Title: Genetic Tools for Colony Management
Description: Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical
Approach for Designing Breeding Groups to Maximize Genetic Diversity in a
Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatto')".
It provides a 'Shiny' application with an exposed API.
The application supports five groups of functions:
(1) Quality control of studbooks contained in text files or 'Excel'
workbooks and of pedigrees within 'LabKey' Electronic Health Records
(EHR);
(2) Creation of pedigrees from a list of animals using the 'LabKey' EHR
integration;
(3) Creation and display of an age by sex pyramid plot of the living
animals within the designated pedigree;
(4) Generation of genetic value analysis reports; and
(5) Creation of potential breeding groups with and without proscribed sex
ratios and defined maximum kinships.
Author: Michael Raboin [aut],
Terry Therneau [aut],
Amanda Vinson [aut, dtc],
R. Mark Sharp [aut, cre, cph, dtc] ,
Matthew Schultz [aut] ,
Southwest National Primate Research Center NIH grant P51 RR13986 [fnd],
Oregon National Primate Research Center grant P [...truncated...]
Maintainer: R. Mark Sharp <rmsharp@me.com>
Diff between nprcgenekeepr versions 1.0.7 dated 2025-04-24 and 1.0.8 dated 2025-07-25
DESCRIPTION | 16 + MD5 | 111 ++++++------- NEWS.md | 55 +++--- R/convertDate.R | 2 R/convertFromCenter.R | 2 R/fillGroupMembersWithSexRatio.R | 2 R/getLkDirectAncestors.R | 4 R/getLkDirectRelatives.R | 8 R/getLogo.R | 4 R/getMinParentAge.R | 3 R/getParamDef.R | 3 R/getPotentialSires.R | 8 R/getProbandPedigree.R | 2 R/getProductionStatus.R | 2 R/getPyramidAgeDist.R | 2 R/getSimSires.R | 8 R/getSiteInfo.R | 4 R/getTokenList.R | 2 R/groupAddAssign.R | 11 - R/hasGenotype.R | 4 R/headerDisplayNames.R | 2 R/initializeHaremGroups.R | 16 - R/insertSeparators.R | 25 +- R/makeSimPed.R | 4 R/obfuscateDate.R | 8 R/removePotentialSires.R | 4 README.md | 12 - build/vignette.rds |binary inst/application/server.r | 2 inst/application/uitpBreedingGroupFormation.R | 4 inst/application/uitpGeneticValueAnalysis.R | 3 inst/application/uitpGvAndBgDesc.R | 3 inst/application/uitpInput.R | 2 inst/application/uitpPedigreeBrowser.R | 5 inst/application/uitpSummaryStatistics.R | 6 inst/doc/a2interactive.Rmd | 4 inst/doc/a2interactive.html | 26 +-- inst/doc/a3manual.R | 2 inst/doc/a3manual.html | 2 inst/doc/simulatedKValues.Rmd | 8 inst/doc/simulatedKValues.html | 8 inst/extdata/create_nprcgenekeepr_hexbadge.R | 3 inst/extdata/software_design_doc.qmd |only man/getPotentialSires.Rd | 14 - man/getProbandPedigree.Rd | 2 man/groupAddAssign.Rd | 16 - man/obfuscateDate.Rd | 10 - man/removePotentialSires.Rd | 2 tests/testthat/test_addBackSecondParents.R | 1 tests/testthat/test_addErrTxt.R | 1 tests/testthat/test_get_elapsed_time_str.R | 31 +++ tests/testthat/test_groupAddAssign.R | 16 - tests/testthat/test_makeGroupMembers.R | 6 tests/testthat/test_obfuscateDate.R | 10 - vignettes/a2interactive.Rmd | 4 vignettes/manual_components/_running_shiny_application.Rmd | 2 vignettes/simulatedKValues.Rmd | 8 57 files changed, 286 insertions(+), 239 deletions(-)
Title: Raven Hydrological Modelling Framework R Support and Analysis
Description: Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files.
The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>.
The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.
Author: Robert Chlumsky [cre, aut] ,
James Craig [ctb, aut] ,
Leland Scantlebury [ctb, aut],
Simon Lin [ctb, aut],
Sarah Grass [ctb, aut],
Genevieve Brown [ctb, aut],
Rezgar Arabzadeh [ctb, aut]
Maintainer: Robert Chlumsky <rchlumsk@uwaterloo.ca>
Diff between RavenR versions 2.2.2 dated 2024-05-06 and 2.2.3 dated 2025-07-25
RavenR-2.2.2/RavenR/R/rvn_forcing_data.R |only RavenR-2.2.2/RavenR/data/rvn_forcing_data.RData |only RavenR-2.2.2/RavenR/man/rvn_forcing_data.Rd |only RavenR-2.2.3/RavenR/DESCRIPTION | 13 RavenR-2.2.3/RavenR/MD5 | 56 RavenR-2.2.3/RavenR/NAMESPACE | 2 RavenR-2.2.3/RavenR/R/rvn_apply_wyearly.R | 3 RavenR-2.2.3/RavenR/R/rvn_forcings_plot.R | 18 RavenR-2.2.3/RavenR/R/rvn_met_recordplot.R | 28 RavenR-2.2.3/RavenR/R/rvn_rvi_process_diagrammer.R | 2 RavenR-2.2.3/RavenR/R/rvn_rvt_tidyhydat.R | 11 RavenR-2.2.3/RavenR/R/rvn_rvt_write.R | 3 RavenR-2.2.3/RavenR/R/rvn_utilities.R | 30 RavenR-2.2.3/RavenR/R/rvn_write_Raven_table.R | 4 RavenR-2.2.3/RavenR/R/rvn_wyear_indices.R | 7 RavenR-2.2.3/RavenR/inst/doc/Introduction_to_RavenR.R | 8 RavenR-2.2.3/RavenR/inst/doc/Introduction_to_RavenR.Rmd | 10 RavenR-2.2.3/RavenR/inst/doc/Introduction_to_RavenR.html | 49 RavenR-2.2.3/RavenR/inst/extdata/RavenParameters.dat | 3 RavenR-2.2.3/RavenR/inst/extdata/run1_ForcingFunctions.csv | 1464 ++++++------- RavenR-2.2.3/RavenR/man/cmax.Rd | 4 RavenR-2.2.3/RavenR/man/ggplotColours.Rd |only RavenR-2.2.3/RavenR/man/rvn_apply_wyearly.Rd | 3 RavenR-2.2.3/RavenR/man/rvn_forcings_plot.Rd | 4 RavenR-2.2.3/RavenR/man/rvn_num_days_month.Rd | 5 RavenR-2.2.3/RavenR/man/rvn_rvi_process_diagrammer.Rd | 2 RavenR-2.2.3/RavenR/man/rvn_rvt_tidyhydat.Rd | 8 RavenR-2.2.3/RavenR/man/rvn_write_Raven_table.Rd | 4 RavenR-2.2.3/RavenR/man/rvn_wyear_indices.Rd | 7 RavenR-2.2.3/RavenR/tests/testthat/test_time.series.R | 8 RavenR-2.2.3/RavenR/vignettes/Introduction_to_RavenR.Rmd | 10 31 files changed, 905 insertions(+), 861 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing sparse priors to
promote exact sparsity leads to efficient Bayesian shrinkage estimation, variable
selection and statistical inference. In this package, we have implemented robust
Bayesian variable selection with spike-and-slab priors under high-dimensional
linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models with spike-and-slab priors include
robust Bayesian group LASSO and robust binary Bayesian LASSO (Fan and Wu (2025)
<doi:10.1002/sta4.70078>). The Markov Chain Monte Carlo (MCMC) algorithms
of the proposed and alternative models are implemented in C++.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.1.3 dated 2025-05-15 and 1.1.4 dated 2025-07-25
DESCRIPTION | 15 - MD5 | 82 +++--- NAMESPACE | 24 +- NEWS.md | 98 ++++---- R/NonRobust.R | 150 ++++++------ R/NonRobust_vc.R | 150 ++++++------ R/Robust_vc.R | 164 ++++++------- R/coverage_lin.R | 22 - R/coverage_vc.R | 88 +++---- R/data.R | 148 ++++++------ R/estimation_lin.R | 24 +- R/estimation_vc.R | 126 +++++----- R/nonrobust_bin.R | 76 +++--- R/nonrobust_g.R | 80 +++--- R/nonrobust_lin.R | 76 +++--- R/pqrBayes-package.R | 3 R/pqrBayes.R | 3 R/pqrBayes_bin.R | 66 ++--- R/pqrBayes_g.R | 38 +-- R/pqrBayes_lin.R | 64 ++--- R/pqrBayes_vc.R | 38 +-- R/predict_bin.R | 106 ++++---- R/predict_lin.R | 114 ++++----- R/predict_vc.R | 148 ++++++------ R/print.pqrBayes.R | 106 ++++---- R/robust_bin.R | 86 +++---- R/robust_g.R | 94 +++---- R/robust_lin.R | 86 +++---- R/select.pqrBayes.R | 178 +++++++------- R/select_lin.R | 78 +++--- R/select_vc.R | 88 +++---- README.md | 516 +++++++++++++++++++++---------------------- man/coverage.Rd | 74 +++--- man/data.Rd | 154 ++++++------ man/estimation.pqrBayes.Rd | 80 +++--- man/pqrBayes-package.Rd | 125 +++++----- man/pqrBayes.Rd | 407 +++++++++++++++++---------------- man/predict_pqrBayes.Rd | 100 ++++---- man/print.pqrBayes.Rd | 48 ++-- man/print.pqrBayes.pred.Rd | 48 ++-- man/print.pqrBayes.select.Rd | 48 ++-- man/select.pqrBayes.Rd | 156 ++++++------- 42 files changed, 2196 insertions(+), 2179 deletions(-)
Title: Survival Analysis for Weighted Composite Endpoints
Description: Analyze given data frame with multiple endpoints and return Kaplan-Meier survival probabilities together with the specified confidence interval. See Nabipoor M, Westerhout CM, Rathwell S, and Bakal JA (2023) <doi:10.1186/s12874-023-01857-0>.
Author: Majid Nabipoor [aut] ,
Cynthia Westerhout [aut] ,
Jeffrey Bakal [aut] ,
Sarah Rathwell [cre]
Maintainer: Sarah Rathwell <srathwel@ualberta.ca>
Diff between wcep versions 1.0.2 dated 2023-12-19 and 1.0.3 dated 2025-07-25
DESCRIPTION | 19 ++++++++++--------- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/wcep.R | 2 +- README.md | 2 ++ build/partial.rdb |binary man/wcep-package.Rd | 3 +-- man/wcep.Rd | 2 +- 8 files changed, 28 insertions(+), 20 deletions(-)
Title: Bayesian Estimation of Naloxone Kit Number Under-Reporting
Description: Bayesian model and associated tools for generating estimates of
total naloxone kit numbers distributed and used from naloxone kit orders
data. Provides functions for generating simulated data of naloxone kit use
and functions for generating samples from the posterior.
