Title: Grain-Size Statistics and Description of Sediment
Description: Full descriptive statistics, physical description of sediment,
metric or phi sieves. Includes a Shiny web application for
interactive grain size analysis and visualization.
Author: Regis K. Gallon [aut, cre] ,
Jerome Fournier [aut]
Maintainer: Regis K. Gallon <regis.gallon@lecnam.net>
Diff between G2Sd versions 2.1.5 dated 2015-12-07 and 2.2 dated 2025-11-11
G2Sd-2.1.5/G2Sd/data/coord_gran.rda |only G2Sd-2.1.5/G2Sd/inst/extdata/www/R_logo.png |only G2Sd-2.1.5/G2Sd/inst/extdata/www/bootstrap3.css |only G2Sd-2.1.5/G2Sd/inst/extdata/www/cnrs.gif |only G2Sd-2.1.5/G2Sd/inst/extdata/www/mnhn.gif |only G2Sd-2.1.5/G2Sd/man/coord_gran.Rd |only G2Sd-2.2/G2Sd/DESCRIPTION | 33 G2Sd-2.2/G2Sd/MD5 | 41 G2Sd-2.2/G2Sd/NAMESPACE | 44 G2Sd-2.2/G2Sd/NEWS | 18 G2Sd-2.2/G2Sd/R/G2Sd-internal.R | 1068 +++++++++++------------- G2Sd-2.2/G2Sd/R/grandistrib.R | 83 + G2Sd-2.2/G2Sd/R/granplot.R | 292 +++++- G2Sd-2.2/G2Sd/R/granstat.R | 215 ++-- G2Sd-2.2/G2Sd/README.md |only G2Sd-2.2/G2Sd/inst/CITATION | 11 G2Sd-2.2/G2Sd/inst/INDEX | 16 G2Sd-2.2/G2Sd/inst/extdata/server.R | 880 ++++++++++++++++--- G2Sd-2.2/G2Sd/inst/extdata/ui.R | 442 ++++++++- G2Sd-2.2/G2Sd/inst/extdata/www/G2SdLogo.png |only G2Sd-2.2/G2Sd/inst/extdata/www/cnam_logo.png |only G2Sd-2.2/G2Sd/man/G2Sd-package.Rd | 102 +- G2Sd-2.2/G2Sd/man/grandistrib.Rd | 96 +- G2Sd-2.2/G2Sd/man/granplot.Rd | 20 G2Sd-2.2/G2Sd/man/granstat.Rd | 245 ++--- G2Sd-2.2/G2Sd/man/granulo.Rd | 56 - 26 files changed, 2413 insertions(+), 1249 deletions(-)
Title: Test Robustness with Directed Acyclic Graphs
Description: Provides robustness checks to align estimands with the identification
that they require. Given a 'dagitty' object and a model specification,
'DAGassist' classifies variables by causal roles, flags problematic controls,
and generates a report comparing the original model with minimal and canonical
adjustment sets. Exports publication-grade reports in 'LaTeX', 'Word', 'Excel',
'dotwhisker', or plain text/'markdown'. 'DAGassist' is built on 'dagitty', an
'R' package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for
creating and analyzing DAGs. Methods draw on Pearl (2009) <doi:10.1017/CBO9780511803161>
and Textor et al. (2016) <doi:10.1093/ije/dyw341>.
Author: Graham Goff [aut, cre] ,
Michael Denly [aut]
Maintainer: Graham Goff <goffgrahamc@gmail.com>
Diff between DAGassist versions 0.2.4 dated 2025-09-21 and 0.2.7 dated 2025-11-11
DESCRIPTION | 36 - MD5 | 57 +-- NAMESPACE | 1 NEWS.md | 31 + R/assist.R | 817 ++++++++++++++++++++++++++++++++----------- R/assist_helpers.R | 173 ++++++++- R/classify.R | 273 +++++++------- R/dotwhisker.R |only R/export_helpers.R | 18 R/report_excel.R | 33 + R/report_latex.R | 224 ++++++++--- R/report_text.R | 65 ++- R/report_word.R | 36 + R/validate.R | 21 - README.md | 71 ++- inst/doc/get-started.R | 115 +++--- inst/doc/get-started.Rmd | 186 ++++++--- inst/doc/get-started.html | 616 ++++++++++++++++---------------- inst/doc/making-reports.R | 50 ++ inst/doc/making-reports.Rmd | 74 +++ inst/doc/making-reports.html | 406 +++++++++++++++++++-- inst/doc/quick-tour.R | 29 + inst/doc/quick-tour.Rmd | 34 + inst/doc/quick-tour.html | 48 +- man/DAGassist.Rd | 147 +++++-- man/art |only man/classify_nodes.Rd | 61 +-- man/figures/logo.png |only vignettes/get-started.Rmd | 186 ++++++--- vignettes/making-reports.Rmd | 74 +++ vignettes/quick-tour.Rmd | 34 + 31 files changed, 2752 insertions(+), 1164 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, rational expectations, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control, by A. Luciani (2022) <doi:10.13140/RG.2.2.31160.83202>.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 4.1.1 dated 2025-10-30 and 4.1.2 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/bimets_ts_functions.R | 2 +- README.md | 10 +++++----- inst/doc/bimets.pdf |binary inst/doc/frb2bimets.pdf |binary man/MDL.Rd | 4 ++-- man/RENORM.Rd | 2 +- man/SIMULATE.Rd | 4 ++-- man/STOCHSIMULATE.Rd | 2 +- man/bimets-package.Rd | 6 ++---- 12 files changed, 35 insertions(+), 31 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.1.2 dated 2025-11-05 and 2.1.3 dated 2025-11-11
DESCRIPTION | 6 MD5 | 52 ++-- NAMESPACE | 48 ++-- NEWS.md | 2 R/BayesChange-package.R | 24 +- inst/doc/tutorial.html | 209 ++++++++++--------- man/BayesChange-package.Rd | 58 ++--- man/ClustCpObj.Rd | 104 ++++----- man/DetectCpObj.Rd | 116 +++++------ man/clust_cp.Rd | 358 +++++++++++++++++----------------- man/clust_cp_epi.Rd | 186 ++++++++--------- man/clust_cp_multi.Rd | 160 +++++++-------- man/clust_cp_uni.Rd | 128 ++++++------ man/detect_cp.Rd | 288 +++++++++++++-------------- man/detect_cp_multi.Rd | 134 ++++++------ man/detect_cp_uni.Rd | 118 +++++------ man/plot.ClustCpObj.Rd | 174 ++++++++-------- man/plot.DetectCpObj.Rd | 110 +++++----- man/posterior_estimate.ClustCpObj.Rd | 116 +++++------ man/posterior_estimate.DetectCpObj.Rd | 106 +++++----- man/posterior_estimate.Rd | 24 +- man/print.ClustCpObj.Rd | 64 +++--- man/print.DetectCpObj.Rd | 62 ++--- man/sim_epi_data.Rd | 72 +++--- man/summary.ClustCpObj.Rd | 64 +++--- man/summary.DetectCpObj.Rd | 64 +++--- tests/testthat.R | 24 +- 27 files changed, 1444 insertions(+), 1427 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.4 dated 2025-06-16 and 0.1.5 dated 2025-11-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/trajmsm_ipw.R | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: A Simulation Framework for Spatiotemporal Population Genetics
Description: A framework for simulating spatially explicit genomic data which
leverages real cartographic information for programmatic and visual encoding
of spatiotemporal population dynamics on real geographic landscapes. Population
genetic models are then automatically executed by the 'SLiM' software by Haller
et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom
built-in simulation 'SLiM' script. Additionally, fully abstract spatial models
not tied to a specific geographic location are supported, and users can also
simulate data from standard, non-spatial, random-mating models. These can be
simulated either with the 'SLiM' built-in back-end script, or using an efficient
coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022)
<doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the
R package. Simulated genomic data is saved in a tree-sequence format and can be
loaded, manipulated, and summarised using tree-sequen [...truncated...]
Author: Martin Petr [aut, cre]
Maintainer: Martin Petr <contact@bodkan.net>
Diff between slendr versions 1.2.0 dated 2025-07-31 and 1.3.0 dated 2025-11-11
slendr-1.2.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-312.pyc |only slendr-1.3.0/slendr/DESCRIPTION | 13 - slendr-1.3.0/slendr/MD5 | 130 +++++----- slendr-1.3.0/slendr/NAMESPACE | 1 slendr-1.3.0/slendr/NEWS.md | 12 slendr-1.3.0/slendr/R/interface.R | 1 slendr-1.3.0/slendr/R/shiny.R | 83 +++--- slendr-1.3.0/slendr/R/tree-sequences.R | 28 +- slendr-1.3.0/slendr/R/visualization.R | 46 +-- slendr-1.3.0/slendr/R/zzz.R | 6 slendr-1.3.0/slendr/build/partial.rdb |binary slendr-1.3.0/slendr/build/vignette.rds |binary slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-01-tutorial.html | 28 +- slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-02-grid-model.html | 16 - slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-03-interactions.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-04-nonspatial-models.html | 2 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.R | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/inst/doc/vignette-05-tree-sequences.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/inst/doc/vignette-06-locations.html | 22 - slendr-1.3.0/slendr/inst/doc/vignette-07-engines.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-07-engines.html | 10 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.R | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/inst/doc/vignette-08-nonslendr-tskit.html | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.R | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/inst/doc/vignette-10-tracts.html | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.R | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.Rmd | 6 slendr-1.3.0/slendr/inst/doc/vignette-11-extensions.html | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/__pycache__/script.cpython-313.pyc |only slendr-1.3.0/slendr/inst/extdata/models/introgression/checksums.tsv | 2 slendr-1.3.0/slendr/inst/extdata/models/introgression/ranges.rds |binary slendr-1.3.0/slendr/inst/extdata/models/introgression/script.py | 4 slendr-1.3.0/slendr/inst/extdata/models/introgression/script.slim | 44 +-- slendr-1.3.0/slendr/inst/extdata/models/introgression_msprime.trees |binary slendr-1.3.0/slendr/inst/extdata/models/introgression_slim.trees |binary slendr-1.3.0/slendr/inst/extdata/models/msprime.trees |binary slendr-1.3.0/slendr/inst/scripts/script.slim | 42 +-- slendr-1.3.0/slendr/man/plot_map.Rd | 5 slendr-1.3.0/slendr/tests/testthat/afs_Linux.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/distances.tsv.gz |binary slendr-1.3.0/slendr/tests/testthat/test-interaction-changes.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime-geneflow.R | 2 slendr-1.3.0/slendr/tests/testthat/test-msprime.R | 2 slendr-1.3.0/slendr/vignettes/vignette-01-tutorial.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-02-grid-model.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-03-interactions.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-04-nonspatial-models.Rmd | 6 slendr-1.3.0/slendr/vignettes/vignette-05-tree-sequences.Rmd | 12 slendr-1.3.0/slendr/vignettes/vignette-06-locations.Rmd | 10 slendr-1.3.0/slendr/vignettes/vignette-07-engines.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-08-nonslendr-tskit.Rmd | 8 slendr-1.3.0/slendr/vignettes/vignette-10-tracts.Rmd | 4 slendr-1.3.0/slendr/vignettes/vignette-11-extensions.Rmd | 6 67 files changed, 344 insertions(+), 379 deletions(-)
Title: Plots for the Quantitative Analysis of Textual Data
Description: Plotting functions for visualising textual data. Extends 'quanteda' and
related packages with plot methods designed specifically for text data, textual statistics,
and models fit to textual data. Plot types include word clouds, lexical dispersion plots,
scaling plots, network visualisations, and word 'keyness' plots.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
Ian Fellows [cph] ),
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textplots versions 0.96 dated 2025-09-03 and 0.96.1 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/textplot_keyness.R | 2 +- R/textplot_xray.R | 10 ++++++---- README.md | 8 +++----- man/textplot_xray.Rd | 7 ++++--- 6 files changed, 23 insertions(+), 22 deletions(-)
More information about quanteda.textplots at CRAN
Permanent link
Title: Access and Analyse Data from the 'CVD Prevent' API
Description: Provides an R interface to the 'CVD Prevent' application
programming interface (API), allowing users to retrieve and analyse
cardiovascular disease prevention data from primary care records
across England. The Cardiovascular Disease Prevention Audit
(CVDPREVENT) automatically extracts routinely held GP health data to
support national reporting and improvement initiatives. See the API
documentation for details:
<https://bmchealthdocs.atlassian.net/wiki/spaces/CP/pages/317882369/CVDPREVENT+API+Documentation>.
Author: Craig Parylo [aut, cre, cph] ,
Cardiovascular Disease Prevention Audit [ant]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between cvdprevent versions 0.2.3 dated 2025-11-05 and 0.2.4 dated 2025-11-11
DESCRIPTION | 6 MD5 | 15 NAMESPACE | 1 NEWS.md | 64 R/cvd_memoise.R | 62 README.md | 20 build/vignette.rds |binary inst/doc/using_cvdprevent.html | 4182 ++++++++++++++++++++--------------------- man/cvd_clear_cache.Rd |only 9 files changed, 2213 insertions(+), 2137 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjaerde [trl],
Brad J. Biggerstaff [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 3.0.1 dated 2024-08-29 and 3.1.0 dated 2025-11-11
DESCRIPTION | 9 MD5 | 225 ++++++------ NEWS.md | 6 R/Adjusted_inv_sinh_CI_OR_2x2.R | 1 R/Adjusted_inv_sinh_CI_ratio_2x2.R | 1 R/Adjusted_log_CI_2x2.R | 1 R/AgrestiCaffo_CI_2x2.R | 1 R/BaptistaPike_exact_conditional_CI_2x2.R | 1 R/BaptistaPike_midP_CI_2x2.R | 1 R/CochranMantelHaenszel_test_stratified_2x2.R | 1 R/Cornfield_exact_conditional_CI_2x2.R | 1 R/Cornfield_midP_CI_2x2.R | 1 R/Exact_unconditional_test_2x2.R | 23 - R/Fisher_exact_test_2x2.R | 7 R/Fisher_midP_test_2x2.R | 1 R/Gart_adjusted_logit_CI_2x2.R | 1 R/Independence_smoothed_logit_CI_2x2.R | 1 R/Inv_sinh_CI_OR_2x2.R | 1 R/Inv_sinh_CI_ratio_2x2.R | 1 R/Katz_log_CI_2x2.R | 1 R/Koopman_asymptotic_score_CI_2x2.R | 1 R/LR_test_2x2.R | 1 R/MOVER_R_Wilson_CI_OR_2x2.R | 1 R/MOVER_R_Wilson_CI_ratio_2x2.R | 1 R/MantelHaenszel_estimate_stratified_2x2.R | 1 R/McNemar_asymptotic_test_CC_paired_2x2.R | 1 R/McNemar_asymptotic_test_paired_2x2.R | 1 R/Mee_asymptotic_score_CI_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_OR_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_difference_2x2.R | 1 R/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.R | 1 R/Newcombe_hybrid_score_CI_2x2.R | 1 R/Newcombe_square_and_add_CI_paired_2x2.R | 1 R/Pearson_LR_test_common_effect_stratified_2x2.R | 1 R/Pearson_chi_squared_test_2x2.R | 4 R/Pearson_chi_squared_test_CC_2x2.R | 1 R/PriceBonett_approximate_Bayes_CI_2x2.R | 1 R/Transformed_Blaker_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_exact_CI_paired_2x2.R | 1 R/Transformed_Clopper_Pearson_midP_CI_paired_2x2.R | 1 R/Uncorrected_asymptotic_score_CI_2x2.R | 1 R/Wald_CI_2x2.R | 1 R/Wald_CI_AgrestiMin_paired_2x2.R | 1 R/Wald_CI_CC_2x2.R | 1 R/Wald_CI_OR_paired_2x2.R | 1 R/Wald_CI_ratio_paired_2x2.R | 1 R/Wald_test_and_CI_common_diff_stratified_2x2.R | 1 R/Wald_test_and_CI_common_ratio_stratified_2x2.R | 1 R/Woolf_logit_CI_2x2.R | 1 R/Z_unpooled_test_2x2.R | 1 R/chapters.R | 15 R/the_2x2_table_CIs_OR.R | 1 R/the_2x2_table_CIs_difference.R | 1 R/the_2x2_table_CIs_ratio.R | 1 R/the_2x2_table_tests.R | 1 R/the_paired_2x2_table_CIs_OR.R | 1 man/Adjusted_inv_sinh_CI_OR_2x2.Rd | 8 man/Adjusted_inv_sinh_CI_ratio_2x2.Rd | 8 man/Adjusted_log_CI_2x2.Rd | 8 man/AgrestiCaffo_CI_2x2.Rd | 8 man/BaptistaPike_exact_conditional_CI_2x2.Rd | 8 man/BaptistaPike_midP_CI_2x2.Rd | 8 man/CochranMantelHaenszel_test_stratified_2x2.Rd | 8 man/Cornfield_exact_conditional_CI_2x2.Rd | 8 man/Cornfield_midP_CI_2x2.Rd | 8 man/Exact_unconditional_test_2x2.Rd | 8 man/Fisher_exact_test_2x2.Rd | 8 man/Fisher_midP_test_2x2.Rd | 8 man/Gart_adjusted_logit_CI_2x2.Rd | 8 man/Independence_smoothed_logit_CI_2x2.Rd | 8 man/Inv_sinh_CI_OR_2x2.Rd | 8 man/Inv_sinh_CI_ratio_2x2.Rd | 8 man/Katz_log_CI_2x2.Rd | 8 man/Koopman_asymptotic_score_CI_2x2.Rd | 8 man/LR_test_2x2.Rd | 8 man/MOVER_R_Wilson_CI_OR_2x2.Rd | 8 man/MOVER_R_Wilson_CI_ratio_2x2.Rd | 8 man/MantelHaenszel_estimate_stratified_2x2.Rd | 8 man/McNemar_asymptotic_test_CC_paired_2x2.Rd | 8 man/McNemar_asymptotic_test_paired_2x2.Rd | 8 man/Mee_asymptotic_score_CI_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_OR_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_difference_2x2.Rd | 8 man/MiettinenNurminen_asymptotic_score_CI_ratio_2x2.Rd | 8 man/Newcombe_hybrid_score_CI_2x2.Rd | 8 man/Newcombe_square_and_add_CI_paired_2x2.Rd | 8 man/Pearson_LR_test_common_effect_stratified_2x2.Rd | 8 man/Pearson_chi_squared_test_2x2.Rd | 8 man/Pearson_chi_squared_test_CC_2x2.Rd | 8 man/PriceBonett_approximate_Bayes_CI_2x2.Rd | 8 man/Transformed_Blaker_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_exact_CI_paired_2x2.Rd | 8 man/Transformed_Clopper_Pearson_midP_CI_paired_2x2.Rd | 8 man/Uncorrected_asymptotic_score_CI_2x2.Rd | 8 man/Wald_CI_2x2.Rd | 8 man/Wald_CI_AgrestiMin_paired_2x2.Rd | 8 man/Wald_CI_CC_2x2.Rd | 8 man/Wald_CI_OR_paired_2x2.Rd | 8 man/Wald_CI_ratio_paired_2x2.Rd | 8 man/Wald_test_and_CI_common_diff_stratified_2x2.Rd | 8 man/Wald_test_and_CI_common_ratio_stratified_2x2.Rd | 8 man/Woolf_logit_CI_2x2.Rd | 8 man/Z_unpooled_test_2x2.Rd | 8 man/chap10.Rd | 8 man/chap4.Rd | 8 man/chap8.Rd | 8 man/the_2x2_table_CIs_OR.Rd | 8 man/the_2x2_table_CIs_difference.Rd | 8 man/the_2x2_table_CIs_ratio.Rd | 8 man/the_2x2_table_tests.Rd | 8 man/the_paired_2x2_table_CIs_OR.Rd | 8 tests/testthat/Rplots.pdf |only tests/testthat/test-ch4.R | 18 tests/testthat/test-validation.R | 4 114 files changed, 667 insertions(+), 133 deletions(-)
More information about contingencytables at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-15 0.2.4
2018-04-30 0.2.3
2016-04-29 0.2.2
2015-07-17 0.2
2014-01-12 0.1
Title: Power Analysis for Research Experiments
Description: Provides tools for calculating statistical power for experiments
analyzed using linear mixed models. It supports standard designs, including
randomized block, split-plot, and Latin Square designs, while offering flexibility
to accommodate a variety of other complex study designs.
Author: Kai Wang [aut, cre, cph] ,
Mutian Niu [aut, cph]
Maintainer: Kai Wang <kai.wang@usys.ethz.ch>
Diff between pwr4exp versions 1.0.0 dated 2025-03-17 and 1.0.1 dated 2025-11-11
DESCRIPTION | 11 ++-- MD5 | 48 ++++++++++++------- NAMESPACE | 20 ++++++++ NEWS.md | 8 ++- R/corClasses.R |only R/df_utils.R | 6 +- R/mkdesign.R | 22 ++++++-- R/standard_designs.R | 6 +- R/utils.R | 125 ++++++++++++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/CITATION | 14 +++-- inst/doc/pwr4exp.R | 4 - inst/doc/pwr4exp.Rmd | 6 +- inst/doc/pwr4exp.html | 23 ++++----- man/corAR1.Rd |only man/corARMA.Rd |only man/corCAR1.Rd |only man/corClasses.Rd |only man/corCompSymm.Rd |only man/corExp.Rd |only man/corGaus.Rd |only man/corLin.Rd |only man/corRatio.Rd |only man/corSpher.Rd |only man/corSymm.Rd |only man/create_designs.Rd | 4 - man/df.lsd.Rd | 4 - man/mkRTrms.Rd | 6 +- man/mkStruct.Rd | 4 - man/mkdesign.Rd | 9 ++- vignettes/pwr4exp.Rmd | 6 +- 31 files changed, 213 insertions(+), 113 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Author: Hajk-Georg Drost [aut, cre] ,
Stefan Manolache [aut, ctb] ,
Jaruwatana Sodai Lotharukpong [aut, ctb] ,
Nikola Kalabova [aut, ctb] ,
Filipa Martins Costa [aut, ctb],
Kristian K Ullrich [aut, ctb]
Maintainer: Hajk-Georg Drost <hajk-georg.drost@tuebingen.mpg.de>
Diff between myTAI versions 2.3.3 dated 2025-11-07 and 2.3.4 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 74 +++++++-------- NEWS.md | 10 +- R/plot_contribution.R | 13 ++ R/plot_gene_heatmap.R | 17 --- R/taxid.R | 32 ++++++ README.md | 12 -- inst/doc/myTAI.Rmd | 1 inst/doc/myTAI.html | 2 inst/doc/other-strata.Rmd | 1 inst/doc/other-strata.html | 4 inst/doc/phylo-expression-object.R | 12 +- inst/doc/phylo-expression-object.Rmd | 13 +- inst/doc/phylo-expression-object.html | 160 ++++++++++++---------------------- inst/doc/phylostratigraphy.Rmd | 9 + inst/doc/phylostratigraphy.html | 20 ++-- inst/doc/tai-breaker.Rmd | 1 inst/doc/tai-gallery.Rmd | 1 inst/doc/tai-gallery.html | 72 +++++++-------- inst/doc/tai-stats.Rmd | 1 inst/doc/tai-stats.html | 56 +++++------ inst/doc/tai-transform.Rmd | 3 inst/doc/tai-transform.html | 20 ++-- inst/doc/taxonomy.R | 30 +++--- inst/doc/taxonomy.Rmd | 31 ++++-- inst/doc/taxonomy.html | 52 ++++++----- man/dot-plot_gene_heatmap_impl.Rd | 3 man/plot_gene_heatmap.Rd | 3 tests/testthat/test-plotting.R | 15 +++ vignettes/myTAI.Rmd | 1 vignettes/other-strata.Rmd | 1 vignettes/phylo-expression-object.Rmd | 13 +- vignettes/phylostratigraphy.Rmd | 9 + vignettes/tai-breaker.Rmd | 1 vignettes/tai-gallery.Rmd | 1 vignettes/tai-stats.Rmd | 1 vignettes/tai-transform.Rmd | 3 vignettes/taxonomy.Rmd | 31 ++++-- 38 files changed, 384 insertions(+), 353 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Maria Jose Ginzo Villamayor [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
Diff between FORTLS versions 1.6.0 dated 2025-07-29 and 1.6.1 dated 2025-11-11
FORTLS-1.6.0/FORTLS/R/geometric.features.R |only FORTLS-1.6.0/FORTLS/man/geometric.features.Rd |only FORTLS-1.6.0/FORTLS/man/geometric_features_point.Rd |only FORTLS-1.6.0/FORTLS/man/sort_sublists.Rd |only FORTLS-1.6.0/FORTLS/man/subset_matrix_by_indices.Rd |only FORTLS-1.6.0/FORTLS/src/geometric.features.cpp |only FORTLS-1.6.1/FORTLS/DESCRIPTION | 18 FORTLS-1.6.1/FORTLS/MD5 | 72 - FORTLS-1.6.1/FORTLS/R/RcppExports.R | 8 FORTLS-1.6.1/FORTLS/R/auxiliary.functions.R | 142 +- FORTLS-1.6.1/FORTLS/R/install_fortls_python_deps.R | 3 FORTLS-1.6.1/FORTLS/R/normalize.R | 12 FORTLS-1.6.1/FORTLS/R/tree.detection.multi.scan.R | 216 --- FORTLS-1.6.1/FORTLS/R/tree.detection.several.plots.R | 15 FORTLS-1.6.1/FORTLS/R/tree.detection.single.scan.R | 238 --- FORTLS-1.6.1/FORTLS/README.md | 5 FORTLS-1.6.1/FORTLS/build/partial.rdb |binary FORTLS-1.6.1/FORTLS/build/vignette.rds |binary FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.R | 2 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/plot_design_optimization.html | 8 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/inst/doc/stand_level.html | 4 FORTLS-1.6.1/FORTLS/inst/doc/tree_level.R | 78 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.Rmd | 88 - FORTLS-1.6.1/FORTLS/inst/doc/tree_level.html | 875 +++++++------ FORTLS-1.6.1/FORTLS/man/Rioja.data.Rd | 2 FORTLS-1.6.1/FORTLS/man/Rioja.simulations.Rd | 12 FORTLS-1.6.1/FORTLS/man/geometric_features_dist.Rd |only FORTLS-1.6.1/FORTLS/man/geometric_features_knn.Rd |only FORTLS-1.6.1/FORTLS/man/normalize.Rd | 5 FORTLS-1.6.1/FORTLS/man/tree.detection.multi.scan.Rd | 12 FORTLS-1.6.1/FORTLS/man/tree.detection.several.plots.Rd | 11 FORTLS-1.6.1/FORTLS/man/tree.detection.single.scan.Rd | 8 FORTLS-1.6.1/FORTLS/src/RcppExports.cpp | 88 - FORTLS-1.6.1/FORTLS/src/geometric_features_dist.cpp |only FORTLS-1.6.1/FORTLS/src/geometric_features_knn.cpp |only FORTLS-1.6.1/FORTLS/vignettes/plot_design_optimization.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/stand_level.Rmd | 4 FORTLS-1.6.1/FORTLS/vignettes/tree.list.multi.tls.csv | 40 FORTLS-1.6.1/FORTLS/vignettes/tree.list.single.tls.csv | 27 FORTLS-1.6.1/FORTLS/vignettes/tree_level.Rmd | 88 - 42 files changed, 1024 insertions(+), 1069 deletions(-)
Title: Diagnosis of Metabolic Dysfunction Associated Fatty Liver
Disease
Description: The latest guidelines proposed by International Expert Consensus are used for the clinical diagnosis of Metabolic Associated Fatty Liver Disease (MAFLD). The new definition takes hepatic steatosis (determined by elastography or histology or biomarker-based fatty liver index) as a major criterion. In addition, race, gender, body mass index (BMI), waist circumference (WC), fasting plasma glucose (FPG), systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides (TG), high-density lipoprotein cholesterol (HDLC), homeostatic model assessment of insulin resistance (HOMAIR), high sensitive c-reactive protein (HsCRP) for the diagnosis of MAFLD. Each parameter has to be interpreted based on the proposed cut-offs, making the diagnosis slightly complex and error-prone. This package is developed by incorporating the latest international expert consensus guidelines, and it will aid in the easy and quick diagnosis of MAFLD based on FibroScan in busy healthcare settings and also for [...truncated...]
