Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman [aut, cre] ,
Hao Wu [aut],
Gary Churchill [ctb] ,
Saunak Sen [ctb] ,
Danny Arends [ctb] ,
Robert Corty [ctb],
Timothee Flutre [ctb],
Ritsert Jansen [ctb],
Pjotr Prins [ctb] ,
Lars Ronnegard [ctb],
Rohan Shah [ctb],
Laura Shannon [ctb],
[...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.72 dated 2025-11-19 and 1.74 dated 2025-12-08
DESCRIPTION | 8 +-- MD5 | 110 +++++++++++++++++++++--------------------- NEWS.md | 5 + inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary src/countXO.c | 1 src/discan.c | 1 src/discan_covar.c | 1 src/effectscan.c | 1 src/findDupMarkers_notexact.c | 1 src/fitqtl_hk.c | 1 src/fitqtl_hk_binary.c | 1 src/fitqtl_imp.c | 1 src/fitqtl_imp_binary.c | 1 src/hmm_4way.c | 1 src/hmm_bc.c | 1 src/hmm_bci.c | 1 src/hmm_bcsft.c | 1 src/hmm_bgmagic16.c | 1 src/hmm_f2.c | 1 src/hmm_f2i.c | 1 src/hmm_main.c | 1 src/hmm_ri4self.c | 1 src/hmm_ri4sib.c | 1 src/hmm_ri8self.c | 1 src/hmm_ri8selfIRIP1.c | 1 src/hmm_ri8sib.c | 1 src/hmm_util.c | 1 src/inferFounderHap.c | 1 src/info.c | 1 src/lapackutil.c | 1 src/markerlrt.c | 1 src/pickMarkerSubset.c | 1 src/ril48_reorg.c | 2 src/ripple.c | 1 src/scanone_ehk.c | 1 src/scanone_em.c | 1 src/scanone_em_covar.c | 1 src/scanone_hk.c | 1 src/scanone_hk_binary.c | 1 src/scanone_imp.c | 1 src/scanone_mr.c | 1 src/scanone_np.c | 1 src/scantwo_binary_em.c | 1 src/scantwo_binary_hk.c | 1 src/scantwo_em.c | 1 src/scantwo_hk.c | 1 src/scantwo_imp.c | 1 src/scantwo_mr.c | 1 src/scantwopermhk.c | 1 src/simulate.c | 1 src/simulate_ril.c | 1 src/stahl_mf.c | 1 src/summary_scantwo.c | 1 src/test_bcsft.c | 1 56 files changed, 64 insertions(+), 110 deletions(-)
Title: Detecting Changes in Autocorrelated and Fluctuating Signals
Description: Detect abrupt changes in time series with local fluctuations as a random walk process and autocorrelated noise as an AR(1) process. See Romano, G., Rigaill, G., Runge, V., Fearnhead, P. (2021) <doi:10.1080/01621459.2021.1909598>.
Author: Gaetano Romano [aut, cre],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between DeCAFS versions 3.3.3 dated 2023-01-06 and 3.3.5 dated 2025-12-08
DeCAFS-3.3.3/DeCAFS/src/Makevars |only DeCAFS-3.3.5/DeCAFS/DESCRIPTION | 12 ++++++------ DeCAFS-3.3.5/DeCAFS/MD5 | 7 +++---- DeCAFS-3.3.5/DeCAFS/NEWS.md | 14 ++++++++++++++ DeCAFS-3.3.5/DeCAFS/build/partial.rdb |binary 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Multilevel Latent Time Series Models with 'R' and 'Stan'
Description: Fit multilevel manifest or latent time-series models, including popular Dynamic Structural Equation Models (DSEM).
The models can be set up and modified with user-friendly functions and are fit to the data using 'Stan' for Bayesian inference.
Path models and formulas for user-defined models can be easily created with functions using 'knitr'.
Asparouhov, Hamaker, & Muthen (2018) <doi:10.1080/10705511.2017.1406803>.
Author: Kenneth Koslowski [aut, cre, cph] ,
Fabian Muench [aut] ,
Tobias Koch [aut] ,
Jana Holtmann [aut]
Maintainer: Kenneth Koslowski <kenneth.koslowski@uni-leipzig.de>
Diff between mlts versions 1.0.0 dated 2024-06-27 and 2.0.0 dated 2025-12-08
DESCRIPTION | 19 MD5 | 156 NAMESPACE | 39 NEWS.md | 27 R/VARprepare.R | 701 +- R/ar1_data.R | 26 R/create_missings.R | 309 - R/mlts-package.R | 26 R/mlts_fit.R | 998 ++- R/mlts_model.R | 880 ++- R/mlts_model_betw.R | 362 - R/mlts_model_check.R | 52 R/mlts_model_constraint.R | 325 - R/mlts_model_eval.R | 938 +-- R/mlts_model_formula.R | 1761 +++--- R/mlts_model_measurement.R | 529 +- R/mlts_model_paths.R | 2449 ++++----- R/mlts_param_labels.R | 332 - R/mlts_paths.R |only R/mlts_plot.R | 692 +- R/mlts_posterior_sample.R |only R/mlts_pp_check.R |only R/mlts_sim.R | 965 +-- R/mlts_standardized.R | 4 R/mlts_standardized_btw.R | 616 +- R/mlts_standardized_within.R | 414 - R/model_helper_functions.R | 653 ++ R/prepare_data.R | 417 - R/sim_helper_functions.R |only R/stanmodels.R | 56 R/summary.R | 671 +- R/ts_data.R | 28 README.md | 634 +- build/partial.rdb |binary build/vignette.rds |binary configure.win | 10 inst/CITATION | 36 inst/doc/betw_predictors.R | 170 inst/doc/betw_predictors.html | 1466 ++--- inst/doc/manifest_ar.R | 91 inst/doc/manifest_ar.Rmd | 290 - inst/doc/manifest_ar.html | 1201 ++-- inst/doc/manifest_var.R | 18 inst/doc/manifest_var.Rmd | 44 inst/doc/manifest_var.html | 723 +- inst/rmarkdown/templates/formula/skeleton/skeleton.Rmd | 32 inst/rmarkdown/templates/formula/template.yaml | 8 inst/rmarkdown/templates/pathmodel/skeleton/skeleton.Rmd | 48 inst/rmarkdown/templates/pathmodel/template.yaml | 8 inst/stan/VAR_latent.stan | 782 +-- inst/stan/VAR_latentCovsFix.stan | 731 +- inst/stan/VAR_manifest.stan | 565 +- inst/stan/VAR_manifestCovsFix.stan | 530 +- inst/stan/include/license.stan | 28 man/ar1_data.Rd | 54 man/create_missings.Rd | 90 man/figures/README-ar1_plot-1.png |binary man/figures/README-unnamed-chunk-5-1.png |only man/mlts-package.Rd | 60 man/mlts_fit.Rd | 339 - man/mlts_model.Rd | 400 - man/mlts_model_formula.Rd | 104 man/mlts_model_paths.Rd | 110 man/mlts_paths.Rd |only man/mlts_plot.Rd | 228 man/mlts_posterior_sample.Rd |only man/mlts_pp_check.Rd |only man/mlts_sim.Rd | 177 man/mlts_standardized.Rd | 113 man/summary.mltsfit.Rd | 124 man/ts_data.Rd | 56 tests/local/test-mlts_model_formula.R | 174 tests/local/test-mlts_model_paths.R | 172 tests/testthat.R | 24 tests/testthat/test-create_missings.R | 104 tests/testthat/test-mlts_model.R | 56 tests/testthat/test-prepare_data.R | 36 vignettes/apa.csl | 3828 +++++++-------- vignettes/ar1_fit.rds |binary vignettes/betw_preds_fit1.txt | 90 vignettes/betw_preds_fit2.txt | 110 vignettes/manifest_ar.Rmd | 290 - vignettes/manifest_var.Rmd | 44 83 files changed, 15085 insertions(+), 13558 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.13.0 dated 2025-08-30 and 0.13.1 dated 2025-12-08
DESCRIPTION | 24 - MD5 | 107 ++++---- NAMESPACE | 4 NEWS.md | 21 + R/as.data.frame.R |only R/estimate_contrasts.R | 24 + R/estimate_contrasts_effectsize.R | 41 ++- R/estimate_grouplevel.R | 206 +++++++++++----- R/estimate_means.R | 83 ++++-- R/estimate_slopes.R | 1 R/format.R | 54 +++- R/get_inequalitycontrasts.R | 2 R/get_marginalcontrasts.R | 35 +- R/get_marginaleffects_type.R | 36 +- R/get_marginalmeans.R | 108 +++++--- R/get_marginaltrends.R | 3 R/options.R | 10 R/residualize_over_grid.R | 2 R/standardize_methods.R | 12 R/summary.R | 2 R/table_footer.R | 28 ++ R/tinyplot.R | 95 ++++++- R/visualisation_recipe.R | 6 R/visualisation_recipe_internal.R | 2 README.md | 20 + build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 100 ++----- inst/doc/overview_of_vignettes.Rmd | 1 inst/doc/overview_of_vignettes.html | 2 man/as.data.frame.estimate_contrasts.Rd |only man/describe_nonlinear.Rd | 2 man/estimate_contrasts.Rd | 8 man/estimate_expectation.Rd | 2 man/estimate_grouplevel.Rd | 35 +- man/estimate_means.Rd | 48 +++ man/estimate_slopes.Rd | 4 man/figures/unnamed-chunk-3-1.png |binary man/get_emmeans.Rd | 10 man/modelbased-options.Rd | 9 man/pool_contrasts.Rd | 2 man/pool_predictions.Rd | 2 man/print.estimate_contrasts.Rd | 13 - man/puppy_love.Rd | 64 ++-- man/residualize_over_grid.Rd | 2 man/visualisation_recipe.estimate_predicted.Rd | 51 ++- tests/testthat/test-as.data.frame.R |only tests/testthat/test-attributes_estimatefun.R | 38 ++ tests/testthat/test-equivalence.R |only tests/testthat/test-estimate_contrasts_counterfactual.R |only tests/testthat/test-estimate_contrasts_effectsize.R | 106 ++++++-- tests/testthat/test-estimate_filter.R | 19 + tests/testthat/test-estimate_grouplevel.R | 145 +++++++++++ tests/testthat/test-keep_iterations.R | 47 ++- tests/testthat/test-ordinal.R | 1 tests/testthat/test-plot-grouplevel.R | 2 vignettes/overview_of_vignettes.Rmd | 1 57 files changed, 1180 insertions(+), 460 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-11 dated 2025-10-08 and 1.1-12 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++++----- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.pdf |binary tests/AFT-Ex.Rout.save |only tests/KM-Ex.Rout.save |only tests/faithful.Rout.save |only tests/orm-Ex.Rout.save |only tests/timedep_covar.Rout.save |only tests/truncreg-Ex.Rout.save |only vignettes/defs.tex | 2 +- 12 files changed, 24 insertions(+), 10 deletions(-)
Title: Dice Plot Visualization for 'ggplot2'
Description: Provides 'ggplot2' extensions for creating dice-based visualizations
where each dot position represents a specific categorical variable. The package
includes geom_dice() for displaying presence/absence of categorical variables
using traditional dice patterns. Each dice position (1-6) represents a different
category, with dots shown only when that category is present. This allows
intuitive visualization of up to 6 categorical variables simultaneously.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between ggdiceplot versions 0.1.1 dated 2025-10-14 and 1.0.1 dated 2025-12-08
ggdiceplot-0.1.1/ggdiceplot/R/geom-dice-ggproto.R |only ggdiceplot-0.1.1/ggdiceplot/inst |only ggdiceplot-1.0.1/ggdiceplot/DESCRIPTION | 16 +- ggdiceplot-1.0.1/ggdiceplot/MD5 | 19 +- ggdiceplot-1.0.1/ggdiceplot/R/geom-dice-ggprotto.R | 17 +- ggdiceplot-1.0.1/ggdiceplot/R/sample_datasets.R |only ggdiceplot-1.0.1/ggdiceplot/README.md | 123 +++++++++-------- ggdiceplot-1.0.1/ggdiceplot/data/sample_dice_miRNA.rda |only ggdiceplot-1.0.1/ggdiceplot/man/geom_dice.Rd | 2 ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data1.Rd | 51 ++----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_data2.Rd | 45 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_large.Rd | 48 +----- ggdiceplot-1.0.1/ggdiceplot/man/sample_dice_miRNA.Rd |only 13 files changed, 137 insertions(+), 184 deletions(-)
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Pascal Bondon [aut],
Valderio A. Reisen [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between alqrfe versions 1.2 dated 2025-07-03 and 1.3 dated 2025-12-08
alqrfe-1.2/alqrfe/R/LQRFE_main_v3.R |only alqrfe-1.3/alqrfe/DESCRIPTION | 10 +++-- alqrfe-1.3/alqrfe/MD5 | 21 ++++++----- alqrfe-1.3/alqrfe/R/LQRFE_main.R |only alqrfe-1.3/alqrfe/R/RcppExports.R | 17 ++++++--- alqrfe-1.3/alqrfe/man/clean_data.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr.Rd | 2 - alqrfe-1.3/alqrfe/man/mqr_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_alpha.Rd | 2 - alqrfe-1.3/alqrfe/man/plot_taus.Rd | 2 - alqrfe-1.3/alqrfe/man/qr.Rd | 19 +++++++++- alqrfe-1.3/alqrfe/src/LQRFE_arma.cpp | 62 +++++++++++++++++------------------ alqrfe-1.3/alqrfe/tests |only 13 files changed, 80 insertions(+), 59 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-07 1.10
2015-07-20 1.07
2014-12-05 1.06
2013-12-11 1.05
2009-02-10 1.04
2008-02-16 1.03
2007-09-11 1.02
2006-08-03 1.01
Title: Simulation of Legal Exemption System for European Cartel Law
Description: Monte Carlo simulations of a game-theoretic model for the
legal exemption system of the European cartel law are implemented
in order to estimate the (mean) deterrent effect of this system.
The input and output parameters of the simulated cartel
opportunities can be visualized by three-dimensional projections.
A description of the model is given in Moritz et al. (2018)
<doi:10.1515/bejeap-2017-0235>.
Author: Martin Becker [aut, cre]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between SimEUCartelLaw versions 1.0.3 dated 2022-06-13 and 1.0.4 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- src/SimEUCartelLaw.c | 1 - 3 files changed, 8 insertions(+), 8 deletions(-)
More information about SimEUCartelLaw at CRAN
Permanent link
Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has
already an implementation in package 'Synth') are implemented: first,
'MSCMT' allows for using multiple outcome variables, second, time series
can be supplied as economic predictors, and third, a well-defined
cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
A detailed description of the main algorithms is given in
Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] ,
Stefan Kloessner [aut],
Karline Soetaert [com],
Jack Dongarra [cph],
R.J. Hanson [cph],
K.H. Haskell [cph],
Cleve Moler [cph],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.4.0 dated 2024-03-19 and 1.4.1 dated 2025-12-08
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NEWS | 7 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/CheckingSynth.R | 2 +- inst/doc/CheckingSynth.html | 6 +++--- inst/doc/UsingTimeSeries.R | 2 +- inst/doc/WorkingWithMSCMT.R | 2 +- inst/doc/WorkingWithMSCMT.html | 32 ++++++++++++++++---------------- src/MSCMT.c | 2 +- 11 files changed, 46 insertions(+), 38 deletions(-)
Title: Extracts the Backbone from Networks
Description: An implementation of methods for extracting a sparse unweighted network (i.e. a backbone)
from an unweighted network (e.g., Hamann et al., 2016 <doi:10.1007/s13278-016-0332-2>), a weighted network
(e.g., Serrano et al., 2009 <doi:10.1073/pnas.0808904106>), or a weighted projection (e.g., Neal et al., 2021
<doi:10.1038/s41598-021-03238-3>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [ctb],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 3.0.2 dated 2025-10-06 and 3.0.3 dated 2025-12-08
backbone-3.0.2/backbone/R/utils.R |only backbone-3.0.3/backbone/DESCRIPTION | 8 backbone-3.0.3/backbone/MD5 | 37 +- backbone-3.0.3/backbone/NAMESPACE | 3 backbone-3.0.3/backbone/NEWS.md | 5 backbone-3.0.3/backbone/R/backbone.R | 9 backbone-3.0.3/backbone/R/backbone_from_projection.R | 4 backbone-3.0.3/backbone/R/backbone_from_unweighted.R | 26 +- backbone-3.0.3/backbone/R/backbone_from_weighted.R | 8 backbone-3.0.3/backbone/R/functions_s3.R |only backbone-3.0.3/backbone/R/functions_unweighted.R | 3 backbone-3.0.3/backbone/R/functions_util.R |only backbone-3.0.3/backbone/R/functions_weighted.R | 6 backbone-3.0.3/backbone/inst/doc/backbone.R | 24 + backbone-3.0.3/backbone/inst/doc/backbone.Rmd | 37 ++ backbone-3.0.3/backbone/inst/doc/backbone.html | 241 +++++++++---------- backbone-3.0.3/backbone/inst/doc/senate.html | 25 + backbone-3.0.3/backbone/man/backbone.Rd | 4 backbone-3.0.3/backbone/man/bicm.Rd | 2 backbone-3.0.3/backbone/man/fastball.Rd | 2 backbone-3.0.3/backbone/vignettes/backbone.Rmd | 37 ++ 21 files changed, 270 insertions(+), 211 deletions(-)
Title: Penalized Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.
Author: Ian Meneghel Danilevicz [aut, cre] ,
Valderio A Reisen [aut],
Pascal Bondon [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between pqrfe versions 1.2 dated 2025-11-14 and 1.3 dated 2025-12-08
pqrfe-1.2/pqrfe/build |only pqrfe-1.2/pqrfe/inst |only pqrfe-1.2/pqrfe/man/check_lambda.Rd |only pqrfe-1.2/pqrfe/man/choice_p.Rd |only pqrfe-1.2/pqrfe/man/d_psi_als.Rd |only pqrfe-1.2/pqrfe/man/d_psi_mq.Rd |only pqrfe-1.2/pqrfe/man/f_den.Rd |only pqrfe-1.2/pqrfe/man/f_tab.Rd |only pqrfe-1.2/pqrfe/man/loss_er.Rd |only pqrfe-1.2/pqrfe/man/loss_erfe.Rd |only pqrfe-1.2/pqrfe/man/loss_erlasso.Rd |only pqrfe-1.2/pqrfe/man/loss_mqr.Rd |only pqrfe-1.2/pqrfe/man/loss_mqrfe.Rd |only pqrfe-1.2/pqrfe/man/loss_mqrlasso.Rd |only pqrfe-1.2/pqrfe/man/loss_qr.Rd |only pqrfe-1.2/pqrfe/man/loss_qrfe.Rd |only pqrfe-1.2/pqrfe/man/loss_qrlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_er.Rd |only pqrfe-1.2/pqrfe/man/optim_erfe.Rd |only pqrfe-1.2/pqrfe/man/optim_erlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_mqr.Rd |only pqrfe-1.2/pqrfe/man/optim_mqrfe.Rd |only pqrfe-1.2/pqrfe/man/optim_mqrlasso.Rd |only pqrfe-1.2/pqrfe/man/optim_qr.Rd |only pqrfe-1.2/pqrfe/man/optim_qrfe.Rd |only pqrfe-1.2/pqrfe/man/optim_qrlasso.Rd |only pqrfe-1.2/pqrfe/man/pqrfe-package.Rd |only pqrfe-1.2/pqrfe/man/print.PQR.Rd |only pqrfe-1.2/pqrfe/man/psi_als.Rd |only pqrfe-1.2/pqrfe/man/psi_mq.Rd |only pqrfe-1.2/pqrfe/man/q_cov.Rd |only pqrfe-1.2/pqrfe/man/rho_koenker.Rd |only pqrfe-1.2/pqrfe/man/rho_mq.Rd |only pqrfe-1.2/pqrfe/man/sgf.Rd |only pqrfe-1.2/pqrfe/src/Makevars |only pqrfe-1.2/pqrfe/tests/tinytest.R |only pqrfe-1.3/pqrfe/DESCRIPTION | 14 pqrfe-1.3/pqrfe/MD5 | 53 --- pqrfe-1.3/pqrfe/NAMESPACE | 13 pqrfe-1.3/pqrfe/R/PQRFE_main.R | 219 ++++++++------- pqrfe-1.3/pqrfe/R/RcppExports.R | 487 +++++++++++++++++----------------- pqrfe-1.3/pqrfe/man/pqr.Rd | 17 + pqrfe-1.3/pqrfe/src/Makevars.win | 13 pqrfe-1.3/pqrfe/src/PQRFE_arma.cpp | 296 +++++++++----------- pqrfe-1.3/pqrfe/src/RcppExports.cpp | 77 ----- pqrfe-1.3/pqrfe/tests/testthat |only 46 files changed, 562 insertions(+), 627 deletions(-)
Title: Machine-Readable Data Analysis Results with Function Wrappers
Description: You can use the set of wrappers for analytical schemata
to reduce the effort in writing machine-readable data. The set of all-in-one
wrappers will cover widely used functions from data analysis packages.
Author: Olga Lezhnina [aut] ,
Manuel Prinz [aut] ,
Markus Stocker [aut, cre] ,
Open Research Knowledge Graph Project and Contributors [cph]
Maintainer: Markus Stocker <markus.stocker@tib.eu>
Diff between mrap versions 1.0.0 dated 2025-11-25 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NEWS.md | 4 ++++ man/mrap-package.Rd | 4 ++-- 4 files changed, 18 insertions(+), 14 deletions(-)
Title: Estimate Inverse Probability Weights
Description: Functions to estimate the probability to receive the observed treatment, based on
individual characteristics. The inverse of these probabilities can be used as weights when
estimating causal effects from observational data via marginal structural models. Both point
treatment situations and longitudinal studies can be analysed. The same functions can be used to
correct for informative censoring.
Author: Hung Thai Tran [aut, cre],
Willem M. van der Wal [aut],
Ronald B. Geskus [aut]
Maintainer: Hung Thai Tran <hungtt@oucru.org>
Diff between ipw versions 1.2.1.1 dated 2025-07-28 and 1.2.2 dated 2025-12-08
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 8 ++++---- R/ipwpoint.R | 43 +++++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/ipwpoint.Rd | 12 +++++++----- 5 files changed, 69 insertions(+), 17 deletions(-)
Title: Automated Multicollinearity Management
Description: Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single function: (1) target encoding of categorical variables based on response values (Micci-Barreca, 2001 (Micci-Barreca, D. 2001 <doi:10.1145/507533.507538>); (2) automated feature prioritization to preserve key predictors during filtering; (3 and 4) pairwise correlation and VIF filtering across all variable types (numeric–numeric, numeric–categorical, and categorical–categorical); (5) adaptive correlation and VIF thresholds. Together, these methods enable a reliable multicollinearity management in most use cases while maintaining model integrity. The package also supports parallel processing and progress tracking via the packages 'future' and 'progressr', and provides seamless integration with the 'tidymodels' ecosystem through a dedicated recipe step.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 2.0.0 dated 2024-11-08 and 3.0.0 dated 2025-12-08
collinear-2.0.0/collinear/R/cor_cramer_v.R |only collinear-2.0.0/collinear/R/identify.R |only collinear-2.0.0/collinear/R/imports.R |only collinear-2.0.0/collinear/R/performance_score_auc.R |only collinear-2.0.0/collinear/R/performance_score_r2.R |only collinear-2.0.0/collinear/R/performance_score_v.R |only collinear-2.0.0/collinear/R/preference_order_collinear.R |only collinear-2.0.0/collinear/R/preference_order_methods.R |only collinear-2.0.0/collinear/R/target_encoding_methods.R |only collinear-2.0.0/collinear/R/validate.R |only collinear-2.0.0/collinear/man/add_white_noise.Rd |only collinear-2.0.0/collinear/man/collinear-package.Rd |only collinear-2.0.0/collinear/man/cor_cramer_v.Rd |only collinear-2.0.0/collinear/man/encoded_predictor_name.Rd |only collinear-2.0.0/collinear/man/f_auc.Rd |only collinear-2.0.0/collinear/man/f_r2.Rd |only collinear-2.0.0/collinear/man/f_r2_counts.Rd |only collinear-2.0.0/collinear/man/f_v.Rd |only collinear-2.0.0/collinear/man/f_v_rf_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors.Rd |only collinear-2.0.0/collinear/man/identify_predictors_categorical.Rd |only collinear-2.0.0/collinear/man/identify_predictors_numeric.Rd |only collinear-2.0.0/collinear/man/identify_predictors_type.Rd |only collinear-2.0.0/collinear/man/identify_predictors_zero_variance.Rd |only collinear-2.0.0/collinear/man/performance_score_auc.Rd |only collinear-2.0.0/collinear/man/performance_score_r2.Rd |only collinear-2.0.0/collinear/man/performance_score_v.Rd |only collinear-2.0.0/collinear/man/preference_order_collinear.Rd |only collinear-2.0.0/collinear/man/validate_data_cor.Rd |only collinear-2.0.0/collinear/man/validate_data_vif.Rd |only collinear-2.0.0/collinear/man/validate_df.Rd |only collinear-2.0.0/collinear/man/validate_encoding_arguments.Rd |only collinear-2.0.0/collinear/man/validate_predictors.Rd |only collinear-2.0.0/collinear/man/validate_preference_order.Rd |only collinear-2.0.0/collinear/man/validate_response.Rd |only collinear-2.0.0/collinear/tests/testthat/test-auc.R |only collinear-2.0.0/collinear/tests/testthat/test-cramer_v.R |only collinear-2.0.0/collinear/tests/testthat/test-identify.R |only collinear-2.0.0/collinear/tests/testthat/test-preference_order_methods.R |only collinear-2.0.0/collinear/tests/testthat/test-target_encoding_methods.R |only collinear-2.0.0/collinear/tests/testthat/test-validate.R |only collinear-3.0.0/collinear/DESCRIPTION | 19 collinear-3.0.0/collinear/LICENSE | 4 collinear-3.0.0/collinear/MD5 | 303 ++- collinear-3.0.0/collinear/NAMESPACE | 90 - collinear-3.0.0/collinear/NEWS.md | 208 +- collinear-3.0.0/collinear/R/case_weights.R | 88 - collinear-3.0.0/collinear/R/collinear.R | 819 ++++++---- collinear-3.0.0/collinear/R/collinear_select.R |only collinear-3.0.0/collinear/R/collinear_stats.R |only collinear-3.0.0/collinear/R/cor_clusters.R | 148 + collinear-3.0.0/collinear/R/cor_cramer.R |only collinear-3.0.0/collinear/R/cor_df.R | 622 +++---- collinear-3.0.0/collinear/R/cor_matrix.R | 144 + collinear-3.0.0/collinear/R/cor_select.R | 239 -- collinear-3.0.0/collinear/R/cor_stats.R |only collinear-3.0.0/collinear/R/data.R | 165 +- collinear-3.0.0/collinear/R/drop_geometry_column.R | 58 collinear-3.0.0/collinear/R/f_auto.R |only collinear-3.0.0/collinear/R/f_auto_rules.R |only collinear-3.0.0/collinear/R/f_binomial_gam.R |only collinear-3.0.0/collinear/R/f_binomial_glm.R |only collinear-3.0.0/collinear/R/f_binomial_rf.R |only collinear-3.0.0/collinear/R/f_categorical_rf.R |only collinear-3.0.0/collinear/R/f_count_gam.R |only collinear-3.0.0/collinear/R/f_count_glm.R |only collinear-3.0.0/collinear/R/f_count_rf.R |only collinear-3.0.0/collinear/R/f_functions.R |only collinear-3.0.0/collinear/R/f_numeric_gam.R |only collinear-3.0.0/collinear/R/f_numeric_glm.R |only collinear-3.0.0/collinear/R/f_numeric_rf.R |only collinear-3.0.0/collinear/R/identify_categorical_variables.R |only collinear-3.0.0/collinear/R/identify_logical_variables.R |only collinear-3.0.0/collinear/R/identify_numeric_variables.R |only collinear-3.0.0/collinear/R/identify_response_type.R |only collinear-3.0.0/collinear/R/identify_valid_variables.R |only collinear-3.0.0/collinear/R/identify_zero_variance_variables.R |only collinear-3.0.0/collinear/R/model_formula.R | 341 +--- collinear-3.0.0/collinear/R/preference_order.R | 619 +++++-- collinear-3.0.0/collinear/R/print.collinear_output.R |only collinear-3.0.0/collinear/R/print.collinear_selection.R |only collinear-3.0.0/collinear/R/score_auc.R |only collinear-3.0.0/collinear/R/score_cramer.R |only collinear-3.0.0/collinear/R/score_r2.R |only collinear-3.0.0/collinear/R/step_collinear.R |only collinear-3.0.0/collinear/R/summary.collinear_output.R |only collinear-3.0.0/collinear/R/summary.collinear_selection.R |only collinear-3.0.0/collinear/R/target_encoding_lab.R | 352 ++-- collinear-3.0.0/collinear/R/target_encoding_loo.R |only collinear-3.0.0/collinear/R/target_encoding_mean.R |only collinear-3.0.0/collinear/R/target_encoding_rank.R |only collinear-3.0.0/collinear/R/validate_arg_df.R |only collinear-3.0.0/collinear/R/validate_arg_df_not_null.R |only collinear-3.0.0/collinear/R/validate_arg_encoding_method.R |only collinear-3.0.0/collinear/R/validate_arg_f.R |only collinear-3.0.0/collinear/R/validate_arg_function_name.R |only collinear-3.0.0/collinear/R/validate_arg_max_cor.R |only collinear-3.0.0/collinear/R/validate_arg_max_vif.R |only collinear-3.0.0/collinear/R/validate_arg_predictors.R |only collinear-3.0.0/collinear/R/validate_arg_preference_order.R |only collinear-3.0.0/collinear/R/validate_arg_quiet.R |only collinear-3.0.0/collinear/R/validate_arg_responses.R |only collinear-3.0.0/collinear/R/vif.R |only collinear-3.0.0/collinear/R/vif_df.R | 259 +-- collinear-3.0.0/collinear/R/vif_select.R | 331 ---- collinear-3.0.0/collinear/R/vif_stats.R |only collinear-3.0.0/collinear/README.md | 624 +++++-- collinear-3.0.0/collinear/data/experiment_adaptive_thresholds.rda |only collinear-3.0.0/collinear/data/experiment_cor_vs_vif.rda |only collinear-3.0.0/collinear/data/gam_cor_to_vif.rda |only collinear-3.0.0/collinear/data/prediction_cor_to_vif.rda |only collinear-3.0.0/collinear/data/vi.rda |binary collinear-3.0.0/collinear/data/vi_predictors.rda |binary collinear-3.0.0/collinear/data/vi_predictors_categorical.rda |binary collinear-3.0.0/collinear/data/vi_predictors_numeric.rda |binary collinear-3.0.0/collinear/data/vi_responses.rda |only collinear-3.0.0/collinear/data/vi_smol.rda |only collinear-3.0.0/collinear/inst/WORDLIST | 55 collinear-3.0.0/collinear/inst/experiments |only collinear-3.0.0/collinear/man/case_weights.Rd | 43 collinear-3.0.0/collinear/man/collinear.Rd | 269 +-- collinear-3.0.0/collinear/man/collinear_select.Rd |only collinear-3.0.0/collinear/man/collinear_stats.Rd |only collinear-3.0.0/collinear/man/cor_clusters.Rd | 90 - 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collinear-3.0.0/collinear/man/vif_select.Rd | 200 -- collinear-3.0.0/collinear/man/vif_stats.Rd |only collinear-3.0.0/collinear/tests/testthat/test-case_weights.R | 119 + collinear-3.0.0/collinear/tests/testthat/test-collinear.R | 720 ++++++-- collinear-3.0.0/collinear/tests/testthat/test-collinear_select.R |only collinear-3.0.0/collinear/tests/testthat/test-collinear_stats.R |only collinear-3.0.0/collinear/tests/testthat/test-cor_clusters.R | 31 collinear-3.0.0/collinear/tests/testthat/test-cor_cramer.R |only collinear-3.0.0/collinear/tests/testthat/test-cor_df.R | 113 - collinear-3.0.0/collinear/tests/testthat/test-cor_matrix.R | 135 + collinear-3.0.0/collinear/tests/testthat/test-cor_select.R | 128 - collinear-3.0.0/collinear/tests/testthat/test-cor_stats.R |only collinear-3.0.0/collinear/tests/testthat/test-drop_geometry_column.R |only collinear-3.0.0/collinear/tests/testthat/test-f_auto.R |only collinear-3.0.0/collinear/tests/testthat/test-f_auto_rules.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_binomial_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_categorical_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_count_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-f_functions.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_gam.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_glm.R |only collinear-3.0.0/collinear/tests/testthat/test-f_numeric_rf.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_categorical_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_logical_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_numeric_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_response_type.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_valid_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-identify_zero_variance_variables.R |only collinear-3.0.0/collinear/tests/testthat/test-model_formula.R |only collinear-3.0.0/collinear/tests/testthat/test-preference_order.R | 334 +++- collinear-3.0.0/collinear/tests/testthat/test-print.collinear_output.R |only collinear-3.0.0/collinear/tests/testthat/test-print.collinear_selection.R |only collinear-3.0.0/collinear/tests/testthat/test-score_auc.R |only collinear-3.0.0/collinear/tests/testthat/test-score_cramer.R |only collinear-3.0.0/collinear/tests/testthat/test-score_r2.R |only collinear-3.0.0/collinear/tests/testthat/test-step_collinear.R |only collinear-3.0.0/collinear/tests/testthat/test-summary.collinear_output.R |only collinear-3.0.0/collinear/tests/testthat/test-summary.collinear_selection.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_lab.R | 144 + collinear-3.0.0/collinear/tests/testthat/test-target_encoding_loo.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_mean.R |only collinear-3.0.0/collinear/tests/testthat/test-target_encoding_rank.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_df.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_df_not_null.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_encoding_method.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_f.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_function_name.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_max_cor.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_max_vif.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_predictors.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_preference_order.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_quiet.R |only collinear-3.0.0/collinear/tests/testthat/test-validate_arg_responses.R |only collinear-3.0.0/collinear/tests/testthat/test-vif.R |only collinear-3.0.0/collinear/tests/testthat/test-vif_df.R | 131 - collinear-3.0.0/collinear/tests/testthat/test-vif_select.R | 141 - collinear-3.0.0/collinear/tests/testthat/test-vif_stats.R |only 247 files changed, 5604 insertions(+), 3741 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.90 dated 2025-10-10 and 0.92 dated 2025-12-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ data/numbers-cap.RData |binary data/numbers.RData |binary src/normalize.c | 1 - src/runningmean.c | 1 - src/runningratio2.c | 1 - 8 files changed, 16 insertions(+), 14 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model. See, for example,
Broman and Weber (2000) <doi:10.1086/302923>.
Author: Karl W Broman [aut, cre] ,
Il-Youp Kwak [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between xoi versions 0.72 dated 2023-03-22 and 0.74 dated 2025-12-08
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ data/bssbsb.RData |binary src/GammaS.h | 1 - src/kfunc.c | 1 - src/kwak_coincidence.c | 1 - src/kwak_get_n_xo.c | 1 - src/kwak_identify.c | 1 - src/kwak_intensity.c | 1 - 10 files changed, 22 insertions(+), 22 deletions(-)
Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial
data in regulatory settings. We provide a framework for the specific
formatting features often used when displaying large datasets in that
context.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Joe Zhu [aut, cre] ,
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rlistings versions 0.2.12 dated 2025-06-15 and 0.2.13 dated 2025-12-08
DESCRIPTION | 19 ++-- MD5 | 44 +++++------ NAMESPACE | 2 NEWS.md | 5 + R/rlistings.R | 50 +++++++----- R/rlistings_methods.R | 45 +++++++++-- inst/WORDLIST | 2 inst/doc/col_formatting.html | 91 +++++++++++------------ inst/doc/large_list.R | 20 +++-- inst/doc/large_list.Rmd | 21 +++-- inst/doc/large_list.html | 79 +++++++++++--------- inst/doc/pagination.html | 7 + inst/doc/ref_footnotes.html | 7 + inst/doc/rlistings.html | 33 ++++---- man/listing_methods.Rd | 16 ++-- man/listings.Rd | 7 + man/make_row_df-listing_df-method.Rd | 13 ++- man/matrix_form-listing_df-method.Rd | 13 ++- man/vec_nlines.Rd | 15 +++ tests/testthat/test-listings.R | 129 ++++++++++++++++++++++++++++++--- tests/testthat/test-paginate_listing.R | 37 +++++++++ tests/testthat/test-print.R | 44 ++++++----- vignettes/large_list.Rmd | 21 +++-- 23 files changed, 496 insertions(+), 224 deletions(-)
Title: Estimating the Number of Essential Genes in a Genome
Description: Estimating the number of essential genes in a genome on
the basis of data from a random transposon mutagenesis experiment,
through the use of a Gibbs sampler.
Lamichhane et al. (2003) <doi:10.1073/pnas.1231432100>.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between negenes versions 1.2 dated 2025-05-11 and 1.4 dated 2025-12-08
DESCRIPTION | 10 ++--- MD5 | 10 ++--- NEWS.md | 5 ++ build/partial.rdb |binary data/Mtb80.RData |binary src/negenes.c | 94 +++++++++++++++++++++++++----------------------------- 6 files changed, 60 insertions(+), 59 deletions(-)
Title: m-Out-of-n Bootstrap Functions
Description: Functions and examples based on the m-out-of-n bootstrap suggested by
Politis, D.N. and Romano, J.P. (1994) <doi:10.1214/aos/1176325770>.
Additionally there are functions to estimate the scaling factor tau
and the subsampling size m. For a detailed description and a full list
of references, see Dalitz, C. and Lögler, F. (2025)
<doi:10.32614/RJ-2025-031>.
Author: Christoph Dalitz [aut, cre],
Felix Loegler [aut]
Maintainer: Christoph Dalitz <christoph.dalitz@hs-niederrhein.de>
Diff between moonboot versions 1.0.1 dated 2025-02-21 and 2.0.1 dated 2025-12-08
Changelog | 19 ++++++++++++ DESCRIPTION | 12 ++++---- MD5 | 26 ++++++++--------- R/distpower.R | 2 - R/moonboot.R | 78 ++++++++++++++++++++++++++++++---------------------- R/sherman.R | 6 ++-- README.md | 6 ++-- build/partial.rdb |binary inst/CITATION | 16 ++++++---- man/distPower.Rd | 2 - man/estimate.m.Rd | 11 ++++--- man/estimate.tau.Rd | 17 ++++++----- man/mboot.Rd | 4 +- man/mboot.ci.Rd | 20 +++++++++---- 14 files changed, 133 insertions(+), 86 deletions(-)
Title: An Accurate kNN Implementation with Multiple Distance Measures
Description: Similarly to the 'FNN' package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix.
The implementation is based on cover trees introduced by
Alina Beygelzimer, Sham Kakade, and John Langford (2006) <doi:10.1145/1143844.1143857>.
Author: Philipp Angerer [cre, aut] ,
David Crane [cph, aut]
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>
Diff between knn.covertree versions 1.0 dated 2019-10-28 and 1.1 dated 2025-12-08
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ R/knn.covertree-package.r | 3 +-- README.md | 10 ++++++---- build |only man/knn.Rd | 10 ++++++++-- man/knn.covertree-package.Rd | 21 +++++++++++++++++++-- src/RcppExports.cpp | 5 +++++ 8 files changed, 53 insertions(+), 23 deletions(-)
Title: Fair Gated Algorithm for Targeted Equity
Description: Tools for training and analysing fairness-aware gated neural
networks for subgroup-aware prediction and interpretation in clinical datasets.
Methods draw on prior work in mixture-of-experts neural networks by
Jordan and Jacobs (1994) <doi:10.1007/978-1-4471-2097-1_113>,
fairness-aware learning by Hardt, Price, and Srebro (2016) <doi:10.48550/arXiv.1610.02413>,
and personalised treatment prediction for depression by Iniesta, Stahl, and McGuffin (2016)
<doi:10.1016/j.jpsychires.2016.03.016>.
Author: Rhys Holland [aut, cre],
Raquel Iniesta [aut]
Maintainer: Rhys Holland <rhys.holland@icloud.com>
Diff between fairGATE versions 0.1.0 dated 2025-11-19 and 0.1.1 dated 2025-12-08
DESCRIPTION | 17 +++++++++----- MD5 | 4 +-- inst/doc/introduction-to-fairGATE.html | 40 ++++++++++++++++----------------- 3 files changed, 34 insertions(+), 27 deletions(-)
Title: Ecological Inference in 2x2 Tables
Description: Implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008 <doi:10.1093/pan/mpm017>) and (2011 <doi:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
Author: Kosuke Imai [aut, cre],
Ying Lu [aut],
Aaron Strauss [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@Harvard.Edu>
Diff between eco versions 4.0-5 dated 2025-10-23 and 4.0-6 dated 2025-12-08
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/fintegrate.c | 2 +- src/gibbsEM.c | 2 +- src/rand.c | 2 +- src/vector.c | 2 +- 7 files changed, 15 insertions(+), 14 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 fitting cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM',
as well as network comparison fitted using the '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 0.2.1 dated 2024-10-17 and 0.3.1 dated 2025-12-08
easybgm-0.2.1/easybgm/R/sparse_dense.R |only easybgm-0.2.1/easybgm/man/sparse_or_dense.Rd |only easybgm-0.2.1/easybgm/tests/testthat/_snaps |only easybgm-0.3.1/easybgm/DESCRIPTION | 29 - easybgm-0.3.1/easybgm/MD5 | 58 +- easybgm-0.3.1/easybgm/NAMESPACE | 20 easybgm-0.3.1/easybgm/R/AuxiliaryFunctions.R | 319 +++++++------- easybgm-0.3.1/easybgm/R/bgm_plot_class.R | 118 ++--- easybgm-0.3.1/easybgm/R/easybgm.R | 92 ++-- easybgm-0.3.1/easybgm/R/easybgm_compare.R |only easybgm-0.3.1/easybgm/R/functions.bdgraph.R | 43 + easybgm-0.3.1/easybgm/R/functions.bggm.R | 9 easybgm-0.3.1/easybgm/R/functions.bggmcompare.R |only easybgm-0.3.1/easybgm/R/functions.bgms.R | 278 ++++++++---- easybgm-0.3.1/easybgm/R/functions.bgmscompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgmCompare.R |only easybgm-0.3.1/easybgm/R/plottingfunctions.bgms.R | 99 +++- easybgm-0.3.1/easybgm/R/plottingfunctions.easybgm.R | 249 +++++++++- easybgm-0.3.1/easybgm/R/summary.easybgm.R | 255 ++++++++--- easybgm-0.3.1/easybgm/R/summary.easybgm_compare.R |only easybgm-0.3.1/easybgm/man/HDI.Rd | 4 easybgm-0.3.1/easybgm/man/centrality.Rd | 12 easybgm-0.3.1/easybgm/man/clusterBayesfactor.Rd |only easybgm-0.3.1/easybgm/man/complexity_probs.Rd | 2 easybgm-0.3.1/easybgm/man/easybgm.Rd | 48 +- easybgm-0.3.1/easybgm/man/easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/edgeevidence.Rd | 11 easybgm-0.3.1/easybgm/man/network.Rd | 2 easybgm-0.3.1/easybgm/man/print.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/man/prior_sensitivity.Rd | 8 easybgm-0.3.1/easybgm/man/structure.Rd | 2 easybgm-0.3.1/easybgm/man/structure_probs.Rd | 2 easybgm-0.3.1/easybgm/man/summary.easybgm.Rd | 6 easybgm-0.3.1/easybgm/man/summary.easybgm_compare.Rd |only easybgm-0.3.1/easybgm/tests/testthat/Rplots.pdf |binary easybgm-0.3.1/easybgm/tests/testthat/test-easybgm.R | 385 +++++++++++------ 36 files changed, 1410 insertions(+), 641 deletions(-)
Title: Create Scale Linkage Scores
Description: Perform a 'probabilistic' linkage of two data files using a scaling procedure using the methods described in Goldstein, H., Harron, K. and Cortina-Borja, M. (2017) <doi:10.1002/sim.7287>.
