Title: Comprehensive Unit Root and Stationarity Tests
Description: A unified framework for unit root and stationarity testing
including quantile ADF tests (Koenker and Xiao, 2004)
<doi:10.1198/016214504000001114>, GARCH-based unit root tests with
endogenous structural breaks (Narayan and Liu, 2015)
<doi:10.1016/j.eneco.2014.11.021>, and comprehensive Dickey-Fuller,
Phillips-Perron, KPSS, ERS/DF-GLS, Zivot-Andrews, and
Kobayashi-McAleer tests with an Elder-Kennedy decision strategy
(Elder and Kennedy, 2001) <doi:10.1080/00220480109595179>.
Author: Muhammad Abdullah Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between unitrootests versions 1.0.0 dated 2026-03-27 and 1.1.0 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 55 +++++++++++++++++++++++++++---------------------------- R/garchur_main.R | 1 + R/qadf_main.R | 48 +++++++----------------------------------------- R/qadf_methods.R | 6 +----- R/urstat_main.R | 4 ++++ 7 files changed, 50 insertions(+), 84 deletions(-)
Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] ,
Chris Wallace [aut] ,
Olly Burren [ctb]
Maintainer: Guillermo Reales <grealesm@gmail.com>
This is a re-admission after prior archival of version 2.3.1 dated 2025-02-19
Diff between RapidoPGS versions 2.3.1 dated 2025-02-19 and 2.3.2 dated 2026-04-02
DESCRIPTION | 21 MD5 | 64 - NAMESPACE | 56 NEWS.md | 219 ++- R/data.R | 152 +- R/globals.R | 2 R/rapfunc.R | 1798 ++++++++++++++++---------------- README.md | 142 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 inst/doc/Computing_RapidoPGSmulti.R | 60 - inst/doc/Computing_RapidoPGSmulti.Rmd | 708 ++++++------ inst/doc/Computing_RapidoPGSmulti.html | 1476 +++++++++++++------------- inst/doc/Computing_RapidoPGSsingle.R | 102 - inst/doc/Computing_RapidoPGSsingle.Rmd | 356 +++--- inst/doc/Computing_RapidoPGSsingle.html | 1251 +++++++++++----------- man/EUR_ld.blocks19.Rd | 52 man/EUR_ld.blocks38.Rd | 54 man/create_1000G.Rd | 98 - man/find_file_in_ftp.Rd | 52 man/gwascat.download.Rd | 60 - man/logsum.Rd | 42 man/michailidou19.Rd | 64 - man/michailidou38.Rd | 64 - man/rapidopgs_multi.Rd | 248 ++-- man/rapidopgs_single.Rd | 214 +-- man/sd.prior.est.Rd | 84 - man/sdY.est.Rd | 60 - man/wakefield_pp.Rd | 60 - man/wakefield_pp_quant.Rd | 68 - vignettes/Computing_RapidoPGSmulti.Rmd | 708 ++++++------ vignettes/Computing_RapidoPGSsingle.Rmd | 356 +++--- 33 files changed, 4369 insertions(+), 4360 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation (Rue et al., 2009)
<doi:10.1111/j.1467-9868.2008.00700.x> as described in Jamil and Rue
(2026a) <doi:10.48550/arXiv.2603.25690>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax. See also the companion paper on implementation and
workflows, Jamil and Rue (2026b) <doi:10.48550/arXiv.2604.00671>.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.3 dated 2026-01-28 and 0.2.4 dated 2026-04-02
INLAvaan-0.2.3/INLAvaan/R/zzz_OLD_log-likelihood-and-grad.R |only INLAvaan-0.2.3/INLAvaan/R/zzz_OLD_log-prior-and-grad.R |only INLAvaan-0.2.3/INLAvaan/inst/examples/heywood.R |only INLAvaan-0.2.3/INLAvaan/man/fitMeasures.Rd |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-ecmerkle.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-mismatch.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-variance_estimation.R |only INLAvaan-0.2.3/INLAvaan/vignettes/glycemic-table.png |only INLAvaan-0.2.4/INLAvaan/DESCRIPTION | 23 INLAvaan-0.2.4/INLAvaan/MD5 | 189 - INLAvaan-0.2.4/INLAvaan/NAMESPACE | 59 INLAvaan-0.2.4/INLAvaan/NEWS.md | 35 INLAvaan-0.2.4/INLAvaan/R/INLAvaan-class.R | 26 INLAvaan-0.2.4/INLAvaan/R/INLAvaan-package.R | 48 INLAvaan-0.2.4/INLAvaan/R/compare.R | 217 + INLAvaan-0.2.4/INLAvaan/R/create_lav_from_inlavaan_internal.R | 5 INLAvaan-0.2.4/INLAvaan/R/globals.R |only INLAvaan-0.2.4/INLAvaan/R/inlavaan.R | 481 +-- INLAvaan-0.2.4/INLAvaan/R/lavaan-unexported.R | 12 INLAvaan-0.2.4/INLAvaan/R/log-likelihood-and-grad.R | 8 INLAvaan-0.2.4/INLAvaan/R/log-prior-and-grad.R | 98 INLAvaan-0.2.4/INLAvaan/R/method-diagnostics.R |only INLAvaan-0.2.4/INLAvaan/R/method-fitmeasures.R | 502 +++ INLAvaan-0.2.4/INLAvaan/R/method-others.R |only INLAvaan-0.2.4/INLAvaan/R/method-plot.R | 271 + INLAvaan-0.2.4/INLAvaan/R/method-predict.R | 1224 +++++++- INLAvaan-0.2.4/INLAvaan/R/method-sampling.R |only INLAvaan-0.2.4/INLAvaan/R/method-show.R | 2 INLAvaan-0.2.4/INLAvaan/R/method-simulate.R |only INLAvaan-0.2.4/INLAvaan/R/method-summary.R | 77 INLAvaan-0.2.4/INLAvaan/R/method-timing.R |only INLAvaan-0.2.4/INLAvaan/R/method-vcov.R | 50 INLAvaan-0.2.4/INLAvaan/R/norta.R |only INLAvaan-0.2.4/INLAvaan/R/pars_to_x.R | 4 INLAvaan-0.2.4/INLAvaan/R/partable.R | 4 INLAvaan-0.2.4/INLAvaan/R/posterior-marginals.R | 64 INLAvaan-0.2.4/INLAvaan/R/posterior-sampling.R | 408 +- INLAvaan-0.2.4/INLAvaan/R/priors_for.R |only INLAvaan-0.2.4/INLAvaan/R/qsnorm_fast.R | 114 INLAvaan-0.2.4/INLAvaan/R/rgeneric.R | 8 INLAvaan-0.2.4/INLAvaan/R/skew-normal.R | 19 INLAvaan-0.2.4/INLAvaan/R/sobol.R |only INLAvaan-0.2.4/INLAvaan/R/standardisedsolution.R | 16 INLAvaan-0.2.4/INLAvaan/R/sysdata.rda |only INLAvaan-0.2.4/INLAvaan/R/utils-compare_mcmc.R | 623 +++- INLAvaan-0.2.4/INLAvaan/R/utils-inlavaan.R |only INLAvaan-0.2.4/INLAvaan/R/utils-optim.R |only INLAvaan-0.2.4/INLAvaan/R/utils-visual_debug.R | 213 + INLAvaan-0.2.4/INLAvaan/R/utils.R | 175 - INLAvaan-0.2.4/INLAvaan/R/zzz.R | 26 INLAvaan-0.2.4/INLAvaan/README.md | 180 - INLAvaan-0.2.4/INLAvaan/demo |only INLAvaan-0.2.4/INLAvaan/inst/CITATION |only INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.R | 21 INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.html | 369 +- INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.qmd | 56 INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.R | 2 INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.html | 1470 +++++++--- INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.qmd | 2 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-model_comparison.R | 8 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-sampling.R |only INLAvaan-0.2.4/INLAvaan/inst/examples/ex-simulate.R |only INLAvaan-0.2.4/INLAvaan/inst/examples/ex-skewnorm-fit.R | 49 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-stdsoln.R | 12 INLAvaan-0.2.4/INLAvaan/inst/validation-tests |only INLAvaan-0.2.4/INLAvaan/man/INLAvaan-class.Rd | 69 INLAvaan-0.2.4/INLAvaan/man/INLAvaan-package.Rd | 14 INLAvaan-0.2.4/INLAvaan/man/acfa.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/agrowth.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/asem.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/bfit_indices.Rd |only INLAvaan-0.2.4/INLAvaan/man/compare.Rd | 57 INLAvaan-0.2.4/INLAvaan/man/diagnostics.Rd |only INLAvaan-0.2.4/INLAvaan/man/figures/README-fig-compare-poldem-1.png |binary INLAvaan-0.2.4/INLAvaan/man/fit_skew_normal.Rd | 49 INLAvaan-0.2.4/INLAvaan/man/fitmeasures.Rd |only INLAvaan-0.2.4/INLAvaan/man/get_inlavaan_internal.Rd |only INLAvaan-0.2.4/INLAvaan/man/inlavaan.Rd | 64 INLAvaan-0.2.4/INLAvaan/man/plot.Rd |only INLAvaan-0.2.4/INLAvaan/man/predict.Rd |only INLAvaan-0.2.4/INLAvaan/man/priors_for.Rd |only INLAvaan-0.2.4/INLAvaan/man/qsnorm_fast.Rd | 7 INLAvaan-0.2.4/INLAvaan/man/sampling.Rd |only INLAvaan-0.2.4/INLAvaan/man/simulate.Rd |only INLAvaan-0.2.4/INLAvaan/man/standardisedsolution.Rd | 15 INLAvaan-0.2.4/INLAvaan/man/timing.Rd |only INLAvaan-0.2.4/INLAvaan/man/vcov.Rd |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-binary.R | 25 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-cfa.R | 24 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-compare.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-diagnostics.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-equality_constraints.R | 48 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-fast_jacobian.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-fitmeasures.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-growth.R | 74 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-loglik.R | 2 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-multilevel.R | 117 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-mvn_loglik.R | 2 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-norta.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-plot.R | 42 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-predict.R | 121 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-priors.R | 108 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-priors_for.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-qsnorm_fast.R | 26 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sampling.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sem.R | 65 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-simulate.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sobol.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-standardised_solution.R | 29 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-utils.R | 37 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-vcov.R |only INLAvaan-0.2.4/INLAvaan/vignettes/INLAvaan.qmd | 56 INLAvaan-0.2.4/INLAvaan/vignettes/mediation.qmd | 2 INLAvaan-0.2.4/INLAvaan/vignettes/refs.bib | 42 114 files changed, 6133 insertions(+), 2342 deletions(-)
Title: Bayesian Quantile Regression Models for Complex Survey Data
Analysis
Description: Provides Bayesian quantile regression models for complex survey data
under informative sampling using survey-weighted estimators. Both single- and
multiple-output models are supported. To accelerate computation, all algorithms
are implemented in 'C++' using 'Rcpp', 'RcppArmadillo', and 'RcppEigen', and
are called from 'R'. See Nascimento and Gonçalves (2024) <doi:10.1093/jssam/smae015>
and Nascimento and Gonçalves (2025, in press) <https://academic.oup.com/jssam>.
Author: Tomas Rodriguez Taborda [aut, cre],
Johnatan Cardona Jimenez [aut],
Marcus L. Nascimento [aut],
Kelly Cristina Mota Goncalves [aut]
Maintainer: Tomas Rodriguez Taborda <torodriguezt@unal.edu.co>
Diff between bayesQRsurvey versions 0.2.0 dated 2026-03-27 and 0.2.1 dated 2026-04-02
DESCRIPTION | 8 +- MD5 | 19 +++--- NEWS.md | 25 ++++++++- R/bqr.svy.R | 2 R/mo.bqr.svy.R | 2 R/plot_quantile.R | 150 ++++++++++++++++++++++++++++++++---------------------- build |only data/Anthro.rda |binary man/Anthro.Rd | 2 man/bqr.svy.Rd | 2 man/mo.bqr.svy.Rd | 2 11 files changed, 133 insertions(+), 79 deletions(-)
Title: 'LiDAR' Terrain Analysis and Change Detection from Above
Description: Terrain change detection, cut and fill volume estimation,
terrain profiling, flood inundation analysis, slope and aspect
computation, hillshade generation, contour extraction, reclamation
monitoring, erosion analysis, and engineering export (LandXML, STL)
from 'LiDAR' (Light Detection and Ranging) point clouds and digital
elevation models ('DEMs'). Applications include surface mine
reclamation monitoring, sediment pond capacity tracking, highwall
safety classification, and erosion channel detection. Built on 'lidR'
for point cloud I/O and 'terra' for raster operations. Includes
access utilities for 'KyFromAbove' cloud-native elevation data on
Amazon Web Services ('AWS') <https://kyfromabove.ky.gov/>. Methods
for terrain change detection and volume estimation follow Li and
others (2005) <doi:10.1016/j.geomorph.2004.10.007>.
Author: Chris Lyons [aut, cre]
Maintainer: Chris Lyons <chris.lyons@ky.gov>
Diff between aboveR versions 0.1.0 dated 2026-03-19 and 1.0.0 dated 2026-04-02
DESCRIPTION | 32 - MD5 | 75 ++- NAMESPACE | 79 ++- NEWS.md |only R/export.R |only R/flood.R |only R/highwall.R | 228 +++++++--- R/kfa_counties.R |only R/kfa_read.R | 374 ++++++++--------- R/kfa_stac.R | 72 ++- R/kfa_tiles.R | 260 +++++------ R/security.R |only R/terrain.R |only R/utils.R | 346 +++++++-------- R/visualize.R | 90 ++-- README.md | 197 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/getting-started.R | 114 ++--- inst/doc/getting-started.html | 890 ++++++++++++++++++++--------------------- man/aboveR-package.Rd | 50 +- man/bench_detection.Rd |only man/change_colors.Rd |only man/contour_lines.Rd |only man/export_landxml.Rd |only man/export_stl.Rd |only man/flood_colors.Rd |only man/flood_depth.Rd |only man/flood_inundation.Rd |only man/has_s3_access.Rd | 40 - man/height_above_drainage.Rd |only man/hillshade.Rd |only man/kfa_county_bbox.Rd |only man/kfa_find_tiles.Rd | 94 ++-- man/kfa_list_counties.Rd |only man/kfa_read_dem.Rd | 70 +-- man/kfa_read_ortho.Rd | 64 +- man/kfa_read_pointcloud.Rd | 60 +- man/kfa_stac_search.Rd | 62 +- man/kfa_tile_index.Rd | 58 +- man/slope_aspect.Rd |only man/terrain_colors.Rd |only man/zonal_stats.Rd |only tests/testthat/test-counties.R |only tests/testthat/test-export.R |only tests/testthat/test-exports.R | 75 ++- tests/testthat/test-flood.R |only tests/testthat/test-highwall.R | 69 +-- tests/testthat/test-kfa.R | 2 tests/testthat/test-security.R |only tests/testthat/test-terrain.R |only 52 files changed, 1823 insertions(+), 1578 deletions(-)
Title: Using Relative Abundance Data to Estimate of Multiplicative
Differences in Mean Absolute Abundance
Description: A differential abundance method for the analysis of microbiome data. 'radEmu' estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) <doi:10.1093/biomet/asag009>.
Author: David Clausen [aut],
Amy D Willis [aut, cre] ,
Sarah Teichman [aut]
Maintainer: Amy D Willis <adwillis@uw.edu>
Diff between radEmu versions 2.3.1.0 dated 2026-03-26 and 2.3.2.0 dated 2026-04-02
DESCRIPTION | 6 - MD5 | 30 +++--- README.md | 8 + inst/doc/intro_radEmu.html | 4 inst/doc/intro_radEmu_with_phyloseq.html | 4 inst/doc/intro_radEmu_with_tse.html | 4 inst/doc/parallel_radEmu.html | 4 inst/doc/quick_start.html | 4 inst/doc/radEmu_clustered_data.html | 4 inst/doc/radEmu_with_reference_taxon.html | 4 tests/testthat/test-X_cup_from_X.R | 3 tests/testthat/test-emuFit_micro.R | 123 +------------------------- tests/testthat/test-emuFit_micro_penalized.R | 3 tests/testthat/test-fit_null_discrete.R | 2 tests/testthat/test-get_G_for_augmentations.R | 2 tests/testthat/test-macro_fisher_null.R | 97 -------------------- 16 files changed, 52 insertions(+), 250 deletions(-)
Title: Standardization-Based Effect Estimation with Optional Prior
Covariance Adjustment
Description: The Prognostic Regression Offsets with Propagation of
ERrors (for Treatment Effect Estimation) package facilitates
direct adjustment for experiments and observational studies that
is compatible with a range of study designs and covariance
adjustment strategies. It uses explicit specification of clusters,
blocks and treatment allocations to furnish probability of
assignment-based weights targeting any of several average
treatment effect parameters, and for standard error calculations
reflecting these design parameters. For covariance adjustment of
its Hajek and (one-way) fixed effects estimates, it enables
offsetting the outcome against predictions from a dedicated
covariance model, with standard error calculations propagating
error as appropriate from the covariance model.
Author: Josh Errickson [cre, aut],
Josh Wasserman [aut],
Mark Fredrickson [ctb],
Adam Sales [ctb],
Xinhe Wang [ctb],
Ben Hansen [aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between propertee versions 1.0.4 dated 2026-01-23 and 1.0.5 dated 2026-04-02
DESCRIPTION | 6 MD5 | 34 ++-- NEWS.md | 9 + R/SandwichLayerVariance.R | 136 +++++++++------- R/teeMod.R | 230 ++++++++++++++++------------ R/weights_internal.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/RDD.html | 4 inst/doc/intro-to-propertee.html | 4 inst/doc/non-binary-treatment.html | 4 man/bread.teeMod.Rd | 4 man/dot-align_and_extend_estfuns.Rd | 15 + man/dot-check_df_moderator_estimates.Rd | 1 man/estfun.teeMod.Rd | 10 - man/sandwich_elements_calc.Rd | 6 tests/testthat/test.SandwichLayerVariance.R | 62 ++++++- tests/testthat/test.teeMod.R | 192 +++++++++++++++++++++-- 18 files changed, 511 insertions(+), 209 deletions(-)
Title: Adaptive Sample Size Simulator
Description: A simulations-first sample size determination package that aims at making sample size formulae obsolete for most easily computable statistical experiments ; the main envisioned use case is clinical trials. The proposed clinical trial must be written by the user in the form of a function that takes as argument a sample size and returns a boolean (for whether or not the trial is a success). The 'adsasi' functions will then use it to find the correct sample size empirically. The unavoidable mis-specification is obviated by trying sample size values close to the right value, the latter being understood as the value that gives the probability of success the user wants (usually 80 or 90% in biostatistics, corresponding to 20 or 10% type II error).
Author: Skerdi Haviari [aut, cre]
Maintainer: Skerdi Haviari <skerdi.haviari@aphp.fr>
Diff between adsasi versions 0.9.0.1 dated 2026-02-01 and 0.9.0.2 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/adsasi_0d.r | 24 ++++++++++++------------ R/adsasi_1d.r | 52 ++++++++++++++++++++++++++-------------------------- man/adsasi_0d.Rd | 2 +- man/adsasi_1d.Rd | 4 ++-- 6 files changed, 49 insertions(+), 49 deletions(-)
Title: Stationary Subspace Analysis
Description: Stationary subspace analysis (SSA) is a blind source separation (BSS) variant where stationary components are separated from non-stationary components. Several SSA methods for multivariate time series are provided here (Flumian et al. (2024) <doi:10.1016/j.cam.2023.115379>; Hara et al. (2010) <doi:10.1007/978-3-642-17537-4_52>) along with functions to simulate time series with time-varying variance and autocovariance (Patilea and Raissi(2014) <doi:10.1080/01621459.2014.884504>).
Author: Markus Matilainen [cre, aut] ,
Lea Flumian [aut],
Klaus Nordhausen [aut] ,
Sara Taskinen [aut]
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between ssaBSS versions 0.1.1 dated 2022-12-01 and 0.1.2 dated 2026-04-02
DESCRIPTION | 21 +++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 4 +++- inst/ChangeLog | 5 +++++ man/SSAcomb.Rd | 2 +- man/SSAcor.Rd | 2 +- man/SSAsave.Rd | 2 +- man/SSAsir.Rd | 2 +- man/ssaBSS-package.Rd | 20 ++++++++++---------- 9 files changed, 41 insertions(+), 33 deletions(-)
Title: Fast and Effortless Calibration of Agent-Based Models using
Machine Learning
Description: Provides tools and pre-trained Machine Learning [ML] models for
calibration of Agent-Based Models [ABMs] built with the R package
'epiworldR'. Implements methods described in Najafzadehkhoei, Vega Yon,
Modenesi, and Meyer (2025) <doi:10.48550/arXiv.2509.07013>. Users can
automatically calibrate ABMs in seconds with pre-trained ML models,
effectively focusing on simulation rather than calibration. Bridges a gap
by allowing public health practitioners to run their own ABMs without the
advanced technical expertise often required by calibration.
Author: Sima Najafzadehkhoei [aut, cre] ,
George Vega Yon [aut] ,
Jake Wagoner [aut],
Bernardo Modenesi [aut],
Centers for Disease Control and Prevention [fnd]
Maintainer: Sima Najafzadehkhoei <sima.njf@utah.edu>
Diff between epiworldRcalibrate versions 0.1.2 dated 2026-02-18 and 0.1.4 dated 2026-04-02
epiworldRcalibrate-0.1.2/epiworldRcalibrate/man/dot-find_python.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/DESCRIPTION | 12 epiworldRcalibrate-0.1.4/epiworldRcalibrate/MD5 | 21 epiworldRcalibrate-0.1.4/epiworldRcalibrate/NAMESPACE | 1 epiworldRcalibrate-0.1.4/epiworldRcalibrate/R/calibrate_sir.R | 615 ++++------ epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.bib |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.html |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.md | 329 +++-- epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/check_python_setup.Rd | 5 epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-required_python_modules.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-required_python_packages.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-resolve_python_target.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-verify_python_imports.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/epiworldRcalibrate-package.Rd | 1 epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/setup_python_deps.Rd | 22 15 files changed, 520 insertions(+), 486 deletions(-)
More information about epiworldRcalibrate at CRAN
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Title: Sensitivity Analysis with 'mrgsolve'
Description: Perform sensitivity analysis on ordinary differential equation
based models, including ad-hoc graphical analyses based on structured
sequences of parameters as well as local sensitivity analysis. Functions
are provided for creating inputs, simulating scenarios and plotting outputs.
Author: Kyle Baron [aut, cre]
Maintainer: Kyle Baron <kylebtwin@imap.cc>
Diff between mrgsim.sa versions 0.2.0 dated 2023-12-08 and 0.3.0 dated 2026-04-02
DESCRIPTION | 15 +- MD5 | 82 ++++++------- NAMESPACE | 5 NEWS.md | 26 ++++ R/AAA.R | 39 +++--- R/lsa.R | 43 ++++--- R/parseq.R | 23 +-- R/sens.R | 2 R/sens_each.R | 6 R/sens_grid.R | 1 R/sens_plot.R | 183 ++++++++++++++++++++++++++---- R/sens_run.R | 4 R/seq.R | 31 ++--- R/utils.R | 17 ++ build/vignette.rds |binary inst/doc/mrgsim.sa.R | 27 ++-- inst/doc/mrgsim.sa.Rmd | 31 +++-- inst/doc/mrgsim.sa.html | 36 +++-- man/as.data.frame.sens_each.Rd | 2 man/denest.Rd | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/lsa.Rd | 8 - man/mrgsim.sa.Rd | 10 + man/parseq_cv.Rd | 4 man/parseq_fct.Rd | 2 man/parseq_range.Rd | 2 man/plot.lsa.Rd | 10 + man/select_par.Rd | 4 man/sens_fun.Rd | 2 man/sens_plot.Rd | 55 ++++++++- man/sens_run.Rd | 4 man/seq_cv.Rd | 2 man/seq_fct.Rd | 2 tests/testthat/test-lsa.R | 15 ++ tests/testthat/test-sens-plot.R | 158 +++++++++++++++++++++++++ tests/testthat/test-sens_grid.R | 15 ++ vignettes/mrgsim.sa.Rmd | 31 +++-- 42 files changed, 704 insertions(+), 195 deletions(-)
Title: Fit Difference-in-Differences Models with Staggered
Interventions
Description: Fits linear difference-in-differences models in scenarios where
intervention roll-outs are staggered over time. The package implements a
version of an approach proposed by Sun and Abraham (2021)
<doi:10.1016/j.jeconom.2020.09.006> to estimate cohort- and
time-since-treatment specific difference-in-differences parameters, and it
provides convenience functions both for specifying the model and for
flexibly aggregating coefficients to answer a variety of research questions.
Author: Kyle Hart [aut, cre, cph] ,
Stephan Lindner [aut]
Maintainer: Kyle Hart <hartky@ohsu.edu>
Diff between staggR versions 0.1.1 dated 2026-01-14 and 0.2.0 dated 2026-04-02
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++++--------- NAMESPACE | 2 + NEWS.md | 5 ++++ R/detrend.R |only R/detrend_factor.R |only R/pick_time_refs.R | 6 +++++ R/sdid.R | 36 ++++++++++++++++++++++++++--------- inst/doc/staggR.R | 37 ++++++++++++++++++++++++++++++++---- inst/doc/staggR.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++----- inst/doc/staggR.html | 51 +++++++++++++++++++++++++++++++++++++++++++++----- man/detrend.Rd |only man/detrend_factor.Rd |only vignettes/staggR.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++----- 14 files changed, 217 insertions(+), 40 deletions(-)
Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Man Chen [aut],
Daniel M. Swan [aut],
Paulina Grekov [ctb],
Amy Cai [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.7.3 dated 2024-09-07 and 0.7.4 dated 2026-04-02
DESCRIPTION | 22 MD5 | 18 NEWS.md | 4 R/calculate-effect-sizes.R | 22 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Effect-size-definitions.html | 23 inst/doc/Using-SingleCaseES.R | 18 inst/doc/Using-SingleCaseES.html | 858 ++++++++------------------- tests/testthat/test-SCD-effect-sizes.R | 1037 ++++++++++++++++----------------- 10 files changed, 841 insertions(+), 1161 deletions(-)
Title: Core File Structures and Workflows for 'RAVE'
Description: Defines storage standard for Read, process, and analyze
intracranial electroencephalography and deep-brain stimulation in 'RAVE',
a reproducible framework for analysis and visualization of iEEG
by Magnotti, Wang, and Beauchamp, (2020,
<doi:10.1016/j.neuroimage.2020.117341>).
Supports brain imaging data structure (BIDS)
<https://bids.neuroimaging.io> and native file structure to
ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5),
European data format (EDF), BrainVision core data format (BVCDF), or
BlackRock Microsystem (NEV/NSx); process images in
Neuroimaging informatics technology initiative (NIfTI) and
'FreeSurfer' formats, providing brain imaging normalization to template
brain, facilitating 'threeBrain' package for comprehensive electrode
localization via 'YAEL' (your advanced electrode localizer) by Wang,
Magnotti, Zhang, and Beauchamp
(2023, <doi:10.1523/ENEURO.0328-23.2023>).
Author: Zhengjia Wang [aut, cre] ,
Xiang Zhang [aut],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravecore versions 0.1.0 dated 2025-09-23 and 0.1.1 dated 2026-04-02
DESCRIPTION | 10 MD5 | 259 +++++---- NAMESPACE | 4 NEWS.md | 44 + R/aaa-cmd.R | 27 - R/aaa-common.R | 29 - R/aaa-constants.R | 6 R/class002-project.R | 114 ++-- R/class003-subject-internal.R | 176 +++--- R/class004-epoch.R | 60 +- R/class005-subject.R | 308 +++++------ R/class006-rawsubject.R | 246 ++++----- R/class007-abstract_electrode.R | 142 ++--- R/class008-LFP_electrode.R | 264 +++++----- R/class008-LFP_reference.R | 254 ++++----- R/class009-Auxiliary_channel.R | 134 ++--- R/class010-Spike_channel.R | 142 ++--- R/class011-YAEL_process.R | 163 +++--- R/class012-rave_brain.R | 50 + R/class100-base_repository.R | 96 ++- R/class101-epoched_repository.R | 64 +- R/class102-epoched_rawvoltage.R | 18 R/class103-epoched_voltage.R | 16 R/class104-epoched_time-frequency.R | 22 R/class111-recording_blocks_repository.R | 28 - R/class112-recording_blocks_rawvoltage.R | 30 - R/class112-recording_blocks_voltage.R | 28 - R/class113-recording_blocks_coefs.R | 18 R/cmd-tools.R | 72 +- R/import-brainvision.R | 36 - R/import-edf.R | 42 - R/import-h5_matlab_per_block.R | 36 - R/import-h5_matlab_per_channel.R | 38 - R/import-nev.R | 50 - R/internal.R | 53 +- R/legacy-convert_backwards.R | 18 R/math-baseline_power.R | 50 - R/math-collapse_arrays.R | 60 +- R/utils-ants.R | 8 R/utils-bezier.R | 50 + R/utils-csv.R | 81 +-- R/utils-fs.R | 124 ++-- R/utils-matlab.R | 34 - R/utils-nifti2svg.R | 40 - R/utils-openneuro.R | 23 R/utils-operators.R | 7 R/utils-package.R | 8 R/utils-snapshot.R |only R/utils-spikeinterface.R |only R/utils-string.R | 22 R/utils-sys.R | 10 R/utils-tables.R | 64 +- R/validator-brainvision.R | 28 - R/validator-edf.R | 32 - R/validator-h5_matlab_per_block.R | 30 - R/validator-h5_matlab_per_channel.R | 66 +- R/validator-nev.R | 32 - R/validator-subject.R | 418 ++++++++-------- R/validator-time_windows.R | 18 R/visualization-plotly_signals.R | 146 ++--- R/visualization-voltage_repository.R | 160 +++--- R/workflow-ANTs_ct_mri_coregistration.R | 38 - R/workflow-afni_3dallineate.R | 18 R/workflow-archive-subject.R | 158 +++--- R/workflow-compose_channel.R | 74 +- R/workflow-dcm2niix.R | 38 - R/workflow-freesurfer_recon_all.R | 46 - R/workflow-fsl_flirt.R | 17 R/workflow-generate_reference.R | 20 R/workflow-import_electrode_coordinates.R | 20 R/workflow-niftyreg.R | 10 R/workflow-nipy_coreg.R | 14 R/workflow-template_mapping.R | 96 +-- R/workflow-volumetric_atlases.R |only R/workflow-wavelet.R | 76 +- R/workflow-yael_preprocess.R | 96 ++- R/zzz.R |only build/partial.rdb |binary inst/WORDLIST | 7 inst/ravecorepy |only inst/reports |only inst/shell-templates/rave-ants-coregistration.R | 8 inst/shell-templates/rave-ants-mri-to-template.R | 2 inst/shell-templates/rave-nifty-coregistration.R | 6 inst/shell-templates/rave-nipy-coregistration.R | 12 inst/shell-templates/yael-preprocess.R | 39 - man/RAVESubjectBaseRepository.Rd | 13 man/RAVESubjectEpochPhaseRepository.Rd | 1 man/RAVESubjectEpochPowerRepository.Rd | 1 man/RAVESubjectEpochRawVoltageRepository.Rd | 3 man/RAVESubjectEpochRepository.Rd | 3 man/RAVESubjectEpochTimeFreqBaseRepository.Rd | 3 man/RAVESubjectEpochTimeFreqCoefRepository.Rd | 1 man/RAVESubjectEpochVoltageRepository.Rd | 3 man/RAVESubjectRecordingBlockPhaseRepository.Rd | 3 man/RAVESubjectRecordingBlockPowerRepository.Rd | 3 man/RAVESubjectRecordingBlockRawVoltageRepository.Rd | 1 man/RAVESubjectRecordingBlockRepository.Rd | 3 man/RAVESubjectRecordingBlockTimeFreqBaseRepository.Rd | 1 man/RAVESubjectRecordingBlockTimeFreqCoefRepository.Rd | 3 man/RAVESubjectRecordingBlockVoltageRepository.Rd | 1 man/YAELProcess.Rd | 17 man/cmd_run_yael_preprocess.Rd | 7 man/generate_atlases_from_template.Rd |only man/get_available_morph_to_template.Rd |only man/prepare_subject_bare.Rd | 2 man/prepare_subject_with_epochs.Rd | 2 man/rave_brain.Rd | 2 man/snapshot_project.Rd |only man/transform_point_to_template.Rd | 2 tests/testthat/test-class008-LFP_electrode.R | 4 tests/testthat/test-class008-LFP_reference.R | 10 tests/testthat/test-class009-Auxiliary_channel.R | 4 tests/testthat/test-class011-YAEL_process.R | 2 tests/testthat/test-class100-base_repository.R | 28 - tests/testthat/test-class101-epoched_repository.R | 52 - tests/testthat/test-class103-epoched_voltage.R | 82 +-- tests/testthat/test-class104-epoched_time-frequency.R | 80 +-- tests/testthat/test-class112-recording_blocks_voltage.R | 70 +- tests/testthat/test-math-collapse_arrays.R | 18 120 files changed, 3095 insertions(+), 2733 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS
Optimization
Description: Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the
'Scilab' optimization documentation located at
<https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Bill Denney [ctb] ,
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukha [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.1-12 dated 2024-09-17 and 6.0.1-13 dated 2026-04-02
DESCRIPTION | 16 +++++++----- MD5 | 27 ++++++++++----------- NEWS.md | 10 +++++++ R/n1qn1.R | 2 - README.md | 3 ++ man/n1qn1.Rd | 2 - src/RcppExpMod.cpp | 22 ++++++++++++----- src/ajour.c | 24 +++++++++--------- src/calmaj.c | 2 - src/n1qn1_all.c | 46 ++++++++++++++++++------------------ src/proj.c | 2 - src/satur.c | 10 +++---- tests/testthat.R | 8 ++++++ tests/testthat/test-banana.R | 1 tests/testthat/test-memory-safety.R |only 15 files changed, 105 insertions(+), 70 deletions(-)
Title: Joint Model of Heterogeneous Repeated Measures and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data in the presence of heterogeneous within-subject variability, proposed by Li and colleagues (2023) <doi:10.48550/arXiv.2506.12741>.
The proposed method models the within-subject variability of the biomarker and associates it with the risk of the competing risks event. The time-to-event data is modeled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates.
The longitudinal outcome is modeled using a mixed-effects location and scale model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm. This is the final release of the 'JMH' package. Active development has been moved to the 'FastJM' package, which provides improved functionality and ongoing support. Users are strongly encouraged to transition to 'FastJM'.
Author: Shanpeng Li [aut, cre],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between JMH versions 1.0.3 dated 2024-02-20 and 1.0.4 dated 2026-04-02
JMH-1.0.3/JMH/R/bootsfit.R |only JMH-1.0.3/JMH/R/bootsfitMESA.R |only JMH-1.0.3/JMH/R/bootsfitRI.R |only JMH-1.0.3/JMH/R/bootsfitRISF.R |only JMH-1.0.3/JMH/R/bootsfitRISF_Brier.R |only JMH-1.0.3/JMH/R/bootsfitRISF_MAEQ.R |only JMH-1.0.3/JMH/R/bootsfitRI_Brier.R |only JMH-1.0.3/JMH/R/bootsfitRI_MAEQ.R |only JMH-1.0.3/JMH/R/bootsfitRI_MAEQ2.R |only JMH-1.0.3/JMH/R/bootsfitRIhomo.R |only JMH-1.0.3/JMH/R/bootsfitSF.R |only JMH-1.0.3/JMH/R/simJMMESA.R |only JMH-1.0.3/JMH/R/simJMdata.R |only JMH-1.0.3/JMH/R/simJMdataRI.R |only JMH-1.0.3/JMH/R/simJMdataRISF.R |only JMH-1.0.3/JMH/R/simJMdataRIhomo.R |only JMH-1.0.3/JMH/R/simJMdataSF.R |only JMH-1.0.3/JMH/R/simfit.R |only JMH-1.0.3/JMH/R/simfitMESA.R |only JMH-1.0.3/JMH/R/simfitRI.R |only JMH-1.0.3/JMH/R/simfitRISF.R |only JMH-1.0.3/JMH/R/simfitRISF_DPBrier.R |only JMH-1.0.3/JMH/R/simfitRISF_DPMAEQ.R |only JMH-1.0.3/JMH/R/simfitRI_DPBrier.R |only JMH-1.0.3/JMH/R/simfitRI_DPMAEQ.R |only JMH-1.0.3/JMH/R/simfitRIhomo.R |only JMH-1.0.3/JMH/R/simfitSF.R |only JMH-1.0.3/JMH/man/summary.AUCJMMLSM.Rd |only JMH-1.0.3/JMH/man/summary.MAEQJMMLSM.Rd |only JMH-1.0.3/JMH/man/summary.PEJMMLSM.Rd |only JMH-1.0.4/JMH/DESCRIPTION | 25 ++--- JMH-1.0.4/JMH/MD5 | 113 +++++++++-------------- JMH-1.0.4/JMH/NAMESPACE | 10 +- JMH-1.0.4/JMH/R/AUCJMMLSM.R | 111 ++++++++++++++++------- JMH-1.0.4/JMH/R/CindexCR.R |only JMH-1.0.4/JMH/R/ConcordanceJMMLSM.R |only JMH-1.0.4/JMH/R/GetBayes.R |only JMH-1.0.4/JMH/R/GetGHmatrix.R | 111 +++-------------------- JMH-1.0.4/JMH/R/Getinit.R | 2 JMH-1.0.4/JMH/R/JMH.R | 7 - JMH-1.0.4/JMH/R/JMMLSM.R | 10 +- JMH-1.0.4/JMH/R/MAEQJMMLSM.R | 26 ++++- JMH-1.0.4/JMH/R/PEJMMLSM.R | 40 +++++++- JMH-1.0.4/JMH/R/RcppExports.R | 12 ++ JMH-1.0.4/JMH/R/logLik.R | 4 JMH-1.0.4/JMH/R/logLikCR.R | 4 JMH-1.0.4/JMH/R/print.JMMLSM.R | 28 ++++- JMH-1.0.4/JMH/R/sortdata.R | 6 - JMH-1.0.4/JMH/R/summary.AUCJMMLSM.R | 24 +++-- JMH-1.0.4/JMH/R/summary.ConcordanceJMMLSM.R |only JMH-1.0.4/JMH/R/summary.JMMLSM.R | 10 ++ JMH-1.0.4/JMH/R/summary.MAEQJMMLSM.R | 5 - JMH-1.0.4/JMH/R/summary.PEJMMLSM.R | 4 JMH-1.0.4/JMH/R/survfitJMMLSM.R | 46 ++++++++- JMH-1.0.4/JMH/R/timeROC.R |only JMH-1.0.4/JMH/R/vcov.JMMLSM.R | 88 ++++++++++-------- JMH-1.0.4/JMH/README.md | 35 +++++-- JMH-1.0.4/JMH/inst |only JMH-1.0.4/JMH/man/AUCJMMLSM.Rd | 30 +++++- JMH-1.0.4/JMH/man/ConcordanceJMMLSM.Rd |only JMH-1.0.4/JMH/man/JMMLSM.Rd | 6 + JMH-1.0.4/JMH/man/MAEQJMMLSM.Rd | 11 ++ JMH-1.0.4/JMH/man/PEJMMLSM.Rd | 17 +++ JMH-1.0.4/JMH/man/summary.Rd |only JMH-1.0.4/JMH/man/survfitJMMLSM.Rd | 11 ++ JMH-1.0.4/JMH/src/RcppExports.cpp | 84 +++++++++++++++++ JMH-1.0.4/JMH/src/basics.cpp | 134 ++++++++++++++++++++++++++++ JMH-1.0.4/JMH/src/basics.h | 18 +++ JMH-1.0.4/JMH/src/getCov.cpp | 8 + JMH-1.0.4/JMH/src/getCovSF.cpp | 8 + JMH-1.0.4/JMH/src/getEC.cpp | 16 ++- JMH-1.0.4/JMH/src/getECIFall.cpp |only JMH-1.0.4/JMH/src/getECSF.cpp | 15 +-- JMH-1.0.4/JMH/src/getECSFad.cpp | 12 +- JMH-1.0.4/JMH/src/getECad.cpp | 23 ++-- JMH-1.0.4/JMH/src/getMC.cpp | 26 +++-- JMH-1.0.4/JMH/src/getMCSF.cpp | 18 ++- 77 files changed, 809 insertions(+), 349 deletions(-)
Title: Pre-Processing of 'GENEActiv' Data
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events.
For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
Author: Joss Langford [aut],
Ian Long [aut],
Jia Ying Chua [aut, cre],
Activinsights Ltd [cph]
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Diff between GENEAcore versions 1.1.2 dated 2025-11-21 and 1.2.0 dated 2026-04-02
GENEAcore-1.1.2/GENEAcore/inst/extdata/100650Hz_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/1008667Hz.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/20Hz_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/667Hz.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/GENEAcore_Data_Dictionary_21Nov2025.pdf |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Incomplete_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Multi_page_reset_config_time.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Not_a_GENEActiv_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Not_contiguous.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/One_page_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/One_page_reset_config_time.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Short_header.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Zero_data_pages.bin |only GENEAcore-1.2.0/GENEAcore/DESCRIPTION | 11 GENEAcore-1.2.0/GENEAcore/MD5 | 169 + GENEAcore-1.2.0/GENEAcore/NAMESPACE | 27 GENEAcore-1.2.0/GENEAcore/NEWS.md | 26 GENEAcore-1.2.0/GENEAcore/R/MPI_calibrate.R | 12 GENEAcore-1.2.0/GENEAcore/R/MPI_create.R | 169 + GENEAcore-1.2.0/GENEAcore/R/MPI_detect.R | 387 +-- GENEAcore-1.2.0/GENEAcore/R/aggregate_periods.R | 9 GENEAcore-1.2.0/GENEAcore/R/apply_measures.R | 3 GENEAcore-1.2.0/GENEAcore/R/coel_json_builder.R |only GENEAcore-1.2.0/GENEAcore/R/coel_json_create.R |only GENEAcore-1.2.0/GENEAcore/R/daily_measures.R |only GENEAcore-1.2.0/GENEAcore/R/geneabout.R |only GENEAcore-1.2.0/GENEAcore/R/geneabout_functions.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore.R | 324 --- GENEAcore-1.2.0/GENEAcore/R/geneacore_part1.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part2.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part3.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part4.R |only GENEAcore-1.2.0/GENEAcore/R/math.R |only GENEAcore-1.2.0/GENEAcore/R/sample_binfile.R | 346 +-- GENEAcore-1.2.0/GENEAcore/R/step_counter.R | 64 GENEAcore-1.2.0/GENEAcore/R/utils.R | 576 ++++- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.R | 532 +++-- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.Rmd | 646 ++++-- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.html | 685 +++++- GENEAcore-1.2.0/GENEAcore/inst/doc/breaking-changes.html | 1 GENEAcore-1.2.0/GENEAcore/inst/extdata/GENEAcore_Data_Dictionary_2Apr26.pdf |only GENEAcore-1.2.0/GENEAcore/inst/extdata/behavioural-bout-model-v1.0-to-coel-model-v2.0.csv |only GENEAcore-1.2.0/GENEAcore/inst/extdata/geneabout_functions.png |only GENEAcore-1.2.0/GENEAcore/inst/extdata/geneacore_functions.png |binary GENEAcore-1.2.0/GENEAcore/inst/extdata/math_example_13Mar26.R |only GENEAcore-1.2.0/GENEAcore/inst/extdata/rest-activity-model-v1.0-to-coel-model-v2.0.csv |only GENEAcore-1.2.0/GENEAcore/man/MPI_summary.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/MPI_toJSON.Rd |only GENEAcore-1.2.0/GENEAcore/man/aggregate_periods.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/apply_all.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/apply_calibration.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/binfile_summary.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/bouts_decision_tree.Rd |only GENEAcore-1.2.0/GENEAcore/man/calc_autocalparams.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/calculate_daily_activity_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/calculate_daily_sleep_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/check_MPI.Rd | 48 GENEAcore-1.2.0/GENEAcore/man/create_MPI.Rd | 2 GENEAcore-1.2.0/GENEAcore/man/create_coel_atoms_json.Rd |only GENEAcore-1.2.0/GENEAcore/man/create_event_mapping.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/create_summary.Rd | 10 GENEAcore-1.2.0/GENEAcore/man/cx_percentile.Rd |only GENEAcore-1.2.0/GENEAcore/man/detect_nonmovement.Rd | 26 GENEAcore-1.2.0/GENEAcore/man/detect_transitions.Rd | 32 GENEAcore-1.2.0/GENEAcore/man/expected_last_timestamp.Rd |only GENEAcore-1.2.0/GENEAcore/man/find_rest_intervals.Rd |only GENEAcore-1.2.0/GENEAcore/man/folder_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/fx_count.Rd |only 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GENEAcore-1.2.0/GENEAcore/man/single_file_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/step_counter.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/valid_day_nonwear.Rd |only GENEAcore-1.2.0/GENEAcore/man/weighted_mean.Rd |only GENEAcore-1.2.0/GENEAcore/man/weighted_sum.Rd |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-MPI_create.R | 664 +++--- GENEAcore-1.2.0/GENEAcore/tests/testthat/test-MPI_detect.R | 131 - GENEAcore-1.2.0/GENEAcore/tests/testthat/test-apply_measures.R | 132 - GENEAcore-1.2.0/GENEAcore/tests/testthat/test-coel_json_create.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-daily_measures.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-geneabout_functions.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-geneacore.R | 381 +++ GENEAcore-1.2.0/GENEAcore/tests/testthat/test-math.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-sample_binfile.R | 264 +- GENEAcore-1.2.0/GENEAcore/tests/testthat/test-step_counter.R | 95 GENEAcore-1.2.0/GENEAcore/tests/testthat/test-utils.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test_aggregate_periods.R | 1026 +++++----- GENEAcore-1.2.0/GENEAcore/tests/testthat/testdata |only GENEAcore-1.2.0/GENEAcore/vignettes/GENEAcore.Rmd | 646 ++++-- 104 files changed, 4623 insertions(+), 2950 deletions(-)
Title: Check Text Files Content at a Glance
Description: Tools to help text files importation. It can return the
number of lines; print the first and last lines; convert encoding;
guess delimiters and file encoding. Operations are made without
reading the entire file before starting, resulting in good
performances with large files. This package provides an alternative to
a simple use of the 'head', 'tail', 'wc' and 'iconv' programs that are
not always available on machine where R is installed.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between fpeek versions 0.2.0 dated 2026-02-09 and 0.2.1 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/peek-guess-delim.R | 6 ++++-- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM',
as well as network comparison tests fitted using the packages 'bgms' and 'BBGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.3.1 dated 2025-12-08 and 0.4.0 dated 2026-04-02
DESCRIPTION | 10 MD5 | 65 ++--- NAMESPACE | 2 R/AuxiliaryFunctions.R | 69 +++--- R/bgm_plot_class.R | 81 ++++--- R/easybgm.R | 27 +- R/easybgm_compare.R | 15 - R/functions.bdgraph.R | 77 +++--- R/functions.bggm.R | 9 R/functions.bgms.R | 86 ++++--- R/functions.bgmscompare.R | 144 ++++++++---- R/plottingfunctions.bgmCompare.R | 254 +++++++++++++++++----- R/plottingfunctions.bgms.R | 145 +++++++++++-- R/plottingfunctions.easybgm.R | 220 +++++++++++++++---- R/summary.easybgm.R | 76 +++++- R/summary.easybgm_compare.R | 139 +++++++++--- README.md | 135 ++++++++---- man/HDI.Rd | 4 man/centrality.Rd | 4 man/complexity_probs.Rd | 2 man/easybgm.Rd | 13 - man/easybgm_compare.Rd | 10 man/edgeevidence.Rd | 23 +- man/network.Rd | 17 + man/prior_sensitivity.Rd | 19 + man/readme_plots/easybgm_sticker.svg |only man/readme_plots/plot_edgeevidence.png |binary man/readme_plots/plot_network.png |binary man/structure.Rd | 4 man/structure_probs.Rd | 2 man/summary.easybgm.Rd | 15 + man/summary.easybgm_compare.Rd | 14 + tests/testthat/Rplots.pdf |binary tests/testthat/test-easybgm.R | 367 +++++++++++++++++---------------- 34 files changed, 1391 insertions(+), 657 deletions(-)
Title: Preprocessing and Feature Engineering Steps for Modeling
Description: A recipe prepares your data for modeling. We provide an
extensible framework for pipeable sequences of feature engineering
steps provides preprocessing tools to be applied to data. Statistical
parameters for the steps can be estimated from an initial data set and
then applied to other data sets. The resulting processed output can
then be used as inputs for statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Emil Hvitfeldt [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between recipes versions 1.3.1 dated 2025-05-21 and 1.3.2 dated 2026-04-02
recipes-1.3.1/recipes/tests/testthat/_snaps/R4.2 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.3 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.4 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.5 |only recipes-1.3.2/recipes/DESCRIPTION | 18 recipes-1.3.2/recipes/MD5 | 249 +-- recipes-1.3.2/recipes/NEWS.md | 6 recipes-1.3.2/recipes/R/corr.R | 10 recipes-1.3.2/recipes/R/dummy.R | 4 recipes-1.3.2/recipes/R/impute_linear.R | 2 recipes-1.3.2/recipes/R/impute_mean.R | 4 recipes-1.3.2/recipes/R/impute_mode.R | 3 recipes-1.3.2/recipes/R/isomap.R | 26 recipes-1.3.2/recipes/R/misc.R | 7 recipes-1.3.2/recipes/R/newvalues.R | 4 recipes-1.3.2/recipes/R/nnmf.R | 15 recipes-1.3.2/recipes/R/pls.R | 4 recipes-1.3.2/recipes/R/select.R | 2 recipes-1.3.2/recipes/build/partial.rdb |binary recipes-1.3.2/recipes/build/vignette.rds |binary recipes-1.3.2/recipes/inst/doc/Dummies.html | 5 recipes-1.3.2/recipes/inst/doc/Roles.html | 5 recipes-1.3.2/recipes/inst/doc/Selecting_Variables.html | 5 recipes-1.3.2/recipes/inst/doc/Skipping.html | 5 recipes-1.3.2/recipes/inst/doc/recipes.html | 5 recipes-1.3.2/recipes/man/bake.Rd | 2 recipes-1.3.2/recipes/man/check_class.Rd | 2 recipes-1.3.2/recipes/man/check_cols.Rd | 2 recipes-1.3.2/recipes/man/check_missing.Rd | 2 recipes-1.3.2/recipes/man/check_new_values.Rd | 2 recipes-1.3.2/recipes/man/discretize.Rd | 2 recipes-1.3.2/recipes/man/get_data_types.Rd | 2 recipes-1.3.2/recipes/man/has_role.Rd | 6 recipes-1.3.2/recipes/man/prep.Rd | 2 recipes-1.3.2/recipes/man/recipe.Rd | 2 recipes-1.3.2/recipes/man/recipes.Rd | 2 recipes-1.3.2/recipes/man/recipes_argument_select.Rd | 2 recipes-1.3.2/recipes/man/recipes_eval_select.Rd | 2 recipes-1.3.2/recipes/man/rmd/num_comp.Rmd | 2 recipes-1.3.2/recipes/man/rmd/tunable-args.Rmd | 2 recipes-1.3.2/recipes/man/roles.Rd | 2 recipes-1.3.2/recipes/man/step_YeoJohnson.Rd | 2 recipes-1.3.2/recipes/man/step_bin2factor.Rd | 2 recipes-1.3.2/recipes/man/step_bs.Rd | 2 recipes-1.3.2/recipes/man/step_center.Rd | 2 recipes-1.3.2/recipes/man/step_classdist.Rd | 2 recipes-1.3.2/recipes/man/step_classdist_shrunken.Rd | 2 recipes-1.3.2/recipes/man/step_corr.Rd | 8 recipes-1.3.2/recipes/man/step_count.Rd | 2 recipes-1.3.2/recipes/man/step_depth.Rd | 2 recipes-1.3.2/recipes/man/step_discretize.Rd | 2 recipes-1.3.2/recipes/man/step_dummy.Rd | 2 recipes-1.3.2/recipes/man/step_dummy_extract.Rd | 2 recipes-1.3.2/recipes/man/step_dummy_multi_choice.Rd | 2 recipes-1.3.2/recipes/man/step_factor2string.Rd | 2 recipes-1.3.2/recipes/man/step_filter_missing.Rd | 4 recipes-1.3.2/recipes/man/step_geodist.Rd | 2 recipes-1.3.2/recipes/man/step_harmonic.Rd | 4 recipes-1.3.2/recipes/man/step_ica.Rd | 6 recipes-1.3.2/recipes/man/step_impute_bag.Rd | 4 recipes-1.3.2/recipes/man/step_impute_knn.Rd | 4 recipes-1.3.2/recipes/man/step_impute_linear.Rd | 4 recipes-1.3.2/recipes/man/step_impute_lower.Rd | 2 recipes-1.3.2/recipes/man/step_impute_mean.Rd | 4 recipes-1.3.2/recipes/man/step_impute_median.Rd | 2 recipes-1.3.2/recipes/man/step_impute_mode.Rd | 2 recipes-1.3.2/recipes/man/step_indicate_na.Rd | 2 recipes-1.3.2/recipes/man/step_integer.Rd | 2 recipes-1.3.2/recipes/man/step_interact.Rd | 2 recipes-1.3.2/recipes/man/step_intercept.Rd | 2 recipes-1.3.2/recipes/man/step_invlogit.Rd | 2 recipes-1.3.2/recipes/man/step_isomap.Rd | 6 recipes-1.3.2/recipes/man/step_kpca.Rd | 4 recipes-1.3.2/recipes/man/step_kpca_poly.Rd | 4 recipes-1.3.2/recipes/man/step_kpca_rbf.Rd | 4 recipes-1.3.2/recipes/man/step_lincomb.Rd | 2 recipes-1.3.2/recipes/man/step_nnmf.Rd | 17 recipes-1.3.2/recipes/man/step_nnmf_sparse.Rd | 4 recipes-1.3.2/recipes/man/step_normalize.Rd | 2 recipes-1.3.2/recipes/man/step_novel.Rd | 2 recipes-1.3.2/recipes/man/step_ns.Rd | 4 recipes-1.3.2/recipes/man/step_num2factor.Rd | 2 recipes-1.3.2/recipes/man/step_nzv.Rd | 2 recipes-1.3.2/recipes/man/step_other.Rd | 4 recipes-1.3.2/recipes/man/step_pca.Rd | 2 recipes-1.3.2/recipes/man/step_percentile.Rd | 2 recipes-1.3.2/recipes/man/step_pls.Rd | 4 recipes-1.3.2/recipes/man/step_poly.Rd | 4 recipes-1.3.2/recipes/man/step_poly_bernstein.Rd | 4 recipes-1.3.2/recipes/man/step_profile.Rd | 2 recipes-1.3.2/recipes/man/step_range.Rd | 2 recipes-1.3.2/recipes/man/step_ratio.Rd | 2 recipes-1.3.2/recipes/man/step_regex.Rd | 2 recipes-1.3.2/recipes/man/step_relevel.Rd | 2 recipes-1.3.2/recipes/man/step_relu.Rd | 2 recipes-1.3.2/recipes/man/step_rm.Rd | 2 recipes-1.3.2/recipes/man/step_scale.Rd | 2 recipes-1.3.2/recipes/man/step_spatialsign.Rd | 2 recipes-1.3.2/recipes/man/step_spline_b.Rd | 2 recipes-1.3.2/recipes/man/step_spline_convex.Rd | 2 recipes-1.3.2/recipes/man/step_spline_monotone.Rd | 2 recipes-1.3.2/recipes/man/step_spline_natural.Rd | 4 recipes-1.3.2/recipes/man/step_spline_nonnegative.Rd | 2 recipes-1.3.2/recipes/man/step_string2factor.Rd | 2 recipes-1.3.2/recipes/man/step_unknown.Rd | 2 recipes-1.3.2/recipes/man/step_window.Rd | 2 recipes-1.3.2/recipes/man/step_zv.Rd | 2 recipes-1.3.2/recipes/man/tidy.recipe.Rd | 2 recipes-1.3.2/recipes/man/update.step.Rd | 2 recipes-1.3.2/recipes/tests/testthat/_snaps/discretize.md | 12 recipes-1.3.2/recipes/tests/testthat/_snaps/isomap.md | 35 recipes-1.3.2/recipes/tests/testthat/_snaps/nnmf.md |only recipes-1.3.2/recipes/tests/testthat/_snaps/select.md | 2 recipes-1.3.2/recipes/tests/testthat/_snaps/selections.md | 10 recipes-1.3.2/recipes/tests/testthat/test-colcheck.R | 6 recipes-1.3.2/recipes/tests/testthat/test-date.R | 4 recipes-1.3.2/recipes/tests/testthat/test-discretize.R | 11 recipes-1.3.2/recipes/tests/testthat/test-dummy_extract.R | 20 recipes-1.3.2/recipes/tests/testthat/test-dummy_multi_choice.R | 55 recipes-1.3.2/recipes/tests/testthat/test-impute_knn.R | 39 recipes-1.3.2/recipes/tests/testthat/test-isomap.R | 73 recipes-1.3.2/recipes/tests/testthat/test-kpca_poly.R | 8 recipes-1.3.2/recipes/tests/testthat/test-nnmf.R |only recipes-1.3.2/recipes/tests/testthat/test-pls.R | 106 - recipes-1.3.2/recipes/tests/testthat/test-selections.R | 4 recipes-1.3.2/recipes/tests/testthat/test-term_info.R | 801 ++-------- 126 files changed, 694 insertions(+), 1104 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.3-0 dated 2026-02-28 and 2.3-1 dated 2026-04-02
Changelog | 174 +-- DESCRIPTION | 15 MD5 | 28 NAMESPACE | 1 R/kmassess.R | 47 R/kmsassess.R | 7 R/kmsurmiserelation.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/kstMatrix.R | 48 - inst/doc/kstMatrix.Rmd | 505 +++++----- inst/doc/kstMatrix.html | 2240 ++++++----------------------------------------- man/kmassess.Rd | 10 man/kmsurmiserelation.Rd | 5 vignettes/kstMatrix.Rmd | 505 +++++----- 15 files changed, 1001 insertions(+), 2589 deletions(-)
Title: General-Purpose Unconstrained Non-Linear Optimization
Description: An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is
designed for easy interchange with 'optim'.
