Title: Una implementación de funciones de uso interno
Description: Una herramienta rápida y consistente para la disposición de
microdatos y la visualización de las cifras y estadísticas oficiales
de la Universidad Nacional de Colombia <https://unal.edu.co>. Contiene
una biblioteca de funciones gráficas, tanto estáticas como
interactivas, que ofrece numerosos tipos de gráficos con una sintaxis
altamente configurable y simple. Entre estos encontramos la
visualización de tablas HTML, series, gráficos de barras y circulares,
mapas, etc. Todo lo anterior apoyado en bibliotecas de JavaScript.
English: A fast and consistent tool for the arrangement of microdata
and the visualization of official figures and statistics from the
National University of Colombia <https://unal.edu.co>. It includes a
library of graphical functions, both static and interactive, offering
numerous types of charts with a highly configurable and simple syntax.
Among these, we find the visualization of HTML tables, series, bar and
pie charts, maps, etc. It provides the capabi [...truncated...]
Author: Jeison Alarcon [aut, cre, ctr] ,
Alberto Rodriguez [aut, rev],
Direccion Nacional de Planeacion y Estadistica Universidad Nacional de
Colombia [cph, fnd]
Maintainer: Jeison Alarcon <jmalarconbe@unal.edu.co>
Diff between UnalR versions 1.0.0 dated 2024-05-25 and 1.0.1 dated 2025-09-18
UnalR-1.0.0/UnalR/man/figures/PlotExample1.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample10.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample2.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample3.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample4.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample5.png |only UnalR-1.0.0/UnalR/man/figures/PlotExample6.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample7.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample8.PNG |only UnalR-1.0.0/UnalR/man/figures/PlotExample9.PNG |only UnalR-1.0.0/UnalR/man/figures/lifecycle-deprecated.svg |only UnalR-1.0.1/UnalR/DESCRIPTION | 78 UnalR-1.0.1/UnalR/MD5 | 75 UnalR-1.0.1/UnalR/NAMESPACE | 218 +- UnalR-1.0.1/UnalR/NEWS.md | 9 UnalR-1.0.1/UnalR/R/Auxiliares.R | 2 UnalR-1.0.1/UnalR/R/Plot_Boxplot.R | 601 ++++-- UnalR-1.0.1/UnalR/R/Plot_Mapa.R | 1628 ++++++++++++----- UnalR-1.0.1/UnalR/R/Plot_Mundo.R | 845 ++++++-- UnalR-1.0.1/UnalR/R/Plot_Series.R | 4 UnalR-1.0.1/UnalR/README.md | 61 UnalR-1.0.1/UnalR/man/Agregar.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Apiladas.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Barras.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Boxplot.Rd | 10 UnalR-1.0.1/UnalR/man/Plot.Drilldown.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Mapa.Rd | 16 UnalR-1.0.1/UnalR/man/Plot.Mundo.Rd | 32 UnalR-1.0.1/UnalR/man/Plot.Radar.Rd | 2 UnalR-1.0.1/UnalR/man/Plot.Series.Rd | 8 UnalR-1.0.1/UnalR/man/Plot.Torta.Rd | 4 UnalR-1.0.1/UnalR/man/Plot.Treemap.Rd | 6 UnalR-1.0.1/UnalR/man/StaticPlot.Rd | 2 UnalR-1.0.1/UnalR/man/Tabla.General.Rd | 4 UnalR-1.0.1/UnalR/man/Tabla.Rd | 6 UnalR-1.0.1/UnalR/man/ejConsolidadoGrad.Rd | 2 UnalR-1.0.1/UnalR/man/ejConsolidadoSaberPro2019.Rd | 2 UnalR-1.0.1/UnalR/man/ejGraduados.Rd | 2 UnalR-1.0.1/UnalR/man/ejMiniAspirantesPre.Rd | 2 UnalR-1.0.1/UnalR/man/ejMiniConsolidadoAsp.Rd | 2 UnalR-1.0.1/UnalR/man/ejSaberPro2020.Rd | 2 UnalR-1.0.1/UnalR/man/read_example.Rd | 2 UnalR-1.0.1/UnalR/tests/testthat.R | 10 UnalR-1.0.1/UnalR/tests/testthat/test-Plot_Series.R | 3 44 files changed, 2606 insertions(+), 1044 deletions(-)
Title: Multiple-Instance Logistic Regression with LASSO Penalty
Description: The multiple instance data set consists of many independent
subjects (called bags) and each subject is composed of several components
(called instances). The outcomes of such data set are binary or categorical responses,
and, we can only observe the subject-level outcomes. For example, in manufacturing
processes, a subject is labeled as "defective" if at least one of its own
components is defective, and otherwise, is labeled as "non-defective". The
'milr' package focuses on the predictive model for the multiple instance
data set with binary outcomes and performs the maximum likelihood estimation
with the Expectation-Maximization algorithm under the framework of logistic
regression. Moreover, the LASSO penalty is attached to the likelihood function
for simultaneous parameter estimation and variable selection.
Author: Ping-Yang Chen [aut, cre],
ChingChuan Chen [aut],
Chun-Hao Yang [aut],
Sheng-Mao Chang [aut]
Maintainer: Ping-Yang Chen <pychen.ping@gmail.com>
Diff between milr versions 0.3.1 dated 2020-10-31 and 0.4.1 dated 2025-09-18
milr-0.3.1/milr/tests |only milr-0.4.1/milr/DESCRIPTION | 12 milr-0.4.1/milr/MD5 | 30 milr-0.4.1/milr/R/milr-package.R | 5 milr-0.4.1/milr/R/milr.R | 2 milr-0.4.1/milr/build/vignette.rds |binary milr-0.4.1/milr/inst/doc/milr-intro.R | 12 milr-0.4.1/milr/inst/doc/milr-intro.html | 1176 ++++++++++++++++++++----------- milr-0.4.1/milr/man/milr-package.Rd | 19 milr-0.4.1/milr/man/milr.Rd | 2 milr-0.4.1/milr/src/Makevars | 2 milr-0.4.1/milr/src/RcppExports.cpp | 5 milr-0.4.1/milr/src/common.cpp | 3 milr-0.4.1/milr/vignettes/musk1norm.svm | 954 ++++++++++++------------- 14 files changed, 1306 insertions(+), 916 deletions(-)
Title: Network Meta-Analysis Based on Multivariate Meta-Analysis and
Meta-Regression Models
Description: Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2025) <doi:10.1101/2025.09.15.25335823>). Comprehensive analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available through simple commands. For inconsistency assessment, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model are available. In addition, the side-splitting methods and Jackson's random inconsistency model can be applied. Standard graphical tools for network meta-analysis, including network plots, ranked forest plots, and transitivity analyses, are also provided. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) <doi:10.1002/jrsm.1652> <doi:10.1002/jrsm.1651>) are adopted as the default methods.
Author: Hisashi Noma [aut, cre] ,
Kazushi Maruo [aut],
Shiro Tanaka [aut],
Toshi A. Furukawa [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between NMA versions 1.4-3 dated 2024-05-17 and 2.1-1 dated 2025-09-18
DESCRIPTION | 22 ++++--- MD5 | 86 ++++++++++++++++------------ NAMESPACE | 3 + NEWS.md | 5 + R/global.ict.r | 2 R/local.ict.r | 2 R/netplot.r | 2 R/nmaforest.r | 4 - R/nmaleague.r | 2 R/nmaweight.r | 2 R/obj.forest.r | 4 - R/pairwise.r | 150 ++++++++++++++++++++++++++++++++++++++++++++++++-- R/random.icm.r | 47 +++++++++++++++ R/setup.r | 114 +++++++++++++++++++++++++++++++++++--- R/sidesplit.r | 2 R/trans.armdata.r |only R/trans.armdataP.r |only build/partial.rdb |binary data/exdataMD.RData |only data/exdataP.RData |only data/exdataRR.RData |only data/woods1.RData |only data/woods2.RData |only man/NMA-package.Rd | 10 ++- man/antidiabetic.Rd | 2 man/diabetes.Rd | 2 man/exdataMD.Rd |only man/exdataP.Rd |only man/exdataRR.Rd |only man/global.ict.Rd | 4 + man/heartfailure.Rd | 2 man/local.ict.Rd | 4 - man/netplot.Rd | 4 - man/nma.Rd | 4 - man/nmaQ.Rd | 4 - man/nmafunnel.Rd | 4 - man/nmaleague.Rd | 10 ++- man/nmarank.Rd | 6 +- man/nmareg.Rd | 4 - man/nmaweight.Rd | 2 man/obj.forest.Rd | 4 - man/pairwise.Rd | 13 +++- man/random.icm.Rd | 6 +- man/setup.Rd | 39 ++++++++++--- man/sidesplit.Rd | 4 - man/smoking.Rd | 2 man/trans.armdata.Rd |only man/trans.armdataP.Rd |only man/transitivity.Rd | 4 + man/woods1.Rd |only man/woods2.Rd |only 51 files changed, 459 insertions(+), 122 deletions(-)
Title: Custom 'MetaphoneBR' Phonetic Encoding for Brazilian Names
Description: Simplifies Brazilian names phonetically using a custom 'metaphoneBR' algorithm that preserves ending vowels.
Useful for name matching processing preserving gender information carried generally by ending vowels in Portuguese.
Mation (2025) <doi:10.6082/uchicago.15104>.
Author: Rodrigo Borges [aut, cre] ,
Lucas Mation [aut] ,
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rodrigo Borges <rodrigoesborges@gmail.com>
Diff between metaphonebr versions 0.0.4 dated 2025-07-17 and 0.0.5 dated 2025-09-18
DESCRIPTION | 13 +++---------- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 14 ++++++++++---- man/metaphonebr-package.Rd | 1 - 5 files changed, 21 insertions(+), 19 deletions(-)
Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality
assurance and quality control (QA/QC) of eddy covariance flux tower
data processing. It generates data-point removal code via
user-directed selection from a scatterplot, and can export a cleaned
.csv with removed points set to NA plus an R script for
reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>
Diff between fluxtools versions 0.6.2 dated 2025-08-28 and 0.7.0 dated 2025-09-18
DESCRIPTION | 6 MD5 | 35 NEWS.md | 10 R/prm.R | 1072 ++++++++--------- R/run_app.R | 70 - R/zzz-deps.R | 14 R/zzz.R | 20 README.md | 65 - inst/CITATION | 32 inst/app/app.R | 2408 +++++++++++++++++++++++++++------------- inst/doc/introduction.Rmd | 394 +++--- inst/doc/introduction.html | 118 + inst/extdata/app_V3.R |only inst/extdata/test.R | 94 - man/apply_prm.Rd | 60 man/get_prm_rules.Rd | 28 man/run_fluxtools.Rd | 40 tests/testthat/test-apply_prm.R | 354 ++--- vignettes/introduction.Rmd | 394 +++--- 19 files changed, 3117 insertions(+), 2097 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Christophe Dutang [ctb] ,
Reinhold Kainhofer [ctb] ,
Kevin J Owens [ctb],
Ernesto Schirmacher [ctb],
Gian Paolo Clemente [ctb] ,
Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.3.12 dated 2024-09-29 and 1.4.3 dated 2025-09-18
lifecontingencies-1.3.12/lifecontingencies/man/AExn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/DAxn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/IAxn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/axn.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/axn_1.Rd |only lifecontingencies-1.3.12/lifecontingencies/man/pureendowment.Rd |only lifecontingencies-1.4.3/lifecontingencies/DESCRIPTION | 21 lifecontingencies-1.4.3/lifecontingencies/MD5 | 60 - lifecontingencies-1.4.3/lifecontingencies/NEWS.md | 448 +++++----- lifecontingencies-1.4.3/lifecontingencies/R/2_commonMethods.R | 22 lifecontingencies-1.4.3/lifecontingencies/R/5_actuarialFunctions.R | 235 ++++- lifecontingencies-1.4.3/lifecontingencies/README.md | 6 lifecontingencies-1.4.3/lifecontingencies/build/vignette.rds |binary lifecontingencies-1.4.3/lifecontingencies/data/AF92Lt.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/AM92Lt.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/SoAISTdata.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/de_angelis_di_falco.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoCanada.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoChina.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoFrance.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoGermany.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoIta.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoJapan.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoUk.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/demoUsa.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soa08.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soa08Act.rda |binary lifecontingencies-1.4.3/lifecontingencies/data/soaLt.rda |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/PensionPlanVal.html | 13 lifecontingencies-1.4.3/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/compute-detail.html | 7 lifecontingencies-1.4.3/lifecontingencies/inst/doc/mortality_projection.pdf |binary lifecontingencies-1.4.3/lifecontingencies/inst/doc/pensionfunding.html | 11 lifecontingencies-1.4.3/lifecontingencies/man/arithmetic_variation_insurances.Rd |only lifecontingencies-1.4.3/lifecontingencies/man/endowment_trio.Rd |only 35 files changed, 485 insertions(+), 338 deletions(-)
More information about lifecontingencies 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 1.0.8 dated 2025-07-25 and 1.0.9 dated 2025-09-18
DESCRIPTION | 6 MD5 | 12 - NAMESPACE | 3 R/wtLHDs.R | 484 ++++++++++++++++++++++++++++++++-------------------- R/wtLHDs_prime.R | 462 +++++++++++++++++++++++++++++++++++++------------ man/wtLHDs.Rd | 8 man/wtLHDs_prime.Rd | 6 7 files changed, 674 insertions(+), 307 deletions(-)
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Description: Estimate haplotypic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
and Gerard (2021b) <doi:10.1038/s41437-021-00462-5>.