Author: Mike Irvine [aut, cre, cph] ,
Samantha Bardwell [ctb],
Andrew Johnson [ctb]
Maintainer: Mike Irvine <mike.irvine@bccdc.ca>
Diff between bennu versions 0.3.0 dated 2023-09-13 and 0.3.1 dated 2025-07-25
bennu-0.3.0/bennu/src/Makevars |only bennu-0.3.1/bennu/DESCRIPTION | 22 bennu-0.3.1/bennu/MD5 | 67 - bennu-0.3.1/bennu/NEWS.md | 15 bennu-0.3.1/bennu/R/aaa.R |only bennu-0.3.1/bennu/R/bennu-package.R | 3 bennu-0.3.1/bennu/R/data.R |only bennu-0.3.1/bennu/R/est_naloxone.R | 82 + bennu-0.3.1/bennu/R/generate_model_data.R | 2 bennu-0.3.1/bennu/R/utils-plot.R | 110 + bennu-0.3.1/bennu/R/utils-table.R | 102 + bennu-0.3.1/bennu/README.md | 17 bennu-0.3.1/bennu/build/vignette.rds |binary bennu-0.3.1/bennu/configure | 1 bennu-0.3.1/bennu/configure.win | 1 bennu-0.3.1/bennu/data |only bennu-0.3.1/bennu/inst/doc/Introduction.R | 97 + bennu-0.3.1/bennu/inst/doc/Introduction.Rmd | 125 +- bennu-0.3.1/bennu/inst/doc/Introduction.html | 479 ++++--- bennu-0.3.1/bennu/inst/doc/simulation_validation_experiments.R |only bennu-0.3.1/bennu/inst/doc/simulation_validation_experiments.Rmd |only bennu-0.3.1/bennu/inst/doc/simulation_validation_experiments.html |only bennu-0.3.1/bennu/inst/stan/distribution_covariate_model.stan | 25 bennu-0.3.1/bennu/man/bennu-package.Rd | 18 bennu-0.3.1/bennu/man/est_naloxone.Rd | 27 bennu-0.3.1/bennu/man/est_naloxone_vec.Rd | 18 bennu-0.3.1/bennu/man/experimental_validation_data.Rd |only bennu-0.3.1/bennu/man/figures/README-example-1.png |binary bennu-0.3.1/bennu/man/generate_model_data.Rd | 2 bennu-0.3.1/bennu/man/kit_summary_table.Rd | 13 bennu-0.3.1/bennu/man/missing_data_validation.Rd |only bennu-0.3.1/bennu/man/plot_kit_use.Rd | 12 bennu-0.3.1/bennu/src/stanExports_distribution_covariate_model.h | 605 +++++----- bennu-0.3.1/bennu/tests/testthat/setup.R | 5 bennu-0.3.1/bennu/tests/testthat/test-est_naloxone.R | 64 + bennu-0.3.1/bennu/tests/testthat/test-kit_summary_table.R | 5 bennu-0.3.1/bennu/tests/testthat/test-plot_kit_use.R | 26 bennu-0.3.1/bennu/vignettes/Introduction.Rmd | 125 +- bennu-0.3.1/bennu/vignettes/simulation_validation_experiments.Rmd |only 39 files changed, 1384 insertions(+), 684 deletions(-)
Title: Stepwise Clustered Ensemble
Description: Implementation of Stepwise Clustered Ensemble (SCE) and Stepwise Cluster Analysis (SCA) for multivariate data analysis. The package provides comprehensive tools for feature selection, model training, prediction, and evaluation in hydrological and environmental modeling applications. Key functionalities include recursive feature elimination (RFE), Wilks feature importance analysis, model validation through out-of-bag (OOB) validation, and ensemble prediction capabilities. The package supports both single and multivariate response variables, making it suitable for complex environmental modeling scenarios. For more details see Li et al. (2021) <doi:10.5194/hess-25-4947-2021>.
Author: Kailong Li [aut, cre]
Maintainer: Kailong Li <lkl98509509@gmail.com>
Diff between SCE versions 1.1.0 dated 2025-07-02 and 1.1.1 dated 2025-07-25
DESCRIPTION | 6 MD5 | 38 +-- NAMESPACE | 16 - NEWS.md | 10 R/Model_evaluation.R | 304 +++++++++++++------------- R/Model_simulation.R | 6 R/RFE_SCE.R | 76 ++---- R/SCA.R | 588 +++++++++++++++++++++++++-------------------------- R/SCE.R | 54 +--- R/Wilks_importance.R | 6 README.md | 10 man/Air_quality.Rd | 4 man/Plot_RFE.Rd |only man/RFE_SCE.Rd | 285 ++++-------------------- man/SCA.Rd |only man/SCE.Rd | 281 +++--------------------- man/Streamflow.Rd | 116 ++-------- man/evaluate.Rd | 130 +---------- man/importance.Rd | 91 ------- man/predict.Rd | 140 +----------- man/print.Rd | 44 +-- 21 files changed, 717 insertions(+), 1488 deletions(-)
Title: Landscape Visualizations in R and 'Unity'
Description: Functions for the retrieval, manipulation, and visualization
of 'geospatial' data, with an aim towards producing '3D' landscape
visualizations in the 'Unity' '3D' rendering engine. Functions are
also provided for retrieving elevation data and base map tiles from
the 'USGS' National Map <https://apps.nationalmap.gov/services/>.
Author: Michael Mahoney [aut, cre] ,
Mike Johnson [rev] for rOpenSci,
see <https://github.com/ropensci/software-review/issues/416>),
Sydney Foks [rev] for rOpenSci,
see <https://github.com/ropensci/software-review/issues/416>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between terrainr versions 0.7.5 dated 2023-10-04 and 0.7.6 dated 2025-07-25
terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_USGSImageryOnly.R |only terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_USGSShadedReliefOnly.R |only terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_USGSTNMBlank.R |only terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_USGSTopo.R |only terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_ecosystems.R |only terrainr-0.7.5/terrainr/tests/testthat/test-2-get_tiles_govunits.R |only terrainr-0.7.6/terrainr/DESCRIPTION | 13 terrainr-0.7.6/terrainr/MD5 | 44 - terrainr-0.7.6/terrainr/NEWS.md | 4 terrainr-0.7.6/terrainr/R/geom_spatial_rgb.R | 353 +++++----- terrainr-0.7.6/terrainr/R/get_tiles.R | 220 +++--- terrainr-0.7.6/terrainr/R/hit_api.R | 125 ++- terrainr-0.7.6/terrainr/README.md | 6 terrainr-0.7.6/terrainr/build/vignette.rds |binary terrainr-0.7.6/terrainr/inst/doc/overview.R | 164 ++-- terrainr-0.7.6/terrainr/inst/doc/overview.html | 22 terrainr-0.7.6/terrainr/inst/doc/unity_instructions.R | 44 - terrainr-0.7.6/terrainr/inst/doc/unity_instructions.html | 4 terrainr-0.7.6/terrainr/man/geom_spatial_rgb.Rd | 84 +- terrainr-0.7.6/terrainr/man/get_tiles.Rd | 1 terrainr-0.7.6/terrainr/man/hit_national_map_api.Rd | 4 terrainr-0.7.6/terrainr/tests/testthat/_snaps/add_bbox_buffer.md | 10 terrainr-0.7.6/terrainr/tests/testthat/test-add_bbox_buffer.R | 52 - terrainr-0.7.6/terrainr/tests/testthat/test-combine_overlays.R | 13 terrainr-0.7.6/terrainr/tests/testthat/test-georeference_overlay.R | 2 terrainr-0.7.6/terrainr/tests/testthat/test-get_tiles.R | 63 - 26 files changed, 686 insertions(+), 542 deletions(-)
Title: Fast Principal Component Analysis for Outlier Detection
Description: Methods to detect genetic markers involved in biological
adaptation. 'pcadapt' provides statistical tools for outlier detection based on
Principal Component Analysis. Implements the method described in (Luu, 2016)
<DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020)
<DOI:10.1093/molbev/msaa053>.
Author: Keurcien Luu [aut],
Michael Blum [aut],
Florian Prive [aut, cre],
Eric Bazin [ctb],
Nicolas Duforet-Frebourg [ctb]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between pcadapt versions 4.4.0 dated 2024-09-24 and 4.4.1 dated 2025-07-25
DESCRIPTION | 14 +- MD5 | 10 - NAMESPACE | 2 R/iram.R | 1 R/plotUtils.R | 275 +++++++++++++++++++++++++--------------------------- man/plot.pcadapt.Rd | 2 6 files changed, 152 insertions(+), 152 deletions(-)
Title: Pacote Para Analise Multivariada
Description: Package with multivariate analysis methodologies for experiment evaluation.
The package estimates dissimilarity measures, builds dendrograms, obtains MANOVA,
principal components, canonical variables, etc. (Pacote com metodologias de analise
multivariada para avaliação de experimentos. O pacote estima medidas de dissimilaridade,
construi de dendogramas, obtem a MANOVA, componentes principais, variaveis canonicas, etc.)
Author: Alcinei Mistico Azevedo [aut, cre]
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>
Diff between MultivariateAnalysis versions 0.5.0 dated 2024-04-08 and 0.5.1 dated 2025-07-25
DESCRIPTION | 12 MD5 | 56 +- NEWS.md | 4 R/ComponentesPrincipais.Misto.R | 2 R/CorrelacaoMantel.R | 2 R/Dendrograma.R | 2 R/Distancia.R | 2 R/MANOVA.R | 1 R/MultivariateAnalysis-package.R | 2 R/SummaryDistancia.R | 2 R/Tocher.R | 2 R/VariaveisCanonicas.R | 1 build/vignette.rds |binary inst/doc/Exemplo_dados_DBC_Misto.html | 312 ++++++++-------- inst/doc/Exemplo_dados_Qualitativos_FMI.html | 416 +++++++++++----------- inst/doc/Exemplo_dados_binarios.html | 118 +++--- inst/doc/Exemplo_dados_misto.html | 240 ++++++------ inst/doc/Exemplo_dados_multicategoricos.html | 184 ++++----- inst/doc/Exemplo_dados_quantitativos_DBC.html | 348 +++++++++--------- inst/doc/Exemplo_dados_quantitativos_DIC.html | 302 +++++++-------- inst/doc/Exemplo_dados_quantitativos_FAT_DBC.html | 362 +++++++++---------- inst/doc/Exemplo_dados_quantitativos_Med.html | 218 +++++------ man/ComponentesPrincipais.Misto.Rd | 2 man/ContribuicaoRelativa.Rd | 4 man/Dendrograma.Rd | 2 man/Kmeans.Rd | 3 man/Kmeans_NumeroOtimo.Rd | 2 man/Kmeans_NumeroOtimo2.Rd | 2 man/MultivariateAnalysis-package.Rd | 1 29 files changed, 1308 insertions(+), 1296 deletions(-)
More information about MultivariateAnalysis at CRAN
Permanent link
Title: Plotting Multi-Dimensional Data - Using 'rgl'
Description: The 'rgl' implementation of plot3D functions.
Author: Karline Soetaert [aut, cre]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3Drgl versions 1.0.4 dated 2023-01-19 and 1.0.5 dated 2025-07-25
DESCRIPTION | 16 +++++++++++----- MD5 | 10 +++++----- man/cutrgl.Rd | 6 +++--- man/imagergl.Rd | 20 ++++++++++---------- man/persp3Drgl.Rd | 14 +++++++------- man/plotrgl.Rd | 14 +++++++------- 6 files changed, 43 insertions(+), 37 deletions(-)
Title: Polygons of Bivariate Density Distributions
Description: With bivariate data, it is possible to calculate
2-dimensional kernel density estimates that return polygons at given
levels of probability. 'densityarea' returns these polygons for
analysis, including for calculating their area.
Author: Josef Fruehwald [aut, cre, cph]
Maintainer: Josef Fruehwald <jofrhwld@gmail.com>
Diff between densityarea versions 0.1.0 dated 2023-10-02 and 0.1.1 dated 2025-07-25
DESCRIPTION | 6 +-- MD5 | 24 +++++++-------- NEWS.md | 7 +++- R/density_area.R | 2 - README.md | 4 ++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/densityarea.R | 2 - inst/doc/densityarea.html | 12 +++---- inst/doc/sf-operations.R | 48 +++++++++++++++---------------- inst/doc/sf-operations.html | 24 +++++++-------- man/density_polygons.Rd | 2 - man/figures/README-unnamed-chunk-2-1.png |binary 13 files changed, 70 insertions(+), 61 deletions(-)
Title: Access to Canadian Election Study Data
Description: Provides tools to easily access and analyze Canadian Election Study data.
