESCRIPTION | 8 MD5 | 32 +- NAMESPACE | 22 - NEWS.md | 22 - R/ExhaustiveSearch-package.R | 10 R/ExhaustiveSearch.R | 600 +++++++++++++++++++++--------------------- R/RcppExports.R | 14 R/print.R | 104 +++---- R/resultFunctions.R | 176 ++++++------ README.md | 298 ++++++++++---------- man/ExhaustiveSearch.Rd | 362 ++++++++++++------------- man/getFeatures.Rd | 82 ++--- man/print.ExhaustiveSearch.Rd | 52 +-- man/resultTable.Rd | 112 +++---- src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 5 17 files changed, 958 insertions(+), 947 deletions(-)
More information about ExhaustiveSearch at CRAN
Permanent link
Title: Compute Energy Landscapes
Description: Compute energy landscapes using a digital elevation model
and body mass of animals.
Author: Emilio Berti [aut, cre],
Marco Davoli [ctb],
Robert Buitenwerf [ctb],
Alexander Dyer [ctb],
Oskar L.P. Hansen [ctb],
Myriam Hirt [ctb],
Jens-Christian Svenning [ctb],
Joerdis F. Terlau [ctb],
Ulrich Brose [ctb],
Fritz Vollrath [ctb]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between enerscape versions 1.1.0 dated 2024-01-29 and 1.2.0 dated 2025-09-19
DESCRIPTION | 23 ++- MD5 | 48 +++--- R/RcppExports.R | 44 +++++- R/enerscape.R | 23 +-- R/humanscape.R |only README.md | 263 +++++++++++++++++++++++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/enerscape.R | 119 +++++++++++----- inst/doc/enerscape.Rmd | 71 +++++++++ inst/doc/enerscape.html | 84 ++++++----- man/energy.Rd | 6 man/energyHuman.Rd |only man/energyscape.Rd | 6 man/energyscapeHuman.Rd |only man/enerscape.Rd | 12 - man/humanscape.Rd |only man/slopeRadiant.Rd |only src/RcppExports.cpp | 62 +++++++- src/distance.cpp |only src/distance.h | 34 ---- src/enerscape.cpp | 20 +- src/humanscape.cpp |only src/neighbours.cpp |only src/neighbours.h | 44 ------ src/slope.cpp |only src/slope.h | 36 ---- tests/testthat/test-cpp-functions.R | 2 vignettes/enerscape.Rmd | 71 +++++++++ 30 files changed, 677 insertions(+), 291 deletions(-)
Title: Two-Stage Difference-in-Differences Following Gardner (2021)
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021) <doi:10.48550/arXiv.2207.05943>. To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
Author: Kyle Butts [aut, cre] ,
John Gardner [aut] ,
Grant McDermott [ctb] ,
Laurent Berge [ctb]
Maintainer: Kyle Butts <buttskyle96@gmail.com>
Diff between did2s versions 1.0.2 dated 2023-04-07 and 1.2.0 dated 2025-09-19
did2s-1.0.2/did2s/R/utils.R |only did2s-1.0.2/did2s/man/figures/es.png |only did2s-1.0.2/did2s/man/figures/resid.png |only did2s-1.0.2/did2s/man/figures/twfe.png |only did2s-1.0.2/did2s/man/figures/twfe_count.png |only did2s-1.0.2/did2s/man/figures/unnamed-chunk-1-1.png |only did2s-1.2.0/did2s/DESCRIPTION | 26 did2s-1.2.0/did2s/MD5 | 64 did2s-1.2.0/did2s/NAMESPACE | 2 did2s-1.2.0/did2s/NEWS.md | 4 did2s-1.2.0/did2s/R/data.R | 2 did2s-1.2.0/did2s/R/did2s.R | 303 ++-- did2s-1.2.0/did2s/R/event_study.R | 752 +++++----- did2s-1.2.0/did2s/R/gen_data.R | 153 +- did2s-1.2.0/did2s/R/honest_did.R |only did2s-1.2.0/did2s/R/zzz.R | 13 did2s-1.2.0/did2s/README.md | 247 ++- did2s-1.2.0/did2s/build/vignette.rds |binary did2s-1.2.0/did2s/data/castle.rda |binary did2s-1.2.0/did2s/data/df_het.rda |binary did2s-1.2.0/did2s/data/df_hom.rda |binary did2s-1.2.0/did2s/inst/CITATION | 15 did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.R | 81 - did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.Rmd | 77 - did2s-1.2.0/did2s/inst/doc/Two-Stage-Difference-in-Differences.html | 223 +- did2s-1.2.0/did2s/man/did2s.Rd | 33 did2s-1.2.0/did2s/man/event_study.Rd | 10 did2s-1.2.0/did2s/man/figures/README-ehec-data-est-1.png |only did2s-1.2.0/did2s/man/figures/README-plot-compare-1.png |binary did2s-1.2.0/did2s/man/figures/README-plot-df-het-1.png |binary did2s-1.2.0/did2s/man/figures/README-plot-es-1.png |binary did2s-1.2.0/did2s/man/figures/README-sensitivity-1.png |only did2s-1.2.0/did2s/man/figures/README-unnamed-chunk-3-1.png |only did2s-1.2.0/did2s/man/get_honestdid_obj_did2s.Rd |only did2s-1.2.0/did2s/man/honest_did_did2s.Rd |only did2s-1.2.0/did2s/man/robust_solve_XtX.Rd |only did2s-1.2.0/did2s/tests/testthat/test-did2s.R | 129 + did2s-1.2.0/did2s/tests/testthat/test-event-study.R | 74 did2s-1.2.0/did2s/tests/testthat/test-robust-solve.R |only did2s-1.2.0/did2s/vignettes/Two-Stage-Difference-in-Differences.Rmd | 77 - 40 files changed, 1396 insertions(+), 889 deletions(-)
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and
Generalized Linear Models
Description: The c060 package provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models.
Author: Martin Sill [aut],
Thomas Hielscher [aut],
Manuela Zucknick [aut],
Natalia Becker [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between c060 versions 0.3-1 dated 2025-08-18 and 0.4-0 dated 2025-09-19
c060-0.3-1/c060/build |only c060-0.3-1/c060/man/coef.intsearch.Rd |only c060-0.3-1/c060/man/figures/logo.png |only c060-0.3-1/c060/man/plot.summary.int.Rd |only c060-0.3-1/c060/man/predictProb.glmnet.Rd |only c060-0.4-0/c060/DESCRIPTION | 25 c060-0.4-0/c060/MD5 | 86 - c060-0.4-0/c060/NAMESPACE | 77 - c060-0.4-0/c060/NEWS.md | 8 c060-0.4-0/c060/R/EPSGO.R | 190 ++ c060-0.4-0/c060/R/balancedFolds.R | 49 c060-0.4-0/c060/R/c060-package.R |only c060-0.4-0/c060/R/coef_intsearch.R | 19 c060-0.4-0/c060/R/peperr_glmnet.R | 299 +++ c060-0.4-0/c060/R/plot_coef_glmnet.R | 45 c060-0.4-0/c060/R/plot_summary_inter_search.R | 58 c060-0.4-0/c060/R/stabilityselection.R | 215 ++ c060-0.4-0/c060/R/summary_inter_search.R | 33 c060-0.4-0/c060/R/tune_glmnet_interval.R | 183 +- c060-0.4-0/c060/README.md | 1071 +++++++++++++- c060-0.4-0/c060/inst/CITATION | 28 c060-0.4-0/c060/inst/_pkgdown.yml |only c060-0.4-0/c060/man/EPSGO.Rd | 221 +- c060-0.4-0/c060/man/PLL.coxnet.Rd | 53 c060-0.4-0/c060/man/Plot.coef.glmnet.Rd | 60 c060-0.4-0/c060/man/Plot.peperr.curves.Rd | 68 c060-0.4-0/c060/man/aggregation.auc.Rd | 63 c060-0.4-0/c060/man/balancedFolds.Rd | 74 c060-0.4-0/c060/man/c060-package.Rd |only c060-0.4-0/c060/man/coef.sum.intsearch.Rd |only c060-0.4-0/c060/man/complexity.glmnet.Rd | 87 - c060-0.4-0/c060/man/figures/README-unnamed-chunk-13-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-42-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-43-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-44-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-45-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-46-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-5-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-50-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-6-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-7-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-8-1.png |only c060-0.4-0/c060/man/figures/README-unnamed-chunk-9-1.png |only c060-0.4-0/c060/man/fit.glmnet.Rd | 75 c060-0.4-0/c060/man/plot.stabpath.Rd | 133 - c060-0.4-0/c060/man/plot.sum.intsearc.Rd |only c060-0.4-0/c060/man/predictProb.coxnet.Rd | 70 c060-0.4-0/c060/man/stabpath.Rd | 141 - c060-0.4-0/c060/man/stabsel.Rd | 101 - c060-0.4-0/c060/man/summary.intsearch.Rd | 76 c060-0.4-0/c060/man/tune.glmnet.interval.Rd | 169 +- c060-0.4-0/c060/tests |only 52 files changed, 3003 insertions(+), 774 deletions(-)
Title: A Family of Beta Mixture Models for Clustering Beta-Valued DNA
Methylation Data
Description: A family of novel beta mixture models (BMMs) has been developed by Majumdar et al. (2022) <doi:10.48550/arXiv.2211.01938> to appositely model the beta-valued cytosine-guanine dinucleotide (CpG) sites, to objectively identify methylation state thresholds and to identify the differentially methylated CpG (DMC) sites using a model-based clustering approach. The family of beta mixture models employs different parameter constraints applicable to different study settings. The EM algorithm is used for parameter estimation, with a novel approximation during the M-step providing tractability and ensuring computational feasibility.
Author: Koyel Majumdar [aut, cre] ,
Romina Silva [aut],
Antoinette Sabrina Perry [aut],
Ronald William Watson [aut],
Andrea Rau [aut] ,
Florence Jaffrezic [aut],
Thomas Brendan Murphy [aut] ,
Isobel Claire Gormley [aut]
Maintainer: Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>
Diff between betaclust versions 1.0.4 dated 2024-09-24 and 1.0.5 dated 2025-09-19
DESCRIPTION | 23 ++- MD5 | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignettes.html | 294 +++++++++++++++++++++++------------------------- 5 files changed, 159 insertions(+), 166 deletions(-)
Title: An API Client for Australian Weather and Climate Data Resources
Description: Provides automated downloading, parsing and formatting of
weather data for Australia through API endpoints provided by the
Department of Primary Industries and Regional Development (DPIRD) of
Western Australia and by the Science and Technology Division of the
Queensland Government's Department of Environment and Science (DES).
As well as the Bureau of Meteorology (BOM) of the Australian
government precis and coastal forecasts,
and downloading and importing radar and satellite imagery files.
DPIRD weather data are accessed through public APIs provided by
DPIRD, <https://www.dpird.wa.gov.au/online-tools/apis/>, providing
access to weather station data from the DPIRD weather station
network. Australia-wide weather data are based on data from the
Australian Bureau of Meteorology (BOM) data and accessed through
SILO (Scientific Information for Land Owners) Jeffrey et al. (2001)
<doi:10.1016/S1364-8152(01)00008-1>. DPIRD data are made available
under a Creative Commons Attribut [...truncated...]
Author: Rodrigo Pires [aut, cre] ,
Anna Hepworth [aut] ,
Rebecca O'Leary [aut],
Jonathan Carroll [aut] ,
James Goldie [aut] ,
Dean Marchiori [aut] ,
Paul Melloy [aut] ,
Mark Padgham [aut] ,
Hugh Parsonage [aut] ,
Keith Pembleton [ctb] ,
Maelle Salmon [ctb] . [...truncated...]
Maintainer: Rodrigo Pires <rodrigo.pires@dpird.wa.gov.au>
This is a re-admission after prior archival of version 2.0.1 dated 2025-04-16
Diff between weatherOz versions 2.0.1 dated 2025-04-16 and 2.0.2 dated 2025-09-19
DESCRIPTION | 108 ++++++++++++++-------------- MD5 | 88 +++++++++++----------- NAMESPACE | 4 + NEWS.md | 28 +++++++ R/data.R | 6 - R/find_nearby_stations.R | 6 - R/find_stations_in.R | 2 R/get_ag_bulletin.R | 4 - R/get_dpird_apsim.R | 2 R/get_dpird_availability.R | 2 R/get_dpird_extremes.R | 2 R/get_dpird_minute.R | 2 R/get_dpird_summaries.R | 2 R/get_key.R | 2 R/get_radar_imagery.R | 1 R/get_satellite_imagery.R | 1 R/get_stations_metadata.R | 2 R/internal_functions.R | 1 R/query_dpird_api.R | 2 README.md | 14 +-- inst/doc/use_case.Rmd | 2 inst/doc/use_case.html | 14 +-- inst/doc/weatherOz.Rmd | 2 inst/doc/weatherOz.html | 15 ++- inst/doc/weatherOz_for_BOM.html | 5 - inst/doc/weatherOz_for_DPIRD.html | 5 - inst/doc/weatherOz_for_SILO.html | 5 - man/dpird_extreme_weather_values.Rd | 2 man/dpird_minute_values.Rd | 2 man/dpird_summary_values.Rd | 2 man/find_nearby_stations.Rd | 4 - man/find_stations_in.Rd | 2 man/get_ag_bulletin.Rd | 6 - man/get_dpird_apsim.Rd | 2 man/get_dpird_availability.Rd | 2 man/get_dpird_extremes.Rd | 2 man/get_dpird_minute.Rd | 2 man/get_dpird_summaries.Rd | 2 man/get_stations_metadata.Rd | 2 man/weatherOz-package.Rd | 2 tests/testthat/test-find_stations_in.R | 6 + tests/testthat/test-get_stations_metadata.R | 3 vignettes/use_case.Rmd | 2 vignettes/weatherOz.Rmd | 2 vignettes/weatherOz.Rmd.orig | 2 45 files changed, 203 insertions(+), 171 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.15.1 dated 2024-11-22 and 0.16.0 dated 2025-09-19
progressr-0.15.1/progressr/inst/doc/progressr-intro.html |only progressr-0.15.1/progressr/inst/doc/progressr-intro.md |only progressr-0.15.1/progressr/vignettes/progressr-intro.md |only progressr-0.16.0/progressr/DESCRIPTION | 14 - progressr-0.16.0/progressr/MD5 | 116 ++++++---- progressr-0.16.0/progressr/NAMESPACE | 2 progressr-0.16.0/progressr/NEWS.md | 31 ++ progressr-0.16.0/progressr/R/delays.R | 28 ++ progressr-0.16.0/progressr/R/global_progression_handler.R | 2 progressr-0.16.0/progressr/R/handler_cli.R | 3 progressr-0.16.0/progressr/R/handler_pbmcapply.R | 3 progressr-0.16.0/progressr/R/handler_progress.R | 3 progressr-0.16.0/progressr/R/handler_slowdown.R |only progressr-0.16.0/progressr/R/handler_tkprogressbar.R | 5 progressr-0.16.0/progressr/R/handler_txtprogressbar.R | 3 progressr-0.16.0/progressr/R/handler_winprogressbar.R | 8 progressr-0.16.0/progressr/R/handlers.R | 2 progressr-0.16.0/progressr/R/make_progression_handler.R | 5 progressr-0.16.0/progressr/R/progressr-package.R | 57 ++-- progressr-0.16.0/progressr/R/rstudio-console.R |only progressr-0.16.0/progressr/R/vignette_engine.R | 1 progressr-0.16.0/progressr/R/zzz.R | 6 progressr-0.16.0/progressr/build/vignette.rds |binary progressr-0.16.0/progressr/inst/WORDLIST | 27 +- progressr-0.16.0/progressr/inst/doc/progressr-01-intro.html |only progressr-0.16.0/progressr/inst/doc/progressr-01-intro.md |only progressr-0.16.0/progressr/inst/doc/progressr-11-handlers.html |only progressr-0.16.0/progressr/inst/doc/progressr-11-handlers.md |only progressr-0.16.0/progressr/inst/doc/progressr-21-map-reduce.html |only progressr-0.16.0/progressr/inst/doc/progressr-21-map-reduce.md |only progressr-0.16.0/progressr/inst/doc/progressr-22-parallel-processing.html |only progressr-0.16.0/progressr/inst/doc/progressr-22-parallel-processing.md |only progressr-0.16.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.html |only progressr-0.16.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.md |only progressr-0.16.0/progressr/inst/doc/progressr-29-debug.html |only progressr-0.16.0/progressr/inst/doc/progressr-29-debug.md |only progressr-0.16.0/progressr/inst/doc/progressr-31-knitr.html |only progressr-0.16.0/progressr/inst/doc/progressr-31-knitr.md |only progressr-0.16.0/progressr/inst/doc/progressr-91-appendix.html |only progressr-0.16.0/progressr/inst/doc/progressr-91-appendix.md |only progressr-0.16.0/progressr/man/figures/handler_cli-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_cli-format-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-adjust-mid.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-adjust-right-complete.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbcol-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_pbmcapply-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-complete.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-format-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_progress-format-2.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char-ansi.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char-width-2.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-char.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-default.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-style-1.svg | 2 progressr-0.16.0/progressr/man/figures/handler_txtprogressbar-style-3.svg | 2 progressr-0.16.0/progressr/man/handler_cli.Rd | 3 progressr-0.16.0/progressr/man/handler_pbmcapply.Rd | 3 progressr-0.16.0/progressr/man/handler_progress.Rd | 3 progressr-0.16.0/progressr/man/handler_slowdown.Rd |only progressr-0.16.0/progressr/man/handler_tkprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handler_txtprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handler_winprogressbar.Rd | 3 progressr-0.16.0/progressr/man/handlers.Rd | 10 progressr-0.16.0/progressr/man/make_progression_handler.Rd | 3 progressr-0.16.0/progressr/man/progressr.Rd | 59 ++--- progressr-0.16.0/progressr/vignettes/progressr-01-intro.md |only progressr-0.16.0/progressr/vignettes/progressr-11-handlers.md |only progressr-0.16.0/progressr/vignettes/progressr-21-map-reduce.md |only progressr-0.16.0/progressr/vignettes/progressr-22-parallel-processing.md |only progressr-0.16.0/progressr/vignettes/progressr-25-replace-cli-with-progressr.md |only progressr-0.16.0/progressr/vignettes/progressr-29-debug.md |only progressr-0.16.0/progressr/vignettes/progressr-31-knitr.md |only progressr-0.16.0/progressr/vignettes/progressr-91-appendix.md |only 74 files changed, 280 insertions(+), 158 deletions(-)
Title: Experimental Data of Cascade Experiments in Genomics
Description: These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between CascadeData versions 1.5 dated 2025-08-21 and 1.6 dated 2025-09-19
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/CascadeData-package.R | 2 +- README.md | 4 +++- inst/CITATION | 4 +++- man/CascadeData-package.Rd | 2 +- tests/testthat.R | 1 - 8 files changed, 28 insertions(+), 20 deletions(-)
Title: Selection, Reverse-Engineering and Prediction in Cascade
Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Laurent Vallat [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Cascade versions 2.2 dated 2025-08-20 and 2.3 dated 2025-09-19
DESCRIPTION | 16 ++--- MD5 | 14 ++--- NEWS.md | 10 +++ R/Cascade-package.R | 2 README.md | 137 +++++++++++++++++++++---------------------------- inst/CITATION | 19 ++++++ inst/_pkgdown.yml | 3 + man/Cascade-package.Rd | 2 8 files changed, 108 insertions(+), 95 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.0.2-1 dated 2025-09-08 and 15.0.2-2 dated 2025-09-19
RcppArmadillo-15.0.2-1/RcppArmadillo/man/armadillo_set_seed_random.Rd |only RcppArmadillo-15.0.2-2/RcppArmadillo/ChangeLog | 30 +++ RcppArmadillo-15.0.2-2/RcppArmadillo/DESCRIPTION | 8 - RcppArmadillo-15.0.2-2/RcppArmadillo/MD5 | 39 ++-- RcppArmadillo-15.0.2-2/RcppArmadillo/R/RcppExports.R | 33 +--- RcppArmadillo-15.0.2-2/RcppArmadillo/README.md | 5 RcppArmadillo-15.0.2-2/RcppArmadillo/configure | 18 +- RcppArmadillo-15.0.2-2/RcppArmadillo/configure.ac | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/NEWS.Rd | 11 + RcppArmadillo-15.0.2-2/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-15.0.2-2/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/RcppArmadillo/interface/RcppArmadilloForward.h | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/RcppArmadillo/version/arma.h | 14 + RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/diskio_bones.hpp | 3 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/diskio_meat.hpp | 79 ++++++---- RcppArmadillo-15.0.2-2/RcppArmadillo/inst/include/current/armadillo_bits/glue_hist_meat.hpp | 2 RcppArmadillo-15.0.2-2/RcppArmadillo/inst/skeleton/Makevars | 16 -- RcppArmadillo-15.0.2-2/RcppArmadillo/inst/skeleton/Makevars.win | 16 -- RcppArmadillo-15.0.2-2/RcppArmadillo/man/armadillo_set_seed.Rd | 42 ++--- RcppArmadillo-15.0.2-2/RcppArmadillo/man/armadillo_version.Rd | 19 +- RcppArmadillo-15.0.2-2/RcppArmadillo/src/RcppArmadillo.cpp | 36 +--- 21 files changed, 191 insertions(+), 184 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, [...truncated...]
Author: Liam J. Revell [aut, cre]
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 2.4-4 dated 2025-01-07 and 2.5-2 dated 2025-09-19
DESCRIPTION | 8 - MD5 | 49 ++++++----- NAMESPACE | 20 +++- R/bounded_bm.R | 19 +++- R/cladebox.R |only R/ctt.R | 10 +- R/fitMk.parallel.R | 4 R/fitPagel.R | 17 +++- R/fitThresh.R | 199 ++++++++++++++++++++++++++++++++++++++++-------- R/fitcontMk.R |only R/fitgammaMk.R | 85 ++++++++++++++++++++ R/fitmultiBM.R | 37 ++++++-- R/fitmultiTrend.R |only R/phenogram.R | 17 ---- R/sim_absorbing.R |only R/utilities.R | 17 ---- man/bmPlot.Rd | 40 ++++++--- man/bounded_bm.Rd | 4 man/cladelabels.Rd | 7 + man/fitMk.Rd | 4 man/fitThresh.Rd | 11 +- man/fitcontMk.Rd |only man/fitmultiBM.Rd | 12 +- man/genSeq.Rd | 2 man/phytools-package.Rd | 2 man/plotSimmap.Rd | 2 man/reorderSimmap.Rd | 2 man/setMap.Rd | 2 28 files changed, 426 insertions(+), 144 deletions(-)
Title: Multiple Geometric Shape Point Layer for 'ggplot2'
Description: To create the multiple polygonal point layer for easily discernible shapes,
we developed the package, it is like the 'geom_point' of 'ggplot2'.
It can be used to draw the scatter plot.
Author: Shuangbin Xu [aut, cre]
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Diff between ggstar versions 1.0.4 dated 2022-11-08 and 1.0.6 dated 2025-09-19
DESCRIPTION | 16 MD5 | 42 - NAMESPACE | 11 NEWS.md | 15 R/draw-key.R | 4 R/geom-star.R | 14 R/geom_star_interactive.R |only R/import.R |only R/primitive.R | 25 R/scale-identity.R | 2 R/scale-interactive.R |only R/scale-manual.R | 74 ++ R/scale-starshape.R | 5 build/vignette.rds |binary inst/doc/ggstar.R | 41 + inst/doc/ggstar.Rmd | 33 + inst/doc/ggstar.html | 1038 ++++++++++++++++++++++++++++++++++++- man/GeomInteractiveStar.Rd |only man/geom_star.Rd | 66 +- man/geom_star_interactive.Rd |only man/scale_manual.Rd | 44 + man/scale_starshape.Rd | 23 man/scale_starshape_identity.Rd | 33 - man/scale_starshape_interactive.Rd |only vignettes/ggstar.Rmd | 33 + 25 files changed, 1388 insertions(+), 131 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.5.0 dated 2025-07-08 and 0.5.1 dated 2025-09-19
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ R/compute.ci.R | 7 ++++++- R/fwb.R | 2 +- R/set_fwb_wtype.R | 2 +- R/utils.R | 8 ++------ R/vcovFWB.R | 6 +++--- R/weighted-statistics.R | 2 +- README.md | 1 + build/stage23.rdb |binary build/vignette.rds |binary inst/doc/fwb-rep.html | 5 +++-- man/fwb.Rd | 2 +- man/set_fwb_wtype.Rd | 2 +- man/vcovFWB.Rd | 6 +++--- man/w_mean.Rd | 2 +- 17 files changed, 49 insertions(+), 42 deletions(-)
Title: Harness ArcGIS Data Services
Description: Enables users of 'ArcGIS Enterprise', 'ArcGIS Online', or
'ArcGIS Platform' to read, write, publish, or manage vector and raster
data via ArcGIS location services REST API endpoints
<https://developers.arcgis.com/rest/>.
Author: Josiah Parry [aut, cre] ,
Eli Pousson [ctb] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Antony Barja [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgislayers versions 0.4.0 dated 2025-04-15 and 0.5.0 dated 2025-09-19
arcgislayers-0.4.0/arcgislayers/R/arc-add-update-delete.R |only arcgislayers-0.4.0/arcgislayers/man/list_service_raster_fns.Rd |only arcgislayers-0.5.0/arcgislayers/DESCRIPTION | 40 arcgislayers-0.5.0/arcgislayers/MD5 | 81 - arcgislayers-0.5.0/arcgislayers/NAMESPACE | 5 arcgislayers-0.5.0/arcgislayers/NEWS.md | 34 arcgislayers-0.5.0/arcgislayers/R/add_item.R | 11 arcgislayers-0.5.0/arcgislayers/R/arc-add-delete.R |only arcgislayers-0.5.0/arcgislayers/R/arc-definition.R |only arcgislayers-0.5.0/arcgislayers/R/arc-open.R | 190 ++-- arcgislayers-0.5.0/arcgislayers/R/arc-raster.R | 2 arcgislayers-0.5.0/arcgislayers/R/arc-read.R | 24 arcgislayers-0.5.0/arcgislayers/R/arc-select.R | 180 +-- arcgislayers-0.5.0/arcgislayers/R/attachments.R | 7 arcgislayers-0.5.0/arcgislayers/R/print-methods.R | 8 arcgislayers-0.5.0/arcgislayers/R/raster-fns.R | 26 arcgislayers-0.5.0/arcgislayers/R/update-attachments.R |only arcgislayers-0.5.0/arcgislayers/R/update-features.R |only arcgislayers-0.5.0/arcgislayers/R/utils-feature-server.R | 8 arcgislayers-0.5.0/arcgislayers/R/utils-validation.R |only arcgislayers-0.5.0/arcgislayers/R/utils.R | 52 - arcgislayers-0.5.0/arcgislayers/man/arc_open.Rd | 30 arcgislayers-0.5.0/arcgislayers/man/arc_raster.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/arc_read.Rd | 4 arcgislayers-0.5.0/arcgislayers/man/arc_select.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/attachments.Rd | 5 arcgislayers-0.5.0/arcgislayers/man/definition.Rd |only arcgislayers-0.5.0/arcgislayers/man/encode_field_values.Rd | 7 arcgislayers-0.5.0/arcgislayers/man/figures/README-unnamed-chunk-7-1.png |only arcgislayers-0.5.0/arcgislayers/man/get_layer.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/get_layer_estimates.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/modify.Rd | 35 arcgislayers-0.5.0/arcgislayers/man/raster_fns.Rd |only arcgislayers-0.5.0/arcgislayers/man/truncate_layer.Rd | 2 arcgislayers-0.5.0/arcgislayers/man/update_attachments.Rd |only arcgislayers-0.5.0/arcgislayers/tests/testthat.R | 8 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-adding-features.R | 22 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_open.R | 97 ++ arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_read.R | 1 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-arc_select.R | 8 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-attachments.R | 4 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-definition.R |only arcgislayers-0.5.0/arcgislayers/tests/testthat/test-delete-feats.R |only arcgislayers-0.5.0/arcgislayers/tests/testthat/test-encode-field-values.R | 459 +++++++++- arcgislayers-0.5.0/arcgislayers/tests/testthat/test-page-size.R | 4 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-raster-fns.R | 5 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-return-geometry.R | 2 arcgislayers-0.5.0/arcgislayers/tests/testthat/test-returned-fields.R | 5 48 files changed, 972 insertions(+), 402 deletions(-)
Title: Una implementación de funciones de uso interno
Description: Una herramienta rápida y consistente para la disposición de
microdatos y la visualización de las cifras y estadísticas oficiales
de la Universidad Nacional de Colombia <https://unal.edu.co>. Contiene
una biblioteca de funciones gráficas, tanto estáticas como
interactivas, que ofrece numerosos tipos de gráficos con una sintaxis
altamente configurable y simple. Entre estos encontramos la
visualización de tablas HTML, series, gráficos de barras y circulares,
mapas, etc. Todo lo anterior apoyado en bibliotecas de JavaScript.
English: A fast and consistent tool for the arrangement of microdata
and the visualization of official figures and statistics from the
National University of Colombia <https://unal.edu.co>. It includes a
library of graphical functions, both static and interactive, offering
numerous types of charts with a highly configurable and simple syntax.
Among these, we find the visualization of HTML tables, series, bar and
pie charts, maps, etc. It provides the capabi [...truncated...]
Author: Jeison Alarcon [aut, cre, ctr] ,
Alberto Rodriguez [aut, rev],
Direccion Nacional de Planeacion y Estadistica Universidad Nacional de
Colombia [cph, fnd]
Maintainer: Jeison Alarcon <jmalarconbe@unal.edu.co>
Diff between UnalR versions 1.0.0 dated 2024-05-25 and 1.0.1 dated 2025-09-18
UnalR-1.0.0/UnalR/man/figures/PlotExample1.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample10.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample2.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample3.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample4.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample5.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample6.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample7.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample8.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample9.PNG |only UnalR-1.0.0/UnalR/man/figures/lifecycle-deprecated.svg |only UnalR-1.0.1/UnalR/DESCRIPTION | 78 UnalR-1.0.1/UnalR/MD5 | 75 UnalR-1.0.1/UnalR/NAMESPACE | 218 +- UnalR-1.0.1/UnalR/NEWS.md | 9 UnalR-1.0.1/UnalR/R/Auxiliares.R | 2 UnalR-1.0.1/UnalR/R/Plot_Boxplot.R | 601 ++++-- UnalR-1.0.1/UnalR/R/Plot_Mapa.R | 1628 ++++++++++++----- UnalR-1.0.1/UnalR/R/Plot_Mundo.R | 845 ++++++-- UnalR-1.0.1/UnalR/R/Plot_Series.R | 4 UnalR-1.0.1/UnalR/README.md | 61 UnalR-1.0.1/UnalR/man/Agregar.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Apiladas.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Barras.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Boxplot.Rd | 10 UnalR-1.0.1/UnalR/man/Plot.Drilldown.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Mapa.Rd | 16 UnalR-1.0.1/UnalR/man/Plot.Mundo.Rd | 32 UnalR-1.0.1/UnalR/man/Plot.Radar.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Series.Rd | 8 UnalR-1.0.1/UnalR/man/Plot.Torta.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Treemap.Rd | 6 UnalR-1.0.1/UnalR/man/StaticPlot.Rd | 2 UnalR-1.0.1/UnalR/man/Tabla.General.Rd | 4 UnalR-1.0.1/UnalR/man/Tabla.Rd | 6 UnalR-1.0.1/UnalR/man/ejConsolidadoGrad.Rd | 2 UnalR-1.0.1/UnalR/man/ejConsolidadoSaberPro2019.Rd | 2 UnalR-1.0.1/UnalR/man/ejGraduados.Rd | 2 UnalR-1.0.1/UnalR/man/ejMiniAspirantesPre.Rd | 2 UnalR-1.0.1/UnalR/man/ejMiniConsolidadoAsp.Rd | 2 UnalR-1.0.1/UnalR/man/ejSaberPro2020.Rd | 2 UnalR-1.0.1/UnalR/man/read_example.Rd | 2 UnalR-1.0.1/UnalR/tests/testthat.R | 10 UnalR-1.0.1/UnalR/tests/testthat/test-Plot_Series.R | 3 44 files changed, 2606 insertions(+), 1044 deletions(-)
Title: Multiple-Instance Logistic Regression with LASSO Penalty
Description: The multiple instance data set consists of many independent
subjects (called bags) and each subject is composed of several components
(called instances). The outcomes of such data set are binary or categorical responses,
and, we can only observe the subject-level outcomes. For example, in manufacturing
processes, a subject is labeled as "defective" if at least one of its own
components is defective, and otherwise, is labeled as "non-defective". The
'milr' package focuses on the predictive model for the multiple instance
data set with binary outcomes and performs the maximum likelihood estimation
with the Expectation-Maximization algorithm under the framework of logistic
regression. Moreover, the LASSO penalty is attached to the likelihood function
for simultaneous parameter estimation and variable selection.
Author: Ping-Yang Chen [aut, cre],
ChingChuan Chen [aut],
Chun-Hao Yang [aut],
Sheng-Mao Chang [aut]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>
Diff between milr versions 0.3.1 dated 2020-10-31 and 0.4.1 dated 2025-09-18
milr-0.3.1/milr/tests |only milr-0.4.1/milr/DESCRIPTION | 12 milr-0.4.1/milr/MD5 | 30 milr-0.4.1/milr/R/milr-package.R | 5 milr-0.4.1/milr/R/milr.R | 2 milr-0.4.1/milr/build/vignette.rds |binary milr-0.4.1/milr/inst/doc/milr-intro.R | 12 milr-0.4.1/milr/inst/doc/milr-intro.html | 1176 ++++++++++++++++++++----------- milr-0.4.1/milr/man/milr-package.Rd | 19 milr-0.4.1/milr/man/milr.Rd | 2 milr-0.4.1/milr/src/Makevars | 2 milr-0.4.1/milr/src/RcppExports.cpp | 5 milr-0.4.1/milr/src/common.cpp | 3 milr-0.4.1/milr/vignettes/musk1norm.svm | 954 ++++++++++++------------- 14 files changed, 1306 insertions(+), 916 deletions(-)
Title: Network Meta-Analysis Based on Multivariate Meta-Analysis and
Meta-Regression Models
Description: Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2025) <doi:10.1101/2025.09.15.25335823>). Comprehensive analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available through simple commands. For inconsistency assessment, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model are available. In addition, the side-splitting methods and Jackson's random inconsistency model can be applied. Standard graphical tools for network meta-analysis, including network plots, ranked forest plots, and transitivity analyses, are also provided. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) <doi:10.1002/jrsm.1652> <doi:10.1002/jrsm.1651>) are adopted as the default methods.
Author: Hisashi Noma [aut, cre] ,
Kazushi Maruo [aut],
Shiro Tanaka [aut],
Toshi A. Furukawa [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between NMA versions 1.4-3 dated 2024-05-17 and 2.1-1 dated 2025-09-18
DESCRIPTION | 22 ++++--- MD5 | 86 ++++++++++++++++------------ NAMESPACE | 3 + NEWS.md | 5 + R/global.ict.r | 2 R/local.ict.r | 2 R/netplot.r | 2 R/nmaforest.r | 4 - R/nmaleague.r | 2 R/nmaweight.r | 2 R/obj.forest.r | 4 - R/pairwise.r | 150 ++++++++++++++++++++++++++++++++++++++++++++++++-- R/random.icm.r | 47 +++++++++++++++ R/setup.r | 114 +++++++++++++++++++++++++++++++++++--- R/sidesplit.r | 2 R/trans.armdata.r |only R/trans.armdataP.r |only build/partial.rdb |binary data/exdataMD.RData |only data/exdataP.RData |only data/exdataRR.RData |only data/woods1.RData |only data/woods2.RData |only man/NMA-package.Rd | 10 ++- man/antidiabetic.Rd | 2 man/diabetes.Rd | 2 man/exdataMD.Rd |only man/exdataP.Rd |only man/exdataRR.Rd |only man/global.ict.Rd | 4 + man/heartfailure.Rd | 2 man/local.ict.Rd | 4 - man/netplot.Rd | 4 - man/nma.Rd | 4 - man/nmaQ.Rd | 4 - man/nmafunnel.Rd | 4 - man/nmaleague.Rd | 10 ++- man/nmarank.Rd | 6 +- man/nmareg.Rd | 4 - man/nmaweight.Rd | 2 man/obj.forest.Rd | 4 - man/pairwise.Rd | 13 +++- man/random.icm.Rd | 6 +- man/setup.Rd | 39 ++++++++++--- man/sidesplit.Rd | 4 - man/smoking.Rd | 2 man/trans.armdata.Rd |only man/trans.armdataP.Rd |only man/transitivity.Rd | 4 + man/woods1.Rd |only man/woods2.Rd |only 51 files changed, 459 insertions(+), 122 deletions(-)
Title: Custom 'MetaphoneBR' Phonetic Encoding for Brazilian Names
Description: Simplifies Brazilian names phonetically using a custom 'metaphoneBR' algorithm that preserves ending vowels.
Useful for name matching processing preserving gender information carried generally by ending vowels in Portuguese.
Mation (2025) <doi:10.6082/uchicago.15104>.
