Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.1.2 dated 2025-01-09 and 1.1.3 dated 2025-07-15
DESCRIPTION | 10 LICENSE | 4 MD5 | 195 NAMESPACE | 1 NEWS | 502 - R/MzTabReader.R | 984 +- R/PTXQC-package.R | 100 R/YAMLClass.R | 282 R/createYaml.R | 358 R/fcn_misc.R | 2560 +++--- R/fcn_mqpar.R | 112 R/fcn_qualities.R | 586 - R/modsToTable.R | 48 R/modsToTableByRaw.R | 82 R/pkg_internal.R | 6 R/qcMetric.R | 3 R/qcMetric_EVD.R | 3061 +++---- R/qcMetric_EVD_modTable.R | 110 R/qcMetric_PAR.R | 166 R/qcMetric_PG.R | 750 - README.md | 368 build/vignette.rds |binary inst/CITATION | 28 inst/doc/PTXQC-Basic_Guide_for_R_users.R | 136 inst/doc/PTXQC-Basic_Guide_for_R_users.Rmd | 234 inst/doc/PTXQC-Basic_Guide_for_R_users.html | 4 inst/doc/PTXQC-CustomizeReport.Rmd | 250 inst/doc/PTXQC-CustomizeReport.html | 4 inst/doc/PTXQC-DragNDrop.Rmd | 128 inst/doc/PTXQC-DragNDrop.html | 8 inst/doc/PTXQC-FAQ.Rmd | 182 inst/doc/PTXQC-FAQ.html | 4 inst/doc/PTXQC-Input_And_Output_Data.R | 2 inst/doc/PTXQC-Input_And_Output_Data.Rmd | 136 inst/doc/PTXQC-Input_And_Output_Data.html | 4 inst/doc/PTXQC-ListOfMetrics.Rmd | 188 inst/doc/PTXQC-ListOfMetrics.html | 21 inst/dragNdrop/QC-dragdrop/_internal/compute_QC_report.R | 102 inst/dragNdrop/QC-dragdrop/createQC_dragNdrop.bat | 440 - inst/dragNdrop/QC-dragdrop/createQC_dragNdrop_withYAML.bat | 72 inst/dragNdrop/README.md | 212 inst/examples/README.md | 88 inst/examples/report_ecoli_small.mzQC | 160 inst/examples/report_v1.1.0__txt_5files_withMatch-100min.html | 4084 +++++----- inst/reportTemplate/PTXQC_report_template.Rmd | 538 - man/CV.Rd | 34 man/LCS.Rd | 40 man/MQDataReader-class.Rd | 258 man/MzTabReader-class.Rd | 80 man/PTXQC-package.Rd | 117 man/PTXQC.Rd |only man/RSD.Rd | 34 man/assembleMZQC.Rd | 38 man/checkEnglishLocale.Rd | 32 man/createReport.Rd | 104 man/del0.Rd | 34 man/getFileEncoding.Rd | 34 man/getHTMLTable.Rd | 52 man/getMQPARValue.Rd | 62 man/getMaxima.Rd | 58 man/getMetaData.Rd | 38 man/getMetricsObjects.Rd | 34 man/getReportFilenames.Rd | 74 man/getRunQualityTemplate.Rd | 38 man/ggText.Rd | 42 man/grapes-plus-grapes.Rd | 38 man/lcpCount.Rd | 34 man/lcsCount.Rd | 34 man/modsToTable.Rd | 54 man/modsToTableByRaw.Rd | 74 man/pasten.Rd | 44 man/pastet.Rd | 44 man/plot_DataOverRT.Rd | 92 man/plot_IDsOverRT.Rd | 56 man/plot_RatiosPG.Rd | 76 man/plot_peptideMods.Rd | 68 man/print.PTXQC_table.Rd | 32 man/printWithFooter.Rd | 42 man/qcMetric-class.Rd | 3 man/qcMetric_MSMSScans_TopNoverRT-class.Rd | 22 man/qualUniform.Rd | 92 man/repEach.Rd | 48 man/scale01linear.Rd | 38 man/theme_blank.Rd | 28 tests/testthat.R | 14 tests/testthat/test_computeQC.R | 176 tests/testthat/test_createYaml.R | 126 tests/testthat/test_misc.R | 276 tests/testthat/test_modsToTable.R | 18 tests/testthat/test_modsToTableByRaw.R | 48 tests/testthat/test_qcMetric.R | 74 tests/testthat/test_qualities.R | 218 vignettes/PTXQC-Basic_Guide_for_R_users.Rmd | 234 vignettes/PTXQC-CustomizeReport.Rmd | 250 vignettes/PTXQC-DragNDrop.Rmd | 128 vignettes/PTXQC-FAQ.Rmd | 182 vignettes/PTXQC-Input_And_Output_Data.Rmd | 136 vignettes/PTXQC-ListOfMetrics.Rmd | 188 vignettes/readme.txt | 62 99 files changed, 10783 insertions(+), 10782 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.5.0 dated 2025-06-14 and 2.5.1 dated 2025-07-15
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ R/clustering.R | 2 +- inst/doc/comparing_results.html | 2 +- inst/doc/intro_vignette.html | 4 ++-- inst/doc/manual_execution.html | 4 ++-- inst/doc/non_hs_analysis.html | 4 ++-- inst/doc/obtain_data.html | 4 ++-- inst/doc/visualization_vignette.html | 4 ++-- tests/testthat/test-clustering.R | 2 +- 11 files changed, 31 insertions(+), 26 deletions(-)
Title: Core Mathematical Functions for Multi-Objective Optimization
Description: Fast implementation of mathematical operations and performance metrics for multi-objective optimization, including filtering and ranking of dominated vectors according to Pareto optimality, computation of the empirical attainment function, V.G. da Fonseca, C.M. Fonseca, A.O. Hall (2001) <doi:10.1007/3-540-44719-9_15>, hypervolume metric, C.M. Fonseca, L. Paquete, M. López-Ibáñez (2006) <doi:10.1109/CEC.2006.1688440>, epsilon indicator, inverted generational distance, and Vorob'ev threshold, expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) <doi:10.1016/j.ejor.2014.07.032>, among others.
Author: Manuel Lopez-Ibanez [aut, cre] ,
Carlos Fonseca [ctb],
Luis Paquete [ctb],
Andreia P. Guerreiro [ctb],
Mickael Binois [ctb],
Michael H. Buselli [cph] ,
Wessel Dankers [cph] ,
NumPy Developers [cph] ,
Jean-Sebastien Roy [cph] ,
Makoto Matsumoto [cph] [...truncated...]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between moocore versions 0.1.7 dated 2025-06-05 and 0.1.8 dated 2025-07-15
moocore-0.1.7/moocore/src/libmoocore/hv-bound.c |only moocore-0.1.7/moocore/src/libmoocore/ndtree.c |only moocore-0.1.7/moocore/src/libmoocore/svnversion.mk |only moocore-0.1.8/moocore/DESCRIPTION | 12 moocore-0.1.8/moocore/MD5 | 136 ++--- moocore-0.1.8/moocore/NAMESPACE | 1 moocore-0.1.8/moocore/NEWS.md | 8 moocore-0.1.8/moocore/R/eaf.R | 79 ++ moocore-0.1.8/moocore/R/hv.R | 47 + moocore-0.1.8/moocore/R/hv_approx.R |only moocore-0.1.8/moocore/R/igd.R | 11 moocore-0.1.8/moocore/R/vorob.R | 47 + moocore-0.1.8/moocore/R/whv.R | 8 moocore-0.1.8/moocore/build/partial.rdb |binary moocore-0.1.8/moocore/inst/COPYRIGHTS | 7 moocore-0.1.8/moocore/inst/extdata/DTLZLinearShape.8d.front.60pts.10 |only moocore-0.1.8/moocore/inst/extdata/ran.10pts.9d.10 |only moocore-0.1.8/moocore/man/Vorob.Rd | 53 + moocore-0.1.8/moocore/man/compute_eaf_call.Rd | 12 moocore-0.1.8/moocore/man/eaf.Rd | 74 ++ moocore-0.1.8/moocore/man/hv_approx.Rd |only moocore-0.1.8/moocore/man/hv_contributions.Rd | 28 - moocore-0.1.8/moocore/man/hypervolume.Rd | 17 moocore-0.1.8/moocore/man/igd.Rd | 11 moocore-0.1.8/moocore/man/whv_hype.Rd | 8 moocore-0.1.8/moocore/src/Makevars | 11 moocore-0.1.8/moocore/src/Rmoocore.c | 41 + moocore-0.1.8/moocore/src/init.h | 2 moocore-0.1.8/moocore/src/install.libs.R | 11 moocore-0.1.8/moocore/src/libmoocore/COPYRIGHTS |only moocore-0.1.8/moocore/src/libmoocore/LICENSE |only moocore-0.1.8/moocore/src/libmoocore/Makefile | 158 +++-- moocore-0.1.8/moocore/src/libmoocore/NEWS.md | 7 moocore-0.1.8/moocore/src/libmoocore/README.md | 9 moocore-0.1.8/moocore/src/libmoocore/avl_tiny.h | 37 + moocore-0.1.8/moocore/src/libmoocore/cmdline.h | 19 moocore-0.1.8/moocore/src/libmoocore/common.h | 34 + moocore-0.1.8/moocore/src/libmoocore/config.h | 5 moocore-0.1.8/moocore/src/libmoocore/cvector.h | 28 - moocore-0.1.8/moocore/src/libmoocore/dominatedsets.c | 22 moocore-0.1.8/moocore/src/libmoocore/eaf.c | 24 moocore-0.1.8/moocore/src/libmoocore/eaf.h | 22 moocore-0.1.8/moocore/src/libmoocore/eaf3d.c | 36 - moocore-0.1.8/moocore/src/libmoocore/eaf_main.c | 24 moocore-0.1.8/moocore/src/libmoocore/epsilon.c | 22 moocore-0.1.8/moocore/src/libmoocore/epsilon.h | 1 moocore-0.1.8/moocore/src/libmoocore/gcc_attribs.h | 61 +- moocore-0.1.8/moocore/src/libmoocore/git_version | 2 moocore-0.1.8/moocore/src/libmoocore/hv.c | 268 ++++------ moocore-0.1.8/moocore/src/libmoocore/hv.h | 50 - moocore-0.1.8/moocore/src/libmoocore/hv3dplus.c | 26 moocore-0.1.8/moocore/src/libmoocore/hv4d.c | 33 - moocore-0.1.8/moocore/src/libmoocore/hv_contrib.c | 196 ++++++- moocore-0.1.8/moocore/src/libmoocore/hv_priv.h | 2 moocore-0.1.8/moocore/src/libmoocore/hvapprox.c |only moocore-0.1.8/moocore/src/libmoocore/hvapprox.h |only moocore-0.1.8/moocore/src/libmoocore/igd.c | 24 moocore-0.1.8/moocore/src/libmoocore/igd.h | 4 moocore-0.1.8/moocore/src/libmoocore/io.c | 22 moocore-0.1.8/moocore/src/libmoocore/io.h | 13 moocore-0.1.8/moocore/src/libmoocore/libhv.mk | 4 moocore-0.1.8/moocore/src/libmoocore/libmoocore-config.h |only moocore-0.1.8/moocore/src/libmoocore/libutil.c | 2 moocore-0.1.8/moocore/src/libmoocore/main-hv.c | 133 ++-- moocore-0.1.8/moocore/src/libmoocore/main-hvapprox.c |only moocore-0.1.8/moocore/src/libmoocore/ndsort.c | 20 moocore-0.1.8/moocore/src/libmoocore/nondominated.c | 39 - moocore-0.1.8/moocore/src/libmoocore/nondominated.h | 41 - moocore-0.1.8/moocore/src/libmoocore/pareto.c | 14 moocore-0.1.8/moocore/src/libmoocore/pow_int.h | 8 moocore-0.1.8/moocore/src/libmoocore/sort.h | 57 ++ moocore-0.1.8/moocore/src/libmoocore/timer.h | 23 moocore-0.1.8/moocore/src/libmoocore/whv.h | 1 moocore-0.1.8/moocore/tests/testthat/test-doctest-hv_approx.R |only moocore-0.1.8/moocore/tests/testthat/test-doctest-igd.R | 2 moocore-0.1.8/moocore/tests/testthat/test-doctest-vorob_t.R | 2 76 files changed, 1195 insertions(+), 924 deletions(-)
Title: Inference About Relationships from DNA Mixtures
Description: Methods for inference about/under complex relationships using
peak height data from DNA mixtures: the most basic example would be testing whether a contributor to
a mixture is the father of a child of known genotype. This provides most of the functionality
of the 'KinMix' package, but with some loss of efficiency and restriction on problem size,
as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'.
The package implements the methods introduced in
Green, P. J. and Mortera, J. (2017) <doi:10.1016/j.fsigen.2017.02.001> and
Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.
Author: Peter Green [aut, cre]
Maintainer: Peter Green <P.J.Green@bristol.ac.uk>
Diff between KinMixLite versions 2.1.1 dated 2024-10-09 and 2.2.0 dated 2025-07-15
DESCRIPTION | 14 MD5 | 20 NAMESPACE | 3 R/KinMix.R | 1844 ++-------------------------------------------------- R/KinMixsubs.R |only R/checkdata.R |only build/partial.rdb |binary demo/KMdemo.R | 18 man/KinMix.Rd |only man/checkdata.Rd |only man/convertIBD.Rd | 2 man/make.profile.Rd | 7 man/wlr.Rd | 2 13 files changed, 139 insertions(+), 1771 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.2.0 dated 2025-07-01 and 0.2.1 dated 2025-07-15
kinesis-0.2.0/kinesis/inst/tinytest/_tinysnapshot/output_plot.txt |only kinesis-0.2.0/kinesis/inst/tinytest/_tinysnapshot/select_calendar.txt |only kinesis-0.2.0/kinesis/inst/tinytest/test_coda_barplot.R |only kinesis-0.2.0/kinesis/inst/tinytest/test_plot.R |only kinesis-0.2.1/kinesis/DESCRIPTION | 10 - kinesis-0.2.1/kinesis/MD5 | 60 +++++----- kinesis-0.2.1/kinesis/NAMESPACE | 2 kinesis-0.2.1/kinesis/NEWS.md | 4 kinesis-0.2.1/kinesis/R/coda_hist.R |only kinesis-0.2.1/kinesis/R/coda_statistics.R | 15 -- kinesis-0.2.1/kinesis/R/kinesis-package.R | 2 kinesis-0.2.1/kinesis/README.md | 35 ++++- kinesis-0.2.1/kinesis/inst/app/source/server.R | 1 kinesis-0.2.1/kinesis/inst/app/source/ui.R | 1 kinesis-0.2.1/kinesis/inst/tinytest/test_calendar.R | 4 kinesis-0.2.1/kinesis/inst/tinytest/test_coda_plot.R |only kinesis-0.2.1/kinesis/inst/tinytest/test_coda_statistics.R | 11 - kinesis-0.2.1/kinesis/inst/tinytest/test_graphics.R | 30 ++--- kinesis-0.2.1/kinesis/man/coda_barplot_server.Rd | 2 kinesis-0.2.1/kinesis/man/coda_barplot_ui.Rd | 2 kinesis-0.2.1/kinesis/man/coda_hclust_server.Rd | 2 kinesis-0.2.1/kinesis/man/coda_hclust_ui.Rd | 2 kinesis-0.2.1/kinesis/man/coda_hist_server.Rd |only kinesis-0.2.1/kinesis/man/coda_hist_ui.Rd |only kinesis-0.2.1/kinesis/man/coda_outliers_server.Rd | 2 kinesis-0.2.1/kinesis/man/coda_outliers_ui.Rd | 2 kinesis-0.2.1/kinesis/man/coda_server.Rd | 2 kinesis-0.2.1/kinesis/man/coda_summary_server.Rd | 2 kinesis-0.2.1/kinesis/man/coda_summary_ui.Rd | 2 kinesis-0.2.1/kinesis/man/coda_ui.Rd | 2 kinesis-0.2.1/kinesis/man/kinesis-package.Rd | 2 kinesis-0.2.1/kinesis/man/logratio_server.Rd | 2 kinesis-0.2.1/kinesis/man/logratio_ui.Rd | 2 kinesis-0.2.1/kinesis/po/R-fr.po | 42 +++---- kinesis-0.2.1/kinesis/po/R-kinesis.pot | 42 +++---- 35 files changed, 154 insertions(+), 131 deletions(-)
Title: An Interface to the 'Arctos' Database
Description: Performs requests to the 'Arctos' API to download data. Provides a
set of builder classes for performing complex requests, as well as a set of
simple functions for automating many common requests and workflows. More
information about 'Arctos' can be found in
Cicero et al. (2024) <doi:10.1371/journal.pone.0296478> or on their website
<https://arctosdb.org/>.
Author: Harlan Williams [aut, cre],
Marlon E. Cobos [aut],
Jocelyn P. Colella [aut],
Michelle S. Koo [aut],
Vijay Barve [aut]
Maintainer: Harlan Williams <harlanrhwilliams@gmail.com>
Diff between ArctosR versions 0.1.0 dated 2025-07-11 and 0.1.1 dated 2025-07-15
DESCRIPTION | 6 - MD5 | 43 +++++----- NAMESPACE | 3 NEWS.md | 5 + R/frontend.R | 124 ++++++++++++++++++++++++++--- R/query.R | 10 +- R/response.R | 7 + R/utils.R | 4 README.md | 7 - inst/doc/overview.R | 174 ++++++++++++++++++++--------------------- inst/doc/overview.Rmd | 18 ++-- inst/doc/overview.html | 81 ++++++------------- man/Response.Rd | 10 ++ man/check_for_status.Rd |only man/expand_column.Rd | 4 man/get_error_response.Rd |only man/get_last_response_url.Rd |only man/get_records.Rd | 2 man/read_response_rds.Rd | 4 man/response_data.Rd | 6 - man/save_response_csv.Rd | 4 man/save_response_rds.Rd | 4 tests/testthat/test-frontend.R | 4 vignettes/overview.Rmd | 18 ++-- 24 files changed, 318 insertions(+), 220 deletions(-)
Title: Transition Network Analysis (TNA)
Description: Provides tools for performing Transition Network Analysis (TNA) to
study relational dynamics, including functions for building and plotting TNA
models, calculating centrality measures, and identifying dominant events and
patterns. TNA statistical techniques (e.g., bootstrapping and permutation
tests) ensure the reliability of observed insights and confirm that
identified dynamics are meaningful. See (Saqr et al., 2025)
<doi:10.1145/3706468.3706513> for more details on TNA.
Author: Mohammed Saqr [aut],
Santtu Tikka [aut],
Sonsoles Lopez-Pernas [aut, cre]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between tna versions 0.5.0 dated 2025-05-26 and 1.0.0 dated 2025-07-15
tna-0.5.0/tna/vignettes/complete_tutorial_cache |only tna-0.5.0/tna/vignettes/ftna_cache |only tna-1.0.0/tna/DESCRIPTION | 8 tna-1.0.0/tna/MD5 | 195 ++--- tna-1.0.0/tna/NAMESPACE | 5 tna-1.0.0/tna/NEWS.md | 13 tna-1.0.0/tna/R/build.R | 16 tna-1.0.0/tna/R/centralities.R | 4 tna-1.0.0/tna/R/check.R | 61 + tna-1.0.0/tna/R/clusters.R | 117 +-- tna-1.0.0/tna/R/colors.R | 2 tna-1.0.0/tna/R/data.R | 21 tna-1.0.0/tna/R/plot.R | 709 +++++++++++++++++--- tna-1.0.0/tna/R/print.R | 4 tna-1.0.0/tna/R/simulate.R | 2 tna-1.0.0/tna/R/utilities.R | 8 tna-1.0.0/tna/build/vignette.rds |binary tna-1.0.0/tna/inst/CITATION | 15 tna-1.0.0/tna/inst/doc/communities_and_cliques.R |only tna-1.0.0/tna/inst/doc/communities_and_cliques.Rmd |only tna-1.0.0/tna/inst/doc/communities_and_cliques.html |only tna-1.0.0/tna/inst/doc/complete_tutorial.R |only tna-1.0.0/tna/inst/doc/complete_tutorial.Rmd |only tna-1.0.0/tna/inst/doc/complete_tutorial.html |only tna-1.0.0/tna/inst/doc/grouped_sequences.R |only tna-1.0.0/tna/inst/doc/grouped_sequences.Rmd |only tna-1.0.0/tna/inst/doc/grouped_sequences.html |only tna-1.0.0/tna/inst/doc/prepare_data.R |only tna-1.0.0/tna/inst/doc/prepare_data.Rmd |only tna-1.0.0/tna/inst/doc/prepare_data.html |only tna-1.0.0/tna/inst/doc/tna.R | 19 tna-1.0.0/tna/inst/doc/tna.Rmd | 5 tna-1.0.0/tna/inst/doc/tna.html | 224 +++--- tna-1.0.0/tna/man/build_model.Rd | 7 tna-1.0.0/tna/man/figures |only tna-1.0.0/tna/man/hist.group_tna.Rd | 4 tna-1.0.0/tna/man/hist.tna.Rd | 4 tna-1.0.0/tna/man/import_data.Rd | 23 tna-1.0.0/tna/man/mmm_stats.Rd | 5 tna-1.0.0/tna/man/plot.group_tna.Rd | 43 + tna-1.0.0/tna/man/plot.group_tna_bootstrap.Rd | 4 tna-1.0.0/tna/man/plot.group_tna_centralities.Rd | 3 tna-1.0.0/tna/man/plot.tna.Rd | 22 tna-1.0.0/tna/man/plot.tna_cliques.Rd | 6 tna-1.0.0/tna/man/plot_compare.group_tna.Rd | 4 tna-1.0.0/tna/man/plot_frequencies.Rd | 18 tna-1.0.0/tna/man/plot_frequencies.group_tna.Rd | 41 + tna-1.0.0/tna/man/plot_model.Rd | 6 tna-1.0.0/tna/man/plot_mosaic.Rd | 4 tna-1.0.0/tna/man/plot_mosaic.group_tna.Rd | 4 tna-1.0.0/tna/man/plot_mosaic.tna_data.Rd | 4 tna-1.0.0/tna/man/plot_sequences.Rd |only tna-1.0.0/tna/man/prepare_data.Rd | 23 tna-1.0.0/tna/man/print.group_tna.Rd | 4 tna-1.0.0/tna/man/print.summary.group_tna.Rd | 4 tna-1.0.0/tna/man/print.summary.tna.Rd | 4 tna-1.0.0/tna/man/print.tna.Rd | 4 tna-1.0.0/tna/man/print.tna_data.Rd | 23 tna-1.0.0/tna/man/simulate.tna.Rd | 23 tna-1.0.0/tna/man/summary.group_tna.Rd | 4 tna-1.0.0/tna/man/summary.tna.Rd | 4 tna-1.0.0/tna/man/tna-package.Rd | 4 tna-1.0.0/tna/tests/testthat/test-check.R | 24 tna-1.0.0/tna/tests/testthat/test-clusters.R | 4 tna-1.0.0/tna/tests/testthat/test-plot.R | 73 ++ tna-1.0.0/tna/vignettes/articles |only tna-1.0.0/tna/vignettes/communities_and_cliques.Rmd |only tna-1.0.0/tna/vignettes/complete_tutorial.Rmd |only tna-1.0.0/tna/vignettes/grouped_sequences.Rmd |only tna-1.0.0/tna/vignettes/prepare_data.Rmd |only tna-1.0.0/tna/vignettes/tna.Rmd | 5 71 files changed, 1194 insertions(+), 639 deletions(-)
Title: Finds Roots, Extrema and Inflection Points of a Curve
Description: Implementation of Taylor Regression Estimator (TRE),
Tulip Extreme Finding Estimator (TEFE), Bell Extreme Finding Estimator (BEFE),
Integration Extreme Finding Estimator (IEFE) and
Integration Root Finding Estimator (IRFE) for roots, extrema and inflections of a curve .
Christopoulos, DT (2019) <doi:10.13140/RG.2.2.17158.32324> .
Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> .
Christopoulos, DT (2016) <https://demovtu.veltech.edu.in/wp-content/uploads/2016/04/Paper-04-2016.pdf> .
Christopoulos, DT (2014) <doi:10.48550/arXiv.1206.5478> .
Author: Demetris T. Christopoulos [aut, cre]
Maintainer: Demetris T. Christopoulos <dchristop@econ.uoa.gr>
Diff between RootsExtremaInflections versions 1.2.1 dated 2019-07-29 and 1.2.5 dated 2025-07-15
DESCRIPTION | 15 +++-- MD5 | 31 ++++++------ NEWS.md | 6 ++ build |only man/RootsExtremaInflections-package.Rd | 4 - man/classify_curve.Rd | 20 +++---- man/extremexi.Rd | 2 man/findextreme.Rd | 15 +++-- man/findmaxbell.Rd | 8 +-- man/findmaxtulip.Rd | 8 +-- man/findroot.Rd | 17 +++--- man/inflexi.Rd | 2 man/rootexinf.Rd | 2 man/rootxi.Rd | 2 man/scan_curve.Rd | 76 +++++++++++++---------------- man/scan_noisy_curve.Rd | 85 +++++++++++++++------------------ man/symextreme.Rd | 17 +++--- 17 files changed, 155 insertions(+), 155 deletions(-)
More information about RootsExtremaInflections at CRAN
Permanent link
Title: Minimalist Async Evaluation Framework for R
Description: Designed for simplicity, a 'mirai' evaluates an R expression
asynchronously in a parallel process, locally or distributed over the
network. Modern networking and concurrency, built on 'nanonext' and
'NNG', ensures reliable scheduling over fast inter-process
communications or TCP/IP secured by TLS. Launch remote resources via
SSH or cluster managers for distributed computing. Scales efficiently
to millions of tasks over thousands of connections, requiring no
storage on the file system due to its inherently queued architecture.
Innovative features include event-driven promises, asynchronous
parallel map, and seamless serialization of otherwise non-exportable
reference objects.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between mirai versions 2.4.0 dated 2025-06-25 and 2.4.1 dated 2025-07-15
mirai-2.4.0/mirai/inst/doc/mirai-map.Rmd |only mirai-2.4.0/mirai/inst/doc/mirai-map.html |only mirai-2.4.0/mirai/inst/doc/mirai-promises.Rmd |only mirai-2.4.0/mirai/inst/doc/mirai-promises.html |only mirai-2.4.0/mirai/inst/doc/mirai-serialization.Rmd |only mirai-2.4.0/mirai/inst/doc/mirai-serialization.html |only mirai-2.4.0/mirai/inst/doc/mirai-xparallel.Rmd |only mirai-2.4.0/mirai/inst/doc/mirai-xparallel.html |only mirai-2.4.0/mirai/inst/doc/packages.Rmd |only mirai-2.4.0/mirai/inst/doc/packages.html |only mirai-2.4.0/mirai/inst/doc/questions.Rmd |only mirai-2.4.0/mirai/inst/doc/questions.html |only mirai-2.4.0/mirai/vignettes/mirai-map.Rmd |only mirai-2.4.0/mirai/vignettes/mirai-promises.Rmd |only mirai-2.4.0/mirai/vignettes/mirai-serialization.Rmd |only mirai-2.4.0/mirai/vignettes/mirai-xparallel.Rmd |only mirai-2.4.0/mirai/vignettes/packages.Rmd |only mirai-2.4.0/mirai/vignettes/questions.Rmd |only mirai-2.4.1/mirai/DESCRIPTION | 21 +-- mirai-2.4.1/mirai/MD5 | 80 ++++++------- mirai-2.4.1/mirai/NEWS.md | 19 +++ mirai-2.4.1/mirai/R/daemons.R | 114 ++++++++++--------- mirai-2.4.1/mirai/R/dispatcher.R | 45 +++---- mirai-2.4.1/mirai/R/launchers.R | 33 ++--- mirai-2.4.1/mirai/R/mirai-package.R | 9 - mirai-2.4.1/mirai/R/mirai.R | 69 +++++------ mirai-2.4.1/mirai/R/next.R | 5 mirai-2.4.1/mirai/README.md | 29 ++-- mirai-2.4.1/mirai/build/vignette.rds |binary mirai-2.4.1/mirai/inst/doc/mirai.Rmd | 117 +++++++++++--------- mirai-2.4.1/mirai/inst/doc/mirai.html | 109 ++++++++++-------- mirai-2.4.1/mirai/inst/doc/v01-map.Rmd |only mirai-2.4.1/mirai/inst/doc/v01-map.html |only mirai-2.4.1/mirai/inst/doc/v02-promises.Rmd |only mirai-2.4.1/mirai/inst/doc/v02-promises.html |only mirai-2.4.1/mirai/inst/doc/v03-serialization.Rmd |only mirai-2.4.1/mirai/inst/doc/v03-serialization.html |only mirai-2.4.1/mirai/inst/doc/v04-parallel.Rmd |only mirai-2.4.1/mirai/inst/doc/v04-parallel.html |only mirai-2.4.1/mirai/inst/doc/v05-packages.Rmd |only mirai-2.4.1/mirai/inst/doc/v05-packages.html |only mirai-2.4.1/mirai/inst/doc/v06-questions.Rmd |only mirai-2.4.1/mirai/inst/doc/v06-questions.html |only mirai-2.4.1/mirai/man/cluster_config.Rd | 6 - mirai-2.4.1/mirai/man/daemons.Rd | 61 +++++----- mirai-2.4.1/mirai/man/daemons_set.Rd | 2 mirai-2.4.1/mirai/man/dispatcher.Rd | 17 -- mirai-2.4.1/mirai/man/everywhere.Rd | 24 +--- mirai-2.4.1/mirai/man/launch_local.Rd | 21 ++- mirai-2.4.1/mirai/man/mirai-package.Rd | 9 - mirai-2.4.1/mirai/man/mirai.Rd | 9 + mirai-2.4.1/mirai/tests/tests.R | 25 ++++ mirai-2.4.1/mirai/vignettes/mirai.Rmd | 117 +++++++++++--------- mirai-2.4.1/mirai/vignettes/v01-map.Rmd |only mirai-2.4.1/mirai/vignettes/v02-promises.Rmd |only mirai-2.4.1/mirai/vignettes/v03-serialization.Rmd |only mirai-2.4.1/mirai/vignettes/v04-parallel.Rmd |only mirai-2.4.1/mirai/vignettes/v05-packages.Rmd |only mirai-2.4.1/mirai/vignettes/v06-questions.Rmd |only 59 files changed, 518 insertions(+), 423 deletions(-)
Title: Graphical User Interface with Integrated 'Diagrammer' for
'Lavaan'
Description: Provides a graphical user interface with an
integrated diagrammer for latent variables from the 'lavaan' package.
It offers two core functions: first, lavaangui() launches a web application
that allows users to specify models by drawing path diagrams, fitting them,
assessing model fit, and more; second, plot_lavaan() creates
interactive path diagrams from models specified in 'lavaan'.
Karch (2024) <doi: 10.31234/osf.io/f4ary> contains a tutorial.
Author: Julian D. Karch [aut, cre, cph]
Maintainer: Julian D. Karch <j.d.karch@fsw.leidenuniv.nl>
Diff between lavaangui versions 0.2.4 dated 2025-02-20 and 0.2.5 dated 2025-07-15
lavaangui-0.2.4/lavaangui/inst/www/assets/index-45781b04.js |only lavaangui-0.2.5/lavaangui/DESCRIPTION | 12 ++++++------ lavaangui-0.2.5/lavaangui/MD5 | 8 ++++---- lavaangui-0.2.5/lavaangui/NEWS.md | 4 ++++ lavaangui-0.2.5/lavaangui/inst/www/assets/index-cf36f4da.js |only lavaangui-0.2.5/lavaangui/inst/www/index.html | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] ,
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] ,
Marco Gallotta [ctb] ,
Johan Renaudie [ctb] ,
The R Core Team [ctb] ,
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvat [...truncated...]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.19.0 dated 2024-11-15 and 1.19.1 dated 2025-07-15
dendextend-1.19.0/dendextend/tests/testthat/Rplots.pdf |only dendextend-1.19.1/dendextend/DESCRIPTION | 8 - dendextend-1.19.1/dendextend/MD5 | 47 ++++------ dendextend-1.19.1/dendextend/NEWS.md | 11 ++ dendextend-1.19.1/dendextend/R/data.R | 3 dendextend-1.19.1/dendextend/R/set.dendrogram.R | 16 +-- dendextend-1.19.1/dendextend/R/zzz.R | 2 dendextend-1.19.1/dendextend/inst/doc/Cluster_Analysis.html | 4 dendextend-1.19.1/dendextend/inst/doc/FAQ.html | 4 dendextend-1.19.1/dendextend/inst/doc/Quick_Introduction.html | 4 dendextend-1.19.1/dendextend/inst/doc/dendextend.html | 8 - dendextend-1.19.1/dendextend/man/khan.Rd | 3 dendextend-1.19.1/dendextend/man/set.Rd | 16 +-- dendextend-1.19.1/dendextend/tests/testthat/test-circlize.R | 8 - dendextend-1.19.1/dendextend/tests/testthat/test-color_branches.R | 6 - dendextend-1.19.1/dendextend/tests/testthat/test-common_subtrees.R | 10 +- dendextend-1.19.1/dendextend/tests/testthat/test-cor.dendlist.R | 6 - dendextend-1.19.1/dendextend/tests/testthat/test-cutree.dendrogram.R | 14 +- dendextend-1.19.1/dendextend/tests/testthat/test-ggdend.R | 13 +- dendextend-1.19.1/dendextend/tests/testthat/test-rainbow_fun.R | 6 - dendextend-1.19.1/dendextend/tests/testthat/test-rect.dendrogram.R | 14 +- dendextend-1.19.1/dendextend/tests/testthat/test-rotate.R | 8 - dendextend-1.19.1/dendextend/tests/testthat/test-seriate_dendrogram.R | 6 - dendextend-1.19.1/dendextend/tests/testthat/test-tanglegram.R | 6 - dendextend-1.19.1/dendextend/tests/testthat/test-untangle.R | 16 +-- 25 files changed, 131 insertions(+), 108 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.7 dated 2025-05-07 and 0.1.8 dated 2025-07-15
DESCRIPTION | 21 - MD5 | 62 +- NAMESPACE | 209 +++++++++- NEWS.md | 4 R/hardReexports.R |only R/monolixControl.R | 2 R/monolixNlmixr2est.R | 13 R/monolixReadData.R | 33 + R/monolixRxUiGetMlxtranParameters.R | 48 ++ R/nonmemRxUiGetErr.R | 4 R/pknca.R | 3 R/poped.R | 73 ++- R/reexport.R | 8 R/reexports.R |only R/utils.R | 206 +++++++++ R/zzz.R | 1 inst/WORDLIST | 2 inst/poped/ex.1.a.PK.1.comp.oral.md.intro.babelmixr2.R | 31 - inst/poped/ex.1.b.PK.1.comp.oral.md.re-parameterize.babelmixr2.R | 25 - inst/poped/ex.1.c.PK.1.comp.oral.md.ODE.compiled.babelmixr2.R | 20 inst/poped/ex.14.PK.IOV.babelmixr2.R | 37 - inst/poped/ex.15.full.covariance.matrix.babelmixr2.R | 51 +- inst/poped/ex.6.PK.1.comp.oral.sd.babelmixr2.R | 53 +- man/popedControl.Rd | 5 man/reexports.Rd | 115 +++++ src/poped.cpp | 6 tests/testthat/test-monolix-read.R | 76 ++- tests/testthat/test-monolix.R | 44 ++ tests/testthat/test-nonmem-pred.R | 2 tests/testthat/test-nonmem-read.R | 4 tests/testthat/test-nonmem.R | 2 tests/testthat/test-pknca.R | 4 tests/testthat/test-poped.R | 64 +-- 33 files changed, 965 insertions(+), 263 deletions(-)
Title: Project Multidimensional Data in 2D Space
Description: An implementation of the radviz projection in R. It enables the visualization of
multidimensional data while maintaining the relation to the original dimensions.
This package provides functions to create and plot radviz projections, and a number of summary
plots that enable comparison and analysis. For reference see Hoffman *et al.* (1999)
(<doi:10.1145/331770.331775>) for original implementation,
see Di Caro *et al* (2012) (<doi:10.1007/978-3-642-13672-6_13>),
for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007)
(<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.
Author: Yann Abraham [aut, cre],
Nicolas Sauwen [aut]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
Diff between Radviz versions 0.9.4 dated 2025-05-09 and 0.9.5 dated 2025-07-15
DESCRIPTION | 12 +-- MD5 | 10 +- NAMESPACE | 1 R/plot.radviz.R | 4 - inst/doc/multivariate_analysis.html | 123 +++++++++++++++++----------------- inst/doc/single_cell_projections.html | 123 +++++++++++++++++----------------- 6 files changed, 138 insertions(+), 135 deletions(-)
Title: Biogeographic Regionalization and Macroecology
Description: Computational infrastructure for biogeography, community ecology,
and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>.
It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>.
The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013>
on patterns and processes of biogeographical regionalization. Additionally, the package
contains fast and efficient functions to compute more standard conservation measures
such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness
and global endangerment, as well as compositional turnover (e.g., beta diversity).
Author: Barnabas H. Daru [aut, cre, cph] ,
Piyal Karunarathne [aut] ,
Klaus Schliep [aut] ,
Xiaobei Zhao [ctb],
Albin Sandelin [ctb],
Luciano Pataro [ctb]
Maintainer: Barnabas H. Daru <darunabas@gmail.com>
Diff between phyloregion versions 1.0.8 dated 2023-08-15 and 1.0.9 dated 2025-07-15
DESCRIPTION | 19 - MD5 | 78 +++--- NAMESPACE | 19 + NEWS.md | 13 + R/Choropleth.R |only R/PD_ses.R | 6 R/background.R |only R/coldspots.R | 51 +++- R/fitgom.R | 6 R/pd.R | 33 ++ R/phylo_beta.R | 19 - R/phyloregion-package.R | 3 R/phyloregion.R | 19 - R/plot_pie.R | 61 ++++- R/rast_quantile.R |only R/sdm.R | 445 ++++++++++++++++++++++---------------- R/treeSampler.R |only R/utils.R | 30 +- R/visualize_phyloregions.R | 2 build/vignette.rds |binary inst/doc/Benchmark.Rmd | 2 inst/doc/Benchmark.html | 213 +++++++++--------- inst/doc/ed.Rmd | 2 inst/doc/ed.html | 42 +-- inst/doc/phyloregion-intro.R | 18 - inst/doc/phyloregion-intro.Rmd | 2 inst/doc/phyloregion-intro.html | 293 ++++++++++++------------- man/PD.Rd | 8 man/backg.Rd |only man/beta_diss.Rd | 8 man/choropleth.Rd |only man/coldspots.Rd | 22 + man/dirpath.Rd |only man/fitgom.Rd | 6 man/phylobeta.Rd | 11 man/phyloregion-package.Rd | 28 ++ man/plot_pie.Rd | 17 - man/rast_quantile.Rd |only man/sdm.Rd | 35 +- man/tree_sampler.Rd |only vignettes/Benchmark.Rmd | 2 vignettes/Rbuildignore.txt |only vignettes/ed.Rmd | 2 vignettes/gitignore.txt |only vignettes/homogenization.Rmd.orig |only vignettes/phyloregion-intro.Rmd | 2 46 files changed, 905 insertions(+), 612 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime HERVE [aut, cre]
Maintainer: Maxime HERVE <maxime.herve@univ-rennes.fr>
Diff between RVAideMemoire versions 0.9-83-11 dated 2025-04-22 and 0.9-83-12 dated 2025-07-15
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ NEWS | 3 +++ R/rating.emmeans.R | 2 +- R/zzz.R | 2 +- man/RVAideMemoire-package.Rd | 4 ++-- man/adonis.II.Rd | 4 ++-- 7 files changed, 22 insertions(+), 18 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.1.9 dated 2025-06-21 and 0.2.0 dated 2025-07-15
DESCRIPTION | 10 +++++----- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ NEWS.md | 4 ++++ R/geom-xspline.R |only inst/doc/ggfun.html | 26 +++++++++++++------------- man/element_roundrect.Rd | 6 ++---- man/geom_xspline.Rd |only 8 files changed, 36 insertions(+), 27 deletions(-)
Title: Extract Tox Info from Various Databases
Description: Extract toxicological and chemical information from databases
maintained by scientific agencies and resources, including the
Comparative Toxicogenomics Database <https://ctdbase.org/>, the
Integrated Chemical Environment <https://ice.ntp.niehs.nih.gov/>, the
PubChem <https://pubchem.ncbi.nlm.nih.gov/>, and others EPA databases
s.
Author: Claudio Zanettini [aut, cre, cph] ,
Lucio Queiroz [aut]
Maintainer: Claudio Zanettini <claudio.zanettini@gmail.com>
Diff between extractox versions 1.0.0 dated 2025-01-07 and 1.2.0 dated 2025-07-15
extractox-1.0.0/extractox/man/with_extr_sandbox.Rd |only extractox-1.0.0/extractox/tests/testthat/test_pprtv.R |only extractox-1.2.0/extractox/DESCRIPTION | 23 - extractox-1.2.0/extractox/MD5 | 64 +- extractox-1.2.0/extractox/NAMESPACE | 3 extractox-1.2.0/extractox/NEWS.md | 29 + extractox-1.2.0/extractox/R/cache.R | 103 +++- extractox-1.2.0/extractox/R/checks.R | 61 ++ extractox-1.2.0/extractox/R/extr_comptox.R | 297 +++++++++---- extractox-1.2.0/extractox/R/extr_ctd.R | 6 extractox-1.2.0/extractox/R/extr_iris.R | 107 ++++ extractox-1.2.0/extractox/R/extr_pprtv.R | 37 - extractox-1.2.0/extractox/R/extr_pubchem.R | 220 +++++++-- extractox-1.2.0/extractox/R/extr_tox.R | 13 extractox-1.2.0/extractox/R/utils.R | 99 +++- extractox-1.2.0/extractox/README.md | 47 +- extractox-1.2.0/extractox/build/partial.rdb |binary extractox-1.2.0/extractox/man/extr_chem_info.Rd | 34 + extractox-1.2.0/extractox/man/extr_comptox.Rd | 137 +++-- extractox-1.2.0/extractox/man/extr_ctd.Rd | 2 extractox-1.2.0/extractox/man/extr_iris.Rd | 11 extractox-1.2.0/extractox/man/extr_pprtv.Rd | 37 - extractox-1.2.0/extractox/man/extr_pubchem_fema.Rd | 21 extractox-1.2.0/extractox/man/extr_pubchem_ghs.Rd | 24 - extractox-1.2.0/extractox/man/extr_tetramer.Rd | 4 extractox-1.2.0/extractox/man/extr_tox.Rd | 10 extractox-1.2.0/extractox/man/search_and_match.Rd | 14 extractox-1.2.0/extractox/man/with_sandbox_dir.Rd |only extractox-1.2.0/extractox/man/write_dataframes_to_excel.Rd | 8 extractox-1.2.0/extractox/tests/testthat/setup.R | 59 ++ extractox-1.2.0/extractox/tests/testthat/test-cache.R | 20 extractox-1.2.0/extractox/tests/testthat/test-comptox.R | 29 - extractox-1.2.0/extractox/tests/testthat/test-iris.R | 6 extractox-1.2.0/extractox/tests/testthat/test-pprtv.R |only extractox-1.2.0/extractox/tests/testthat/test-pubchem.R | 22 35 files changed, 1104 insertions(+), 443 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joeseph Zemm [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.19 dated 2025-06-27 and 2.7.20 dated 2025-07-15
dataRetrieval-2.7.19/dataRetrieval/inst/doc/qwdata_changes.R |only dataRetrieval-2.7.19/dataRetrieval/inst/doc/qwdata_changes.Rmd |only dataRetrieval-2.7.19/dataRetrieval/inst/doc/qwdata_changes.html |only dataRetrieval-2.7.19/dataRetrieval/vignettes/Wide_data_example.xlsx |only dataRetrieval-2.7.19/dataRetrieval/vignettes/nwisData.rds |only dataRetrieval-2.7.19/dataRetrieval/vignettes/qwdata_changes.Rmd |only dataRetrieval-2.7.19/dataRetrieval/vignettes/wqpData.rds |only dataRetrieval-2.7.20/dataRetrieval/DESCRIPTION | 6 dataRetrieval-2.7.20/dataRetrieval/MD5 | 61 ++++----- dataRetrieval-2.7.20/dataRetrieval/NAMESPACE | 2 dataRetrieval-2.7.20/dataRetrieval/NEWS | 7 + dataRetrieval-2.7.20/dataRetrieval/R/AAA.R | 11 + dataRetrieval-2.7.20/dataRetrieval/R/construct_api_requests.R | 65 +++++++--- dataRetrieval-2.7.20/dataRetrieval/R/readNWISpCode.R | 15 -- dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata.R | 22 +++ dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_daily.R | 6 dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_latest_continuous.R | 15 +- dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_metadata.R |only dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_monitoring_location.R | 6 dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_parameter_codes.R |only dataRetrieval-2.7.20/dataRetrieval/R/read_waterdata_ts_meta.R | 2 dataRetrieval-2.7.20/dataRetrieval/R/walk_pages.R | 18 -- dataRetrieval-2.7.20/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.7.20/dataRetrieval/inst/CITATION | 4 dataRetrieval-2.7.20/dataRetrieval/inst/doc/dataRetrieval.R | 11 - dataRetrieval-2.7.20/dataRetrieval/inst/doc/dataRetrieval.Rmd | 15 +- dataRetrieval-2.7.20/dataRetrieval/inst/doc/dataRetrieval.html | 20 +-- dataRetrieval-2.7.20/dataRetrieval/man/readNWISpCode.Rd | 11 - dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata.Rd | 13 ++ dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_daily.Rd | 6 dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_latest_continuous.Rd | 15 +- dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_metadata.Rd |only dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_monitoring_location.Rd | 6 dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_parameter_codes.Rd |only dataRetrieval-2.7.20/dataRetrieval/man/read_waterdata_ts_meta.Rd | 2 dataRetrieval-2.7.20/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 25 +-- dataRetrieval-2.7.20/dataRetrieval/vignettes/dataRetrieval.Rmd | 15 +- 37 files changed, 226 insertions(+), 153 deletions(-)
Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Atorus/GSK JPT [cp [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.4.2 dated 2025-01-07 and 0.4.3 dated 2025-07-15
DESCRIPTION | 8 LICENSE | 4 MD5 | 146 NAMESPACE | 180 NEWS.md | 248 R/data.R | 220 R/df_label.R | 178 R/format.R | 510 - R/label.R | 278 R/length.R | 342 - R/messages.R | 524 - R/metadata.R | 130 R/options.R | 184 R/order.R | 276 R/split.R | 100 R/support-test.R | 384 - R/type.R | 370 - R/utils-xportr.R | 948 +-- R/write.R | 474 - R/xportr-package.R | 274 R/xportr.R | 142 R/zzz.R | 92 README.md | 386 - build/vignette.rds |binary inst/WORDLIST | 154 inst/doc/agency_standards.Rmd | 508 - inst/doc/agency_standards.html | 1140 ++-- inst/doc/deepdive.R | 562 +- inst/doc/deepdive.Rmd | 1038 +-- inst/doc/deepdive.html | 8938 ++++++++++++++++---------------- inst/doc/xportr.R | 320 - inst/doc/xportr.Rmd | 564 +- inst/doc/xportr.html | 7192 ++++++++++++------------- man/adsl_xportr.Rd | 150 man/dataset_spec.Rd | 60 man/expect_attr_width.Rd | 42 man/metadata.Rd | 114 man/minimal_metadata.Rd | 96 man/minimal_table.Rd | 44 man/multiple_vars_in_spec_helper.Rd | 24 man/multiple_vars_in_spec_helper2.Rd | 24 man/var_spec.Rd | 80 man/xportr-package.Rd | 276 man/xportr.Rd | 162 man/xportr_df_label.Rd | 116 man/xportr_format.Rd | 252 man/xportr_label.Rd | 174 man/xportr_length.Rd | 184 man/xportr_options.Rd | 152 man/xportr_options_list.Rd | 32 man/xportr_order.Rd | 182 man/xportr_split.Rd | 86 man/xportr_type.Rd | 200 man/xportr_write.Rd | 180 man/xpt_validate.Rd | 36 tests/testthat.R | 8 tests/testthat/test-deprecation.R | 226 tests/testthat/test-df_label.R | 18 tests/testthat/test-format.R | 602 +- tests/testthat/test-label.R | 88 tests/testthat/test-length.R | 516 - tests/testthat/test-messages.R | 214 tests/testthat/test-metadata.R | 1686 +++--- tests/testthat/test-options.R | 90 tests/testthat/test-order.R | 401 - tests/testthat/test-pkg-load.R | 46 tests/testthat/test-support-for-tests.R | 74 tests/testthat/test-type.R | 694 +- tests/testthat/test-utils-xportr.R | 284 - tests/testthat/test-write.R | 702 +- tests/testthat/test-xportr.R | 92 vignettes/agency_standards.Rmd | 508 - vignettes/deepdive.Rmd | 1038 +-- vignettes/xportr.Rmd | 564 +- 74 files changed, 18677 insertions(+), 18654 deletions(-)
Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database.
<https://api.neotomadb.org/api-docs/>.