The package simplifies the process of downloading, cleaning, and using 'CES' datasets
for political science research and analysis. The Canadian Election Study ('CES')
has been conducted during federal elections since 1965, surveying Canadians
on their political preferences, engagement, and demographics. Data is accessed
from multiple sources including the 'Borealis' Data repository
<https://borealisdata.ca/> and the official 'Canadian Election Study' website
<https://ces-eec.arts.ubc.ca/>. This package is not officially affiliated
with the Canadian Election Study, 'Borealis' Data, or the University of British
Columbia, and users should cite the original data sources in their work.
Author: Laurence-Olivier M. Foisy [aut, cre]
Maintainer: Laurence-Olivier M. Foisy <mail@mfoisy.com>
Diff between ces versions 1.0.0 dated 2025-07-23 and 1.0.1 dated 2025-07-25
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 16 ++++++++++++++++ R/download_all_ces_datasets.R | 7 ++++--- R/download_ces_dataset.R | 6 +++--- R/download_pdf_codebook.R | 6 +++--- R/get_ces.R | 2 +- R/sysdata.rda |binary man/download_all_ces_datasets.Rd | 7 ++++--- man/download_ces_dataset.Rd | 6 +++--- man/download_pdf_codebook.Rd | 6 +++--- man/get_ces.Rd | 2 +- 12 files changed, 52 insertions(+), 34 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-25 1.0.2
More information about StablePopulation at CRAN
Permanent link
Title: Latent Hidden Markov Models for Response Process Data
Description: Provides functions for simulating from and fitting the latent hidden
Markov models for response process data (Tang, 2024) <doi:10.1007/s11336-023-09938-1>.
It also includes functions for simulating from and fitting ordinary hidden Markov models.
Author: Xueying Tang [aut, cre, cph]
Maintainer: Xueying Tang <xueyingtang1989@gmail.com>
Diff between proclhmm versions 1.0.0 dated 2024-06-05 and 1.0.1 dated 2025-07-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/lhmm_mmle.R | 2 +- build/partial.rdb |binary man/lhmm.Rd | 2 +- 6 files changed, 14 insertions(+), 10 deletions(-)
Title: Plotting Multi-Dimensional Data
Description: Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.
Author: Karline Soetaert [aut, cre]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3D versions 1.4.1 dated 2024-02-06 and 1.4.2 dated 2025-07-25
DESCRIPTION | 16 +++++++++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/plot3D.pdf |binary inst/doc/volcano.pdf |binary man/slice3D.Rd | 2 +- 6 files changed, 17 insertions(+), 11 deletions(-)
Title: Visualisation of Oceanographic Data and Model Output
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Author: Karline Soetaert [aut, cre]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between OceanView versions 1.0.7 dated 2024-02-06 and 1.0.8 dated 2025-07-25
DESCRIPTION | 16 - MD5 | 28 +- build/vignette.rds |binary inst/doc/Northsea.pdf |binary inst/doc/OceanView.pdf |binary man/Chesapeake.Rd | 384 +++++++++++++++--------------- man/Sylt.Rd | 624 ++++++++++++++++++++++++------------------------- man/TempTraject.Rd | 270 ++++++++++----------- man/WSnioz.Rd | 8 man/moviepersp.Rd | 6 man/movieslice.Rd | 8 man/quiver.Rd | 14 - man/tracers2D.Rd | 8 man/tracers3D.Rd | 6 man/vectorplot.Rd | 6 15 files changed, 692 insertions(+), 686 deletions(-)
More information about TreeOrderTests at CRAN
Permanent link
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.7 dated 2025-05-11 and 1.6.9 dated 2025-07-25
rstpm2-1.6.7/rstpm2/inst/Rcpp-tests.R |only rstpm2-1.6.7/rstpm2/inst/Thumbs.db |only rstpm2-1.6.7/rstpm2/inst/aft.aux |only rstpm2-1.6.7/rstpm2/inst/aft.pdf |only rstpm2-1.6.7/rstpm2/inst/doc/equations.html |only rstpm2-1.6.7/rstpm2/inst/doc/equations.org |only rstpm2-1.6.7/rstpm2/inst/doc/equations.pdf |only rstpm2-1.6.7/rstpm2/inst/integrateRcpp.cpp |only rstpm2-1.6.7/rstpm2/inst/integration.cpp |only rstpm2-1.6.7/rstpm2/inst/math.aux |only rstpm2-1.6.7/rstpm2/inst/math.fdb_latexmk |only rstpm2-1.6.7/rstpm2/inst/math.fls |only rstpm2-1.6.7/rstpm2/inst/math.html |only rstpm2-1.6.7/rstpm2/inst/math.out |only rstpm2-1.6.7/rstpm2/inst/math.toc |only rstpm2-1.6.7/rstpm2/inst/model.bug |only rstpm2-1.6.7/rstpm2/inst/pstpm2.out |only rstpm2-1.6.7/rstpm2/inst/tmp.cpp |only rstpm2-1.6.7/rstpm2/inst/tutorial/haz_1.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/hazz_1.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/histo_1.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/histo_2.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/surv_1.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/surv_1_age.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/surv_5_age.png |only rstpm2-1.6.7/rstpm2/inst/tutorial/timevar.html |only rstpm2-1.6.7/rstpm2/inst/tutorial/timevar.pdf |only rstpm2-1.6.7/rstpm2/inst/tutorial/timevar2.html |only rstpm2-1.6.7/rstpm2/inst/vintegrateRcpp.cpp |only rstpm2-1.6.7/rstpm2/inst/vintegrateRcpp2.cpp |only rstpm2-1.6.7/rstpm2/inst/vintegration.cpp |only rstpm2-1.6.7/rstpm2/inst/vintegrationRcpp.cpp |only rstpm2-1.6.7/rstpm2/man/update-methods.Rd |only rstpm2-1.6.7/rstpm2/vignettes/SimpleGuide-004.jpg |only rstpm2-1.6.7/rstpm2/vignettes/SimpleGuide-005.jpg |only rstpm2-1.6.7/rstpm2/vignettes/SimpleGuide-006.jpg |only rstpm2-1.6.7/rstpm2/vignettes/SimpleGuide-007.jpg |only rstpm2-1.6.7/rstpm2/vignettes/competing.R |only rstpm2-1.6.7/rstpm2/vignettes/jsslogo.jpg |only rstpm2-1.6.7/rstpm2/vignettes/multistate-fig-1.pdf |only rstpm2-1.6.7/rstpm2/vignettes/multistate-fig-2.pdf |only rstpm2-1.6.7/rstpm2/vignettes/test.org |only rstpm2-1.6.9/rstpm2/DESCRIPTION | 7 rstpm2-1.6.9/rstpm2/MD5 | 79 - rstpm2-1.6.9/rstpm2/NAMESPACE | 9 rstpm2-1.6.9/rstpm2/R/multistate.R | 7 rstpm2-1.6.9/rstpm2/R/pm2-3.R | 72 + rstpm2-1.6.9/rstpm2/R/zzz.R | 4 rstpm2-1.6.9/rstpm2/inst/doc/Introduction.pdf |binary rstpm2-1.6.9/rstpm2/inst/doc/SimpleGuide.pdf |binary rstpm2-1.6.9/rstpm2/inst/doc/multistate.Rnw | 4 rstpm2-1.6.9/rstpm2/inst/doc/multistate.pdf |binary rstpm2-1.6.9/rstpm2/inst/doc/predictnl.pdf |binary rstpm2-1.6.9/rstpm2/inst/equations.org |only rstpm2-1.6.9/rstpm2/inst/working_code.R | 20 rstpm2-1.6.9/rstpm2/man/aft-class.Rd | 4 rstpm2-1.6.9/rstpm2/man/predictnl-methods.Rd | 69 + rstpm2-1.6.9/rstpm2/man/pstpm2-class.Rd | 6 rstpm2-1.6.9/rstpm2/man/stpm2-class.Rd | 26 rstpm2-1.6.9/rstpm2/src/aft.cpp | 1004 +++++++++++++-------- rstpm2-1.6.9/rstpm2/vignettes/multistate.Rnw | 4 rstpm2-1.6.9/rstpm2/vignettes/multistate_fig-1.pdf |only rstpm2-1.6.9/rstpm2/vignettes/multistate_fig-2.pdf |only 63 files changed, 868 insertions(+), 447 deletions(-)
Title: The MBESS R Package
Description: Implements methods that are useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but MBESS became
more general and now contains methods applicable and used in a wide variety of fields and [...truncated...]
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.9.3 dated 2023-10-26 and 4.9.41 dated 2025-07-25
DESCRIPTION | 14 +- MD5 | 26 ++-- R/ci.c.R | 25 ++-- R/cor2cov.R | 26 ++-- R/ss.aipe.c.R | 16 +- R/ss.aipe.sc.R | 167 ++++++++++++++--------------- R/ss.aipe.sc.ancova.R | 7 - R/ss.aipe.sc.ancova.sensitivity.R | 7 - R/ss.aipe.sc.sensitivity.R | 207 ++++++++++++++++++------------------ man/MBESS-package.Rd | 8 - man/cor2cov.Rd | 69 +++++------- man/power.density.equivalence.md.Rd | 3 man/power.equivalence.md.Rd | 3 man/upsilon.Rd | 12 +- 14 files changed, 302 insertions(+), 288 deletions(-)
Title: A Flexible Modelling Environment for Inverse Modelling,
Sensitivity, Identifiability and Monte Carlo Analysis
Description: Provides functions to help in fitting models to data, to
perform Monte Carlo, sensitivity and identifiability analysis. It is
intended to work with models be written as a set of differential
equations that are solved either by an integration routine from
package 'deSolve', or a steady-state solver from package
'rootSolve'. However, the methods can also be used with other types of
functions.
Author: Karline Soetaert [aut, cre] ,
Thomas Petzoldt [aut]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between FME versions 1.3.6.3 dated 2023-07-05 and 1.3.6.4 dated 2025-07-25
FME-1.3.6.3/FME/inst/doc/examples |only FME-1.3.6.4/FME/DESCRIPTION | 11 - FME-1.3.6.4/FME/MD5 | 28 +--- FME-1.3.6.4/FME/build/partial.rdb |binary FME-1.3.6.4/FME/build/vignette.rds |binary FME-1.3.6.4/FME/inst/doc/FME.pdf |binary FME-1.3.6.4/FME/inst/doc/FMEdyna.pdf |binary FME-1.3.6.4/FME/inst/doc/FMEmcmc.pdf |binary FME-1.3.6.4/FME/inst/doc/FMEother.pdf |binary FME-1.3.6.4/FME/inst/doc/FMEsteady.pdf |binary FME-1.3.6.4/FME/man/obsplot.Rd | 210 ++++++++++++++++----------------- 11 files changed, 120 insertions(+), 129 deletions(-)
Title: Create Networks of Dendrochronological Series using Pairwise
Similarity
Description: Creating dendrochronological networks based on the similarity between tree-ring series or chronologies. The package includes various functions to compare tree-ring curves building upon the 'dplR' package. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance of wood as described in Visser (2021) <DOI:10.5334/jcaa.79> or wood-use within a structure/context/site as described in Visser and Vorst (2022) <DOI:10.1163/27723194-bja10014>.