Author: K Herve Dakpo [ctb, cre],
Hans Bruun Nielsen [aut],
Stig Bousgaard Mortensen [aut]
Maintainer: K Herve Dakpo <k-herve.dakpo@inrae.fr>
Diff between ucminf versions 1.2.2 dated 2024-06-24 and 1.2.3 dated 2026-04-02
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 50 +++-- R/ucminf.R | 512 ++++++++++++++++++++++++++++---------------------------- README.md | 202 +++++++++++----------- man/ucminf.Rd | 330 ++++++++++++++++++------------------ src/init.c | 3 src/interface.c | 150 +++++++++------- 8 files changed, 649 insertions(+), 620 deletions(-)
Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility and supervised dimension reduction problem for multivariate time series. Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace. The package is fully described in Nordhausen, Matilainen, Miettinen, Virta and Taskinen (2021) <doi:10.18637/jss.v098.i15>.
Author: Markus Matilainen [cre, aut] ,
Christophe Croux [aut],
Jari Miettinen [aut] ,
Klaus Nordhausen [aut] ,
Hannu Oja [aut],
Sara Taskinen [aut] ,
Joni Virta [aut]
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 1.0.0 dated 2021-07-10 and 1.0.1 dated 2026-04-02
DESCRIPTION | 24 +++++++++++++----------- MD5 | 14 +++++++------- NAMESPACE | 4 +++- inst/ChangeLog | 4 ++++ man/WeeklyReturnsData.Rd | 2 +- man/tsBSS-package.Rd | 28 ++++++++++++++-------------- src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 44 insertions(+), 36 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.4.0 dated 2026-03-17 and 2.5.0 dated 2026-04-02
GitStats-2.4.0/GitStats/R/gitstats_functions.R |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.R |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.Rmd |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.html |only GitStats-2.4.0/GitStats/vignettes/get_repos_with_code.Rmd |only GitStats-2.5.0/GitStats/DESCRIPTION | 14 GitStats-2.5.0/GitStats/MD5 | 122 +- GitStats-2.5.0/GitStats/NAMESPACE | 11 GitStats-2.5.0/GitStats/NEWS.md | 16 GitStats-2.5.0/GitStats/R/EngineGraphQL.R | 13 GitStats-2.5.0/GitStats/R/EngineGraphQLGitHub.R | 118 -- GitStats-2.5.0/GitStats/R/EngineGraphQLGitLab.R | 143 -- GitStats-2.5.0/GitStats/R/EngineRestGitHub.R | 33 GitStats-2.5.0/GitStats/R/EngineRestGitLab.R | 70 + GitStats-2.5.0/GitStats/R/GQLQueryGitHub.R | 18 GitStats-2.5.0/GitStats/R/GQLQueryGitLab.R | 75 - GitStats-2.5.0/GitStats/R/GitHost.R | 117 +- GitStats-2.5.0/GitStats/R/GitHostGitHub.R | 44 GitStats-2.5.0/GitStats/R/GitHostGitLab.R | 206 +++- GitStats-2.5.0/GitStats/R/GitStats-package.R | 1 GitStats-2.5.0/GitStats/R/GitStats.R | 486 ++++++++-- GitStats-2.5.0/GitStats/R/Storage.R |only GitStats-2.5.0/GitStats/R/get_repos.R | 16 GitStats-2.5.0/GitStats/R/global.R | 1 GitStats-2.5.0/GitStats/R/utils.R | 59 + GitStats-2.5.0/GitStats/README.md | 37 GitStats-2.5.0/GitStats/build/vignette.rds |binary GitStats-2.5.0/GitStats/inst/doc/set_hosts.R | 24 GitStats-2.5.0/GitStats/inst/doc/set_hosts.Rmd | 4 GitStats-2.5.0/GitStats/inst/doc/store_data.R |only GitStats-2.5.0/GitStats/inst/doc/store_data.Rmd |only GitStats-2.5.0/GitStats/inst/doc/store_data.html |only GitStats-2.5.0/GitStats/man/create_gitstats.Rd | 2 GitStats-2.5.0/GitStats/man/get_repos.Rd | 14 GitStats-2.5.0/GitStats/man/get_storage.Rd | 2 GitStats-2.5.0/GitStats/man/get_storage_metadata.Rd |only GitStats-2.5.0/GitStats/man/is_verbose.Rd | 2 GitStats-2.5.0/GitStats/man/remove_from_storage.Rd |only GitStats-2.5.0/GitStats/man/remove_postgres_storage.Rd |only GitStats-2.5.0/GitStats/man/remove_sqlite_storage.Rd |only GitStats-2.5.0/GitStats/man/set_local_storage.Rd |only GitStats-2.5.0/GitStats/man/set_parallel.Rd |only GitStats-2.5.0/GitStats/man/set_postgres_storage.Rd |only GitStats-2.5.0/GitStats/man/set_sqlite_storage.Rd |only GitStats-2.5.0/GitStats/man/show_hosts.Rd | 2 GitStats-2.5.0/GitStats/man/show_orgs.Rd | 2 GitStats-2.5.0/GitStats/man/verbose_off.Rd | 2 GitStats-2.5.0/GitStats/man/verbose_on.Rd | 2 GitStats-2.5.0/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 4 GitStats-2.5.0/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 33 GitStats-2.5.0/GitStats/tests/testthat/_snaps/02-get_commits-GitLab.md | 2 GitStats-2.5.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitHub.md | 15 GitStats-2.5.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md | 13 GitStats-2.5.0/GitStats/tests/testthat/_snaps/z-GitStats.md | 8 GitStats-2.5.0/GitStats/tests/testthat/helper-fixtures-repos.R | 71 + GitStats-2.5.0/GitStats/tests/testthat/helper.R | 13 GitStats-2.5.0/GitStats/tests/testthat/setup.R | 2 GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 6 GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 394 +++++++- GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 5 GitStats-2.5.0/GitStats/tests/testthat/test-03-get_files_structure-GitHub.R | 190 --- GitStats-2.5.0/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R | 201 ---- GitStats-2.5.0/GitStats/tests/testthat/test-GitHost-helpers.R | 37 GitStats-2.5.0/GitStats/tests/testthat/test-get_files_tree-REST.R |only GitStats-2.5.0/GitStats/tests/testthat/test-get_storage.R | 6 GitStats-2.5.0/GitStats/tests/testthat/test-get_urls_repos-GitStats.R | 21 GitStats-2.5.0/GitStats/tests/testthat/test-incremental-cache.R |only GitStats-2.5.0/GitStats/tests/testthat/test-parallel.R |only GitStats-2.5.0/GitStats/tests/testthat/test-set_storage.R |only GitStats-2.5.0/GitStats/tests/testthat/test-utils.R | 114 ++ GitStats-2.5.0/GitStats/tests/testthat/test-z-GitStats.R | 44 GitStats-2.5.0/GitStats/vignettes/set_hosts.Rmd | 4 GitStats-2.5.0/GitStats/vignettes/store_data.Rmd |only 73 files changed, 1887 insertions(+), 952 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.2.0 dated 2026-03-02 and 1.2.1 dated 2026-04-02
DESCRIPTION | 10 MD5 | 48 +-- NEWS.md | 4 R/check_api_access.R | 2 R/firstlib.R | 7 R/get_municipalities.R | 4 R/get_municipality_pop.R | 4 R/get_population_grid.R | 4 R/get_statistical_grid.R | 4 R/get_zipcodes.R | 4 R/ogc_api_nls.R | 1 R/wfs_api.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/geofi_datasets.html | 4 inst/doc/geofi_joining_attribute_data.html | 4 inst/doc/geofi_making_maps.html | 365 ++++++++++++----------------- inst/doc/geofi_nls_ogc.html | 4 inst/doc/geofi_spatial_analysis.Rmd | 2 inst/doc/geofi_spatial_analysis.html | 6 inst/doc/geofi_statfi_ogc.html | 4 inst/extdata/wfs_providers.yaml | 4 man/check_api_access.Rd | 2 man/wfs_api.Rd | 4 vignettes/geofi_spatial_analysis.Rmd | 2 25 files changed, 222 insertions(+), 279 deletions(-)
Title: F1 Pit Stop Datasets
Description: Formula 1 pit stop data. The package provides information on teams and drivers across seasons (2019 or higher). It also includes a function to visualize pit stop performance.
Author: Jose Jordan-Soria [aut, cre]
Maintainer: Jose Jordan-Soria <jjose.jjordan@gmail.com>
Diff between f1pits versions 0.2.0 dated 2026-03-08 and 1.2.0 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 1 + NEWS.md | 14 ++++++++++++-- R/pitchamp.R |only R/pitplot.R | 3 +++ R/pits.R | 2 +- inst/CITATION | 2 +- inst/doc/f1pits-intro.R | 6 ++++++ inst/doc/f1pits-intro.Rmd | 13 +++++++++++-- inst/doc/f1pits-intro.html | 22 +++++++++++++++++----- man/pitchamp.Rd |only man/pits.Rd | 2 +- tests/testthat/test-pitchamp.R |only tests/testthat/testdata/2015.csv |only vignettes/f1pits-intro.Rmd | 13 +++++++++++-- 16 files changed, 83 insertions(+), 29 deletions(-)
Title: Functions for Declared Missing Values
Description: A zero dependency package containing functions to declare labels
and missing values, coupled with associated functions to create (weighted)
tables of frequencies and various other summary measures.
Some of the base functions have been rewritten to make use of the specific
information about the missing values, most importantly to distinguish
between empty NA and declared NA values.
Some functions have similar functionality with the corresponding ones from
packages "haven" and "labelled". The aim is to ensure as much compatibility
as possible with these packages, while offering an alternative in the
objects of class "declared".
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.25 dated 2024-09-08 and 0.26 dated 2026-04-02
declared-0.25/declared/R/w_IQR.R |only declared-0.25/declared/R/w_fivenum.R |only declared-0.25/declared/R/w_mean.R |only declared-0.25/declared/R/w_median.R |only declared-0.25/declared/R/w_mode.R |only declared-0.25/declared/R/w_quantile.R |only declared-0.25/declared/R/w_sd.R |only declared-0.25/declared/R/w_standardize.R |only declared-0.25/declared/R/w_summary.R |only declared-0.25/declared/R/w_table.R |only declared-0.25/declared/R/w_var.R |only declared-0.26/declared/DESCRIPTION | 16 -- declared-0.26/declared/MD5 | 54 ++++----- declared-0.26/declared/NAMESPACE | 18 ++- declared-0.26/declared/R/class_methods.R | 22 +++ declared-0.26/declared/R/declared.R | 87 ++++++++++++++- declared-0.26/declared/R/declared_package.R | 4 declared-0.26/declared/R/drop_undeclare.R | 2 declared-0.26/declared/R/internals.R | 38 +++--- declared-0.26/declared/R/measurement.R | 6 - declared-0.26/declared/R/onLoad.R | 137 ++++++++++++++++++++++++ declared-0.26/declared/R/print.R | 92 ++++++++++------ declared-0.26/declared/R/wIQR.R |only declared-0.26/declared/R/wfivenum.R |only declared-0.26/declared/R/wmean.R |only declared-0.26/declared/R/wmedian.R |only declared-0.26/declared/R/wmode.R |only declared-0.26/declared/R/wquantile.R |only declared-0.26/declared/R/wsd.R |only declared-0.26/declared/R/wstandardize.R |only declared-0.26/declared/R/wsummary.R |only declared-0.26/declared/R/wtable.R |only declared-0.26/declared/R/wvar.R |only declared-0.26/declared/man/declared.Rd | 8 + declared-0.26/declared/man/declared_internal.Rd | 51 ++++++++ declared-0.26/declared/man/declared_package.Rd | 4 declared-0.26/declared/man/measurement.Rd | 4 declared-0.26/declared/man/weighted.Rd | 88 +++++++-------- declared-0.26/declared/src/declared.c | 19 +++ 39 files changed, 496 insertions(+), 154 deletions(-)
Title: Acknowledge all Contributors to a Project
Description: Acknowledge all contributors to a project via a single
function call. The function appends to a 'README' or other specified
file(s) a table with names of all individuals who contributed via code
or repository issues. The package also includes several additional
functions to extract and quantify contributions to any repository.
Author: Mark Padgham [aut, cre],
Chris Hartgerink [aut],
Maelle Salmon [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between allcontributors versions 0.2.2 dated 2024-10-23 and 0.2.3 dated 2026-04-02
allcontributors-0.2.2/allcontributors/tests/testthat/getcontribs/gh-api/geodist/contributors-7ad99d-38c41e.json |only allcontributors-0.2.2/allcontributors/tests/testthat/getcontribs/gh-api/rate_limit-38c41e.json |only allcontributors-0.2.3/allcontributors/DESCRIPTION | 9 allcontributors-0.2.3/allcontributors/MD5 | 30 +- allcontributors-0.2.3/allcontributors/NEWS.md | 16 + allcontributors-0.2.3/allcontributors/R/add-contributors.R | 4 allcontributors-0.2.3/allcontributors/R/github.R | 20 + allcontributors-0.2.3/allcontributors/README.md | 148 +++++++++- allcontributors-0.2.3/allcontributors/build/vignette.rds |binary allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.R | 2 allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.Rmd | 2 allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.html | 50 +-- allcontributors-0.2.3/allcontributors/man/get_contributors.Rd | 4 allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/geodist/contributors-7ad99d.json |only allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/graphql-8cf72c-POST.json | 130 ++++++++ allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/rate_limit.json |only allcontributors-0.2.3/allcontributors/tests/testthat/test-get-contribs.R | 6 allcontributors-0.2.3/allcontributors/vignettes/allcontributors.Rmd | 2 18 files changed, 347 insertions(+), 76 deletions(-)
More information about allcontributors at CRAN
Permanent link
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and computing. Includes functions for logging, parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.4.3 dated 2026-03-06 and 0.4.4 dated 2026-04-02
DESCRIPTION | 12 MD5 | 53 ++- NAMESPACE | 10 NEWS.md | 16 + R/RcppExports.R | 18 - R/computation.R | 37 +- R/lisi.R |only R/log_message.R | 647 +++++++++++++++++++++++++++++++++++-------- R/parallelize_fun.R | 253 +++++++++++----- R/reexports.R | 2 R/sparse_cor.R | 5 R/thisutils-package.R | 2 R/utils.R | 57 ++- README.md | 2 man/compute_lisi.Rd |only man/compute_simpson_index.Rd |only man/is_apple_silicon.Rd |only man/is_linux.Rd |only man/is_osx.Rd |only man/is_windows.Rd |only man/log_message.Rd | 22 + man/parallelize_fun.Rd | 4 man/unnest_fun.Rd | 2 src/RcppExports.cpp | 55 +++ src/lisi.cpp |only src/matrix_to_table.cpp | 12 src/table_to_matrix.cpp | 55 ++- tests |only 28 files changed, 986 insertions(+), 278 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.8.4 dated 2026-01-29 and 1.8.5 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/altrep_compact_replication.cpp | 5 +++-- src/rlasstreamer.cpp | 4 ++-- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.5.0 dated 2026-02-27 and 1.6.0 dated 2026-04-02
mlr3-1.5.0/mlr3/man/figures/block.png |only mlr3-1.5.0/mlr3/man/figures/block.svg |only mlr3-1.5.0/mlr3/man/figures/mlr3verse.svg |only mlr3-1.6.0/mlr3/DESCRIPTION | 8 mlr3-1.6.0/mlr3/MD5 | 457 ++++------ mlr3-1.6.0/mlr3/NEWS.md | 8 mlr3-1.6.0/mlr3/R/BenchmarkResult.R | 184 ++-- mlr3-1.6.0/mlr3/R/CallbackResample.R | 48 - mlr3-1.6.0/mlr3/R/ContextResample.R | 5 mlr3-1.6.0/mlr3/R/DataBackend.R | 4 mlr3-1.6.0/mlr3/R/DataBackendCbind.R | 7 mlr3-1.6.0/mlr3/R/DataBackendDataTable.R | 11 mlr3-1.6.0/mlr3/R/DataBackendRbind.R | 7 mlr3-1.6.0/mlr3/R/DataBackendRename.R | 6 mlr3-1.6.0/mlr3/R/HotstartStack.R | 38 mlr3-1.6.0/mlr3/R/Learner.R | 327 +++++-- mlr3-1.6.0/mlr3/R/LearnerClassif.R | 40 mlr3-1.6.0/mlr3/R/LearnerClassifDebug.R | 90 + mlr3-1.6.0/mlr3/R/LearnerClassifFeatureless.R | 27 mlr3-1.6.0/mlr3/R/LearnerClassifRpart.R | 29 mlr3-1.6.0/mlr3/R/LearnerRegr.R | 57 - mlr3-1.6.0/mlr3/R/LearnerRegrDebug.R | 14 mlr3-1.6.0/mlr3/R/LearnerRegrFeatureless.R | 19 mlr3-1.6.0/mlr3/R/LearnerRegrRpart.R | 17 mlr3-1.6.0/mlr3/R/Measure.R | 155 ++- mlr3-1.6.0/mlr3/R/MeasureAIC.R | 18 mlr3-1.6.0/mlr3/R/MeasureBIC.R | 18 mlr3-1.6.0/mlr3/R/MeasureClassif.R | 39 mlr3-1.6.0/mlr3/R/MeasureClassifCosts.R | 12 mlr3-1.6.0/mlr3/R/MeasureDebug.R | 3 mlr3-1.6.0/mlr3/R/MeasureElapsedTime.R | 10 mlr3-1.6.0/mlr3/R/MeasureInternalValidScore.R | 3 mlr3-1.6.0/mlr3/R/MeasureOOBError.R | 3 mlr3-1.6.0/mlr3/R/MeasureRegr.R | 39 mlr3-1.6.0/mlr3/R/MeasureRegrPinball.R | 3 mlr3-1.6.0/mlr3/R/MeasureRegrRQR.R | 7 mlr3-1.6.0/mlr3/R/MeasureRegrRSQ.R | 13 mlr3-1.6.0/mlr3/R/MeasureSelectedFeatures.R | 3 mlr3-1.6.0/mlr3/R/MeasureSimilarity.R | 38 mlr3-1.6.0/mlr3/R/MeasureSimple.R | 60 - mlr3-1.6.0/mlr3/R/Prediction.R | 29 mlr3-1.6.0/mlr3/R/PredictionClassif.R | 29 mlr3-1.6.0/mlr3/R/PredictionData.R | 13 mlr3-1.6.0/mlr3/R/PredictionDataClassif.R | 26 mlr3-1.6.0/mlr3/R/PredictionDataRegr.R | 26 mlr3-1.6.0/mlr3/R/PredictionRegr.R | 33 mlr3-1.6.0/mlr3/R/ResampleResult.R | 65 + mlr3-1.6.0/mlr3/R/Resampling.R | 36 mlr3-1.6.0/mlr3/R/ResamplingBootstrap.R | 15 mlr3-1.6.0/mlr3/R/ResamplingCV.R | 8 mlr3-1.6.0/mlr3/R/ResamplingCustom.R | 12 mlr3-1.6.0/mlr3/R/ResamplingCustomCV.R | 12 mlr3-1.6.0/mlr3/R/ResamplingHoldout.R | 9 mlr3-1.6.0/mlr3/R/ResamplingInsample.R | 9 mlr3-1.6.0/mlr3/R/ResamplingLOO.R | 4 mlr3-1.6.0/mlr3/R/ResamplingRepeatedCV.R | 15 mlr3-1.6.0/mlr3/R/ResamplingSubsampling.R | 28 mlr3-1.6.0/mlr3/R/ResultData.R | 165 ++- mlr3-1.6.0/mlr3/R/Task.R | 298 ++++-- mlr3-1.6.0/mlr3/R/TaskClassif.R | 12 mlr3-1.6.0/mlr3/R/TaskClassif_breast_cancer.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_german_credit.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_penguins.R | 9 mlr3-1.6.0/mlr3/R/TaskClassif_pima.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_sonar.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_spam.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_wine.R | 6 mlr3-1.6.0/mlr3/R/TaskGenerator.R | 22 mlr3-1.6.0/mlr3/R/TaskGenerator2DNormals.R | 15 mlr3-1.6.0/mlr3/R/TaskGeneratorCassini.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorCircle.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorFriedman1.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorMoons.R | 12 mlr3-1.6.0/mlr3/R/TaskGeneratorSimplex.R | 19 mlr3-1.6.0/mlr3/R/TaskGeneratorSmiley.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorSpirals.R | 15 mlr3-1.6.0/mlr3/R/TaskGeneratorXor.R | 13 mlr3-1.6.0/mlr3/R/TaskRegr.R | 12 mlr3-1.6.0/mlr3/R/TaskSupervised.R | 5 mlr3-1.6.0/mlr3/R/TaskUnsupervised.R | 6 mlr3-1.6.0/mlr3/R/as_benchmark_result.R | 6 mlr3-1.6.0/mlr3/R/as_data_backend.R | 9 mlr3-1.6.0/mlr3/R/as_learner.R | 15 mlr3-1.6.0/mlr3/R/as_measure.R | 21 mlr3-1.6.0/mlr3/R/as_prediction.R | 16 mlr3-1.6.0/mlr3/R/as_prediction_classif.R | 11 mlr3-1.6.0/mlr3/R/as_prediction_data.R | 13 mlr3-1.6.0/mlr3/R/as_prediction_regr.R | 6 mlr3-1.6.0/mlr3/R/as_resample_result.R | 19 mlr3-1.6.0/mlr3/R/as_resampling.R | 15 mlr3-1.6.0/mlr3/R/as_result_data.R | 38 mlr3-1.6.0/mlr3/R/as_task.R | 15 mlr3-1.6.0/mlr3/R/as_task_classif.R | 42 mlr3-1.6.0/mlr3/R/as_task_regr.R | 21 mlr3-1.6.0/mlr3/R/as_task_unsupervised.R | 15 mlr3-1.6.0/mlr3/R/assertions.R | 211 +++- mlr3-1.6.0/mlr3/R/auto_convert.R | 7 mlr3-1.6.0/mlr3/R/benchmark.R | 52 - 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Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- common effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- three-level meta-analysis model;
- generalised linear mixed model;
- logistic regression with penalised likelihood for rare events;
- Hartung-Knapp method for random effects model;
- Kenward-Roger method for random effects model;
- prediction interval and density of the prediction distribution;
- expected proportion of comparable studies with clinically important benefit or harm;
- statistical tests for funnel plot asymmetry;
- trim-and-fill method to evaluate bias in meta-analysis;
- meta-regression;
- cumulative meta-analysis and leave-one-out meta-analysis;
- import data from 'RevMan 5';
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between meta versions 8.2-1 dated 2025-09-01 and 8.3-0 dated 2026-04-02
DESCRIPTION | 20 MD5 | 321 +++--- NAMESPACE | 12 NEWS.md | 102 + R/JAMAlabels.R | 17 R/amlodipine.R | 11 R/as.data.frame.meta.R | 57 - R/barplot.rob.R | 29 R/baujat.R | 77 - R/blup.meta.R | 15 R/bracket.longarm.R | 6 R/bracket.pairwise.R | 6 R/bubble.R | 8 R/caffeine.R | 8 R/catmeth-internal.R | 40 R/catmeth.R | 298 ++--- R/ci.R | 15 R/cidprop.R | 141 +- R/compsplit.R | 2 R/drapery.R | 275 ++--- R/estimates.R | 263 ++-- R/forest-internal.R | 437 ++++---- R/forest.R | 472 +++++--- R/forest.metabind.R | 190 +-- R/forest.metacum.R | 14 R/forest.metainf.R | 23 R/funnel.R | 247 ++-- R/gm.R | 38 R/gs.R | 1 R/hetcalc.R | 219 ++-- R/labbe.R | 186 +-- R/labels.meta.R | 19 R/longarm-internal.R | 10 R/longarm.R | 151 +- R/mean-sd-internal.R | 130 +- R/meta-aux.R | 286 ++--- R/meta-chk.R | 166 +-- R/meta-ci.R | 78 - R/meta-format.R | 50 R/meta-het.R | 80 - R/meta-internal.R | 355 +++--- R/meta-is.R | 14 R/meta-math.R | 200 +-- R/meta-object.R | 81 - R/meta-package.R | 21 R/meta-set.R | 64 - R/meta-transf.R | 123 +- R/meta-xlab.R | 70 - R/metaadd.R | 51 R/metabias.R | 276 ++--- R/metabias.rm5.R | 42 R/metabin.R | 547 +++++----- R/metabind-internal.R | 234 ++-- R/metabind.R | 377 +++---- R/metacont.R | 645 ++++++------ R/metacor.R | 355 +++--- R/metacr.R | 375 +++---- R/metacum.R | 226 ++-- R/metagen.R | 805 +++++++-------- R/metainc.R | 407 +++---- R/metainf.R | 234 ++-- R/metamean.R | 533 ++++------ R/metamerge-internal.R | 248 ++-- R/metamerge.R | 459 ++++---- R/metaprop.R | 531 ++++----- R/metarate.R | 469 ++++---- R/metareg.R | 133 +- R/nnt.R | 233 ++-- R/or2smd.R | 99 - R/pairwise-internal.R |only R/pairwise.R | 2395 +++++++++++++++++++++++---------------------- R/plot.cidprop.R | 19 R/print.meta.R | 514 ++++----- R/print.metacum.R | 12 R/print.metainf.R | 10 R/print.rm5.R | 25 R/print.summary.meta.R | 259 ++-- R/radial.R | 104 - R/rd.R |only R/read.cdir.R | 210 +-- R/read.mtv.R | 55 - R/read.rm5-internal.R | 484 ++++----- R/read.rm5.R | 19 R/rob-internal.R | 48 R/rob.R | 244 ++-- R/se-internal.R | 58 - R/settings.meta-internal.R | 56 - R/settings.meta.R | 459 ++++---- R/smd2or.R | 107 -- R/smlab.R | 4 R/smoking.R | 9 R/subgroup-internal.R | 16 R/subgroup.R | 456 ++++---- R/subset.longarm.R | 21 R/subset.pairwise.R | 18 R/summary.meta.R | 114 +- R/summary.rm5.R | 48 R/traffic_light.R | 31 R/trimfill.R | 326 +++--- R/trimfill.rm5.R | 68 - R/update.meta.R | 648 ++++++------ R/weights.meta.R | 29 R/woodyplants.R | 13 build/vignette.rds |binary inst/CITATION | 4 inst/doc/meta-tutorial.pdf |binary inst/doc/meta-workflow.pdf |binary man/amlodipine.Rd | 10 man/as.data.frame.meta.Rd | 12 man/barplot.rob.Rd | 8 man/baujat.meta.Rd | 20 man/blup.meta.Rd | 15 man/bubble.metareg.Rd | 6 man/caffeine.Rd | 8 man/cidprop.Rd | 12 man/drapery.Rd | 10 man/estimates.Rd | 25 man/forest.meta.Rd | 183 ++- man/forest.metabind.Rd | 12 man/forest.metacum.Rd | 14 man/forest.metainf.Rd | 14 man/funnel.meta.Rd | 12 man/labbe.Rd | 16 man/meta-object.Rd | 81 - man/meta-package.Rd | 13 man/metaadd.Rd | 10 man/metabias.Rd | 30 man/metabin.Rd | 66 - man/metabind.Rd | 32 man/metacont.Rd | 26 man/metacor.Rd | 18 man/metacr.Rd | 4 man/metacum.Rd | 24 man/metagen.Rd | 16 man/metainc.Rd | 20 man/metainf.Rd | 32 man/metamean.Rd | 20 man/metamerge.Rd | 66 - man/metaprop.Rd | 92 - man/metarate.Rd | 34 man/metareg.Rd | 48 man/nnt.Rd | 6 man/or2smd.Rd | 8 man/pairwise.Rd | 104 + man/plot.cidprop.Rd | 10 man/print.metacum.Rd | 10 man/print.metainf.Rd | 10 man/print.summary.meta.Rd | 10 man/radial.Rd | 4 man/rd.Rd |only man/rob.Rd | 8 man/smd2or.Rd | 10 man/smoking.Rd | 8 man/sub-.longarm.Rd | 4 man/sub-.pairwise.Rd | 4 man/subset.longarm.Rd | 2 man/subset.pairwise.Rd | 4 man/summary.meta.Rd | 10 man/traffic_light.Rd | 8 man/trimfill.Rd | 16 man/update.meta.Rd | 14 man/woodyplants.Rd | 12 vignettes/references.bib | 2 163 files changed, 10728 insertions(+), 10155 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] ,
Florian De Boissieu [ctb] ,
Andrew Sanchez Meador [ctb] for
segment_snags),
Bourdon Jean-Francois [ctb] for
track_sensor),
Gatziolis Demetrios [ctb] for
track_sensor),
Leon Steinmeier [c [...truncated...]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between lidR versions 4.2.3 dated 2026-01-08 and 4.3.0 dated 2026-04-02
DESCRIPTION | 8 - MD5 | 78 ++++++++++++------- NAMESPACE | 4 NEWS.md | 8 + R/RcppExports.R | 8 + R/algorithm-dsm.R | 97 ++++++++++++++++++++++++ R/algorithm-gnd.R | 84 ++++++++++++++++++++ R/catalog_boundaries.R | 22 +++++ R/classify.R | 4 inst/doc/lidR-LAS-class.html | 5 - inst/doc/lidR-LAScatalog-class.html | 5 - inst/doc/lidR-LAScatalog-engine.html | 5 - inst/doc/lidR-catalog-apply-examples.html | 5 - inst/doc/lidR-computation-speed-LAScatalog.html | 5 - inst/include/lidR/Grid3D.h | 2 man/catalog_split_clusters.Rd |only man/classify.Rd | 4 man/dsm_pitfree.Rd | 1 man/dsm_point2raster.Rd | 1 man/dsm_spikefree.Rd |only man/dsm_tin.Rd | 3 man/gnd_csf.Rd | 3 man/gnd_mcc.Rd | 3 man/gnd_pmf.Rd | 3 man/ptd.Rd |only src/C_ptd.cpp |only src/C_spikefree.cpp |only src/LAS.cpp | 8 - src/Makevars | 22 +++++ src/RcppExports.cpp | 34 ++++++++ src/hporro |only src/knn.cpp | 2 src/nanoflann |only src/ptd |only src/spikefree |only tests/testthat/Rplots.pdf |binary tests/testthat/test-classify_ground.R | 15 +++ tests/testthat/test-rasterize_canopy.R | 18 ++++ 38 files changed, 401 insertions(+), 56 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cf-convention.github.io/Data/cf-conventions/cf-conventions-1.13/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.7.2 dated 2025-11-12 and 1.7.3 dated 2026-04-02
DESCRIPTION | 8 - LICENSE | 2 MD5 | 68 +++++----- NAMESPACE | 1 NEWS.md | 141 ++++++---------------- R/CFCalendar.R | 17 ++ R/CFCalendar360.R | 10 + R/CFCalendar365.R | 11 + R/CFCalendar366.R | 11 + R/CFCalendarNone.R | 13 ++ R/CFCalendarProleptic.R | 2 R/CFClimatology.R | 10 - R/CFtime-package.R | 7 - R/CFtime.R | 224 +++++++++++++++++++++--------------- R/api.R | 125 ++++++++++++-------- R/helpers.R | 8 - README.md | 36 +++-- TODO | 1 man/CFCalendar.Rd | 28 ++++ man/CFCalendar360.Rd | 24 +++ man/CFCalendar365.Rd | 24 +++ man/CFCalendar366.Rd | 24 +++ man/CFCalendarJulian.Rd | 1 man/CFCalendarNone.Rd | 23 +++ man/CFCalendarProleptic.Rd | 1 man/CFCalendarStandard.Rd | 1 man/CFCalendarTAI.Rd | 1 man/CFCalendarUTC.Rd | 1 man/CFClimatology.Rd | 3 man/CFTime.Rd | 52 +++++--- man/CFtime-package.Rd | 7 - man/plus-.CFTime.Rd | 56 +++++---- tests/testthat/test-CFtime.R | 18 +- tests/testthat/test-functions.R | 34 +++-- tests/testthat/test-parse_deparse.R | 22 +-- 35 files changed, 629 insertions(+), 386 deletions(-)
Title: Utility Functions for Plotting
Description: Provides utility functions for plotting. Includes functions for color manipulation, plot customization, panel size control, data optimization for plots, and layout adjustments.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisplot versions 0.3.6 dated 2026-03-07 and 0.3.7 dated 2026-04-02
DESCRIPTION | 19 - MD5 | 26 +- NAMESPACE | 2 NEWS.md | 14 + R/GraphPlot.R |only R/StatPlot.R | 74 +++++- R/compute_velocity_on_grid.R |only R/heatmap.R | 5 R/palettes.R | 2 R/sankey.R | 371 +++++++++++++++++++++------------- README.md | 2 man/GraphPlot.Rd |only man/annotation_block_fill_graphics.Rd | 2 man/build_heatmap_annotation.Rd | 2 man/compute_velocity_on_grid.Rd |only man/palette_colors.Rd | 2 16 files changed, 342 insertions(+), 179 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.5-1 dated 2026-02-01 and 3.6-0 dated 2026-04-02
DESCRIPTION | 16 +- MD5 | 36 ++--- NEWS | 10 + build/vignette.rds |binary inst/doc/NAobjects.pdf |binary inst/doc/bugfixes.Rnw | 10 + inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 323 +++++++++++++++++++++++++++++++++++++++++++-- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 1 man/macros/defns.Rd | 3 vignettes/bugfixes.Rnw | 10 + vignettes/updates.Rnw | 323 +++++++++++++++++++++++++++++++++++++++++++-- 19 files changed, 677 insertions(+), 56 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically regular time series and air quality
measurement, meteorological data and dispersion model output can be
analysed. The package is described in Carslaw and Ropkins (2012,
<doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre] ,
Jack Davison [aut] ,
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.19.0 dated 2025-08-28 and 3.0.0 dated 2026-04-02
openair-2.19.0/openair/R/calcFno2.R |only openair-2.19.0/openair/R/date.breaks.R |only openair-2.19.0/openair/R/drawOpenKey.R |only openair-2.19.0/openair/R/linearRelation.R |only openair-2.19.0/openair/R/samp.boot.block.R |only openair-2.19.0/openair/R/summaryPlot.R |only openair-2.19.0/openair/R/zzz.R |only openair-2.19.0/openair/man/calcFno2.Rd |only openair-2.19.0/openair/man/drawOpenKey.Rd |only openair-2.19.0/openair/man/linearRelation.Rd |only openair-2.19.0/openair/man/summaryPlot.Rd |only openair-2.19.0/openair/src/Makevars |only openair-2.19.0/openair/src/Makevars.win |only openair-2.19.0/openair/src/init.c |only openair-2.19.0/openair/tests/testthat/test-bootMean.R |only openair-2.19.0/openair/tests/testthat/test-utilities.R |only openair-3.0.0/openair/DESCRIPTION | 23 openair-3.0.0/openair/MD5 | 300 openair-3.0.0/openair/NAMESPACE | 215 openair-3.0.0/openair/NEWS.md | 2558 +++--- openair-3.0.0/openair/R/GaussianSmooth.R |only openair-3.0.0/openair/R/RColorBrewer.R | 3586 ++++----- openair-3.0.0/openair/R/RcppExports.R |only openair-3.0.0/openair/R/TaylorDiagram.R | 1484 +-- openair-3.0.0/openair/R/TheilSen.R | 1498 +--- openair-3.0.0/openair/R/WhittakerSmooth.R |only openair-3.0.0/openair/R/aqStats.R | 746 -- openair-3.0.0/openair/R/bootMeans.R | 570 - openair-3.0.0/openair/R/calcPercentile.R | 262 openair-3.0.0/openair/R/calendarPlot.R | 1497 ++-- openair-3.0.0/openair/R/checkPrep.R | 345 openair-3.0.0/openair/R/conditionalEval.R | 1080 +- openair-3.0.0/openair/R/conditionalQuantile.R | 870 +- openair-3.0.0/openair/R/corPlot.R | 1172 +-- openair-3.0.0/openair/R/cutData.R | 1653 ++-- openair-3.0.0/openair/R/datePad.R |only openair-3.0.0/openair/R/facet_wd.R |only openair-3.0.0/openair/R/ggplot2-utils.R |only openair-3.0.0/openair/R/importADMS.R | 2461 +++--- openair-3.0.0/openair/R/importEurope.R | 435 - openair-3.0.0/openair/R/importImperial.R | 876 +- openair-3.0.0/openair/R/importMeta.R | 747 +- openair-3.0.0/openair/R/importTraj.R | 360 openair-3.0.0/openair/R/importUKAQ-utils.R | 1144 +-- openair-3.0.0/openair/R/importUKAQ.R | 1439 +-- openair-3.0.0/openair/R/layer_stroked_path.R |only openair-3.0.0/openair/R/layer_windflow.R |only openair-3.0.0/openair/R/modStats.R | 808 +- openair-3.0.0/openair/R/mydata.R | 62 openair-3.0.0/openair/R/openColours.R | 1190 +-- openair-3.0.0/openair/R/openair-package.R | 267 openair-3.0.0/openair/R/openair.generics.R | 74 openair-3.0.0/openair/R/percentileRose.R | 1277 +-- openair-3.0.0/openair/R/polarAnnulus.R | 1521 +--- openair-3.0.0/openair/R/polarCluster.R | 999 +- openair-3.0.0/openair/R/polarDiff.R | 401 - openair-3.0.0/openair/R/polarFreq.R | 948 +- openair-3.0.0/openair/R/polarPlot.R | 3559 ++++----- openair-3.0.0/openair/R/quickText.R | 438 - openair-3.0.0/openair/R/rollingMean.R | 276 openair-3.0.0/openair/R/rollingQuantile.R |only openair-3.0.0/openair/R/runRegression.R | 329 openair-3.0.0/openair/R/scatterPlot.R | 3715 ++++------ openair-3.0.0/openair/R/selectByDate.R | 359 openair-3.0.0/openair/R/selectRunning.R | 309 openair-3.0.0/openair/R/senTheil.R | 22 openair-3.0.0/openair/R/shared-docs.R |only openair-3.0.0/openair/R/smoothTrend.R | 1278 +-- openair-3.0.0/openair/R/splitByDate.R | 252 openair-3.0.0/openair/R/timeAverage.R | 1353 +-- openair-3.0.0/openair/R/timePlot.R | 1636 ++-- openair-3.0.0/openair/R/timeProp.R | 698 - openair-3.0.0/openair/R/timeVariation.R | 1924 +---- openair-3.0.0/openair/R/trajCluster.R | 587 - openair-3.0.0/openair/R/trajLevel.R | 1662 ++-- openair-3.0.0/openair/R/trajPlot.R | 771 -- openair-3.0.0/openair/R/trendLevel.R | 1313 +-- openair-3.0.0/openair/R/utilities.R | 1158 --- openair-3.0.0/openair/R/variationPlot.R |only openair-3.0.0/openair/R/windRose.R | 2225 +++-- openair-3.0.0/openair/R/windflowOpts.R |only openair-3.0.0/openair/README.md | 196 openair-3.0.0/openair/build/partial.rdb |binary openair-3.0.0/openair/inst/CITATION | 42 openair-3.0.0/openair/inst/WORDLIST | 1007 +- openair-3.0.0/openair/man/GaussianSmooth.Rd |only openair-3.0.0/openair/man/TaylorDiagram.Rd | 585 - openair-3.0.0/openair/man/TheilSen.Rd | 577 - openair-3.0.0/openair/man/WhittakerSmooth.Rd |only openair-3.0.0/openair/man/aqStats.Rd | 228 openair-3.0.0/openair/man/bootMeans.Rd | 179 openair-3.0.0/openair/man/calcPercentile.Rd | 242 openair-3.0.0/openair/man/calc_sqtba_cpp.Rd |only openair-3.0.0/openair/man/calendarPlot.Rd | 518 - openair-3.0.0/openair/man/conditionalEval.Rd | 359 openair-3.0.0/openair/man/conditionalQuantile.Rd | 374 - openair-3.0.0/openair/man/corPlot.Rd | 353 openair-3.0.0/openair/man/cutData.Rd | 318 openair-3.0.0/openair/man/datePad.Rd |only openair-3.0.0/openair/man/distAngle.Rd |only openair-3.0.0/openair/man/distEuclid.Rd |only openair-3.0.0/openair/man/figures/feature-banner.png |binary openair-3.0.0/openair/man/importADMS.Rd | 386 - openair-3.0.0/openair/man/importEurope.Rd | 124 openair-3.0.0/openair/man/importImperial.Rd | 392 - openair-3.0.0/openair/man/importMeta.Rd | 236 openair-3.0.0/openair/man/importTraj.Rd | 312 openair-3.0.0/openair/man/importUKAQ-wrapper.Rd | 506 - openair-3.0.0/openair/man/importUKAQ.Rd | 472 - openair-3.0.0/openair/man/modStats.Rd | 378 - openair-3.0.0/openair/man/mydata.Rd | 98 openair-3.0.0/openair/man/openColours.Rd | 252 openair-3.0.0/openair/man/openair-package.Rd | 249 openair-3.0.0/openair/man/percentileRose.Rd | 432 - openair-3.0.0/openair/man/polarAnnulus.Rd | 570 - openair-3.0.0/openair/man/polarCluster.Rd | 805 +- openair-3.0.0/openair/man/polarDiff.Rd | 615 - openair-3.0.0/openair/man/polarFreq.Rd | 503 - openair-3.0.0/openair/man/polarPlot.Rd | 948 +- openair-3.0.0/openair/man/pollutionRose.Rd | 464 - openair-3.0.0/openair/man/quickText.Rd | 104 openair-3.0.0/openair/man/rollingMean.Rd | 134 openair-3.0.0/openair/man/rollingQuantile.Rd |only openair-3.0.0/openair/man/rolling_gaussian_cpp.Rd |only openair-3.0.0/openair/man/runRegression.Rd | 145 openair-3.0.0/openair/man/scatterPlot.Rd | 736 - openair-3.0.0/openair/man/selectByDate.Rd | 145 openair-3.0.0/openair/man/selectRunning.Rd | 164 openair-3.0.0/openair/man/shared_openair_params.Rd |only openair-3.0.0/openair/man/smoothTrend.Rd | 498 - openair-3.0.0/openair/man/splitByDate.Rd | 142 openair-3.0.0/openair/man/timeAverage.Rd | 420 - openair-3.0.0/openair/man/timePlot.Rd | 679 - openair-3.0.0/openair/man/timeProp.Rd | 338 openair-3.0.0/openair/man/timeVariation.Rd | 647 - openair-3.0.0/openair/man/trajCluster.Rd | 308 openair-3.0.0/openair/man/trajLevel.Rd | 619 - openair-3.0.0/openair/man/trajPlot.Rd | 428 - openair-3.0.0/openair/man/trendLevel.Rd | 429 - openair-3.0.0/openair/man/variationPlot.Rd |only openair-3.0.0/openair/man/windRose.Rd | 548 - openair-3.0.0/openair/man/windflowOpts.Rd |only openair-3.0.0/openair/src/Gaus_smooth.cpp |only openair-3.0.0/openair/src/RcppExports.cpp |only openair-3.0.0/openair/src/cluster.cpp | 180 openair-3.0.0/openair/src/rolling.cpp | 258 openair-3.0.0/openair/src/sqtba.cpp |only openair-3.0.0/openair/src/time_average.cpp |only openair-3.0.0/openair/src/whittaker_baseline.cpp |only openair-3.0.0/openair/src/whittaker_gcv.cpp |only openair-3.0.0/openair/tests/testthat.R | 26 openair-3.0.0/openair/tests/testthat/test-GaussianSmooth.R |only openair-3.0.0/openair/tests/testthat/test-TaylorDiagram.R |only openair-3.0.0/openair/tests/testthat/test-TheilSen.R |only openair-3.0.0/openair/tests/testthat/test-WhittakerSmooth.R |only openair-3.0.0/openair/tests/testthat/test-aqStats.R | 203 openair-3.0.0/openair/tests/testthat/test-bootMeans.R |only openair-3.0.0/openair/tests/testthat/test-calcPercentile.R | 189 openair-3.0.0/openair/tests/testthat/test-calendarPlot.R |only openair-3.0.0/openair/tests/testthat/test-conditionalEval.R |only openair-3.0.0/openair/tests/testthat/test-conditionalQuantile.R |only openair-3.0.0/openair/tests/testthat/test-corPlot.R |only openair-3.0.0/openair/tests/testthat/test-cutData.R | 310 openair-3.0.0/openair/tests/testthat/test-datePad.R |only openair-3.0.0/openair/tests/testthat/test-modStats.R |only openair-3.0.0/openair/tests/testthat/test-openColours.R | 240 openair-3.0.0/openair/tests/testthat/test-percentileRose.R |only openair-3.0.0/openair/tests/testthat/test-polarAnnulus.R |only openair-3.0.0/openair/tests/testthat/test-polarCluster.R |only openair-3.0.0/openair/tests/testthat/test-polarDiff.R |only openair-3.0.0/openair/tests/testthat/test-polarFreq.R |only openair-3.0.0/openair/tests/testthat/test-polarPlot.R |only openair-3.0.0/openair/tests/testthat/test-rollingMean.R | 232 openair-3.0.0/openair/tests/testthat/test-rollingQuantile.R |only openair-3.0.0/openair/tests/testthat/test-scatterPlot.R |only openair-3.0.0/openair/tests/testthat/test-selectByDate.R |only openair-3.0.0/openair/tests/testthat/test-selectRunning.R | 239 openair-3.0.0/openair/tests/testthat/test-smoothTrend.R |only openair-3.0.0/openair/tests/testthat/test-splitByDate.R | 152 openair-3.0.0/openair/tests/testthat/test-timeAverage.R | 389 - openair-3.0.0/openair/tests/testthat/test-timePlot.R |only openair-3.0.0/openair/tests/testthat/test-timeProp.R |only openair-3.0.0/openair/tests/testthat/test-trajCluster.R |only openair-3.0.0/openair/tests/testthat/test-trajLevel.R |only openair-3.0.0/openair/tests/testthat/test-trajPlot.R |only openair-3.0.0/openair/tests/testthat/test-trendLevel.R |only openair-3.0.0/openair/tests/testthat/test-variationPlot.R |only openair-3.0.0/openair/tests/testthat/test-windRose.R |only 188 files changed, 38150 insertions(+), 40204 deletions(-)
Title: Download and Analyze Spatial Development Data from 'INKAR'
Description: A professional R interface to download and analyze spatial
development indicators from the 'BBSR' 'INKAR' (Indikatoren und Karten zur Raum-
und Stadtentwicklung) database. Features a bilingual interactive wizard,
fuzzy search, multi-indicator downloads with automatic tidy merging (long/wide),
robust disk caching, and premium 'ggplot2' themes for regional mapping.
Author: Omer Furkan Coban [aut, cre]
Maintainer: Omer Furkan Coban <oemer.furkan.coban@uni-oldenburg.de>
This is a re-admission after prior archival of version 0.6.1 dated 2026-03-17
Diff between inkaR versions 0.6.1 dated 2026-03-17 and 0.6.2 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 12 ++++++++++++ R/api.R | 16 ++++++++++++++-- 4 files changed, 32 insertions(+), 8 deletions(-)
Title: Estimating and Testing the Number of Interesting Components in
Linear Dimension Reduction
Description: For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.
Author: Klaus Nordhausen [aut, cre] ,
Hannu Oja [aut] ,
Katariina Perkonoja [aut] ,
David E. Tyler [aut],
Joni Virta [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICtest versions 0.3-6 dated 2025-05-27 and 0.3-7 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/components.R | 3 ++- inst/ChangeLog | 5 +++++ inst/doc/ICA.html | 8 ++++---- inst/doc/PCA.html | 10 +++++----- inst/doc/SIR.html | 10 +++++----- man/components.ictest.Rd | 11 +++++++---- src/Makevars | 2 +- src/Makevars.win | 3 +-- 11 files changed, 45 insertions(+), 37 deletions(-)
Title: Making "Deduplicated" Functions
Description: Contains one main function deduped() which speeds up slow,
vectorized functions by only performing computations on the unique values
of the input and expanding the results at the end.
Author: Or Gadish [aut, cre, cph]
Maintainer: Or Gadish <orgadish@gmail.com>
Diff between deduped versions 0.3.0 dated 2025-11-29 and 0.4.0 dated 2026-04-02
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 13 ++++++++ R/deduped.R | 42 ++++++++++++++++++++++------ README.md | 54 ++++++++++++++++++++++++++++++------- inst/WORDLIST | 1 man/deduped.Rd | 5 ++- tests/testthat/test-deduped.R | 39 ++++++++++++++++++++++++++ tests/testthat/test-with_deduped.R | 25 ++++++++++++++--- 9 files changed, 167 insertions(+), 38 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.4 dated 2025-09-26 and 1.3.0 dated 2026-04-02
rio-1.2.4/rio/po |only rio-1.2.4/rio/tests/testthat/test_format_qs.R |only rio-1.3.0/rio/DESCRIPTION | 10 - rio-1.3.0/rio/MD5 | 38 +++--- rio-1.3.0/rio/NAMESPACE | 2 rio-1.3.0/rio/NEWS.md | 12 ++ rio-1.3.0/rio/R/export.R | 5 rio-1.3.0/rio/R/export_methods.R | 8 - rio-1.3.0/rio/R/import.R | 5 rio-1.3.0/rio/R/import_methods.R | 6 - rio-1.3.0/rio/R/sysdata.rda |binary rio-1.3.0/rio/README.md | 142 ++++++++++++------------ rio-1.3.0/rio/build/vignette.rds |binary rio-1.3.0/rio/inst/doc/labelled.html | 4 rio-1.3.0/rio/inst/doc/philosophy.Rmd | 2 rio-1.3.0/rio/inst/doc/philosophy.html | 2 rio-1.3.0/rio/inst/doc/rio.html | 32 ++--- rio-1.3.0/rio/man/export.Rd | 5 rio-1.3.0/rio/man/import.Rd | 5 rio-1.3.0/rio/tests/testthat/test_import_list.R | 3 rio-1.3.0/rio/vignettes/philosophy.Rmd | 2 21 files changed, 130 insertions(+), 153 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: Provides a self-contained, static build of the 'HDF5'
(Hierarchical Data Format 5) 'C' library (release 2.1.1) for R
package developers. Designed for use in the 'LinkingTo' field,
it enables zero-dependency integration by building the library
entirely from source during installation. Additionally, it compiles
and internally links a comprehensive suite of advanced compression
filters and their 'HDF5' plugins (Zstd, LZ4, Blosc/Blosc2, Snappy,
ZFP, Bzip2, LZF, Bitshuffle, szip, and gzip). These plugins are
integrated out-of-the-box, allowing downstream packages to utilize
high-performance compression directly through the standard 'HDF5'
API while keeping the underlying third-party headers fully
encapsulated. 'HDF5' is developed by The HDF Group
<https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd],
The HDF Group [ctb, cph] ,
The Board of Trustees of the University of Illinois [cph] ,
Jean-loup Gailly [ctb, cph] ,
Mark Adler [ctb, cph] ,
Kiyoshi Masui [...truncated...]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.0.0.6 dated 2026-02-19 and 2.1.1.0 dated 2026-04-02
hdf5lib-2.0.0.6/hdf5lib/src/H5pubconf.h |only hdf5lib-2.0.0.6/hdf5lib/src/find_byte_widths.c |only hdf5lib-2.0.0.6/hdf5lib/src/hdf5-2.0.0.tar.gz |only hdf5lib-2.0.0.6/hdf5lib/src/zlib-1.3.1.tar.gz |only hdf5lib-2.0.0.6/hdf5lib/tests/src |only hdf5lib-2.0.0.6/hdf5lib/tests/testthat |only hdf5lib-2.0.0.6/hdf5lib/tests/testthat.r |only hdf5lib-2.1.1.0/hdf5lib/DESCRIPTION | 79 +++- hdf5lib-2.1.1.0/hdf5lib/LICENSE | 2 hdf5lib-2.1.1.0/hdf5lib/MD5 | 105 +++++- hdf5lib-2.1.1.0/hdf5lib/NEWS.md | 8 hdf5lib-2.1.1.0/hdf5lib/R/flags.r | 52 +- hdf5lib-2.1.1.0/hdf5lib/README.md | 86 ++-- hdf5lib-2.1.1.0/hdf5lib/configure | 434 ++++++++++++++++++++----- hdf5lib-2.1.1.0/hdf5lib/inst/COPYRIGHTS | 310 +++++++++++++++++ hdf5lib-2.1.1.0/hdf5lib/man/figures/logo.png |binary hdf5lib-2.1.1.0/hdf5lib/src/config |only hdf5lib-2.1.1.0/hdf5lib/src/dummy.c |only hdf5lib-2.1.1.0/hdf5lib/src/filters |only hdf5lib-2.1.1.0/hdf5lib/src/hdf5-2.1.0.tar.gz |only hdf5lib-2.1.1.0/hdf5lib/src/hdf5-2.1.1.tar.gz |only hdf5lib-2.1.1.0/hdf5lib/src/install.libs.R |only hdf5lib-2.1.1.0/hdf5lib/src/lib |only hdf5lib-2.1.1.0/hdf5lib/src/patches |only hdf5lib-2.1.1.0/hdf5lib/src/plugins |only hdf5lib-2.1.1.0/hdf5lib/tests/Makevars |only hdf5lib-2.1.1.0/hdf5lib/tests/interop |only hdf5lib-2.1.1.0/hdf5lib/tests/smoke_test.c |only hdf5lib-2.1.1.0/hdf5lib/tests/test-flags.r |only hdf5lib-2.1.1.0/hdf5lib/tests/test-hdf5.r |only 30 files changed, 885 insertions(+), 191 deletions(-)
Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, MDS maps and biplots obtained by PCA, PFA or WALS (weighted alternating least squares); See Graffelman & De Leeuw (2023) <doi: 10.1080/00031305.2023.2186952>.
Author: Jan Graffelman [aut, cre],
Jan De Leeuw [aut]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between Correlplot versions 1.1.2 dated 2025-07-25 and 1.1.3 dated 2026-04-02
DESCRIPTION | 8 MD5 | 48 ++- NAMESPACE | 4 R/FitAllModelsRxy.R |only R/FitRxy.R |only R/LastFunctions.R |only R/genloss.R |only R/ggbplot.R | 132 ++++++---- R/ggtally.R | 139 ++++++++-- R/rmse.rxy.R |only data/achievement.rda |only inst/doc/CorrelplotManual.R | 288 ++++++++++++++++++++-- inst/doc/CorrelplotManual.Rmd | 357 +++++++++++++++++++++++++-- inst/doc/CorrelplotManual.html | 526 +++++++++++++++++++++++++++++++++-------- man/FitAllModelsRxy.Rd |only man/FitRDeltaQSym.Rd | 3 man/FitRwithPCAandWALS.Rd | 4 man/FitRxy.Rd |only man/Keller.Rd | 2 man/achievement.Rd |only man/ggbplot.Rd | 42 +-- man/ggtally.Rd | 37 ++ man/ipSymLS.Rd | 2 man/rmse.Rd | 3 man/rmse.rxy.Rd |only man/rmsePCAandWALS.Rd | 2 man/tally.Rd | 4 man/wAddPCA.Rd | 2 vignettes/Correlplot.bib | 13 - vignettes/CorrelplotManual.Rmd | 357 +++++++++++++++++++++++++-- 30 files changed, 1651 insertions(+), 322 deletions(-)
Title: Design-Based Causal Inference Method for Incomplete Block
Designs
Description: This R package implements methods for estimation and inference under Incomplete Block Designs and Balanced Incomplete Block Designs within a design-based finite-population framework. Based on 'Koo and Pashley' (2026) <doi:10.1093/biomet/asag013>, it includes block-level estimators and extends to unit-level effects using 'Horvitz-Thompson' and 'Hájek' estimators. The package also provides asymptotic confidence intervals to support valid statistical inference.
Author: Taehyeon Koo [aut, cre],
Nicole Pashley [ctb]
Maintainer: Taehyeon Koo <tk3077@cumc.columbia.edu>
Diff between IBDInfer versions 0.0.1 dated 2025-04-16 and 0.1.0 dated 2026-04-01
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/IBDInfer.R | 44 ++++++++++++++++++++++++++++++++++---------- 3 files changed, 42 insertions(+), 18 deletions(-)
Title: R Wrappers for EXPOKIT; Other Matrix Functions
Description: Wraps some of the matrix exponentiation
utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>),
a FORTRAN library that is widely recommended for matrix
exponentiation (Sidje RB, 1998. "Expokit: A Software Package
for Computing Matrix Exponentials." ACM Trans. Math. Softw.
24(1): 130-156). EXPOKIT includes functions for
exponentiating both small, dense matrices, and large, sparse
matrices (in sparse matrices, most of the cells have value 0).
Rapid matrix exponentiation is useful in phylogenetics when we
have a large number of states (as we do when we are inferring
the history of transitions between the possible geographic
ranges of a species), but is probably useful in other ways as
well. NOTE: In case FORTRAN checks temporarily get rexpokit
archived on CRAN, see archived binaries at GitHub in:
nmatzke/Matzke_R_binaries (binaries install without compilation
of source code).