Author: Dominguez Vidana Socorro [aut, cre] ,
Simon Goring [aut]
Maintainer: Dominguez Vidana Socorro <s.dominguez@ht-data.com>
Diff between neotoma2 versions 1.0.6 dated 2025-06-25 and 1.0.7 dated 2025-07-14
neotoma2-1.0.6/neotoma2/R/check_args.R |only neotoma2-1.0.6/neotoma2/R/getids.r |only neotoma2-1.0.6/neotoma2/R/parse_body.R |only neotoma2-1.0.6/neotoma2/R/parse_location.R |only neotoma2-1.0.6/neotoma2/R/pingNeotoma.r |only neotoma2-1.0.6/neotoma2/R/specimen-methods.R |only neotoma2-1.0.6/neotoma2/R/specimens.R |only neotoma2-1.0.6/neotoma2/R/toJSON.R |only neotoma2-1.0.6/neotoma2/man/as.data.frame-specimen-method.Rd |only neotoma2-1.0.6/neotoma2/man/as.data.frame-specimens-method.Rd |only neotoma2-1.0.6/neotoma2/man/build_chron.Rd |only neotoma2-1.0.6/neotoma2/man/build_collunits.Rd |only neotoma2-1.0.6/neotoma2/man/build_dataset.Rd |only neotoma2-1.0.6/neotoma2/man/build_sample.Rd |only neotoma2-1.0.6/neotoma2/man/build_sites.Rd |only neotoma2-1.0.6/neotoma2/man/c-specimens-method.Rd |only neotoma2-1.0.6/neotoma2/man/cash-set-specimen-method.Rd |only neotoma2-1.0.6/neotoma2/man/cash-specimen-method.Rd |only neotoma2-1.0.6/neotoma2/man/cash-specimens-method.Rd |only neotoma2-1.0.6/neotoma2/man/check_args.Rd |only neotoma2-1.0.6/neotoma2/man/get_downloads.character.Rd |only neotoma2-1.0.6/neotoma2/man/get_sites.sites.Rd |only neotoma2-1.0.6/neotoma2/man/get_specimens.Rd |only neotoma2-1.0.6/neotoma2/man/get_specimens.default.Rd |only neotoma2-1.0.6/neotoma2/man/get_specimens.numeric.Rd |only neotoma2-1.0.6/neotoma2/man/get_specimens.sites.Rd |only neotoma2-1.0.6/neotoma2/man/length-specimens-method.Rd |only neotoma2-1.0.6/neotoma2/man/names-specimen-method.Rd |only neotoma2-1.0.6/neotoma2/man/newURL.Rd |only neotoma2-1.0.6/neotoma2/man/parseURL.Rd |only neotoma2-1.0.6/neotoma2/man/parse_site.Rd |only neotoma2-1.0.6/neotoma2/man/parsebody.Rd |only neotoma2-1.0.6/neotoma2/man/show-specimen-method.Rd |only neotoma2-1.0.6/neotoma2/man/show-specimens-method.Rd |only neotoma2-1.0.6/neotoma2/man/specimens-collunit-method.Rd |only neotoma2-1.0.6/neotoma2/man/specimens-collunits-method.Rd |only neotoma2-1.0.6/neotoma2/man/specimens-site-method.Rd |only neotoma2-1.0.6/neotoma2/man/specimens-sites-method.Rd |only neotoma2-1.0.6/neotoma2/man/specimens.Rd |only neotoma2-1.0.6/neotoma2/man/sub-specimens-numeric-method.Rd |only neotoma2-1.0.6/neotoma2/man/sub-sub-specimens-numeric-method.Rd |only neotoma2-1.0.6/neotoma2/man/sub-subset-specimens-ANY-ANY-ANY-method.Rd |only neotoma2-1.0.6/neotoma2/man/subset-specimen-character-ANY-ANY-method.Rd |only neotoma2-1.0.6/neotoma2/man/subset-specimen-numeric-ANY-ANY-method.Rd |only neotoma2-1.0.6/neotoma2/man/toJSON-sites-method.Rd |only neotoma2-1.0.6/neotoma2/man/toJSON.Rd |only neotoma2-1.0.6/neotoma2/man/write.csv-specimens-method.Rd |only neotoma2-1.0.7/neotoma2/DESCRIPTION | 14 neotoma2-1.0.7/neotoma2/MD5 | 192 +--- neotoma2-1.0.7/neotoma2/NAMESPACE | 19 neotoma2-1.0.7/neotoma2/NEWS.md | 10 neotoma2-1.0.7/neotoma2/R/01_classDefinitions.R | 42 - neotoma2-1.0.7/neotoma2/R/02_genericDefinitions.R | 36 neotoma2-1.0.7/neotoma2/R/build_chron.R | 107 +- neotoma2-1.0.7/neotoma2/R/build_collunit.R | 71 - neotoma2-1.0.7/neotoma2/R/build_dataset.R | 47 - neotoma2-1.0.7/neotoma2/R/build_sample.R | 6 neotoma2-1.0.7/neotoma2/R/build_site.R | 85 -- neotoma2-1.0.7/neotoma2/R/chronology-methods.R | 4 neotoma2-1.0.7/neotoma2/R/cleanNULL.R | 22 neotoma2-1.0.7/neotoma2/R/dataset-methods.R | 6 neotoma2-1.0.7/neotoma2/R/filter.R | 12 neotoma2-1.0.7/neotoma2/R/get0_params.R |only neotoma2-1.0.7/neotoma2/R/get_datasets.R | 273 +------ neotoma2-1.0.7/neotoma2/R/get_downloads.R | 161 ---- neotoma2-1.0.7/neotoma2/R/get_publications.R | 68 - neotoma2-1.0.7/neotoma2/R/get_sites.R | 202 ----- neotoma2-1.0.7/neotoma2/R/get_specimens.R | 44 - neotoma2-1.0.7/neotoma2/R/get_stats.R | 4 neotoma2-1.0.7/neotoma2/R/get_table.R | 9 neotoma2-1.0.7/neotoma2/R/get_taxon.R | 11 neotoma2-1.0.7/neotoma2/R/getids.R |only neotoma2-1.0.7/neotoma2/R/group_data.R |only neotoma2-1.0.7/neotoma2/R/parseLocation.R |only neotoma2-1.0.7/neotoma2/R/parseURL.R | 387 +++------- neotoma2-1.0.7/neotoma2/R/parse_site.R |only neotoma2-1.0.7/neotoma2/R/pingNeotoma.R |only neotoma2-1.0.7/neotoma2/R/publication-methods.R | 1 neotoma2-1.0.7/neotoma2/R/samples-methods.R | 45 + neotoma2-1.0.7/neotoma2/R/samples.R | 6 neotoma2-1.0.7/neotoma2/R/set_chronology.R | 56 - neotoma2-1.0.7/neotoma2/R/set_collunit.R | 7 neotoma2-1.0.7/neotoma2/R/set_contacts.R | 3 neotoma2-1.0.7/neotoma2/R/set_dataset.R | 13 neotoma2-1.0.7/neotoma2/R/set_sample.R | 3 neotoma2-1.0.7/neotoma2/R/set_site.R | 5 neotoma2-1.0.7/neotoma2/R/site-methods.R | 12 neotoma2-1.0.7/neotoma2/R/testNull.R | 4 neotoma2-1.0.7/neotoma2/R/use_na.R | 29 neotoma2-1.0.7/neotoma2/inst/doc/neotoma2-package.R | 63 - neotoma2-1.0.7/neotoma2/inst/doc/neotoma2-package.Rmd | 63 - neotoma2-1.0.7/neotoma2/inst/doc/neotoma2-package.html | 145 +-- neotoma2-1.0.7/neotoma2/man/c-samples-method.Rd |only neotoma2-1.0.7/neotoma2/man/filter.sites.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_datasets.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_datasets.default.Rd | 17 neotoma2-1.0.7/neotoma2/man/get_downloads.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_downloads.numeric.Rd | 4 neotoma2-1.0.7/neotoma2/man/get_publications.publication.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_publications.publications.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_sites.Rd | 10 neotoma2-1.0.7/neotoma2/man/get_sites.default.Rd | 2 neotoma2-1.0.7/neotoma2/man/get_stats.Rd | 2 neotoma2-1.0.7/neotoma2/man/getids.Rd | 2 neotoma2-1.0.7/neotoma2/man/getids.collunit.Rd | 2 neotoma2-1.0.7/neotoma2/man/getids.collunits.Rd | 2 neotoma2-1.0.7/neotoma2/man/getids.site.Rd | 2 neotoma2-1.0.7/neotoma2/man/getids.sites.Rd | 2 neotoma2-1.0.7/neotoma2/man/pingNeotoma.Rd | 2 neotoma2-1.0.7/neotoma2/man/plotLeaflet.Rd | 2 neotoma2-1.0.7/neotoma2/man/set_collunit.Rd | 4 neotoma2-1.0.7/neotoma2/man/set_dataset.Rd | 11 neotoma2-1.0.7/neotoma2/man/set_site.Rd | 2 neotoma2-1.0.7/neotoma2/man/sub-subset-samples-ANY-ANY-ANY-method.Rd |only neotoma2-1.0.7/neotoma2/man/subset-sample-character-ANY-ANY-method.Rd |only neotoma2-1.0.7/neotoma2/tests/testthat/test-parse_location.R | 24 neotoma2-1.0.7/neotoma2/tests/testthat/test-set_server.R | 2 neotoma2-1.0.7/neotoma2/tests/testthat/test-toJSON.R | 27 neotoma2-1.0.7/neotoma2/tests/testthat/test_chroncontrols.R | 7 neotoma2-1.0.7/neotoma2/tests/testthat/test_datasets.R | 2 neotoma2-1.0.7/neotoma2/tests/testthat/test_download.R | 4 neotoma2-1.0.7/neotoma2/tests/testthat/test_generaltests.R | 39 - neotoma2-1.0.7/neotoma2/tests/testthat/test_sites.R | 54 - neotoma2-1.0.7/neotoma2/tests/testthat/test_specimens.R | 6 neotoma2-1.0.7/neotoma2/vignettes/neotoma2-package.Rmd | 63 - 125 files changed, 909 insertions(+), 1682 deletions(-)
Title: Bayesian Geostatistics Using Predictive Stacking
Description: Fits Bayesian hierarchical spatial and spatial-temporal process
models for point-referenced Gaussian, Poisson, binomial, and binary data
using stacking of predictive densities. It involves sampling from
analytically available posterior distributions conditional upon candidate
values of the spatial process parameters and, subsequently assimilate
inference from these individual posterior distributions using Bayesian
predictive stacking. Our algorithm is highly parallelizable and hence, much
faster than traditional Markov chain Monte Carlo algorithms while delivering
competitive predictive performance. See Zhang, Tang, and Banerjee (2025)
<doi:10.48550/arXiv.2304.12414>, and, Pan, Zhang, Bradley, and Banerjee
(2025) <doi:10.48550/arXiv.2406.04655> for details.
Author: Soumyakanti Pan [aut, cre] ,
Sudipto Banerjee [aut]
Maintainer: Soumyakanti Pan <span18@ucla.edu>
Diff between spStack versions 1.1.0 dated 2025-07-11 and 1.1.1 dated 2025-07-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 +++++++--- inst/doc/spatial.html | 4 ++-- src/util.cpp | 14 ++++---------- 5 files changed, 20 insertions(+), 22 deletions(-)
Title: Parallel Low-Rank Approximation with Nonnegativity Constraints
Description: 'Rcpp' bindings for 'PLANC', a highly parallel
and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library.
Wraps algorithms described in
Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and
Eswar et. al (2021) <doi:10.1145/3432185>.
Implements algorithms described in
Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>,
Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and
Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Author: Andrew Robbins [aut, cre] ,
Yichen Wang [aut],
Joshua Welch [cph] ,
Ramakrishnan Kannan [cph] ,
Conrad Sanderson [cph] ,
Blue Brain Project/EPFL [cph] ,
UT-Batelle [cph]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between RcppPlanc versions 2.0.12 dated 2025-05-29 and 2.0.13 dated 2025-07-14
DESCRIPTION | 10 MD5 | 30 - NEWS.md | 6 README.md | 36 +- build/vignette.rds |binary configure | 1 inst/doc/RcppPlanc.html | 10 src/planc/CMakeLists.txt | 61 ++- src/planc/common/progressWrapper.cpp | 9 src/planc/common/progressWrapper.h | 4 src/planc/nmf/NMFDriver.hpp | 2 src/planc/pyproject.toml | 9 tools/patches/00_remove_stdio.patch | 500 +++++++++++++--------------- tools/patches/01_remove_sprintf.patch | 196 ++++------ tools/patches/02_adjust_windows_types.patch | 14 tools/patches/03_remove_abort.patch | 47 -- 16 files changed, 454 insertions(+), 481 deletions(-)
Title: A Centralized Metadata Object Focus on Clinical Trial Data
Programming Workflows
Description: Create an immutable container holding metadata for the
purpose of better enabling programming activities and functionality of
other packages within the clinical programming workflow.
Author: Liam Hobby [aut, cre],
Christina Fillmore [aut] ,
Bill Denney [aut],
Maya Gans [aut] ,
Ashley Tarasiewicz [aut],
Mike Stackhouse [aut] ,
Tamara Senior [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Liam Hobby <liam.f.hobby@gsk.com>
Diff between metacore versions 0.1.3 dated 2024-05-02 and 0.2.0 dated 2025-07-14
metacore-0.1.3/metacore/inst/extdata/ADaM_define.xml |only metacore-0.2.0/metacore/DESCRIPTION | 74 metacore-0.2.0/metacore/LICENSE | 4 metacore-0.2.0/metacore/MD5 | 131 metacore-0.2.0/metacore/NAMESPACE | 247 metacore-0.2.0/metacore/NEWS.md | 105 metacore-0.2.0/metacore/R/DatasetMeta.R |only metacore-0.2.0/metacore/R/checks.R | 172 metacore-0.2.0/metacore/R/metacore.R | 1066 - metacore-0.2.0/metacore/R/spec_builder.R | 1557 - metacore-0.2.0/metacore/R/utils-pipe.R | 22 metacore-0.2.0/metacore/R/utils.R | 248 metacore-0.2.0/metacore/R/validators.R | 750 metacore-0.2.0/metacore/R/xml_builders.R | 831 metacore-0.2.0/metacore/R/xml_helpers.R | 58 metacore-0.2.0/metacore/R/zzz.R | 81 metacore-0.2.0/metacore/README.md | 451 metacore-0.2.0/metacore/build/vignette.rds |binary metacore-0.2.0/metacore/inst/doc/Building_Specification_Readers.R | 206 metacore-0.2.0/metacore/inst/doc/Building_Specification_Readers.Rmd | 476 metacore-0.2.0/metacore/inst/doc/Building_Specification_Readers.html | 1894 -- metacore-0.2.0/metacore/inst/doc/Example.R | 72 metacore-0.2.0/metacore/inst/doc/Example.Rmd | 132 metacore-0.2.0/metacore/inst/doc/Example.html | 905 - metacore-0.2.0/metacore/inst/extdata/ADaM_define_CDISC_pilot3.xml |only metacore-0.2.0/metacore/inst/extdata/SDTM_define.xml | 4228 ++-- metacore-0.2.0/metacore/inst/extdata/pilot_ADaM.rda |binary metacore-0.2.0/metacore/man/MetaCore_filter.Rd | 28 metacore-0.2.0/metacore/man/check_columns.Rd | 68 metacore-0.2.0/metacore/man/check_structure.Rd | 44 metacore-0.2.0/metacore/man/check_words.Rd | 32 metacore-0.2.0/metacore/man/checks.Rd | 88 metacore-0.2.0/metacore/man/create_tbl.Rd | 44 metacore-0.2.0/metacore/man/define_to_metacore.Rd | 38 metacore-0.2.0/metacore/man/get_control_term.Rd | 64 metacore-0.2.0/metacore/man/get_keys.Rd | 52 metacore-0.2.0/metacore/man/is_DatasetMeta.Rd |only metacore-0.2.0/metacore/man/is_metacore.Rd | 46 metacore-0.2.0/metacore/man/load_metacore.Rd | 34 metacore-0.2.0/metacore/man/metacore.Rd | 86 metacore-0.2.0/metacore/man/metacore_example.Rd | 42 metacore-0.2.0/metacore/man/pipe.Rd | 24 metacore-0.2.0/metacore/man/read_all_sheets.Rd | 34 metacore-0.2.0/metacore/man/save_metacore.Rd | 38 metacore-0.2.0/metacore/man/select_dataset.Rd | 45 metacore-0.2.0/metacore/man/spec_to_metacore.Rd | 52 metacore-0.2.0/metacore/man/spec_type.Rd | 34 metacore-0.2.0/metacore/man/spec_type_to_codelist.Rd | 114 metacore-0.2.0/metacore/man/spec_type_to_derivations.Rd | 92 metacore-0.2.0/metacore/man/spec_type_to_ds_spec.Rd | 78 metacore-0.2.0/metacore/man/spec_type_to_ds_vars.Rd | 98 metacore-0.2.0/metacore/man/spec_type_to_value_spec.Rd | 116 metacore-0.2.0/metacore/man/spec_type_to_var_spec.Rd | 80 metacore-0.2.0/metacore/man/verify_DatasetMeta.Rd |only metacore-0.2.0/metacore/man/xml_to_codelist.Rd | 58 metacore-0.2.0/metacore/man/xml_to_derivations.Rd | 54 metacore-0.2.0/metacore/man/xml_to_ds_spec.Rd | 52 metacore-0.2.0/metacore/man/xml_to_ds_vars.Rd | 52 metacore-0.2.0/metacore/man/xml_to_value_spec.Rd | 56 metacore-0.2.0/metacore/man/xml_to_var_spec.Rd | 56 metacore-0.2.0/metacore/tests/testthat.R | 8 metacore-0.2.0/metacore/tests/testthat/define-2021.xml | 4226 ++-- metacore-0.2.0/metacore/tests/testthat/define2-0-0.xsl | 8592 +++++----- metacore-0.2.0/metacore/tests/testthat/test-checks.R | 89 metacore-0.2.0/metacore/tests/testthat/test-metacore.R | 308 metacore-0.2.0/metacore/tests/testthat/test-utils.R | 106 metacore-0.2.0/metacore/tests/testthat/test-validators.R | 236 metacore-0.2.0/metacore/vignettes/Building_Specification_Readers.Rmd | 476 metacore-0.2.0/metacore/vignettes/Example.Rmd | 132 69 files changed, 14838 insertions(+), 14844 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Sturges (1926) <doi:10.1080/01621459.1926.10502161> formula.
CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt).
FishPar(): Calculates length-based [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.7 dated 2024-11-21 and 0.1.8 dated 2025-07-14
DESCRIPTION | 15 MD5 | 39 +- NAMESPACE | 17 + R/DataDescription.R | 84 +++-- R/FishPar.R | 631 ++++++++++++++++++++++------------------ R/FishSS.R | 2 R/FrequencyTable.R | 128 ++++---- R/LWR.R |only build/vignette.rds |binary data/LWdata.rda |only inst/doc/Introduction.R | 53 +++ inst/doc/Introduction.Rmd | 146 +++++++-- inst/doc/Introduction.html | 704 ++++++++++++++++++++++++++++----------------- inst/exdata/LWdata.xlsx |only man/CPdata.Rd | 28 - man/ExData.Rd | 10 man/FishPar.Rd | 31 + man/FrequencyTable.Rd | 44 +- man/LWR.Rd |only man/LWdata.Rd |only man/lenfreq01.Rd | 10 man/lenfreq02.Rd | 10 vignettes/Introduction.Rmd | 146 +++++++-- 23 files changed, 1314 insertions(+), 784 deletions(-)
Title: Speaker Recognition, Voice Analysis and Mood Inference via Music
Theory
Description: Provides tools for audio data analysis, including feature extraction, pitch detection, and speaker identification. Designed for voice research and signal processing applications.
Author: Zabala Filipe J. [cre, aut]
Maintainer: Zabala Filipe J. <filipezabala@gmail.com>
Diff between voice versions 0.4.21 dated 2023-04-19 and 0.5.4 dated 2025-07-14
voice-0.4.21/voice/inst/doc/voicegnette_R.R |only voice-0.4.21/voice/inst/doc/voicegnette_R.Rmd |only voice-0.4.21/voice/inst/doc/voicegnette_R.html |only voice-0.4.21/voice/vignettes/index_2021-08-15.html |only voice-0.4.21/voice/vignettes/index_2021-09-03.html |only voice-0.4.21/voice/vignettes/index_2021-09-16_143012.html |only voice-0.4.21/voice/vignettes/index_2021-09-17_000220.html |only voice-0.4.21/voice/vignettes/index_2021-11-08.html |only voice-0.4.21/voice/vignettes/index_2022-09-07.html |only voice-0.4.21/voice/vignettes/index_2022-09-14.html |only voice-0.4.21/voice/vignettes/musescore.png |only voice-0.4.21/voice/vignettes/rttm.png |only voice-0.4.21/voice/vignettes/split.png |only voice-0.4.21/voice/vignettes/test.WAV |only voice-0.4.21/voice/vignettes/vignettes_old.zip |only voice-0.4.21/voice/vignettes/voicegnette_R.Rmd |only voice-0.5.4/voice/DESCRIPTION | 27 voice-0.5.4/voice/MD5 | 81 - voice-0.5.4/voice/NAMESPACE | 12 voice-0.5.4/voice/NEWS.md | 920 +++++++------- voice-0.5.4/voice/R/assign_notes.R |only voice-0.5.4/voice/R/check_chords.R |only voice-0.5.4/voice/R/cut_audio.R |only voice-0.5.4/voice/R/diarize.R | 11 voice-0.5.4/voice/R/embed_media.R |only voice-0.5.4/voice/R/extract_features.R | 22 voice-0.5.4/voice/R/media_files.R |only voice-0.5.4/voice/R/notes.R | 18 voice-0.5.4/voice/R/notes_freq.R | 2 voice-0.5.4/voice/R/piano_plot.R |only voice-0.5.4/voice/R/splitw.R | 2 voice-0.5.4/voice/R/spn2abc.R |only voice-0.5.4/voice/R/utils.R |only voice-0.5.4/voice/README.md | 326 ---- voice-0.5.4/voice/build/partial.rdb |binary voice-0.5.4/voice/build/vignette.rds |binary voice-0.5.4/voice/inst/doc/voicegnette_CRAN.R |only voice-0.5.4/voice/inst/doc/voicegnette_CRAN.Rmd |only voice-0.5.4/voice/inst/doc/voicegnette_CRAN.html |only voice-0.5.4/voice/inst/media |only voice-0.5.4/voice/man/assign_notes.Rd |only voice-0.5.4/voice/man/check_chords.Rd |only voice-0.5.4/voice/man/cut_audio.Rd |only voice-0.5.4/voice/man/diarize.Rd | 9 voice-0.5.4/voice/man/embed_audio.Rd |only voice-0.5.4/voice/man/embed_video.Rd |only voice-0.5.4/voice/man/extract_features.Rd | 19 voice-0.5.4/voice/man/is.audio.Rd |only voice-0.5.4/voice/man/is.hosted.Rd |only voice-0.5.4/voice/man/is.local.Rd |only voice-0.5.4/voice/man/is.url.Rd |only voice-0.5.4/voice/man/is.video.Rd |only voice-0.5.4/voice/man/media-files.Rd |only voice-0.5.4/voice/man/notes.Rd | 2 voice-0.5.4/voice/man/notes_freq.Rd | 2 voice-0.5.4/voice/man/piano_plot.Rd |only voice-0.5.4/voice/man/spn2abc.Rd |only voice-0.5.4/voice/man/url.exists.Rd |only voice-0.5.4/voice/vignettes/img |only voice-0.5.4/voice/vignettes/index.html | 803 ++++++++---- voice-0.5.4/voice/vignettes/voicegnette_CRAN.Rmd |only 61 files changed, 1249 insertions(+), 1007 deletions(-)
Title: Truncated Harmonic Mean Estimator of the Marginal Likelihood
Description: Implements the truncated harmonic mean estimator (THAMES)
of the reciprocal marginal likelihood using posterior samples and
unnormalized log posterior values via reciprocal importance sampling.
Metodiev, Perrot-Dockès, Ouadah, Irons, Latouche, & Raftery (2024).
Bayesian Analysis. <doi:10.1214/24-BA1422>.
Author: Nicholas J. Irons [aut, cre] ,
Marie Perrot-Dockes [aut],
Martin Metodiev [aut]
Maintainer: Nicholas J. Irons <nicholasjonirons@gmail.com>
Diff between thames versions 0.1.1 dated 2023-10-27 and 0.1.2 dated 2025-07-14
DESCRIPTION | 20 +-- MD5 | 19 +-- NAMESPACE | 4 R/bound_par_cor.R | 3 R/thames.R | 7 - R/uniformly_functions.R |only build/vignette.rds |binary inst/doc/multivariate-gaussian.R | 2 inst/doc/multivariate-gaussian.html | 202 ++++++++++++++---------------------- man/runif_ellipsoid.Rd |only man/runif_sphere.Rd |only man/thames.Rd | 7 - 12 files changed, 118 insertions(+), 146 deletions(-)
Title: Bindings to 'GDAL'
Description: API bindings to the Geospatial Data Abstraction Library ('GDAL',
<https://gdal.org>). Implements the 'GDAL' Raster and Vector Data Models.
Bindings are implemented with 'Rcpp' modules. Exposed C++ classes and
stand-alone functions wrap much of the 'GDAL' API and provide additional
functionality. Calling signatures resemble the native C, C++ and Python APIs
provided by the 'GDAL' project. Class 'GDALRaster' encapsulates a
'GDALDataset' and its raster band objects. Class 'GDALVector' encapsulates
an 'OGRLayer' and the 'GDALDataset' that contains it. Class 'VSIFile'
provides bindings to the 'GDAL' 'VSIVirtualHandle' API. Additional classes
include 'CmbTable' for counting unique combinations of integers, and
'RunningStats' for computing summary statistics efficiently on large data
streams. C++ stand-alone functions provide bindings to most 'GDAL' raster
and vector utilities including 'OGR' facilities for vector geoprocessing,
several algorithms, the Geometry API ('GEOS' via 'GDAL' he [...truncated...]
Author: Chris Toney [aut, cre] ,
Michael D. Sumner [ctb],
Frank Warmerdam [ctb, cph] ,
Even Rouault [ctb, cph] ,
Marius Appel [ctb, cph] ,
Daniel James [ctb, cph] ,
Peter Dimov [ctb, cph]
Maintainer: Chris Toney <jctoney@gmail.com>
Diff between gdalraster versions 2.0.0 dated 2025-05-11 and 2.1.0 dated 2025-07-14
gdalraster-2.0.0/gdalraster/man/g_buffer.Rd |only gdalraster-2.0.0/gdalraster/man/g_make_valid.Rd |only gdalraster-2.0.0/gdalraster/man/g_simplify.Rd |only gdalraster-2.0.0/gdalraster/man/g_swap_xy.Rd |only gdalraster-2.1.0/gdalraster/DESCRIPTION | 10 gdalraster-2.1.0/gdalraster/MD5 | 173 - gdalraster-2.1.0/gdalraster/NEWS.md | 55 gdalraster-2.1.0/gdalraster/R/RcppExports.R | 151 - gdalraster-2.1.0/gdalraster/R/cmb_table.R | 4 gdalraster-2.1.0/gdalraster/R/display.R | 4 gdalraster-2.1.0/gdalraster/R/gdal_create.R | 85 gdalraster-2.1.0/gdalraster/R/gdal_helpers.R | 8 gdalraster-2.1.0/gdalraster/R/gdal_rat.R | 6 gdalraster-2.1.0/gdalraster/R/gdal_util.R | 2 gdalraster-2.1.0/gdalraster/R/gdalraster_proc.R | 262 +- gdalraster-2.1.0/gdalraster/R/gdalvector.R | 35 gdalraster-2.1.0/gdalraster/R/geom.R | 1217 ++++++--- gdalraster-2.1.0/gdalraster/R/ogr_define.R | 329 ++ gdalraster-2.1.0/gdalraster/R/ogr_manage.R | 441 ++- gdalraster-2.1.0/gdalraster/R/running_stats.R | 2 gdalraster-2.1.0/gdalraster/R/s3_methods.R | 15 gdalraster-2.1.0/gdalraster/README.md | 56 gdalraster-2.1.0/gdalraster/build/vignette.rds |binary gdalraster-2.1.0/gdalraster/configure | 36 gdalraster-2.1.0/gdalraster/configure.ac | 2 gdalraster-2.1.0/gdalraster/inst/doc/raster-api-tutorial.html | 2 gdalraster-2.1.0/gdalraster/inst/doc/raster-attribute-tables.html | 110 gdalraster-2.1.0/gdalraster/inst/doc/vector-api-overview.Rmd | 9 gdalraster-2.1.0/gdalraster/inst/doc/vector-api-overview.html | 67 gdalraster-2.1.0/gdalraster/inst/extdata/domains.gdb.zip |only gdalraster-2.1.0/gdalraster/inst/extdata/test_ogr_geojson_mixed_timezone.geojson |only gdalraster-2.1.0/gdalraster/man/CmbTable-class.Rd | 4 gdalraster-2.1.0/gdalraster/man/GDALVector-class.Rd | 37 gdalraster-2.1.0/gdalraster/man/RunningStats-class.Rd | 2 gdalraster-2.1.0/gdalraster/man/addFilesInZip.Rd | 8 gdalraster-2.1.0/gdalraster/man/bandCopyWholeRaster.Rd | 6 gdalraster-2.1.0/gdalraster/man/buildRAT.Rd | 6 gdalraster-2.1.0/gdalraster/man/buildVRT.Rd | 2 gdalraster-2.1.0/gdalraster/man/calc.Rd | 2 gdalraster-2.1.0/gdalraster/man/create.Rd | 4 gdalraster-2.1.0/gdalraster/man/createColorRamp.Rd | 8 gdalraster-2.1.0/gdalraster/man/fillNodata.Rd | 2 gdalraster-2.1.0/gdalraster/man/g_binary_op.Rd | 6 gdalraster-2.1.0/gdalraster/man/g_binary_pred.Rd | 8 gdalraster-2.1.0/gdalraster/man/g_envelope.Rd | 20 gdalraster-2.1.0/gdalraster/man/g_measures.Rd | 13 gdalraster-2.1.0/gdalraster/man/g_query.Rd | 11 gdalraster-2.1.0/gdalraster/man/g_transform.Rd | 6 gdalraster-2.1.0/gdalraster/man/g_unary_op.Rd |only gdalraster-2.1.0/gdalraster/man/g_util.Rd |only gdalraster-2.1.0/gdalraster/man/g_wk2wk.Rd | 12 gdalraster-2.1.0/gdalraster/man/gdalraster-package.Rd | 10 gdalraster-2.1.0/gdalraster/man/ogr_define.Rd | 135 - gdalraster-2.1.0/gdalraster/man/ogr_manage.Rd | 116 gdalraster-2.1.0/gdalraster/man/pixel_extract.Rd | 66 gdalraster-2.1.0/gdalraster/man/rasterFromRaster.Rd | 18 gdalraster-2.1.0/gdalraster/man/rasterToVRT.Rd | 24 gdalraster-2.1.0/gdalraster/man/rasterize.Rd | 4 gdalraster-2.1.0/gdalraster/man/read_ds.Rd | 4 gdalraster-2.1.0/gdalraster/man/srs_convert.Rd | 48 gdalraster-2.1.0/gdalraster/man/transform_bounds.Rd | 21 gdalraster-2.1.0/gdalraster/man/warp.Rd | 2 gdalraster-2.1.0/gdalraster/src/RcppExports.cpp | 343 +- gdalraster-2.1.0/gdalraster/src/gdal_exp.cpp | 48 gdalraster-2.1.0/gdalraster/src/gdal_vsi.cpp | 2 gdalraster-2.1.0/gdalraster/src/gdal_vsi.h | 2 gdalraster-2.1.0/gdalraster/src/gdalraster.cpp | 70 gdalraster-2.1.0/gdalraster/src/gdalraster.h | 16 gdalraster-2.1.0/gdalraster/src/gdalvector.cpp | 422 ++- gdalraster-2.1.0/gdalraster/src/gdalvector.h | 3 gdalraster-2.1.0/gdalraster/src/geom_api.cpp | 1309 +++++++--- gdalraster-2.1.0/gdalraster/src/geom_api.h | 109 gdalraster-2.1.0/gdalraster/src/ogr_util.cpp | 902 ++++++ gdalraster-2.1.0/gdalraster/src/ogr_util.h | 21 gdalraster-2.1.0/gdalraster/src/rcpp_util.cpp | 2 gdalraster-2.1.0/gdalraster/src/rcpp_util.h | 4 gdalraster-2.1.0/gdalraster/src/srs_api.cpp | 118 gdalraster-2.1.0/gdalraster/src/srs_api.h | 5 gdalraster-2.1.0/gdalraster/src/transform.cpp | 140 - gdalraster-2.1.0/gdalraster/src/transform.h | 13 gdalraster-2.1.0/gdalraster/src/vsifile.cpp | 4 gdalraster-2.1.0/gdalraster/src/vsifile.h | 4 gdalraster-2.1.0/gdalraster/tests/testthat/test-GDALVector-class.R | 789 +++++- gdalraster-2.1.0/gdalraster/tests/testthat/test-gdal_create.R |only gdalraster-2.1.0/gdalraster/tests/testthat/test-gdal_vsi.R | 2 gdalraster-2.1.0/gdalraster/tests/testthat/test-gdalraster_proc.R | 170 + gdalraster-2.1.0/gdalraster/tests/testthat/test-geom.R | 651 ++++ gdalraster-2.1.0/gdalraster/tests/testthat/test-ogr_manage.R | 284 ++ gdalraster-2.1.0/gdalraster/tests/testthat/test-s3_methods.R | 12 gdalraster-2.1.0/gdalraster/tests/testthat/test-srs_api.R | 6 gdalraster-2.1.0/gdalraster/tests/testthat/test-transform.R | 61 gdalraster-2.1.0/gdalraster/vignettes/vector-api-overview.Rmd | 9 92 files changed, 7272 insertions(+), 1935 deletions(-)
Title: Access Data from 'GISCO'
Description: Access data related to the European union from 'GISCO'
<https://ec.europa.eu/eurostat/web/gisco>, the Geographic Information
System of the European Commission, via its rest API at
<https://gisco-services.ec.europa.eu>.
This package tries to make it easier to get these data into R.
Author: Vilmos Prokaj [aut, cre]
Maintainer: Vilmos Prokaj <prokaj.vilmos@gmail.com>
Diff between eudata versions 0.1.2 dated 2025-07-09 and 0.1.3 dated 2025-07-14
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NAMESPACE | 79 ------------------------------------------- R/eudata-package.R | 90 -------------------------------------------------- inst/doc/example.html | 30 ++++++---------- 5 files changed, 20 insertions(+), 195 deletions(-)
Title: Visualizing Classification Results
Description: Tools to visualize the results of a classification or a regression.
The graphical displays include stacked plots, silhouette plots, quasi residual plots, class maps, predictions plots, and predictions correlation plots.
Implements the techniques described and illustrated in Raymaekers J., Rousseeuw P.J., Hubert M. (2022). Class maps for visualizing classification results. \emph{Technometrics}, 64(2), 151–165. \doi{10.1080/00401706.2021.1927849}
(open access), Raymaekers J., Rousseeuw P.J.(2022). Silhouettes and quasi residual plots for neural nets and tree-based classifiers. \emph{Journal of Computational and Graphical Statistics}, 31(4), 1332–1343. \doi{10.1080/10618600.2022.2050249}, and Rousseeuw, P.J. (2025). Explainable Linear and Generalized Linear Models by the Predictions Plot. <doi:10.48550/arXiv.2412.16980> (open access).
Examples can be found in the vignettes:
"Discriminant_analysis_examples","K_nearest_neighbors_examples",
"Support_vector_machine_examples", "Rpart_exa [...truncated...]
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between classmap versions 1.2.5 dated 2025-06-18 and 1.2.6 dated 2025-07-14
DESCRIPTION | 23 ++++++++++---------- MD5 | 29 ++++++++++++++++---------- NAMESPACE | 12 ++++++++-- R/predsplot.R |only build/vignette.rds |binary inst/doc/Discriminant_analysis_examples.html | 6 ++--- inst/doc/K_nearest_neighbors_examples.html | 4 +-- inst/doc/Neural_net_examples.html | 4 +-- inst/doc/Random_forest_examples.html | 4 +-- inst/doc/Rpart_examples.html | 4 +-- inst/doc/Support_vector_machine_examples.Rmd | 3 -- inst/doc/Support_vector_machine_examples.html | 11 ++++----- inst/doc/predsplot_examples.R |only inst/doc/predsplot_examples.Rmd |only inst/doc/predsplot_examples.html |only man/predscor.Rd |only man/predsplot.Rd |only vignettes/Support_vector_machine_examples.Rmd | 3 -- vignettes/predsplot_examples.Rmd |only 19 files changed, 57 insertions(+), 46 deletions(-)
Title: Air Quality Evaluation
Description: Developed for use by those tasked with the routine detection, characterisation and quantification of
discrete changes in air quality time-series, such as identifying the impacts of air quality policy
interventions. The main functions use signal isolation then break-point/segment (BP/S) methods based
on 'strucchange' and 'segmented' methods to detect and quantify change events (Ropkins & Tate, 2021,
<doi:10.1016/j.scitotenv.2020.142374>).
Author: Karl Ropkins [aut, cre] ,
Anthony Walker [aut] ,
James Tate [aut]
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>
Diff between AQEval versions 0.6.0 dated 2025-01-09 and 0.6.2 dated 2025-07-14
DESCRIPTION | 35 +++++++++++++++++------------------ MD5 | 20 ++++++++++++++------ NEWS.md | 3 +++ R/calculate.stats.R | 6 +++++- R/isolate.signal.R | 34 ++++++++++++++++++++++++++++++++-- build/partial.rdb |binary inst/tinytest |only man/isolate.signal.Rd | 4 ++++ tests |only 9 files changed, 75 insertions(+), 27 deletions(-)
Title: Annotate Package Load Calls
Description: Provides non-invasive annotation of package load calls
such as \code{library()}, \code{p_load()}, and \code{require()} so that we can have an idea of what
the packages we are loading are meant for.
Author: Luis D. Verde Arregoitia [aut, cre] ,
Juan Cruz Rodriguez [ctb],
Hadley Wickham [ctb]
Maintainer: Luis D. Verde Arregoitia <luis@liomys.mx>
Diff between annotater versions 0.2.3 dated 2024-01-26 and 0.2.4 dated 2025-07-14
annotater-0.2.3/annotater/inst/media |only annotater-0.2.4/annotater/DESCRIPTION | 18 annotater-0.2.4/annotater/MD5 | 51 +- annotater-0.2.4/annotater/NAMESPACE | 7 annotater-0.2.4/annotater/NEWS.md | 5 annotater-0.2.4/annotater/R/annotate_active_file.R | 5 annotater-0.2.4/annotater/R/annotate_fun_calls.R | 38 + annotater-0.2.4/annotater/R/annotate_fun_calls_active_file.R | 7 annotater-0.2.4/annotater/R/annotate_pkg_datasets_active.R | 5 annotater-0.2.4/annotater/R/annotate_r_version.R |only annotater-0.2.4/annotater/R/annotate_repo_source.R | 16 annotater-0.2.4/annotater/R/annotate_repos_active_file.R | 5 annotater-0.2.4/annotater/R/annotate_repostitle.R | 44 +- annotater-0.2.4/annotater/R/annotate_repostitle_active.R | 5 annotater-0.2.4/annotater/R/expand_metapackages_active.R | 5 annotater-0.2.4/annotater/R/globals.R |only annotater-0.2.4/annotater/README.md | 221 ++++++++--- annotater-0.2.4/annotater/build/vignette.rds |binary annotater-0.2.4/annotater/inst/doc/annotater_intro.R | 4 annotater-0.2.4/annotater/inst/doc/annotater_intro.Rmd | 4 annotater-0.2.4/annotater/inst/doc/annotater_intro.html | 12 annotater-0.2.4/annotater/inst/rstudio/addins.dcf | 5 annotater-0.2.4/annotater/man/annotate_r_version.Rd |only annotater-0.2.4/annotater/man/annotate_repo_source.Rd | 2 annotater-0.2.4/annotater/man/annotate_repostitle.Rd | 2 annotater-0.2.4/annotater/vignettes/annotater_intro.Rmd | 4 26 files changed, 301 insertions(+), 164 deletions(-)
Title: Truncated Harmonic Mean Estimator of the Marginal Likelihood for
Mixtures
Description: Implements the truncated harmonic mean estimator (THAMES)
of the reciprocal marginal likelihood for uni- and multivariate mixture
models using posterior samples and unnormalized log posterior values via
reciprocal importance sampling.
Metodiev, Irons, Perrot-Dockès, Latouche & Raftery (2025)
<doi:10.48550/arXiv.2504.21812>.
Author: Martin Metodiev [aut, cre, cph] ,
Nicholas J. Irons [aut] ,
Marie Perrot-Dockes [aut]
Maintainer: Martin Metodiev <m.metodiev@tutanota.com>
Diff between thamesmix versions 0.1.2 dated 2025-06-26 and 0.1.3 dated 2025-07-14
DESCRIPTION | 10 +++++----- MD5 | 19 +++++++++++-------- NAMESPACE | 4 +++- NEWS.md | 9 ++------- R/compute_W_c_volB.R | 3 +-- R/unformly_functions.R |only inst/doc/thames_mixtures_vignette.R | 1 - inst/doc/thames_mixtures_vignette.Rmd | 1 - inst/doc/thames_mixtures_vignette.html | 2 +- man/runif_ellipsoid.Rd |only man/runif_sphere.Rd |only vignettes/thames_mixtures_vignette.Rmd | 1 - 12 files changed, 23 insertions(+), 27 deletions(-)
Title: Bayesian Estimation of Multivariate Threshold Autoregressive
Models
Description: Estimation, inference and forecasting using the Bayesian approach for multivariate threshold autoregressive (TAR) models in which the distribution used to describe the noise process belongs to the class of Gaussian variance mixtures.
Author: Luis Hernando Vanegas [aut, cre],
Sergio Alejandro Calderon [aut],
Luz Marina Rondon [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between mtarm versions 0.1.5 dated 2025-05-07 and 0.1.6 dated 2025-07-14
DESCRIPTION | 6 +-- MD5 | 6 +-- R/mtar.R | 102 ++++++++++++++++++++++++++++++++++++++-------------------- man/simtar.Rd | 9 ++--- 4 files changed, 78 insertions(+), 45 deletions(-)
Title: Logic Forest
Description: Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
Author: Bethany Wolf [aut],
Melica Nikahd [ctb, cre],
Andrew Gothard [ctb],
Madison Hyer [ctb]
Maintainer: Melica Nikahd <melica.nikahd@osumc.edu>
Diff between LogicForest versions 2.1.1 dated 2024-03-13 and 2.1.2 dated 2025-07-14
LogicForest-2.1.1/LogicForest/R/LF.data.R |only LogicForest-2.1.1/LogicForest/R/LogicForest-package.R |only LogicForest-2.1.1/LogicForest/R/Perms.R |only LogicForest-2.1.1/LogicForest/R/pimp.mat_.R |only LogicForest-2.1.1/LogicForest/build/vignette.rds |only LogicForest-2.1.1/LogicForest/data |only LogicForest-2.1.1/LogicForest/inst |only LogicForest-2.1.1/LogicForest/man/LF.data.Rd |only LogicForest-2.1.1/LogicForest/man/pimp.mat.Rd |only LogicForest-2.1.1/LogicForest/vignettes |only LogicForest-2.1.2/LogicForest/DESCRIPTION | 16 - LogicForest-2.1.2/LogicForest/MD5 | 64 ++-- LogicForest-2.1.2/LogicForest/NAMESPACE | 9 LogicForest-2.1.2/LogicForest/R/TTab.R | 28 + LogicForest-2.1.2/LogicForest/R/a.frame.logreg2.R |only LogicForest-2.1.2/LogicForest/R/find.ctree.R |only LogicForest-2.1.2/LogicForest/R/logforest.R | 226 +++++++++++---- LogicForest-2.1.2/LogicForest/R/p.combos.R | 37 +- LogicForest-2.1.2/LogicForest/R/perms.R |only LogicForest-2.1.2/LogicForest/R/pimp.import.R | 216 +++++++++++--- LogicForest-2.1.2/LogicForest/R/pimp.mat.bin.R |only LogicForest-2.1.2/LogicForest/R/pimp.mat.nonbin.R |only LogicForest-2.1.2/LogicForest/R/predict.logforest.R | 76 ++++- LogicForest-2.1.2/LogicForest/R/predict.logreg2.R |only LogicForest-2.1.2/LogicForest/R/prime.imp.R | 29 - LogicForest-2.1.2/LogicForest/R/print.LFprediction.R | 16 - LogicForest-2.1.2/LogicForest/R/print.logforest.R | 35 +- LogicForest-2.1.2/LogicForest/R/proportion.positive.R | 59 ++- LogicForest-2.1.2/LogicForest/R/zzz_globals.R |only LogicForest-2.1.2/LogicForest/build/partial.rdb |only LogicForest-2.1.2/LogicForest/man/Perms.Rd | 8 LogicForest-2.1.2/LogicForest/man/TTab.Rd | 26 + LogicForest-2.1.2/LogicForest/man/find.ctree.Rd |only LogicForest-2.1.2/LogicForest/man/frame.logreg2.Rd |only LogicForest-2.1.2/LogicForest/man/logforest.Rd | 103 +++++- LogicForest-2.1.2/LogicForest/man/p.combos.Rd | 8 LogicForest-2.1.2/LogicForest/man/pimp.import.Rd | 48 ++- LogicForest-2.1.2/LogicForest/man/pimp.mat.bin.Rd |only LogicForest-2.1.2/LogicForest/man/pimp.mat.nonbin.Rd |only LogicForest-2.1.2/LogicForest/man/predict.logforest.Rd |only LogicForest-2.1.2/LogicForest/man/predict.logreg2.Rd |only LogicForest-2.1.2/LogicForest/man/prime.imp.Rd | 16 - LogicForest-2.1.2/LogicForest/man/print.LFprediction.Rd |only LogicForest-2.1.2/LogicForest/man/print.logforest.Rd |only LogicForest-2.1.2/LogicForest/man/proportion.positive.Rd | 10 45 files changed, 784 insertions(+), 246 deletions(-)
Title: A System of Plotting Optimized for Speed and Modularity
Description: A high-level plotting system, compatible with `ggplot2` objects,
maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the
'grid' package. The objective of the package is to provide a plotting system
that is built for speed and modularity. This is useful for quick visualizations
when testing code and for plotting multiple figures to the same device from
independent sources that may be independent of one another (i.e., different
function or modules the create the visualizations).
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
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 quickPlot versions 1.0.2 dated 2023-07-02 and 1.0.4 dated 2025-07-14
quickPlot-1.0.2/quickPlot/tests/testthat/_snaps/Plot |only quickPlot-1.0.4/quickPlot/DESCRIPTION | 32 quickPlot-1.0.4/quickPlot/MD5 | 253 +- quickPlot-1.0.4/quickPlot/NAMESPACE | 12 quickPlot-1.0.4/quickPlot/NEWS.md | 60 quickPlot-1.0.4/quickPlot/R/plotting-colours.R | 21 quickPlot-1.0.4/quickPlot/R/plotting-helpers.R | 1000 +++++----- quickPlot-1.0.4/quickPlot/R/plotting-other.R | 135 - quickPlot-1.0.4/quickPlot/R/plotting.R | 129 - quickPlot-1.0.4/quickPlot/R/quickPlot-package.R | 26 quickPlot-1.0.4/quickPlot/R/testing-helpers.R | 46 quickPlot-1.0.4/quickPlot/README.md | 10 quickPlot-1.0.4/quickPlot/build/vignette.rds |binary quickPlot-1.0.4/quickPlot/inst/WORDLIST | 3 quickPlot-1.0.4/quickPlot/inst/doc/iii-plotting.R | 150 - quickPlot-1.0.4/quickPlot/inst/doc/iii-plotting.Rmd | 92 quickPlot-1.0.4/quickPlot/inst/doc/iii-plotting.html | 366 +-- quickPlot-1.0.4/quickPlot/man/Plot-internal.Rd | 6 quickPlot-1.0.4/quickPlot/man/Plot.Rd | 14 quickPlot-1.0.4/quickPlot/man/coordinates.Rd | 8 quickPlot-1.0.4/quickPlot/man/dev.Rd | 2 quickPlot-1.0.4/quickPlot/man/extent.Rd | 25 quickPlot-1.0.4/quickPlot/man/layerNames.Rd | 8 quickPlot-1.0.4/quickPlot/man/newPlot.Rd | 8 quickPlot-1.0.4/quickPlot/man/parseArgs.Rd | 2 quickPlot-1.0.4/quickPlot/man/plotGrob.Rd | 11 quickPlot-1.0.4/quickPlot/man/quickPlot-package.Rd | 4 quickPlot-1.0.4/quickPlot/man/quickPlotMouseClicks.Rd | 4 quickPlot-1.0.4/quickPlot/man/sp2sl.Rd | 16 quickPlot-1.0.4/quickPlot/man/thin.Rd | 8 quickPlot-1.0.4/quickPlot/man/whereInStack.Rd | 6 quickPlot-1.0.4/quickPlot/tests/testthat/_snaps/Plot-snapshots |only quickPlot-1.0.4/quickPlot/tests/testthat/helper-testInit.R | 50 quickPlot-1.0.4/quickPlot/tests/testthat/setup.R | 1 quickPlot-1.0.4/quickPlot/tests/testthat/test-Plot-do-call.R | 4 quickPlot-1.0.4/quickPlot/tests/testthat/test-Plot-nonVisual.R | 10 quickPlot-1.0.4/quickPlot/tests/testthat/test-Plot-snapshots.R |only quickPlot-1.0.4/quickPlot/tests/testthat/test-Plot.R | 838 -------- quickPlot-1.0.4/quickPlot/tests/testthat/test-examples.R | 1 quickPlot-1.0.4/quickPlot/vignettes/iii-plotting.Rmd | 92 40 files changed, 1449 insertions(+), 2004 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends <doi:10.32614/RJ-2021-048>. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The recommended approach is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.1.1 dated 2025-06-06 and 1.1.2 dated 2025-07-14
DESCRIPTION | 6 +++--- MD5 | 18 ++++++++++-------- NEWS.md | 11 +++++++++++ R/globals.R | 4 ++-- R/utils-debug.R | 33 ++++++++++++--------------------- R/with.DoPar.R | 6 +++--- R/zzz.R | 7 +++++++ build/vignette.rds |binary inst/testme/test-with.DoPar.R |only man/with.DoPar.Rd | 2 +- tests/test-with.DoPar.R |only 11 files changed, 49 insertions(+), 38 deletions(-)
Title: Bayesian Cost Effectiveness Analysis
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
This package computes the most cost-effective alternative and
produces graphical summaries and probabilistic sensitivity analysis,
see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.
Author: Gianluca Baio [aut, cre, cph] ,
Andrea Berardi [aut] ,
Anna Heath [aut] ,
Nathan Green [aut]
Maintainer: Gianluca Baio <g.baio@ucl.ac.uk>
Diff between BCEA versions 2.4.8 dated 2025-07-04 and 2.4.81 dated 2025-07-14
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS.md | 11 ++++++++++- R/ceac_plot_graph.R | 4 ++-- R/compute_xxx.R | 43 ++++++++++++++++++++++++++++++------------- R/multi.ce.R | 1 + R/summary.pairwise.R | 6 +++--- R/zzz.R | 2 +- build/partial.rdb |binary man/BCEA-package.Rd | 4 ++-- 10 files changed, 64 insertions(+), 37 deletions(-)
Title: Fast and Vectorized Base 64 Engine
Description: Provides a fast, lightweight, and vectorized base 64 engine
to encode and decode character and raw vectors as well as files stored
on disk. Common base 64 alphabets are supported out of the box
including the standard, URL-safe, bcrypt, crypt, 'BinHex', and
IMAP-modified UTF-7 alphabets. Custom engines can be created to
support unique base 64 encoding and decoding needs.
Author: Josiah Parry [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between b64 versions 0.1.6 dated 2025-05-19 and 0.1.7 dated 2025-07-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ src/rust/Cargo.lock | 19 +++++++++++-------- src/rust/Cargo.toml | 15 ++++++--------- src/rust/src/lib.rs | 8 ++++---- src/rust/vendor-config.toml | 4 ---- src/rust/vendor.tar.xz |binary 8 files changed, 37 insertions(+), 36 deletions(-)
Title: Multivariate Normal Probabilities using Vecchia Approximation
Description: Under a different representation of the multivariate normal (MVN) probability, we can use the Vecchia approximation to sample the integrand at a linear complexity with respect to n. Additionally, both the SOV algorithm from Genz (92) and the exponential-tilting method from Botev (2017) can be adapted to linear complexity. The reference for the method implemented in this package is Jian Cao and Matthias Katzfuss (2024) "Linear-Cost Vecchia Approximation of Multivariate Normal Probabilities" <doi:10.48550/arXiv.2311.09426>. Two major references for the development of our method are Alan Genz (1992) "Numerical Computation of Multivariate Normal Probabilities" <doi:10.1080/10618600.1992.10477010> and Z. I. Botev (2017) "The Normal Law Under Linear Restrictions: Simulation and Estimation via Minimax Tilting" <doi:10.48550/arXiv.1603.04166>.
Author: Jian Cao [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Jian Cao <jcao2416@gmail.com>
Diff between VeccTMVN versions 1.2.1 dated 2024-11-26 and 1.3.0 dated 2025-07-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++-- R/mvnrnd_cwrap.R | 7 ++++++- R/rnd_TMVN.R | 4 ++++ R/rnd_TMVT.R | 4 ++++ 6 files changed, 26 insertions(+), 12 deletions(-)
Title: Parsing, Anonymizing and Visualizing Exported 'WhatsApp' Chat
Logs
Description: Imports 'WhatsApp' chat logs and parses them into
a usable dataframe object. The parser works on chats exported
from Android or iOS phones and on Linux, macOS and Windows. The parser has multiple options for extracting smileys and emojis
from the messages, extracting URLs and domains from the messages, extracting names and types of sent
media files from the messages, extracting timestamps from messages, extracting and anonymizing author
names from messages. Can be used to create anonymized versions of data.