Author: Jagadish Ramasamy [aut, cre]
Maintainer: Jagadish Ramasamy <iamjagankmr@gmail.com>
Diff between MAFLD versions 3.0.0 dated 2025-09-14 and 4.0.0 dated 2025-11-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/MAFLD.R | 11 ++++++++++- R/data.R | 1 + README.md | 8 ++++++-- data/x.rda |binary man/x.Rd | 1 + 8 files changed, 33 insertions(+), 14 deletions(-)
More information about SelectBoost.beta at CRAN
Permanent link
Title: Visualising How Nonlinear Dimension Reduction Warps Your Data
Description: To construct a model in 2-D space from 2-D nonlinear
dimension reduction data and then lift it to the high-dimensional
space. Additionally, provides tools to visualise the model overlay the
data in 2-D and high-dimensional space. Furthermore, provides
summaries and diagnostics to evaluate the nonlinear dimension
reduction layout.
Author: Jayani P. Gamage [aut, cre] ,
Dianne Cook [aut] ,
Paul Harrison [aut] ,
Michael Lydeamore [aut] ,
Thiyanga S. Talagala [aut]
Maintainer: Jayani P. Gamage <jayanilakshika76@gmail.com>
Diff between quollr versions 0.3.13 dated 2025-09-23 and 1.0.1 dated 2025-11-11
quollr-0.3.13/quollr/man/plot_rmse_layouts.Rd |only quollr-1.0.1/quollr/DESCRIPTION | 6 quollr-1.0.1/quollr/MD5 | 52 - quollr-1.0.1/quollr/NAMESPACE | 2 quollr-1.0.1/quollr/NEWS.md | 2 quollr-1.0.1/quollr/R/prediction.R | 28 quollr-1.0.1/quollr/data/scurve_plts.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse2.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse3.rda |binary quollr-1.0.1/quollr/data/scurve_umap_rmse4.rda |binary quollr-1.0.1/quollr/inst/doc/quollr4algo.html | 321 ++++++---- quollr-1.0.1/quollr/inst/doc/quollr5summary.html | 2 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.R | 8 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/inst/doc/quollr6bestbinwidth.html | 32 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.R | 4 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/inst/doc/quollr7bestfit.html | 21 quollr-1.0.1/quollr/man/gen_diffbin1_errors.Rd | 4 quollr-1.0.1/quollr/man/glance.highd_vis_model.Rd | 2 quollr-1.0.1/quollr/man/plot_hbe_layouts.Rd |only quollr-1.0.1/quollr/src/prediction.cpp | 6 quollr-1.0.1/quollr/tests/testthat/_snaps/prediction.md | 54 - quollr-1.0.1/quollr/tests/testthat/test-prediction.R | 4 quollr-1.0.1/quollr/vignettes/quollr6bestbinwidth.Rmd | 14 quollr-1.0.1/quollr/vignettes/quollr7bestfit.Rmd | 10 quollr-1.0.1/quollr/vignettes/quollr7bestfit_files/figure-html/unnamed-chunk-3-1.png |binary 28 files changed, 345 insertions(+), 251 deletions(-)
Title: Efficient Evaluation of Quadratic Forms
Description: A range of quadratic forms are evaluated, using efficient methods.
Unnecessary transposes are not performed. Complex values are handled
consistently.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between quadform versions 0.0-2 dated 2024-05-14 and 0.0-4 dated 2025-11-11
quadform-0.0-2/quadform/build |only quadform-0.0-2/quadform/inst |only quadform-0.0-4/quadform/DESCRIPTION | 12 +-- quadform-0.0-4/quadform/MD5 | 15 +--- quadform-0.0-4/quadform/NAMESPACE | 40 ++++++++++- quadform-0.0-4/quadform/NEWS.md | 12 +++ quadform-0.0-4/quadform/R/quadform.R | 108 +++++++++++++++++++++++-------- quadform-0.0-4/quadform/README.md | 18 ++--- quadform-0.0-4/quadform/man/quad.form.Rd | 106 +++++++++++++++--------------- 9 files changed, 206 insertions(+), 105 deletions(-)
Title: Estimate Bayesian Multilevel Models for Compositional Data
Description: Implement Bayesian multilevel modelling for compositional data.
Compute multilevel compositional data and
perform log-ratio transforms at between and within-person levels,
fit Bayesian multilevel models for compositional predictors and outcomes,
and run post-hoc analyses such as isotemporal substitution models.
References:
Le, Stanford, Dumuid, and Wiley (2025) <doi:10.1037/met0000750>,
Le, Dumuid, Stanford, and Wiley (2025) <doi:10.1080/00273171.2025.2565598>.
Author: Flora Le [aut, cre] ,
Joshua F. Wiley [aut]
Maintainer: Flora Le <floralebui@gmail.com>
This is a re-admission after prior archival of version 1.3.2 dated 2025-05-25
Diff between multilevelcoda versions 1.3.2 dated 2025-05-25 and 1.3.3 dated 2025-11-11
multilevelcoda-1.3.2/multilevelcoda/R/substitution-bsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-sub-margins.R |only multilevelcoda-1.3.2/multilevelcoda/R/substitution-wsubmargins.R |only multilevelcoda-1.3.2/multilevelcoda/man/bsubmargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/build.basesub.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/create_substitution.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/print.summary.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/submargins.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/update.complr.Rd |only multilevelcoda-1.3.2/multilevelcoda/man/wsubmargins.Rd |only multilevelcoda-1.3.3/multilevelcoda/DESCRIPTION | 16 multilevelcoda-1.3.3/multilevelcoda/MD5 | 184 multilevelcoda-1.3.3/multilevelcoda/NAMESPACE | 33 multilevelcoda-1.3.3/multilevelcoda/NEWS.md | 11 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda-methods.R | 91 multilevelcoda-1.3.3/multilevelcoda/R/brmcoda.R | 107 multilevelcoda-1.3.3/multilevelcoda/R/build.R | 338 + multilevelcoda-1.3.3/multilevelcoda/R/complr-methods.R | 144 multilevelcoda-1.3.3/multilevelcoda/R/complr.R | 465 +- multilevelcoda-1.3.3/multilevelcoda/R/get.R |only multilevelcoda-1.3.3/multilevelcoda/R/internal.R | 127 multilevelcoda-1.3.3/multilevelcoda/R/optimise.R |only multilevelcoda-1.3.3/multilevelcoda/R/pivot-coord.R | 371 - multilevelcoda-1.3.3/multilevelcoda/R/plot.R | 169 multilevelcoda-1.3.3/multilevelcoda/R/posterior.R | 397 - multilevelcoda-1.3.3/multilevelcoda/R/shiny.R | 484 +- multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsub.R | 41 multilevelcoda-1.3.3/multilevelcoda/R/substitution-bsubmargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-helpers.R | 2310 +++++----- multilevelcoda-1.3.3/multilevelcoda/R/substitution-sub.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-submargin.R |only multilevelcoda-1.3.3/multilevelcoda/R/substitution-wsub.R | 39 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More information about multilevelcoda at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-10 1.14.6.4
Title: Provides Batch Functions and Visualisation for Basic Statistical
Procedures
Description: Designed to streamline data analysis and statistical testing, reducing the length of R
scripts while generating well-formatted outputs in 'pdf', 'Microsoft Word', and 'Microsoft Excel'
formats. In essence, the package contains functions which are sophisticated wrappers around
existing R functions that are called by using 'f_' (user f_riendly) prefix followed by the normal
function name. This first version of the 'rfriend' package focuses primarily on data exploration,
including tools for creating summary tables, f_summary(), performing data transformations,
f_boxcox() in part based on 'MASS/boxcox' and 'rcompanion', and f_bestNormalize()
which wraps and extends functionality from the 'bestNormalize' package. Furthermore, 'rfriend'
can automatically (or on request) generate visualizations such as boxplots, f_boxplot(),
QQ-plots, f_qqnorm(), histograms f_hist(), and density plots. Additionally, the package includes
four statistical test functions: f_aov(), f_kruskal_test(), f_glm(), f_c [...truncated...]
Author: Sander H. van Delden [aut, cre]
Maintainer: Sander H. van Delden <plantmind@proton.me>
Diff between rfriend versions 1.0.0 dated 2025-07-16 and 2.0.0 dated 2025-11-11
DESCRIPTION | 8 - MD5 | 60 ++++---- NAMESPACE | 2 NEWS.md |only R/faov.R | 306 ++++++++++++++++++++++++++++--------------- R/fbestnormalize.R | 242 +++++++++++++++++++++++----------- R/fboxcox.R | 219 ++++++++++++++++++++---------- R/fboxplot.R | 139 ++++++++++++++----- R/fclear.R | 15 -- R/fcorplot.R | 252 +++++++++++++++++++++++------------ R/ffactors.R | 21 +- R/fglm.R | 183 ++++++++++++++++--------- R/fhist.R | 58 +++----- R/fkruskal_test.R | 204 +++++++++++++++++++--------- R/fmodel_compare.R | 2 R/fqqnorm.R | 57 +++----- R/fsummary.R | 125 ++++++++--------- R/helper_extract_extension.R |only R/helper_get_save_path.R |only R/import.R | 2 README.md |only man/f_aov.Rd | 23 +-- man/f_bestNormalize.Rd | 17 +- man/f_boxcox.Rd | 40 ++--- man/f_boxplot.Rd | 24 ++- man/f_corplot.Rd | 21 +- man/f_factors.Rd | 17 +- man/f_glm.Rd | 20 +- man/f_hist.Rd | 14 + man/f_kruskal_test.Rd | 25 +-- man/f_qqnorm.Rd | 14 + man/f_summary.Rd | 21 +- man/print.f_summary.Rd | 2 33 files changed, 1339 insertions(+), 794 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive. This package is the successor of 'ProTrackR' providing
better performance.
Author: Pepijn de Vries [aut, cre] ,
Olav Soerensen [aut]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR2 versions 0.0.5 dated 2024-11-09 and 0.1.0 dated 2025-11-11
DESCRIPTION | 21 MD5 | 177 +++--- NAMESPACE | 208 ++++--- NEWS.md | 88 +-- R/cell.R | 92 ++- R/command.R | 188 +++--- R/cpp11.R | 56 -- R/data.R | 32 - R/demo.R | 16 R/instrument.R | 131 ++-- R/mod_info.R | 61 ++ R/note.R | 198 +++---- R/pattern.R | 79 +- R/play.R |only R/render.R | 100 ++- R/s3.R | 186 +++--- R/samples.R | 290 +++++++++- R/select_ops.R | 649 ++++++++++++----------- README.md | 137 ++--- build/vignette.rds |binary inst/doc/ProTrackR_vs_ProTrackR2.R | 87 ++- inst/doc/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- inst/doc/ProTrackR_vs_ProTrackR2.html | 472 +++++------------ inst/doc/effect_commands.R | 72 ++ inst/doc/effect_commands.Rmd | 214 +++++-- inst/doc/effect_commands.html | 133 ++++ inst/doc/s3class.R | 2 inst/doc/s3class.Rmd | 607 +++++++++++----------- inst/doc/s3class.html | 110 +--- inst/doc/sel_assign.Rmd | 360 ++++++------- inst/doc/sel_assign.html | 44 - inst/mod.intro |binary man/ProTrackR2-package.Rd | 62 +- man/as_modplug_pattern.Rd | 56 +- man/as_pt2cell.Rd |only man/effect_commands.Rd | 48 - man/figures/logo.svg | 396 +++++++------- man/mod_info.Rd | 159 +++-- man/mod_io.Rd | 68 +- man/play.Rd | 119 ++-- man/pt2_cell.Rd | 68 +- man/pt2_command.Rd | 100 +-- man/pt2_demo.Rd | 36 - man/pt2_duration.Rd | 74 +- man/pt2_instrument.Rd | 98 +-- man/pt2_new_mod.Rd | 50 - man/pt2_new_pattern.Rd | 54 - man/pt2_note.Rd | 112 ++-- man/pt2_note_to_period.Rd | 68 +- man/pt2_pattern.Rd | 60 +- man/pt2_render.Rd | 112 ++-- man/pt2_render_options.Rd | 85 +-- man/pt2_sample.Rd | 60 +- man/pt2_sample_to_audio.Rd |only man/pt2_validate.Rd | 62 +- man/s3methods.Rd | 362 +++++++------ man/samp_io.Rd | 74 +- man/sample_properties.Rd |only man/select_assign.Rd | 160 +++-- src/cpp11.cpp | 140 +---- src/get_mod.cpp | 2 src/get_mod.h | 2 src/mod_header.cpp | 37 - src/mod_header.h | 4 src/mod_io.cpp | 26 src/mod_render.cpp | 29 - src/patterns.cpp | 24 src/pt2-clone.h |only src/pt2-clone/LICENSE.txt | 50 - src/pt2-clone/pt2_audio.c | 870 ++++++++++++++++---------------- src/pt2-clone/pt2_module_loader.c | 84 +-- src/pt2-clone/pt2_module_loader.h | 2 src/pt2-clone/pt2_sampler.c | 566 ++++++++++---------- src/pt2-clone/smploaders/pt2_load_wav.c | 9 src/pt_cell.cpp | 329 +----------- src/pt_cell.h | 5 src/pt_cleanup.cpp | 2 src/pt_init.cpp | 3 src/samp_io.cpp | 44 - src/samples.cpp | 87 +-- src/samples.h | 4 tests |only vignettes/ProTrackR_vs_ProTrackR2.Rmd | 293 ++++++---- vignettes/effect_commands.Rmd | 214 +++++-- vignettes/s3class.Rmd | 607 +++++++++++----------- vignettes/sel_assign.Rmd | 360 ++++++------- 86 files changed, 6044 insertions(+), 5395 deletions(-)
Title: Model Based Phylogenetic Analysis
Description: A collection of functions to do model-based phylogenetic analysis.
It includes functions to calculate community phylogenetic diversity,
to estimate correlations among functional traits while accounting for
phylogenetic relationships, and to fit phylogenetic generalized linear
mixed models. The Bayesian phylogenetic generalized linear mixed models
are fitted with the 'INLA' package (<https://www.r-inla.org>).
Author: Anthony Ives [aut],
Russell Dinnage [aut] ,
Lucas A. Nell [aut] ,
Matthew Helmus [aut],
Daijiang Li [aut, cre]
Maintainer: Daijiang Li <daijianglee@gmail.com>
Diff between phyr versions 1.1.0 dated 2020-12-18 and 1.1.3 dated 2025-11-11
DESCRIPTION | 17 MD5 | 61 +- NAMESPACE | 2 NEWS.md | 8 R/RcppExports.R | 28 + R/cor_phylo.R | 234 ++++++----- R/pglmm-utils.R | 262 ++++++++++-- R/pglmm.R | 25 - R/pglmm_compare.R | 8 R/utils.R | 1 README.md | 81 ++- build/vignette.rds |binary inst/doc/benchmarks.R | 246 +++++------ inst/doc/benchmarks.html | 728 ++++++++++++++++++++++------------ inst/doc/pglmm.html | 375 ++++++++++++++--- inst/doc/plot-re.html | 753 +++++++++++++++++++++++++----------- man/cor_phylo.Rd | 118 ++--- man/figures |only man/nobs.communityPGLMM.Rd | 4 man/pglmm-profile-LRT.Rd | 14 man/refit_boots.Rd | 12 man/simulate.communityPGLMM.Rd | 25 + src/RcppExports.cpp | 76 +++ src/binaryPGLMM.cpp | 2 src/cor_phylo.cpp | 544 +++++++++++++------------- src/cor_phylo.h | 157 ++----- tests/testthat/test-cor_phylo.R | 36 + tests/testthat/test-pcd.R | 16 tests/testthat/test-pglmm.R | 57 +- tests/testthat/test-pglmm_compare.R | 2 tests/testthat/test-psv.R | 6 tests/testthat/test_pglmm_utils.R | 24 - 32 files changed, 2522 insertions(+), 1400 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.4.5 dated 2025-01-08 and 0.5.1 dated 2025-11-11
DESCRIPTION | 12 - MD5 | 18 + NEWS.md | 4 R/HashStreetName.R | 94 ++++----- R/download_latlon_data.R | 142 +++++++-------- R/fillPostcodeStreets.R | 63 +++--- R/read_locality_by_postcode.R | 2 inst/extdata/LOCALITY_BY_POSTCODE.qdata |only inst/extdata/POSTCODE-STREET_TYPE_CODE-STREET_NAME.qdata |only man/download_latlon_data.Rd | 7 tests/tinytest.R | 10 - 11 files changed, 179 insertions(+), 173 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects.
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg [aut, cre],
Uku Raudvere [aut]
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.2.3 dated 2024-02-23 and 0.2.4 dated 2025-11-11
DESCRIPTION | 14 ++-- MD5 | 24 +++---- NAMESPACE | 1 R/gprofiler2.R | 107 ++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/gprofiler2.R | 60 +++++++++--------- inst/doc/gprofiler2.Rmd | 6 - inst/doc/gprofiler2.html | 154 ++++++++++++++++++++++++----------------------- inst/extdata |only man/gostplot.Rd | 3 man/gprofiler_request.Rd |only man/publish_gostplot.Rd | 3 man/publish_gosttable.Rd | 3 vignettes/gprofiler2.Rmd | 6 - 14 files changed, 218 insertions(+), 163 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.3 dated 2025-09-25 and 1.3.4 dated 2025-11-11
DESCRIPTION | 8 MD5 | 88 ++--- NEWS.md | 5 R/flux_fitting.R | 27 - R/flux_fitting_exptz.R | 9 R/flux_fitting_hm.R | 7 R/flux_fitting_lm.R | 7 R/flux_fitting_quadratic.R | 9 R/flux_fitting_zhao18.R | 9 R/flux_fortify.R | 10 R/flux_fortify_exp.R | 7 R/flux_fortify_lin.R | 5 R/flux_fortify_quadratic.R | 5 R/flux_param_exp.R | 12 R/flux_param_kappamax.R | 12 R/flux_param_lm.R | 12 R/flux_param_qua.R | 12 R/flux_plot.R | 2 R/flux_plot_flag.R | 2 README.md | 71 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 inst/doc/two-gases.html | 4 man/figures/README-short-example-1.png |binary man/figures/logo.png |binary man/flux_fitting.Rd | 4 man/flux_fitting_exptz.Rd | 4 man/flux_fitting_hm.Rd | 4 man/flux_fitting_lm.Rd | 5 man/flux_fitting_quadratic.Rd | 13 man/flux_fitting_zhao18.Rd | 4 man/flux_fortify_exp.Rd | 4 man/flux_fortify_lin.Rd | 4 man/flux_fortify_quadratic.Rd | 4 man/flux_param_exp.Rd | 4 man/flux_param_kappamax.Rd | 4 man/flux_param_lm.Rd | 4 man/flux_param_qua.Rd | 4 tests/testthat/_snaps/flux_fitting.md | 47 +- tests/testthat/_snaps/flux_plot.md | 32 ++ tests/testthat/_snaps/flux_plot/flux-diff-and-lm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-hm.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-tz.svg |only tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-quadratic.svg |only tests/testthat/test-flux_fitting.R | 27 + tests/testthat/test-flux_plot.R | 158 ++++++++++ 47 files changed, 456 insertions(+), 202 deletions(-)
Title: Dynamic ICAR Spatiotemporal Factor Models
Description: Bayesian factor models are effective tools for dimension reduction. This is especially applicable to multivariate large-scale datasets. It allows researchers to understand the latent factors of the data which are the linear or non-linear combination of the variables. Dynamic Intrinsic Conditional Autocorrelative Priors (ICAR) Spatiotemporal Factor Models 'DIFM' package provides function to run Markov Chain Monte Carlo (MCMC), evaluation methods and visual plots from Shin and Ferreira (2023)<doi:10.1016/j.spasta.2023.100763>. Our method is a class of Bayesian factor model which can account for spatial and temporal correlations. By incorporating these correlations, the model can capture specific behaviors and provide predictions.
Author: Hwasoo Shin [aut, cre],
Marco Ferreira [aut]
Maintainer: Hwasoo Shin <hshin2@hfhs.org>
Diff between DIFM versions 1.0 dated 2024-04-12 and 1.0.1 dated 2025-11-11
DESCRIPTION | 15 ++++----- MD5 | 14 ++++---- R/RcppExports.R | 15 ++------- build/partial.rdb |binary inst/doc/DIFMvignette.html | 24 +++++++------- src/marginal.d.cpp | 31 +++++++++---------- src/sigma2.simulation.cpp | 65 ++++++++++++++++++++-------------------- src/tau.simulation.cpp | 73 +++++++++++++++++++++++---------------------- 8 files changed, 117 insertions(+), 120 deletions(-)
Title: General Unified Threshold Model of Survival for Bees using
Bayesian Inference
Description: Tools to calibrate, validate, and make predictions with the
General Unified Threshold model of Survival adapted for Bee species. The
model is presented in the publication from Baas, J., Goussen, B., Miles, M.,
Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and
Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G.,
van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the
GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011)
<doi:10.1021/es103092a>.
The authors are grateful to Bayer A.G. for its financial support.
Author: Benoit Goussen [aut] ,
Liubov Zakharova [ctb],
Carlo Romoli [aut, cre],
Bayer AG [cph, fnd],
ibacon GmbH [cph]
Maintainer: Carlo Romoli <carlo.romoli@ibacon.com>
Diff between BeeGUTS versions 1.3.0 dated 2024-10-23 and 1.4.0 dated 2025-11-11
DESCRIPTION | 26 +++++++-------- MD5 | 36 +++++++++++----------- NEWS.md | 3 + R/BeeGUTS-package.R | 29 +++++++++++++++++ R/ppc.R | 6 +++ README.md | 44 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary data/valBetacyfluthrinChronic.rda |only inst/doc/Tutorial.html | 43 ++++++++++++-------------- man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |binary man/figures/README-example-5.png |binary man/ppc.beeSurvValidation.Rd | 6 +++ man/valBetacyfluthrinChronic.Rd |only vignettes/man/figures/Tutorial-example-2.png |binary vignettes/man/figures/Tutorial-example-3.png |binary vignettes/man/figures/Tutorial-example-4.png |binary vignettes/man/figures/Tutorial-example-5.png |binary 20 files changed, 118 insertions(+), 75 deletions(-)
Title: Value Added Receiver Operating Characteristics Curve
Description: A continuous version of the receiver operating characteristics (ROC) curve to assess both classification and continuity performances of biomarkers, diagnostic tests, or risk prediction models.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between varoc versions 0.4.0 dated 2025-06-21 and 1.0.0 dated 2025-11-11
varoc-0.4.0/varoc/R/tmd.R |only varoc-1.0.0/varoc/DESCRIPTION | 11 +- varoc-1.0.0/varoc/MD5 | 12 +-- varoc-1.0.0/varoc/NAMESPACE | 6 - varoc-1.0.0/varoc/R/tmd_ft.R |only varoc-1.0.0/varoc/R/varoc.R | 152 ++++++++++++++++++--------------------- varoc-1.0.0/varoc/R/varoc3d.R |only varoc-1.0.0/varoc/man/varoc.Rd | 43 ++++------- varoc-1.0.0/varoc/man/varoc3d.Rd |only 9 files changed, 105 insertions(+), 119 deletions(-)
Title: Identify and Measure Tree Rings on X-Ray Micro-Density Profiles
Description: Contains functions to identify tree-ring borders based on X-ray micro-density profiles and a Graphical User Interface (GUI) to visualize density profiles and correct tree-ring borders. Campelo F, Mayer K, Grabner M. (2019) <doi:10.1016/j.dendro.2018.11.002>.
Author: Filipe Campelo [aut, cre, cph],
Konrad Mayer [ctb]
Maintainer: Filipe Campelo <fcampelo@ci.uc.pt>
Diff between xRing versions 0.1.1 dated 2022-04-22 and 0.1.2 dated 2025-11-11
xRing-0.1.1/xRing/man/plot.Rd |only xRing-0.1.1/xRing/man/print.Rd |only xRing-0.1.2/xRing/DESCRIPTION | 28 ++--- xRing-0.1.2/xRing/MD5 | 75 +++++++-------- xRing-0.1.2/xRing/R/calibrateFilm.R | 4 xRing-0.1.2/xRing/R/detectRings.R | 2 xRing-0.1.2/xRing/R/imDisplay.R | 2 xRing-0.1.2/xRing/R/imRead.R | 6 - xRing-0.1.2/xRing/R/plot.R | 34 +++--- xRing-0.1.2/xRing/R/plotRings.R | 2 xRing-0.1.2/xRing/R/print.R | 24 ++-- xRing-0.1.2/xRing/R/toxRing.R | 2 xRing-0.1.2/xRing/R/toxRingList.R | 2 xRing-0.1.2/xRing/inst/img/AFO1046.1200dpi_AFO1046.RData |only xRing-0.1.2/xRing/man/PaPiRaw.Rd | 13 ++ xRing-0.1.2/xRing/man/PaPiSpan.Rd | 10 ++ xRing-0.1.2/xRing/man/addRing.Rd | 2 xRing-0.1.2/xRing/man/calibrateFilm.Rd | 2 xRing-0.1.2/xRing/man/combineFrag.Rd | 2 xRing-0.1.2/xRing/man/correctRings.Rd | 2 xRing-0.1.2/xRing/man/detectEwLw.Rd | 2 xRing-0.1.2/xRing/man/detectRings.Rd | 4 xRing-0.1.2/xRing/man/fitCalibrationModel.Rd | 6 - xRing-0.1.2/xRing/man/getBorders.Rd | 2 xRing-0.1.2/xRing/man/getDensity.Rd | 2 xRing-0.1.2/xRing/man/getRwls.Rd | 2 xRing-0.1.2/xRing/man/getSteps.Rd | 2 xRing-0.1.2/xRing/man/imCrop.Rd | 2 xRing-0.1.2/xRing/man/imDisplay.Rd | 4 xRing-0.1.2/xRing/man/imRead.Rd | 8 + xRing-0.1.2/xRing/man/measureProfiles.Rd | 2 xRing-0.1.2/xRing/man/plot.xRing.Rd |only xRing-0.1.2/xRing/man/plot.xRingList.Rd |only xRing-0.1.2/xRing/man/plotRings.Rd | 4 xRing-0.1.2/xRing/man/print.xRing.Rd |only xRing-0.1.2/xRing/man/print.xRingList.Rd |only xRing-0.1.2/xRing/man/removeRing.Rd | 2 xRing-0.1.2/xRing/man/selectProfiles.Rd | 2 xRing-0.1.2/xRing/man/setLastYear.Rd | 2 xRing-0.1.2/xRing/man/stepIncrease.Rd | 2 xRing-0.1.2/xRing/man/toxRing.Rd | 4 xRing-0.1.2/xRing/man/toxRingList.Rd | 4 42 files changed, 170 insertions(+), 98 deletions(-)
Title: Seamless Access to World Bank International Debt Statistics
(IDS)
Description: Access and analyze the World Bank's International Debt Statistics
(IDS) <https://www.worldbank.org/en/programs/debt-statistics/ids>.
IDS provides creditor-debtor relationships between countries, regions, and
institutions. 'wbids' enables users to download, process and work with IDS
series across multiple geographies, counterparts, and time periods.