Author: Chris Charlton [aut, cre],
Harvey Goldstein [aut]
Maintainer: Chris Charlton <c.charlton@bristol.ac.uk>
Diff between Scalelink versions 1.0 dated 2019-02-20 and 1.0-2 dated 2025-12-08
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/pkgname.R | 5 ++--- man/Scalelink.Rd | 6 ++---- man/calcScores.Rd | 10 ++++++++-- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 5 +++++ src/rcpp_build_astar.cpp | 5 ++--- 10 files changed, 42 insertions(+), 29 deletions(-)
Title: An Interface to the Nexus Class Library
Description: An interface to the Nexus Class Library which allows parsing
of NEXUS, Newick and other phylogenetic tree file formats. It provides
elements of the file that can be used to build phylogenetic objects
such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality
is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
Author: Francois Michonneau [aut, cre] ,
Ben Bolker [aut] ,
Mark Holder [aut] ,
Paul Lewis [aut] ,
Brian O'Meara [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rncl versions 0.8.7 dated 2023-01-08 and 0.8.8 dated 2025-12-08
DESCRIPTION | 20 +++++++++--------- MD5 | 18 ++++++++-------- NAMESPACE | 1 NEWS.md | 4 +++ R/collapse_singles.R | 1 R/rncl-package.R | 3 -- R/rncl.R | 36 ++++++++++++++------------------- README.md | 7 +++--- build/partial.rdb |binary man/rncl.Rd | 55 ++++++++++++++++++++++++++++++++------------------- 10 files changed, 79 insertions(+), 66 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity. A detailed vignette can be found in the open-access paper
"Analyzing Intraday Financial Data in R: The highfrequency Package"
by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>).
Author: Kris Boudt [aut, cre] ,
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] ,
Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>
Diff between highfrequency versions 1.0.1 dated 2023-10-04 and 1.0.2 dated 2025-12-08
highfrequency-1.0.1/highfrequency/man/MDtest.Rd |only highfrequency-1.0.1/highfrequency/man/RBPCov_bi.Rd |only highfrequency-1.0.1/highfrequency/man/cholCovrMRCov.Rd |only highfrequency-1.0.2/highfrequency/DESCRIPTION | 14 - highfrequency-1.0.2/highfrequency/MD5 | 75 +++--- highfrequency-1.0.2/highfrequency/NEWS.md | 6 highfrequency-1.0.2/highfrequency/R/HARmodel.R | 4 highfrequency-1.0.2/highfrequency/R/HEAVYmodel.R | 2 highfrequency-1.0.2/highfrequency/R/dataHandling.R | 15 - highfrequency-1.0.2/highfrequency/R/driftBursts.R | 4 highfrequency-1.0.2/highfrequency/R/internalRealizedMeasures.R | 51 +--- highfrequency-1.0.2/highfrequency/R/internalSpotVolAndDrift.R | 24 -- highfrequency-1.0.2/highfrequency/R/liquidityMeasures.R | 2 highfrequency-1.0.2/highfrequency/R/realizedMeasures.R | 13 - highfrequency-1.0.2/highfrequency/R/spotVolAndDrift.R | 114 +++++----- highfrequency-1.0.2/highfrequency/man/AJjumpTest.Rd | 2 highfrequency-1.0.2/highfrequency/man/HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDI.Rd | 2 highfrequency-1.0.2/highfrequency/man/ReMeDIAsymptoticVariance.Rd | 2 highfrequency-1.0.2/highfrequency/man/aggregatePrice.Rd | 2 highfrequency-1.0.2/highfrequency/man/businessTimeAggregation.Rd | 2 highfrequency-1.0.2/highfrequency/man/driftBursts.Rd | 2 highfrequency-1.0.2/highfrequency/man/getLiquidityMeasures.Rd | 2 highfrequency-1.0.2/highfrequency/man/getTradeDirection.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/plot.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/plot.HEAVYmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/predict.HARmodel.Rd | 2 highfrequency-1.0.2/highfrequency/man/print.DBH.Rd | 4 highfrequency-1.0.2/highfrequency/man/quotesCleanup.Rd | 2 highfrequency-1.0.2/highfrequency/man/rQPVar.Rd | 2 highfrequency-1.0.2/highfrequency/man/rSemiCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rTSCov.Rd | 2 highfrequency-1.0.2/highfrequency/man/rThresholdCov.Rd | 9 highfrequency-1.0.2/highfrequency/man/spotDrift.Rd | 18 - highfrequency-1.0.2/highfrequency/man/spotVol.Rd | 75 +++--- highfrequency-1.0.2/highfrequency/tests/testthat/Rplots.pdf |binary highfrequency-1.0.2/highfrequency/tests/testthat/tests_models.R | 8 highfrequency-1.0.2/highfrequency/tests/testthat/tests_spotvol_and_drift.R | 2 40 files changed, 241 insertions(+), 237 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.16 dated 2024-02-20 and 0.4.17 dated 2025-12-08
DESCRIPTION | 14 - LICENSE | 2 MD5 | 48 +++--- NAMESPACE | 7 NEWS | 20 ++ R/chordDiagram.R | 9 - R/circos.heatmap.R | 36 ++++ R/genomic.R | 15 + R/global.R | 1 R/link.R | 42 ++--- R/low_level.R | 271 ++++++++++++++++++++++++++++++----- R/plot.R | 9 - R/utils.R | 198 +++++++++++++++++++++++++ build/vignette.rds |binary inst/CITATION | 24 +-- inst/doc/circlize.Rmd | 10 - inst/doc/circlize.html | 221 ++++++++++++++++++++++++++-- man/chordDiagram.Rd | 183 +++++++++++++++-------- man/circos.dendrogram.Rd | 3 man/circos.heatmap.get.x.Rd |only man/circos.initializeWithIdeogram.Rd | 2 man/circos.raster.Rd | 3 man/circos.rect.Rd | 3 man/circos.stackedText.Rd |only man/circos.trackPlotRegion.Rd | 2 vignettes/circlize.Rmd | 10 - 26 files changed, 929 insertions(+), 204 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.2.1 dated 2025-07-22 and 1.2.2 dated 2025-12-08
DESCRIPTION | 14 +-- MD5 | 73 ++++++++--------- NAMESPACE | 1 NEWS.md | 10 ++ R/iterate-responses.R | 15 ++- R/oauth-flow-auth-code.R | 4 R/otel.R |only R/pooled-request.R | 14 +++ R/req-cache.R | 2 R/req-dry-run.R | 2 R/req-error.R | 7 + R/req-perform-connection.R | 36 ++++++-- R/req-perform.R | 53 +++++++++--- R/req-promise.R | 7 - R/req-throttle.R | 22 ++++- R/req-url.R | 8 - R/url.R | 13 +-- R/zzz.R | 1 README.md | 16 +-- inst/doc/httr2.Rmd | 2 inst/doc/httr2.html | 41 +++++---- man/StreamingBody.Rd | 3 man/req_auth_aws_v4.Rd | 2 man/req_cache.Rd | 2 man/req_oauth_auth_code.Rd | 2 man/resps_successes.Rd | 16 ++- tests/testthat/_snaps/req-perform-connection.md | 10 ++ tests/testthat/test-req-body.R | 2 tests/testthat/test-req-dry-run.R | 2 tests/testthat/test-req-perform-connection.R | 99 ++++++++++++++++++++++++ tests/testthat/test-req-perform-parallel.R | 63 +++++++++++++++ tests/testthat/test-req-perform.R | 92 ++++++++++++++++++++++ tests/testthat/test-req-promise.R | 65 +++++++++++++++ tests/testthat/test-req-throttle.R | 53 ++++++++++++ tests/testthat/test-resp-url.R | 2 tests/testthat/test-resp.R | 1 tests/testthat/test-url.R | 18 ++++ vignettes/httr2.Rmd | 2 38 files changed, 627 insertions(+), 148 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.11 dated 2025-04-09 and 0.5.12 dated 2025-12-08
DESCRIPTION | 28 ++++++------ MD5 | 61 +++++++++++++-------------- NAMESPACE | 5 ++ NEWS.md | 8 +++ R/format_value.R | 61 +++++++++++++++++++++++---- R/generics.R | 71 ++++++++++++++++++++++++++++++- R/matrix_form.R | 87 +++++++++++++++++++++++++-------------- R/mpf_exporters.R | 13 +++-- R/pagination.R | 76 +++++++++++++++++++++------------- R/tostring.R | 12 ++--- build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/formatters.html | 9 ++-- man/MatrixPrintForm.Rd | 7 ++- man/export_as_pdf.Rd | 13 ++++- man/export_as_rtf.Rd | 10 ++++ man/export_as_txt.Rd | 13 ++++- man/format_value.Rd | 13 ++++- man/list_formats.Rd | 7 +++ man/make_row_df.Rd | 15 ++++-- man/matrix_form.Rd | 15 ++++-- man/mpf_to_rtf.Rd | 8 +-- man/obj_round_type.Rd |only man/paginate_indices.Rd | 17 ++++--- man/propose_column_widths.Rd | 13 ++++- man/round_fmt.Rd | 26 +++++++++-- man/test_matrix_form.Rd | 12 ++++- man/tostring.Rd | 8 +-- man/vert_pag_indices.Rd | 17 ++++--- tests/testthat/test-formatters.R | 87 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-listings.R | 2 tests/testthat/test-pagination.R | 53 +++++++++++++++++++++++ 32 files changed, 582 insertions(+), 188 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.1.1 dated 2025-07-08 and 1.1.2 dated 2025-12-08
CHANGELOG | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/prelim.R | 14 +++++++++----- R/sf-ks-prelim.R | 11 ++++++----- build/vignette.rds |binary inst/doc/tidysf_kde.html | 22 ++++++++++++---------- man/contour.Rd | 9 +++++++-- man/tidyst_as_kde.Rd | 1 + 10 files changed, 55 insertions(+), 38 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, Ising model reconstruction <doi:10.1080/01621459.2025.2571245>, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Zezhi Wang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj1jqx@gmail.com>
Diff between abess versions 0.4.10 dated 2025-04-05 and 0.4.11 dated 2025-12-08
DESCRIPTION | 24 ++++++++++++------------ MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/abess.R | 2 +- R/abessgraph.R |only R/generate.graph.R |only man/abess-package.Rd | 1 - man/abess.Rd | 2 +- man/generate.bmn.data.Rd |only man/slide.Rd |only src/AlgorithmGLM.h | 4 ++-- src/api.cpp | 27 +++++++++++++++++++-------- 13 files changed, 53 insertions(+), 33 deletions(-)
Title: Odds Ratio Tools for Logistic Regression
Description: Produces odds ratio analyses with comprehensive reporting tools. Generates
plots, summary tables, and diagnostic checks for logistic regression models
fitted with 'glm()' using binomial family. Provides visualisation methods,
formatted reporting tables via 'gt', and tools to assess logistic regression
model assumptions.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 0.7.0 dated 2025-07-01 and 0.8.0 dated 2025-12-08
plotor-0.7.0/plotor/tests/testthat/test_data/df_correlated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/df_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_four.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_correlated_two.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_diabetes.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_infert.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_separated.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_streptb.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_titanic.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/lr_triple_outcome.Rds |only plotor-0.7.0/plotor/tests/testthat/test_data/nonlr_streptb.Rds |only plotor-0.8.0/plotor/DESCRIPTION | 29 plotor-0.8.0/plotor/LICENSE | 4 plotor-0.8.0/plotor/MD5 | 61 plotor-0.8.0/plotor/NAMESPACE | 14 plotor-0.8.0/plotor/NEWS.md | 299 plotor-0.8.0/plotor/R/gt_extras.R | 806 - plotor-0.8.0/plotor/R/plot_or.R | 4550 ++++++---- plotor-0.8.0/plotor/R/plotor-package.R | 16 plotor-0.8.0/plotor/README.md | 481 - plotor-0.8.0/plotor/build/vignette.rds |binary plotor-0.8.0/plotor/inst/doc/using_plotor.R | 334 plotor-0.8.0/plotor/inst/doc/using_plotor.Rmd | 762 - plotor-0.8.0/plotor/inst/doc/using_plotor.html | 3163 +++--- plotor-0.8.0/plotor/man/check_or.Rd | 84 plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.png |binary plotor-0.8.0/plotor/man/figures/README-unnamed-chunk-4-1.svg | 2370 ++--- plotor-0.8.0/plotor/man/plot_or.Rd | 123 plotor-0.8.0/plotor/man/plotor-package.Rd | 52 plotor-0.8.0/plotor/man/table_or.Rd | 181 plotor-0.8.0/plotor/tests/testthat.R | 24 plotor-0.8.0/plotor/tests/testthat/helper_generate_data.R |only plotor-0.8.0/plotor/tests/testthat/test-plot_or.R | 536 - plotor-0.8.0/plotor/tests/testthat/test_data/make_test_data.R | 1288 +- plotor-0.8.0/plotor/vignettes/using_plotor.Rmd | 762 - 40 files changed, 8824 insertions(+), 7115 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph] ,
Thibaut Jombart [aut, cph] ,
Zhian N. Kamvar [aut, cph] ,
Brian Knaus [aut, cph] ,
Klaus Schliep [aut, cph] ,
Alastair Potts [aut, cph] ,
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 1.3 dated 2023-12-13 and 1.4 dated 2025-12-08
DESCRIPTION | 29 ++++++----- MD5 | 48 +++++++++---------- NEWS | 38 +++++++++++++++ R/dist.asd.R | 6 +- R/haplotype.R | 111 ++++++++++++++++++++++++++++++++++++++------- R/mjn.R | 52 ++++++++++++--------- R/zzz.R | 5 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PlotHaploNet.R | 46 +++++++++--------- inst/doc/PlotHaploNet.Rnw | 3 - inst/doc/PlotHaploNet.pdf |binary inst/doc/ReadingFiles.pdf |binary man/Fst.Rd | 2 man/alleles2loci.Rd | 2 man/amova.Rd | 3 - man/conversion.Rd | 13 ++--- man/hap.div.Rd | 4 + man/haplotype.Rd | 8 ++- man/hw.test.Rd | 4 - man/jaguar.Rd | 2 man/mst.Rd | 45 ++++++++++++------ man/read.gtx.Rd | 3 - man/utilities.Rd | 2 vignettes/PlotHaploNet.Rnw | 3 - 25 files changed, 295 insertions(+), 134 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.22 dated 2025-09-14 and 0.2.23 dated 2025-12-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/JAGS-diagnostics.R | 7 ++++++- R/model-averaging-plots.R | 8 ++++---- build/partial.rdb |binary inst/doc/ComparisonR.html | 6 +++--- inst/doc/SpikeAndSlab.html | 4 ++-- 8 files changed, 29 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-25 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-06 0.4.1
Title: Propensity Score Matching of Non-Binary Treatments
Description: Propensity score matching for non-binary treatments.
Author: Jason Bryer [aut, cre]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between TriMatch versions 1.0.0 dated 2025-04-03 and 1.0.1 dated 2025-12-08
DESCRIPTION | 18 +++++++++--------- MD5 | 27 +++++++++++++++------------ NAMESPACE | 5 ++++- NEWS.md | 5 +++++ R/TriMatch-package.R | 1 - R/ezANOVA.R |only R/ezANOVA_main.R |only R/plot.balance.R | 2 +- R/summary.triangle.matches.R | 2 +- build/vignette.rds |binary inst/doc/TriMatch.R | 16 +++++++--------- inst/doc/TriMatch.Rmd | 10 ++++------ inst/doc/TriMatch.pdf |binary man/ezANOVA.Rd |only man/summary.triangle.matches.Rd | 2 +- vignettes/TriMatch.Rmd | 10 ++++------ 16 files changed, 51 insertions(+), 47 deletions(-)
Title: The Plate Plot for Network Meta-Analysis Results
Description: A graphical display of results from network meta-analysis (NMA).
It is suitable for outcomes like odds ratio (OR), risk ratio (RR),
risk difference (RD) and standardized mean difference (SMD).
It also has an option to visually display and compare
the surface under the cumulative ranking (SUCRA) of different treatments.
Author: Zhenxun Wang [aut, cre],
Lifeng Lin [ctb],
Shanshan Zhao [ctb],
Haitao Chu [ctb]
Maintainer: Zhenxun Wang <wang6795@alumni.umn.edu>
Diff between nmaplateplot versions 1.0.2 dated 2024-04-07 and 1.0.3 dated 2025-12-08
DESCRIPTION | 10 MD5 | 22 NEWS.md | 6 R/nmaplateplot.R | 97 R/pe_text_conversion.R | 87 build/vignette.rds |binary inst/doc/nmaplateplot-intro.R | 118 inst/doc/nmaplateplot-intro.Rmd | 135 inst/doc/nmaplateplot-intro.html |20037 +++++++++++++++++++++++++++++++++++++-- man/nmaplateplot-package.Rd | 2 man/plateplot.Rd | 45 vignettes/nmaplateplot-intro.Rmd | 135 12 files changed, 19573 insertions(+), 1121 deletions(-)
Title: Generalized Gamma Probability Distribution
Description: Density, distribution function, quantile function and random generation for the Generalized Gamma proposed in Stacy, E. W. (1962) <doi:10.1214/aoms/1177704481>.
Author: Matheus H. J. Saldanha [aut, cre],
Adriano K. Suzuki [aut]
Maintainer: Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Diff between ggamma versions 1.0.1 dated 2019-12-15 and 1.0.2 dated 2025-12-08
ggamma-1.0.1/ggamma/man/ggamma.Rd |only ggamma-1.0.2/ggamma/DESCRIPTION | 11 +++++------ ggamma-1.0.2/ggamma/MD5 | 7 ++++--- ggamma-1.0.2/ggamma/NEWS.md |only ggamma-1.0.2/ggamma/R/ggamma-package.R | 5 +---- ggamma-1.0.2/ggamma/man/ggamma-package.Rd |only 6 files changed, 10 insertions(+), 13 deletions(-)
Title: Construct Reproducible Analytic Data Sets as R Packages
Description: A framework to help construct R data packages in a
reproducible manner. Potentially time consuming processing of raw data
sets into analysis ready data sets is done in a reproducible manner
and decoupled from the usual 'R CMD build' process so that data sets
can be processed into R objects in the data package and the data
package can then be shared, built, and installed by others without the
need to repeat computationally costly data processing. The package
maintains data provenance by turning the data processing scripts into
package vignettes, as well as enforcing documentation and version
checking of included data objects. Data packages can be version
controlled on 'GitHub', and used to share data for manuscripts,
collaboration and reproducible research.
Author: Greg Finak [aut, cph] ,
Paul Obrecht [ctb],
Ellis Hughes [ctb] ,
Jimmy Fulp [ctb],
Marie Vendettuoli [ctb] ,
Dave Slager [ctb, cre] ,
Jason Taylor [ctb],
Kara Woo [rev] ,
William Landau [rev]
Maintainer: Dave Slager <dslager@fredhutch.org>
Diff between DataPackageR versions 0.16.1 dated 2024-09-17 and 0.16.2 dated 2025-12-08
DataPackageR-0.16.1/DataPackageR/R/logger.R |only DataPackageR-0.16.1/DataPackageR/tests/testthat/test-logger.R |only DataPackageR-0.16.2/DataPackageR/DESCRIPTION | 19 +- DataPackageR-0.16.2/DataPackageR/MD5 | 48 ++--- DataPackageR-0.16.2/DataPackageR/NAMESPACE | 14 - DataPackageR-0.16.2/DataPackageR/NEWS.md | 17 + DataPackageR-0.16.2/DataPackageR/R/build.R | 44 +---- DataPackageR-0.16.2/DataPackageR/R/digests.R | 21 -- DataPackageR-0.16.2/DataPackageR/R/load_save.R | 1 DataPackageR-0.16.2/DataPackageR/R/processData.R | 87 +--------- DataPackageR-0.16.2/DataPackageR/R/prompt.R | 1 DataPackageR-0.16.2/DataPackageR/R/skeleton.R | 15 - DataPackageR-0.16.2/DataPackageR/R/use.R | 6 DataPackageR-0.16.2/DataPackageR/R/yamlR.R | 17 - DataPackageR-0.16.2/DataPackageR/README.md | 50 ++--- DataPackageR-0.16.2/DataPackageR/build/vignette.rds |binary DataPackageR-0.16.2/DataPackageR/inst/WORDLIST | 2 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.Rmd | 6 DataPackageR-0.16.2/DataPackageR/inst/doc/Using_DataPackageR.html | 60 +++--- DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.R | 12 - DataPackageR-0.16.2/DataPackageR/inst/doc/YAML_Configuration_Details.html | 21 +- DataPackageR-0.16.2/DataPackageR/man/package_build.Rd | 3 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-data-name-change.R | 5 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-edge-cases.R | 2 DataPackageR-0.16.2/DataPackageR/tests/testthat/test-project-path.R | 2 DataPackageR-0.16.2/DataPackageR/vignettes/Using_DataPackageR.Rmd | 6 26 files changed, 166 insertions(+), 293 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.1.3 dated 2024-04-05 and 1.1.4 dated 2025-12-08
DESCRIPTION | 8 MD5 | 35 +- NAMESPACE | 5 NEWS.md | 6 R/common.R | 2 R/operators.R | 541 +++++++++++++++++++++++++++++++++++++++- README.md | 23 + build/vignette.rds |binary inst/doc/common.R | 2 inst/doc/common.Rmd | 33 +- inst/doc/common.html | 47 ++- man/common.Rd | 2 man/grapes-eq-grapes.Rd | 11 man/grapes-ge-grapes.Rd |only man/grapes-gt-grapes.Rd |only man/grapes-le-grapes.Rd |only man/grapes-lt-grapes.Rd |only man/grapes-ne-grapes.Rd |only man/grapes-p-grapes.Rd | 10 tests/testthat/test-operators.R | 224 ++++++++++++++++ vignettes/common.Rmd | 33 +- 21 files changed, 915 insertions(+), 67 deletions(-)
Title: Aster Models
Description: Aster models (Geyer, Wagenius, and Shaw, 2007,
<doi:10.1093/biomet/asm030>; Shaw, Geyer, Wagenius, Hangelbroek, and
Etterson, 2008, <doi:10.1086/588063>; Geyer, Ridley, Latta, Etterson,
and Shaw, 2013, <doi:10.1214/13-AOAS653>) are exponential family
regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, life table analysis,
zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the ex [...truncated...]
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between aster versions 1.3-6 dated 2025-10-20 and 1.3-7 dated 2025-12-08
CHANGES | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/reaster.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/delta.pdf |binary inst/doc/linkingTo.pdf |binary inst/doc/re.pdf |binary inst/doc/trunc.pdf |binary inst/doc/tutor.pdf |binary 11 files changed, 17 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-21 0.1.8.17
2024-03-01 0.1.8.10
2023-12-04 0.1.8.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-25 1.0.2
2025-11-23 1.0.1
2023-06-19 0.5.5
2023-03-03 0.3.4
2021-09-23 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-30 0.3.0
2022-03-08 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-02 1.1.1
2025-04-09 1.1.0
2025-01-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-03 0.1.1
Title: R Commander Plug-in for the EZR (Easy R) Package
Description: EZR (Easy R) adds a variety of statistical functions, including survival analyses, ROC analyses, metaanalyses, sample size calculation, and so on, to the R commander. EZR enables point-and-click easy access to statistical functions, especially for medical statistics. EZR is platform-independent and runs on Windows, Mac OS X, and UNIX. Its complete manual is available only in Japanese (Chugai Igakusha, ISBN: 978-4-498-10918-6, Nankodo, ISBN: 978-4-524-21861-5, Ohmsha, ISBN: 978-4-274-22632-8), but an report that introduced the investigation of EZR was published in Bone Marrow Transplantation (Nature Publishing Group) as an Open article. This report can be used as a simple manual. It can be freely downloaded from the journal website as shown below. This report has been cited in more than 14,000 scientific articles.
Author: Yoshinobu Kanda [aut, cre]
Maintainer: Yoshinobu Kanda <ycanda-tky@umin.ac.jp>
Diff between RcmdrPlugin.EZR versions 1.68 dated 2024-06-25 and 1.70 dated 2025-12-07
RcmdrPlugin.EZR-1.68/RcmdrPlugin.EZR/inst/etc/menus.txt.262 |only RcmdrPlugin.EZR-1.68/RcmdrPlugin.EZR/inst/etc/menus_old.txt |only RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/DESCRIPTION | 15 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/MD5 | 25 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/NEWS | 6 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/R/EZR.R | 171 ++++- RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/CHANGES | 6 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/doc/EZR.htm | 315 ++++------ RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/doc/EZR.pdf |binary RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/etc/menus.txt | 1 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/inst/po/ja/LC_MESSAGES/R-RcmdrPlugin.EZR.mo |binary RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/man/EZR.Rd | 9 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/man/EZR.dialogs.Rd | 1 RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/po/R-RcmdrPlugin.EZR.mo |only RcmdrPlugin.EZR-1.70/RcmdrPlugin.EZR/po/R-RcmdrPlugin.EZR.po | 11 15 files changed, 358 insertions(+), 202 deletions(-)
More information about RcmdrPlugin.EZR at CRAN
Permanent link
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
re [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.25.0 dated 2025-08-26 and 1.25.1 dated 2025-12-07
DESCRIPTION | 16 ++- MD5 | 55 ++++++------- NAMESPACE | 4 NEWS.md | 12 ++ R/ctrLoadQueryIntoDbCtgov2.R | 26 ++++-- R/ctrLoadQueryIntoDbCtis.R | 40 ++++++++- R/ctrLoadQueryIntoDbIsrctn.R | 8 - R/ctrdata-registers.R | 38 ++++----- R/ctrdata-trial-concepts.R | 2 R/dbFindIdsUniqueTrials.R | 3 R/dfTrials2Long.R | 4 R/f_isUniqueTrial.R | 1 R/util_functions.R | 4 README.md | 76 ++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/WORDLIST | 4 inst/doc/ctrdata_install.R | 3 inst/doc/ctrdata_install.Rmd | 16 +++ inst/doc/ctrdata_install.html | 32 +++++-- inst/js/euctr2ndjson.js | 5 - inst/tinytest/ctrdata_ctgov2.R | 10 ++ inst/tinytest/test_ctrdata_function_activesubstance.R | 2 man/ctrdata-package.Rd | 2 man/ctrdata-registers.Rd | 35 ++++---- man/ctrdata-trial-concepts.Rd | 2 man/f.isUniqueTrial.Rd | 1 vignettes/ctrdata_install.Rmd | 16 +++ 29 files changed, 270 insertions(+), 147 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing two major classes of shrinkage priors
(the spike-and-slab priors and the horseshoe family of priors) leads to efficient Bayesian
shrinkage estimation, variable selection and valid statistical inference. In this package,
we have implemented robust Bayesian variable selection with spike-and-slab priors under
high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models with spike-and-slab priors include
robust Bayesian group LASSO and robust binary Bayesian LASSO (Fan and Wu (2025)
<doi:10.1002/sta4.70078>). Besides, robust sparse Bayesian regression with the horseshoe
family of (hor [...truncated...]
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.1.4 dated 2025-07-25 and 1.2.0 dated 2025-12-07
pqrBayes-1.1.4/pqrBayes/R/NonRobust.R |only pqrBayes-1.2.0/pqrBayes/DESCRIPTION | 27 - pqrBayes-1.2.0/pqrBayes/MD5 | 77 +-- pqrBayes-1.2.0/pqrBayes/NEWS.md | 8 pqrBayes-1.2.0/pqrBayes/R/NonRobust_vc.R | 11 pqrBayes-1.2.0/pqrBayes/R/RcppExports.R | 24 + pqrBayes-1.2.0/pqrBayes/R/Robust_vc.R | 11 pqrBayes-1.2.0/pqrBayes/R/coverage.R | 10 pqrBayes-1.2.0/pqrBayes/R/estimation.R | 10 pqrBayes-1.2.0/pqrBayes/R/nonrobust_bin.R | 10 pqrBayes-1.2.0/pqrBayes/R/nonrobust_g.R | 11 pqrBayes-1.2.0/pqrBayes/R/nonrobust_lin.R | 29 + pqrBayes-1.2.0/pqrBayes/R/pqrBayes-package.R | 21 - pqrBayes-1.2.0/pqrBayes/R/pqrBayes.R | 90 +--- pqrBayes-1.2.0/pqrBayes/R/pqrBayes_bin.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_g.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_lin.R | 6 pqrBayes-1.2.0/pqrBayes/R/pqrBayes_vc.R | 10 pqrBayes-1.2.0/pqrBayes/R/predict.pqrBayes.R | 14 pqrBayes-1.2.0/pqrBayes/R/robust_bin.R | 11 pqrBayes-1.2.0/pqrBayes/R/robust_g.R | 11 pqrBayes-1.2.0/pqrBayes/R/robust_lin.R | 30 + pqrBayes-1.2.0/pqrBayes/R/select.pqrBayes.R | 40 - pqrBayes-1.2.0/pqrBayes/R/select_lin.R | 10 pqrBayes-1.2.0/pqrBayes/R/select_vc.R | 12 pqrBayes-1.2.0/pqrBayes/README.md | 297 +++++++++++--- pqrBayes-1.2.0/pqrBayes/man/coverage.Rd | 74 +-- pqrBayes-1.2.0/pqrBayes/man/data.Rd | 154 +++---- pqrBayes-1.2.0/pqrBayes/man/estimation.pqrBayes.Rd | 80 +-- pqrBayes-1.2.0/pqrBayes/man/pqrBayes-package.Rd | 133 +++--- pqrBayes-1.2.0/pqrBayes/man/pqrBayes.Rd | 394 +++++++++---------- pqrBayes-1.2.0/pqrBayes/man/predict_pqrBayes.Rd | 100 ++-- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.pred.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/print.pqrBayes.select.Rd | 48 +- pqrBayes-1.2.0/pqrBayes/man/select.pqrBayes.Rd | 148 +++---- pqrBayes-1.2.0/pqrBayes/src/RcppExports.cpp | 175 ++++++++ pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe+.cpp |only pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe.cpp |only pqrBayes-1.2.0/pqrBayes/src/Rhorseshoe_reg.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe+.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe.cpp |only pqrBayes-1.2.0/pqrBayes/src/horseshoe_reg.cpp |only 43 files changed, 1320 insertions(+), 874 deletions(-)
Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct simultaneous confidence intervals for
the ranks of means mu_1,...,mu_n based on an independent Gaussian sample
using multiple testing techniques.
Author: Diaa Al Mohamad [aut, cre],
Erik W. van Zwet [aut],
Jelle J. Goeman [aut]
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>
Diff between ICRanks versions 3.1 dated 2019-06-21 and 3.2 dated 2025-12-07
DESCRIPTION | 34 +++++++++++++++++++++++++--------- MD5 | 6 +++--- R/ic.ranks.R | 16 ++++++++-------- man/ic.ranks.Rd | 36 ++++++++++++++++++++---------------- 4 files changed, 56 insertions(+), 36 deletions(-)
Title: Kumaraswamy Complementary Weibull Geometric (Kw-CWG) Probability
Distribution
Description: Density, distribution function, quantile function
and random generation for the Kumaraswamy Complementary Weibull
Geometric (Kw-CWG) lifetime probability distribution proposed
in Afify, A.Z. et al (2017) <doi:10.1214/16-BJPS322>.
Author: Matheus H. J. Saldanha [aut, cre],
Adriano K. Suzuki [aut]
Maintainer: Matheus H. J. Saldanha <mhjsaldanha@gmail.com>
Diff between elfDistr versions 1.0.0 dated 2019-10-07 and 1.0.1 dated 2025-12-07
elfDistr-1.0.0/elfDistr/man/elfDistr.Rd |only elfDistr-1.0.1/elfDistr/DESCRIPTION | 10 -- elfDistr-1.0.1/elfDistr/MD5 | 17 ++-- elfDistr-1.0.1/elfDistr/NEWS.md |only elfDistr-1.0.1/elfDistr/R/elfDistr-package.R | 5 - elfDistr-1.0.1/elfDistr/man/Kw-CWG.Rd | 1 elfDistr-1.0.1/elfDistr/man/elfDistr-package.Rd |only elfDistr-1.0.1/elfDistr/src/Makevars | 5 - elfDistr-1.0.1/elfDistr/src/RcppExports.cpp | 5 + elfDistr-1.0.1/elfDistr/src/kwcwg-distribution.cpp | 82 ++++++++++++-------- elfDistr-1.0.1/elfDistr/tests/testthat/test_kwcwg.R | 53 +++++------- 11 files changed, 97 insertions(+), 81 deletions(-)
Title: Export Data from 'R' to 'DataGraph'
Description: Functions to pipe data from 'R' to 'DataGraph', a graphing and analysis application for mac OS. Create a live connection using either '.dtable' or '.dtbin' files that can be read by 'DataGraph'. Can save a data frame, collection of data frames and sequences of data frames and individual vectors. For more information see <https://community.visualdatatools.com/datagraph/knowledge-base/r-package/>.
Author: David Adalsteinsson [aut, cre]
Maintainer: David Adalsteinsson <david@visualdatatools.com>
Diff between DataGraph versions 1.2.14 dated 2023-03-02 and 1.2.15 dated 2025-12-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Driver.cpp | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Multivariate Conditional Volatility Modelling and Forecasting
Description: Methods and tools for estimating, simulating and forecasting of so-called BEKK-models (named after Baba, Engle, Kraft and Kroner) based on the fast Berndt–Hall–Hall–Hausman (BHHH) algorithm described in Hafner and Herwartz (2008) <doi:10.1007/s00184-007-0130-y>. For an overview, we refer the reader to Fülle et al. (2024) <doi:10.18637/jss.v111.i04>.
Author: Markus J. Fuelle [aut, cre],
Alexander Lange [aut],
Christian M. Hafner [aut],
Helmut Herwartz [aut]
Maintainer: Markus J. Fuelle <markus.fuelle@gmail.com>
Diff between BEKKs versions 1.4.5 dated 2024-11-25 and 1.4.6 dated 2025-12-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NAMESPACE | 4 +++- R/BEKKs.R | 2 -- R/backtest.R | 9 ++++----- R/bekk_functions.R | 4 ++-- R/bekk_mc_eval.R | 3 ++- R/summary.backtest.R | 20 ++++++++++---------- build/stage23.rdb |binary man/BEKKs.Rd | 3 --- 10 files changed, 35 insertions(+), 38 deletions(-)
Title: Multiple Imputation Through 'XGBoost'
Description: Multiple imputation using 'XGBoost', subsampling, and predictive mean
matching as described in Deng and Lumley (2023)
<doi:10.1080/10618600.2023.2252501>. The package supports various types of
variables, offers flexible settings, and enables saving an imputation model to impute
new data. Data processing and memory usage have been optimised to speed up
the imputation process.
Author: Yongshi Deng [aut, cre] ,
Thomas Lumley [ths]
Maintainer: Yongshi Deng <agnes.yongshideng@gmail.com>
Diff between mixgb versions 1.5.3 dated 2025-04-06 and 2.0.3 dated 2025-12-07
mixgb-1.5.3/mixgb/R/mixgb_boot.R |only mixgb-1.5.3/mixgb/R/mixgb_boot_xgb_save.R |only mixgb-1.5.3/mixgb/R/mixgb_bootsave.R |only mixgb-2.0.3/mixgb/DESCRIPTION | 17 - mixgb-2.0.3/mixgb/MD5 | 44 +-- mixgb-2.0.3/mixgb/NEWS.md | 37 +++ mixgb-2.0.3/mixgb/R/impute_each.R |only mixgb-2.0.3/mixgb/R/mixgb.R | 2 mixgb-2.0.3/mixgb/R/mixgb_cv.R | 30 +- mixgb-2.0.3/mixgb/R/mixgb_load_use.R | 2 mixgb-2.0.3/mixgb/R/mixgb_null.R | 278 ++--------------------- mixgb-2.0.3/mixgb/R/mixgb_save.R | 122 ++++++---- mixgb-2.0.3/mixgb/R/mixgb_use.R | 2 mixgb-2.0.3/mixgb/R/mixgb_xgb_save.R | 119 +++++---- mixgb-2.0.3/mixgb/R/save_yhatobs.R | 121 ++++++---- mixgb-2.0.3/mixgb/build/partial.rdb |binary mixgb-2.0.3/mixgb/build/vignette.rds |binary mixgb-2.0.3/mixgb/inst/doc/Imputing-newdata.R | 24 - mixgb-2.0.3/mixgb/inst/doc/Imputing-newdata.html | 9 mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.R | 38 +-- mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.Rmd | 5 mixgb-2.0.3/mixgb/inst/doc/Using-mixgb.html | 91 ++++--- mixgb-2.0.3/mixgb/man/default_params.Rd | 2 mixgb-2.0.3/mixgb/src/Makevars | 2 mixgb-2.0.3/mixgb/vignettes/Using-mixgb.Rmd | 5 25 files changed, 435 insertions(+), 515 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.0 dated 2025-07-02 and 1.1.0.8 dated 2025-12-07
Rcpp-1.1.0.8/Rcpp/ChangeLog | 116 +++++++++++++++ Rcpp-1.1.0.8/Rcpp/DESCRIPTION | 9 - Rcpp-1.1.0.8/Rcpp/MD5 | 123 +++++++--------- Rcpp-1.1.0.8/Rcpp/NAMESPACE | 4 Rcpp-1.1.0.8/Rcpp/R/Attributes.R | 70 ++++++++- Rcpp-1.1.0.8/Rcpp/R/RcppLdpath.R | 6 Rcpp-1.1.0.8/Rcpp/R/asis.R |only Rcpp-1.1.0.8/Rcpp/R/zzz.R | 9 - Rcpp-1.1.0.8/Rcpp/build/partial.rdb |binary Rcpp-1.1.0.8/Rcpp/build/vignette.rds |binary Rcpp-1.1.0.8/Rcpp/inst/NEWS.Rd | 38 ++++ Rcpp-1.1.0.8/Rcpp/inst/bib/Rcpp.bib | 15 + Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-FAQ.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-attributes.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-extending.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-introduction.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-jss-2011.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-jss-2011.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-libraries.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-libraries.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-modules.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-package.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-quickref.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-1.1.0.8/Rcpp/inst/doc/Rcpp-sugar.pdf.asis |only Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/exceptions_impl.h | 29 +-- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/hash/IndexHash.h | 22 +- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/hash/SelfHash.h | 28 ++- Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/internal/wrap.h | 2 Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/r/check_r_headers.h |only Rcpp-1.1.0.8/Rcpp/inst/include/Rcpp/r/headers.h | 2 Rcpp-1.1.0.8/Rcpp/inst/include/RcppCommon.h | 5 Rcpp-1.1.0.8/Rcpp/inst/skeleton/zzz.R | 13 - Rcpp-1.1.0.8/Rcpp/inst/tinytest/testRcppModule/R/zzz.R | 9 - Rcpp-1.1.0.8/Rcpp/inst/tinytest/test_sugar.R | 5 Rcpp-1.1.0.8/Rcpp/man/Rcpp-deprecated.Rd | 3 Rcpp-1.1.0.8/Rcpp/man/asisWeave.Rd |only Rcpp-1.1.0.8/Rcpp/man/loadModule.Rd | 3 Rcpp-1.1.0.8/Rcpp/src/api.cpp | 1 Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-FAQ.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-attributes.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-extending.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-introduction.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-jss-2011.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-libraries.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-modules.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-package.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-quickref.pdf.asis |only Rcpp-1.1.0.8/Rcpp/vignettes/Rcpp-sugar.pdf.asis |only Rcpp-1.1.0/Rcpp/R/compilerCheck.R |only Rcpp-1.1.0/Rcpp/R/loadRcppModules.R |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-FAQ.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-attributes.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-extending.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-introduction.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-jss-2011.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-libraries.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-modules.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-package.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-quickref.Rnw |only Rcpp-1.1.0/Rcpp/inst/doc/Rcpp-sugar.Rnw |only Rcpp-1.1.0/Rcpp/man/compilerCheck.Rd |only Rcpp-1.1.0/Rcpp/man/loadRcppModules-deprecated.Rd |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-FAQ.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-attributes.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-extending.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-introduction.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-jss-2011.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-libraries.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-modules.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-package.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-quickref.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/Rcpp-sugar.Rnw |only Rcpp-1.1.0/Rcpp/vignettes/pdf |only 82 files changed, 364 insertions(+), 152 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified JSON document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut],
Ivan Tarbakou [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.13.1 dated 2025-06-26 and 0.14.0 dated 2025-12-07
DESCRIPTION | 11 +++-- MD5 | 28 +++++++------- NEWS.md | 8 ++++ R/query.R | 85 +++++++++++++++---------------------------- R/src_couchdb.R | 2 - R/src_duckdb.R | 2 - R/src_elastic.R | 2 - R/src_mongo.R | 2 - R/src_postgres.R | 3 + R/src_sqlite.R | 4 +- R/update.R | 6 ++- R/zzz.R | 5 +- inst/doc/nodbi-overview.html | 2 - tests/testthat/core-nodbi.R | 27 ++++++++++--- tests/testthat/helper.R | 10 +++++ 15 files changed, 108 insertions(+), 89 deletions(-)
Title: Convert and Impute Dates to ISO Standard ("International
Organization for Standardization")
Description: Provides functions to convert and impute date values to the ISO 8601
standard format. The package automatically recognizes date patterns within a
data frame and transforms them into consistent ISO-formatted dates. It also
supports imputing missing month or day components in partial date strings
using user-defined rules. Only one date format can be applied within a single
data frame column.
Author: Lukasz Andrzejewski [aut, cre]
Maintainer: Lukasz Andrzejewski <lukasz.coding@gmail.com>
Diff between datetoiso versions 1.1.1 dated 2025-11-18 and 1.2.0 dated 2025-12-07
DESCRIPTION | 8 +- MD5 | 20 +++-- NAMESPACE | 4 - NEWS.md | 110 +++++++++++++++------------ R/impute_date.R | 20 +---- R/reconcile.R |only man/compare_rows_with_same_index.Rd |only man/get_same_class.Rd |only man/impute_date.Rd | 144 ++++++++++++++++++------------------ man/impute_date_dmy.Rd | 134 ++++++++++++++++----------------- man/impute_date_ymd.Rd | 134 ++++++++++++++++----------------- man/reconcile.Rd |only man/reconcile_without_index.Rd |only tests/testthat/test-reconcile.R |only 14 files changed, 287 insertions(+), 287 deletions(-)
Title: Analyzing Censored Factor Models
Description: Provides generation and estimation of censored factor models for high-dimensional data with censored errors (normal, t, logistic). Includes Sparse Orthogonal Principal Components (SOPC), and evaluation metrics. Based on Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Tong Meng [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between CFM versions 0.7.0 dated 2025-11-13 and 0.8.0 dated 2025-12-07
DESCRIPTION | 6 +++--- MD5 | 11 ++++++++++- R/Aids2.R |only R/bcdata.R |only R/data_yoghurt.R |only data |only man/Aids2.Rd |only man/bcdata.Rd |only man/yoghurt.Rd |only 9 files changed, 13 insertions(+), 4 deletions(-)
Title: WOFOST Crop Growth Simulation Model
Description: An implementation of the WOFOST ("World Food Studies") crop growth model. WOFOST is a dynamic simulation model that uses daily weather data, and crop, soil and management parameters to simulate crop growth and development. See De Wit et al. (2019) <doi:10.1016/j.agsy.2018.06.018> for a recent review of the history and use of the model.
Author: Robert J. Hijmans [cre, aut],
Huang Fang [ctb],
C.A. van Diepen [ctb],
Allard de Wit [ctb],
Daniel van Kraalingen [ctb],
Tamme van der Wal [ctb],
C. Rappoldt [ctb],
Hendrik Boogard [ctb],
I.G.A.M. Noy [ctb],
Alterra, Wageningen-UR [cph]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between Rwofost versions 0.8-6 dated 2025-12-04 and 0.8-7 dated 2025-12-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/partial.rdb |binary src/wofost.cpp | 15 ++++++++++----- 4 files changed, 17 insertions(+), 12 deletions(-)
Title: Spectral Modularity Clustering
Description: Implements the network clustering algorithm described in
Newman (2006) <doi:10.1103/PhysRevE.74.036104>. The complete
iterative algorithm comprises of two steps. In the first step, the
network is expressed in terms of its leading eigenvalue and
eigenvector and recursively partition into two communities.
Partitioning occurs if the maximum positive
eigenvalue is greater than the tolerance (10e-5) for the current
partition, and if it results in a positive contribution to the
Modularity.
Given an initial separation using the leading eigen step, 'rSpectral'
then continues to maximise for the change in Modularity using a
fine-tuning step - or variate thereof. The first stage here is to
find the node which, when moved from one community to another,
gives the maximum change in Modularity. This node’s community is
then fixed and we repeat the process until all nodes have been moved.
The whole process is repeated from this new state until the change
in the Modularity, between the new and o [...truncated...]