Author: Ronald Visser [aut, cre] ,
Angelino Salentino [ctb] ,
Andy Bunn [ctb] ,
Kaija Gahm [rev] ,
Zachary Gajewski [rev]
Maintainer: Ronald Visser <r.m.visser@saxion.nl>
Diff between dendroNetwork versions 0.5.4 dated 2024-04-30 and 0.5.5 dated 2025-07-25
DESCRIPTION | 18 +++--- MD5 | 54 ++++++++++---------- NEWS.md | 10 +++ R/cor_mat_overlap.R | 2 R/cyto_clean_styles.R | 2 R/cyto_create_graph.R | 2 R/dendro_network.R | 25 +++++++-- R/find_all_cpm_com.R | 7 ++ R/globals.R | 2 R/gn_names.R | 6 +- R/wuchswerte.R | 6 +- README.md | 23 ++++++-- inst/doc/dendroNetwork.html | 8 +- man/cor_mat_overlap.Rd | 2 man/cyto_clean_styles.Rd | 4 - man/cyto_create_graph.Rd | 2 man/dendroNetwork-package.Rd | 2 man/dendro_network.Rd | 12 +++- man/figures/README-flowchart_workflow-1.png |binary man/figures/README-network_hollstein_1980-1.png |binary man/figures/README-network_hollstein_1980-2.png |binary man/find_all_cpm_com.Rd | 8 ++ man/gn_names.Rd | 9 ++- man/wuchswerte.Rd | 8 +- tests/testthat/_snaps/clique_community_names.md | 14 +++-- tests/testthat/_snaps/clique_community_names_par.md | 34 ++++++------ tests/testthat/_snaps/find_all_cpm_com.md | 14 +++-- tests/testthat/_snaps/gn_names.md | 32 +++++++---- 28 files changed, 192 insertions(+), 114 deletions(-)
Title: Interface for 'Semestry TermTime' Services
Description: Provides an R interface for interacting with the 'Semestry TermTime' services.
It allows users to retrieve scheduling data from the API. see
<https://github.com/vusaverse/vvtermtime/blob/main/openapi_7.7.0.pdf> for details.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvtermtime versions 0.0.1 dated 2023-08-07 and 0.1.0 dated 2025-07-25
DESCRIPTION | 8 MD5 | 50 ++ NAMESPACE | 18 NEWS.md | 2 R/get_activities.R |only R/get_activity_groups.R |only R/get_activity_templates.R |only R/get_activity_types.R |only R/get_assessment_types.R |only R/get_booking_types.R |only R/get_capabilities.R |only R/get_contact_requirements.R |only R/get_floors.R |only R/get_ping.R |only R/get_room_relationships.R |only R/get_staff_groups.R |only R/get_student_groups.R |only R/get_supergroups.R |only R/get_timetable_module.R |only R/get_timetable_room.R |only R/get_timetable_staff.R |only R/get_timetable_student.R |only README.md | 6 build/vignette.rds |binary inst/doc/getting_started.R | 44 +- inst/doc/getting_started.html | 840 ++++++++++++++++++++-------------------- man/get_activities.Rd |only man/get_activity_groups.Rd |only man/get_activity_templates.Rd |only man/get_activity_types.Rd |only man/get_assessment_types.Rd |only man/get_booking_types.Rd |only man/get_capabilities.Rd |only man/get_contact_requirements.Rd |only man/get_floors.Rd |only man/get_ping.Rd |only man/get_room_relationships.Rd |only man/get_staff_groups.Rd |only man/get_student_groups.Rd |only man/get_supergroups.Rd |only man/get_timetable_module.Rd |only man/get_timetable_room.Rd |only man/get_timetable_staff.Rd |only man/get_timetable_student.Rd |only 44 files changed, 514 insertions(+), 454 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.8.4 dated 2025-05-27 and 0.8.5 dated 2025-07-25
DESCRIPTION | 11 +++-- MD5 | 49 ++++++++++++------------ NAMESPACE | 3 - NEWS.md | 5 ++ R/RcppExports.R | 18 +++------ R/client.R | 67 +++++++++++++++++++++++----------- R/config.R | 28 ++++++++++---- R/convert.R | 4 +- R/credential_providers.R | 20 +++++++--- R/custom_rds.R | 8 +++- R/custom_s3.R | 25 +++++++++--- R/handlers_restjson.R | 12 ++++-- R/jsonutil.R | 8 +++- R/populateutil.R | 20 +++++++--- R/queryutil.R | 8 +++- R/request.R | 16 ++++++-- R/service.R | 4 +- R/service_parameter_helper.R | 5 +- R/signer_v1.R | 4 +- R/signer_v4.R | 4 +- R/xmlutil.R | 16 ++++++-- man/set_service_parameter.Rd | 3 + src/RcppExports.cpp | 40 ++++++-------------- src/fstring.cpp |only src/resolve_endpoint.cpp | 47 ----------------------- tests/testthat/test_endpoint_vendor.R | 32 ++++++++++++++++ 26 files changed, 272 insertions(+), 185 deletions(-)
Title: Item Maker
Description: This is an Automatic Item Generator for Psychological Assessment. Items created with the 'IMak' package should not be used in applied settings as part of the working protocol without ensuring first that the items meet the required psychometric quality standards (see Blum & Holling, 2018) <DOI:10.3389/fpsyg.2018.01286>.
Author: Diego Blum [aut, cre]
Maintainer: Diego Blum <blumworx@gmail.com>
Diff between IMak versions 2.1.0 dated 2022-05-02 and 2.1.1 dated 2025-07-25
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- NEWS.md |only R/plotfa.R | 12 ++++++------ 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Graphical Markov Models with Mixed Graphs
Description: Provides functions for defining
mixed graphs containing three types of edges, directed,
undirected and bi-directed, with possibly multiple edges.
These graphs are useful because they capture fundamental
independence structures in multivariate distributions
and in the induced distributions after marginalization
and conditioning.
The package is especially concerned with Gaussian graphical
models for
(i) ML estimation for directed acyclic graphs, undirected and
bi-directed graphs and ancestral graph models
(ii) testing several conditional independencies
(iii) checking global identification of DAG Gaussian models
with one latent variable
(iv) testing Markov equivalences and generating Markov
equivalent graphs of specific types.
Author: Giovanni M. Marchetti [aut, cre] ,
Mathias Drton [aut] ,
Kayvan Sadeghi [aut]
Maintainer: Giovanni M. Marchetti <giovanni.marchetti@unifi.it>
Diff between ggm versions 2.5.1 dated 2024-01-25 and 2.5.2 dated 2025-07-25
DESCRIPTION | 16 +++--- MD5 | 40 ++++++++-------- NEWS | 2 R/all_functions.R | 4 + man/AG.Rd | 2 man/MAG.Rd | 2 man/MRG.Rd | 2 man/MSG.Rd | 2 man/MarkEqMag.Rd | 118 ++++++++++++++++++++++++------------------------- man/MarkEqRcg.Rd | 2 man/Max.Rd | 2 man/RG.Rd | 2 man/RepMarBG.Rd | 128 +++++++++++++++++++++++++++--------------------------- man/RepMarDAG.Rd | 126 ++++++++++++++++++++++++++--------------------------- man/RepMarUG.Rd | 126 ++++++++++++++++++++++++++--------------------------- man/SG.Rd | 2 man/ggm.Rd | 2 man/grMAT.Rd | 2 man/msep.Rd | 2 man/null.Rd | 2 man/plotGraph.Rd | 10 ++-- 21 files changed, 299 insertions(+), 295 deletions(-)
Title: Tool-Kit for Dynamic Materials Model and Thermal Processing Maps
Description: Provides a simple approach for constructing dynamic materials
modeling suggested by Prasad and Gegel (1984) <doi:10.1007/BF02664902>. It
can easily generate various processing-maps based on this model as well. The
calculation result in this package contains full materials constants, information
about power dissipation efficiency factor, and rheological properties, can
be exported completely also, through which further analysis and customized
plots will be applicable as well.
Author: Chen Zhang [aut, cre, cph] ,
Huakang Bian [ctb],
Kenta Yamanaka [ths] ,
Akihiko Chiba [ths]
Maintainer: Chen Zhang <chen.zhang_06sept@foxmail.com>
Diff between TPMplt versions 0.1.6 dated 2024-10-01 and 0.1.7 dated 2025-07-25
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 2 +- R/PLTblder.R | 2 +- inst/doc/TPMplt-vignette.html | 8 ++++---- 5 files changed, 17 insertions(+), 16 deletions(-)
Title: 'DataSHIELD' Implementation on Local Datasets
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This 'DataSHIELD Interface' implementation is for analyzing datasets living
in the current R session. The purpose of this is primarily for lightweight
'DataSHIELD' analysis package development.
Author: Yannick Marcon [aut, cre]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between DSLite versions 1.4.0 dated 2022-10-07 and 1.4.1 dated 2025-07-25
DESCRIPTION | 15 MD5 | 100 +++--- R/DSLiteConnection.R | 52 +-- R/DSLiteDriver.R | 2 R/DSLiteResult.R | 8 R/getDSLiteData.R | 6 R/setupCNSIMTest.R | 2 R/setupDASIMTest.R | 2 R/setupDATASETTest.R | 2 R/setupDISCORDANTTest.R | 2 R/setupDSLiteServer.R | 2 R/setupSURVIVALTest.R | 2 build/vignette.rds |binary inst/doc/developing-with-dslite.R | 68 ++-- inst/doc/developing-with-dslite.Rmd | 2 inst/doc/developing-with-dslite.html | 351 +++++++++++++--------- man/DSLiteConnection-class.Rd | 2 man/DSLiteDriver-class.Rd | 2 man/DSLiteResult-class.Rd | 2 man/dsAggregate-DSLiteConnection-method.Rd | 2 man/dsAssignExpr-DSLiteConnection-method.Rd | 4 man/dsAssignResource-DSLiteConnection-method.Rd | 4 man/dsAssignTable-DSLiteConnection-method.Rd | 4 man/dsConnect-DSLiteDriver-method.Rd | 4 man/dsDisconnect-DSLiteConnection-method.Rd | 2 man/dsFetch-DSLiteResult-method.Rd | 2 man/dsGetInfo-DSLiteResult-method.Rd | 2 man/dsHasResource-DSLiteConnection-method.Rd | 2 man/dsHasTable-DSLiteConnection-method.Rd | 2 man/dsIsAsync-DSLiteConnection-method.Rd | 2 man/dsIsCompleted-DSLiteResult-method.Rd | 2 man/dsKeepAlive-DSLiteConnection-method.Rd | 2 man/dsListMethods-DSLiteConnection-method.Rd | 2 man/dsListPackages-DSLiteConnection-method.Rd | 2 man/dsListProfiles-DSLiteConnection-method.Rd | 2 man/dsListResources-DSLiteConnection-method.Rd | 2 man/dsListSymbols-DSLiteConnection-method.Rd | 2 man/dsListTables-DSLiteConnection-method.Rd | 2 man/dsListWorkspaces-DSLiteConnection-method.Rd | 2 man/dsRestoreWorkspace-DSLiteConnection-method.Rd | 2 man/dsRmSymbol-DSLiteConnection-method.Rd | 2 man/dsRmWorkspace-DSLiteConnection-method.Rd | 2 man/dsSaveWorkspace-DSLiteConnection-method.Rd | 2 man/getDSLiteData.Rd | 6 man/setupCNSIMTest.Rd | 2 man/setupDASIMTest.Rd | 2 man/setupDATASETTest.Rd | 2 man/setupDISCORDANTTest.Rd | 2 man/setupDSLiteServer.Rd | 2 man/setupSURVIVALTest.Rd | 2 vignettes/developing-with-dslite.Rmd | 2 51 files changed, 396 insertions(+), 302 deletions(-)
Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, MDS maps and biplots obtained by PCA, PFA or WALS (weighted alternating least squares); See Graffelman & De Leeuw (2023) <doi: 10.1080/00031305.2023.2186952>.
