Title: Evaluation of Presence-Absence Models
Description: Collection of functions to evaluate presence-absence models. It
comprises functions to adjust discrimination statistics for the
representativeness effect through case-weighting, along with functions for
visualizing the outcomes. Originally outlined in:
Jiménez-Valverde (2022) The uniform AUC: dealing with the
representativeness effect in presence-absence models. Methods Ecol. Evol,
13, 1224-1236.
Author: Alberto Jimenez-Valverde [aut, cre]
Maintainer: Alberto Jimenez-Valverde <alberto.jimenez.valverde@gmail.com>
Diff between vandalico versions 0.1.0 dated 2024-09-06 and 0.2.0 dated 2025-10-29
DESCRIPTION | 20 ++++++++++++-------- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 +++ NEWS.md | 14 ++++++++++++-- R/AUCuniform.2.R |only R/AUCuniform.R | 30 ++++++++++++++---------------- R/AUCuniform_trap.R | 45 +++++++++++++++++++++------------------------ R/CALplot.R | 11 +++++------ R/HSgraph.R | 18 ++++++++---------- man/AUCuniform.2.Rd |only man/AUCuniform.Rd | 6 +++--- man/CALplot.Rd | 4 ++-- man/HSgraph.Rd | 4 ++-- 13 files changed, 94 insertions(+), 83 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.3.0 dated 2025-04-23 and 5.3.1 dated 2025-10-29
DESCRIPTION | 55 ++--- MD5 | 85 +++---- NAMESPACE | 8 NEWS.md | 29 ++ R/clustering.R | 254 +++++++++++++++-------- R/convenience.R | 3 R/differential_expression.R | 29 +- R/dimensional_reduction.R | 86 ++++++- R/integration.R | 108 ++++------ R/mixscape.R | 58 ++--- R/objects.R | 40 +-- R/preprocessing.R | 83 ++++--- R/preprocessing5.R | 14 - R/sketching.R | 104 +++++++-- R/utilities.R | 66 ++++-- R/visualization.R | 324 +++++++++++++++++------------- R/zzz.R | 4 build/Seurat.pdf |binary build/stage23.rdb |binary man/AddModuleScore.Rd | 2 man/BuildNicheAssay.Rd | 9 man/ColorDimSplit.Rd | 4 man/DEenrichRPlot.Rd | 2 man/DimPlot.Rd | 8 man/FeaturePlot.Rd | 6 man/FindClusters.Rd | 11 + man/MixscapeHeatmap.Rd | 2 man/MixscapeLDA.Rd | 2 man/PrepLDA.Rd | 2 man/PrepSCTFindMarkers.Rd | 2 man/ReadAkoya.Rd | 2 man/ReadNanostring.Rd | 2 man/ReadVitessce.Rd | 2 man/ReadVizgen.Rd | 2 man/RunICA.Rd | 2 man/RunLeiden.Rd | 17 + man/RunUMAP.Rd | 9 man/STARmap-class.Rd | 2 man/Seurat-package.Rd | 2 man/SlideSeq-class.Rd | 2 man/roxygen/templates/section-progressr.R | 2 tests/testthat/test_dimplot.R |only tests/testthat/test_find_clusters.R | 2 tests/testthat/test_integration.R | 2 44 files changed, 912 insertions(+), 536 deletions(-)
Title: Toolbox for Regression Discontinuity Design ('RDD')
Description: Set of functions for Regression Discontinuity Design ('RDD'), for
data visualisation, estimation and testing.