Author: Colin Mclean [aut] ,
Anatoly Sorokin [aut, cre]
Maintainer: Anatoly Sorokin <lptolik@gmail.com>
This is a re-admission after prior archival of version 1.0.0.10 dated 2023-01-18
Diff between rSpectral versions 1.0.0.10 dated 2023-01-18 and 1.0.0.14 dated 2025-12-07
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++++----------- R/igraph.R | 2 - R/rSpectral-package.R | 2 - README.md | 6 +++++ build/partial.rdb |binary inst/CITATION | 19 ++++++++-------- man/figures/README-karate.example-1.png |binary man/figures/README-plot.rspec.default-1.png |binary man/figures/README-plot.rspec.fixneig-1.png |binary man/figures/README-plot.rspec.fixneig.cnmin-1.png |binary man/rSpectral.Rd | 4 +-- man/spectral_igraph_communities.Rd | 2 - src/Makevars | 1 14 files changed, 38 insertions(+), 32 deletions(-)
Title: Reduced-Rank Regression
Description: Multivariate regression methodologies including
classical reduced-rank regression (RRR)
studied by Anderson (1951) <doi:10.1214/aoms/1177729580> and
Reinsel and Velu (1998) <doi:10.1007/978-1-4757-2853-8>,
reduced-rank regression via adaptive nuclear norm penalization
proposed by Chen et al. (2013) <doi:10.1093/biomet/ast036> and
Mukherjee et al. (2015) <doi:10.1093/biomet/asx080>,
robust reduced-rank regression (R4) proposed by
She and Chen (2017) <doi:10.1093/biomet/asx032>,
generalized/mixed-response reduced-rank regression (mRRR) proposed by
Luo et al. (2018) <doi:10.1016/j.jmva.2018.04.011>,
row-sparse reduced-rank regression (SRRR) proposed by
Chen and Huang (2012) <doi:10.1080/01621459.2012.734178>,
reduced-rank regression with a sparse singular value decomposition (RSSVD)
proposed by Chen et al. (2012) <doi:10.1111/j.1467-9868.2011.01002.x>
and sparse and orthogonal factor regression (SOFAR) proposed by
Uematsu et al. (2019) <d [...truncated...]
Author: Kun Chen [aut, cre] ,
Wenjie Wang [aut] ,
Jun Yan [ctb]
Maintainer: Kun Chen <kun.chen@uconn.edu>
Diff between rrpack versions 0.1-13 dated 2022-06-16 and 0.1-14 dated 2025-12-07
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- R/mrrr.R | 16 ++++++++-------- man/mrrr.Rd | 16 ++++++++-------- src/Makevars | 1 - 5 files changed, 27 insertions(+), 28 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951, Stuiver & Suess 1966, Pearson & Stuiver 1986) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre] ,
Christopher Bronk Ramsey [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.3.0 dated 2025-07-09 and 1.3.1 dated 2025-12-07
rintcal-1.3.0/rintcal/inst/extdata/Arnold_Libby_1951.txt |only rintcal-1.3.1/rintcal/DESCRIPTION | 10 rintcal-1.3.1/rintcal/MD5 | 30 +- rintcal-1.3.1/rintcal/NEWS.md | 4 rintcal-1.3.1/rintcal/R/data.R | 27 +- rintcal-1.3.1/rintcal/R/rintcal.R | 77 ++++--- rintcal-1.3.1/rintcal/build/partial.rdb |binary rintcal-1.3.1/rintcal/build/vignette.rds |binary rintcal-1.3.1/rintcal/inst/doc/rintcal.R | 18 - rintcal-1.3.1/rintcal/inst/doc/rintcal.Rmd | 48 ++-- rintcal-1.3.1/rintcal/inst/doc/rintcal.html | 128 ++++++------ rintcal-1.3.1/rintcal/inst/extdata/Arnold_Libby_1951.14C |only rintcal-1.3.1/rintcal/inst/extdata/Pearson_Stuiver_1986.14C |only rintcal-1.3.1/rintcal/inst/extdata/Stuiver_Suess_1966.14C |only rintcal-1.3.1/rintcal/man/ccurve.Rd | 15 + rintcal-1.3.1/rintcal/man/glue.ccurves.Rd | 4 rintcal-1.3.1/rintcal/man/intcal.data.Rd | 5 rintcal-1.3.1/rintcal/vignettes/rintcal.Rmd | 48 ++-- 18 files changed, 230 insertions(+), 184 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.21 dated 2025-10-31 and 1.22 dated 2025-12-07
openxlsx2-1.21/openxlsx2/R/onUnload.R |only openxlsx2-1.21/openxlsx2/man/figures/tableoptions.pdf |only openxlsx2-1.21/openxlsx2/man/figures/tableoptions.png |only openxlsx2-1.22/openxlsx2/DESCRIPTION | 11 openxlsx2-1.22/openxlsx2/MD5 | 214 +-- openxlsx2-1.22/openxlsx2/NAMESPACE | 2 openxlsx2-1.22/openxlsx2/NEWS.md | 41 openxlsx2-1.22/openxlsx2/R/RcppExports.R | 12 openxlsx2-1.22/openxlsx2/R/class-comment.R | 109 + openxlsx2-1.22/openxlsx2/R/class-workbook-utils.R | 3 openxlsx2-1.22/openxlsx2/R/class-workbook-wrappers.R | 164 +- openxlsx2-1.22/openxlsx2/R/class-workbook.R | 110 - openxlsx2-1.22/openxlsx2/R/converters.R | 22 openxlsx2-1.22/openxlsx2/R/dates.R | 13 openxlsx2-1.22/openxlsx2/R/deprecate.R | 103 - openxlsx2-1.22/openxlsx2/R/get-named-regions.R | 2 openxlsx2-1.22/openxlsx2/R/helper-functions.R | 8 openxlsx2-1.22/openxlsx2/R/openxlsx2-package.R | 10 openxlsx2-1.22/openxlsx2/R/read.R | 89 - openxlsx2-1.22/openxlsx2/R/utils.R | 144 ++ openxlsx2-1.22/openxlsx2/R/wb_functions.R | 109 + openxlsx2-1.22/openxlsx2/R/wb_load.R | 13 openxlsx2-1.22/openxlsx2/R/wb_styles.R | 10 openxlsx2-1.22/openxlsx2/R/write.R | 22 openxlsx2-1.22/openxlsx2/R/xl_open.R | 115 +- openxlsx2-1.22/openxlsx2/R/zzz.R |only openxlsx2-1.22/openxlsx2/build/vignette.rds |binary openxlsx2-1.22/openxlsx2/inst/WORDLIST | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.R | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/Update-from-openxlsx.html | 2 openxlsx2-1.22/openxlsx2/inst/doc/conditional-formatting.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/conditional-formatting.html | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2.Rmd | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2.html | 6 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.R | 2 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.Rmd | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_read_to_df.html | 6 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.R | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 4 openxlsx2-1.22/openxlsx2/inst/doc/openxlsx2_style_manual.html | 4 openxlsx2-1.22/openxlsx2/man/col2int.Rd | 5 openxlsx2-1.22/openxlsx2/man/col_widths-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/convertToExcelDate.Rd | 2 openxlsx2-1.22/openxlsx2/man/convert_date.Rd | 8 openxlsx2-1.22/openxlsx2/man/create_hyperlink.Rd | 6 openxlsx2-1.22/openxlsx2/man/delete_data.Rd | 2 openxlsx2-1.22/openxlsx2/man/dims_to_dataframe.Rd | 4 openxlsx2-1.22/openxlsx2/man/filter-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/int2col.Rd | 5 openxlsx2-1.22/openxlsx2/man/named_region-wb.Rd | 2 openxlsx2-1.22/openxlsx2/man/openxlsx2-package.Rd | 4 openxlsx2-1.22/openxlsx2/man/openxlsx2_options.Rd | 3 openxlsx2-1.22/openxlsx2/man/row_heights-wb.Rd | 5 openxlsx2-1.22/openxlsx2/man/wbWorkbook.Rd | 15 openxlsx2-1.22/openxlsx2/man/wb_add_conditional_formatting.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_add_data.Rd | 3 openxlsx2-1.22/openxlsx2/man/wb_add_data_table.Rd | 12 openxlsx2-1.22/openxlsx2/man/wb_add_data_validation.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_add_page_break.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_get_tables.Rd | 4 openxlsx2-1.22/openxlsx2/man/wb_open.Rd | 6 openxlsx2-1.22/openxlsx2/man/wb_remove_tables.Rd | 2 openxlsx2-1.22/openxlsx2/man/wb_save.Rd | 31 openxlsx2-1.22/openxlsx2/man/wb_to_df.Rd | 13 openxlsx2-1.22/openxlsx2/man/wb_workbook.Rd | 18 openxlsx2-1.22/openxlsx2/man/write_data.Rd | 2 openxlsx2-1.22/openxlsx2/man/write_datatable.Rd | 14 openxlsx2-1.22/openxlsx2/man/write_formula.Rd | 4 openxlsx2-1.22/openxlsx2/man/xl_open.Rd | 3 openxlsx2-1.22/openxlsx2/src/RcppExports.cpp | 36 openxlsx2-1.22/openxlsx2/src/date.cpp | 14 openxlsx2-1.22/openxlsx2/src/helper_functions.cpp | 406 ++++--- openxlsx2-1.22/openxlsx2/src/load_workbook.cpp | 49 openxlsx2-1.22/openxlsx2/src/openxlsx2.h | 250 +--- openxlsx2-1.22/openxlsx2/src/pugi.cpp | 50 openxlsx2-1.22/openxlsx2/src/styles_xml.cpp | 27 openxlsx2-1.22/openxlsx2/src/write_file.cpp | 41 openxlsx2-1.22/openxlsx2/src/xlsb.cpp | 26 openxlsx2-1.22/openxlsx2/src/xlsb_flags.h | 574 ++++------ openxlsx2-1.22/openxlsx2/src/xlsb_funs.h | 42 openxlsx2-1.22/openxlsx2/tests/testthat/helper.R | 28 openxlsx2-1.22/openxlsx2/tests/testthat/test-Workbook_properties.R | 1 openxlsx2-1.22/openxlsx2/tests/testthat/test-class-comment.R | 77 - 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Title: Negative Binomial Mixed Models Using Large-Sample Approximation
for Differential Expression Analysis of ScRNA-Seq Data
Description: A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.
Author: Liang He [aut, cre],
Raghav Sharma [ctb]
Maintainer: Liang He <hyx520101@gmail.com>
Diff between nebula versions 1.5.3 dated 2024-02-15 and 1.5.6 dated 2025-12-07
DESCRIPTION | 8 +- MD5 | 20 +++--- R/nebula.R | 39 +++++++++--- R/utils.R | 29 +++++---- README.md | 116 +++++++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/nebula_example.Rmd | 8 +- inst/doc/nebula_example.html | 136 +++++++++++++++++++++---------------------- man/nebula.Rd | 2 vignettes/nebula_example.Rmd | 8 +- 11 files changed, 206 insertions(+), 160 deletions(-)
Title: Generate Isolines and Isobands from Regularly Spaced Elevation
Grids
Description: A fast C++ implementation to generate contour lines
(isolines) and contour polygons (isobands) from regularly spaced grids
containing elevation data.
Author: Hadley Wickham [aut] ,
Claus O. Wilke [aut] ,
Thomas Lin Pedersen [aut, cre] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between isoband versions 0.2.7 dated 2022-12-20 and 0.3.0 dated 2025-12-07
isoband-0.2.7/isoband/R/isoband.R |only isoband-0.2.7/isoband/src/init.cpp |only isoband-0.2.7/isoband/src/utils.h |only isoband-0.3.0/isoband/DESCRIPTION | 38 isoband-0.3.0/isoband/LICENSE | 4 isoband-0.3.0/isoband/MD5 | 89 isoband-0.3.0/isoband/NAMESPACE | 1 isoband-0.3.0/isoband/NEWS.md | 11 isoband-0.3.0/isoband/R/clip-lines.R | 20 isoband-0.3.0/isoband/R/cpp11.R |only isoband-0.3.0/isoband/R/iso-to-sfg.R | 16 isoband-0.3.0/isoband/R/isoband-package.R |only isoband-0.3.0/isoband/R/isobands-grob.R | 28 isoband-0.3.0/isoband/R/isobands.R | 36 isoband-0.3.0/isoband/R/isolines-grob.R | 126 isoband-0.3.0/isoband/R/label-placer.R | 74 isoband-0.3.0/isoband/R/plot-iso.R | 64 isoband-0.3.0/isoband/R/utilities.R | 9 isoband-0.3.0/isoband/README.md | 4 isoband-0.3.0/isoband/build/vignette.rds |binary isoband-0.3.0/isoband/inst/doc/isoband1.R | 4 isoband-0.3.0/isoband/inst/doc/isoband1.Rmd | 6 isoband-0.3.0/isoband/inst/doc/isoband1.html | 216 - isoband-0.3.0/isoband/inst/doc/isoband3.R | 2 isoband-0.3.0/isoband/inst/doc/isoband3.Rmd | 4 isoband-0.3.0/isoband/inst/doc/isoband3.html | 211 - isoband-0.3.0/isoband/man/figures/README-basic-example-plot-1.png |binary isoband-0.3.0/isoband/man/figures/README-volcano-1.png |binary isoband-0.3.0/isoband/man/isoband-package.Rd | 14 isoband-0.3.0/isoband/src/Makevars | 1 isoband-0.3.0/isoband/src/Makevars.win | 1 isoband-0.3.0/isoband/src/clip-lines.cpp | 92 isoband-0.3.0/isoband/src/clip-lines.h | 12 isoband-0.3.0/isoband/src/cpp11.cpp |only isoband-0.3.0/isoband/src/isoband.cpp | 191 - isoband-0.3.0/isoband/src/polygon.h | 6 isoband-0.3.0/isoband/src/separate-polygons.cpp | 69 isoband-0.3.0/isoband/src/separate-polygons.h | 5 isoband-0.3.0/isoband/tests/testthat.R | 8 isoband-0.3.0/isoband/tests/testthat/_snaps |only isoband-0.3.0/isoband/tests/testthat/test-clip-lines.R | 92 isoband-0.3.0/isoband/tests/testthat/test-iso-to-sfg.R | 250 + isoband-0.3.0/isoband/tests/testthat/test-isobands.R | 1503 ++++++++-- isoband-0.3.0/isoband/tests/testthat/test-isolines-grob.R | 61 isoband-0.3.0/isoband/tests/testthat/test-isolines.R | 207 + isoband-0.3.0/isoband/tests/testthat/test-label-placer.R | 39 isoband-0.3.0/isoband/vignettes/isoband1.Rmd | 6 isoband-0.3.0/isoband/vignettes/isoband3.Rmd | 4 48 files changed, 2543 insertions(+), 981 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Description: Provides HE plot and other functions for visualizing hypothesis
tests in multivariate linear models. HE plots represent sums-of-squares-and-products
matrices for linear hypotheses and for error using ellipses (in two
dimensions) and ellipsoids (in three dimensions). It also provides other tools for analysis and graphical display of the models
such as robust methods and homogeneity of variance covariance matrices.
The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when
there are more than a few response variables.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Georges Monette [aut] ,
Phil Chalmers [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between heplots versions 1.7.8 dated 2025-08-18 and 1.8.1 dated 2025-12-07
DESCRIPTION | 18 MD5 | 270 ++-- NAMESPACE | 5 NEWS.md | 27 R/Ellipsoid.R | 16 R/Mahalanobis.R | 15 R/arrow3d.R | 7 R/bartlettTests.R | 13 R/bbox3d.R | 7 R/boxM.R | 453 +++++--- R/coefplot.mlm.R | 18 R/colDevs.R | 14 R/covEllipses.R | 110 + R/cqplot.R | 56 - R/cross3d.R | 3 R/datasets.R | 896 ++++++++-------- R/distancePlot.R | 29 R/ellipse.axes.R | 32 R/ellipse.box.R | 14 R/ellipse3d.axes.R | 13 R/etasq.R | 26 R/glance.mlm.R | 19 R/gsorth.R | 22 R/heplot.R | 293 ++--- R/heplot1d.R | 99 - R/heplot3d.R | 128 +- R/heplots-package.R | 49 R/interpPlot.R | 18 R/label.ellipse.R | 214 ++- R/leveneTests.R | 25 R/logdetCI.R | 22 R/mark.H0.R | 8 R/noteworthy.R | 32 R/pairs.mlm.R | 37 R/plot.boxM.R | 63 - R/plot.robmlm.R | 59 - R/rel_diff.R | 8 R/robmlm.R | 45 R/schoolsites.R | 24 R/statList.R | 26 R/termMeans.R | 6 R/text_usr.R |only R/trans.colors.R | 4 R/uniStats.R | 4 inst/CITATION | 2 inst/doc/HE_manova.html | 27 inst/doc/HE_mmra.html | 25 inst/doc/Robust.html | 11 inst/doc/datasets.R | 29 inst/doc/datasets.Rmd | 48 inst/doc/datasets.html | 1323 +++++++++++++++++++----- man/AddHealth.Rd | 17 man/Adopted.Rd | 20 man/Bees.Rd | 22 man/Diabetes.Rd | 18 man/Ellipsoid.Rd | 6 man/FootHead.Rd | 16 man/Headache.Rd | 32 man/Hernior.Rd | 30 man/Iwasaki_Big_Five.Rd | 30 man/Mahalanobis.Rd | 14 man/MockJury.Rd | 38 man/NLSY.Rd | 18 man/NeuroCog.Rd | 30 man/Oslo.Rd | 50 man/Overdose.Rd | 148 +- man/Parenting.Rd | 12 man/Plastic.Rd | 12 man/Pottery2.Rd | 44 man/Probe.Rd | 32 man/RatWeight.Rd | 16 man/ReactTime.Rd | 18 man/Rohwer.Rd | 41 man/RootStock.Rd | 12 man/Sake.Rd | 22 man/Skulls.Rd | 28 man/SocGrades.Rd | 24 man/SocialCog.Rd | 16 man/TIPI.Rd | 57 - man/VocabGrowth.Rd | 12 man/WeightLoss.Rd | 16 man/arrow3d.Rd | 9 man/bartlettTests.Rd | 8 man/bbox3d.Rd | 13 man/boxM.Rd | 147 +- man/coefplot.Rd | 9 man/colDevs.Rd | 4 man/covEllipses.Rd | 45 man/cqplot.Rd | 27 man/cross3d.Rd | 9 man/distancePlot.Rd | 250 ++-- man/dogfood.Rd | 18 man/ellipse.axes.Rd | 6 man/ellipse.box.Rd | 141 +- man/ellipse3d.axes.Rd | 17 man/etasq.Rd | 27 man/figures/README-iris4-1.png |binary man/glance.mlm.Rd | 19 man/heplot.Rd | 65 - man/heplot1d.Rd | 41 man/heplot3d.Rd | 38 man/heplots-package.Rd | 31 man/interpPlot.Rd | 6 man/label.ellipse.Rd | 137 +- man/leveneTests.Rd | 16 man/logdetCI.Rd | 11 man/mathscore.Rd | 10 man/noteworthy.Rd | 180 +-- man/oral.Rd | 18 man/pairs.mlm.Rd | 18 man/peng.Rd | 172 +-- man/plot.boxM.Rd | 18 man/plot.robmlm.Rd | 37 man/robmlm.Rd | 30 man/schooldata.Rd | 27 man/schoolsites.Rd | 108 - man/statList.Rd | 8 man/termMeans.Rd | 8 man/text_usr.Rd |only man/trans.colors.Rd | 2 man/uniStats.Rd | 4 vignettes/datasets.Rmd | 48 vignettes/fig/manova-addhealth-means-each-1.png |binary vignettes/fig/manova-addhealth-means-plot-1.png |binary vignettes/fig/manova-jury-mod1-pairs-1.png |binary vignettes/fig/manova-plastic1-1.png |binary vignettes/fig/manova-plastic1a-1.png |binary vignettes/fig/manova-plastic2-1.png |binary vignettes/fig/manova-skulls-HE-pairs-1.png |binary vignettes/fig/mmra-grades-pairs-1.png |binary vignettes/fig/mmra-hern-pairs-1.png |binary vignettes/fig/mmra-rohwer-HE1-1.png |binary vignettes/fig/mmra-rohwer-HE2-1.png |binary vignettes/fig/mmra-rohwer-HE2-2.png |binary vignettes/fig/mmra-rohwer-HE3-1.png |binary vignettes/fig/mmra-rohwer-long-ggplot-1.png |binary vignettes/fig/robust-pottery-pairs-1.png |binary 137 files changed, 4429 insertions(+), 2916 deletions(-)
Title: Rmetrics - Markets and Basic Statistics
Description: Provides a collection of functions to
explore and to investigate basic properties of financial returns
and related quantities.
The covered fields include techniques of explorative data analysis
and the investigation of distributional properties, including
parameter estimation and hypothesis testing. Even more there are
several utility functions for data handling and management.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
CRAN Team [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fBasics versions 4041.97 dated 2024-08-19 and 4052.98 dated 2025-12-07
DESCRIPTION | 17 ++++-- MD5 | 46 +++++++++--------- NEWS.md | 17 ++++++ data/Capitalization.rda |binary data/DowJones30.csv.gz |binary data/HedgeFund.rda |binary data/PensionFund.csv.gz |binary data/SWXLP.csv.gz |binary data/cars2.csv.gz |binary data/msft.dat.rda |binary data/nyse.csv.gz |binary data/swissEconomy.rda |binary data/usdthb.csv.gz |binary inst/pkgdown.yml | 4 - man/plot-acfPlot.Rd | 105 +++++++++++++++++++++++++++---------------- man/plot-boxPlot.Rd | 40 ++++++++++++---- man/plot-histPlot.Rd | 31 +++++++++++- man/plot-qqPlot.Rd | 88 +++++++++++++++++++++++++----------- man/plot-returnSeriesGUI.Rd | 47 ++++++++++++++----- man/plot-scalinglawPlot.Rd | 62 ++++++++++++++++--------- man/plot-seriesPlot.Rd | 57 +++++++++++++++-------- man/stableSlider.Rd | 30 +++++++++++- man/utils-interactivePlot.Rd | 43 ++++++++++++++--- src/nig.c | 14 +---- 24 files changed, 420 insertions(+), 181 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.4.3 dated 2025-10-30 and 1.4.5 dated 2025-12-07
Colossus-1.4.3/Colossus/man/Check_Iters.Rd |only Colossus-1.4.3/Colossus/man/RunCaseControlRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunCoxRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunLogisticRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/RunPoissonRegression_Omnibus.Rd |only Colossus-1.4.3/Colossus/man/apply_norm.Rd |only Colossus-1.4.5/Colossus/DESCRIPTION | 8 Colossus-1.4.5/Colossus/MD5 | 207 +- Colossus-1.4.5/Colossus/NAMESPACE | 5 Colossus-1.4.5/Colossus/NEWS.md | 11 Colossus-1.4.5/Colossus/R/BasicRun.R | 602 +++++++ Colossus-1.4.5/Colossus/R/CaseControl_Regression.R | 26 Colossus-1.4.5/Colossus/R/Cox_Regression.R | 69 Colossus-1.4.5/Colossus/R/LogitRegression.R | 8 Colossus-1.4.5/Colossus/R/ObjValidate.R | 45 Colossus-1.4.5/Colossus/R/Poisson_Regression.R | 109 - Colossus-1.4.5/Colossus/R/RcppExports.R | 34 Colossus-1.4.5/Colossus/R/SurvTypes.R | 138 + Colossus-1.4.5/Colossus/R/Utility.R | 451 ++++- Colossus-1.4.5/Colossus/R/zzz.R | 45 Colossus-1.4.5/Colossus/README.md | 40 Colossus-1.4.5/Colossus/build/vignette.rds |binary Colossus-1.4.5/Colossus/inst/WORDLIST | 8 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.R | 8 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.Rmd | 12 Colossus-1.4.5/Colossus/inst/doc/Alt_Run_Opt.html | 533 ++---- Colossus-1.4.5/Colossus/inst/doc/Control_Options.html | 157 -- Colossus-1.4.5/Colossus/inst/doc/Dose_Formula_Inputs.html | 186 +- Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.R | 2 Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.Rmd | 2 Colossus-1.4.5/Colossus/inst/doc/Equation_Expression.html | 365 ++-- Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.R | 16 Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.Rmd | 21 Colossus-1.4.5/Colossus/inst/doc/Excess_and_Predicted_Cases.html | 198 +- Colossus-1.4.5/Colossus/inst/doc/Grad_Hess.html | 489 ++---- Colossus-1.4.5/Colossus/inst/doc/Logistic.R | 11 Colossus-1.4.5/Colossus/inst/doc/Logistic.Rmd | 11 Colossus-1.4.5/Colossus/inst/doc/Logistic.html | 433 ++--- Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.R | 10 Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.Rmd | 10 Colossus-1.4.5/Colossus/inst/doc/Matched_Case_Control.html | 407 ++--- Colossus-1.4.5/Colossus/inst/doc/Multi_Realization.html | 210 +- Colossus-1.4.5/Colossus/inst/doc/Plotting_And_Analysis.html | 492 +++--- Colossus-1.4.5/Colossus/inst/doc/SMR_Analysis.html | 278 +-- Colossus-1.4.5/Colossus/inst/doc/Script_Comparison_Epicure.html | 230 +- Colossus-1.4.5/Colossus/inst/doc/Starting-Description.Rmd | 5 Colossus-1.4.5/Colossus/inst/doc/Starting-Description.html | 634 +++----- Colossus-1.4.5/Colossus/inst/doc/Time_Dep_Cov.html | 398 ++--- Colossus-1.4.5/Colossus/inst/doc/Wald_and_Log_Bound.Rmd | 2 Colossus-1.4.5/Colossus/inst/doc/Wald_and_Log_Bound.html | 783 ++++------ Colossus-1.4.5/Colossus/inst/doc/count_time_tables.html | 600 +++---- Colossus-1.4.5/Colossus/man/CaseControlRun.Rd | 4 Colossus-1.4.5/Colossus/man/CoxRun.Rd | 3 Colossus-1.4.5/Colossus/man/CoxRunMulti.Rd | 3 Colossus-1.4.5/Colossus/man/Date_Shift.Rd | 2 Colossus-1.4.5/Colossus/man/EventAssignment.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/EventAssignment.poisresbound.Rd |only Colossus-1.4.5/Colossus/man/Event_Count_Gen.Rd | 2 Colossus-1.4.5/Colossus/man/Event_Time_Gen.Rd | 2 Colossus-1.4.5/Colossus/man/Joint_Multiple_Events.Rd | 2 Colossus-1.4.5/Colossus/man/LikelihoodBound.coxres.Rd | 3 Colossus-1.4.5/Colossus/man/LikelihoodBound.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/LogisticRun.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRun.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRunJoint.Rd | 4 Colossus-1.4.5/Colossus/man/PoisRunMulti.Rd | 4 Colossus-1.4.5/Colossus/man/Replace_Missing.Rd | 2 Colossus-1.4.5/Colossus/man/Residual.poisres.Rd | 4 Colossus-1.4.5/Colossus/man/Time_Since.Rd | 2 Colossus-1.4.5/Colossus/man/factorize.Rd | 2 Colossus-1.4.5/Colossus/man/gen_time_dep.Rd | 2 Colossus-1.4.5/Colossus/src/Calc_Repeated.cpp | 168 -- Colossus-1.4.5/Colossus/src/Main_Bound.cpp | 145 - Colossus-1.4.5/Colossus/src/Main_Functions.cpp | 145 - Colossus-1.4.5/Colossus/src/Main_Multi.cpp | 57 Colossus-1.4.5/Colossus/src/Omnibus_Pieces.cpp | 137 - Colossus-1.4.5/Colossus/src/Omnibus_Pieces.h | 2 Colossus-1.4.5/Colossus/src/Plot_Extensions.cpp | 21 Colossus-1.4.5/Colossus/src/R_Interface.cpp | 108 - Colossus-1.4.5/Colossus/src/R_Interface.h | 6 Colossus-1.4.5/Colossus/src/RcppExports.cpp | 37 Colossus-1.4.5/Colossus/src/Step_Calc.cpp | 3 Colossus-1.4.5/Colossus/src/Step_Grad.cpp | 4 Colossus-1.4.5/Colossus/src/Step_Newton.cpp | 7 Colossus-1.4.5/Colossus/src/Subterms_Risk.cpp | 247 +-- Colossus-1.4.5/Colossus/src/Subterms_Risk.h | 6 Colossus-1.4.5/Colossus/tests/testthat/test-Assigned.R | 100 - Colossus-1.4.5/Colossus/tests/testthat/test-CaseControl.R | 67 Colossus-1.4.5/Colossus/tests/testthat/test-Cox_Plot.R | 167 -- Colossus-1.4.5/Colossus/tests/testthat/test-Cox_Regression.R | 179 -- Colossus-1.4.5/Colossus/tests/testthat/test-Formula.R | 109 - Colossus-1.4.5/Colossus/tests/testthat/test-Gradient.R | 119 - Colossus-1.4.5/Colossus/tests/testthat/test-Joint.R | 63 Colossus-1.4.5/Colossus/tests/testthat/test-Logbound.R | 118 - Colossus-1.4.5/Colossus/tests/testthat/test-Logit.R | 12 Colossus-1.4.5/Colossus/tests/testthat/test-Multidose.R | 156 - Colossus-1.4.5/Colossus/tests/testthat/test-Norm.R | 59 Colossus-1.4.5/Colossus/tests/testthat/test-Omnibus.R | 58 Colossus-1.4.5/Colossus/tests/testthat/test-Poisson_Regression.R | 77 Colossus-1.4.5/Colossus/tests/testthat/test-Poisson_Residual.R | 27 Colossus-1.4.5/Colossus/tests/testthat/test-Utility.R | 127 + Colossus-1.4.5/Colossus/vignettes/Alt_Run_Opt.Rmd | 12 Colossus-1.4.5/Colossus/vignettes/Equation_Expression.Rmd | 2 Colossus-1.4.5/Colossus/vignettes/Excess_and_Predicted_Cases.Rmd | 21 Colossus-1.4.5/Colossus/vignettes/Logistic.Rmd | 11 Colossus-1.4.5/Colossus/vignettes/Matched_Case_Control.Rmd | 10 Colossus-1.4.5/Colossus/vignettes/Starting-Description.Rmd | 5 Colossus-1.4.5/Colossus/vignettes/Wald_and_Log_Bound.Rmd | 2 108 files changed, 4966 insertions(+), 5994 deletions(-)
Title: Client for World Banks's 'Indicators' and 'Poverty and
Inequality Platform (PIP)' APIs
Description: Download and search data from the 'World Bank Indicators
API', which provides access to nearly 16,000 time series indicators.
See
<https://datahelpdesk.worldbank.org/knowledgebase/articles/889392-about-the-indicators-api-documentation>
for further details about the API.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
This is a re-admission after prior archival of version 0.7.0 dated 2025-11-10
Diff between worldbank versions 0.7.0 dated 2025-11-10 and 0.7.1 dated 2025-12-06
worldbank-0.7.0/worldbank/tests/testthat/setup.R |only worldbank-0.7.1/worldbank/DESCRIPTION | 8 +- worldbank-0.7.1/worldbank/MD5 | 31 ++++----- worldbank-0.7.1/worldbank/NEWS.md | 4 + worldbank-0.7.1/worldbank/R/indicators.R | 18 +++++ worldbank-0.7.1/worldbank/man/wb_country.Rd | 2 worldbank-0.7.1/worldbank/man/wb_data.Rd | 2 worldbank-0.7.1/worldbank/man/wb_income_level.Rd | 2 worldbank-0.7.1/worldbank/man/wb_indicator.Rd | 2 worldbank-0.7.1/worldbank/man/wb_language.Rd | 2 worldbank-0.7.1/worldbank/man/wb_lending_type.Rd | 2 worldbank-0.7.1/worldbank/man/wb_region.Rd | 2 worldbank-0.7.1/worldbank/man/wb_source.Rd | 2 worldbank-0.7.1/worldbank/man/wb_topic.Rd | 2 worldbank-0.7.1/worldbank/tests/testthat/test-fone.R | 4 - worldbank-0.7.1/worldbank/tests/testthat/test-indicators.R | 43 ++++++------- worldbank-0.7.1/worldbank/tests/testthat/test-pip.R | 2 17 files changed, 84 insertions(+), 44 deletions(-)
Title: Collecting 'TikTok' Data
Description: Getting 'TikTok' data (<https://www.tiktok.com/>) through the official
and unofficial APIs—in other words, you can track 'TikTok'.
Author: Johannes B. Gruber [aut, cre]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2025-11-24
Diff between traktok versions 0.1.0 dated 2025-11-24 and 0.1.1 dated 2025-12-06
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 2 R/utils.R | 3 README.md | 10 inst/WORDLIST | 5 inst/doc/research-api.Rmd | 2 inst/doc/research-api.html | 3 inst/doc/unofficial-api.Rmd | 492 +++++++++++++++++++++---------------------- vignettes/research-api.Rmd | 2 vignettes/unofficial-api.Rmd | 492 +++++++++++++++++++++---------------------- 11 files changed, 524 insertions(+), 513 deletions(-)
Title: Estimation of the Rasch Model for Multistage Tests
Description: Provides conditional maximum likelihood (CML) item parameter estimation of both sequential and cumulative deterministic multistage designs (Zwitser & Maris, 2015, <doi:10.1007/s11336-013-9369-6>) and probabilistic sequential and cumulative multistage designs (Steinfeld & Robitzsch, 2024, <doi:10.1007/s41237-024-00228-3>). Supports CML item parameter estimation of conventional linear designs and additional functions for the likelihood ratio test (Andersen, 1973, <doi:10.1007/BF02291180>) as well as functions for simulating various types of multistage designs.
Author: Jan Steinfeld [cre, aut] ,
Alexander Robitzsch [aut]
Maintainer: Jan Steinfeld <jan.d.steinfeld@gmail.com>
Diff between tmt versions 0.3.6-0 dated 2025-06-20 and 0.3.6-4 dated 2025-12-06
DESCRIPTION | 14 +- MD5 | 34 ++--- NEWS.md | 3 R/helper_functions.R | 3 R/raschmodel.mst.R | 40 ++++++ R/sim.rm.R | 11 + R/tmt_gmc.R | 6 + R/tmt_mstdesign.R | 115 ++++++++++++++++++- R/tmt_msttemplate.R | 38 +++++- R/tmt_sim.R | 161 +++++++++++++++++++++++++-- README.md | 22 ++- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 8 + inst/doc/introduction_to_tmt.html | 8 - src/esf_mst_sum_vector.cpp | 201 ++++++++++++++++++++++++++++++++-- src/esf_mst_sum_vector_s2.h | 151 ++++++++++++++++++++++++- tests/testthat/test-helperfunctions.R | 26 ++-- 18 files changed, 748 insertions(+), 93 deletions(-)
Title: Tidy Methods for Bayesian Treatment Effect Models
Description: Functions for extracting tidy data from Bayesian treatment effect models, in particular BART, but extensions are possible. Functionality includes extracting tidy posterior summaries as in 'tidybayes' <https://github.com/mjskay/tidybayes>, estimating (average) treatment effects, common support calculations, and plotting useful summaries of these.
Author: Joshua J Bon [aut, cre]
Maintainer: Joshua J Bon <joshuajbon@gmail.com>
Diff between tidytreatment versions 0.3.1 dated 2025-01-10 and 0.3.2 dated 2025-12-06
tidytreatment-0.3.1/tidytreatment/man/fitted_draws.bartMachine.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.lbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.mbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.mbart2.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.pbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws.wbart.Rd |only tidytreatment-0.3.1/tidytreatment/man/fitted_draws_BART.Rd |only tidytreatment-0.3.2/tidytreatment/DESCRIPTION | 15 - tidytreatment-0.3.2/tidytreatment/MD5 | 90 +++--- tidytreatment-0.3.2/tidytreatment/NAMESPACE | 16 - tidytreatment-0.3.2/tidytreatment/NEWS.md | 5 tidytreatment-0.3.2/tidytreatment/R/average-treatment-effects-posterior.R | 6 tidytreatment-0.3.2/tidytreatment/R/common-support.R | 12 tidytreatment-0.3.2/tidytreatment/R/helper.R | 2 tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-BART.R | 141 +++++++--- tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-bartMachine.R | 26 - tidytreatment-0.3.2/tidytreatment/R/tidy-posterior-stan4bart.R | 40 -- tidytreatment-0.3.2/tidytreatment/R/tidytreatment-package.R | 2 tidytreatment-0.3.2/tidytreatment/R/treatment-effects-bartCause.R | 2 tidytreatment-0.3.2/tidytreatment/R/treatment-effects-posterior.R | 11 tidytreatment-0.3.2/tidytreatment/R/tree-extract-BART.R | 2 tidytreatment-0.3.2/tidytreatment/build/vignette.rds |binary tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.R |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.Rmd |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART-binary-outcome.html |only tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.R | 10 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.Rmd | 10 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-BART.html | 85 +++--- tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.R | 4 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.Rmd | 4 tidytreatment-0.3.2/tidytreatment/inst/doc/use-tidytreatment-bartCause.html | 75 ++--- tidytreatment-0.3.2/tidytreatment/man/avg_treatment_effects.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/epred_draws.bartMachine.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.lbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.mbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.mbart2.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.pbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws.stan4bartFit.Rd | 4 tidytreatment-0.3.2/tidytreatment/man/epred_draws.wbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/epred_draws_BART.Rd |only tidytreatment-0.3.2/tidytreatment/man/has_common_support.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/linpred_draws.stan4bartFit.Rd | 6 tidytreatment-0.3.2/tidytreatment/man/predicted_draws.lbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/predicted_draws.pbart.Rd |only tidytreatment-0.3.2/tidytreatment/man/predicted_draws.stan4bartFit.Rd | 10 tidytreatment-0.3.2/tidytreatment/man/predicted_draws_BART.Rd | 6 tidytreatment-0.3.2/tidytreatment/man/tidy_ate.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/tidy_att.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/tidytreatment.Rd | 4 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.bartcFit.Rd | 2 tidytreatment-0.3.2/tidytreatment/man/treatment_effects.default.Rd | 2 tidytreatment-0.3.2/tidytreatment/tests/testthat/test-fitted.R | 2 tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-BART-binary-outcome.Rmd |only tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-BART.Rmd | 10 tidytreatment-0.3.2/tidytreatment/vignettes/use-tidytreatment-bartCause.Rmd | 4 56 files changed, 362 insertions(+), 256 deletions(-)
Title: Robust Exponential Factor Analysis
Description: A robust alternative to the traditional principal component estimator is proposed within the framework of factor models, known as Robust Exponential Factor Analysis, specifically designed for the modeling of high-dimensional datasets with heavy-tailed distributions. The algorithm estimates the latent factors and the loading by minimizing the exponential squared loss function. To determine the appropriate number of factors, we propose a modified rank minimization technique, which has been shown to significantly enhance finite-sample performance. For more detail of Robust Exponential Factor Analysis, please refer to Hu et al. (2026) <doi:10.1016/j.jmva.2025.105567>.
Author: Jiaqi Hu [cre, aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between REFA versions 0.1.0 dated 2023-11-19 and 0.2.0 dated 2025-12-06
DESCRIPTION | 16 +++---- MD5 | 28 ++++++------- NAMESPACE | 29 +++++++------- NEWS.md | 2 R/FA.R | 37 ++++++++++++++++++ R/REFA.R | 54 ++++++++++++++++++++++++++ R/auxiliary.R | 67 ++++++++++++++++++++++++++++++--- R/gendata.R | 115 ++++++++++++++++++++++++++++++++++++++------------------- man/ECC.Rd | 28 ++++++++----- man/FA.Rd | 35 +++++++++-------- man/REFA.Rd | 47 +++++++++++++---------- man/REFA_FN.Rd | 50 ++++++++++++++---------- man/TR.Rd | 19 ++++++--- man/est_num.Rd | 25 +++++++----- man/gendata.Rd | 41 +++++++++++--------- 15 files changed, 417 insertions(+), 176 deletions(-)
Title: Bindings for 'Open Source Routing Machine'
Description: Install and control 'Open Source Routing Machine' ('OSRM')
backend executables to prepare routing data and run/stop a local
'OSRM' server. For computations with the running server use the 'osrm'
R package (<https://cran.r-project.org/package=osrm>).
Author: Egor Kotov [aut, cre, cph]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between osrm.backend versions 0.1.0 dated 2025-12-03 and 0.1.1 dated 2025-12-06
osrm.backend-0.1.0/osrm.backend/inst/doc/osrm-backend.qmd |only osrm.backend-0.1.0/osrm.backend/man/print.osrm_job.Rd |only osrm.backend-0.1.0/osrm.backend/vignettes/osrm-backend.qmd |only osrm.backend-0.1.1/osrm.backend/DESCRIPTION | 10 osrm.backend-0.1.1/osrm.backend/MD5 | 26 osrm.backend-0.1.1/osrm.backend/NEWS.md | 4 osrm.backend-0.1.1/osrm.backend/R/utils.R | 29 osrm.backend-0.1.1/osrm.backend/README.md | 11 osrm.backend-0.1.1/osrm.backend/build/vignette.rds |binary osrm.backend-0.1.1/osrm.backend/inst/CITATION | 5 osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.R | 64 - osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.Rmd |only osrm.backend-0.1.1/osrm.backend/inst/doc/osrm-backend.html | 443 ++++++++-- osrm.backend-0.1.1/osrm.backend/tests/testthat/setup-osrm.R | 61 - osrm.backend-0.1.1/osrm.backend/tests/testthat/teardown.R |only osrm.backend-0.1.1/osrm.backend/tests/testthat/test-osrm_server.R | 10 osrm.backend-0.1.1/osrm.backend/vignettes/osrm-backend.Rmd |only 17 files changed, 472 insertions(+), 191 deletions(-)
Title: Model Selection and Tuning Utilities
Description: Provides a lightweight framework for model selection
and hyperparameter tuning in R. The package offers intuitive tools for
grid search, cross-validation, and combined grid search with cross-validation
that work seamlessly with virtually any modeling package. Designed for
flexibility and ease of use, it standardizes tuning workflows while
remaining fully compatible with a wide range of model interfaces and
estimation functions.
Author: Daniel Molitor [aut, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between modeltuning versions 0.1.2 dated 2025-10-28 and 0.1.3 dated 2025-12-06
DESCRIPTION | 11 ++++++----- MD5 | 13 +++++++------ NEWS.md |only README.md | 20 +++++++++++++------- inst/doc/basic-usage.html | 18 +++++++++--------- inst/doc/data-masking.html | 36 +++++++++++++++++++----------------- inst/doc/scaling-with-aws.html | 16 ++++++++-------- man/modeltuning-package.Rd | 1 + 8 files changed, 63 insertions(+), 52 deletions(-)
Title: Bootstrap Analyses of Sampling Uncertainty in Goodness-of-Fit
Statistics
Description: Uses jackknife and bootstrap methods to quantify the sampling uncertainty in goodness-of-fit statistics. Full details are in Clark et al. (2021), "The abuse of popular performance metrics in hydrologic modeling", Water Resources Research, <doi:10.1029/2020WR029001>.
Author: Martyn Clark [aut],
Kevin Shook [aut, trl, cre]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between gumboot versions 1.0.1 dated 2023-10-18 and 1.0.2 dated 2025-12-06
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/gumboot-package.R | 3 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/using_gumboot.R | 10 +++++----- inst/doc/using_gumboot.html | 21 +++++++++++---------- man/gumboot-package.Rd | 2 ++ 8 files changed, 33 insertions(+), 29 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.7.0 dated 2025-08-25 and 3.8.0 dated 2025-12-06
DESCRIPTION | 8 MD5 | 102 NEWS.md | 43 R/gsMethods.R | 9 R/gsqplot.R | 6 R/nNormal.R | 4 R/sfXG.R | 2 inst/doc/ConditionalErrorSpending.html | 351 +- inst/doc/PoissonMixtureModel.html | 693 ++--- inst/doc/VaccineEfficacy.html | 468 +-- inst/doc/binomialSPRTExample.html | 222 - inst/doc/binomialTwoSample.html | 1488 +++++------- inst/doc/gsSurvBasicExamples.html | 355 +- inst/doc/nNormal.html | 2 man/gsDesign-package.Rd | 2 man/nNormal.Rd | 4 tests/testthat/_snaps |only tests/testthat/test-independent-test-plot.gsBinomialExact.R | 10 tests/testthat/test-independent-test-plot.gsDesign.R | 18 tests/testthat/test-independent-test-plot.gsProbability.R | 10 tests/testthat/test-independent-test-sfXG.R |only tests/testthat/test-independent-test-toBinomialExact.R |only tests/testthat/test-independent-test-xtable.R |only 23 files changed, 1933 insertions(+), 1864 deletions(-)
Title: Group Factor Analysis
Description: Implements statistical methods for group factor analysis, focusing on estimating the number of global and local factors and extracting them. Several algorithms are implemented, including Canonical Correlation-based Estimation by Choi et al. (2021) <doi:10.1016/j.jeconom.2021.09.008>, Generalised Canonical Correlation Estimation by Lin and Shin (2023) <doi:10.2139/ssrn.4295429>, Circularly Projected Estimation by Chen (2022) <doi:10.1080/07350015.2022.2051520>, and the Aggregated Projection Method by Hu et al. (2025) <doi:10.1080/01621459.2025.2491154>.
