Title: Generalized Kumaraswamy Distribution Family
Description: Implements the five-parameter Generalized Kumaraswamy ('gkw')
distribution proposed by 'Carrasco, Ferrari and Cordeiro (2010)'
<doi:10.48550/arXiv.1004.0911> and its seven nested sub-families for
modeling bounded continuous data on the unit interval (0,1). The 'gkw'
distribution extends the Kumaraswamy distribution described by Jones (2009)
<doi:10.1016/j.stamet.2008.04.001>. Provides density, distribution,
quantile, and random generation functions, along with analytical
log-likelihood, gradient, and Hessian functions implemented in 'C++' via
'RcppArmadillo' for maximum computational efficiency. Suitable for modeling
proportions, rates, percentages, and indices exhibiting complex features
such as asymmetry, or heavy tails and other shapes not adequately captured by
standard distributions like simple Beta or Kumaraswamy.
Author: Jose Evandeilton Lopes [aut, cre]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between gkwdist versions 1.1.5 dated 2026-08-23 and 1.1.7 dated 2026-09-26
gkwdist-1.1.5/gkwdist/inst/doc/into-gkwdist.R |only gkwdist-1.1.5/gkwdist/inst/doc/into-gkwdist.Rmd |only gkwdist-1.1.5/gkwdist/inst/doc/into-gkwdist.html |only gkwdist-1.1.5/gkwdist/vignettes/into-gkwdist.Rmd |only gkwdist-1.1.7/gkwdist/DESCRIPTION | 11 gkwdist-1.1.7/gkwdist/LICENSE | 2 gkwdist-1.1.7/gkwdist/MD5 | 195 - gkwdist-1.1.7/gkwdist/NAMESPACE | 3 gkwdist-1.1.7/gkwdist/NEWS.md | 1579 ++++++++++ gkwdist-1.1.7/gkwdist/R/RcppExports.R | 64 gkwdist-1.1.7/gkwdist/R/aaa-shape.R |only gkwdist-1.1.7/gkwdist/R/beta.R | 177 - gkwdist-1.1.7/gkwdist/R/bkw.R | 221 - gkwdist-1.1.7/gkwdist/R/bpmc.R | 611 +-- gkwdist-1.1.7/gkwdist/R/ekw.R | 199 - gkwdist-1.1.7/gkwdist/R/gkw.R | 276 + gkwdist-1.1.7/gkwdist/R/gkwdist-package.R | 28 gkwdist-1.1.7/gkwdist/R/kkw.R | 267 + gkwdist-1.1.7/gkwdist/R/kw.R | 158 - gkwdist-1.1.7/gkwdist/R/zzz.R | 23 gkwdist-1.1.7/gkwdist/README.md | 778 ---- gkwdist-1.1.7/gkwdist/build/vignette.rds |binary gkwdist-1.1.7/gkwdist/inst/CITATION | 20 gkwdist-1.1.7/gkwdist/inst/WORDLIST |only gkwdist-1.1.7/gkwdist/inst/doc/gkwdist.R |only gkwdist-1.1.7/gkwdist/inst/doc/gkwdist.Rmd |only gkwdist-1.1.7/gkwdist/inst/doc/gkwdist.html |only gkwdist-1.1.7/gkwdist/inst/doc/theory-gkwdist.html | 4 gkwdist-1.1.7/gkwdist/man/dbeta_.Rd | 29 gkwdist-1.1.7/gkwdist/man/dbkw.Rd | 30 gkwdist-1.1.7/gkwdist/man/dekw.Rd | 28 gkwdist-1.1.7/gkwdist/man/dgkw.Rd | 36 gkwdist-1.1.7/gkwdist/man/dkkw.Rd | 40 gkwdist-1.1.7/gkwdist/man/dkw.Rd | 27 gkwdist-1.1.7/gkwdist/man/dmc.Rd | 34 gkwdist-1.1.7/gkwdist/man/gkwdist-package.Rd | 28 gkwdist-1.1.7/gkwdist/man/gkwgetstartvalues.Rd | 64 gkwdist-1.1.7/gkwdist/man/grbeta.Rd | 25 gkwdist-1.1.7/gkwdist/man/grbkw.Rd | 35 gkwdist-1.1.7/gkwdist/man/grekw.Rd | 35 gkwdist-1.1.7/gkwdist/man/grgkw.Rd | 33 gkwdist-1.1.7/gkwdist/man/grkkw.Rd | 33 gkwdist-1.1.7/gkwdist/man/grkw.Rd | 17 gkwdist-1.1.7/gkwdist/man/grmc.Rd | 416 -- gkwdist-1.1.7/gkwdist/man/hsbeta.Rd | 25 gkwdist-1.1.7/gkwdist/man/hsbkw.Rd | 35 gkwdist-1.1.7/gkwdist/man/hsekw.Rd | 35 gkwdist-1.1.7/gkwdist/man/hsgkw.Rd | 39 gkwdist-1.1.7/gkwdist/man/hskkw.Rd | 41 gkwdist-1.1.7/gkwdist/man/hskw.Rd | 23 gkwdist-1.1.7/gkwdist/man/hsmc.Rd | 48 gkwdist-1.1.7/gkwdist/man/llbeta.Rd | 26 gkwdist-1.1.7/gkwdist/man/llbkw.Rd | 28 gkwdist-1.1.7/gkwdist/man/llekw.Rd | 24 gkwdist-1.1.7/gkwdist/man/llgkw.Rd | 33 gkwdist-1.1.7/gkwdist/man/llkkw.Rd | 30 gkwdist-1.1.7/gkwdist/man/llkw.Rd | 26 gkwdist-1.1.7/gkwdist/man/llmc.Rd | 28 gkwdist-1.1.7/gkwdist/man/pbeta_.Rd | 32 gkwdist-1.1.7/gkwdist/man/pbkw.Rd | 30 gkwdist-1.1.7/gkwdist/man/pekw.Rd | 28 gkwdist-1.1.7/gkwdist/man/pgkw.Rd | 44 gkwdist-1.1.7/gkwdist/man/pipe.Rd | 13 gkwdist-1.1.7/gkwdist/man/pkkw.Rd | 40 gkwdist-1.1.7/gkwdist/man/pkw.Rd | 28 gkwdist-1.1.7/gkwdist/man/pmc.Rd | 34 gkwdist-1.1.7/gkwdist/man/qbeta_.Rd | 26 gkwdist-1.1.7/gkwdist/man/qbkw.Rd | 26 gkwdist-1.1.7/gkwdist/man/qekw.Rd | 24 gkwdist-1.1.7/gkwdist/man/qgkw.Rd | 38 gkwdist-1.1.7/gkwdist/man/qkkw.Rd | 30 gkwdist-1.1.7/gkwdist/man/qkw.Rd | 24 gkwdist-1.1.7/gkwdist/man/qmc.Rd | 28 gkwdist-1.1.7/gkwdist/man/rbeta_.Rd | 26 gkwdist-1.1.7/gkwdist/man/rbkw.Rd | 23 gkwdist-1.1.7/gkwdist/man/rekw.Rd | 22 gkwdist-1.1.7/gkwdist/man/rgkw.Rd | 31 gkwdist-1.1.7/gkwdist/man/rkkw.Rd | 39 gkwdist-1.1.7/gkwdist/man/rkw.Rd | 22 gkwdist-1.1.7/gkwdist/man/rmc.Rd | 26 gkwdist-1.1.7/gkwdist/src/beta_.cpp | 143 gkwdist-1.1.7/gkwdist/src/bkw.cpp | 550 ++- gkwdist-1.1.7/gkwdist/src/bpmc.cpp | 506 +-- gkwdist-1.1.7/gkwdist/src/ekw.cpp | 409 +- gkwdist-1.1.7/gkwdist/src/gkw.cpp | 1086 +++--- gkwdist-1.1.7/gkwdist/src/gkwinit.cpp | 238 + gkwdist-1.1.7/gkwdist/src/kkw.cpp | 671 ++-- gkwdist-1.1.7/gkwdist/src/kw.cpp | 349 +- gkwdist-1.1.7/gkwdist/src/utils.h | 305 + gkwdist-1.1.7/gkwdist/tests/testthat/test-argument-contract.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-bkw-kkw-log-space.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-cdf-log-space.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-cdf-upper-tail.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-deep-tail-precision.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-density-closed-boundary.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-density-near-upper-bound.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-derivatives-validation.R | 17 gkwdist-1.1.7/gkwdist/tests/testthat/test-gkw-log-chain.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-hessian-degenerate.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-invalid-parameter-warning.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-kw-derivatives-log-space.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-log1mexp-region-boundary.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-loglik-invalid-data.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-loglikelihood-functions.R | 71 gkwdist-1.1.7/gkwdist/tests/testthat/test-mcdonald-no-clamping.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-mcdonald-precision.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-mle-performance.R | 32 gkwdist-1.1.7/gkwdist/tests/testthat/test-quantile-log-space.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-return-contract.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-rng-log-space.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-startvalues-contract.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-subnormal-band.R |only gkwdist-1.1.7/gkwdist/tests/testthat/test-zero-length-input.R |only gkwdist-1.1.7/gkwdist/vignettes/gkwdist.Rmd |only 114 files changed, 6947 insertions(+), 4031 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide substitution,
copy number alteration, etc. are the major force for cancer
initialization and development. Due to the specificity of molecular
lesions caused by genomic alterations, we can generate characteristic
alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021)
<DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al.
(2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al.
(2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to
extract, analyze and visualize signatures from genomic alteration
records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] ,
Ziyu Tao [aut] ,
Huimin Li [aut] ,
Tao Wu [aut] ,
Xue-Song Liu [aut, ctb] ,
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.3.1 dated 2024-05-11 and 2.3.3 dated 2026-09-26
DESCRIPTION | 29 +++-- MD5 | 55 +++++------ NEWS.md | 15 ++- R/best_practice.R | 18 ++- R/get_sv.R | 2 R/read_maf.R | 8 + R/show_group_enrichment.R | 4 R/sig_estimate.R | 18 +++ R/sig_extract.R | 12 ++ R/sig_fit_bootstrap_batch.R | 2 R/sig_tally.R | 6 + R/sigprofiler.R | 24 +++- README.md | 51 +++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/cnsignature.html | 154 +++++++++++++++++-------------- inst/doc/sigminer.R | 24 ++-- inst/doc/sigminer.html | 27 ++++- inst/extdata/human_hg19_gene_info.rds |only man/bp.Rd | 4 man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary 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-9-1.png |binary man/sig_tally.Rd | 2 man/sigprofiler.Rd | 10 +- 29 files changed, 287 insertions(+), 178 deletions(-)
Title: Miscellaneous Mathematical Tools
Description: Some basic math calculators for finding angles for triangles and for finding the greatest common divisor of two numbers and so on.