Author: Julian Kohne [aut, cre]
Maintainer: Julian Kohne <julian.kohne@gesis.org>
Diff between WhatsR versions 1.0.4 dated 2024-01-29 and 1.0.6 dated 2025-07-14
WhatsR-1.0.4/WhatsR/README.md |only WhatsR-1.0.4/WhatsR/man/figures/plot_location().png |only WhatsR-1.0.6/WhatsR/DESCRIPTION | 22 +- WhatsR-1.0.6/WhatsR/MD5 | 170 ++++++++-------- WhatsR-1.0.6/WhatsR/NAMESPACE | 9 WhatsR-1.0.6/WhatsR/R/download_emoji.R | 1 WhatsR-1.0.6/WhatsR/R/parse_android.R | 9 WhatsR-1.0.6/WhatsR/R/parse_chat.R | 79 ++++++- WhatsR-1.0.6/WhatsR/R/parse_ios.R | 9 WhatsR-1.0.6/WhatsR/R/plot_locations.R | 111 +++------- WhatsR-1.0.6/WhatsR/R/plot_network.R | 5 WhatsR-1.0.6/WhatsR/inst/CITATION | 20 + WhatsR-1.0.6/WhatsR/inst/EnglishAndroid24H_default.rds |binary WhatsR-1.0.6/WhatsR/inst/EnglishAndroidAMPM_default.rds |binary WhatsR-1.0.6/WhatsR/inst/EnglishIos24H_default.rds |binary WhatsR-1.0.6/WhatsR/inst/EnglishIosAMPM_default.rds |binary WhatsR-1.0.6/WhatsR/inst/GermanAndroid24H_default.rds |binary WhatsR-1.0.6/WhatsR/inst/GermanAndroidAMPM_default.rds |binary WhatsR-1.0.6/WhatsR/inst/GermanIos24H_default.rds |binary WhatsR-1.0.6/WhatsR/inst/GermanIosAMPM_default.rds |binary WhatsR-1.0.6/WhatsR/inst/Languages.csv | 10 WhatsR-1.0.6/WhatsR/inst/TailoredData1.rds |binary WhatsR-1.0.6/WhatsR/inst/TailoredData2.rds |binary WhatsR-1.0.6/WhatsR/inst/TailoredData3.rds |binary WhatsR-1.0.6/WhatsR/inst/TailoredData4.rds |binary WhatsR-1.0.6/WhatsR/inst/englishandroid24h.txt | 2 WhatsR-1.0.6/WhatsR/inst/englishandroidampm.txt | 2 WhatsR-1.0.6/WhatsR/inst/englishios24h.txt | 2 WhatsR-1.0.6/WhatsR/inst/englishiosampm.txt | 2 WhatsR-1.0.6/WhatsR/inst/germanandroid24h.txt | 2 WhatsR-1.0.6/WhatsR/inst/germanandroidampm.txt | 2 WhatsR-1.0.6/WhatsR/inst/germanios24h.txt | 2 WhatsR-1.0.6/WhatsR/inst/germaniosampm.txt | 2 WhatsR-1.0.6/WhatsR/inst/summarize_chat1.rds |binary WhatsR-1.0.6/WhatsR/inst/summarize_chat2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_emoji1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_emoji2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_emoji3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_emoji4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_lediplo1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_lediplo2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_lediplo3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_lediplo4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_links1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_links2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_links3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_links4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_location1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_location2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_location3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_location4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_media1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_media2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_media3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_media4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_messages1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_messages2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_messages3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_messages4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_network1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_network2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_network3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_network4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_replytimes1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_replytimes2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_replytimes3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_replytimes4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_smilies1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_smilies2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_smilies3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_smilies4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tokens1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tokens2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tokens3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tokens4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tot1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tot2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tot3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_tot4.rds |binary WhatsR-1.0.6/WhatsR/inst/test_wc1.rds |binary WhatsR-1.0.6/WhatsR/inst/test_wc2.rds |binary WhatsR-1.0.6/WhatsR/inst/test_wc3.rds |binary WhatsR-1.0.6/WhatsR/inst/test_wc4.rds |binary WhatsR-1.0.6/WhatsR/man/figures/plot_locations().png |only WhatsR-1.0.6/WhatsR/man/plot_locations.Rd | 17 - WhatsR-1.0.6/WhatsR/man/plot_network.Rd | 2 WhatsR-1.0.6/WhatsR/tests/testthat/Rplots.pdf |only WhatsR-1.0.6/WhatsR/tests/testthat/test-WhatsR-tests.R | 110 +++++++--- 88 files changed, 351 insertions(+), 239 deletions(-)
Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre],
Luke Winslow [aut],
Scott Chamberlain [ctb],
Alison Appling [ctb],
Jordan Read [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between sbtools versions 1.4.0 dated 2025-07-07 and 1.4.1 dated 2025-07-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/gql_helpers.R | 13 +++++++++++++ R/item_replace_files.R | 2 +- R/item_rm.R | 2 +- R/item_rm_files.R | 20 +++++++++++++------- inst/doc/sbtools.html | 20 ++++++++++---------- man/item_rm_recursive.Rd | 2 +- 9 files changed, 54 insertions(+), 31 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.11 dated 2024-12-19 and 0.3.12 dated 2025-07-14
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 15 ++++++++------- MD5 | 18 ++++++++++-------- R/anytime.R | 7 ++++++- README.md | 15 ++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary configure |only inst/NEWS.Rd | 12 +++++++++++- inst/doc/anytime-introduction.pdf |binary inst/tinytest/test_gh_issue_135.R |only 11 files changed, 77 insertions(+), 20 deletions(-)
Title: Interfacing 'NaileR' with 'Shiny'
Description: A very small package for more convenient use of 'NaileR'. You provide a data set containing a latent variable you want to understand. It generates a description and an interpretation of this latent variable using a Large Language Model. For perceptual data, it describes the stimuli used in the experiment.
Author: Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Diff between PolisheR versions 1.1.0 dated 2025-07-13 and 1.1.1 dated 2025-07-14
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 11 ++++++ R/shiny_nail_catdes.R | 81 ++++++++++++++++++++++++++++++++--------------- R/shiny_nail_condes.R | 24 ++++++++----- man/shiny_nail_catdes.Rd | 9 +++-- 6 files changed, 95 insertions(+), 46 deletions(-)
Title: Search and Get Data from the I14Y Interoperability Platform of
Switzerland
Description: Search and download Swiss data and metadata from the I14Y
interoperability platform of Switzerland using its public APIs
<https://www.i14y.admin.ch/api/index.html>.
Author: Felix Luginbuhl [aut, cre, cph] ,
Felix Lorenz [ctr]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between I14Y versions 0.1.4 dated 2025-06-09 and 0.1.5 dated 2025-07-14
I14Y-0.1.4/I14Y/R/i14y_get_data_element.R |only I14Y-0.1.4/I14Y/R/i14y_get_dataset_description.R |only I14Y-0.1.4/I14Y/R/i14y_get_dataset_distributions.R |only I14Y-0.1.4/I14Y/man/i14y_get_data_element.Rd |only I14Y-0.1.4/I14Y/man/i14y_get_dataset_description.Rd |only I14Y-0.1.4/I14Y/man/i14y_get_dataset_distributions.Rd |only I14Y-0.1.4/I14Y/tests/testthat/test-i14y_get_data_element.R |only I14Y-0.1.4/I14Y/tests/testthat/test-i14y_get_dataset_description.R |only I14Y-0.1.4/I14Y/tests/testthat/test-i14y_get_dataset_distributions.R |only I14Y-0.1.4/I14Y/tests/testthat/testthat-problems.rds |only I14Y-0.1.5/I14Y/DESCRIPTION | 17 I14Y-0.1.5/I14Y/MD5 | 51 - I14Y-0.1.5/I14Y/NAMESPACE | 4 I14Y-0.1.5/I14Y/NEWS.md | 12 I14Y-0.1.5/I14Y/R/i14y_get_dataset_metadata.R |only I14Y-0.1.5/I14Y/R/i14y_search_catalog.R | 4 I14Y-0.1.5/I14Y/R/i14y_search_concept.R | 50 + I14Y-0.1.5/I14Y/README.md | 271 +++++----- I14Y-0.1.5/I14Y/man/i14y_get_codelist.Rd | 50 - I14Y-0.1.5/I14Y/man/i14y_get_concept.Rd | 50 - I14Y-0.1.5/I14Y/man/i14y_get_concept_all_versions.Rd | 50 - I14Y-0.1.5/I14Y/man/i14y_get_content_information.Rd | 44 - I14Y-0.1.5/I14Y/man/i14y_get_data_service.Rd | 50 - I14Y-0.1.5/I14Y/man/i14y_get_data_structure.Rd | 48 - I14Y-0.1.5/I14Y/man/i14y_get_dataset_metadata.Rd |only I14Y-0.1.5/I14Y/man/i14y_get_nomenclature_level.Rd | 68 +- I14Y-0.1.5/I14Y/man/i14y_get_nomenclature_level_multiple.Rd | 92 +-- I14Y-0.1.5/I14Y/man/i14y_search_catalog.Rd | 110 ++-- I14Y-0.1.5/I14Y/man/i14y_search_concept.Rd | 80 +- I14Y-0.1.5/I14Y/man/i14y_search_nomenclature.Rd | 68 +- I14Y-0.1.5/I14Y/tests/testthat.R | 24 I14Y-0.1.5/I14Y/tests/testthat/test-i14y_get_dataset_metadata.R |only I14Y-0.1.5/I14Y/tests/testthat/test-i14y_search_concept.R | 10 33 files changed, 590 insertions(+), 563 deletions(-)
Title: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site
Motifs
Description: A comprehensive suite of helper functions designed to facilitate the analysis of genomic annotations from the 'GENCODE' database <https://www.gencodegenes.org/>, supporting both human and mouse genomes. This toolkit enables users to extract, filter, and analyze a wide range of annotation features including genes, transcripts, exons, and introns across different 'GENCODE' releases. It provides functionality for cross-version comparisons, allowing researchers to systematically track annotation updates, structural changes, and feature-level differences between releases. In addition, the package can generate high-quality FASTA files containing donor and acceptor splice site motifs, which are formatted for direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004 <doi:10.1089/1066527041410418>), enabling accurate calculation of splice site strength scores.
Author: Monah Abou Alezz [aut, cre, cph] ,
Lorenzo Salviati [ctb],
Roberta Alfieri [ctb],
Silvia Bione [ctb]
Maintainer: Monah Abou Alezz <aboualezz.monah@hsr.it>
Diff between GencoDymo2 versions 1.0.1 dated 2025-05-15 and 1.0.2 dated 2025-07-14
GencoDymo2-1.0.1/GencoDymo2/tests |only GencoDymo2-1.0.2/GencoDymo2/DESCRIPTION | 21 GencoDymo2-1.0.2/GencoDymo2/MD5 | 38 GencoDymo2-1.0.2/GencoDymo2/NAMESPACE | 2 GencoDymo2-1.0.2/GencoDymo2/NEWS.md | 10 GencoDymo2-1.0.2/GencoDymo2/R/files.R | 6 GencoDymo2-1.0.2/GencoDymo2/R/introns.R | 199 GencoDymo2-1.0.2/GencoDymo2/R/utils.R | 96 GencoDymo2-1.0.2/GencoDymo2/README.md | 258 GencoDymo2-1.0.2/GencoDymo2/build/vignette.rds |binary GencoDymo2-1.0.2/GencoDymo2/inst/doc/GencoDymo2_vignette.R | 410 GencoDymo2-1.0.2/GencoDymo2/inst/doc/GencoDymo2_vignette.html | 4223 +++++----- GencoDymo2-1.0.2/GencoDymo2/man/assign_splice_sites.Rd | 40 GencoDymo2-1.0.2/GencoDymo2/man/calculate_gc_content.Rd | 17 GencoDymo2-1.0.2/GencoDymo2/man/extract_cds_sequences.Rd | 29 GencoDymo2-1.0.2/GencoDymo2/man/extract_ss_motif.Rd | 55 GencoDymo2-1.0.2/GencoDymo2/man/find_cryptic_splice_sites.Rd | 18 GencoDymo2-1.0.2/GencoDymo2/man/get_gff3.Rd | 2 GencoDymo2-1.0.2/GencoDymo2/man/get_gtf.Rd | 2 GencoDymo2-1.0.2/GencoDymo2/man/get_latest_release.Rd | 2 20 files changed, 2706 insertions(+), 2722 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.2.5 dated 2025-04-05 and 0.2.6 dated 2025-07-14
CopernicusMarine-0.2.5/CopernicusMarine/tests/testthat/test_stac.r |only CopernicusMarine-0.2.6/CopernicusMarine/DESCRIPTION | 23 - CopernicusMarine-0.2.6/CopernicusMarine/MD5 | 67 ++-- CopernicusMarine-0.2.6/CopernicusMarine/NAMESPACE | 8 CopernicusMarine-0.2.6/CopernicusMarine/NEWS.md | 11 CopernicusMarine-0.2.6/CopernicusMarine/R/cms_catalogue_entry.R |only CopernicusMarine-0.2.6/CopernicusMarine/R/cms_cite_product.r | 3 CopernicusMarine-0.2.6/CopernicusMarine/R/cms_download_native.R |only CopernicusMarine-0.2.6/CopernicusMarine/R/cms_download_stac.r | 88 +----- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_download_subset.r | 94 ------ CopernicusMarine-0.2.6/CopernicusMarine/R/cms_list_stac_files.r | 80 ----- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_login.r | 136 +++++++--- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_product_details.r | 64 ++-- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_product_metadata.r | 62 ++-- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_product_services.r | 40 +- CopernicusMarine-0.2.6/CopernicusMarine/R/cms_products_list.r | 20 + CopernicusMarine-0.2.6/CopernicusMarine/R/cms_stac_properties.r | 25 - CopernicusMarine-0.2.6/CopernicusMarine/R/cms_wmts.r | 11 CopernicusMarine-0.2.6/CopernicusMarine/R/generics.r | 99 ++++--- CopernicusMarine-0.2.6/CopernicusMarine/README.md | 117 +++++--- CopernicusMarine-0.2.6/CopernicusMarine/man/account.Rd |only CopernicusMarine-0.2.6/CopernicusMarine/man/cms_cite_product.Rd | 1 CopernicusMarine-0.2.6/CopernicusMarine/man/cms_download_native.Rd |only CopernicusMarine-0.2.6/CopernicusMarine/man/cms_download_subset.Rd | 12 CopernicusMarine-0.2.6/CopernicusMarine/man/cms_get_client_info.Rd |only CopernicusMarine-0.2.6/CopernicusMarine/man/cms_login.Rd | 25 - CopernicusMarine-0.2.6/CopernicusMarine/man/cms_product_details.Rd | 31 -- CopernicusMarine-0.2.6/CopernicusMarine/man/cms_product_metadata.Rd | 28 -- CopernicusMarine-0.2.6/CopernicusMarine/man/cms_product_services.Rd | 11 CopernicusMarine-0.2.6/CopernicusMarine/man/cms_products_list.Rd | 8 CopernicusMarine-0.2.6/CopernicusMarine/man/cms_stac.Rd | 45 --- CopernicusMarine-0.2.6/CopernicusMarine/man/figures/README-leaflet-1.png |binary CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/helper.r | 38 +- CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_dev.r | 47 +-- CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_login.r |only CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_native.r |only CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_product.r |only CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_subset.r | 43 --- CopernicusMarine-0.2.6/CopernicusMarine/tests/testthat/test_wmts.r | 69 ++++- 39 files changed, 617 insertions(+), 689 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
NNG is a socket library for reliable, high-performance messaging over
in-process, IPC, TCP, WebSocket and secure TLS transports. Implements
'Scalability Protocols', a standard for common communications patterns
including publish/subscribe, request/reply and service discovery. As
its own threaded concurrency framework, provides a toolkit for
asynchronous programming and distributed computing. Intuitive 'aio'
objects resolve automatically when asynchronous operations complete,
and synchronisation primitives allow R to wait upon events signalled
by concurrent threads.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.6.1 dated 2025-06-23 and 1.6.2 dated 2025-07-14
DESCRIPTION | 8 - MD5 | 24 ++--- NEWS.md | 6 + R/context.R | 6 - man/nanonext-package.Rd | 2 man/request.Rd | 6 - src/aio.c | 124 +++++++++++++++++++++--------- src/core.c | 65 --------------- src/nanonext.h | 37 +++++++-- src/ncurl.c | 197 +++++++++++++++++++++++++----------------------- src/sync.c | 48 +++++++++++ src/thread.c | 6 - tests/tests.R | 4 13 files changed, 303 insertions(+), 230 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.14 dated 2025-06-09 and 0.2.15 dated 2025-07-14
DESCRIPTION | 8 MD5 | 123 NAMESPACE | 7 NEWS.md | 32 R/RcppExports.R | 285 + R/getDesignMeans.R | 634 ++- R/getDesignProportions.R | 353 ++ R/getDesignSurvivals.R | 121 R/lrstat-package.R | 4 R/prints.R | 178 - R/wrappers.R | 403 ++ inst/doc/maxcombo.html | 93 inst/shinyApp/app.R | 5544 ++++++++++++++++----------------- man/BOINTable.Rd | 6 man/ClopperPearsonCI.Rd | 6 man/getDesignANOVA.Rd | 2 man/getDesignANOVAContrast.Rd | 2 man/getDesignEquiv.Rd | 14 man/getDesignMeanDiffCarryover.Rd | 7 man/getDesignMeanDiffCarryoverEquiv.Rd | 7 man/getDesignMeanDiffMMRM.Rd | 73 man/getDesignOddsRatio.Rd | 419 +- man/getDesignOneMultinom.Rd | 152 man/getDesignOneProportion.Rd | 8 man/getDesignOneSlope.Rd | 19 man/getDesignOrderedBinom.Rd | 169 - man/getDesignPairedPropMcNemar.Rd | 424 +- man/getDesignRepeatedANOVA.Rd | 6 man/getDesignRiskDiff.Rd | 418 +- man/getDesignRiskRatio.Rd | 417 +- man/getDesignRiskRatioFM.Rd | 422 +- man/getDesignSlopeDiff.Rd | 28 man/getDesignSlopeDiffMMRM.Rd | 55 man/getDesignTwoMultinom.Rd | 166 man/getDesignTwoOrdinal.Rd | 181 - man/getDesignUnorderedBinom.Rd | 154 man/getDesignUnorderedMultinom.Rd | 184 - man/getDesignWilcoxon.Rd | 32 man/hazard_pd.Rd |only man/hazard_sub.Rd |only man/hedgesg.Rd | 10 man/liferegr.Rd | 8 man/logisregr.Rd | 5 man/lrschoenfeld.Rd | 442 +- man/lrsim2e.Rd | 4 man/lrsim2e3a.Rd | 4 man/lrsim3a.Rd | 2 man/lrsimsub.Rd |only man/mTPI2Table.Rd | 5 man/pbvnorm.Rd |only man/phregr.Rd | 5 man/pwexpcuts.Rd | 23 man/pwexploglik.Rd | 117 man/rmvnorm.Rd |only src/RcppExports.cpp | 153 src/kmstat.cpp | 73 src/logistic_regression.cpp | 16 src/logistic_regression.h | 1 src/lrsim.cpp | 1820 ++++++++-- src/lrstat.cpp | 83 src/rmstat.cpp | 80 src/survival_analysis.cpp | 791 +--- src/survival_analysis.h | 8 src/utilities.cpp | 175 - src/utilities.h | 20 65 files changed, 9255 insertions(+), 5746 deletions(-)
Title: Quasi Analysis of Variance for K-Functions
Description: One-way and two-way analysis of variance for replicated point
patterns, grouped by one or two classification factors, on the
basis of the corresponding K-functions.
Author: Rolf Turner [aut, cre]
Maintainer: Rolf Turner <rolfturner@posteo.net>
Diff between kanova versions 0.3-18 dated 2025-07-03 and 0.3-19 dated 2025-07-13
kanova-0.3-18/kanova/inst/preVignettes/testStat.pdf |only kanova-0.3-19/kanova/ChangeLog | 12 ++++++ kanova-0.3-19/kanova/DESCRIPTION | 8 ++-- kanova-0.3-19/kanova/MD5 | 17 ++++---- kanova-0.3-19/kanova/R/kanova.R | 2 - kanova-0.3-19/kanova/data/stomata.rda |binary kanova-0.3-19/kanova/inst/doc/testStat.pdf |binary kanova-0.3-19/kanova/inst/preVignettes/testStat.log | 4 +- kanova-0.3-19/kanova/inst/preVignettes/testStat.tex | 16 ++++---- kanova-0.3-19/kanova/man/kanova.Rd | 39 +++++++++----------- 10 files changed, 54 insertions(+), 44 deletions(-)
Title: Relational Operators for Intervals
Description: Evaluating if values
of vectors are within different open/closed intervals
(`x %[]% c(a, b)`), or if two closed
intervals overlap (`c(a1, b1) %[]o[]% c(a2, b2)`).
Operators for negation and directional relations also implemented.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between intrval versions 0.1-3 dated 2024-05-20 and 1.0-0 dated 2025-07-13
DESCRIPTION | 18 ++++++++---- MD5 | 12 ++++---- NAMESPACE | 5 ++- R/intrnals.R | 80 +++++++++++++++++++++++++++++++++++++++++------------- R/zzz.R |only build/partial.rdb |binary man/opts.Rd |only tests/tests.R | 1 8 files changed, 87 insertions(+), 29 deletions(-)
Title: Analysis of Niche Evolution using Niche and Distribution Models
Description: Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Author: Dan Warren [aut, cre] ,
Russell Dinnage [aut]
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between ENMTools versions 1.1.2 dated 2024-01-16 and 1.1.4 dated 2025-07-13
DESCRIPTION | 16 +++++++++------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 22 ++++++++++++++++++++++ R/background.buffer.R | 6 +++--- R/combine.species.R | 45 ++++++++++++++++++++++++++------------------- R/enmtools.bc.R | 6 +++--- R/enmtools.dm.R | 6 +++--- R/enmtools.ecospat.id.R | 16 ++++++++-------- R/enmtools.gam.R | 6 +++--- R/enmtools.glm.R | 6 +++--- R/enmtools.maxent.R | 6 +++--- R/enmtools.rf.R | 6 +++--- R/enmtools.rf.ranger.R | 6 +++--- R/enmtools.vip.R | 20 ++++++++++---------- R/moses.list.R | 4 ++-- R/visualize.enm.R | 45 +++++++++++++++++++++++++++++++-------------- man/visualize.enm.Rd | 6 +++--- 17 files changed, 151 insertions(+), 103 deletions(-)
Title: Tools for Manipulating Gas Exchange Data
Description: Set of tools for manipulating gas exchange data from cardiopulmonary exercise testing.
Author: Felipe Mattioni Maturana [aut, cre]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between whippr versions 0.1.3 dated 2024-02-19 and 0.1.4 dated 2025-07-13
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/averages.R | 28 +++++++++++++++++++++++----- R/max.R | 2 +- R/read-data.R | 4 ++-- README.md | 26 +++++++++++++------------- man/perform_average.Rd | 13 +++++++++++++ 8 files changed, 71 insertions(+), 34 deletions(-)
Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb] ,
Dianne Cook [aut, cre] ,
Nick Spyrison [ctb] ,
Ursula Laa [ctb] ,
H. Sherry Zhang [ctb] ,
Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between tourr versions 1.2.4 dated 2025-02-13 and 1.2.6 dated 2025-07-13
DESCRIPTION | 27 ++++++++++++++------------- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/animate.r | 4 ++++ build/vignette.rds |binary inst/doc/edges.html | 4 ++-- 6 files changed, 33 insertions(+), 20 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) <https://apps.dtic.mil/sti/citations/ADA020296>, Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.1.4 dated 2025-05-16 and 0.1.5 dated 2025-07-13
ReliaGrowR-0.1.4/ReliaGrowR/inst/Abstract.Rmd |only ReliaGrowR-0.1.4/ReliaGrowR/inst/Abstract.html |only ReliaGrowR-0.1.4/ReliaGrowR/inst/Abstract.log |only ReliaGrowR-0.1.4/ReliaGrowR/inst/Abstract.tex |only ReliaGrowR-0.1.5/ReliaGrowR/DESCRIPTION | 6 ReliaGrowR-0.1.5/ReliaGrowR/MD5 | 39 ++-- ReliaGrowR-0.1.5/ReliaGrowR/NAMESPACE | 2 ReliaGrowR-0.1.5/ReliaGrowR/NEWS.md | 5 ReliaGrowR-0.1.5/ReliaGrowR/R/plot_rga.R | 87 +++++---- ReliaGrowR-0.1.5/ReliaGrowR/R/rga.R | 49 ++--- ReliaGrowR-0.1.5/ReliaGrowR/inst/doc/RGA.R | 6 ReliaGrowR-0.1.5/ReliaGrowR/inst/doc/RGA.Rmd | 22 +- ReliaGrowR-0.1.5/ReliaGrowR/inst/doc/RGA.html | 64 +++--- ReliaGrowR-0.1.5/ReliaGrowR/inst/paper.Rmd |only ReliaGrowR-0.1.5/ReliaGrowR/inst/paper.docx |only ReliaGrowR-0.1.5/ReliaGrowR/inst/paper.html |only ReliaGrowR-0.1.5/ReliaGrowR/inst/paper.log |only ReliaGrowR-0.1.5/ReliaGrowR/inst/paper.tex |only ReliaGrowR-0.1.5/ReliaGrowR/man/figures/README-unnamed-chunk-4-1.png |binary ReliaGrowR-0.1.5/ReliaGrowR/man/plot_rga.Rd | 5 ReliaGrowR-0.1.5/ReliaGrowR/man/rga.Rd | 8 ReliaGrowR-0.1.5/ReliaGrowR/tests/testthat/Rplots.pdf |binary ReliaGrowR-0.1.5/ReliaGrowR/tests/testthat/test-plot-rga.R | 70 ++++--- ReliaGrowR-0.1.5/ReliaGrowR/tests/testthat/test-rga.R | 94 +++------- ReliaGrowR-0.1.5/ReliaGrowR/vignettes/RGA.Rmd | 22 +- 25 files changed, 243 insertions(+), 236 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between mefa4 versions 0.3-11 dated 2024-05-20 and 0.3-12 dated 2025-07-13
DESCRIPTION | 17 ++++++++++++----- MD5 | 6 +++--- build/partial.rdb |binary man/Xtab.Rd | 2 +- 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Hierarchical Models Made Easy with Data Cloning
Description: S4 classes around infrastructure provided by the
'coda' and 'dclone' packages to make package development easy as a breeze
with data cloning for hierarchical models.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between dcmle versions 0.4-1 dated 2023-07-04 and 0.4-2 dated 2025-07-13
DESCRIPTION | 17 ++++++++++++----- MD5 | 6 +++--- man/dcFit-class.Rd | 2 +- man/gsFit-class.Rd | 2 +- 4 files changed, 17 insertions(+), 10 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing
maximum likelihood estimating procedures for
complex models using data cloning and Bayesian
Markov chain Monte Carlo methods
as described in Solymos 2010 <doi:10.32614/RJ-2010-011>.
Sequential and parallel MCMC support
for 'JAGS', 'WinBUGS', 'OpenBUGS', and 'Stan'.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between dclone versions 2.3-2 dated 2023-07-03 and 2.3-3 dated 2025-07-13
DESCRIPTION | 17 +++++++--- MD5 | 72 ++++++++++++++++++++++---------------------- NEWS.md | 5 +++ man/DcloneEnv.Rd | 2 - man/bugs.fit.Rd | 2 - man/bugs.parfit.Rd | 2 - man/clusterSize.Rd | 2 - man/clusterSplitSB.Rd | 2 - man/codaSamples.Rd | 2 - man/coef.mcmc.list.Rd | 2 - man/dc.fit.Rd | 2 - man/dc.parfit.Rd | 2 - man/dcFit.Rd | 2 - man/dclone-package.Rd | 2 - man/dclone.Rd | 2 - man/dcoptions.Rd | 4 +- man/dctable.Rd | 2 - man/errlines.Rd | 2 - man/evalParallelArgument.Rd | 2 - man/jags.fit.Rd | 2 - man/jags.parfit.Rd | 2 - man/jagsModel.Rd | 2 - man/lambdamax.diag.Rd | 2 - man/make.symmetric.Rd | 2 - man/mcmcapply.Rd | 2 - man/nclones.Rd | 2 - man/pairs.mcmc.list.Rd | 2 - man/parCodaSamples.Rd | 2 - man/parDosa.Rd | 2 - man/parJagsModel.Rd | 2 - man/parLoadModule.Rd | 2 - man/parSetFactory.Rd | 2 - man/parUpdate.Rd | 2 - man/parallel.inits.Rd | 2 - man/stan.fit.Rd | 2 - man/update.mcmc.list.Rd | 2 - man/write.jags.model.Rd | 2 - 37 files changed, 88 insertions(+), 76 deletions(-)
Title: Weighted-Average Least Squares Model Averaging
Description: Implements Weighted-Average Least Squares model averaging
for negative binomial regression models of Huynh (2024) <doi:10.48550/arXiv.2404.11324>,
generalized linear models of De Luca, Magnus, Peracchi (2018)
<doi:10.1016/j.jeconom.2017.12.007> and linear regression models of
Magnus, Powell, Pruefer (2010) <doi:10.1016/j.jeconom.2009.07.004>, see also
Magnus, De Luca (2016) <doi:10.1111/joes.12094>. Weighted-Average Least Squares
for the linear regression model is based on the original 'MATLAB' code by
Magnus and De Luca <https://www.janmagnus.nl/items/WALS.pdf>, see also
Kumar, Magnus (2013) <doi:10.1007/s13571-013-0060-9> and
De Luca, Magnus (2011) <doi:10.1177/1536867X1201100402>.
Author: Kevin Huynh [aut, cre]
Maintainer: Kevin Huynh <kevin.huynh-dev@gmx.ch>
Diff between WALS versions 0.2.5 dated 2024-06-21 and 0.2.6 dated 2025-07-13
DESCRIPTION | 16 MD5 | 108 +- NAMESPACE | 122 +- NEWS.md | 54 - R/WALS-package.R | 10 R/computePosterior.R | 226 ++--- R/data.R | 272 +++--- R/familyPrior.R | 452 +++++----- R/familyWALS.R | 824 +++++++++--------- R/fitNB2.R | 292 +++--- R/predictCounts.R | 128 +- R/tools.R | 1276 ++++++++++++++--------------- R/wals.R | 1666 ++++++++++++++++++------------------- R/walsGLM.R | 1694 +++++++++++++++++++------------------- R/walsNB.R | 1848 +++++++++++++++++++++--------------------- build/partial.rdb |binary inst/CITATION | 36 inst/REFERENCES.bib | 374 ++++---- man/GrowthMP.Rd | 194 ++-- man/GrowthMPP.Rd | 122 +- man/checkSingularitySVD.Rd | 44 - man/computeGamma1.Rd | 186 ++-- man/computeGamma1r.Rd | 138 +-- man/computeGammaUnSVD.Rd | 144 +-- man/computePosterior.Rd | 110 +- man/computeX2M1X2.Rd | 136 +-- man/controlGLM.Rd | 72 - man/controlNB.Rd | 126 +- man/ddweibull.Rd | 72 - man/dlaplace.Rd | 66 - man/dsubbotin.Rd | 74 - man/familyPrior.Rd | 206 ++-- man/familyWALS.Rd | 276 +++--- man/fitNB2.Rd | 112 +- man/gammaToBeta.Rd | 134 +-- man/negativeBinomial.Rd | 50 - man/predict.wals.Rd | 372 ++++---- man/predict.walsGLM.Rd | 464 +++++----- man/predictCounts.Rd | 102 +- man/semiorthogonalize.Rd | 160 +-- man/snbinom.Rd | 68 - man/svdLSplus.Rd | 114 +- man/vcov.walsNB.Rd | 42 man/wals.Rd | 432 ++++----- man/walsFit.Rd | 274 +++--- man/walsGLM.Rd | 404 ++++----- man/walsGLMfit.Rd | 198 ++-- man/walsGLMfitIterate.Rd | 244 ++--- man/walsNB.Rd | 420 ++++----- man/walsNBfit.Rd | 422 ++++----- man/walsNBfitIterate.Rd | 260 ++--- tests/testthat.R | 8 tests/testthat/test-wals.R | 460 +++++----- tests/testthat/test-walsGLM.R | 348 +++---- tests/testthat/test-walsNB.R | 514 +++++------ 55 files changed, 8483 insertions(+), 8483 deletions(-)
Title: Models and Data Sets for the Study of Species-Area Relationships
Description: Hierarchical models for the analysis of species-area
relationships (SARs) by combining several data sets and covariates;
with a global data set combining individual SAR studies;
as described in Solymos and Lele
(2012) <doi:10.1111/j.1466-8238.2011.00655.x>.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between sharx versions 1.0-6 dated 2024-05-21 and 1.0-7 dated 2025-07-13
DESCRIPTION | 17 ++++++++++++----- MD5 | 4 ++-- inst/ChangeLog | 3 +++ 3 files changed, 17 insertions(+), 7 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem [aut],
Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between PVAClone versions 0.1-7 dated 2024-01-23 and 0.1-8 dated 2025-07-13
PVAClone-0.1-7/PVAClone/data/paurelia.R |only PVAClone-0.1-7/PVAClone/data/redstart.R |only PVAClone-0.1-7/PVAClone/data/songsparrow.R |only PVAClone-0.1-8/PVAClone/DESCRIPTION | 20 +++++++++++++++----- PVAClone-0.1-8/PVAClone/MD5 | 12 ++++++------ PVAClone-0.1-8/PVAClone/build/partial.rdb |binary PVAClone-0.1-8/PVAClone/data/paurelia.rda |only PVAClone-0.1-8/PVAClone/data/redstart.rda |only PVAClone-0.1-8/PVAClone/data/songsparrow.rda |only PVAClone-0.1-8/PVAClone/man/pva-class.Rd | 2 +- 10 files changed, 22 insertions(+), 12 deletions(-)
Title: Likelihood Based Optimal Partitioning and Indicator Species
Analysis
Description: Likelihood based optimal partitioning and indicator
species analysis. Finding the best binary partition for each species
based on model selection, with the possibility to take into account
modifying/confounding variables as described
in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>.
The package implements binary and multi-level response models,
various measures of uncertainty, Lorenz-curve based thresholding,
with native support for parallel computations.
Author: Peter Solymos [aut, cre] ,
Ermias T. Azeria [ctb]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between opticut versions 0.1-3 dated 2024-05-21 and 0.1-4 dated 2025-07-13
DESCRIPTION | 22 +++++++++++++++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 19 insertions(+), 7 deletions(-)
Title: Agent-Based Bird Point Count Simulator
Description: A highly scientific and utterly addictive
bird point count simulator
to test statistical assumptions, aid survey design,
and have fun while doing it (Solymos 2024 <doi:10.1007/s42977-023-00183-2>).
The simulations follow time-removal and distance sampling models
based on Matsuoka et al. (2012) <doi:10.1525/auk.2012.11190>,
Solymos et al. (2013) <doi:10.1111/2041-210X.12106>,
and Solymos et al. (2018) <doi:10.1650/CONDOR-18-32.1>,
and sound attenuation experiments by
Yip et al. (2017) <doi:10.1650/CONDOR-16-93.1>.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between bSims versions 0.3-2 dated 2024-05-21 and 0.3-3 dated 2025-07-13
DESCRIPTION | 17 MD5 | 14 NEWS.md | 4 build/vignette.rds |binary inst/doc/bsims02-layers.R | 20 - inst/doc/bsims02-layers.html | 705 ++++++++++++++++++++--------------------- inst/doc/bsims03-workflow.R | 18 - inst/doc/bsims03-workflow.html | 323 +++++++++--------- 8 files changed, 555 insertions(+), 546 deletions(-)
Title: Multivariate Data Handling in Ecology and Biogeography
Description: A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.
Author: Peter Solymos [aut, cre]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between mefa versions 3.2-9 dated 2024-05-20 and 3.2-10 dated 2025-07-13
DESCRIPTION | 17 ++++++++++++----- MD5 | 6 +++--- build/partial.rdb |binary inst/ChangeLog | 4 ++++ 4 files changed, 19 insertions(+), 8 deletions(-)
Title: Set Alpha Based on Sample Size Using Bayes Factors
Description: Sets the alpha level for coefficients in a regression model
as a decreasing function of the sample size through the use of
Jeffreys' Approximate Bayes factor. You tell alphaN() your sample
size, and it tells you to which value you must lower alpha to avoid
Lindley's Paradox. For details, see Wulff and Taylor (2024)
<doi:10.1177/14761270231214429>.
Author: Jesper Wulff [aut, cre] ,
Luke Taylor [aut]
Maintainer: Jesper Wulff <jwulff@econ.au.dk>
Diff between alphaN versions 0.1.0 dated 2023-01-12 and 0.1.2 dated 2025-07-13
alphaN-0.1.0/alphaN/inst/CITATION |only alphaN-0.1.2/alphaN/DESCRIPTION | 15 +- alphaN-0.1.2/alphaN/MD5 | 18 +-- alphaN-0.1.2/alphaN/NEWS.md | 6 + alphaN-0.1.2/alphaN/README.md | 27 ++++- alphaN-0.1.2/alphaN/build/vignette.rds |binary alphaN-0.1.2/alphaN/inst/doc/intro-alphaN.R | 26 ----- alphaN-0.1.2/alphaN/inst/doc/intro-alphaN.Rmd | 56 ---------- alphaN-0.1.2/alphaN/inst/doc/intro-alphaN.html | 129 ++----------------------- alphaN-0.1.2/alphaN/man/figures |only alphaN-0.1.2/alphaN/vignettes/intro-alphaN.Rmd | 56 ---------- 11 files changed, 59 insertions(+), 274 deletions(-)
Title: Find Routes for Supersonic Aircraft
Description: For supersonic aircraft, flying subsonic over land,
find the best route between airports. Allow for coastal buffer and
potentially closed regions. Use a minimal model of aircraft
performance: the focus is on time saved versus subsonic flight, rather
than on vertical flight profile. For modelling and forecasting, not for planning your
flight!
Author: David Marsh [aut, cre],
Enrico Spinielli [ctb],
EUROCONTROL [fnd, cph]
Maintainer: David Marsh <david6marsh@gmail.com>
Diff between himach versions 0.3.2 dated 2023-09-20 and 1.0.0 dated 2025-07-13
himach-0.3.2/himach/vignettes/EDDF_KBOS_speed.png |only himach-0.3.2/himach/vignettes/EDDF_KBOS_time.png |only himach-0.3.2/himach/vignettes/polar_examples.png |only himach-0.3.2/himach/vignettes/refuel_examples_pacific.png |only himach-0.3.2/himach/vignettes/three_routes.png |only himach-1.0.0/himach/DESCRIPTION | 25 ++-- himach-1.0.0/himach/MD5 | 50 ++++---- himach-1.0.0/himach/NEWS.md | 6 + himach-1.0.0/himach/R/grids.R | 22 +-- himach-1.0.0/himach/R/routes.R | 52 ++++---- himach-1.0.0/himach/README.md | 10 - himach-1.0.0/himach/build/vignette.rds |binary himach-1.0.0/himach/inst/doc/Supersonic_Routes.R | 6 - himach-1.0.0/himach/inst/doc/Supersonic_Routes.Rmd | 8 - himach-1.0.0/himach/inst/doc/Supersonic_Routes.html | 58 ++++----- himach-1.0.0/himach/inst/doc/Supersonic_Routes_in_depth.R | 66 +++++------ himach-1.0.0/himach/inst/doc/Supersonic_Routes_in_depth.Rmd | 6 - himach-1.0.0/himach/inst/doc/Supersonic_Routes_in_depth.html | 30 ++--- himach-1.0.0/himach/man/figures |only himach-1.0.0/himach/man/find_leg.Rd | 2 himach-1.0.0/himach/man/find_route.Rd | 2 himach-1.0.0/himach/man/find_routes.Rd | 2 himach-1.0.0/himach/man/himach-package.Rd | 3 himach-1.0.0/himach/tests/testthat/test_grid.R | 8 - himach-1.0.0/himach/tests/testthat/test_routes.R | 18 +-- himach-1.0.0/himach/vignettes/Supersonic_Routes.Rmd | 8 - himach-1.0.0/himach/vignettes/Supersonic_Routes_in_depth.Rmd | 6 - 27 files changed, 194 insertions(+), 194 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.65.0 dated 2025-06-29 and 0.65.1 dated 2025-07-13
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 8 +++++++- R/export.R | 8 +++++--- R/export.sc_trend.R | 12 ++++++++---- R/plm.R | 2 +- R/plm_contrasts.R | 8 +++++--- R/print-export-plm.R | 28 +++++++++++++++------------- R/private-utilities.R | 26 ++++++++++++-------------- man/bplm.Rd | 3 +-- man/export.Rd | 7 +++---- man/hplm.Rd | 3 +-- man/pand.Rd | 3 +-- man/plm.Rd | 3 +++ man/tau_u.Rd | 3 +-- 15 files changed, 81 insertions(+), 69 deletions(-)
Title: Fit Log-Ratio Lasso Regression for Compositional Data
Description: Log-ratio Lasso regression for continuous, binary, and survival outcomes with (longitudinal) compositional features. See Fei and others (2024) <doi:10.1016/j.crmeth.2024.100899>.
Author: Teng Fei [aut, cre, cph] ,
Tyler Funnell [aut] ,
Nicholas Waters [aut] ,
Sandeep Raj [aut]
Maintainer: Teng Fei <feit1@mskcc.org>
Diff between FLORAL versions 0.4.0 dated 2025-02-17 and 0.5.0 dated 2025-07-13
DESCRIPTION | 17 - MD5 | 29 - NEWS.md | 8 R/sysdata.rda |only README.md | 62 ++-- inst/WORDLIST | 6 inst/doc/Using-FLORAL-for-Microbiome-Analysis.Rmd | 322 ++++++++++----------- inst/doc/Using-FLORAL-for-Microbiome-Analysis.html | 138 ++++----- inst/doc/Using-FLORAL-with-phyloseq.R | 11 inst/doc/Using-FLORAL-with-phyloseq.Rmd | 11 inst/doc/Using-FLORAL-with-phyloseq.html | 25 - man/figures/README-plot-1.png |binary man/figures/README-plot-2.png |binary tests/testthat/test-utils.R | 6 vignettes/Using-FLORAL-for-Microbiome-Analysis.Rmd | 322 ++++++++++----------- vignettes/Using-FLORAL-with-phyloseq.Rmd | 11 16 files changed, 489 insertions(+), 479 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.8.1 dated 2025-04-29 and 2.8.2 dated 2025-07-13
DESCRIPTION | 10 ++--- MD5 | 32 +++++++++--------- NEWS.md | 17 +++++++++ R/getMap.R | 20 +++++++---- R/marker_distribute.R | 80 ++++++++++++++++++++++++++++++++------------- R/marker_setattr.R | 63 ++++++++++++++++++++++------------- R/marker_setattr_inplace.R | 2 - R/ped_plot.R | 23 +++++++----- R/plot_methods.R | 71 ++++++++++++++++++++++++++++++++++----- R/setMutmod.R | 8 ++-- build/vignette.rds |binary inst/doc/pedtools.html | 4 +- man/getMap.Rd | 4 +- man/marker_setattr.Rd | 13 +++---- man/plot.ped.Rd | 20 ++++++----- man/plotmethods.Rd | 20 ++++++++--- man/setSNPs.Rd | 17 ++++++--- 17 files changed, 278 insertions(+), 126 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.10.0-2 dated 2025-05-16 and 1.10.0-3 dated 2025-07-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/highs.R | 5 ++++- 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
or Robitzsch and George (2019, <doi:10.1007/978-3-030-05584-4_26>)
for further details on estimation and the package structure.
For tutorial [...truncated...]
Author: Alexander Robitzsch [aut, cre],
Thomas Kiefer [aut],
Ann Cathrice George [aut],
Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 8.2-6 dated 2022-08-25 and 8.3-14 dated 2025-07-13
CDM-8.2-6/CDM/R/vcov.loglike.din.R |only CDM-8.3-14/CDM/DESCRIPTION | 30 + CDM-8.3-14/CDM/MD5 | 164 +++++----- CDM-8.3-14/CDM/NAMESPACE | 2 CDM-8.3-14/CDM/R/IRT.RMSD.R | 2 CDM-8.3-14/CDM/R/IRT.modelfit.R | 10 CDM-8.3-14/CDM/R/IRT_RMSD_calc_rmsd.R | 11 CDM-8.3-14/CDM/R/IRT_RMSD_summary_print_statistics.R | 4 CDM-8.3-14/CDM/R/RcppExports.R | 2 CDM-8.3-14/CDM/R/array3_sum.R | 6 CDM-8.3-14/CDM/R/attach_environment.R | 4 CDM-8.3-14/CDM/R/cat_paste.R | 4 CDM-8.3-14/CDM/R/cdi.kli.R | 12 CDM-8.3-14/CDM/R/cdm.est.calc.accuracy.R | 4 CDM-8.3-14/CDM/R/cdm_attach_exported_function.R | 4 CDM-8.3-14/CDM/R/cdm_attach_internal_function.R | 4 CDM-8.3-14/CDM/R/cdm_calc_increment.R | 4 CDM-8.3-14/CDM/R/cdm_calc_posterior.R | 8 CDM-8.3-14/CDM/R/cdm_est_calc_accuracy_version1.R | 34 +- CDM-8.3-14/CDM/R/cdm_est_calc_accuracy_version1_computation.R | 6 CDM-8.3-14/CDM/R/din.R | 10 CDM-8.3-14/CDM/R/gdina.R | 18 - CDM-8.3-14/CDM/R/gdina_attr_rpf_hogdina.R | 7 CDM-8.3-14/CDM/R/gdina_attribute_structure_hogdina.R | 9 CDM-8.3-14/CDM/R/gdina_calc_expected_counts.R | 12 CDM-8.3-14/CDM/R/gdina_calc_ic.R | 6 CDM-8.3-14/CDM/R/gdina_calc_individual_likelihood.R | 8 CDM-8.3-14/CDM/R/gdina_calc_loglikelihood.R | 27 - CDM-8.3-14/CDM/R/numerical_Hessian.R | 5 CDM-8.3-14/CDM/R/slca.R | 28 - CDM-8.3-14/CDM/R/slca_est_skillspace.R | 9 CDM-8.3-14/CDM/R/vcov.din.R | 10 CDM-8.3-14/CDM/R/vcov_loglike_din.R |only CDM-8.3-14/CDM/README.md | 4 CDM-8.3-14/CDM/build/partial.rdb |binary CDM-8.3-14/CDM/data/data.Students.rda |binary CDM-8.3-14/CDM/data/data.cdm01.rda |binary CDM-8.3-14/CDM/data/data.cdm02.rda |binary CDM-8.3-14/CDM/data/data.cdm03.rda |binary CDM-8.3-14/CDM/data/data.cdm04.rda |binary CDM-8.3-14/CDM/data/data.cdm05.rda |binary CDM-8.3-14/CDM/data/data.cdm06.rda |binary CDM-8.3-14/CDM/data/data.cdm07.rda |binary CDM-8.3-14/CDM/data/data.cdm08.rda |binary CDM-8.3-14/CDM/data/data.cdm09.rda |binary CDM-8.3-14/CDM/data/data.cdm10.rda |binary CDM-8.3-14/CDM/data/data.dcm.rda |binary CDM-8.3-14/CDM/data/data.dtmr.rda |binary CDM-8.3-14/CDM/data/data.ecpe.rda |binary CDM-8.3-14/CDM/data/data.fraction1.rda |binary CDM-8.3-14/CDM/data/data.fraction2.rda |binary CDM-8.3-14/CDM/data/data.fraction3.rda |binary CDM-8.3-14/CDM/data/data.fraction4.rda |binary CDM-8.3-14/CDM/data/data.fraction5.rda |binary CDM-8.3-14/CDM/data/data.hr.rda |binary CDM-8.3-14/CDM/data/data.jang.rda |binary CDM-8.3-14/CDM/data/data.melab.rda |binary CDM-8.3-14/CDM/data/data.mg.rda |binary CDM-8.3-14/CDM/data/data.pgdina.rda |binary CDM-8.3-14/CDM/data/data.pisa00R.cc.rda |binary CDM-8.3-14/CDM/data/data.pisa00R.ct.rda |binary CDM-8.3-14/CDM/data/data.sda6.rda |binary CDM-8.3-14/CDM/data/data.timss03.G8.su.rda |binary CDM-8.3-14/CDM/data/data.timss07.G4.Qdomains.rda |binary CDM-8.3-14/CDM/data/data.timss07.G4.lee.rda |binary CDM-8.3-14/CDM/data/data.timss07.G4.py.rda |binary CDM-8.3-14/CDM/data/data.timss11.G4.AUT.part.rda |binary CDM-8.3-14/CDM/data/data.timss11.G4.AUT.rda |binary CDM-8.3-14/CDM/data/data.timss11.G4.sa.rda |binary CDM-8.3-14/CDM/data/fraction.subtraction.data.rda |binary CDM-8.3-14/CDM/data/fraction.subtraction.qmatrix.rda |binary CDM-8.3-14/CDM/data/sim.dina.rda |binary CDM-8.3-14/CDM/data/sim.dino.rda |binary CDM-8.3-14/CDM/data/sim.qmatrix.rda |binary CDM-8.3-14/CDM/inst/CITATION | 6 CDM-8.3-14/CDM/inst/NEWS | 11 CDM-8.3-14/CDM/man/IRT.modelfit.Rd | 8 CDM-8.3-14/CDM/man/data.dtmr.Rd | 10 CDM-8.3-14/CDM/man/data.ecpe.Rd | 4 CDM-8.3-14/CDM/man/data.fraction.Rd | 4 CDM-8.3-14/CDM/man/discrim.index.Rd | 4 CDM-8.3-14/CDM/src/RcppExports.cpp | 2 CDM-8.3-14/CDM/src/cdm_rcpp_kli.cpp | 11 CDM-8.3-14/CDM/src/init.c | 2 84 files changed, 292 insertions(+), 238 deletions(-)
Title: Interfacing 'NaileR' with 'Shiny'
Description: A very small package for more convenient use of 'NaileR'. You provide a data set containing a latent variable you want to understand. It generates a description and an interpretation of this latent variable using a Large Language Model. For perceptual data, it describes the stimuli used in the experiment.
Author: Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Diff between PolisheR versions 1.0.0 dated 2024-11-29 and 1.1.0 dated 2025-07-13
DESCRIPTION | 13 +- MD5 | 10 +- NAMESPACE | 6 + R/shiny_nail_catdes.R |only R/shiny_nail_condes.R |only R/shiny_nail_qda.R | 219 ++++++++++++++++++++++------------------------- man/shiny_nail_catdes.Rd |only man/shiny_nail_condes.Rd |only 8 files changed, 125 insertions(+), 123 deletions(-)
Title: Interpreting Latent Variables with AI
Description: A small package designed for interpreting continuous and categorical latent variables. You provide a data set with a latent variable you want to understand and some other explanatory variables. It provides a description of the latent variable based on the explanatory variables. It also provides a name to the latent variable.
Author: Nel Herve [aut],
Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Diff between NaileR versions 1.2.2 dated 2025-02-18 and 1.2.3 dated 2025-07-13
DESCRIPTION | 11 - MD5 | 26 ++- NAMESPACE | 5 NEWS.md |only R/nail_catdes.R | 387 ++++++++++++++++++++++++++++++++++++----------------- R/nail_condes.R | 83 ++++++++++- R/nail_qda.R | 4 R/nail_sort.R | 145 ++++++++++++++----- README.md | 8 - build |only inst |only man/nail_condes.Rd | 3 man/nail_sort.Rd | 38 ++++- vignettes |only 14 files changed, 518 insertions(+), 192 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre] ,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.18 dated 2025-05-16 and 0.1.19 dated 2025-07-13
DESCRIPTION | 13 ++--- MD5 | 31 ++++++------ NAMESPACE | 4 + R/check_installation.R | 9 +-- R/github.R | 17 +++--- R/github_actions.R | 16 ++++++ R/targets.R | 4 - R/testthat.R |only R/worcs_project.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/citation.html | 9 +-- man/add_testthat.Rd |only man/git_release_publish.Rd |only man/git_remote_create.Rd | 81 ++++++++++---------------------- man/github_action_check_endpoints.Rd | 63 +++++++++++++------------ man/list_endpoints.Rd | 76 +++++++++++++++--------------- man/remove_endpoint.Rd | 88 +++++++++++++++++------------------ 18 files changed, 207 insertions(+), 206 deletions(-)
Title: FAIR Theory Construction
Description: An integrated suite of tools for creating, maintaining, and reusing
FAIR (Findable, Accessible, Interoperable, Reusable) theories.
Designed to support transparent and collaborative theory development,
the package enables users to formalize theories,
track changes with version control,
assess pre-empirical coherence,
and derive testable hypotheses.
Aligning with open science principles and workflows,
'theorytools' facilitates the systematic improvement of theoretical frameworks
and enhances their discoverability and usability.
Author: Caspar J. Van Lissa [aut, cre]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between theorytools versions 0.1.1 dated 2025-06-23 and 0.1.2 dated 2025-07-13
DESCRIPTION | 6 MD5 | 54 ++-- NAMESPACE | 2 NEWS.md | 6 R/dagitty.R | 46 +++ R/derive_formula.R | 3 R/download_theory.R | 2 build/vignette.rds |binary inst/doc/causal-inference.Rmd | 8 inst/doc/causal-inference.html | 30 +- inst/doc/computational_social_science.R |only inst/doc/computational_social_science.Rmd |only inst/doc/computational_social_science.html |only inst/doc/dunning-kruger.R | 13 - inst/doc/dunning-kruger.Rmd | 21 + inst/doc/dunning-kruger.html | 8 inst/doc/fair-theory.Rmd | 4 inst/doc/fair-theory.html | 4 inst/doc/readme.Rmd | 2 inst/doc/readme.html | 2 man/prune_dag.Rd |only tests/testthat/tests-empty_formula.R |only vignettes/causal-inference.Rmd | 8 vignettes/computational.bib |only vignettes/computational_social_science.Rmd |only vignettes/dunning-kruger.Rmd | 21 + vignettes/fair-theory.Rmd | 4 vignettes/readme.Rmd | 2 vignettes/theory |only vignettes/vignettes.bib | 362 ++++++++++++++++------------- vignettes/visnetwork.png |only 31 files changed, 377 insertions(+), 231 deletions(-)
Title: Confounder-Adjusted Survival Curves and Cumulative Incidence
Functions
Description: Estimate and plot confounder-adjusted survival curves using
either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values',
various forms of 'Inverse Probability of Treatment Weighting', two
forms of 'Augmented Inverse Probability of Treatment Weighting',
'Empirical Likelihood Estimation' or 'Targeted Maximum Likelihood Estimation'.