Author: Jiaqi Hu [cre, aut],
Ting Li [aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between GrFA versions 0.2.1 dated 2024-12-22 and 0.2.2 dated 2025-12-06
DESCRIPTION | 30 ++--- MD5 | 41 ++++---- NAMESPACE | 26 ++--- NEWS.md |only R/APM.R | 234 +++++++++++++++++++++++++++++----------------- R/CCA.R | 233 +++++++++++++++++++++++++++++----------------- R/CPE.R | 177 +++++++++++++++++++++++----------- R/FA.R | 208 ++++++++++++++++++++++++++--------------- R/GCC.R | 199 ++++++++++++++++++++++++--------------- R/auxiliary.R | 129 +++++++++++++++++++------ R/data.R |only R/gendata.R | 263 +++++++++++++++++++++++++++++++--------------------- man/APM.Rd | 78 ++++++++++----- man/CCA.Rd | 71 ++++++++------ man/CP.Rd | 57 ++++++----- man/FA.Rd | 31 +++--- man/GCC.Rd | 55 ++++++---- man/TraceRatio.Rd | 26 +++-- man/UShouseprice.Rd | 91 +++++++++-------- man/est_num.Rd | 32 ++++-- man/gendata.Rd | 96 +++++++++++------- man/print.GFA.Rd | 18 +-- man/print.GFD.Rd |only 23 files changed, 1322 insertions(+), 773 deletions(-)
Title: Factor Analysis for All
Description: Provides a comprehensive Shiny-based graphical user interface for conducting
a wide range of factor analysis procedures. 'FAfA' (Factor Analysis for All)
guides users through data uploading, assumption checking (descriptives,
collinearity, multivariate normality, outliers), data wrangling (variable
exclusion, data splitting), factor retention analysis (e.g., Parallel Analysis,
Hull method, EGA), Exploratory Factor Analysis (EFA) with various rotation
and extraction methods, Confirmatory Factor Analysis (CFA) for model testing,
Reliability Analysis (e.g., Cronbach's Alpha, McDonald's Omega), Measurement
Invariance testing across groups, and item weighting techniques. The application
leverages established R packages such as 'lavaan' and 'psych' to perform
these analyses, offering an accessible platform for researchers and students.
Results are presented in user-friendly tables and plots, with options for
downloading outputs.
Author: Abdullah Faruk KILIC [aut, cre]
Maintainer: Abdullah Faruk KILIC <afarukkilic@trakya.edu.tr>
Diff between FAfA versions 0.3 dated 2025-05-23 and 0.4 dated 2025-12-06
DESCRIPTION | 17 ++- MD5 | 8 - R/mod_about_server.r | 224 +++++++++++++++++++++++++------------------------- R/mod_cfa_server.r | 43 +++++++-- inst/golem-config.yml | 2 5 files changed, 161 insertions(+), 133 deletions(-)
Title: A Method to Identify Single CpG Sites for Classification and
Deconvolution
Description: DNA methylation signatures are usually based on multivariate
approaches that require hundreds of sites for predictions. 'CimpleG'
is a method for the detection of small CpG methylation signatures used
for cell-type classification and deconvolution. 'CimpleG' is time
efficient and performs as well as top performing methods for cell-type
classification of blood cells and other somatic cells, while basing
its prediction on a single DNA methylation site per cell type (but
users can also select more sites if they so wish). Users can train
cell type classifiers ('CimpleG' based, and others) and directly apply
these in a deconvolution of cell mixes context. Altogether, 'CimpleG'
provides a complete computational framework for the delineation of
DNAm signatures and cellular deconvolution. For more details see Maié
et al. (2023) <doi:10.1186/s13059-023-03000-0>.
Author: Tiago F.V. Maie [aut, cre]
Maintainer: Tiago F.V. Maie <tiagomaie@hotmail.com>
Diff between CimpleG versions 1.0.0 dated 2025-12-03 and 1.0.1 dated 2025-12-06
DESCRIPTION | 18 ++-- MD5 | 10 +- README.md | 130 +++++++++++++++++++++------------ inst/doc/generate-signatures.html | 12 +-- inst/doc/save_load_objects.html | 4 - tests/testthat/test3-CimpleG-xgboost.R | 10 +- 6 files changed, 112 insertions(+), 72 deletions(-)
Title: Outlier Detection and Influence Diagnostics for Meta-Analysis
Description: Computational tools for outlier detection and influence diagnostics in meta-analysis (Noma et al. (2025) <doi:10.1101/2025.09.18.25336125>). Bootstrap distributions of influence statistics are computed, and explicit thresholds for identifying outliers are provided. These methods can also be applied to the analysis of influential centers or regions in multicenter or multiregional clinical trials (Aoki, Noma and Gosho (2021) <doi:10.1080/24709360.2021.1921944>, Nakamura and Noma (2021) <doi:10.5691/jjb.41.117>).
Author: Hisashi Noma [aut, cre],
Kazushi Maruo [aut],
Masahiko Gosho [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between boutliers versions 2.1-2 dated 2025-11-25 and 2.1-3 dated 2025-12-06
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 3 +++ NEWS.md | 4 ++++ 4 files changed, 15 insertions(+), 8 deletions(-)
Title: Tools for Preprocessing Visual World Data
Description: Gaze data from the Visual World Paradigm requires significant
preprocessing prior to plotting and analyzing the data. This package
provides functions for preparing visual world eye-tracking data for
statistical analysis and plotting. It can prepare data for linear
analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as
well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM).
Additionally, it contains various plotting functions for creating grand average and
conditional average plots. See the vignette for samples of the functionality.
Currently, the functions in this package are designed for handling data
collected with SR Research Eyelink eye trackers using Sample Reports created
in SR Research Data Viewer. While we would like to add functionality
for data collected with other systems in the future, the current package is
considered to be feature-complete; further updates will mainly entail maintenance
and the addition of minor functionality.
Author: Vincent Porretta [aut, cre],
Aki-Juhani Kyroelaeinen [aut],
Jacolien van Rij [ctb],
Juhani Jaervikivi [ctb]
Maintainer: Vincent Porretta <vincentporretta@gmail.com>
Diff between VWPre versions 1.2.4 dated 2020-11-29 and 1.2.5 dated 2025-12-06
DESCRIPTION | 12 MD5 | 48 - R/VWPre.R | 3 R/calculations.R | 2 R/formatting.R | 27 R/plotting.R | 2 build/vignette.rds |binary inst/NEWS | 879 ++++++++++++++++---------------- inst/doc/VWPre_Basic_Preprocessing.R | 100 +-- inst/doc/VWPre_Basic_Preprocessing.Rmd | 6 inst/doc/VWPre_Basic_Preprocessing.html | 611 ++++++++++++++++------ inst/doc/VWPre_Interest_Areas.R | 34 - inst/doc/VWPre_Interest_Areas.html | 270 ++++++--- inst/doc/VWPre_Message_Alignment.R | 22 inst/doc/VWPre_Message_Alignment.Rmd | 272 ++++----- inst/doc/VWPre_Message_Alignment.html | 273 +++++++-- inst/doc/VWPre_Plotting.R | 64 +- inst/doc/VWPre_Plotting.Rmd | 7 inst/doc/VWPre_Plotting.html | 597 +++++++++++++-------- man/VWPre.Rd | 4 man/bin_prop.Rd | 2 man/plot_avg_contour.Rd | 2 vignettes/VWPre_Basic_Preprocessing.Rmd | 6 vignettes/VWPre_Message_Alignment.Rmd | 272 ++++----- vignettes/VWPre_Plotting.Rmd | 7 25 files changed, 2103 insertions(+), 1419 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The functions
are pipe-friendly and provide a consistent syntax to work with tidy
data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.7.1 dated 2025-07-27 and 1.7.2 dated 2025-12-06
DESCRIPTION | 20 +-- MD5 | 24 ++-- NEWS.md | 4 R/globals.R | 109 +++++++++--------- R/one-sample-test.R | 208 ++++++++++++++++++------------------ README.md | 14 +- build/vignette.rds |binary inst/doc/statsExpressions.Rmd | 3 inst/doc/statsExpressions.html | 18 +-- man/figures/README-t_two-1.png |binary tests/testthat/_snaps/one-sample.md | 76 ++++++------- tests/testthat/test-one-sample.R | 2 vignettes/statsExpressions.Rmd | 3 13 files changed, 240 insertions(+), 241 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Text Analysis for All
Description: An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs.
It is a versatile, general-purpose tool for analyzing textual data.
'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Author: Massimo Aria [aut, cre, cph] ,
Maria Spano [aut] ,
Luca D'Aniello [aut] ,
Corrado Cuccurullo [ctb] ,
Michelangelo Misuraca [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between tall versions 0.4.0 dated 2025-10-23 and 0.5.0 dated 2025-12-06
DESCRIPTION | 21 MD5 | 63 NAMESPACE | 7 NEWS.md | 49 R/RcppExports.R | 24 R/calculate_ngram_is.R |only R/reinert.R | 153 R/txt_recode_fast.R |only R/zzz.R | 9 inst/CITATION |only inst/tall/cssTags.R |only inst/tall/doc_classification.R |only inst/tall/documents.R |only inst/tall/edit.R |only inst/tall/featureroles.R |only inst/tall/filters_groups.R |only inst/tall/header.R |only inst/tall/helpContent.R | 469 ++ inst/tall/home.R |only inst/tall/import.R |only inst/tall/keyness.R |only inst/tall/libraries.R | 1108 ++++- inst/tall/overview.R |only inst/tall/preprocessing.R |only inst/tall/report.R |only inst/tall/server.R | 5040 ------------------------ inst/tall/settings.R |only inst/tall/tallAI.R | 1399 ++++-- inst/tall/tallFunctions.R | 8405 ++++++++++++++++++++++++++++++++--------- inst/tall/ui.R | 4153 -------------------- inst/tall/words.R |only inst/tall/www/images |only inst/tall/www/tall_logo.jpg |binary man/calculate_ngram_is.Rd |only man/process_multiwords_fast.Rd |only man/reinert.Rd | 4 man/txt_recode_batch_cpp.Rd |only man/txt_recode_cpp.Rd |only man/txt_recode_fast.Rd |only man/txt_recode_ngram_cpp.Rd |only man/txt_recode_ngram_fast.Rd |only src/RcppExports.cpp | 87 src/is_calculation.cpp |only src/ngram_generation.cpp |only src/text_recode.cpp |only 45 files changed, 9320 insertions(+), 11671 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist',
'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet',
Ocean 'Biogeographic' Information System ('OBIS'), and
Atlas of Living Australia ('ALA'). Includes functionality for retrieving
species occurrence data, and combining those data.
Author: Hannah Owens [aut, cre] ,
Vijay Barve [aut] ,
Scott Chamberlain [aut] ,
Karthik Ram [ctb],
Ted Hart [ctb],
rOpenSci [fnd]
Maintainer: Hannah Owens <hannah.owens@gmail.com>
Diff between spocc versions 1.2.3 dated 2024-03-06 and 1.2.4 dated 2025-12-06
DESCRIPTION | 45 +++++++++++++++++------------------ MD5 | 16 +++++++----- NEWS.md | 7 +++++ R/as.idigbio.R | 6 ++-- man/as.idigbio.Rd | 4 +-- tests/testthat/_problems |only tests/testthat/test-as.idigbio.R | 2 - tests/testthat/test-geometry.R | 29 +++++++++++----------- tests/testthat/testthat-problems.rds |only 9 files changed, 60 insertions(+), 49 deletions(-)
Title: A Simple Package for Testing R Packages
Description: Provides two convenience functions assert() and test_pkg() to
facilitate testing R packages.
Author: Yihui Xie [aut, cre] ,
Tomas Kalibera [ctb],
Steven Mortimer [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between testit versions 0.13 dated 2021-04-14 and 0.14 dated 2025-12-06
DESCRIPTION | 19 +++++++----- LICENSE |only MD5 | 11 +++---- R/testit.R | 35 +++-------------------- man/assert.Rd | 38 ++----------------------- tests/testit/test-assert.R | 68 +++++++++++++++++++++------------------------ tests/testit/test-utils.R | 27 +++++++---------- 7 files changed, 70 insertions(+), 128 deletions(-)
Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tile map display from spatial polygons. Each
polygon is represented by a hexagon tile, placed as close to it's original
centroid as possible, with a focus on maintaining spatial relationship to
a focal point. Developed to aid visualisation and analysis of spatial
distributions across Australia, which can be challenging due to the
concentration of the population on the coast and wide open interior.
Author: Dianne Cook [aut, cre, ths] ,
Stephanie Kobakian [aut] ,
Matt Cowgill [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between sugarbag versions 0.1.6 dated 2022-11-09 and 0.1.9 dated 2025-12-06
sugarbag-0.1.6/sugarbag/R/read_shape.R |only sugarbag-0.1.6/sugarbag/man/read_shape.Rd |only sugarbag-0.1.9/sugarbag/DESCRIPTION | 29 - sugarbag-0.1.9/sugarbag/MD5 | 37 - sugarbag-0.1.9/sugarbag/NAMESPACE | 1 sugarbag-0.1.9/sugarbag/NEWS.md | 15 sugarbag-0.1.9/sugarbag/R/allocate.R | 14 sugarbag-0.1.9/sugarbag/R/data.R | 17 sugarbag-0.1.9/sugarbag/R/fortify_sfc.R | 7 sugarbag-0.1.9/sugarbag/README.md | 171 ++---- sugarbag-0.1.9/sugarbag/build/vignette.rds |binary sugarbag-0.1.9/sugarbag/inst/CITATION | 23 sugarbag-0.1.9/sugarbag/inst/doc/Tasmania.R | 36 - sugarbag-0.1.9/sugarbag/inst/doc/Tasmania.Rmd | 2 sugarbag-0.1.9/sugarbag/inst/doc/Tasmania.html | 267 +++++----- sugarbag-0.1.9/sugarbag/inst/france |only sugarbag-0.1.9/sugarbag/man/figures/README-unnamed-chunk-2-1.png |only sugarbag-0.1.9/sugarbag/man/figures/README-unnamed-chunk-4-1.png |only sugarbag-0.1.9/sugarbag/man/figures/README-unnamed-chunk-5-1.png |only sugarbag-0.1.9/sugarbag/man/figures/README-unnamed-chunk-6-1.png |only sugarbag-0.1.9/sugarbag/man/fp19.Rd | 17 sugarbag-0.1.9/sugarbag/man/sugarbag-package.Rd | 9 sugarbag-0.1.9/sugarbag/vignettes/Tasmania.Rmd | 2 23 files changed, 330 insertions(+), 317 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2025)<Forthcoming>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 3.2-1 dated 2025-11-24 and 4.1-1 dated 2025-12-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++++------ NAMESPACE | 4 +++- NEWS.md | 4 ++++ R/rqlm.r | 2 +- R/ttemsm.r |only data/exdata04.RData |only man/exdata04.Rd |only man/qlogist.Rd | 2 +- man/rqlm.Rd | 5 +++-- man/ttemsm.Rd |only 11 files changed, 26 insertions(+), 15 deletions(-)
Title: Bayesian Estimation of the Evolutionary Rate Matrix
Description: The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
Author: Daniel Caetano [aut, cre],
Luke Harmon [aut]
Maintainer: Daniel Caetano <caetanods1@gmail.com>
Diff between ratematrix versions 1.2.4 dated 2022-06-03 and 1.2.5 dated 2025-12-06
ratematrix-1.2.4/ratematrix/inst/doc/Intro_on_the_package.html |only ratematrix-1.2.4/ratematrix/inst/doc/Making_prior_on_ratematrix.html |only ratematrix-1.2.4/ratematrix/inst/doc/Set_custom_starting_point.html |only ratematrix-1.2.5/ratematrix/DESCRIPTION | 8 - ratematrix-1.2.5/ratematrix/MD5 | 44 ++++---- ratematrix-1.2.5/ratematrix/NAMESPACE | 3 ratematrix-1.2.5/ratematrix/R/ratematrix-package.R | 2 ratematrix-1.2.5/ratematrix/R/ratematrixJointMCMC.R | 48 ++++++++- ratematrix-1.2.5/ratematrix/R/ratematrixMCMC.R | 15 ++- ratematrix-1.2.5/ratematrix/build/vignette.rds |binary ratematrix-1.2.5/ratematrix/inst/doc/Intro_on_the_package.R | 18 +-- ratematrix-1.2.5/ratematrix/inst/doc/Intro_on_the_package.Rmd | 4 ratematrix-1.2.5/ratematrix/inst/doc/Intro_on_the_package.pdf |only ratematrix-1.2.5/ratematrix/inst/doc/Making_prior_on_ratematrix.R | 50 +++++----- ratematrix-1.2.5/ratematrix/inst/doc/Making_prior_on_ratematrix.Rmd | 4 ratematrix-1.2.5/ratematrix/inst/doc/Making_prior_on_ratematrix.pdf |only ratematrix-1.2.5/ratematrix/inst/doc/Set_custom_starting_point.R | 22 ++-- ratematrix-1.2.5/ratematrix/inst/doc/Set_custom_starting_point.Rmd | 4 ratematrix-1.2.5/ratematrix/inst/doc/Set_custom_starting_point.pdf |only ratematrix-1.2.5/ratematrix/man/ratematrix.Rd | 1 ratematrix-1.2.5/ratematrix/man/ratematrixJointMCMC.Rd | 2 ratematrix-1.2.5/ratematrix/src/Makevars | 2 ratematrix-1.2.5/ratematrix/src/Makevars.win | 2 ratematrix-1.2.5/ratematrix/vignettes/Intro_on_the_package.Rmd | 4 ratematrix-1.2.5/ratematrix/vignettes/Making_prior_on_ratematrix.Rmd | 4 ratematrix-1.2.5/ratematrix/vignettes/Set_custom_starting_point.Rmd | 4 26 files changed, 142 insertions(+), 99 deletions(-)
Title: Detecting Differentially Variable Genes Using the Mixture of
Marginal Distributions
Description: Gene selection based on variance using the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions. Please see the reference: Li X, Fu Y, Wang X, DeMeo DL, Tantisira K, Weiss ST, Qiu W. (2018) <doi:10.1155/2018/6591634>.
Author: Xuan Li [aut, ctb],
Yuejiao Fu [aut, ctb],
Xiaogang Wang [aut, ctb],
Dawn L. DeMeo [aut, ctb],
Kelan Tantisira [aut, ctb],
Scott T. Weiss [aut, ctb],
Weiliang Qiu [aut, cre]
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
Diff between MMDvariance versions 0.0.9 dated 2018-07-27 and 0.1.0 dated 2025-12-06
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS | 2 + man/gsMMD.v.Rd | 41 +++++++++++++++++++-------------- man/plotHistDensity.v.Rd | 57 ++++++++++++++++++++++++----------------------- 5 files changed, 64 insertions(+), 52 deletions(-)
Title: A Bridge Between 'keras' and 'tidymodels'
Description: Provides a seamless bridge between 'keras' and the 'tidymodels'
frameworks. It allows for the dynamic creation of 'parsnip' model
specifications for 'keras' models.
Author: David Diaz [aut, cre]
Maintainer: David Diaz <daviddrsch@gmail.com>
Diff between kerasnip versions 0.0.3 dated 2025-09-18 and 0.1.0 dated 2025-12-06
DESCRIPTION | 8 MD5 | 48 R/create_keras_spec_helpers.R | 518 ++++---- README.md | 13 build/vignette.rds |binary inst/doc/applications.html | 58 inst/doc/autoplot_uniqueness.html | 38 inst/doc/functional_api.R | 6 inst/doc/functional_api.Rmd | 6 inst/doc/functional_api.html | 18 inst/doc/getting_started.html | 214 +-- inst/doc/tuning_fit_compile_args.html | 376 +++--- inst/doc/workflows_functional.R | 16 inst/doc/workflows_functional.Rmd | 18 inst/doc/workflows_functional.html | 607 ++++----- inst/doc/workflows_sequential.R | 8 inst/doc/workflows_sequential.Rmd | 8 inst/doc/workflows_sequential.html | 1616 ++++++++++++-------------- man/inp_spec.Rd | 15 tests/testthat/test_e2e_func_classification.R | 8 tests/testthat/test_e2e_func_regression.R | 456 +++---- tests/testthat/test_inp_spec.R | 87 - vignettes/functional_api.Rmd | 6 vignettes/workflows_functional.Rmd | 18 vignettes/workflows_sequential.Rmd | 8 25 files changed, 2116 insertions(+), 2058 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.3.0 dated 2025-04-09 and 2.4.0 dated 2025-12-06
EGAnet-2.3.0/EGAnet/R/EGM.R |only EGAnet-2.3.0/EGAnet/R/EGM.compare.R |only EGAnet-2.3.0/EGAnet/R/network.generalizability.R |only EGAnet-2.3.0/EGAnet/R/network.nonconvex.R |only EGAnet-2.3.0/EGAnet/man/EGM.Rd |only EGAnet-2.3.0/EGAnet/man/EGM.compare.Rd |only EGAnet-2.3.0/EGAnet/man/network.nonconvex.Rd |only EGAnet-2.4.0/EGAnet/DESCRIPTION | 30 EGAnet-2.4.0/EGAnet/MD5 | 95 +- EGAnet-2.4.0/EGAnet/NAMESPACE | 20 EGAnet-2.4.0/EGAnet/NEWS | 43 EGAnet-2.4.0/EGAnet/R/EGA.R | 8 EGAnet-2.4.0/EGAnet/R/EGAnet.R | 2 EGAnet-2.4.0/EGAnet/R/EGM.optimizations.R | 777 +++++++++------- EGAnet-2.4.0/EGAnet/R/auto.correlate.R | 29 EGAnet-2.4.0/EGAnet/R/bootEGA.R | 17 EGAnet-2.4.0/EGAnet/R/community.unidimensional.R | 228 ++-- EGAnet-2.4.0/EGAnet/R/compare.EGA.plots.R | 108 +- EGAnet-2.4.0/EGAnet/R/dynEGA.R | 923 +++++++++++++++----- EGAnet-2.4.0/EGAnet/R/dynEGA.ind.pop.R | 68 + EGAnet-2.4.0/EGAnet/R/dynamic.network.compare.R |only EGAnet-2.4.0/EGAnet/R/genTEFI.R | 64 - EGAnet-2.4.0/EGAnet/R/glla.R | 259 ++++- EGAnet-2.4.0/EGAnet/R/helpers.R | 21 EGAnet-2.4.0/EGAnet/R/hierEGA.R | 10 EGAnet-2.4.0/EGAnet/R/itemDiagnostics.R | 84 + EGAnet-2.4.0/EGAnet/R/known.graph.R |only EGAnet-2.4.0/EGAnet/R/net.loads.R | 102 +- EGAnet-2.4.0/EGAnet/R/network.compare.R | 24 EGAnet-2.4.0/EGAnet/R/network.estimation.R | 47 - EGAnet-2.4.0/EGAnet/R/network.fit.R |only EGAnet-2.4.0/EGAnet/R/network.predictability.R | 17 EGAnet-2.4.0/EGAnet/R/network.regularization.R |only EGAnet-2.4.0/EGAnet/R/plot_clusters.R |only EGAnet-2.4.0/EGAnet/R/regularization.R |only EGAnet-2.4.0/EGAnet/R/riEGA.R | 17 EGAnet-2.4.0/EGAnet/R/simEGM.R | 628 +++++++++++-- EGAnet-2.4.0/EGAnet/R/tefi.R | 357 +++---- EGAnet-2.4.0/EGAnet/inst/eganet-qr.png |only EGAnet-2.4.0/EGAnet/man/EGA.Rd | 3 EGAnet-2.4.0/EGAnet/man/auto.correlate.Rd | 6 EGAnet-2.4.0/EGAnet/man/community.unidimensional.Rd | 24 EGAnet-2.4.0/EGAnet/man/compare.EGA.plots.Rd | 6 EGAnet-2.4.0/EGAnet/man/dynEGA.Rd | 71 + EGAnet-2.4.0/EGAnet/man/dynEGA.ind.pop.Rd | 57 + EGAnet-2.4.0/EGAnet/man/dynamic.network.compare.Rd |only EGAnet-2.4.0/EGAnet/man/genTEFI.Rd | 32 EGAnet-2.4.0/EGAnet/man/glla.Rd | 54 - EGAnet-2.4.0/EGAnet/man/itemDiagnostics.Rd | 8 EGAnet-2.4.0/EGAnet/man/known.graph.Rd |only EGAnet-2.4.0/EGAnet/man/net.loads.Rd | 21 EGAnet-2.4.0/EGAnet/man/network.fit.Rd |only EGAnet-2.4.0/EGAnet/man/network.predictability.Rd | 12 EGAnet-2.4.0/EGAnet/man/network.regularization.Rd |only EGAnet-2.4.0/EGAnet/man/plot_clusters.Rd |only EGAnet-2.4.0/EGAnet/man/riEGA.Rd | 7 EGAnet-2.4.0/EGAnet/man/simEGM.Rd | 60 - EGAnet-2.4.0/EGAnet/man/tefi.Rd | 8 58 files changed, 3016 insertions(+), 1331 deletions(-)
Title: Cytokine Profiling Analysis Tool
Description: Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.
Author: Shubh Saraswat [cre, aut, cph] ,
Xiaohua Douglas Zhang [aut]
Maintainer: Shubh Saraswat <shubh.saraswat00@gmail.com>
Diff between CytoProfile versions 0.2.2 dated 2025-09-04 and 0.2.3 dated 2025-12-06
DESCRIPTION | 10 - MD5 | 54 +++---- NAMESPACE | 1 NEWS.md | 8 + R/CytoProfile-package.R | 1 R/cyt_xgb.R | 241 +++++++++++++++++++-------------- README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/getting_started.R | 9 - inst/doc/getting_started.Rmd | 12 - inst/doc/getting_started.html | 45 +++--- man/cyt_xgb.Rd | 45 ++++-- man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/readme-ML1-1.png |binary man/figures/readme-ML1-2.png |binary man/figures/readme-Multivariate2-1.png |binary man/figures/readme-Multivariate2-2.png |binary man/figures/readme-Multivariate2-3.png |binary man/figures/readme-Multivariate2-4.png |binary man/figures/readme-Multivariate2-5.png |binary man/figures/readme-Multivariate2-6.png |binary man/figures/readme-Multivariate2-7.png |binary man/figures/readme-Multivariate2-8.png |binary man/figures/readme-Multivariate2-9.png |binary vignettes/getting_started.Rmd | 12 - 30 files changed, 259 insertions(+), 186 deletions(-)
Title: Bayesian Methods for State Space Models
Description: Implements methods for Bayesian analysis of State Space Models.
Includes implementations of the Particle Marginal Metropolis-Hastings
algorithm described in Andrieu et al. (2010)
<doi:10.1111/j.1467-9868.2009.00736.x> and automatic tuning inspired by
Pitt et al. (2012) <doi:10.1016/j.jeconom.2012.06.004> and J. Dahlin and
T. B. Schön (2019) <doi:10.18637/jss.v088.c02>.
Author: Bjarke Hautop [aut, cre, cph]
Maintainer: Bjarke Hautop <bjarke.hautop@gmail.com>
Diff between bayesSSM versions 0.7.0 dated 2025-08-26 and 0.7.1 dated 2025-12-06
bayesSSM-0.7.0/bayesSSM/R/ess.R |only bayesSSM-0.7.0/bayesSSM/tests/testthat/test-ess.R |only bayesSSM-0.7.1/bayesSSM/DESCRIPTION | 8 bayesSSM-0.7.1/bayesSSM/LICENSE | 4 bayesSSM-0.7.1/bayesSSM/MD5 | 101 bayesSSM-0.7.1/bayesSSM/NAMESPACE | 66 bayesSSM-0.7.1/bayesSSM/NEWS.md | 4 bayesSSM-0.7.1/bayesSSM/R/ESS.R |only bayesSSM-0.7.1/bayesSSM/R/RcppExports.R | 30 bayesSSM-0.7.1/bayesSSM/R/auxiliary_filter.R | 431 +-- bayesSSM-0.7.1/bayesSSM/R/bayesSSM-package.R | 30 bayesSSM-0.7.1/bayesSSM/R/bootstrap_filter.R | 341 +- bayesSSM-0.7.1/bayesSSM/R/particle_filter-doc.R | 194 - bayesSSM-0.7.1/bayesSSM/R/particle_filter.R | 30 bayesSSM-0.7.1/bayesSSM/R/particle_filter_core.R | 535 +-- bayesSSM-0.7.1/bayesSSM/R/pmmh.R | 1249 ++++---- bayesSSM-0.7.1/bayesSSM/R/pmmh_tuning.R | 635 ++-- bayesSSM-0.7.1/bayesSSM/R/print.R | 132 bayesSSM-0.7.1/bayesSSM/R/resample_move_filter.R | 472 +-- bayesSSM-0.7.1/bayesSSM/R/resampling.R | 138 bayesSSM-0.7.1/bayesSSM/R/resampling_old.R | 304 +- bayesSSM-0.7.1/bayesSSM/R/rhat.R | 214 - bayesSSM-0.7.1/bayesSSM/R/summary.R | 108 bayesSSM-0.7.1/bayesSSM/R/utils.R | 305 +- bayesSSM-0.7.1/bayesSSM/README.md | 449 +-- bayesSSM-0.7.1/bayesSSM/build/partial.rdb |binary bayesSSM-0.7.1/bayesSSM/build/vignette.rds |binary bayesSSM-0.7.1/bayesSSM/inst/WORDLIST |only bayesSSM-0.7.1/bayesSSM/inst/doc/bayesSSM.R | 218 - bayesSSM-0.7.1/bayesSSM/inst/doc/bayesSSM.Rmd | 392 +- bayesSSM-0.7.1/bayesSSM/inst/doc/bayesSSM.html | 1072 +++---- bayesSSM-0.7.1/bayesSSM/man/auxiliary_filter.Rd | 6 bayesSSM-0.7.1/bayesSSM/man/bayesSSM-package.Rd | 4 bayesSSM-0.7.1/bayesSSM/man/bootstrap_filter.Rd | 6 bayesSSM-0.7.1/bayesSSM/man/dot-particle_filter_core.Rd | 6 bayesSSM-0.7.1/bayesSSM/man/ess.Rd | 4 bayesSSM-0.7.1/bayesSSM/man/particle_filter.Rd | 34 bayesSSM-0.7.1/bayesSSM/man/particle_filter_common_params.Rd | 2 bayesSSM-0.7.1/bayesSSM/man/particle_filter_model_specification.Rd | 4 bayesSSM-0.7.1/bayesSSM/man/pmmh.Rd | 488 +-- bayesSSM-0.7.1/bayesSSM/man/resample_move_filter.Rd | 10 bayesSSM-0.7.1/bayesSSM/tests/testthat/test-ESS.R |only bayesSSM-0.7.1/bayesSSM/tests/testthat/test-auxiliary_filter.R | 108 bayesSSM-0.7.1/bayesSSM/tests/testthat/test-bootstrap_filter.R | 460 +-- bayesSSM-0.7.1/bayesSSM/tests/testthat/test-particle_filter_core.R | 216 - bayesSSM-0.7.1/bayesSSM/tests/testthat/test-pmmh.R | 1341 ++++----- bayesSSM-0.7.1/bayesSSM/tests/testthat/test-pmmh_tuning.R | 1422 +++++----- bayesSSM-0.7.1/bayesSSM/tests/testthat/test-resample_move_filter.R | 124 bayesSSM-0.7.1/bayesSSM/tests/testthat/test-resampling.R | 441 +-- bayesSSM-0.7.1/bayesSSM/tests/testthat/test-resampling_old.R | 300 +- bayesSSM-0.7.1/bayesSSM/tests/testthat/test-rhat.R | 164 - bayesSSM-0.7.1/bayesSSM/tests/testthat/test-summary.R | 52 bayesSSM-0.7.1/bayesSSM/tests/testthat/test-utils.R | 120 bayesSSM-0.7.1/bayesSSM/vignettes/bayesSSM.Rmd | 392 +- 54 files changed, 6587 insertions(+), 6579 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.3 dated 2025-09-05 and 1.6.4 dated 2025-12-06
DESCRIPTION | 8 +- MD5 | 64 ++++++++++---------- NEWS.md | 12 +++ R/dbi-connection.R | 22 +++++++ R/dbi-driver.R | 15 +++- R/dbi-result.R | 8 ++ R/dbi-table.R | 14 ++++ R/driver-databricks.R | 4 - R/driver-oracle.R | 4 - R/driver-redshift.R | 4 - R/driver-snowflake.R | 6 + R/odbc-package.R | 2 R/odbc.R | 3 build/vignette.rds |binary man/ConnectionAttributes.Rd | 18 +++++ man/OdbcConnection.Rd | 4 - man/databricks.Rd | 2 man/dbConnect-OdbcDriver-method.Rd | 9 ++ man/dbListTables-OdbcConnection-method.Rd | 4 - man/driver-Snowflake.Rd | 4 - man/odbc-package.Rd | 3 man/odbcListConfig.Rd | 2 man/odbcListDrivers.Rd | 2 man/odbcSetTransactionIsolationLevel.Rd | 4 - man/redshift.Rd | 2 man/snowflake.Rd | 2 src/cctz/src/time_zone_info.cc | 34 ++++++----- src/nanodbc/nanodbc.cpp | 2 src/odbc_result.cpp | 92 ++++++++++++++++-------------- src/odbc_result.h | 4 - src/r_types.h | 6 + tests/testthat/test-driver-oracle.R | 27 ++++++++ tests/testthat/test-driver-sql-server.R | 27 ++++++++ 33 files changed, 286 insertions(+), 128 deletions(-)
Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database.
<https://api.neotomadb.org/api-docs/>.
Author: Dominguez Vidana Socorro [aut, cre] ,
Simon Goring [aut]
Maintainer: Dominguez Vidana Socorro <dominguezvid@wisc.edu>
Diff between neotoma2 versions 1.0.9 dated 2025-11-25 and 1.0.10 dated 2025-12-06
DESCRIPTION | 8 +++---- MD5 | 36 ++++++++++++++++----------------- NEWS.md | 5 ++++ inst/doc/neotoma2-package.R | 32 +++++++++-------------------- inst/doc/neotoma2-package.Rmd | 34 +++++++++++-------------------- inst/doc/neotoma2-package.html | 8 +++---- tests/testthat/test_c.R | 1 tests/testthat/test_doi.R | 3 -- tests/testthat/test_filter.R | 4 ++- tests/testthat/test_get_contacts.R | 2 + tests/testthat/test_get_publications.R | 3 ++ tests/testthat/test_get_table.R | 13 +++++++---- tests/testthat/test_get_taxa.R | 1 tests/testthat/test_get_taxon.R | 1 tests/testthat/test_parse_location.R | 1 tests/testthat/test_sites.R | 21 ------------------- tests/testthat/test_specimens.R | 7 ------ tests/testthat/test_speleothems.R | 17 --------------- vignettes/neotoma2-package.Rmd | 34 +++++++++++-------------------- 19 files changed, 88 insertions(+), 143 deletions(-)
Title: Sample Generalized Random Dot Product Graphs in Linear Time
Description: Samples generalized random product graphs, a generalization of
a broad class of network models. Given matrices X, S, and Y with with
non-negative entries, samples a matrix with expectation X S Y^T and
independent Poisson or Bernoulli entries using the fastRG algorithm of
Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The
algorithm first samples the number of edges and then puts them down
one-by-one. As a result it is O(m) where m is the number of edges, a
dramatic improvement over element-wise algorithms that which require
O(n^2) operations to sample a random graph, where n is the number of
nodes.
Author: Alex Hayes [aut, cre, cph] ,
Karl Rohe [aut, cph],
Jun Tao [aut],
Xintian Han [aut],
Norbert Binkiewicz [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between fastRG versions 0.3.3 dated 2025-07-24 and 0.4.0 dated 2025-12-06
DESCRIPTION | 10 + MD5 | 70 +++++++------ NEWS.md | 30 +++++ R/directed_dcsbm.R | 69 ++++++++----- R/directed_erdos_renyi.R | 33 ++++-- R/directed_factor_model.R | 34 ++++-- R/expected-degrees.R | 37 +++---- R/expected-spectra.R | 37 ++++--- R/sample_edgelist.R | 47 +++++--- R/sample_igraph.R | 23 ++-- R/sample_sparse.R | 15 +- R/sample_tidygraph.R | 15 +- R/undirected_chung_lu.R | 19 ++- R/undirected_dcsbm.R | 131 +++++++++++++++++++----- R/undirected_erdos_renyi.R | 20 ++- R/undirected_factor_model.R | 36 ++++-- R/undirected_mmsbm.R | 46 +++++--- R/undirected_overlapping_sbm.R | 47 +++++--- R/undirected_planted_partition.R | 32 +++--- R/undirected_sbm.R | 36 +++++- README.md | 78 +++++++------- build |only inst |only man/dcsbm.Rd | 31 ++++- man/expected_edges.Rd | 8 - man/mmsbm.Rd | 2 man/planted_partition.Rd | 17 ++- man/sample_edgelist.matrix.Rd | 6 - man/sbm.Rd | 36 +++++- tests/testthat/test-allow_self_loops.R | 19 ++- tests/testthat/test-degree-scaling.R | 147 +++++++++------------------- tests/testthat/test-directedness.R | 3 tests/testthat/test-poisson_edges.R | 22 ++-- tests/testthat/test-population-spectra.R |only tests/testthat/test-retain-isolated-nodes.R | 4 tests/testthat/test-sampling-index-bug.R | 18 +++ vignettes |only 37 files changed, 732 insertions(+), 446 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.3.21 dated 2025-03-21 and 10.0.0 dated 2025-12-06
rswipl-10.0.0/rswipl/DESCRIPTION | 12 rswipl-10.0.0/rswipl/MD5 | 5195 +++++++++++----------- rswipl-10.0.0/rswipl/NEWS.md | 56 rswipl-10.0.0/rswipl/R/rswipl.R | 25 rswipl-10.0.0/rswipl/inst/patch/02-clib.patch | 4 rswipl-10.0.0/rswipl/inst/patch/03-cpp.patch | 4 rswipl-10.0.0/rswipl/inst/patch/04-cpp.patch | 4 rswipl-10.0.0/rswipl/inst/patch/patches.sh | 2 rswipl-10.0.0/rswipl/src/Makevars | 9 rswipl-10.0.0/rswipl/src/Makevars.win | 27 rswipl-10.0.0/rswipl/src/install.libs.R | 8 rswipl-10.0.0/rswipl/src/rswipl.cpp | 45 rswipl-10.0.0/rswipl/src/swipl |only rswipl-10.0.0/rswipl/tests/testthat/test-rswipl.R | 19 rswipl-9.3.21/rswipl/configure |only rswipl-9.3.21/rswipl/configure.win |only rswipl-9.3.21/rswipl/inst/patch/01-ssl.patch |only rswipl-9.3.21/rswipl/src/swipl-devel |only 18 files changed, 2792 insertions(+), 2618 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.7 dated 2025-10-16 and 2.3.8 dated 2025-12-06
GitStats-2.3.7/GitStats/tests/testthat/test-show_orgs.R |only GitStats-2.3.8/GitStats/DESCRIPTION | 8 GitStats-2.3.8/GitStats/MD5 | 141 +++++----- GitStats-2.3.8/GitStats/NAMESPACE | 1 GitStats-2.3.8/GitStats/NEWS.md | 8 GitStats-2.3.8/GitStats/R/EngineGraphQL.R | 14 GitStats-2.3.8/GitStats/R/EngineGraphQLGitHub.R | 16 - GitStats-2.3.8/GitStats/R/EngineGraphQLGitLab.R | 40 +- GitStats-2.3.8/GitStats/R/EngineRest.R | 16 - GitStats-2.3.8/GitStats/R/EngineRestGitHub.R | 12 GitStats-2.3.8/GitStats/R/EngineRestGitLab.R | 22 - GitStats-2.3.8/GitStats/R/GitHost.R | 22 - GitStats-2.3.8/GitStats/R/GitHostGitHub.R | 10 GitStats-2.3.8/GitStats/R/GitHostGitLab.R | 4 GitStats-2.3.8/GitStats/R/GitStats.R | 141 +++++----- GitStats-2.3.8/GitStats/R/get_commits.R | 14 GitStats-2.3.8/GitStats/R/get_files.R | 8 GitStats-2.3.8/GitStats/R/get_issues.R | 14 GitStats-2.3.8/GitStats/R/get_orgs.R | 6 GitStats-2.3.8/GitStats/R/get_release_logs.R | 10 GitStats-2.3.8/GitStats/R/get_repos.R | 34 -- GitStats-2.3.8/GitStats/R/get_users.R | 12 GitStats-2.3.8/GitStats/R/gitstats_functions.R | 12 GitStats-2.3.8/GitStats/R/message_handler.R | 2 GitStats-2.3.8/GitStats/R/set_host.R | 4 GitStats-2.3.8/GitStats/R/utils.R | 6 GitStats-2.3.8/GitStats/inst/doc/get_repos_with_code.R | 4 GitStats-2.3.8/GitStats/inst/doc/get_repos_with_code.Rmd | 4 GitStats-2.3.8/GitStats/inst/doc/get_repos_with_code.html | 4 GitStats-2.3.8/GitStats/man/get_commits.Rd | 8 GitStats-2.3.8/GitStats/man/get_commits_stats.Rd | 2 GitStats-2.3.8/GitStats/man/get_files.Rd | 4 GitStats-2.3.8/GitStats/man/get_issues.Rd | 8 GitStats-2.3.8/GitStats/man/get_issues_stats.Rd | 2 GitStats-2.3.8/GitStats/man/get_orgs.Rd | 2 GitStats-2.3.8/GitStats/man/get_release_logs.Rd | 6 GitStats-2.3.8/GitStats/man/get_repos.Rd | 8 GitStats-2.3.8/GitStats/man/get_repos_trees.Rd | 6 GitStats-2.3.8/GitStats/man/get_repos_urls.Rd | 8 GitStats-2.3.8/GitStats/man/get_storage.Rd | 2 GitStats-2.3.8/GitStats/man/get_users.Rd | 6 GitStats-2.3.8/GitStats/man/set_github_host.Rd | 2 GitStats-2.3.8/GitStats/man/set_gitlab_host.Rd | 2 GitStats-2.3.8/GitStats/man/show_hosts.Rd |only GitStats-2.3.8/GitStats/tests/testthat/_snaps/00-get_orgs-GitStats.md | 8 GitStats-2.3.8/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 2 GitStats-2.3.8/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 2 GitStats-2.3.8/GitStats/tests/testthat/_snaps/01-get_repos-GitStats.md | 1 GitStats-2.3.8/GitStats/tests/testthat/_snaps/02-get_commits-GitLab.md | 2 GitStats-2.3.8/GitStats/tests/testthat/_snaps/02-get_commits-GitStats.md | 10 GitStats-2.3.8/GitStats/tests/testthat/_snaps/03-get_files_structure-GitHub.md | 8 GitStats-2.3.8/GitStats/tests/testthat/_snaps/03-get_repos_trees-GitStats.md | 3 GitStats-2.3.8/GitStats/tests/testthat/_snaps/04-get_files_content-GitLab.md | 1 GitStats-2.3.8/GitStats/tests/testthat/_snaps/05-get_files.md | 9 GitStats-2.3.8/GitStats/tests/testthat/_snaps/06-get_issues-GitStats.md | 10 GitStats-2.3.8/GitStats/tests/testthat/_snaps/get_release-GitStats.md | 10 GitStats-2.3.8/GitStats/tests/testthat/_snaps/set_host.md | 28 - GitStats-2.3.8/GitStats/tests/testthat/helper-expect-responses.R | 4 GitStats-2.3.8/GitStats/tests/testthat/helper-fixtures.R | 8 GitStats-2.3.8/GitStats/tests/testthat/helper.R | 1 GitStats-2.3.8/GitStats/tests/testthat/test-00-api-requests.R | 3 GitStats-2.3.8/GitStats/tests/testthat/test-00-get_orgs-GitLab.R | 13 GitStats-2.3.8/GitStats/tests/testthat/test-00-get_orgs-GitStats.R | 7 GitStats-2.3.8/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 28 + GitStats-2.3.8/GitStats/tests/testthat/test-02-get_commits-GitStats.R | 13 GitStats-2.3.8/GitStats/tests/testthat/test-05-get_files.R | 18 + GitStats-2.3.8/GitStats/tests/testthat/test-06-get_issues-GitStats.R | 15 - GitStats-2.3.8/GitStats/tests/testthat/test-get_release-GitStats.R | 11 GitStats-2.3.8/GitStats/tests/testthat/test-get_storage.R | 14 GitStats-2.3.8/GitStats/tests/testthat/test-set_host.R | 30 +- GitStats-2.3.8/GitStats/tests/testthat/test-show.R |only GitStats-2.3.8/GitStats/tests/testthat/test-z-GitStats.R | 9 GitStats-2.3.8/GitStats/vignettes/get_repos_with_code.Rmd | 4 73 files changed, 556 insertions(+), 371 deletions(-)
Title: Flexible, Ensemble-Based Variable Selection with Potentially
Missing Data
Description: Perform variable selection in settings with possibly missing data
based on extrinsic (algorithm-specific) and intrinsic (population-level)
variable importance. Uses a Super Learner ensemble to estimate the
underlying prediction functions that give rise to estimates of variable importance.
For more information about the methods, please see Williamson and Huang (2024) <doi:10.1515/ijb-2023-0059>.