Author: W.J. Braun [aut, cre]
Maintainer: W.J. Braun <john.braun@ubc.ca>
Diff between MiscMath versions 1.1 dated 2025-04-13 and 1.2 dated 2026-09-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/rAlias.R | 21 ++++++++++----------- 3 files changed, 15 insertions(+), 16 deletions(-)
Title: Generate Postestimation Quantities for Bayesian MCMC Estimation
Description: An implementation of functions to generate and plot postestimation quantities after estimating Bayesian regression models using Markov chain Monte Carlo (MCMC). Functionality includes the estimation of the Precision-Recall curves (see Beger, 2016 <doi:10.2139/ssrn.2765419>), the implementation of the observed values method of calculating predicted probabilities by Hanmer and Kalkan (2013) <doi:10.1111/j.1540-5907.2012.00602.x>, the implementation of the average value method of calculating predicted probabilities (see King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>), and the generation and plotting of first differences to summarize typical effects across covariates (see Long 1997, ISBN:9780803973749; King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>). This package can be used with MCMC output generated by any Bayesian estimation tool including 'JAGS', 'BUGS', 'MCMCpack', and 'Stan'.
Author: Johannes Karreth [aut] ,
Shana Scogin [aut, cre] ,
Rob Williams [aut] ,
Andreas Beger [aut] ,
Myunghee Lee [ctb],
Neil Williams [ctb]
Maintainer: Shana Scogin <shanarscogin@gmail.com>
Diff between BayesPostEst versions 0.4.0 dated 2025-08-18 and 0.4.1 dated 2026-09-26
DESCRIPTION | 17 MD5 | 20 NEWS.md | 9 build/partial.rdb |binary inst/doc/getting_started.html | 810 ++++++++++++++--------------- tests/testthat/setup-data/brms-logit.R | 28 - tests/testthat/setup-data/mcmcpack-logit.R | 47 - tests/testthat/setup-data/rstan-logit.R | 96 +-- tests/testthat/setup-data/rstanarm-logit.R | 45 - tests/testthat/setup.R | 83 ++ tests/testthat/test_mcmcRocPrc.R | 43 + 11 files changed, 664 insertions(+), 534 deletions(-)
Title: Regional Association Score for Genome-Wide Association Studies
Description: Implements the Regional Association Score (RAS) method for
genome-wide association studies (GWAS). For each single nucleotide
polymorphism (SNP), RAS quantifies the strength of association within its
surrounding genomic region, arranges these regional scores along the
chromosome into a signal profile, and locates association regions on that
profile with one of two detectors: the original changepoint detector, or a
box-scan region detector that also delimits broad plateau-shaped regions.
Genotypes can be streamed from a chunked on-disk format through compiled
code so that peak memory no longer grows with chromosome size, and the
regional weights can be taken from an independent external GWAS
(harmonised summary statistics) instead of a within-sample split. The
method is described in Jiang and Zhang (2025) <doi:10.1073/pnas.2419721122>.
Author: Jiahe Jin [aut],
Yiran Jiang [aut],
Heping Zhang [aut, cre]
Maintainer: Heping Zhang <heping.zhang@yale.edu>
Diff between RAS versions 1.0.3 dated 2026-07-24 and 1.1.2 dated 2026-09-26
RAS-1.0.3/RAS/R/screening.R |only RAS-1.0.3/RAS/tests/testthat/test-screening.R |only RAS-1.1.2/RAS/DESCRIPTION | 35 RAS-1.1.2/RAS/MD5 | 114 + RAS-1.1.2/RAS/NAMESPACE | 89 + RAS-1.1.2/RAS/NEWS.md | 115 + RAS-1.1.2/RAS/R/RAS-package.R | 154 +- RAS-1.1.2/RAS/R/aliases.R |only RAS-1.1.2/RAS/R/box_scan.R |only RAS-1.1.2/RAS/R/changepoint.R | 105 + RAS-1.1.2/RAS/R/detect.R |only RAS-1.1.2/RAS/R/detect_dispatch.R |only RAS-1.1.2/RAS/R/gwas.R | 406 ++----- RAS-1.1.2/RAS/R/gwas_original.R |only RAS-1.1.2/RAS/R/pipeline.R | 926 ++++++++-------- RAS-1.1.2/RAS/R/pipeline_original.R |only RAS-1.1.2/RAS/R/plink_fast.R |only RAS-1.1.2/RAS/R/plot.R | 105 + RAS-1.1.2/RAS/R/rasbin.R |only RAS-1.1.2/RAS/R/release_memory.R | 24 RAS-1.1.2/RAS/R/scan.R |only RAS-1.1.2/RAS/R/screening_original.R |only RAS-1.1.2/RAS/R/sumstats.R |only RAS-1.1.2/RAS/R/utils.R | 12 RAS-1.1.2/RAS/README.md | 237 ++-- RAS-1.1.2/RAS/inst/WORDLIST |only RAS-1.1.2/RAS/man/RAS-package.Rd | 160 +- RAS-1.1.2/RAS/man/bed_to_rasbin.Rd |only RAS-1.1.2/RAS/man/compute_gwas_weights.Rd | 119 -- RAS-1.1.2/RAS/man/compute_gwas_weights_original.Rd |only RAS-1.1.2/RAS/man/compute_pgs_matrix.Rd | 8 RAS-1.1.2/RAS/man/geno_to_rasbin.Rd |only RAS-1.1.2/RAS/man/get_break_points.Rd | 2 RAS-1.1.2/RAS/man/get_local_maximum.Rd | 2 RAS-1.1.2/RAS/man/plot.ras.Rd | 12 RAS-1.1.2/RAS/man/plot_ras_scan.Rd | 4 RAS-1.1.2/RAS/man/ras-aliases.Rd |only RAS-1.1.2/RAS/man/ras.Rd | 353 +++--- RAS-1.1.2/RAS/man/ras_box_calibrate.Rd |only RAS-1.1.2/RAS/man/ras_box_detect.Rd |only RAS-1.1.2/RAS/man/ras_box_stat.Rd |only RAS-1.1.2/RAS/man/ras_detect.Rd | 137 -- RAS-1.1.2/RAS/man/ras_detect_original.Rd |only RAS-1.1.2/RAS/man/ras_harmonize_sumstats.Rd |only RAS-1.1.2/RAS/man/ras_liftover_sumstats.Rd |only RAS-1.1.2/RAS/man/ras_map_ids_to_rsid.Rd |only RAS-1.1.2/RAS/man/ras_memory.Rd | 8 RAS-1.1.2/RAS/man/ras_original.Rd |only RAS-1.1.2/RAS/man/ras_read_variant_dictionary.Rd |only RAS-1.1.2/RAS/man/ras_scan.Rd | 243 +--- RAS-1.1.2/RAS/man/ras_scan_external.Rd |only RAS-1.1.2/RAS/man/ras_scan_external_original.Rd |only RAS-1.1.2/RAS/man/ras_scan_original.Rd |only RAS-1.1.2/RAS/man/ras_sumstats_report.Rd |only RAS-1.1.2/RAS/man/ras_validate.Rd | 23 RAS-1.1.2/RAS/man/ras_weights_from_sumstats.Rd |only RAS-1.1.2/RAS/man/rasbin_header.Rd |only RAS-1.1.2/RAS/man/rasbin_read_chunk.Rd |only RAS-1.1.2/RAS/man/release_memory.Rd | 17 RAS-1.1.2/RAS/man/screen_forward_max_region.Rd | 207 --- RAS-1.1.2/RAS/man/screen_forward_max_region_original.Rd |only RAS-1.1.2/RAS/man/slope_test.Rd | 4 RAS-1.1.2/RAS/src/brent.h |only RAS-1.1.2/RAS/src/detect_c.c |only RAS-1.1.2/RAS/src/geno_io.c |only RAS-1.1.2/RAS/src/gwas_c.c |only RAS-1.1.2/RAS/src/init.c | 42 RAS-1.1.2/RAS/src/linalg.h |only RAS-1.1.2/RAS/src/malloc_trim.c | 17 RAS-1.1.2/RAS/src/plink_io.c |only RAS-1.1.2/RAS/src/rasbin.h |only RAS-1.1.2/RAS/src/scan_c.c |only RAS-1.1.2/RAS/src/smalllinalg.h |only RAS-1.1.2/RAS/tests/testthat/test-box-scan.R |only RAS-1.1.2/RAS/tests/testthat/test-changepoint.R | 97 + RAS-1.1.2/RAS/tests/testthat/test-detect.R |only RAS-1.1.2/RAS/tests/testthat/test-gwas-original.R |only RAS-1.1.2/RAS/tests/testthat/test-gwas.R | 122 +- RAS-1.1.2/RAS/tests/testthat/test-pipeline.R |only RAS-1.1.2/RAS/tests/testthat/test-plink-fast.R |only RAS-1.1.2/RAS/tests/testthat/test-rasbin.R |only RAS-1.1.2/RAS/tests/testthat/test-release-memory.R | 24 RAS-1.1.2/RAS/tests/testthat/test-scan.R |only RAS-1.1.2/RAS/tests/testthat/test-screening-original.R |only 84 files changed, 2122 insertions(+), 1801 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock Assessment
Description: Provides tools for estimating length-based indicators (LBIs) from length-frequency data to assess fish stock status and evaluate growth and recruitment overfishing in data-limited fisheries. Implements the sustainability indicators of Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x>, empirical biological reference points from Froese and Binohlan (2000) <doi:10.1111/j.1095-8649.2000.tb00870.x>, and the decision framework of Cope and Punt (2009) <doi:10.1577/C08-025.1>. Incorporates a three-tier Monte Carlo and bootstrap uncertainty propagation framework for sustainability indicators, optimum bin size calculations following Wang et al. (2020) <doi:10.1016/j.fishres.2019.105474>, multi-month length-frequency harmonization, and length-weight relationship fitting. Methodology is detailed in Ali et al. (2025) <doi:10.1016/j.fishres.2025.107467>.