Author: Matthieu Stigler [aut, cre] ,
Bastiaan Quast [aut]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
This is a re-admission after prior archival of version 2.0.1 dated 2025-07-02
Diff between rddtools versions 2.0.1 dated 2025-07-02 and 2.0.2 dated 2025-10-29
DESCRIPTION | 21 ++++++++++++++------- MD5 | 19 +++++++++++-------- NAMESPACE | 9 ++++++++- NEWS.md | 7 ++++++- R/dens_test.R | 17 ++++++++++------- R/rdd_pkg_old_DCdensity.R |only R/rdd_pkg_old_kernelwts.R |only build/partial.rdb |only inst/devtools_internal_tests.R | 7 ++++++- inst/doc/morocco.html | 17 ++++++++++++----- inst/doc/rddtools.html | 9 +++++---- man/dens_test.Rd | 19 +++++++++++++------ 12 files changed, 85 insertions(+), 40 deletions(-)
Title: Support for Parallel Computation, Logging, and Function
Automation
Description: Support for parallel computation with progress bar, and option to stop or proceed on errors. Also provides logging to console and disk,
and the logging persists in the parallel threads. Additional functions support function call automation with delayed execution (e.g. for executing functions in
parallel).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between ParallelLogger versions 3.5.0 dated 2025-08-27 and 3.5.1 dated 2025-10-29
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/Cluster.R | 4 ++-- inst/doc/Logging.pdf |binary inst/doc/Parallel.pdf |binary man/makeCluster.Rd | 2 +- 7 files changed, 21 insertions(+), 14 deletions(-)
More information about ParallelLogger at CRAN
Permanent link
Title: Imputation Procedures and Quality Tests for Fuzzy Data
Description: Special procedures for the imputation of missing fuzzy numbers are still underdeveloped. The goal of the package is to provide the new d-imputation method (DIMP for short, Romaniuk, M. and Grzegorzewski, P. (2023) "Fuzzy Data Imputation with DIMP and FGAIN" RB/23/2023) and covert some classical ones applied in R packages ('missForest','miceRanger','knn') for use with fuzzy datasets. Additionally, specially tailored benchmarking tests are provided to check and compare these imputation procedures with fuzzy datasets.
Author: Maciej Romaniuk [cre, aut]
Maintainer: Maciej Romaniuk <mroman@ibspan.waw.pl>
Diff between FuzzyImputationTest versions 0.5.1 dated 2025-05-15 and 0.5.2 dated 2025-10-29
DESCRIPTION | 8 MD5 | 18 R/FuzzyImputation.R | 22 R/FuzzyNumbersToMatrix.R | 4 man/FuzzyImputation.Rd | 9 tests/testthat/_snaps/FuzzyImputation.md | 148 +- tests/testthat/_snaps/FuzzyNumbersToMatrix.md | 16 tests/testthat/_snaps/MethodsComparison.md | 1578 +++++++++++++------------- tests/testthat/test-FuzzyImputation.R | 6 tests/testthat/test-MethodsComparison.R | 4 10 files changed, 936 insertions(+), 877 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: Clean and Standardize Epidemiological Data
Description: Cleaning and standardizing tabular data package, tailored
specifically for curating epidemiological data. It streamlines various
data cleaning tasks that are typically expected when working with
datasets in epidemiology. It returns the processed data in the same
format, and generates a comprehensive report detailing the outcomes of
each cleaning task.
Author: Karim Mane [aut] ,
Thibaut Jombart [ctb] .),
Abdoelnaser Degoot [aut] ,
Bankole Ahadzie [aut],
Nuredin Mohammed [aut],
Bubacarr Bah [aut, cre] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [rev] ,
James M. Azam [rev] ,
Joshua W. Lambert [rev, ctb] ,
Chr [...truncated...]
Maintainer: Bubacarr Bah <Bubacarr.Bah1@lshtm.ac.uk>
Diff between cleanepi versions 1.1.1 dated 2025-07-16 and 1.1.2 dated 2025-10-29
DESCRIPTION | 21 MD5 | 45 - NEWS.md | 24 R/correct_misspelled_values.R | 25 R/find_and_remove_duplicates.R | 12 R/print_report.R | 133 ++- R/replace_missing_values.R | 9 R/standardize_subject_ids.R | 32 R/utils.R | 11 README.md | 424 ------------ inst/WORDLIST | 3 inst/doc/cleanepi.html | 4 inst/extdata/logo.svg |only inst/po/fr/LC_MESSAGES/R-cleanepi.mo |binary inst/rmarkdown/templates/printing-rmd/skeleton/skeleton.Rmd | 12 man/cleanepi-package.Rd | 6 man/find_duplicates.Rd | 9 man/print_report.Rd | 99 +- man/replace_missing_values.Rd | 3 man/unnest_report.Rd | 2 po/R-cleanepi.pot | 87 +- po/R-fr.po | 102 +- tests/testthat/test-correct_misspelled_values.R | 16 tests/testthat/test-replace_missing_values.R | 9 24 files changed, 413 insertions(+), 675 deletions(-)
Title: Spatial Coverage Sampling and Random Sampling from Compact
Geographical Strata
Description: Spatial coverage sampling and random sampling from compact
geographical strata created by k-means. See Walvoort et al. (2010)
<doi:10.1016/j.cageo.2010.04.005> for details.