Author: Teal Emery [aut, cre],
Teal Insights [cph],
Christoph Scheuch [aut] ,
Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Diff between wbids versions 1.1.0 dated 2025-09-04 and 1.1.1 dated 2025-11-11
DESCRIPTION | 6 LICENSE | 4 MD5 | 98 NAMESPACE | 46 NEWS.md | 5 R/global-variables.R | 24 R/ids_bulk.R | 562 +- R/ids_bulk_files.R | 79 R/ids_bulk_series.R | 82 R/ids_get.R | 1082 ++--- R/ids_list_counterparts.R | 58 R/ids_list_entities.R | 130 R/ids_list_series.R | 56 R/ids_list_series_topics.R | 48 R/perform_request.R | 208 R/read_bulk_info.R | 42 R/sysdata.R | 54 R/wbids-package.R | 26 README.md | 294 - build/vignette.rds |binary inst/doc/data-model.R | 94 inst/doc/data-model.html | 5729 +++++++++++++-------------- inst/doc/data-model.qmd | 250 - man/counterparts.Rd | 32 man/entities.Rd | 32 man/ids_bulk.Rd | 116 man/ids_bulk_files.Rd | 56 man/ids_bulk_series.Rd | 66 man/ids_get.Rd | 288 - man/ids_list_counterparts.Rd | 66 man/ids_list_entities.Rd | 88 man/ids_list_geographies.Rd | 90 man/ids_list_series.Rd | 64 man/ids_list_series_topics.Rd | 56 man/read_bulk_info.Rd | 32 man/series.Rd | 32 man/series_topics.Rd | 32 man/wbids-package.Rd | 70 tests/testthat.R | 24 tests/testthat/test-ids_bulk.R | 812 +-- tests/testthat/test-ids_bulk_files.R | 30 tests/testthat/test-ids_bulk_series.R | 30 tests/testthat/test-ids_get.R | 1292 +++--- tests/testthat/test-ids_list_counterparts.R | 20 tests/testthat/test-ids_list_entities.R | 48 tests/testthat/test-ids_list_series.R | 18 tests/testthat/test-ids_list_series_topics.R | 16 tests/testthat/test-perform_request.R | 230 - tests/testthat/test-read_bulk_info.R | 19 vignettes/data-model.qmd | 250 - 50 files changed, 6532 insertions(+), 6354 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between SLOPE versions 1.1.0 dated 2025-10-30 and 1.2.0 dated 2025-11-11
DESCRIPTION | 6 - MD5 | 47 +++++++------- NEWS.md | 26 ++++++++ R/plot.R | 2 R/regularization_weights.R | 2 R/slope.R | 4 - README.md | 60 +++++++++++++++--- inst/CITATION | 99 +++++++++++-------------------- inst/WORDLIST | 4 + inst/doc/introduction.html | 6 - inst/doc/solvers.html | 8 +- inst/include/slope/cv.h | 11 ++- inst/include/slope/eigen_compat.h |only inst/include/slope/folds.h | 7 +- inst/include/slope/math.h | 4 - inst/include/slope/ols.h | 4 - inst/include/slope/slope.h | 74 +++++++++++++++++++---- inst/include/slope/solvers/hybrid_cd.h | 3 inst/include/slope/solvers/pgd.h | 4 - inst/include/slope/utils.h | 40 +++++++++++- man/SLOPE.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/regularizationWeights.Rd | 2 src/rcpp_slope.cpp | 16 ++++- tests/testthat/test-coef.R | 26 ++++++++ 26 files changed, 318 insertions(+), 139 deletions(-)
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 11.0.0 dated 2022-05-20 and 12.0.0 dated 2025-11-11
praznik-11.0.0/praznik/R/pure.R |only praznik-11.0.0/praznik/tests/testthat |only praznik-11.0.0/praznik/tests/testthat.R |only praznik-12.0.0/praznik/DESCRIPTION | 16 ++++----- praznik-12.0.0/praznik/MD5 | 50 +++++++++++++++-------------- praznik-12.0.0/praznik/NAMESPACE | 1 praznik-12.0.0/praznik/R/transforms.R | 30 +++++++++++++++++ praznik-12.0.0/praznik/inst/CITATION | 24 ++++--------- praznik-12.0.0/praznik/inst/NEWS | 4 ++ praznik-12.0.0/praznik/inst/tinytest |only praznik-12.0.0/praznik/man/tspTransform.Rd |only praznik-12.0.0/praznik/src/cmis.h | 6 +-- praznik-12.0.0/praznik/src/hs.h | 4 +- praznik-12.0.0/praznik/src/ims.h | 2 - praznik-12.0.0/praznik/src/jmis.h | 4 +- praznik-12.0.0/praznik/src/kt.h | 4 +- praznik-12.0.0/praznik/src/minmaxs.h | 4 +- praznik-12.0.0/praznik/src/mis.h | 4 +- praznik-12.0.0/praznik/src/praznik.c | 5 ++ praznik-12.0.0/praznik/src/shared.h | 4 +- praznik-12.0.0/praznik/src/trips.h | 2 - praznik-12.0.0/praznik/src/tsp.h |only praznik-12.0.0/praznik/tests/tinytest.R |only 23 files changed, 98 insertions(+), 66 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.2 dated 2025-10-13 and 1.3.3 dated 2025-11-11
DESCRIPTION | 8 MD5 | 38 - NAMESPACE | 1 NEWS.md | 7 R/OMOPGenerics-package.R | 1 R/assert.R | 5 R/classCdmReference.R | 19 R/classCdmTable.R | 10 R/classConceptSetExpression.R | 32 - R/compute.R | 108 +-- R/exportConceptSetExpression.R | 2 R/exportSummarisedResult.R | 18 R/importConceptSetExpression.R | 17 R/logger.R | 47 - inst/doc/logging.html | 52 - inst/doc/summarised_result.html | 886 +++++++++++++++---------------- man/assertLogical.Rd | 3 man/exportSummarisedResult.Rd | 5 tests/testthat/test-logger.R | 6 tests/testthat/test-methodComputeTable.R | 11 20 files changed, 647 insertions(+), 629 deletions(-)
Title: Modelling of Extreme Values
Description: Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes (Dombry, Engelke and Oesting, 2016, <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Author: Leo Belzile [aut, cre] ,
Jennifer L. Wadsworth [aut],
Paul J. Northrop [aut] ,
Raphael Huser [aut] ,
Scott D. Grimshaw [aut] ,
Jin Zhang [ctb],
Michael A. Stephens [ctb],
Art B. Owen [ctb]
Maintainer: Leo Belzile <belzilel@gmail.com>
Diff between mev versions 2.0 dated 2025-10-22 and 2.1 dated 2025-11-11
DESCRIPTION | 6 MD5 | 50 ++--- NAMESPACE | 7 NEWS.md | 25 ++ R/NCdiag.R | 2 R/coefvariation.R | 14 - R/extgp.R | 363 ++++++++++++++++++++++++++++++++------ R/infomattest.R | 41 +++- R/penultimate.R | 91 +++++++-- R/pickands.R | 4 R/tailindex.R | 23 +- R/threshold.R | 240 +++++++++++++++---------- R/thselect.R | 114 +++++++++++ R/vartymetric.R | 29 ++- inst/doc/mev-vignette.html | 10 - inst/tinytest/test-distribution.R | 122 ++++++++++++ inst/tinytest/test-egp.R | 268 ++++++++++++++-------------- man/egpdist.Rd | 3 man/smith.penult.Rd | 74 +++++-- man/thselect.cbm.Rd |only man/thselect.egp.Rd |only man/thselect.rbm.Rd | 5 man/thselect.sdinfo.Rd | 4 man/thselect.vmetric.Rd | 17 + man/tstab.cv.Rd | 14 - man/tstab.egp.Rd | 13 + man/tstab.gpd.Rd | 4 27 files changed, 1160 insertions(+), 383 deletions(-)
Title: Ecological Trajectory Analysis
Description: Analysis of temporal changes (i.e. dynamics) of ecological entities, defined as trajectories on a chosen multivariate space, by providing a set of
trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>;
and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions
to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as
metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also
provided to estimate the ecological quality of ecosystem with respect to reference conditions
[Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].
Author: Miquel De Caceres [aut, cre] ,
Nicolas Djeghri [aut] ,
Anthony Sturbois [aut] ,
Javier De la Casa [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between ecotraj versions 1.1.1 dated 2025-08-28 and 1.2.0 dated 2025-11-11
DESCRIPTION | 15 ++-- MD5 | 30 ++++++--- NAMESPACE | 10 ++- NEWS.md | 5 + R/cycleShiftArrows.R |only R/ecotraj-package.R | 5 - R/trajectoryComparison.R | 121 ++++++++++++++++++++++++++++++++------- R/trajectoryConvergencePlot.R |only R/trajectoryCyclical.R | 4 - R/trajectoryCyclicalPlots.R | 6 - R/trajectoryRMA.R |only R/trajectoryRMAPlot.R |only build/partial.rdb |binary man/cycleShiftArrows.Rd |only man/trajectoryComparison.Rd | 25 +++++++- man/trajectoryConvergencePlot.Rd |only man/trajectoryCyclical.Rd | 4 - man/trajectoryCyclicalPlots.Rd | 6 - man/trajectoryRMA.Rd |only man/trajectoryRMAPlot.Rd |only 20 files changed, 176 insertions(+), 55 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as i [...truncated...]
Author: Peter Rossi [aut, cre],
Robert McCulloch [ctb],
Wayne Taylor [ctb],
Dan Yavorsky [ctb]
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.1-6 dated 2023-09-23 and 3.1-7 dated 2025-11-11
DESCRIPTION | 21 +- MD5 | 33 ++-- NEWS.md |only build/vignette.rds |binary data/Scotch.rda |binary data/bank.rda |binary data/camera.RData |binary data/cheese.rda |binary data/customerSat.rda |binary data/detailing.rda |binary data/margarine.rda |binary data/orangeJuice.rda |binary data/tuna.rda |binary inst/doc/Constrained_MNL_Vignette.R | 32 ++-- inst/doc/Constrained_MNL_Vignette.html | 249 ++++++++++++++++----------------- inst/doc/bayesm_Overview_Vignette.R | 64 ++++---- inst/doc/bayesm_Overview_Vignette.html | 221 ++++++++++++++--------------- src/clusterMix_rcpp_loop.cpp | 2 18 files changed, 311 insertions(+), 311 deletions(-)
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.2.1 dated 2023-12-12 and 1.5.0 dated 2025-11-11
DESCRIPTION | 13 ++-- MD5 | 57 +++++++++--------- NAMESPACE | 1 NEWS.md | 18 +++++ R/data.R | 3 R/ibd.R | 131 ++++++++++++++++++++++++++++--------------- R/plot.R | 99 ++++++++++++++++++++++---------- R/prep.R | 80 +++++++++++++++----------- R/probUxUy.R | 40 ++++--------- build/vignette.rds |binary inst/doc/vignetteDcifer.R | 72 ++++++++++++----------- inst/doc/vignetteDcifer.Rmd | 41 ++++++------- inst/doc/vignetteDcifer.pdf |binary man/dsmp.Rd | 3 man/format.Rd | 14 ++-- man/getCOI.Rd | 2 man/ibdDat.Rd | 10 ++- man/ibdEstM.Rd | 6 + man/ibdPair.Rd | 6 + man/matchAfreq.Rd | 15 +++- man/mixMat.Rd |only man/plotColorbar.Rd | 3 man/plotRel.Rd | 36 ++++++----- src/logr.c | 21 ++++-- src/pUxUy.c | 75 +++++++++++++++++------- src/pUxUy0.c | 42 ++++++++++--- src/pUxUy0M1.c | 82 ++++++++++++++++++++------ src/pUxUyEqr.c | 55 ++++++++++++++---- src/pUxUyM1.c | 105 ++++++++++++++++++++++++---------- vignettes/vignetteDcifer.Rmd | 41 ++++++------- 30 files changed, 691 insertions(+), 380 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-27 0.2.0
2023-08-21 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-12 0.1.1
Title: Creates New Folders and Loads Standard Practices for Monterey
County Office of Education
Description: Basic Setup for Projects in R for Monterey County Office of Education. It contains functions often used in the analysis of education data in the county office including seeing if an item is not in a list, rounding in the manner the general public expects, including logos for districts, switching between district names and their county-district-school codes, accessing the local 'SQL' table and making thematically consistent graphs.
Author: David Dobrowski [aut, cre, cph]
Maintainer: David Dobrowski <ddobrowski@montereycoe.org>
Diff between MCOE versions 0.4.0 dated 2024-02-06 and 0.6.0 dated 2025-11-10
DESCRIPTION | 10 - MD5 | 8 - NEWS.md | 5 R/setup_dir.R | 367 +++++++++++++++++++++++++----------------------------- man/mcoe_theme.Rd | 2 5 files changed, 190 insertions(+), 202 deletions(-)
Title: Extending Base 'R' Lists
Description: Extends the functionality of base 'R' lists and provides
specialized data structures 'deque', 'set', 'dict', and 'dict.table',
the latter to extend the 'data.table' package.
Author: Roman Pahl [aut, cre]
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between container versions 1.0.5 dated 2024-12-02 and 1.1.0 dated 2025-11-10
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Title: 'Targets' Extension for 'SQL' Queries
Description: Provides an extension for 'SQL' queries as separate file
within 'targets' pipelines. The shorthand creates two targets,
the query file and the query result.
Author: David Ranzolin [aut, cre, cph],
Roy Storey [ctb]
Maintainer: David Ranzolin <daranzolin@gmail.com>
Diff between sqltargets versions 0.2.1 dated 2024-10-02 and 0.3.0 dated 2025-11-10
DESCRIPTION | 12 ++-- MD5 | 16 ++--- NEWS.md | 10 +++ R/source_sql_to_dataframe.R | 14 ++++ R/sqltargets-option.R | 2 R/utils.R | 2 README.md | 30 +++++++++- tests/testthat/test-tar-sql-deps.R | 3 - tests/testthat/test-tar-sql.R | 110 +++++++++++++++++++++++++++++++++++++ 9 files changed, 179 insertions(+), 20 deletions(-)
Title: Multivariate Joint Modeling for Longitudinal and Time-to-Event
Outcomes with 'INLA'
Description: Estimation of joint models for multivariate longitudinal markers (with various distributions available) and survival outcomes (possibly accounting for competing risks) with Integrated Nested Laplace Approximations (INLA). The flexible and user friendly function joint() facilitates the use of the fast and reliable inference technique implemented in the 'INLA' package for joint modeling. More details are given in the help page of the joint() function (accessible via ?joint in the R console) and the vignette associated to the joint() function (accessible via vignette("INLAjoint") in the R console).
Author: Denis Rustand [cre, aut] ,
Elias Teixeira Krainski [aut] ,
Haavard Rue [aut] ,
Janet van Niekerk [aut]
Maintainer: Denis Rustand <INLAjoint@gmail.com>
Diff between INLAjoint versions 24.3.25 dated 2024-03-25 and 25.11.10 dated 2025-11-10
DESCRIPTION | 23 MD5 | 34 NAMESPACE | 3 R/joint.R | 1371 +++++++++++++++++++++++------ R/joint.run.R |only R/plot.INLAjoint.R | 327 ++++++- R/predict.INLAjoint.R | 2036 ++++++++++++++++++++++++++++++++++---------- R/print.plot.INLAjoint.R | 8 R/print.summary.INLAjoint.R | 30 R/setupFonctions.R | 109 ++ R/summary.INLAjoint.R | 286 +++++- R/zzz.R | 38 README.md | 8 build/vignette.rds |binary inst/CITATION | 2 man/joint.Rd | 37 man/joint.run.Rd |only man/predict.INLAjoint.Rd | 54 - vignettes/INLAjoint.Rmd | 2 19 files changed, 3547 insertions(+), 821 deletions(-)
Title: Output Results from 'rms' Models for Medical Journals
Description: Provides streamlined functions for summarising and visualising
regression models fitted with the 'rms' package, in the preferred format for medical journals.
The 'modelsummary_rms()' function produces concise summaries for linear, logistic, and
Cox regression models, including automatic handling of models containing restricted
cubic spline (RCS) terms. The resulting summary dataframe can be easily converted into
publication-ready documents using the 'flextable' and 'officer' packages. The 'ggrmsMD()'
function creates clear and customizable plots ('ggplot2' objects) to visualise RCS terms.
Author: Samuel Tingle [aut, cre] ,
Georgios Kourounis [aut]
Maintainer: Samuel Tingle <samjamestingle@gmail.com>
Diff between rmsMD versions 1.0.0 dated 2025-06-17 and 1.0.1 dated 2025-11-10
DESCRIPTION | 12 - MD5 | 26 +- NEWS.md |only R/ggrmsMD.R | 5 R/zzz.R | 10 README.md | 28 ++ build/vignette.rds |binary inst/CITATION |only inst/doc/Further_details_ggrmsMD.html | 22 - inst/doc/Further_details_modelsummary_rms.Rmd | 4 inst/doc/Further_details_modelsummary_rms.html | 6 inst/doc/Standard_workflow_with_restricted_cubic_splines.html | 6 tests/testthat/_snaps/snapshot.md | 111 ++++++++++ tests/testthat/test-snapshot.R | 51 ++++ vignettes/Further_details_modelsummary_rms.Rmd | 4 15 files changed, 245 insertions(+), 40 deletions(-)
Title: Riemannian Metrics for Symmetric Positive Definite Matrices
Description: Implements various Riemannian metrics for symmetric positive definite matrices, including AIRM (Affine Invariant Riemannian Metric, <doi:10.1007/s11263-005-3222-z>), Log-Euclidean (<doi:10.1002/mrm.20965>), Euclidean, Log-Cholesky (<doi:10.1137/18M1221084>), and Bures-Wasserstein metrics (<doi:10.1016/j.exmath.2018.01.002>). Provides functions for computing logarithmic and exponential maps, vectorization, and statistical operations on the manifold of positive definite matrices.
Author: Nicolas Escobar [aut, cre] ,
Jaroslaw Harezlak [ths]
Maintainer: Nicolas Escobar <nescoba@iu.edu>
Diff between riemtan versions 0.1.0 dated 2025-04-23 and 0.2.5 dated 2025-11-10
riemtan-0.1.0/riemtan/man/solve_lyapunov.Rd |only riemtan-0.2.5/riemtan/DESCRIPTION | 23 riemtan-0.2.5/riemtan/LICENSE | 2 riemtan-0.2.5/riemtan/MD5 | 193 + riemtan-0.2.5/riemtan/NAMESPACE | 112 - riemtan-0.2.5/riemtan/NEWS.md | 206 + riemtan-0.2.5/riemtan/R/RcppExports.R |only riemtan-0.2.5/riemtan/R/airm.R | 368 +-- riemtan-0.2.5/riemtan/R/bures-wasserstein.R | 187 - riemtan-0.2.5/riemtan/R/data.R | 60 riemtan-0.2.5/riemtan/R/euclidean.R | 130 - riemtan-0.2.5/riemtan/R/log_cholesky.R | 306 +- riemtan-0.2.5/riemtan/R/log_euclidean.R | 158 - riemtan-0.2.5/riemtan/R/other_utils.R | 1049 +++++---- riemtan-0.2.5/riemtan/R/parallel_config.R |only riemtan-0.2.5/riemtan/R/parquet_backend.R |only riemtan-0.2.5/riemtan/R/parquet_io.R |only riemtan-0.2.5/riemtan/R/progress_utils.R |only riemtan-0.2.5/riemtan/R/riemtan-package.R | 18 riemtan-0.2.5/riemtan/R/sample.R | 762 ++++-- riemtan-0.2.5/riemtan/R/super_sample.R |only riemtan-0.2.5/riemtan/R/tangent_handler.R | 364 ++- riemtan-0.2.5/riemtan/README | 168 - 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Title: Confidence Interval Post-Selection of Variable
Description: Calculates confidence intervals after variable selection using repeated data splits. The package offers methods to address the challenges of post-selection inference, ensuring more accurate confidence intervals in models involving variable selection. The two main functions are 'lmps', which records the different models selected across multiple data splits as well as the corresponding coefficient estimates, and 'cips', which takes the lmps object as input to select variables and perform inferences using two types of voting.
Author: Boubacar DIALLO [aut, cre]
Maintainer: Boubacar DIALLO <boubacar.diallo0@yahoo.com>
Diff between CIpostSelect versions 0.2.1 dated 2024-10-22 and 0.2.2 dated 2025-11-10
DESCRIPTION | 8 MD5 | 4 R/uneFonction.R | 761 -------------------------------------------------------- 3 files changed, 13 insertions(+), 760 deletions(-)
Title: Weierstrass and Jacobi Elliptic Functions
Description: A suite of elliptic and related functions including Weierstrass and
Jacobi forms. Also includes various tools for manipulating and
visualizing complex functions.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between elliptic versions 1.5-0 dated 2025-09-18 and 1.5-1 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/elliptic.pdf |binary inst/doc/residuetheorem.R | 10 +++++----- inst/doc/residuetheorem.Rnw | 36 +++++++++++++++++++++--------------- inst/doc/residuetheorem.pdf |binary man/theta.neville.Rd | 2 +- vignettes/residuetheorem.Rnw | 36 +++++++++++++++++++++--------------- 11 files changed, 65 insertions(+), 49 deletions(-)
Title: Effects of External Conditions on Air Quality
Description: Analyzes the impact of external conditions on air quality using counterfactual approaches, featuring methods for data preparation, modeling, and visualization.
Author: Raphael Franke [aut],
Imke Voss [aut, cre]
Maintainer: Imke Voss <imke.voss@uba.de>
Diff between ubair versions 1.1.0 dated 2025-01-27 and 1.1.1 dated 2025-11-10
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++----------- NEWS.md | 5 ++ R/counterfactual_model.R | 2 - R/data_loading.R | 9 +++- R/sample_data_DESN025.R | 39 ++++---------------- R/utils.R | 2 - R/visualisation.R | 4 +- README.md | 26 ++----------- build/vignette.rds |binary inst/doc/neun_euro_ticket_demonstrator.R |only inst/doc/neun_euro_ticket_demonstrator.Rmd |only inst/doc/neun_euro_ticket_demonstrator.html |only inst/doc/user_sample_1.html | 4 +- inst/doc/user_sample_2.html | 2 - inst/doc/user_sample_3.html | 6 +-- inst/sticker/stickers-ubair-1.png |binary man/figures/README-counterfactual-scenario-1.png |binary man/figures/README-feature_importance-1.png |binary man/figures/README-feature_importance-2.png |binary man/figures/README-plot-meteo-data-1.png |binary man/load_uba_data_from_dir.Rd | 2 + man/run_counterfactual.Rd | 2 - man/sample_data_DESN025.Rd | 35 ++++-------------- vignettes/neun_euro_ticket_demonstrator.Rmd |only 25 files changed, 72 insertions(+), 116 deletions(-)
Title: Build a Docker Image from a Directory or Project
Description: Simple utilities to generate a Dockerfile from a directory or
project, build the corresponding Docker image, push the image to
DockerHub, and publicly share the project via Binder.
Author: Daniel Molitor [aut, cph, cre]
Maintainer: Daniel Molitor <molitdj97@gmail.com>
Diff between tugboat versions 0.1.4 dated 2025-10-31 and 0.1.5 dated 2025-11-10
DESCRIPTION | 6 +- MD5 | 14 ++--- NEWS.md | 13 +++++ R/binderize.R | 5 ++ R/build.R | 100 ++++++++++++++++++++++++++++++++-------- R/utils.R | 13 +++++ man/build.Rd | 6 ++ tests/testthat/test-binderize.R | 6 ++ 8 files changed, 132 insertions(+), 31 deletions(-)
Title: A Unified Pipeline for Pupillometry Data
Description: Provides a unified pipeline to clean, prepare, plot,
and run basic analyses on pupillometry experiments.
Author: Samuel Forbes [aut, cre],
David Robinson [ctb]
Maintainer: Samuel Forbes <samuel.h.forbes@gmail.com>
Diff between PupillometryR versions 0.0.5 dated 2023-09-15 and 0.0.6 dated 2025-11-10
DESCRIPTION | 12 +++--- MD5 | 30 +++++++-------- NEWS.md | 5 ++ R/clean_and_downsample.R | 59 ++++++++++++++++++------------- R/functional_data.R | 1 R/make_smoothed_data.R | 17 +++++--- R/plot_pupil_data.R | 1 README.md | 15 ++++--- build/vignette.rds |binary inst/doc/PupillometryR.R | 2 - inst/doc/PupillometryR.Rmd | 4 +- inst/doc/PupillometryR.html | 56 +++++++++++++++-------------- man/clean_missing_data.Rd | 41 ++++++++++++--------- man/figures/README-unnamed-chunk-2-1.png |binary man/interpolate_data.Rd | 5 ++ vignettes/PupillometryR.Rmd | 4 +- 16 files changed, 147 insertions(+), 105 deletions(-)
Title: Estimating Peer Effects Using Partial Network Data
Description: Implements IV-estimator and Bayesian estimator for linear-in-means Spatial Autoregressive (SAR) model (see LeSage, 1997 <doi:10.1177/016001769702000107>; Lee, 2004 <doi:10.1111/j.1468-0262.2004.00558.x>; Bramoullé et al., 2009 <doi:10.1016/j.jeconom.2008.12.021>), while assuming that only a partial information about the network structure is available. Examples are when the adjacency matrix is not fully observed or when only consistent estimation of the network formation model is available (see Boucher and Houndetoungan, 2025 <doi:10.48550/arXiv.2509.08145>).
Author: Vincent Boucher [aut],
Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between PartialNetwork versions 1.1.1 dated 2025-09-24 and 1.1.2 dated 2025-11-10
DESCRIPTION | 12 +-- MD5 | 36 ++++++---- NAMESPACE | 3 NEWS.md | 11 ++- R/RcppExports.R | 4 + R/mcmcSAR.R | 5 - R/simIV.R | 88 +++++++++++++------------- R/simSAR.R |only R/smmSAR.R | 4 - inst/CITATION |only inst/doc/PartialNetwork_vignette.R | 102 +++++++++++++----------------- inst/doc/PartialNetwork_vignette.Rmd | 113 +++++++++++++++------------------- inst/doc/PartialNetwork_vignette.pdf |binary man/mcmcSAR.Rd | 5 - man/sim.IV.Rd | 88 +++++++++++++------------- man/simSAR.Rd |only man/smmSAR.Rd | 4 - src/RcppExports.cpp | 19 +++++ src/simSAR.cpp |only vignettes/PartialNetwork_vignette.Rmd | 113 +++++++++++++++------------------- vignettes/References.bib | 8 +- 21 files changed, 313 insertions(+), 302 deletions(-)
More information about PartialNetwork at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-25 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-10 0.1.1
2020-06-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-06 0.4.1
2024-11-29 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-23 0.3.3
2018-09-12 0.2.0
2017-02-08 0.1.2
2016-12-29 0.1.1
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.4.0 dated 2025-10-22 and 0.5.0 dated 2025-11-10
DESCRIPTION | 14 - MD5 | 36 +-- NAMESPACE | 1 NEWS.md | 7 R/RcppExports.R | 4 R/download_data.R | 357 ++++++++++++++++++----------------- R/resourcecode-package.R | 22 +- R/spectral_data_download.R | 62 ++++-- R/sysdata.rda |binary R/weather_windows.R |only data/rscd_dir.rda |binary data/rscd_freq.rda |binary man/compute_sea_state_2d_spectrum.Rd | 2 man/get_parameters.Rd | 3 man/weather_windows.Rd |only src/RcppExports.cpp | 15 + src/ww_calc_cpp.cpp |only tests/testthat.R | 24 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-data_download.R | 317 ++++++++++++++++++------------- tests/testthat/test_ww_calc.R |only 21 files changed, 493 insertions(+), 371 deletions(-)
Title: Detecting Extremal Values in a Normal Linear Model
Description: Provides a method to detect values poorly explained by a Gaussian linear model. The procedure is based on the maximum of the absolute value of the studentized residuals, which is a parameter-free statistic. This approach generalizes several procedures used to detect abnormal values during longitudinal monitoring of biological markers. For methodological details, see: Berthelot G., Saulière G., Dedecker J. (2025). "DEViaN-LM An R Package for Detecting Abnormal Values in the Gaussian Linear Model". HAL Id: hal-05230549. <https://hal.science/hal-05230549>.