Author: Ataher Ali [aut, cre] ,
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.9 dated 2026-01-10 and 0.2.0 dated 2026-09-26
DESCRIPTION | 32 MD5 | 37 NAMESPACE | 25 R/FishPar.R | 1046 ++++++++++------- R/FishSS.R | 125 +- R/FreqTM.R | 290 ++-- R/FrequencyTable.R | 188 +-- R/LWR.R | 274 ++-- README.md | 194 ++- build/vignette.rds |binary inst/WORDLIST |only inst/doc/Introduction.R | 538 ++++++-- inst/doc/Introduction.Rmd | 1309 +++++++++++++++++---- inst/doc/Introduction.html | 2759 +++++++++++++++++++++++++++++++++------------ man/FishPar.Rd | 80 + man/FishSS.Rd | 43 man/FreqTM.Rd | 54 man/FrequencyTable.Rd | 51 man/LWR.Rd | 63 - vignettes/Introduction.Rmd | 1309 +++++++++++++++++---- 20 files changed, 6140 insertions(+), 2277 deletions(-)
Title: Penalized Principal Machine for Sufficient Dimension Reduction
Description: A unified, computation-friendly framework for penalized principal
machines (P2M), a class of sparse sufficient dimension reduction (SDR)
estimators for regression and binary classification. Principal machines
(PM) estimate the central subspace by solving a family of convex-loss
problems over several cutoffs; their penalized counterparts (P2M) add a
row-group sparsity penalty so that dimension reduction and variable
selection are performed simultaneously. All estimators are fitted by a
single group coordinate descent (GCD) algorithm that accommodates least
squares, logistic, asymmetric least squares, L2-hinge, hinge (support
vector machine, SVM) and quantile losses, together with the least absolute
shrinkage and selection operator (LASSO), the smoothly clipped absolute
deviation (SCAD) penalty and the minimax concave penalty (MCP). Methods are
described in Li, Artemiou and Li (2011) <doi:10.1214/11-AOS932>, Shin and
Artemiou (2017) <doi:10.1016/j.csda.2016.12.003>, Artemiou, [...truncated...]
Author: Jungmin Shin [aut, cre] ,
Seung Jun Shin [aut]
Maintainer: Jungmin Shin <c16267@gmail.com>
Diff between ppmSDR versions 2.0.0 dated 2026-06-19 and 3.0.1 dated 2026-09-26
ppmSDR-2.0.0/ppmSDR/inst/doc/ppmSDR.html |only ppmSDR-3.0.1/ppmSDR/DESCRIPTION | 8 ppmSDR-3.0.1/ppmSDR/MD5 | 38 ppmSDR-3.0.1/ppmSDR/NAMESPACE | 8 ppmSDR-3.0.1/ppmSDR/R/estimators.R | 912 ++++++++++++--------- ppmSDR-3.0.1/ppmSDR/R/methods.R | 39 ppmSDR-3.0.1/ppmSDR/R/ppm.R | 205 ++++ ppmSDR-3.0.1/ppmSDR/R/ppmSDR-package.R | 12 ppmSDR-3.0.1/ppmSDR/R/ppm_tune.R | 39 ppmSDR-3.0.1/ppmSDR/R/utils-internal.R | 134 +++ ppmSDR-3.0.1/ppmSDR/README.md | 77 + ppmSDR-3.0.1/ppmSDR/build/partial.rdb |binary ppmSDR-3.0.1/ppmSDR/build/vignette.rds |binary ppmSDR-3.0.1/ppmSDR/inst/doc/ppmSDR.R | 40 ppmSDR-3.0.1/ppmSDR/inst/doc/ppmSDR.Rmd | 124 ++ ppmSDR-3.0.1/ppmSDR/inst/doc/ppmSDR.pdf |only ppmSDR-3.0.1/ppmSDR/man/ppm.Rd | 131 ++- ppmSDR-3.0.1/ppmSDR/man/ppmSDR-package.Rd | 12 ppmSDR-3.0.1/ppmSDR/man/ppm_tune.Rd | 48 - ppmSDR-3.0.1/ppmSDR/vignettes/ppmSDR.Rmd | 124 ++ ppmSDR-3.0.1/ppmSDR/vignettes/ppmSDR.html |only ppmSDR-3.0.1/ppmSDR/vignettes/ppmSDR_vignette.diff |only 22 files changed, 1434 insertions(+), 517 deletions(-)
Title: Work with Microsoft Access Files
Description: Work with Microsoft Access '.mdb' and '.accdb' files using the
open source 'MDB Tools' library <https://github.com/mdbtools/mdbtools/>.
The library is compiled and bundled with the package, so no external
installation is required. Provides high-level helpers for reading tables,
exporting to CSV or JSON, inspecting table definitions, and running SQL queries.
Also exposes a full read-only 'DBI' interface for use with standard
database workflows.
Author: Kiernan Nicholls [aut, cre, cph] ,
Bruno Tremblay [ctb]
Maintainer: Kiernan Nicholls <k5cents@gmail.com>
Diff between mdbr versions 0.3.2 dated 2026-07-18 and 0.4.0 dated 2026-09-26
mdbr-0.3.2/mdbr/inst/extdata/nycflights13.mdb |only mdbr-0.3.2/mdbr/tests/testthat/mdbtestdata/data/nwind.mdb |only mdbr-0.4.0/mdbr/DESCRIPTION | 6 mdbr-0.4.0/mdbr/MD5 | 60 ++++--- mdbr-0.4.0/mdbr/NAMESPACE | 1 mdbr-0.4.0/mdbr/NEWS.md | 29 +++ mdbr-0.4.0/mdbr/R/dbi.R | 108 ++++++++++++-- mdbr-0.4.0/mdbr/R/example.R | 10 - mdbr-0.4.0/mdbr/R/export.R | 2 mdbr-0.4.0/mdbr/R/native.R | 34 ++-- mdbr-0.4.0/mdbr/R/read.R | 12 - mdbr-0.4.0/mdbr/R/stream.R |only mdbr-0.4.0/mdbr/README.md | 84 +++------- mdbr-0.4.0/mdbr/inst/extdata/nwind.mdb |only mdbr-0.4.0/mdbr/man/export_mdb.Rd | 2 mdbr-0.4.0/mdbr/man/mdb.Rd | 5 mdbr-0.4.0/mdbr/man/mdb_example.Rd | 10 - mdbr-0.4.0/mdbr/man/mdb_stream_table.Rd |only mdbr-0.4.0/mdbr/man/read_mdb.Rd | 6 mdbr-0.4.0/mdbr/src/Makevars.in | 2 mdbr-0.4.0/mdbr/src/Makevars.win | 2 mdbr-0.4.0/mdbr/src/init.c | 8 + mdbr-0.4.0/mdbr/src/mdb_cursor.c |only mdbr-0.4.0/mdbr/src/mdbtools/include/mdbtools.h | 1 mdbr-0.4.0/mdbr/src/mdbtools/src/libmdb/data.c | 1 mdbr-0.4.0/mdbr/tests/testthat/_snaps |only mdbr-0.4.0/mdbr/tests/testthat/decimal.accdb |only mdbr-0.4.0/mdbr/tests/testthat/decimal.mdb |only mdbr-0.4.0/mdbr/tests/testthat/test-dbi.R | 36 ++++ mdbr-0.4.0/mdbr/tests/testthat/test-examples.R | 5 mdbr-0.4.0/mdbr/tests/testthat/test-export.R | 8 - mdbr-0.4.0/mdbr/tests/testthat/test-native.R | 27 +-- mdbr-0.4.0/mdbr/tests/testthat/test-read.R | 20 +- mdbr-0.4.0/mdbr/tests/testthat/test-schema.R | 6 mdbr-0.4.0/mdbr/tests/testthat/test-stream.R |only mdbr-0.4.0/mdbr/tests/testthat/test-tables.R | 2 36 files changed, 310 insertions(+), 177 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The
'gurobi' package, which is not on CRAN, is optional and comes with
an installation of the Gurobi Optimizer, available at
<https://www.gurobi.com>.)
Author: Daniel Ho [aut] ,
Kosuke Imai [aut] ,
Gary King [aut] ,
Elizabeth Stuart [aut] ,
Alex Whitworth [ctb],
Noah Greifer [cre, aut]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.8.0 dated 2026-09-16 and 4.8.1 dated 2026-09-26
DESCRIPTION | 6 MD5 | 108 +++---- NEWS.md | 28 + R/RcppExports.R | 16 - R/aux_functions.R | 4 R/dist_functions.R | 7 R/get_weights_from_subclass.R | 25 - R/match.qoi.R | 95 +++--- R/matchit.R | 15 - R/matchit2cardinality.R | 38 ++ R/matchit2cem.R | 16 - R/matchit2full.R | 25 + R/matchit2genetic.R | 11 R/matchit2nearest.R | 170 ++++++----- R/matchit2optimal.R | 62 +++- R/matchit2quick.R | 21 + R/summary.matchit.R | 73 +++-- R/utils.R | 27 + build/stage23.rdb |binary inst/doc/MatchIt.Rmd | 23 - inst/doc/MatchIt.html | 93 +++--- inst/doc/assessing-balance.Rmd | 40 +- inst/doc/assessing-balance.html | 191 ++++++------- inst/doc/estimating-effects.Rmd | 24 - inst/doc/estimating-effects.html | 50 +-- inst/doc/matching-methods.Rmd | 42 +- inst/doc/matching-methods.html | 215 +++++++-------- inst/doc/sampling-weights.Rmd | 4 inst/doc/sampling-weights.html | 21 - man/method_cardinality.Rd | 10 src/RcppExports.cpp | 40 +- src/internal.cpp | 413 ++++++++++++++++++++++++++--- src/internal.h | 105 +++++++ src/nn_matchC_distmat.cpp | 68 ++++ src/nn_matchC_distmat_closest.cpp | 31 +- src/nn_matchC_mahcovs.cpp | 90 +++--- src/nn_matchC_mahcovs_closest.cpp | 67 +--- src/nn_matchC_vec.cpp | 23 + src/nn_matchC_vec_closest.cpp | 23 + src/pairdistC.cpp | 119 +++++++- tests/testthat/_snaps/method_quick.md | 4 tests/testthat/_snaps/nearest_snapshots.md | 218 +++++++++++++++ tests/testthat/test-method_cardinality.R | 59 +++- tests/testthat/test-method_cem.R | 20 + tests/testthat/test-method_full.R | 20 + tests/testthat/test-method_nearest.R | 194 +++++++++++++ tests/testthat/test-method_optimal.R | 42 ++ tests/testthat/test-method_quick.R | 6 tests/testthat/test-nearest_snapshots.R | 69 ++++ tests/testthat/test-summary.R | 174 ++++++++++++ vignettes/MatchIt.Rmd | 23 - vignettes/assessing-balance.Rmd | 40 +- vignettes/estimating-effects.Rmd | 24 - vignettes/matching-methods.Rmd | 42 +- vignettes/sampling-weights.Rmd | 4 55 files changed, 2455 insertions(+), 923 deletions(-)
Title: Core C++ Sampling Engine for 'glmbayes'
Description: Core C++ engine for 'glmbayes': envelope-based iid linear and
generalized linear model samplers, prior-family routing, and optional
'OpenCL' acceleration. Sampling for supported non-conjugate models uses
accept-reject methods based on likelihood subgradients as in Nygren and
Nygren (2006) <doi:10.1198/016214506000000357>. Intended as a developer
backend for the 'glmbayes' formula interface; end users should use
'glmbayes' for modelling with interfaces analogous to 'lm' and 'glm'.