Author: David Gerard [aut, cre]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between ldsep versions 2.1.5 dated 2022-10-18 and 2.1.6 dated 2025-09-18
DESCRIPTION | 14 MD5 | 128 +-- NAMESPACE | 46 - NEWS.md | 4 R/RcppExports.R | 26 R/data.R | 120 +-- R/fast.R | 748 +++++++++---------- R/generics.R | 400 +++++----- R/ldgeno.R | 1396 ++++++++++++++++++------------------ R/ldsep-package.R | 53 - R/maxd.R | 414 +++++----- R/mds.R | 180 ++-- R/mom.R | 1098 ++++++++++++++-------------- R/multild.R | 896 +++++++++++------------ R/sliding_window.R | 178 ++-- README.md | 254 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fast.R | 8 inst/doc/fast.Rmd | 6 inst/doc/fast.html | 174 ++-- inst/doc/vcf.R | 94 +- inst/doc/vcf.Rmd | 10 inst/doc/vcf.html | 365 ++++----- inst/extdata/subuit.vcf | 1164 +++++++++++++++--------------- man/Dprime.Rd | 104 +- man/format_lddf.Rd | 102 +- man/get_prob_array.Rd | 64 - man/gl_to_gp.Rd | 66 - man/glike.Rd | 60 - man/gp.Rd | 60 - man/is.lddf.Rd | 52 - man/ldest.Rd | 570 +++++++------- man/ldest_comp.Rd | 310 +++---- man/ldest_hap.Rd | 382 ++++----- man/ldfast.Rd | 358 ++++----- man/ldsep-package.Rd | 71 - man/ldshrink.Rd | 76 - man/mldest.Rd | 340 ++++---- man/pbnorm_dist.Rd | 54 - man/plot.lddf.Rd | 178 ++-- man/pvcalc.Rd | 58 - man/slcor.Rd | 74 - man/sldest.Rd | 332 ++++---- man/uit.Rd | 54 - man/zshrink.Rd | 80 +- src/Makevars | 3 src/Makevars.win | 3 src/derivatives.cpp | 28 src/genolike.cpp | 6 src/utils.cpp | 2 tests/testthat.R | 8 tests/testthat/test-cube.R | 104 +- tests/testthat/test-derivatives.R | 750 +++++++++---------- tests/testthat/test-em_vs_grad.R | 98 +- tests/testthat/test-hessian.R | 290 +++---- tests/testthat/test-ld_from_gmat.R | 44 - tests/testthat/test-ldfast.R | 136 +-- tests/testthat/test-lp.R | 110 +- tests/testthat/test-multinomial.R | 92 +- tests/testthat/test-pbnorm.R | 80 +- tests/testthat/test-posteriormean.R | 366 ++++----- tests/testthat/test-problem_data.R | 212 ++--- vignettes/fast.Rmd | 6 vignettes/vcf.Rmd | 10 65 files changed, 6745 insertions(+), 6824 deletions(-)
Title: Data from the Ecuador Truth Commission
Description: Provides access to data collected by the Ecuadorian Truth Commission.
Allows users to extract and analyze systematized information for human rights
research in Ecuador. The package contains datasets documenting human rights
violations from 1984-2008, including victim information, violation types,
perpetrators, and geographic distribution.
Author: Adriana Robles [aut] ,
Javier Borja [aut, cre]
Maintainer: Javier Borja <javier@demografiando.pro>
Diff between verdadecu versions 0.2.0 dated 2025-08-21 and 1.0.0 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++++----- NEWS.md | 34 ++++++++++++++++++++++++++++++++++ README.md | 28 ++++++++++++++++++++++++++++ inst/CITATION | 4 ++-- inst/doc/verdadecu.html | 4 ++-- tests |only 7 files changed, 80 insertions(+), 13 deletions(-)
Title: Result Model Manager
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
Informatics programme. 'ResultModelManager' provides utility functions to allow package
maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Diff between ResultModelManager versions 0.5.11 dated 2024-09-19 and 0.6.0 dated 2025-09-18
DESCRIPTION | 13 - MD5 | 79 ++++++---- NAMESPACE | 19 -- NEWS.md | 15 ++ R/ConnectionHandler.R | 32 +--- R/DataMigrationManager.R | 25 ++- R/DataModel.R | 210 ++++++++++++++++++----------- R/PooledConnectionHandler.R | 11 - R/PyFunctions.R |only R/QueryNamespace.R | 17 +- R/ResultExportManager.R | 110 +++++++++------ R/ResultModelManager.R | 7 R/SchemaGenerator.R | 6 R/Utils.R | 4 README.md | 5 build/vignette.rds |binary inst/doc/CreatingMigrations.pdf |binary inst/doc/PackageDesign.pdf |binary inst/doc/UploadFunctionality.pdf |binary inst/doc/UsingAnExportManager.pdf |binary inst/doc/UsingConnectionHandlers.pdf |binary inst/doc/UsingPythonUploads.R |only inst/doc/UsingPythonUploads.Rmd |only inst/doc/UsingPythonUploads.pdf |only inst/doc/UsingQueryNamespaces.pdf |binary inst/pg_upload.py |only man/ConnectionHandler.Rd | 28 +-- man/DataMigrationManager.Rd | 16 +- man/QueryNamespace.Rd | 15 +- man/ResultExportManager.Rd | 10 + man/ResultModelManager-package.Rd | 2 man/disablePythonUploads.Rd |only man/enablePythonUploads.Rd |only man/install_psycopg2.Rd |only man/pyPgUploadEnabled.Rd |only man/pyUploadCsv.Rd |only man/pyUploadDataFrame.Rd |only tests/testthat/helper-packageMaintainer.R | 2 tests/testthat/test-ConnectionHandler.R | 10 - tests/testthat/test-DataMigrationManager.R | 13 - tests/testthat/test-DataModel.R | 46 +++--- tests/testthat/test-DataModelFunctions.R | 168 +++++++++++++++++++++++ tests/testthat/test-PooledConnection.R | 12 - tests/testthat/test-PyFunctions.R |only tests/testthat/test-QueryNamespace.R | 12 + tests/testthat/test-ResultExportManager.R | 14 + vignettes/UsingPythonUploads.Rmd |only 47 files changed, 600 insertions(+), 301 deletions(-)
More information about ResultModelManager at CRAN
Permanent link
Title: Ready-to-Use Omics Formatting, Analysis, and Visualization
Pipeline
Description: Provides a flexible and streamlined pipeline for formatting, analyzing, and
visualizing omics data, regardless of omics type (e.g. transcriptomics, proteomics,
metabolomics). The package includes tools for shaping input data into analysis-ready
structures, fitting linear or mixed-effect models, extracting key contrasts, and
generating a rich variety of ready-to-use publication-quality plots.
Designed for transparency and reproducibility across a wide range of study designs,
with customizable components for statistical modeling.
Author: Laura Martinez-Gili [cre, aut, cph]
Maintainer: Laura Martinez-Gili <martinez.gili.laura@gmail.com>
Diff between readyomics versions 0.1.1 dated 2025-08-27 and 0.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/ready_plots.R | 3 +-- R/utils_analysis.R | 1 - inst/doc/readyomics.html | 17 +++++++++-------- 6 files changed, 23 insertions(+), 20 deletions(-)
Title: Sample Size Calculation for the Proportional Hazards Mixture
Cure Model
Description: An R-package for calculating sample size of a survival trial with or without cure fractions.
Author: Chao Cai [aut, cre],
Songfeng Wang [aut],
Wenbin Lu [aut],
Jiajia Zhang [aut]
Maintainer: Chao Cai <caic@mailbox.sc.edu>
Diff between NPHMC versions 2.3 dated 2022-05-08 and 2.4.2 dated 2025-09-18
DESCRIPTION | 30 +++++++++++++++++++++++------- MD5 | 4 ++-- man/NPHMC-package.Rd | 2 +- 3 files changed, 26 insertions(+), 10 deletions(-)
Title: Approximate Optimal Transport Between Two-Dimensional Grids
Description: Can be used for optimal transport between two-dimensional grids with respect to separable cost functions of l^p form. It utilizes the Frank-Wolfe algorithm to approximate so-called pivot measures: One-dimensional transport plans that fully describe the full transport, see G. Auricchio (2023) <doi:10.4171/RLM/1026>. For these, it offers methods for visualization and to extract the corresponding transport plans and costs. Additionally, related functions for one-dimensional optimal transport are available.
Author: Michel Groppe [aut, cre],
Nicholas Bonneel [ctb],
Egervary Research Group on Combinatorial Optimization [cph]
Maintainer: Michel Groppe <michel.groppe@uni-goettingen.de>
Diff between gridOT versions 1.0.1 dated 2022-10-18 and 1.0.2 dated 2025-09-18
DESCRIPTION | 19 ++++++++++--------- MD5 | 13 +++++++------ R/gridOT-package.R | 10 ++++++---- R/transport_costmat.R | 10 +++++----- build |only man/gridOT-package.Rd | 12 +++++++----- src/Makevars | 6 +++--- src/Makevars.win | 6 +++--- 8 files changed, 41 insertions(+), 35 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 1.3.0 dated 2025-07-15 and 1.3.1 dated 2025-09-18
DESCRIPTION | 13 MD5 | 84 - NAMESPACE | 20 NEWS.md | 17 R/casting.R | 24 R/classAchillesTable.R | 3 R/classCdmReference.R | 50 - R/classCodelist.R | 6 R/classCohortTable.R | 5 R/classConceptSetExpression.R | 27 R/classOmopTable.R | 4 R/compute.R | 51 - R/importConceptSetExpression.R | 2 R/methodInsertTable.R | 7 R/omopDataFolder.R |only R/overwriteClasses.R | 99 + R/recordCohortAttrition.R | 17 R/sysdata.rda |binary R/validate.R | 10 build/vignette.rds |binary inst/doc/cdm_reference.Rmd | 2 inst/doc/codelists.Rmd | 2 inst/doc/cohorts.Rmd | 2 inst/doc/cohorts.html | 126 +- inst/doc/logging.html | 52 - inst/doc/summarised_result.R | 10 inst/doc/summarised_result.Rmd | 32 inst/doc/summarised_result.html | 1199 +++++++++++------------- inst/doc/suppression.R |only inst/doc/suppression.Rmd |only inst/doc/suppression.html |only man/emptyConceptSetExpression.Rd |only man/insertTable.Rd | 4 man/newConceptSetExpression.Rd | 6 man/omopDataFolder.Rd |only man/validateConceptSetArgument.Rd | 8 tests/testthat/test-assert.R | 12 tests/testthat/test-classCdmReference.R | 8 tests/testthat/test-classCodelist.R | 1 tests/testthat/test-classCohortTable.R | 2 tests/testthat/test-classConceptSetExpression.R | 7 tests/testthat/test-omopDataFolder.R |only vignettes/cdm_reference.Rmd | 2 vignettes/codelists.Rmd | 2 vignettes/cohorts.Rmd | 2 vignettes/summarised_result.Rmd | 32 vignettes/suppression.Rmd |only 47 files changed, 1019 insertions(+), 931 deletions(-)
Title: A Super K-Nearest Neighbor (SKNN) Classification Algorithm
Description: It's a Super K-Nearest Neighbor(SKNN) classification method with using kernel density to describe weight of the distance between a training observation and the testing sample. Comparison of performance between SKNN and KNN shows that SKNN is significantly superior to KNN.