Author: Rodrigo Borges [aut, cre] ,
Lucas Mation [aut] ,
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rodrigo Borges <rodrigoesborges@gmail.com>
Diff between metaphonebr versions 0.0.4 dated 2025-07-17 and 0.0.5 dated 2025-09-18
DESCRIPTION | 13 +++---------- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 14 ++++++++++---- man/metaphonebr-package.Rd | 1 - 5 files changed, 21 insertions(+), 19 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 0.6.2 dated 2025-08-28 and 0.7.0 dated 2025-09-18
DESCRIPTION | 6 MD5 | 35 NEWS.md | 10 R/prm.R | 1072 ++++++++--------- R/run_app.R | 70 - R/zzz-deps.R | 14 R/zzz.R | 20 README.md | 65 - inst/CITATION | 32 inst/app/app.R | 2408 +++++++++++++++++++++++++++------------- inst/doc/introduction.Rmd | 394 +++--- inst/doc/introduction.html | 118 + inst/extdata/app_V3.R |only inst/extdata/test.R | 94 - 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 | 394 +++--- 19 files changed, 3117 insertions(+), 2097 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Christophe Dutang [ctb] ,
Reinhold Kainhofer [ctb] ,
Kevin J Owens [ctb],
Ernesto Schirmacher [ctb],
Gian Paolo Clemente [ctb] ,
Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.3.12 dated 2024-09-29 and 1.4.3 dated 2025-09-18
lifecontingencies-1.3.12/lifecontingencies/man/AExn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/DAxn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/IAxn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/axn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/axn_1.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/pureendowment.Rd |only lifecontingencies-1.4.3/lifecontingencies/DESCRIPTION | 21 lifecontingencies-1.4.3/lifecontingencies/MD5 | 60 - lifecontingencies-1.4.3/lifecontingencies/NEWS.md | 448 +++++----- lifecontingencies-1.4.3/lifecontingencies/R/2_commonMethods.R | 22 lifecontingencies-1.4.3/lifecontingencies/R/5_actuarialFunctions.R | 235 ++++- lifecontingencies-1.4.3/lifecontingencies/README.md | 6 lifecontingencies-1.4.3/lifecontingencies/build/vignette.rds |binary lifecontingencies-1.4.3/lifecontingencies/data/AF92Lt.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/AM92Lt.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/SoAISTdata.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/de_angelis_di_falco.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoCanada.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoChina.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoFrance.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoGermany.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoIta.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoJapan.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoUk.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoUsa.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soa08.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soa08Act.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soaLt.rda |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/PensionPlanVal.html | 13 lifecontingencies-1.4.3/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/compute-detail.html | 7 lifecontingencies-1.4.3/lifecontingencies/inst/doc/mortality_projection.pdf |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/pensionfunding.html | 11 lifecontingencies-1.4.3/lifecontingencies/man/arithmetic_variation_insurances.Rd |only lifecontingencies-1.4.3/lifecontingencies/man/endowment_trio.Rd |only 35 files changed, 485 insertions(+), 338 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: Designs for Computer Experimentations
Description: In computer experiments space-filling designs are having great impact. Most popularly used space-filling designs are Uniform designs (UDs), Latin hypercube designs (LHDs) etc. For further references one can see Mckay (1979) <DOI:10.1080/00401706.1979.10489755> and Fang (1980) <https://cir.nii.ac.jp/crid/1570291225616774784>. In this package, we have provided algorithms for generate efficient LHDs and UDs. Here, generated LHDs are efficient as they possess lower value of Maxpro measure, Phi_p value and Maximum Absolute Correlation (MAC) value based on the weightage given to each criterion. On the other hand, the produced UDs are having good space-filling property as they always attain the lower bound of Discrete Discrepancy measure. Further, some useful functions added in this package for adding more value to this package.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between CompExpDes versions 1.0.8 dated 2025-07-25 and 1.0.9 dated 2025-09-18
DESCRIPTION | 6 MD5 | 12 - NAMESPACE | 3 R/wtLHDs.R | 484 ++++++++++++++++++++++++++++++++-------------------- R/wtLHDs_prime.R | 462 +++++++++++++++++++++++++++++++++++++------------ man/wtLHDs.Rd | 8 man/wtLHDs_prime.Rd | 6 7 files changed, 674 insertions(+), 307 deletions(-)
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Description: Estimate haplotypic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.
Author: David Gerard [aut, cre]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between ldsep versions 2.1.5 dated 2022-10-18 and 2.1.6 dated 2025-09-18
DESCRIPTION | 14 MD5 | 128 +-- NAMESPACE | 46 - NEWS.md | 4 R/RcppExports.R | 26 R/data.R | 120 +-- R/fast.R | 748 +++++++++---------- R/generics.R | 400 +++++----- R/ldgeno.R | 1396 ++++++++++++++++++------------------ R/ldsep-package.R | 53 - R/maxd.R | 414 +++++----- R/mds.R | 180 ++-- R/mom.R | 1098 ++++++++++++++-------------- R/multild.R | 896 +++++++++++------------ R/sliding_window.R | 178 ++-- README.md | 254 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fast.R | 8 inst/doc/fast.Rmd | 6 inst/doc/fast.html | 174 ++-- inst/doc/vcf.R | 94 +- inst/doc/vcf.Rmd | 10 inst/doc/vcf.html | 365 ++++----- inst/extdata/subuit.vcf | 1164 +++++++++++++++--------------- man/Dprime.Rd | 104 +- man/format_lddf.Rd | 102 +- man/get_prob_array.Rd | 64 - man/gl_to_gp.Rd | 66 - man/glike.Rd | 60 - man/gp.Rd | 60 - man/is.lddf.Rd | 52 - man/ldest.Rd | 570 +++++++------- man/ldest_comp.Rd | 310 +++---- man/ldest_hap.Rd | 382 ++++----- man/ldfast.Rd | 358 ++++----- man/ldsep-package.Rd | 71 - man/ldshrink.Rd | 76 - man/mldest.Rd | 340 ++++---- man/pbnorm_dist.Rd | 54 - man/plot.lddf.Rd | 178 ++-- man/pvcalc.Rd | 58 - man/slcor.Rd | 74 - man/sldest.Rd | 332 ++++---- man/uit.Rd | 54 - man/zshrink.Rd | 80 +- src/Makevars | 3 src/Makevars.win | 3 src/derivatives.cpp | 28 src/genolike.cpp | 6 src/utils.cpp | 2 tests/testthat.R | 8 tests/testthat/test-cube.R | 104 +- tests/testthat/test-derivatives.R | 750 +++++++++---------- tests/testthat/test-em_vs_grad.R | 98 +- tests/testthat/test-hessian.R | 290 +++---- tests/testthat/test-ld_from_gmat.R | 44 - tests/testthat/test-ldfast.R | 136 +-- tests/testthat/test-lp.R | 110 +- tests/testthat/test-multinomial.R | 92 +- tests/testthat/test-pbnorm.R | 80 +- tests/testthat/test-posteriormean.R | 366 ++++----- tests/testthat/test-problem_data.R | 212 ++--- vignettes/fast.Rmd | 6 vignettes/vcf.Rmd | 10 65 files changed, 6745 insertions(+), 6824 deletions(-)
Title: Data from the Ecuador Truth Commission
Description: Provides access to data collected by the Ecuadorian Truth Commission.
Allows users to extract and analyze systematized information for human rights
research in Ecuador. The package contains datasets documenting human rights
violations from 1984-2008, including victim information, violation types,
perpetrators, and geographic distribution.
Author: Adriana Robles [aut] ,
Javier Borja [aut, cre]
Maintainer: Javier Borja <javier@demografiando.pro>
Diff between verdadecu versions 0.2.0 dated 2025-08-21 and 1.0.0 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++++----- NEWS.md | 34 ++++++++++++++++++++++++++++++++++ README.md | 28 ++++++++++++++++++++++++++++ inst/CITATION | 4 ++-- inst/doc/verdadecu.html | 4 ++-- tests |only 7 files changed, 80 insertions(+), 13 deletions(-)
Title: Result Model Manager
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
Informatics programme. 'ResultModelManager' provides utility functions to allow package
maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Diff between ResultModelManager versions 0.5.11 dated 2024-09-19 and 0.6.0 dated 2025-09-18
DESCRIPTION | 13 - MD5 | 79 ++++++---- NAMESPACE | 19 -- NEWS.md | 15 ++ R/ConnectionHandler.R | 32 +--- R/DataMigrationManager.R | 25 ++- R/DataModel.R | 210 ++++++++++++++++++----------- R/PooledConnectionHandler.R | 11 - R/PyFunctions.R |only R/QueryNamespace.R | 17 +- R/ResultExportManager.R | 110 +++++++++------ R/ResultModelManager.R | 7 R/SchemaGenerator.R | 6 R/Utils.R | 4 README.md | 5 build/vignette.rds |binary inst/doc/CreatingMigrations.pdf |binary inst/doc/PackageDesign.pdf |binary inst/doc/UploadFunctionality.pdf |binary inst/doc/UsingAnExportManager.pdf |binary inst/doc/UsingConnectionHandlers.pdf |binary inst/doc/UsingPythonUploads.R |only inst/doc/UsingPythonUploads.Rmd |only inst/doc/UsingPythonUploads.pdf |only inst/doc/UsingQueryNamespaces.pdf |binary inst/pg_upload.py |only man/ConnectionHandler.Rd | 28 +-- man/DataMigrationManager.Rd | 16 +- man/QueryNamespace.Rd | 15 +- man/ResultExportManager.Rd | 10 + man/ResultModelManager-package.Rd | 2 man/disablePythonUploads.Rd |only man/enablePythonUploads.Rd |only man/install_psycopg2.Rd |only man/pyPgUploadEnabled.Rd |only man/pyUploadCsv.Rd |only man/pyUploadDataFrame.Rd |only tests/testthat/helper-packageMaintainer.R | 2 tests/testthat/test-ConnectionHandler.R | 10 - tests/testthat/test-DataMigrationManager.R | 13 - tests/testthat/test-DataModel.R | 46 +++--- tests/testthat/test-DataModelFunctions.R | 168 +++++++++++++++++++++++ tests/testthat/test-PooledConnection.R | 12 - tests/testthat/test-PyFunctions.R |only tests/testthat/test-QueryNamespace.R | 12 + tests/testthat/test-ResultExportManager.R | 14 + vignettes/UsingPythonUploads.Rmd |only 47 files changed, 600 insertions(+), 301 deletions(-)
More information about ResultModelManager at CRAN
Permanent link
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 0.1.1 dated 2025-08-27 and 0.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/ready_plots.R | 3 +-- R/utils_analysis.R | 1 - inst/doc/readyomics.html | 17 +++++++++-------- 6 files changed, 23 insertions(+), 20 deletions(-)
Title: Sample Size Calculation for the Proportional Hazards Mixture
Cure Model
Description: An R-package for calculating sample size of a survival trial with or without cure fractions.
Author: Chao Cai [aut, cre],
Songfeng Wang [aut],
Wenbin Lu [aut],
Jiajia Zhang [aut]
Maintainer: Chao Cai <caic@mailbox.sc.edu>
Diff between NPHMC versions 2.3 dated 2022-05-08 and 2.4.2 dated 2025-09-18
DESCRIPTION | 30 +++++++++++++++++++++++------- MD5 | 4 ++-- man/NPHMC-package.Rd | 2 +- 3 files changed, 26 insertions(+), 10 deletions(-)
Title: Approximate Optimal Transport Between Two-Dimensional Grids
Description: Can be used for optimal transport between two-dimensional grids with respect to separable cost functions of l^p form. It utilizes the Frank-Wolfe algorithm to approximate so-called pivot measures: One-dimensional transport plans that fully describe the full transport, see G. Auricchio (2023) <doi:10.4171/RLM/1026>. For these, it offers methods for visualization and to extract the corresponding transport plans and costs. Additionally, related functions for one-dimensional optimal transport are available.
Author: Michel Groppe [aut, cre],
Nicholas Bonneel [ctb],
Egervary Research Group on Combinatorial Optimization [cph]
Maintainer: Michel Groppe <michel.groppe@uni-goettingen.de>
Diff between gridOT versions 1.0.1 dated 2022-10-18 and 1.0.2 dated 2025-09-18
DESCRIPTION | 19 ++++++++++--------- MD5 | 13 +++++++------ R/gridOT-package.R | 10 ++++++---- R/transport_costmat.R | 10 +++++----- build |only man/gridOT-package.Rd | 12 +++++++----- src/Makevars | 6 +++--- src/Makevars.win | 6 +++--- 8 files changed, 41 insertions(+), 35 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.0 dated 2025-07-15 and 1.3.1 dated 2025-09-18
DESCRIPTION | 13 MD5 | 84 - NAMESPACE | 20 NEWS.md | 17 R/casting.R | 24 R/classAchillesTable.R | 3 R/classCdmReference.R | 50 - R/classCodelist.R | 6 R/classCohortTable.R | 5 R/classConceptSetExpression.R | 27 R/classOmopTable.R | 4 R/compute.R | 51 - R/importConceptSetExpression.R | 2 R/methodInsertTable.R | 7 R/omopDataFolder.R |only R/overwriteClasses.R | 99 + R/recordCohortAttrition.R | 17 R/sysdata.rda |binary R/validate.R | 10 build/vignette.rds |binary inst/doc/cdm_reference.Rmd | 2 inst/doc/codelists.Rmd | 2 inst/doc/cohorts.Rmd | 2 inst/doc/cohorts.html | 126 +- inst/doc/logging.html | 52 - inst/doc/summarised_result.R | 10 inst/doc/summarised_result.Rmd | 32 inst/doc/summarised_result.html | 1199 +++++++++++------------- inst/doc/suppression.R |only inst/doc/suppression.Rmd |only inst/doc/suppression.html |only man/emptyConceptSetExpression.Rd |only man/insertTable.Rd | 4 man/newConceptSetExpression.Rd | 6 man/omopDataFolder.Rd |only man/validateConceptSetArgument.Rd | 8 tests/testthat/test-assert.R | 12 tests/testthat/test-classCdmReference.R | 8 tests/testthat/test-classCodelist.R | 1 tests/testthat/test-classCohortTable.R | 2 tests/testthat/test-classConceptSetExpression.R | 7 tests/testthat/test-omopDataFolder.R |only vignettes/cdm_reference.Rmd | 2 vignettes/codelists.Rmd | 2 vignettes/cohorts.Rmd | 2 vignettes/summarised_result.Rmd | 32 vignettes/suppression.Rmd |only 47 files changed, 1019 insertions(+), 931 deletions(-)
Title: A Super K-Nearest Neighbor (SKNN) Classification Algorithm
Description: It's a Super K-Nearest Neighbor(SKNN) classification method with using kernel density to describe weight of the distance between a training observation and the testing sample. Comparison of performance between SKNN and KNN shows that SKNN is significantly superior to KNN.
Author: Yarong Yang [aut, cre],
Nader Ebrahimi [ctb],
Yoram Rubin [ctb],
Jacob Zhang [ctb]
Maintainer: Yarong Yang <Yi.YA_yaya@hotmail.com>
Diff between SKNN versions 4.1.1 dated 2025-09-09 and 4.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/PCAy.Rd | 2 +- man/PCAyd-class.Rd | 4 ++-- man/SKNN-package.Rd | 6 +++--- man/SKNN.Rd | 2 +- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.20.0 dated 2025-07-16 and 2.21 dated 2025-09-18
DESCRIPTION | 8 ++--- MD5 | 62 +++++++++++++++++++-------------------- NAMESPACE | 2 + NEWS.md | 25 +++++++++++++++ R/Attach.R | 19 ++++++++++- R/Design.R | 18 +++++++++-- R/PBA.R | 2 - R/RobbinsMonro.R | 2 - R/SimDesign.R | 1 R/SimExtract.R | 2 - R/SimShiny.R | 4 +- R/SimSolve.R | 3 + R/runArraySimulation.R | 29 +++++++++++------- R/runSimulation.R | 41 +++++++++++++++++++++---- inst/doc/Catch_errors.html | 27 +++++----------- inst/doc/Fixed_obj_fun.html | 10 +++--- inst/doc/HPC-computing.html | 4 +- inst/doc/MultipleAnalyses.html | 4 +- inst/doc/Parallel-computing.html | 4 +- inst/doc/Saving-results.html | 46 +++------------------------- inst/doc/SimDesign-intro.html | 42 +++++--------------------- man/Attach.Rd | 7 +++- man/PBA.Rd | 2 - man/RobbinsMonro.Rd | 2 - man/SimExtract.Rd | 2 - man/SimShiny.Rd | 4 +- man/SimSolve.Rd | 2 - man/createDesign.Rd | 12 ++++++- man/expandReplications.Rd | 2 - man/runArraySimulation.Rd | 2 - man/runSimulation.Rd | 20 +++++++++++- tests/tests/test-01-core.R | 26 ++++++++++++++++ 32 files changed, 256 insertions(+), 180 deletions(-)
Title: Holistic Multimodel Domain Analysis for Exploratory Machine
Learning
Description: Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological cond [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
This is a re-admission after prior archival of version 0.1 dated 2025-03-27
Diff between HMDA versions 0.1 dated 2025-03-27 and 0.1.1 dated 2025-09-18
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
Title: Discrete Statistical Distributions
Description: Implementation of new discrete statistical distributions. Each distribution includes the traditional functions as well as an additional function called the family function, which can be used to estimate parameters within the 'gamlss' framework.
Author: Freddy Hernandez-Barajas [aut, cre] ,
Fernando Marmolejo-Ramos [aut] ,
Olga Usuga-Manco [aut]
Maintainer: Freddy Hernandez-Barajas <fhernanb@unal.edu.co>
Diff between DiscreteDists versions 1.1.0 dated 2025-09-08 and 1.1.1 dated 2025-09-18
DiscreteDists-1.1.0/DiscreteDists/man/d1_dldm_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d1_vec_dldm_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d2_dldd_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d2_vec_dldd_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dCOMPO_single.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dCOMPO_vec.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dHYPERPO_single.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dHYPERPO_vec.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/f11_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/figures |only DiscreteDists-1.1.0/DiscreteDists/man/z_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/z_vec_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/src/dDMOLBE.cpp |only DiscreteDists-1.1.1/DiscreteDists/DESCRIPTION | 6 DiscreteDists-1.1.1/DiscreteDists/MD5 | 83 +++---- DiscreteDists-1.1.1/DiscreteDists/NAMESPACE | 11 DiscreteDists-1.1.1/DiscreteDists/NEWS.md | 2 DiscreteDists-1.1.1/DiscreteDists/R/DMOLBE.R | 83 ++++--- DiscreteDists-1.1.1/DiscreteDists/R/HYPERPO.R | 8 DiscreteDists-1.1.1/DiscreteDists/R/RcppExports.R | 100 -------- DiscreteDists-1.1.1/DiscreteDists/R/dDMOLBE.R | 21 - DiscreteDists-1.1.1/DiscreteDists/R/utils.R | 21 + DiscreteDists-1.1.1/DiscreteDists/inst/include |only DiscreteDists-1.1.1/DiscreteDists/man/AR.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/F11.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_DBH.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_DLD.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_POISXL.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_DGEII.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_DIKUM.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_GGEO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_HYPERPO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_HYPERPO2.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DBH.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DGEII.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DIKUM.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DLD.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_GGEO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_HYPERPO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_HYPERPO2.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_POISXL.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/obtaining_lambda.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/simulate_hp.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/stopping.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/src/RcppExports.cpp | 113 ++++------ DiscreteDists-1.1.1/DiscreteDists/src/dCOMPO.cpp | 57 ----- DiscreteDists-1.1.1/DiscreteDists/src/dDMOLBDE.cpp |only DiscreteDists-1.1.1/DiscreteDists/src/dHP.cpp | 67 ----- DiscreteDists-1.1.1/DiscreteDists/src/shared.cpp |only DiscreteDists-1.1.1/DiscreteDists/src/shared.h |only DiscreteDists-1.1.1/DiscreteDists/src/shared_inline.h |only 51 files changed, 207 insertions(+), 386 deletions(-)
Title: Visual Model Checking for Nonlinear Mixed Effect Model
Description: Various visual and numerical diagnosis methods for the nonlinear mixed effect model, including visual predictive checks, numerical predictive checks, and coverage plots (Karlsson and Holford, 2008, <https://www.page-meeting.org/?abstract=1434>).
Author: Eun-Kyung Lee [aut, cre],
Eun-Hwa Kang [aut]
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between nlmeVPC versions 2.6 dated 2022-12-22 and 2.8 dated 2025-09-18
DESCRIPTION | 10 +++++----- MD5 | 44 ++++++++++++++++++++++---------------------- R/BootVPC.R | 5 ++--- R/Misc.R | 24 ++++++++++++------------ R/NumericalCheck.R | 4 ---- R/VPCgraph.R | 6 ++---- R/aqrVPC.R | 5 ++--- R/asVPC.R | 8 +++----- R/coverage.R | 14 ++++++-------- R/coverageDetailplot.R | 4 +--- R/optK.R | 9 ++++----- R/quantVPC.R | 5 ++--- man/NumericalCheck.Rd | 2 -- man/VPCgraph.Rd | 4 +--- man/aqrVPC.Rd | 4 +--- man/asVPC.Rd | 7 ++----- man/bootVPC.Rd | 4 +--- man/coverageDetailplot.Rd | 4 +--- man/coverageplot.Rd | 5 +---- man/optK.Rd | 2 -- man/quantVPC.Rd | 4 +--- src/Makevars | 3 ++- src/Makevars.win | 2 +- 23 files changed, 72 insertions(+), 107 deletions(-)
Title: Construct Mixed Type Data Structures with Vectors of Vectors
Description: Mixed type vectors are useful for combining semantically similar classes. Some examples of semantically related classes include time across different granularities (e.g. daily, monthly, annual) and probability distributions (e.g. Normal, Uniform, Poisson). These groups of vector types typically share common statistical operations which vary in results with the attributes of each vector. The 'vecvec' data structure facilitates efficient storage and computation across multiple vectors within the same object.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vecvec versions 0.1.0 dated 2025-06-29 and 0.2.0 dated 2025-09-18
DESCRIPTION | 6 +++--- MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS.md |only R/vecvec.R | 34 +++++++++++++++++++++------------- R/vecvec_apply.R |only R/vecvec_math.R | 33 +++++++++++++++++++++++---------- R/zzz.R | 2 +- man/vecvec.Rd | 4 +++- man/vecvec_apply.Rd |only 10 files changed, 62 insertions(+), 34 deletions(-)
Title: Random Forest Prediction Decomposition and Feature Importance
Measure
Description: An R re-implementation of the 'treeinterpreter' package on PyPI
<https://pypi.org/project/treeinterpreter/>. Each prediction can be
decomposed as 'prediction = bias + feature_1_contribution + ... +
feature_n_contribution'. This decomposition is then used to calculate
the Mean Decrease Impurity (MDI) and Mean Decrease Impurity using
out-of-bag samples (MDI-oob) feature importance measures based on the
work of Li et al. (2019) <doi:10.48550/arXiv.1906.10845>.
Author: Qingyao Sun [aut, cre]
Maintainer: Qingyao Sun <sunqingyao19970825@gmail.com>
Diff between tree.interpreter versions 0.1.1 dated 2020-02-05 and 0.1.3 dated 2025-09-18
tree.interpreter-0.1.1/tree.interpreter/src/RcppExports-d25771d5.o.tmp |only tree.interpreter-0.1.3/tree.interpreter/DESCRIPTION | 18 tree.interpreter-0.1.3/tree.interpreter/MD5 | 21 tree.interpreter-0.1.3/tree.interpreter/README.md | 6 tree.interpreter-0.1.3/tree.interpreter/build/vignette.rds |binary tree.interpreter-0.1.3/tree.interpreter/configure | 4 tree.interpreter-0.1.3/tree.interpreter/inst/CITATION | 51 tree.interpreter-0.1.3/tree.interpreter/inst/doc/MDI.R | 2 tree.interpreter-0.1.3/tree.interpreter/inst/doc/MDI.html | 516 ++++------ tree.interpreter-0.1.3/tree.interpreter/src/Makevars.template | 13 tree.interpreter-0.1.3/tree.interpreter/src/Makevars.win | 13 tree.interpreter-0.1.3/tree.interpreter/vignettes/MDI.bib | 4 12 files changed, 306 insertions(+), 342 deletions(-)
More information about tree.interpreter at CRAN
Permanent link
Title: Transparent Assessment Framework for Reproducible Research
Description: General framework to organize data, methods, and results used in
reproducible scientific analyses. A TAF analysis consists of four scripts
(data.R, model.R, output.R, report.R) that are run sequentially. Each script
starts by reading files from a previous step and ends with writing out files
for the next step. Convenience functions are provided to version control the
required data and software, run analyses, clean residues from previous runs,
manage files, manipulate tables, and produce figures. With a focus on
stability and reproducible analyses, the TAF package comes with no
dependencies. TAF forms a base layer for the 'icesTAF' package and other
scientific applications.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Iago Mosqueira [aut],
Alexandros Kokkalis [ctb],
Ibrahim Umar [ctb],
Hjalte Parner [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between TAF versions 4.3.0 dated 2025-09-02 and 4.3.1 dated 2025-09-18
DESCRIPTION | 10 +++--- MD5 | 78 +++++++++++++++++++++++++-------------------------- NEWS.md | 7 ++++ R/div.R | 2 - R/download.R | 2 - R/make.R | 2 - R/make.all.R | 2 - R/make.taf.R | 2 - R/msg.R | 2 - R/pdeps.R | 2 - R/read.taf.R | 2 - R/rnd.R | 2 - R/source.all.R | 2 - R/source.dir.R | 2 - R/taf.boot.R | 2 - R/taf.boot.path.R | 2 - R/taf.data.path.R | 2 - R/taf.png.R | 2 - R/taf.unzip.R | 2 - R/wide2long.R | 12 +++++++ R/write.taf.R | 2 - R/zoom.R | 2 - man/div.Rd | 2 - man/download.Rd | 2 - man/make.Rd | 2 - man/make.all.Rd | 2 - man/make.taf.Rd | 2 - man/msg.Rd | 2 - man/pdeps.Rd | 2 - man/read.taf.Rd | 2 - man/rnd.Rd | 2 - man/source.all.Rd | 2 - man/source.dir.Rd | 2 - man/taf.boot.Rd | 2 - man/taf.boot.path.Rd | 2 - man/taf.data.path.Rd | 2 - man/taf.png.Rd | 2 - man/taf.unzip.Rd | 2 - man/write.taf.Rd | 2 - man/zoom.Rd | 2 - 40 files changed, 98 insertions(+), 81 deletions(-)
Title: Weighted Mean SHAP and CI for Robust Feature Assessment in ML
Grid
Description: This R package introduces Weighted Mean SHapley Additive exPlanations (WMSHAP), an innovative method for calculating SHAP values for a grid of fine-tuned base-learner machine learning models as well as stacked ensembles, a method not previously available due to the common reliance on single best-performing models. By integrating the weighted mean SHAP values from individual base-learners comprising the ensemble or individual base-learners in a tuning grid search, the package weights SHAP contributions according to each model's performance, assessed by multiple either R squared (for both regression and classification models). alternatively, this software also offers weighting SHAP values based on the area under the precision-recall curve (AUCPR), the area under the curve (AUC), and F2 measures for binary classifiers. It further extends this framework to implement weighted confidence intervals for weighted mean SHAP values, offering a more comprehensive and robust feature importance eval [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
This is a re-admission after prior archival of version 0.5 dated 2025-03-18
Diff between shapley versions 0.5 dated 2025-03-18 and 0.5.1 dated 2025-09-18
DESCRIPTION | 13 +++++------- MD5 | 14 ++++++------- NAMESPACE | 1 R/shapley.domain.R | 3 -- R/shapley.plot.R | 53 +++++++++++++++++++++++++------------------------- README.md | 12 +++++++---- man/shapley.domain.Rd | 1 man/shapley.plot.Rd | 1 8 files changed, 49 insertions(+), 49 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of Machine Learning
(ML) techniques as easy and accessible as possible, particularly within the framework of
the Knowledge Discovery in Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive or classification
modeling workflow, aligning closely with the fundamental steps of the KDD methodology,
from data selection and preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis. The 'MLwrap' workflow
is organized into four core steps; preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to data preparation and
transformation, model construction, hyperparameter optimization, and sensitivity analysis.
The user can access comprehensive model evaluation results including fit assessment metrics,
plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
This is a re-admission after prior archival of version 0.1.0 dated 2025-07-22
Diff between MLwrap versions 0.1.0 dated 2025-07-22 and 0.1.1 dated 2025-09-18
DESCRIPTION | 60 ++++++++++------------ MD5 | 80 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 11 ++-- R/InterpretableML.R | 16 +++--- R/SOBOL.R | 2 R/evaluate_model.R | 27 ++++++++++ R/fine_tuning.R | 6 +- R/model_creation.R | 4 - R/plotting_utils.R | 72 +++++++++++++-------------- R/results_binary_classification.R | 6 +- R/results_regression.R | 2 R/table_utils.R | 52 +++++++++---------- README.md | 20 +++---- man/build_model.Rd | 4 - man/fine_tuning.Rd | 6 +- man/plot_calibration_curve.Rd | 4 - man/plot_confusion_matrix.Rd | 4 - man/plot_distribution_by_class.Rd | 4 - man/plot_gain_curve.Rd | 4 - man/plot_graph_nn.Rd | 4 - man/plot_integrated_gradients.Rd | 4 - man/plot_lift_curve.Rd | 4 - man/plot_loss_curve.Rd | 4 - man/plot_olden.Rd | 4 - man/plot_pfi.Rd | 4 - man/plot_residuals_distribution.Rd | 4 - man/plot_roc_curve.Rd | 4 - man/plot_scatter_predictions.Rd | 4 - man/plot_scatter_residuals.Rd | 4 - man/plot_shap.Rd | 4 - man/plot_sobol_jansen.Rd | 4 - man/plot_tuning_results.Rd | 4 - man/sensitivity_analysis.Rd | 16 +++--- man/table_best_hyperparameters.Rd | 4 - man/table_evaluation_results.Rd | 4 - man/table_integrated_gradients_results.Rd | 4 - man/table_olden_results.Rd | 4 - man/table_pfi_results.Rd | 4 - man/table_shap_results.Rd | 4 - man/table_sobol_jansen_results.Rd | 4 - 41 files changed, 257 insertions(+), 225 deletions(-)
Title: Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Description: Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data.
Includes Cauchit, Compl. Log-Log, Logistic, and Probit link functions for Bernoulli Distributed RR data.
RR Designs: Warner, Forced Response, Unrelated Question, Kuk, Crosswise, and Triangular.
Reference: Fox, J-P, Veen, D. and Klotzke, K. (2018). Generalized Linear Mixed Models for Randomized Responses. Methodology. <doi:10.1027/1614-2241/a000153>.
Author: Jean-Paul Fox [aut, cre],
Konrad Klotzke [aut],
Duco Veen [aut]
Maintainer: Jean-Paul Fox <jpfox00@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2021-01-13
Diff between GLMMRR versions 0.5.0 dated 2021-01-13 and 0.6.0 dated 2025-09-18
DESCRIPTION | 24 + MD5 | 91 ++--- NAMESPACE | 96 ++--- R/ETHBE.R | 96 ++--- R/MTURK.R | 92 ++--- R/Plagiarism.R | 84 ++--- R/RRbinomial.R | 132 ++++---- R/RRglm.R | 8 R/RRglmGOF.R | 374 +++++++++++----------- R/RRglmer.R | 12 R/RRlink_cauchit.R | 52 +-- R/RRlink_cloglog.R | 52 +-- R/RRlink_logit.R | 52 +-- R/RRlink_probit.R | 52 +-- R/getMLPrevalence.R | 44 +- R/getRRparameters.R | 262 +++++++-------- R/plot.R | 658 ++++++++++++++++++++-------------------- R/print.R | 564 +++++++++++++++++----------------- R/residuals.R | 8 R/summary.R | 326 +++++++++---------- R/tools.R | 160 ++++----- README.md |only build/partial.rdb |binary man/Plagiarism.Rd | 106 +++--- man/RRbinomial.Rd | 52 +-- man/RRglm.Rd | 106 +++--- man/RRglmGOF.Rd | 80 ++-- man/RRglmer.Rd | 150 ++++----- man/RRlink.cauchit.Rd | 38 +- man/RRlink.cloglog.Rd | 38 +- man/RRlink.logit.Rd | 38 +- man/RRlink.probit.Rd | 38 +- man/getCellMeans.Rd | 42 +- man/getCellSizes.Rd | 42 +- man/getMLPrevalence.Rd | 46 +- man/getRRparameters.Rd | 42 +- man/getUniqueGroups.Rd | 34 +- man/intDotplot.Rd | 34 +- man/plot.RRglm.Rd | 76 ++-- man/plot.RRglmerMod.Rd | 60 +-- man/print.RRglmGOF.Rd | 36 +- man/print.summary.RRglm.Rd | 62 +-- man/print.summary.RRglmerMod.Rd | 62 +-- man/residuals.RRglm.Rd | 66 ++-- man/residuals.RRglmerMod.Rd | 62 +-- man/summary.RRglm.Rd | 42 +- man/summary.RRglmerMod.Rd | 42 +- 47 files changed, 2323 insertions(+), 2310 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.3.3 dated 2025-09-10 and 1.4.0 dated 2025-09-18
DESCRIPTION | 6 MD5 | 70 ++++++----- NAMESPACE | 3 NEWS.md | 21 +++ R/backend-dbplyr__duckdb_connection.R | 7 - R/dbGetInfo__duckdb_driver.R | 8 - R/duckdb-package.R |only R/duckdb.R | 8 - R/progress_display.R | 2 R/release.R |only R/sql.R | 75 ++++++++++-- R/version.R | 2 man/backend-duckdb.Rd | 4 man/default_conn.Rd |only man/duckdb-package.Rd | 2 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/sql_query.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/duckdb.tar.xz |binary src/include/rapi.hpp | 2 src/include/rfuns_extension.hpp | 2 src/include/sources.mk | 2 src/include/typesr.hpp | 2 src/relational.cpp | 7 - src/reltoaltrep.cpp | 166 ++++++++++++++++++++++----- src/rfuns.cpp | 54 ++++---- src/transform.cpp | 16 +- src/utils.cpp | 2 tests/testthat/_snaps/explain.md | 8 - tests/testthat/_snaps/relational.md | 2 tests/testthat/_snaps/sql.md |only tests/testthat/_snaps/types.md | 2 tests/testthat/test-date.R | 3 tests/testthat/test-sql.R |only tests/testthat/test-struct.R | 146 +++++++++++++++++++++++ tests/testthat/test-tbl__duckdb_connection.R | 13 ++ tests/testthat/test-types.R | 2 41 files changed, 492 insertions(+), 149 deletions(-)
Title: 'DataSHIELD' Server Side Base Functions
Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
been designed to only share non disclosive summary statistics, with built in automated output
checking based on statistical disclosure control. With data sites setting the threshold values for
the automated output checks. For more details, see 'citation("dsBase")'.
Author: Paul Burton [aut] ,
Rebecca Wilson [aut] ,
Olly Butters [aut] ,
Patricia Ryser-Welch [aut] ,
Alex Westerberg [aut],
Leire Abarrategui [aut],
Roberto Villegas-Diaz [aut] ,
Demetris Avraam [aut] ,
Yannick Marcon [aut] ,
Tom Bishop [aut],
Amadou Gaye [a [...truncated...]
Maintainer: Stuart Wheater <stuart.wheater@arjuna.com>
This is a re-admission after prior archival of version 6.3.3 dated 2025-07-19
Diff between dsBase versions 6.3.3 dated 2025-07-19 and 6.3.4 dated 2025-09-18
dsBase-6.3.3/dsBase/R/zzz.R |only dsBase-6.3.4/dsBase/DESCRIPTION | 49 ++++-- dsBase-6.3.4/dsBase/MD5 | 130 ++++++++-------- dsBase-6.3.4/dsBase/R/BooleDS.R | 2 dsBase-6.3.4/dsBase/R/asDataMatrixDS.R | 2 dsBase-6.3.4/dsBase/R/blackBoxDS.R | 7 dsBase-6.3.4/dsBase/R/blackBoxRanksDS.R | 7 dsBase-6.3.4/dsBase/R/cbindDS.R | 2 dsBase-6.3.4/dsBase/R/checkNegValueDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSortDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSubsetDS1.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSubsetDS2.R | 2 dsBase-6.3.4/dsBase/R/densityGridDS.R | 2 dsBase-6.3.4/dsBase/R/dmtC2SDS.R | 4 dsBase-6.3.4/dsBase/R/dsBase-package.R |only dsBase-6.3.4/dsBase/R/gamlssDS.R | 2 dsBase-6.3.4/dsBase/R/glmerSLMADS.assign.R | 2 dsBase-6.3.4/dsBase/R/global.R | 3 dsBase-6.3.4/dsBase/R/heatmapPlotDS.R | 7 dsBase-6.3.4/dsBase/R/hetcorDS.R | 2 dsBase-6.3.4/dsBase/R/histogramDS1.R | 7 dsBase-6.3.4/dsBase/R/histogramDS2.R | 7 dsBase-6.3.4/dsBase/R/levelsDS.R | 2 dsBase-6.3.4/dsBase/R/lexisDS2.R | 2 dsBase-6.3.4/dsBase/R/lmerSLMADS.assign.R | 4 dsBase-6.3.4/dsBase/R/meanDS.R | 2 dsBase-6.3.4/dsBase/R/metadataDS.R | 2 dsBase-6.3.4/dsBase/R/minMaxRandDS.R | 7 dsBase-6.3.4/dsBase/R/qlsplineDS.R | 2 dsBase-6.3.4/dsBase/R/rangeDS.R | 7 dsBase-6.3.4/dsBase/R/reShapeDS.R | 2 dsBase-6.3.4/dsBase/R/recodeLevelsDS.R | 2 dsBase-6.3.4/dsBase/R/recodeValuesDS.R | 2 dsBase-6.3.4/dsBase/R/repDS.R | 2 dsBase-6.3.4/dsBase/R/rmDS.R | 2 dsBase-6.3.4/dsBase/R/scatterPlotDS.R | 7 dsBase-6.3.4/dsBase/R/subsetByClassDS.R | 2 dsBase-6.3.4/dsBase/R/subsetDS.R | 2 dsBase-6.3.4/dsBase/R/table1DDS.R | 2 dsBase-6.3.4/dsBase/R/tableDS.R | 6 dsBase-6.3.4/dsBase/R/tableDS.assign.R | 6 dsBase-6.3.4/dsBase/R/tableDS2.R | 6 dsBase-6.3.4/dsBase/R/vectorDS.R | 2 dsBase-6.3.4/dsBase/README.md | 75 ++++++++- dsBase-6.3.4/dsBase/inst/CITATION | 10 - dsBase-6.3.4/dsBase/inst/DATASHIELD | 14 + dsBase-6.3.4/dsBase/inst/WORDLIST |only dsBase-6.3.4/dsBase/man/asDataMatrixDS.Rd | 2 dsBase-6.3.4/dsBase/man/checkNegValueDS.Rd | 2 dsBase-6.3.4/dsBase/man/densityGridDS.Rd | 2 dsBase-6.3.4/dsBase/man/dmtC2SDS.Rd | 4 dsBase-6.3.4/dsBase/man/dsBase-package.Rd |only dsBase-6.3.4/dsBase/man/gamlssDS.Rd | 2 dsBase-6.3.4/dsBase/man/glmerSLMADS.assign.Rd | 2 dsBase-6.3.4/dsBase/man/hetcorDS.Rd | 2 dsBase-6.3.4/dsBase/man/lexisDS2.Rd | 2 dsBase-6.3.4/dsBase/man/lmerSLMADS.assign.Rd | 4 dsBase-6.3.4/dsBase/man/meanDS.Rd | 2 dsBase-6.3.4/dsBase/man/metadataDS.Rd | 2 dsBase-6.3.4/dsBase/man/qlsplineDS.Rd | 2 dsBase-6.3.4/dsBase/man/repDS.Rd | 2 dsBase-6.3.4/dsBase/man/rmDS.Rd | 2 dsBase-6.3.4/dsBase/man/table1DDS.Rd | 2 dsBase-6.3.4/dsBase/man/tableDS.Rd | 6 dsBase-6.3.4/dsBase/man/tableDS.assign.Rd | 6 dsBase-6.3.4/dsBase/man/tableDS2.Rd | 6 dsBase-6.3.4/dsBase/tests/testthat/test-smk-corTestDS.R | 3 68 files changed, 295 insertions(+), 175 deletions(-)
Title: Crafting Print-Ready Maps and Layered Visualizations
Description: Simplifying the creation of print-ready maps, this package offers a user-friendly interface derived from 'ggplot2' for handling OpenStreetMap data. It streamlines the map-making process, allowing users to focus on the story their maps tell. Transforming raw geospatial data into informative visualizations is made easy with simple features 'sf' geometries. Whether for urban planning, environmental studies, or impactful public presentations, this tool facilitates straightforward and effective map creation. Enhance the dissemination of spatial information with high-quality, narrative-driven visualizations!