Mixed-model engines are planned for a future release.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb] ,
The Khronos Group Inc [cph] )
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between glmbayesCore versions 0.5.3 dated 2026-08-05 and 0.5.4 dated 2026-09-26
glmbayesCore-0.5.3/glmbayesCore/src/glmbayes_getRegisteredNamespace.cpp |only glmbayesCore-0.5.3/glmbayesCore/src/glmbayes_getRegisteredNamespace.h |only glmbayesCore-0.5.3/glmbayesCore/tools |only glmbayesCore-0.5.4/glmbayesCore/DESCRIPTION | 8 glmbayesCore-0.5.4/glmbayesCore/MD5 | 26 +- glmbayesCore-0.5.4/glmbayesCore/NAMESPACE | 5 glmbayesCore-0.5.4/glmbayesCore/NEWS.md | 110 ++++++---- glmbayesCore-0.5.4/glmbayesCore/R/glmbayesCore-package.R | 4 glmbayesCore-0.5.4/glmbayesCore/R/residuals.rglmb.R | 18 + glmbayesCore-0.5.4/glmbayesCore/build/partial.rdb |binary glmbayesCore-0.5.4/glmbayesCore/configure | 92 +++++--- glmbayesCore-0.5.4/glmbayesCore/configure.win | 41 --- glmbayesCore-0.5.4/glmbayesCore/inst/WORDLIST | 13 + glmbayesCore-0.5.4/glmbayesCore/man/residuals.rglmb.Rd | 8 glmbayesCore-0.5.4/glmbayesCore/src/Makevars.win | 3 15 files changed, 192 insertions(+), 136 deletions(-)
Title: Develop Hybridization Probes
Description: Hybridization probes for target sequences can be made based on melting temperature value calculated by R package 'TmCalculator' <https://CRAN.R-project.org/package=TmCalculator> and methods extended from Beliveau, B. J.,(2018) <doi:10.1073/pnas.1714530115>, and those hybridization probes can be used to capture specific target regions in fluorescence in situ hybridization and next generation sequence experiments.
Author: Junhui Li [cre, aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ProbeDeveloper versions 1.1.2 dated 2026-06-13 and 1.1.3 dated 2026-09-26
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 2 +- R/ProbeMake.R | 17 ++++++++++------- 4 files changed, 20 insertions(+), 16 deletions(-)
More information about ProbeDeveloper at CRAN
Permanent link
Title: Managing and Visualizing Brain Surface Data
Description: Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <https://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Author: Tim Schaefer [aut, cre] ,
The General Hospital Corporation [cph] ,
Van Essen Lab [cph] ,
Alexander Schaefer [cph] ,
Ru Kong [cph] ,
Lingzhong Fan [cph] ,
Edmund T. Rolls [cph] ,
Matthew F. Glasser [cph] ,
Kathryn Mills [cph]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between fsbrain versions 0.8.0 dated 2026-09-14 and 1.0.0 dated 2026-09-26
DESCRIPTION | 13 MD5 | 264 ++++++++++----- NAMESPACE | 16 R/brainview_magick.R | 22 + R/cbar.R | 10 R/coloredmesh.R | 109 +++++- R/coloredpaths.R |only R/connectome.R |only R/helpers.R | 36 +- R/optdata.R | 42 ++ R/renderable_transform.R | 9 R/scimesh_bridge.R | 215 +++++++++++- R/sphere_cloud.R |only R/tracts.R |only R/tracts_data.R |only R/vis_mesh_atlas.R |only R/vis_meshes.R | 69 +++ R/vis_multiview.R | 10 R/vis_surface_background.R | 18 - R/vis_volume_3d.R | 208 ++++++++++- R/vis_volume_clusters.R |only R/vol2surf.R |only R/volume.R | 45 ++ R/volvis_shells.R |only build/partial.rdb |only inst/doc/fsbrain.R | 4 inst/doc/fsbrain.Rmd | 26 + inst/doc/fsbrain.html | 105 +++-- inst/doc/fsbrain_with_scimesh.R | 10 inst/doc/fsbrain_with_scimesh.Rmd | 18 + inst/doc/fsbrain_with_scimesh.html | 151 ++++---- inst/extdata/pkgfilecache_manifest_fs_LR_32_labels.csv |only inst/extdata/pkgfilecache_manifest_fsaverage_atlases.csv | 9 inst/extdata/pkgfilecache_manifest_xtract_tracts.csv |only man/FSBRAIN_SCIMESH_DEFAULT_AA.Rd |only man/Triangles3D.to.coloredmesh.Rd | 1 man/apply.affine.to.coords.Rd |only man/apply.transform.Rd | 23 + man/apply.transform.matrix.Rd |only man/apply.transform.to.tracts.Rd |only man/as.tract.bundle.list.Rd |only man/check.segment.points.Rd |only man/check.transform.matrix.Rd |only man/cluster.shell.alpha.Rd |only man/coloredmesh.from.annot.Rd | 1 man/coloredmesh.from.color.Rd | 22 + man/coloredmesh.from.label.Rd | 1 man/coloredmesh.from.mask.Rd | 1 man/coloredmesh.from.morph.native.Rd | 1 man/coloredmesh.from.morph.standard.Rd | 1 man/coloredmesh.from.morphdata.Rd | 1 man/coloredmesh.from.spheres.Rd |only man/coloredmeshes.from.color.Rd | 8 man/coloredpaths.length.Rd |only man/coloredpaths_to_scimesh.Rd |only man/combine_bboxes.Rd |only man/connectivity.matrix.from.edge.list.Rd |only man/context.mesh.resolve.subjects.dir.Rd |only man/download_fs_LR_32_atlases.Rd | 6 man/download_fs_LR_32_labels.Rd |only man/download_fs_LR_32_meshes.Rd | 6 man/download_fsaverage_atlases.Rd | 2 man/download_optional_data.Rd | 2 man/download_xtract_tracts.Rd |only man/find.subjectsdir.of.Rd | 4 man/fs.coloredpaths.Rd |only man/fsbrain.renderable.Rd | 2 man/get.fsbrain.scimesh.aa.samples.Rd |only man/get.rglstyle.Rd | 3 man/get.rglstyle.parameters.Rd | 2 man/group.start.rows.Rd |only man/highlight.vertices.on.subject.Rd | 2 man/highlight.vertices.on.subject.spheres.Rd | 2 man/index2ras_tkr.Rd |only man/is.fs.coloredpaths.Rd |only man/list.tract.bundle.files.Rd |only man/match.bundle.values.Rd |only man/mesh.atlas.all.regions.hidden.Rd |only man/mesh.atlas.check.files.Rd |only man/mesh.atlas.context.layer.Rd |only man/mesh.atlas.file.paths.Rd |only man/mesh.atlas.hide.nan.vertices.Rd |only man/mesh.atlas.resolve.subjects.dir.Rd |only man/mesh.atlas.restrict.faces.Rd |only man/mesh.weld.Rd |only man/normalize.region.names.Rd |only man/print.fs.coloredpaths.Rd |only man/ras2vox_tkr.Rd | 1 man/read.tract.bundles.Rd |only man/renderables_to_line_layers.Rd |only man/resolve.template.subjects.dir.Rd |only man/segment.orientation.colors.Rd |only man/segment_bbox.Rd |only man/shell.backend.Rd |only man/shell.coloredmeshes.Rd |only man/shell.cut.away.Rd |only man/shell.extract.mesh.Rd |only man/shell.levels.Rd |only man/shell.palette.Rd |only man/shell.volume.data.Rd |only man/spheres.mesh.Rd |only man/streamlines.to.segments.Rd |only man/streamlines.to.tracts.Rd |only man/subdivide.triangles.Rd |only man/subject.dir.has.core.files.Rd |only man/subject.region.centroids.Rd |only man/subject.vol2surf.Rd |only man/surface.interpolate.frac.Rd |only man/template.vol2surf.Rd |only man/tract.bundle.name.from.file.Rd |only man/translation.matrix.Rd |only man/unit.icosphere.Rd |only man/values.to.colorlayer.Rd |only man/values.to.range.Rd |only man/view_angle_to_scimesh_camera.Rd | 7 man/vis.color.on.subject.Rd | 2 man/vis.coloredmeshes.Rd | 2 man/vis.coloredpaths.Rd |only man/vis.connectome.Rd |only man/vis.data.on.fsaverage.Rd | 2 man/vis.data.on.subject.Rd | 2 man/vis.labeldata.on.subject.Rd | 2 man/vis.mask.on.subject.Rd | 2 man/vis.region.values.on.subject.Rd | 3 man/vis.renderable.Rd | 2 man/vis.rglwidget.Rd | 2 man/vis.subcortical.region.values.Rd |only man/vis.subject.annot.Rd | 5 man/vis.subject.label.Rd | 2 man/vis.subject.morph.native.Rd | 2 man/vis.subject.morph.standard.Rd | 2 man/vis.subject.pre.Rd | 2 man/vis.symmetric.data.on.subject.Rd | 2 man/vis.tracts.Rd |only man/vis.volume.clusters.Rd |only man/vis.volume.on.surface.Rd | 5 man/vislayout.from.coloredmeshes.Rd | 2 man/vol.apply.cortex.mask.Rd |only man/vol.check.interpolation.Rd |only man/vol.check.surface.frac.Rd |only man/vol.find.file.Rd |only man/vol.frac.vertices.Rd |only man/vol.load.Rd |only man/vol.read.file.with.affine.Rd |only man/vol.sample.at.coords.Rd |only man/vol.sample.nearest.Rd |only man/vol.sample.trilinear.Rd |only man/vol.select.frame.Rd |only man/vol.tkreg.affine.Rd |only man/vol.vol2surf.hemilist.Rd |only man/vol.warn.outside.Rd |only man/volume.boxblur.Rd |only man/volume.boxblur.axis.Rd |only man/volume.cluster.extremes.Rd |only man/volume.cluster.levels.Rd |only man/volume.cluster.threshold.Rd |only man/volume.clusters.colormap.Rd |only man/volume.subsample.Rd |only man/volume.subsample.matrix.Rd |only man/volvis.lb.Rd | 1 man/volvis.lb.with.surface.Rd | 1 man/volvis.lightbox.Rd | 1 man/volvis.shells.Rd |only man/volvis.slices.with.surface.Rd | 1 man/volvis.voxels.Rd | 2 man/vox2ras_tkr.Rd | 1 tests/testthat/fsbrain_issue50_export.png |binary tests/testthat/setup-cran.R |only tests/testthat/teardown-cran.R | 35 + tests/testthat/test-cbar.R | 16 tests/testthat/test-coloredpaths.R |only tests/testthat/test-connectome.R |only tests/testthat/test-scimesh_bridge.R | 134 +++++++ tests/testthat/test-tracts.R |only tests/testthat/test-u_find_subjectsdir.R |only tests/testthat/test-u_vis_volume_3d.R | 203 +++++++++++ tests/testthat/test-u_vis_volume_clusters.R |only tests/testthat/test-u_volvis_shells.R |only tests/testthat/test-vis-volume-on-surface.R | 1 tests/testthat/test-vis_mesh_atlas.R |only tests/testthat/test-vol2surf.R |only tests/testthat/test-volume.R | 7 tests/testthat/test-w_vis_group.R | 1 tests/testthat/test-x_vis_meshes.R | 28 + tests/testthat/test-z_vis_surface_background.R | 24 + vignettes/fsbrain.Rmd | 26 + vignettes/fsbrain_with_scimesh.Rmd | 18 + 187 files changed, 1742 insertions(+), 307 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.7 dated 2026-06-25 and 0.2.8 dated 2026-09-26