Author: Guillaume Sauliere [aut, cre] ,
Geoffroy Berthelot [aut],
Jerome Dedecker [aut]
Maintainer: Guillaume Sauliere <guillaumesauliere@hotmail.com>
Diff between devianLM versions 1.0.4 dated 2025-10-05 and 1.0.5 dated 2025-11-10
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 8 +++ R/devianlm_stats.R | 4 - man/devianlm_stats.Rd | 126 +++++++++++++++++++++++++------------------------- 5 files changed, 81 insertions(+), 73 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 0.5.7
2023-05-10 0.5.6.1
2023-03-28 0.5.5
2023-03-13 0.5.4
2023-02-20 0.5.3
2023-01-30 0.5.1
2023-01-13 0.5.0
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.0 dated 2025-11-06 and 1.3.2 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/internal_hazard.R | 2 +- R/internal_misc.R | 33 ++++++++++++++++----------------- R/internal_survival.R | 23 +++++++++++------------ tests/testthat/test_survival.R | 8 ++++++++ 6 files changed, 44 insertions(+), 38 deletions(-)
Title: A Fast Permutation-Based Split-Half Reliability Algorithm
Description: Accurately estimates the reliability of cognitive tasks using a fast and flexible permutation-based split-half reliability algorithm that supports stratified splitting while maintaining equal split sizes. See Kahveci, Bathke, and Blechert (2025) <doi:10.3758/s13423-024-02597-y> for details.
Author: Sercan Kahveci [aut, cre]
Maintainer: Sercan Kahveci <sercan.kahveci@plus.ac.at>
Diff between rapidsplithalf versions 0.5 dated 2025-11-06 and 0.6 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rapidsplit.R | 29 ++++++++--------------------- inst/doc/rapidsplithalf.html | 14 +++++++------- man/figures/README-iatrel-1.png |binary man/figures/README-plotter-1.png |binary man/figures/README-plotter2-1.png |binary man/rapidsplit.Rd | 27 +++++++-------------------- 8 files changed, 32 insertions(+), 58 deletions(-)
More information about rapidsplithalf at CRAN
Permanent link
Title: 'Canvas' LMS API Integration
Description: Allow R users to interact with the 'Canvas' Learning Management System (LMS) API (see
<https://canvas.instructure.com/doc/api/all_resources.html> for details).
It provides a set of functions to access and manipulate course data, assignments, grades, users,
and other resources available through the 'Canvas' API.
Author: Tomer Iwan [aut, cre],
Niels Smits [ctb] ,
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvcanvas versions 0.0.6 dated 2025-09-05 and 0.0.7 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 13 +++++++++++-- R/get_assignment_submissions.R | 32 ++++++++++++++++++-------------- README.md | 9 --------- man/get_assignment_submissions.Rd | 18 +++++++----------- 6 files changed, 44 insertions(+), 44 deletions(-)
Title: Provider-Agnostic OAuth Authentication for 'shiny' Applications
Description: Provides a simple, configurable, provider-agnostic 'OAuth 2.0' and
'OpenID Connect' (OIDC) authentication framework for 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval, asynchronous
flows, and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.1.1 dated 2025-11-09 and 0.1.3 dated 2025-11-10
DESCRIPTION | 6 LICENSE | 2 MD5 | 36 ++-- NAMESPACE | 76 +++++----- NEWS.md | 6 README.md | 14 + build/vignette.rds |binary inst/doc/authentication-flow.Rmd | 162 +++++++++++++-------- inst/doc/authentication-flow.html | 227 +++++++++++++++--------------- man/handle_callback.Rd | 166 ++++++++++----------- man/prepare_call.Rd | 120 +++++++-------- man/state_payload_decrypt_validate.Rd | 48 +++--- man/state_store_get_remove.Rd | 46 +++--- man/use_shinyOAuth.Rd | 66 ++++---- tests/testthat/test-introspect-token.R | 1 tests/testthat/test-module-server-async.R | 3 tests/testthat/test-refresh-races.R | 1 tests/testthat/test-state-fail-delay.R | 3 vignettes/authentication-flow.Rmd | 162 +++++++++++++-------- 19 files changed, 630 insertions(+), 515 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac, uniform or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] ,
Branislav Panic [ctb] ,
Jernej Klemenc [ctb] ,
Simon Oman [ctb]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.17.0 dated 2025-11-06 and 2.17.1 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- R/EMMIX.R | 2 +- R/RCLRMIX.R | 2 +- R/RCLSMIX.R | 4 ++-- R/REBMIX.R | 2 +- R/RNGMIX.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 2 +- inst/doc/rebmix.Rnw | 4 ++-- inst/doc/rebmix.pdf |binary src/init.c | 8 ++++---- src/rebmixf.cpp | 2 +- src/rngmixf.cpp | 2 +- vignettes/rebmix.Rnw | 4 ++-- 16 files changed, 35 insertions(+), 35 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph R Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 8.0.6 dated 2025-01-09 and 8.1.0 dated 2025-11-10
prioritizr-8.0.6/prioritizr/R/add_loglinear_targets.R |only prioritizr-8.0.6/prioritizr/R/all_binary.R |only prioritizr-8.0.6/prioritizr/R/all_columns_any_finite.R |only prioritizr-8.0.6/prioritizr/R/all_columns_inherit.R |only prioritizr-8.0.6/prioritizr/R/all_finite.R |only prioritizr-8.0.6/prioritizr/R/all_positive.R |only prioritizr-8.0.6/prioritizr/R/all_proportion.R |only prioritizr-8.0.6/prioritizr/R/any_nonNA.R |only prioritizr-8.0.6/prioritizr/R/any_nonzero.R |only prioritizr-8.0.6/prioritizr/R/as_Matrix.R |only prioritizr-8.0.6/prioritizr/R/assertions.R |only prioritizr-8.0.6/prioritizr/R/assertions_class.R |only prioritizr-8.0.6/prioritizr/R/assertions_misc.R |only prioritizr-8.0.6/prioritizr/R/assertions_raster.R |only prioritizr-8.0.6/prioritizr/R/assertions_sf.R |only prioritizr-8.0.6/prioritizr/R/assertions_vector.R |only prioritizr-8.0.6/prioritizr/R/cli.R |only prioritizr-8.0.6/prioritizr/R/get_crs.R |only prioritizr-8.0.6/prioritizr/R/is_numeric_values.R |only prioritizr-8.0.6/prioritizr/R/is_same_crs.R |only prioritizr-8.0.6/prioritizr/R/is_spatial_extents_overlap.R |only prioritizr-8.0.6/prioritizr/R/list_text.R |only prioritizr-8.0.6/prioritizr/R/repr.R |only prioritizr-8.0.6/prioritizr/R/st_geometry_classes.R |only prioritizr-8.0.6/prioritizr/man/add_loglinear_targets.Rd |only prioritizr-8.0.6/prioritizr/src/rcpp_apply_feature_weights.cpp |only prioritizr-8.0.6/prioritizr/tests/testthat/_snaps/assertions.md |only prioritizr-8.0.6/prioritizr/tests/testthat/test_add_boundary_penalties.R |only prioritizr-8.0.6/prioritizr/tests/testthat/test_add_loglinear_targets.R |only prioritizr-8.0.6/prioritizr/tests/testthat/test_assertions.R |only prioritizr-8.1.0/prioritizr/DESCRIPTION | 141 prioritizr-8.1.0/prioritizr/MD5 | 995 + prioritizr-8.1.0/prioritizr/NAMESPACE | 760 - prioritizr-8.1.0/prioritizr/NEWS.md | 5386 +++++----- prioritizr-8.1.0/prioritizr/R/ConservationModifier-class.R | 232 prioritizr-8.1.0/prioritizr/R/ConservationProblem-class.R | 2136 ++- prioritizr-8.1.0/prioritizr/R/Constraint-class.R | 66 prioritizr-8.1.0/prioritizr/R/Decision-class.R | 66 prioritizr-8.1.0/prioritizr/R/Objective-class.R | 89 prioritizr-8.1.0/prioritizr/R/OptimizationProblem-class.R | 524 prioritizr-8.1.0/prioritizr/R/OptimizationProblem-methods.R | 717 - prioritizr-8.1.0/prioritizr/R/Penalty-class.R | 66 prioritizr-8.1.0/prioritizr/R/Portfolio-class.R | 68 prioritizr-8.1.0/prioritizr/R/RcppExports.R | 442 prioritizr-8.1.0/prioritizr/R/Solver-class.R | 259 prioritizr-8.1.0/prioritizr/R/Target-class.R | 64 prioritizr-8.1.0/prioritizr/R/TargetMethod-class.R |only prioritizr-8.1.0/prioritizr/R/Weight-class.R |only prioritizr-8.1.0/prioritizr/R/add_absolute_targets.R | 635 - prioritizr-8.1.0/prioritizr/R/add_asym_connectivity_penalties.R | 775 - prioritizr-8.1.0/prioritizr/R/add_auto_targets.R |only prioritizr-8.1.0/prioritizr/R/add_binary_decisions.R | 192 prioritizr-8.1.0/prioritizr/R/add_boundary_penalties.R | 959 - prioritizr-8.1.0/prioritizr/R/add_cbc_solver.R | 636 - prioritizr-8.1.0/prioritizr/R/add_compile_solver.R | 112 prioritizr-8.1.0/prioritizr/R/add_connectivity_penalties.R | 1199 +- prioritizr-8.1.0/prioritizr/R/add_contiguity_constraints.R | 760 - prioritizr-8.1.0/prioritizr/R/add_cplex_solver.R | 720 - prioritizr-8.1.0/prioritizr/R/add_cuts_portfolio.R | 280 prioritizr-8.1.0/prioritizr/R/add_default_portfolio.R | 80 prioritizr-8.1.0/prioritizr/R/add_default_solver.R | 186 prioritizr-8.1.0/prioritizr/R/add_extra_portfolio.R | 273 prioritizr-8.1.0/prioritizr/R/add_feature_contiguity_constraints.R | 902 - prioritizr-8.1.0/prioritizr/R/add_feature_weights.R | 682 - prioritizr-8.1.0/prioritizr/R/add_gap_portfolio.R | 363 prioritizr-8.1.0/prioritizr/R/add_group_targets.R |only prioritizr-8.1.0/prioritizr/R/add_gurobi_solver.R | 774 - prioritizr-8.1.0/prioritizr/R/add_highs_solver.R | 471 prioritizr-8.1.0/prioritizr/R/add_linear_constraints.R | 888 - prioritizr-8.1.0/prioritizr/R/add_linear_penalties.R | 864 - prioritizr-8.1.0/prioritizr/R/add_locked_in_constraints.R | 1077 + prioritizr-8.1.0/prioritizr/R/add_locked_out_constraints.R | 926 - prioritizr-8.1.0/prioritizr/R/add_lpsymphony_solver.R | 474 prioritizr-8.1.0/prioritizr/R/add_mandatory_allocation_constraints.R | 206 prioritizr-8.1.0/prioritizr/R/add_manual_bounded_constraints.R | 541 - prioritizr-8.1.0/prioritizr/R/add_manual_locked_constraints.R | 646 - prioritizr-8.1.0/prioritizr/R/add_manual_targets.R | 797 - prioritizr-8.1.0/prioritizr/R/add_max_cover_objective.R | 402 prioritizr-8.1.0/prioritizr/R/add_max_features_objective.R | 334 prioritizr-8.1.0/prioritizr/R/add_max_phylo_div_objective.R | 555 - prioritizr-8.1.0/prioritizr/R/add_max_phylo_end_objective.R | 641 - prioritizr-8.1.0/prioritizr/R/add_max_utility_objective.R | 330 prioritizr-8.1.0/prioritizr/R/add_min_largest_shortfall_objective.R | 325 prioritizr-8.1.0/prioritizr/R/add_min_penalties_objective.R | 321 prioritizr-8.1.0/prioritizr/R/add_min_set_objective.R | 259 prioritizr-8.1.0/prioritizr/R/add_min_shortfall_objective.R | 333 prioritizr-8.1.0/prioritizr/R/add_neighbor_constraints.R | 895 - prioritizr-8.1.0/prioritizr/R/add_neighbor_penalties.R |only prioritizr-8.1.0/prioritizr/R/add_proportion_decisions.R | 178 prioritizr-8.1.0/prioritizr/R/add_relative_targets.R | 462 prioritizr-8.1.0/prioritizr/R/add_rsymphony_solver.R | 441 prioritizr-8.1.0/prioritizr/R/add_semicontinuous_decisions.R | 210 prioritizr-8.1.0/prioritizr/R/add_shuffle_portfolio.R | 484 prioritizr-8.1.0/prioritizr/R/add_top_portfolio.R | 297 prioritizr-8.1.0/prioritizr/R/adjacency_matrix.R | 389 prioritizr-8.1.0/prioritizr/R/as.R | 80 prioritizr-8.1.0/prioritizr/R/as_units.R |only prioritizr-8.1.0/prioritizr/R/binary_stack.R | 186 prioritizr-8.1.0/prioritizr/R/boundary_matrix.R | 479 prioritizr-8.1.0/prioritizr/R/branch_matrix.R | 122 prioritizr-8.1.0/prioritizr/R/calibrate_cohon_penalty.R |only prioritizr-8.1.0/prioritizr/R/category_layer.R | 145 prioritizr-8.1.0/prioritizr/R/category_vector.R | 170 prioritizr-8.1.0/prioritizr/R/compile.R | 592 - prioritizr-8.1.0/prioritizr/R/connectivity_matrix.R | 672 - prioritizr-8.1.0/prioritizr/R/constraints.R | 233 prioritizr-8.1.0/prioritizr/R/data.R | 751 - prioritizr-8.1.0/prioritizr/R/decisions.R | 170 prioritizr-8.1.0/prioritizr/R/deprecated.R | 430 prioritizr-8.1.0/prioritizr/R/eval_asym_connectivity_summary.R | 664 - prioritizr-8.1.0/prioritizr/R/eval_boundary_summary.R | 550 - prioritizr-8.1.0/prioritizr/R/eval_connectivity_summary.R | 656 - prioritizr-8.1.0/prioritizr/R/eval_cost_summary.R | 378 prioritizr-8.1.0/prioritizr/R/eval_feature_representation_summary.R | 577 - prioritizr-8.1.0/prioritizr/R/eval_ferrier_importance.R | 793 - prioritizr-8.1.0/prioritizr/R/eval_n_summary.R | 316 prioritizr-8.1.0/prioritizr/R/eval_rank_importance.R | 2034 +-- prioritizr-8.1.0/prioritizr/R/eval_rare_richness_importance.R | 573 - 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Title: Structural Equation Modeling with Deep Neural Network and
Machine Learning Algorithms
Description: Training and validation of a custom (or data-driven) Structural
Equation Models using layer-wise Deep Neural Networks or node-wise
Machine Learning algorithms, which extend the fitting procedures of
the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.
Author: Mario Grassi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMdeep versions 1.0.0 dated 2025-01-23 and 1.1.0 dated 2025-11-10
DESCRIPTION | 16 MD5 | 42 - NAMESPACE | 4 NEWS.md | 24 - R/DNNhelp.R |only R/SEMdnn.R | 1005 ++++++++++++++++++++++++++----------------- R/SEMhelp.R | 184 ++++--- R/SEMml.R | 481 ++++++++++++-------- README.md | 12 man/SEMdnn.Rd | 158 ++++-- man/SEMml.Rd | 49 -- man/crossValidation.Rd | 4 man/getConnectionWeight.Rd | 35 - man/getGradientWeight.Rd | 38 - man/getLOCO.Rd |only man/getShapleyR2.Rd | 63 +- man/getSignificanceTest.Rd | 56 +- man/getVariableImportance.Rd | 5 man/mapGraph.Rd | 10 man/nplot.Rd | 28 - man/predict.DNN.Rd | 16 man/predict.ML.Rd | 6 man/predict.SEM.Rd | 15 23 files changed, 1317 insertions(+), 934 deletions(-)
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.5.4 dated 2025-06-04 and 1.6.0 dated 2025-11-10
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Title: Wrapper for the Gnu Scientific Library
Description: An R wrapper for some of the functionality of the
Gnu Scientific Library.
Author: Robin K. S. Hankin [aut, cre] ,
Andrew Clausen [ctb] ,
Duncan Murdoch [ctb]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 2.1-8 dated 2023-01-24 and 2.1-9 dated 2025-11-10
DESCRIPTION | 11 ++++++----- INSTALL | 16 +++++++++++++++- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ README.md | 3 +-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 15 ++++----------- inst/doc/gsl.Rnw | 4 ++-- inst/doc/gsl.pdf |binary man/figures/gsl.png |binary src/qrng.c | 22 +++++++++++----------- src/rng.c | 6 +++--- vignettes/gsl.Rnw | 4 ++-- 14 files changed, 63 insertions(+), 50 deletions(-)
Title: Cancer RADAR Project Tool
Description: Cancer RADAR is a project which aim is to develop an
infrastructure that allows quantifying the risk of cancer by migration
background across Europe. This package contains a set of functions
cancer registries partners should use to reshape 5 year-age group
cancer incidence data into a set of summary statistics (see Boyle &
Parkin (1991, ISBN:978-92-832-1195-2)) in lines with Cancer RADAR data
protections rules.
Author: Nienke Alberts [aut],
Damien Georges [aut, cre] ,
Stefano Rosso [aut],
Iacopo Baussano [aut]
Maintainer: Damien Georges <georgesd@iarc.who.int>
Diff between cancerradarr versions 2.0.0 dated 2025-10-28 and 2.1.0 dated 2025-11-10
DESCRIPTION | 6 +-- MD5 | 28 +++++++-------- R/chop_vector.R | 2 - R/create_static_report.R | 4 +- R/custom_ageg_aggregation.R | 6 +-- R/data.R | 8 ++-- R/proportional_rates.R | 2 - README.md | 4 +- inst/extdata/static_report.Rmd | 72 +++++++++++++++++++++-------------------- man/chop_vector.Rd | 2 - man/chopped.vector.list.Rd | 2 - man/custom_ageg_aggregation.Rd | 2 - man/dat.asr.cat.Rd | 4 +- man/globocan.2022.eu.Rd | 2 - man/proportional_rates.Rd | 2 - 15 files changed, 76 insertions(+), 70 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 0.6.1 dated 2025-08-29
Diff between worldbank versions 0.6.1 dated 2025-08-29 and 0.7.0 dated 2025-11-10
worldbank-0.6.1/worldbank/man/wb_country_indicator.Rd |only worldbank-0.7.0/worldbank/DESCRIPTION | 12 +- worldbank-0.7.0/worldbank/MD5 | 58 +++++---- worldbank-0.7.0/worldbank/NAMESPACE | 3 worldbank-0.7.0/worldbank/NEWS.md | 7 + worldbank-0.7.0/worldbank/R/cache.R |only worldbank-0.7.0/worldbank/R/fone.R | 15 +- worldbank-0.7.0/worldbank/R/indicators.R | 96 ++++++++-------- worldbank-0.7.0/worldbank/R/pip.R | 39 ++++-- worldbank-0.7.0/worldbank/R/utils.R | 7 + worldbank-0.7.0/worldbank/R/worldbank-package.R | 1 worldbank-0.7.0/worldbank/README.md | 29 ++++ worldbank-0.7.0/worldbank/man/cache.Rd |only worldbank-0.7.0/worldbank/man/figures/README-demo-1.png |only worldbank-0.7.0/worldbank/man/fone.Rd | 9 + worldbank-0.7.0/worldbank/man/pip_aux.Rd | 11 + worldbank-0.7.0/worldbank/man/pip_citation.Rd | 2 worldbank-0.7.0/worldbank/man/pip_data.Rd | 5 worldbank-0.7.0/worldbank/man/pip_group.Rd | 5 worldbank-0.7.0/worldbank/man/pip_health_check.Rd | 2 worldbank-0.7.0/worldbank/man/pip_info.Rd | 2 worldbank-0.7.0/worldbank/man/pip_valid_params.Rd | 5 worldbank-0.7.0/worldbank/man/pip_versions.Rd | 5 worldbank-0.7.0/worldbank/man/wb_country.Rd | 5 worldbank-0.7.0/worldbank/man/wb_data.Rd |only worldbank-0.7.0/worldbank/man/wb_income_level.Rd | 2 worldbank-0.7.0/worldbank/man/wb_indicator.Rd | 2 worldbank-0.7.0/worldbank/man/wb_language.Rd | 2 worldbank-0.7.0/worldbank/man/wb_lending_type.Rd | 2 worldbank-0.7.0/worldbank/man/wb_region.Rd | 5 worldbank-0.7.0/worldbank/man/wb_source.Rd | 5 worldbank-0.7.0/worldbank/man/wb_topic.Rd | 5 worldbank-0.7.0/worldbank/tests/testthat/setup.R |only 33 files changed, 226 insertions(+), 115 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in
R. The framework is unopinionated when it comes to how HTTP requests
and WebSocket messages are handled and supports all levels of app
complexity; from serving static content to full-blown dynamic
web-apps. Fiery does not hold your hand as much as e.g. the shiny
package does, but instead sets you free to create your web app the way
you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.3.0 dated 2025-08-20 and 1.4.0 dated 2025-11-10
DESCRIPTION | 18 MD5 | 45 - NAMESPACE | 5 NEWS.md | 10 R/Fire.R | 610 ++++++++++++----- R/HandlerStack.R | 17 R/PromiseStack.R | 55 + R/aaa.R | 13 R/additional_type_checks.R | 34 R/fake_request.R | 42 - R/fiery-package.R | 4 R/loggers.R | 129 +++ R/otel.R |only R/request_store.R | 2 README.md | 2 build/vignette.rds |binary man/loggers.Rd | 3 tests/testthat/_snaps/Fire.md | 8 tests/testthat/helper.R | 20 tests/testthat/test-Fire.R | 1279 ++++++++++++++++++++----------------- tests/testthat/test-HandlerStack.R | 141 ++-- tests/testthat/test-PromiseStack.R | 174 ++--- tests/testthat/test-fake_request.R | 201 +++-- tests/testthat/test-loggers.R | 121 +-- 24 files changed, 1792 insertions(+), 1141 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at the country, region, state, and city levels. The package also downloads world-level COVID-19 data from Johns Hopkins University's repository. COVID-19 data is available from the start of follow-up until to May 5, 2023, when the World Health Organization (WHO) declared an end to the Public Health Emergency of International Concern (PHEIC) for COVID-19.
Author: Fabio Demarqui [aut, cre, cph],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
This is a re-admission after prior archival of version 1.0.0 dated 2025-08-18
Diff between covid19br versions 1.0.0 dated 2025-08-18 and 1.0.0.1 dated 2025-11-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/downloadData.R | 1 + tests/testthat/test_covid19br.R | 21 +++++++++++++-------- 5 files changed, 26 insertions(+), 16 deletions(-)
Title: Automatic Time Series Analysis and Forecasting using the Ata
Method
Description: The Ata method (Yapar et al. (2019) <doi:10.15672/hujms.461032>), an alternative to exponential smoothing (described in Yapar (2016) <doi:10.15672/HJMS.201614320580>,
Yapar et al. (2017) <doi:10.15672/HJMS.2017.493>), is a new univariate time series forecasting method which provides innovative solutions to issues faced during the
initialization and optimization stages of existing forecasting methods. Forecasting performance of the Ata method is superior to existing methods both in terms of easy
implementation and accurate forecasting. It can be applied to non-seasonal or seasonal time series which can be decomposed into four components (remainder, level, trend
and seasonal). This methodology performed well on the M3 and M4-competition data. This package was written based on Ali Sabri Taylan’s PhD dissertation.
Author: Ali Sabri Taylan [aut, cre, cph] ,
Hanife Taylan Selamlar [aut, cph] ,
Guckan Yapar [aut, ths, cph]
Maintainer: Ali Sabri Taylan <alisabritaylan@gmail.com>
Diff between ATAforecasting versions 0.0.60 dated 2023-06-12 and 0.0.61 dated 2025-11-10
DESCRIPTION | 25 ++++++----- MD5 | 20 +++++---- R/ATA.R | 7 +-- R/ATA_BoxCoxAttributes.r | 2 R/ATA_Decomposition.r | 31 ++++++++++++-- README.md | 91 +++++++++++++++++++++++++++++++++++++++--- build/partial.rdb |binary inst/COPYRIGHT.md |only man/ATA.BoxCoxAttr.Rd | 2 man/ATA.Decomposition.Rd | 11 ++++- man/ATAforecasting-package.Rd | 21 +++++++-- man/figures |only 12 files changed, 170 insertions(+), 40 deletions(-)
More information about ATAforecasting at CRAN
Permanent link
Title: Weighted Random Sampling without Replacement
Description: A collection of implementations of classical and
novel algorithms for weighted sampling without replacement.
Implementations include the algorithm of Efraimidis and Spirakis (2006)
<doi:10.1016/j.ipl.2005.11.003> and Wong and Easton (1980)
<doi:10.1137/0209009>.