Author: Dennis Walvoort [aut, cre, cph] ,
Dick Brus [aut, cph] ,
Jaap de Gruijter [aut, cph]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between spcosa versions 0.4-5 dated 2025-10-14 and 0.4-6 dated 2025-10-29
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- inst/NEWS.Rd | 6 ++++ man/estimate-methods.Rd | 60 +++++++++++++++++++++++++----------------------- man/spsample-methods.Rd | 47 ++++++++++++++++++++----------------- man/stratify-methods.Rd | 28 ++++++++++++---------- 6 files changed, 87 insertions(+), 72 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.16 dated 2025-10-27 and 0.0.17 dated 2025-10-29
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/zzz.R | 2 +- build/partial.rdb |binary inst/CITATION | 19 +++++++++++++++---- inst/doc/choice-of-SEL-weights.html | 4 ++-- inst/doc/non-parametric-rcpp.html | 29 ++++++++++++++--------------- tests/testthat/test-ExEL1.R | 2 +- tests/testthat/test-ExEL2.R | 2 +- 10 files changed, 50 insertions(+), 36 deletions(-)
Title: Non-Local Prior Based Iterative Variable Selection Tool for
Genome-Wide Association Studies
Description: Performs variable selection with data from Genome-wide association studies (GWAS), or other high-dimensional data with continuous, binary or survival outcomes, combining in an iterative framework the computational efficiency of the structured screen-and-select variable selection strategy based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors (see Sanyal et al., 2019 <DOI:10.1093/bioinformatics/bty472>).
Author: Nilotpal Sanyal [aut, cre]
Maintainer: Nilotpal Sanyal <nilotpal.sanyal@gmail.com>
This is a re-admission after prior archival of version 2.3 dated 2024-10-20
Diff between GWASinlps versions 2.3 dated 2024-10-20 and 2.4 dated 2025-10-29
DESCRIPTION | 13 +++---- MD5 | 16 ++++---- NAMESPACE | 1 NEWS | 4 ++ NEWS.md | 4 ++ R/GWASinlps.R | 84 ++++++++++++++++++++++++++--------------------- man/GWASinlps-package.Rd | 4 +- man/GWASinlps.Rd | 10 ++--- man/nlps.Rd | 8 ++-- 9 files changed, 81 insertions(+), 63 deletions(-)
Title: Chi-Square and G-Square Test of Independence, Power and Residual
Analysis, Measures of Categorical Association
Description: Provides the facility to perform the chi-square and G-square test of independence, calculates the retrospective power of the traditional chi-square test, compute permutation and Monte Carlo p-value, and provides measures of association for tables of any size such as Phi, Phi corrected, odds ratio with 95 percent CI and p-value, Yule' Q and Y, adjusted contingency coefficient, Cramer's V, V corrected, V standardised, bias-corrected V, W, Cohen's w, Goodman-Kruskal's lambda, and tau. It also calculates standardised, moment-corrected standardised, and adjusted standardised residuals, and their significance, as well as the Quetelet Index, IJ association factor, and adjusted standardised counts. It also computes the chi-square-maximising version of the input table. Different outputs are returned in nicely formatted tables.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between chisquare versions 1.1.1 dated 2024-10-27 and 1.2 dated 2025-10-29
DESCRIPTION | 6 MD5 | 18 NAMESPACE | 1 NEWS.md | 39 R/chisquare.r | 1756 ++++++++++++++++++++++++++------- R/compute_median_polish_residuals.R |only R/gk_tau_se.R |only R/multiple_ORs.R | 1 README.md | 5 man/chisquare.Rd | 732 ++++++++++--- man/compute_gk_tau_se.Rd |only man/compute_median_polish_residuals.Rd |only 12 files changed, 2018 insertions(+), 540 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.5 dated 2025-10-02 and 4.5.1 dated 2025-10-29