Author: Nicholas J. Matzke [aut, cre, cph],
Roger B. Sidje [aut, cph],
Drew Schmidt [aut]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>
This is a re-admission after prior archival of version 0.26.6.14 dated 2023-11-22
Diff between rexpokit versions 0.26.6.14 dated 2023-11-22 and 0.26.6.15 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 3 ++- NEWS | 22 ++++++++++++++++++++++ R/expm.r | 2 +- R/rexpokit-package.R | 4 ++-- build/partial.rdb |binary demo/expm.r | 2 +- demo/expm_check.r | 2 +- man/00_rexpokit-package.Rd | 7 ++----- man/01_expm.Rd | 14 ++++++-------- tests/expm.R | 8 ++++---- 12 files changed, 57 insertions(+), 39 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [aut]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.1.0 dated 2026-02-13 and 0.2.0 dated 2026-04-01
MFF-0.1.0/MFF/man/dot-weight_kmeans.Rd |only MFF-0.2.0/MFF/DESCRIPTION | 11 +- MFF-0.2.0/MFF/MD5 | 25 ++--- MFF-0.2.0/MFF/NAMESPACE | 9 + MFF-0.2.0/MFF/R/MFF-package.R | 27 +++-- MFF-0.2.0/MFF/R/boot.train.R |only MFF-0.2.0/MFF/R/evaluate.R | 2 MFF-0.2.0/MFF/R/mff.R | 80 ++++++++++++++--- MFF-0.2.0/MFF/R/tune.mff.R | 153 +++++++++++++++++---------------- MFF-0.2.0/MFF/R/utils-clustering.R | 1 MFF-0.2.0/MFF/man/MFF-package.Rd | 24 +++-- MFF-0.2.0/MFF/man/boot.train.Rd |only MFF-0.2.0/MFF/man/evaluate.Rd | 2 MFF-0.2.0/MFF/man/mff.Rd | 30 ++++-- MFF-0.2.0/MFF/man/tune.mff.Rd | 20 +++- 15 files changed, 252 insertions(+), 132 deletions(-)
Title: Ensemble Models for Lactation Curves
Description: Lactation curves describe temporal changes in milk yield and are key to breeding and managing dairy animals more efficiently. The use of ensemble modeling, which consists of combining predictions from multiple models, has the potential to yields more accurate and robust estimates of lactation patterns than relying solely on single model estimates. The package EMOTIONS fits 47 models for lactation curves and creates ensemble models using model averaging based on Akaike information criterion (AIC), Bayesian information criterion (BIC), root mean square percentage error (RMSPE) and mean squared error (MAE), variance of the predictions, cosine similarity for each model's predictions, and Bayesian Model Average (BMA). The daily production values predicted through the ensemble models can be used to estimate resilience indicators in the package. The package allows the graphical visualization of the model ranks and the predicted lactation curves. Additionally, the packages allows the user to d [...truncated...]
Author: Pablo Fonseca [aut, cre],
Marcos Prates [aut],
Aroa Suarez-Vega [aut],
Ruth Arribas Gonzalo [aut],
Beatriz Gutierrez-Gil [aut],
Juan Jose Arranz [aut]
Maintainer: Pablo Fonseca <p.fonseca@csic.es>
Diff between EMOTIONS versions 1.2 dated 2026-03-27 and 1.3 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 6 ++---- R/PlotMilkLoss.R | 46 +++++++++++++++++++++++++++++++++++++--------- R/global_variables.R | 2 +- inst/doc/EMOTIONS.html | 6 +++--- 7 files changed, 53 insertions(+), 26 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
This is a re-admission after prior archival of version 1.5.2 dated 2024-02-26
Diff between conos versions 1.5.2 dated 2024-02-26 and 1.5.3 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 2 +- src/Makevars | 2 +- src/Makevars.win | 2 +- tests/testthat/test_functions.R | 28 ++++++++++++++++++++++++++-- 6 files changed, 37 insertions(+), 13 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between RTMBdist versions 1.0.2 dated 2026-03-16 and 1.0.3 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 6 ++++++ R/aaa_utils.R | 9 +++++---- R/skewt.R | 12 ++++++------ R/skewt2.R | 4 ++-- R/zibeta.R | 2 +- R/zibinom.R | 2 +- R/zigamma.R | 3 +-- R/ziinvgauss.R | 2 +- R/zilnorm.R | 2 +- R/zipois.R | 2 +- R/ziweibull.R |only R/zoibeta.R | 8 ++++++-- build/vignette.rds |binary inst/doc/Examples.html | 10 +++++----- inst/doc/distlist.Rmd | 10 ++++++---- inst/doc/distlist.html | 15 +++++++++------ man/ziweibull.Rd |only vignettes/distlist.Rmd | 10 ++++++---- 20 files changed, 81 insertions(+), 62 deletions(-)
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Mans Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adiguezel [ctb],
Jacob Socolar [ctb],
Noa Kallioinen [ctb],
Teemu Saeilynoja [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.6.1 dated 2025-02-27 and 1.7.0 dated 2026-04-01
posterior-1.6.1/posterior/man/figures/stanlogo.png |only posterior-1.7.0/posterior/DESCRIPTION | 21 - posterior-1.7.0/posterior/MD5 | 96 +++--- posterior-1.7.0/posterior/NAMESPACE | 19 + posterior-1.7.0/posterior/NEWS.md | 17 + posterior-1.7.0/posterior/R/extract_list_of_variable_arrays.R |only posterior-1.7.0/posterior/R/extract_variable_array.R | 39 ++ posterior-1.7.0/posterior/R/gpd.R | 141 +++++++-- posterior-1.7.0/posterior/R/misc.R | 28 + posterior-1.7.0/posterior/R/pareto_smooth.R | 152 +++++----- posterior-1.7.0/posterior/R/pit.R |only posterior-1.7.0/posterior/R/posterior-package.R | 2 posterior-1.7.0/posterior/R/rvar-.R | 1 posterior-1.7.0/posterior/R/rvar-print.R | 2 posterior-1.7.0/posterior/R/rvar-slice.R | 2 posterior-1.7.0/posterior/R/subset_draws.R | 12 posterior-1.7.0/posterior/R/uniformity_test.R |only posterior-1.7.0/posterior/R/weight_draws.R | 3 posterior-1.7.0/posterior/README.md | 98 +++--- posterior-1.7.0/posterior/build/partial.rdb |binary posterior-1.7.0/posterior/build/vignette.rds |binary posterior-1.7.0/posterior/inst/doc/pareto_diagnostics.html | 43 +- posterior-1.7.0/posterior/inst/doc/posterior.R | 12 posterior-1.7.0/posterior/inst/doc/posterior.html | 3 posterior-1.7.0/posterior/inst/doc/rvar.R | 2 posterior-1.7.0/posterior/inst/doc/rvar.html | 16 - posterior-1.7.0/posterior/man/extract_list_of_variable_arrays.Rd |only posterior-1.7.0/posterior/man/extract_variable.Rd | 8 posterior-1.7.0/posterior/man/extract_variable_array.Rd | 19 - posterior-1.7.0/posterior/man/extract_variable_matrix.Rd | 8 posterior-1.7.0/posterior/man/figures/logo.svg | 97 ------ posterior-1.7.0/posterior/man/gpdfit.Rd |only posterior-1.7.0/posterior/man/is_constant.Rd |only posterior-1.7.0/posterior/man/pareto_pit.Rd |only posterior-1.7.0/posterior/man/pgeneralized_pareto.Rd |only posterior-1.7.0/posterior/man/pit.Rd |only posterior-1.7.0/posterior/man/posterior-package.Rd | 5 posterior-1.7.0/posterior/man/print.rvar.Rd | 2 posterior-1.7.0/posterior/man/ps_convergence_rate.Rd | 1 posterior-1.7.0/posterior/man/ps_khat_threshold.Rd | 1 posterior-1.7.0/posterior/man/ps_min_ss.Rd | 1 posterior-1.7.0/posterior/man/ps_tail.Rd |only posterior-1.7.0/posterior/man/ps_tail_length.Rd | 1 posterior-1.7.0/posterior/man/qgeneralized_pareto.Rd |only posterior-1.7.0/posterior/man/rvar-slice.Rd | 2 posterior-1.7.0/posterior/man/subset_draws.Rd | 4 posterior-1.7.0/posterior/man/uniformity_test.Rd |only posterior-1.7.0/posterior/tests/testthat/test-draws-index.R | 5 posterior-1.7.0/posterior/tests/testthat/test-extract_list_of_variable_arrays.R |only posterior-1.7.0/posterior/tests/testthat/test-extract_variable_array.R | 130 +++++++- posterior-1.7.0/posterior/tests/testthat/test-gpd-distributions.R |only posterior-1.7.0/posterior/tests/testthat/test-gpdfit.R |only posterior-1.7.0/posterior/tests/testthat/test-log_sum_exp.R |only posterior-1.7.0/posterior/tests/testthat/test-pareto_pit.R |only posterior-1.7.0/posterior/tests/testthat/test-pareto_smooth.R | 61 +++- posterior-1.7.0/posterior/tests/testthat/test-pit.R |only posterior-1.7.0/posterior/tests/testthat/test-rvar-.R | 5 posterior-1.7.0/posterior/tests/testthat/test-subset_draws.R | 97 ++++++ posterior-1.7.0/posterior/tests/testthat/test-uniformity_test.R |only 59 files changed, 787 insertions(+), 369 deletions(-)
Title: Lagged Cross-Correlation Analysis of Environmental Time Series
Description: Tools for analysing lagged relationships between environmental variables and ecological or epidemiological time series. The package implements a workflow to aggregate meteorological data over multiple lagged intervals, fit regression models, including mixed-effect models using 'glmmTMB', for each lag window, and visualise varied models outcomes (effect strength and direction, model prediction error...) using cross-correlation maps ('CCM').
Author: Nicolas Moiroux [aut, cre] ,
Colombine Bartholomee [aut] ,
Paul Taconet [aut]
Maintainer: Nicolas Moiroux <nicolas.moiroux@ird.fr>
Diff between ecoXCorr versions 0.1.9 dated 2026-03-24 and 0.2.1 dated 2026-04-01
DESCRIPTION | 6 MD5 | 18 - NEWS.md |only R/funs.R | 284 +++++++++++++---------- README.md | 217 +++++++++++++---- build/partial.rdb |binary inst/CITATION | 2 man/aggregate_lagged_intervals.Rd | 25 +- man/ecoXCorr.Rd | 4 man/plotCCM.Rd | 8 tests/testthat/test-aggregate_lagged_intervals.R |only 11 files changed, 381 insertions(+), 183 deletions(-)
Title: Parse 'User-Agent' Strings
Description: Despite there being a section in RFC 7231
<https://datatracker.ietf.org/doc/html/rfc7231#section-5.5.3> defining a suggested
structure for 'User-Agent' headers this data is notoriously difficult
to parse consistently. Tools are provided that will take in user agent
strings and return structured R objects. This is a 'V8'-backed package
based on the 'ua-parser' project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.3.6 dated 2026-03-23 and 0.3.7 dated 2026-04-01
uaparserjs-0.3.6/uaparserjs/inst/js/bld |only uaparserjs-0.3.6/uaparserjs/inst/js/index.js |only uaparserjs-0.3.6/uaparserjs/inst/js/newbuild |only uaparserjs-0.3.7/uaparserjs/DESCRIPTION | 18 +++--- uaparserjs-0.3.7/uaparserjs/LICENSE | 4 - uaparserjs-0.3.7/uaparserjs/MD5 | 31 ++++++------ uaparserjs-0.3.7/uaparserjs/NEWS.md | 9 +++ uaparserjs-0.3.7/uaparserjs/R/uaparser.R | 21 +++++++- uaparserjs-0.3.7/uaparserjs/R/uaparserjs-package.R | 22 +++++++- uaparserjs-0.3.7/uaparserjs/R/utils-mappers.R | 17 +++++- uaparserjs-0.3.7/uaparserjs/R/zzz.r | 14 +++++ uaparserjs-0.3.7/uaparserjs/inst/js/bundle.js | 9 --- uaparserjs-0.3.7/uaparserjs/inst/tinytest/test_exhaustive.R |only uaparserjs-0.3.7/uaparserjs/inst/tinytest/test_uaparserjs.R | 15 +++++ uaparserjs-0.3.7/uaparserjs/inst/tinytest/tests |only uaparserjs-0.3.7/uaparserjs/man/ua_parse.Rd | 4 - uaparserjs-0.3.7/uaparserjs/man/uaparserjs.Rd | 14 +++++ uaparserjs-0.3.7/uaparserjs/tests/tinytest.R | 14 +++++ 18 files changed, 147 insertions(+), 45 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can
check if a background process is running; wait on a background process
to finish; get the exit status of finished processes; kill background
processes. It can read the standard output and error of the processes,
using non-blocking connections. 'processx' can poll a process for
standard output or error, with a timeout. It can also poll several
processes at once.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
Posit Software, PBC [cph, fnd] ,
Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between processx versions 3.8.6 dated 2025-02-21 and 3.8.7 dated 2026-04-01
DESCRIPTION | 17 - LICENSE | 2 MD5 | 141 +++++---- NEWS.md | 4 R/aaa-import-standalone-rstudio-detect.R | 78 ++--- R/aaassertthat.R | 39 +- R/assertions.R | 21 - R/base64.R | 1 R/cleancall.R | 1 R/client-lib.R | 20 - R/connections.R | 112 +++++-- R/initialize.R | 97 ++++-- R/io.R | 37 +- R/named_pipe.R | 12 R/on-load.R | 11 R/poll.R | 4 R/print.R | 6 R/process-helpers.R | 1 R/process.R | 343 ++++++++++++------------ R/run.R | 273 ++++++++++++++----- R/standalone-errors.R | 414 +++++++++++++++++++---------- R/supervisor.R | 49 +-- R/utils.R | 87 +++--- README.md | 21 - man/process.Rd | 31 +- src/cleancall.c | 6 src/init.c | 2 src/install.libs.R | 10 tests/testthat.R | 8 tests/testthat/_snaps/Darwin |only tests/testthat/_snaps/Linux |only tests/testthat/_snaps/Windows |only tests/testthat/_snaps/assertions.md |only tests/testthat/_snaps/fifo.md |only tests/testthat/_snaps/io.md |only tests/testthat/_snaps/process.md |only tests/testthat/_snaps/pty.md |only tests/testthat/_snaps/standalone-errors.md | 36 +- tests/testthat/_snaps/unix-sockets.md |only tests/testthat/_snaps/utils.md |only tests/testthat/helper.R | 92 +++++- tests/testthat/test-assertions.R | 62 ++-- tests/testthat/test-chr-io.R | 4 tests/testthat/test-cleanup.R | 3 tests/testthat/test-client-lib.R | 31 +- tests/testthat/test-connections.R | 27 - tests/testthat/test-env.R | 7 tests/testthat/test-err-output.R | 66 +++- tests/testthat/test-errors.R | 31 +- tests/testthat/test-extra-connections.R | 34 +- tests/testthat/test-fifo.R | 24 + tests/testthat/test-io.R | 47 +-- tests/testthat/test-kill-tree.R | 91 ++++-- tests/testthat/test-poll-connections.R | 12 tests/testthat/test-poll-curl.R | 65 +++- tests/testthat/test-poll-stress.R | 11 tests/testthat/test-poll.R | 92 ++++-- tests/testthat/test-poll2.R | 29 +- tests/testthat/test-poll3.R | 56 ++- tests/testthat/test-print.R | 2 tests/testthat/test-process.R | 40 ++ tests/testthat/test-ps-methods.R | 9 tests/testthat/test-pty.R | 34 +- tests/testthat/test-run.R | 53 ++- tests/testthat/test-set-std.R | 16 - tests/testthat/test-sigchld.R | 33 +- tests/testthat/test-standalone-errors.R | 199 ++++--------- tests/testthat/test-stdin.R | 6 tests/testthat/test-stress.R | 12 tests/testthat/test-unix-sockets.R | 62 +++- tests/testthat/test-utf8.R | 5 tests/testthat/test-utils.R | 31 +- tests/testthat/test-wait.R | 18 - tools |only 74 files changed, 1953 insertions(+), 1235 deletions(-)
Title: Download Data from the FAOSTAT Database
Description: Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations.
A list of functions to download statistics from FAOSTAT (database of the FAO <https://www.fao.org/faostat/>)
and WDI (database of the World Bank <https://data.worldbank.org/>), and to perform some harmonization operations.
Author: Michael C. J. [aut],
Markus Gesmann [aut],
Filippo Gheri [aut],
Paul Rougieux [aut, cre],
Sebastian Campbell [aut]
Maintainer: Paul Rougieux <paul.rougieux@gmail.com>
Diff between FAOSTAT versions 2.4.0 dated 2024-05-22 and 2.4.2 dated 2026-04-01
DESCRIPTION | 34 +++++- MD5 | 31 +++-- NAMESPACE | 3 R/faostat_bulk_download.R | 110 ++++++++++++++------- R/read_fao.R | 2 R/rest.R | 88 ++++++++++++++++ R/utils.R | 4 build/vignette.rds |binary data/FAOregionProfile.RData |binary inst/doc/FAOSTAT.R | 224 ++++++++++++++++++++++--------------------- inst/doc/FAOSTAT.Rnw | 58 ++++++++--- inst/doc/FAOSTAT.pdf |binary man/FAOSTAT-package.Rd | 12 ++ man/change_case.Rd | 4 man/download_faostat_bulk.Rd | 46 ++++++-- man/faostat_login.Rd |only vignettes/FAOSTAT.Rnw | 58 ++++++++--- 17 files changed, 463 insertions(+), 211 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <stuartt@a-star.edu.sg>
Diff between Signac versions 1.16.0 dated 2025-10-10 and 1.17.0 dated 2026-04-01
Signac-1.16.0/Signac/man/AddChromatinModule.Rd |only Signac-1.16.0/Signac/man/RunChromVAR.Rd |only Signac-1.17.0/Signac/DESCRIPTION | 29 Signac-1.17.0/Signac/MD5 | 262 ++-- Signac-1.17.0/Signac/NAMESPACE | 36 Signac-1.17.0/Signac/NEWS.md | 35 Signac-1.17.0/Signac/R/Signac-package.R |only Signac-1.17.0/Signac/R/data.R | 61 Signac-1.17.0/Signac/R/dimension_reduction.R | 93 - Signac-1.17.0/Signac/R/footprinting.R | 12 Signac-1.17.0/Signac/R/fragments.R | 40 Signac-1.17.0/Signac/R/generics.R | 161 +- Signac-1.17.0/Signac/R/genomeinfodb-methods.R | 12 Signac-1.17.0/Signac/R/granges-methods.R | 14 Signac-1.17.0/Signac/R/heatmaps.R | 4 Signac-1.17.0/Signac/R/iranges-methods.R | 78 - Signac-1.17.0/Signac/R/links.R | 22 Signac-1.17.0/Signac/R/mito.R | 14 Signac-1.17.0/Signac/R/motifs.R | 144 -- Signac-1.17.0/Signac/R/objects.R | 74 - Signac-1.17.0/Signac/R/ontology.R |only Signac-1.17.0/Signac/R/peaks.R | 22 Signac-1.17.0/Signac/R/preprocessing.R | 770 +++++++++++- Signac-1.17.0/Signac/R/quantification.R | 24 Signac-1.17.0/Signac/R/region-enrichment.R | 7 Signac-1.17.0/Signac/R/utilities.R | 129 -- Signac-1.17.0/Signac/R/visualization.R | 103 - Signac-1.17.0/Signac/README.md | 12 Signac-1.17.0/Signac/data/blacklist_ce10.rda |binary Signac-1.17.0/Signac/data/blacklist_ce11.rda |binary Signac-1.17.0/Signac/data/blacklist_dm3.rda |binary Signac-1.17.0/Signac/data/blacklist_dm6.rda |binary Signac-1.17.0/Signac/data/blacklist_hg19.rda |binary Signac-1.17.0/Signac/data/blacklist_hg38.rda |binary Signac-1.17.0/Signac/data/blacklist_hg38_unified.rda |binary Signac-1.17.0/Signac/data/blacklist_mm10.rda |binary Signac-1.17.0/Signac/man/ATACqc.Rd |only Signac-1.17.0/Signac/man/AddMotifs.Rd | 6 Signac-1.17.0/Signac/man/AggregateTiles.Rd | 4 Signac-1.17.0/Signac/man/AlleleFreq.Rd | 2 Signac-1.17.0/Signac/man/Annotation.Rd | 4 Signac-1.17.0/Signac/man/AnnotationPlot.Rd | 4 Signac-1.17.0/Signac/man/BigwigTrack.Rd | 2 Signac-1.17.0/Signac/man/BinarizeCounts.Rd | 4 Signac-1.17.0/Signac/man/CallPeaks.Rd | 8 Signac-1.17.0/Signac/man/Cells.Rd | 8 Signac-1.17.0/Signac/man/ChromatinAssay-class.Rd | 24 Signac-1.17.0/Signac/man/ClosestFeature.Rd | 4 Signac-1.17.0/Signac/man/ClusterClonotypes.Rd | 2 Signac-1.17.0/Signac/man/ConnectionsToLinks.Rd | 2 Signac-1.17.0/Signac/man/CountFragments.Rd | 10 Signac-1.17.0/Signac/man/CountsInRegion.Rd | 4 Signac-1.17.0/Signac/man/CoverageBrowser.Rd | 6 Signac-1.17.0/Signac/man/CoveragePlot.Rd | 8 Signac-1.17.0/Signac/man/CreateChromatinAssay.Rd | 26 Signac-1.17.0/Signac/man/CreateMotifMatrix.Rd | 8 Signac-1.17.0/Signac/man/CreateMotifObject.Rd | 6 Signac-1.17.0/Signac/man/DepthCor.Rd | 6 Signac-1.17.0/Signac/man/DownsampleFeatures.Rd | 4 Signac-1.17.0/Signac/man/EnrichedTerms.Rd |only Signac-1.17.0/Signac/man/Extend.Rd | 2 Signac-1.17.0/Signac/man/FRiP.Rd | 6 Signac-1.17.0/Signac/man/FeatureMatrix.Rd | 6 Signac-1.17.0/Signac/man/FindClonotypes.Rd | 8 Signac-1.17.0/Signac/man/FindMotifs.Rd | 6 Signac-1.17.0/Signac/man/FindTopFeatures.Rd | 10 Signac-1.17.0/Signac/man/FitMeanVar.Rd |only Signac-1.17.0/Signac/man/Footprint.Rd | 2 Signac-1.17.0/Signac/man/FractionCountsInRegion.Rd | 4 Signac-1.17.0/Signac/man/Fragment-class.Rd | 2 Signac-1.17.0/Signac/man/FragmentHistogram.Rd | 2 Signac-1.17.0/Signac/man/Fragments.Rd | 4 Signac-1.17.0/Signac/man/GRangesToString.Rd | 3 Signac-1.17.0/Signac/man/GenomeBinMatrix.Rd | 6 Signac-1.17.0/Signac/man/GetFootprintData.Rd | 14 Signac-1.17.0/Signac/man/GetFragmentData.Rd | 4 Signac-1.17.0/Signac/man/GetGRangesFromEnsDb.Rd | 2 Signac-1.17.0/Signac/man/GetIntersectingFeatures.Rd | 4 Signac-1.17.0/Signac/man/GetMotifData.Rd | 2 Signac-1.17.0/Signac/man/InsertionBias.Rd | 2 Signac-1.17.0/Signac/man/IntersectMatrix.Rd | 4 Signac-1.17.0/Signac/man/LinkPeaks.Rd | 16 Signac-1.17.0/Signac/man/LinkPlot.Rd | 4 Signac-1.17.0/Signac/man/Links.Rd | 2 Signac-1.17.0/Signac/man/MatchRegionStats.Rd | 4 Signac-1.17.0/Signac/man/Motif-class.Rd | 2 Signac-1.17.0/Signac/man/MotifCounts.Rd | 6 Signac-1.17.0/Signac/man/MotifPlot.Rd | 4 Signac-1.17.0/Signac/man/Motifs.Rd | 2 Signac-1.17.0/Signac/man/NucleosomeSignal.Rd | 4 Signac-1.17.0/Signac/man/PeakPlot.Rd | 6 Signac-1.17.0/Signac/man/PearsonResidualVar.Rd |only Signac-1.17.0/Signac/man/RegionHeatmap.Rd | 10 Signac-1.17.0/Signac/man/RegionMatrix.Rd | 4 Signac-1.17.0/Signac/man/RegionPlot.Rd | 8 Signac-1.17.0/Signac/man/RegionStats.Rd | 4 Signac-1.17.0/Signac/man/RunSVD.Rd | 43 Signac-1.17.0/Signac/man/RunTFIDF.Rd | 26 Signac-1.17.0/Signac/man/SetMotifData.Rd | 2 Signac-1.17.0/Signac/man/Signac-package.Rd | 16 Signac-1.17.0/Signac/man/SortIdents.Rd | 6 Signac-1.17.0/Signac/man/StringToGRanges.Rd | 5 Signac-1.17.0/Signac/man/TSSEnrichment.Rd | 4 Signac-1.17.0/Signac/man/TSSPlot.Rd | 9 Signac-1.17.0/Signac/man/TilePlot.Rd | 2 Signac-1.17.0/Signac/man/UnifyPeaks.Rd | 8 Signac-1.17.0/Signac/man/UpdatePath.Rd | 4 Signac-1.17.0/Signac/man/ValidateCells.Rd | 4 Signac-1.17.0/Signac/man/ValidateFragments.Rd | 4 Signac-1.17.0/Signac/man/ValidateHash.Rd | 2 Signac-1.17.0/Signac/man/VariantPlot.Rd | 2 Signac-1.17.0/Signac/man/as.ChromatinAssay.Rd | 16 Signac-1.17.0/Signac/man/atac_small.Rd | 8 Signac-1.17.0/Signac/man/blacklist_ce10.Rd | 3 Signac-1.17.0/Signac/man/blacklist_ce11.Rd | 3 Signac-1.17.0/Signac/man/blacklist_dm3.Rd | 3 Signac-1.17.0/Signac/man/blacklist_dm6.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg19.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg38.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg38_unified.Rd | 4 Signac-1.17.0/Signac/man/blacklist_mm10.Rd | 3 Signac-1.17.0/Signac/man/corSparse.Rd | 2 Signac-1.17.0/Signac/man/coverage-ChromatinAssay-method.Rd | 22 Signac-1.17.0/Signac/man/figures/lifecycle-deprecated.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-experimental.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-stable.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-superseded.svg |only Signac-1.17.0/Signac/man/findOverlaps-methods.Rd | 22 Signac-1.17.0/Signac/man/granges-methods.Rd | 16 Signac-1.17.0/Signac/man/head.Fragment.Rd | 2 Signac-1.17.0/Signac/man/inter-range-methods.Rd | 22 Signac-1.17.0/Signac/man/nearest-methods.Rd | 24 Signac-1.17.0/Signac/man/seqinfo-methods.Rd | 12 Signac-1.17.0/Signac/man/subset.Fragment.Rd | 6 Signac-1.17.0/Signac/man/subset.Motif.Rd | 6 Signac-1.17.0/Signac/man/theme_browser.Rd | 2 Signac-1.17.0/Signac/tests/testthat/test-dimreduc.R | 4 Signac-1.17.0/Signac/tests/testthat/test-preprocessing.R | 2 138 files changed, 1777 insertions(+), 1030 deletions(-)
Title: Convert Gene IDs Between Each Other and Fetch Annotations from
Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but
that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function
in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the
'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes"
can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol()
attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre],
Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Diff between convertid versions 0.2.1 dated 2026-02-05 and 0.3.0 dated 2026-04-01
convertid-0.2.1/convertid/R/get_symbol_aliases.R |only convertid-0.3.0/convertid/DESCRIPTION | 13 +++--- convertid-0.3.0/convertid/MD5 | 19 ++++++--- convertid-0.3.0/convertid/NAMESPACE | 1 convertid-0.3.0/convertid/R/convertId2.R | 6 ++- convertid-0.3.0/convertid/R/likely_symbol.R |only convertid-0.3.0/convertid/R/unify_gene_ids.R |only convertid-0.3.0/convertid/man/convert.bm.Rd | 3 + convertid-0.3.0/convertid/man/likely_symbol.Rd | 46 ++++++++++++++++++++--- convertid-0.3.0/convertid/man/unify_gene_ids.Rd |only convertid-0.3.0/convertid/tests |only 11 files changed, 68 insertions(+), 20 deletions(-)
Title: Classify Names by Gender, U.S. Ethnicity, and Leaf Nationality
Description: Functions to use the 'NamePrism' API <https://www.name-prism.com/api> or 'NamSor' API v2 <https://namsor.app/> for classifying names based on gender, 6 U.S. ethnicities, or 39 leaf nationalities. Updated to work with current API endpoints.
Author: Charles Crabtree [aut, cre],
Volha Chykina [aut],
Micah Gell-Redman [aut],
Christian Chacua [aut]
Maintainer: Charles Crabtree <charles.crabtree@monash.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2017-11-04
Diff between nomine versions 1.0.0 dated 2017-11-04 and 1.0.2 dated 2026-04-01
DESCRIPTION | 27 ++++---- LICENSE | 4 - MD5 | 18 ++--- R/ethnicites.R | 56 +++++++++++++----- R/gender.r | 26 ++++---- R/nationalities.r | 95 +++++++++++++++++-------------- README.md | 143 ++++++++++++++++++++++++++++++++++++++++++----- man/get_ethnicities.Rd | 30 +++++++-- man/get_gender.Rd | 20 +++--- man/get_nationalities.Rd | 28 +++++++-- 10 files changed, 315 insertions(+), 132 deletions(-)
Title: A Multi-Modal Simulator for Spearheading Single-Cell Omics
Analyses
Description: A novel, multi-modal simulation engine for
studying dynamic cellular processes at single-cell resolution. 'dyngen'
is more flexible than current single-cell simulation engines. It
allows better method development and benchmarking, thereby stimulating
development and testing of novel computational methods. Cannoodt et
al. (2021) <doi:10.1038/s41467-021-24152-2>.
Author: Robrecht Cannoodt [aut, cre, cph] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dyngen versions 1.1.0 dated 2026-03-17 and 1.1.1 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/8_convert.R | 12 ++++++++---- build/vignette.rds |binary man/convert.Rd | 12 ++++++++---- 6 files changed, 28 insertions(+), 16 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. Multi-phase and multi-baseline designs are
supported. Analysing methods include regression models
(multilevel, multivariate, bayesian), between case standardised mean difference,
overlap indices ('PND', 'PEM', 'PAND', 'NAP', 'PET', 'tau-u', 'IRD', 'baseline corrected tau',
'CDC'), and randomization tests. Data preparation functions support outlier
detection, handling missing values, scaling, and custom transformations.
An export function helps to generate html, word, and latex tables in a
publication friendly style. A shiny app allows to use scan in a graphical
user interface.
More details can be found in the online book 'Analyzing single-case data with
R and scan', Juergen Wilbert (2026)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.67.0 dated 2025-09-11 and 0.68.0 dated 2026-04-01
scan-0.67.0/scan/man/example_data.Rd |only scan-0.68.0/scan/DESCRIPTION | 17 scan-0.68.0/scan/MD5 | 332 ++++++++-------- scan-0.68.0/scan/NAMESPACE | 2 scan-0.68.0/scan/NEWS.md | 25 + scan-0.68.0/scan/R/add_l2.R | 43 +- scan-0.68.0/scan/R/anova.R | 17 scan-0.68.0/scan/R/as.data.frame.scdf.R | 7 scan-0.68.0/scan/R/autocorr.R | 9 scan-0.68.0/scan/R/batch_apply.R | 10 scan-0.68.0/scan/R/between_smd.R | 10 scan-0.68.0/scan/R/bplm.R | 44 +- scan-0.68.0/scan/R/cdc.R | 5 scan-0.68.0/scan/R/coefficents.sc_plm.R | 4 scan-0.68.0/scan/R/convert.R | 14 scan-0.68.0/scan/R/corrected_tau.R | 73 ++- scan-0.68.0/scan/R/describe.R | 8 scan-0.68.0/scan/R/design.R | 10 scan-0.68.0/scan/R/estimate_design.R | 33 + scan-0.68.0/scan/R/export.R | 8 scan-0.68.0/scan/R/export.sc_desc.R | 5 scan-0.68.0/scan/R/fetch.R | 35 + scan-0.68.0/scan/R/fill_missing.R | 156 +++++-- scan-0.68.0/scan/R/hplm.R | 61 ++- scan-0.68.0/scan/R/importer-gadget.R | 37 + scan-0.68.0/scan/R/inherit_roxygen_descriptions.R | 10 scan-0.68.0/scan/R/ird.R | 5 scan-0.68.0/scan/R/mplm.R | 10 scan-0.68.0/scan/R/nap.R | 9 scan-0.68.0/scan/R/outlier.R | 3 scan-0.68.0/scan/R/overlap.R | 6 scan-0.68.0/scan/R/pand.R | 5 scan-0.68.0/scan/R/pem.R | 12 scan-0.68.0/scan/R/pet.R | 10 scan-0.68.0/scan/R/plm.R | 22 - scan-0.68.0/scan/R/plm_contrasts.R | 7 scan-0.68.0/scan/R/pnd.R | 8 scan-0.68.0/scan/R/power_test.R | 8 scan-0.68.0/scan/R/print-export-plm.R | 1 scan-0.68.0/scan/R/private_check.R | 21 - scan-0.68.0/scan/R/private_kendall.R | 2 scan-0.68.0/scan/R/private_options.R | 2 scan-0.68.0/scan/R/rand_test.R | 20 - scan-0.68.0/scan/R/random_scdf.R | 12 scan-0.68.0/scan/R/rci.R | 12 scan-0.68.0/scan/R/read_scdf.R | 5 scan-0.68.0/scan/R/rescale.R | 7 scan-0.68.0/scan/R/sample_names.R | 14 scan-0.68.0/scan/R/scan-Data.R | 156 +++++-- scan-0.68.0/scan/R/scan-package.R | 3 scan-0.68.0/scan/R/scdf-functions.R | 39 + scan-0.68.0/scan/R/scdf.R | 36 + scan-0.68.0/scan/R/select_cases.R | 10 scan-0.68.0/scan/R/select_phases.R | 25 + scan-0.68.0/scan/R/set_vars.R | 8 scan-0.68.0/scan/R/shinyscan.R | 4 scan-0.68.0/scan/R/smd.R | 6 scan-0.68.0/scan/R/subset.scdf.R | 7 scan-0.68.0/scan/R/summary.scdf.R | 13 scan-0.68.0/scan/R/tau_u.R | 12 scan-0.68.0/scan/R/transform.scdf.R | 4 scan-0.68.0/scan/R/trend.R | 21 - scan-0.68.0/scan/R/write_scdf.R | 13 scan-0.68.0/scan/README.md | 48 +- scan-0.68.0/scan/data/Beretvas2008.rda |binary scan-0.68.0/scan/data/Borckardt2014.rda |binary scan-0.68.0/scan/data/Grosche2011.rda |binary scan-0.68.0/scan/data/Grosche2014.rda |binary scan-0.68.0/scan/data/GruenkeWilbert2014.rda |binary scan-0.68.0/scan/data/Huber2014.rda |binary scan-0.68.0/scan/data/Huitema2000.rda |binary scan-0.68.0/scan/data/Leidig2018.rda |binary scan-0.68.0/scan/data/Leidig2018_l2.rda |binary scan-0.68.0/scan/data/Lenz2013.rda |binary scan-0.68.0/scan/data/Parker2007.rda |binary scan-0.68.0/scan/data/Parker2009.rda |binary scan-0.68.0/scan/data/Parker2009b.rda |binary scan-0.68.0/scan/data/Parker2011.rda |binary scan-0.68.0/scan/data/Parker2011b.rda |binary scan-0.68.0/scan/data/SSDforR2017.rda |binary scan-0.68.0/scan/data/Tarlow2017.rda |binary scan-0.68.0/scan/data/Waddell2011.rda |binary scan-0.68.0/scan/data/byHeart2011.rda |binary scan-0.68.0/scan/data/exampleA1B1A2B2.rda |binary scan-0.68.0/scan/data/exampleA1B1A2B2_zvt.rda |binary scan-0.68.0/scan/data/exampleAB.rda |binary scan-0.68.0/scan/data/exampleABAB.rda |binary scan-0.68.0/scan/data/exampleABC.rda |binary scan-0.68.0/scan/data/exampleABC_150.rda |binary scan-0.68.0/scan/data/exampleABC_outlier.rda |binary scan-0.68.0/scan/data/exampleAB_50.l2.rda |binary scan-0.68.0/scan/data/exampleAB_50.rda |binary scan-0.68.0/scan/data/exampleAB_add.rda |binary scan-0.68.0/scan/data/exampleAB_decreasing.rda |binary scan-0.68.0/scan/data/exampleAB_mpd.rda |binary scan-0.68.0/scan/data/exampleAB_score.rda |binary scan-0.68.0/scan/data/exampleAB_simple.rda |binary scan-0.68.0/scan/data/example_A24.rda |binary scan-0.68.0/scan/data/example_atd.rda |only scan-0.68.0/scan/data/example_stranger.rda |only scan-0.68.0/scan/inst/CITATION | 6 scan-0.68.0/scan/inst/shiny_scan/resources.R | 89 +--- scan-0.68.0/scan/inst/shiny_scan/server.R | 412 +++++++-------------- scan-0.68.0/scan/inst/shiny_scan/ui.R | 266 +++++++------ scan-0.68.0/scan/man/Subsetting.Rd | 13 scan-0.68.0/scan/man/add_dummy_variables.Rd | 5 scan-0.68.0/scan/man/add_l2.Rd | 18 scan-0.68.0/scan/man/anova.sc_plm.Rd | 18 scan-0.68.0/scan/man/as.data.frame.scdf.Rd | 7 scan-0.68.0/scan/man/as_scdf.Rd | 1 scan-0.68.0/scan/man/autocorr.Rd | 11 scan-0.68.0/scan/man/batch_apply.Rd | 30 + scan-0.68.0/scan/man/between_smd.Rd | 12 scan-0.68.0/scan/man/bplm.Rd | 35 + scan-0.68.0/scan/man/cdc.Rd | 3 scan-0.68.0/scan/man/check_args.Rd |only scan-0.68.0/scan/man/combine.Rd | 11 scan-0.68.0/scan/man/convert.Rd | 17 scan-0.68.0/scan/man/corrected_tau.Rd | 8 scan-0.68.0/scan/man/describe.Rd | 7 scan-0.68.0/scan/man/design.Rd | 8 scan-0.68.0/scan/man/dot-inheritParams.Rd | 13 scan-0.68.0/scan/man/estimate_design.Rd | 34 + scan-0.68.0/scan/man/example_data_sets.Rd |only scan-0.68.0/scan/man/export.Rd | 9 scan-0.68.0/scan/man/fetch.Rd | 42 +- scan-0.68.0/scan/man/fill_missing.Rd | 62 ++- scan-0.68.0/scan/man/hplm.Rd | 76 +++ scan-0.68.0/scan/man/ird.Rd | 1 scan-0.68.0/scan/man/is.scdf.Rd | 11 scan-0.68.0/scan/man/mplm.Rd | 14 scan-0.68.0/scan/man/na.omit.scdf.Rd | 9 scan-0.68.0/scan/man/nap.Rd | 11 scan-0.68.0/scan/man/outlier.Rd | 4 scan-0.68.0/scan/man/overlap.Rd | 8 scan-0.68.0/scan/man/pand.Rd | 1 scan-0.68.0/scan/man/pem.Rd | 14 scan-0.68.0/scan/man/pet.Rd | 12 scan-0.68.0/scan/man/plm.Rd | 16 scan-0.68.0/scan/man/pnd.Rd | 10 scan-0.68.0/scan/man/power_test.Rd | 12 scan-0.68.0/scan/man/rand_test.Rd | 15 scan-0.68.0/scan/man/random_scdf.Rd | 14 scan-0.68.0/scan/man/ranks.Rd | 1 scan-0.68.0/scan/man/rci.Rd | 11 scan-0.68.0/scan/man/read_scdf.Rd | 6 scan-0.68.0/scan/man/rescale.Rd | 8 scan-0.68.0/scan/man/sample_names.Rd | 15 scan-0.68.0/scan/man/scdf.Rd | 35 + scan-0.68.0/scan/man/select_cases.Rd | 12 scan-0.68.0/scan/man/select_phases.Rd | 39 + scan-0.68.0/scan/man/set_vars.Rd | 12 scan-0.68.0/scan/man/shift.Rd | 1 scan-0.68.0/scan/man/shinyscan.Rd | 6 scan-0.68.0/scan/man/smd.Rd | 6 scan-0.68.0/scan/man/smooth_cases.Rd | 1 scan-0.68.0/scan/man/standardize.Rd | 1 scan-0.68.0/scan/man/subset.scdf.Rd | 7 scan-0.68.0/scan/man/summary.scdf.Rd | 17 scan-0.68.0/scan/man/tau_u.Rd | 10 scan-0.68.0/scan/man/transform.scdf.Rd | 5 scan-0.68.0/scan/man/trend.Rd | 20 - scan-0.68.0/scan/man/truncate_phase.Rd | 1 scan-0.68.0/scan/man/write_scdf.Rd | 14 scan-0.68.0/scan/tests/testthat/helper-checksum.R |only scan-0.68.0/scan/tests/testthat/test-add_l2.R | 14 scan-0.68.0/scan/tests/testthat/test-anova.R |only scan-0.68.0/scan/tests/testthat/test-bacht_apply.R |only scan-0.68.0/scan/tests/testthat/test-between_smd.R |only scan-0.68.0/scan/tests/testthat/test-cdc.R | 8 scan-0.68.0/scan/tests/testthat/test-corrected.R | 10 scan-0.68.0/scan/tests/testthat/test-ird.R |only 172 files changed, 2099 insertions(+), 1107 deletions(-)
Title: Utilities to Support Lidar Applications at the Landscape,
Forest, and Tree Scale
Description: Implements algorithms for terrestrial, mobile, and airborne lidar processing, tree detection,
segmentation, and attribute estimation (Donager et al., 2021)
<doi:10.3390/rs13122297>, and a hierarchical patch delineation algorithm
'PatchMorph' (Girvetz & Greco, 2007) <doi:10.1007/s10980-007-9104-8>. Tree
detection uses rasterized point cloud metrics (relative neighborhood density and
verticality) combined with RANSAC cylinder fitting to locate tree boles and estimate
diameter at breast height. Tree segmentation applies graph-theory approaches inspired
by Tao et al. (2015) <doi:10.1016/j.isprsjprs.2015.08.007> with cylinder fitting
methods from de Conto et al. (2017) <doi:10.1016/j.compag.2017.07.019>. PatchMorph
delineates habitat patches across spatial scales using organism-specific thresholds.
Built on 'lidR' (Roussel et al., 2020) <doi:10.1016/j.rse.2020.112061>.
Author: Andrew Sanchez Meador [aut, cre, ctb] ,
Jonathon Donager [aut, ctb] ,
Blackburn Ryan [aut, ctb] ,
Cannon Jeffery [ctb] ,
Tiago de Conto [ctb, cph] ,
Keith O'Hara [ctb, cph]
Maintainer: Andrew Sanchez Meador <Andrew.SanchezMeador@nau.edu>
Diff between spanner versions 1.0.3 dated 2026-03-26 and 1.0.4 dated 2026-04-01
DESCRIPTION | 8 MD5 | 38 +- NEWS.md | 163 ++++----- R/Patch_Morph.R | 404 +++++++++++------------ R/PostProcess_TreeLocations.R | 492 ++++++++++++++-------------- R/Segment_Graph.R | 630 ++++++++++++++++++------------------ R/spanner-package.R | 38 +- R/utils.R | 62 ++- build/stage23.rdb |binary man/colorize_las.Rd | 180 +++++----- man/compute_pcv.Rd | 72 ++-- man/compute_ssao.Rd | 90 ++--- man/create_rotation_gif.Rd | 33 - man/download_naip_for_las.Rd | 126 +++---- man/eigen_metrics.Rd | 126 +++---- man/merge_las_colors.Rd | 124 +++---- man/segment_graph.Rd | 304 ++++++++--------- src/Progress.cpp | 5 tests/testthat/test-eigen-metrics.R | 120 +++--- tests/testthat/test-segmentation.R | 224 ++++++------ 20 files changed, 1627 insertions(+), 1612 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.6 dated 2026-01-13 and 0.2.7 dated 2026-04-01
DESCRIPTION | 10 - MD5 | 56 +++---- NAMESPACE | 4 NEWS.md | 10 + R/assess_last_30_bugs_status.R | 10 - R/metric_score.R | 7 R/pkg_ref_cache.R | 2 R/pkg_ref_cache_archive_release_date.R | 1 R/pkg_ref_cache_bug_reports.R | 5 R/pkg_ref_cache_description.R | 4 R/pkg_ref_cache_examples.R | 2 R/pkg_ref_cache_help_aliases.R | 4 R/pkg_ref_cache_license.R | 3 R/pkg_ref_cache_maintainer.R | 5 R/pkg_ref_cache_news.R | 6 R/pkg_ref_cache_r_cmd_check.R | 1 R/pkg_ref_cache_release_date.R | 6 R/pkg_ref_cache_repo_base_url.R | 3 R/pkg_ref_cache_tarball_url.R | 3 R/pkg_ref_cache_vignettes.R | 8 - R/pkg_ref_cache_web_url.R | 4 R/pkg_ref_cache_website_urls.R | 6 R/pkg_ref_class.R | 238 ++++++++++++++++++++------------- inst/doc/extending-riskmetric.R | 6 inst/doc/extending-riskmetric.html | 14 - inst/doc/riskmetric.R | 16 +- inst/doc/riskmetric.html | 30 ++-- man/pkg_ref.Rd | 28 +-- tests/testthat/setup_test_packages.R | 63 +++++--- 29 files changed, 322 insertions(+), 233 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.2 dated 2026-03-20 and 0.3.3 dated 2026-04-01
DESCRIPTION | 6 ++--- MD5 | 15 ++++++------- NAMESPACE | 1 NEWS.md | 12 +++------- R/evaluate_performance.R | 45 ++++++++++++++++++++++++++++++++++++--- R/print.quickSentiment_eval.R | 30 ++++++++++++++++++++++++++ README.md | 1 man/evaluate_performance.Rd | 4 ++- man/print.quickSentiment_eval.Rd |only 9 files changed, 92 insertions(+), 22 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.5.0 dated 2026-02-03 and 1.5.1 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/namespace-env.R | 5 ++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989) <DOI:10.2307/1912557>.
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is partially based on
work supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle [aut, cre],
Dongjun You [aut],
Lennart Schneider [ctb],
Mauricio Garnier-Villarreal [ctb],
Seongho Bae [ctb],
Phil Chalmers [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.5-8 dated 2024-08-28 and 0.5-9 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NEWS | 4 ++++ R/icci.R | 4 ++-- R/vuongtest.R | 9 ++++++--- README.md | 28 ++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/nonnest2.R | 10 +++++----- inst/doc/nonnest2.pdf |binary tests/testthat/test_discreteclass.R |only 10 files changed, 59 insertions(+), 23 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace
Approximation, deterministic nested approximations, Monte Carlo Expectation
Maximization, and some other tools.
The nimbleFunction system makes it easy to do things like implement new MCMC
samplers from R, customize the assignment of samplers to different parts of
a model from R, and compile the new samplers automatically via C++ alongside
the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language
by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think
of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models,
one can use 'NIMBLE' for writing arbitrary other kinds of model-generic
al [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodriguez [aut] ,
Duncan Temple Lang [aut] ,
Wei Zhang [aut] ,
[...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 1.4.1 dated 2026-02-13 and 1.4.2 dated 2026-04-01
DESCRIPTION | 8 INSTALL | 6 MD5 | 30 +-- R/MCMC_configuration.R | 10 - R/cppDefs_nimbleFunction.R | 2 R/cppDefs_nimbleList.R | 50 +---- inst/CppCode/RcppNimbleUtils.cpp | 162 ++++++++--------- inst/CppCode/RcppUtils.cpp | 77 ++++---- inst/CppCode/accessorClasses.cpp | 56 ++---- inst/CppCode/eigenUsingClasses.cpp | 54 ++--- inst/CppCode/nimOptim.cpp | 16 - inst/CppCode/predefinedNimbleLists.cpp | 306 ++++++++++++++------------------- inst/NEWS.md | 12 + inst/include/nimble/RcppNimbleUtils.h | 57 ++---- inst/include/nimble/Utils.h | 52 +++++ inst/include/nimble/accessorClasses.h | 215 ++++------------------- 16 files changed, 489 insertions(+), 624 deletions(-)
Title: Multimodal Access and Interactive Data Representation
Description: Provides accessible, interactive visualizations through the 'MAIDR'
(Multimodal Access and Interactive Data Representation) system. Converts
'ggplot2' and Base R plots into accessible HTML/SVG formats with keyboard
navigation, screen reader support, and 'sonification' capabilities. Supports
bar charts (simple, grouped, stacked), histograms, line plots, scatter plots,
box plots, violin plots, heat maps, density/smooth curves, faceted plots,
multi-panel layouts (including patchwork), and multi-layered plot combinations. Enables
data exploration for users with visual impairments through multiple sensory
modalities. For more details see the 'MAIDR' project
<https://maidr.ai/>.
Author: JooYoung Seo [aut, cph],
Niranjan Kalaiselvan [aut, cre]
Maintainer: Niranjan Kalaiselvan <nk46@illinois.edu>
Diff between maidr versions 0.2.0 dated 2026-03-07 and 0.3.0 dated 2026-04-01
maidr-0.2.0/maidr/inst/doc/plot-types.R |only maidr-0.2.0/maidr/inst/doc/plot-types.Rmd |only maidr-0.2.0/maidr/inst/doc/plot-types.html |only maidr-0.2.0/maidr/inst/htmlwidgets/lib/maidr-3.55.2 |only maidr-0.2.0/maidr/vignettes/plot-types.Rmd |only maidr-0.3.0/maidr/DESCRIPTION | 9 maidr-0.3.0/maidr/MD5 | 49 ++-- maidr-0.3.0/maidr/R/base_r_point_layer_processor.R | 94 +++++++ maidr-0.3.0/maidr/R/base_r_processor_factory.R | 2 maidr-0.3.0/maidr/R/examples.R | 12 + maidr-0.3.0/maidr/R/ggplot2_line_layer_processor.R | 4 maidr-0.3.0/maidr/R/ggplot2_point_layer_processor.R | 120 +++++++++- maidr-0.3.0/maidr/R/html_dependencies.R | 2 maidr-0.3.0/maidr/R/maidr-package.R |only maidr-0.3.0/maidr/R/svg_utils.R | 4 maidr-0.3.0/maidr/build/vignette.rds |binary maidr-0.3.0/maidr/inst/doc/getting-started.Rmd | 4 maidr-0.3.0/maidr/inst/doc/getting-started.html | 10 maidr-0.3.0/maidr/inst/doc/shiny-integration.Rmd | 2 maidr-0.3.0/maidr/inst/doc/shiny-integration.html | 8 maidr-0.3.0/maidr/inst/htmlwidgets/lib/maidr-3.59.0 |only maidr-0.3.0/maidr/man/BaseRPointLayerProcessor.Rd | 10 maidr-0.3.0/maidr/man/Ggplot2PointLayerProcessor.Rd | 49 +++- maidr-0.3.0/maidr/man/maidr-package.Rd |only maidr-0.3.0/maidr/tests/testthat/Rplots.pdf |binary maidr-0.3.0/maidr/tests/testthat/test-base-r-point-layer-processor.R | 114 ++++++++- maidr-0.3.0/maidr/tests/testthat/test-ggplot2-point-layer-processor.R |only maidr-0.3.0/maidr/vignettes/getting-started.Rmd | 4 maidr-0.3.0/maidr/vignettes/shiny-integration.Rmd | 2 29 files changed, 426 insertions(+), 73 deletions(-)
Title: Calculation of Sample Size and Power for ICC
Description: Provides functions to calculate the requisite sample size for studies where ICC is
the primary outcome. Can also be used for calculation of power. In both cases it
allows the user to test the impact of changing input variables by calculating the outcome
for several different values of input variables. Based off the work of Zou.
Zou, G. Y. (2012). Sample size formulas for estimating intraclass correlation coefficients with
precision and assurance. Statistics in medicine, 31(29), 3972-3981.
Author: Alasdair Rathbone [aut, cre],
Saurabh Shaw [aut],
Dinesh Kumbhare [aut]
Maintainer: Alasdair Rathbone <alasdair.rathbone@gmail.com>
Diff between ICC.Sample.Size versions 1.0 dated 2015-09-03 and 1.1 dated 2026-04-01
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 11 ++++++----- NEWS.md |only R/calculateAchievablep0.R | 11 +++++------ man/calculateAchieveablep0.Rd | 2 +- man/calculateIccPower.Rd | 2 +- man/calculateIccSampleSize.Rd | 2 +- 7 files changed, 33 insertions(+), 21 deletions(-)
More information about ICC.Sample.Size at CRAN
Permanent link
Title: Robust Inference in Difference-in-Differences and Event Study
Designs
Description: Provides functions to conduct robust inference in difference-in-differences and event study designs by implementing the methods developed in Rambachan & Roth (2023) <doi:10.1093/restud/rdad018>, "A More Credible Approach to Parallel Trends" [Previously titled "An Honest Approach..."]. Inference is conducted under a weaker version of the parallel trends assumption. Uniformly valid confidence sets are constructed based upon conditional confidence sets, fixed-length confidence sets and hybridized confidence sets.
Author: Ashesh Rambachan [aut, cph, cre],
Jonathan Roth [aut, cph]
Maintainer: Ashesh Rambachan <ashesh.a.rambachan@gmail.com>
Diff between HonestDiD versions 0.2.6 dated 2024-07-14 and 0.2.7 dated 2026-04-01
DESCRIPTION | 8 +++---- MD5 | 11 +++++----- NEWS.md |only R/arp-nuisance.R | 4 +-- R/flci.R | 53 ++++++++++++++++++++++++++++++++++++------------- R/sensitivityresults.R | 4 +++ R/utilities.R | 30 ++++++++++++++++++++++----- 7 files changed, 80 insertions(+), 30 deletions(-)
Title: Parallelize Common Functions via One Magic Function
Description: The futurize() function transpiles calls to sequential map-reduce functions such as base::lapply(), purrr::map(), 'foreach::foreach() %do% { ... }' into concurrent alternatives, providing you with a simple, straightforward path to scalable parallel computing via the 'future' ecosystem <doi:10.32614/RJ-2021-048>. By combining this function with R's native pipe operator, you have a convenient way for speeding up iterative computations with minimal refactoring, e.g. 'lapply(xs, fcn) |> futurize()', 'purrr::map(xs, fcn) |> futurize()', and 'foreach::foreach(x = xs) %do% { fcn(x) } |> futurize()'. Other map-reduce packages that can be "futurized" are 'BiocParallel', 'plyr', 'crossmap', 'pbapply' packages. There is also support for a growing set of domain-specific packages on CRAN (e.g. 'boot', 'caret', 'fgsea', 'fwb', 'gamlss', 'glmmTMB', 'glmnet', 'kernelshap', 'lme4', 'metafor', 'mgcv', 'partykit', 'riskRegression', 'seriation', 'shapr', 'SimDesign', 'strucchange', 'tm', 'T [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between futurize versions 0.2.0 dated 2026-03-18 and 0.3.0 dated 2026-04-01
futurize-0.2.0/futurize/inst/testme/test-furrr-future_invoke-map.R |only futurize-0.2.0/futurize/tests/test-furrr-future_invoke-map.R |only futurize-0.3.0/futurize/DESCRIPTION | 9 futurize-0.3.0/futurize/MD5 | 218 ++++------ futurize-0.3.0/futurize/NAMESPACE | 1 futurize-0.3.0/futurize/NEWS.md | 20 futurize-0.3.0/futurize/R/000.bquote.R | 2 futurize-0.3.0/futurize/R/addons-BiocParallel.R | 11 futurize-0.3.0/futurize/R/addons-DESeq2.R | 6 futurize-0.3.0/futurize/R/addons-GSVA.R | 5 futurize-0.3.0/futurize/R/addons-GenomicAlignments.R | 5 futurize-0.3.0/futurize/R/addons-Rsamtools.R | 5 futurize-0.3.0/futurize/R/addons-SimDesign.R | 12 futurize-0.3.0/futurize/R/addons-SingleCellExperiment.R | 5 futurize-0.3.0/futurize/R/addons-TSP.R | 6 futurize-0.3.0/futurize/R/addons-boot.R | 12 futurize-0.3.0/futurize/R/addons-caret.R | 15 futurize-0.3.0/futurize/R/addons-fgsea.R | 5 futurize-0.3.0/futurize/R/addons-foreach.R | 8 futurize-0.3.0/futurize/R/addons-fwb.R | 24 - futurize-0.3.0/futurize/R/addons-gamlss.R | 21 futurize-0.3.0/futurize/R/addons-glmmTMB.R | 14 futurize-0.3.0/futurize/R/addons-glmnet.R | 5 futurize-0.3.0/futurize/R/addons-kernelshap.R | 6 futurize-0.3.0/futurize/R/addons-lme4.R | 5 futurize-0.3.0/futurize/R/addons-metafor.R | 15 futurize-0.3.0/futurize/R/addons-mgcv.R | 11 futurize-0.3.0/futurize/R/addons-partykit.R | 3 futurize-0.3.0/futurize/R/addons-pbapply.R | 11 futurize-0.3.0/futurize/R/addons-plyr.R | 8 futurize-0.3.0/futurize/R/addons-riskRegression.R | 10 futurize-0.3.0/futurize/R/addons-scater.R | 5 futurize-0.3.0/futurize/R/addons-scuttle.R | 5 futurize-0.3.0/futurize/R/addons-seriation.R | 6 futurize-0.3.0/futurize/R/addons-shapr.R | 10 futurize-0.3.0/futurize/R/addons-strucchange.R | 5 futurize-0.3.0/futurize/R/addons-sva.R | 5 futurize-0.3.0/futurize/R/addons-tm.R | 11 futurize-0.3.0/futurize/R/addons-vegan.R | 2 futurize-0.3.0/futurize/R/make_addon_transpilers.R | 11 futurize-0.3.0/futurize/R/make_options_for_furrr.R | 16 futurize-0.3.0/futurize/R/make_options_for_future.apply.R | 5 futurize-0.3.0/futurize/R/transpile.R | 17 futurize-0.3.0/futurize/R/transpiler-unwrap.R | 3 futurize-0.3.0/futurize/README.md | 2 futurize-0.3.0/futurize/inst/doc/futurize-21-purrr.html | 9 futurize-0.3.0/futurize/inst/doc/futurize-21-purrr.md | 9 futurize-0.3.0/futurize/inst/doc/futurize-22-crossmap.html | 2 futurize-0.3.0/futurize/inst/doc/futurize-22-crossmap.md | 2 futurize-0.3.0/futurize/inst/testme/run.R | 15 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,errors.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_colon.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_dofuture.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,rng.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture-options,nested.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-times.R | 1 futurize-0.3.0/futurize/inst/testme/test-furrr-future_imap.R | 6 futurize-0.3.0/futurize/inst/testme/test-furrr-future_map.R | 11 futurize-0.3.0/futurize/inst/testme/test-furrr-future_map2.R | 12 futurize-0.3.0/futurize/inst/testme/test-furrr-future_modify.R | 1 futurize-0.3.0/futurize/inst/testme/test-furrr-future_pmap.R | 12 futurize-0.3.0/futurize/inst/testme/test-furrr-future_walk.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_Filter.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_apply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_by.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_eapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_kernapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply,RNG.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply.R | 2 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_mapply,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_mapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_replicate.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_sapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_tapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_vapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-globals,tricky2.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-globals,tricky_recursive.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-options,nested.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-stdout.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-BiocParallel.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-DESeq2.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-Rsamtools.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-SimDesign.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-TSP.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-base-stats.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-boot.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-caret.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-crossmap.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-fgsea.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-foreach.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-fwb.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-gamlss.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-kernelshap.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-lme4.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-metafor.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-mgcv.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-partykit.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-purrr.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-seriation.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-shapr.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-strucchange.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-tm.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-vegan.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-wrapped.R | 28 + futurize-0.3.0/futurize/inst/testme/test-internals-futurize.R | 1 futurize-0.3.0/futurize/man/transpile.Rd | 4 futurize-0.3.0/futurize/vignettes/futurize-21-purrr.md | 9 futurize-0.3.0/futurize/vignettes/futurize-22-crossmap.md | 2 111 files changed, 471 insertions(+), 285 deletions(-)
Title: Breaks for Additive Season and Trend
Description: Decomposition of time series into
trend, seasonal, and remainder components with methods for detecting and
characterizing abrupt changes within the trend and seasonal components. 'BFAST'
can be used to analyze different types of satellite image time series and can
be applied to other disciplines dealing with seasonal or non-seasonal time
series, such as hydrology, climatology, and econometrics. The algorithm can be
extended to label detected changes with information on the parameters of the
fitted piecewise linear models. 'BFAST' monitoring functionality is described
in Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor'
provides functionality to detect disturbance in near real-time based on 'BFAST'-
type models, and is described in Verbesselt et al. (2012) <doi:10.1016/j.rse.2012.02.022>.