Author: David Willinger [aut, cre, cph]
Maintainer: David Willinger <david.willinger@gmail.com>
Diff between cartographr versions 0.2.3 dated 2025-08-19 and 0.2.4 dated 2025-09-18
DESCRIPTION | 12 - MD5 | 19 - NEWS.md | 8 R/cartographr.R | 401 +++++++++++++++++++++++++------------- R/palette.R | 4 R/set.R | 10 R/utils.R | 153 +++++++++++++- README.md | 6 man/dot-make_border_ring.Rd |only tests/testthat/test-cartographr.R | 30 +- tests/testthat/test-utils.R | 4 11 files changed, 467 insertions(+), 180 deletions(-)
Title: Breeding Insight Genomics Functions for Polyploid and Diploid
Species
Description: Functions developed within Breeding Insight to analyze
diploid and polyploid breeding and genetic data. 'BIGr' provides the
ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs)
from diversity arrays technology missing allele discovery count (DArT MADC) files,
and manipulate genotype data for both diploid and polyploid species. It
also serves as the core dependency for the 'BIGapp' 'Shiny' app, which
provides a user-friendly interface for performing routine genotype
analysis tasks such as dosage calling, filtering, principal component analysis (PCA),
genome-wide association studies (GWAS), and
genomic prediction. For more details about the included 'breedTools'
functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and
the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
Author: Alexander M. Sandercock [cre, aut],
Cristiane Taniguti [aut],
Josue Chinchilla-Vargas [aut],
Shufen Chen [ctb],
Manoj Sapkota [ctb],
Meng Lin [ctb],
Dongyan Zhao [ctb],
Cornell University [cph]
Maintainer: Alexander M. Sandercock <sandercock.alex@gmail.com>
Diff between BIGr versions 0.5.5 dated 2025-05-19 and 0.6.2 dated 2025-09-18
DESCRIPTION | 15 +++---- MD5 | 35 ++++++++++------ NAMESPACE | 7 +++ NEWS.md | 59 ++++++++++++++++----------- R/breedtools_functions.R | 4 - R/filterMADC.R |only R/madc2gmat.R |only R/madc2vcf_all.R | 26 +++++++----- R/madc2vcf_targets.R | 39 +++++++++++++++--- R/thinSNP.R |only R/updog2vcf.R | 34 ++++++++++++++-- R/utils.R | 7 ++- README.md | 1 inst/CITATION | 70 ++++++++++++++++++++++++--------- man/allele_freq_poly.Rd |only man/filterMADC.Rd |only man/madc2gmat.Rd |only man/solve_composition_poly.Rd |only man/thinSNP.Rd |only man/updog2vcf.Rd | 10 ++++ tests/testthat/test-filterMADC.R |only tests/testthat/test-madc2gmat.R |only tests/testthat/test-madc2vcf_targets.R | 55 +++++++++++++++++++++++++ tests/testthat/test-thinSNP.R |only 24 files changed, 277 insertions(+), 85 deletions(-)
Title: Vaccine Extension Package for ADaM in 'R' Asset Library
Description: Programming vaccine specific Clinical Data Interchange
Standards Consortium (CDISC) compliant Analysis Data Model (ADaM)
datasets in 'R'. Flat model is followed as per Center for Biologics
Evaluation and Research (CBER) guidelines for creating vaccine
specific domains. ADaM datasets are a mandatory part of any New Drug
or Biologics License Application submitted to the United States Food
and Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team (2021),
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
The package is an extension package of the 'admiral' package.
Author: Arjun Rubalingam [aut, cre],
Sukalpo Saha [aut, ctb],
Ben Straub [aut],
Vikram S [aut],
Dhivya Kanagaraj [aut],
Federico Baratin [aut],
Yamini Purna Bollu [aut],
Ilse Augustyns [aut],
Kalyani Bodicherla [aut],
Hilde Delanghe [aut],
Lee Armishaw [aut] [...truncated...]
Maintainer: Arjun Rubalingam <arjun.rubalingam@pfizer.com>
Diff between admiralvaccine versions 0.4.0 dated 2025-01-31 and 0.5.0 dated 2025-09-18
DESCRIPTION | 40 +++++++++++++-------------- MD5 | 55 +++++++++++++++++++------------------ NEWS.md | 10 ++++++ R/derive_diam_to_sev_records.R | 4 +- R/derive_fever_records.R | 2 - R/derive_vars_crit.R | 2 - R/derive_vars_merged_vaccine.R | 4 +- R/derive_vars_params.R | 2 - R/derive_vars_vaxdt.R | 2 - README.md | 22 ++++----------- build/vignette.rds |binary inst/doc/adce.html | 2 - inst/doc/adface.R | 3 +- inst/doc/adface.Rmd | 3 +- inst/doc/adface.html | 30 +++++++++++--------- inst/doc/adis.html | 2 - inst/doc/admiralvaccine.html | 2 - inst/doc/adsl.R | 6 ++-- inst/doc/adsl.Rmd | 6 ++-- inst/doc/adsl.html | 60 +++++++++++++++++++++-------------------- inst/templates/ad_adface.R | 3 +- inst/templates/ad_adis.R | 9 ++++-- inst/templates/ad_adsl.R | 6 ++-- man/admiralvaccine-package.Rd | 4 +- man/figures/gsk_logo.png |only man/figures/jnj_logo.png |only man/figures/pfizer_logo.png |only tests/testthat.R | 6 +--- vignettes/adface.Rmd | 3 +- vignettes/adsl.Rmd | 6 ++-- 30 files changed, 159 insertions(+), 135 deletions(-)
More information about admiralvaccine at CRAN
Permanent link
Title: Flexible Multidimensional Scaling and 'smacof' Extensions
Description: Flexible multidimensional scaling (MDS) methods and extensions to the package 'smacof'. This package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models. These are: Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459) with powers, Sammon mapping (Sammon, 1969, <doi:10.1109/T-C.1969.222678>) with ratio and interval optimal scaling, Multiscale MDS (Ramsay, 1977, <doi:10.1007/BF02294052>) with ratio and interval optimal scaling, s-stress MDS (ALSCAL; Takane, Young & De Leeuw, 1977, <doi:10.1007/BF02293745>) with ratio and interval optimal scaling, elastic scaling (McGee, 1966, <doi:10.1111/j.2044-8317.1966.tb00367.x>) with ratio and interval optimal scaling, r-stress MDS (De Leeuw, Groenen & Mair, 2016, <https://rpubs.com/deleeuw/142619>) with ratio, interval, splines and nonmetric optimal scaling, power-stress MDS (POST-MDS; Buja & Swayne, 2002 <doi: [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Jan de Leeuw [aut],
Lisha Chen [aut],
Patrick Mair [aut]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between smacofx versions 1.21-1 dated 2025-07-07 and 1.22-0 dated 2025-09-18
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 2 ++ NEWS | 4 ++++ R/alignplot.R |only man/alignplot.Rd |only 6 files changed, 14 insertions(+), 6 deletions(-)
Title: Create Visualisations for BART Models
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut],
Claus Wilke [ctb]
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Diff between bartMan versions 0.2.0 dated 2025-08-22 and 0.2.1 dated 2025-09-18
DESCRIPTION | 15 +- MD5 | 29 ++--- NAMESPACE | 15 -- R/VSUP.R | 60 ++++------ R/bartDiag.R | 277 ++++++++++++++++++++++++++++++++----------------- R/generic_functions.R | 3 R/globals.R | 2 R/plotSingleTree.R | 8 + R/plot_all_trees.R | 22 +++ R/treeBarPlot.R | 37 +++++- R/vimpPlot.R | 35 +++--- R/vintPlot.R | 18 +-- R/viviBartMatrix.R | 12 ++ man/bartDiag.Rd | 4 man/bartReorder.Rd |only man/bivariate_scale.Rd | 4 16 files changed, 334 insertions(+), 207 deletions(-)
Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen <mehmet.suzen@physics.org>
Diff between isingLenzMC versions 0.2.5 dated 2016-07-01 and 0.2.7 dated 2025-09-18
isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/analyseData.R |only isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/functions.R |only isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/generateData.R |only isingLenzMC-0.2.7/isingLenzMC/DESCRIPTION | 8 +- isingLenzMC-0.2.7/isingLenzMC/MD5 | 18 ++--- isingLenzMC-0.2.7/isingLenzMC/NAMESPACE | 2 isingLenzMC-0.2.7/isingLenzMC/README.md | 34 +++++++++- isingLenzMC-0.2.7/isingLenzMC/build/vignette.rds |binary isingLenzMC-0.2.7/isingLenzMC/inst/CITATION | 3 isingLenzMC-0.2.7/isingLenzMC/inst/doc/isingLenzMC.pdf |binary isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/README.md |only isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/data_analysis.ipynb |only isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/data_generate.ipynb |only 13 files changed, 46 insertions(+), 19 deletions(-)
Title: Weierstrass and Jacobi Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and
Jacobi forms. Also includes various tools for manipulating and
visualizing complex functions.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between elliptic versions 1.4-0 dated 2019-03-14 and 1.5-0 dated 2025-09-18
elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.R |only elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.Rnw |only elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.pdf |only elliptic-1.4-0/elliptic/tests/aaa.R |only elliptic-1.4-0/elliptic/vignettes/ellipticpaper.Rnw |only elliptic-1.4-0/elliptic/vignettes/semicircular_path.pdf |only elliptic-1.4-0/elliptic/vignettes/semicircular_path.svg |only elliptic-1.5-0/elliptic/DESCRIPTION | 14 elliptic-1.5-0/elliptic/MD5 | 81 ++- elliptic-1.5-0/elliptic/NEWS.md |only elliptic-1.5-0/elliptic/R/elliptic.R | 98 ++-- elliptic-1.5-0/elliptic/README.md |only elliptic-1.5-0/elliptic/build/partial.rdb |binary elliptic-1.5-0/elliptic/build/vignette.rds |binary elliptic-1.5-0/elliptic/inst/CITATION | 19 elliptic-1.5-0/elliptic/inst/doc/elliptic.R |only elliptic-1.5-0/elliptic/inst/doc/elliptic.Rnw |only elliptic-1.5-0/elliptic/inst/doc/elliptic.pdf |only elliptic-1.5-0/elliptic/inst/doc/residuetheorem.R | 62 +-- elliptic-1.5-0/elliptic/inst/doc/residuetheorem.Rnw | 325 ++++++++++------ elliptic-1.5-0/elliptic/inst/doc/residuetheorem.pdf |binary elliptic-1.5-0/elliptic/inst/semicircular_path.pdf |only elliptic-1.5-0/elliptic/inst/semicircular_path.svg |only elliptic-1.5-0/elliptic/man/J.Rd | 24 - elliptic-1.5-0/elliptic/man/K.fun.Rd | 4 elliptic-1.5-0/elliptic/man/as.primitive.Rd | 8 elliptic-1.5-0/elliptic/man/ck.Rd | 14 elliptic-1.5-0/elliptic/man/divisor.Rd | 2 elliptic-1.5-0/elliptic/man/elliptic-package.Rd | 44 -- elliptic-1.5-0/elliptic/man/eta.Rd | 4 elliptic-1.5-0/elliptic/man/figures |only elliptic-1.5-0/elliptic/man/fpp.Rd | 15 elliptic-1.5-0/elliptic/man/half.periods.Rd | 6 elliptic-1.5-0/elliptic/man/latplot.Rd | 6 elliptic-1.5-0/elliptic/man/misc.Rd | 1 elliptic-1.5-0/elliptic/man/myintegrate.Rd | 73 +-- elliptic-1.5-0/elliptic/man/newton_raphson.Rd | 16 elliptic-1.5-0/elliptic/man/p1.tau.Rd | 2 elliptic-1.5-0/elliptic/man/parameters.Rd | 10 elliptic-1.5-0/elliptic/man/sn.Rd | 4 elliptic-1.5-0/elliptic/man/theta.Rd | 33 - elliptic-1.5-0/elliptic/man/theta.neville.Rd | 22 + elliptic-1.5-0/elliptic/man/theta1dash.Rd | 11 elliptic-1.5-0/elliptic/man/unimodular.Rd | 2 elliptic-1.5-0/elliptic/man/view.Rd | 2 elliptic-1.5-0/elliptic/tests/testthat |only elliptic-1.5-0/elliptic/tests/testthat.R |only elliptic-1.5-0/elliptic/vignettes/elliptic.Rnw |only elliptic-1.5-0/elliptic/vignettes/elliptic.bib | 38 + elliptic-1.5-0/elliptic/vignettes/residuetheorem.Rnw | 325 ++++++++++------ 50 files changed, 745 insertions(+), 520 deletions(-)
Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Author: Lars Snipen [aut, cre],
Kristian Hovde Liland [aut]
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between microseq versions 2.1.6 dated 2023-08-21 and 2.1.7 dated 2025-09-18
microseq-2.1.6/microseq/build |only microseq-2.1.6/microseq/inst/doc |only microseq-2.1.6/microseq/man/microseq-package.Rd |only microseq-2.1.6/microseq/vignettes |only microseq-2.1.7/microseq/DESCRIPTION | 26 - microseq-2.1.7/microseq/MD5 | 36 - microseq-2.1.7/microseq/R/fasta.R | 202 ++++---- microseq-2.1.7/microseq/R/fastq.R | 202 ++++---- microseq-2.1.7/microseq/R/gff.R | 352 +++++++------- microseq-2.1.7/microseq/R/microseq-package.R | 45 - microseq-2.1.7/microseq/R/multialign.R | 438 +++++++++--------- microseq-2.1.7/microseq/R/orfs.R | 570 ++++++++++++------------ microseq-2.1.7/microseq/man/findOrfs.Rd | 4 microseq-2.1.7/microseq/man/gff2fasta.Rd | 4 microseq-2.1.7/microseq/man/lorfs.Rd | 2 microseq-2.1.7/microseq/man/microseq.Rd |only microseq-2.1.7/microseq/man/msalign.Rd | 4 microseq-2.1.7/microseq/man/readFasta.Rd | 12 microseq-2.1.7/microseq/man/readFastq.Rd | 8 microseq-2.1.7/microseq/man/readGFF.Rd | 4 20 files changed, 955 insertions(+), 954 deletions(-)
Title: Downscaling Species Occupancy
Description: Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Author: Charles Marsh [aut, cre, cph]
Maintainer: Charles Marsh <charlie.marsh@mailbox.org>
Diff between downscale versions 5.0.0 dated 2023-05-31 and 5.1.3 dated 2025-09-18
downscale-5.0.0/downscale/man/figures/Thumbs.db |only downscale-5.1.3/downscale/DESCRIPTION | 11 downscale-5.1.3/downscale/MD5 | 29 downscale-5.1.3/downscale/NEWS.md | 16 downscale-5.1.3/downscale/R/checkInputs.R | 10 downscale-5.1.3/downscale/R/predict.downscale.R | 7 downscale-5.1.3/downscale/build/vignette.rds |binary downscale-5.1.3/downscale/inst/doc/Downscaling.R | 24 downscale-5.1.3/downscale/inst/doc/Downscaling.html | 949 +++++++++----------- downscale-5.1.3/downscale/inst/doc/Upgraining.R | 22 downscale-5.1.3/downscale/inst/doc/Upgraining.html | 99 +- downscale-5.1.3/downscale/man/Downscale-package.Rd | 9 downscale-5.1.3/downscale/man/downscale.Rd | 4 downscale-5.1.3/downscale/man/ensemble.downscale.Rd | 4 downscale-5.1.3/downscale/man/hui.downscale.Rd | 2 downscale-5.1.3/downscale/man/predict.downscale.Rd | 2 16 files changed, 598 insertions(+), 590 deletions(-)
Title: Automatic Database Normalisation for Data Frames
Description: Automatic normalisation of a data frame to third normal form, with
the intention of easing the process of data cleaning. (Usage to design your
actual database for you is not advised.)
Originally inspired by the 'AutoNormalize' library for 'Python' by 'Alteryx'
(<https://github.com/alteryx/autonormalize>), with various changes and
improvements. Automatic discovery of functional or approximate dependencies,
normalisation based on those, and plotting of the resulting "database" via
'Graphviz', with options to exclude some attributes at discovery time, or
remove discovered dependencies at normalisation time.
Author: Mark Webster [aut, cre]
Maintainer: Mark Webster <markwebster204@yahoo.co.uk>
Diff between autodb versions 3.0.0 dated 2025-06-25 and 3.1.0 dated 2025-09-18
DESCRIPTION | 6 - MD5 | 27 ++-- NEWS.md | 7 + R/autoref.r | 91 ++++++++++++---- R/database.r | 56 +++++++--- R/decompose.r | 9 + R/plot.r | 250 ++++++++++++++++++++++++++++++++++++++++++--- inst/doc/autodb.html | 144 ++++++++++++------------- man/d2.Rd |only man/d2.data.frame.Rd |only man/d2.relation_schema.Rd |only man/database.Rd | 23 +++- man/gv.relation.Rd | 58 +++++----- man/gv.relation_schema.Rd | 62 +++++------ tests/testthat/setup.r | 2 tests/testthat/test-plot.r | 167 ++++++++++++++++++++++++++++++ 16 files changed, 699 insertions(+), 203 deletions(-)
Title: Procedures Related to the Zadeh's Extension Principle for Fuzzy
Data
Description: Procedures for calculation, plotting, animation, and approximation of the outputs for fuzzy numbers (see A.I. Ban, L. Coroianu, P. Grzegorzewski "Fuzzy Numbers: Approximations, Ranking and Applications" (2015)) based on the Zadeh's Extension Principle (see de Barros, L.C., Bassanezi, R.C., Lodwick, W.A. (2017) <doi:10.1007/978-3-662-53324-6_2>).
Author: Maciej Romaniuk [cre, aut] ),
Abbas Parchami [aut] ),
Przemyslaw Grzegorzewski [ctb] )
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between ZEP versions 0.1.5 dated 2025-06-22 and 0.2.0 dated 2025-09-18
DESCRIPTION | 10 +++---- MD5 | 30 +++++++++++++++------ NAMESPACE | 1 R/AnimateZFunction.R |only R/ApplyZFunction.R | 9 +++++- R/ApproximationAmbValPres.R |only R/FuzzyApproximation.R | 54 +++++++++++++++++++++++++++++++++++---- R/PlotZFunction.R | 9 +++++- R/approximationMehodsInside.R | 2 - R/utils.R | 2 - man/AnimateZFunction.Rd |only man/FuzzyApproximation.Rd | 7 +++-- man/approximationMehodsInside.Rd | 2 - tests |only 14 files changed, 98 insertions(+), 28 deletions(-)
Title: A Bridge Between 'keras' and 'tidymodels'
Description: Provides a seamless bridge between 'keras' and the 'tidymodels'
frameworks. It allows for the dynamic creation of 'parsnip' model
specifications for 'keras' models.
Author: David Diaz [aut, cre]
Maintainer: David Diaz <daviddrsch@gmail.com>
Diff between kerasnip versions 0.0.1 dated 2025-09-03 and 0.0.3 dated 2025-09-18
kerasnip-0.0.1/kerasnip/tests/testthat/helper_keras.R |only kerasnip-0.0.3/kerasnip/DESCRIPTION | 8 kerasnip-0.0.3/kerasnip/MD5 | 84 kerasnip-0.0.3/kerasnip/NAMESPACE | 1 kerasnip-0.0.3/kerasnip/R/compile_keras_grid.R | 678 ++-- kerasnip-0.0.3/kerasnip/R/create_keras_functional_spec.R | 281 - kerasnip-0.0.3/kerasnip/R/create_keras_sequential_spec.R | 245 - kerasnip-0.0.3/kerasnip/R/dials.R |only kerasnip-0.0.3/kerasnip/R/generic_functional_fit.R | 233 - kerasnip-0.0.3/kerasnip/R/generic_sequential_fit.R | 233 - kerasnip-0.0.3/kerasnip/R/keras_tools.R | 294 - kerasnip-0.0.3/kerasnip/R/register_model_args.R | 21 kerasnip-0.0.3/kerasnip/R/remove_keras_spec.R | 190 - kerasnip-0.0.3/kerasnip/R/utils.R | 824 ++--- kerasnip-0.0.3/kerasnip/README.md | 6 kerasnip-0.0.3/kerasnip/build/vignette.rds |binary kerasnip-0.0.3/kerasnip/inst/doc/applications.R |only kerasnip-0.0.3/kerasnip/inst/doc/applications.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/applications.html |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.R |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.html |only kerasnip-0.0.3/kerasnip/inst/doc/functional_api.html | 49 kerasnip-0.0.3/kerasnip/inst/doc/getting_started.html | 222 - kerasnip-0.0.3/kerasnip/inst/doc/sequential_model.html | 6 kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.R |only kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.html |only kerasnip-0.0.3/kerasnip/inst/doc/workflows_functional.html | 511 +-- kerasnip-0.0.3/kerasnip/inst/doc/workflows_sequential.html | 1570 +++++----- kerasnip-0.0.3/kerasnip/man/compile_keras_grid.Rd | 35 kerasnip-0.0.3/kerasnip/man/create_keras_functional_spec.Rd | 1 kerasnip-0.0.3/kerasnip/man/create_keras_sequential_spec.Rd | 5 kerasnip-0.0.3/kerasnip/man/extract_valid_grid.Rd | 58 kerasnip-0.0.3/kerasnip/man/generic_functional_fit.Rd | 9 kerasnip-0.0.3/kerasnip/man/generic_sequential_fit.Rd | 9 kerasnip-0.0.3/kerasnip/man/inform_errors.Rd | 57 kerasnip-0.0.3/kerasnip/man/keras_evaluate.Rd | 32 kerasnip-0.0.3/kerasnip/man/loss_function_keras.Rd | 38 kerasnip-0.0.3/kerasnip/man/model_exists.Rd |only kerasnip-0.0.3/kerasnip/man/optimizer_function.Rd | 38 kerasnip-0.0.3/kerasnip/man/remove_keras_spec.Rd | 2 kerasnip-0.0.3/kerasnip/tests/testthat/helper_tests.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_autoplot_uniqueness.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_fit_compile_tuning.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_func_classification.R | 587 +-- kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_func_regression.R | 16 kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_spec_removal.R | 41 kerasnip-0.0.3/kerasnip/tests/testthat/test_generic_fit_helpers.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_postprocessing_helpers.R |only kerasnip-0.0.3/kerasnip/vignettes/applications.Rmd |only kerasnip-0.0.3/kerasnip/vignettes/autoplot_uniqueness.Rmd |only kerasnip-0.0.3/kerasnip/vignettes/tuning_fit_compile_args.Rmd |only 53 files changed, 3356 insertions(+), 3028 deletions(-)
Title: 'shiny' Application for Statistical Test Assumption Checking and
Guidance
Description: A 'shiny' application to assess statistical assumptions and guide users toward appropriate tests. The app is designed for researchers with minimal statistical training and provides diagnostics, plots, and test recommendations for a wide range of analyses. Many statistical assumptions are implemented using the package 'rstatix' (Kassambara, 2019) <doi:10.32614/CRAN.package.rstatix> and 'performance' (Lüdecke et al., 2021) <doi:10.21105/joss.03139>.
Author: Ahmed Bargheet [aut, cre]
Maintainer: Ahmed Bargheet <ahmed.bargheet@yahoo.com>
Diff between AssumpSure versions 1.1.0 dated 2025-08-18 and 1.1.1 dated 2025-09-18
DESCRIPTION | 11 +- MD5 | 9 - NEWS.md | 15 ++ R/launch_app.R | 14 ++ R/zzz.R |only inst/app/app.R | 306 +++++++++++++++++++++++++++++++++++++++++++++------------ 6 files changed, 285 insertions(+), 70 deletions(-)
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb],
Robert Corty [ctb],
Thomas Neitmann [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.4.9 dated 2020-12-05 and 0.5.0 dated 2025-09-18
DESCRIPTION | 11 MD5 | 30 - NAMESPACE | 77 +-- NEWS.md | 132 ++--- R/as-raster.R | 42 - R/hexSticker-package.R |only R/sticker.R | 767 ++++++++++++++++---------------- inst/fonts/Aller/Aller_Font_License.txt | 182 +++---- man/geom_hexagon.Rd | 48 +- man/geom_pkgname.Rd | 86 +-- man/geom_url.Rd | 92 +-- man/hexSticker-package.Rd |only man/reexports.Rd | 40 - man/save_sticker.Rd | 42 - man/sticker.Rd | 264 +++++------ man/sticker_dev.Rd | 34 - man/theme_sticker.Rd | 44 - 17 files changed, 949 insertions(+), 942 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for
performance. Offers convenient utilities for working with in-memory and
larger-than-memory data while retaining full 'dplyr' compatibility.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 1.1.1 dated 2025-07-30 and 1.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 37 +++++++++++++++++++------------------ NEWS.md | 15 +++++++++++++++ R/aaa-meta.R | 1 + R/bisect_reduce.R |only R/duckplyr_df.R | 8 ++++++-- R/read_file_duckdb.R | 15 +++++++++------ R/relational-duckdb.R | 4 ++-- R/translate.R | 14 ++++++++++---- inst/doc/developers.html | 8 ++++---- inst/doc/duckdb.html | 10 +++++----- inst/doc/extend.html | 4 ++-- inst/doc/fallback.html | 2 +- inst/doc/large.html | 4 ++-- inst/doc/limits.html | 8 ++++---- inst/doc/prudence.Rmd | 18 +++++++++++++++++- inst/doc/prudence.html | 28 ++++++++++++++++++++++------ tests/testthat/helper-taxi.R | 2 ++ tests/testthat/test-fallback.R | 20 ++++++++++++++++++++ vignettes/prudence.Rmd | 18 +++++++++++++++++- 20 files changed, 162 insertions(+), 62 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parametric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.4.0 dated 2025-02-24 and 1.5.0 dated 2025-09-18
DESCRIPTION | 15 - MD5 | 166 ++++++----- NAMESPACE | 4 NEWS.md | 34 ++ R/ESS.R | 20 - R/WeightIt-package.R | 1 R/anova.glm_weightit.R | 48 +-- R/as.weightit.R | 50 ++- R/calibrate.R | 29 +- R/dist_functions.R | 21 - R/functions_for_processing.R | 416 +++++++++++++++++------------ R/get_w_from_ps.R | 40 +- R/glm_weightit-methods.R | 163 +++++------ R/glm_weightit.R | 33 +- R/glm_weightit_helpers.R | 110 ++++--- R/make_full_rank.R | 36 +- R/multinom_weightit.R | 52 ++- R/ordinal_weightit.R | 35 +- R/plot.weightit.R | 17 - R/predict.glm_weightit.R | 110 ++++++- R/sbps.R | 70 ++--- R/summary.weightit.R | 268 ++++++++++--------- R/treat.R |only R/trim.R | 188 ++++++------- R/utils.R | 444 ++++++++++++++++++++----------- R/weightit.R | 164 +++++------ R/weightit.fit.R | 119 +++----- R/weightit2bart.R | 104 ++++--- R/weightit2cbps.R | 532 ++++++++++++++++++++------------------ R/weightit2ebal.R | 421 +++++++++++++++++++++++------- R/weightit2energy.R | 447 +++++++++++++++++++++---------- R/weightit2gbm.R | 278 ++++++++++--------- R/weightit2glm.R | 256 +++++++++--------- R/weightit2ipt.R | 128 ++++----- R/weightit2npcbps.R | 85 +++--- R/weightit2optweight.R | 470 ++++++++++++++++----------------- R/weightit2ps.R | 22 - R/weightit2super.R | 129 +++++---- R/weightit2user.R | 39 +- R/weightitMSM.R | 228 +++++++--------- R/weightit_methods.R | 45 +-- README.md | 149 +++++----- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/WeightIt.Rmd | 63 ++-- inst/doc/WeightIt.html | 235 ++++++++-------- inst/doc/estimating-effects.Rmd | 48 +-- inst/doc/estimating-effects.html | 469 +++++++++++++++++---------------- inst/doc/installing-packages.Rmd | 74 ++--- inst/doc/installing-packages.html | 203 +++++++------- man/ESS.Rd | 14 - man/anova.glm_weightit.Rd | 7 man/as.weightit.Rd | 6 man/calibrate.Rd | 16 - man/dot-weightit_methods.Rd | 13 man/get_w_from_ps.Rd | 5 man/glm_weightit-methods.Rd | 4 man/glm_weightit.Rd | 19 - man/make_full_rank.Rd | 14 - man/method_bart.Rd | 48 ++- man/method_cbps.Rd | 36 +- man/method_ebal.Rd | 66 ++-- man/method_energy.Rd | 82 +++-- man/method_gbm.Rd | 143 +++++----- man/method_glm.Rd | 62 +--- man/method_ipt.Rd | 29 +- man/method_npcbps.Rd | 36 +- man/method_optweight.Rd | 97 +++--- man/method_super.Rd | 53 ++- man/method_user.Rd | 20 - man/plot.weightit.Rd | 8 man/predict.glm_weightit.Rd | 21 - man/sbps.Rd | 3 man/summary.weightit.Rd | 33 +- man/trim.Rd | 27 - man/weightit.Rd | 75 +---- man/weightit.fit.Rd | 30 -- man/weightitMSM.Rd | 63 +--- tests/testthat/helpers.R | 2 tests/testthat/test-moments.R |only tests/testthat/test-update.R | 62 ++-- vignettes/WeightIt.Rmd | 63 ++-- vignettes/estimating-effects.Rmd | 48 +-- vignettes/installing-packages.Rmd | 74 ++--- vignettes/references.bib | 92 ++---- 85 files changed, 4648 insertions(+), 3801 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] ,
Andreas Alfons [aut],
Gregor de Cillia [aut],
Bernd Prantner [ctb],
Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 6.2.2 dated 2022-08-25 and 6.2.6 dated 2025-09-18
DESCRIPTION | 20 MD5 | 95 +- NAMESPACE | 11 NEWS.md | 9 R/VIM-package.R | 16 R/evaluation.R | 1 R/gowerD.R | 14 R/hotdeck.R | 3 R/imputeRobust.R |only R/imputeRobustChain.R |only R/irmi.R | 20 R/kNN.R | 11 R/matchImpute.R | 6 R/rangerImpute.R | 34 R/regressionImp.R | 3 R/xgboostImpute.R |only R/zzz.R | 5 build/vignette.rds |binary inst/doc/VIM.R | 2 inst/doc/VIM.html | 40 - inst/doc/VisualImp.R | 7 inst/doc/VisualImp.Rmd | 5 inst/doc/VisualImp.html | 173 ++--- inst/doc/donorImp.R | 13 inst/doc/donorImp.Rmd | 7 inst/doc/donorImp.html | 1267 +++++++++++------------------------- inst/doc/irmi.R | 11 inst/doc/irmi.Rmd | 7 inst/doc/irmi.html | 1261 +++++++++++------------------------- inst/doc/modelImp.R | 13 inst/doc/modelImp.Rmd | 7 inst/doc/modelImp.html | 1275 +++++++++++-------------------------- inst/tinytest/test_matchImpute.R |only inst/tinytest/test_xgboostImpute.R |only man/VIM-package.Rd | 19 man/hotdeck.Rd | 3 man/impPCA.Rd | 3 man/imputeRobust.Rd |only man/imputeRobustChain.Rd |only man/irmi.Rd | 10 man/kNN.Rd | 6 man/matchImpute.Rd | 3 man/medianSamp.Rd | 3 man/prepare.Rd | 4 man/rangerImpute.Rd | 3 man/regressionImp.Rd | 6 man/sampleCat.Rd | 3 man/xgboostImpute.Rd |only tests/test_imputeRobust.R |only vignettes/VisualImp.Rmd | 5 vignettes/donorImp.Rmd | 7 vignettes/irmi.Rmd | 7 vignettes/modelImp.Rmd | 7 53 files changed, 1532 insertions(+), 2893 deletions(-)
Title: Manual Tours, Manual Control of Dynamic Projections of Numeric
Multivariate Data
Description: Data visualization tours animates linear projection
of multivariate data as its basis (ie. orientation) changes. The 'spinifex'
packages generates paths for manual tours by manipulating the contribution of
a single variable at a time Cook & Buja (1997)
<doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand
(random walk) and guided (optimizing some objective function) are available
in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>.
'spinifex' builds on 'tourr' and can render tours with 'gganimate' and
'plotly' graphics, and allows for exporting as an .html widget and as an .gif,
respectively. This work is fully discussed in Spyrison & Cook (2020)
<doi:10.32614/RJ-2020-027>.
Author: Nicholas Spyrison [aut, cre] ,
Dianne Cook [aut, ths]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between spinifex versions 0.3.9 dated 2025-08-22 and 0.3.10 dated 2025-09-18
DESCRIPTION | 6 +- MD5 | 23 ++++---- NAMESPACE | 1 NEWS.md | 8 ++ R/0_util.r | 63 ++++++++++++++++++++++ R/2_ggproto_visualize.r | 37 ++++++------- inst/WORDLIST | 79 +++++++++++----------------- inst/doc/getting_started_with_spinifex.html | 10 +-- inst/doc/ggproto_api.Rmd | 2 inst/doc/ggproto_api.html | 10 +-- man/ide.Rd |only tests/testthat/test-2_ggproto_visualize.r | 50 ++++++++--------- vignettes/ggproto_api.Rmd | 2 13 files changed, 173 insertions(+), 118 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system to
implement a complete data-to-decisions, reproducible workflow.
The core components facilitate the development of modular pieces,
and enable the user to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the within-project dependencies.
The suggested package 'NLMR' can be installed from the repository
(<https://PredictiveEcology.r-universe.dev>).