DESCRIPTION | 8 - MD5 | 122 ++++++++++++++++------------ NAMESPACE | 13 +++ NEWS.md | 9 ++ R/ipcw.R | 19 +++- R/ipe.R | 18 +++- R/msm.R | 21 +++- R/plot.ipcw.R | 4 R/plot.ipe.R | 174 +++++++++++++++++++++++++++------------- R/plot.msm.R | 4 R/plot.rpsftm.R | 93 ++++++++++++++++++--- R/plot.tsegest.R | 72 ++++++++++++++-- R/plot.tsesimp.R | 91 ++++++++++++++++++--- R/print.ipcw.R | 6 + R/print.ipe.R | 6 + R/print.liferegr.R | 1 R/print.msm.R | 6 + R/print.phregr.R | 1 R/print.rpsftm.R | 6 + R/print.tsegest.R | 6 + R/print.tsesimp.R | 6 + R/rpsftm.R | 18 +++- R/summary.ipcw.R |only R/summary.ipe.R |only R/summary.msm.R |only R/summary.rpsftm.R |only R/summary.tsegest.R |only R/summary.tsesimp.R |only R/trtswitch-package.R | 2 R/tsegest.R | 21 ++++ R/tsesimp.R | 31 ++++++- R/utilities.R | 23 +++++ build/vignette.rds |binary inst/doc/tsegest.html | 2 man/figures/logo.svg | 18 ++-- man/ipcw.Rd | 12 ++ man/ipe.Rd | 9 +- man/msm.Rd | 12 ++ man/plot.ipcw.Rd | 4 man/plot.ipe.Rd | 7 + man/plot.msm.Rd | 4 man/plot.rpsftm.Rd | 10 +- man/plot.tsegest.Rd | 5 - man/plot.tsesimp.Rd | 8 + man/print.summary.ipcw.Rd |only man/print.summary.ipe.Rd |only man/print.summary.msm.Rd |only man/print.summary.rpsftm.Rd |only man/print.summary.tsegest.Rd |only man/print.summary.tsesimp.Rd |only man/rpsftm.Rd | 9 +- man/summary.ipcw.Rd |only man/summary.ipe.Rd |only man/summary.msm.Rd |only man/summary.rpsftm.Rd |only man/summary.tsegest.Rd |only man/summary.tsesimp.Rd |only man/tsegest.Rd | 12 ++ man/tsesimp.Rd | 18 +++- src/ipcw.cpp | 79 ++++++++++++++++++ src/msm.cpp | 81 ++++++++++++++++++- src/survival_analysis.cpp | 117 +++++++++++++++++++++++---- src/tsegest.cpp | 54 ++++++++++++ src/tsesimp.cpp | 116 +++++++++++++++++++++++++++ tests/testthat/test-ipcw.R | 155 +++++++++++++++++++++++++++++++++++- tests/testthat/test-ipe.R | 132 ++++++++++++++++++++++++++++++ tests/testthat/test-kmest.R | 12 ++ tests/testthat/test-msm.R | 136 +++++++++++++++++++++++++++++++ tests/testthat/test-rpsftm.R | 179 ++++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-tsegest.R | 148 ++++++++++++++++++++++++++++++++++ tests/testthat/test-tsesimp.R | 138 ++++++++++++++++++++++++++++++++ 71 files changed, 2027 insertions(+), 231 deletions(-)
Title: 3D Prioritization Algorithm
Description: Three-dimensional systematic conservation planning, conducting
nested prioritization analyses across multiple depth levels and
ensuring efficient resource allocation throughout the water column.
It provides a structured workflow designed to address biodiversity
conservation and management challenges in the 3 dimensions, while
facilitating users’ choices and parameterization (Doxa et al. 2025
<doi:10.1016/j.ecolmodel.2024.110919>).
Author: Aggeliki Doxa [aut] ,
Christos Adam [aut, cre] ,
Nikolaos Nagkoulis [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between prior3D versions 0.1.5 dated 2025-01-25 and 0.1.6 dated 2026-09-26
DESCRIPTION | 22 MD5 | 70 NAMESPACE | 32 NEWS.md | 7 R/rfunctions.R | 2 README.md | 17 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 20 inst/doc/Introduction.Rmd | 13 inst/doc/Introduction.html | 15 inst/test_datasets/biodiv_df.csv | 4142 ++++++++++++++++---------------- man/Compare_2D_3D.Rd | 566 ++-- man/biodiv_df.Rd | 50 man/coherence.Rd | 200 - man/evaluate_3D.Rd | 158 - man/get_biodiv_raster.Rd | 62 man/get_depth_raster.Rd | 60 man/get_rast.Rd | 56 man/plot_3D.Rd | 188 - man/plot_Compare_2D_3D.Rd | 158 - man/plot_sumrast.Rd | 88 man/prioritize_3D.Rd | 486 +-- man/split_rast.Rd | 172 - man/sumrast.Rd | 72 man/terra_jaccard.Rd | 74 tests/testthat/test-biodiv_df.r | 26 tests/testthat/test-get_biodiv_raster.r | 12 tests/testthat/test-get_depth_raster.r | 4 tests/testthat/test-get_rast.r | 14 tests/testthat/test-plot_sumrast.r | 42 tests/testthat/test-prioritize_3D.r | 14 tests/testthat/test-split_rast.r | 474 +-- tests/testthat/test-sumrast.r | 24 tests/testthat/test-terra_jaccard.r | 14 vignettes/Introduction.Rmd | 13 36 files changed, 3702 insertions(+), 3665 deletions(-)
Title: Visualize Simon's Two-Stage Design
Description: To visualize the probabilities of early termination, fail and success of Simon's two-stage design. To evaluate and visualize the operating characteristics of Simon's two-stage design.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between VisualizeSimon2Stage versions 0.2.2 dated 2025-04-27 and 0.2.3 dated 2026-09-26
DESCRIPTION | 28 +- MD5 | 30 +-- NAMESPACE | 64 ++++-- R/0PACKAGE.R | 5 R/Sprintf.R | 17 + R/autoplot.R | 1 R/bibs.R |only R/power.R |only R/r_simon.R | 2 R/show.R | 3 build/vignette.rds |binary inst/doc/intro.R | 115 ++++++----- inst/doc/intro.html | 360 ++++++++++++++++++++++++------------ inst/doc/intro.qmd | 147 ++++++++------ man/VisualizeSimon2Stage-package.Rd | 16 + man/power_ph2simon.Rd |only man/simon_bib.Rd |only vignettes/intro.qmd | 147 ++++++++------ 18 files changed, 588 insertions(+), 347 deletions(-)
More information about VisualizeSimon2Stage at CRAN
Permanent link
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Jakub Grzywaczewski [aut, cre],
Tymoteusz Kwiecinski [aut] ,
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Jakub Grzywaczewski <jakubzgrzywaczewski@gmail.com>
Diff between SerolyzeR versions 1.4.1 dated 2026-02-20 and 1.5.0 dated 2026-09-26
DESCRIPTION | 14 - MD5 | 44 ++- NAMESPACE | 18 + R/helpers.R | 2 R/parser.R | 5 R/plots-levey_jennings.R | 6 R/process-dir.R | 55 +++- R/run_gui.R |only build/partial.rdb |binary build/vignette.rds |binary inst/app |only inst/doc/example_script.html | 68 +++--- inst/img/EU.jpg |binary man/Model.Rd | 217 +++++++++---------- man/Plate.Rd | 352 +++++++++++++++---------------- man/PlateBuilder.Rd | 420 +++++++++++++++++++------------------- man/detect_mba_format.Rd | 9 man/plot_levey_jennings.Rd | 6 man/process_dir.Rd | 4 man/read_luminex_data.Rd | 6 man/run_gui.Rd |only tests/testthat/normalised_data |only tests/testthat/test-process-dir.R | 8 23 files changed, 652 insertions(+), 582 deletions(-)
Title: Graph Community Detection Methods into Systematic Conservation
Planning
Description: An innovative tool-set that incorporates graph community detection
methods into systematic conservation planning. It is designed to
enhance spatial prioritization by focusing on the protection of
areas with high ecological connectivity. Unlike traditional
approaches that prioritize individual planning units, 'priorCON'
focuses on clusters of features that exhibit strong ecological
linkages. The 'priorCON' package is built upon the 'prioritizr'
package <doi:10.32614/CRAN.package.prioritizr>, using commercial
and open-source exact algorithm solvers that ensure optimal
solutions to prioritization problems.
Author: Christos Adam [aut, cre] ,
Aggeliki Doxa [aut] ,
Nikolaos Nagkoulis [aut] ,
Maria Papazekou [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between priorCON versions 0.1.7 dated 2025-11-03 and 0.1.8 dated 2026-09-26
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 2 +- NEWS.md | 9 +++++++++ R/functions_connect.R | 4 ++-- README.md | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 18 +++++++++--------- inst/doc/Introduction.html | 18 +++++++++--------- man/basic_scenario.Rd | 2 +- man/connectivity_scenario.Rd | 2 +- man/get_metrics.Rd | 4 ++-- man/get_outputs.Rd | 2 -- man/preprocess_graphs.Rd | 8 -------- vignettes/Introduction.Rmd | 18 +++++++++--------- 16 files changed, 72 insertions(+), 73 deletions(-)
More information about drisdiagnostics at CRAN
Permanent link
Title: Download, Clean, Classify, Enrich and Export Biodiversity
Occurrence Data
Description: Downloads, imports, cleans, classifies, enriches and exports biodiversity
occurrence data, with an emphasis on reproducible Global Biodiversity
Information Facility (GBIF) <https://api.gbif.org/v1/> workflows. The package
supports batch occurrence downloads, taxonomic standardisation, coordinate
cleaning, optional spatial thinning, spatial attribution and structured
export of processed occurrence records and audit outputs. Terrestrial and
freshwater workflows can join records to administrative units, protected
areas, freshwater ecoregions, basins, rivers, lakes, reservoirs, wetlands and
other contextual spatial overlays. Marine workflows support offshore and
coastal records through joins to Marine Regions
<https://www.marineregions.org/> style layers, Exclusive Economic Zone (EEZ)
units, marine ecoregions, Large Marine Ecosystems and user-supplied marine
overlays. The package also supports native-range and invasive-status evidence
workflows using the World Register of Marin [...truncated...]