'BFAST Lite' approach is a flexible approach that handles missing data
without interpolation, and will be described in an upcoming paper.
Furthermore, different mode [...truncated...]
Author: Jan Verbesselt [aut],
Dainius Masiliūnas [aut, cre] ,
Achim Zeileis [aut],
Rob Hyndman [ctb],
Marius Appel [aut],
Martin Jung [ctb],
Andrei Mîrț [ctb] ,
Paulo Negri Bernardino [ctb],
Dongdong Kong [ctb]
Maintainer: Dainius Masiliūnas <pastas4@gmail.com>
Diff between bfast versions 1.7.1 dated 2025-08-18 and 1.7.2 dated 2026-04-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ build/partial.rdb |binary man/bfastlite.Rd | 3 ++- man/bfastpp.Rd | 6 +++--- tests/Examples/bfast-Ex.Rout.save | 12 +++++++++--- 7 files changed, 29 insertions(+), 17 deletions(-)
Title: Spatial Component Analysis for Spatial Sequencing Data
Description: Spatial components offer tools for dimension reduction and
spatially variable gene detection for high dimensional spatial transcriptomics
data. Construction of a projection onto low-dimensional feature space of
spatially dependent metagenes offers pre-processing to clustering, testing for
spatial variability and denoising of spatial expression patterns. For more
details, see Koehler et al. (2026) <doi:10.1093/bioinformatics/btag052>.
Author: David Koehler [aut, cre]
Maintainer: David Koehler <koehler@imbie.uni-bonn.de>
Diff between SPACO versions 1.0.0 dated 2026-03-31 and 1.0.1 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Rcpp_Functions.cpp | 3 +++ tests/testthat/test-SCA.R | 13 +++++++++---- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Simulate and Analyse Social Interaction Data
Description: Provides tools to simulate and analyse datasets of social interactions
between individuals using hierarchical Bayesian models implemented in Stan.
Model fitting is performed via the 'rstan' package. Users can generate
realistic interaction data where individual phenotypes influence and respond
to those of their partners, with control over sampling design parameters such
as the number of individuals, partners, and repeated dyads. The simulation
framework allows flexible control over variation and correlation in mean trait
values, social responsiveness, and social impact, making it suitable for
research on interacting phenotypes and on direct and indirect genetic effects
('DGEs' and 'IGEs'). The package also includes functions to fit and compare
alternative models of social effects, including impact–responsiveness,
variance–partitioning, and trait-based models, and to summarise model
performance in terms of bias and dispersion. For a more detailed description
of the available models and [...truncated...]
Author: Rori Efrain Wijnhorst [aut, cre]
Maintainer: Rori Efrain Wijnhorst <roriwijnhorst@proton.me>
Diff between socialSim versions 0.1.8 dated 2026-01-30 and 0.1.9 dated 2026-03-31
DESCRIPTION | 12 - MD5 | 28 +-- NEWS.md | 8 R/run_model.R | 302 +++++++++++++++++------------------ R/simulate_data.R | 362 +++++++++++++++++++++--------------------- R/summarise_results.R | 164 +++++++++---------- README.md | 8 inst/doc/getting-started.Rmd | 198 +++++++++++----------- inst/stan/I&R.stan | 250 ++++++++++++++--------------- inst/stan/Trait.stan | 250 ++++++++++++++--------------- inst/stan/Trait_EIV.stan | 218 ++++++++++++------------- inst/stan/Trait_RS.stan | 260 +++++++++++++++--------------- inst/stan/Trait_only.stan | 180 ++++++++++---------- inst/stan/VP.stan | 160 +++++++++--------- vignettes/getting-started.Rmd | 198 +++++++++++----------- 15 files changed, 1299 insertions(+), 1299 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Paul Madley-Dowd [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.6 dated 2026-02-16 and 1.4.1 dated 2026-03-31
DESCRIPTION | 17 +- MD5 | 115 +++++++++--------- NAMESPACE | 1 NEWS.md | 55 ++++++++ R/SEQexpand.R | 50 ++++---- R/SEQopts.R | 34 ++++- R/SEQuential.R | 74 +++++++++-- R/class_definitions.R | 9 - R/class_methods.R | 66 ++++++---- R/class_setters.R | 6 R/data.R | 12 - R/internal_analysis.R | 58 +++++---- R/internal_fatglmHelpers.R | 46 +++---- R/internal_hazard.R | 28 ++-- R/internal_misc.R | 67 +++++++--- R/internal_models.R | 2 R/internal_multinomial.R | 84 ++++++++----- R/internal_plot.R | 5 R/internal_survival.R | 145 ++++++++++++++--------- R/internal_weights.R | 103 ++++++++-------- README.md | 34 +++-- build/vignette.rds |binary data/SEQdata.LTFU.rda |binary data/SEQdata.multitreatment.rda |binary data/SEQdata.rda |binary inst/doc/ITT.R | 2 inst/doc/ITT.Rmd | 2 inst/doc/SEQuential.R | 4 inst/doc/SEQuential.Rmd | 15 +- inst/doc/SEQuential.html | 248 +++++++++++++++++++++++++++++++--------- inst/doc/censoring.R | 10 - inst/doc/censoring.Rmd | 10 - inst/doc/censoring.html | 172 ++++++++++----------------- inst/doc/doseresponse.R | 2 inst/doc/doseresponse.Rmd | 12 + inst/doc/doseresponse.html | 8 - man/SEQdata.LTFU.Rd | 5 man/SEQdata.Rd | 6 man/SEQdata.multitreatment.Rd | 2 man/SEQopts.Rd | 12 - man/SEQuential.Rd | 2 man/check_separation.Rd |only man/compevent.Rd | 2 man/create.risk.Rd | 2 man/denominator.Rd | 2 man/dot-coef_table.Rd |only man/hazard_ratio.Rd | 2 man/km_curve.Rd | 2 man/km_data.Rd | 2 man/prepare.output.Rd | 1 tests/testthat/test_coverage.R |only tests/testthat/test_errors.R | 13 ++ tests/testthat/test_methods.R | 4 tests/testthat/test_misc.R | 12 + tests/testthat/test_survival.R | 19 ++- tests/testthat/test_warnings.R | 23 +++ vignettes/ITT.Rmd | 2 vignettes/SEQuential.Rmd | 15 +- vignettes/censoring.Rmd | 10 - vignettes/doseresponse.Rmd | 12 + 60 files changed, 1031 insertions(+), 615 deletions(-)
Title: Analyzing Revisions in Real-Time Time Series Vintages
Description: Analyzes revisions in real-time time series vintages. The
package converts between wide revision triangles and tidy long
vintages, extracts selected releases, computes revision series,
visualizes vintage paths, and summarizes revision properties such as
bias, dispersion, autocorrelation, and news-noise diagnostics. It
also identifies efficient releases and estimates state-space models
for revision nowcasting. Methods are based on Howrey (1978)
<doi:10.2307/1924972>, Jacobs and Van Norden (2011)
<doi:10.1016/j.jeconom.2010.04.010>, and Kishor and Koenig (2012)
<doi:10.1198/jbes.2010.08169>.
Author: Marc Burri [aut, cre, cph] ,
Philipp Wegmueller [aut, cph]
Maintainer: Marc Burri <marc.burri91@gmail.com>
Diff between reviser versions 0.1.0 dated 2026-03-29 and 0.1.1 dated 2026-03-31
reviser-0.1.0/reviser/man/figures/README-unnamed-chunk-3-1.png |only reviser-0.1.0/reviser/tests/testthat/tests-kk.R |only reviser-0.1.1/reviser/DESCRIPTION | 11 - reviser-0.1.1/reviser/MD5 | 22 +- reviser-0.1.1/reviser/NEWS.md | 13 + reviser-0.1.1/reviser/R/jvn.R | 55 +++---- reviser-0.1.1/reviser/R/kk.R | 19 +- reviser-0.1.1/reviser/R/reviser-package.R | 4 reviser-0.1.1/reviser/README.md | 75 ++++++---- reviser-0.1.1/reviser/inst/CITATION | 5 reviser-0.1.1/reviser/inst/examples/sticker.R | 2 reviser-0.1.1/reviser/man/figures/README-readme-example-1.png |only reviser-0.1.1/reviser/man/reviser-package.Rd | 11 + reviser-0.1.1/reviser/tests/testthat/test-kk.R |only 14 files changed, 132 insertions(+), 85 deletions(-)
Title: Spatial Estimation and Prediction for Censored/Missing Responses
Description: It provides functions for estimating parameters in linear spatial models with censored or missing responses using the Expectation-Maximization (EM), Stochastic Approximation EM (SAEM), and Monte Carlo EM (MCEM) algorithms. These methods are widely used to obtain maximum likelihood (ML) estimates in the presence of incomplete data. The EM algorithm computes ML estimates when a closed-form expression for the conditional expectation of the complete-data log-likelihood is available. The MCEM algorithm replaces this expectation with a Monte Carlo approximation based on independent simulations of the missing data. In contrast, the SAEM algorithm decomposes the E-step into simulation and stochastic approximation steps, improving computational efficiency in complex settings. In addition, the package provides standard error estimation based on the Louis method. It also includes functionality for spatial prediction at new locations.
References used for this package: Galarza, C. E., Matos, L. A., [...truncated...]
Author: Katherine A. L. Valeriano [aut, cre] ,
Christian Galarza Morales [ctb] ,
Larissa Avila Matos [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>
This is a re-admission after prior archival of version 0.3.0 dated 2022-06-27
Diff between RcppCensSpatial versions 0.3.0 dated 2022-06-27 and 1.0.0 dated 2026-03-31
DESCRIPTION | 40 ++++---------- MD5 | 44 +++++++-------- NEWS.md | 16 +++-- R/Algorithm_utils.R | 19 +++++- R/AuxiliaryFunctions_USER.R | 20 +++---- R/EstEMspatial_USER.R | 26 ++++----- R/EstMCEMspatial_USER.R | 29 +++++----- R/EstSAEMspatial_USER.R | 40 +++++++------- R/RcppExports.R | 8 +- R/rCensspatial_USER.R | 6 +- README.md | 125 ++++++++++++++++++++++---------------------- build/partial.rdb |binary man/CovMat.Rd | 4 - man/EM.sclm.Rd | 26 ++++----- man/MCEM.sclm.Rd | 29 +++++----- man/SAEM.sclm.Rd | 40 +++++++------- man/dist2Dmatrix.Rd | 4 - man/predict.sclm.Rd | 8 +- man/rCensSp.Rd | 6 +- src/AuxiliaryFunctions.cpp | 14 +--- src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 18 +++--- 23 files changed, 262 insertions(+), 262 deletions(-)
More information about RcppCensSpatial at CRAN
Permanent link
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharche [...truncated...]
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Rasmus Rydbirk [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
This is a re-admission after prior archival of version 1.0.14 dated 2026-03-08
Diff between pagoda2 versions 1.0.14 dated 2026-03-08 and 1.0.15 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Measles Epidemiological Models
Description: A specialized collection of measles epidemiological models built on the 'epiworldR' framework. This package is a spinoff from 'epiworldR' focusing specifically on measles transmission dynamics. It includes models for school settings with quarantine and isolation policies, mixing models with population groups, and risk-based quarantine strategies. The models use Agent-Based Models (ABM) with a fast 'C++' backend from the 'epiworld' library. Ideal for studying measles outbreaks, vaccination strategies, and intervention policies.
Author: George Vega Yon [aut, cre] ,
Damon Toth [ctb] ,
Jake Wagoner [ctb] ,
Olivia Banks [ctb] ,
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2026-02-21
Diff between measles versions 0.1.1 dated 2026-02-21 and 0.2.0 dated 2026-03-31
DESCRIPTION | 8 MD5 | 35 +-- NEWS.md | 13 + R/ModelMeaslesMixing.R | 22 ++ R/ModelMeaslesMixingRiskQuarantine.R | 3 R/ModelMeaslesSchool.R | 3 README.md | 256 ++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/short-creek.R | 17 + inst/doc/short-creek.html | 147 +++++++------- inst/doc/short-creek.qmd | 25 +- inst/tinytest/test-measles-quarantine-errors.R | 1 inst/tinytest/test-measles-quarantine-math.R | 16 - man/ModelMeaslesMixing.Rd | 22 ++ man/ModelMeaslesMixingRiskQuarantine.Rd | 3 man/ModelMeaslesSchool.Rd | 3 man/figures/README-outbreak-size-plot-1.png |only vignettes/short-creek.qmd | 25 +- 19 files changed, 483 insertions(+), 116 deletions(-)
Title: Model-Based Geostatistics
Description: Modern model-based geostatistics for point-referenced data. This package provides a
simple interface to run spatial machine learning models and geostatistical models
that estimate a continuous (raster) surface from point-referenced outcomes and,
optionally, a set of raster covariates. The package also includes functions to
summarize raster outcomes by (polygon) region while preserving uncertainty.
Author: Nathaniel Henry [aut, cre] ,
Benjamin Mayala [aut],
Roy Burstein [ctb] ,
Nafis Sadat [ctb],
Michael Richards [ctb],
Michael Collison [ctb],
Michael Cork [ctb]
Maintainer: Nathaniel Henry <nat@henryspatialanalysis.com>
Diff between mbg versions 1.1.2 dated 2026-03-10 and 1.2.0 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/aggregate_grid_to_polygons.R | 4 ++++ 3 files changed, 9 insertions(+), 5 deletions(-)
Title: Image Statistics Based on Processing Fluency
Description: Get image statistics based on processing fluency theory. The
functions provide scores for several basic aesthetic principles that
facilitate fluent cognitive processing of images: contrast,
complexity / simplicity, self-similarity, symmetry, and typicality.
See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr
(2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Author: Stefan Mayer [aut, cre]
Maintainer: Stefan Mayer <stefan@mayer-de.com>
This is a re-admission after prior archival of version 0.2.5 dated 2024-02-22
Diff between imagefluency versions 0.2.5 dated 2024-02-22 and 1.0.0 dated 2026-03-31
DESCRIPTION | 17 MD5 | 75 +- NEWS.md | 12 R/complexity.R | 147 +--- R/contrast.R | 8 R/imagefluency-package.R | 2 R/self-similarity.R | 74 +- R/simplicity.R | 2 R/symmetry.R | 15 R/typicality.R | 15 R/utils.R | 48 + README.md | 42 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.R | 152 ++-- inst/doc/getting-started.Rmd | 26 inst/doc/getting-started.html | 831 +++++++++++++++++------ inst/imagefluencyApp/app.R | 1228 ++++++++++++++++++++++++++++------ man/dot-compl.Rd | 2 man/dot-compress_and_get_size.Rd |only man/dot-typ.Rd | 2 man/figures/dashboard.png |only man/imagefluency-package.Rd | 2 man/img_complexity.Rd | 2 man/img_simplicity.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test_complexity.R | 34 tests/testthat/test_contrast.R | 6 tests/testthat/test_imagefluencyApp.R | 2 tests/testthat/test_self_similarity.R | 13 tests/testthat/test_symmetry.R | 3 tests/testthat/test_typicality.R | 6 tests/testthat/test_utils.R | 8 vignettes/example_images |only vignettes/getting-started.Rmd | 26 35 files changed, 2051 insertions(+), 753 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut],
Idris A. Eckley [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.2 dated 2026-03-30 and 0.1.3 dated 2026-03-31
DESCRIPTION | 6 MD5 | 28 +- R/RcppExports.R | 59 ++--- README.md | 18 - man/detector_candidates.Rd | 4 man/detector_info_n.Rd | 4 man/detector_info_sn.Rd | 4 man/detector_pieces_len.Rd | 4 man/detector_update.Rd | 4 man/focus_offline.Rd | 9 man/generate_projection_indexes.Rd | 12 - man/get_statistics.Rd | 4 src/MultivariateInfo.h | 378 +++++++++++-------------------------- src/RcppExports.cpp | 56 ++--- src/focus_rcpp_module.cpp | 61 ++--- 15 files changed, 242 insertions(+), 409 deletions(-)
Title: Representing and Inferring Single-Cell Trajectories
Description: Provides functionality to infer trajectories from single-cell data,
represent them into a common format, and adapt them. Other biological information
can also be added, such as cellular grouping, RNA velocity and annotation.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
This is a re-admission after prior archival of version 1.2.5 dated 2025-11-26
Diff between dynwrap versions 1.2.5 dated 2025-11-26 and 1.3.0 dated 2026-03-31
dynwrap-1.2.5/dynwrap/man/dynwrap.Rd |only dynwrap-1.3.0/dynwrap/DESCRIPTION | 14 dynwrap-1.3.0/dynwrap/MD5 | 180 +++++----- dynwrap-1.3.0/dynwrap/NAMESPACE | 4 dynwrap-1.3.0/dynwrap/NEWS.md | 18 + dynwrap-1.3.0/dynwrap/R/adapt_orient_topology.R | 22 - dynwrap-1.3.0/dynwrap/R/add_regulatory_network.R | 2 dynwrap-1.3.0/dynwrap/R/calculate_average.R | 6 dynwrap-1.3.0/dynwrap/R/calculate_geodesic_distances.R | 69 +-- dynwrap-1.3.0/dynwrap/R/calculate_trajectory_dimred.R | 72 +--- dynwrap-1.3.0/dynwrap/R/classify_milestone_network.R | 8 dynwrap-1.3.0/dynwrap/R/convert_milestone_percentages_to_progressions.R | 28 - dynwrap-1.3.0/dynwrap/R/convert_progressions_to_milestone_percentages.R | 20 - dynwrap-1.3.0/dynwrap/R/method_create_ti_method_container.R | 6 dynwrap-1.3.0/dynwrap/R/method_create_ti_method_r.R | 6 dynwrap-1.3.0/dynwrap/R/method_execute.R | 6 dynwrap-1.3.0/dynwrap/R/method_extract_args.R | 16 dynwrap-1.3.0/dynwrap/R/method_get_ti_methods.R | 12 dynwrap-1.3.0/dynwrap/R/method_process_definition.R | 2 dynwrap-1.3.0/dynwrap/R/package.R | 7 dynwrap-1.3.0/dynwrap/R/project_waypoints.R | 4 dynwrap-1.3.0/dynwrap/R/simplify_igraph_network.R | 72 ++-- dynwrap-1.3.0/dynwrap/R/simplify_trajectory.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_branch_trajectory.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_cell_graph.R | 53 +- dynwrap-1.3.0/dynwrap/R/wrap_add_cell_waypoints.R | 52 +- dynwrap-1.3.0/dynwrap/R/wrap_add_cluster_graph.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_cyclic_trajectory.R | 10 dynwrap-1.3.0/dynwrap/R/wrap_add_dimred.R | 36 +- dynwrap-1.3.0/dynwrap/R/wrap_add_dimred_projection.R | 26 - dynwrap-1.3.0/dynwrap/R/wrap_add_end_state_probabilities.R | 14 dynwrap-1.3.0/dynwrap/R/wrap_add_expression.R | 4 dynwrap-1.3.0/dynwrap/R/wrap_add_feature_importance.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_grouping.R | 42 +- dynwrap-1.3.0/dynwrap/R/wrap_add_prior_information.R | 26 - dynwrap-1.3.0/dynwrap/R/wrap_add_pseudotime.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_root.R | 27 - dynwrap-1.3.0/dynwrap/R/wrap_add_timings.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_trajectory.R | 42 +- dynwrap-1.3.0/dynwrap/R/wrap_add_waypoints.R | 60 +-- dynwrap-1.3.0/dynwrap/R/wrap_data.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_gather_cells_at_milestones.R | 10 dynwrap-1.3.0/dynwrap/R/wrap_label_milestones.R | 28 - dynwrap-1.3.0/dynwrap/build/vignette.rds |binary dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_container.Rmd | 4 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_container.html | 28 - dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_definition.Rmd | 6 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_definition.html | 13 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_r.Rmd | 2 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_r.html | 6 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_wrappers.html | 44 +- dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_comp1.R | 10 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_identity.R | 8 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_random.R | 10 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_shuffle.R | 12 dynwrap-1.3.0/dynwrap/man/add_trajectory.Rd | 6 dynwrap-1.3.0/dynwrap/man/create_ti_method_r.Rd | 2 dynwrap-1.3.0/dynwrap/man/dynwrap-package.Rd |only dynwrap-1.3.0/dynwrap/man/simplify_igraph_network.Rd | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-adapt_orient_topology.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_average.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_geodesic_distances.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_trajectory_dimred.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-classify_milestone_network.R | 24 - dynwrap-1.3.0/dynwrap/tests/testthat/test-method_create_ti_method_r.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-method_infer_trajectory.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-method_parse_parameter_definition.R | 22 - dynwrap-1.3.0/dynwrap/tests/testthat/test-milestone_convertors.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-simplify_igraph_network.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-simplify_trajectory.R | 44 +- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_branch_trajectory.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cell_graph.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cell_waypoints.R | 18 - dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cyclic_trajectory.R | 12 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_dimred.R | 50 +- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_dimred_projection.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_end_state_probabilities.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_expression.R | 16 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_grouping.R | 12 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_linear_trajectory.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_prior_information.R | 84 ++-- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_pseudotime.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_root_and_add_pseudotime.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_timings.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_trajectory.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_waypoints.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_cell_group.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_cluster_graph.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_label_milestones.R | 8 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_container.Rmd | 4 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_definition.Rmd | 6 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_r.Rmd | 2 92 files changed, 858 insertions(+), 857 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse 'intraspecific' trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in 'Taudiere' and 'Violle' (2016) <doi:10.1111/ecog.01433>.
Author: Adrien Taudiere [aut, cre, cph] ,
Cyrille Violle [aut] ,
Francois Munoz [ctb]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between cati versions 0.99.4 dated 2022-02-25 and 0.99.6 dated 2026-03-31
DESCRIPTION | 37 MD5 | 62 NAMESPACE | 112 NEWS.md |only R/allfunctions_cati.R |10942 +++++++++++++++++++++++++++++----------------- R/cati-package.R |only README.md |only build |only inst/CITATION | 26 inst/WORDLIST |only man/ComIndex.Rd | 2 man/ComIndexMulti.Rd | 61 man/Fred.Rd | 20 man/IndexByGroups.Rd | 4 man/MinMaxMST.Rd | 4 man/RaoRel.Rd | 71 man/SumBL.Rd | 4 man/Tstats.Rd | 26 man/as.listofindex.Rd | 2 man/cati-package.Rd |only man/decompCTRE.Rd | 8 man/partvar.Rd | 2 man/plotCorTstats.Rd | 2 man/plotDistri.Rd | 2 man/plotRandtest.Rd | 22 man/plotSESvar.Rd | 2 man/plotSpPop.Rd | 2 man/plotSpVar.Rd | 2 man/samplingSubsetData.Rd | 8 man/ses.Rd | 2 man/ses.listofindex.Rd | 10 man/traitflex.anova.Rd | 11 tests |only 33 files changed, 7341 insertions(+), 4105 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus
genotype-by-environment) and GGB (genotype plus
genotype-by-block-of-environments) models. See Laffont et al. (2013)
<doi:10.2135/cropsci2013.03.0178>.
Author: Kevin Wright [aut, cre, cph] ,
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.9 dated 2024-10-28 and 1.10 dated 2026-03-31
gge-1.10/gge/DESCRIPTION | 11 ++++---- gge-1.10/gge/MD5 | 22 ++++++++-------- gge-1.10/gge/NAMESPACE | 1 gge-1.10/gge/NEWS.md | 11 +++++--- gge-1.10/gge/R/gge.r |only gge-1.10/gge/build/partial.rdb |binary gge-1.10/gge/build/vignette.rds |binary gge-1.10/gge/inst/doc/gge_examples.R | 44 ++++++++++++++++---------------- gge-1.10/gge/inst/doc/gge_examples.html | 19 +++++++------ gge-1.10/gge/man/RedGrayBlue.Rd | 2 - gge-1.10/gge/man/gge.Rd | 17 ++++++++---- gge-1.10/gge/tests/testthat/test_gge.R | 37 ++++++++++++++++++++++---- gge-1.9/gge/R/gge.R |only 13 files changed, 100 insertions(+), 64 deletions(-)
Title: Automated Analysis of Phenotypic Data
Description: Provides functions to analyze and visualize meristic and mensural
phenotypic data in a comparative framework. The package implements an
automated pipeline that summarizes traits, identifies diagnostic variables
among groups, performs multivariate and univariate statistical analyses, and
produces publication-ready graphics. Earlier implementation are
described in Torres (2025) <doi:10.64898/2025.12.18.695244> (v1.0.0)
and Torres (2026) <doi:10.1002/ece3.73111> (v2.0.0).
Author: Javier Torres [aut, cre]
Maintainer: Javier Torres <metalofis@gmail.com>
Diff between Orangutan versions 2.0.0 dated 2026-02-04 and 2.1.0 dated 2026-03-31
DESCRIPTION | 17 MD5 | 16 NAMESPACE | 11 R/Orangutan.R | 1269 ++++++++++++++++++++++++++++++-------------- R/globals.R | 4 R/html_report.R |only R/imports.R | 17 README.md |only man/categorical_analyses.Rd |only man/generate_html_report.Rd |only man/run_orangutan.Rd | 6 11 files changed, 924 insertions(+), 416 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230818.1400 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.5-0 dated 2025-08-19 and 1.5-1 dated 2026-03-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/nzilbb.labbcat.R | 20 +++++++++++++------- build/partial.rdb |binary tests/testthat/test-getMatches.R | 3 ++- 6 files changed, 30 insertions(+), 17 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Run 'shiny' Applications in the Browser
Description: Exporting 'shiny' applications with 'shinylive' allows you to
run them entirely in a web browser, without the need for a separate R
server. The traditional way of deploying 'shiny' applications involves
in a separate server and client: the server runs R and 'shiny', and
clients connect via the web browser. When an application is deployed
with 'shinylive', R and 'shiny' run in the web browser (via 'webR'):
the browser is effectively both the client and server for the
application. This allows for your 'shiny' application exported by
'shinylive' to be hosted by a static web server.
Author: Barret Schloerke [aut, cre] ,
Winston Chang [aut] ,
George Stagg [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinylive versions 0.3.0 dated 2024-11-12 and 0.4.0 dated 2026-03-31
DESCRIPTION | 26 +++--- MD5 | 53 +++++++------ NAMESPACE | 1 NEWS.md | 24 ++++++ R/app_json.R | 46 +++++++---- R/assets.R | 45 ++++++----- R/cli.R | 39 +++++++-- R/deps.R | 47 +++++++---- R/export.R | 58 +++++++------- R/packages.R | 136 +++++++++++++++++++++++++--------- R/quarto_ext.R | 39 ++++++--- R/shinylive-package.R | 1 R/utils.R | 42 ++++++++-- R/version.R | 4 - README.md | 2 inst/WORDLIST | 6 - man/export.Rd | 6 - man/figures |only man/shinylive-package.Rd | 2 tests/testthat/apps/app-r/app.R | 2 tests/testthat/apps/server-r/global.R | 2 tests/testthat/apps/server-r/server.R | 2 tests/testthat/apps/server-r/ui.R | 2 tests/testthat/setup-skip.R | 5 + tests/testthat/test-assertions.R |only tests/testthat/test-export.R | 53 ++++++++++--- tests/testthat/test-quarto_ext.R | 50 +++++++++++- 27 files changed, 485 insertions(+), 208 deletions(-)
Title: Analysis and Visualization of Complex Networks
Description: Provides tools for the analysis, visualization, and manipulation
of dynamical, social (Saqr et al. (2024) <doi:10.1007/978-3-031-54464-4_10>) and
complex networks (Saqr et al. (2025) <doi:10.1145/3706468.3706513>). The package
supports multiple network formats and offers flexible tools for heterogeneous,
multi-layer, and hierarchical network analysis with simple syntax and
extensive toolset.
Author: Mohammed Saqr [aut, cph],
Sonsoles Lopez-Pernas [aut, cre, cph],
Santtu Tikka [aut]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between cograph versions 1.5.2 dated 2026-03-02 and 2.0.0 dated 2026-03-31
cograph-1.5.2/cograph/inst/doc/basic_example.R |only cograph-1.5.2/cograph/inst/doc/basic_example.Rmd |only cograph-1.5.2/cograph/inst/doc/basic_example.html |only cograph-1.5.2/cograph/inst/doc/co_pvalue.R |only cograph-1.5.2/cograph/inst/doc/co_pvalue.Rmd |only cograph-1.5.2/cograph/inst/doc/co_pvalue.html |only cograph-1.5.2/cograph/inst/doc/multi_network.R |only cograph-1.5.2/cograph/inst/doc/multi_network.Rmd |only cograph-1.5.2/cograph/inst/doc/multi_network.html |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.R |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.Rmd |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.html |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.R |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.Rmd |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.html |only cograph-1.5.2/cograph/man/as_cograph_network.Rd |only cograph-1.5.2/cograph/man/figures/README-unnamed-chunk-10-1.jpeg |only 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cograph-2.0.0/cograph/tests/testthat/test-sn-edges.R | 132 - cograph-2.0.0/cograph/tests/testthat/test-sn-nodes.R | 169 -- cograph-2.0.0/cograph/tests/testthat/test-sn-save.R | 9 cograph-2.0.0/cograph/tests/testthat/test-soplot.R | 199 -- cograph-2.0.0/cograph/tests/testthat/test-splot.R | 557 +------ cograph-2.0.0/cograph/tests/testthat/test-themes-extended.R | 12 cograph-2.0.0/cograph/tests/testthat/test-tna-integration.R |only cograph-2.0.0/cograph/tests/testthat/test-tna-temporal.R |only cograph-2.0.0/cograph/tests/testthat/test-validate-nestimate-bootstrap-permutation.R |only cograph-2.0.0/cograph/vignettes/articles |only cograph-2.0.0/cograph/vignettes/input-formats.Rmd |only cograph-2.0.0/cograph/vignettes/introduction.Rmd |only 590 files changed, 6724 insertions(+), 4121 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.2 dated 2025-11-06 and 0.8.3 dated 2026-03-31
vcfppR-0.8.2/vcfppR/src/vcf-popgen.cpp |only vcfppR-0.8.3/vcfppR/DESCRIPTION | 6 vcfppR-0.8.3/vcfppR/MD5 | 33 +- vcfppR-0.8.3/vcfppR/NAMESPACE | 2 vcfppR-0.8.3/vcfppR/NEWS.md | 4 vcfppR-0.8.3/vcfppR/R/RcppExports.R | 16 vcfppR-0.8.3/vcfppR/R/common.R | 60 ++- vcfppR-0.8.3/vcfppR/R/vcf-compare.R | 6 vcfppR-0.8.3/vcfppR/R/vcf-info.R | 4 vcfppR-0.8.3/vcfppR/R/vcf-plot.R | 273 +++++++++++++++++ vcfppR-0.8.3/vcfppR/inst/include/vcfpp.h | 32 + vcfppR-0.8.3/vcfppR/man/plot_variants_per_haplotype.Rd |only vcfppR-0.8.3/vcfppR/man/vcfpp_calc_info_persite.Rd |only vcfppR-0.8.3/vcfppR/man/vcfreader.Rd | 2 vcfppR-0.8.3/vcfppR/src/RcppExports.cpp | 44 +- vcfppR-0.8.3/vcfppR/src/htslib-1.21/config.status | 12 vcfppR-0.8.3/vcfppR/src/vcf-reader.cpp | 3 vcfppR-0.8.3/vcfppR/src/vcf-utils.cpp |only vcfppR-0.8.3/vcfppR/tests/testthat/test-clearinfo.R |only vcfppR-0.8.3/vcfppR/tests/testthat/test-vcf-plot.R | 69 +++- 20 files changed, 496 insertions(+), 70 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/data-documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between rscorecard versions 0.32.0 dated 2025-05-12 and 0.33.0 dated 2026-03-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/sysdata.rda |binary 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Compact Inline Widgets for 'shiny' Apps
Description: Provides a basic set of compact widgets for 'shiny' apps which
occupy less space and can appear inline with surrounding text.
Author: Nick Davies [aut, cre]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between inshiny versions 0.1.3 dated 2026-03-20 and 0.1.4 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 6 ++++++ R/date.R | 5 +++-- R/inline.R | 18 ++++++++++++++++++ R/number.R | 5 +++-- R/select.R | 6 ++++-- R/slider.R | 4 ++-- R/text.R | 10 ++++++++-- inst/www/inshiny/inshiny.css | 18 +++++++++++++++++- man/inline.Rd | 18 ++++++++++++++++++ man/inline_date.Rd | 6 ++++++ man/inline_number.Rd | 16 +++++++++++----- man/inline_select.Rd | 14 +++++++++++++- man/inline_slider.Rd | 8 +++++++- man/inline_text.Rd | 13 ++++++++++++- tests/testthat/_snaps/date.md | 2 +- tests/testthat/_snaps/number.md | 2 +- tests/testthat/_snaps/select.md | 2 +- tests/testthat/_snaps/slider.md | 2 +- tests/testthat/_snaps/text.md | 2 +- 21 files changed, 156 insertions(+), 47 deletions(-)
Title: Nonlinear Longitudinal Process in Structural Equation Modeling
Description: Provides computational tools for nonlinear longitudinal models, in particular the intrinsically nonlinear models, in four scenarios: (1) univariate longitudinal processes with growth factors, with or without covariates including time-invariant covariates (TICs) and time-varying covariates (TVCs); (2) multivariate longitudinal processes that facilitate the assessment of correlation or causation between multiple longitudinal variables; (3) multiple-group models for scenarios (1) and (2) to evaluate differences among manifested groups, and (4) longitudinal mixture models for scenarios (1) and (2), with an assumption that trajectories are from multiple latent classes. The methods implemented are introduced in Liu (2025) <doi:10.3758/s13428-025-02596-4>.
Author: Jin Liu [aut, cre]
Maintainer: Jin Liu <Veronica.Liu0206@gmail.com>
Diff between nlpsem versions 0.3 dated 2023-09-12 and 0.4 dated 2026-03-31
nlpsem-0.3/nlpsem/man/getFitFig.Rd |only nlpsem-0.3/nlpsem/man/getLCSM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getLCSM.output.Rd |only nlpsem-0.3/nlpsem/man/getLGCM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getLGCM.output.Rd |only nlpsem-0.3/nlpsem/man/getMED.initial.Rd |only nlpsem-0.3/nlpsem/man/getMED.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMED.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMED.output.Rd |only nlpsem-0.3/nlpsem/man/getMGM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMGM.output.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.initial.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.output.Rd |only nlpsem-0.3/nlpsem/man/getMIX.initial.Rd |only nlpsem-0.3/nlpsem/man/getMIX.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMIX.output.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MED.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MULTI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MULTI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMIX_TVC.info.Rd |only nlpsem-0.3/nlpsem/man/getMIX_UNI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMIX_UNI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.initial.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getTVC.info.Rd |only nlpsem-0.3/nlpsem/man/getTVC.initial.Rd |only nlpsem-0.3/nlpsem/man/getTVC.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getTVC.output.Rd |only nlpsem-0.3/nlpsem/man/getUNI.GF.Rd |only nlpsem-0.3/nlpsem/man/getUNI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getUNI.initial.Rd |only nlpsem-0.3/nlpsem/man/getUNI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getsub.LCSM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.LCSM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.LGCM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.LGCM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.MED_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.MED_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.MGM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.MGM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.TVC_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.TVC_m.Rd |only nlpsem-0.4/nlpsem/DESCRIPTION | 21 nlpsem-0.4/nlpsem/MD5 | 309 +-- nlpsem-0.4/nlpsem/NAMESPACE | 9 nlpsem-0.4/nlpsem/NEWS.md |only nlpsem-0.4/nlpsem/R/FitFig_helper.R | 164 + nlpsem-0.4/nlpsem/R/LCSM.mxModel_helper.R | 189 - nlpsem-0.4/nlpsem/R/LCSM.output_helper.R | 38 nlpsem-0.4/nlpsem/R/LGCM.mxModel_helper.R | 253 +- nlpsem-0.4/nlpsem/R/LGCM.output_helper.R | 11 nlpsem-0.4/nlpsem/R/MED.Initial_helper.R | 117 - nlpsem-0.4/nlpsem/R/MED.loading_helper.R | 7 nlpsem-0.4/nlpsem/R/MED.mxModel_helper.R | 189 - nlpsem-0.4/nlpsem/R/MED.output_helper.R | 17 nlpsem-0.4/nlpsem/R/MGM.mxModel_helper.R | 226 +- nlpsem-0.4/nlpsem/R/MGM.output_helper.R | 45 nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.LCSM_helper.R | 213 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.LGCM_helper.R | 279 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.MED_helper.R | 147 - nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.MGM_helper.R | 226 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.TVC_helper.R | 1175 +++++------ nlpsem-0.4/nlpsem/R/MGroup.initial_helper.R | 26 nlpsem-0.4/nlpsem/R/MGroup.mxModel_helper.R | 1 nlpsem-0.4/nlpsem/R/MGroup.output_helper.R | 529 ++--- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.LCSM_helper.R | 237 +- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.LGCM_helper.R | 311 +-- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.MED_helper.R | 155 - nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.MGM_helper.R | 254 +- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.TVC_helper.R | 1287 ++++++------- nlpsem-0.4/nlpsem/R/MIX.initial_helper.R | 63 nlpsem-0.4/nlpsem/R/MIX.mxModel_helper.R | 5 nlpsem-0.4/nlpsem/R/MIX.output_helper.R | 532 ++--- nlpsem-0.4/nlpsem/R/MIX_MED.loading_helper.R | 7 nlpsem-0.4/nlpsem/R/MIX_MULTI.addpara_helper.R | 11 nlpsem-0.4/nlpsem/R/MIX_MULTI.loading_helper.R | 11 nlpsem-0.4/nlpsem/R/MIX_TVC.info_helper.R | 41 nlpsem-0.4/nlpsem/R/MIX_UNI.addpara_helper.R | 9 nlpsem-0.4/nlpsem/R/MIX_UNI.loading_helper.R | 10 nlpsem-0.4/nlpsem/R/MULTI.addpara_helper.R | 11 nlpsem-0.4/nlpsem/R/MULTI.initial_helper.R | 168 + nlpsem-0.4/nlpsem/R/MULTI.loading_helper.R | 13 nlpsem-0.4/nlpsem/R/StandardMethods.R | 118 - nlpsem-0.4/nlpsem/R/TVC.info_helper.R | 41 nlpsem-0.4/nlpsem/R/TVC.initial_helper.R | 284 ++ nlpsem-0.4/nlpsem/R/TVC.mxModel_helper.R | 1109 +++++------ nlpsem-0.4/nlpsem/R/TVC.output_helper.R | 18 nlpsem-0.4/nlpsem/R/UNI.GF_helper.R | 254 ++ nlpsem-0.4/nlpsem/R/UNI.addpara_helper.R | 9 nlpsem-0.4/nlpsem/R/UNI.initial_helper.R | 159 + nlpsem-0.4/nlpsem/R/UNI.loading_helper.R | 10 nlpsem-0.4/nlpsem/R/getEstimateStats.R | 110 - nlpsem-0.4/nlpsem/R/getFigure.R | 160 - nlpsem-0.4/nlpsem/R/getIndFS.R | 7 nlpsem-0.4/nlpsem/R/getLCSM.R | 37 nlpsem-0.4/nlpsem/R/getLGCM.R | 49 nlpsem-0.4/nlpsem/R/getLRT.R | 8 nlpsem-0.4/nlpsem/R/getLatentKappa.R | 20 nlpsem-0.4/nlpsem/R/getMGM.R | 64 nlpsem-0.4/nlpsem/R/getMGroup.R | 117 - nlpsem-0.4/nlpsem/R/getMIX.R | 118 - nlpsem-0.4/nlpsem/R/getMediation.R | 64 nlpsem-0.4/nlpsem/R/getPosterior.R | 38 nlpsem-0.4/nlpsem/R/getSummary.R | 22 nlpsem-0.4/nlpsem/R/getTVCmodel.R | 75 nlpsem-0.4/nlpsem/R/global_vars.R | 21 nlpsem-0.4/nlpsem/R/initial_helpers_common.R |only nlpsem-0.4/nlpsem/R/multi_cov_helpers.R |only nlpsem-0.4/nlpsem/R/output_helpers_common.R |only nlpsem-0.4/nlpsem/R/paramNames_helper.R |only nlpsem-0.4/nlpsem/R/validation_helpers.R |only nlpsem-0.4/nlpsem/build/partial.rdb |binary nlpsem-0.4/nlpsem/build/vignette.rds |binary nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.R | 118 - nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.Rmd | 30 nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.html | 61 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.R | 90 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.Rmd | 18 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.html | 89 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.R | 85 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.Rmd | 28 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.html | 46 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.R | 83 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.Rmd | 39 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.html | 50 nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.R | 114 - nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.Rmd | 37 nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.html | 209 +- nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.R | 102 - nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.Rmd | 44 nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.html | 257 +- nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.R | 152 - nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.Rmd | 52 nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.html | 183 - nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.R |only nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.Rmd |only nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.html |only nlpsem-0.4/nlpsem/inst/extdata/getLCSM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getLGCM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMGM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMGroup_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMIX_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMediation_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getTVCmodel_examples.RData |binary nlpsem-0.4/nlpsem/man/KappaOutput-class.Rd | 2 nlpsem-0.4/nlpsem/man/ModelSummary-myMxOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/ModelSummary.Rd | 26 nlpsem-0.4/nlpsem/man/getEstimateStats.Rd | 28 nlpsem-0.4/nlpsem/man/getFigure.Rd | 31 nlpsem-0.4/nlpsem/man/getIndFS.Rd | 8 nlpsem-0.4/nlpsem/man/getLCSM.Rd | 16 nlpsem-0.4/nlpsem/man/getLGCM.Rd | 27 nlpsem-0.4/nlpsem/man/getLRT.Rd | 7 nlpsem-0.4/nlpsem/man/getLatentKappa.Rd | 12 nlpsem-0.4/nlpsem/man/getMGM.Rd | 41 nlpsem-0.4/nlpsem/man/getMGroup.Rd | 53 nlpsem-0.4/nlpsem/man/getMIX.Rd | 59 nlpsem-0.4/nlpsem/man/getMediation.Rd | 47 nlpsem-0.4/nlpsem/man/getPosterior.Rd | 9 nlpsem-0.4/nlpsem/man/getSummary.Rd | 11 nlpsem-0.4/nlpsem/man/getTVCmodel.Rd | 52 nlpsem-0.4/nlpsem/man/myMxOutput-class.Rd | 2 nlpsem-0.4/nlpsem/man/printTable-FSOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-KappaOutput-method.Rd | 8 nlpsem-0.4/nlpsem/man/printTable-StatsOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-myMxOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-postOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable.Rd | 28 nlpsem-0.4/nlpsem/man/show-figOutput-method.Rd | 3 nlpsem-0.4/nlpsem/tests |only nlpsem-0.4/nlpsem/vignettes/getLCSM_examples.Rmd | 30 nlpsem-0.4/nlpsem/vignettes/getLGCM_examples.Rmd | 18 nlpsem-0.4/nlpsem/vignettes/getMGM_examples.Rmd | 28 nlpsem-0.4/nlpsem/vignettes/getMGroup_examples.Rmd | 39 nlpsem-0.4/nlpsem/vignettes/getMIX_examples.Rmd | 37 nlpsem-0.4/nlpsem/vignettes/getMediation_examples.Rmd | 44 nlpsem-0.4/nlpsem/vignettes/getTVCmodel_examples.Rmd | 52 nlpsem-0.4/nlpsem/vignettes/nlpsem_overview.Rmd |only 180 files changed, 6751 insertions(+), 6102 deletions(-)
Title: Income Tax Calculations (UK)
Description: Income tax calculations for England, Northern Ireland and Wales. Estimate annual income tax within the different taxation bands at specified levels of both taxable income and the Personal Allowance, emulating the results obtained at <https://www.gov.uk/estimate-income-tax>. Calculate the standard Personal Allowance at various levels of taxable income. Estimate the personal allowance required to recoup a specified amount of income tax.
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark@markeisler.com>
Diff between Fiscal versions 1.0.1 dated 2026-03-24 and 1.0.2 dated 2026-03-31
DESCRIPTION | 8 ++--- MD5 | 20 +++++++------- NEWS.md | 6 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/incometax.R | 12 ++++++-- inst/doc/incometax.Rnw | 67 +++++++++++++++++++++++++++--------------------- inst/doc/incometax.pdf |binary man/allowance.Rd | 14 +++++----- man/tax_opts.Rd | 31 ++++++++++------------ vignettes/incometax.Rnw | 67 +++++++++++++++++++++++++++--------------------- 11 files changed, 127 insertions(+), 98 deletions(-)
Title: Surrogate Functional False Discovery Rates for Genome-Wide
Association Studies
Description: Pleiotropy-informed significance analysis of genome-wide association studies with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and $q$-value, and uses these estimates to derive a functional $p$-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization).
Author: Andrew Bass [aut, cre],
Chris Wallace [aut]
Maintainer: Andrew Bass <ab3105@cam.ac.uk>
Diff between sffdr versions 1.1.0 dated 2026-02-11 and 1.1.2 dated 2026-03-31
DESCRIPTION | 11 - MD5 | 62 +++--- NAMESPACE | 14 + NEWS.md | 10 + R/RcppExports.R |only R/fpi0est.R | 300 ++++++++++++++++++++++++++------ R/fpvalues.R | 42 ---- R/kernelEstimator.R | 204 ++++++++++++++------- R/null_overlap.R |only R/pi0_model.R | 290 +++++++++++++++++++++++------- R/plot.R | 3 R/sffdr.R | 130 ++++++++++++- README.md | 48 ++++- inst/doc/sffdr.R | 17 + inst/doc/sffdr.Rmd | 39 +++- inst/doc/sffdr.html | 219 ++++++++++++++--------- man/decorrelate_informative.Rd |only man/discover_empirical_nulls.Rd |only man/estimate_rho_overlap.Rd |only man/fit_bivariate_density.Rd | 6 man/fit_strategy_final.Rd | 3 man/fit_univariate_density.Rd | 2 man/fpi0est.Rd | 9 man/kernelEstimator.Rd | 27 +- man/monoSmooth_conditional.Rd |only man/monoSmooth_pava.Rd |only man/overlap_null_density.Rd |only man/pi0_model.Rd | 21 +- man/plot.sffdr.Rd | 3 man/run_empirical_overlap_correction.Rd |only man/sffdr.Rd | 20 ++ src |only tests/testthat/test-fpi0est.R | 127 +++++++++++++ tests/testthat/test-kernelEstimator.R | 25 -- tests/testthat/test-null_overlap.R |only tests/testthat/test-sffdr.R | 151 ++++++++++++++++ vignettes/sffdr.Rmd | 39 +++- 37 files changed, 1408 insertions(+), 414 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) (No. AMSAATR138), Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.3.2 dated 2025-12-09 and 0.4 dated 2026-03-31
DESCRIPTION | 10 MD5 | 60 ++-- NAMESPACE | 9 NEWS.md | 21 + R/ReliaGrowR-package.R | 68 ++++ R/grwr_api.R | 4 R/rdt.R | 25 + R/rga.R | 470 +++++++++++++++++++++++++++++++-- R/sim_failures.R |only build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 3 inst/doc/RGF.R |only inst/doc/RGF.Rmd |only inst/doc/RGF.html |only inst/plumber/plumb-duane.R | 152 ---------- inst/plumber/plumb-gof.R | 80 ----- inst/plumber/plumb-rga.R | 218 --------------- inst/plumber/plumber.R | 354 +++++++++++++++++++----- man/ReliaGrowR-package.Rd | 70 ++++ man/grwr_api.Rd | 5 man/plot.rga.Rd | 3 man/plot.rga_predict.Rd |only man/predict_rga.Rd |only man/print.rga.Rd | 3 man/print.rga_predict.Rd |only man/rdt.Rd | 15 - man/rga.Rd | 38 ++ man/sim_failures.Rd |only man/weibull_to_rga.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-srr-duane.R | 3 tests/testthat/test-srr-rga.R | 376 +++++++++++++++++++++++++- tests/testthat/test-srr-sim_failures.R |only tests/testthat/test-srr_rdt.R | 94 ++++++ vignettes/RGF.Rmd |only 36 files changed, 1497 insertions(+), 594 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.9.1 dated 2025-04-12 and 1.9.2 dated 2026-03-31
DESCRIPTION | 12 LICENSE | 2 MD5 | 99 +-- NAMESPACE | 1 NEWS.md | 4 R/cleancall.R | 1 R/compat-vctrs.R | 1003 ++++++++++++++++----------------- R/disk.R | 16 R/errno.R | 1 R/error.R | 4 R/glob.R | 21 R/iso-date.R | 49 - R/kill-tree.R | 9 R/linux.R | 127 ++-- R/low-level.R | 180 +++-- R/macos.R | 36 - R/memoize.R | 7 R/memory.R | 76 +- R/os.R | 17 R/package.R | 7 R/posix.R | 6 R/ps.R | 193 ++++-- R/rematch2.R | 14 R/string.R |only R/system.R | 63 +- R/testthat-reporter.R | 149 +++- R/utils.R | 126 ++-- README.md | 297 +++++---- inst/tools/error-codes.R | 23 inst/tools/winver.R | 21 man/ps_handle.Rd | 4 man/ps_string.Rd |only src/cleancall.c | 6 src/install.libs.R | 9 tests/testthat.R | 7 tests/testthat/helpers.R | 57 + tests/testthat/test-cleanup-reporter.R | 253 +++++--- tests/testthat/test-common.R | 30 tests/testthat/test-connections.R | 152 +++-- tests/testthat/test-finished.R | 21 tests/testthat/test-kill-tree.R | 88 ++ tests/testthat/test-linux.R | 12 tests/testthat/test-macos.R | 5 tests/testthat/test-pid-reuse.R | 17 tests/testthat/test-posix-zombie.R | 5 tests/testthat/test-posix.R | 29 tests/testthat/test-ps.R | 5 tests/testthat/test-system.R | 12 tests/testthat/test-utils.R | 3 tests/testthat/test-windows.R | 5 tests/testthat/test-winver.R | 26 tests/testthat/test-z-string.R |only 52 files changed, 1954 insertions(+), 1356 deletions(-)
Title: Apply Mapping Functions in Parallel using Futures
Description: Implementations of the family of map() functions from 'purrr'
that can be resolved using any 'future'-supported backend, e.g.
parallel on the local machine or distributed on a compute cluster.