Author: Yarong Yang [aut, cre],
Nader Ebrahimi [ctb],
Yoram Rubin [ctb],
Jacob Zhang [ctb]
Maintainer: Yarong Yang <Yi.YA_yaya@hotmail.com>
Diff between SKNN versions 4.1.1 dated 2025-09-09 and 4.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/PCAy.Rd | 2 +- man/PCAyd-class.Rd | 4 ++-- man/SKNN-package.Rd | 6 +++--- man/SKNN.Rd | 2 +- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.20.0 dated 2025-07-16 and 2.21 dated 2025-09-18
DESCRIPTION | 8 ++--- MD5 | 62 +++++++++++++++++++-------------------- NAMESPACE | 2 + NEWS.md | 25 +++++++++++++++ R/Attach.R | 19 ++++++++++- R/Design.R | 18 +++++++++-- R/PBA.R | 2 - R/RobbinsMonro.R | 2 - R/SimDesign.R | 1 R/SimExtract.R | 2 - R/SimShiny.R | 4 +- R/SimSolve.R | 3 + R/runArraySimulation.R | 29 +++++++++++------- R/runSimulation.R | 41 +++++++++++++++++++++---- inst/doc/Catch_errors.html | 27 +++++----------- inst/doc/Fixed_obj_fun.html | 10 +++--- inst/doc/HPC-computing.html | 4 +- inst/doc/MultipleAnalyses.html | 4 +- inst/doc/Parallel-computing.html | 4 +- inst/doc/Saving-results.html | 46 +++------------------------- inst/doc/SimDesign-intro.html | 42 +++++--------------------- man/Attach.Rd | 7 +++- man/PBA.Rd | 2 - man/RobbinsMonro.Rd | 2 - man/SimExtract.Rd | 2 - man/SimShiny.Rd | 4 +- man/SimSolve.Rd | 2 - man/createDesign.Rd | 12 ++++++- man/expandReplications.Rd | 2 - man/runArraySimulation.Rd | 2 - man/runSimulation.Rd | 20 +++++++++++- tests/tests/test-01-core.R | 26 ++++++++++++++++ 32 files changed, 256 insertions(+), 180 deletions(-)
Title: Holistic Multimodel Domain Analysis for Exploratory Machine
Learning
Description: Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological cond [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
This is a re-admission after prior archival of version 0.1 dated 2025-03-27
Diff between HMDA versions 0.1 dated 2025-03-27 and 0.1.1 dated 2025-09-18
DESCRIPTION | 9 ++++----- MD5 | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-)
Title: Discrete Statistical Distributions
Description: Implementation of new discrete statistical distributions. Each distribution includes the traditional functions as well as an additional function called the family function, which can be used to estimate parameters within the 'gamlss' framework.
Author: Freddy Hernandez-Barajas [aut, cre] ,
Fernando Marmolejo-Ramos [aut] ,
Olga Usuga-Manco [aut]
Maintainer: Freddy Hernandez-Barajas <fhernanb@unal.edu.co>
Diff between DiscreteDists versions 1.1.0 dated 2025-09-08 and 1.1.1 dated 2025-09-18
DiscreteDists-1.1.0/DiscreteDists/man/d1_dldm_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d1_vec_dldm_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d2_dldd_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/d2_vec_dldd_compo_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dCOMPO_single.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dCOMPO_vec.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dHYPERPO_single.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/dHYPERPO_vec.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/f11_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/figures |only DiscreteDists-1.1.0/DiscreteDists/man/z_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/man/z_vec_cpp.Rd |only DiscreteDists-1.1.0/DiscreteDists/src/dDMOLBE.cpp |only DiscreteDists-1.1.1/DiscreteDists/DESCRIPTION | 6 DiscreteDists-1.1.1/DiscreteDists/MD5 | 83 +++---- DiscreteDists-1.1.1/DiscreteDists/NAMESPACE | 11 DiscreteDists-1.1.1/DiscreteDists/NEWS.md | 2 DiscreteDists-1.1.1/DiscreteDists/R/DMOLBE.R | 83 ++++--- DiscreteDists-1.1.1/DiscreteDists/R/HYPERPO.R | 8 DiscreteDists-1.1.1/DiscreteDists/R/RcppExports.R | 100 -------- DiscreteDists-1.1.1/DiscreteDists/R/dDMOLBE.R | 21 - DiscreteDists-1.1.1/DiscreteDists/R/utils.R | 21 + DiscreteDists-1.1.1/DiscreteDists/inst/include |only DiscreteDists-1.1.1/DiscreteDists/man/AR.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/F11.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_DBH.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_DLD.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_POISXL.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_DGEII.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_DIKUM.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_GGEO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_HYPERPO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/estim_mu_sigma_HYPERPO2.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DBH.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DGEII.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DIKUM.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_DLD.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_GGEO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_HYPERPO.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_HYPERPO2.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/logLik_POISXL.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/obtaining_lambda.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/simulate_hp.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/man/stopping.Rd | 1 DiscreteDists-1.1.1/DiscreteDists/src/RcppExports.cpp | 113 ++++------ DiscreteDists-1.1.1/DiscreteDists/src/dCOMPO.cpp | 57 ----- DiscreteDists-1.1.1/DiscreteDists/src/dDMOLBDE.cpp |only DiscreteDists-1.1.1/DiscreteDists/src/dHP.cpp | 67 ----- DiscreteDists-1.1.1/DiscreteDists/src/shared.cpp |only DiscreteDists-1.1.1/DiscreteDists/src/shared.h |only DiscreteDists-1.1.1/DiscreteDists/src/shared_inline.h |only 51 files changed, 207 insertions(+), 386 deletions(-)
Title: Visual Model Checking for Nonlinear Mixed Effect Model
Description: Various visual and numerical diagnosis methods for the nonlinear mixed effect model, including visual predictive checks, numerical predictive checks, and coverage plots (Karlsson and Holford, 2008, <https://www.page-meeting.org/?abstract=1434>).
Author: Eun-Kyung Lee [aut, cre],
Eun-Hwa Kang [aut]
Maintainer: Eun-Kyung Lee <lee.eunk@gmail.com>
Diff between nlmeVPC versions 2.6 dated 2022-12-22 and 2.8 dated 2025-09-18
DESCRIPTION | 10 +++++----- MD5 | 44 ++++++++++++++++++++++---------------------- R/BootVPC.R | 5 ++--- R/Misc.R | 24 ++++++++++++------------ R/NumericalCheck.R | 4 ---- R/VPCgraph.R | 6 ++---- R/aqrVPC.R | 5 ++--- R/asVPC.R | 8 +++----- R/coverage.R | 14 ++++++-------- R/coverageDetailplot.R | 4 +--- R/optK.R | 9 ++++----- R/quantVPC.R | 5 ++--- man/NumericalCheck.Rd | 2 -- man/VPCgraph.Rd | 4 +--- man/aqrVPC.Rd | 4 +--- man/asVPC.Rd | 7 ++----- man/bootVPC.Rd | 4 +--- man/coverageDetailplot.Rd | 4 +--- man/coverageplot.Rd | 5 +---- man/optK.Rd | 2 -- man/quantVPC.Rd | 4 +--- src/Makevars | 3 ++- src/Makevars.win | 2 +- 23 files changed, 72 insertions(+), 107 deletions(-)
Title: Construct Mixed Type Data Structures with Vectors of Vectors
Description: Mixed type vectors are useful for combining semantically similar classes. Some examples of semantically related classes include time across different granularities (e.g. daily, monthly, annual) and probability distributions (e.g. Normal, Uniform, Poisson). These groups of vector types typically share common statistical operations which vary in results with the attributes of each vector. The 'vecvec' data structure facilitates efficient storage and computation across multiple vectors within the same object.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vecvec versions 0.1.0 dated 2025-06-29 and 0.2.0 dated 2025-09-18
DESCRIPTION | 6 +++--- MD5 | 15 +++++++++------ NAMESPACE | 2 ++ NEWS.md |only R/vecvec.R | 34 +++++++++++++++++++++------------- R/vecvec_apply.R |only R/vecvec_math.R | 33 +++++++++++++++++++++++---------- R/zzz.R | 2 +- man/vecvec.Rd | 4 +++- man/vecvec_apply.Rd |only 10 files changed, 62 insertions(+), 34 deletions(-)
Title: Random Forest Prediction Decomposition and Feature Importance
Measure
Description: An R re-implementation of the 'treeinterpreter' package on PyPI
<https://pypi.org/project/treeinterpreter/>. Each prediction can be
decomposed as 'prediction = bias + feature_1_contribution + ... +
feature_n_contribution'. This decomposition is then used to calculate
the Mean Decrease Impurity (MDI) and Mean Decrease Impurity using
out-of-bag samples (MDI-oob) feature importance measures based on the
work of Li et al. (2019) <doi:10.48550/arXiv.1906.10845>.
Author: Qingyao Sun [aut, cre]
Maintainer: Qingyao Sun <sunqingyao19970825@gmail.com>
Diff between tree.interpreter versions 0.1.1 dated 2020-02-05 and 0.1.3 dated 2025-09-18
tree.interpreter-0.1.1/tree.interpreter/src/RcppExports-d25771d5.o.tmp |only tree.interpreter-0.1.3/tree.interpreter/DESCRIPTION | 18 tree.interpreter-0.1.3/tree.interpreter/MD5 | 21 tree.interpreter-0.1.3/tree.interpreter/README.md | 6 tree.interpreter-0.1.3/tree.interpreter/build/vignette.rds |binary tree.interpreter-0.1.3/tree.interpreter/configure | 4 tree.interpreter-0.1.3/tree.interpreter/inst/CITATION | 51 tree.interpreter-0.1.3/tree.interpreter/inst/doc/MDI.R | 2 tree.interpreter-0.1.3/tree.interpreter/inst/doc/MDI.html | 516 ++++------ tree.interpreter-0.1.3/tree.interpreter/src/Makevars.template | 13 tree.interpreter-0.1.3/tree.interpreter/src/Makevars.win | 13 tree.interpreter-0.1.3/tree.interpreter/vignettes/MDI.bib | 4 12 files changed, 306 insertions(+), 342 deletions(-)
More information about tree.interpreter at CRAN
Permanent link
Title: Transparent Assessment Framework for Reproducible Research
Description: General framework to organize data, methods, and results used in
reproducible scientific analyses. A TAF analysis consists of four scripts
(data.R, model.R, output.R, report.R) that are run sequentially. Each script
starts by reading files from a previous step and ends with writing out files
for the next step. Convenience functions are provided to version control the
required data and software, run analyses, clean residues from previous runs,
manage files, manipulate tables, and produce figures. With a focus on
stability and reproducible analyses, the TAF package comes with no
dependencies. TAF forms a base layer for the 'icesTAF' package and other
scientific applications.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Iago Mosqueira [aut],
Alexandros Kokkalis [ctb],
Ibrahim Umar [ctb],
Hjalte Parner [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between TAF versions 4.3.0 dated 2025-09-02 and 4.3.1 dated 2025-09-18
DESCRIPTION | 10 +++--- MD5 | 78 +++++++++++++++++++++++++-------------------------- NEWS.md | 7 ++++ R/div.R | 2 - R/download.R | 2 - R/make.R | 2 - R/make.all.R | 2 - R/make.taf.R | 2 - R/msg.R | 2 - R/pdeps.R | 2 - R/read.taf.R | 2 - R/rnd.R | 2 - R/source.all.R | 2 - R/source.dir.R | 2 - R/taf.boot.R | 2 - R/taf.boot.path.R | 2 - R/taf.data.path.R | 2 - R/taf.png.R | 2 - R/taf.unzip.R | 2 - R/wide2long.R | 12 +++++++ R/write.taf.R | 2 - R/zoom.R | 2 - man/div.Rd | 2 - man/download.Rd | 2 - man/make.Rd | 2 - man/make.all.Rd | 2 - man/make.taf.Rd | 2 - man/msg.Rd | 2 - man/pdeps.Rd | 2 - man/read.taf.Rd | 2 - man/rnd.Rd | 2 - man/source.all.Rd | 2 - man/source.dir.Rd | 2 - man/taf.boot.Rd | 2 - man/taf.boot.path.Rd | 2 - man/taf.data.path.Rd | 2 - man/taf.png.Rd | 2 - man/taf.unzip.Rd | 2 - man/write.taf.Rd | 2 - man/zoom.Rd | 2 - 40 files changed, 98 insertions(+), 81 deletions(-)
Title: Weighted Mean SHAP and CI for Robust Feature Assessment in ML
Grid
Description: This R package introduces Weighted Mean SHapley Additive exPlanations (WMSHAP), an innovative method for calculating SHAP values for a grid of fine-tuned base-learner machine learning models as well as stacked ensembles, a method not previously available due to the common reliance on single best-performing models. By integrating the weighted mean SHAP values from individual base-learners comprising the ensemble or individual base-learners in a tuning grid search, the package weights SHAP contributions according to each model's performance, assessed by multiple either R squared (for both regression and classification models). alternatively, this software also offers weighting SHAP values based on the area under the precision-recall curve (AUCPR), the area under the curve (AUC), and F2 measures for binary classifiers. It further extends this framework to implement weighted confidence intervals for weighted mean SHAP values, offering a more comprehensive and robust feature importance eval [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
This is a re-admission after prior archival of version 0.5 dated 2025-03-18
Diff between shapley versions 0.5 dated 2025-03-18 and 0.5.1 dated 2025-09-18
DESCRIPTION | 13 +++++------- MD5 | 14 ++++++------- NAMESPACE | 1 R/shapley.domain.R | 3 -- R/shapley.plot.R | 53 +++++++++++++++++++++++++------------------------- README.md | 12 +++++++---- man/shapley.domain.Rd | 1 man/shapley.plot.Rd | 1 8 files changed, 49 insertions(+), 49 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of Machine Learning
(ML) techniques as easy and accessible as possible, particularly within the framework of
the Knowledge Discovery in Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive or classification
modeling workflow, aligning closely with the fundamental steps of the KDD methodology,
from data selection and preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis. The 'MLwrap' workflow
is organized into four core steps; preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to data preparation and
transformation, model construction, hyperparameter optimization, and sensitivity analysis.