Author: Alex M Chubaty [aut] ,
Eliot J B McIntire [aut, cre] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between SpaDES.core versions 2.1.6 dated 2025-09-02 and 2.1.8 dated 2025-09-18
DESCRIPTION | 10 MD5 | 576 NAMESPACE | 968 - NEWS.md | 1288 - R/Plots.R | 948 - R/cache.R | 2583 +-- R/check.R | 512 R/checkpoint.R | 258 R/code-checking.R | 1338 - R/convertToPackage.R | 842 - R/copy.R | 254 R/debugging.R | 78 R/downloadData.R | 646 R/environment.R | 34 R/helpers.R | 818 - R/load.R | 814 - R/memory-leaks.R | 156 R/memory.R | 512 R/misc-methods.R | 864 - R/modActiveBinding.R | 144 R/module-define.R | 1598 +- R/module-dependencies-class.R | 484 R/module-dependencies-methods.R | 676 R/module-param-check.R | 238 R/module-repository.R | 856 - R/module-template.R | 1844 +- R/moduleCoverage.R | 222 R/moduleMetadata.R | 656 R/objectSynonyms.R | 332 R/options.R | 472 R/paths.R | 433 R/plotting-diagrams.R | 1146 - R/plotting.R | 182 R/priority.R | 82 R/progress.R | 260 R/project-template.R | 194 R/reexports.R | 50 R/restart.R | 1132 - R/save.R | 532 R/saveLoadSimList.R | 1142 - R/simList-accessors.R | 6976 +++++----- R/simList-class.R | 544 R/simulation-parseModule.R | 1290 - R/simulation-simInit.R | 3814 ++--- R/simulation-spades.R | 4952 +++---- R/spades-classes.R | 36 R/spades-core-deprecated.R | 90 R/spades-core-package.R | 998 - R/suppliedElsewhere.R | 276 R/times.R | 910 - R/zzz.R | 208 README.md | 130 build/vignette.rds |binary inst/WORDLIST | 207 inst/doc/i-introduction.R | 142 inst/doc/i-introduction.Rmd | 724 - inst/doc/i-introduction.html | 2000 +- inst/doc/ii-modules.R | 608 inst/doc/ii-modules.Rmd | 1574 +- inst/doc/ii-modules.html | 3229 ++-- inst/doc/iii-cache.R | 226 inst/doc/iii-cache.Rmd | 538 inst/doc/iii-cache.html | 1765 +- inst/doc/iv-advanced.R | 26 inst/doc/iv-advanced.Rmd | 104 inst/doc/iv-advanced.html | 848 - inst/doc/v-automated-testing.R | 16 inst/doc/v-automated-testing.Rmd | 174 inst/doc/v-automated-testing.html | 926 - inst/examples/example_inputs.R | 144 inst/examples/example_moduleMetadata.R | 46 inst/examples/example_moduleParamsInputsOuputs.R | 26 inst/examples/example_moduleVersion.R | 34 inst/examples/example_outputs.R | 130 inst/extdata/abundRaster.tif.aux.xml | 10 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R | 64 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd | 92 inst/sampleModules/caribouMovement/caribouMovement.R | 342 inst/sampleModules/fireSpread/fireSpread.R | 400 inst/sampleModules/randomLandscapes/randomLandscapes.R | 318 inst/templates/LICENSE.template | 16 inst/templates/NEWS.template | 6 inst/templates/README.template | 16 inst/templates/citation.bib.template | 16 inst/templates/data-gitignore.template | 12 inst/templates/module.R.template | 42 inst/templates/module.Rmd.template | 216 inst/templates/module.inputObjects.R.template | 50 inst/templates/moduleEvent1.R.template | 22 inst/templates/moduleEvent2.R.template | 22 inst/templates/moduleInit.R.template | 16 inst/templates/modulePartialEvents.R.template | 326 inst/templates/modulePartialMeta.R.template | 60 inst/templates/moduleSave.R.template | 20 inst/templates/moduledoEvent.R.template | 146 inst/templates/moduleggplotFn.R.template | 10 inst/templates/moduleplotFn.R.template | 22 inst/templates/project.R.template | 72 inst/templates/render-module-rmd.yaml.template | 154 inst/templates/test-template.R.template | 148 inst/templates/unitTests.R.template | 16 man/Copy.Rd | 98 man/FilterRecursive.Rd | 34 man/Plot.Rd | 302 man/Plots.Rd | 338 man/SpaDES.core-package.Rd | 1064 - 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Title: Global Sensitivity Analysis of Model Outputs and Importance
Measures
Description: A collection of functions for sensitivity analysis of model outputs (factor screening, global sensitivity analysis and robustness analysis), for variable importance measures of data, as well as for interpretability of machine learning models. Most of the functions have to be applied on scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss [aut, cre],
Sebastien Da Veiga [aut],
Alexandre Janon [aut],
Gilles Pujol [aut]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.30.1 dated 2024-08-28 and 1.30.2 dated 2025-09-18
DESCRIPTION | 6 MD5 | 26 - NEWS | 22 + R/lmg.R | 8 R/morris.R | 2 R/pmvd.R | 8 R/sensiHSIC.R | 601 ++++++++++++++++++++++++++++--------- R/testHSIC.R | 620 +++++++++++++++++++++++++++++++++++---- man/PLIsuperquantile_multivar.Rd | 2 man/sensiHSIC.Rd | 139 +++++--- man/testHSIC.Rd | 253 ++++++++++++--- man/testmodels.Rd | 2 src/RcppExports.cpp | 1 src/nested.cpp | 1 14 files changed, 1337 insertions(+), 354 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.4.3 dated 2025-05-13 and 3.4.4 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/labkey.deleteRows.R | 1 + R/labkey.experiment.R | 4 ++++ R/labkey.importRows.R | 1 + R/labkey.insertRows.R | 1 + R/labkey.updateRows.R | 1 + R/makeDF.R | 2 +- man/Rlabkey-package.Rd | 4 ++-- 10 files changed, 28 insertions(+), 16 deletions(-)
Title: NFL Logo Plots in 'ggplot2' and 'gt'
Description: A set of functions to visualize National Football League
analysis in 'ggplot2' plots and 'gt' tables.
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflplotR versions 1.4.0 dated 2024-08-21 and 1.5.0 dated 2025-09-18
DESCRIPTION | 21 LICENSE | 4 MD5 | 136 +- NAMESPACE | 89 - NEWS.md | 9 R/build_grobs.R | 188 +-- R/geom_lines.R | 48 R/geom_nfl_headshots.R | 277 ++--- R/geom_nfl_logos.R | 284 ++--- R/geom_nfl_wordmarks.R | 272 ++--- R/ggpreview.R | 134 +- R/gt_nfl.R | 40 R/nfl_team_factors.R | 184 +-- R/nfl_team_tiers.R | 312 +++--- R/nflplotR-package.R | 36 R/scale_nfl.R | 222 ++-- R/sysdata.rda |binary R/theme-elements.R | 630 +++++------- R/utils.R | 8 R/zzz.R | 137 +- README.md | 174 +-- man/dot-nflplotR_clear_cache.Rd | 34 man/element.Rd | 369 +++---- man/figures/lifecycle-deprecated.svg | 42 man/geom_from_path.Rd | 310 +++--- man/geom_lines.Rd | 217 ++-- man/geom_nfl_headshots.Rd | 348 +++---- man/geom_nfl_logos.Rd | 358 +++---- man/geom_nfl_wordmarks.Rd | 346 +++--- man/ggpreview.Rd | 177 +-- man/gt_nfl_cols_label.Rd | 142 +- man/gt_nfl_headshots.Rd | 150 +-- man/gt_nfl_logos.Rd | 136 +- man/gt_render_image.Rd | 76 - man/nfl_team_factor.Rd | 150 +-- man/nfl_team_tiers.Rd | 218 ++-- man/nflplotR-package.Rd | 88 - man/nflverse_sitrep.Rd | 22 man/reexports.Rd |only man/scale_nfl.Rd | 291 +++-- man/valid_team_names.Rd | 52 - tests/testthat.R | 8 tests/testthat/_snaps/geom_from_path/p1.svg | 67 - tests/testthat/_snaps/geom_lines/p1.svg | 199 ++-- tests/testthat/_snaps/geom_lines/p2.svg | 195 +-- tests/testthat/_snaps/geom_lines/p3.svg | 195 +-- tests/testthat/_snaps/geom_lines/p4.svg | 199 ++-- tests/testthat/_snaps/geom_nfl_logos.md |only tests/testthat/_snaps/geom_nfl_logos/p1.svg | 131 +- tests/testthat/_snaps/geom_nfl_logos/p2.svg | 137 +- tests/testthat/_snaps/geom_nfl_logos/p3.svg | 131 +- tests/testthat/_snaps/geom_nfl_wordmarks.md |only tests/testthat/_snaps/geom_nfl_wordmarks/p1.svg | 161 +-- tests/testthat/_snaps/geom_nfl_wordmarks/p2.svg | 161 +-- tests/testthat/_snaps/nfl_team_factors/p1.svg | 1187 ++++++++++++------------ tests/testthat/_snaps/nfl_team_factors/p2.svg | 1187 ++++++++++++------------ tests/testthat/_snaps/nfl_team_tiers/p1.svg | 150 +-- tests/testthat/_snaps/scale_nfl/p1.svg | 289 ++--- tests/testthat/_snaps/theme-elements.md |only tests/testthat/_snaps/theme-elements/p1.svg | 73 - tests/testthat/_snaps/theme-elements/p2.svg | 73 - tests/testthat/test-geom_from_path.R | 46 tests/testthat/test-geom_lines.R | 72 - tests/testthat/test-geom_nfl_logos.R | 123 +- tests/testthat/test-geom_nfl_wordmarks.R | 109 +- tests/testthat/test-nfl_team_factors.R | 80 - tests/testthat/test-nfl_team_tiers.R | 60 - tests/testthat/test-scale_nfl.R | 44 tests/testthat/test-theme-elements.R | 78 - tests/testthat/test-utils.R | 24 tools/check.env | 18 71 files changed, 5963 insertions(+), 5965 deletions(-)
Title: L-Moments and Quantile Mixtures
Description: Contains functions to estimate
L-moments and trimmed L-moments from the data. Also
contains functions to estimate the parameters of the normal
polynomial quantile mixture and the Cauchy polynomial quantile
mixture from L-moments and trimmed L-moments.
Author: Juha Karvanen [cre, aut],
Santeri Karppinen [aut]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>
Diff between Lmoments versions 1.3-1 dated 2019-03-15 and 1.3-2 dated 2025-09-18
Lmoments-1.3-1/Lmoments/COPYING |only Lmoments-1.3-2/Lmoments/DESCRIPTION | 13 +++---- Lmoments-1.3-2/Lmoments/MD5 | 25 ++++++------- Lmoments-1.3-2/Lmoments/inst/CITATION | 45 ++++++++----------------- Lmoments-1.3-2/Lmoments/inst/News | 22 ++++++------ Lmoments-1.3-2/Lmoments/man/Lmoments.Rd | 18 +++++----- Lmoments-1.3-2/Lmoments/man/cauchypoly.Rd | 24 ++++++------- Lmoments-1.3-2/Lmoments/man/covnormpoly4.Rd | 2 - Lmoments-1.3-2/Lmoments/man/data2cauchypoly.Rd | 20 +++++------ Lmoments-1.3-2/Lmoments/man/data2normpoly.Rd | 18 +++++----- Lmoments-1.3-2/Lmoments/man/normpoly.Rd | 22 ++++++------ Lmoments-1.3-2/Lmoments/man/t1lmoments.Rd | 20 +++++------ Lmoments-1.3-2/Lmoments/src/Makevars | 12 ------ Lmoments-1.3-2/Lmoments/src/Makevars.win | 12 ------ 14 files changed, 110 insertions(+), 143 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love [aut, cre, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 2.6.3 dated 2024-09-07 and 2.7.7 dated 2025-09-18
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/analysis.R | 9 ++++++++- R/image.R | 11 +++++++++++ R/options.R | 6 ++++++ R/output.R | 3 ++- R/results.R | 6 ++++-- 7 files changed, 42 insertions(+), 15 deletions(-)
Title: R-ArcGIS Bridge Utility Functions
Description: Developer oriented utility functions designed to be used as
the building blocks of R packages that work with ArcGIS Location
Services. It provides functionality for authorization, Esri JSON
construction and parsing, as well as other utilities pertaining to
geometry and Esri type conversions. To support 'ArcGIS Pro' users,
authorization can be done via 'arcgisbinding'. Installation
instructions for 'arcgisbinding' can be found at
<https://developers.arcgis.com/r-bridge/installation/>.
Author: Josiah Parry [aut, cre] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Eli Pousson [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisutils versions 0.3.3 dated 2025-04-10 and 0.4.0 dated 2025-09-18
arcgisutils-0.3.3/arcgisutils/R/self.R |only arcgisutils-0.3.3/arcgisutils/man/arc_self_meta.Rd |only arcgisutils-0.4.0/arcgisutils/DESCRIPTION | 33 arcgisutils-0.4.0/arcgisutils/MD5 | 86 +- arcgisutils-0.4.0/arcgisutils/NAMESPACE | 53 + arcgisutils-0.4.0/arcgisutils/NEWS.md | 30 arcgisutils-0.4.0/arcgisutils/R/arc-auth.R | 84 +- arcgisutils-0.4.0/arcgisutils/R/arc-base-req.R | 2 arcgisutils-0.4.0/arcgisutils/R/arc-paginate-req.R |only arcgisutils-0.4.0/arcgisutils/R/arcgisutils-package.R | 3 arcgisutils-0.4.0/arcgisutils/R/esri-featureset-list.R | 10 arcgisutils-0.4.0/arcgisutils/R/esri-field-mapping.R | 120 +-- arcgisutils-0.4.0/arcgisutils/R/geoprocessing-class.R |only arcgisutils-0.4.0/arcgisutils/R/geoprocessing-types.R |only arcgisutils-0.4.0/arcgisutils/R/portal-resources.R |only arcgisutils-0.4.0/arcgisutils/R/portal-self.R |only arcgisutils-0.4.0/arcgisutils/R/portal-servers.R |only arcgisutils-0.4.0/arcgisutils/R/portal-types.R |only arcgisutils-0.4.0/arcgisutils/R/portal-users.R |only arcgisutils-0.4.0/arcgisutils/R/search.R |only arcgisutils-0.4.0/arcgisutils/R/sharing.R |only arcgisutils-0.4.0/arcgisutils/R/user-group-content.R |only arcgisutils-0.4.0/arcgisutils/R/user-self.R |only arcgisutils-0.4.0/arcgisutils/R/util-parse-esri-json.R | 17 arcgisutils-0.4.0/arcgisutils/R/utils-dates.R | 2 arcgisutils-0.4.0/arcgisutils/R/utils-requests.R | 8 arcgisutils-0.4.0/arcgisutils/R/utils-url.R |only arcgisutils-0.4.0/arcgisutils/R/utils.R | 16 arcgisutils-0.4.0/arcgisutils/R/zzz.R |only arcgisutils-0.4.0/arcgisutils/README.md | 385 ++++++++-- arcgisutils-0.4.0/arcgisutils/man/arc_base_req.Rd | 3 arcgisutils-0.4.0/arcgisutils/man/arc_form_params.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_group.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_item.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_item_data.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_job_status.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_paginate_req.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_portal_resources.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_portal_servers.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_portal_urls.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_portal_users.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_user.Rd |only arcgisutils-0.4.0/arcgisutils/man/arc_user_self.Rd |only arcgisutils-0.4.0/arcgisutils/man/auth.Rd | 6 arcgisutils-0.4.0/arcgisutils/man/content.Rd |only arcgisutils-0.4.0/arcgisutils/man/featureset.Rd | 3 arcgisutils-0.4.0/arcgisutils/man/field_mapping.Rd | 42 - arcgisutils-0.4.0/arcgisutils/man/figures/README-unnamed-chunk-17-1.png |only arcgisutils-0.4.0/arcgisutils/man/figures/lifecycle-deprecated.svg |only arcgisutils-0.4.0/arcgisutils/man/figures/lifecycle-experimental.svg |only arcgisutils-0.4.0/arcgisutils/man/figures/lifecycle-stable.svg |only arcgisutils-0.4.0/arcgisutils/man/figures/lifecycle-superseded.svg |only arcgisutils-0.4.0/arcgisutils/man/gp_job.Rd |only arcgisutils-0.4.0/arcgisutils/man/gp_params.Rd |only arcgisutils-0.4.0/arcgisutils/man/portal_types.Rd |only arcgisutils-0.4.0/arcgisutils/man/search_items.Rd |only arcgisutils-0.4.0/arcgisutils/man/self.Rd |only arcgisutils-0.4.0/arcgisutils/man/url.Rd |only arcgisutils-0.4.0/arcgisutils/man/utilities.Rd | 7 arcgisutils-0.4.0/arcgisutils/src/Makevars.in | 18 arcgisutils-0.4.0/arcgisutils/src/Makevars.win.in | 12 arcgisutils-0.4.0/arcgisutils/src/rust/Cargo.toml | 10 arcgisutils-0.4.0/arcgisutils/tests/testthat/test-sharing.R |only arcgisutils-0.4.0/arcgisutils/tests/testthat/test-utils-url.R |only arcgisutils-0.4.0/arcgisutils/tools/config.R | 45 + 65 files changed, 714 insertions(+), 281 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker [aut, cph],
Jonathon Love [aut, cre, cph],
Damian Dropmann [aut, cph],
Victor Moreno [ctb, cph],
Maurizio Agosti [ctb, cph],
Sebastian Jentschke [ctb, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 2.7.0 dated 2025-06-11 and 2.7.7 dated 2025-09-17
jmv-2.7.0/jmv/tests/testthat/testthat-problems.rds |only jmv-2.7.7/jmv/DESCRIPTION | 8 ++++---- jmv-2.7.7/jmv/MD5 | 13 ++++++------- jmv-2.7.7/jmv/R/ttestis.b.R | 2 ++ jmv-2.7.7/jmv/R/ttestones.b.R | 1 + jmv-2.7.7/jmv/R/ttestps.b.R | 2 +- jmv-2.7.7/jmv/tests/testthat/testerrors.R | 14 +++++++------- jmv-2.7.7/jmv/tests/testthat/testttestis.R | 4 ++-- 8 files changed, 23 insertions(+), 21 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 0.1.6 dated 2025-07-11 and 1.0.4 dated 2025-09-17
spinebil-0.1.6/spinebil/NEWS |only spinebil-0.1.6/spinebil/R/indexFunctions.R |only spinebil-0.1.6/spinebil/R/samplingFunctions.R |only spinebil-0.1.6/spinebil/R/spinebil-package.R |only spinebil-0.1.6/spinebil/R/utils-tourr.R |only spinebil-0.1.6/spinebil/man/basisMatrix.Rd |only spinebil-0.1.6/spinebil/man/basisVector.Rd |only spinebil-0.1.6/spinebil/man/compareSmoothing.Rd |only spinebil-0.1.6/spinebil/man/distanceDist.Rd |only spinebil-0.1.6/spinebil/man/distanceToSp.Rd |only spinebil-0.1.6/spinebil/man/getIndexMean.Rd |only spinebil-0.1.6/spinebil/man/getTrace.Rd |only spinebil-0.1.6/spinebil/man/jitterAngle.Rd |only spinebil-0.1.6/spinebil/man/jitterPoints.Rd |only spinebil-0.1.6/spinebil/man/pipeData.Rd |only spinebil-0.1.6/spinebil/man/plotRotation.Rd |only spinebil-0.1.6/spinebil/man/plotSmoothingComparison.Rd |only spinebil-0.1.6/spinebil/man/plotTrace.Rd |only spinebil-0.1.6/spinebil/man/profileRotation.Rd |only spinebil-0.1.6/spinebil/man/scagIndex.Rd |only spinebil-0.1.6/spinebil/man/sinData.Rd |only spinebil-0.1.6/spinebil/man/spiralData.Rd |only spinebil-0.1.6/spinebil/man/squintAngleEstimate.Rd |only spinebil-0.1.6/spinebil/man/timeSequence.Rd |only spinebil-1.0.4/spinebil/DESCRIPTION | 12 + spinebil-1.0.4/spinebil/MD5 | 101 +++++++++------ spinebil-1.0.4/spinebil/NAMESPACE | 57 +++++--- spinebil-1.0.4/spinebil/NEWS.md |only spinebil-1.0.4/spinebil/R/distances.R | 46 ++---- spinebil-1.0.4/spinebil/R/index_functions.R |only spinebil-1.0.4/spinebil/R/index_mean.R |only spinebil-1.0.4/spinebil/R/index_noise_threshold.R |only spinebil-1.0.4/spinebil/R/index_scale.R |only spinebil-1.0.4/spinebil/R/rotation.R | 36 ++--- spinebil-1.0.4/spinebil/R/sample_size_effect.R |only spinebil-1.0.4/spinebil/R/sampling_functions.R |only spinebil-1.0.4/spinebil/R/smoothing.R | 50 +++---- spinebil-1.0.4/spinebil/R/spinebil_package.R |only spinebil-1.0.4/spinebil/R/timer.R | 8 - spinebil-1.0.4/spinebil/R/tracing.R | 44 +++--- spinebil-1.0.4/spinebil/R/utils.R | 6 spinebil-1.0.4/spinebil/R/utils_data.R |only spinebil-1.0.4/spinebil/R/utils_tourr.R |only spinebil-1.0.4/spinebil/README.md | 68 +--------- spinebil-1.0.4/spinebil/build |only spinebil-1.0.4/spinebil/inst/doc |only spinebil-1.0.4/spinebil/man/basis_matrix.Rd |only spinebil-1.0.4/spinebil/man/basis_nearby.Rd | 2 spinebil-1.0.4/spinebil/man/basis_vector.Rd |only spinebil-1.0.4/spinebil/man/compare_smoothing.Rd |only spinebil-1.0.4/spinebil/man/data_gen.Rd |only spinebil-1.0.4/spinebil/man/distance_dist.Rd |only spinebil-1.0.4/spinebil/man/distance_to_sp.Rd |only spinebil-1.0.4/spinebil/man/figures/README-example-1.png |binary spinebil-1.0.4/spinebil/man/figures/spinebil.png |only spinebil-1.0.4/spinebil/man/geodesic_info.Rd | 2 spinebil-1.0.4/spinebil/man/get_index_mean.Rd |only spinebil-1.0.4/spinebil/man/get_trace.Rd |only spinebil-1.0.4/spinebil/man/jitter_angle.Rd |only spinebil-1.0.4/spinebil/man/jitter_points.Rd |only spinebil-1.0.4/spinebil/man/noise_gen.Rd |only spinebil-1.0.4/spinebil/man/pipe_data.Rd |only spinebil-1.0.4/spinebil/man/plot_rotation.Rd |only spinebil-1.0.4/spinebil/man/plot_smoothing_comparison.Rd |only spinebil-1.0.4/spinebil/man/plot_trace.Rd |only spinebil-1.0.4/spinebil/man/ppi_mean.Rd |only spinebil-1.0.4/spinebil/man/ppi_noise_threshold.Rd |only spinebil-1.0.4/spinebil/man/ppi_samplesize_effect.Rd |only spinebil-1.0.4/spinebil/man/ppi_scale.Rd |only spinebil-1.0.4/spinebil/man/profile_rotation.Rd |only spinebil-1.0.4/spinebil/man/scag_index.Rd |only spinebil-1.0.4/spinebil/man/sin_data.Rd |only spinebil-1.0.4/spinebil/man/spinebil-package.Rd | 12 - spinebil-1.0.4/spinebil/man/spiral_data.Rd |only spinebil-1.0.4/spinebil/man/squint_angle_estimate.Rd |only spinebil-1.0.4/spinebil/man/step_fraction.Rd | 2 spinebil-1.0.4/spinebil/man/time_sequence.Rd |only spinebil-1.0.4/spinebil/vignettes |only 78 files changed, 214 insertions(+), 232 deletions(-)
Title: Rcpp Hidden Markov Model
Description: Collection of functions to evaluate sequences, decode hidden states and estimate parameters from a single or multiple sequences of a discrete time Hidden Markov Model. The observed values can be modeled by a multinomial distribution for categorical/labeled emissions, a mixture of Gaussians for continuous data and also a mixture of Poissons for discrete values. It includes functions for random initialization, simulation, backward or forward sequence evaluation, Viterbi or forward-backward decoding and parameter estimation using an Expectation-Maximization approach.
Author: Roberto A. Cardenas-Ovando [aut, cre],
Julieta Noguez [aut],
Claudia Rangel-Escareno [aut]
Maintainer: Roberto A. Cardenas-Ovando <robalecarova@gmail.com>
Diff between RcppHMM versions 1.2.2 dated 2017-11-21 and 1.2.2.1 dated 2025-09-17
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 6 +++--- src/Makevars | 2 +- src/Makevars.win | 2 +- 4 files changed, 24 insertions(+), 13 deletions(-)
Title: Analysis of Incubation Data
Description: Suite of functions to study animal incubation.
At the core of incR
lies an algorithm that allows for the scoring of
incubation behaviour. Additionally, several functions
extract biologically relevant metrics of incubation such as off-bout number
and off-bout duration - for a review of avian incubation studies,
see Nests, Eggs, and Incubation: New ideas about avian reproduction (2015)
edited by D. Charles Deeming and S. James Reynolds <doi:10.1093/acprof:oso/9780198718666.001.0001>.
Author: Pablo Capilla-Lasheras [aut, cre]
Maintainer: Pablo Capilla-Lasheras <pacapilla@gmail.com>
Diff between incR versions 2.1.0 dated 2023-04-18 and 2.1.1 dated 2025-09-17
DESCRIPTION | 10 MD5 | 35 - NAMESPACE | 1 NEWS.md | 4 R/inRt.R | 506 ++++++++--------- R/incRact.R | 136 ++-- R/incRplot.R | 158 ++--- R/incRprep.R | 164 ++--- R/incRscan.R | 2 R/incRscan_v3.R | 635 +++++++++++---------- README.md | 56 - build/vignette.rds |binary inst/doc/incR_pipeline.R | 216 +++---- inst/doc/incR_pipeline.html | 1278 ++++++++++++++++++++++---------------------- man/incR.Rd | 5 man/incRplot.Rd | 4 man/incRprep.Rd | 4 man/incRscan_v3.Rd |only man/incRt.Rd | 8 19 files changed, 1633 insertions(+), 1589 deletions(-)
Title: Interactively Explore Local Explanations with the Radial Tour
Description: Given a non-linear model, calculate the local explanation.
We purpose view the data space, explanation
space, and model residuals as ensemble graphic interactive on a shiny
application. After an observation of interest is identified, the normalized
variable importance of the local explanation is used as a 1D projection
basis. The support of the local explanation is then explored by changing
the basis with the use of the radial tour <doi:10.32614/RJ-2020-027>;
<doi:10.1080/10618600.1997.10474754>.
Author: Nicholas Spyrison [aut, cre]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between cheem versions 0.4.1 dated 2025-08-26 and 0.4.2 dated 2025-09-17
cheem-0.4.1/cheem/inst/shiny_apps/cheem/rsconnect |only cheem-0.4.1/cheem/man/rnorm_from.Rd |only cheem-0.4.2/cheem/DESCRIPTION | 10 - cheem-0.4.2/cheem/MD5 | 44 +++--- cheem-0.4.2/cheem/NAMESPACE | 1 cheem-0.4.2/cheem/NEWS.md | 7 + cheem-0.4.2/cheem/R/0_util.r | 86 ++++++------- cheem-0.4.2/cheem/build/vignette.rds |binary cheem-0.4.2/cheem/inst/doc/getting-started-with-cheem.html | 10 - cheem-0.4.2/cheem/man/as_logical_index.Rd | 1 cheem-0.4.2/cheem/man/cheem.Rd | 2 cheem-0.4.2/cheem/man/color_scale_of.Rd | 1 cheem-0.4.2/cheem/man/contains_nonnumeric.Rd | 1 cheem-0.4.2/cheem/man/is_discrete.Rd | 1 cheem-0.4.2/cheem/man/is_diverging.Rd | 1 cheem-0.4.2/cheem/man/linear_tform.Rd | 1 cheem-0.4.2/cheem/man/logistic_tform.Rd | 1 cheem-0.4.2/cheem/man/problem_type.Rd | 1 cheem-0.4.2/cheem/man/radial_cheem_tour.Rd | 2 cheem-0.4.2/cheem/man/run_app.Rd | 2 cheem-0.4.2/cheem/man/sug_basis.Rd | 1 cheem-0.4.2/cheem/man/sug_manip_var.Rd | 1 cheem-0.4.2/cheem/tests/testthat/test-1_cheem_lists.R | 6 cheem-0.4.2/cheem/tests/testthat/test-2_visualization.r | 18 +- 24 files changed, 98 insertions(+), 100 deletions(-)
Title: Probabilistic Two Sample Mendelian Randomization
Description: Efficient statistical inference of two-sample MR (Mendelian Randomization) analysis.
It can account for the correlated instruments and the horizontal pleiotropy,
and can provide the accurate estimates of both causal effect and horizontal
pleiotropy effect as well as the two corresponding p-values. There are two main
functions in the 'PPMR' package. One is PMR_individual() for individual level data,
the other is PMR_summary() for summary data.
Author: Zhongshang Yuan [aut],
Xiang Zhou [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between PPMR versions 1.0 dated 2019-08-09 and 1.0.1 dated 2025-09-17
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 10 - R/RcppExports.R | 249 ++++++++++++++++++++++++++--------------------- R/data.R | 62 +++++------ README.md | 70 ++++++------- man/Exampleindividual.Rd | 42 ++++--- man/Examplesummary.Rd | 46 ++++---- man/PMR_individual.Rd | 150 ++++++++++++++++------------ man/PMR_summary.Rd | 151 +++++++++++++++------------- src/Makevars | 3 src/Makevars.win | 4 src/PMR_summary.cpp | 66 ++++++++++-- src/PPMR.cpp | 83 ++++++++++++++- src/RcppExports.cpp | 43 ++++---- 15 files changed, 614 insertions(+), 401 deletions(-)
Title: Deconvolution and Alignment of 1d NMR Spectra
Description: A framework for deconvolution, alignment and postprocessing
of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in
a data matrix of aligned signal integrals. The deconvolution part uses the
algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>.
The alignment part is based on functions from the 'speaq' package, described
in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al.
(2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation
of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in
Haeckl et al. (2021) <doi:10.3390/metabo11070452>.
Author: Tobias Schmidt [aut, cre, cph],
Martina Haeckl [aut, cph],
Yanren Linda Hu [ctb],
Wolfram Gronwald [aut, cph]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Diff between metabodecon versions 1.2.6 dated 2025-01-21 and 1.6.2 dated 2025-09-17
metabodecon-1.2.6/metabodecon/R/10_spec.R |only metabodecon-1.2.6/metabodecon/R/20_deconv.R |only metabodecon-1.2.6/metabodecon/R/30_align.R |only metabodecon-1.2.6/metabodecon/R/40_plot.R |only metabodecon-1.2.6/metabodecon/R/50_util.R |only metabodecon-1.2.6/metabodecon/R/60_data.R |only metabodecon-1.2.6/metabodecon/R/70_depr.R |only metabodecon-1.2.6/metabodecon/R/80_class.R |only metabodecon-1.2.6/metabodecon/R/90_testing.R |only metabodecon-1.2.6/metabodecon/man/metabodecon_classes.Rd |only metabodecon-1.2.6/metabodecon/tests/testthat/test-convert_sfr.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-convert_wsr.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-deconvolute_ispec.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-deconvolute_ispecs.R |only metabodecon-1.2.6/metabodecon/tests/testthat/test-init_lorentz_curves.R |only metabodecon-1.6.2/metabodecon/DESCRIPTION | 22 metabodecon-1.6.2/metabodecon/MD5 | 161 metabodecon-1.6.2/metabodecon/NAMESPACE 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metabodecon-1.6.2/metabodecon/man/calculate_lorentz_curves.Rd | 18 metabodecon-1.6.2/metabodecon/man/check_mdrb.Rd |only metabodecon-1.6.2/metabodecon/man/combine_peaks.Rd | 79 metabodecon-1.6.2/metabodecon/man/convert_pos.Rd | 5 metabodecon-1.6.2/metabodecon/man/datadir.Rd | 20 metabodecon-1.6.2/metabodecon/man/datadir_persistent.Rd | 6 metabodecon-1.6.2/metabodecon/man/datadir_temp.Rd | 6 metabodecon-1.6.2/metabodecon/man/deconvolute.Rd | 147 metabodecon-1.6.2/metabodecon/man/dohCluster.Rd | 44 metabodecon-1.6.2/metabodecon/man/download_example_datasets.Rd | 6 metabodecon-1.6.2/metabodecon/man/draw_spectrum.Rd | 94 metabodecon-1.6.2/metabodecon/man/evalwith.Rd | 5 metabodecon-1.6.2/metabodecon/man/gen_feat_mat.Rd | 18 metabodecon-1.6.2/metabodecon/man/generate_lorentz_curves.Rd |only metabodecon-1.6.2/metabodecon/man/get_data_dir.Rd | 5 metabodecon-1.6.2/metabodecon/man/get_ppm_range.Rd | 13 metabodecon-1.6.2/metabodecon/man/get_si_mat.Rd |only metabodecon-1.6.2/metabodecon/man/install_mdrb.Rd |only metabodecon-1.6.2/metabodecon/man/is_metabodecon_class.Rd | 48 metabodecon-1.6.2/metabodecon/man/make_spectrum.Rd | 7 metabodecon-1.6.2/metabodecon/man/metabodecon-package.Rd |only metabodecon-1.6.2/metabodecon/man/metabodecon_file.Rd | 5 metabodecon-1.6.2/metabodecon/man/plot_lorentz_curves_save_as_png.Rd | 12 metabodecon-1.6.2/metabodecon/man/plot_spectra.Rd | 14 metabodecon-1.6.2/metabodecon/man/plot_spectrum.Rd | 18 metabodecon-1.6.2/metabodecon/man/plot_spectrum_superposition_save_as_png.Rd | 4 metabodecon-1.6.2/metabodecon/man/plot_triplets.Rd | 6 metabodecon-1.6.2/metabodecon/man/print_methods.Rd | 29 metabodecon-1.6.2/metabodecon/man/read_spectra.Rd | 7 metabodecon-1.6.2/metabodecon/man/read_spectrum.Rd | 7 metabodecon-1.6.2/metabodecon/man/sap.Rd | 2 metabodecon-1.6.2/metabodecon/man/sim.Rd | 4 metabodecon-1.6.2/metabodecon/man/simulate_spectrum.Rd | 8 metabodecon-1.6.2/metabodecon/man/speaq_align.Rd | 32 metabodecon-1.6.2/metabodecon/man/tmpdir.Rd | 5 metabodecon-1.6.2/metabodecon/man/transp.Rd | 5 metabodecon-1.6.2/metabodecon/man/tree.Rd | 5 metabodecon-1.6.2/metabodecon/man/width.Rd | 5 metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/draw_spectrum/draw-spectrum.svg | 6633 +++++----- metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_sfr |only metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_spectrum/plot-spectrum.svg | 5460 ++++---- metabodecon-1.6.2/metabodecon/tests/testthat/_snaps/plot_ws |only metabodecon-1.6.2/metabodecon/tests/testthat/test-aaa_Get_Started.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-align.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-as_decon.R | 270 metabodecon-1.6.2/metabodecon/tests/testthat/test-confirm_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute.R | 91 metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute_spectra.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-deconvolute_spectrum.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-draw_spectrum.R | 51 metabodecon-1.6.2/metabodecon/tests/testthat/test-enrich_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-enrich_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-evalwith.R | 2 metabodecon-1.6.2/metabodecon/tests/testthat/test-find_peaks_fast2.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-generate_lorentz_curves.R | 2 metabodecon-1.6.2/metabodecon/tests/testthat/test-get_names.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_right_borders_fast.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_si_mat.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_smopts.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-get_wshw.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-init_lc.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-install_mdrb.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-lorentz_int.R | 22 metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_sfr.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_spectrum.R | 121 metabodecon-1.6.2/metabodecon/tests/testthat/test-plot_ws.R |only metabodecon-1.6.2/metabodecon/tests/testthat/test-smooth_signals.R | 13 metabodecon-1.6.2/metabodecon/tests/testthat/test-speaq_align.R | 17 metabodecon-1.6.2/metabodecon/vignettes |only 108 files changed, 7807 insertions(+), 6080 deletions(-)
Title: Computationally Efficient Maximum Likelihood Identification of
Linear Dynamical Systems
Description: Provides implementations of computationally efficient maximum likelihood parameter estimation algorithms for models representing linear dynamical systems. Currently, two such algorithms (one offline and one online) are implemented for the single-output cumulative structural equation model with an additive-noise output measurement equation and assumptions of normality and independence. The corresponding scientific papers are referenced in the descriptions of the functions implementing these algorithms.
Author: Vytautas Dulskis [cre, aut],
Leonidas Sakalauskas [aut]
Maintainer: Vytautas Dulskis <vytautas.dulskis@gmail.com>
Diff between EMLI versions 0.2.0 dated 2022-11-20 and 0.3.0 dated 2025-09-17
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/calculate_likelihood.R | 6 +++--- R/estimate_parameters.R | 9 ++++++--- R/estimate_parameters_on.R |only R/evaluate_estimates.R | 4 ++-- R/generate_data.R | 8 ++++---- man/calculate_likelihood.Rd | 6 +++--- man/estimate_parameters.Rd | 9 ++++++--- man/estimate_parameters_on.Rd |only man/evaluate_estimates.Rd | 4 ++-- man/generate_data.Rd | 8 ++++---- 14 files changed, 56 insertions(+), 40 deletions(-)
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
four different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; 'Nager.Date' for public holidays;
and 'REST Countries API' for general country information. The package enables
users to explore various aspects of Colombia such as geographic locations,
cultural attractions, economic indicators, demographic data, and public
holidays. Additionally, 'ColombiAPI' includes curated datasets covering
Bogota air stations, business and holiday dates, public schools, Colombian
coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota,
making it a comprehensive tool for exploring Colombia's multifaceted data
landscape. For more information on the APIs, see:
'API-Colombia' <https://api-colombia.com/>,
'Nager.Da [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.1.1 dated 2025-02-16 and 0.2.0 dated 2025-09-17
ColombiAPI-0.1.1/ColombiAPI/R/get_Colombia_info.R |only ColombiAPI-0.1.1/ColombiAPI/R/get_airports_list.R |only ColombiAPI-0.1.1/ColombiAPI/R/get_departments_list.R |only ColombiAPI-0.1.1/ColombiAPI/R/get_presidents_list.R |only ColombiAPI-0.1.1/ColombiAPI/R/get_regions_list.R |only ColombiAPI-0.1.1/ColombiAPI/R/view_datasets.R |only ColombiAPI-0.1.1/ColombiAPI/man/get_Colombia_info.Rd |only ColombiAPI-0.1.1/ColombiAPI/man/get_airports_list.Rd |only ColombiAPI-0.1.1/ColombiAPI/man/get_departments_list.Rd |only ColombiAPI-0.1.1/ColombiAPI/man/get_presidents_list.Rd |only ColombiAPI-0.1.1/ColombiAPI/man/get_regions_list.Rd |only ColombiAPI-0.1.1/ColombiAPI/man/view_datasets.Rd |only ColombiAPI-0.1.1/ColombiAPI/tests/testthat/test-get_Colombia_info.R |only ColombiAPI-0.1.1/ColombiAPI/tests/testthat/test-get_airports_list.R |only ColombiAPI-0.1.1/ColombiAPI/tests/testthat/test-get_departments_list.R |only ColombiAPI-0.1.1/ColombiAPI/tests/testthat/test-get_presidents_list.R |only 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Title: Compute Global Sensitivity Analysis Indices Using Optimal
Transport
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
Author: Leonardo Chiani [aut, cre, cph] ,
Emanuele Borgonovo [rev],
Elmar Plischke [rev],
Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Diff between gsaot versions 1.1.0 dated 2025-07-18 and 1.1.1 dated 2025-09-17
gsaot-1.1.0/gsaot/tests |only gsaot-1.1.1/gsaot/DESCRIPTION | 8 +-- gsaot-1.1.1/gsaot/MD5 | 25 ++++----- gsaot-1.1.1/gsaot/NEWS.md | 6 ++ gsaot-1.1.1/gsaot/R/check_solver_optns.R | 6 +- gsaot-1.1.1/gsaot/R/test_functions.R | 2 gsaot-1.1.1/gsaot/README.md | 34 ++++++------- gsaot-1.1.1/gsaot/build/partial.rdb |binary gsaot-1.1.1/gsaot/build/vignette.rds |binary gsaot-1.1.1/gsaot/inst/CITATION |only gsaot-1.1.1/gsaot/inst/doc/gaussian-model-sensitivity.R | 3 - gsaot-1.1.1/gsaot/inst/doc/gaussian-model-sensitivity.Rmd | 4 - gsaot-1.1.1/gsaot/inst/doc/gaussian-model-sensitivity.html | 21 +++----- gsaot-1.1.1/gsaot/vignettes/gaussian-model-sensitivity.Rmd | 4 - 14 files changed, 56 insertions(+), 57 deletions(-)
Title: Advanced Processing and Chart Generation from activPAL Events
Files
Description: Contains functions to generate pre-defined summary statistics from activPAL
events files <https://www.palt.com/>. The package also contains functions to produce informative
graphics that visualise physical activity behaviour and trends. This includes
generating graphs that align physical activity behaviour with additional time based
observations described by other data sets, such as sleep diaries and continuous glucose
monitoring data.