Author: Davis Vaughan [aut, cre] ,
Henrik Bengtsson [aut] ,
Matt Dancho [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between furrr versions 0.3.1 dated 2022-08-15 and 0.4.0 dated 2026-03-31
furrr-0.3.1/furrr/R/future-invoke-map.R |only furrr-0.3.1/furrr/man/future_invoke_map.Rd |only furrr-0.3.1/furrr/man/future_options.Rd |only furrr-0.3.1/furrr/tests/testthat/_snaps/deprecation.md |only furrr-0.3.1/furrr/tests/testthat/test-deprecation.R |only furrr-0.3.1/furrr/tests/testthat/test-future-invoke-map.R |only furrr-0.4.0/furrr/DESCRIPTION | 37 - furrr-0.4.0/furrr/MD5 | 80 +-- furrr-0.4.0/furrr/NAMESPACE | 17 furrr-0.4.0/furrr/NEWS.md | 79 ++- furrr-0.4.0/furrr/R/chunks.R | 24 furrr-0.4.0/furrr/R/furrr-options.R | 159 +++--- furrr-0.4.0/furrr/R/future-imap.R | 129 +++-- furrr-0.4.0/furrr/R/future-map.R | 261 ++++++---- furrr-0.4.0/furrr/R/future-map2.R | 190 ++++--- furrr-0.4.0/furrr/R/future-modify.R | 341 +++++++------- furrr-0.4.0/furrr/R/future-pmap.R | 148 +++--- furrr-0.4.0/furrr/R/future-walk.R | 67 +- furrr-0.4.0/furrr/R/globals.R | 28 - furrr-0.4.0/furrr/R/progress.R | 7 furrr-0.4.0/furrr/R/recycle.R | 10 furrr-0.4.0/furrr/R/seed.R | 28 - furrr-0.4.0/furrr/R/template.R | 193 +++++-- furrr-0.4.0/furrr/R/utils-purrr.R | 34 + furrr-0.4.0/furrr/R/utils.R | 1 furrr-0.4.0/furrr/README.md | 42 - furrr-0.4.0/furrr/man/furrr-package.Rd | 9 furrr-0.4.0/furrr/man/furrr_options.Rd | 40 + furrr-0.4.0/furrr/man/future_imap.Rd | 50 +- furrr-0.4.0/furrr/man/future_map.Rd | 64 +- furrr-0.4.0/furrr/man/future_map2.Rd | 71 +- furrr-0.4.0/furrr/man/future_map_if.Rd | 56 +- furrr-0.4.0/furrr/man/future_modify.Rd | 54 +- furrr-0.4.0/furrr/tests/testthat/_snaps/future-map.md |only furrr-0.4.0/furrr/tests/testthat/_snaps/future-map2.md |only furrr-0.4.0/furrr/tests/testthat/_snaps/future-pmap.md |only furrr-0.4.0/furrr/tests/testthat/helper-furrr-test-that.R | 12 furrr-0.4.0/furrr/tests/testthat/helper-state.R |only furrr-0.4.0/furrr/tests/testthat/test-chunks.R | 19 furrr-0.4.0/furrr/tests/testthat/test-furrr-options.R | 78 ++- furrr-0.4.0/furrr/tests/testthat/test-future-imap.R | 48 + furrr-0.4.0/furrr/tests/testthat/test-future-map.R | 99 +++- furrr-0.4.0/furrr/tests/testthat/test-future-map2.R | 121 +++- furrr-0.4.0/furrr/tests/testthat/test-future-modify.R | 61 ++ furrr-0.4.0/furrr/tests/testthat/test-future-pmap.R | 139 ++++- furrr-0.4.0/furrr/tests/testthat/test-future-walk.R | 24 46 files changed, 1799 insertions(+), 1021 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joseph Zemme [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.23 dated 2026-03-10 and 2.7.24 dated 2026-03-31
DESCRIPTION | 9 MD5 | 162 +++--- NEWS | 7 R/AAA.R | 135 +++-- R/addWaterYear.R | 41 + R/checkWQPdates.R | 12 R/citations.R | 68 +- R/constructNWISURL.R | 552 ++++++++++---------- R/construct_api_requests.R | 572 +++++++++++---------- R/dataRetrieval-package.R | 29 - R/deal_with_empty.R | 72 +- R/findNLDI.R | 94 ++- R/getWebServiceData.R | 90 +-- R/get_ogc_data.R | 228 ++++---- R/get_ogc_documentation.R | 129 ++-- R/importNGWMN_wml2.R | 162 ++++-- R/importRDB1.R | 150 +++-- R/importWQP.R | 225 ++++---- R/importWaterML1.R | 193 +++++-- R/pcode_to_name.R | 44 - R/readNGWMNdata.R | 88 ++- R/readNWISdata.R | 365 ++++++++----- R/readNWISdv.R | 33 - R/readNWISpCode.R | 50 + R/readNWISsite.R | 36 - R/readNWISunit.R | 121 ++-- R/readWQPdata.R | 282 +++++----- R/readWQPdots.R | 65 +- R/readWQPqw.R | 48 - R/read_waterdata.R | 96 +-- R/read_waterdata_channel.R | 98 +-- R/read_waterdata_combined_meta.R | 180 +++--- R/read_waterdata_continuous.R | 114 ++-- R/read_waterdata_daily.R | 84 +-- R/read_waterdata_field_measurements.R | 94 +-- R/read_waterdata_field_meta.R | 74 +- R/read_waterdata_latest_continuous.R | 76 +- R/read_waterdata_latest_daily.R | 76 +- R/read_waterdata_metadata.R | 40 - R/read_waterdata_monitoring_location.R | 125 ++-- R/read_waterdata_parameter_codes.R | 62 +- R/read_waterdata_samples.R | 795 +++++++++++++++--------------- R/read_waterdata_stats.R | 233 ++++---- R/read_waterdata_ts_meta.R | 100 +-- R/rejigger_cols.R | 58 +- R/renameColumns.R | 24 R/setAccess.R | 22 R/walk_pages.R | 147 +++-- R/whatNWISdata.R | 89 ++- R/whatNWISsites.R | 65 +- R/whatWQPdata.R | 216 ++++---- R/whatWQPsites.R | 79 +- build/vignette.rds |binary inst/CITATION | 4 inst/doc/dataRetrieval.html | 6 man/create_NWIS_bib.Rd | 4 man/importNGWMN.Rd | 2 man/importWaterML1.Rd | 6 man/parse_WQP.Rd | 2 man/readWQPdata.Rd | 22 man/readWQPqw.Rd | 8 man/read_waterdata.Rd | 2 man/read_waterdata_channel.Rd | 5 man/read_waterdata_combined_meta.Rd | 10 man/read_waterdata_continuous.Rd | 19 man/read_waterdata_daily.Rd | 14 man/read_waterdata_field_measurements.Rd | 8 man/read_waterdata_field_meta.Rd | 4 man/read_waterdata_latest_continuous.Rd | 6 man/read_waterdata_latest_daily.Rd | 4 man/read_waterdata_monitoring_location.Rd | 15 man/read_waterdata_parameter_codes.Rd | 4 man/read_waterdata_samples.Rd | 6 man/read_waterdata_stats.Rd | 10 man/read_waterdata_ts_meta.Rd | 4 man/wqp_check_status.Rd | 2 tests/testthat/test_waterdata_stats.R | 140 ++--- tests/testthat/tests_general.R | 512 +++++++++++-------- tests/testthat/tests_imports.R | 152 +++-- tests/testthat/tests_nldi.R | 196 +++++-- tests/testthat/tests_samples.R | 203 ++++--- tests/testthat/tests_userFriendly_fxns.R | 446 ++++++++++------ 82 files changed, 4975 insertions(+), 3850 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Giulio Genovese [cph] ,
DuckDB C Extension API Authors [ctb]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 0.1.3-0.0.2 dated 2026-02-24 and 1.1.4-0.0.1 dated 2026-03-31
DESCRIPTION | 11 MD5 | 117 +- NAMESPACE | 12 NEWS.md | 60 + R/bootstrap.R | 37 R/duckhts.R | 804 +++++++++++++++- configure | 2 configure.win | 2 inst/duckhts_extension/bam_reader.c | 168 ++- inst/duckhts_extension/bcf_reader.c | 150 ++ inst/duckhts_extension/bcftools_filter.c |only inst/duckhts_extension/bcftools_shim.c |only inst/duckhts_extension/bgzip.c |only inst/duckhts_extension/duckhts.c | 226 ++++ inst/duckhts_extension/hts_index_builder.c |only inst/duckhts_extension/hts_meta_reader.c | 288 +++-- inst/duckhts_extension/include/bcftools_filter_config.h |only inst/duckhts_extension/include/bcftools_shim.h |only inst/duckhts_extension/include/filter.h |only inst/duckhts_extension/include/quality_encoding.h |only inst/duckhts_extension/include/seq_encoding.h |only inst/duckhts_extension/include/vep_parser.h | 10 inst/duckhts_extension/interval_udf.c |only inst/duckhts_extension/kmer_udf.c |only inst/duckhts_extension/liftover_udf.c |only inst/duckhts_extension/munge_udf.c |only inst/duckhts_extension/quality_encoding.c |only inst/duckhts_extension/quality_encoding_reader.c |only inst/duckhts_extension/score_udf.c |only inst/duckhts_extension/seq_reader.c | 235 ++++ inst/duckhts_extension/tabix_reader.c | 17 inst/duckhts_extension/vep_parser.c | 247 ++++ inst/extdata/colheaders.tsv |only inst/extdata/legacy_phred64.fq |only inst/extdata/score_as.vcf |only inst/extdata/score_chrprefix.vcf |only inst/extdata/score_columns.tsv |only inst/extdata/score_dosage.vcf |only inst/extdata/score_gwas_summary.vcf |only inst/extdata/score_input.vcf |only inst/extdata/score_missing_ds.vcf |only inst/extdata/score_missing_gt.vcf |only inst/extdata/score_regions.txt |only inst/extdata/score_summary.tsv |only inst/extdata/score_summary_bolt.tsv |only inst/extdata/score_summary_custom.tsv |only inst/extdata/score_summary_log10p.tsv |only inst/extdata/score_summary_metal.tsv |only inst/extdata/score_summary_mismatch.tsv |only inst/extdata/score_summary_na.tsv |only inst/extdata/score_summary_no_snp.tsv |only inst/extdata/score_summary_or.tsv |only inst/extdata/score_summary_pgs.tsv |only inst/extdata/score_summary_plink2.tsv |only inst/extdata/score_summary_regenie.tsv |only inst/extdata/score_summary_rsid.tsv |only inst/extdata/score_summary_saige.tsv |only inst/extdata/score_summary_smallp.tsv |only inst/extdata/score_summary_ssf.tsv |only inst/extdata/score_targets.txt |only inst/extdata/targets.bed |only inst/function_catalog |only inst/tinytest/test_basic.R | 154 ++- inst/tinytest/test_cigar_utils.R |only inst/tinytest/test_indexes_bgzip.R |only inst/tinytest/test_integration.R | 39 inst/tinytest/test_intervals.R |only inst/tinytest/test_liftover.R |only inst/tinytest/test_liftover_stress.R |only inst/tinytest/test_munge.R |only inst/tinytest/test_quality_encoding.R |only inst/tinytest/test_score.R |only inst/tinytest/test_seq_ops.R |only man/Rduckhts.Rd | 1 man/rduckhts_bam.Rd | 18 man/rduckhts_bam_index.Rd |only man/rduckhts_bcf.Rd | 4 man/rduckhts_bcf_index.Rd |only man/rduckhts_bed.Rd |only man/rduckhts_bgunzip.Rd |only man/rduckhts_bgzip.Rd |only man/rduckhts_detect_quality_encoding.Rd |only man/rduckhts_fasta.Rd | 5 man/rduckhts_fasta_nuc.Rd |only man/rduckhts_fastq.Rd | 15 man/rduckhts_functions.Rd |only man/rduckhts_gff.Rd | 15 man/rduckhts_gtf.Rd | 15 man/rduckhts_liftover.Rd |only man/rduckhts_munge.Rd |only man/rduckhts_score.Rd |only man/rduckhts_tabix_index.Rd |only 92 files changed, 2362 insertions(+), 290 deletions(-)
Title: Approximate Optimal Experimental Designs Using Generalised
Linear Mixed Models
Description: Optimal design analysis algorithms for any study design that can be represented or
modelled as a generalised linear mixed model including cluster randomised trials,
cohort studies, spatial and temporal epidemiological studies, and split-plot designs.
See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a
detailed manual on model specification. A detailed discussion of the methods in this
package can be found in Watson, Hemming, and Girling (2023) <doi:10.1177/09622802231202379>.
Author: Sam Watson [aut, cre],
Yi Pan [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrOptim versions 0.3.6 dated 2024-12-17 and 0.3.7 dated 2026-03-31
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/R6designspace.R | 4 ++-- build/partial.rdb |binary inst/include/optim/optimclass.h | 1 + src/gd_search.cpp | 1 + 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Tools for Various R Functions Helpers
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 2026.2.28 dated 2026-02-28 and 2026.3.31 dated 2026-03-31
HelpersMG-2026.2.28/HelpersMG/R/Probability_Best_Model_WAIC.R |only HelpersMG-2026.2.28/HelpersMG/man/Probability_Best_Model_WAIC.Rd |only HelpersMG-2026.3.31/HelpersMG/DESCRIPTION | 10 - HelpersMG-2026.3.31/HelpersMG/MD5 | 54 +++++----- HelpersMG-2026.3.31/HelpersMG/NAMESPACE | 6 - HelpersMG-2026.3.31/HelpersMG/NEWS | 15 ++ HelpersMG-2026.3.31/HelpersMG/R/AddPriors.R |only HelpersMG-2026.3.31/HelpersMG/R/ELPDweight.R |only HelpersMG-2026.3.31/HelpersMG/R/HelpersMG-package.R | 4 HelpersMG-2026.3.31/HelpersMG/R/MHalgoGen.R | 49 +++++++-- HelpersMG-2026.3.31/HelpersMG/R/plot.mcmcComposite.R | 21 +++ HelpersMG-2026.3.31/HelpersMG/R/setPriors1.R |only HelpersMG-2026.3.31/HelpersMG/inst/shiny/cutter/ui.R | 2 HelpersMG-2026.3.31/HelpersMG/man/ELPDweight.Rd |only HelpersMG-2026.3.31/HelpersMG/man/ExtractAIC.glm.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/FormatCompareAIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/HelpersMG-package.Rd | 4 HelpersMG-2026.3.31/HelpersMG/man/MHalgoGen.Rd | 21 +++ HelpersMG-2026.3.31/HelpersMG/man/as.mcmc.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/as.parameters.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/as.quantiles.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_AIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_AICc.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_BIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/figures/TB.png |binary HelpersMG-2026.3.31/HelpersMG/man/merge.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plot.PriorsmcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plot.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plus-.PriorsmcmcComposite.Rd |only HelpersMG-2026.3.31/HelpersMG/man/setPriors.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/setPriors1.Rd |only HelpersMG-2026.3.31/HelpersMG/man/summary.mcmcComposite.Rd | 4 32 files changed, 156 insertions(+), 58 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.2.1 dated 2026-01-27 and 1.3.0 dated 2026-03-31
glmmrBase-1.2.1/glmmrBase/inst/include/glmmr/modelmcmc.hpp |only glmmrBase-1.3.0/glmmrBase/DESCRIPTION | 8 glmmrBase-1.3.0/glmmrBase/MD5 | 35 glmmrBase-1.3.0/glmmrBase/R/Betadist.R | 4 glmmrBase-1.3.0/glmmrBase/R/R6Model.R | 229 ++-- glmmrBase-1.3.0/glmmrBase/R/R6covariance.R | 33 glmmrBase-1.3.0/glmmrBase/R/RcppExports.R | 12 glmmrBase-1.3.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/covariance.hpp | 42 glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/hsgpcovariance.hpp | 498 +++++++-- glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 147 ++ glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 515 +++++++++- glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/nngpcovariance.hpp | 100 - glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/randomeffects.hpp | 71 + glmmrBase-1.3.0/glmmrBase/man/Model.Rd | 48 glmmrBase-1.3.0/glmmrBase/man/exponential.Rd | 34 glmmrBase-1.3.0/glmmrBase/src/RcppExports.cpp | 35 glmmrBase-1.3.0/glmmrBase/src/model_module.cpp | 40 glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.cc | 34 19 files changed, 1317 insertions(+), 568 deletions(-)
Title: An Abstracted System for Easily Working with Databases with
Large Datasets
Description: Provides object-oriented database management tools for working with large datasets across multiple database systems. Features include robust connection management for 'PostgreSQL' databases, advanced table operations with bulk data loading and upsert functionality, comprehensive data validation through customizable field type and content validators, efficient index management, and cross-database compatibility. Designed for high-performance data operations in surveillance systems and large-scale data processing workflows.
Author: Richard Aubrey White [aut, cre] ,
August Soerli Mathisen [aut]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdb versions 2025.7.30 dated 2025-08-18 and 2026.2.2 dated 2026-03-31
DESCRIPTION | 22 +++++++--------- MD5 | 18 +++++++------ NAMESPACE | 2 + NEWS.md | 10 +++++++ R/3_onAttach.R | 8 ++--- R/r6_DBConnection_v9.R | 63 +++++++++++++++++++++++++++++++++++++++++++++- README.md | 36 ++++---------------------- build/vignette.rds |binary inst/doc/csdb.html | 5 ++- man/csdb_get_auth_hook.Rd |only man/csdb_set_auth_hook.Rd |only 11 files changed, 107 insertions(+), 57 deletions(-)
Title: Pan-European Phenological Data Analysis
Description: Provides a framework for quality-aware analysis of ground-based
phenological data from the PEP725 Pan-European Phenology Database
(Templ et al. (2018) <doi:10.1007/s00484-018-1512-8>;
Templ et al. (2026) <doi:10.1111/nph.70869>) and similar observation
networks. Implements station-level data quality grading, outlier
detection, phenological normals (climate baselines), anomaly detection,
elevation and latitude gradient estimation with robust regression,
spatial synchrony quantification, partial least squares (PLS) regression
for identifying temperature-sensitive periods, and sequential
Mann-Kendall trend analysis. Supports data import from PEP725 files,
conversion of user-supplied data, and downloadable synthetic datasets
for teaching without barriers of registration.
All analysis outputs provide 'print', 'summary', and
'plot' methods. Interactive spatial visualization is available via
'leaflet'.
Author: Matthias Templ [aut, cre] ,
Barbara Templ [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between pep725 versions 1.0.0 dated 2026-03-09 and 1.0.2 dated 2026-03-31
DESCRIPTION | 6 MD5 | 22 NEWS.md | 11 R/pep_class.R | 13 R/pep_download.R | 29 R/pep_simulate.R | 5 inst/doc/data-quality.html | 787 ++++++++-------- inst/doc/getting-started.html | 1696 +++++++++++++++++------------------- inst/doc/phenological-analysis.html | 1605 +++++++++++++++++----------------- inst/doc/spatial-patterns.html | 1197 ++++++++++++------------- man/pep_coverage.Rd | 13 man/pep_simulate.Rd | 5 12 files changed, 2705 insertions(+), 2684 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.3.3 dated 2026-03-15 and 0.3.4 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/OrgHeatmap.R | 13 ++++++------- README.md | 2 +- inst/doc/introduction.Rmd | 2 +- inst/doc/introduction.html | 2 +- man/OrgHeatmap.Rd | 3 +++ vignettes/introduction.Rmd | 2 +- 9 files changed, 30 insertions(+), 22 deletions(-)
Title: Reinforcement Learning Tools for Multi-Armed Bandit
Description: A flexible general-purpose toolbox for implementing Rescorla-Wagner models
in multi-armed bandit tasks.
As the successor and functional extension of the 'binaryRL' package,
'multiRL' modularizes the Markov Decision Process (MDP) into six core
components. This framework enables users to construct custom models via
intuitive if-else syntax and define latent learning rules for agents.
For parameter estimation, it provides both likelihood-based
inference (MLE and MAP) and simulation-based inference (ABC and
RNN), with full support for parallel processing across subjects.
The workflow is highly standardized, featuring four main functions
that strictly follow the four-step protocol (and ten rules)
proposed by Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Beyond the three built-in models (TD, RSTD, and Utility), users
can easily derive new variants by declaring which variables are
treated as free parameters.
Author: YuKi [aut, cre] ,
Xinyu [aut]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between multiRL versions 0.2.3 dated 2026-01-26 and 0.3.7 dated 2026-03-31
DESCRIPTION | 10 MD5 | 187 +++++++------ NAMESPACE | 3 R/base_plot.R | 7 R/base_setClass.R | 5 R/base_summary.R | 3 R/document_algorithm.R | 22 - R/document_behrule.R | 6 R/document_colnames.R | 4 R/document_control.R | 563 +++++++++++++++++++++++++++--------------- R/document_data.R | 2 R/document_estimate.R | 209 ++++++++------- R/document_funcs.R | 285 ++++++++++----------- R/document_layer.R |only R/document_params.R | 538 ++++++++++++++++++++++------------------ R/document_reduction.R |only R/engine_ABC.R | 16 - R/engine_RNN.R | 347 +++++++++++++++++++------ R/engine_RNN3.R |only R/estimate_0_ENV.R | 6 R/estimate_1_LBI.R | 225 ++++++++++------ R/estimate_1_MAP.R | 308 ++++++++++++---------- R/estimate_1_MLE.R | 199 +++++++------- R/estimate_2_ABC.R | 338 ++++++++++++++----------- R/estimate_2_RNN.R | 140 +++++++--- R/estimate_2_SBI.R | 17 - R/estimation_methods.R | 115 ++++---- R/func_alpha.R | 20 + R/func_beta.R | 27 +- R/func_delta.R | 94 ++++++- R/func_epsilon.R | 56 +--- R/func_gamma.R | 20 + R/func_zeta.R | 20 + R/model_RSTD.R | 2 R/model_TD.R | 2 R/model_Utility.R | 2 R/multiRL-package.R | 12 R/plot_fitting.R | 62 +--- R/plot_recovery.R | 150 ++++++++++- R/process_1_input.R | 6 R/process_3_record.R | 4 R/process_4_output.R | 91 ++++-- R/process_5_metric.R | 30 +- R/step_1_run_m.R | 6 R/step_2_rcv_d.R | 246 +++++++++--------- R/step_3_fit_p.R | 202 ++++++++------- R/step_4_rpl_e.R | 2 R/tool_check_dependency.R | 18 - R/tool_df2matrix.R | 64 ++-- R/tool_extract_abc.R | 6 R/tool_fix_params.r |only R/tool_for_abc.R | 28 +- R/tool_name_abcouts.R |only R/tool_name_rnnouts.R |only R/tool_reduce_sumstats.R |only R/tool_remove_slot.R | 4 R/tool_replay.R | 43 +-- R/tool_restructure_settings.R | 4 R/tool_return_result.R | 2 R/zzz.R | 13 build/partial.rdb |binary man/RSTD.Rd | 2 man/TD.Rd | 2 man/Utility.Rd | 2 man/algorithm.Rd | 22 - man/behrule.Rd | 6 man/colnames.Rd | 4 man/control.Rd | 541 ++++++++++++++++++++++++++-------------- man/data.Rd | 2 man/engine_ABC.Rd | 2 man/engine_RNN.Rd | 41 ++- man/estimate.Rd | 167 ++++++------ man/estimate_0_ENV.Rd | 2 man/estimate_1_LBI.Rd | 23 - man/estimate_1_MAP.Rd | 24 - man/estimate_1_MLE.Rd | 16 - man/estimate_2_ABC.Rd | 10 man/estimate_2_RNN.Rd | 8 man/estimate_2_SBI.Rd | 6 man/estimation_methods.Rd | 20 - man/fit_p.Rd | 21 - man/func_alpha.Rd | 20 + man/func_beta.Rd | 26 + man/func_delta.Rd | 55 +++- man/func_epsilon.Rd | 39 +- man/func_gamma.Rd | 19 + man/func_zeta.Rd | 20 + man/funcs.Rd | 229 ++++++++--------- man/layer.Rd |only man/multiRL-package.Rd | 12 man/params.Rd | 506 +++++++++++++++++++++---------------- man/plot.multiRL.replay.Rd | 5 man/rcv_d.Rd | 35 +- man/reduction.Rd |only man/rpl_e.Rd | 2 man/run_m.Rd | 6 src/process_4_output.cpp | 100 +++++-- src/tool_record_shown.cpp | 9 src/tool_sample_choice.cpp | 40 +- 99 files changed, 4122 insertions(+), 2713 deletions(-)
Title: Functions and Data for "Epidemics: Models and Data in R (2nd
Edition)"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <doi:10.1007/978-3-031-12056-5>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
This is a re-admission after prior archival of version 1.0-9 dated 2022-12-15
Diff between epimdr2 versions 1.0-9 dated 2022-12-15 and 1.1-1 dated 2026-03-31
epimdr2-1.0-9/epimdr2/man/integrandpc.Rd |only epimdr2-1.1-1/epimdr2/CHANGES | 4 +++ epimdr2-1.1-1/epimdr2/DESCRIPTION | 20 ++++++--------- epimdr2-1.1-1/epimdr2/MD5 | 40 ++++++++++++++++--------------- epimdr2-1.1-1/epimdr2/NAMESPACE | 4 +-- epimdr2-1.1-1/epimdr2/NEWS.md |only epimdr2-1.1-1/epimdr2/R/data.R | 5 +-- epimdr2-1.1-1/epimdr2/R/flowField.R |only epimdr2-1.1-1/epimdr2/R/network.R | 4 +-- epimdr2-1.1-1/epimdr2/R/rfuncs.R | 32 +++++++++++------------- epimdr2-1.1-1/epimdr2/R/shiny2strain.r | 3 +- epimdr2-1.1-1/epimdr2/R/shinypara.R | 1 epimdr2-1.1-1/epimdr2/R/shinyross.r | 1 epimdr2-1.1-1/epimdr2/R/spatsir.R | 2 - epimdr2-1.1-1/epimdr2/README.md | 6 ++-- epimdr2-1.1-1/epimdr2/man/cspring.Rd | 2 - epimdr2-1.1-1/epimdr2/man/ebola.Rd | 2 - epimdr2-1.1-1/epimdr2/man/flowField.Rd |only epimdr2-1.1-1/epimdr2/man/llik.pc.Rd | 4 +-- epimdr2-1.1-1/epimdr2/man/plot.cm.Rd | 2 - epimdr2-1.1-1/epimdr2/man/sirNetmod.Rd | 2 - epimdr2-1.1-1/epimdr2/man/sirSpatmod.Rd | 2 - epimdr2-1.1-1/epimdr2/man/variants.Rd | 4 --- 23 files changed, 68 insertions(+), 72 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.7.3 dated 2026-01-23 and 0.8.0 dated 2026-03-31
joinspy-0.7.3/joinspy/inst/doc/introduction.R |only joinspy-0.7.3/joinspy/inst/doc/introduction.Rmd |only joinspy-0.7.3/joinspy/inst/doc/introduction.html |only joinspy-0.7.3/joinspy/vignettes/introduction.Rmd |only joinspy-0.8.0/joinspy/DESCRIPTION | 8 joinspy-0.8.0/joinspy/MD5 | 63 joinspy-0.8.0/joinspy/NEWS.md | 21 joinspy-0.8.0/joinspy/R/advanced_patterns.R | 7 joinspy-0.8.0/joinspy/R/backends.R |only joinspy-0.8.0/joinspy/R/join_strict.R | 18 joinspy-0.8.0/joinspy/R/join_wrappers.R | 40 joinspy-0.8.0/joinspy/README.md | 385 +-- joinspy-0.8.0/joinspy/build/vignette.rds |binary joinspy-0.8.0/joinspy/inst/doc/backends.R |only joinspy-0.8.0/joinspy/inst/doc/backends.Rmd |only joinspy-0.8.0/joinspy/inst/doc/backends.html |only joinspy-0.8.0/joinspy/inst/doc/common-issues.R | 255 +- joinspy-0.8.0/joinspy/inst/doc/common-issues.Rmd | 804 ++++--- joinspy-0.8.0/joinspy/inst/doc/common-issues.html | 1085 +++++----- joinspy-0.8.0/joinspy/inst/doc/production.R |only joinspy-0.8.0/joinspy/inst/doc/production.Rmd |only joinspy-0.8.0/joinspy/inst/doc/production.html |only joinspy-0.8.0/joinspy/inst/doc/quickstart.R |only joinspy-0.8.0/joinspy/inst/doc/quickstart.Rmd |only joinspy-0.8.0/joinspy/inst/doc/quickstart.html |only joinspy-0.8.0/joinspy/inst/doc/why-keys-dont-match.R |only joinspy-0.8.0/joinspy/inst/doc/why-keys-dont-match.Rmd |only joinspy-0.8.0/joinspy/inst/doc/why-keys-dont-match.html |only joinspy-0.8.0/joinspy/man/dot-detect_backend.Rd |only joinspy-0.8.0/joinspy/man/dot-join_spy_impl.Rd | 6 joinspy-0.8.0/joinspy/man/dot-perform_join.Rd |only joinspy-0.8.0/joinspy/man/full_join_spy.Rd | 7 joinspy-0.8.0/joinspy/man/inner_join_spy.Rd | 7 joinspy-0.8.0/joinspy/man/join_strict.Rd | 4 joinspy-0.8.0/joinspy/man/joinspy-package.Rd | 2 joinspy-0.8.0/joinspy/man/left_join_spy.Rd | 7 joinspy-0.8.0/joinspy/man/right_join_spy.Rd | 7 joinspy-0.8.0/joinspy/tests/testthat/Rplots.pdf |binary joinspy-0.8.0/joinspy/tests/testthat/test-backends-integration.R |only joinspy-0.8.0/joinspy/tests/testthat/test-backends.R |only joinspy-0.8.0/joinspy/vignettes/backends.Rmd |only joinspy-0.8.0/joinspy/vignettes/common-issues.Rmd | 804 ++++--- joinspy-0.8.0/joinspy/vignettes/production.Rmd |only joinspy-0.8.0/joinspy/vignettes/quickstart.Rmd |only joinspy-0.8.0/joinspy/vignettes/why-keys-dont-match.Rmd |only 45 files changed, 2066 insertions(+), 1464 deletions(-)
Title: Structural Data for Norway
Description: Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.
Author: Richard Aubrey White [aut, cre] ,
Chi Zhang [aut]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdata versions 2024.4.26 dated 2024-04-26 and 2026.3.30 dated 2026-03-31
DESCRIPTION | 28 - MD5 | 22 NEWS.md | 15 R/1_onAttach.R | 2 R/sysdata.rda |binary README.md | 37 - build/vignette.rds |binary inst/doc/csdata.Rmd | 2 inst/doc/csdata.html | 450 +++++++++---------- inst/doc/locations_norway.html | 116 ++-- inst/doc/population_norway.html | 945 +++++++++++++++++++++------------------- vignettes/csdata.Rmd | 2 12 files changed, 848 insertions(+), 771 deletions(-)
Title: An Inclusive, Unifying API for Progress Updates
Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will als [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between progressr versions 0.18.0 dated 2025-11-06 and 0.19.0 dated 2026-03-31
progressr-0.18.0/progressr/R/progress.R |only progressr-0.18.0/progressr/man/progress.Rd |only progressr-0.18.0/progressr/vignettes/imgs/three_in_chinese.gif |only progressr-0.19.0/progressr/DESCRIPTION | 8 progressr-0.19.0/progressr/MD5 | 156 +- progressr-0.19.0/progressr/NAMESPACE | 2 progressr-0.19.0/progressr/NEWS.md | 69 - progressr-0.19.0/progressr/R/delays.R | 32 progressr-0.19.0/progressr/R/handler_brrr.R |only progressr-0.19.0/progressr/R/handler_cli.R | 12 progressr-0.19.0/progressr/R/handlers.R | 34 progressr-0.19.0/progressr/R/make_progression_handler.R | 1 progressr-0.19.0/progressr/R/progressor.R | 9 progressr-0.19.0/progressr/R/progressr-package.R | 3 progressr-0.19.0/progressr/R/with_progress.R | 14 progressr-0.19.0/progressr/build/vignette.rds |binary progressr-0.19.0/progressr/inst/doc/progressr-01-intro.html | 25 progressr-0.19.0/progressr/inst/doc/progressr-01-intro.md | 28 progressr-0.19.0/progressr/inst/doc/progressr-11-handlers.html | 2 progressr-0.19.0/progressr/inst/doc/progressr-11-handlers.md | 2 progressr-0.19.0/progressr/inst/doc/progressr-21-map-reduce.html | 6 progressr-0.19.0/progressr/inst/doc/progressr-21-map-reduce.md | 6 progressr-0.19.0/progressr/inst/doc/progressr-22-parallel-processing.html | 14 progressr-0.19.0/progressr/inst/doc/progressr-22-parallel-processing.md | 14 progressr-0.19.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.html | 4 progressr-0.19.0/progressr/inst/doc/progressr-25-replace-cli-with-progressr.md | 6 progressr-0.19.0/progressr/inst/doc/progressr-31-knitr.html | 4 progressr-0.19.0/progressr/inst/doc/progressr-31-knitr.md | 6 progressr-0.19.0/progressr/inst/doc/progressr-91-appendix.html | 28 progressr-0.19.0/progressr/inst/doc/progressr-91-appendix.md | 32 progressr-0.19.0/progressr/inst/testme/_prologue/060.utils.R | 2 progressr-0.19.0/progressr/inst/testme/_prologue/080.options.R | 2 progressr-0.19.0/progressr/inst/testme/deploy.R | 2 progressr-0.19.0/progressr/inst/testme/run.R | 562 +++++----- progressr-0.19.0/progressr/inst/testme/test-debug.R | 11 progressr-0.19.0/progressr/inst/testme/test-handlers.R | 20 progressr-0.19.0/progressr/inst/testme/test-progression.R | 18 progressr-0.19.0/progressr/inst/testme/test-with_progress,delay.R | 2 progressr-0.19.0/progressr/inst/testme/test-with_progress,delay_stdout.R |only progressr-0.19.0/progressr/inst/testme/test-with_progress.R | 11 progressr-0.19.0/progressr/man/figures/progressr-logo.png |only progressr-0.19.0/progressr/man/handler_brrr.Rd |only progressr-0.19.0/progressr/man/handlers.Rd | 23 progressr-0.19.0/progressr/man/progressor.Rd | 4 progressr-0.19.0/progressr/man/progressr.Rd | 3 progressr-0.19.0/progressr/man/with_progress.Rd | 14 progressr-0.19.0/progressr/tests/test-debug.R | 1 progressr-0.19.0/progressr/tests/test-demo.R | 1 progressr-0.19.0/progressr/tests/test-exceptions.R | 1 progressr-0.19.0/progressr/tests/test-globals,relay.R | 1 progressr-0.19.0/progressr/tests/test-handler_cli.R | 1 progressr-0.19.0/progressr/tests/test-handler_filesize.R | 1 progressr-0.19.0/progressr/tests/test-handler_make_progression.R | 1 progressr-0.19.0/progressr/tests/test-handler_pbmcapply.R | 1 progressr-0.19.0/progressr/tests/test-handler_progress.R | 1 progressr-0.19.0/progressr/tests/test-handler_rstudio.R | 1 progressr-0.19.0/progressr/tests/test-handler_shiny.R | 1 progressr-0.19.0/progressr/tests/test-handler_tkprogressbar.R | 1 progressr-0.19.0/progressr/tests/test-handler_txtprogressbar.R | 1 progressr-0.19.0/progressr/tests/test-handlers.R | 1 progressr-0.19.0/progressr/tests/test-progress_aggregator.R | 1 progressr-0.19.0/progressr/tests/test-progression.R | 1 progressr-0.19.0/progressr/tests/test-progressor.R | 1 progressr-0.19.0/progressr/tests/test-utils.R | 1 progressr-0.19.0/progressr/tests/test-with_progress,delay.R | 1 progressr-0.19.0/progressr/tests/test-with_progress,delay_stdout.R |only progressr-0.19.0/progressr/tests/test-with_progress,relay.R | 1 progressr-0.19.0/progressr/tests/test-with_progress.R | 1 progressr-0.19.0/progressr/tests/test-without_progress.R | 1 progressr-0.19.0/progressr/tests/test-zzz,doFuture.R | 1 progressr-0.19.0/progressr/tests/test-zzz,foreach_do.R | 1 progressr-0.19.0/progressr/tests/test-zzz,furrr.R | 1 progressr-0.19.0/progressr/tests/test-zzz,future.apply.R | 1 progressr-0.19.0/progressr/tests/test-zzz,plyr.R | 1 progressr-0.19.0/progressr/tests/test-zzz,purrr.R | 1 progressr-0.19.0/progressr/tests/test-zzz,shiny.R | 1 progressr-0.19.0/progressr/vignettes/progressr-01-intro.md | 28 progressr-0.19.0/progressr/vignettes/progressr-11-handlers.md | 2 progressr-0.19.0/progressr/vignettes/progressr-21-map-reduce.md | 6 progressr-0.19.0/progressr/vignettes/progressr-22-parallel-processing.md | 14 progressr-0.19.0/progressr/vignettes/progressr-25-replace-cli-with-progressr.md | 6 progressr-0.19.0/progressr/vignettes/progressr-31-knitr.md | 6 progressr-0.19.0/progressr/vignettes/progressr-91-appendix.md | 32 83 files changed, 777 insertions(+), 537 deletions(-)
Title: Access the Bangladesh Environmental Mobility Panel Dataset
Description: Provides functions to download and work with the Bangladesh
Environmental Mobility Panel (BEMP), a household panel survey tracing
the impacts of riverbank erosion and flooding on (im)mobility,
socio-economic outcomes, and political attitudes along the Jamuna River
in Bangladesh (2021-2024). Wave datasets (20 files across 14 survey
rounds) are hosted on Zenodo
(<doi:10.5281/zenodo.18229497>) and downloaded on demand with
local caching. Bundled data include a merged cross-wave codebook and
wave metadata.
Author: Jan Freihardt [aut, cre]
Maintainer: Jan Freihardt <fjan@ethz.ch>
Diff between BEMPdata versions 0.2.1 dated 2026-03-09 and 0.2.3 dated 2026-03-31
DESCRIPTION | 11 MD5 | 29 R/data.R | 2 R/get_codebook.R | 6 R/get_wave.R | 6 R/utils.R | 4 README.md | 187 - data/codebook.rda |binary inst/shiny/bemp_explorer/global.R | 164 + inst/shiny/bemp_explorer/rsconnect/shinyapps.io/b68gkn-janfreihardt/bemp-explorer.dcf | 2 inst/shiny/bemp_explorer/server.R | 1343 ++++++++-- inst/shiny/bemp_explorer/ui.R | 226 + man/codebook.Rd | 2 man/get_codebook.Rd | 6 man/get_wave.Rd | 6 tests/testthat/setup.R |only 16 files changed, 1677 insertions(+), 317 deletions(-)
Title: High-Dimensional Functional Time Series Analysis
Description: Offers methods for visualising, modelling, and forecasting high-dimensional functional time series, also known as functional panel data. Documentation about 'hdftsa' is initially provided via the paper by Cristian F. Jimenez-Varon, Ying Sun and Han Lin Shang (2024, Journal of Computational and Graphical Statistics).
Author: Han Lin Shang [aut, cre]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between hdftsa versions 1.0 dated 2025-01-24 and 1.1 dated 2026-03-31
hdftsa-1.0/hdftsa/R/FANOVA.R |only hdftsa-1.0/hdftsa/R/One_way_Residuals.R |only hdftsa-1.0/hdftsa/R/Two_way_Residuals.R |only hdftsa-1.0/hdftsa/R/Two_way_Residuals_means.R |only hdftsa-1.0/hdftsa/man/FANOVA.Rd |only hdftsa-1.0/hdftsa/man/One_way_Residuals.Rd |only hdftsa-1.0/hdftsa/man/Two_way_Residuals.Rd |only hdftsa-1.0/hdftsa/man/Two_way_Residuals_means.Rd |only hdftsa-1.1/hdftsa/ChangeLog |only hdftsa-1.1/hdftsa/DESCRIPTION | 20 ++-- hdftsa-1.1/hdftsa/MD5 | 61 +++++++++++---- hdftsa-1.1/hdftsa/NAMESPACE | 24 ++++- hdftsa-1.1/hdftsa/R/FRE_means_oneway.R |only hdftsa-1.1/hdftsa/R/LOS.R |only hdftsa-1.1/hdftsa/R/MFPCA.R |only hdftsa-1.1/hdftsa/R/One_way_mean.R |only hdftsa-1.1/hdftsa/R/One_way_mean_residuals.R |only hdftsa-1.1/hdftsa/R/One_way_median_polish_residuals.R |only hdftsa-1.1/hdftsa/R/Two_way_mean.R |only hdftsa-1.1/hdftsa/R/Two_way_mean_residuals.R |only hdftsa-1.1/hdftsa/R/Two_way_median_polish_residuals.R |only hdftsa-1.1/hdftsa/R/dfpca.R |only hdftsa-1.1/hdftsa/R/dmfpca.R |only hdftsa-1.1/hdftsa/R/forecast.hdfpca.R |only hdftsa-1.1/hdftsa/R/hdfpca.R |only hdftsa-1.1/hdftsa/R/hdpca.R |only hdftsa-1.1/hdftsa/R/mftsc.R |only hdftsa-1.1/hdftsa/R/mftsc_DFPCA.R |only hdftsa-1.1/hdftsa/R/mu_hat_oneway.R |only hdftsa-1.1/hdftsa/R/sco.resamp.R |only hdftsa-1.1/hdftsa/R/tsse.R |only hdftsa-1.1/hdftsa/R/wtflat.R |only hdftsa-1.1/hdftsa/build/partial.rdb |binary hdftsa-1.1/hdftsa/data |only hdftsa-1.1/hdftsa/man/MFPCA.Rd |only hdftsa-1.1/hdftsa/man/One_way_mean.Rd |only hdftsa-1.1/hdftsa/man/One_way_mean_residuals.Rd |only hdftsa-1.1/hdftsa/man/One_way_median_polish.Rd | 14 +-- hdftsa-1.1/hdftsa/man/One_way_median_polish_residuals.Rd |only hdftsa-1.1/hdftsa/man/Two_way_mean.Rd |only hdftsa-1.1/hdftsa/man/Two_way_mean_residuals.Rd |only hdftsa-1.1/hdftsa/man/Two_way_median_polish.Rd | 2 hdftsa-1.1/hdftsa/man/Two_way_median_polish_residuals.Rd |only hdftsa-1.1/hdftsa/man/all_hmd_female_data.Rd |only hdftsa-1.1/hdftsa/man/all_hmd_male_data.Rd |only hdftsa-1.1/hdftsa/man/dmfpca.Rd |only hdftsa-1.1/hdftsa/man/forecast.hdfpca.Rd |only hdftsa-1.1/hdftsa/man/hd_data.Rd |only hdftsa-1.1/hdftsa/man/hdfpca.Rd |only hdftsa-1.1/hdftsa/man/hdftsa-package.Rd | 18 +++- hdftsa-1.1/hdftsa/man/mftsc.Rd |only hdftsa-1.1/hdftsa/man/sim_ex_cluster.Rd |only 52 files changed, 101 insertions(+), 38 deletions(-)
Title: Draw Venn Diagrams
Description: A close to zero dependency package to draw and display Venn
diagrams up to 7 sets, and any Boolean union of set intersections.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between venn versions 1.12 dated 2024-01-08 and 1.13 dated 2026-03-31
DESCRIPTION | 11 MD5 | 29 R/checkZone.R | 91 +- R/extractDisjunctions.R |only R/extractInfo.R | 202 +++--- R/getCentroid.R | 105 +-- R/getZones.R | 358 ++++++----- R/openPlot.R | 145 ++-- R/plotRules.R | 723 ++++++++++++---------- R/sysdata.rda |binary R/utils.R | 15 R/venn.R | 1542 ++++++++++++++++++++++++++---------------------- inst/ChangeLog | 177 ++--- man/extractInfo.Rd | 24 man/venn.Rd | 4 man/venn_package.Rd | 78 +- 16 files changed, 1941 insertions(+), 1563 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] ,
Han Lin Shang [aut, cre, cph]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between ftsa versions 6.6 dated 2025-02-22 and 6.7 dated 2026-03-31
ftsa-6.6/ftsa/R/DFPCA.R |only ftsa-6.6/ftsa/R/LOS.R |only ftsa-6.6/ftsa/R/MFPCA.R |only ftsa-6.6/ftsa/R/dmfpca.R |only ftsa-6.6/ftsa/R/forecast.hdfpca.R |only ftsa-6.6/ftsa/R/hdfpca.R |only ftsa-6.6/ftsa/R/mftsc.R |only ftsa-6.6/ftsa/R/tsse.R |only ftsa-6.6/ftsa/data/all_hmd_female_data.rda |only ftsa-6.6/ftsa/data/all_hmd_male_data.rda |only ftsa-6.6/ftsa/data/hd_data.rda |only ftsa-6.6/ftsa/data/sim_ex_cluster.rda |only ftsa-6.6/ftsa/data/sim_ex_cluster.smooth.rda |only ftsa-6.6/ftsa/man/MFPCA.Rd |only ftsa-6.6/ftsa/man/all_hmd_female_data.Rd |only ftsa-6.6/ftsa/man/all_hmd_male_data.Rd |only ftsa-6.6/ftsa/man/dmfpca.Rd |only ftsa-6.6/ftsa/man/forecast.hdfpca.Rd |only ftsa-6.6/ftsa/man/hd_data.Rd |only ftsa-6.6/ftsa/man/hdfpca.Rd |only ftsa-6.6/ftsa/man/mftsc.Rd |only ftsa-6.6/ftsa/man/sim_ex_cluster.Rd |only ftsa-6.7/ftsa/ChangeLog | 8 ++++ ftsa-6.7/ftsa/DESCRIPTION | 13 +++---- ftsa-6.7/ftsa/MD5 | 43 ++++++++--------------- ftsa-6.7/ftsa/NAMESPACE | 11 ++---- ftsa-6.7/ftsa/R/BrownMat.R |only ftsa-6.7/ftsa/R/H_estimate_RS.R |only ftsa-6.7/ftsa/R/MAphi.R |only ftsa-6.7/ftsa/R/dfpca.R |only ftsa-6.7/ftsa/R/fdpca.R | 2 - ftsa-6.7/ftsa/R/funARMat.R |only ftsa-6.7/ftsa/R/funIntegral.R |only ftsa-6.7/ftsa/R/funKernel.R |only ftsa-6.7/ftsa/R/funMAMat.R |only ftsa-6.7/ftsa/R/sim_FARMA.R |only ftsa-6.7/ftsa/man/H_estimate_RS.Rd |only ftsa-6.7/ftsa/man/ftsa-package.Rd | 49 +++++++++++++++++++++++---- ftsa-6.7/ftsa/man/sim_FARMA.Rd |only 39 files changed, 78 insertions(+), 48 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like 'csv',
'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut] ,
Hadley Wickham [aut] ,
Jennifer Bryan [aut, cre] ,
Shelby Bearrows [ctb],
https://github.com/mandreyel/ [cph] ,
Jukka Jylaenki [cph] ,
Mikkel Joergensen [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between vroom versions 1.7.0 dated 2026-01-27 and 1.7.1 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ inst/doc/vroom.html | 8 ++++---- src/vroom_errors.h | 6 ++++-- src/vroom_write.cc | 2 +- tests/testthat/test-connection.R | 12 ++++++++---- tests/testthat/test-vroom_fwf.R | 3 ++- 8 files changed, 35 insertions(+), 22 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.4-1 dated 2026-01-31 and 3.5-0 dated 2026-03-31
DESCRIPTION | 16 ++++---- MD5 | 48 ++++++++++++------------ NAMESPACE | 2 + NEWS | 46 +++++++++++++++++++++++ R/envelopelpp.R | 4 ++ R/linearK.R | 78 ---------------------------------------- R/linearKmulti.R | 15 ++++--- R/linearpcfmulti.R | 17 +++++--- R/lintess.R | 18 ++++++++- R/quadratcountlpp.R | 9 +++- R/resolve.lambdalpp.R |only build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Smooth.lpp.Rd | 3 + man/density.lpp.Rd | 5 +- man/envelope.lpp.Rd | 14 +++++-- man/linearKcross.inhom.Rd | 23 +++++++++-- man/linearKdot.inhom.Rd | 40 ++++++++++++++++++-- man/linearpcfcross.inhom.Rd | 23 +++++++++-- man/linearpcfdot.inhom.Rd | 40 ++++++++++++++++++-- man/macros/defns.Rd | 3 + man/mergeTiles.lintess.Rd |only man/spatstat.linnet-internal.Rd | 6 +-- tests/testsAtoK.R | 2 - tests/testsL.R | 14 +++++++ 26 files changed, 279 insertions(+), 149 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Roenkkoe [aut],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.24 dated 2026-02-24 and 2.25 dated 2026-03-31
DESCRIPTION | 10 +- MD5 | 138 ++++++++++++++------------- NAMESPACE | 11 ++ NEWS.md | 20 +++- R/RobbinsMonro.R | 2 R/SimAnova.R | 2 R/SimCheck.R | 2 R/SimClean.R | 3 R/SimCollect.R | 2 R/SimDesign.R | 4 R/SimErrors.R |only R/SimExtract.R | 12 +- R/SimFunctions.R | 4 R/SimResults.R | 11 +- R/SimSolve.R | 4 R/SimWarnings.R |only R/analysis.R | 9 + R/descript.R | 110 +++++++++------------- R/manageMessages.R | 2 R/manageWarnings.R | 2 R/reSummarise.R | 2 R/rtruncate.R | 2 R/runArraySimulation.R | 15 +-- R/runSimulation.R | 76 +++++++++------ R/util.R | 32 +++++- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Catch_errors.R | 102 +++++++++++--------- inst/doc/Catch_errors.Rmd | 152 +++++++++++++++++------------- inst/doc/Catch_errors.html | 193 +++++++++++++++++++++++---------------- inst/doc/Fixed_obj_fun.Rmd | 2 inst/doc/Fixed_obj_fun.html | 12 +- inst/doc/HPC-computing.R | 8 + inst/doc/HPC-computing.Rmd | 13 +- inst/doc/HPC-computing.html | 21 ++-- inst/doc/MultipleAnalyses.html | 4 inst/doc/Parallel-computing.Rmd | 6 - inst/doc/Parallel-computing.html | 10 +- inst/doc/Saving-results.R | 2 inst/doc/Saving-results.Rmd | 6 - inst/doc/Saving-results.html | 18 ++- inst/doc/SimDesign-intro.R | 8 + inst/doc/SimDesign-intro.Rmd | 13 ++ inst/doc/SimDesign-intro.html | 112 ++++++++++++++++++++++ man/BF_sim.Rd | 2 man/RobbinsMonro.Rd | 2 man/SimAnova.Rd | 2 man/SimClean.Rd | 3 man/SimErrors.Rd |only man/SimExtract.Rd | 13 +- man/SimFunctions.Rd | 2 man/SimRead.Rd |only man/SimResults.Rd | 9 + man/SimSolve.Rd | 2 man/SimWarnings.Rd |only man/descript.Rd | 31 ++++-- man/manageMessages.Rd | 2 man/manageWarnings.Rd | 2 man/reexports.Rd |only man/rtruncate.Rd | 2 man/runArraySimulation.Rd | 15 +-- man/runSimulation.Rd | 53 ++++++---- tests/tests/mysim-1 |only tests/tests/mysim-1rds |only tests/tests/test-01-core.R | 2 tests/tests/test-02-aggregate.R | 2 tests/tests/test-03-array.R | 2 vignettes/Catch_errors.Rmd | 152 +++++++++++++++++------------- vignettes/Fixed_obj_fun.Rmd | 2 vignettes/HPC-computing.Rmd | 13 +- vignettes/Parallel-computing.Rmd | 6 - vignettes/Saving-results.Rmd | 6 - vignettes/SimDesign-intro.Rmd | 13 ++ 74 files changed, 924 insertions(+), 575 deletions(-)
Title: Sampling Algorithms and Spatially Balanced Sampling
Description: Fast tools for unequal probability sampling in multi-dimensional spaces, implemented in Rust for high performance.
The package offers a wide range of methods, including Sampford (Sampford, 1967, <doi:10.1093/biomet/54.3-4.499>) and correlated Poisson sampling (Bondesson and Thorburn, 2008, <doi:10.1111/j.1467-9469.2008.00596.x>), pivotal sampling (Deville and Tillé, 1998, <doi:10.1093/biomet/91.4.893>), and balanced sampling such as the cube method (Deville and Tillé, 2004, <doi:10.1093/biomet/91.4.893>) to ensure auxiliary totals are respected.
Spatially balanced approaches, including the local pivotal method (Grafström et al., 2012, <doi:10.1111/j.1541-0420.2011.01699.x>), spatially correlated Poisson sampling (Grafström, 2012, <doi:10.1016/j.jspi.2011.07.003>), and locally correlated Poisson sampling (Prentius, 2024, <doi:10.1002/env.2832>), provide efficient designs when the target variable is linked to auxiliary information.
Author: Wilmer Prentius [aut, cre] ,
Anton Grafstroem [ctb] ,
Authors of the dependent Rust crates [aut]
Maintainer: Wilmer Prentius <wilmer.prentius@slu.se>
Diff between rsamplr versions 0.1.1 dated 2025-09-11 and 0.2.0 dated 2026-03-31
DESCRIPTION | 12 - LICENSE.note | 48 ++--- MD5 | 48 +++-- NAMESPACE | 12 + R/000-wrappers.R | 34 +++ R/distributional_designs.R |only R/draw.R |only R/spatial_balance.R | 92 ++++++++++ R/unequal_probability_sampling.R | 13 - R/utils.R | 10 - configure | 26 +++ inst/AUTHORS.md | 29 +-- man/distributional_designs.Rd |only man/distributional_designs_iter.Rd |only man/dot-dbd_defaults.Rd |only man/dot-sampling_defaults.Rd | 4 man/draw.dbd.Rd |only man/spatial_balance_measure.Rd | 66 +++++++ src/Makevars.in | 4 src/init.c | 42 +++- src/rust/Cargo.lock | 72 ++++---- src/rust/Cargo.toml | 18 +- src/rust/api.h | 8 src/rust/src/lib.rs | 316 +++++++++++++++++++++++++++---------- src/rust/src/matrix.rs | 11 - src/rust/src/random.rs | 37 ++-- src/rust/src/utils.rs | 6 src/rust/vendor.tar.xz |binary 28 files changed, 650 insertions(+), 258 deletions(-)
Title: Visualize Simple 2-D Decision Tree Partitions
Description: Visualize the partitions of simple decision trees, involving one or
two predictors, on the scale of the original data. Provides an intuitive
alternative to traditional tree diagrams, by visualizing how a decision tree
divides the predictor space in a simple 2D plot alongside the original data.
The 'parttree' package supports both classification and regression trees
from 'rpart' and 'partykit', as well as trees produced by popular frontend
systems like 'tidymodels' and 'mlr3'. Visualization methods are provided for
both base R graphics and 'ggplot2'.
Author: Grant McDermott [aut, cre] ,
Achim Zeileis [ctb] ,
Brian Heseung Kim [ctb] ,
Julia Silge [ctb]
Maintainer: Grant McDermott <contact@grantmcdermott.com>
Diff between parttree versions 0.1.2 dated 2026-01-15 and 0.1.3 dated 2026-03-31
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 8 ++++++++ build/vignette.rds |binary 4 files changed, 17 insertions(+), 9 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 1.5 dated 2026-03-11 and 1.5.1 dated 2026-03-31
huge-1.5.1/huge/DESCRIPTION | 6 - huge-1.5.1/huge/MD5 | 37 +++---- huge-1.5.1/huge/NEWS.md | 15 ++ huge-1.5.1/huge/R/huge.R | 6 - huge-1.5.1/huge/R/huge.ct.R | 2 huge-1.5.1/huge/R/huge.generator.R | 3 huge-1.5.1/huge/R/huge.glasso.R | 2 huge-1.5.1/huge/R/huge.mb.R | 5 huge-1.5.1/huge/R/huge.select.R | 18 +++ huge-1.5.1/huge/R/huge.tiger.R | 4 huge-1.5.1/huge/inst/doc/huge.pdf |binary huge-1.5.1/huge/man/huge.Rd | 4 huge-1.5.1/huge/man/huge.ct.Rd | 2 huge-1.5.1/huge/man/huge.glasso.Rd | 4 huge-1.5.1/huge/man/huge.mb.Rd | 4 huge-1.5.1/huge/man/huge.select.Rd | 2 huge-1.5.1/huge/man/huge.tiger.Rd | 2 huge-1.5.1/huge/man/plot.huge.Rd | 2 huge-1.5.1/huge/src/huge_core.cpp | 194 +++++++++++-------------------------- huge-1.5/huge/build |only 20 files changed, 133 insertions(+), 179 deletions(-)
Title: Fit the Vector Autoregressive Model for Multiple Individuals
Description: Fit the vector autoregressive model for multiple individuals
using the 'OpenMx' package (Hunter, 2017 <doi:10.1080/10705511.2017.1369354>).
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between fitVARMxID versions 1.0.2 dated 2026-02-27 and 1.0.3 dated 2026-03-31
DESCRIPTION | 8 MD5 | 34 - NEWS.md | 8 R/fitVARMxID-algebras-dot.R | 178 ---------- R/fitVARMxID-beta-dot.R | 36 +- R/fitVARMxID-build-model-id-dot.R | 30 - R/fitVARMxID-fit-dt-var-mx-id-dot.R | 24 - R/fitVARMxID-fit-dt-var-mx-id.R | 22 - R/mxHelper-ctvar-beta-values-dot.R | 2 R/mxHelper-ensure-good-hessian-dot.R | 2 R/mxHelper-run-dot.R | 9 build/partial.rdb |binary man/FitVARMxID.Rd | 30 + man/LDL.Rd | 6 man/Softplus.Rd | 6 man/fitVARMxID-package.Rd | 5 tests/testthat/test-fitVARMxID-beta-fixed-false-null-ct.R | 19 - tests/testthat/test-fitVARMxID-beta-fixed-false-null-values-ct.R | 6 18 files changed, 136 insertions(+), 289 deletions(-)
Title: Adjust Estimates of Learning for Guessing
Description: Provides tools to adjust estimates of learning for guessing-related
bias in educational and survey research. Implements standard guessing
correction methods and a sophisticated latent class model that leverages
informative pre-post test transitions to account for guessing behavior.
The package helps researchers obtain more accurate estimates of actual
learning when respondents may guess on closed-ended knowledge items.
For theoretical background and empirical validation, see Cor and Sood (2018)
<https://gsood.com/research/papers/guess.pdf>.
Author: Gaurav Sood [aut, cre],
Ken Cor [aut]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between guess versions 0.2.1 dated 2025-12-15 and 0.3.0 dated 2026-03-31
guess-0.2.1/guess/tests/README.html |only guess-0.2.1/guess/tests/README.md |only guess-0.3.0/guess/DESCRIPTION | 8 guess-0.3.0/guess/MD5 | 59 ++- guess-0.3.0/guess/NAMESPACE | 7 guess-0.3.0/guess/NEWS.md | 39 ++ guess-0.3.0/guess/R/fit_unified.R | 9 guess-0.3.0/guess/R/group_adj.R | 4 guess-0.3.0/guess/R/internal-helpers.R | 11 guess-0.3.0/guess/R/lca_cor.R | 12 guess-0.3.0/guess/R/lca_subset.R | 4 guess-0.3.0/guess/R/multi_transmat.R | 7 guess-0.3.0/guess/R/nona.R | 9 guess-0.3.0/guess/R/transmat.R | 20 - guess-0.3.0/guess/R/utils-matrix.R | 2 guess-0.3.0/guess/R/utils-validation.R | 151 +++++++--- guess-0.3.0/guess/README.md | 28 + guess-0.3.0/guess/build/vignette.rds |binary guess-0.3.0/guess/inst/WORDLIST | 2 guess-0.3.0/guess/inst/doc/using_guess.html | 4 guess-0.3.0/guess/man/validate_dk.Rd |only guess-0.3.0/guess/man/validate_equal_length.Rd |only guess-0.3.0/guess/man/validate_matrix.Rd |only guess-0.3.0/guess/man/validate_required.Rd |only guess-0.3.0/guess/man/validate_subgroup.Rd |only guess-0.3.0/guess/man/zero1.Rd |only guess-0.3.0/guess/tests/testthat/helper-simulation.R |only guess-0.3.0/guess/tests/testthat/test-comprehensive-battery.R | 4 guess-0.3.0/guess/tests/testthat/test-econometric-formula-derivation.R |only guess-0.3.0/guess/tests/testthat/test-econometric-identification.R |only guess-0.3.0/guess/tests/testthat/test-econometric-likelihood.R |only guess-0.3.0/guess/tests/testthat/test-econometric-parameter-recovery.R |only guess-0.3.0/guess/tests/testthat/test-econometric-se-validation.R |only guess-0.3.0/guess/tests/testthat/test-fit-unified.R | 8 guess-0.3.0/guess/tests/testthat/test-lca-adj.R |only guess-0.3.0/guess/tests/testthat/test-lca-cor.R | 12 guess-0.3.0/guess/tests/testthat/test-multi-transmat.R | 12 guess-0.3.0/guess/tests/testthat/test-utils.R | 62 ++-- 38 files changed, 322 insertions(+), 152 deletions(-)
Title: An 'Shiny' App for Exploring scRNA-seq Data Processed in
'Seurat'
Description: A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.