Author: Jan Graffelman [aut, cre],
Jan De Leeuw [aut]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between Correlplot versions 1.1.0 dated 2024-01-23 and 1.1.2 dated 2025-07-25
DESCRIPTION | 10 +- MD5 | 26 +++---- R/FitRDeltaQSym.R | 152 +++++++++++++++++++++++++++++------------ R/ggtally.R | 22 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/CorrelplotManual.R | 5 - inst/doc/CorrelplotManual.Rmd | 5 - inst/doc/CorrelplotManual.html | 49 ++++++++----- man/FitRDeltaQSym.Rd | 27 ++++--- man/ggbplot.Rd | 2 man/pfa.Rd | 2 man/tally.Rd | 2 vignettes/CorrelplotManual.Rmd | 5 - 14 files changed, 199 insertions(+), 108 deletions(-)
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP (Lundberg and Lee,
2017, <doi:10.48550/arXiv.1705.07874>) permutation SHAP, and additive
SHAP for model interpretability. For Kernel SHAP and permutation
SHAP, if the number of features is too large for exact calculations,
the algorithms iterate until the SHAP values are sufficiently precise
in terms of their standard errors. The package integrates smoothly
with meta-learning packages such as 'tidymodels', 'caret' or 'mlr3'.
It supports multi-output models, case weights, and parallel
computations. Visualizations can be done using the R package
'shapviz'.
Author: Michael Mayer [aut, cre] ,
David Watson [aut] ,
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.8.0 dated 2025-07-08 and 0.9.0 dated 2025-07-25
DESCRIPTION | 10 - MD5 | 30 ++--- NAMESPACE | 2 NEWS.md | 50 ++++++++ R/kernelshap.R | 82 ++++++-------- R/permshap.R | 51 ++++---- R/utils.R | 51 ++++---- R/utils_kernelshap.R | 130 +++++++++++----------- R/utils_permshap.R | 105 ++++++++---------- README.md | 34 ++--- man/kernelshap.Rd | 67 +++++------ man/permshap.Rd | 49 ++++---- tests/testthat/test-basic.R | 190 ++++++++++++++++++++++++++++----- tests/testthat/test-kernelshap-utils.R | 34 +++++ tests/testthat/test-permshap-utils.R | 5 tests/testthat/test-utils.R | 21 ++- 16 files changed, 566 insertions(+), 345 deletions(-)
Title: 'DataSHIELD' Implementation for 'Opal'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation for 'Opal', which is
the data integration application for biobanks by 'OBiBa'. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is the reference implementation of the 'DataSHIELD' infrastructure.
Author: Yannick Marcon [aut, cre] ,
Becca Wilson [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between DSOpal versions 1.4.0 dated 2022-10-06 and 1.4.1 dated 2025-07-25
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- R/OpalConnection.R | 2 +- R/OpalDriver.R | 2 +- R/OpalResult.R | 2 +- man/DSOpal-package.Rd | 2 +- man/OpalConnection-class.Rd | 2 +- man/OpalDriver-class.Rd | 2 +- man/OpalResult-class.Rd | 2 +- 9 files changed, 23 insertions(+), 22 deletions(-)
Title: Quantile-Based Estimator
Description: Quantile-based estimators (Q-estimators) can be used to fit any parametric distribution, using its quantile function. Q-estimators are usually more robust than standard maximum likelihood estimators. The method is described in: Sottile G. and Frumento P. (2022). Robust estimation and regression with parametric quantile functions. <doi:10.1016/j.csda.2022.107471>.
Author: Gianluca Sottile [aut, cre],
Paolo Frumento [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between Qest versions 1.0.1 dated 2024-01-23 and 1.0.2 dated 2025-07-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- build/partial.rdb |binary man/Qcoxph.Rd | 6 +++--- man/Qest-package.Rd | 4 ++-- man/Qest.control.Rd | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Develop Clinical Prediction Models Using the Common Data Model
Description: A user friendly way to create patient level prediction models using
the Observational Medical Outcomes Partnership Common Data Model. Given a cohort
of interest and an outcome of interest, the package can use data in the Common
Data Model to build a large set of features. These features can then be used to
fit a predictive model with a number of machine learning algorithms. This is
further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Author: Egill Fridgeirsson [aut, cre],
Jenna Reps [aut],
Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Peter Rijnbeek [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Egill Fridgeirsson <e.fridgeirsson@erasmusmc.nl>
Diff between PatientLevelPrediction versions 6.4.1 dated 2025-04-20 and 6.5.0 dated 2025-07-25
DESCRIPTION | 8 MD5 | 232 ++++++++++++------------- NEWS.md | 10 + R/CalibrationSummary.R | 2 R/CovariateSummary.R | 2 R/CyclopsModels.R | 4 R/DataSplitting.R | 2 R/DemographicSummary.R | 2 R/EvaluatePlp.R | 2 R/ExistingSklearn.R | 8 R/ExternalValidatePlp.R | 4 R/ExtractData.R | 6 R/FeatureEngineering.R | 13 + R/FeatureImportance.R | 2 R/Fit.R | 2 R/Formatting.R | 2 R/Glm.R | 12 - R/ImportFromCsv.R | 2 R/LearningCurve.R | 4 R/Plotting.R | 28 +-- R/PopulationSettings.R | 2 R/Predict.R | 2 R/PreprocessingData.R | 2 R/RClassifier.R | 4 R/Recalibration.R | 4 R/RunMultiplePlp.R | 7 R/RunPlp.R | 2 R/Sampling.R | 7 R/SaveLoadPlp.R | 20 +- R/Simulation.R | 21 ++ R/SklearnClassifier.R | 4 R/ViewShinyPlp.R | 2 R/uploadToDatabase.R | 23 +- R/uploadToDatabaseModelDesign.R | 2 demo/EnsembleModelDemo.R | 3 demo/SingleModelDemo.R | 2 inst/doc/AddingCustomFeatureEngineering.html | 6 inst/doc/AddingCustomModels.html | 6 inst/doc/AddingCustomSamples.html | 6 inst/doc/AddingCustomSplitting.html | 6 inst/doc/BenchmarkTasks.html | 4 inst/doc/BestPractices.html | 4 inst/doc/BuildingMultiplePredictiveModels.html | 6 inst/doc/BuildingPredictiveModels.Rmd | 2 inst/doc/BuildingPredictiveModels.html | 27 +- inst/doc/ClinicalModels.html | 4 inst/doc/ConstrainedPredictors.html | 6 inst/doc/CreatingLearningCurves.R | 3 inst/doc/CreatingLearningCurves.Rmd | 3 inst/doc/CreatingLearningCurves.html | 11 - inst/doc/CreatingNetworkStudies.Rmd | 54 ++++- inst/doc/CreatingNetworkStudies.html | 195 ++++++++++++++++++--- inst/doc/GISExample.html | 6 inst/doc/InstallationGuide.html | 6 man/covariateSummary.Rd | 2 man/createGlmModel.Rd | 2 man/createLearningCurve.Rd | 2 man/createStudyPopulation.Rd | 2 man/evaluatePlp.Rd | 2 man/externalValidateDbPlp.Rd | 2 man/extractDatabaseToCsv.Rd | 2 man/fitPlp.Rd | 2 man/getCalibrationSummary.Rd | 2 man/getDemographicSummary.Rd | 2 man/insertCsvToDatabase.Rd | 2 man/insertResultsToSqlite.Rd | 5 man/loadPlpData.Rd | 2 man/loadPlpModel.Rd | 2 man/loadPlpResult.Rd | 2 man/loadPlpShareable.Rd | 2 man/loadPrediction.Rd | 2 man/outcomeSurvivalPlot.Rd | 2 man/pfi.Rd | 2 man/plotDemographicSummary.Rd | 2 man/plotF1Measure.Rd | 2 man/plotGeneralizability.Rd | 2 man/plotLearningCurve.Rd | 2 man/plotNetBenefit.Rd | 2 man/plotPlp.Rd | 2 man/plotPrecisionRecall.Rd | 2 man/plotPredictedPDF.Rd | 2 man/plotPredictionDistribution.Rd | 2 man/plotPreferencePDF.Rd | 2 man/plotSparseCalibration.Rd | 2 man/plotSparseCalibration2.Rd | 2 man/plotSparseRoc.Rd | 2 man/plotVariableScatterplot.Rd | 2 man/predictCyclops.Rd | 4 man/predictGlm.Rd | 2 man/predictPlp.Rd | 2 man/preprocessData.Rd | 2 man/print.plpData.Rd | 2 man/print.summary.plpData.Rd | 2 man/recalibratePlpRefit.Rd | 4 man/runMultiplePlp.Rd | 3 man/runPlp.Rd | 2 man/savePlpData.Rd | 2 man/savePlpModel.Rd | 2 man/savePlpResult.Rd | 2 man/savePlpShareable.Rd | 2 man/simulatePlpData.Rd | 6 man/splitData.Rd | 2 man/summary.plpData.Rd | 2 man/toSparseM.Rd | 2 man/validateExternal.Rd | 2 man/viewPlp.Rd | 2 tests/testthat/helper-expectations.R | 6 tests/testthat/setup.R | 3 tests/testthat/test-featureEngineering.R | 2 tests/testthat/test-normalizers.R | 67 +++++++ tests/testthat/test-rclassifier.R | 13 + tests/testthat/test-sampling.R | 10 + tests/testthat/test-simulation.R | 2 tests/testthat/test-sklearnClassifier.R | 66 +++++++ vignettes/BuildingPredictiveModels.Rmd | 2 vignettes/CreatingLearningCurves.Rmd | 3 vignettes/CreatingNetworkStudies.Rmd | 54 ++++- 117 files changed, 802 insertions(+), 351 deletions(-)
More information about PatientLevelPrediction at CRAN
Permanent link
Title: Designs for Computer Experimentations
Description: In computer experiments space-filling designs are having great impact. Most popularly used space-filling designs are Uniform designs (UDs), Latin hypercube designs (LHDs) etc. For further references one can see Mckay (1979) <DOI:10.1080/00401706.1979.10489755> and Fang (1980) <https://cir.nii.ac.jp/crid/1570291225616774784>. In this package, we have provided algorithms for generate efficient LHDs and UDs. Here, generated LHDs are efficient as they possess lower value of Maxpro measure, Phi_p value and Maximum Absolute Correlation (MAC) value based on the weightage given to each criterion. On the other hand, the produced UDs are having good space-filling property as they always attain the lower bound of Discrete Discrepancy measure. Further, some useful functions added in this package for adding more value to this package.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between CompExpDes versions 1.0.7 dated 2025-03-28 and 1.0.8 dated 2025-07-25
CompExpDes-1.0.7/CompExpDes/R/Meeting_Number.R |only CompExpDes-1.0.8/CompExpDes/DESCRIPTION | 8 CompExpDes-1.0.8/CompExpDes/MD5 | 16 CompExpDes-1.0.8/CompExpDes/NAMESPACE | 3 CompExpDes-1.0.8/CompExpDes/R/max_coincidence_number.R |only CompExpDes-1.0.8/CompExpDes/R/wtLHDs.R | 345 ++++++++++------- CompExpDes-1.0.8/CompExpDes/R/wtLHDs_prime.R | 263 +++++++----- CompExpDes-1.0.8/CompExpDes/man/Meeting_Number.Rd | 8 CompExpDes-1.0.8/CompExpDes/man/wtLHDs.Rd | 59 +- CompExpDes-1.0.8/CompExpDes/man/wtLHDs_prime.Rd | 58 +- 10 files changed, 463 insertions(+), 297 deletions(-)
Title: 'VigiBase' Pharmacovigilance Database Toolbox
Description: Perform the analysis of the World Health Organization
(WHO) Pharmacovigilance database 'VigiBase' (Extract Case Level version),
<https://who-umc.org/>
e.g., load data, perform data management,
disproportionality analysis, and descriptive statistics. Intended for
pharmacovigilance routine use or studies.