Author: Darren Stuart [aut, cre]
Maintainer: Darren Stuart <dstuart04@qub.ac.uk>
Diff between biofetchR versions 0.1.1 dated 2026-08-19 and 0.1.2 dated 2026-09-26
DESCRIPTION | 10 MD5 | 172 NAMESPACE | 26 NEWS.md |only R/marine_pipeline.R | 4264 ++++++------- R/terrestrial_freshwater_pipeline.R | 6231 ++++++++++---------- R/utils_core_helpers.R | 2 R/utils_download_helpers.R | 49 R/utils_encoding.R | 4 R/utils_native_range_sinas.R | 2003 +++--- R/utils_native_range_web_sources.R | 2417 +++---- R/utils_pipeline_origin_gates.R | 4 R/utils_raster_context_layers.R | 790 +- R/utils_sinas_download.R | 594 + build/vignette.rds |binary inst/doc/biofetchR-auditing-and-scaling.html | 65 inst/doc/biofetchR-batch-pipelines.html | 2 inst/doc/biofetchR-origin-evidence.html | 2 man/append_summary_row.Rd | 6 man/bf_attach_griis_status.Rd | 16 man/bf_attach_native_status.Rd | 14 man/bf_available_marine_overlays.Rd | 6 man/bf_available_native_web_sources.Rd | 21 man/bf_download_griis.Rd | 16 man/bf_download_sinas_resources.Rd | 106 man/bf_enrich_raster_context.Rd | 4 man/bf_enrich_raster_context_from_sources.Rd | 4 man/bf_fetch_native_ranges_sinas.Rd | 51 man/bf_fetch_native_ranges_web.Rd | 65 man/bf_filter_griis_invasive.Rd | 16 man/bf_filter_native.Rd | 14 man/bf_filter_non_native.Rd | 14 man/bf_find_griis_table.Rd | 16 man/bf_griis_lookup.Rd | 16 man/bf_load_basins.Rd | 10 man/bf_load_biosphere_reserve.Rd | 6 man/bf_load_feow.Rd | 10 man/bf_load_gdw_barriers.Rd | 6 man/bf_load_gdw_reservoirs.Rd | 6 man/bf_load_global_mining.Rd | 6 man/bf_load_gloric.Rd | 6 man/bf_load_hydrowaste.Rd | 6 man/bf_load_lakes.Rd | 10 man/bf_load_marine_regions_overlay.Rd | 6 man/bf_load_ne_admin1.Rd | 6 man/bf_load_ne_urban.Rd | 6 man/bf_load_ne_urban_areas.Rd | 10 man/bf_load_ramsar.Rd | 4 man/bf_load_resolve2017.Rd | 6 man/bf_load_resolve_ecoregions2017.Rd | 10 man/bf_load_rivers.Rd | 10 man/bf_load_teow.Rd | 10 man/bf_load_wdpa.Rd | 4 man/bf_marine_overlay_canonical.Rd | 6 man/bf_name_rivers_osm.Rd | 10 man/bf_native_range_lookup.Rd | 14 man/bf_native_status_summary.Rd | 14 man/bf_read_griis.Rd | 16 man/bf_reconcile_griis_native_status.Rd | 14 man/bf_sinas_default_urls.Rd | 31 man/bf_standardise_griis.Rd | 16 man/bf_standardise_native_ranges.Rd | 14 man/bf_teow_cache_info.Rd | 10 man/bf_teow_clear_cache.Rd | 10 man/bf_unpack_griis.Rd | 16 man/bf_web_native_gbif.Rd | 44 man/bf_web_native_worms.Rd | 43 man/bf_write_native_web_outputs.Rd | 57 man/biofetchR-package.Rd | 5 man/check_gbif_presence.Rd | 6 man/download_gbif_batch.Rd | 6 man/download_gbif_batch_gadm.Rd | 8 man/eez_join.Rd | 4 man/filter_by_status.Rd | 4 man/gadm_join.Rd | 6 man/get_taxon_key.Rd | 6 man/initialize_summary.Rd | 4 man/list_status_presets.Rd | 4 man/load_all_gadm.Rd | 6 man/load_gadm.Rd | 6 man/overlay_join.Rd | 4 man/process_gbif_eez_pipeline.Rd | 4 man/process_gbif_marine_pipeline.Rd | 8 man/process_gbif_terrestrial_freshwater_pipeline.Rd | 4 man/wait_and_import_gbif.Rd | 6 man/wait_and_import_gbif_safe.Rd | 6 tests/testthat/test-curl-path.R |only tests/testthat/test-sinas-3-2.R |only tests/testthat/test-strict-overlay-loading.R |only 89 files changed, 8890 insertions(+), 8680 deletions(-)
Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep (CTS, for one or
several conditions), Outcome Threshold Sweep (OTS), and Dual Threshold
Sweep (DTS) for systematic exploration of threshold calibration effects on
crisp-set QCA results. These methods extend traditional robustness
approaches by treating threshold variation as an explicit analytical
dimension and recording the sufficiency solution obtained at each
threshold setting. Also provides Fiss (2011)
<doi:10.5465/amj.2011.60263120> core/peripheral condition classification
via compute_fiss_core() and generate_fiss_chart(), enabling four-symbol
configuration charts that distinguish core conditions (conditions of the
parsimonious term contained in each configuration) from peripheral
conditions (intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.7 dated 2026-09-24 and 2.0.8 dated 2026-09-26
ThSQCA-2.0.7/ThSQCA/man/build_parsim_status_map.Rd |only ThSQCA-2.0.7/ThSQCA/man/classify_term_conditions.Rd |only ThSQCA-2.0.7/ThSQCA/man/extract_cond_status_map.Rd |only ThSQCA-2.0.8/ThSQCA/DESCRIPTION | 14 ThSQCA-2.0.8/ThSQCA/MD5 | 47 - ThSQCA-2.0.8/ThSQCA/NEWS.md | 76 ++ ThSQCA-2.0.8/ThSQCA/R/tsqca_config_chart.R | 25 ThSQCA-2.0.8/ThSQCA/R/tsqca_fiss_core.R | 513 +++++++++----- ThSQCA-2.0.8/ThSQCA/R/tsqca_report.R | 18 ThSQCA-2.0.8/ThSQCA/README.md | 7 ThSQCA-2.0.8/ThSQCA/inst/doc/ThSQCA_Reproducible_EN.Rmd | 25 ThSQCA-2.0.8/ThSQCA/inst/doc/ThSQCA_Reproducible_EN.html | 31 ThSQCA-2.0.8/ThSQCA/inst/doc/ThSQCA_Tutorial_EN.R | 4 ThSQCA-2.0.8/ThSQCA/inst/doc/ThSQCA_Tutorial_EN.Rmd | 56 + ThSQCA-2.0.8/ThSQCA/inst/doc/ThSQCA_Tutorial_EN.html | 72 + ThSQCA-2.0.8/ThSQCA/man/ThSQCA-package.Rd | 2 ThSQCA-2.0.8/ThSQCA/man/classify_term_fiss.Rd |only ThSQCA-2.0.8/ThSQCA/man/compute_fiss_core.Rd | 102 ++ ThSQCA-2.0.8/ThSQCA/man/fiss_threshold_label.Rd |only ThSQCA-2.0.8/ThSQCA/man/format_models_expr.Rd |only ThSQCA-2.0.8/ThSQCA/man/generate_fiss_chart.Rd | 6 ThSQCA-2.0.8/ThSQCA/man/generate_report.Rd | 4 ThSQCA-2.0.8/ThSQCA/man/model_key.Rd |only ThSQCA-2.0.8/ThSQCA/man/nested_core_conditions.Rd |only ThSQCA-2.0.8/ThSQCA/man/term_status.Rd |only ThSQCA-2.0.8/ThSQCA/man/trace_intermediate_sources.Rd |only ThSQCA-2.0.8/ThSQCA/tests/testthat/test-fiss-derivation.R |only ThSQCA-2.0.8/ThSQCA/tests/testthat/test-fiss-polarity.R | 57 - ThSQCA-2.0.8/ThSQCA/vignettes/ThSQCA_Reproducible_EN.Rmd | 25 ThSQCA-2.0.8/ThSQCA/vignettes/ThSQCA_Tutorial_EN.Rmd | 56 + 30 files changed, 833 insertions(+), 307 deletions(-)
Title: Manage 'RStudio' Preferences and Addin Shortcuts
Description: Provides an interface for working with 'RStudio' preference files
to modify settings and addin shortcuts without using point-and-click option
menus. Useful for ensuring a unified experience across devices and for
enforcing best practices. Also exposes some settings not available in the
Global Options dialog.