Also includes a significance test for the difference
between two adjusted survival curves and the calculation of adjusted
restricted mean survival times. Additionally enables the user to
estimate and plot cause-specific confounder-adjusted cumulative
incidence functions in the competing risks setting using the same
methods (with some exceptions).
For details, see Denz et. al (2023) <doi:10.1002/sim.9681>.
Author: Robin Denz [aut, cre]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between adjustedCurves versions 0.11.2 dated 2024-07-29 and 0.11.3 dated 2025-07-13
adjustedCurves-0.11.2/adjustedCurves/inst/doc/introduction.R |only adjustedCurves-0.11.2/adjustedCurves/inst/doc/introduction.Rmd |only adjustedCurves-0.11.2/adjustedCurves/inst/doc/introduction.html |only adjustedCurves-0.11.2/adjustedCurves/vignettes/introduction.Rmd |only adjustedCurves-0.11.3/adjustedCurves/DESCRIPTION | 8 adjustedCurves-0.11.3/adjustedCurves/MD5 | 89 adjustedCurves-0.11.3/adjustedCurves/NEWS.md | 98 adjustedCurves-0.11.3/adjustedCurves/R/adjusted_auc.r | 38 adjustedCurves-0.11.3/adjustedCurves/R/adjusted_curve_diff.r | 194 - adjustedCurves-0.11.3/adjustedCurves/R/adjusted_curve_test.r | 1334 ++++------ adjustedCurves-0.11.3/adjustedCurves/R/adjusted_surv_quantile.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/adjustedcif.r | 48 adjustedCurves-0.11.3/adjustedCurves/R/adjustedsurv.r | 47 adjustedCurves-0.11.3/adjustedCurves/R/ce_model_mi.r | 108 adjustedCurves-0.11.3/adjustedCurves/R/helper_functions.r | 27 adjustedCurves-0.11.3/adjustedCurves/R/input_checks.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/integral_calculation.r | 432 +-- adjustedCurves-0.11.3/adjustedCurves/R/method_aiptw.r | 16 adjustedCurves-0.11.3/adjustedCurves/R/method_aiptw_pseudo.r | 348 +- adjustedCurves-0.11.3/adjustedCurves/R/method_direct.r | 33 adjustedCurves-0.11.3/adjustedCurves/R/method_direct_pseudo.r | 270 -- adjustedCurves-0.11.3/adjustedCurves/R/method_emp_lik.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/method_iptw.r | 22 adjustedCurves-0.11.3/adjustedCurves/R/method_iptw_pseudo.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/method_matching.r | 220 - adjustedCurves-0.11.3/adjustedCurves/R/method_stratification.r | 586 ++-- adjustedCurves-0.11.3/adjustedCurves/R/method_unadjusted.r | 184 - adjustedCurves-0.11.3/adjustedCurves/R/plot.adjustedcif.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/plot.adjustedsurv.r | 964 +++---- adjustedCurves-0.11.3/adjustedCurves/R/plot_auc_curve.r | 14 adjustedCurves-0.11.3/adjustedCurves/R/plot_curve_diff.r | 716 ++--- adjustedCurves-0.11.3/adjustedCurves/R/risk_tables.r | 648 ++-- adjustedCurves-0.11.3/adjustedCurves/R/simulation_functions.r | 596 ++-- adjustedCurves-0.11.3/adjustedCurves/README.md | 95 adjustedCurves-0.11.3/adjustedCurves/build/vignette.rds |binary adjustedCurves-0.11.3/adjustedCurves/inst/doc/adjustedCurves.R |only adjustedCurves-0.11.3/adjustedCurves/inst/doc/adjustedCurves.Rmd |only adjustedCurves-0.11.3/adjustedCurves/inst/doc/adjustedCurves.html |only adjustedCurves-0.11.3/adjustedCurves/inst/doc/comparing_groups.R | 2 adjustedCurves-0.11.3/adjustedCurves/inst/doc/comparing_groups.html | 28 adjustedCurves-0.11.3/adjustedCurves/inst/doc/plot_customization.R | 2 adjustedCurves-0.11.3/adjustedCurves/inst/doc/plot_customization.html | 56 adjustedCurves-0.11.3/adjustedCurves/man/adjustedCurves.Rd | 2 adjustedCurves-0.11.3/adjustedCurves/man/adjusted_rmst.Rd | 7 adjustedCurves-0.11.3/adjustedCurves/man/adjusted_rmtl.Rd | 7 adjustedCurves-0.11.3/adjustedCurves/man/figures/README-unnamed-chunk-4-1.png |only adjustedCurves-0.11.3/adjustedCurves/man/figures/README-unnamed-chunk-5-1.png |only adjustedCurves-0.11.3/adjustedCurves/man/figures/README-unnamed-chunk-6-1.png |only adjustedCurves-0.11.3/adjustedCurves/man/surv_iptw_km.Rd | 3 adjustedCurves-0.11.3/adjustedCurves/tests/testthat/test_general_stuff.r | 80 adjustedCurves-0.11.3/adjustedCurves/vignettes/adjustedCurves.Rmd |only 51 files changed, 3601 insertions(+), 3791 deletions(-)
More information about adjustedCurves at CRAN
Permanent link
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).
Author: Jenni Niku [aut, cre],
Wesley Brooks [aut],
Riki Herliansyah [aut],
Francis K.C. Hui [aut],
Pekka Korhonen [aut],
Sara Taskinen [aut],
Bert van der Veen [aut],
David I. Warton [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 2.0.2 dated 2025-04-08 and 2.0.5 dated 2025-07-13
DESCRIPTION | 8 MD5 | 80 ++--- NAMESPACE | 2 NEWS.md | 44 +++ R/TMBtrait.R | 255 ++++++++++-------- R/VP.gllvm.R | 17 - R/coefplot.gllvm.R | 17 - R/confint.gllvm.R | 13 R/getEnvironCov.gllvm.R | 18 + R/getResidualCov.gllvm.R | 22 - R/gllvm.R | 155 ++++++----- R/gllvm.TMB.R | 356 ++++++++++++++----------- R/gllvm.auxiliary.R | 605 ++++++++++++++++++++++---------------------- R/gllvm.iter.R | 2 R/goodnessOfFit.gllvm.R | 2 R/ordiplot.gllvm.R | 209 ++++++++------- R/predict.gllvm.R | 32 +- R/randomCoefplot.R | 33 +- R/residuals.gllvm.R | 44 ++- R/se.gllvm.R | 55 +++- R/simulate.gllvm.R | 18 + R/update.gllvm.R | 43 ++- inst/doc/vignette1.Rmd | 6 inst/doc/vignette1.html | 162 +++-------- inst/doc/vignette2.html | 26 - inst/doc/vignette3.html | 346 ++++++++++++------------- inst/doc/vignette4.html | 134 ++++----- inst/doc/vignette5.html | 8 inst/doc/vignette8.html | 6 man/Skabbholmen.Rd | 22 - man/coefplot.gllvm.Rd | 3 man/fungi.Rd | 3 man/getEnvironCov.gllvm.Rd | 6 man/gllvm.Rd | 18 - man/goodnessOfFit.Rd | 118 ++++---- man/ordiplot.gllvm.Rd | 2 man/randomCoefplot.gllvm.Rd | 3 src/distrib.h | 2 src/gllvm.cpp | 523 ++++++++++++++++++++++++++++++-------- src/utils.h | 115 ++++++++ vignettes/vignette1.Rmd | 6 41 files changed, 2119 insertions(+), 1420 deletions(-)
Title: Fast Serializable Random Forests Based on 'ranger'
Description: An updated implementation of R package 'ranger' by Wright et al,
(2017) <doi:10.18637/jss.v077.i01> for training and predicting from random
forests, particularly suited to high-dimensional data, and for embedding in
'Multiple Imputation by Chained Equations' (MICE) by van Buuren (2007)
<doi:10.1177/0962280206074463>. Ensembles of classification and regression
trees are currently supported. Sparse data of class 'dgCMatrix' (R package
'Matrix') can be directly analyzed. Conventional bagged predictions are
available alongside an efficient prediction for MICE via the algorithm
proposed by Doove et al (2014) <doi:10.1016/j.csda.2013.10.025>. Trained
forests can be written to and read from storage. Survival and probability
forests are not supported in the update, nor is data of class 'gwaa.data'
(R package 'GenABEL'); use the original 'ranger' package for these analyses.
Author: Stephen Wade [aut, cre] ,
Marvin N Wright [ctb]
Maintainer: Stephen Wade <stephematician@gmail.com>
Diff between literanger versions 0.1.1 dated 2024-09-22 and 0.2.0 dated 2025-07-13
literanger-0.1.1/literanger/src/literanger/TreeParameters.h |only literanger-0.2.0/literanger/DESCRIPTION | 21 literanger-0.2.0/literanger/MD5 | 107 +- literanger-0.2.0/literanger/NAMESPACE | 1 literanger-0.2.0/literanger/NEWS.md | 14 literanger-0.2.0/literanger/R/cpp11.R | 4 literanger-0.2.0/literanger/R/io.R | 32 literanger-0.2.0/literanger/R/literanger-package.R | 7 literanger-0.2.0/literanger/R/merge.R |only literanger-0.2.0/literanger/R/predict.R | 32 literanger-0.2.0/literanger/R/train.R | 89 +- literanger-0.2.0/literanger/README.md | 16 literanger-0.2.0/literanger/build/partial.rdb |binary literanger-0.2.0/literanger/man/literanger-package.Rd | 7 literanger-0.2.0/literanger/man/merge.literanger.Rd |only literanger-0.2.0/literanger/man/predict.literanger.Rd | 16 literanger-0.2.0/literanger/man/read_literanger.Rd | 2 literanger-0.2.0/literanger/man/train.Rd | 34 literanger-0.2.0/literanger/man/write_literanger.Rd | 10 literanger-0.2.0/literanger/src/cpp11.cpp | 8 literanger-0.2.0/literanger/src/cpp11_io.cpp | 106 -- literanger-0.2.0/literanger/src/cpp11_merge.cpp |only literanger-0.2.0/literanger/src/cpp11_merge.decl.h |only literanger-0.2.0/literanger/src/cpp11_predict.cpp | 32 literanger-0.2.0/literanger/src/cpp11_predict.decl.h | 18 literanger-0.2.0/literanger/src/cpp11_train.cpp | 83 -- literanger-0.2.0/literanger/src/cpp11_train.decl.h | 20 literanger-0.2.0/literanger/src/cpp11_utility.h | 2 literanger-0.2.0/literanger/src/literanger/Data.decl.h | 111 +-- literanger-0.2.0/literanger/src/literanger/Data.defn.h | 95 +- literanger-0.2.0/literanger/src/literanger/DataVector.h | 40 - literanger-0.2.0/literanger/src/literanger/Forest.decl.h | 106 +- literanger-0.2.0/literanger/src/literanger/Forest.defn.h | 87 +- literanger-0.2.0/literanger/src/literanger/ForestBase.decl.h | 129 ++- literanger-0.2.0/literanger/src/literanger/ForestBase.defn.h | 63 - literanger-0.2.0/literanger/src/literanger/ForestClassification.decl.h | 115 +-- literanger-0.2.0/literanger/src/literanger/ForestClassification.defn.h | 145 +-- literanger-0.2.0/literanger/src/literanger/ForestRegression.decl.h | 84 +- literanger-0.2.0/literanger/src/literanger/ForestRegression.defn.h | 72 + literanger-0.2.0/literanger/src/literanger/TrainingParameters.h |only literanger-0.2.0/literanger/src/literanger/Tree.decl.h | 119 ++- literanger-0.2.0/literanger/src/literanger/Tree.defn.h | 228 ++++-- literanger-0.2.0/literanger/src/literanger/TreeBase.decl.h | 252 +++--- literanger-0.2.0/literanger/src/literanger/TreeBase.defn.h | 222 +++--- literanger-0.2.0/literanger/src/literanger/TreeClassification.decl.h | 177 +++- literanger-0.2.0/literanger/src/literanger/TreeClassification.defn.h | 330 ++++----- literanger-0.2.0/literanger/src/literanger/TreeRegression.decl.h | 164 +++- literanger-0.2.0/literanger/src/literanger/TreeRegression.defn.h | 365 +++++----- literanger-0.2.0/literanger/src/literanger/enum_types.h | 46 - literanger-0.2.0/literanger/src/literanger/globals.h | 15 literanger-0.2.0/literanger/src/literanger/utility_draw.h | 25 literanger-0.2.0/literanger/src/literanger/utility_math.h | 21 literanger-0.2.0/literanger/tests/testthat/test-classification.R | 20 literanger-0.2.0/literanger/tests/testthat/test-merge.R |only literanger-0.2.0/literanger/tests/testthat/test-regression.R | 11 literanger-0.2.0/literanger/tests/testthat/test-sparse.R | 4 literanger-0.2.0/literanger/tests/testthat/test-train.R | 10 literanger-0.2.0/literanger/tests/testthat/test-unordered.R | 8 58 files changed, 2041 insertions(+), 1684 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.16.0 dated 2023-11-28 and 0.17.0 dated 2025-07-13
stringfish-0.16.0/stringfish/R/sf_functions.r |only stringfish-0.16.0/stringfish/inst/extra_tests/benchmark_test.r |only stringfish-0.17.0/stringfish/ChangeLog | 4 stringfish-0.17.0/stringfish/DESCRIPTION | 14 stringfish-0.17.0/stringfish/MD5 | 34 stringfish-0.17.0/stringfish/R/sf_functions.R |only stringfish-0.17.0/stringfish/README.md | 4 stringfish-0.17.0/stringfish/build/vignette.rds |binary stringfish-0.17.0/stringfish/configure | 709 +++++----- stringfish-0.17.0/stringfish/inst/doc/vignette.R | 4 stringfish-0.17.0/stringfish/inst/doc/vignette.html | 187 +- stringfish-0.17.0/stringfish/inst/doc/vignette.rmd | 4 stringfish-0.17.0/stringfish/inst/extra_tests/benchmark_test.R |only stringfish-0.17.0/stringfish/inst/include/sf_internal.h | 15 stringfish-0.17.0/stringfish/src/Makevars.in | 1 stringfish-0.17.0/stringfish/src/Makevars.win | 2 stringfish-0.17.0/stringfish/src/sf_altrep.h | 7 stringfish-0.17.0/stringfish/src/sf_functions.cpp | 2 stringfish-0.17.0/stringfish/tests/tests.R | 16 stringfish-0.17.0/stringfish/vignettes/vignette.rmd | 4 20 files changed, 546 insertions(+), 461 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.1.2 dated 2025-03-26 and 1.2.0 dated 2025-07-13
httr2-1.1.2/httr2/cleanup |only httr2-1.1.2/httr2/configure |only httr2-1.1.2/httr2/configure.win |only httr2-1.1.2/httr2/man/multi_req_perform.Rd |only httr2-1.1.2/httr2/tools |only httr2-1.2.0/httr2/DESCRIPTION | 15 httr2-1.2.0/httr2/MD5 | 310 +++++----- httr2-1.2.0/httr2/NAMESPACE | 20 httr2-1.2.0/httr2/NEWS.md | 68 ++ httr2-1.2.0/httr2/R/content-type.R | 25 httr2-1.2.0/httr2/R/curl.R | 31 - httr2-1.2.0/httr2/R/headers.R | 135 ++-- httr2-1.2.0/httr2/R/httr2-package.R | 1 httr2-1.2.0/httr2/R/iterate-helpers.R | 18 httr2-1.2.0/httr2/R/jwt.R | 18 httr2-1.2.0/httr2/R/last.R |only httr2-1.2.0/httr2/R/oauth-client.R | 62 +- httr2-1.2.0/httr2/R/oauth-flow-auth-code.R | 121 +-- httr2-1.2.0/httr2/R/oauth-flow-client-credentials.R | 22 httr2-1.2.0/httr2/R/oauth-flow-device.R | 78 +- httr2-1.2.0/httr2/R/oauth-flow-jwt.R | 34 - httr2-1.2.0/httr2/R/oauth-flow-password.R | 38 - httr2-1.2.0/httr2/R/oauth-flow-refresh.R | 26 httr2-1.2.0/httr2/R/oauth-flow-token-exchange.R | 46 - httr2-1.2.0/httr2/R/oauth-flow.R | 12 httr2-1.2.0/httr2/R/oauth-token.R | 29 httr2-1.2.0/httr2/R/oauth.R | 28 httr2-1.2.0/httr2/R/pooled-request.R | 28 httr2-1.2.0/httr2/R/req-auth-aws.R | 111 ++- httr2-1.2.0/httr2/R/req-auth-sign.R | 7 httr2-1.2.0/httr2/R/req-body.R | 278 +++++--- httr2-1.2.0/httr2/R/req-cache.R | 87 ++ httr2-1.2.0/httr2/R/req-dry-run.R | 24 httr2-1.2.0/httr2/R/req-error.R | 4 httr2-1.2.0/httr2/R/req-headers.R | 46 + httr2-1.2.0/httr2/R/req-method.R | 24 httr2-1.2.0/httr2/R/req-mock.R | 34 - httr2-1.2.0/httr2/R/req-options.R | 17 httr2-1.2.0/httr2/R/req-perform-connection.R | 116 +++ httr2-1.2.0/httr2/R/req-perform-iterative.R | 50 - httr2-1.2.0/httr2/R/req-perform-parallel.R | 108 +-- httr2-1.2.0/httr2/R/req-perform-sequential.R | 64 +- httr2-1.2.0/httr2/R/req-perform-stream.R | 73 +- httr2-1.2.0/httr2/R/req-perform.R | 63 -- httr2-1.2.0/httr2/R/req-progress.R | 10 httr2-1.2.0/httr2/R/req-promise.R | 28 httr2-1.2.0/httr2/R/req-retries.R | 41 - httr2-1.2.0/httr2/R/req-template.R | 28 httr2-1.2.0/httr2/R/req-throttle.R | 6 httr2-1.2.0/httr2/R/req-url.R | 28 httr2-1.2.0/httr2/R/req-verbose.R | 28 httr2-1.2.0/httr2/R/req.R | 38 - httr2-1.2.0/httr2/R/resp-body.R | 29 httr2-1.2.0/httr2/R/resp-headers.R | 11 httr2-1.2.0/httr2/R/resp-status.R | 4 httr2-1.2.0/httr2/R/resp-stream-aws.R | 11 httr2-1.2.0/httr2/R/resp-stream.R | 72 +- httr2-1.2.0/httr2/R/resp-timing.R |only httr2-1.2.0/httr2/R/resp-url.R | 3 httr2-1.2.0/httr2/R/resp.R | 150 +++- httr2-1.2.0/httr2/R/roxygen2.R | 21 httr2-1.2.0/httr2/R/secret.R | 20 httr2-1.2.0/httr2/R/test.R | 11 httr2-1.2.0/httr2/R/url.R | 153 ++-- httr2-1.2.0/httr2/R/utils-multi.R | 36 - httr2-1.2.0/httr2/R/utils-redacted.R |only httr2-1.2.0/httr2/R/utils.R | 126 ++-- httr2-1.2.0/httr2/README.md | 6 httr2-1.2.0/httr2/build/vignette.rds |binary httr2-1.2.0/httr2/inst/doc/httr2.Rmd | 2 httr2-1.2.0/httr2/inst/doc/httr2.html | 45 - httr2-1.2.0/httr2/man/StreamingBody.Rd |only httr2-1.2.0/httr2/man/last_response.Rd | 41 + httr2-1.2.0/httr2/man/new_response.Rd |only httr2-1.2.0/httr2/man/req_body.Rd | 11 httr2-1.2.0/httr2/man/req_get_body_type.Rd |only httr2-1.2.0/httr2/man/req_get_headers.Rd |only httr2-1.2.0/httr2/man/req_get_method.Rd |only httr2-1.2.0/httr2/man/req_get_url.Rd |only httr2-1.2.0/httr2/man/req_oauth_auth_code.Rd | 13 httr2-1.2.0/httr2/man/req_oauth_device.Rd | 6 httr2-1.2.0/httr2/man/req_perform.Rd | 4 httr2-1.2.0/httr2/man/req_perform_connection.Rd | 12 httr2-1.2.0/httr2/man/req_perform_iterative.Rd | 6 httr2-1.2.0/httr2/man/req_perform_parallel.Rd | 12 httr2-1.2.0/httr2/man/req_perform_promise.Rd | 16 httr2-1.2.0/httr2/man/req_perform_sequential.Rd | 6 httr2-1.2.0/httr2/man/req_perform_stream.Rd | 19 httr2-1.2.0/httr2/man/resp_status.Rd | 2 httr2-1.2.0/httr2/man/resp_timing.Rd |only httr2-1.2.0/httr2/man/resp_url.Rd | 3 httr2-1.2.0/httr2/man/response.Rd | 25 httr2-1.2.0/httr2/man/with_mocked_responses.Rd | 12 httr2-1.2.0/httr2/tests/testthat/_snaps/curl.md | 62 +- httr2-1.2.0/httr2/tests/testthat/_snaps/headers.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/last.md |only httr2-1.2.0/httr2/tests/testthat/_snaps/oauth-client.md | 6 httr2-1.2.0/httr2/tests/testthat/_snaps/oauth-flow-auth-code.md | 26 httr2-1.2.0/httr2/tests/testthat/_snaps/oauth-token.md | 4 httr2-1.2.0/httr2/tests/testthat/_snaps/req-auth-aws.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/req-body.md | 42 + httr2-1.2.0/httr2/tests/testthat/_snaps/req-dry-run.md | 12 httr2-1.2.0/httr2/tests/testthat/_snaps/req-error.md | 27 httr2-1.2.0/httr2/tests/testthat/_snaps/req-headers.md | 2 httr2-1.2.0/httr2/tests/testthat/_snaps/req-mock.md | 17 httr2-1.2.0/httr2/tests/testthat/_snaps/req-options.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/req-perform-connection.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/req-perform-parallel.md | 21 httr2-1.2.0/httr2/tests/testthat/_snaps/req-perform-stream.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/req-perform.md | 2 httr2-1.2.0/httr2/tests/testthat/_snaps/req-url.md | 8 httr2-1.2.0/httr2/tests/testthat/_snaps/req.md | 18 httr2-1.2.0/httr2/tests/testthat/_snaps/resp-body.md | 4 httr2-1.2.0/httr2/tests/testthat/_snaps/resp.md | 52 + httr2-1.2.0/httr2/tests/testthat/_snaps/url.md | 21 httr2-1.2.0/httr2/tests/testthat/_snaps/utils-redacted.md |only httr2-1.2.0/httr2/tests/testthat/helper-sync.R | 18 httr2-1.2.0/httr2/tests/testthat/helper.R | 2 httr2-1.2.0/httr2/tests/testthat/test-content-type.R | 22 httr2-1.2.0/httr2/tests/testthat/test-curl.R | 46 + httr2-1.2.0/httr2/tests/testthat/test-headers.R | 64 +- httr2-1.2.0/httr2/tests/testthat/test-last.R |only httr2-1.2.0/httr2/tests/testthat/test-oauth-client.R | 25 httr2-1.2.0/httr2/tests/testthat/test-oauth-flow-auth-code.R | 29 httr2-1.2.0/httr2/tests/testthat/test-oauth-flow-jwt.R | 18 httr2-1.2.0/httr2/tests/testthat/test-oauth-flow-refresh.R | 4 httr2-1.2.0/httr2/tests/testthat/test-oauth-flow.R | 5 httr2-1.2.0/httr2/tests/testthat/test-oauth.R | 5 httr2-1.2.0/httr2/tests/testthat/test-parse.R | 4 httr2-1.2.0/httr2/tests/testthat/test-req-auth-aws.R | 33 - httr2-1.2.0/httr2/tests/testthat/test-req-auth.R | 6 httr2-1.2.0/httr2/tests/testthat/test-req-body.R | 216 ++++-- httr2-1.2.0/httr2/tests/testthat/test-req-cache.R | 78 +- httr2-1.2.0/httr2/tests/testthat/test-req-cookies.R | 24 httr2-1.2.0/httr2/tests/testthat/test-req-dry-run.R | 12 httr2-1.2.0/httr2/tests/testthat/test-req-error.R | 28 httr2-1.2.0/httr2/tests/testthat/test-req-headers.R | 52 + httr2-1.2.0/httr2/tests/testthat/test-req-method.R | 6 httr2-1.2.0/httr2/tests/testthat/test-req-mock.R | 24 httr2-1.2.0/httr2/tests/testthat/test-req-options.R | 20 httr2-1.2.0/httr2/tests/testthat/test-req-perform-connection.R | 45 + httr2-1.2.0/httr2/tests/testthat/test-req-perform-iterative.R | 56 + httr2-1.2.0/httr2/tests/testthat/test-req-perform-parallel.R | 91 +- httr2-1.2.0/httr2/tests/testthat/test-req-perform-sequential.R | 17 httr2-1.2.0/httr2/tests/testthat/test-req-perform-stream.R | 35 - httr2-1.2.0/httr2/tests/testthat/test-req-perform.R | 104 ++- httr2-1.2.0/httr2/tests/testthat/test-req-promise.R | 53 + httr2-1.2.0/httr2/tests/testthat/test-req-retries.R | 41 - httr2-1.2.0/httr2/tests/testthat/test-req-template.R | 10 httr2-1.2.0/httr2/tests/testthat/test-req-throttle.R | 10 httr2-1.2.0/httr2/tests/testthat/test-req-url.R | 108 ++- httr2-1.2.0/httr2/tests/testthat/test-req-verbose.R | 56 + httr2-1.2.0/httr2/tests/testthat/test-req.R | 12 httr2-1.2.0/httr2/tests/testthat/test-resp-body.R | 31 - httr2-1.2.0/httr2/tests/testthat/test-resp-headers.R | 36 - httr2-1.2.0/httr2/tests/testthat/test-resp-status.R | 10 httr2-1.2.0/httr2/tests/testthat/test-resp-stream-aws.R | 28 httr2-1.2.0/httr2/tests/testthat/test-resp-stream.R | 39 - httr2-1.2.0/httr2/tests/testthat/test-resp-timing.R |only httr2-1.2.0/httr2/tests/testthat/test-resp-url.R | 3 httr2-1.2.0/httr2/tests/testthat/test-resp.R | 20 httr2-1.2.0/httr2/tests/testthat/test-secret.R | 13 httr2-1.2.0/httr2/tests/testthat/test-url.R | 47 - httr2-1.2.0/httr2/tests/testthat/test-utils-multi.R | 19 httr2-1.2.0/httr2/tests/testthat/test-utils-redacted.R |only httr2-1.2.0/httr2/vignettes/httr2.Rmd | 2 166 files changed, 3326 insertions(+), 2031 deletions(-)
Title: Distribution Function of Quadratic Forms in Normal Variables
Description: Computes the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.
Author: Pierre Lafaye De Micheaux [aut, cre],
Pierre Duchesne [aut],
Robert B. Davies [aut],
R. W. Farebrother [aut],
J. Sheil [aut],
I. O Muircheartaigh [aut]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
Diff between CompQuadForm versions 1.4.3 dated 2017-04-12 and 1.4.4 dated 2025-07-13
DESCRIPTION | 26 +++++--- MD5 | 12 +-- TODO | 186 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ inst/CITATION | 7 +- inst/HISTORY | 8 ++ src/qfc.cpp | 4 + src/ruben.cpp | 13 +++- 7 files changed, 237 insertions(+), 19 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.18.0 dated 2025-05-27 and 0.19.0 dated 2025-07-13
DESCRIPTION | 6 MD5 | 82 +- NAMESPACE | 1 R/adbc.R | 7 R/driver_void.R | 88 ++ R/utils.R | 26 man/adbc_driver_load.Rd |only man/adbc_driver_void.Rd | 10 man/adbc_load_flags.Rd |only src/Makevars | 2 src/Makevars.win |only src/c/driver/common/utils.c | 80 +- src/c/driver/common/utils.h | 94 +- src/c/driver/postgresql/bind_stream.h | 2 src/c/driver/postgresql/connection.cc | 67 + src/c/driver/postgresql/copy/postgres_copy_test_common.h | 23 src/c/driver/postgresql/copy/reader.h | 25 src/c/driver/postgresql/copy/writer.h | 6 src/c/driver/postgresql/database.cc | 22 src/c/driver/postgresql/database.h | 7 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/postgresql/postgresql.cc | 28 src/c/driver/postgresql/result_helper.h | 2 src/c/driver/postgresql/statement.cc | 101 +- src/c/driver/sqlite/sqlite.cc | 39 - src/c/driver/sqlite/statement_reader.c | 290 ++++--- src/c/driver/sqlite/statement_reader.h | 23 src/c/driver_manager/adbc_driver_manager.cc | 547 ++++++++++++++- src/c/driver_manager/current_arch.h |only src/c/include/arrow-adbc/adbc.h | 14 src/c/include/arrow-adbc/adbc_driver_manager.h | 78 ++ src/c/include/arrow-adbc/driver |only src/c/integration |only src/c/validation/adbc_validation_connection.cc | 16 src/c/validation/adbc_validation_util.cc | 2 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/toml++ |only src/driver_test.cc | 23 src/init.c | 18 src/options.cc | 6 src/radbc.cc | 92 +- tests/testthat/test-driver_void.R | 63 + tests/testthat/test-radbc.R | 2 43 files changed, 1413 insertions(+), 501 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.18.0 dated 2025-05-27 and 0.19.0 dated 2025-07-13
DESCRIPTION | 6 MD5 | 61 - cleanup | 1 configure | 3 src/c/driver/common/utils.c | 80 +- src/c/driver/common/utils.h | 94 +- src/c/driver/postgresql/bind_stream.h | 2 src/c/driver/postgresql/connection.cc | 67 + src/c/driver/postgresql/copy/postgres_copy_test_common.h | 23 src/c/driver/postgresql/copy/reader.h | 25 src/c/driver/postgresql/copy/writer.h | 6 src/c/driver/postgresql/database.cc | 22 src/c/driver/postgresql/database.h | 7 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/postgresql/postgresql.cc | 28 src/c/driver/postgresql/result_helper.h | 2 src/c/driver/postgresql/statement.cc | 101 +- src/c/driver/sqlite/sqlite.cc | 39 - src/c/driver/sqlite/statement_reader.c | 290 ++++--- src/c/driver/sqlite/statement_reader.h | 23 src/c/driver_manager/adbc_driver_manager.cc | 547 ++++++++++++++- src/c/driver_manager/current_arch.h |only src/c/include/arrow-adbc/adbc.h | 14 src/c/include/arrow-adbc/adbc_driver_manager.h | 78 ++ src/c/include/arrow-adbc/driver |only src/c/integration |only src/c/validation/adbc_validation_connection.cc | 16 src/c/validation/adbc_validation_util.cc | 2 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/toml++ |only src/init.cc | 5 31 files changed, 1122 insertions(+), 442 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.18.0 dated 2025-05-27 and 0.19.0 dated 2025-07-13
DESCRIPTION | 6 MD5 | 55 - src/c/driver/common/utils.c | 80 +- src/c/driver/common/utils.h | 94 +- src/c/driver/postgresql/bind_stream.h | 2 src/c/driver/postgresql/connection.cc | 67 + src/c/driver/postgresql/copy/postgres_copy_test_common.h | 23 src/c/driver/postgresql/copy/reader.h | 25 src/c/driver/postgresql/copy/writer.h | 6 src/c/driver/postgresql/database.cc | 22 src/c/driver/postgresql/database.h | 7 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/postgresql/postgresql.cc | 28 src/c/driver/postgresql/result_helper.h | 2 src/c/driver/postgresql/statement.cc | 101 +- src/c/driver/sqlite/sqlite.cc | 39 - src/c/driver/sqlite/statement_reader.c | 290 ++++--- src/c/driver/sqlite/statement_reader.h | 23 src/c/driver_manager/adbc_driver_manager.cc | 547 ++++++++++++++- src/c/driver_manager/current_arch.h |only src/c/include/arrow-adbc/adbc.h | 14 src/c/include/arrow-adbc/adbc_driver_manager.h | 78 ++ src/c/include/arrow-adbc/driver |only src/c/integration |only src/c/validation/adbc_validation_connection.cc | 16 src/c/validation/adbc_validation_util.cc | 2 src/c/validation/adbc_validation_util.h | 4 src/c/vendor/toml++ |only 28 files changed, 1114 insertions(+), 435 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph] ,
Tilman M. Davies [aut, ctb, cph] ,
Martin L. Hazelton [aut, ctb, cph] ,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.1-3 dated 2025-05-07 and 3.1-4 dated 2025-07-12
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS | 16 ++++ R/weightedStats.R | 148 +++++++++++++++++++++++++++++++++------------ inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/macros/defns.Rd | 25 ++++--- man/weighted.median.Rd | 141 +++++++++++++++++++++++++++++++++++++----- tests/all.R | 20 +++++- 9 files changed, 296 insertions(+), 80 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi [aut, cre] ,
Miguel B. Araujo [aut]
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.2-55 dated 2025-01-11 and 1.2-59 dated 2025-07-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/niche.R | 5 +++-- R/replicate.R | 6 +++--- R/responseCurve.R | 6 +++--- R/sdmData.R | 6 +++--- build/vignette.rds |binary 8 files changed, 25 insertions(+), 24 deletions(-)
Title: Vectors Representing Random Variables
Description: Random vectors, called rvecs. An rvec holds
multiple draws, but tries to behave like a standard
R vector, including working well in data frames.
Rvecs are useful for analysing
output from a simulation or a Bayesian analysis.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between rvec versions 0.0.7 dated 2024-09-15 and 0.0.8 dated 2025-07-12
DESCRIPTION | 16 +-- MD5 | 41 ++++---- NAMESPACE | 3 NEWS.md | 16 +++ R/constructors.R | 7 + R/distributions.R | 54 ++++++++++ R/draws.R | 58 +++++++++++ R/util.R | 12 ++ build/vignette.rds |binary inst/doc/vig1_overview.html | 12 +- man/dbinom_rvec.Rd | 8 + man/dgeom_rvec.Rd | 8 + man/dhyper_rvec.Rd | 8 + man/dmultinom_rvec.Rd | 8 + man/dnbinom_rvec.Rd | 8 + man/dpois_rvec.Rd | 8 + man/prob.Rd |only tests/testthat/test-constructors.R | 20 ++++ tests/testthat/test-distributions.R | 178 +++++++++++++++++++++++------------- tests/testthat/test-draws.R | 48 +++++++++ tests/testthat/test-plot.R | 58 ++++++----- tests/testthat/test-util.R | 9 + 22 files changed, 453 insertions(+), 127 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.7.1 dated 2025-06-20 and 0.7.2 dated 2025-07-12
DESCRIPTION | 16 MD5 | 55 - NAMESPACE | 2 R/boxviolinplot.R | 7 R/data.R | 23 R/dimplot.R | 281 +++-- R/heatmap.R | 1970 ++++++++++++++++++++---------------- R/spatialplot.R | 75 + R/velocityplot.R |only R/volcanoplot.R | 22 README.md | 11 data/dim_example.rda |only man/BoxViolinPlot-internal.Rd | 3 man/BoxViolinPlotAtomic.Rd | 3 man/DimPlotAtomic.Rd | 95 + man/Heatmap.Rd | 591 +++++----- man/HeatmapAtomic.Rd | 302 ++--- man/VelocityPlot.Rd |only man/VolcanoPlot.Rd | 15 man/VolcanoPlotAtomic.Rd | 1 man/boxviolinplot.Rd | 3 man/dim_example.Rd |only man/dimplot.Rd | 255 +++- man/dot-compute_velocity_on_grid.Rd |only man/enrich_example.Rd | 4 man/enrich_multidb_example.Rd | 4 man/figures/dimplot.png |binary man/gsea_example.Rd | 4 man/heatmap-layer.Rd | 22 man/join_heatmap_meta.Rd |only man/process_heatmap_data.Rd |only man/spatialplots.Rd | 28 32 files changed, 2256 insertions(+), 1536 deletions(-)
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider [aut, cre],
Eric Chicken [aut],
Rachel Becvarik [aut]
Maintainer: Grant Schneider <gschneidz@gmail.com>
Diff between NSM3 versions 1.19 dated 2024-11-04 and 1.20 dated 2025-07-12
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS.md |only R/pLepage.R | 8 +++++--- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Generating Synthetic Versions of Sensitive Microdata for
Statistical Disclosure Control
Description: A tool for producing synthetic versions of microdata containing confidential information so that they are safe to be released to users for exploratory analysis. The key objective of generating synthetic data is to replace sensitive original values with synthetic ones causing minimal distortion of the statistical information contained in the data set. Variables, which can be categorical or continuous, are synthesised one-by-one using sequential modelling. Replacements are generated by drawing from conditional distributions fitted to the original data using parametric or classification and regression trees models. Data are synthesised via the function syn() which can be largely automated, if default settings are used, or with methods defined by the user. Optional parameters can be used to influence the disclosure risk and the analytical quality of the synthesised data. For a description of the implemented method see Nowok, Raab and Dibben (2016) <doi:10.18637/jss.v074.i11>. Functio [...truncated...]
Author: Beata Nowok [aut, cre],
Gillian M Raab [aut],
Chris Dibben [ctb],
Joshua Snoke [ctb],
Caspar van Lissa [ctb],
Lotte Pater [ctb]
Maintainer: Beata Nowok <beata.nowok@gmail.com>
Diff between synthpop versions 1.9-1.1 dated 2025-06-03 and 1.9-2 dated 2025-07-12
DESCRIPTION | 9 - MD5 | 42 ++-- NEWS | 7 R/methods.syn.r | 2 build/partial.rdb |binary build/vignette.rds |binary data/SD2011.rda |binary inst/doc/disclosure.R | 130 +++++++------- inst/doc/disclosure.Rnw | 28 +-- inst/doc/disclosure.pdf |binary inst/doc/inference.R | 420 +++++++++++++++++++++++------------------------ inst/doc/inference.pdf |binary inst/doc/synthpop.R | 418 +++++++++++++++++++++++----------------------- inst/doc/synthpop.pdf |binary inst/doc/utility.R | 286 ++++++++++++++++---------------- inst/doc/utility.Rnw | 2 inst/doc/utility.pdf |binary man/synthpop-package.Rd | 4 vignettes/disclosure.Rnw | 28 +-- vignettes/disclosure.bib | 36 +--- vignettes/utility.Rnw | 2 vignettes/utility.bib | 4 22 files changed, 709 insertions(+), 709 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' to 'heatmap.2' with the advantage of speed
('plotly.js' is able to han [...truncated...]
Author: Tal Galili [aut, cre, cph] ,
Alan O'Callaghan [aut] ,
Jonathan Sidi [ctb] ,
Jaehyun Joo [ctb] ,
Yoav Benjamini [ths],
Mathew Simenc [ctb]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 1.5.0 dated 2023-10-06 and 1.6.0 dated 2025-07-12
DESCRIPTION | 17 + MD5 | 32 +-- NEWS | 11 + NEWS.md | 11 + R/RColorBrewer.R | 4 R/heatmaply.R | 30 ++- R/heatmapr.R | 9 R/plots.R | 36 ++- R/zzz.R | 4 build/vignette.rds |binary inst/doc/heatmaply.R | 34 +-- inst/doc/heatmaply.html | 337 +++++++++++++++++------------------ man/RColorBrewer_colors.Rd | 4 man/heatmaply.Rd | 14 + man/heatmapr.Rd | 2 man/is.plotly.Rd | 2 tests/testthat/test_heatmaply_misc.R | 1 17 files changed, 305 insertions(+), 243 deletions(-)
Title: Linear Innovations State Space Unobserved Components Model
Description: Unobserved components time series model using the linear innovations state space representation (single source of error) with choice of error distributions and option for dynamic variance. Methods for estimation using automatic differentiation, automatic model selection and ensembling, prediction, filtering, simulation and backtesting. Based on the model described in Hyndman et al (2012) <doi:10.1198/jasa.2011.tm09771>.
Author: Alexios Galanos [aut, cre]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsissm versions 1.0.1 dated 2025-04-28 and 1.0.2 dated 2025-07-12
DESCRIPTION | 9 +- MD5 | 31 +++---- NAMESPACE | 1 NEWS.md | 7 + R/backtest.R | 30 +++++-- R/constraint.R | 146 +++++++++++++++++++++++++++++++++++ R/estimation.R | 124 +++++++++++++++++------------ R/solvers.R | 43 +++++++--- R/tsprofile.R | 16 ++- inst/doc/demo_ensembling.html | 41 +++++---- inst/doc/demo_missing_data.html | 16 ++- inst/doc/demo_variance_dynamics.html | 89 +++++++++++++-------- inst/doc/issm_introduction.pdf |binary man/estimate.Rd | 17 ++-- man/solver_control.Rd |only man/tsbacktest.Rd | 8 + man/tsprofile.Rd | 17 +++- 17 files changed, 438 insertions(+), 157 deletions(-)
Title: Testing for Population Trends Using Low-Cost Ecological Count
Data
Description: A Bayesian tool to test for population trends and changes in trends under arbitrary designs, including before-after (BA), control-intervention (CI) and before-after-control-intervention (BACI) designs commonly used to assess conservation impact. It infers changes in trends jointly from data obtained with multiple survey methods, as well as from limited and noisy data not necessarily collected in standardized ecological surveys. Observed counts can be modeled as following either a Poisson or a negative binomial model, and both deterministic and stochastic trend models are available. For more details on the model see Singer et al. (2025) <doi:10.1101/2025.01.08.631844>, and the file 'AUTHORS' for a list of copyright holders and contributors.
Author: Madleina Caduff [aut, cre],
Daniel Wegmann [aut],
Liam Singer [aut],
Raphael Eckel [ctb],
Andreas Fueglistaler [ctb]
Maintainer: Madleina Caduff <madleina.caduff@unifr.ch>
Diff between birp versions 0.0.4 dated 2025-07-06 and 0.0.5 dated 2025-07-12
DESCRIPTION | 8 - MD5 | 26 ++--- NEWS.md | 6 + build/partial.rdb |binary configure | 2 configure.win | 2 inst/doc/birp-introduction.html | 82 +++++++++--------- src/libs/CMakeLists.txt | 2 src/libs/coretools/CMakeLists.txt | 4 src/libs/coretools/FindR.cmake | 10 +- src/libs/coretools/core/coretools/Files/TInputRcpp.h | 7 - src/libs/coretools/core/coretools/Files/TOutputRcpp.h | 13 +- src/libs/coretools/core/coretools/Main/TRcppData.h | 2 src/libs/coretools/core/coretools/Main/TRcppResults.h | 2 14 files changed, 90 insertions(+), 76 deletions(-)
Title: Identifies Package Differences
Description: Identifies differences between
versions of a package. Specifically, the functions help
determine if there are breaking changes from one package version
to the next. The package also includes a stability assessment,
to help you determine the overall stability of a package, or even
an entire repository.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Kevin Putschko [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between pkgdiff versions 0.2.0 dated 2025-04-13 and 0.2.1 dated 2025-07-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ tests/testthat/test-reports.R | 2 ++ tests/testthat/test-stability.R | 12 +++++++++--- 5 files changed, 22 insertions(+), 10 deletions(-)
Title: 'Shiny' Applications for the R Package 'Luminescence'
Description: A collection of 'shiny' applications for the R package
'Luminescence'. These mainly, but not exclusively, include applications for
plotting chronometric data from e.g. luminescence or radiocarbon dating. It
further provides access to bootstraps tooltip and popover functionality and
contains the 'jscolor.js' library with a custom 'shiny' output binding.
Author: Christoph Burow [aut, cre] ,
Urs Tilmann Wolpert [aut],
Sebastian Kreutzer [aut] ,
Marco Colombo [aut] ,
R Luminescence Package Team [ctb],
Jan Odvarko [cph] ,
AnalytixWare [cph] ,
RStudio [cph]
Maintainer: Christoph Burow <christoph.burow@gmx.net>
Diff between RLumShiny versions 0.2.4 dated 2025-03-23 and 0.2.5 dated 2025-07-12
DESCRIPTION | 59 LICENSE |only LICENSE.note | 16 MD5 | 205 +-- NAMESPACE | 46 NEWS.md | 387 +++-- R/RLumShiny.R | 50 R/addin.R | 533 ++++---- R/app_RLum.R | 216 +-- R/chooser.R | 88 - R/jscolor.R | 140 +- R/module_aboutTab.R | 46 R/module_exportTab.R | 198 +-- R/module_printCode.R | 97 - R/popover.R | 158 +- R/tooltip.R | 200 +-- R/zzz.R | 28 inst/rstudio/addins.dcf | 6 inst/shiny/KDE/Global.R | 20 inst/shiny/KDE/server.R | 486 +++---- inst/shiny/KDE/ui.R | 448 +++--- inst/shiny/KDE/www/style.css | 140 +- inst/shiny/RCarb/global.R | 48 inst/shiny/RCarb/server.R | 408 +++--- inst/shiny/RCarb/ui.R | 202 +-- inst/shiny/abanico/Global.R | 20 inst/shiny/abanico/server.R | 908 ++++++------- inst/shiny/abanico/ui.R | 1618 ++++++++++++------------ inst/shiny/abanico/www/style.css | 140 +- inst/shiny/aliquotsize |only inst/shiny/convert/global.R | 16 inst/shiny/convert/select.R | 130 - inst/shiny/convert/server.R | 268 ++-- inst/shiny/convert/ui.R | 126 - inst/shiny/convert/www/style.css | 140 +- inst/shiny/cosmicdose/Global.R | 14 inst/shiny/cosmicdose/server.R | 250 +-- inst/shiny/cosmicdose/ui.R | 280 ++-- inst/shiny/cosmicdose/www/style.css | 168 +- inst/shiny/doserecovery/Global.R | 20 inst/shiny/doserecovery/server.R | 496 +++---- inst/shiny/doserecovery/ui.R | 647 ++++----- inst/shiny/doserecovery/www/style.css | 140 +- inst/shiny/fading/global.R | 18 inst/shiny/fading/server.R | 340 ++--- inst/shiny/fading/ui.R | 209 +-- inst/shiny/fading/www/style.css | 140 +- inst/shiny/fastratio/Global.R | 18 inst/shiny/fastratio/Server.R | 292 ++-- inst/shiny/fastratio/UI.R | 513 +++---- inst/shiny/fastratio/www/style.css | 140 +- inst/shiny/filter/global.R | 64 inst/shiny/filter/server.R | 572 ++++---- inst/shiny/filter/ui.R | 418 +++--- inst/shiny/finitemixture |only inst/shiny/histogram/Global.R | 22 inst/shiny/histogram/server.R | 311 ++-- inst/shiny/histogram/ui.R | 615 ++++----- inst/shiny/histogram/www/style.css | 140 +- inst/shiny/huntley2006 |only inst/shiny/irsarRF |only inst/shiny/lmcurve |only inst/shiny/portableOSL |only inst/shiny/radialplot/Global.R | 20 inst/shiny/radialplot/server.R | 716 +++++----- inst/shiny/radialplot/ui.R | 1062 ++++++++-------- inst/shiny/radialplot/www/style.css | 140 +- inst/shiny/scalegamma/global.R | 44 inst/shiny/scalegamma/server.R | 396 +++--- inst/shiny/scalegamma/ui.R | 143 +- inst/shiny/scalegamma/www/style.css | 140 +- inst/shiny/surfaceexposure/global.R | 34 inst/shiny/surfaceexposure/server.R | 610 ++++----- inst/shiny/surfaceexposure/ui.R | 579 ++++---- inst/shiny/surfaceexposure/www/style.css | 148 +- inst/shiny/teststimulationpower/global.R | 44 inst/shiny/teststimulationpower/server.R | 496 +++---- inst/shiny/teststimulationpower/ui.R | 166 +- inst/shiny/transformCW/Global.R | 18 inst/shiny/transformCW/Server.R | 310 ++-- inst/shiny/transformCW/UI.R | 337 ++--- inst/shiny/transformCW/www/style.css | 140 +- inst/www/chooser_inputBinding.js | 218 +-- inst/www/jscolor/demo.html | 24 inst/www/jscolor/jscolor.js | 2020 +++++++++++++++---------------- inst/www/jscolor_inputBinding.js | 36 man/RLumShiny-package.Rd | 100 - man/RLumShinyAddin.Rd | 22 man/app_RLum.Rd | 160 +- man/jscolorInput.Rd | 144 +- man/popover.Rd | 130 - man/tooltip.Rd | 174 +- 92 files changed, 11087 insertions(+), 10902 deletions(-)
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.7 dated 2025-06-05 and 0.1.8 dated 2025-07-12
DESCRIPTION | 14 MD5 | 114 +++--- NAMESPACE | 4 NEWS.md | 12 R/RcppExports.R | 203 ++++++++++- R/ipcw.R | 36 +- R/ipe.R | 20 - R/liferegr.R | 34 + R/logisregr.R | 29 - R/msm.R |only R/phregr.R | 30 + R/residuals_liferegr.R | 15 R/residuals_phregr.R | 15 R/rpsftm.R | 37 +- R/survfit_phregr.R | 11 R/trtswitch-package.R | 2 R/tsegest.R | 29 - R/tsesimp.R | 27 - build/vignette.rds |binary inst/doc/ipcw.Rmd | 6 inst/doc/ipcw.html | 5 inst/doc/ipe.Rmd | 2 inst/doc/ipe.html | 4 inst/doc/msm.R |only inst/doc/msm.Rmd |only inst/doc/msm.html |only inst/doc/rpsftm.Rmd | 120 ++---- inst/doc/rpsftm.html | 227 ++++-------- inst/doc/tsesimp.html | 12 man/ipcw.Rd | 3 man/ipe.Rd | 3 man/liferegr.Rd | 8 man/logisregr.Rd | 5 man/msm.Rd |only man/phregr.Rd | 5 man/recensor_sim_rpsftm.Rd |only man/rpsftm.Rd | 20 - man/tsegest.Rd | 3 man/tsegestsim.Rd | 4 man/tsesimp.Rd | 3 man/tssim.Rd | 70 +++ src/RcppExports.cpp | 99 ++++- src/ipcw.cpp | 112 +++--- src/ipe.cpp | 47 +- src/logistic_regression.cpp | 16 src/logistic_regression.h | 6 src/msm.cpp |only src/recensor_sim_rpsftm.cpp |only src/rpsftm.cpp | 60 ++- src/survival_analysis.cpp | 791 +++++++++++++++++--------------------------- src/survival_analysis.h | 7 src/tsegest.cpp | 62 ++- src/tsegestsim.cpp | 36 +- src/tsesimp.cpp | 47 +- src/tssim.cpp | 72 +++- src/utilities.cpp | 5 src/utilities.h | 3 tests/testthat/test-ipcw.R | 8 tests/testthat/test-msm.R |only vignettes/ipcw.Rmd | 6 vignettes/ipe.Rmd | 2 vignettes/msm.Rmd |only vignettes/rpsftm.Rmd | 120 ++---- 63 files changed, 1478 insertions(+), 1153 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia [aut],
Silvia Castiglione [aut, cre],
Carmela Serio [aut],
Giorgia Girardi [aut],
Alessandro Mondanaro [aut],
Marina Melchionna [aut],
Mirko Di Febbraro [aut],
Antonio Profico [aut],
Francesco Carotenuto [aut]
Maintainer: Silvia Castiglione <silvia.castiglione@unina.it>
Diff between RRphylo versions 3.0.0 dated 2025-03-23 and 3.0.1 dated 2025-07-12
DESCRIPTION | 8 +-- MD5 | 32 +++++++-------- R/RRphylo.R | 11 +++-- R/conv.map.R | 2 R/rate.map.R | 2 R/search.conv.R | 5 +- build/vignette.rds |binary inst/doc/Alternative-trees.html | 11 ++--- inst/doc/Plotting-tools.html | 5 +- inst/doc/RRphylo.html | 19 ++++----- inst/doc/Tree-Manipulation.Rmd | 2 inst/doc/Tree-Manipulation.html | 29 +++++++------ inst/doc/overfit.html | 5 +- inst/doc/search.conv.html | 83 +++++++++++++++++++++++++++------------- inst/doc/search.shift.html | 9 ++-- inst/doc/search.trend.html | 11 ++--- vignettes/Tree-Manipulation.Rmd | 2 17 files changed, 141 insertions(+), 95 deletions(-)
Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R.