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/Analyze.Multinomial.R | 30 ++++++++++++++++++++---------- man/Sequential-package.Rd | 9 ++++++--- 4 files changed, 33 insertions(+), 20 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.11.3 dated 2025-09-11 and 2.11.4 dated 2025-10-29
DESCRIPTION | 6 MD5 | 270 +- NEWS.md | 7 R/exportUserRoleAssignments.R | 22 R/importUserRoleAssignments.R | 74 R/logging.R | 24 R/redcapConnection.R | 1156 +++++----- R/redcapDataStructure.R | 17 inst/doc/redcapAPI-best-practices.pdf |binary inst/doc/redcapAPI-casting-data.pdf |binary inst/doc/redcapAPI-data-validation.pdf |binary inst/doc/redcapAPI-faq.pdf |binary inst/doc/redcapAPI-getting-started-connecting.pdf |binary inst/doc/redcapAPI-missing-data-detection.pdf |binary inst/doc/redcapAPI-offline-connection.pdf |binary inst/extdata/offlineConnectionFiles/TestRedcapAPI_UserRoleAssignments.csv | 4 man/redcapConnection.Rd | 12 tests/testthat/test-001-packageSetup.R | 68 tests/testthat/test-002-projectSetup.R | 6 tests/testthat/test-020-redcapConnection-ArgumentValidation.R | 70 tests/testthat/test-021-redcapConnection-caching.R | 160 - tests/testthat/test-022-offlineConnection-ArgumentValidation.R | 40 tests/testthat/test-022-offlineConnection-Functionality.R | 346 +- tests/testthat/test-024-unlockREDCap-ArgumentValidation.R | 2 tests/testthat/test-024-unlockREDCap.R | 2 tests/testthat/test-050-makeApiCall.R | 2 tests/testthat/test-051-stringCleanup.R | 62 tests/testthat/test-052-unitsFieldAnnotation.R | 11 tests/testthat/test-053-fieldValidationAndCasting.R | 988 ++++---- tests/testthat/test-054-fieldChoiceMapping.R | 78 tests/testthat/test-055-filterEmptyRow.R | 68 tests/testthat/test-056-redcapError.R | 22 tests/testthat/test-057-vectorToApiBodyList.R | 17 tests/testthat/test-058-writeDataForImport.R | 26 tests/testthat/test-059-isZeroCodedCheckField.R | 80 tests/testthat/test-060-reviewInvalidRecords.R | 42 tests/testthat/test-061-regularExpressions.R | 32 tests/testthat/test-100-projectInfo-ArgumentValidation.R | 144 - tests/testthat/test-100-projectInfo-functionality.R | 35 tests/testthat/test-101-userMethods-ArgumentValidation.R | 140 - tests/testthat/test-101-userMethods-Functionality.R | 112 tests/testthat/test-102-userRoleMethods-ArgumentValidation.R | 98 tests/testthat/test-102-userRoleMethods-Functionality.R | 74 tests/testthat/test-103-userRoleAssignmentMethods-ArgumentValidation.R | 114 tests/testthat/test-103-userRoleAssignmentMethods-Functionality.R | 66 tests/testthat/test-104-dagMethods-ArgumentValidation.R | 98 tests/testthat/test-104-dagMethods-Functionality.R | 62 tests/testthat/test-105-dagAssignment-ArgumentValidation.R | 82 tests/testthat/test-105-dagAssignment-Functionality.R | 60 tests/testthat/test-106-armsMethods-ArgumentValidation.R | 82 tests/testthat/test-106-armsMethods-Functionality.R | 228 - tests/testthat/test-107-eventsMethods-ArgumentValidation.R | 111 tests/testthat/test-107-eventsMethods-Functionality.R | 186 - tests/testthat/test-108-metadataMethods-ArgumentValidation.R | 300 +- tests/testthat/test-108-metadataMethods-Functionality.R | 38 tests/testthat/test-109-instrumentMethods-ArgumentValidation.R | 247 +- tests/testthat/test-109-instrumentMethods-Functionality.R | 2 