The user can access comprehensive model evaluation results including fit assessment metrics,
plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
This is a re-admission after prior archival of version 0.1.0 dated 2025-07-22
Diff between MLwrap versions 0.1.0 dated 2025-07-22 and 0.1.1 dated 2025-09-18
DESCRIPTION | 60 ++++++++++------------ MD5 | 80 +++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 11 ++-- R/InterpretableML.R | 16 +++--- R/SOBOL.R | 2 R/evaluate_model.R | 27 ++++++++++ R/fine_tuning.R | 6 +- R/model_creation.R | 4 - R/plotting_utils.R | 72 +++++++++++++-------------- R/results_binary_classification.R | 6 +- R/results_regression.R | 2 R/table_utils.R | 52 +++++++++---------- README.md | 20 +++---- man/build_model.Rd | 4 - man/fine_tuning.Rd | 6 +- man/plot_calibration_curve.Rd | 4 - man/plot_confusion_matrix.Rd | 4 - man/plot_distribution_by_class.Rd | 4 - man/plot_gain_curve.Rd | 4 - man/plot_graph_nn.Rd | 4 - man/plot_integrated_gradients.Rd | 4 - man/plot_lift_curve.Rd | 4 - man/plot_loss_curve.Rd | 4 - man/plot_olden.Rd | 4 - man/plot_pfi.Rd | 4 - man/plot_residuals_distribution.Rd | 4 - man/plot_roc_curve.Rd | 4 - man/plot_scatter_predictions.Rd | 4 - man/plot_scatter_residuals.Rd | 4 - man/plot_shap.Rd | 4 - man/plot_sobol_jansen.Rd | 4 - man/plot_tuning_results.Rd | 4 - man/sensitivity_analysis.Rd | 16 +++--- man/table_best_hyperparameters.Rd | 4 - man/table_evaluation_results.Rd | 4 - man/table_integrated_gradients_results.Rd | 4 - man/table_olden_results.Rd | 4 - man/table_pfi_results.Rd | 4 - man/table_shap_results.Rd | 4 - man/table_sobol_jansen_results.Rd | 4 - 41 files changed, 257 insertions(+), 225 deletions(-)
Title: Generalized Linear Mixed Model (GLMM) for Binary Randomized
Response Data
Description: Generalized Linear Mixed Model (GLMM) for Binary Randomized Response Data.
Includes Cauchit, Compl. Log-Log, Logistic, and Probit link functions for Bernoulli Distributed RR data.
RR Designs: Warner, Forced Response, Unrelated Question, Kuk, Crosswise, and Triangular.
Reference: Fox, J-P, Veen, D. and Klotzke, K. (2018). Generalized Linear Mixed Models for Randomized Responses. Methodology. <doi:10.1027/1614-2241/a000153>.
Author: Jean-Paul Fox [aut, cre],
Konrad Klotzke [aut],
Duco Veen [aut]
Maintainer: Jean-Paul Fox <jpfox00@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2021-01-13
Diff between GLMMRR versions 0.5.0 dated 2021-01-13 and 0.6.0 dated 2025-09-18
DESCRIPTION | 24 + MD5 | 91 ++--- NAMESPACE | 96 ++--- R/ETHBE.R | 96 ++--- R/MTURK.R | 92 ++--- R/Plagiarism.R | 84 ++--- R/RRbinomial.R | 132 ++++---- R/RRglm.R | 8 R/RRglmGOF.R | 374 +++++++++++----------- R/RRglmer.R | 12 R/RRlink_cauchit.R | 52 +-- R/RRlink_cloglog.R | 52 +-- R/RRlink_logit.R | 52 +-- R/RRlink_probit.R | 52 +-- R/getMLPrevalence.R | 44 +- R/getRRparameters.R | 262 +++++++-------- R/plot.R | 658 ++++++++++++++++++++-------------------- R/print.R | 564 +++++++++++++++++----------------- R/residuals.R | 8 R/summary.R | 326 +++++++++---------- R/tools.R | 160 ++++----- README.md |only build/partial.rdb |binary man/Plagiarism.Rd | 106 +++--- man/RRbinomial.Rd | 52 +-- man/RRglm.Rd | 106 +++--- man/RRglmGOF.Rd | 80 ++-- man/RRglmer.Rd | 150 ++++----- man/RRlink.cauchit.Rd | 38 +- man/RRlink.cloglog.Rd | 38 +- man/RRlink.logit.Rd | 38 +- man/RRlink.probit.Rd | 38 +- man/getCellMeans.Rd | 42 +- man/getCellSizes.Rd | 42 +- man/getMLPrevalence.Rd | 46 +- man/getRRparameters.Rd | 42 +- man/getUniqueGroups.Rd | 34 +- man/intDotplot.Rd | 34 +- man/plot.RRglm.Rd | 76 ++-- man/plot.RRglmerMod.Rd | 60 +-- man/print.RRglmGOF.Rd | 36 +- man/print.summary.RRglm.Rd | 62 +-- man/print.summary.RRglmerMod.Rd | 62 +-- man/residuals.RRglm.Rd | 66 ++-- man/residuals.RRglmerMod.Rd | 62 +-- man/summary.RRglm.Rd | 42 +- man/summary.RRglmerMod.Rd | 42 +- 47 files changed, 2323 insertions(+), 2310 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.3.3 dated 2025-09-10 and 1.4.0 dated 2025-09-18
DESCRIPTION | 6 MD5 | 70 ++++++----- NAMESPACE | 3 NEWS.md | 21 +++ R/backend-dbplyr__duckdb_connection.R | 7 - R/dbGetInfo__duckdb_driver.R | 8 - R/duckdb-package.R |only R/duckdb.R | 8 - R/progress_display.R | 2 R/release.R |only R/sql.R | 75 ++++++++++-- R/version.R | 2 man/backend-duckdb.Rd | 4 man/default_conn.Rd |only man/duckdb-package.Rd | 2 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/sql_query.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/duckdb.tar.xz |binary src/include/rapi.hpp | 2 src/include/rfuns_extension.hpp | 2 src/include/sources.mk | 2 src/include/typesr.hpp | 2 src/relational.cpp | 7 - src/reltoaltrep.cpp | 166 ++++++++++++++++++++++----- src/rfuns.cpp | 54 ++++---- src/transform.cpp | 16 +- src/utils.cpp | 2 tests/testthat/_snaps/explain.md | 8 - tests/testthat/_snaps/relational.md | 2 tests/testthat/_snaps/sql.md |only tests/testthat/_snaps/types.md | 2 tests/testthat/test-date.R | 3 tests/testthat/test-sql.R |only tests/testthat/test-struct.R | 146 +++++++++++++++++++++++ tests/testthat/test-tbl__duckdb_connection.R | 13 ++ tests/testthat/test-types.R | 2 41 files changed, 492 insertions(+), 149 deletions(-)
Title: 'DataSHIELD' Server Side Base Functions
Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
been designed to only share non disclosive summary statistics, with built in automated output
checking based on statistical disclosure control. With data sites setting the threshold values for
the automated output checks. For more details, see 'citation("dsBase")'.
Author: Paul Burton [aut] ,
Rebecca Wilson [aut] ,
Olly Butters [aut] ,
Patricia Ryser-Welch [aut] ,
Alex Westerberg [aut],
Leire Abarrategui [aut],
Roberto Villegas-Diaz [aut] ,
Demetris Avraam [aut] ,
Yannick Marcon [aut] ,
Tom Bishop [aut],
Amadou Gaye [a [...truncated...]
Maintainer: Stuart Wheater <stuart.wheater@arjuna.com>
This is a re-admission after prior archival of version 6.3.3 dated 2025-07-19
Diff between dsBase versions 6.3.3 dated 2025-07-19 and 6.3.4 dated 2025-09-18
dsBase-6.3.3/dsBase/R/zzz.R |only dsBase-6.3.4/dsBase/DESCRIPTION | 49 ++++-- dsBase-6.3.4/dsBase/MD5 | 130 ++++++++-------- dsBase-6.3.4/dsBase/R/BooleDS.R | 2 dsBase-6.3.4/dsBase/R/asDataMatrixDS.R | 2 dsBase-6.3.4/dsBase/R/blackBoxDS.R | 7 dsBase-6.3.4/dsBase/R/blackBoxRanksDS.R | 7 dsBase-6.3.4/dsBase/R/cbindDS.R | 2 dsBase-6.3.4/dsBase/R/checkNegValueDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSortDS.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSubsetDS1.R | 2 dsBase-6.3.4/dsBase/R/dataFrameSubsetDS2.R | 2 dsBase-6.3.4/dsBase/R/densityGridDS.R | 2 dsBase-6.3.4/dsBase/R/dmtC2SDS.R | 4 dsBase-6.3.4/dsBase/R/dsBase-package.R |only dsBase-6.3.4/dsBase/R/gamlssDS.R | 2 dsBase-6.3.4/dsBase/R/glmerSLMADS.assign.R | 2 dsBase-6.3.4/dsBase/R/global.R | 3 dsBase-6.3.4/dsBase/R/heatmapPlotDS.R | 7 dsBase-6.3.4/dsBase/R/hetcorDS.R | 2 dsBase-6.3.4/dsBase/R/histogramDS1.R | 7 dsBase-6.3.4/dsBase/R/histogramDS2.R | 7 dsBase-6.3.4/dsBase/R/levelsDS.R | 2 dsBase-6.3.4/dsBase/R/lexisDS2.R | 2 dsBase-6.3.4/dsBase/R/lmerSLMADS.assign.R | 4 dsBase-6.3.4/dsBase/R/meanDS.R | 2 dsBase-6.3.4/dsBase/R/metadataDS.R | 2 dsBase-6.3.4/dsBase/R/minMaxRandDS.R | 7 dsBase-6.3.4/dsBase/R/qlsplineDS.R | 2 dsBase-6.3.4/dsBase/R/rangeDS.R | 7 dsBase-6.3.4/dsBase/R/reShapeDS.R | 2 dsBase-6.3.4/dsBase/R/recodeLevelsDS.R | 2 dsBase-6.3.4/dsBase/R/recodeValuesDS.R | 2 dsBase-6.3.4/dsBase/R/repDS.R | 2 dsBase-6.3.4/dsBase/R/rmDS.R | 2 dsBase-6.3.4/dsBase/R/scatterPlotDS.R | 7 dsBase-6.3.4/dsBase/R/subsetByClassDS.R | 2 dsBase-6.3.4/dsBase/R/subsetDS.R | 2 dsBase-6.3.4/dsBase/R/table1DDS.R | 2 dsBase-6.3.4/dsBase/R/tableDS.R | 6 dsBase-6.3.4/dsBase/R/tableDS.assign.R | 6 dsBase-6.3.4/dsBase/R/tableDS2.R | 6 dsBase-6.3.4/dsBase/R/vectorDS.R | 2 dsBase-6.3.4/dsBase/README.md | 75 ++++++++- dsBase-6.3.4/dsBase/inst/CITATION | 10 - dsBase-6.3.4/dsBase/inst/DATASHIELD | 14 + dsBase-6.3.4/dsBase/inst/WORDLIST |only dsBase-6.3.4/dsBase/man/asDataMatrixDS.Rd | 2 dsBase-6.3.4/dsBase/man/checkNegValueDS.Rd | 2 dsBase-6.3.4/dsBase/man/densityGridDS.Rd | 2 dsBase-6.3.4/dsBase/man/dmtC2SDS.Rd | 4 dsBase-6.3.4/dsBase/man/dsBase-package.Rd |only dsBase-6.3.4/dsBase/man/gamlssDS.Rd | 2 dsBase-6.3.4/dsBase/man/glmerSLMADS.assign.Rd | 2 dsBase-6.3.4/dsBase/man/hetcorDS.Rd | 2 dsBase-6.3.4/dsBase/man/lexisDS2.Rd | 2 dsBase-6.3.4/dsBase/man/lmerSLMADS.assign.Rd | 4 dsBase-6.3.4/dsBase/man/meanDS.Rd | 2 dsBase-6.3.4/dsBase/man/metadataDS.Rd | 2 dsBase-6.3.4/dsBase/man/qlsplineDS.Rd | 2 dsBase-6.3.4/dsBase/man/repDS.Rd | 2 dsBase-6.3.4/dsBase/man/rmDS.Rd | 2 dsBase-6.3.4/dsBase/man/table1DDS.Rd | 2 dsBase-6.3.4/dsBase/man/tableDS.Rd | 6 dsBase-6.3.4/dsBase/man/tableDS.assign.Rd | 6 dsBase-6.3.4/dsBase/man/tableDS2.Rd | 6 dsBase-6.3.4/dsBase/tests/testthat/test-smk-corTestDS.R | 3 68 files changed, 295 insertions(+), 175 deletions(-)
Title: Crafting Print-Ready Maps and Layered Visualizations
Description: Simplifying the creation of print-ready maps, this package offers a user-friendly interface derived from 'ggplot2' for handling OpenStreetMap data. It streamlines the map-making process, allowing users to focus on the story their maps tell. Transforming raw geospatial data into informative visualizations is made easy with simple features 'sf' geometries. Whether for urban planning, environmental studies, or impactful public presentations, this tool facilitates straightforward and effective map creation. Enhance the dissemination of spatial information with high-quality, narrative-driven visualizations!
