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(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-07 1.0.9
2024-04-14 1.0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-17 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-13 0.2.2
2022-09-05 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-12 0.5.0
2024-03-11 0.4.5
2024-02-01 0.4.4
2022-09-08 0.4.3
2022-03-22 0.4.2
2022-03-15 0.4.1
2019-08-09 0.3.1
2018-10-30 0.3.0
2018-01-22 0.2.3
2017-06-26 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-13 0.2.2
2024-01-29 0.2.1
2022-09-06 0.2.0
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(-)