tests/testthat/test-110-repeatingInstruments-ArgumentValidation.R | 32 tests/testthat/test-110-repeatingInstruments-Functionality.R | 116 - tests/testthat/test-111-switchDag-ArgumentValidation.R | 24 tests/testthat/test-111-switchDag-Functionality.R | 6 tests/testthat/test-150-importDeleteRecords-ArgumentValidation.R | 274 +- tests/testthat/test-150-importDeleteRecords-Functionality.R | 232 -- tests/testthat/test-151-exportRecords-ArgumentValidation.R | 6 tests/testthat/test-151-exportRecords-Functionality.R | 6 tests/testthat/test-152-exportRecordsWithDags.R | 6 tests/testthat/test-153-exportRecordsWithEvents.R | 6 tests/testthat/test-154-exportRecordsWithSurveys.R | 2 tests/testthat/test-155-exportRecordsWithRepeatingInstruments.R | 6 tests/testthat/test-180-exportRecordsOffline-ArgumentValidation.R | 6 tests/testthat/test-180-exportRecordsOffline-Functionality.R | 6 tests/testthat/test-190-exportReports-ArgumentValidation.R | 8 tests/testthat/test-190-exportReports-Functionality.R | 8 tests/testthat/test-200-exportTypedRecords-ArgumentValidation.R | 6 tests/testthat/test-200-exportTypedRecords-Functionality.R | 334 +- tests/testthat/test-201-exportTypedRecords-withDAGs.R | 42 tests/testthat/test-202-exportTypedRecords-withEvents.R | 32 tests/testthat/test-203-exportTypedRecords-withSurveys.R | 2 tests/testthat/test-204-exportTypedRecords-withRepeatingInstruments.R | 54 tests/testthat/test-205-exportTypedRecords-offline-ArgumentValidation.R | 70 tests/testthat/test-205-exportTypedRecords-offline-Functionality.R | 156 - tests/testthat/test-206-exportBulkRecords.R | 6 tests/testthat/test-210-exportSAS.R | 2 tests/testthat/test-240-exportTypedReports-ArgumentValidation.R | 18 tests/testthat/test-240-exportTypedReports-Functionality.R | 74 tests/testthat/test-250-recastRecords.R | 2 tests/testthat/test-251-castForImport.R | 682 ++--- tests/testthat/test-252-guessCast.R | 16 tests/testthat/test-253-guessDate.R | 4 tests/testthat/test-254-mChoiceCast.R | 21 tests/testthat/test-255-splitForms.R | 90 tests/testthat/test-256-dropRepeatingNA.R | 68 tests/testthat/test-300-reconstituteFileFromExport.R | 121 - tests/testthat/test-301-fileMethods-ArgumentValidation.R | 322 +- tests/testthat/test-301-fileMethods-Functionality.R | 144 - tests/testthat/test-302-createFileRepository-ArgumentValidation.R | 124 - tests/testthat/test-302-createFileRepository-Functionality.R | 6 tests/testthat/test-303-fileRepository-SingleFileMethods-ArgumentValidation.R | 161 - tests/testthat/test-303-fileRepository-SingleFileMethods-Functionality.R | 108 tests/testthat/test-304-fileRepository-BulkFileMethods-ArgumentValidation.R | 160 - tests/testthat/test-304-fileRepository-BulkFileMethods-Functionality.R | 116 - tests/testthat/test-305-exportFileRepositoryListing.R | 68 tests/testthat/test-306-fileRepositoryPath.R | 64 tests/testthat/test-350-exportNextRecordName-ArgumentValidation.R | 26 tests/testthat/test-350-exportNextRecordName-Functionality.R | 10 tests/testthat/test-351-exportVersion.R | 28 tests/testthat/test-352-savePurgeRestoreProject-ArgumentValidation.R | 250 +- tests/testthat/test-352-savePurgeRestoreProject-Functionality.R | 2 tests/testthat/test-353-allocationTable-ArgumentValidation.R | 259 +- tests/testthat/test-353-allocationTable-Functionality.R | 14 tests/testthat/test-354-getProjectIdFields.R | 26 tests/testthat/test-355-invalid.R | 14 tests/testthat/test-356-missingSummary.R | 102 