This package is NOT supported nor reflect the opinion of the WHO, or the
Uppsala Monitoring Centre.
Disproportionality methods are described by Norén et
al (2013) <doi:10.1177/0962280211403604>.
Author: Charles Dolladille [aut, cre] ,
Basile Chretien [aut] ,
Universite de Caen Normandie [cph] ,
Unite de pharmaco-epidemiologie [cph]
Maintainer: Charles Dolladille <cdolladille@hotmail.com>
Diff between vigicaen versions 0.15.6 dated 2025-03-13 and 0.16.1 dated 2025-07-25
vigicaen-0.15.6/vigicaen/tests/testthat/_snaps/vigi_routine/case-tto-below-median.svg |only vigicaen-0.16.1/vigicaen/DESCRIPTION | 11 vigicaen-0.16.1/vigicaen/MD5 | 117 vigicaen-0.16.1/vigicaen/NAMESPACE | 1 vigicaen-0.16.1/vigicaen/NEWS.md | 687 ++-- vigicaen-0.16.1/vigicaen/R/add_adr.R | 2 vigicaen-0.16.1/vigicaen/R/add_drug.R | 2 vigicaen-0.16.1/vigicaen/R/create_example_tables.R | 98 vigicaen-0.16.1/vigicaen/R/desc_tto.R | 216 - vigicaen-0.16.1/vigicaen/R/dt_fst.R | 86 vigicaen-0.16.1/vigicaen/R/get_atc_code.R | 276 - vigicaen-0.16.1/vigicaen/R/get_drecno.R | 1340 ++++---- vigicaen-0.16.1/vigicaen/R/get_llt_smq.R | 866 ++--- vigicaen-0.16.1/vigicaen/R/tb_vigibase.R | 1161 +++--- vigicaen-0.16.1/vigicaen/R/vigi_routine.R | 224 - vigicaen-0.16.1/vigicaen/build/partial.rdb |binary vigicaen-0.16.1/vigicaen/build/vignette.rds |binary vigicaen-0.16.1/vigicaen/inst/doc/basic_workflow.html | 2 vigicaen-0.16.1/vigicaen/inst/doc/descriptive.html | 2 vigicaen-0.16.1/vigicaen/inst/doc/getting_started.R | 9 vigicaen-0.16.1/vigicaen/inst/doc/getting_started.Rmd | 28 vigicaen-0.16.1/vigicaen/inst/doc/getting_started.html | 41 vigicaen-0.16.1/vigicaen/inst/doc/interactions.html | 2 vigicaen-0.16.1/vigicaen/inst/doc/routine_pharmacovigilance.R | 27 vigicaen-0.16.1/vigicaen/inst/doc/routine_pharmacovigilance.Rmd | 584 +-- vigicaen-0.16.1/vigicaen/inst/doc/routine_pharmacovigilance.html | 52 vigicaen-0.16.1/vigicaen/inst/doc/template_dictionary.html | 2 vigicaen-0.16.1/vigicaen/inst/doc/template_main.html | 2 vigicaen-0.16.1/vigicaen/inst/doc/template_routine.html | 2 vigicaen-0.16.1/vigicaen/man/create_example_tables.Rd | 13 vigicaen-0.16.1/vigicaen/man/desc_tto.Rd | 2 vigicaen-0.16.1/vigicaen/man/dt_fst.Rd | 18 vigicaen-0.16.1/vigicaen/man/figures/README-render_graph-1.png |binary vigicaen-0.16.1/vigicaen/man/figures/vg.png |binary vigicaen-0.16.1/vigicaen/man/get_atc_code.Rd | 4 vigicaen-0.16.1/vigicaen/man/get_llt_smq.Rd | 4 vigicaen-0.16.1/vigicaen/man/tb_vigibase.Rd | 17 vigicaen-0.16.1/vigicaen/man/vigi_routine.Rd | 10 vigicaen-0.16.1/vigicaen/tests/testthat/Rplots.pdf |binary vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/dt_fst.md |only vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/tb_vigibase.md | 569 ++- vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine.md | 46 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/arrow-table.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/base-graphic.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/case-time-to-onset.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/case-tto-above-90-days.svg |only vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/case-tto-below-90-days.svg |only vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/custom-drug-and-adr-labels.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/dual-drug-analysis.svg |only vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/exporting.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/ic025-below-0.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/no-cases.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/no-rechallenge.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/no-time-to-onset-export.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/no-time-to-onset-with-2-drugs.svg |only vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/no-time-to-onset.svg | 102 vigicaen-0.16.1/vigicaen/tests/testthat/_snaps/vigi_routine/suspect-only-true.svg |only vigicaen-0.16.1/vigicaen/tests/testthat/test-create_example_tables.R | 24 vigicaen-0.16.1/vigicaen/tests/testthat/test-dt_fst.R | 67 vigicaen-0.16.1/vigicaen/tests/testthat/test-tb_vigibase.R | 413 ++ vigicaen-0.16.1/vigicaen/tests/testthat/test-vigi_routine.R | 1667 +++++----- vigicaen-0.16.1/vigicaen/vignettes/getting_started.Rmd | 28 vigicaen-0.16.1/vigicaen/vignettes/routine_pharmacovigilance.Rmd | 584 +-- 63 files changed, 5828 insertions(+), 4498 deletions(-)
Title: Unify Dimensionality Reduction Results
Description: Dimensionality reduction (DR) is widely used in many domain for analyzing and visualizing high-dimensional data. 'tidydr' provides uniform output and is compatible with multiple methods, including 'prcomp', 'mds', 'Rtsne'. etc.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut] ,
Erqiang Hu [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidydr versions 0.0.5 dated 2023-03-08 and 0.0.6 dated 2025-07-25
DESCRIPTION | 16 - MD5 | 52 ++--- NAMESPACE | 101 +++++---- NEWS.md | 100 +++++---- R/available_methods.R | 98 ++++----- R/dr.R | 118 +++++------ R/element_line2.R | 110 +++++----- R/method-autoplot.R | 173 +++++++++------- R/method-dr-extract.R | 238 ++++++++++++---------- R/method-drawDetails.R | 30 +- R/method-fortify.R | 58 ++--- R/silinfo.R |only R/theme.R | 84 ++++---- R/tidydr-package.R |only R/utilities.R | 25 +- build/vignette.rds |binary inst/doc/tidydr.R | 52 ++--- inst/doc/tidydr.Rmd | 144 ++++++------- inst/doc/tidydr.html | 488 +++++++++++++++++++++++------------------------ man/available_methods.Rd | 46 ++-- man/dr-extract.Rd | 40 +-- man/dr.Rd | 64 +++--- man/element_line2.Rd | 104 +++++----- man/nk.Rd |only man/reexports.Rd | 34 +-- man/theme_dr.Rd | 56 ++--- man/theme_noaxis.Rd | 40 +-- man/tidydr-package.Rd |only vignettes/tidydr.Rmd | 144 ++++++------- 29 files changed, 1253 insertions(+), 1162 deletions(-)
Title: Nonlinear and Penalized Quantile Regression Coefficients
Modeling
Description: Nonlinear and Penalized parametric modeling of quantile regression coefficient functions. Sottile G, Frumento P, Chiodi M and Bottai M (2020) <doi:10.1177/1471082X19825523>.
Author: Gianluca Sottile [aut, cre],
Paolo Frumento [aut, ctb]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between qrcmNP versions 0.2.1 dated 2024-01-23 and 0.2.2 dated 2025-07-25
DESCRIPTION | 11 +++++++---- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ man/piqr.Rd | 8 ++++---- man/predict.piqr.Rd | 4 ++-- man/qrcmNP-package.Rd | 4 ++-- man/summary.piqr.Rd | 2 +- 7 files changed, 29 insertions(+), 19 deletions(-)
Title: Retrieve and Analyze Clinical Trials Data from Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Protocols, statistical analysis plans, informed consent sheets and other
documents in registers associated with trials can also be downloaded.
Other functions implement trial concepts canonically across registers,
identify deduplicated records, easily find and extract variables
(fields) of interest even from complex nested data as used by the
re [...truncated...]
Author: Ralf Herold [aut, cre] ,
Marek Kubica [cph] ,
Ivan Bozhanov [cph]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.24.0 dated 2025-07-21 and 1.24.1 dated 2025-07-25
ctrdata-1.24.0/ctrdata/man/figures/README-ctrdata_json_mongodb.jpg |only ctrdata-1.24.0/ctrdata/man/figures/README-ctrdata_json_sqlite.jpg |only ctrdata-1.24.1/ctrdata/DESCRIPTION | 6 ctrdata-1.24.1/ctrdata/MD5 | 78 - ctrdata-1.24.1/ctrdata/NEWS.md | 6 ctrdata-1.24.1/ctrdata/R/ctrGenerateQueries.R | 65 - ctrdata-1.24.1/ctrdata/R/ctrGetQueryUrl.R | 8 ctrdata-1.24.1/ctrdata/R/ctrLoadQueryIntoDb.R | 34 ctrdata-1.24.1/ctrdata/R/ctrOpenSearchPagesInBrowser.R | 7 ctrdata-1.24.1/ctrdata/R/ctrShowOneTrial.R | 8 ctrdata-1.24.1/ctrdata/R/ctrdata-package.R | 2 ctrdata-1.24.1/ctrdata/R/ctrdata-registers.R | 18 ctrdata-1.24.1/ctrdata/R/ctrdata-trial-concepts.R | 21 ctrdata-1.24.1/ctrdata/R/dbFindFields.R | 11 ctrdata-1.24.1/ctrdata/R/dbFindIdsUniqueTrials.R | 4 ctrdata-1.24.1/ctrdata/R/dbQueryHistory.R | 2 ctrdata-1.24.1/ctrdata/R/dfMergeVariablesRelevel.R | 17 ctrdata-1.24.1/ctrdata/R/dfName2Value.R | 8 ctrdata-1.24.1/ctrdata/R/f_numSites.R | 2 ctrdata-1.24.1/ctrdata/R/f_primaryEndpointResults.R | 6 ctrdata-1.24.1/ctrdata/R/util_fields.R | 497 +++++----- ctrdata-1.24.1/ctrdata/R/util_functions.R | 6 ctrdata-1.24.1/ctrdata/README.md | 258 ++--- ctrdata-1.24.1/ctrdata/inst/WORDLIST | 4 ctrdata-1.24.1/ctrdata/inst/tinytest/test_ctrdata_function_ctrgeneratequeries.R | 211 ++-- ctrdata-1.24.1/ctrdata/man/ctrGenerateQueries.Rd | 9 ctrdata-1.24.1/ctrdata/man/ctrGetQueryUrl.Rd | 9 ctrdata-1.24.1/ctrdata/man/ctrLoadQueryIntoDb.Rd | 34 ctrdata-1.24.1/ctrdata/man/ctrOpenSearchPagesInBrowser.Rd | 7 ctrdata-1.24.1/ctrdata/man/ctrShowOneTrial.Rd | 6 ctrdata-1.24.1/ctrdata/man/ctrdata-registers.Rd | 18 ctrdata-1.24.1/ctrdata/man/ctrdata-trial-concepts.Rd | 21 ctrdata-1.24.1/ctrdata/man/ctrdata.Rd | 2 ctrdata-1.24.1/ctrdata/man/dbFindFields.Rd | 11 ctrdata-1.24.1/ctrdata/man/dbFindIdsUniqueTrials.Rd | 4 ctrdata-1.24.1/ctrdata/man/dbQueryHistory.Rd | 4 ctrdata-1.24.1/ctrdata/man/dfMergeVariablesRelevel.Rd | 17 ctrdata-1.24.1/ctrdata/man/dfName2Value.Rd | 6 ctrdata-1.24.1/ctrdata/man/figures/README-ctrdata_across_registers.png |binary ctrdata-1.24.1/ctrdata/man/figures/README-ctrdata_results_neuroblastoma.png |binary ctrdata-1.24.1/ctrdata/man/figures/ctrdata_ctrShowOneTrial.jpg |binary 41 files changed, 760 insertions(+), 667 deletions(-)
Title: Change-Points Detections for Changes in Variance
Description: Detection of change-points for variance of heteroscedastic Gaussian variables with piecewise constant variance function. Adelfio, G. (2012), Change-point detection for variance piecewise constant models, Communications in Statistics, Simulation and Computation, 41:4, 437-448, <doi:10.1080/03610918.2011.592248>.