Author: Craig Speirs [aut, cre],
Kate Lyden [ctb],
Douglas Maxwell [ctb],
David Loudon [ctb]
Maintainer: Craig Speirs <craig@paltechnologies.com>
Diff between activPAL versions 0.1.3 dated 2019-07-18 and 0.1.4 dated 2025-09-17
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
Title: Scatter Plot Combined with Ridgelines in 'ggplot2'
Description: The function combines a scatter plot with ridgelines to better visualise the distribution between sample groups. The plot is created with 'ggplot2'.
Author: Matthieu Bourgery [aut, cre]
Maintainer: Matthieu Bourgery <matthieu.bourgery@gmail.com>
This is a re-admission after prior archival of version 0.1.2 dated 2025-05-13
Diff between ggScatRidges versions 0.1.2 dated 2025-05-13 and 1.1.0 dated 2025-09-17
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 4 +--- R/Scatter_ridges_function.R | 20 +++++++++----------- man/ggScatRidges.Rd | 8 ++++---- 5 files changed, 23 insertions(+), 28 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.1 dated 2025-09-17 and 0.2.2 dated 2025-09-17
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 2 +- R/zzz.R |only README.md | 2 +- inst/CITATION | 2 +- inst/doc/vignettes.R | 6 ------ inst/doc/vignettes.Rmd | 10 ++-------- inst/doc/vignettes.pdf |binary vignettes/vignettes.Rmd | 10 ++-------- 10 files changed, 19 insertions(+), 36 deletions(-)
Title: Weibull Regression for a Right-Censored Endpoint with
Interval-Censored Covariate
Description: The function SurvRegCens() of this package allows estimation of a Weibull Regression for a right-censored endpoint, one interval-censored covariate, and an arbitrary number of non-censored covariates. Additional functions allow to switch between different parametrizations of Weibull regression used by different R functions, inference for the mean difference of two arbitrarily censored Normal samples, and estimation of canonical parameters from censored samples for several distributional assumptions. Hubeaux, S. and Rufibach, K. (2014) <doi:10.48550/arXiv.1402.0432>.
Author: Stanislas Hubeaux [aut, cre],
Kaspar Rufibach [aut]
Maintainer: Stanislas Hubeaux <stan.hubeaux@bluewin.ch>
Diff between SurvRegCensCov versions 1.7 dated 2023-09-27 and 1.8 dated 2025-09-17
DESCRIPTION | 23 ++++++++++----- MD5 | 24 +++++++-------- NAMESPACE | 70 +++++++++++++++++++++++----------------------- NEWS | 5 +++ build/vignette.rds |binary inst/doc/weibull.pdf |binary man/ConvertWeibull.Rd | 6 +-- man/NormalMeanDiffCens.Rd | 4 +- man/ParamSampleCens.Rd | 2 - man/SurvRegCens.Rd | 8 ++--- man/WeibullDiag.Rd | 6 +-- man/WeibullReg.Rd | 8 ++--- man/censorContVar.Rd | 2 - 13 files changed, 86 insertions(+), 72 deletions(-)
More information about SurvRegCensCov at CRAN
Permanent link
Title: Estimating Marginal Effects with Prognostic Covariate Adjustment
Description: Conduct power analyses and inference of marginal effects.
Uses plug-in estimation and influence functions to perform robust inference,
optionally leveraging historical data to increase precision with
prognostic covariate adjustment. The methods are described in
Højbjerre-Frandsen et al. (2025) <doi:10.48550/arXiv.2503.22284>.
Author: Mathias Lerbech Jeppesen [aut, cre],
Emilie Hojbjerre-Frandsen [aut],
Novo Nordisk A/S [cph]
Maintainer: Mathias Lerbech Jeppesen <mathiasljeppesen@outlook.com>
Diff between postcard versions 1.0.1 dated 2025-07-01 and 1.1.0 dated 2025-09-17
postcard-1.0.1/postcard/tests/testthat/_snaps/power.md |only postcard-1.0.1/postcard/tests/testthat/test-power.R |only postcard-1.1.0/postcard/DESCRIPTION | 16 postcard-1.1.0/postcard/MD5 | 106 +-- postcard-1.1.0/postcard/NAMESPACE | 15 postcard-1.1.0/postcard/NEWS.md | 11 postcard-1.1.0/postcard/R/create_example_data.R | 15 postcard-1.1.0/postcard/R/fit_best_learner.R | 2 postcard-1.1.0/postcard/R/postcard-package.R | 8 postcard-1.1.0/postcard/R/power_linear.R | 120 ++- postcard-1.1.0/postcard/R/power_marginaleffect.R | 18 postcard-1.1.0/postcard/R/rctglm.R | 5 postcard-1.1.0/postcard/R/rctglm_methods.R | 22 postcard-1.1.0/postcard/R/rctglm_prog_methods.R | 6 postcard-1.1.0/postcard/R/rctglm_utils.R | 4 postcard-1.1.0/postcard/R/rctglm_with_prognosticscore.R | 6 postcard-1.1.0/postcard/R/repeat_power_plot.R |only postcard-1.1.0/postcard/R/utils.R | 126 +++ postcard-1.1.0/postcard/R/zzz.R | 6 postcard-1.1.0/postcard/README.md | 21 postcard-1.1.0/postcard/build/partial.rdb |binary postcard-1.1.0/postcard/build/vignette.rds |binary postcard-1.1.0/postcard/inst/doc/model-fit.R | 18 postcard-1.1.0/postcard/inst/doc/model-fit.Rmd | 22 postcard-1.1.0/postcard/inst/doc/model-fit.html | 71 +- postcard-1.1.0/postcard/inst/doc/postcard.R | 48 - postcard-1.1.0/postcard/inst/doc/postcard.Rmd | 90 +- postcard-1.1.0/postcard/inst/doc/postcard.html | 275 +++++--- postcard-1.1.0/postcard/inst/doc/prospective-power.R | 201 +---- postcard-1.1.0/postcard/inst/doc/prospective-power.Rmd | 242 +------ postcard-1.1.0/postcard/inst/doc/prospective-power.html | 342 +++------- postcard-1.1.0/postcard/man/glm_data.Rd | 15 postcard-1.1.0/postcard/man/postcard-package.Rd | 2 postcard-1.1.0/postcard/man/power_linear.Rd | 35 - postcard-1.1.0/postcard/man/power_marginaleffect.Rd | 2 postcard-1.1.0/postcard/man/prog.Rd | 6 postcard-1.1.0/postcard/man/rctglm.Rd | 3 postcard-1.1.0/postcard/man/rctglm_methods.Rd | 17 postcard-1.1.0/postcard/man/rctglm_with_prognosticscore.Rd | 9 postcard-1.1.0/postcard/man/repeat_power_linear.Rd |only postcard-1.1.0/postcard/man/repeat_power_marginaleffect.Rd |only postcard-1.1.0/postcard/tests/testthat/_snaps/power-linear.md |only postcard-1.1.0/postcard/tests/testthat/_snaps/power_marginaleffect.md | 52 + postcard-1.1.0/postcard/tests/testthat/_snaps/rctglm_prog_methods.md | 307 ++++---- postcard-1.1.0/postcard/tests/testthat/_snaps/rctglm_with_prognosticscore.md | 234 +++--- postcard-1.1.0/postcard/tests/testthat/_snaps/repeat_power_plot |only postcard-1.1.0/postcard/tests/testthat/_snaps/repeat_power_plot.md |only postcard-1.1.0/postcard/tests/testthat/helper-vdiffr.R |only postcard-1.1.0/postcard/tests/testthat/test-power-linear.R |only postcard-1.1.0/postcard/tests/testthat/test-power_marginaleffect.R | 17 postcard-1.1.0/postcard/tests/testthat/test-rctglm.R | 42 - postcard-1.1.0/postcard/tests/testthat/test-rctglm_prog_methods.R | 6 postcard-1.1.0/postcard/tests/testthat/test-rctglm_with_prognosticscore.R | 24 postcard-1.1.0/postcard/tests/testthat/test-repeat_power_plot.R |only postcard-1.1.0/postcard/tests/testthat/test-utils.R | 120 +++ postcard-1.1.0/postcard/vignettes/model-fit.Rmd | 22 postcard-1.1.0/postcard/vignettes/postcard.Rmd | 90 +- postcard-1.1.0/postcard/vignettes/prospective-power.Rmd | 242 +------ 58 files changed, 1594 insertions(+), 1467 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Asbjoern Risom [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2025.05.20 dated 2025-05-20 and 2025.09.17 dated 2025-09-17
DESCRIPTION | 15 - MD5 | 61 ++--- NAMESPACE | 1 R/Brier.binary.R | 12 - R/CSC.R | 6 R/IPA.R | 10 R/IPACompute.R |only R/Score.R | 50 ++-- R/ate-pointEstimate.R | 8 R/ate.R | 39 ++- R/ate_initArgs.R | 6 R/calcSeCox.R | 8 R/computePerformance.R | 21 + R/coxLP.R | 8 R/iidCox.R | 25 +- R/predict.CauseSpecificCox.R | 2 R/predictCox.R | 9 R/predictRisk.R | 12 - R/print.Score.R | 26 +- R/summary.Score.R | 33 +- R/synthesize.R | 4 build/vignette.rds |binary inst/doc/IPA.html | 380 +++++++++++++++++---------------- man/CSC.Rd | 6 man/Score.Rd | 7 man/predictCox.Rd | 6 man/riskRegression-package.Rd | 3 src/Makevars | 20 - src/Makevars.win | 3 tests/testthat/test-iidCox.R | 6 tests/testthat/test-score-train-test.R | 131 +++++++---- tests/testthat/test-score.R | 22 - 32 files changed, 522 insertions(+), 418 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between pillar versions 1.11.0 dated 2025-07-04 and 1.11.1 dated 2025-09-17
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 9 ++++++--- R/glimpse.R | 15 +++++++++++---- R/tbl-format-setup.R | 4 ++++ README.md | 2 +- build/vignette.rds |binary inst/doc/printing.html | 4 ++-- man/scale_x_num.Rd | 10 ++++++---- tests/testthat/_snaps/tbl-format-header.md | 2 +- tests/testthat/_snaps/tbl-format-setup.md | 14 +++++++------- tests/testthat/helper-unknown-rows.R | 5 ++++- tests/testthat/test-format_decimal.R | 4 ++-- 14 files changed, 62 insertions(+), 42 deletions(-)
Title: Robust Image Rendering Support for 'ggplot2'
Description: A 'ggplot2' extension that enables robust image grobs in
panels and theme elements.
Author: Sebastian Carl [aut, cre, cph]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between ggpath versions 1.0.2 dated 2024-08-20 and 1.1.0 dated 2025-09-17
DESCRIPTION | 16 - LICENSE | 4 MD5 | 65 ++-- NAMESPACE | 39 +- NEWS.md | 10 R/build_grobs.R | 196 ++++++------ R/geom_from_path.R | 230 +++++++------- R/geom_lines.R | 353 ++++++++++------------ R/ggpath-package.R | 10 R/theme_element.R | 217 ++++++++----- R/utils.R |only R/zzz.R | 3 README.md | 443 +++++++++++++--------------- man/element_path.Rd | 46 +- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/geom_from_path.Rd | 296 +++++++++--------- man/geom_lines.Rd | 287 +++++++++--------- man/ggpath-package.Rd | 78 ++-- tests/testthat.R | 8 tests/testthat/_snaps/geom_from_path/p1.svg | 129 ++++---- tests/testthat/_snaps/geom_lines/p1.svg | 199 ++++++------ tests/testthat/_snaps/geom_lines/p2.svg | 195 ++++++------ tests/testthat/_snaps/geom_lines/p3.svg | 195 ++++++------ tests/testthat/_snaps/geom_lines/p4.svg | 199 ++++++------ tests/testthat/_snaps/geom_lines/p5.svg | 181 +++++------ tests/testthat/_snaps/theme-elements/p1.svg | 103 +++--- tests/testthat/_snaps/theme-elements/p2.svg | 103 +++--- tests/testthat/_snaps/theme-elements/p3.svg | 152 ++++----- tests/testthat/test-geom_from_path.R | 98 +++--- tests/testthat/test-geom_lines.R | 118 +++---- tests/testthat/test-theme-elements.R | 42 +- 34 files changed, 2037 insertions(+), 1978 deletions(-)
Title: Scalable Joint Species Distribution Modeling
Description: A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) [...truncated...]
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.6 dated 2024-08-19 and 1.0.7 dated 2025-09-17
DESCRIPTION | 15 MD5 | 40 - NEWS.md | 9 R/anova.R | 24 - R/importance.R | 101 ++-- R/installation_help.R | 8 R/internalStructure.R | 231 ++++++++--- R/sjSDM.R | 4 R/sjSDM_cv.R | 5 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/sjSDM_Introduction.Rmd | 8 inst/doc/sjSDM_Introduction.html | 24 - inst/python/sjSDM_py/__pycache__/dist_mvp.cpython-310.pyc |binary inst/python/sjSDM_py/__pycache__/model_sjSDM.cpython-310.pyc |binary inst/python/sjSDM_py/dist_mvp.py | 4 inst/python/sjSDM_py/model_sjSDM.py | 35 + man/installation_help.Rd | 8 tests/testthat/test-5-importance.R | 218 +++++----- vignettes/sjSDM_Introduction.Rmd | 8 vignettes/sjSDM_Introduction.orig | 8 21 files changed, 458 insertions(+), 292 deletions(-)
Title: Bootstrapping Helpers for Structural Equation Modelling
Description: A collection of helper functions for forming
bootstrapping confidence intervals and examining bootstrap
estimates in structural equation modelling. Currently
supports models fitted by the 'lavaan' package by
Rosseel (2012) <doi: 10.18637/jss.v048.i02>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between semboottools versions 0.1.0 dated 2025-04-01 and 0.1.1 dated 2025-09-17
DESCRIPTION | 12 MD5 | 8 NEWS.md | 78 +++++- README.md | 13 - man/hist_qq_boot.Rd | 662 ++++++++++++++++++++++++++-------------------------- 5 files changed, 424 insertions(+), 349 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.21.0 dated 2025-04-24 and 1.22.0 dated 2025-09-17
broom.helpers-1.21.0/broom.helpers/R/select_utilities.R |only broom.helpers-1.21.0/broom.helpers/man/dot-formula_list_to_named_list.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-generic_selector.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-select_to_varnames.Rd |only broom.helpers-1.22.0/broom.helpers/DESCRIPTION | 20 broom.helpers-1.22.0/broom.helpers/MD5 | 96 +- broom.helpers-1.22.0/broom.helpers/NAMESPACE | 8 broom.helpers-1.22.0/broom.helpers/NEWS.md | 17 broom.helpers-1.22.0/broom.helpers/R/broom.helpers-package.R | 2 broom.helpers-1.22.0/broom.helpers/R/custom_tidiers.R | 43 - broom.helpers-1.22.0/broom.helpers/R/model_get_assign.R | 13 broom.helpers-1.22.0/broom.helpers/R/model_get_contrasts.R | 10 broom.helpers-1.22.0/broom.helpers/R/model_get_model_frame.R | 9 broom.helpers-1.22.0/broom.helpers/R/model_get_model_matrix.R | 14 broom.helpers-1.22.0/broom.helpers/R/model_get_weights.R | 10 broom.helpers-1.22.0/broom.helpers/build/vignette.rds |binary broom.helpers-1.22.0/broom.helpers/data/supported_models.rda |binary broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.R | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.Rmd | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.html | 394 +++++----- broom.helpers-1.22.0/broom.helpers/man/model_get_assign.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_contrasts.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_model_matrix.Rd | 7 broom.helpers-1.22.0/broom.helpers/man/model_get_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/model_get_weights.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_list_variables.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/select_helpers.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/supported_models.Rd | 1 broom.helpers-1.22.0/broom.helpers/man/tidy_add_estimate_to_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_header_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_all_effects.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_comparisons.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_slopes.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_broom.Rd | 4 broom.helpers-1.22.0/broom.helpers/man/tidy_ggpredict.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_group_by.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_predictions.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_margins.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_multgee.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_parameters.Rd | 10 broom.helpers-1.22.0/broom.helpers/man/tidy_plus_plus.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_svy_vglm.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_vgam.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_with_broom_or_parameters.Rd | 9 broom.helpers-1.22.0/broom.helpers/man/tidy_zeroinfl.Rd | 6 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-model_get_n.R | 25 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-tidy_plus_plus.R | 36 broom.helpers-1.22.0/broom.helpers/vignettes/broom-helpers.Rmd | 2 51 files changed, 466 insertions(+), 333 deletions(-)
Title: R Interface to the A/B Street Transport System Simulation
Software
Description: Provides functions to convert origin-destination data,
represented as straight 'desire lines' in the 'sf' Simple Features
class system, into JSON files that can be directly imported into
A/B Street <https://www.abstreet.org>, a free and open source tool
for simulating urban transport systems and scenarios of change
<doi:10.1007/s10109-020-00342-2>.
Author: Robin Lovelace [aut, cre] ,
Nathanael Sheehan [aut] ,
Trevor Nederlof [aut],
Lucas Dias [ctb],
Dustin Carlino [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between abstr versions 0.4.1 dated 2021-11-30 and 0.4.2 dated 2025-09-17
DESCRIPTION | 29 MD5 | 90 +- NAMESPACE | 18 NEWS.md | 57 + R/ab_scenario.R | 680 +++++++++++----------- R/data.R | 12 R/montlake_buildings.R | 54 - R/montlake_od.R | 38 - R/montlake_zones.R | 32 - R/sao_paulo_activity_df_20.R | 124 ++-- R/utils-pipe.R | 38 - README.md | 538 +++++++++-------- build/vignette.rds |binary inst/doc/abstr.R | 96 +-- inst/doc/abstr.Rmd | 352 +++++------ inst/doc/abstr.html | 841 ++++++++++++++++++--------- inst/doc/activity.R | 234 +++---- inst/doc/activity.Rmd | 496 ++++++++-------- inst/doc/activity.html | 1002 ++++++++++++++++++++------------- inst/doc/montlake.R | 254 ++++---- inst/doc/montlake.Rmd | 452 +++++++------- inst/doc/montlake.html | 921 +++++++++++++++++++----------- inst/doc/pct_to_abstr.R | 404 ++++++------- inst/doc/pct_to_abstr.Rmd | 679 +++++++++++----------- inst/doc/pct_to_abstr.html | 1087 ++++++++++++++++++++++-------------- inst/extdata/activity_leeds.json | 188 +++--- inst/extdata/minimal_scenario.json | 86 +- inst/extdata/minimal_scenario2.json | 162 ++--- man/ab_json.Rd | 132 ++-- man/ab_save.Rd | 38 - man/ab_scenario.Rd | 180 ++--- man/ab_sf.Rd | 76 +- man/ab_time_normal.Rd | 64 +- man/figures/README-input-1.png |binary man/figures/README-outputplot-1.png |binary man/leeds_site_area.Rd | 26 man/montlake_buildings.Rd | 70 +- man/montlake_od.Rd | 60 - man/montlake_zones.Rd | 54 - man/pipe.Rd | 40 - man/sao_paulo_activity_df_20.Rd | 86 +- man/sao_paulo_activity_sf_20.Rd | 84 +- vignettes/abstr.Rmd | 352 +++++------ vignettes/activity.Rmd | 496 ++++++++-------- vignettes/montlake.Rmd | 452 +++++++------- vignettes/pct_to_abstr.Rmd | 679 +++++++++++----------- 46 files changed, 6443 insertions(+), 5410 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.6.0 dated 2025-07-18 and 1.7.0 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 57 ++++++++++++++++++++++++++------------------- NEWS.md | 15 +++++++++++ R/rd-GHR04.R | 16 ++++++++---- R/rd-Lipset59.R | 11 +++++--- R/rd-Weede84.R |only R/rd-mmb_war.R |only R/rd-stevesteps.R |only build/partial.rdb |binary data/DJIA.rda |binary data/ESS10NO.rda |binary data/GHR04.rda |binary data/PPGE.rda |binary data/USFAHR.rda |binary data/Weede84.rda |only data/chile88.rda |binary data/china_peace.rda |binary data/coffee_imports.rda |binary data/country_isocodes.rda |binary data/eu_ua_fta24.rda |binary data/mmb_war.rda |only data/rok_unga.rda |binary data/scb_regions.rda |binary data/states_war.rda |binary data/stevesteps.rda |only data/thatcher_approval.rda |binary data/turnips.rda |binary data/wb_groups.rda |binary data/wbd_example.rda |binary man/GHR04.Rd | 16 ++++++++---- man/Lipset59.Rd | 11 +++++--- man/Weede84.Rd |only man/mmb_war.Rd |only man/stevesteps.Rd |only 34 files changed, 87 insertions(+), 45 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>
Diff between SEQTaRget versions 0.13.1 dated 2025-09-15 and 1.0.0 dated 2025-09-17
DESCRIPTION | 18 +++++++++++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/SEQopts.R | 3 ++- R/SEQuential.R | 4 ++-- R/class_definitions.R | 2 +- README.md | 37 +++++++++++++++++++------------------ inst/doc/ITT.html | 2 +- inst/doc/SEQuential.html | 2 +- inst/doc/censoring.html | 2 +- inst/doc/doseresponse.html | 2 +- man/SEQopts.Rd | 2 +- man/SEQuential.Rd | 4 ++-- 13 files changed, 57 insertions(+), 46 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.5 dated 2025-08-18 and 2.3.6 dated 2025-09-17
GitStats-2.3.5/GitStats/inst/cache_workflow.R |only GitStats-2.3.5/GitStats/inst/example_workflow.R |only GitStats-2.3.5/GitStats/inst/get_commits_workflow.R |only GitStats-2.3.5/GitStats/inst/get_files_workflow.R |only GitStats-2.3.5/GitStats/inst/get_issues_workflow.R |only GitStats-2.3.5/GitStats/inst/get_orgs_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_for_individual_users.R |only GitStats-2.3.5/GitStats/inst/get_repos_tree_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_urls_workflow.R |only GitStats-2.3.5/GitStats/inst/get_storage_workflow.R |only GitStats-2.3.5/GitStats/inst/set_hosts.R |only GitStats-2.3.5/GitStats/inst/set_many_repos.R |only GitStats-2.3.5/GitStats/inst/set_tokens.R |only GitStats-2.3.5/GitStats/inst/verbose_workflow.R |only GitStats-2.3.5/GitStats/tests/testthat/_snaps/00-api-requests.md |only GitStats-2.3.6/GitStats/DESCRIPTION | 6 GitStats-2.3.6/GitStats/MD5 | 93 +--- GitStats-2.3.6/GitStats/NEWS.md | 13 GitStats-2.3.6/GitStats/R/EngineGraphQL.R | 58 +- GitStats-2.3.6/GitStats/R/EngineGraphQLGitHub.R | 231 +++++----- GitStats-2.3.6/GitStats/R/EngineGraphQLGitLab.R | 156 ++++-- GitStats-2.3.6/GitStats/R/EngineRest.R | 31 - GitStats-2.3.6/GitStats/R/EngineRestGitHub.R | 106 ++-- GitStats-2.3.6/GitStats/R/EngineRestGitLab.R | 129 +++-- GitStats-2.3.6/GitStats/R/GQLQueryGitHub.R | 17 GitStats-2.3.6/GitStats/R/GQLQueryGitLab.R | 17 GitStats-2.3.6/GitStats/R/GitHost.R | 124 +++-- GitStats-2.3.6/GitStats/R/GitHostGitHub.R | 7 GitStats-2.3.6/GitStats/R/GitHostGitLab.R | 32 - GitStats-2.3.6/GitStats/R/GitStats.R | 67 +- GitStats-2.3.6/GitStats/R/get_repos.R | 4 GitStats-2.3.6/GitStats/man/get_repos.Rd | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/00-get_orgs-GitLab.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 30 - GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 6 GitStats-2.3.6/GitStats/tests/testthat/_snaps/02-get_commits-GitHub.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitHub.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitLab.md | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/helpers.md | 2 GitStats-2.3.6/GitStats/tests/testthat/helper-error-fixtures.R | 16 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-responses.R | 10 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-tables.R | 21 GitStats-2.3.6/GitStats/tests/testthat/helper-fixtures.R | 100 +++- GitStats-2.3.6/GitStats/tests/testthat/test-00-api-requests.R | 29 - GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitHub.R | 19 GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitLab.R | 20 GitStats-2.3.6/GitStats/tests/testthat/test-00-graphql_errors.R | 11 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 170 ++++--- GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 17 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 2 GitStats-2.3.6/GitStats/tests/testthat/test-02-get_commits-GitHub.R | 41 + GitStats-2.3.6/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R | 4 GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitHub.R |only GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitLab.R |only GitStats-2.3.6/GitStats/tests/testthat/test-06-get_issues-GitHub.R | 19 56 files changed, 1000 insertions(+), 636 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 2.1.1 dated 2025-07-26 and 3.0.0 dated 2025-09-17
eyeris-2.1.1/eyeris/R/utils-alert.R |only eyeris-2.1.1/eyeris/man/alert.Rd |only eyeris-3.0.0/eyeris/DESCRIPTION | 16 eyeris-3.0.0/eyeris/MD5 | 254 eyeris-3.0.0/eyeris/NAMESPACE | 15 eyeris-3.0.0/eyeris/NEWS.md | 141 eyeris-3.0.0/eyeris/R/constants.R | 10 eyeris-3.0.0/eyeris/R/core-logging.R |only eyeris-3.0.0/eyeris/R/eyeris-package.R | 3 eyeris-3.0.0/eyeris/R/pipeline-bidsify.R | 2881 ++++------ eyeris-3.0.0/eyeris/R/pipeline-bin.R | 36 eyeris-3.0.0/eyeris/R/pipeline-confounds.R | 243 eyeris-3.0.0/eyeris/R/pipeline-deblink.R | 29 eyeris-3.0.0/eyeris/R/pipeline-detransient.R | 10 eyeris-3.0.0/eyeris/R/pipeline-detrend.R | 9 eyeris-3.0.0/eyeris/R/pipeline-downsample.R | 48 eyeris-3.0.0/eyeris/R/pipeline-epoch.R | 266 eyeris-3.0.0/eyeris/R/pipeline-glassbox.R | 504 - eyeris-3.0.0/eyeris/R/pipeline-handler.R | 74 eyeris-3.0.0/eyeris/R/pipeline-interpolate.R | 23 eyeris-3.0.0/eyeris/R/pipeline-loadasc.R | 79 eyeris-3.0.0/eyeris/R/pipeline-lpfilt.R | 25 eyeris-3.0.0/eyeris/R/pipeline-zscore.R | 46 eyeris-3.0.0/eyeris/R/plot.eyeris.R | 287 eyeris-3.0.0/eyeris/R/utils-baseline.R | 51 eyeris-3.0.0/eyeris/R/utils-checks.R | 128 eyeris-3.0.0/eyeris/R/utils-database.R |only eyeris-3.0.0/eyeris/R/utils-epoch.R | 110 eyeris-3.0.0/eyeris/R/utils-error_handler.R | 2 eyeris-3.0.0/eyeris/R/utils-eyelogger.R | 6 eyeris-3.0.0/eyeris/R/utils-gallery.R | 350 + eyeris-3.0.0/eyeris/R/utils-parquet-split.R |only eyeris-3.0.0/eyeris/R/utils-parsers.R | 32 eyeris-3.0.0/eyeris/R/utils-progress_bar.R | 9 eyeris-3.0.0/eyeris/R/utils-render_report.R | 160 eyeris-3.0.0/eyeris/R/utils-zip-cleanup.R |only eyeris-3.0.0/eyeris/R/utils-zip-gallery.R |only eyeris-3.0.0/eyeris/R/zzz.R | 35 eyeris-3.0.0/eyeris/README.md | 267 eyeris-3.0.0/eyeris/build/vignette.rds |binary eyeris-3.0.0/eyeris/inst/WORDLIST | 42 eyeris-3.0.0/eyeris/inst/doc/anatomy.html | 5 eyeris-3.0.0/eyeris/inst/doc/chunked-database-export.R |only 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Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 2.1.0 dated 2025-05-07 and 2.2.0 dated 2025-09-17
DESCRIPTION | 6 +- MD5 | 8 +-- R/cctest.R | 126 ++++++++++++++++++++++++++---------------------------- build/partial.rdb |binary man/cctest.Rd | 114 ++++++++++++++++++++++++++---------------------- 5 files changed, 130 insertions(+), 124 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.0 dated 2025-09-16 and 0.2.1 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------- NEWS.md | 6 ++++ README.md | 2 - inst/CITATION | 2 - inst/doc/vignettes.R | 6 ++++ inst/doc/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- inst/doc/vignettes.pdf |binary vignettes/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- 9 files changed, 88 insertions(+), 66 deletions(-)
Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API'
<http://core.telegram.org/bots/api>. In addition to the pure API
implementation, it features a number of tools to make the development of
'Telegram' bots with R easy and straightforward, providing an easy-to-use
interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre],
Chris Stefano [ctb]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Diff between telegram.bot versions 3.0.0 dated 2022-09-07 and 3.0.1 dated 2025-09-17
DESCRIPTION | 8 MD5 | 226 - NAMESPACE | 104 NEWS.md | 190 - R/base.R | 216 - R/basefilter.R | 157 - R/bot.R | 3585 +++++++++++------------- R/callbackqueryhandler.R | 121 R/commandhandler.R | 257 - R/dispatcher.R | 329 +- R/errorhandler.R | 97 R/filters.R | 121 R/handler.R | 283 - R/inlinequeryresult.R | 101 R/messagehandler.R | 165 - R/replymarkup.R | 713 ++-- R/telegram.bot-package.R | 107 R/update.R | 427 +- R/updater.R | 481 +-- R/utils.R | 171 - R/webhook.R | 872 ++--- README.md | 424 +- build/vignette.rds |binary inst/doc/telegrambot-advanced-filters.R | 85 inst/doc/telegrambot-advanced-filters.Rmd | 213 - inst/doc/telegrambot-advanced-filters.html | 896 +++-- inst/doc/telegrambot-basic-functionalities.R | 96 inst/doc/telegrambot-basic-functionalities.Rmd | 210 - inst/doc/telegrambot-basic-functionalities.html | 925 +++--- inst/doc/telegrambot-building-a-bot.R | 68 inst/doc/telegrambot-building-a-bot.Rmd | 208 - inst/doc/telegrambot-building-a-bot.html | 901 +++--- inst/doc/telegrambot-introduction.R | 160 - inst/doc/telegrambot-introduction.Rmd | 360 +- inst/doc/telegrambot-introduction.html | 1113 +++---- inst/doc/telegrambot-set-a-proxy.R | 24 inst/doc/telegrambot-set-a-proxy.Rmd | 62 inst/doc/telegrambot-set-a-proxy.html | 743 ++-- inst/doc/telegrambot-the-add-operator.R | 108 inst/doc/telegrambot-the-add-operator.Rmd | 198 - inst/doc/telegrambot-the-add-operator.html | 845 ++--- man/BaseFilter.Rd | 86 man/Bot.Rd | 186 - man/CallbackQueryHandler.Rd | 44 man/CommandHandler.Rd | 116 man/Dispatcher.Rd | 64 man/ErrorHandler.Rd | 78 man/ForceReply.Rd | 66 man/Handler.Rd | 180 - man/InlineKeyboardButton.Rd | 104 man/InlineKeyboardMarkup.Rd | 124 man/InlineQueryResult.Rd | 88 man/KeyboardButton.Rd | 70 man/MessageFilters.Rd | 98 man/MessageHandler.Rd | 70 man/ReplyKeyboardMarkup.Rd | 116 man/ReplyKeyboardRemove.Rd | 110 man/TelegramObject-add.Rd | 126 man/TelegramObject.Rd | 86 man/Update.Rd | 76 man/Updater.Rd | 184 - man/Webhook.Rd | 298 - man/add_error_handler.Rd | 70 man/add_handler.Rd | 66 man/answerCallbackQuery.Rd | 76 man/answerInlineQuery.Rd | 130 man/bot_token.Rd | 54 man/check_update.Rd | 32 man/clean_updates.Rd | 24 man/deleteMessage.Rd | 54 man/deleteWebhook.Rd | 30 man/editMessageCaption.Rd | 94 man/editMessageReplyMarkup.Rd | 78 man/editMessageText.Rd | 102 man/effective_chat.Rd | 28 man/effective_message.Rd | 28 man/effective_user.Rd | 24 man/filtersLogic.Rd | 68 man/forwardMessage.Rd | 52 man/from_chat_id.Rd | 22 man/from_user_id.Rd | 22 man/getFile.Rd | 82 man/getMe.Rd | 28 man/getUpdates.Rd | 106 man/getUserProfilePhotos.Rd | 66 man/getWebhookInfo.Rd | 34 man/handle_update.Rd | 44 man/leaveChat.Rd | 36 man/running.Rd | 22 man/sendAnimation.Rd | 146 man/sendAudio.Rd | 152 - man/sendChatAction.Rd | 92 man/sendDocument.Rd | 138 man/sendLocation.Rd | 110 man/sendMessage.Rd | 124 man/sendPhoto.Rd | 130 man/sendSticker.Rd | 110 man/sendVideo.Rd | 154 - man/sendVideoNote.Rd | 122 man/sendVoice.Rd | 138 man/setWebhook.Rd | 132 man/set_token.Rd | 28 man/start_polling.Rd | 96 man/start_server.Rd | 98 man/stop_polling.Rd | 60 man/stop_server.Rd | 56 man/telegram.bot.Rd | 132 man/user_id.Rd | 54 vignettes/telegrambot-advanced-filters.Rmd | 213 - vignettes/telegrambot-basic-functionalities.Rmd | 210 - vignettes/telegrambot-building-a-bot.Rmd | 208 - vignettes/telegrambot-introduction.Rmd | 360 +- vignettes/telegrambot-set-a-proxy.Rmd | 62 vignettes/telegrambot-the-add-operator.Rmd | 198 - 114 files changed, 11819 insertions(+), 11716 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry [aut, cre],
Amy Gill [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.8.0 dated 2024-03-01 and 0.9.0 dated 2025-09-17
DESCRIPTION | 23 ++++++++++----- MD5 | 16 +++++++--- NAMESPACE | 1 R/fit_recommender_model.R |only R/results_us_election_2012.R |only build/partial.rdb |binary data/polls_us_election_2016.rda |binary data/results_us_election_2012.rda |only inst/script/make-polls_us_election_2016.R | 41 +++++++++++++++------------- inst/script/make-results_us_election_2012.R |only man/fit_recommender_model.Rd |only man/results_us_election_2012.Rd |only 12 files changed, 51 insertions(+), 30 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.7 dated 2025-08-18 and 7.8 dated 2025-09-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/mkde.R | 26 ++++++++++++++++---------- man/Compositional-package.Rd | 4 ++-- man/mkde.Rd | 5 ++++- 6 files changed, 32 insertions(+), 23 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.2 dated 2025-02-15 and 2.2-1 dated 2025-09-17