tests/testthat/test-357-prepUserImportData.R | 42 tests/testthat/test-358-renameRecord-ArgumentValidation.R | 34 tests/testthat/test-358-renameRecord-Functionality.R | 42 tests/testthat/test-359-exportProjectXml-ArgumentValidation.R | 136 - tests/testthat/test-359-exportProjectXml-Functionality.R | 64 tests/testthat/test-360-createRedcapProject-ArgumentValidation.R | 150 - tests/testthat/test-361-userStructureVersion.R | 18 tests/testthat/test-400-exportSurveyParticipants-ArgumentValidation.R | 44 tests/testthat/test-400-exportSurveyParticipants-Functionality.R | 4 tests/testthat/test-401-exportSurveyLink-ArgumentValidation.R | 108 tests/testthat/test-401-exportSurveyLink-Functionality.R | 4 tests/testthat/test-402-exportSurveyQueueLink-ArgumentValidation.R | 54 tests/testthat/test-402-exportSurveyQueueLink-Functionality.R | 4 tests/testthat/test-403-exportSurveyReturnCode-ArgumentValidation.R | 108 tests/testthat/test-403-exportSurveyReturnCode-Functionality.R | 4 tests/testthat/test-800-exportLogging-Functionality.R | 120 - tests/testthat/test-800-exportLogging-argumentValidation.R | 74 tests/testthat/test-801-changedRecords.R | 2 tests/testthat/test-900-checkbox_suffixes.R | 42 tests/testthat/test-901-fieldToVar.R | 26 tests/testthat/test-902-fieldToVar-mChoice.R | 16 tests/testthat/test-903-validateImport_methods.R | 1 tests/testthat/test-904-exportDataQuality.R | 12 136 files changed, 5715 insertions(+), 5935 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.4.3 dated 2025-10-01 and 1.4.4 dated 2025-10-29
DESCRIPTION | 6 - MD5 | 22 ++-- NEWS.md | 12 ++ R/addConceptIntersect.R | 10 + R/addDemographics.R | 40 ++++++- R/addDemographicsQuery.R | 19 +++ R/addIntersect.R | 4 inst/doc/cohort-intersect.html | 68 ++++++------- inst/doc/concept-intersect.html | 96 +++++++++--------- inst/doc/demographics.html | 208 ++++++++++++++++++++-------------------- inst/doc/summarise.html | 152 ++++++++++++++--------------- inst/doc/table-intersect.html | 92 ++++++++--------- 12 files changed, 398 insertions(+), 331 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: 'Shiny' Modules for General Tasks
Description: 'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between formods versions 0.2.1 dated 2025-06-12 and 0.2.2 dated 2025-10-29
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/FG_Server.R | 6 ++---- build/vignette.rds |binary inst/doc/included_modules.html | 2 +- inst/doc/making_modules.html | 4 ++-- 6 files changed, 13 insertions(+), 15 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cph],
Julia Piaskowski [cre, aut],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Julia Piaskowski <julia.piask@gmail.com>
Diff between emmeans versions 1.11.2-8 dated 2025-08-27 and 2.0.0 dated 2025-10-29
emmeans-1.11.2-8/emmeans/data/autonoise.RData |only emmeans-1.11.2-8/emmeans/vignettes/rvlstyle.html |only emmeans-2.0.0/emmeans/DESCRIPTION | 29 +- emmeans-2.0.0/emmeans/MD5 | 99 ++++----- emmeans-2.0.0/emmeans/NAMESPACE | 7 emmeans-2.0.0/emmeans/NEWS.md | 22 ++ emmeans-2.0.0/emmeans/R/MCMC-support.R | 9 emmeans-2.0.0/emmeans/R/emm-contr.R | 2 emmeans-2.0.0/emmeans/R/emmGrid-methods.R | 30 ++ emmeans-2.0.0/emmeans/R/emmip.R | 145 +++++++++++-- emmeans-2.0.0/emmeans/R/multiv.R | 2 emmeans-2.0.0/emmeans/R/ordinal-support.R | 1 emmeans-2.0.0/emmeans/R/plot.emm.R | 98 ++++++--- emmeans-2.0.0/emmeans/R/pwpp.R | 17 - emmeans-2.0.0/emmeans/R/qdrg.R | 156 ++++++++------- emmeans-2.0.0/emmeans/R/summary.R | 11 - emmeans-2.0.0/emmeans/R/zzz.R | 13 - emmeans-2.0.0/emmeans/README.md | 25 -- emmeans-2.0.0/emmeans/build/vignette.rds |binary emmeans-2.0.0/emmeans/data/auto.noise.RData |only emmeans-2.0.0/emmeans/inst/doc/AQuickStart.html | 4 emmeans-2.0.0/emmeans/inst/doc/FAQs.html | 8 emmeans-2.0.0/emmeans/inst/doc/basics.html | 16 - emmeans-2.0.0/emmeans/inst/doc/comparisons.html | 18 - emmeans-2.0.0/emmeans/inst/doc/confidence-intervals.html | 12 - emmeans-2.0.0/emmeans/inst/doc/interactions.html | 28 +- emmeans-2.0.0/emmeans/inst/doc/messy-data.html | 14 - emmeans-2.0.0/emmeans/inst/doc/models.html | 4 emmeans-2.0.0/emmeans/inst/doc/predictions.html | 6 emmeans-2.0.0/emmeans/inst/doc/re-engineering-clds.html | 4 emmeans-2.0.0/emmeans/inst/doc/sophisticated.html | 8 emmeans-2.0.0/emmeans/inst/doc/transformations.html | 16 - emmeans-2.0.0/emmeans/inst/doc/utilities.html | 4 emmeans-2.0.0/emmeans/inst/doc/vignette-topics.Rmd | 6 emmeans-2.0.0/emmeans/inst/doc/vignette-topics.html | 15 + emmeans-2.0.0/emmeans/inst/doc/xplanations.html | 14 - emmeans-2.0.0/emmeans/inst/doc/xtending.R | 17 + emmeans-2.0.0/emmeans/inst/doc/xtending.Rmd | 62 +++++ emmeans-2.0.0/emmeans/inst/doc/xtending.html | 106 ++++++++-- emmeans-2.0.0/emmeans/man/emm_options.Rd | 28 ++ emmeans-2.0.0/emmeans/man/emmc-functions.Rd | 2 emmeans-2.0.0/emmeans/man/emmip.Rd | 35 ++- emmeans-2.0.0/emmeans/man/extending-emmeans.Rd | 6 emmeans-2.0.0/emmeans/man/figures/logo.png |binary emmeans-2.0.0/emmeans/man/hpd.summary.Rd | 5 emmeans-2.0.0/emmeans/man/mvregrid.Rd | 102 ++++----- emmeans-2.0.0/emmeans/man/plot.Rd | 30 +- emmeans-2.0.0/emmeans/man/qdrg.Rd | 44 ++-- emmeans-2.0.0/emmeans/man/summary.emmGrid.Rd | 11 - emmeans-2.0.0/emmeans/man/untidy.Rd | 62 ++--- emmeans-2.0.0/emmeans/vignettes/vignette-topics.Rmd | 6 emmeans-2.0.0/emmeans/vignettes/xtending.Rmd | 62 +++++ 52 files changed, 948 insertions(+), 473 deletions(-)
Title: Retrieve Records from the Urban Institute's Education Data
Portal API
Description: Allows R users to retrieve and parse data from the Urban
Institute's Education Data API <https://educationdata.urban.org/> into a
'data.frame' for analysis.
Author: Erika Tyagi [cre],
Kyle Ueyama [aut],
Andrew Martin [ctb] ,
The Urban Institute [cph]
Maintainer: Erika Tyagi <etyagi@urban.org>
Diff between educationdata versions 0.1.3 dated 2022-09-29 and 0.1.5 dated 2025-10-29
educationdata-0.1.3/educationdata/build |only educationdata-0.1.3/educationdata/inst |only educationdata-0.1.3/educationdata/vignettes |only educationdata-0.1.5/educationdata/DESCRIPTION | 12 educationdata-0.1.5/educationdata/MD5 | 24 educationdata-0.1.5/educationdata/NEWS.md | 11 educationdata-0.1.5/educationdata/R/download-csv.R | 10 educationdata-0.1.5/educationdata/R/get-page-data.R | 20 educationdata-0.1.5/educationdata/R/get_education_data.R | 23 educationdata-0.1.5/educationdata/R/validate-args.R | 1 educationdata-0.1.5/educationdata/README.md | 338 +++++----- educationdata-0.1.5/educationdata/man/figures |only educationdata-0.1.5/educationdata/man/get_education_data.Rd | 5 educationdata-0.1.5/educationdata/tests/testthat/test-validation.R | 15 14 files changed, 253 insertions(+), 206 deletions(-)
Title: Messages, Warnings, Strings with Ascii Animals
Description: Allows printing of character strings as messages/warnings/etc.
with ASCII animals, including cats, cows, frogs, chickens, ghosts,
and more.