Author: Mohamed El Fodil Ihaddaden [aut, cre],
Ezekiel Ogundepo [ctb],
Romain Francois [ctb]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between ralger versions 2.2.4 dated 2021-03-17 and 2.3.0 dated 2025-07-12
DESCRIPTION | 17 LICENSE | 4 MD5 | 83 +- NAMESPACE | 63 - NEWS.md | 140 ++- R/attribute_scrap.R | 184 ++--- R/comments_scrap.R |only R/files_scrap.R |only R/images_noalt_scrap.R | 154 ++-- R/images_scrap.R | 291 ++++---- R/paragraphs_scrap.R | 249 +++---- R/preview_images.R | 206 ++--- R/scrap.R | 201 ++--- R/table_scrap.R | 243 +++--- R/tidy_scrap.R | 267 +++---- R/titles_scrap.R | 202 ++--- R/weblink_scrap.R | 193 ++--- README.md | 868 ++++++++++++------------ build/vignette.rds |binary inst/doc/Functions_Overview.R | 256 ++++--- inst/doc/Functions_Overview.Rmd | 558 +++++++++------ inst/doc/Functions_Overview.html | 1165 ++++++++++++++++++++------------- man/comments_scrap.Rd |only man/csv_scrap.Rd |only man/images_preview.Rd | 2 man/images_scrap.Rd | 4 man/paragraphs_scrap.Rd | 80 +- man/pdf_scrap.Rd |only man/scrap.Rd | 66 - man/table_scrap.Rd | 66 - man/tidy_scrap.Rd | 71 -- man/titles_scrap.Rd | 64 - man/weblink_scrap.Rd | 66 - man/xls_scrap.Rd |only man/xlsx_scrap.Rd |only tests/testthat.R | 8 tests/testthat/test-attribute_scrap.R | 148 ++-- tests/testthat/test-images_scrap.R | 82 +- tests/testthat/test-paragraphs_scrap.R | 86 +- tests/testthat/test-preview_images.R | 79 +- tests/testthat/test-scrap.R | 132 +-- tests/testthat/test-table_scrap.R | 156 ++-- tests/testthat/test-tidy_scrap.R | 154 ++-- tests/testthat/test-titles_scrap.R | 92 +- tests/testthat/test-weblink_scrap.R | 108 +-- vignettes/Functions_Overview.Rmd | 558 +++++++++------ 46 files changed, 3977 insertions(+), 3389 deletions(-)
Title: Customizing Structural Equation Modelling Plots
Description: Most function focus on specific ways to customize a graph.
They use a 'qgraph' output as the first argument, and return a
modified 'qgraph' object. This allows the functions to be chained
by a pipe operator.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semptools versions 0.3.1 dated 2024-11-09 and 0.3.2 dated 2025-07-12
DESCRIPTION | 14 - MD5 | 61 ++++-- NAMESPACE | 12 + NEWS.md | 53 +++++- R/add_rsq.R | 2 R/auto_layout.R |only R/auto_layout_helpers.R |only R/mark_sig.R | 141 ++++++++++++++-- R/move_node.R |only R/quickplots.R |only R/safe_edge_label_positions.R |only R/safe_edge_label_positions_helpers.R |only R/safe_resid_position.R |only R/safe_resid_position_helpers.R |only README.md | 2 build/vignette.rds |binary inst/doc/keep_or_drop_nodes.html | 10 - inst/doc/layout_matrix.html | 16 - inst/doc/quick_start_cfa.R | 18 +- inst/doc/quick_start_cfa.html | 16 - inst/doc/quick_start_sem.R | 26 +- inst/doc/quick_start_sem.html | 16 - inst/doc/second_order.html | 4 inst/doc/semptools.R | 22 +- inst/doc/semptools.html | 38 ++-- man/auto_layout_mediation.Rd |only man/mark_sig.Rd | 41 ++++ man/move_node.Rd |only man/quick_sem_plot.Rd |only man/safe_edge_label_position.Rd |only man/safe_resid_position.Rd |only tests/testthat/test-add_rsq.R | 35 +++ tests/testthat/test-auto_layout_mediation.R |only tests/testthat/test-auto_layout_mediation_complicated.R |only tests/testthat/test-auto_layout_mediation_middle.R |only tests/testthat/test-auto_layout_mediation_qgraph.R |only tests/testthat/test-auto_rotate_resid.R |only tests/testthat/test-mark_mg.R |only tests/testthat/test-mark_sig_rsq.R |only tests/testthat/test-move_ndoe.R |only tests/testthat/test-quickplots_mediation_parallel.R |only tests/testthat/test-quickplots_mediation_serial.R |only tests/testthat/test-quickplots_mediation_simple.R |only tests/testthat/test-safe_edge_label_positions.R |only 44 files changed, 398 insertions(+), 129 deletions(-)
Title: Finding Files in Project Subdirectories
Description: Robust, reliable and flexible paths to files below
a project root. The 'root' of a project is defined as a directory that
matches a certain criterion, e.g., it contains a certain regular file.
Author: Kirill Mueller [aut, cre]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between rprojroot versions 2.0.4 dated 2023-11-05 and 2.1.0 dated 2025-07-12
DESCRIPTION | 18 - MD5 | 43 +- NAMESPACE | 2 NEWS.md | 35 ++ R/criterion.R | 9 R/root.R | 45 ++ R/utils.R | 2 README.md | 156 +++++---- build/vignette.rds |binary inst/doc/rprojroot.R | 114 +++--- inst/doc/rprojroot.Rmd | 8 inst/doc/rprojroot.html | 35 +- man/criteria.Rd | 10 man/find_root.Rd | 5 man/root_criterion.Rd | 9 tests/testthat/_snaps/root.md | 10 tests/testthat/package/tests/testthat.R | 1 tests/testthat/package/tests/testthat/test-something.R | 1 tests/testthat/test-absolute.R | 1 tests/testthat/test-file.R | 59 +-- tests/testthat/test-root.R | 282 ++++++++--------- tests/testthat/test-utils.R |only vignettes/rprojroot.Rmd | 8 23 files changed, 482 insertions(+), 371 deletions(-)
Title: Neo-Normal Distribution
Description: Calculating the density, cumulative distribution, quantile, and random number of
neo-normal distribution. It also interfaces with the 'brms' package,
allowing the use of the neo-normal distribution as a custom family.
This integration enables the application of various 'brms' formulas
for neo-normal regression. Modified to be Stable as Normal from Burr (MSNBurr),
Modified to be Stable as Normal from Burr-IIa (MSNBurr-IIa), Generalized of MSNBurr (GMSNBurr),
Jones-Faddy Skew-t, Fernandez-Osiewalski-Steel Skew Exponential Power,
and Jones Skew Exponential Power distributions are supported.
References: Choir, A. S. (2020).Unpublished Dissertation, Iriawan, N. (2000).Unpublished Dissertation,
Rigby, R. A., Stasinopoulos, M. D., Heller, G. Z., & Bastiani, F. D. (2019) <doi:10.1201/9780429298547>.
Author: Achmad Syahrul Choir [aut, cre] ,
Anisa Faoziah [aut],
Nur Iriawan [aut] ,
Almira Utami [ctb],
Meischa Zahra Nur Adhelia [ctb]
Maintainer: Achmad Syahrul Choir <madsyair@stis.ac.id>
Diff between neodistr versions 0.1.1 dated 2024-06-26 and 0.1.2 dated 2025-07-12
neodistr-0.1.1/neodistr/.aspell |only neodistr-0.1.1/neodistr/README.md |only neodistr-0.1.1/neodistr/tests/testthat/test.R |only neodistr-0.1.2/neodistr/DESCRIPTION | 64 +- neodistr-0.1.2/neodistr/MD5 | 87 ++-- neodistr-0.1.2/neodistr/NAMESPACE | 15 neodistr-0.1.2/neodistr/R/bnrm.R | 46 +- neodistr-0.1.2/neodistr/R/brms_custom.R | 107 ++++ neodistr-0.1.2/neodistr/R/fossep_distribution.R |only neodistr-0.1.2/neodistr/R/gmsnburr_distribution.R | 4 neodistr-0.1.2/neodistr/R/jfst_distribution.R | 2 neodistr-0.1.2/neodistr/R/jsep_distribution.R |only neodistr-0.1.2/neodistr/R/msnburr2a_distribution.R | 6 neodistr-0.1.2/neodistr/R/msnburr_distribution.R | 6 neodistr-0.1.2/neodistr/R/neonormal_stanfunc.R | 111 ++++- neodistr-0.1.2/neodistr/R/stanf_fossep.R |only neodistr-0.1.2/neodistr/R/stanf_gmsnburr.R | 8 neodistr-0.1.2/neodistr/R/stanf_jfst.R | 6 neodistr-0.1.2/neodistr/R/stanf_jsep.R |only neodistr-0.1.2/neodistr/R/stanf_msnburr.R | 8 neodistr-0.1.2/neodistr/R/stanf_msnburr2a.R | 8 neodistr-0.1.2/neodistr/R/summary_dist.R | 86 +++ neodistr-0.1.2/neodistr/build |only neodistr-0.1.2/neodistr/inst/CITATION |only neodistr-0.1.2/neodistr/inst/WORDLIST |only neodistr-0.1.2/neodistr/inst/data_precomputed |only neodistr-0.1.2/neodistr/inst/doc |only neodistr-0.1.2/neodistr/inst/shiny/server.R | 304 +++++++++++++- neodistr-0.1.2/neodistr/inst/shiny/ui.R | 38 + neodistr-0.1.2/neodistr/man/bnrm.Rd | 8 neodistr-0.1.2/neodistr/man/brms_custom_family.Rd | 8 neodistr-0.1.2/neodistr/man/fossep.Rd |only neodistr-0.1.2/neodistr/man/gmsnburr.Rd | 4 neodistr-0.1.2/neodistr/man/jfst.Rd | 2 neodistr-0.1.2/neodistr/man/jsep.Rd |only neodistr-0.1.2/neodistr/man/msnburr.Rd | 4 neodistr-0.1.2/neodistr/man/msnburr2a.Rd | 4 neodistr-0.1.2/neodistr/man/stanf_fossep.Rd |only neodistr-0.1.2/neodistr/man/stanf_gmsnburr.Rd | 8 neodistr-0.1.2/neodistr/man/stanf_jfst.Rd | 6 neodistr-0.1.2/neodistr/man/stanf_jsep.Rd |only neodistr-0.1.2/neodistr/man/stanf_msnburr.Rd | 8 neodistr-0.1.2/neodistr/man/stanf_msnburr2a.Rd | 8 neodistr-0.1.2/neodistr/man/summary_dist.Rd | 10 neodistr-0.1.2/neodistr/tests/spelling.R |only neodistr-0.1.2/neodistr/tests/testthat/test_fossep_r.R |only neodistr-0.1.2/neodistr/tests/testthat/test_gmsnburr_r.R |only neodistr-0.1.2/neodistr/tests/testthat/test_jfst_r.R |only neodistr-0.1.2/neodistr/tests/testthat/test_jsep_r.R |only neodistr-0.1.2/neodistr/tests/testthat/test_msnburr2a_r.R |only neodistr-0.1.2/neodistr/tests/testthat/test_msnburr_r.R |only neodistr-0.1.2/neodistr/vignettes |only 52 files changed, 810 insertions(+), 166 deletions(-)
Title: Demographic Analysis and Data Manipulation
Description: Perform tasks commonly encountered when
preparing and analysing demographic data.
Some functions are intended for end users, and
others for developers. Includes functions for
working with life tables.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between poputils versions 0.4.1 dated 2025-03-27 and 0.4.2 dated 2025-07-12
DESCRIPTION | 6 ++-- MD5 | 19 ++++++------ NEWS.md | 9 ++++++ R/cpp11.R | 4 ++ R/rr3.R | 62 ++++++++++++++++-------------------------- build/vignette.rds |binary man/rr3.Rd | 2 - src/cpp11.cpp | 8 +++++ src/rr3.cpp |only tests/testthat/test-lifetab.R | 4 +- tests/testthat/test-rr3.R | 14 ++++++++- 11 files changed, 74 insertions(+), 54 deletions(-)
Title: Multinomial Logit Models
Description: Maximum likelihood estimation of random utility discrete
choice models. The software is described in Croissant (2020)
<doi:10.18637/jss.v095.i11> and the underlying methods in
Train (2009) <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.1-2 dated 2025-04-28 and 1.1-3 dated 2025-07-12
mlogit-1.1-2/mlogit/tests |only mlogit-1.1-3/mlogit/DESCRIPTION | 8 ++++---- mlogit-1.1-3/mlogit/MD5 | 21 ++++++++------------- mlogit-1.1-3/mlogit/NEWS.md | 4 ++++ mlogit-1.1-3/mlogit/build/partial.rdb |binary mlogit-1.1-3/mlogit/inst/doc/c2.formula.data.html | 3 +-- mlogit-1.1-3/mlogit/inst/doc/e1mlogit.html | 4 ++-- mlogit-1.1-3/mlogit/inst/doc/e2nlogit.html | 4 ++-- mlogit-1.1-3/mlogit/inst/doc/e3mxlogit.html | 8 ++++---- mlogit-1.1-3/mlogit/inst/doc/e4mprobit.html | 4 ++-- 10 files changed, 27 insertions(+), 29 deletions(-)
Title: Bayesian Geostatistics Using Predictive Stacking
Description: Fits Bayesian hierarchical spatial and spatial-temporal process
models for point-referenced Gaussian, Poisson, binomial, and binary data
using stacking of predictive densities. It involves sampling from
analytically available posterior distributions conditional upon candidate
values of the spatial process parameters and, subsequently assimilate
inference from these individual posterior distributions using Bayesian
predictive stacking. Our algorithm is highly parallelizable and hence, much
faster than traditional Markov chain Monte Carlo algorithms while delivering
competitive predictive performance. See Zhang, Tang, and Banerjee (2025)
<doi:10.48550/arXiv.2304.12414>, and, Pan, Zhang, Bradley, and Banerjee
(2025) <doi:10.48550/arXiv.2406.04655> for details.
Author: Soumyakanti Pan [aut, cre] ,
Sudipto Banerjee [aut]
Maintainer: Soumyakanti Pan <span18@ucla.edu>
Diff between spStack versions 1.0.1 dated 2024-10-08 and 1.1.0 dated 2025-07-11
DESCRIPTION | 37 - MD5 | 103 ++-- NAMESPACE | 7 NEWS.md | 8 R/predict.R |only R/recoverGLMscale.R |only R/sim_stvcPoisson.R |only R/spGLMexact.R | 28 - R/spGLMstack.R | 30 - R/spLMexact.R | 12 R/spLMstack.R | 23 R/spStack-package.R | 6 R/stackedSampler.R | 93 ++- R/stacking_weights.R | 1 R/stvcGLMexact.R |only R/stvcGLMstack.R |only R/utils.R | 175 ++++++- README.md | 14 build/partial.rdb |binary build/vignette.rds |binary data/sim_stvcPoisson.rda |only inst/doc/posterior-predictive.R |only inst/doc/posterior-predictive.Rmd |only inst/doc/posterior-predictive.html |only inst/doc/spStack.R | 238 ++-------- inst/doc/spStack.Rmd | 413 ++++------------- inst/doc/spStack.html | 879 +++++++++---------------------------- inst/doc/spatial-temporal.R |only inst/doc/spatial-temporal.Rmd |only inst/doc/spatial-temporal.html |only inst/doc/spatial.R |only inst/doc/spatial.Rmd |only inst/doc/spatial.html |only inst/doc/technical_overview.R |only inst/doc/technical_overview.Rmd |only inst/doc/technical_overview.html |only man/candidateModels.Rd |only man/figures/logo.png |binary man/get_stacking_weights.Rd | 1 man/posteriorPredict.Rd |only man/recoverGLMscale.Rd |only man/sim_stvcPoisson.Rd |only man/spGLMstack.Rd | 1 man/spLMstack.Rd | 1 man/spStack-package.Rd | 7 man/stackedSampler.Rd | 18 man/stvcGLMexact.Rd |only man/stvcGLMstack.Rd |only src/MatrixAlgos.cpp | 277 +++++++++++ src/MatrixAlgos.h | 17 src/init.cpp | 9 src/predict_spGLM.cpp |only src/predict_spLM.cpp |only src/predict_stvcGLM.cpp |only src/recoverScale_spGLM.cpp |only src/recoverScale_stvcGLM.cpp |only src/spGLMexact.cpp | 10 src/spGLMexactLOO.cpp | 8 src/spLMexactLOO.cpp | 261 +++++++--- src/spStack.h | 37 + src/stvcGLMexact.cpp |only src/stvcGLMexactLOO.cpp |only src/util.cpp | 391 ++++++++++++++++ src/util.h | 30 + vignettes/posterior-predictive.Rmd |only vignettes/refs.bib | 25 - vignettes/spStack.Rmd | 413 ++++------------- vignettes/spatial-temporal.Rmd |only vignettes/spatial.Rmd |only vignettes/technical_overview.Rmd |only 70 files changed, 1861 insertions(+), 1712 deletions(-)
Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support
for automatic legends, facets, themes, and various other enhancements.
Author: Grant McDermott [aut, cre] ,
Vincent Arel-Bundock [aut] ,
Achim Zeileis [aut] ,
Etienne Bacher [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between tinyplot versions 0.4.1 dated 2025-06-02 and 0.4.2 dated 2025-07-11
DESCRIPTION | 12 ++-- MD5 | 39 +++++++------- NEWS.md | 31 +++++++++++ R/environment.R |only R/hooks.R |only R/tinyplot.R | 21 +++++-- R/tinyplot_add.R | 15 ----- R/tinytheme.R | 3 - R/tpar.R | 16 +++-- R/type_abline.R | 138 ++++++++++++++++++++++++++++++++++++++++++-------- R/type_barplot.R | 15 ++++- R/type_hline.R | 53 ++++++++++++++----- R/type_spineplot.R | 30 ++++++++-- R/type_text.R | 39 +++++++++++--- R/type_vline.R | 52 ++++++++++++++---- R/zzz.R | 18 ++---- man/set_hooks.Rd |only man/tinyplot_add.Rd | 14 ----- man/type_abline.Rd | 72 +++++++++++++++++++++++--- man/type_barplot.Rd | 9 ++- man/type_spineplot.Rd | 12 +++- man/type_text.Rd | 29 +++++++++- 22 files changed, 460 insertions(+), 158 deletions(-)
Title: Regularized Bayesian Estimator for Two-Level Latent Variable
Models
Description: Implements a regularized Bayesian estimator that optimizes the estimation
of between-group coefficients for multilevel latent variable models by minimizing
mean squared error (MSE) and balancing variance and bias. The package provides more reliable
estimates in scenarios with limited data, offering a robust solution for accurate
parameter estimation in two-level latent variable models. It is designed for
researchers in psychology, education, and related fields who face challenges in
estimating between-group effects under small sample sizes and low intraclass
correlation coefficients. Dashuk et al. (2024) <doi:10.13140/RG.2.2.18148.39048>
derived the optimal regularized Bayesian estimator;
Dashuk et al. (2024) <doi:10.13140/RG.2.2.34350.01604> extended it to
the multivariate case; and Luedtke et al. (2008) <doi:10.1037/a0012869>
formalized the two-level latent variable framework.
Author: Valerii Dashuk [aut, cre],
Binayak Timilsina [aut],
Martin Hecht [aut],
Steffen Zitzmann [aut]
Maintainer: Valerii Dashuk <vadashuk@gmail.com>
Diff between MultiLevelOptimalBayes versions 0.0.1.6 dated 2025-05-29 and 0.0.2.0 dated 2025-07-11
DESCRIPTION | 6 +-- MD5 | 14 ++++----- R/mlob.R | 45 ++++++++++++++++------------- README.md | 34 ++++++++++----------- inst/doc/MultiLevelOptimalBayes-Intro.Rmd | 18 +++++------ inst/doc/MultiLevelOptimalBayes-Intro.html | 24 +++++++-------- man/mlob.Rd | 2 + vignettes/MultiLevelOptimalBayes-Intro.Rmd | 18 +++++------ 8 files changed, 85 insertions(+), 76 deletions(-)
More information about MultiLevelOptimalBayes at CRAN
Permanent link
Title: Integrative Pathway Enrichment Analysis of Multivariate Omics
Data
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.
Author: Juri Reimand [aut, cre],
Jonathan Barenboim [ctb],
Mykhaylo Slobodyanyuk [aut]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Diff between ActivePathways versions 2.0.5 dated 2024-07-28 and 2.0.6 dated 2025-07-11
DESCRIPTION | 8 - MD5 | 18 +-- NAMESPACE | 2 NEWS.md | 5 R/merge_results.r |only inst/doc/ActivePathways-vignette.R | 31 +++++ inst/doc/ActivePathways-vignette.Rmd | 55 ++++++++- inst/doc/ActivePathways-vignette.html | 202 +++++++++++++++++++++++----------- man/merge_gmt.Rd |only man/merge_results.Rd |only tests/testthat/test_merge_results.r |only vignettes/ActivePathways-vignette.Rmd | 55 ++++++++- 12 files changed, 295 insertions(+), 81 deletions(-)
More information about ActivePathways at CRAN
Permanent link
Title: Parametric Time-Dependent Receiver Operating Characteristic
Description: Producing the time-dependent receiver operating characteristic (ROC) curve through parametric approaches. Tools for
generating random data, fitting, predicting and check goodness of fit are prepared. The methods are
developed from the theoretical framework of proportional hazard model and copula functions.
Using this package, users can now simulate parametric time-dependent ROC and run experiment
to understand the behavior of the curve under different scenario.
Author: Faiz Azhar [aut, cre, cph] ,
Adina Najwa Kamarudin [cph, ths] ,
Universiti Teknologi Malaysia, UTM [cph],
Universiti Malaya, UM [cph]
Maintainer: Faiz Azhar <faiz.azhar241@gmail.com>
Diff between parTimeROC versions 0.1.1 dated 2025-04-11 and 0.2.0 dated 2025-07-11
DESCRIPTION | 21 ++++++++++++--------- MD5 | 4 ++-- NEWS.md | 2 ++ 3 files changed, 16 insertions(+), 11 deletions(-)
Title: ISO 3166-1 Country Codes
Description: ISO 3166-1 country codes and ISO 4217 currency codes provided
by the International Organization for Standardization.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between isocountry versions 0.4.0 dated 2025-06-06 and 0.5.0 dated 2025-07-11
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/data.R | 16 +++++++++++++--- README.md | 7 ++++--- data/isocountry.rda |binary data/isocurrency.rda |binary man/isocountry.Rd | 14 ++++++++++++-- man/isocurrency.Rd | 2 +- 9 files changed, 46 insertions(+), 20 deletions(-)
Title: Tools for Wikidata and Wikipedia
Description: A set of wrappers intended to check, read and download information from the Wikimedia sources. It is specifically created to work with names of celebrities, in which case their information and statistics can be downloaded. Additionally, it also builds links and snippets to use in combination with the function gallery() in netCoin package.
Author: Modesto Escobar [aut, cph, cre] ,
Angel Zazo [aut],
Carlos Prieto [aut] ,
David Barrios [aut],
Cristina Calvo [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between wikiTools versions 1.2.8 dated 2025-03-31 and 1.2.14 dated 2025-07-11
DESCRIPTION | 20 +++++--- MD5 | 48 ++++++++++---------- NAMESPACE | 3 + R/w_Exhibit.R |only R/wikiTools.R | 44 ++++++++++++++++++ R/wiki_utils.R | 30 ++++++------ README.md | 4 - build/vignette.rds |binary inst/doc/wiki_utils.html | 30 ++++++------ man/extractWiki.Rd | 2 man/filext.Rd | 58 ++++++++++++------------ man/getFiles.Rd | 102 +++++++++++++++++++++---------------------- man/getWikiFiles.Rd | 88 ++++++++++++++++++------------------- man/httrGetJSON.Rd | 62 +++++++++++++------------- man/nametoWikiFrame.Rd | 74 +++++++++++++++---------------- man/nametoWikiHtml.Rd | 70 ++++++++++++++--------------- man/nametoWikiURL.Rd | 74 +++++++++++++++---------------- man/pop_up.Rd |only man/preName.Rd | 60 ++++++++++++------------- man/searchWiki.Rd | 96 ++++++++++++++++++++-------------------- man/selectLang.Rd |only man/urltoFrame.Rd | 70 ++++++++++++++--------------- man/urltoHtml.Rd | 86 ++++++++++++++++++------------------ man/validUrl.Rd | 56 +++++++++++------------ man/w_Exhibit.Rd |only man/w_SearchByAuthority.Rd | 6 +- man/w_SearchByIdentifiers.Rd | 6 +- 27 files changed, 573 insertions(+), 516 deletions(-)
Title: Find Differences Between R Objects
Description: Compare complex R objects and reveal the key differences.
Designed particularly for use in testing packages where being able to
quickly isolate key differences makes understanding test failures much
easier.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between waldo versions 0.6.1 dated 2024-11-07 and 0.6.2 dated 2025-07-11
DESCRIPTION | 6 MD5 | 36 ++--- NEWS.md | 8 + R/compare-class.R | 6 R/compare-data-frame.R | 16 +- R/compare-opts.R | 24 +-- R/compare-value.R | 86 ++++++++---- R/compare.R | 219 ++++++++++++++++++++++--------- R/diff.R | 104 +++++++++----- R/ses.R | 13 + R/utils.R | 13 - tests/testthat/_snaps/compare.md | 72 ++++++---- tests/testthat/f2.R | 4 tests/testthat/test-compare-data-frame.R | 5 tests/testthat/test-compare-value.R | 30 +++- tests/testthat/test-compare.R | 189 +++++++++++++++++--------- tests/testthat/test-proxy.R | 2 tests/testthat/test-ses.R | 3 tests/testthat/test-utils.R | 10 + 19 files changed, 573 insertions(+), 273 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, cre, cph],
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],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.11.1 dated 2025-05-04 and 1.11.2 dated 2025-07-11
DESCRIPTION | 8 +++---- MD5 | 40 ++++++++++++++++++------------------- NEWS.md | 7 ++++++ R/ordinal-support.R | 4 +-- R/ref-grid.R | 16 +++++--------- inst/doc/AQuickStart.html | 4 +-- inst/doc/FAQs.html | 4 +-- inst/doc/basics.html | 6 ++--- inst/doc/comparisons.html | 10 ++++----- inst/doc/confidence-intervals.html | 14 ++++++------ inst/doc/interactions.html | 18 ++++++++-------- inst/doc/messy-data.html | 4 +-- inst/doc/models.html | 4 +-- inst/doc/predictions.html | 4 +-- inst/doc/re-engineering-clds.html | 4 +-- inst/doc/sophisticated.html | 4 +-- inst/doc/transformations.html | 6 ++--- inst/doc/utilities.html | 4 +-- inst/doc/vignette-topics.html | 4 +-- inst/doc/xplanations.html | 4 +-- inst/doc/xtending.html | 8 +++---- 21 files changed, 90 insertions(+), 87 deletions(-)
Title: Multilevel Hidden Markov Models Using Bayesian Estimation
Description: An implementation of the multilevel (also known as mixed or random
effects) hidden Markov model using Bayesian estimation in R. The multilevel
hidden Markov model (HMM) is a generalization of the well-known hidden
Markov model, for the latter see Rabiner (1989) <doi:10.1109/5.18626>. The
multilevel HMM is tailored to accommodate (intense) longitudinal data of
multiple individuals simultaneously, see e.g., de Haan-Rietdijk et al.
<doi:10.1080/00273171.2017.1370364>. Using a multilevel framework, we allow
for heterogeneity in the model parameters (transition probability matrix and
conditional distribution), while estimating one overall HMM. The model can
be fitted on multivariate data with either a categorical, normal, or Poisson
distribution, and include individual level covariates (allowing for e.g.,
group comparisons on model parameters). Parameters are estimated using
Bayesian estimation utilizing the forward-backward recursion within a hybrid
Metropolis within Gibbs samp [...truncated...]
Author: Emmeke Aarts [aut, cre],
Sebastian Mildiner Moraga [aut]
Maintainer: Emmeke Aarts <e.aarts@uu.nl>
Diff between mHMMbayes versions 1.1.0 dated 2024-04-01 and 1.1.1 dated 2025-07-11
mHMMbayes-1.1.0/mHMMbayes/inst/doc/estimation-mhmm.R |only mHMMbayes-1.1.0/mHMMbayes/inst/doc/estimation-mhmm.Rmd |only mHMMbayes-1.1.0/mHMMbayes/inst/doc/estimation-mhmm.pdf |only mHMMbayes-1.1.0/mHMMbayes/vignettes/estimation-mhmm.Rmd |only mHMMbayes-1.1.1/mHMMbayes/DESCRIPTION | 8 mHMMbayes-1.1.1/mHMMbayes/MD5 | 40 - mHMMbayes-1.1.1/mHMMbayes/NEWS.md | 8 mHMMbayes-1.1.1/mHMMbayes/R/mHMM.R | 310 ++++++----- mHMMbayes-1.1.1/mHMMbayes/R/obtain_emiss.R | 14 mHMMbayes-1.1.1/mHMMbayes/R/obtain_gamma.R | 3 mHMMbayes-1.1.1/mHMMbayes/R/plot.mHMM.R | 6 mHMMbayes-1.1.1/mHMMbayes/R/sim_mHMM.R | 19 mHMMbayes-1.1.1/mHMMbayes/R/summary.mHMM.R | 14 mHMMbayes-1.1.1/mHMMbayes/R/vit_mHMM.R | 4 mHMMbayes-1.1.1/mHMMbayes/README.md | 84 ++ mHMMbayes-1.1.1/mHMMbayes/build/partial.rdb |binary mHMMbayes-1.1.1/mHMMbayes/build/vignette.rds |binary mHMMbayes-1.1.1/mHMMbayes/inst/doc/estimation-mhmm-html.R |only mHMMbayes-1.1.1/mHMMbayes/inst/doc/estimation-mhmm-html.Rmd |only mHMMbayes-1.1.1/mHMMbayes/inst/doc/estimation-mhmm-html.html |only mHMMbayes-1.1.1/mHMMbayes/inst/doc/tutorial-mhmm.R | 114 ++-- mHMMbayes-1.1.1/mHMMbayes/inst/doc/tutorial-mhmm.Rmd | 10 mHMMbayes-1.1.1/mHMMbayes/inst/doc/tutorial-mhmm.html | 38 - mHMMbayes-1.1.1/mHMMbayes/vignettes/estimation-mhmm-html.Rmd |only mHMMbayes-1.1.1/mHMMbayes/vignettes/tutorial-mhmm.Rmd | 10 25 files changed, 419 insertions(+), 263 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Stratification and covariate adju [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.7.2 dated 2025-05-14 and 0.8.0 dated 2025-07-11
hce-0.7.2/hce/R/simADHCE.R |only hce-0.7.2/hce/man/simADHCE.Rd |only hce-0.8.0/hce/DESCRIPTION | 10 +++--- hce-0.8.0/hce/MD5 | 48 +++++++++++++++--------------- hce-0.8.0/hce/NAMESPACE | 2 - hce-0.8.0/hce/NEWS.md | 7 ++++ hce-0.8.0/hce/R/as_hce.data.frame.R | 41 +++++++++++++++++++++++-- hce-0.8.0/hce/R/simHCE.R | 43 +++++++++++++++++++++----- hce-0.8.0/hce/R/simKHCE.R |only hce-0.8.0/hce/R/simORD.R | 2 - hce-0.8.0/hce/R/summaryWO_data_frame.R | 2 - hce-0.8.0/hce/R/summaryWO_formula.R | 5 +-- hce-0.8.0/hce/R/summaryWO_hce.R | 2 - hce-0.8.0/hce/data/KHCE.rda |binary hce-0.8.0/hce/inst/doc/Introduction.Rmd | 4 +- hce-0.8.0/hce/inst/doc/Introduction.html | 39 ++++++++++++------------ hce-0.8.0/hce/inst/doc/Wins.html | 4 +- hce-0.8.0/hce/inst/doc/hce.html | 4 +- hce-0.8.0/hce/inst/doc/maraca.html | 4 +- hce-0.8.0/hce/man/simHCE.Rd | 7 +++- hce-0.8.0/hce/man/simKHCE.Rd |only hce-0.8.0/hce/man/simORD.Rd | 2 - hce-0.8.0/hce/man/summaryWO.data.frame.Rd | 2 - hce-0.8.0/hce/man/summaryWO.formula.Rd | 3 + hce-0.8.0/hce/man/summaryWO.hce.Rd | 2 - hce-0.8.0/hce/vignettes/Introduction.Rmd | 4 +- hce-0.8.0/hce/vignettes/REFERENCES.bib | 2 - 27 files changed, 157 insertions(+), 82 deletions(-)
Title: Implement Download Buttons in 'rmarkdown'
Description: Implement download buttons in HTML output from 'rmarkdown' without the need for 'runtime:shiny'.
Author: Felipe Mattioni Maturana [aut, cre] ,
John Coene [ctb]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between downloadthis versions 0.4.1 dated 2024-10-14 and 0.5.0 dated 2025-07-11
downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-brands-400.eot |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-brands-400.svg |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-brands-400.woff |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-regular-400.eot |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-regular-400.svg |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-regular-400.woff |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-solid-900.eot |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-solid-900.svg |only downloadthis-0.4.1/downloadthis/inst/assets/webfonts/fa-solid-900.woff |only downloadthis-0.5.0/downloadthis/DESCRIPTION | 14 +-- downloadthis-0.5.0/downloadthis/MD5 | 45 ++++------ downloadthis-0.5.0/downloadthis/NEWS.md | 5 + downloadthis-0.5.0/downloadthis/R/utils.R | 8 - downloadthis-0.5.0/downloadthis/build/vignette.rds |binary downloadthis-0.5.0/downloadthis/inst/assets/css/all.min.css | 8 - downloadthis-0.5.0/downloadthis/inst/assets/css/v4-shims.min.css | 4 downloadthis-0.5.0/downloadthis/inst/assets/js/script.js | 2 downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-brands-400.ttf |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-brands-400.woff2 |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-regular-400.ttf |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-regular-400.woff2 |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-solid-900.ttf |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-solid-900.woff2 |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-v4compatibility.ttf |binary downloadthis-0.5.0/downloadthis/inst/assets/webfonts/fa-v4compatibility.woff2 |binary downloadthis-0.5.0/downloadthis/inst/doc/button_types.html | 8 - downloadthis-0.5.0/downloadthis/inst/doc/customization.html | 2 downloadthis-0.5.0/downloadthis/inst/doc/downloadthis.html | 14 +-- 28 files changed, 53 insertions(+), 57 deletions(-)
Title: Profiling a Log-Likelihood to Calculate Confidence Intervals
Description: Provides tools for profiling a user-supplied log-likelihood
function to calculate confidence intervals for model parameters. Speed of
computation can be improved by adjusting the step sizes in the profiling
and/or starting the profiling from limits based on the approximate large
sample normal distribution for the maximum likelihood estimator of a
parameter. The accuracy of the limits can be set by the user. A plot method
visualises the log-likelihood and confidence interval. Cases where the
profile log-likelihood flattens above the value at which a confidence limit
is defined can be handled, leading to a limit at plus or minus infinity.
Disjoint confidence intervals will not be found.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between profileCI versions 1.0.0 dated 2025-06-04 and 1.1.0 dated 2025-07-11
DESCRIPTION | 15 MD5 | 37 + NAMESPACE | 1 NEWS.md |only R/profileCI-internal.R | 584 ++++++++++++++++++++----------- R/profileCI-logLikFn.R | 34 + R/profileCI-methods.R | 6 R/profileCI-package.R | 8 R/profileCI.R | 79 +++- README.md | 20 - man/figures/README-unnamed-chunk-5-1.png |binary man/logLikFn.Rd | 15 man/profileCI-internal.Rd | 21 + man/profileCI-package.Rd | 6 man/profileCI.Rd | 46 ++ tests/testthat.R | 24 - tests/testthat/setup.R | 2 tests/testthat/test-profileCI-bounds.R |only tests/testthat/test-profileCI-flat.R |only tests/testthat/test-profileCI-methods.R | 4 tests/testthat/test-profileCI.R | 1 21 files changed, 646 insertions(+), 257 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.4.3 dated 2025-05-13 and 1.5.0 dated 2025-07-11
praatpicture-1.4.3/praatpicture/R/praat_pitchRawAC.R |only praatpicture-1.4.3/praatpicture/R/zzz.R |only praatpicture-1.4.3/praatpicture/man/praat_pitchRawAC.Rd |only praatpicture-1.5.0/praatpicture/DESCRIPTION | 16 praatpicture-1.5.0/praatpicture/MD5 | 59 praatpicture-1.5.0/praatpicture/NAMESPACE | 3 praatpicture-1.5.0/praatpicture/NEWS.md | 284 - praatpicture-1.5.0/praatpicture/R/conv2sc.R | 88 praatpicture-1.5.0/praatpicture/R/draw_arrow.R | 58 praatpicture-1.5.0/praatpicture/R/draw_rectangle.R | 56 praatpicture-1.5.0/praatpicture/R/formantplot.R | 485 +- praatpicture-1.5.0/praatpicture/R/intensity_overlay.R |only praatpicture-1.5.0/praatpicture/R/intensityplot.R | 287 - praatpicture-1.5.0/praatpicture/R/make_TextGrid.R | 154 praatpicture-1.5.0/praatpicture/R/make_annot.R | 68 praatpicture-1.5.0/praatpicture/R/pitch_overlay.R |only praatpicture-1.5.0/praatpicture/R/pitchplot.R | 446 +- praatpicture-1.5.0/praatpicture/R/praatpicture.R | 1783 +++++----- praatpicture-1.5.0/praatpicture/R/shiny_praatpicture.R | 30 praatpicture-1.5.0/praatpicture/R/specplot.R | 994 ++--- praatpicture-1.5.0/praatpicture/R/talking_praatpicture.R | 174 praatpicture-1.5.0/praatpicture/R/tg_createTier.R | 208 - praatpicture-1.5.0/praatpicture/R/waveplot.R | 413 +- praatpicture-1.5.0/praatpicture/inst/shiny/shiny_praatpicture/server.R | 1624 ++++----- praatpicture-1.5.0/praatpicture/inst/shiny/shiny_praatpicture/ui.R | 744 ++-- praatpicture-1.5.0/praatpicture/man/formantplot.Rd | 9 praatpicture-1.5.0/praatpicture/man/intensity_overlay.Rd |only praatpicture-1.5.0/praatpicture/man/intensityplot.Rd | 9 praatpicture-1.5.0/praatpicture/man/make_annot.Rd | 62 praatpicture-1.5.0/praatpicture/man/pitch_overlay.Rd |only praatpicture-1.5.0/praatpicture/man/pitchplot.Rd | 7 praatpicture-1.5.0/praatpicture/man/praatpicture.Rd | 15 praatpicture-1.5.0/praatpicture/man/shiny_praatpicture.Rd | 38 praatpicture-1.5.0/praatpicture/man/waveplot.Rd | 104 34 files changed, 4190 insertions(+), 4028 deletions(-)
Title: Checking and Simplifying Validation Rule Sets
Description: Rule sets with validation rules may contain redundancies or contradictions.
Functions for finding redundancies and problematic rules are provided,
given a set a rules formulated with 'validate'.
Author: Edwin de Jonge [aut, cre] ,
Mark van der Loo [aut],
Jacco Daalmans [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between validatetools versions 0.5.2 dated 2023-09-30 and 0.6.1 dated 2025-07-11
DESCRIPTION | 13 +- MD5 | 91 +++++++++--------- NAMESPACE | 2 NEWS.md | 17 +++ R/categorical.R | 4 R/conditional.R | 4 R/contradicted.R | 29 ++++- R/detect_boundary.R | 25 ++--- R/detect_contradicting_if_rules.R |only R/detect_fixed_variables.R | 13 +- R/dnf.R | 34 ++++++ R/feasible.R | 99 +++++++++++++++----- R/implied_by.R | 26 ++++- R/linear.R | 4 R/mip_lpsolve.R | 3 R/mip_rule.R | 1 R/redundancy.R | 41 ++++++-- R/simplify_conditional.R | 41 +++++++- R/simplify_rules.R | 15 +-- R/soft-rule.R | 6 + R/substitute_values.R | 7 - R/utils.R | 6 - R/validatetools-package.R | 29 +++-- man/detect_boundary_cat.Rd | 11 +- man/detect_boundary_num.Rd | 14 +- man/detect_contradicting_if_rules.Rd |only man/detect_fixed_variables.Rd | 7 - man/detect_infeasible_rules.Rd | 23 +++- man/detect_redundancy.Rd | 18 ++- man/expect_values.Rd | 1 man/is_categorical.Rd | 4 man/is_conditional.Rd | 4 man/is_contradicted_by.Rd | 21 +++- man/is_implied_by.Rd | 16 ++- man/is_infeasible.Rd | 27 ++++- man/is_linear.Rd | 2 man/make_feasible.Rd | 33 ++++-- man/remove_redundancy.Rd | 16 +-- man/simplify_conditional.Rd | 15 ++- man/simplify_fixed_variables.Rd | 6 - man/simplify_rules.Rd | 16 ++- man/substitute_values.Rd | 3 man/translate_mip_lp.Rd | 1 man/validatetools.Rd | 49 +++++++-- tests/testthat/detect_contradicting_if_rules.txt |only tests/testthat/test-cat_domain.R |only tests/testthat/test-detect_contradicting_if_rules.R |only tests/testthat/test-feasible.R | 2 tests/testthat/test-simplify_conditional.R | 15 +++ 49 files changed, 568 insertions(+), 246 deletions(-)
Title: Response Item Networks
Description: Contains various tools to perform and visualize Response Item Networks ('ResIN's'). 'ResIN' binarizes ordered-categorical and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Author: Philip Warncke [cre, aut],
Dino Carpentras [aut],
Adrian Lueders [aut]
Maintainer: Philip Warncke <pwarncke@live.unc.edu>
Diff between ResIN versions 2.1.0 dated 2025-06-13 and 2.2.0 dated 2025-07-11
DESCRIPTION | 6 - MD5 | 30 ++--- R/Boostrap_example.R | 2 R/ResIN.R | 27 ++-- R/ResIN_boots_extract.R | 68 ++++-------- R/ResIN_boots_prepare.R | 8 - R/globals.R | 1 data/Bootstrap_example.rda |binary inst/doc/ResIN-VIGNETTE.R | 29 ++--- inst/doc/ResIN-VIGNETTE.Rmd | 51 ++++----- inst/doc/ResIN-VIGNETTE.html | 235 +++++++++++++++++++++---------------------- man/Bootstrap_example.Rd | 2 man/ResIN.Rd | 3 man/ResIN_boots_extract.Rd | 2 man/ResIN_boots_prepare.Rd | 4 vignettes/ResIN-VIGNETTE.Rmd | 51 ++++----- 16 files changed, 252 insertions(+), 267 deletions(-)
Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <https://iucn.org/> for more information) red list criteria.
Author: Pedro Cardoso [aut] ,
Vasco V. Branco [cre, aut]
Maintainer: Vasco V. Branco <vasco.branco@helsinki.fi>
Diff between red versions 1.6.2 dated 2025-05-10 and 1.6.3 dated 2025-07-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/main.R | 29 +++++++++++++++-------------- man/aoo.Rd | 6 ++++-- 4 files changed, 26 insertions(+), 23 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.2.6 dated 2025-05-14 and 0.2.7 dated 2025-07-11
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 5 R/Get_AdmUnNames.R | 5 R/Get_BroadBand.R | 306 ++++++++++++++++++++++------------------------ R/Get_School2mun.R | 158 ++++++++++++----------- R/Group_BroadBand.R | 2 R/Set_DB.R | 3 R/Util_BroadBand2mun.R |only README.md | 9 - man/Get_BroadBand.Rd | 42 ++++-- man/Util_BroadBand2mun.Rd |only 12 files changed, 292 insertions(+), 266 deletions(-)
Title: Framework for Easy Statistical Modeling, Visualization, and
Reporting
Description: A meta-package that installs and loads a set of packages from
'easystats' ecosystem in a single step. This collection of packages provide
a unifying and consistent framework for statistical modeling, visualization,
and reporting. Additionally, it provides articles targeted at instructors for
teaching 'easystats', and a dashboard targeted at new R users for easily
conducting statistical analysis by accessing summary results, model fit indices,
and visualizations with minimal programming.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Etienne Bacher [aut] ,
Remi Theriault [aut]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between easystats versions 0.7.4 dated 2025-02-06 and 0.7.5 dated 2025-07-11
DESCRIPTION | 36 ++++++++++++++++++--------------- MD5 | 39 +++++++++++++++++++----------------- NAMESPACE | 11 ++++++++++ NEWS.md | 9 ++++++++ R/easystats_citations.R |only R/easystats_update.R | 7 ++++-- R/install_easystats.R | 29 ++++++++++++++++++++------ R/install_suggested.R | 17 ++++++--------- README.md | 27 +++++++++++++++++++++++- build/vignette.rds |binary inst/WORDLIST | 2 + inst/doc/overview_of_vignettes.Rmd | 5 +++- inst/doc/overview_of_vignettes.html | 9 ++++++-- inst/templates/easydashboard.Rmd | 10 --------- man/easystats_citations.Rd |only man/easystats_update.Rd | 6 ++++- man/figures/README-6-1.png |binary man/figures/depnetwork-1.png |binary man/install_latest.Rd | 14 ++++++++---- man/install_suggested.Rd | 13 ++++++------ man/reexports.Rd |only vignettes/overview_of_vignettes.Rmd | 5 +++- 22 files changed, 159 insertions(+), 80 deletions(-)
Title: Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
Description: Datasets and Functionality from
'Jan Beran' (1994). Statistics for Long-Memory Processes; Chapman & Hall.
Estimation of Hurst (and more) parameters for fractional Gaussian noise,
'fARIMA' and 'FEXP' models.
Author: Jan Beran [aut] ,
Martin Maechler [cre, aut] ,
Brandon Whitcher [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between longmemo versions 1.1-3 dated 2024-07-30 and 1.1-4 dated 2025-07-11
ChangeLog | 17 +++++ DESCRIPTION | 10 +-- MD5 | 22 ++++--- R/WhittleEst.R | 54 ++++++++++-------- build/vignette.rds |binary inst/doc/BspecFGN.pdf |binary inst/doc/Done |only man/CetaARIMA.Rd | 7 +- man/specARIMA.Rd | 9 ++- man/specFGN.Rd | 8 ++ tests/ceta-ex.R | 50 +++++++++++++---- tests/ceta-ex.Rout.save | 138 +++++++++++++++++++----------------------------- tests/ceta-ex.Rout_noLD |only 13 files changed, 175 insertions(+), 140 deletions(-)
Title: Conditional Method Agreement Trees (COAT)
Description: Agreement of continuously scaled measurements made by two techniques, devices or methods is usually
evaluated by the well-established Bland-Altman analysis or plot. Conditional method agreement trees (COAT),
proposed by Karapetyan, Zeileis, Henriksen, and Hapfelmeier (2025) <doi:10.1093/jrsssc/qlae077>,
embed the Bland-Altman analysis in the framework of recursive partitioning to explore heterogeneous method
agreement in dependence of covariates. COAT can also be used to perform a Bland-Altman test for differences
in method agreement.
Author: Alexander Hapfelmeier [aut, cre] ,
Siranush Karapetyan [aut] ,
Achim Zeileis [aut]
Maintainer: Alexander Hapfelmeier <Alexander.Hapfelmeier@mri.tum.de>
Diff between coat versions 0.2.1 dated 2025-06-27 and 0.2.2 dated 2025-07-11
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 46 +++++++++++++++++++++++++--------------------- R/batest.R | 5 +++++ R/coat.R | 16 ++++++++-------- build/partial.rdb |binary inst/CITATION | 30 ++++++++++++++++-------------- man/batest.Rd | 6 ++++++ man/coat.Rd | 8 ++++---- 9 files changed, 77 insertions(+), 60 deletions(-)
Title: 'HJ-Biplot' using Different Ways of Penalization Plotting with
'ggplot2'
Description: The 'HJ-Biplot' is a multivariate method that represents high-dimensional data in a low-dimensional subspace, capturing most of the information’s variability in just a few dimensions. This package implements three new regularized versions of the HJ-Biplot: Ridge, LASSO, and Elastic Net. These versions introduce restrictions that shrink or zero-out variable weights to improve interpretability based on regularization theory. All methods provide graphical representations using 'ggplot2'.
Author: Mitzi Isabel Cubilla-Montilla [aut, cre],
Carlos Alfredo Torres-Cubilla [aut],
Maria Purificacion Galindo Villardon [aut],
Ana Belen Nieto-Librero [aut]
Maintainer: Mitzi Isabel Cubilla-Montilla <mitzi@usal.es>
Diff between SparseBiplots versions 4.0.2 dated 2025-05-26 and 4.1.1 dated 2025-07-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/Plot_Biplot.R | 25 +++++++++++++++++++------ README.md | 3 +++ man/Plot_Biplot.Rd | 7 +++++++ 5 files changed, 36 insertions(+), 13 deletions(-)
Title: A System of Soil Classification for Making and Interpreting Soil
Surveys
Description: Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy.
Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation.
Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the "higher" taxonomic levels: Order, Suborder, Great Group, and Subgroup.
Author: Andrew Brown [aut, cre],
Dylan Beaudette [aut]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between SoilTaxonomy versions 0.2.7 dated 2025-04-05 and 0.2.8 dated 2025-07-11
DESCRIPTION | 9 +++---- MD5 | 42 ++++++++++++++++++------------------ NEWS.md | 4 +++ R/family-classes.R | 6 ----- R/taxonTree.R | 5 +--- README.md | 37 ++++++++++++++++--------------- build/vignette.rds |binary data/ST.rda |binary data/ST_SMR_13th.rda |binary data/ST_criteria_13th.rda |binary data/ST_family_classes.rda |binary data/ST_features.rda |binary data/ST_formative_elements.rda |binary data/ST_higher_taxa_codes_12th.rda |binary data/ST_higher_taxa_codes_13th.rda |binary data/ST_unique_list.rda |binary inst/CITATION | 7 ++---- inst/doc/family-level_taxonomy.html | 34 ++++++++++++++--------------- man/ST_family_classes.Rd | 2 - man/SoilTaxonomy-package.Rd | 1 man/taxonTree.Rd | 4 +-- tests/testthat/test-parseFamily.R | 8 ++++-- 22 files changed, 78 insertions(+), 81 deletions(-)
Title: Interface Between 'GRASS' Geographical Information System and
'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [aut] ,
Sebastian Jeworutzki [ctb] ,
Rainer Krug [ctb] ,
Robin Lovelace [ctb] ,
Markus Neteler [ctb] ,
Steven Pawley [cre, aut] ,
Floris Vanderhaeghe [ctb]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>
Diff between rgrass versions 0.5-2 dated 2025-02-14 and 0.5-3 dated 2025-07-11
rgrass-0.5-2/rgrass/R/AAA.R |only rgrass-0.5-2/rgrass/inst/etc |only rgrass-0.5-2/rgrass/inst/pre_git_ChangeLog |only rgrass-0.5-3/rgrass/DESCRIPTION | 25 +++++----- rgrass-0.5-3/rgrass/MD5 | 29 +++++------ rgrass-0.5-3/rgrass/NEWS.md | 4 + rgrass-0.5-3/rgrass/R/initGRASS.R | 49 +++++++++++++------- rgrass-0.5-3/rgrass/R/zzz.R |only rgrass-0.5-3/rgrass/build/vignette.rds |binary rgrass-0.5-3/rgrass/inst/doc/coerce.html | 19 +++---- rgrass-0.5-3/rgrass/tests/testthat/helper.R | 45 +++++++++--------- rgrass-0.5-3/rgrass/tests/testthat/test-execGRASS.R | 2 rgrass-0.5-3/rgrass/tests/testthat/test-gmeta.R | 1 rgrass-0.5-3/rgrass/tests/testthat/test-initGRASS.R | 3 + rgrass-0.5-3/rgrass/tests/testthat/test-options.R | 12 ++++ rgrass-0.5-3/rgrass/tests/testthat/test-read_RAST.R | 4 + rgrass-0.5-3/rgrass/tests/testthat/test-read_VECT.R | 3 + 17 files changed, 122 insertions(+), 74 deletions(-)
Title: NASA 'EarthData' Access Utilities
Description: Providing easy, portable access to NASA 'EarthData' products
through the use of bearer tokens. Much of NASA's public data catalogs hosted
and maintained by its 12 Distributed Active Archive Centers ('DAACs') are
now made available on the Amazon Web Services 'S3' storage. However,
accessing this data through the standard 'S3' API is restricted to only to
compute resources running inside 'us-west-2' Data Center in Portland, Oregon,
which allows NASA to avoid being charged data egress rates. This package
provides public access to the data from any networked device by using the
'EarthData' login application programming interface (API),
<https://www.earthdata.nasa.gov/data/earthdata-login>,
providing convenient authentication and access to cloud-hosted NASA 'EarthData'
products. This makes access to a wide range of earth observation data from
any location straight forward and compatible with R packages that are
widely used with cloud native earth observation data (such as 'terra',
's [...truncated...]