Author: Brian D. Williamson [aut, cre]
Maintainer: Brian D. Williamson <brian.d.williamson@kp.org>
Diff between flevr versions 0.0.4 dated 2023-11-30 and 0.0.5 dated 2025-12-06
flevr-0.0.4/flevr/man/flevr.Rd |only flevr-0.0.5/flevr/DESCRIPTION | 15 +- flevr-0.0.5/flevr/MD5 | 42 +++--- flevr-0.0.5/flevr/NEWS.md | 9 + flevr-0.0.5/flevr/R/biomarkers.R | 76 ++++++------ flevr-0.0.5/flevr/R/extract_importance_svm.R | 11 + flevr-0.0.5/flevr/R/extract_importance_xgboost.R | 12 + flevr-0.0.5/flevr/R/flevr-package.R | 7 - flevr-0.0.5/flevr/R/get_base_set.R | 13 +- flevr-0.0.5/flevr/README.md | 8 - flevr-0.0.5/flevr/build/partial.rdb |only flevr-0.0.5/flevr/build/vignette.rds |binary flevr-0.0.5/flevr/inst/doc/extrinsic_selection.R | 60 ++++----- flevr-0.0.5/flevr/inst/doc/extrinsic_selection.html | 10 - flevr-0.0.5/flevr/inst/doc/intrinsic_selection.R | 48 +++---- flevr-0.0.5/flevr/inst/doc/intrinsic_selection.html | 49 +++---- flevr-0.0.5/flevr/inst/doc/introduction_to_flevr.R | 8 - flevr-0.0.5/flevr/inst/doc/introduction_to_flevr.html | 2 flevr-0.0.5/flevr/man/extract_importance_svm.Rd | 7 - flevr-0.0.5/flevr/man/extract_importance_xgboost.Rd | 10 - flevr-0.0.5/flevr/man/figures |only flevr-0.0.5/flevr/man/flevr-package.Rd |only flevr-0.0.5/flevr/man/get_base_set.Rd | 2 flevr-0.0.5/flevr/tests/testthat/test-extrinsic_selection.R | 2 24 files changed, 208 insertions(+), 183 deletions(-)
Title: R Bindings to the Feather 'API'
Description: Read and write feather files, a lightweight binary columnar
data store designed for maximum speed.
Author: Hadley Wickham [aut, cre],
RStudio [cph],
LevelDB Authors [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between feather versions 0.3.5 dated 2019-09-14 and 0.4.0 dated 2025-12-06
feather-0.3.5/feather/R/RcppExports.R |only feather-0.3.5/feather/configure |only feather-0.3.5/feather/man/feather_metadata.Rd |only feather-0.3.5/feather/src |only feather-0.4.0/feather/DESCRIPTION | 22 - feather-0.4.0/feather/MD5 | 127 +--------- feather-0.4.0/feather/NAMESPACE | 18 - feather-0.4.0/feather/NEWS.md | 12 + feather-0.4.0/feather/R/class.R | 129 ----------- feather-0.4.0/feather/R/feather.R | 63 +---- feather-0.4.0/feather/R/utils.R | 17 - feather-0.4.0/feather/README.md | 2 feather-0.4.0/feather/man/feather.Rd | 13 - feather-0.4.0/feather/man/read_feather.Rd | 16 + feather-0.4.0/feather/tests/testthat.R | 8 feather-0.4.0/feather/tests/testthat/helper-roundtrip.R | 9 feather-0.4.0/feather/tests/testthat/test-class.R | 40 --- feather-0.4.0/feather/tests/testthat/test-overwrite.R | 2 feather-0.4.0/feather/tests/testthat/test-read.R | 8 feather-0.4.0/feather/tests/testthat/test-roundtrip-vector.R | 26 -- 20 files changed, 119 insertions(+), 393 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.6.2 dated 2025-11-18 and 1.7.0 dated 2025-12-06
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 13 +++ R/deployApp.R | 134 ++++++++++++++++++++++++++++++++----- R/http.R | 4 - man/deployApp.Rd | 16 ++++ tests/testthat/_snaps/deployApp.md | 36 +++++++++ tests/testthat/test-deployApp.R | 93 +++++++++++++++++++++++++ 8 files changed, 286 insertions(+), 30 deletions(-)
Title: Compiler for R
Description: Compile R functions annotated with type and shape
declarations for extremely fast performance and robust runtime
type checking. Supports both just-in-time (JIT) and ahead-of-time
(AOT) compilation. Compilation is performed by lowering R code to
Fortran.
Author: Tomasz Kalinowski [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between quickr versions 0.2.0 dated 2025-08-25 and 0.2.1 dated 2025-12-06
DESCRIPTION | 8 - MD5 | 53 +++++----- NEWS.md | 15 ++ R/c-wrapper.R | 105 ++++++++++++++++---- R/manifest.R | 7 - R/preprocess-lang.R | 47 ++++++++ R/r2f.R | 84 ++++++++++------ R/subroutine.R | 16 ++- tests/testthat/_snaps/add.md | 6 - tests/testthat/_snaps/dims2f.md | 6 - tests/testthat/_snaps/div-cast.md | 18 +-- tests/testthat/_snaps/div-mod.md | 8 - tests/testthat/_snaps/example-convolve.md | 4 tests/testthat/_snaps/example-heat_diffusion.md | 14 +- tests/testthat/_snaps/example-roll_mean.md | 6 - tests/testthat/_snaps/example-viterbi.md | 20 +-- tests/testthat/_snaps/hoist-mask.md | 4 tests/testthat/_snaps/logical.md | 22 ++-- tests/testthat/_snaps/loops.md | 14 +- tests/testthat/_snaps/matrix.md | 12 +- tests/testthat/_snaps/runif.md | 20 +-- tests/testthat/_snaps/size-constraint.md | 4 tests/testthat/_snaps/unary-intrinsics.md | 126 ++++++++++++++++++------ tests/testthat/_snaps/which.md | 10 - tests/testthat/test-as-double.R | 2 tests/testthat/test-loops.R | 1 tests/testthat/test-multiple-return.R |only tests/testthat/test-unary-intrinsics.R | 57 ++++++++++ 28 files changed, 482 insertions(+), 207 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>)
with or without multilevel or additive terms (Catalina, Bürkner, and
Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for
some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2025,
<doi:10.1007/s00180-024-01506-0>), and for many other regression models
(using the latent projection by Catalina, Bürkner, and Vehtari, 2021,
<doi:10.48550/arXiv.2109.04702>, which can also be applied to most of the
former models). The package is compatible with the 'rstanarm' and 'brms'
packages, but other reference models can also be used. See the vignettes and
the documentation for more information and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [aut],
Osvaldo Martin [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb],
Brian Sullivan [ctb], [...truncated...]
Maintainer: Osvaldo Martin <aloctavodia@gmail.com>
Diff between projpred versions 2.9.1 dated 2025-10-28 and 2.10.0 dated 2025-12-06
DESCRIPTION | 20 - MD5 | 92 ++++---- NEWS.md | 14 + R/cv_varsel.R | 17 + R/divergence_minimizers.R | 6 R/extend_family.R | 45 +++- R/formula.R | 10 R/latent.R | 20 + R/methods.R | 27 +- R/misc.R | 7 R/projfun.R | 2 R/refmodel.R | 3 R/summary_funs.R | 11 R/varsel.R | 11 build/partial.rdb |binary build/vignette.rds |binary inst/doc/latent.R | 268 ++++++++++++++++++++++++ inst/doc/latent.Rmd | 318 ++++++++++++++++++++++++++++ inst/doc/latent.html | 409 +++++++++++++++++++++++++++++++++---- inst/doc/projpred.R | 14 - inst/doc/projpred.Rmd | 25 +- inst/doc/projpred.html | 93 ++++---- man/as.matrix.projection.Rd | 2 man/as_draws_matrix.projection.Rd | 2 man/cv_varsel.Rd | 2 man/extend_family.Rd | 28 ++ man/figures/logo.svg | 97 -------- man/force_search_terms.Rd | 2 man/performances.Rd | 2 man/plot.cv_proportions.Rd | 2 man/plot.vsel.Rd | 2 man/pred-projection.Rd | 2 man/predictor_terms.Rd | 2 man/project.Rd | 2 man/refmodel-init-get.Rd | 2 man/run_cvfun.Rd | 2 man/suggest_size.Rd | 2 man/summary.vsel.Rd | 2 man/varsel.Rd | 6 tests/testthat/helpers/testers.R | 3 tests/testthat/test_augdat.R | 2 tests/testthat/test_latent.R | 35 +++ tests/testthat/test_methods_vsel.R | 33 +- tests/testthat/test_proj_predfun.R | 9 tests/testthat/test_refmodel.R | 12 - vignettes/latent.Rmd | 318 ++++++++++++++++++++++++++++ vignettes/projpred.Rmd | 25 +- 47 files changed, 1671 insertions(+), 337 deletions(-)
Title: Armadillo Client for the Armadillo Service
Description: A set of functions to manage data shared on a
'MOLGENIS Armadillo' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
Morris Swertz [aut] ,
Tim Cadman [aut]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between MolgenisArmadillo versions 2.9.1 dated 2025-06-13 and 2.9.3 dated 2025-12-06
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS.md | 3 R/utils.R | 4 + inst/doc/MolgenisArmadillo.Rmd | 2 inst/doc/MolgenisArmadillo.html | 5 - tests/testthat/test-object.R | 140 ++++++++++++++++++++-------------------- tests/testthat/test-utils.R | 9 +- vignettes/MolgenisArmadillo.Rmd | 2 9 files changed, 98 insertions(+), 91 deletions(-)
More information about MolgenisArmadillo at CRAN
Permanent link
Title: Laplace Factor Model Analysis and Evaluation
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between LFM versions 0.3.2 dated 2025-10-10 and 0.3.3 dated 2025-12-06
DESCRIPTION | 10 +- MD5 | 14 ++- NAMESPACE | 12 ++- R/DGulPC.R |only R/DPPC.R |only R/Ftest.R | 207 +++++++++++++++++++++++++++++++++++++++++++++++----- R/factor.tests.R |only man/DGulPC.Rd |only man/DPPC.Rd |only man/Ftest.Rd | 18 ++++ man/factor.tests.Rd |only 11 files changed, 230 insertions(+), 31 deletions(-)
Title: Transforms Institutional Data into Text Files for IPEDS
Automated Import/Upload
Description: Starting from user-supplied institutional data, these scripts
transform, aggregate, and reshape the information to produce
key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System)
through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes.
Final files are saved locally to a location of the user's choice.
User-friendly readable files can also be produced for purposes of data review and validation.
Author: Alison Lanski [aut, cre],
Shiloh Fling [aut],
Edwin Welch [aut]
Maintainer: Alison Lanski <alanski@nd.edu>
Diff between IPEDSuploadables versions 2.11.0 dated 2025-09-09 and 3.0.0 dated 2025-12-06
DESCRIPTION | 18 +++---- MD5 | 62 +++++++++++++++++++-------- NAMESPACE | 9 +++ NEWS.md | 3 + R/adm_students.R |only R/create_dummy_data_adm.R |only R/make_adm_part_B.R |only R/make_adm_part_C.R |only R/make_adm_part_D.R |only R/make_adm_part_F.R |only R/make_adm_part_G.R |only R/make_adm_part_H.R |only R/prep_adm_data_frame.R |only R/produce_adm_report.R |only R/specs_ADM.R |only README.md | 3 - build/vignette.rds |binary data/adm_students.rda |only data/part_outputs.rda |binary data/specs_ADM.rda |only data/specs_COM.rda |binary inst/doc/howto_overall_ipedsuploadables.Rmd | 18 +++++-- inst/doc/howto_overall_ipedsuploadables.html | 57 ++++++++++++++++-------- inst/doc/howto_use_autoformat.Rmd | 7 --- inst/doc/howto_use_autoformat.html | 15 ++---- inst/doc/setup_for_admissions.R |only inst/doc/setup_for_admissions.Rmd |only inst/doc/setup_for_admissions.html |only inst/doc/setup_for_completions.html | 14 ++++++ man/IPEDSuploadables-package.Rd | 3 - man/adm_students.Rd |only man/create_dummy_data_adm.Rd |only man/make_adm_part_B.Rd |only man/make_adm_part_C.Rd |only man/make_adm_part_D.Rd |only man/make_adm_part_F.Rd |only man/make_adm_part_G.Rd |only man/make_adm_part_H.Rd |only man/prep_adm_data_frame.Rd |only man/produce_adm_report.Rd |only man/specs_ADM.Rd |only tests/testthat/test-part-outputs.R | 24 ++++++++++ tests/testthat/test-prep-scripts.R | 14 ++++++ vignettes/howto_overall_ipedsuploadables.Rmd | 18 +++++-- vignettes/howto_use_autoformat.Rmd | 7 --- vignettes/setup_for_admissions.Rmd |only 46 files changed, 193 insertions(+), 79 deletions(-)
More information about IPEDSuploadables at CRAN
Permanent link
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb] ,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between insight versions 1.4.3 dated 2025-11-24 and 1.4.4 dated 2025-12-06
DESCRIPTION | 6 MD5 | 24 +- NEWS.md | 9 R/get_data.R | 2 R/is_converged.R | 58 ++++- inst/WORDLIST | 3 inst/doc/display.html | 370 ++++++++++++++++++------------------ man/is_converged.Rd | 27 ++ tests/testthat/test-fixest.R | 8 tests/testthat/test-get_predicted.R | 7 tests/testthat/test-is_converged.R | 17 + tests/testthat/test-panelr.R | 10 tests/testthat/test-tidymodels.R | 2 13 files changed, 326 insertions(+), 217 deletions(-)
Title: Supplements the 'gtsummary' Package for Pharmaceutical Reporting
Description: Tables summarizing clinical trial results are often complex
and require detailed tailoring prior to submission to a health
authority. The 'crane' package supplements the functionality of the
'gtsummary' package for creating these often highly bespoke tables in
the pharmaceutical industry.
Author: Daniel D. Sjoberg [aut, cre] ,
Emily de la Rua [aut] ,
Davide Garolini [aut],
Abinaya Yogasekaram [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between crane versions 0.2.0 dated 2025-08-29 and 0.3.0 dated 2025-12-06
DESCRIPTION | 10 MD5 | 104 +++++----- NAMESPACE | 8 NEWS.md | 22 ++ R/add_difference_row.R |only R/add_hierarchical_count_row.R | 2 R/import-standalone-check_pkg_installed.R | 95 +++------ R/import-standalone-cli_call_env.R | 7 R/label_roche.R | 66 +++++- R/reexport.R | 4 R/tbl_baseline_chg.R | 42 ++-- R/tbl_hierarchical_rate_and_count.R | 22 +- R/tbl_listing.R | 8 R/tbl_null_report.R |only R/tbl_roche_summary.R | 17 + R/tbl_shift.R | 7 R/tbl_survfit_quantiles.R | 12 - R/tbl_survfit_times.R | 17 + R/theme_gtsummary_roche.R | 9 R/utils.R | 46 ++++ README.md | 17 + inst/WORDLIST | 1 man/figures/README-tbl_print_simple-1.png |binary man/label_roche.Rd | 40 +++ man/reexports.Rd | 4 man/tbl_baseline_chg.Rd | 4 man/tbl_hierarchical_rate_and_count.Rd | 10 man/tbl_hierarchical_rate_by_grade.Rd | 2 man/tbl_listing.Rd | 2 man/tbl_null_report.Rd |only man/tbl_roche_summary.Rd | 3 man/tbl_shift.Rd | 6 man/tbl_survfit_quantiles.Rd | 8 man/tbl_survfit_times.Rd | 64 +++++- man/theme_gtsummary_roche.Rd | 1 tests/testthat/_snaps/add_difference_row.md |only tests/testthat/_snaps/tbl_baseline_chg.md | 156 +++++++-------- tests/testthat/_snaps/tbl_hierarchical_rate_and_count.md | 2 tests/testthat/_snaps/tbl_listing.md | 61 +++-- tests/testthat/_snaps/tbl_roche_summary.md | 23 ++ tests/testthat/_snaps/tbl_shift.md | 98 ++++----- tests/testthat/_snaps/tbl_survfit_quantiles.md | 3 tests/testthat/_snaps/tbl_survfit_times.md | 28 +- tests/testthat/_snaps/theme_gtsummary_roche.md | 13 - tests/testthat/test-add_difference_row.R |only tests/testthat/test-label_roche.R | 14 + tests/testthat/test-tbl_baseline_chg.R | 16 + tests/testthat/test-tbl_hierarchical_rate_and_count.R | 11 - tests/testthat/test-tbl_hierarchical_rate_by_grade.R | 2 tests/testthat/test-tbl_listing.R | 26 +- tests/testthat/test-tbl_null_report.R |only tests/testthat/test-tbl_roche_summary.R | 19 + tests/testthat/test-tbl_shift.R | 101 +++++---- tests/testthat/test-tbl_survfit_quantiles.R | 4 tests/testthat/test-tbl_survfit_times.R | 2 tests/testthat/test-theme_gtsummary_roche.R | 5 56 files changed, 794 insertions(+), 450 deletions(-)
Title: Graphical Web-Framework for Data Manipulation and Visualization
Description: A framework for data manipulation and visualization using a
web-based point and click user interface where analysis pipelines are decomposed into re-usable and parameterizable blocks.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut],
Christoph Sax [aut],
Karma Tarap [ctb],
John Coene [ctb],
Bristol Myers Squibb [fnd]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.core versions 0.1.0 dated 2025-05-20 and 0.1.1 dated 2025-12-06
blockr.core-0.1.0/blockr.core/R/aaa.R |only blockr.core-0.1.0/blockr.core/R/pkg.R |only blockr.core-0.1.0/blockr.core/R/plugin-serialize.R |only blockr.core-0.1.0/blockr.core/R/registry.R |only blockr.core-0.1.0/blockr.core/R/utils-json.R |only blockr.core-0.1.0/blockr.core/R/zzz.R |only blockr.core-0.1.0/blockr.core/man/figures |only blockr.core-0.1.0/blockr.core/tests/testthat/_snaps/serve |only blockr.core-0.1.0/blockr.core/tests/testthat/test-json.R |only blockr.core-0.1.0/blockr.core/tests/testthat/test-plugin-serialize.R |only blockr.core-0.1.0/blockr.core/tests/testthat/test-registry.R |only blockr.core-0.1.0/blockr.core/tests/testthat/test-serve.R |only blockr.core-0.1.1/blockr.core/DESCRIPTION | 32 blockr.core-0.1.1/blockr.core/MD5 | 278 +-- blockr.core-0.1.1/blockr.core/NAMESPACE | 202 ++ blockr.core-0.1.1/blockr.core/NEWS.md | 34 blockr.core-0.1.1/blockr.core/R/block-class.R | 234 -- blockr.core-0.1.1/blockr.core/R/block-registry.R |only blockr.core-0.1.1/blockr.core/R/block-server.R | 388 ++-- blockr.core-0.1.1/blockr.core/R/block-ui.R | 2 blockr.core-0.1.1/blockr.core/R/blocks-class.R | 17 blockr.core-0.1.1/blockr.core/R/board-class.R | 188 +- blockr.core-0.1.1/blockr.core/R/board-option.R |only blockr.core-0.1.1/blockr.core/R/board-options.R | 520 +++--- blockr.core-0.1.1/blockr.core/R/board-plugins.R | 121 + blockr.core-0.1.1/blockr.core/R/board-server.R | 809 ++++++---- blockr.core-0.1.1/blockr.core/R/board-ui.R | 133 - 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blockr.core-0.1.1/blockr.core/inst/doc/create-block.R | 2 blockr.core-0.1.1/blockr.core/inst/doc/create-block.html | 182 +- blockr.core-0.1.1/blockr.core/inst/doc/create-block.qmd | 2 blockr.core-0.1.1/blockr.core/inst/doc/extend-blockr.R | 20 blockr.core-0.1.1/blockr.core/inst/doc/extend-blockr.html | 254 ++- blockr.core-0.1.1/blockr.core/inst/doc/extend-blockr.qmd | 22 blockr.core-0.1.1/blockr.core/inst/doc/get-started.html | 180 +- blockr.core-0.1.1/blockr.core/inst/doc/testing-blocks.html | 180 +- blockr.core-0.1.1/blockr.core/man/assertions.Rd |only blockr.core-0.1.1/blockr.core/man/block_server.Rd | 15 blockr.core-0.1.1/blockr.core/man/blockr_abort.Rd |only blockr.core-0.1.1/blockr.core/man/blockr_option.Rd | 5 blockr.core-0.1.1/blockr.core/man/blockr_ser.Rd | 40 blockr.core-0.1.1/blockr.core/man/board_blocks.Rd | 58 blockr.core-0.1.1/blockr.core/man/board_server.Rd | 16 blockr.core-0.1.1/blockr.core/man/board_ui.Rd | 44 blockr.core-0.1.1/blockr.core/man/chr_ply.Rd |only blockr.core-0.1.1/blockr.core/man/edit_block.Rd | 8 blockr.core-0.1.1/blockr.core/man/export_code.Rd |only blockr.core-0.1.1/blockr.core/man/generate_code.Rd | 2 blockr.core-0.1.1/blockr.core/man/get_session.Rd |only blockr.core-0.1.1/blockr.core/man/new_block.Rd | 13 blockr.core-0.1.1/blockr.core/man/new_board.Rd | 6 blockr.core-0.1.1/blockr.core/man/new_board_options.Rd | 227 ++ blockr.core-0.1.1/blockr.core/man/new_file_block.Rd | 8 blockr.core-0.1.1/blockr.core/man/new_link.Rd | 14 blockr.core-0.1.1/blockr.core/man/new_plugin.Rd | 28 blockr.core-0.1.1/blockr.core/man/new_stack.Rd | 14 blockr.core-0.1.1/blockr.core/man/new_text_block.Rd |only blockr.core-0.1.1/blockr.core/man/new_transform_block.Rd | 20 blockr.core-0.1.1/blockr.core/man/notify_user.Rd | 5 blockr.core-0.1.1/blockr.core/man/preserve_board.Rd | 18 blockr.core-0.1.1/blockr.core/man/rand_names.Rd | 64 blockr.core-0.1.1/blockr.core/man/register_block.Rd | 37 blockr.core-0.1.1/blockr.core/man/serve.Rd | 25 blockr.core-0.1.1/blockr.core/man/set_names.Rd |only blockr.core-0.1.1/blockr.core/man/stack_ui.Rd | 42 blockr.core-0.1.1/blockr.core/man/testing.Rd |only blockr.core-0.1.1/blockr.core/man/write_log.Rd | 62 blockr.core-0.1.1/blockr.core/tests/testthat/_snaps/block-class.md | 4 blockr.core-0.1.1/blockr.core/tests/testthat/_snaps/blocks-class.md | 4 blockr.core-0.1.1/blockr.core/tests/testthat/_snaps/board-class.md | 57 blockr.core-0.1.1/blockr.core/tests/testthat/_snaps/board-option.md |only blockr.core-0.1.1/blockr.core/tests/testthat/_snaps/utils-serve |only blockr.core-0.1.1/blockr.core/tests/testthat/helpers.R | 58 blockr.core-0.1.1/blockr.core/tests/testthat/setup.R |only blockr.core-0.1.1/blockr.core/tests/testthat/test-block-class.R | 9 blockr.core-0.1.1/blockr.core/tests/testthat/test-block-registry.R |only blockr.core-0.1.1/blockr.core/tests/testthat/test-block-server.R | 212 ++ blockr.core-0.1.1/blockr.core/tests/testthat/test-board-class.R | 109 + blockr.core-0.1.1/blockr.core/tests/testthat/test-board-option.R |only blockr.core-0.1.1/blockr.core/tests/testthat/test-board-options.R |only blockr.core-0.1.1/blockr.core/tests/testthat/test-board-plugins.R | 11 blockr.core-0.1.1/blockr.core/tests/testthat/test-board-server.R | 276 +++ blockr.core-0.1.1/blockr.core/tests/testthat/test-file-browser.R | 15 blockr.core-0.1.1/blockr.core/tests/testthat/test-plot-scatter.R | 4 blockr.core-0.1.1/blockr.core/tests/testthat/test-plugin-block.R | 53 blockr.core-0.1.1/blockr.core/tests/testthat/test-plugin-blocks.R | 16 blockr.core-0.1.1/blockr.core/tests/testthat/test-plugin-code.R | 32 blockr.core-0.1.1/blockr.core/tests/testthat/test-plugin-links.R | 46 blockr.core-0.1.1/blockr.core/tests/testthat/test-plugin-notification.R | 86 - 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Title: Biostatistics and Clinical Data Analysis
Description: Biostatistical and clinical data analysis, including descriptive
statistics, exploratory data analysis, sample size and power calculations,
statistical inference, and data visualization. Normality tests are
implemented following Mishra et al. (2019) <doi:10.4103/aca.ACA_157_18>,
omnibus test procedures are based on Blanca et al. (2017)
<doi:10.3758/s13428-017-0918-2> and Field et al. (2012, ISBN:9781446200469),
while sample size and power calculation methods follow Chow et al. (2017)
<doi:10.1201/9781315183084>.
Author: Sebastian Quirarte-Justo [aut, cre] ,
Angela Carolina Montano-Ruiz [aut] ,
Jose Maria Torres-Arellano [aut] ,
Laboratorios Sophia S.A. de C.V. [cph, fnd]
Maintainer: Sebastian Quirarte-Justo <sebastian.quirarte@sophia.com.mx>
Diff between biostats versions 1.0.0 dated 2025-11-13 and 1.1.0 dated 2025-12-06
DESCRIPTION | 8 +++--- MD5 | 24 +++++++++--------- NAMESPACE | 2 - NEWS.md | 18 +++++++++++++ R/normality.R | 27 +++++++++++++------- R/plot_bar.R | 8 ++++++ R/summary_table.R | 7 +++-- R/util-summary_table.R | 4 +-- README.md | 39 +++++++++++++++--------------- man/figures/README-unnamed-chunk-24-2.png |binary man/normality.Rd | 10 ++++++- man/summary_table.Rd | 2 - tests/testthat/test-normality.R | 2 - 13 files changed, 98 insertions(+), 53 deletions(-)
Title: Dynamic Model of Ammonia Emission from Field-Applied Manure
Description: An implementation of the ALFAM2 dynamic emission model for ammonia volatilization from field-applied animal slurry (manure with dry matter below about 15%). The model can be used to predict cumulative emission and emission rate of ammonia following field application of slurry. Predictions may be useful for emission inventory calculations, fertilizer management, assessment of mitigation strategies, or research aimed at understanding ammonia emission. Default parameter sets include effects of application method, slurry composition, and weather. The model structure is based on a simplified representation of the physical-chemical slurry-soil-atmosphere system. More information is available via citation("ALFAM2").
Author: Sasha D. Hafner [aut, cre] ,
Christoph Haeni [aut] ,
Roland Fuss [aut] ,
Frederik Dalby [aut] ,
Johanna Pedersen [ctb] ,
Valdemar Petersen [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@bce.au.dk>
Diff between ALFAM2 versions 4.2 dated 2024-11-08 and 4.2.14 dated 2025-12-06
DESCRIPTION | 21 +++--- MD5 | 32 +++++---- NAMESPACE | 2 NEWS.md | 10 ++ R/aggregate2.R |only R/alfam2.R | 24 +++---- R/alfami.R |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 5 - inst/doc/ALFAM2-start.R | 150 ++++++++++++++++++++++---------------------- inst/doc/ALFAM2-start.Rmd | 14 +--- inst/doc/ALFAM2-start.html | 76 +++++++++++----------- inst/tinytest/test_alfam2.R | 5 + man/alfam2.Rd | 16 ++-- man/alfam2pars.Rd | 10 +- man/alfami.Rd |only vignettes/ALFAM2-start.Rmd | 14 +--- vignettes/dev |only 19 files changed, 199 insertions(+), 180 deletions(-)
Title: A Two-Stage Estimation Approach to Cox Regression Using M-Spline
Function
Description: Implements a two-stage estimation approach for Cox
regression using five-parameter M-spline functions to model the baseline hazard. It allows
for flexible hazard shapes and model selection based on log-likelihood criteria as described in
Teranishi et al.(2025).
In addition, the package provides functions for constructing and evaluating B-spline copulas
based on five M-spline or I-spline basis functions, allowing users to flexibly model and
compute bivariate dependence structures. Both the copula function and its density can be evaluated.
Furthermore, the package supports computation of dependence measures such as Kendall's tau and
Spearman's rho, derived analytically from the copula parameters.
Author: Ren Teranishi [aut, cre]
Maintainer: Ren Teranishi <ren.teranishi1227@gmail.com>
Diff between splineCox versions 0.0.5 dated 2025-07-10 and 0.0.7 dated 2025-12-06
DESCRIPTION | 10 +- MD5 | 24 ++--- NAMESPACE | 8 + NEWS.md | 9 + R/splineCoxreg1.R | 21 ++-- R/splineCoxreg2.R | 23 ++-- R/splinecopula.R | 124 +++++++++++++++----------- R/splinecopulasim.R |only inst/WORDLIST | 7 + inst/doc/splineCox-introduction.html | 13 ++ man/spline.copula.Rd | 105 +++++++++++++--------- man/spline.copula.simu.Rd |only man/splineCox.reg1.Rd | 163 ++++++++++++++++++---------------- man/splineCox.reg2.Rd | 165 +++++++++++++++++------------------ 14 files changed, 380 insertions(+), 292 deletions(-)
Title: Load Configuration Values
Description: A simple approach to configuring R projects with different
parameter values. Configurations are specified using a reduced subset of base
R and parsed accordingly.
Author: Tim Taylor [aut, cre, cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ronfig versions 0.0.6 dated 2025-11-21 and 0.0.7 dated 2025-12-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/load_config.R | 2 +- tests/testthat/test-load_config.R | 30 ++++++++++++++++++++++++++++++ 5 files changed, 42 insertions(+), 8 deletions(-)
Title: Gradient-Based Recognition of Spatial Patterns in Environmental
Data
Description: Provides algorithms for detection of spatial patterns from oceanographic data using image processing methods based on Gradient Recognition.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between grec versions 1.6.2 dated 2025-09-04 and 1.6.3 dated 2025-12-06
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 3 +++ R/grec-package.R | 2 +- build/partial.rdb |binary 6 files changed, 15 insertions(+), 12 deletions(-)
Title: Add Uncertainty to Data Visualisations
Description: A 'ggplot2' extension for visualising uncertainty with the goal
of signal suppression. Usually, uncertainty visualisation focuses on
expressing uncertainty as a distribution or probability, whereas
'ggdibbler' differentiates itself by viewing an uncertainty
visualisation as an adjustment to an existing graphic that
incorporates the inherent uncertainty in the estimates. You provide
the code for an existing plot, but replace any of the variables with a
vector of distributions, and it will convert the visualisation into
it's signal suppression counterpart.
Author: Harriet Mason [aut, cre] ,
Dianne Cook [aut, ths] ,
Sarah Goodwin [aut, ths] ,
Susan VanderPlas [aut, ths]
Maintainer: Harriet Mason <harriet.m.mason@gmail.com>
Diff between ggdibbler versions 0.1.0 dated 2025-07-31 and 0.6.1 dated 2025-12-06
ggdibbler-0.1.0/ggdibbler/R/geom_sf_sample.R |only ggdibbler-0.1.0/ggdibbler/R/scale_type.R |only ggdibbler-0.1.0/ggdibbler/R/stat_sample.R |only ggdibbler-0.1.0/ggdibbler/inst/bivar.R |only ggdibbler-0.1.0/ggdibbler/inst/dibble.R |only ggdibbler-0.1.0/ggdibbler/inst/doc/ggdibbler-vignette.R |only ggdibbler-0.1.0/ggdibbler/inst/doc/ggdibbler-vignette.Rmd |only ggdibbler-0.1.0/ggdibbler/inst/doc/ggdibbler-vignette.html |only ggdibbler-0.1.0/ggdibbler/inst/geom.R |only ggdibbler-0.1.0/ggdibbler/inst/ggdibbler-package.R |only ggdibbler-0.1.0/ggdibbler/inst/listofdists.R |only ggdibbler-0.1.0/ggdibbler/inst/meanplot.R |only ggdibbler-0.1.0/ggdibbler/inst/meanvarplot.R |only ggdibbler-0.1.0/ggdibbler/inst/oldvsup.R |only ggdibbler-0.1.0/ggdibbler/inst/sampleplot.R |only ggdibbler-0.1.0/ggdibbler/inst/stat.R |only ggdibbler-0.1.0/ggdibbler/inst/subdividedebug.R |only ggdibbler-0.1.0/ggdibbler/inst/test-bivar.R |only ggdibbler-0.1.0/ggdibbler/inst/testcolour.R |only ggdibbler-0.1.0/ggdibbler/inst/vsup.R |only ggdibbler-0.1.0/ggdibbler/tests/testthat/_snaps/geom_sf_sample |only ggdibbler-0.1.0/ggdibbler/tests/testthat/_snaps/stat_sample |only ggdibbler-0.1.0/ggdibbler/tests/testthat/test-geom_sf_sample.R |only ggdibbler-0.1.0/ggdibbler/tests/testthat/test-stat_sample.R |only ggdibbler-0.1.0/ggdibbler/vignettes/ggdibbler-vignette.Rmd |only ggdibbler-0.6.1/ggdibbler/DESCRIPTION | 33 ggdibbler-0.6.1/ggdibbler/MD5 | 380 +++++++++- ggdibbler-0.6.1/ggdibbler/NAMESPACE | 223 +++++ ggdibbler-0.6.1/ggdibbler/NEWS.md | 121 +++ ggdibbler-0.6.1/ggdibbler/R/data.R | 154 ++++ ggdibbler-0.6.1/ggdibbler/R/geom-abline-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-bar-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-bin2d-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-boxplot-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-col-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-contour-sample.R |only ggdibbler-0.6.1/ggdibbler/R/geom-count-sample.R |only 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ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-linerange-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-path-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-point-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-pointrange-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-polygon-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-quantile-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-raster-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-rect-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-ribbon-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-rug-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-segment-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-sf-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-smooth-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-spoke-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-text-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-tile-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-violin-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-geom-vline-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-nest-position.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-nested-position-dodge.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-nested-position-stack.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-position-identity-nested.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-position-nesting-utils.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-position-subdivide.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-scale-continuous-distribution.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-scale-type.R | 10 ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-connect-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-ecdf-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-ellipse-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-manual-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-qq-line-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-qq-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-sf-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-summary-2d-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-summary-bin-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-summary-hex-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-summary-sample.R |only ggdibbler-0.6.1/ggdibbler/tests/testthat/test-stat-unique-sample.R |only ggdibbler-0.6.1/ggdibbler/vignettes/A_how-to-guide.Rmd |only ggdibbler-0.6.1/ggdibbler/vignettes/B_ggdibbler-philosophy.Rmd |only ggdibbler-0.6.1/ggdibbler/vignettes/C_random-plots.Rmd |only ggdibbler-0.6.1/ggdibbler/vignettes/D_extender-info.Rmd |only 312 files changed, 880 insertions(+), 96 deletions(-)
Title: Distributed Laplace Factor Model
Description: Distributed estimation method is based on a Laplace factor model to solve the estimates of load and specific variance. The philosophy of the package is described in Guangbao Guo. (2022). <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between DLFM versions 0.1.1 dated 2025-11-14 and 0.1.4 dated 2025-12-06
DESCRIPTION | 9 -- MD5 | 14 ++- NAMESPACE | 4 R/DSAPC.R |only R/Dfactor.tests.R |only R/Ftest.R | 209 ++++++++++++++++++++++++++++++++++++++++++++++----- R/SAPC.R |only man/DSAPC.Rd |only man/Dfactor.tests.Rd |only man/Ftest.Rd | 18 +++- man/SAPC.Rd |only 11 files changed, 222 insertions(+), 32 deletions(-)
Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance, phylogenetic trees), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution, biostratigraphy or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.7.0 dated 2025-11-24 and 0.7.1 dated 2025-12-06
DESCRIPTION | 8 +-- MD5 | 77 ++++++++++++++++++------------- NAMESPACE | 5 ++ NEWS.md | 14 +++++ R/apply_niche.R | 9 +++ R/apply_taphonomy.R | 18 ++++++- R/as_char_mat.R |only R/is_char_mat.R |only R/scenarioA.R | 11 ++-- R/strat_filter.R |only build/vignette.rds |binary data/scenarioA.rda |binary inst/WORDLIST | 12 ++++ inst/doc/FossilSim_integration.html | 17 +++--- inst/doc/StratPal.Rmd | 6 +- inst/doc/StratPal.html | 37 ++++++++------ inst/doc/StratPal_docs.Rmd | 27 ++++++++++ inst/doc/StratPal_docs.html | 33 +++++++++++++ inst/doc/advanced_functionality.Rmd | 4 + inst/doc/advanced_functionality.html | 11 +++- inst/doc/event_data.R | 2 inst/doc/event_data.Rmd | 6 -- inst/doc/event_data.html | 40 ++++++---------- inst/doc/paleoTS_functionality.html | 12 ++-- inst/doc/phenotypic_evolution.html | 10 ++-- inst/doc/stratigraphic_architecture.R |only inst/doc/stratigraphic_architecture.Rmd |only inst/doc/stratigraphic_architecture.html |only man/apply_niche.Rd | 3 - man/apply_taphonomy.Rd | 4 + man/as_char_mat.Rd |only man/is_char_mat.Rd |only man/scenarioA.Rd | 13 ++--- man/strat_filter.Rd |only tests/testthat/test_apply_niche.R | 14 +++++ tests/testthat/test_apply_taphonomy.R | 23 +++++++++ tests/testthat/test_as_char_mat.R |only tests/testthat/test_is_char_mat.R |only tests/testthat/test_strat_filter.R |only vignettes/StratPal.Rmd | 6 +- vignettes/StratPal_docs.Rmd | 27 ++++++++++ vignettes/advanced_functionality.Rmd | 4 + vignettes/event_data.Rmd | 6 -- vignettes/platform_production_curve.png |only vignettes/platform_profile.png |only vignettes/platform_summary.png |only vignettes/platform_wheeler_diagram.png |only vignettes/stratigraphic_architecture.Rmd |only 48 files changed, 331 insertions(+), 128 deletions(-)
Title: File Sharing Shiny Module
Description: Shiny module for easily sharing files between users. Admin can add, remove, edit and download file.
User can only download file. It's also possible to manage files using R functions directly.
Author: Benoit Thieurmel [aut, cre],
Thibaut Dubois [aut],
Jeremy Boussaguet [ctb]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>
Diff between shinydrive versions 0.1.3 dated 2022-09-29 and 0.1.5 dated 2025-12-06
shinydrive-0.1.3/shinydrive/inst/demo_app/rsconnect |only shinydrive-0.1.5/shinydrive/DESCRIPTION | 16 shinydrive-0.1.5/shinydrive/MD5 | 29 shinydrive-0.1.5/shinydrive/NAMESPACE | 5 shinydrive-0.1.5/shinydrive/NEWS.md | 8 shinydrive-0.1.5/shinydrive/R/shiny_module.R | 759 ++++++++--- shinydrive-0.1.5/shinydrive/R/utils.R | 20 shinydrive-0.1.5/shinydrive/R/yaml_tools.R | 750 ++++++++++ shinydrive-0.1.5/shinydrive/README.md | 3 shinydrive-0.1.5/shinydrive/inst/demo_app/ui.R | 10 shinydrive-0.1.5/shinydrive/inst/demo_app/www/css/custom.css | 10 shinydrive-0.1.5/shinydrive/inst/translate/translate.csv | 15 shinydrive-0.1.5/shinydrive/man/combine_yaml_recursive.Rd |only shinydrive-0.1.5/shinydrive/man/delete_config.Rd |only shinydrive-0.1.5/shinydrive/man/delete_old_config.Rd |only shinydrive-0.1.5/shinydrive/man/file_manager.Rd | 246 +-- shinydrive-0.1.5/shinydrive/man/init_config.Rd |only shinydrive-0.1.5/shinydrive/man/shiny_drive_module.Rd | 166 +- 18 files changed, 1624 insertions(+), 413 deletions(-)
Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.11.3 dated 2025-01-25 and 0.11.5 dated 2025-12-06
DESCRIPTION | 15 MD5 | 378 +++++----- NEWS.md | 16 R/loglike_at.R | 4 R/loglike_at_user.R | 4 R/semlbci.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary tests/testthat/test-check_sem_out.R | 3 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_cfa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_cfa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_pa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_pa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_sem.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_mg_std_sem_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_cfa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_cfa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_pa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_pa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_sem.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_rb_std_sem_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_cfa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_cfa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_pa.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_pa_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_sem.R | 2 tests/testthat/test-ci_bound_wn_i_int_comp_std_sem_user_eq.R | 2 tests/testthat/test-ci_bound_wn_i_mg_rb_std_cfa.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_std_cfa_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_std_cfa_user.R | 12 tests/testthat/test-ci_bound_wn_i_mg_rb_std_cfa_user_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_std_pa.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_std_pa_eq.R | 12 tests/testthat/test-ci_bound_wn_i_mg_rb_std_pa_user.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_std_pa_user_eq.R | 26 tests/testthat/test-ci_bound_wn_i_mg_rb_std_sem.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_std_sem_eq.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_std_sem_user.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_std_sem_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_cfa.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_cfa_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_cfa_user.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_cfa_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_pa.R | 26 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_pa_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_pa_user.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_pa_user_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_sem.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_sem_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_sem_user.R | 7 tests/testthat/test-ci_bound_wn_i_mg_rb_ustd_sem_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_mg_std_cfa.R | 14 tests/testthat/test-ci_bound_wn_i_mg_std_cfa_eq.R | 14 tests/testthat/test-ci_bound_wn_i_mg_std_cfa_user.R | 14 tests/testthat/test-ci_bound_wn_i_mg_std_cfa_user_eq.R | 14 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tests/testthat/test-ci_bound_wn_i_std_sem_user.R | 7 tests/testthat/test-ci_bound_wn_i_std_sem_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_cfa.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_cfa_eq.R | 6 tests/testthat/test-ci_bound_wn_i_ustd_cfa_user.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_cfa_user_eq.R | 6 tests/testthat/test-ci_bound_wn_i_ustd_pa.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_pa_eq.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_pa_user.R | 14 tests/testthat/test-ci_bound_wn_i_ustd_pa_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_sem.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_sem_eq.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_sem_user.R | 7 tests/testthat/test-ci_bound_wn_i_ustd_sem_user_eq.R | 7 tests/testthat/test-ci_bound_wn_i_z_print_maxtime.R | 2 tests/testthat/test-ci_i_one_rb_std_pa.R | 7 tests/testthat/test-ci_i_one_rb_ustd_pa.R | 7 tests/testthat/test-ci_i_one_std_pa.R | 7 tests/testthat/test-ci_i_one_std_pa_ur.R | 2 tests/testthat/test-ci_i_one_ustd_pa_ur.R | 2 tests/testthat/test-confint_semlbci.R | 2 tests/testthat/test-extra_arguments.R | 20 tests/testthat/test-gen_unique_name.R | 2 tests/testthat/test-get_i_from_lor.R | 8 tests/testthat/test-get_lhs_op_rhs.R | 2 tests/testthat/test-get_names_from_ptable.R | 6 tests/testthat/test-i_to_names.R | 2 tests/testthat/test-lav_mod_to_ram.R | 24 tests/testthat/test-pars_op.R | 2 tests/testthat/test-plot_likelihood.R | 2 tests/testthat/test-plot_likelihood_ur.R | 2 tests/testthat/test-ram_to_lav_mod.R | 8 tests/testthat/test-remove_intercepts.R | 2 tests/testthat/test-remove_variances.R | 2 tests/testthat/test-scaling_factor3_mg_rb_std_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_mg_rb_ustd_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_mg_wn_sem_std.R | 4 tests/testthat/test-scaling_factor3_mg_wn_sem_ustd.R | 4 tests/testthat/test-scaling_factor3_std_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_ustd_sem_user_eq.R | 2 tests/testthat/test-scaling_factor3_wn_sem_std.R | 4 tests/testthat/test-scaling_factor3_wn_sem_ustd.R | 4 tests/testthat/test-scaling_factor_int_comp_mg_wn_sem_std.R | 4 tests/testthat/test-scaling_factor_int_comp_wn_sem_std.R | 4 tests/testthat/test-semlbci_lavaan_cfa.R | 2 tests/testthat/test-semlbci_lavaan_cfa_mg.R | 2 tests/testthat/test-semlbci_lavaan_indirect.R | 2 tests/testthat/test-semlbci_lavaan_sem.R | 2 tests/testthat/test-semlbci_lavaan_sem_ur.R | 2 tests/testthat/test-semlbci_lavaan_sem_ur_rb.R | 2 tests/testthat/test-semlbci_nearby_rb_std.R | 2 tests/testthat/test-semlbci_print_text.R | 2 tests/testthat/test-semlbci_rb_std_pa.R | 2 tests/testthat/test-semlbci_rb_ustd_pa.R | 2 tests/testthat/test-semlbci_std_wn.R | 2 tests/testthat/test-semlbci_std_wn_derived_parameter.R | 2 tests/testthat/test-semlbci_std_wn_eq_constr.R | 2 tests/testthat/test-semlbci_update_wn_mg_ustd_cfa_user_eq.R | 2 tests/testthat/test-semlbci_wn_mg_ustd_cfa_user_eq.R | 6 tests/testthat/test-semlbci_wn_mg_ustd_pa_user_eq.R | 2 tests/testthat/test-semlbci_wn_mg_ustd_sem_user_eq.R | 5 tests/testthat/test-set_constraint_wn.R | 12 tests/testthat/test-std_lav.R | 2 tests/testthat/test-std_lav_one_factor.R | 2 tests/testthat/test-std_ram.R | 4 tests/testthat/test-syntax_to_i_mg.R | 2 tests/testthat/test-ur_add_func.R | 5 tests/testthat/test-ur_ci_bound_ur_i_mg_std_1.R | 2 tests/testthat/test-ur_ci_bound_ur_i_mg_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_i_rb_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_i_std_1.R | 2 tests/testthat/test-ur_ci_bound_ur_i_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_mg_std_1.R | 2 tests/testthat/test-ur_ci_bound_ur_mg_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_rb_mg_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_rb_ustd_1.R | 2 tests/testthat/test-ur_ci_bound_ur_std_1.R | 2 tests/testthat/test-ur_ci_bound_ur_ustd_1.R | 2 tests/testthat/test-ur_gen_est_i.R | 2 tests/testthat/test-ur_gen_userp.R | 5 190 files changed, 1015 insertions(+), 622 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
MOLGENIS org [cph, fnd]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between DSMolgenisArmadillo versions 3.0.1 dated 2025-09-16 and 3.0.2 dated 2025-12-06
DESCRIPTION | 12 MD5 | 26 - NAMESPACE | 5 NEWS.md | 3 R/ArmadilloConnection.R | 97 ++--- R/ArmadilloDriver.R | 31 - R/ArmadilloOAuth.R | 152 ++++---- R/ArmadilloResult.R | 14 R/utils.R | 21 - tests/testthat/test-ArmadilloConnection.R | 496 ++++++++++++++-------------- tests/testthat/test-ArmadilloDriver.R | 189 ++++++----- tests/testthat/test-ArmadilloOAuth.R | 514 +++++++++++++++--------------- tests/testthat/test-ArmadilloResult.R | 160 +++++---- tests/testthat/test-utils.R | 229 ++++++++----- 14 files changed, 1052 insertions(+), 897 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Layout Manager Widget for R and 'shiny' Apps
Description: Provides R bindings to the 'dockview' 'JavaScript' library <https://dockview.dev/>.