Author: S.A. van der Wulp [aut, cre, cph],
Daniel D. Sjoberg [aut, cph]
Maintainer: S.A. van der Wulp <vdwulp@gmail.com>
Diff between rstudio.prefs versions 0.2.0 dated 2026-08-20 and 0.3.0 dated 2026-09-26
rstudio.prefs-0.2.0/rstudio.prefs/R/fetch_rstudio_prefs.R |only rstudio.prefs-0.2.0/rstudio.prefs/R/pretty.R |only rstudio.prefs-0.2.0/rstudio.prefs/tests/testthat/test-check_prefs_consistency.R |only rstudio.prefs-0.2.0/rstudio.prefs/tests/testthat/test-fetch_rstudio_settings_table.R |only rstudio.prefs-0.2.0/rstudio.prefs/tests/testthat/test-invert_list_names_and_values.R |only rstudio.prefs-0.2.0/rstudio.prefs/tests/testthat/test-repo_string_as_named_list.R |only rstudio.prefs-0.2.0/rstudio.prefs/tests/testthat/test-write_json.R |only rstudio.prefs-0.3.0/rstudio.prefs/DESCRIPTION | 8 rstudio.prefs-0.3.0/rstudio.prefs/MD5 | 51 rstudio.prefs-0.3.0/rstudio.prefs/NEWS.md | 280 +-- rstudio.prefs-0.3.0/rstudio.prefs/R/pretty_print_updates.R |only rstudio.prefs-0.3.0/rstudio.prefs/R/sysdata.rda |binary rstudio.prefs-0.3.0/rstudio.prefs/R/use_rstudio_keyboard_shortcut.R | 270 +- rstudio.prefs-0.3.0/rstudio.prefs/R/use_rstudio_prefs.R | 322 ++- rstudio.prefs-0.3.0/rstudio.prefs/R/use_rstudio_secondary_repo.R | 266 +- rstudio.prefs-0.3.0/rstudio.prefs/R/utils.R | 364 +-- rstudio.prefs-0.3.0/rstudio.prefs/README.md | 44 rstudio.prefs-0.3.0/rstudio.prefs/inst/WORDLIST | 30 rstudio.prefs-0.3.0/rstudio.prefs/man/check_min_rstudio_version.Rd | 51 rstudio.prefs-0.3.0/rstudio.prefs/man/fetch_rstudio_prefs.Rd | 52 rstudio.prefs-0.3.0/rstudio.prefs/man/figures |only rstudio.prefs-0.3.0/rstudio.prefs/man/repo_string_as_named_list.Rd | 9 rstudio.prefs-0.3.0/rstudio.prefs/man/rstudio.prefs-package.Rd | 2 rstudio.prefs-0.3.0/rstudio.prefs/man/use_rstudio_keyboard_shortcut.Rd | 4 rstudio.prefs-0.3.0/rstudio.prefs/man/use_rstudio_prefs.Rd | 93 - rstudio.prefs-0.3.0/rstudio.prefs/man/use_rstudio_secondary_repo.Rd | 27 rstudio.prefs-0.3.0/rstudio.prefs/tests/spelling.R | 6 rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-add_ins.R |only rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-pretty_print_updates.R | 193 ++ rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-use_rstudio_keyboard_shortcut.R | 913 +++++----- rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-use_rstudio_prefs.R |only rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-use_rstudio_secondary_repo.R |only rstudio.prefs-0.3.0/rstudio.prefs/tests/testthat/test-utils.R |only 33 files changed, 1718 insertions(+), 1267 deletions(-)
Title: Testing Workbench for Precision-Recall Curves
Description: A testing workbench to evaluate tools that calculate precision-recall curves.
Saito and Rehmsmeier (2015) <doi:10.1371/journal.pone.0118432>.
Author: Takaya Saito [aut, cre] ,
Marc Rehmsmeier [aut] ,
The scikit-learn developers [cph] ; see inst/COPYRIGHTS)
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between prcbench versions 1.1.10 dated 2025-05-14 and 1.1.16 dated 2026-09-26
DESCRIPTION | 26 +- MD5 | 70 +++---- NAMESPACE | 16 + NEWS.md | 62 ++++++ R/data_interface.R | 10 - R/main_benchmark.R | 11 + R/main_evalcurves.R | 2 R/prcbench.R | 19 + R/tool_interface.R | 87 ++++++-- R/tool_rlib.R | 39 +++ R/tool_sklearn.R |only R/tool_zzz.R | 159 ++++++++++++++++ README.md | 106 +++++++--- build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/introduction.R | 52 +++-- inst/doc/introduction.Rmd | 113 ++++++++--- inst/doc/introduction.html | 335 ++++++++++++++++++++++------------ inst/python |only man/TestDataB.Rd | 200 +++++++++++--------- man/TestDataC.Rd | 310 ++++++++++++++++--------------- man/ToolAUCCalculator.Rd | 178 +++++++++--------- man/ToolIFBase.Rd | 277 +++++++++++++++------------- man/ToolPRROC.Rd | 178 +++++++++--------- man/ToolPerfMeas.Rd | 62 +++--- man/ToolROCR.Rd | 62 +++--- man/Toolprecrec.Rd | 120 ++++++------ man/Toolsklearn.Rd |only man/Toolyardstick.Rd |only man/create_testset.Rd | 10 - man/create_toolset.Rd | 49 +++- man/prcbench.Rd | 25 ++ man/run_benchmark.Rd | 11 + tests/testthat/Rplots.pdf |only tests/testthat/setup.R | 9 tests/testthat/test_main_evalcurves.R | 48 ++-- tests/testthat/test_tool_sklearn.R |only tests/testthat/test_tool_tools.R | 164 ++++++++++++++-- tests/testthat/test_tool_yardstick.R |only vignettes/introduction.Rmd | 113 ++++++++--- 40 files changed, 1899 insertions(+), 1024 deletions(-)
Title: Tools for Graphical Inference
Description: Tools for visual inference. Generate null data sets
and null plots using permutation and simulation. Calculate distance metrics
for a lineup, and examine the distributions of metrics.
Author: Hadley Wickham [aut, ctb] ,
Niladri Roy Chowdhury [aut, ctb],
Di Cook [aut, cre] ,
Heike Hofmann [aut, ctb] ,
Mans Thulin [aut, ctb]
Maintainer: Di Cook <dicook@monash.edu>
Diff between nullabor versions 0.3.15 dated 2025-02-10 and 0.3.16 dated 2026-09-26
DESCRIPTION | 20 ++++---- MD5 | 30 ++++++------ NAMESPACE | 2 NEWS.md | 5 ++ R/distances.r | 16 +++--- R/opt_diff.r | 68 +++++++++++++++++----------- R/protocols.r | 13 +++-- build/vignette.rds |binary inst/doc/distances.html | 83 +++++++++++++++++------------------ inst/doc/nullabor-distributions.html | 74 +++++++++++++++++-------------- inst/doc/nullabor-examples.html | 23 +++++---- inst/doc/nullabor-regression.html | 15 +++--- inst/doc/nullabor.html | 83 ++++++++++++++++++----------------- man/bin_dist.Rd | 2 man/calc_diff.Rd | 25 +++++----- man/calc_mean_dist.Rd | 13 ++--- 16 files changed, 258 insertions(+), 214 deletions(-)
Title: Bayesian Federated Inference
Description: The Bayesian Federated Inference ('BFI') method combines inference results obtained from local data sets in the separate centers. In this version of the package, the 'BFI' methodology is programmed for linear, logistic and survival regression models. For GLMs, see Jonker, Pazira and Coolen (2024) <doi:10.1002/sim.10072>; for survival models, see Pazira, Massa, Weijers, Coolen and Jonker (2026) <doi:10.1080/02664763.2025.2511932>; and for heterogeneous populations, see Jonker, Pazira and Coolen (2025) <doi:10.1017/rsm.2025.6>.
Author: Hassan Pazira [aut, cre] ,
Emanuele Massa [aut] ,
Marianne A. Jonker [aut]
Maintainer: Hassan Pazira <h.pazira@arq.org>
Diff between BFI versions 3.1.0 dated 2025-05-24 and 3.2.0 dated 2026-09-26
DESCRIPTION | 17 LICENSE | 4 MD5 | 72 - NAMESPACE | 75 - NEWS.md | 139 +- R/A.l.maker.R | 570 ++++---- R/BFI.R | 1600 ++++++++++++----------- R/coef.bfi.R |only R/print.bfi.R |only R/summary.bfi.R | 283 ++-- R/vcov.bfi.R |only README.md | 432 +++--- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 26 inst/doc/BFI.R | 246 +-- inst/doc/BFI.Rmd | 453 +++--- inst/doc/BFI.html | 827 ++++++------ inst/doc/Python.R | 232 +-- inst/doc/Python.Rmd | 1228 +++++++++--------- inst/doc/Python.html | 1316 +++++++++---------- inst/doc/SAS.R | 12 inst/doc/SAS.Rmd | 674 +++++----- inst/doc/SAS.html | 878 ++++++------- man/BFI-internal.Rd | 68 - man/BFI-package.Rd | 72 - man/BFI.Rd | 1614 ++++++++++++------------ man/MAP.estimation.Rd | 710 +++++----- man/b.diag.Rd | 102 - man/bfi-methods.Rd |only man/hazards.fun.Rd | 268 ++- man/inv.prior.cov.Rd | 353 ++--- man/n.par.Rd | 136 +- man/summary.bfi.Rd | 249 +-- man/surv.simulate.Rd | 323 ++-- tests/testthat/test-A-l-maker-prior-curvature.R |only tests/testthat/test-A-l-maker.R |only tests/testthat/test-poly-parameter-order.R |only vignettes/BFI.Rmd | 453 +++--- vignettes/Python.Rmd | 1228 +++++++++--------- vignettes/SAS.Rmd | 674 +++++----- 41 files changed, 7793 insertions(+), 7541 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration
tests for binary logistic regression, runnable in a single call via
'run.all.gof()'. Around twenty-five tests spanning five decades of
literature are aggregated and grouped by the departure each is built to
detect: global and standardized statistics, partition tests such as
Hosmer-Lemeshow, directed and covariate-space tests, smoothing and
resampling tests, and calibration tests. Each is obtained from its own
package where installed and attributed to its authors. The package also
implements the author's own procedures for sparse data, where the
Hosmer-Lemeshow test loses power: the omnibus Ebrahim-Farrington test
'ef.gof()', the directed 'edge.gof()' and its covariate-space variant
'cdef.gof()', the Cauchy-combination ensemble 'edges.gof()', 'DeepGOF-1'
(a pretrained convolutional statistic whose level comes from the analyst's
own parametric bootstrap rather than from the network), and 'legoft()'
(a frozen-weight combination [...truncated...]