Author: Carl Boettiger [aut, cre, cph] ,
Luis Lopez [aut] ,
Yuvi Panda [aut],
Bri Lind [aut] ,
Andy Teucher [ctb] ,
Openscapes [fnd]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between earthdatalogin versions 0.0.2 dated 2023-12-15 and 0.0.3 dated 2025-07-11
earthdatalogin-0.0.2/earthdatalogin/inst/examples/search.R |only earthdatalogin-0.0.2/earthdatalogin/inst/vignette-sources/img |only earthdatalogin-0.0.2/earthdatalogin/tests/testthat/test-edl_download-alternatives.R |only earthdatalogin-0.0.3/earthdatalogin/DESCRIPTION | 28 + earthdatalogin-0.0.3/earthdatalogin/MD5 | 71 ++-- earthdatalogin-0.0.3/earthdatalogin/NAMESPACE | 7 earthdatalogin-0.0.3/earthdatalogin/NEWS.md | 20 + earthdatalogin-0.0.3/earthdatalogin/R/default_auth.R | 21 - earthdatalogin-0.0.3/earthdatalogin/R/edl_download.R | 30 -- earthdatalogin-0.0.3/earthdatalogin/R/edl_s3_token.R | 128 +++++++- earthdatalogin-0.0.3/earthdatalogin/R/edl_search.R |only earthdatalogin-0.0.3/earthdatalogin/R/edl_set_token.R | 12 earthdatalogin-0.0.3/earthdatalogin/R/list-nasa-stacs.R |only earthdatalogin-0.0.3/earthdatalogin/R/stac-collections_fetch.R |only earthdatalogin-0.0.3/earthdatalogin/README.md | 24 - earthdatalogin-0.0.3/earthdatalogin/build/vignette.rds |binary earthdatalogin-0.0.3/earthdatalogin/inst/WORDLIST | 17 - earthdatalogin-0.0.3/earthdatalogin/inst/doc/data-formats.html | 6 earthdatalogin-0.0.3/earthdatalogin/inst/doc/gdalcubes-stac-cog.Rmd | 129 +++++++- earthdatalogin-0.0.3/earthdatalogin/inst/doc/gdalcubes-stac-cog.html | 149 +++++++--- earthdatalogin-0.0.3/earthdatalogin/inst/doc/legacy-formats.html | 8 earthdatalogin-0.0.3/earthdatalogin/inst/doc/non-egressed.R | 76 ++--- earthdatalogin-0.0.3/earthdatalogin/inst/doc/non-egressed.Rmd | 2 earthdatalogin-0.0.3/earthdatalogin/inst/doc/non-egressed.html | 6 earthdatalogin-0.0.3/earthdatalogin/inst/vignette-sources/gdalcubes-stac-cog-explore.Rmd |only earthdatalogin-0.0.3/earthdatalogin/inst/vignette-sources/gdalcubes-stac-cog.Rmd | 103 +++++- earthdatalogin-0.0.3/earthdatalogin/inst/vignette-sources/legacy-formats.Rmd | 6 earthdatalogin-0.0.3/earthdatalogin/man/collections_fetch.Rd |only earthdatalogin-0.0.3/earthdatalogin/man/edl_download.Rd | 2 earthdatalogin-0.0.3/earthdatalogin/man/edl_extract_urls.Rd |only earthdatalogin-0.0.3/earthdatalogin/man/edl_s3_token.Rd | 44 ++ earthdatalogin-0.0.3/earthdatalogin/man/edl_search.Rd |only earthdatalogin-0.0.3/earthdatalogin/man/get_nasa_stac_url.Rd |only earthdatalogin-0.0.3/earthdatalogin/man/list_nasa_stacs.Rd |only earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-edl_download.R | 4 earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-edl_netrc.R | 29 + earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-edl_s3.R | 4 earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-edl_search.R |only earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-list-nasa-stacs.R |only earthdatalogin-0.0.3/earthdatalogin/tests/testthat/test-stac-collections_fetch.R |only earthdatalogin-0.0.3/earthdatalogin/vignettes/gdalcubes-stac-cog.Rmd | 129 +++++++- earthdatalogin-0.0.3/earthdatalogin/vignettes/img/unnamed-chunk-51-1.png |only earthdatalogin-0.0.3/earthdatalogin/vignettes/img/unnamed-chunk-7-1.png |only earthdatalogin-0.0.3/earthdatalogin/vignettes/img/unnamed-chunk-8-1.png |only earthdatalogin-0.0.3/earthdatalogin/vignettes/img/unnamed-chunk-9-1.png |only earthdatalogin-0.0.3/earthdatalogin/vignettes/non-egressed.Rmd | 2 46 files changed, 778 insertions(+), 279 deletions(-)
More information about earthdatalogin at CRAN
Permanent link
Title: Acceptance Sampling Plans Design
Description: Provides tools for designing and analyzing Acceptance Sampling plans.
Supports both Attributes Sampling (Binomial and Poisson distributions) and
Variables Sampling (Normal and Beta distributions), enabling quality control
for fractional and compositional data. Uses nonlinear programming for sampling
plan optimization, minimizing sample size while controlling producer's and
consumer's risks. Operating Characteristic curves are available for plan visualization.
Author: Ha Truong [aut, cre, cph],
Victor Miranda [ths, rev],
Roger Kissling [ths, rev]
Maintainer: Ha Truong <truongvietha87@gmail.com>
Diff between AccSamplingDesign versions 0.0.4 dated 2025-06-26 and 0.0.5 dated 2025-07-11
AccSamplingDesign-0.0.4/AccSamplingDesign/man/OCdata-accessors.Rd |only AccSamplingDesign-0.0.5/AccSamplingDesign/DESCRIPTION | 6 AccSamplingDesign-0.0.5/AccSamplingDesign/MD5 | 25 AccSamplingDesign-0.0.5/AccSamplingDesign/NAMESPACE | 24 AccSamplingDesign-0.0.5/AccSamplingDesign/R/OCdata.R | 311 ++-------- AccSamplingDesign-0.0.5/AccSamplingDesign/R/manualPlan.R |only AccSamplingDesign-0.0.5/AccSamplingDesign/R/optVarPlan.R | 8 AccSamplingDesign-0.0.5/AccSamplingDesign/R/summary.R | 75 +- AccSamplingDesign-0.0.5/AccSamplingDesign/README.md | 23 AccSamplingDesign-0.0.5/AccSamplingDesign/inst/doc/introduction.R | 36 - AccSamplingDesign-0.0.5/AccSamplingDesign/inst/doc/introduction.Rmd | 36 - AccSamplingDesign-0.0.5/AccSamplingDesign/inst/doc/introduction.html | 252 +++----- AccSamplingDesign-0.0.5/AccSamplingDesign/man/OCdata.Rd | 125 ---- AccSamplingDesign-0.0.5/AccSamplingDesign/man/manualPlan.Rd |only AccSamplingDesign-0.0.5/AccSamplingDesign/vignettes/introduction.Rmd | 36 - 15 files changed, 374 insertions(+), 583 deletions(-)
More information about AccSamplingDesign at CRAN
Permanent link
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.9 dated 2025-04-05 and 2.8.11 dated 2025-07-10
soilDB-2.8.11/soilDB/DESCRIPTION | 17 soilDB-2.8.11/soilDB/MD5 | 254 - soilDB-2.8.11/soilDB/NAMESPACE | 4 soilDB-2.8.11/soilDB/NEWS.md | 12 soilDB-2.8.11/soilDB/R/ISSR800.R | 7 soilDB-2.8.11/soilDB/R/KSSL_VG_model.R | 27 soilDB-2.8.11/soilDB/R/OSDquery.R | 4 soilDB-2.8.11/soilDB/R/ROSETTA.R | 4 soilDB-2.8.11/soilDB/R/SDA-spatial.R | 2 soilDB-2.8.11/soilDB/R/SDA_query.R | 91 soilDB-2.8.11/soilDB/R/SSURGO_spatial_query.R | 6 soilDB-2.8.11/soilDB/R/STR.R | 142 soilDB-2.8.11/soilDB/R/SoilDataViewer.R | 4 soilDB-2.8.11/soilDB/R/WCS-utils.R | 2 soilDB-2.8.11/soilDB/R/createSSURGO.R | 13 soilDB-2.8.11/soilDB/R/createStaticNASIS.R | 54 soilDB-2.8.11/soilDB/R/fetchHWSD.R |only soilDB-2.8.11/soilDB/R/fetchHenry.R | 30 soilDB-2.8.11/soilDB/R/fetchKSSL.R | 41 soilDB-2.8.11/soilDB/R/fetchLDM.R | 12 soilDB-2.8.11/soilDB/R/fetchNASIS.R | 117 soilDB-2.8.11/soilDB/R/fetchNASISLabData.R | 7 soilDB-2.8.11/soilDB/R/fetchNASISWebReport.R | 46 soilDB-2.8.11/soilDB/R/fetchNASIS_components.R | 11 soilDB-2.8.11/soilDB/R/fetchNASIS_pedons.R | 107 soilDB-2.8.11/soilDB/R/fetchNASIS_report.R | 38 soilDB-2.8.11/soilDB/R/fetchNOAA.R | 3 soilDB-2.8.11/soilDB/R/fetchOSD.R | 2 soilDB-2.8.11/soilDB/R/fetchRaCA.R | 26 soilDB-2.8.11/soilDB/R/fetchSCAN.R | 10 soilDB-2.8.11/soilDB/R/fetchSDA_spatial.R | 10 soilDB-2.8.11/soilDB/R/fetchSOLUS.R | 2 soilDB-2.8.11/soilDB/R/fetchSoilGrids.R | 151 soilDB-2.8.11/soilDB/R/fetchVegdata.R | 41 soilDB-2.8.11/soilDB/R/getHzErrorsNASIS.R | 2 soilDB-2.8.11/soilDB/R/getHzErrorsPedonPC.R | 2 soilDB-2.8.11/soilDB/R/get_NASIS_table_name_by_purpose.R | 5 soilDB-2.8.11/soilDB/R/get_RMF_from_NASIS_db.R | 2 soilDB-2.8.11/soilDB/R/get_SDA_coecoclass.R | 9 soilDB-2.8.11/soilDB/R/get_SDA_cosurfmorph.R | 8 soilDB-2.8.11/soilDB/R/get_SDA_interpretation.R | 22 soilDB-2.8.11/soilDB/R/get_SDA_property.R | 96 soilDB-2.8.11/soilDB/R/get_SSURGO_utils.R | 11 soilDB-2.8.11/soilDB/R/get_colors_from_NASIS_db.R | 2 soilDB-2.8.11/soilDB/R/get_component_data_from_NASIS_db.R | 42 soilDB-2.8.11/soilDB/R/get_component_from_GDB.R | 70 soilDB-2.8.11/soilDB/R/get_component_from_SDA.R | 109 soilDB-2.8.11/soilDB/R/get_concentrations_from_NASIS_db.R | 2 soilDB-2.8.11/soilDB/R/get_cosoilmoist_from_NASIS.R | 2 soilDB-2.8.11/soilDB/R/get_cosoilmoist_from_NASISWebReport.R |only soilDB-2.8.11/soilDB/R/get_cosoilmoist_from_SDA.R | 4 soilDB-2.8.11/soilDB/R/get_ecosite_history_from_NASIS_db.R | 2 soilDB-2.8.11/soilDB/R/get_extended_data_from_NASIS_db.R | 41 soilDB-2.8.11/soilDB/R/get_extended_data_from_pedon_db.R | 5 soilDB-2.8.11/soilDB/R/get_hz_data_from_NASIS_db.R | 3 soilDB-2.8.11/soilDB/R/get_hz_data_from_pedon_db.R | 11 soilDB-2.8.11/soilDB/R/get_lablayer_data_from_NASIS_db.R | 4 soilDB-2.8.11/soilDB/R/get_labpedon_data_from_NASIS_db.R | 3 soilDB-2.8.11/soilDB/R/get_mapunit_from_NASIS.R | 104 soilDB-2.8.11/soilDB/R/get_phfmp_from_NASIS_db.R | 2 soilDB-2.8.11/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 4 soilDB-2.8.11/soilDB/R/get_phroots_from_NASIS_db.R |only soilDB-2.8.11/soilDB/R/get_project_from_NASIS.R | 4 soilDB-2.8.11/soilDB/R/get_site_data_from_NASIS_db.R | 6 soilDB-2.8.11/soilDB/R/get_site_data_from_pedon_db.R | 10 soilDB-2.8.11/soilDB/R/get_soilseries_from_NASIS.R | 4 soilDB-2.8.11/soilDB/R/get_text_notes_from_NASIS_db.R | 6 soilDB-2.8.11/soilDB/R/get_veg_data_from_NASIS_db.R | 4 soilDB-2.8.11/soilDB/R/get_vegplot_data_from_NASIS_db.R | 22 soilDB-2.8.11/soilDB/R/mukey-WCS.R | 21 soilDB-2.8.11/soilDB/R/parseWebReport.R | 5 soilDB-2.8.11/soilDB/R/siblings.R | 2 soilDB-2.8.11/soilDB/R/simplifyArtifactData.R | 2 soilDB-2.8.11/soilDB/R/simplifyColorData.R | 4 soilDB-2.8.11/soilDB/R/simplifyFragmentData.R | 4 soilDB-2.8.11/soilDB/R/soilColorWCS.R | 9 soilDB-2.8.11/soilDB/R/soilDB_user_dir.R |only soilDB-2.8.11/soilDB/R/utils.R | 170 soilDB-2.8.11/soilDB/build/partial.rdb |binary soilDB-2.8.11/soilDB/build/vignette.rds |binary soilDB-2.8.11/soilDB/data/metadata.rda |binary soilDB-2.8.11/soilDB/inst/CITATION | 4 soilDB-2.8.11/soilDB/inst/doc/fetchNASIS.R | 192 soilDB-2.8.11/soilDB/inst/doc/fetchNASIS.html | 1995 ---------- soilDB-2.8.11/soilDB/inst/doc/wcs-ssurgo.R | 992 ++-- soilDB-2.8.11/soilDB/inst/doc/wcs-ssurgo.html | 587 -- soilDB-2.8.11/soilDB/man/createStaticNASIS.Rd | 22 soilDB-2.8.11/soilDB/man/fetchHWSD.Rd |only soilDB-2.8.11/soilDB/man/fetchNASIS.Rd | 100 soilDB-2.8.11/soilDB/man/fetchNASISLabData.Rd | 4 soilDB-2.8.11/soilDB/man/fetchSoilGrids.Rd | 92 soilDB-2.8.11/soilDB/man/fetchVegdata.Rd | 30 soilDB-2.8.11/soilDB/man/get_labpedon_data_from_NASIS_db.Rd | 4 soilDB-2.8.11/soilDB/man/get_phroots_from_NASIS_db.Rd |only soilDB-2.8.11/soilDB/man/soilDB_user_dir.Rd |only soilDB-2.8.11/soilDB/tests/testthat/test-ISSR800.R | 8 soilDB-2.8.11/soilDB/tests/testthat/test-SDA_query.R | 27 soilDB-2.8.11/soilDB/tests/testthat/test-SoilDataViewer.R | 4 soilDB-2.8.11/soilDB/tests/testthat/test-dbQueryNASIS.R | 2 soilDB-2.8.11/soilDB/tests/testthat/test-estimateColorMixture.R | 4 soilDB-2.8.11/soilDB/tests/testthat/test-estimateSTR.R | 86 soilDB-2.8.11/soilDB/tests/testthat/test-fetchEDIT_tools.R | 15 soilDB-2.8.11/soilDB/tests/testthat/test-fetchHenry.R | 38 soilDB-2.8.11/soilDB/tests/testthat/test-fetchKSSL.R | 10 soilDB-2.8.11/soilDB/tests/testthat/test-fetchLDM.R | 15 soilDB-2.8.11/soilDB/tests/testthat/test-fetchNASIS.R | 22 soilDB-2.8.11/soilDB/tests/testthat/test-fetchNASISLabData.R | 10 soilDB-2.8.11/soilDB/tests/testthat/test-fetchNASISWebReport.R | 12 soilDB-2.8.11/soilDB/tests/testthat/test-fetchOSD.R | 12 soilDB-2.8.11/soilDB/tests/testthat/test-fetchSCAN.R | 4 soilDB-2.8.11/soilDB/tests/testthat/test-fetchSDA_component.R | 14 soilDB-2.8.11/soilDB/tests/testthat/test-fetchSDA_spatial.R | 12 soilDB-2.8.11/soilDB/tests/testthat/test-fetchSOLUS.R | 6 soilDB-2.8.11/soilDB/tests/testthat/test-fetchSoilGrids.R | 6 soilDB-2.8.11/soilDB/tests/testthat/test-get_OSD.R | 7 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_coecoclass.R | 18 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_hydric.R | 12 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_interpretation.R | 14 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_muaggatt.R | 4 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_pmgroupname.R | 12 soilDB-2.8.11/soilDB/tests/testthat/test-get_SDA_property.R | 36 soilDB-2.8.11/soilDB/tests/testthat/test-get_SSURGO_utils.R | 4 soilDB-2.8.11/soilDB/tests/testthat/test-mukey-WCS.R | 2 soilDB-2.8.11/soilDB/tests/testthat/test-multi-row-simplification.R | 10 soilDB-2.8.11/soilDB/tests/testthat/test-siblings.R | 10 soilDB-2.8.11/soilDB/tests/testthat/test-simplifyArtifactData.R | 63 soilDB-2.8.11/soilDB/tests/testthat/test-simplifyColorData.R | 32 soilDB-2.8.11/soilDB/tests/testthat/test-simplifyFragmentData.R | 167 soilDB-2.8.11/soilDB/tests/testthat/test-soilDBdata.R | 8 soilDB-2.8.11/soilDB/tests/testthat/test-uncode.R | 20 soilDB-2.8.11/soilDB/tests/testthat/test-waterDayYear.R | 28 soilDB-2.8.9/soilDB/R/get_cosoilmoist_from_LIMS.R |only 132 files changed, 2379 insertions(+), 4534 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided. See
Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
methods and <https://distancesampling.org/resources/vignettes.html> for example analyses.
Author: Laura Marshall [cre],
David Miller [aut],
T.J. Clark-Wolf [aut],
Len Thomas [ctb],
Jeff Laake [ctb],
Eric Rexstad [rev]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between Distance versions 2.0.0 dated 2024-10-24 and 2.0.1 dated 2025-07-10
Distance-2.0.0/Distance/NEWS |only Distance-2.0.1/Distance/DESCRIPTION | 20 - Distance-2.0.1/Distance/MD5 | 72 +++--- Distance-2.0.1/Distance/NAMESPACE | 4 Distance-2.0.1/Distance/NEWS.md |only Distance-2.0.1/Distance/R/Distance-package.R | 5 Distance-2.0.1/Distance/R/ER_var_f.R | 10 Distance-2.0.1/Distance/R/bootdht.R | 2 Distance-2.0.1/Distance/R/bootdht_Dhat_summarize.R | 2 Distance-2.0.1/Distance/R/bootdht_Nhat_summarize.R | 2 Distance-2.0.1/Distance/R/checkdata.R | 20 + Distance-2.0.1/Distance/R/dht2.R | 52 +--- Distance-2.0.1/Distance/R/ds.R | 87 +++---- Distance-2.0.1/Distance/R/get_truncation.R | 120 +++++----- Distance-2.0.1/Distance/R/p_dist_table.R | 2 Distance-2.0.1/Distance/R/print.dht_result.R | 47 ++- Distance-2.0.1/Distance/R/summarize_ds_models.R | 44 ++- Distance-2.0.1/Distance/R/varNhat.R | 20 + Distance-2.0.1/Distance/R/variance_contributions.R | 5 Distance-2.0.1/Distance/build/partial.rdb |binary Distance-2.0.1/Distance/inst/REFERENCES.bib |only Distance-2.0.1/Distance/man/Distance-package.Rd | 2 Distance-2.0.1/Distance/man/bootdht.Rd | 2 Distance-2.0.1/Distance/man/bootdht_Dhat_summarize.Rd | 2 Distance-2.0.1/Distance/man/bootdht_Nhat_summarize.Rd | 2 Distance-2.0.1/Distance/man/dht2.Rd | 38 --- Distance-2.0.1/Distance/man/ds.Rd | 59 ++-- Distance-2.0.1/Distance/man/flatfile.Rd | 2 Distance-2.0.1/Distance/man/p_dist_table.Rd | 2 Distance-2.0.1/Distance/man/print.dht_result.Rd | 5 Distance-2.0.1/Distance/man/summarize_ds_models.Rd | 13 - Distance-2.0.1/Distance/tests/testthat/test_binned.R |only Distance-2.0.1/Distance/tests/testthat/test_dht2.R | 91 +++++++ Distance-2.0.1/Distance/tests/testthat/test_ds.R | 15 + Distance-2.0.1/Distance/tests/testthat/test_golftees.R | 4 Distance-2.0.1/Distance/tests/testthat/test_summarize.R | 37 ++- Distance-2.0.1/Distance/tests/testthat/test_systematic_var2.R | 5 Distance-2.0.1/Distance/tests/testthat/test_truncation.R | 49 +++- Distance-2.0.1/Distance/tests/testthat/test_variance.R | 14 - 39 files changed, 531 insertions(+), 325 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length
as input, the function returns the numerator and denominator coefficients
for the Padé approximant of appropriate order (Baker, 1975)
<ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 1.0.7 dated 2024-06-19 and 1.0.8 dated 2025-07-10
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- R/Pade.R | 2 +- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 9 +++++++++ inst/tinytest/test_Pade.R | 5 +---- inst/tinytest/test_package_metadata.R | 10 ++++++---- 8 files changed, 31 insertions(+), 22 deletions(-)
Title: A 'Tidyverse' Extension for Ordinations and Biplots
Description: Ordination comprises several multivariate exploratory and
explanatory techniques with theoretical foundations in geometric data
analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and
applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for
foundations.
Greenacre (2010, ISBN:978-84-923846) shows how the most established of
these, including principal components analysis, correspondence analysis,
multidimensional scaling, factor analysis, and discriminant analysis,
rely on eigen-decompositions or singular value decompositions of
pre-processed numeric matrix data.
These decompositions give rise to a set of shared coordinates along which
the row and column elements can be measured. The overlay of their
scatterplots on these axes, introduced by Gabriel (1971)
<doi:10.1093/biomet/58.3.453>, is called a biplot.
'ordr' provides inspection, extraction, manipulation, and visualization
tools for several popular ordination classes supported by a set of r [...truncated...]
Author: Jason Cory Brunson [aut, cre] ,
Emily Paul [ctb],
John Gracey [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ordr versions 0.1.2 dated 2025-07-02 and 0.2.0 dated 2025-07-10
ordr-0.1.2/ordr/R/geom-axis.r |only ordr-0.1.2/ordr/R/geom-intervals.r |only ordr-0.1.2/ordr/R/geom-isoline.r |only ordr-0.1.2/ordr/R/geom-text-radiate.r |only ordr-0.1.2/ordr/R/geom-unit-circle.r |only ordr-0.1.2/ordr/R/geom-vector.r |only ordr-0.1.2/ordr/R/stat-center.r |only ordr-0.1.2/ordr/R/stat-chull.r |only ordr-0.1.2/ordr/R/stat-cone.r |only ordr-0.1.2/ordr/R/stat-scale.r |only ordr-0.1.2/ordr/R/stat-spantree.r |only ordr-0.1.2/ordr/R/themes.r |only ordr-0.1.2/ordr/inst/examples/ex-geom-axis-diabetes.r |only ordr-0.1.2/ordr/inst/examples/ex-geom-intervals-glass.r |only ordr-0.1.2/ordr/inst/examples/ex-geom-isoline-diabetes.r |only ordr-0.1.2/ordr/inst/examples/ex-methods-eigen-qswur.r |only ordr-0.1.2/ordr/inst/examples/ex-stat-center-iris.r |only ordr-0.1.2/ordr/inst/examples/ex-stat-chull-haireye.r |only ordr-0.1.2/ordr/inst/examples/ex-stat-chull-spend.r |only ordr-0.1.2/ordr/inst/examples/ex-stat-ellipse-iris.r |only ordr-0.1.2/ordr/inst/examples/ex-stat-spantree-eurodist.r |only ordr-0.1.2/ordr/man/geom_axis.Rd |only ordr-0.1.2/ordr/man/geom_isoline.Rd |only ordr-0.1.2/ordr/man/geom_lineranges.Rd |only ordr-0.1.2/ordr/man/geom_text_radiate.Rd |only ordr-0.1.2/ordr/man/geom_unit_circle.Rd |only ordr-0.1.2/ordr/man/geom_vector.Rd |only ordr-0.1.2/ordr/man/stat_center.Rd |only ordr-0.1.2/ordr/man/stat_chull.Rd |only ordr-0.1.2/ordr/man/stat_cone.Rd |only ordr-0.1.2/ordr/man/stat_scale.Rd |only ordr-0.1.2/ordr/man/stat_spantree.Rd |only ordr-0.1.2/ordr/man/theme_biplot.Rd |only ordr-0.1.2/ordr/tests/testthat/test-stat-spantree.r |only ordr-0.2.0/ordr/DESCRIPTION | 46 ordr-0.2.0/ordr/MD5 | 240 - ordr-0.2.0/ordr/NAMESPACE | 125 ordr-0.2.0/ordr/NEWS.md | 98 ordr-0.2.0/ordr/R/biplot.r | 69 ordr-0.2.0/ordr/R/coord-scaffold.r |only ordr-0.2.0/ordr/R/dplyr-verbs.r | 6 ordr-0.2.0/ordr/R/fun-lda.r | 24 ordr-0.2.0/ordr/R/geom-interpolation.r |only ordr-0.2.0/ordr/R/geom-origin.r | 127 ordr-0.2.0/ordr/R/geom-utils.r | 289 +- ordr-0.2.0/ordr/R/layer-utils.r |only ordr-0.2.0/ordr/R/methods-base-eigen.r | 10 ordr-0.2.0/ordr/R/methods-base-svd.r | 4 ordr-0.2.0/ordr/R/methods-mass-correspondence.r | 4 ordr-0.2.0/ordr/R/methods-mass-lda.r | 6 ordr-0.2.0/ordr/R/methods-mass-mca.r | 6 ordr-0.2.0/ordr/R/methods-ordr-lra.r | 4 ordr-0.2.0/ordr/R/methods-stats-cancor.r | 16 ordr-0.2.0/ordr/R/methods-stats-cmds.r | 4 ordr-0.2.0/ordr/R/methods-stats-factanal.r | 25 ordr-0.2.0/ordr/R/methods-stats-kmeans.r | 4 ordr-0.2.0/ordr/R/methods-stats-prcomp.r | 4 ordr-0.2.0/ordr/R/methods-stats-princomp.r | 43 ordr-0.2.0/ordr/R/ord-annotation.r | 4 ordr-0.2.0/ordr/R/ord-format.r | 33 ordr-0.2.0/ordr/R/ord-plot.r | 2 ordr-0.2.0/ordr/R/ordr.r | 12 ordr-0.2.0/ordr/R/stat-matrix.r | 8 ordr-0.2.0/ordr/R/stat-projection.r |only ordr-0.2.0/ordr/R/stat-utils.r |only ordr-0.2.0/ordr/R/theme-scaffold.r |only ordr-0.2.0/ordr/R/utils.r | 166 - ordr-0.2.0/ordr/R/zzz-biplot-geoms.r | 1363 ++++++---- ordr-0.2.0/ordr/R/zzz-biplot-stats.r | 1042 +++++-- ordr-0.2.0/ordr/README.md | 98 ordr-0.2.0/ordr/inst/doc/cmds-variables.R | 24 ordr-0.2.0/ordr/inst/doc/cmds-variables.html | 95 ordr-0.2.0/ordr/inst/doc/cmds-variables.rmd | 36 ordr-0.2.0/ordr/inst/doc/ordr.html | 119 ordr-0.2.0/ordr/inst/doc/ordr.rmd | 2 ordr-0.2.0/ordr/inst/examples/ex-coord-rect.r |only ordr-0.2.0/ordr/inst/examples/ex-coord-scaffold.r |only ordr-0.2.0/ordr/inst/examples/ex-dplyr-verbs-iris-lda.r | 4 ordr-0.2.0/ordr/inst/examples/ex-fun-lda-iris.r | 51 ordr-0.2.0/ordr/inst/examples/ex-fun-lra-arrests.r | 4 ordr-0.2.0/ordr/inst/examples/ex-geom-axis.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-bagplot.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-interpolation.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-intervals-ord-glass.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-intervals.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-isoline-glass.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-isoline.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-origin.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-rule.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-unit-circle-ord-glass.r |only ordr-0.2.0/ordr/inst/examples/ex-geom-unit-circle.r | 41 ordr-0.2.0/ordr/inst/examples/ex-geom-vector-iris.r | 3 ordr-0.2.0/ordr/inst/examples/ex-geom-vector.r |only ordr-0.2.0/ordr/inst/examples/ex-ggbiplot-key-iris.r | 5 ordr-0.2.0/ordr/inst/examples/ex-ggbiplot-lm-mtcars.r | 2 ordr-0.2.0/ordr/inst/examples/ex-ggbiplot-prediction-iris.r | 15 ordr-0.2.0/ordr/inst/examples/ex-ggbiplot-secaxis-iris.r | 18 ordr-0.2.0/ordr/inst/examples/ex-methods-cancor-savings.r | 15 ordr-0.2.0/ordr/inst/examples/ex-methods-eigen.r |only ordr-0.2.0/ordr/inst/examples/ex-methods-factanal-swiss.r | 3 ordr-0.2.0/ordr/inst/examples/ex-methods-kmeans-iris.r | 4 ordr-0.2.0/ordr/inst/examples/ex-methods-lra-arrests.r | 8 ordr-0.2.0/ordr/inst/examples/ex-ord-format.r |only ordr-0.2.0/ordr/inst/examples/ex-ordinate.r | 2 ordr-0.2.0/ordr/inst/examples/ex-stat-bagplot-ord-iris.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-bagplot.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-center-ord-iris.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-center.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-chull-ord-haireye.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-chull.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-cone-ord-spend.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-cone.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-depth.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-ellipse-ord-iris.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-matrix-swiss.r | 5 ordr-0.2.0/ordr/inst/examples/ex-stat-peel-ord-judges.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-projection-ord-iris.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-projection.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-referent.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-rule-ord-glass.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-rule.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-spantree-ord-eurodist.r |only ordr-0.2.0/ordr/inst/examples/ex-stat-spantree.r |only ordr-0.2.0/ordr/man/biplot-geoms.Rd | 484 +++ ordr-0.2.0/ordr/man/biplot-stats.Rd | 594 ++++ ordr-0.2.0/ordr/man/coord_scaffold.Rd |only ordr-0.2.0/ordr/man/dplyr-verbs.Rd | 4 ordr-0.2.0/ordr/man/draw-key.Rd | 5 ordr-0.2.0/ordr/man/format.Rd | 20 ordr-0.2.0/ordr/man/geom_interpolation.Rd |only ordr-0.2.0/ordr/man/geom_origin.Rd | 98 ordr-0.2.0/ordr/man/ggbiplot.Rd | 42 ordr-0.2.0/ordr/man/lda-ord.Rd | 65 ordr-0.2.0/ordr/man/lra-ord.Rd | 4 ordr-0.2.0/ordr/man/methods-cancor.Rd | 16 ordr-0.2.0/ordr/man/methods-cmds.Rd | 3 ordr-0.2.0/ordr/man/methods-correspondence.Rd | 1 ordr-0.2.0/ordr/man/methods-eigen.Rd | 35 ordr-0.2.0/ordr/man/methods-factanal.Rd | 6 ordr-0.2.0/ordr/man/methods-kmeans.Rd | 4 ordr-0.2.0/ordr/man/methods-lda.Rd | 1 ordr-0.2.0/ordr/man/methods-lra.Rd | 9 ordr-0.2.0/ordr/man/methods-mca.Rd | 1 ordr-0.2.0/ordr/man/methods-prcomp.Rd | 1 ordr-0.2.0/ordr/man/methods-princomp.Rd | 26 ordr-0.2.0/ordr/man/methods-svd.Rd | 3 ordr-0.2.0/ordr/man/ordinate.Rd | 2 ordr-0.2.0/ordr/man/ordr-ggproto.Rd | 43 ordr-0.2.0/ordr/man/ordr.Rd | 16 ordr-0.2.0/ordr/man/plot.tbl_ord.Rd | 6 ordr-0.2.0/ordr/man/reexports.Rd | 30 ordr-0.2.0/ordr/man/stat_projection.Rd |only ordr-0.2.0/ordr/man/stat_rows.Rd | 9 ordr-0.2.0/ordr/man/sync.Rd |only ordr-0.2.0/ordr/man/theme_scaffold.Rd |only ordr-0.2.0/ordr/tests/testthat/test-format.r | 21 ordr-0.2.0/ordr/tests/testthat/test-geom-origin.r |only ordr-0.2.0/ordr/tests/testthat/test-ordr-ldaord.r | 4 ordr-0.2.0/ordr/tests/testthat/test-stat-projection.r |only ordr-0.2.0/ordr/vignettes/cmds-variables.rmd | 36 ordr-0.2.0/ordr/vignettes/ordr.rmd | 2 161 files changed, 4167 insertions(+), 1762 deletions(-)
Title: Bayesian Mortality Modelling
Description: Fit Bayesian graduation mortality using the Heligman-Pollard model, as seen in Heligman, L., & Pollard, J. H. (1980) <doi:10.1017/S0020268100040257> and Dellaportas, Petros, et al. (2001) <doi:10.1111/1467-985X.00202>, and dynamic linear model (Campagnoli, P., Petris, G., and Petrone, S. (2009) <doi:10.1007/b135794_2>). While Heligman-Pollard has parameters with a straightforward interpretation yielding some rich analysis, the dynamic linear model provides a very flexible adjustment of the mortality curves by controlling the discount factor value. Closing methods for both Heligman-Pollard and dynamic linear model were also implemented according to Dodd, Erengul, et al. (2018) <https://www.jstor.org/stable/48547511>. The Bayesian Lee-Carter model is also implemented to fit historical mortality tables time series to predict the mortality in the following years and to do improvement analysis, as seen in Lee, R. D., & Carter, L. R. (1992) <doi:10.1080/016 [...truncated...]
Author: Luiz F. V. Figueiredo [aut, cre] ,
Lucas M. F. Silva [aut] ,
Viviana G. R. Lobo [aut] ,
Thais C. O. Fonseca [aut] ,
Mariane B. Alves [aut]
Maintainer: Luiz F. V. Figueiredo <labmapackage@gmail.com>
Diff between BayesMortalityPlus versions 0.2.4 dated 2024-06-04 and 1.0.0 dated 2025-07-10
DESCRIPTION | 37 +++++++++++++++++++++++++++++++------ MD5 | 15 ++++++++------- R/blc.R | 1 + R/dlm.R | 1 + R/hp.R | 1 + inst |only man/blc.Rd | 2 ++ man/dlm.Rd | 2 ++ man/hp.Rd | 2 ++ 9 files changed, 48 insertions(+), 13 deletions(-)
More information about BayesMortalityPlus at CRAN
Permanent link
Title: A Two-Stage Estimation Approach to Cox Regression Using M-Spline
Function
Description: Implements a two-stage estimation approach for Cox
regression using five-parameter M-spline functions to model the baseline hazard. It allows
for flexible hazard shapes and model selection based on log-likelihood criteria as described in
Teranishi et al.(2025).
In addition, the package provides functions for constructing and evaluating B-spline copulas
based on five M-spline or I-spline basis functions, allowing users to flexibly model and
compute bivariate dependence structures. Both the copula function and its density can be evaluated.
Furthermore, the package supports computation of dependence measures such as Kendall's tau and
Spearman's rho, derived analytically from the copula parameters.
Author: Ren Teranishi [aut, cre]
Maintainer: Ren Teranishi <ren.teranishi1227@gmail.com>
Diff between splineCox versions 0.0.4 dated 2025-06-12 and 0.0.5 dated 2025-07-10
DESCRIPTION | 8 ++- MD5 | 18 ++++---- NAMESPACE | 1 NEWS.md | 5 ++ R/splinecopula.R | 75 ++++++++++++++++++++++++++++++++--- inst/doc/splineCox-introduction.R | 8 +++ inst/doc/splineCox-introduction.Rmd | 14 ++++++ inst/doc/splineCox-introduction.html | 18 +++++++- man/spline.copula.Rd | 32 +++++++++++++- vignettes/splineCox-introduction.Rmd | 14 ++++++ 10 files changed, 170 insertions(+), 23 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Luedecke [aut, cre] ,
Alexander Bartel [ctb] ,
Carsten Schwemmer [ctb],
Chuck Powell [ctb] ,
Amir Djalovski [ctb],
Johannes Titz [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.17 dated 2024-11-29 and 2.9.0 dated 2025-07-10
sjPlot-2.8.17/sjPlot/R/plot_kfold_cv.R |only sjPlot-2.8.17/sjPlot/R/sjPlotAnova.R |only sjPlot-2.8.17/sjPlot/R/sjPlotCorr.R |only sjPlot-2.8.17/sjPlot/R/zzz.R |only sjPlot-2.8.17/sjPlot/man/plot_kfold_cv.Rd |only sjPlot-2.8.17/sjPlot/man/sjp.aov1.Rd |only sjPlot-2.8.17/sjPlot/man/sjp.corr.Rd |only sjPlot-2.9.0/sjPlot/DESCRIPTION | 31 sjPlot-2.9.0/sjPlot/MD5 | 195 ++--- sjPlot-2.9.0/sjPlot/NAMESPACE | 119 --- sjPlot-2.9.0/sjPlot/NEWS.md | 12 sjPlot-2.9.0/sjPlot/R/S3-methods.R | 39 - sjPlot-2.9.0/sjPlot/R/color_utils.R | 2 sjPlot-2.9.0/sjPlot/R/helpfunctions.R | 150 ++- sjPlot-2.9.0/sjPlot/R/html_print.R | 13 sjPlot-2.9.0/sjPlot/R/html_print_utils.R | 1 sjPlot-2.9.0/sjPlot/R/plot_diag_linear.R | 184 +++- sjPlot-2.9.0/sjPlot/R/plot_diag_stan.R | 126 ++- sjPlot-2.9.0/sjPlot/R/plot_frq.R | 575 ++++++++++----- sjPlot-2.9.0/sjPlot/R/plot_gpt.R | 261 +++++- sjPlot-2.9.0/sjPlot/R/plot_grid.R | 14 sjPlot-2.9.0/sjPlot/R/plot_grpfrq.R | 546 +++++++++----- sjPlot-2.9.0/sjPlot/R/plot_likert.R | 545 ++++++++------ sjPlot-2.9.0/sjPlot/R/plot_model.R | 35 sjPlot-2.9.0/sjPlot/R/plot_model_estimates.R | 3 sjPlot-2.9.0/sjPlot/R/plot_models.R | 271 +++---- sjPlot-2.9.0/sjPlot/R/plot_point_estimates.R | 291 ++++--- sjPlot-2.9.0/sjPlot/R/plot_residuals.R | 33 sjPlot-2.9.0/sjPlot/R/plot_scatter.R | 262 +++++- sjPlot-2.9.0/sjPlot/R/plot_stackfrq.R | 242 ++++-- sjPlot-2.9.0/sjPlot/R/plot_type_eff.R | 123 +-- sjPlot-2.9.0/sjPlot/R/plot_type_est.R | 139 +-- sjPlot-2.9.0/sjPlot/R/plot_type_int.R | 159 ++-- sjPlot-2.9.0/sjPlot/R/plot_type_ranef.R | 2 sjPlot-2.9.0/sjPlot/R/plot_type_slope.R | 28 sjPlot-2.9.0/sjPlot/R/plot_xtab.R | 405 +++++++--- sjPlot-2.9.0/sjPlot/R/save_plot.R | 10 sjPlot-2.9.0/sjPlot/R/select_helpers.R | 2 sjPlot-2.9.0/sjPlot/R/sjPlotDist.R | 420 ++++++---- sjPlot-2.9.0/sjPlot/R/sjPlotPearsonsChi2Test.R | 84 +- sjPlot-2.9.0/sjPlot/R/sjPlotPolynomials.R | 121 ++- sjPlot-2.9.0/sjPlot/R/sjPlotSetTheme.R | 341 ++++++-- sjPlot-2.9.0/sjPlot/R/sjplot.R | 37 sjPlot-2.9.0/sjPlot/R/sjplot_themes.R | 175 ++-- sjPlot-2.9.0/sjPlot/R/tab_corr.R | 308 ++++++-- sjPlot-2.9.0/sjPlot/R/tab_fa.R | 2 sjPlot-2.9.0/sjPlot/R/tab_itemscale.R | 6 sjPlot-2.9.0/sjPlot/R/tab_model.R | 171 ++-- sjPlot-2.9.0/sjPlot/R/tab_pca.R | 4 sjPlot-2.9.0/sjPlot/R/tab_stackfrq.R | 2 sjPlot-2.9.0/sjPlot/R/tab_xtab.R | 8 sjPlot-2.9.0/sjPlot/R/tidiers.R | 21 sjPlot-2.9.0/sjPlot/R/utils.R | 52 - sjPlot-2.9.0/sjPlot/R/view_df.R | 6 sjPlot-2.9.0/sjPlot/build/vignette.rds |binary sjPlot-2.9.0/sjPlot/inst/doc/blackwhitefigures.R | 6 sjPlot-2.9.0/sjPlot/inst/doc/blackwhitefigures.Rmd | 6 sjPlot-2.9.0/sjPlot/inst/doc/blackwhitefigures.html | 12 sjPlot-2.9.0/sjPlot/inst/doc/custplot.R | 56 - sjPlot-2.9.0/sjPlot/inst/doc/custplot.Rmd | 61 - sjPlot-2.9.0/sjPlot/inst/doc/custplot.html | 66 - sjPlot-2.9.0/sjPlot/inst/doc/plot_interactions.html | 4 sjPlot-2.9.0/sjPlot/inst/doc/plot_likert_scales.R | 2 sjPlot-2.9.0/sjPlot/inst/doc/plot_likert_scales.Rmd | 2 sjPlot-2.9.0/sjPlot/inst/doc/plot_likert_scales.html | 20 sjPlot-2.9.0/sjPlot/inst/doc/plot_marginal_effects.R | 14 sjPlot-2.9.0/sjPlot/inst/doc/plot_marginal_effects.Rmd | 12 sjPlot-2.9.0/sjPlot/inst/doc/plot_marginal_effects.html | 10 sjPlot-2.9.0/sjPlot/inst/doc/plot_model_estimates.R | 10 sjPlot-2.9.0/sjPlot/inst/doc/plot_model_estimates.Rmd | 24 sjPlot-2.9.0/sjPlot/inst/doc/plot_model_estimates.html | 18 sjPlot-2.9.0/sjPlot/inst/doc/sjtitemanalysis.R | 6 sjPlot-2.9.0/sjPlot/inst/doc/sjtitemanalysis.Rmd | 7 sjPlot-2.9.0/sjPlot/inst/doc/sjtitemanalysis.html | 15 sjPlot-2.9.0/sjPlot/inst/doc/tab_bayes.R | 2 sjPlot-2.9.0/sjPlot/inst/doc/tab_bayes.html | 26 sjPlot-2.9.0/sjPlot/inst/doc/tab_mixed.R | 2 sjPlot-2.9.0/sjPlot/inst/doc/tab_mixed.html | 4 sjPlot-2.9.0/sjPlot/inst/doc/tab_model_estimates.html | 4 sjPlot-2.9.0/sjPlot/inst/doc/tab_model_robust.R | 2 sjPlot-2.9.0/sjPlot/inst/doc/table_css.html | 4 sjPlot-2.9.0/sjPlot/man/plot_frq.Rd | 12 sjPlot-2.9.0/sjPlot/man/plot_grid.Rd | 8 sjPlot-2.9.0/sjPlot/man/plot_likert.Rd | 2 sjPlot-2.9.0/sjPlot/man/plot_model.Rd | 30 sjPlot-2.9.0/sjPlot/man/plot_models.Rd | 10 sjPlot-2.9.0/sjPlot/man/plot_stackfrq.Rd | 6 sjPlot-2.9.0/sjPlot/man/plot_xtab.Rd | 2 sjPlot-2.9.0/sjPlot/man/save_plot.Rd | 4 sjPlot-2.9.0/sjPlot/man/set_theme.Rd | 2 sjPlot-2.9.0/sjPlot/man/sjplot.Rd | 17 sjPlot-2.9.0/sjPlot/man/tab_itemscale.Rd | 2 sjPlot-2.9.0/sjPlot/man/tab_model.Rd | 33 sjPlot-2.9.0/sjPlot/tests/testthat/test-plot_grpfrq.R | 8 sjPlot-2.9.0/sjPlot/tests/testthat/test-plot_model_std.R | 2 sjPlot-2.9.0/sjPlot/tests/testthat/test-tab_model.R | 8 sjPlot-2.9.0/sjPlot/vignettes/blackwhitefigures.Rmd | 6 sjPlot-2.9.0/sjPlot/vignettes/custplot.Rmd | 61 - sjPlot-2.9.0/sjPlot/vignettes/plot_likert_scales.Rmd | 2 sjPlot-2.9.0/sjPlot/vignettes/plot_marginal_effects.Rmd | 12 sjPlot-2.9.0/sjPlot/vignettes/plot_model_estimates.Rmd | 24 sjPlot-2.9.0/sjPlot/vignettes/sjtitemanalysis.Rmd | 7 102 files changed, 4374 insertions(+), 2855 deletions(-)
Title: Survey Sampling
Description: Functions to draw random samples using different sampling schemes are available. Functions are also provided to obtain (generalized) calibration weights, different estimators, as well some variance estimators.
Author: Yves Tille [aut],
Alina Matei [aut, cre]
Maintainer: Alina Matei <alina.matei@unine.ch>
Diff between sampling versions 2.10 dated 2023-10-29 and 2.11 dated 2025-07-10
DESCRIPTION | 24 +++++++++++++++------ MD5 | 24 ++++++++++----------- NAMESPACE | 2 - R/UPopips.r | 26 +++++++++++++---------- R/writesample.R | 44 ++++++--------------------------------- build/vignette.rds |binary data/rec99.rda |binary inst/doc/HT_Hajek_estimators.pdf |binary inst/doc/UPexamples.pdf |binary inst/doc/calibration.pdf |binary man/UPopips.Rd | 16 +++++++------- man/rec99.Rd | 5 ++-- man/writesample.Rd | 2 - 13 files changed, 65 insertions(+), 78 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for
R.
Author: Hadley Wickham [aut, cre] ,
Lionel Henry [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between purrr versions 1.0.4 dated 2025-02-05 and 1.1.0 dated 2025-07-10
purrr-1.0.4/purrr/cleanup |only purrr-1.0.4/purrr/configure |only purrr-1.0.4/purrr/configure.win |only purrr-1.0.4/purrr/tools |only purrr-1.1.0/purrr/DESCRIPTION | 20 purrr-1.1.0/purrr/MD5 | 204 ++++----- purrr-1.1.0/purrr/NAMESPACE | 1 purrr-1.1.0/purrr/NEWS.md | 8 purrr-1.1.0/purrr/R/adverb-auto-browse.R | 12 purrr-1.1.0/purrr/R/adverb-partial.R | 22 - purrr-1.1.0/purrr/R/adverb-possibly.R | 11 purrr-1.1.0/purrr/R/adverb-safely.R | 3 purrr-1.1.0/purrr/R/coerce.R | 7 purrr-1.1.0/purrr/R/compat-obj-type.R | 30 - purrr-1.1.0/purrr/R/compat-types-check.R | 236 ++++++----- purrr-1.1.0/purrr/R/conditions.R | 48 +- purrr-1.1.0/purrr/R/deprec-cross.R | 6 purrr-1.1.0/purrr/R/deprec-invoke.R | 18 purrr-1.1.0/purrr/R/deprec-lift.R | 8 purrr-1.1.0/purrr/R/deprec-rerun.R | 2 purrr-1.1.0/purrr/R/deprec-when.R | 19 purrr-1.1.0/purrr/R/detect.R | 28 + purrr-1.1.0/purrr/R/head-tail.R | 8 purrr-1.1.0/purrr/R/imap.R | 10 purrr-1.1.0/purrr/R/keep.R | 7 purrr-1.1.0/purrr/R/list-combine.R | 24 - purrr-1.1.0/purrr/R/list-flatten.R | 10 purrr-1.1.0/purrr/R/list-modify.R | 15 purrr-1.1.0/purrr/R/list-simplify.R | 32 - purrr-1.1.0/purrr/R/list-transpose.R | 24 - purrr-1.1.0/purrr/R/lmap.R | 14 purrr-1.1.0/purrr/R/map-depth.R | 57 ++ purrr-1.1.0/purrr/R/map-if-at.R | 8 purrr-1.1.0/purrr/R/map-mapper.R | 13 purrr-1.1.0/purrr/R/map.R | 121 +++++ purrr-1.1.0/purrr/R/map2.R | 44 +- purrr-1.1.0/purrr/R/modify-tree.R | 20 purrr-1.1.0/purrr/R/modify.R | 8 purrr-1.1.0/purrr/R/parallelization.R |only purrr-1.1.0/purrr/R/pmap.R | 53 +- purrr-1.1.0/purrr/R/rate.R | 18 purrr-1.1.0/purrr/R/reduce.R | 47 +- purrr-1.1.0/purrr/R/reexport-pipe.R | 1 purrr-1.1.0/purrr/R/superseded-map-df.R | 66 ++- purrr-1.1.0/purrr/R/superseded-simplify.R | 33 + purrr-1.1.0/purrr/R/superseded-transpose.R | 1 purrr-1.1.0/purrr/R/utils.R | 37 - purrr-1.1.0/purrr/README.md | 9 purrr-1.1.0/purrr/inst/doc/base.R | 10 purrr-1.1.0/purrr/inst/doc/base.Rmd | 17 purrr-1.1.0/purrr/inst/doc/base.html | 32 - purrr-1.1.0/purrr/man/as_mapper.Rd | 14 purrr-1.1.0/purrr/man/detect.Rd | 3 purrr-1.1.0/purrr/man/every.Rd | 3 purrr-1.1.0/purrr/man/imap.Rd | 12 purrr-1.1.0/purrr/man/in_parallel.Rd |only purrr-1.1.0/purrr/man/keep.Rd | 3 purrr-1.1.0/purrr/man/keep_at.Rd | 4 purrr-1.1.0/purrr/man/map.Rd | 42 + purrr-1.1.0/purrr/man/map2.Rd | 13 purrr-1.1.0/purrr/man/map_depth.Rd | 11 purrr-1.1.0/purrr/man/map_if.Rd | 11 purrr-1.1.0/purrr/man/negate.Rd | 3 purrr-1.1.0/purrr/man/pmap.Rd | 11 purrr-1.1.0/purrr/man/purrr-package.Rd | 2 purrr-1.1.0/purrr/src/pluck.c | 8 purrr-1.1.0/purrr/tests/testthat/_snaps/deprec-when.md | 2 purrr-1.1.0/purrr/tests/testthat/_snaps/parallel.md |only purrr-1.1.0/purrr/tests/testthat/test-adverb-compose.R | 17 purrr-1.1.0/purrr/tests/testthat/test-adverb-partial.R | 64 ++ purrr-1.1.0/purrr/tests/testthat/test-adverb-possibly.R | 10 purrr-1.1.0/purrr/tests/testthat/test-adverb-quietly.R | 15 purrr-1.1.0/purrr/tests/testthat/test-adverb-safely.R | 7 purrr-1.1.0/purrr/tests/testthat/test-coerce.R | 3 purrr-1.1.0/purrr/tests/testthat/test-conditions.R | 37 + purrr-1.1.0/purrr/tests/testthat/test-deprec-cross.R | 2 purrr-1.1.0/purrr/tests/testthat/test-deprec-lift.R | 17 purrr-1.1.0/purrr/tests/testthat/test-deprec-prepend.R | 7 purrr-1.1.0/purrr/tests/testthat/test-deprec-rerun.R | 1 purrr-1.1.0/purrr/tests/testthat/test-deprec-splice.R | 3 purrr-1.1.0/purrr/tests/testthat/test-deprec-utils.R | 1 purrr-1.1.0/purrr/tests/testthat/test-deprec-when.R | 32 - purrr-1.1.0/purrr/tests/testthat/test-detect.R | 5 purrr-1.1.0/purrr/tests/testthat/test-head-tail.R | 2 purrr-1.1.0/purrr/tests/testthat/test-imap.R | 2 purrr-1.1.0/purrr/tests/testthat/test-keep.R | 4 purrr-1.1.0/purrr/tests/testthat/test-list-combine.R | 12 purrr-1.1.0/purrr/tests/testthat/test-list-modify.R | 11 purrr-1.1.0/purrr/tests/testthat/test-list-simplify.R | 10 purrr-1.1.0/purrr/tests/testthat/test-lmap.R | 4 purrr-1.1.0/purrr/tests/testthat/test-map-depth.R | 1 purrr-1.1.0/purrr/tests/testthat/test-map-if-at.R | 7 purrr-1.1.0/purrr/tests/testthat/test-map-raw.R | 10 purrr-1.1.0/purrr/tests/testthat/test-map.R | 13 purrr-1.1.0/purrr/tests/testthat/test-map2.R | 20 purrr-1.1.0/purrr/tests/testthat/test-modify-tree.R | 2 purrr-1.1.0/purrr/tests/testthat/test-modify.R | 77 ++- purrr-1.1.0/purrr/tests/testthat/test-parallel.R |only purrr-1.1.0/purrr/tests/testthat/test-pluck-assign.R | 8 purrr-1.1.0/purrr/tests/testthat/test-pluck.R | 9 purrr-1.1.0/purrr/tests/testthat/test-pmap.R | 41 + purrr-1.1.0/purrr/tests/testthat/test-rate.R | 1 purrr-1.1.0/purrr/tests/testthat/test-reduce.R | 87 +++- purrr-1.1.0/purrr/tests/testthat/test-superseded-map-df.R | 8 purrr-1.1.0/purrr/tests/testthat/test-superseded-transpose.R | 12 purrr-1.1.0/purrr/tests/testthat/test-utils.R | 20 purrr-1.1.0/purrr/vignettes/base.Rmd | 17 107 files changed, 1372 insertions(+), 791 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.11.2 dated 2025-05-30 and 0.12.0 dated 2025-07-10
DESCRIPTION | 28 ++--- MD5 | 93 ++++++++--------- NAMESPACE | 9 + NEWS.md | 42 +++++++ R/clean_names.R | 3 R/display.R |only R/estimate_contrast_methods.R | 4 R/estimate_contrasts.R | 143 +++++++++++++++++++++------ R/estimate_means.R | 11 +- R/estimate_predicted.R | 13 ++ R/estimate_slopes.R | 13 +- R/format.R | 93 +++++++++++++---- R/get_emcontrasts.R | 5 R/get_marginalcontrasts.R | 51 +++++++++ R/get_marginalmeans.R | 8 - R/get_marginaltrends.R | 4 R/joint_test.R | 2 R/p_adjust.R | 100 +++++++++++++++++- R/reexports.R | 4 R/table_footer.R | 64 ++++-------- R/utils.R | 2 R/visualisation_recipe_internal.R | 54 +++++++--- README.md | 41 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 16 ++- inst/doc/overview_of_vignettes.Rmd | 3 inst/doc/overview_of_vignettes.html | 4 man/estimate_contrasts.Rd | 87 ++++++++++++++-- man/estimate_expectation.Rd | 14 ++ man/estimate_means.Rd | 13 ++ man/estimate_slopes.Rd | 15 ++ man/figures/unnamed-chunk-3-1.png |binary man/get_emmeans.Rd | 21 +++ man/puppy_love.Rd | 64 ++++++------ man/reexports.Rd | 3 tests/testthat/test-attributes_estimatefun.R | 14 +- tests/testthat/test-brms-marginaleffects.R | 67 ++++++------ tests/testthat/test-estimate_contrasts.R | 122 +++++++++++++++++++++++ tests/testthat/test-estimate_slopes.R | 22 +++- tests/testthat/test-joint_test.R | 21 +++ tests/testthat/test-keep_iterations.R | 4 tests/testthat/test-ordinal.R | 17 +++ tests/testthat/test-plot-ordinal.R | 41 +++++++ tests/testthat/test-plot-slopes.R | 20 +++ tests/testthat/test-plot.R | 19 +++ vignettes/overview_of_vignettes.Rmd | 3 48 files changed, 1084 insertions(+), 295 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Franziska Eidloth [aut],
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.7 dated 2025-04-22 and 0.9.8 dated 2025-07-10
DESCRIPTION | 17 MD5 | 48 - NAMESPACE | 3 NEWS.md | 6 R/basefunctions.R | 30 R/biotech.R | 8 R/clin_estimates.R | 16 R/descriptives.R | 668 +++++++++++++--------- R/pkgstart.R | 7 R/plots.R | 8 R/tests.R | 968 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/wrappedtools.html | 8 man/cat_desc_table.Rd | 6 man/compare2numvars.Rd | 11 man/compare_n_numvars.Rd | 2 man/ksnormal.Rd | 2 man/meansd.Rd | 16 man/median_quart.Rd | 18 man/wrappedtools-package.Rd | 2 tests/testthat/compare2numvars_out.rda |binary tests/testthat/meansdout.rda |binary tests/testthat/medianquart.rda |binary tests/testthat/test-compare_2_numvars.R | 107 +-- tests/testthat/test-meansd.R | 2 25 files changed, 1109 insertions(+), 844 deletions(-)
Title: Cluster Distances Through Trees
Description: Create a measure of inter-point dissimilarity useful
for clustering mixed data, and, optionally, perform the clustering.