Author: David Willinger [aut, cre, cph]
Maintainer: David Willinger <david.willinger@gmail.com>
Diff between cartographr versions 0.2.3 dated 2025-08-19 and 0.2.4 dated 2025-09-18
DESCRIPTION | 12 - MD5 | 19 - NEWS.md | 8 R/cartographr.R | 401 +++++++++++++++++++++++++------------- R/palette.R | 4 R/set.R | 10 R/utils.R | 153 +++++++++++++- README.md | 6 man/dot-make_border_ring.Rd |only tests/testthat/test-cartographr.R | 30 +- tests/testthat/test-utils.R | 4 11 files changed, 467 insertions(+), 180 deletions(-)
Title: Breeding Insight Genomics Functions for Polyploid and Diploid
Species
Description: Functions developed within Breeding Insight to analyze
diploid and polyploid breeding and genetic data. 'BIGr' provides the
ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs)
from diversity arrays technology missing allele discovery count (DArT MADC) files,
and manipulate genotype data for both diploid and polyploid species. It
also serves as the core dependency for the 'BIGapp' 'Shiny' app, which
provides a user-friendly interface for performing routine genotype
analysis tasks such as dosage calling, filtering, principal component analysis (PCA),
genome-wide association studies (GWAS), and
genomic prediction. For more details about the included 'breedTools'
functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and
the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.
Author: Alexander M. Sandercock [cre, aut],
Cristiane Taniguti [aut],
Josue Chinchilla-Vargas [aut],
Shufen Chen [ctb],
Manoj Sapkota [ctb],
Meng Lin [ctb],
Dongyan Zhao [ctb],
Cornell University [cph]
Maintainer: Alexander M. Sandercock <sandercock.alex@gmail.com>
Diff between BIGr versions 0.5.5 dated 2025-05-19 and 0.6.2 dated 2025-09-18
DESCRIPTION | 15 +++---- MD5 | 35 ++++++++++------ NAMESPACE | 7 +++ NEWS.md | 59 ++++++++++++++++----------- R/breedtools_functions.R | 4 - R/filterMADC.R |only R/madc2gmat.R |only R/madc2vcf_all.R | 26 +++++++----- R/madc2vcf_targets.R | 39 +++++++++++++++--- R/thinSNP.R |only R/updog2vcf.R | 34 ++++++++++++++-- R/utils.R | 7 ++- README.md | 1 inst/CITATION | 70 ++++++++++++++++++++++++--------- man/allele_freq_poly.Rd |only man/filterMADC.Rd |only man/madc2gmat.Rd |only man/solve_composition_poly.Rd |only man/thinSNP.Rd |only man/updog2vcf.Rd | 10 ++++ tests/testthat/test-filterMADC.R |only tests/testthat/test-madc2gmat.R |only tests/testthat/test-madc2vcf_targets.R | 55 +++++++++++++++++++++++++ tests/testthat/test-thinSNP.R |only 24 files changed, 277 insertions(+), 85 deletions(-)
Title: Vaccine Extension Package for ADaM in 'R' Asset Library
Description: Programming vaccine specific Clinical Data Interchange
Standards Consortium (CDISC) compliant Analysis Data Model (ADaM)
datasets in 'R'. Flat model is followed as per Center for Biologics
Evaluation and Research (CBER) guidelines for creating vaccine
specific domains. ADaM datasets are a mandatory part of any New Drug
or Biologics License Application submitted to the United States Food
and Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team (2021),
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
The package is an extension package of the 'admiral' package.
Author: Arjun Rubalingam [aut, cre],
Sukalpo Saha [aut, ctb],
Ben Straub [aut],
Vikram S [aut],
Dhivya Kanagaraj [aut],
Federico Baratin [aut],
Yamini Purna Bollu [aut],
Ilse Augustyns [aut],
Kalyani Bodicherla [aut],
Hilde Delanghe [aut],
Lee Armishaw [aut] [...truncated...]
Maintainer: Arjun Rubalingam <arjun.rubalingam@pfizer.com>
Diff between admiralvaccine versions 0.4.0 dated 2025-01-31 and 0.5.0 dated 2025-09-18
DESCRIPTION | 40 +++++++++++++-------------- MD5 | 55 +++++++++++++++++++------------------ NEWS.md | 10 ++++++ R/derive_diam_to_sev_records.R | 4 +- R/derive_fever_records.R | 2 - R/derive_vars_crit.R | 2 - R/derive_vars_merged_vaccine.R | 4 +- R/derive_vars_params.R | 2 - R/derive_vars_vaxdt.R | 2 - README.md | 22 ++++----------- build/vignette.rds |binary inst/doc/adce.html | 2 - inst/doc/adface.R | 3 +- inst/doc/adface.Rmd | 3 +- inst/doc/adface.html | 30 +++++++++++--------- inst/doc/adis.html | 2 - inst/doc/admiralvaccine.html | 2 - inst/doc/adsl.R | 6 ++-- inst/doc/adsl.Rmd | 6 ++-- inst/doc/adsl.html | 60 +++++++++++++++++++++-------------------- inst/templates/ad_adface.R | 3 +- inst/templates/ad_adis.R | 9 ++++-- inst/templates/ad_adsl.R | 6 ++-- man/admiralvaccine-package.Rd | 4 +- man/figures/gsk_logo.png |only man/figures/jnj_logo.png |only man/figures/pfizer_logo.png |only tests/testthat.R | 6 +--- vignettes/adface.Rmd | 3 +- vignettes/adsl.Rmd | 6 ++-- 30 files changed, 159 insertions(+), 135 deletions(-)
More information about admiralvaccine at CRAN
Permanent link
Title: Flexible Multidimensional Scaling and 'smacof' Extensions
Description: Flexible multidimensional scaling (MDS) methods and extensions to the package 'smacof'. This package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models. These are: Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459) with powers, Sammon mapping (Sammon, 1969, <doi:10.1109/T-C.1969.222678>) with ratio and interval optimal scaling, Multiscale MDS (Ramsay, 1977, <doi:10.1007/BF02294052>) with ratio and interval optimal scaling, s-stress MDS (ALSCAL; Takane, Young & De Leeuw, 1977, <doi:10.1007/BF02293745>) with ratio and interval optimal scaling, elastic scaling (McGee, 1966, <doi:10.1111/j.2044-8317.1966.tb00367.x>) with ratio and interval optimal scaling, r-stress MDS (De Leeuw, Groenen & Mair, 2016, <https://rpubs.com/deleeuw/142619>) with ratio, interval, splines and nonmetric optimal scaling, power-stress MDS (POST-MDS; Buja & Swayne, 2002 <doi: [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Jan de Leeuw [aut],
Lisha Chen [aut],
Patrick Mair [aut]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between smacofx versions 1.21-1 dated 2025-07-07 and 1.22-0 dated 2025-09-18
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 2 ++ NEWS | 4 ++++ R/alignplot.R |only man/alignplot.Rd |only 6 files changed, 14 insertions(+), 6 deletions(-)
Title: Create Visualisations for BART Models
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut],
Claus Wilke [ctb]
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Diff between bartMan versions 0.2.0 dated 2025-08-22 and 0.2.1 dated 2025-09-18
DESCRIPTION | 15 +- MD5 | 29 ++--- NAMESPACE | 15 -- R/VSUP.R | 60 ++++------ R/bartDiag.R | 277 ++++++++++++++++++++++++++++++++----------------- R/generic_functions.R | 3 R/globals.R | 2 R/plotSingleTree.R | 8 + R/plot_all_trees.R | 22 +++ R/treeBarPlot.R | 37 +++++- R/vimpPlot.R | 35 +++--- R/vintPlot.R | 18 +-- R/viviBartMatrix.R | 12 ++ man/bartDiag.Rd | 4 man/bartReorder.Rd |only man/bivariate_scale.Rd | 4 16 files changed, 334 insertions(+), 207 deletions(-)
Title: Monte Carlo for Classical Ising Model
Description: Classical Ising Model is a land mark system in statistical physics.The model explains the physics of spin glasses and magnetic materials, and cooperative phenomenon in general, for example phase transitions and neural networks.This package provides utilities to simulate one dimensional Ising Model with Metropolis and Glauber Monte Carlo with single flip dynamics in periodic boundary conditions. Utility functions for exact solutions are provided.