Create fully customizable grid layouts (docks) in seconds to include in interactive R reports with R Markdown or 'Quarto' or
in 'shiny' apps <https://shiny.posit.co/>. In 'shiny' mode, modify docks by dynamically adding, removing or moving panels or
groups of panels from the server function. Choose among 8 stunning themes (dark and light),
serialise the state of a dock to restore it later.
Author: David Granjon [aut, cre],
Nelson Stevens [aut],
Nicolas Bennett [aut],
mathuo [cph],
cynkra GmbH [fnd]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between dockViewR versions 0.2.0 dated 2025-07-10 and 0.3.0 dated 2025-12-06
dockViewR-0.2.0/dockViewR/R/add_panel.R |only dockViewR-0.2.0/dockViewR/R/move_group.R |only dockViewR-0.2.0/dockViewR/R/move_group2.R |only dockViewR-0.2.0/dockViewR/R/move_panel.R |only dockViewR-0.2.0/dockViewR/R/remove_panel.R |only dockViewR-0.2.0/dockViewR/R/select_panel.R |only dockViewR-0.2.0/dockViewR/inst/examples/replace_panel_content |only dockViewR-0.2.0/dockViewR/man/add_panel.Rd |only dockViewR-0.2.0/dockViewR/man/move_group.Rd |only dockViewR-0.2.0/dockViewR/man/move_group2.Rd |only dockViewR-0.2.0/dockViewR/man/move_panel.Rd |only dockViewR-0.2.0/dockViewR/man/remove_panel.Rd |only dockViewR-0.2.0/dockViewR/man/select_panel.Rd |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/add_panel |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/add_panel.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_group |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_group.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_group2 |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_group2.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_panel |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/move_panel.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/remove_panel |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/remove_panel.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/select_panel |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/select_panel.md |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/update-dock_view |only dockViewR-0.2.0/dockViewR/tests/testthat/_snaps/update-dock_view.md |only dockViewR-0.2.0/dockViewR/tests/testthat/test-add_panel.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-move_group.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-move_group2.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-move_panel.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-remove_panel.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-select_panel.R |only dockViewR-0.2.0/dockViewR/tests/testthat/test-update-dock_view.R |only dockViewR-0.3.0/dockViewR/DESCRIPTION | 11 dockViewR-0.3.0/dockViewR/MD5 | 194 dockViewR-0.3.0/dockViewR/NAMESPACE | 14 dockViewR-0.3.0/dockViewR/NEWS.md | 35 dockViewR-0.3.0/dockViewR/R/dock_state.R | 110 dockViewR-0.3.0/dockViewR/R/dock_view.R | 157 dockViewR-0.3.0/dockViewR/R/plugins.R |only dockViewR-0.3.0/dockViewR/R/proxy.R |only dockViewR-0.3.0/dockViewR/R/utils.R | 46 dockViewR-0.3.0/dockViewR/inst/doc/dockViewR.R | 34 dockViewR-0.3.0/dockViewR/inst/doc/dockViewR.html | 2079 +++++----- dockViewR-0.3.0/dockViewR/inst/doc/dockViewR.qmd | 66 dockViewR-0.3.0/dockViewR/inst/examples/add_panel/app.R | 39 dockViewR-0.3.0/dockViewR/inst/examples/demo/app.R | 8 dockViewR-0.3.0/dockViewR/inst/examples/move_group/app.R | 20 dockViewR-0.3.0/dockViewR/inst/examples/move_group2/app.R | 16 dockViewR-0.3.0/dockViewR/inst/examples/move_panel/app.R | 22 dockViewR-0.3.0/dockViewR/inst/examples/remove_panel/app.R | 16 dockViewR-0.3.0/dockViewR/inst/examples/select_panel/app.R | 16 dockViewR-0.3.0/dockViewR/inst/examples/serialise/app.R | 36 dockViewR-0.3.0/dockViewR/inst/examples/set_panel_title |only dockViewR-0.3.0/dockViewR/inst/examples/update_theme/app.R | 10 dockViewR-0.3.0/dockViewR/inst/htmlwidgets/dockview.js | 2 dockViewR-0.3.0/dockViewR/inst/wip |only dockViewR-0.3.0/dockViewR/man/default_add_tab_callback.Rd |only dockViewR-0.3.0/dockViewR/man/default_remove_tab_callback.Rd |only dockViewR-0.3.0/dockViewR/man/dock-state.Rd | 39 dockViewR-0.3.0/dockViewR/man/dock_view.Rd | 11 dockViewR-0.3.0/dockViewR/man/dock_view_plugins.Rd |only dockViewR-0.3.0/dockViewR/man/dockview-proxy.Rd |only dockViewR-0.3.0/dockViewR/man/is_add_tab_plugin.Rd |only dockViewR-0.3.0/dockViewR/man/is_dock_view_plugin.Rd |only dockViewR-0.3.0/dockViewR/man/is_remove_tab_plugin.Rd |only dockViewR-0.3.0/dockViewR/man/panel-operations.Rd |only dockViewR-0.3.0/dockViewR/man/panel.Rd | 5 dockViewR-0.3.0/dockViewR/man/update_dock_view.Rd | 8 dockViewR-0.3.0/dockViewR/man/validate_plugins.Rd |only dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-001.json | 59 dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-001_.png |binary dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-002.json | 23 dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-002.new.json |only dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-002_.png |binary dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-003.json |only dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_state/dock_state-003_.png |only dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/dock_view.md | 8 dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/proxy |only dockViewR-0.3.0/dockViewR/tests/testthat/_snaps/proxy.md |only dockViewR-0.3.0/dockViewR/tests/testthat/test-dock_state.R | 37 dockViewR-0.3.0/dockViewR/tests/testthat/test-dock_view.R | 22 dockViewR-0.3.0/dockViewR/tests/testthat/test-plugins.R |only dockViewR-0.3.0/dockViewR/tests/testthat/test-proxy.R |only dockViewR-0.3.0/dockViewR/vignettes/dockViewR.qmd | 66 86 files changed, 1683 insertions(+), 1526 deletions(-)
Title: Discrete Laplace Mixture Inference using the EM Algorithm
Description: Make inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used for modelling the distribution of Y chromosomal haplotypes as described in [1, 2] (refer to the URL section).
Author: Mikkel Meyer Andersen [aut, cre],
Poul Svante Eriksen [aut]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between disclapmix versions 1.7.4 dated 2022-06-29 and 1.7.5 dated 2025-12-06
DESCRIPTION | 19 -- MD5 | 55 +++-- NAMESPACE | 4 NEWS | 19 ++ R/RcppExports.R | 4 R/disclapmix-package.R | 3 R/disclapmix.R | 11 - R/disclapmix_adaptive.R | 83 ++++++++- R/disclapmix_robust.R | 35 +++ R/export.R |only R/helper.R | 378 ++++++++++++++++++++++------------------- README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/adaptive-fitting.R |only inst/doc/adaptive-fitting.Rmd |only inst/doc/adaptive-fitting.html |only inst/doc/introduction.R | 8 inst/doc/introduction.html | 253 ++++++++++++++------------- inst/doc/mixtures.R | 2 inst/doc/mixtures.html | 181 ++++++++++--------- man/disclapmix-package.Rd | 9 man/disclapmix.Rd | 2 man/disclapmix_adaptive.Rd | 21 ++ man/disclapmix_robust.Rd | 13 + man/export_compact_fit.Rd |only man/predict.disclapmixfit.Rd | 9 man/simulate.disclapmixfit.Rd | 5 src/RcppExports.cpp | 15 + src/helper.cpp | 27 ++ tests/testthat/test-adaptive.R |only tests/testthat/test-predict.R |only vignettes/adaptive-fitting.Rmd |only 33 files changed, 714 insertions(+), 444 deletions(-)
Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal processes. The
models may include covariates and can be specified with familiar formula
syntax as in glm() and package 'flexsurv'. The methodology is described by
Kharrat et all (2019) <doi:10.18637/jss.v090.i13> (included as vignette
'Countr_guide' in the package).
Author: Tarak Kharrat [aut] ,
Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Countr versions 3.5.8 dated 2024-01-14 and 3.6 dated 2025-12-06
Countr-3.5.8/Countr/R/probpredict.R |only Countr-3.5.8/Countr/inst/auto |only Countr-3.5.8/Countr/man/prob_predict.Rd |only Countr-3.6/Countr/DESCRIPTION | 36 +- Countr-3.6/Countr/MD5 | 102 +++--- Countr-3.6/Countr/NAMESPACE | 20 - Countr-3.6/Countr/NEWS.md | 14 Countr-3.6/Countr/R/Countr-package.R | 16 - Countr-3.6/Countr/R/RcppExports.R | 66 ++++ Countr-3.6/Countr/R/coefnames.R | 5 Countr-3.6/Countr/R/convCount_moments.R | 8 Countr-3.6/Countr/R/convCount_probs.R | 2 Countr-3.6/Countr/R/dBivariateWeibull.R |only Countr-3.6/Countr/R/dWeibull.R | 2 Countr-3.6/Countr/R/dWeibullgamma.R | 2 Countr-3.6/Countr/R/data.R | 2 Countr-3.6/Countr/R/renewal_cstr.R | 19 - Countr-3.6/Countr/R/renewal_methods.R | 13 Countr-3.6/Countr/R/renewal_tools.R | 47 --- Countr-3.6/Countr/README.md | 5 Countr-3.6/Countr/build/partial.rdb |binary Countr-3.6/Countr/build/vignette.rds |binary Countr-3.6/Countr/inst/REFERENCES.bib | 17 - Countr-3.6/Countr/inst/doc/ComputationalPerformance.pdf |binary Countr-3.6/Countr/inst/doc/Countr_guide.pdf |binary Countr-3.6/Countr/inst/doc/ModelSelectionAndComparison.pdf |binary Countr-3.6/Countr/inst/doc/VarianceCovariance.pdf |binary Countr-3.6/Countr/inst/doc/exampleFertility.pdf |binary Countr-3.6/Countr/inst/doc/exampleFootball.pdf |binary Countr-3.6/Countr/inst/include/BivWei_series.h |only Countr-3.6/Countr/inst/include/Biv_utils.h |only Countr-3.6/Countr/inst/include/Countr_RcppExports.h | 84 +++++ Countr-3.6/Countr/inst/include/utils.h | 1 Countr-3.6/Countr/man/Countr-package.Rd | 26 + Countr-3.6/Countr/man/dBivariateWeibullCountFrankCopula.Rd |only Countr-3.6/Countr/man/dCount_allProbs_bi.Rd | 4 Countr-3.6/Countr/man/dCount_conv_bi.Rd | 6 Countr-3.6/Countr/man/dCount_conv_loglik_bi.Rd | 2 Countr-3.6/Countr/man/dCount_dePril_bi.Rd | 3 Countr-3.6/Countr/man/dCount_naive_bi.Rd | 19 - Countr-3.6/Countr/man/dRenewalFrankCopula_user.Rd |only Countr-3.6/Countr/man/dWeibullCount.Rd | 2 Countr-3.6/Countr/man/dWeibullgammaCount.Rd | 2 Countr-3.6/Countr/man/evCount_conv_bi.Rd | 8 Countr-3.6/Countr/man/fertility.Rd | 2 Countr-3.6/Countr/man/getParNames.Rd | 4 Countr-3.6/Countr/man/renewalCoef.Rd | 3 Countr-3.6/Countr/man/renewalCount.Rd | 19 - Countr-3.6/Countr/man/surv.Rd | 6 Countr-3.6/Countr/src/Biv_utils.cpp |only Countr-3.6/Countr/src/RcppExports.cpp | 192 +++++++++++++ Countr-3.6/Countr/src/built_in_distributions.cpp | 2 Countr-3.6/Countr/src/conv_dePril.cpp | 1 Countr-3.6/Countr/src/conv_naive.cpp | 1 Countr-3.6/Countr/src/series_weibull.cpp | 110 +++++++ Countr-3.6/Countr/src/utils.cpp | 9 Countr-3.6/Countr/tests/testthat/test-BivariateWeibull.R |only 57 files changed, 666 insertions(+), 216 deletions(-)
Title: Determining Groups in Multiples Curves
Description: A method for determining groups in multiple
curves with an automatic selection of their number based on k-means or
k-medians algorithms. The selection of the optimal number is provided by
bootstrap methods or other approaches with lower computational cost. The methodology can be applied both in regression and survival framework.
Implemented methods are:
Grouping multiple survival curves described by Villanueva et al. (2018) <doi:10.1002/sim.8016>.
Author: Nora M. Villanueva [aut, cre] ,
Marta Sestelo [aut]
Maintainer: Nora M. Villanueva <nmvillanueva@uvigo.es>
Diff between clustcurv versions 3.0.0 dated 2025-11-14 and 3.0.1 dated 2025-12-06
DESCRIPTION | 8 - MD5 | 8 - NEWS | 4 R/auxfun_surv.R | 1 inst/doc/clustcurv.html | 212 +++++++++++++++++++++++------------------------- 5 files changed, 117 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-28 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-10 0.7.0
2025-08-29 0.6.1
2025-05-29 0.6.0
2025-01-27 0.5.0
2024-12-09 0.4.0
2024-08-26 0.3.0
2024-07-31 0.2.0
2024-07-02 0.1.0
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by recording real 'HTTP'
requests/responses on disk in 'cassettes', and then replaying
matching responses on subsequent requests.
Author: Scott Chamberlain [aut, cre] ,
Aaron Wolen [aut] ,
Maelle Salmon [aut] ,
Daniel Possenriede [aut] ,
Hadley Wickham [aut],
rOpenSci [fnd]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between vcr versions 2.0.0 dated 2025-07-23 and 2.1.0 dated 2025-12-05
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 7 ++++++- build/vignette.rds |binary inst/doc/debugging.html | 24 ++++++++++++------------ inst/doc/knitr-test.html | 4 ++-- inst/doc/vcr.html | 24 ++++++++++++------------ tests/testthat/_snaps/check_cassette_names.md | 2 +- tests/testthat/_snaps/lightswitch.md | 2 +- tests/testthat/test-ause_cassette_re_record.R | 4 ++-- tests/testthat/test-check_cassette_names.R | 3 ++- 11 files changed, 51 insertions(+), 45 deletions(-)
Title: Tests for Geophysical Eigenvalues
Description: The eigenvalues of observed symmetric matrices are often of intense scientific interest. This package offers single sample tests for the eigenvalues of the population mean or the eigenvalue-multiplicity of the population mean. For k-samples, this package offers tests for equal eigenvalues between samples. Included is support for matrices with constraints common to geophysical tensors (constant trace, sum of squared eigenvalues, or both) and eigenvectors are usually considered nuisance parameters. Pivotal bootstrap methods enable these tests to have good performance for small samples (n=15 for 3x3 matrices). These methods were developed and studied by Hingee, Scealy and Wood (2026, "Nonparametric bootstrap inference for the eigenvalues of geophysical tensors", accepted by the Journal of American Statistical Association). Also available is a 2-sample test using a Gaussian orthogonal ensemble approximation and an eigenvalue-multiplicity test that assumes orthogonally-invariant covariance.
Author: Kassel Liam Hingee [aut, cre] ,
Art B. Owen [cph] ,
Board of Trustees Leland Stanford Junior University [cph]
Maintainer: Kassel Liam Hingee <kassel.hingee@anu.edu.au>
Diff between TFORGE versions 0.1.14 dated 2025-12-04 and 0.1.15 dated 2025-12-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ build/partial.rdb |binary tests/testthat/test-multiplicity.R | 17 ++++++++++++++++- 5 files changed, 26 insertions(+), 8 deletions(-)
Title: Benchmark for Publication Bias Correction Methods
Description: Implements a unified interface for benchmarking meta-analytic
publication bias correction methods through simulation studies (see
Bartoš et al., 2025, <doi:10.48550/arXiv.2510.19489>). It provides
1) predefined data-generating mechanisms from the literature, 2) functions
for running meta-analytic methods on simulated data, 3) pre-simulated
datasets and pre-computed results for reproducible benchmarks, 4) tools for
visualizing and comparing method performance.
Author: Frantisek Bartos [aut, cre] ,
Samuel Pawel [aut] ,
Bjoern S. Siepe [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between PublicationBiasBenchmark versions 0.1.2 dated 2025-11-26 and 0.1.3 dated 2025-12-05
DESCRIPTION | 6 +- MD5 | 28 +++++----- NAMESPACE | 30 +++++++++++ NEWS.md | 9 +++ R/dgm.R | 12 ++++ R/download.R | 2 R/measures.R | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++ R/measures_compute.R | 42 +++++----------- R/method-RoBMA.R | 4 + R/method.R | 12 ++++ R/utilities.R | 16 +++--- build/partial.rdb |binary inst/REFERENCES.bib | 9 +++ man/measure.Rd |only man/measure_mcse.Rd |only man/method.RoBMA.Rd | 4 + 16 files changed, 248 insertions(+), 56 deletions(-)
More information about PublicationBiasBenchmark at CRAN
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Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Emily de la Rua [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Malcolm Barrett [ctb] ,
Esther Drill [ctb] ,
Jessica Flynn [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.4.0 dated 2025-08-28 and 2.5.0 dated 2025-12-05
DESCRIPTION | 10 MD5 | 348 ++--- NAMESPACE | 6 NEWS.md | 32 R/add_ci.R | 4 R/add_ci.tbl_svysummary.R | 4 R/add_overall.R | 12 R/assign_summary_type.R | 6 R/brdg_summary.R | 4 R/deprecated.R | 6 R/gather_ard.R | 2 R/gtsummary-package.R | 1 R/head.R |only R/import-standalone-check_pkg_installed.R | 95 - R/import-standalone-cli_call_env.R | 4 R/modify_abbreviation.R | 3 R/modify_footnote.R | 1 R/modify_source_note.R | 2 R/sort_hierarchical.R | 57 R/sysdata.rda |binary R/tbl_ard_hierarchical.R | 10 R/tbl_ard_strata.R |only R/tbl_hierarchical.R | 10 R/tbl_merge.R | 58 R/tbl_strata.R | 4 R/tbl_strata_nested_stack.R | 18 R/tbl_summary.R | 24 R/tbl_wide_summary.R | 2 R/utils-add_p_tests.R | 40 R/utils-as.R | 1 build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/gtsummary_definition.Rmd | 6 inst/doc/gtsummary_definition.html | 1129 +++++++++---------- man/add_ci.Rd | 2 man/add_ci.tbl_svysummary.Rd | 2 man/add_difference.tbl_summary.Rd | 2 man/add_difference.tbl_svysummary.Rd | 2 man/add_difference_row.tbl_summary.Rd | 2 man/add_glance.Rd | 2 man/add_global_p.Rd | 2 man/add_n.tbl_survfit.Rd | 2 man/add_n_regression.Rd | 2 man/add_n_summary.Rd | 2 man/add_nevent.tbl_survfit.Rd | 2 man/add_nevent_regression.Rd | 2 man/add_p.tbl_continuous.Rd | 2 man/add_p.tbl_summary.Rd | 2 man/add_p.tbl_survfit.Rd | 2 man/add_p.tbl_svysummary.Rd | 2 man/add_q.Rd | 2 man/add_significance_stars.Rd | 2 man/add_variable_group_header.Rd | 2 man/add_vif.Rd | 2 man/as_flex_table.Rd | 2 man/as_hux_table.Rd | 2 man/as_kable_extra.Rd | 2 man/combine_terms.Rd | 2 man/custom_tidiers.Rd | 2 man/filter_hierarchical.Rd | 2 man/gather_ard.Rd | 2 man/glance_fun_s3.Rd | 2 man/global_pvalue_fun.Rd | 2 man/head.gtsummary.Rd |only man/inline_text.tbl_regression.Rd | 2 man/inline_text.tbl_survfit.Rd | 2 man/inline_text.tbl_uvregression.Rd | 2 man/modify.Rd | 2 man/modify_abbreviation.Rd | 7 man/modify_bold_italic.Rd | 2 man/modify_column_merge.Rd | 2 man/modify_footnote2.Rd | 5 man/modify_missing_symbol.Rd | 2 man/modify_source_note.Rd | 6 man/plot.Rd | 2 man/proportion_summary.Rd | 2 man/sort_hierarchical.Rd | 16 man/tbl_ard_hierarchical.Rd | 2 man/tbl_ard_strata.Rd |only man/tbl_butcher.Rd | 2 man/tbl_continuous.Rd | 2 man/tbl_hierarchical.Rd | 3 man/tbl_merge.Rd | 14 man/tbl_regression.Rd | 2 man/tbl_split_by.Rd | 2 man/tbl_stack.Rd | 2 man/tbl_strata.Rd | 13 man/tbl_summary.Rd | 5 man/tbl_survfit.Rd | 2 man/tbl_svysummary.Rd | 2 man/tbl_uvregression.Rd | 2 man/tbl_wide_summary.Rd | 4 tests/testthat/_snaps/add_p.tbl_summary.md | 134 -- tests/testthat/_snaps/filter_hierarchical.md | 44 tests/testthat/_snaps/gather_ard.md |only tests/testthat/_snaps/sort_hierarchical.md | 82 - tests/testthat/_snaps/tbl_ard_strata.md |only tests/testthat/_snaps/tbl_hierarchical.md | 195 +-- tests/testthat/_snaps/tbl_merge.md | 3 tests/testthat/_snaps/tbl_summary.md | 39 tests/testthat/test-add_ci.tbl_summary.R | 2 tests/testthat/test-add_ci.tbl_svysummary.R | 5 tests/testthat/test-add_difference.tbl_summary.R | 16 tests/testthat/test-add_difference.tbl_svysummary.R | 6 tests/testthat/test-add_difference_row.tbl_summary.R | 8 tests/testthat/test-add_glance.R | 5 tests/testthat/test-add_global_p.tbl_regression.R | 3 tests/testthat/test-add_global_p.tbl_uvregression.R | 2 tests/testthat/test-add_n.tbl_regression.R | 2 tests/testthat/test-add_n.tbl_svysummary.R | 2 tests/testthat/test-add_n.tbl_uvregression.R | 2 tests/testthat/test-add_nevent.tbl_regression.R | 2 tests/testthat/test-add_nevent.tbl_uvregression.R | 2 tests/testthat/test-add_overall.tbl_custom_summary.R | 2 tests/testthat/test-add_overall.tbl_hierarchical.R | 2 tests/testthat/test-add_overall.tbl_svysummary.R | 2 tests/testthat/test-add_p.tbl_continuous.R | 2 tests/testthat/test-add_p.tbl_summary.R | 28 tests/testthat/test-add_p.tbl_survfit.R | 2 tests/testthat/test-add_p.tbl_svysummary.R | 6 tests/testthat/test-add_significance_stars.R | 2 tests/testthat/test-add_stat.R | 2 tests/testthat/test-add_stat_label.tbl_ard_summary.R | 2 tests/testthat/test-add_stat_label.tbl_svysummary.R | 2 tests/testthat/test-add_variable_group_header.R | 2 tests/testthat/test-add_vif.R | 2 tests/testthat/test-as_flex_table.R | 7 tests/testthat/test-as_gt.R | 2 tests/testthat/test-as_hux_table.R | 8 tests/testthat/test-as_kable.R | 6 tests/testthat/test-as_kable_extra.R | 4 tests/testthat/test-as_tibble.R | 2 tests/testthat/test-combine_terms.R | 8 tests/testthat/test-custom_tidiers.R | 10 tests/testthat/test-filter_hierarchical.R | 18 tests/testthat/test-gather_ard.R | 9 tests/testthat/test-head.R |only tests/testthat/test-inline_text.R | 6 tests/testthat/test-label_style.R | 2 tests/testthat/test-modify_abbreviation.R | 2 tests/testthat/test-modify_bold_italic.R | 2 tests/testthat/test-modify_caption.R | 7 tests/testthat/test-modify_column_alignment.R | 2 tests/testthat/test-modify_column_hide.R | 2 tests/testthat/test-modify_column_merge.R | 2 tests/testthat/test-modify_fmt_fun.R | 2 tests/testthat/test-modify_footnote.R | 6 tests/testthat/test-modify_header.R | 6 tests/testthat/test-modify_missing_symbol.R | 2 tests/testthat/test-modify_spanning_header.R | 7 tests/testthat/test-modify_table_body.R | 2 tests/testthat/test-modify_table_styling.R | 2 tests/testthat/test-plot.tbl_regression.R | 2 tests/testthat/test-plot.tbl_uvregression.R | 2 tests/testthat/test-remove_row_type.R | 2 tests/testthat/test-select_helpers.R | 2 tests/testthat/test-separate_p_footnotes.R | 4 tests/testthat/test-show_header_names.R | 2 tests/testthat/test-sort_filter_p.R | 2 tests/testthat/test-sort_hierarchical.R | 16 tests/testthat/test-tbl_ard_hierarchical.R | 23 tests/testthat/test-tbl_ard_strata.R |only tests/testthat/test-tbl_ard_summary.R | 2 tests/testthat/test-tbl_butcher.R | 2 tests/testthat/test-tbl_hierarchical.R | 22 tests/testthat/test-tbl_likert.R | 2 tests/testthat/test-tbl_merge.R | 25 tests/testthat/test-tbl_regression.R | 2 tests/testthat/test-tbl_regression_methods.R | 18 tests/testthat/test-tbl_stack.R | 2 tests/testthat/test-tbl_strata.R | 5 tests/testthat/test-tbl_strata_nested_stack.R | 38 tests/testthat/test-tbl_summary.R | 45 tests/testthat/test-tbl_survfit.R | 2 tests/testthat/test-tbl_svysummary.R | 2 tests/testthat/test-tbl_uvregression.R | 2 tests/testthat/test-theme_elements_gtsummary.R | 290 ++++ tests/testthat/test-theme_gtsummary.R | 4 vignettes/gtsummary_definition.Rmd | 6 179 files changed, 1962 insertions(+), 1368 deletions(-)
Title: Genome-Wide Robust Analysis for Biobank Data (GRAB)
Description: Provides a comprehensive suite of genome-wide association study (GWAS) methods
specifically designed for biobank-scale data, including but not limited to, robust approaches
for time-to-event traits (Li et al., 2025 <doi:10.1038/s43588-025-00864-z>) and ordinal
categorical traits (Bi et al., 2021 <doi:10.1016/j.ajhg.2021.03.019>). The package also offers
general frameworks for GWAS of any trait type (Bi et al., 2020 <doi:10.1016/j.ajhg.2020.06.003>),
while accounting for sample relatedness (Xu et al., 2025 <doi:10.1038/s41467-025-56669-1>) or
population structure (Ma et al., 2025 <doi:10.1186/s13059-025-03827-9>). By accurately
approximating score statistic distributions using saddlepoint approximation (SPA), these
methods can effectively control type I error rates for rare variants and in the presence of
unbalanced phenotype distributions. Additionally, the package includes functions for simulating
genotype and phenotype data to support research and method [...truncated...]
Author: Wenjian Bi [aut],
Wei Zhou [aut],
Rounak Dey [aut],
Zhangchen Zhao [aut],
Seunggeun Lee [aut],
Woody Miao [cre]
Maintainer: Woody Miao <miaolin@pku.edu.cn>
Diff between GRAB versions 0.2.3 dated 2025-08-19 and 0.2.4 dated 2025-12-05
GRAB-0.2.3/GRAB/R/CCT.R |only GRAB-0.2.3/GRAB/R/DenseGRM.R |only GRAB-0.2.3/GRAB/R/PairwiseIBD.R |only GRAB-0.2.3/GRAB/R/SparseGRM.R |only GRAB-0.2.3/GRAB/R/control.R |only GRAB-0.2.3/GRAB/R/formula.R |only GRAB-0.2.3/GRAB/man/Batcheffect.Test.Rd |only GRAB-0.2.3/GRAB/man/checkIfSampleIDsExist.Rd |only GRAB-0.2.3/GRAB/man/getDenseGRM.Rd |only GRAB-0.2.3/GRAB/man/getSampleIDsFromBGEN.Rd |only GRAB-0.2.3/GRAB/man/getVersionFromBGEN.Rd |only GRAB-0.2.3/GRAB/man/handleFormula.Rd |only GRAB-0.2.3/GRAB/man/makeGroup.Rd |only GRAB-0.2.3/GRAB/man/setDenseGRM.Rd |only GRAB-0.2.4/GRAB/DESCRIPTION | 28 GRAB-0.2.4/GRAB/MD5 | 114 - GRAB-0.2.4/GRAB/NAMESPACE | 16 GRAB-0.2.4/GRAB/R/GRAB_Marker.R | 505 +++---- GRAB-0.2.4/GRAB/R/GRAB_Null_Model.R | 528 +++----- GRAB-0.2.4/GRAB/R/GRAB_Region.R | 1070 ++++++++-------- GRAB-0.2.4/GRAB/R/GRAB_Simu.R | 1358 ++++++++++++-------- GRAB-0.2.4/GRAB/R/GRM_IBD.R |only GRAB-0.2.4/GRAB/R/Geno.R | 565 +++++--- GRAB-0.2.4/GRAB/R/POLMM.R | 766 +++++++---- GRAB-0.2.4/GRAB/R/RcppExports.R | 32 GRAB-0.2.4/GRAB/R/SAGELD.R | 527 ++++---- GRAB-0.2.4/GRAB/R/SPACox.R | 266 ++-- GRAB-0.2.4/GRAB/R/SPAGRM.R | 1511 ++++++++++------------- GRAB-0.2.4/GRAB/R/SPAmix.R | 333 +++-- GRAB-0.2.4/GRAB/R/Util.R | 572 ++++---- GRAB-0.2.4/GRAB/R/WtCoxG.R | 785 ++++++----- GRAB-0.2.4/GRAB/R/zzz.R | 10 GRAB-0.2.4/GRAB/README.md | 6 GRAB-0.2.4/GRAB/build |only GRAB-0.2.4/GRAB/man/CCT.Rd | 48 GRAB-0.2.4/GRAB/man/GRAB.Marker.Rd | 183 -- GRAB-0.2.4/GRAB/man/GRAB.NullModel.Rd | 217 --- GRAB-0.2.4/GRAB/man/GRAB.POLMM.Rd | 159 +- GRAB-0.2.4/GRAB/man/GRAB.POLMM.Region.Rd |only GRAB-0.2.4/GRAB/man/GRAB.ReadGeno.Rd | 103 - GRAB-0.2.4/GRAB/man/GRAB.Region.Rd | 158 -- GRAB-0.2.4/GRAB/man/GRAB.SAGELD.Rd | 5 GRAB-0.2.4/GRAB/man/GRAB.SPACox.Rd | 78 - GRAB-0.2.4/GRAB/man/GRAB.SPAGRM.Rd | 55 GRAB-0.2.4/GRAB/man/GRAB.SPAmix.Rd | 97 - GRAB-0.2.4/GRAB/man/GRAB.SimuGMat.Rd | 51 GRAB-0.2.4/GRAB/man/GRAB.SimuGMatFromGenoFile.Rd | 56 GRAB-0.2.4/GRAB/man/GRAB.SimuPheno.Rd | 37 GRAB-0.2.4/GRAB/man/GRAB.SimubVec.Rd | 32 GRAB-0.2.4/GRAB/man/GRAB.WtCoxG.Rd | 102 - GRAB-0.2.4/GRAB/man/GRAB.getGenoInfo.Rd | 34 GRAB-0.2.4/GRAB/man/GRAB.makePlink.Rd | 58 GRAB-0.2.4/GRAB/man/SAGELD.NullModel.Rd | 71 - GRAB-0.2.4/GRAB/man/SPAGRM.NullModel.Rd | 30 GRAB-0.2.4/GRAB/man/TestforBatchEffect.Rd | 24 GRAB-0.2.4/GRAB/man/fitNullModel.POLMM.Rd |only GRAB-0.2.4/GRAB/man/fitNullModel.SPACox.Rd |only GRAB-0.2.4/GRAB/man/fitNullModel.SPAmix.Rd |only GRAB-0.2.4/GRAB/man/fitNullModel.WtCoxG.Rd |only GRAB-0.2.4/GRAB/man/getPairwiseIBD.Rd |only GRAB-0.2.4/GRAB/man/getSparseGRM.Rd | 53 GRAB-0.2.4/GRAB/man/getTempFilesFullGRM.Rd | 39 GRAB-0.2.4/GRAB/src/Main.cpp | 401 +----- GRAB-0.2.4/GRAB/src/POLMM.cpp | 3 GRAB-0.2.4/GRAB/src/RcppExports.cpp | 85 - GRAB-0.2.4/GRAB/src/SAGELD.h | 2 GRAB-0.2.4/GRAB/src/SPAGRM.h | 2 GRAB-0.2.4/GRAB/src/WtCoxG.cpp | 624 ++++----- GRAB-0.2.4/GRAB/src/WtCoxG.h | 208 +-- 69 files changed, 6154 insertions(+), 5853 deletions(-)
Title: Data Utilities for Congressional Research
Description: Provides easy-to-understand and consistent interfaces for
accessing data on the U.S. Congress. The functions in 'filibustr'
streamline the process for importing data on Congress into R, removing
the need to download and work from CSV files and the like. Data
sources include 'Voteview' (<https://voteview.com/>), the U.S. Senate
website (<https://www.senate.gov/>), and more.
Author: Max Feinleib [aut, cre, cph]
Maintainer: Max Feinleib <mhfeinleib@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2025-10-26
Diff between filibustr versions 0.5.0 dated 2025-10-26 and 0.5.1 dated 2025-12-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 3 +++ R/read_html_table.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary man/read_html_table.Rd | 4 ++-- tests/testthat/test-utils_data_cleaning.R | 4 ++-- 8 files changed, 19 insertions(+), 16 deletions(-)
Title: Excess Mortality
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Author: Rafael A. Irizarry [aut, cre],
Rolando Acosta [aut],
Monica Robles-Fontan [aut],
Ferenci Tamas [ctb]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between excessmort versions 0.8.1 dated 2025-04-07 and 0.8.2 dated 2025-12-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/compute_expected.R | 24 ++++++++++++++++++------ R/excess_plot.R | 2 +- R/expected_diagnostic.R | 26 +++++++++++++------------- R/expected_plot.R | 2 +- build/vignette.rds |binary inst/doc/excessmort.html | 23 ++++++++++++----------- 8 files changed, 55 insertions(+), 42 deletions(-)
Title: Search Download and Handle Data from Copernicus Climate Data
Service
Description: Subset and download data from EU Copernicus Climate Data Service:
<https://cds.climate.copernicus.eu/>. Import information about the Earth's
past, present and future climate from Copernicus into R without the need of
external software.
Author: Pepijn de Vries [aut, cre]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusClimate versions 0.0.3 dated 2025-10-23 and 0.0.4 dated 2025-12-05
DESCRIPTION | 13 ++-- MD5 | 32 ++++++------ NEWS.md | 7 ++ R/cite.R | 2 R/jobs.R | 2 R/retrieve.R | 23 +++++++- R/token.R | 6 +- inst/doc/download.R | 2 inst/doc/download.Rmd | 4 - inst/doc/download.html | 104 ++++++++++++++++++++++++--------------- man/CopernicusClimate-package.Rd | 2 man/cds_account_metrics.Rd | 4 - man/cds_delete_job.Rd | 2 man/cds_get_token.Rd | 2 tests/testthat/test-download.R | 21 +++++++ tests/testthat/test-exceptions.R | 2 vignettes/download.Rmd | 4 - 17 files changed, 149 insertions(+), 83 deletions(-)
More information about CopernicusClimate at CRAN
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Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.4.0 dated 2025-11-19 and 1.4.1 dated 2025-12-05
DESCRIPTION | 6 MD5 | 12 NEWS.md | 761 +++++++++++++++--------------- R/downloading_tools.R | 824 ++++++++++++++++----------------- R/oafeat_tools.R | 42 + inst/CITATION | 26 - tests/testthat/test_03_get_functions.R | 6 7 files changed, 855 insertions(+), 822 deletions(-)
Title: Linear Mixed Models with Sparse Matrix Methods and Smoothing
Description: Provides tools for fitting linear mixed models using sparse matrix
methods and variance component estimation. Applications include spline-based
modeling of spatial and temporal trends using penalized splines (Boer, 2023)
<doi:10.1177/1471082X231178591>.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.11 dated 2025-08-20 and 1.0.12 dated 2025-12-05
LMMsolver-1.0.11/LMMsolver/man/predictTest.Rd |only LMMsolver-1.0.12/LMMsolver/DESCRIPTION | 21 LMMsolver-1.0.12/LMMsolver/MD5 | 112 +-- LMMsolver-1.0.12/LMMsolver/NAMESPACE | 1 LMMsolver-1.0.12/LMMsolver/NEWS.md | 11 LMMsolver-1.0.12/LMMsolver/R/LMMsolve-class.R | 97 +- LMMsolver-1.0.12/LMMsolver/R/LMMsolve.R | 14 LMMsolver-1.0.12/LMMsolver/R/RcppExports.R | 4 LMMsolver-1.0.12/LMMsolver/R/constructRinv.R | 6 LMMsolver-1.0.12/LMMsolver/R/data.R | 34 LMMsolver-1.0.12/LMMsolver/R/diagnosticsMME.R | 6 LMMsolver-1.0.12/LMMsolver/R/displayMME.R | 6 LMMsolver-1.0.12/LMMsolver/R/effDim.R |only LMMsolver-1.0.12/LMMsolver/R/obtainSmoothTrend.R | 6 LMMsolver-1.0.12/LMMsolver/R/predictFunctions.R | 222 +++--- LMMsolver-1.0.12/LMMsolver/R/spl1D.R | 6 LMMsolver-1.0.12/LMMsolver/R/splinesFunctions.R | 3 LMMsolver-1.0.12/LMMsolver/README.md | 51 - LMMsolver-1.0.12/LMMsolver/build/partial.rdb |binary LMMsolver-1.0.12/LMMsolver/build/vignette.rds |binary LMMsolver-1.0.12/LMMsolver/data/barley.uniformity.trial.rda |only LMMsolver-1.0.12/LMMsolver/data/oats.data.rda |only LMMsolver-1.0.12/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.R | 34 LMMsolver-1.0.12/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.Rmd | 88 +- LMMsolver-1.0.12/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.html | 350 +++++----- LMMsolver-1.0.12/LMMsolver/inst/tinytest/effDim0 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/pred7 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/pred8 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/pred9 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/spl2DFull2 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/spl2DFull3 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/spl3DFull2 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/spl3DFull3 |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_LMMsolve.R | 20 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_MME_functions.R |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_conditionalFactor.R | 16 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_effDim.R |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_gam.R | 9 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_internal_functions.R |only LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_mLogLik.R | 6 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_multinomial.R | 6 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_obtainSmoothTrend.R | 29 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_predict.R | 54 + LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_spl1D.R | 50 - LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_spl2D.R | 19 LMMsolver-1.0.12/LMMsolver/inst/tinytest/test_spl3D.R | 19 LMMsolver-1.0.12/LMMsolver/inst/tinytest/testdata.rda |binary LMMsolver-1.0.12/LMMsolver/man/LMMsolve.Rd | 10 LMMsolver-1.0.12/LMMsolver/man/barley.uniformity.trial.Rd |only LMMsolver-1.0.12/LMMsolver/man/coef.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/deviance.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/diagnosticsMME.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/displayMME.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/effDim.Rd |only LMMsolver-1.0.12/LMMsolver/man/fitted.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/logLik.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/oats.data.Rd |only LMMsolver-1.0.12/LMMsolver/man/obtainSmoothTrend.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/residuals.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/spl1D.Rd | 6 LMMsolver-1.0.12/LMMsolver/man/summary.LMMsolve.Rd | 6 LMMsolver-1.0.12/LMMsolver/src/ADcholesky.cpp | 38 - LMMsolver-1.0.12/LMMsolver/src/RcppExports.cpp | 12 LMMsolver-1.0.12/LMMsolver/src/SparseMatrix.cpp | 13 LMMsolver-1.0.12/LMMsolver/vignettes/Solving_Linear_Mixed_Models.Rmd | 88 +- LMMsolver-1.0.12/LMMsolver/vignettes/bibliography.bib | 34 66 files changed, 915 insertions(+), 640 deletions(-)
Title: Tools for Analysing Forensic Genetic DNA Data
Description: Computationally efficient tools for comparing all pairs of profiles
in a DNA database. The expectation and covariance of the summary statistic
is implemented for fast computing. Routines for estimating proportions of
close related individuals are available. The use of wildcards (also called F-
designation) is implemented. Dedicated functions ease plotting the results.
See Tvedebrink et al. (2012) <doi:10.1016/j.fsigen.2011.08.001>.
Compute the distribution of the numbers of alleles in DNA mixtures.
See Tvedebrink (2013) <doi:10.1016/j.fsigss.2013.10.142>.
Author: Torben Tvedebrink [aut],
James Curran [aut],
Mikkel Meyer Andersen [aut, cre]
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between DNAtools versions 0.2-4 dated 2022-03-17 and 0.2-5 dated 2025-12-05
DESCRIPTION | 17 +- MD5 | 36 ++--- NEWS | 4 R/DNAtools-package.R | 3 R/dbcompare.R | 4 README.md | 158 ++++++++++++------------ build/vignette.rds |binary inst/CITATION | 36 +++-- inst/doc/db_vignette.R | 6 inst/doc/db_vignette.html | 223 ++++++++++++++++++----------------- inst/doc/dna_vignette.R | 8 - inst/doc/dna_vignette.html | 157 ++++++++++++------------ inst/doc/noa_vignette.R | 28 ++-- inst/doc/noa_vignette.html | 266 +++++++++++++++++++++--------------------- man/DNAtools-package.Rd | 7 + src/Makevars | 1 src/Makevars.win | 1 src/compare_threaded.cpp | 10 + tests/testthat/test-compare.R | 8 + 19 files changed, 506 insertions(+), 467 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-19 0.1.0
Title: Shared Memory Multithreading
Description: This project extends 'R' with a mechanism for efficient parallel data access by utilizing 'C++' shared memory. Large data objects can be accessed and manipulated directly from 'R' without redundant copying, providing both speed and memory efficiency.