Author: Sam Buttrey [aut, cre]
Maintainer: Sam Buttrey <buttrey@nps.edu>
Diff between treeClust versions 1.1-7 dated 2018-05-11 and 1.1-7.1 dated 2025-07-10
DESCRIPTION | 14 +++++++++----- MD5 | 8 ++++---- man/rpart.predict.leaves.Rd | 2 +- man/treeClust.Rd | 2 +- man/treeClust.dist.Rd | 2 +- 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Package including functions and interactive shiny application
for the psychometric analysis of educational tests, psychological
assessments, health-related and other types of multi-item
measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre] ,
Adela Hladka [aut] ,
Jan Netik [aut] ,
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.5.4 dated 2025-02-08 and 1.5.5 dated 2025-07-10
ShinyItemAnalysis-1.5.4/ShinyItemAnalysis/inst/ShinyItemAnalysis/www/flag_CR.png |only ShinyItemAnalysis-1.5.4/ShinyItemAnalysis/inst/ShinyItemAnalysis/www/flag_USA.png |only ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/DESCRIPTION | 28 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/MD5 | 49 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/NAMESPACE | 1 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/NEWS.md | 732 ++++------ ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/R/data_EPIA.R | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/R/gDiscrim.R | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/R/package_options.R | 14 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/R/plotDistractorAnalysis.R | 4 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/R/startShinyItemAnalysis.R | 27 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/README.md | 12 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/build/partial.rdb |binary ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/reporthtml.Rmd | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/reportpdf.Rmd | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/server/DIF.R | 10 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/server/Data.R | 7 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/server/Modules.R | 181 +- ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/ui.R | 4 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/ui/uiAbout.R | 15 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/inst/ShinyItemAnalysis/ui/uiReferences.R | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/EPIA.Rd | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/ShinyItemAnalysis-package.Rd | 2 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/figures |only ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/gDiscrim.Rd | 7 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/plotDistractorAnalysis.Rd | 4 ShinyItemAnalysis-1.5.5/ShinyItemAnalysis/man/startShinyItemAnalysis.Rd | 6 27 files changed, 575 insertions(+), 540 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Numeric Extensions for the 'rebus' Package
Description: Build regular expressions piece by piece using human readable code.
This package contains number-related functionality, and is primarily intended
to be used by package developers.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus.numbers versions 0.0-1 dated 2015-12-16 and 0.0-1.1 dated 2025-07-10
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- R/number_range.R | 2 +- man/number_range.Rd | 3 +-- man/roman.Rd | 7 ++++--- 5 files changed, 14 insertions(+), 15 deletions(-)
Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, depends on GLPK Version >= 4.42.
Author: Mihail Anton [cre],
Mayo Roettger [ctb],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Mihail Anton <mihail.anton@chalmers.se>
Diff between glpkAPI versions 1.3.4 dated 2022-11-10 and 1.3.4.1 dated 2025-07-10
DESCRIPTION | 6 MD5 | 20 build/vignette.rds |binary configure | 2756 +++++++++++++++++++++++-------------------- configure.ac | 14 inst/doc/glpk-gmpl-intro.pdf |binary inst/doc/glpkAPI.pdf |binary man/getRiiGLPK.Rd | 2 man/getSjjGLPK.Rd | 2 man/setRiiGLPK.Rd | 2 man/setSjjGLPK.Rd | 2 11 files changed, 1537 insertions(+), 1267 deletions(-)
Title: 'ggplot' Visualizations for the 'partykit' Package
Description: Extends 'ggplot2' functionality to the 'partykit' package. 'ggparty' provides the necessary tools to create clearly structured and highly customizable visualizations for tree-objects of the class 'party'.
Author: Martin Borkovec [aut, cre],
Niyaz Madin [aut],
Hadley Wickham [ctb],
Winston Chang [ctb],
Lionel Henry [ctb],
Thomas Lin Pedersen [ctb],
Kohske Takahashi [ctb],
Claus Wilke [ctb],
Kara Woo [ctb],
Hiroaki Yutani [ctb]
Maintainer: Martin Borkovec <martin.borkovec@skyforge.at>
Diff between ggparty versions 1.0.0 dated 2019-07-18 and 1.0.0.1 dated 2025-07-10
DESCRIPTION | 9 MD5 | 30 R/geom_node_plot.R | 2 R/ggparty.R | 10 build/vignette.rds |binary inst/doc/ggparty-graphic-partying.R | 1166 +++++++------- inst/doc/ggparty-graphic-partying.html | 2681 ++++++++++++++++++--------------- inst/doc/on-the-edge.R | 210 +- inst/doc/on-the-edge.html | 970 ++++++----- man/autoplot.party.Rd | 7 man/geom_edge.Rd | 14 man/geom_edge_label.Rd | 21 man/geom_node_label.Rd | 398 ++-- man/geom_node_plot.Rd | 43 man/get_predictions.Rd | 10 man/ggparty.Rd | 57 16 files changed, 3053 insertions(+), 2575 deletions(-)
Title: Join Tables Together on Inexact Matching
Description: Join tables together based not on whether columns
match exactly, but whether they are similar by some comparison.
Implementations include string distance and regular expression
matching.
Author: David Robinson [aut, cre],
Jennifer Bryan [ctb],
Joran Elias [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between fuzzyjoin versions 0.1.6 dated 2020-05-15 and 0.1.6.1 dated 2025-07-10
DESCRIPTION | 8 MD5 | 20 - R/misspellings.R | 2 R/regex_join.R | 2 R/stringdist_join.R | 2 build/vignette.rds |binary data/misspellings.rda |binary inst/doc/stringdist_join.html | 500 ++++++++++++++++++++++++++++++++---------- man/misspellings.Rd | 2 man/regex_join.Rd | 2 man/stringdist_join.Rd | 2 11 files changed, 406 insertions(+), 134 deletions(-)
Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.callr versions 0.10.0 dated 2025-06-05 and 0.10.1 dated 2025-07-10
DESCRIPTION | 6 +-- MD5 | 14 ++++---- NEWS.md | 9 +++++ R/CallrFutureBackend-class.R | 50 +++++++++++++++++++++++--------- R/utils-debug.R | 39 ++++++++++-------------- build/vignette.rds |binary inst/WORDLIST | 1 inst/testme/test-callr,launch-failure.R | 11 ++----- 8 files changed, 77 insertions(+), 53 deletions(-)
Title: Cluster Validation Techniques
Description: Contains most of the popular internal and external
cluster validation methods ready to use for the most of the
outputs produced by functions coming from package "cluster".
Package contains also functions and examples of usage for
cluster stability approach that might be applied to algorithms
implemented in "cluster" package as well as user defined
clustering algorithms.
Author: Lukasz Nieweglowski [aut, cre]
Maintainer: Lukasz Nieweglowski <wookashn@gmail.com>
Diff between clv versions 0.3-2.4 dated 2023-09-28 and 0.3-2.5 dated 2025-07-10
DESCRIPTION | 15 +++++++++------ MD5 | 15 ++++++++------- R/SD_SDbw_indicies.R | 2 +- R/cluster_stability_usr.R | 2 +- build |only man/cluster_stability.Rd | 7 ++++--- man/cluster_stability_usr.Rd | 5 +++-- man/dot_product.Rd | 5 +++-- man/similarity_index.Rd | 5 +++-- 9 files changed, 32 insertions(+), 24 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 machine learning framework with
spatio-temporal resampling methods to account for the presence of
spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
cause highly biased performance estimates in cross-validation if
ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.3.2 dated 2024-11-29 and 2.3.3 dated 2025-07-10
DESCRIPTION | 15 MD5 | 68 - NEWS.md | 12 R/ResamplingRepeatedSpCVBlock.R | 1 R/ResamplingRepeatedSpCVCoords.R | 1 R/ResamplingRepeatedSpCVDisc.R | 1 R/ResamplingRepeatedSpCVEnv.R | 1 R/ResamplingRepeatedSpCVTiles.R | 1 R/ResamplingRepeatedSpCVknndm.R | 1 R/ResamplingRepeatedSptCVCstf.R | 1 R/ResamplingSpCVBlock.R | 1 R/ResamplingSpCVBuffer.R | 1 R/ResamplingSpCVCoords.R | 1 R/ResamplingSpCVDisc.R | 1 R/ResamplingSpCVEnv.R | 1 R/ResamplingSpCVKnndm.R | 1 R/ResamplingSpCVTiles.R | 1 R/ResamplingSptCVCstf.R | 1 R/autoplot.R | 13 R/autoplot_multi_fold_list.R | 11 R/autoplot_spcv_cstf.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mlr3spatiotempcv.html | 80 +- inst/doc/spatiotemp-viz.R | 76 - inst/doc/spatiotemp-viz.html | 7 tests/testthat/_snaps/2-autoplot/repsptcvcstf-2d-space-var-fold-1-2-rep-2.svg | 136 +-- tests/testthat/_snaps/2-autoplot/repsptcvcstf-2d-space-var-fold-1-rep-2.svg | 141 +-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-all-test-sets.svg | 120 +-- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1-2.svg | 387 ++++------ tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1.svg | 175 ++-- tests/testthat/test-1-autoplot.R | 70 - tests/testthat/test-2-autoplot.R | 91 ++ tests/testthat/test-autoplot_buffer.R | 23 35 files changed, 766 insertions(+), 678 deletions(-)
More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Layout Manager Widget for R and 'shiny' Apps
Description: Provides R bindings to the 'dockview' 'JavaScript' library <https://dockview.dev/>.
Create fully customizable grid layouts (docks) in seconds to include in interactive R reports with R Markdown or 'Quarto' or
in 'shiny' apps <https://shiny.posit.co/>. In 'shiny' mode, modify docks by dynamically adding, removing or moving panels or
groups of panels from the server function. Choose among 8 stunning themes (dark and light),
serialise the state of a dock to restore it later.
Author: David Granjon [aut, cre],
Nelson Stevens [aut],
Nicolas Bennett [aut],
mathuo [cph],
cynkra GmbH [fnd]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between dockViewR versions 0.1.0 dated 2025-05-09 and 0.2.0 dated 2025-07-10
DESCRIPTION | 8 MD5 | 49 NAMESPACE | 2 NEWS.md | 12 R/dock_view.R | 113 R/select_panel.R |only R/utils.R | 5 README.md | 25 inst/doc/dockViewR.html | 167 inst/doc/dockViewR.qmd | 2 inst/examples/add_panel/app.R | 22 inst/examples/replace_panel_content/app.R | 1 inst/examples/select_panel |only inst/examples/update_theme |only inst/htmlwidgets/dockview.js |14373 ------------------------------ man/dock_view.Rd | 5 man/panel.Rd | 16 man/select_panel.Rd |only man/update_dock_view.Rd |only tests/testthat/_snaps/select_panel |only tests/testthat/_snaps/select_panel.md |only tests/testthat/_snaps/update-dock_view |only tests/testthat/_snaps/update-dock_view.md |only tests/testthat/test-add_panel.R | 6 tests/testthat/test-dock_state.R | 3 tests/testthat/test-select_panel.R |only tests/testthat/test-update-dock_view.R |only vignettes/dockViewR.qmd | 2 28 files changed, 326 insertions(+), 14485 deletions(-)
Title: Multivariate Random Forest with Compositional Responses
Description: Multivariate random forests with compositional responses and Euclidean predictors is performed. The compositional data are first transformed using the additive log-ratio transformation, and then the multivariate random forest of Rahman R., Otridge J. and Pal R. (2017), <doi:10.1093/bioinformatics/btw765>, is applied.
Author: Michail Tsagris [aut, cre],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalRF versions 1.2 dated 2025-05-29 and 1.3 dated 2025-07-10
DESCRIPTION | 13 +++--- MD5 | 20 +++++----- NAMESPACE | 4 -- R/cv.alfacomprf.R | 6 +-- R/cv.comprf.R | 80 +++++++++++------------------------------ man/CompositionalRF-package.Rd | 6 +-- man/alfa.comp.rf.Rd | 10 ++--- man/comp.rf.Rd | 2 - man/cv.alfacomprf.Rd | 6 +-- man/cv.comprf.Rd | 2 - man/mrf.Rd | 2 - 11 files changed, 56 insertions(+), 95 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: Compute Scores for Different Implicit Measures
Description: A tool for computing the scores for the Implicit Association Test
(IAT; Greenwald, McGhee & Schwartz (1998) <doi:10.1037/0022-3514.74.6.1464>)
and the Single Category-IAT (SC-IAT: Karpinski & Steinman
(2006) <doi:10.1037/0022-3514.91.1.16>). Functions for preparing the data
(both for the IAT and the SC-IAT), plotting the results, and obtaining a
table with the scores of implicit measures descriptive statistics are
provided.
Author: Ottavia M. Epifania [aut, cre],
Pasquale Anselmi [ctb],
Egidio Robusto [ctb]
Maintainer: Ottavia M. Epifania <otta.epifania@gmail.com>
Diff between implicitMeasures versions 0.2.1 dated 2022-02-16 and 0.3.0 dated 2025-07-10
DESCRIPTION | 26 MD5 | 68 +- NEWS.md | 11 R/d_density.R | 18 R/multi_dsciat.R | 18 R/multi_dscore.R | 10 README.md | 53 + build/vignette.rds |binary inst/doc/IAT-example.R | 20 inst/doc/IAT-example.Rmd | 20 inst/doc/IAT-example.html | 809 ++++++++++++++++++++--------- inst/doc/SC-IAT-example.R | 26 inst/doc/SC-IAT-example.Rmd | 28 - inst/doc/SC-IAT-example.html | 825 ++++++++++++++++++++---------- inst/doc/implicitMeasures.R | 27 inst/doc/implicitMeasures.Rmd | 33 - inst/doc/implicitMeasures.html | 838 +++++++++++++++++++++---------- man/IAT_rel.Rd | 86 +-- man/clean_iat.Rd | 208 +++---- man/clean_sciat.Rd | 190 +++---- man/compute_iat.Rd | 168 +++--- man/compute_sciat.Rd | 184 +++--- man/d_density.Rd | 182 +++--- man/d_point.Rd | 184 +++--- man/descript_d.Rd | 134 ++-- man/dsciat1.Rd | 38 - man/dsciat2.Rd | 38 - man/figures/README-unnamed-chunk-3-1.png |binary man/iatdscores.Rd | 40 - man/multi_dsciat.Rd | 160 ++--- man/multi_dscore.Rd | 110 ++-- man/raw_data.Rd | 120 ++-- vignettes/IAT-example.Rmd | 20 vignettes/SC-IAT-example.Rmd | 28 - vignettes/implicitMeasures.Rmd | 33 - 35 files changed, 2845 insertions(+), 1908 deletions(-)
More information about implicitMeasures at CRAN
Permanent link
Title: Client for US Treasury XML Feed and Published Data
Description: Download daily interest rates from the US Treasury XML feed.
Leveraging
<https://home.treasury.gov/treasury-daily-interest-rate-xml-feed>,
this package serves as a wrapper, facilitating the retrieval of daily
treasury rates across various categories, including par yield curves,
treasury bills, long-term rates, and real yield curves.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between treasury versions 0.2.0 dated 2024-07-05 and 0.3.0 dated 2025-07-10
treasury-0.2.0/treasury/R/utils.R |only treasury-0.3.0/treasury/DESCRIPTION | 17 - treasury-0.3.0/treasury/MD5 | 32 +-- treasury-0.3.0/treasury/NAMESPACE | 2 treasury-0.3.0/treasury/NEWS.md | 5 treasury-0.3.0/treasury/R/assertions.R |only treasury-0.3.0/treasury/R/interest-rate.R | 115 +++++------- treasury-0.3.0/treasury/R/treasury-package.R | 10 - treasury-0.3.0/treasury/R/yield-curve.R | 112 ++++++----- treasury-0.3.0/treasury/README.md | 19 - treasury-0.3.0/treasury/man/tr_bill_rates.Rd | 4 treasury-0.3.0/treasury/man/tr_curve_rate.Rd | 8 treasury-0.3.0/treasury/man/tr_long_term_rate.Rd | 6 treasury-0.3.0/treasury/man/tr_real_long_term.Rd | 6 treasury-0.3.0/treasury/man/tr_real_yield_curve.Rd | 4 treasury-0.3.0/treasury/man/tr_yield_curve.Rd | 4 treasury-0.3.0/treasury/man/treasury-package.Rd | 2 treasury-0.3.0/treasury/tests/testthat/test-interest-rate.R | 64 ++++-- 18 files changed, 219 insertions(+), 191 deletions(-)
Title: Fast, Robust, and High-Quality Synthetic Data Generation with a
Tuneable Privacy-Utility Trade-Off
Description: Synthesize numeric, categorical, mixed and time series data. Data
circumstances including mixed (or zero-inflated) distributions and missing
data patterns are reproduced in the synthetic data. A single parameter allows
balancing between high-quality synthetic data that represents correlations of
the original data and lower quality but more privacy safe synthetic data
without correlations. Tuning can be done per variable or for the whole
dataset.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between synthesizer versions 0.4.0 dated 2025-02-07 and 0.5.0 dated 2025-07-10
synthesizer-0.4.0/synthesizer/R/measures.R |only synthesizer-0.4.0/synthesizer/man/pmse.Rd |only synthesizer-0.5.0/synthesizer/DESCRIPTION | 28 synthesizer-0.5.0/synthesizer/MD5 | 36 synthesizer-0.5.0/synthesizer/NAMESPACE | 43 synthesizer-0.5.0/synthesizer/NEWS | 46 synthesizer-0.5.0/synthesizer/R/synthesizer.R | 472 ++++----- synthesizer-0.5.0/synthesizer/R/synthesizer_package.R | 14 synthesizer-0.5.0/synthesizer/build/vignette.rds |binary synthesizer-0.5.0/synthesizer/inst/doc/introduction.R | 104 -- synthesizer-0.5.0/synthesizer/inst/doc/introduction.html | 508 ++++------ synthesizer-0.5.0/synthesizer/inst/doc/introduction.md | 358 +++---- synthesizer-0.5.0/synthesizer/inst/tinytest/test_clustering.R | 74 - synthesizer-0.5.0/synthesizer/inst/tinytest/test_synthesizer.R | 175 +-- synthesizer-0.5.0/synthesizer/man/make_synthesizer.Rd | 21 synthesizer-0.5.0/synthesizer/man/synthesize.Rd | 9 synthesizer-0.5.0/synthesizer/man/synthesizer-package.Rd | 4 synthesizer-0.5.0/synthesizer/tests/tinytest.R | 10 synthesizer-0.5.0/synthesizer/vignettes/introduction.md | 358 +++---- synthesizer-0.5.0/synthesizer/vignettes/style.css | 88 - 20 files changed, 1146 insertions(+), 1202 deletions(-)
Title: The Interpretation of Adjusted Cp Statistic
Description: Several methods may be found for selecting a subset of regressors from a set of k candidate variables in multiple linear regression.
One possibility is to evaluate all possible regression models and comparing them using Mallows's Cp statistic (Cp) according to Gilmour original study.
Full model is calculated, all possible combinations of regressors are generated, adjusted Cp for each submodel are computed, and the submodel with the minimum adjusted value Cp (ModelMin) is calculated.
To identify the final model, the package applies a sequence of hypothesis tests on submodels nested within ModelMin, following the approach outlined in Gilmour's original paper.
For more details see the help of the function final_model() and the original study (1996) <doi:10.2307/2348411>.
Author: Josef Dolejs [aut, cre]
Maintainer: Josef Dolejs <josef.dolejs@uhk.cz>
Diff between gilmour versions 0.1.0 dated 2025-07-01 and 0.1.1 dated 2025-07-10
gilmour-0.1.0/gilmour/LICENSE |only gilmour-0.1.1/gilmour/DESCRIPTION | 8 ++++---- gilmour-0.1.1/gilmour/MD5 | 5 ++--- gilmour-0.1.1/gilmour/inst/doc/gilmour-spec.html | 4 ++-- 4 files changed, 8 insertions(+), 9 deletions(-)
Title: Exploratory Analysis of Temporal and Spatio-Temporal Health Data
Description: A collection of commonly used visualizations of temporal and
spatio-temporal health data including case counts, incidence rates, and
covariates. The available plot types include time series, heatmaps,
seasonality plots, maps and more. The package supports standard data
transformations such as temporal and spatial aggregations, while
offering extensive customization options for the resulting figures.
Author: Carles Mila [aut, cre] ,
Giovenale Moirano [aut] ,
Anna B. Kawiecki [aut] ,
Rachel Lowe [aut, cph]
Maintainer: Carles Mila <carles.milagarcia@bsc.es>
Diff between GHRexplore versions 0.1.0 dated 2025-07-05 and 0.1.1 dated 2025-07-10
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 5 +++++ R/plot_heatmap.R | 6 +++--- R/plot_map.R | 11 ++++++----- README.md | 8 ++++++-- man/figures/GHRexplore.png |only tests/testthat/test-plot_combine.R | 13 ++++++------- tests/testthat/test-plot_map.R | 3 ++- tests/testthat/test-plot_seasonality.R | 13 +------------ 10 files changed, 41 insertions(+), 41 deletions(-)
Title: Monthly Climate Data for Germany, Usable for Heating and Cooling
Calculations
Description: This data package contains monthly climate data in Germany, it can be used for heating and
cooling calculations (external temperature, heating / cooling days, solar radiation).
Author: Tobias Loga [aut] ,
Guillaume Behem [aut],
Jens Calisti [cre]
Maintainer: Jens Calisti <jens@tangled.de>
Diff between clidamonger versions 1.3.0 dated 2025-02-07 and 1.4.0 dated 2025-07-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 10 +++++++++- README.md | 4 ++-- data/data.sol.rda |binary data/data.ta.hd.rda |binary data/list.station.ta.rda |binary man/data.ta.hd.Rd | 2 +- man/list.station.ta.Rd | 2 +- 9 files changed, 26 insertions(+), 18 deletions(-)
Title: Build Species Distribution Modeling using 'caret'
Description: Use machine learning algorithms and advanced geographic information system tools to
build Species Distribution Modeling in a extensible and modern fashion.
Author: Dayani Bailly [aut] ,
Edivando Couto [aut] ,
Jose Hilario Delconte Ferreira [aut] ,
Reginaldo Re [aut] ,
Valeria Batista [aut] ,
Luiz Fernando Esser [aut, cre, cph]
Maintainer: Luiz Fernando Esser <luizesser@gmail.com>
Diff between caretSDM versions 1.1.0 dated 2025-07-09 and 1.1.0.1 dated 2025-07-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/train_sdm.R | 40 ++++++++++++++++++++++++++++++---------- README.md | 2 ++ tests/testthat/test-sdm_area.R | 34 +++++++++++++++++----------------- 5 files changed, 56 insertions(+), 34 deletions(-)
Title: Feature Extraction and Document Classification with Noisy Labels
Description: Extract features and classify documents with noisy labels given by document-meta data or keyword matching Watanabe & Zhou (2020) <doi:10.1177/0894439320907027>.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordmap versions 0.9.4 dated 2025-06-29 and 0.9.5 dated 2025-07-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-textmodel.R | 7 ++++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: A Service for Tidy Transcriptomics Software Suite
Description: It provides generic methods that are used by more than one package, avoiding conflicts. This package will be imported by 'tidySingleCellExperiment' and 'tidyseurat'.
Author: Stefano Mangiola [aut, cre]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between ttservice versions 0.4.1 dated 2024-06-07 and 0.5.3 dated 2025-07-10
DESCRIPTION | 14 + MD5 | 15 + NAMESPACE | 39 ++-- R/methods.R | 49 +++++- man/aggregate_cells.Rd | 80 +++++----- man/append_samples.Rd |only man/dplyr-methods.Rd | 134 ++++++++--------- man/join_features.Rd | 92 +++++------ man/plot_ly.Rd | 384 ++++++++++++++++++++++++------------------------- 9 files changed, 422 insertions(+), 385 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible, and comprehensive framework for
quantitative text analysis in R. Provides functionality for corpus management,
creating and manipulating tokens and n-grams, exploring keywords in context,
forming and manipulating sparse matrices
of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and
distances, applying content dictionaries, applying supervised and unsupervised machine learning,
visually representing text and text analyses, and more.
Author: Kenneth Benoit [cre, aut, cph] ,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Paul Nulty [aut] ,
Adam Obeng [aut] ,
Stefan Mueller [aut] ,
Akitaka Matsuo [aut] ,
William Lowe [aut] ,
Christian Mueller [ctb],
Olivier Delmarcelle [ctb] ,
European Research [...truncated...]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 4.3.0 dated 2025-05-20 and 4.3.1 dated 2025-07-10
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS.md | 11 ++++++++ README.md | 2 - data/data_corpus_inaugural.rda |binary inst/doc/quickstart.html | 48 ++++++++++++++++++------------------ src/tokens_xptr.cpp | 8 +++--- tests/testthat/test-corpus_chunk.R | 2 - tests/testthat/test-dfm_subset.R | 20 +++++++-------- tests/testthat/test-tokens_subset.R | 16 ++++++------ 10 files changed, 72 insertions(+), 59 deletions(-)
Title: Semi-Supervised Model for Geographical Document Classification
Description: Semissupervised model for geographical document classification (Watanabe 2018) <doi:10.1080/21670811.2017.1293487>.
This package currently contains seed dictionaries in English, German, French, Spanish, Italian, Russian, Hebrew, Arabic, Turkish, Japanese and Chinese (Simplified and Traditional).
Author: Kohei Watanabe [aut, cre, cph],
Stefan Mueller [aut],
Dani Madrid-Morales [aut],
Katerina Tertytchnaya [aut],
Ke Cheng [aut],
Chung-hong Chan [aut],
Claude Grasland [aut],
Giuseppe Carteny [aut],
Elad Segev [aut],
Dai Yamao [aut],
Barbara Ellynes Zucc [...truncated...]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between newsmap versions 0.9.0 dated 2024-05-22 and 0.9.2 dated 2025-07-10
DESCRIPTION | 8 +++--- MD5 | 12 +++++----- NAMESPACE | 2 + NEWS.md | 8 ++++++ R/textmodel.R | 48 ++++++++++++++++++++++++---------------- man/textmodel_newsmap.Rd | 12 ++++++---- tests/testthat/test-textmodel.R | 30 ++++++++++++++++++++++--- 7 files changed, 84 insertions(+), 36 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 2.1.0 dated 2025-06-25 and 2.1.1 dated 2025-07-10
DESCRIPTION | 6 - MD5 | 40 ++++++------- NEWS.md | 5 + R/Eunomia.R | 2 R/copyCdmTo.R | 2 R/generateCohortSet.R | 87 +++++++--------------------- R/summariseQuantile.R | 60 +++++++++++++++---- README.md | 19 ++---- inst/doc/a01_getting-started.Rmd | 4 - inst/doc/a01_getting-started.html | 52 ++++++++--------- inst/doc/a02_cohorts.Rmd | 2 inst/doc/a02_cohorts.html | 100 ++++++++++++++++----------------- inst/doc/a06_using_cdm_attributes.html | 4 - man/CDMConnector-package.Rd | 2 man/copyCdmTo.Rd | 2 man/eunomiaIsAvailable.Rd | 2 man/figures/logo.png |only man/figures/logo_small.png |only man/generateCohortSet.Rd | 2 tests/testthat/setup.R | 8 +- vignettes/a01_getting-started.Rmd | 4 - vignettes/a02_cohorts.Rmd | 2 22 files changed, 201 insertions(+), 204 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.15.0 dated 2025-06-23 and 0.15.1 dated 2025-07-10
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS.md | 4 +- R/backends.R | 2 - R/cuda.R | 2 - R/install.R | 34 +++++++++++------ R/save.R | 2 - R/utils-data-dataloader.R | 2 - build/partial.rdb |binary inst/po/fr/LC_MESSAGES/R-torch.mo |binary man/torch_install_path.Rd | 5 ++ po/R-fr.po | 75 ++++---------------------------------- po/R-torch.pot | 64 +------------------------------- tests/testthat/test-install.R | 2 - 14 files changed, 61 insertions(+), 163 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.14.0 dated 2025-05-22 and 0.15.0 dated 2025-07-10
DESCRIPTION | 36 +++--- MD5 | 70 ++++++----- NAMESPACE | 47 +++++++ NEWS.md | 44 +++++++ R/check_itemscale.R | 105 ++++++++++++----- R/check_normality.R | 47 +++++++ R/check_outliers.R | 151 ++++++++++++++++++++----- R/check_predictions.R | 93 ++++++++++++--- R/check_residuals.R | 22 +++ R/cronbachs_alpha.R | 39 ++++-- R/display.R | 15 ++ R/item_difficulty.R | 49 +++++--- R/item_discrimination.R | 128 ++++++++++++++++++--- R/item_omega.R |only R/item_reliability.R | 156 ++++++++++++++++++++------ R/model_performance.psych.R |only R/performance_reliability.R | 21 +-- R/print_md.R | 22 --- R/test_likelihoodratio.R | 47 ++++++- R/test_performance.R | 7 - build/partial.rdb |binary inst/WORDLIST | 8 + man/check_itemscale.Rd | 32 +++-- man/check_outliers.Rd | 26 ++-- man/cronbachs_alpha.Rd | 33 ++++- man/item_difficulty.Rd | 26 ++-- man/item_discrimination.Rd | 68 +++++++++-- man/item_omega.Rd |only man/item_reliability.Rd | 64 +++++++--- man/model_performance.fa.Rd |only man/performance_reliability.Rd | 6 - tests/testthat/test-check_itemscale.R | 31 +++++ tests/testthat/test-check_outliers.R | 15 ++ tests/testthat/test-check_predictions.R | 61 ++++++++++ tests/testthat/test-item_discrimination.R | 12 ++ tests/testthat/test-item_omega.R |only tests/testthat/test-item_reliability.R | 31 +++-- tests/testthat/test-model_performance.psych.R |only tests/testthat/test-test_likelihoodratio.R | 10 + 39 files changed, 1175 insertions(+), 347 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.1-3 dated 2025-02-04 and 2.1-4 dated 2025-07-10
gstat-2.1-3/gstat/tests/unproj.R |only gstat-2.1-3/gstat/tests/unproj.Rout.save |only gstat-2.1-4/gstat/DESCRIPTION | 9 +- gstat-2.1-4/gstat/MD5 | 50 +++++------ gstat-2.1-4/gstat/build/vignette.rds |binary gstat-2.1-4/gstat/data/DE_RB_2005.rda |binary gstat-2.1-4/gstat/data/coalash.rda |binary gstat-2.1-4/gstat/data/fulmar.rda |binary gstat-2.1-4/gstat/data/jura.rda |binary gstat-2.1-4/gstat/data/meuse.all.rda |binary gstat-2.1-4/gstat/data/meuse.alt.rda |binary gstat-2.1-4/gstat/data/ncp.grid.rda |binary gstat-2.1-4/gstat/data/oxford.rda |binary gstat-2.1-4/gstat/data/pcb.rda |binary gstat-2.1-4/gstat/data/sic2004.rda |binary gstat-2.1-4/gstat/data/sic97.rda |binary gstat-2.1-4/gstat/data/tull.rda |binary gstat-2.1-4/gstat/data/vv.rda |binary gstat-2.1-4/gstat/data/walker.rda |binary gstat-2.1-4/gstat/data/wind.rda |binary gstat-2.1-4/gstat/inst/CITATION | 1 gstat-2.1-4/gstat/inst/doc/gstat.pdf |binary gstat-2.1-4/gstat/inst/doc/prs.pdf |binary gstat-2.1-4/gstat/inst/doc/spatio-temporal-kriging.pdf |binary gstat-2.1-4/gstat/inst/doc/st.pdf |binary gstat-2.1-4/gstat/tests/stars.R | 5 + gstat-2.1-4/gstat/tests/stars.Rout.save | 73 +++++++++-------- 27 files changed, 74 insertions(+), 64 deletions(-)
Title: A 'Future' API for Parallel Processing using 'mirai'
Description: Implementation of the 'Future' API <doi:10.32614/RJ-2021-048> on top of the 'mirai' package <doi:10.5281/zenodo.7912722>. By using this package, you get to take advantage of the benefits of 'mirai' plus everything else that 'future' and the 'Futureverse' adds on top of it. It allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local machine or across remote machines. Contrary to back-ends relying on the 'parallel' package (e.g. 'multisession') and socket connections, 'mirai_cluster' and 'mirai_multisession', provided here, can run more than 125 parallel R processes. As a reminder, regardless which future backend is used by the user, the code does not have to change, it gives identical results, and behaves exactly the same.
Author: Henrik Bengtsson [aut, cre, cph] ,
Charlie Gao [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.mirai versions 0.10.0 dated 2025-06-05 and 0.10.1 dated 2025-07-10
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 20 ++++++++++++++ R/MiraiFutureBackend-class.R | 58 ++++++++++++++++++++++++++++++------------- R/utils-debug.R | 39 ++++++++++++---------------- R/zzz.R | 20 ++++++++++---- man/mirai_multisession.Rd | 5 ++- 7 files changed, 105 insertions(+), 55 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre] ,
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut] ,
Toby Hocking [aut] ,
Benjamin Schwendinger [aut] ,
Ivan Krylov [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduar [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.17.6 dated 2025-06-16 and 1.17.8 dated 2025-07-10
DESCRIPTION | 6 +- MD5 | 34 ++++++------ NEWS.md | 9 +-- build/vignette.rds |binary inst/cc | 2 inst/doc/datatable-benchmarking.html | 2 inst/doc/datatable-faq.html | 2 inst/doc/datatable-importing.html | 2 inst/doc/datatable-intro.html | 2 inst/doc/datatable-joins.html | 2 inst/doc/datatable-keys-fast-subset.html | 8 +- inst/doc/datatable-programming.html | 2 inst/doc/datatable-reference-semantics.html | 2 inst/doc/datatable-reshape.html | 2 inst/doc/datatable-sd-usage.html | 6 +- inst/doc/datatable-secondary-indices-and-auto-indexing.html | 12 ++-- src/data.table.h | 13 +++- src/init.c | 2 18 files changed, 59 insertions(+), 49 deletions(-)
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.3 dated 2025-01-21 and 1.0.4 dated 2025-07-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/BPLSR.R | 3 ++- data/milk_MIR.rda |binary 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Multiblock Exploratory and Predictive Data Analysis
Description: Exploratory and predictive methods for the analysis of several blocks of variables measured on the same individuals.
Author: Benjamin Mahieu [aut, cre],
Essomanda Tchandao Mangamana [aut],
Evelyne Vigneau [aut],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MBAnalysis versions 2.0.2 dated 2023-10-24 and 2.1.0 dated 2025-07-10
MBAnalysis-2.0.2/MBAnalysis/R/Beta.R |only MBAnalysis-2.0.2/MBAnalysis/man/Beta.Rd |only MBAnalysis-2.1.0/MBAnalysis/DESCRIPTION | 10 +- MBAnalysis-2.1.0/MBAnalysis/MD5 | 60 +++++++----- MBAnalysis-2.1.0/MBAnalysis/NAMESPACE | 7 + MBAnalysis-2.1.0/MBAnalysis/R/ComDim.R | 10 +- MBAnalysis-2.1.0/MBAnalysis/R/MBPCA.R | 8 - MBAnalysis-2.1.0/MBAnalysis/R/MBPLS.R | 8 - MBAnalysis-2.1.0/MBAnalysis/R/MBValidation.R | 28 +++-- MBAnalysis-2.1.0/MBAnalysis/R/MBWCov.R | 8 - MBAnalysis-2.1.0/MBAnalysis/R/MBplotBlocks.R | 9 + MBAnalysis-2.1.0/MBAnalysis/R/MBplotVars.R | 4 MBAnalysis-2.1.0/MBAnalysis/R/coef.MBPLS.R |only MBAnalysis-2.1.0/MBAnalysis/R/coef.MBWCov.R |only MBAnalysis-2.1.0/MBAnalysis/R/plot.ComDim.R | 100 ++++++++++----------- MBAnalysis-2.1.0/MBAnalysis/R/plot.MBPCA.R | 100 ++++++++++----------- MBAnalysis-2.1.0/MBAnalysis/R/plot.MBPLS.R | 104 ++++++++++------------ MBAnalysis-2.1.0/MBAnalysis/R/plot.MBWCov.R | 104 ++++++++++------------ MBAnalysis-2.1.0/MBAnalysis/R/predict.MBPLS.R | 102 ++++++++++----------- MBAnalysis-2.1.0/MBAnalysis/R/predict.MBWCov.R | 8 - MBAnalysis-2.1.0/MBAnalysis/R/print.ComDim.R |only MBAnalysis-2.1.0/MBAnalysis/R/print.MBPCA.R |only MBAnalysis-2.1.0/MBAnalysis/R/print.MBPLS.R |only MBAnalysis-2.1.0/MBAnalysis/R/print.MBWCov.R |only MBAnalysis-2.1.0/MBAnalysis/R/summary.ComDim.R | 76 +++++++--------- MBAnalysis-2.1.0/MBAnalysis/R/summary.MBPCA.R | 76 +++++++--------- MBAnalysis-2.1.0/MBAnalysis/R/summary.MBPLS.R | 78 ++++++++-------- MBAnalysis-2.1.0/MBAnalysis/R/summary.MBWCov.R | 78 ++++++++-------- MBAnalysis-2.1.0/MBAnalysis/build/partial.rdb |binary MBAnalysis-2.1.0/MBAnalysis/man/ComDim.Rd | 2 MBAnalysis-2.1.0/MBAnalysis/man/coef.MBPLS.Rd |only MBAnalysis-2.1.0/MBAnalysis/man/coef.MBWCov.Rd |only MBAnalysis-2.1.0/MBAnalysis/man/predict.MBPLS.Rd | 2 MBAnalysis-2.1.0/MBAnalysis/man/predict.MBWCov.Rd | 2 MBAnalysis-2.1.0/MBAnalysis/man/print.ComDim.Rd |only MBAnalysis-2.1.0/MBAnalysis/man/print.MBPCA.Rd |only MBAnalysis-2.1.0/MBAnalysis/man/print.MBPLS.Rd |only MBAnalysis-2.1.0/MBAnalysis/man/print.MBWCov.Rd |only 38 files changed, 496 insertions(+), 488 deletions(-)
Title: Analyse and Interpret Time Series Features
Description: Provides a suite of functions for analysing, interpreting, and visualising
time-series features calculated from different feature sets from the 'theft' package.
Implements statistical learning methodologies described in Henderson, T.,
Bryant, A., and Fulcher, B. (2023) <doi:10.48550/arXiv.2303.17809>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theftdlc versions 0.1.2 dated 2024-10-04 and 0.2.0 dated 2025-07-10
theftdlc-0.1.2/theftdlc/man/figures/theft-ecosystem.png |only theftdlc-0.2.0/theftdlc/DESCRIPTION | 23 theftdlc-0.2.0/theftdlc/LICENSE | 4 theftdlc-0.2.0/theftdlc/MD5 | 103 theftdlc-0.2.0/theftdlc/NAMESPACE | 154 theftdlc-0.2.0/theftdlc/R/classify.R | 533 +- theftdlc-0.2.0/theftdlc/R/cluster.R | 307 - theftdlc-0.2.0/theftdlc/R/compare_features.R | 332 - theftdlc-0.2.0/theftdlc/R/filter_duplicates.R | 288 - theftdlc-0.2.0/theftdlc/R/find_good_features.R | 104 theftdlc-0.2.0/theftdlc/R/fit_models.R | 172 theftdlc-0.2.0/theftdlc/R/get_rescale_vals.R | 82 theftdlc-0.2.0/theftdlc/R/interval.R | 322 - theftdlc-0.2.0/theftdlc/R/mywhere.R | 32 theftdlc-0.2.0/theftdlc/R/plots.R | 997 ++-- theftdlc-0.2.0/theftdlc/R/project.R | 367 - theftdlc-0.2.0/theftdlc/R/resample_data.R | 176 theftdlc-0.2.0/theftdlc/R/select_stat_cols.R | 124 theftdlc-0.2.0/theftdlc/R/shrink.R |only theftdlc-0.2.0/theftdlc/R/stat_test.R | 328 - theftdlc-0.2.0/theftdlc/R/theftdlc.R | 54 theftdlc-0.2.0/theftdlc/README.md | 318 - theftdlc-0.2.0/theftdlc/build/vignette.rds |binary theftdlc-0.2.0/theftdlc/inst/doc/theftdlc.R | 339 - theftdlc-0.2.0/theftdlc/inst/doc/theftdlc.Rmd | 775 +-- theftdlc-0.2.0/theftdlc/inst/doc/theftdlc.html | 2258 +++++----- theftdlc-0.2.0/theftdlc/man/classify.Rd | 127 theftdlc-0.2.0/theftdlc/man/cluster.Rd | 115 theftdlc-0.2.0/theftdlc/man/compare_features.Rd | 112 theftdlc-0.2.0/theftdlc/man/figures/logo.png |binary theftdlc-0.2.0/theftdlc/man/figures/theft-packages.png |binary theftdlc-0.2.0/theftdlc/man/figures/workflow-graphic_ecosystem-final.png |only theftdlc-0.2.0/theftdlc/man/filter_duplicates.Rd | 48 theftdlc-0.2.0/theftdlc/man/filter_good_features.Rd | 48 theftdlc-0.2.0/theftdlc/man/find_good_features.Rd | 44 theftdlc-0.2.0/theftdlc/man/fit_models.Rd | 56 theftdlc-0.2.0/theftdlc/man/get_rescale_vals.Rd | 40 theftdlc-0.2.0/theftdlc/man/interval.Rd | 131 theftdlc-0.2.0/theftdlc/man/make_title.Rd | 40 theftdlc-0.2.0/theftdlc/man/plot.feature_calculations.Rd | 88 theftdlc-0.2.0/theftdlc/man/plot.feature_projection.Rd | 48 theftdlc-0.2.0/theftdlc/man/plot.interval_calculations.Rd |only theftdlc-0.2.0/theftdlc/man/project.Rd | 131 theftdlc-0.2.0/theftdlc/man/resample_data.Rd | 60 theftdlc-0.2.0/theftdlc/man/rescale_zscore.Rd | 44 theftdlc-0.2.0/theftdlc/man/select_stat_cols.Rd | 52 theftdlc-0.2.0/theftdlc/man/shrink.Rd |only theftdlc-0.2.0/theftdlc/man/stat_test.Rd | 86 theftdlc-0.2.0/theftdlc/man/theftdlc.Rd | 18 theftdlc-0.2.0/theftdlc/tests/testthat.R | 8 theftdlc-0.2.0/theftdlc/tests/testthat/helper-core_data.R | 18 theftdlc-0.2.0/theftdlc/tests/testthat/test-classify.R | 38 theftdlc-0.2.0/theftdlc/tests/testthat/test-cluster.R | 12 theftdlc-0.2.0/theftdlc/tests/testthat/test-compare_features.R | 30 theftdlc-0.2.0/theftdlc/vignettes/theftdlc.Rmd | 775 +-- 55 files changed, 5280 insertions(+), 5081 deletions(-)
Title: Hyperband for 'mlr3'
Description: Successive Halving (Jamieson and Talwalkar (2016)
<doi:10.48550/arXiv.1502.07943>) and Hyperband (Li et al. 2018
<doi:10.48550/arXiv.1603.06560>) optimization algorithm for the mlr3
ecosystem. The implementation in mlr3hyperband features improved
scheduling and parallelizes the evaluation of configurations. The
package includes tuners for hyperparameter optimization in mlr3tuning
and optimizers for black-box optimization in bbotk.
Author: Marc Becker [aut, cre] ,
Sebastian Gruber [aut] ,
Jakob Richter [aut] ,
Julia Moosbauer [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3hyperband versions 0.6.0 dated 2024-06-29 and 1.0.0 dated 2025-07-10
mlr3hyperband-0.6.0/mlr3hyperband/tests/testthat/test_TunerHyperband.R |only mlr3hyperband-0.6.0/mlr3hyperband/tests/testthat/test_TunerSuccessiveHalving.R |only mlr3hyperband-1.0.0/mlr3hyperband/DESCRIPTION | 47 ++++----- mlr3hyperband-1.0.0/mlr3hyperband/MD5 | 27 +++-- mlr3hyperband-1.0.0/mlr3hyperband/NAMESPACE | 3 mlr3hyperband-1.0.0/mlr3hyperband/NEWS.md | 6 - mlr3hyperband-1.0.0/mlr3hyperband/R/OptimizerAsyncSuccessiveHalving.R |only mlr3hyperband-1.0.0/mlr3hyperband/R/OptimizerBatchHyperband.R | 4 mlr3hyperband-1.0.0/mlr3hyperband/R/TunerAsyncSuccessiveHalving.R |only mlr3hyperband-1.0.0/mlr3hyperband/R/bibentries.R | 15 ++ mlr3hyperband-1.0.0/mlr3hyperband/R/helper.R | 2 mlr3hyperband-1.0.0/mlr3hyperband/R/zzz.R | 1 mlr3hyperband-1.0.0/mlr3hyperband/build/partial.rdb |binary mlr3hyperband-1.0.0/mlr3hyperband/man/mlr_optimizers_async_successive_halving.Rd |only mlr3hyperband-1.0.0/mlr3hyperband/man/mlr_tuners_async_successive_halving.Rd |only mlr3hyperband-1.0.0/mlr3hyperband/tests/testthat/helper.R | 51 ++++++++++ mlr3hyperband-1.0.0/mlr3hyperband/tests/testthat/test_TunerAsyncSuccessiveHalving.R |only mlr3hyperband-1.0.0/mlr3hyperband/tests/testthat/test_TunerBatchHyperband.R |only mlr3hyperband-1.0.0/mlr3hyperband/tests/testthat/test_TunerBatchSuccessiveHalving.R |only 19 files changed, 117 insertions(+), 39 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 1.2.4 dated 2025-07-04 and 1.2.5 dated 2025-07-10
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 196 +++++++++++------------ inst/doc/example_ssd.html | 272 ++++++++++++++++---------------- man/adj_val.Rd | 92 +++++------ man/qcond_weibullPH.Rd | 52 +++--- man/qtimecov.Rd | 348 +++++++++++++++++++++--------------------- man/random_stream.Rd | 88 +++++----- tests/testthat/test-input_f.R | 25 +-- 9 files changed, 550 insertions(+), 547 deletions(-)
Title: Tools for Handling Extraction of Features from Time Series
Description: Consolidates and calculates different sets of time-series features from multiple
'R' and 'Python' packages including 'Rcatch22' Henderson, T. (2021) <doi:10.5281/zenodo.5546815>,
'feasts' O'Hara-Wild, M., Hyndman, R., and Wang, E. (2021) <https://CRAN.R-project.org/package=feasts>,
'tsfeatures' Hyndman, R., Kang, Y., Montero-Manso, P., Talagala, T., Wang, E., Yang, Y., and O'Hara-Wild, M. (2020)
<https://CRAN.R-project.org/package=tsfeatures>, 'tsfresh' Christ, M., Braun, N., Neuffer, J.,
and Kempa-Liehr A.W. (2018) <doi:10.1016/j.neucom.2018.03.067>, 'TSFEL' Barandas, M., et al. (2020)
<doi:10.1016/j.softx.2020.100456>, and 'Kats' Facebook Infrastructure Data Science (2021)
<https://facebookresearch.github.io/Kats/>.