Author: Yongchao Zhang [aut, cre]
Maintainer: Yongchao Zhang <zhangyongchao@nibs.ac.cn>
Diff between SeuratExplorer versions 0.1.2 dated 2026-01-19 and 0.1.4 dated 2026-03-30
SeuratExplorer-0.1.2/SeuratExplorer/README.md |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/CellRatio-Splited.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/CellRatio.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Dimplot-splited.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/DotPlot-Splited.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/DotPlot.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Featureplot-splited.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Featureplot.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Heatmap-CellLevel.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Heatmap-GroupLevel-2.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/Heatmap-GroupLevel.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/RidgePlot.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/ViolinPlot-Stack.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/ViolinPlot-splited-Stack.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/ViolinPlot-splited.png |only SeuratExplorer-0.1.2/SeuratExplorer/inst/extdata/www/ViolinPlot.png |only SeuratExplorer-0.1.4/SeuratExplorer/DESCRIPTION | 15 SeuratExplorer-0.1.4/SeuratExplorer/MD5 | 48 SeuratExplorer-0.1.4/SeuratExplorer/NAMESPACE | 5 SeuratExplorer-0.1.4/SeuratExplorer/R/functions.R | 166 + SeuratExplorer-0.1.4/SeuratExplorer/R/server.R | 1243 ++++++++-- SeuratExplorer-0.1.4/SeuratExplorer/R/ui.R | 93 SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/README.Rmd |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/Dimplot-1-highlight.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/Dimplot-1.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/Dimplot-2.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/cell-ratio-2.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/cell-ratio.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/dotplot-1.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/dotplot.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/featureplot-1.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/featureplot-2.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/featureplot-3.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/heatmap-cell-level.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/heatmap-group-level.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/ridge-plot-2.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/ridge-plot.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-1.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-2.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-3.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-4.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-5.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-6.png |only SeuratExplorer-0.1.4/SeuratExplorer/inst/extdata/www/violin-7.png |only 44 files changed, 1258 insertions(+), 312 deletions(-)
More information about SeuratExplorer at CRAN
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Title: Bayesian Estimation of Nonlinear Data (BEND)
Description: Provides a set of models to estimate nonlinear longitudinal data using Bayesian estimation methods. These models include the: 1) Bayesian Piecewise Random Effects Model (Bayes_PREM()) which estimates a piecewise random effects (mixture) model for a given number of latent classes and a latent number of possible changepoints in each class, and can incorporate class and outcome predictive covariates (see Lamm (2022) <https://hdl.handle.net/11299/252533> and Lock et al., (2018) <doi:10.1007/s11336-017-9594-5>), 2) Bayesian Crossed Random Effects Model (Bayes_CREM()) which estimates a linear, quadratic, exponential, or piecewise crossed random effects models where individuals are changing groups over time (e.g., students and schools; see Rohloff et al., (2024) <doi:10.1111/bmsp.12334>), and 3) Bayesian Bivariate Piecewise Random Effects Model (Bayes_BPREM()) which estimates a bivariate piecewise random effects model to jointly model two related outcomes (e.g., reading and [...truncated...]
Author: Corissa T. Rohloff [aut, cre] ,
Rik Lamm [aut] ,
Yadira Peralta [aut] ,
Nidhi Kohli [aut] ,
Eric F. Lock [aut]
Maintainer: Corissa T. Rohloff <corissa.wurth@gmail.com>
Diff between BEND versions 1.1 dated 2025-09-23 and 2.0.0 dated 2026-03-30
DESCRIPTION | 8 +- MD5 | 77 +++++++++++++++++++--------- NAMESPACE | 46 ++++++++++++++++ NEWS.md | 6 ++ R/Bayes_BPREM.R | 56 +++++++++++++------- R/Bayes_CREM.R | 53 +++++++++++++------ R/Bayes_PREM.R | 86 +++++++++++++++++-------------- R/data.R |only R/getClassProb.R |only R/getCoef.R |only R/getFitted.R |only R/getFixEf.R |only R/getKProb.R |only R/getModelFit.R |only R/getRanEf.R |only R/getVarCov.R |only R/plot_BPREM.R |only R/plot_CREM.R |only R/plot_PREM.R |only R/print_BPREM.R |only R/print_CREM.R |only R/print_PREM.R |only R/summary_BPREM.R | 121 +++++++++++++++++++++++++++----------------- R/summary_CREM.R | 113 +++++++++++++++++++++++++++-------------- R/summary_PREM.R | 134 +++++++++++++++++++++++++++++-------------------- data/results_bprem.rda |binary data/results_pcrem.rda |binary data/results_prem.rda |binary man/Bayes_BPREM.Rd | 19 ++---- man/Bayes_CREM.Rd | 17 ++---- man/Bayes_PREM.Rd | 35 +++--------- man/SimData_BPREM.Rd | 17 +++++- man/SimData_PCREM.Rd | 17 +++++- man/SimData_PREM.Rd | 19 ++++++ man/getClassProb.Rd |only man/getCoef.Rd |only man/getFitted.Rd |only man/getFixEf.Rd |only man/getKProb.Rd |only man/getModelFit.Rd |only man/getRanEf.Rd |only man/getVarCov.Rd |only man/plot.BPREM.Rd |only man/plot.CREM.Rd |only man/plot.PREM.Rd |only man/print.BPREM.Rd |only man/print.CREM.Rd |only man/print.PREM.Rd |only man/results_bprem.Rd | 22 +++++++- man/results_pcrem.Rd | 22 +++++++- man/results_prem.Rd | 22 +++++++- man/summary.BPREM.Rd | 7 ++ man/summary.CREM.Rd | 7 ++ man/summary.PREM.Rd | 7 ++ 54 files changed, 612 insertions(+), 299 deletions(-)
Title: Utilities for Importing Data from Plain Text Accounting Files
Description: Utilities for querying plain text accounting files from 'Ledger', 'HLedger', and 'Beancount'.
Author: Trevor L. Davis [aut, cre] ,
Jenya Sovetkin [ctb],
Chris Lloyd [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ledger versions 2.0.11 dated 2024-05-20 and 2.0.13 dated 2026-03-30
ledger-2.0.11/ledger/R/net_worth.r |only ledger-2.0.11/ledger/R/prune_coa.r |only ledger-2.0.11/ledger/R/register.r |only ledger-2.0.11/ledger/tests/testthat/test-ledger.R |only ledger-2.0.11/ledger/tests/testthat/test-numeric.R |only ledger-2.0.13/ledger/DESCRIPTION | 17 - ledger-2.0.13/ledger/MD5 | 33 +- ledger-2.0.13/ledger/NEWS.md | 28 + ledger-2.0.13/ledger/R/net_worth.R |only ledger-2.0.13/ledger/R/prune_coa.R |only ledger-2.0.13/ledger/R/register.R |only ledger-2.0.13/ledger/R/to_numeric.R | 8 ledger-2.0.13/ledger/R/zzz.R | 19 - ledger-2.0.13/ledger/README.md | 278 ++++++++---------- ledger-2.0.13/ledger/inst/extdata/example.ledger | 4 ledger-2.0.13/ledger/man/default_toolchain.Rd | 2 ledger-2.0.13/ledger/man/net_worth.Rd | 4 ledger-2.0.13/ledger/man/prune_coa.Rd | 2 ledger-2.0.13/ledger/man/register.Rd | 4 ledger-2.0.13/ledger/tests/testthat/test-net_worth.R |only ledger-2.0.13/ledger/tests/testthat/test-prune_coa.R | 44 +- ledger-2.0.13/ledger/tests/testthat/test-register.R |only ledger-2.0.13/ledger/tests/testthat/test-to_numeric.R |only 23 files changed, 232 insertions(+), 211 deletions(-)
Title: Neural Output Visualization and Analysis
Description: A comprehensive toolkit for analyzing and visualizing neural data
outputs, including Principal Component Analysis (PCA) trajectory plotting,
Multi-Electrode Array (MEA) heatmap generation, and variable importance
analysis. Provides publication-ready visualizations with flexible
customization options for neuroscience research applications.
Author: Alex Tudoras [aut, cre]
Maintainer: Alex Tudoras <alex.tudorasmiravet@ucsf.edu>
Diff between NOVA versions 0.1.1 dated 2025-10-16 and 0.1.5 dated 2026-03-30
DESCRIPTION | 14 MD5 | 26 - NAMESPACE | 10 R/data_handling.R | 166 ++++---- R/metric_plots.R |only R/pca_analysis.R | 53 +- R/plots.R | 689 +++++++++++++++++++++++------------ R/zzz.R | 5 README.md | 244 +++++++----- man/create_mea_heatmaps_enhanced.Rd | 25 + man/plot_mea_metric.Rd |only man/plot_pca_trajectories_general.Rd | 6 tests |only 13 files changed, 800 insertions(+), 438 deletions(-)
Title: Time Varying Mediation Analysis
Description: Provides functions for estimating mediation effects that vary over
time as described in Cai X, Coffman DL, Piper ME, Li R.
Estimation and inference for the mediation effect in a time-varying mediation model.
BMC Med Res Methodol. 2022;22(1):1-12.
Author: Donna Coffman [aut, cre] ,
Xizhen Cai [aut] ,
Yajnaseni Chakraborti [aut] ,
Harry Zobel [ctb]
Maintainer: Donna Coffman <dcoffman@mailbox.sc.edu>
This is a re-admission after prior archival of version 1.1.0 dated 2022-05-25
Diff between tvmediation versions 1.1.0 dated 2022-05-25 and 1.1.1 dated 2026-03-30
DESCRIPTION | 24 - MD5 | 30 +- NEWS.md | 6 R/estBootCIs.R | 10 R/tvma.R | 2 R/tvma_3trt.R | 2 R/tvmb.R | 2 build/vignette.rds |binary inst/CITATION | 12 inst/doc/TVMA_Function_3_Treatment.html | 337 ++++++++++++------------- inst/doc/TVMB_Function_for_Binary_Outcome.html | 289 ++++++++++----------- inst/doc/Time_Varying_Mediation_Analysis.html | 287 ++++++++++----------- man/estBootCIs.Rd | 11 man/tvma.Rd | 2 man/tvma_3trt.Rd | 2 man/tvmb.Rd | 2 16 files changed, 525 insertions(+), 493 deletions(-)
Title: Plastome Assembly Coverage Visualization
Description: Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) <doi:10.1186/s12859-020-3475-0>.
Author: Michael Gruenstaeudl [aut, cre] ,
Gregory Smith [ctb],
Nils Jenke [ctb]
Maintainer: Michael Gruenstaeudl <m_gruenstaeudl@fhsu.edu>
Diff between PACVr versions 1.0.11 dated 2024-04-09 and 1.1.4 dated 2026-03-30
DESCRIPTION | 26 LICENSE | 6 MD5 | 79 NAMESPACE | 35 R/AnalysisSpecs.R | 162 R/Coverage.R |only R/GBKData.R | 266 R/IROps.R | 374 R/OutputSpecs.R | 236 R/PACVr-package.R | 41 R/PACVr.R | 276 R/RCircosOps.R | 1094 +- R/compileStats.R | 78 R/coverageCalcOps.R | 702 - R/customRead.gb.R | 440 - R/helpers.R | 140 R/parsingOps.R | 142 R/quadripOps.R | 366 R/readingOps.R | 608 - R/visualisationOps.R | 522 - R/writingOps.R | 103 R/zzz.R | 14 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 26 inst/doc/PACVr_Vignette.Rnw | 360 inst/doc/PACVr_Vignette.pdf |binary inst/extdata/MG936619/MG936619.gb | 1164 +- inst/extdata/NC_045072/NC_045072.gb | 9358 +++++++++++------------ inst/extdata/PACVr_Rscript.R | 236 inst/extdata/PACVr_run_parallel.R | 116 inst/extdata/README_USAGE/Mitochondrial_Genome.R | 28 inst/extdata/README_USAGE/Plastid_Genome.R | 56 man/PACVr-package.Rd | 58 man/PACVr.complete.Rd | 164 man/RCircos.Env.Rd | 28 tests |only vignettes/PACVr_Vignette.Rnw | 360 38 files changed, 8817 insertions(+), 8847 deletions(-)
Title: Fast and Scalable Approximate k-Nearest Neighbor Search Methods
using 'N2' Library
Description: Implements methods to perform fast approximate K-nearest neighbor search on input matrix. Algorithm based on the 'N2' implementation of an approximate nearest neighbor search using hierarchical Navigable Small World (NSW) graphs. The original algorithm is described in "Efficient and Robust Approximate Nearest Neighbor Search Using Hierarchical Navigable Small World Graphs", Y. Malkov and D. Yashunin, <doi:10.1109/TPAMI.2018.2889473>, <doi:10.48550/arXiv.1603.09320>.
Author: Peter Kharchenko [aut],
Viktor Petukhov [aut],
Dirk Eddelbuettel [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2026-03-06
Diff between N2R versions 1.0.4 dated 2026-03-06 and 1.0.5 dated 2026-03-30
N2R-1.0.4/N2R/src/n2/base.cc |only N2R-1.0.4/N2R/src/n2/distance.cc |only N2R-1.0.4/N2R/src/n2/include/n2/base.h |only N2R-1.0.4/N2R/src/n2/include/n2/simd.h |only N2R-1.0.5/N2R/DESCRIPTION | 10 N2R-1.0.5/N2R/MD5 | 53 - N2R-1.0.5/N2R/README.md | 2 N2R-1.0.5/N2R/src/Makevars | 2 N2R-1.0.5/N2R/src/n2/LICENSE | 2 N2R-1.0.5/N2R/src/n2/Makefile | 4 N2R-1.0.5/N2R/src/n2/Makefile.win | 5 N2R-1.0.5/N2R/src/n2/heuristic.cc | 81 + N2R-1.0.5/N2R/src/n2/hnsw.cc | 915 +-------------------- N2R-1.0.5/N2R/src/n2/hnsw_build.cc |only N2R-1.0.5/N2R/src/n2/hnsw_model.cc |only N2R-1.0.5/N2R/src/n2/hnsw_node.cc | 22 N2R-1.0.5/N2R/src/n2/hnsw_search.cc |only N2R-1.0.5/N2R/src/n2/include/n2/common.h | 23 N2R-1.0.5/N2R/src/n2/include/n2/data.h |only N2R-1.0.5/N2R/src/n2/include/n2/distance.h | 63 - N2R-1.0.5/N2R/src/n2/include/n2/heuristic.h | 20 N2R-1.0.5/N2R/src/n2/include/n2/hnsw.h | 347 +++++-- N2R-1.0.5/N2R/src/n2/include/n2/hnsw_build.h |only N2R-1.0.5/N2R/src/n2/include/n2/hnsw_model.h |only N2R-1.0.5/N2R/src/n2/include/n2/hnsw_node.h | 30 N2R-1.0.5/N2R/src/n2/include/n2/hnsw_search.h |only N2R-1.0.5/N2R/src/n2/include/n2/hnsw_search_impl.h |only N2R-1.0.5/N2R/src/n2/include/n2/max_heap.h |only N2R-1.0.5/N2R/src/n2/include/n2/min_heap.h | 26 N2R-1.0.5/N2R/src/n2/include/n2/mmap.h | 8 N2R-1.0.5/N2R/src/n2/include/n2/sort.h | 9 N2R-1.0.5/N2R/src/n2/include/n2/utils.h |only N2R-1.0.5/N2R/src/n2/include/n2/visited_list.h |only N2R-1.0.5/N2R/src/n2/mmap.cc | 117 -- N2R-1.0.5/N2R/src/n2knn.cpp | 7 35 files changed, 564 insertions(+), 1182 deletions(-)
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Maximilian Muecke [aut, cre] ,
Sebastian Fischer [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3fda versions 0.3.0 dated 2025-10-15 and 0.4.0 dated 2026-03-30
mlr3fda-0.3.0/mlr3fda/tests/testthat/test_PipeOpFDAInterpolate.R |only mlr3fda-0.4.0/mlr3fda/DESCRIPTION | 39 ++-- mlr3fda-0.4.0/mlr3fda/MD5 | 95 +++++----- mlr3fda-0.4.0/mlr3fda/NAMESPACE | 1 mlr3fda-0.4.0/mlr3fda/NEWS.md | 6 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDABsignal.R | 7 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDACor.R | 6 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAExtract.R | 2 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAFlatten.R | 4 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAFourier.R |only mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAInterpol.R | 4 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDARandomEffect.R | 5 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAScaleRange.R | 4 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDASmooth.R | 2 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDATsfeatures.R | 5 mlr3fda-0.4.0/mlr3fda/R/PipeOpFDAWavelets.R | 5 mlr3fda-0.4.0/mlr3fda/R/PipeOpFPCA.R | 2 mlr3fda-0.4.0/mlr3fda/R/TaskRegr_dti.R | 4 mlr3fda-0.4.0/mlr3fda/R/TaskRegr_fuel.R | 4 mlr3fda-0.4.0/mlr3fda/R/bibentries.R | 8 mlr3fda-0.4.0/mlr3fda/R/hash_input.R | 4 mlr3fda-0.4.0/mlr3fda/R/zzz.R | 4 mlr3fda-0.4.0/mlr3fda/README.md | 6 mlr3fda-0.4.0/mlr3fda/build/partial.rdb |binary mlr3fda-0.4.0/mlr3fda/data/fuel.rda |binary mlr3fda-0.4.0/mlr3fda/man/mlr3fda-package.Rd | 4 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.bsignal.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.cor.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.extract.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.flatten.Rd | 4 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.fourier.Rd |only mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.fpca.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.scalerange.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_pipeops_fda.smooth.Rd | 2 mlr3fda-0.4.0/mlr3fda/man/mlr_tasks_dti.Rd | 9 mlr3fda-0.4.0/mlr3fda/man/mlr_tasks_fuel.Rd | 7 mlr3fda-0.4.0/mlr3fda/man/mlr_tasks_phoneme.Rd | 5 mlr3fda-0.4.0/mlr3fda/tests/testthat/_snaps/PipeOpFDASmooth.md | 2 mlr3fda-0.4.0/mlr3fda/tests/testthat/_snaps/PipeOpFDAWavelets.md | 2 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDABsignal.R | 4 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDACor.R | 2 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAFlatten.R | 6 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAFourier.R |only mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAInterpol.R |only mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDARandomEffect.R | 6 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAScaleRange.R | 2 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDATsfeatures.R | 12 - mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAWavelets.R | 12 - mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFDAZoom.R | 4 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_PipeOpFPCA.R | 8 mlr3fda-0.4.0/mlr3fda/tests/testthat/test_hash_input.R | 2 51 files changed, 166 insertions(+), 154 deletions(-)
Title: Conducts Analyses Informing Ecosystem Restoration Decisions
Description: Three sets of data and functions for informing ecosystem restoration
decisions, particularly in the context of the U.S. Army Corps of Engineers.
First, model parameters are compiled as a data set and associated metadata
for over 300 habitat suitability models developed by the U.S. Fish and
Wildlife Service (USFWS 1980, <https://www.fws.gov/policy-library/870fw1>).
Second, functions for conducting habitat suitability analyses both for the
models described above as well as generic user-specified model parameterizations.
Third, a suite of decision support tools for conducting cost-effectiveness and
incremental cost analyses (Robinson et al. 1995, IWR Report 95-R-1, U.S.
Army Corps of Engineers).
Author: S. Kyle McKay [aut, cre] ,
Darixa D. Hernandez-Abrams [aut],
Kiara C. Cushway [aut]
Maintainer: S. Kyle McKay <skmckay@gmail.com>
Diff between ecorest versions 2.0.1 dated 2025-09-19 and 2.0.2 dated 2026-03-30
DESCRIPTION | 8 +-- MD5 | 44 +++++++++---------- R/BBfinder.R | 109 +++++++++++++++++++++++++++++++++++++++++-------- R/CEfinder.R | 49 ++++++++++++++++------ R/HSIarimean.R | 14 +++--- R/HSIeqtn.R | 22 ++++++--- R/HSIgeomean.R | 15 +++--- R/HSImin.R | 15 +++--- R/HSIplotter.R | 33 ++++++++++++++ R/HSIwarimean.R | 25 ++++------- R/HUcalc.R | 26 +++++++---- R/SIcalc.R | 74 ++++++++++++++++++++++----------- R/annualizer.R | 54 ++++++++++++++++++------ data/HSImetadata.RData |binary man/HSIarimean.Rd | 5 -- man/HSIeqtn.Rd | 11 ++-- man/HSIgeomean.Rd | 5 -- man/HSImin.Rd | 5 -- man/HSIplotter.Rd | 21 ++++++++- man/HSIwarimean.Rd | 11 ---- man/HUcalc.Rd | 8 ++- man/SIcalc.Rd | 33 ++++++-------- man/annualizer.Rd | 2 23 files changed, 389 insertions(+), 200 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.16.2 dated 2026-02-27 and 0.16.3 dated 2026-03-30
DESCRIPTION | 12 MD5 | 30 NEWS.md | 9 R/data.R | 2 R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/eq5d.html | 4 inst/shiny/server.R | 1530 ++++++++++++------------------------------ inst/shiny/ui.R | 199 ++--- man/RCWVH.Rd | 2 man/VT.Rd | 3 man/Y3L.Rd | 3 man/eq5d-package.Rd | 2 tests/testthat/test-eq5d5l.R | 8 tests/testthat/test-eq5dy3l.R | 6 16 files changed, 603 insertions(+), 1207 deletions(-)
Title: R Interface to 'DuckDB' Database with Spatial Extension
Description: Fast & memory-efficient functions to analyze and manipulate large
spatial data data sets. It leverages the fast analytical
capabilities of 'DuckDB' and its spatial extension (see <https://duckdb.org/docs/stable/core_extensions/spatial/overview>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckspatial versions 0.9.0 dated 2026-01-10 and 1.0.0 dated 2026-03-30
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duckspatial-1.0.0/duckspatial/tests/testthat/test-collect_options.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-compatibility.R | 37 duckspatial-1.0.0/duckspatial/tests/testthat/test-connection-management.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-db_read.R | 59 duckspatial-1.0.0/duckspatial/tests/testthat/test-db_register.R | 91 duckspatial-1.0.0/duckspatial/tests/testthat/test-db_write.R | 148 duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_affine.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_as_spatial.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_collect.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_crs.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_extent_funs.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_filter.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_generate_points.R | 197 - duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_geom_conversion.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_geom_validation.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_interpolate_aw.R | 64 duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_join.R | 130 duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_measure.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_open_dataset.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_ops_binary.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_ops_unary.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_options.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_predicates.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_quadkey.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_transform.R | 375 + duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_union.R | 488 +- duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_write_dataset-fid.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_write_dataset-validation.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_write_dataset.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-ddbs_write_vector_cross_connection.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-duckdbfs-interop.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-duckspatial_df.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-duckspatial_df_dplyr_methods.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-duckspatial_df_sf_methods.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-formats_autodetect.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-get_query_list.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-helper-temp-spatial-files.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-import-strategies.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-import_view_to_connection.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-mixed-inputs.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-normalize_spatial_input.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-regression-inefficient-fallback.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-resolve_connections.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-resources.R |only duckspatial-1.0.0/duckspatial/tests/testthat/test-tmp_conn.R |only duckspatial-1.0.0/duckspatial/vignettes/aw_interpolation.qmd |only duckspatial-1.0.0/duckspatial/vignettes/benchmark.qmd |only duckspatial-1.0.0/duckspatial/vignettes/duckspatial.qmd |only duckspatial-1.0.0/duckspatial/vignettes/spatial_joins.qmd |only 263 files changed, 8857 insertions(+), 7785 deletions(-)
Title: Temporal Empirical Dynamic Modeling
Description: Inferring causation from time series data through empirical dynamic modeling (EDM), with methods such as convergent cross mapping from Sugihara et al. (2012) <doi:10.1126/science.1227079>, partial cross mapping introduced by Leng et al. (2020) <doi:10.1038/s41467-020-16238-0>, and cross mapping cardinality described in Tao et al. (2023) <doi:10.1016/j.fmre.2023.01.007>, following a systematic description proposed in Lyu et al. (2026) <doi:10.1016/j.compenvurbsys.2026.102435>.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between tEDM versions 1.2 dated 2026-01-14 and 1.3 dated 2026-03-30
DESCRIPTION | 14 MD5 | 50 - NEWS.md | 10 R/Agenerics.R | 26 R/logostic_map.R | 74 +- README.md | 213 +++--- build/vignette.rds |binary inst/CITATION | 19 inst/doc/tEDM.Rmd | 1287 +++++++++++++++++++--------------------- inst/doc/tEDM.html | 163 ++--- inst/include/tEDM.h | 6 man/ccm.Rd | 162 ++--- man/cmc.Rd | 146 ++-- man/figures/edm/fig_case3-1.png |binary man/ic.Rd | 126 +-- man/multispatialccm.Rd | 170 ++--- man/pcm.Rd | 182 ++--- man/simplex.Rd | 156 ++-- man/smap.Rd | 134 ++-- src/CppDistances.cpp | 4 src/CppDistances.h | 4 src/Embed.cpp | 49 - src/NumericUtils.h | 2 src/StatsExp.cpp | 38 - vignettes/tEDM.Rmd | 1287 +++++++++++++++++++--------------------- vignettes/tEDM.Rmd.orig | 5 26 files changed, 2180 insertions(+), 2147 deletions(-)
Title: Forecasting Tipping Points at the Community Level
Description: Rolling and expanding window approaches to assessing abundance based early warning signals, non-equilibrium resilience measures, and machine learning. See Dakos et al. (2012) <doi:10.1371/journal.pone.0041010>, Deb et al. (2022) <doi:10.1098/rsos.211475>, Drake and Griffen (2010) <doi:10.1038/nature09389>, Ushio et al. (2018) <doi:10.1038/nature25504> and Weinans et al. (2021) <doi:10.1038/s41598-021-87839-y> for methodological details. Graphical presentation of the outputs are also provided for clear and publishable figures. Visit the 'EWSmethods' website for more information, and tutorials.
Author: Duncan O'Brien [aut, cre, cph] ,
Smita Deb [aut] ,
Sahil Sidheekh [aut],
Narayanan Krishnan [aut],
Partha Dutta [aut] ,
Christopher Clements [aut]
Maintainer: Duncan O'Brien <duncan.a.obrien@gmail.com>
Diff between EWSmethods versions 1.3.1 dated 2024-05-15 and 1.3.3 dated 2026-03-30
EWSmethods-1.3.1/EWSmethods/inst/python/src/inference/__pycache__/ewsnet_pred_rand.cpython-39.pyc |only EWSmethods-1.3.3/EWSmethods/DESCRIPTION | 25 +-- EWSmethods-1.3.3/EWSmethods/MD5 | 78 +++++----- EWSmethods-1.3.3/EWSmethods/NAMESPACE | 10 - EWSmethods-1.3.3/EWSmethods/NEWS.md | 8 - EWSmethods-1.3.3/EWSmethods/R/II.R | 24 ++- EWSmethods-1.3.3/EWSmethods/R/deseason_ts.R | 12 - EWSmethods-1.3.3/EWSmethods/R/detrend_ts.R | 4 EWSmethods-1.3.3/EWSmethods/R/embed_ts.R | 24 +-- EWSmethods-1.3.3/EWSmethods/R/ewsnet_init.R | 24 ++- EWSmethods-1.3.3/EWSmethods/R/imbalance_gain.R | 4 EWSmethods-1.3.3/EWSmethods/R/multiAR.R | 2 EWSmethods-1.3.3/EWSmethods/R/multivariate_resilience_indicators.R | 26 +-- EWSmethods-1.3.3/EWSmethods/R/no_plot_rolling_ews_fn.R | 26 --- EWSmethods-1.3.3/EWSmethods/R/plotEWS.R | 16 +- EWSmethods-1.3.3/EWSmethods/R/reset_ewsnet.R | 17 +- EWSmethods-1.3.3/EWSmethods/R/reset_sewsnet.R |only EWSmethods-1.3.3/EWSmethods/R/rnk_matrix.R | 13 + EWSmethods-1.3.3/EWSmethods/R/sewsnet_predict.R |only EWSmethods-1.3.3/EWSmethods/R/tuneII.R | 8 - EWSmethods-1.3.3/EWSmethods/R/uniAR.R | 7 EWSmethods-1.3.3/EWSmethods/R/univariate_composite_ews_wrapper.R | 2 EWSmethods-1.3.3/EWSmethods/R/w_composite_ews_fn.R | 10 - EWSmethods-1.3.3/EWSmethods/README.md | 44 ++--- EWSmethods-1.3.3/EWSmethods/build/vignette.rds |binary EWSmethods-1.3.3/EWSmethods/inst/doc/ews_assessments.Rmd | 4 EWSmethods-1.3.3/EWSmethods/inst/doc/ews_assessments.html | 52 +++--- EWSmethods-1.3.3/EWSmethods/inst/python/src/inference/__pycache__/ewsnet_pred_rand.cpython-310.pyc |binary EWSmethods-1.3.3/EWSmethods/man/II.Rd | 4 EWSmethods-1.3.3/EWSmethods/man/default_sewsnet_path.Rd |only EWSmethods-1.3.3/EWSmethods/man/ewsnet_reset.Rd | 4 EWSmethods-1.3.3/EWSmethods/man/figures/README-expanding_oct_plot-1.png |binary EWSmethods-1.3.3/EWSmethods/man/figures/README-expanding_plot-1.png |binary EWSmethods-1.3.3/EWSmethods/man/figures/README-expanding_plot_trait-1.png |binary EWSmethods-1.3.3/EWSmethods/man/figures/README-rolling_plot-1.png |binary EWSmethods-1.3.3/EWSmethods/man/imbalance_gain.Rd | 4 EWSmethods-1.3.3/EWSmethods/man/multiAR.Rd | 2 EWSmethods-1.3.3/EWSmethods/man/sewsnet_predict.Rd |only EWSmethods-1.3.3/EWSmethods/man/sewsnet_reset.Rd |only EWSmethods-1.3.3/EWSmethods/man/tuneII.Rd | 8 - EWSmethods-1.3.3/EWSmethods/man/uniAR.Rd | 2 EWSmethods-1.3.3/EWSmethods/tests/testthat/test-ii.R | 2 EWSmethods-1.3.3/EWSmethods/vignettes/ews_assessments.Rmd | 4 43 files changed, 254 insertions(+), 216 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Renato Hilario [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pmcardoso@ciencias.ulisboa.pt>
Diff between BAT versions 2.11.0 dated 2025-07-29 and 2.11.1 dated 2026-03-30
DESCRIPTION | 10 ++-- MD5 | 12 ++--- R/BAT.R | 107 ++++++++++++++++++++++++++++++++++++---------------- man/cwm.Rd | 8 +++ man/hyper.build.Rd | 6 ++ man/kernel.build.Rd | 1 man/standard.Rd | 1 7 files changed, 99 insertions(+), 46 deletions(-)
Title: Analysis of Event Data with Two Time Scales
Description: Analyse time to event data with two time scales by estimating a smooth hazard that varies over two time scales. If covariates are available, estimate a proportional hazards model with such a two-dimensional baseline hazard.
Functions are provided to prepare the raw data for estimation, to fit the model and to plot the two-dimensional smooth hazard.
Extension to a competing risks model are implemented. For details about the method please refer to Carollo et al. (2025) <doi:10.1002/sim.10297>.
Author: Angela Carollo [aut, cre, cph] ,
Paul H.C. Eilers [aut],
Jutta Gampe [aut]
Maintainer: Angela Carollo <carollo@demogr.mpg.de>
Diff between TwoTimeScales versions 1.2.0 dated 2026-03-25 and 1.2.1 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- R/select_model2ts.R | 4 ++-- man/figures/logo.png |only man/select_model2ts.Rd | 4 ++-- 5 files changed, 11 insertions(+), 10 deletions(-)
Title: Rearrangement Distances Between Phylogenetic Trees
Description: Fast calculation of tree rearrangement distances.
For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and
Reconnection (TBR), and Replug distances, using the algorithms of Whidden
and Matsen (2017) <doi:10.48550/arXiv.1511.07529>.
For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter
algorithms of Whidden, Beiko, and Zeh (2013) <doi:10.1137/110845045>.
Author: Martin R. Smith [aut, cre, cph] ,
Chris Whidden [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TBRDist versions 1.0.3 dated 2025-11-28 and 2.0.0 dated 2026-03-30
DESCRIPTION | 42 +++-- MD5 | 148 ++++++++++++++++++-- NAMESPACE | 2 NEWS.md | 24 +++ R/RcppExports.R | 17 ++ R/rspr.R |only R/uspr.R | 2 build/partial.rdb |only inst/CITATION | 66 +++++++- inst/doc/TBRDist.html | 4 man/RSPRDist.Rd |only man/dot-CheckRooted.Rd |only man/rspr_dist.Rd |only src/RcppExports.cpp | 15 ++ src/rspr |only src/rspr.cpp |only src/spr |only src/spr_lookup.cpp |only src/uspr/tbr.h | 143 ++++++++----------- src/uspr/tree_numbering.h |only src/uspr/uforest.h | 8 + src/uspr/unode.h | 272 +++++++++++++++++++++++-------------- src/uspr/unode_arena.h |only src/uspr/uspr.h | 267 ++++++++++++++++++++++++++++-------- src/uspr/uspr_neighbors.h | 4 src/uspr/uspr_neighbors_numbered.h |only src/uspr/utree.h | 57 +++---- tests/testthat/test-rspr.R |only tests/testthat/test-src.R | 2 29 files changed, 759 insertions(+), 314 deletions(-)
Title: Scalable Gaussian Process Regression with Hierarchical Shrinkage
Priors
Description: Efficient variational inference methods for fully Bayesian univariate
and multivariate Gaussian and t-process regression models. Hierarchical shrinkage priors,
including the triple gamma prior, are used for effective variable selection and
covariance shrinkage in high-dimensional settings. The package leverages normalizing
flows to approximate complex posterior distributions. For details on implementation,
see Knaus (2025) <doi:10.48550/arXiv.2501.13173>.
Author: Peter Knaus [aut, cre]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
This is a re-admission after prior archival of version 1.1.1 dated 2025-10-01
Diff between shrinkGPR versions 1.1.1 dated 2025-10-01 and 2.0.0 dated 2026-03-30
DESCRIPTION | 16 - MD5 | 79 +++-- NAMESPACE | 11 NEWS.md | 17 + R/GPR_class.R | 89 ++++-- R/MVGPR_class.R |only R/MVTPR_class.R |only R/TPR_class.R | 107 +++----- R/internal_utils.R | 134 ++++++---- R/kernel_funcs.R | 178 ++++++------- R/plot_functions.R | 93 +++++- R/pred_functions.R | 409 +++++++++++++++++++++++------- R/save_load.R |only R/shrinkGPR.R | 127 +++------ R/shrinkGPR_package.R | 94 +++++-- R/shrinkMVGPR.R |only R/shrinkMVTPR.R |only R/shrinkTPR.R | 142 +++------- R/simGPR.R | 452 +++++++++++++++++----------------- R/simMVGPR.R |only R/sylvester.R | 12 man/LPDS.Rd | 7 man/calc_pred_moments.Rd | 26 + man/eval_pred_dens.Rd | 12 man/gen_marginal_samples.Rd | 160 ++++++------ man/gen_posterior_samples.Rd | 29 +- man/kernel_functions.Rd | 8 man/load_shrinkGPR.Rd |only man/plot.shrinkGPR.Rd | 96 +++---- man/plot.shrinkGPR_marg_samples_1D.Rd | 137 +++++----- man/plot.shrinkGPR_marg_samples_2D.Rd | 151 +++++------ man/plot.shrinkMVGPR.Rd |only man/plot.shrinkTPR.Rd | 96 +++---- man/predict.shrinkMVGPR.Rd |only man/predict.shrinkTPR.Rd | 6 man/save_shrinkGPR.Rd |only man/shrinkGPR.Rd | 435 +++++++++++++++----------------- man/shrinkMVGPR.Rd |only man/shrinkMVTPR.Rd |only man/shrinkTPR.Rd | 446 +++++++++++++++------------------ man/simGPR.Rd | 176 ++++++------- man/simMVGPR.Rd |only man/sylvester.Rd | 126 ++++----- tests/testthat/Rplots.pdf |binary tests/testthat/test_shrinkGPR.R | 22 + tests/testthat/test_shrinkMVGPR.R |only tests/testthat/test_shrinkMVTPR.R |only tests/testthat/test_shrinkTPR.R | 24 + 48 files changed, 2135 insertions(+), 1782 deletions(-)
Title: Accelerated Estimation of Robust Location and Scale
Description: Estimates robust location and scale parameters using
platform-specific Single Instruction, Multiple Data (SIMD) vectorization
and Intel Threading Building Blocks (TBB) for parallel processing.
Implements a novel variance-weighted ensemble estimator that adaptively
combines all available statistics. Methods include logistic
M-estimators, the estimators of Rousseeuw and Croux (1993), the Gini
mean difference, the scaled Median Absolute Deviation (MAD), the scaled
Interquartile Range (IQR), and unbiased standard deviations. Achieves
substantial speedups over existing implementations through an 'Rcpp'
backend with fused single-buffer algorithms that halve memory traffic
for MAD and M-scale estimation, and a unified dispatcher that
automatically selects the optimal estimator based on sample size.
Author: Dennis Alexis Valin Dittrich [aut, cre, cph]
Maintainer: Dennis Alexis Valin Dittrich <davd@economicscience.net>
Diff between robscale versions 0.5.3 dated 2026-03-29 and 0.5.4 dated 2026-03-30
DESCRIPTION | 8 - MD5 | 61 ++++++----- NEWS.md | 67 +++++++++++++ R/RcppExports.R | 8 - R/robLoc.R | 2 R/robScale.R | 2 configure | 111 +++++++++++++-------- inst/CITATION | 2 inst/doc/robscale-intro.Rmd | 25 ++-- inst/doc/robscale-intro.html | 47 ++++----- man/robLoc.Rd | 2 man/robScale.Rd | 2 src/Makevars.in | 2 src/RcppExports.cpp | 22 ---- src/adm.cpp | 24 ++++ src/diag.cpp | 60 +---------- src/ensemble.cpp | 26 +++-- src/estimators_internal.h | 29 +++-- src/gmd.cpp | 4 src/iqr.cpp | 14 +- src/pdq_select.h | 2 src/qn_estimator.cpp | 2 src/qnsn_hardware_info.h | 21 +++- src/qnsn_kernels.h | 2 src/rob_loc.cpp | 12 +- src/rob_scale.cpp | 22 ++-- src/robscale_config.h | 44 ++++---- src/robust_core.h | 180 +++++++++++++++-------------------- src/simd_median.h |only src/sn_estimator.cpp | 4 tests/testthat/test-runtime-config.R | 8 - vignettes/robscale-intro.Rmd | 25 ++-- 32 files changed, 446 insertions(+), 394 deletions(-)
Title: UNHCR Refugee Population Statistics Database
Description: The Refugee Population Statistics Database published by
The Office of The United Nations High Commissioner for Refugees (UNHCR)
contains information about forcibly displaced populations
spanning more than 70 years of statistical activities.
It covers displaced populations such as refugees, asylum-seekers and
internally displaced people, including their demographics.
Stateless people are also included, most of who have never been displaced.
The database also reflects the different types of solutions
for displaced populations such as repatriation or resettlement.
More information on the data and methodology can be found on
the UNHCR Refugee Data Finder <https://www.unhcr.org/refugee-statistics/>.
Author: Hisham Galal [aut],
Ahmadou Dicko [aut],
Janis Kreuder [cre],
UNHCR [cph]
Maintainer: Janis Kreuder <kreuder@unhcr.org>
Diff between refugees versions 2025.06.0 dated 2025-11-19 and 2025.06.1 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ data/asylum_applications.rda |binary data/asylum_decisions.rda |binary data/countries.rda |binary data/demographics.rda |binary data/flows.rda |binary data/idmc.rda |binary data/population.rda |binary data/solutions.rda |binary data/unrwa.rda |binary 12 files changed, 18 insertions(+), 14 deletions(-)
Title: Quantile-Frequency Analysis (QFA) of Time Series and Spline
Quantile Regression (SQR)
Description: Implementation of quantile frequency analysis (QFA) for time series based on trigonometric quantile regression and of spline quantile regression (SQR) for estimating the coefficients in linear quantile regression models as smooth functions of the quantile level.
References:
[1] Li, T.-H. (2012). ''Quantile periodograms,'' J. of the American Statistical Association,
107, 765–776. <doi:10.1080/01621459.2012.682815>
[2] Li, T.-H. (2014). Time Series with Mixed Spectra, CRC Press. <doi:10.1201/b15154>
[3] Li, T.-H. (2025). ''Quantile Fourier transform, quantile series, and nonparametric
estimation of quantile spectra,'' Communications in Statistics: Simulation and
Computation, 1–22. <doi:10.1080/03610918.2025.2509820>
[4] Li, T.-H. (2025). ''Quantile-crossing spectrum and spline autoregression estimation,''
Statistical Inference for Stochastic Processes, 28, 20. <doi:10.1007/s11203-025-09336-7>
[5] Li, T.-H. (2025). ''Spline autoregression method for estimation of q [...truncated...]
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl024@outlook.com>
Diff between qfa versions 4.2 dated 2025-09-11 and 5.0 dated 2026-03-30
qfa-4.2/qfa/R/qfa4.2.R |only qfa-5.0/qfa/DESCRIPTION | 44 ++++++++++-------- qfa-5.0/qfa/MD5 | 86 ++++++++++++++++++++---------------- qfa-5.0/qfa/NAMESPACE | 14 +++++ qfa-5.0/qfa/R/datasets.R | 39 ++++++++++++---- qfa-5.0/qfa/R/qfa5.0.R |only qfa-5.0/qfa/build |only qfa-5.0/qfa/data/finIndex.rda |only qfa-5.0/qfa/data/yearssn2024.rda |only qfa-5.0/qfa/man/birthweight.Rd | 8 ++- qfa-5.0/qfa/man/boot.sqr.Rd |only qfa-5.0/qfa/man/engel.Rd | 4 - qfa-5.0/qfa/man/finIndex.Rd |only qfa-5.0/qfa/man/per.Rd | 2 qfa-5.0/qfa/man/qacf.Rd | 2 qfa-5.0/qfa/man/qcser.Rd | 2 qfa-5.0/qfa/man/qdft.Rd | 2 qfa-5.0/qfa/man/qdft2qacf.Rd | 2 qfa-5.0/qfa/man/qdft2qper.Rd | 2 qfa-5.0/qfa/man/qdft2qser.Rd | 2 qfa-5.0/qfa/man/qfa.plot.Rd | 7 ++ qfa-5.0/qfa/man/qkl.divergence.Rd | 2 qfa-5.0/qfa/man/qper.Rd | 2 qfa-5.0/qfa/man/qper2.Rd | 2 qfa-5.0/qfa/man/qser.Rd | 2 qfa-5.0/qfa/man/qser2ar.Rd | 9 ++- qfa-5.0/qfa/man/qser2qacf.Rd | 2 qfa-5.0/qfa/man/qser2sar.Rd | 6 ++ qfa-5.0/qfa/man/qspec.ar.Rd | 16 ++++-- qfa-5.0/qfa/man/qspec.lw.Rd | 2 qfa-5.0/qfa/man/qspec.sar.Rd | 5 +- qfa-5.0/qfa/man/qspec2qcoh.Rd | 2 qfa-5.0/qfa/man/sar.eq.bootstrap.Rd | 5 +- qfa-5.0/qfa/man/sar.eq.test.Rd | 2 qfa-5.0/qfa/man/sar.gc.bootstrap.Rd | 5 +- qfa-5.0/qfa/man/sar.gc.coef.Rd | 2 qfa-5.0/qfa/man/sar.gc.test.Rd | 2 qfa-5.0/qfa/man/sqdft.Rd | 48 ++++++++++++++------ qfa-5.0/qfa/man/sqdft.fit.Rd | 41 ++++++++++++----- qfa-5.0/qfa/man/sqr.Rd | 84 ++++++++++++++++++++++++----------- qfa-5.0/qfa/man/sqr.fit.Rd | 45 ++++++++++++------ qfa-5.0/qfa/man/sqr.fit.optim.Rd | 10 ++-- qfa-5.0/qfa/man/sqr.plot.Rd |only qfa-5.0/qfa/man/sqr1.fit.Rd |only qfa-5.0/qfa/man/sqr3.fit.Rd |only qfa-5.0/qfa/man/sqr_deriv.plot.Rd |only qfa-5.0/qfa/man/tqr.fit.Rd | 6 +- qfa-5.0/qfa/man/tsqr.fit.Rd | 49 ++++++++++++++------ qfa-5.0/qfa/man/yearssn.Rd | 9 ++- qfa-5.0/qfa/man/yearssn2.Rd |only 50 files changed, 379 insertions(+), 195 deletions(-)
Title: Standard Methods for Use in Public Health Scotland
Description: A collection of methods for commonly undertaken analytical
tasks, primarily developed for Public Health Scotland (PHS) analysts,
but the package is also generally useful to others working in the
healthcare space, particularly since it has functions for working with
Community Health Index (CHI) numbers. The package can help to make
data manipulation and analysis more efficient and reproducible.
Author: Public Health Scotland [cph],
David Caldwell [aut],
Lucinda Lawrie [rev],
Jack Hannah [aut],
Tina Fu [aut, cre],
Ciara Gribben [aut],
Chris Deans [aut],
Jaime Villacampa [aut],
Graeme Gowans [aut],
Alice Byers [ctb],
Alan Yeung [ctb],
James Hayes [au [...truncated...]
Maintainer: Tina Fu <Yuyan.Fu2@phs.scot>
Diff between phsmethods versions 1.0.2 dated 2024-01-08 and 1.1.0 dated 2026-03-30
phsmethods-1.0.2/phsmethods/R/phsmethods.R |only phsmethods-1.0.2/phsmethods/R/rename.R |only phsmethods-1.0.2/phsmethods/man/make_inheritance_checks.Rd |only phsmethods-1.0.2/phsmethods/man/phsmethods.Rd |only phsmethods-1.0.2/phsmethods/man/rename.Rd |only phsmethods-1.0.2/phsmethods/tests/testthat/test-rename.R |only phsmethods-1.1.0/phsmethods/DESCRIPTION | 22 phsmethods-1.1.0/phsmethods/MD5 | 133 phsmethods-1.1.0/phsmethods/NAMESPACE | 60 phsmethods-1.1.0/phsmethods/NEWS.md | 203 - phsmethods-1.1.0/phsmethods/R/age_calculate.R | 161 - phsmethods-1.1.0/phsmethods/R/age_from_chi.R |only phsmethods-1.1.0/phsmethods/R/chi_check.R | 240 - phsmethods-1.1.0/phsmethods/R/chi_pad.R | 78 phsmethods-1.1.0/phsmethods/R/create_age_groups.R | 140 phsmethods-1.1.0/phsmethods/R/data.R | 45 phsmethods-1.1.0/phsmethods/R/dob_from_chi.R | 461 +- phsmethods-1.1.0/phsmethods/R/extract_fin_year.R | 72 phsmethods-1.1.0/phsmethods/R/file_size.R | 245 - phsmethods-1.1.0/phsmethods/R/format_postcode.R | 314 - phsmethods-1.1.0/phsmethods/R/make_inheritance_checks.R | 129 phsmethods-1.1.0/phsmethods/R/match_area.R | 176 - phsmethods-1.1.0/phsmethods/R/percent.R |only phsmethods-1.1.0/phsmethods/R/phsmethods-package.R |only phsmethods-1.1.0/phsmethods/R/qtr.R | 496 +-- phsmethods-1.1.0/phsmethods/R/sex_from_chi.R | 192 - phsmethods-1.1.0/phsmethods/README.md | 361 +- phsmethods-1.1.0/phsmethods/build/vignette.rds |binary phsmethods-1.1.0/phsmethods/inst/WORDLIST | 50 phsmethods-1.1.0/phsmethods/inst/doc/chi-operations.R | 320 +- phsmethods-1.1.0/phsmethods/inst/doc/chi-operations.Rmd | 488 +-- phsmethods-1.1.0/phsmethods/inst/doc/chi-operations.html | 1583 +++++----- phsmethods-1.1.0/phsmethods/inst/doc/percent.R |only phsmethods-1.1.0/phsmethods/inst/doc/percent.Rmd |only phsmethods-1.1.0/phsmethods/inst/doc/percent.html |only phsmethods-1.1.0/phsmethods/man/age_calculate.Rd | 108 phsmethods-1.1.0/phsmethods/man/age_from_chi.Rd | 134 phsmethods-1.1.0/phsmethods/man/area_lookup.Rd | 71 phsmethods-1.1.0/phsmethods/man/chi_check.Rd | 146 phsmethods-1.1.0/phsmethods/man/chi_pad.Rd | 78 phsmethods-1.1.0/phsmethods/man/create_age_groups.Rd | 108 phsmethods-1.1.0/phsmethods/man/dob_from_chi.Rd | 108 phsmethods-1.1.0/phsmethods/man/extract_fin_year.Rd | 58 phsmethods-1.1.0/phsmethods/man/file_size.Rd | 179 - phsmethods-1.1.0/phsmethods/man/format_postcode.Rd | 162 - phsmethods-1.1.0/phsmethods/man/match_area.Rd | 116 phsmethods-1.1.0/phsmethods/man/percent.Rd |only phsmethods-1.1.0/phsmethods/man/phsmethods-package.Rd |only phsmethods-1.1.0/phsmethods/man/qtr.Rd | 120 phsmethods-1.1.0/phsmethods/man/sex_from_chi.Rd | 134 phsmethods-1.1.0/phsmethods/tests/spelling.R | 12 phsmethods-1.1.0/phsmethods/tests/testthat.R | 8 phsmethods-1.1.0/phsmethods/tests/testthat/_snaps/UNIX/file_size.md | 77 phsmethods-1.1.0/phsmethods/tests/testthat/_snaps/extract_fin_year.md | 226 - phsmethods-1.1.0/phsmethods/tests/testthat/_snaps/format_postcode.md | 148 phsmethods-1.1.0/phsmethods/tests/testthat/_snaps/rename.md | 486 +-- phsmethods-1.1.0/phsmethods/tests/testthat/_snaps/windows/file_size.md | 77 phsmethods-1.1.0/phsmethods/tests/testthat/files/iris.csv | 302 - phsmethods-1.1.0/phsmethods/tests/testthat/files/puromycin.txt | 48 phsmethods-1.1.0/phsmethods/tests/testthat/files/swiss.tsv | 96 phsmethods-1.1.0/phsmethods/tests/testthat/test-age_calculate.R | 597 ++- phsmethods-1.1.0/phsmethods/tests/testthat/test-age_from_chi.R |only phsmethods-1.1.0/phsmethods/tests/testthat/test-chi_check.R | 198 - phsmethods-1.1.0/phsmethods/tests/testthat/test-chi_pad.R | 76 phsmethods-1.1.0/phsmethods/tests/testthat/test-create_age_groups.R | 134 phsmethods-1.1.0/phsmethods/tests/testthat/test-dob_from_chi.R | 859 ++--- phsmethods-1.1.0/phsmethods/tests/testthat/test-extract_fin_year.R | 228 - phsmethods-1.1.0/phsmethods/tests/testthat/test-file_size.R | 132 phsmethods-1.1.0/phsmethods/tests/testthat/test-format_postcode.R | 304 - phsmethods-1.1.0/phsmethods/tests/testthat/test-make_inheritance_checks.R | 118 phsmethods-1.1.0/phsmethods/tests/testthat/test-match_area.R | 118 phsmethods-1.1.0/phsmethods/tests/testthat/test-percent.R |only phsmethods-1.1.0/phsmethods/tests/testthat/test-qtr.R | 152 phsmethods-1.1.0/phsmethods/tests/testthat/test-sex_from_chi.R | 214 - phsmethods-1.1.0/phsmethods/vignettes/chi-operations.Rmd | 488 +-- phsmethods-1.1.0/phsmethods/vignettes/percent.Rmd |only 76 files changed, 6523 insertions(+), 6066 deletions(-)
Title: Penalized Estimation of Multiple-Subject Vector Autoregressive
Models
Description: Simulate, estimate, and forecast vector autoregressive (VAR)
models for multiple-subject data using structured penalization. Decomposes
dynamics into shared (common) and subject-specific (unique) components via
adaptive LASSO with FISTA optimization. Supports cross-validation and
extended BIC model selection and subgroup detection, and time-varying
parameters.
Author: Zachary Fisher [aut, cre],
Christopher Crawford [aut],
Younghoon Kim [ctb],
Vladas Pipiras [ctb]
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between multivar versions 1.3.0 dated 2026-03-17 and 1.4.0 dated 2026-03-30
DESCRIPTION | 33 +++++--- MD5 | 38 ++++++---- R/constructModel.R | 27 +++++-- R/est_base_weight_mat.R | 48 ++++++++----- R/estimate_initial_coefs.R | 107 +++++++++++++++++++++++++++-- R/maity_debiasing.R |only R/multivarObjectClass.R | 18 +++- R/select_by_ebic.R | 129 +++++++++++++++++++++++++++++++---- README.md |only man/adaptive_weights.Rd | 6 + man/aggregate_common_redescending.Rd |only man/build_theta_nodewise.Rd |only man/compute_ebic.Rd | 23 ++++-- man/constructModel.Rd | 16 ++-- man/count_block_df.Rd |only man/debias_var1_single.Rd |only man/debias_var1_subjects.Rd |only man/estimate_glmnet_alasso.Rd |only man/estimate_initial_coefs.Rd | 5 + man/estimate_maity_effects.Rd |only man/estimate_raw_effects.Rd | 2 man/maity_debiasing.Rd |only man/multivar-class.Rd | 6 + man/multivar-package.Rd | 4 - man/redescending_aggregate.Rd |only man/soft_threshold_matrix.Rd |only 26 files changed, 367 insertions(+), 95 deletions(-)
Title: Information-Theoretic Measures for Revealing Variable
Interactions
Description: Implements information-theoretic measures to explore variable interactions, including KSG mutual information estimation for continuous variables from Kraskov et al. (2004) <doi:10.1103/PhysRevE.69.066138>, knockoff conditional mutual information described in Zhang & Chen (2025) <doi:10.1126/sciadv.adu6464>, synergistic-unique-redundant decomposition introduced by Martinez-Sanchez et al. (2024) <doi:10.1038/s41467-024-53373-4>, allowing detection of complex and diverse relationships among variables.
Author: Wenbo Lyu [aut, cre, cph]
Maintainer: Wenbo Lyu <lyu.geosocial@gmail.com>
Diff between infoxtr versions 0.1 dated 2026-03-19 and 0.2 dated 2026-03-30
DESCRIPTION | 10 - MD5 | 57 +++--- NEWS.md | 12 + R/RcppExports.R | 4 R/entropy.R | 16 - R/internal_utility.R | 76 ++++----- R/kocmi.R | 8 R/surd.R | 130 ++++++++------- R/te.R | 8 README.md | 38 ++-- build/vignette.rds |binary inst/CITATION | 2 inst/doc/surd.Rmd | 20 +- inst/doc/surd.html | 281 +++++++++++++++++----------------- inst/include/infoxtr.h | 1 inst/include/infoxtr/kocmi.hpp | 16 + inst/include/infoxtr/numericutils.hpp | 111 +++++++++++++ inst/include/infoxtr/symdync.hpp |only man/figures/surd/fig_surd_cvds-1.png |binary man/figures/surd/fig_surd_npp-1.png |binary man/figures/surd/fig_surd_popd-1.png |binary man/kocmi.Rd | 3 man/surd.Rd | 16 + man/te.Rd | 3 src/InfotheoExps.cpp | 39 ++-- src/KOCMI.cpp | 2 src/RcppExports.cpp | 10 - src/SURD.cpp | 123 ++++++++++++-- vignettes/surd.Rmd | 20 +- vignettes/surd.Rmd.orig | 18 +- 30 files changed, 651 insertions(+), 373 deletions(-)
Title: Curated Datasets and Tools for Epidemiological Data Analysis
Description: Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, 'DIVINE' makes the process more efficient, transparent, and reproducible.
Author: Natalia Pallares [aut, cre],
Joao Carmezim [aut],
Pau Satorra [aut],
Lucia Blanc [aut],
Cristian Tebe [aut]
Maintainer: Natalia Pallares <napallares@recerca.clinic.cat>
Diff between DIVINE versions 0.1.1 dated 2025-12-11 and 0.1.2 dated 2026-03-30
DESCRIPTION | 10 +- MD5 | 26 +++---- NEWS.md | 28 ++++---- R/end_followup.R | 4 - R/icu.R | 6 - R/impute_missing.R | 174 ++++++++++++++++++++++++++++++++++++++------------ README.md | 4 + build/vignette.rds |binary inst/doc/DIVINE.Rmd | 5 + inst/doc/DIVINE.html | 12 ++- man/end_followup.Rd | 4 - man/icu.Rd | 6 - man/impute_missing.Rd | 6 + vignettes/DIVINE.Rmd | 5 + 14 files changed, 208 insertions(+), 82 deletions(-)
Title: Bias-Corrected Bayesian Classification with Selected Features
Description: Fully Bayesian Classification with a subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.