Author: Mehmet Suzen [aut, cre]
Maintainer: Mehmet Suzen <mehmet.suzen@physics.org>
Diff between isingLenzMC versions 0.2.5 dated 2016-07-01 and 0.2.7 dated 2025-09-18
isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/analyseData.R |only isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/functions.R |only isingLenzMC-0.2.5/isingLenzMC/inst/examples/powerLawErgodicity/generateData.R |only isingLenzMC-0.2.7/isingLenzMC/DESCRIPTION | 8 +- isingLenzMC-0.2.7/isingLenzMC/MD5 | 18 ++--- isingLenzMC-0.2.7/isingLenzMC/NAMESPACE | 2 isingLenzMC-0.2.7/isingLenzMC/README.md | 34 +++++++++- isingLenzMC-0.2.7/isingLenzMC/build/vignette.rds |binary isingLenzMC-0.2.7/isingLenzMC/inst/CITATION | 3 isingLenzMC-0.2.7/isingLenzMC/inst/doc/isingLenzMC.pdf |binary isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/README.md |only isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/data_analysis.ipynb |only isingLenzMC-0.2.7/isingLenzMC/inst/examples/powerLawErgodicity/data_generate.ipynb |only 13 files changed, 46 insertions(+), 19 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 1.4-0 dated 2019-03-14 and 1.5-0 dated 2025-09-18
elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.R |only elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.Rnw |only elliptic-1.4-0/elliptic/inst/doc/ellipticpaper.pdf |only elliptic-1.4-0/elliptic/tests/aaa.R |only elliptic-1.4-0/elliptic/vignettes/ellipticpaper.Rnw |only elliptic-1.4-0/elliptic/vignettes/semicircular_path.pdf |only elliptic-1.4-0/elliptic/vignettes/semicircular_path.svg |only elliptic-1.5-0/elliptic/DESCRIPTION | 14 elliptic-1.5-0/elliptic/MD5 | 81 ++- elliptic-1.5-0/elliptic/NEWS.md |only elliptic-1.5-0/elliptic/R/elliptic.R | 98 ++-- elliptic-1.5-0/elliptic/README.md |only elliptic-1.5-0/elliptic/build/partial.rdb |binary elliptic-1.5-0/elliptic/build/vignette.rds |binary elliptic-1.5-0/elliptic/inst/CITATION | 19 elliptic-1.5-0/elliptic/inst/doc/elliptic.R |only elliptic-1.5-0/elliptic/inst/doc/elliptic.Rnw |only elliptic-1.5-0/elliptic/inst/doc/elliptic.pdf |only elliptic-1.5-0/elliptic/inst/doc/residuetheorem.R | 62 +-- elliptic-1.5-0/elliptic/inst/doc/residuetheorem.Rnw | 325 ++++++++++------ elliptic-1.5-0/elliptic/inst/doc/residuetheorem.pdf |binary elliptic-1.5-0/elliptic/inst/semicircular_path.pdf |only elliptic-1.5-0/elliptic/inst/semicircular_path.svg |only elliptic-1.5-0/elliptic/man/J.Rd | 24 - elliptic-1.5-0/elliptic/man/K.fun.Rd | 4 elliptic-1.5-0/elliptic/man/as.primitive.Rd | 8 elliptic-1.5-0/elliptic/man/ck.Rd | 14 elliptic-1.5-0/elliptic/man/divisor.Rd | 2 elliptic-1.5-0/elliptic/man/elliptic-package.Rd | 44 -- elliptic-1.5-0/elliptic/man/eta.Rd | 4 elliptic-1.5-0/elliptic/man/figures |only elliptic-1.5-0/elliptic/man/fpp.Rd | 15 elliptic-1.5-0/elliptic/man/half.periods.Rd | 6 elliptic-1.5-0/elliptic/man/latplot.Rd | 6 elliptic-1.5-0/elliptic/man/misc.Rd | 1 elliptic-1.5-0/elliptic/man/myintegrate.Rd | 73 +-- elliptic-1.5-0/elliptic/man/newton_raphson.Rd | 16 elliptic-1.5-0/elliptic/man/p1.tau.Rd | 2 elliptic-1.5-0/elliptic/man/parameters.Rd | 10 elliptic-1.5-0/elliptic/man/sn.Rd | 4 elliptic-1.5-0/elliptic/man/theta.Rd | 33 - elliptic-1.5-0/elliptic/man/theta.neville.Rd | 22 + elliptic-1.5-0/elliptic/man/theta1dash.Rd | 11 elliptic-1.5-0/elliptic/man/unimodular.Rd | 2 elliptic-1.5-0/elliptic/man/view.Rd | 2 elliptic-1.5-0/elliptic/tests/testthat |only elliptic-1.5-0/elliptic/tests/testthat.R |only elliptic-1.5-0/elliptic/vignettes/elliptic.Rnw |only elliptic-1.5-0/elliptic/vignettes/elliptic.bib | 38 + elliptic-1.5-0/elliptic/vignettes/residuetheorem.Rnw | 325 ++++++++++------ 50 files changed, 745 insertions(+), 520 deletions(-)
More information about CompositionalClust at CRAN
Permanent link
Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Author: Lars Snipen [aut, cre],
Kristian Hovde Liland [aut]
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between microseq versions 2.1.6 dated 2023-08-21 and 2.1.7 dated 2025-09-18
microseq-2.1.6/microseq/build |only microseq-2.1.6/microseq/inst/doc |only microseq-2.1.6/microseq/man/microseq-package.Rd |only microseq-2.1.6/microseq/vignettes |only microseq-2.1.7/microseq/DESCRIPTION | 26 - microseq-2.1.7/microseq/MD5 | 36 - microseq-2.1.7/microseq/R/fasta.R | 202 ++++---- microseq-2.1.7/microseq/R/fastq.R | 202 ++++---- microseq-2.1.7/microseq/R/gff.R | 352 +++++++------- microseq-2.1.7/microseq/R/microseq-package.R | 45 - microseq-2.1.7/microseq/R/multialign.R | 438 +++++++++--------- microseq-2.1.7/microseq/R/orfs.R | 570 ++++++++++++------------ microseq-2.1.7/microseq/man/findOrfs.Rd | 4 microseq-2.1.7/microseq/man/gff2fasta.Rd | 4 microseq-2.1.7/microseq/man/lorfs.Rd | 2 microseq-2.1.7/microseq/man/microseq.Rd |only microseq-2.1.7/microseq/man/msalign.Rd | 4 microseq-2.1.7/microseq/man/readFasta.Rd | 12 microseq-2.1.7/microseq/man/readFastq.Rd | 8 microseq-2.1.7/microseq/man/readGFF.Rd | 4 20 files changed, 955 insertions(+), 954 deletions(-)
Title: Downscaling Species Occupancy
Description: Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Author: Charles Marsh [aut, cre, cph]
Maintainer: Charles Marsh <charlie.marsh@mailbox.org>
Diff between downscale versions 5.0.0 dated 2023-05-31 and 5.1.3 dated 2025-09-18
downscale-5.0.0/downscale/man/figures/Thumbs.db |only downscale-5.1.3/downscale/DESCRIPTION | 11 downscale-5.1.3/downscale/MD5 | 29 downscale-5.1.3/downscale/NEWS.md | 16 downscale-5.1.3/downscale/R/checkInputs.R | 10 downscale-5.1.3/downscale/R/predict.downscale.R | 7 downscale-5.1.3/downscale/build/vignette.rds |binary downscale-5.1.3/downscale/inst/doc/Downscaling.R | 24 downscale-5.1.3/downscale/inst/doc/Downscaling.html | 949 +++++++++----------- downscale-5.1.3/downscale/inst/doc/Upgraining.R | 22 downscale-5.1.3/downscale/inst/doc/Upgraining.html | 99 +- downscale-5.1.3/downscale/man/Downscale-package.Rd | 9 downscale-5.1.3/downscale/man/downscale.Rd | 4 downscale-5.1.3/downscale/man/ensemble.downscale.Rd | 4 downscale-5.1.3/downscale/man/hui.downscale.Rd | 2 downscale-5.1.3/downscale/man/predict.downscale.Rd | 2 16 files changed, 598 insertions(+), 590 deletions(-)
Title: Automatic Database Normalisation for Data Frames
Description: Automatic normalisation of a data frame to third normal form, with
the intention of easing the process of data cleaning. (Usage to design your
actual database for you is not advised.)
Originally inspired by the 'AutoNormalize' library for 'Python' by 'Alteryx'
(<https://github.com/alteryx/autonormalize>), with various changes and
improvements. Automatic discovery of functional or approximate dependencies,
normalisation based on those, and plotting of the resulting "database" via
'Graphviz', with options to exclude some attributes at discovery time, or
remove discovered dependencies at normalisation time.
Author: Mark Webster [aut, cre]
Maintainer: Mark Webster <markwebster204@yahoo.co.uk>
Diff between autodb versions 3.0.0 dated 2025-06-25 and 3.1.0 dated 2025-09-18
DESCRIPTION | 6 - MD5 | 27 ++-- NEWS.md | 7 + R/autoref.r | 91 ++++++++++++---- R/database.r | 56 +++++++--- R/decompose.r | 9 + R/plot.r | 250 ++++++++++++++++++++++++++++++++++++++++++--- inst/doc/autodb.html | 144 ++++++++++++------------- man/d2.Rd |only man/d2.data.frame.Rd |only man/d2.relation_schema.Rd |only man/database.Rd | 23 +++- man/gv.relation.Rd | 58 +++++----- man/gv.relation_schema.Rd | 62 +++++------ tests/testthat/setup.r | 2 tests/testthat/test-plot.r | 167 ++++++++++++++++++++++++++++++ 16 files changed, 699 insertions(+), 203 deletions(-)
Title: Procedures Related to the Zadeh's Extension Principle for Fuzzy
Data
Description: Procedures for calculation, plotting, animation, and approximation of the outputs for fuzzy numbers (see A.I. Ban, L. Coroianu, P. Grzegorzewski "Fuzzy Numbers: Approximations, Ranking and Applications" (2015)) based on the Zadeh's Extension Principle (see de Barros, L.C., Bassanezi, R.C., Lodwick, W.A. (2017) <doi:10.1007/978-3-662-53324-6_2>).
Author: Maciej Romaniuk [cre, aut] ),
Abbas Parchami [aut] ),
Przemyslaw Grzegorzewski [ctb] )
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between ZEP versions 0.1.5 dated 2025-06-22 and 0.2.0 dated 2025-09-18
DESCRIPTION | 10 +++---- MD5 | 30 +++++++++++++++------ NAMESPACE | 1 R/AnimateZFunction.R |only R/ApplyZFunction.R | 9 +++++- R/ApproximationAmbValPres.R |only R/FuzzyApproximation.R | 54 +++++++++++++++++++++++++++++++++++---- R/PlotZFunction.R | 9 +++++- R/approximationMehodsInside.R | 2 - R/utils.R | 2 - man/AnimateZFunction.Rd |only man/FuzzyApproximation.Rd | 7 +++-- man/approximationMehodsInside.Rd | 2 - tests |only 14 files changed, 98 insertions(+), 28 deletions(-)
Title: A Bridge Between 'keras' and 'tidymodels'
Description: Provides a seamless bridge between 'keras' and the 'tidymodels'
frameworks. It allows for the dynamic creation of 'parsnip' model
specifications for 'keras' models.
Author: David Diaz [aut, cre]
Maintainer: David Diaz <daviddrsch@gmail.com>
Diff between kerasnip versions 0.0.1 dated 2025-09-03 and 0.0.3 dated 2025-09-18
kerasnip-0.0.1/kerasnip/tests/testthat/helper_keras.R |only kerasnip-0.0.3/kerasnip/DESCRIPTION | 8 kerasnip-0.0.3/kerasnip/MD5 | 84 kerasnip-0.0.3/kerasnip/NAMESPACE | 1 kerasnip-0.0.3/kerasnip/R/compile_keras_grid.R | 678 ++-- kerasnip-0.0.3/kerasnip/R/create_keras_functional_spec.R | 281 - kerasnip-0.0.3/kerasnip/R/create_keras_sequential_spec.R | 245 - kerasnip-0.0.3/kerasnip/R/dials.R |only kerasnip-0.0.3/kerasnip/R/generic_functional_fit.R | 233 - kerasnip-0.0.3/kerasnip/R/generic_sequential_fit.R | 233 - kerasnip-0.0.3/kerasnip/R/keras_tools.R | 294 - kerasnip-0.0.3/kerasnip/R/register_model_args.R | 21 kerasnip-0.0.3/kerasnip/R/remove_keras_spec.R | 190 - kerasnip-0.0.3/kerasnip/R/utils.R | 824 ++--- kerasnip-0.0.3/kerasnip/README.md | 6 kerasnip-0.0.3/kerasnip/build/vignette.rds |binary kerasnip-0.0.3/kerasnip/inst/doc/applications.R |only kerasnip-0.0.3/kerasnip/inst/doc/applications.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/applications.html |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.R |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/autoplot_uniqueness.html |only kerasnip-0.0.3/kerasnip/inst/doc/functional_api.html | 49 kerasnip-0.0.3/kerasnip/inst/doc/getting_started.html | 222 - kerasnip-0.0.3/kerasnip/inst/doc/sequential_model.html | 6 kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.R |only kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.Rmd |only kerasnip-0.0.3/kerasnip/inst/doc/tuning_fit_compile_args.html |only kerasnip-0.0.3/kerasnip/inst/doc/workflows_functional.html | 511 +-- kerasnip-0.0.3/kerasnip/inst/doc/workflows_sequential.html | 1570 +++++----- kerasnip-0.0.3/kerasnip/man/compile_keras_grid.Rd | 35 kerasnip-0.0.3/kerasnip/man/create_keras_functional_spec.Rd | 1 kerasnip-0.0.3/kerasnip/man/create_keras_sequential_spec.Rd | 5 kerasnip-0.0.3/kerasnip/man/extract_valid_grid.Rd | 58 kerasnip-0.0.3/kerasnip/man/generic_functional_fit.Rd | 9 kerasnip-0.0.3/kerasnip/man/generic_sequential_fit.Rd | 9 kerasnip-0.0.3/kerasnip/man/inform_errors.Rd | 57 kerasnip-0.0.3/kerasnip/man/keras_evaluate.Rd | 32 kerasnip-0.0.3/kerasnip/man/loss_function_keras.Rd | 38 kerasnip-0.0.3/kerasnip/man/model_exists.Rd |only kerasnip-0.0.3/kerasnip/man/optimizer_function.Rd | 38 kerasnip-0.0.3/kerasnip/man/remove_keras_spec.Rd | 2 kerasnip-0.0.3/kerasnip/tests/testthat/helper_tests.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_autoplot_uniqueness.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_fit_compile_tuning.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_func_classification.R | 587 +-- kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_func_regression.R | 16 kerasnip-0.0.3/kerasnip/tests/testthat/test_e2e_spec_removal.R | 41 kerasnip-0.0.3/kerasnip/tests/testthat/test_generic_fit_helpers.R |only kerasnip-0.0.3/kerasnip/tests/testthat/test_postprocessing_helpers.R |only kerasnip-0.0.3/kerasnip/vignettes/applications.Rmd |only kerasnip-0.0.3/kerasnip/vignettes/autoplot_uniqueness.Rmd |only kerasnip-0.0.3/kerasnip/vignettes/tuning_fit_compile_args.Rmd |only 53 files changed, 3356 insertions(+), 3028 deletions(-)
Title: 'shiny' Application for Statistical Test Assumption Checking and
Guidance
Description: A 'shiny' application to assess statistical assumptions and guide users toward appropriate tests. The app is designed for researchers with minimal statistical training and provides diagnostics, plots, and test recommendations for a wide range of analyses. Many statistical assumptions are implemented using the package 'rstatix' (Kassambara, 2019) <doi:10.32614/CRAN.package.rstatix> and 'performance' (Lüdecke et al., 2021) <doi:10.21105/joss.03139>.