Author: Trent Henderson [cre, aut],
Annie Bryant [ctb]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between theft versions 0.6.3 dated 2024-10-03 and 0.8.1 dated 2025-07-10
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Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
appropriate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.6.0 dated 2025-02-08 and 0.6.1 dated 2025-07-09
DESCRIPTION | 11 ++++++----- MD5 | 31 ++++++++++++++++++------------- NEWS.md | 27 +++++++++++++++++---------- R/inclusion_prob.R | 28 +++++++++++++++++++++------- R/sps.R | 6 +++++- R/zzz.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/sps.R | 4 ++-- inst/doc/sps.Rmd | 4 ++-- inst/doc/sps.html | 4 ++-- inst/doc/take-all.R |only inst/doc/take-all.Rmd |only inst/doc/take-all.html |only man/inclusion_prob.Rd | 7 ++++++- man/sps.Rd | 4 ++++ tests/testthat/test-sps.R | 17 ++++++++++++++++- vignettes/sps.Rmd | 4 ++-- vignettes/take-all.Rmd |only 19 files changed, 101 insertions(+), 46 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.12.0 dated 2024-11-21 and 2.13.0 dated 2025-07-09
inlabru-2.12.0/inlabru/man/bru_component.Rd |only inlabru-2.12.0/inlabru/man/bru_component_eval.Rd |only inlabru-2.12.0/inlabru/man/bru_component_list.Rd |only inlabru-2.12.0/inlabru/man/bru_like_methods.Rd |only inlabru-2.12.0/inlabru/man/bru_like_print.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_aggregate.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_collect.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_const.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_factor.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_1d.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_2d.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_fmesher.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_harmonics.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_index.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_linear.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_logsumexp.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_marginal.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_matrix.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_mesh_B.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_multi.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_pipe.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_repeat.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_scale.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_shift.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_summary.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_taylor.Rd |only inlabru-2.12.0/inlabru/man/code.components.Rd |only inlabru-2.12.0/inlabru/man/comp_lin_eval.Rd |only inlabru-2.12.0/inlabru/man/eval_in_data_context.Rd |only inlabru-2.12.0/inlabru/man/evaluate_comp_lin.Rd |only inlabru-2.12.0/inlabru/man/evaluate_comp_simple.Rd |only inlabru-2.12.0/inlabru/man/evaluate_index.Rd |only inlabru-2.12.0/inlabru/man/evaluate_inputs.Rd |only inlabru-2.12.0/inlabru/man/index_eval.Rd |only inlabru-2.12.0/inlabru/man/input_eval.Rd |only inlabru-2.12.0/inlabru/man/summary.component.Rd |only inlabru-2.13.0/inlabru/DESCRIPTION | 29 inlabru-2.13.0/inlabru/MD5 | 301 - inlabru-2.13.0/inlabru/NAMESPACE | 419 + inlabru-2.13.0/inlabru/NEWS.md | 83 inlabru-2.13.0/inlabru/R/bru.gof.R | 4 inlabru-2.13.0/inlabru/R/bru.inference.R | 2195 ++++++---- inlabru-2.13.0/inlabru/R/bru_conversion.R |only inlabru-2.13.0/inlabru/R/bru_index.R |only inlabru-2.13.0/inlabru/R/bru_input.R |only inlabru-2.13.0/inlabru/R/data.gorillas.R | 18 inlabru-2.13.0/inlabru/R/data.shrimp.R | 3 inlabru-2.13.0/inlabru/R/deltaIC.R | 16 inlabru-2.13.0/inlabru/R/effect.R | 1522 ++---- inlabru-2.13.0/inlabru/R/environment.R | 126 inlabru-2.13.0/inlabru/R/ggplot.R | 29 inlabru-2.13.0/inlabru/R/inla.R | 5 inlabru-2.13.0/inlabru/R/inlabru-package.R | 2 inlabru-2.13.0/inlabru/R/local_testthat.R | 135 inlabru-2.13.0/inlabru/R/mapper_collect.R |only inlabru-2.13.0/inlabru/R/mapper_repeat.R | 251 - inlabru-2.13.0/inlabru/R/mapper_sum.R |only inlabru-2.13.0/inlabru/R/mappers.R | 1949 ++++---- inlabru-2.13.0/inlabru/R/model.R | 569 +- 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21 inlabru-2.13.0/inlabru/inst/examples/devel.cvmeasure.R | 196 inlabru-2.13.0/inlabru/inst/examples/predict.bru.R | 52 inlabru-2.13.0/inlabru/inst/examples/rgl.R | 2 inlabru-2.13.0/inlabru/man/add_mappers.Rd | 23 inlabru-2.13.0/inlabru/man/as_bru_comp.Rd |only inlabru-2.13.0/inlabru/man/as_bru_mapper.Rd |only inlabru-2.13.0/inlabru/man/as_bru_obs.Rd |only inlabru-2.13.0/inlabru/man/bm_aggregate.Rd |only inlabru-2.13.0/inlabru/man/bm_collect.Rd |only inlabru-2.13.0/inlabru/man/bm_const.Rd |only inlabru-2.13.0/inlabru/man/bm_factor.Rd |only inlabru-2.13.0/inlabru/man/bm_fm_mesh_1d.Rd |only inlabru-2.13.0/inlabru/man/bm_fm_mesh_2d.Rd |only inlabru-2.13.0/inlabru/man/bm_fmesher.Rd |only inlabru-2.13.0/inlabru/man/bm_harmonics.Rd |only inlabru-2.13.0/inlabru/man/bm_index.Rd |only inlabru-2.13.0/inlabru/man/bm_linear.Rd |only inlabru-2.13.0/inlabru/man/bm_list.Rd | 33 inlabru-2.13.0/inlabru/man/bm_logsumexp.Rd |only inlabru-2.13.0/inlabru/man/bm_marginal.Rd |only 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inlabru-2.13.0/inlabru/man/evaluate_effect.Rd | 34 inlabru-2.13.0/inlabru/man/evaluate_model.Rd | 6 inlabru-2.13.0/inlabru/man/evaluate_predictor.Rd | 9 inlabru-2.13.0/inlabru/man/figures/README-plot-1.png |binary inlabru-2.13.0/inlabru/man/generate.Rd | 31 inlabru-2.13.0/inlabru/man/gg.bru_prediction.Rd | 3 inlabru-2.13.0/inlabru/man/gg.fm_mesh_1d.Rd | 15 inlabru-2.13.0/inlabru/man/gg.fm_mesh_2d.Rd | 26 inlabru-2.13.0/inlabru/man/globe.Rd | 2 inlabru-2.13.0/inlabru/man/glplot.Rd | 9 inlabru-2.13.0/inlabru/man/gorillas_sf.Rd | 18 inlabru-2.13.0/inlabru/man/iinla.Rd | 5 inlabru-2.13.0/inlabru/man/inla_subset_eval.Rd | 8 inlabru-2.13.0/inlabru/man/inlabru-package.Rd | 2 inlabru-2.13.0/inlabru/man/lgcp.Rd | 17 inlabru-2.13.0/inlabru/man/local_testthat.Rd | 21 inlabru-2.13.0/inlabru/man/materncov.bands.Rd | 4 inlabru-2.13.0/inlabru/man/predict.bru.Rd | 82 inlabru-2.13.0/inlabru/man/shrimp.Rd | 3 inlabru-2.13.0/inlabru/man/spde.posterior.Rd | 4 inlabru-2.13.0/inlabru/man/summary.bru.Rd | 2 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inlabru-2.13.0/inlabru/tests/testthat/test-latent_factor.R | 4 inlabru-2.13.0/inlabru/tests/testthat/test-latent_fixed_effects.R | 5 inlabru-2.13.0/inlabru/tests/testthat/test-latent_linear.R | 131 inlabru-2.13.0/inlabru/tests/testthat/test-latent_rw2.R | 4 inlabru-2.13.0/inlabru/tests/testthat/test-latent_spde_2d.R | 57 inlabru-2.13.0/inlabru/tests/testthat/test-lgcp_1d.R | 9 inlabru-2.13.0/inlabru/tests/testthat/test-lgcp_1d_nonlinear.R | 7 inlabru-2.13.0/inlabru/tests/testthat/test-lgcp_2d_covars.R | 65 inlabru-2.13.0/inlabru/tests/testthat/test-lgcp_2d_plotsample.R | 10 inlabru-2.13.0/inlabru/tests/testthat/test-linearisation.R | 26 inlabru-2.13.0/inlabru/tests/testthat/test-mapper.R | 206 inlabru-2.13.0/inlabru/tests/testthat/test-mdata.R | 2 inlabru-2.13.0/inlabru/tests/testthat/test-multi_like.R | 15 inlabru-2.13.0/inlabru/tests/testthat/test-response_size.R | 79 inlabru-2.13.0/inlabru/vignettes/bru_mapper.Rmd | 147 inlabru-2.13.0/inlabru/vignettes/prediction_scores.Rmd | 313 + 193 files changed, 7998 insertions(+), 5503 deletions(-)
Title: Assess Water Quality Trends with Generalized Additive Models
Description: Assess Water Quality Trends for Long-Term Monitoring Data in Estuaries using
Generalized Additive Models following Wood (2017) <doi:10.1201/9781315370279> and Error
Propagation with Mixed-Effects Meta-Analysis following Sera et al. (2019) <doi:10.1002/sim.8362>.
Methods are available for model fitting, assessment of fit, annual and seasonal trend tests, and
visualization of results.
Author: Marcus Beck [aut, cre] ,
Perry de Valpine [aut],
Rebecca Murphy [aut],
Ian Wren [aut],
Ariella Chelsky [aut],
Melissa Foley [aut] ,
David Senn [aut]
Maintainer: Marcus Beck <mbeck@tbep.org>
Diff between wqtrends versions 1.5.0 dated 2024-09-04 and 1.5.1 dated 2025-07-09
DESCRIPTION | 16 ++--- MD5 | 30 +++++----- NEWS.md | 5 + R/show_metseason.R | 12 ++-- R/show_prddoy.R | 9 ++- R/show_prdseason.R | 5 + R/show_prdseries.R | 9 ++- build/vignette.rds |binary inst/doc/wqtrends.html | 102 +++++++++++++++++------------------ man/show_metseason.Rd | 6 ++ man/show_prddoy.Rd | 7 ++ man/show_prdseason.Rd | 11 +++ man/show_prdseries.Rd | 6 ++ tests/testthat/test-show_prddoy.R | 8 ++ tests/testthat/test-show_prdseason.R | 7 ++ tests/testthat/test-show_prdseries.R | 8 ++ 16 files changed, 157 insertions(+), 84 deletions(-)
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.5.0 dated 2025-07-01 and 1.5.1 dated 2025-07-09
DESCRIPTION | 6 +- MD5 | 22 +++---- R/getAbundance.R | 15 ++--- R/getAbundanceAnomaly.R | 51 +++++++++++++---- R/getInfectionRate.R | 7 +- R/getVectorIndex.R | 9 +-- R/globals.R | 2 inst/doc/vectorsurvR.html | 130 ++++++++++++++++++++++++--------------------- man/getAbundance.Rd | 2 man/getAbundanceAnomaly.Rd | 2 man/getInfectionRate.Rd | 4 - man/getVectorIndex.Rd | 4 - 12 files changed, 147 insertions(+), 107 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre] ,
Christopher Bronk Ramsey [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.2.1 dated 2025-06-10 and 1.3.0 dated 2025-07-09
DESCRIPTION | 6 - MD5 | 28 +++--- NAMESPACE | 3 NEWS.md | 7 + R/intcal_json.R | 177 +++++++++++++++++++++++++++++++++++++++++++ R/rintcal-package.R | 1 R/rintcal.R | 131 ++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rintcal.R | 4 inst/doc/rintcal.Rmd | 8 + inst/doc/rintcal.html | 21 +++-- man/glue.ccurves.Rd | 3 man/intcal.extract.record.Rd |only man/intcal.plot.record.Rd |only vignettes/rintcal.Rmd | 8 + 16 files changed, 306 insertions(+), 91 deletions(-)
Title: Flexible and Robust GARCH-X Modelling
Description: Flexible and robust estimation and inference of Generalised Autoregressive Conditional Heteroscedasticity (GARCH) models with covariates ('X') based on the results by Francq and Thieu (2019) <doi:10.1017/S0266466617000512>. Coefficients can straightforwardly be set to zero by omission, and quasi maximum likelihood methods ensure estimates are generally consistent and inference valid, even when the standardised innovations are non-normal and/or dependent over time. See <doi:10.32614/RJ-2021-057> for an overview of the package.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between garchx versions 1.5 dated 2022-09-13 and 1.6 dated 2025-07-09
DESCRIPTION | 14 +++-- MD5 | 33 ++++++------- NAMESPACE | 9 +-- NEWS | 44 ++++++++++------- R/garchx-internal.R | 2 R/garchx-source-code.R | 124 +++++++++++++++++++++++++++++++++++++++++++------ build |only man/coef.garchx.Rd | 18 ++++--- man/garchx-package.Rd | 6 +- man/garchx.Rd | 13 ++--- man/garchxAvar.Rd | 4 - man/garchxObjective.Rd | 2 man/garchxSim.Rd | 6 +- man/gdiff.Rd | 8 +-- man/glag.Rd | 6 +- man/refit.Rd | 2 man/rmnorm.Rd | 2 man/ttest0.Rd | 2 18 files changed, 207 insertions(+), 88 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 1.3.1 dated 2025-06-23 and 1.3.2 dated 2025-07-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++++ src/duckdb.tar.xz |binary 4 files changed, 13 insertions(+), 6 deletions(-)
Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology (Pinheiro et al. (2014)
<doi:10.1002/sim.6052>).
Author: Bjoern Bornkamp [aut] ,
Jose Pinheiro [aut],
Frank Bretz [aut],
Ludger Sandig [aut],
Marius Thomas [aut, cre],
Daniel Sabanes Bove [aut] ,
Novartis Pharma AG [cph, fnd]
Maintainer: Marius Thomas <marius.thomas@novartis.com>
Diff between DoseFinding versions 1.3-1 dated 2025-03-11 and 1.4-1 dated 2025-07-09
DoseFinding-1.3-1/DoseFinding/tests/testssampSize.R |only DoseFinding-1.4-1/DoseFinding/DESCRIPTION | 25 + DoseFinding-1.4-1/DoseFinding/MD5 | 133 +++++----- DoseFinding-1.4-1/DoseFinding/NAMESPACE | 2 DoseFinding-1.4-1/DoseFinding/NEWS.md | 8 DoseFinding-1.4-1/DoseFinding/R/DoseFinding-package.R | 120 ++++----- DoseFinding-1.4-1/DoseFinding/R/MCPMod.R | 34 +- DoseFinding-1.4-1/DoseFinding/R/MCTtest.R | 26 - DoseFinding-1.4-1/DoseFinding/R/Mods.R | 32 +- DoseFinding-1.4-1/DoseFinding/R/bFitMod.R | 36 +- DoseFinding-1.4-1/DoseFinding/R/bMCTtest.R | 10 DoseFinding-1.4-1/DoseFinding/R/drmodels.R | 19 - DoseFinding-1.4-1/DoseFinding/R/fitMod.R | 31 -- DoseFinding-1.4-1/DoseFinding/R/guesst.R | 12 DoseFinding-1.4-1/DoseFinding/R/maFitMod.R | 10 DoseFinding-1.4-1/DoseFinding/R/optContr.R | 11 DoseFinding-1.4-1/DoseFinding/R/optDesign.R | 19 - DoseFinding-1.4-1/DoseFinding/R/planMod.R | 31 +- DoseFinding-1.4-1/DoseFinding/R/powMCT.R | 12 DoseFinding-1.4-1/DoseFinding/R/powMCTInterim.R |only DoseFinding-1.4-1/DoseFinding/R/sampSize.R | 22 - DoseFinding-1.4-1/DoseFinding/README.md | 3 DoseFinding-1.4-1/DoseFinding/build/vignette.rds |binary DoseFinding-1.4-1/DoseFinding/inst/doc/binary_data.R | 9 DoseFinding-1.4-1/DoseFinding/inst/doc/binary_data.Rmd | 9 DoseFinding-1.4-1/DoseFinding/inst/doc/binary_data.html | 13 DoseFinding-1.4-1/DoseFinding/inst/doc/longitudinal_data.R |only DoseFinding-1.4-1/DoseFinding/inst/doc/longitudinal_data.Rmd |only DoseFinding-1.4-1/DoseFinding/inst/doc/longitudinal_data.html |only DoseFinding-1.4-1/DoseFinding/inst/doc/mult_regimen.html | 16 - DoseFinding-1.4-1/DoseFinding/man/DoseFinding-package.Rd | 25 - DoseFinding-1.4-1/DoseFinding/man/IBScovars.Rd | 12 DoseFinding-1.4-1/DoseFinding/man/MCTpval.Rd | 10 DoseFinding-1.4-1/DoseFinding/man/Mods.Rd | 16 - DoseFinding-1.4-1/DoseFinding/man/bMCTtest.Rd | 18 - DoseFinding-1.4-1/DoseFinding/man/biom.Rd | 8 DoseFinding-1.4-1/DoseFinding/man/critVal.Rd | 4 DoseFinding-1.4-1/DoseFinding/man/drmodels.Rd | 42 +-- DoseFinding-1.4-1/DoseFinding/man/figures/README-example1-1.png |binary DoseFinding-1.4-1/DoseFinding/man/figures/README-example3-1.png |binary DoseFinding-1.4-1/DoseFinding/man/figures/logo.png |only DoseFinding-1.4-1/DoseFinding/man/fitMod.Rd | 52 +-- DoseFinding-1.4-1/DoseFinding/man/glycobrom.Rd | 18 - DoseFinding-1.4-1/DoseFinding/man/guesst.Rd | 12 DoseFinding-1.4-1/DoseFinding/man/maFitMod.Rd | 14 - DoseFinding-1.4-1/DoseFinding/man/migraine.Rd | 12 DoseFinding-1.4-1/DoseFinding/man/neurodeg.Rd | 14 - DoseFinding-1.4-1/DoseFinding/man/optContr.Rd | 10 DoseFinding-1.4-1/DoseFinding/man/optDesign.Rd | 72 ++--- DoseFinding-1.4-1/DoseFinding/man/planMod.Rd | 18 - DoseFinding-1.4-1/DoseFinding/man/powMCT.Rd | 8 DoseFinding-1.4-1/DoseFinding/man/powMCTInterim.Rd |only DoseFinding-1.4-1/DoseFinding/man/sampSize.Rd | 14 - DoseFinding-1.4-1/DoseFinding/man/targdose.Rd | 8 DoseFinding-1.4-1/DoseFinding/tests/testssamplMod.R | 1 DoseFinding-1.4-1/DoseFinding/tests/testthat.R | 3 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-DesignMCPModApp.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-MCTtest.R | 12 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-bMCTtest.R | 28 +- DoseFinding-1.4-1/DoseFinding/tests/testthat/test-drmodels.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-fitMod.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-guesst.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-maFitMod.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-optContr.R | 4 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-optDesign.R | 18 - DoseFinding-1.4-1/DoseFinding/tests/testthat/test-planMod.R | 6 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-powMCTBinCount.R | 2 DoseFinding-1.4-1/DoseFinding/tests/testthat/test-powMCTInterim.R |only DoseFinding-1.4-1/DoseFinding/tests/testthat/test-sampSize.R | 9 DoseFinding-1.4-1/DoseFinding/vignettes/binary_data.Rmd | 9 DoseFinding-1.4-1/DoseFinding/vignettes/longitudinal_data.Rmd |only DoseFinding-1.4-1/DoseFinding/vignettes/refs.bib | 10 72 files changed, 571 insertions(+), 571 deletions(-)
Title: A Tidy Framework for Changepoint Detection Analysis
Description: Changepoint detection algorithms for R are widespread but have
different interfaces and reporting conventions.
This makes the comparative analysis of results difficult.
We solve this problem by providing a tidy, unified interface for several
different changepoint detection algorithms.
We also provide consistent numerical and graphical reporting leveraging
the 'broom' and 'ggplot2' packages.
Author: Benjamin S. Baumer [aut, cre, cph] ,
Biviana Marcela Suarez Sierra [aut] ,
Arrigo Coen [aut] ,
Carlos A. Taimal [aut] ,
Xueheng Shi [ctb]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between tidychangepoint versions 1.0.0 dated 2025-01-31 and 1.0.1 dated 2025-07-09
DESCRIPTION | 25 ++++++------ MD5 | 73 +++++++++++++++++++----------------- NAMESPACE | 20 +++++++++ NEWS.md | 9 ++++ R/class-mod_cpt.R | 22 ++++++++++ R/class-seg_cpt.R | 30 ++++++++++++++ R/class-tidycpt.R | 46 +++++++++++++++++++++- R/pkg-GA.R | 1 R/pkg-changepoint.R | 1 R/pkg-changepointGA.R |only R/pkg-segmented.R |only R/pkg-stats.R | 57 ++++++++++++++++++++++++++++ R/pkg-wbs.R | 5 +- R/segment.R | 10 ++++ R/segment_cga.R |only R/tidychangepoint-package.R | 6 ++ README.md | 16 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tidychangepoint.html | 4 - man/as.segmenter.Rd | 8 +++ man/changepoints.Rd | 16 +++++++ man/fit_arima.Rd |only man/fit_lmshift.Rd | 1 man/fit_meanshift.Rd | 1 man/fit_meanvar.Rd | 1 man/fit_nhpp.Rd | 1 man/fitness.Rd | 23 ++++++++++- man/fun_cpt.Rd | 1 man/model_args.Rd | 6 ++ man/model_name.Rd | 9 +++- man/reexports.Rd | 35 +++++++++++++++-- man/seg_cpt.Rd | 3 + man/seg_params.Rd | 8 +++ man/segment.Rd | 4 + man/segment_cga.Rd |only man/whomademe.Rd | 1 tests/testthat/test-changepointGA.R |only tests/testthat/test-segmented.R |only tests/testthat/test-stats.R | 9 +++- tests/testthat/test-tidycpt.R | 3 + 41 files changed, 384 insertions(+), 71 deletions(-)
More information about tidychangepoint at CRAN
Permanent link
Title: Sign-Simplicity-Regression-Solver
Description: Implementation of the SSR-Algorithm. The Sign-Simplicity-Regression model is a nonparametric statistical model which is based on residual signs and simplicity assumptions on the regression function. Goal is to calculate the most parsimonious regression function satisfying the statistical adequacy requirements. Theory and functions are specified in Metzner (2020, ISBN: 979-8-68239-420-3, "Trendbasierte Prognostik") and Metzner (2021, ISBN: 979-8-59347-027-0, "Adäquates Maschinelles Lernen").
Author: Lars Metzner [aut, cre]
Maintainer: Lars Metzner <lars.metzner@ppi.de>
Diff between sisireg versions 1.1.2 dated 2024-12-13 and 1.2.1 dated 2025-07-09
DESCRIPTION | 6 +++--- MD5 | 17 ++++++++++++----- NAMESPACE | 2 +- R/ssrMLP.R | 4 ++++ R/ssrMLP2.R |only R/ssrnd.R | 2 +- R/ssrnd2.R |only man/psplotnd2.Rd |only man/ssrmlp2_train.Rd |only man/ssrnd2.Rd |only man/ssrnd2NN.Rd |only man/ssrnd2_predict.Rd |only src/ssrnd.c | 9 ++++++--- 13 files changed, 27 insertions(+), 13 deletions(-)
Title: Construct Process Maps Using Event Data
Description: Visualize event logs using directed graphs, i.e. process maps. Part of the 'bupaR' framework.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Benoît Depaire [ctb],
Felix Mannhardt [ctb],
Thijs Beuving [ctb],
urvikalia [ctb],
Hasselt University [cph]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between processmapR versions 0.5.6 dated 2024-12-03 and 0.5.7 dated 2025-07-09
DESCRIPTION | 6 ++-- MD5 | 14 +++++------ R/process_map.R | 40 +++++++++++++++++++------------- R/trace_explorer.R | 6 ++-- build/vignette.rds |binary inst/doc/processmapr.html | 4 +-- man/trace_explorer.Rd | 4 +-- tests/testthat/_snaps/trace_explorer.md | 8 +++--- 8 files changed, 45 insertions(+), 37 deletions(-)
Title: Microeconometrics with R
Description: Functions, data sets and examples for the book: Yves Croissant (2025) "Microeconometrics with R", Chapman and Hall/CRC The R Series <doi:10.1201/9781003100263>. The package includes a set of estimators for models used in microeconometrics, especially for count data and limited dependent variables. Test functions include score test, Hausman test, Vuong test, Sargan test and conditional moment test. A small subset of the data set used in the book is also included.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between micsr versions 0.1-2 dated 2025-06-08 and 0.1-3 dated 2025-07-09
DESCRIPTION | 12 +-- MD5 | 85 ++++++++++----------- NAMESPACE | 10 ++ NEWS.md | 7 + R/binomreg.R | 66 ++++++++-------- R/gaze.R | 62 +++++++++++---- R/lnl_tobit1.R | 11 ++ R/methods.R | 112 ++++++++++++++-------------- R/ordreg.R | 2 R/poisreg.R | 24 ++++-- R/predict.R |only R/tobit1.R | 42 ++++++---- R/tools.R | 33 +++++++- R/weibreg.R | 2 build/partial.rdb |binary data/random_group.rda |binary inst/doc/charitable.R | 27 +++++- inst/doc/charitable.pdf |binary inst/doc/charitable.qmd | 64 ++++++++-------- inst/doc/escount.R | 7 + inst/doc/escount.pdf |binary inst/doc/escount.qmd | 153 ++++++++++++++++++-------------------- inst/doc/expreg.R | 12 +-- inst/doc/expreg.pdf |binary inst/doc/expreg.qmd | 175 ++++++++++++++++++++++--------------------- inst/doc/lm_function.R | 4 - inst/doc/lm_function.pdf |binary inst/doc/lm_function.qmd | 43 +++++----- inst/doc/micsr_objects.R | 2 inst/doc/micsr_objects.pdf |binary inst/doc/micsr_objects.qmd | 62 ++++++++------- inst/doc/ndvuong.R | 21 +++-- inst/doc/ndvuong.pdf |binary inst/doc/ndvuong.qmd | 176 ++++++++++++++++++++++++-------------------- man/binomreg.Rd | 8 -- man/gaze.Rd | 16 +--- man/micsr.Rd | 51 ++++++++++-- man/select_coef.Rd | 11 ++ vignettes/charitable.qmd | 64 ++++++++-------- vignettes/escount.qmd | 153 ++++++++++++++++++-------------------- vignettes/expreg.qmd | 175 ++++++++++++++++++++++--------------------- vignettes/lm_function.qmd | 43 +++++----- vignettes/micsr_objects.qmd | 62 ++++++++------- vignettes/ndvuong.qmd | 176 ++++++++++++++++++++++++-------------------- 44 files changed, 1087 insertions(+), 886 deletions(-)
Title: Translate Text
Description: Provide easy methods to translate pieces of text.
Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between polyglotr versions 1.6.0 dated 2025-05-14 and 1.6.1 dated 2025-07-09
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 91 +++++++++++++++++----------------- data/google_supported_languages.rda |binary man/replace_urls_with_placeholders.Rd | 46 ++++++++--------- man/restore_urls_from_placeholders.Rd | 40 +++++++------- 6 files changed, 99 insertions(+), 96 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 1.4.1 dated 2025-06-27 and 1.4.2 dated 2025-07-09
DESCRIPTION | 12 +- MD5 | 16 +- NEWS.md | 4 R/summariseResult.R | 7 + inst/doc/cohort-intersect.html | 98 ++++++++-------- inst/doc/concept-intersect.html | 94 +++++++-------- inst/doc/demographics.html | 240 ++++++++++++++++++++-------------------- inst/doc/summarise.html | 152 ++++++++++++------------- inst/doc/table-intersect.html | 86 +++++++------- 9 files changed, 359 insertions(+), 350 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between parameters versions 0.26.0 dated 2025-05-22 and 0.27.0 dated 2025-07-09
DESCRIPTION | 35 +-- MD5 | 123 +++++----- NAMESPACE | 15 + NEWS.md | 41 +++ R/1_model_parameters.R | 19 + R/bootstrap_model.R | 4 R/display.R | 108 +++++++-- R/equivalence_test.R | 2 R/factor_analysis.R | 122 +++++----- R/factor_scores.R |only R/format_p_adjust.R | 190 ++++++++++++---- R/format_parameters.R | 9 R/methods_brms.R | 3 R/methods_glmmTMB.R | 7 R/methods_psych.R | 288 ++++++++++++++++--------- R/methods_rstanarm.R | 2 R/n_clusters_easystats.R | 2 R/n_factors.R | 158 ++++++------- R/p_direction.R | 2 R/p_significance.R | 2 R/principal_components.R | 165 ++++++++------ R/print_html.R | 57 ++++ R/print_md.R | 34 ++ R/standardize_info.R | 3 R/standardize_parameters.R | 2 R/utils_model_parameters.R | 27 ++ R/utils_pca_efa.R | 217 ++++++++++++------ README.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 5 man/compare_parameters.Rd | 11 man/convert_efa_to_cfa.Rd | 5 man/display.parameters_model.Rd | 5 man/equivalence_test.lm.Rd | 2 man/factor_scores.Rd |only man/get_scores.Rd | 59 +++-- man/model_parameters.Rd | 7 man/model_parameters.aov.Rd | 11 man/model_parameters.cgam.Rd | 11 man/model_parameters.default.Rd | 11 man/model_parameters.glimML.Rd | 11 man/model_parameters.glmmTMB.Rd | 11 man/model_parameters.mira.Rd | 11 man/model_parameters.mlm.Rd | 11 man/model_parameters.principal.Rd | 140 ++++++------ man/model_parameters.zcpglm.Rd | 11 man/n_factors.Rd | 10 man/p_direction.lm.Rd | 2 man/p_significance.lm.Rd | 2 man/principal_components.Rd | 150 ++++++++----- man/reduce_parameters.Rd | 16 - man/reshape_loadings.Rd | 8 man/standardize_parameters.Rd | 2 tests/testthat/test-bootstrap_parameters.R | 15 + tests/testthat/test-compare_parameters.R | 2 tests/testthat/test-factor_analysis.R |only tests/testthat/test-get_scores.R | 1 tests/testthat/test-model_parameters.mediate.R | 5 tests/testthat/test-p_adjust.R | 63 +++++ tests/testthat/test-pca.R | 2 tests/testthat/test-pool_parameters.R | 2 tests/testthat/test-pretty_names.R | 25 ++ tests/testthat/test-standardize_parameters.R | 1 64 files changed, 1500 insertions(+), 768 deletions(-)
Title: Multidimensional Top Scoring for Creativity Research
Description: Implementation of Multidimensional Top Scoring
method for creativity assessment proposed in
Boris Forthmann, Maciej Karwowski, Roger E. Beaty (2023) <doi:10.1037/aca0000571>.
Author: Jakub Jedrusiak [aut, cre, cph] ,
Boris Forthmann [aut, rev] ,
Roger E. Beaty [aut] ,
Maciej Karwowski [aut]
Maintainer: Jakub Jedrusiak <jakub.jedrusiak2@uwr.edu.pl>
Diff between mtscr versions 1.0.2 dated 2024-12-12 and 2.0.0 dated 2025-07-09
mtscr-1.0.2/mtscr/R/utils-tidy-eval.R |only mtscr-1.0.2/mtscr/man/tidyeval.Rd |only mtscr-1.0.2/mtscr/tests/testthat/test-mtscr_model.R |only mtscr-1.0.2/mtscr/tests/testthat/test-mtscr_model_summary.R |only mtscr-1.0.2/mtscr/tests/testthat/test-mtscr_prepare.R |only mtscr-1.0.2/mtscr/tests/testthat/test-mtscr_score.R |only mtscr-2.0.0/mtscr/DESCRIPTION | 28 + mtscr-2.0.0/mtscr/MD5 | 60 ++-- mtscr-2.0.0/mtscr/NAMESPACE | 19 - mtscr-2.0.0/mtscr/NEWS.md | 4 mtscr-2.0.0/mtscr/R/constructors.R |only mtscr-2.0.0/mtscr/R/data.R | 6 mtscr-2.0.0/mtscr/R/methods-mtscr.R |only mtscr-2.0.0/mtscr/R/mtscr-package.R | 7 mtscr-2.0.0/mtscr/R/mtscr.R |only mtscr-2.0.0/mtscr/R/mtscr_app.R | 52 ++- mtscr-2.0.0/mtscr/R/mtscr_model.R | 41 ++ mtscr-2.0.0/mtscr/R/mtscr_model_summary.R | 10 mtscr-2.0.0/mtscr/R/mtscr_prepare.R | 79 +++-- mtscr-2.0.0/mtscr/R/mtscr_score.R | 51 +++ mtscr-2.0.0/mtscr/R/mtscr_wrangle.R |only mtscr-2.0.0/mtscr/README.md | 171 ++++++++---- mtscr-2.0.0/mtscr/build/partial.rdb |binary mtscr-2.0.0/mtscr/inst/GUI/app.R | 92 ++++-- mtscr-2.0.0/mtscr/inst/GUI/www/article_citation.html | 3 mtscr-2.0.0/mtscr/man/mtscr-package.Rd | 1 mtscr-2.0.0/mtscr/man/mtscr.Rd |only mtscr-2.0.0/mtscr/man/mtscr_app.Rd | 26 - mtscr-2.0.0/mtscr/man/mtscr_creativity.Rd | 2 mtscr-2.0.0/mtscr/man/mtscr_model.Rd | 7 mtscr-2.0.0/mtscr/man/mtscr_model_summary.Rd | 8 mtscr-2.0.0/mtscr/man/mtscr_prepare.Rd | 11 mtscr-2.0.0/mtscr/man/mtscr_score.Rd | 10 mtscr-2.0.0/mtscr/man/mtscr_self_rank.Rd | 4 mtscr-2.0.0/mtscr/man/mtscr_wrangle.Rd |only mtscr-2.0.0/mtscr/man/new_mtscr.Rd |only mtscr-2.0.0/mtscr/man/predict.mtscr.Rd |only mtscr-2.0.0/mtscr/man/summary.mtscr.Rd |only mtscr-2.0.0/mtscr/tests/testthat/test_mtscr.R |only 39 files changed, 473 insertions(+), 219 deletions(-)
Title: Local Polynomial (Ridge) Regression
Description: Local Polynomial Regression with Ridging.
Author: Burkhardt Seifert [aut] ,
Martin Maechler [cre, aut]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between lpridge versions 1.1-0 dated 2023-12-08 and 1.1-1 dated 2025-07-09
ChangeLog | 4 ++++ DESCRIPTION | 20 +++++++++++++------- MD5 | 4 ++-- 3 files changed, 19 insertions(+), 9 deletions(-)
Title: Extra Appenders for 'lgr'
Description: Additional appenders for the logging package 'lgr' that
support logging to databases, email and push notifications.
Author: Stefan Fleck [aut, cre] ,
Jimmy Briggs [ctb, rev]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgrExtra versions 0.1.0 dated 2025-06-20 and 0.1.1 dated 2025-07-09
DESCRIPTION | 9 +++--- MD5 | 14 +++++----- NEWS.md | 5 +++ R/AppenderDynatrace.R | 23 ++++------------- README.md | 12 +++----- inst/WORDLIST | 2 + man/AppenderDynatrace.Rd | 43 ++++---------------------------- tests/testthat/test_AppenderDynatrace.R | 10 +++++-- 8 files changed, 44 insertions(+), 74 deletions(-)
Title: Selected Utilities Extending 'ggplot2'
Description: Selected utilities, in particular 'geoms' and 'stats'
functions, extending the 'ggplot2' package. This package imports
functions from 'EnvStats' <doi:10.1007/978-1-4614-8456-1> by Millard
(2013), 'ggpp' <https://CRAN.R-project.org/package=ggpp> by Aphalo et
al. (2023) and 'ggstats' <doi:10.5281/zenodo.10183964> by Larmarange
(2023), and then exports them. This package also contains modified
code from 'ggquickeda' <https://CRAN.R-project.org/package=ggquickeda>
by Mouksassi et al. (2023) for Kaplan-Meier lines and ticks additions
to plots. All functions are tested to make sure that they work
reliably.
Author: Daniel Sabanes Bove [aut, cre],
Samer Mouksassi [aut] ,
Michael Sachs [aut] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between ggplot2.utils versions 0.3.2 dated 2024-06-25 and 0.3.3 dated 2025-07-09
ggplot2.utils-0.3.2/ggplot2.utils/man/figures/logo.png |only ggplot2.utils-0.3.3/ggplot2.utils/DESCRIPTION | 10 ggplot2.utils-0.3.3/ggplot2.utils/MD5 | 96 +-- ggplot2.utils-0.3.3/ggplot2.utils/NAMESPACE | 82 +- ggplot2.utils-0.3.3/ggplot2.utils/NEWS.md | 72 +- ggplot2.utils-0.3.3/ggplot2.utils/R/geom_km.R | 148 ++--- ggplot2.utils-0.3.3/ggplot2.utils/R/geom_km_ticks.R | 186 +++--- ggplot2.utils-0.3.3/ggplot2.utils/R/geom_table.R | 30 - ggplot2.utils-0.3.3/ggplot2.utils/R/ggproto.R | 32 - ggplot2.utils-0.3.3/ggplot2.utils/R/package.R | 32 - ggplot2.utils-0.3.3/ggplot2.utils/R/stat_km.R | 120 ++-- ggplot2.utils-0.3.3/ggplot2.utils/R/stat_km_compute.R | 112 +-- ggplot2.utils-0.3.3/ggplot2.utils/R/stat_km_ticks.R | 132 ++-- ggplot2.utils-0.3.3/ggplot2.utils/R/stat_n_text.R | 28 ggplot2.utils-0.3.3/ggplot2.utils/R/stat_prop.R | 30 - ggplot2.utils-0.3.3/ggplot2.utils/R/table_themes.R | 64 +- ggplot2.utils-0.3.3/ggplot2.utils/R/ttheme_set.R | 38 - ggplot2.utils-0.3.3/ggplot2.utils/inst/WORDLIST | 44 - ggplot2.utils-0.3.3/ggplot2.utils/man/figures/logo.svg |only ggplot2.utils-0.3.3/ggplot2.utils/man/geom_km.Rd | 284 ++++----- ggplot2.utils-0.3.3/ggplot2.utils/man/geom_km_ticks.Rd | 288 +++++----- ggplot2.utils-0.3.3/ggplot2.utils/man/geom_table.Rd | 28 ggplot2.utils-0.3.3/ggplot2.utils/man/ggplot2.utils-package.Rd | 84 +- ggplot2.utils-0.3.3/ggplot2.utils/man/ggproto.Rd | 86 +- ggplot2.utils-0.3.3/ggplot2.utils/man/h_surv_fit.Rd | 38 - ggplot2.utils-0.3.3/ggplot2.utils/man/stat_km.Rd | 266 ++++----- ggplot2.utils-0.3.3/ggplot2.utils/man/stat_km_compute.Rd | 40 - ggplot2.utils-0.3.3/ggplot2.utils/man/stat_km_ticks.Rd | 276 ++++----- ggplot2.utils-0.3.3/ggplot2.utils/man/stat_km_ticks_compute.Rd | 42 - ggplot2.utils-0.3.3/ggplot2.utils/man/stat_n_text.Rd | 26 ggplot2.utils-0.3.3/ggplot2.utils/man/stat_prop.Rd | 28 ggplot2.utils-0.3.3/ggplot2.utils/man/ttheme_gtdefault.Rd | 42 - ggplot2.utils-0.3.3/ggplot2.utils/man/ttheme_set.Rd | 38 - ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat.R | 8 ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/_snaps/geom_km/geom-km-single-group.svg | 104 +-- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/_snaps/geom_km/geom-km-two-groups.svg | 122 ++-- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/_snaps/geom_km_ticks/geom-km-ticks-single-group.svg | 122 ++-- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/_snaps/geom_km_ticks/geom-km-ticks-two-groups.svg | 146 ++--- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/_snaps/stat_km_compute.md | 48 - ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/helper-data.R | 16 ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-geom_km.R | 71 +- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-geom_km_ticks.R | 75 +- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-geom_table.R | 70 +- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-stat_km.R | 44 - ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-stat_km_compute.R | 78 +- ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-stat_km_ticks.R | 48 + ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-stat_n_text.R | 18 ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-stat_prop.R | 20 ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-table_themes.R | 54 - ggplot2.utils-0.3.3/ggplot2.utils/tests/testthat/test-ttheme_set.R | 90 +-- 50 files changed, 2005 insertions(+), 1951 deletions(-)
Title: Curly Braces for 'ggplot2'
Description: Provides curly braces and square brackets in 'ggplot2' plus matching text.
stat_brace() plots braces/brackets to embrace data.
stat_bracetext() plots corresponding text, fitting to the braces from stat_brace().
Author: Nicolas Huber [aut, cre, cph]
Maintainer: Nicolas Huber <info.huber@aol.de>
Diff between ggbrace versions 0.1.1 dated 2024-02-20 and 0.1.2 dated 2025-07-09
DESCRIPTION | 13 +- MD5 | 24 +-- R/StatBrace.R | 11 + R/StatBraceLabel.R | 8 - R/coordCorrection.R | 32 +++-- R/seekBrace.R | 27 +++- R/stat_brace.R | 45 ++++--- R/stat_bracetext.R | 4 README.md | 271 +++++++++++++++++++++++---------------------- man/dot-coordCorrection.Rd | 90 +++++++------- man/dot-seekBrace.Rd | 50 ++++---- man/stat_brace.Rd | 89 ++++++++------ man/stat_bracetext.Rd | 240 +++++++++++++++++++++++---------------- 13 files changed, 514 insertions(+), 390 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper "An Approximation Based Theory of Linear Regression". Only four simple equations are required. Moreover the Gaussian P-values can be simply derived from standard F P-values. Furthermore [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.1.7 dated 2025-07-05 and 1.1.8 dated 2025-07-09
gausscov-1.1.7/gausscov/R/fpsired.R |only gausscov-1.1.7/gausscov/man/fpsired.Rd |only gausscov-1.1.8/gausscov/DESCRIPTION | 6 +++--- gausscov-1.1.8/gausscov/MD5 | 10 ++++++---- gausscov-1.1.8/gausscov/R/fdecode.R |only gausscov-1.1.8/gausscov/R/fselect.R |only gausscov-1.1.8/gausscov/man/fdecode.Rd |only gausscov-1.1.8/gausscov/man/fselect.Rd |only gausscov-1.1.8/gausscov/src/gaucov.f | 25 +++++++++++++------------ 9 files changed, 22 insertions(+), 19 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Marijke Swennen [ctb],
Ivan Esin [ctb],
Hasselt University [cph]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between edeaR versions 0.9.4 dated 2023-04-27 and 0.9.5 dated 2025-07-09
DESCRIPTION | 11 - MD5 | 115 +++++++------- NAMESPACE | 1 R/filter_case_condition.R | 56 ------- R/idle_time.R | 18 +- R/idle_time_flow.R |only R/processing_time.R | 16 +- R/processing_time_activity_instance.R | 55 ++++-- R/processing_time_case.R | 16 +- R/repetitions_all.R | 8 - R/repetitions_redo.R | 8 - R/repetitions_repeat.R | 4 R/rework_base.R | 4 R/selfloops_all.R | 8 - R/selfloops_redo.R | 6 R/selfloops_repeat.R | 4 R/setdiff.R | 2 R/throughput_time.R | 19 +- R/throughput_time_activity.R |only R/throughput_time_activity_instance.R |only R/utils.R | 18 +- build/vignette.rds |binary inst/doc/filters.html | 98 ++++++------ inst/doc/metrics.html | 90 +++++------ inst/doc/queue.R | 2 inst/doc/queue.html | 248 +++++++++++++++---------------- inst/doc/work_schedules.html | 129 ++++++++-------- man/edeaR.Rd | 2 man/filter_activity.Rd | 16 +- man/filter_activity_frequency.Rd | 18 +- man/filter_activity_instance.Rd | 18 +- man/filter_activity_presence.Rd | 18 +- man/filter_case.Rd | 16 +- man/filter_case_condition.Rd | 50 +----- man/filter_endpoints.Rd | 16 +- man/filter_endpoints_condition.Rd | 16 +- man/filter_flow_time.Rd | 18 +- man/filter_idle_time.Rd | 18 +- man/filter_infrequent_flows.Rd | 18 +- man/filter_lifecycle.Rd | 16 +- man/filter_lifecycle_presence.Rd | 16 +- man/filter_precedence.Rd | 16 +- man/filter_precedence_condition.Rd | 18 +- man/filter_precedence_resource.Rd | 18 +- man/filter_processing_time.Rd | 18 +- man/filter_resource.Rd | 16 +- man/filter_resource_frequency.Rd | 16 +- man/filter_throughput_time.Rd | 18 +- man/filter_time_period.Rd | 18 +- man/filter_trace.Rd | 16 +- man/filter_trace_frequency.Rd | 18 +- man/filter_trace_length.Rd | 18 +- man/filter_trim.Rd | 14 - man/filter_trim_lifecycle.Rd | 14 - man/idle_time.Rd | 10 - man/processing_time.Rd | 15 + man/setdiff.Rd | 16 -- man/throughput_time.Rd | 15 + tests/testthat/test_activity_frequency.R | 16 +- tests/testthat/test_processing_time.R | 14 - 60 files changed, 743 insertions(+), 753 deletions(-)
Title: Bayesian Cluster Validity Index
Description: Algorithms for computing and generating plots with and without error bars for Bayesian cluster validity index (BCVI) (O. Preedasawakul, and N. Wiroonsri, A Bayesian Cluster Validity Index, Computational Statistics & Data Analysis, 202, 108053, 2025. <doi:10.1016/j.csda.2024.108053>) based on several underlying cluster validity indexes (CVIs) including Calinski-Harabasz, Chou-Su-Lai, Davies-Bouldin, Dunn, Pakhira-Bandyopadhyay-Maulik, Point biserial correlation, the score function, Starczewski, and Wiroonsri indices for hard clustering, and Correlation Cluster Validity, the generalized C, HF, KWON, KWON2, Modified Pakhira-Bandyopadhyay-Maulik, Pakhira-Bandyopadhyay-Maulik, Tang, Wiroonsri-Preedasawakul, Wu-Li, and Xie-Beni indices for soft clustering. The package is compatible with K-means, fuzzy C means, EM clustering, and hierarchical clustering (single, average, and complete linkage). Though BCVI is compatible with any underlying existing CVIs, we recommend users to use ei [...truncated...]
Author: Nathakhun Wiroonsri [aut] ,
Onthada Preedasawakul [cre, aut]
Maintainer: Onthada Preedasawakul <o.preedasawakul@gmail.com>
Diff between BayesCVI versions 1.0.1 dated 2024-09-04 and 1.0.2 dated 2025-07-09
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NAMESPACE | 3 +-- NEWS.md | 4 +++- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.3.0 dated 2025-04-15 and 0.4.0 dated 2025-07-08
OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.R |only OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.Rmd |only OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.html |only OmopViewer-0.3.0/OmopViewer/vignettes/configured_panels.Rmd |only OmopViewer-0.4.0/OmopViewer/DESCRIPTION | 36 OmopViewer-0.4.0/OmopViewer/MD5 | 84 - OmopViewer-0.4.0/OmopViewer/NAMESPACE | 1 OmopViewer-0.4.0/OmopViewer/R/appDynamic.R | 37 OmopViewer-0.4.0/OmopViewer/R/appStatic.R | 36 OmopViewer-0.4.0/OmopViewer/R/background.R | 2 OmopViewer-0.4.0/OmopViewer/R/buttons.R | 68 + OmopViewer-0.4.0/OmopViewer/R/classes.R | 23 OmopViewer-0.4.0/OmopViewer/R/createServer.R | 74 + OmopViewer-0.4.0/OmopViewer/R/createUi.R | 25 OmopViewer-0.4.0/OmopViewer/R/defaultPanels.R | 30 OmopViewer-0.4.0/OmopViewer/R/functions.R | 267 +---- OmopViewer-0.4.0/OmopViewer/R/omopViewer-package.R | 1 OmopViewer-0.4.0/OmopViewer/R/populatePanelDetailsOptions.R | 34 OmopViewer-0.4.0/OmopViewer/R/sysdata.rda |binary OmopViewer-0.4.0/OmopViewer/R/utilities.R | 3 OmopViewer-0.4.0/OmopViewer/build/vignette.rds |binary OmopViewer-0.4.0/OmopViewer/data/omopViewerPanels.rda |binary OmopViewer-0.4.0/OmopViewer/data/omopViewerResults.rda |binary OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.R |only OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.Rmd |only OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.html |only OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.R | 51 + OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.Rmd | 95 + OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.html | 97 +- OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.R | 38 OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.Rmd | 106 ++ OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.html | 477 ++++++++-- OmopViewer-0.4.0/OmopViewer/inst/functions.R | 262 ----- OmopViewer-0.4.0/OmopViewer/man/exportStaticApp.Rd | 17 OmopViewer-0.4.0/OmopViewer/man/figures |only OmopViewer-0.4.0/OmopViewer/man/getPanel.Rd | 2 OmopViewer-0.4.0/OmopViewer/man/launchDynamicApp.Rd | 2 OmopViewer-0.4.0/OmopViewer/man/omopViewerPanels.Rd | 8 OmopViewer-0.4.0/OmopViewer/man/omopViewerResults.Rd | 10 OmopViewer-0.4.0/OmopViewer/man/panelDetailsFromResult.Rd | 8 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-appStatic.R | 4 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-background.R | 2 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-choices.R | 79 + OmopViewer-0.4.0/OmopViewer/vignettes/dynamic_app.Rmd |only OmopViewer-0.4.0/OmopViewer/vignettes/edit_static_content.Rmd | 95 + OmopViewer-0.4.0/OmopViewer/vignettes/export_static_app.Rmd | 106 ++ 46 files changed, 1466 insertions(+), 714 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.9 dated 2025-06-27 and 0.1.10 dated 2025-07-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/LONBGLSS.R | 8 ++++---- R/LONRBGLSS.R | 4 ++-- R/mixedBayes.R | 11 ++++++----- R/selection.R | 8 ++++---- R/selection_nonsparse.R | 8 ++++---- R/selection_sparse.R | 8 ++++---- README.md | 4 ++-- man/selection.Rd | 2 +- src/BGL.cpp | 2 +- src/BLSS.cpp | 6 +++--- 13 files changed, 51 insertions(+), 46 deletions(-)
Title: Spatio-Temporal Point Pattern Methods, Model Fitting,
Diagnostics, Simulation, Local Tests
Description: Toolbox for different kinds of spatio-temporal analyses to be performed on observed point patterns, following the growing stream of literature on point process theory. This R package implements functions to perform different kinds of analyses on point processes, proposed in the papers (Siino, Adelfio, and Mateu 2018<doi:10.1007/s00477-018-1579-0>; Siino et al. 2018<doi:10.1002/env.2463>; Adelfio et al. 2020<doi:10.1007/s00477-019-01748-1>; D’Angelo, Adelfio, and Mateu 2021<doi:10.1016/j.spasta.2021.100534>; D’Angelo, Adelfio, and Mateu 2022<doi:10.1007/s00362-022-01338-4>; D’Angelo, Adelfio, and Mateu 2023<doi:10.1016/j.csda.2022.107679>). The main topics include modeling, statistical inference, and simulation issues on spatio-temporal point processes on Euclidean space and linear networks. Version 1.0.0 has been updated for accompanying the journal publication D Angelo and Adelfio 2025 <doi:10.18637/jss.v113.i10>.
Author: Nicoletta D'Angelo [aut, cre] ,
Giada Adelfio [aut]
Maintainer: Nicoletta D'Angelo <nicoletta.dangelo@unipa.it>
Diff between stopp versions 0.2.4 dated 2024-06-04 and 1.0.0 dated 2025-07-08
DESCRIPTION | 19 +++++++++-------- MD5 | 53 ++++++++++++++++++++++++------------------------- R/globaldiag.R | 4 +-- R/internals.R | 5 ++++ R/localSTLKinhom.R | 2 - R/localdiag.R | 2 - R/localtest.R | 2 - R/plot.globaldiag.R | 2 - R/plot.locstppm.R | 4 +-- R/plot.sepstppm.R | 4 +-- R/plot.stlgcppm.R | 4 +-- R/plot.stlp.R | 2 - R/plot.stppm.R | 4 +-- R/sepstlppm.R | 2 - R/sepstppm.R | 2 - inst |only man/globaldiag.Rd | 4 +-- man/localSTLKinhom.Rd | 2 - man/localdiag.Rd | 2 - man/localtest.Rd | 2 - man/plot.globaldiag.Rd | 2 - man/plot.locstppm.Rd | 4 +-- man/plot.sepstppm.Rd | 4 +-- man/plot.stlgcppm.Rd | 4 +-- man/plot.stlp.Rd | 2 - man/plot.stppm.Rd | 4 +-- man/sepstlppm.Rd | 2 - man/sepstppm.Rd | 2 - 28 files changed, 76 insertions(+), 69 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>. 'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.8.0 dated 2025-06-10 and 0.8.3 dated 2025-07-08
DESCRIPTION | 8 +- MD5 | 24 +++--- R/RcppExports.R | 20 +++++ R/data_functions.R | 13 ++- R/griddata_class.R | 117 +++++++++++++++++++++---------- build/partial.rdb |binary inst/include/rts/regionlinearpredictor.h | 33 +++++++- inst/include/rts/rtsmodelbits.h | 6 - inst/include/rts/rtsregionmodel.h | 11 +- man/create_points.Rd | 2 man/grid.Rd | 4 + src/RcppExports.cpp | 78 ++++++++++++++++++++ src/model_module.cpp | 88 ++++++++++++++++++++++- 13 files changed, 330 insertions(+), 74 deletions(-)