Author: Longhai Li [aut, cre]
Maintainer: Longhai Li <longhai.li@usask.ca>
Diff between BCBCSF versions 1.0-1 dated 2015-09-25 and 1.0-2 dated 2026-03-30
DESCRIPTION | 18 ++++++++++++------ MD5 | 11 ++++++----- R/comp_pred.r | 47 ++++++++++++++++++++++++++++++----------------- R/tr-pr.r | 2 +- man/example.Rd | 11 +++++++++-- man/fitpred.Rd | 24 ++++++++++++++++++++---- src/init.c |only 7 files changed, 78 insertions(+), 35 deletions(-)
Title: Credential Chain for Seamless 'OAuth 2.0' Authentication to
'Azure Services'
Description: Implements a credential chain for 'Azure OAuth 2.0' authentication
based on the package 'httr2''s 'OAuth' framework. Sequentially attempts authentication
methods until one succeeds. During development allows interactive
browser-based flows ('Device Code' and 'Auth Code' flows) and non-interactive
flow ('Client Secret') in batch mode.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between azr versions 0.3.1 dated 2026-03-04 and 0.3.2 dated 2026-03-30
azr-0.3.1/azr/inst/code.html |only azr-0.3.2/azr/DESCRIPTION | 6 - azr-0.3.2/azr/MD5 | 16 ++-- azr-0.3.2/azr/NEWS.md | 5 + azr-0.3.2/azr/R/api-client.R | 98 +++++++++++--------------- azr-0.3.2/azr/R/credential-azure-cli.R | 2 azr-0.3.2/azr/R/import-funs.R | 32 +++++++- azr-0.3.2/azr/inst/www |only azr-0.3.2/azr/man/default_response_handler.Rd | 34 ++------- azr-0.3.2/azr/man/is_hosted_session.Rd | 11 +- 10 files changed, 107 insertions(+), 97 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Lina Patil [aut, cre],
Stefan Bundfuss [aut] ,
Kristin Dahnert [aut],
Fanny Gautier [aut] ,
Edoardo Mancini [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Gerardo Jose Rodriguez [aut] ,
Vladyslav Shuliar [aut] ,
Cytel Inc. [cph, fnd],
F. Hoffmann-L [...truncated...]
Maintainer: Lina Patil <lina.patil@cytel.com>
Diff between pharmaversesdtm versions 1.4.0 dated 2026-01-10 and 1.4.1 dated 2026-03-30
DESCRIPTION | 16 +++++++---- MD5 | 58 ++++++++++++++++++++++++----------------- NEWS.md | 26 ++++++++++++++++++ R/be.R |only R/dm.R | 4 ++ R/dm_metabolic.R | 4 ++ R/dm_neuro.R | 5 ++- R/dm_peds.R | 6 ++-- R/dm_vaccine.R | 4 ++ R/mb.R |only R/ms.R |only README.md | 20 +++++++++----- data/be.rda |only data/dm.rda |binary data/dm_metabolic.rda |binary data/dm_neuro.rda |binary data/dm_peds.rda |binary data/dm_vaccine.rda |binary data/mb.rda |only data/ms.rda |only inst/WORDLIST | 17 ++++++++++++ inst/extdata/sdtms-specs.json | 21 ++++++++++++++ inst/extdata/ts.json |only man/be.Rd |only man/dm.Rd | 4 ++ man/dm_metabolic.Rd | 4 ++ man/dm_neuro.Rd | 5 ++- man/dm_peds.Rd | 6 ++-- man/dm_vaccine.Rd | 4 ++ man/figures/gsk_logo.png |binary man/figures/logo.png |binary man/figures/roche_logo.png |binary man/mb.Rd |only man/ms.Rd |only man/pharmaversesdtm-package.Rd | 1 35 files changed, 155 insertions(+), 50 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
Title: Statistical Methodology for Graphical Extreme Value Models
Description: Statistical methodology for sparse multivariate extreme value models. Methods are
provided for exact simulation and statistical inference for multivariate Pareto distributions
on graphical structures as described in the paper 'Graphical Models for Extremes' by
Engelke and Hitz (2020) <doi:10.1111/rssb.12355>.
Author: Sebastian Engelke [aut, cre],
Adrien S. Hitz [aut],
Nicola Gnecco [aut],
Manuel Hentschel [aut]
Maintainer: Sebastian Engelke <sebastian.engelke@unige.ch>
Diff between graphicalExtremes versions 0.3.4 dated 2025-06-13 and 0.3.5 dated 2026-03-30
DESCRIPTION | 8 MD5 | 22 R/eglatent.R | 38 - R/matrix_completions_main.R | 23 build/partial.rdb |binary build/vignette.rds |binary data/flights.rda |binary inst/doc/applicationDanube.R | 532 +++++++------- inst/doc/applicationDanube.html | 1474 +++++++++++++++++---------------------- inst/doc/applicationFlights.R | 412 +++++----- inst/doc/applicationFlights.html | 992 ++++++++++---------------- man/complete_Gamma.Rd | 8 12 files changed, 1583 insertions(+), 1926 deletions(-)
More information about graphicalExtremes at CRAN
Permanent link
Title: Adaptive Trial Simulator
Description: Package that simulates adaptive (multi-arm, multi-stage) clinical
trials using adaptive stopping, adaptive arm dropping, and/or adaptive
randomisation. Developed as part of the INCEPT (Intensive Care Platform
Trial) project (<https://incept.dk/>), primarily supported by a grant
from Sygeforsikringen "danmark" (<https://www.sygeforsikring.dk/>).
Author: Anders Granholm [aut, cre] ,
Benjamin Skov Kaas-Hansen [aut] ,
Aksel Karl Georg Jensen [ctb] ,
Theis Lange [ctb]
Maintainer: Anders Granholm <andersgran@gmail.com>
Diff between adaptr versions 1.4.0 dated 2024-05-03 and 1.5.0 dated 2026-03-30
DESCRIPTION | 22 MD5 | 232 - NEWS.md | 46 R/adaptr-package.R | 11 R/calibrate_trial.R | 4 R/check_performance.R | 16 R/check_remaining_arms.R | 2 R/extract_results.R | 31 R/find_beta_params.R | 16 R/get_ys_and_draws.R | 21 R/plot_history.R | 46 R/plot_metrics_ecdf.R | 2 R/plot_status.R | 6 R/print.R | 24 R/prob_funs.R | 36 R/run_trial.R | 110 R/run_trials.R | 2 R/setup_trial.R | 149 R/summary.R | 2 R/update_saved.R | 118 R/utils.R | 2 R/utils_plots.R | 8 R/zzz.R | 2 README.md | 130 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 25 inst/doc/Advanced-example.R | 18 inst/doc/Advanced-example.Rmd | 69 inst/doc/Advanced-example.html | 545 +- inst/doc/Basic-examples.R | 25 inst/doc/Basic-examples.Rmd | 41 inst/doc/Basic-examples.html | 1038 ++--- inst/doc/Overview.R | 49 inst/doc/Overview.Rmd | 102 inst/doc/Overview.html | 836 ++-- inst/extdata |only inst/testdata/binom___calibration___setup2_arms__no_difference___rar.RData |binary inst/testdata/binom__result__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__result__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/binom__results__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__softened__sparse.RData |binary inst/testdata/binom__results__3_arms__no_control__equivalence__stopping.RData |binary inst/testdata/binom__setup__3_arms__common_control__equivalence__futility__softened.RData |binary inst/testdata/binom__setup__3_arms__no_control__equivalence__softened.RData |binary inst/testdata/norm__result__3_arms__common_control__fixed__all_arms_fixed.RData |binary inst/testdata/norm__results__3_arms__common_control__fixed__all_arms_fixed.RData |binary inst/testdata/norm__setup__3_arms__common_control__fixed__all_arms_fixed.RData |binary inst/testdata/norm__setup__3_arms__common_control__matched__varying_probs.RData |binary man/adaptr-package.Rd | 11 man/calibrate_trial.Rd | 4 man/check_performance.Rd | 41 man/check_remaining_arms.Rd | 2 man/cond_rescale_prob.Rd |only man/extract_history.Rd | 28 man/extract_results.Rd | 31 man/extract_statuses.Rd | 12 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/find_beta_params.Rd | 16 man/fmt_pct.Rd | 2 man/get_draws_binom.Rd | 6 man/get_draws_generic.Rd | 6 man/get_draws_norm.Rd | 17 man/make_x_scale.Rd | 6 man/make_y_scale.Rd | 12 man/plot_convergence.Rd | 25 man/plot_history.Rd | 18 man/plot_metrics_ecdf.Rd | 25 man/plot_status.Rd | 6 man/print.Rd | 25 man/prog_breaks.Rd | 2 man/run_trial.Rd | 74 man/setup_trial.Rd | 110 man/setup_trial_binom.Rd | 78 man/setup_trial_norm.Rd | 67 man/summary.Rd | 27 man/update_saved_calibration.Rd | 2 man/update_saved_trials.Rd | 12 man/validate_trial.Rd | 67 tests/testthat/_snaps/calibrate_trial/gaussian-process-based-calibration-plot.svg | 1 tests/testthat/_snaps/check_performance.md | 718 +-- tests/testthat/_snaps/extract.md | 1828 +++++----- tests/testthat/_snaps/plot_convergence/convergence-plot-binomial-prob-concl-prob-sup-idp.svg | 37 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-followed-n-2-cores.svg | 9 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-followed-n.svg | 9 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct-total-n.svg | 9 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-pct.svg | 7 tests/testthat/_snaps/plot_history/history-plot-binomial-multiple-prob.svg | 7 tests/testthat/_snaps/plot_history/history-plot-binomial-single-n-look.svg | 3 tests/testthat/_snaps/plot_history/history-plot-binomial-single-pct-all-look.svg | 1 tests/testthat/_snaps/plot_history/history-plot-binomial-single-pct-look.svg | 1 tests/testthat/_snaps/plot_history/history-plot-binomial-single-prob-followed-n.svg | 3 tests/testthat/_snaps/plot_history/history-plot-binomial-single-prob-total-n.svg | 3 tests/testthat/_snaps/plot_history/history-plot-binomial-single-prob.svg | 1 tests/testthat/_snaps/plot_history/history-plot-binomial-single-ratio-ys-all-look.svg | 1 tests/testthat/_snaps/plot_history/history-plot-binomial-single-ratio-ys-look.svg | 1 tests/testthat/_snaps/plot_metrics_ecdf/errors.svg | 12 tests/testthat/_snaps/plot_metrics_ecdf/no-restriction.svg | 6 tests/testthat/_snaps/plot_metrics_ecdf/selected.svg | 6 tests/testthat/_snaps/plot_metrics_ecdf/size-only.svg | 2 tests/testthat/_snaps/plot_metrics_ecdf/superior.svg | 6 tests/testthat/_snaps/plot_status/status-plot-across-arms-binomial.svg | 9 tests/testthat/_snaps/plot_status/status-plot-for-all-arms-binomial.svg | 13 tests/testthat/_snaps/plot_status/status-plot-for-arm-c-binom.svg | 13 tests/testthat/_snaps/run_trials.md | 1364 ++++--- tests/testthat/_snaps/setup_trial.md | 28 tests/testthat/_snaps/summary-print.md | 746 ++-- tests/testthat/test-plot_convergence.R | 4 tests/testthat/test-prob_funs.R | 12 tests/testthat/test-run_trials.R | 45 tests/testthat/test-setup_trial.R | 15 tests/testthat/test-update_saved.R | 28 vignettes/Advanced-example.Rmd | 69 vignettes/Basic-examples.Rmd | 41 vignettes/Overview.Rmd | 102 118 files changed, 5247 insertions(+), 4431 deletions(-)
Title: Parse Tabled Content to Text Vector and Extract Statistical
Standard Results
Description: Features include the ability to extract tabled content from NISO-JATS-coded XML, any native HTML or HML file, DOCX, and PDF documents, and then collapse it into a text format that is readable by humans by mimicking the actions of a screen reader. As tables within PDF documents are extracted with the 'tabulapdf' package, and the table captions and footnotes cannot be extracted, the results on tables within PDF documents have to be considered less precise. The function table2matrix() returns a list of the tables within a document as character matrices. table2text() collapses the matrix content into a list of character strings by imitating the behavior of a screen reader. The textual representation of characters and numbers can be unified with unifyMatrix() before parsing. The function table2stats() extracts the tabled statistical test results from the collapsed text with the function standardStats() from the 'JATSdecoder' package and, if activated, checks the reported and coded p-values [...truncated...]
Author: Ingmar Boeschen [aut, cre]
Maintainer: Ingmar Boeschen <ingmar.boeschen@uni-hamburg.de>
Diff between tableParser versions 1.0.3 dated 2026-02-20 and 1.0.4 dated 2026-03-30
DESCRIPTION | 12 - MD5 | 26 +-- NAMESPACE | 1 R/legendCodings.R | 82 ++++++---- R/matrix2text.R | 4 R/parseMatrixContent.R | 41 +++-- R/prepareMatrix.R | 2 R/table2matrix.R | 11 - R/table2stats.R | 20 +- R/table2text.R | 2 R/tableClass.R | 17 +- R/tableFunctions.R | 382 ++++++++++++++++++++++++++++++++++++++++--------- R/unifyMatrixContent.R | 8 - man/tableClass.Rd | 2 14 files changed, 457 insertions(+), 153 deletions(-)
Title: Simulate Data from a (Time-Dependent) Causal DAG
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression or any other function. Also includes a comprehensive framework for discrete-time
simulation, discrete-event simulation, and networks-based simulation which can generate even more complex longitudinal and dependent data.
For more details, see Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.5.1 dated 2026-03-10 and 0.5.2 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ inst/doc/simDAG.html | 2 +- inst/doc/v_cookbook.html | 12 ++++++------ man/rtexp.Rd | 2 +- tests/testthat/test_network.r | 2 +- tests/testthat/test_node_lmer.r | 22 +++++++++++----------- 8 files changed, 36 insertions(+), 30 deletions(-)
Title: Estimation of Multivariate Long-Memory Models Parameters
Description: Computation of an estimation of the long-memory parameters and
the long-run covariance matrix using a multivariate model
(Lobato (1999) <doi:10.1016/S0304-4076(98)00038-4>; Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>). Two semi-parametric methods are
implemented: a Fourier based approach (Shimotsu (2007) <doi:10.1016/j.jeconom.2006.01.003>) and a wavelet based
approach (Achard and Gannaz (2016) <doi:10.1111/jtsa.12170>; Achard and Gannaz (2024) <doi:10.1111/jtsa.12719>). Real and complex wavelets are implemented.
Author: Sophie Achard [aut],
Irene Gannaz [aut, cre]
Maintainer: Irene Gannaz <irene.gannaz@grenoble-inp.fr>
Diff between multiwave versions 1.4 dated 2019-05-06 and 2.0 dated 2026-03-30
multiwave-1.4/multiwave/data/brainHCP.txt.gz |only multiwave-2.0/multiwave/DESCRIPTION | 19 +- multiwave-2.0/multiwave/MD5 | 57 ++++--- multiwave-2.0/multiwave/NAMESPACE | 5 multiwave-2.0/multiwave/R/DWTcomplex.R |only multiwave-2.0/multiwave/R/DWTexact.R | 13 - multiwave-2.0/multiwave/R/K_eval.R | 34 +--- multiwave-2.0/multiwave/R/convmtx.R |only multiwave-2.0/multiwave/R/hwlet.R |only multiwave-2.0/multiwave/R/mcw.R |only multiwave-2.0/multiwave/R/mcw_wav.R |only multiwave-2.0/multiwave/R/mcw_wav_cov_eval.R |only multiwave-2.0/multiwave/R/mcw_wav_eval.R |only multiwave-2.0/multiwave/R/mww_eval.R | 17 +- multiwave-2.0/multiwave/R/mww_wav_eval.R | 24 +-- multiwave-2.0/multiwave/R/psi_hat_exact.R | 146 ++++++++++++++----- multiwave-2.0/multiwave/R/scaling_function.R | 98 ++++-------- multiwave-2.0/multiwave/R/sfact.R |only multiwave-2.0/multiwave/data/brainHCP.RData |only multiwave-2.0/multiwave/man/DWTcomplex.Rd |only multiwave-2.0/multiwave/man/DWTexact.Rd | 2 multiwave-2.0/multiwave/man/K_eval.Rd | 4 multiwave-2.0/multiwave/man/convmtx.Rd |only multiwave-2.0/multiwave/man/hwlet.Rd |only multiwave-2.0/multiwave/man/leja.Rd |only multiwave-2.0/multiwave/man/mcw.Rd |only multiwave-2.0/multiwave/man/mcw_wav.Rd |only multiwave-2.0/multiwave/man/mcw_wav_cov_eval.Rd |only multiwave-2.0/multiwave/man/mcw_wav_eval.Rd |only multiwave-2.0/multiwave/man/multiwave-package.Rd | 7 multiwave-2.0/multiwave/man/mww.Rd | 6 multiwave-2.0/multiwave/man/mww_cov_eval.Rd | 4 multiwave-2.0/multiwave/man/mww_eval.Rd | 6 multiwave-2.0/multiwave/man/mww_wav.Rd | 4 multiwave-2.0/multiwave/man/mww_wav_cov_eval.Rd | 4 multiwave-2.0/multiwave/man/mww_wav_eval.Rd | 4 multiwave-2.0/multiwave/man/psi_hat_exact.Rd | 7 multiwave-2.0/multiwave/man/psi_hat_exact_complex.Rd |only multiwave-2.0/multiwave/man/seprts.Rd |only multiwave-2.0/multiwave/man/sfact.Rd |only 40 files changed, 270 insertions(+), 191 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2023) <doi:10.31234/osf.io/umt57>.
Author: Vencislav Popov [aut, cre, cph] ,
Gidon T. Frischkorn [aut, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Vencislav Popov <vencislav.popov@gmail.com>
Diff between bmm versions 1.2.0 dated 2025-07-24 and 1.3.0 dated 2026-03-30
DESCRIPTION | 24 MD5 | 134 +- NAMESPACE | 45 NEWS.md | 45 R/bmm.R | 9 R/bmmformula.R | 3 R/conditional_effects.R |only R/data.R | 28 R/distributions.R | 1338 +++++++++++++++++++++++++- R/emmeans.R |only R/helpers-data.R | 720 +++++++++++++ R/helpers-inits.R |only R/helpers-model.R | 330 ++++++ R/helpers-parameters.R | 257 ++++ R/model_cswald.R |only R/model_ddm.R |only R/model_ezdm.R |only R/model_mixture2p.R | 2 R/model_mixture3p.R | 4 R/model_sdm.R | 7 R/pp_check.R |only R/reexports.R | 8 R/utils.R | 58 - R/zzz.R | 2 README.md | 34 build/partial.rdb |binary data/data_color_judgement_task.rda |only inst/stan_chunks/cswald_crisk_functions.stan |only inst/stan_chunks/cswald_helper_functions.stan |only inst/stan_chunks/cswald_simple_functions.stan |only inst/stan_chunks/ddm_functions.stan |only inst/stan_chunks/ezdm_3par_functions.stan |only inst/stan_chunks/ezdm_4par_functions.stan |only man/SDMdist.Rd | 4 man/adjust_ezdm_accuracy.Rd |only man/bmm-package.Rd | 4 man/bmm.Rd | 9 man/c_parametrizations.Rd | 2 man/conditional_effects.bmmfit.Rd |only man/configure_model.Rd | 2 man/configure_prior.Rd | 2 man/create_initfun.Rd |only man/cswald.Rd |only man/cswald_dist.Rd |only man/data_color_judgement_task.Rd |only man/ddm.Rd |only man/ddm_dist.Rd |only man/emmeans-bmmfit.Rd |only man/extract_parameter_dimensions.Rd |only man/extract_stan_blocks.Rd |only man/ezdm.Rd |only man/ezdm_dist.Rd |only man/ezdm_summary_stats.Rd |only man/figures/logo.png |only man/fit_info.Rd | 2 man/flag_contaminant_rts.Rd |only man/imm.Rd | 2 man/m3.Rd | 2 man/m3dist.Rd | 89 + man/mixture2p.Rd | 4 man/mixture3p.Rd | 4 man/parameters.Rd |only man/postprocess_brm.Rd | 2 man/pp_check.bmmfit.Rd |only man/restructure.bmmfit.Rd | 2 man/revert_postprocess_brm.Rd | 2 man/sdm.Rd | 4 man/softmax.Rd | 14 man/summary.bmmfit.Rd | 2 man/update.bmmfit.Rd | 2 man/use_model_template.Rd | 2 man/validate_fast_guesses.Rd |only tests/testthat/test-conditional_effects.R |only tests/testthat/test-distributions.R | 1044 ++++++++++++++++++++ tests/testthat/test-emmeans.R |only tests/testthat/test-helpers-data.R | 697 +++++++++++++ tests/testthat/test-helpers-formula.R | 9 tests/testthat/test-helpers-init.R |only tests/testthat/test-helpers-model.R | 316 ++++++ tests/testthat/test-helpers-parameters.R | 171 +++ tests/testthat/test-model_cswald.R |only tests/testthat/test-model_ddm.R |only tests/testthat/test-model_ezdm.R |only tests/testthat/test-parameters.R |only tests/testthat/test-pkgdown.R |only tests/testthat/test-pp_check.R |only tests/testthat/test-summary.R | 6 tests/testthat/test-update.R | 6 tests/testthat/test-utils.R | 138 ++ 89 files changed, 5372 insertions(+), 219 deletions(-)
Title: Visualization of Spline Effects in GAM and GLM Models
Description: Creates 'ggplot2'-based visualizations of smooth effects from GAM (Generalized Additive Models)
fitted with 'mgcv' and spline effects from GLM (Generalized Linear Models). Supports survey-weighted
models ('svyglm', 'svycoxph') from the 'survey' package, interaction terms, and provides hazard ratio
plots with histograms for survival analysis.
Wood (2017, ISBN:9781498728331) provides comprehensive methodology for generalized additive models.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between splineplot versions 0.2.1 dated 2025-11-19 and 0.3.0 dated 2026-03-30
DESCRIPTION | 19 ++--- MD5 | 12 +-- NAMESPACE | 1 NEWS.md | 19 +++++ R/splineplot.R | 190 +++++++++++++++++++++++++++++++++++++++++++++++------ build/vignette.rds |binary man/splineplot.Rd | 2 7 files changed, 207 insertions(+), 36 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Binary/Text Encoding
Functions
Description: Fast and memory-efficient streaming hash functions,
binary/text encoding and serialization. Hashes strings and raw vectors
directly. Stream hashes files which can be larger than memory, as
well as in-memory objects through R's serialization mechanism.
Implements the SHA-256, SHA-3 and 'Keccak' cryptographic hash
functions, SHAKE256 extendable-output function (XOF), 'SipHash'
pseudo-random function, base64 and base58 encoding, 'CBOR' and 'JSON'
serialization.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between secretbase versions 1.2.0 dated 2026-02-05 and 1.2.1 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/base64.c | 4 ++++ src/json.c | 53 +++++++++++++++++++++++++++-------------------------- tests/tests.R | 2 +- 6 files changed, 44 insertions(+), 35 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut],
Jaewoong Heo [aut],
Mingu Jee [aut],
Yujeong Yoon [aut],
Minhyuk Kim [aut],
Wonbin Hahn [aut],
Taehong K [...truncated...]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.24 dated 2026-02-24 and 1.3.25 dated 2026-03-30
DESCRIPTION | 10 +- MD5 | 18 ++-- NEWS.md | 9 ++ R/forestcox.R | 34 +++---- R/forestglm.R | 60 +++++++------ R/svyCreateTableOneJS.R | 74 +++++++++++++--- R/utils.R | 9 +- inst/doc/jstable.html | 30 +++--- inst/doc/jstable_competing_risk_analysis.html | 4 inst/doc/jstable_options.html | 116 +++++++++++++------------- 10 files changed, 215 insertions(+), 149 deletions(-)
Title: Regression under Interference in Connected Populations
Description: An implementation of generalized linear models (GLMs) for studying relationships among attributes in connected populations, where responses of connected units can be dependent, as introduced by Fritz et al. (2025) <doi:10.1080/01621459.2025.2565851>. 'igml' extends GLMs for independent responses to dependent responses and can be used for studying spillover in connected populations and other network-mediated phenomena.
Author: Cornelius Fritz [aut, cre],
Michael Schweinberger [aut]
Maintainer: Cornelius Fritz <corneliusfritz2010@gmail.com>
Diff between iglm versions 1.2.1 dated 2026-03-18 and 1.2.2 dated 2026-03-30
DESCRIPTION | 6 - MD5 | 8 - inst/doc/iglm.html | 6 - inst/include/iglm/helper_functions.h | 3 src/xyz_sampling.cpp | 202 +++++++++++++++++++++++++++++++++-- 5 files changed, 202 insertions(+), 23 deletions(-)
Title: Bayesian Estimation of (Sparse) Latent Factor Stochastic
Volatility Models
Description: Markov chain Monte Carlo (MCMC) sampler for fully Bayesian estimation of latent factor stochastic volatility models with interweaving <doi:10.1080/10618600.2017.1322091>. Sparsity can be achieved through the usage of Normal-Gamma priors on the factor loading matrix <doi:10.1016/j.jeconom.2018.11.007>.
Author: Gregor Kastner [aut, cre] ,
Darjus Hosszejni [ctb] ,
Luis Gruber [ctb]
Maintainer: Gregor Kastner <gregor.kastner@aau.at>
Diff between factorstochvol versions 1.1.1 dated 2026-03-02 and 1.1.2 dated 2026-03-30
factorstochvol-1.1.1/factorstochvol/src/testrgig.cpp |only factorstochvol-1.1.2/factorstochvol/DESCRIPTION | 10 factorstochvol-1.1.2/factorstochvol/MD5 | 95 - factorstochvol-1.1.2/factorstochvol/NEWS | 8 factorstochvol-1.1.2/factorstochvol/R/RcppExports.R |only factorstochvol-1.1.2/factorstochvol/R/factorstochvol-package.R | 8 factorstochvol-1.1.2/factorstochvol/R/generics.R | 6 factorstochvol-1.1.2/factorstochvol/R/imports.R | 6 factorstochvol-1.1.2/factorstochvol/R/plotting.R | 6 factorstochvol-1.1.2/factorstochvol/R/register.R |only factorstochvol-1.1.2/factorstochvol/R/simulation.R | 6 factorstochvol-1.1.2/factorstochvol/R/utilities_fsvdraws.R | 6 factorstochvol-1.1.2/factorstochvol/R/utilities_other.R | 6 factorstochvol-1.1.2/factorstochvol/R/wrappers.R | 42 factorstochvol-1.1.2/factorstochvol/R/zzz.R | 6 factorstochvol-1.1.2/factorstochvol/build/partial.rdb |binary factorstochvol-1.1.2/factorstochvol/build/vignette.rds |binary factorstochvol-1.1.2/factorstochvol/inst/CITATION | 2 factorstochvol-1.1.2/factorstochvol/inst/doc/paper.Rtex | 30 factorstochvol-1.1.2/factorstochvol/inst/doc/paper.pdf |binary factorstochvol-1.1.2/factorstochvol/inst/include/factorstochvol.h | 120 - factorstochvol-1.1.2/factorstochvol/man/factorstochvol-package.Rd | 2 factorstochvol-1.1.2/factorstochvol/src/RcppExports.cpp |only factorstochvol-1.1.2/factorstochvol/src/dmvnorm.cpp | 16 factorstochvol-1.1.2/factorstochvol/src/dmvnorm.h | 10 factorstochvol-1.1.2/factorstochvol/src/predict.cpp | 23 factorstochvol-1.1.2/factorstochvol/src/predict.h | 10 factorstochvol-1.1.2/factorstochvol/src/progutils.cpp | 112 - factorstochvol-1.1.2/factorstochvol/src/progutils.h | 6 factorstochvol-1.1.2/factorstochvol/src/register.cpp | 35 factorstochvol-1.1.2/factorstochvol/src/sampler.cpp | 860 +--------- factorstochvol-1.1.2/factorstochvol/src/sampler.h | 17 factorstochvol-1.1.2/factorstochvol/src/update_fsv.cpp | 42 factorstochvol-1.1.2/factorstochvol/src/update_fsv.h | 6 factorstochvol-1.1.2/factorstochvol/tests/testthat/test-iterative-use.R |only factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-comtimeplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-corimageplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-cortimeplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-evdiag-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-fsvprepdata-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-loadplot2-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-loadplot2-2.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-logdetcovn-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-plotsvlpred-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-preddist-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-svlbetaplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-svlplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-varplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-varplot2-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/Figures/jss3813-voltimeplot-1.pdf |binary factorstochvol-1.1.2/factorstochvol/vignettes/paper.Rtex | 30 51 files changed, 416 insertions(+), 1110 deletions(-)
More information about factorstochvol at CRAN
Permanent link
Title: Code Sharing at the Department of Epidemiology Research at
Statens Serum Institut
Description: This is a collection of assorted functions and examples collected
from various projects. Currently we have functionalities for simplifying
overlapping time intervals, Charlson comorbidity score constructors for
Danish data, getting frequency for multiple variables, getting standardized
output from logistic and log-linear regressions, sibling design linear
regression functionalities a method for calculating the confidence intervals
for functions of parameters from a GLM, Bayes equivalent for hypothesis
testing with asymptotic Bayes factor, and several help functions for
generalized random forest analysis using 'grf'.
Author: Anders Husby [aut] ,
Anna Laksafoss [aut] ,
Emilia Myrup Thiesson [aut] ,
Kim Daniel Jakobsen [aut, cre] ,
Mikael Andersson [aut] ,
Klaus Rostgaard [aut]
Maintainer: Kim Daniel Jakobsen <kija@ssi.dk>
This is a re-admission after prior archival of version 0.2.1 dated 2026-03-19
Diff between EpiForsk versions 0.2.1 dated 2026-03-19 and 0.2.2 dated 2026-03-30
DESCRIPTION | 6 MD5 | 24 R/adls_flatten_dates_dt.R | 362 ++--- R/aso_odds_ratio_function.R | 1802 +++++++++++++------------- R/aso_odds_ratio_function_repeated.R | 770 +++++------ R/kija_covariate_balance.R | 2378 +++++++++++++++++------------------ R/kija_fct_confint.R | 2241 ++++++++++++++++---------------- R/klp_AsympBF.R | 402 ++--- build/vignette.rds |binary inst/doc/Contributing.html | 11 inst/doc/andh_forest_plot.html | 32 man/asympBF.Rd | 248 +-- man/dot-datatable.aware.Rd | 34 13 files changed, 4158 insertions(+), 4152 deletions(-)
Title: Data Management Tools for Pharmacometrics
Description: Tools and functions to efficiently create datasets used in pharmacometric analysis.
Additional functionality is added to create documentation and prepare files for submission and
quality control purposes.
Author: Richard Hooijmaijers [aut, cre, cph],
LAPP Consultants [fnd, cph]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Diff between amp.dm versions 0.2.0 dated 2026-03-13 and 0.2.1 dated 2026-03-30
DESCRIPTION | 6 - MD5 | 38 ++++----- NEWS.md | 6 + R/attr_extract.r | 2 R/get_script.r | 4 R/impute_covar.r | 2 R/impute_dose.r | 10 +- R/make_readonly.r | 8 + R/output_data.r | 5 - R/session_tbl.r | 4 README.md | 8 + inst/doc/example_study.pdf |binary man/attr_extract.Rd | 2 man/impute_covar.Rd | 2 man/impute_dose.Rd | 2 man/make_readonly.Rd | 8 + man/session_tbl.Rd | 3 tests/testthat/test_dataio.R | 165 ++++------------------------------------- tests/testthat/test_dosefunc.R | 13 ++- tests/testthat/test_tabulate.R | 10 +- 20 files changed, 102 insertions(+), 196 deletions(-)
Title: Read, Write, Visualize and Manipulate PDB Files
Description: Provides tools to read, write, visualize Protein Data Bank (PDB) files and
perform some structural manipulations.
Author: Leonard Mada [cre, ctb],
Julien Ide [aut]
Maintainer: Leonard Mada <lmada@umft.ro>
Diff between Rpdb versions 2.4.3 dated 2026-03-16 and 2.4.4 dated 2026-03-30
Rpdb-2.4.3/Rpdb/R/conect.R |only Rpdb-2.4.3/Rpdb/man/conect.Rd |only Rpdb-2.4.4/Rpdb/DESCRIPTION | 10 - Rpdb-2.4.4/Rpdb/MD5 | 72 ++++--- Rpdb-2.4.4/Rpdb/NAMESPACE | 26 ++ Rpdb-2.4.4/Rpdb/NEWS.md | 47 ++++- Rpdb-2.4.4/Rpdb/R/Graphics.Tools.R |only Rpdb-2.4.4/Rpdb/R/addAxes.R | 330 ++++++++++++++++++++++++------------ Rpdb-2.4.4/Rpdb/R/atoms.R | 117 ++++++++++-- Rpdb-2.4.4/Rpdb/R/backbone.R | 109 ++++++++++- Rpdb-2.4.4/Rpdb/R/chains.R |only Rpdb-2.4.4/Rpdb/R/connect.R |only Rpdb-2.4.4/Rpdb/R/crystal.R | 9 Rpdb-2.4.4/Rpdb/R/distances.R | 72 +++++-- Rpdb-2.4.4/Rpdb/R/elements.R | 25 +- Rpdb-2.4.4/Rpdb/R/merge.coords.R | 18 - Rpdb-2.4.4/Rpdb/R/pdb.R | 43 ++-- Rpdb-2.4.4/Rpdb/R/read.pdb.R | 199 ++++++++++----------- Rpdb-2.4.4/Rpdb/R/reindex.R | 25 +- Rpdb-2.4.4/Rpdb/R/replicate.R | 8 Rpdb-2.4.4/Rpdb/R/select.R |only Rpdb-2.4.4/Rpdb/R/split.pdb.R | 37 ++-- Rpdb-2.4.4/Rpdb/R/subset.atoms.R | 15 - Rpdb-2.4.4/Rpdb/R/toSymbols.R | 31 ++- Rpdb-2.4.4/Rpdb/R/visualize.R | 121 +++++++------ Rpdb-2.4.4/Rpdb/R/write.pdb.R | 21 +- Rpdb-2.4.4/Rpdb/man/addAxes.Rd | 48 +++-- Rpdb-2.4.4/Rpdb/man/atoms.Rd | 32 ++- Rpdb-2.4.4/Rpdb/man/chains.Rd |only Rpdb-2.4.4/Rpdb/man/connect.Rd |only Rpdb-2.4.4/Rpdb/man/distances.Rd | 59 +++--- Rpdb-2.4.4/Rpdb/man/elements.Rd | 25 +- Rpdb-2.4.4/Rpdb/man/merge.coords.Rd | 2 Rpdb-2.4.4/Rpdb/man/pdb.Rd | 37 ++-- Rpdb-2.4.4/Rpdb/man/read.pdb.Rd | 23 +- Rpdb-2.4.4/Rpdb/man/reindex.Rd | 2 Rpdb-2.4.4/Rpdb/man/select.Rd |only Rpdb-2.4.4/Rpdb/man/split.pdb.Rd | 4 Rpdb-2.4.4/Rpdb/man/subset.atoms.Rd | 6 Rpdb-2.4.4/Rpdb/man/translate.Rd |only Rpdb-2.4.4/Rpdb/man/visualize.Rd | 22 +- Rpdb-2.4.4/Rpdb/man/write.pdb.Rd | 4 42 files changed, 1043 insertions(+), 556 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://ec.europa.eu/eurostat/web/user-guides/data-browser/api-data-access/api-detailed-guidelines/sdmx2-1>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.24.5 dated 2026-02-04 and 0.25.0 dated 2026-03-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/get_eurostat_data.R | 14 -------------- R/get_eurostat_toc.R | 3 +++ R/load_cfg.R | 1 - inst/tinytest/test_restatapi.R | 3 +-- 7 files changed, 20 insertions(+), 27 deletions(-)
Title: Simulation Based Sample Size Estimation
Description: Estimates the sample size for a test or a trial based on repeated simulation using a model based approach.
Implements a method by Maruo et al. (2018) <doi:10.1080/19466315.2017.1349689> and an extension.
Author: Lukas Baumann [aut, cre] ,
Bjoern Bornkamp [ctb]
Maintainer: Lukas Baumann <baumann@imbi.uni-heidelberg.de>
Diff between findn versions 0.1.0 dated 2026-02-03 and 0.2.0 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/findn.R | 15 ++++++++------- R/plot.findn.R | 2 +- R/print.findn.R | 22 +++++++++++----------- tests/testthat/test-print.findn.R | 2 +- 6 files changed, 29 insertions(+), 28 deletions(-)
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload and download of files.
Author: Emmanuel Blondel [aut, cre] ,
Julien Barde [ctb] ,
Stephen Eglen [ctb] ,
Hans Van Calster [ctb] ,
Floris Vanderhaeghe [ctb] ,
Jemma Stachelek [ctb] ,
Collin Schwantes [ctb] ,
Nicholas Tierney [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.10.4 dated 2025-12-18 and 0.10.5 dated 2026-03-30
DESCRIPTION | 8 - MD5 | 28 ++-- NAMESPACE | 1 NEWS.md | 15 ++ R/ZenodoException.R |only R/ZenodoManager.R | 318 ++++++++++++++++++++++++++++--------------------- R/ZenodoRecord.R | 8 + R/ZenodoRequest.R | 21 ++- R/zen4R_citation.R | 1 R/zen4R_downloader.R | 1 R/zen4R_exporter.R | 1 R/zen4R_getter.R | 2 R/zen4R_versioning.R | 1 README.md | 2 man/ZenodoException.Rd |only man/ZenodoRequest.Rd | 14 ++ 16 files changed, 262 insertions(+), 159 deletions(-)
Title: Wasserstein Regression and Inference
Description: Implementation of the methodologies described in 1) Alexander Petersen, Xi Liu and Afshin A. Divani (2021) <doi:10.1214/20-aos1971>, including global F tests, partial F tests, intrinsic Wasserstein-infinity bands and Wasserstein density bands, and 2) Chao Zhang, Piotr Kokoszka and Alexander Petersen (2022) <doi:10.1111/jtsa.12590>, including estimation, prediction, and inference of the Wasserstein autoregressive models.
Author: Alexander Petersen [aut, cre],
Xi Liu [aut],
Chao Zhang [aut],
Matthew Coleman [aut]
Maintainer: Alexander Petersen <petersen@stat.byu.edu>
Diff between WRI versions 0.2.2 dated 2026-03-28 and 0.2.3 dated 2026-03-30
DESCRIPTION | 20 ++++++++++---------- MD5 | 4 ++-- inst/doc/WRI-vignette.html | 14 +++++++------- 3 files changed, 19 insertions(+), 19 deletions(-)
Title: Tidying, Analysis, and Fast Visualization of Animal and Plant
Pedigrees
Description: Provides tools for the analysis and visualization of animal and
plant pedigrees. Analytical methods include equivalent complete generations,
generation intervals, effective population size (via inbreeding, coancestry,
and demographic approaches), founder and ancestor contributions, partial
inbreeding, genetic diversity indices, and additive (A), dominance (D), and
epistatic (AA) relationship matrices. Core algorithms — ancestry tracing,
topological sorting, inbreeding coefficients, and matrix construction — are
implemented in C++ ('Rcpp', 'RcppArmadillo') and 'data.table', scaling to
pedigrees with over one million individuals. Pedigree graphs are rendered
via 'igraph' with support for compact full-sib family display; relationship
matrices can be visualized as heatmaps. Supports complex mating systems,
including selfing and pedigrees in which the same individual can appear as
both sire and dam.
Author: Sheng Luan [aut, cre]
Maintainer: Sheng Luan <luansheng@gmail.com>
Diff between visPedigree versions 1.0.1 dated 2026-02-23 and 1.8.1 dated 2026-03-30
visPedigree-1.0.1/visPedigree/LICENSE |only visPedigree-1.0.1/visPedigree/tests/manual |only visPedigree-1.0.1/visPedigree/tests/testthat/Rplots.pdf |only visPedigree-1.8.1/visPedigree/DESCRIPTION | 39 visPedigree-1.8.1/visPedigree/MD5 | 154 + visPedigree-1.8.1/visPedigree/NAMESPACE | 26 visPedigree-1.8.1/visPedigree/NEWS.md | 317 +++ visPedigree-1.8.1/visPedigree/R/RcppExports.R | 32 visPedigree-1.8.1/visPedigree/R/data.R | 37 visPedigree-1.8.1/visPedigree/R/globals.R | 8 visPedigree-1.8.1/visPedigree/R/inbreed.R | 49 visPedigree-1.8.1/visPedigree/R/pedanalysis.R |only visPedigree-1.8.1/visPedigree/R/pedhalflife.R |only visPedigree-1.8.1/visPedigree/R/pedmatrix.R | 142 + visPedigree-1.8.1/visPedigree/R/splitped.R | 20 visPedigree-1.8.1/visPedigree/R/tidyped.R | 396 +++- visPedigree-1.8.1/visPedigree/R/utils-s3.R | 433 +++++ visPedigree-1.8.1/visPedigree/R/vismat.R | 522 ++++-- visPedigree-1.8.1/visPedigree/R/visped.R | 56 visPedigree-1.8.1/visPedigree/R/visped_graph.R | 56 visPedigree-1.8.1/visPedigree/R/visped_layout.R | 10 visPedigree-1.8.1/visPedigree/R/visped_render.R | 27 visPedigree-1.8.1/visPedigree/R/visped_style.R | 103 + visPedigree-1.8.1/visPedigree/R/vispstat.R |only visPedigree-1.8.1/visPedigree/README.md | 49 visPedigree-1.8.1/visPedigree/build/vignette.rds |binary visPedigree-1.8.1/visPedigree/data/complex_ped.rda |only visPedigree-1.8.1/visPedigree/data/half_founder_ped.rda |only visPedigree-1.8.1/visPedigree/data/inbred_ped.rda |only visPedigree-1.8.1/visPedigree/inst/doc/draw-pedigree.R | 3 visPedigree-1.8.1/visPedigree/inst/doc/draw-pedigree.Rmd | 10 visPedigree-1.8.1/visPedigree/inst/doc/draw-pedigree.html | 232 +- visPedigree-1.8.1/visPedigree/inst/doc/efficient-visPedigree-workflows.R |only visPedigree-1.8.1/visPedigree/inst/doc/efficient-visPedigree-workflows.Rmd |only visPedigree-1.8.1/visPedigree/inst/doc/efficient-visPedigree-workflows.html |only visPedigree-1.8.1/visPedigree/inst/doc/pedigree-analysis.R |only visPedigree-1.8.1/visPedigree/inst/doc/pedigree-analysis.Rmd |only visPedigree-1.8.1/visPedigree/inst/doc/pedigree-analysis.html |only visPedigree-1.8.1/visPedigree/inst/doc/relationship-matrix.R | 51 visPedigree-1.8.1/visPedigree/inst/doc/relationship-matrix.Rmd | 115 + visPedigree-1.8.1/visPedigree/inst/doc/relationship-matrix.html | 510 +----- visPedigree-1.8.1/visPedigree/inst/doc/tidy-pedigree.Rmd | 10 visPedigree-1.8.1/visPedigree/inst/doc/tidy-pedigree.html | 256 +-- visPedigree-1.8.1/visPedigree/inst/doc/tidyped-structure.Rmd |only visPedigree-1.8.1/visPedigree/inst/doc/tidyped-structure.html |only visPedigree-1.8.1/visPedigree/man/as_tidyped.Rd |only visPedigree-1.8.1/visPedigree/man/build_ped_meta.Rd |only visPedigree-1.8.1/visPedigree/man/complex_ped.Rd |only visPedigree-1.8.1/visPedigree/man/ensure_complete_tidyped.Rd |only visPedigree-1.8.1/visPedigree/man/ensure_tidyped.Rd |only visPedigree-1.8.1/visPedigree/man/half_founder_ped.Rd |only visPedigree-1.8.1/visPedigree/man/has_candidates.Rd |only visPedigree-1.8.1/visPedigree/man/has_inbreeding.Rd |only visPedigree-1.8.1/visPedigree/man/inbred_ped.Rd |only visPedigree-1.8.1/visPedigree/man/inbreed.Rd | 21 visPedigree-1.8.1/visPedigree/man/is_complete_pedigree.Rd |only visPedigree-1.8.1/visPedigree/man/is_tidyped.Rd |only visPedigree-1.8.1/visPedigree/man/pedancestry.Rd |only visPedigree-1.8.1/visPedigree/man/pedcontrib.Rd |only visPedigree-1.8.1/visPedigree/man/pedecg.Rd |only visPedigree-1.8.1/visPedigree/man/pedfclass.Rd |only visPedigree-1.8.1/visPedigree/man/pedgenint.Rd |only visPedigree-1.8.1/visPedigree/man/pedhalflife.Rd |only visPedigree-1.8.1/visPedigree/man/pediv.Rd |only visPedigree-1.8.1/visPedigree/man/pedmat.Rd | 4 visPedigree-1.8.1/visPedigree/man/pedmeta.Rd |only visPedigree-1.8.1/visPedigree/man/pedne.Rd |only visPedigree-1.8.1/visPedigree/man/pedpartial.Rd |only visPedigree-1.8.1/visPedigree/man/pedrel.Rd |only visPedigree-1.8.1/visPedigree/man/pedstats.Rd |only visPedigree-1.8.1/visPedigree/man/pedsubpop.Rd |only visPedigree-1.8.1/visPedigree/man/plot_ped_igraph.Rd | 2 visPedigree-1.8.1/visPedigree/man/print.pedcontrib.Rd |only visPedigree-1.8.1/visPedigree/man/print.pediv.Rd |only visPedigree-1.8.1/visPedigree/man/print.pedstats.Rd |only visPedigree-1.8.1/visPedigree/man/require_complete_pedigree.Rd |only visPedigree-1.8.1/visPedigree/man/sub-.tidyped.Rd |only visPedigree-1.8.1/visPedigree/man/tidyped.Rd | 25 visPedigree-1.8.1/visPedigree/man/validate_tidyped.Rd | 6 visPedigree-1.8.1/visPedigree/man/vismat.Rd | 188 +- visPedigree-1.8.1/visPedigree/man/visped.Rd | 13 visPedigree-1.8.1/visPedigree/man/vispstat.Rd |only visPedigree-1.8.1/visPedigree/src/RcppExports.cpp | 116 + visPedigree-1.8.1/visPedigree/src/pedigree_calculators.cpp | 802 +++++++++- visPedigree-1.8.1/visPedigree/tests/testthat/test-as-tidyped.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-edge-cases.R | 6 visPedigree-1.8.1/visPedigree/tests/testthat/test-inbreed.R | 4 visPedigree-1.8.1/visPedigree/tests/testthat/test-pedanalysis.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-pedcontrib.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-pedhalflife.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-pediv.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-selfing.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-splitped.R | 8 visPedigree-1.8.1/visPedigree/tests/testthat/test-summary-pedmat-vismat-vispstat.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-summary-tidyped.R | 1 visPedigree-1.8.1/visPedigree/tests/testthat/test-tidyped-workflows.R |only visPedigree-1.8.1/visPedigree/tests/testthat/test-visped.R | 48 visPedigree-1.8.1/visPedigree/tests/testthat/test_highlight_edges.R | 2 visPedigree-1.8.1/visPedigree/vignettes/draw-pedigree.Rmd | 10 visPedigree-1.8.1/visPedigree/vignettes/efficient-visPedigree-workflows.Rmd |only visPedigree-1.8.1/visPedigree/vignettes/pedigree-analysis.Rmd |only visPedigree-1.8.1/visPedigree/vignettes/relationship-matrix.Rmd | 115 + visPedigree-1.8.1/visPedigree/vignettes/tidy-pedigree.Rmd | 10 visPedigree-1.8.1/visPedigree/vignettes/tidyped-structure.Rmd |only 104 files changed, 3761 insertions(+), 1283 deletions(-)
Title: Bayesian CAR Models for Road-Segment Traffic
Description: Tools for simulating and modeling traffic flow on road networks
using spatial conditional autoregressive (CAR) models. The package
represents road systems as graphs derived from 'OpenStreetMap' data
<https://www.openstreetmap.org/> and
supports network-based spatial dependence, basic preprocessing, and
visualization for spatial traffic analysis.
Author: Madison Ell [aut, cre]
Maintainer: Madison Ell <mell@stat.tamu.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2026-01-27
Diff between trafficCAR versions 0.1.0 dated 2026-01-27 and 0.1.1 dated 2026-03-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/plot-model-fit-diagnostics-spatial.html | 8 ++++---- tests/testthat/test-car-precision.R | 3 ++- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Predict Gender from Brazilian First Names
Description: A generalized method to predict and report gender from Brazilian first names
using the Brazilian Institute of Geography and Statistics' Census data and
neural networks.
Author: Fernando Meireles [aut, cre]
Maintainer: Fernando Meireles <fernando.meireles@iesp.uerj.br>
Diff between genderBR versions 1.2.0 dated 2026-01-15 and 1.3.0 dated 2026-03-30
DESCRIPTION | 17 +-- MD5 | 31 ++++- NAMESPACE | 4 NEWS.md | 12 ++ R/get_gender.R | 39 ++++--- R/get_gender_nn.R |only R/map_gender.R | 5 R/model.R |only R/utils.R | 11 +- README.md | 158 +++++++++++++++++++++++------ inst |only man/clear_nn_cache.Rd |only man/download_gender_model.Rd |only man/get_gender.Rd | 15 ++ man/get_gender_nn.Rd |only man/map_gender.Rd | 5 tests/testthat/test-get_gender-api.R |only tests/testthat/test-get_gender-nn-option.R |only tests/testthat/test-get_gender_nn-inputs.R |only tests/testthat/test-map_gender.R |only tests/testthat/test-model.R |only tests/testthat/test-predict-nn.R |only 22 files changed, 223 insertions(+), 74 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.6.2 dated 2026-03-08 and 0.6.3 dated 2026-03-30
DESCRIPTION | 8 +-- MD5 | 32 ++++++------ R/copyCohorts.R | 7 ++ R/deathCohort.R | 14 +++-- R/measurementCohort.R | 80 ++++++++++++++++++++++++++++--- R/requireDemographics.R | 8 +-- R/requireIsEntry.R | 4 - R/subsetCohorts.R | 26 +++++++++- inst/doc/a01_building_base_cohorts.html | 40 ++++++++------- man/requireIsEntry.Rd | 4 - man/subsetCohorts.Rd | 5 + tests/testthat/test-conceptCohort.R | 6 -- tests/testthat/test-copyCohorts.R | 18 ++++++ tests/testthat/test-deathCohort.R | 26 +++++++--- tests/testthat/test-demographicsCohort.R | 5 + tests/testthat/test-measurementCohort.R | 21 ++++++-- tests/testthat/test-subsetCohorts.R | 16 ++++++ 17 files changed, 247 insertions(+), 73 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Descriptive Statistics, Summary Tables, and Data Management
Tools
Description: Provides tools for descriptive data analysis,
variable inspection, data management, and tabulation workflows in 'R'.
Summarizes variable metadata, labels, classes, missing values, and
representative values, with support for readable frequency tables,
cross-tabulations, association measures for contingency tables
(Cramer's V, Phi, Goodman-Kruskal Gamma, Kendall's Tau-b, Somers' D,
and others), categorical and continuous summary tables, including
APA-style reporting outputs. Includes helpers for interactive
codebooks, variable label extraction, clipboard export, and row-wise
descriptive summaries. Designed to make descriptive analysis faster,
clearer, and easier to work with in practice.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.6.0 dated 2026-03-23 and 0.7.0 dated 2026-03-30
spicy-0.6.0/spicy/R/table_apa.R |only spicy-0.6.0/spicy/inst/doc/table-apa.R |only spicy-0.6.0/spicy/inst/doc/table-apa.Rmd |only spicy-0.6.0/spicy/inst/doc/table-apa.html |only spicy-0.6.0/spicy/man/table_apa.Rd |only spicy-0.6.0/spicy/tests/testthat/test-table_apa.R |only spicy-0.6.0/spicy/vignettes/table-apa.Rmd |only spicy-0.7.0/spicy/DESCRIPTION | 26 spicy-0.7.0/spicy/MD5 | 80 - spicy-0.7.0/spicy/NAMESPACE | 19 spicy-0.7.0/spicy/NEWS.md | 296 ++-- spicy-0.7.0/spicy/R/flextable_helpers.R |only spicy-0.7.0/spicy/R/selection_helpers.R |only spicy-0.7.0/spicy/R/table_categorical.R |only spicy-0.7.0/spicy/R/table_categorical_print.R |only spicy-0.7.0/spicy/R/table_continuous.R |only spicy-0.7.0/spicy/R/table_continuous_print.R |only spicy-0.7.0/spicy/R/tables_ascii.R | 253 +++ spicy-0.7.0/spicy/README.md | 300 +++- spicy-0.7.0/spicy/build/vignette.rds |binary spicy-0.7.0/spicy/inst/CITATION | 6 spicy-0.7.0/spicy/inst/doc/association-measures.Rmd | 8 spicy-0.7.0/spicy/inst/doc/association-measures.html | 97 - spicy-0.7.0/spicy/inst/doc/frequency-tables.R |only spicy-0.7.0/spicy/inst/doc/frequency-tables.Rmd |only spicy-0.7.0/spicy/inst/doc/frequency-tables.html |only spicy-0.7.0/spicy/inst/doc/spicy.R | 26 spicy-0.7.0/spicy/inst/doc/spicy.Rmd | 352 ++--- spicy-0.7.0/spicy/inst/doc/spicy.html | 892 ++------------ spicy-0.7.0/spicy/inst/doc/summary-tables-reporting.R |only spicy-0.7.0/spicy/inst/doc/summary-tables-reporting.Rmd |only spicy-0.7.0/spicy/inst/doc/summary-tables-reporting.html |only spicy-0.7.0/spicy/inst/doc/table-categorical.R |only spicy-0.7.0/spicy/inst/doc/table-categorical.Rmd |only spicy-0.7.0/spicy/inst/doc/table-categorical.html |only spicy-0.7.0/spicy/inst/doc/table-continuous.R |only spicy-0.7.0/spicy/inst/doc/table-continuous.Rmd |only spicy-0.7.0/spicy/inst/doc/table-continuous.html |only spicy-0.7.0/spicy/inst/doc/variable-exploration.R |only spicy-0.7.0/spicy/inst/doc/variable-exploration.Rmd |only spicy-0.7.0/spicy/inst/doc/variable-exploration.html |only spicy-0.7.0/spicy/man/build_ascii_table.Rd | 10 spicy-0.7.0/spicy/man/print.spicy_categorical_table.Rd |only spicy-0.7.0/spicy/man/print.spicy_continuous_table.Rd |only spicy-0.7.0/spicy/man/spicy-package.Rd | 4 spicy-0.7.0/spicy/man/spicy_print_table.Rd | 10 spicy-0.7.0/spicy/man/table_categorical.Rd |only spicy-0.7.0/spicy/man/table_continuous.Rd |only spicy-0.7.0/spicy/tests/testthat/test-code_book.R | 28 spicy-0.7.0/spicy/tests/testthat/test-copy_clipboard.R | 181 ++ spicy-0.7.0/spicy/tests/testthat/test-flextable_helpers.R |only spicy-0.7.0/spicy/tests/testthat/test-table_categorical.R |only spicy-0.7.0/spicy/tests/testthat/test-table_continuous.R |only spicy-0.7.0/spicy/tests/testthat/test-tables_ascii.R | 63 spicy-0.7.0/spicy/vignettes/association-measures.Rmd | 8 spicy-0.7.0/spicy/vignettes/frequency-tables.Rmd |only spicy-0.7.0/spicy/vignettes/spicy.Rmd | 352 ++--- spicy-0.7.0/spicy/vignettes/summary-tables-reporting.Rmd |only spicy-0.7.0/spicy/vignettes/table-categorical.Rmd |only spicy-0.7.0/spicy/vignettes/table-continuous.Rmd |only spicy-0.7.0/spicy/vignettes/variable-exploration.Rmd |only 61 files changed, 1598 insertions(+), 1413 deletions(-)
Title: Fast and Scalable Cellwise-Robust Ensemble
Description: Functions to perform robust variable selection and regression using the Fast and Scalable
Cellwise-Robust Ensemble (FSCRE) algorithm. The approach establishes a robust foundation
using the Detect Deviating Cells (DDC) algorithm and robust correlation estimates. It then
employs a competitive ensemble architecture where a robust Least Angle Regression (LARS)
engine proposes candidate variables and cross-validation arbitrates their assignment. A final
robust MM-estimator is applied to the selected predictors.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between srlars versions 2.0.0 dated 2026-03-02 and 2.0.1 dated 2026-03-30
DESCRIPTION | 8 ++-- MD5 | 6 +-- NEWS.md | 3 + README.md | 109 ++++++++++++++++++++++++++++++++++-------------------------- 4 files changed, 72 insertions(+), 54 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.1-5 dated 2026-02-13 and 2.1-6 dated 2026-03-30
DESCRIPTION | 6 +-- MD5 | 54 ++++++++++++++++---------------- NEWS.md | 4 ++ build/vignette.rds |binary data/DE_RB_2005.rda |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.Rnw | 2 - inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/tull.Rd | 6 --- tests/stars.R | 2 - tests/stars.Rout.save | 57 ---------------------------------- vignettes/spatio-temporal-kriging.Rnw | 2 - 28 files changed, 36 insertions(+), 97 deletions(-)
Title: Dimension Reduction Methods for Multivariate Time Series
Description: Estimates VAR and VARX models with Structured Penalties.