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between wrswoR versions 1.1.1 dated 2020-07-26 and 1.2.0 dated 2025-11-10
.aspell |only DESCRIPTION | 32 ++++-- MD5 | 32 +++--- NAMESPACE | 1 NEWS.md | 17 +++ R/RcppExports.R | 6 + R/sample_int_rank.R | 38 ++++++-- R/sample_int_rej.R | 2 README.md | 4 man/sample_int.Rd | 26 ++++- man/wrswoR-package.Rd | 8 + src/RcppExports.cpp | 19 ++++ src/sample_int_crank.cpp | 192 ++++++++++++++++++++++++++++++++--------- tests/testthat.R | 10 +- tests/testthat/test-corner.R | 2 tests/testthat/test-error.R | 47 +++++++++- tests/testthat/test-harmonic.R | 2 tests/testthat/test-unique.R | 2 18 files changed, 341 insertions(+), 99 deletions(-)
Title: Simple Features for R
Description: Support for simple feature access, a standardized way to
encode and analyze spatial vector data. Binds to 'GDAL'
<doi:10.5281/zenodo.5884351> for reading and writing data, to 'GEOS'
<doi:10.5281/zenodo.11396894> for geometrical operations,
and to 'PROJ' <doi:10.5281/zenodo.5884394> for projection
conversions and datum transformations. Uses by default the 's2'
package for geometry operations on geodetic (long/lat degree)
coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-21 dated 2025-05-15 and 1.0-22 dated 2025-11-10
DESCRIPTION | 8 MD5 | 136 +- NAMESPACE | 1 NEWS.md | 18 R/geom-measures.R | 23 R/geom-transformers.R | 55 R/plot.R | 32 R/sf.R | 19 R/sfc.R | 5 R/sfg.R | 6 R/spatstat.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/sf1.R | 2 inst/doc/sf1.Rmd | 12 inst/doc/sf1.html | 2600 +++++++++++++++++++++++++++++++------------ inst/doc/sf2.R | 2 inst/doc/sf2.Rmd | 12 inst/doc/sf2.html | 1996 ++++++++++++++++++++++++++------- inst/doc/sf3.R | 2 inst/doc/sf3.Rmd | 12 inst/doc/sf3.html | 2412 +++++++++++++++++++++++++++++---------- inst/doc/sf4.R | 2 inst/doc/sf4.Rmd | 12 inst/doc/sf4.html | 2086 +++++++++++++++++++++++++++------- inst/doc/sf5.Rmd | 12 inst/doc/sf5.html | 1883 +++++++++++++++++++++++++------ inst/doc/sf6.R | 2 inst/doc/sf6.Rmd | 12 inst/doc/sf6.html | 1782 ++++++++++++++++++++++++----- inst/doc/sf7.R | 2 inst/doc/sf7.Rmd | 12 inst/doc/sf7.html | 2056 ++++++++++++++++++++++++++-------- inst/docker/gdal/Dockerfile | 67 - inst/nc/ones.zarr.zip |only inst/nc/zarr.py |only man/geos_unary.Rd | 31 man/st_line_project_point.Rd | 6 src/stars.cpp | 5 tests/aggregate.Rout.save | 10 tests/cast.Rout.save | 8 tests/crs.Rout.save | 8 tests/dist.Rout.save | 8 tests/dplyr.Rout.save | 8 tests/empty.Rout.save | 8 tests/full.Rout.save | 8 tests/gdal_geom.Rout.save | 8 tests/geos.Rout.save | 8 tests/graticule.Rout.save | 8 tests/grid.Rout.save | 8 tests/maps.Rout.save | 8 tests/plot.Rout.save | 8 tests/read.Rout.save | 8 tests/roundtrip.Rout.save | 8 tests/s2.Rout.save | 8 tests/sample.Rout.save | 8 tests/sfc.Rout.save | 10 tests/sfg.Rout.save | 8 tests/spatstat.Rout.save | 38 tests/stars.R | 9 tests/stars.Rout.save | 67 + tests/units.Rout.save | 8 tests/wkb.Rout.save | 8 vignettes/sf1.Rmd | 12 vignettes/sf2.Rmd | 12 vignettes/sf3.Rmd | 12 vignettes/sf4.Rmd | 12 vignettes/sf5.Rmd | 12 vignettes/sf6.Rmd | 12 vignettes/sf7.Rmd | 12 70 files changed, 12190 insertions(+), 3506 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine (version 3.51.0) and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.4.3 dated 2025-08-20 and 2.4.4 dated 2025-11-10
DESCRIPTION | 12 MD5 | 18 NEWS.md | 13 src/SqliteResultImpl.h | 4 src/vendor/extensions/regexp.c | 118 src/vendor/extensions/series.c | 529 ++- src/vendor/extensions/sqlite3ext.h | 7 src/vendor/sqlite3/sqlite3.c | 5519 ++++++++++++++++++++++++++++--------- src/vendor/sqlite3/sqlite3.h | 413 ++ tests/testthat/test-dbConnect.R | 7 10 files changed, 4968 insertions(+), 1672 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.1 dated 2025-10-16 and 0.8.2 dated 2025-11-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/gsea.R | 2 ++ 3 files changed, 7 insertions(+), 5 deletions(-)
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
This is a re-admission after prior archival of version 1.1-2 dated 2025-10-20
Diff between clifford versions 1.1-2 dated 2025-10-20 and 1.1-3 dated 2025-11-10
clifford-1.1-2/clifford/inst/clifford_arxiv.Rnw |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.R |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/cramer_clifford.html |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.R |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/determinants_clifford.html |only clifford-1.1-2/clifford/inst/doc/getcoeffs.R |only clifford-1.1-2/clifford/inst/doc/getcoeffs.Rmd |only clifford-1.1-2/clifford/inst/doc/getcoeffs.html |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.R |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/lorentz_clifford.html |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.R |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/pauli_clifford.html |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.R |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.Rmd |only clifford-1.1-2/clifford/inst/doc/pseudoscalar.html |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.R |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.Rmd |only clifford-1.1-2/clifford/inst/doc/quaternion_clifford.html |only clifford-1.1-2/clifford/inst/dot.Rmd |only clifford-1.1-2/clifford/inst/hankin_aaca_revision.tex |only clifford-1.1-2/clifford/inst/hankin_aaca_revision2.tex |only clifford-1.1-2/clifford/inst/hankin_aaca_revision3.tex |only clifford-1.1-2/clifford/inst/hankin_aca.Rnw |only clifford-1.1-2/clifford/inst/hitzer.Rmd |only clifford-1.1-2/clifford/inst/nectarines.Rmd |only clifford-1.1-2/clifford/inst/read.me |only clifford-1.1-2/clifford/inst/referee_comments.tex |only clifford-1.1-2/clifford/inst/referee_comments2.tex |only clifford-1.1-2/clifford/inst/spheres.R |only clifford-1.1-2/clifford/vignettes/cramer_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/determinants_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/getcoeffs.Rmd |only clifford-1.1-2/clifford/vignettes/lorentz_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/pauli_clifford.Rmd |only clifford-1.1-2/clifford/vignettes/pseudoscalar.Rmd |only clifford-1.1-2/clifford/vignettes/quaternion_clifford.Rmd |only clifford-1.1-3/clifford/DESCRIPTION | 6 clifford-1.1-3/clifford/MD5 | 78 ++-------- clifford-1.1-3/clifford/README.md | 36 +++- clifford-1.1-3/clifford/build/partial.rdb |binary clifford-1.1-3/clifford/build/vignette.rds |binary clifford-1.1-3/clifford/data/dot.rda |binary clifford-1.1-3/clifford/inst/CITATION | 2 clifford-1.1-3/clifford/inst/doc/clifford.pdf |binary clifford-1.1-3/clifford/inst/doc/complex_clifford.Rmd | 2 clifford-1.1-3/clifford/inst/doc/complex_clifford.html | 6 clifford-1.1-3/clifford/inst/doc/conformal_algebra_clifford.html | 10 - clifford-1.1-3/clifford/inst/doc/signature.R | 22 +- clifford-1.1-3/clifford/inst/doc/signature.Rmd | 1 clifford-1.1-3/clifford/inst/doc/signature.html | 17 +- clifford-1.1-3/clifford/man/Ops.clifford.Rd | 2 clifford-1.1-3/clifford/man/antivector.Rd | 8 - clifford-1.1-3/clifford/man/print.Rd | 12 - clifford-1.1-3/clifford/vignettes/clifford.bib | 4 clifford-1.1-3/clifford/vignettes/complex_clifford.Rmd | 2 clifford-1.1-3/clifford/vignettes/signature.Rmd | 1 60 files changed, 100 insertions(+), 109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-17 0.2.1
2023-01-17 0.2.0
2022-11-01 0.1.1
2022-07-20 0.1.0
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb],
Wouter van der Bijl [ctb],
Hugo Gruson [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.3 dated 2025-02-24 and 0.2.4 dated 2025-11-10
DESCRIPTION | 14 ++++++++------ MD5 | 16 ++++++++-------- NEWS.md | 21 +++++++++++++++++++++ R/init.R | 2 +- R/util.R | 6 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/uwot.html | 5 +++-- tests/testthat/test_output.R | 2 +- 9 files changed, 47 insertions(+), 19 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The 'netgwas' package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The 'netgwas'
implements the methodological developments in Behrouzi and Wit (2017)
<doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
Author: Pariya Behrouzi [aut, cre] ,
Ernst C. Wit [ctb]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.14.3 dated 2024-03-19 and 1.14.4 dated 2025-11-10
DESCRIPTION | 9 +-- MD5 | 12 ++-- R/selectnet.R | 150 ++++++++++++++++++++++++++-------------------------- inst/CITATION | 5 - man/plot.select.Rd | 24 ++++---- man/print.select.Rd | 64 +++++++++++----------- man/selectnet.Rd | 16 ++--- 7 files changed, 139 insertions(+), 141 deletions(-)
Title: Depth Importance in Precision Medicine (DIPM) Method
Description: An implementation by Chen, Li, and Zhang (2022) <doi: 10.1093/bioadv/vbac041> of the Depth Importance in Precision Medicine (DIPM) method
in Chen and Zhang (2022) <doi:10.1093/biostatistics/kxaa021> and Chen and
Zhang (2020) <doi:10.1007/978-3-030-46161-4_16>. The DIPM method is a classification
tree that searches for subgroups with especially poor or strong performance in a given treatment group.
Author: Cai Li [aut, cre],
Victoria Chen [aut],
Heping Zhang [aut]
Maintainer: Cai Li <cai.li.stats@gmail.com>
Diff between dipm versions 1.11 dated 2025-06-15 and 1.12 dated 2025-11-10
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 3 ++- R/node_dipm.R | 13 +++++++------ 4 files changed, 18 insertions(+), 15 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.8.1 dated 2025-08-24 and 2.0.0 dated 2025-11-10
DESCRIPTION | 8 MD5 | 202 ++--- NEWS.md | 10 R/baseline.R | 13 R/baseline_binomial.R | 26 R/baseline_gaussian.R | 45 - R/baseline_multinomial.R | 29 R/baseline_wrappers.R | 13 R/call_validate.R | 12 R/choosing_metrics_functions.R | 6 R/combine_predictors.R | 21 R/combine_predictors_prepare_args.R | 16 R/computational_grid.R | 10 R/confusion_matrix.R | 91 +- R/cross_validate.R | 34 R/cross_validate_list.R | 42 - R/data_documentation.R | 22 R/evaluate.R | 195 ++--- R/evaluate_predictions_binomial.R | 25 R/evaluate_predictions_gaussian.R | 45 - R/evaluate_predictions_multinomial.R | 112 +-- R/evaluate_residuals.R | 6 R/extract_model_effects.R | 7 R/extract_probabilities_of.R | 22 R/extract_special_fn_specific_hparams.R | 2 R/fit_model.R | 1 R/fit_predict_model_fn.R | 46 - R/get_nested_model_coefficients.R | 120 +-- R/helpers.R | 168 ++-- R/internal_evaluate_model.R | 1 R/internal_evaluate_predictions.R | 51 - R/metrics.R | 8 R/model_functions.R | 10 R/most_challenging.R | 277 ++++--- R/multiclass_probability_tibble.R | 16 R/nesting_predictions.R | 11 R/plot_confusion_matrix.R | 359 +++++----- R/plot_metric_density.R | 80 +- R/plot_probabilities.R | 131 +-- R/plot_probabilities_ecdf.R | 80 +- R/plot_probability_violins.R | 2 R/plotting_utilities.R | 173 ++-- R/predict_functions.R | 1 R/prepare_evaluation.R | 22 R/prepare_train_test.R | 72 +- R/preprocess_functions.R | 19 R/process_info.R | 110 +-- R/reconstruct_formulas.R | 3 R/run_model_fitting.R | 36 - R/run_prediction_process.R | 35 R/run_quietly.R | 30 R/select_definitions.R | 15 R/select_metrics.R | 10 R/set_info_cols.R | 3 R/set_metrics.R | 25 R/simplify_formula.R | 30 R/softmax.R | 26 R/summarize_metrics.R | 27 R/table_of_content_markdown.R | 4 R/update_hyperparameters.R | 25 R/update_model_specifics.R | 5 R/validate.R | 33 R/validate_fold.R | 4 R/validate_list.R | 45 - build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 22 inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.html | 10 inst/doc/evaluate_by_id.html | 6 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 8 man/baseline.Rd | 8 man/baseline_binomial.Rd | 2 man/baseline_gaussian.Rd | 2 man/baseline_multinomial.Rd | 4 man/cross_validate.Rd | 11 man/evaluate.Rd | 98 +- man/most_challenging.Rd | 12 man/plot_confusion_matrix.Rd | 42 - man/plot_metric_density.Rd | 12 man/plot_probabilities.Rd | 1 man/plot_probabilities_ecdf.Rd | 1 man/predicted.musicians.Rd | 20 man/preprocess_functions.Rd | 2 man/summarize_metrics.Rd | 8 man/update_hyperparameters.Rd | 3 man/validate.Rd | 9 tests/testthat/test_cross_validate.R | 169 ++++ tests/testthat/test_evaluate.R | 44 - tests/testthat/test_validate.R | 8 vignettes/man/figures/vignette_conf_mat-unnamed-chunk-12-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-13-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-15-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-2.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-17-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-18-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-5-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-6-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-9-1.png |binary vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-3-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-5-1.png |binary 102 files changed, 1891 insertions(+), 1743 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.8.4 dated 2025-10-02 and 0.8.7 dated 2025-11-09
DESCRIPTION | 8 +-- MD5 | 40 ++++++++--------- NAMESPACE | 3 - R/methods.R | 30 ++++--------- R/methods_DEPRECATED.R | 6 +- README.md | 26 +++++------ build/stage23.rdb |binary inst/NEWS.rd | 6 ++ inst/doc/figures_article.html | 2 inst/doc/introduction.R | 2 inst/doc/introduction.html | 83 ++++++++++++++++++------------------- man/figures/pc_plot-1.png |binary man/figures/plot1-1.png |binary man/figures/plot2-1.png |binary man/figures/unnamed-chunk-15-1.png |binary man/fragments/intro.Rmd | 4 - man/join_features.Rd | 2 man/join_transcripts.Rd | 2 man/plotly.Rd | 2 man/tidy.Rd | 19 +++----- tests/testthat/test-methods.R | 8 +++ 21 files changed, 121 insertions(+), 122 deletions(-)
Title: Robust Sufficient Dimension Reduction
Description: A novel sufficient-dimension reduction method is robust against outliers using alpha-distance covariance and manifold-learning in dimensionality reduction problems. Please refer Hsin-Hsiung Huang, Feng Yu & Teng Zhang (2024) <doi:10.1080/10485252.2024.2313137> for the details.
Author: Sheau-Chiann Chen [aut, cre] ,
Shilin Zhao [aut],
Hsin-Hsiung Bill Huang [aut]
Maintainer: Sheau-Chiann Chen <sheau-chiann.chen.1@vumc.org>
Diff between rSDR versions 1.0.2.1 dated 2025-10-28 and 1.0.3.0 dated 2025-11-09
DESCRIPTION | 14 +- MD5 | 22 ++-- R/cost_fun_esting.R | 20 ++-- R/optimal_alpha_boot.R | 5 - R/optimal_alpha_cv.R | 2 R/rSDR.R | 38 +++++--- inst/doc/rSDR_vignette.R | 28 ++--- inst/doc/rSDR_vignette.Rmd | 37 +++---- inst/doc/rSDR_vignette.html | 208 +++++++++++++++++++++----------------------- man/optimal_alpha_boot.Rd | 3 man/optimal_alpha_cv.Rd | 2 vignettes/rSDR_vignette.Rmd | 37 +++---- 12 files changed, 211 insertions(+), 205 deletions(-)
Title: Network Representations of Attitudes
Description: A tool for computing network representations of attitudes,
extracted from tabular data such as sociological surveys. Development of
surveygraph software and training materials was initially funded by the
European Union under the ERC Proof-of-concept programme (ERC,
Attitude-Maps-4-All, project number: 101069264). Views and opinions expressed
are however those of the author(s) only and do not necessarily reflect those
of the European Union or the European Research Council Executive Agency.
Neither the European Union nor the granting authority can be held responsible
for them.
Author: Samuel Unicomb [aut, cre],
Ana Jovancevic [aut],
Caoimhe O'Reilly [aut],
Alejandro Dinkelberg [aut],
Padraig MacCarron [aut],
David O'Sullivan [aut],
Paul Maher [aut],
Mike Quayle [aut]
Maintainer: Samuel Unicomb <samuelunicomb@gmail.com>
Diff between surveygraph versions 0.1.2 dated 2024-06-04 and 1.0.0 dated 2025-11-09
surveygraph-0.1.2/surveygraph/R/projection.R |only surveygraph-0.1.2/surveygraph/R/synthetic-data.R |only surveygraph-0.1.2/surveygraph/R/threshold-profile.R |only surveygraph-0.1.2/surveygraph/src/build_graphs.cc |only surveygraph-0.1.2/surveygraph/src/components.cc |only surveygraph-0.1.2/surveygraph/src/graph.h |only surveygraph-0.1.2/surveygraph/src/make_projection.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_agent_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_projection_symbolic_pilot.cc |only surveygraph-0.1.2/surveygraph/src/make_threshold_profile.cc |only surveygraph-0.1.2/surveygraph/tests/README.md |only surveygraph-0.1.2/surveygraph/tests/testthat/test-projection.R |only surveygraph-0.1.2/surveygraph/tests/testthat/test-synthetic-data.R |only surveygraph-1.0.0/surveygraph/DESCRIPTION | 18 - surveygraph-1.0.0/surveygraph/MD5 | 54 +-- surveygraph-1.0.0/surveygraph/NAMESPACE | 5 surveygraph-1.0.0/surveygraph/NEWS.md | 4 surveygraph-1.0.0/surveygraph/R/data-preprocess.R |only surveygraph-1.0.0/surveygraph/R/make-projection.R |only surveygraph-1.0.0/surveygraph/R/make-synthetic-data.R |only surveygraph-1.0.0/surveygraph/R/make-threshold-profile.R |only surveygraph-1.0.0/surveygraph/R/surveygraph.R | 6 surveygraph-1.0.0/surveygraph/README.md | 33 + surveygraph-1.0.0/surveygraph/build |only surveygraph-1.0.0/surveygraph/inst/doc |only surveygraph-1.0.0/surveygraph/man/data_preprocess.Rd |only surveygraph-1.0.0/surveygraph/man/make_projection.Rd | 77 +++- surveygraph-1.0.0/surveygraph/man/make_synthetic_data.Rd | 20 - surveygraph-1.0.0/surveygraph/man/make_threshold_profile.Rd | 25 + surveygraph-1.0.0/surveygraph/man/surveygraph.Rd | 32 + surveygraph-1.0.0/surveygraph/src/edge.h |only surveygraph-1.0.0/surveygraph/src/init.cc | 70 +--- surveygraph-1.0.0/surveygraph/src/make_projection_pilot.cc |only surveygraph-1.0.0/surveygraph/src/make_threshold_profile_pilot.cc | 175 ++++++---- surveygraph-1.0.0/surveygraph/src/surveygraph.h | 110 +++--- surveygraph-1.0.0/surveygraph/src/surveygraph_edgelist.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_projection.cc |only surveygraph-1.0.0/surveygraph/src/surveygraph_make_threshold_profile.cc |only surveygraph-1.0.0/surveygraph/src/unionfind.h |only surveygraph-1.0.0/surveygraph/tests/testthat/test_make_projection_comparisons.R |only surveygraph-1.0.0/surveygraph/vignettes |only 41 files changed, 400 insertions(+), 229 deletions(-)
Title: Analysis and Manipulation of Data from Minecraft Bedrock Edition
Description: Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
Author: Reed Cartwright [aut, cre] ,
Rich FitzJohn [ctb],
Christian Stigen Larsen [ctb],
The LevelDB Authors [cph]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between rbedrock versions 0.4.1 dated 2025-08-24 and 0.4.2 dated 2025-11-09
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/finalized_state.R | 2 +- R/legacy-checksums.R | 2 +- data/biome_df.rda |binary data/vanilla_block_list.rda |binary data/vanilla_block_property_type_list.rda |binary data/vanilla_block_states_df.rda |binary man/FinalizedState.Rd | 2 +- tests/testthat/test_legacy-checksums.R | 2 +- 11 files changed, 23 insertions(+), 17 deletions(-)
Title: Plot and Analyse Time-Intensity Data
Description: Plots and analyzes time-intensity curve data, such as data from
(contrast-enhanced) ultrasound. Values such as peak intensity, time to
peak, area under the curve, wash in rate and wash out rate are calculated.
Author: Samuel James Tingle [aut, cre]
Maintainer: Samuel James Tingle <samjamestingle@gmail.com>
Diff between tican versions 1.0.3 dated 2025-05-26 and 1.1.0 dated 2025-11-09
DESCRIPTION | 10 +- MD5 | 32 ++++---- NAMESPACE | 3 NEWS.md | 4 + R/tic_analyse.R | 102 ++++++++++++++++----------- R/tic_auc.R | 22 ----- R/tic_wir.R |only R/tic_wor.R |only R/ttpeak.R | 24 ------ build/vignette.rds |binary inst/doc/tican-vignette.R | 76 ++++++++++++++++---- inst/doc/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- inst/doc/tican-vignette.html | 162 ++++++++++++++++++++++++------------------- man/tic_analyse.Rd | 35 +++------ man/tic_auc.Rd | 21 ----- man/tic_wir.Rd |only man/tic_wor.Rd |only man/ttpeak.Rd | 23 ------ vignettes/tican-vignette.Rmd | 105 +++++++++++++++++++++++---- 19 files changed, 443 insertions(+), 281 deletions(-)
Title: Quantum Computing for Analyzing CD4 Lymphocytes and
Antiretroviral Therapy
Description: Resources, tutorials, and code snippets dedicated to exploring the intersection of quantum computing and artificial intelligence (AI) in the context of analyzing Cluster of Differentiation 4 (CD4) lymphocytes and optimizing antiretroviral therapy (ART) for human immunodeficiency virus (HIV). With the emergence of quantum artificial intelligence and the development of small-scale quantum computers, there's an unprecedented opportunity to revolutionize the understanding of HIV dynamics and treatment strategies. This project leverages the R package 'qsimulatR' (Ostmeyer and Urbach, 2023, <https://CRAN.R-project.org/package=qsimulatR>), a quantum computer simulator, to explore these applications in quantum computing techniques, addressing the challenges in studying CD4 lymphocytes and enhancing ART efficacy.
Author: Juan Pablo Acuna Gonzalez [aut, cre, cph]
Maintainer: Juan Pablo Acuna Gonzalez <22253567@uagro.mx>
Diff between qvirus versions 0.0.4 dated 2025-05-20 and 0.0.5 dated 2025-11-09
DESCRIPTION | 12 MD5 | 74 +-- NAMESPACE | 38 - NEWS.md | 54 ++ R/InteractionClassification.R | 90 ++-- R/cd_diff.R | 70 +-- R/cds_diff.R | 70 +-- R/data.R | 328 ++++++++-------- R/estimate_payoffs.R | 84 ++-- R/mse.InteractionClassification.R | 126 +++--- R/mse.payoffs.R | 116 ++--- R/nearest_payoff.R | 64 +-- R/payoffs_list.R | 112 ++--- R/phen_hiv.R | 132 +++--- R/run_bb84_simulation.R |only R/run_e91_simulation.R |only R/summary.InteractionClassification.R | 116 ++--- R/summary.payoffs.R | 94 ++-- R/vl_diff.R | 72 +-- R/vlog_diff.R | 76 +-- R/vlogs_diff.R | 82 ++-- README.md | 44 +- build/partial.rdb |binary man/run_bb84_simulation.Rd |only man/run_e91_simulation.Rd |only tests/testthat/test-InteractionClassification.R | 24 - tests/testthat/test-cd_diff.R | 14 tests/testthat/test-cds_diff.R | 12 tests/testthat/test-estimate_payoffs.R | 26 - tests/testthat/test-mse.InteractionClassification.R | 24 - tests/testthat/test-mse.payoffs.R | 26 - tests/testthat/test-nearest_payoff.R | 18 tests/testthat/test-payoffs_list.R | 18 tests/testthat/test-phen_hiv.R | 22 - tests/testthat/test-run_bb84_simulation.R |only tests/testthat/test-run_e91_simulation.R |only tests/testthat/test-summary.InteractionClassification.R | 24 - tests/testthat/test-summary.payoffs.R | 28 - tests/testthat/test-vl_diff.R | 16 tests/testthat/test-vlog_diff.R | 14 tests/testthat/test-vlogs_diff.R | 12 41 files changed, 1086 insertions(+), 1046 deletions(-)
Title: Structure Learning with Copula Graphical Model
Description: Statistical tool for learning the structure of direct associations among variables for
continuous data, discrete data and mixed discrete-continuous data. The package is based
on the copula graphical model in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>.
Author: Pariya Behrouzi [aut, cre]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between nutriNetwork versions 0.1.2 dated 2023-07-05 and 0.2.0 dated 2025-11-09
DESCRIPTION | 17 +++-- MD5 | 9 +-- R/selectnet.R | 156 ++++++++++++++++++++++++++--------------------------- inst |only man/plot.select.Rd | 21 +++---- man/selectnet.Rd | 32 +++++----- 6 files changed, 120 insertions(+), 115 deletions(-)
Title: Sampling from the von Mises-Fisher Distribution
Description: Provides fast sampling from von Mises-Fisher distribution using the method proposed by Andrew T.A Wood (1994) <doi:10.1080/03610919408813161>.
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between vMF versions 0.0.3 dated 2024-03-09 and 0.0.4 dated 2025-11-09
vMF-0.0.3/vMF/README.md |only vMF-0.0.4/vMF/DESCRIPTION | 16 ++++++------ vMF-0.0.4/vMF/MD5 | 20 +++++++-------- vMF-0.0.4/vMF/build/partial.rdb |binary vMF-0.0.4/vMF/build/vignette.rds |binary vMF-0.0.4/vMF/inst/doc/vMF.R | 52 +++++++++++++++++++-------------------- vMF-0.0.4/vMF/inst/doc/vMF.Rmd | 12 ++++----- vMF-0.0.4/vMF/inst/doc/vMF.pdf |binary vMF-0.0.4/vMF/man/vMF-package.Rd |only vMF-0.0.4/vMF/src/Makevars | 13 --------- vMF-0.0.4/vMF/src/Makevars.win | 9 ------ vMF-0.0.4/vMF/vignettes/vMF.Rmd | 12 ++++----- 12 files changed, 58 insertions(+), 76 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or
'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Mueller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyz [...truncated...]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.6.4 dated 2023-11-09 and 3.6.5 dated 2025-11-09
covr-3.6.4/covr/tests/testthat/test-tally_coverage.R |only covr-3.6.5/covr/DESCRIPTION | 18 covr-3.6.5/covr/MD5 | 159 +- covr-3.6.5/covr/NAMESPACE | 6 covr-3.6.5/covr/NEWS.md | 31 covr-3.6.5/covr/R/R6.R | 26 covr-3.6.5/covr/R/S7.R |only covr-3.6.5/covr/R/box.R |only covr-3.6.5/covr/R/cobertura.R | 6 covr-3.6.5/covr/R/codecov.R | 14 covr-3.6.5/covr/R/compiled.R | 47 covr-3.6.5/covr/R/coveralls.R | 6 covr-3.6.5/covr/R/covr.R | 71 - covr-3.6.5/covr/R/exclusions.R | 10 covr-3.6.5/covr/R/gitlab.R | 2 covr-3.6.5/covr/R/icc.R | 2 covr-3.6.5/covr/R/parse_data.R | 20 covr-3.6.5/covr/R/replace.R | 4 covr-3.6.5/covr/R/summary_functions.R | 30 covr-3.6.5/covr/R/trace_calls.R | 24 covr-3.6.5/covr/R/trace_tests.R | 146 +- covr-3.6.5/covr/R/utils.R | 11 covr-3.6.5/covr/README.md | 2 covr-3.6.5/covr/build/vignette.rds |binary covr-3.6.5/covr/inst/doc/how_it_works.R | 2 covr-3.6.5/covr/inst/doc/how_it_works.Rmd | 3 covr-3.6.5/covr/inst/doc/how_it_works.html | 25 covr-3.6.5/covr/man/covr.record_tests.Rd | 27 covr-3.6.5/covr/man/current_test_call_count.Rd |only covr-3.6.5/covr/man/current_test_index.Rd |only covr-3.6.5/covr/man/current_test_key.Rd |only covr-3.6.5/covr/man/gitlab.Rd | 2 covr-3.6.5/covr/src/reassign.c | 132 +- covr-3.6.5/covr/tests/testthat.R | 20 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/Test+Char/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple-header.h | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/src/simple.cc | 2 covr-3.6.5/covr/tests/testthat/TestCompiled/tests/testthat/test-TestCompiled.R | 1 covr-3.6.5/covr/tests/testthat/TestCompiledSubdir/src/lib/simple.c | 2 covr-3.6.5/covr/tests/testthat/TestS7 |only covr-3.6.5/covr/tests/testthat/Testbox |only covr-3.6.5/covr/tests/testthat/Testbox_R6 |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions |only covr-3.6.5/covr/tests/testthat/Testbox_attached_modules_functions_R6 |only covr-3.6.5/covr/tests/testthat/_snaps |only covr-3.6.5/covr/tests/testthat/test-Compiled.R | 30 covr-3.6.5/covr/tests/testthat/test-R6.R | 2 covr-3.6.5/covr/tests/testthat/test-RC.R | 1 covr-3.6.5/covr/tests/testthat/test-S4.R | 1 covr-3.6.5/covr/tests/testthat/test-S7.R |only covr-3.6.5/covr/tests/testthat/test-box-R6.R |only covr-3.6.5/covr/tests/testthat/test-box.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions-R6.R |only covr-3.6.5/covr/tests/testthat/test-box_attached_modules_functions.R |only covr-3.6.5/covr/tests/testthat/test-braceless.R | 2 covr-3.6.5/covr/tests/testthat/test-cobertura.R | 2 covr-3.6.5/covr/tests/testthat/test-codecov.R | 649 ++++------ covr-3.6.5/covr/tests/testthat/test-corner-cases.R | 2 covr-3.6.5/covr/tests/testthat/test-coveralls.R | 182 +- covr-3.6.5/covr/tests/testthat/test-covr.R | 3 covr-3.6.5/covr/tests/testthat/test-exclusions.R | 4 covr-3.6.5/covr/tests/testthat/test-file_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-functions.R | 1 covr-3.6.5/covr/tests/testthat/test-gcov.R | 105 - covr-3.6.5/covr/tests/testthat/test-gitlab.R | 2 covr-3.6.5/covr/tests/testthat/test-memoised.R | 1 covr-3.6.5/covr/tests/testthat/test-null.R | 2 covr-3.6.5/covr/tests/testthat/test-package_coverage.R | 1 covr-3.6.5/covr/tests/testthat/test-parallel.R | 5 covr-3.6.5/covr/tests/testthat/test-print.R | 18 covr-3.6.5/covr/tests/testthat/test-record_tests.R | 24 covr-3.6.5/covr/tests/testthat/test-report.R | 4 covr-3.6.5/covr/tests/testthat/test-sonarqube.R | 2 covr-3.6.5/covr/tests/testthat/test-summary.R | 4 covr-3.6.5/covr/tests/testthat/test-trace_calls.R | 1 covr-3.6.5/covr/tests/testthat/test-utils.R | 66 - covr-3.6.5/covr/tests/testthat/test-vectorized.R | 1 covr-3.6.5/covr/vignettes/how_it_works.Rmd | 3 79 files changed, 1163 insertions(+), 812 deletions(-)
Title: Econometrics of Network Data
Description: Simulating and estimating peer effect models and network formation models. The class of peer effect models includes linear-in-means models (Lee, 2004; <doi:10.1111/j.1468-0262.2004.00558.x>), Tobit models (Xu and Lee, 2015; <doi:10.1016/j.jeconom.2015.05.004>), and discrete numerical data models (Houndetoungan, 2025; <doi:10.48550/arXiv.2405.17290>). The network formation models include pair-wise regressions with degree heterogeneity (Graham, 2017; <doi:10.3982/ECTA12679>) and exponential random graph models (Mele, 2017; <doi:10.3982/ECTA10400>).