Author: Scott Chamberlain [aut, cre],
Amanda Dobbyn [aut],
Tyler Rinker [ctb],
Thomas Leeper [ctb],
Noam Ross [ctb],
Rich FitzJohn [ctb],
Carson Sievert [ctb],
Kiyoko Gotanda [ctb],
Andy Teucher [ctb],
Karl Broman [ctb],
Franz-Sebastian Krah [ctb],
Lucy D'Ag [...truncated...]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between cowsay versions 1.2.0 dated 2025-03-28 and 1.2.2 dated 2025-10-29
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- NEWS.md | 5 +++ R/constants.R | 2 - R/say.R | 40 +++++++++++------------- README.md | 83 +++++++++++++++++++-------------------------------- build/vignette.rds |binary inst/doc/cowsay.html | 6 +-- man/say.Rd | 6 --- 9 files changed, 70 insertions(+), 96 deletions(-)
Title: R Graphics Device using Cairo Graphics Library for Creating
High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
PostScript) and Display (X11 and Win32) Output
Description: R graphics device using cairographics library that can be used to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek [aut, cre, cph] ,
Jeffrey Horner [aut]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Cairo versions 1.6-5 dated 2025-08-20 and 1.7-0 dated 2025-10-29
DESCRIPTION | 8 - MD5 | 13 +- NEWS | 16 ++- configure.win | 2 src/cairogd.c | 10 - src/cairogd.h | 21 +++- src/cairotalk.c | 288 ++++++++++++++++++++++++++++++++++++++++---------------- src/coreutil.c |only 8 files changed, 256 insertions(+), 102 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.17-3 dated 2025-08-18 and 2.17-4 dated 2025-10-29
DESCRIPTION | 11 ++- MD5 | 8 +- R/ensemble.blockCV.R | 56 ++++++++++++++------ inst/ChangeLog | 8 ++ man/ensemble.blockCV.Rd | 133 +++++++++++++++++++++--------------------------- 5 files changed, 119 insertions(+), 97 deletions(-)
Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut],
Egill Fridgeirsson [aut],
Martijn Schuemie [aut, cre],
Marc A. Suchard [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between Andromeda versions 1.1.1 dated 2025-08-22 and 1.2.0 dated 2025-10-29
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 14 ++++++++++++++ R/Object.R | 30 +++++++++++++++++++++++++----- R/Operations.R | 23 ++++++++++++++++++++--- inst/doc/UsingAndromeda.html | 6 +++--- man/flushAndromeda.Rd | 4 +++- tests/testthat/test-object.R | 2 +- 8 files changed, 79 insertions(+), 26 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download comprehensive datasets of local,
state, and federal election results in Germany from 1990 to 2025. The package
facilitates access to data on turnout, vote shares for major parties, and
demographic information across different levels of government (municipal, state,
and federal). It offers access to geographically harmonized datasets
that account for changes in municipal boundaries over time and incorporate
mail-in voting districts. Users can easily retrieve, clean, and standardize
German electoral data, making it ready for analysis. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.2.1 dated 2025-10-06 and 0.3.0 dated 2025-10-29
DESCRIPTION | 8 +-- MD5 | 22 +++++--- NAMESPACE | 3 + NEWS.md | 20 +++++++- R/gerda_covariates.R |only R/sysdata.rda |binary README.md | 44 +++++++++++++++++ inst/doc/gerda.R | 32 +++++++++++++ inst/doc/gerda.Rmd | 75 ++++++++++++++++++++++++++++++ inst/doc/gerda.html | 96 +++++++++++++++++++++++++++++++++++---- man/add_gerda_covariates.Rd |only man/gerda_covariates.Rd |only man/gerda_covariates_codebook.Rd |only vignettes/gerda.Rmd | 75 ++++++++++++++++++++++++++++++ 14 files changed, 352 insertions(+), 23 deletions(-)
Title: Fetch and Explore the Cornell Lab of Ornithology Open Tree of
Life Avian Phylogeny
Description: Fetches the Cornell Lab of Ornithology Open Tree of Life (clootl) tree in a specified taxonomy. Optionally prune it to a given set of study taxa. Provide a recommended citation list for the studies that informed the extracted tree. Tree generated as described in McTavish et al. (2024) <doi:10.1101/2024.05.20.595017>.
Author: Eliot Miller [aut, cre],
Emily Jane McTavish [aut],
Luna L. Sanchez Reyes [ctb, aut]
Maintainer: Eliot Miller <clootlmaintainers@gmail.com>
Diff between clootl versions 0.1.1 dated 2025-04-10 and 0.1.2 dated 2025-10-29
DESCRIPTION | 8 +-- MD5 | 40 ++++++++-------- NAMESPACE | 1 NEWS.md | 3 + R/data.R | 100 +++++++++++++++++++++++++++++++++--------- R/extractTree.R | 84 +++++++++++++++++++---------------- R/getCitations.R | 70 +++++++++++++++-------------- R/sampleTrees.R | 25 +++++++--- R/utils.R | 66 +++++++-------------------- R/zzz.R | 2 README.md | 9 +++ data/clootl_data.rda |binary man/clootl_data.Rd | 97 +++++++++++++++++++++++++++++++++------- man/extractTree.Rd | 44 ++++++++++-------- man/getCitations.Rd | 62 ++++++++++++++------------ man/get_avesdata_repo.Rd | 14 ++++- man/sampleTrees.Rd | 20 +++++--- man/set_avesdata_repo_path.Rd | 7 ++ man/taxonomyGet.Rd | 18 ++++--- man/treeGet.Rd | 27 +---------- tests/testthat/test_basics.R | 15 +++--- 21 files changed, 430 insertions(+), 282 deletions(-)