Author: Julian Maerte [aut, ctr] ,
Romain Francois [ctb],
Michael Thrun [aut, ths, rev, cph, cre]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between memshare versions 1.0.3 dated 2025-11-08 and 1.1.0 dated 2025-12-05
DESCRIPTION | 11 - MD5 | 40 +++-- R/memApply.R | 15 +- R/memLapply.R | 11 + README.md | 329 ++++++++++++++++++++++++------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/memshare.Rmd | 2 inst/doc/memshare.html | 4 src/altrep.cpp | 5 src/metadata.cpp | 2 src/register.cpp | 1 src/register.h | 1 src/retrieve.cpp | 8 - src/shared_memory.cpp | 13 + src/shared_memory.h | 11 + tests |only vignettes/memshare.Rmd | 2 19 files changed, 248 insertions(+), 207 deletions(-)
Title: Geospatial Tools for Visibility Analysis
Description: Provides tools for visibility analysis in geospatial data. It
offers functionality to perform isovist calculations, using arbitrary
geometries as both viewpoints and occluders.
Author: Claudiu Forgaci [aut, cre, cph] ,
Francesco Nattino [aut] ,
Netherlands eScience Center [fnd]
Maintainer: Claudiu Forgaci <c.forgaci@tudelft.nl>
Diff between visor versions 0.1.0 dated 2025-04-07 and 0.1.1 dated 2025-12-05
DESCRIPTION | 18 ++++++++++-------- MD5 | 14 +++++++------- NEWS.md | 10 +++++++++- R/isovist.R | 16 +++++++++++++--- README.md | 4 +++- build/vignette.rds |binary man/figures/logo.png |binary tests/testthat/test-isovist.R | 11 +++++++++++ 8 files changed, 53 insertions(+), 20 deletions(-)
Title: Triangulate and Simplify 3D Terrain Meshes
Description: Provides triangulations of regular height fields, based on the methods described in "Fast Polygonal Approximation of Terrains and Height Fields" Michael Garland and Paul S. Heckbert (1995) <https://www.mgarland.org/files/papers/scape.pdf> using code from the 'hmm' library written by Michael Fogleman <https://github.com/fogleman/hmm>.
Author: Tyler Morgan-Wall [aut, cph, cre] ,
Michael Fogleman [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between terrainmeshr versions 0.1.0 dated 2020-04-29 and 1.0.1 dated 2025-12-05
terrainmeshr-0.1.0/terrainmeshr/R/RcppExports.R |only terrainmeshr-0.1.0/terrainmeshr/src/RcppExports.cpp |only terrainmeshr-1.0.1/terrainmeshr/DESCRIPTION | 22 -- terrainmeshr-1.0.1/terrainmeshr/MD5 | 31 ++- terrainmeshr-1.0.1/terrainmeshr/NAMESPACE | 2 terrainmeshr-1.0.1/terrainmeshr/R/terrainmeshr-package.R | 1 terrainmeshr-1.0.1/terrainmeshr/R/terrainmeshrRcpp.R | 1 terrainmeshr-1.0.1/terrainmeshr/R/triangulate_matrix.R | 52 +++-- terrainmeshr-1.0.1/terrainmeshr/README.md |only terrainmeshr-1.0.1/terrainmeshr/man/figures |only terrainmeshr-1.0.1/terrainmeshr/src/heightmap.cpp | 1 terrainmeshr-1.0.1/terrainmeshr/src/heightmap.h | 3 terrainmeshr-1.0.1/terrainmeshr/src/triangular_mesh.cpp | 150 +++++++++++---- 13 files changed, 178 insertions(+), 85 deletions(-)
Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Description: Produces ANOVA tables in the format used by Judd, McClelland,
and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook,
Data Analysis. This includes proportional reduction in error and
formatting to improve ease the transition between the book and R.
Author: Adam Blake [cre, aut] ,
Jeff Chrabaszcz [aut],
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between supernova versions 3.0.0 dated 2024-02-07 and 3.0.1 dated 2025-12-05
DESCRIPTION | 23 +-- MD5 | 45 +++---- NEWS.md | 17 ++ R/generate_models.R | 21 +++ R/pairwise.R | 32 ++--- R/supernova.R | 18 +- R/utils-formula.R | 61 +++++++++- R/utils.R | 5 README.md | 8 - inst/WORDLIST | 3 man/anova_tbl.Rd | 2 man/find_bars.Rd |only man/level_pairs.Rd | 5 man/new_pairwise_tbl.Rd | 2 man/no_bars.Rd |only man/normalize_term.Rd |only man/row_blank.Rd | 2 man/row_error.Rd | 6 man/row_term.Rd | 6 man/supernova.Rd | 4 tests/testthat/_snaps/pairwise/bonferroni-one-variable.svg | 2 tests/testthat/_snaps/pairwise/multiple-plots-term-factor-am.svg | 2 tests/testthat/_snaps/pairwise/multiple-plots-term-factor-cyl.svg | 2 tests/testthat/_snaps/pairwise/t-test-one-variable.svg | 2 tests/testthat/_snaps/pairwise/tukey-one-variable.svg | 2 25 files changed, 183 insertions(+), 87 deletions(-)
Title: Syntax Highlighter
Description: Syntax highlighter for R code based on the results of the R
parser. Rendering in HTML and latex markup. Custom Sweave driver
performing syntax highlighting of R code chunks.
Author: Hadley Wickham [cre],
Romain Francois [aut],
Andre Simon [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between highlight versions 0.5.1 dated 2023-01-18 and 0.5.2 dated 2025-12-05
highlight-0.5.1/highlight/NEWS |only highlight-0.5.2/highlight/DESCRIPTION | 8 highlight-0.5.2/highlight/MD5 | 59 highlight-0.5.2/highlight/NEWS.md | 105 + highlight-0.5.2/highlight/R/00_sizes.R | 15 highlight-0.5.2/highlight/R/SweaveLatexDriver.R | 1019 ++++++++-------- highlight-0.5.2/highlight/R/css.R | 249 +-- highlight-0.5.2/highlight/R/detectives.R | 91 - highlight-0.5.2/highlight/R/external_highlight.R | 295 ++-- highlight-0.5.2/highlight/R/highlight.R | 285 ++-- highlight-0.5.2/highlight/R/renderer.R | 772 ++++++------ highlight-0.5.2/highlight/R/utils.R | 50 highlight-0.5.2/highlight/R/zzz.R | 15 highlight-0.5.2/highlight/README.md | 4 highlight-0.5.2/highlight/man/HighlightWeaveLatex.Rd | 20 highlight-0.5.2/highlight/man/Hweave.Rd | 14 highlight-0.5.2/highlight/man/boxes_latex.Rd | 6 highlight-0.5.2/highlight/man/css.parser.Rd | 30 highlight-0.5.2/highlight/man/external_highlight.Rd | 8 highlight-0.5.2/highlight/man/header_html.Rd | 12 highlight-0.5.2/highlight/man/header_latex.Rd | 3 highlight-0.5.2/highlight/man/highlight-package.Rd | 40 highlight-0.5.2/highlight/man/highlight.Rd | 30 highlight-0.5.2/highlight/man/renderer.Rd | 40 highlight-0.5.2/highlight/man/renderer_html.Rd | 22 highlight-0.5.2/highlight/man/renderer_latex.Rd | 16 highlight-0.5.2/highlight/man/simple_detective.Rd | 4 highlight-0.5.2/highlight/man/styler.Rd | 16 highlight-0.5.2/highlight/man/styler_assistant_latex.Rd | 8 highlight-0.5.2/highlight/src/Makevars | 1 highlight-0.5.2/highlight/src/Makevars.win | 1 31 files changed, 1817 insertions(+), 1421 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Includes implementation of a new [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.8.5 dated 2025-08-22 and 0.8.8 dated 2025-12-05
DESCRIPTION | 10 - MD5 | 80 +++++++------- NAMESPACE | 1 NEWS.md | 42 +++++++ R/as_hce.R | 2 R/as_hce.data.frame.R | 2 R/as_hce.default.R | 4 R/calcWINS_data_frame.R | 135 ++++++++++++++++++------ R/calcWINS_formula.R | 8 + R/calcWINS_hce.R | 8 + R/data.R | 22 ++++ R/simHCE.R | 5 R/simKHCE.R | 144 +++++++++++++++++++------- R/simTTE.R |only R/summaryWO.R | 2 R/summaryWO_adhce.R | 40 ++++++- R/summaryWO_formula.R | 7 + R/summaryWO_hce.R | 6 - inst/doc/Introduction.R | 10 + inst/doc/Introduction.Rmd | 16 ++ inst/doc/Introduction.html | 105 ++++++++++++------- inst/doc/Wins.html | 19 +-- inst/doc/hce.R | 49 +++++++- inst/doc/hce.Rmd | 92 +++++++++++++--- inst/doc/hce.html | 246 +++++++++++++++++++++++++++++++-------------- inst/doc/maraca.html | 4 man/KHCE.Rd | 22 ++++ man/as_hce.Rd | 2 man/as_hce.default.Rd | 1 man/calcWINS.data.frame.Rd | 50 ++++++--- man/calcWINS.formula.Rd | 10 + man/calcWINS.hce.Rd | 10 + man/simHCE.Rd | 4 man/simKHCE.Rd | 36 +++++- man/simTTE.Rd |only man/summaryWO.Rd | 2 man/summaryWO.adhce.Rd | 21 +++ man/summaryWO.formula.Rd | 5 man/summaryWO.hce.Rd | 6 - vignettes/Introduction.Rmd | 16 ++ vignettes/REFERENCES.bib | 4 vignettes/hce.Rmd | 92 +++++++++++++--- 42 files changed, 1006 insertions(+), 334 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.45 dated 2025-10-03 and 0.46 dated 2025-12-05
DESCRIPTION | 10 ++--- MD5 | 8 ++-- R/publish.R | 85 ++++++++++++++++++++++++---------------------- man/publish_book.Rd | 36 ++++--------------- tests/testit/test-utils.R | 29 +-------------- 5 files changed, 66 insertions(+), 102 deletions(-)
Title: Functions for Time Series Analysis
Description: Nonparametric estimators and tests for time series analysis. The functions use bootstrap techniques and robust nonparametric difference-based estimators to test for the presence of possibly non-monotonic trends and for synchronicity of trends in multiple time series.
Author: Vyacheslav Lyubchich [aut, cre] ,
Yulia R. Gel [aut],
Alexander Brenning [ctb],
Calvin Chu [ctb],
Xin Huang [ctb],
Umar Islambekov [ctb],
Palina Niamkova [ctb],
Dorcas Ofori-Boateng [ctb],
Ethan D. Schaeffer [ctb],
Srishti Vishwakarma [aut],
Xingyu W [...truncated...]
Maintainer: Vyacheslav Lyubchich <lyubchich@umces.edu>
Diff between funtimes versions 9.1 dated 2023-03-21 and 10.0 dated 2025-12-05
funtimes-10.0/funtimes/DESCRIPTION | 17 - funtimes-10.0/funtimes/MD5 | 79 ++---- funtimes-10.0/funtimes/NAMESPACE | 13 - funtimes-10.0/funtimes/R/AuePolyReg_test.R | 2 funtimes-10.0/funtimes/R/GombayCPA_test.R | 2 funtimes-10.0/funtimes/R/VAR.R | 22 + funtimes-10.0/funtimes/R/VARselect.R | 22 + funtimes-10.0/funtimes/R/causality_pred.R | 109 ++++---- funtimes-10.0/funtimes/R/cumsumCPA_test.R | 2 funtimes-10.0/funtimes/R/fun_causality.R | 13 + funtimes-10.0/funtimes/R/fun_cusum.R | 16 + funtimes-10.0/funtimes/R/fun_trend.R |only funtimes-10.0/funtimes/R/fun_trust.R | 17 + funtimes-10.0/funtimes/R/funtimes.R | 1 funtimes-10.0/funtimes/R/notrend_test.R | 4 funtimes-10.0/funtimes/R/r_crit.R |only funtimes-10.0/funtimes/R/tails_i.R | 2 funtimes-10.0/funtimes/R/tails_q.R | 2 funtimes-10.0/funtimes/R/toMlm.R | 29 +- funtimes-10.0/funtimes/build/partial.rdb |binary funtimes-10.0/funtimes/build/vignette.rds |binary funtimes-10.0/funtimes/inst/doc/beales.R | 8 funtimes-10.0/funtimes/inst/doc/beales.html | 111 ++++---- funtimes-10.0/funtimes/inst/doc/trendtests.R | 10 funtimes-10.0/funtimes/inst/doc/trendtests.html | 228 ++++++++--------- funtimes-10.0/funtimes/inst/doc/tsclusters.R | 16 - funtimes-10.0/funtimes/inst/doc/tsclusters.html | 281 +++++++++++----------- funtimes-10.0/funtimes/man/AuePolyReg_test.Rd | 2 funtimes-10.0/funtimes/man/GombayCPA_test.Rd | 2 funtimes-10.0/funtimes/man/causality_pred.Rd | 5 funtimes-10.0/funtimes/man/cumsumCPA_test.Rd | 2 funtimes-10.0/funtimes/man/funtimes-defunct.Rd | 74 ----- funtimes-10.0/funtimes/man/r_crit.Rd |only funtimes-10.0/funtimes/man/tails_i.Rd | 2 funtimes-10.0/funtimes/man/tails_q.Rd | 2 funtimes-9.1/funtimes/R/i.tails.R |only funtimes-9.1/funtimes/R/mcusum.test.R |only funtimes-9.1/funtimes/R/notrend.test.R |only funtimes-9.1/funtimes/R/q.tails.R |only funtimes-9.1/funtimes/R/sync.cluster.R |only funtimes-9.1/funtimes/R/sync.test.R |only funtimes-9.1/funtimes/R/wavk.test.R |only funtimes-9.1/funtimes/man/i.tails-defunct.Rd |only funtimes-9.1/funtimes/man/mcusum.test-defunct.Rd |only funtimes-9.1/funtimes/man/notrend.test-defunct.Rd |only funtimes-9.1/funtimes/man/q.tails-defunct.Rd |only funtimes-9.1/funtimes/man/sync.cluster-defunct.Rd |only funtimes-9.1/funtimes/man/sync.test-defunct.Rd |only funtimes-9.1/funtimes/man/wavk.test-defunct.Rd |only 49 files changed, 546 insertions(+), 549 deletions(-)
Title: Kornbrot's Rank Difference Test
Description: Implements Kornbrot's rank difference test as described in
<doi:10.1111/j.2044-8317.1990.tb00939.x>. This method is a modified
Wilcoxon signed-rank test which produces consistent and meaningful
results for ordinal or monotonically-transformed data.
Author: Brett Klamer [aut, cre]
Maintainer: Brett Klamer <code@brettklamer.com>
Diff between rankdifferencetest versions 2025.4.21 dated 2025-04-22 and 2025.12.4 dated 2025-12-04
rankdifferencetest-2025.12.4/rankdifferencetest/DESCRIPTION | 22 rankdifferencetest-2025.12.4/rankdifferencetest/MD5 | 73 - rankdifferencetest-2025.12.4/rankdifferencetest/NAMESPACE | 63 rankdifferencetest-2025.12.4/rankdifferencetest/NEWS.md | 33 rankdifferencetest-2025.12.4/rankdifferencetest/R/as.data.frame.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/bkbase.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/data.r | 15 rankdifferencetest-2025.12.4/rankdifferencetest/R/pmedian.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/print.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/rankdifferencetest-package.r | 1 rankdifferencetest-2025.12.4/rankdifferencetest/R/rdpmedian.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/rdt.r | 695 ++++++---- rankdifferencetest-2025.12.4/rankdifferencetest/R/rdt_data.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_data.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_method.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_pmedian.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_pvalue.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_ranks.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_result.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/srt_statistic.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/tidy.r |only rankdifferencetest-2025.12.4/rankdifferencetest/R/utils.r | 94 - rankdifferencetest-2025.12.4/rankdifferencetest/README.md | 43 rankdifferencetest-2025.12.4/rankdifferencetest/build/partial.rdb |binary rankdifferencetest-2025.12.4/rankdifferencetest/inst/REFERENCES.bib | 178 ++ rankdifferencetest-2025.12.4/rankdifferencetest/inst/tinytest |only rankdifferencetest-2025.12.4/rankdifferencetest/man/as.data.frame.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/kornbrot_table1.Rd | 14 rankdifferencetest-2025.12.4/rankdifferencetest/man/pmedian.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/print.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/rankdifferencetest-package.Rd | 1 rankdifferencetest-2025.12.4/rankdifferencetest/man/rdpmedian.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/rdt.Rd | 333 ++-- rankdifferencetest-2025.12.4/rankdifferencetest/man/rdt_data.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/reexports.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_data.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_method.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_pmedian.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_pvalue.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_ranks.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_result.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/srt_statistic.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/man/tidy.Rd |only rankdifferencetest-2025.12.4/rankdifferencetest/tests/manual |only rankdifferencetest-2025.12.4/rankdifferencetest/tests/tinytest.r |only rankdifferencetest-2025.4.21/rankdifferencetest/LICENSE |only rankdifferencetest-2025.4.21/rankdifferencetest/tests/test-all.R |only rankdifferencetest-2025.4.21/rankdifferencetest/tests/testit |only 50 files changed, 1113 insertions(+), 452 deletions(-)
More information about rankdifferencetest at CRAN
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Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.1.2 dated 2025-11-28 and 1.1.4 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/utility_functions.R | 4 +++- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: WOFOST Crop Growth Simulation Model
Description: An implementation of the WOFOST ("World Food Studies") crop growth model. WOFOST is a dynamic simulation model that uses daily weather data, and crop, soil and management parameters to simulate crop growth and development. See De Wit et al. (2019) <doi:10.1016/j.agsy.2018.06.018> for a recent review of the history and use of the model.
Author: Robert J. Hijmans [cre, aut],
Huang Fang [ctb],
C.A. van Diepen [ctb],
Allard de Wit [ctb],
Daniel van Kraalingen [ctb],
Tamme van der Wal [ctb],
C. Rappoldt [ctb],
Hendrik Boogard [ctb],
I.G.A.M. Noy [ctb],
Alterra, Wageningen-UR [cph]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between Rwofost versions 0.8-3 dated 2021-10-01 and 0.8-6 dated 2025-12-04
DESCRIPTION | 9 +++--- MD5 | 33 +++++++++++++------------ R/RcppExports.R | 2 - R/show.R |only R/spatial.R | 64 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary man/Rwofost-package.Rd | 3 +- man/predict.Rd | 12 ++++----- man/wofost.Rd | 2 - man/wofost_control.Rd | 3 +- man/wofost_crop.Rd | 4 +-- man/wofost_model.Rd | 2 - man/wofost_soil.Rd | 3 +- src/RcppExports.cpp | 5 +++ src/batch.cpp | 57 ++++++++++++++++++++++++++----------------- src/cropsi.cpp | 1 src/wofost.cpp | 17 ++++++++----- src/wofost.h | 22 +++++++++++++--- 18 files changed, 148 insertions(+), 91 deletions(-)
Title: Adaptive Rejection Metropolis Sampling (ARMS) via 'Rcpp'
Description: An efficient 'Rcpp' implementation of the Adaptive Rejection Metropolis Sampling (ARMS) algorithm proposed by Gilks, W. R., Best, N. G. and Tan, K. K. C. (1995) <doi:10.2307/2986138>. This allows for sampling from a univariate target probability distribution specified by its (potentially unnormalised) log density.
Author: Michael Bertolacci [aut, cre]
Maintainer: Michael Bertolacci <m.bertolacci@gmail.com>
Diff between armspp versions 0.0.2 dated 2019-05-24 and 0.0.3 dated 2025-12-04
DESCRIPTION | 9 - MD5 | 22 ++-- R/arms.R | 2 build/vignette.rds |binary inst/doc/arms.R | 8 - inst/doc/arms.Rmd | 2 inst/doc/arms.html | 271 ++++++++++++++++++++++++++++++++-------------------- man/arms.Rd | 20 ++- man/arms_gibbs.Rd | 20 ++- src/Makevars | 1 src/RcppExports.cpp | 5 vignettes/arms.Rmd | 2 12 files changed, 222 insertions(+), 140 deletions(-)
Title: eXtreme RuleFit
Description: An implementation of the RuleFit algorithm as described in
Friedman & Popescu (2008) <doi:10.1214/07-AOAS148>. eXtreme Gradient
Boosting ('XGBoost') is used to build rules, and 'glmnet' is used to
fit a sparse linear model on the raw and rule features. The result is
a model that learns similarly to a tree ensemble, while often offering
improved interpretability and achieving improved scoring runtime in
live applications. Several algorithms for reducing rule complexity are
provided, most notably hyperrectangle de-overlapping. All algorithms
scale to several million rows and support sparse representations to
handle tens of thousands of dimensions.
Author: Karl Holub [aut, cre]
Maintainer: Karl Holub <karljholub@gmail.com>
Diff between xrf versions 0.2.2 dated 2022-10-04 and 0.3.0 dated 2025-12-04
DESCRIPTION | 39 +- MD5 | 26 - NAMESPACE | 1 R/glmnot.R | 118 ++++--- R/hyperrectangle_overlap.R | 350 +++++++++++++-------- R/utils.R | 49 ++- R/xrf.R | 624 ++++++++++++++++++++++++++------------- README.md | 19 - inst |only man/xrf.formula.Rd | 7 tests/testthat.R | 8 tests/testthat/helpers.R |only tests/testthat/test_deoverlap.R | 69 ++-- tests/testthat/test_model.R | 159 +++++---- tests/testthat/test_xgb_1_7_11.R |only 15 files changed, 941 insertions(+), 528 deletions(-)
Title: R6-Based ML Survival Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners for survival analysis. The package
provides R6-based survival learners for the following algorithms:
'glmnet' <https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'rpart'
<https://CRAN.R-project.org/package=rpart>. These can be used directly
with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mlsurvlrnrs versions 0.0.6 dated 2025-09-09 and 0.0.7 dated 2025-12-04
DESCRIPTION | 13 MD5 | 84 +- NAMESPACE | 24 R/learner_surv_coxph_cox.R | 316 +++---- R/learner_surv_glmnet_cox.R | 526 ++++++------ R/learner_surv_ranger_cox.R | 587 +++++++------- R/learner_surv_xgboost_aft.R | 514 ++++++------ R/learner_surv_xgboost_cox.R | 335 ++++---- R/surv_c_index.R | 54 - R/zzz.R | 50 - build/vignette.rds |binary inst/doc/mlsurvlrnrs_glmnet_survival.html | 180 +++- inst/doc/mlsurvlrnrs_glmnet_survival.qmd | 1022 ++++++++++++------------- inst/doc/mlsurvlrnrs_ranger_survival.R | 55 - inst/doc/mlsurvlrnrs_ranger_survival.html | 235 ++++- inst/doc/mlsurvlrnrs_ranger_survival.qmd | 907 +++++++++++----------- inst/doc/mlsurvlrnrs_rpart_survival.html | 180 +++- inst/doc/mlsurvlrnrs_rpart_survival.qmd | 868 ++++++++++----------- inst/doc/mlsurvlrnrs_xgboost_survival_aft.R | 139 +-- inst/doc/mlsurvlrnrs_xgboost_survival_aft.html | 377 ++++++--- inst/doc/mlsurvlrnrs_xgboost_survival_aft.qmd | 933 +++++++++++----------- inst/doc/mlsurvlrnrs_xgboost_survival_cox.R | 150 ++- inst/doc/mlsurvlrnrs_xgboost_survival_cox.html | 330 +++++--- inst/doc/mlsurvlrnrs_xgboost_survival_cox.qmd | 938 +++++++++++----------- man/LearnerSurvCoxPHCox.Rd | 284 +++--- man/LearnerSurvGlmnetCox.Rd | 308 +++---- man/LearnerSurvRangerCox.Rd | 314 +++---- man/LearnerSurvRpartCox.Rd | 342 ++++---- man/LearnerSurvXgboostAft.Rd | 356 ++++---- man/LearnerSurvXgboostCox.Rd | 348 ++++---- man/c_index.Rd | 66 - tests/testthat.R | 30 tests/testthat/test-lints.R | 26 tests/testthat/test-surv_glmnet_cox.R | 214 ++--- tests/testthat/test-surv_ranger_cox.R | 236 ++--- tests/testthat/test-surv_rpart_cox.R | 230 ++--- tests/testthat/test-surv_xgboost_aft.R | 295 ++++--- tests/testthat/test-surv_xgboost_cox.R | 296 ++++--- vignettes/mlsurvlrnrs_glmnet_survival.qmd | 1022 ++++++++++++------------- vignettes/mlsurvlrnrs_ranger_survival.qmd | 907 +++++++++++----------- vignettes/mlsurvlrnrs_rpart_survival.qmd | 868 ++++++++++----------- vignettes/mlsurvlrnrs_xgboost_survival_aft.qmd | 933 +++++++++++----------- vignettes/mlsurvlrnrs_xgboost_survival_cox.qmd | 938 +++++++++++----------- 43 files changed, 8849 insertions(+), 7981 deletions(-)
Title: Web Framework Inspired by 'Express.js'
Description: A web framework inspired by 'express.js' to build
any web service from multi-page websites to 'RESTful'
application programming interfaces.
Author: John Coene [aut] ,
Opifex [fnd],
Kennedy Mwavu [cre] ,
Julio Collazos [ctb]
Maintainer: Kennedy Mwavu <mwavukennedy@gmail.com>
Diff between ambiorix versions 2.2.1 dated 2025-07-29 and 2.2.2 dated 2025-12-04
DESCRIPTION | 18 ++--- MD5 | 29 ++++---- NEWS.md | 17 ++++ R/ambiorix.R | 15 +++- R/assertions.R | 12 +++ R/parser.R | 3 R/render.R | 2 R/response.R | 21 +++++- R/route.R | 3 R/routing.R | 138 +++++++++++++++++++++++++++++++++++----- man/Ambiorix.Rd | 2 man/Router.Rd | 2 man/Routing.Rd | 104 ++++++++++++++++++++++++++++++ tests/testthat/test-param.R |only tests/testthat/test-parser.R | 77 +++++++++++++++++----- tests/testthat/test-serialise.R | 48 +++++++++++++ 16 files changed, 427 insertions(+), 64 deletions(-)
Title: An 'Armadillo' Interface
Description: Provides function declarations and inline function definitions that
facilitate communication between R and the 'Armadillo' 'C++' library for
linear algebra and scientific computing. This implementation is derived
from Vargas Sepulveda and Schneider Malamud (2024)
<doi:10.1016/j.softx.2025.102087>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Jonathan Schneider Malamud [ctb],
Conrad Sanderson [aut] )
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between armadillo4r versions 0.6.0 dated 2025-11-03 and 0.7.0 dated 2025-12-04
armadillo4r-0.6.0/armadillo4r/inst/extdata/src/00_main.h |only armadillo4r-0.6.0/armadillo4r/inst/extdata/src/01_ols.cpp |only armadillo4r-0.6.0/armadillo4r/inst/extdata/src/02_your_functions.cpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/cond_rel_bones.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/cond_rel_meat.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eps.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_shift.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/op_misc_bones.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/op_misc_meat.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/op_shift_bones.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/op_shift_meat.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_shift_bones.hpp |only armadillo4r-0.6.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_shift_meat.hpp |only armadillo4r-0.7.0/armadillo4r/DESCRIPTION | 6 armadillo4r-0.7.0/armadillo4r/MD5 | 1318 - armadillo4r-0.7.0/armadillo4r/NEWS.md | 7 armadillo4r-0.7.0/armadillo4r/R/unvendor.R | 29 armadillo4r-0.7.0/armadillo4r/R/vendor.R | 12 armadillo4r-0.7.0/armadillo4r/R/version.R | 4 armadillo4r-0.7.0/armadillo4r/README.md | 2 armadillo4r-0.7.0/armadillo4r/configure | 30 armadillo4r-0.7.0/armadillo4r/inst/extdata/configure | 25 armadillo4r-0.7.0/armadillo4r/inst/extdata/src/01_ols.h |only armadillo4r-0.7.0/armadillo4r/inst/extdata/src/02_your_functions.h |only armadillo4r-0.7.0/armadillo4r/inst/extdata/src/Makevars.in | 4 armadillo4r-0.7.0/armadillo4r/inst/extdata/src/main.cpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r.hpp | 35 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo.hpp | 73 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/BaseCube_bones.hpp | 105 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/BaseCube_meat.hpp | 609 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Base_bones.hpp | 247 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Base_meat.hpp | 1316 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Col_bones.hpp | 418 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Col_meat.hpp | 2243 + armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/CubeToMatOp_bones.hpp | 49 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/CubeToMatOp_meat.hpp | 47 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Cube_bones.hpp | 1031 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Cube_meat.hpp | 7262 +++-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/GenCube_bones.hpp | 63 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/GenCube_meat.hpp | 213 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Gen_bones.hpp | 72 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Gen_meat.hpp | 278 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/GlueCube_bones.hpp | 32 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/GlueCube_meat.hpp | 38 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Glue_bones.hpp | 75 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Glue_meat.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/MapMat_bones.hpp | 277 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/MapMat_meat.hpp | 2080 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Mat_bones.hpp | 1692 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Mat_meat.hpp |12789 ++++++---- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/OpCube_bones.hpp | 53 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/OpCube_meat.hpp | 111 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Op_bones.hpp | 77 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Op_meat.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Proxy.hpp | 4087 +-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/ProxyCube.hpp | 791 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Row_bones.hpp | 421 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/Row_meat.hpp | 2252 + armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SizeCube_bones.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SizeCube_meat.hpp | 188 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SizeMat_bones.hpp | 33 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SizeMat_meat.hpp | 160 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpBase_bones.hpp | 167 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpBase_meat.hpp | 1070 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpCol_bones.hpp | 116 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpCol_meat.hpp | 467 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpGlue_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpGlue_meat.hpp | 63 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpMat_bones.hpp | 1195 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpMat_iterators_meat.hpp | 965 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpMat_meat.hpp | 8291 +++--- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpOp_bones.hpp | 49 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpOp_meat.hpp | 74 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpProxy.hpp | 1293 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpRow_bones.hpp | 113 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpRow_meat.hpp | 470 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpSubview_bones.hpp | 606 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpSubview_col_list_bones.hpp | 134 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpSubview_col_list_meat.hpp | 847 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpSubview_iterators_meat.hpp | 1000 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpSubview_meat.hpp | 2436 + armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpToDGlue_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpToDGlue_meat.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpToDOp_bones.hpp | 59 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpToDOp_meat.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpValProxy_bones.hpp | 71 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/SpValProxy_meat.hpp | 360 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/access.hpp | 74 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_cmath.hpp | 565 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_config.hpp | 436 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_forward.hpp | 807 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_ostream_bones.hpp | 119 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_ostream_meat.hpp | 1504 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_rel_comparators.hpp | 159 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_rng.hpp | 1479 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_rng_cxx03.hpp | 197 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_static_check.hpp | 22 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_str.hpp | 757 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arma_version.hpp | 52 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arrayops_bones.hpp | 360 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/arrayops_meat.hpp | 1330 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/auxlib_bones.hpp | 923 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/auxlib_meat.hpp |11344 ++++---- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/band_helper.hpp | 491 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/compiler_check.hpp | 83 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/compiler_setup.hpp | 636 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/compiler_setup_post.hpp | 16 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/cond_rel.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/config.hpp | 326 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/config.hpp.cmake | 83 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/constants.hpp | 459 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/constants_old.hpp | 130 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/csv_name.hpp | 216 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/debug.hpp | 1852 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_arpack.hpp | 290 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_atlas.hpp | 154 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_blas.hpp | 354 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_fftw3.hpp | 57 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_lapack.hpp | 3918 --- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/def_superlu.hpp | 180 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/diagmat_proxy.hpp | 509 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/diagview_bones.hpp | 140 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/diagview_meat.hpp | 1307 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/diskio_bones.hpp | 494 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/diskio_meat.hpp | 6863 ++--- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/distr_param.hpp | 111 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eGlueCube_bones.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eGlueCube_meat.hpp | 189 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eGlue_bones.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eGlue_meat.hpp | 185 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eOpCube_bones.hpp | 78 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eOpCube_meat.hpp | 219 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eOp_bones.hpp | 73 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eOp_meat.hpp | 172 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eglue_core_bones.hpp | 100 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eglue_core_meat.hpp | 1938 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eop_aux.hpp | 552 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eop_core_bones.hpp | 200 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/eop_core_meat.hpp | 1690 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fft_engine_fftw3.hpp | 202 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fft_engine_kissfft.hpp | 497 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/field_bones.hpp | 627 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/field_meat.hpp | 3552 +- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fill.hpp | 284 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_accu.hpp | 1143 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_all.hpp | 100 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_any.hpp | 100 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_approx_equal.hpp | 702 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_as_scalar.hpp | 544 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_balance.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_chi2rnd.hpp | 207 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_chol.hpp | 174 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_circshift.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_clamp.hpp | 147 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cond_rcond.hpp | 81 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_conv.hpp | 80 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_conv_to.hpp | 1258 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cor.hpp | 48 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cov.hpp | 48 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cross.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cumprod.hpp | 90 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_cumsum.hpp | 90 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_det.hpp | 77 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_diagmat.hpp | 95 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_diags_spdiags.hpp | 163 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_diagvec.hpp | 61 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_diff.hpp | 91 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_dot.hpp | 439 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eig_gen.hpp | 222 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eig_pair.hpp | 179 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eig_sym.hpp | 190 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eigs_gen.hpp | 509 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eigs_sym.hpp | 309 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_elem.hpp | 1428 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_expmat.hpp | 100 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_eye.hpp | 124 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_fft.hpp | 158 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_fft2.hpp | 147 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_find.hpp | 568 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_find_unique.hpp | 67 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_flip.hpp | 75 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_hess.hpp | 194 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_hist.hpp | 81 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_histc.hpp | 59 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_index_max.hpp | 179 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_index_min.hpp | 179 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_inplace_strans.hpp | 106 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_inplace_trans.hpp | 131 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_interp1.hpp | 431 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_interp2.hpp | 350 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_intersect.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_inv.hpp | 143 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_inv_sympd.hpp | 142 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_join.hpp | 574 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_kmeans.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_kron.hpp | 95 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_log_det.hpp | 163 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_log_normpdf.hpp | 230 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_logmat.hpp | 143 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_lu.hpp | 84 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_max.hpp | 312 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_mean.hpp | 160 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_median.hpp | 74 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_min.hpp | 312 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_misc.hpp | 703 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_mvnrnd.hpp | 117 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_n_unique.hpp | 141 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_nonzeros.hpp | 42 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_norm.hpp | 442 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_normalise.hpp | 123 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_normcdf.hpp | 220 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_normpdf.hpp | 228 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_numel.hpp | 92 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_omit.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_ones.hpp | 167 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_orth_null.hpp | 95 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_pinv.hpp | 126 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_polyfit.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_polyval.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_powext.hpp | 199 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_powmat.hpp | 113 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_princomp.hpp | 166 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_prod.hpp | 82 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_qr.hpp | 149 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_quantile.hpp | 57 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_qz.hpp | 60 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_rande.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_randg.hpp | 276 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_randi.hpp | 301 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_randn.hpp | 410 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_randperm.hpp | 182 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_randu.hpp | 402 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_range.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_rank.hpp | 58 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_regspace.hpp | 319 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_repelem.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_repmat.hpp | 88 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_reshape.hpp | 197 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_resize.hpp | 158 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_reverse.hpp | 102 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_roots.hpp | 63 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_schur.hpp | 107 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_shuffle.hpp | 88 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_size.hpp | 347 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_solve.hpp | 263 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sort.hpp | 166 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sort_index.hpp | 117 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_speye.hpp | 91 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_spones.hpp | 40 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sprandn.hpp | 132 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sprandu.hpp | 132 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_spsolve.hpp | 227 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sqrtmat.hpp | 137 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_stddev.hpp | 155 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_strans.hpp | 105 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sum.hpp | 159 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_svd.hpp | 266 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_svds.hpp | 435 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_sylvester.hpp | 154 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_symmat.hpp | 142 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_toeplitz.hpp | 59 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trace.hpp | 751 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trans.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trapz.hpp | 53 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trig.hpp | 517 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trimat.hpp | 150 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trimat_ind.hpp | 143 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trunc_exp.hpp | 99 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_trunc_log.hpp | 106 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_unique.hpp | 58 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_var.hpp | 158 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_vecnorm.hpp | 456 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_vectorise.hpp | 111 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_wishrnd.hpp | 213 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/fn_zeros.hpp | 209 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_affmul_bones.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_affmul_meat.hpp | 685 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_atan2_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_atan2_meat.hpp | 250 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_conv_bones.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_conv_meat.hpp | 462 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cor_bones.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cor_meat.hpp | 76 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cov_bones.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cov_meat.hpp | 72 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cross_bones.hpp | 35 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_cross_meat.hpp | 84 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_hist_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_hist_meat.hpp | 308 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_histc_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_histc_meat.hpp | 212 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_hypot_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_hypot_meat.hpp | 187 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_intersect_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_intersect_meat.hpp | 156 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_join_bones.hpp | 124 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_join_meat.hpp | 553 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_kron_bones.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_kron_meat.hpp | 175 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_max_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_max_meat.hpp | 201 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_min_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_min_meat.hpp | 201 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_mixed_bones.hpp | 136 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_mixed_meat.hpp | 716 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_mvnrnd_bones.hpp | 66 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_mvnrnd_meat.hpp | 212 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_polyfit_bones.hpp | 54 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_polyfit_meat.hpp | 204 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_polyval_bones.hpp | 40 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_polyval_meat.hpp | 97 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_powext_bones.hpp | 98 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_powext_meat.hpp | 775 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_quantile_bones.hpp | 67 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_quantile_meat.hpp | 303 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_relational_bones.hpp | 190 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_relational_meat.hpp | 527 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_solve_bones.hpp | 299 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_solve_meat.hpp | 964 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_times_bones.hpp | 254 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_times_meat.hpp | 1583 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_times_misc_bones.hpp | 122 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_times_misc_meat.hpp | 782 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_toeplitz_bones.hpp | 27 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_toeplitz_meat.hpp | 72 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_trapz_bones.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/glue_trapz_meat.hpp | 231 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_diag_bones.hpp | 305 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_diag_meat.hpp | 3560 +- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_full_bones.hpp | 289 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_full_meat.hpp | 3683 +- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_misc_bones.hpp | 142 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/gmm_misc_meat.hpp | 203 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/hdf5_misc.hpp | 846 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/hdf5_name.hpp | 133 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/include_hdf5.hpp | 63 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/include_superlu.hpp | 633 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/injector_bones.hpp | 79 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/injector_meat.hpp | 424 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/memory.hpp | 301 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mp_misc.hpp | 101 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtGlueCube_bones.hpp | 37 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtGlueCube_meat.hpp | 51 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtGlue_bones.hpp | 47 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtGlue_meat.hpp | 66 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtOpCube_bones.hpp | 66 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtOpCube_meat.hpp | 135 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtOp_bones.hpp | 72 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtOp_meat.hpp | 138 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpGlue_bones.hpp | 43 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpGlue_meat.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpOp_bones.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpOp_meat.hpp | 102 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpReduceOp_bones.hpp | 67 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mtSpReduceOp_meat.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mul_gemm.hpp | 732 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mul_gemm_mixed.hpp | 378 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mul_gemv.hpp | 731 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mul_herk.hpp | 667 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/mul_syrk.hpp | 647 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_DenseGenMatProd_bones.hpp | 34 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_DenseGenMatProd_meat.hpp | 47 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_DoubleShiftQR_bones.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_DoubleShiftQR_meat.hpp | 322 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_EigsSelect.hpp | 57 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_GenEigsSolver_bones.hpp | 118 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_GenEigsSolver_meat.hpp | 418 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SortEigenvalue.hpp | 235 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SparseGenMatProd_bones.hpp | 38 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SparseGenMatProd_meat.hpp | 58 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SparseGenRealShiftSolve_bones.hpp | 52 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SparseGenRealShiftSolve_meat.hpp | 180 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SymEigsShiftSolver_bones.hpp | 33 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SymEigsShiftSolver_meat.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SymEigsSolver_bones.hpp | 108 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_SymEigsSolver_meat.hpp | 404 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_TridiagEigen_bones.hpp | 38 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_TridiagEigen_meat.hpp | 165 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_UpperHessenbergEigen_bones.hpp | 56 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_UpperHessenbergEigen_meat.hpp | 201 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_UpperHessenbergQR_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_UpperHessenbergQR_meat.hpp | 234 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/newarp_cx_attrib.hpp | 44 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_accu_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_accu_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_all_bones.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_all_meat.hpp | 605 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_any_bones.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_any_meat.hpp | 599 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_chi2rnd_bones.hpp | 47 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_chi2rnd_meat.hpp | 189 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_chol_bones.hpp | 34 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_chol_meat.hpp | 89 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_circshift_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_circshift_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_clamp_bones.hpp | 111 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_clamp_meat.hpp | 744 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_col_as_mat_bones.hpp | 25 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_col_as_mat_meat.hpp | 49 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cond_bones.hpp | 34 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cond_meat.hpp | 217 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cor_bones.hpp | 30 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cor_meat.hpp | 144 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cov_bones.hpp | 30 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cov_meat.hpp | 116 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cumprod_bones.hpp | 51 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cumprod_meat.hpp | 226 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cumsum_bones.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cumsum_meat.hpp | 226 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cx_scalar_bones.hpp | 221 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_cx_scalar_meat.hpp | 739 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_det_bones.hpp | 58 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_det_meat.hpp | 223 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diagmat_bones.hpp | 72 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diagmat_meat.hpp | 944 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diagvec_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diagvec_meat.hpp | 609 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diff_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_diff_meat.hpp | 311 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_dot_bones.hpp | 167 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_dot_meat.hpp | 806 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_dotext_bones.hpp | 57 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_dotext_meat.hpp | 227 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_elem_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_elem_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_expmat_bones.hpp | 58 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_expmat_meat.hpp | 337 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_fft_bones.hpp | 67 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_fft_meat.hpp | 437 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_find_bones.hpp | 156 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_find_meat.hpp | 1025 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_find_unique_bones.hpp | 84 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_find_unique_meat.hpp | 162 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_flip_bones.hpp | 73 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_flip_meat.hpp | 395 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_hist_bones.hpp | 30 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_hist_meat.hpp | 167 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_htrans_bones.hpp | 161 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_htrans_meat.hpp | 499 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_index_max_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_index_max_meat.hpp | 509 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_index_min_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_index_min_meat.hpp | 509 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_inv_gen_bones.hpp | 223 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_inv_gen_meat.hpp | 574 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_inv_spd_bones.hpp | 92 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_inv_spd_meat.hpp | 472 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_log_det_bones.hpp | 60 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_log_det_meat.hpp | 303 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_logmat_bones.hpp | 112 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_logmat_meat.hpp | 763 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_max_bones.hpp | 177 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_max_meat.hpp | 1725 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_mean_bones.hpp | 148 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_mean_meat.hpp | 837 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_median_bones.hpp | 95 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_median_meat.hpp | 399 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_min_bones.hpp | 179 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_min_meat.hpp | 1725 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_nonzeros_bones.hpp | 35 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_nonzeros_meat.hpp | 127 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_norm2est_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_norm2est_meat.hpp | 317 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_norm_bones.hpp | 92 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_norm_meat.hpp | 1366 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_normalise_bones.hpp | 48 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_normalise_meat.hpp | 166 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_omit_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_omit_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_orth_null_bones.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_orth_null_meat.hpp | 245 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_pinv_bones.hpp | 74 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_pinv_meat.hpp | 461 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_powmat_bones.hpp | 61 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_powmat_meat.hpp | 386 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_princomp_bones.hpp | 89 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_princomp_meat.hpp | 366 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_prod_bones.hpp | 34 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_prod_meat.hpp | 232 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_range_bones.hpp | 31 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_range_meat.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_rank_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_rank_meat.hpp | 273 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_rcond_bones.hpp | 23 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_rcond_meat.hpp | 119 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_relational_bones.hpp | 181 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_relational_meat.hpp | 746 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_repelem_bones.hpp | 34 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_repelem_meat.hpp | 104 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_repmat_bones.hpp | 44 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_repmat_meat.hpp | 193 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_reshape_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_reshape_meat.hpp | 360 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_resize_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_resize_meat.hpp | 233 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_reverse_bones.hpp | 49 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_reverse_meat.hpp | 210 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_roots_bones.hpp | 42 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_roots_meat.hpp | 170 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_row_as_mat_bones.hpp | 25 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_row_as_mat_meat.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_shuffle_bones.hpp | 47 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_shuffle_meat.hpp | 254 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sort_bones.hpp | 62 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sort_index_bones.hpp | 169 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sort_index_meat.hpp | 229 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sort_meat.hpp | 415 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_as_dense_bones.hpp | 25 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_as_dense_meat.hpp | 27 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_diagvec_bones.hpp | 28 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_diagvec_meat.hpp | 59 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_max_bones.hpp | 86 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_max_meat.hpp | 739 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_mean_bones.hpp | 80 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_mean_meat.hpp | 428 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_min_bones.hpp | 86 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_min_meat.hpp | 787 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_minus_bones.hpp | 69 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_minus_meat.hpp | 180 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_nonzeros_bones.hpp | 28 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_nonzeros_meat.hpp | 101 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_plus_bones.hpp | 41 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_plus_meat.hpp | 94 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_stddev_bones.hpp | 37 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_stddev_meat.hpp | 181 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_sum_bones.hpp | 28 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_sum_meat.hpp | 156 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_var_bones.hpp | 70 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_var_meat.hpp | 348 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_vecnorm_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sp_vecnorm_meat.hpp | 233 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sqrtmat_bones.hpp | 108 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sqrtmat_meat.hpp | 673 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_stddev_bones.hpp | 55 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_stddev_meat.hpp | 211 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_strans_bones.hpp | 107 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_strans_meat.hpp | 636 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sum_bones.hpp | 97 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_sum_meat.hpp | 747 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_symmat_bones.hpp | 75 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_symmat_meat.hpp | 325 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_toeplitz_bones.hpp | 43 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_toeplitz_meat.hpp | 137 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_trimat_bones.hpp | 93 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_trimat_meat.hpp | 484 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_unique_bones.hpp | 91 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_unique_meat.hpp | 220 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_var_bones.hpp | 85 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_var_meat.hpp | 466 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_vecnorm_bones.hpp | 69 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_vecnorm_meat.hpp | 303 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_vectorise_bones.hpp | 116 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_vectorise_meat.hpp | 580 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_wishrnd_bones.hpp | 64 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/op_wishrnd_meat.hpp | 368 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_div.hpp | 217 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_minus.hpp | 234 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_plus.hpp | 234 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_relational.hpp | 333 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_schur.hpp | 135 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_cube_times.hpp | 129 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_div.hpp | 440 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_minus.hpp | 570 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_ostream.hpp | 181 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_plus.hpp | 499 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_relational.hpp | 819 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_schur.hpp | 446 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/operator_times.hpp | 556 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/podarray_bones.hpp | 94 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/podarray_meat.hpp | 340 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/promote_type.hpp | 855 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/restrictors.hpp | 738 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/running_stat_bones.hpp | 146 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/running_stat_meat.hpp | 522 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/running_stat_vec_bones.hpp | 242 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/running_stat_vec_meat.hpp | 771 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/sp_auxlib_bones.hpp | 413 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/sp_auxlib_meat.hpp | 3902 +-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/span.hpp | 81 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spdiagview_bones.hpp | 135 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spdiagview_meat.hpp | 1297 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_join_bones.hpp | 109 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_join_meat.hpp | 438 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_kron_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_kron_meat.hpp | 157 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_max_bones.hpp | 68 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_max_meat.hpp | 231 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_merge_bones.hpp | 36 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_merge_meat.hpp | 625 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_min_bones.hpp | 68 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_min_meat.hpp | 229 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_minus_bones.hpp | 80 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_minus_meat.hpp | 408 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_plus_bones.hpp | 70 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_plus_meat.hpp | 348 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_relational_bones.hpp | 103 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_relational_meat.hpp | 564 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_schur_bones.hpp | 86 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_schur_meat.hpp | 470 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_times_bones.hpp | 76 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spglue_times_meat.hpp | 386 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_accu_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_accu_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_circshift_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_circshift_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_diagmat_bones.hpp | 85 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_diagmat_meat.hpp | 566 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_htrans_bones.hpp | 49 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_htrans_meat.hpp | 87 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_misc_bones.hpp | 372 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_misc_meat.hpp | 766 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_norm_bones.hpp | 45 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_norm_meat.hpp | 170 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_normalise_bones.hpp | 28 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_normalise_meat.hpp | 147 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_omit_bones.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_omit_meat.hpp |only armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_relational_bones.hpp | 163 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_relational_meat.hpp | 671 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_repmat_bones.hpp | 40 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_repmat_meat.hpp | 143 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_reverse_bones.hpp | 35 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_reverse_meat.hpp | 208 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_strans_bones.hpp | 53 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_strans_meat.hpp | 183 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_symmat_bones.hpp | 43 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_symmat_meat.hpp | 106 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_trimat_bones.hpp | 83 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_trimat_meat.hpp | 417 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_vectorise_bones.hpp | 66 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spop_vectorise_meat.hpp | 126 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spsolve_factoriser_bones.hpp | 65 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/spsolve_factoriser_meat.hpp | 349 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/strip.hpp | 234 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_bones.hpp | 1004 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_bones.hpp | 351 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_each_bones.hpp | 240 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_each_meat.hpp | 1229 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_meat.hpp | 3547 +- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_slices_bones.hpp | 122 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_cube_slices_meat.hpp | 670 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_each_bones.hpp | 255 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_each_meat.hpp | 1729 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_elem1_bones.hpp | 158 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_elem1_meat.hpp | 1316 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_elem2_bones.hpp | 165 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_elem2_meat.hpp | 1346 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_field_bones.hpp | 119 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_field_meat.hpp | 751 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/subview_meat.hpp | 6534 +++-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/sym_helper.hpp | 676 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/traits.hpp | 2241 - armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_arpack.hpp | 302 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_atlas.hpp | 445 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_blas.hpp | 511 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_fftw3.hpp | 139 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_lapack.hpp | 3906 +-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/translate_superlu.hpp | 509 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/trimat_helper.hpp | 204 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/typedef_elem.hpp | 233 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/typedef_elem_check.hpp | 59 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/typedef_mat.hpp | 224 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/typedef_mat_fixed.hpp | 163 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/unwrap.hpp | 4250 +-- armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/unwrap_cube.hpp | 144 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/unwrap_spmat.hpp | 259 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/upgrade_val.hpp | 310 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/wall_clock_bones.hpp | 46 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/wall_clock_meat.hpp | 119 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/xtrans_mat_bones.hpp | 50 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/xtrans_mat_meat.hpp | 87 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/xvec_htrans_bones.hpp | 48 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/armadillo/xvec_htrans_meat.hpp | 106 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/wrappers/matrices.hpp | 11 armadillo4r-0.7.0/armadillo4r/inst/include/armadillo4r/wrappers/vectors.hpp | 25 armadillo4r-0.7.0/armadillo4r/inst/include/update_instructions.md |only armadillo4r-0.7.0/armadillo4r/man/armadillo4r-package.Rd | 2 armadillo4r-0.7.0/armadillo4r/tests/testthat/test-version.R | 2 678 files changed, 147139 insertions(+), 118546 deletions(-)
Title: 'RSpace' API Wrapper
Description: Wrapper for the 'RSpace' Electronic Lab Notebook (<https://www.researchspace.com/>)
API. This packages provides convenience functions to browse, search, create,
and edit your 'RSpace' documents. In addition, it enables filling 'RSpace' templates
from R Markdown/Quarto templates or tabular data (e.g., 'Excel' files).