Author: Gianluca Sottile [cre],
Giada Adelfio [aut]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>
Diff between changepointsVar versions 0.1.1 dated 2024-01-23 and 0.1.2 dated 2025-07-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/changepointsVar-internal.Rd | 1 - man/changepointsVar-package.Rd | 6 +++--- man/jumpointsVar.Rd | 2 +- 5 files changed, 11 insertions(+), 12 deletions(-)
More information about changepointsVar at CRAN
Permanent link
Title: Generalized and Classical Blockmodeling of Valued Networks
Description: This is primarily meant as an implementation of generalized blockmodeling for valued networks.
In addition, measures of similarity or dissimilarity based on structural equivalence and
regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted:
Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>,
Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>.
Author: Ales Ziberna [aut, cre],
Marjan Cugmas [ctb]
Maintainer: Ales Ziberna <ales.ziberna@gmail.com>
Diff between blockmodeling versions 1.1.7 dated 2025-07-24 and 1.1.8 dated 2025-07-25
CHANGES | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/blockmodeling-package.R | 3 +-- build/partial.rdb |binary src/init.c | 8 ++++---- 6 files changed, 19 insertions(+), 16 deletions(-)
More information about BoneDensityMapping at CRAN
Permanent link
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.6 dated 2025-07-22 and 0.2.7 dated 2025-07-25
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More information about autoslider.core at CRAN
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Title: Bootstrap Tests for Cointegration and Autocorrelation in VARs
Description: Implements wild bootstrap tests for autocorrelation in Vector
Autoregressive (VAR) models based on Ahlgren and Catani (2016)
<doi:10.1007/s00362-016-0744-0>, a combined Lagrange Multiplier (LM)
test for Autoregressive Conditional Heteroskedasticity (ARCH) in VAR
models from Catani and Ahlgren (2016) <doi:10.1016/j.ecosta.2016.10.006>,
and bootstrap-based methods for determining the cointegration rank from
Cavaliere, Rahbek, and Taylor (2012) <doi:10.3982/ECTA9099> and
Cavaliere, Rahbek, and Taylor (2014) <doi:10.1080/07474938.2013.825175>.
Author: Markus Belfrage [aut, cre],
Paul Catani [ctb],
Niklas Ahlgren [ctb]
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
This is a re-admission after prior archival of version 2.0.5 dated 2018-11-02
Diff between VARtests versions 2.0.5 dated 2018-11-02 and 2.0.7 dated 2025-07-25
DESCRIPTION | 56 ++++++++++++++++++++++++++++------------ MD5 | 33 ++++++++++++----------- R/ACtest.R | 3 -- R/VARfit.R | 4 -- R/archBootTest.R | 19 +++++++------ R/cointBootTest.R | 31 ++++++++++++++-------- R/wildBoot.R | 29 ++++++++++++--------- inst/WORDLIST |only man/ACtest.Rd | 69 +++++++++++++++++++++++--------------------------- man/VARfit-methods.Rd | 23 ++++++++++++---- man/VARfit.Rd | 7 +---- man/VARsim.Rd | 30 ++------------------- man/archBootTest.Rd | 47 +++++++++++++++------------------- man/cointBootTest.Rd | 43 ++++++++++++++----------------- man/wildBoot.Rd | 12 +++++--- src/Makevars | 2 - src/Makevars.win | 2 - src/RcppExports.cpp | 5 +++ 18 files changed, 216 insertions(+), 199 deletions(-)
Title: Dose Rate Modelling of Carbonate-Rich Samples
Description: Translation of the 'MATLAB' program 'Carb' (Nathan and Mauz 2008 <DOI:10.1016/j.radmeas.2007.12.012>; Mauz and Hoffmann 2014) for dose rate modelling for carbonate-rich samples in the context of trapped charged dating (e.g., luminescence dating) applications.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Roger P. Nathan [aut, cph],
Barbara Mauz [aut, cph]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@uni-heidelberg.de>
Diff between RCarb versions 0.1.6 dated 2022-08-08 and 0.1.7 dated 2025-07-25
DESCRIPTION | 25 ++-- MD5 | 36 +++--- NEWS.md | 5 R/RCarb-package.R | 44 ++++--- R/calc_DoseRate.R | 2 R/model_DoseRate.R | 2 README.md | 37 +++--- build/partial.rdb |binary build/vignette.rds |binary data/Reference_Data.rda |binary data/datalist | 2 inst/doc/GetStarted.html | 203 ++++++++++++++++++----------------- man/Example_Data.Rd | 6 - man/RCarb-package.Rd | 33 ++++- man/Reference_Data.Rd | 21 ++- man/model_DoseRate.Rd | 4 man/write_InputTemplate.Rd | 2 tests/testthat/test_model_DoseRate.R | 2 vignettes/GetStarted.Rmd | 3 19 files changed, 233 insertions(+), 194 deletions(-)
Title: The Moving Epidemic Method
Description: The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.18 dated 2023-06-20 and 2.19 dated 2025-07-25
DESCRIPTION | 10 - MD5 | 182 ++++++++++---------- NAMESPACE | 1 R/add.alpha.R | 3 R/calcular.indicadores.2.timings.R | 73 ++++---- R/calcular.indicadores.R | 105 +++++------ R/calcular.map.R | 2 R/calcular.optimo.R | 14 - R/calcular.optimo.criterio.R | 4 R/calcular.optimo.derivada.R | 5 R/calcular.optimo.original.R | 1 R/calcular.optimo.pendiente.R | 8 R/comparar.metodos.R | 10 - R/create.calendar.R | 4 R/extraer.datos.curva.map.R | 2 R/extraer.datos.optimo.map.R | 1 R/flucyl.R | 20 +- R/flucylraw.R | 2 R/full.series.graph.R | 43 ++-- R/iconfianza.R | 2 R/iconfianza.aritmetica.R | 9 - R/iconfianza.completo.R | 8 R/iconfianza.geometrica.R | 4 R/iconfianza.logx.R | 4 R/iconfianza.percentil.boot.R | 17 + R/iconfianza.percentil.eqnpar.R | 18 +- R/iconfianza.percentil.kc.R | 3 R/iconfianza.x.R | 9 - R/maxFixNA.R | 2 R/maxnvalores.R | 2 R/mem.R | 2 R/memevolution.R | 27 +-- R/memgoodness.R | 95 ++++++---- R/memmodel.R | 241 ++++++++++++-------------- R/memstability.R | 11 - R/memsurveillance.R | 85 ++++----- R/memsurveillance.animated.R | 28 +-- R/memtiming.R | 53 ++--- R/memtrend.R | 20 +- R/minFixNA.R | 2 R/minnvalores.R | 2 R/optimal.tickmarks.R | 2 R/optimum.by.inspection.R | 66 ++++--- R/output.ci.R | 24 ++ R/percentage.added.R | 8 R/processPlots.R | 53 ++--- R/roc.analysis.R | 119 ++++++++----- R/transformdata.R | 18 +- R/transformdata.back.R | 31 +-- R/transformseries.R | 34 +-- R/transformseries.loess.R | 10 - R/transformseries.moving.average.R | 10 - R/transformseries.multiple.R | 304 ++++++++++++++++++---------------- R/transformseries.odd.R | 7 R/transformseries.spline.R | 10 - R/transformseries.twowaves.R | 52 +++-- build/partial.rdb |binary man/calcular.indicadores.2.timings.Rd | 10 - man/calcular.indicadores.Rd | 12 + man/fill.missing.Rd | 2 man/flucyl.Rd | 20 +- man/flucylraw.Rd | 2 man/full.series.graph.Rd | 8 man/iconfianza.Rd | 4 man/iconfianza.aritmetica.Rd | 2 man/iconfianza.completo.Rd | 2 man/iconfianza.geometrica.Rd | 2 man/iconfianza.logx.Rd | 2 man/iconfianza.percentil.boot.Rd | 2 man/iconfianza.percentil.eqnpar.Rd | 2 man/iconfianza.percentil.kc.Rd | 4 man/iconfianza.x.Rd | 2 man/maxFixNA.Rd | 24 +- man/maxnvalores.Rd | 24 +- man/memevolution.Rd | 18 +- man/memgoodness.Rd | 52 +++-- man/memmodel.Rd | 55 +++--- man/memstability.Rd | 6 man/memsurveillance.Rd | 20 +- man/memsurveillance.animated.Rd | 4 man/memtiming.Rd | 42 ++-- man/memtrend.Rd | 17 + man/minFixNA.Rd | 24 +- man/minnvalores.Rd | 24 +- man/optimal.tickmarks.Rd | 4 man/optimum.by.inspection.Rd | 21 +- man/roc.analysis.Rd | 20 +- man/transformseries.Rd | 22 +- man/transformseries.loess.Rd | 2 man/transformseries.moving.average.Rd | 24 +- man/transformseries.multiple.Rd | 9 - man/transformseries.spline.Rd | 2 92 files changed, 1261 insertions(+), 1111 deletions(-)
Title: Tools for ABC Analyses
Description: Tools for approximate Bayesian computation including summary statistic selection and assessing coverage.
See Nunes and Prangle (2015) <doi:10.32614/RJ-2015-030> and Rodrigues, Prangle and Sisson (2018) <doi:10.1016/j.csda.2018.04.004>.
Author: Matt Nunes [aut, cre],
Dennis Prangle [aut],
Guilherme Rodrigues [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between abctools versions 1.1.7 dated 2023-09-18 and 1.1.8 dated 2025-07-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- data/coal.rda |binary data/coalobs.rda |binary man/abctools-package.Rd | 2 +- man/cov.pi.Rd | 12 ++++++------ 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure
to analyse temporal trend in the framework of the OSPAR convention.
The analysis process run through 4 successive steps : 1) manipulate your data, 2)
select the parameters you want to analyse, 3) build your regulated
time series, 4) perform diagnosis and analysis and 5) read the results.
Statistical analysis call other package function such as Kendall tests
or cusum() function.