Author: Will Nicholson [cre, aut],
David Matteson [aut],
Jacob Bien [aut]
Maintainer: Will Nicholson <wbn8@cornell.edu>
Diff between BigVAR versions 1.1.4 dated 2025-11-04 and 1.1.5 dated 2026-03-30
DESCRIPTION | 10 +++---- MD5 | 22 +++++++++++------ R/data.R | 40 ++++++++++++++++++++++++++++++ data/CPI.RData |only data/FFR.RData |only data/GDP.RData |only data/M1.RData |only inst/doc/BigVAR.R | 66 ++++++++++++++++++++++++++++----------------------- inst/doc/BigVAR.Rmd | 17 ++++++++++--- inst/doc/BigVAR.html | 47 +++++++++++++++++------------------- man/CPI.Rd |only man/FFR.Rd |only man/GDP.Rd |only man/M1.Rd |only man/Y1.Rd | 2 - vignettes/BigVAR.Rmd | 17 ++++++++++--- 16 files changed, 145 insertions(+), 76 deletions(-)
Title: Robust Instrumental Variable Methods in Linear Models
Description: Inference for the treatment effect with possibly invalid instrumental variables via TSHT ('Guo et al.' (2018) <doi:10.1111/rssb.12275>) and SearchingSampling ('Guo' (2023) <doi:10.1093/jrsssb/qkad049>), which are effective for both low- and high-dimensional covariates and instrumental variables; test of endogeneity in high dimensions ('Guo et al.' (2018) <doi:10.1016/j.jeconom.2018.07.002>).
Author: Taehyeon Koo [aut],
Zhenyu Wang [aut],
Hyunseung Kang [ctb],
Dylan Small [ctb],
Zijian Guo [aut, cre, cph]
Maintainer: Zijian Guo <zijguo@stat.rutgers.edu>
Diff between RobustIV versions 0.2.5 dated 2022-12-19 and 0.3.1 dated 2026-03-29
DESCRIPTION | 10 +++--- MD5 | 21 +++++++------- R/Projection_Directions-LF.R | 12 ++++---- R/SearchingSampling.R | 20 ++++++++----- R/TSHT.R | 16 +--------- R/endo-test.R | 26 +++-------------- R/helpers-TSHT.R | 34 +++++++--------------- R/helpers-endo.test.R | 64 ++++++++++++++----------------------------- README.md |only man/SearchingSampling.Rd | 4 +- man/TSHT.Rd | 4 +- man/endo.test.Rd | 5 +-- 12 files changed, 79 insertions(+), 137 deletions(-)
Title: Discovery of Motifs in Spatial-Time Series
Description: Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Heraldo Borges [aut, cre] ,
Amin Bazaz [aut] ,
Esther Pacciti [aut] ,
Eduardo Ogasawara [aut]
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>
Diff between STMotif versions 2.0.2 dated 2024-02-23 and 2.0.3 dated 2026-03-29
STMotif-2.0.2/STMotif/LICENSE |only STMotif-2.0.2/STMotif/man/STMotif.Rd |only STMotif-2.0.3/STMotif/DESCRIPTION | 21 - STMotif-2.0.3/STMotif/MD5 | 47 +- STMotif-2.0.3/STMotif/NAMESPACE | 8 STMotif-2.0.3/STMotif/NEWS.md | 10 STMotif-2.0.3/STMotif/R/STMotif.R | 33 +- STMotif-2.0.3/STMotif/R/example_dataset.R | 17 - STMotif-2.0.3/STMotif/R/mainFunction.R | 193 ++++++----- STMotif-2.0.3/STMotif/R/subFunction.R | 277 ++++++++++------ STMotif-2.0.3/STMotif/R/visualization.R | 329 +++++++++++++++----- STMotif-2.0.3/STMotif/build/vignette.rds |binary STMotif-2.0.3/STMotif/inst/doc/STMotif.R | 63 +-- STMotif-2.0.3/STMotif/inst/doc/STMotif.Rmd | 110 ++---- STMotif-2.0.3/STMotif/inst/doc/STMotif.html | 155 ++++----- STMotif-2.0.3/STMotif/man/CSAMiningProcess.Rd | 49 +- STMotif-2.0.3/STMotif/man/NormSAX.Rd | 15 STMotif-2.0.3/STMotif/man/RankSTMotifs.Rd | 20 - STMotif-2.0.3/STMotif/man/STMotif-package.Rd |only STMotif-2.0.3/STMotif/man/STSADatasetAdjust.Rd | 17 - STMotif-2.0.3/STMotif/man/SearchSTMotifs.Rd | 44 +- STMotif-2.0.3/STMotif/man/display_motifsDataset.Rd | 30 + STMotif-2.0.3/STMotif/man/display_motifsSTSeries.Rd | 32 + STMotif-2.0.3/STMotif/man/example_dataset.Rd | 21 + STMotif-2.0.3/STMotif/tests |only STMotif-2.0.3/STMotif/vignettes/STMotif.Rmd | 110 ++---- 26 files changed, 970 insertions(+), 631 deletions(-)
Title: Quick and Flexible Survey Weighting
Description: Quickly and flexibly calculates weights for survey data, in order to correct
for survey non-response or other sampling issues. Uses rake weighting, a common technique
also know as rim weighting or iterative proportional fitting. This technique allows for weighting
on multiple variables, even when the interlocked distribution of the two
variables is not known. Interacts with Thomas Lumley's 'survey' package, as described in
Lumley, Thomas (2011, ISBN:978-1-118-21093-2). Adds additional functionality, more adaptable syntax, and error-checking
to the base weighting functionality in 'survey.'
Author: Ben Mainwaring [aut, cre]
Maintainer: Ben Mainwaring <mainwaringb@gmail.com>
Diff between svyweight versions 0.1.0 dated 2022-05-03 and 0.1.1 dated 2026-03-29
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/data.R | 5 ++--- R/quality_functions.R | 2 +- R/svyweight.R | 2 +- R/w8margin_functions.R | 2 +- README.md | 10 ---------- man/eff_n.Rd | 2 +- man/gles17.Rd | 5 ++--- man/svyweight.Rd | 1 + tests/testthat/all_w8margin.rds |binary tests/testthat/benchmark_onevar_out.rds |binary tests/testthat/benchmark_out.rds |binary tests/testthat/helper.R | 5 +++-- tests/testthat/test-rake.R | 12 ++++++------ 15 files changed, 36 insertions(+), 46 deletions(-)
Title: Hidden Markov Model for Predicting Time Sequences with Mixture
Sampling
Description: An algorithm for time series analysis that leverages hidden Markov models, cluster analysis, and mixture distributions to segment data, detect patterns and predict future sequences.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between hmix versions 1.0.2 dated 2024-09-10 and 1.0.3 dated 2026-03-29
DESCRIPTION | 14 ++--- MD5 | 14 ++--- NAMESPACE | 6 ++ NEWS.md | 5 +- R/dummy_set.R | 2 R/main1.R | 129 +++++++++++++++++++++++++++++++++++++++++++++++++++++-- man/dummy_set.Rd | 2 man/hmix.Rd | 2 8 files changed, 152 insertions(+), 22 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Principal component analysis (PCA) is also supported for a two-way data matrix. Uses component weights from one mode of a Parafac, Parafac2, or PCA model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel', 'doParallel', and 'doRNG' packages.
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-6 dated 2026-02-06 and 1.2-7 dated 2026-03-29
ChangeLog | 47 + DESCRIPTION | 10 MD5 | 44 - NAMESPACE | 5 R/cpfa.R | 304 +++++-- R/plotcpfa.R | 71 + R/predict.tunecpfa.R | 245 ++++-- R/print.tunecpfa.R | 11 R/simcpfa.R | 1825 +++++++++++++++++++++++++----------------------- R/tunecpfa.R | 184 ++++ build/vignette.rds |binary inst/doc/cpfa.R | 94 ++ inst/doc/cpfa.Rmd | 222 ++++- inst/doc/cpfa.pdf |binary man/cpfa.Rd | 186 +++- man/cpm.Rd | 5 man/cpm.all.Rd | 5 man/plotcpfa.Rd | 56 + man/predict.tunecpfa.Rd | 52 - man/print.tunecpfa.Rd | 4 man/simcpfa.Rd | 171 ++-- man/tunecpfa.Rd | 106 +- vignettes/cpfa.Rmd | 222 ++++- 23 files changed, 2471 insertions(+), 1398 deletions(-)
Title: Probabilistic Time Series Forecasting with XGBoost and Conformal
Inference
Description: Implements a probabilistic approach to time series forecasting combining XGBoost regression with conformal inference methods. The package provides functionality for generating predictive distributions, evaluating uncertainty, and optimizing hyperparameters using Bayesian, coarse-to-fine, or random search strategies.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between xpect versions 1.1 dated 2026-02-14 and 1.2 dated 2026-03-29
DESCRIPTION | 10 ++-- MD5 | 8 +-- NAMESPACE | 7 ++- NEWS.md | 3 + R/main.R | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- 5 files changed, 145 insertions(+), 14 deletions(-)
Title: 'GGML' Tensor Operations for Machine Learning
Description: Provides 'R' bindings to the 'GGML' tensor library for machine
learning, designed primarily for 'Vulkan' GPU acceleration with full CPU
fallback. 'Vulkan' support is auto-detected at build time on Linux (when
'libvulkan-dev' and 'glslc' are installed) and on Windows (when 'Vulkan'
'SDK' is installed and 'VULKAN_SDK' environment variable is set); all
operations fall back to CPU transparently when no GPU is available.
Supports tensors up to 5D natively (GGML_MAX_DIMS=5).
Implements tensor operations, neural network layers, quantization, and a
'Keras'-like sequential model API for building and training networks.
Includes 'AdamW' (Adam with Weight decay) and 'SGD' (Stochastic Gradient
Descent) optimizers with 'MSE' (Mean Squared Error) and cross-entropy
losses. Also provides a dynamic 'autograd' engine ('PyTorch'-style) with
data-parallel training via 'dp_train()', broadcast arithmetic, 'f16'
(half-precision) support on 'Vulkan' GPU, and a multi-head attention layer
for building Transforme [...truncated...]
Author: Yuri Baramykov [aut, cre],
Georgi Gerganov [ctb, cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
Mozilla Foundation [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between ggmlR versions 0.6.3 dated 2026-03-18 and 0.6.7 dated 2026-03-29
DESCRIPTION | 20 MD5 | 98 NEWS.md | 95 R/nn_functional.R | 135 - R/nn_model.R | 224 - R/onnx.R | 19 README.md | 52 inst/examples/benchmark_onnx.R | 4 inst/examples/benchmark_onnx_fp16.R |only inst/examples/test_all_onnx.R |only inst/examples/titanic_classification.R |only man/ggmlR-package.Rd | 2 man/nn_build_graph.Rd | 2 man/onnx_load.Rd | 14 src/Makevars.in | 3 src/Makevars.win.in | 2 src/ggml-backend.cpp | 9 src/ggml-cpu/ggml-cpu-backend.c | 5 src/ggml-cpu/ops.cpp | 146 - src/ggml-cpu/ops.h | 1 src/ggml-vulkan/ggml-vulkan.cpp | 92 src/ggml-vulkan/vulkan-shaders/scatter_elements.comp |only src/ggml-vulkan/vulkan-shaders/vulkan-shaders-gen.cpp | 4 src/ggml.c | 196 + src/ggml.h | 58 src/onnx/nms.c |only src/onnx/nms.h |only src/onnx/onnx_ggml.c | 2173 +++++++++++++---- src/onnx/onnx_ggml.h | 100 src/onnx/r_onnx.c | 22 src/onnx/roi_align.c |only src/onnx/roi_align.h |only src/r_interface.c | 10 tests/testthat.R | 33 tests/testthat/helper-onnx.R | 21 tests/testthat/test-chain-ag-early-stopping.R |only tests/testthat/test-chain-patterns.R |only tests/testthat/test-chain-sequential-batchnorm.R |only tests/testthat/test-nn-functional.R | 2 tests/testthat/test-onnx-chain-attn-mask.R |only tests/testthat/test-onnx-chain-audio.R |only tests/testthat/test-onnx-chain-batched-matmul.R |only tests/testthat/test-onnx-chain-bert-mlp.R |only tests/testthat/test-onnx-chain-broadcast-strict.R |only tests/testthat/test-onnx-chain-cast.R |only tests/testthat/test-onnx-chain-classify.R |only tests/testthat/test-onnx-chain-constantofshape-int64.R |only tests/testthat/test-onnx-chain-convtranspose.R |only tests/testthat/test-onnx-chain-decoder.R |only tests/testthat/test-onnx-chain-detect.R |only tests/testthat/test-onnx-chain-erf-gelu.R |only tests/testthat/test-onnx-chain-eyelike.R |only tests/testthat/test-onnx-chain-fpn.R |only tests/testthat/test-onnx-chain-maskrcnn-broadcast.R |only tests/testthat/test-onnx-chain-pooling.R |only tests/testthat/test-onnx-chain-position.R |only tests/testthat/test-onnx-chain-postprocess.R |only tests/testthat/test-onnx-chain-powernorm.R |only tests/testthat/test-onnx-chain-preprocess.R |only tests/testthat/test-onnx-chain-qlinearconv.R |only tests/testthat/test-onnx-chain-quant.R |only tests/testthat/test-onnx-chain-resize-broadcast.R |only tests/testthat/test-onnx-chain-roberta-attn.R |only tests/testthat/test-onnx-chain-roialign-nms.R |only tests/testthat/test-onnx-chain-scatter-gnn.R |only tests/testthat/test-onnx-chain-superres.R |only tests/testthat/test-onnx-chain-transformer.R |only tests/testthat/test-onnx-chain-uncovered-ops.R |only tests/testthat/test-onnx-chain-unet.R |only tests/testthat/test-onnx-chain-xcit-dynamic.R |only tests/testthat/test-onnx-meta.R | 23 71 files changed, 2783 insertions(+), 782 deletions(-)
Title: Transformed Ornstein-Uhlenbeck Model for Adsorption Kinetics
Description: Estimates the parameters of a Transformed Ornstein-Uhlenbeck (TOU) stochastic model for adsorption data and also the parameters of the related pseudo-n-order (PNO) model, such as the maximum adsorption capacity (qe), the adsorption rate constant (kn) and the order of the model (n).
Author: Silvia Rodriguez-Narciso [aut] ,
Juan Antonio Lozano-Alvarez [aut] ,
Rogelio Salinas-Gutierrez [aut, cre] ,
Netzahualcoyotl Castaneda-Leyva [aut]
Maintainer: Rogelio Salinas-Gutierrez <rsalinas@correo.uaa.mx>
This is a re-admission after prior archival of version 0.1.0 dated 2022-10-11
Diff between TOU versions 0.1.0 dated 2022-10-11 and 0.2.0 dated 2026-03-29
TOU-0.1.0/TOU/R/draw_model_tou.R |only TOU-0.1.0/TOU/R/fit_model_tou.R |only TOU-0.1.0/TOU/man/draw.model.tou.Rd |only TOU-0.1.0/TOU/man/fit.model.tou.Rd |only TOU-0.2.0/TOU/DESCRIPTION | 26 +++++++++++++------------- TOU-0.2.0/TOU/MD5 | 14 +++++++------- TOU-0.2.0/TOU/NAMESPACE | 4 ++-- TOU-0.2.0/TOU/R/tou_fit_params.R |only TOU-0.2.0/TOU/R/tou_plot.R |only TOU-0.2.0/TOU/build/partial.rdb |binary TOU-0.2.0/TOU/man/tou.fit.params.Rd |only TOU-0.2.0/TOU/man/tou.plot.Rd |only 12 files changed, 22 insertions(+), 22 deletions(-)
Title: Generate Multi-Dimensional Open Simplex Noise
Description: Generate 2, 3 or 4-dimensional gradient noise.
The noise function is comparable to classic Perlin noise,
but with less directional artefacts and lower computational overhead.
It can have applications in procedural generation or (flow fields)
simulations.
Author: Pepijn de Vries [aut, cre] ,
Marco Ciaramella [aut, cph],
KdotJPG [aut, cph]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between opensimplex2 versions 0.0.2 dated 2026-03-25 and 0.0.3 dated 2026-03-29
DESCRIPTION | 9 +++--- MD5 | 21 ++++++++------ NEWS.md | 7 ++++ README.md | 13 ++++++-- build |only inst |only man/opensimplex2-package.Rd | 2 - src/OpenSimplex2F.c | 66 ++++++++++++++++++++++---------------------- src/OpenSimplex2S.c | 14 ++++----- src/opensimplex2_ctypes.h | 4 +- src/simplex2r.cpp | 2 - vignettes |only 12 files changed, 79 insertions(+), 59 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: The 'leaflet' JavaScript library provides many plugins some of which
are available in the core 'leaflet' package, but there are many more. It is not
possible to support them all in the core 'leaflet' package. This package serves
as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet'
plugins.
Author: Sebastian Gatscha [aut],
Sebastien Plutniak [cre] ,
Bhaskar Karambelkar [aut],
Barret Schloerke [aut],
Bangyou Zheng [ctb] ,
Robin Cura [ctb] ,
Markus Voge [ctb] ,
Markus Dumke [ctb] ,
Mapbox [ctb, cph] ,
Henry Thasler [ctb, cph] ,
Dennis Wilhelm [ct [...truncated...]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
This is a re-admission after prior archival of version 2.0.1 dated 2024-08-19
Diff between leaflet.extras versions 2.0.1 dated 2024-08-19 and 2.0.2 dated 2026-03-29
leaflet.extras-2.0.1/leaflet.extras/R/leaflet.extras-package.R |only leaflet.extras-2.0.1/leaflet.extras/inst/examples/shiny/search/search_google_app.R |only leaflet.extras-2.0.1/leaflet.extras/inst/examples/shiny/search/www |only leaflet.extras-2.0.1/leaflet.extras/inst/htmlwidgets/build/lfx-search/18cd91b6672b08907d35.png |only leaflet.extras-2.0.2/leaflet.extras/DESCRIPTION | 30 leaflet.extras-2.0.2/leaflet.extras/LICENSE | 1348 ++++---- leaflet.extras-2.0.2/leaflet.extras/MD5 | 214 - leaflet.extras-2.0.2/leaflet.extras/NAMESPACE | 195 - leaflet.extras-2.0.2/leaflet.extras/NEWS.md | 17 leaflet.extras-2.0.2/leaflet.extras/R/TileLayer.PouchDBCached.R | 46 leaflet.extras-2.0.2/leaflet.extras/R/bounceMarker.R | 138 leaflet.extras-2.0.2/leaflet.extras/R/draw.R | 317 - leaflet.extras-2.0.2/leaflet.extras/R/drawOptions.R | 911 ++--- leaflet.extras-2.0.2/leaflet.extras/R/fullscreen.R | 57 leaflet.extras-2.0.2/leaflet.extras/R/geodesic.R | 442 +- leaflet.extras-2.0.2/leaflet.extras/R/gps.R | 178 - 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leaflet.extras-2.0.2/leaflet.extras/inst/examples/wmsLegend.R | 46 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-choropleth/lfx-choropleth-prod.js.LICENSE.txt | 112 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-draw-drag/lfx-draw-drag-prod.js.LICENSE.txt | 24 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-geodesic/lfx-geodesic-prod.js.LICENSE.txt | 2 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-groupedlayercontrol |only leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-measure-path/lfx-measure-path-bindings.js | 2 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-search/lfx-search-bindings.js | 2 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-search/lfx-search-prod.css | 2 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-search/lfx-search-prod.js | 2 leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-styleeditor/887fb08b2baa4a1d3975.svg | 228 - leaflet.extras-2.0.2/leaflet.extras/inst/htmlwidgets/build/lfx-weather-markers/86a76ca5e882e8285706.svg | 512 +-- leaflet.extras-2.0.2/leaflet.extras/man/GroupedLayersControl.Rd |only leaflet.extras-2.0.2/leaflet.extras/man/TileCaching.Rd | 44 leaflet.extras-2.0.2/leaflet.extras/man/addAwesomeMarkersDependencies.Rd | 32 leaflet.extras-2.0.2/leaflet.extras/man/addBingTiles.Rd | 76 leaflet.extras-2.0.2/leaflet.extras/man/addBootstrapDependency.Rd | 28 leaflet.extras-2.0.2/leaflet.extras/man/addBounceMarkers.Rd | 174 - 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leaflet.extras-2.0.2/leaflet.extras/man/search-features.Rd | 74 leaflet.extras-2.0.2/leaflet.extras/man/search-geocoding.Rd | 288 - leaflet.extras-2.0.2/leaflet.extras/man/search-options.Rd | 233 - leaflet.extras-2.0.2/leaflet.extras/man/sleep.Rd | 86 leaflet.extras-2.0.2/leaflet.extras/man/style-editor.Rd | 94 leaflet.extras-2.0.2/leaflet.extras/man/toolbarOptions.Rd | 96 leaflet.extras-2.0.2/leaflet.extras/man/utils.Rd | 132 leaflet.extras-2.0.2/leaflet.extras/man/weatherMarkers.Rd | 268 - leaflet.extras-2.0.2/leaflet.extras/man/webglheatmap.Rd | 497 +-- leaflet.extras-2.0.2/leaflet.extras/man/wms-legend.Rd | 116 leaflet.extras-2.0.2/leaflet.extras/tests/testthat.R | 26 leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-geodesic.R | 1086 +++--- leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-geojson.R | 690 ++-- leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-geojson_mini.R | 683 ++-- leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-groupedlayerscontrol.R |only leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-heatmaps.R | 744 ++-- leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-layers.R | 88 leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-map-controls.R | 1615 +++++----- leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-maputils.R | 94 leaflet.extras-2.0.2/leaflet.extras/tests/testthat/test-marker.R | 764 ++-- 113 files changed, 13004 insertions(+), 12764 deletions(-)
More information about leaflet.extras at CRAN
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Title: Utility Functions for Data Analysis and Visualization
Description: A utility toolkit for data analysis and visualization in R.
Provides ~50 functions covering package management, color palette management,
data visualization (bar, pie, density, Venn, forest plots), statistical
testing (t-test, ANOVA, chi-square, correlation, power analysis), bioinformatics
utilities (gene ID conversion, GMT parsing, GEO access), and custom infix
operators. Implementation follows tidyverse principles (Wickham et al. (2019)
<doi:10.21105/joss.01686>).
Author: Evan Zhou [aut, cre]
Maintainer: Evan Zhou <evanzhou.bio@gmail.com>
Diff between evanverse versions 0.4.4 dated 2026-03-10 and 0.5.1 dated 2026-03-29
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Title: Income Polarization Index
Description: Extremely fast and memory efficient computation of the DER (or PaF) income polarization index as proposed by Duclos J. Y., Esteban, J. and Ray D. (2004). "Polarization: concepts, measurement, estimation". Econometrica, 72(6): 1737--1772. <doi:10.1111/j.1468-0262.2004.00552.x>. The index may be computed for a single or for a range of values of the alpha-parameter and bootstrapping is also available.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between DER versions 1.3 dated 2025-11-12 and 1.5 dated 2026-03-29
DESCRIPTION | 16 ++++++++-------- MD5 | 22 +++++++++++----------- NAMESPACE | 3 ++- R/paf.boot.R | 2 +- R/paf2.boot.R | 2 +- man/DER-package.Rd | 4 ++-- src/colpafs.cpp | 2 ++ src/colpafs2.cpp | 2 ++ src/kde.cpp | 9 ++++++++- src/paf.cpp | 2 ++ src/paf2.cpp | 6 ++++++ src/pafF_helper.cpp | 6 ++++++ 12 files changed, 51 insertions(+), 25 deletions(-)
Title: Bounded Outcome Risk Guard for Model Evaluation
Description: Comprehensive toolkit for valid spatial, temporal, and grouped model
evaluation. Automatically detects data dependencies (spatial autocorrelation,
temporal structure, clustered observations), generates appropriate
cross-validation schemes (spatial blocking, checkerboard, hexagonal, KNNDM,
environmental blocking, leave-location-out, purged CV), and validates
evaluation pipelines for leakage. Includes area of applicability (AOA)
assessment following Meyer & Pebesma (2021) <doi:10.1111/2041-210X.13650>,
forward feature selection with blocked CV, spatial thinning, block-permutation
variable importance, extrapolation detection, and interactive visualizations.
Integrates with 'tidymodels', 'caret', 'mlr3', 'ENMeval', and 'biomod2'.
Based on evaluation principles described in
Roberts et al. (2017) <doi:10.1111/ecog.02881>,
Kaufman et al. (2012) <doi:10.1145/2382577.2382579>,
Kapoor & Narayanan (2023) <doi:10.1016/j.patter.2023.100804>, and
Linnenbrink et al. (2 [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between BORG versions 0.2.5 dated 2026-03-20 and 0.3.1 dated 2026-03-29
DESCRIPTION | 34 - MD5 | 169 ++++- NAMESPACE | 121 +++ NEWS.md | 25 R/BORG-package.R | 2 R/BorgRisk.R | 55 + R/borg.R | 139 ++++ R/borg_adversarial.R |only R/borg_aoa.R |only R/borg_autoplot.R |only R/borg_block_size.R |only R/borg_bootstrap.R |only R/borg_cache.R |only R/borg_calibration.R |only R/borg_check.R |only R/borg_check_residuals.R |only R/borg_classification_metrics.R |only R/borg_compare.R | 4 R/borg_compare_models.R |only R/borg_conformal.R |only R/borg_cv.R | 1116 ++++++++++++++++++++++++++++++----- R/borg_debias.R |only R/borg_diagnose.R | 21 R/borg_disc_cv.R |only R/borg_drift.R |only R/borg_ensemble.R |only R/borg_error_profile.R |only R/borg_explain.R |only R/borg_extract.R |only R/borg_extrapolation.R |only R/borg_fairness.R |only R/borg_ffs.R |only R/borg_fold_performance.R |only R/borg_geodist.R |only R/borg_html_report.R |only R/borg_importance.R |only R/borg_inspect.R | 11 R/borg_leaflet.R |only R/borg_literature_check.R |only R/borg_mlr3_resampling.R |only R/borg_multiscale.R |only R/borg_null_test.R |only R/borg_predict_raster.R |only R/borg_prediction_map.R |only R/borg_repeated_cv.R |only R/borg_rewrite.R | 110 +-- R/borg_rset.R |only R/borg_sample_design.R |only R/borg_sf_utils.R |only R/borg_shap.R |only R/borg_simulate.R |only R/borg_spatial_loo.R |only R/borg_spatial_metrics.R |only R/borg_stability.R |only R/borg_stability_map.R |only R/borg_stratify.R |only R/borg_thin.R |only R/borg_transferability.R |only R/borg_workflow.R |only R/borg_wrappers.R | 92 ++ R/diagnose_spatial.R | 69 +- R/inspect_feature_engineering.R |only R/inspect_nested_cv.R | 132 ++++ R/inspect_preprocessing.R | 65 -- R/inspect_resampling.R | 8 R/inspect_sdm.R |only R/spatial_utils.R |only inst/WORDLIST | 119 +++ inst/doc/frameworks.html | 138 ++-- inst/doc/quickstart.html | 39 - inst/doc/risk-taxonomy.html | 37 - man/BORG-package.Rd | 2 man/autoplot.BorgDiagnosis.Rd |only man/autoplot.BorgRisk.Rd |only man/autoplot.borg_comparison.Rd |only man/autoplot.borg_cv.Rd |only man/autoplot.borg_fold_perf.Rd |only man/autoplot.borg_result.Rd |only man/borg.Rd | 24 man/borg_adversarial.Rd |only man/borg_aoa.Rd |only man/borg_best_subset.Rd |only man/borg_block_size.Rd |only man/borg_bootstrap.Rd |only man/borg_cache.Rd |only man/borg_calibration.Rd |only man/borg_check.Rd |only man/borg_check_coverage.Rd |only man/borg_check_nested_cv.Rd |only man/borg_check_residuals.Rd |only man/borg_compare_models.Rd |only man/borg_conformal.Rd |only man/borg_cv.Rd | 25 man/borg_debias.Rd |only man/borg_di.Rd |only man/borg_diagnose.Rd | 4 man/borg_disc_cv.Rd |only man/borg_drift.Rd |only man/borg_ensemble.Rd |only man/borg_error_profile.Rd |only man/borg_explain_risk.Rd |only man/borg_extract.Rd |only man/borg_extrapolation.Rd |only man/borg_fairness.Rd |only man/borg_fold_performance.Rd |only man/borg_fold_similarity.Rd |only man/borg_forward_selection.Rd |only man/borg_geodist.Rd |only man/borg_global_validation.Rd |only man/borg_importance.Rd |only man/borg_leaflet.Rd |only man/borg_literature_check.Rd |only man/borg_local_moran.Rd |only man/borg_metrics.Rd |only man/borg_multiscale.Rd |only man/borg_null_test.Rd |only man/borg_predict_raster.Rd |only man/borg_prediction_map.Rd |only man/borg_repeated_cv.Rd |only man/borg_report.Rd |only man/borg_rset.Rd |only man/borg_sample_design.Rd |only man/borg_shap.Rd |only man/borg_simulate.Rd |only man/borg_spatial_cv.Rd |only man/borg_spatial_loo.Rd |only man/borg_stability.Rd |only man/borg_stability_map.Rd |only man/borg_temporal_cv.Rd |only man/borg_thin.Rd |only man/borg_to_biomod2.Rd |only man/borg_to_enmeval.Rd |only man/borg_to_mlr3.Rd |only man/borg_transferability.Rd |only man/borg_willmott.Rd |only man/borg_workflow.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-BorgRisk.R | 3 tests/testthat/test-borg.R | 6 tests/testthat/test-borg_autoplot.R |only tests/testthat/test-new_features.R |only tests/testthat/test-sf_terra_input.R |only tests/testthat/test-spatial_utils.R |only 143 files changed, 2114 insertions(+), 456 deletions(-)
Title: Comparison of Bioregionalization Methods
Description: The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Author: Maxime Lenormand [aut, cre] ,
Boris Leroy [aut] ,
Pierre Denelle [aut]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
This is a re-admission after prior archival of version 1.3.0 dated 2026-01-23
Diff between bioregion versions 1.3.0 dated 2026-01-23 and 1.4.0 dated 2026-03-29
bioregion-1.3.0/bioregion/R/clustermetrics.R |only bioregion-1.3.0/bioregion/R/elbow_method.R |only bioregion-1.3.0/bioregion/R/iterative_hierarchical_consensus_tree.R |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.R |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_2_summary_metrics.html |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.R |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/a5_3_compare_bioregionalizations.html |only bioregion-1.3.0/bioregion/inst/doc/citations.Rmd |only bioregion-1.3.0/bioregion/inst/doc/citations.html |only bioregion-1.3.0/bioregion/vignettes/a5_2_summary_metrics.Rmd |only bioregion-1.3.0/bioregion/vignettes/a5_3_compare_bioregionalizations.Rmd |only bioregion-1.3.0/bioregion/vignettes/citations.Rmd |only bioregion-1.4.0/bioregion/DESCRIPTION | 10 bioregion-1.4.0/bioregion/MD5 | 147 +-- bioregion-1.4.0/bioregion/NAMESPACE | 46 - bioregion-1.4.0/bioregion/R/IHCT.R |only bioregion-1.4.0/bioregion/R/as_bioregion_pairwise.R | 2 bioregion-1.4.0/bioregion/R/betapart_to_bioregion.R | 42 - bioregion-1.4.0/bioregion/R/bioregion_colors.R | 6 bioregion-1.4.0/bioregion/R/bioregion_metrics.R | 328 ++++---- bioregion-1.4.0/bioregion/R/bioregionalization_metrics.R | 39 bioregion-1.4.0/bioregion/R/compare_bioregionalizations.R | 4 bioregion-1.4.0/bioregion/R/cut_tree.R | 3 bioregion-1.4.0/bioregion/R/data.R | 14 bioregion-1.4.0/bioregion/R/find_optimal_n.R | 14 bioregion-1.4.0/bioregion/R/generic_functions.R | 3 bioregion-1.4.0/bioregion/R/hclu_diana.R | 19 bioregion-1.4.0/bioregion/R/hclu_hierarclust.R | 170 +--- bioregion-1.4.0/bioregion/R/hclu_optics.R | 11 bioregion-1.4.0/bioregion/R/map_bioregions.R | 396 ++++------ bioregion-1.4.0/bioregion/R/mat_to_net.R | 5 bioregion-1.4.0/bioregion/R/net_to_mat.R | 3 bioregion-1.4.0/bioregion/R/netclu_beckett.R | 15 bioregion-1.4.0/bioregion/R/netclu_greedy.R | 2 bioregion-1.4.0/bioregion/R/netclu_labelprop.R | 16 bioregion-1.4.0/bioregion/R/netclu_leadingeigen.R | 2 bioregion-1.4.0/bioregion/R/netclu_leiden.R | 35 bioregion-1.4.0/bioregion/R/netclu_louvain.R | 16 bioregion-1.4.0/bioregion/R/netclu_walktrap.R | 2 bioregion-1.4.0/bioregion/R/nhclu_affprop.R | 89 -- bioregion-1.4.0/bioregion/R/nhclu_clara.R | 47 - bioregion-1.4.0/bioregion/R/nhclu_clarans.R | 38 bioregion-1.4.0/bioregion/R/nhclu_dbscan.R | 6 bioregion-1.4.0/bioregion/R/nhclu_kmeans.R | 36 bioregion-1.4.0/bioregion/R/nhclu_pam.R | 46 - bioregion-1.4.0/bioregion/R/package.R | 2 bioregion-1.4.0/bioregion/R/site_species_metrics.R | 2 bioregion-1.4.0/bioregion/R/site_species_subset.R | 41 - bioregion-1.4.0/bioregion/R/utils.R | 316 +++++++ bioregion-1.4.0/bioregion/build/partial.rdb |binary bioregion-1.4.0/bioregion/build/vignette.rds |binary bioregion-1.4.0/bioregion/data/fishdf.rda |binary bioregion-1.4.0/bioregion/data/fishmat.rda |binary bioregion-1.4.0/bioregion/data/fishsf.rda |binary bioregion-1.4.0/bioregion/data/vegedf.rda |binary bioregion-1.4.0/bioregion/data/vegemat.rda |binary bioregion-1.4.0/bioregion/data/vegesf.rda |binary bioregion-1.4.0/bioregion/inst/doc/bioregion.Rmd | 14 bioregion-1.4.0/bioregion/inst/doc/bioregion.html | 16 bioregion-1.4.0/bioregion/man/as_bioregion_pairwise.Rd | 2 bioregion-1.4.0/bioregion/man/betapart_to_bioregion.Rd | 4 bioregion-1.4.0/bioregion/man/bioregion_colors.Rd | 7 bioregion-1.4.0/bioregion/man/bioregion_metrics.Rd | 39 bioregion-1.4.0/bioregion/man/bioregionalization_metrics.Rd | 3 bioregion-1.4.0/bioregion/man/compare_bioregionalizations.Rd | 2 bioregion-1.4.0/bioregion/man/fishmat.Rd | 4 bioregion-1.4.0/bioregion/man/fishsf.Rd | 4 bioregion-1.4.0/bioregion/man/hclu_diana.Rd | 1 bioregion-1.4.0/bioregion/man/hclu_hierarclust.Rd | 4 bioregion-1.4.0/bioregion/man/map_bioregions.Rd | 106 +- bioregion-1.4.0/bioregion/man/netclu_labelprop.Rd | 1 bioregion-1.4.0/bioregion/man/nhclu_affprop.Rd | 2 bioregion-1.4.0/bioregion/man/nhclu_clara.Rd | 2 bioregion-1.4.0/bioregion/man/nhclu_clarans.Rd | 2 bioregion-1.4.0/bioregion/man/nhclu_kmeans.Rd | 2 bioregion-1.4.0/bioregion/man/nhclu_pam.Rd | 2 bioregion-1.4.0/bioregion/man/site_species_metrics.Rd | 2 bioregion-1.4.0/bioregion/man/site_species_subset.Rd | 10 bioregion-1.4.0/bioregion/man/vegesf.Rd | 6 bioregion-1.4.0/bioregion/vignettes/bioregion.Rmd | 14 82 files changed, 1128 insertions(+), 1094 deletions(-)
Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0)
"Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences".
This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting
functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between HDANOVA versions 0.8.4 dated 2025-08-30 and 0.8.5 dated 2026-03-29
DESCRIPTION | 15 - MD5 | 47 ++-- NAMESPACE | 6 NEWS | 5 R/HDANOVA-package.R | 2 R/ML_variance_partition.R | 8 R/RcppExports.R |only R/apca.R | 2 R/apls.R | 2 R/asca_plots.R | 27 +- R/asca_results.R | 8 R/permutation.R | 422 ++++++++++++++++++++++++++++++++---- R/pls.R | 2 R/rotation.R |only R/utilities.R | 2 README.md | 1 build/vignette.rds |binary inst/doc/vignette_A_data.html | 16 - inst/doc/vignette_B_ANOVA.html | 9 inst/doc/vignette_C_ASCA.html | 67 ++--- inst/doc/vignette_D_additional.html | 83 +++---- man/asca_plots.Rd | 3 man/permutation.Rd | 63 ++++- man/rotation.Rd |only src |only 25 files changed, 617 insertions(+), 173 deletions(-)
Title: Genetic Algorithms in Regression
Description: Provides a genetic algorithm framework for regression problems requiring discrete optimization over model spaces with unknown or varying dimension, where gradient-based methods and exhaustive enumeration are impractical. Uses a compact chromosome representation for tasks including spline knot placement and best-subset variable selection, with constraint-preserving crossover and mutation, exact uniform initialization under spacing constraints, steady-state replacement, and optional island-model parallelization from Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). The computation is built on the 'GA' engine of Scrucca (2017, <doi:10.32614/RJ-2017-008>) and 'changepointGA' engine from Li and Lu (2024, <doi:10.48550/arXiv.2410.15571>). In challenging high-dimensional settings, 'GAReg' enables efficient search and delivers near-optimal solutions when alternative algorithms are not well-justified.
Author: Mo Li [aut, cre],
QiQi Lu [aut],
Robert Lund [aut],
Xueheng Shi [aut]
Maintainer: Mo Li <mo.li@louisiana.edu>
Diff between GAReg versions 0.1.0 dated 2026-02-09 and 0.1.1 dated 2026-03-29
DESCRIPTION | 9 ++++---- MD5 | 13 +++++++----- R/data-nhtr2005.R |only R/gareg_knots.R | 8 +++---- R/gareg_subset.R | 6 ++--- data |only inst/doc/vignette.html | 53 ++++++++++++++++++++++++------------------------- man/gareg_subset.Rd | 6 ++--- man/nhtr2005.Rd |only 9 files changed, 50 insertions(+), 45 deletions(-)
Title: Plot Function for Single-Case Data Frames
Description: Add-on for the 'scan' package that creates plots
from single-case data frames ('scdf'). It includes functions for styling
single-case plots, adding phase-based lines to indicate various statistical
parameters, and predefined themes for presentations and publications. More
information and in depth examples can be found in the online book
"Analyzing Single-Case Data with R and 'scan"
Jürgen Wilbert (2026) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scplot versions 0.6.1 dated 2026-02-25 and 0.7.0 dated 2026-03-29
DESCRIPTION | 10 MD5 | 69 - NAMESPACE | 2 NEWS.md | 41 + R/add_arrow.R | 26 R/add_legend.R | 36 R/add_line.R | 2 R/add_staircase.R |only R/add_statline.R | 155 ++- R/as_ggplot.R | 185 +--- R/background_panel.R | 4 R/message_system.R |only R/print.scplot.R | 16 R/private-scplot.R | 8 R/private-statline.R | 324 +++----- R/private-theil_sen.R |only R/private-themes.R | 1976 +++++++++++++++++++++++++++++++++++++++++++++++--- R/private_check.R | 70 - R/scplot-package.R | 1 R/scplot.R | 13 R/scplot.sc_hplm.R | 9 R/scplot.sc_rand.R | 2 R/scplot.sc_tauu.R | 5 R/set_dataline.R | 99 +- R/set_separator.R | 6 R/split_dataline.R |only R/startup.R | 2 R/theme.R | 15 R/title_caption.R | 8 README.md | 6 inst/CITATION | 2 man/abort.Rd |only man/add_arrow.Rd | 24 man/add_legend.Rd | 31 man/add_statline.Rd | 52 - man/as_ggplot.Rd | 19 man/notify.Rd |only man/set_dataline.Rd | 28 man/split_dataline.Rd |only 39 files changed, 2541 insertions(+), 705 deletions(-)
Title: Evidence Accumulation Models
Description: Simulation-based evidence accumulation models for analyzing responses
and reaction times in single- and multi-response tasks. The package includes
simulation engines for five representative models: the Diffusion Decision
Model (DDM), Leaky Competing Accumulator (LCA), Linear Ballistic Accumulator
(LBA), Racing Diffusion Model (RDM), and Levy Flight Model (LFM), and
extends these frameworks to multi-response settings. The package supports
user-defined functions for item-level parameterization and the incorporation
of covariates, enabling flexible customization and the development of new
model variants based on existing architectures. Inference is performed using
simulation-based methods, including Approximate Bayesian Computation (ABC)
and Amortized Bayesian Inference (ABI), which allow parameter estimation
without requiring tractable likelihood functions. In addition to core
inference tools, the package provides modules for parameter recovery,
posterior predictive checks, and model com [...truncated...]
Author: Guangyu Zhu [aut] ,
Guang Yang [aut, cre]
Maintainer: Guang Yang <guang.spike.yang@gmail.com>
Diff between eam versions 1.1.0 dated 2026-02-09 and 1.2.0 dated 2026-03-29
DESCRIPTION | 9 MD5 | 66 ++-- NAMESPACE | 12 NEWS.md | 66 +++- R/abc_abc.R |only R/abc_cv.R |only R/abc_input.R | 12 R/abc_posterior.R | 2 R/abc_resample.R | 14 R/abi_assess.R |only R/abi_estimate.R |only R/abi_input.R | 68 +++- R/abi_julia_interface.R |only R/abi_sample_posterior.R |only R/abi_train.R |only R/plot_accuracy.R | 42 -- R/plot_cv_recovery.R | 553 +++++++++++++++++++++++++++++++++- R/plot_posterior_parameters.R | 54 --- R/plot_rt.R | 61 ++- R/posterior_predictive_check.R |only R/simulation_config.R | 213 +++++++++++++ R/simulation_router.R | 3 R/summarise_posterior_parameters.R | 97 +++++ inst/CITATION |only inst/julia |only man/abc_abc.Rd |only man/abc_cv.Rd |only man/abc_posterior_bootstrap.Rd | 2 man/abc_posterior_predictive_check.Rd |only man/abc_resample.Rd | 2 man/abi_assess.Rd |only man/abi_estimate.Rd |only man/abi_posterior_predictive_check.Rd |only man/abi_sample_posterior.Rd |only man/abi_train.Rd |only man/build_abc_input.Rd | 10 man/build_abi_input.Rd | 201 ++++++------ man/init_julia_env.Rd |only man/plot_cv_recovery.Rd | 158 ++++++--- man/plot_posterior_parameters.Rd | 113 +++--- man/plot_rt.Rd | 7 man/summarise_posterior_parameters.Rd | 94 +++-- man/update_config_from_posterior.Rd |only 43 files changed, 1437 insertions(+), 422 deletions(-)
Title: Accelerated Estimation of Robust Location and Scale
Description: Estimates robust location and scale parameters using
platform-specific Single Instruction, Multiple Data (SIMD) vectorization
and Intel Threading Building Blocks (TBB) for parallel processing.
Implements a novel variance-weighted ensemble estimator that adaptively
combines all available statistics. Methods include logistic
M-estimators, the estimators of Rousseeuw and Croux (1993), the Gini
mean difference, the scaled Median Absolute Deviation (MAD), the scaled
Interquartile Range (IQR), and unbiased standard deviations. Achieves
substantial speedups over existing implementations through an 'Rcpp'
backend with fused single-buffer algorithms that halve memory traffic
for MAD and M-scale estimation, and a unified dispatcher that
automatically selects the optimal estimator based on sample size.
Author: Dennis Alexis Valin Dittrich [aut, cre, cph]
Maintainer: Dennis Alexis Valin Dittrich <davd@economicscience.net>
Diff between robscale versions 0.2.1 dated 2026-03-16 and 0.5.3 dated 2026-03-29
DESCRIPTION | 25 MD5 | 164 NEWS.md | 370 R/RcppExports.R | 24 R/adm.R | 38 R/ci_utils.R | 49 R/gmd.R | 19 R/iqr_scaled.R | 17 R/mad_scaled.R | 23 R/qn.R | 36 R/robLoc.R | 45 R/robScale.R | 62 R/robscale-package.R | 1 R/scale_robust.R | 188 R/sd_c4.R | 17 R/sn.R | 30 build/vignette.rds |only configure | 130 inst/CITATION | 2 inst/doc |only inst/references.bib |only man/adm.Rd | 24 man/gmd.Rd | 2 man/mad_scaled.Rd | 2 man/print.robscale_ci.Rd |only man/print.robscale_ensemble_ci.Rd |only man/qn.Rd | 10 man/robLoc.Rd | 32 man/robScale.Rd | 34 man/scale_robust.Rd | 64 man/sn.Rd | 4 src/Makevars.in | 4 src/RcppExports.cpp | 94 src/adm.cpp | 66 src/diag.cpp |only src/ensemble.cpp | 758 + src/estimators_internal.h | 212 src/gmd.cpp | 83 src/iqr.cpp | 87 src/mad.cpp | 105 src/pdq_select.h | 2 src/qn_estimator.cpp | 306 src/qnsn_constants.h | 2 src/qnsn_hardware_info.h | 142 src/qnsn_kernels.h | 37 src/qnsn_runtime_config.h | 10 src/qnsn_sort_utils.h | 21 src/rob_loc.cpp | 310 src/rob_scale.cpp | 398 src/robscale_config.h | 101 src/robust_core.h | 291 src/sd_c4.cpp | 6 src/selection.h | 5 src/sn_estimator.cpp | 293 src/sort_net.h |12258 ++++++++++++++++++++++++++- src/sort_net_inst.cpp |only src/validate_finite.h |only src/vshaped_mad.h |only src/worker_compat.h |only tests/testthat/fixtures |only tests/testthat/test-adm-cancellation.R |only tests/testthat/test-adm-opt.R |only tests/testthat/test-adm.R | 37 tests/testthat/test-bca-jackknife-remap.R |only tests/testthat/test-build-config.R | 3 tests/testthat/test-ci.R | 2 tests/testthat/test-cpp-validate-finite.R |only tests/testthat/test-cross-check.R | 183 tests/testthat/test-ensemble.R | 6 tests/testthat/test-factors-boundary.R |only tests/testthat/test-fuse1-nr-step.R |only tests/testthat/test-gmd-opt.R |only tests/testthat/test-gmd1-weighted-sum.R |only tests/testthat/test-implosion-guard.R |only tests/testthat/test-input-validation.R |only tests/testthat/test-iqr-correctness.R |only tests/testthat/test-iqr-opt.R |only tests/testthat/test-layout1-transpose.R |only tests/testthat/test-mad-microbuf.R |only tests/testthat/test-mad-opt.R |only tests/testthat/test-mad-scaled.R | 7 tests/testthat/test-qn-constants.R | 14 tests/testthat/test-qn-opt.R |only tests/testthat/test-qnsn-config.R |only tests/testthat/test-qnsn.R | 7 tests/testthat/test-refactor-robloc.R | 6 tests/testthat/test-rob-scale-opt.R |only tests/testthat/test-robScale-nr-production.R |only tests/testthat/test-robScale-oscillation.R |only tests/testthat/test-robScale.R | 41 tests/testthat/test-robloc-aitken.R |only tests/testthat/test-robloc-convergence.R |only tests/testthat/test-robloc-opt.R |only tests/testthat/test-robscale-nr.R |only tests/testthat/test-scale-robust.R | 99 tests/testthat/test-sn-constants.R | 12 tests/testthat/test-sn-correctness.R |only tests/testthat/test-sn-opt.R |only tests/testthat/test-sort-threshold.R |only vignettes |only 100 files changed, 16135 insertions(+), 1285 deletions(-)
Title: Power Analysis for Generalised Linear Mixed Models by Simulation
Description: Calculate power for generalised linear mixed models, using
simulation. Designed to work with models fit using the 'lme4' package.
Described in Green and MacLeod, 2016 <doi:10.1111/2041-210X.12504>.
Author: Peter Green [aut, cre] ,
Catriona MacLeod [aut],
Phillip Alday [ctb]
Maintainer: Peter Green <simr.peter@gmail.com>
Diff between simr versions 1.0.8 dated 2025-08-18 and 1.0.9 dated 2026-03-29
DESCRIPTION | 15 ++++----- MD5 | 40 ++++++++++++------------ NEWS.md | 8 ++++ R/extend.R | 4 +- R/maybe.R | 47 +++++++++++++++++++++++++++- R/modify.R | 62 +++++++++++++++++++++++++++++++++++--- R/new.R | 2 - R/powerCurve.R | 1 R/powerSim.R | 1 R/print.R | 26 +++++++++++---- R/simr.R | 6 +-- R/testLibrary.R | 22 +++++++++++-- build/vignette.rds |binary inst/doc/examples.R | 4 +- inst/doc/examples.html | 29 ++++++++--------- inst/doc/fromscratch.html | 47 +++++++--------------------- tests/testthat/helper_setup.R | 4 +- tests/testthat/test_modify.R | 28 ++++++++++++++++- tests/testthat/test_new.R | 10 ++++++ tests/testthat/test_testLibrary.R | 5 +++ tests/testthat/test_zzz.r | 3 + 21 files changed, 258 insertions(+), 106 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short
cgeneric, to define a Gaussian Markov random (GMRF) model.
The cgeneric contain code to specify GMRF elements such as
the graph and the precision matrix, and also the initial and
prior for its parameters, useful for model inference.
It can be accessed from a C program and is the recommended
way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>).
The 'INLAtools' implement functions to evaluate
each one of the model specifications from R.
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
A very useful functionality is the Kronecker product method
that creates a new model from multiple cgeneric models.
It also works with the rgeneric, the R version of the
cgeneric intended to easy try implementation of new GMRF models.
The Kronecker between two cgeneric models was used in
Sterr [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.0.9 dated 2026-02-12 and 0.1.0 dated 2026-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/aaa_methods.R | 8 +------- R/cgeneric.R | 7 ++++--- src/cgeneric_kronecker.c | 19 +++++++++---------- 5 files changed, 21 insertions(+), 27 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.6-1 dated 2026-01-29 and 3.7-0 dated 2026-03-29
DESCRIPTION | 16 +- MD5 | 71 +++++----- NAMESPACE | 33 ++++ NEWS | 40 +++++ R/Kmodel.R | 4 R/clusterprocess.R | 15 ++ R/detPPF-class.R | 6 R/dppmclass.R | 4 R/envelope.R | 272 ++++++++++++++++++++++++++++++---------- R/kppm.R | 19 ++ R/percy.R | 9 + R/ppmclass.R | 9 - R/quadrattest.R | 2 R/slrm.R | 4 R/sysdata.rda |binary R/zclustermodel.R | 5 build/partial.rdb |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/Kmodel.Rd | 30 ++-- man/Kmodel.clusterprocess.Rd |only man/Kmodel.dppm.Rd | 6 man/Kmodel.kppm.Rd | 6 man/Kmodel.ppm.Rd | 6 man/Triplets.Rd | 8 + man/clusterstrength.Rd | 31 ++-- man/envelope.Rd | 83 +++++++++--- man/is.poissonclusterprocess.Rd | 6 man/macros/defns.Rd | 3 man/methods.zclustermodel.Rd | 3 man/panysib.Rd | 4 man/persist.Rd | 29 +++- man/psib.Rd | 7 - man/spatstat.model-internal.Rd | 19 +- man/varcount.Rd | 4 man/zclustermodel.Rd | 2 tests/testsK.R | 30 ++-- 37 files changed, 591 insertions(+), 199 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Parallel Utilities for Lambda Selection along a Regularization
Path
Description: Model selection for penalized graphical models using the Stability Approach to Regularization Selection ('StARS'), with options for speed-ups including Bounded StARS (B-StARS), batch computing, and other stability metrics (e.g., graphlet stability G-StARS). Christian L. Müller, Richard Bonneau, Zachary Kurtz (2016) <doi:10.48550/arXiv.1605.07072>.
Author: Zachary Kurtz [aut, cre],
Christian Mueller [aut, ctb]
Maintainer: Zachary Kurtz <zdkurtz@gmail.com>
Diff between pulsar versions 0.3.12 dated 2026-03-19 and 0.3.13 dated 2026-03-29
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS | 6 +++++ R/mcPulsarSelect.R | 40 +++++++++++++++++++++-------------- R/pulsar-package.R | 4 --- man/pulsar.Rd | 2 - tests/testthat/test_errorreporting.R | 4 --- 7 files changed, 42 insertions(+), 32 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets and
association rules). Also provides C implementations of the
association mining algorithms Apriori and Eclat. Hahsler, Gruen and
Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph] ,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph] ,
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7.13 dated 2026-01-10 and 1.7.14 dated 2026-03-29
arules-1.7.13/arules/src/arrayIndex.c |only arules-1.7.14/arules/DESCRIPTION | 8 arules-1.7.14/arules/MD5 | 21 arules-1.7.14/arules/NEWS.md | 4 arules-1.7.14/arules/inst/doc/arules.pdf |binary arules-1.7.14/arules/src/dll.c | 22 arules-1.7.14/arules/src/matrix.c | 833 ++++------ arules-1.7.14/arules/src/ptree.c | 801 +++++----- arules-1.7.14/arules/src/rapriori.c | 1698 +++++++++------------- arules-1.7.14/arules/src/similarity.c | 277 ++- arules-1.7.14/arules/src/warm.c | 623 ++++---- arules-1.7.14/arules/tests/testthat/test-matrix.R | 10 12 files changed, 2023 insertions(+), 2274 deletions(-)
Title: 'Copernicus Data Space Ecosystem' API Wrapper
Description: Provides interface to the 'Copernicus Data Space Ecosystem' API
<https://dataspace.copernicus.eu/analyse/apis>, mainly for searching the catalog of available
data from Copernicus Sentinel missions and obtaining the images for just the area of interest
based on selected spectral bands. The package uses the 'Sentinel Hub' REST API interface
<https://dataspace.copernicus.eu/analyse/apis/sentinel-hub> that provides access to various
satellite imagery archives. It allows you to access raw satellite data, rendered images,
statistical analysis, and other features.
This package is in no way officially related to or endorsed by Copernicus.
Author: Zivan Karaman [aut, cre, cph]
Maintainer: Zivan Karaman <zivan.karaman@gmail.com>
Diff between CDSE versions 0.3.0 dated 2025-09-02 and 0.3.2 dated 2026-03-28
CDSE-0.3.0/CDSE/inst/CITATION |only CDSE-0.3.2/CDSE/DESCRIPTION | 15 ++-- CDSE-0.3.2/CDSE/MD5 | 53 ++++++++--------- CDSE-0.3.2/CDSE/NAMESPACE | 15 ++++ CDSE-0.3.2/CDSE/NEWS.md | 16 +++-- CDSE-0.3.2/CDSE/R/Authentication.R | 1 CDSE-0.3.2/CDSE/R/CheckCRS.R | 7 ++ CDSE-0.3.2/CDSE/R/GetArchiveImage.R | 6 - CDSE-0.3.2/CDSE/R/GetCollections.R | 2 CDSE-0.3.2/CDSE/R/GetImage.R | 6 - CDSE-0.3.2/CDSE/R/GetImageBy.R | 5 - CDSE-0.3.2/CDSE/R/GetQueryables.R | 6 - CDSE-0.3.2/CDSE/R/GetStatistics.R | 4 - CDSE-0.3.2/CDSE/R/GetStatisticsBy.R | 4 - CDSE-0.3.2/CDSE/R/MakeEvalScript.R | 63 +++++++++++--------- CDSE-0.3.2/CDSE/R/Point2Bbox.R | 2 CDSE-0.3.2/CDSE/R/SearchCatalog.R | 6 - CDSE-0.3.2/CDSE/R/SeasonalFilter.R | 1 CDSE-0.3.2/CDSE/R/SetPathAPI.R |only CDSE-0.3.2/CDSE/R/UniqueCatalog.R | 1 CDSE-0.3.2/CDSE/R/internals.R | 87 +++++++++++++++++++++++++++- CDSE-0.3.2/CDSE/R/zzz.R | 6 + CDSE-0.3.2/CDSE/inst/doc/BeforeYouStart.Rmd | 4 - CDSE-0.3.2/CDSE/inst/doc/BeforeYouStart.pdf |binary CDSE-0.3.2/CDSE/inst/doc/CDSE.R | 13 ++-- CDSE-0.3.2/CDSE/inst/doc/CDSE.Rmd | 40 ++++++------ CDSE-0.3.2/CDSE/inst/doc/CDSE.pdf |binary CDSE-0.3.2/CDSE/man/MakeEvalScript.Rd | 26 +++++--- CDSE-0.3.2/CDSE/man/SetPathAPI.Rd |only 29 files changed, 257 insertions(+), 132 deletions(-)
Title: Wasserstein Regression and Inference
Description: Implementation of the methodologies described in 1) Alexander Petersen, Xi Liu and Afshin A. Divani (2021) <doi:10.1214/20-aos1971>, including global F tests, partial F tests, intrinsic Wasserstein-infinity bands and Wasserstein density bands, and 2) Chao Zhang, Piotr Kokoszka and Alexander Petersen (2022) <doi:10.1111/jtsa.12590>, including estimation, prediction, and inference of the Wasserstein autoregressive models.
Author: Xi Liu [aut, cre],
Chao Zhang [aut],
Matthew Coleman [aut],
Alexander Petersen [aut]
Maintainer: Xi Liu <xiliu@ucsb.edu>
Diff between WRI versions 0.2.1 dated 2025-12-16 and 0.2.2 dated 2026-03-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/confidenceBands.R | 4 ++-- R/partialFtest.R | 4 ++-- R/quadrcticQ.R | 2 +- inst/doc/WRI-vignette.html | 28 ++++++++++++++-------------- 6 files changed, 29 insertions(+), 29 deletions(-)