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@ecn.ulaval.ca>
Diff between CDatanet versions 2.2.1 dated 2025-01-07 and 2.2.2 dated 2025-11-09
DESCRIPTION | 18 MD5 | 40 + NAMESPACE | 9 NEWS.md | 14 R/CDatanet.R | 2 R/RcppExports.R | 52 ++ R/auxfunc.R | 1 R/cdnet.R | 214 +++++----- R/homophily.fe.R | 58 ++ R/homophily.re.R | 15 R/meffects.R |only R/sart.R | 144 +++---- build/partial.rdb |binary man/CDatanet-package.Rd | 4 man/meffects.Rd |only man/simcdnet.Rd | 6 man/simsart.Rd | 16 src/RcppExports.cpp | 261 +++++++++++- src/cdnet.cpp | 987 ++++++++++++++++++++++++++++++++---------------- src/homophily.cpp | 2 src/sartcomplet.cpp | 82 +-- src/sartincomplet.cpp | 421 +++++++++++++++----- 22 files changed, 1638 insertions(+), 708 deletions(-)
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
Author: Lissandro Costa de Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Diff between adcontabil versions 1.1.0 dated 2025-11-08 and 1.1.8 dated 2025-11-09
DESCRIPTION | 6 +- MD5 | 12 ++-- R/AV_AH.R | 136 ++++++++++++++++++++++++++++++------------------- R/indicadores.R | 31 +++++++++++ R/padronizar_balanco.R | 8 +- man/calcular_AV_AH.Rd | 38 ++++++------- man/indicadores.Rd | 32 +++++++++++ 7 files changed, 178 insertions(+), 85 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions,
without making copies.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like, and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra functions for st [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.5.3 dated 2025-10-10 and 0.1.6.1 dated 2025-11-09
broadcast-0.1.5.3/broadcast/R/internal_cast.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bycolumn.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-bylayer.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/acast/test-acast-byrow.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/class/test-class.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/internal/test-orthogonal.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-bc_dim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-ndim.R |only broadcast-0.1.5.3/broadcast/inst/tinytest/test-rep_dim.R |only broadcast-0.1.5.3/broadcast/src/C_bindhelper_vdims.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_equal.c |only broadcast-0.1.5.3/broadcast/src/C_dims_all_orthogonal.c |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_dec.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_str.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcFact_int.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_normalize_dims.cpp |only broadcast-0.1.6.1/broadcast/DESCRIPTION | 9 broadcast-0.1.6.1/broadcast/MD5 | 297 +- broadcast-0.1.6.1/broadcast/NAMESPACE | 10 broadcast-0.1.6.1/broadcast/NEWS.md | 20 broadcast-0.1.6.1/broadcast/R/RcppExports.R | 220 +- broadcast-0.1.6.1/broadcast/R/aaa00_broadcast_help.R | 7 broadcast-0.1.6.1/broadcast/R/aaa02_broadcast_casting.R | 10 broadcast-0.1.6.1/broadcast/R/aaa03_broadcast_bind.R | 20 broadcast-0.1.6.1/broadcast/R/aaa04_broadcast_linearalgebra.R | 2 broadcast-0.1.6.1/broadcast/R/acast.R | 45 broadcast-0.1.6.1/broadcast/R/bc_b.R | 16 broadcast-0.1.6.1/broadcast/R/bc_bit.R | 16 broadcast-0.1.6.1/broadcast/R/bc_cplx.R | 16 broadcast-0.1.6.1/broadcast/R/bc_d.R | 49 broadcast-0.1.6.1/broadcast/R/bc_i.R | 40 broadcast-0.1.6.1/broadcast/R/bc_ifelse.R | 16 broadcast-0.1.6.1/broadcast/R/bc_list.R | 15 broadcast-0.1.6.1/broadcast/R/bc_raw.R | 8 broadcast-0.1.6.1/broadcast/R/bc_str.R | 30 broadcast-0.1.6.1/broadcast/R/bc_strrep.R |only broadcast-0.1.6.1/broadcast/R/bcapply.R | 12 broadcast-0.1.6.1/broadcast/R/bind_array.R | 18 broadcast-0.1.6.1/broadcast/R/broadcastWrappers.R | 55 broadcast-0.1.6.1/broadcast/R/broadcaster.R | 85 broadcast-0.1.6.1/broadcast/R/cast_dim2hier.R | 6 broadcast-0.1.6.1/broadcast/R/cast_hier2dim.R | 30 broadcast-0.1.6.1/broadcast/R/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/R/dropnests.R | 2 broadcast-0.1.6.1/broadcast/R/hier2dim.R | 110 - broadcast-0.1.6.1/broadcast/R/internal_acast.R |only broadcast-0.1.6.1/broadcast/R/internal_acast_names.R |only broadcast-0.1.6.1/broadcast/R/internal_binary.R | 104 - broadcast-0.1.6.1/broadcast/R/internal_binary_names.R | 18 broadcast-0.1.6.1/broadcast/R/internal_bind.R | 123 - broadcast-0.1.6.1/broadcast/R/internal_bind_names.R | 4 broadcast-0.1.6.1/broadcast/R/internal_functions.R | 8 broadcast-0.1.6.1/broadcast/R/internal_hiercast.R |only broadcast-0.1.6.1/broadcast/R/internal_opfuns.R | 2 broadcast-0.1.6.1/broadcast/R/internal_typefuns.R | 38 broadcast-0.1.6.1/broadcast/R/linear_algebra_stats.R | 3 broadcast-0.1.6.1/broadcast/R/meta_functions.R | 142 + broadcast-0.1.6.1/broadcast/R/ndim.R | 2 broadcast-0.1.6.1/broadcast/R/overload_ops_math.R | 6 broadcast-0.1.6.1/broadcast/R/overload_relops.R | 8 broadcast-0.1.6.1/broadcast/R/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/examples/bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/examples/bind_array.R | 8 broadcast-0.1.6.1/broadcast/inst/examples/broadcaster.R | 32 broadcast-0.1.6.1/broadcast/inst/examples/cast_shallow2atomic.R |only broadcast-0.1.6.1/broadcast/inst/examples/vector2array.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-backtransform.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bycolumn_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-bylayer_named.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-byrow_namedR.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-crashtest.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-edgecases.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-acast-errors.R | 62 broadcast-0.1.6.1/broadcast/inst/tinytest/acast/test-simple.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_b/test-bc_b.R | 1026 +--------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_cplx/test-bc_cplx_math.R | 352 --- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-bc_strrep.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bc_general/test-binaryerrors.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_list/test-bc_list.R | 2 broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_d_math.R | 662 ------ broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_math.R | 791 ------- broadcast-0.1.6.1/broadcast/inst/tinytest/bc_num/test-bc_i_rel.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-1d.R | 38 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-array.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-between.R | 32 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-ortho.R | 39 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-vector.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/binary_names/test-zerolen.R | 37 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-broadcaster.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array-errors.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-bind_array_internal.R | 30 broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_1_basic/test-partialdimnames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/bind_array_3_row/test-rbind_bc.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim-nonames.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-cast_hier2dim_names.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-errors.R | 4 broadcast-0.1.6.1/broadcast/inst/tinytest/cast/test-hiernames2dimnames-nonames.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-broadcaster_set.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/class/test-mbroadcasters.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/count/count_tests.R | 6 broadcast-0.1.6.1/broadcast/inst/tinytest/helper |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-conformable.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimmode.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-dimnames_fit.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/internal/test-mini.R | 1 broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx.R | 362 --- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_cplx_by_other.R | 600 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/overload/test-math_d.R | 535 ----- broadcast-0.1.6.1/broadcast/inst/tinytest/shallow2atomic |only broadcast-0.1.6.1/broadcast/inst/tinytest/source.R |only broadcast-0.1.6.1/broadcast/inst/tinytest/test-S4error-callerenv.R | 3 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary1d.R | 27 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_attr_broadcaster.R | 28 broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_errors.R | 109 - broadcast-0.1.6.1/broadcast/inst/tinytest/test-binary_zerolen.R | 24 broadcast-0.1.6.1/broadcast/inst/tinytest/test-ellipsis.R | 17 broadcast-0.1.6.1/broadcast/man/aaa00_broadcast_help.Rd | 9 broadcast-0.1.6.1/broadcast/man/aaa01_broadcast_operators.Rd | 32 broadcast-0.1.6.1/broadcast/man/aaa02_broadcast_casting.Rd | 10 broadcast-0.1.6.1/broadcast/man/acast.Rd | 31 broadcast-0.1.6.1/broadcast/man/bc_ifelse.Rd | 4 broadcast-0.1.6.1/broadcast/man/bc_strrep.Rd |only broadcast-0.1.6.1/broadcast/man/bcapply.Rd | 2 broadcast-0.1.6.1/broadcast/man/bind_array.Rd | 27 broadcast-0.1.6.1/broadcast/man/broadcaster.Rd | 69 broadcast-0.1.6.1/broadcast/man/cast_dim2hier.Rd | 2 broadcast-0.1.6.1/broadcast/man/cast_hier2dim.Rd | 8 broadcast-0.1.6.1/broadcast/man/cast_shallow2atomic.Rd |only broadcast-0.1.6.1/broadcast/man/hier2dim.Rd | 5 broadcast-0.1.6.1/broadcast/man/linear_algebra_stats.Rd | 2 broadcast-0.1.6.1/broadcast/man/ndim.Rd | 2 broadcast-0.1.6.1/broadcast/man/vector2array.Rd |only broadcast-0.1.6.1/broadcast/src/C_any_nonarray.c |only broadcast-0.1.6.1/broadcast/src/C_arraysize_overflow.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_get_alongdims.c |only broadcast-0.1.6.1/broadcast/src/C_bindhelper_need_coerce.c |only broadcast-0.1.6.1/broadcast/src/C_check_conf_dim.c | 51 broadcast-0.1.6.1/broadcast/src/C_determine_dimmode.c |only broadcast-0.1.6.1/broadcast/src/C_dims_allge.c |only broadcast-0.1.6.1/broadcast/src/C_make_dcp.c | 9 broadcast-0.1.6.1/broadcast/src/C_sd_lc.c | 34 broadcast-0.1.6.1/broadcast/src/C_unlisthelper_maxlen.c |only broadcast-0.1.6.1/broadcast/src/RcppExports.cpp | 687 +++++- broadcast-0.1.6.1/broadcast/src/broadcast.h | 808 +++---- broadcast-0.1.6.1/broadcast/src/rcpp_bcD_dec.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_int.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcD_str.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_b.cpp | 43 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_cplx.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_int.cpp | 31 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bcRel_str.cpp | 34 broadcast-0.1.6.1/broadcast/src/rcpp_bc_b.cpp | 184 + broadcast-0.1.6.1/broadcast/src/rcpp_bc_bind.cpp | 62 broadcast-0.1.6.1/broadcast/src/rcpp_bc_bit.cpp | 48 broadcast-0.1.6.1/broadcast/src/rcpp_bc_cplx.cpp | 44 broadcast-0.1.6.1/broadcast/src/rcpp_bc_dec.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_ifelse.cpp | 38 broadcast-0.1.6.1/broadcast/src/rcpp_bc_int.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_list.cpp | 29 broadcast-0.1.6.1/broadcast/src/rcpp_bc_raw.cpp | 30 broadcast-0.1.6.1/broadcast/src/rcpp_bc_str.cpp | 32 broadcast-0.1.6.1/broadcast/src/rcpp_bc_strrep.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_bcapply.cpp | 21 broadcast-0.1.6.1/broadcast/src/rcpp_bindhelpers.cpp | 81 broadcast-0.1.6.1/broadcast/src/rcpp_cast_shallow2atomic.cpp |only broadcast-0.1.6.1/broadcast/src/rcpp_set_attr.cpp | 44 broadcast-0.1.6.1/broadcast/tests/tinytest.R | 12 173 files changed, 3769 insertions(+), 6105 deletions(-)
Title: Assessing Normality of Stationary Process
Description: Despite that several tests for normality in stationary processes have been proposed in the literature, consistent implementations of these tests in programming languages are limited. Seven normality test are implemented. The asymptotic Lobato & Velasco's, asymptotic Epps, Psaradakis and Vávra, Lobato & Velasco's and Epps sieve bootstrap approximations, El bouch et al., and the random projections tests for univariate stationary process. Some other diagnostics such as, unit root test for stationarity, seasonal tests for seasonality, and arch effect test for volatility; are also performed. Additionally, the El bouch test performs normality tests for bivariate time series. The package also offers residual diagnostic for linear time series models developed in several packages.
Author: Asael Alonzo Matamoros [aut, cre],
Alicia Nieto-Reyes [aut],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb],
Trapletti A. [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between nortsTest versions 1.1.2 dated 2024-01-25 and 1.1.3 dated 2025-11-09
DESCRIPTION | 10 ++--- MD5 | 17 +++++---- NEWS.md | 15 ++++++++ R/autoplot.R | 4 +- R/epps_test.R | 21 +++++++++--- R/nortsTest-package.R | 60 +++++++++++++++------------------- README.md | 2 - man/autoplot.ts.Rd | 4 +- man/nortsTest-package.Rd | 78 ++++++++++++++++++++++++++++----------------- tests/testthat/test-epps.r |only 10 files changed, 126 insertions(+), 85 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Supports Gaussian and binomial responses. Also implements the randomized permutation whole-model test for SVEM with Gaussian responses (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Some parts of the package code were drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 2.3.1 dated 2025-10-13 and 2.5.4 dated 2025-11-09
SVEMnet-2.3.1/SVEMnet/R/predict_with_ci.R |only SVEMnet-2.3.1/SVEMnet/R/svem_significance_test.R |only SVEMnet-2.3.1/SVEMnet/man/predict_with_ci.Rd |only SVEMnet-2.3.1/SVEMnet/man/svem_significance_test.Rd |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/bic_sim_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_c2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_aicc_cvglm.R |only SVEMnet-2.3.1/SVEMnet/vignettes/debias_and_objective.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_26AUG25.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_27AUG25_second_script_pp.R |only SVEMnet-2.3.1/SVEMnet/vignettes/sim_28AUG25_script.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svem_vs_lassoCV_par_v2.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_identity.R |only SVEMnet-2.3.1/SVEMnet/vignettes/svemnet_sim_mixture_v2.R |only SVEMnet-2.5.4/SVEMnet/DESCRIPTION | 19 SVEMnet-2.5.4/SVEMnet/MD5 | 109 - SVEMnet-2.5.4/SVEMnet/NAMESPACE | 13 SVEMnet-2.5.4/SVEMnet/NEWS | 3 SVEMnet-2.5.4/SVEMnet/R/SVEMnet-package.R | 29 SVEMnet-2.5.4/SVEMnet/R/SVEMnet.R | 539 ++++- SVEMnet-2.5.4/SVEMnet/R/bigexp.R | 702 +++++-- SVEMnet-2.5.4/SVEMnet/R/coef.R | 178 + SVEMnet-2.5.4/SVEMnet/R/glmnet_with_cv.R | 386 +++ SVEMnet-2.5.4/SVEMnet/R/globals.R | 2 SVEMnet-2.5.4/SVEMnet/R/lipid_screen.R | 111 - SVEMnet-2.5.4/SVEMnet/R/plot.svemnet.R | 270 ++ SVEMnet-2.5.4/SVEMnet/R/plot.svemtest.R | 60 SVEMnet-2.5.4/SVEMnet/R/predict.cv.R | 155 + SVEMnet-2.5.4/SVEMnet/R/predict.svem_lasso.R | 405 ++-- SVEMnet-2.5.4/SVEMnet/R/svem_optimize_random.R | 987 +++++++--- SVEMnet-2.5.4/SVEMnet/R/svem_random_table_multi.R | 101 - SVEMnet-2.5.4/SVEMnet/R/svem_significance_test_parallel.R | 249 +- SVEMnet-2.5.4/SVEMnet/data/lipid_screen.rda |binary SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.R | 89 SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/inst/doc/SVEMnet_vignette.html | 430 +--- SVEMnet-2.5.4/SVEMnet/man/SVEMnet-package.Rd | 34 SVEMnet-2.5.4/SVEMnet/man/SVEMnet.Rd | 171 + SVEMnet-2.5.4/SVEMnet/man/bigexp_formula.Rd | 31 SVEMnet-2.5.4/SVEMnet/man/bigexp_model_matrix.Rd | 30 SVEMnet-2.5.4/SVEMnet/man/bigexp_prepare.Rd | 63 SVEMnet-2.5.4/SVEMnet/man/bigexp_terms.Rd | 138 + SVEMnet-2.5.4/SVEMnet/man/bigexp_train.Rd | 54 SVEMnet-2.5.4/SVEMnet/man/coef.svem_model.Rd | 66 SVEMnet-2.5.4/SVEMnet/man/glmnet_with_cv.Rd | 277 ++ SVEMnet-2.5.4/SVEMnet/man/lipid_screen.Rd | 141 + SVEMnet-2.5.4/SVEMnet/man/plot.svem_binomial.Rd |only SVEMnet-2.5.4/SVEMnet/man/plot.svem_model.Rd | 49 SVEMnet-2.5.4/SVEMnet/man/plot.svem_significance_test.Rd | 21 SVEMnet-2.5.4/SVEMnet/man/predict.svem_model.Rd | 194 + SVEMnet-2.5.4/SVEMnet/man/predict_cv.Rd | 90 SVEMnet-2.5.4/SVEMnet/man/print.bigexp_spec.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_nonzero.Rd |only SVEMnet-2.5.4/SVEMnet/man/svem_optimize_random.Rd | 384 ++- SVEMnet-2.5.4/SVEMnet/man/svem_random_table_multi.Rd | 81 SVEMnet-2.5.4/SVEMnet/man/svem_significance_test_parallel.Rd | 170 + SVEMnet-2.5.4/SVEMnet/man/with_bigexp_contrasts.Rd | 31 SVEMnet-2.5.4/SVEMnet/tests/testthat/test-fit-and-predict.R | 369 +++ SVEMnet-2.5.4/SVEMnet/tests/testthat/test-optimize-random.R | 109 - SVEMnet-2.5.4/SVEMnet/tests/testthat/test-significance-tests.R | 4 SVEMnet-2.5.4/SVEMnet/vignettes/SVEMnet_vignette.Rmd | 158 - SVEMnet-2.5.4/SVEMnet/vignettes/binary_sim_05NOV25.R |only 67 files changed, 5403 insertions(+), 2257 deletions(-)
Title: Uniformity Tests on the Circle, Sphere, and Hypersphere
Description: Implementation of uniformity tests on the circle and
(hyper)sphere. The main function of the package is unif_test(), which
conveniently collects more than 35 tests for assessing uniformity on
S^{p-1} = {x in R^p : ||x|| = 1}, p >= 2. The test statistics are
implemented in the unif_stat() function, which allows computing several
statistics for different samples within a single call, thus facilitating
Monte Carlo experiments. Furthermore, the unif_stat_MC() function allows
parallelizing them in a simple way. The asymptotic null distributions of
the statistics are available through the function unif_stat_distr(). The
core of 'sphunif' is coded in C++ by relying on the 'Rcpp' package.
The package also provides several novel datasets and gives the replicability
for the data applications/simulations in García-Portugués et al. (2021)
<doi:10.1007/978-3-030-69944-4_12>, García-Portugués et al. (2023)
<doi:10.3150/21-BEJ1454>, Fernández-de-Marcos and
García-Portugués (2024) <d [...truncated...]
Author: Eduardo Garcia-Portugues [aut, cre] ,
Thomas Verdebout [aut] ,
Alberto Fernandez-de-Marcos [ctb],
Paula Navarro [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between sphunif versions 1.4.2 dated 2025-08-18 and 1.4.3 dated 2025-11-09
DESCRIPTION | 10 - MD5 | 78 +++++++------- NEWS.md | 8 + R/Pn.R | 2 R/Sobolev.R | 29 +++-- R/cir_distr.R | 2 R/cir_stat.R | 5 R/data.R | 14 +- R/harmonics.R | 12 +- R/locdev.R | 2 R/sph_distr.R | 1 R/sph_stat.R | 2 R/sphunif-package.R | 20 +-- R/unif_stat.R | 2 R/unif_stat_distr.R | 57 ++++++---- R/unif_test.R | 6 - inst/WORDLIST | 2 inst/doc/sphunif.R | 4 inst/doc/sphunif.Rmd | 21 ++- inst/doc/sphunif.html | 181 ++++++++++++++++++---------------- man/Pn.Rd | 2 man/Sobolev.Rd | 3 man/Sobolev_coefs.Rd | 4 man/avail_tests.Rd | 2 man/cir_stat.Rd | 5 man/cir_stat_distr.Rd | 5 man/comets.Rd | 2 man/craters.Rd | 12 +- man/harmonics.Rd | 12 +- man/locdev.Rd | 2 man/sph_stat.Rd | 2 man/sphunif-package.Rd | 20 +-- man/unif_stat.Rd | 2 man/unif_stat_distr.Rd | 5 man/unif_test.Rd | 4 tests/testthat/test_Sobolev.R | 15 ++ tests/testthat/test_unif_stat.R | 4 tests/testthat/test_unif_stat_distr.R | 66 ++++++++++++ vignettes/sphunif.Rmd | 21 ++- vignettes/sphunif.bib | 15 +- 40 files changed, 398 insertions(+), 263 deletions(-)
Title: Longitudinal Surrogate Marker Analysis
Description: Assess the proportion of treatment effect explained by a longitudinal surrogate marker as described in Agniel D and Parast L (2021) <doi:10.1111/biom.13310>; and estimate the treatment effect on a longitudinal surrogate marker as described in Wang et al. (2025) <doi:10.1093/biomtc/ujaf104>. A tutorial for this package can be found at <https://www.laylaparast.com/longsurr>.
Author: Layla Parast [aut, cre],
Denis Agniel [aut],
Xuan Wang [aut]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between longsurr versions 1.0 dated 2022-09-29 and 1.1 dated 2025-11-09
DESCRIPTION | 16 - MD5 | 12 - NAMESPACE | 8 R/longsurr.functions.R | 416 ++++++++++++++++++++++++++++++++++++++++++++- data/data_sjm.RData |only man/data_sjm.Rd |only man/resam.Rd |only man/resam_nonlinear.Rd |only man/sjm_linear_estimate.Rd |only man/sjm_nl_estimate.Rd |only 10 files changed, 436 insertions(+), 16 deletions(-)
Title: Meta-Analysis of Quantiles and Functions of Quantiles
Description: Implements a novel density-based approach for estimating unknown parameters, distribution visualisations and meta-analyses of quantiles and ther functions.
A detailed vignettes with example datasets and code to prepare data and analyses is available at <https://bookdown.org/a2delivera/metaquant/>.
The methods are described in the pre-print by De Livera, Prendergast and Kumaranathunga (2024, <doi:10.48550/arXiv.2411.10971>).
Author: Udara Kumaranathunga [aut, cre],
Alysha De Livera [aut],
Luke Prendergast [aut]
Maintainer: Udara Kumaranathunga <U.Kumaranathunga@latrobe.edu.au>
Diff between metaquant versions 0.1.2 dated 2025-08-21 and 0.1.3 dated 2025-11-09
metaquant-0.1.2/metaquant/build |only metaquant-0.1.2/metaquant/man/est.density.five.Rd |only metaquant-0.1.2/metaquant/man/est.density.minq2max.Rd |only metaquant-0.1.2/metaquant/man/est.density.q1q2q3.Rd |only metaquant-0.1.3/metaquant/DESCRIPTION | 20 - metaquant-0.1.3/metaquant/MD5 | 29 - metaquant-0.1.3/metaquant/NAMESPACE | 11 metaquant-0.1.3/metaquant/R/est.mean.R | 99 ++--- metaquant-0.1.3/metaquant/R/est.sd.R | 26 - metaquant-0.1.3/metaquant/R/helper.functions.R | 308 +++++++++++++++++- metaquant-0.1.3/metaquant/R/metaquant.R |only metaquant-0.1.3/metaquant/R/plotdist.R | 201 ----------- metaquant-0.1.3/metaquant/man/est.gld.five.Rd |only metaquant-0.1.3/metaquant/man/est.mean.Rd | 18 - metaquant-0.1.3/metaquant/man/est.q.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.r.study.level.Rd |only metaquant-0.1.3/metaquant/man/est.sd.Rd | 8 metaquant-0.1.3/metaquant/man/est.sld.minq2max.Rd |only metaquant-0.1.3/metaquant/man/est.sld.q1q2q3.Rd |only metaquant-0.1.3/metaquant/man/metaquant.Rd |only metaquant-0.1.3/metaquant/man/plotdist.Rd | 10 21 files changed, 413 insertions(+), 317 deletions(-)
Title: Neat Data for Presentation
Description: Utilities for unambiguous, neat and legible
representation of data (date, time stamp, numbers, percentages and strings)
for presentation of analysis , aiming for elegance and consistency.
The purpose of this package is to format data, that is better
for presentation and any automation jobs that reports numbers.
Author: Shivaprakash Suresh [aut, cre, cph]
Maintainer: Shivaprakash Suresh <dswithai@gmail.com>
This is a re-admission after prior archival of version 0.2.0 dated 2023-03-23
Diff between neatR versions 0.2.0 dated 2023-03-23 and 0.2.1 dated 2025-11-09
DESCRIPTION | 8 - MD5 | 28 ++--- R/src.R | 248 +++++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/neat-data.R | 54 +++++----- inst/doc/neat-data.Rmd | 70 ++++++------- inst/doc/neat-data.html | 213 ++++++++++++++++++++--------------------- man/ndate.Rd | 10 - man/nday.Rd | 8 - man/nnumber.Rd | 8 - man/npercent.Rd | 23 ++-- man/nstring.Rd | 20 +-- man/ntimestamp.Rd | 28 ++--- tests/testthat/tests.R | 32 +++--- vignettes/neat-data.Rmd | 70 ++++++------- 15 files changed, 432 insertions(+), 388 deletions(-)
Title: Access Infectious and Epidemiological Data via 'disease.sh API'
Description: Provides functions to access real-time infectious disease data from the 'disease.sh API',
including COVID-19 global, US states, continent, and country statistics, vaccination coverage,
influenza-like illness data from the Centers for Disease Control and Prevention (CDC), and more.