Author: Ahmed Bargheet [aut, cre]
Maintainer: Ahmed Bargheet <ahmed.bargheet@yahoo.com>
Diff between AssumpSure versions 1.1.0 dated 2025-08-18 and 1.1.1 dated 2025-09-18
DESCRIPTION | 11 +- MD5 | 9 - NEWS.md | 15 ++ R/launch_app.R | 14 ++ R/zzz.R |only inst/app/app.R | 306 +++++++++++++++++++++++++++++++++++++++++++++------------ 6 files changed, 285 insertions(+), 70 deletions(-)
Title: Create Hexagon Sticker in R
Description: Helper functions for creating reproducible hexagon sticker purely in R.
Author: Guangchuang Yu [aut, cre],
Laurent Gatto [ctb],
Johannes Rainer [ctb],
Sebastian Gibb [ctb],
Robert Corty [ctb],
Thomas Neitmann [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between hexSticker versions 0.4.9 dated 2020-12-05 and 0.5.0 dated 2025-09-18
DESCRIPTION | 11 MD5 | 30 - NAMESPACE | 77 +-- NEWS.md | 132 ++--- R/as-raster.R | 42 - R/hexSticker-package.R |only R/sticker.R | 767 ++++++++++++++++---------------- inst/fonts/Aller/Aller_Font_License.txt | 182 +++---- man/geom_hexagon.Rd | 48 +- man/geom_pkgname.Rd | 86 +-- man/geom_url.Rd | 92 +-- man/hexSticker-package.Rd |only man/reexports.Rd | 40 - man/save_sticker.Rd | 42 - man/sticker.Rd | 264 +++++------ man/sticker_dev.Rd | 34 - man/theme_sticker.Rd | 44 - 17 files changed, 949 insertions(+), 942 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for
performance. Offers convenient utilities for working with in-memory and
larger-than-memory data while retaining full 'dplyr' compatibility.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 1.1.1 dated 2025-07-30 and 1.1.2 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 37 +++++++++++++++++++------------------ NEWS.md | 15 +++++++++++++++ R/aaa-meta.R | 1 + R/bisect_reduce.R |only R/duckplyr_df.R | 8 ++++++-- R/read_file_duckdb.R | 15 +++++++++------ R/relational-duckdb.R | 4 ++-- R/translate.R | 14 ++++++++++---- inst/doc/developers.html | 8 ++++---- inst/doc/duckdb.html | 10 +++++----- inst/doc/extend.html | 4 ++-- inst/doc/fallback.html | 2 +- inst/doc/large.html | 4 ++-- inst/doc/limits.html | 8 ++++---- inst/doc/prudence.Rmd | 18 +++++++++++++++++- inst/doc/prudence.html | 28 ++++++++++++++++++++++------ tests/testthat/helper-taxi.R | 2 ++ tests/testthat/test-fallback.R | 20 ++++++++++++++++++++ vignettes/prudence.Rmd | 18 +++++++++++++++++- 20 files changed, 162 insertions(+), 62 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-27 0.9-2.2
2025-07-23 0.9-2.1
2025-07-22 0.9-2
2025-01-15 0.9-1
2024-10-02 0.9-0.4
2024-08-27 0.9-0.1
2024-08-23 0.9-0
2023-11-28 0.8-0.1
2023-06-23 0.8-0
2023-02-13 0.7-4.3
2023-02-02 0.7-4.2
2023-01-17 0.7-4.1
2023-01-14 0.7-4
2023-01-12 0.7-3.1
2023-01-09 0.7-3
2023-01-06 0.7-2
2022-09-22 0.7-0
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parametric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.4.0 dated 2025-02-24 and 1.5.0 dated 2025-09-18
DESCRIPTION | 15 - MD5 | 166 ++++++----- NAMESPACE | 4 NEWS.md | 34 ++ R/ESS.R | 20 - R/WeightIt-package.R | 1 R/anova.glm_weightit.R | 48 +-- R/as.weightit.R | 50 ++- R/calibrate.R | 29 +- R/dist_functions.R | 21 - R/functions_for_processing.R | 416 +++++++++++++++++------------ R/get_w_from_ps.R | 40 +- R/glm_weightit-methods.R | 163 +++++------ R/glm_weightit.R | 33 +- R/glm_weightit_helpers.R | 110 ++++--- R/make_full_rank.R | 36 +- R/multinom_weightit.R | 52 ++- R/ordinal_weightit.R | 35 +- R/plot.weightit.R | 17 - R/predict.glm_weightit.R | 110 ++++++- R/sbps.R | 70 ++--- R/summary.weightit.R | 268 ++++++++++--------- R/treat.R |only R/trim.R | 188 ++++++------- R/utils.R | 444 ++++++++++++++++++++----------- R/weightit.R | 164 +++++------ R/weightit.fit.R | 119 +++----- R/weightit2bart.R | 104 ++++--- R/weightit2cbps.R | 532 ++++++++++++++++++++------------------ R/weightit2ebal.R | 421 +++++++++++++++++++++++------- R/weightit2energy.R | 447 +++++++++++++++++++++---------- R/weightit2gbm.R | 278 ++++++++++--------- R/weightit2glm.R | 256 +++++++++--------- R/weightit2ipt.R | 128 ++++----- R/weightit2npcbps.R | 85 +++--- R/weightit2optweight.R | 470 ++++++++++++++++----------------- R/weightit2ps.R | 22 - R/weightit2super.R | 129 +++++---- R/weightit2user.R | 39 +- R/weightitMSM.R | 228 +++++++--------- R/weightit_methods.R | 45 +-- README.md | 149 +++++----- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/WeightIt.Rmd | 63 ++-- inst/doc/WeightIt.html | 235 ++++++++-------- inst/doc/estimating-effects.Rmd | 48 +-- inst/doc/estimating-effects.html | 469 +++++++++++++++++---------------- inst/doc/installing-packages.Rmd | 74 ++--- inst/doc/installing-packages.html | 203 +++++++------- man/ESS.Rd | 14 - man/anova.glm_weightit.Rd | 7 man/as.weightit.Rd | 6 man/calibrate.Rd | 16 - man/dot-weightit_methods.Rd | 13 man/get_w_from_ps.Rd | 5 man/glm_weightit-methods.Rd | 4 man/glm_weightit.Rd | 19 - man/make_full_rank.Rd | 14 - man/method_bart.Rd | 48 ++- man/method_cbps.Rd | 36 +- man/method_ebal.Rd | 66 ++-- man/method_energy.Rd | 82 +++-- man/method_gbm.Rd | 143 +++++----- man/method_glm.Rd | 62 +--- man/method_ipt.Rd | 29 +- man/method_npcbps.Rd | 36 +- man/method_optweight.Rd | 97 +++--- man/method_super.Rd | 53 ++- man/method_user.Rd | 20 - man/plot.weightit.Rd | 8 man/predict.glm_weightit.Rd | 21 - man/sbps.Rd | 3 man/summary.weightit.Rd | 33 +- man/trim.Rd | 27 - man/weightit.Rd | 75 +---- man/weightit.fit.Rd | 30 -- man/weightitMSM.Rd | 63 +--- tests/testthat/helpers.R | 2 tests/testthat/test-moments.R |only tests/testthat/test-update.R | 62 ++-- vignettes/WeightIt.Rmd | 63 ++-- vignettes/estimating-effects.Rmd | 48 +-- vignettes/installing-packages.Rmd | 74 ++--- vignettes/references.bib | 92 ++---- 85 files changed, 4648 insertions(+), 3801 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] ,
Andreas Alfons [aut],
Gregor de Cillia [aut],
Bernd Prantner [ctb],
Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 6.2.2 dated 2022-08-25 and 6.2.6 dated 2025-09-18
DESCRIPTION | 20 MD5 | 95 +- NAMESPACE | 11 NEWS.md | 9 R/VIM-package.R | 16 R/evaluation.R | 1 R/gowerD.R | 14 R/hotdeck.R | 3 R/imputeRobust.R |only R/imputeRobustChain.R |only R/irmi.R | 20 R/kNN.R | 11 R/matchImpute.R | 6 R/rangerImpute.R | 34 R/regressionImp.R | 3 R/xgboostImpute.R |only R/zzz.R | 5 build/vignette.rds |binary inst/doc/VIM.R | 2 inst/doc/VIM.html | 40 - inst/doc/VisualImp.R | 7 inst/doc/VisualImp.Rmd | 5 inst/doc/VisualImp.html | 173 ++--- inst/doc/donorImp.R | 13 inst/doc/donorImp.Rmd | 7 inst/doc/donorImp.html | 1267 +++++++++++------------------------- inst/doc/irmi.R | 11 inst/doc/irmi.Rmd | 7 inst/doc/irmi.html | 1261 +++++++++++------------------------- inst/doc/modelImp.R | 13 inst/doc/modelImp.Rmd | 7 inst/doc/modelImp.html | 1275 +++++++++++-------------------------- inst/tinytest/test_matchImpute.R |only inst/tinytest/test_xgboostImpute.R |only man/VIM-package.Rd | 19 man/hotdeck.Rd | 3 man/impPCA.Rd | 3 man/imputeRobust.Rd |only man/imputeRobustChain.Rd |only man/irmi.Rd | 10 man/kNN.Rd | 6 man/matchImpute.Rd | 3 man/medianSamp.Rd | 3 man/prepare.Rd | 4 man/rangerImpute.Rd | 3 man/regressionImp.Rd | 6 man/sampleCat.Rd | 3 man/xgboostImpute.Rd |only tests/test_imputeRobust.R |only vignettes/VisualImp.Rmd | 5 vignettes/donorImp.Rmd | 7 vignettes/irmi.Rmd | 7 vignettes/modelImp.Rmd | 7 53 files changed, 1532 insertions(+), 2893 deletions(-)
Title: Manual Tours, Manual Control of Dynamic Projections of Numeric
Multivariate Data
Description: Data visualization tours animates linear projection
of multivariate data as its basis (ie. orientation) changes. The 'spinifex'
packages generates paths for manual tours by manipulating the contribution of
a single variable at a time Cook & Buja (1997)
<doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand
(random walk) and guided (optimizing some objective function) are available
in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>.
'spinifex' builds on 'tourr' and can render tours with 'gganimate' and
'plotly' graphics, and allows for exporting as an .html widget and as an .gif,
respectively. This work is fully discussed in Spyrison & Cook (2020)
<doi:10.32614/RJ-2020-027>.
Author: Nicholas Spyrison [aut, cre] ,
Dianne Cook [aut, ths]
Maintainer: Nicholas Spyrison <spyrison@gmail.com>
Diff between spinifex versions 0.3.9 dated 2025-08-22 and 0.3.10 dated 2025-09-18
DESCRIPTION | 6 +- MD5 | 23 ++++---- NAMESPACE | 1 NEWS.md | 8 ++ R/0_util.r | 63 ++++++++++++++++++++++ R/2_ggproto_visualize.r | 37 ++++++------- inst/WORDLIST | 79 +++++++++++----------------- inst/doc/getting_started_with_spinifex.html | 10 +-- inst/doc/ggproto_api.Rmd | 2 inst/doc/ggproto_api.html | 10 +-- man/ide.Rd |only tests/testthat/test-2_ggproto_visualize.r | 50 ++++++++--------- vignettes/ggproto_api.Rmd | 2 13 files changed, 173 insertions(+), 118 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system to
implement a complete data-to-decisions, reproducible workflow.
The core components facilitate the development of modular pieces,
and enable the user to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the within-project dependencies.
The suggested package 'NLMR' can be installed from the repository
(<https://PredictiveEcology.r-universe.dev>).