aqp-2.2-1/aqp/DESCRIPTION | 11 aqp-2.2-1/aqp/MD5 | 109 +++----- aqp-2.2-1/aqp/NAMESPACE | 3 aqp-2.2-1/aqp/NEWS.md | 12 aqp-2.2-1/aqp/R/NCSP.R | 100 ++++--- aqp-2.2-1/aqp/R/SoilProfileCollection-metadata.R | 3 aqp-2.2-1/aqp/R/accumulateDepths.R | 22 + aqp-2.2-1/aqp/R/aqp-package.R | 2 aqp-2.2-1/aqp/R/col2Munsell.R | 8 aqp-2.2-1/aqp/R/colorChart.R | 6 aqp-2.2-1/aqp/R/data-documentation.R | 6 aqp-2.2-1/aqp/R/evalMissingData.R | 10 aqp-2.2-1/aqp/R/fragmentClasses.R | 2 aqp-2.2-1/aqp/R/hzTransitionProbabilities.R | 2 aqp-2.2-1/aqp/R/mixMunsell.R | 4 aqp-2.2-1/aqp/R/mostLikelyHzSequence.R | 2 aqp-2.2-1/aqp/R/munsell2rgb.R | 14 - aqp-2.2-1/aqp/R/particleSizeClasses.R |only aqp-2.2-1/aqp/R/random_profile.R | 57 ++++ aqp-2.2-1/aqp/build/partial.rdb |binary aqp-2.2-1/aqp/build/vignette.rds |binary aqp-2.2-1/aqp/data/munsell.spectra.rda |binary aqp-2.2-1/aqp/data/munsell.spectra.wide.rda |binary aqp-2.2-1/aqp/data/munsellHuePosition.rda |binary aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 136 +++++----- aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.R | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.html | 4 aqp-2.2-1/aqp/inst/doc/NCSP.R | 4 aqp-2.2-1/aqp/inst/doc/NCSP.Rmd | 4 aqp-2.2-1/aqp/inst/doc/NCSP.html | 12 aqp-2.2-1/aqp/inst/doc/label-placement.R | 19 - aqp-2.2-1/aqp/inst/doc/label-placement.Rmd | 20 - aqp-2.2-1/aqp/inst/doc/label-placement.html | 134 +++++---- aqp-2.2-1/aqp/man/NCSP.Rd | 28 -- aqp-2.2-1/aqp/man/accumulateDepths.Rd | 6 aqp-2.2-1/aqp/man/col2Munsell.Rd | 10 aqp-2.2-1/aqp/man/colorChart.Rd | 2 aqp-2.2-1/aqp/man/mixMunsell.Rd | 4 aqp-2.2-1/aqp/man/munsell.spectra.Rd | 4 aqp-2.2-1/aqp/man/munsell2rgb.Rd | 6 aqp-2.2-1/aqp/man/random_profile.Rd | 5 aqp-2.2-1/aqp/man/rgb2munsell.Rd | 10 aqp-2.2-1/aqp/man/rp.Rd |only aqp-2.2-1/aqp/tests/testthat/Rplots.pdf |binary aqp-2.2-1/aqp/tests/testthat/test-NCSP.R | 37 ++ aqp-2.2-1/aqp/tests/testthat/test-spec2Munsell.R | 42 +++ aqp-2.2-1/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/vignettes/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/vignettes/NCSP.Rmd | 4 aqp-2.2-1/aqp/vignettes/label-placement.Rmd | 20 - aqp-2.2/aqp/R/unroll.R |only aqp-2.2/aqp/inst/_pkgdown.yml |only aqp-2.2/aqp/inst/doc/missing-data.R |only aqp-2.2/aqp/inst/doc/missing-data.Rmd |only aqp-2.2/aqp/inst/doc/missing-data.html |only aqp-2.2/aqp/man/unroll.Rd |only aqp-2.2/aqp/vignettes/missing-data.Rmd |only 60 files changed, 540 insertions(+), 356 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.19.0-1 dated 2025-07-20 and 0.20.0 dated 2025-09-17
DESCRIPTION | 6 MD5 | 38 - R/driver_void.R | 15 man/adbc_driver_load.Rd | 6 man/adbc_load_flags.Rd | 11 src/Makevars | 3 src/Makevars.win | 3 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/sqlite/sqlite.cc | 17 src/c/driver/sqlite/statement_reader.c | 56 ++ src/c/driver/sqlite/statement_reader.h | 6 src/c/driver_manager/adbc_driver_manager.cc | 522 ++++++++++++++++++++----- src/c/driver_manager/current_arch.h | 53 ++ src/c/include/arrow-adbc/adbc_driver_manager.h | 33 + src/c/vendor/nanoarrow/nanoarrow.c | 251 +++++++++++- src/c/vendor/nanoarrow/nanoarrow.h | 447 ++++++++++++++------- src/c/vendor/nanoarrow/nanoarrow.hpp | 473 +++++++++++++++------- src/init.c | 5 src/radbc.cc | 9 tests/testthat/test-driver_void.R | 5 20 files changed, 1508 insertions(+), 469 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elementary indexes are first calculated for a collection
of elementary aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.8.2 dated 2025-03-19 and 0.8.3 dated 2025-09-17
piar-0.8.2/piar/R/elemental_index.R |only piar-0.8.2/piar/man/elemental_index.Rd |only piar-0.8.3/piar/DESCRIPTION | 13 piar-0.8.3/piar/MD5 | 259 +-- piar-0.8.3/piar/NAMESPACE | 6 piar-0.8.3/piar/NEWS.md | 39 piar-0.8.3/piar/R/aggregate.piar_index.R | 196 +- piar-0.8.3/piar/R/aggregation_structure-class.R | 25 piar-0.8.3/piar/R/aggregation_structure.R | 32 piar-0.8.3/piar/R/as_aggregation_structure.R | 10 piar-0.8.3/piar/R/as_index.R | 21 piar-0.8.3/piar/R/chain.R | 14 piar-0.8.3/piar/R/coerce-aggregation_structure.R | 22 piar-0.8.3/piar/R/coerce-index.R | 24 piar-0.8.3/piar/R/contrib.R | 82 - piar-0.8.3/piar/R/cut.piar_aggregation_structure.R | 14 piar-0.8.3/piar/R/elementary_index.R |only piar-0.8.3/piar/R/expand_classification.R | 17 piar-0.8.3/piar/R/extract.piar_index.R | 8 piar-0.8.3/piar/R/head.piar_index.R | 10 piar-0.8.3/piar/R/helpers.R | 145 +- piar-0.8.3/piar/R/impute_prices.R | 51 piar-0.8.3/piar/R/index-class.R | 41 piar-0.8.3/piar/R/is.na.piar_index.R | 2 piar-0.8.3/piar/R/levels.piar_index.R | 2 piar-0.8.3/piar/R/mean.piar_index.R | 87 - piar-0.8.3/piar/R/merge.piar_index.R | 6 piar-0.8.3/piar/R/split.piar_index.R | 32 piar-0.8.3/piar/R/split_classification.R | 10 piar-0.8.3/piar/R/stack.piar_index.R | 4 piar-0.8.3/piar/R/time.piar_index.R | 4 piar-0.8.3/piar/R/update.aggregation_structure.R | 16 piar-0.8.3/piar/R/weights.piar_aggregation_structure.R | 22 piar-0.8.3/piar/R/window.piar_index.R | 14 piar-0.8.3/piar/R/zzz.R |only piar-0.8.3/piar/README.md | 65 piar-0.8.3/piar/build/partial.rdb |binary piar-0.8.3/piar/build/vignette.rds |binary piar-0.8.3/piar/inst/doc/adjust-weights.R | 16 piar-0.8.3/piar/inst/doc/adjust-weights.Rmd | 24 piar-0.8.3/piar/inst/doc/adjust-weights.html | 94 - piar-0.8.3/piar/inst/doc/contributions.R | 6 piar-0.8.3/piar/inst/doc/contributions.Rmd | 12 piar-0.8.3/piar/inst/doc/contributions.html | 67 piar-0.8.3/piar/inst/doc/imputation.R | 2 piar-0.8.3/piar/inst/doc/imputation.Rmd | 20 piar-0.8.3/piar/inst/doc/imputation.html | 49 piar-0.8.3/piar/inst/doc/index-number-formulas.R | 40 piar-0.8.3/piar/inst/doc/index-number-formulas.Rmd | 64 piar-0.8.3/piar/inst/doc/index-number-formulas.html | 150 +- piar-0.8.3/piar/inst/doc/matrix-aggregation.R | 6 piar-0.8.3/piar/inst/doc/matrix-aggregation.Rmd | 22 piar-0.8.3/piar/inst/doc/matrix-aggregation.html | 88 - piar-0.8.3/piar/inst/doc/multiple-baskets.R | 12 piar-0.8.3/piar/inst/doc/multiple-baskets.Rmd | 20 piar-0.8.3/piar/inst/doc/multiple-baskets.html | 101 - piar-0.8.3/piar/inst/doc/multiple-data-sources.R | 6 piar-0.8.3/piar/inst/doc/multiple-data-sources.Rmd | 10 piar-0.8.3/piar/inst/doc/multiple-data-sources.html | 50 piar-0.8.3/piar/inst/doc/multiple-dimensions.R | 6 piar-0.8.3/piar/inst/doc/multiple-dimensions.Rmd | 8 piar-0.8.3/piar/inst/doc/multiple-dimensions.html | 59 piar-0.8.3/piar/inst/doc/piar.R | 4 piar-0.8.3/piar/inst/doc/piar.Rmd | 36 piar-0.8.3/piar/inst/doc/piar.html | 150 +- piar-0.8.3/piar/inst/doc/spatial-price-index.html | 30 piar-0.8.3/piar/inst/doc/subperiods.R | 2 piar-0.8.3/piar/inst/doc/subperiods.Rmd | 4 piar-0.8.3/piar/inst/doc/subperiods.html | 63 piar-0.8.3/piar/inst/doc/superlative-aggregation.R | 2 piar-0.8.3/piar/inst/doc/superlative-aggregation.Rmd | 12 piar-0.8.3/piar/inst/doc/superlative-aggregation.html | 59 piar-0.8.3/piar/man/aggregate.piar_index.Rd | 56 piar-0.8.3/piar/man/aggregation_structure.Rd | 18 piar-0.8.3/piar/man/as.data.frame.piar_index.Rd | 2 piar-0.8.3/piar/man/as.matrix.piar_aggregation_structure.Rd | 4 piar-0.8.3/piar/man/as.ts.piar_index.Rd | 2 piar-0.8.3/piar/man/as_aggregation_structure.Rd | 8 piar-0.8.3/piar/man/as_index.Rd | 4 piar-0.8.3/piar/man/chain.Rd | 2 piar-0.8.3/piar/man/contrib.Rd | 7 piar-0.8.3/piar/man/elementary_index.Rd |only piar-0.8.3/piar/man/expand_classification.Rd | 10 piar-0.8.3/piar/man/head.piar_index.Rd | 2 piar-0.8.3/piar/man/impute_prices.Rd | 16 piar-0.8.3/piar/man/is.na.piar_index.Rd | 2 piar-0.8.3/piar/man/levels.piar_index.Rd | 2 piar-0.8.3/piar/man/mean.piar_index.Rd | 25 piar-0.8.3/piar/man/merge.piar_index.Rd | 4 piar-0.8.3/piar/man/piar-package.Rd | 2 piar-0.8.3/piar/man/split.piar_index.Rd | 2 piar-0.8.3/piar/man/split_classification.Rd | 7 piar-0.8.3/piar/man/stack.piar_index.Rd | 2 piar-0.8.3/piar/man/sub-.piar_index.Rd | 2 piar-0.8.3/piar/man/time.piar_index.Rd | 2 piar-0.8.3/piar/man/weights.piar_aggregation_structure.Rd | 6 piar-0.8.3/piar/man/window.piar_index.Rd | 2 piar-0.8.3/piar/tests/Examples/piar-Ex.Rout.save | 250 ++- piar-0.8.3/piar/tests/test-making-price-indexes.R | 84 - piar-0.8.3/piar/tests/test-making-price-indexes.Rout.save | 674 +++++----- piar-0.8.3/piar/tests/testthat/test-aggregate.R | 623 ++++++--- piar-0.8.3/piar/tests/testthat/test-aggregation-structure-attributes.R | 24 piar-0.8.3/piar/tests/testthat/test-as.ts.R | 7 piar-0.8.3/piar/tests/testthat/test-as_index.R | 47 piar-0.8.3/piar/tests/testthat/test-chain.R | 60 piar-0.8.3/piar/tests/testthat/test-coerce-aggregation-structure.R | 37 piar-0.8.3/piar/tests/testthat/test-coerce-index.R | 64 piar-0.8.3/piar/tests/testthat/test-contrib.R | 100 - piar-0.8.3/piar/tests/testthat/test-cut.R | 18 piar-0.8.3/piar/tests/testthat/test-elemental_index.R | 108 + piar-0.8.3/piar/tests/testthat/test-expand_classification.R | 105 + piar-0.8.3/piar/tests/testthat/test-extract-index.R | 107 + piar-0.8.3/piar/tests/testthat/test-impute-prices.R | 107 + piar-0.8.3/piar/tests/testthat/test-index-attributes.R | 28 piar-0.8.3/piar/tests/testthat/test-is.na.R | 21 piar-0.8.3/piar/tests/testthat/test-known-values.R | 16 piar-0.8.3/piar/tests/testthat/test-mean.R | 68 - piar-0.8.3/piar/tests/testthat/test-merge.R | 32 piar-0.8.3/piar/tests/testthat/test-split.R | 20 piar-0.8.3/piar/tests/testthat/test-split_classification.R | 37 piar-0.8.3/piar/tests/testthat/test-stack.R | 22 piar-0.8.3/piar/tests/testthat/test-update.R | 6 piar-0.8.3/piar/vignettes/adjust-weights.Rmd | 24 piar-0.8.3/piar/vignettes/contributions.Rmd | 12 piar-0.8.3/piar/vignettes/imputation.Rmd | 20 piar-0.8.3/piar/vignettes/index-number-formulas.Rmd | 64 piar-0.8.3/piar/vignettes/matrix-aggregation.Rmd | 22 piar-0.8.3/piar/vignettes/multiple-baskets.Rmd | 20 piar-0.8.3/piar/vignettes/multiple-data-sources.Rmd | 10 piar-0.8.3/piar/vignettes/multiple-dimensions.Rmd | 8 piar-0.8.3/piar/vignettes/piar.Rmd | 36 piar-0.8.3/piar/vignettes/subperiods.Rmd | 4 piar-0.8.3/piar/vignettes/superlative-aggregation.Rmd | 12 133 files changed, 3371 insertions(+), 2302 deletions(-)
Title: Bivariate Automatic Analysis
Description: Simplify bivariate and regression analyses by automating
result generation, including summary tables, statistical tests, and
customizable graphs. It supports tests for continuous and dichotomous
data, as well as stepwise regression for linear, logistic, and Firth
penalized logistic models. While not a substitute for tailored
analysis, 'BiVariAn' accelerates workflows and is expanding features
like multilingual interpretations of results.The methods for selecting
significant statistical tests, as well as the predictor selection in
prediction functions, can be referenced in the works of Marc Kery
(2003) <doi:10.1890/0012-9623(2003)84[92:NORDIG]2.0.CO;2> and Rainer
Puhr (2017) <doi:10.1002/sim.7273>.
Author: Jose Andres Flores-Garcia [cre, aut, cph] ,
Antonio Augusto Gordillo-Moscoso [aut] ,
Jhoselin Marian Castro-Rodriguez [aut]
Maintainer: Jose Andres Flores-Garcia <andres.flores@uaslp.mx>
Diff between BiVariAn versions 1.0.1 dated 2025-03-05 and 1.0.2 dated 2025-09-16
DESCRIPTION | 24 +-- MD5 | 51 +++---- NAMESPACE | 1 NEWS.md | 2 R/auto_bar_categ.R | 166 +++++++++++------------ R/auto_bar_cont.R | 3 R/auto_bp_cont.R | 5 R/auto_dens_cont.R | 2 R/continuous_corr_test.R | 1 R/logistf_summary.R | 73 ++++------ R/step_bw_firth.R | 243 +++++++++++++++------------------- R/step_bw_p.R | 237 +++++++++++++++++---------------- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 8 - inst/doc/bivarian-description.html | 9 - man/auto_bar_categ.Rd | 4 man/logistf_summary.Rd | 13 - man/step_bw_firth.Rd | 64 +++++--- man/step_bw_p.Rd | 43 +++--- tests/testthat/test-auto_bar_categ.R | 148 ++++++++++++-------- tests/testthat/test-auto_bar_cont.R | 2 tests/testthat/test-auto_viol_cont.R | 3 tests/testthat/test-logistf_summary.R |only tests/testthat/test-step_bw_firth.R | 82 ++++++++--- tests/testthat/test-step_bw_p.R | 70 +++++---- 27 files changed, 668 insertions(+), 590 deletions(-)
Title: Conditionally Symmetric Multidimensional Gaussian Mixture Model
Description: Implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (Journal of the American Statistical Association 2025, <doi:10.1080/01621459.2024.2422124>).
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between csmGmm versions 0.3.0 dated 2024-12-03 and 0.4.0 dated 2025-09-16
DESCRIPTION | 8 MD5 | 10 inst/doc/csmGmm_tutorial.R | 134 ++++++++++-- inst/doc/csmGmm_tutorial.Rmd | 166 +++++++++++++-- inst/doc/csmGmm_tutorial.html | 441 ++++++++++++++++++++++++++---------------- vignettes/csmGmm_tutorial.Rmd | 166 +++++++++++++-- 6 files changed, 678 insertions(+), 247 deletions(-)
Title: Stabilize Function Arguments
Description: A set of consistent, opinionated functions to quickly check
function arguments, coerce them to the desired configuration, or
deliver informative error messages when that is not possible.
Author: Jon Harmon [aut, cre, cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between stbl versions 0.1.1 dated 2024-05-23 and 0.2.0 dated 2025-09-16
stbl-0.1.1/stbl/R/aaa-shared-args.R |only stbl-0.1.1/stbl/R/msgs_common.R |only stbl-0.1.1/stbl/R/stabilize_arg_scalar.R |only stbl-0.1.1/stbl/R/stabilize_chr_scalar.R |only stbl-0.1.1/stbl/R/stabilize_fct_scalar.R |only stbl-0.1.1/stbl/R/stabilize_int_scalar.R |only stbl-0.1.1/stbl/R/stabilize_lgl_scalar.R |only stbl-0.1.1/stbl/R/to_chr_scalar.R |only stbl-0.1.1/stbl/R/to_fct_scalar.R |only stbl-0.1.1/stbl/R/to_int_scalar.R |only stbl-0.1.1/stbl/R/to_lgl_scalar.R |only stbl-0.1.1/stbl/man/dot-coerce-params.Rd |only stbl-0.1.1/stbl/tests/testthat/_snaps/stabilize_arg_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/stabilize_chr_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/stabilize_int_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/stabilize_lgl_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/to_chr_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/to_fct_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/to_int_scalar.md |only stbl-0.1.1/stbl/tests/testthat/_snaps/to_lgl_scalar.md |only stbl-0.1.1/stbl/tests/testthat/test-msgs_common.R |only stbl-0.1.1/stbl/tests/testthat/test-stabilize_arg_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-stabilize_chr_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-stabilize_fct_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-stabilize_int_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-stabilize_lgl_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-to_chr_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-to_fct_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-to_int_scalar.R |only stbl-0.1.1/stbl/tests/testthat/test-to_lgl_scalar.R |only stbl-0.2.0/stbl/DESCRIPTION | 26 stbl-0.2.0/stbl/MD5 | 204 +++--- stbl-0.2.0/stbl/NAMESPACE | 62 + stbl-0.2.0/stbl/NEWS.md | 22 stbl-0.2.0/stbl/R/aaa-conditions.R |only stbl-0.2.0/stbl/R/aaa-shared_params.R |only stbl-0.2.0/stbl/R/are_chr_ish.R |only stbl-0.2.0/stbl/R/are_dbl_ish.R |only stbl-0.2.0/stbl/R/are_fct_ish.R |only stbl-0.2.0/stbl/R/are_int_ish.R |only stbl-0.2.0/stbl/R/are_lgl_ish.R |only stbl-0.2.0/stbl/R/check.R | 142 +++- stbl-0.2.0/stbl/R/cls_unexported.R | 215 +++++- stbl-0.2.0/stbl/R/object_type.R | 8 stbl-0.2.0/stbl/R/regex.R |only stbl-0.2.0/stbl/R/stabilize_arg.R | 51 + stbl-0.2.0/stbl/R/stabilize_chr.R | 328 ++++++---- stbl-0.2.0/stbl/R/stabilize_dbl.R |only stbl-0.2.0/stbl/R/stabilize_fct.R | 171 +++-- stbl-0.2.0/stbl/R/stabilize_int.R | 240 +++---- stbl-0.2.0/stbl/R/stabilize_lgl.R | 157 ++-- stbl-0.2.0/stbl/R/stbl-package.R | 2 stbl-0.2.0/stbl/R/to_chr.R | 105 ++- stbl-0.2.0/stbl/R/to_dbl.R |only stbl-0.2.0/stbl/R/to_fct.R | 262 +++++-- stbl-0.2.0/stbl/R/to_int.R | 219 ++++-- stbl-0.2.0/stbl/R/to_lgl.R | 149 +++- stbl-0.2.0/stbl/R/to_null.R | 25 stbl-0.2.0/stbl/R/utils.R | 106 ++- stbl-0.2.0/stbl/README.md | 52 + stbl-0.2.0/stbl/build |only stbl-0.2.0/stbl/inst |only stbl-0.2.0/stbl/man/are_chr_ish.Rd |only stbl-0.2.0/stbl/man/are_dbl_ish.Rd |only stbl-0.2.0/stbl/man/are_fct_ish.Rd |only stbl-0.2.0/stbl/man/are_int_ish.Rd |only stbl-0.2.0/stbl/man/are_lgl_ish.Rd |only stbl-0.2.0/stbl/man/dot-apply_regex_rule.Rd |only stbl-0.2.0/stbl/man/dot-are_not_dbl_ish_chr.Rd |only stbl-0.2.0/stbl/man/dot-are_not_fct_ish_chr.Rd |only stbl-0.2.0/stbl/man/dot-are_not_int_ish_chr.Rd |only stbl-0.2.0/stbl/man/dot-check_cast_failures.Rd |only stbl-0.2.0/stbl/man/dot-check_chr_to_int_failures.Rd |only stbl-0.2.0/stbl/man/dot-check_na.Rd |only stbl-0.2.0/stbl/man/dot-check_scalar.Rd |only stbl-0.2.0/stbl/man/dot-check_size.Rd |only stbl-0.2.0/stbl/man/dot-check_value_chr.Rd |only stbl-0.2.0/stbl/man/dot-check_value_dbl.Rd |only stbl-0.2.0/stbl/man/dot-check_x_no_more_than_y.Rd |only stbl-0.2.0/stbl/man/dot-cli_escape.Rd |only stbl-0.2.0/stbl/man/dot-cli_mark.Rd |only stbl-0.2.0/stbl/man/dot-coerce_fct_levels.Rd |only stbl-0.2.0/stbl/man/dot-coerce_fct_levels_impl.Rd |only stbl-0.2.0/stbl/man/dot-coerce_fct_to_na.Rd |only stbl-0.2.0/stbl/man/dot-compile_error_class.Rd |only stbl-0.2.0/stbl/man/dot-define_main_msg.Rd |only stbl-0.2.0/stbl/man/dot-describe_failure_chr.Rd |only stbl-0.2.0/stbl/man/dot-elements_are_cls_ish.Rd |only stbl-0.2.0/stbl/man/dot-fast_false.Rd |only stbl-0.2.0/stbl/man/dot-find_failures.Rd |only stbl-0.2.0/stbl/man/dot-glue2.Rd |only stbl-0.2.0/stbl/man/dot-has_regex_pattern.Rd |only stbl-0.2.0/stbl/man/dot-is_allowed_null.Rd |only stbl-0.2.0/stbl/man/dot-shared-params-check.Rd |only stbl-0.2.0/stbl/man/dot-shared-params.Rd |only stbl-0.2.0/stbl/man/dot-stabilize_cls.Rd |only stbl-0.2.0/stbl/man/dot-stabilize_cls_scalar.Rd |only stbl-0.2.0/stbl/man/dot-stbl_abort.Rd |only stbl-0.2.0/stbl/man/dot-stop_bad_levels.Rd |only stbl-0.2.0/stbl/man/dot-stop_cant_coerce.Rd |only stbl-0.2.0/stbl/man/dot-stop_incompatible.Rd |only stbl-0.2.0/stbl/man/dot-stop_must.Rd |only stbl-0.2.0/stbl/man/dot-stop_null.Rd |only stbl-0.2.0/stbl/man/dot-to_cls_from_fct.Rd |only stbl-0.2.0/stbl/man/dot-to_cls_from_list.Rd |only stbl-0.2.0/stbl/man/dot-to_cls_scalar.Rd |only stbl-0.2.0/stbl/man/dot-to_null.Rd |only stbl-0.2.0/stbl/man/dot-to_num_from_complex.Rd |only stbl-0.2.0/stbl/man/grapes-and-and-grapes.Rd |only stbl-0.2.0/stbl/man/reexports.Rd | 2 stbl-0.2.0/stbl/man/regex_must_match.Rd |only stbl-0.2.0/stbl/man/regex_must_not_match.Rd |only stbl-0.2.0/stbl/man/stabilize_arg.Rd | 35 - stbl-0.2.0/stbl/man/stabilize_chr.Rd | 63 + stbl-0.2.0/stbl/man/stabilize_dbl.Rd |only stbl-0.2.0/stbl/man/stabilize_fct.Rd | 56 - stbl-0.2.0/stbl/man/stabilize_int.Rd | 88 +- stbl-0.2.0/stbl/man/stabilize_lgl.Rd | 42 - stbl-0.2.0/stbl/man/stbl-package.Rd | 6 stbl-0.2.0/stbl/tests/testthat/_snaps/aaa-conditions.md |only stbl-0.2.0/stbl/tests/testthat/_snaps/check.md |only stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_arg.md | 86 ++ stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_chr.md | 137 +++- stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_dbl.md |only stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_fct.md |only stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_int.md | 34 - stbl-0.2.0/stbl/tests/testthat/_snaps/stabilize_lgl.md | 42 - stbl-0.2.0/stbl/tests/testthat/_snaps/to_chr.md | 117 +++ stbl-0.2.0/stbl/tests/testthat/_snaps/to_dbl.md |only stbl-0.2.0/stbl/tests/testthat/_snaps/to_fct.md | 88 ++ stbl-0.2.0/stbl/tests/testthat/_snaps/to_int.md | 98 +- stbl-0.2.0/stbl/tests/testthat/_snaps/to_lgl.md | 110 ++- stbl-0.2.0/stbl/tests/testthat/_snaps/to_null.md | 104 +-- stbl-0.2.0/stbl/tests/testthat/helper-wrap.R |only stbl-0.2.0/stbl/tests/testthat/test-aaa-conditions.R |only stbl-0.2.0/stbl/tests/testthat/test-are_chr_ish.R |only stbl-0.2.0/stbl/tests/testthat/test-are_dbl_ish.R |only stbl-0.2.0/stbl/tests/testthat/test-are_fct_ish.R |only stbl-0.2.0/stbl/tests/testthat/test-are_int_ish.R |only stbl-0.2.0/stbl/tests/testthat/test-are_lgl_ish.R |only stbl-0.2.0/stbl/tests/testthat/test-check.R |only stbl-0.2.0/stbl/tests/testthat/test-cls_unexported.R |only stbl-0.2.0/stbl/tests/testthat/test-object_type.R |only stbl-0.2.0/stbl/tests/testthat/test-regex.R |only stbl-0.2.0/stbl/tests/testthat/test-stabilize_arg.R | 111 ++- stbl-0.2.0/stbl/tests/testthat/test-stabilize_chr.R | 194 +++++ stbl-0.2.0/stbl/tests/testthat/test-stabilize_dbl.R |only stbl-0.2.0/stbl/tests/testthat/test-stabilize_fct.R | 38 + stbl-0.2.0/stbl/tests/testthat/test-stabilize_int.R | 50 + stbl-0.2.0/stbl/tests/testthat/test-stabilize_lgl.R | 55 + stbl-0.2.0/stbl/tests/testthat/test-to_chr.R | 156 +++- stbl-0.2.0/stbl/tests/testthat/test-to_dbl.R |only stbl-0.2.0/stbl/tests/testthat/test-to_fct.R | 118 ++- stbl-0.2.0/stbl/tests/testthat/test-to_int.R | 130 ++- stbl-0.2.0/stbl/tests/testthat/test-to_lgl.R | 206 ++++-- stbl-0.2.0/stbl/tests/testthat/test-to_null.R | 56 + stbl-0.2.0/stbl/tests/testthat/test-utils.R |only stbl-0.2.0/stbl/vignettes |only 158 files changed, 3342 insertions(+), 1426 deletions(-)
Title: Variable Selection Using a Smooth Information Criterion
Description: Implementation of the SIC epsilon-telescope method, either
using single or distributional (multiparameter) regression. Includes classical regression
with normally distributed errors and robust regression, where the errors are from
the Laplace distribution. The "smooth generalized normal distribution" is used,
where the estimation of an additional shape parameter allows the user to move
smoothly between both types of regression. See O'Neill and Burke (2022)
"Robust Distributional Regression with Automatic Variable Selection" for more details.
<doi:10.48550/arXiv.2212.07317>. This package also contains the data analyses from O'Neill and
Burke (2023). "Variable selection using a smooth information criterion for distributional
regression models". <doi:10.1007/s11222-023-10204-8>.
Author: Meadhbh O'Neill [aut, cre],
Kevin Burke [aut]
Maintainer: Meadhbh O'Neill <meadhbhon@gmail.com>
Diff between smoothic versions 1.2.0 dated 2023-08-22 and 1.2.1 dated 2025-09-16
DESCRIPTION | 15 +- MD5 | 36 +++--- NAMESPACE | 66 ++++++------ NEWS.md | 5 R/smoothic_functions.R | 10 - README.md | 2 build/vignette.rds |binary inst/doc/sgnd-boston.R | 6 - inst/doc/sgnd-boston.html | 55 +++++----- man/bostonhouseprice.Rd | 78 +++++++------- man/bostonhouseprice2.Rd | 86 ++++++++-------- man/diabetes.Rd | 72 ++++++------- man/pcancer.Rd | 76 +++++++------- man/plot_effects.Rd | 158 +++++++++++++++--------------- man/plot_paths.Rd | 2 man/predict.smoothic.Rd | 74 +++++++------- man/smoothic.Rd | 242 +++++++++++++++++++++++----------------------- man/sniffer.Rd | 66 ++++++------ man/summary.smoothic.Rd | 82 +++++++-------- 19 files changed, 569 insertions(+), 562 deletions(-)
Title: Washington Soil Health Initiative Branding
Description: Create plots and tables in a consistent style with WaSHI
(Washington Soil Health Initiative) branding. Use 'washi' to easily
style your 'ggplot2' plots and 'flextable' tables.
Author: Jadey Ryan [aut, cre],
Molly McIlquham [aut],
Dani Gelardi [aut],
Washington State Department of Agriculture [cph, fnd]
Maintainer: Jadey Ryan <jryan@agr.wa.gov>
Diff between washi versions 0.2.0 dated 2023-09-07 and 0.2.1 dated 2025-09-16
washi-0.2.0/washi/tests/testthat/_snaps/palettes |only washi-0.2.1/washi/DESCRIPTION | 14 washi-0.2.1/washi/MD5 | 56 washi-0.2.1/washi/NEWS.md | 5 washi-0.2.1/washi/R/data.R | 8 washi-0.2.1/washi/R/flextable.R | 218 washi-0.2.1/washi/R/palettes.R | 424 - washi-0.2.1/washi/R/scales.R | 141 washi-0.2.1/washi/R/theme.R | 547 - washi-0.2.1/washi/README.md | 42 washi-0.2.1/washi/data/example_data_long.rda |binary washi-0.2.1/washi/data/example_data_wide.rda |binary washi-0.2.1/washi/inst/extdata/example_data_long.csv | 3602 +++++----- washi-0.2.1/washi/inst/extdata/example_data_wide.csv | 62 washi-0.2.1/washi/man/example_data_long.Rd | 4 washi-0.2.1/washi/man/example_data_wide.Rd | 4 washi-0.2.1/washi/man/figures/README-barplot-1.png |binary washi-0.2.1/washi/man/figures/README-loom.png |only washi-0.2.1/washi/man/figures/README-plot-workflow-1.png |binary washi-0.2.1/washi/man/figures/README-scatter-plot-1.png |binary washi-0.2.1/washi/man/figures/README-table-1.png |binary washi-0.2.1/washi/man/figures/logo.png |binary washi-0.2.1/washi/man/washi_flextable.Rd | 6 washi-0.2.1/washi/man/washi_pal_setup.Rd | 4 washi-0.2.1/washi/man/washi_pal_view.Rd | 4 washi-0.2.1/washi/man/washi_scale.Rd | 4 washi-0.2.1/washi/man/washi_theme.Rd | 7 washi-0.2.1/washi/tests/testthat/_snaps/theme/washi-theme.svg | 4 washi-0.2.1/washi/tests/testthat/test-scales.R | 14 washi-0.2.1/washi/tests/testthat/test-theme.R | 172 30 files changed, 2678 insertions(+), 2664 deletions(-)
Title: 'Base Dos Dados' R Client
Description: An R interface to the 'Base dos Dados' API <https://basedosdados.org/docs/api_reference_python/>). Authenticate your project, query our tables, save data to disk and memory, all from R.
Author: Pedro Cavalcante [aut, cre],
Daniel Herszenhut [aut] ,
Rodrigo Dornelles [aut]
Maintainer: Pedro Cavalcante <pedrocolrj@gmail.com>
Diff between basedosdados versions 0.2.2 dated 2023-03-06 and 0.2.3 dated 2025-09-16
basedosdados-0.2.2/basedosdados/R/bd_connection.R |only basedosdados-0.2.2/basedosdados/R/http_client.R |only basedosdados-0.2.2/basedosdados/R/query_table.R |only basedosdados-0.2.2/basedosdados/R/utils-typed.R |only basedosdados-0.2.3/basedosdados/DESCRIPTION | 22 basedosdados-0.2.3/basedosdados/LICENSE | 4 basedosdados-0.2.3/basedosdados/MD5 | 60 - basedosdados-0.2.3/basedosdados/NAMESPACE | 112 +- basedosdados-0.2.3/basedosdados/R/bd-connection.R |only basedosdados-0.2.3/basedosdados/R/bdplyr.R | 10 basedosdados-0.2.3/basedosdados/R/download.R | 438 +++++----- basedosdados-0.2.3/basedosdados/R/http-client.R |only basedosdados-0.2.3/basedosdados/R/metadata.R | 83 + basedosdados-0.2.3/basedosdados/R/partition.R | 128 +- basedosdados-0.2.3/basedosdados/R/query-table.R |only basedosdados-0.2.3/basedosdados/R/utils-pipe.R | 28 basedosdados-0.2.3/basedosdados/R/zzzz.R | 4 basedosdados-0.2.3/basedosdados/README.md | 52 - basedosdados-0.2.3/basedosdados/man/BaseDosDadosConnection-class.Rd | 36 basedosdados-0.2.3/basedosdados/man/bd_collect.Rd | 136 +-- basedosdados-0.2.3/basedosdados/man/bd_request.Rd |only basedosdados-0.2.3/basedosdados/man/bd_write.Rd | 265 ++---- basedosdados-0.2.3/basedosdados/man/bdplyr.Rd | 208 ++-- basedosdados-0.2.3/basedosdados/man/download.Rd | 108 +- basedosdados-0.2.3/basedosdados/man/get_billing_id.Rd | 28 basedosdados-0.2.3/basedosdados/man/get_dataset_description.Rd | 48 - basedosdados-0.2.3/basedosdados/man/get_table_description.Rd | 51 - basedosdados-0.2.3/basedosdados/man/list_dataset_tables.Rd | 44 - basedosdados-0.2.3/basedosdados/man/partition_table.Rd | 74 - basedosdados-0.2.3/basedosdados/man/pipe.Rd | 40 basedosdados-0.2.3/basedosdados/man/read_sql.Rd | 100 +- basedosdados-0.2.3/basedosdados/man/set_billing_id.Rd | 70 - basedosdados-0.2.3/basedosdados/tests/testthat/test-bd_metadata.R | 170 +-- basedosdados-0.2.3/basedosdados/tests/testthat/test-bdplyr.R | 332 +++---- basedosdados-0.2.3/basedosdados/tests/testthat/test-download.R | 262 +++-- 35 files changed, 1471 insertions(+), 1442 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.19.0 dated 2025-07-13 and 0.20.0 dated 2025-09-16
DESCRIPTION | 6 MD5 | 22 - src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/sqlite/sqlite.cc | 17 src/c/driver/sqlite/statement_reader.c | 56 ++ src/c/driver/sqlite/statement_reader.h | 6 src/c/driver_manager/adbc_driver_manager.cc | 522 ++++++++++++++++++++----- src/c/driver_manager/current_arch.h | 55 ++ src/c/include/arrow-adbc/adbc_driver_manager.h | 33 + src/c/vendor/nanoarrow/nanoarrow.c | 251 +++++++++++- src/c/vendor/nanoarrow/nanoarrow.h | 447 ++++++++++++++------- src/c/vendor/nanoarrow/nanoarrow.hpp | 473 +++++++++++++++------- 12 files changed, 1466 insertions(+), 440 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.19.0 dated 2025-07-13 and 0.20.0 dated 2025-09-16
DESCRIPTION | 6 MD5 | 22 - src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/sqlite/sqlite.cc | 17 src/c/driver/sqlite/statement_reader.c | 56 ++ src/c/driver/sqlite/statement_reader.h | 6 src/c/driver_manager/adbc_driver_manager.cc | 522 ++++++++++++++++++++----- src/c/driver_manager/current_arch.h | 55 ++ src/c/include/arrow-adbc/adbc_driver_manager.h | 33 + src/c/vendor/nanoarrow/nanoarrow.c | 251 +++++++++++- src/c/vendor/nanoarrow/nanoarrow.h | 447 ++++++++++++++------- src/c/vendor/nanoarrow/nanoarrow.hpp | 473 +++++++++++++++------- 12 files changed, 1466 insertions(+), 440 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 1.8.2 dated 2025-04-25 and 1.9.0 dated 2025-09-16
DESCRIPTION | 8 MD5 | 98 +-- R/attribute_generation_functions.R |only R/calc_conservative_anticoef.R | 2 R/calculate_gefficiency.R | 2 R/calculate_power_curves.R | 18 R/convert_blockcolumn_rownames.R | 79 +- R/design_df_to_processed.R |only R/effectpower.R | 14 R/eval_design.R | 967 +++++++++++++++++------------------ R/eval_design_custom_mc.R | 27 R/eval_design_mc.R | 240 ++++---- R/eval_design_survival_mc.R | 172 +++--- R/gen_design.R | 201 ++++--- R/get_attribute.R | 14 R/get_moment_matrix.R | 47 + R/get_optimality.R | 20 R/methods.R | 2 R/parameterpower.R | 18 R/plot_correlations.R | 98 +-- R/plot_fds.R | 207 +++++-- R/remove_skpr_blockcols.R | 20 R/skprGUI.R | 17 man/calculate_power_curves.Rd | 40 - man/contr.simplex.Rd | 4 man/convert_blockcolumn_rownames.Rd | 9 man/convert_model_dots.Rd | 2 man/convhull_halfspace.Rd | 10 man/effectpowermc.Rd | 4 man/eval_design.Rd | 37 - man/eval_design_custom_mc.Rd | 26 man/eval_design_mc.Rd | 58 +- man/eval_design_survival_mc.Rd | 17 man/gen_design.Rd | 86 +-- man/gen_momentsmatrix_constrained.Rd | 8 man/get_attribute.Rd | 92 +-- man/get_block_groups.Rd | 2 man/get_moment_matrix.Rd | 2 man/get_optimality.Rd | 16 man/get_power_curve_output.Rd | 4 man/interpolate_convex_hull.Rd | 8 man/normalize_design.Rd | 2 man/plot_correlations.Rd | 12 man/plot_fds.Rd | 44 + man/print.skpr_eval_output.Rd | 4 man/print.skpr_power_curve_output.Rd | 4 man/remove_skpr_blockcols.Rd | 6 man/skprGUI.Rd | 8 src/genOptimalDesign.cpp | 6 src/genSplitPlotOptimalDesign.cpp | 4 src/getBlockedOptimalDesign.cpp | 6 51 files changed, 1519 insertions(+), 1273 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.14.1 dated 2025-05-06 and 2.15.0 dated 2025-09-16
DESCRIPTION | 10 +- MD5 | 53 ++++++------- NAMESPACE | 56 ++++++++++++++ NEWS.md | 8 ++ R/copy_labels.R | 37 +++++++-- R/drop_unused_value_labels.R | 11 ++ R/na_values.R | 87 +++++++++++++++++++++- R/remove_attributes.R | 9 ++ R/remove_labels.R | 55 +++++++++++++- R/tagged_na.R | 21 +++++ R/to_character.R | 26 ++++++ R/to_factor.R | 49 ++++++++++++ R/to_na.R | 18 ++++ R/update_with.R | 40 ++++++++++ R/val_labels.R | 113 +++++++++++++++++++++++++++-- R/var_label.R | 60 +++++++++++++-- build/vignette.rds |binary man/copy_labels.Rd | 4 - man/drop_unused_value_labels.Rd | 2 man/na_values.Rd | 4 - man/remove_labels.Rd | 2 man/tagged_na_to_user_na.Rd | 2 man/to_character.Rd | 11 ++ man/to_factor.Rd | 18 ++++ man/update_variable_labels_with.Rd | 3 man/val_labels.Rd | 6 - man/var_label.Rd | 26 ++++-- tests/testthat/test-survey-compatibility.R |only 28 files changed, 651 insertions(+), 80 deletions(-)
Title: Robust Estimators for Multi-Group and Spatial Data
Description: Estimation of robust estimators for multi-group and spatial data including the casewise robust Spatially Smoothed Minimum Regularized Determinant (ssMRCD) estimator and its usage for local outlier detection as described in Puchhammer and Filzmoser (2023) <doi:10.1080/10618600.2023.2277875> as well as for sparse robust PCA for multi-source data described in Puchhammer, Wilms and Filzmoser (2024) <doi:10.48550/arXiv.2407.16299>. Moreover, a cellwise robust multi-group Gaussian mixture model (MG-GMM) is implemented as described in Puchhammer, Wilms and Filzmoser (2024) <doi:10.48550/arXiv.2504.02547>. Included are also complementary visualization and parameter tuning tools.