This R package is not developed or endorsed by 'Research Space'.
Author: Gerhard Burger [aut, cre] ,
Hanneke Leegwater [aut] ,
Leiden University [cph, fnd]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between rspacer versions 0.3.0 dated 2025-10-17 and 0.3.1 dated 2025-12-04
rspacer-0.3.0/rspacer/inst/doc/rspacer.Rmd |only rspacer-0.3.0/rspacer/vignettes/rspacer.Rmd |only rspacer-0.3.0/rspacer/vignettes/rspacer.Rmd.in |only rspacer-0.3.1/rspacer/DESCRIPTION | 22 rspacer-0.3.1/rspacer/MD5 | 18 rspacer-0.3.1/rspacer/NEWS.md | 5 rspacer-0.3.1/rspacer/R/rspacer-package.R | 7 rspacer-0.3.1/rspacer/build/vignette.rds |binary rspacer-0.3.1/rspacer/inst/doc/rspacer.html | 1503 +++++++++----------- rspacer-0.3.1/rspacer/inst/doc/rspacer.qmd |only rspacer-0.3.1/rspacer/vignettes/prebuild_vignette.R | 11 rspacer-0.3.1/rspacer/vignettes/rspacer.qmd |only rspacer-0.3.1/rspacer/vignettes/rspacer.qmd.in |only 13 files changed, 789 insertions(+), 777 deletions(-)
Title: Analysis of Antimicrobial Minimum Inhibitory Concentration Data
Description: Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data.
Validate the results of an MIC experiment by comparing observed MIC values to
a gold standard assay, in line with standards from the International Organization for
Standardization (2021) <https://www.iso.org/standard/79377.html>.
Author: Alessandro Gerada [aut, cre, cph]
Maintainer: Alessandro Gerada <alessandro.gerada@liverpool.ac.uk>
Diff between MIC versions 1.2.0 dated 2025-10-12 and 2.0.0 dated 2025-12-04
MIC-1.2.0/MIC/R/RcppExports.R |only MIC-1.2.0/MIC/R/cv.R |only MIC-1.2.0/MIC/R/data_converters.R |only MIC-1.2.0/MIC/R/kmer_batch.R |only MIC-1.2.0/MIC/R/meta_data.R |only MIC-1.2.0/MIC/R/patric.R |only MIC-1.2.0/MIC/build |only MIC-1.2.0/MIC/inst |only MIC-1.2.0/MIC/man/combined_file_system.Rd |only MIC-1.2.0/MIC/man/download_patric_db.Rd |only MIC-1.2.0/MIC/man/figures/lifecycle-deprecated.svg |only MIC-1.2.0/MIC/man/figures/lifecycle-experimental.svg |only MIC-1.2.0/MIC/man/figures/lifecycle-stable.svg |only MIC-1.2.0/MIC/man/figures/lifecycle-superseded.svg |only MIC-1.2.0/MIC/man/genome_to_libsvm.Rd |only MIC-1.2.0/MIC/man/genomes_to_kmer_libsvm.Rd |only MIC-1.2.0/MIC/man/kmers.Rd |only MIC-1.2.0/MIC/man/load_patric_db.Rd |only MIC-1.2.0/MIC/man/move_files.Rd |only MIC-1.2.0/MIC/man/pull_PATRIC_genomes.Rd |only MIC-1.2.0/MIC/man/replace_multiple_slashes.Rd |only MIC-1.2.0/MIC/man/reverse_complement.Rd |only MIC-1.2.0/MIC/man/split_and_combine_files.Rd |only MIC-1.2.0/MIC/man/squeezed_index_to_str.Rd |only MIC-1.2.0/MIC/man/squeezed_mers.Rd |only MIC-1.2.0/MIC/man/tidy_patric_meta_data.Rd |only MIC-1.2.0/MIC/man/train_test_filesystem.Rd |only MIC-1.2.0/MIC/man/unsqueezed_index_to_str.Rd |only MIC-1.2.0/MIC/man/unsqueezed_mers.Rd |only MIC-1.2.0/MIC/man/xgb.cv.lowmem.Rd |only MIC-1.2.0/MIC/src |only MIC-1.2.0/MIC/tests/testthat/fixtures |only MIC-1.2.0/MIC/tests/testthat/test-cv.R |only MIC-1.2.0/MIC/tests/testthat/test-data_converters.R |only MIC-1.2.0/MIC/tests/testthat/test-kmer_batch.R |only MIC-1.2.0/MIC/tests/testthat/test-kmers.R |only MIC-1.2.0/MIC/tests/testthat/test-meta_data.R |only MIC-1.2.0/MIC/tests/testthat/test-patric.R |only MIC-2.0.0/MIC/DESCRIPTION | 22 +-- MIC-2.0.0/MIC/MD5 | 122 ++++++------------- MIC-2.0.0/MIC/NAMESPACE | 30 ---- MIC-2.0.0/MIC/NEWS.md | 9 + MIC-2.0.0/MIC/R/MIC-package.R | 18 -- MIC-2.0.0/MIC/R/data.R | 2 MIC-2.0.0/MIC/R/mic_manipulation.R |only MIC-2.0.0/MIC/R/plotting.R |only MIC-2.0.0/MIC/R/qc.R |only MIC-2.0.0/MIC/R/validation.R |only MIC-2.0.0/MIC/README.md | 11 - MIC-2.0.0/MIC/man/MIC-package.Rd | 2 MIC-2.0.0/MIC/man/as.sir_vectorised.Rd | 2 MIC-2.0.0/MIC/man/bias.Rd | 2 MIC-2.0.0/MIC/man/clean_raw_mic.Rd | 2 MIC-2.0.0/MIC/man/compare_mic.Rd | 2 MIC-2.0.0/MIC/man/compare_sir.Rd | 2 MIC-2.0.0/MIC/man/droplevels.mic_validation.Rd | 2 MIC-2.0.0/MIC/man/ecoffs.Rd | 2 MIC-2.0.0/MIC/man/essential_agreement.Rd | 2 MIC-2.0.0/MIC/man/fill_dilution_levels.Rd | 2 MIC-2.0.0/MIC/man/force_mic.Rd | 2 MIC-2.0.0/MIC/man/get_mic.Rd | 2 MIC-2.0.0/MIC/man/mic_censor.Rd | 2 MIC-2.0.0/MIC/man/mic_r_breakpoint.Rd | 2 MIC-2.0.0/MIC/man/mic_range.Rd | 2 MIC-2.0.0/MIC/man/mic_s_breakpoint.Rd | 2 MIC-2.0.0/MIC/man/mic_uncensor.Rd | 6 MIC-2.0.0/MIC/man/plot.mic_validation.Rd | 2 MIC-2.0.0/MIC/man/print.mic_validation.Rd | 2 MIC-2.0.0/MIC/man/print.mic_validation_summary.Rd | 2 MIC-2.0.0/MIC/man/qc_in_range.Rd | 2 MIC-2.0.0/MIC/man/qc_on_target.Rd | 2 MIC-2.0.0/MIC/man/standardise_mic.Rd | 2 MIC-2.0.0/MIC/man/subset.mic_validation.Rd | 2 MIC-2.0.0/MIC/man/summary.mic_validation.Rd | 2 MIC-2.0.0/MIC/man/table.Rd | 2 MIC-2.0.0/MIC/tests/testthat/test-mic_manipulation.R |only MIC-2.0.0/MIC/tests/testthat/test-plotting.R |only MIC-2.0.0/MIC/tests/testthat/test-qc.R |only MIC-2.0.0/MIC/tests/testthat/test-validation.R |only 79 files changed, 92 insertions(+), 178 deletions(-)
Title: Create Interactive Gantt Charts with Work Breakdown Structure
Description: Create Primavera-style interactive Gantt charts with Work Breakdown
Structure (WBS) hierarchy and activities. Features include color-coded WBS
items, indented labels, scrollable views for large projects, dynamic date
formatting, and the ability to dim past activities. Built on top of 'plotly'
for interactive visualizations.
Author: Ahmed Aredah [aut, cre]
Maintainer: Ahmed Aredah <Ahmed.Aredah@gmail.com>
Diff between ganttify versions 0.1.1 dated 2025-10-28 and 0.1.7 dated 2025-12-04
DESCRIPTION | 10 MD5 | 15 NAMESPACE | 1 NEWS.md |only R/Ganttify.R | 2767 +++++++++++++++++++++++++++++++++------------------- R/data.R | 2 README.md | 531 ++++++--- man/Ganttify.Rd | 224 +++- man/test_project.Rd | 2 9 files changed, 2290 insertions(+), 1262 deletions(-)
Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superb(), return a plot. It can
also be used to obtain a dataframe with the statistics and their precision intervals
so that other plotting environments (e.g., Excel)
can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109>
or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001> for specific references.
The documentation is available at <https://dcousin3.github.io/superb/> .
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 1.0.0 dated 2025-08-18 and 1.0.1 dated 2025-12-04
DESCRIPTION | 36 +- MD5 | 66 ++-- NEWS.md | 6 R/grd.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/CustomizingSuperbPlots.R | 10 inst/doc/CustomizingSuperbPlots.Rmd | 10 inst/doc/CustomizingSuperbPlots.html | 158 +++++----- inst/doc/TheMakingOf.html | 12 inst/doc/Vignette3.html | 4 inst/doc/Vignette4.html | 4 inst/doc/Vignette5.html | 22 - inst/doc/Vignette6.html | 46 +- inst/doc/Vignette7.html | 2 inst/doc/Vignette8.html | 2 inst/doc/Vignette9.html | 12 inst/doc/VignetteA.html | 32 +- inst/doc/VignetteB.html | 4 inst/doc/VignetteC.Rmd | 6 inst/doc/VignetteC.html | 18 - inst/doc/VignetteE.html | 2 inst/doc/VignetteF.R | 4 inst/doc/VignetteF.Rmd | 4 inst/doc/VignetteF.html | 6 inst/doc/VignetteH.html | 14 inst/superbShiny/App.R | 8 inst/superbShiny/rsconnect/shinyapps.io/dcousin3/superbshiny.dcf | 2 man/GRD.Rd | 2 tests/testthat/test_GRD.R | 29 + vignettes/CustomizingSuperbPlots.Rmd | 10 vignettes/VignetteC.Rmd | 6 vignettes/VignetteF.Rmd | 4 34 files changed, 283 insertions(+), 262 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-10 dated 2024-09-04 and 0.0-11 dated 2025-12-04
DESCRIPTION | 39 - MD5 | 8 R/lme4_functions.R | 1482 ++++++++++++++++++++++++++++++----------------------- configure | 5 configure.ac | 5 5 files changed, 871 insertions(+), 668 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.
Author: Guillermo Vinue [aut, cre],
Irene Epifanio [aut],
Amelia Simo [aut],
M. Victoria Ibanez [aut],
Juan Domingo [aut],
Guillermo Ayala [aut]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between Anthropometry versions 1.20 dated 2025-07-23 and 1.21 dated 2025-12-04
Anthropometry-1.20/Anthropometry/R/CCbiclustAnthropo.R |only Anthropometry-1.20/Anthropometry/R/overlapBiclustersByRows.R |only Anthropometry-1.20/Anthropometry/man/CCbiclustAnthropo.Rd |only Anthropometry-1.20/Anthropometry/man/overlapBiclustersByRows.Rd |only Anthropometry-1.21/Anthropometry/DESCRIPTION | 11 +++---- Anthropometry-1.21/Anthropometry/MD5 | 14 +++------- Anthropometry-1.21/Anthropometry/NAMESPACE | 6 ---- Anthropometry-1.21/Anthropometry/NEWS | 4 ++ Anthropometry-1.21/Anthropometry/inst/doc/Anthropometry.pdf |binary Anthropometry-1.21/Anthropometry/man/Anthropometry-package.Rd | 6 +--- 10 files changed, 16 insertions(+), 25 deletions(-)
Title: Interface for Multilevel Regression and Poststratification
Description: Dual interfaces, graphical and programmatic, designed for
intuitive applications of Multilevel Regression and Poststratification (MRP).
Users can apply the method to a variety of datasets, from electronic health records
to sample survey data, through an end-to-end Bayesian data analysis workflow.
The package provides robust tools for data cleaning, exploratory analysis,
flexible model building, and insightful result visualization. For more details, see
Si et al. (2020) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2020002/article/00003-eng.pdf?st=iF1_Fbrh>
and Si (2025) <doi:10.1214/24-STS932>.
Author: Toan Tran [cre, aut, cph],
Jonah Gabry [aut, cph],
Yajuan Si [aut, cph]
Maintainer: Toan Tran <trannttoan97@gmail.com>
Diff between shinymrp versions 0.9.1 dated 2025-11-11 and 0.10.0 dated 2025-12-04
shinymrp-0.10.0/shinymrp/DESCRIPTION | 12 shinymrp-0.10.0/shinymrp/MD5 | 65 - shinymrp-0.10.0/shinymrp/NEWS.md | 12 shinymrp-0.10.0/shinymrp/R/fct_data.R | 7 shinymrp-0.10.0/shinymrp/R/fct_data_geo.R |only shinymrp-0.10.0/shinymrp/R/fct_model.R | 410 +++++++--- shinymrp-0.10.0/shinymrp/R/global.R | 10 shinymrp-0.10.0/shinymrp/R/mod_analyze_model.R | 42 - shinymrp-0.10.0/shinymrp/R/mod_learn_interface.R | 28 shinymrp-0.10.0/shinymrp/R/model.R | 3 shinymrp-0.10.0/shinymrp/R/shiny_model.R | 3 shinymrp-0.10.0/shinymrp/R/utils_model.R | 109 ++ shinymrp-0.10.0/shinymrp/R/utils_ui.R | 38 shinymrp-0.10.0/shinymrp/R/workflow.R | 36 shinymrp-0.10.0/shinymrp/build/vignette.rds |binary shinymrp-0.10.0/shinymrp/inst/doc/data-prep.Rmd | 1 shinymrp-0.10.0/shinymrp/inst/doc/data-prep.html | 3 shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.R |only shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.Rmd |only shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.html |only shinymrp-0.10.0/shinymrp/inst/doc/workflow.R | 6 shinymrp-0.10.0/shinymrp/inst/doc/workflow.Rmd | 8 shinymrp-0.10.0/shinymrp/inst/doc/workflow.html | 25 shinymrp-0.10.0/shinymrp/inst/scripts/utils.R | 4 shinymrp-0.10.0/shinymrp/man/MRPModel-method-summary.Rd | 3 shinymrp-0.10.0/shinymrp/man/MRPWorkflow-method-create_model.Rd | 13 shinymrp-0.10.0/shinymrp/tests/testthat/test-model-helper.R |only shinymrp-0.10.0/shinymrp/tests/testthat/test-mrp-model.R | 2 shinymrp-0.10.0/shinymrp/vignettes/data-prep.Rmd | 1 shinymrp-0.10.0/shinymrp/vignettes/data/spatial_prior |only shinymrp-0.10.0/shinymrp/vignettes/data/workflow |only shinymrp-0.10.0/shinymrp/vignettes/figures/sample_size_map.png |only shinymrp-0.10.0/shinymrp/vignettes/spatial-prior.Rmd |only shinymrp-0.10.0/shinymrp/vignettes/workflow.Rmd | 8 shinymrp-0.9.1/shinymrp/vignettes/data/loo.csv |only shinymrp-0.9.1/shinymrp/vignettes/data/model.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/data/workflow.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/spatial_prior.html |only 38 files changed, 607 insertions(+), 242 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 2.0.3 dated 2025-11-08 and 2.0.4 dated 2025-12-04
DESCRIPTION | 6 MD5 | 61 +++++---- R/package_data.r | 66 +++++----- R/qpcrANOVAFC.r | 6 data/Lee_etal2020qPCR.rda |binary data/Taylor_etal2019.rda |binary data/data_1factor.rda |binary data/data_2factor.rda |binary data/data_2factorBlock.rda |binary data/data_3factor.rda |binary data/data_repeated_measure_1.rda |binary data/data_repeated_measure_2.rda |binary data/data_withTechRep.rda |binary inst/CITATION |only inst/doc/vignette.html | 192 +++++++++++++++---------------- inst/extdata/Lee_etal2020qPCR.csv | 2 inst/extdata/data_1factor.csv | 2 inst/extdata/data_2factor.csv | 2 inst/extdata/data_2factorBlock.csv | 2 inst/extdata/data_3factor.csv | 2 inst/extdata/data_repeated_measure_1.csv | 2 inst/extdata/data_repeated_measure_2.csv | 2 inst/extdata/data_withTechRep.csv | 2 man/Lee_etal2020qPCR.Rd | 8 - man/data_1factor.Rd | 10 - man/data_2factor.Rd | 8 - man/data_2factorBlock.Rd | 8 - man/data_3factor.Rd | 8 - man/data_repeated_measure_1.Rd | 8 - man/data_repeated_measure_2.Rd | 8 - man/data_withTechRep.Rd | 8 - man/qpcrANOVAFC.Rd | 6 32 files changed, 209 insertions(+), 210 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.7.0-1 dated 2025-09-24 and 0.7.0-2 dated 2025-12-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/convert-array.R | 2 ++ tests/testthat/test-altrep.R | 20 ++++++++++++++------ tests/testthat/test-convert-array.R | 12 ------------ 5 files changed, 23 insertions(+), 25 deletions(-)
Title: Statistical Tools for the Analysis of Psychophysical Data
Description: Tools for the analysis of psychophysical data in R. This package allows to estimate the Point of Subjective Equivalence (PSE)
and the Just Noticeable Difference (JND), either from a psychometric function or from a Generalized Linear Mixed Model (GLMM).
Additionally, the package allows plotting the fitted models and the response data, simulating psychometric functions of different shapes, and simulating data sets.
For a description of the use of GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012).
Author: Alessandro Moscatelli [aut, cre] ,
Priscilla Balestrucci [aut]
Maintainer: Alessandro Moscatelli <moskante@gmail.com>
Diff between MixedPsy versions 1.2.0 dated 2025-02-18 and 1.3.0 dated 2025-12-04
DESCRIPTION | 15 ++++---- MD5 | 9 ++--- NAMESPACE | 1 NEWS.md | 5 ++ R/mix_utils.R | 90 +++++++++++++++++++++++++++++++++++++++++++++++--- man/MixInterpolate.Rd |only 6 files changed, 104 insertions(+), 16 deletions(-)
Title: Ensemble Learning Framework for Diagnostic and Prognostic
Modeling
Description: Provides a framework to build and evaluate diagnosis or
prognosis models using stacking, voting, and bagging ensemble
techniques with various base learners. The package also includes
tools for visualization and interpretation of models. The development
version of the package is available on 'GitHub' at
<https://github.com/xiaojie0519/E2E>. The methods
are based on the foundational work of Breiman (1996) <doi:10.1007/BF00058655>
on bagging and Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1>
on stacking.
Author: Shanjie Luan [aut, cre]
Maintainer: Shanjie Luan <Luan20050519@163.com>
Diff between E2E versions 0.1.1 dated 2025-11-28 and 0.1.2 dated 2025-12-04
DESCRIPTION | 12 ++--- MD5 | 40 +++++++++---------- NAMESPACE | 1 R/diagnosis.R | 21 +-------- R/prognosis.R | 35 ++++++++++------ inst/doc/advanced-features.R | 4 - inst/doc/advanced-features.Rmd | 4 - inst/doc/advanced-features.html | 8 +-- inst/doc/diagnostic-workflow.R | 16 +++---- inst/doc/diagnostic-workflow.Rmd | 16 +++---- inst/doc/diagnostic-workflow.html | 80 +++++++++++++++++++++++++++----------- inst/doc/getting-started.html | 2 inst/doc/integrated-pipeline.R | 6 +- inst/doc/integrated-pipeline.Rmd | 6 +- inst/doc/integrated-pipeline.html | 8 +-- inst/doc/prognostic-workflow.html | 2 man/imbalance_dia.Rd | 6 +- man/xb_dia.Rd | 16 ------- vignettes/advanced-features.Rmd | 4 - vignettes/diagnostic-workflow.Rmd | 16 +++---- vignettes/integrated-pipeline.Rmd | 6 +- 21 files changed, 162 insertions(+), 147 deletions(-)
Title: Hydro-Meteorological Catchments Datasets for the 'airGR'
Packages
Description: Sample of hydro-meteorological datasets extracted from the 'CAMELS-FR' French database <doi:10.57745/WH7FJR>.
It provides metadata and catchment-scale aggregated hydro-meteorological time series on a pool of French catchments for use by the 'airGR' packages.
Author: Olivier Delaigue [aut, cre] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut] ,
Benoît Genot [ctb],
Guilherme Mendoza Guimaraes [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRdatasets versions 0.2.2 dated 2025-11-18 and 0.2.3 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS.md | 9 +++++++++ README.md | 2 +- build/partial.rdb |binary data/A273011002.rda |binary data/A605102001.rda |binary data/B222001001.rda |binary data/E540031001.rda |binary data/E645651001.rda |binary data/F439000101.rda |binary data/H010002001.rda |binary data/H120101001.rda |binary data/H622101001.rda |binary data/J171171001.rda |binary data/J421191001.rda |binary data/K134181001.rda |binary data/K265401001.rda |binary data/K731261001.rda |binary data/V123521001.rda |binary data/X031001001.rda |binary data/X045401001.rda |binary data/Y643401001.rda |binary data/Y862000101.rda |binary 24 files changed, 37 insertions(+), 28 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.3-0 dated 2025-11-18 and 1.3-1 dated 2025-12-04
tram-1.3-0/tram/vignettes/COXME-margsurv-plot-1.pdf |only tram-1.3-0/tram/vignettes/HTECOX-DFS-plot-1.pdf |only tram-1.3-0/tram/vignettes/TVAR-DFS-plot-1.pdf |only tram-1.3-0/tram/vignettes/TVAR-iDFS-plot-1.pdf |only tram-1.3-1/tram/DESCRIPTION | 8 tram-1.3-1/tram/MD5 | 44 - tram-1.3-1/tram/demo/mtram.Rout.save | 48 - tram-1.3-1/tram/demo/survtram.R | 10 tram-1.3-1/tram/demo/survtram.Rout.save | 334 +++++++---- tram-1.3-1/tram/inst/NEWS.Rd | 8 tram-1.3-1/tram/inst/doc/NAMI.Rnw | 2 tram-1.3-1/tram/inst/doc/NAMI.pdf |binary tram-1.3-1/tram/inst/doc/mtram.R | 35 - tram-1.3-1/tram/inst/doc/mtram.Rnw | 43 - tram-1.3-1/tram/inst/doc/mtram.pdf |binary tram-1.3-1/tram/inst/doc/survtram.R | 36 - tram-1.3-1/tram/inst/doc/survtram.Rnw | 215 +++---- tram-1.3-1/tram/inst/doc/survtram.pdf |binary tram-1.3-1/tram/inst/doc/tram.pdf |binary tram-1.3-1/tram/vignettes/NAMI.Rnw | 2 tram-1.3-1/tram/vignettes/mtram.Rnw | 43 - tram-1.3-1/tram/vignettes/survtram-COXME-margsurv-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-HTECOX-DFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-TVAR-DFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-TVAR-iDFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram.Rnw | 215 +++---- tram-1.3-1/tram/vignettes/survtram.bib | 15 27 files changed, 600 insertions(+), 458 deletions(-)
Title: A Universal Differential Expression Prediction Tool for
Single-Cell and Spatial Genomics Data
Description: One key exploratory analysis step in single-cell genomics data analysis
is the prediction of features with different activity levels. For example, we want
to predict differentially expressed genes (DEGs) in single-cell RNA-seq data,
spatial DEGs in spatial transcriptomics data, or differentially accessible
regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially
active features in single cell omics datasets without relying on the clustering
of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler
divergence to find features (e.g., genes, genomic regions, etc) that are active
in subsets of cells that are non-randomly positioned inside an input space (such as
1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For
the theoretical background of 'singleCellHaystack' we refer to our original paper
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>
and our update Vandenbon and Diez [...truncated...]
Author: Alexis Vandenbon [aut, cre] ,
Diego Diez [aut]
Maintainer: Alexis Vandenbon <alexis.vandenbon@gmail.com>
Diff between singleCellHaystack versions 1.0.2 dated 2024-01-11 and 1.0.3 dated 2025-12-04
DESCRIPTION | 11 LICENSE | 4 MD5 | 144 - NAMESPACE | 118 - NEWS.md | 78 - R/data.R | 28 R/debug.R | 146 - R/haystack.R | 1276 ++++++++-------- R/haystack_IO.R | 104 - R/haystack_clustering.R | 202 +- R/haystack_clustering_highD.R | 412 ++--- R/haystack_continuous.R | 1394 +++++++++--------- R/haystack_highD.R | 874 +++++------ R/haystack_visualization.R | 474 +++--- R/randomization.R | 98 - R/s3.R | 506 +++--- R/singleCellHaystack-package.R | 20 R/sparse.R | 98 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 60 inst/doc/a01_toy_example.R | 144 - inst/doc/a01_toy_example.Rmd | 240 +-- inst/doc/a01_toy_example.html | 980 ++++++------ man/dat.expression.Rd | 20 man/dat.tsne.Rd | 20 man/default_bandwidth.nrd.Rd | 34 man/extract_row_dgRMatrix.Rd | 42 man/extract_row_lgRMatrix.Rd | 42 man/get_D_KL.Rd | 46 man/get_D_KL_continuous_highD.Rd | 56 man/get_D_KL_highD.Rd | 46 man/get_density.Rd | 62 man/get_dist_two_sets.Rd | 38 man/get_euclidean_distance.Rd | 38 man/get_grid_points.Rd | 42 man/get_log_p_D_KL.Rd | 46 man/get_log_p_D_KL_continuous.Rd | 68 man/get_parameters_haystack.Rd | 42 man/get_reference.Rd | 38 man/haystack.Rd | 184 +- man/haystack_2D.Rd | 62 man/haystack_continuous_highD.Rd | 120 - man/haystack_highD.Rd | 82 - man/hclust_haystack.Rd | 102 - man/hclust_haystack_highD.Rd | 74 man/hclust_haystack_raw.Rd | 50 man/kde2d_faster.Rd | 32 man/kmeans_haystack.Rd | 56 man/kmeans_haystack_highD.Rd | 80 - man/kmeans_haystack_raw.Rd | 54 man/plot_compare_ranks.Rd | 36 man/plot_gene_haystack.Rd | 106 - man/plot_gene_haystack_raw.Rd | 80 - man/plot_gene_set_haystack.Rd | 106 - man/plot_gene_set_haystack_raw.Rd | 74 man/plot_rand_KLD.Rd | 46 man/plot_rand_fit.Rd | 38 man/read_haystack.Rd | 34 man/show_result_haystack.Rd | 114 - man/singleCellHaystack-package.Rd | 58 man/write_haystack.Rd | 32 tests/testthat.R | 8 tests/testthat/test-extract_row.R | 40 tests/testthat/test-haystack_continuous.R | 64 tests/testthat/test-haystack_sparse.R | 78 - vignettes/a01_toy_example.Rmd | 240 +-- vignettes/examples/a02_example_scRNAseq.Rmd | 288 +-- vignettes/examples/a03_example_spatial_visium.Rmd | 198 +- vignettes/examples/a04_example_spatial_slideseqV2.Rmd | 198 +- vignettes/examples/a05_moca_100k.Rmd | 182 +- vignettes/examples/a07_gene_sets.Rmd | 174 +- vignettes/examples/a08_gene_clustering.Rmd | 268 +-- 73 files changed, 5727 insertions(+), 5722 deletions(-)
More information about singleCellHaystack at CRAN
Permanent link
Title: Spectrally Deconfounded Models
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).
Author: Markus Ulmer [aut, cre, cph] ,
Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Diff between SDModels versions 1.0.13 dated 2025-06-05 and 2.0.0 dated 2025-12-04
SDModels-1.0.13/SDModels/R/List.R |only SDModels-1.0.13/SDModels/R/copy.R |only SDModels-1.0.13/SDModels/man/copy.SDForest.Rd |only SDModels-1.0.13/SDModels/man/copy.SDTree.Rd |only SDModels-1.0.13/SDModels/man/fromList.SDForest.Rd |only SDModels-1.0.13/SDModels/man/fromList.SDTree.Rd |only SDModels-1.0.13/SDModels/man/print.SDTree.Rd |only SDModels-1.0.13/SDModels/man/toList.SDForest.Rd |only SDModels-1.0.13/SDModels/man/toList.SDTree.Rd |only SDModels-2.0.0/SDModels/DESCRIPTION | 16 - SDModels-2.0.0/SDModels/MD5 | 88 ++---- SDModels-2.0.0/SDModels/NAMESPACE | 12 SDModels-2.0.0/SDModels/NEWS.md | 9 SDModels-2.0.0/SDModels/R/SDAM.R | 2 SDModels-2.0.0/SDModels/R/SDForest.R | 122 +++----- SDModels-2.0.0/SDModels/R/SDTree.R | 176 ++++-------- SDModels-2.0.0/SDModels/R/cvSDTree.R | 56 +-- SDModels-2.0.0/SDModels/R/get_cp_seq.R | 4 SDModels-2.0.0/SDModels/R/paths.R | 14 SDModels-2.0.0/SDModels/R/plot.R | 66 +++- SDModels-2.0.0/SDModels/R/predict.R | 50 ++- SDModels-2.0.0/SDModels/R/print.R | 24 - SDModels-2.0.0/SDModels/R/prune.R | 22 - SDModels-2.0.0/SDModels/R/simData.R | 80 +++-- SDModels-2.0.0/SDModels/R/transformations.R | 20 - SDModels-2.0.0/SDModels/R/utility.R | 93 ++---- SDModels-2.0.0/SDModels/R/varImp.R | 18 - SDModels-2.0.0/SDModels/README.md | 26 - SDModels-2.0.0/SDModels/build/partial.rdb |binary SDModels-2.0.0/SDModels/build/vignette.rds |binary SDModels-2.0.0/SDModels/inst/CITATION | 10 SDModels-2.0.0/SDModels/inst/REFERENCES.bib | 17 - SDModels-2.0.0/SDModels/inst/doc/Runtime.R | 5 SDModels-2.0.0/SDModels/inst/doc/Runtime.Rmd | 9 SDModels-2.0.0/SDModels/inst/doc/Runtime.html | 36 -- SDModels-2.0.0/SDModels/man/SDForest.Rd | 9 SDModels-2.0.0/SDModels/man/SDTree.Rd | 13 SDModels-2.0.0/SDModels/man/cvSDTree.Rd | 9 SDModels-2.0.0/SDModels/man/figures/README-SDTree-1.png |binary SDModels-2.0.0/SDModels/man/figures/README-SDTreeplot-1.png |only SDModels-2.0.0/SDModels/man/get_Q.Rd | 5 SDModels-2.0.0/SDModels/man/get_W.Rd | 5 SDModels-2.0.0/SDModels/man/plot.SDTree.Rd | 17 - SDModels-2.0.0/SDModels/man/prune.SDForest.Rd | 4 SDModels-2.0.0/SDModels/man/prune.SDTree.Rd | 5 SDModels-2.0.0/SDModels/man/regPath.SDForest.Rd | 6 SDModels-2.0.0/SDModels/man/simulate_data_step.Rd | 19 - SDModels-2.0.0/SDModels/tests/testthat/test-parallel.R | 4 SDModels-2.0.0/SDModels/tests/testthat/test-tree.R | 7 SDModels-2.0.0/SDModels/vignettes/Runtime.Rmd | 9 50 files changed, 488 insertions(+), 599 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted
analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user
to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R
packages that undertake higher level analysis and visualization of text. This affords the user a more efficient
and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other
areas of Text Mining/ Natural Language Processing.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.4.6 dated 2023-05-11 and 2.4.6.1 dated 2025-12-04
DESCRIPTION | 8 +-- MD5 | 73 +++++++++++++++++----------------- R/check_text.R | 2 R/lexical_classification.R | 2 R/new_project.R | 18 ++++---- R/qdap-package.R | 2 R/trans_venn.R | 2 R/word_stats.R | 2 build |only data/DATA.SPLIT.rda |binary data/DATA.rda |binary data/DATA2.rda |binary data/env.syl.rda |binary data/hamlet.rda |binary data/mraja1.rda |binary data/mraja1spl.rda |binary data/pres_debate_raw2012.rda |binary data/pres_debates2012.rda |binary data/raj.act.1.rda |binary data/raj.act.1POS.rda |binary data/raj.act.2.rda |binary data/raj.act.3.rda |binary data/raj.act.4.rda |binary data/raj.act.5.rda |binary data/raj.demographics.rda |binary data/raj.rda |binary data/rajPOS.rda |binary data/rajSPLIT.rda |binary data/raw.time.span.rda |binary data/sample.time.span.rda |binary man/check_text.Rd | 2 man/env.syl.Rd | 2 man/new_project.Rd | 16 +++---- man/plot.lexical.Rd | 2 man/qdap.Rd | 19 ++++++++ man/trans_venn.Rd | 2 man/word_stats.Rd | 2 tests/testthat/test-dispersion_plot.R | 2 38 files changed, 88 insertions(+), 68 deletions(-)
Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2022) <doi:10.48550/arXiv.2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.6.1 dated 2025-12-01 and 1.6.2 dated 2025-12-04
DESCRIPTION | 6 +-- MD5 | 22 +++++------ R/g_models.R | 52 ++++++++++++++++----------- R/q_models.R | 55 ++++++++++++++++------------ inst/doc/policy_data.html | 6 +-- inst/doc/policy_eval.html | 6 +-- inst/doc/policy_learn.html | 6 +-- man/g_model.Rd | 14 +++---- man/q_model.Rd | 14 +++---- tests/testthat/test-g_xgboost.R | 77 +++++++++++++++++++++------------------- tests/testthat/test-q_sl.R | 3 + tests/testthat/test-q_xgboost.R | 31 ++++++++++------ 12 files changed, 162 insertions(+), 130 deletions(-)
Title: Download and Manipulate Data from Istat
Description: Download data from ISTAT (Italian Institute of Statistics) database, both old and new provider (respectively, <http://dati.istat.it/> and <https://esploradati.istat.it/databrowser/>). Additional functions for manipulating data are provided. Moreover, a 'shiny' application called 'shinyIstat' can be used to search, download and filter datasets in an easier way.
Author: Elena Gradi [aut, cre],
Alissa Lelli [aut],
Daniela Ichim [aut]
Maintainer: Elena Gradi <elenaagradi@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2024-09-10
Diff between istat versions 1.0 dated 2024-09-10 and 1.1.1 dated 2025-12-04
DESCRIPTION | 12 MD5 | 54 - NAMESPACE | 178 +-- R/filter_istat.R | 118 +- R/filter_istat_interactive.R | 178 +-- R/get_i_stat.R | 233 ++-- R/get_istatdata.R | 218 ++-- R/list_i_stat.R | 97 + R/list_istatdata.R | 479 ++++----- R/plot_interactive.R | 196 +-- R/search_i_stat.R | 181 +-- R/search_istatdata.R | 566 +++++----- R/shinyIstat.R | 704 ++++++++----- build/vignette.rds |binary inst/doc/Get_started_with_istat_package.R | 18 inst/doc/Get_started_with_istat_package.Rmd | 646 +++++------- inst/doc/Get_started_with_istat_package.html | 1407 +++++++++++++-------------- man/filter_istat.Rd | 64 - man/filter_istat_interactive.Rd | 50 man/get_i_stat.Rd | 104 + man/get_istatdata.Rd | 104 + man/list_i_stat.Rd | 40 man/list_istatdata.Rd | 40 man/plot_interactive.Rd | 50 man/search_i_stat.Rd | 54 - man/search_istatdata.Rd | 54 - man/shinyIstat.Rd | 44 vignettes/Get_started_with_istat_package.Rmd | 646 +++++------- 28 files changed, 3400 insertions(+), 3135 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanes Bove et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [a [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.0.0 dated 2025-11-29 and 2.0.1 dated 2025-12-04
DESCRIPTION | 6 MD5 | 48 +-- NEWS.md | 6 R/Model-validity.R | 2 build/partial.rdb |binary inst/doc/ordinal-crm.html | 88 +++--- inst/doc/tidy_method.html | 28 +- inst/doc/trial_analysis.html | 348 +++++++++++++-------------- inst/doc/trial_definition.html | 2 inst/doc/upgrading_from_the_old_crmPack.html | 15 - man/nextBest.Rd | 29 +- man/stopTrial.Rd | 57 +--- tests/testthat/helper-testthat.R | 23 + tests/testthat/test-Design-methods.R | 50 +-- tests/testthat/test-Model-class.R | 156 ++++++------ tests/testthat/test-Model-methods.R | 4 tests/testthat/test-Model-validity.R | 30 +- tests/testthat/test-Rules-methods.R | 62 ++-- tests/testthat/test-Samples-methods.R | 50 +-- tests/testthat/test-Simulations-methods.R | 32 +- tests/testthat/test-fromQuantiles.R | 8 tests/testthat/test-helpers_jags.R | 4 tests/testthat/test-helpers_knitr.R | 16 - tests/testthat/test-sas-results-part-1.R | 8 tests/testthat/test-sas-results-part-2.R | 8 25 files changed, 547 insertions(+), 533 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.2.1 dated 2025-09-03 and 0.2.2 dated 2025-12-04
DESCRIPTION | 10 ++-- MD5 | 14 +++--- build/vignette.rds |binary data/dataADaMCDISCP01.RData |binary data/dataSDTMCDISCP01.RData |binary inst/NEWS | 2 inst/doc/clinUtils-vignette.html | 81 +++++++++++++++++++-------------------- tests/testthat/test_getClinDT.R | 6 +- 8 files changed, 58 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-17 0.3.3
2022-06-20 0.3.1
2020-06-10 0.3.0
2020-01-08 0.2.3
2019-06-05 0.2.2
2019-01-02 0.2.1
2018-04-20 0.1.4
2018-04-20 0.1.5
2017-11-18 0.1.3
2017-09-10 0.1.2
2017-06-09 0.1.1
2016-10-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-10 1.21
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-19 2.1.0
2024-11-22 2.0.1
2024-09-12 2.0.0
2024-01-09 1.2.1
2023-09-12 1.2.0
2023-04-15 1.1.0
2023-01-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-08 1.2.3
2021-03-18 1.2.2
2020-10-07 1.2.1
2020-09-22 1.2.0
2020-06-04 1.1.0
2020-05-18 1.0.0