Also includes curated datasets on a variety of infectious diseases such as influenza, measles, dengue,
Ebola, tuberculosis, meningitis, AIDS, and others. The package supports epidemiological research
and data analysis by combining API access with high-quality historical and survey datasets on infectious diseases.
For more details on the 'disease.sh API', see <https://disease.sh/>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between infectiousR versions 0.1.0 dated 2025-06-16 and 0.1.1 dated 2025-11-09
DESCRIPTION | 19 +- MD5 | 132 +++++++++--------- NAMESPACE | 2 NEWS.md |only R/data-documentation.R | 2 R/get_covid_stats_by_continent.R | 71 ++++++--- R/get_covid_stats_by_country.R | 73 +++++++-- R/get_covid_stats_by_country_name.R | 76 ++++++++-- R/get_covid_stats_for_state.R | 80 ++++++++-- R/get_global_covid_stats.R | 89 ++++++++---- R/get_influenza_cdc_ili.R | 103 +++++++++++--- R/get_us_states_covid_stats.R | 90 ++++++++---- R/infectiousR-package.R | 2 R/utils.R | 2 R/view_datasets_infectiousR.R | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/infectiousR_vignette.html | 5 man/get_covid_stats_by_continent.Rd | 13 + man/get_covid_stats_by_country.Rd | 13 + man/get_covid_stats_by_country_name.Rd | 13 + man/get_covid_stats_for_state.Rd | 9 - man/get_global_covid_stats.Rd | 18 +- man/get_influenza_cdc_ili.Rd | 12 + man/get_us_states_covid_stats.Rd | 10 - tests/testthat/test-active_hepatitis_df.R | 2 tests/testthat/test-aids_azt_df.R | 2 tests/testthat/test-bcg_vaccine_df.R | 2 tests/testthat/test-campy_infections_ts.R | 2 tests/testthat/test-china_dengue_tbl_df.R | 2 tests/testthat/test-contagious_diseases_df.R | 2 tests/testthat/test-covid_mortality_df.R | 2 tests/testthat/test-covid_new_york_df.R | 2 tests/testthat/test-covid_severity_df.R | 2 tests/testthat/test-diphtheria_philly_df.R | 2 tests/testthat/test-ebola_cases_df.R | 2 tests/testthat/test-ebola_sleone_df.R | 2 tests/testthat/test-ebola_survey_tbl_df.R | 2 tests/testthat/test-ecoli_infections_df.R | 2 tests/testthat/test-ehec_infections_df.R | 2 tests/testthat/test-flu_enrich_df.R | 2 tests/testthat/test-fungal_infections_df.R | 2 tests/testthat/test-get_covid_stats_by_continent.R |only tests/testthat/test-get_covid_stats_by_country.R |only tests/testthat/test-get_covid_stats_by_country_name.R |only tests/testthat/test-get_covid_stats_for_state.R |only tests/testthat/test-get_global_covid_stats.R |only tests/testthat/test-get_influenza_cdc_ili.R |only tests/testthat/test-get_us_states_covid_stats.R |only tests/testthat/test-gonorrhea_ma_df.R | 2 tests/testthat/test-hepatitisA_df.R | 2 tests/testthat/test-india_dengue_tbl_df.R | 2 tests/testthat/test-influenza_ice_df.R | 2 tests/testthat/test-influenza_infections_df.R | 2 tests/testthat/test-influenza_pneumonia_ts.R | 2 tests/testthat/test-influenza_vax_survey_df.R | 2 tests/testthat/test-korea_dengue_tbl_df.R | 2 tests/testthat/test-malaria_mice_df.R | 2 tests/testthat/test-measles_infections_df.R | 2 tests/testthat/test-measles_survey_df.R | 2 tests/testthat/test-meningitis_df.R | 2 tests/testthat/test-rubella_austria_df.R | 2 tests/testthat/test-rubella_peru_df.R | 2 tests/testthat/test-sars_canada_df.R | 2 tests/testthat/test-smallpox_nigeria_df.R | 2 tests/testthat/test-spanish_flu_df.R | 2 tests/testthat/test-streptomycin_tbl_df.R | 2 tests/testthat/test-us_covid_cases_df.R | 2 tests/testthat/test-view_datasets_infectiousR.R | 2 tests/testthat/test-zika_girardot_df.R | 2 tests/testthat/test-zika_sanandres_df.R | 2 71 files changed, 621 insertions(+), 295 deletions(-)
Title: Fast, Vectorized Hashmap
Description: A fast, vectorized hashmap that is built on top of 'C++' std::unordered_map <https://en.cppreference.com/w/cpp/container/unordered_map.html>.
The map can hold any 'R' object as key / value as long as it is serializable and supports
vectorized insertion, lookup, and deletion.
Author: Sven Glinz [aut, cre]
Maintainer: Sven Glinz <svenglinz@proton.me>
Diff between hashmapR versions 1.0.0 dated 2025-11-07 and 1.0.1 dated 2025-11-09
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- README.md | 6 ++++++ src/hashmap.cpp | 10 +++++----- src/init.c | 35 +++++++++++++++++------------------ tests/testthat/test_map.R | 3 ++- 6 files changed, 40 insertions(+), 35 deletions(-)
Title: Bayesian Hierarchical Modeling for Label-Free Proteomics
Description: Statistical decision in proteomics data using a hierarchical
Bayesian model. There are two regression models for describing the
mean-variance trend, a gamma regression or a latent gamma mixture
regression. The regression model is then used as an Empirical Bayes
estimator for the prior on the variance in a peptide. Further, it assumes
that each measurement has an uncertainty (increased variance) associated
with it that is also inferred. Finally, it tries to estimate the posterior
distribution (by Hamiltonian Monte Carlo) for the differences in means for
each peptide in the data. Once the posterior is inferred, it integrates the
tails to estimate the probability of error from which a statistical decision
can be made.
See Berg and Popescu for details (<doi:10.1016/j.mcpro.2023.100658>).
Author: Philip Berg [aut, cre]
Maintainer: Philip Berg <pberg@live.se>
Diff between baldur versions 0.0.3 dated 2023-09-18 and 0.0.4 dated 2025-11-09
baldur-0.0.3/baldur/inst/doc/baldur_yeast_tutorial.Rmd |only baldur-0.0.3/baldur/inst/doc/baldur_yeast_tutorial.html |only baldur-0.0.3/baldur/vignettes/baldur_yeast_tutorial.Rmd |only baldur-0.0.4/baldur/DESCRIPTION | 16 baldur-0.0.4/baldur/MD5 | 88 baldur-0.0.4/baldur/NEWS.md | 9 baldur-0.0.4/baldur/R/baldur-package.R | 87 baldur-0.0.4/baldur/R/calculate_mean_sd_trends.R | 16 baldur-0.0.4/baldur/R/fit_lgmr.R | 2 baldur-0.0.4/baldur/R/psrn.R | 258 +- baldur-0.0.4/baldur/R/sample_posterior.R | 901 +++---- baldur-0.0.4/baldur/README.md | 177 + baldur-0.0.4/baldur/build/partial.rdb |binary baldur-0.0.4/baldur/build/vignette.rds |binary baldur-0.0.4/baldur/inst/CITATION |only baldur-0.0.4/baldur/inst/doc/Baldur_Yeast_Tutorial.Rmd |only baldur-0.0.4/baldur/inst/doc/Baldur_Yeast_Tutorial.html |only baldur-0.0.4/baldur/inst/doc/baldur_ups_tutorial.Rmd | 414 +-- baldur-0.0.4/baldur/inst/doc/baldur_ups_tutorial.html | 131 - baldur-0.0.4/baldur/inst/stan/empirical_bayes.stan | 104 baldur-0.0.4/baldur/inst/stan/lgmr_model.stan | 134 - baldur-0.0.4/baldur/inst/stan/weakly_informative.stan | 98 baldur-0.0.4/baldur/man/baldur-package.Rd | 66 baldur-0.0.4/baldur/man/calculate_mean_sd_trends.Rd | 74 baldur-0.0.4/baldur/man/fit_lgmr.Rd | 2 baldur-0.0.4/baldur/man/infer_data_and_decision_model.Rd | 20 baldur-0.0.4/baldur/src/stanExports_empirical_bayes.cc | 34 baldur-0.0.4/baldur/src/stanExports_empirical_bayes.h | 1292 +++++------ baldur-0.0.4/baldur/src/stanExports_lgmr_model.cc | 34 baldur-0.0.4/baldur/src/stanExports_lgmr_model.h | 1138 ++++----- baldur-0.0.4/baldur/src/stanExports_weakly_informative.cc | 34 baldur-0.0.4/baldur/src/stanExports_weakly_informative.h | 1210 +++++----- baldur-0.0.4/baldur/vignettes/Baldur_Yeast_Tutorial.Rmd |only baldur-0.0.4/baldur/vignettes/baldur_ups_tutorial.Rmd | 414 +-- baldur-0.0.4/baldur/vignettes/baldur_ups_tutorial.Rmd.orig | 36 baldur-0.0.4/baldur/vignettes/baldur_yeast_tutorial.Rmd.orig | 13 baldur-0.0.4/baldur/vignettes/compile_vignettes.R |only baldur-0.0.4/baldur/vignettes/plotting_lgmr-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_lgmr_yeast-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_sa_yeast-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc-2.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc_yeast-1.png |binary baldur-0.0.4/baldur/vignettes/plotting_volc_yeast-2.png |binary 49 files changed, 3426 insertions(+), 3376 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.7.5 dated 2025-10-28 and 0.8.0 dated 2025-11-09
glyrepr-0.7.5/glyrepr/R/composition-utils.R |only glyrepr-0.7.5/glyrepr/man/normalize_substituents.Rd |only glyrepr-0.8.0/glyrepr/DESCRIPTION | 10 glyrepr-0.8.0/glyrepr/MD5 | 46 +- glyrepr-0.8.0/glyrepr/NAMESPACE | 2 glyrepr-0.8.0/glyrepr/NEWS.md | 22 + glyrepr-0.8.0/glyrepr/R/composition.R | 170 +++++--- glyrepr-0.8.0/glyrepr/R/count-mono.R |only glyrepr-0.8.0/glyrepr/R/get-structure-level.R |only glyrepr-0.8.0/glyrepr/R/linkage.R | 40 + glyrepr-0.8.0/glyrepr/R/substituent.R | 3 glyrepr-0.8.0/glyrepr/README.md | 2 glyrepr-0.8.0/glyrepr/inst/doc/glycan-graph.html | 6 glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.R | 12 glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.Rmd | 42 ++ glyrepr-0.8.0/glyrepr/inst/doc/glyrepr.html | 201 +++++----- glyrepr-0.8.0/glyrepr/inst/doc/smap.html | 8 glyrepr-0.8.0/glyrepr/man/as_glycan_composition.Rd | 18 glyrepr-0.8.0/glyrepr/man/count_mono.Rd | 16 glyrepr-0.8.0/glyrepr/man/get_structure_level.Rd |only glyrepr-0.8.0/glyrepr/man/glyrepr-package.Rd | 2 glyrepr-0.8.0/glyrepr/man/has_linkages.Rd | 22 - glyrepr-0.8.0/glyrepr/tests/testthat/test-composition.R | 48 +- glyrepr-0.8.0/glyrepr/tests/testthat/test-count-mono.R | 5 glyrepr-0.8.0/glyrepr/tests/testthat/test-get-structure-level.R |only glyrepr-0.8.0/glyrepr/tests/testthat/test-linkage.R | 7 glyrepr-0.8.0/glyrepr/vignettes/glyrepr.Rmd | 42 ++ 27 files changed, 495 insertions(+), 229 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-03 1.0.1
2023-12-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-24 2.2.8
2023-07-16 2.2.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-26 0.1.0
Title: Fuzzy Rank Tests and Confidence Intervals
Description: Does fuzzy tests and confidence intervals (following Geyer
and Meeden, Statistical Science, 2005, <doi:10.1214/088342305000000340>)
for sign test and Wilcoxon signed rank and rank sum tests.
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between fuzzyRankTests versions 0.4 dated 2021-08-14 and 0.5 dated 2025-11-09
fuzzyRankTests-0.4/fuzzyRankTests/.Rinstignore |only fuzzyRankTests-0.4/fuzzyRankTests/inst/doc/design.tex |only fuzzyRankTests-0.5/fuzzyRankTests/ChangeLog | 3 fuzzyRankTests-0.5/fuzzyRankTests/DESCRIPTION | 18 +- fuzzyRankTests-0.5/fuzzyRankTests/MD5 | 42 +++--- fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.ranksum.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.ranksum.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.sign.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.sign.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.signrank.ci.R | 2 fuzzyRankTests-0.5/fuzzyRankTests/R/fuzzy.signrank.test.R | 6 fuzzyRankTests-0.5/fuzzyRankTests/R/plot.fuzzyrankci.R | 4 fuzzyRankTests-0.5/fuzzyRankTests/build |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/design.Rnw |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/design.pdf |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.R |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.Rnw |only fuzzyRankTests-0.5/fuzzyRankTests/inst/doc/intro.pdf |only fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.ranksum.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.sign.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/man/fuzzy.signrank.test.Rd | 16 +- fuzzyRankTests-0.5/fuzzyRankTests/tests/ranksum.R | 10 - fuzzyRankTests-0.5/fuzzyRankTests/tests/ranksum.Rout.save | 38 +---- fuzzyRankTests-0.5/fuzzyRankTests/tests/signrank.R | 12 - fuzzyRankTests-0.5/fuzzyRankTests/tests/signrank.Rout.save | 72 ++--------- fuzzyRankTests-0.5/fuzzyRankTests/vignettes |only 26 files changed, 119 insertions(+), 152 deletions(-)
More information about fuzzyRankTests at CRAN
Permanent link
Title: Build 'pkgdown' Websites Offline
Description: Provides support for building 'pkgdown' websites without an
internet connection. Works by bundling cached dependencies and
implementing drop-in replacements for key 'pkgdown' functions.
Enables package documentation websites to be built in environments
where internet access is unavailable or restricted.
For more details on generating 'pkgdown' websites, see
Wickham et al. (2025) <doi:10.32614/CRAN.package.pkgdown>.
Author: Nan Xiao [aut, cre, cph] ,
John Blischak [aut] ,
Algolia, Inc. and other contributors [ctb, cph] ,
Aidan Feldman [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Williams [ctb, cph] ,
Julian Kuehnel [ctb, cph] ,
Kiro Risk [ctb, cph] ,
Khan Academy and other [...truncated...]
Maintainer: Nan Xiao <me@nanx.me>
Diff between pkgdown.offline versions 0.1.1 dated 2025-05-25 and 0.1.2 dated 2025-11-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/build.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/cache/MD5 | 7 +++++++ 7 files changed, 28 insertions(+), 10 deletions(-)
More information about pkgdown.offline at CRAN
Permanent link
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.5.1 dated 2025-10-21 and 0.6.0 dated 2025-11-08
DESCRIPTION | 18 +++++++-------- MD5 | 34 +++++++++++++++++++----------- NAMESPACE | 9 +++++++ NEWS.md | 13 +++++++++++ R/grouped_tbl_pivot_wider.R | 4 +-- R/gtsummary_utilities.R |only R/long_to_periods.R | 2 - R/plot_multiple_answers.R | 4 +-- R/plot_proportions.R | 9 ++++--- R/plot_trajectories.R |only R/proportion.R | 34 ++++++++++++++++-------------- R/view_dictionary.R |only README.md | 2 - inst/WORDLIST | 4 +++ inst/rstudio |only man/gtsummary_utilities.Rd |only man/plot_multiple_answers.Rd | 2 - man/plot_proportions.Rd | 2 - man/plot_trajectories.Rd |only man/view_dictionary.Rd |only tests/testthat/test-gtsummary-utilities.R |only tests/testthat/test-plot_trajectories.R |only tests/testthat/test-view_dictionary.R |only 23 files changed, 89 insertions(+), 48 deletions(-)
Title: Sparse Principal Component Regression
Description: The sparse principal component regression is computed. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano <skawano@math.kyushu-u.ac.jp>
This is a re-admission after prior archival of version 2.1.1 dated 2022-10-16
Diff between spcr versions 2.1.1 dated 2022-10-16 and 2.1.1 dated 2025-11-08
0 files changed
Title: Sparse Group Partial Least Square Methods
Description: Regularized version of partial least square approaches
providing sparse, group, and sparse group versions of partial
least square regression models (Liquet, B., Lafaye de Micheaux, P.,
Hejblum B., Thiebaut, R. (2016) <doi:10.1093/bioinformatics/btv535>).
Version of PLS Discriminant analysis is also provided.
Author: Benoit Liquet [aut, cre],
Pierre Lafaye de Micheaux [aut],
Camilo Broc [aut]
Maintainer: Benoit Liquet <benoit.liquet@univ-pau.fr>
Diff between sgPLS versions 1.8 dated 2023-10-05 and 1.8.1 dated 2025-11-08
DESCRIPTION | 28 +++++++++++++++++++--------- MD5 | 10 +++++----- man/gPLS.Rd | 2 +- man/gPLSda.Rd | 4 ++-- man/sPLSda.Rd | 4 ++-- man/sgPLSda.Rd | 4 ++-- 6 files changed, 31 insertions(+), 21 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>
This is a re-admission after prior archival of version 2.0.3 dated 2025-06-04
Diff between rtpcr versions 2.0.3 dated 2025-06-04 and 2.0.3 dated 2025-11-08
0 files changed
Title: Histone ChIP-Seq qPCR Analyzer
Description: Quality control of chromatin immunoprecipitation libraries (ChIP-seq) by quantitative polymerase chain reaction (qPCR). This function calculates Enrichment value with respect to reference for each histone modification (specific to 'Vii7' software <http://www.thermofisher.com/ca/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/viia-7-real-time-pcr-system/viia-7-software.html>). This function is applicable to full panel of histone modifications described by International Human Epigenomic Consortium (IHEC).
Author: Alireza Lorzadeh
Maintainer: Alireza Lorzadeh <alorzadeh@bcgsc.ca>
This is a re-admission after prior archival of version 1.5 dated 2018-02-08
Diff between qcQpcr versions 1.5 dated 2018-02-08 and 1.5 dated 2025-11-08
0 files changed
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 1.0.3.1 dated 2025-11-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/memshare.Rmd | 2 +- vignettes/memshare.Rmd | 2 +- 6 files changed, 11 insertions(+), 11 deletions(-)
Title: Bayesian Analysis of qRT-PCR Data
Description: Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <https://matzlab.weebly.com/uploads/7/6/2/2/76229469/mcmc.qpcr.tutorial.v1.2.4.pdf>.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
This is a re-admission after prior archival of version 1.2.4 dated 2020-03-29
Diff between MCMC.qpcr versions 1.2.4 dated 2020-03-29 and 1.2.4 dated 2025-11-08
0 files changed
Title: Land Use Change Modelling in R
Description: Classes and methods for spatially explicit land use change
modelling in R.
Author: Simon Moulds <sim.moulds@gmail.com>
Maintainer: Simon Moulds <sim.moulds@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2019-03-01
Diff between lulcc versions 1.0.4 dated 2019-03-01 and 1.0.4 dated 2025-11-08
0 files changed
Title: Generalized Supervised Principal Component Regression
Description: Generalization of supervised principal component regression (SPCR;
Bair et al., 2006, <doi:10.1198/016214505000000628>) to support continuous,
binary, and discrete variables as outcomes and predictors
(inspired by the 'superpc' R package <https://cran.r-project.org/package=superpc>).
Author: Edoardo Costantini [aut, cre]
Maintainer: Edoardo Costantini <costantini.edoardo@yahoo.com>
This is a re-admission after prior archival of version 0.9.5 dated 2024-04-12
Diff between gspcr versions 0.9.5 dated 2024-04-12 and 0.9.5 dated 2025-11-08
0 files changed
Title: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk
Samples
Description: Interval estimation of the population allele frequency from qPCR analysis based on the restriction enzyme digestion (RED)-DeltaDeltaCq method (Osakabe et al. 2017, <doi:10.1016/j.pestbp.2017.04.003>), as well as general DeltaDeltaCq analysis. Compatible with the Cq measurement of DNA extracted from multiple individuals at once, so called "group-testing", this model assumes that the quantity of DNA extracted from an individual organism follows a gamma distribution. Therefore, the point estimate is robust regarding the uncertainty of the DNA yield.
Author: Masaaki Sudo [aut, cre]
Maintainer: Masaaki Sudo <masaaki@sudori.info>
This is a re-admission after prior archival of version 0.4.0 dated 2022-01-27
Diff between freqpcr versions 0.4.0 dated 2022-01-27 and 0.4.0 dated 2025-11-08
0 files changed
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
This is a re-admission after prior archival of version 1.15.2 dated 2023-08-20
Diff between ddpcr versions 1.15.2 dated 2023-08-20 and 1.15.2 dated 2025-11-08
0 files changed
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <doi:10.1016/j.jprot.2019.103613>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 2.5.0 dated 2025-06-15 and 2.5.1 dated 2025-11-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/GetSequences.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.5 dated 2025-10-08 and 0.1.6 dated 2025-11-08
DESCRIPTION | 6 - MD5 | 14 +- build/vignette.rds |binary data/bullet.rda |binary data/place_prefecture.rda |binary data/sex_prefecture.rda |binary inst/doc/jpinfect.html | 204 +++++++++++++++++++++---------------------- inst/extdata/1999_Syu_11.xls |binary 8 files changed, 112 insertions(+), 112 deletions(-)
Title: Accounting Analysis
Description: Provides methods for processing corporate balance sheets with a focus on the Brazilian reporting format. Includes data standardization, classification by accounting categories, and aggregation of values. Supports accounting and financial analyses of companies, improving efficiency and ensuring reproducibility of empirical studies.
Author: Lissandro Costa de Sousa [cre, aut],
Francisco Gildemir Ferreira da Silva [ths, aut]
Maintainer: Lissandro Costa de Sousa <lisandrosousa54@gmail.com>
Diff between adcontabil versions 1.0.4 dated 2025-10-03 and 1.1.0 dated 2025-11-08
adcontabil-1.0.4/adcontabil/man/categorias.Rd |only adcontabil-1.0.4/adcontabil/man/classificar_conta.Rd |only adcontabil-1.1.0/adcontabil/DESCRIPTION | 6 adcontabil-1.1.0/adcontabil/MD5 | 28 + adcontabil-1.1.0/adcontabil/NAMESPACE | 2 adcontabil-1.1.0/adcontabil/R/AV_AH.R | 21 - adcontabil-1.1.0/adcontabil/R/indicadores.R | 238 ++++++++++----- adcontabil-1.1.0/adcontabil/R/padronizar_balanco.R | 8 adcontabil-1.1.0/adcontabil/R/padronizar_dre.R |only adcontabil-1.1.0/adcontabil/R/zzz.R | 103 +++++- adcontabil-1.1.0/adcontabil/man/calcular_AV_AH.Rd | 7 adcontabil-1.1.0/adcontabil/man/categorias_bp.Rd |only adcontabil-1.1.0/adcontabil/man/categorias_dre.Rd |only adcontabil-1.1.0/adcontabil/man/classificar_conta_bp.Rd |only adcontabil-1.1.0/adcontabil/man/classificar_conta_dre.Rd |only adcontabil-1.1.0/adcontabil/man/indicadores.Rd | 86 +++-- adcontabil-1.1.0/adcontabil/man/normalizar_texto.Rd | 10 adcontabil-1.1.0/adcontabil/man/padronizar_balanco.Rd | 2 adcontabil-1.1.0/adcontabil/man/padronizar_dre.Rd |only 19 files changed, 344 insertions(+), 167 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb] ,
Audrey Martin [ctb] ,
Philip Greenspoon [ctb] ,
Ros Craddock [ctb] ,
Jana Obsteter [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 2.0.0 dated 2025-09-01 and 2.1.0 dated 2025-11-08
DESCRIPTION | 21 +++--- MD5 | 42 ++++++------ NAMESPACE | 3 NEWS.md | 16 ++++ R/AlphaSimR.R | 34 +++++----- R/Class-Pop.R | 16 +++- R/RcppExports.R | 6 - R/misc.R | 19 +++++ R/popSummary.R | 129 ++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 2 inst/doc/AlphaSimR.html | 11 +-- inst/doc/traits.pdf |binary man/AlphaSimR-package.Rd | 27 ++++---- man/mendelianSampling.Rd |only man/parentAverage.Rd |only man/popVar.Rd | 2 man/popVarCpp.Rd |only src/RcppExports.cpp | 10 +-- src/misc.cpp | 4 - src/packHaplo.cpp | 4 + src/simulator.cpp | 5 + tests/testthat/test-popSummary.R |only 24 files changed, 270 insertions(+), 81 deletions(-)
Title: Multivariate Bayesian Sparse Group Selection with Spike and Slab
Description: An implementation of a Bayesian sparse group model using spike and slab priors in a regression context. It is designed for regression with a multivariate response variable, but also provides an implementation for univariate response.
Author: Benoit Liquet [aut, cre],
Matthew Sutton [aut]
Maintainer: Benoit Liquet <benoit.liquet@univ-pau.fr>
Diff between MBSGS versions 1.1.0 dated 2017-08-09 and 1.2.0 dated 2025-11-08
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- R/MBSGS-internal.R | 4 ++-- man/BGLSS.Rd | 4 +--- man/BSGSSS.Rd | 2 +- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: Processing Hemispherical Canopy Images
Description: Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.
Author: Francesco Chianucci [aut, cre] ,
Martin Macek [aut]
Maintainer: Francesco Chianucci <fchianucci@gmail.com>
Diff between hemispheR versions 1.1.7 dated 2025-09-03 and 1.1.8 dated 2025-11-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/binarize_fisheye.R | 10 +++++++++- R/import_fisheye.R | 6 ++++-- 6 files changed, 26 insertions(+), 11 deletions(-)
Title: Exponential Integral and Incomplete Gamma Function
Description: The exponential integrals E_1(x), E_2(x), E_n(x) and
Ei(x), and the incomplete gamma function G(a, x) defined for
negative values of its first argument. The package also gives easy
access to the underlying C routines through an API; see the package
vignette for details. A test package included in sub-directory
example_API provides an implementation. C routines derived from the
GNU Scientific Library <https://www.gnu.org/software/gsl/>.