Author: Patricia Puchhammer [aut, cre, cph],
Peter Filzmoser [aut]
Maintainer: Patricia Puchhammer <patricia.puchhammer@tuwien.ac.at>
Diff between ssMRCD versions 2.0.0 dated 2025-09-11 and 2.0.1 dated 2025-09-16
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/SRPCAMS.R | 11 +++++++---- R/SRPCAMS_helpers.R | 14 ++++++++------ R/SRPCAMS_internal.R | 4 ++++ R/locOuts.R | 2 +- R/ssMRCD.R | 3 ++- R/ssMRCD_methods.R | 2 +- inst/doc/SRPCAMS.html | 17 ++--------------- man/msPCA.Rd | 9 ++++++--- man/residuals.ssMRCD.Rd | 2 +- man/scores.Rd | 14 ++++++++------ man/ssMRCD.Rd | 3 ++- src/cellMGGMM.cpp | 38 ++++++++++++++++++-------------------- 14 files changed, 76 insertions(+), 75 deletions(-)
Title: Visualizing and Quantifying Decision Uncertainty
Description: A suite of tools to help modelers and decision-makers effectively
interpret and communicate decision risk when evaluating multiple policy options.
It uses model outputs from uncertainty analysis for baseline scenarios and policy
alternatives to generate visual representations of uncertainty and quantitative
measures for assessing associated risks. For more details see <https://dut.ihe.ca/>.
Author: Megan Wiggins [aut, cre] ,
Marie Betsy Varughese [aut] ,
Ellen Rafferty [aut] ,
Sasha van Katwyk [aut] ,
Christopher McCabe [aut] ,
Jeff Round [aut] ,
Erin Kirwin [aut] ,
Institute of Health Economics [cph, aut],
Canadian Network for Modelling Infect [...truncated...]
Maintainer: Megan Wiggins <mwiggins@ihe.ca>
Diff between DUToolkit versions 1.0.0 dated 2025-09-14 and 1.0.1 dated 2025-09-16
DESCRIPTION | 6 +-- MD5 | 20 +++++----- NEWS.md | 11 +++++ inst/doc/Fan_Plots.html | 4 +- inst/doc/density_plots.html | 4 +- inst/doc/rain_plot.html | 2 - inst/doc/temporal_plot.html | 2 - tests/testthat/test-plot_density.R | 26 ++++++------- tests/testthat/test-plot_fan.R | 70 +++++++++++++++++------------------ tests/testthat/test-plot_raincloud.R | 29 +++++++------- tests/testthat/test-plot_temporal.R | 27 +++++++------ 11 files changed, 107 insertions(+), 94 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
MOLGENIS org [cph, fnd]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
This is a re-admission after prior archival of version 3.0.0 dated 2025-07-24
Diff between DSMolgenisArmadillo versions 3.0.0 dated 2025-07-24 and 3.0.1 dated 2025-09-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ tests/testthat/test-ArmadilloOAuth.R | 20 +++++++++++++------- 4 files changed, 22 insertions(+), 13 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Detection and Attribution Analysis of Climate Change
Description: Detection and attribution of climate change using methods including optimal fingerprinting via
generalized total least squares or an estimating equation approach (Li et al., 2025,
<doi:10.1175/JCLI-D-24-0193.1>; Ma et al., 2023, <doi:10.1175/JCLI-D-22-0681.1>).
Provides shrinkage estimators for the covariance matrix following
Ledoit and Wolf (2004, <doi:10.1016/S0047-259X(03)00096-4>) and
Ledoit and Wolf (2017, <doi:10.2139/ssrn.2383361>).
Author: Yan Li [aut, cre],
Kun Chen [aut],
Jun Yan [aut]
Maintainer: Yan Li <yan.4.li@uconn.edu>
This is a re-admission after prior archival of version 0.0-6 dated 2025-01-24
Diff between dacc versions 0.0-6 dated 2025-01-24 and 0.0-7 dated 2025-09-16
DESCRIPTION | 18 MD5 | 17 NAMESPACE | 2 R/fingerprint.R | 73 +++- R/fingerprintCEE.R | 956 ++++++++++++++++++++++++++--------------------------- R/fingerprintTLS.R | 931 ++++++++++++++++++++++++++------------------------- R/fingerprintTS.R | 425 +++++++++++------------ R/fpPrep.R | 4 inst |only man/fingerprint.Rd | 259 +++++++------- 10 files changed, 1388 insertions(+), 1297 deletions(-)
Title: Proportional Testing for Colocalisation Analysis
Description: Colocalisation analysis tests whether two traits share a causal
genetic variant in a specified genomic region. Proportional testing for
colocalisation has been previously proposed
[Wallace (2013) <doi:10.1002/gepi.21765>], but is reimplemented here to
overcome barriers to its adoption. Its use is complementary to the fine-
mapping based colocalisation method in the 'coloc' package, and may be used in
particular to identify false "H3" conclusions in 'coloc'.
Author: Chris Wallace [aut, cre]
Maintainer: Chris Wallace <cew54@cam.ac.uk>
Diff between colocPropTest versions 0.9.2 dated 2025-09-08 and 0.9.3 dated 2025-09-16
DESCRIPTION | 8 +++---- MD5 | 13 ++++++------ R/proportional.R | 46 ++++++++++++++++++++++++++----------------- build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.html | 4 +-- man/colocPropTest-package.Rd | 4 +-- man/run_proptests.Rd | 45 +++++++++++++++++++++++++----------------- 8 files changed, 70 insertions(+), 50 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 2.1.1 dated 2025-07-10 and 2.2.0 dated 2025-09-16
CDMConnector-2.1.1/CDMConnector/tests/testthat/test-db-dplyr.R |only CDMConnector-2.1.1/CDMConnector/tests/testthat/test-zzz-DBI.R |only CDMConnector-2.1.1/CDMConnector/tests/testthat/test-zzz-dplyr.R |only CDMConnector-2.2.0/CDMConnector/DESCRIPTION | 8 CDMConnector-2.2.0/CDMConnector/MD5 | 76 +- CDMConnector-2.2.0/CDMConnector/NAMESPACE | 2 CDMConnector-2.2.0/CDMConnector/NEWS.md | 10 CDMConnector-2.2.0/CDMConnector/R/Eunomia.R | 15 CDMConnector-2.2.0/CDMConnector/R/cdm.R | 27 - CDMConnector-2.2.0/CDMConnector/R/compute.R | 23 CDMConnector-2.2.0/CDMConnector/R/dateadd.R | 9 CDMConnector-2.2.0/CDMConnector/R/dbSource.R | 28 - CDMConnector-2.2.0/CDMConnector/R/generateCohortSet.R | 71 +- CDMConnector-2.2.0/CDMConnector/R/summariseQuantile.R | 2 CDMConnector-2.2.0/CDMConnector/R/utils.R | 224 +++++++- CDMConnector-2.2.0/CDMConnector/build/vignette.rds |binary CDMConnector-2.2.0/CDMConnector/inst/doc/a01_getting-started.html | 129 ++--- CDMConnector-2.2.0/CDMConnector/inst/doc/a02_cohorts.html | 98 +-- CDMConnector-2.2.0/CDMConnector/inst/doc/a03_dbplyr.html | 14 CDMConnector-2.2.0/CDMConnector/inst/doc/a04_DBI_connection_examples.R | 134 ++++- CDMConnector-2.2.0/CDMConnector/inst/doc/a04_DBI_connection_examples.Rmd | 182 ++++++- CDMConnector-2.2.0/CDMConnector/inst/doc/a04_DBI_connection_examples.html | 254 +++++++--- CDMConnector-2.2.0/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 4 CDMConnector-2.2.0/CDMConnector/man/computeDataHashByTable.Rd |only CDMConnector-2.2.0/CDMConnector/man/snapshot.Rd | 4 CDMConnector-2.2.0/CDMConnector/tests/testthat/old_tests/test-zzz-DBI.R |only CDMConnector-2.2.0/CDMConnector/tests/testthat/old_tests/test-zzz-dplyr.R |only CDMConnector-2.2.0/CDMConnector/tests/testthat/setup.R | 71 +- CDMConnector-2.2.0/CDMConnector/tests/testthat/test-02-db-cdm.R | 9 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-03-db-generateCohortSet.R | 14 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-04-db-generateConceptCohortSet.R | 15 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-10-db-summariseQuantile.R | 24 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-12-db-dplyr.R | 30 + CDMConnector-2.2.0/CDMConnector/tests/testthat/test-Eunomia.R | 2 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-db-utils.R | 19 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-deprecations.R | 1 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-memory-issue.R | 1 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-omopgenerics.R | 1 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-pool.R | 1 CDMConnector-2.2.0/CDMConnector/tests/testthat/test-writePrefixDropUseCase.R | 178 +++---- CDMConnector-2.2.0/CDMConnector/tests/testthat/test-write_prefix.r | 1 CDMConnector-2.2.0/CDMConnector/vignettes/a04_DBI_connection_examples.Rmd | 182 ++++++- 42 files changed, 1385 insertions(+), 478 deletions(-)
Title: Bias Reduction in Binomial-Response Generalized Linear Models
Description: Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved frequentist properties (bias, mean squared error) that are always finite even in cases where the maximum likelihood estimates are infinite (data separation). Fitting takes place by fitting generalized linear models on iteratively updated pseudo-data. The interface is essentially the same as 'glm'. More flexibility is provided by the fact that custom pseudo-data representations can be specified and used for model fitting. Functions are provided for the construction of confidence intervals for the reduced-bias estimates.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm versions 0.7.2 dated 2021-04-22 and 0.7.3 dated 2025-09-16
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- inst/CHANGES | 4 ++++ man/brglm.Rd | 16 ++++++++-------- man/profile.brglm.Rd | 2 +- 5 files changed, 22 insertions(+), 17 deletions(-)
Title: Statistics Netherlands (CBS) Open Data API Client
Description: The data and meta data from Statistics
Netherlands (<https://www.cbs.nl>) can be browsed and downloaded. The client uses
the open data API of Statistics Netherlands.
Author: Edwin de Jonge [aut, cre],
Sara Houweling [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between cbsodataR versions 1.1 dated 2024-09-25 and 1.2.1 dated 2025-09-16
DESCRIPTION | 7 ++++--- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 9 +++++++++ R/cbs_download_data.R | 5 +++-- R/cbs_download_meta.R | 3 ++- R/cbs_get_data.R | 11 ++++++----- R/cbs_get_meta.R | 2 +- R/cbsopendata.R | 24 ++++++++++++++++++++++++ R/get-meta.R | 2 +- build/vignette.rds |binary inst/doc/cbsodata.html | 9 +++++---- inst/doc/maps.html | 9 +++++---- man/cbs_download_data.Rd | 29 ++++++++++++++++++++++++++++- man/cbs_download_meta.Rd | 29 ++++++++++++++++++++++++++++- man/cbs_get_data.Rd | 29 ++++++++++++++++++++++++++++- man/cbsodataR-package.Rd | 27 +++++++++++++++++++++++++++ man/download_data-deprecated.Rd | 29 ++++++++++++++++++++++++++++- man/download_meta-deprecated.Rd | 29 ++++++++++++++++++++++++++++- man/get_data-deprecated.Rd | 29 ++++++++++++++++++++++++++++- 19 files changed, 273 insertions(+), 45 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.1.1 dated 2025-08-19 and 0.2.0 dated 2025-09-16
BKP-0.1.1/BKP/R/get_prior_dkp.R |only BKP-0.1.1/BKP/R/loss_fun_dkp.R |only BKP-0.1.1/BKP/man/figures/elapsed_time.pdf |only BKP-0.1.1/BKP/man/figures/ex1.pdf |only BKP-0.1.1/BKP/man/figures/ex1_sim.pdf |only BKP-0.1.1/BKP/man/figures/ex1class001.pdf |only BKP-0.1.1/BKP/man/figures/ex1class2.pdf |only BKP-0.1.1/BKP/man/figures/ex2.pdf |only BKP-0.1.1/BKP/man/figures/ex2_sim.pdf |only BKP-0.1.1/BKP/man/figures/ex3.pdf |only BKP-0.1.1/BKP/man/figures/ex3_true.pdf |only BKP-0.1.1/BKP/man/figures/ex4.pdf |only BKP-0.1.1/BKP/man/figures/ex4LGP.pdf |only BKP-0.1.1/BKP/man/figures/ex4roc.pdf |only BKP-0.1.1/BKP/man/figures/ex4rocLGP.pdf |only BKP-0.1.1/BKP/man/figures/ex5.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class1.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class1_true.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class2.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class2_true.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class3.pdf |only BKP-0.1.1/BKP/man/figures/ex6_class3_true.pdf |only BKP-0.1.1/BKP/man/figures/ex7.pdf |only BKP-0.1.1/BKP/man/figures/ex7LGP.pdf |only BKP-0.1.1/BKP/man/figures/ex7roc.pdf |only BKP-0.1.1/BKP/man/figures/ex7rocLGP.pdf |only BKP-0.1.1/BKP/man/fit.BKP.Rd |only BKP-0.1.1/BKP/man/fit.DKP.Rd |only BKP-0.1.1/BKP/man/get_prior_dkp.Rd |only BKP-0.1.1/BKP/man/loss_fun_dkp.Rd |only BKP-0.1.1/BKP/tests/testthat/test-get_prior_dkp.R |only BKP-0.1.1/BKP/tests/testthat/test-loss_fun_dkp.R |only BKP-0.2.0/BKP/DESCRIPTION | 13 BKP-0.2.0/BKP/MD5 | 146 +- BKP-0.2.0/BKP/NAMESPACE | 26 BKP-0.2.0/BKP/NEWS.md | 14 BKP-0.2.0/BKP/R/BKP-package.R | 43 BKP-0.2.0/BKP/R/fit_BKP.R | 477 ++++---- BKP-0.2.0/BKP/R/fit_DKP.R | 446 ++++---- BKP-0.2.0/BKP/R/fitted_BKP.R |only BKP-0.2.0/BKP/R/fitted_DKP.R |only BKP-0.2.0/BKP/R/get_prior.R | 305 +++-- BKP-0.2.0/BKP/R/kernel_matrix.R | 295 ++--- BKP-0.2.0/BKP/R/loss_fun.R | 216 ++-- BKP-0.2.0/BKP/R/parameter_BKP.R |only BKP-0.2.0/BKP/R/parameter_DKP.R |only BKP-0.2.0/BKP/R/plot_BKP.R | 163 +-- BKP-0.2.0/BKP/R/plot_DKP.R | 117 +- BKP-0.2.0/BKP/R/predict_BKP.R | 411 ++++--- BKP-0.2.0/BKP/R/predict_DKP.R | 304 +++-- BKP-0.2.0/BKP/R/print_BKP.R | 322 ++++- BKP-0.2.0/BKP/R/print_DKP.R | 457 ++++++-- BKP-0.2.0/BKP/R/quantile_BKP.R |only BKP-0.2.0/BKP/R/quantile_DKP.R |only BKP-0.2.0/BKP/R/simulate_BKP.R | 358 +++--- BKP-0.2.0/BKP/R/simulate_DKP.R | 157 +- BKP-0.2.0/BKP/R/summary_BKP.R | 221 ++-- BKP-0.2.0/BKP/R/summary_DKP.R | 54 - BKP-0.2.0/BKP/R/utils.R | 138 +- BKP-0.2.0/BKP/README.md | 2 BKP-0.2.0/BKP/inst/CITATION | 44 BKP-0.2.0/BKP/inst/doc/vignettes.R | 719 +++++++++++++ BKP-0.2.0/BKP/inst/doc/vignettes.Rmd | 1188 ++++++++++++++++++---- BKP-0.2.0/BKP/inst/doc/vignettes.pdf |binary BKP-0.2.0/BKP/man/BKP-package.Rd | 36 BKP-0.2.0/BKP/man/fit_BKP.Rd |only BKP-0.2.0/BKP/man/fit_DKP.Rd |only BKP-0.2.0/BKP/man/fitted.Rd |only BKP-0.2.0/BKP/man/get_prior.Rd | 118 +- BKP-0.2.0/BKP/man/loss_fun.Rd | 71 - BKP-0.2.0/BKP/man/parameter.Rd |only BKP-0.2.0/BKP/man/plot.Rd | 93 + BKP-0.2.0/BKP/man/predict.Rd | 134 +- BKP-0.2.0/BKP/man/print.Rd | 99 + BKP-0.2.0/BKP/man/quantile.Rd |only BKP-0.2.0/BKP/man/simulate.Rd | 102 + BKP-0.2.0/BKP/man/summary.Rd | 62 - BKP-0.2.0/BKP/tests/testthat/Rplots.pdf |only BKP-0.2.0/BKP/tests/testthat/test-fit_BKP.R | 196 +-- BKP-0.2.0/BKP/tests/testthat/test-fit_DKP.R | 265 ++-- BKP-0.2.0/BKP/tests/testthat/test-fitted_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-fitted_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-get_prior.R | 131 +- BKP-0.2.0/BKP/tests/testthat/test-kernel_matrix.R | 114 -- BKP-0.2.0/BKP/tests/testthat/test-loss_fun.R | 74 + BKP-0.2.0/BKP/tests/testthat/test-parameter_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-parameter_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-plot_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-plot_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-predict_BKP.R | 95 + BKP-0.2.0/BKP/tests/testthat/test-predict_DKP.R | 111 +- BKP-0.2.0/BKP/tests/testthat/test-print_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-print_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-quantile_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-quantile_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-simualte_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-simulate_BKP.R | 125 +- BKP-0.2.0/BKP/tests/testthat/test-simulate_DKP.R | 18 BKP-0.2.0/BKP/tests/testthat/test-summary_BKP.R |only BKP-0.2.0/BKP/tests/testthat/test-summary_DKP.R |only BKP-0.2.0/BKP/tests/testthat/test-utils.R |only BKP-0.2.0/BKP/vignettes/refs.bib | 897 ++++++++-------- BKP-0.2.0/BKP/vignettes/vignettes.Rmd | 1188 ++++++++++++++++++---- 103 files changed, 7214 insertions(+), 3351 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 0.3.0 dated 2025-07-31 and 0.3.1 dated 2025-09-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 2 ++ R/Rush.R | 14 ++++++++------ man/Rush.Rd | 13 ++++++++----- 5 files changed, 27 insertions(+), 20 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.9.0 dated 2025-08-18 and 0.9.1 dated 2025-09-16
DESCRIPTION | 10 +-- MD5 | 38 +++++++-------- NEWS.md | 9 +++ R/facet_interactive.R | 2 R/geom_boxplot_interactive.R | 88 +++++++++++++++++----------------- R/geom_col_interactive.R | 11 +++- R/geom_crossbar_interactive.R | 10 +++ R/geom_errorbar_interactive.R | 2 R/geom_errorbarh_interactive.R | 28 ++++++----- R/geom_linerange_interactive.R | 6 +- R/geom_pointrange_interactive.R | 31 +++++------- R/geom_violin_interactive.R | 67 +++++--------------------- R/tracers.R | 2 R/utils_ggplot2.R | 2 man/geom_abline_interactive.Rd | 2 man/geom_crossbar_interactive.Rd | 2 man/geom_errorbarh_interactive.Rd | 15 ----- man/geom_sf_interactive.Rd | 2 man/ggiraph-ggproto.Rd | 2 man/guide_bins_interactive.Rd | 96 +++++++++++++++++++------------------- 20 files changed, 201 insertions(+), 224 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.4.0 dated 2025-04-22 and 0.4.1 dated 2025-09-16
DESCRIPTION | 11 +++---- MD5 | 12 +++---- NEWS.md | 10 +++++- R/install_dependencies.R | 24 +++++++++++---- inst/WORDLIST | 2 - man/grouped_tbl_pivot_wider.Rd | 2 - man/install_dependencies.Rd | 62 +++++++++++++++++++++-------------------- 7 files changed, 72 insertions(+), 51 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.4 dated 2025-06-16 and 1.1.5 dated 2025-09-16
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/executeChecks.R | 1 + R/mockDrugExposure.R | 2 +- inst/doc/DrugSig.html | 2 +- inst/doc/IntroductionToDrugExposureDiagnostics.html | 11 +++++------ inst/shiny/ResultsExplorer/utils.R | 1 + tests/testthat/test-SyntheaSqlServer.R | 2 +- tests/testthat/test-checkTimeBetween.R | 8 ++++---- 10 files changed, 30 insertions(+), 25 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Scalable Bayesian Disease Mapping Models for High-Dimensional
Data
Description: Implements several spatial and spatio-temporal scalable disease mapping models for high-dimensional count data using the INLA technique for approximate Bayesian inference in latent Gaussian models (Orozco-Acosta et al., 2021 <doi:10.1016/j.spasta.2021.100496>; Orozco-Acosta et al., 2023 <doi:10.1016/j.cmpb.2023.107403> and Vicente et al., 2023 <doi:10.1007/s11222-023-10263-x>). The creation and develpment of this package has been supported by Project MTM2017-82553-R (AEI/FEDER, UE) and Project PID2020-113125RB-I00/MCIN/AEI/10.13039/501100011033. It has also been partially funded by the Public University of Navarra (project PJUPNA2001).
Author: Aritz Adin [aut, cre] ,
Erick Orozco-Acosta [aut] ,
Maria Dolores Ugarte [aut]
Maintainer: Aritz Adin <aritz.adin@unavarra.es>
Diff between bigDM versions 0.5.6 dated 2025-03-25 and 0.5.7 dated 2025-09-16
DESCRIPTION | 16 +++++---- MD5 | 24 +++++++------- NEWS | 3 + R/CAR_INLA.R | 52 +++++++++++++++++++++++++------ R/MCAR_INLA.R | 2 - R/STCAR_INLA.R | 48 +++++++++++++++++++++++------ R/divide_carto.R | 11 +++++- R/mergeINLA.R | 89 ++++++++++++++++++++++++++++++++++++++---------------- README.md | 7 +++- build/partial.rdb |binary inst/CITATION | 6 +-- man/CAR_INLA.Rd | 4 +- man/STCAR_INLA.Rd | 2 - 13 files changed, 189 insertions(+), 75 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre],
Niklas von Hertzen [aut]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.6.7 dated 2024-10-23 and 1.6.8 dated 2025-09-16
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/radiant.R | 14 ++++++++++---- inst/app/radiant.R | 8 ++++---- 5 files changed, 27 insertions(+), 17 deletions(-)
Title: Statistical Power and Sample Size Calculation Tools
Description: The 'pwrss' R package provides flexible and comprehensive functions for
statistical power and minimum required sample size calculations across a wide
range of commonly used hypothesis tests in psychological, biomedical, and
social sciences.
Author: Metin Bulus [aut, cre],
Sebastian Jentschke [ctb]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between pwrss versions 0.3.1 dated 2023-04-11 and 1.0.0 dated 2025-09-16
pwrss-0.3.1/pwrss/R/pwrss.R |only pwrss-0.3.1/pwrss/README.md |only pwrss-0.3.1/pwrss/man/0-Generic-Chi-square-Test.Rd |only pwrss-0.3.1/pwrss/man/0-Generic-F-Test.Rd |only pwrss-0.3.1/pwrss/man/0-Generic-t-Test.Rd |only pwrss-0.3.1/pwrss/man/0-Generic-z-Test.Rd |only pwrss-0.3.1/pwrss/man/1-One-Correlation.Rd |only pwrss-0.3.1/pwrss/man/1-One-Mean.Rd |only pwrss-0.3.1/pwrss/man/1-One-Proportion.Rd |only pwrss-0.3.1/pwrss/man/2-Two-Correlations.Rd |only pwrss-0.3.1/pwrss/man/2-Two-Groups-NP.Rd |only pwrss-0.3.1/pwrss/man/2-Two-Means.Rd |only pwrss-0.3.1/pwrss/man/2-Two-Proportions.Rd |only pwrss-0.3.1/pwrss/man/4-Indirect-Effect-in-Mediation.Rd |only pwrss-0.3.1/pwrss/man/4-Linear-Regression-Beta.Rd |only pwrss-0.3.1/pwrss/man/4-Linear-Regression-Rsquared.Rd |only pwrss-0.3.1/pwrss/man/4-Logistic-Regression-Beta.Rd |only pwrss-0.3.1/pwrss/man/4-Poisson-Regression-Beta.Rd |only pwrss-0.3.1/pwrss/man/5-ANOVA-and-ANCOVA.Rd |only pwrss-0.3.1/pwrss/man/5-GOF-or-Independence.Rd |only pwrss-0.3.1/pwrss/man/5-Repeated-Measures-ANOVA.Rd |only pwrss-0.3.1/pwrss/man/6-Plot-Type-I-and-II-Errors.Rd |only pwrss-1.0.0/pwrss/DESCRIPTION | 23 pwrss-1.0.0/pwrss/MD5 | 118 pwrss-1.0.0/pwrss/NAMESPACE | 99 pwrss-1.0.0/pwrss/NEWS.md | 51 pwrss-1.0.0/pwrss/R/ancova.R |only pwrss-1.0.0/pwrss/R/anova.mixed.R |only pwrss-1.0.0/pwrss/R/checks.R |only pwrss-1.0.0/pwrss/R/correlations.R |only pwrss-1.0.0/pwrss/R/generic.binom.test.R |only pwrss-1.0.0/pwrss/R/generic.chisq.test.R |only pwrss-1.0.0/pwrss/R/generic.f.test.R |only pwrss-1.0.0/pwrss/R/generic.t.test.R |only pwrss-1.0.0/pwrss/R/generic.z.test.R |only pwrss-1.0.0/pwrss/R/means.student.R |only pwrss-1.0.0/pwrss/R/means.wilcoxon.R |only pwrss-1.0.0/pwrss/R/plot.binom.R |only pwrss-1.0.0/pwrss/R/plot.chisq.R |only pwrss-1.0.0/pwrss/R/plot.f.R |only pwrss-1.0.0/pwrss/R/plot.t.R |only pwrss-1.0.0/pwrss/R/plots.R |only pwrss-1.0.0/pwrss/R/printing.R |only pwrss-1.0.0/pwrss/R/printing.pretty.R |only pwrss-1.0.0/pwrss/R/proportions.fisher.R |only pwrss-1.0.0/pwrss/R/proportions.gof.R |only pwrss-1.0.0/pwrss/R/proportions.mcnemar.R |only pwrss-1.0.0/pwrss/R/proportions.onetwo.R |only pwrss-1.0.0/pwrss/R/regression.linear.R |only pwrss-1.0.0/pwrss/R/regression.logistic.R |only pwrss-1.0.0/pwrss/R/regression.mediation.R |only pwrss-1.0.0/pwrss/R/regression.poisson.R |only pwrss-1.0.0/pwrss/R/utils.R |only pwrss-1.0.0/pwrss/build/partial.rdb |only pwrss-1.0.0/pwrss/build/vignette.rds |binary pwrss-1.0.0/pwrss/inst/CITATION | 14 pwrss-1.0.0/pwrss/inst/WORDLIST |only pwrss-1.0.0/pwrss/inst/doc/examples.R | 1445 ++ pwrss-1.0.0/pwrss/inst/doc/examples.Rmd | 2417 +++- pwrss-1.0.0/pwrss/inst/doc/examples.html | 8360 ++++++++++++---- pwrss-1.0.0/pwrss/man/ancova.Rd |only pwrss-1.0.0/pwrss/man/ancova.contrasts.Rd |only pwrss-1.0.0/pwrss/man/ancova.factorial.contrasts.Rd |only pwrss-1.0.0/pwrss/man/ancova.keppel.Rd |only pwrss-1.0.0/pwrss/man/ancova.shieh.Rd |only pwrss-1.0.0/pwrss/man/anova.mixed.Rd |only pwrss-1.0.0/pwrss/man/conversion.cors.to.q.Rd |only pwrss-1.0.0/pwrss/man/conversion.d.to.cles.Rd |only pwrss-1.0.0/pwrss/man/conversion.f.to.etasq.Rd |only pwrss-1.0.0/pwrss/man/conversion.mcnemar.probs.Rd |only pwrss-1.0.0/pwrss/man/conversion.means.to.d.Rd |only pwrss-1.0.0/pwrss/man/conversion.probs.to.h.Rd |only pwrss-1.0.0/pwrss/man/conversion.probs.to.w.Rd |only pwrss-1.0.0/pwrss/man/conversion.rsq.to.f.Rd |only pwrss-1.0.0/pwrss/man/correlations.one.Rd |only pwrss-1.0.0/pwrss/man/correlations.steiger.Rd |only pwrss-1.0.0/pwrss/man/correlations.two.Rd |only pwrss-1.0.0/pwrss/man/figures |only pwrss-1.0.0/pwrss/man/generic.binom.test.Rd |only pwrss-1.0.0/pwrss/man/generic.chisq.test.Rd |only pwrss-1.0.0/pwrss/man/generic.f.test.Rd |only pwrss-1.0.0/pwrss/man/generic.t.test.Rd |only pwrss-1.0.0/pwrss/man/generic.z.test.Rd |only pwrss-1.0.0/pwrss/man/means.student.welch.Rd |only pwrss-1.0.0/pwrss/man/means.wilcoxon.Rd |only pwrss-1.0.0/pwrss/man/proportions.fisher.Rd |only pwrss-1.0.0/pwrss/man/proportions.gof.Rd |only pwrss-1.0.0/pwrss/man/proportions.mcnemar.Rd |only pwrss-1.0.0/pwrss/man/proportions.oneprop.Rd |only pwrss-1.0.0/pwrss/man/proportions.twoprops.Rd |only pwrss-1.0.0/pwrss/man/regression.linear.f.Rd |only pwrss-1.0.0/pwrss/man/regression.linear.t.Rd |only pwrss-1.0.0/pwrss/man/regression.logistic.Rd |only pwrss-1.0.0/pwrss/man/regression.mediation.Rd |only pwrss-1.0.0/pwrss/man/regression.poisson.Rd |only pwrss-1.0.0/pwrss/man/utils.attrition.Rd |only pwrss-1.0.0/pwrss/vignettes/app.png |binary pwrss-1.0.0/pwrss/vignettes/examples.Rmd | 2417 +++- pwrss-1.0.0/pwrss/vignettes/hex.png |binary pwrss-1.0.0/pwrss/vignettes/license.png |binary pwrss-1.0.0/pwrss/vignettes/med.png |binary 101 files changed, 11510 insertions(+), 3434 deletions(-)
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] ,
Vonage Holdings Corp. [ctb, cph] ,
Ian Galpin [ctb, cph] ,
Ben Gertzfield [ctb, cph]
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 8.13.36 dated 2024-05-03 and 9.0.14 dated 2025-09-16
dialrjars-8.13.36/dialrjars/inst/java/carrier-1.220.jar |only dialrjars-8.13.36/dialrjars/inst/java/geocoder-2.230.jar |only dialrjars-8.13.36/dialrjars/inst/java/libphonenumber-8.13.36.jar |only dialrjars-8.13.36/dialrjars/inst/java/prefixmapper-2.230.jar |only dialrjars-9.0.14/dialrjars/DESCRIPTION | 8 dialrjars-9.0.14/dialrjars/MD5 | 12 dialrjars-9.0.14/dialrjars/NEWS.md | 300 ++++++++++ dialrjars-9.0.14/dialrjars/inst/java/carrier-2.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/geocoder-3.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/libphonenumber-9.0.14.jar |only dialrjars-9.0.14/dialrjars/inst/java/prefixmapper-3.14.jar |only 11 files changed, 310 insertions(+), 10 deletions(-)
Title: 'juice' + 'markdown': Convert 'R Markdown' into 'HTML' with
Inline Styles
Description: A convenience tool to create 'HTML' with inline styles using
'juicyjuice' and 'markdown' packages. It is particularly useful when working
on a content management system (CMS) whose code editor eliminates style and
link tags. The main use case of the package is the learning management system,
'Moodle'. Additional helper functions for teaching purposes are provided. Learn
more about 'juicedown' at <https://kenjisato.github.io/juicedown/>.
Author: Kenji Sato [aut, cre, cph]
Maintainer: Kenji Sato <kenji@kenjisato.jp>
Diff between juicedown versions 0.1.1 dated 2023-09-05 and 0.1.2 dated 2025-09-15
DESCRIPTION | 15 +++++++++------ MD5 | 14 +++++++------- NEWS.md | 7 ++++++- R/includeFlickr.R | 2 +- R/includeMedia.R | 4 ++-- man/includeAudio.Rd | 2 +- man/includeText.Rd | 2 +- man/juicedown-package.Rd | 2 ++ 8 files changed, 29 insertions(+), 19 deletions(-)
Title: Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre] ,
Maurice Goodman [ctb] ,
Wouter van der Bijl [ctb] ,
Giovanni M. Marchetti [ctr]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.6.0 dated 2025-03-21 and 1.7.0 dated 2025-09-15
dsem-1.6.0/dsem/inst/doc/vignette.R |only dsem-1.6.0/dsem/inst/doc/vignette.Rmd |only dsem-1.6.0/dsem/inst/doc/vignette.html |only dsem-1.6.0/dsem/vignettes/vignette.Rmd |only dsem-1.7.0/dsem/DESCRIPTION | 20 +- dsem-1.7.0/dsem/MD5 | 72 ++++--- dsem-1.7.0/dsem/NAMESPACE | 2 dsem-1.7.0/dsem/NEWS.md | 12 + dsem-1.7.0/dsem/R/compute_nll.R | 6 dsem-1.7.0/dsem/R/dsem.R | 59 +++++- dsem-1.7.0/dsem/R/make_dsem_ram.R | 14 - dsem-1.7.0/dsem/R/make_matrices.R | 17 + dsem-1.7.0/dsem/R/stepwise_selection.R | 17 + dsem-1.7.0/dsem/R/utility.R | 174 ++++++++++++++++-- dsem-1.7.0/dsem/README.md | 6 dsem-1.7.0/dsem/build/partial.rdb |binary dsem-1.7.0/dsem/build/vignette.rds |binary dsem-1.7.0/dsem/inst/doc/dynamic_factor_analysis.html | 34 +-- dsem-1.7.0/dsem/inst/doc/features.R |only dsem-1.7.0/dsem/inst/doc/features.Rmd |only dsem-1.7.0/dsem/inst/doc/features.html |only dsem-1.7.0/dsem/inst/doc/model-description.R |only dsem-1.7.0/dsem/inst/doc/model-description.Rmd |only dsem-1.7.0/dsem/inst/doc/model-description.html |only dsem-1.7.0/dsem/inst/doc/spatial_diffusion.html | 3 dsem-1.7.0/dsem/man/cAIC.Rd | 4 dsem-1.7.0/dsem/man/classify_variables.Rd | 2 dsem-1.7.0/dsem/man/convert_equations.Rd | 4 dsem-1.7.0/dsem/man/dsem.Rd | 92 +++++---- dsem-1.7.0/dsem/man/dsemRTMB.Rd | 16 - dsem-1.7.0/dsem/man/dsem_control.Rd | 31 +-- dsem-1.7.0/dsem/man/figures |only dsem-1.7.0/dsem/man/logLik.dsem.Rd | 4 dsem-1.7.0/dsem/man/loo_residuals.Rd | 2 dsem-1.7.0/dsem/man/make_dsem_ram.Rd | 76 ++++--- dsem-1.7.0/dsem/man/make_matrices.Rd | 4 dsem-1.7.0/dsem/man/parse_path.Rd | 2 dsem-1.7.0/dsem/man/partition_variance.Rd |only dsem-1.7.0/dsem/man/stepwise_selection.Rd | 9 dsem-1.7.0/dsem/man/test_dsep.Rd | 2 dsem-1.7.0/dsem/man/total_effect.Rd | 59 ++++-- dsem-1.7.0/dsem/src/dsem.cpp | 103 ++++++++++ dsem-1.7.0/dsem/vignettes/features.Rmd |only dsem-1.7.0/dsem/vignettes/model-description.Rmd |only 44 files changed, 622 insertions(+), 224 deletions(-)
Title: Model Classifier for Binary Classification
Description: A collection of tools that support data splitting, predictive modeling, and model evaluation.