Author: Ebrahim Khaled Ebrahim [aut, cre] ,
Jiawei Zhang [ctb, cph] ,
Jie Ding [ctb, cph] ,
Yuhong Yang [ctb, cph]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.7.0 dated 2026-09-09 and 2.8.0 dated 2026-09-26
DESCRIPTION | 34 MD5 | 110 +- NAMESPACE | 105 +- NEWS.md | 1305 ++++++++++++++++++--------------- R/bagoft_fast.R |only R/calm_gof.R | 764 +++++++++---------- R/cdef_gof.R | 456 +++++------ R/data.R | 180 ++-- R/deepgof.R | 440 +++++------ R/def_ensemble_gof.R | 342 ++++---- R/def_gof.R | 517 ++++++++----- R/ebrahim.gof-package.R | 176 ++-- R/ebrahim_farrington_test.R | 680 ++++++++--------- R/edge_gof.R | 117 +- R/install_suggests.R | 246 +++--- R/legoft.R | 494 ++++++------ R/proj_gof.R |only R/run_all_gof.R | 334 ++++++-- R/shrink_gof.R | 432 +++++----- R/zzz.R | 50 - README.md | 1087 +++++++++++++-------------- inst/CITATION | 88 +- inst/WORDLIST | 136 +-- inst/doc/ebrahim-farrington-intro.Rmd | 630 +++++++-------- inst/doc/ebrahim-farrington-intro.html | 29 inst/doc/ebrahim-gof-toolbox.Rmd | 366 ++++----- inst/doc/ebrahim-gof-toolbox.html | 58 - man/bagoft.fast.Rd |only man/calm.gof.Rd | 270 +++--- man/cdef.gof.Rd | 166 ++-- man/deepgof1.Rd | 170 ++-- man/def.ensemble.gof.Rd | 17 man/def.gof.Rd | 70 + man/deploy.gof.Rd | 82 +- man/ebrahim.gof-package.Rd | 215 ++--- man/edge.gof.Rd | 186 ++-- man/edges.gof.Rd | 96 +- man/gof.features.Rd | 72 - man/gof_demo.Rd | 102 +- man/gof_demo_grouped.Rd | 128 +-- man/gof_install_suggests.Rd | 101 +- man/legoft.Rd | 106 +- man/legoft.localize.Rd | 112 +- man/plot.gof_battery.Rd | 42 - man/print.gof_battery.Rd | 46 - man/projection.gof.Rd |only man/run.all.gof.Rd | 121 ++- man/shrink.gof.Rd | 204 ++--- tests/testthat/test-bagoft-fast.R |only tests/testthat/test-deepgof1.R | 136 ++- tests/testthat/test-def-ensemble-gof.R | 12 tests/testthat/test-def-gof.R | 198 ++++- tests/testthat/test-exports-smoke.R | 250 +++--- tests/testthat/test-lecessie-algebra.R | 202 ++--- tests/testthat/test-parallel.R | 106 +- tests/testthat/test-proj-gof.R |only tests/testthat/test-run-all-gof.R | 501 ++++++++---- vignettes/ebrahim-farrington-intro.Rmd | 630 +++++++-------- vignettes/ebrahim-gof-toolbox.Rmd | 366 ++++----- 59 files changed, 7490 insertions(+), 6393 deletions(-)
Title: Complex Partial Least Squares Structural Equation Modeling
Description: Estimate complex Structural Equation Models (SEMs) by fitting Partial
Least Squares Structural Equation Modeling (PLS-SEM) and Partial Least
Squares consistent Structural Equation Modeling (PLSc-SEM) specifications
that handle categorical data, non-linear relations, and multilevel
structures. The implementation follows Lohmöller (1989) for the classic PLS-SEM
algorithm, Dijkstra and Henseler (2015) for consistent PLSc-SEM, Dijkstra et al.,
(2014) for nonlinear PLSc-SEM, and Schuberth, Henseler, Dijkstra (2018)
for ordinal PLS-SEM and PLSc-SEM. Additional extensions are under development.
The MC-OrdPLSc algorithm, used to handle ordinal interaction models is detailed
in Slupphaug et al., (2026).
References:
Lohmöller, J.-B. (1989, ISBN:9783790803002).
"Latent Variable Path Modeling with Partial Least Squares."
Dijkstra, T. K., & Henseler, J. (2015).
<doi:10.1016/j.jmva.2015.06.002>.
"Consistent partial least squares path modeling."
Dijkstra, T. K., & Schermelleh-Engel, K. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between plssem versions 0.1.4 dated 2026-08-24 and 0.1.5 dated 2026-09-26
DESCRIPTION | 14 - MD5 | 48 ++- NAMESPACE | 12 R/RcppExports.R |only R/bootstrap.R | 87 ------ R/ho_helpers.R | 3 R/mcpls.R | 536 +++++++++++++++++++++++++++++------------ R/mcpls_robbins_monro.R | 122 +++++++-- R/model_accessors.R | 19 + R/model_generics.R | 9 R/model_specification.R | 137 +++++++--- R/model_state.R | 51 ++- R/parallel.R |only R/pls.R | 116 ++++++-- R/pls_fit.R | 196 ++++++++++++-- R/pls_steps.R | 218 +++------------- R/plssem-package.R |only R/simulate_data.R | 211 +++++++++++++--- R/utils_matrices.R | 5 build/partial.rdb |only man/pls.Rd | 37 ++ man/plssem-package.Rd |only man/summary-PlsModel-method.Rd | 6 src |only tests/testthat/test_oneint.R | 2 tests/testthat/test_tpb.R | 2 26 files changed, 1208 insertions(+), 623 deletions(-)
Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment and forecasting of weekly data.
The package provides a user-friendly interface for computing seasonally
adjusted estimates and forecasts of weekly time series and includes
functions for the construction of country-specific prior adjustment
variables, as well as diagnostic tools to assess the quality of the
adjustments. The methodology is described in more detail in
Ginker (2024) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph] ,
Jon Lachman [ctb]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between boiwsa versions 1.1.4 dated 2025-12-14 and 1.1.5 dated 2026-09-26
DESCRIPTION | 10 - MD5 | 27 +- NAMESPACE | 2 NEWS.md | 4 R/generic_functions.R | 151 ++++++++++++++++ README.md | 68 +++++-- man/figures/README-gasoline-patterns-original-1.png |only man/figures/README-unemployment-patterns-original-1.png |only man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-3-1.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-8-1.png |binary man/plot_weekly_patterns.Rd |only 16 files changed, 229 insertions(+), 33 deletions(-)
Title: Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson [...truncated...]
Author: Jeffrey Doser [aut, cre],
Hunter Stanke [aut],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between rFIA versions 1.1.4 dated 2026-06-26 and 1.2.0 dated 2026-09-26
DESCRIPTION | 9 - MD5 | 118 +++++++-------- NEWS.md | 366 +++++++++++++++++++++++++++++++++++++++++++++++++ R/area.R | 5 R/areaChange.R | 5 R/areaChangeStarter.R | 15 +- R/areaStarter.R | 24 ++- R/biomass.R | 19 -- R/biomassStarter.R | 106 ++++++++------ R/carbon.R | 5 R/carbonStarter.R | 9 + R/customPSE.R | 23 ++- R/diversity.R | 29 ++- R/diversityStarter.R | 109 +++++++++----- R/dwm.R | 4 R/dwmStarter.R | 79 +++++++++- R/fsi.R | 65 ++++---- R/fsiHelper.R | 13 + R/fsiStarter.R | 5 R/globalVars.R | 6 R/growMort.R | 7 R/growMortStarter.R | 216 +++++++++++++++++++++------- R/invasive.R | 4 R/invasiveStarter.R | 83 +++++++---- R/plotFIA.R | 8 - R/seedling.R | 5 R/seedlingStarter.R | 53 ++++--- R/standStruct.R | 5 R/standStructStarter.R | 25 +++ R/sysdata.rda |binary R/tpa.R | 5 R/tpaStarter.R | 21 +- R/util.R | 297 ++++++++++++++++++++++----------------- R/vegStruct.R | 4 R/vegStructStarter.R | 50 +++++- R/vitalRates.R | 5 R/vitalRatesStarter.R | 145 +++++++++++++++---- R/volume.R | 5 R/volumeStarter.R | 69 +++++++-- R/writeFIA.R | 18 ++ README.md | 105 +++++++------- inst/extdata/qrLM.jag | 2 inst/extdata/qrLMM.jag | 2 man/area.Rd | 18 ++ man/areaChange.Rd | 18 ++ man/biomass.Rd | 57 ++++--- man/carbon.Rd | 18 ++ man/customPSE.Rd | 4 man/diversity.Rd | 22 ++ man/dwm.Rd | 2 man/fsi.Rd | 22 ++ man/growMort.Rd | 19 ++ man/intersectFIA.Rd | 2 man/invasive.Rd | 3 man/seedling.Rd | 23 ++- man/standStruct.Rd | 24 ++- man/tpa.Rd | 20 ++ man/vegStruct.Rd | 25 ++- man/vitalRates.Rd | 18 ++ man/volume.Rd | 18 ++ 60 files changed, 1796 insertions(+), 665 deletions(-)
Title: Fast C++ Primitives for the 'NeuroAnatomy Toolbox'
Description: Fast functions implemented in C++ via 'Rcpp' to support the
'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large
speed-ups for basic manipulation of neuronal skeletons over pure R
functions found in the 'nat' package. The expectation is that end
users will not use this package directly, but instead the 'nat'
package will automatically use routines from this package when it is
available to enable large performance gains.
Author: Gregory Jefferis [aut, cre] ,
libigl contributors [ctb, cph] ; see src/vendor/README.md)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between natcpp versions 0.3.1 dated 2026-07-20 and 0.3.2 dated 2026-09-26
DESCRIPTION | 27 +++++++++++-------- MD5 | 40 +++++++++++++++++++++------- NAMESPACE | 1 NEWS.md | 27 +++++++++++++++++++ R/RcppExports.R | 30 ++++++--------------- R/inside_mesh.R |only R/utils.R |only R/weighted_jaccard.R | 49 ++++++++++++++++++++++++++++++++--- man/c_pointsinside.Rd |only man/c_weighted_jaccard_dense.Rd | 31 +++++++++++++++++----- man/c_weighted_jaccard_sparse.Rd | 8 +++-- man/natcpp-package.Rd | 5 +++ src/RcppExports.cpp | 34 +++++++++++++++++++++++- src/fast_inside_mesh.cpp |only src/inside_mesh.cpp |only src/vendor |only src/weighted_jaccard.cpp | 25 ++--------------- tests/testthat/test-inside-mesh.R |only tests/testthat/test-utils.R |only tests/testthat/testdata/ca1_mesh.rds |only 20 files changed, 200 insertions(+), 77 deletions(-)
Title: Neutrosophic Analysis of Incomplete Block Designs
Description: Provides methods for neutrosophic analysis of variance
(NANOVA) and neutrosophic analysis of covariance (NANCOVA)
for interval-valued data arising from incomplete block design
experiments. The package supports balanced incomplete block
designs (BIBDs), partially balanced incomplete block designs
(PBIBDs), and lattice designs. Functions are included for
treatment comparisons, least significant difference (LSD)
tests, and interval-based statistical inference under
neutrosophic environments.
Author: Neethu R.S. [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Vinaykumar L.N. [aut, cre]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between NeutroIBDAnalysis versions 0.1.1 dated 2026-06-05 and 0.1.2 dated 2026-09-26
DESCRIPTION | 8 - MD5 | 18 ++-- R/IBDnsANCOVA.R | 55 ++++++------ R/IBDnsANOVA.R | 61 +++++++++---- R/LDnsANCOVA.R | 234 ++++++++++++++++++++++------------------------------- R/LDnsANOVA.R | 54 +++++++----- man/IBDnsANCOVA.Rd | 21 ++-- man/IBDnsANOVA.Rd | 7 - man/LDnsANCOVA.Rd | 14 +-- man/LDnsANOVA.Rd | 7 - 10 files changed, 233 insertions(+), 246 deletions(-)
More information about NeutroIBDAnalysis at CRAN
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