Author: Alex M Chubaty [aut] ,
Eliot J B McIntire [aut, cre] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between SpaDES.core versions 2.1.6 dated 2025-09-02 and 2.1.8 dated 2025-09-18
DESCRIPTION | 10 MD5 | 576 NAMESPACE | 968 - NEWS.md | 1288 - R/Plots.R | 948 - R/cache.R | 2583 +-- R/check.R | 512 R/checkpoint.R | 258 R/code-checking.R | 1338 - R/convertToPackage.R | 842 - R/copy.R | 254 R/debugging.R | 78 R/downloadData.R | 646 R/environment.R | 34 R/helpers.R | 818 - R/load.R | 814 - R/memory-leaks.R | 156 R/memory.R | 512 R/misc-methods.R | 864 - R/modActiveBinding.R | 144 R/module-define.R | 1598 +- R/module-dependencies-class.R | 484 R/module-dependencies-methods.R | 676 R/module-param-check.R | 238 R/module-repository.R | 856 - R/module-template.R | 1844 +- R/moduleCoverage.R | 222 R/moduleMetadata.R | 656 R/objectSynonyms.R | 332 R/options.R | 472 R/paths.R | 433 R/plotting-diagrams.R | 1146 - R/plotting.R | 182 R/priority.R | 82 R/progress.R | 260 R/project-template.R | 194 R/reexports.R | 50 R/restart.R | 1132 - R/save.R | 532 R/saveLoadSimList.R | 1142 - R/simList-accessors.R | 6976 +++++----- R/simList-class.R | 544 R/simulation-parseModule.R | 1290 - R/simulation-simInit.R | 3814 ++--- R/simulation-spades.R | 4952 +++---- R/spades-classes.R | 36 R/spades-core-deprecated.R | 90 R/spades-core-package.R | 998 - R/suppliedElsewhere.R | 276 R/times.R | 910 - R/zzz.R | 208 README.md | 130 build/vignette.rds |binary inst/WORDLIST | 207 inst/doc/i-introduction.R | 142 inst/doc/i-introduction.Rmd | 724 - inst/doc/i-introduction.html | 2000 +- inst/doc/ii-modules.R | 608 inst/doc/ii-modules.Rmd | 1574 +- inst/doc/ii-modules.html | 3229 ++-- inst/doc/iii-cache.R | 226 inst/doc/iii-cache.Rmd | 538 inst/doc/iii-cache.html | 1765 +- inst/doc/iv-advanced.R | 26 inst/doc/iv-advanced.Rmd | 104 inst/doc/iv-advanced.html | 848 - inst/doc/v-automated-testing.R | 16 inst/doc/v-automated-testing.Rmd | 174 inst/doc/v-automated-testing.html | 926 - inst/examples/example_inputs.R | 144 inst/examples/example_moduleMetadata.R | 46 inst/examples/example_moduleParamsInputsOuputs.R | 26 inst/examples/example_moduleVersion.R | 34 inst/examples/example_outputs.R | 130 inst/extdata/abundRaster.tif.aux.xml | 10 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R | 64 inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.Rmd | 92 inst/sampleModules/caribouMovement/caribouMovement.R | 342 inst/sampleModules/fireSpread/fireSpread.R | 400 inst/sampleModules/randomLandscapes/randomLandscapes.R | 318 inst/templates/LICENSE.template | 16 inst/templates/NEWS.template | 6 inst/templates/README.template | 16 inst/templates/citation.bib.template | 16 inst/templates/data-gitignore.template | 12 inst/templates/module.R.template | 42 inst/templates/module.Rmd.template | 216 inst/templates/module.inputObjects.R.template | 50 inst/templates/moduleEvent1.R.template | 22 inst/templates/moduleEvent2.R.template | 22 inst/templates/moduleInit.R.template | 16 inst/templates/modulePartialEvents.R.template | 326 inst/templates/modulePartialMeta.R.template | 60 inst/templates/moduleSave.R.template | 20 inst/templates/moduledoEvent.R.template | 146 inst/templates/moduleggplotFn.R.template | 10 inst/templates/moduleplotFn.R.template | 22 inst/templates/project.R.template | 72 inst/templates/render-module-rmd.yaml.template | 154 inst/templates/test-template.R.template | 148 inst/templates/unitTests.R.template | 16 man/Copy.Rd | 98 man/FilterRecursive.Rd | 34 man/Plot.Rd | 302 man/Plots.Rd | 338 man/SpaDES.core-package.Rd | 1064 - 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Title: Global Sensitivity Analysis of Model Outputs and Importance
Measures
Description: A collection of functions for sensitivity analysis of model outputs (factor screening, global sensitivity analysis and robustness analysis), for variable importance measures of data, as well as for interpretability of machine learning models. Most of the functions have to be applied on scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss [aut, cre],
Sebastien Da Veiga [aut],
Alexandre Janon [aut],
Gilles Pujol [aut]
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.30.1 dated 2024-08-28 and 1.30.2 dated 2025-09-18
DESCRIPTION | 6 MD5 | 26 - NEWS | 22 + R/lmg.R | 8 R/morris.R | 2 R/pmvd.R | 8 R/sensiHSIC.R | 601 ++++++++++++++++++++++++++++--------- R/testHSIC.R | 620 +++++++++++++++++++++++++++++++++++---- man/PLIsuperquantile_multivar.Rd | 2 man/sensiHSIC.Rd | 139 +++++--- man/testHSIC.Rd | 253 ++++++++++++--- man/testmodels.Rd | 2 src/RcppExports.cpp | 1 src/nested.cpp | 1 14 files changed, 1337 insertions(+), 354 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.4.3 dated 2025-05-13 and 3.4.4 dated 2025-09-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/labkey.deleteRows.R | 1 + R/labkey.experiment.R | 4 ++++ R/labkey.importRows.R | 1 + R/labkey.insertRows.R | 1 + R/labkey.updateRows.R | 1 + R/makeDF.R | 2 +- man/Rlabkey-package.Rd | 4 ++-- 10 files changed, 28 insertions(+), 16 deletions(-)
Title: NFL Logo Plots in 'ggplot2' and 'gt'
Description: A set of functions to visualize National Football League
analysis in 'ggplot2' plots and 'gt' tables.
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflplotR versions 1.4.0 dated 2024-08-21 and 1.5.0 dated 2025-09-18
DESCRIPTION | 21 LICENSE | 4 MD5 | 136 +- NAMESPACE | 89 - NEWS.md | 9 R/build_grobs.R | 188 +-- R/geom_lines.R | 48 R/geom_nfl_headshots.R | 277 ++--- R/geom_nfl_logos.R | 284 ++--- R/geom_nfl_wordmarks.R | 272 ++--- R/ggpreview.R | 134 +- R/gt_nfl.R | 40 R/nfl_team_factors.R | 184 +-- R/nfl_team_tiers.R | 312 +++--- R/nflplotR-package.R | 36 R/scale_nfl.R | 222 ++-- R/sysdata.rda |binary R/theme-elements.R | 630 +++++------- R/utils.R | 8 R/zzz.R | 137 +- README.md | 174 +-- man/dot-nflplotR_clear_cache.Rd | 34 man/element.Rd | 369 +++---- man/figures/lifecycle-deprecated.svg | 42 man/geom_from_path.Rd | 310 +++--- man/geom_lines.Rd | 217 ++-- man/geom_nfl_headshots.Rd | 348 +++---- man/geom_nfl_logos.Rd | 358 +++---- man/geom_nfl_wordmarks.Rd | 346 +++--- man/ggpreview.Rd | 177 +-- man/gt_nfl_cols_label.Rd | 142 +- man/gt_nfl_headshots.Rd | 150 +-- man/gt_nfl_logos.Rd | 136 +- man/gt_render_image.Rd | 76 - man/nfl_team_factor.Rd | 150 +-- man/nfl_team_tiers.Rd | 218 ++-- man/nflplotR-package.Rd | 88 - man/nflverse_sitrep.Rd | 22 man/reexports.Rd |only man/scale_nfl.Rd | 291 +++-- man/valid_team_names.Rd | 52 - tests/testthat.R | 8 tests/testthat/_snaps/geom_from_path/p1.svg | 67 - tests/testthat/_snaps/geom_lines/p1.svg | 199 ++-- tests/testthat/_snaps/geom_lines/p2.svg | 195 +-- tests/testthat/_snaps/geom_lines/p3.svg | 195 +-- tests/testthat/_snaps/geom_lines/p4.svg | 199 ++-- tests/testthat/_snaps/geom_nfl_logos.md |only tests/testthat/_snaps/geom_nfl_logos/p1.svg | 131 +- tests/testthat/_snaps/geom_nfl_logos/p2.svg | 137 +- tests/testthat/_snaps/geom_nfl_logos/p3.svg | 131 +- tests/testthat/_snaps/geom_nfl_wordmarks.md |only tests/testthat/_snaps/geom_nfl_wordmarks/p1.svg | 161 +-- tests/testthat/_snaps/geom_nfl_wordmarks/p2.svg | 161 +-- tests/testthat/_snaps/nfl_team_factors/p1.svg | 1187 ++++++++++++------------ tests/testthat/_snaps/nfl_team_factors/p2.svg | 1187 ++++++++++++------------ tests/testthat/_snaps/nfl_team_tiers/p1.svg | 150 +-- tests/testthat/_snaps/scale_nfl/p1.svg | 289 ++--- tests/testthat/_snaps/theme-elements.md |only tests/testthat/_snaps/theme-elements/p1.svg | 73 - tests/testthat/_snaps/theme-elements/p2.svg | 73 - tests/testthat/test-geom_from_path.R | 46 tests/testthat/test-geom_lines.R | 72 - tests/testthat/test-geom_nfl_logos.R | 123 +- tests/testthat/test-geom_nfl_wordmarks.R | 109 +- tests/testthat/test-nfl_team_factors.R | 80 - tests/testthat/test-nfl_team_tiers.R | 60 - tests/testthat/test-scale_nfl.R | 44 tests/testthat/test-theme-elements.R | 78 - tests/testthat/test-utils.R | 24 tools/check.env | 18 71 files changed, 5963 insertions(+), 5965 deletions(-)
Title: L-Moments and Quantile Mixtures
Description: Contains functions to estimate
L-moments and trimmed L-moments from the data. Also
contains functions to estimate the parameters of the normal
polynomial quantile mixture and the Cauchy polynomial quantile
mixture from L-moments and trimmed L-moments.
Author: Juha Karvanen [cre, aut],
Santeri Karppinen [aut]
Maintainer: Juha Karvanen <juha.karvanen@iki.fi>
Diff between Lmoments versions 1.3-1 dated 2019-03-15 and 1.3-2 dated 2025-09-18
Lmoments-1.3-1/Lmoments/COPYING |only Lmoments-1.3-2/Lmoments/DESCRIPTION | 13 +++---- Lmoments-1.3-2/Lmoments/MD5 | 25 ++++++------- Lmoments-1.3-2/Lmoments/inst/CITATION | 45 ++++++++----------------- Lmoments-1.3-2/Lmoments/inst/News | 22 ++++++------ Lmoments-1.3-2/Lmoments/man/Lmoments.Rd | 18 +++++----- Lmoments-1.3-2/Lmoments/man/cauchypoly.Rd | 24 ++++++------- Lmoments-1.3-2/Lmoments/man/covnormpoly4.Rd | 2 - Lmoments-1.3-2/Lmoments/man/data2cauchypoly.Rd | 20 +++++------ Lmoments-1.3-2/Lmoments/man/data2normpoly.Rd | 18 +++++----- Lmoments-1.3-2/Lmoments/man/normpoly.Rd | 22 ++++++------ Lmoments-1.3-2/Lmoments/man/t1lmoments.Rd | 20 +++++------ Lmoments-1.3-2/Lmoments/src/Makevars | 12 ------ Lmoments-1.3-2/Lmoments/src/Makevars.win | 12 ------ 14 files changed, 110 insertions(+), 143 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love [aut, cre, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 2.6.3 dated 2024-09-07 and 2.7.7 dated 2025-09-18
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/analysis.R | 9 ++++++++- R/image.R | 11 +++++++++++ R/options.R | 6 ++++++ R/output.R | 3 ++- R/results.R | 6 ++++-- 7 files changed, 42 insertions(+), 15 deletions(-)
Title: R-ArcGIS Bridge Utility Functions
Description: Developer oriented utility functions designed to be used as
the building blocks of R packages that work with ArcGIS Location
Services. It provides functionality for authorization, Esri JSON
construction and parsing, as well as other utilities pertaining to
geometry and Esri type conversions. To support 'ArcGIS Pro' users,
authorization can be done via 'arcgisbinding'. Installation
instructions for 'arcgisbinding' can be found at
<https://developers.arcgis.com/r-bridge/installation/>.
Author: Josiah Parry [aut, cre] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb] ,
Eli Pousson [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisutils versions 0.3.3 dated 2025-04-10 and 0.4.0 dated 2025-09-18
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