Author: Vincent Goulet [cre, aut],
Gerard Jungman [aut] ,
Brian Gough [aut] ,
Jeffrey A. Ryan [aut] ,
Robert Gentleman [aut] ,
Ross Ihaka [aut] ,
R Core Team [aut] ,
R Foundation [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between expint versions 0.1-8 dated 2022-10-28 and 0.1-9 dated 2025-11-08
expint-0.1-8/expint/vignettes/auto |only expint-0.1-9/expint/DESCRIPTION | 8 +-- expint-0.1-9/expint/MD5 | 27 ++++++------ expint-0.1-9/expint/build/partial.rdb |binary expint-0.1-9/expint/build/vignette.rds |binary expint-0.1-9/expint/inst/CITATION | 19 +------- expint-0.1-9/expint/inst/NEWS.Rd | 13 +++++- expint-0.1-9/expint/inst/doc/expint.R | 18 ++++---- expint-0.1-9/expint/inst/doc/expint.Rnw | 66 ------------------------------- expint-0.1-9/expint/inst/doc/expint.pdf |binary expint-0.1-9/expint/src/expint.c | 33 +++++---------- expint-0.1-9/expint/src/expint.h | 8 +-- expint-0.1-9/expint/src/gamma_inc.c | 18 ++------ expint-0.1-9/expint/vignettes/Makefile |only expint-0.1-9/expint/vignettes/expint.Rnw | 66 ------------------------------- expint-0.1-9/expint/vignettes/share |only 16 files changed, 67 insertions(+), 209 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb, cre] ,
Duncan Temple Lang [aut] ,
Tomas Kalibera [ctb],
Ivan Krylov [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between XML versions 3.99-0.19 dated 2025-08-22 and 3.99-0.20 dated 2025-11-08
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 7 +++++++ R/tree.R | 2 +- src/DocParse.c | 3 +++ src/RUtils.c | 2 +- src/XMLEventParse.c | 11 +++++++++++ 8 files changed, 37 insertions(+), 12 deletions(-)
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 1.0.2 dated 2025-09-10 and 1.0.3 dated 2025-11-08
memshare-1.0.2/memshare/src/Makevars |only memshare-1.0.2/memshare/src/Makevars.win |only memshare-1.0.3/memshare/DESCRIPTION | 11 + memshare-1.0.3/memshare/MD5 | 34 +++-- memshare-1.0.3/memshare/README.md | 52 ++++++++ memshare-1.0.3/memshare/build/partial.rdb |binary memshare-1.0.3/memshare/build/vignette.rds |only memshare-1.0.3/memshare/inst |only memshare-1.0.3/memshare/man/memApply.Rd | 134 ++++++++++++++-------- memshare-1.0.3/memshare/man/memLapply.Rd | 134 ++++++++++++++-------- memshare-1.0.3/memshare/man/memshare-package.Rd | 58 +++++++++ memshare-1.0.3/memshare/man/pageList.Rd | 87 +++++++------- memshare-1.0.3/memshare/man/releaseVariables.Rd | 85 +++++++------- memshare-1.0.3/memshare/man/releaseViews.Rd | 106 +++++++++-------- memshare-1.0.3/memshare/man/retrieveMetadata.Rd | 111 +++++++++--------- memshare-1.0.3/memshare/man/retrieveViews.Rd | 144 +++++++++++++----------- memshare-1.0.3/memshare/man/viewList.Rd | 109 +++++++++--------- memshare-1.0.3/memshare/src/memory_page.cpp | 20 ++- memshare-1.0.3/memshare/src/memory_page.h | 22 ++- memshare-1.0.3/memshare/vignettes |only 20 files changed, 662 insertions(+), 445 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: A joint model for large-scale, competing risks time-to-event data with singular or multiple longitudinal biomarkers, implemented with the efficient algorithms developed by Li and colleagues (2022) <doi:10.1155/2022/1362913> and <doi:10.48550/arXiv.2506.12741>.
The time-to-event data is modelled using a (cause-specific) Cox
proportional hazards regression model with time-fixed covariates.
The longitudinal biomarkers are modelled using a linear mixed
effects model. The association between the longitudinal submodel
and the survival submodel is captured through shared random
effects. It allows researchers to analyze large-scale data to
model biomarker trajectories, estimate their effects on event
outcomes, and dynamically predict future events from patients’
past histories. A function for simulating survival and longitudinal
data for multiple biomarkers is also included alongside built-in
datasets.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Emily Ouyang [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.5.2 dated 2025-10-18 and 1.5.3 dated 2025-11-08
DESCRIPTION | 29 +++-- MD5 | 29 ++--- NAMESPACE | 4 NEWS.md | 5 R/CIF1mv.SF.R |only R/FastJM.R | 2 R/MAEQjmcs.R | 4 R/Pkmv.us_SF.R |only R/logLikCRmv.R | 2 R/logLikSFmv.R |only R/print.jmcs.R | 207 +++++++++++++++++++----------------- R/print.survfitmvjmcs.R |only R/summary.jmcs.R | 29 +++-- R/survfitmvjmcs.R | 258 ++++++++++++++++++++++----------------------- README.md | 162 ++++++++++++++++++++++++++-- inst/WORDLIST | 6 + man/print.survfitmvjmcs.Rd |only man/survfitmvjmcs.Rd | 2 18 files changed, 469 insertions(+), 270 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.1.1 dated 2025-09-02 and 5.2.0 dated 2025-11-08
DESCRIPTION | 19 MD5 | 94 NAMESPACE | 31 NEWS | 27 R/apiOA2df.R | 294 R/apply_citation_matching.R |only R/assignEvolutionColors.R |only R/authorBio.r |only R/convert2df.R | 110 R/csvScopus2df.R | 48 R/findAuthorWorks.r |only R/histNetwork.R | 127 R/lifeCycle.R |only R/ltwa.R |only R/networkPlot.R | 401 - R/plotThematicEvolution.R | 315 R/thematicEvolution.R | 219 R/thematicMap.R | 860 +- R/zzz.R | 291 build/partial.rdb |binary data/bibtag.rda |binary data/countries.rda |binary data/customTheme.rda |binary data/logo.rda |binary data/ltwa.rda |only data/stopwords.rda |binary inst/biblioshiny/article_summary.R |only inst/biblioshiny/biblioAI.R | 2147 ++++- inst/biblioshiny/biblioShot.R | 3 inst/biblioshiny/contentAnalysisServer.R |only inst/biblioshiny/contentAnalysisUI.R |only inst/biblioshiny/cssTags.R |only inst/biblioshiny/helpContent.R | 2110 +++++ inst/biblioshiny/libraries.R | 16 inst/biblioshiny/lifeCycleUI.R |only inst/biblioshiny/openalex_api.R |only inst/biblioshiny/pubmed_api.R |only inst/biblioshiny/server.R |11235 ++++++++++++++++++++++--------- inst/biblioshiny/ui.R |10324 ++++++++++++++++++++-------- inst/biblioshiny/utils.R | 2503 +++++- inst/biblioshiny/utils_old.R |only inst/biblioshiny/www/ORCID.jpg |only inst/biblioshiny/www/openalex.jpg |only man/abbreviate_journal_title.Rd |only man/abbreviate_term.Rd |only man/applyCitationMatching.Rd |only man/assignEvolutionColors.Rd |only man/authorBio.Rd |only man/convert_scopus_new_to_classic.Rd |only man/create_journal_iso4_lookup.Rd |only man/findAuthorWorks.Rd |only man/get_authors_summary.Rd |only man/get_iso4_stop_words.Rd |only man/lifeCycle.Rd |only man/ltwa.Rd |only man/mergeKeywords.Rd | 4 man/networkPlot.Rd | 16 man/normalize_citations.Rd |only man/normalize_journal_to_iso4.Rd |only man/plotThematicEvolution.Rd | 40 man/prepare_ltwa_lookup.Rd |only man/print_author_works_summary.Rd |only man/remove_diacritics.Rd |only man/thematicEvolution.Rd | 13 man/thematicMap.Rd | 22 65 files changed, 23084 insertions(+), 8185 deletions(-)
Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@fu-berlin.de>
Diff between DrDimont versions 0.1.4 dated 2022-09-23 and 0.1.6 dated 2025-11-08
DrDimont-0.1.4/DrDimont/man/calculate_interaction_score.Rd |only DrDimont-0.1.4/DrDimont/man/check_connection.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_target.Rd |only DrDimont-0.1.4/DrDimont/man/check_drug_targets_in_layers.Rd |only DrDimont-0.1.4/DrDimont/man/check_layer.Rd |only DrDimont-0.1.4/DrDimont/man/check_sensible_connections.Rd |only DrDimont-0.1.4/DrDimont/man/chunk.Rd |only DrDimont-0.1.4/DrDimont/man/chunk_2gether.Rd |only DrDimont-0.1.4/DrDimont/man/combine_graphs.Rd |only DrDimont-0.1.4/DrDimont/man/corPvalueStudentParallel.Rd |only DrDimont-0.1.4/DrDimont/man/create_unique_layer_node_ids.Rd |only DrDimont-0.1.4/DrDimont/man/find_targets.Rd |only DrDimont-0.1.4/DrDimont/man/generate_reduced_graph.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer.Rd |only DrDimont-0.1.4/DrDimont/man/get_layer_setting.Rd |only DrDimont-0.1.4/DrDimont/man/graph_metrics.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_id.Rd |only DrDimont-0.1.4/DrDimont/man/inter_layer_edgelist_by_table.Rd |only DrDimont-0.1.4/DrDimont/man/load_interaction_score_output.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_p_value.Rd |only DrDimont-0.1.4/DrDimont/man/network_reduction_by_pickHardThreshold.Rd |only DrDimont-0.1.4/DrDimont/man/sample_size.Rd |only DrDimont-0.1.4/DrDimont/man/set_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/shutdown_cluster.Rd |only DrDimont-0.1.4/DrDimont/man/target_edge_list.Rd |only DrDimont-0.1.4/DrDimont/man/write_interaction_score_input.Rd |only DrDimont-0.1.6/DrDimont/DESCRIPTION | 36 DrDimont-0.1.6/DrDimont/LICENSE | 2 DrDimont-0.1.6/DrDimont/MD5 | 148 DrDimont-0.1.6/DrDimont/NAMESPACE | 26 DrDimont-0.1.6/DrDimont/R/checks.R | 48 DrDimont-0.1.6/DrDimont/R/data_documentations.R | 90 DrDimont-0.1.6/DrDimont/R/drug_targets.R | 20 DrDimont-0.1.6/DrDimont/R/graph_combination.R | 10 DrDimont-0.1.6/DrDimont/R/interaction_score.R | 18 DrDimont-0.1.6/DrDimont/R/network_generation.R | 87 DrDimont-0.1.6/DrDimont/R/network_reduction.R | 66 DrDimont-0.1.6/DrDimont/R/pipeline_functions.R | 63 DrDimont-0.1.6/DrDimont/R/settings.R | 34 DrDimont-0.1.6/DrDimont/R/utilities.R | 114 DrDimont-0.1.6/DrDimont/R/utils-pipe.R | 4 DrDimont-0.1.6/DrDimont/build/vignette.rds |binary DrDimont-0.1.6/DrDimont/data/combined_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/correlation_matrices_example.rda |binary DrDimont-0.1.6/DrDimont/data/differential_graph_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_gene_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/drug_response_scores_example.rda |binary DrDimont-0.1.6/DrDimont/data/drug_target_edges_example.rda |binary DrDimont-0.1.6/DrDimont/data/individual_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/interaction_score_graphs_example.rda |binary DrDimont-0.1.6/DrDimont/data/layers_example.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_data.rda |binary DrDimont-0.1.6/DrDimont/data/metabolite_protein_interactions.rda |binary DrDimont-0.1.6/DrDimont/data/mrna_data.rda |binary DrDimont-0.1.6/DrDimont/data/phosphosite_data.rda |binary DrDimont-0.1.6/DrDimont/data/protein_data.rda |binary DrDimont-0.1.6/DrDimont/inst/CITATION | 9 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.R | 407 - DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.Rmd | 141 DrDimont-0.1.6/DrDimont/inst/doc/DrDimont_Vignette.html | 2197 +++++----- DrDimont-0.1.6/DrDimont/inst/python_igraph_interaction_score.py | 19 DrDimont-0.1.6/DrDimont/man/check_input.Rd | 2 DrDimont-0.1.6/DrDimont/man/combined_graphs_example.Rd | 6 DrDimont-0.1.6/DrDimont/man/compute_correlation_matrices.Rd | 2 DrDimont-0.1.6/DrDimont/man/compute_drug_response_scores.Rd | 2 DrDimont-0.1.6/DrDimont/man/correlation_matrices_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/determine_drug_targets.Rd | 4 DrDimont-0.1.6/DrDimont/man/differential_graph_example.Rd | 2 DrDimont-0.1.6/DrDimont/man/drdimont_settings.Rd | 33 DrDimont-0.1.6/DrDimont/man/drug_gene_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/drug_response_scores_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/drug_target_edges_example.Rd | 8 DrDimont-0.1.6/DrDimont/man/generate_combined_graphs.Rd | 2 DrDimont-0.1.6/DrDimont/man/generate_individual_graphs.Rd | 6 DrDimont-0.1.6/DrDimont/man/generate_interaction_score_graphs.Rd | 4 DrDimont-0.1.6/DrDimont/man/individual_graphs_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/interaction_score_graphs_example.Rd | 4 DrDimont-0.1.6/DrDimont/man/layers_example.Rd | 10 DrDimont-0.1.6/DrDimont/man/make_drug_target.Rd | 2 DrDimont-0.1.6/DrDimont/man/make_layer.Rd | 6 DrDimont-0.1.6/DrDimont/man/metabolite_data.Rd | 8 DrDimont-0.1.6/DrDimont/man/metabolite_protein_interactions.Rd | 6 DrDimont-0.1.6/DrDimont/man/mrna_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/phosphosite_data.Rd | 4 DrDimont-0.1.6/DrDimont/man/pipe.Rd | 4 DrDimont-0.1.6/DrDimont/man/protein_data.Rd | 2 DrDimont-0.1.6/DrDimont/man/run_pipeline.Rd | 4 DrDimont-0.1.6/DrDimont/vignettes/DrDimont_Vignette.Rmd | 141 88 files changed, 1927 insertions(+), 1912 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-24 1.6.0
2025-10-08 1.5.5
2025-08-25 1.5.4
2025-08-18 1.5.3
2025-07-24 1.5.2
2025-07-15 1.5.0
2025-07-07 1.4.4
2025-07-07 1.4.5
Title: Plot Null Hypothesis Significance Tests
Description: Illustrate graphically the most common Null Hypothesis Significance Testing procedures. More specifically, this package provides functions to plot Chi-Squared, F, t (one- and two-tailed) and z (one- and two-tailed) tests, by plotting the probability density under the null hypothesis as a function of the different test statistic values. Although highly flexible (color theme, fonts, etc.), only the minimal number of arguments (observed test statistic, degrees of freedom) are necessary for a clear and useful graph to be plotted, with the observed test statistic and the p value, as well as their corresponding value labels. The axes are automatically scaled to present the relevant part and the overall shape of the probability density function. This package is especially intended for education purposes, as it provides a helpful support to help explain the Null Hypothesis Significance Testing process, its use and/or shortcomings.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between nhstplot versions 1.4.0 dated 2025-07-30 and 1.4.1 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ NEWS.md | 5 ++- R/plot.chisqtest.R | 10 +++---- R/plot.ftest.R | 10 +++---- R/plot.ttest.R | 32 +++++++++++------------ R/plot.ztest.R | 34 ++++++++++++------------ build/vignette.rds |binary inst/doc/nhstplot.html | 67 +++++++++++++++++++++++++++---------------------- 9 files changed, 96 insertions(+), 84 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.0 dated 2025-09-10 and 3.2.1 dated 2025-11-08
scCustomize-3.2.0/scCustomize/man/Liger_to_Seurat.Rd |only scCustomize-3.2.0/scCustomize/man/deprecated.Rd |only scCustomize-3.2.1/scCustomize/DESCRIPTION | 10 scCustomize-3.2.1/scCustomize/MD5 | 72 - scCustomize-3.2.1/scCustomize/NAMESPACE | 5 scCustomize-3.2.1/scCustomize/NEWS.md | 33 scCustomize-3.2.1/scCustomize/R/Color_Palettes.R | 11 scCustomize-3.2.1/scCustomize/R/Deprecated.R | 18 scCustomize-3.2.1/scCustomize/R/Generics.R | 3 scCustomize-3.2.1/scCustomize/R/Internal_Utilities.R | 633 ++++++++-- scCustomize-3.2.1/scCustomize/R/LIGER_Internal_Utilities.R | 16 scCustomize-3.2.1/scCustomize/R/LIGER_Plotting.R | 1 scCustomize-3.2.1/scCustomize/R/LIGER_Utilities.R | 56 scCustomize-3.2.1/scCustomize/R/Object_Conversion.R | 483 +++---- scCustomize-3.2.1/scCustomize/R/Object_Utilities.R | 337 ++++- scCustomize-3.2.1/scCustomize/R/Plotting_Nebulosa.R | 7 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seq_10X.R | 30 scCustomize-3.2.1/scCustomize/R/Plotting_QC_Seurat.R | 2 scCustomize-3.2.1/scCustomize/R/Plotting_Seurat.R | 265 +++- scCustomize-3.2.1/scCustomize/R/Plotting_Seurat_Iterative.R | 14 scCustomize-3.2.1/scCustomize/R/Plotting_Shared.R | 1 scCustomize-3.2.1/scCustomize/R/Plotting_Statistics.R | 8 scCustomize-3.2.1/scCustomize/R/Plotting_Utilities_Internal.R | 39 scCustomize-3.2.1/scCustomize/R/QC_Utilities_Seurat.R | 12 scCustomize-3.2.1/scCustomize/R/Read_&_Write_Data.R | 54 scCustomize-3.2.1/scCustomize/R/Statistics.R | 5 scCustomize-3.2.1/scCustomize/R/Utilities.R | 39 scCustomize-3.2.1/scCustomize/R/zzz.R | 2 scCustomize-3.2.1/scCustomize/man/Clustered_DotPlot.Rd | 6 scCustomize-3.2.1/scCustomize/man/DimPlot_scCustom.Rd | 10 scCustomize-3.2.1/scCustomize/man/ElbowPlot_scCustom.Rd |only scCustomize-3.2.1/scCustomize/man/Extract_Sample_Meta.Rd | 7 scCustomize-3.2.1/scCustomize/man/Fetch_Meta.Rd | 8 scCustomize-3.2.1/scCustomize/man/Map_New_Meta.Rd |only scCustomize-3.2.1/scCustomize/man/NavyAndOrange.Rd | 2 scCustomize-3.2.1/scCustomize/man/Random_Cells_Downsample.Rd | 4 scCustomize-3.2.1/scCustomize/man/Read_CellBender_h5_Multi_Directory.Rd | 3 scCustomize-3.2.1/scCustomize/man/Stacked_VlnPlot.Rd | 4 scCustomize-3.2.1/scCustomize/man/VlnPlot_scCustom.Rd | 2 39 files changed, 1465 insertions(+), 737 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph],
Edward Fuselier [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 5.3 dated 2023-01-26 and 6.0 dated 2025-11-08
molaR-5.3/molaR/R/ARC_Legend.R |only molaR-5.3/molaR/R/DNE_Discard_Legend.R |only molaR-5.3/molaR/R/DNE_Legend.R |only molaR-5.3/molaR/R/OPC_Legend.R |only molaR-5.3/molaR/R/RFI_Legend.R |only molaR-5.3/molaR/R/Slope_Legend.R |only molaR-5.3/molaR/R/molaR_bgplot.R |only molaR-6.0/molaR/DESCRIPTION | 12 molaR-6.0/molaR/MD5 | 61 molaR-6.0/molaR/NAMESPACE | 2 molaR-6.0/molaR/R/ARC3d.R | 310 ++ molaR-6.0/molaR/R/Check2D.R | 218 + molaR-6.0/molaR/R/DNE3d.R | 490 ++-- molaR-6.0/molaR/R/DNE3dDiscard.R | 328 +- molaR-6.0/molaR/R/Face_Normals.R | 2 molaR-6.0/molaR/R/OPC3d.R | 644 +++-- molaR-6.0/molaR/R/RFI3d.R | 462 ++-- molaR-6.0/molaR/R/Slope3d.R | 375 ++- molaR-6.0/molaR/R/clipDisplay.R | 20 molaR-6.0/molaR/R/meshClip.R | 330 +- molaR-6.0/molaR/R/plyPlaneCut.R | 428 +-- molaR-6.0/molaR/R/zzz.R |only molaR-6.0/molaR/build/vignette.rds |binary molaR-6.0/molaR/inst/doc/molaR_vignette.R | 125 - molaR-6.0/molaR/inst/doc/molaR_vignette.Rmd | 45 molaR-6.0/molaR/inst/doc/molaR_vignette.html | 3067 +++++++++------------------ molaR-6.0/molaR/man/ARC3d.Rd | 86 molaR-6.0/molaR/man/Check2D.Rd | 84 molaR-6.0/molaR/man/DNE3d.Rd | 110 molaR-6.0/molaR/man/DNE3dDiscard.Rd | 104 molaR-6.0/molaR/man/OPC3d.Rd | 131 - molaR-6.0/molaR/man/RFI3d.Rd | 113 molaR-6.0/molaR/man/Slope3d.Rd | 91 molaR-6.0/molaR/man/meshClip.Rd |only molaR-6.0/molaR/man/plyPlaneCut.Rd | 151 - molaR-6.0/molaR/vignettes/molaR_vignette.Rmd | 45 36 files changed, 3914 insertions(+), 3920 deletions(-)
Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between prome versions 2.0.1.9 dated 2025-10-08 and 3.0.1.5 dated 2025-11-08
prome-2.0.1.9/prome/R/blindinglogit.R |only prome-2.0.1.9/prome/man/lslogit.Rd |only prome-3.0.1.5/prome/DESCRIPTION | 10 +++++----- prome-3.0.1.5/prome/MD5 | 20 +++++++++++++++----- prome-3.0.1.5/prome/NAMESPACE | 11 +++++++---- prome-3.0.1.5/prome/R/blindingCPE.R |only prome-3.0.1.5/prome/R/blindingTEST.R |only prome-3.0.1.5/prome/R/zzz.R |only prome-3.0.1.5/prome/data/bd010.rda |only prome-3.0.1.5/prome/data/bd011.rda |only prome-3.0.1.5/prome/data/bd012.rda |only prome-3.0.1.5/prome/data/datalist | 3 +++ prome-3.0.1.5/prome/inst/extdata |only prome-3.0.1.5/prome/man/blindingcpe.Rd |only prome-3.0.1.5/prome/man/blindingdata.Rd |only prome-3.0.1.5/prome/man/blindingtest.Rd |only 16 files changed, 30 insertions(+), 14 deletions(-)
Title: Run Any CLI Tool on a 'Conda' Environment
Description: Simplifies the execution of command line interface (CLI)
tools within isolated and reproducible environments. It enables users
to effortlessly manage 'Conda' environments, execute command line
tools, handle dependencies, and ensure reproducibility in their data
analysis workflows.
Author: Lucio Queiroz [aut, cre, cph] ,
Claudio Zanettini [aut, ctb]
Maintainer: Lucio Queiroz <luciorqueiroz@gmail.com>
Diff between condathis versions 0.1.2 dated 2025-06-02 and 0.1.3 dated 2025-11-08
DESCRIPTION | 19 - MD5 | 117 +++---- NAMESPACE | 1 NEWS.md | 70 +++- R/check_micromamba_version.R | 5 R/clean_cache.R | 42 +- R/create_base_env.R | 2 R/create_env.R | 93 +++-- R/define_platform.R | 16 R/env_exists.R | 2 R/format_channels_args.R | 1 R/get_best_micromamba_path.R | 22 + R/get_env_dir.R | 2 R/get_install_dir.R | 8 R/get_sys_arch.R | 2 R/install_micromamba.R | 64 ++- R/install_packages.R | 53 ++- R/list_envs.R | 4 R/list_packages.R | 41 +- R/micromamba_bin_path.R | 8 R/native_cmd.R | 49 +- R/packages_search_native.R | 25 - R/parse_output.R | 63 +++ R/parse_quiet_flag.R | 2 R/parse_strategy_verbose.R | 103 ++++-- R/remove_env.R | 33 + R/rethrow_error_run.R | 14 R/run.R | 146 +++++--- R/run_bin.R | 46 +- R/run_internal_native.R | 44 +- R/symlink_micromamba_bin.R | 8 README.md | 284 +++++------------ build |only inst/doc |only man/clean_cache.Rd |only man/condathis-package.Rd | 1 man/create_env.Rd | 26 + man/env_exists.Rd | 22 + man/get_install_dir.Rd | 8 man/install_micromamba.Rd | 8 man/install_packages.Rd | 24 + man/list_packages.Rd | 33 + man/parse_output.Rd | 25 + man/remove_env.Rd | 27 + man/run.Rd | 84 +++-- man/run_bin.Rd | 54 ++- tests/testthat.R | 2 tests/testthat/test-clean_cache.R |only tests/testthat/test-create_base_env.R | 6 tests/testthat/test-create_env.R | 76 ++-- tests/testthat/test-create_nested_env.R | 10 tests/testthat/test-format_channels_args.R | 5 tests/testthat/test-get_env_dir.R | 2 tests/testthat/test-get_sys_arch.R | 9 tests/testthat/test-is_micromamba_available_for_arch.R | 15 tests/testthat/test-parse_output.R |only tests/testthat/test-parse_strategy_verbose.R | 141 +++++++- tests/testthat/test-rethrow_error.R | 26 + tests/testthat/test-run_bin.R | 20 - tests/testthat/test-run_output_file.R | 26 - tests/testthat/test-run_verbose_levels.R |only vignettes |only 62 files changed, 1338 insertions(+), 701 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.57.4 dated 2025-07-22 and 1.58.7 dated 2025-11-08
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++--------- NEWS.md | 4 ++ build/vignette.rds |binary inst/README-known_issues.md | 2 + inst/doc/additional_examples.html | 4 +- inst/doc/getting_started.html | 4 +- inst/htmlwidgets/canvasXpress.yaml | 2 - inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 8 ++--- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 ++-- inst/ui-examples/cX-function.R.gz |binary tests/testthat/test-other-decorations.R | 7 ++++ tests/testthat/test-other-piping.R | 1 tests/testthat/test-ui-heatmap.R | 8 +++++ 14 files changed, 48 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-18 4.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-19 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-22 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-01 0.2.1
2022-02-03 0.2
2021-09-12 0.1.1
2021-09-09 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-18 0.1.4
2020-12-03 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-12 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-16 2.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-09 1.0.3
2022-01-10 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-08 1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-13 1.3.0
2020-06-09 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-04 2.0.3
2025-03-25 2.0.2
2025-02-13 2.0.1
2024-07-07 2.0.0
2024-05-30 1.0.9
2024-05-16 1.0.8
2024-05-10 1.0.7
2024-04-29 1.0.6
2024-04-21 1.0.5
2024-04-20 1.0.4
2024-04-13 1.0.3
2024-04-10 1.0.2
2024-04-05 1.0.1
2024-04-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-03 0.6.1
2022-07-18 0.6.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-28 1.5.0
2016-08-27 1.0.0
2016-04-26 0.0.3
2016-03-29 0.0.2
2016-03-03 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-14 0.1.3
2023-06-19 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-17 2.3.0
2016-01-21 2.2.1
2015-02-19 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-12 0.1.6
2023-04-25 0.1.5
2022-10-26 0.1.4
2020-08-25 0.1.3
2020-05-26 0.1.2
2020-04-08 0.1.1
2020-03-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-19 0.3.0
2022-03-25 0.2.0
2021-05-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-16 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-11 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-04 1.1.1
2022-02-10 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-18 0.0.25
2024-07-17 0.0.22
2022-08-12 0.0.18
2022-07-11 0.0.17
2022-07-08 0.0.16
2022-03-02 0.0.15
2022-01-05 0.0.14
2021-11-19 0.0.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-05 1.1.0
2023-01-11 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-01 1.2.2
2020-02-25 1.2.1
2019-10-03 1.2.0
2018-07-24 1.1.2
2018-06-23 1.1.1
2017-11-20 1.1.0
2017-11-03 1.0.0
2017-11-03 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-17 0.1.1
2022-06-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-02 0.5.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-10-02 0.4.0
2017-03-28 0.3.3
2017-03-07 0.3.0
2016-07-12 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-25 1.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-18 1.3.4
2021-08-13 1.3.2
2021-07-15 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-19 0.5.0
2021-11-17 0.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-01 1.0.4
2019-01-24 1.0.3
2017-03-27 1.0.2
2015-08-19 1.0.1
2015-07-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-16 0.2.5
2022-10-21 0.2.4
2022-06-27 0.2.2
2022-06-09 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-11 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-20 2.0.0
2023-02-09 1.0.2
2022-10-20 1.0.1
2022-09-22 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-30 1.0.1
2024-06-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-25 0.3.0
2018-07-05 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-13 1.3
2014-08-09 1.2
2014-05-05 1.1
2014-03-29 1.0