A typical function is to split a dataset into a training dataset and a test dataset.
Then compare the data distribution of the two datasets.
Another feature is to support the development of predictive models and to compare the performance of several predictive models,
helping to select the best model.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between alookr versions 0.3.91 dated 2025-08-24 and 0.4.0 dated 2025-09-15
alookr |only 1 file changed
Title: Methods for ''A Fast Alternative for the R x C Ecological
Inference Case''
Description: Estimates the probability matrix for the R×C Ecological Inference problem using the Expectation-Maximization Algorithm with four approximation methods for the E-Step, and an exact method as well. It also provides a bootstrap function to estimate the standard deviation of the estimated probabilities. In addition, it has functions that aggregate rows optimally to have more reliable estimates in cases of having few data points. For comparing the probability estimates of two groups, a Wald test routine is implemented. The library has data from the first round of the Chilean Presidential Election 2021 and can also generate synthetic election data. Methods described in Thraves, Charles; Ubilla, Pablo; Hermosilla, Daniel (2024) ''A Fast Ecological Inference Algorithm for the R×C case'' <doi:10.2139/ssrn.4832834>.
Author: Charles Thraves [aut] ,
Pablo Ubilla [aut],
Daniel Hermosilla [aut, cre],
Hanson Troy [ctb, cph]
Maintainer: Daniel Hermosilla <daniel.hermosilla.r@ug.uchile.cl>
Diff between fastei versions 0.0.0.9 dated 2025-07-18 and 0.0.0.10 dated 2025-09-15
fastei-0.0.0.10/fastei/DESCRIPTION | 12 fastei-0.0.0.10/fastei/MD5 | 80 +- fastei-0.0.0.10/fastei/NAMESPACE | 2 fastei-0.0.0.10/fastei/R/RcppExports.R | 20 fastei-0.0.0.10/fastei/R/data-utils.R | 2 fastei-0.0.0.10/fastei/R/eim-class.R | 118 +++- fastei-0.0.0.10/fastei/R/instancer.R | 19 fastei-0.0.0.10/fastei/R/internal.R | 30 - fastei-0.0.0.10/fastei/inst/doc/demonstration.html | 17 fastei-0.0.0.10/fastei/man/fastei-package.Rd | 2 fastei-0.0.0.10/fastei/man/get_eim_chile.Rd | 2 fastei-0.0.0.10/fastei/man/run_em.Rd | 19 fastei-0.0.0.10/fastei/man/simulate_election.Rd | 1 fastei-0.0.0.10/fastei/src/LP.c |only fastei-0.0.0.10/fastei/src/LP.h |only fastei-0.0.0.10/fastei/src/MCMC.c |only fastei-0.0.0.10/fastei/src/MCMC.h |only fastei-0.0.0.10/fastei/src/Makevars | 3 fastei-0.0.0.10/fastei/src/RcppExports.cpp | 62 +- fastei-0.0.0.10/fastei/src/bootstrap.c | 45 - fastei-0.0.0.10/fastei/src/bootstrap.h | 2 fastei-0.0.0.10/fastei/src/dynamic_program.c | 76 +- fastei-0.0.0.10/fastei/src/dynamic_program.h | 22 fastei-0.0.0.10/fastei/src/exact.c | 209 ++----- fastei-0.0.0.10/fastei/src/exact.h | 23 fastei-0.0.0.10/fastei/src/globals.h | 92 ++- fastei-0.0.0.10/fastei/src/main.c | 601 ++++++++++++++------- fastei-0.0.0.10/fastei/src/main.h | 89 --- fastei-0.0.0.10/fastei/src/multinomial.c | 54 - fastei-0.0.0.10/fastei/src/multinomial.h | 4 fastei-0.0.0.10/fastei/src/multivariate-cdf.c | 431 ++++++++++----- fastei-0.0.0.10/fastei/src/multivariate-cdf.h | 2 fastei-0.0.0.10/fastei/src/multivariate-pdf.c | 254 ++++---- fastei-0.0.0.10/fastei/src/multivariate-pdf.h | 2 fastei-0.0.0.10/fastei/src/utils_hash.c | 2 fastei-0.0.0.10/fastei/src/utils_hash.h | 6 fastei-0.0.0.10/fastei/src/utils_matrix.c | 118 +++- fastei-0.0.0.10/fastei/src/utils_matrix.h | 21 fastei-0.0.0.10/fastei/src/utils_multivariate.c | 9 fastei-0.0.0.10/fastei/src/utils_multivariate.h | 4 fastei-0.0.0.10/fastei/src/wrapper.cpp | 149 ++--- fastei-0.0.0.10/fastei/src/wrapper.h | 71 +- fastei-0.0.0.9/fastei/src/hitAndRun.c |only fastei-0.0.0.9/fastei/src/hitAndRun.h |only 44 files changed, 1612 insertions(+), 1063 deletions(-)
Title: Produce Forest Plots to Visualize Covariate Effects
Description: Produce forest plots to visualize covariate effects using either
the command line or an interactive 'Shiny' application.
Author: Samer Mouksassi [aut, cre] ,
Benjamin Rich [aut],
Dean Attali [ctb]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between coveffectsplot versions 1.0.6 dated 2025-01-12 and 1.0.7 dated 2025-09-15
coveffectsplot-1.0.6/coveffectsplot/inst/shiny/rsconnect |only coveffectsplot-1.0.6/coveffectsplot/vignettes/Figure_8_4.png |only coveffectsplot-1.0.7/coveffectsplot/DESCRIPTION | 17 coveffectsplot-1.0.7/coveffectsplot/MD5 | 74 coveffectsplot-1.0.7/coveffectsplot/NEWS.md | 5 coveffectsplot-1.0.7/coveffectsplot/R/forest_plot.R | 12 coveffectsplot-1.0.7/coveffectsplot/build/vignette.rds |binary coveffectsplot-1.0.7/coveffectsplot/inst/doc/Exposure_Response_Example.R | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/Exposure_Response_Example.Rmd | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/Exposure_Response_Example.html | 21 coveffectsplot-1.0.7/coveffectsplot/inst/doc/PKPD_Example.html | 15 coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example.R | 5 coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example.Rmd | 56 coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example.html | 144 - coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example_full.R | 122 + coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example_full.Rmd | 127 + coveffectsplot-1.0.7/coveffectsplot/inst/doc/PK_Example_full.html | 331 ++- coveffectsplot-1.0.7/coveffectsplot/inst/doc/Pediatric_Cov_Sim.R | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/Pediatric_Cov_Sim.Rmd | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/Pediatric_Cov_Sim.html | 44 coveffectsplot-1.0.7/coveffectsplot/inst/doc/app.html | 2 coveffectsplot-1.0.7/coveffectsplot/inst/doc/introduction_to_coveffectsplot.R | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/introduction_to_coveffectsplot.Rmd | 1 coveffectsplot-1.0.7/coveffectsplot/inst/doc/introduction_to_coveffectsplot.html | 23 coveffectsplot-1.0.7/coveffectsplot/inst/shiny/global.r | 20 coveffectsplot-1.0.7/coveffectsplot/inst/shiny/server.R | 27 coveffectsplot-1.0.7/coveffectsplot/inst/shiny/text/howto.md | 48 coveffectsplot-1.0.7/coveffectsplot/inst/shiny/ui.R | 14 coveffectsplot-1.0.7/coveffectsplot/man/covdatasim.Rd | 52 coveffectsplot-1.0.7/coveffectsplot/man/deltamethod.Rd | 202 - coveffectsplot-1.0.7/coveffectsplot/man/draw_key.Rd | 52 coveffectsplot-1.0.7/coveffectsplot/man/expand_modelframe.Rd | 60 coveffectsplot-1.0.7/coveffectsplot/man/forest_plot.Rd | 1040 +++++----- coveffectsplot-1.0.7/coveffectsplot/man/wtage.Rd | 70 coveffectsplot-1.0.7/coveffectsplot/vignettes/Exposure_Response_Example.Rmd | 1 coveffectsplot-1.0.7/coveffectsplot/vignettes/PK_Example.Rmd | 56 coveffectsplot-1.0.7/coveffectsplot/vignettes/PK_Example_full.Rmd | 127 + coveffectsplot-1.0.7/coveffectsplot/vignettes/Pediatric_Cov_Sim.Rmd | 1 coveffectsplot-1.0.7/coveffectsplot/vignettes/introduction_to_coveffectsplot.Rmd | 1 39 files changed, 1690 insertions(+), 1085 deletions(-)
More information about coveffectsplot at CRAN
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Title: Test Surveys by Simulating Spatially-Correlated Populations
Description: Simulate age-structured populations that vary in space and time and
explore the efficacy of a range of built-in or user-defined sampling
protocols to reproduce the population parameters of the known population.
(See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more
details).
Author: Paul Regular [aut, cre] ,
Jonathan Babyn [ctb],
Greg Robertson [ctb]
Maintainer: Paul Regular <Paul.Regular@dfo-mpo.gc.ca>
Diff between SimSurvey versions 0.1.7 dated 2025-08-22 and 0.1.8 dated 2025-09-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 ++ NEWS.md | 3 +++ R/data.R | 6 +++++- man/land.Rd | 2 +- 6 files changed, 20 insertions(+), 11 deletions(-)
Title: Feel at Home using R, Thanks to Shortcuts Functions Making it
Simple
Description: A collection of personal functions designed to simplify and streamline
common R programming tasks. This package provides reusable tools and shortcuts
for frequently used calculations and workflows.
Author: Raphael Flambard [aut, cre],
Adrien Cocuaud [ctb]
Maintainer: Raphael Flambard <raphael@ralpha.fr>
Diff between R.AlphA.Home versions 1.0.0 dated 2025-02-11 and 1.1.0 dated 2025-09-15
DESCRIPTION | 27 +- MD5 | 87 ++++--- NAMESPACE | 119 ++++++---- NEWS.md |only R/Rtimer.R |only R/cols_pad.R | 66 ++--- R/compareVars.R | 100 ++++---- R/countSwitches.R | 190 ++++++++-------- R/foldAllBr.R | 557 +++++++++++++++++++++++++----------------------- R/globalVariables.R | 200 ++++++++--------- R/importAll.R | 347 ++++++++++++++++++----------- R/left_join_checks.R | 329 ++++++++++++++-------------- R/loadCheck.R |only R/lum_0_100.R | 74 +++--- R/printif.R |only R/quickExport.R |only R/quickSave.R | 150 ++++++------ R/ralpha_fold.R |only R/ralpha_unfold.R |only R/rdate.R | 108 ++++----- R/ret_lum.R | 72 +++--- R/root.R | 38 +-- R/sepThsd.R | 64 ++--- R/setOption.R |only R/shiny_lum_0_100.R | 74 +++--- R/show_diff.R |only R/timer.R | 184 +++++++-------- R/utils-position.R |only README.md | 93 +++++++- inst/rstudio/addins.dcf | 14 - man/Rtimer.Rd |only man/cols_pad.Rd | 64 ++--- man/compareVars.Rd | 94 ++++---- man/countSwitches.Rd | 144 ++++++------ man/figures |only man/foldAllBr.Rd | 93 ++++---- man/importAll.Rd | 161 +++++++------ man/left_join_checks.Rd | 152 ++++++------- man/loadCheck.Rd |only man/lum_0_100.Rd | 46 +-- man/printif.Rd |only man/quickExport.Rd |only man/quickSave.Rd | 72 +++--- man/ralpha_fold.Rd |only man/ralpha_unfold.Rd |only man/rdate.Rd | 92 +++---- man/ret_lum.Rd | 68 ++--- man/root.Rd | 42 +-- man/sepThsd.Rd | 70 +++--- man/setOption.Rd |only man/shiny_lum_0_100.Rd | 42 +-- man/show_diff.Rd |only man/timer.Rd | 128 +++++------ tests |only 54 files changed, 2226 insertions(+), 1935 deletions(-)
Title: Deal with One and Two (Normal) Samples
Description: We introduce an R function
one_two_sample() which can deal with one and two (normal)
samples, Ying-Ying Zhang, Yi Wei (2012) <doi:10.2991/asshm-13.2013.29>.
For one normal sample x, the function reports
descriptive statistics, plot, interval estimation and test of
hypothesis of x. For two normal samples x and y, the function
reports descriptive statistics, plot, interval estimation and
test of hypothesis of x and y, respectively. It also reports
interval estimation and test of hypothesis of mu1-mu2 (the
difference of the means of x and y) and sigma1^2 / sigma2^2
(the ratio of the variances of x and y), tests whether x and y
are from the same population, finds the correlation coefficient
of x and y if x and y have the same length.
Author: Frederic Bertrand [cre] ,
Ying-Ying Zhang [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between OneTwoSamples versions 1.1-0 dated 2023-03-28 and 1.2-0 dated 2025-09-15
OneTwoSamples-1.1-0/OneTwoSamples/tests/tests_OneTwoSamples.R |only OneTwoSamples-1.1-0/OneTwoSamples/vignettes/RnwToTex.R |only OneTwoSamples-1.2-0/OneTwoSamples/DESCRIPTION | 20 - OneTwoSamples-1.2-0/OneTwoSamples/MD5 | 157 +++++++++- OneTwoSamples-1.2-0/OneTwoSamples/NEWS.md | 12 OneTwoSamples-1.2-0/OneTwoSamples/build/partial.rdb |binary OneTwoSamples-1.2-0/OneTwoSamples/build/vignette.rds |binary OneTwoSamples-1.2-0/OneTwoSamples/inst/CITATION |only OneTwoSamples-1.2-0/OneTwoSamples/inst/_pkgdown.yml |only OneTwoSamples-1.2-0/OneTwoSamples/inst/doc/OneTwoSamples.pdf |binary OneTwoSamples-1.2-0/OneTwoSamples/man/OneTwoSamples-package.Rd | 2 OneTwoSamples-1.2-0/OneTwoSamples/man/one_sample.Rd | 2 OneTwoSamples-1.2-0/OneTwoSamples/tests/testthat |only OneTwoSamples-1.2-0/OneTwoSamples/tests/testthat.R |only 14 files changed, 172 insertions(+), 21 deletions(-)
Title: Deciphering Biological Networks with Patterned Heterogeneous
Measurements
Description: A modeling tool dedicated to biological network modeling (Bertrand and others 2020, <doi:10.1093/bioinformatics/btaa855>). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, <doi:10.1093/bioinformati [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between Patterns versions 1.6 dated 2025-07-02 and 1.7 dated 2025-09-15
DESCRIPTION | 24 +++-- MD5 | 49 +++++++---- NAMESPACE | 1 NEWS.md | 6 + R/Patterns-package.R | 4 R/datasets.R | 30 +++++++ R/omics_array.R | 5 - README.md | 147 ++++++++++++++++++----------------- data/datalist | 9 +- data/jetsetscores.RData |only inst/CITATION | 6 + inst/_pkgdown.yml |only inst/doc/ExampleCLL.Rmd | 2 inst/doc/ExampleCLL.html | 6 - inst/doc/IntroPatterns.Rmd | 2 inst/doc/IntroPatterns.html | 6 - man/Patterns-package.Rd | 4 man/jetsetscores.Rd |only man/probeMerge-omics_array-method.Rd | 5 - tests |only vignettes/ExampleCLL.Rmd | 2 vignettes/IntroPatterns.Rmd | 2 22 files changed, 188 insertions(+), 122 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva [aut, cre],
Paula Brito [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Diff between MAINT.Data versions 2.7.1 dated 2023-04-04 and 2.7.2 dated 2025-09-15
CHANGELOG | 6 ++++ DESCRIPTION | 14 +++++----- MD5 | 58 +++++++++++++++++++++--------------------- R/ClasGenMetDef.R | 8 ++--- R/IdtMclust_methods.R | 48 ++++++++++++++++++++++++++-------- R/IdtOutl_methods.R | 42 +++++++++++++++++++++--------- R/fasttle.R | 7 ++--- R/lqda.R | 7 +---- man/IdtOutl-methods.Rd | 6 +++- man/MAINT.Data-package.Rd | 4 +- man/RepLOptim.Rd | 2 - man/RobEstControl-class.Rd | 20 +++++++------- man/Robda-methods.Rd | 2 - man/fasttle-methods.Rd | 2 - man/pcoordplot-methos.Rd | 8 ++++- src/AdMatAlgFoo.h | 2 + src/AuxFoo.cpp | 1 src/AuxFoo.h | 2 + src/CEMGauss.cpp | 1 src/MDataGaussLogLik.h | 2 + src/Makevars | 2 - src/MinMaxEgval.h | 2 + src/fulltle.cpp | 1 src/msnCP_Aux.cpp | 3 +- src/msnCP_Aux.h | 1 src/msnCP_dev.h | 2 + src/msnCP_dev_grad.h | 2 + src/registerDynamicSimbol.cpp | 2 - src/sampleint.h | 3 +- src/tle.h | 5 +-- 30 files changed, 164 insertions(+), 101 deletions(-)
Title: Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary
Tables
Description: Quickly and easily perform exploratory data analysis by uploading your
data as a 'csv' file. Start generating insights using 'ggplot2' plots and
'table1' tables with descriptive stats, all using an easy-to-use point and click
'Shiny' interface.
Author: Samer Mouksassi [aut, cre] ,
Dean Attali [aut],
James Craig [aut] ,
Benjamin Rich [aut] ,
Michael Sachs [aut]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between ggquickeda versions 0.3.1 dated 2024-01-15 and 0.3.2 dated 2025-09-15
ggquickeda-0.3.1/ggquickeda/inst/shinyapp/rsconnect |only ggquickeda-0.3.2/ggquickeda/DESCRIPTION | 25 ggquickeda-0.3.2/ggquickeda/MD5 | 53 ggquickeda-0.3.2/ggquickeda/NAMESPACE | 4 ggquickeda-0.3.2/ggquickeda/NEWS.md | 26 ggquickeda-0.3.2/ggquickeda/R/ggcontinuousexpdist.R | 1264 ++++++++-- ggquickeda-0.3.2/ggquickeda/R/ggkm.R | 6 ggquickeda-0.3.2/ggquickeda/R/ggkmrisktable.R | 217 + ggquickeda-0.3.2/ggquickeda/R/gglogisticexpdist.R | 1065 ++++++-- ggquickeda-0.3.2/ggquickeda/R/ggresponseexpdist.R |only ggquickeda-0.3.2/ggquickeda/build/vignette.rds |binary ggquickeda-0.3.2/ggquickeda/inst/doc/AdditionalPlotsStats.html | 22 ggquickeda-0.3.2/ggquickeda/inst/doc/Visualizing_Summary_Data.html | 23 ggquickeda-0.3.2/ggquickeda/inst/doc/app.html | 2 ggquickeda-0.3.2/ggquickeda/inst/doc/ggquickeda.html | 16 ggquickeda-0.3.2/ggquickeda/inst/shinyapp/global.R | 26 ggquickeda-0.3.2/ggquickeda/inst/shinyapp/server.R | 311 +- ggquickeda-0.3.2/ggquickeda/inst/shinyapp/ui.R | 28 ggquickeda-0.3.2/ggquickeda/man/geom_km.Rd | 71 ggquickeda-0.3.2/ggquickeda/man/geom_kmband.Rd | 71 ggquickeda-0.3.2/ggquickeda/man/geom_kmticks.Rd | 71 ggquickeda-0.3.2/ggquickeda/man/ggcontinuousexpdist.Rd | 136 - ggquickeda-0.3.2/ggquickeda/man/ggkmrisktable.Rd | 41 ggquickeda-0.3.2/ggquickeda/man/gglogisticexpdist.Rd | 169 + ggquickeda-0.3.2/ggquickeda/man/ggresponseexpdist.Rd |only ggquickeda-0.3.2/ggquickeda/man/stat_km.Rd | 41 ggquickeda-0.3.2/ggquickeda/man/stat_kmband.Rd | 37 ggquickeda-0.3.2/ggquickeda/man/stat_kmticks.Rd | 43 28 files changed, 2999 insertions(+), 769 deletions(-)
Title: Conformal Inference Tools for Regression with Multivariate
Response
Description: It computes full conformal, split conformal and multi-split conformal
prediction regions when the response variable is multivariate (i.e.
dimension is greater than one). Moreover, the package also contains
plot functions to visualize the output of the full and split conformal
functions. To guarantee consistency, the package structure mimics the
univariate package 'conformalInference' by Ryan Tibshirani.
See Lei, G’sell, Rinaldo, Tibshirani, & Wasserman (2018) <doi:10.1080/01621459.2017.1307116>
for full and split conformal prediction in regression, and Barber, Candès,
Ramdas, & Tibshirani (2023) <doi:10.1214/23-AOS2276> for extensions beyond exchangeability.
Author: Jacopo Diquigiovanni [aut, ths],
Matteo Fontana [aut, ths],
Aldo Solari [aut, ths],
Simone Vantini [aut, ths],
Paolo Vergottini [aut, cre],
Ryan Tibshirani [ctb]
Maintainer: Paolo Vergottini <paolo.vergottini@gmail.com>
This is a re-admission after prior archival of version 1.1.1 dated 2022-03-16
Diff between conformalInference.multi versions 1.1.1 dated 2022-03-16 and 1.1.2 dated 2025-09-15
conformalInference.multi-1.1.1/conformalInference.multi/NEWS.md |only conformalInference.multi-1.1.1/conformalInference.multi/R/bikeMi.R |only conformalInference.multi-1.1.1/conformalInference.multi/R/common.R |only conformalInference.multi-1.1.1/conformalInference.multi/R/jackplus.R |only conformalInference.multi-1.1.1/conformalInference.multi/R/msplit.R |only conformalInference.multi-1.1.1/conformalInference.multi/R/plot.multidim.R |only conformalInference.multi-1.1.1/conformalInference.multi/R/s.regression.R |only conformalInference.multi-1.1.1/conformalInference.multi/data |only conformalInference.multi-1.1.1/conformalInference.multi/inst/examples/ex.jackplus.R |only conformalInference.multi-1.1.1/conformalInference.multi/man/bikeMi.Rd |only conformalInference.multi-1.1.1/conformalInference.multi/man/conformal.multidim.jackplus.Rd |only conformalInference.multi-1.1.2/conformalInference.multi/DESCRIPTION | 49 conformalInference.multi-1.1.2/conformalInference.multi/LICENSE |only conformalInference.multi-1.1.2/conformalInference.multi/MD5 | 62 - conformalInference.multi-1.1.2/conformalInference.multi/NAMESPACE | 2 conformalInference.multi-1.1.2/conformalInference.multi/R/check.R | 500 ++++------ conformalInference.multi-1.1.2/conformalInference.multi/R/conformalInference.multi-package.R | 33 conformalInference.multi-1.1.2/conformalInference.multi/R/full.R | 384 +++---- conformalInference.multi-1.1.2/conformalInference.multi/R/glmnet.R | 288 ++--- conformalInference.multi-1.1.2/conformalInference.multi/R/interval.build.R |only conformalInference.multi-1.1.2/conformalInference.multi/R/lm.R | 120 +- conformalInference.multi-1.1.2/conformalInference.multi/R/mean.R | 98 + conformalInference.multi-1.1.2/conformalInference.multi/R/multisplit.R |only conformalInference.multi-1.1.2/conformalInference.multi/R/plot.full.R |only conformalInference.multi-1.1.2/conformalInference.multi/R/plot.split.R |only conformalInference.multi-1.1.2/conformalInference.multi/R/s_regression.R |only conformalInference.multi-1.1.2/conformalInference.multi/R/split.R | 382 +++---- conformalInference.multi-1.1.2/conformalInference.multi/README.md |only conformalInference.multi-1.1.2/conformalInference.multi/build |only conformalInference.multi-1.1.2/conformalInference.multi/inst/examples/ex.full.R | 48 conformalInference.multi-1.1.2/conformalInference.multi/inst/examples/ex.msplit.R | 50 - conformalInference.multi-1.1.2/conformalInference.multi/inst/examples/ex.split.R | 50 - conformalInference.multi-1.1.2/conformalInference.multi/man/computing_s_regression.Rd | 29 conformalInference.multi-1.1.2/conformalInference.multi/man/conformal.multidim.full.Rd | 46 conformalInference.multi-1.1.2/conformalInference.multi/man/conformal.multidim.msplit.Rd | 152 +-- conformalInference.multi-1.1.2/conformalInference.multi/man/conformal.multidim.split.Rd | 58 - conformalInference.multi-1.1.2/conformalInference.multi/man/conformalInference.multi-package.Rd | 31 conformalInference.multi-1.1.2/conformalInference.multi/man/glmnet.funs.Rd | 11 conformalInference.multi-1.1.2/conformalInference.multi/man/lm_multi.Rd | 29 conformalInference.multi-1.1.2/conformalInference.multi/man/mean_multi.Rd | 28 conformalInference.multi-1.1.2/conformalInference.multi/man/plot_multidim.Rd | 77 - conformalInference.multi-1.1.2/conformalInference.multi/man/plot_multidim_full.Rd |only 42 files changed, 1184 insertions(+), 1343 deletions(-)
More information about conformalInference.multi at CRAN
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Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, counterfactual analysis, and
computation of impulse response functions, generalized impulse response functions,
generalized forecast error variance decompositions, as well as historical
decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.1016/j.jedc.2025.105162>,
Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.2.1 dated 2025-06-19 and 1.2.2 dated 2025-09-15
DESCRIPTION | 10 ++-- MD5 | 84 +++++++++++++++++++------------------- NEWS.md | 8 +++ R/MAINest.R | 4 - R/STVARconstruction.R | 75 ++++++++++++++++++++++++---------- R/argumentChecks.R | 4 - R/data.R | 8 +-- R/geneticAlgorithm.R | 13 ++--- R/loglikelihood.R | 4 - README.md | 4 - configure | 14 +++--- data/usacpu.rda |binary inst/doc/sstvars-vignette.Rnw | 89 ++++++++++++++++++++--------------------- inst/doc/sstvars-vignette.pdf |binary man/GAfit.Rd | 6 +- man/STVAR.Rd | 4 - man/alt_stvar.Rd | 4 - man/change_regime.Rd | 4 - man/check_params.Rd | 4 - man/diagnostic_plot.Rd | 4 - man/fitSTVAR.Rd | 4 - man/get_alpha_mt.Rd | 4 - man/get_residuals.Rd | 4 - man/in_paramspace.Rd | 4 - man/iterate_more.Rd | 4 - man/loglikelihood.Rd | 4 - man/n_params.Rd | 4 - man/plot_struct_shocks.Rd | 4 - man/predict.stvar.Rd | 4 - man/profile_logliks.Rd | 4 - man/random_covmat.Rd | 2 man/random_ind.Rd | 6 +- man/reform_constrained_pars.Rd | 4 - man/regime_distance.Rd | 4 - man/simulate.stvar.Rd | 4 - man/simulate_from_regime.Rd | 4 - man/simulate_stvar_int.Rd | 4 - man/smart_ind.Rd | 6 +- man/standard_errors.Rd | 4 - man/swap_parametrization.Rd | 4 - man/usacpu.Rd | 8 +-- vignettes/refs.bib | 8 ++- vignettes/sstvars-vignette.Rnw | 89 ++++++++++++++++++++--------------------- 43 files changed, 286 insertions(+), 244 deletions(-)
Title: Access South Korean Data via Public APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'Nager.Date', 'World Bank API', and 'REST Countries API', retrieving real-time or historical
data related to South Korea, such as holidays, economic indicators, and international
demographic and geopolitical indicators. Additionally, the package includes one of the largest
curated collections of open datasets focused on South Korea, covering topics such as public health
outbreaks, demographics, social surveys, elections, economic indicators, natural disasters,
administrative divisions, air quality, climate data, energy consumption, cultural information,
and financial markets. The package supports reproducible research and teaching by integrating
reliable international APIs and structured datasets from public, academic, and government sources.
For more information on the APIs, see:
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
[...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between SouthKoreAPIs versions 0.1.0 dated 2025-09-01 and 0.1.1 dated 2025-09-15
DESCRIPTION | 6 - MD5 | 103 +++++++++---------- NEWS.md |only R/data-documentation.R | 2 R/get_country_info_kr.R | 50 ++++----- R/get_southkorea_child_mortality.R | 2 R/get_southkorea_cpi.R | 2 R/get_southkorea_energy_use.R | 2 R/get_southkorea_gdp.R | 2 R/get_southkorea_holidays.R | 2 R/get_southkorea_hospital_beds.R | 2 R/get_southkorea_life_expectancy.R | 2 R/get_southkorea_literacy_rate.R | 2 R/get_southkorea_population.R | 2 R/get_southkorea_unemployment.R | 2 R/southkoreapis-package.R | 2 R/utils.R | 2 R/view_datasets_SouthKoreAPIs.R | 2 inst/CITATION | 2 inst/doc/SouthKoreAPIs_vignette.html | 5 man/get_country_info_kr.Rd | 18 --- tests/testthat/test-AutoOwnershipKorea_df.R | 2 tests/testthat/test-GasSales_Korea_tbl_df.R | 2 tests/testthat/test-HeptathlonSeoul1988_df.R | 2 tests/testthat/test-KOSPI200_list.R | 2 tests/testthat/test-KPopIdols_tbl_df.R | 2 tests/testthat/test-KoreanBoneDensity_df.R | 2 tests/testthat/test-KoreanElection2017_df.R | 2 tests/testthat/test-KoreanSocialSurvey_tbl_df.R | 2 tests/testthat/test-MERSKorea2015_list.R | 2 tests/testthat/test-NFIColumnNames_df.R | 2 tests/testthat/test-RegionalKorea_df.R | 2 tests/testthat/test-SeoulAdminAreas_sf.R | 2 tests/testthat/test-SeoulDistrictPop_df.R | 2 tests/testthat/test-SeoulH3Data_tbl_df.R | 2 tests/testthat/test-SeoulMosquito_tbl_df.R | 2 tests/testthat/test-SolarRadiation_df.R | 2 tests/testthat/test-SouthKoreaBirths_tbl_df.R | 2 tests/testthat/test-SouthKoreaCovid19_tbl_df.R | 2 tests/testthat/test-demographicsKR_tbl_df.R | 2 tests/testthat/test-get_country_info_kr.R | 19 ++- tests/testthat/test-get_southkorea_child_mortality.R | 2 tests/testthat/test-get_southkorea_cpi.R | 2 tests/testthat/test-get_southkorea_energy_use.R | 2 tests/testthat/test-get_southkorea_gdp.R | 2 tests/testthat/test-get_southkorea_holidays.R | 2 tests/testthat/test-get_southkorea_hospital_beds.R | 2 tests/testthat/test-get_southkorea_life_expectancy.R | 2 tests/testthat/test-get_southkorea_literacy_rate.R | 2 tests/testthat/test-get_southkorea_population.R | 2 tests/testthat/test-get_southkorea_unemployment.R | 2 tests/testthat/test-migrationflows_tbl_df.R | 2 tests/testthat/test-view_datasets_SouthKoreAPIs.R | 2 53 files changed, 147 insertions(+), 146 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 2.6.2 dated 2023-08-08 and 2.6.3 dated 2025-09-15
noctua-2.6.2/noctua/man/Query.Rd |only noctua-2.6.2/noctua/man/backend_dbplyr_v2.Rd |only noctua-2.6.2/noctua/man/dbClearResult.Rd |only noctua-2.6.2/noctua/man/dbColumnInfo.Rd |only noctua-2.6.2/noctua/man/dbDataType.Rd |only noctua-2.6.2/noctua/man/dbDisconnect.Rd |only noctua-2.6.2/noctua/man/dbExistsTable.Rd |only noctua-2.6.2/noctua/man/dbFetch.Rd |only noctua-2.6.2/noctua/man/dbGetInfo.Rd |only noctua-2.6.2/noctua/man/dbGetPartition.Rd |only noctua-2.6.2/noctua/man/dbGetQuery.Rd |only noctua-2.6.2/noctua/man/dbGetStatement.Rd |only noctua-2.6.2/noctua/man/dbGetTables.Rd |only noctua-2.6.2/noctua/man/dbHasCompleted.Rd |only noctua-2.6.2/noctua/man/dbIsValid.Rd |only noctua-2.6.2/noctua/man/dbListFields.Rd |only noctua-2.6.2/noctua/man/dbQuote.Rd |only noctua-2.6.2/noctua/man/dbRemoveTable.Rd |only noctua-2.6.2/noctua/man/dbShow.Rd |only noctua-2.6.2/noctua/man/dbStatistics.Rd |only noctua-2.6.3/noctua/DESCRIPTION | 13 noctua-2.6.3/noctua/MD5 | 130 - noctua-2.6.3/noctua/NAMESPACE | 14 noctua-2.6.3/noctua/NEWS.md | 11 noctua-2.6.3/noctua/R/Connection.R | 922 +++------- noctua-2.6.3/noctua/R/DataTypes.R | 126 - noctua-2.6.3/noctua/R/Driver.R | 152 - noctua-2.6.3/noctua/R/File_Parser.R | 305 ++- noctua-2.6.3/noctua/R/Options.R | 293 ++- noctua-2.6.3/noctua/R/Result.R | 339 +-- noctua-2.6.3/noctua/R/Table.R | 456 +++- noctua-2.6.3/noctua/R/View.R | 294 +-- noctua-2.6.3/noctua/R/athena_low_api.R | 99 - noctua-2.6.3/noctua/R/dplyr_integration.R | 293 +-- noctua-2.6.3/noctua/R/fetch_utils.R | 2 noctua-2.6.3/noctua/R/sql_translate_env.R | 202 +- noctua-2.6.3/noctua/R/utils.R | 246 +- noctua-2.6.3/noctua/R/zzz.R | 34 noctua-2.6.3/noctua/README.md | 2 noctua-2.6.3/noctua/build/vignette.rds |binary noctua-2.6.3/noctua/inst/doc/aws_athena_query_caching.html | 1 noctua-2.6.3/noctua/inst/doc/aws_athena_unload.html | 1 noctua-2.6.3/noctua/inst/doc/aws_s3_backend.R | 2 noctua-2.6.3/noctua/inst/doc/aws_s3_backend.Rmd | 2 noctua-2.6.3/noctua/inst/doc/aws_s3_backend.html | 5 noctua-2.6.3/noctua/inst/doc/changing_backend_file_parser.html | 1 noctua-2.6.3/noctua/inst/doc/convert_and_save_cost.Rmd | 2 noctua-2.6.3/noctua/inst/doc/convert_and_save_cost.html | 3 noctua-2.6.3/noctua/inst/doc/getting_started.html | 1 noctua-2.6.3/noctua/inst/doc/how_to_retry.html | 1 noctua-2.6.3/noctua/man/AthenaConnection.Rd | 133 + noctua-2.6.3/noctua/man/AthenaDriver.Rd | 14 noctua-2.6.3/noctua/man/AthenaListObjects.Rd |only noctua-2.6.3/noctua/man/AthenaPreviewObject.Rd |only noctua-2.6.3/noctua/man/AthenaResult.Rd |only noctua-2.6.3/noctua/man/AthenaWriteTables.Rd | 16 noctua-2.6.3/noctua/man/assume_role.Rd | 4 noctua-2.6.3/noctua/man/athena.Rd | 4 noctua-2.6.3/noctua/man/backend_dbplyr.Rd |only noctua-2.6.3/noctua/man/backend_dbplyr_v1.Rd | 3 noctua-2.6.3/noctua/man/dbConnect-AthenaDriver-method.Rd | 71 noctua-2.6.3/noctua/man/dbConvertTable.Rd | 47 noctua-2.6.3/noctua/man/dbListTables.Rd | 4 noctua-2.6.3/noctua/man/db_compute.Rd | 36 noctua-2.6.3/noctua/man/db_connection_describe.Rd | 2 noctua-2.6.3/noctua/man/db_copy_to.Rd | 8 noctua-2.6.3/noctua/man/db_desc.Rd | 2 noctua-2.6.3/noctua/man/dbplyr_edition.Rd | 4 noctua-2.6.3/noctua/man/noctua-package.Rd | 3 noctua-2.6.3/noctua/man/noctua_options.Rd | 20 noctua-2.6.3/noctua/man/session_token.Rd | 2 noctua-2.6.3/noctua/man/sqlCreateTable.Rd | 4 noctua-2.6.3/noctua/man/sqlData.Rd | 4 noctua-2.6.3/noctua/man/sql_translate_env.Rd | 12 noctua-2.6.3/noctua/man/work_group.Rd | 21 noctua-2.6.3/noctua/tests/testthat/test-dplyr-compute.R | 49 noctua-2.6.3/noctua/vignettes/aws_s3_backend.Rmd | 2 noctua-2.6.3/noctua/vignettes/convert_and_save_cost.Rmd | 2 78 files changed, 2428 insertions(+), 1991 deletions(-)