Author: David DEVREKER [aut, cre],
Alain LEFEBVRE [aut]
Maintainer: David DEVREKER <David.Devreker@ifremer.fr>
Diff between TTAinterfaceTrendAnalysis versions 1.5.10 dated 2024-01-23 and 1.5.11 dated 2025-07-25
DESCRIPTION | 11 +- MD5 | 28 ++--- NAMESPACE | 3 NEWS | 2 R/FULLoption.r | 239 +++++++++++++++++++++++++------------------- R/TTAinterface.R | 44 +++++--- R/aide3.r | 2 R/fixdata.R | 35 +++--- R/selectdirectory.R | 37 +++--- build/vignette.rds |binary inst/doc/TTAVignette.pdf |binary man/FULLoption.Rd | 36 ++---- man/TTAinterface-package.Rd | 4 man/TTAinterface.Rd | 6 - man/fixdata.Rd | 5 15 files changed, 254 insertions(+), 198 deletions(-)
More information about TTAinterfaceTrendAnalysis at CRAN
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Title: Stochastic Blockmodeling of One-Mode and Linked Networks
Description: Stochastic blockmodeling of one-mode and linked networks as presented in Škulj and Žiberna (2022) <doi:10.1016/j.socnet.2022.02.001>. The optimization is done via CEM (Classification Expectation Maximization) algorithm that can be initialized by random partitions or the results of k-means algorithm. The development of this package is financially supported by the Slovenian Research Agency (<https://www.arrs.si/>) within the research programs P5-0168 and the research projects J7-8279 (Blockmodeling multilevel and temporal networks) and J5-2557 (Comparison and evaluation of different approaches to blockmodeling dynamic networks by simulations with application to Slovenian co-authorship networks).
Author: Ales Ziberna [aut, cre] ,
Fabio Ashtar Telarico [ctb]
Maintainer: Ales Ziberna <ales.ziberna@fdv.uni-lj.si>
Diff between StochBlock versions 0.1.2 dated 2023-01-24 and 0.1.5 dated 2025-07-25
CHANGES | 20 DESCRIPTION | 19 MD5 | 26 NAMESPACE | 3 R/StochBlock-package.R | 5 R/stochBlock.r | 1465 +++++++++++++++++++++++----------------------- R/upAndDownSearch.R |only inst/CITATION | 43 - man/StochBlock-package.Rd | 55 + man/llStochBlock.Rd | 6 man/stochBlock.Rd | 4 man/stochBlockORP.Rd | 13 man/upAndDownSearch.Rd |only src/Makevars | 2 src/Makevars.win | 2 15 files changed, 880 insertions(+), 783 deletions(-)
Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed
Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] ,
Ana W. Capuano [aut],
Emmanuelle Comets [ctb]
Maintainer: Maude Wagner <maude_wagner@rush.edu>
Diff between nlive versions 0.7.0 dated 2025-02-14 and 0.8.0 dated 2025-07-25
DESCRIPTION | 13 +++--- MD5 | 10 ++-- NAMESPACE | 2 R/globals.R | 5 -- R/nlive.splines.R | 108 ++++++++++++++++++++++++++------------------------- man/nlive.splines.Rd | 25 ++++++----- 6 files changed, 83 insertions(+), 80 deletions(-)
Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
Author: Thibaut Jombart [aut, cre],
Anne Cori [aut],
Zhian N. Kamvar [ctb],
Dirk Schumacher [ctb],
Flavio Finger [aut],
Charlie Whittaker [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between epitrix versions 0.4.0 dated 2023-01-13 and 0.4.1 dated 2025-07-25
DESCRIPTION | 8 MD5 | 32 NEWS.md | 205 ++-- R/fit_discrete.R | 267 ++--- R/gamma_tools.R | 260 ++--- build/vignette.rds |binary inst/doc/epitrix.R | 192 ++-- inst/doc/epitrix.html | 1177 +++++++++++++------------- inst/doc/estimate_incubation.R | 92 +- inst/doc/estimate_incubation.html | 999 +++++++++++----------- man/fit_disc_gamma.Rd | 5 man/gamma_tools.Rd | 11 vignettes/figs-overview/fit_i-1.png |binary vignettes/figs-overview/sample_R0-1.png |binary vignettes/figs-overview/si-1.png |binary vignettes/figs-overview/unnamed-chunk-4-1.png |binary vignettes/figs-overview/unnamed-chunk-5-1.png |binary 17 files changed, 1649 insertions(+), 1599 deletions(-)
Title: Jackknife(+) Predictive Intervals for Bayesian Models
Description: Provides functions to construct finite-sample calibrated predictive
intervals for Bayesian models, following the approach in Barber et al.
(2021) <doi:10.1214/20-AOS1965>. These intervals are calculated efficiently
using importance sampling for the leave-one-out residuals. By default,
the intervals will also reflect the relative uncertainty in the Bayesian
model, using the locally-weighted conformal methods of Lei et al. (2018)
<doi:10.1080/01621459.2017.1307116>.
Author: Cory McCartan [aut, cre]
Maintainer: Cory McCartan <mccartan@psu.edu>
This is a re-admission after prior archival of version 0.1.2 dated 2022-08-12
Diff between conformalbayes versions 0.1.2 dated 2022-08-12 and 0.1.4 dated 2025-07-25
DESCRIPTION | 15 +- MD5 | 24 +-- NEWS.md | 4 R/loo_conformal.R | 72 ++++++--- R/predictive_interval.R | 13 + README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/conformalbayes.R | 4 inst/doc/conformalbayes.html | 256 ++++++++++++++++++----------------- man/conformalbayes-package.Rd | 2 man/loo_conformal.Rd | 41 ++++- man/predictive_interval.conformal.Rd | 7 13 files changed, 257 insertions(+), 187 deletions(-)
More information about conformalbayes at CRAN
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Title: Fitting Point Process Models via the Palm Likelihood
Description: Functions to fit point process models using the Palm likelihood. First proposed by Tanaka, Ogata, and Stoyan (2008) <DOI:10.1002/bimj.200610339>, maximisation of the Palm likelihood can provide computationally efficient parameter estimation for point process models in situations where the full likelihood is intractable. This package is chiefly focused on Neyman-Scott point processes, but can also fit the void processes proposed by Jones-Todd et al. (2019) <DOI:10.1002/sim.8046>. The development of this package was motivated by the analysis of capture-recapture surveys on which individuals cannot be identified---the data from which can conceptually be seen as a clustered point process (Stevenson, Borchers, and Fewster, 2019 <DOI:10.1111/biom.12983>). As such, some of the functions in this package are specifically for the estimation of cetacean density from two-camera aerial surveys.
Author: Ben Stevenson [aut, cre]
Maintainer: Ben Stevenson <ben.stevenson@auckland.ac.nz>
Diff between palm versions 1.1.5 dated 2023-09-22 and 1.1.6 dated 2025-07-25
palm-1.1.5/palm/man/palm.Rd |only palm-1.1.6/palm/DESCRIPTION | 18 +++++++++++------- palm-1.1.6/palm/MD5 | 18 +++++++++--------- palm-1.1.6/palm/NEWS | 5 +++++ palm-1.1.6/palm/R/fit-ns.r | 10 +++++----- palm-1.1.6/palm/R/methods.r | 2 +- palm-1.1.6/palm/R/palm.r | 6 ++---- palm-1.1.6/palm/man/confint.palm.Rd | 2 +- palm-1.1.6/palm/man/fit.ns.Rd | 10 +++++----- palm-1.1.6/palm/man/fit.void.Rd | 10 +++++----- palm-1.1.6/palm/man/palm-package.Rd |only 11 files changed, 44 insertions(+), 37 deletions(-)
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Using tidy data principles can make many text mining tasks
easier, more effective, and consistent with tools already in wide use.
Much of the infrastructure needed for text mining with tidy data
frames already exists in packages like 'dplyr', 'broom', 'tidyr', and
'ggplot2'. In this package, we provide functions and supporting data
sets to allow conversion of text to and from tidy formats, and to
switch seamlessly between tidy tools and existing text mining
packages.
Author: Gabriela De Queiroz [ctb],
Colin Fay [ctb] ,
Emil Hvitfeldt [ctb],
Os Keyes [ctb] ,
Kanishka Misra [ctb],
Tim Mastny [ctb],
Jeff Erickson [ctb],
David Robinson [aut],
Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.4.2 dated 2024-04-10 and 0.4.3 dated 2025-07-25
DESCRIPTION | 14 +- MD5 | 80 ++++++------ NEWS.md | 4 R/bind_tf_idf.R | 11 + R/compat_lazyeval.R | 49 ++++--- R/corpus_tidiers.R | 16 +- R/dictionary_tidiers.R | 4 R/globals.R | 35 ++++- R/lda_tidiers.R | 8 - R/mallet_tidiers.R | 10 + R/reorder_within.R | 5 R/sentiments.R | 15 +- R/sparse_casters.R | 31 +++-- R/sparse_tidiers.R | 12 - R/stm_tidiers.R | 70 +++++++---- R/unnest_char.R | 50 ++++---- R/unnest_ngrams.R | 54 ++++---- R/unnest_ptb.R | 21 +-- R/unnest_regex.R | 23 +-- R/unnest_sentence.R | 68 +++++------ R/unnest_tokens.R | 107 +++++++++++------ R/unnest_tweets.R | 2 README.md | 27 ++-- build/vignette.rds |binary inst/doc/tf_idf.html | 9 - inst/doc/tidying_casting.html | 102 +++++++++------- inst/doc/tidytext.html | 26 +++- man/cast_sparse.Rd | 2 man/document_term_casters.Rd | 2 tests/testthat/helper-funs.R | 23 +-- tests/testthat/test-corpus-tidiers.R | 9 - tests/testthat/test-dictionary-tidiers.R | 1 tests/testthat/test-lda-tidiers.R | 1 tests/testthat/test-reorder-within.R | 21 +-- tests/testthat/test-sparse-casters.R | 2 tests/testthat/test-sparse-tidiers.R | 7 - tests/testthat/test-stm-tidiers.R | 71 ++++++++--- tests/testthat/test-tf-idf.R | 36 ++++- tests/testthat/test-unnest-char.R | 11 + tests/testthat/test-unnest-sentence.R | 45 ++++--- tests/testthat/test-unnest-tokens.R | 191 +++++++++++++++++-------------- 41 files changed, 754 insertions(+), 521 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.3-3 dated 2025-05-24 and 3.4-0 dated 2025-07-25
DESCRIPTION | 16 ++-- MD5 | 36 ++++----- NEWS | 11 +++ build/vignette.rds |binary demo/spatstat.R | 22 ++++-- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 3 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 17 ++-- inst/doc/updates.Rnw | 163 ++++++++++++++++++++++++++++++++++++++++++--- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 3 man/macros/defns.Rd | 25 ++++-- man/spatstat-package.Rd | 17 ++++ vignettes/updates.Rnw | 163 ++++++++++++++++++++++++++++++++++++++++++--- 19 files changed, 408 insertions(+), 68 deletions(-)
Title: Recursive Partitioning Based on Psychometric Models
Description: Recursive partitioning based on psychometric models,
employing the general MOB algorithm (from package partykit) to obtain
Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and
MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial
credit models.
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
David Dreifuss [aut],
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotree versions 0.16-1 dated 2024-04-11 and 0.16-2 dated 2025-07-25
DESCRIPTION | 18 ++++++++++-------- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 1 + inst/doc/raschtree.pdf |binary man/CEMSChoice.Rd | 6 +++--- man/EuropeanValuesStudy.Rd | 4 ++-- man/SPISA.Rd | 4 ++-- man/Topmodel2007.Rd | 4 ++-- man/bttree.Rd | 2 ++ man/gpcmtree.Rd | 2 ++ man/mpttree.Rd | 3 +++ man/npltree.Rd | 3 +++ man/pctree.Rd | 3 +++ man/raschtree.Rd | 3 +++ man/rstree.Rd | 3 +++ vignettes/psychotree.bib | 7 ++++--- 19 files changed, 66 insertions(+), 38 deletions(-)